run_metadata: 39766

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
39766	SRR2136165	SRX1125641	SRS1017713	SRP061852	PRJNA291530	DNA methylome patterns of zebrafish cells under cold pressure	GSE71567	Other	In this study MeDIP seq and RNA seq were performed to reveal a genome wide methylation profile of zebrafish Danio rerio embryonic fibroblast cell line ZF4 and its variation under cold environment.This study puts a new insight into the genome wide epigenetic regulation under cold environment. Overall design: ZF4 cells were cultured at 28 °C as control and at 18 °C for 5 days and 30 days seperately. Each condition has three biological replica.				ZF4 18d5dRNA2	GSM1838564		tissue:embryonic fibroblast cells\|cell type:fibroblast cell line\|growth:cultured at 18°C for 5 days\|treatment:cold treatment for 5 days	ZF4 18d5dRNA2	Illumina Casava1.7 software was used for basecalling. The fastx toolkit program was used to filter off low quality sequences from raw sequencing data. Sequences were aligned with Zebrafish genomeZR9/danRer7 downloaded from iGenome using Bowtie2. MeDIP seq peaks were called with the Model based Analysis of MeDIP Seq MACS software with default parameters with alignment results. The three peak sets generated by MACS were merged using Bedtools for peaks with at least 1bp overlap to get a reference peak set REF for following analysis. Genome build: ZR9/danRer7 Supplementary files format and content: .txt	embryonic fibroblast cells	For cold treatment cells were grown at 18 °C 5% CO2 in the same medium for up to 30 days.	For MeDIP seq genomic DNAs were isolated and sonicated. End repair adenylation adapter ligation methylated DNA enrichment and methylated DNA library construction were all performed with The NEXTflex™ Methyl Seq 1 Kit BIOO LIFE SCIENCE PRODUCTS Cat No. 5118 01 according to the manufacturer’s instruction. For RNA seq total RNA was isolated using TRlzol reagent Invitrogen life Technologies.	The zebrafish embryonic fibroblast cell line ZF4 was purchased from the American Type Culture Collection ATCC CRL 2050; Driever and Rangini 1993. The cells were grown at 28 °C 5% CO2 in Dulbecco's modified Eagle's medium/F12 nutrient mix DMEM/F12 supplemented with 10% FBS 1% l glutamine 100 u/ml penicillin 100 μg/ml streptomycin. For cold treatment cells were grown at 18 °C 5% CO2 in the same medium for up to 30 days. All cell culture medium components were purchased from Gibco BRL Life Technologies Ltd USA.	cell type:fibroblast cell line\|growth:cultured at 18°C for 5 days\|treatment:cold treatment for 5 days	GSM1838564	GSM1838564: ZF4 18d5dRNA2; Danio rerio; RNA Seq	GSM1838564		1	For MeDIP seq genomic DNAs were isolated and sonicated. End repair adenylation adapter ligation methylated DNA enrichment and methylated DNA library construction were all performed with The NEXTflex™ Methyl Seq 1 Kit BIOO LIFE SCIENCE PRODUCTS Cat No. 5118 01 according to the manufacturer’s instruction. For RNA seq total RNA was isolated using TRlzol reagent Invitrogen life Technologies. MeDIP DNA libraries were prepared with The NEXTflex™ Methyl Seq 1 Kit BIOO LIFE SCIENCE PRODUCTS Cat No. 5118 01 according to the manufacturer’s instruction. RNA libraries were prepared for sequencing using standard Illumina protocols．	GEO Accession:GSM1838564	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP061852			18_5_replica2_2.fastq.gz 18_5_replica2_1.fastq.gz	fastq fastq	2948189798.0	14594999.0	GSM1838564 r1	0:101 1:101	A:784972120;C:694695628;G:681782943;T:786426712;N:312395	101	101			784972120	694695628	681782943	786426712	312395	SRX1125641	SRS1017713	SRA281140	GEO	College of fishery and life science, Shanghai Ocean University	2	0.94304	0.94274	0.10665	0.10697	0.72383	0.72508	0.48863	0.4889	101	101	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown		China	2015-07-30	Undetermined	Embryo	Embryo Imprecise	All anatomical structures