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Sample GSM1035407 Query DataSets for GSM1035407
Status Public on Nov 20, 2013
Title EGFP KD,replicate B
Sample type RNA
Source name embryonic stem cells, KD replicate B
Organism Mus musculus
Characteristics development stage: E14
treatment: control
Treatment protocol In one 10 cm2 dish, 1X10^6 cells were infected with 30 ul of concentrated lentivirus. After 12-15 hours, the media was replaced and cells were cultured until 72 hours post-infection.
Growth protocol Feeder-free growth on gelatin coated dishes in standatd ES medium: KO DMEM + 10% FBS, glutamine, LIF, non-essential amino acids, beta-mercaptoethanol.
Extracted molecule total RNA
Extraction protocol Trizol, followed by Zymo RNA columns.
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 5 ug of total RNA using Low Input Quick Amp Labeling Kit protocol (Agilent) with minor modifications. Briefly, cRNA was amplified by in vitro transcription with amino-allyl UTP (3:2 ratio for amino-ally UTP: UTP) overnight at 37°C. Then, cRNA was purified using Zymo RNA purification columns (Zymo, Irvine, CA) and labelled with Cy3 (GE healthcare) at RT for 60 minutes in the dark. The fluorescence intensity of Cy3 was determined by NanoDrop ND-1000 Spectrophotometer.
Hybridization protocol Fifty picomoles of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 125 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 125 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent 4X44K Whole Mouse Genome Microarrays 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 on the Agilent scanner (G2565CA) immediately after washing.
Description gene expression in indicated KD
Data processing The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters (protocol GE1-107 and Grid: 026655_D_F_20120201) to obtain background subtracted and spatially detrended Processed Signal intensities. We used the quantile normalization in R (bioconductor) to obtain the value in the Sample data tables.
Submission date Nov 09, 2012
Last update date Nov 20, 2013
Contact name Benson Chen
Organization name UC San Diego
Department Cellular and Molecular Medicine
Lab Bing Ren
Street address 9500 Gilman Dr. CMM East, Room 2071
City La Jolla
State/province CA
ZIP/Postal code 92093-0653
Country USA
Platform ID GPL10333
Series (2)
GSE42208 Hdac6 regulates Tip60-p400 function in stem cells (gene expression)
GSE42329 Hdac6 regulates Tip60-p400 function in stem cells

Data table header descriptions
VALUE Log2 Normalized signal intensity

Data table
12 7.909031613
13 7.898057861
14 8.433803671
15 7.990622612
16 10.75492334
17 11.67613616
18 6.793790911
19 7.118910605
20 9.453902187
21 6.129123026
22 8.834816861
23 12.34768048
24 10.93321245
25 12.56588111
26 10.34539554
27 12.50979868
28 9.648494634
30 9.056518865
31 12.16960363
32 6.446347244

Total number of rows: 39429

Table truncated, full table size 679 Kbytes.

Supplementary file Size Download File type/resource
GSM1035407_EGFP_B.txt.gz 9.0 Mb (ftp)(http) TXT
Processed data included within Sample table

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