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Sample GSM2629878 Query DataSets for GSM2629878
Status Public on Jun 23, 2020
Title MCF7-LTED
Sample type genomic
 
Source name MCF7-LTED, resistant to estrogen deprivation
Organism Homo sapiens
Characteristics cell type: MCF7-LTED
cell line: MCF7-LTED
compound: resistant to estrogen deprivation
Treatment protocol wt cells were treated long term with palobociclib until thay develop resistance.
Growth protocol Cell lines were grown according to standard conditions.
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted from target cell lines using QIAamp DNA mini kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, PicoGreen and agarose gel electrophoresis.
Label Biotin
Label protocol As per manufacturer (Affymetrix)
 
Hybridization protocol DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.
Scan protocol The Arrays were then washed using Affymetrix fluidics stations, and scanned using the GeneChip® Scanner 3000 7G with AutoLoader.
Description basal
Data processing SNPs were called using the Birdseed v2 algorithm (.CHP files), and copy number variations were called using the CN5 algorithm (.CNCHP files) using Affymetrix Genotyping Console 4.0 (Affymetrix). Sample table and .CNCHP data are based on genome build GRCh37 (hg19). HapMap samples were used as a reference.
Genotype Call (SNP call): AA, AB, BB, and NoCall; 'Signal' = Summarized signal
 
Submission date May 17, 2017
Last update date Jun 23, 2020
Contact name Alice Gao
E-mail(s) alice.gao@icr.ac.uk
Organization name The Institute of Cancer Research
Department Breast Cancer Now
Lab Molecular Cell Biology
Street address 237 Fulham Road
City London
State/province London
ZIP/Postal code SW3 6JB
Country United Kingdom
 
Platform ID GPL6801
Series (2)
GSE99002 Resistance to Palbociclib involves multiple mechanisms amenable to targeting with drug holidays or drug switching to improve therapeutic outcome [Affymetrix]
GSE99003 Resistance to Palbociclib involves multiple mechanisms amenable to targeting with drug holidays or drug switching to improve therapeutic outcome

Data table header descriptions
ID_REF PROBE SET NAME
VALUE CALL
CONFIDENCE
FORCED CALL
SIGNAL A
SIGNAL B

Data table
ID_REF VALUE CONFIDENCE FORCED CALL SIGNAL A SIGNAL B
SNP_A-2131660 BB 0.006493 BB 571.438904 1036.740234
SNP_A-1967418 BB 0.002186 BB 315.025879 769.906067
SNP_A-1969580 BB 0.006842 BB 825.638123 2804.608398
SNP_A-4263484 BB 0.007649 BB 448.104065 1558.453613
SNP_A-1978185 AA 0.013323 AA 1328.449219 625.068359
SNP_A-4264431 AB 0.008720 AB 857.584839 719.253845
SNP_A-1980898 BB 0.004392 BB 239.127121 1006.532227
SNP_A-1983139 AA 0.012532 AA 2025.931641 817.295959
SNP_A-4265735 NC 0.112355 AB 402.398682 1298.432495
SNP_A-1995832 AB 0.005432 AB 896.182739 841.072571
SNP_A-1995893 BB 0.004463 BB 848.711792 1742.603882
SNP_A-1997689 BB 0.003308 BB 643.337891 2621.195801
SNP_A-1997709 AA 0.005262 AA 1263.751953 235.233154
SNP_A-1997896 AA 0.004173 AA 1739.931274 562.863708
SNP_A-1997922 AB 0.007078 AB 995.858398 877.848083
SNP_A-2000230 AA 0.005402 AA 2392.323730 1819.358398
SNP_A-2000332 AA 0.005812 AA 3157.939209 1771.302490
SNP_A-2000337 AA 0.003019 AA 1142.864624 339.702148
SNP_A-2000342 AA 0.002390 AA 3257.288574 945.557190
SNP_A-4268173 AB 0.005464 AB 1097.129761 1006.674866

Total number of rows: 909622

Table truncated, full table size 46157 Kbytes.




Supplementary file Size Download File type/resource
GSM2629878_A3198-03.CEL.gz 26.3 Mb (ftp)(http) CEL
GSM2629878_A3198-03.birdseed-v2.chp.gz 13.6 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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