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Sample GSM2214886 Query DataSets for GSM2214886
Status Public on Jun 28, 2016
Title EGFR_p.D837A_rep1_TA.OE014_A549_96H_X1_B19:N03
Sample type RNA
 
Source name A549
Organism Homo sapiens
Characteristics cell line: A549
genetic modification: EGFR_p.D837A
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]

Data table header descriptions
ID_REF
VALUE Gene expression levels that have been normalized.

Data table
ID_REF VALUE
201000_at 10.8900
203192_at 9.3400
209380_s_at 4.4900
200045_at 8.9200
202394_s_at 8.3600
218581_at 9.1400
221552_at 7.2200
202123_s_at 9.1800
214274_s_at 8.1800
209608_s_at 9.1400
202324_s_at 7.1400
204617_s_at 8.3700
210337_s_at 11.5700
221641_s_at 10.5200
202604_x_at 9.5700
219384_s_at 6.7200
218168_s_at 4.3000
208847_s_at 10.3500
217761_at 8.5500
212500_at 7.2600

Total number of rows: 978

Table truncated, full table size 17 Kbytes.




Supplementary file Size Download File type/resource
GSM2214886_TA.OE014_A549_96H_X1_B19_N03.lxb.gz 738.8 Kb (ftp)(http) LXB
Processed data included within Sample table
Processed data are available on Series record

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