 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Feb 12, 2019 |
| Title |
H1_EXP3_1 |
| Sample type |
SRA |
| |
|
| Source name |
Whole blood
|
| Organism |
Homo sapiens |
| Characteristics |
subject id: H1
tissue: whole blood
sampling day: 3 (after vaccination)
repeat: 1
|
| 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 |
SAMN08518764 |
| SRA |
SRX3683174 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
