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| Status |
Public on Feb 02, 2015 |
| Title |
MB_Kap1_ChIPSeq |
| Sample type |
SRA |
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| Source name |
C2C12 myoblasts
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| Organism |
Mus musculus |
| Characteristics |
strain: C3H
developmental stage: proliferating myoblasts
chip antibody (epitope/name): Kap1 - homemade rabbit polylconal antibody
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| Treatment protocol |
For differentiation, cells were placed in media containing Dulbecco's Modified Eagle Medium (DMEM) supplemented with 2% horse serum, penicillin/streptomycin and insulin-Transferrin-selenium-A.
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| Growth protocol |
C2C12 myoblasts were routinely grown in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal calf serum (FCS) and penicillin/streptomycin.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
C2C12 cells at various stages were washed 2x (in PBS + Protease inhibitor), counted to normalize by cell number, cross-linked (ten minutes rotation in 1% formaldehyde), quenched with glycine (at 125mM on ice), washed 3x (PBS+PI) and pelleted at 10e7 cells per eppendorf. Pellets were lysed, resuspended in 1ml sonication buffer on ice (10mM Tris pH 8, 200mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% NaDOC, 0.25% NLS and protease inhibitors), transferred to glass 12x12mm tubes (Covaris: 520081) and sonicated (Covaris settings: 5% duty cycle, PIP 140, 200cyles/ burst, 25 minutes). Sonication was then assessed by reverse cross-linking overnight in the presence of proteinase K and RNase, followed by DNA extraction and quantification on a Bioanalyzer (Agilent 2100 machine). Libraries were prepared according to Illumina's instructions.
Libraries were prepared according to Illumina's instructions
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Raw reads were mapped to the human genome (mm9) using Bowtie 2.2.1 in sensitive mode
Peaks were called using MACS
Genome_build: mm9
Supplementary_files_format_and_content: bedfiles contain the results of the peakcalled using MACS
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| Submission date |
Oct 23, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Evarist Planet |
| E-mail(s) |
evarist.planet@epfl.ch
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| Organization name |
EPFL
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| Lab |
LVG
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| Street address |
Route Cantonale
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| City |
Lausanne |
| State/province |
Vaud |
| ZIP/Postal code |
1015 |
| Country |
Switzerland |
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| Platform ID |
GPL13112 |
| Series (2) |
| GSE62660 |
A KAP1 phosphorylation switch controls MyoD function during skeletal muscle differentiation (ChIP-seq) |
| GSE62664 |
A KAP1 phosphorylation switch controls MyoD function during skeletal muscle differentiation |
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| Relations |
| BioSample |
SAMN03140309 |
| SRA |
SRX739773 |
| Named Annotation |
GSM1531007_c2_MB_kap1_peaks_p7.bed.gz |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1531007_c2_MB_kap1_peaks_p7.bed.gz |
279.9 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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