run_metadata: 52233

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
52233	SRR9022957	SRX5800871	SRS4730903	SRP195753	PRJNA541476	Transcriptomic profiling of zebrafish livers with nAtf6 overexpression at collected at 78 hpf and 120 hpf	GSE130800	Transcriptome Analysis	Activting transcription factor 6 Atf6 is one of three main mediators of the Unfolded Protein Response and it gets cleaved cleaved in the Golgi and its N terminal consisting of the bZip domain translocates into the nucleus to generate a transcriptional response nAtf6. This study carries out RNAseq on an established transgenic overexpression of nAtf6 in zebrafish hepatocytes tgfabp10:nAtf6 cherry; cmlc2:GFP C allele. Samples were collected at 78 hpf and 120 hpf to detect gene expression changes at early and late time points post nAtf6 is overexpressed. Overall design: We used two transgenic lines: Tgfabp10a: CAAX EGFP to use as a marker of the liver for dissction and tgfabp10:nAtf6 cherry; cmlc2:GFP C allele to overexpress nAtf6 specifically in hepatocytes.This experiment was conducted by natural spawnings between tg:fabp10:nAtf6 cherry; cmlc2:GFP C and tgfabp10a:CAAX EGFP . Using GFP to guide microdissscion of 20 25 livers at 78 hpf and 120 hpf . Total RNA isolated using TRIZOL and treated by DNAse I. Libraries were prepared using RiboZero for 120 hpf samples or polyA selection for 78 hpf samples. Samples from 2 clutches collected at 78 hpf and 3 clutches at 120 hpf. Samples were sequenced on NextSeq550 Illumina	parent bioproject:PRJNA541472			sibslivr1: 5 dpf Livers non transgenic siblings 1	GSM3754093		source name:liver/pooled\|tissue:pooled liver\|genotype/variation:WT	sibslivr1: 5 dpf Livers non transgenic siblings 1	Illumina Casava1.8 software used for basecalling. The raw reads were quality assessed using FastQC v0.11.5. The raw reads were then quality trimmed using Trimmomatic trimmomatic adapter.fa:2:30:10 TRAILING:3 LEADING:3 SLIDINGWINDOW:4:15 MINLEN:36 Alignments of trimmed reads were performed using tophat2 v2.1.0 with the parameters “–no novel junctions” and “–G” Accepted bam files were used for counting gene read numbers with HTSeq a 10 s no Test of differential expression of each transposonis was implemented by DESeq2 in Bioconductor Genome build: GRCz10 Supplementary files format and content: .txt Reads count of genes	liver/pooled		Tgfabp10:nAtf6 cherry; cmlc2:GFPC+/ were outcrossed to WT TAB 14 and the embryos were sorted and segregated basing on the expression of Cmlc2:GFP. The three different clutches of embryos were collected and dissected over three different days. The embryos were collected inbetween 10 11 AM. The Liver dissection was also performed on the 5dpf larvae before noon. 25 livers from 5dpf embryos were pooled per sample Transgenic and WT siblings in two different tubes and RNA extracted with Trizol as per manufacturer's instructions.The RNA was later treated with DNAse to remove any DNA. They RNA concentration was taken on the Q bit and then analysed on the Bioanalyser for the integrety and quality of RNA. The RIN score for the samples was above 8.5 RNA seq libraries were prepared according to Illumina TruSeq RNA sample preparation version 2 protocol with Ribo Zero Gold Catalog #: RS 122 2501		tissue:pooled liver\|genotype/variation:WT	GSM3754093	GSM3754093: sibslivr1: 5 dpf Livers non transgenic siblings 1; Danio rerio; RNA Seq	GSM3754093		1	Tgfabp10:nAtf6 cherry; cmlc2:GFPC+/ were outcrossed to WT TAB 14 and the embryos were sorted and segregated basing on the expression of Cmlc2:GFP. The three different clutches of embryos were collected and dissected over three different days. The embryos were collected inbetween 10 11 AM. The Liver dissection was also performed on the 5dpf larvae before noon. 25 livers from 5dpf embryos were pooled per sample Transgenic and WT siblings in two different tubes and RNA extracted with Trizol as per manufacturer's instructions.The RNA was later treated with DNAse to remove any DNA. They RNA concentration was taken on the Q bit and then analysed on the Bioanalyser for the integrety and quality of RNA. The RIN score for the samples was above 8.5 RNA seq libraries were prepared according to Illumina TruSeq RNA sample preparation version 2 protocol with Ribo Zero Gold Catalog #: RS 122 2501	GEO Accession:GSM3754093	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500		SRP195753			Sample_sibslivr1_read1.fastq.gz Sample_sibslivr1_read2.fastq.gz	fastq fastq	6725147216.0	33292808.0	GSM3754093 r1	0:101 1:101	A:1807945249;C:1550856849;G:1534573991;T:1826050327;N:5720800	101	101			1807945249	1550856849	1534573991	1826050327	5720800	SRX5800871	SRS4730903	SRA883585	GEO	Biology, New York University Abu Dhabi	2	0.90678	0.9037	0.2571	0.25652	0.76278	0.76577	0.58002	0.58511	101	101	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	ribozero	bulk	unknown	unknown		United Arab Emirates	2019-05-07	Larval	Larval	Liver	Liver and Biliary System