|
| Status |
Public on Feb 24, 2012 |
| Title |
H3K4me3_ChIPSeq |
| Sample type |
SRA |
| |
|
| Source name |
NIH-3T3_H3K4me3_ChIPSeq
|
| Organism |
Mus musculus |
| Characteristics |
cell line: NIH-3T3
cell type: Mouse embryonic fibroblast cell
chip antibody: H3K4me3
chip antibody vendor: Millipore
chip antibody cat. #: 04-745
chip antibody lot/batch #: DAM1541166
|
| Treatment protocol |
Cells were cross-linked with 1% formaldehyde in cell culture medium for 10 min at 37C. After quenching with the addition of 125 mM glycine for 5 min at 37C, the cells were washed twice with ice-cold PBS containing proteinase inhibitor. Cells were collected after each wash by centrifugation at 2,500g for 3 min. Finally cells were aliquoted, frozen and kept at -80C.
|
| Growth protocol |
Standard 3T3 growth conditions: 37C, .05% CO2. Medium was DMEM (Gibco) with 10% FCS (Hyclone). Cells were split 1:8 every 2-3 days.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. Libraries were prepared as follows: 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 (32 to 52 exo minus) 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 DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer II following the manufacturer's protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
32754.0
|
| Data processing |
Sequence reads were mapped to the mouse genome assembly mm8 using MAQ v 0.7.1, and these alignments were converted to BED format. Read density maps were produced using IGVTools v 1.5.10 to generate a WIG file, which was then converted to BigWig format using the UCSC WigToBigWig conversion utility v 4.
Genome Build:
315BDAAXX.6.bed: mm8
315BDAAXX.6.bw: mm8
|
| |
|
| Submission date |
Feb 23, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Joseph M Zullo |
| E-mail(s) |
joseph_zullo@hms.harvard.edu, jmz4@uchicago.edu
|
| Organization name |
University of Chicago
|
| Department |
MGCB
|
| Lab |
Singh
|
| Street address |
929 E 57th Street
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60637 |
| Country |
USA |
| |
|
| Platform ID |
GPL9250 |
| Series (2) |
| GSE36048 |
A molecular mechanism for compartmentalization and silencing of chromatin domains at the nuclear lamina [ChIP-seq] |
| GSE36049 |
A molecular mechanism for compartmentalization and silencing of chromatin domains at the nuclear lamina |
|
| Relations |
| SRA |
SRX121863 |
| BioSample |
SAMN00792227 |
| Named Annotation |
GSM879920_315BDAAXX.6.bed.gz |
| Named Annotation |
GSM879920_315BDAAXX.6.bw |
