{"database": "metadata", "table": "run_metadata", "rows": [[41845, "SRR5259816", "SRX2564547", "SRS1981208", "SRP099850", "PRJNA374872", "Genomic dissection of conserved transcriptional regulation in intestinal epithelial cells [zebrafish]", "GSE94933", "Other", "We profiled genome wide accesssible chromatin data and RNA seq from four species zebrafish  stickleback  mouse  and human to identify commonly regulated genes and regulatory metods in intestinal epithelial cells IECs.  We identify a group genes that are commonly expressed in IECs and genes that are commonly expressed along the length of the intestine in fish and mammals.  Using accessible chromatin data we identified enriched transcription factor binding site motifs In IECs and sites that are commonly accessible in IECs in all species.  Finally  we confirm the ability for these regions from multiple species to drive conserved expression in IECs using a zebrafish reporter assay. Overall design: Examination of expression levels and chromatin accessibility in intestinal epithelaial cells in zebrafish", "parent bioproject:PRJNA374867", "pubmed:28850571", null, "zIEC2 mRNA", "GSM2492107", null, "tissue:Intestinal Epithelial Cells RNA seq|strain:TL|cell type:Zebrafish Adult Intestinal Epithelial Cells", "zIEC2 mRNA", "Paired End Adapter trimmed reads from Duke Sequencing and Genomic Technologies Shared Resource were mapped to the danRer7 genome using Tophat2v2.0.9 with default conditions using Galaxy0.5 Cufflinks v2.0.2 was used to generate FPKM values using default peramaters and Zv9/danRer7 Ensembl annotationsEnsemble genes 71 using Galaxy0.0.5 bigWig files were generated using bamCoverage Galaxy verion 2.2.3.0 and read normalized Genome build: danRer7 Supplementary files format and content: Bigwig represents single base pair genomewide sequencing coverage; Bed files are tabular files containing peak coordinates; Tabular Files Contain Gene Expression Information", "Intestinal Epithelial Cells RNA seq", null, "To isolate zebrafish IECs  intestines were dissected  splayed  and washed extensively with ice cold 1x PBS with care taken to remove as much intestine associated fascia  adipocytes  and blood vessels as possible. Three washed intestines were transferred into dissociation reagent 1 DR1; 30 mM EDTA  1.5 mM DTT  0.5x Complete protease inhibitors Roche  in 1x PBS for 15 minutes on ice. Segments were transferred to Dissociation Reagent 2 DR2; 30 mM EDTA  0.5x Complete protease inhibitors Roche  in PBS and moderately shaken by hand for 5 minutes until most epithelial cells were isolated in the suspension. Intestinal lamina propria was removed and 8 ml of cold 1x PBS was added to the cells on ice. Cells were pelleted at 500 x G at 4\u00b0C  washed once with 13 ml of cold 1X PBS  and re suspended in 0.5 ml cold 1x PBS. A 0.4 ml fraction was used for FAIRE  and 0.1 ml fraction was reserved for RNA extraction. Isolated IECs were placed in TRIzol Reagent for RNA extraction. For FAIRE  freshly isolated intestinal epithelial cells were directly fixed for 5 10 minutes in 10 ml of 1 3% w/v Formaldehyde solution in 1x PBS at room temperature and gentle rocking. Glycine 2.5M was added to a final concentration of 125 mM to quench the formaldehyde. Cells were pelleted at 600 x G and washed three times in cold 1x PBS without xxx the pellet. Fixed and washed cell pellets were flash frozen and stored at  80\u00b0C. Cells were lysed in 2 ml Lysis Buffer A 10 mMTris HCl pH8.0  2% vol/vol Triton X 100  1% SDS  100 mM NaCl and 1 mM EDTA and sonicated using a Branson Sonifier 450D equipped with a microtip for 6 13 cycles 1 second burst  0.5 second pause  for 30 seconds/cycle at 70% intensity allowing samples to cool on ice for 1 minute between cycles. Isolated IECs were placed in TRIzol Reagent. UNC Highthrough put Sequencing Core performed TruSeq library preperation.", "TL strain zebrafish at Aquaculture Core Facility at UNC Chapel Hill were grown using standard zebrafish diets", "strain:TL|cell type:Zebrafish Adult Intestinal Epithelial Cells", "GSM2492107", "GSM2492107: zIEC2 mRNA; Danio rerio; RNA Seq", "GSM2492107", null, "1", "To isolate zebrafish IECs  intestines were dissected  splayed  and washed extensively with ice cold 1x PBS with care taken to remove as much intestine associated fascia  adipocytes  and blood vessels as possible. Three washed intestines were transferred into dissociation reagent 1 DR1; 30 mM EDTA  1.5 mM DTT  0.5x Complete protease inhibitors Roche  in 1x PBS for 15 minutes on ice. Segments were transferred to Dissociation Reagent 2 DR2; 30 mM EDTA  0.5x Complete protease inhibitors Roche  in PBS and moderately shaken by hand for 5 minutes until most epithelial cells were isolated in the suspension. Intestinal lamina propria was removed and 8 ml of cold 1x PBS was added to the cells on ice. Cells were pelleted at 500 x G at 4\u00b0C  washed once with 13 ml of cold 1X PBS  and re suspended in 0.5 ml cold 1x PBS. A 0.4 ml fraction was used for FAIRE  and 0.1 ml fraction was reserved for RNA extraction. Isolated IECs were placed in TRIzol Reagent for RNA extraction. For FAIRE  freshly isolated intestinal epithelial cells were directly fixed for 5 10 minutes in 10 ml of 1 3% w/v Formaldehyde solution in 1x PBS at room temperature and gentle rocking. Glycine 2.5M was added to a final concentration of 125 mM to quench the formaldehyde. Cells were pelleted at 600 x G and washed three times in cold 1x PBS without xxx the pellet. Fixed and washed cell pellets were flash frozen and stored at  80\u00b0C. Cells were lysed in 2 ml Lysis Buffer A 10 mMTris HCl pH8.0  2% vol/vol Triton X 100  1% SDS  100 mM NaCl and 1 mM EDTA and sonicated using a Branson Sonifier 450D equipped with a microtip for 6 13 cycles 1 second burst  0.5 second pause  for 30 seconds/cycle at 70% intensity allowing samples to cool on ice for 1 minute between cycles. Isolated IECs were placed in TRIzol Reagent. UNC Highthrough put Sequencing Core performed TruSeq library preperation.", "GEO Accession:GSM2492107", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP099850", null, null, "ZIEC2_GCCAAT_L005_R1_001.fastq.gz ZIEC2_GCCAAT_L005_R2_001.fastq.gz", "fastq fastq", 1785594816.0, 18599946.0, "GSM2492107 r1", "0:48 1:48", "A:466092820;C:422828003;G:420238032;T:476324795;N:111166", 48, 48, null, null, 466092820, 422828003, 420238032, 476324795, 111166, "SRX2564547", "SRS1981208", "SRA538156", "GEO", "John Rawls, Duke University", 2, 0.85545, 0.86359, 0.08337, 0.08488, 0.74635, 0.74677, 0.52663, 0.53064, 48, 48, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2017-02-15", "Adult", "Adult", "Gut", "Digestive 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": ["41845"], "units": {}, "query_ms": 9.898878008243628}