|
| Status |
Public on Mar 22, 2015 |
| Title |
dim-3 H3K9me3 ChIPseq |
| Sample type |
SRA |
| |
|
| Source name |
N2108 (dim-3) Selker lab
|
| Organism |
Neurospora crassa |
| Characteristics |
strain: dim-3
time point in light: 0
growth medium: 1x Vogels, 1.5% sucrose
chip antibody: Active Motif Cat# 39162 (H3K9me3)
|
| Growth protocol |
grown under standard dark cycle in 1xVogels medium + 1.5% sucrose (minimum medium) for 16 hours on rocking shaker at 32oC
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were generated from sonicated wet tissue, and histone-DNA complexes were isolated with H3K9me3 antibody
Libraries were prepared according to Illumina's standard protocol (TruSeq kit, ref# IP-202-1012)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
raw data .fastq files were mapped to the Ncrassa10 genome using Bowtie2, generating .sam files
using samtools, .sam files were converted to .bam files, duplicates were removed (rmdup), and the .bam file was sorted
the sorted .bam file was indexed, and then used for building the .tdf file on igvtools (below)
Genome_build: Ncrassa version10
Supplementary_files_format_and_content: .tdf files were generated using the "count" function in igvtools (Integrative Genomics Viewer; Broad Institute, Robinson et al, 2011), using a window size of 200bp, showing peaks of H3K9me3 enrichment
|
| |
|
| Submission date |
Sep 05, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Andrew David Klocko |
| E-mail(s) |
aklocko@uccs.edu
|
| Phone |
719-255-3255
|
| Organization name |
University of Colorado Colorado Springs
|
| Department |
Chemistry and Biochemistry
|
| Lab |
Klocko
|
| Street address |
278 Centennial Hall, 1420 Austin Bluffs Pkwy
|
| City |
Colorado Springs |
| State/province |
Colorado |
| ZIP/Postal code |
80918 |
| Country |
USA |
| |
|
| Platform ID |
GPL16164 |
| Series (2) |
| GSE61173 |
H3K9me3 ChIP-seq from Neurospora crassa wild type (WT) and dim-3 (severely reduced H3K9me3 levels) strains |
| GSE61175 |
Neurospora importin alpha compromises H3K9me3 and cytosine methylation levels through inappropriate localization of the heterochromatin machinery |
|
| Relations |
| BioSample |
SAMN03020660 |
| SRA |
SRX693078 |
