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Sample GSM1846543 Query DataSets for GSM1846543
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 SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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