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Sample GSM2096055 Query DataSets for GSM2096055
Status Public on Mar 22, 2019
Title NHAC-kn_P6_4w_SCB 2
Sample type RNA
Source name NHAC-kn, passage 6, cryopreserved with STEM-CELLBANKER for 4 weeks
Organism Homo sapiens
Characteristics cell characters: articular chondrocyte from adult knee
cell provider: Lonza
cell line name: NHAC-kn - Human Articular Chondrocytes - Knee, CC-2550
cell lot: 8F3303
passage number: 6
cryoprotectant medium: STEM-CELLBANKER
cryopreservation period: 4 weeks
Treatment protocol Each viable cells were suspended in either STEM-CELLBANKER (ZENOAQ), STEM-CELLBANKER DMSO Free (ZENOAQ), or 10% DMSO (SIGMA, D2650) in 20% Fetal Bovine Serum, MSC-Qualified (FBS) (Invitrogen) containing culture medium. The cell suspension was dispensed into a cryopreservation tube (Corning, 430488) and was frozen in a BICELL freezing vessel (Nippon freezer) at -80℃ for overnight, and was transferred into a liquid nitrogen tank or -150°C refrigerator for more than 4 weeks or 1 year. The frozen cells were quickly thaw in a 37°C water bath and were plated into culture vessel. When the cell confluency becomes 60–90 %, the cells were subcultured. The cell confluency becomes 70–90 % again, then the cells were harvested for DNA microarray analysis.
Growth protocol ADSCs were maintained in MesenPRO RS Medium (Invitrogen), according to the manufacturer’s instructions. UC-MSCs were maintained using Mesenchymal Stem Cell Growth Kit for Adipose and Umbilical-derived MSCs - Low Serum (ATCC, PCS-500-040) plus Mesenchymal Stem Cell Basal Medium for Adipose, Umbilical and Bone Marrow-derived MSCs (ATCC, PCS-500-030), according to the manufacturer’s instructions. Yub621c and Yub625 were cultured in 1x Penicillin-Streptomycin (gibco)-containing MesenPRO RS Medium (Invitrogen), according to the manufacturer’s instructions. NHAC-kn and H-1303 were maintained using CGM Chondrocyte Growth Medium BulletKit (Lonza, CC-3216) and Chondrocyte ReagentPack Subculture Reagents (Lonza, CC-3233), according to the manufacturer’s instructions.
Extracted molecule total RNA
Extraction protocol Total RNA was prepared using ISOGEN (Nippon Gene) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer.
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 150 ng of total RNA using Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
Hybridization protocol 0.6 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x HiRPM Hybridization Buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE 8x60K Microarray Kit (G4851A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.
Scan protocol Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides.
Description Gene expression in human cell
Data processing The scanned images were analyzed with Feature Extraction Software GX13.1 (Agilent) using default parameters.
Submission date Mar 22, 2016
Last update date Mar 22, 2019
Contact name Yuzuru Ito
Organization name National Institute of Advanced Industrial Science and Technology (AIST)
Department Biotechnology Research Institute for Drug Discovery
Street address Central 6, Higashi 1-1-1
City Tsukuba
State/province Ibaraki
ZIP/Postal code 3058566
Country Japan
Platform ID GPL13607
Series (1)
GSE79496 DMSO-free chemically defined cryopreservation of human mesenchymal stem cells and chondrocytes

Data table header descriptions
VALUE processed Cy3 signal intensity (Agilent gProcessedSignal)

Data table
1 8.905807e+004
2 4.481238e+000
3 4.491275e+000
4 3.115985e+002
5 2.454554e+003
6 5.533272e+001
7 6.746711e+003
8 1.876805e+003
9 4.519880e+000
10 4.380834e+001
11 4.521160e+000
12 1.157628e+003
13 8.624134e+002
14 8.025490e+002
15 1.567712e+004
16 6.278499e+000
17 2.969728e+002
18 4.498487e+000
19 7.012961e+002
20 1.062680e+003

Total number of rows: 62976

Table truncated, full table size 1219 Kbytes.

Supplementary file Size Download File type/resource
GSM2096055_YuzuruIto_US91703677_252800421644_S01_GE1_1105_Oct12_2_4.txt.gz 3.0 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data provided as supplementary file

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