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Status |
Public on Feb 12, 2019 |
Title |
H10_EXP7_1 |
Sample type |
SRA |
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Source name |
Whole blood
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Organism |
Homo sapiens |
Characteristics |
subject id: H10 tissue: whole blood sampling day: 7 (after vaccination) repeat: 1
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Treatment protocol |
Whole blood samples were collected in Paxgene Blood RNA tubes (PreAnalytiX), containing a lysis buffer and RNA stabilizator.
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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).
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NextSeq 500 |
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Description |
combined_lane_counts.txt
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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".
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Submission date |
Feb 12, 2018 |
Last update date |
Feb 12, 2019 |
Contact name |
Nicolas De Neuter |
Organization name |
University of Antwerp
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Street address |
Middelheimlaan 1
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City |
Antwerpen |
ZIP/Postal code |
2020 |
Country |
Belgium |
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Platform ID |
GPL18573 |
Series (1) |
GSE110480 |
Transcriptomic profiling following de novo hepatitis B vaccination reveals role of granulocytes in non-responders |
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Relations |
BioSample |
SAMN08518760 |
SRA |
SRX3683182 |
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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