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| Status |
Public on Aug 14, 2018 |
| Title |
npf H3K27me3 ChIPseq |
| Sample type |
SRA |
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| Source name |
germinated conidia
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| Organism |
Neurospora crassa |
| Characteristics |
cell type: conidium
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
none provided by the submitter
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
ChIP-seq 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).
Supplementary_files_format_and_content: For Poly-A mRNA files: Text files contain counts for every gene as outlined in process above.
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| Submission date |
Aug 13, 2018 |
| Last update date |
Aug 14, 2018 |
| Contact name |
Vincent T Bicocca |
| E-mail(s) |
bicocca@uoregon.edu
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| Organization name |
University of Oregon
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| Department |
Biology
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| Lab |
Selker
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| Street address |
1229 University of Oregon
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| City |
Eugene |
| State/province |
OR |
| ZIP/Postal code |
97403 |
| Country |
USA |
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| Platform ID |
GPL20660 |
| Series (1) |
| GSE118495 |
ASH-1-catalyzed H3K36 methylation drives gene repression and marks H3K27me2/3-competent chromatin |
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| Relations |
| BioSample |
SAMN09828192 |
| SRA |
SRX4549863 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3330997_Galaxy217-_bamCoverage_CTGTCA_N4721.npf.K27me3_.bigwig |
7.8 Mb |
(ftp)(http) |
BIGWIG |
| GSM3330997_Galaxy228-_Sorted_K27npf_wt_loss_to_gain_.txt.gz |
14.2 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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