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Status |
Public on Jun 27, 2019 |
Title |
R_BEN-015_S20_L002 |
Sample type |
SRA |
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Source name |
Whole blood
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Organism |
Homo sapiens |
Characteristics |
infected with/healthy control: juvenile idiopathic arthritis tissue: whole blood library name: BEN-015__S20
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Extracted molecule |
total RNA |
Extraction protocol |
Paxgene blood RNA extraction (pre-analytix): RNA extraction from blood, collected in Paxgene blood RNA tubes (Pre-analytix) Lexogen QuantSeq 3mRNA library preparation FWD kit
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NextSeq 500 |
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Description |
180321_NB501809_0276_AHJJ3LBGX5_readcounts.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. One output file containing counts is created for each SAM file. Genome_build: GRCh38 Supplementary_files_format_and_content: Format: tsv (tab-separated file); Content: raw read counts for each gene and sample/lane combination (genes as rows and sample/lane as columns). For example, sample 1 (AZT11_C_S34) was sequenced on four lanes from a single flow cell and resulted in the following files, each resulting in a separate column: AZT_16_C_S2_L001_R1_001.fastq.gz, AZT_16_C_S2_L002_R1_001.fastq.gz, AZT_16_C_S2_L003_R1_001.fastq.gz, AZT_16_C_S2_L004_R1_001.fastq.gz. One file is provided per sequencing run.
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Submission date |
Jun 26, 2019 |
Last update date |
Jun 30, 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) |
GSE133378 |
Diagnosing enterovirus meningitis via blood transcriptomics: an alternative for lumbar puncture? |
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Relations |
BioSample |
SAMN12143311 |
SRA |
SRX6368725 |
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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