|
| Status |
Public on Oct 17, 2017 |
| Title |
s02_170602_T6E_shMafB_H3K27ac_27656648_S2 |
| Sample type |
SRA |
| |
|
| Source name |
T6E cell line
|
| Organism |
Mus musculus |
| Characteristics |
cell line: T6E
transduction: MafB shRNA
condition: knockdown
chip andibody: ab4729, Abcam
|
| Treatment protocol |
T6E cells were retrovirally transduced with either MigR1-scrambled shRNA or MigR1-MafB shRNA and were sorted for expression of GFP at day3 and were fixed for ChIP assay.
|
| Growth protocol |
T6E cells (Pear et al., 1996) were grown in RPMI 1640 (Corning cellgro) supplemented with penicillin/streptomycin, 20% fetal bovine serum, 2mM L-glutamine, nonessential amino acids, 1 mM sodium pyruvate, and 5 uM 2-mercaptoethanol under standard culture conditions and were maintained in the culture until reaching passage 10.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were cross-linked with 1% formaldehyde for 10min and fixation was quenched with 0.125M glycin for 5min, fixed cells were washed with PBS and nuclear extracts were lysed and DNA was sonicated to 200- 400 bp fragments. Antibodies were incubated with lysates overnight at 4℃. Antibody-chromatin complexes were captured with protein G–conjugated beads, washed, and eluted. After RNase (37℃) and proteinase K (56℃) treatments, cross-links were reversed overnight and DNA was purified using Qiagen PCR purification kit.
Libraries were prepared using NEBNext® Ultra II DNA Library Prep Kit
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
bcl2fastq for creation of fastq files
trimming adaptors with trim_galore
alignment with bwa aln
removing unmapped, reads not maped on propare pair, and low quality reads
remove black list and duplicate reads
Genome_build: GRCm38
Supplementary_files_format_and_content: bigwig
|
| |
|
| Submission date |
Oct 16, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Robert Babak Faryabi |
| E-mail(s) |
faryabi@pennmedicine.upenn.edu
|
| Phone |
215-573-8220
|
| Organization name |
University of Pennsylvania
|
| Department |
Pathology
|
| Lab |
Faryabi Lab
|
| Street address |
Room 553 BRB II/III, 421 Curie Boulevard
|
| City |
Philadelphia |
| State/province |
Pennsylvania |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE104992 |
MafB enhances oncogenic Notch signaling in T-ALL [ChIP-Seq] |
| GSE104993 |
MafB enhances oncogenic Notch signaling in T-ALL |
|
| Relations |
| BioSample |
SAMN07787119 |
| SRA |
SRX3286326 |
