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| Status |
Public on Sep 24, 2022 |
| Title |
L4 Larvae, whole worm, biol rep 3 |
| Sample type |
SRA |
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| Source name |
whole worm
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| Organism |
Oscheius tipulae |
| Characteristics |
strain: CEW1
tissue: whole worm
developmental stage: L4 Larvae
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| Extracted molecule |
total RNA |
| Extraction protocol |
Egg-laying worms were washed off plates and passed through a 70-µm mesh. This step allows existing eggs to fall through the mesh, leaving the mature worms on the top. These worms were then bleached with sodium hypochlorite solution (Sigma Cat# 425044-250ML, 0.5 M NaOH, 3% bleach) to collect embryos (largely 2-4 cell stage, Fig. S1). Early embryos were further developed in Virgin S Basal (VSB) medium (100 mM NaCl, 5.7 mM K2HPO4, 44.1 mM KH2PO4) at 25°C to reach to the desired embryonic stages. To prepare larval stages, the flow-through of the 70-µm mesh was further passed through a 25-µm mesh to separate mixed embryos from various stages of worms. These mixed embryos were developed in the VSB medium until all embryos reach to L1. The arrested L1s were plated on NGM with a robust OP50 lawn to develop at 20°C to synchronous stages of larvae, young adults, and mature adults. Alternatively, post-dauer larvae and worm samples were collected starting from the dauer harvested from the liquid culture. For adult males, we handpicked 200 males from the HIM-1 mutant for RNA-seq library replicate.
Total RNA was prepared using TRIzol (Invitrogen Cat# 15596026) protocol. The quality of the RNA was evaluated with the TapeStation 4200 (Agilent) and quantified with the Qubit™ 4 Fluorometer (Thermo Fisher). The ribosomal RNAs were removed using the RiboCop rRNA Depletion Kit (LEXOGEN Cat# No 144). The RNA-seq libraries were constructed using the CORALL Total RNA-Seq Library Prep Kit (LEXOGEN Cat# No 146)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
L4_rep3
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| Data processing |
Ribosomal RNA reads were filtered out using Bowtie2 (v2.4.2). The non-rRNA reads from each sample were mapped to the O. tipulae genome with STAR (v2.7.10).
The transcripts for each sample were assembled separately using the StringTie (v2.2.0) and merged into a non-redundant set of transcripts. The predicted coding regions (https://github.com/TransDecoder) from the transcripts were used to further evaluated and to remove artifacts, cryptic transcripts, and transcriptional noises based on their coding capacity (< 50%), the lack of splicing, and/or low expression.
For expression analysis, we used the HTSeq (v2.0.2) to get the read count for all transcripts.
Assembly: Oscheius tipulae ASM1342590v1
Supplementary files format and content: tab deliminated file containing normalized expression data
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| Submission date |
Sep 21, 2022 |
| Last update date |
Sep 24, 2022 |
| Contact name |
Jianbin Wang |
| E-mail(s) |
jianbin.wang@utk.edu
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| Phone |
865-974-4085
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| Organization name |
University of Tennessee Knoxville
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| Department |
Biochemistry & Cellular and Molecular Biology
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| Lab |
420C
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| Street address |
1311 Cumberland Avenue
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| City |
Knoxville |
| State/province |
TN |
| ZIP/Postal code |
37996 |
| Country |
USA |
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| Platform ID |
GPL32681 |
| Series (2) |
| GSE213885 |
The Nematode Oscheius tipulae as A Genetic Model for Programmed DNA Elimination [RNA-seq] |
| GSE213886 |
The Nematode Oscheius tipulae as A Genetic Model for Programmed DNA Elimination |
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| Relations |
| BioSample |
SAMN30952833 |
| SRA |
SRX17661505 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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