run_metadata: 69003

This data as json

rowid	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	study.PMIDs	sample.description	sample.title	sample.alias	sample.centername	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.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.spot_descriptor	experiment.study_ref	run.title	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	tech_variant	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
69003	SRR18290761	SRX14428458	SRS12237028	SRP363388	PRJNA814612	Shear stress switches the association of endothelial enhancers from ETV/ETS to KLF transcription factor binding sites	GSE198221	Other	The study shows transcriptional and chromatin changes in human umbilical cord endothelial cells HUVEC exposed to shear stress. In addition transcriptional changes in zebrafish endothelial cells in response to blood flow block are shown Overall design: HUVEC were exposed to shear stress of 18 dyn/cm2 for 6 h and used for RNA Seq ATAC Seq and H3K27ac ChIP Seq. Blood flow was stopped in zebrafish embryos 48 hpf for 4 h and endothelial cells were used for RNA Seq		pubmed:35314737		Zebrafish Control RNA Seq Rep1	GSM5941046		tissue:Endothelial cells\|treatment:DMSO\|transgene:Tgkdrl:H2B EGFPmu122	Zebrafish Control RNA Seq Rep1	Sequencing reads were aligned to hg19 human or danRer10 zebrafish genomes RNA Seq. Data was mapped using TopHat2 v2.1.1. and differential gene expression analysis between flow treated samples and static controls was performed using DESeq2. Read counts were obtained with HTSeq ChIP Seq. Sequencing reads from ChIP and input samples were mapped with Bowtie 2 v2.3.5. and Samtools v1.9.was used to edit the alignments. Reads were downsampled to equivalent read depth. Peak calling was performed with Genrich https://github.com/jsh58/Genrich applying the following parameters: genrich v e Y MT E blacklist.bed t Sample1ChIP.bam Sample2ChIP.bam c Sample1Input.bam Sample2Input.bam o Sample.narrowPeak k Sample.bedGraphish. Differential peak analysis was performed with DiffBind 50and peaks with FDR < 0.05 were used for further analysis. ATAC Seq. Sequencing reads were mapped with Bowtie2 downsampled to equivalent read depth and peak calling was performed with Genrich in ATAC Seq mode using the following parameters: genrich j v y r e Y MT E blacklist.bed t Sample1.bam Sample2.bam o Sample.narrowPeak k Sample.bedGraphish. Differential peak analysis was performed with DiffBind 50 and peaks with FDR < 0.05 were used for further analysis. ChIP Seq and ATAC Seq tracks were produced with deepTools bamCoverage and normalized to sequencing depth Assembly: hg19 Assembly: danRer10	Endothelial cells	The maximum flow of 18 dyn/cm2 was achieved by computer controlled cone rotation in culture medium containing 3% polyvinylpyrrolidone PVP within ten minutes ramp function and then kept constant for the required time. The experiments were perfomed in in a BioTechFlow system BTF system; MOS Technologies at 37°C and under constant CO2 perfusion. Static controls were incubated in a cell culture incubator. 48 hpf Tgkdrl:H2B EGFPmu122 zebrafish embryos were dechorionated at 48 hpf using pronase and treated for 4 h with nifedipine 12.5 nM Biomol # Cay11106 and tricaine 1.3 mM Sigma Aldrich # A5040 to stop the heart beat or with a corresponding amount of DMSO as a control.	RNA for RNA Seq was extracted with RNeasy Micro Kit Qiagen. Cells were cross linked with formaldehyde final concentration 1 % for 5 min sonicated and the cromatin was used for H3K27ac ChIP. For ATAC HUVEC were first frozen in the medium containing 10 % DMSO and used for OMNI ATAC post thawing. For zebrafish RNA Seq 300 embryos per condition were collected in ice cold 10 % DMSO and kept at 80°C for 2 min. postwards embryos were washed twice with 1x Hanks’Balanced Salt Solution HBSS Gibco # 14185 052and deyolked with calcium free Ringer’s solution. Embryos were then dissociated with trypsin EDTA 0.5 % and collagenase type IV 50 mg/ml. The reaction was stopped by addition of FCS 5 % andcells were collected by centrifugation at 350 g for 5 min at 4°C and washed twice with 1x HBSS followed by centrifugation. post a final wash cells were resuspended in 1x HBSS passed through a 40 m nylon filter to obtain a single cell suspension which was subjected to fluorescence activated cell sorting FACS. EGFP positive ECs were collected in RLT buffer RNeasy Micro kit Qiagen. RNA Seq libraries were prepared using TruSeq Stranded Total RNA Sample Prep with RiboZero depletion. ChIP Seq libraries were prepared using TruSeq ChIP Sample Preparation Kit Illumina. ATAC Seq libraries were prepared using the protocol by Buenorosto et al Buenorosto Nat Met 2013	HUVEC were seeded on 6 cm BTF glass plates coated with cross linked gelatin and cultured to confluence approximately 105 cells/cm2 in EC growth medium. Zebrafish were grown and crossed under standard conditions	treatment:DMSO\|transgene:Tgkdrl:H2B EGFPmu122	GSM5941046	GSM5941046: Zebrafish Control RNA Seq Rep1; Danio rerio; RNA Seq	GSM5941046 r1	GSM5941046	1	RNA for RNA Seq was extracted with RNeasy Micro Kit Qiagen. Cells were cross linked with formaldehyde final concentration 1 % for 5 min sonicated and the cromatin was used for H3K27ac ChIP. For ATAC HUVEC were first frozen in the medium containing 10 % DMSO and used for OMNI ATAC post thawing. For zebrafish RNA Seq 300 embryos per condition were collected in ice cold 10 % DMSO and kept at 80°C for 2 min. postwards embryos were washed twice with 1x Hanks'Balanced Salt Solution HBSS Gibco # 14185 052and deyolked with calcium free Ringer's solution. Embryos were then dissociated with trypsin EDTA 0.5 % and collagenase type IV 50 mg/ml. The reaction was stopped by addition of FCS 5 % andcells were collected by centrifugation at 350 g for 5 min at 4°C and washed twice with 1x HBSS followed by centrifugation. post a final wash cells were resuspended in 1x HBSS passed through a 40 m nylon filter to obtain a single cell suspension which was subjected to fluorescence activated cell sorting FACS. EGFP positive ECs were collected in RLT buffer RNeasy Micro kit Qiagen. RNA Seq libraries were prepared using TruSeq Stranded Total RNA Sample Prep with RiboZero depletion. ChIP Seq libraries were prepared using TruSeq ChIP Sample Preparation Kit Illumina. ATAC Seq libraries were prepared using the protocol by Buenorosto et al Buenorosto Nat Met 2013		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina MiSeq		SRP363388		loader:fastq load.py	DMSO1_S1_L001_R1_001.fastq DMSO1_S1_L001_R2_001.fastq	fastq fastq	1241823302.0	8016001.0	GSM5941046 r1	0:77.51 1:77.41	A:328337938;C:289285295;G:287437001;T:336735414;N:27654	77	77			328337938	289285295	287437001	336735414	27654	SRX14428458	SRS12237028	SRA1385237	Arndt Siekmann, Perelman School of Medicine, UNIVERSITY OF PENNSYLVANIA	Arndt Siekmann, Perelman School of Medicine, UNIVERSITY OF PENNSYLVANIA	2	0.93546	0.93858	0.24555	0.24639	0.71494	0.71508	0.60726	0.60144	78	78	B	B	biological fallback assumption	illumina	miseq	unknown	rrna_depletion	trueseq	bulk	unknown	unknown		United States	2022-03-09	Hatching	Embryo	Endothelium	Cardiovascular System