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Sample GSM2527772 Query DataSets for GSM2527772
Status Public on Aug 08, 2019
Title Day 3 -2
Sample type RNA
 
Source name iPS cells during chondrocyte differentiation by the 2C method at day 3
Organism Homo sapiens
Characteristics cell type: iPS
day: 3
Treatment protocol Human iPS cells were differentiated to chondrocytes by the 2C method for 9 days.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from the chondrocytes using RNeasy mini kits (Qiagen) according to manufacturer’s protocol.
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1ug Total RNA using the Low Input Quick Amp Labeling Kit(Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.
 
Hybridization protocol 0.6ug of Cy3-labelled 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 manufacturer’s instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE 8x60K Microarray (Agilent) 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 the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).
Data processing The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.
 
Submission date Mar 09, 2017
Last update date Aug 08, 2019
Contact name Taku Saito
E-mail(s) tasaitou-tky@umin.ac.jp
Organization name The University of Tokyo
Department Orthopaedic Surgery, Faculty of Medicine
Street address 7-3-1 Hongo, Bunkyo-ku
City TOKYO
ZIP/Postal code 113-8655
Country Japan
 
Platform ID GPL21185
Series (1)
GSE96036 Gene expression during chondrocyte differentiation from human iPS cells by the 2C method

Data table header descriptions
ID_REF
VALUE normalized signal intensity

Data table
ID_REF VALUE
GE_BrightCorner 15.774198
DarkCorner 2.204256
A_21_P0014386 2.5693033
A_33_P3396872 2.2632706
A_33_P3267760 2.512954
A_32_P194264 6.8729296
A_23_P153745 9.217218
A_33_P3352837 2.3118346
A_21_P0011260 2.5423617
A_33_P3235816 2.3305595
A_21_P0014180 2.3387563
A_24_P944991 4.9844127
A_21_P0006507 2.3527164
A_23_P208706 12.659863
A_33_P3388806 2.3638952
A_33_P3324839 5.5813594
A_24_P333494 10.647153
A_22_P00006274 2.375691
A_23_P161615 9.059406
A_33_P3384958 4.953528

Total number of rows: 58341

Table truncated, full table size 1332 Kbytes.




Supplementary file Size Download File type/resource
GSM2527772_Day3-2.txt.gz 3.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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