|
| Status |
Public on Dec 26, 2018 |
| Title |
2b_woman_HH2376 [T00279473] |
| Sample type |
RNA |
| |
|
| Source name |
female_frozen lactotrop tumor_2b
|
| Organism |
Homo sapiens |
| Characteristics |
gender: female
classification: 2b
tissue: lactotroph pituitary tumor
|
| Treatment protocol |
no treatment before resection
|
| Growth protocol |
All included tumors were resected between 1989 and 2005 by the transsphenoidal route and were further shown to be positive for prolactin expression by immunohistochemistry. The tumors were rapidly frozen after resection
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from pituitary tumors using Trizol (Invitrogen), according to the manufacturer’s protocol (Invitrogen, Carlsbad, California, USA)
|
| Label |
biotin
|
| Label protocol |
Total RNA (2 µg) was amplified and biotin-labeled by a round of in vitro transcription with a Message Amp aRNA kit (Ambion, Austin, Texas, USA) following the manufacturer’s protocol
|
| |
|
| Hybridization protocol |
Ten micrograms of biotin-labelled aRNA was fragmented using 5 μl of fragmentation buffer in a final volume of 20 µl and was then mixed with 240 µl of Amersham hybridization solution (GE Healthcare Europe GmbH, Freiburg, Germany) and injected onto CodeLink Uniset Human Whole Genome bioarrays containing 55000 human oligonucleotide gene probes (GE Healthcare Europe GmbH, Freiburg, Germany)
|
| Scan protocol |
The slides were scanned using a Genepix 4000B scanner (Axon, Union City, USA) and Genepix software, with the laser set at 635 mm, the laser power at 100%, and the photomultiplier tube voltage at 60%.
|
| Description |
2b_woman_HH2376
|
| Data processing |
The scanned image files were analyzed using CodeLink expression software, version 4.2 (GE Healthcare), which produces both a raw and a normalized hybridization signal for each spot on the array. CodeLink software was used to normalize the raw hybridization signal on each array to the median of the array (median intensity is 1 after normalization) for better cross-array comparison. The threshold of detection was calculated using the normalized signal intensity of the 100 negative control samples in the array: spot with signal intensity below this threshold was referred as ‘absent’. The quality of processing was evaluated by generating scatter plots of positive signal distribution.
The complete_data.txt contains raw (SIGNAL_RAW), normalized data (VALUE) and quality flag data.
|
| |
|
| Submission date |
Sep 24, 2018 |
| Last update date |
Dec 26, 2018 |
| Contact name |
Anne Wierinckx |
| E-mail(s) |
anne.wierinckx@univ-lyon1.fr
|
| Organization name |
University Lyon1
|
| Street address |
8, av Rockefeller
|
| City |
Lyon |
| State/province |
select a state |
| ZIP/Postal code |
69008 |
| Country |
France |
| |
|
| Platform ID |
GPL2895 |
| Series (1) |
| GSE120350 |
Sex-related differences in lactotroph tumor aggressiveness are associated with a specific gene-expression signature and genome instability |
|
