|
| Status |
Public on Feb 07, 2023 |
| Title |
Chordoma Sample 10 |
| Sample type |
SRA |
| |
|
| Source name |
Chordoma
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Chordoma
cell type: Tumor
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extracted with Trizol and a bead beater
Nugen Ovation Pico WTA kit followed by WT-Ovation Exon Module then Illumina DNA Sample Prep Kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Data processing |
Reads mapping to human rRNA (using Bowtie 0.12.7) were removed
Reads mapped using STAR (version 2.7.10a)
Gene read counts generated using STAR (--quantMode GeneCounts), unstranded RNA-seq read counts shown in processed files
Assembly: GRCh38 primary assembly and Gencode v40 annotations
Supplementary files format and content: Tab-delimited text file exported from STAR; Column 1: Gene ID; Column 2: Read counts
|
| |
|
| Submission date |
Jun 03, 2022 |
| Last update date |
Feb 07, 2023 |
| Contact name |
Stefan Halvorsen |
| E-mail(s) |
shalvorsen@mgh.harvard.edu
|
| Organization name |
Massachusetts General Hospital
|
| Department |
Center for Computational and Integrative Biology
|
| Lab |
Seed Lab
|
| Street address |
185 Cambridge Street
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02114 |
| Country |
USA |
| |
|
| Platform ID |
GPL9115 |
| Series (2) |
| GSE205457 |
Expression data from chordoma and notochord (RNA-Seq) |
| GSE205458 |
Expression data from chordoma and notochord |
|
| Relations |
| BioSample |
SAMN28860888 |
| SRA |
SRX15591241 |
