run_metadata: 56828

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
56828	SRR11114799	SRX7751802	SRS6171093	SRP250035	PRJNA607563	Transcriptomic profile of zebrafish liver cells in thioacetamide TAA model	GSE145564	Transcriptome Analysis	Zebrafish transgenic lines Tgfabp10a:dsRed Tghand2:EGFP and Tgkdrl:ras mCherry in AB wild type background were anesthetized with MS 222 and adult females were injected intraperitoneally with 500 mg/kg thioacetamide TAA or sterile water as a control 6 times over the course of 2 weeks. We have characterized transcriptomic profiles of FACS isolated hepatocytes dsRed+ stellate cells EGFP+ and liver endothelial cells mCherry+ from fishes treated with TAA or sterile water. Cells negative for the fluorescence were used as a control. Overall design: Examination of transcriptomic profile of zebrafish hepatocytes stellate cells and liver enothelial cells treated with thioacetamide TAA and control sterile water cell specific reporters: fabp = hep hepatocytes hand = hsc hepatic stellate cells kdlr = ec endothelial cells	parent bioproject:PRJNA607562	pubmed:34920711		RNA kdlr pos 2 TAA	GSM4321574		tissue:FACS sorted liver cells\|treatment:TAA\|genetic background:AB\|genotype:Tgkdrl:ras mCherry\|fluorescence:mCherry positive\|Sex:female\|cell type:FACS sorted liver cells	RNA kdlr pos 2 TAA	Raw RNA seq and ATAC seq reads were quality checked using Fastqc 0.11.8 Adapters were removed using Cutadapt 1.18 Reads quality filtering was performed using SAMtools 1.9 RNA seq reads were aligned to the zebrafish reference genome GRCz11 using STAR 2.6 Gene counts were calculated by using R GenomicRanges Bioconductor package and tranformed to regularized logarithm DESeq2 Bioconductor package Genome build: GRCz11 Supplementary files format and content: comma separated file containing normalized read counts rlog of Ensembl annotated genes organized in columns for each sample separately	FACS sorted liver cells	Adult females were anesthetized with MS 222 Sigma Aldrich Germany as previously described and injected intraperitoneally with 500 mg/kg thioacetamide TAA or sterile water as a control 6 times over the course of 2 weeks.	For RNA sequencing 100 000 of fluorescent liver cells were sorted directly to TRIzol LS Thermo Fisher Scientific USA. post ethanol precipitation RNA was depleted of DNA by using DNase I treatment and purified on columns by using RNA Clean & Concentrator™ 5 Zymo Research USA Sequencing libraries were performed from total RNA by using SMARTer low input RNA Kit Clontech according to manufacturer protocol.	Zebrafish transgenic lines Tgfabp10a:dsRed Tghand2:EGFP and Tgkdrl:ras mCherry in AB wild type background were maintained in the IIMCB zebrafish facility License no. PL14656251 according to standard procedures.	treatment:TAA\|genetic background:AB\|genotype:Tgkdrl:ras mCherry\|fluorescence:mCherry positive\|Sex:female\|cell type:FACS sorted liver cells	GSM4321574	GSM4321574: RNA kdlr pos 2 TAA; Danio rerio; RNA Seq	GSM4321574		1	For RNA sequencing 100 000 of fluorescent liver cells were sorted directly to TRIzol LS Thermo Fisher Scientific USA. post ethanol precipitation RNA was depleted of DNA by using DNase I treatment and purified on columns by using RNA Clean & Concentrator™ 5 Zymo Research USA Sequencing libraries were performed from total RNA by using SMARTer low input RNA Kit Clontech according to manufacturer protocol.	GEO Accession:GSM4321574	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP250035			RNA_kdlr_pos_2_TAA_R1.fastq.gz RNA_kdlr_pos_2_TAA_R2.fastq.gz	fastq fastq	5569241392.0	36639746.0	GSM4321574 r1	0:76 1:76	A:1021150275;C:1717497658;G:1851818735;T:978010673;N:764051	76	76			1021150275	1717497658	1851818735	978010673	764051	SRX7751802	SRS6171093	SRA1044822	GEO	Zebrafish Developmental Genomics Lab, International Institute of Molecular and Cell Biology	2	0.94843	0.95051	0.07004	0.06371	0.92732	0.94838	0.62057	0.63854	76	76	B	B	biological fallback assumption	illumina	nextseq	full_length	cdna_unspecified	smarter	bulk	unknown	unknown		Poland	2020-02-19	Larval	Larval	Liver	Liver and Biliary System