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| Status |
Public on Nov 23, 2021 |
| Title |
QM-3 |
| Sample type |
SRA |
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| Source name |
jmjd-5 (zr1234);jmjd-3.1 (gk384);jmjd-3.2 (tm3121);jmjd-3.3 (tm3197) quadruple mutant
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| Organism |
Caenorhabditis elegans |
| Characteristics |
genotype: jmjd-5 (zr1234);jmjd-3.1 (gk384);jmjd-3.2 (tm3121);jmjd-3.3 (tm3197) quadruple mutant
developmental stage: Young adults
temperature of growth: 25 C
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| 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.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Young adults grown at 25°C at F3 generation were collected and washed in M9 to remove residual bacteria, flash-frozen in liquid nitrogen and stored at -80°C before RNA extraction. RNA was isolated from 4 independent cultures for each strain using TRIzol reagent and RNase-Free DNase Set. Sequencing libraries was constructed using TruSeq RNA Library Prep Kit v2.
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).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| 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
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| Submission date |
May 18, 2021 |
| Last update date |
Nov 23, 2021 |
| Contact name |
Diego Pasini |
| E-mail(s) |
lab.pasini@gmail.com
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| Organization name |
European Institute of Oncology
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| Street address |
Via Adamello, 16
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| City |
Milano |
| ZIP/Postal code |
20139 |
| Country |
Italy |
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| Platform ID |
GPL19757 |
| Series (1) |
| GSE174652 |
Coordinated Maintenance of H3K36/K27 Methylation by Histone Demethylases Preserves Germ Cell Identity and Immortality |
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| Relations |
| BioSample |
SAMN19244591 |
| SRA |
SRX10925667 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5321712_QM-rep3.counts.txt.gz |
162.6 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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