|
| Status |
Public on Sep 03, 2021 |
| Title |
RNA-Seq Person living with HIV sample 20, Alveolar macrophage, Mycobacterium tuberculosis challenged library |
| Sample type |
SRA |
| |
|
| Source name |
bronchoalveolar lavage
|
| Organism |
Homo sapiens |
| Characteristics |
ethnicity: Caucasian
Sex: M
age: 58
medical.history: HIV (1997)
sexually transmitted infections: no
quantiferon tb reagent: no
cd4 count: 727
viral load: not detected
prescription drugs: Truvada, Tybost, Prezista
active ingredient: Emtricitabine, Tenofovir_DF, Cobiscistat, Darunavir
art start year: 1997
recreational drugs: cannabis
cigarette smoker: no
bal sampling date: 2018/05/30
mtb challenged: yes
rin: 8.9
average library size: 317
sequencing run: centre1_batch3
lane: L1
|
| Treatment protocol |
Bronchoalveolar lavage samples were filtered to remove macro contaminants and alveolar macrophages (AM) cells enrich via tube adhesion method. 1 x 106 AM cells were cultured with media (not challenged) or media + Mtb (challenged) for 20h.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were lysed with Trizol and kept at -80°C until extraction. RNA isolation was performed with miRNeasy kit and RNA integrity (RIN) was assessed with the Agilent 2100 Bioanalyzer.
RNA libraries were prepared for sequencing using standard unstrand Illumina protocols (TruSeq RNA Library Preparation Kit v2, Set A ).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Person living with HIV sample 20, Alveolar macrophage, Mycobacterium tuberculosis challenged library
mRNA, poly-A selected
PLWH.AMV20.MTB.1_RNA_R1_quant.sf
|
| Data processing |
Basecalling was done with Illumina Casava 1.8.2 and fastq files generated via bcl2fastq v2.18.
Fastq files were trimmed to remove leftover adaptor sequences and < phred 20 bases using cutadapt v2.6.
Read alignment was performed with STAR v2.7.3a and resulting alignments in transcriptomic coordinates was input to Salmon v1.1.0 for gene expression estimation.
Gene level estimated counts matrix was created in R v3.6.1, using tximport v1.12.3 with the option “lengthScaledTPM”.
Libray depth and compositional bias scaling factors were calculated via the function calcNormFactors from edgeR v3.26.8 and used by limma’s voom function (v3.40.6) to generate the normalized log2(CPM) expression matrix.
Genome_build: GRCh38.p13 (ENSEMBL v99)
Supplementary_files_format_and_content: tab-delimited text files including transcript estimated counts and TPM values for each sample.
Supplementary_files_format_and_content: tab-delimited matrix table with raw estimated gene counts for every gene and sample (lengthScaledTPM).
Supplementary_files_format_and_content: tab-delimited matrix table with normalized gene expression in log2 scale for tested genes (created with limma's voom function). Covariates not regressed out.
|
| |
|
| Submission date |
Jan 28, 2021 |
| Last update date |
Sep 03, 2021 |
| Contact name |
Erwin Schurr |
| E-mail(s) |
erwin.schurr@mcgill.ca
|
| Organization name |
McGill University Health Centre
|
| Street address |
1001 boulevard Decarie
|
| City |
Montreal |
| ZIP/Postal code |
H4A 3J1 |
| Country |
Canada |
| |
|
| Platform ID |
GPL20301 |
| Series (2) |
| GSE165708 |
Epigenetic impairment and blunted transcriptional response to Mycobacterium tuberculosis of alveolar macrophages from persons living with HIV (RNA-Seq) |
| GSE165709 |
Epigenetic impairment and blunted transcriptional response to Mycobacterium tuberculosis of alveolar macrophages from persons living with HIV |
|
| Relations |
| BioSample |
SAMN17615578 |
| SRA |
SRX9969469 |
