run_metadata: 76413

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
76413	SRR24921921	SRX20682433	SRS17977026	SRP443822	PRJNA983848	Transcriptomic analysis of the liver from control sibling and mutant uhrf1 hi272 zebrafish larvae at 120 hpf treated with DMSO or Palbociclib PD	GSE234993	Transcriptome Analysis	This study was carried out to compare the changes in gene expression in livers of 120 hpf control sibling and mutant uhrf1 hi272 zebrafish larvae in response to treatment with DMSO or Palbociclib PD Overall design: 48 hpf embryos from an incross of uhrf1 hi272+/ zebrafish adults with Tgfabp10a:CAAX EGFP to mark the livers were treated with either 0.5% DMSO or 20 microM PD in 0.5% DMSO in 6 well plates. At 120 hpf 15 20 livers from were dissected from larvae treated with PD or DMSO treated and individual livers were immediately placed in TRIzol and stored at 80 while the carcass of each larvae was genotyped. The individual livers from uhrf1hi272 / mutants and from WT in each treatment batch were pooled RNA was extracted per standard TRIzol/Chloroform method and concentrated DNAse 1 treated and resuspended in DNase/RNase free water. For library preparation high quality RNA was identified based on bioanalyzer analysis and quantified so that 100 ng of total RNA was used to initiate the library preparation using Ribo Zero rRNA Removal Kit Human/Mouse/Rat. The RNA sample was chemically fragmented and random primed for reverse transcription using Illumina TruSeq V2 RNA sample Prep Kit and first strand cDNA reverse transcribed using random primers. Following second strand cDNA synthesis and end repair. TrueSeq adapter index was ligated to cDNA libraries and PCR amplification of 12 cycles was done for enrichment producing a 350 400?bp fragment including adapters. The fragment sizes and purity of the libraries were confirmed by analyzing on a Bioanalyzer 2100 and were sequenced using the Illumina NextSeq 550 system with a Paired end HO V2.5 kit 150 cycles.		pubmed:38321933		Liv 3 hi272 DMSO Control	GSM7488239		source name:embryo livers\|strain:ABNYU\|genotype:Control\|treatment:DMSO\|tissue:embryo livers\|geo loc name:missing\|collection date:missing	Liv 3 hi272 DMSO Control	Illumina Casava1.8 software used for basecalling Sequenced reads where first assessed for quality using FastQC v0.11.5. Trimmomatic v0.36 was used for quality trimming and adapter sequence removal with the parameters ILLUMINACLIP: trimmomatic adapter.fa:2:30:10 TRAILING:3 LEADING:3 SLIDINGWINDOW:4:15 MINLEN:36 The resulting transcripts from the raw counts were used for further downstream analysis Supplementary files format and content: txt containing raw counts	embryo livers	None	TRIzol/Choloform Extraction RNA seq libraries were prepared with Ribo Zero kit by the staff in the NYUAD genomics facility and quality controled by Bioanalyzer.	Zebrafish larvae were kept in 6 well plate at a density of 2 larvae/ per 1 mL embyro medium in a 10:14 light/dark cycle	strain:ABNYU\|genotype:Control\|treatment:DMSO\|tissue:embryo livers	GSM7488239	GSM7488239: Liv 3 hi272 DMSO Control; Danio rerio; RNA Seq	GSM7488239 r1	GSM7488239	1	TRIzol/Choloform Extraction RNA seq libraries were prepared with Ribo Zero kit by the staff in the NYUAD genomics facility and quality controled by Bioanalyzer.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 550		SRP443822		loader:fastq load.py	Liv_3_hi272_DMSO_Control_S3_read1.fastq.gz Liv_3_hi272_DMSO_Control_S3_read2.fastq.gz	fastq fastq	3834724728.0	12697764.0	GSM7488239 r1	0:151 1:151	A:734283230;C:1173806209;G:1211329655;T:715252057;N:53577	151	151			734283230	1173806209	1211329655	715252057	53577	SRX20682433	SRS17977026	SRA1656736	Biology, New York University Abu Dhabi	Biology, New York University Abu Dhabi	2	0.58761	0.58614	0.06162	0.06136	0.8253	0.82485	0.73148	0.734	151	151	B	B	biological fallback assumption	illumina	nextseq	unknown	rrna_depletion	ribozero	bulk	bulk	bulk		United Arab Emirates	2023-06-14	Larval	Larval	Liver	Liver and Biliary System