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| Status |
Public on Mar 08, 2022 |
| Title |
RNAseq_crf4_3_N7966 |
| Sample type |
SRA |
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| Source name |
nuclei from germinated condia
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| Organism |
Neurospora crassa |
| Characteristics |
sample type: nuclei
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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 room temperature.
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| Growth protocol |
5 ml cultures were grown in Vogels medium and 1.5% sucrose (standard minimal medium), 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 |
RNA-seq
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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)
Batch effect were corrected using R package, limma (version 3.44.1).
FDR < 0.05 and log2 fold-change > 2 were used as a threshold to identify significantly up- or downreagulated genes.
neurospora crassa genome (OR74A)
tab-deliminated text files of gene ID and expected read count obtained from RSEM calculation
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| Submission date |
Mar 04, 2021 |
| Last update date |
Mar 08, 2022 |
| Contact name |
Hideki Tanizawa |
| E-mail(s) |
[email protected]
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| Organization name |
University of Oregon
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| Department |
Institute of Molecular Biology
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| Street address |
1370 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) |
| GSE168277 |
The ACF chromatin remodeling complex is essential for Polycomb repression |
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| Relations |
| BioSample |
SAMN18141460 |
| SRA |
SRX10240498 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5135463_RNAseq_crf4_3_N7966_count.txt.gz |
41.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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