|
| Status |
Public on Aug 11, 2017 |
| Title |
SX2966_input_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
whole animal,mixed population
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
strain: SX2966
antibody: none
|
| Growth protocol |
All strains were grown on NGM plates seeded with HB101 E coli
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
After fixation with formaldehyde, C elegans lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to a modifed Illumina protocol (Ethan Ford's protocol). Briefly, DNA was end-repaired using the NEB ENd repair enzyme Mix. The blunt, phosphorylated ends were treated with Klenow fragment (exo minus, NEB) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were size selected with AMPure XP beads.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Data processing |
Reads were aligned using BWA v. 0.7.7
SAMtools v. 0.1.19 ‘view’ utility was used to convert the alignments to BAM format
Normalized ChIP-seq coverage tracks were generated using the R implementation of BEADS algorithm
Initial ChIP-seq peaks were called using MACS v. 2.1.1. To generate combined peak calls, we used the modified IDR procedure with an IDR threshold of 0.05 to combine replicates
Genome_build: WS220/ce10 assembly of the C. elegans genome
Supplementary_files_format_and_content: narrowpeak file was generated using a modified IDR procedure from the encode project with an IDR threshold of 0.05 to combine replicates
Supplementary_files_format_and_content: wig files were generated using the R implementation of BEADS algorithm and contain normalised Chip-seq coverage tracks.
|
| |
|
| Submission date |
Feb 22, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Eric Alexander Miska |
| E-mail(s) |
eam29@cam.ac.uk
|
| Organization name |
University of Cambridge
|
| Department |
Gurdon Institute
|
| Street address |
Tennis Court Road
|
| City |
Cambridge |
| ZIP/Postal code |
CB2 1QN |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL18730 |
| Series (2) |
| GSE95228 |
Role of STA-1 and SID-3 upon Orsay virus infection in C. elegans (ChIP-Seq) |
| GSE95230 |
Role of STA-1 and SID-3 upon Orsay virus infection in C. elegans |
|
| Relations |
| BioSample |
SAMN06392917 |
| SRA |
SRX2582952 |
