|
| Status |
Public on Mar 13, 2024 |
| Title |
CD3_O2R65 |
| Sample type |
SRA |
| |
|
| Source name |
colon
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: colon
age (years): 55
Sex: Male
ethnicity: White
blood pressure: Unknown (not stated)
bmi: 24.01
height (cm): Unknown (not stated)
weight (kg): Unknown (not stated)
smoking: No
drinking: Yes, <14 units/week, couple times a month
major reason_for_surgery: None
medical history: crohn's disease. Symptoms since his 30s (always had abdominal cramping, diarrhea issues) but was diagnosed at age 47 when he presented w bloody diarrhea. Montreal Classification: CD: A3 >40 L1 ileal B2 stricturing.
acute medication: Current therapy: Infliximab. Past therapy: Prednisone x 6months. Current Outpatient Medications: • Cholecalciferol (Vitamin D) • inFLIXimab 100 MG Recon Soln, • iron polysaccharides (Ferrex 150) 150 MG capsule.
chronic medication: Unknown (not stated)
treatment: KO-947
|
| Treatment protocol |
Culture plates were incubated in media with either test compounds (10 uM) or vehicle. Tissues were treated with Staphylococcus enterotoxin B (List Biological Laboratories, Campbell, CA) to stimulate inflammatory cytokine secretion.
|
| Growth protocol |
Biopsy tissues were cultured in triplicate in 12-well plates containing a modified Connaught Medical Research Laboratory (CMRL)–based cell-culture media at 37 °C, 5% CO2.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted by proprietary process by REPROCELL. Briefly, tissue lysates were treated with Proteinase K. NA was eluted with an elution solution of concentration ≥20 ng/μL. The lysates were then centrifuged, ethanol was added to the supernatant, and the solutions were loaded onto spin-columns. DNase digestion was performed on column to remove any traces of DNA and RNA.
RNA libraries for 150bp paired-end sequencing were prepared by an mRNA library prep kit for sequencing by an Illumina Novaseq 6000.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
male CD patient; aged 55 years
|
| Data processing |
Sequence reads were aligned to GRCh38 using STAR alignment software.
Gene expression was calculated (in fragments per kilobase of transcript per million mapped reads) using the RSEM software package.
Assembly: hg38
Supplementary files format and content: Comma-delimited text file includes FPKM values for each sample.
|
| |
|
| Submission date |
Mar 08, 2024 |
| Last update date |
Mar 13, 2024 |
| Contact name |
Susan Dina Ghiassian |
| Organization name |
Scipher Medicine
|
| Street address |
500 Totten Pond Rd, 6th Floor
|
| City |
Waltham |
| ZIP/Postal code |
02451 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE261205 |
A network-based framework to discover treatment-response-predicting biomarkers for complex diseases |
|
