|
| Status |
Public on Mar 06, 2024 |
| Title |
GIST-T1, control, rep1 |
| Sample type |
SRA |
| |
|
| Source name |
GIST-T1
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: GIST-T1
cell type: cell line established from a metastatic GIST
genotype: WT
|
| Growth protocol |
GIST-T1 cell line was obtained from Cosmo Biosciences. Cells were passaged in DMEM with 10% serum, 1X antibiotics and 1X Glutamax (Life Technologies).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using an RNeasy Plus Kit (Qiagen). RNA concentration was measured by NanoDrop (Thermo Scientific) and quality was determined by TapeStation (Agilent).
For each sample, 1 μg of the total RNA was used for RNA-seq library preparation using the NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
RNA-seq reads were aligned using STAR 2.5.3 to the hg38 human reference
RSEM (v1.3.2) was used for obtaining read counts and transcripts per million.
DESeq2 (v1.38.3) was used for differential expression genes
Assembly: hg38
Supplementary files format and content: tab-delimited text files include read counts and TPM values for each Sample
|
| |
|
| Submission date |
Aug 30, 2023 |
| Last update date |
Mar 06, 2024 |
| Contact name |
Kyung Lock Kim |
| E-mail(s) |
postclassic@gmail.com
|
| Phone |
6177589374
|
| Organization name |
Dana-Farber Cancer Institute
|
| Department |
Cancer Biology
|
| Lab |
Bradley E. Bernstein
|
| Street address |
450 Brookline Avenue
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL21697 |
| Series (2) |
| GSE241926 |
Dissection of a CTCF insulator and its impact on chromosome topology and oncogene expression in gastrointestinal stromal tumor (RNA-Seq) |
| GSE241927 |
Dissection of a CTCF topological boundary uncovers principles of enhancer-oncogene regulation |
|
| Relations |
| BioSample |
SAMN37200046 |
| SRA |
SRX21530539 |
