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Sample GSM186251 Query DataSets for GSM186251
Status Public on Apr 21, 2008
Title BR2 5/20 CD34- vs. BR2 5/20 CD34+ Cy3: BR2 5/20 CD34+ Cy5: BR2 5/20 CD34-
Sample type RNA
 
Channel 1
Source name BR2 5/20 CD34+
Organism Mus musculus
Characteristics treated
Treatment protocol Keratinocytes were harvested from adult mouse skin (7 weeks of age) following digestion in 0.25% trypsin for 2 hours at 32 C. Single cell preparations were made after epidermal cells were scraped into fresh media (SMEM supplemented with 10% fetal bovine serum and 1X gentamicin). Cells were stained with antibodies to CD34 (rat anti-mouse CD34 RAM clone and rat anti-human alpha-6 integrin) and sorted into alpha6+CD34+ (stem and progenitor cells) and alpha6+CD34- (basal cells) using fluorescence activated cell sorting (FACS).
Extracted molecule total RNA
Extraction protocol The CD34+ and CD34- cells were pelleted and lysed in 1 ml lysis buffer with beta-mercaptoethanol (Qiagen Rnasesy kit), then total RNA extracted following manufacturer’s protocol.
Label Cy3
Label protocol Total RNA was amplified using the Agilent Low RNA Input Fluorescent Linear Amplification Kit protocol. Starting with 0.5µg of total RNA, Cy3 or Cy5 labeled cRNA was produced according to manufacturer's protocol.
 
Channel 2
Source name BR2 5/20 CD34-
Organism Mus musculus
Characteristics control
Treatment protocol Keratinocytes were harvested from adult mouse skin (7 weeks of age) following digestion in 0.25% trypsin for 2 hours at 32 C. Single cell preparations were made after epidermal cells were scraped into fresh media (SMEM supplemented with 10% fetal bovine serum and 1X gentamicin). Cells were stained with antibodies to CD34 (rat anti-mouse CD34 RAM clone and rat anti-human alpha-6 integrin) and sorted into alpha6+CD34+ (stem and progenitor cells) and alpha6+CD34- (basal cells) using fluorescence activated cell sorting (FACS).
Extracted molecule total RNA
Extraction protocol The CD34+ and CD34- cells were pelleted and lysed in 1 ml lysis buffer with beta-mercaptoethanol (Qiagen Rnasesy kit), then total RNA extracted following manufacturer’s protocol.
Label Cy5
Label protocol Total RNA was amplified using the Agilent Low RNA Input Fluorescent Linear Amplification Kit protocol. Starting with 0.5µg of total RNA, Cy3 or Cy5 labeled cRNA was produced according to manufacturer's protocol.
 
 
Hybridization protocol For each two color comparison, 750ng of each Cy3 and Cy5 labeled cRNAs were mixed and fragmented using the Agilent In Situ Hybridization Kit protocol. Hybridizations were performed for 17 hours in a rotating hybridization oven using the Agilent 60-mer oligo microarray processing protocol.
Scan protocol Chips were scanned with an Agilent Scanner and processed with the Agilent Feature Extraction Software (v7.5).
Description Total RNA was amplified using the Agilent Low RNA Input Fluorescent Linear Amplification Kit protocol. Starting with 500ng of total RNA, Cy3 or Cy5 labeled cRNA was produced according to manufacturer's protocol. For each two color comparison, 750ng of each Cy3 and Cy5 labeled cRNAs were mixed and fragmented using the Agilent In Situ Hybridization Kit protocol. Hybridizations were performed for 17 hours in a rotating hybridization oven using the Agilent 60-mer oligo microarray processing protocol. Chips were scanned with an Agilent Scanner and processed with the Agilent Feature Extraction Software (v7.5).
Data processing Agilent Feature Extraction protocol for 44K arrays, log2ratio Treated/Control
 
Submission date May 02, 2007
Last update date Apr 21, 2008
Contact name NIEHS Microarray Core
E-mail(s) microarray@niehs.nih.gov, liuliw@niehs.nih.gov
Organization name NIEHS
Department DIR
Lab Microarray Core
Street address 111 T.W. Alexander Drive
City RTP
State/province NC
ZIP/Postal code 27709
Country USA
 
Platform ID GPL891
Series (1)
GSE7690 Comprehensive Microarray Transcriptome Profiling of CD34-Enriched Mouse Keratinocyte Stem Cells

Data table header descriptions
ID_REF Feature IDs from the Agilent oligo array
VALUE log base 10 ratio of Normalized Treated to Reference

Data table
ID_REF VALUE
1 0.7400697796
2 0.2112073879
3 0.05056824632
4 0.07512064844
5 -0.4293948928
6 -0.0433558674
7 1.826819525
8 -0.06823351654
9 -0.2129588407
10 -0.008896817038
11 0.01316394288
12 0.04070305752
13 -0.006252706337
14 1.813874205
15 -0.1257964723
16 0.1360757119
17 0.0192355708
18 -0.5315077628
19 0.01655410926
20 0.08682835172

Total number of rows: 22393

Table truncated, full table size 424 Kbytes.




Supplementary file Size Download File type/resource
GSM186251.tif.gz 25.2 Mb (ftp)(http) TIFF
GSM186251.txt.gz 5.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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