|
| Status |
Public on Jun 01, 2014 |
| Title |
GHP7/9_H3K4me2_rep1 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
wildtype female XEN cells H3K4me2 ChIP DNA
|
| Organism |
Mus musculus |
| Characteristics |
strain: Htz 129/129.Pgk1a
genotype/variation: XHprt-/XWT
gender: female
cell type: Extra-embryonic endoderm Stem cells isolated from E3.5 blastocysts
chip antibody: H3K4me2
chip antibody vendor: Abcam
chip antibody cat. #: ab7766
|
| Treatment protocol |
No treatment
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin was fixed in 1% formaldehyde for 10 min, sheared to 200-700 bp using a Bioruptor (Diagenode). It was immunoprecipitated using the indicated antibody. Genomic DNA was isolated from the precipitated material as well as from the sheared chromatin input by phenol extraction and ethanol precipitation. The ChIP material was amplified using whole genome amplification (WGA-2, SIGMA). For detailed protocol see (Navarro et al., Genes Dev, 2005).
|
| Label |
Cy3
|
| Label protocol |
Labelling was performed by NimbleGen using 4 ug of ChIP DNA and 4 ug of Input DNA (http://www.nimblegen.com/products/chip/tutorial.html)
|
| |
|
| Channel 2 |
| Source name |
input DNA from wildtype female XEN cells H3K4me2 ChIP DNA
|
| Organism |
Mus musculus |
| Characteristics |
strain: Htz 129/129.Pgk1a
genotype/variation: XHprt-/XWT
cell type: Extra-embryonic endoderm Stem cells isolated from E3.5 blastocysts
chip antibody: none, input DNA
|
| Treatment protocol |
No treatment
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin was fixed in 1% formaldehyde for 10 min, sheared to 200-700 bp using a Bioruptor (Diagenode). It was immunoprecipitated using the indicated antibody. Genomic DNA was isolated from the precipitated material as well as from the sheared chromatin input by phenol extraction and ethanol precipitation. The ChIP material was amplified using whole genome amplification (WGA-2, SIGMA). For detailed protocol see (Navarro et al., Genes Dev, 2005).
|
| Label |
Cy5
|
| Label protocol |
Labelling was performed by NimbleGen using 4 ug of ChIP DNA and 4 ug of Input DNA (http://www.nimblegen.com/products/chip/tutorial.html)
|
| |
|
| |
| Hybridization protocol |
Hybridisation was performed by NimbleGen (http://www.nimblegen.com/products/chip/)
|
| Scan protocol |
Scanning was performed by NimbleGen (http://www.nimblegen.com/products/chip/)
|
| Description |
Sample 13
|
| Data processing |
Reproducibility and quality control of the data were assessed using the “R” software combined with an algorithm especially developed for ChIP-on-Chip data analysis of histone modifications (http://www.epigenome-noe.net/WWW/researchtools/protocol.php?protid=43). Briefly, the global hybridisation patterns across each array were controlled by MA-plotting of all the probe signals on the array and by calculating the Pearson correlation coefficients between pairs of replicates (all the coefficients were > 0.8). The two replicates showing the highest Pearson correlation coefficient were used for further analysis. We applied a Lowess normalisation to each dataset and the 'SAM' algorithms to determined statistically enriched probe (Tusher et al., PNAS, 2001). A VSN (variance stabilization) normalisation of each array was also performed independently, then a SAM algorithm and a lfdr > 0,2 (local false discovery rate probability test) to determine the significance of enrichment of each probel were applied (data not included in this submission but available upon request).
|
| |
|
| Submission date |
Sep 04, 2013 |
| Last update date |
Jun 01, 2014 |
| Contact name |
Celine Morey |
| E-mail(s) |
[email protected]
|
| Phone |
+33 1 57278930
|
| Organization name |
UMR7216-Epigenetics and stem cell
|
| Department |
University Paris 7
|
| Lab |
Non-coding RNAs, differentiation and development
|
| Street address |
35 rue Hélène Brion
|
| City |
Paris |
| ZIP/Postal code |
75013 |
| Country |
France |
| |
|
| Platform ID |
GPL14676 |
| Series (1) |
| GSE50587 |
H3K27me3 and H3K4me2 profiles along the length of the X chromosome in trophoblast stem (TS) cells and Extra-embryonic endoderm stem cells (XEN), ChIP-chip |
|
