|
| Status |
Public on Jul 01, 2016 |
| Title |
FDC-P1 RUNX-ERt2_Runx1_ChIPSeq |
| Sample type |
SRA |
| |
|
| Source name |
FDC-P1 wt
|
| Organism |
Mus musculus |
| Characteristics |
cell line: FDC-P1
infection: GFP
chip antibody: Runx1, rabbit (Aziz-Aloya R, 1998)
|
| Treatment protocol |
FDCP1_RUNX1-ERt2 were treated with 1 µM 4-OHT for 48h prior to assay
|
| Growth protocol |
FDCP1 and FDCP1_RUNX1-ERt2 cells were cultured in DMEM 10%FCS + IL3
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP was performed using the EZ-ChIP Kit (Upstate/Millipore) on murine FDCP1 cells. After chromatin-crosslinking with 1% formaldehyde, cells were lysed and nuclei were isolated by centrifugation. Chromatin was extracted from the isolated nuclei and fragmented by sonication to an average length of 200–500 bp. Material from 1x10e7 cells was pre-cleared with protein-G agarose beads to reduce non-specific background. Chromatin immunoprecipitation was performed with either rabbit anti-Runx1 antibody, generated against a C-terminal peptide,2 or rabbit IgG (Abcam). Bound protein-DNA complexes were captured with Protein G Sepharose 4 Fast Flow (GE Healthcare) and chromatin eluted 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 200-400 bp were isolated using PippinPrep (Sage Science) and quantified and sized on a microfluidics-based Bioanalyzer 2100 using a High Sensitivity DNA Kit (Agilent)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
RUNX1-ERt2_Runx1_IgG.bed
|
| Data processing |
Basecalls performed using RTA 1.13.48.0 (for HiSeq2000) or RTA 1.17.20.0 (for HiSeq2500)
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie version 0.12.8 with the following configurations: --threads 6 --best --strata –m 1
peaks were called using MACS version 1.4.1 using default setting
Genome_build: mm9
Supplementary_files_format_and_content: bed files were generated using MACS14
|
| |
|
| Submission date |
May 06, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Kira Behrens |
| Organization name |
Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology
|
| Lab |
Retroviral Pathogenesis
|
| Street address |
Martinistrasse 52
|
| City |
Hamburg |
| ZIP/Postal code |
20251 |
| Country |
Germany |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE81179 |
Genome-wide Runx1 binding sites in early hematopoietic progenitors (FDCP1) |
| GSE81182 |
Runx1 downregulates stem cell and megakaryocytic transcription programs that support niche interactions |
|
| Relations |
| BioSample |
SAMN04958095 |
| SRA |
SRX1744939 |
