|
| Status |
Public on Oct 24, 2013 |
| Title |
MEF_FAIRE |
| Sample type |
SRA |
| |
|
| Source name |
embryonic fibroblasts
|
| Organism |
Mus musculus |
| Characteristics |
cell type: embryonic fibroblasts
strain: C57BL/6
|
| Treatment protocol |
Approximately 5-10x106 MEFs were crosslinked with 1% formaldehyde for 7 minutes.
|
| Growth protocol |
Faire-seq protocol was followed as previously described (Giresi et al., 2007) in order to identify regions in MEFs genome that are nucleosomal-free and could be associated with regulatory activity.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
The isolated DNA was RNase treated and purified.
For sequencing libraries we followed Illumina’s protocol.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
genome build: mm9
Raw reads were uniquely mapped to mouse reference genome (NCBI37/mm9) using bowtie (version 0.12.6) allowing maximum one mismatch (Langmead et al., 2009).
For Chip-Seq, peaks for each sample were called using MACs algorithm (version 1.4.2). For FAIRE-Seq, peaks were called using ZINBA.
Supplementary_files_format_and_content: The processed file is in bed format with called peaks.
|
| |
|
| Submission date |
Jul 17, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Kun Qu |
| E-mail(s) |
kqu@stanford.edu
|
| Organization name |
Stanford University
|
| Department |
Dermatology
|
| Lab |
Howard Chang
|
| Street address |
269 Campus Dr. CCSR 2150
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE43916 |
Hierarchical mechanisms for transcription factor-mediated reprogramming of fibroblasts to neurons |
|
| Relations |
| BioSample |
SAMN02256185 |
| SRA |
SRX323580 |
