|
| Status |
Public on Dec 09, 2020 |
| Title |
328-4_bd_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
N. crassa culture, control
|
| Organism |
Neurospora crassa |
| Characteristics |
strain: 328-4: ras-1bd MAT A
genotype: wt
|
| Growth protocol |
A mycelial disc was cut from respective strain using a 6 mm cork borer, transferred into a flask containing Bird 1.8% glucose medium, and grown for 48 hours, 25C, constant light, and ~100 RPM shaking.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Neurospora tissue was isolated by vacuum filtration and frozen in liquid nitrogen. Frozen tissue was ground under liquid nitrogen using a mortar and pestle. Total RNA was extracted using Trizol (Invitrogen) as described (PMID: 19262566).
Novogene procedures: total RNA QC pass (Agilent 2100 Bioanalyzer), polyA(+) enrichment for mRNA using oligo(dT) beads, NEB directional library preparation kit, library QC pass (concentration & insert size), Illumina NovaSeq 6000 sequencing, 150 bp stranded PE reads returned for each sample
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
wt_s1
|
| Data processing |
Align reads: STAR --runThreadN 1 --runMode alignReads --genomeDir /N_crassa_NC12/STAR_genomebuild/ --sjdbGTFfile /N_crassa_NC12/neurospora_crassa_or74a_12_transcripts.gtf --readFilesIn ./*_1.fq ./*_2.fq --outFilterType BySJout --alignIntronMin 10 --alignIntronMax 3000 --outFileNamePrefix ./STAR_out/ --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical
Quantify transcripts: cuffquant --library-type=fr-firststrand /N_crassa_NC12/neurospora_crassa_or74a_12_transcripts.gtf Aligned.out.sorted.sam
Normalize samples together: cuffnorm /N_crassa_NC12/neurospora_crassa_or74a_12_transcripts.gtf *.cxb
Output: Fragments Per Kilobase of transcript per Million mapped reads (FPKM) at the gene level (i.e. not isoforms) used for analysis.
Genome_build: Neurospora crassa OR74A NC12 genome, accessed 9/28/17: ftp://ftp.broadinstitute.org/pub/annotation/fungi/neurospora_crassa/assembly/
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each Sample
|
| |
|
| Submission date |
Aug 10, 2020 |
| Last update date |
Dec 09, 2020 |
| Contact name |
Christina M Kelliher |
| E-mail(s) |
Christina.M.Kelliher@dartmouth.edu
|
| Organization name |
Geisel School of Medicine at Dartmouth
|
| Department |
Molecular & Systems Biology
|
| Street address |
7400 Hinman
|
| City |
Hanover |
| State/province |
NH |
| ZIP/Postal code |
03755 |
| Country |
USA |
| |
|
| Platform ID |
GPL26551 |
| Series (1) |
| GSE155999 |
Nonsense mediated decay and a novel protein Period-2 regulate casein kinase I in an opposing manner to control circadian period in Neurospora crassa |
|
| Relations |
| BioSample |
SAMN15776660 |
| SRA |
SRX8920395 |
