|
| Status |
Public on Apr 11, 2024 |
| Title |
41N |
| Sample type |
SRA |
| |
|
| Source name |
Rectum
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Rectum
age at_surgery: 81
tumor stage: NA
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Tumors and adjacent colonic segments were surgically resected and aliquots were stored in RNAlater (Thermo Fisher) preservative. Samples were homogenized with a pestle and chloroform was added. The samples were centrifuged at 12,000 x g for 15 minutes. The aqueous layer was purified with RNAEasy Mini Kit (Qiagen). Samples were selected for poly-adenylation, and cDNA libraries were made and sequenced on MiSeq2500 (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
41N
|
| Data processing |
Base calling with Illumina MiSeq2500
Alignment with STAR version 2.7.3
HTSeq counting of aligned reads
Assembly: hg38
Supplementary files format and content: Count files contain raw counts for sequences aligning to each transcript.
|
| |
|
| Submission date |
Dec 21, 2023 |
| Last update date |
Apr 11, 2024 |
| Contact name |
Gregory Yochum |
| E-mail(s) |
gyochum@pennstatehealth.psu.edu
|
| Organization name |
Penn State College of Medicine
|
| Department |
Biochemistry, Colorectal Surgery
|
| Street address |
700 HMC Crescent Road
|
| City |
Hershey |
| State/province |
PA |
| ZIP/Postal code |
17033 |
| Country |
USA |
| |
|
| Platform ID |
GPL15520 |
| Series (1) |
| GSE251845 |
Identification of unique gene expression and splicing events in early-onset colorectal cancer |
|
| Relations |
| BioSample |
SAMN39058866 |
| SRA |
SRX22997908 |
