|
| Status |
Public on Jan 09, 2019 |
| Title |
nhr-86(tm2590) R24 rep1 |
| Sample type |
SRA |
| |
|
| Source name |
nhr-86(tm2590) R24, whole animal
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
developmental stage: L4
strain: N2
treatment: R24
genotype: nhr-86(tm2590)
tissue: Whole animal
|
| Treatment protocol |
Synchronized L1 staged C. elegans wild-type and nhr-86 loss of function animals were grown to L4 to young adult stage, transferred to 70 μM R24 or solvent control (DMSO, 1% final concentration) assay and incubated at 20°C overnight.
|
| 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 |
mRNA-seq data analysis was performed by BGI Americas Corp.
Supplementary_files_format_and_content: FPKM values for each sample
|
| |
|
| Submission date |
Jul 26, 2018 |
| Last update date |
Jan 09, 2019 |
| 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 (2) |
| GSE117700 |
The nuclear hormone receptor NHR-86 controls anti-pathogen responses in C. elegans [RNA-seq] |
| GSE117724 |
The nuclear hormone receptor NHR-86 controls anti-pathogen responses in C. elegans |
|
| Relations |
| BioSample |
SAMN09723204 |
| SRA |
SRX4472668 |
