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Sample GSM4629957

Query DataSets for GSM4629957

Status

Public on Apr 14, 2021

Title

GPU rep1 [OD1]

Sample type

SRA

Source name

hyphae

Organism

Neurospora crassa

Characteristics

strain: GUL-1
rna immunoprecipitation: pull-dow
agent: none
genotype: Pccg1-gul-1-sgfp::his-3 hph::deltagul-1 (GUL-1;;GFP) A
fraction: pull-down RNA

Treatment protocol

For cell wall stress induction, relevant cultures were supplemented with 10-5 M Nikkomycin Z, for the last hour prior to RNA extraction.

Growth protocol

Strains were grown in either liquid or solid (supplemented with 1.5% agar) Vogel's minimal medium with 1.5% (w/v) sucrose (Vs) as described by Davis, 2000) or is available at http://www.fgsc.net/Neurospora/NeurosporaProtocolGuide.htm.

Extracted molecule

total RNA

Extraction protocol

RNA extraction, DNase treatment, cDNA and RT PCR (primers are listed in Table 2) were performed as previously described (Herold and Yarden, 2017).
For purified total RNA collected from samples, strand-specific sequencing libraries were produced following the Illumina TruSeq stranded protocol.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina NovaSeq 6000

Description

OD1

Data processing

According to Illumina protocol, the libraries underwent 101-bp paired-end sequencing using an Illumina NovaSeq (S4).. Basecalls performed using CASAVA version 1.8.2
For each read, the first 6 and the last nucleotides were trimmed to the point where the Phred score of an examined base fell below 20 using in-house scripts. If, after trimming, the read was shorter than 45 bp, the whole read was discarded.
Trimmed reads were mapped to the Neurospora crassa OR74A reference genome (FungiDB release 43) with hisat2 v2.1.0 indicating that reads correspond to the reverse complement of the transcripts. Alignments with quality score below 20 were excluded from further analysis.
Gene counts were produced with stringtie v1.3.3b and the python script “prepde.py” provided in the package. Stringtie was limited to reads matching the reference annotation.
Genome_build: Neurospora crassa OR74A (FungiDB release 43)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

Submission date

Jun 22, 2020

Last update date

Apr 15, 2021

Contact name

Francesc Lopez

E-mail(s)

francesc.lopez@yale.edu

Organization name

Yale University

Department

Department of Genetics