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| Status |
Public on Apr 01, 2022 |
| Title |
ICOV1-007 |
| Sample type |
SRA |
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| Source name |
PBMC
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| Organism |
Homo sapiens |
| Characteristics |
cell type: Monocytes CD14+
disease state: Healthy
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
20 000 to 50 000 sorted CD14+ monocytes were collected in 1mL of RPMI media supplemented with 10% FCS at 4°C.Cells were centrifuged, then cell pellets were resuspended in 50 μL of lysis buffer (Tris HCl 10 mM, NaCl 10 mM, MgCl2 3 mM, Igepal 0,1%) and centrifuged (500 g) for 10 minutes at 4°C. Supernatant was discarded and nuclei were resuspended in 50 μL of reaction buffer (Tn5 transposase 2,5 μL, TD buffer 22,5 μL and 25 μL H2O – Nextera DNA sample preparation kit, Illumina). Tagmentation was performed for 30 minutes at 37°C. DNA was purified using the MinElute purification kit (QIAGEN).
Purified DNA was amplified and indexed by PCR using NEBNext High-Fidelity 2× PCR Master Mix (New England Biolabs) with 10-12 cycles. Llibraries were purified using MinElute PCR Purification Kit (Qiagen) and quality controlled using a Bioanalyzer High-Sensitivity DNA Analysis kit (Agilent).
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
Monocytes CD14+ Healthy
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| Data processing |
Adapters were removed with TrimmomaticPE with the following parameters : LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Reads were aligned to hg38 by Bowtie2 with the following parameters: –X 2000 –fr –very-sensitive –no-discordant –no-mixed –non-deterministic
Reads from the alignment were sorted and indexed according to chromosomes
Duplicate reads were filtered out using MarkDuplicate tool from Picard suite
Reads mapping within the blacklist of the ENCODE project were removed with a custom script and samtools view
Peak calling was performed with MACS2 callpeak, using standard parameters for paired-end reads and q-value threshold=0.05
Assembly: hg38
Supplementary files format and content: txt: peaks and fold change and p-value, bigwig: signal
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| Submission date |
Mar 09, 2022 |
| Last update date |
Apr 01, 2022 |
| Contact name |
Abdulkader AZOUZ |
| E-mail(s) |
Abdulkader.azouz@ulb.be
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| Organization name |
Université Libre de Bruxelles
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| Street address |
Rue Adrienne Bolland, 8
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| City |
GOSSELIES |
| ZIP/Postal code |
6041 |
| Country |
Belgium |
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| Platform ID |
GPL24676 |
| Series (2) |
| GSE198255 |
Functional reprogramming of monocytes in acute and convalescent severe COVID-19 patients [ATAC-seq] |
| GSE198257 |
Functional reprogramming of monocytes in acute and convalescent severe COVID-19 patients |
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| Relations |
| BioSample |
SAMN26543152 |
| SRA |
SRX14418922 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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