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| Status |
Public on Mar 13, 2024 |
| Title |
CD7_O2R49 |
| Sample type |
SRA |
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| Source name |
colon
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| Organism |
Homo sapiens |
| Characteristics |
tissue: colon
age (years): 30
Sex: Female
ethnicity: White
blood pressure: Unknown (not stated)
bmi: 27.17
height (cm): Unknown (not stated)
weight (kg): Unknown (not stated)
smoking: No
drinking: Past
major reason_for_surgery: None
medical history: Significant history of stricturing ileocolonic Crohn's disease with perianal involvement. Diagnosed (age): 2016 (25). Status post total colectomy with end ileostomy due to steroid and Remicade refractory disease while inpatient. It was recommended to resume Remicade as she had only received 2 infusions before her surgery. Current therapy: Remicade since 2019. Past therapy: prednisone. No family GI history. Prior medical history: CXrohn's, colitis, depression, supraventricular tachycardia, anxiety, ovarian cyst
acute medication: Current medication list which includes the following prescription(s): acetaminophen (TYLENOL), chlorhexidine (HIBICLENS), clindamycin (CLEOCIN T), hydrocortisone (ANUSOL-HC), hyoscyamine (LEVSIN), infliximab (REMICADE), ondansetron (ZOFRAN), and promethazine hcl (PHENERGAN
chronic medication: Unknown (not stated)
treatment: KO-947
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| 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.
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| 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.
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
female CD patient; aged 30 years
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| 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.
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| Submission date |
Mar 08, 2024 |
| Last update date |
Mar 13, 2024 |
| Contact name |
Susan Dina Ghiassian |
| Organization name |
Scipher Medicine
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| Street address |
500 Totten Pond Rd, 6th Floor
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| City |
Waltham |
| ZIP/Postal code |
02451 |
| Country |
USA |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE261205 |
A network-based framework to discover treatment-response-predicting biomarkers for complex diseases |
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| Supplementary data files not provided |
| Raw data not provided for this record |
| Processed data are available on Series record |
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