|
| Status |
Public on Jul 26, 2022 |
| Title |
43_baseline_IFX_R_RNA |
| Sample type |
SRA |
| |
|
| Source name |
Peripheral Whole-Blood
|
| Organism |
Homo sapiens |
| Characteristics |
patient: 43
cohort: Discovery - Infliximab
treatment: Infliximab
remission at week 14: Remission
time point: baseline
diagnosis: UC
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Patient peripheral blood was collected in 2.5mL tubes PAXgene Blood RNA Tubes, RNA was automated isolated in QIAGEN’s QIAcube using the PAXgene Blood miRNA Kit from QIAGEN PreAnalytiX.
RNA Sequencing libraries were prepared from Paxgene™ Blood RNA Tubes (Qiagen) according to the Illumina TruSeq® messenger RNA (mRNA) sequencing protocol (TruSeq® RNA Seq Library Prep Kit v2)
Paired-end sequencing (2x75bp) was performed on Illumina HiSeq 4000
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Fastq files were mapped and aligned using nf-core ((https://github.com/nf-core/rnaseq)) rnaseq pipeline.
Adapters and low-quality bases from the RNA-seq reads were removed using Trim Galore (version 0.4.4), which is a wrapper tool for Cutadapt and FastQC. Reads that were shorter than 35 bp after trimming were discarded.
The filtered reads were mapped to the human genome (GRCh38, gencode version 25) using STAR aligner (version 2.5.2b).
featureCounts (version 1.5.2) was used to estimate the expression counts of the genes.
Genome_build: (GRCh38, gencode version 25)
Supplementary_files_format_and_content: tab-delimited text files include feature counts
|
| |
|
| Submission date |
Dec 20, 2021 |
| Last update date |
Jul 26, 2022 |
| Contact name |
Neha Mishra |
| E-mail(s) |
[email protected]
|
| Organization name |
Institute of Clinical Molecular Biology
|
| Lab |
Cell biology Lab
|
| Street address |
Rosalind-Franklin-Str. 12
|
| City |
Kiel |
| ZIP/Postal code |
24105 |
| Country |
Germany |
| |
|
| Platform ID |
GPL20301 |
| Series (2) |
| GSE191328 |
Longitudinal multi-omics analysis identifies early blood-based predictors of anti-TNF therapy response in inflammatory bowel disease [RNA-Seq] |
| GSE191331 |
Longitudinal multi-omics analysis identifies early blood-based predictors of anti-TNF therapy response in inflammatory bowel disease |
|
| Relations |
| BioSample |
SAMN24254641 |
| SRA |
SRX13460752 |
