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Sample GSM1035410 Query DataSets for GSM1035410
Status Public on Nov 20, 2013
Title Hdac6 KD,replicate A
Sample type RNA
Source name embryonic stem cells, KD replicate A
Organism Mus musculus
Characteristics development stage: E14
treatment: Lentiviral-based shRNA was used for Hdac6 knock down
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 8.027119546
13 7.753356367
14 8.805942686
15 7.795219161
16 10.74774503
17 11.56265423
18 7.072500434
19 6.848636606
20 8.665020218
21 5.231722897
22 8.656620676
23 12.10676682
24 10.45446592
25 11.51985359
26 9.27639619
27 12.26603959
28 8.375679085
30 9.606349713
31 12.1666407
32 5.978645569

Total number of rows: 39429

Table truncated, full table size 679 Kbytes.

Supplementary file Size Download File type/resource
GSM1035410_Hdac6_A.txt.gz 8.9 Mb (ftp)(http) TXT
Processed data included within Sample table

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