|
| Status |
Public on Mar 06, 2014 |
| Title |
M106A H3K4me3 |
| Sample type |
SRA |
| |
|
| Source name |
106A cell line
|
| Organism |
Mus musculus |
| Characteristics |
cell line: 106A cell line
chip antibody: H3K4me3
sample type: Cytokine independent
strain: C57BL/6
cell type: NUP98-PHF23 pre-T LBL derived cell line
source: NUP98-PHF23 pre-T LBL derived cell line, mouse 106
|
| 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 |
lymphoblast
|
| 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 |
SAMN02630900 |
| SRA |
SRX467483 |
