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Sample GSM1213156 Query DataSets for GSM1213156
Status Public on Dec 03, 2013
Title WT Mtb-infected, rep 2
Sample type SRA
 
Source name Macrophages, infected with WT Mtb
Organism Mus musculus
Characteristics cell type: macrophages
treatment: infected with wild-type Mycobacterium tuberculosis
Treatment protocol Uninfected, or infected with WT or rv0431 mutant Mycobacterium tuberculosis (Mtb).
Extracted molecule total RNA
Extraction protocol Cells were lysed with Trizol, and RNA was extracted with a kit from Qiagen.
cDNA libraries were synthesized following the protocol of Illumina Inc. (San Diego) and sequenced on an Illumina GA2x SR40.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer IIx
 
Data processing Illumina Casava1.8 software was used for basecalling.
Sequence reads were aligned to RefSeq transcripts (mm9) using BWA with default parameters.
RPKMs were calculated as described in Mortazavi et al., 2008 (PMID 18516045).
Genome_build: MGSCv37
Supplementary_files_format_and_content: Tab-delimited text file containing RPKM values for each RefSeq transcript.
 
Submission date Aug 20, 2013
Last update date May 15, 2019
Contact name Olivier Elemento
E-mail(s) ole2001@med.cornell.edu
Organization name WEILL MEDICAL COLLEGE OF CORNELL UNIV
Street address 1305 York Avenue
City New York
State/province NY
ZIP/Postal code 10021
Country USA
 
Platform ID GPL11002
Series (1)
GSE50050 A Novel Gene Regulates Vesiculogenesis and Immunomodulation in Mycobacterium tuberculosis
Relations
BioSample SAMN02324076
SRA SRX337468

Supplementary file Size Download File type/resource
GSM1213156_WT-2_RPKM.txt.gz 164.3 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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