|
| Status |
Public on Mar 23, 2021 |
| Title |
COLO205_single cell derived_Selumetinib resistant-5b |
| Sample type |
genomic |
| |
|
| Source name |
Colorectal cancer cell line
|
| Organism |
Homo sapiens |
| Characteristics |
growth media: RPMI-1640 + 1µM selumetinib
molecule: Genomic DNA
|
| Treatment protocol |
Cells were seeded in 25 cm2 flasks and treated with fresh growth media or media containing 1 µM selumetinib 24 hours later. Media and drug were changed weekly until colonies (>50 cells) of proliferating cells were formed in culture.
|
| Growth protocol |
Parental and selumetinib resistant COLO205 cell lines were grown in RPMI-1640 media supplemented with 10% (v/v) foetal bovine serum, penicillin (100 U/mL), streptomycin (100 mg/mL) and 2 mM glutamine in the absence or presence of 1 µM selumetinib respectively at 37 °C in a humidified incubator with 5% (v/v) CO2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells grown in growth media were harvested by trypsinisation, centrifuged (300 x g for 3 minutes) and washed once in PBS. Genomic DNA from cells was extracted using a a Qiagen DNeasy Blood and Tissue kit (Qiagen, 69504)
|
| Label |
Cy3 and Cy5
|
| Label protocol |
200 ng of genomic DNA was amplified in a reaction mix containing multi-sample amplification Mix 1, multi-sample amplification mix 2 and multi- sample master mix according to the instructions provided by the manufacturer (Illumina). See https://emea.support.illumina.com/downloads/infinium-cytosnp-850k-reference-guide-15046990.html
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| |
|
| Hybridization protocol |
Amplified and fragmented DNA samples were hybridised to BeadChips according to the instructions provided by the manufacturer (Illumina). See https://emea.support.illumina.com/downloads/infinium-cytosnp-850k-reference-guide-15046990.html
|
| Scan protocol |
BeadChips were scaned using the iScan system according to the instructions provided by the manufacturer (Illumina) See https://emea.support.illumina.com/downloads/infinium-cytosnp-850k-reference-guide-15046990.html
|
| Description |
SAMPLE 16
|
| Data processing |
The raw intensity data (.idat) files were converted to genotype call (.gtc) files using Beeline version 4.5 and then imported to BlueFuse multi version 4.5 and analysed using BlueFuse algorithm with default settings(10 contiguous markers for CNV and 500 contiguous markers for loss of heterozygosity (LOH)).Samples 1-8 processed on Illumina CytoSNP 850K v1.1 were analysed using the cluster file CytoSNP850Kv1-1_iScan_C1_ClusterFile.egt and manifest file CytoSNP-850Kv1-1_iScan_C1.bpm. Samples 9-16 processed on Illumina CytoSNP 850K v1.2 beadchips were analysed using the cluster file CytoSNP850Kv1-2_iScan_B1_ClusterFile.egt and CytoSNP-850Kv1-2_iScan_B3.bpm. The annotation file used for the analysis was BG_Annotation_Ens74_20180801.db (genome build 37).
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| |
|
| Submission date |
Mar 10, 2021 |
| Last update date |
Sep 14, 2022 |
| Contact name |
Laura Biggins |
| E-mail(s) |
laura.biggins@babraham.ac.uk
|
| Organization name |
The Babraham Institute
|
| Department |
Bioinformatics
|
| Street address |
Babraham Research Campus
|
| City |
Cambridge |
| ZIP/Postal code |
CB22 3AT |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL19718 |
| Series (2) |
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