|
| Status |
Public on Oct 24, 2013 |
| Title |
Ascl1_BAM_48hrs_input_R1 |
| Sample type |
SRA |
| |
|
| Source name |
embryonic fibroblasts treated with BAM factors
|
| Organism |
Mus musculus |
| Characteristics |
cell type: embryonic fibroblasts treated with BAM factors
strain: C57BL/6
antibody: none (input)
|
| Treatment protocol |
ChIP-qPCR and ChIP-seq were carried out following the Farnham protocol (O'Geen et al., 2011) in Ascl1- and BAM-infected MEFs 48 hours after dox, and in Ascl1-infected NPCs 18 hours after induction
|
| Growth protocol |
Embryonic fibroblasts were isolated as previously described from the distal extremities of E14.5 homozygous TauEGFP mice embryos (Vierbuchen et al., 2010). iN cells were generated following the previously described protocol (Vierbuchen et al., 2010).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
The isolated DNA was RNase treated and purified using Qiagen columns.
For sequencing libraries we followed Illumina’s protocol.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| 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 |
SAMN02256172 |
| SRA |
SRX323560 |
