NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2991952 Query DataSets for GSM2991952
Status Public on Feb 12, 2019
Title H1_EXP7_2
Sample type SRA
 
Source name Whole blood
Organism Homo sapiens
Characteristics subject id: H1
tissue: whole blood
sampling day: 7 (after vaccination)
repeat: 2
Treatment protocol Whole blood samples were collected in Paxgene Blood RNA tubes (PreAnalytiX), containing a lysis buffer and RNA stabilizator.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from the Paxgene-blood samples with the Paxgene RNA extraction kit (Qiagen) following the supplier instructions. To concentrate the RNA even more, the clean and concentrator-5 kit (Zymo Research) was used.
Libraries were prepared (following supplier instructions) with QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen GmbH).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description combined_lane_counts.txt
Data processing trimming of low quality bases. name: Trimmomatic, version: 0.36, parameters: -phred33 HEADCROP:20 SLIDINGWINDOW:4:15 MINLEN:30
removal of polyA tails. custom Perl script, removes polyA tails at the end of reads if the read ends with 7 or more As; also removes reads with length <= 20
read mapping. name: HISAT2, version: 2.0.4, parameters: -x GRCh38_noalt_h2, outputs SAM files
read counting. custom Python script, uses the Python library HTSeq to count how many reads map to each gene. Uses GCF_000001405.31_GRCh38.p5_genomic.gff as an annotation source. (https://ftp.ncbi.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCF_000001405.31_GRCh38.p5/GCF_000001405.31_GRCh38.p5_genomic.gff.gz). One output file containing counts is created for each SAM file.
combining read counts. custom Python script, sums up read counts across lanes for a given sample, then combines all samples (columns) into a single count file with genes as rows
Genome_build: GRCh38
Supplementary_files_format_and_content: format: tsv (tab-separated file); content: raw read counts per gene, combined from four sequencing lanes, for each sample (genes as rows and samples as columns). The file genes.txt provides a key to the gene IDs in "combined_lane_counts.txt".
 
Submission date Feb 12, 2018
Last update date Feb 12, 2019
Contact name Nicolas De Neuter
Organization name University of Antwerp
Street address Middelheimlaan 1
City Antwerpen
ZIP/Postal code 2020
Country Belgium
 
Platform ID GPL18573
Series (1)
GSE110480 Transcriptomic profiling following de novo hepatitis B vaccination reveals role of granulocytes in non-responders
Relations
BioSample SAMN08518766
SRA SRX3683177

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

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap