|
| Status |
Public on Apr 10, 2013 |
| Title |
WCE_DicerKO_R2 |
| Sample type |
SRA |
| |
|
| Source name |
Dicer -/- murine MSC cell line
|
| Organism |
Mus musculus |
| Characteristics |
cell type: murine MSC cell line
genotype: Dicer -/-
strain: C57BL/6
chip antibody: none
|
| Treatment protocol |
Dicer WT and KO cells were crosslinked for 10 minutes at room temperature by the addition of one-tenth of the volume of 11% formaldehyde solution (11% formaldehyde, 50mM Hepes pH 7.3, 100mM NaCl, 1mM EDTA pH 8.0, 0.5mM EGTA pH 8.0) to the growth media. Cells were washed twice with PBS, supernatant was aspirated and the cell pellet was flash frozen in liquid nitrogen. Frozen crosslinked cells were stored at -80oC. 50ul of Dynal magnetic beads (Sigma) were blocked with 0.5% BSA (w/v) in PBS. Magnetic beads were bound with 5ug of the indicated antibody unless otherwise indicated.
|
| Growth protocol |
Monoclonal immortalized Dicer WT and KO MSCs were cultured in Alpha-MEM supplemented with pen/strep and 10% fetal bovine serum.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Genomic DNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Illumina pipeline version 1.3+ used for basecalling and sequence read generation
Reads were aligned to the mouse genome (genome build mm9). Read mapping was performed with Bowtie version 0.12.7 for uniquely mapping reads with 0 mismatches. Peaks were called using MACS version 1.4.0beta.
Genome_build: mm9
Supplementary_files_format_and_content: BED files for peaks were generated using MACS version 1.4.0beta. Score column represents: -10log10(pvalue). For each histone mark and replicate number (r1/r2) the *_WCE_r[12].bed files per sample are peaks called with the genotype-matched WCE (whole cell extract) sample as control input. For each histone mark and replicate number (r1/r2) the *_Diff_r[12].bed files per sample are peaks called using the opposite genotype as control input.
|
| |
|
| Submission date |
Feb 07, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
A Bhutkar |
| Organization name |
MIT
|
| Street address |
77 Massachusetts Avenue
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02139 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE44159 |
Let-7 represses Nr6a1 and a mid-gestation developmental program in adult fibroblasts [ChIP-seq_histone] |
| GSE44163 |
Let-7 represses Nr6a1 and a mid-gestation developmental program in adult fibroblasts |
|
| Relations |
| SRA |
SRX228661 |
| BioSample |
SAMN01915294 |
