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Sample GSM4002742 Query DataSets for GSM4002742
Status Public on Aug 02, 2020
Title RNA_AH21
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 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
Phone +3226509586
Organization name Université Libre de Bruxelles
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
BioSample SAMN12430319
SRA SRX6640555

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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