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SRX23747040: GSM8113792: UC71_LC_S13; Homo sapiens; RNA-Seq
1 ILLUMINA (Illumina NovaSeq 6000) run: 30.4M spots, 6.1G bases, 1.9Gb downloads

External Id: GSM8113792_r1
Submitted by: Boolean, Pediatrics, UCSD
Study: A "living biobank" of Crohn's Disease
show Abstracthide Abstract
Patient-derived organoids (PDOs) from the colons of patients with Crohn's Disease (or healthy controls) were subjected to in-depth genotype, transcriptome and phenotype assessment. These studies revealed that CD may be classified broadly into two molecular subtypes, each with its unique profile of dysregulated celluar processes. We further show that these phenotypes can be rectified with matched therapeutics, hence making such intervention personalized. Findings show that CD-PDOs could serve as pre-clinical platforms for drug discovery and personalized medicine. Overall design: Patients representing various subtypes of Crohn's disease (CD) [Montreal classification-B1/2/3, perianal] were enrolled into this study to obtain tissue biopsies which would serve as source of adult stem cells for the generation of patient-derived organoids (PDOs). Standard cell biological, biochemical, functional and phenotypic assays were used to assess the PDOs for: 1) barrier integrity, 2) apoptosis, 3) proliferation, 4) ROS induced DNA/RNA damage; 5) senescence and DNA damage; 6) bacterial clearance, 7) induction of inflammatory cytokines, and morphology/growth characteristics. Please note that the cell biological, biochemical, and functional assays are not done on these GEO samples prior to RNA analysis, but characterization that is independent of the samples sequenced. The current records are the content of the associated manuscript to validate RNA seq findings.
Sample: UC71_LC_S13
SAMN40144375 • SRS20573726 • All experiments • All runs
Organism: Homo sapiens
Library:
Name: GSM8113792
Instrument: Illumina NovaSeq 6000
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: cDNA
Layout: PAIRED
Construction protocol: Cell recovery was used to extract the organoids from the matrigel domes. Organoids and EDMs were lysed with RNA lysis buffer following the manufacturer's instructions for the Zymo Research Quick-RNA MicroPrep Kit. RNA sequencing libraries were generated using the Illumina TruSeq Stranded Total RNA Library Prep Gold with TruSeq Unique Dual Indexes (Illumina, San Diego, CA). Samples were processed following manufacturer's instructions, except modifying RNA shear time to five minutes. Resulting libraries were multiplexed and sequenced with 100 basepair (bp) Paired End (PE100) to a depth of approximately 25-40 million reads per sample on an Illumina NovaSeq 6000. Samples were demuxltiplexed using bcl2fastq v2.20 Conversion Software (Illumina, San Diego, CA).
Runs: 1 run, 30.4M spots, 6.1G bases, 1.9Gb
Run# of Spots# of BasesSizePublished
SRR2810161630,396,3806.1G1.9Gb2024-03-31

ID:
32037124

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