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Sample GSM1655622

Query DataSets for GSM1655622

Status

Public on Feb 29, 2016

Title

KP363T_snp

Sample type

genomic

Source name

CRC

Organism

Characteristics

tissue: colorectal cancer
gender: M
tumor location: Left-sided colon
tumor type: Adenocarcinoma
tumor stage (dukes): B2

Extracted molecule

genomic DNA

Extraction protocol

DNA was isolated using the Wizard genomic DNA isolation kit

Label

Cy3,Cy5

Label protocol

200 ng of DNA was labelled according to the standard illumina protocol

Hybridization protocol

Standard illumina protocol

Scan protocol

Standard illumina protocol

Description

Genomic DNA isolated from novel CRC cell lines was genotyped using the Illumina HumanExome-12 v1.0 BeadChip

Data processing

Data were processed in GenomeStudio. The file HumanExome-12_v1.0_signal.txt contains the raw signals and is available on the series record.

Submission date

Apr 10, 2015

Last update date

Feb 29, 2016

Contact name

Arnoud Boot

Organization name

Duke-NUS Medical School

Street address

8 college road

City

Singapore

State/province

Singapore

ZIP/Postal code

169857

Country

Singapore

Platform ID

Series (2)

GSE67773	SNP-array profiling of 21 novel primary and metastatic colorectal cancer cell lines [Illumina HumanExome-12 v1.0 BeadChip]
GSE67775	Omics profiling of 21 novel primary and metastatic colorectal cancer cell lines

Data table header descriptions
ID_REF
VALUE	genotype call
KP363T_B_Allele_Freq
KP363T_GC_SCORE
KP363T_Log_R_Ratio
KP363T_R
KP363T_Theta

Data table
ID_REF	VALUE	KP363T_B_Allele_Freq	KP363T_GC_SCORE	KP363T_Log_R_Ratio	KP363T_R	KP363T_Theta
exm-IND1-200449980-0_M_R_1990486447	BB	1	0.404	0.389	0.441	0.987
exm-IND1-201453487-0_M_R_1990486448	BB	0.9961	0.9136	-0.1329	1.062	0.989
exm-IND1-85310248-0_P_F_1990486624	AA	0.0077	0.8485	-0.1992	0.429	0.017
exm-IND10-102817747-0_P_F_1990486569	BB	0.9669	0.838	0.1667	1.193	0.963
exm-IND10-18329639-0_M_R_1990486442	AA	7.00E-04	0.4358	0.0971	1.357	0.044
exm-IND10-27476467-0_M_R_1990486443	BB	1	0.8748	0.1328	1.403	0.995
exm-IND10-27727540-0_M_R_1990486444	BB	1	0.9589	0.0794	0.694	0.994
exm-IND10-74560589-0_P_F_1990486573	AA	0	0.9469	0.4864	0.799	0.016
exm-IND11-102094357-0_P_F_1990486575	AA	0.0029	0.7873	-0.1168	1.364	0.006
exm-IND11-60867390-0_M_R_1990486445	BB	1	0.8699	0.0385	0.737	0.968
exm-IND11-73463127-0_P_F_1990486580	AA	0	0.7674	0.2369	1.726	0.016
exm-IND12-4584372-0_P_F_1990486581	AA	0.0076	0.7497	0.2661	1.773	0.026
exm-IND12-46829523-0_M_R_1990486450	AA	0.0032	0.7742	0.2898	1.779	0.011
exm-IND12-49036005-0_P_F_1990486582	AA	0.0081	0.8497	0.4149	1.245	0.025
exm-IND12-51232970-0_P_F_1990486584	BB	1	0.8459	0.1482	1.008	0.977
exm-IND12-54361914-0_M_R_1990486452	AA	6.00E-04	0.6786	0.3008	2.203	0.034
exm-IND12-67380833-0_P_F_1990486586	AA	0.0051	0.5335	0.3542	0.907	0.012
exm-IND12-83947680-0_M_R_1990486453	AA	0	0.7839	-0.0588	0.381	0
exm-IND12-8887191-0_M_R_1990486455	BB	1	0.9335	0.0051	0.866	0.994
exm-IND13-47565698-0_P_F_1990486590	AA	0	0.8752	0.216	1.17	0.018

Total number of rows: 247870

Table truncated, full table size 14997 Kbytes.

Supplementary file	Size	Download	File type/resource
GSM1655622_7539041023_R06C02_Grn.idat.gz	2.1 Mb	(ftp)(http)	IDAT
GSM1655622_7539041023_R06C02_Red.idat.gz	2.0 Mb	(ftp)(http)	IDAT
Processed data included within Sample table

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