|
| Status |
Public on Mar 01, 2016 |
| Title |
C1 |
| Sample type |
SRA |
| |
|
| Source name |
Uninfected BMDMs
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57Bl/6
tissue: bone marrow derived macrophages (BMDMs)
m.tb strain: None
infection period: N/A
m.tb culturing coonditions: N/A
|
| Treatment protocol |
On day 7, BMDMs were infected with either R5527 or R1507 M.tb for 12 hours
|
| Growth protocol |
BMDMs were allowed 7 days to differentiate prior to infection with M.tb.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
BMDM RNA was extracted using the RNeasy® Plus Mini Kit and mRNA enrichment was performed using the Dynabeads® mRNA DIRECT™ Kit (Cat. No. 61012, Ambion, Life Technologies, Oslo, Norway)
AB Library Builder™ Whole Transcriptome Core Kit for 5500 Genetic Analysis Systems (Cat. No. 4472690, Applied Biosystems, Life Technologies), SOLiD® EZ Bead™ System (Cat. No. 4448419, Applied Biosystems, Life Technologies)
Paired end (75/35)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
AB 5500xl Genetic Analyzer |
| |
|
| Description |
Differentiated to macrophages using L-CSF
|
| Data processing |
Basecalling by SOLiD
Mapped using Lifescope, export .BAM files for mapped reads
Quantified to transcriptome in Partek (EM method)
Differential expression, Normalise RPKM, (Gene Specific Analysis- Partek), read count of 0 reset to 1.0E-4
Filer for data with FDR<0.05 and fold change >|2| Remove genes with less than 60 reads
Genome_build: Mus Musculus mm10
Supplementary_files_format_and_content: text files containing unfiltered gene counts and RPKM values
|
| |
|
| Submission date |
Feb 26, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Abhilasha Madhvi |
| Organization name |
Stellenbosch University
|
| Street address |
Francie van Zijl Drive. Tygerberg
|
| City |
Bellville |
| State/province |
Western Cape |
| ZIP/Postal code |
7505 |
| Country |
South Africa |
| |
|
| Platform ID |
GPL15907 |
| Series (1) |
| GSE78706 |
RNAseq Reveals Virulence-Specific Host Responses to M. tuberculosis infection |
|
| Relations |
| BioSample |
SAMN04517743 |
| SRA |
SRX1602206 |
