metadata: run_metadata: 34 rows where experiment.library_strategy = "RNA-Seq", tissue_curation = "Pharyngeal Arch" and tissue_curation

34 rows where experiment.library_strategy = "RNA-Seq", tissue_curation = "Pharyngeal Arch" and tissue_curation_coarse = "Multi-system"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.PMIDs	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.extractprotocol	GEOsample.growthprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.r3_length	run.r4_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.Ncount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.mapping_rate.mate2	seqdetective.nofeature_rate.mate1	seqdetective.nofeature_rate.mate2	seqdetective.sparsity.mate1	seqdetective.sparsity.mate2	seqdetective.pos_strand_rate.mate1	seqdetective.pos_strand_rate.mate2	seqdetective.readlen.mate1	seqdetective.readlen.mate2	seqdetective.judgement.mate1	seqdetective.judgement.mate2	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
25133	25133	SRR25634296	SRX21361065	SRS18605555	SRP454944	PRJNA1005241	Nkx2.7 is a Conserved Regulator of Craniofacial Development	GSE240780	Transcriptome Analysis	Pharyngeal arch cells are comprised of endoderm mesoderm and neural crest layers. We used single cell RNA sequencing scRNA seq to analyze the genetic differences in pharyngeal arch cell types between wild type and nkx2.7 / samples. Overall design: Pharyngeal arch cells were obtained through manual dissection of wild type and nkx2.7 / embryos at 26 hpf. All embryos were positive for TgBACtcf21:mcherry NTR which was used as a visual guide for dissection. Cells were FACS sorted to eliminate dead cells from sequencing. 2 wild type embryos and 2 nkx2.7 / samples were pooled for submission.	pubmed:40268889	KC002 scRNAseq	GSM7709162	source name:Pharyngeal arches\|genotype:nkx2.7 / \|tissue:Pharyngeal arches\|strain:AB\|developmental stage:26 hpf\|geo loc name:missing\|collection date:missing	KC002 scRNAseq	The read alignment and gene counting were made using the Cell Ranger software v6.1.2 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: GRCz11 version 105 Supplementary files format and content: Tab separated values files and matrix files	Pharyngeal arches	From the offspring of an intercross of nkx2.7+/ ;Tgtcf21:NTRO mCherrypd108 two wild type and two nkx2.7 / embryos were identified by genotyping. The pharyngeal arches and surrounding tissue were dissected dissociated and submitted for flow cytometry. Cellular dissociation was performed with liberase solution in PBS at 28°C with pipetting every five minutes until adequately homogenized in solution. Fetal Bovine Serum FBS 5% of volume was then added to each sample to arrest the dissociation and each sample was centrifuged at 4°C. The excess supernatant was removed and the pellet was resuspended in PBS/1% FBS and filtered through a 40 m cell strainer. Finally DAPI and DRAQ5 were added and cells were sorted using a SORP FACSAriaTM Cell Sorter BD Biosciences under gentle conditions with the 130 μm nozzle at 12 PSI. NERL Diluent 2 Thermo Fisher DIL5522 solution was used for sheath fluid. The FACSAria was calibrated per the standard protocol in the CSCI Flow Cytometry Core Facility using Cytometer Setup and Tracking Beads BD Biosciences 655051 SPHERO Rainbow Calibration Particles 8 Peaks 3.0 m 5 mL Spherotech RCP 30 5A followed by optimization of the drop charge delay using BD FACS Accudrop Beads BD Biosciences 345249. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. Briefly GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.		genotype:nkx2.7 / \|tissue:Pharyngeal arches\|strain:AB\|developmental stage:26 hpf	GSM7709162	GSM7709162: KC002 scRNAseq; Danio rerio; RNA Seq	GSM7709162 r1	GSM7709162	1	From the offspring of an intercross of nkx2.7+/ ;Tgtcf21:NTRO mCherrypd108 two wild type and two nkx2.7 / embryos were identified by genotyping. The pharyngeal arches and surrounding tissue were dissected dissociated and submitted for flow cytometry. Cellular dissociation was performed with liberase solution in PBS at 28°C with pipetting every five minutes until adequately homogenized in solution. Fetal Bovine Serum FBS 5% of volume was then added to each sample to arrest the dissociation and each sample was centrifuged at 4°C. The excess supernatant was removed and the pellet was resuspended in PBS/1% FBS and filtered through a 40 m cell strainer. Finally DAPI and DRAQ5 were added and cells were sorted using a SORP FACSAriaTM Cell Sorter BD Biosciences under gentle conditions with the 130 μm nozzle at 12 PSI. NERL Diluent 2 Thermo Fisher DIL5522 solution was used for sheath fluid. The FACSAria was calibrated per the standard protocol in the CSCI Flow Cytometry Core Facility using Cytometer Setup and Tracking Beads BD Biosciences 655051 SPHERO Rainbow Calibration Particles 8 Peaks 3.0 m 5 mL Spherotech RCP 30 5A followed by optimization of the drop charge delay using BD FACS Accudrop Beads BD Biosciences 345249. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. Briefly GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index we…		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP454944	loader:fastq load.py\|options: readTypes=TTBB read1PairFiles=KC002 S1 L004 I1 001.fastq.gz read2PairFiles=KC002 S1 L004 I2 001.fastq.gz read3PairFiles=KC002 S1 L004 R1 001.fastq.gz read4PairFiles=KC002 S1 L004 R2 001.fastq.gz	KC002_S1_L004_I1_001.fastq.gz KC002_S1_L004_I2_001.fastq.gz KC002_S1_L004_R1_001.fastq.gz KC002_S1_L004_R2_001.fastq.gz	fastq fastq fastq fastq	65825988564.0	296513462.0	GSM7709162 r1	0:10 1:10 2:101 3:101	A:14990994149;C:11485312838;G:11921291570;T:21497933732;N:187035	10	10	101	101	14990994149	11485312838	11921291570	21497933732	187035	SRX21361065	SRS18605555	SRA1692494	SangesLab Computational Genomics, NEUROSCIENCE, SISSA	SangesLab Computational Genomics, NEUROSCIENCE, SISSA	2	0.00059	0.93473	2e-05	0.14487	0.99949	0.78364	0.5	0.52799	101	101	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Italy	2023-08-14	Pharyngula	Embryo	Pharyngeal Arch	Multi-system
25134	25134	SRR25634297	SRX21361064	SRS18605556	SRP454944	PRJNA1005241	Nkx2.7 is a Conserved Regulator of Craniofacial Development	GSE240780	Transcriptome Analysis	Pharyngeal arch cells are comprised of endoderm mesoderm and neural crest layers. We used single cell RNA sequencing scRNA seq to analyze the genetic differences in pharyngeal arch cell types between wild type and nkx2.7 / samples. Overall design: Pharyngeal arch cells were obtained through manual dissection of wild type and nkx2.7 / embryos at 26 hpf. All embryos were positive for TgBACtcf21:mcherry NTR which was used as a visual guide for dissection. Cells were FACS sorted to eliminate dead cells from sequencing. 2 wild type embryos and 2 nkx2.7 / samples were pooled for submission.	pubmed:40268889	KC001 scRNAseq	GSM7709161	source name:Pharyngeal arches\|genotype:wild type\|tissue:Pharyngeal arches\|strain:AB\|developmental stage:26 hpf\|geo loc name:missing\|collection date:missing	KC001 scRNAseq	The read alignment and gene counting were made using the Cell Ranger software v6.1.2 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: GRCz11 version 105 Supplementary files format and content: Tab separated values files and matrix files	Pharyngeal arches	From the offspring of an intercross of nkx2.7+/ ;Tgtcf21:NTRO mCherrypd108 two wild type and two nkx2.7 / embryos were identified by genotyping. The pharyngeal arches and surrounding tissue were dissected dissociated and submitted for flow cytometry. Cellular dissociation was performed with liberase solution in PBS at 28°C with pipetting every five minutes until adequately homogenized in solution. Fetal Bovine Serum FBS 5% of volume was then added to each sample to arrest the dissociation and each sample was centrifuged at 4°C. The excess supernatant was removed and the pellet was resuspended in PBS/1% FBS and filtered through a 40 m cell strainer. Finally DAPI and DRAQ5 were added and cells were sorted using a SORP FACSAriaTM Cell Sorter BD Biosciences under gentle conditions with the 130 μm nozzle at 12 PSI. NERL Diluent 2 Thermo Fisher DIL5522 solution was used for sheath fluid. The FACSAria was calibrated per the standard protocol in the CSCI Flow Cytometry Core Facility using Cytometer Setup and Tracking Beads BD Biosciences 655051 SPHERO Rainbow Calibration Particles 8 Peaks 3.0 m 5 mL Spherotech RCP 30 5A followed by optimization of the drop charge delay using BD FACS Accudrop Beads BD Biosciences 345249. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. Briefly GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.		genotype:wild type\|tissue:Pharyngeal arches\|strain:AB\|developmental stage:26 hpf	GSM7709161	GSM7709161: KC001 scRNAseq; Danio rerio; RNA Seq	GSM7709161 r1	GSM7709161	1	From the offspring of an intercross of nkx2.7+/ ;Tgtcf21:NTRO mCherrypd108 two wild type and two nkx2.7 / embryos were identified by genotyping. The pharyngeal arches and surrounding tissue were dissected dissociated and submitted for flow cytometry. Cellular dissociation was performed with liberase solution in PBS at 28°C with pipetting every five minutes until adequately homogenized in solution. Fetal Bovine Serum FBS 5% of volume was then added to each sample to arrest the dissociation and each sample was centrifuged at 4°C. The excess supernatant was removed and the pellet was resuspended in PBS/1% FBS and filtered through a 40 m cell strainer. Finally DAPI and DRAQ5 were added and cells were sorted using a SORP FACSAriaTM Cell Sorter BD Biosciences under gentle conditions with the 130 μm nozzle at 12 PSI. NERL Diluent 2 Thermo Fisher DIL5522 solution was used for sheath fluid. The FACSAria was calibrated per the standard protocol in the CSCI Flow Cytometry Core Facility using Cytometer Setup and Tracking Beads BD Biosciences 655051 SPHERO Rainbow Calibration Particles 8 Peaks 3.0 m 5 mL Spherotech RCP 30 5A followed by optimization of the drop charge delay using BD FACS Accudrop Beads BD Biosciences 345249. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. Briefly GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index we…		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP454944	loader:fastq load.py\|options: readTypes=TTBB read1PairFiles=KC001 S1 L004 I1 001.fastq.gz read2PairFiles=KC001 S1 L004 I2 001.fastq.gz read3PairFiles=KC001 S1 L004 R1 001.fastq.gz read4PairFiles=KC001 S1 L004 R2 001.fastq.gz	KC001_S1_L004_I1_001.fastq.gz KC001_S1_L004_I2_001.fastq.gz KC001_S1_L004_R1_001.fastq.gz KC001_S1_L004_R2_001.fastq.gz	fastq fastq fastq fastq	69380677872.0	312525576.0	GSM7709161 r1	0:10 1:10 2:101 3:101	A:16018222868;C:11704492905;G:12161620273;T:23245625739;N:204567	10	10	101	101	16018222868	11704492905	12161620273	23245625739	204567	SRX21361064	SRS18605556	SRA1692494	SangesLab Computational Genomics, NEUROSCIENCE, SISSA	SangesLab Computational Genomics, NEUROSCIENCE, SISSA	2	0.00071	0.93976	0.0001	0.12725	0.99945	0.78457	0.75	0.50121	101	101	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Italy	2023-08-14	Pharyngula	Embryo	Pharyngeal Arch	Multi-system
39921	39921	SRR2392494	SRX1240723	SRS1067356	SRP063659	PRJNA295533	Accelerated cartilage differentiation distinguishes the lower from the upper vertebrate face	GSE72985	Transcriptome Analysis	Distinct shaping of the upper versus lower facial skeleton is essential for function of the vertebrate jaw and middle ear yet the cellular mechanisms by which this occurs have remained unclear. Here we show that Endothelin1 Edn1 signaling accelerates mesenchymal condensation and subsequent cartilage formation in the lower face through antagonism of Jagged Notch signaling and Prrx1 transcription factors. A genomic analysis of facial skeletal precursors in mutants and overexpression embryos reveals that Jagged Notch signaling represses genes that are strongly induced as pharyngeal arch neural crest derived cells begin skeletal differentiation. In wild types initial Jagged Notch repression dorsally ensures that barx1+ condensations and cartilage differentiation occur first in ventral intermediate zones of the pharyngeal arches. Reduced Jagged Notch signaling results in an expansion of pre cartilage condensations in the upper face with loss of barx1 partially restoring dorsal cartilage shapes in jag1b mutants. Further by studying new mutants for zebrafish prrx1a and prrx1b we find that Prrx1 genes function in parallel to Jagged Notch signaling to restrict the formation of dorsal barx1+ pre cartilage condensations. Consistently combined losses of jag1b and prrx1a/b robustly rescue ventral barx1+ condensations and lower facial cartilage development in edn1 mutants. Together our work suggests that Edn1 works through parallel inhibition of Jagged Notch and Prrx1 pathways to promote an earlier and more extensive establishment of cartilage condensations in the lower face. Overall design: We performed RNAseq on FACS sorted neural crest derived pharyngeal arch cells fli1a:GFP; sox10:DsRed double positive from wild type embryos at 3 different stages 20 28 and 36 hpf and embryos with altered levels of Edn1 and Notch signaling edn1 mutants and hsp70I:Gal4; UAS:Edn1 transgenics; jag1b mutants dibenzazepine treated embryos and hsp70I:Gal4; UAS:NICD transgenics. We also sequenced RNA from heat shocked UAS:Edn1+ and hsp…	pubmed:27058748	UASEdn1 36hpf DP	GSM1876262	source name:Pharyngeal arches\|tissue:Pharyngeal arches\|developmental stage:embryo\|age:36 hpf\|genotype:UASEdn1\|treatment:Heat shocked	UASEdn1 36hpf DP	Raw sequencing data in Fastq format was imported into the Partek Flow® interface for alignment and quantification. Pre alignment QC showed that the reads from all samples had generally high quality with the average Phred quality score for each sample being above 30. Reads were then trimmed from both ends based on Phred quality score with a minimum end quality level of 20 and a minimum acceptable read length of 25. The TopHat 2 algorithm was used to align the trimmed reads to the zebrafish GRCz10 genome assembly Ensembl v80. Aligned reads were then quantified using the Partek E/M algorithm with default parameters to yield the RPKM values. Genome build: GRCz10 Supplementary files format and content: csv text files include RPKM values for each gene in each sample	Pharyngeal arches	GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol and quantified on a NanoDrop 2000 spectrophotometer NanoDrop Products Wilmington DE USA. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer V3 kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.		tissue:Pharyngeal arches\|developmental stage:embryo\|age:36 hpf\|genotype:UASEdn1\|treatment:Heat shocked	GSM1876262	GSM1876262: UASEdn1 36hpf DP; Danio rerio; RNA Seq	GSM1876262		1	GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol and quantified on a NanoDrop 2000 spectrophotometer NanoDrop Products Wilmington DE USA. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer V3 kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.	GEO Accession:GSM1876262	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP063659		GC-68_L000_R1_001.fastq.gz GC-68_L000_R2_001.fastq.gz	fastq fastq	7552509120.0	49687560.0	GSM1876262 r1	0:76 1:76	A:2200651776;C:1439090377;G:1524077665;T:2388535092;N:154210	76	76			2200651776	1439090377	1524077665	2388535092	154210	SRX1240723	SRS1067356	SRA297650	GEO	Crump Lab, Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California	2	0.87955	0.93035	0.13705	0.14804	0.76274	0.77796	0.48221	0.47595	76	76	B	B	biological fallback assumption	illumina	nextseq	full_length	cdna_unspecified	smarter	bulk	unknown	unknown	United States	2015-09-14	Pharyngula	Embryo	Pharyngeal Arch	Multi-system
39922	39922	SRR2392493	SRX1240722	SRS1067357	SRP063659	PRJNA295533	Accelerated cartilage differentiation distinguishes the lower from the upper vertebrate face	GSE72985	Transcriptome Analysis	Distinct shaping of the upper versus lower facial skeleton is essential for function of the vertebrate jaw and middle ear yet the cellular mechanisms by which this occurs have remained unclear. Here we show that Endothelin1 Edn1 signaling accelerates mesenchymal condensation and subsequent cartilage formation in the lower face through antagonism of Jagged Notch signaling and Prrx1 transcription factors. A genomic analysis of facial skeletal precursors in mutants and overexpression embryos reveals that Jagged Notch signaling represses genes that are strongly induced as pharyngeal arch neural crest derived cells begin skeletal differentiation. In wild types initial Jagged Notch repression dorsally ensures that barx1+ condensations and cartilage differentiation occur first in ventral intermediate zones of the pharyngeal arches. Reduced Jagged Notch signaling results in an expansion of pre cartilage condensations in the upper face with loss of barx1 partially restoring dorsal cartilage shapes in jag1b mutants. Further by studying new mutants for zebrafish prrx1a and prrx1b we find that Prrx1 genes function in parallel to Jagged Notch signaling to restrict the formation of dorsal barx1+ pre cartilage condensations. Consistently combined losses of jag1b and prrx1a/b robustly rescue ventral barx1+ condensations and lower facial cartilage development in edn1 mutants. Together our work suggests that Edn1 works through parallel inhibition of Jagged Notch and Prrx1 pathways to promote an earlier and more extensive establishment of cartilage condensations in the lower face. Overall design: We performed RNAseq on FACS sorted neural crest derived pharyngeal arch cells fli1a:GFP; sox10:DsRed double positive from wild type embryos at 3 different stages 20 28 and 36 hpf and embryos with altered levels of Edn1 and Notch signaling edn1 mutants and hsp70I:Gal4; UAS:Edn1 transgenics; jag1b mutants dibenzazepine treated embryos and hsp70I:Gal4; UAS:NICD transgenics. We also sequenced RNA from heat shocked UAS:Edn1+ and hsp…	pubmed:27058748	hspGal4 36hpf DP	GSM1876261	source name:Pharyngeal arches\|tissue:Pharyngeal arches\|developmental stage:embryo\|age:36 hpf\|genotype:hspGal4\|treatment:Heat shocked	hspGal4 36hpf DP	Raw sequencing data in Fastq format was imported into the Partek Flow® interface for alignment and quantification. Pre alignment QC showed that the reads from all samples had generally high quality with the average Phred quality score for each sample being above 30. Reads were then trimmed from both ends based on Phred quality score with a minimum end quality level of 20 and a minimum acceptable read length of 25. The TopHat 2 algorithm was used to align the trimmed reads to the zebrafish GRCz10 genome assembly Ensembl v80. Aligned reads were then quantified using the Partek E/M algorithm with default parameters to yield the RPKM values. Genome build: GRCz10 Supplementary files format and content: csv text files include RPKM values for each gene in each sample	Pharyngeal arches	GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol and quantified on a NanoDrop 2000 spectrophotometer NanoDrop Products Wilmington DE USA. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer V3 kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.		tissue:Pharyngeal arches\|developmental stage:embryo\|age:36 hpf\|genotype:hspGal4\|treatment:Heat shocked	GSM1876261	GSM1876261: hspGal4 36hpf DP; Danio rerio; RNA Seq	GSM1876261		1	GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol and quantified on a NanoDrop 2000 spectrophotometer NanoDrop Products Wilmington DE USA. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer V3 kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.	GEO Accession:GSM1876261	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP063659		GC-67_L000_R1_001.fastq.gz GC-67_L000_R2_001.fastq.gz	fastq fastq	12101492616.0	79615083.0	GSM1876261 r1	0:76 1:76	A:3579849331;C:2226140960;G:2397001824;T:3898240336;N:260165	76	76			3579849331	2226140960	2397001824	3898240336	260165	SRX1240722	SRS1067357	SRA297650	GEO	Crump Lab, Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California	2	0.85987	0.92528	0.14437	0.15795	0.7624	0.7781	0.50831	0.50375	76	76	B	B	biological fallback assumption	illumina	nextseq	full_length	cdna_unspecified	smarter	bulk	unknown	unknown	United States	2015-09-14	Pharyngula	Embryo	Pharyngeal Arch	Multi-system
39923	39923	SRR2392492	SRX1240721	SRS1067358	SRP063659	PRJNA295533	Accelerated cartilage differentiation distinguishes the lower from the upper vertebrate face	GSE72985	Transcriptome Analysis	Distinct shaping of the upper versus lower facial skeleton is essential for function of the vertebrate jaw and middle ear yet the cellular mechanisms by which this occurs have remained unclear. Here we show that Endothelin1 Edn1 signaling accelerates mesenchymal condensation and subsequent cartilage formation in the lower face through antagonism of Jagged Notch signaling and Prrx1 transcription factors. A genomic analysis of facial skeletal precursors in mutants and overexpression embryos reveals that Jagged Notch signaling represses genes that are strongly induced as pharyngeal arch neural crest derived cells begin skeletal differentiation. In wild types initial Jagged Notch repression dorsally ensures that barx1+ condensations and cartilage differentiation occur first in ventral intermediate zones of the pharyngeal arches. Reduced Jagged Notch signaling results in an expansion of pre cartilage condensations in the upper face with loss of barx1 partially restoring dorsal cartilage shapes in jag1b mutants. Further by studying new mutants for zebrafish prrx1a and prrx1b we find that Prrx1 genes function in parallel to Jagged Notch signaling to restrict the formation of dorsal barx1+ pre cartilage condensations. Consistently combined losses of jag1b and prrx1a/b robustly rescue ventral barx1+ condensations and lower facial cartilage development in edn1 mutants. Together our work suggests that Edn1 works through parallel inhibition of Jagged Notch and Prrx1 pathways to promote an earlier and more extensive establishment of cartilage condensations in the lower face. Overall design: We performed RNAseq on FACS sorted neural crest derived pharyngeal arch cells fli1a:GFP; sox10:DsRed double positive from wild type embryos at 3 different stages 20 28 and 36 hpf and embryos with altered levels of Edn1 and Notch signaling edn1 mutants and hsp70I:Gal4; UAS:Edn1 transgenics; jag1b mutants dibenzazepine treated embryos and hsp70I:Gal4; UAS:NICD transgenics. We also sequenced RNA from heat shocked UAS:Edn1+ and hsp…	pubmed:27058748	jag1b++ 36hpf DP	GSM1876260	source name:Pharyngeal arches\|tissue:Pharyngeal arches\|developmental stage:embryo\|age:36 hpf\|genotype:WT\|treatment:Genotyped	jag1b++ 36hpf DP	Raw sequencing data in Fastq format was imported into the Partek Flow® interface for alignment and quantification. Pre alignment QC showed that the reads from all samples had generally high quality with the average Phred quality score for each sample being above 30. Reads were then trimmed from both ends based on Phred quality score with a minimum end quality level of 20 and a minimum acceptable read length of 25. The TopHat 2 algorithm was used to align the trimmed reads to the zebrafish GRCz10 genome assembly Ensembl v80. Aligned reads were then quantified using the Partek E/M algorithm with default parameters to yield the RPKM values. Genome build: GRCz10 Supplementary files format and content: csv text files include RPKM values for each gene in each sample	Pharyngeal arches	GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol and quantified on a NanoDrop 2000 spectrophotometer NanoDrop Products Wilmington DE USA. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer V3 kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.		tissue:Pharyngeal arches\|developmental stage:embryo\|age:36 hpf\|genotype:WT\|treatment:Genotyped	GSM1876260	GSM1876260: jag1b++ 36hpf DP; Danio rerio; RNA Seq	GSM1876260		1	GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol and quantified on a NanoDrop 2000 spectrophotometer NanoDrop Products Wilmington DE USA. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer V3 kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.	GEO Accession:GSM1876260	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP063659		GC-62_L000_R1_001.fastq.gz GC-62_L000_R2_001.fastq.gz	fastq fastq	9196789944.0	60505197.0	GSM1876260 r1	0:76 1:76	A:2617231956;C:1761629764;G:1849570227;T:2965452565;N:2905432	76	76			2617231956	1761629764	1849570227	2965452565	2905432	SRX1240721	SRS1067358	SRA297650	GEO	Crump Lab, Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California	2	0.87575	0.84626	0.14246	0.13869	0.76426	0.78595	0.49695	0.49462	76	76	B	B	biological fallback assumption	illumina	nextseq	full_length	cdna_unspecified	smarter	bulk	unknown	unknown	United States	2015-09-14	Pharyngula	Embryo	Pharyngeal Arch	Multi-system
39924	39924	SRR2392491	SRX1240720	SRS1067359	SRP063659	PRJNA295533	Accelerated cartilage differentiation distinguishes the lower from the upper vertebrate face	GSE72985	Transcriptome Analysis	Distinct shaping of the upper versus lower facial skeleton is essential for function of the vertebrate jaw and middle ear yet the cellular mechanisms by which this occurs have remained unclear. Here we show that Endothelin1 Edn1 signaling accelerates mesenchymal condensation and subsequent cartilage formation in the lower face through antagonism of Jagged Notch signaling and Prrx1 transcription factors. A genomic analysis of facial skeletal precursors in mutants and overexpression embryos reveals that Jagged Notch signaling represses genes that are strongly induced as pharyngeal arch neural crest derived cells begin skeletal differentiation. In wild types initial Jagged Notch repression dorsally ensures that barx1+ condensations and cartilage differentiation occur first in ventral intermediate zones of the pharyngeal arches. Reduced Jagged Notch signaling results in an expansion of pre cartilage condensations in the upper face with loss of barx1 partially restoring dorsal cartilage shapes in jag1b mutants. Further by studying new mutants for zebrafish prrx1a and prrx1b we find that Prrx1 genes function in parallel to Jagged Notch signaling to restrict the formation of dorsal barx1+ pre cartilage condensations. Consistently combined losses of jag1b and prrx1a/b robustly rescue ventral barx1+ condensations and lower facial cartilage development in edn1 mutants. Together our work suggests that Edn1 works through parallel inhibition of Jagged Notch and Prrx1 pathways to promote an earlier and more extensive establishment of cartilage condensations in the lower face. Overall design: We performed RNAseq on FACS sorted neural crest derived pharyngeal arch cells fli1a:GFP; sox10:DsRed double positive from wild type embryos at 3 different stages 20 28 and 36 hpf and embryos with altered levels of Edn1 and Notch signaling edn1 mutants and hsp70I:Gal4; UAS:Edn1 transgenics; jag1b mutants dibenzazepine treated embryos and hsp70I:Gal4; UAS:NICD transgenics. We also sequenced RNA from heat shocked UAS:Edn1+ and hsp…	pubmed:27058748	hspEdn1 36hpf DP	GSM1876259	source name:Pharyngeal arches\|tissue:Pharyngeal arches\|developmental stage:embryo\|age:36 hpf\|genotype:hspGal4 ; UASEdn1\|treatment:Heat shocked	hspEdn1 36hpf DP	Raw sequencing data in Fastq format was imported into the Partek Flow® interface for alignment and quantification. Pre alignment QC showed that the reads from all samples had generally high quality with the average Phred quality score for each sample being above 30. Reads were then trimmed from both ends based on Phred quality score with a minimum end quality level of 20 and a minimum acceptable read length of 25. The TopHat 2 algorithm was used to align the trimmed reads to the zebrafish GRCz10 genome assembly Ensembl v80. Aligned reads were then quantified using the Partek E/M algorithm with default parameters to yield the RPKM values. Genome build: GRCz10 Supplementary files format and content: csv text files include RPKM values for each gene in each sample	Pharyngeal arches	GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol and quantified on a NanoDrop 2000 spectrophotometer NanoDrop Products Wilmington DE USA. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer V3 kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.		tissue:Pharyngeal arches\|developmental stage:embryo\|age:36 hpf\|genotype:hspGal4 ; UASEdn1\|treatment:Heat shocked	GSM1876259	GSM1876259: hspEdn1 36hpf DP; Danio rerio; RNA Seq	GSM1876259		1	GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol and quantified on a NanoDrop 2000 spectrophotometer NanoDrop Products Wilmington DE USA. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer V3 kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.	GEO Accession:GSM1876259	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP063659		GC-63_L000_R1_001.fastq.gz GC-63_L000_R2_001.fastq.gz	fastq fastq	8241464016.0	54220158.0	GSM1876259 r1	0:76 1:76	A:2338801834;C:1581411340;G:1652427014;T:2666281574;N:2542254	76	76			2338801834	1581411340	1652427014	2666281574	2542254	SRX1240720	SRS1067359	SRA297650	GEO	Crump Lab, Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California	2	0.88843	0.85822	0.15095	0.14812	0.75978	0.7751	0.49125	0.48482	76	76	B	B	biological fallback assumption	illumina	nextseq	full_length	cdna_unspecified	smarter	bulk	unknown	unknown	United States	2015-09-14	Pharyngula	Embryo	Pharyngeal Arch	Multi-system
39925	39925	SRR2392490	SRX1240719	SRS1067360	SRP063659	PRJNA295533	Accelerated cartilage differentiation distinguishes the lower from the upper vertebrate face	GSE72985	Transcriptome Analysis	Distinct shaping of the upper versus lower facial skeleton is essential for function of the vertebrate jaw and middle ear yet the cellular mechanisms by which this occurs have remained unclear. Here we show that Endothelin1 Edn1 signaling accelerates mesenchymal condensation and subsequent cartilage formation in the lower face through antagonism of Jagged Notch signaling and Prrx1 transcription factors. A genomic analysis of facial skeletal precursors in mutants and overexpression embryos reveals that Jagged Notch signaling represses genes that are strongly induced as pharyngeal arch neural crest derived cells begin skeletal differentiation. In wild types initial Jagged Notch repression dorsally ensures that barx1+ condensations and cartilage differentiation occur first in ventral intermediate zones of the pharyngeal arches. Reduced Jagged Notch signaling results in an expansion of pre cartilage condensations in the upper face with loss of barx1 partially restoring dorsal cartilage shapes in jag1b mutants. Further by studying new mutants for zebrafish prrx1a and prrx1b we find that Prrx1 genes function in parallel to Jagged Notch signaling to restrict the formation of dorsal barx1+ pre cartilage condensations. Consistently combined losses of jag1b and prrx1a/b robustly rescue ventral barx1+ condensations and lower facial cartilage development in edn1 mutants. Together our work suggests that Edn1 works through parallel inhibition of Jagged Notch and Prrx1 pathways to promote an earlier and more extensive establishment of cartilage condensations in the lower face. Overall design: We performed RNAseq on FACS sorted neural crest derived pharyngeal arch cells fli1a:GFP; sox10:DsRed double positive from wild type embryos at 3 different stages 20 28 and 36 hpf and embryos with altered levels of Edn1 and Notch signaling edn1 mutants and hsp70I:Gal4; UAS:Edn1 transgenics; jag1b mutants dibenzazepine treated embryos and hsp70I:Gal4; UAS:NICD transgenics. We also sequenced RNA from heat shocked UAS:Edn1+ and hsp…	pubmed:27058748	hspNICD 36hpf DP	GSM1876258	source name:Pharyngeal arches\|tissue:Pharyngeal arches\|developmental stage:embryo\|age:36 hpf\|genotype:hspGal4 ; UASNICD\|treatment:Heat shocked	hspNICD 36hpf DP	Raw sequencing data in Fastq format was imported into the Partek Flow® interface for alignment and quantification. Pre alignment QC showed that the reads from all samples had generally high quality with the average Phred quality score for each sample being above 30. Reads were then trimmed from both ends based on Phred quality score with a minimum end quality level of 20 and a minimum acceptable read length of 25. The TopHat 2 algorithm was used to align the trimmed reads to the zebrafish GRCz10 genome assembly Ensembl v80. Aligned reads were then quantified using the Partek E/M algorithm with default parameters to yield the RPKM values. Genome build: GRCz10 Supplementary files format and content: csv text files include RPKM values for each gene in each sample	Pharyngeal arches	GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol and quantified on a NanoDrop 2000 spectrophotometer NanoDrop Products Wilmington DE USA. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer V3 kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.		tissue:Pharyngeal arches\|developmental stage:embryo\|age:36 hpf\|genotype:hspGal4 ; UASNICD\|treatment:Heat shocked	GSM1876258	GSM1876258: hspNICD 36hpf DP; Danio rerio; RNA Seq	GSM1876258		1	GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol and quantified on a NanoDrop 2000 spectrophotometer NanoDrop Products Wilmington DE USA. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer V3 kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.	GEO Accession:GSM1876258	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP063659		GC-71_L000_R1_001.fastq.gz GC-71_L000_R2_001.fastq.gz	fastq fastq	8181679072.0	53826836.0	GSM1876258 r1	0:76 1:76	A:2319439232;C:1614438452;G:1687303013;T:2557951732;N:2546643	76	76			2319439232	1614438452	1687303013	2557951732	2546643	SRX1240719	SRS1067360	SRA297650	GEO	Crump Lab, Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California	2	0.90043	0.87604	0.13901	0.13824	0.74937	0.76777	0.48827	0.47857	76	76	B	B	biological fallback assumption	illumina	nextseq	full_length	cdna_unspecified	smarter	bulk	unknown	unknown	United States	2015-09-14	Pharyngula	Embryo	Pharyngeal Arch	Multi-system
39926	39926	SRR2392489	SRX1240718	SRS1067361	SRP063659	PRJNA295533	Accelerated cartilage differentiation distinguishes the lower from the upper vertebrate face	GSE72985	Transcriptome Analysis	Distinct shaping of the upper versus lower facial skeleton is essential for function of the vertebrate jaw and middle ear yet the cellular mechanisms by which this occurs have remained unclear. Here we show that Endothelin1 Edn1 signaling accelerates mesenchymal condensation and subsequent cartilage formation in the lower face through antagonism of Jagged Notch signaling and Prrx1 transcription factors. A genomic analysis of facial skeletal precursors in mutants and overexpression embryos reveals that Jagged Notch signaling represses genes that are strongly induced as pharyngeal arch neural crest derived cells begin skeletal differentiation. In wild types initial Jagged Notch repression dorsally ensures that barx1+ condensations and cartilage differentiation occur first in ventral intermediate zones of the pharyngeal arches. Reduced Jagged Notch signaling results in an expansion of pre cartilage condensations in the upper face with loss of barx1 partially restoring dorsal cartilage shapes in jag1b mutants. Further by studying new mutants for zebrafish prrx1a and prrx1b we find that Prrx1 genes function in parallel to Jagged Notch signaling to restrict the formation of dorsal barx1+ pre cartilage condensations. Consistently combined losses of jag1b and prrx1a/b robustly rescue ventral barx1+ condensations and lower facial cartilage development in edn1 mutants. Together our work suggests that Edn1 works through parallel inhibition of Jagged Notch and Prrx1 pathways to promote an earlier and more extensive establishment of cartilage condensations in the lower face. Overall design: We performed RNAseq on FACS sorted neural crest derived pharyngeal arch cells fli1a:GFP; sox10:DsRed double positive from wild type embryos at 3 different stages 20 28 and 36 hpf and embryos with altered levels of Edn1 and Notch signaling edn1 mutants and hsp70I:Gal4; UAS:Edn1 transgenics; jag1b mutants dibenzazepine treated embryos and hsp70I:Gal4; UAS:NICD transgenics. We also sequenced RNA from heat shocked UAS:Edn1+ and hsp…	pubmed:27058748	DBZ 36hpf DP	GSM1876257	source name:Pharyngeal arches\|tissue:Pharyngeal arches\|developmental stage:embryo\|age:36 hpf\|genotype:WT\|treatment:DBZ treated	DBZ 36hpf DP	Raw sequencing data in Fastq format was imported into the Partek Flow® interface for alignment and quantification. Pre alignment QC showed that the reads from all samples had generally high quality with the average Phred quality score for each sample being above 30. Reads were then trimmed from both ends based on Phred quality score with a minimum end quality level of 20 and a minimum acceptable read length of 25. The TopHat 2 algorithm was used to align the trimmed reads to the zebrafish GRCz10 genome assembly Ensembl v80. Aligned reads were then quantified using the Partek E/M algorithm with default parameters to yield the RPKM values. Genome build: GRCz10 Supplementary files format and content: csv text files include RPKM values for each gene in each sample	Pharyngeal arches	GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol and quantified on a NanoDrop 2000 spectrophotometer NanoDrop Products Wilmington DE USA. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer V3 kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.		tissue:Pharyngeal arches\|developmental stage:embryo\|age:36 hpf\|genotype:WT\|treatment:DBZ treated	GSM1876257	GSM1876257: DBZ 36hpf DP; Danio rerio; RNA Seq	GSM1876257		1	GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol and quantified on a NanoDrop 2000 spectrophotometer NanoDrop Products Wilmington DE USA. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer V3 kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.	GEO Accession:GSM1876257	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP063659		GC-41_L000_R1_001.fastq.gz GC-41_L000_R2_001.fastq.gz	fastq fastq	10477585112.0	68931481.0	GSM1876257 r1	0:76 1:76	A:3034271232;C:2011126753;G:2224836663;T:3203537953;N:3812511	76	76			3034271232	2011126753	2224836663	3203537953	3812511	SRX1240718	SRS1067361	SRA297650	GEO	Crump Lab, Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California	2	0.86576	0.91066	0.12989	0.13947	0.77273	0.78804	0.49193	0.49239	76	76	B	B	biological fallback assumption	illumina	nextseq	full_length	cdna_unspecified	smarter	bulk	unknown	unknown	United States	2015-09-14	Pharyngula	Embryo	Pharyngeal Arch	Multi-system
39927	39927	SRR2392488	SRX1240717	SRS1067362	SRP063659	PRJNA295533	Accelerated cartilage differentiation distinguishes the lower from the upper vertebrate face	GSE72985	Transcriptome Analysis	Distinct shaping of the upper versus lower facial skeleton is essential for function of the vertebrate jaw and middle ear yet the cellular mechanisms by which this occurs have remained unclear. Here we show that Endothelin1 Edn1 signaling accelerates mesenchymal condensation and subsequent cartilage formation in the lower face through antagonism of Jagged Notch signaling and Prrx1 transcription factors. A genomic analysis of facial skeletal precursors in mutants and overexpression embryos reveals that Jagged Notch signaling represses genes that are strongly induced as pharyngeal arch neural crest derived cells begin skeletal differentiation. In wild types initial Jagged Notch repression dorsally ensures that barx1+ condensations and cartilage differentiation occur first in ventral intermediate zones of the pharyngeal arches. Reduced Jagged Notch signaling results in an expansion of pre cartilage condensations in the upper face with loss of barx1 partially restoring dorsal cartilage shapes in jag1b mutants. Further by studying new mutants for zebrafish prrx1a and prrx1b we find that Prrx1 genes function in parallel to Jagged Notch signaling to restrict the formation of dorsal barx1+ pre cartilage condensations. Consistently combined losses of jag1b and prrx1a/b robustly rescue ventral barx1+ condensations and lower facial cartilage development in edn1 mutants. Together our work suggests that Edn1 works through parallel inhibition of Jagged Notch and Prrx1 pathways to promote an earlier and more extensive establishment of cartilage condensations in the lower face. Overall design: We performed RNAseq on FACS sorted neural crest derived pharyngeal arch cells fli1a:GFP; sox10:DsRed double positive from wild type embryos at 3 different stages 20 28 and 36 hpf and embryos with altered levels of Edn1 and Notch signaling edn1 mutants and hsp70I:Gal4; UAS:Edn1 transgenics; jag1b mutants dibenzazepine treated embryos and hsp70I:Gal4; UAS:NICD transgenics. We also sequenced RNA from heat shocked UAS:Edn1+ and hsp…	pubmed:27058748	jag1b 36hpf DP	GSM1876256	source name:Pharyngeal arches\|tissue:Pharyngeal arches\|developmental stage:embryo\|age:36 hpf\|genotype:jag1b / \|treatment:Genotyped	jag1b 36hpf DP	Raw sequencing data in Fastq format was imported into the Partek Flow® interface for alignment and quantification. Pre alignment QC showed that the reads from all samples had generally high quality with the average Phred quality score for each sample being above 30. Reads were then trimmed from both ends based on Phred quality score with a minimum end quality level of 20 and a minimum acceptable read length of 25. The TopHat 2 algorithm was used to align the trimmed reads to the zebrafish GRCz10 genome assembly Ensembl v80. Aligned reads were then quantified using the Partek E/M algorithm with default parameters to yield the RPKM values. Genome build: GRCz10 Supplementary files format and content: csv text files include RPKM values for each gene in each sample	Pharyngeal arches	GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol and quantified on a NanoDrop 2000 spectrophotometer NanoDrop Products Wilmington DE USA. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer V3 kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.		tissue:Pharyngeal arches\|developmental stage:embryo\|age:36 hpf\|genotype:jag1b / \|treatment:Genotyped	GSM1876256	GSM1876256: jag1b 36hpf DP; Danio rerio; RNA Seq	GSM1876256		1	GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol and quantified on a NanoDrop 2000 spectrophotometer NanoDrop Products Wilmington DE USA. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer V3 kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.	GEO Accession:GSM1876256	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP063659		GC-61_L000_R2_001.fastq.gz GC-61_L000_R1_001.fastq.gz	fastq fastq	7981914592.0	52512596.0	GSM1876256 r1	0:76 1:76	A:2278594852;C:1520667450;G:1610295025;T:2569901477;N:2455788	76	76			2278594852	1520667450	1610295025	2569901477	2455788	SRX1240717	SRS1067362	SRA297650	GEO	Crump Lab, Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California	2	0.88292	0.85134	0.15785	0.15494	0.7643	0.78222	0.5054	0.49691	76	76	B	B	biological fallback assumption	illumina	nextseq	full_length	cdna_unspecified	smarter	bulk	unknown	unknown	United States	2015-09-14	Pharyngula	Embryo	Pharyngeal Arch	Multi-system
39928	39928	SRR2392487	SRX1240716	SRS1067363	SRP063659	PRJNA295533	Accelerated cartilage differentiation distinguishes the lower from the upper vertebrate face	GSE72985	Transcriptome Analysis	Distinct shaping of the upper versus lower facial skeleton is essential for function of the vertebrate jaw and middle ear yet the cellular mechanisms by which this occurs have remained unclear. Here we show that Endothelin1 Edn1 signaling accelerates mesenchymal condensation and subsequent cartilage formation in the lower face through antagonism of Jagged Notch signaling and Prrx1 transcription factors. A genomic analysis of facial skeletal precursors in mutants and overexpression embryos reveals that Jagged Notch signaling represses genes that are strongly induced as pharyngeal arch neural crest derived cells begin skeletal differentiation. In wild types initial Jagged Notch repression dorsally ensures that barx1+ condensations and cartilage differentiation occur first in ventral intermediate zones of the pharyngeal arches. Reduced Jagged Notch signaling results in an expansion of pre cartilage condensations in the upper face with loss of barx1 partially restoring dorsal cartilage shapes in jag1b mutants. Further by studying new mutants for zebrafish prrx1a and prrx1b we find that Prrx1 genes function in parallel to Jagged Notch signaling to restrict the formation of dorsal barx1+ pre cartilage condensations. Consistently combined losses of jag1b and prrx1a/b robustly rescue ventral barx1+ condensations and lower facial cartilage development in edn1 mutants. Together our work suggests that Edn1 works through parallel inhibition of Jagged Notch and Prrx1 pathways to promote an earlier and more extensive establishment of cartilage condensations in the lower face. Overall design: We performed RNAseq on FACS sorted neural crest derived pharyngeal arch cells fli1a:GFP; sox10:DsRed double positive from wild type embryos at 3 different stages 20 28 and 36 hpf and embryos with altered levels of Edn1 and Notch signaling edn1 mutants and hsp70I:Gal4; UAS:Edn1 transgenics; jag1b mutants dibenzazepine treated embryos and hsp70I:Gal4; UAS:NICD transgenics. We also sequenced RNA from heat shocked UAS:Edn1+ and hsp…	pubmed:27058748	edn1 36hpf DP	GSM1876255	source name:Pharyngeal arches\|tissue:Pharyngeal arches\|developmental stage:embryo\|age:36 hpf\|genotype:edn1 / \|treatment:N1	edn1 36hpf DP	Raw sequencing data in Fastq format was imported into the Partek Flow® interface for alignment and quantification. Pre alignment QC showed that the reads from all samples had generally high quality with the average Phred quality score for each sample being above 30. Reads were then trimmed from both ends based on Phred quality score with a minimum end quality level of 20 and a minimum acceptable read length of 25. The TopHat 2 algorithm was used to align the trimmed reads to the zebrafish GRCz10 genome assembly Ensembl v80. Aligned reads were then quantified using the Partek E/M algorithm with default parameters to yield the RPKM values. Genome build: GRCz10 Supplementary files format and content: csv text files include RPKM values for each gene in each sample	Pharyngeal arches	GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol and quantified on a NanoDrop 2000 spectrophotometer NanoDrop Products Wilmington DE USA. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer V3 kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.		tissue:Pharyngeal arches\|developmental stage:embryo\|age:36 hpf\|genotype:edn1 / \|treatment:N1	GSM1876255	GSM1876255: edn1 36hpf DP; Danio rerio; RNA Seq	GSM1876255		1	GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol and quantified on a NanoDrop 2000 spectrophotometer NanoDrop Products Wilmington DE USA. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer V3 kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.	GEO Accession:GSM1876255	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP063659		GC-34_CAGATC_L008_R1_001.fastq.gz GC-34_CAGATC_L008_R2_001.fastq.gz	fastq fastq	3805470400.0	38054704.0	GSM1876255 r1	0:50 1:50	A:1039863232;C:811509659;G:855601660;T:1094752796;N:3743053	50	50			1039863232	811509659	855601660	1094752796	3743053	SRX1240716	SRS1067363	SRA297650	GEO	Crump Lab, Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California	2	0.90373	0.77103	0.11765	0.1006	0.75982	0.77565	0.48596	0.4847	50	50	B	B	biological fallback assumption	illumina	hiseq_era	full_length	cdna_unspecified	smarter	bulk	unknown	unknown	United States	2015-09-14	Pharyngula	Embryo	Pharyngeal Arch	Multi-system
39929	39929	SRR2392486	SRX1240715	SRS1067364	SRP063659	PRJNA295533	Accelerated cartilage differentiation distinguishes the lower from the upper vertebrate face	GSE72985	Transcriptome Analysis	Distinct shaping of the upper versus lower facial skeleton is essential for function of the vertebrate jaw and middle ear yet the cellular mechanisms by which this occurs have remained unclear. Here we show that Endothelin1 Edn1 signaling accelerates mesenchymal condensation and subsequent cartilage formation in the lower face through antagonism of Jagged Notch signaling and Prrx1 transcription factors. A genomic analysis of facial skeletal precursors in mutants and overexpression embryos reveals that Jagged Notch signaling represses genes that are strongly induced as pharyngeal arch neural crest derived cells begin skeletal differentiation. In wild types initial Jagged Notch repression dorsally ensures that barx1+ condensations and cartilage differentiation occur first in ventral intermediate zones of the pharyngeal arches. Reduced Jagged Notch signaling results in an expansion of pre cartilage condensations in the upper face with loss of barx1 partially restoring dorsal cartilage shapes in jag1b mutants. Further by studying new mutants for zebrafish prrx1a and prrx1b we find that Prrx1 genes function in parallel to Jagged Notch signaling to restrict the formation of dorsal barx1+ pre cartilage condensations. Consistently combined losses of jag1b and prrx1a/b robustly rescue ventral barx1+ condensations and lower facial cartilage development in edn1 mutants. Together our work suggests that Edn1 works through parallel inhibition of Jagged Notch and Prrx1 pathways to promote an earlier and more extensive establishment of cartilage condensations in the lower face. Overall design: We performed RNAseq on FACS sorted neural crest derived pharyngeal arch cells fli1a:GFP; sox10:DsRed double positive from wild type embryos at 3 different stages 20 28 and 36 hpf and embryos with altered levels of Edn1 and Notch signaling edn1 mutants and hsp70I:Gal4; UAS:Edn1 transgenics; jag1b mutants dibenzazepine treated embryos and hsp70I:Gal4; UAS:NICD transgenics. We also sequenced RNA from heat shocked UAS:Edn1+ and hsp…	pubmed:27058748	WT 28hpf DP	GSM1876254	source name:Pharyngeal arches\|tissue:Pharyngeal arches\|developmental stage:embryo\|age:28 hpf\|genotype:WT\|treatment:N1	WT 28hpf DP	Raw sequencing data in Fastq format was imported into the Partek Flow® interface for alignment and quantification. Pre alignment QC showed that the reads from all samples had generally high quality with the average Phred quality score for each sample being above 30. Reads were then trimmed from both ends based on Phred quality score with a minimum end quality level of 20 and a minimum acceptable read length of 25. The TopHat 2 algorithm was used to align the trimmed reads to the zebrafish GRCz10 genome assembly Ensembl v80. Aligned reads were then quantified using the Partek E/M algorithm with default parameters to yield the RPKM values. Genome build: GRCz10 Supplementary files format and content: csv text files include RPKM values for each gene in each sample	Pharyngeal arches	GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol and quantified on a NanoDrop 2000 spectrophotometer NanoDrop Products Wilmington DE USA. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer V3 kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.		tissue:Pharyngeal arches\|developmental stage:embryo\|age:28 hpf\|genotype:WT\|treatment:N1	GSM1876254	GSM1876254: WT 28hpf DP; Danio rerio; RNA Seq	GSM1876254		1	GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol and quantified on a NanoDrop 2000 spectrophotometer NanoDrop Products Wilmington DE USA. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer V3 kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.	GEO Accession:GSM1876254	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP063659		GC-53_L000_R1_001.fastq.gz GC-53_L000_R2_001.fastq.gz	fastq fastq	8894656200.0	58517475.0	GSM1876254 r1	0:76 1:76	A:2518354811;C:1741233873;G:1824297464;T:2807980201;N:2789851	76	76			2518354811	1741233873	1824297464	2807980201	2789851	SRX1240715	SRS1067364	SRA297650	GEO	Crump Lab, Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California	2	0.89587	0.86799	0.11918	0.11489	0.74846	0.76528	0.49754	0.49063	76	76	B	B	biological fallback assumption	illumina	nextseq	full_length	cdna_unspecified	smarter	bulk	unknown	unknown	United States	2015-09-14	Pharyngula	Embryo	Pharyngeal Arch	Multi-system
39930	39930	SRR2392485	SRX1240714	SRS1067365	SRP063659	PRJNA295533	Accelerated cartilage differentiation distinguishes the lower from the upper vertebrate face	GSE72985	Transcriptome Analysis	Distinct shaping of the upper versus lower facial skeleton is essential for function of the vertebrate jaw and middle ear yet the cellular mechanisms by which this occurs have remained unclear. Here we show that Endothelin1 Edn1 signaling accelerates mesenchymal condensation and subsequent cartilage formation in the lower face through antagonism of Jagged Notch signaling and Prrx1 transcription factors. A genomic analysis of facial skeletal precursors in mutants and overexpression embryos reveals that Jagged Notch signaling represses genes that are strongly induced as pharyngeal arch neural crest derived cells begin skeletal differentiation. In wild types initial Jagged Notch repression dorsally ensures that barx1+ condensations and cartilage differentiation occur first in ventral intermediate zones of the pharyngeal arches. Reduced Jagged Notch signaling results in an expansion of pre cartilage condensations in the upper face with loss of barx1 partially restoring dorsal cartilage shapes in jag1b mutants. Further by studying new mutants for zebrafish prrx1a and prrx1b we find that Prrx1 genes function in parallel to Jagged Notch signaling to restrict the formation of dorsal barx1+ pre cartilage condensations. Consistently combined losses of jag1b and prrx1a/b robustly rescue ventral barx1+ condensations and lower facial cartilage development in edn1 mutants. Together our work suggests that Edn1 works through parallel inhibition of Jagged Notch and Prrx1 pathways to promote an earlier and more extensive establishment of cartilage condensations in the lower face. Overall design: We performed RNAseq on FACS sorted neural crest derived pharyngeal arch cells fli1a:GFP; sox10:DsRed double positive from wild type embryos at 3 different stages 20 28 and 36 hpf and embryos with altered levels of Edn1 and Notch signaling edn1 mutants and hsp70I:Gal4; UAS:Edn1 transgenics; jag1b mutants dibenzazepine treated embryos and hsp70I:Gal4; UAS:NICD transgenics. We also sequenced RNA from heat shocked UAS:Edn1+ and hsp…	pubmed:27058748	WT 20hpf DP	GSM1876253	source name:Pharyngeal arches\|tissue:Pharyngeal arches\|developmental stage:embryo\|age:20 hpf\|genotype:WT\|treatment:N1	WT 20hpf DP	Raw sequencing data in Fastq format was imported into the Partek Flow® interface for alignment and quantification. Pre alignment QC showed that the reads from all samples had generally high quality with the average Phred quality score for each sample being above 30. Reads were then trimmed from both ends based on Phred quality score with a minimum end quality level of 20 and a minimum acceptable read length of 25. The TopHat 2 algorithm was used to align the trimmed reads to the zebrafish GRCz10 genome assembly Ensembl v80. Aligned reads were then quantified using the Partek E/M algorithm with default parameters to yield the RPKM values. Genome build: GRCz10 Supplementary files format and content: csv text files include RPKM values for each gene in each sample	Pharyngeal arches	GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol and quantified on a NanoDrop 2000 spectrophotometer NanoDrop Products Wilmington DE USA. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer V3 kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.		tissue:Pharyngeal arches\|developmental stage:embryo\|age:20 hpf\|genotype:WT\|treatment:N1	GSM1876253	GSM1876253: WT 20hpf DP; Danio rerio; RNA Seq	GSM1876253		1	GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol and quantified on a NanoDrop 2000 spectrophotometer NanoDrop Products Wilmington DE USA. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer V3 kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.	GEO Accession:GSM1876253	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP063659		GC-51_L000_R2_001.fastq.gz GC-51_L000_R1_001.fastq.gz	fastq fastq	8748773288.0	57557719.0	GSM1876253 r1	0:76 1:76	A:2470411775;C:1715400097;G:1801773754;T:2758442284;N:2745378	76	76			2470411775	1715400097	1801773754	2758442284	2745378	SRX1240714	SRS1067365	SRA297650	GEO	Crump Lab, Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California	2	0.9023	0.87479	0.11683	0.11569	0.75592	0.77327	0.48431	0.49574	76	76	B	B	biological fallback assumption	illumina	nextseq	full_length	cdna_unspecified	smarter	bulk	unknown	unknown	United States	2015-09-14	Segmentation	Embryo	Pharyngeal Arch	Multi-system
39931	39931	SRR2392484	SRX1240713	SRS1067366	SRP063659	PRJNA295533	Accelerated cartilage differentiation distinguishes the lower from the upper vertebrate face	GSE72985	Transcriptome Analysis	Distinct shaping of the upper versus lower facial skeleton is essential for function of the vertebrate jaw and middle ear yet the cellular mechanisms by which this occurs have remained unclear. Here we show that Endothelin1 Edn1 signaling accelerates mesenchymal condensation and subsequent cartilage formation in the lower face through antagonism of Jagged Notch signaling and Prrx1 transcription factors. A genomic analysis of facial skeletal precursors in mutants and overexpression embryos reveals that Jagged Notch signaling represses genes that are strongly induced as pharyngeal arch neural crest derived cells begin skeletal differentiation. In wild types initial Jagged Notch repression dorsally ensures that barx1+ condensations and cartilage differentiation occur first in ventral intermediate zones of the pharyngeal arches. Reduced Jagged Notch signaling results in an expansion of pre cartilage condensations in the upper face with loss of barx1 partially restoring dorsal cartilage shapes in jag1b mutants. Further by studying new mutants for zebrafish prrx1a and prrx1b we find that Prrx1 genes function in parallel to Jagged Notch signaling to restrict the formation of dorsal barx1+ pre cartilage condensations. Consistently combined losses of jag1b and prrx1a/b robustly rescue ventral barx1+ condensations and lower facial cartilage development in edn1 mutants. Together our work suggests that Edn1 works through parallel inhibition of Jagged Notch and Prrx1 pathways to promote an earlier and more extensive establishment of cartilage condensations in the lower face. Overall design: We performed RNAseq on FACS sorted neural crest derived pharyngeal arch cells fli1a:GFP; sox10:DsRed double positive from wild type embryos at 3 different stages 20 28 and 36 hpf and embryos with altered levels of Edn1 and Notch signaling edn1 mutants and hsp70I:Gal4; UAS:Edn1 transgenics; jag1b mutants dibenzazepine treated embryos and hsp70I:Gal4; UAS:NICD transgenics. We also sequenced RNA from heat shocked UAS:Edn1+ and hsp…	pubmed:27058748	WT 36hpf DP	GSM1876252	source name:Pharyngeal arches\|tissue:Pharyngeal arches\|developmental stage:embryo\|age:36 hpf\|genotype:WT\|treatment:N1	WT 36hpf DP	Raw sequencing data in Fastq format was imported into the Partek Flow® interface for alignment and quantification. Pre alignment QC showed that the reads from all samples had generally high quality with the average Phred quality score for each sample being above 30. Reads were then trimmed from both ends based on Phred quality score with a minimum end quality level of 20 and a minimum acceptable read length of 25. The TopHat 2 algorithm was used to align the trimmed reads to the zebrafish GRCz10 genome assembly Ensembl v80. Aligned reads were then quantified using the Partek E/M algorithm with default parameters to yield the RPKM values. Genome build: GRCz10 Supplementary files format and content: csv text files include RPKM values for each gene in each sample	Pharyngeal arches	GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol and quantified on a NanoDrop 2000 spectrophotometer NanoDrop Products Wilmington DE USA. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer V3 kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.		tissue:Pharyngeal arches\|developmental stage:embryo\|age:36 hpf\|genotype:WT\|treatment:N1	GSM1876252	GSM1876252: WT 36hpf DP; Danio rerio; RNA Seq	GSM1876252		1	GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol and quantified on a NanoDrop 2000 spectrophotometer NanoDrop Products Wilmington DE USA. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer V3 kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.	GEO Accession:GSM1876252	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP063659		GC-24_ATTCCT_L001_R1_001.fastq.gz GC-24_ATTCCT_L001_R2_001.fastq.gz	fastq fastq	5577850800.0	55778508.0	GSM1876252 r1	0:50 1:50	A:1539279722;C:1164400006;G:1236602222;T:1636301311;N:1267539	50	50			1539279722	1164400006	1236602222	1636301311	1267539	SRX1240713	SRS1067366	SRA297650	GEO	Crump Lab, Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California	2	0.90764	0.74515	0.17719	0.14848	0.75566	0.77737	0.49598	0.48654	50	50	B	B	biological fallback assumption	illumina	hiseq_era	full_length	cdna_unspecified	smarter	bulk	unknown	unknown	United States	2015-09-14	Pharyngula	Embryo	Pharyngeal Arch	Multi-system
41879	41879	SRR5320530	SRX2619935	SRS2029898	SRP101558	PRJNA378498	Functional Analysis of Regional Gene Expression in Zebrafish Craniofacial Development	GSE95812	Transcriptome Analysis	Patterning of the facial skeleton involves the precise deployment of thousands of genes in distinct regions of the pharyngeal arches. Despite their significance for craniofacial development how genetic programs drive this regionalization remains poorly understood. Here we use combinatorial labeling of zebrafish cranial neural crest derived cells CNCCs to define global gene expression along the dorsoventral axis of the developing arches. Intersection of region specific transcriptomes with expression changes in response to signaling perturbations demonstrates complex roles for Endothelin1 Edn1 signaling in the intermediate joint forming region yet a surprisingly minor role in ventral most regions. Analysis of co variance across multiple sequencing experiments further reveals clusters of co regulated genes with in situ hybridization confirming the expression of novel genes with domain specific expression. We then performed mutational analysis of a number of these genes which uncovered antagonistic functions of two Edn1 targets follistatin a fsta and emx2 in regulating cartilaginous joints in the hyoid arch. Our unbiased discovery and functional analysis of genes with regional expression in arch CNCCs reveals complex regulation by Edn1 and points to novel candidates for craniofacial disorders. Overall design: mRNA profiles of 3 distinct populations of zebrafish pharyngeal arch cells isolated using FACS from 36 hpf wild type WT zebrafish. fli1a:GFP+;sox10:DsRed and fli1a:GFP ;sox10:DsRed+ populations were also isolated at the same time and sequenced as controls 3 replicate each. Additionally there are mRNA profiles of zebrafish pharyngeal arches all domains combined isolated by FACS from 36 hpf zebrafish with the following genotypes: edn1 / 2 replicates jag1b / jag1b+/+ control hsp70I:Gal4; UAS:Edn1 hsp70I:Gal4; UAS:Nicd and hsp70I:Gal4 control.	pubmed:28705894	hspGal4 fli1a sox10	GSM2526409	tissue:Pharyngeal arches\|developmental stage:36 hpf\|genotype:hspGal4\|treatment:Heat shocked	hspGal4 fli1a sox10	Raw sequencing data in Fastq format was imported into the Partek Flow® interface for alignment and quantification. Pre alignment QC showed that the reads from all samples had generally high quality with the average Phred quality score for each sample being above 30. Reads were then trimmed from both ends based on Phred quality score with a minimum end quality level of 20 and a minimum acceptable read length of 25. The TopHat 2 algorithm was used to align the trimmed reads to the zebrafish GRCz10 genome assembly Ensembl v80. Aligned reads were then quantified using the Partek E/M algorithm with default parameters to yield the TPM values. Genome build: GRCz10 Supplementary files format and content: csv text files include TPM values for each gene in each sample	Pharyngeal arches	GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.		developmental stage:36 hpf\|genotype:hspGal4\|treatment:Heat shocked	GSM2526409	GSM2526409: hspGal4 fli1a sox10; Danio rerio; RNA Seq	GSM2526409		1	GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.	GEO Accession:GSM2526409	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP101558				12101492616.0	79615083.0	GSM2526409 r1	0:76 1:76	A:3579849331;C:2226140960;G:2397001824;T:3898240336;N:260165	76	76			3579849331	2226140960	2397001824	3898240336	260165	SRX2619935	SRS2029898	SRA543392	GEO	Crump Lab, Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California	2	0.85984	0.92526	0.14429	0.15831	0.76226	0.77816	0.50873	0.50352	76	76	B	B	biological fallback assumption	illumina	nextseq	full_length	cdna_unspecified	smarter	bulk	unknown	unknown	United States	2017-03-08	Pharyngula	Embryo	Pharyngeal Arch	Multi-system
41880	41880	SRR5320529	SRX2619934	SRS2029897	SRP101558	PRJNA378498	Functional Analysis of Regional Gene Expression in Zebrafish Craniofacial Development	GSE95812	Transcriptome Analysis	Patterning of the facial skeleton involves the precise deployment of thousands of genes in distinct regions of the pharyngeal arches. Despite their significance for craniofacial development how genetic programs drive this regionalization remains poorly understood. Here we use combinatorial labeling of zebrafish cranial neural crest derived cells CNCCs to define global gene expression along the dorsoventral axis of the developing arches. Intersection of region specific transcriptomes with expression changes in response to signaling perturbations demonstrates complex roles for Endothelin1 Edn1 signaling in the intermediate joint forming region yet a surprisingly minor role in ventral most regions. Analysis of co variance across multiple sequencing experiments further reveals clusters of co regulated genes with in situ hybridization confirming the expression of novel genes with domain specific expression. We then performed mutational analysis of a number of these genes which uncovered antagonistic functions of two Edn1 targets follistatin a fsta and emx2 in regulating cartilaginous joints in the hyoid arch. Our unbiased discovery and functional analysis of genes with regional expression in arch CNCCs reveals complex regulation by Edn1 and points to novel candidates for craniofacial disorders. Overall design: mRNA profiles of 3 distinct populations of zebrafish pharyngeal arch cells isolated using FACS from 36 hpf wild type WT zebrafish. fli1a:GFP+;sox10:DsRed and fli1a:GFP ;sox10:DsRed+ populations were also isolated at the same time and sequenced as controls 3 replicate each. Additionally there are mRNA profiles of zebrafish pharyngeal arches all domains combined isolated by FACS from 36 hpf zebrafish with the following genotypes: edn1 / 2 replicates jag1b / jag1b+/+ control hsp70I:Gal4; UAS:Edn1 hsp70I:Gal4; UAS:Nicd and hsp70I:Gal4 control.	pubmed:28705894	hspNICD fli1a sox10	GSM2526408	tissue:Pharyngeal arches\|developmental stage:36 hpf\|genotype:hspGal4 ; UASNICD\|treatment:Heat shocked	hspNICD fli1a sox10	Raw sequencing data in Fastq format was imported into the Partek Flow® interface for alignment and quantification. Pre alignment QC showed that the reads from all samples had generally high quality with the average Phred quality score for each sample being above 30. Reads were then trimmed from both ends based on Phred quality score with a minimum end quality level of 20 and a minimum acceptable read length of 25. The TopHat 2 algorithm was used to align the trimmed reads to the zebrafish GRCz10 genome assembly Ensembl v80. Aligned reads were then quantified using the Partek E/M algorithm with default parameters to yield the TPM values. Genome build: GRCz10 Supplementary files format and content: csv text files include TPM values for each gene in each sample	Pharyngeal arches	GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.		developmental stage:36 hpf\|genotype:hspGal4 ; UASNICD\|treatment:Heat shocked	GSM2526408	GSM2526408: hspNICD fli1a sox10; Danio rerio; RNA Seq	GSM2526408		1	GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.	GEO Accession:GSM2526408	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP101558				8181679072.0	53826836.0	GSM2526408 r1												SRX2619934	SRS2029897	SRA543392	GEO	Crump Lab, Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California	2	0.83613	0.71682	0.12705	0.11094	0.74158	0.75611	0.48765	0.48307	76	76	B	B	biological fallback assumption	illumina	nextseq	full_length	cdna_unspecified	smarter	bulk	unknown	unknown	United States	2017-03-08	Pharyngula	Embryo	Pharyngeal Arch	Multi-system
41881	41881	SRR5320528	SRX2619933	SRS2029896	SRP101558	PRJNA378498	Functional Analysis of Regional Gene Expression in Zebrafish Craniofacial Development	GSE95812	Transcriptome Analysis	Patterning of the facial skeleton involves the precise deployment of thousands of genes in distinct regions of the pharyngeal arches. Despite their significance for craniofacial development how genetic programs drive this regionalization remains poorly understood. Here we use combinatorial labeling of zebrafish cranial neural crest derived cells CNCCs to define global gene expression along the dorsoventral axis of the developing arches. Intersection of region specific transcriptomes with expression changes in response to signaling perturbations demonstrates complex roles for Endothelin1 Edn1 signaling in the intermediate joint forming region yet a surprisingly minor role in ventral most regions. Analysis of co variance across multiple sequencing experiments further reveals clusters of co regulated genes with in situ hybridization confirming the expression of novel genes with domain specific expression. We then performed mutational analysis of a number of these genes which uncovered antagonistic functions of two Edn1 targets follistatin a fsta and emx2 in regulating cartilaginous joints in the hyoid arch. Our unbiased discovery and functional analysis of genes with regional expression in arch CNCCs reveals complex regulation by Edn1 and points to novel candidates for craniofacial disorders. Overall design: mRNA profiles of 3 distinct populations of zebrafish pharyngeal arch cells isolated using FACS from 36 hpf wild type WT zebrafish. fli1a:GFP+;sox10:DsRed and fli1a:GFP ;sox10:DsRed+ populations were also isolated at the same time and sequenced as controls 3 replicate each. Additionally there are mRNA profiles of zebrafish pharyngeal arches all domains combined isolated by FACS from 36 hpf zebrafish with the following genotypes: edn1 / 2 replicates jag1b / jag1b+/+ control hsp70I:Gal4; UAS:Edn1 hsp70I:Gal4; UAS:Nicd and hsp70I:Gal4 control.	pubmed:28705894	hspEdn1 fli1a sox10	GSM2526407	tissue:Pharyngeal arches\|developmental stage:36 hpf\|genotype:hspGal4 ; UASEdn1\|treatment:Heat shocked	hspEdn1 fli1a sox10	Raw sequencing data in Fastq format was imported into the Partek Flow® interface for alignment and quantification. Pre alignment QC showed that the reads from all samples had generally high quality with the average Phred quality score for each sample being above 30. Reads were then trimmed from both ends based on Phred quality score with a minimum end quality level of 20 and a minimum acceptable read length of 25. The TopHat 2 algorithm was used to align the trimmed reads to the zebrafish GRCz10 genome assembly Ensembl v80. Aligned reads were then quantified using the Partek E/M algorithm with default parameters to yield the TPM values. Genome build: GRCz10 Supplementary files format and content: csv text files include TPM values for each gene in each sample	Pharyngeal arches	GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.		developmental stage:36 hpf\|genotype:hspGal4 ; UASEdn1\|treatment:Heat shocked	GSM2526407	GSM2526407: hspEdn1 fli1a sox10; Danio rerio; RNA Seq	GSM2526407		1	GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.	GEO Accession:GSM2526407	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP101558				8241464016.0	54220158.0	GSM2526407 r1	0:76 1:76	A:2338801834;C:1581411340;G:1652427014;T:2666281574;N:2542254	76	76			2338801834	1581411340	1652427014	2666281574	2542254	SRX2619933	SRS2029896	SRA543392	GEO	Crump Lab, Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California	2	0.8884	0.85826	0.15095	0.14838	0.75958	0.77538	0.49126	0.48522	76	76	B	B	biological fallback assumption	illumina	nextseq	full_length	cdna_unspecified	smarter	bulk	unknown	unknown	United States	2017-03-08	Pharyngula	Embryo	Pharyngeal Arch	Multi-system
41882	41882	SRR5320527	SRX2619932	SRS2029895	SRP101558	PRJNA378498	Functional Analysis of Regional Gene Expression in Zebrafish Craniofacial Development	GSE95812	Transcriptome Analysis	Patterning of the facial skeleton involves the precise deployment of thousands of genes in distinct regions of the pharyngeal arches. Despite their significance for craniofacial development how genetic programs drive this regionalization remains poorly understood. Here we use combinatorial labeling of zebrafish cranial neural crest derived cells CNCCs to define global gene expression along the dorsoventral axis of the developing arches. Intersection of region specific transcriptomes with expression changes in response to signaling perturbations demonstrates complex roles for Endothelin1 Edn1 signaling in the intermediate joint forming region yet a surprisingly minor role in ventral most regions. Analysis of co variance across multiple sequencing experiments further reveals clusters of co regulated genes with in situ hybridization confirming the expression of novel genes with domain specific expression. We then performed mutational analysis of a number of these genes which uncovered antagonistic functions of two Edn1 targets follistatin a fsta and emx2 in regulating cartilaginous joints in the hyoid arch. Our unbiased discovery and functional analysis of genes with regional expression in arch CNCCs reveals complex regulation by Edn1 and points to novel candidates for craniofacial disorders. Overall design: mRNA profiles of 3 distinct populations of zebrafish pharyngeal arch cells isolated using FACS from 36 hpf wild type WT zebrafish. fli1a:GFP+;sox10:DsRed and fli1a:GFP ;sox10:DsRed+ populations were also isolated at the same time and sequenced as controls 3 replicate each. Additionally there are mRNA profiles of zebrafish pharyngeal arches all domains combined isolated by FACS from 36 hpf zebrafish with the following genotypes: edn1 / 2 replicates jag1b / jag1b+/+ control hsp70I:Gal4; UAS:Edn1 hsp70I:Gal4; UAS:Nicd and hsp70I:Gal4 control.	pubmed:28705894	jag1b++ fli1a sox10	GSM2526406	tissue:Pharyngeal arches\|developmental stage:36 hpf\|genotype:jag1b+/+\|treatment:Genotyped	jag1b++ fli1a sox10	Raw sequencing data in Fastq format was imported into the Partek Flow® interface for alignment and quantification. Pre alignment QC showed that the reads from all samples had generally high quality with the average Phred quality score for each sample being above 30. Reads were then trimmed from both ends based on Phred quality score with a minimum end quality level of 20 and a minimum acceptable read length of 25. The TopHat 2 algorithm was used to align the trimmed reads to the zebrafish GRCz10 genome assembly Ensembl v80. Aligned reads were then quantified using the Partek E/M algorithm with default parameters to yield the TPM values. Genome build: GRCz10 Supplementary files format and content: csv text files include TPM values for each gene in each sample	Pharyngeal arches	GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.		developmental stage:36 hpf\|genotype:jag1b+/+\|treatment:Genotyped	GSM2526406	GSM2526406: jag1b++ fli1a sox10; Danio rerio; RNA Seq	GSM2526406		1	GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.	GEO Accession:GSM2526406	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP101558				9196789944.0	60505197.0	GSM2526406 r1	0:76 1:76	A:2617231956;C:1761629764;G:1849570227;T:2965452565;N:2905432	76	76			2617231956	1761629764	1849570227	2965452565	2905432	SRX2619932	SRS2029895	SRA543392	GEO	Crump Lab, Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California	2	0.87578	0.84631	0.14233	0.13848	0.7641	0.78602	0.49727	0.49394	76	76	B	B	biological fallback assumption	illumina	nextseq	full_length	cdna_unspecified	smarter	bulk	unknown	unknown	United States	2017-03-08	Pharyngula	Embryo	Pharyngeal Arch	Multi-system
41883	41883	SRR5320526	SRX2619931	SRS2029894	SRP101558	PRJNA378498	Functional Analysis of Regional Gene Expression in Zebrafish Craniofacial Development	GSE95812	Transcriptome Analysis	Patterning of the facial skeleton involves the precise deployment of thousands of genes in distinct regions of the pharyngeal arches. Despite their significance for craniofacial development how genetic programs drive this regionalization remains poorly understood. Here we use combinatorial labeling of zebrafish cranial neural crest derived cells CNCCs to define global gene expression along the dorsoventral axis of the developing arches. Intersection of region specific transcriptomes with expression changes in response to signaling perturbations demonstrates complex roles for Endothelin1 Edn1 signaling in the intermediate joint forming region yet a surprisingly minor role in ventral most regions. Analysis of co variance across multiple sequencing experiments further reveals clusters of co regulated genes with in situ hybridization confirming the expression of novel genes with domain specific expression. We then performed mutational analysis of a number of these genes which uncovered antagonistic functions of two Edn1 targets follistatin a fsta and emx2 in regulating cartilaginous joints in the hyoid arch. Our unbiased discovery and functional analysis of genes with regional expression in arch CNCCs reveals complex regulation by Edn1 and points to novel candidates for craniofacial disorders. Overall design: mRNA profiles of 3 distinct populations of zebrafish pharyngeal arch cells isolated using FACS from 36 hpf wild type WT zebrafish. fli1a:GFP+;sox10:DsRed and fli1a:GFP ;sox10:DsRed+ populations were also isolated at the same time and sequenced as controls 3 replicate each. Additionally there are mRNA profiles of zebrafish pharyngeal arches all domains combined isolated by FACS from 36 hpf zebrafish with the following genotypes: edn1 / 2 replicates jag1b / jag1b+/+ control hsp70I:Gal4; UAS:Edn1 hsp70I:Gal4; UAS:Nicd and hsp70I:Gal4 control.	pubmed:28705894	jag1b fli1a sox10	GSM2526405	tissue:Pharyngeal arches\|developmental stage:36 hpf\|genotype:jag1b / \|treatment:Genotyped	jag1b fli1a sox10	Raw sequencing data in Fastq format was imported into the Partek Flow® interface for alignment and quantification. Pre alignment QC showed that the reads from all samples had generally high quality with the average Phred quality score for each sample being above 30. Reads were then trimmed from both ends based on Phred quality score with a minimum end quality level of 20 and a minimum acceptable read length of 25. The TopHat 2 algorithm was used to align the trimmed reads to the zebrafish GRCz10 genome assembly Ensembl v80. Aligned reads were then quantified using the Partek E/M algorithm with default parameters to yield the TPM values. Genome build: GRCz10 Supplementary files format and content: csv text files include TPM values for each gene in each sample	Pharyngeal arches	GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.		developmental stage:36 hpf\|genotype:jag1b / \|treatment:Genotyped	GSM2526405	GSM2526405: jag1b fli1a sox10; Danio rerio; RNA Seq	GSM2526405		1	GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.	GEO Accession:GSM2526405	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP101558				7981914592.0	52512596.0	GSM2526405 r1	0:76 1:76	A:2278594852;C:1520667450;G:1610295025;T:2569901477;N:2455788	76	76			2278594852	1520667450	1610295025	2569901477	2455788	SRX2619931	SRS2029894	SRA543392	GEO	Crump Lab, Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California	2	0.88292	0.85135	0.1578	0.15478	0.76435	0.78175	0.50571	0.49719	76	76	B	B	biological fallback assumption	illumina	nextseq	full_length	cdna_unspecified	smarter	bulk	unknown	unknown	United States	2017-03-08	Pharyngula	Embryo	Pharyngeal Arch	Multi-system
41884	41884	SRR5320525	SRX2619930	SRS2029893	SRP101558	PRJNA378498	Functional Analysis of Regional Gene Expression in Zebrafish Craniofacial Development	GSE95812	Transcriptome Analysis	Patterning of the facial skeleton involves the precise deployment of thousands of genes in distinct regions of the pharyngeal arches. Despite their significance for craniofacial development how genetic programs drive this regionalization remains poorly understood. Here we use combinatorial labeling of zebrafish cranial neural crest derived cells CNCCs to define global gene expression along the dorsoventral axis of the developing arches. Intersection of region specific transcriptomes with expression changes in response to signaling perturbations demonstrates complex roles for Endothelin1 Edn1 signaling in the intermediate joint forming region yet a surprisingly minor role in ventral most regions. Analysis of co variance across multiple sequencing experiments further reveals clusters of co regulated genes with in situ hybridization confirming the expression of novel genes with domain specific expression. We then performed mutational analysis of a number of these genes which uncovered antagonistic functions of two Edn1 targets follistatin a fsta and emx2 in regulating cartilaginous joints in the hyoid arch. Our unbiased discovery and functional analysis of genes with regional expression in arch CNCCs reveals complex regulation by Edn1 and points to novel candidates for craniofacial disorders. Overall design: mRNA profiles of 3 distinct populations of zebrafish pharyngeal arch cells isolated using FACS from 36 hpf wild type WT zebrafish. fli1a:GFP+;sox10:DsRed and fli1a:GFP ;sox10:DsRed+ populations were also isolated at the same time and sequenced as controls 3 replicate each. Additionally there are mRNA profiles of zebrafish pharyngeal arches all domains combined isolated by FACS from 36 hpf zebrafish with the following genotypes: edn1 / 2 replicates jag1b / jag1b+/+ control hsp70I:Gal4; UAS:Edn1 hsp70I:Gal4; UAS:Nicd and hsp70I:Gal4 control.	pubmed:28705894	edn1 fli1a sox10 2	GSM2526404	tissue:Pharyngeal arches\|developmental stage:36 hpf\|genotype:edn1 / \|treatment:Genotyped	edn1 fli1a sox10 2	Raw sequencing data in Fastq format was imported into the Partek Flow® interface for alignment and quantification. Pre alignment QC showed that the reads from all samples had generally high quality with the average Phred quality score for each sample being above 30. Reads were then trimmed from both ends based on Phred quality score with a minimum end quality level of 20 and a minimum acceptable read length of 25. The TopHat 2 algorithm was used to align the trimmed reads to the zebrafish GRCz10 genome assembly Ensembl v80. Aligned reads were then quantified using the Partek E/M algorithm with default parameters to yield the TPM values. Genome build: GRCz10 Supplementary files format and content: csv text files include TPM values for each gene in each sample	Pharyngeal arches	GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.		developmental stage:36 hpf\|genotype:edn1 / \|treatment:Genotyped	GSM2526404	GSM2526404: edn1 fli1a sox10 2; Danio rerio; RNA Seq	GSM2526404		1	GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.	GEO Accession:GSM2526404	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP101558		GC-805_L000_R1_001.fastq.gz GC-805_L000_R2_001.fastq.gz	fastq fastq	8083094760.0	53178255.0	GSM2526404 r1	0:76 1:76	A:2289691443;C:1736629919;G:1749357479;T:2306964200;N:451719	76	76			2289691443	1736629919	1749357479	2306964200	451719	SRX2619930	SRS2029893	SRA543392	GEO	Crump Lab, Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California	2	0.9383	0.92923	0.13857	0.13758	0.73641	0.74416	0.44748	0.48421	76	76	B	B	biological fallback assumption	illumina	nextseq	full_length	cdna_unspecified	smarter	bulk	unknown	unknown	United States	2017-03-08	Pharyngula	Embryo	Pharyngeal Arch	Multi-system
41885	41885	SRR5320524	SRX2619929	SRS2029892	SRP101558	PRJNA378498	Functional Analysis of Regional Gene Expression in Zebrafish Craniofacial Development	GSE95812	Transcriptome Analysis	Patterning of the facial skeleton involves the precise deployment of thousands of genes in distinct regions of the pharyngeal arches. Despite their significance for craniofacial development how genetic programs drive this regionalization remains poorly understood. Here we use combinatorial labeling of zebrafish cranial neural crest derived cells CNCCs to define global gene expression along the dorsoventral axis of the developing arches. Intersection of region specific transcriptomes with expression changes in response to signaling perturbations demonstrates complex roles for Endothelin1 Edn1 signaling in the intermediate joint forming region yet a surprisingly minor role in ventral most regions. Analysis of co variance across multiple sequencing experiments further reveals clusters of co regulated genes with in situ hybridization confirming the expression of novel genes with domain specific expression. We then performed mutational analysis of a number of these genes which uncovered antagonistic functions of two Edn1 targets follistatin a fsta and emx2 in regulating cartilaginous joints in the hyoid arch. Our unbiased discovery and functional analysis of genes with regional expression in arch CNCCs reveals complex regulation by Edn1 and points to novel candidates for craniofacial disorders. Overall design: mRNA profiles of 3 distinct populations of zebrafish pharyngeal arch cells isolated using FACS from 36 hpf wild type WT zebrafish. fli1a:GFP+;sox10:DsRed and fli1a:GFP ;sox10:DsRed+ populations were also isolated at the same time and sequenced as controls 3 replicate each. Additionally there are mRNA profiles of zebrafish pharyngeal arches all domains combined isolated by FACS from 36 hpf zebrafish with the following genotypes: edn1 / 2 replicates jag1b / jag1b+/+ control hsp70I:Gal4; UAS:Edn1 hsp70I:Gal4; UAS:Nicd and hsp70I:Gal4 control.	pubmed:28705894	edn1 fli1a sox10 1	GSM2526403	tissue:Pharyngeal arches\|developmental stage:36 hpf\|genotype:edn1 / \|treatment:Genotyped	edn1 fli1a sox10 1	Raw sequencing data in Fastq format was imported into the Partek Flow® interface for alignment and quantification. Pre alignment QC showed that the reads from all samples had generally high quality with the average Phred quality score for each sample being above 30. Reads were then trimmed from both ends based on Phred quality score with a minimum end quality level of 20 and a minimum acceptable read length of 25. The TopHat 2 algorithm was used to align the trimmed reads to the zebrafish GRCz10 genome assembly Ensembl v80. Aligned reads were then quantified using the Partek E/M algorithm with default parameters to yield the TPM values. Genome build: GRCz10 Supplementary files format and content: csv text files include TPM values for each gene in each sample	Pharyngeal arches	GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.		developmental stage:36 hpf\|genotype:edn1 / \|treatment:Genotyped	GSM2526403	GSM2526403: edn1 fli1a sox10 1; Danio rerio; RNA Seq	GSM2526403		1	GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.	GEO Accession:GSM2526403	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP101558				3805470400.0	38054704.0	GSM2526403 r1	0:50 1:50	A:1039863232;C:811509659;G:855601660;T:1094752796;N:3743053	50	50			1039863232	811509659	855601660	1094752796	3743053	SRX2619929	SRS2029892	SRA543392	GEO	Crump Lab, Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California	2	0.90375	0.77106	0.11778	0.10051	0.76037	0.77571	0.48632	0.48462	50	50	B	B	biological fallback assumption	illumina	hiseq_era	full_length	cdna_unspecified	smarter	bulk	unknown	unknown	United States	2017-03-08	Pharyngula	Embryo	Pharyngeal Arch	Multi-system
41892	41892	SRR5320517	SRX2619922	SRS2029885	SRP101558	PRJNA378498	Functional Analysis of Regional Gene Expression in Zebrafish Craniofacial Development	GSE95812	Transcriptome Analysis	Patterning of the facial skeleton involves the precise deployment of thousands of genes in distinct regions of the pharyngeal arches. Despite their significance for craniofacial development how genetic programs drive this regionalization remains poorly understood. Here we use combinatorial labeling of zebrafish cranial neural crest derived cells CNCCs to define global gene expression along the dorsoventral axis of the developing arches. Intersection of region specific transcriptomes with expression changes in response to signaling perturbations demonstrates complex roles for Endothelin1 Edn1 signaling in the intermediate joint forming region yet a surprisingly minor role in ventral most regions. Analysis of co variance across multiple sequencing experiments further reveals clusters of co regulated genes with in situ hybridization confirming the expression of novel genes with domain specific expression. We then performed mutational analysis of a number of these genes which uncovered antagonistic functions of two Edn1 targets follistatin a fsta and emx2 in regulating cartilaginous joints in the hyoid arch. Our unbiased discovery and functional analysis of genes with regional expression in arch CNCCs reveals complex regulation by Edn1 and points to novel candidates for craniofacial disorders. Overall design: mRNA profiles of 3 distinct populations of zebrafish pharyngeal arch cells isolated using FACS from 36 hpf wild type WT zebrafish. fli1a:GFP+;sox10:DsRed and fli1a:GFP ;sox10:DsRed+ populations were also isolated at the same time and sequenced as controls 3 replicate each. Additionally there are mRNA profiles of zebrafish pharyngeal arches all domains combined isolated by FACS from 36 hpf zebrafish with the following genotypes: edn1 / 2 replicates jag1b / jag1b+/+ control hsp70I:Gal4; UAS:Edn1 hsp70I:Gal4; UAS:Nicd and hsp70I:Gal4 control.	pubmed:28705894	WT hand2 sox10 2	GSM2526396	tissue:Pharyngeal arches\|developmental stage:36 hpf\|genotype:WT\|treatment:N1	WT hand2 sox10 2	Raw sequencing data in Fastq format was imported into the Partek Flow® interface for alignment and quantification. Pre alignment QC showed that the reads from all samples had generally high quality with the average Phred quality score for each sample being above 30. Reads were then trimmed from both ends based on Phred quality score with a minimum end quality level of 20 and a minimum acceptable read length of 25. The TopHat 2 algorithm was used to align the trimmed reads to the zebrafish GRCz10 genome assembly Ensembl v80. Aligned reads were then quantified using the Partek E/M algorithm with default parameters to yield the TPM values. Genome build: GRCz10 Supplementary files format and content: csv text files include TPM values for each gene in each sample	Pharyngeal arches	GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.		developmental stage:36 hpf\|genotype:WT\|treatment:N1	GSM2526396	GSM2526396: WT hand2 sox10 2; Danio rerio; RNA Seq	GSM2526396		1	GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.	GEO Accession:GSM2526396	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP101558		GC-99_L000_R1_001.fastq.gz GC-99_L000_R2_001.fastq.gz	fastq fastq	5678291208.0	37357179.0	GSM2526396 r1	0:76 1:76	A:1598205402;C:1219592650;G:1242882414;T:1613938733;N:3672009	76	76			1598205402	1219592650	1242882414	1613938733	3672009	SRX2619922	SRS2029885	SRA543392	GEO	Crump Lab, Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California	2	0.95476	0.95009	0.12808	0.12848	0.74602	0.76008	0.45997	0.46118	76	76	B	B	biological fallback assumption	illumina	nextseq	full_length	cdna_unspecified	smarter	bulk	unknown	unknown	United States	2017-03-08	Pharyngula	Embryo	Pharyngeal Arch	Multi-system
41893	41893	SRR5320516	SRX2619921	SRS2029884	SRP101558	PRJNA378498	Functional Analysis of Regional Gene Expression in Zebrafish Craniofacial Development	GSE95812	Transcriptome Analysis	Patterning of the facial skeleton involves the precise deployment of thousands of genes in distinct regions of the pharyngeal arches. Despite their significance for craniofacial development how genetic programs drive this regionalization remains poorly understood. Here we use combinatorial labeling of zebrafish cranial neural crest derived cells CNCCs to define global gene expression along the dorsoventral axis of the developing arches. Intersection of region specific transcriptomes with expression changes in response to signaling perturbations demonstrates complex roles for Endothelin1 Edn1 signaling in the intermediate joint forming region yet a surprisingly minor role in ventral most regions. Analysis of co variance across multiple sequencing experiments further reveals clusters of co regulated genes with in situ hybridization confirming the expression of novel genes with domain specific expression. We then performed mutational analysis of a number of these genes which uncovered antagonistic functions of two Edn1 targets follistatin a fsta and emx2 in regulating cartilaginous joints in the hyoid arch. Our unbiased discovery and functional analysis of genes with regional expression in arch CNCCs reveals complex regulation by Edn1 and points to novel candidates for craniofacial disorders. Overall design: mRNA profiles of 3 distinct populations of zebrafish pharyngeal arch cells isolated using FACS from 36 hpf wild type WT zebrafish. fli1a:GFP+;sox10:DsRed and fli1a:GFP ;sox10:DsRed+ populations were also isolated at the same time and sequenced as controls 3 replicate each. Additionally there are mRNA profiles of zebrafish pharyngeal arches all domains combined isolated by FACS from 36 hpf zebrafish with the following genotypes: edn1 / 2 replicates jag1b / jag1b+/+ control hsp70I:Gal4; UAS:Edn1 hsp70I:Gal4; UAS:Nicd and hsp70I:Gal4 control.	pubmed:28705894	WT hand2 sox10 1	GSM2526395	tissue:Pharyngeal arches\|developmental stage:36 hpf\|genotype:WT\|treatment:N1	WT hand2 sox10 1	Raw sequencing data in Fastq format was imported into the Partek Flow® interface for alignment and quantification. Pre alignment QC showed that the reads from all samples had generally high quality with the average Phred quality score for each sample being above 30. Reads were then trimmed from both ends based on Phred quality score with a minimum end quality level of 20 and a minimum acceptable read length of 25. The TopHat 2 algorithm was used to align the trimmed reads to the zebrafish GRCz10 genome assembly Ensembl v80. Aligned reads were then quantified using the Partek E/M algorithm with default parameters to yield the TPM values. Genome build: GRCz10 Supplementary files format and content: csv text files include TPM values for each gene in each sample	Pharyngeal arches	GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.		developmental stage:36 hpf\|genotype:WT\|treatment:N1	GSM2526395	GSM2526395: WT hand2 sox10 1; Danio rerio; RNA Seq	GSM2526395		1	GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.	GEO Accession:GSM2526395	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP101558		GC-32_ACTGAT_L008_R1_001.fastq.gz GC-32_ACTGAT_L008_R2_001.fastq.gz	fastq fastq	4507512700.0	45075127.0	GSM2526395 r1	0:50 1:50	A:1231085820;C:944462783;G:1008951826;T:1318567555;N:4444716	50	50			1231085820	944462783	1008951826	1318567555	4444716	SRX2619921	SRS2029884	SRA543392	GEO	Crump Lab, Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California	2	0.9285	0.75484	0.0986	0.08168	0.75751	0.77863	0.49299	0.48494	50	50	B	B	biological fallback assumption	illumina	hiseq_era	full_length	cdna_unspecified	smarter	bulk	unknown	unknown	United States	2017-03-08	Pharyngula	Embryo	Pharyngeal Arch	Multi-system
41894	41894	SRR5320515	SRX2619920	SRS2029883	SRP101558	PRJNA378498	Functional Analysis of Regional Gene Expression in Zebrafish Craniofacial Development	GSE95812	Transcriptome Analysis	Patterning of the facial skeleton involves the precise deployment of thousands of genes in distinct regions of the pharyngeal arches. Despite their significance for craniofacial development how genetic programs drive this regionalization remains poorly understood. Here we use combinatorial labeling of zebrafish cranial neural crest derived cells CNCCs to define global gene expression along the dorsoventral axis of the developing arches. Intersection of region specific transcriptomes with expression changes in response to signaling perturbations demonstrates complex roles for Endothelin1 Edn1 signaling in the intermediate joint forming region yet a surprisingly minor role in ventral most regions. Analysis of co variance across multiple sequencing experiments further reveals clusters of co regulated genes with in situ hybridization confirming the expression of novel genes with domain specific expression. We then performed mutational analysis of a number of these genes which uncovered antagonistic functions of two Edn1 targets follistatin a fsta and emx2 in regulating cartilaginous joints in the hyoid arch. Our unbiased discovery and functional analysis of genes with regional expression in arch CNCCs reveals complex regulation by Edn1 and points to novel candidates for craniofacial disorders. Overall design: mRNA profiles of 3 distinct populations of zebrafish pharyngeal arch cells isolated using FACS from 36 hpf wild type WT zebrafish. fli1a:GFP+;sox10:DsRed and fli1a:GFP ;sox10:DsRed+ populations were also isolated at the same time and sequenced as controls 3 replicate each. Additionally there are mRNA profiles of zebrafish pharyngeal arches all domains combined isolated by FACS from 36 hpf zebrafish with the following genotypes: edn1 / 2 replicates jag1b / jag1b+/+ control hsp70I:Gal4; UAS:Edn1 hsp70I:Gal4; UAS:Nicd and hsp70I:Gal4 control.	pubmed:28705894	WT dlx5a sox10	GSM2526394	tissue:Pharyngeal arches\|developmental stage:36 hpf\|genotype:WT\|treatment:N1	WT dlx5a sox10	Raw sequencing data in Fastq format was imported into the Partek Flow® interface for alignment and quantification. Pre alignment QC showed that the reads from all samples had generally high quality with the average Phred quality score for each sample being above 30. Reads were then trimmed from both ends based on Phred quality score with a minimum end quality level of 20 and a minimum acceptable read length of 25. The TopHat 2 algorithm was used to align the trimmed reads to the zebrafish GRCz10 genome assembly Ensembl v80. Aligned reads were then quantified using the Partek E/M algorithm with default parameters to yield the TPM values. Genome build: GRCz10 Supplementary files format and content: csv text files include TPM values for each gene in each sample	Pharyngeal arches	GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.		developmental stage:36 hpf\|genotype:WT\|treatment:N1	GSM2526394	GSM2526394: WT dlx5a sox10; Danio rerio; RNA Seq	GSM2526394		1	GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.	GEO Accession:GSM2526394	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP101558		GC-807_L000_R1_001.fastq.gz GC-807_L000_R2_001.fastq.gz	fastq fastq	8131381360.0	53495930.0	GSM2526394 r1	0:76 1:76	A:2329666125;C:1728067909;G:1735452315;T:2337737035;N:457976	76	76			2329666125	1728067909	1735452315	2337737035	457976	SRX2619920	SRS2029883	SRA543392	GEO	Crump Lab, Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California	2	0.94883	0.93771	0.12915	0.12662	0.75112	0.7597	0.48692	0.48304	76	76	B	B	biological fallback assumption	illumina	nextseq	full_length	cdna_unspecified	smarter	bulk	unknown	unknown	United States	2017-03-08	Pharyngula	Embryo	Pharyngeal Arch	Multi-system
41895	41895	SRR5320514	SRX2619919	SRS2029882	SRP101558	PRJNA378498	Functional Analysis of Regional Gene Expression in Zebrafish Craniofacial Development	GSE95812	Transcriptome Analysis	Patterning of the facial skeleton involves the precise deployment of thousands of genes in distinct regions of the pharyngeal arches. Despite their significance for craniofacial development how genetic programs drive this regionalization remains poorly understood. Here we use combinatorial labeling of zebrafish cranial neural crest derived cells CNCCs to define global gene expression along the dorsoventral axis of the developing arches. Intersection of region specific transcriptomes with expression changes in response to signaling perturbations demonstrates complex roles for Endothelin1 Edn1 signaling in the intermediate joint forming region yet a surprisingly minor role in ventral most regions. Analysis of co variance across multiple sequencing experiments further reveals clusters of co regulated genes with in situ hybridization confirming the expression of novel genes with domain specific expression. We then performed mutational analysis of a number of these genes which uncovered antagonistic functions of two Edn1 targets follistatin a fsta and emx2 in regulating cartilaginous joints in the hyoid arch. Our unbiased discovery and functional analysis of genes with regional expression in arch CNCCs reveals complex regulation by Edn1 and points to novel candidates for craniofacial disorders. Overall design: mRNA profiles of 3 distinct populations of zebrafish pharyngeal arch cells isolated using FACS from 36 hpf wild type WT zebrafish. fli1a:GFP+;sox10:DsRed and fli1a:GFP ;sox10:DsRed+ populations were also isolated at the same time and sequenced as controls 3 replicate each. Additionally there are mRNA profiles of zebrafish pharyngeal arches all domains combined isolated by FACS from 36 hpf zebrafish with the following genotypes: edn1 / 2 replicates jag1b / jag1b+/+ control hsp70I:Gal4; UAS:Edn1 hsp70I:Gal4; UAS:Nicd and hsp70I:Gal4 control.	pubmed:28705894	WT fli1a sox10 3	GSM2526393	tissue:Pharyngeal arches\|developmental stage:36 hpf\|genotype:WT\|treatment:N1	WT fli1a sox10 3	Raw sequencing data in Fastq format was imported into the Partek Flow® interface for alignment and quantification. Pre alignment QC showed that the reads from all samples had generally high quality with the average Phred quality score for each sample being above 30. Reads were then trimmed from both ends based on Phred quality score with a minimum end quality level of 20 and a minimum acceptable read length of 25. The TopHat 2 algorithm was used to align the trimmed reads to the zebrafish GRCz10 genome assembly Ensembl v80. Aligned reads were then quantified using the Partek E/M algorithm with default parameters to yield the TPM values. Genome build: GRCz10 Supplementary files format and content: csv text files include TPM values for each gene in each sample	Pharyngeal arches	GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.		developmental stage:36 hpf\|genotype:WT\|treatment:N1	GSM2526393	GSM2526393: WT fli1a sox10 3; Danio rerio; RNA Seq	GSM2526393		1	GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.	GEO Accession:GSM2526393	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP101558		GC-94_L000_R1_001.fastq.gz GC-94_L000_R2_001.fastq.gz	fastq fastq	7177187832.0	47218341.0	GSM2526393 r1	0:76 1:76	A:1987437090;C:1523180428;G:1579096104;T:2080512802;N:6961408	76	76			1987437090	1523180428	1579096104	2080512802	6961408	SRX2619919	SRS2029882	SRA543392	GEO	Crump Lab, Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California	2	0.9383	0.92453	0.13099	0.12672	0.74152	0.76055	0.47365	0.46661	76	76	B	B	biological fallback assumption	illumina	nextseq	full_length	cdna_unspecified	smarter	bulk	unknown	unknown	United States	2017-03-08	Pharyngula	Embryo	Pharyngeal Arch	Multi-system
41896	41896	SRR5320513	SRX2619918	SRS2029881	SRP101558	PRJNA378498	Functional Analysis of Regional Gene Expression in Zebrafish Craniofacial Development	GSE95812	Transcriptome Analysis	Patterning of the facial skeleton involves the precise deployment of thousands of genes in distinct regions of the pharyngeal arches. Despite their significance for craniofacial development how genetic programs drive this regionalization remains poorly understood. Here we use combinatorial labeling of zebrafish cranial neural crest derived cells CNCCs to define global gene expression along the dorsoventral axis of the developing arches. Intersection of region specific transcriptomes with expression changes in response to signaling perturbations demonstrates complex roles for Endothelin1 Edn1 signaling in the intermediate joint forming region yet a surprisingly minor role in ventral most regions. Analysis of co variance across multiple sequencing experiments further reveals clusters of co regulated genes with in situ hybridization confirming the expression of novel genes with domain specific expression. We then performed mutational analysis of a number of these genes which uncovered antagonistic functions of two Edn1 targets follistatin a fsta and emx2 in regulating cartilaginous joints in the hyoid arch. Our unbiased discovery and functional analysis of genes with regional expression in arch CNCCs reveals complex regulation by Edn1 and points to novel candidates for craniofacial disorders. Overall design: mRNA profiles of 3 distinct populations of zebrafish pharyngeal arch cells isolated using FACS from 36 hpf wild type WT zebrafish. fli1a:GFP+;sox10:DsRed and fli1a:GFP ;sox10:DsRed+ populations were also isolated at the same time and sequenced as controls 3 replicate each. Additionally there are mRNA profiles of zebrafish pharyngeal arches all domains combined isolated by FACS from 36 hpf zebrafish with the following genotypes: edn1 / 2 replicates jag1b / jag1b+/+ control hsp70I:Gal4; UAS:Edn1 hsp70I:Gal4; UAS:Nicd and hsp70I:Gal4 control.	pubmed:28705894	WT fli1a sox10 2	GSM2526392	tissue:Pharyngeal arches\|developmental stage:36 hpf\|genotype:WT\|treatment:N1	WT fli1a sox10 2	Raw sequencing data in Fastq format was imported into the Partek Flow® interface for alignment and quantification. Pre alignment QC showed that the reads from all samples had generally high quality with the average Phred quality score for each sample being above 30. Reads were then trimmed from both ends based on Phred quality score with a minimum end quality level of 20 and a minimum acceptable read length of 25. The TopHat 2 algorithm was used to align the trimmed reads to the zebrafish GRCz10 genome assembly Ensembl v80. Aligned reads were then quantified using the Partek E/M algorithm with default parameters to yield the TPM values. Genome build: GRCz10 Supplementary files format and content: csv text files include TPM values for each gene in each sample	Pharyngeal arches	GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.		developmental stage:36 hpf\|genotype:WT\|treatment:N1	GSM2526392	GSM2526392: WT fli1a sox10 2; Danio rerio; RNA Seq	GSM2526392		1	GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.	GEO Accession:GSM2526392	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP101558		GC-804_L000_R1_001.fastq.gz GC-804_L000_R2_001.fastq.gz	fastq fastq	7744827272.0	50952811.0	GSM2526392 r1	0:76 1:76	A:2194582167;C:1674810287;G:1681888119;T:2193114686;N:432013	76	76			2194582167	1674810287	1681888119	2193114686	432013	SRX2619918	SRS2029881	SRA543392	GEO	Crump Lab, Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California	2	0.94738	0.94045	0.1245	0.12381	0.7389	0.74955	0.47046	0.47075	76	76	B	B	biological fallback assumption	illumina	nextseq	full_length	cdna_unspecified	smarter	bulk	unknown	unknown	United States	2017-03-08	Pharyngula	Embryo	Pharyngeal Arch	Multi-system
41897	41897	SRR5320512	SRX2619917	SRS2029880	SRP101558	PRJNA378498	Functional Analysis of Regional Gene Expression in Zebrafish Craniofacial Development	GSE95812	Transcriptome Analysis	Patterning of the facial skeleton involves the precise deployment of thousands of genes in distinct regions of the pharyngeal arches. Despite their significance for craniofacial development how genetic programs drive this regionalization remains poorly understood. Here we use combinatorial labeling of zebrafish cranial neural crest derived cells CNCCs to define global gene expression along the dorsoventral axis of the developing arches. Intersection of region specific transcriptomes with expression changes in response to signaling perturbations demonstrates complex roles for Endothelin1 Edn1 signaling in the intermediate joint forming region yet a surprisingly minor role in ventral most regions. Analysis of co variance across multiple sequencing experiments further reveals clusters of co regulated genes with in situ hybridization confirming the expression of novel genes with domain specific expression. We then performed mutational analysis of a number of these genes which uncovered antagonistic functions of two Edn1 targets follistatin a fsta and emx2 in regulating cartilaginous joints in the hyoid arch. Our unbiased discovery and functional analysis of genes with regional expression in arch CNCCs reveals complex regulation by Edn1 and points to novel candidates for craniofacial disorders. Overall design: mRNA profiles of 3 distinct populations of zebrafish pharyngeal arch cells isolated using FACS from 36 hpf wild type WT zebrafish. fli1a:GFP+;sox10:DsRed and fli1a:GFP ;sox10:DsRed+ populations were also isolated at the same time and sequenced as controls 3 replicate each. Additionally there are mRNA profiles of zebrafish pharyngeal arches all domains combined isolated by FACS from 36 hpf zebrafish with the following genotypes: edn1 / 2 replicates jag1b / jag1b+/+ control hsp70I:Gal4; UAS:Edn1 hsp70I:Gal4; UAS:Nicd and hsp70I:Gal4 control.	pubmed:28705894	WT fli1a sox10 1	GSM2526391	tissue:Pharyngeal arches\|developmental stage:36 hpf\|genotype:WT\|treatment:N1	WT fli1a sox10 1	Raw sequencing data in Fastq format was imported into the Partek Flow® interface for alignment and quantification. Pre alignment QC showed that the reads from all samples had generally high quality with the average Phred quality score for each sample being above 30. Reads were then trimmed from both ends based on Phred quality score with a minimum end quality level of 20 and a minimum acceptable read length of 25. The TopHat 2 algorithm was used to align the trimmed reads to the zebrafish GRCz10 genome assembly Ensembl v80. Aligned reads were then quantified using the Partek E/M algorithm with default parameters to yield the TPM values. Genome build: GRCz10 Supplementary files format and content: csv text files include TPM values for each gene in each sample	Pharyngeal arches	GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.		developmental stage:36 hpf\|genotype:WT\|treatment:N1	GSM2526391	GSM2526391: WT fli1a sox10 1; Danio rerio; RNA Seq	GSM2526391		1	GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.	GEO Accession:GSM2526391	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP101558				5577850800.0	55778508.0	GSM2526391 r1	0:50 1:50	A:1539279722;C:1164400006;G:1236602222;T:1636301311;N:1267539	50	50			1539279722	1164400006	1236602222	1636301311	1267539	SRX2619917	SRS2029880	SRA543392	GEO	Crump Lab, Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California	2	0.90764	0.74518	0.17723	0.14872	0.75546	0.77741	0.49639	0.48675	50	50	B	B	biological fallback assumption	illumina	hiseq_era	full_length	cdna_unspecified	smarter	bulk	unknown	unknown	United States	2017-03-08	Pharyngula	Embryo	Pharyngeal Arch	Multi-system
42954	42954	SRR5855387	SRX3024626	SRS2373891	SRP113259	PRJNA395253	Nr2f transcription factors promote the identity of the vertebrate upper jaw	GSE101719	Transcriptome Analysis	The jaws are complementary in form and function but develop asymmetrically as the lower but not upper jaw bone forms around a prominent cartilage template. How such differences in skeletal composition are patterned is unclear. Here we identify four Nuclear receptor 2f genes nr2f1a nr2f1b nr2f2 and nr2f5 as enriched in zebrafish upper jaw precursors. Whereas loss of Nr2f genes results in expansion of upper jaw cartilage to resemble that of the lower jaw Nr2f5 misexpression inhibits lower jaw cartilage formation. Genome wide analyses show that Nr2f genes prevent expansion of lower jaw associated gene expression into the upper jaw territory. Further restriction of Nr2f expression by Endothelin1 signaling is critical for lower jaw development as reducing Nr2f dosage fully restores lower jaw development in edn1 mutants. We propose that Nr2f genes drive jaw asymmetry by limiting early cartilage differentiation in the upper jaw to preserve more precursors for later osteogenesis. Overall design: Zebrafish pharyngeal arch cells expressing both fli1a:GFP and sox10:DsRed were isolated by FACS from 36 hpf nr2f2; nr2f5 double mutant embryos 2 replicates: n = 37 & 84; 18 858 & 30 655 cells sox10:Gal4+ embryos n = 69; 86 517 cells sox10:Gal4; UAS:Nr2f5 embryos n = 84; 56 866 cells.	pubmed:29358039	sox10:Gal4 fli1a:GFP+ sox10:DsRed+	GSM2713941	tissue:pharyngeal arch cells\|Stage:36 hpf\|genotype/variation:sox10:Gal4\|identification:fin biopsies taken at 24 hpf genotyped for Gal4 and the UAS allele	sox10:Gal4 fli1a:GFP+ sox10:DsRed+	Raw sequencing data in Fastq format were imported into Partek Flow® for alignment and quantification. In pre alignment QC the reads from all samples were generally of high quality with the average quality score for each sample exceeding 33. The reads were then trimmed at both ends based on the Phred quality score with a minimum end quality level of 20 and a minimum acceptable read length of 25. Trimmed reads were aligned to the Danio rerio GRCz10 genome assembly Emsembl v80 using the TopHat 2 algorithm. Aligned reads were quantified with the Partek E/M algorithm using default parameters to generate TPM values. Genome build: GRCz10 Supplementary files format and content: The csv text files have the TPM values for each gene in each sample.	pharyngeal arch cells	GFP/DsRed double positive cells populations were collected into RLT lysis buffer Qiagen and total RNA was immediately extracted using the RNeasy Micro kit Qiagen according to the manufacturer’s instructions. The purified RNA was evaluated for quality and quantity on a BioAnalyzer Pico RNA chip Agilent Santa Clara CA and then reverse transcribed into cDNA using the SMARTer kit Clontech Mountain View CA. cDNA amplification was adjusted based on the RNA input quantity and the size and amount of generated cDNA was measured by BioAnalyzer. The samples were sonicated on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommendations. DNA libraries were assembled using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA with NextFlex adapters Bioo Scientific Austin TX. Libraries were assessed by Bioanalyzer and quantified using qPCR Kapa Library Quantification kit. Sequencing was performed on a NextSeq 500 75 bp paired end reads Illumina San Diego CA. Library construction and sequencing were performed at the USC Molecular Genomics Core at the USC Norris Comprehensive Cancer Center.	Embryos were maintained at 28.5 degrees C until 27 hpf and then transferred to 22 degrees C to slow their development. Embryos were dissociated and sorted once they achieved morphological criteria corresponding to the standard 36 hpf stage	Stage:36 hpf\|genotype/variation:sox10:Gal4\|identification:fin biopsies taken at 24 hpf genotyped for Gal4 and the UAS allele	GSM2713941	GSM2713941: sox10:Gal4 fli1a:GFP+ sox10:DsRed+; Danio rerio; RNA Seq	GSM2713941		1	GFP/DsRed double positive cells populations were collected into RLT lysis buffer Qiagen and total RNA was immediately extracted using the RNeasy Micro kit Qiagen according to the manufacturer’s instructions. The purified RNA was evaluated for quality and quantity on a BioAnalyzer Pico RNA chip Agilent Santa Clara CA and then reverse transcribed into cDNA using the SMARTer kit Clontech Mountain View CA. cDNA amplification was adjusted based on the RNA input quantity and the size and amount of generated cDNA was measured by BioAnalyzer. The samples were sonicated on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommendations. DNA libraries were assembled using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA with NextFlex adapters Bioo Scientific Austin TX. Libraries were assessed by Bioanalyzer and quantified using qPCR Kapa Library Quantification kit. Sequencing was performed on a NextSeq 500 75 bp paired end reads Illumina San Diego CA. Library construction and sequencing were performed at the USC Molecular Genomics Core at the USC Norris Comprehensive Cancer Center.	GEO Accession:GSM2713941	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP113259		sox10Gal4_GC104_S5_R2_001.fastq.gz sox10Gal4_GC104_S5_R1_001.fastq.gz	fastq fastq	5174277752.0	34041301.0	GSM2713941 r1	0:76 1:76	A:829112690;C:1697763956;G:1785211548;T:861259657;N:929901	76	76			829112690	1697763956	1785211548	861259657	929901	SRX3024626	SRS2373891	SRA589735	GEO	Crump Lab, Stem Cell Biology and Regenerative Medicine, University of Southern California	2	0.89781	0.89904	0.07767	0.07318	0.83378	0.84287	0.79941	0.84864	76	76	B	B	biological fallback assumption	illumina	nextseq	full_length	cdna_unspecified	smarter	bulk	unknown	unknown	United States	2017-07-20	Pharyngula	Embryo	Pharyngeal Arch	Multi-system
42955	42955	SRR5855386	SRX3024625	SRS2373890	SRP113259	PRJNA395253	Nr2f transcription factors promote the identity of the vertebrate upper jaw	GSE101719	Transcriptome Analysis	The jaws are complementary in form and function but develop asymmetrically as the lower but not upper jaw bone forms around a prominent cartilage template. How such differences in skeletal composition are patterned is unclear. Here we identify four Nuclear receptor 2f genes nr2f1a nr2f1b nr2f2 and nr2f5 as enriched in zebrafish upper jaw precursors. Whereas loss of Nr2f genes results in expansion of upper jaw cartilage to resemble that of the lower jaw Nr2f5 misexpression inhibits lower jaw cartilage formation. Genome wide analyses show that Nr2f genes prevent expansion of lower jaw associated gene expression into the upper jaw territory. Further restriction of Nr2f expression by Endothelin1 signaling is critical for lower jaw development as reducing Nr2f dosage fully restores lower jaw development in edn1 mutants. We propose that Nr2f genes drive jaw asymmetry by limiting early cartilage differentiation in the upper jaw to preserve more precursors for later osteogenesis. Overall design: Zebrafish pharyngeal arch cells expressing both fli1a:GFP and sox10:DsRed were isolated by FACS from 36 hpf nr2f2; nr2f5 double mutant embryos 2 replicates: n = 37 & 84; 18 858 & 30 655 cells sox10:Gal4+ embryos n = 69; 86 517 cells sox10:Gal4; UAS:Nr2f5 embryos n = 84; 56 866 cells.	pubmed:29358039	sox10:Gal4; UAS:Nr2f5 fli1a:GFP+ sox10:DsRed+	GSM2713940	tissue:pharyngeal arch cells\|Stage:36 hpf\|genotype/variation:sox10:Gal4; UAS:Nr2f5\|identification:fin biopsies taken at 24 hpf genotyped for Gal4 and the UAS allele	sox10:Gal4; UAS:Nr2f5 fli1a:GFP+ sox10:DsRed+	Raw sequencing data in Fastq format were imported into Partek Flow® for alignment and quantification. In pre alignment QC the reads from all samples were generally of high quality with the average quality score for each sample exceeding 33. The reads were then trimmed at both ends based on the Phred quality score with a minimum end quality level of 20 and a minimum acceptable read length of 25. Trimmed reads were aligned to the Danio rerio GRCz10 genome assembly Emsembl v80 using the TopHat 2 algorithm. Aligned reads were quantified with the Partek E/M algorithm using default parameters to generate TPM values. Genome build: GRCz10 Supplementary files format and content: The csv text files have the TPM values for each gene in each sample.	pharyngeal arch cells	GFP/DsRed double positive cells populations were collected into RLT lysis buffer Qiagen and total RNA was immediately extracted using the RNeasy Micro kit Qiagen according to the manufacturer’s instructions. The purified RNA was evaluated for quality and quantity on a BioAnalyzer Pico RNA chip Agilent Santa Clara CA and then reverse transcribed into cDNA using the SMARTer kit Clontech Mountain View CA. cDNA amplification was adjusted based on the RNA input quantity and the size and amount of generated cDNA was measured by BioAnalyzer. The samples were sonicated on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommendations. DNA libraries were assembled using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA with NextFlex adapters Bioo Scientific Austin TX. Libraries were assessed by Bioanalyzer and quantified using qPCR Kapa Library Quantification kit. Sequencing was performed on a NextSeq 500 75 bp paired end reads Illumina San Diego CA. Library construction and sequencing were performed at the USC Molecular Genomics Core at the USC Norris Comprehensive Cancer Center.	Embryos were maintained at 28.5 degrees C until 27 hpf and then transferred to 22 degrees C to slow their development. Embryos were dissociated and sorted once they achieved morphological criteria corresponding to the standard 36 hpf stage	Stage:36 hpf\|genotype/variation:sox10:Gal4; UAS:Nr2f5\|identification:fin biopsies taken at 24 hpf genotyped for Gal4 and the UAS allele	GSM2713940	GSM2713940: sox10:Gal4; UAS:Nr2f5 fli1a:GFP+ sox10:DsRed+; Danio rerio; RNA Seq	GSM2713940		1	GFP/DsRed double positive cells populations were collected into RLT lysis buffer Qiagen and total RNA was immediately extracted using the RNeasy Micro kit Qiagen according to the manufacturer’s instructions. The purified RNA was evaluated for quality and quantity on a BioAnalyzer Pico RNA chip Agilent Santa Clara CA and then reverse transcribed into cDNA using the SMARTer kit Clontech Mountain View CA. cDNA amplification was adjusted based on the RNA input quantity and the size and amount of generated cDNA was measured by BioAnalyzer. The samples were sonicated on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommendations. DNA libraries were assembled using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA with NextFlex adapters Bioo Scientific Austin TX. Libraries were assessed by Bioanalyzer and quantified using qPCR Kapa Library Quantification kit. Sequencing was performed on a NextSeq 500 75 bp paired end reads Illumina San Diego CA. Library construction and sequencing were performed at the USC Molecular Genomics Core at the USC Norris Comprehensive Cancer Center.	GEO Accession:GSM2713940	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP113259		sox10Gal4UASNr2f5_GC103_S4_R1_001.fastq.gz sox10Gal4UASNr2f5_GC103_S4_R2_001.fastq.gz	fastq fastq	1876943424.0	12348312.0	GSM2713940 r1	0:76 1:76	A:277876402;C:637297214;G:668302099;T:293137389;N:330320	76	76			277876402	637297214	668302099	293137389	330320	SRX3024625	SRS2373890	SRA589735	GEO	Crump Lab, Stem Cell Biology and Regenerative Medicine, University of Southern California	2	0.95473	0.94996	0.08065	0.07608	0.84177	0.85127	0.82239	0.8689	76	76	B	B	biological fallback assumption	illumina	nextseq	full_length	cdna_unspecified	smarter	bulk	unknown	unknown	United States	2017-07-20	Pharyngula	Embryo	Pharyngeal Arch	Multi-system
42956	42956	SRR5855385	SRX3024624	SRS2373889	SRP113259	PRJNA395253	Nr2f transcription factors promote the identity of the vertebrate upper jaw	GSE101719	Transcriptome Analysis	The jaws are complementary in form and function but develop asymmetrically as the lower but not upper jaw bone forms around a prominent cartilage template. How such differences in skeletal composition are patterned is unclear. Here we identify four Nuclear receptor 2f genes nr2f1a nr2f1b nr2f2 and nr2f5 as enriched in zebrafish upper jaw precursors. Whereas loss of Nr2f genes results in expansion of upper jaw cartilage to resemble that of the lower jaw Nr2f5 misexpression inhibits lower jaw cartilage formation. Genome wide analyses show that Nr2f genes prevent expansion of lower jaw associated gene expression into the upper jaw territory. Further restriction of Nr2f expression by Endothelin1 signaling is critical for lower jaw development as reducing Nr2f dosage fully restores lower jaw development in edn1 mutants. We propose that Nr2f genes drive jaw asymmetry by limiting early cartilage differentiation in the upper jaw to preserve more precursors for later osteogenesis. Overall design: Zebrafish pharyngeal arch cells expressing both fli1a:GFP and sox10:DsRed were isolated by FACS from 36 hpf nr2f2; nr2f5 double mutant embryos 2 replicates: n = 37 & 84; 18 858 & 30 655 cells sox10:Gal4+ embryos n = 69; 86 517 cells sox10:Gal4; UAS:Nr2f5 embryos n = 84; 56 866 cells.	pubmed:29358039	nr2f2; nr2f5 mutant 2 fli1a:GFP+ sox10:DsRed+	GSM2713939	tissue:pharyngeal arch cells\|Stage:36 hpf\|genotype/variation:nr2f2; nr2f5 mutant\|identification:ocular coloboma	nr2f2; nr2f5 mutant 2 fli1a:GFP+ sox10:DsRed+	Raw sequencing data in Fastq format were imported into Partek Flow® for alignment and quantification. In pre alignment QC the reads from all samples were generally of high quality with the average quality score for each sample exceeding 33. The reads were then trimmed at both ends based on the Phred quality score with a minimum end quality level of 20 and a minimum acceptable read length of 25. Trimmed reads were aligned to the Danio rerio GRCz10 genome assembly Emsembl v80 using the TopHat 2 algorithm. Aligned reads were quantified with the Partek E/M algorithm using default parameters to generate TPM values. Genome build: GRCz10 Supplementary files format and content: The csv text files have the TPM values for each gene in each sample.	pharyngeal arch cells	GFP/DsRed double positive cells populations were collected into RLT lysis buffer Qiagen and total RNA was immediately extracted using the RNeasy Micro kit Qiagen according to the manufacturer’s instructions. The purified RNA was evaluated for quality and quantity on a BioAnalyzer Pico RNA chip Agilent Santa Clara CA and then reverse transcribed into cDNA using the SMARTer kit Clontech Mountain View CA. cDNA amplification was adjusted based on the RNA input quantity and the size and amount of generated cDNA was measured by BioAnalyzer. The samples were sonicated on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommendations. DNA libraries were assembled using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA with NextFlex adapters Bioo Scientific Austin TX. Libraries were assessed by Bioanalyzer and quantified using qPCR Kapa Library Quantification kit. Sequencing was performed on a NextSeq 500 75 bp paired end reads Illumina San Diego CA. Library construction and sequencing were performed at the USC Molecular Genomics Core at the USC Norris Comprehensive Cancer Center.	Embryos were maintained at 28.5 degrees C until 27 hpf and then transferred to 22 degrees C to slow their development. Embryos were dissociated and sorted once they achieved morphological criteria corresponding to the standard 36 hpf stage	Stage:36 hpf\|genotype/variation:nr2f2; nr2f5 mutant\|identification:ocular coloboma	GSM2713939	GSM2713939: nr2f2; nr2f5 mutant 2 fli1a:GFP+ sox10:DsRed+; Danio rerio; RNA Seq	GSM2713939		1	GFP/DsRed double positive cells populations were collected into RLT lysis buffer Qiagen and total RNA was immediately extracted using the RNeasy Micro kit Qiagen according to the manufacturer’s instructions. The purified RNA was evaluated for quality and quantity on a BioAnalyzer Pico RNA chip Agilent Santa Clara CA and then reverse transcribed into cDNA using the SMARTer kit Clontech Mountain View CA. cDNA amplification was adjusted based on the RNA input quantity and the size and amount of generated cDNA was measured by BioAnalyzer. The samples were sonicated on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommendations. DNA libraries were assembled using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA with NextFlex adapters Bioo Scientific Austin TX. Libraries were assessed by Bioanalyzer and quantified using qPCR Kapa Library Quantification kit. Sequencing was performed on a NextSeq 500 75 bp paired end reads Illumina San Diego CA. Library construction and sequencing were performed at the USC Molecular Genomics Core at the USC Norris Comprehensive Cancer Center.	GEO Accession:GSM2713939	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP113259		nr2f25mut2_GC102_S3_R1_001.fastq.gz nr2f25mut2_GC102_S3_R2_001.fastq.gz	fastq fastq	4425393512.0	29114431.0	GSM2713939 r1	0:76 1:76	A:742522706;C:1435550593;G:1473779857;T:772748815;N:791541	76	76			742522706	1435550593	1473779857	772748815	791541	SRX3024624	SRS2373889	SRA589735	GEO	Crump Lab, Stem Cell Biology and Regenerative Medicine, University of Southern California	2	0.83264	0.83706	0.0728	0.07018	0.85208	0.85823	0.81134	0.83008	76	76	B	B	biological fallback assumption	illumina	nextseq	full_length	cdna_unspecified	smarter	bulk	unknown	unknown	United States	2017-07-20	Pharyngula	Embryo	Pharyngeal Arch	Multi-system
42957	42957	SRR5855384	SRX3024623	SRS2373888	SRP113259	PRJNA395253	Nr2f transcription factors promote the identity of the vertebrate upper jaw	GSE101719	Transcriptome Analysis	The jaws are complementary in form and function but develop asymmetrically as the lower but not upper jaw bone forms around a prominent cartilage template. How such differences in skeletal composition are patterned is unclear. Here we identify four Nuclear receptor 2f genes nr2f1a nr2f1b nr2f2 and nr2f5 as enriched in zebrafish upper jaw precursors. Whereas loss of Nr2f genes results in expansion of upper jaw cartilage to resemble that of the lower jaw Nr2f5 misexpression inhibits lower jaw cartilage formation. Genome wide analyses show that Nr2f genes prevent expansion of lower jaw associated gene expression into the upper jaw territory. Further restriction of Nr2f expression by Endothelin1 signaling is critical for lower jaw development as reducing Nr2f dosage fully restores lower jaw development in edn1 mutants. We propose that Nr2f genes drive jaw asymmetry by limiting early cartilage differentiation in the upper jaw to preserve more precursors for later osteogenesis. Overall design: Zebrafish pharyngeal arch cells expressing both fli1a:GFP and sox10:DsRed were isolated by FACS from 36 hpf nr2f2; nr2f5 double mutant embryos 2 replicates: n = 37 & 84; 18 858 & 30 655 cells sox10:Gal4+ embryos n = 69; 86 517 cells sox10:Gal4; UAS:Nr2f5 embryos n = 84; 56 866 cells.	pubmed:29358039	nr2f2; nr2f5 mutant 1 fli1a:GFP+ sox10:DsRed+	GSM2713938	tissue:pharyngeal arch cells\|Stage:36 hpf\|genotype/variation:nr2f2; nr2f5 mutant\|identification:ocular coloboma	nr2f2; nr2f5 mutant 1 fli1a:GFP+ sox10:DsRed+	Raw sequencing data in Fastq format were imported into Partek Flow® for alignment and quantification. In pre alignment QC the reads from all samples were generally of high quality with the average quality score for each sample exceeding 33. The reads were then trimmed at both ends based on the Phred quality score with a minimum end quality level of 20 and a minimum acceptable read length of 25. Trimmed reads were aligned to the Danio rerio GRCz10 genome assembly Emsembl v80 using the TopHat 2 algorithm. Aligned reads were quantified with the Partek E/M algorithm using default parameters to generate TPM values. Genome build: GRCz10 Supplementary files format and content: The csv text files have the TPM values for each gene in each sample.	pharyngeal arch cells	GFP/DsRed double positive cells populations were collected into RLT lysis buffer Qiagen and total RNA was immediately extracted using the RNeasy Micro kit Qiagen according to the manufacturer’s instructions. The purified RNA was evaluated for quality and quantity on a BioAnalyzer Pico RNA chip Agilent Santa Clara CA and then reverse transcribed into cDNA using the SMARTer kit Clontech Mountain View CA. cDNA amplification was adjusted based on the RNA input quantity and the size and amount of generated cDNA was measured by BioAnalyzer. The samples were sonicated on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommendations. DNA libraries were assembled using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA with NextFlex adapters Bioo Scientific Austin TX. Libraries were assessed by Bioanalyzer and quantified using qPCR Kapa Library Quantification kit. Sequencing was performed on a NextSeq 500 75 bp paired end reads Illumina San Diego CA. Library construction and sequencing were performed at the USC Molecular Genomics Core at the USC Norris Comprehensive Cancer Center.	Embryos were maintained at 28.5 degrees C until 27 hpf and then transferred to 22 degrees C to slow their development. Embryos were dissociated and sorted once they achieved morphological criteria corresponding to the standard 36 hpf stage	Stage:36 hpf\|genotype/variation:nr2f2; nr2f5 mutant\|identification:ocular coloboma	GSM2713938	GSM2713938: nr2f2; nr2f5 mutant 1 fli1a:GFP+ sox10:DsRed+; Danio rerio; RNA Seq	GSM2713938		1	GFP/DsRed double positive cells populations were collected into RLT lysis buffer Qiagen and total RNA was immediately extracted using the RNeasy Micro kit Qiagen according to the manufacturer’s instructions. The purified RNA was evaluated for quality and quantity on a BioAnalyzer Pico RNA chip Agilent Santa Clara CA and then reverse transcribed into cDNA using the SMARTer kit Clontech Mountain View CA. cDNA amplification was adjusted based on the RNA input quantity and the size and amount of generated cDNA was measured by BioAnalyzer. The samples were sonicated on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommendations. DNA libraries were assembled using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA with NextFlex adapters Bioo Scientific Austin TX. Libraries were assessed by Bioanalyzer and quantified using qPCR Kapa Library Quantification kit. Sequencing was performed on a NextSeq 500 75 bp paired end reads Illumina San Diego CA. Library construction and sequencing were performed at the USC Molecular Genomics Core at the USC Norris Comprehensive Cancer Center.	GEO Accession:GSM2713938	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP113259		nr2f25mut1_GC101_S2_R1_001.fastq.gz nr2f25mut1_GC101_S2_R2_001.fastq.gz	fastq fastq	4981028448.0	32769924.0	GSM2713938 r1	0:76 1:76	A:840950063;C:1614355757;G:1644774381;T:880078202;N:870045	76	76			840950063	1614355757	1644774381	880078202	870045	SRX3024623	SRS2373888	SRA589735	GEO	Crump Lab, Stem Cell Biology and Regenerative Medicine, University of Southern California	2	0.92321	0.92152	0.11945	0.11592	0.82627	0.83368	0.7663	0.79383	76	76	B	B	biological fallback assumption	illumina	nextseq	full_length	cdna_unspecified	smarter	bulk	unknown	unknown	United States	2017-07-20	Pharyngula	Embryo	Pharyngeal Arch	Multi-system
67550	67550	SRR17201124	SRX13381108	SRS11285137	SRP350317	PRJNA788011	pharyngeal arch region in zebrafish embryos at 48 hpf	PRJNA788011	Other	pharyngeal arch regions in wild type sibling and mutant zebrafish embryos at 48 hpf			homo 48h2	strain:Tubingen\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:48 hpf stage:not applicable\|sex:not determined\|tissue:pharyngeal arch\|genotype:homozygotic mutant 2\|BioSampleModel:Model organism or animal								RNA seq of Danio rerio: 48hpf homozygotic mutant pharyngeal arch 2	homo 48h2	homo 48h2	Poly A RNA is purified from 1g total RNA using Dynabeads Oligo dT25 61005 Thermo Fisher CA USA using two rounds of purification. Then the polyA RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module NEB cat.e6150 USA under 94 5 7min. Then the cleaved RNA fragments were reverse transcribed to create the cDNA by SuperScript II Reverse Transcriptase Invitrogen cat. 1896649 USA which were next used to synthesise U labeled second stranded DNAs with E. coli DNA polymerase I NEB cat.m0209 USA RNase H NEB cat.m0297 USA and dUTP Solution Thermo Fisher cat.R0133 USA. An A base is then added to the blunt ends of each strand preparing them for ligation to the indexed adapters. Each adapter contains a T base overhang for ligating the adapter to the A tailed fragmented DNA. Single or dual index adapters are ligated to the fragments and size selection was performed with AMPureXP beads. post the heat labile UDG enzyme NEB cat.m0280 USA treatment of the U labeled second stranded DNAs the ligated products are amplified with PCR by the following conditions: initial denaturation at 95 for 3 min; 8 cycles of denaturation at 98 for 15 sec annealing at 60 for 15 sec and extension at 72 for 30 sec; and then final extension at 72 for 5 min. The average insert size for the final cDNA library was 30050 bp.			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP350317		homo_48h2_Clean_Data1.fq.gz homo_48h2_Clean_Data2.fq.gz	fastq fastq	5736708800.0	20741445.0	homo 48h2 Clean Data1.fq.gz	0:138.30 1:138.28	A:1509851615;C:1356120916;G:1368270971;T:1502443004;N:22294	138	138			1509851615	1356120916	1368270971	1502443004	22294	SRX13381108	SRS11285137	SRA1341839	Ocean University of China\|School of Medicine and Pharmacy	Ocean University of China	2	0.95037	0.95325	0.06985	0.06953	0.68763	0.68678	0.47361	0.46423	141	141	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-12-11	Hatching	Embryo	Pharyngeal Arch	Multi-system
67551	67551	SRR17201125	SRX13381107	SRS11285136	SRP350317	PRJNA788011	pharyngeal arch region in zebrafish embryos at 48 hpf	PRJNA788011	Other	pharyngeal arch regions in wild type sibling and mutant zebrafish embryos at 48 hpf			homo 48h1	strain:Tubingen\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:48 hpf stage:not applicable\|sex:not determined\|tissue:pharyngeal arch\|genotype:homozygotic mutant 1\|BioSampleModel:Model organism or animal								RNA seq of Danio rerio: 48hpf homozygotic mutant pharyngeal arch 1	homo 48h1	homo 48h1	Poly A RNA is purified from 1g total RNA using Dynabeads Oligo dT25 61005 Thermo Fisher CA USA using two rounds of purification. Then the polyA RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module NEB cat.e6150 USA under 94 5 7min. Then the cleaved RNA fragments were reverse transcribed to create the cDNA by SuperScript II Reverse Transcriptase Invitrogen cat. 1896649 USA which were next used to synthesise U labeled second stranded DNAs with E. coli DNA polymerase I NEB cat.m0209 USA RNase H NEB cat.m0297 USA and dUTP Solution Thermo Fisher cat.R0133 USA. An A base is then added to the blunt ends of each strand preparing them for ligation to the indexed adapters. Each adapter contains a T base overhang for ligating the adapter to the A tailed fragmented DNA. Single or dual index adapters are ligated to the fragments and size selection was performed with AMPureXP beads. post the heat labile UDG enzyme NEB cat.m0280 USA treatment of the U labeled second stranded DNAs the ligated products are amplified with PCR by the following conditions: initial denaturation at 95 for 3 min; 8 cycles of denaturation at 98 for 15 sec annealing at 60 for 15 sec and extension at 72 for 30 sec; and then final extension at 72 for 5 min. The average insert size for the final cDNA library was 30050 bp.			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP350317		homo_48h1_Clean_Data1.fq.gz homo_48h1_Clean_Data2.fq.gz	fastq fastq	6066639719.0	21885656.0	homo 48h1 Clean Data1.fq.gz	0:138.61 1:138.59	A:1589936586;C:1439665676;G:1452172800;T:1584841034;N:23623	138	138			1589936586	1439665676	1452172800	1584841034	23623	SRX13381107	SRS11285136	SRA1341839	Ocean University of China\|School of Medicine and Pharmacy	Ocean University of China	2	0.95081	0.95275	0.07088	0.07055	0.68357	0.68355	0.45424	0.45004	141	141	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-12-11	Hatching	Embryo	Pharyngeal Arch	Multi-system
67552	67552	SRR17201126	SRX13381106	SRS11285135	SRP350317	PRJNA788011	pharyngeal arch region in zebrafish embryos at 48 hpf	PRJNA788011	Other	pharyngeal arch regions in wild type sibling and mutant zebrafish embryos at 48 hpf			WT 48h2	strain:Tubingen\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:48 hpf stage:not applicable\|sex:not determined\|tissue:pharyngeal arch\|genotype:wild type 2\|BioSampleModel:Model organism or animal								RNA seq of Danio rerio: 48hpf wt pharyngeal arch 2	WT 48h2	WT 48h2	Poly A RNA is purified from 1g total RNA using Dynabeads Oligo dT25 61005 Thermo Fisher CA USA using two rounds of purification. Then the polyA RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module NEB cat.e6150 USA under 94 5 7min. Then the cleaved RNA fragments were reverse transcribed to create the cDNA by SuperScript II Reverse Transcriptase Invitrogen cat. 1896649 USA which were next used to synthesise U labeled second stranded DNAs with E. coli DNA polymerase I NEB cat.m0209 USA RNase H NEB cat.m0297 USA and dUTP Solution Thermo Fisher cat.R0133 USA. An A base is then added to the blunt ends of each strand preparing them for ligation to the indexed adapters. Each adapter contains a T base overhang for ligating the adapter to the A tailed fragmented DNA. Single or dual index adapters are ligated to the fragments and size selection was performed with AMPureXP beads. post the heat labile UDG enzyme NEB cat.m0280 USA treatment of the U labeled second stranded DNAs the ligated products are amplified with PCR by the following conditions: initial denaturation at 95 for 3 min; 8 cycles of denaturation at 98 for 15 sec annealing at 60 for 15 sec and extension at 72 for 30 sec; and then final extension at 72 for 5 min. The average insert size for the final cDNA library was 30050 bp.			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP350317		WT_48h2_Clean_Data1.fq.gz WT_48h2_Clean_Data2.fq.gz	fastq fastq	6235089330.0	22675108.0	WT 48h2 Clean Data1.fq.gz	0:137.49 1:137.48	A:1652157697;C:1463853803;G:1478688188;T:1640365014;N:24628	137	137			1652157697	1463853803	1478688188	1640365014	24628	SRX13381106	SRS11285135	SRA1341839	Ocean University of China\|School of Medicine and Pharmacy	Ocean University of China	2	0.94927	0.95075	0.0714	0.07087	0.69073	0.69035	0.47367	0.47498	141	141	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-12-11	Hatching	Embryo	Pharyngeal Arch	Multi-system
67553	67553	SRR17201127	SRX13381105	SRS11285134	SRP350317	PRJNA788011	pharyngeal arch region in zebrafish embryos at 48 hpf	PRJNA788011	Other	pharyngeal arch regions in wild type sibling and mutant zebrafish embryos at 48 hpf			WT 48h1	strain:Tubingen\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:48 hpf stage:not applicable\|sex:not determined\|tissue:pharyngeal arch\|genotype:wild type 1\|BioSampleModel:Model organism or animal								RNA seq of Danio rerio: 48hpf wt pharyngeal arch 1	WT 48h1	WT 48h1	Poly A RNA is purified from 1g total RNA using Dynabeads Oligo dT25 61005 Thermo Fisher CA USA using two rounds of purification. Then the polyA RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module NEB cat.e6150 USA under 94 5 7min. Then the cleaved RNA fragments were reverse transcribed to create the cDNA by SuperScript II Reverse Transcriptase Invitrogen cat. 1896649 USA which were next used to synthesise U labeled second stranded DNAs with E. coli DNA polymerase I NEB cat.m0209 USA RNase H NEB cat.m0297 USA and dUTP Solution Thermo Fisher cat.R0133 USA. An A base is then added to the blunt ends of each strand preparing them for ligation to the indexed adapters. Each adapter contains a T base overhang for ligating the adapter to the A tailed fragmented DNA. Single or dual index adapters are ligated to the fragments and size selection was performed with AMPureXP beads. post the heat labile UDG enzyme NEB cat.m0280 USA treatment of the U labeled second stranded DNAs the ligated products are amplified with PCR by the following conditions: initial denaturation at 95 for 3 min; 8 cycles of denaturation at 98 for 15 sec annealing at 60 for 15 sec and extension at 72 for 30 sec; and then final extension at 72 for 5 min. The average insert size for the final cDNA library was 30050 bp.			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP350317		WT_48h1_Clean_Data1.fq.gz WT_48h1_Clean_Data2.fq.gz	fastq fastq	6015762217.0	21777982.0	WT 48h1 Clean Data1.fq.gz	0:138.12 1:138.11	A:1585826267;C:1419329854;G:1432062628;T:1578519780;N:23688	138	138			1585826267	1419329854	1432062628	1578519780	23688	SRX13381105	SRS11285134	SRA1341839	Ocean University of China\|School of Medicine and Pharmacy	Ocean University of China	2	0.95017	0.95204	0.07598	0.07505	0.68004	0.6786	0.46827	0.46952	111	111	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-12-11	Hatching	Embryo	Pharyngeal Arch	Multi-system

Advanced export

JSON shape: default, array, newline-delimited

CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;