|
| Status |
Public on Jul 26, 2017 |
| Title |
ev 2 |
| Sample type |
SRA |
| |
|
| Source name |
whole body
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
strain: N2
age: one day old adults
media: NGM
|
| Treatment protocol |
Glucose was mixed in the NGM media
|
| Growth protocol |
worms were grown on NGM seeded with E.coli OP50 at 20oC
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Worms were picked, washed, flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
basecalls performed by basespace (Illumina)
reads alignment, transcripts assembly and quantification and differential expression analysis were performed using tuxedo software suite (v2.1.1). Read were aligned to known transcriptome of WS220 C.elegans genome assembly (Ensembl) using tophat with the following paramters: --b2-sensitive, --no-novel junctions.
Transcripts assembly and quantification was performed by cufflinks with default parameters.
Differential expression analysis was performed by cuffdiff with default parameters.
Genome_build: Ensembl WS220
Supplementary_files_format_and_content: gene_exp.diff, genes.fpkm_tracking
|
| |
|
| Submission date |
May 05, 2017 |
| Last update date |
Jul 26, 2017 |
| Contact name |
Ivan Gusarov |
| E-mail(s) |
[email protected]
|
| Organization name |
NYU School of Medicine
|
| Department |
Biochemistry
|
| Street address |
450E 29th street
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10016 |
| Country |
USA |
| |
|
| Platform ID |
GPL19757 |
| Series (1) |
| GSE98576 |
Global transcriptional responce in C.elegans on a high glucose diet |
|
| Relations |
| BioSample |
SAMN06894128 |
