|
| Status |
Public on May 27, 2015 |
| Title |
BJ Nucleus-2 hours |
| Sample type |
SRA |
| |
|
| Source name |
BJ
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: skin
cell type: fibroblast cells
cell line: BJ
treatment: 0.2mM H2O2
tiime: 4 hours
|
| Treatment protocol |
Fibroblast cells were treated with H2O2 (final concentration 0.2mM) for 30 minutes and 2 hours.
|
| Growth protocol |
Fibroblast cells were routinely generated typically by re-plating 1-2 10e6 cells into a 140x20mm plate on uncoated plastic in DMEM medium (Gibco, Life technologies) supplemented with BSF and penicillin/streptomycin.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was harvested using Trizol reagent. Applied Biosystems SOLiD System (3.5 and 4) directional RNA-Seq was used with 5 ug of total RNA for the construction of sequencing libraries.Total RNA was depleted twice from rRNA using the RiboMinus Eukaryote Kit for RNA-Seq (ABI, #A1083708)
RNA libraries were prepared for sequencing using standard ABI SOLiD protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
AB SOLiD System 3.0 |
| |
|
| Description |
rRNA-depleted total RNA
|
| Data processing |
The sequenced reads were mapped to hg19 build of the human genome using TopHat version 1.1.4 with the aligner Bowtie 0.12.7 with their default parameters except –m 1 and –segment-mismatches 2.
The mapped reads were further manipulated by removing the reads that mapped to multiple locations (-q 0) using SAMtools.
Genome_build: hg19
Supplementary_files_format_and_content: Each BAM alignment file was divided into two groups based on their relative DNA strand using SAMtools. Each BAM files was converted into Wig file format using BedTools genomeCoverageBed (v2.16.2). Bigwig files generated by converting Wig files using wigToBigWig from UCSC.
|
| |
|
| Submission date |
Feb 19, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Jingxian Zhang |
| E-mail(s) |
zhangjingxian.nus@gmail.com
|
| Organization name |
Institute of Molecular and Cell Biology (IMCB), A-Star, Singapore
|
| Department |
IMCB
|
| Street address |
61 Biopolis Drive Proteos
|
| City |
Singapore |
| State/province |
Singpaore |
| ZIP/Postal code |
138673 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL9442 |
| Series (2) |
| GSE55169 |
Pervasive genomic transcription during oxidative stress generates thousands of previously uncharacterized lncRNAs (RNA-Seq) |
| GSE55172 |
Pervasive genomic transcription during oxidative stress generates thousands of previously uncharacterized lncRNAs |
|
| Relations |
| BioSample |
SAMN02645867 |
| SRA |
SRX472882 |
| Named Annotation |
GSM1330716_BJ_H2O2_N_2h.plus.bw |
| Named Annotation |
GSM1330716_BJ_H2O2_N_2h.minus.bw |
