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| Status |
Public on Mar 13, 2024 |
| Title |
UC4_O2R41 |
| Sample type |
SRA |
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| Source name |
colon
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| Organism |
Homo sapiens |
| Characteristics |
tissue: colon
age (years): 34
Sex: Male
ethnicity: White
blood pressure: Unknown (not stated)
bmi: Unknown (not stated)
height (cm): Unknown (not stated)
weight (kg): Unknown (not stated)
smoking: Unknown (not stated)
drinking: Unknown (not stated)
major reason_for_surgery: BACK SURGERY ﾠ ﾠ ﾠ bone was fused to his back at age 6 " PR COLONOSCOPY FLX DX W/COLLJ SPEC WHEN PFRMD N/A 2021 " PR SIGMOIDOSCOPY FLX WITH WITH BAND LIGATION(S) N/A 2021 Abdominal CT 2021: radiology impression:ﾠActive IBD related inflammation involving a long segment of colon from the splenic flexure through the rectum. Subjectively, the degree of inflammation has worsened from 2021 Abdominal CT 2021: radiology impression:ﾠFindings of active colitis, moderately improved extending from the distal transverse colon to the rectum when compared to 2021 examination in this patient with history of ulcerative colitis.ﾠ ﾠ Colonoscopy 2021:ﾠﾠPancolitis ulcerative colitis. Inflammation was found from the anus to the ascending colon. This was severe. Biopsied. ﾠ /2021:ﾠﾠSevere (Mayo Score 3) pancolitis ulcerative colitis;ﾠﾠBiopsies were taken with a cold forceps for histology in the right colon, transverse colon, left colon, and rectum. ﾠ Pathology 2021: diagnosis:ﾠﾠCOLON, RANDOM, BIOPSY: SEVERELY ACTIVE CHRONIC COLITIS (CRYPT ABSCESSES AND CRYPTITIS) AND FOCAL EROSION
medical history: Blood clotting disorder (CMS/HCC) ﾠ " Chronic diarrhea may " Irritable bowel syndrome ﾠ " Scoliosis ﾠ " Ulcerative colitis (CMS/HCC) 2021 5 month history of bloody diarrhea consistent with active ulcerative colitis. He first started experiencing occasional episodes of diarrhea in 2016 and was diagnosed with colitis after a colonoscopy at an outside facility. Sinceﾠ2016, he reports having occasional episodes of diarrhea, often triggered by consumption of fried foods. These episodes increased in frequency and severity up until 2021. In 2021, he was hospitalized at --- due to bloody diarrhea and was diagnosed with ulcerative colitis. --- has also since been hospitalized multiple times at --- since 2021, including 2-3 ED visits and at least 2 inpatient stays. He has been on a low-fiber diet since his hospitalization in 2021 as well as a weight loss of about 70 lbs since then
acute medication: Remicade, prednisone
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 |
male UC patient; aged 34 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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