|
| Status |
Public on Dec 02, 2019 |
| Title |
CSF3R.T618I-INPUT |
| Sample type |
SRA |
| |
|
| Source name |
Bone marrow
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Bone marrow
cell type: HoxB8
vector: CSF3R.T618I only
chip marker: none (input)
|
| Treatment protocol |
Cells were retrovirally transduced with retrovirus harboring oncogenes, sorted for expression of both fluorescent proteins and allowed to recover for 1 week. Cells were washed 4x and cultured for 24 hours in estrogen free media
|
| Growth protocol |
HoxB8 cells were grown in RPMI +10% FCS and SCF-CHO conditioned media +estrogen as preaviously described (Wang et al, Nat Methods, 2006)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were fixed and lysed to extract chromatin. Fixed chromatin was sheared and appropriate antibodies were used to perform the pull down. Aliquotes of the sheared chromatin were used as input.
ChIP and INPUT libraries were prepared using the NEB Ultra II kit (E7645S) according to manufacturer's instructions. Briefly, samples were end-prepped, adaptor ligated and cleaned with Agencourt Ampure XP magnetic beads. Adaptor ligated samples were then barcoded during PCR (10 cycles) and cleaned up.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Cells immortalized through retroviral transduction with CSF3R.T618I
|
| Data processing |
Read qualities were evaluated using FastQC.
Reads were aligned to the mm10 reference using bwa-mem, with default single-end settings.
Using Samtools, alignments were converted to bam format and filtered to remove reads with mapping quality <30.
Alignments were combined between biological replicates.
We used MACS2 to predict ChIP-seq peaks and generate fold enrichment tracks againts appropriate INPUT sample.
Genome_build: mm10
Supplementary_files_format_and_content: BedGraph tracks contain fold enrichment values (calculated by MACS2, relative to INPUT) for each combination of ChIP for each of the cell groups.
|
| |
|
| Submission date |
Nov 05, 2018 |
| Last update date |
Dec 02, 2019 |
| Contact name |
Theodore Paul Braun |
| E-mail(s) |
braunt@ohsu.edu
|
| Organization name |
OHSU
|
| Department |
Knight Cancer Institute
|
| Lab |
3181 SW Sam Jackson Park Road
|
| Street address |
3181 SW Sam Jackson Park Road
|
| City |
Portland |
| State/province |
OR |
| ZIP/Postal code |
97239 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE122162 |
CEBPA Dysfunction Intiates CSF3R Mutant Acute Myeloid Leukemia Through Disruption of Myeloid Lineage Enhancers (ChIP-seq) |
| GSE122166 |
CEBPA Dysfunction Intiates CSF3R Mutant Acute Myeloid Leukemia Through Disruption of Myeloid Lineage Enhancers |
|
| Relations |
| BioSample |
SAMN10380374 |
| SRA |
SRX4980170 |
