|
| Status |
Public on Sep 03, 2021 |
| Title |
ChIP-Seq Person living with HIV sample 23, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library |
| Sample type |
SRA |
| |
|
| Source name |
bronchoalveolar lavage
|
| Organism |
Homo sapiens |
| Characteristics |
ethnicity: Caucasian
Sex: M
age: 33
medical.history: HIV (2017)
sexually transmitted infections: no
quantiferon tb reagent: no
cd4 count: 633
prescription drugs: Genvoya
active ingredient: Emtricitabine, Tenofovir_AF, Cobicistat, Elvitegravir
art start year: 2017
recreational drugs: cannabis
cigarette smoker: yes
bal sampling date: 2018/07/11
mtb challenged: no
fragments in clean bam: 1
|
| 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 ChIP-seq, AM were crosslinked with 1% w/v formaldehyde for 10 min and then sonicated to 150-500 bp using a S220 (Covaris).
ChIP-DNA was prepared using a manual chromatin immunoprecipitation method with an Antibody-Antigen for H3K27ac (Abcam, Ab4729, GR3211959-1). incubation of 18 hrs., followed by bead incubation for 135 minutes, and 6 x 5-minutes washing steps.
ATACseq libraries were prepared for sequencing using standard single end sequencing.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Person living with HIV sample 23, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library
|
| Data processing |
Fastq files were trimmed to remove adaptors and < phred 10 using cutadapt v2.6 with TrimGalore v0.6.5
Reads were aligned to the human genome (hg38) using BWA v0.7.17 default parameters. PICARD v2.18.9 was used to mark duplicates. Reads aligning to the mitochondrial genome were removed with samtools v1.9
alignmentSieve v3.3.2 was used to: (i) select unique single-end reads using the --samFlagExclude 1796; (ii) remove ENCODE hg38 blacklisted regions.
Peaks were called with MACS2 v2.2.6 callpeak was used with --call-summits with --shift -37 and --extsize 73 flags. 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 reads 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 reads 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 |
GPL24676 |
| Series (2) |
| GSE165705 |
Epigenetic impairment and blunted transcriptional response to Mycobacterium tuberculosis of alveolar macrophages from persons living with HIV (ChIP-Seq) |
| GSE165709 |
Epigenetic impairment and blunted transcriptional response to Mycobacterium tuberculosis of alveolar macrophages from persons living with HIV |
|
| Relations |
| BioSample |
SAMN17615437 |
| SRA |
SRX9969396 |
