|
| Status |
Public on Jan 27, 2015 |
| Title |
biological rep264 |
| Sample type |
RNA |
| |
|
| Source name |
pouch
|
| Organism |
Homo sapiens |
| Characteristics |
batch: 4
gender: F
individual: IND173
diagnosis: FAP
|
| Treatment protocol |
not applicable
|
| Growth protocol |
not applicable
|
| Extracted molecule |
total RNA |
| Extraction protocol |
miRNeasy Mini Kit (QIAGEN)
|
| Label |
biotin
|
| Label protocol |
GeneChip WT Terminal Labeling and Controls Kit (Affymetrix)
|
| |
|
| Hybridization protocol |
GeneChip Hybridization, Wash, and Stain Kit (Affymetrix)
|
| Scan protocol |
Affymetrix GeneChip Scanner 3000
|
| Description |
tissue biopsy from human, post IPAA subjects
|
| Data processing |
Summarized probe cell intensity data were generated with an Affymetrix GeneChip Command Console. Probe-level summarization files were produced and the data were background-adjusted, normalized and log-transformed with a robust multiarray average (RMA) algorithm in Affymetrix Expression Console. The empirical Bayes (EB) method described by Johnson, W.E. et al. (2007) was applied to the normalized data to correct for batch effects which may have resulted from a non-linear sample extraction and microarray processing schedule. Lastly, duplicate and ambiguous Affymetrix probesets (Release 32) as well as those which no longer mapped to a gene in the current human genome build (GRCh37.p5) were removed from further analysis.
HuGene-1_0-st-v1.r4.pgf
HuGene-1_0-st-v1.r4.mps
|
| |
|
| Submission date |
Jan 26, 2015 |
| Last update date |
Jan 27, 2015 |
| Contact name |
Boyko Kabakchiev |
| Organization name |
Mount Sinai Hospital
|
| Department |
Samuel Lunenfeld Research Institute
|
| Lab |
Silverberg Lab
|
| Street address |
60 Murray Street, Room L3-004
|
| City |
Toronto |
| State/province |
Ontario |
| ZIP/Postal code |
M5T 3L9 |
| Country |
Canada |
| |
|
| Platform ID |
GPL6244 |
| Series (1) |
| GSE65270 |
Associations between host gene expression, the mucosal microbiome, and clinical outcome in the pelvic pouch of patients with inflammatory bowel disease. |
|
