|
| Status |
Public on Jun 22, 2017 |
| Title |
Bloodlinc_ChIRP-seq_oddProbes |
| Sample type |
SRA |
| |
|
| Source name |
MEL
|
| Organism |
Mus musculus |
| Characteristics |
protocol: 2% DMSO day 5
cell type: MEL
|
| Growth protocol |
40 million MEL cells were harvested after 5 days of 2% DMSO-induced differentiation
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIRP-seq was conducted as described (Chu et al. 2011; Chu et al. 2012).
Non-strand-specific cDNA libraries were sequenced on an Illumina HiSeq2000 platform.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Library strategy: ChiRP-seq
Reads were mapped to mm9 using bowtie2 (Langmead and Salzberg 2012). Peak calling was performed on uniquely-mapped reads relative to input control using MACS (Zhang et al. 2008) with default parameters and “--bw=300 --mfold 10 30”. High-confidence peaks were identified based on several criteria. First, peak coverage was quantified using BEDTools (Quinlan and Hall 2010), and only peaks with an average per-base coverage greater than 10 reads were considered. Then only peaks with a relative read density >10-fold over the background model and an absolute read pileup >100 for the complete probe set or >50 for the split probe sets were retained. Finally, peaks in treated samples overlapping peaks in the input, RNase, or untreated controls were excluded from further analysis.
Genome_build: mm9
Supplementary_files_format_and_content: Uniquely-mapped reads in bigwig format. Peaks in text format.
|
| |
|
| Submission date |
Jun 21, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Juan R Alvarez-Dominguez |
| Organization name |
Harvard University
|
| Department |
Stem Cell and Regenerative Biology
|
| Street address |
7 Divinity Ave
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02138 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE97119 |
The super-enhancer derived alncRNA-EC7/Bloodlinc potentiates red blood cell development in trans (ChIRP-seq) |
| GSE97121 |
The super-enhancer derived alncRNA-EC7/Bloodlinc potentiates red blood cell development in trans |
|
| Relations |
| BioSample |
SAMN07260763 |
| SRA |
SRX2940982 |
