|
| Status |
Public on Nov 28, 2011 |
| Title |
Brain RNA |
| Sample type |
mixed |
| |
|
| Channel 1 |
| Source name |
Total RNA from E12.5 mouse brain
|
| Organism |
Mus musculus |
| Characteristics |
age: E12.5
developmental stage: embryo
tissue: Forebrain
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Presumptive digits and forebrains were dissected from E12.5 mouse embryos and stored in RNAlater reagent (Qiagen). For each replicate, RNA was extracted from pools of 8 autopods or 2 forebrains using RNeasy mini-kit (Qiagen).
|
| Label |
biotin
|
| Label protocol |
rRNA was depleted using RiboMinus Human/Mouse Transcriptome Isolation kit (Affymetrix). After cRNA amplification, double-stranded cDNA was generated using the GeneChip Whole Transcript Amplified Double-Stranded Target Assay kit (Affymetrix) according to manufacturer’s instructions. cDNA was fragmented and labeled using GeneChip WT Double-Stranded DNA Terminal Labeling Kit (Affymetrix). The control genomic DNA samples were fragmented with DNAse I.
|
| |
|
| Channel 2 |
| Source name |
genomic DNA from mouse kidney
|
| Organism |
Mus musculus |
| Characteristics |
age: 3 month
deveopmental stage: adult
tissue: kidney
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Presumptive digits and forebrains were dissected from E12.5 mouse embryos and stored in RNAlater reagent (Qiagen). For each replicate, RNA was extracted from pools of 8 autopods or 2 forebrains using RNeasy mini-kit (Qiagen).
|
| Label |
biotin
|
| Label protocol |
rRNA was depleted using RiboMinus Human/Mouse Transcriptome Isolation kit (Affymetrix). After cRNA amplification, double-stranded cDNA was generated using the GeneChip Whole Transcript Amplified Double-Stranded Target Assay kit (Affymetrix) according to manufacturer’s instructions. cDNA was fragmented and labeled using GeneChip WT Double-Stranded DNA Terminal Labeling Kit (Affymetrix). The control genomic DNA samples were fragmented with DNAse I.
|
| |
|
| |
| Hybridization protocol |
7μg of cDNA was hybridzed per array for 16 hours at 45° at 60rpm using the Affymetrix hybridization kit.
|
| Scan protocol |
Arrays were scanned on an Affymetrix Scanner 3000 7G
|
| Description |
Total RNA Forebrain, Biological Rep 1-2
|
| 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 80 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.
|
| |
|
| Submission date |
Aug 25, 2011 |
| Last update date |
Nov 28, 2011 |
| Contact name |
Thomas Montavon |
| Organization name |
EPFL
|
| Street address |
SV 2843, Station 19
|
| City |
Lausanne |
| ZIP/Postal code |
1015 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL14183 |
| Series (2) |
| GSE31656 |
Transcription landscape at the HoxD locus in developing limbs and brain |
| GSE31659 |
HoxD locus in the developing limb, digit, and brain |
|
