|
| Status |
Public on Mar 11, 2017 |
| Title |
let-418(n3536)_YA_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
young adults, let-418(n3536), condition1
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
strain/background: N2
genotype/variation: let-418(n3536)
tissue: whole body
age: young adults
growth condition: condition1
|
| Growth protocol |
Samples were grown under condition 1 or condition 2:
Condition 1: Starved L1s were grown at 20C until L4 stage, shifted to 25C, then collected as young adults.
Condition 2: Starved L1s were grown at 15C until L4 stage, shifted to 25C, then collected as young adults.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted in TriPure Reagent (Roche), treated with baseline zero DNase (Epicentre), and purified with Zymo Research RNA Clean and Concentrator-5 (Cambridge Bioscience), all according to the manufacturers' instructions. Ribosomal RNA was depleted using the Ribo-Zero rRNA Removal Kit (Human/Mouse/Rat) (Illumina).
Ribosomal RNA-depleted RNA was used to make strand-specific libraries using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs) according to the manufacturer's instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Description |
Ribosomal RNA-depleted RNA.
|
| Data processing |
Libraries were sequenced using Illumina HiSeq and de-multiplexed FASTQ files were obtained from Illumina BaseSpace.
Reads were aligned to the WS220/ce10 assembly of the C. elegans genome using BWA v. 0.7.7 with default settings (BWA-backtrack algorithm).
The SAMtools v. 0.1.19 ‘view’ utility was used to convert the alignments to BAM format.
Pileups tracks were generated in R and normalised for depth of coverage by dividing by number of millions of reads in the library (RPM).
Genome_build: WS220/ce10
Supplementary_files_format_and_content: BigWiggle binary track file
|
| |
|
| Submission date |
Sep 30, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Julie Ahringer |
| E-mail(s) |
ja219@cam.ac.uk
|
| Organization name |
University of Cambridge
|
| Department |
The Gurdon Institute
|
| Street address |
Tennis Court Road
|
| City |
Cambridge |
| ZIP/Postal code |
CB2 1QN |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL18730 |
| Series (2) |
| GSE87523 |
A team of heterochromatin factors collaborates with small RNA pathways to combat repetitive elements and germline stress [RNA-seq] |
| GSE87524 |
A team of heterochromatin factors collaborates with small RNA pathways to combat repetitive elements and germline stress |
|
| Relations |
| BioSample |
SAMN05855022 |
| SRA |
SRX2202801 |
