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Sample GSM5414110 Query DataSets for GSM5414110
Status Public on Mar 01, 2022
Title Vehicle [Sample2]
Sample type SRA
Source name Human ATL43Tb (-) cell lines
Organism Homo sapiens
Characteristics tissue: ATL43Tbeta (-) xenograft tumor
mouse strain: NOD scid gamma
treatment: Vehicle
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 Sample2
Adult T cell leukemia cell lines
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
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
BioSample SAMN19998732
SRA SRX11329414

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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