|
| Status |
Public on Jul 08, 2017 |
| Title |
IP_Pol II_KDIno80NC2 |
| Sample type |
SRA |
| |
|
| Source name |
ESC cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: ESC cells
antibody: Anti Pol II antibody (QED Bioscience)
|
| Treatment protocol |
Cells were transfected with siRNA following the protocol of Lipofectamine RNAiMAX Transfection Reagent. 72 hours post transfection, cells were harvested for experiments
|
| Growth protocol |
E14 cells were grown on feeder-free tissue culture plates (0.5% gelatin treated before use) in ESC media: knockout DMEM supplemented with 15% fetal bovine serum, leukemia inhibiting factor, L-glutamine, non-essential amino acids, penicillin/streptomycin and 2-mercaptoethanol. Cells were passaged at least twice before treatment.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For ChIP-seq, cells were harvested and crosslinked in suspension with 1% formaldehyde for 10 minute at room temperature. Crosslinked cells were lysed, sonicated and chromatin was collected for IP. 2-5 ug of antibody was used for each IP. IPed chromatin was captured by Protein A beads. After washing, bound complexes were eluted and crosslinking was reversed. DNA was extracted using phenol-chloroform and purified by ethanol precipitation.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Fastq files were used to map reads to mouse genome(mm9) with Bowtie 0.12.9
Mapped reads were counted and shuffled to similar reads.
Shuffled reads were used to calculate the p value and log2 ratio of Ip vs Input or histone modifications in knockdown vs control
log2 ratio of Ip vs input at significant windows were used to plot with metagene profiles or center with TSS
log2 ratio of H3K79Me3 in mutant vs control at all windowns was used for metagene profile
genome_build: mm9
|
| |
|
| Submission date |
Mar 02, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Siavash K Kurdistani |
| E-mail(s) |
Skurdistani@mednet.ucla.edu
|
| Organization name |
UCLA
|
| Department |
Biological Chemistry
|
| Lab |
Kurdistani
|
| Street address |
615 Charles E Young Dr South
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE95633 |
MINC Regulates Pervasive Transcription in Yeast and Mammals |
|
| Relations |
| BioSample |
SAMN06470321 |
| SRA |
SRX2609743 |
