|
| Status |
Public on Apr 01, 2021 |
| Title |
067-0 [lib37226] |
| Sample type |
SRA |
| |
|
| Source name |
Nasal Brush Epithelial Cell
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Nasal brush epithelial cells
age: 11 years
Sex: Male
site: UNBS4
atopy: Atopic
phenotypeage10: TW-LA
asthmaage10: No
total number of cells counted: 300
number of ciliated epithelial cells: 197
percent ciliated epithelial cells: 0.6567
number of non-ciliated epithelial cells: 0
percent non-ciliated epithelial cells: 0.0000
number of leukocytes: 103
percent leukocytes: 0.3433
fev1/fvc percent: 84.5
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were provided in RLT/1%BME; Dual RNA and DNA extraction (AllPrep Kit).
Reverse transcription was performed followed by PCR amplification to generate full length amplified cDNA. Sequencing libraries were constructed using the NexteraXT DNA sample preparation kit (Illumina) to generate Illumina-compatible barcoded libraries. Libraries were pooled and quantified using a Qubit® Fluorometer (Life Technologies).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
lib37226
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv
|
| 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 STAR aligner; 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, STAR, Samtools, and htseq-count.
Genome_build: GRCh38 release 91
Supplementary_files_format_and_content: P216-2_CD3JAANXX_190311_combined_counts.csv is a comma-separated value file. The first column contains Ensembl gene IDs. The remaining columns include raw read counts assigned for each library.
|
| |
|
| Submission date |
Feb 18, 2020 |
| Last update date |
Jan 03, 2024 |
| Contact name |
Stephanie Osmond |
| E-mail(s) |
sosmond@benaroyaresearch.org
|
| Organization name |
Benaroya Research Institute
|
| Street address |
1201 9th Ave
|
| City |
Seattle, |
| State/province |
WA |
| ZIP/Postal code |
98101 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE145505 |
Endotype of Allergic Asthma with Airway Obstruction in Urban Children |
|
| Relations |
| BioSample |
SAMN14130442 |
| SRA |
SRX7745203 |
