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Sample GSM5321723

Query DataSets for GSM5321723

Status

Public on Nov 23, 2021

Title

12C01N2_15C_LTSO180412_R2

Sample type

SRA

Source name

N2 (wild type)

Organism

Caenorhabditis elegans

Characteristics

genotype: N2 (wild type)
developmental stage: Germline
temperature of growth: 15 C

Growth protocol

N2 and jmjd-5(zr1234) young adult worms ) were collected at the indicated temperature and generations, washed 3 times in M9 and flash-frozen in liquid nitrogen.

Extracted molecule

total RNA

Extraction protocol

Libraries for sequencing were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB E7645S) and Multiplex Oligos for Illumina (NEB E7335S, E7500S). Quality and size of the libraries were checked by Bioanalyzer (Agilent 2100 Bioanalyzer).

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina NextSeq 500

Data processing

For ChIP-seq, fastq reads were aligned to C. elegans and drosophila reference genomes (downloaded from wormbase, PRJNA13758, and UCSC, dm6, respectively) using bowtie with default parameters, discarding multimapping reads. PCR duplicates were removed using samblaster. Reads aligning to both PRJNA13758 and dm6 genomes were removed. Peaks were called with MACS2 with a p-value threshold of 1e-5 and were further annotated with ChIPseeker. To eliminate differences in library size and to perform a calibrated quantification of ChIP-seq signal, we calculated a normalization factor based on the reads aligning to the spike-in genome as described in (Orlando et al 2014).
For the RNA-seq of whole worm analyses, reads were aligned to C.elegans reference genome, ce10, using STAR with default parameters and removing multimapping reads. PCR duplicates were removed with samblaster and gene quantification was performed using featureCounts with default parameters. Differential expression analyses were performed with the R package DESeq2. P-values and log2 fold changes were further corrected with ihw and apeglm R packages, respectively, with default parameters. Finally, genes with an adjusted p-value < 0.01 and absolute log2FC >= 1 were considered differentially expressed
Genome_build: ce10
Supplementary_files_format_and_content: MACS2 narrowPeak and DESeq2 differtial expression analysis (tsv); raw counts

Submission date

May 18, 2021

Last update date

Nov 23, 2021

Contact name

Diego Pasini

E-mail(s)

lab.pasini@gmail.com

Organization name

European Institute of Oncology

Street address

Via Adamello, 16