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Sample GSM647885 Query DataSets for GSM647885
Status Public on Jan 04, 2011
Title S6_GRA2_Hy5
Sample type RNA
 
Source name FACS sorted P4 Early Bulge cells
Organism Mus musculus
Characteristics tissue: skin
strain: CD-1
genotype: K14-RFP/Sox9-GFP
age: P4
Treatment protocol Hair follicle cells were isolated from P4 Backskin (Dox since P3 for 24hrs) of DTG (K14-rtTA/TRE-miR-125b/K14-H2BGFP), TRE (TRE-miR-125b/K14-H2BGFP), KrtA (K14-rtTA/K14-H2BGFP) as following: interfollicular epidermis sheet was pealed from hair follicle & dermis after dispase treatment.The hair follicle & dermis were first digested by collagenase (Sigma). Intact hair follicles were separated from dermal cells by low speed spinning (20g). The hair follicles were then digested by Trypsin and filtered by 40 µm cell strainers. The isolated hair follicle cells were FACS sorted. During FACS, cells were first gated against CD34 (endothelial cells), CD45 (immune cells), CD114 (melanocytes) and DAPI (dead cells). ORS cells were sorted from the remaining cells as α6HiGFPHi
Growth protocol Standard mouse growth protocol
Extracted molecule total RNA
Extraction protocol miRNeasy kit (Qiagen) extraction of total RNA was performed according to the manufacturer's instructions.
Label Hy5
Label protocol Standard Exiqon miRCURY™ Hy3™/Hy5™ power labeling kit protocol according to he manufacturer's instructions
 
Hybridization protocol Standard Exiqon miRCURY™ LNA Array (v.11.0) hybridization protocol according to he manufacturer's instructions
Scan protocol Standard Exiqon miRCURY™ LNA Array (v.11.0) scanning protocol according to he manufacturer's instructions
Description miRNA expression data from FACS sorted cells
Data processing Analysis of the scanned slides showed that the labeling was successful as all capture probes for the control spike-in oligo nucleotides produced signals in the expected range. The quantified signals (background correction) were normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm.
Background correction, refers to adjustments to the data intended to remove nonbiological contributions (background) to the measured signal.
Normalization method, refers to computational data transformations intended to remove certain systematic biases from microarray data, such as dye effects or intensity dependence. We have good experience with using the non-linear regression method (LOESS) to apply this transformation to the data. The positive effect from normalization is illustrated on each slide sheet (slide 1 - 8) with a MA plot before and after normalization. After normalization the spots appear symmetrically scattered around the horizontal line M=0. The difference between the two channels (M) is now independent of the average intensity level of the two channels (A).
 
Submission date Jan 03, 2011
Last update date Jan 04, 2011
Contact name liang zhang
E-mail(s) liangz@colorado.edu
Organization name university of colorado at boulder
Street address University of Colorado at Boulder, Han lab, Department of MCD Biology, Campus box 0347
City Boulder
State/province CO
ZIP/Postal code 80309-0347
Country USA
 
Platform ID GPL7723
Series (2)
GSE26395 miRNA Expression data of P4 stage hair follicle ORS cells from DTG (K14-rtTA,TRE-miR-125b) and control littermates
GSE26396 Specific MicroRNAs Are Preferentially Expressed by Skin Stem Cells To Balance Self-Renewal and Early Lineage Commitment

Data table header descriptions
ID_REF
VALUE The quantified signals (background correction) were normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm.

Data table
ID_REF VALUE
11279 5038.565565
11278 562.7944956
46207 546.4396137
46209 24.4111842
17492 71.44903136
17614 40.38290741
10899
14257
10907
10905
14262
10906
10904
14264
14263
14261
46197 34.6040105
46198 31.55096022
46203 37.55378792
46199 35.03949497

Total number of rows: 2002

Table truncated, full table size 34 Kbytes.




Supplementary file Size Download File type/resource
GSM647885.txt.gz 766.2 Kb (ftp)(http) TXT
Processed data included within Sample table

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