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Sample GSM3948560 Query DataSets for GSM3948560
Status Public on Oct 19, 2022
Title set-2_H3K9me3_ChIP-seq
Sample type SRA
Source name germinated conidia
Organism Neurospora crassa
Characteristics genotype/variation: set-2
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
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
BioSample SAMN12307229
SRA SRX6458537

Supplementary file Size Download File type/resource
GSM3948560_Galaxy761-_bamCoverage_GATCAAGG_N5761_H3K9me3_1_051019_.bigwig 9.6 Mb (ftp)(http) BIGWIG
GSM3948560_Galaxy763-_bamCoverage_TCTTCGAC_N5761_H3K9me3_2_051019_.bigwig 9.1 Mb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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