|
| Status |
Public on Nov 10, 2021 |
| Title |
Treated human monocytes, rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
Human monocytes
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Human monocytes
treatment: MV130
|
| Treatment protocol |
1.5E+6 human monocytes were plated in in 10 cm Petri dishes and stimulated at day 0 with MV130 (3.0E+6 bacteria/plate) or excipient. After 24 hours cells were washed and left resting for 5 days.
|
| Growth protocol |
Buffy coats from healthy volunteers were obtained from Andalusian Biobank. Human peripheral blood mononuclear cells (hPBMCs) were isolated by differential centrifugation using Biocoll Separating Solution and human monocytes were selected by adhesion.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
At day 5, human monocytes were detached and 50.000 cells were colleceted in ice-cold Flow cytometry buffer and immediately processed following a previously published protocol (Buenrostro et al, 2013). The transposition reaction was started by adding Nextera’s Tn5 Transposase in reaction buffer and mantained by incubation for 30 minutes at 37°C. DNA was purified using a Quiagen MinElute PCR purification kit.
ATAC-seq libraries were generated following Buenrostro et al (2013), purified using a PCR purification MinElute kit (Quiagen) and quantified using a 2100 Bioanalyzer instrument (Agilent). Finally, libraries were sequenced 2x50 in a paired end flowcell (PE) run on Illuminaa NextSeq 2000 System.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
NextSeq 2000 |
| |
|
| Data processing |
Illumina Casava software used for basecalling and bcl2fastq for demultiplexing.
Illumina and Nextera adapter contaminations were removed from reads using Cutadapt.
Processed reads were mapped against HG38 whole genome using bowtie2.
Alignments were filtered with samtools to retain only properly mapped, non duplicate reads, with mapping quality above 0, not aligning to unlocalized or unassembled contigs, the mitochondrial genome, or chromosome Y.
Peaks were called with MACS3, using parameters "--nomodel --shift -100 --extsize 200", and "-q 0.05" as the false discovery rate cut-off.
Genome_build: HG38
Supplementary_files_format_and_content: ENCODE narrow peak files (extended bed format) including coordinates, score and qvalue for ATAC-seq peaks, using MACS3.
|
| |
|
| Submission date |
Sep 05, 2021 |
| Last update date |
Nov 10, 2021 |
| Contact name |
Manuel J Gomez |
| E-mail(s) |
mjgomezr@cnic.es
|
| Organization name |
CNIC
|
| Lab |
Bioinformatics Unit
|
| Street address |
Melchor Fernández Almagro, 3
|
| City |
Madrid |
| State/province |
Madrid |
| ZIP/Postal code |
28029 |
| Country |
Spain |
| |
|
| Platform ID |
GPL30173 |
| Series (2) |
| GSE183485 |
ATAC-Seq based chromatin accessibilty profile of human monocytes treated with MV130 or its excipient |
| GSE183721 |
Trained immunity induction by the inactivated mucosal vaccine MV130 protects against experimental viral respiratory infections |
|
| Relations |
| BioSample |
SAMN21239478 |
| SRA |
SRX12020759 |
