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Sample GSM1090233 Query DataSets for GSM1090233
Status Public on Oct 20, 2013
Title Scalp dermal papillae-intact tissue-donor D6
Sample type RNA
 
Source name Intact dermal papilla tissue
Organism Homo sapiens
Characteristics gender: male
donor id: D6
tissue origin: Occipital Scalp
tissue/cell type: Intact dermal papilla tissue
Treatment protocol Cells were cultured in dMEM containing 10% FBS. No antibiotics were used during cell culture. Cells were passaged using Trypsin-EDTA. Cells were fed every four days, and when RNA was collected, it was done so 72 hours post feeding cells that were 70% confluent. For spheroids, RNA was collected 48 hours after hanging drop cultures were started.
Growth protocol Intact papillae were isolated from occipital scalp skin from 3 male donors undergoing hair transplantation procedures. 27G needles were used for microdissection. For culture, isolated papillae were adhered in 35mm dishes, at which point they collapsed, and cells migrate out from the papillae forming an explant (passage 0). Spheroids containing 3000 cells were established from cells cultured at passage 3, using hanging drop culture.
Extracted molecule total RNA
Extraction protocol Cells and tissues were collected in RLT buffer containing BME. Total RNA was isolated using the mRNA micro Kit from Qiagen.
Label biotin
Label protocol The Affymetrix two-cycle amplification kit was used to generate biotin labelled cRNA. Two rounds of amplification were performed, following the manufacturers instructions.
 
Hybridization protocol Following fragmentation, 15ug cRNA was hybridized onto U133 Plus 2.0 genechips from Affymetrix. The Affymetrix GeneChip Hybridization Oven 640, and the GeneChip Fluidics Station 450 were used for hybridization and chip processing.
Scan protocol Chips were scanned using the Affymetrix GeneChip Scanner 3000.
Description Gene expression data from intact scalp dermal papillae
DP2
Data processing Data was analyzed using GeneSpring 12.0 software. Data was RMA normalized, baseline transformed (baseline to median of all samples), and log2 transformed for analysis within GeneSpring. We used a one way ANOVA, coupled with a Benjamini-Hochberg multiple testing correction to perform paired comparisons between cells at different stages in culture respective to intact papilla. Other analytical software was also employed. We used iPAGE (RMA normalized values used here), and GEDI (RMA normalized, baseline and log2 transformed values used) to identify pathways and metagenes with interesting changes in gene expression.
 
Submission date Mar 01, 2013
Last update date Oct 20, 2013
Contact name Claire A Higgins
E-mail(s) ch2609@columbia.edu
Organization name Columbia University
Department Department of Dermatology
Lab Christiano Lab
Street address 1150 St Nicholas Avenue, Russ Berrie 307
City New York
State/province NY
ZIP/Postal code 10032
Country USA
 
Platform ID GPL570
Series (1)
GSE44765 Global profiling of human hair follicle scalp dermal papilla cells using Affymetrix microarrays

Data table header descriptions
ID_REF
VALUE RMA normalized (prior to baseline and log2 transformation)

Data table
ID_REF VALUE
AFFX-BioB-5_at 209.423
AFFX-BioB-M_at 333.4725
AFFX-BioB-3_at 182.16281
AFFX-BioC-5_at 565.72015
AFFX-BioC-3_at 571.8808
AFFX-BioDn-5_at 1344.5469
AFFX-BioDn-3_at 3327.7903
AFFX-CreX-5_at 7755.86
AFFX-CreX-3_at 7922.5796
AFFX-DapX-5_at 11.877437
AFFX-DapX-M_at 10.988341
AFFX-DapX-3_at 9.853212
AFFX-LysX-5_at 8.776267
AFFX-LysX-M_at 14.082085
AFFX-LysX-3_at 9.685067
AFFX-PheX-5_at 14.394031
AFFX-PheX-M_at 9.700029
AFFX-PheX-3_at 32.823006
AFFX-ThrX-5_at 15.135152
AFFX-ThrX-M_at 12.475583

Total number of rows: 54675

Table truncated, full table size 1093 Kbytes.




Supplementary file Size Download File type/resource
GSM1090233_DP2.CEL.gz 4.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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