|
| Status |
Public on Mar 02, 2007 |
| Title |
Microarray profile of Cervical Cancer Cell Line- SiHa |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Cervical Cancer Cell Line
|
| Organism |
Homo sapiens |
| Characteristics |
This line was established from fragments of a primary tissue sample obtained after surgery from a Japanese patient. Electron microscopic observations revealed presence of typical desmosomes at the cell junctions and an abundance of tonofilaments in the cytoplasm.
The line is reported to contain an integrated human papillomavirus type 16 genome (HPV-16, 1 to 2 copies per cell). {Information obtained from: http://www.atcc.org/common/catalog/numSearch/numResults.cfm )
|
| Biomaterial provider |
Dr. Sudhir Krishna, National center for Biological Sciences, Bangalore, India
|
| Treatment protocol |
No treatment, Grown in prescribed media till subconfluent.
|
| Growth protocol |
Dulbecco's Minimum essential medium with 10%
fetal bovine serum, Temperature: 37.0C
|
| 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 |
none
|
| 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 |
Mar 01, 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 |
GPL3515 |
| Series (1) |
| GSE4482 |
Microarray based Gene expression profiling of Cervical Cancer in India |
|
