|
| Status |
Public on Sep 03, 2021 |
| Title |
ATAC-Seq Person living with HIV sample 4, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library |
| Sample type |
SRA |
| |
|
| Source name |
bronchoalveolar lavage
|
| Organism |
Homo sapiens |
| Characteristics |
ethnicity: Caucasian
Sex: M
age: 56
medical.history: HIV (2002)
sexually transmitted infections: no
quantiferon tb reagent: no
cd4 count: 1172
prescription drugs: Biktarvy
active ingredient: Emtricitabine, Tenofovir_AF, Bictegravir
art start year: 2002
recreational drugs: cannabis
cigarette smoker: yes
bal sampling date: 2019/12/04
mtb challenged: no
average tagmented library size: 1245
fragments in clean bam: 43512856
sequencing run: 6
lane: 1,2
|
| 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 |
genomic DNA |
| Extraction protocol |
Cells were lysed with Trizol and kept at -80°C until extraction. For ATAC-seq, 50,000 cell were isolated and incubated with Tn5 transposase for DNA tagmentation. The fragment length distribution was assessed with the Agilent 2100 Bioanalyzer.
ATACseq libraries were prepared for sequencing using standard paired end sequencing.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Person living with HIV sample 4, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library
Tn5 transposase
|
| Data processing |
Fastq files were trimmed to remove nextera adaptors and < phred 10 using cutadapt v2.6 with TrimGalore v0.6.5
Reads were aligned to both human (hg38) and Mtb (H37rv) genomes using BWA v0.7.17 default parameters. PICARD v2.18.9 was used to mark duplicates and to assess the fragment length distribution. Reads aligning to the mitochondrial genome were removed with samtools v1.9
alignmentSieve v3.3.2 was used to: (i) select unique paired-end reads using the --samFlagExclude 1804; (ii) remove ENCODE hg38 blacklisted regions; and (iii) to extract fragments between 40 – 2000bp in length
Peaks were called with MACS2 v2.2.6 callpeak was used with --call-summits in BAMPE mode. The summit of each peak was extended 250bp in both directions resulting in fixed-width peaks of exactly 501bp. Fiixed-width peaks overlapping in at least two samples were merged with bedtools v2.26
featureCounts v1.6.3 was used to count the number of unique fragments overlapping the targeted regions.
Libray depth and was calculated via calcNormFactors in edgeR v3.26.8 and used by limma’s voom function (v3.40.6) to generate the normalized log2(CPM) expression matrix.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files including the number of fragmentes overlaping assessed peaks for each sample.
Supplementary_files_format_and_content: tab-delimited matrix table with normalized peak quantification in log2 scale for every sample. 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) |
| GSE165703 |
Epigenetic impairment and blunted transcriptional response to Mycobacterium tuberculosis of alveolar macrophages from persons living with HIV (ATAC-Seq) |
| GSE165709 |
Epigenetic impairment and blunted transcriptional response to Mycobacterium tuberculosis of alveolar macrophages from persons living with HIV |
|
| Relations |
| BioSample |
SAMN17615469 |
| SRA |
SRX9969347 |
