|
| Status |
Public on Jun 18, 2015 |
| Title |
RCC112s |
| Sample type |
RNA |
| |
|
| Source name |
Renal Cell Carcinoma
|
| Organism |
Homo sapiens |
| Characteristics |
sampletype: S
data set: Data 1
batch: 11
pretreatment: None
chipversion: Illumina HumanHT-12_v3
Stage: IV
grade: Sarcomatoid
flagged: TRUE
|
| Treatment protocol |
N/A
|
| Growth protocol |
N/A
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Epicentre MasterPure Complete DNA and RNA Purification Kit
|
| Label |
biotin
|
| Label protocol |
Illumina DASL Protocol Inoculate PCR (one product labeled with fluorescent dye and the other is biotynylated
|
| |
|
| Hybridization protocol |
Illumina DASL Expression Chip Protocol
|
| Scan protocol |
Illumina Bead Array Reader DirectHyb Gene Expression
|
| Description |
X5367784020_D
|
| Data processing |
There are 3 sets of raw data. “Data 1” contains batches 10, 11, 15 and 16. “Data 2” only contains batch 17. “Data 3” contains batches K04 and K05. “Data 1” was obtained by Illumina HumanHT-12_v3 and “Data 2” and “Data 2” were obtained by Illumina HumanHT-12_v4. We normalized data using “Data 1” and “Data 2” (“Quantile normalized Data1+Data2”). We also use all three data sets to normalize (“Quantile normalized All”). Since there are different number of probe sets between V3 and V4, we used common probes for normalization. The data were log 2 transformed and normalized using quantile normalization.
|
| |
|
| Submission date |
Jul 09, 2014 |
| Last update date |
Jun 18, 2015 |
| Contact name |
Kanishka Sircar |
| E-mail(s) |
ksircar@mdanderson.org
|
| Organization name |
MD Anderson Cancer Center
|
| Street address |
1515 Holcombe Blvd., G1.3623
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL6947 |
| Series (2) |
| GSE59264 |
Genome wide transcriptomic analysis of sarcomatoid (E/S), rhabdoid (E/R) and non-sarcomatoid (E*) clear cell renal cell carcinoma |
| GSE59266 |
Genome wide analysis of sarcomatoid and non-sarcomatoid clear cell renal cell carcinoma |
|
