|
| Status |
Public on Oct 19, 2023 |
| Title |
R008_PRE |
| Sample type |
SRA |
| |
|
| Source name |
Metastatic Triple-Negative Breast Cancer PRE treatment
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: primary breast tissue biopsy
treatment: Carboplatin, Nab-Paclitaxel, and Pembrolizumab
overall response: Partial Response
os: 16.3285420944559
pfs: 6.07802874743327
os event: 1
pfs event: 1
age: 50
biomaterial provider: Alberto J. Montero,[email protected]
collection date: 2017-11-08
geo loc_name: Cleveland, OH, USA
Sex: female
tissue: breast
disease: TNBC
disease stage: stage IV
race: Not specified
|
| Treatment protocol |
Pre-treatment samples were collected from patients with stage IV triple negative breast cancer prior to receiving chemo-immunotherapy with the following regimen which was administered intravenously on a 21 day cycle: carboplatin (C) day 1 (AUC 4.5), nab-paclitaxel (N) days 1,8,15 (75 mg/m2), and pembrolizumab (P) 200 mg on day 15. An optional post-therapy biopsy was obtained after the 3rd cycle of CNP chemo-immunotherapy
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was isolated from frozen core biopsies of primary or metastatic TNBC tissue using the Qiagen AllPrep DNA/RNA kit.Libraries were prepared using the Takara SMART-Seq v4 Ultra Low Input RNA kit and sequenced on an Illumina NovaSeq for a target of 40 million reads per sample.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Single-Arm Phase II Trial
|
| Data processing |
Raw reads in the FASTQ format were aligned to the mm10 reference genome using STAR aligner v2.7.6a. The featureCounts read summarization program was used to count mapped reads for each gene in the annotation file (Human GENECODE: Release 42 (GRCh38.p13)). Count files were then merged by an in-house R script and differential gene expression analysis was performed using DESeq2. DESeq2 normalizes the count data to account for differences in sequencing depth and composition. This is done using the median of ratios method, which involves dividing each gene's raw count by a size factor that accounts for library size and composition. DESeq2 models the variation in gene expression using a negative binomial distribution. The dispersion estimates are used to model the relationship between mean expression and variance, which is critical for accurate detection of differentially expressed genes.
Assembly: Human GENECODE: Release 42 (GRCh38.p13)
Supplementary files format and content: Raw (raw_count_matrix.csv) and DESeq normalized (DeseqNormalizedCount.csv) matrices are made available along with the FASTQ files used in current study.
|
| |
|
| Submission date |
Aug 29, 2023 |
| Last update date |
Oct 19, 2023 |
| Contact name |
Vladimir Makarov |
| E-mail(s) |
[email protected]
|
| Phone |
2162879971
|
| Organization name |
CLEVELAND CLINIC LERNER COM-CWRU
|
| Street address |
9500 Euclid Ave
|
| City |
Cleveland |
| State/province |
OH |
| ZIP/Postal code |
44195 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE241876 |
Distinct Transcriptional Landscapes Identified by Radiographic Response in Metastatic Triple-Negative Breast Cancer Treated with Carboplatin, Nab-Paclitaxel, and Pembrolizumab in a Single-Arm Phase II Trial |
|
| Relations |
| BioSample |
SAMN37200077 |
| SRA |
SRX21505134 |
