|
| Status |
Public on Aug 02, 2020 |
| Title |
ATAC_AH49 |
| Sample type |
SRA |
| |
|
| Source name |
monocytes from human donnor with Severe Alcoholic Hepatitis
|
| Organism |
Homo sapiens |
| Characteristics |
subject status: Severe Alcoholic Hepatitis
tissue: Peripheral Blood
cell type: monocyte CD14+
|
| Growth protocol |
PBMCs were isolated from sodium-heparinised whole blood by Ficoll and 10-20 million PBMCs were frozen in FBS with 20% DMSO in liquid nitrogen. PBMCs were thawed and CD14hi monocytes were isolated by fluorescence-activated cells sorting (FACS) on a BD FACS Aria III
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
20000 to 50000 sorted monocytes were washed with cold PBS and resuspended in cold lysis buffer (10 mM Tris·Cl, pH 7.4, 10 mM NaCl,3 mM MgCl2, 0.1% (v/v) Igepal CA-630).
Nuclei were subject to transposition reaction in 1x TD Buffer containing 2.5 μl transposase Nextera enzyme and DNA was purified. Purified DNA was amplified by PCR with 10-12 cycles. Amplified libraries were purified and quality controlled.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
ATAC-seq in liver monocytes from human donnor with Severe Alcoholic Hepatitis
|
| Data processing |
Adapters were removed with Trimmomatic-0.36 with the following parameters : Nextera1.fa:1:25:6 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Reads were aligned to GRCh38 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 chromosome positions
Duplicate reads were filtered out using MarkDuplicate tool from Picard suite
Reads mapping in chrM 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
Genome_build: GRCh38
Supplementary_files_format_and_content: Bed: peaks ; bigwig: signal
|
| |
|
| Submission date |
Aug 02, 2019 |
| Last update date |
Aug 03, 2020 |
| Contact name |
Stanislas Goriely |
| E-mail(s) |
stgoriel@ulb.ac.be
|
| Phone |
+3226509586
|
| Organization name |
Université Libre de Bruxelles
|
| Lab |
IMI
|
| Street address |
Rue Adrienne Bolland 8
|
| City |
Gosselies |
| ZIP/Postal code |
B-6041 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE135284 |
Epigenetic basis for monocyte dysfunction in acute-on-chronic liver failure and alcoholic hepatitis [ATAC-seq] |
| GSE135286 |
Epigenetic basis for monocyte dysfunction in acute-on-chronic liver failure and alcoholic hepatitis |
|
| Relations |
| BioSample |
SAMN12430308 |
| SRA |
SRX6640541 |
