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Sample GSM4811886

Query DataSets for GSM4811886

Status

Public on Oct 01, 2020

Title

cel1N2L2

Sample type

SRA

Source name

whole worm mRNA extract

Organism

Caenorhabditis elegans

Characteristics

tissue: whole worm
condition: wild type L2 larvae
age: L2 larvae
genotype: wild type

Growth protocol

C. elegans strains were maintained under standard conditions, on NGM plates seeded with OP50 bacteria at 20°C degrees.

Extracted molecule

polyA RNA

Extraction protocol

The total nucleic acid extraction of wild-type and mutant animals was conducted by TRI Reagent® (Molecular Research Center, Inc, Cincinnati, Ohio USA) as recommended by the manufacturer. The crude extract was further purified with RNeasy Mini Kit (Qiagen, Hilden, Germany) using the manufacturer’s protocol. To remove DNA contamination which might interfere with downstream applications, Column DNase treatment with Qiagen RNase free DNase kit was applied. To purify pure mature polyA-tailed mRNA, we performed a magnetic bead based separation on the purified total RNA with NEB NEXT Poly(A) mRNA magnetic Isolation Module (New England Biolabs, Ipswich, MA, USA). 100 ng of mature polyA-tailed mRNA per sample was used to construct RNA-SEQ libraries.
NEB NEXT ULTRA II Directional RNA Library Preparation Kit (Illumina,San Diego, CA, USA)

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina MiSeq

Description

cel1N2L2

Data processing

FASTQ Generation | Version: 1.0.0 on Illumina BaseSpaceFS version: 2.0.1018 system
Sequenced reads were trimmed for adaptor and low-quality sequence with trim_galore version 0.4.1 and cutadapt version 1.14
The trimmed sequence sets were aligned to the WBcel235 genome with TopHat v2.1.0 (bowtie2-align-s version 2.3.4.3), using default parameters
Performed union-exon based count with R Rsubread package version 1.34.7 , and count processing and rpkm calculation with R edgeR package version 3.26.8
Genome_build: C. elegans WBcel235 genome Ensembl release 94
Supplementary_files_format_and_content: tab-delimited text files include union-exon based RPKM values and annotation information for each Sample

Submission date

Sep 30, 2020

Last update date

Oct 01, 2020

Contact name

István Likó

E-mail(s)

istvanliko@gmail.com

Organization name

Semmelweis University

Lab

HAS-SE Momentum Hereditary Endocrine Tumour Syndromes Research Group, Hungarian Academy of Sciences and Semmelweis University