run_metadata: 34638

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
34638	SRR32145169	SRX27491066	SRS23912864	SRP560249	PRJNA1216300	Insulin like growth factor signalling regulates zebrafish lymphatic vessel development	GSE288160	Transcriptome Analysis	RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.				WT Replicate 3	GSM8760181		tissue:Chondrocyte\|cell type:Chondrocyte\|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry\|geo loc name:missing\|collection date:missing	WT Replicate 3	The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column	Chondrocyte		At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer	Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees.	cell type:Chondrocyte\|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry	GSM8760181	GSM8760181: WT Replicate 3; Danio rerio; RNA Seq	GSM8760181 r1	GSM8760181	1	At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP560249			WT3_S7_L001_R1_001.fastq.gz	fastq	1039833292.0	13682017.0	GSM8760181 r1	0:76	A:250507910;C:247806634;G:245922610;T:295415371;N:180767	76				250507910	247806634	245922610	295415371	180767	SRX27491066	SRS23912864	SRA2062832	Molecular Medicine and Pathology, University of Auckland	Molecular Medicine and Pathology, University of Auckland												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown		New Zealand	2025-01-27	Larval	Larval	Bone or Cartilage	Skeletal Element