|
| Status |
Public on Jul 05, 2024 |
| Title |
Sample20 |
| Sample type |
SRA |
| |
|
| Source name |
Nasal-epithelial
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Nasal-epithelial
vape 6mo_lab: Did_Not_Vape_in_Last_6_Months
Sex: Female
age (yrs): 14
ruv k1: -0.0460018085438091
ruv k2: 0.155375132867788
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the Qiagen RNeasy Mini Kit (Qiagen, Valencia, CA) and sequenced using Illumina chemistry (Nugen Universal Plus mRNASEQ kit [Redwood City, CA]; NovaSeq6000 [Illumina: San Diego, CA]) through the Genomics and Microarray Core at the University of Colorado Anschutz Medical Campus.
Sequencing libraries will be prepared using the standard TruSeq RNA Sample Prep Kit v2 Protocol (Illumina, San Diego, CA).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
examined the quality of the sequencing reads (FastQC) and removed adaptors and low quality base calls (Cutadapt).
Sequences were aligned to the human genome (GENCODE GRCh37)
Read counts overlapping each gene were reported using STAR
Removed genes detected with 0 reads in greater than or equal to 75% of samples or with a range of reads less than or equal to 100.
Corrected for unwanted technical effects using two normalization factors estimated using Removal of Unwanted Variance using Residuals (RUVr) using RUVSeq (ver.
Assembly: GENCODE GRCh37
Supplementary files format and content: Filename: seq_express_filter.csv; Format: Raw gene counts aligned to the genome and filtered to remove those with 0 reads in greater than or equal to 75% of samples or with a range of reads less than or equal to 100.
Supplementary files format and content: Filename: seq_express_norm.csv; Format: Normalized gene counts from DESeq2 Model adjusting for vape status, age, sex, recruitment center, and two normalization (RUVr) factors.
|
| |
|
| Submission date |
Jul 25, 2023 |
| Last update date |
Jul 05, 2024 |
| Contact name |
Sunita Sharma |
| E-mail(s) |
sunita.sharma@cuanschutz.edu
|
| Organization name |
University of Colorado - Anschutz Medical Campus
|
| Department |
Anschutz Campus - Sch of Med - Pulmonary Sciences
|
| Street address |
13001 East 17th Place
|
| City |
Aurora |
| State/province |
CO |
| ZIP/Postal code |
80045 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE238235 |
The impact of vaping on adolescent lung function and nasal epithelial gene expression [RNA-seq] |
| GSE240132 |
The impact of vaping on adolescent lung function and nasal epithelial gene expression |
|
| Relations |
| BioSample |
SAMN36704293 |
| SRA |
SRX21155577 |
