GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM765568 Query DataSets for GSM765568
Status Public on Sep 01, 2011
Title, biological replicate 2
Sample type SRA
Source name Id2-HPC cells induced under B-cell conditions, Cd19+, 120h, H3K4me1 ChIP
Organism Mus musculus
Characteristics genetic background: C57BL/6
genotype: human ID2 transgenic
cell type: Cd19+ B cells
hpc induction: B-cell conditions
induction duration: 120 hrs
chip antibody: H3K4me1
antibody vendor: Abcam
antibody catalog#: ab8895
antibody lot#: 937164
Treatment protocol None.
Growth protocol Cells were cultured for up to 5 days in IMDM medium supplemented with 10% FCS/2% PSG/β-me and IL-7 and SCF cytokines on S17 feeder cells in the presence of 1 ug/mL doxycycline, or alternatively, in alpha-MEM medium in the presence of cytokines and on Tst-4 stromal cells.
Extracted molecule genomic DNA
Extraction protocol Lysates were clarified from sonicated cells and protein-DNA complexes were isolated with antibody. Libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (minus exo) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters, which have a single 'T' base overhang at the 3’ end. After adapter ligation, ChIP DNA was PCR-amplified with Illumina primers for 18 cycles and library fragments (ChIP) (insert plus adaptor and PCR primer sequences) were size selected from a 8% polyacrylamide gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer II or IIx following the manufacturer's protocols.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer IIx
Description Chromatin IP against H3K4me1 of induced CD19+ B cells, biological replicate #2.
Data processing Fastq files were generated by CASAVA.
Alignment: Reads were aligned to the mouse mm8 genome (NCBI Build 36) using Bowtie. Only reads that mapped to a single, unique position were used for downstream analysis.
Custom HOMER software was used for downstream analysis (HOMER, available at
Submission date Jul 21, 2011
Last update date May 15, 2019
Contact name Yin Chun Lin
Organization name UCSD
Department Division of Biological Sciences
Lab Cornelis Murre
Street address 9500 Gilman Drive
City La Jolla
State/province CA
ZIP/Postal code 92093-0377
Country USA
Platform ID GPL11002
Series (2)
GSE30858 Establishment of Enhancer Repertoires that Orchestrate the Myeloid and Lymphoid Cell Fates (ChIP-Seq dataset)
GSE30859 Multilineage Priming of Enhancer Repertoires Precedes Commitment to the B and Myeloid Cell Lineages in Hematopoietic Progenitors
SRA SRX084834
BioSample SAMN00672709

Supplementary file Size Download File type/resource 195.1 Mb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap