 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Aug 14, 2017 |
| Title |
H2Bub_ChIPseq |
| Sample type |
SRA |
| |
|
| Source name |
Kc167
|
| Organism |
Drosophila melanogaster |
| Characteristics |
cell type: Kc167 Drosophila Embryonic Cell Line
chip-antibody: H2Bub (Millipore 05-1312)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were crosslinked with 1% formaldehyde for 10 min at room temperature and quenched with glycine. For ChIP-seq, nuclear lysates were sonicated to generate 200-500 bp fragments . Chromatin was precleared with Protein A or G Dynabeads at 4°C for 2 hours and incubated with antibody overnight at 4°C. Isolated chromatin was washed, eluted, reverse crosslinked and purified by standard methods. For HiChIP nuclei were isolated and chromatin digested by DpnII, filled in with biotin-dCTP, and ligated. After ligation, chromatin was sonicated and precleared with Protein A and G Dynabeads at 4°C for 2 hours, then precipitated using anti-CP190 or anti-Pol2phosphoSerine2 antibody overnight. Isolated chromatin was washed, eluted, reverse crosslinked and purified by standard methods, after which ligation events were enriched by streptavidin precipitation.
Libraries were constructed using the standard protocol. Genomic fragments were end repaired (NEBNext End Repair Module), A-tailed by adding adenosine to the 3’ ends of fragment using Klenow fragment (3’ to 5’ exo minus, New England Biolabs), and adaptors were ligatedat room temperature for 1 hr with T4 DNA ligase (New England Biolabs). Libraries were amplified with Illumina primers using the KAPA SYBR FAST qPCR Master Mix.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
ChIP-seq for H2B ubiquitinylated
|
| Data processing |
ChIP-seq reads were aligned to the dm6 reference genome using bowtie2 and PCR duplicates were removed. HiChIP and ChIAPET reads were processed using the Juicer pipeline.
Genome_build: dm6
Supplementary_files_format_and_content: bigWig containing coverage of ChIP-seq and .hic containing Hi-C contact matrices.
|
| |
|
| Submission date |
Feb 14, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
M Jordan Rowley |
| E-mail(s) |
jordan.rowley@unmc.edu, jordrow@gmail.com
|
| Phone |
7343580454
|
| Organization name |
Univ of Nebraska Medical Center
|
| Department |
GCBA
|
| Lab |
Rowley
|
| Street address |
601 S Saddle Creek Rd
|
| City |
Omaha |
| State/province |
NE |
| ZIP/Postal code |
68106 |
| Country |
USA |
| |
|
| Platform ID |
GPL13304 |
| Series (1) |
| GSE89244 |
Evolutionary Principles Predict 3D Chromatin Organization |
|
| Relations |
| BioSample |
SAMN06330340 |
| SRA |
SRX2559032 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2487551_H2Bub.bw.gz |
64.7 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
