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Sample GSM334240 Query DataSets for GSM334240
Status Public on Nov 26, 2008
Title ES cells_untreated_H1AcK26-IP
Sample type genomic
 
Channel 1
Source name mouse embryonic stem (ES) cells
Organism Mus musculus
Characteristics C57BL/6x129Sv F1
Input fraction
Treatment protocol no treatment
Growth protocol standard growth conditions
Extracted molecule genomic DNA
Extraction protocol Mouse embryonic stem (ES) cells were fixed in 1% formaldehyde for 20 min at 37 degree Celsius, cells were than lysed and processed using the Upstate Chromatin IP Kit following the manufacturer's instructions. Samples were sonicated 5 times for 10 s and subjected to 1h preclear and o/n IP using Rabbit anti Sir2 (Upstate), Rabbit Ig (Upstate) or Rabbit anti-acetyl H1K26 (Vaquero et al., Mol Cell 2004). Input and IP samples were amplified using LM-PCR following the NImblegen protocol.
Label Cy3
Label protocol 1 µg ChIP DNA was directly labeled by Klenow (New England Biolabs) random priming per manufacturer's protocol. Input DNA was labeled with Cy3, IP DNA was labeled with Cy5 (http://www.nimblegen.com/products/lit/lit.html).
 
Channel 2
Source name mouse embryonic stem (ES) cells
Organism Mus musculus
Characteristics C57BL/6x129Sv F1
IP fraction
Treatment protocol no treatment
Growth protocol standard growth conditions
Extracted molecule genomic DNA
Extraction protocol Mouse embryonic stem (ES) cells were fixed in 1% formaldehyde for 20 min at 37 degree Celsius, cells were than lysed and processed using the Upstate Chromatin IP Kit following the manufacturer's instructions. Samples were sonicated 5 times for 10 s and subjected to 1h preclear and o/n IP using Rabbit anti Sir2 (Upstate), Rabbit Ig (Upstate) or Rabbit anti-acetyl H1K26 (Vaquero et al., Mol Cell 2004). Input and IP samples were amplified using LM-PCR following the NImblegen protocol.
Label Cy5
Label protocol 1 µg ChIP DNA was directly labeled by Klenow (New England Biolabs) random priming per manufacturer's protocol. Input DNA was labeled with Cy3, IP DNA was labeled with Cy5 (http://www.nimblegen.com/products/lit/lit.html).
 
 
Hybridization protocol The labeled ChIP DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in a total volume of 35 ul using 2X Hybridization Buffer (composition is proprietary) and hybridization component A (composition is priorietary). 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).
Description no additional information
Data processing Arrays were processed using Nimblegens standard protocol for Nimblescan 2.4 ChIP data extraction.
 
Submission date Oct 16, 2008
Last update date Nov 26, 2008
Contact name Philipp Oberdoerffer
E-mail(s) philober@hms.harvard.edu
Organization name Harvard Medical School
Department Pathology
Lab Sinclair
Street address 77 Avenue Louis Pasteur
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
 
Platform ID GPL7496
Series (2)
GSE13075 SIRT1 and H1AcK26 promoter-association in mouse ES cells changes upon oxidative stress
GSE13121 SIRT1 redistribution on chromatin promotes genome stability but alters gene expression during aging

Data table header descriptions
ID_REF
VALUE scaled, log2 (ChIP/Input) ratio

Data table
ID_REF VALUE
MMUS0407S00000001 -0.05
MMUS0407S00000002 0.048
MMUS0407S00000003 0.018
MMUS0407S00000004 0.098
MMUS0407S00000005 0.128
MMUS0407S00000006 0.037
MMUS0407S00000007 0.049
MMUS0407S00000008 0.333
MMUS0407S00000009 0.7
MMUS0407S00000011 0.981
MMUS0407S00000012 0.341
MMUS0407S00000013 0.211
MMUS0407S00000015 1.241
MMUS0407S00000016 0.009
MMUS0407S00000017 -0.126
MMUS0407S00000019 2.838
MMUS0407S00000022 0.079
MMUS0407S00000024 0.085
MMUS0407S00000026 0.006
MMUS0407S00000028 0.054

Total number of rows: 26275

Table truncated, full table size 615 Kbytes.




Supplementary file Size Download File type/resource
GSM334240_ES_NT_H1_IP_Cy5.pair.gz 6.2 Mb (ftp)(http) PAIR
GSM334240_ES_NT_H1_input_Cy3.pair.gz 6.4 Mb (ftp)(http) PAIR
Processed data included within Sample table

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