|
| Status |
Public on Jan 10, 2011 |
| Title |
mESC-Dicer_Null-3 |
| Sample type |
RNA |
| |
|
| Source name |
mESC
|
| Organism |
Mus musculus |
| Characteristics |
cell type: mESC
genotype: Dicer Null
genetic background: mixed 129/B6
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was collected using Trizol (Invitrogen) independently from three 10cm dishes of Dicer wild-type and Dicer null mESCs that were plated with 2E6 cells 48hrs prior to collection.
|
| Label |
biotin
|
| Label protocol |
Performed according to manufacturer's instructions (Affymetrix) for Affymetrix Mouse Exon 1.0 ST arrays.
|
| |
|
| Hybridization protocol |
Performed according to manufacturer's instructions (Affymetrix) for Affymetrix Mouse Exon 1.0 ST arrays.
|
| Scan protocol |
Affymetrix Gene ChIP Scanner 3000 7G; GeneChip® Command Console.
|
| Description |
Total RNA from Dicer Null mESCs
|
| Data processing |
Data were processed using Partek Genomics Suite 6.4 software. RMA was used to summarize and normalize the probe data into probe set expression values. The list of utilized probe sets was defined by custom .ps and .mps files designed to include all core probes and all probes targeting miRNA transcripts. The RMA procedure used included the options adjusted for GC content, probe sequence, RMA background correction, Quantile Normalization and median polish probe set summarization. Expression values for probesets were summarized to a single value per gene based on the same custom .mps file mentioned above using the outlier excluded mean method. This procedure excludes probe set values that are more than 3 standard deviations above the mean or more and 2 standard deviations below the mean. The log fold change (LFC) value for WT/Dcr_null was defined as the difference between the mean expression in Dicer WT mESCs (Dcr_WT) and the mean expression in Dicer null mESCs (Dcr_null).
MoEx-1_0-st-v1.r2.pgf
MoEx-1_0-st-v1.na25.mm9.core+miRNA.SH.11023.mps (Custom .mps file designed to include all core probes and all probes targeting miRNA transcripts ; mouse genome version mm9)
|
| |
|
| Submission date |
Jan 10, 2011 |
| Last update date |
Jan 10, 2011 |
| Contact name |
A Bhutkar |
| Organization name |
MIT
|
| Street address |
77 Massachusetts Avenue
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02139 |
| Country |
USA |
| |
|
| Platform ID |
GPL11410 |
| Series (1) |
| GSE25310 |
Genome-wide identification of Ago2 binding sites from mouse embryonic stem cells with and without mature microRNAs |
|
