|
| Status |
Public on Mar 18, 2021 |
| Title |
Ctrl-PolII-S5 |
| Sample type |
SRA |
| |
|
| Source name |
Satellite cells/Myoblasts
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
chip antibody: PolII-S5 (Abcam Cat.No.ab5131)
cell type: Satellite cells
|
| Treatment protocol |
Satellite cells were treated with 4-OHT for 72 hrs for CreERT2 activation. Before proceeding for experiment cells were cultured in 4-OHT free media for 24 hrs
|
| Growth protocol |
Satellite cells isolated from mice muscle tissue were cultured in F10 media with 20% BGS and bFGF (2.5 ng/ml)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were fixed with 1% formaldehyde for 20 min and quenched for 10 min in 125 mM glycine. Cells were sonicated in 1% SDS containing sonication buffer for extracting sonicated chromatin
Library was constructed using KAPA HyperPrep Kit (Roche 07962363001-KAPA KK8504 ). End Repair/A-tailing step then ligation of IDT for Illumina TruSeq UD Indexes (Illumina-20022370) followed by dual SPRI size selection Left 1.0 - 0.52 Right and 11 cycles of PCR enrichment.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Mapping: Satellite cells/Myoblasts
PeakCalling: Uniquely mapped reads were used for peak calling using MACS2
Visualization: Mapped reads were converted to bigWigs with RPKM normalization
Peak calls were converted to bigBed files
Genome_build: MM10
Supplementary_files_format_and_content: narrowPeak [peak information, location]
|
| |
|
| Submission date |
May 11, 2020 |
| Last update date |
Dec 02, 2023 |
| Contact name |
Jeffrey Dilworth |
| E-mail(s) |
fdilworth@wisc.edu
|
| Phone |
6082653758
|
| Organization name |
University of Wisconsin
|
| Street address |
1111 Highland Ave
|
| City |
Madison |
| State/province |
Wisconsin |
| ZIP/Postal code |
53705 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (2) |
| GSE150276 |
Negative Elongation Factor (NELF) regulates muscle progenitor expansion for efficient myofiber repair and stem cell pool repopulation {ChIP-seq] |
| GSE150280 |
Negative Elongation Factor (NELF) regulates muscle progenitor expansion for efficient myofiber repair and stem cell pool repopulation |
|
| Relations |
| BioSample |
SAMN14887057 |
| SRA |
SRX8321720 |
