GEO Accession viewer

NCBI > GEO > Accession Display

Not logged in | Login

GEO help: Mouse over screen elements for information.

Sample GSM5221640

Query DataSets for GSM5221640

Status

Public on Dec 08, 2021

Title

MC38_Baseline_2

Sample type

SRA

Source name

Tumor

Organism

Mus musculus

Characteristics

replicate group: MC38_Baseline
treatment: none
cell line: MC38
time point: na
genotype: WT

Treatment protocol

WT mice were randomized day 7 post-tumor implant and for PD-1 antibody (Ab) experiments, mice were dosed intraperitoneally every 4 days on 4 separate occasions with 5 mg/kg anti-mouse PD-1 Ab muDX400. PD-1cKO mice were randomized day 7 post-tumor implant and tamoxifen (Sigma-Aldrich) dissolved in 1:9 ratio of ethanol:sunflower oil at a stock concentration of 10 mg/mL was injected intraperitoneally at a dose of 40 mg/kg on 5 consecutive days. Tamoxifen injections were administered to both PD-1cKO and littermate controls.

Growth protocol

WT mice were subcutaneously injected on the right flank with MC-38 cells (1x106) and received PD-1 Ab injection day 7, 11 and day 15 post-tumor implant. PD-1cKO and littermate control mice were subcutaneously injected on the right flank with MC-38 cells (1x106) and day 6-7 post-tumor cell injection the mice received injections of tamoxifen on 5 consecutive days.

Extracted molecule

total RNA

Extraction protocol

For tumor tissue RNA isolation, organs were homogenized into RNA STAT-60 (Tel-Test Inc., Friendswood, TX) using a polytron homogenizer, then total RNA extracted according to the manufacturer's instructions. After isopropanol precipitation, total RNA was re-extracted with phenol:chloroform:isoamyl alcohol (25:24:1) (Sigma-Aldrich, St. Louis, MO).
Sequencing was performed using the Truseq stranded total RNA RiboZero library preparation kit (Catalog #: RS-122-2201) according to the manufacturer’s instructions (Illumina, San Diego, CA). The resulting cDNA libraries were sequenced on an Illumina (HiSeqTM 4000) using a 50-base paired-end run.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 4000

Description

US-1377657

Data processing

Cleaned reads were aligned to the Mouse.B38 genome reference using the Omicsoft Aligner with a maximum of 2 allowed mismatches.
Gene level raw counts, and FPKM, were determined by the OSA algorithm as implemented in Omicsoft Array Studio and using Ensembl.R86 gene models.
Genome_build: Mouse.B38
Supplementary_files_format_and_content: Tab-delimited text file include FPKM values for each Sample. Each column corresponds to one sample (barcode).

Submission date

Mar 31, 2021

Last update date

Dec 08, 2021

Contact name

Eric Muise

E-mail(s)

[email protected]

Phone

6179923514

Organization name

Merck