|
| Status |
Public on Oct 19, 2017 |
| Title |
WT rep2 (RNA-Seq) |
| Sample type |
SRA |
| |
|
| Source name |
whole organism
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
developmental stage: L4
genotype: wildtype N2
tissue: whole organism
|
| Treatment protocol |
No special treatment
|
| Growth protocol |
WT Caenorhabditis elegans (N2 Bristol) animals were cultured on OP50 bacteria at 25°C, and collected at the last larval stage (mid-L4 – 29 h time point). Standard worm synchronization methods were used.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with Trizol and DNAse treated.
These samples were prepared for sequencing by rRNA depletion with Ribo-Zero rRNA Removal Mix – Gold (Illumina), and the TruSeq Stranded Total RNA Library Prep Kit (Illumina) according to the Low Sample Protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Read counts were quantified using kallisto.
These were then aligned to C. elegans genome WS247.
Genome_build: WS247
Supplementary_files_format_and_content: Csv; Contains tpm values for each replicate
|
| |
|
| Submission date |
Oct 02, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Amy Pasquinelli |
| E-mail(s) |
apasquinelli@ucsd.edu
|
| Organization name |
University of California, San Diego
|
| Department |
Biological Sciences
|
| Lab |
Pasquinelli Lab
|
| Street address |
9500 Gilman Drive
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093 |
| Country |
USA |
| |
|
| Platform ID |
GPL18245 |
| Series (2) |
| GSE104500 |
RNA-Seq of L4 C. elegans |
| GSE104502 |
Short Poly(A) Tails are a Conserved Feature of Highly Expressed Genes |
|
| Relations |
| BioSample |
SAMN07730914 |
| SRA |
SRX3237805 |
