metadata: run_metadata: 6 rows where experiment.library_source = "TRANSCRIPTOMIC", technology = "bulk" and tissue_curation

6 rows where experiment.library_source = "TRANSCRIPTOMIC", technology = "bulk" and tissue_curation_coarse = "Cell Line"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	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.library_name	experiment.design_description	experiment.library_construction_protocol	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.r2_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.Ncount	run.experiment	run.pool_member	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
71391	71391	SRR21563983	SRX17566322	SRS15108370	SRP397072	PRJNA880540	A chronic signaling TGFb zebrafish reporter identifies immune response in melanoma [RNA seq ZMEL]	GSE213328	Transcriptome Analysis	Developmental signaling pathways associated with growth factors such as TGFb are commonly dysregulated in melanoma. Here we identified a human TGFb enhancer that was specifically activated in melanoma cells treated with TGFB1 ligand. We generated stable transgenic zebrafish with this enhancer driving green fluorescent protein TIE:EGFP. EGFP was not expressed in normal melanocytes or early melanomas but was expressed in spatially distinct regions of mature melanomas. Single cell RNA sequencing revealed that TIE:EGFP+ melanoma cells down regulated interferon response while up regulating a novel set of chronic TGFb target genes. AP 1 factor binding is required for activation of this chronic TGFb reporter. Overexpression of the chromatin remodeler SATB2 which is associated with tumor spreading shows activation of TGFb signaling in melanoma precursor zones and early melanomas. Confocal imaging and flow cytometric analysis showed that macrophages are recruited to EGFP positive regions and preferentially phagocytose TIE:EGFP+ cells. This work identifies a TGFb induced immune response and demonstrates the need for the development of chronic TGFb biomarkers to predict patient response to TGFb inhibitors. Overall design: RNA seq +/ TGFB1 Bulk RNA seq on ZMEL1 treated with 10ng/mL TGFB1 ligand or vehicle control ZMEL1 cells were serum starved for 2 hours then treated with 10ng/mL human recombinant TGFB1 or 4mM HCl containing 1 mg/mL BSA vehicle control for an additional two hours. Experiment performed in technical triplicate.	parent bioproject:PRJNA880593	10ng/mL TGFB1 treated ZMEL1 Replicate 3	GSM6579025	tissue:ZMEL1 Cells\|cell line:ZMEL1 Cells\|treatment:TGFB1\|geo loc name:missing\|collection date:missing	10ng/mL TGFB1 treated ZMEL1 Replicate 3	Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence using cutadapt then mapped to Ensembl GRCz11 whole genome using tophat 2.1 Transcript abundance were calculated with Htseq count Assembly: GRCz11 Supplementary files format and content: raw count file	ZMEL1 Cells	Cells were starved for 2 hours. Treated with 10ng/mL TGFB1 ligand or 4mM HCl containing 1mg/mL BSA vehicle control for 2 hours.	RNA was collected from adherent cells using the Qiagen RNeasy Plus Mini Kit Qiagen #74134. One microgram of RNA was ribodepleted using NEBNext rRNA Depletion Kit NEB #E6310. Ribodepleted RNA was fragmented reverse transcribed and library prepped NEB #E7530 NEB #E7335.	ZMEL1 were grown in filter sterilized DMEM 10% FBS 1% PenStrep 1% Glutamine at 28°C	cell line:ZMEL1 Cells\|treatment:TGFB1	GSM6579025	GSM6579025: 10ng/mL TGFB1 treated ZMEL1 Replicate 3; Danio rerio; RNA Seq	GSM6579025 r1	GSM6579025	1	RNA was collected from adherent cells using the Qiagen RNeasy Plus Mini Kit Qiagen #74134. One microgram of RNA was ribodepleted using NEBNext rRNA Depletion Kit NEB #E6310. Ribodepleted RNA was fragmented reverse transcribed and library prepped NEB #E7530 NEB #E7335.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP397072	HN74_R1_001.fastq.gz HN74_R2_001.fastq.gz	fastq fastq	10636363800.0	35454546.0	GSM6579025 r1	0:150 1:150	A:2029842779;C:3291717009;G:3355095939;T:1958873670;N:834403	150	150	2029842779	3291717009	3355095939	1958873670	834403	SRX17566322	SRS15108370	Oncology/Hematology, Boston Children's Hospital	2	0.93331	0.94647	0.18347	0.19102	0.85163	0.86429	0.71853	0.75127	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	rrna_depletion	nebnext	sc_generic	bulk	bulk	United States	2022-09-14	Undetermined	Undetermined	Cell Line	Cell Line
71392	71392	SRR21563984	SRX17566321	SRS15108369	SRP397072	PRJNA880540	A chronic signaling TGFb zebrafish reporter identifies immune response in melanoma [RNA seq ZMEL]	GSE213328	Transcriptome Analysis	Developmental signaling pathways associated with growth factors such as TGFb are commonly dysregulated in melanoma. Here we identified a human TGFb enhancer that was specifically activated in melanoma cells treated with TGFB1 ligand. We generated stable transgenic zebrafish with this enhancer driving green fluorescent protein TIE:EGFP. EGFP was not expressed in normal melanocytes or early melanomas but was expressed in spatially distinct regions of mature melanomas. Single cell RNA sequencing revealed that TIE:EGFP+ melanoma cells down regulated interferon response while up regulating a novel set of chronic TGFb target genes. AP 1 factor binding is required for activation of this chronic TGFb reporter. Overexpression of the chromatin remodeler SATB2 which is associated with tumor spreading shows activation of TGFb signaling in melanoma precursor zones and early melanomas. Confocal imaging and flow cytometric analysis showed that macrophages are recruited to EGFP positive regions and preferentially phagocytose TIE:EGFP+ cells. This work identifies a TGFb induced immune response and demonstrates the need for the development of chronic TGFb biomarkers to predict patient response to TGFb inhibitors. Overall design: RNA seq +/ TGFB1 Bulk RNA seq on ZMEL1 treated with 10ng/mL TGFB1 ligand or vehicle control ZMEL1 cells were serum starved for 2 hours then treated with 10ng/mL human recombinant TGFB1 or 4mM HCl containing 1 mg/mL BSA vehicle control for an additional two hours. Experiment performed in technical triplicate.	parent bioproject:PRJNA880593	10ng/mL TGFB1 treated ZMEL1 Replicate 2	GSM6579024	tissue:ZMEL1 Cells\|cell line:ZMEL1 Cells\|treatment:TGFB1\|geo loc name:missing\|collection date:missing	10ng/mL TGFB1 treated ZMEL1 Replicate 2	Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence using cutadapt then mapped to Ensembl GRCz11 whole genome using tophat 2.1 Transcript abundance were calculated with Htseq count Assembly: GRCz11 Supplementary files format and content: raw count file	ZMEL1 Cells	Cells were starved for 2 hours. Treated with 10ng/mL TGFB1 ligand or 4mM HCl containing 1mg/mL BSA vehicle control for 2 hours.	RNA was collected from adherent cells using the Qiagen RNeasy Plus Mini Kit Qiagen #74134. One microgram of RNA was ribodepleted using NEBNext rRNA Depletion Kit NEB #E6310. Ribodepleted RNA was fragmented reverse transcribed and library prepped NEB #E7530 NEB #E7335.	ZMEL1 were grown in filter sterilized DMEM 10% FBS 1% PenStrep 1% Glutamine at 28°C	cell line:ZMEL1 Cells\|treatment:TGFB1	GSM6579024	GSM6579024: 10ng/mL TGFB1 treated ZMEL1 Replicate 2; Danio rerio; RNA Seq	GSM6579024 r1	GSM6579024	1	RNA was collected from adherent cells using the Qiagen RNeasy Plus Mini Kit Qiagen #74134. One microgram of RNA was ribodepleted using NEBNext rRNA Depletion Kit NEB #E6310. Ribodepleted RNA was fragmented reverse transcribed and library prepped NEB #E7530 NEB #E7335.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP397072	HN73_R1_001.fastq.gz HN73_R2_001.fastq.gz	fastq fastq	8998062900.0	29993543.0	GSM6579024 r1	0:150 1:150	A:1717609888;C:2782898315;G:2831578316;T:1665301010;N:675371	150	150	1717609888	2782898315	2831578316	1665301010	675371	SRX17566321	SRS15108369	Oncology/Hematology, Boston Children's Hospital	2	0.93781	0.94782	0.184	0.19138	0.8449	0.86014	0.71335	0.71676	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	rrna_depletion	nebnext	sc_generic	bulk	bulk	United States	2022-09-14	Undetermined	Undetermined	Cell Line	Cell Line
71393	71393	SRR21563985	SRX17566320	SRS15108368	SRP397072	PRJNA880540	A chronic signaling TGFb zebrafish reporter identifies immune response in melanoma [RNA seq ZMEL]	GSE213328	Transcriptome Analysis	Developmental signaling pathways associated with growth factors such as TGFb are commonly dysregulated in melanoma. Here we identified a human TGFb enhancer that was specifically activated in melanoma cells treated with TGFB1 ligand. We generated stable transgenic zebrafish with this enhancer driving green fluorescent protein TIE:EGFP. EGFP was not expressed in normal melanocytes or early melanomas but was expressed in spatially distinct regions of mature melanomas. Single cell RNA sequencing revealed that TIE:EGFP+ melanoma cells down regulated interferon response while up regulating a novel set of chronic TGFb target genes. AP 1 factor binding is required for activation of this chronic TGFb reporter. Overexpression of the chromatin remodeler SATB2 which is associated with tumor spreading shows activation of TGFb signaling in melanoma precursor zones and early melanomas. Confocal imaging and flow cytometric analysis showed that macrophages are recruited to EGFP positive regions and preferentially phagocytose TIE:EGFP+ cells. This work identifies a TGFb induced immune response and demonstrates the need for the development of chronic TGFb biomarkers to predict patient response to TGFb inhibitors. Overall design: RNA seq +/ TGFB1 Bulk RNA seq on ZMEL1 treated with 10ng/mL TGFB1 ligand or vehicle control ZMEL1 cells were serum starved for 2 hours then treated with 10ng/mL human recombinant TGFB1 or 4mM HCl containing 1 mg/mL BSA vehicle control for an additional two hours. Experiment performed in technical triplicate.	parent bioproject:PRJNA880593	10ng/mL TGFB1 treated ZMEL1 Replicate 1	GSM6579023	tissue:ZMEL1 Cells\|cell line:ZMEL1 Cells\|treatment:TGFB1\|geo loc name:missing\|collection date:missing	10ng/mL TGFB1 treated ZMEL1 Replicate 1	Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence using cutadapt then mapped to Ensembl GRCz11 whole genome using tophat 2.1 Transcript abundance were calculated with Htseq count Assembly: GRCz11 Supplementary files format and content: raw count file	ZMEL1 Cells	Cells were starved for 2 hours. Treated with 10ng/mL TGFB1 ligand or 4mM HCl containing 1mg/mL BSA vehicle control for 2 hours.	RNA was collected from adherent cells using the Qiagen RNeasy Plus Mini Kit Qiagen #74134. One microgram of RNA was ribodepleted using NEBNext rRNA Depletion Kit NEB #E6310. Ribodepleted RNA was fragmented reverse transcribed and library prepped NEB #E7530 NEB #E7335.	ZMEL1 were grown in filter sterilized DMEM 10% FBS 1% PenStrep 1% Glutamine at 28°C	cell line:ZMEL1 Cells\|treatment:TGFB1	GSM6579023	GSM6579023: 10ng/mL TGFB1 treated ZMEL1 Replicate 1; Danio rerio; RNA Seq	GSM6579023 r1	GSM6579023	1	RNA was collected from adherent cells using the Qiagen RNeasy Plus Mini Kit Qiagen #74134. One microgram of RNA was ribodepleted using NEBNext rRNA Depletion Kit NEB #E6310. Ribodepleted RNA was fragmented reverse transcribed and library prepped NEB #E7530 NEB #E7335.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP397072	HN72_R1_001.fastq.gz HN72_R2_001.fastq.gz	fastq fastq	9469796100.0	31565987.0	GSM6579023 r1	0:150 1:150	A:1779087329;C:2959081502;G:3015100670;T:1715714055;N:812544	150	150	1779087329	2959081502	3015100670	1715714055	812544	SRX17566320	SRS15108368	Oncology/Hematology, Boston Children's Hospital	2	0.93963	0.94978	0.17963	0.18558	0.84691	0.86032	0.72223	0.75653	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	rrna_depletion	nebnext	sc_generic	bulk	bulk	United States	2022-09-14	Undetermined	Undetermined	Cell Line	Cell Line
71394	71394	SRR21563986	SRX17566319	SRS15108367	SRP397072	PRJNA880540	A chronic signaling TGFb zebrafish reporter identifies immune response in melanoma [RNA seq ZMEL]	GSE213328	Transcriptome Analysis	Developmental signaling pathways associated with growth factors such as TGFb are commonly dysregulated in melanoma. Here we identified a human TGFb enhancer that was specifically activated in melanoma cells treated with TGFB1 ligand. We generated stable transgenic zebrafish with this enhancer driving green fluorescent protein TIE:EGFP. EGFP was not expressed in normal melanocytes or early melanomas but was expressed in spatially distinct regions of mature melanomas. Single cell RNA sequencing revealed that TIE:EGFP+ melanoma cells down regulated interferon response while up regulating a novel set of chronic TGFb target genes. AP 1 factor binding is required for activation of this chronic TGFb reporter. Overexpression of the chromatin remodeler SATB2 which is associated with tumor spreading shows activation of TGFb signaling in melanoma precursor zones and early melanomas. Confocal imaging and flow cytometric analysis showed that macrophages are recruited to EGFP positive regions and preferentially phagocytose TIE:EGFP+ cells. This work identifies a TGFb induced immune response and demonstrates the need for the development of chronic TGFb biomarkers to predict patient response to TGFb inhibitors. Overall design: RNA seq +/ TGFB1 Bulk RNA seq on ZMEL1 treated with 10ng/mL TGFB1 ligand or vehicle control ZMEL1 cells were serum starved for 2 hours then treated with 10ng/mL human recombinant TGFB1 or 4mM HCl containing 1 mg/mL BSA vehicle control for an additional two hours. Experiment performed in technical triplicate.	parent bioproject:PRJNA880593	Vehicle Control treated ZMEL1 Replicate 3	GSM6579022	tissue:ZMEL1 Cells\|cell line:ZMEL1 Cells\|treatment:Vehicle\|geo loc name:missing\|collection date:missing	Vehicle Control treated ZMEL1 Replicate 3	Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence using cutadapt then mapped to Ensembl GRCz11 whole genome using tophat 2.1 Transcript abundance were calculated with Htseq count Assembly: GRCz11 Supplementary files format and content: raw count file	ZMEL1 Cells	Cells were starved for 2 hours. Treated with 10ng/mL TGFB1 ligand or 4mM HCl containing 1mg/mL BSA vehicle control for 2 hours.	RNA was collected from adherent cells using the Qiagen RNeasy Plus Mini Kit Qiagen #74134. One microgram of RNA was ribodepleted using NEBNext rRNA Depletion Kit NEB #E6310. Ribodepleted RNA was fragmented reverse transcribed and library prepped NEB #E7530 NEB #E7335.	ZMEL1 were grown in filter sterilized DMEM 10% FBS 1% PenStrep 1% Glutamine at 28°C	cell line:ZMEL1 Cells\|treatment:Vehicle	GSM6579022	GSM6579022: Vehicle Control treated ZMEL1 Replicate 3; Danio rerio; RNA Seq	GSM6579022 r1	GSM6579022	1	RNA was collected from adherent cells using the Qiagen RNeasy Plus Mini Kit Qiagen #74134. One microgram of RNA was ribodepleted using NEBNext rRNA Depletion Kit NEB #E6310. Ribodepleted RNA was fragmented reverse transcribed and library prepped NEB #E7530 NEB #E7335.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP397072	HN71_R1_001.fastq.gz HN71_R2_001.fastq.gz	fastq fastq	7971184800.0	26570616.0	GSM6579022 r1	0:150 1:150	A:1508647225;C:2475104436;G:2532882877;T:1453950842;N:599420	150	150	1508647225	2475104436	2532882877	1453950842	599420	SRX17566319	SRS15108367	Oncology/Hematology, Boston Children's Hospital	2	0.93862	0.94897	0.18002	0.18677	0.84555	0.86198	0.7493	0.75354	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	rrna_depletion	nebnext	sc_generic	bulk	bulk	United States	2022-09-14	Undetermined	Undetermined	Cell Line	Cell Line
71395	71395	SRR21563987	SRX17566318	SRS15108366	SRP397072	PRJNA880540	A chronic signaling TGFb zebrafish reporter identifies immune response in melanoma [RNA seq ZMEL]	GSE213328	Transcriptome Analysis	Developmental signaling pathways associated with growth factors such as TGFb are commonly dysregulated in melanoma. Here we identified a human TGFb enhancer that was specifically activated in melanoma cells treated with TGFB1 ligand. We generated stable transgenic zebrafish with this enhancer driving green fluorescent protein TIE:EGFP. EGFP was not expressed in normal melanocytes or early melanomas but was expressed in spatially distinct regions of mature melanomas. Single cell RNA sequencing revealed that TIE:EGFP+ melanoma cells down regulated interferon response while up regulating a novel set of chronic TGFb target genes. AP 1 factor binding is required for activation of this chronic TGFb reporter. Overexpression of the chromatin remodeler SATB2 which is associated with tumor spreading shows activation of TGFb signaling in melanoma precursor zones and early melanomas. Confocal imaging and flow cytometric analysis showed that macrophages are recruited to EGFP positive regions and preferentially phagocytose TIE:EGFP+ cells. This work identifies a TGFb induced immune response and demonstrates the need for the development of chronic TGFb biomarkers to predict patient response to TGFb inhibitors. Overall design: RNA seq +/ TGFB1 Bulk RNA seq on ZMEL1 treated with 10ng/mL TGFB1 ligand or vehicle control ZMEL1 cells were serum starved for 2 hours then treated with 10ng/mL human recombinant TGFB1 or 4mM HCl containing 1 mg/mL BSA vehicle control for an additional two hours. Experiment performed in technical triplicate.	parent bioproject:PRJNA880593	Vehicle Control treated ZMEL1 Replicate 2	GSM6579021	tissue:ZMEL1 Cells\|cell line:ZMEL1 Cells\|treatment:Vehicle\|geo loc name:missing\|collection date:missing	Vehicle Control treated ZMEL1 Replicate 2	Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence using cutadapt then mapped to Ensembl GRCz11 whole genome using tophat 2.1 Transcript abundance were calculated with Htseq count Assembly: GRCz11 Supplementary files format and content: raw count file	ZMEL1 Cells	Cells were starved for 2 hours. Treated with 10ng/mL TGFB1 ligand or 4mM HCl containing 1mg/mL BSA vehicle control for 2 hours.	RNA was collected from adherent cells using the Qiagen RNeasy Plus Mini Kit Qiagen #74134. One microgram of RNA was ribodepleted using NEBNext rRNA Depletion Kit NEB #E6310. Ribodepleted RNA was fragmented reverse transcribed and library prepped NEB #E7530 NEB #E7335.	ZMEL1 were grown in filter sterilized DMEM 10% FBS 1% PenStrep 1% Glutamine at 28°C	cell line:ZMEL1 Cells\|treatment:Vehicle	GSM6579021	GSM6579021: Vehicle Control treated ZMEL1 Replicate 2; Danio rerio; RNA Seq	GSM6579021 r1	GSM6579021	1	RNA was collected from adherent cells using the Qiagen RNeasy Plus Mini Kit Qiagen #74134. One microgram of RNA was ribodepleted using NEBNext rRNA Depletion Kit NEB #E6310. Ribodepleted RNA was fragmented reverse transcribed and library prepped NEB #E7530 NEB #E7335.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP397072	HN70_R1_001.fastq.gz HN70_R2_001.fastq.gz	fastq fastq	11384890800.0	37949636.0	GSM6579021 r1	0:150 1:150	A:2150820071;C:3536644295;G:3597916072;T:2098730563;N:779799	150	150	2150820071	3536644295	3597916072	2098730563	779799	SRX17566318	SRS15108366	Oncology/Hematology, Boston Children's Hospital	2	0.93899	0.94702	0.17416	0.18046	0.84147	0.85433	0.75163	0.66088	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	rrna_depletion	nebnext	sc_generic	bulk	bulk	United States	2022-09-14	Undetermined	Undetermined	Cell Line	Cell Line
71396	71396	SRR21563988	SRX17566317	SRS15108365	SRP397072	PRJNA880540	A chronic signaling TGFb zebrafish reporter identifies immune response in melanoma [RNA seq ZMEL]	GSE213328	Transcriptome Analysis	Developmental signaling pathways associated with growth factors such as TGFb are commonly dysregulated in melanoma. Here we identified a human TGFb enhancer that was specifically activated in melanoma cells treated with TGFB1 ligand. We generated stable transgenic zebrafish with this enhancer driving green fluorescent protein TIE:EGFP. EGFP was not expressed in normal melanocytes or early melanomas but was expressed in spatially distinct regions of mature melanomas. Single cell RNA sequencing revealed that TIE:EGFP+ melanoma cells down regulated interferon response while up regulating a novel set of chronic TGFb target genes. AP 1 factor binding is required for activation of this chronic TGFb reporter. Overexpression of the chromatin remodeler SATB2 which is associated with tumor spreading shows activation of TGFb signaling in melanoma precursor zones and early melanomas. Confocal imaging and flow cytometric analysis showed that macrophages are recruited to EGFP positive regions and preferentially phagocytose TIE:EGFP+ cells. This work identifies a TGFb induced immune response and demonstrates the need for the development of chronic TGFb biomarkers to predict patient response to TGFb inhibitors. Overall design: RNA seq +/ TGFB1 Bulk RNA seq on ZMEL1 treated with 10ng/mL TGFB1 ligand or vehicle control ZMEL1 cells were serum starved for 2 hours then treated with 10ng/mL human recombinant TGFB1 or 4mM HCl containing 1 mg/mL BSA vehicle control for an additional two hours. Experiment performed in technical triplicate.	parent bioproject:PRJNA880593	Vehicle Control treated ZMEL1 Replicate 1	GSM6579020	tissue:ZMEL1 Cells\|cell line:ZMEL1 Cells\|treatment:Vehicle\|geo loc name:missing\|collection date:missing	Vehicle Control treated ZMEL1 Replicate 1	Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence using cutadapt then mapped to Ensembl GRCz11 whole genome using tophat 2.1 Transcript abundance were calculated with Htseq count Assembly: GRCz11 Supplementary files format and content: raw count file	ZMEL1 Cells	Cells were starved for 2 hours. Treated with 10ng/mL TGFB1 ligand or 4mM HCl containing 1mg/mL BSA vehicle control for 2 hours.	RNA was collected from adherent cells using the Qiagen RNeasy Plus Mini Kit Qiagen #74134. One microgram of RNA was ribodepleted using NEBNext rRNA Depletion Kit NEB #E6310. Ribodepleted RNA was fragmented reverse transcribed and library prepped NEB #E7530 NEB #E7335.	ZMEL1 were grown in filter sterilized DMEM 10% FBS 1% PenStrep 1% Glutamine at 28°C	cell line:ZMEL1 Cells\|treatment:Vehicle	GSM6579020	GSM6579020: Vehicle Control treated ZMEL1 Replicate 1; Danio rerio; RNA Seq	GSM6579020 r1	GSM6579020	1	RNA was collected from adherent cells using the Qiagen RNeasy Plus Mini Kit Qiagen #74134. One microgram of RNA was ribodepleted using NEBNext rRNA Depletion Kit NEB #E6310. Ribodepleted RNA was fragmented reverse transcribed and library prepped NEB #E7530 NEB #E7335.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP397072	HN69_R1_001.fastq.gz HN69_R2_001.fastq.gz	fastq fastq	7923946200.0	26413154.0	GSM6579020 r1	0:150 1:150	A:1526034388;C:2436567275;G:2481233024;T:1479490022;N:621491	150	150	1526034388	2436567275	2481233024	1479490022	621491	SRX17566317	SRS15108365	Oncology/Hematology, Boston Children's Hospital	2	0.93823	0.94638	0.18016	0.18529	0.83481	0.84928	0.71588	0.74024	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	rrna_depletion	nebnext	sc_generic	bulk	bulk	United States	2022-09-14	Undetermined	Undetermined	Cell Line	Cell Line

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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");;