|
| Status |
Public on Oct 19, 2022 |
| Title |
SET-2; H3G34R RNAseq |
| Sample type |
SRA |
| |
|
| Source name |
germinated conidia
|
| Organism |
Neurospora crassa |
| Characteristics |
genotype/variation: SET-2; H3G34R
tissue: mycelia
|
| Growth protocol |
Strains were grown, crossed, and maintained according to standard procedures (Davis RH, 2000). Briefly, polyA RNA was isolated from strains grown at 32°C with shaking for 18 hours in Vogel’s liquid medium.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated ( D), Dnase treated (ThermoFisher Scientific) and cleaned (Agencourt RNAClean XP beads; Beckman Coulter)
Poly-A+RNA-seq libraries were prepared using KAPA Stranded mRNA-seq kit (KAPA Biosystems)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Reads were mapped and gene counts generated using RNA STAR (2.6.0)
DESeq2 version 1.18.1 was used to generate differential count files.
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: Tabular files contain counts for every gene as outlined in process above. Excel workbook files (.xlsx) include the differential gene expression values for each mutant background as determined by DESeq2.
|
| |
|
| Submission date |
Jul 17, 2019 |
| Last update date |
Oct 19, 2022 |
| Contact name |
Elizabeth Toomey Wiles |
| E-mail(s) |
tishw@uoregon.edu
|
| 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) |
| GSE134451 |
The histone H3G34R mutation disrupts the epigenome via catalytic inactivation of the ASH1 H3K36 methyltransferase [RNA-seq] |
| GSE134452 |
The histone H3G34R mutation disrupts the epigenome via catalytic inactivation of the ASH1 H3K36 methyltransferase |
|
| Relations |
| BioSample |
SAMN12307378 |
| SRA |
SRX6458547 |
