|
| Status |
Public on Jun 21, 2013 |
| Title |
Celeg-1-ST-RPF |
| Sample type |
SRA |
| |
|
| Source name |
population-whole animal
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
developmental stage: L1 diapause
batch: 1
strain: N2
rna subtype: ribosome protected fragments
|
| Growth protocol |
36 million embryos were grown in S-complete liquid media at 20 C. Animals were starved for 24 hours and either harvested by freezing in liquid nitrogen (diapause animals) or fed for three hours with E. coli HB101 at 15 mg/mL.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total mRNA was isolated using Ambion's micro-poly(A) purist kit, fragmented by alkali and heat, followed by library preparation. Ribosome profiling was carried out as described in Ingolia et al (2009) with modifications as Stadler and Fire (2011).
Libraries were constructed using the circligase protocol as described in Ingolia et al. (2009) with modifications described in Stadler and Fire (2013).
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Library strategy: RPF
Basecalls performed standard Illumina software
Reads that map multiply to the genome were removed
Remaining reads were mapped to the CDS sequences + 18 nucleotides of genomic flanking regions using Bowtie v0.12.7
Raw counts for each experiment were determined from mappings
Normalization, fold-change, and significance calculations performed using DESeq (Anders and Huber 2010) software package in R.
Genome_build: WS234
Supplementary_files_format_and_content: Matrix of normalized counts, fold change, and statistical output for genes listed by their associated protein name.
|
| |
|
| Submission date |
Jun 20, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Michael Stadler |
| E-mail(s) |
mstadler@stanford.edu
|
| Phone |
3522466938
|
| Organization name |
Stanford University
|
| Department |
Pathology
|
| Lab |
Fire
|
| Street address |
300 Pasteur Dr.
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL13657 |
| Series (1) |
| GSE48140 |
mRNA and Ribosome Profiling in Four Nematode Species Traversing a Shared Developmental Transition |
|
| Relations |
| BioSample |
SAMN02209113 |
| SRA |
SRX311780 |
