|
| Status |
Public on May 27, 2013 |
| Title |
IgG_ChIPseq |
| Sample type |
SRA |
| |
|
| Source name |
BMiFLT3 (15-3) cells
|
| Organism |
Mus musculus |
| Characteristics |
cell line: BMiFLT3(15-3)
cell type: proB cells from a murine BCP-ALL
genetic modification: cells transduced with Runx1-ERt2
chip-seq antibody: rabbit anti-IgG [Abcam,catalog #37415, lot #905012]
|
| Treatment protocol |
24 hours before DNA extraction, cells were either treated with 0.2 µM Tamoxifen to ensure Runx1-ERt2 translocation into the nucleus or treated with the appropriate amount of ethanol as a control.
|
| Growth protocol |
Cells were routinely grown in α-MEM with 10% FCS, glutamine and sodium pyruvate.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP experiments using anti-Runx1 or anti-IgG antibodies were performed using the EZ-ChIP Kit (Upstate/Millipore) according to the manufacturer’s protocol.
Purified DNA from chromatin immunoprecipitations (10-50 ng) was adapter-ligated using the Illumina-compatible NEXTflexTM ChIP Seq-Kit (Bioo Scientific) for DNA inserts ≥70 bps.DNA fragments between 350-550 bp were isolated using PippinPrep (Sage Science) and quantified and sized on a microfluidics-based Bioanalyzer 1200 using a High Sensitivity DNA Kit (Agilent).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
Illumina Casava 1.8.2 software was used for base calling.
Sequence tags were aligned to the mm9 assembly (NCBI Build 37) with Bowtie (v. 0.12.8) reporting only top scoring unique mapping tags.
The MACS algorithm was used to identify bound regions by comparing the enrichment of the Runx1-IP sample against a control IgG-IP for background correction. MACS version 1.4.01 was run with all parameters at their default settings, except m-fold, which was set at 8,30, to identify Runx1-bound regions.
Genome_build: mm9
Supplementary_files_format_and_content: Bed file identifies Runx1-bound regions
|
| |
|
| Submission date |
Mar 21, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Neele Margarete Kriebitzsch |
| E-mail(s) |
neele.kriebitzsch@hpi.uni-hamburg.de
|
| Organization name |
Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology
|
| Lab |
Molecular Pathology
|
| Street address |
Martinistraße 52
|
| City |
Hamburg |
| ZIP/Postal code |
20251 |
| Country |
Germany |
| |
|
| Platform ID |
GPL11002 |
| Series (2) |
| GSE45377 |
Genome-wide mapping of Runx1-bound sites in early B-cell progenitors |
| GSE45425 |
Runx1 targets in early B-cell progenitors |
|
| Relations |
| SRA |
SRX253193 |
| BioSample |
SAMN01985486 |
