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| Status |
Public on Apr 08, 2019 |
| Title |
lib15336_CAJMRANXX |
| Sample type |
SRA |
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| Source name |
SUB195211
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Nasal Lavage
flowcell: CAJMRANXX
used in analaysis: Yes
age.in.years: 11
Sex: M
analysis.visit: Visit 1a
case.or.control.status.matched: Control
case.or.control.status.original: Control
viral.type.at.visit: Viral
hrv.type.at.visit: RV-Cpat28
virus.type.ev.hrv: Yes
virus.type.adv: No
virus.type.boca: No
virus.type.rsv.a: No
virus.type.rsv.b: No
virus.type.cov.hku1: No
virus.type.cov.nl63: No
virus.type.piv.1: No
virus.type.piv.4: No
virus.type.mpv: No
virus.type.piv.2: No
virus.type.piv.3: No
virus.type.flu.b: No
virus.type.cov.229e: No
nasal.neutrophil.percentage: 78.21
nasal.lymphocyte.percentage: 1.98
nasal.eosinophil.percentage: 5.94
nasal.macrophage.percentage: 12.87
nasal.wbc.percentage: 99
nasal.epithelial.percentage: 0
nasal.squamous.percentage: 1
nasal.epi.squa.percentage: 1
libcounts: 10.951106
mediancvcoverage: 0.513174
percentaligned: 0.932457754
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from TRIzol following the manufacturer’s protocol (Invitrogen)
RNA quality was assessed using RNA electrophoresis (Agilent). All samples had RIN values ≥7. Sequencing libraries were constructed from total RNA using TruSeq RNA Sample Preparation Kits v2 (Illumina)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
100017157_S22_L001
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| Data processing |
Base-calling was performed using CASAVA v.1.8.2.
FASTQ reads were trimmed using fastq-mcf (ea-utils, v.1.1.2) to remove SMARTer adapter sequences.
Reads were aligned in Galaxy using bowtie and TopHat (Tophat for Illumina tool, v.1.5.0); duplicate alignments were marked and removed using Picard MarkDuplicates.
Read counts per Ensembl gene ID were estimated in Galaxy using htseq-count (htseq-count tool, v.0.4.1).
Sequencing, alignment, and quantitation metrics were obtained for FASTQ, BAM/SAM, and count files in Galaxy using FastQC, Picard, TopHat, Samtools, and htseq-count.
Genome_build: GRCh37
Supplementary_files_format_and_content: raw_counts_nasal_muppits500.txt is a tab-delimited matrix. The first column contains Ensembl gene IDs The remaining columns include raw read counts assigned for each library. Outlier samples have been removed but data have not been gene filtered or normalized.
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| Submission date |
Jun 13, 2018 |
| Last update date |
Jan 03, 2024 |
| Contact name |
Stephanie Osmond |
| E-mail(s) |
sosmond@benaroyaresearch.org
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| Organization name |
Benaroya Research Institute
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| Street address |
1201 9th Ave
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| City |
Seattle, |
| State/province |
WA |
| ZIP/Postal code |
98101 |
| Country |
USA |
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| Platform ID |
GPL16791 |
| Series (2) |
| GSE115770 |
A network of transcriptome modules demonstrates mechanistic pathways of both virus induced and non-viral asthma exacerbations in children [nasal] |
| GSE115824 |
A network of transcriptome modules demonstrates mechanistic pathways of both virus induced and non-viral asthma exacerbations in children |
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| Relations |
| BioSample |
SAMN09407660 |
| SRA |
SRX4212443 |
| 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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