|
| Status |
Public on Mar 01, 2022 |
| Title |
Triple combination [Sample5] |
| Sample type |
SRA |
| |
|
| Source name |
Human ATL43Tb (-) cell lines
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: ATL43Tbeta (-) xenograft tumor
mouse strain: NOD scid gamma
treatment: IBET762+Copanlisib+Bardoxolone methyl
|
| Treatment protocol |
IBET762+Copanlisib+Bardoxolone methyl were administered for 5 days (alternate days).
|
| Growth protocol |
The xenograft tumor model was established by subcutaneous injection of 1×10^7 ATL43Tβ (-) cells into the flank of NSG mice for 10 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from ATL43Tβ (-) tumor isolated from NSG mice after 5-day treatment with the triple combination using an RNeasy kit.
RNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
| |
|
| Description |
Sample5
Adult T cell leukemia cell lines
mRNA-seq
|
| Data processing |
The sequencing quality of the reads was assessed per sample using FastQC (version 0.11.5).
Preseq (version 2.0.3), Picard tools (version 1.119) and RSeQC (version 2.6.4).
Sequencing reads were trimmed of low quality bases and adapter sequences were removed using Cutadapt (version 1.18).
The trimmed reads were aligned to the GRCh38 (GENCODE hg38, version 30).
Gene and isoform expression levels are quantified using RSEM (version 1.3.0).
Genome_build: Human_hg38 (GRCh38)
Supplementary_files_format_and_content: RawCountFile_rsemgenes.txt: Tab-delimited text file includes raw counts.
Supplementary_files_format_and_content: TreatedvsVehical_voom_deg.csv: Comma-separated text file includes DEG table.
|
| |
|
| Submission date |
Jul 01, 2021 |
| Last update date |
Mar 01, 2022 |
| Contact name |
Anusara Daenthanasanmak |
| E-mail(s) |
anusara.daenthanasanmak@nih.gov
|
| Organization name |
National Institutes of Health
|
| Department |
Lymphoid Malignancies Branch
|
| Street address |
10 Center Dr
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL30173 |
| Series (1) |
| GSE179307 |
Triple combination of BET plus pan-PI3K and NF-κB inhibitors exhibit synergistic activity in adult T cell leukemia/lymphoma |
|
| Relations |
| BioSample |
SAMN19998727 |
| SRA |
SRX11329417 |
