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Sample GSM6500927

Query DataSets for GSM6500927

Status

Public on Oct 01, 2022

Title

yeast wild-type reference, auxin induced, rep2

Sample type

SRA

Source name

yeast

Organism

Saccharomyces cerevisiae

Characteristics

cell type: yeast
genotype: leu2{delta}0, his3{delta}1, ura3{delta}0, met15{delta}0, Mat a
strain: BY4741
treatment: 1H IAA 100µM, ßoestradiol 1µM
Stage: exponential phase

Treatment protocol

1H IAA 100µM, ßoestradiol 1µM

Growth protocol

30°C in YPD, exponential phase (OD 600=0,4)

Extracted molecule

total RNA

Extraction protocol

Standard hot phenol protocol
Direct RNA sequencing (ONT kit SQK-RNA002)

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

MinION

Data processing

Basecalling using guppy (ONT, see sequencing.summary.txt for each sample)
Mapping to the SC288 reference genome Saccer3.fa using minimap2.1 with options -k 14 -ax map-ont –secondary = no and processed with samtools 1.9 (samtools view -b -o).
The poly(A) tail lengths for each read were estimated using the Nanopolish 0.13.2 polya function (Workman, R. E. et al. Nat. Methods 1–9. https://doi.org/10.1038/s41592-019-0617-2 (2019))
Assembly: Saccer3.fa
Supplementary files format and content: Fast5 (raw data)
Supplementary files format and content: Fastq
Supplementary files format and content: sequencin.summary.txt (from basecalling process)

Submission date

Aug 22, 2022

Last update date

Oct 07, 2022

Contact name

Cosmin Saveanu

E-mail(s)

csaveanu@pasteur.fr

Phone

+33144389280

Organization name

Institut Pasteur