|
| Status |
Public on Dec 03, 2013 |
| Title |
Uninfected, rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
Macrophages, uninfected
|
| Organism |
Mus musculus |
| Characteristics |
cell type: macrophages
treatment: none
|
| 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 |
SAMN02324074 |
| SRA |
SRX337466 |
