|
| Status |
Public on Mar 01, 2007 |
| Title |
Normal (non-malignant) cervical tissue (India: NCx128) |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Normal (non-malignant) cervical tissue
|
| Organism |
Homo sapiens |
| Characteristics |
Gender: Female
Tissue: Non-malignant cervical tissue obtained from radical hysterectomy
|
| Biomaterial provider |
King Edward Memorial Hospital, Mumbai, India
|
| Treatment protocol |
NONE
|
| Growth protocol |
NONE
|
| Extracted molecule |
total RNA |
| Extraction protocol |
TriZol Extraction protocol with an additional chloroform extraction step followed by quantitation in spectrophotometer and checking on formaldehyde-agarose gel. RNA stored in 10mM Sodium Citrate Buffer (Ambion).
|
| Label |
Cy5
|
| Label protocol |
Amino-allyl dUTP based indirect labelling protocol described by Pat Brown Lab, available at http://cmgm.stanford.edu/pbrown/protocols/index.html
|
| |
|
| Channel 2 |
| Source name |
Human Universal Reference RNA
|
| Organism |
Homo sapiens |
| Characteristics |
Purchased from (Stratagene, Cat No. 740000),the Human Universal Reference RNA comprises of a pool of RNA made from 10 different human cell lines including: Adenocarcinoma, mammary gland Melanoma, Hepatoblastoma, liver Liposarcoma Adenocarcinoma, cervix Histiocytic lymphoma; macrophage; histocyte, Embryonal carcinoma, testis Lymphoblastic leukemia, T lymphoblast, Glioblastoma, brain, Plasmacytoma; myeloma; B lymphocyte
|
| Biomaterial provider |
Stratagene, Cat No. 740000
|
| Treatment protocol |
NONE
|
| Growth protocol |
NONE
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Commercial RNA
|
| Label |
Cy3
|
| Label protocol |
Amino-allyl dUTP based indirect labelling protocol described by Pat Brown Lab, available at http://cmgm.stanford.edu/pbrown/protocols/index.html
|
| |
|
| |
| Hybridization protocol |
Hybridization in 2XHyb buffer containing 50%formamide, 10X SSC and 0.2%SDS (adapted from Quackenbush protocol) in a 42 degrees Centigrade waterbath overnight in a Hyb chamber, with the probe under a coverslip, as described by Pat Brown Lab http://cmgm.stanford.edu/pbrown/protocols/index.html
|
| Scan protocol |
Scanned in Axon 4200A Professional according to the manufacturer's instructions.
|
| Description |
It is important to note that the data provides comparison of test sample against the universal reference RNA, and not cancer versus normal ratios.
|
| Data processing |
Slides have been scanned by Axon scanner 4200A and data analyzed by GenePix Version 5.0. 'Value' column represents normalized, log transformed, ratio of medians of CH1/CH2. Normalization has been carried out with respect to 'all normalization features' using GenePix software. Normalization features meet the following criteria:[F532 Median]>= 250 And [F635 Median]>= 250 And [F Pixels]>=30 And [Dia.]>=50 And[% >B635+1SD]>55 And[% >B532+1SD]>55
|
| |
|
| Submission date |
Jan 23, 2007 |
| Last update date |
Mar 13, 2007 |
| Contact name |
Chandan Kumar |
| E-mail(s) |
ckumar@actrec.res.in, drchandan.kumar@gmail.com
|
| Phone |
+91-22-27405068
|
| Fax |
+91-22-27412894
|
| Organization name |
Tata Memorial Center
|
| Department |
ACTREC
|
| Lab |
CHANDAN Lab
|
| Street address |
Kharghar Node
|
| City |
Navi Mumbai |
| State/province |
Maharashtra |
| ZIP/Postal code |
410208 |
| Country |
India |
| |
|
| Platform ID |
GPL3516 |
| Series (1) |
| GSE4482 |
Microarray based Gene expression profiling of Cervical Cancer in India |
|
