|
| Status |
Public on Jan 30, 2012 |
| Title |
H3K4me3_ChIPSeq |
| Sample type |
SRA |
| |
|
| Source name |
sorted erythroid cells (Ter119+)
|
| Organism |
Mus musculus |
| Characteristics |
tissue: erythroid cells
strain: C57BL/6/CBA
chip antibody: antiH3K4me3 Millipore catalog number 05-745R clone 15-10C-E4 lot DAM1605007
|
| Treatment protocol |
Mouse primary erythroid cells were sorted from the spleens of acetylphenylhydrazine-treated mice based on the expression of Ter119 (Spivak et al., 1973; Vernimmen et al., 2009).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIPs were performed according to the Millipore ChIP protocol, as described previously (De Gobbi et al., 2007). For ChIP-Seq experiments, Ter119+ cells were fixed with 1% formaldehyde for 10 minutes at RT and chromatin was sonicated to a size <500 bp. Immunoprecipitations were performed, after an overnight incubation with the appropriate antibody, with protein A agarose (Millipore). A sample containing no antibody was used as a negative control. Immunoprecipitations were performed after an overnight incubation with the appropriate antibody with protein A agarose (Millipore). A sample containing no antibody was used as a negative control. Input and immunoprecipitated DNA were purified by phenol and chloroform extraction followed by ethanol precipitation. Subsequently the material was analysed by real time PCR (ABI Prism 7000 Sequence Detection System, Applied Biosystems) using a series of PCR amplicons and 5'FAM-3'TAMRA probes across the alpha-globin locus.
The library was constructed using Illumina protocol. The library was amplified prior to size selection (150-200bp).
Model- GAIIx Chemistry-SBS v4 cBot single generation kit with v4 flow cell SCS 2.8 RTA 1.8 Recipe v7.4
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
Chromatin IP against H3K4me3
|
| Data processing |
The reads were aligned to the mm9 mouse genome build using bowtie (version 0.12.3) with indices on m2 (map twice to the genome). Before downstream analysis duplicate reads of the same chromosome and start position were collapsed to a single representative read to exclude overrepresented PCR products. All aligned reads starts were summed in sliding windows of 300 bp to create summary windows.
|
| |
|
| Submission date |
Mar 12, 2011 |
| Last update date |
Jun 11, 2013 |
| Contact name |
Monika S Kowalczyk |
| E-mail(s) |
monika.kowalczyk@imm.ox.ac.uk
|
| URL |
http://www.imm.ox.ac.uk/wimm-research/molhaem/doug-higgs
|
| Organization name |
Weatherall Institute of Molecular Medicine, University of Oxford
|
| Department |
MRC Molecular Haematology Unit
|
| Lab |
Higgs Group
|
| Street address |
Headley Way
|
| City |
Oxford |
| State/province |
Oxfordshire |
| ZIP/Postal code |
OX3 9DS |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL9250 |
| Series (2) |
| GSE27918 |
Genome-wide maps of chromatin state in mouse erythroid cells. |
| GSE27921 |
Intragenic enhancers act as alternative promoters |
|
| Relations |
| BioSample |
SAMN02196927 |
