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Sample GSM5444460 Query DataSets for GSM5444460
Status Public on Apr 30, 2023
Title Breast tumor 3, soft gel, rep1 [B43202]
Sample type SRA
Source name Human breast tumor cells implanted into mouse
Organism Homo sapiens
Characteristics original patient-derived tumor number: 3
soft or stiff collagen gel: soft
replicate: 1
Treatment protocol soft and stiff tumors from three different patient-derived xenografts, 3 replicates of each
Growth protocol Rat tail collagen-1 (High concentration, Corning, Cat. #: 354249) was incubated with 0.1% acetic acid or 0.1%acetic acid (non-crosslinked; SOFT) with 2500mM L-ribose (Chem Impex International, Cat. #: 28127) (cross-linked; STIFF) for at least 10 days before preparation of collagen/reconstituted basement membrane (rBM) hydrogels for orthotopic implantation of tumor cells or tumor fragments26,48. Collagen-1 mixtures were then combined with basement membrane extract (R&D Systems, Cultrex BME, type 2, Pathclear, Cat. #: 3532-005-02) (20% final volume), PBS and 1N NaOH to a slightly acidic pH (pH ~6.5) as determined by pH strips. For PDX tissues, collagen/rBM with and without L-ribose was injected orthotopically into a cleared inguinal fat pad and allowed to set for 3-5 minutes prior to implantation of a PDX tissue fragment approximately 2x2mm in size.
Extracted molecule total RNA
Extraction protocol RNA was isolated using TRIzol (Invitrogen, Cat. #: 15596018) followed by chloroform extraction.
RNAseq library preparation and sequencing was performed by the Vincent J. Coates Genomics Sequencing Laboratory, University of California, Berkeley. Samples were sequenced in NovaSeq 6000 S4 lanes with 150bp paired-end reads with approximately 25 million read pairs per sample.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
Description B43202_S130_L002
Data processing RNAseq fastq files were mapped to the primary assembly of the Gencode v33 human genome using Rsubread (version 2.0.1) and counted using featureCounts
Lowly expressed genes were filtered out if they did not have at least one CPM in at least 4 samples
Data normalization was performed using calcNormFactors in edgeR (version 3.28.1)
Gene ontology was performed using Gage (version 2.36.0) with gene lists from MsigDB version 7.2
Genome_build: hs33
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Gene ontology table with p-values, q-values, and set sizes for each term enriched in soft or stiff collagen gels
Submission date Jul 13, 2021
Last update date Apr 30, 2023
Contact name Valerie M Weaver
Organization name UCSF
Department Surgery
Lab Weaver Lab
Street address 513 Parnassus Avenue, HSE 560
City San Francisco
State/province CA
ZIP/Postal code 94143
Country USA
Platform ID GPL24676
Series (1)
GSE179983 A convolutional neural network STIFMap reveals associations between stromal stiffness and EMT in breast cancer
BioSample SAMN20181903
SRA SRX11424011

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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