|
| Status |
Public on Mar 17, 2023 |
| Title |
TMD8_CSKi_6h bio replicate2 |
| Sample type |
SRA |
| |
|
| Source name |
TMD8
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: TMD8
cell type: human DLBCL cell line
genotype: Cas9 engineered
treatment: CSKi (500nm)_6h
|
| Treatment protocol |
All cells were grown at 0.5 x 10^6 cells/ml and either treated in duplicates with vehicle (DMSO) or CSKi (500nm) for 1h, 3h, 6h, and 24h.
|
| Growth protocol |
All cells were grown in advanced RPMI supplemented with 5% FBS with pen/strep and glutamine.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the Qiagen RNeasy Mini kit.
Libraries were generated using TruSeq stranded mRNA library prep (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
| |
|
| Description |
TMD8_CSKi_6h_R2
2x75 cycle
paired-end RNA-Seq
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 human genome using STAR2.
Raw read counts per gene were called with Htseq-Count.
FPKM and median shift.
Assembly: hg19
Supplementary files format and content: DLBCL_CSKi_RNAseq_Normalized_log2.txt
|
| |
|
| Submission date |
Mar 07, 2023 |
| Last update date |
Mar 17, 2023 |
| Contact name |
David Huang |
| Organization name |
National Cancer Institute
|
| Street address |
9000 Rockville Pike
|
| City |
Bethesda |
| State/province |
Maryland |
| ZIP/Postal code |
20892-0001 |
| Country |
USA |
| |
|
| Platform ID |
GPL30173 |
| Series (2) |
| GSE225858 |
Targeting oncogenic BCR signaling therapeutically by glucocorticoids and CSK inhibition |
| GSE226866 |
RNA sequencing/Gene expression studies of CSK inhibitor (CSKi) in diffuse large B-cell lymphoma (DLBCL) [JC2] |
|
| Relations |
| BioSample |
SAMN33618620 |
| SRA |
SRX19580736 |
