|
| Status |
Public on Apr 14, 2021 |
| Title |
pt05 |
| Sample type |
SRA |
| |
|
| Source name |
ductal breast cancer tissue
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: ductal breast cancer
subtype: TNBC
response: Non-responder
progression-free survival indicator: 1
progression-free survival: 1.84 months
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from 11 ductal breast cancer tissues and 32 breast cancer cell line samples. Ribosomal RNA were further removed.
RNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Raw fastq files were assessed by FastQC (v0.11.5).
The adapters and low-quality sequence were trimmed by cutadapt (v-1.13).
The gene expression quantification analysis was performed by Salmon (v-0.9.1) based on the reference genome hg38 (GRCh38) with gene annotation from GENCODE (release 28).
The raw counts of reads mapped to each gene were extracted and used for subsequent analysis.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include TPM and raw counts values for each Sample
|
| |
|
| Submission date |
Apr 14, 2020 |
| Last update date |
Apr 15, 2021 |
| Contact name |
Qingfei Pan |
| E-mail(s) |
Qingfei.Pan@stjude.org
|
| Phone |
1-901-356-6214
|
| Organization name |
St. Jude Children's Research Hospital
|
| Department |
Department of Computational Biology
|
| Lab |
Yu Lab
|
| Street address |
262 Danny Thomas Place
|
| City |
Memphis |
| State/province |
TN |
| ZIP/Postal code |
38105 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE148623 |
Network-based assessment of HDAC6 activity is highly predictive of pre-clinical and clinical responses to the HDAC6 inhibitor ricolinostat [high throughput sequencing] |
| GSE180607 |
Network-based assessment of HDAC6 activity is highly predictive of pre-clinical and clinical responses to the HDAC6 inhibitor ricolinostat |
|
| Relations |
| BioSample |
SAMN14595216 |
| SRA |
SRX8111588 |
