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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jun 27, 2019 |
| Title |
R_BEN-011_S18_L002 |
| Sample type |
SRA |
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| Source name |
Whole blood
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| Organism |
Homo sapiens |
| Characteristics |
infected with/healthy control: systemic onset juvenile arthritis
tissue: whole blood
library name: BEN-011__S18
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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 |
SAMN12143275 |
| SRA |
SRX6368713 |
| 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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