{"database": "metadata", "table": "run_metadata", "rows": [[39764, "SRR2136167", "SRX1125643", "SRS1017711", "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 \u00b0C as control and at 18 \u00b0C for 5 days and 30 days  seperately. Each condition has three biological replica.", null, null, null, "ZF4 18d30dRNA1", "GSM1838566", null, "tissue:embryonic fibroblast cells|cell type:fibroblast cell line|growth:cultured at 18\u00b0C for 30 days|treatment:cold treatment for 30 days", "ZF4 18d30dRNA1", "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 \u00b0C  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\u2122 Methyl  Seq 1 Kit BIOO LIFE SCIENCE PRODUCTS  Cat No. 5118 01  according to the manufacturer\u2019s 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 \u00b0C  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 \u03bcg/ml streptomycin.  For cold treatment  cells were grown at 18 \u00b0C  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\u00b0C for 30 days|treatment:cold treatment for 30 days", "GSM1838566", "GSM1838566: ZF4 18d30dRNA1; Danio rerio; RNA Seq", "GSM1838566", null, "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\u2122 Methyl  Seq 1 Kit BIOO LIFE SCIENCE PRODUCTS  Cat No. 5118 01  according to the manufacturer\u2019s instruction. For RNA seq  total RNA was isolated using TRlzol reagent Invitrogen life Technologies. MeDIP DNA libraries were prepared with The NEXTflex\u2122 Methyl  Seq 1 Kit BIOO LIFE SCIENCE PRODUCTS  Cat No. 5118 01  according to the manufacturer\u2019s instruction. RNA libraries were prepared for sequencing using standard Illumina protocols\uff0e", "GEO Accession:GSM1838566", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP061852", null, null, "18_30_replica1_1.fastq.gz 18_30_replica1_2.fastq.gz", "fastq fastq", 2287951443.0, 11382843.0, "GSM1838566 r1", "0:100 1:101", "A:605485570;C:541783445;G:533913145;T:606360277;N:409006", 100, 101, null, null, 605485570, 541783445, 533913145, 606360277, 409006, "SRX1125643", "SRS1017711", "SRA281140", "GEO", "College of fishery and life science, Shanghai Ocean University", 2, 0.93784, 0.93575, 0.10431, 0.10502, 0.72153, 0.72472, 0.49277, 0.49322, 100, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2015-07-30", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"]], "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": ["39764"], "units": {}, "query_ms": 10.255510998831596}