35876	1	Jonas Maaskola	Select microRNAs are essential for early development in the sea urchin.	microRNAs (miRNAs) are small noncoding RNAs that mediate post-transcriptional gene regulation and have emerged as essential regulators of many develop	Jonas Maaskola, Jia Song, Marlon Stoeckius, Marc Friedländer, Nadezda  Stepicheva, Celina  Juliano, Svetlana  Lebedeva, William  Thompson, Nikolaus  Rajewsky, Gary Wessel	Small RNA expression profiling in early sea urchin development	22155525	42264	SRP010973	SRR409091	https://sra-downloadb.st-va.ncbi.nlm.nih.gov/sos2/sra-pub-run-6/SRR409091/SRR409091.3	GSM877247	SRA050178	SRX120407	RNA-Seq	SINGLE	SRP010973	PRJNA151931
35876	2	Jonas Maaskola	Select microRNAs are essential for early development in the sea urchin.	microRNAs (miRNAs) are small noncoding RNAs that mediate post-transcriptional gene regulation and have emerged as essential regulators of many develop	Jonas Maaskola, Jia Song, Marlon Stoeckius, Marc Friedländer, Nadezda  Stepicheva, Celina  Juliano, Svetlana  Lebedeva, William  Thompson, Nikolaus  Rajewsky, Gary Wessel	Small RNA expression profiling in early sea urchin development	22155525	42264	SRP010973	SRR409092	https://sra-downloadb.st-va.ncbi.nlm.nih.gov/sos2/sra-pub-run-6/SRR409092/SRR409092.3	GSM877248	SRA050178	SRX120408	RNA-Seq	SINGLE	SRP010973	PRJNA151931
35876	3	Jonas Maaskola	Select microRNAs are essential for early development in the sea urchin.	microRNAs (miRNAs) are small noncoding RNAs that mediate post-transcriptional gene regulation and have emerged as essential regulators of many develop	Jonas Maaskola, Jia Song, Marlon Stoeckius, Marc Friedländer, Nadezda  Stepicheva, Celina  Juliano, Svetlana  Lebedeva, William  Thompson, Nikolaus  Rajewsky, Gary Wessel	Small RNA expression profiling in early sea urchin development	22155525	42264	SRP010973	SRR409093	https://sra-downloadb.st-va.ncbi.nlm.nih.gov/sos2/sra-pub-run-6/SRR409093/SRR409093.3	GSM877249	SRA050178	SRX120409	RNA-Seq	SINGLE	SRP010973	PRJNA151931
35876	4	Jonas Maaskola	Select microRNAs are essential for early development in the sea urchin.	microRNAs (miRNAs) are small noncoding RNAs that mediate post-transcriptional gene regulation and have emerged as essential regulators of many develop	Jonas Maaskola, Jia Song, Marlon Stoeckius, Marc Friedländer, Nadezda  Stepicheva, Celina  Juliano, Svetlana  Lebedeva, William  Thompson, Nikolaus  Rajewsky, Gary Wessel	Small RNA expression profiling in early sea urchin development	22155525	42264	SRP010973	SRR409094	https://sra-downloadb.st-va.ncbi.nlm.nih.gov/sos2/sra-pub-run-6/SRR409094/SRR409094.3	GSM877250	SRA050178	SRX120410	RNA-Seq	SINGLE	SRP010973	PRJNA151931
35876	5	Jonas Maaskola	Select microRNAs are essential for early development in the sea urchin.	microRNAs (miRNAs) are small noncoding RNAs that mediate post-transcriptional gene regulation and have emerged as essential regulators of many develop	Jonas Maaskola, Jia Song, Marlon Stoeckius, Marc Friedländer, Nadezda  Stepicheva, Celina  Juliano, Svetlana  Lebedeva, William  Thompson, Nikolaus  Rajewsky, Gary Wessel	Small RNA expression profiling in early sea urchin development	22155525	42264	SRP010973	SRR409095	https://sra-downloadb.st-va.ncbi.nlm.nih.gov/sos2/sra-pub-run-6/SRR409095/SRR409095.3	GSM877251	SRA050178	SRX120411	RNA-Seq	SINGLE	SRP010973	PRJNA151931
35876	6	Jonas Maaskola	Select microRNAs are essential for early development in the sea urchin.	microRNAs (miRNAs) are small noncoding RNAs that mediate post-transcriptional gene regulation and have emerged as essential regulators of many develop	Jonas Maaskola, Jia Song, Marlon Stoeckius, Marc Friedländer, Nadezda  Stepicheva, Celina  Juliano, Svetlana  Lebedeva, William  Thompson, Nikolaus  Rajewsky, Gary Wessel	Small RNA expression profiling in early sea urchin development	22155525	42264	SRP010973	SRR409096	https://sra-downloadb.st-va.ncbi.nlm.nih.gov/sos2/sra-pub-run-6/SRR409096/SRR409096.3	GSM877252	SRA050178	SRX120412	RNA-Seq	SINGLE	SRP010973	PRJNA151931
38606	1	Daniel Runcie	Genetics of gene expression responses to temperature stress in a sea urchin gene network (HTS)	Stress responses play an important role in shaping species distributions and robustness to climate change. We investigated how stress responses alter 	Daniel Runcie, Daniel Runcie, David Garfield, Courtney Babbitt, Jennifer Wygoda, Sayan Mukherjee, Gregory Wray	7 RNAseq samples representing embryos grown at 2 temperatures, from 3 female parents and 2 male parents	22856327	42522	SRP013629	SRR505583	https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-2/SRR505583/SRR505583.1	GSM946005	SRA053596	SRX152581	RNA-Seq	SINGLE	SRP013629	PRJNA168291
38606	2	Daniel Runcie	Genetics of gene expression responses to temperature stress in a sea urchin gene network (HTS)	Stress responses play an important role in shaping species distributions and robustness to climate change. We investigated how stress responses alter 	Daniel Runcie, Daniel Runcie, David Garfield, Courtney Babbitt, Jennifer Wygoda, Sayan Mukherjee, Gregory Wray	7 RNAseq samples representing embryos grown at 2 temperatures, from 3 female parents and 2 male parents	22856327	42522	SRP013629	SRR505584	https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-2/SRR505584/SRR505584.1	GSM946006	SRA053596	SRX152582	RNA-Seq	SINGLE	SRP013629	PRJNA168291
38606	3	Daniel Runcie	Genetics of gene expression responses to temperature stress in a sea urchin gene network (HTS)	Stress responses play an important role in shaping species distributions and robustness to climate change. We investigated how stress responses alter 	Daniel Runcie, Daniel Runcie, David Garfield, Courtney Babbitt, Jennifer Wygoda, Sayan Mukherjee, Gregory Wray	7 RNAseq samples representing embryos grown at 2 temperatures, from 3 female parents and 2 male parents	22856327	42522	SRP013629	SRR505585	https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-2/SRR505585/SRR505585.1	GSM946007	SRA053596	SRX152583	RNA-Seq	SINGLE	SRP013629	PRJNA168291
38606	4	Daniel Runcie	Genetics of gene expression responses to temperature stress in a sea urchin gene network (HTS)	Stress responses play an important role in shaping species distributions and robustness to climate change. We investigated how stress responses alter 	Daniel Runcie, Daniel Runcie, David Garfield, Courtney Babbitt, Jennifer Wygoda, Sayan Mukherjee, Gregory Wray	7 RNAseq samples representing embryos grown at 2 temperatures, from 3 female parents and 2 male parents	22856327	42522	SRP013629	SRR505586	https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-2/SRR505586/SRR505586.1	GSM946008	SRA053596	SRX152584	RNA-Seq	SINGLE	SRP013629	PRJNA168291
38606	5	Daniel Runcie	Genetics of gene expression responses to temperature stress in a sea urchin gene network (HTS)	Stress responses play an important role in shaping species distributions and robustness to climate change. We investigated how stress responses alter 	Daniel Runcie, Daniel Runcie, David Garfield, Courtney Babbitt, Jennifer Wygoda, Sayan Mukherjee, Gregory Wray	7 RNAseq samples representing embryos grown at 2 temperatures, from 3 female parents and 2 male parents	22856327	42522	SRP013629	SRR505587	https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-2/SRR505587/SRR505587.1	GSM946009	SRA053596	SRX152585	RNA-Seq	SINGLE	SRP013629	PRJNA168291
38606	6	Daniel Runcie	Genetics of gene expression responses to temperature stress in a sea urchin gene network (HTS)	Stress responses play an important role in shaping species distributions and robustness to climate change. We investigated how stress responses alter 	Daniel Runcie, Daniel Runcie, David Garfield, Courtney Babbitt, Jennifer Wygoda, Sayan Mukherjee, Gregory Wray	7 RNAseq samples representing embryos grown at 2 temperatures, from 3 female parents and 2 male parents	22856327	42522	SRP013629	SRR505588	https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-2/SRR505588/SRR505588.1	GSM946010	SRA053596	SRX152586	RNA-Seq	SINGLE	SRP013629	PRJNA168291
38606	7	Daniel Runcie	Genetics of gene expression responses to temperature stress in a sea urchin gene network (HTS)	Stress responses play an important role in shaping species distributions and robustness to climate change. We investigated how stress responses alter 	Daniel Runcie, Daniel Runcie, David Garfield, Courtney Babbitt, Jennifer Wygoda, Sayan Mukherjee, Gregory Wray	7 RNAseq samples representing embryos grown at 2 temperatures, from 3 female parents and 2 male parents	22856327	42522	SRP013629	SRR505589	https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-2/SRR505589/SRR505589.1	GSM946011	SRA053596	SRX152587	RNA-Seq	SINGLE	SRP013629	PRJNA168291
76067	1	Robert Angerer	Gene expression alterations in SoxC knockdown sea urchin embryos	Transcription factor SoxC is required for all neural development in purple sea urchin S. purpuratus embryos. To begin to develop a gene regulatory net	Robert Angerer, Zheng Wei, Lynne Angerer, Robert Angerer	SoxC function was knocked down by morpholino oligo injection. RNA from about 1000 embryos were collected for both control and knockdown samples.	26657764	44383	SRP067439	SRR3017856	https://sra-downloadb.st-va.ncbi.nlm.nih.gov/sos2/sra-pub-run-6/SRR3017856/SRR3017856.1	GSM1973611	SRA320117	SRX1485315	RNA-Seq	PAIRED	SRP067439	PRJNA306145
76067	2	Robert Angerer	Gene expression alterations in SoxC knockdown sea urchin embryos	Transcription factor SoxC is required for all neural development in purple sea urchin S. purpuratus embryos. To begin to develop a gene regulatory net	Robert Angerer, Zheng Wei, Lynne Angerer, Robert Angerer	SoxC function was knocked down by morpholino oligo injection. RNA from about 1000 embryos were collected for both control and knockdown samples.	26657764	44383	SRP067439	SRR3017857	https://sra-downloadb.st-va.ncbi.nlm.nih.gov/sos2/sra-pub-run-6/SRR3017857/SRR3017857.1	GSM1973612	SRA320117	SRX1485316	RNA-Seq	PAIRED	SRP067439	PRJNA306145
89863	1	Gregory Cary	RNA-seq assessment of morpholino knockdown of the sea star (Patiria miniata) Pm-Tbr transcription factor in early embryos	Purpose: The Tbrain transcription factor has demonstrated an evolved preference for low-affinity, secondary site binding motifs between the sea star a	Gregory Cary, Gregory Cary, Veronica Hinman	mRNA sensitive to PmTbr knockdown were determined by measuring RNA from blastula embryos injected with either anti-Pm-Tbr morpholino antisense oligonucleotides or a control MASO, in triplicate, followed by sequencing using Illumina HiSeq 2500	28584099	45554	SRP096041	SRR5022456	https://sra-downloadb.st-va.ncbi.nlm.nih.gov/sos2/sra-pub-run-3/SRR5022456/SRR5022456.1	GSM2391750	SRA494250	SRX2349182	RNA-Seq	SINGLE	SRP096041	PRJNA354525
89863	2	Gregory Cary	RNA-seq assessment of morpholino knockdown of the sea star (Patiria miniata) Pm-Tbr transcription factor in early embryos	Purpose: The Tbrain transcription factor has demonstrated an evolved preference for low-affinity, secondary site binding motifs between the sea star a	Gregory Cary, Gregory Cary, Veronica Hinman	mRNA sensitive to PmTbr knockdown were determined by measuring RNA from blastula embryos injected with either anti-Pm-Tbr morpholino antisense oligonucleotides or a control MASO, in triplicate, followed by sequencing using Illumina HiSeq 2500	28584099	45554	SRP096041	SRR5022457	https://sra-downloadb.st-va.ncbi.nlm.nih.gov/sos2/sra-pub-run-3/SRR5022457/SRR5022457.1	GSM2391751	SRA494250	SRX2349183	RNA-Seq	SINGLE	SRP096041	PRJNA354525
89863	3	Gregory Cary	RNA-seq assessment of morpholino knockdown of the sea star (Patiria miniata) Pm-Tbr transcription factor in early embryos	Purpose: The Tbrain transcription factor has demonstrated an evolved preference for low-affinity, secondary site binding motifs between the sea star a	Gregory Cary, Gregory Cary, Veronica Hinman	mRNA sensitive to PmTbr knockdown were determined by measuring RNA from blastula embryos injected with either anti-Pm-Tbr morpholino antisense oligonucleotides or a control MASO, in triplicate, followed by sequencing using Illumina HiSeq 2500	28584099	45554	SRP096041	SRR5022458	https://sra-downloadb.st-va.ncbi.nlm.nih.gov/sos2/sra-pub-run-3/SRR5022458/SRR5022458.1	GSM2391752	SRA494250	SRX2349184	RNA-Seq	SINGLE	SRP096041	PRJNA354525
89863	4	Gregory Cary	RNA-seq assessment of morpholino knockdown of the sea star (Patiria miniata) Pm-Tbr transcription factor in early embryos	Purpose: The Tbrain transcription factor has demonstrated an evolved preference for low-affinity, secondary site binding motifs between the sea star a	Gregory Cary, Gregory Cary, Veronica Hinman	mRNA sensitive to PmTbr knockdown were determined by measuring RNA from blastula embryos injected with either anti-Pm-Tbr morpholino antisense oligonucleotides or a control MASO, in triplicate, followed by sequencing using Illumina HiSeq 2500	28584099	45554	SRP096041	SRR5022459	https://sra-downloadb.st-va.ncbi.nlm.nih.gov/sos1/sra-pub-run-10/SRR5022459/SRR5022459.1	GSM2391753	SRA494250	SRX2349185	RNA-Seq	SINGLE	SRP096041	PRJNA354525
89863	5	Gregory Cary	RNA-seq assessment of morpholino knockdown of the sea star (Patiria miniata) Pm-Tbr transcription factor in early embryos	Purpose: The Tbrain transcription factor has demonstrated an evolved preference for low-affinity, secondary site binding motifs between the sea star a	Gregory Cary, Gregory Cary, Veronica Hinman	mRNA sensitive to PmTbr knockdown were determined by measuring RNA from blastula embryos injected with either anti-Pm-Tbr morpholino antisense oligonucleotides or a control MASO, in triplicate, followed by sequencing using Illumina HiSeq 2500	28584099	45554	SRP096041	SRR5022460	https://sra-downloadb.st-va.ncbi.nlm.nih.gov/sos1/sra-pub-run-10/SRR5022460/SRR5022460.1	GSM2391754	SRA494250	SRX2349186	RNA-Seq	SINGLE	SRP096041	PRJNA354525
89863	6	Gregory Cary	RNA-seq assessment of morpholino knockdown of the sea star (Patiria miniata) Pm-Tbr transcription factor in early embryos	Purpose: The Tbrain transcription factor has demonstrated an evolved preference for low-affinity, secondary site binding motifs between the sea star a	Gregory Cary, Gregory Cary, Veronica Hinman	mRNA sensitive to PmTbr knockdown were determined by measuring RNA from blastula embryos injected with either anti-Pm-Tbr morpholino antisense oligonucleotides or a control MASO, in triplicate, followed by sequencing using Illumina HiSeq 2500	28584099	45554	SRP096041	SRR5022461	https://sra-downloadb.st-va.ncbi.nlm.nih.gov/sos1/sra-pub-run-10/SRR5022461/SRR5022461.1	GSM2391755	SRA494250	SRX2349187	RNA-Seq	SINGLE	SRP096041	PRJNA354525
97448	1	Katherine Buckley	Gene expression in tissues from an immune challenged adult sea urchin (Strongylocentrotus purpuratus)	To induce an immune response, a single adult animal was injected intracoelomically with complex microbiota isolated from the gut of another adult anim	Katherine Buckley, Katherine Buckley, Jonathan Rast	A single immune-challenged animal was the source of the two tissues analyzed for gene expression (coelomocytes and gut).	0	51283	SRP103125	SRR5420081	https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR5420081/SRR5420081.1	GSM2564784	SRA551960	SRX2711611	RNA-Seq	PAIRED	SRP103125	PRJNA381801
134350	1	Gary Wessel	Single cell RNA‐seq in the sea urchin embryo show marked cell‐type specificity in the Delta/Notch pathway	Overall, we conclude that single cell RNA‐seq analysis in this embryo is revealing of the cell types present during development, of the changes in 	Gary Wessel, Stephany Foster	Adult S. purpuratus were obtained from South Coast Bio‐Marine info@scbiomarine.com and were spawned using 0.5 M KCl injections intracoelomically. DAPT (Tocris) was added at fertilization to 8 μM, a concentration previously determined to effectively perturb Delta/Notch signaling without affecting overall development (Materna & Davidson, 2012). C59 (Cellagen) was added at 0.5 μM at fertilization as previously described (Cui et al., 2014). Embryos were cultured and, at appropriate developmental stages, were dissociated into single cells as described (McClay, 2004). We started with 50 ml cultures containing 0.25% of embryos (125 ul of embryos in 50 ml). The full volume was dissociated into single cells. We obtained 12 million single cells from which 5,000 were used for the DropSeq.The single‐cell RNA‐seq protocol was performed using the ChromiumTM Single Cell 3′ reagent kit v2 chemistry and cells were loaded on a GemCode Single Cell Instrument (10× Genomics, Pleasanton, CA).	31199038	47260	SRP214801	SRR9693264	https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-15/SRR9693264/SRR9693264.1	GSM3943022	SRA921486	SRX6451538	RNA-Seq	PAIRED	SRP214801	PRJNA554833
134350	2	Gary Wessel	Single cell RNA‐seq in the sea urchin embryo show marked cell‐type specificity in the Delta/Notch pathway	Overall, we conclude that single cell RNA‐seq analysis in this embryo is revealing of the cell types present during development, of the changes in 	Gary Wessel, Stephany Foster	Adult S. purpuratus were obtained from South Coast Bio‐Marine info@scbiomarine.com and were spawned using 0.5 M KCl injections intracoelomically. DAPT (Tocris) was added at fertilization to 8 μM, a concentration previously determined to effectively perturb Delta/Notch signaling without affecting overall development (Materna & Davidson, 2012). C59 (Cellagen) was added at 0.5 μM at fertilization as previously described (Cui et al., 2014). Embryos were cultured and, at appropriate developmental stages, were dissociated into single cells as described (McClay, 2004). We started with 50 ml cultures containing 0.25% of embryos (125 ul of embryos in 50 ml). The full volume was dissociated into single cells. We obtained 12 million single cells from which 5,000 were used for the DropSeq.The single‐cell RNA‐seq protocol was performed using the ChromiumTM Single Cell 3′ reagent kit v2 chemistry and cells were loaded on a GemCode Single Cell Instrument (10× Genomics, Pleasanton, CA).	31199038	47260	SRP214801	SRR9693265	https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-15/SRR9693265/SRR9693265.1	GSM3943023	SRA921486	SRX6451539	RNA-Seq	PAIRED	SRP214801	PRJNA554833
134350	3	Gary Wessel	Single cell RNA‐seq in the sea urchin embryo show marked cell‐type specificity in the Delta/Notch pathway	Overall, we conclude that single cell RNA‐seq analysis in this embryo is revealing of the cell types present during development, of the changes in 	Gary Wessel, Stephany Foster	Adult S. purpuratus were obtained from South Coast Bio‐Marine info@scbiomarine.com and were spawned using 0.5 M KCl injections intracoelomically. DAPT (Tocris) was added at fertilization to 8 μM, a concentration previously determined to effectively perturb Delta/Notch signaling without affecting overall development (Materna & Davidson, 2012). C59 (Cellagen) was added at 0.5 μM at fertilization as previously described (Cui et al., 2014). Embryos were cultured and, at appropriate developmental stages, were dissociated into single cells as described (McClay, 2004). We started with 50 ml cultures containing 0.25% of embryos (125 ul of embryos in 50 ml). The full volume was dissociated into single cells. We obtained 12 million single cells from which 5,000 were used for the DropSeq.The single‐cell RNA‐seq protocol was performed using the ChromiumTM Single Cell 3′ reagent kit v2 chemistry and cells were loaded on a GemCode Single Cell Instrument (10× Genomics, Pleasanton, CA).	31199038	47260	SRP214801	SRR9693266	https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-15/SRR9693266/SRR9693266.1	GSM3943024	SRA921486	SRX6451540	RNA-Seq	PAIRED	SRP214801	PRJNA554833
149221	1	Gary Wessel	A single cell RNA-seq resource for early sea urchin development	Here we leverage the sea urchin embryo for its rich history of developmental transitions, its well-established gene regulatory network, and the abilit	Gary Wessel, Stephany Foster, Nathalie Oulhen	Eggs and sperm of S.purpuratus were spawned by injection of 0.5M KCl into the adult coelomic cavity. Fertilization was accomplished in sea water containing 10mM p-aminobenzoic acid to reduce cross-linking of the fertilization envelope, and which was washed out after 30 minutes. Embryos were cultured in filtered (0.2micron) sea water collected at the Marine Biological laboratories in Woods Hole MA, until the appropriate stage for dissociation. Multiple fertilizations were initiated in this study and timed such that the appropriate stages of embryonic development were reached at a common endpoint. The embryos were then collected and washed twice with calcium-free sea water, and then suspended hyalin-extraction media (HEM) for 10-15 minutes, depending on the stage of dissociation.  When cells were beginning to dissociate, the embryos were collected and washed in 0.5M NaCl, gently sheared with a pipette, run through a 40micron Nitex mesh, counted on a hemocytometer, and diluted to reach the appropriate concentration for the scmRNA-seq protocol. Equal numbers of embryos were used in each time point and at no time were cells or embryos pelleted in a centrifuge. 	32816969	48861	SRP258127	SRR11599813	https://sra-download.ncbi.nlm.nih.gov/traces/sra71/SRR/011327/SRR11599813	GSM4494538	SRA1068313	SRX8166534	RNA-Seq	PAIRED	SRP258127	PRJNA627693
149221	2	Gary Wessel	A single cell RNA-seq resource for early sea urchin development	Here we leverage the sea urchin embryo for its rich history of developmental transitions, its well-established gene regulatory network, and the abilit	Gary Wessel, Stephany Foster, Nathalie Oulhen	Eggs and sperm of S.purpuratus were spawned by injection of 0.5M KCl into the adult coelomic cavity. Fertilization was accomplished in sea water containing 10mM p-aminobenzoic acid to reduce cross-linking of the fertilization envelope, and which was washed out after 30 minutes. Embryos were cultured in filtered (0.2micron) sea water collected at the Marine Biological laboratories in Woods Hole MA, until the appropriate stage for dissociation. Multiple fertilizations were initiated in this study and timed such that the appropriate stages of embryonic development were reached at a common endpoint. The embryos were then collected and washed twice with calcium-free sea water, and then suspended hyalin-extraction media (HEM) for 10-15 minutes, depending on the stage of dissociation.  When cells were beginning to dissociate, the embryos were collected and washed in 0.5M NaCl, gently sheared with a pipette, run through a 40micron Nitex mesh, counted on a hemocytometer, and diluted to reach the appropriate concentration for the scmRNA-seq protocol. Equal numbers of embryos were used in each time point and at no time were cells or embryos pelleted in a centrifuge. 	32816969	48861	SRP258127	SRR11599814	https://sra-download.ncbi.nlm.nih.gov/traces/sra20/SRR/011327/SRR11599814	GSM4494539	SRA1068313	SRX8166535	RNA-Seq	PAIRED	SRP258127	PRJNA627693
149221	3	Gary Wessel	A single cell RNA-seq resource for early sea urchin development	Here we leverage the sea urchin embryo for its rich history of developmental transitions, its well-established gene regulatory network, and the abilit	Gary Wessel, Stephany Foster, Nathalie Oulhen	Eggs and sperm of S.purpuratus were spawned by injection of 0.5M KCl into the adult coelomic cavity. Fertilization was accomplished in sea water containing 10mM p-aminobenzoic acid to reduce cross-linking of the fertilization envelope, and which was washed out after 30 minutes. Embryos were cultured in filtered (0.2micron) sea water collected at the Marine Biological laboratories in Woods Hole MA, until the appropriate stage for dissociation. Multiple fertilizations were initiated in this study and timed such that the appropriate stages of embryonic development were reached at a common endpoint. The embryos were then collected and washed twice with calcium-free sea water, and then suspended hyalin-extraction media (HEM) for 10-15 minutes, depending on the stage of dissociation.  When cells were beginning to dissociate, the embryos were collected and washed in 0.5M NaCl, gently sheared with a pipette, run through a 40micron Nitex mesh, counted on a hemocytometer, and diluted to reach the appropriate concentration for the scmRNA-seq protocol. Equal numbers of embryos were used in each time point and at no time were cells or embryos pelleted in a centrifuge. 	32816969	48861	SRP258127	SRR11599815	https://sra-download.ncbi.nlm.nih.gov/traces/sra65/SRR/011327/SRR11599815	GSM4494540	SRA1068313	SRX8166536	RNA-Seq	PAIRED	SRP258127	PRJNA627693
149221	4	Gary Wessel	A single cell RNA-seq resource for early sea urchin development	Here we leverage the sea urchin embryo for its rich history of developmental transitions, its well-established gene regulatory network, and the abilit	Gary Wessel, Stephany Foster, Nathalie Oulhen	Eggs and sperm of S.purpuratus were spawned by injection of 0.5M KCl into the adult coelomic cavity. Fertilization was accomplished in sea water containing 10mM p-aminobenzoic acid to reduce cross-linking of the fertilization envelope, and which was washed out after 30 minutes. Embryos were cultured in filtered (0.2micron) sea water collected at the Marine Biological laboratories in Woods Hole MA, until the appropriate stage for dissociation. Multiple fertilizations were initiated in this study and timed such that the appropriate stages of embryonic development were reached at a common endpoint. The embryos were then collected and washed twice with calcium-free sea water, and then suspended hyalin-extraction media (HEM) for 10-15 minutes, depending on the stage of dissociation.  When cells were beginning to dissociate, the embryos were collected and washed in 0.5M NaCl, gently sheared with a pipette, run through a 40micron Nitex mesh, counted on a hemocytometer, and diluted to reach the appropriate concentration for the scmRNA-seq protocol. Equal numbers of embryos were used in each time point and at no time were cells or embryos pelleted in a centrifuge. 	32816969	48861	SRP258127	SRR11599816	https://sra-download.ncbi.nlm.nih.gov/traces/sra42/SRR/011327/SRR11599816	GSM4494541	SRA1068313	SRX8166537	RNA-Seq	PAIRED	SRP258127	PRJNA627693
149221	5	Gary Wessel	A single cell RNA-seq resource for early sea urchin development	Here we leverage the sea urchin embryo for its rich history of developmental transitions, its well-established gene regulatory network, and the abilit	Gary Wessel, Stephany Foster, Nathalie Oulhen	Eggs and sperm of S.purpuratus were spawned by injection of 0.5M KCl into the adult coelomic cavity. Fertilization was accomplished in sea water containing 10mM p-aminobenzoic acid to reduce cross-linking of the fertilization envelope, and which was washed out after 30 minutes. Embryos were cultured in filtered (0.2micron) sea water collected at the Marine Biological laboratories in Woods Hole MA, until the appropriate stage for dissociation. Multiple fertilizations were initiated in this study and timed such that the appropriate stages of embryonic development were reached at a common endpoint. The embryos were then collected and washed twice with calcium-free sea water, and then suspended hyalin-extraction media (HEM) for 10-15 minutes, depending on the stage of dissociation.  When cells were beginning to dissociate, the embryos were collected and washed in 0.5M NaCl, gently sheared with a pipette, run through a 40micron Nitex mesh, counted on a hemocytometer, and diluted to reach the appropriate concentration for the scmRNA-seq protocol. Equal numbers of embryos were used in each time point and at no time were cells or embryos pelleted in a centrifuge. 	32816969	48861	SRP258127	SRR11599817	https://sra-download.ncbi.nlm.nih.gov/traces/sra67/SRR/011327/SRR11599817	GSM4494542	SRA1068313	SRX8166538	RNA-Seq	PAIRED	SRP258127	PRJNA627693
149221	6	Gary Wessel	A single cell RNA-seq resource for early sea urchin development	Here we leverage the sea urchin embryo for its rich history of developmental transitions, its well-established gene regulatory network, and the abilit	Gary Wessel, Stephany Foster, Nathalie Oulhen	Eggs and sperm of S.purpuratus were spawned by injection of 0.5M KCl into the adult coelomic cavity. Fertilization was accomplished in sea water containing 10mM p-aminobenzoic acid to reduce cross-linking of the fertilization envelope, and which was washed out after 30 minutes. Embryos were cultured in filtered (0.2micron) sea water collected at the Marine Biological laboratories in Woods Hole MA, until the appropriate stage for dissociation. Multiple fertilizations were initiated in this study and timed such that the appropriate stages of embryonic development were reached at a common endpoint. The embryos were then collected and washed twice with calcium-free sea water, and then suspended hyalin-extraction media (HEM) for 10-15 minutes, depending on the stage of dissociation.  When cells were beginning to dissociate, the embryos were collected and washed in 0.5M NaCl, gently sheared with a pipette, run through a 40micron Nitex mesh, counted on a hemocytometer, and diluted to reach the appropriate concentration for the scmRNA-seq protocol. Equal numbers of embryos were used in each time point and at no time were cells or embryos pelleted in a centrifuge. 	32816969	48861	SRP258127	SRR11599818	https://sra-download.ncbi.nlm.nih.gov/traces/sra42/SRR/011327/SRR11599818	GSM4494542	SRA1068313	SRX8166538	RNA-Seq	PAIRED	SRP258127	PRJNA627693
149221	7	Gary Wessel	A single cell RNA-seq resource for early sea urchin development	Here we leverage the sea urchin embryo for its rich history of developmental transitions, its well-established gene regulatory network, and the abilit	Gary Wessel, Stephany Foster, Nathalie Oulhen	Eggs and sperm of S.purpuratus were spawned by injection of 0.5M KCl into the adult coelomic cavity. Fertilization was accomplished in sea water containing 10mM p-aminobenzoic acid to reduce cross-linking of the fertilization envelope, and which was washed out after 30 minutes. Embryos were cultured in filtered (0.2micron) sea water collected at the Marine Biological laboratories in Woods Hole MA, until the appropriate stage for dissociation. Multiple fertilizations were initiated in this study and timed such that the appropriate stages of embryonic development were reached at a common endpoint. The embryos were then collected and washed twice with calcium-free sea water, and then suspended hyalin-extraction media (HEM) for 10-15 minutes, depending on the stage of dissociation.  When cells were beginning to dissociate, the embryos were collected and washed in 0.5M NaCl, gently sheared with a pipette, run through a 40micron Nitex mesh, counted on a hemocytometer, and diluted to reach the appropriate concentration for the scmRNA-seq protocol. Equal numbers of embryos were used in each time point and at no time were cells or embryos pelleted in a centrifuge. 	32816969	48861	SRP258127	SRR11599819	https://sra-download.ncbi.nlm.nih.gov/traces/sra54/SRR/011327/SRR11599819	GSM4494543	SRA1068313	SRX8166539	RNA-Seq	PAIRED	SRP258127	PRJNA627693
149221	8	Gary Wessel	A single cell RNA-seq resource for early sea urchin development	Here we leverage the sea urchin embryo for its rich history of developmental transitions, its well-established gene regulatory network, and the abilit	Gary Wessel, Stephany Foster, Nathalie Oulhen	Eggs and sperm of S.purpuratus were spawned by injection of 0.5M KCl into the adult coelomic cavity. Fertilization was accomplished in sea water containing 10mM p-aminobenzoic acid to reduce cross-linking of the fertilization envelope, and which was washed out after 30 minutes. Embryos were cultured in filtered (0.2micron) sea water collected at the Marine Biological laboratories in Woods Hole MA, until the appropriate stage for dissociation. Multiple fertilizations were initiated in this study and timed such that the appropriate stages of embryonic development were reached at a common endpoint. The embryos were then collected and washed twice with calcium-free sea water, and then suspended hyalin-extraction media (HEM) for 10-15 minutes, depending on the stage of dissociation.  When cells were beginning to dissociate, the embryos were collected and washed in 0.5M NaCl, gently sheared with a pipette, run through a 40micron Nitex mesh, counted on a hemocytometer, and diluted to reach the appropriate concentration for the scmRNA-seq protocol. Equal numbers of embryos were used in each time point and at no time were cells or embryos pelleted in a centrifuge. 	32816969	48861	SRP258127	SRR11599820	https://sra-download.ncbi.nlm.nih.gov/traces/sra29/SRR/011327/SRR11599820	GSM4494543	SRA1068313	SRX8166539	RNA-Seq	PAIRED	SRP258127	PRJNA627693
149221	9	Gary Wessel	A single cell RNA-seq resource for early sea urchin development	Here we leverage the sea urchin embryo for its rich history of developmental transitions, its well-established gene regulatory network, and the abilit	Gary Wessel, Stephany Foster, Nathalie Oulhen	Eggs and sperm of S.purpuratus were spawned by injection of 0.5M KCl into the adult coelomic cavity. Fertilization was accomplished in sea water containing 10mM p-aminobenzoic acid to reduce cross-linking of the fertilization envelope, and which was washed out after 30 minutes. Embryos were cultured in filtered (0.2micron) sea water collected at the Marine Biological laboratories in Woods Hole MA, until the appropriate stage for dissociation. Multiple fertilizations were initiated in this study and timed such that the appropriate stages of embryonic development were reached at a common endpoint. The embryos were then collected and washed twice with calcium-free sea water, and then suspended hyalin-extraction media (HEM) for 10-15 minutes, depending on the stage of dissociation.  When cells were beginning to dissociate, the embryos were collected and washed in 0.5M NaCl, gently sheared with a pipette, run through a 40micron Nitex mesh, counted on a hemocytometer, and diluted to reach the appropriate concentration for the scmRNA-seq protocol. Equal numbers of embryos were used in each time point and at no time were cells or embryos pelleted in a centrifuge. 	32816969	48861	SRP258127	SRR11599821	https://sra-download.ncbi.nlm.nih.gov/traces/sra34/SRR/011327/SRR11599821	GSM4494544	SRA1068313	SRX8166540	RNA-Seq	PAIRED	SRP258127	PRJNA627693
149221	10	Gary Wessel	A single cell RNA-seq resource for early sea urchin development	Here we leverage the sea urchin embryo for its rich history of developmental transitions, its well-established gene regulatory network, and the abilit	Gary Wessel, Stephany Foster, Nathalie Oulhen	Eggs and sperm of S.purpuratus were spawned by injection of 0.5M KCl into the adult coelomic cavity. Fertilization was accomplished in sea water containing 10mM p-aminobenzoic acid to reduce cross-linking of the fertilization envelope, and which was washed out after 30 minutes. Embryos were cultured in filtered (0.2micron) sea water collected at the Marine Biological laboratories in Woods Hole MA, until the appropriate stage for dissociation. Multiple fertilizations were initiated in this study and timed such that the appropriate stages of embryonic development were reached at a common endpoint. The embryos were then collected and washed twice with calcium-free sea water, and then suspended hyalin-extraction media (HEM) for 10-15 minutes, depending on the stage of dissociation.  When cells were beginning to dissociate, the embryos were collected and washed in 0.5M NaCl, gently sheared with a pipette, run through a 40micron Nitex mesh, counted on a hemocytometer, and diluted to reach the appropriate concentration for the scmRNA-seq protocol. Equal numbers of embryos were used in each time point and at no time were cells or embryos pelleted in a centrifuge. 	32816969	48861	SRP258127	SRR11599822	https://sra-download.ncbi.nlm.nih.gov/traces/sra76/SRR/011327/SRR11599822	GSM4494544	SRA1068313	SRX8166540	RNA-Seq	PAIRED	SRP258127	PRJNA627693
149221	11	Gary Wessel	A single cell RNA-seq resource for early sea urchin development	Here we leverage the sea urchin embryo for its rich history of developmental transitions, its well-established gene regulatory network, and the abilit	Gary Wessel, Stephany Foster, Nathalie Oulhen	Eggs and sperm of S.purpuratus were spawned by injection of 0.5M KCl into the adult coelomic cavity. Fertilization was accomplished in sea water containing 10mM p-aminobenzoic acid to reduce cross-linking of the fertilization envelope, and which was washed out after 30 minutes. Embryos were cultured in filtered (0.2micron) sea water collected at the Marine Biological laboratories in Woods Hole MA, until the appropriate stage for dissociation. Multiple fertilizations were initiated in this study and timed such that the appropriate stages of embryonic development were reached at a common endpoint. The embryos were then collected and washed twice with calcium-free sea water, and then suspended hyalin-extraction media (HEM) for 10-15 minutes, depending on the stage of dissociation.  When cells were beginning to dissociate, the embryos were collected and washed in 0.5M NaCl, gently sheared with a pipette, run through a 40micron Nitex mesh, counted on a hemocytometer, and diluted to reach the appropriate concentration for the scmRNA-seq protocol. Equal numbers of embryos were used in each time point and at no time were cells or embryos pelleted in a centrifuge. 	32816969	48861	SRP258127	SRR11599823	https://sra-download.ncbi.nlm.nih.gov/traces/sra39/SRR/011327/SRR11599823	GSM4494545	SRA1068313	SRX8166541	RNA-Seq	PAIRED	SRP258127	PRJNA627693
149221	12	Gary Wessel	A single cell RNA-seq resource for early sea urchin development	Here we leverage the sea urchin embryo for its rich history of developmental transitions, its well-established gene regulatory network, and the abilit	Gary Wessel, Stephany Foster, Nathalie Oulhen	Eggs and sperm of S.purpuratus were spawned by injection of 0.5M KCl into the adult coelomic cavity. Fertilization was accomplished in sea water containing 10mM p-aminobenzoic acid to reduce cross-linking of the fertilization envelope, and which was washed out after 30 minutes. Embryos were cultured in filtered (0.2micron) sea water collected at the Marine Biological laboratories in Woods Hole MA, until the appropriate stage for dissociation. Multiple fertilizations were initiated in this study and timed such that the appropriate stages of embryonic development were reached at a common endpoint. The embryos were then collected and washed twice with calcium-free sea water, and then suspended hyalin-extraction media (HEM) for 10-15 minutes, depending on the stage of dissociation.  When cells were beginning to dissociate, the embryos were collected and washed in 0.5M NaCl, gently sheared with a pipette, run through a 40micron Nitex mesh, counted on a hemocytometer, and diluted to reach the appropriate concentration for the scmRNA-seq protocol. Equal numbers of embryos were used in each time point and at no time were cells or embryos pelleted in a centrifuge. 	32816969	48861	SRP258127	SRR11599824	https://sra-download.ncbi.nlm.nih.gov/traces/sra67/SRR/011327/SRR11599824	GSM4494545	SRA1068313	SRX8166541	RNA-Seq	PAIRED	SRP258127	PRJNA627693
155427	1	nathalie oulhen	Regulation of dynamic pigment cell states at single-cell resolution	Pigment cells bear molecules with diverse physiological roles across phylogeny and are often under strict evolutionary selection. Thus, the mechanisms	nathalie oulhen, Margherita Perillo, Stephany Foster, Maxwell Spurrell, Cristina Calestani, Gary Wessel	Eggs and sperm of S.purpuratus were spawned by injection of 0.5M KCl into the adult coelomic cavity. Embryos were cultured in filtered (0.2micron) sea water collected at the Marine Biological laboratories in Woods Hole MA, until the appropriate stage for dissociation (48 and 72 hours post fertilization). To test the function of gcm, eggs were dejelled before fertilization by washing in pH4.0 seawater, and injected post fertilization in presence of 1mM 3-AT with either a control morpholino or the gcm morpholino used at a concentration of 0.5mM. The resulting wild type controls and albino embryos were collected at 48 hpf. These 4 samples (non injected 48 and 72 hpf, control morpholino injected 48 hpf and gcm morpholino injected 48 hpf embryos) were used for single cell RNA seq. Briefly, the collected embryos were washed twice with calcium-free sea water, and then suspended hyalin-extraction media (HEM) for 10-15 minutes, depending on the stage of dissociation. When cells were beginning to dissociate, the embryos were collected and washed in 0.5M NaCl, gently sheared with a pipette, run through a 40micron Nitex mesh, counted on a hemocytometer, and diluted to reach the appropriate concentration for the single cell RNA-seq protocol using the 10X Chromium technology (v3 Chemistry).	32812865	48862	SRP274329	SRR12353949	https://sra-download.ncbi.nlm.nih.gov/traces/sra21/SRR/012064/SRR12353949	GSM4704280	SRA1105741	SRX8853396	RNA-Seq	PAIRED	SRP274329	PRJNA649738
155427	2	nathalie oulhen	Regulation of dynamic pigment cell states at single-cell resolution	Pigment cells bear molecules with diverse physiological roles across phylogeny and are often under strict evolutionary selection. Thus, the mechanisms	nathalie oulhen, Margherita Perillo, Stephany Foster, Maxwell Spurrell, Cristina Calestani, Gary Wessel	Eggs and sperm of S.purpuratus were spawned by injection of 0.5M KCl into the adult coelomic cavity. Embryos were cultured in filtered (0.2micron) sea water collected at the Marine Biological laboratories in Woods Hole MA, until the appropriate stage for dissociation (48 and 72 hours post fertilization). To test the function of gcm, eggs were dejelled before fertilization by washing in pH4.0 seawater, and injected post fertilization in presence of 1mM 3-AT with either a control morpholino or the gcm morpholino used at a concentration of 0.5mM. The resulting wild type controls and albino embryos were collected at 48 hpf. These 4 samples (non injected 48 and 72 hpf, control morpholino injected 48 hpf and gcm morpholino injected 48 hpf embryos) were used for single cell RNA seq. Briefly, the collected embryos were washed twice with calcium-free sea water, and then suspended hyalin-extraction media (HEM) for 10-15 minutes, depending on the stage of dissociation. When cells were beginning to dissociate, the embryos were collected and washed in 0.5M NaCl, gently sheared with a pipette, run through a 40micron Nitex mesh, counted on a hemocytometer, and diluted to reach the appropriate concentration for the single cell RNA-seq protocol using the 10X Chromium technology (v3 Chemistry).	32812865	48862	SRP274329	SRR12353950	https://sra-download.ncbi.nlm.nih.gov/traces/sra69/SRR/012064/SRR12353950	GSM4704281	SRA1105741	SRX8853397	RNA-Seq	PAIRED	SRP274329	PRJNA649738
155427	3	nathalie oulhen	Regulation of dynamic pigment cell states at single-cell resolution	Pigment cells bear molecules with diverse physiological roles across phylogeny and are often under strict evolutionary selection. Thus, the mechanisms	nathalie oulhen, Margherita Perillo, Stephany Foster, Maxwell Spurrell, Cristina Calestani, Gary Wessel	Eggs and sperm of S.purpuratus were spawned by injection of 0.5M KCl into the adult coelomic cavity. Embryos were cultured in filtered (0.2micron) sea water collected at the Marine Biological laboratories in Woods Hole MA, until the appropriate stage for dissociation (48 and 72 hours post fertilization). To test the function of gcm, eggs were dejelled before fertilization by washing in pH4.0 seawater, and injected post fertilization in presence of 1mM 3-AT with either a control morpholino or the gcm morpholino used at a concentration of 0.5mM. The resulting wild type controls and albino embryos were collected at 48 hpf. These 4 samples (non injected 48 and 72 hpf, control morpholino injected 48 hpf and gcm morpholino injected 48 hpf embryos) were used for single cell RNA seq. Briefly, the collected embryos were washed twice with calcium-free sea water, and then suspended hyalin-extraction media (HEM) for 10-15 minutes, depending on the stage of dissociation. When cells were beginning to dissociate, the embryos were collected and washed in 0.5M NaCl, gently sheared with a pipette, run through a 40micron Nitex mesh, counted on a hemocytometer, and diluted to reach the appropriate concentration for the single cell RNA-seq protocol using the 10X Chromium technology (v3 Chemistry).	32812865	48862	SRP274329	SRR12353951	https://sra-download.ncbi.nlm.nih.gov/traces/sra77/SRR/012064/SRR12353951	GSM4704282	SRA1105741	SRX8853398	RNA-Seq	PAIRED	SRP274329	PRJNA649738
155427	4	nathalie oulhen	Regulation of dynamic pigment cell states at single-cell resolution	Pigment cells bear molecules with diverse physiological roles across phylogeny and are often under strict evolutionary selection. Thus, the mechanisms	nathalie oulhen, Margherita Perillo, Stephany Foster, Maxwell Spurrell, Cristina Calestani, Gary Wessel	Eggs and sperm of S.purpuratus were spawned by injection of 0.5M KCl into the adult coelomic cavity. Embryos were cultured in filtered (0.2micron) sea water collected at the Marine Biological laboratories in Woods Hole MA, until the appropriate stage for dissociation (48 and 72 hours post fertilization). To test the function of gcm, eggs were dejelled before fertilization by washing in pH4.0 seawater, and injected post fertilization in presence of 1mM 3-AT with either a control morpholino or the gcm morpholino used at a concentration of 0.5mM. The resulting wild type controls and albino embryos were collected at 48 hpf. These 4 samples (non injected 48 and 72 hpf, control morpholino injected 48 hpf and gcm morpholino injected 48 hpf embryos) were used for single cell RNA seq. Briefly, the collected embryos were washed twice with calcium-free sea water, and then suspended hyalin-extraction media (HEM) for 10-15 minutes, depending on the stage of dissociation. When cells were beginning to dissociate, the embryos were collected and washed in 0.5M NaCl, gently sheared with a pipette, run through a 40micron Nitex mesh, counted on a hemocytometer, and diluted to reach the appropriate concentration for the single cell RNA-seq protocol using the 10X Chromium technology (v3 Chemistry).	32812865	48862	SRP274329	SRR12353952	https://sra-download.ncbi.nlm.nih.gov/traces/sra27/SRR/012064/SRR12353952	GSM4704283	SRA1105741	SRX8853399	RNA-Seq	PAIRED	SRP274329	PRJNA649738