|
| Status |
Public on Oct 21, 2018 |
| Title |
cDC PU.1 ChIP-seq Rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
Conventional dendritic cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Conventional dendritic cells
strain: C56BL/6
chip antibody: PU.1 antibody
|
| Growth protocol |
Dendritic cells were generated in Flt3L culture.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
10^7 cells were crosslinked 1% paraformaldehyde (Sigma-Aldrich) in PBS then lysed (1%SDS + 1mM EDTA + proteases inhibitors). Cross-linked DNA was sonicated with the Bioruptor (Diagenode). Protein G Dynabeads (Invitrogen) were incubated with 20 μg of PU.1 antibody (Santa Cruz, T-20) according to the manufacturer’s protocol. Coupled antibody was added to 100 μg of chromatin and incubated overnight at 4°C. Unbound chromatin was removed using a series of four washes. Following elution, bound chromatin was reverse cross-linked and subjected phenol/chloroform immunoprecipitation.
Libraries were prepared at the Beijing Genomic Institute (BGI) according to Illumina's instructions and standard BGI ChIP-seq protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
FASTQ files were output using standard Illumina protocols and software at the Beijing Genomics Institute (BGI).
Reads were aligned to the mouse genome using Subread 1.4.4.
Reads were assigned to genomic windows using the R package csaw version 1.4.1. The window width was set to 10 with spacing of 50bp. Single-end reads were extended directionally to make up a fragment length of 170. Windows were filtered if their count was less than 3-fold higher than background, leaving 329996 windows.
Genome_build: mm10 (NCBI build 38.1)
Supplementary_files_format_and_content: The process files are tab-delimited text files with two columns representing the genomic window coordinates and the number of reads or DNA fragments overlapping that window. The supplementary file 'WindowCounts.tsv.gz' collates the counts for all five samples of this series into one file. The supplementary file 'GenomicWindows.bed.gz' gives the coordinates of each genomic window in BED format.
|
| |
|
| Submission date |
Oct 20, 2018 |
| Last update date |
Oct 22, 2018 |
| Contact name |
Gordon K Smyth |
| E-mail(s) |
smyth@wehi.edu.au
|
| Phone |
(+61 3) 9345 2326
|
| Fax |
(+61 3) 9347 0852
|
| URL |
http://www.wehi.edu.au
|
| Organization name |
Walter and Eliza Hall Institute of Medical Research
|
| Department |
Bioinformatics
|
| Lab |
Smyth
|
| Street address |
1G Royal Pde
|
| City |
Parkville |
| State/province |
Vic |
| ZIP/Postal code |
3052 |
| Country |
Australia |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE121544 |
ChIP-seq profiling of PU.1 binding sites in plasmacytoid and conventional mouse dendritic cells |
|
| Relations |
| BioSample |
SAMN10265178 |
| SRA |
SRX4909227 |
