Comment[ArrayExpressAccession] E-GEOD-49224 MAGE-TAB Version 1.1 Public Release Date 2013-07-26 Investigation Title ChIP-Seq for transcriptional regulators and RNA Polymerase II in tumor cells treated with JQ1 Comment[Submitted Name] ChIP-Seq for transcriptional regulators and RNA Polymerase II in tumor cells treated with JQ1 Experiment Description ChIP-Seq of RNA Polymerase II, and transcriptional regulators in multiple myeloma (MM.1S), glioblastoma (U87-MG), and small cell lung carcinoma (H2171) treated with the BET bromodomain inhibitor JQ1. Cell lines (MM.1S, U87-MG, and H2171) representing multiple myeloma, glioblastoma, and small cell lung carcinoma, were treated with varying concentrations (5nM to 5µM) of the BET bromodomain inhibitor JQ1 followed by ChIP-Seq for RNA Polymerase II and transcriptional regulators.  Other datasets from this series of experiments have been release as a part of GSE42355. Term Source Name ArrayExpress EFO Term Source File http://www.ebi.ac.uk/arrayexpress/ http://www.ebi.ac.uk/efo/efo.owl Person Last Name Young Hoke Lars Sigova DAlessio Young Person First Name Richard Heather Anders Alla Ana Richard Person Mid Initials A A A Person Email young_computation@wi.mit.edu Person Affiliation Whitehead Institute for Biomedical Research Person Phone 617-258-5219 Person Address Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA, USA Person Roles submitter Protocol Name P-GSE49224-30 P-GSE49224-27 P-GSE49224-31 P-GSE49224-22 P-GSE49224-8 P-GSE49224-11 P-GSE49224-28 P-GSE49224-25 P-GSE49224-15 P-GSE49224-6 P-GSE49224-17 P-GSE49224-4 P-GSE49224-29 P-GSE49224-18 P-GSE49224-33 P-GSE49224-7 P-GSE49224-13 P-GSE49224-20 P-GSE49224-24 P-GSE49224-16 P-GSE49224-14 P-GSE49224-5 P-GSE49224-12 P-GSE49224-21 P-GSE49224-32 P-GSE49224-1 P-GSE49224-23 P-GSE49224-19 P-GSE49224-9 P-GSE49224-3 P-GSE49224-26 P-GSE49224-10 P-GSE49224-2 Protocol Description Images analysis and base calling was done using the solexa pipeline. For all samples reads were aligned to their indicated build using bowtie with parameters -e 70 -k 2 -m 2 -n 2 --best --concise. Seed length (-l) was set to read length for each dataset. Genome_build: hg18 and mm8 Supplementary_files_format_and_content: WIG files: For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown. Genome Build: 01182013_C1FJWACXX_5.AGTTCC.wig.gz: hg18 Images analysis and base calling was done using the solexa pipeline. For all samples reads were aligned to their indicated build using bowtie with parameters -e 70 -k 2 -m 2 -n 2 --best --concise. Seed length (-l) was set to read length for each dataset. Genome_build: hg18 and mm8 Supplementary_files_format_and_content: WIG files: For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown. Genome Build: 01182013_C1FJWACXX_2.GCCAAT.wig.gz: hg18 Images analysis and base calling was done using the solexa pipeline. For all samples reads were aligned to their indicated build using bowtie with parameters -e 70 -k 2 -m 2 -n 2 --best --concise. Seed length (-l) was set to read length for each dataset. Genome_build: hg18 and mm8 Supplementary_files_format_and_content: WIG files: For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown. Genome Build: 01182013_C1FJWACXX_5.ATGTCA.wig.gz: hg18 Images analysis and base calling was done using the solexa pipeline. For all samples reads were aligned to their indicated build using bowtie with parameters -e 70 -k 2 -m 2 -n 2 --best --concise. Seed length (-l) was set to read length for each dataset. Genome_build: hg18 and mm8 Supplementary_files_format_and_content: WIG files: For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown. Genome Build: 05242012_D0WUYACXX_4.ACTTGA.wig.gz: hg18 Images analysis and base calling was done using the solexa pipeline. For all samples reads were aligned to their indicated build using bowtie with parameters -e 70 -k 2 -m 2 -n 2 --best --concise. Seed length (-l) was set to read length for each dataset. Genome_build: hg18 and mm8 Supplementary_files_format_and_content: WIG files: For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown. Genome Build: 01312013_D1TBRACXX_6.TGACCA.wig.gz: hg18 Images analysis and base calling was done using the solexa pipeline. For all samples reads were aligned to their indicated build using bowtie with parameters -e 70 -k 2 -m 2 -n 2 --best --concise. Seed length (-l) was set to read length for each dataset. Genome_build: hg18 and mm8 Supplementary_files_format_and_content: WIG files: For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown. Genome Build: 08282012_C1260ACXX_4.AGTTCC.wig.gz: hg18 Images analysis and base calling was done using the solexa pipeline. For all samples reads were aligned to their indicated build using bowtie with parameters -e 70 -k 2 -m 2 -n 2 --best --concise. Seed length (-l) was set to read length for each dataset. Genome_build: hg18 and mm8 Supplementary_files_format_and_content: WIG files: For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown. Genome Build: 01182013_C1FJWACXX_3.CAGATC.wig.gz: hg18 Images analysis and base calling was done using the solexa pipeline. For all samples reads were aligned to their indicated build using bowtie with parameters -e 70 -k 2 -m 2 -n 2 --best --concise. Seed length (-l) was set to read length for each dataset. Genome_build: hg18 and mm8 Supplementary_files_format_and_content: WIG files: For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown. Genome Build: 05242012_D0WUYACXX_5.TAGCTT.wig.gz: hg18 Images analysis and base calling was done using the solexa pipeline. For all samples reads were aligned to their indicated build using bowtie with parameters -e 70 -k 2 -m 2 -n 2 --best --concise. Seed length (-l) was set to read length for each dataset. Genome_build: hg18 and mm8 Supplementary_files_format_and_content: WIG files: For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown. Genome Build: 08282012_C1260ACXX_5.GTCCGC.wig.gz: hg18 Images analysis and base calling was done using the solexa pipeline. For all samples reads were aligned to their indicated build using bowtie with parameters -e 70 -k 2 -m 2 -n 2 --best --concise. Seed length (-l) was set to read length for each dataset. Genome_build: hg18 and mm8 Supplementary_files_format_and_content: WIG files: For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown. Genome Build: 01312013_D1TBRACXX_5.CGATGT.wig.gz: hg18 Images analysis and base calling was done using the solexa pipeline. For all samples reads were aligned to their indicated build using bowtie with parameters -e 70 -k 2 -m 2 -n 2 --best --concise. Seed length (-l) was set to read length for each dataset. Genome_build: hg18 and mm8 Supplementary_files_format_and_content: WIG files: For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown. Genome Build: 08282012_C1260ACXX_7.GAGTGG.wig.gz: hg18 Images analysis and base calling was done using the solexa pipeline. For all samples reads were aligned to their indicated build using bowtie with parameters -e 70 -k 2 -m 2 -n 2 --best --concise. Seed length (-l) was set to read length for each dataset. Genome_build: hg18 and mm8 Supplementary_files_format_and_content: WIG files: For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown. Genome Build: 01312013_D1TBRACXX_5.ATCACG.wig.gz: hg18 Images analysis and base calling was done using the solexa pipeline. For all samples reads were aligned to their indicated build using bowtie with parameters -e 70 -k 2 -m 2 -n 2 --best --concise. Seed length (-l) was set to read length for each dataset. Genome_build: hg18 and mm8 Supplementary_files_format_and_content: WIG files: For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown. Genome Build: 01182013_C1FJWACXX_4.AGTCAA.wig.gz: hg18 Images analysis and base calling was done using the solexa pipeline. For all samples reads were aligned to their indicated build using bowtie with parameters -e 70 -k 2 -m 2 -n 2 --best --concise. Seed length (-l) was set to read length for each dataset. Genome_build: hg18 and mm8 Supplementary_files_format_and_content: WIG files: For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown. Genome Build: 08282012_C1260ACXX_8.CGATGT.wig.gz: hg18 Images analysis and base calling was done using the solexa pipeline. For all samples reads were aligned to their indicated build using bowtie with parameters -e 70 -k 2 -m 2 -n 2 --best --concise. Seed length (-l) was set to read length for each dataset. Genome_build: hg18 and mm8 Supplementary_files_format_and_content: WIG files: For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown. Genome Build: 01182013_C1FJWACXX_5.CCGTCC.wig.gz: hg18 Images analysis and base calling was done using the solexa pipeline. For all samples reads were aligned to their indicated build using bowtie with parameters -e 70 -k 2 -m 2 -n 2 --best --concise. Seed length (-l) was set to read length for each dataset. Genome_build: hg18 and mm8 Supplementary_files_format_and_content: WIG files: For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown. Genome Build: 01312013_D1TBRACXX_5.TTAGGC.wig.gz: hg18 Images analysis and base calling was done using the solexa pipeline. For all samples reads were aligned to their indicated build using bowtie with parameters -e 70 -k 2 -m 2 -n 2 --best --concise. Seed length (-l) was set to read length for each dataset. Genome_build: hg18 and mm8 Supplementary_files_format_and_content: WIG files: For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown. Genome Build: 08282012_C1260ACXX_4.ATGTCA.wig.gz: hg18 Images analysis and base calling was done using the solexa pipeline. For all samples reads were aligned to their indicated build using bowtie with parameters -e 70 -k 2 -m 2 -n 2 --best --concise. Seed length (-l) was set to read length for each dataset. Genome_build: hg18 and mm8 Supplementary_files_format_and_content: WIG files: For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown. Genome Build: 05242012_D0WUYACXX_3.TGACCA.wig.gz: hg18 Images analysis and base calling was done using the solexa pipeline. For all samples reads were aligned to their indicated build using bowtie with parameters -e 70 -k 2 -m 2 -n 2 --best --concise. Seed length (-l) was set to read length for each dataset. Genome_build: hg18 and mm8 Supplementary_files_format_and_content: WIG files: For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown. Genome Build: 05242012_D0WUYACXX_4.GATCAG.wig.gz: hg18 Images analysis and base calling was done using the solexa pipeline. For all samples reads were aligned to their indicated build using bowtie with parameters -e 70 -k 2 -m 2 -n 2 --best --concise. Seed length (-l) was set to read length for each dataset. Genome_build: hg18 and mm8 Supplementary_files_format_and_content: WIG files: For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown. Genome Build: 08282012_C1260ACXX_6.GTTTCG.wig.gz: hg18 5000nM JQ1 for 6h 500nM JQ1 for 6 hours 50nM JQ1 for 6h 5nM JQ1 treatment for 6hr 500nM JQ1 for 6 hoursd 0.05% DMSO for 6 hours 50nM JQ1 treatment for 6hr 150nM JQ1 treatment for 6hr 5nM JQ1 for 6h Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified. RPMI 1640 + 10% FBS RPMI 1640 supplemented with 10% FCS and 1% GlutaMAX The base medium for this cell line is ATCC-formulated Eagle's Minimum Essential Medium (Catalog No. 30-2003)+ 1% GMAX and 10% FBS Protocol Type normalization data transformation protocol normalization data transformation protocol normalization data transformation protocol normalization data transformation protocol normalization data transformation protocol normalization data transformation protocol normalization data transformation protocol normalization data transformation protocol normalization data transformation protocol normalization data transformation protocol normalization data transformation protocol normalization data transformation protocol normalization data transformation protocol normalization data transformation protocol normalization data transformation protocol normalization data transformation protocol normalization data transformation protocol normalization data transformation protocol normalization data transformation protocol normalization data transformation protocol sample treatment protocol sample treatment protocol sample treatment protocol sample treatment protocol sample treatment protocol sample treatment protocol sample treatment protocol sample treatment protocol sample treatment protocol nucleic acid library construction protocol growth protocol growth protocol growth protocol Experimental Factor Name CONCENTRATION CHIP ANTIBODY ANTIBODY CATALOG NUMBER CELL TYPE DRUG Experimental Factor Type concentration chip antibody antibody catalog number cell type drug Comment[SecondaryAccession] GSE49224 Comment[GEOReleaseDate] 2013-07-26 Comment[ArrayExpressSubmissionDate] 2013-07-25 Comment[GEOLastUpdateDate] 2013-08-01 Comment[AEExperimentType] ChIP-seq Comment[SecondaryAccession] SRP028248 Comment[SequenceDataURI] http://www.ebi.ac.uk/ena/data/view/SRR942944-SRR942993 SDRF File E-GEOD-49224.sdrf.txt