|
| Status |
Public on Feb 15, 2018 |
| Title |
exp_succinyllysine_rep_1 |
| Sample type |
SRA |
| |
|
| Source name |
immortalized mouse embryonic fibroblast cell line
|
| Organism |
Mus musculus |
| Characteristics |
cell line: R26M2rtTA/+;TetOcre;Sdhcfl/fl
day: 16
antibody: anti-succinyllysine (PTM Biolabs cat# PTM-401)
|
| Treatment protocol |
Gene rearrangement induced by adding doxycycline to media at 1 microgram/mL final concentration.
|
| Growth protocol |
Cells grown in DMEM (low glucose) containing 10% FBS at 37 degrees Celsius in 5% CO2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells harvested by trypsinization and fixed with formaldehyde prior to lysis. Chromatin prepared via MNase digestion and sonication. Either ChIP-enriched chromatin or non-enriched input chromatin used for library construction.
ThruPLEX DNA-seq 48D Kit (Rubicon Genomics cat# R400406)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
processed data file: succinyllysine_peaks.bed
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie v2.2.3
Peaks were called with MACS
Genome_build: mm10
Supplementary_files_format_and_content: bed files with peaks summarized across replicates and treatments and bedgraph files for each sample.
|
| |
|
| Submission date |
Sep 27, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
John Andrew Smestad |
| Organization name |
Mayo Clinic
|
| Department |
Biochemistry and Molecular Biology
|
| Lab |
Louis (Jim) Maher
|
| Street address |
200 1st St. SW
|
| City |
Rochester |
| State/province |
Minnesota |
| ZIP/Postal code |
55905 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (2) |
| GSE104362 |
iMEF SDHC-loss ChIP-seq |
| GSE129956 |
Functional genomics of iMEF SDHC-loss stable line |
|
| Relations |
| BioSample |
SAMN07714770 |
| SRA |
SRX3227364 |
