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| Status |
Public on Apr 15, 2020 |
| Title |
GFP-EPR-1BAH N7753 ChIP-seq |
| Sample type |
SRA |
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| Source name |
germinated conidia
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| Organism |
Neurospora crassa |
| Characteristics |
genotype: mat A; pNCU05173::hph; pNCU07152::nat-1; his-3+::pCCG::N-GFP::epr-1W184A; epr-1UV1
chip antibody: GFP (MBL #598; lot #079)
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
GFP ChIPs were performed with the same protocol as histone modification ChIP except that cross-linking was done with 1% formaldehyde for 10 minutes, tissue was sonicated with 3x 10 pulses, chromatin was sheared 4x 10 minutes using a Bioruptor, and protein A beads (Sigma) were used for the IP. GFP ChIP-seq libraries were size selected (for fragments 400-800 bp) using Mag-Bind RXNPure Plus Beads (Omega Biotek).
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
ACGTCCAA_N7753_WT_GFP-NCU07505_W184A_122018_S55_L008_R1_001
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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).
RNA-seq processing: Tools available on Galaxy {Afgan:2018gf} were used to map mRNA-sequencing reads (intron size < 1kb) {Dobin:2012fg} against the corrected N. crassa OR74A (NC12) genome {Galazka:2016cm}, count the number of reads per gene {Dobin:2012fg} and determine differentially expressed genes with DESeq2 {Love:2014ka}.
DamID-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: ChIP-seq processed data files are bigwig files generated using DeepTools (Ramirez et al., 2016) using a window size of 25bp
Supplementary_files_format_and_content: RNA-seq processed data files are txt files containing normalized counts for 2 replicates each of wild type, ∆set-7 (both from Klocko et al. 2016; GSE82222) and ∆epr-1 and the output file from DESeq2 (Love et al., 2014) with pairwise comparisons of 2 biological replicates from each genotype.
Supplementary_files_format_and_content: DamID-seq processed data files are bigwig files generated using DeepTools (Ramirez et al., 2016) using a window size of 25bp
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| Submission date |
Mar 14, 2019 |
| Last update date |
Apr 15, 2020 |
| Contact name |
Elizabeth Toomey Wiles |
| E-mail(s) |
[email protected]
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| Organization name |
University of Oregon
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| Department |
Biology, Institute of Molecular Biology
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| Lab |
Selker
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| Street address |
1229 University of Oregon; 1318 Franklin Blvd.
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| City |
Eugene |
| State/province |
OR |
| ZIP/Postal code |
97403 |
| Country |
USA |
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| Platform ID |
GPL23150 |
| Series (1) |
| GSE128317 |
Evolutionarily ancient BAH-PHD protein mediates Polycomb silencing in Neurospora crassa |
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| Relations |
| BioSample |
SAMN11128306 |
| SRA |
SRX5523366 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3671334_ACGTCCAA_N7753_WT_GFP-NCU07505_W184A_122018_S55_L008_R1_001.bigwig |
6.4 Mb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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