metadata: run_metadata: 9 rows where devstage_curation = "Segmentation" and experiment.platform = "BGISEQ"

9 rows where devstage_curation = "Segmentation" and experiment.platform = "BGISEQ"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.treatmentprotocol	GEOsample.extractprotocol	GEOsample.growthprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	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.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.nofeature_rate.mate1	seqdetective.sparsity.mate1	seqdetective.pos_strand_rate.mate1	seqdetective.readlen.mate1	seqdetective.judgement.mate1	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
52944	52944	SRR9609439	SRX6372833	SRS5033898	SRP212216	PRJNA551488	TALE and NF Y dependent Genes in 12 hpf Zebrafish Embryos	GSE133459	Transcriptome Analysis	In this RNA seq experiment we identified genes differentially expressed in 12 hpf zebrafish embryos following disruption with dominant negative TALE PBCAB or NF Y NF YA DN. We normalized each dominant negative condition to GFP. For PBCAB we find 646 downregulated and 854 upregulated genes. For NF YA DN we find 325 downregulated and 577 upregulated genes. Genes downregulated by PBCAB are enriched for transcription development and homeodomain ontologies while genes downregulated by NF YA DN are enriched for transcription and cilia ontologies. 74 genes are downregulated by both PBCAB and NF YA DN; these genes are enriched for transcription development and homeodomain ontologies. Overall design: Zebrafish embryos were injected at the 1 cell stage with either a dominant negative Pbx PBCAB dominant negative NF YA NF YA DN or GFP control. Three replicates of 50 100 embryos per condition were collected at 12 hpf and total RNA was extracted. Libraries of polyadenylated RNAs were prepared and sequenced using the BGISEQ 500 platform.	PBCAB Replicate 3	GSM3909672	tissue:Whole Embryo\|Stage:12 hpf\|treatment:PBCAB	PBCAB Replicate 3	Sequenced reads were trimmed and rRNA reads were filtered out with Bowtie2. Trimmed and filtered reads were aligned to the GRCz10/danrer10 genome build and the transcripts per million were calculated using RSEM v1.2.28 with parameters p4 bowtie e 70 bowtie chunkmbs 100. PBCAB replicate 2 was excluded as an outlier. Differentially expressed genes were determined using DESeq2. Genome build: GRCz10/danrer10 Supplementary files format and content: TSV files contain transcripts per million TPM values for each sample.	Whole Embryo	Zebrafish embryos at the 1 cell stage were injected with a mixture of mRNA 0.1% phenol red and water. The mRNAs encoded either a dominant negative Pbx PBCAB dominant negative NF YA NF YA DN or GFP control.	Embryos were collected in Trizol ThermoFisher Scientific and frozen at 80°C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30μL of water. Sample quality was assessed on a Bioanalyzer Agilent with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI Inc. Polyadenylated RNAs were selected using oligo dT beads fragmented and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.	Injected embryos were raised to 12 hours in egg water 60μg/uL Instant Ocean 0.0002% methylene blue at 29°C.	Stage:12 hpf\|treatment:PBCAB	GSM3909672	GSM3909672: PBCAB Replicate 3; Danio rerio; RNA Seq	GSM3909672	1	Embryos were collected in Trizol ThermoFisher Scientific and frozen at 80°C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30μL of water. Sample quality was assessed on a Bioanalyzer Agilent with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI Inc. Polyadenylated RNAs were selected using oligo dT beads fragmented and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.	GEO Accession:GSM3909672	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	BGISEQ	BGISEQ-500	SRP212216	PBCAB_12hpf_zebrafish_biological_replicate3.fq.gz	fastq	1283013300.0	25660266.0	GSM3909672 r1	0:50	A:339417002;C:304649204;G:297783450;T:341163644;N:0	50	339417002	304649204	297783450	341163644	SRX6372833	SRS5033898	SRA914500	GEO	Charles Sagerström, Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School	1	0.94342	0.10559	0.72401	0.47431	50	B	usable mapping rate	bgi	bgi	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2019-06-27	Segmentation	Embryo	Whole Organism	All anatomical structures
52945	52945	SRR9609438	SRX6372832	SRS5033897	SRP212216	PRJNA551488	TALE and NF Y dependent Genes in 12 hpf Zebrafish Embryos	GSE133459	Transcriptome Analysis	In this RNA seq experiment we identified genes differentially expressed in 12 hpf zebrafish embryos following disruption with dominant negative TALE PBCAB or NF Y NF YA DN. We normalized each dominant negative condition to GFP. For PBCAB we find 646 downregulated and 854 upregulated genes. For NF YA DN we find 325 downregulated and 577 upregulated genes. Genes downregulated by PBCAB are enriched for transcription development and homeodomain ontologies while genes downregulated by NF YA DN are enriched for transcription and cilia ontologies. 74 genes are downregulated by both PBCAB and NF YA DN; these genes are enriched for transcription development and homeodomain ontologies. Overall design: Zebrafish embryos were injected at the 1 cell stage with either a dominant negative Pbx PBCAB dominant negative NF YA NF YA DN or GFP control. Three replicates of 50 100 embryos per condition were collected at 12 hpf and total RNA was extracted. Libraries of polyadenylated RNAs were prepared and sequenced using the BGISEQ 500 platform.	PBCAB Replicate 2	GSM3909671	tissue:Whole Embryo\|Stage:12 hpf\|treatment:PBCAB	PBCAB Replicate 2	Sequenced reads were trimmed and rRNA reads were filtered out with Bowtie2. Trimmed and filtered reads were aligned to the GRCz10/danrer10 genome build and the transcripts per million were calculated using RSEM v1.2.28 with parameters p4 bowtie e 70 bowtie chunkmbs 100. PBCAB replicate 2 was excluded as an outlier. Differentially expressed genes were determined using DESeq2. Genome build: GRCz10/danrer10 Supplementary files format and content: TSV files contain transcripts per million TPM values for each sample.	Whole Embryo	Zebrafish embryos at the 1 cell stage were injected with a mixture of mRNA 0.1% phenol red and water. The mRNAs encoded either a dominant negative Pbx PBCAB dominant negative NF YA NF YA DN or GFP control.	Embryos were collected in Trizol ThermoFisher Scientific and frozen at 80°C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30μL of water. Sample quality was assessed on a Bioanalyzer Agilent with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI Inc. Polyadenylated RNAs were selected using oligo dT beads fragmented and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.	Injected embryos were raised to 12 hours in egg water 60μg/uL Instant Ocean 0.0002% methylene blue at 29°C.	Stage:12 hpf\|treatment:PBCAB	GSM3909671	GSM3909671: PBCAB Replicate 2; Danio rerio; RNA Seq	GSM3909671	1	Embryos were collected in Trizol ThermoFisher Scientific and frozen at 80°C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30μL of water. Sample quality was assessed on a Bioanalyzer Agilent with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI Inc. Polyadenylated RNAs were selected using oligo dT beads fragmented and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.	GEO Accession:GSM3909671	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	BGISEQ	BGISEQ-500	SRP212216	PBCAB_12hpf_zebrafish_biological_replicate2.fq.gz	fastq	1282475700.0	25649514.0	GSM3909671 r1	0:50	A:339635626;C:302447093;G:295507893;T:344885088;N:0	50	339635626	302447093	295507893	344885088	SRX6372832	SRS5033897	SRA914500	GEO	Charles Sagerström, Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School	1	0.94396	0.10502	0.71465	0.47566	50	B	usable mapping rate	bgi	bgi	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2019-06-27	Segmentation	Embryo	Whole Organism	All anatomical structures
52946	52946	SRR9609437	SRX6372831	SRS5033896	SRP212216	PRJNA551488	TALE and NF Y dependent Genes in 12 hpf Zebrafish Embryos	GSE133459	Transcriptome Analysis	In this RNA seq experiment we identified genes differentially expressed in 12 hpf zebrafish embryos following disruption with dominant negative TALE PBCAB or NF Y NF YA DN. We normalized each dominant negative condition to GFP. For PBCAB we find 646 downregulated and 854 upregulated genes. For NF YA DN we find 325 downregulated and 577 upregulated genes. Genes downregulated by PBCAB are enriched for transcription development and homeodomain ontologies while genes downregulated by NF YA DN are enriched for transcription and cilia ontologies. 74 genes are downregulated by both PBCAB and NF YA DN; these genes are enriched for transcription development and homeodomain ontologies. Overall design: Zebrafish embryos were injected at the 1 cell stage with either a dominant negative Pbx PBCAB dominant negative NF YA NF YA DN or GFP control. Three replicates of 50 100 embryos per condition were collected at 12 hpf and total RNA was extracted. Libraries of polyadenylated RNAs were prepared and sequenced using the BGISEQ 500 platform.	PBCAB Replicate 1	GSM3909670	tissue:Whole Embryo\|Stage:12 hpf\|treatment:PBCAB	PBCAB Replicate 1	Sequenced reads were trimmed and rRNA reads were filtered out with Bowtie2. Trimmed and filtered reads were aligned to the GRCz10/danrer10 genome build and the transcripts per million were calculated using RSEM v1.2.28 with parameters p4 bowtie e 70 bowtie chunkmbs 100. PBCAB replicate 2 was excluded as an outlier. Differentially expressed genes were determined using DESeq2. Genome build: GRCz10/danrer10 Supplementary files format and content: TSV files contain transcripts per million TPM values for each sample.	Whole Embryo	Zebrafish embryos at the 1 cell stage were injected with a mixture of mRNA 0.1% phenol red and water. The mRNAs encoded either a dominant negative Pbx PBCAB dominant negative NF YA NF YA DN or GFP control.	Embryos were collected in Trizol ThermoFisher Scientific and frozen at 80°C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30μL of water. Sample quality was assessed on a Bioanalyzer Agilent with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI Inc. Polyadenylated RNAs were selected using oligo dT beads fragmented and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.	Injected embryos were raised to 12 hours in egg water 60μg/uL Instant Ocean 0.0002% methylene blue at 29°C.	Stage:12 hpf\|treatment:PBCAB	GSM3909670	GSM3909670: PBCAB Replicate 1; Danio rerio; RNA Seq	GSM3909670	1	Embryos were collected in Trizol ThermoFisher Scientific and frozen at 80°C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30μL of water. Sample quality was assessed on a Bioanalyzer Agilent with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI Inc. Polyadenylated RNAs were selected using oligo dT beads fragmented and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.	GEO Accession:GSM3909670	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	BGISEQ	BGISEQ-500	SRP212216	PBCAB_12hpf_zebrafish_biological_replicate1.fq.gz	fastq	1147572700.0	22951454.0	GSM3909670 r1	0:50	A:300633532;C:273711082;G:268229512;T:304998574;N:0	50	300633532	273711082	268229512	304998574	SRX6372831	SRS5033896	SRA914500	GEO	Charles Sagerström, Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School	1	0.94418	0.09965	0.72746	0.47644	50	B	usable mapping rate	bgi	bgi	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2019-06-27	Segmentation	Embryo	Whole Organism	All anatomical structures
52947	52947	SRR9609436	SRX6372830	SRS5033895	SRP212216	PRJNA551488	TALE and NF Y dependent Genes in 12 hpf Zebrafish Embryos	GSE133459	Transcriptome Analysis	In this RNA seq experiment we identified genes differentially expressed in 12 hpf zebrafish embryos following disruption with dominant negative TALE PBCAB or NF Y NF YA DN. We normalized each dominant negative condition to GFP. For PBCAB we find 646 downregulated and 854 upregulated genes. For NF YA DN we find 325 downregulated and 577 upregulated genes. Genes downregulated by PBCAB are enriched for transcription development and homeodomain ontologies while genes downregulated by NF YA DN are enriched for transcription and cilia ontologies. 74 genes are downregulated by both PBCAB and NF YA DN; these genes are enriched for transcription development and homeodomain ontologies. Overall design: Zebrafish embryos were injected at the 1 cell stage with either a dominant negative Pbx PBCAB dominant negative NF YA NF YA DN or GFP control. Three replicates of 50 100 embryos per condition were collected at 12 hpf and total RNA was extracted. Libraries of polyadenylated RNAs were prepared and sequenced using the BGISEQ 500 platform.	NF YA DN Replicate 3	GSM3909669	tissue:Whole Embryo\|Stage:12 hpf\|treatment:NF YA DN	NF YA DN Replicate 3	Sequenced reads were trimmed and rRNA reads were filtered out with Bowtie2. Trimmed and filtered reads were aligned to the GRCz10/danrer10 genome build and the transcripts per million were calculated using RSEM v1.2.28 with parameters p4 bowtie e 70 bowtie chunkmbs 100. PBCAB replicate 2 was excluded as an outlier. Differentially expressed genes were determined using DESeq2. Genome build: GRCz10/danrer10 Supplementary files format and content: TSV files contain transcripts per million TPM values for each sample.	Whole Embryo	Zebrafish embryos at the 1 cell stage were injected with a mixture of mRNA 0.1% phenol red and water. The mRNAs encoded either a dominant negative Pbx PBCAB dominant negative NF YA NF YA DN or GFP control.	Embryos were collected in Trizol ThermoFisher Scientific and frozen at 80°C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30μL of water. Sample quality was assessed on a Bioanalyzer Agilent with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI Inc. Polyadenylated RNAs were selected using oligo dT beads fragmented and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.	Injected embryos were raised to 12 hours in egg water 60μg/uL Instant Ocean 0.0002% methylene blue at 29°C.	Stage:12 hpf\|treatment:NF YA DN	GSM3909669	GSM3909669: NF YA DN Replicate 3; Danio rerio; RNA Seq	GSM3909669	1	Embryos were collected in Trizol ThermoFisher Scientific and frozen at 80°C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30μL of water. Sample quality was assessed on a Bioanalyzer Agilent with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI Inc. Polyadenylated RNAs were selected using oligo dT beads fragmented and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.	GEO Accession:GSM3909669	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	BGISEQ	BGISEQ-500	SRP212216	NFYADN_12hpf_zebrafish_biological_replicate3.fq.gz	fastq	1282414400.0	25648288.0	GSM3909669 r1	0:50	A:334687310;C:307161534;G:302070174;T:338495382;N:0	50	334687310	307161534	302070174	338495382	SRX6372830	SRS5033895	SRA914500	GEO	Charles Sagerström, Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School	1	0.94359	0.09476	0.72529	0.47117	50	B	usable mapping rate	bgi	bgi	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2019-06-27	Segmentation	Embryo	Whole Organism	All anatomical structures
52948	52948	SRR9609435	SRX6372829	SRS5033894	SRP212216	PRJNA551488	TALE and NF Y dependent Genes in 12 hpf Zebrafish Embryos	GSE133459	Transcriptome Analysis	In this RNA seq experiment we identified genes differentially expressed in 12 hpf zebrafish embryos following disruption with dominant negative TALE PBCAB or NF Y NF YA DN. We normalized each dominant negative condition to GFP. For PBCAB we find 646 downregulated and 854 upregulated genes. For NF YA DN we find 325 downregulated and 577 upregulated genes. Genes downregulated by PBCAB are enriched for transcription development and homeodomain ontologies while genes downregulated by NF YA DN are enriched for transcription and cilia ontologies. 74 genes are downregulated by both PBCAB and NF YA DN; these genes are enriched for transcription development and homeodomain ontologies. Overall design: Zebrafish embryos were injected at the 1 cell stage with either a dominant negative Pbx PBCAB dominant negative NF YA NF YA DN or GFP control. Three replicates of 50 100 embryos per condition were collected at 12 hpf and total RNA was extracted. Libraries of polyadenylated RNAs were prepared and sequenced using the BGISEQ 500 platform.	NF YA DN Replicate 2	GSM3909668	tissue:Whole Embryo\|Stage:12 hpf\|treatment:NF YA DN	NF YA DN Replicate 2	Sequenced reads were trimmed and rRNA reads were filtered out with Bowtie2. Trimmed and filtered reads were aligned to the GRCz10/danrer10 genome build and the transcripts per million were calculated using RSEM v1.2.28 with parameters p4 bowtie e 70 bowtie chunkmbs 100. PBCAB replicate 2 was excluded as an outlier. Differentially expressed genes were determined using DESeq2. Genome build: GRCz10/danrer10 Supplementary files format and content: TSV files contain transcripts per million TPM values for each sample.	Whole Embryo	Zebrafish embryos at the 1 cell stage were injected with a mixture of mRNA 0.1% phenol red and water. The mRNAs encoded either a dominant negative Pbx PBCAB dominant negative NF YA NF YA DN or GFP control.	Embryos were collected in Trizol ThermoFisher Scientific and frozen at 80°C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30μL of water. Sample quality was assessed on a Bioanalyzer Agilent with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI Inc. Polyadenylated RNAs were selected using oligo dT beads fragmented and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.	Injected embryos were raised to 12 hours in egg water 60μg/uL Instant Ocean 0.0002% methylene blue at 29°C.	Stage:12 hpf\|treatment:NF YA DN	GSM3909668	GSM3909668: NF YA DN Replicate 2; Danio rerio; RNA Seq	GSM3909668	1	Embryos were collected in Trizol ThermoFisher Scientific and frozen at 80°C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30μL of water. Sample quality was assessed on a Bioanalyzer Agilent with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI Inc. Polyadenylated RNAs were selected using oligo dT beads fragmented and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.	GEO Accession:GSM3909668	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	BGISEQ	BGISEQ-500	SRP212216	NFYADN_12hpf_zebrafish_biological_replicate2.fq.gz	fastq	1281370000.0	25627400.0	GSM3909668 r1	0:50	A:335735118;C:306450529;G:298815464;T:340368889;N:0	50	335735118	306450529	298815464	340368889	SRX6372829	SRS5033894	SRA914500	GEO	Charles Sagerström, Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School	1	0.94338	0.09412	0.7204	0.48662	50	B	usable mapping rate	bgi	bgi	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2019-06-27	Segmentation	Embryo	Whole Organism	All anatomical structures
52949	52949	SRR9609434	SRX6372828	SRS5033893	SRP212216	PRJNA551488	TALE and NF Y dependent Genes in 12 hpf Zebrafish Embryos	GSE133459	Transcriptome Analysis	In this RNA seq experiment we identified genes differentially expressed in 12 hpf zebrafish embryos following disruption with dominant negative TALE PBCAB or NF Y NF YA DN. We normalized each dominant negative condition to GFP. For PBCAB we find 646 downregulated and 854 upregulated genes. For NF YA DN we find 325 downregulated and 577 upregulated genes. Genes downregulated by PBCAB are enriched for transcription development and homeodomain ontologies while genes downregulated by NF YA DN are enriched for transcription and cilia ontologies. 74 genes are downregulated by both PBCAB and NF YA DN; these genes are enriched for transcription development and homeodomain ontologies. Overall design: Zebrafish embryos were injected at the 1 cell stage with either a dominant negative Pbx PBCAB dominant negative NF YA NF YA DN or GFP control. Three replicates of 50 100 embryos per condition were collected at 12 hpf and total RNA was extracted. Libraries of polyadenylated RNAs were prepared and sequenced using the BGISEQ 500 platform.	NF YA DN Replicate 1	GSM3909667	tissue:Whole Embryo\|Stage:12 hpf\|treatment:NF YA DN	NF YA DN Replicate 1	Sequenced reads were trimmed and rRNA reads were filtered out with Bowtie2. Trimmed and filtered reads were aligned to the GRCz10/danrer10 genome build and the transcripts per million were calculated using RSEM v1.2.28 with parameters p4 bowtie e 70 bowtie chunkmbs 100. PBCAB replicate 2 was excluded as an outlier. Differentially expressed genes were determined using DESeq2. Genome build: GRCz10/danrer10 Supplementary files format and content: TSV files contain transcripts per million TPM values for each sample.	Whole Embryo	Zebrafish embryos at the 1 cell stage were injected with a mixture of mRNA 0.1% phenol red and water. The mRNAs encoded either a dominant negative Pbx PBCAB dominant negative NF YA NF YA DN or GFP control.	Embryos were collected in Trizol ThermoFisher Scientific and frozen at 80°C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30μL of water. Sample quality was assessed on a Bioanalyzer Agilent with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI Inc. Polyadenylated RNAs were selected using oligo dT beads fragmented and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.	Injected embryos were raised to 12 hours in egg water 60μg/uL Instant Ocean 0.0002% methylene blue at 29°C.	Stage:12 hpf\|treatment:NF YA DN	GSM3909667	GSM3909667: NF YA DN Replicate 1; Danio rerio; RNA Seq	GSM3909667	1	Embryos were collected in Trizol ThermoFisher Scientific and frozen at 80°C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30μL of water. Sample quality was assessed on a Bioanalyzer Agilent with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI Inc. Polyadenylated RNAs were selected using oligo dT beads fragmented and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.	GEO Accession:GSM3909667	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	BGISEQ	BGISEQ-500	SRP212216	NFYADN_12hpf_zebrafish_biological_replicate1.fq.gz	fastq	1278504750.0	25570095.0	GSM3909667 r1	0:50	A:334370606;C:306252389;G:299065406;T:338816349;N:0	50	334370606	306252389	299065406	338816349	SRX6372828	SRS5033893	SRA914500	GEO	Charles Sagerström, Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School	1	0.94373	0.09279	0.7191	0.48836	50	B	usable mapping rate	bgi	bgi	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2019-06-27	Segmentation	Embryo	Whole Organism	All anatomical structures
52950	52950	SRR9609433	SRX6372827	SRS5033892	SRP212216	PRJNA551488	TALE and NF Y dependent Genes in 12 hpf Zebrafish Embryos	GSE133459	Transcriptome Analysis	In this RNA seq experiment we identified genes differentially expressed in 12 hpf zebrafish embryos following disruption with dominant negative TALE PBCAB or NF Y NF YA DN. We normalized each dominant negative condition to GFP. For PBCAB we find 646 downregulated and 854 upregulated genes. For NF YA DN we find 325 downregulated and 577 upregulated genes. Genes downregulated by PBCAB are enriched for transcription development and homeodomain ontologies while genes downregulated by NF YA DN are enriched for transcription and cilia ontologies. 74 genes are downregulated by both PBCAB and NF YA DN; these genes are enriched for transcription development and homeodomain ontologies. Overall design: Zebrafish embryos were injected at the 1 cell stage with either a dominant negative Pbx PBCAB dominant negative NF YA NF YA DN or GFP control. Three replicates of 50 100 embryos per condition were collected at 12 hpf and total RNA was extracted. Libraries of polyadenylated RNAs were prepared and sequenced using the BGISEQ 500 platform.	GFP Replicate 3	GSM3909666	tissue:Whole Embryo\|Stage:12 hpf\|treatment:GFP	GFP Replicate 3	Sequenced reads were trimmed and rRNA reads were filtered out with Bowtie2. Trimmed and filtered reads were aligned to the GRCz10/danrer10 genome build and the transcripts per million were calculated using RSEM v1.2.28 with parameters p4 bowtie e 70 bowtie chunkmbs 100. PBCAB replicate 2 was excluded as an outlier. Differentially expressed genes were determined using DESeq2. Genome build: GRCz10/danrer10 Supplementary files format and content: TSV files contain transcripts per million TPM values for each sample.	Whole Embryo	Zebrafish embryos at the 1 cell stage were injected with a mixture of mRNA 0.1% phenol red and water. The mRNAs encoded either a dominant negative Pbx PBCAB dominant negative NF YA NF YA DN or GFP control.	Embryos were collected in Trizol ThermoFisher Scientific and frozen at 80°C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30μL of water. Sample quality was assessed on a Bioanalyzer Agilent with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI Inc. Polyadenylated RNAs were selected using oligo dT beads fragmented and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.	Injected embryos were raised to 12 hours in egg water 60μg/uL Instant Ocean 0.0002% methylene blue at 29°C.	Stage:12 hpf\|treatment:GFP	GSM3909666	GSM3909666: GFP Replicate 3; Danio rerio; RNA Seq	GSM3909666	1	Embryos were collected in Trizol ThermoFisher Scientific and frozen at 80°C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30μL of water. Sample quality was assessed on a Bioanalyzer Agilent with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI Inc. Polyadenylated RNAs were selected using oligo dT beads fragmented and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.	GEO Accession:GSM3909666	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	BGISEQ	BGISEQ-500	SRP212216	GFP_12hpf_zebrafish_biological_replicate3.fq.gz	fastq	1284828600.0	25696572.0	GSM3909666 r1	0:50	A:340467505;C:302914392;G:291984238;T:349462465;N:0	50	340467505	302914392	291984238	349462465	SRX6372827	SRS5033892	SRA914500	GEO	Charles Sagerström, Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School	1	0.94288	0.0963	0.71713	0.4793	50	B	usable mapping rate	bgi	bgi	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2019-06-27	Segmentation	Embryo	Whole Organism	All anatomical structures
52951	52951	SRR9609432	SRX6372826	SRS5033891	SRP212216	PRJNA551488	TALE and NF Y dependent Genes in 12 hpf Zebrafish Embryos	GSE133459	Transcriptome Analysis	In this RNA seq experiment we identified genes differentially expressed in 12 hpf zebrafish embryos following disruption with dominant negative TALE PBCAB or NF Y NF YA DN. We normalized each dominant negative condition to GFP. For PBCAB we find 646 downregulated and 854 upregulated genes. For NF YA DN we find 325 downregulated and 577 upregulated genes. Genes downregulated by PBCAB are enriched for transcription development and homeodomain ontologies while genes downregulated by NF YA DN are enriched for transcription and cilia ontologies. 74 genes are downregulated by both PBCAB and NF YA DN; these genes are enriched for transcription development and homeodomain ontologies. Overall design: Zebrafish embryos were injected at the 1 cell stage with either a dominant negative Pbx PBCAB dominant negative NF YA NF YA DN or GFP control. Three replicates of 50 100 embryos per condition were collected at 12 hpf and total RNA was extracted. Libraries of polyadenylated RNAs were prepared and sequenced using the BGISEQ 500 platform.	GFP Replicate 2	GSM3909665	tissue:Whole Embryo\|Stage:12 hpf\|treatment:GFP	GFP Replicate 2	Sequenced reads were trimmed and rRNA reads were filtered out with Bowtie2. Trimmed and filtered reads were aligned to the GRCz10/danrer10 genome build and the transcripts per million were calculated using RSEM v1.2.28 with parameters p4 bowtie e 70 bowtie chunkmbs 100. PBCAB replicate 2 was excluded as an outlier. Differentially expressed genes were determined using DESeq2. Genome build: GRCz10/danrer10 Supplementary files format and content: TSV files contain transcripts per million TPM values for each sample.	Whole Embryo	Zebrafish embryos at the 1 cell stage were injected with a mixture of mRNA 0.1% phenol red and water. The mRNAs encoded either a dominant negative Pbx PBCAB dominant negative NF YA NF YA DN or GFP control.	Embryos were collected in Trizol ThermoFisher Scientific and frozen at 80°C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30μL of water. Sample quality was assessed on a Bioanalyzer Agilent with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI Inc. Polyadenylated RNAs were selected using oligo dT beads fragmented and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.	Injected embryos were raised to 12 hours in egg water 60μg/uL Instant Ocean 0.0002% methylene blue at 29°C.	Stage:12 hpf\|treatment:GFP	GSM3909665	GSM3909665: GFP Replicate 2; Danio rerio; RNA Seq	GSM3909665	1	Embryos were collected in Trizol ThermoFisher Scientific and frozen at 80°C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30μL of water. Sample quality was assessed on a Bioanalyzer Agilent with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI Inc. Polyadenylated RNAs were selected using oligo dT beads fragmented and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.	GEO Accession:GSM3909665	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	BGISEQ	BGISEQ-500	SRP212216	GFP_12hpf_zebrafish_biological_replicate2.fq.gz	fastq	1274433150.0	25488663.0	GSM3909665 r1	0:50	A:336050330;C:303141446;G:297353928;T:337887446;N:0	50	336050330	303141446	297353928	337887446	SRX6372826	SRS5033891	SRA914500	GEO	Charles Sagerström, Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School	1	0.94266	0.0966	0.72476	0.47615	50	B	usable mapping rate	bgi	bgi	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2019-06-27	Segmentation	Embryo	Whole Organism	All anatomical structures
52952	52952	SRR9609431	SRX6372825	SRS5033890	SRP212216	PRJNA551488	TALE and NF Y dependent Genes in 12 hpf Zebrafish Embryos	GSE133459	Transcriptome Analysis	In this RNA seq experiment we identified genes differentially expressed in 12 hpf zebrafish embryos following disruption with dominant negative TALE PBCAB or NF Y NF YA DN. We normalized each dominant negative condition to GFP. For PBCAB we find 646 downregulated and 854 upregulated genes. For NF YA DN we find 325 downregulated and 577 upregulated genes. Genes downregulated by PBCAB are enriched for transcription development and homeodomain ontologies while genes downregulated by NF YA DN are enriched for transcription and cilia ontologies. 74 genes are downregulated by both PBCAB and NF YA DN; these genes are enriched for transcription development and homeodomain ontologies. Overall design: Zebrafish embryos were injected at the 1 cell stage with either a dominant negative Pbx PBCAB dominant negative NF YA NF YA DN or GFP control. Three replicates of 50 100 embryos per condition were collected at 12 hpf and total RNA was extracted. Libraries of polyadenylated RNAs were prepared and sequenced using the BGISEQ 500 platform.	GFP Replicate 1	GSM3909664	tissue:Whole Embryo\|Stage:12 hpf\|treatment:GFP	GFP Replicate 1	Sequenced reads were trimmed and rRNA reads were filtered out with Bowtie2. Trimmed and filtered reads were aligned to the GRCz10/danrer10 genome build and the transcripts per million were calculated using RSEM v1.2.28 with parameters p4 bowtie e 70 bowtie chunkmbs 100. PBCAB replicate 2 was excluded as an outlier. Differentially expressed genes were determined using DESeq2. Genome build: GRCz10/danrer10 Supplementary files format and content: TSV files contain transcripts per million TPM values for each sample.	Whole Embryo	Zebrafish embryos at the 1 cell stage were injected with a mixture of mRNA 0.1% phenol red and water. The mRNAs encoded either a dominant negative Pbx PBCAB dominant negative NF YA NF YA DN or GFP control.	Embryos were collected in Trizol ThermoFisher Scientific and frozen at 80°C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30μL of water. Sample quality was assessed on a Bioanalyzer Agilent with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI Inc. Polyadenylated RNAs were selected using oligo dT beads fragmented and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.	Injected embryos were raised to 12 hours in egg water 60μg/uL Instant Ocean 0.0002% methylene blue at 29°C.	Stage:12 hpf\|treatment:GFP	GSM3909664	GSM3909664: GFP Replicate 1; Danio rerio; RNA Seq	GSM3909664	1	Embryos were collected in Trizol ThermoFisher Scientific and frozen at 80°C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30μL of water. Sample quality was assessed on a Bioanalyzer Agilent with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI Inc. Polyadenylated RNAs were selected using oligo dT beads fragmented and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.	GEO Accession:GSM3909664	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	BGISEQ	BGISEQ-500	SRP212216	GFP_12hpf_zebrafish_biological_replicate1.fq.gz	fastq	1278273350.0	25565467.0	GSM3909664 r1	0:50	A:336762127;C:304299745;G:297929933;T:339281545;N:0	50	336762127	304299745	297929933	339281545	SRX6372825	SRS5033890	SRA914500	GEO	Charles Sagerström, Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School	1	0.94207	0.09472	0.72642	0.47988	50	B	usable mapping rate	bgi	bgi	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2019-06-27	Segmentation	Embryo	Whole Organism	All anatomical structures

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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");;