|
Status |
Public on Mar 06, 2014 |
Title |
961C H3K27me3 |
Sample type |
SRA |
|
|
Source name |
961C cell line
|
Organism |
Mus musculus |
Characteristics |
cell line: 961C cell line chip antibody: H3K27me3 sample type: Cytokine independent strain: C57BL/6 cell type: NUP98-PHF23 AML derived cell line source: NUP98-PHF23 AML derived cell line, mouse 961
|
Treatment protocol |
Cells were crosslinked with 1% formaldehyde at room temperature for 15 minutes. The cells were then sheared with a VirSonic 100 sonicator (VirTis) for 40 cycles of 10x 1-second pulses.
|
Growth protocol |
Cell lines grown in IMDM/15% FBS/%1 L-Glut/%1 PenStrep. Cytokine independent.
|
Extracted molecule |
genomic DNA |
Extraction protocol |
ChIP was performed using a ChIP-IT kit from Active Motif (Carlsbad, CA), following the manufacturer’s recommended protocol with minor modifications as described in supplementary methods. Antibodies used were: anti-H3K4me3 (17-614, Millipore), anti-H3K27me3 (07-449, Millipore), anti-V5 (R960-25, Life Technologies), anti-FLAG (M2. Sigma Aldrich) and anti RNA Polymerase II (CTD4H8, Santa Cruz). ChIP DNA (10 ng) was end-repaired and phosphorylated using T4 polymerase, Klenow, and T4 Polynucleotide Kinase. An A-overhang was introduced using exo-Klenow and then ligated to Illumina paired-end adapters with DNA ligase. Ligated products were size selected on a Caliper LabChip XT to a mean size of 240bp +/- 20%. The libraries were amplified with Illumina PCR Primer InPE1.0, PCR Primer InPE2.0 and PCR Primer Indexes and sequenced on Illumina GAIIx or MiSeq sequencers under a single-end run protocol.
|
|
|
Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina Genome Analyzer IIx |
|
|
Description |
myeloblast
|
Data processing |
Basecalls performed using CASAVA version 1.9 ChIP-seq reads were aligned to the mm9 genome assembly using BWA 0.5.9-r26-dev Data were filtered using the following specifications… Peaks were called using in-house developed software Peakfinder (Sven Bilke). Genome_build: mm9
|
|
|
Submission date |
Feb 07, 2014 |
Last update date |
May 15, 2019 |
Contact name |
Yuelin Jack Zhu |
E-mail(s) |
zhujack@mail.nih.gov
|
Phone |
(240)760-7439
|
Organization name |
NCI
|
Department |
Genetics Branch, Center for Cancer Research
|
Lab |
Dr. Paul Meltzer's Lab
|
Street address |
9000 Rockville Pike
|
City |
Bethesda |
State/province |
MD |
ZIP/Postal code |
20892 |
Country |
USA |
|
|
Platform ID |
GPL11002 |
Series (1) |
GSE54786 |
Genome wide localization of chromatin bound NUP98-PHF23 (NP23) |
|
Relations |
BioSample |
SAMN02630894 |
SRA |
SRX467478 |