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Sample GSM1070345 Query DataSets for GSM1070345
Status Public on Apr 19, 2013
Title Atm_SCC_CATCH-IT_Doxo_24h_(538428A01_2)
Sample type genomic
 
Channel 1
Source name Atm_SCC_CATCH-IT_Doxo_24h
Organism Mus musculus
Characteristics cell type: squamous cell carcinoma
genotype/variation: Atm -/-
Extracted molecule genomic DNA
Extraction protocol CATCH-IT was performed as previously described (PMID: 20508129) with some modifications. Briefly, tissue culture medium was replaced with DMEM media without methionine (Invitrogen Cat# 21013-024) supplemented with 1X glutamine, 0.2 mM L-cystine, 10% FBS, and 1% penicillin-streptomycin, and cells were grown at 37C for starvation fro 30 minutes, followed by 30 minutes incubation at 37C with 4 mM azidohomoalanine (Anaspec Cat# 63669) added to the media. Cells were then harvested, washed with 1X PBS, and resuspended in ice-cold TM2 buffer (10 mM Tris, pH=7.5, 2mM MgCl2). Cells were lysed using 0.2% of NP-40 and nuclei were isolated, followed by digestion of micrococcal nuclease for 10 minutes to produce mostly mononucleosomes. Biotin coupling, chrmatin extraction, streptavidin pulldown, urea wash, and DNA isolation were then performed as previously described.
Label Cy5
Label protocol Standard NimbleGen protocol
 
Channel 2
Source name Input
Organism Mus musculus
Characteristics cell type: squamous cell carcinoma
genotype/variation: Atm -/-
Extracted molecule genomic DNA
Extraction protocol CATCH-IT was performed as previously described (PMID: 20508129) with some modifications. Briefly, tissue culture medium was replaced with DMEM media without methionine (Invitrogen Cat# 21013-024) supplemented with 1X glutamine, 0.2 mM L-cystine, 10% FBS, and 1% penicillin-streptomycin, and cells were grown at 37C for starvation fro 30 minutes, followed by 30 minutes incubation at 37C with 4 mM azidohomoalanine (Anaspec Cat# 63669) added to the media. Cells were then harvested, washed with 1X PBS, and resuspended in ice-cold TM2 buffer (10 mM Tris, pH=7.5, 2mM MgCl2). Cells were lysed using 0.2% of NP-40 and nuclei were isolated, followed by digestion of micrococcal nuclease for 10 minutes to produce mostly mononucleosomes. Biotin coupling, chrmatin extraction, streptavidin pulldown, urea wash, and DNA isolation were then performed as previously described.
Label Cy3
Label protocol Standard NimbleGen protocol
 
 
Hybridization protocol Standard NimbleGen protocol
Scan protocol Standard NimbleGen protocol
Description CATCH-IT profiling of Atm -/- SCC cells after 24 hours of doxorubicin treatment.
Data processing The dye-bias correction of Peng, et al (PMID PMC1913544) was applied to bi-weight mean adjusted log base 2 ratios of Cy5/Cy3 computedby NimbleGen. The supplementary gff and wig files contain the bi-weight mean adjusted log base 2 ratios in MM9 coordinates.
 
Submission date Jan 25, 2013
Last update date Apr 21, 2013
Contact name Jorja Henikoff
E-mail(s) jorja@fhcrc.org
Phone 206-667-4850
Organization name Fred Hutchinson Cancer Research Center
Department Basic Sciences
Lab Henikoff
Street address 1100 Fairview AV N, A1-162
City Seattle
State/province WA
ZIP/Postal code 98109-1024
Country USA
 
Platform ID GPL16533
Series (1)
GSE43753 Doxorubicin enhances nucleosome turnover around promoters

Data table header descriptions
ID_REF NimbleGen PROBE_ID
VALUE Dye-bias corrected bi-weight mean adjusted log base 2 (Cy5/Cy3)

Data table
ID_REF VALUE
CHR01FS003521489 -0.603973478598185
CHR01FS003521569 -0.681627587217637
CHR01FS003521689 -0.237152103989655
CHR01FS003521789 -0.275877661233087
CHR01FS003521874 -0.647205276949207
CHR01FS003521969 0.205203579310758
CHR01FS003522069 0.604660156919714
CHR01FS003658583 -0.906074581072103
CHR01FS003658683 -0.291248203971412
CHR01FS003658798 0.471308247482338
CHR01FS003658883 -0.244995730037974
CHR01FS003658993 0.0915183617999855
CHR01FS003659103 0.102375428919824
CHR01FS003659198 -0.141141534388443
CHR01FS003659283 -0.416722265299806
CHR01FS003659383 -0.218685665831072
CHR01FS003659528 -0.314899145238580
CHR01FS003659613 -0.130057815787608
CHR01FS003659728 -0.223158706412167
CHR01FS003659828 -0.376479010922877

Total number of rows: 2082810

Table truncated, full table size 72168 Kbytes.




Supplementary file Size Download File type/resource
GSM1070345_Atm_SCC_CATCH-IT_Doxo_24h.wig.gz 18.7 Mb (ftp)(http) WIG
GSM1070345_Atm_SCC_CATCH-IT_Doxo_24h_532.pair.gz 41.1 Mb (ftp)(http) PAIR
GSM1070345_Atm_SCC_CATCH-IT_Doxo_24h_635.pair.gz 41.0 Mb (ftp)(http) PAIR
GSM1070345_Atm_SCC_CATCH-IT_Doxo_24h_ratio.gff.gz 21.6 Mb (ftp)(http) GFF
Processed data included within Sample table
Processed data provided as supplementary file

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