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Sample GSM5033122 Query DataSets for GSM5033122
Status Public on Apr 28, 2022
Title Mpyr-13-4_RNA-Rep1-156
Sample type SRA
 
Source name Mpyr-13-4
Organism Macrocystis pyrifera
Characteristics strain: Cur6M-Colch-13-4
Sex: Female
tissue: whole organism
Stage: immature gametophyte
phenotype: partial sex reversal
treatment: 1 mg Colchicine (12-16 weeks)
sample code: Rep1-156
Treatment protocol No treatment
Growth protocol Cultures were grown in 140 mm round Petri dishes in natural sea water with 0.01% Provasoli enrichment at 13°C with a 14h/10h day/night cycle and 20 (µmol photons).m-2.s-1 irradiance of red light.
Extracted molecule total RNA
Extraction protocol For each sample, total RNA was extracted from 2 independent bulks of app. 1000 male individuals and 2 bulks of 1000 female individuals (two biological replicates for each sex) using the Qiagen Mini kit (http://www.qiagen.com) as previously described (Lipinska, Cormier, et al. 2015; Arun et al. 2019). RNA from wild-type male and female and variant Mpyr-13-4 line pools was extracted using the protocol described by (Apt et al. 1995).
For each replicate, the RNA was quantified and cDNA was synthesized using an oligo-dT primer. The cDNA was fragmented, cloned, and sequenced by Fasteris (CH-1228 Plan-les-Ouates, Switzerland) using an Illumina Hi-seq 2000 set to generate 150-bp single-end reads.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description Corresponding replicate: Rep2-157
featureCounts_Mpyr-13-4-Wtmale-Wtfemale.tab
deseq_Mpyr134_vs_WT_male.csv
deseq_WT_female_vs_Mpyr134.csv
Mac13-4--156_R1-R1/Mac13-4-156-accepted_hits.bam
Data processing Illumina base calling
Data quality was assessed using the FastQC (Wingett et al. 2018). Reads were trimmed and filtered using Trimmomatic (Bolger et al. 2014) with average quality > 28, a quality threshold of 24 (base calling) and a minimal size of 60 bp.
Filtered reads were mapped to the M. pyrifera genome (Lipinska et al. 2019a) using TopHat2 (Kim et al. 2013) with the Bowtie2 aligner (Langmead and Salzberg 2012).
The mapped sequencing data were then processed with FeatureCounts (Liao et al. 2014) to obtain counts for sequencing reads mapped to exons and counts by gene. Transcript abundances, measured as transcript per million (TPM).
Differential expression analysis was performed with the DESeq2 package (Love et al. 2014) (Bioconductor) using an adjusted P-value cut-off of 0.05 and a minimal fold-change of 2.
Genome_build: M. pyrifera genome (Lipinska et al. 2019, Genome Biol. 20:35)
Supplementary_files_format_and_content: bigWig files were generated from bam files, which were merges of the two replicates, normalised with SES with the signal subtract from the input using deeptools (v3.2.0; Fidel R, Ryan DP, Grüning B, Bhardwaj V, Kilpert F, Richter AS, Heyne S, Dündar F, Manke T. 2016. deepTools2: A next Generation Web Server for Deep-Sequencing Data Analysis. Nucleic Acids Research 44:W160-W165). Peak calling files, based on the bigWig files, are in either narrowPeak (bed9) or broadPeak (bed12) format.
 
Submission date Jan 25, 2021
Last update date Apr 28, 2022
Contact name Olivier GODFROY
E-mail(s) godfroy@sb-roscoff.fr
Organization name CNRS
Department Station Biologique de Roscoff
Lab UMR8227
Street address Place Georges Teissier CS90074
City ROSCOFF
ZIP/Postal code 29680
Country France
 
Platform ID GPL29648
Series (1)
GSE165423 A partially sex-reversed giant kelp sheds light into the mechanisms of sexual differentiation in UV sexual system
Relations
BioSample SAMN17527740
SRA SRX9931405

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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