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| Status |
Public on May 01, 2019 |
| Title |
ev_rep1 |
| Sample type |
SRA |
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| Source name |
L1 larvae
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| Organism |
Caenorhabditis elegans |
| Characteristics |
biological replicate: 1
maternal rnai: empty vector
strain: hrde-1(tm1200)
tissue: Arrested L1 larvae
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| Treatment protocol |
Arrested L1 larvae were snap frozen in liquid nitrogen ~24 hr after bleaching.
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| Growth protocol |
hrde-1(tm1200) animals were bleached and embryos were plated on empty vector, daf-2, or pitr-1 RNAi (HT115). Animals were allowed to develop for 72 hr, after which embryos were released via bleaching and allowed to hatch in the absence of food.
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted using TRIzol with minor modifications to the manufacturer's protocol. 1mL of TRIzol was used per sample. Samples were homogenized using 100uL of acid-washed sand.
Libraries were prepared using the NEB Next Ultra Non-directional mRNA-seq Kit.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
Bowtie version 1.2.2 was used to map reads to the WS210 version of the genome using the commands --best --chunkmbs 256 -k 1 -m 2 -S -p 2
Count files were generated with HTSeq using the GTF file used in Maxwell et al., 2012. This file includes features of the WS210 genome in addition to features of WS220 mapped back to WS210.
Batch correction and differential expression analysis were performed in edgeR using the GLM method as described in section 4.2 of the edgeR manual (Robinson, McCarthy, and Smyth 2010).
Count tables were subsetted to include 12,395 reliably-expressed genes and only the libraries of interest, including empty vector and daf-2 RNAi samples, or empty vector and pitr-1 RNAi samples.
The “calcNormFactors” function was used to normalize libraries. The GLM model was set up using the command model.matrix(~condition + replicate), where condition denotes the RNAi condition, and replicate denotes biological replicate (or batch). The dispersion was estimated, then the model was fit using the “glmQLFit” function and differential expression was determined using “glmQLFTest”.
Genome_build: WS210
Supplementary_files_format_and_content: Count files include the sequence identifier for each gene and the number of counts mapping to that gene (not normalized across libraries). Excel file includes results of differential expression analysis.
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| Submission date |
Mar 30, 2019 |
| Last update date |
May 02, 2019 |
| Contact name |
Amy K Webster |
| E-mail(s) |
awebst10@uoregon.edu
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| Organization name |
University of Oregon
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| Street address |
Institute of Ecology and Evolution
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| City |
Eugene |
| State/province |
Oregon |
| ZIP/Postal code |
97703 |
| Country |
USA |
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| Platform ID |
GPL22765 |
| Series (2) |
| GSE129088 |
mRNA-seq of C. elegans starved L1 progeny of parents fed empty vector, daf-2, or pitr-1 RNAi |
| GSE129089 |
Insulin/IGF signaling and vitellogenin provisioning mediate intergenerational adaptation to nutrient stress |
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| Relations |
| BioSample |
SAMN11290876 |
| SRA |
SRX5608492 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3693115_5364-L1_S13_L003_R1_001.sorted.counts.txt.gz |
131.8 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
| Processed data provided as supplementary file |
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