|
| Status |
Public on Jun 01, 2016 |
| Title |
osm-9_200mM_NaCl_2 |
| Sample type |
SRA |
| |
|
| Source name |
osm-9_200mM_NaCl
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
strain: osm-9
developmental stage: L4
|
| Treatment protocol |
Hypertonic agar plates were generated by adding NaCl to standard nematode growth medium.
|
| Growth protocol |
Worms were cultured at 20 °C using standard methods (Brenner S. The genetics of Caenorhabditis elegans. Genetics 1974 77:71-94).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using TRIzol (Invitrogen, Carlsbad, CA).
PolyA+ TruSeq RNA sequencing libraries were prepared for sequencing using standard Illumina protocols (Illumina, Inc., San Diego, CA).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Reads were aligned to genome build WS235 using Tophat 1.4.1.
Mapped reads were analyzed using Cufflinks 2.0.1 and Ensembl version 71 annotation.
Read counts per gene were analyzed using R/edgeR 3.2.4.
Genome_build: Genome build WS235; Ensembl version 71 annotation.
Supplementary_files_format_and_content: Tab-delimited text file with read counts per gene per sample. Columns are Cufflinks transcript ID, Ensembl gene symbol, Ensembl gene ID, Ensembl transcript IDs (comma-separated), followed by counts per sample.
|
| |
|
| Submission date |
Sep 29, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Benjamin L King |
| E-mail(s) |
benjamin.l.king@maine.edu
|
| Phone |
207-581-2803
|
| Organization name |
University of Maine
|
| Department |
Molecular and Biomedical Sciences
|
| Street address |
5735 Hitchner Hall
|
| City |
Orono |
| State/province |
ME |
| ZIP/Postal code |
04469 |
| Country |
USA |
| |
|
| Platform ID |
GPL18245 |
| Series (1) |
| GSE73589 |
Osmosensory neurons modulate hypertonic stress resistance in C. elegans by controlling protein damage in non-neuronal cells |
|
| Relations |
| BioSample |
SAMN04122857 |
| SRA |
SRX1295775 |
