|
| Status |
Public on Apr 27, 2010 |
| Title |
mouse_ES_input |
| Sample type |
SRA |
| |
|
| Source name |
Embryonic stem cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
cell type: V6.5 embryonic stem cells
chip antibody: none
|
| Treatment protocol |
n/a
|
| Growth protocol |
Murine V6.5 ES cells (C57BL/6(F) x 129/sv(M)) were cultured on inactivated MEFs in DMEM supplemented with 15% FCS, leukemia-inhibiting factor, penicillin/streptomycin, L-glutamine and non-essential amino-acids. Prior to use in ChIP experiments, V6.5 cells were cultured for two passages under feeder-free conditions on 0.2% gelatin
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin Immunoprecipitation was performed with a KDM2A-specific antibody. ChIP DNA was prepared for Illumina Genome Analyzer II sequencing using by blunting the DNA with a mixture of T4 DNA polymerase, Klenow DNA polymerase, and T4 PNK (NEB) according to manufacturer's instruction. dA overhangs were then added and Illumina adapters ligated. Adapter-ligated DNA was subject to 18 cycles of PCR before size selection by agarose gel electrophoresis. Amplified DNA was purified using the Qiaquick gel extraction kit (Qiagen). The purified DNA was quantified both with an Agilent Bioanalyzer and Invitrogen Qubit and diluted to a working concentration of 10 nM prior sequencing. Sequencing on a Illumina Genome Analyzer II instrument was carried out according to the manufacturer’s instructions.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
input DNA
|
| Data processing |
Sequenced tags of 51 bp in length were mapped to the mouse genome (build mm9) using Bowtie aligner. Only uniquely mapped tags with no more than two mismatches in the first 28 base pairs of the read were retained. Positions in genome with the numbers of mapped tags above the significance threshold defined by a Z-score of 7 were identified as anomalous, potentially resulting from amplification bias, and the tags mapped to those positions were discarded. The tag frequency at each genome position was calculated separately for DNA positive and negative strands.
The tab files (processed data) provide information about binding of lysine demethylase enzyme KDM2A in mouse embryonic stem cells.
The tab files (input.tab and kdm2a.tab) list Solexa read coordinates for the input and IP samples used in ChIP-Seq experiment.
The format of these files is as follows:
<chromosome> <strand> <coordinate> <read count in the library>
|
| |
|
| Submission date |
Oct 15, 2009 |
| Last update date |
May 15, 2019 |
| Contact name |
Peter J Park |
| E-mail(s) |
peter_park@harvard.edu
|
| Phone |
617-432-7373
|
| Organization name |
Harvard Medical School
|
| Department |
Center for Biomedical Informatics
|
| Street address |
10 Shattuck St
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL9250 |
| Series (2) |
| GSE18588 |
CpG islands recruit a histone H3 lysine 36 demethylase [Illumina sequencing data] |
| GSE21202 |
CpG islands recruit a histone H3 lysine 36 demethylase |
|
| Relations |
| Reanalyzed by |
GSE80791 |
| SRA |
SRX017109 |
| BioSample |
SAMN00009397 |
