GEO Accession viewer

NCBI > GEO > Accession Display

Not logged in | Login

GEO help: Mouse over screen elements for information.

Series GSE85838

Query DataSets for GSE85838

Status

Public on Aug 31, 2018

Title

Affymetrix SNP array data for cell line and tumor genotype alignment

Organism

Homo sapiens

Experiment type

Genome variation profiling by genome tiling array
Third-party reanalysis

Summary

When characterizing novel cell lines, we used SNP genotyping alignment to compare the tumor to the resulting cell line. In order to do this pairwise comparison as each cell model was developed, we added additional data from the GEO database during the normalization step. These data were either tumor DNA or cancer cell line DNA. These samples were not part of a matched pair and so genotype alignment was not reported for these samples.
The GEO Series and Sample numbers used for each sample grouping is as follows. Wood- Series: GSE21541; Samples: GSM533396, GSM533397, GSM533398, GSM533399, GSM533400, GSM533401, GSM533402, GSM533404, GSM533410. Ferry- Series: GSE16125; Samples: GSM403493, GSM403494, GSM403495, GSM403496, GSM403497, GSM403498, GSM403499, GSM403500, GSM403501. Jacket series 1: GSE15126; samples: GSM385517, GSM385518, GSM385519, GSM385520, GSM385521, GSM385522, GSM385523, GSM385524, GSM385525, GSM385526. Jacket series 2: GSE62407; Samples: GSM1526628, GSM1526648, GSM1526668. DF Series GSE39130; Samples: GSM956523, GSM956524, GSM956525, GSM956526, GSM956527, GSM956528.

Overall design

DNA was extracted from cell lines at several passages and the tumor tissue samples from which they were derived. Genotype was determined by SNP 250K Nsp.

Contributor(s)

Agoston ES, Drapkin RI

Citation missing

Has this study been published? Please login to update or notify GEO.

Submission date

Aug 19, 2016

Last update date

Sep 01, 2018

Contact name

Elin S. Agoston

E-mail(s)

esagoston@cellariabio.com

Organization name

Cellaria Biosciences

Street address

675 West Kendall Street

City

Cambridge

State/province

Massachusetts

ZIP/Postal code

02142

Country

USA

Platforms (1)

GPL3718

[Mapping250K_Nsp] Affymetrix Mapping 250K Nsp SNP Array

Samples (15)

More...

GSM2285347	Wood_20PD
GSM2285348	Wood_40PD
GSM2285349	Wood_150PD

Relations

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

BioProject

Download family	Format
SOFT formatted family file(s)	SOFT
MINiML formatted family file(s)	MINiML
Series Matrix File(s)	TXT

Supplementary file	Size	Download	File type/resource
GSE85838_BRLMM_genotyping_Mapping250K_Nsp.txt.gz	26.7 Mb	(ftp)(http)	TXT
GSE85838_RAW.tar	370.2 Mb	(http)(custom)	TAR (of CEL)
Processed data are available on Series record