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Sample GSM1070349 Query DataSets for GSM1070349
Status Public on Apr 19, 2013
Title WT_SCC_CATCH-IT_Doxo_(529584)
Sample type genomic
 
Channel 1
Source name WT_SCC_CATCH-IT_Doxo
Organism Mus musculus
Characteristics cell type: squamous cell carcinoma
genotype/variation: wild type
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: wild type
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 wild-type SCC cells after 18 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 -0.082176768302125
CHR01FS003521569 0.190462388133756
CHR01FS003521689 0.510456712817316
CHR01FS003521789 -0.7388515779642
CHR01FS003521874 -0.362673672148582
CHR01FS003521969 0.0933092876679067
CHR01FS003522069 0.0287566840833457
CHR01FS003658583 0.195649737474668
CHR01FS003658683 0.145464668272596
CHR01FS003658798 0.206842973157111
CHR01FS003658883 -0.0617049546834788
CHR01FS003658993 -0.0312698522056457
CHR01FS003659103 0.344893981707649
CHR01FS003659198 0.199209839022117
CHR01FS003659283 0.414009302286422
CHR01FS003659383 0.455455730806082
CHR01FS003659528 -0.0410562652973687
CHR01FS003659613 -0.0491793878022461
CHR01FS003659728 0.152991506495028
CHR01FS003659828 0.117499467736532

Total number of rows: 2082810

Table truncated, full table size 72477 Kbytes.




Supplementary file Size Download File type/resource
GSM1070349_WT_SCC_CATCH-IT_Doxo.wig.gz 18.8 Mb (ftp)(http) WIG
GSM1070349_WT_SCC_CATCH-IT_Doxo_532.pair.gz 41.0 Mb (ftp)(http) PAIR
GSM1070349_WT_SCC_CATCH-IT_Doxo_635.pair.gz 40.8 Mb (ftp)(http) PAIR
GSM1070349_WT_SCC_CATCH-IT_Doxo_ratio.gff.gz 21.7 Mb (ftp)(http) GFF
Processed data included within Sample table
Processed data provided as supplementary file

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