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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Apr 30, 2023 |
| Title |
Breast tumor 1, stiff gel, rep3 [B63803] |
| Sample type |
SRA |
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| Source name |
Human breast tumor cells implanted into mouse
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| Organism |
Homo sapiens |
| Characteristics |
original patient-derived tumor number: 1
soft or stiff collagen gel: stiff
replicate: 3
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| Treatment protocol |
soft and stiff tumors from three different patient-derived xenografts, 3 replicates of each
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| 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.
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
B63803_S123_L002
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| 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
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| Submission date |
Jul 13, 2021 |
| Last update date |
Apr 30, 2023 |
| Contact name |
Valerie M Weaver |
| Organization name |
UCSF
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| Department |
Surgery
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| Lab |
Weaver Lab
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| Street address |
513 Parnassus Avenue, HSE 560
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| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94143 |
| Country |
USA |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE179983 |
A convolutional neural network STIFMap reveals associations between stromal stiffness and EMT in breast cancer |
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| Relations |
| BioSample |
SAMN20181894 |
| SRA |
SRX11424004 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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