 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jun 01, 2014 |
| Title |
330 |
| Sample type |
SRA |
| |
|
| Source name |
prostate
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: prostate
|
| Treatment protocol |
The frozen tissues were homogenized by mortar in liquid nitrogen, followed by 1ml TRIZOL/100mg tissue to be homogenized into a falcon tube.
|
| Growth protocol |
we selected tissue samples from 10 anonymous donors.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Add 200ul chloroform plus 1mL TRIZOL, and vortex for 15 seconds, and then centrifuge samples at 12,000g for 15 minutes at 2-8 C. Transfer the aqueous phase to a fresh tube. Add 500ul isopropanol plus 1mL TRIZOL to the this new tube, vortex and centrifuge samples at 12,000g for 10 minutes at 2-8 C again. Following centrifugation, remove the supernatant. Wash RNA pellet with 70% alcohol plus 1ml TRIZOL, vortex, and Centrifuge samples again. Remove supernatant and dry the pellet, then redissolve it in 100ul DEPC water. After Dnase Treatment, RNA was purified using Rneasy Column Purification based on Qiagen’s Rneasy Protocol.
The protocol was based on TruSeq RNA Sample Preparation Kits v2
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
mRNA tissue sample from patient 330
|
| Data processing |
eRNA were developed to process data from mRNA sequencing.
Human genome reference sequences downloaded from NCBI ftp site (Release 103) with Bowtie2
TopHat and Bowtie were used for genome mapping.
Cufflinks were sued for transcripts assembling.
Genome_build: human genome reference sequences downloaded from NCBI ftp site (Release 103) with Bowtie2.
Supplementary_files_format_and_content: Data frame of FPKM of mRNAs in *.txt
|
| |
|
| Submission date |
Dec 18, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Liang Wang |
| E-mail(s) |
liwang@mcw.edu
|
| Phone |
414-955-2574
|
| Organization name |
Medical College of Wisconsin
|
| Department |
Pathology
|
| Street address |
8701 Watertown Plank Rd.
|
| City |
Milwaukee |
| State/province |
Wisconsin |
| ZIP/Postal code |
53226 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE53450 |
eRNA: A graphic user interface-based tool for RNA sequencing data analysis [mRNA-Seq] |
| GSE53452 |
eRNA: A graphic user interface-based tool for RNA sequencing data analysis |
|
| Relations |
| BioSample |
SAMN02463964 |
| SRA |
SRX395557 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1293749_330_genes.fpkm_tracking.gz |
843.2 Kb |
(ftp)(http) |
FPKM_TRACKING |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
