|
| Status |
Public on Jan 04, 2011 |
| Title |
S2_Rall1_Hy5 |
| Sample type |
RNA |
| |
|
| Source name |
FACS sorted P4 RFPall HF 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 |
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