|
| Status |
Public on Aug 02, 2020 |
| Title |
RNA_AH37 |
| Sample type |
SRA |
| |
|
| Source name |
monocytes from human donnor with Severe Alcoholic Hepatitis
|
| Organism |
Homo sapiens |
| Characteristics |
condition: Severe Alcoholic Hepatitis
tissue: Peripheral Blood
cell type: monocyte CD14+
|
| Treatment protocol |
None
|
| 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 |
total RNA |
| Extraction protocol |
80000 to 100,000 CD14hi monocytes were isolated by FACS in RLT buffer and flash frozen. RNA extraction was performed using a RNeasy kit (Qiagen) and sample quality was tested on a 2100 Bioanalyzer (Agilent).
Truseq stranded mRNA Library preparation kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
RNA-seq in liver monocytes from human donnor with Severe Alcoholic Hepatitis
|
| Data processing |
Adapters were removed with Trimmomatic-0.36 with the following parameters : Truseq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 HEADCROP:4
Annotation file Mus_musculus.GRCh38.90.gtf was obtained from the ftp.Ensembl.org server
Reads were aligned to GRCh38 by STAR_2.5.3a
Reads from the alignment were sorted and indexed according to chromosome positions
Duplicated reads were removed by using MarkDuplicates command from Picard tools.
Read counts in the alignment BAM-files that overlap with the gene features were obtained using HTSeq-0.9.1
Genes with no raw read count >=20 in at least 1 sample were filtered out with an R script
Raw read counts were normalized and differential expression analysis was performed with DESeq2 by applying a corrected p value FDR<0.05 and absolute log2-ratio larger than 1.
Genome_build: GRCh38
Supplementary_files_format_and_content: Excel file containing normalized reads counts and differential expression analysis results and tab-delimited text files containing normalized read counts (such as total read count=20M) for each sample and gene
|
| |
|
| Submission date |
Aug 02, 2019 |
| Last update date |
Aug 02, 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) |
| GSE135285 |
Epigenetic basis for monocyte dysfunction in acute-on-chronic liver failure and alcoholic hepatitis [RNA-seq] |
| GSE135286 |
Epigenetic basis for monocyte dysfunction in acute-on-chronic liver failure and alcoholic hepatitis |
|
| Relations |
| BioSample |
SAMN12430318 |
| SRA |
SRX6640556 |
