|
| Status |
Public on Sep 19, 2018 |
| Title |
DEL_Input |
| Sample type |
SRA |
| |
|
| Source name |
MPL-WT-Ba/F3_DEL_Input
|
| Organism |
Mus musculus |
| Characteristics |
cell line: MPL-WT-Ba/F3
cell type: murine pro B cell line
genotype/variation: expressing DEL Calreticuline (CALR)
chip antibody: none (input)
|
| Growth protocol |
RPMI 1640 + 10% h.i. FBS + 10 ng/ml mouse IL-3 or 10%
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were cross-linked in 1% formaldehyde and lysed
Librairires were prepared using NEB ChIP-seq Library Preparation Kit
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Chr3853_DEL_TS11_A12_IGO_08887_11_S53
|
| Data processing |
Peak calls was performed using MACS2 using the command macs2 callpeak with --nomodel --pvalue 0.001 over input. Matched input DNA was used as background for the peak calling.
Reads were trimmed using trimgalore
Trimmed reads were aligned to mm9 using bowtie2
FeatureCount was used to count the reads to the combined peak atlas
DESeq2 was used to normalise samples to the peak atlas
bedtools genomeCoverageBed was used to create normalised bw files using the DESeq2 normfactors. Input bigWig files were kept at depth normalisation to 10M reads.
Genome_build: mm9
Supplementary_files_format_and_content: normalised bigWig files
|
| |
|
| Submission date |
Sep 18, 2018 |
| Last update date |
Sep 19, 2018 |
| Contact name |
Richard Koche |
| E-mail(s) |
kocher@mskcc.org
|
| Organization name |
Memorial Sloan Kettering Cancer Center
|
| Department |
Center for Epigenetic research
|
| Street address |
417 East 68th St
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE120134 |
Targeting the CALR Interactome in Myeloproliferative Neoplasms |
|
| Relations |
| BioSample |
SAMN10086132 |
| SRA |
SRX4712294 |
