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Sample GSM1280870 Query DataSets for GSM1280870
Status Public on Oct 22, 2019
Title HDF CondMed 12h
Sample type RNA
 
Source name HDF_NHK-conditioned medium
Organism Homo sapiens
Characteristics gender: male
tissue: skin
cell type: human dermal fibroblasts (HDF)
stimulated with: normal human keratinocytes (NHK)-conditioned medium
time point: 12h after stimulation
Treatment protocol Conditioned media from normal human keratinocytes (NHK) were used to stimulate cells. Sub-confluent monolayers of fibroblasts were grown in individual flasks, and conditioned medium (0.2-0.3 mL/cm2) was collected as follows: i. NHK conditioned medium (K): KSFM (supplemented with rhEGF and BPE) was added to keratinocyte culture flask and collected after 16h. The After each conditioning treatment the collected media were centrifuged (200 xg/ 5 min) and then was used to stimulate other cells or tested. Time and volume was considered to have adequate soluble factors content and sufficient medium nutrients. RNA was collected fro expression profiling after 1, 2, 3, 4, 5, 6, 7, 8, 10, 12, 18 and 24h of treatment.
Growth protocol Human dermal fibroblasts (HDF) were derived from foreskin as previously described (König & Bruckner-Tuderman, 1994; Stark et al, 1999). HDF obtained from the outgrowth of explants culture and were grown in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal calf serum (FCS), 1% L-glutamate, penicillin G and streptomycin (PAN-Biotech, Aidenbach, Germany). Cells were kept under a humidified environment with 5% CO2 and 3oC. Fibroblasts at passages 2-8 and a density of 5-8 x 10^4 cells/cm^2 were used in all experiments.
Extracted molecule total RNA
Extraction protocol RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.
Label Cy3
Label protocol Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays
 
Hybridization protocol Hybridization was performed at 58°C, in GEX-HCB buffer (Illumina Inc.) at a concentration of 100 ng cRNA/µl, unsealed in a wet chamber for 20h. Spike-in controls for low, medium and highly abundant RNAs were added, as well as mismatch control and biotinylation control oligonucleotides. Microarrays were washed twice in E1BC buffer (Illumina Inc.) at room temperature for 5 minutes. After blocking for 5 min in 4 ml of 1% (wt/vol) Blocker Casein in phosphate buffered saline Hammarsten grade (Pierce Biotechnology, Inc., Rockford, IL), array signals were developed by a 10-min incubation in 2 ml of 1 µg/ml Cy3-streptavidin (Amersham Biosciences, Buckinghamshire, UK) solution and 1% blocking solution. After a final wash in E1BC, the arrays were dried and scanned.
Scan protocol Microarray scanning was done using a Beadstation array scanner, setting adjusted to a scaling factor of 1 and PMT settings at 430. Data extraction was done for all beads individually
Description Array ID: 4675283074
Data processing All arrays were normalized together using the quantile normalization algorithm without background subtraction (Illumina BeadStudio Software).
 
Submission date Dec 05, 2013
Last update date Oct 22, 2019
Contact name Hauke Busch
E-mail(s) hauke.busch@uni-luebeck.de
Phone +49-451-3101-8470
Organization name University of Lübeck
Department Lübeck Institute of Experimental Dermatology
Street address Ratzeburger Allee 160
City Lübeck
State/province Schleswig-Holstein
ZIP/Postal code 23538
Country Germany
 
Platform ID GPL6883
Series (1)
GSE53037 Cell-Cell communication between skin keratinocytes and fibroblasts is non-redundantly coded through inflammatory cytokines

Data table header descriptions
ID_REF
VALUE quantile normalized
Detection Pval

Data table
ID_REF VALUE Detection Pval
ILMN_1802380 482.5082518 2.03101E-26
ILMN_1792389 52.30151663 0.291880355
ILMN_2375156 75.52544821 2.76837E-07
ILMN_1697642 410.6826678 2.99364E-23
ILMN_1681845 295.8143875 1.84138E-18
ILMN_1690979 67.24986644 1.44498E-08
ILMN_1811114 49.76264161 0.022485476
ILMN_1660729 51.66959175 0.166005413
ILMN_2129572 94.19829006 4.31841E-11
ILMN_1705659 58.14966572 0.0500004
ILMN_1670547 50.33427914 0.02225821
ILMN_2342515 95.5041856 1.18737E-11
ILMN_1800425 1289.596003 1.02969E-35
ILMN_1783852 71.65686341 8.34725E-07
ILMN_1721344 294.0501465 1.16809E-21
ILMN_1679973 57.07879728 0.16086477
ILMN_1701854 177.5989583 2.41394E-11
ILMN_1678707 2464.097363 2.08465E-33
ILMN_2276504 52.39781855 0.342579092
ILMN_1778226 339.11475 3.10475E-22

Total number of rows: 24526

Table truncated, full table size 879 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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