|
| Status |
Public on Jan 08, 2019 |
| Title |
wild type untreated (rep 3) |
| Sample type |
SRA |
| |
|
| Source name |
L4 stage whole animal
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
strain: N2
genotype: wt
tissue: whole animals
treatment: none
developmental stage: L4 stage
|
| Treatment protocol |
Bortezomib was added to plates to a final concentration of 20uM and animals were incubated at 20°C for 4 hours. For mock treatment control samples, an equivalent amount of DMSO was added.
|
| Growth protocol |
For all strains and treatments, synchronized L1 animals were grown at 20°C until the L4 stage. For N2, ERT415, and ERT451, animals were then shifted to 25°C for 4 hours before harvesting for RNA extraction. For DMSO and Bortezomib treated N2 animals, treatment was administered and animals were incubated at 20°C for 4 hours before harvesting for RNA extraction.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using TriReagent (Sigma-Aldrich) and cleaned using RNAeasy (Qiagen) column purification. RNA quality was assesed using Tapestation analysis.
Paired-end sequencing libraries were constructed using TruSeq Stranded mRNA (Illumina) prep kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Nematocida.counts.matrix (column 11)
022_a-N2-_S15_L004
|
| Data processing |
Reads were aligned to WS235 using Bowtie 2.
Transcript abundance was estimated using RSEM.
Genome_build: WormBase Release WS235
Supplementary_files_format_and_content: comma-delimited file containing raw counts
|
| |
|
| Submission date |
Aug 10, 2018 |
| Last update date |
Jan 08, 2019 |
| Contact name |
Emily Troemel |
| E-mail(s) |
etroemel@ucsd.edu
|
| Organization name |
University of California, San Diego
|
| Department |
Cell and Developmental Biology
|
| Lab |
Troemel
|
| Street address |
9500 Gilman Dr, #0349
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093 |
| Country |
USA |
| |
|
| Platform ID |
GPL22765 |
| Series (1) |
| GSE118400 |
Transcriptomic Analysis of the Intracellular Pathogen Response (IPR) |
|
| Relations |
| BioSample |
SAMN09791888 |
| SRA |
SRX4528717 |
