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Sample GSM4959959

Query DataSets for GSM4959959

Status

Public on Nov 27, 2023

Title

Primary tumor - bulk RNA seq rep_1

Sample type

SRA

Source name

Pancreatic tumor

Organism

Mus musculus

Characteristics

tissue: Pancreatic tumor tissue
strain: C57BL/6
cell line: FC1242

Treatment protocol

Mice were orthotopically injected with 100,000 murine FC1242 KPC pancreatic cancer cells, either orthotopically in the pancreas or metastatic to the liver. Tumors were harvested after 3 weeks, then either processed for bulk RNA sequencing, or FACS-sorted for CD45+ cells for single cell RNA sequencing via 10X platform.

Extracted molecule

total RNA

Extraction protocol

For bulk RNA-seq, total RNA was extracted from fresh tissue using QIAGEN Rneasy Mini Kit, following the manufacturer's protocol. Single cell RNA sequencing was performed using the 10X Chromium platform, following manufacturer's protocol.
For bulk RNA seq, RNA libraries were prepared for sequencing using standard Illumina protocols. For single cell RNA seq, library construction was performed using the 10X Genomics platform using Chromium™ Single Cell 3' v2 Reagent Kits and a Chromium instrument according to the manufacturer’s protocol

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 4000

Description

Bulk RNA seq
p1

Data processing

For bulk RNA seq, 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 mm10 whole genome
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated to normalize read count by dividing it by the gene length the the total number of reads mapped to protein-coding genes.
For single cell RNA seq, base calling and demultiplexing was performed using Illumina bcl2fastq software.
Additional cell-level demultiplexing and alignment was performed with 10x Cell Ranger software.
Genome_build: mm10
Supplementary_files_format_and_content: Bulk RNAseq: raw counts, fpkm counts, and normalized counts (all .csv files). Single cell RNAseq: genes-barcodes (.tsv files) and matrices (.mtx file)

Submission date

Dec 07, 2020

Last update date

Nov 27, 2023

Contact name

Joshua Caleb Leinwand

Organization name

Columbia University Irving Medical Center

Department

Surgery

Street address

177 Fort Washington Ave, 7th Floor