|
| Status |
Public on Apr 01, 2011 |
| Title |
RCOR3 ChIP-Seq |
| Sample type |
SRA |
| |
|
| Source name |
E14
|
| Organism |
Mus musculus |
| Characteristics |
cell line: E14
passages: 15-18
transgene: V5 tagged RCOR3
chip antibody: V5
chip antibody manufacturer: Invitrogen
chip antibody catalog #: R96125
|
| Growth protocol |
E14 cell were maintained under normal condition for mouse ES cell culture.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and REST and its cofactors DNA complexes were isolated with antibody. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). 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 (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 3â 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 following the manufacturer's protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
Chromatin IP against RCOR3
|
| Data processing |
Alignment: Sequence reads were obtained and mapped to the mouse (Build 36, Feb, 2006) genomes using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained and read starts were summed in sliding windows of 400 bp to create summary windows.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (SCISSRS) algorithm
|
| |
|
| Submission date |
Mar 29, 2011 |
| Last update date |
Jun 11, 2013 |
| Contact name |
hongbing yu |
| E-mail(s) |
[email protected]
|
| Phone |
65 68088488
|
| Fax |
65 68088306
|
| Organization name |
genome institute of singapore
|
| Department |
stem cell and development
|
| Lab |
stem cell 3
|
| Street address |
60 biopolis street, #02-01, genome
|
| City |
Singapore |
| ZIP/Postal code |
138672 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL9185 |
| Series (2) |
| GSE28233 |
Genome-wide maps of REST and its cofactors in mouse E14 cells |
| GSE28289 |
REST ChIP-chip and knockdown expression profiling |
|
| Relations |
| BioSample |
SAMN02198585 |
