|
| Status |
Public on Sep 01, 2011 |
| Title |
ID2-H3K4me1-48h.new, biological replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
Id2-HPC cells induced under B-cell conditions, 48h, H3K4me1 ChIP
|
| Organism |
Mus musculus |
| Characteristics |
genetic background: C57BL/6
genotype: human ID2 transgenic
cell type: B cells
hpc induction: B-cell conditions
induction duration: 48 hrs
chip antibody: H3K4me1
antibody vendor: Abcam
antibody catalog#: ab8895
antibody lot#: 937164
|
| Treatment protocol |
None.
|
| Growth protocol |
Cells were cultured for up to 2 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 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 B cells (48 hours), 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 |
SRX084833 |
| BioSample |
SAMN00672708 |
