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Status |
Public on Jun 28, 2016 |
Title |
EGFR_p.L858R_rep5_TA.OE014_A549_96H_X2_B19:E19 |
Sample type |
RNA |
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Source name |
A549
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Organism |
Homo sapiens |
Characteristics |
cell line: A549 genetic modification: EGFR_p.L858R
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Treatment protocol |
Cells are grown, treated with virus then lysed. Lysate is analyzed using the L1000 assay.
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Growth protocol |
Cells are grown in 384-well plates.
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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.
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Label |
biotin
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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.
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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.
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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.
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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).
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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 |
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Platform ID |
GPL22085 |
Series (1) |
GSE83744 |
High-throughput phenotyping of lung cancer somatic mutations [main experiment] |
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