|
| Status |
Public on Jun 28, 2016 |
| Title |
ARAF_p.D429A_rep1_TA.OE014_A549_96H_X1_B19:H14 |
| Sample type |
RNA |
| |
|
| Source name |
A549
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: A549
genetic modification: ARAF_p.D429A
|
| Treatment protocol |
Cells are grown, treated with virus then lysed. Lysate is analyzed using the L1000 assay.
|
| Growth protocol |
Cells are grown in 384-well plates.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells are lysed in TCL lysate buffer and transferred to Turbocapture plates, which bind the mRNA in the lysate.
|
| Label |
biotin
|
| Label protocol |
mRNA is reverse transcribed and the cDNA product PCR amplified using primers that contain contiguous sequence (barcode) complementary to each L1000 gene; in addition, the upstream primer is biotinylated to enable identification of amplicon-bound beads.
|
| |
|
| Hybridization protocol |
PCR amplicon of each gene is hybridized to barcoded Luminex beads. The barcode incorporated in each amplicon is complementary to a barcode on a Luminex bead, ensuring that each gene from the original lysate mRNA is represented by an amplicon bound to a specific bead.
|
| Scan protocol |
Luminex scanners detect individual beads by color, then measure the fluorescent intensity of the SAPE molecules attached to the biotin label on each amplicon-bound bead.
|
| Data processing |
Raw intensity measurements (LXB) are deconvoluted to provide intensity values for each landmark gene (the 978 directly measured features). Data is then normalized using a calibration curve based on invariant gene sets, and then quantile normalized (Q2NORM). Z-scores are then calculated for each feature with respect to the population of all samples on the plate (Z-SCORES).
|
| |
|
| Submission date |
Jun 27, 2016 |
| Last update date |
Jun 28, 2016 |
| Contact name |
Jesse S. Boehm |
| Organization name |
Broad Institute
|
| Street address |
415 Main Street
|
| City |
Cambridge |
| ZIP/Postal code |
02142 |
| Country |
USA |
| |
|
| Platform ID |
GPL22085 |
| Series (1) |
| GSE83744 |
High-throughput phenotyping of lung cancer somatic mutations [main experiment] |
|
