|
| Status |
Public on Apr 05, 2016 |
| Title |
MM1S_KDM5C70_2 |
| 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 |
SAMN04510402 |
| SRA |
SRX1597477 |
