|
| Status |
Public on May 20, 2021 |
| Title |
Sample008 [Rectal biopsy] |
| Sample type |
SRA |
| |
|
| Source name |
Rectal biopsy
|
| Organism |
Homo sapiens |
| Characteristics |
individual: Ind006
gender: M
age at diagnosis: 11
time of sampling: Baseline
initial treatment: CS-IV
colectomy: 0
disease: pediatric ulcerative colitis
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Rectal biopsy specimens were obtained during diagnostic colonoscopy. RNA was extracted using Qiagen AllPrep DNA/RNA Mini Kit.
RNA sequencing libraries were prepared using the Lexogen QuantSeq 3' Library Prep Kit FWD for Illumina and sequenced on the Illumina NextSeq as single-end 150-bp reads.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
Using FastQC, the single end 150 bp reads were trimmed and adapters were removed.
Reads were mapped to human genome hg19 using hisat2.
The aligned reads were converted into read counts per gene with SAMtools and HTSeq in the default union mode.
The raw read counts were normalized via trimmed mean of M-values normalization with the edgeR R package.
Further adjustment and removal of batch effects was performed with SVA and (SNM).
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file with raw gene counts for each sample.
Supplementary_files_format_and_content: Tab-delimited text file with normalized gene expression for each sample.
|
| |
|
| Submission date |
May 20, 2020 |
| Last update date |
May 20, 2021 |
| Contact name |
Angela Mo |
| E-mail(s) |
[email protected]
|
| Organization name |
Georgia Institute of Technology
|
| Department |
School of Biological Sciences
|
| Street address |
950 Atlantic Drive
|
| City |
Atlanta |
| State/province |
GA |
| ZIP/Postal code |
30332 |
| Country |
USA |
| |
|
| Platform ID |
GPL21697 |
| Series (1) |
| GSE150961 |
Treatment Naïve and Follow-Up Pediatric Ulcerative Colitis Rectal Gene Expression |
|
| Relations |
| BioSample |
SAMN14985423 |
| SRA |
SRX8372262 |
