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Sample GSM2069577 Query DataSets for GSM2069577
Status Public on Apr 05, 2016
Title MM1S_KDM5C70_3
Sample type SRA
 
Source name MM1S Multiple Myeloma cells_KDM5C70
Organism Homo sapiens
Characteristics cell line: MM1S
cell type: Multiple Myeloma cell line
treated with: KDM5-C70
chip antibody: H3K4me3
chip antibody vendor: Millpore
chip antibody cat. #: 07-473
chip antibody lot #: 2207275
Treatment protocol Cells were treated with either KDM5-C70 50uM for 7 days or vehicle control
Growth protocol Cells were grown under standard conditions in RMPI with 10% FGS and 2mmol glutamine supplemented
Extracted molecule genomic DNA
Extraction protocol Cells were fixed in 1% formaldehyde for 8 minutes at room temperature, sonicated on a Bioruptor Pico, incubated for an hour with pre-blocked protein A seppharose beads before being incubated with 1ug of antibody overnight at 4 degrees. The lysate was allowed to incubate with protein A beads before being washed and subejcted to proteinase K digestion
Libraries were constructed using NEBnext Ultra DNA library prep kit according to manufactures instructions
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
 
Data processing Libraries were sequenced on the Illumina NextSeq 500 and Basecalling and demultiplexing performed by their standard pipelines
Adaptors and low quality reads were trimmed using Trim_galore version 0.40
Aligned to GRCh37 using Bowtie v 1.1.2 options -m3 -y --best
Peaks called using macs2 v 2.1.0 and the --gapped option
Homer v4.8 used to create tag directories of all samples and produced bedgraph data normalised to 10^7 reads.
Genome_build: GRCh37
Supplementary_files_format_and_content: bedgraph.gz - coveraged data in bedgraph format noramlised to 10e7 reads. Gapped Peaks file; is in BED12+3 format which contains both the gapped region and narrow peaks. The 5th column is 10*-log10qvalue, to be more compatible to show grey levels on UCSC browser. Tht 7th is the start of the first narrow peak in the region, and the 8th column is the end. The 9th column should be RGB color key, however, we keep 0 here to use the default color, so change it if you want. The 10th column tells how many blocks including the starting 1bp and ending 1bp of gapped regions. The 11th column shows the length of each blocks, and 12th for the starts of each blocks. 13th: fold-change, 14th: -log10pvalue, 15th: -log10qvalue.
 
Submission date Feb 23, 2016
Last update date May 15, 2019
Contact name Udo Oppermann
Organization name University of Oxford
Department Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences
Street address Botnar Research Centre, Nuffield Orthopaedic Centre, Windmill Road
City Oxford
State/province Oxfordshire
ZIP/Postal code OX3 7LD
Country United Kingdom
 
Platform ID GPL18573
Series (1)
GSE78206 H3K4me3 ChIP in multiple myeloma MM1S cells in the presence and absence of KDM5-C70
Relations
BioSample SAMN04510408
SRA SRX1597478

Supplementary file Size Download File type/resource
GSM2069577_KDM5C70_3.bedGraph.gz 46.4 Mb (ftp)(http) BEDGRAPH
GSM2069577_KDM5C70_3_peaks.gappedPeak.gz 1.3 Mb (ftp)(http) GAPPEDPEAK
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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