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Series GSE28108 Query DataSets for GSE28108
Status Public on Dec 01, 2011
Title Expression profile of Gli1-expressing keratinocytes from mouse skin
Organism Mus musculus
Experiment type Expression profiling by array
Summary To assess if Hedgehog (Hh) responding cells in the skin have a unique expression profile, isolated keratinocytes that express the Hh response gene Gli1 were collected by FACS and their gene expression was compared to sorted CD34-expressing cells from the middle bulge region of the hair follicle and to cells from the interfollicular epidermis (IFE) by hybridization of isolated RNA to gene expression microarrays.
Overall design Dissociated keratinocytes isolated form back skin of Gli1-eGFP/+ mice (2 mice pooled for each replicate) in adult telogen were sorted based on GFP expression and immunostaining for CD34. Only viable, single cells with immunostaining for α6 Integrin (to mark basal keratinocytes) were collected. GFP(+) cells were collected as the Gli1 cohort. GFP(-) CD34(+) cells were collected as the CD34 cohort, and GFP(-) CD34(-) cells were collected as interfollicular epidermis (IFE) cohort. Total RNA was extracted from each cell population and labeled for hybridization to gene expression microarrays. The experiment was preformed in triplicate, however RNA from the Gli1(+) cells in one replicate was of insufficient quality to analyze. For staining of isolated keratinocytes, cells were incubated on ice for 1 hour in SMEM containing 1%BSA and 15μL of anti-CD49f-PE antibody (BDBioscience) plus 5μL anti-CD34-APC antibody (eBioscience) for each 100μL total volume for each 2 million cells. Immediately prior to sorting, DAPI (Invitrogen) was added to the washed cells at 1μg/mL final concentration.
Contributor(s) Brownell I, Guevara E, Bai CB, Loomis CA, Joyner AL
Citation(s) 21549329
Submission date Mar 22, 2011
Last update date Jun 14, 2018
Contact name Jeffrey Zhao
Organization name Memorial Sloan Kettering Cancer Center
Department Genomics Core
Street address 1275 York Avenue
City New York
State/province NY
ZIP/Postal code 10065
Country USA
Platforms (1)
GPL6885 Illumina MouseRef-8 v2.0 expression beadchip
Samples (8)
GSM696308 keratinocytes Gli1+ rep2
GSM696309 keratinocytes Gli1+ rep3
GSM696310 keratinocytes Gli1- CD34+ rep1
BioProject PRJNA139697

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE28108_20101012_BrownellI_20101012_BrownellI_nonorm_nobkgd_GEOarchive_Matrix.txt.gz 2.5 Mb (ftp)(http) TXT
GSE28108_RAW.tar 3.1 Mb (http)(custom) TAR
Raw data are available on Series record
Processed data included within Sample table

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