|
| Status |
Public on Feb 07, 2023 |
| Title |
N2_OP50_DMSO_3 |
| Sample type |
SRA |
| |
|
| Source name |
Whole animal
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
developmental stage: L4
strain: N2
bacterial exposure: OP50
chemical treatment: DMSO
|
| Treatment protocol |
Synchronized L1 staged C. elegans wild-type and nhr-8 loss of function animals were grown to L4, transferred to P. aeruginosa or E. coli and incubated at 25°C for 4 hours..
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using TriReagent (Molecular Research Center, Inc.) and purified with RNeasy columns (Qiagen)
Oligo (dT) magnetic beads are used to select mRNA with polyA tail. Fragment the target RNA and reverse transcription to double-strand cDNA (dscDNA) by N6 random primer. End repair the dscDNA with phosphate at 5' end and stickiness 'A' at 3' end, then ligate and adaptor with stickiness 'T' at 3' end to the dscDNA. Two specific primers were used to amplify the ligation product. Denature the PCR product by heat and the single strand DNA is cyclized by splint oligo and DNA ligase.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Data processing |
Raw fastq reads were evaluated by FastQC (version 0.11.5), clean reads were aligned to the C. elegans reference genome (WBcel235) and quantified using Kallisto (version 0.45.0). Differentially expressed genes were identified using Sleuth (version 0.30.0).
Assembly: WBcel235
Supplementary files format and content: tsv files include TPM transcript abundance values for each sample
|
| |
|
| Submission date |
May 04, 2022 |
| Last update date |
Feb 09, 2023 |
| Contact name |
Read Pukkila-Worley |
| E-mail(s) |
read.pukkila-worley@umassmed.edu
|
| Organization name |
University of Massachusetts Medical School
|
| Department |
Medicine
|
| Lab |
Read Pukkila-Worley
|
| Street address |
55 N Lake Ave
|
| City |
Worcester |
| State/province |
Massachusetts |
| ZIP/Postal code |
01655 |
| Country |
USA |
| |
|
| Platform ID |
GPL25145 |
| Series (1) |
| GSE202258 |
Bacterial pattern recognition in C. elegans by the nuclear hormone receptor NHR-86/HNF4 |
|
| Relations |
| BioSample |
SAMN28094581 |
| SRA |
SRX15157692 |
