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| Status |
Public on Jun 01, 2024 |
| Title |
ZD101, PE, biol rep 3 |
| Sample type |
SRA |
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| Source name |
Whole animals
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| Organism |
Caenorhabditis elegans |
| Characteristics |
strain: ZD101
genotype: tir-1(qd4) III
treatment: Standard growth conditions at 20C on NGM plates containing E. coli OP50
developmental stage: Day 1 adults
tissue: Whole animals
Sex: hermaphrodite
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| Growth protocol |
Wild-type and mutant C. elegans animals were synchronized at the L1 stage by egg prep and grown for ~72 hours at 20°C on 10cm NGM Agarose plates (5000 animals/plate) seeded with E. coli OP50 until they reached day 1 of adulthood. For RNAi experiments, synchronized animals were reared on E. coli HT115 bacteria expressing dsRNAs for ~72 hours at 20°C on 10cm NGM Agarose plates containing 5 mM isopropyl-β-D-thiogalactoside (IPTG) and 100 μg/ml ampicillin.
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Animals were harvested in M9 buffer, washed three times, and flash frozen in liquid Nitrogen. Total RNA was isolated using Trizol.
mRNA-Seq libraries were prepared using the Illumina TruSeq RNA Sample Preparation v2 kit. For the tra-1 and tir-1 studies, mRNA-Seq libraries were prepared by Novogene Inc.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
Column names listed in line one for each txt file
FC_gene_read_counts_tir-1_study.txt
DESeq2_norm_gene_counts_tir-1_study.txt
DESeq2_DEGs_ZD101_v_N2_tir-1_study.txt
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| Data processing |
The adapter-trimmed mRNA-Seq reads were mapped to the WS260 genome using the STAR aligner. The mapping was performed using a GTF obtained from Wormbase (c_elegans.PRJNA13758.WS260.canonical_geneset.gtf) with the parameter --outFilterIntronMotifs RemoveNoncanonical.
The gene-level read counts were calculated using the featureCounts algorithm of the subread package (Liao et al., Bioinformatics, 2014), using the following flags: -t exon -g gene_id -a c_elegans.PRJNA13758.WS260.canonical_geneset.gtf.
Differential expression was calculated relative to the N2 wild-type sample using the DESeq2 package using a 1% FDR cutoff (Love et al., 2014). Comparisons between individual mutants were also performed.
Assembly: WS260
Supplementary files format and content: FC_gene_read_counts_study_name.txt: A tab-delimited text file for each sub-study that includes gene level unnormalized read counts for each sample in matrix format generated using the featureCounts aligorithm.
Supplementary files format and content: DESeq2_norm_gene_counts_study_name.txt: A tab-delimited text file that for each sub-study includes gene level normalized read counts for each sample in matrix format generated using the DESeq2 aligorithm.
Supplementary files format and content: DESeq2_DEGs_sample1_v_sample2_study_name.txt: A tab-delimited text file that includes a list of differentially expressed genes, the log2 FC values, and the p values called by DESeq2 at a 1% FDR threshold for sample1 relative to sample2 for each sub-study.
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| Submission date |
May 25, 2024 |
| Last update date |
Jun 01, 2024 |
| Contact name |
Robert Houston Dowen |
| E-mail(s) |
[email protected]
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| Organization name |
University of North Carolina at Chapel Hill
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| Department |
Cell Biology and Physiology
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| Lab |
133 N. Medical Drive
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| Street address |
321 Fordham Hall, CB7100
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| City |
Chapel Hill |
| State/province |
NC |
| ZIP/Postal code |
27599-7100 |
| Country |
USA |
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| Platform ID |
GPL26672 |
| Series (1) |
| GSE268363 |
Next Generation Sequencing and Quantitative Analysis of mRNAs in Caenorhabditis elegans Mutant Animals Exhibiting Impaired Hedgehog, mTORC2, or p38 Signaling |
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| Relations |
| BioSample |
SAMN41590970 |
| SRA |
SRX24703264 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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