|
| Status |
Public on Sep 12, 2023 |
| Title |
K107623 |
| Sample type |
SRA |
| |
|
| Source name |
normal breast tissue core
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: normal breast tissue core
gender: female
age: 61
bmi: 33.7
racial background: WHITE
tyrer-cuzick lifetime_risk_score: 23.4
|
| Growth protocol |
Breast tissue biospies are collected using a vacuum-assisted breast biopsy system (ATEC, Hologic) and fresh frozen whitin 10 min.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the Allprep DNA/RNA/miRNA Universal Kit (QIAGEN, Germantown, MD).
The concentration and quality of total RNA samples were first assessed using Agilent 2100 Bioanalyzer. Then cDNA library was prepared using the KAPA RNA HyperPrep kit (Roche, Wilmington, MA) on a BiomeK Automated worstation (Beckman coulter, Indianapolis, IN)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
normal breast tissue core
|
| Data processing |
The raw RNA-seq reads were cleaned using Trimmomatic version 0.36 (Bolger et al. 2014) setting the cutoff threshold for average base quality score at 20 over a window of 3 bases. Reads shorter than 20 bases post-trimming were excluded.
The cleaned reads were aligned to the human genome reference, GRCh38.p12 using STAR (version STAR_2.5.2b) (Dobin et al. 2013).
Individual gene expression was quantified by counting the number reads mapping to the exon regions of each of the annotated genes from gencode v.28 using featureCounts tool of subread package (version 2.0.0) (Liao et al. 2014). Those reads that mapped to antisense strand, or mapped to multiple regions on the genome or those reads that overlapped with multiple genes were excluded.
|
| |
|
| Submission date |
Jun 08, 2022 |
| Last update date |
Sep 12, 2023 |
| Contact name |
Natascia Marino |
| E-mail(s) |
marinon@iu.edu
|
| Phone |
(317) 274-3340
|
| Organization name |
Indiana University School of Medicine
|
| Department |
Hematology/Oncology Division
|
| Street address |
980 W. Walnut St, R3-C238
|
| City |
Indianapolis |
| State/province |
IN |
| ZIP/Postal code |
46202 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE205725 |
Transcriptome profiling of normal breast tissue |
|
