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Sample GSM1323991 Query DataSets for GSM1323991
Status Public on Mar 06, 2014
Title 961C-V5 NP23
Sample type SRA
Source name 961C cell line
Organism Mus musculus
Characteristics cell line: 961C cell line
chip antibody: NP23
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
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)
BioSample SAMN02630896
SRA SRX467480

Supplementary file Size Download File type/resource
GSM1323991_961C-V5-NP23.bed.gz 38.4 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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