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Sample GSM2572249 Query DataSets for GSM2572249
Status Public on Jan 02, 2019
Title cortex RNA-seq rep2
Sample type SRA
Source name cortex
Organism Mus musculus
Characteristics strain: C57BL/6
age: 8 week
tissue: cortex
Extracted molecule total RNA
Extraction protocol The tissues for the technical replicates are from independent mouse, and at least two replicates are included in different assay as indicated. RNA (Life Tech, at#: 15596-018) were extracted according to the manufacturers’ instructions.
Libraries were prepared using the NEB Ultra™ Directional RNA Library Prep Kit according to the manufacturer’s protocol and sequenced using an Illumina Hiseq 2000.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
Description RNA-seq
Data processing First, the raw FASTQ data files generated by the Illumina HiSeq 2000 platform were mapped to the mouse reference sequence (mm10) for mRNA analysis with the default parameters. Then the normalized FPKM levels of each sample with default parameters using the cufflinks program (cufflinks v2.2.1) were calculated.
genome build: mm10
processed data files format and content: bigwig or text files with 5hmC or 5mC level or gene FPKM. 5hmC or 5mC level calculation is as follows: we counted the number of 'C' bases from sequencing reads as hydroxymethylated or methylated (denoted as NC) and the number of 'T' bases as unmodified (denoted as NT). The hydroxymethylation level or methylation level was estimated as NC/(NC + NT) in 1Mb windows. Bigwig files are available on the series record.
Submission date Apr 10, 2017
Last update date May 15, 2019
Contact name Qin Ma
Organization name Beijing Institute of Genomics
Department Chinese Academy of Sciences
Street address NO.1 Beichen West Road, Chaoyang District
City Beijing
ZIP/Postal code 100101
Country China
Platform ID GPL13112
Series (1)
GSE97568 Whole-genome analysis of 5-hydroxymethylcytosine and 5-methylcytosine at base resolution in the mouse brain
BioSample SAMN06704539
SRA SRX2731668

Supplementary file Size Download File type/resource
GSM2572249_4_cortex_genes.fpkm_tracking.gz 654.5 Kb (ftp)(http) FPKM_TRACKING
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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