|
| Status |
Public on Oct 01, 2018 |
| Title |
SETMAR-FLAG R1 |
| Sample type |
SRA |
| |
|
| Source name |
ChIP-exo of Flag-SETMAR in U2OS-SMF cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: U2OS
chip antibody: Flag M2, F1804
|
| Growth protocol |
U2OS cells were maintained in DMEM with 10% fetal bovine serum and antibiotics.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
RNA extracted with the High Pure RNA isolation kit (Roche Applied Science), following manufacturer's instructions
Libraries were prepared using Illumina's TruSeq RNA Sample Preparation V2 according to manufacturer's instructions
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
AB SOLiD System 3.0 |
| |
|
| Description |
Processed data combined for the two ChIP-seq replicates. Processed data avalable at the foot of this page.
|
| Data processing |
Adapters trimmed with Sythe and Sickle (RNA-seq)
Alignment was done with Tophat2 v. 2.1.0 (RNA-seq) or BWA v. 0.7.5a (ChIP-exo) with default options
Extraction of properly paired and properly mapped reads and Bam files sorting and indexing were done with SAMtools v. 1.3.1
Mapped reads were de-duplicated with Picard (ChIP-exo)
Peak calling was performed with MACS v. 1.3.7.1 (ChIP-exo)
RNA-seq differential expression was performed with HTseq and DESeq2.
Bigwig files were generated with the bedGraphToBigWig script
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files: genome-coverage files for all samples
|
| |
|
| Submission date |
Jan 04, 2018 |
| Last update date |
Oct 01, 2018 |
| Contact name |
Michael Tellier |
| E-mail(s) |
mt477@leicester.ac.uk
|
| Organization name |
University of Leicester
|
| Department |
Department of Molecular and Cell Biology
|
| Lab |
Tellier Lab
|
| Street address |
Lancaster Road
|
| City |
Leicester |
| State/province |
Select State |
| ZIP/Postal code |
LE1 7HB |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL9442 |
| Series (1) |
| GSE108773 |
Human SETMAR is a DNA sequence-specific histone-methylase with a broad effect on the transcriptome |
|
| Relations |
| BioSample |
SAMN08292409 |
| SRA |
SRX3583131 |
