 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Oct 19, 2022 |
| Title |
SET2; H3G34R_H3K9me3_ChIP-seq |
| Sample type |
SRA |
| |
|
| Source name |
germinated conidia
|
| Organism |
Neurospora crassa |
| Characteristics |
genotype/variation: SET2; H3G34R
antibody use: H3K9me3 (ActiveMotif, Cat#39161)
|
| Growth protocol |
Strains were grown, crossed, and maintained according to standard procedures (Davis RH, 2000). Briefly, tissue was harvested from strains grown at 32°C with shaking for 18 hours in Vogel’s liquid medium.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Tissue was cross-linked for 10 min in 0.5% formaldehyde. Tissue was disrupted by sonication and chromatin sheared using a biorupter (Diagenode).
Libraries were prepared using the NEBNext ChIP-seq Library Prep Master Mix for Illumina.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
All sequencing reads were mapped to the corrected N. crassa OR74A (NC12 genome) (Galazka et al., 2016) using Bowtie2 (Langmead and Salzberg, 2012).
ChIP-seq read coverage was averaged, normalized, and analyzed using tools available from deepTools2 on the open-source platform Galaxy (Afgan et al., 2016). Sequencing tracks are displayed as 25-nt-window TDF or bigWig files with the Integrative Genomics Viewer (IGV) (Robinson et al., 2011).
Genome_build: Neurospora crassa assembly 12 Fixed (files: neurospora_crassa_or74a_12_genome_FIXED.fasta, and neurospora_crassa_or74a_12_transcripts_FIXED.gtf; files are found in GEO submission GSE71024)
Supplementary_files_format_and_content: For ChIP-seq files: The tdf files were generated using the "count" function in igvtools (Integrative Genomics Viewer; Broad Institute, Robinson et al, 2011) and bigwig files were generated using DeepTools (Ramirez et al., 2016) using a window size of 20 -200bp (tdf and bigwig files are binary files that shows enrichment peaks for each ChIP sample and have been processed for faster display of the data in IGV).
|
| |
|
| Submission date |
Jul 17, 2019 |
| Last update date |
Oct 19, 2022 |
| Contact name |
Elizabeth Toomey Wiles |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Oregon
|
| Department |
Biology, Institute of Molecular Biology
|
| Lab |
Selker
|
| Street address |
1229 University of Oregon; 1318 Franklin Blvd.
|
| City |
Eugene |
| State/province |
OR |
| ZIP/Postal code |
97403 |
| Country |
USA |
| |
|
| Platform ID |
GPL23150 |
| Series (2) |
| GSE134449 |
The histone H3G34R mutation disrupts the epigenome via catalytic inactivation of the ASH1 H3K36 methyltransferase [ChIP-seq] |
| GSE134452 |
The histone H3G34R mutation disrupts the epigenome via catalytic inactivation of the ASH1 H3K36 methyltransferase |
|
| Relations |
| BioSample |
SAMN12307233 |
| SRA |
SRX6458533 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3948556_Galaxy760-_bamCoverage_CACTTCAC_N6777_H3K9me3_1_051019_.bigwig |
9.1 Mb |
(ftp)(http) |
BIGWIG |
| GSM3948556_Galaxy762-_bamCoverage_TAGCCATG_N6777_H3K9me3_2_051019_.bigwig |
9.5 Mb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
