|
| Status |
Public on Aug 20, 2019 |
| Title |
UC9035 |
| Sample type |
SRA |
| |
|
| Source name |
Liver
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: Normal
tissue: Liver
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from liver biopsies using the miRNeasy Kit (QIAGEN). RNA purity was assessed using the Agilent 2100 Bioanalyzer. Total RNA was converted to cDNA using High-Capacity cDNA Reverse Transcrition Kit (ABI).
The cDNA was then used for Illumina sequencing library preparation by TruSeq Stranded mRNA Library Prep Kit. DNA fragments were further end repaired to generate blunt ends with 5′ phosphatase and 3′ hydroxyls and adapters were ligated for single end or paired end sequencing on Illumina HiSeq 2500.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
The RNA-seq reads were aligned to the human genome (GRCh37/hg19) using TopHat (version 2.1.0)
Transcript quantifications were performed by Cufflinks v2.2.1
Transcript abundances were normalized in reads per kilobase of exon per million mapped reads (RPKM) for single end RNA-seq and fragments per kilobase of exon per million mapped reads (FPKM) for paired end RNA-seq
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM or FPKM values for each sample
|
| |
|
| Submission date |
Nov 08, 2018 |
| Last update date |
Aug 20, 2019 |
| Contact name |
Zhenhua Luo |
| E-mail(s) |
zhenhua.luo@cchmc.org
|
| Phone |
5135171018
|
| Organization name |
Cincinnati Children's Hospital Medical Center
|
| Street address |
3333 Burnet Avenue
|
| City |
Cincinnati |
| State/province |
Ohio |
| ZIP/Postal code |
45229 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE122340 |
A Molecular Signature Predicts 2-Year Outcome of Biliary Atresia and Identifies a Treatment Target to Suppress Fibrosis |
|
| Relations |
| BioSample |
SAMN10396827 |
| SRA |
SRX4997036 |
