|
| Status |
Public on Nov 24, 2024 |
| Title |
blood-CDI_540454_2wk |
| Sample type |
RNA |
| |
|
| Source name |
Whole blood
|
| Organism |
Homo sapiens |
| Characteristics |
participant_id: CDI_540454
condition: CDI
age: 66
Sex: Male
time_point_sample_weeks: 2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Performed using a Tempus Spin RNA Isolation kit according to the manufacturer's instructions.
|
| Label |
Biotin
|
| Label protocol |
cRNA were prepared according to the standard GeneChip protocol from a minimum of 50 ng total RNA (GeneChip™ WT PLUS Reagent Kit USER GUIDE, 2018, Applied Biosystems). Following synthesisation of ss-cDNA from 15 μg of cRNA, the fragmented cDNA (5.5 μg) is labeled by terminal deoxynucleotidyl transferase (TdT) using the proprietary DNA Labeling Reagent that is covalently linked to biotin.
|
| |
|
| Hybridization protocol |
Fragmented and labelled ssDNA were incubate with rotation at 60 rpm for 16 hours at 45°C on Clariom D Human Array. Cartridge arrays were washed and stained in the GeneChip™ Fluidics Station 450 (GeneChip™ WT PLUS Reagent Kit USER GUIDE, 2018, Applied Biosystems).
|
| Scan protocol |
Cartridge arrays were scanned using the GCS3000 scanner (GeneChip™ Command Console™ User Guide).
|
| Data processing |
All processing was performed in R (v4.4.1). CEL files were imported using the oligo package (v1.68.2) and converted to an AnnotatedDataFrame with Biobase (v2.64.0). RMA transformation was performed with the oligo package using default settings, summarised at the 'core' target level. Transcript clusters (TCs) were filtered to those with a transformed probe-intensity greater than 3 in at least 37 samples. The remaining TCs were annotated with Entrez gene IDs using the AnnotationDbi package (v1.66.0) with data obtained from the clariomdhumantranscriptcluster.db package (v8.8.0). TCs assigned to multiple gene IDs were removed, and where gene IDs were assigned to multiple TCs the TC with greatest mean abundance across samples was chosen.
|
| |
|
| Submission date |
Sep 05, 2024 |
| Last update date |
Nov 24, 2024 |
| Contact name |
Maria Tsakiroglou |
| Organization name |
University of Liverpool
|
| Department |
Department of Pharmacology and Therapeutics
|
| Street address |
Block A, Waterhouse Building, 1-5 Brownlow Street,
|
| City |
Liverpool |
| ZIP/Postal code |
L69 3GL |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL23126 |
| Series (1) |
| GSE276395 |
Gene expression dysregulation in whole blood of patients with C. difficile infection |
|
