|
| Status |
Public on Jan 07, 2016 |
| Title |
Ezh2ko H3K27me3 ChIP |
| Sample type |
SRA |
| |
|
| Source name |
Bone marrow
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Bone marrow LSK-cells transformed with NRASQ61K
genotype: Ezh2ko/Cdkn2ako
strain: C57BL/6
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was isolated using standard ChIP protocol
Nugen Ovation Ultra low system V2
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Leukemic cells harvested from a moribund mouse were expanded on OP9DL in the presence of IL7,SCF, Flt3L.
|
| Data processing |
Basecalling was performed by Illumina’s RTA (Real-Time Analysis) software version 1.18.61 with QTable version 6. CASAVA version 1.8.2 was used to demultiplex samples. Illumina Chastity quality filtering was performed.
Alignment was performed using GSNAP (version 2012-07-20): gsnap -d mm9 -v snp128_strict_wholeChrs --gunzip --max-mismatches=0.06 -i2 -n1 -Q --nofails -B5 -t12 -A sam *.fastq.gz > *.sam. Sam format was converted to Bam format using Samtools. Bam-files were sorted using Samtools.
Sorted Bam-files were converted to Bed format and were used as input for Diffreps (PLoS ONE 8(6): e65598.), using ChIP-input input as background controls and using Gtest (-me -gt).
Sorted Bam-files were used to generate peak-files using MACS2, using the callpeak function with parameters -f BAM -g mm --nomodel --broad --nolambda --broad-cutoff 0.25. ChIP-input served as control.
Sorted Bam-files were used to generate Homer Tag-directories. Homer 'makeUCSCfile' was used to generate bedGraph files, which were converted to BigWig format using 'bedGraphToBigWig' (UCSC)
Genome_build: mm9
|
| |
|
| Submission date |
Jan 06, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Tobias Neff |
| E-mail(s) |
Tobias.Neff@ucdenver.edu
|
| Phone |
303-724-7445
|
| Organization name |
University of Colorado Denver AMC
|
| Department |
Pediatric Oncology
|
| Lab |
Neff
|
| Street address |
12800 E. 19th Ave.
|
| City |
Aurora |
| State/province |
CO |
| ZIP/Postal code |
80045 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE76601 |
Tumor suppressor role of Ezh2 in an NRASQ61K driven model of Early T-cell Precursor Acute Lymphoblastic Leukemia (ChIP-Seq) |
| GSE76603 |
Tumor suppressor role of Ezh2 in an NRASQ61K driven model of Early T-cell Precursor Acute Lymphoblastic Leukemia |
|
| Relations |
| BioSample |
SAMN04386851 |
| SRA |
SRX1520515 |
