|
| Status |
Public on Jan 02, 2019 |
| Title |
cortex RNA-seq rep1 |
| 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 |
| E-mail(s) |
qinma@big.ac.cn
|
| 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 |
|
| Relations |
| BioSample |
SAMN06704540 |
| SRA |
SRX2731667 |
