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| Status |
Public on Nov 28, 2011 |
| Title |
Brain H3K4me1 |
| Sample type |
genomic |
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| Channel 1 |
| Source name |
H3K4me1 ChIP DNA from E12.5 mouse brain
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| Organism |
Mus musculus |
| Characteristics |
age: E12.5
developmental stage: embryo
tissue: Forebrain
antibody: H3K4me1
antibody manufacturer: Abcam
antibody catalog number: ab8895
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Presumptive digits and forebrains were dissected from E12.5 mouse embryos, fixed in 1% formaldehyde for 15 minutes at room temperature, washed three times with cold phosphate buffer solution (PBS) and stored at -80°C. Pools of 16 autopods or 2 forebrains were used for each experiment. ChIP was performed according to (Lee et al., 2006) using 2 μg of anti-H3K4me3 (ab8580, Abcam), H3K27me3 (17-622, Millipore), H3K4me1 (ab8895, Abcam), H3K27Ac (ab4729, Abcam), or RNAPII (8WG16, Covance) antibodies, and EZview Red protein G/A Affinity Gel (Sigma). Immunoprecipitated and whole cell extract DNA (input) were treated with RNAseA, proteinase K and purified by two rounds of extraction with phenol/chloroform/isoamyl alcohol. ChIP and input DNA were amplified using ligation-mediated PCR (Lee et al. 2006).
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| Label |
biotin
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| Label protocol |
1 ug of ChIP and input DNA was fragmented and labeled using GeneChip WT Double-Stranded DNA Terminal Labeling Kit (Affymetrix).
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| Channel 2 |
| Source name |
Input DNA from E12.5 mouse limbs
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| Organism |
Mus musculus |
| Characteristics |
age: E12.5
developmental stage: embryo
tissue: Forelimb/ autopod
antibody: none
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Presumptive digits and forebrains were dissected from E12.5 mouse embryos, fixed in 1% formaldehyde for 15 minutes at room temperature, washed three times with cold phosphate buffer solution (PBS) and stored at -80°C. Pools of 16 autopods or 2 forebrains were used for each experiment. ChIP was performed according to (Lee et al., 2006) using 2 μg of anti-H3K4me3 (ab8580, Abcam), H3K27me3 (17-622, Millipore), H3K4me1 (ab8895, Abcam), H3K27Ac (ab4729, Abcam), or RNAPII (8WG16, Covance) antibodies, and EZview Red protein G/A Affinity Gel (Sigma). Immunoprecipitated and whole cell extract DNA (input) were treated with RNAseA, proteinase K and purified by two rounds of extraction with phenol/chloroform/isoamyl alcohol. ChIP and input DNA were amplified using ligation-mediated PCR (Lee et al. 2006).
|
| Label |
biotin
|
| Label protocol |
1 ug of ChIP and input DNA was fragmented and labeled using GeneChip WT Double-Stranded DNA Terminal Labeling Kit (Affymetrix).
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| Hybridization protocol |
1μg of DNA was hybridzed per array for 16 hours at 45° at 60rpm using the Affymetrix hybridization kit.
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| Scan protocol |
Arrays were scanned on an Affymetrix Scanner 3000 7G
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| Description |
H3K4me1 ChIP Brain, Biological Rep 1-2
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| Data processing |
Data were quantile normalized within ChIP/input replicate groups and scaled to medial feature intensity of 100 using TAS software (Affymetrix). For each genomic position, a data set was generated consisting of all (PM-MM) pairs mapping within a sliding window of 250 bp.
signal.bar and pvalue.bar are generated by TAS software (Affymetrix). signal.bar contains log2(IP/Input) fold changes for each probe in a region 2*sliding window+1. pvalue.bar contains -10log10 (IP/Input) for each probe in a region 2*sliding window+1.
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| Submission date |
Aug 25, 2011 |
| Last update date |
Nov 28, 2011 |
| Contact name |
Thomas Montavon |
| Organization name |
EPFL
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| Street address |
SV 2843, Station 19
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| City |
Lausanne |
| ZIP/Postal code |
1015 |
| Country |
Switzerland |
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| Platform ID |
GPL14183 |
| Series (2) |
| GSE31654 |
Chromatin landscape at the HoxD locus in developing digits and forebrain |
| GSE31659 |
HoxD locus in the developing limb, digit, and brain |
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| Supplementary file |
Size |
Download |
File type/resource |
| GSM786023_Brain_H3K4me1_1+2_pvalue.bar.gz |
457.8 Kb |
(ftp)(http) |
BAR |
| GSM786023_Brain_H3K4me1_1+2_signal.bar.gz |
263.8 Kb |
(ftp)(http) |
BAR |
| GSM786023_Brain_H3K4me1_1.CEL.gz |
569.0 Kb |
(ftp)(http) |
CEL |
| GSM786023_Brain_H3K4me1_2.CEL.gz |
595.2 Kb |
(ftp)(http) |
CEL |
| GSM786023_Input_1.CEL.gz |
539.6 Kb |
(ftp)(http) |
CEL |
| GSM786023_Input_2.CEL.gz |
545.9 Kb |
(ftp)(http) |
CEL |
| Processed data provided as supplementary file |
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