|
| Status |
Public on Jul 01, 2020 |
| Title |
CLA-8 |
| Sample type |
SRA |
| |
|
| Source name |
Primary breast tumor
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Primary breast tumor
group: nonresponder
|
| Treatment protocol |
Letrozole was supplied in tablets of 2.5 mg. The physician instructed patients to take the drug after breakfast or lunch and every day at the same time throughout the study. No dose adjustments were permitted. The maximum duration of the neoadjuvant treatment with letrozole defi ned for this study was 12 months. The patients were evaluated every 4 weeks with a clinical examination and every eight weeks with mammograms or breast ultrasounds for the fi rst four months. In the event of absence of clinical improvement after 4 months (tumour reduction below 3 mm in longest diameter), the patient was not evaluable for the primary objective. In the event of clinical or imaging improvement at Month 4, the patients continued treatment with clinical and imaging monitoring every two months. In each control, if response improvement was seen (size reduction over 2 mm), the patients continued treatment for up to 12 months. When complete or no change responses were observed (maximum clinical diameter change.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
H&E-stained FFPE sections were reviewed for assessment of ≥20% tumor cellularity with macrodissection if required. RNA was extracted using the Promega Maxwell® 16 LEV RNA FFPE Purification Kit and instrument, according to the manufacturer’s instructions.
Total RNA was quantified using a Qubit (Life Technologies) and quality was assessed using an Agilent Bioanalyzer. For samples meeting quality requirements, 100 ng of RNA was used for library preparation. First and second strand cDNA synthesis was performed, universal adapters were ligated, and coding regions were selected by two consecutive hybrid captures followed by PCR enrichment. After enrichment, the libraries were quantified with qPCR using the KAPA Library Quantification Kit for Illumina Sequencing platforms and then pooled equimolarly.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
A second run was sequenced on NextSeq500 instrument
|
| Data processing |
fastq reads trimmed with bbduk (v.35.85)
align TopHat (v.2.0.9)
count table htSeq (v.0.6.1)
Genome_build: hg19
|
| |
|
| Submission date |
Feb 14, 2020 |
| Last update date |
Jul 01, 2020 |
| Contact name |
Kyung-min Lee |
| E-mail(s) |
[email protected]
|
| Organization name |
UT SOUTHWESTERN MEDICAL CENTER
|
| Department |
Simmons Comprehensive Cancer Center
|
| Lab |
Arteaga
|
| Street address |
6001 Harry Hines Blvd, NB5. 112
|
| City |
Dallas |
| State/province |
TX |
| ZIP/Postal code |
75390-8807 |
| Country |
USA |
| |
|
| Platform ID |
GPL21290 |
| Series (1) |
| GSE145325 |
RNA sequencing of ER+ breast tumor treated with letrozole |
|
| Relations |
| BioSample |
SAMN14051625 |
| SRA |
SRX7719153 |
| SRA |
SRX7726839 |
