|
| Status |
Public on Apr 11, 2017 |
| Title |
Ulcerative colitis |
| Sample type |
SRA |
| |
|
| Source name |
peripheral whole blood draw
|
| Organism |
Homo sapiens |
| Characteristics |
type: Ulcerative colitis
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Peripheral whole blood was collected into PaxGene tubes. RNA was isolated per the manufacturer's supplied protocol.
Total RNA isolated from PaxGene tubes was purified with the RNeasy MinElute Cleanup kit (Qiagen) using an on-column DNAse treatment to ensure absence of genomic DNA contamination according to the manufacturer’s supplied protocol.
Libraries were constructed using the Illumina TruSeq Stranded mRNA kit (Cat. No. RS-122-2101) following the manufacturer's supplied protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
Illumina Casava1.9 software used for basecalling.
Quality control to filter out bad samples and reads
Alignment to human genome (hg19) using Tophat 2
Read count quantification using HTSeq
Genome_build: hg19
Supplementary_files_format_and_content: text file, FPKM table
|
| |
|
| Submission date |
Dec 15, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Charles F Spurlock III |
| E-mail(s) |
chase.spurlock@vanderbilt.edu
|
| Phone |
6153432363
|
| Organization name |
Vanderbilt University School of Medicine
|
| Department |
Medicine
|
| Lab |
T3113
|
| Street address |
1161 21st Avenue South
|
| City |
Nashville |
| State/province |
Tennessee |
| ZIP/Postal code |
37232 |
| Country |
USA |
| |
|
| Platform ID |
GPL21290 |
| Series (1) |
| GSE92472 |
Expression of long non-coding RNAs in autoimmunity and linkage to enhancer function and autoimmune disease risk genetic variants |
|
| Relations |
| BioSample |
SAMN06146243 |
| SRA |
SRX2430562 |
