|
| Status |
Public on Jul 26, 2021 |
| Title |
1416_UC uninflamed sigmoid colon |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
UC uninflamed sigmoid colon
|
| Organism |
Homo sapiens |
| Characteristics |
Sex: not determined
diagnosis: Ulcerative colitis
inflammation: Uninflamed
tissue: Colon
batch: 7
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with Qiagen RNeasy Plus kit with removal of genomic DNA.
|
| Label |
Cy5
|
| Label protocol |
Total RNA was converted to double-stranded cDNA and then into Cy-dye labeled cRNA using Quick Amp Labeling Kit (Agilent). For all samples, 750 ng of the labeled cRNA was fragmented and hybridized against Cy3-labeled Universal human reference (Stratagene, La Jolla, CA).
|
| |
|
| Channel 2 |
| Source name |
Universal human reference (UHR) from Stratagene
|
| Organism |
Homo sapiens |
| Characteristics |
sample type: pooled human reference RNA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with Qiagen RNeasy Plus kit with removal of genomic DNA.
|
| Label |
Cy3
|
| Label protocol |
Total RNA was converted to double-stranded cDNA and then into Cy-dye labeled cRNA using Quick Amp Labeling Kit (Agilent). For all samples, 750 ng of the labeled cRNA was fragmented and hybridized against Cy3-labeled Universal human reference (Stratagene, La Jolla, CA).
|
| |
|
| |
| Hybridization protocol |
Agilent In Situ Hybridization Kit Plus was used where Cy-dye labeled control and test samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, the arrays were washed twice, dried and then scanned.
|
| Scan protocol |
Scanned on an Agilent scanner, images were processed using Agilent Feature Extraction software version 10.7.
|
| Description |
SAM745532
|
| Data processing |
Raw intensity data were background subtracted using the normal + exponential method from the limma Bioconductor package. The test/reference ratio was log2 transformed and normalized using loess normalization for each array. Loess normalized log2 ratios were then subjected to quantiles normalization across all arrays in the dataset.
|
| |
|
| Submission date |
Jul 01, 2021 |
| Last update date |
Jul 27, 2021 |
| Contact name |
Jason A Hackney |
| E-mail(s) |
hackney.jason@gene.com
|
| Organization name |
Genentech, Inc.
|
| Department |
Department of Bioinformatics and Computational Biology
|
| Street address |
1 DNA Way
|
| City |
South San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94080 |
| Country |
USA |
| |
|
| Platform ID |
GPL6480 |
| Series (1) |
| GSE179285 |
Embark cross-sectional study of inactive and active lesions from the ileum and colon of inflammatory bowel disease patients |
|
