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Sample GSM1020288 Query DataSets for GSM1020288
Status Public on Dec 20, 2012
Title Forward Air Promoter (FAP)
Sample type mixed
 
Channel 1
Source name Forward Air Promoter (FAP) ES cells
Organism Mus musculus
Characteristics cell type: FAP ES cells
day of differentiation: 5
airn length: n.d.
Growth protocol ES cell line was differentiated on gelatinized dishes after feeder cell depletion and LIF withdrawal by 0.27μM retinoic acid for 5 days
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from different tissues or cells. After the treatment of DNase I, total RNA was reverse transcribed, and synthesized to double-stranded cDNA. The genomic DNA isolated from D3 ES cell line was fragmented and used as Input DNA.
Label Cy5
Label protocol 1 µg ds-cDNA was directly labeled by Klenow (New England Biolabs) random priming with Cy3 nonamers per manufacturer's protocol
 
Channel 2
Source name wildtype D3 ESCs_sonicated genomic DNA
Organism Mus musculus
Characteristics cell line background: D3
cell type: Murine embryonic stem (ES) cells
genotype/variation: wild type
Extracted molecule genomic DNA
Extraction protocol Total RNA was extracted from different tissues or cells. After the treatment of DNase I, total RNA was reverse transcribed, and synthesized to double-stranded cDNA. The genomic DNA isolated from D3 ES cell line was fragmented and used as Input DNA.
Label Cy3
Label protocol 1 µg ds-cDNA was directly labeled by Klenow (New England Biolabs) random priming with Cy3 nonamers per manufacturer's protocol
 
 
Hybridization protocol The labeled ds-cDNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in 45 ul of buffer containing 20% formamide, 1.2 M betaine, 0.1 ug/ul herring sperm DNA and 10 ug of human COT1 DNA (Invitrogen). Arrays were hybridized in Maui hybridization stations for 16-18 h at 42C, and then washed in 42C 0.2% SDS/0.2x SSC, room temperature 0.2x SSC, and 0.05x SSC. Hybridization buffers and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html)
Scan protocol Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).
Data processing Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction.
 
Submission date Oct 16, 2012
Last update date Dec 20, 2012
Contact name Florian M Pauler
E-mail(s) florian.pauler@ist.ac.at
Phone +43 2243 9000-7434
Organization name IST Austria
Lab Simon Hippenmeyer
Street address Am Campus 1
City Klosterneuburg
ZIP/Postal code 3400
Country Austria
 
Platform ID GPL11618
Series (1)
GSE41444 Airn transcriptional overlap but not its lncRNA products induce imprinted Igf2r silencing.

Data table header descriptions
ID_REF
VALUE tukey normalized probe-level log2 ratio (Cy5/Cy3)
green
red

Data table
ID_REF VALUE green red
6379_0515_0001 1.36 4154.58 4380.28
6379_0517_0001 -0.58 3364.58 922.94
6379_0519_0001 0.09 7014.44 3058.36
6379_0521_0001 -3.82 41110.95 1194.25
6379_0523_0001 -0.55 3347.69 940.86
6379_0525_0001 -0.22 2898.44 1021.03
6379_0527_0001 -0.2 3005.11 1074.25
6379_0529_0001 0.78 9498.83 6701.75
6379_0531_0001 -0.74 5397.83 1325.36
6379_0533_0001 null null null
6379_0535_0001 -0.48 3838.33 1132.58
6379_0537_0001 null null null
6379_0539_0001 null null null
6379_0541_0001 0 3058.78 1251.81
6379_0543_0001 2.16 4365.11 8010.03
6379_0545_0001 null null null
6379_0547_0001 1.04 6793.36 5725.11
6379_0549_0001 -0.19 3245.06 1171.19
6379_0551_0001 0.1 2481.53 1094.19
6379_0553_0001 -0.06 3317.78 1307.64

Total number of rows: 392778

Table truncated, full table size 13333 Kbytes.




Supplementary file Size Download File type/resource
GSM1020288_3136211.txt.gz 3.9 Mb (ftp)(http) TXT
GSM1020288_3136211_532.pair.gz 5.9 Mb (ftp)(http) PAIR
GSM1020288_3136211_635.pair.gz 5.8 Mb (ftp)(http) PAIR
Processed data included within Sample table
Processed data provided as supplementary file

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