|
Status |
Public on Sep 01, 2011 |
Title |
ID2-H3K4me1-Myeloid.new, biological replicate 2 |
Sample type |
SRA |
|
|
Source name |
Id2-HPC cells induced under myeloid conditions, H3K4me1 ChIP
|
Organism |
Mus musculus |
Characteristics |
genetic background: C57BL/6 genotype: human ID2 transgenic cell type: myeloid cells hpc induction: myeloid conditions chip antibody: H3K4me1 antibody vendor: Abcam antibody catalog#: ab8895 antibody lot#: 937164
|
Treatment protocol |
None.
|
Growth protocol |
Cells were cultured for up to 6 days in IMDM medium supplemented with 10% FCS/2% PSG/β-me and IL3, Flt3L, GMCSF and MCSF cytokines.
|
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 3â 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 myeloid 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 http://biowhat.ucsd.edu/homer/).
|
|
|
Submission date |
Jul 21, 2011 |
Last update date |
May 15, 2019 |
Contact name |
Yin Chun Lin |
E-mail(s) |
yclin@ucsd.edu
|
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 |
|
Relations |
SRA |
SRX084836 |
BioSample |
SAMN00672711 |