|
| Status |
Public on Jan 01, 2020 |
| Title |
D2_Sox2_2 |
| Sample type |
SRA |
| |
|
| Source name |
SKM secondary MEF
|
| Organism |
Mus musculus |
| Characteristics |
sample stage: Day 2 of SKM reprogramming
chip antibody: Sox2 (Millipore, AB5603)
|
| Growth protocol |
MEF cells are cultured in DMEM+10%FBS, and reprogramming cells were cultured in mouse ES medium in presence of doxycycline for 2 days.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatins were cross-linked by 1% formaldehyde and extracted using EZ-ChIP Chromatin Immunoprecipitation kit (Millipore, 17-371). The chromatin was then sonicated to an average DNA fragment length of 100-500 bp on Covaris S2 .
Sequencing libraries were generated, according to the manufacturer’s instructions. Briefly, 4 ng of ChIP product was used for each library preparation. The NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (E7645) was used to ligate adapters and for barcoding and amplification. Libraries was purified using SPRIselect® Reagent magnetic beads (Beckman Coulter, Inc. #B23317), quality-controlled by the Bioanalyzer, and quantified by qPCR.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
base-calling was done using CASAVA 1.8.4.
The alignment was done using bowtie2 with mouse genome build mm9. The result was then filtered by MAPQ scores with smtools to only keep reads with MAPQ larger than 10 (version 0.1.19)
peak calling Macs (version 2.0: macs2 callpeak -t $treatment -c $control --broad -g mm -n $name)， for Klf4 ChIP seq, we used an additional parameter of -p 0.05 to call the peaks.
Genome_build: mm9
Supplementary_files_format_and_content: peaks.narrowPeak bed files from the MACS2
|
| |
|
| Submission date |
Jul 01, 2018 |
| Last update date |
Jan 02, 2020 |
| Contact name |
Sheng Ding |
| E-mail(s) |
sheng.ding@gladstone.ucsf.edu
|
| Organization name |
Gladstone Institute for Cardiovascular Disease
|
| Lab |
Ding lab
|
| Street address |
1650 Owens Street
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94158 |
| Country |
USA |
| |
|
| Platform ID |
GPL21626 |
| Series (1) |
| GSE98280 |
Function of Sox2 and Klf4 during SKM reprogramming |
|
| Relations |
| BioSample |
SAMN09530324 |
| SRA |
SRX4328950 |
