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| Status |
Public on Aug 21, 2024 |
| Title |
RNA-seq ∆sds3 (∆NCU01599) strain: N8194 |
| Sample type |
SRA |
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| Source name |
N8194
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| Organism |
Neurospora crassa |
| Characteristics |
strain: N8194
genotype: [delta]sds3 ([delta]NCU01599)
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| Treatment protocol |
Mycelia were harvested and added to a tube containing ~350uL glass beads (260-300 micrometer, acid washed [Sigma Aldrich] and resuspended in sdH2O), 350uL NETS buffer (10mM Tris pH 7.5, 300mM NaCl, 1mM EDTA, 0.2% SDS) and 350uL phenol:chloroform:isoamyl alcohol (25:24:1) and lysed by a bead beater for 3 minutes at 4oC.
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| Growth protocol |
5 ml cultures were grown in Vogels medium and 1.5% sucrose (standard minimal medium), supplemented with 1x histidine for N6279 strains, with TSA added to samples when indicated, shaking for 16 hours at 32oC.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Samples were cleared by centrifugation, and the aqueous (top) phase was mixed with 350uL of chloroform. After centrifugation, the aqueous phase was divided into two tubes containing 650uL cold 100% EtOH. Samples were precipitated at -20oC, pelleted by centrifugation, washed twice with 1mL 70% EtOH, and resuspended in DEPC-treated dH2O. RNA was treated with DNaseI, amplification grade (Thermo Fisher Scientific) and cleaned (Agencourt® RNAclean XP® beads, Beckman Coulter).
RNA-seq libraries were prepared using the KAPA Stranded mRNA-seq kit (KAPA Biosystems).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
Expression_change_mutant.xlsx
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| Data processing |
Sequence reads were aligned to the Neurospora crassa genome (OR74A) using STAR program (version 2.7.3a)
Total aligned reads per Neurospora gene were calculated using RSEM software (version 1.3.1) and normalized using DESeq2 software (version 1.24.0)
Samples were cleared by centrifugation, and the aqueous (top) phase was mixed with 350uL of chloroform. After centrifugation, the aqueous phase was divided into two tubes containing 650uL cold 100% EtOH. Samples were precipitated at -20oC, pelleted by centrifugation, washed twice with 1mL 70% EtOH, and resuspended in DEPC-treated dH2O. RNA was treated with DNaseI, amplification grade (Thermo Fisher Scientific) and cleaned (Agencourt® RNAclean XP® beads, Beckman Coulter).
Assembly: Neurospora crassa genome (OR74A)
Supplementary files format and content: Excel file with average read count, log2FC, P-value, FDR and category (Up & Down)
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| Submission date |
Mar 11, 2024 |
| Last update date |
Aug 21, 2024 |
| Contact name |
Hideki Tanizawa |
| E-mail(s) |
[email protected]
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| Phone |
011-706-5035
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| Organization name |
Hokkaido University
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| Department |
Institute for Genetic Medicine
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| Lab |
Division of Genome Biology
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| Street address |
Kita 15, Nishi 7, Kita-ku
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| City |
Sapporo |
| State/province |
Hokkaido |
| ZIP/Postal code |
060-8615 |
| Country |
Japan |
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| Platform ID |
GPL23150 |
| Series (1) |
| GSE261319 |
The RPD3L deacetylation complex is required for facultative heterochromatin repression in Neurospora crassa [RNA-seq] |
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| Relations |
| BioSample |
SAMN40378547 |
| SRA |
SRX23900702 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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