|
| Status |
Public on Oct 15, 2013 |
| Title |
Pu1 FDCPmix E [ChIP-seq] |
| Sample type |
SRA |
| |
|
| Source name |
FDCPmix
|
| Organism |
Mus musculus |
| Characteristics |
cell line: FDCPmix
Stage: 5 days erythroid differentiation
chip antibody: Pu1
chip antibody vendor: santa cruz biotechnology
chip antibody cat.#: sc352x
|
| Treatment protocol |
For differentiation, cells were washed and then triplicate samples were cultured in IMDM plus 10% FCS and low IL-3 supplemented with either Epo and hemin (erythroid output) or G-CSF and SCF (neutrophil output). GATA1ERT and Pu.1ERT were subcloned into the pHR-SIN-CSGWEmGFP lentiviral expression construct under control of the SFFV promoter. Gata2 and Pu.1 shRNAs were subcloned into Lentilox 3.7.
|
| Growth protocol |
FDCPmix were routinely maintained in Fischer's medium. For differentiation cells were washed and cultured in IMDM plus 10% FCS and low IL-3 with either Epo+hemin (erythoid) or GCSF+SCF (myeloid)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
FDCPmix cells were cross-linked with 1% formaldehyde and sonicated so that the bulk of the chromatin was between 100-500 bp. ChIP was essentially performed by standard procedures
Libraries were made using the ChIP-Seq sample preparation kit (cat# IP-102-1001, Illumina, San Diego, CA, USA) as per manufacture’s instruction.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
Sample 6
|
| Data processing |
Reads were mapped to the mm9 genome using bowtie (v0.12.3)
Peaks were called against an IgG control with MACS (v1.3.7.1, mfold=15,bw=100) and Peakranger (v1.02, b=100,p=0.01,t=4) where a peak was called so if found by both algorithms within 90bp.
Genome_build: mm9
Supplementary_files_format_and_content: peak files
|
| |
|
| Submission date |
Aug 28, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Shamit Soneji |
| E-mail(s) |
shamit.soneji@med.lu.se
|
| Organization name |
BMC
|
| Street address |
Sölvegatan 19
|
| City |
Lund |
| ZIP/Postal code |
221 84 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL9250 |
| Series (2) |
| GSE49991 |
Dynamic analysis of gene expression and genome wide transcription factor binding during lineage-specification of multipotent progenitors |
| GSE50406 |
Dynamic analysis of gene expression and genome wide transcription factor binding during lineage-specification of multipotent progenitors [ChIP-seq]. |
|
| Relations |
| BioSample |
SAMN02338392 |
| SRA |
SRX340958 |
