|
| Status |
Public on Sep 19, 2022 |
| Title |
E9_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Whole Worm RNA extract
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
gentoye: egl-9(sa307)
|
| Growth protocol |
Developmentally synchronized animals were obtained by hypochlorite treatment of gravid adults and embryos hatched overnight for 15-17 hours in M9. Starvation-arrested L1s were plated on NGM plates and grown at 20°C until L4 stage.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from animals using Trizol (Invitrogen) combined with Bead Beater lysis in four biological replicates for each genotype.
An mRNA library (single-end, 50-bp reads) was prepared for each sample/replicate using Illumina Truseq with PolyA selection
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
E9_rep2
|
| Data processing |
Libraries were sequenced across two lanes on an Illumina HiSeq2000 (GeneWiz) or an Illumina HiSeq 2500 in Rapid Run Mode (RUCDR).
Raw sequences were aligned using STAR 2.5.1a and gene counts, normalization and statistical analysis on gene counts were performed with EdgeR using generalized linear model functionality and tagwise dispersion estimates. Likelihood ratio tests were conducted in a pairwise fashion between genotypes with a Benjamini and Hochberg correction. Genes were considered to be HIF-1-dependent if they were differentially expressed with an FDR<0.01 in the same direction (up or down) in all four of the following pairwise comparisons: (1) egl-9 vs. N2; (2) egl-9 vs. egl-9 hif-1; (3) odIs131; egl-9 vs. N2; (4) odIs131; egl-9 vs. egl-9 hif-1. These pairwise comparisons are in the attached .xlsx file named "DEGenes_All samples and comparisons.xlsx" . This file includes ALL gene fold changes (log2FC) and corresponding p-values and FDR vaues.
Genome_build: WS245/WbCel235
Supplementary_files_format_and_content: EdgeR Excel File with differential gene expression
|
| |
|
| Submission date |
Apr 29, 2021 |
| Last update date |
Sep 19, 2022 |
| Contact name |
Christopher Rongo |
| E-mail(s) |
crongo@waksman.rutgers.edu
|
| Organization name |
Rutgers University
|
| Department |
Waksman Institute
|
| Street address |
190 Frelinghuysen Road, #163
|
| City |
Piscataway |
| State/province |
NJ |
| ZIP/Postal code |
08854 |
| Country |
USA |
| |
|
| Platform ID |
GPL13657 |
| Series (2) |
| GSE173580 |
RNA-seq Files : The Hypoxia Response Pathway Promotes PEP Carboxykinase And Gluconeogenesis In C. elegans |
| GSE173581 |
The Hypoxia Response Pathway Promotes PEP Carboxykinase And Gluconeogenesis In C. elegans |
|
| Relations |
| BioSample |
SAMN18925568 |
| SRA |
SRX10714787 |
