NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM5135465 Query DataSets for GSM5135465
Status Public on Mar 08, 2022
Title RNAseq_NCU09388_N7988
Sample type SRA
 
Source name nuclei from germinated condia
Organism Neurospora crassa
Characteristics sample type: nuclei
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.
Growth protocol 5 ml cultures were grown in Vogels medium and 1.5% sucrose (standard minimal medium), shaking for 16 hours at 32oC.
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).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Description RNA-seq
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
 
Submission date Mar 04, 2021
Last update date Mar 08, 2022
Contact name Hideki Tanizawa
E-mail(s) hidekit@uoregon.edu
Organization name University of Oregon
Department Institute of Molecular Biology
Street address 1370 Franklin Blvd
City Eugene
State/province OR
ZIP/Postal code 97403
Country USA
 
Platform ID GPL23150
Series (1)
GSE168277 The ACF chromatin remodeling complex is essential for Polycomb repression
Relations
BioSample SAMN18141458
SRA SRX10240500

Supplementary file Size Download File type/resource
GSM5135465_RNAseq_NCU09388_N7988_count.txt.gz 41.2 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap