 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Sep 29, 2014 |
| Title |
5metC_MCF7_ChIPSeq |
| Sample type |
SRA |
| |
|
| Source name |
Human breast cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: MCF7
chip antibody: 5metC
antibody vendor: Diagenode
antibody catalog#: Mab-006-100
|
| Growth protocol |
MCF7 and mCF10 human breast cells were plate and incubated during 72 hours in complete medium (DMEM high glucose GutaMAX life Technologies), then the medium was changed by cross-linking medium containing 1% folmaldehyde.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Performed with Illumina protocol. 10Ng of inmunoprecipitated DNA was end-repaired, and Illumina double stranded adapters for single read sequencing were ligated to the DNA. After purification of the sample with a MinElute spin column, we size-selected libraries on a 2% agarose gel and fragments corresponding to an insert size range of around 130bp were recovered. The libraries were finally amplified with an 18-cycle PCR reaction, and library quality was confirmed on the Agilent 2100 Bioanalyzer. The samples were loaded at concentrations of 8-11 pm onto Illumina single read flowcells and sequenced on the Illumina Genome Analyzer IIx using a 40 cycles recipe.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
Supplementary_files_format_and_content: Bedgraph files were generated from peak files built from reads mapping uniquely to the genome with at most 0,1,2 mismatches, using Pyicos (Althammer et al., 2011). Significant ChIP-Seq signal was calculated from the coverage of reads comparing each samples with its specific control sample. The significant peaks per sample in bedgraph format are the following: MCF10-HP1-CTRL.MA.pvalue.bedgraph, MCF7HP1-CTRL.MA.pvalue.bedgraph, 4B8-MCF10-CTRL.MA.pvalue.bedgraph, 4B8-MCF7-CTRL.MA.pvalue.bedgraph, MCF10-5metC-CTRL.MA.pvalue.bedgraph, MCF7-5metC-CTRL.MA.pvalue.bedgraph, MCF10-RNAPII-CTRL.MA.pvalue.bedgraph). AGO1 MCF7 Millipore significant peaks were calculated using Pyicos (Althammer et al., 2011).
|
| |
|
| Submission date |
Apr 15, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Eneritz Agirre |
| Organization name |
Karolinska Institutet
|
| Department |
MBB
|
| Lab |
Castelo-Branco, Molecular Neurobiology
|
| Street address |
Solnavägen 9
|
| City |
Stockholm |
| ZIP/Postal code |
17165 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL10999 |
| Series (2) |
| GSE56826 |
Argonaute-1 binds transcriptional enhancers and controls constitutive and alternative splicing in human cells |
| GSE60094 |
A chromatin code for alternative splicing involving an association between CTCF and HP1α proteins |
|
| Relations |
| BioSample |
SAMN02728383 |
| SRA |
SRX518254 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1369949_5meC_MCF7_ChIPSeq.BEDGRAPH.gz |
138.1 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
