{"database": "metadata", "table": "run_metadata", "rows": [[56827, "SRR11114800", "SRX7751803", "SRS6171094", "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", null, "RNA kdlr pos 3 ctrl", "GSM4321575", null, "tissue:FACS sorted liver cells|treatment:sterile water|genetic background:AB|genotype:Tgkdrl:ras mCherry|fluorescence:mCherry positive|Sex:female|cell type:FACS sorted liver cells", "RNA kdlr pos 3 ctrl", "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\u2122 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:sterile water|genetic background:AB|genotype:Tgkdrl:ras mCherry|fluorescence:mCherry positive|Sex:female|cell type:FACS sorted liver cells", "GSM4321575", "GSM4321575: RNA kdlr pos 3 ctrl; Danio rerio; RNA Seq", "GSM4321575", null, "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\u2122 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:GSM4321575", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP250035", null, null, "RNA_kdlr_pos_3_ctrl_R2.fastq.gz RNA_kdlr_pos_3_ctrl_R1.fastq.gz", "fastq fastq", 4676256819.0, 31322059.0, "GSM4321575 r1", "0:74.66 1:74.64", "A:847890577;C:1438938414;G:1559940415;T:829247648;N:239765", 74, 74, null, null, 847890577, 1438938414, 1559940415, 829247648, 239765, "SRX7751803", "SRS6171094", "SRA1044822", "GEO", "Zebrafish Developmental Genomics Lab, International Institute of Molecular and Cell Biology", 2, 0.95001, 0.96334, 0.12275, 0.12123, 0.86393, 0.8704, 0.75026, 0.75617, 75, 73, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "cdna_unspecified", "smarter", "bulk", "unknown", "unknown", null, "Poland", "2020-02-19", "Larval", "Larval", "Liver", "Liver and Biliary System"]], "columns": ["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"], "primary_keys": ["rowid"], "primary_key_values": ["56827"], "units": {}, "query_ms": 9.889230990665965}