|
| Status |
Public on Mar 13, 2024 |
| Title |
CD4_O2R73 |
| Sample type |
SRA |
| |
|
| Source name |
colon
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: colon
age (years): 55
Sex: Female
ethnicity: White
blood pressure: Unknown (not stated)
bmi: 42.49
height (cm): Unknown (not stated)
weight (kg): Unknown (not stated)
smoking: No
drinking: No
major reason_for_surgery: ectovaginal fistula s/p loop ileostomy in 2017 with later repair with flap complicated by pelvic fluid collection noted in July 2020. Patient was noted to have an additional fistula with active disease during EUA on 12/20. Here for completion proctocolectomy
medical history: hx of fistulizing Crohn's disease and rectovaginal fistula. She has a past medical history of Anemia (09/2017), Crohn disease, Crohn's colitis, with fistula, Essential hypertension, benign, Hyperlipidemia, Ileostomy in place, OSA (obstructive sleep apnea), and Renal disease
acute medication: She continues on therapy with Remicade. She declined adding AZA when she had undetectable drug levels and drug antibodies in the fall.She eclined adding Imuran.She was agreeable to increasing dose of infusion and has remained on 10 mg/kg every8weeks. Had drug levels repeated which showed improved in drug level to 5.1 and antibodies reduced from 10.0 to 6.1.
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 |
female 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 |
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