|
| Status |
Public on Feb 29, 2016 |
| Title |
RNAseq-P2-T |
| Sample type |
SRA |
| |
|
| Source name |
kidney
|
| Organism |
Homo sapiens |
| Characteristics |
gender: female
individual: patient2
tissue: tumor
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tissues of ccRCC and matched normal were removed and frozened in RNA Later and stored in -80°. And RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Paired reads were treated as single end and mapped to hg19 whole genome using bwa with default parameters, followed by extracting uniquly mapped reads.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated. In short, exons from one transcript of a gene (not including microRNA) were used. The number of reads falling in the exons of this gene were counted, followed by being log-transformed, and scaled between 0 and 1. Given a patient, the transformed RPKMs of ccRCC sample were scaled according to the average value of transformed RPKMs of normal tissue.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include normalized RPKM values for each Sample
|
| |
|
| Submission date |
Nov 12, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Jing Zhang |
| E-mail(s) |
henry.jingzhang@gmail.com
|
| Organization name |
Columbia University Medical Center
|
| Street address |
1130 St Nicholas Ave ICRC, room403
|
| City |
Beijing |
| ZIP/Postal code |
10032 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE63183 |
Loss of 5-hydroxymethylcytosine is linked to gene body hypermethylation in kidney cancer |
|
| Relations |
| BioSample |
SAMN03175431 |
| SRA |
SRX757566 |
