 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Feb 02, 2016 |
| Title |
ADAR2_NULL_IFN_REP2 |
| Sample type |
SRA |
| |
|
| Source name |
ADAR2_NULL_IFN
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Mouse Embryonic Fibroblasts
genotype: ADAR2_NULL
replicate: Rep2
treatment: interferon
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from cells
Libraries were prepared by pooling all of the PCR products for a particular sample and barcoding them uniquely using a 15 cycle PCR reaction.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina MiSeq |
| |
|
| Data processing |
Library strategy: mmPCR-seq
Paired-end sequencing reads were combined and mapped as single-end reads onto a combination of the mm9 genome and exonic sequences surrounding known splicing junctions using BWA samse.
We used samtools mpileup to count the number of 'A' and 'G' reads at each editing site to calculate the editing levels.
Genome_build: mm9
Supplementary_files_format_and_content: The processed data files contain editing level measurements. The columns are formatted: editing site chromosome, editing site position, editing site gene, editing site strand, editing site annotation1, editing site annotation2, sequencing coverage, number of edited reads, editing level.
|
| |
|
| Submission date |
Aug 07, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Gokul Ramaswami |
| E-mail(s) |
gokulr@stanford.edu
|
| Organization name |
Stanford University
|
| Street address |
300 Pasteur Drive Alway M305
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL16417 |
| Series (1) |
| GSE71834 |
Quantification of RNA editing in MEF cells of different genetic backgrounds with and without interferon treatment |
|
| Relations |
| SRA |
SRX1136507 |
| BioSample |
SAMN03980153 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1846543_ADAR2_NULL_IFN_2_EditLevels_fixed.txt.gz |
303.5 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
