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Sample GSM7696967

Query DataSets for GSM7696967

Status

Public on Mar 31, 2024

Title

Rv1_WT_Int_SNX631_Rep5

Sample type

SRA

Source name

xenograft

Organism

Homo sapiens

Characteristics

tissue: xenograft
cell line: 22Rv1
cell type: prostate cancer cells
genotype: WT
treatment: Rv1-WT xenograft (WT_Int_Snx_#3) growing intact NSG male mice, SNX631 treatment group (Int-Snx)

Treatment protocol

For SNX631 in vivo treatment, animals were randomly allocated to two study groups when the mean tumor size reached 100-200 mm^3. For Rv1-WT study, the treatment group received SNX631-medicated diet (500 ppm, producing 30-60 mg/kg/day dosage on average) and the control group received the control diet. For Rv1-Luc study, the animals in the control group were dosed with vehicle (70% PEG-400/30% Propylene Glycol, 5 mL/kg, p.o., b.i.d.) and the treatment group was dosed with SNX631 (6 mg/mL solution in the vehicle, 5 mL/kg, p.o., b.i.d.) at 60 mg/kg/day.

Growth protocol

22Rv1 and its derivatives were cultured in RPMI-1640 media supplemented with 2 mM L-glutamine, 1 mM sodium pyruvate, 1.5 g/L sodium bicarbonate, 10 mM HEPES, 0.45% D-glucose, and either 10% fetal bovine serum (FBS) or charcoal stripped FBS (CSS), plus 1% penicillin-streptomycin (P/S). Cells were inoculated s.c. (2x10^6 cells in 0.1 mL 50% Matrigel per animal) in the right flank of intact or castrated male NSG mice to form xenograft tumors

Extracted molecule

total RNA

Extraction protocol

Tumor tissues were first submerged in 500 μL RNA-Later stabilization solution (Thermo Fisher Scientific) at room temperature. After stabilization, RNA samples were extracted from tumor tissues using the mRNeasy Mini Kit (QIAGEN) according to the manufacturer’s protocol. RNA quality was validated on RNA-1000 chip using Bioanalyzer (Agilent)
Sequencing libraries were generated using NEBNext Ultra II Directional RNA Library prep Kit

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 4000

Data processing

Indexed sequences were checked quality by Fastqc
Indexed sequences were trimmed adaptor sequence by cutadapt (v 2.8) with parameters -m 75 -q 30
Reads were aligned to a hybrid reference genome consisting of both the human GRCh38.p13 primary assembly genome and the mouse GRCm39 primary assembly genome, utilizing STAR (v 2.7.2b) with parameter --outFilterMismatchNoverReadLmax 0.01 --outFilterMultimapNmax 1
Read counts over annotated genes were obtained using featureCount (subreads | version: 2.0.3) with parameters -T 12 -B -O --fraction -s 2 -p --countReadPairs -d 50 -D 800 -g gene_id
Assembly: GRCh38.p13 & GRCm39
Supplementary files format and content: tab-delimited text files include human and mouse gene counts for each sample

Submission date

Aug 08, 2023

Last update date

Mar 31, 2024

Contact name

HAO JI

E-mail(s)

ji5@email.sc.edu

Phone

8037774689

Organization name

University of South Carolina