|
| Status |
Public on Aug 10, 2016 |
| Title |
N2-sig-7RNAi-1 |
| Sample type |
SRA |
| |
|
| Source name |
mixed stage early embryos
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
range of embryonic cell stages: 1cell to 350 cell stage
strain: N2
genotype/variation: sig-7 loss
|
| Growth protocol |
Synchronized L1 worms were fed on OP50 bacteria for 72 hrs, then adult worms were treated with standard bleaching solution to collect embryos in utero
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were purified using Trizol/chloroform extraction protocol.
1µg of total RNA was used as starting material, and a sequencing library was prepared using TruSeq Stranded Total RNA Sample Prep Kit after treatment with Ribo-Zero (Human/Mouse/Rat) for rDNA depletion.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
RNA-seq reads were quality-checked using FastQC version 0.5.2
FastQ Quality Trimmer version 1.0 was used to trim reads with less than optimal quality scores.
The DE analysis protocol outlined in Trapnell et. al. was used to perform the DE analysis
The quality filtered reads were mapped to C. elegans (ce10) reference genome using TopHat2 version 0.5.
Cufflinks version 2.1.1 was used to assemble transcripts and estimate their abundance. The transcript assembly outputs from Cufflinks were merged into a unified list of transcripts using Cuffmerge.
Cuffdiff version 2.0.2 was then used to quantify gene and transcript expression levels and test them for significant differences. Default parameters were utilized for all steps.
Genome_build: ce10
Supplementary_files_format_and_content: .txt files, cuffdiff differential expression output (gene-level, isoform-level, primary transcript)
|
| |
|
| Submission date |
Aug 10, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Susan Strome |
| E-mail(s) |
sstrome@ucsc.edu
|
| Organization name |
UC Santa Cruz
|
| Department |
MCD Biology
|
| Street address |
1156 High St
|
| City |
Santa Cruz |
| State/province |
CA |
| ZIP/Postal code |
95064 |
| Country |
USA |
| |
|
| Platform ID |
GPL13657 |
| Series (2) |
| GSE85442 |
Comparison of transcriptomes of sig-7 (RNAi) vs WT C. elegans early stage embryos by RNA-seq |
| GSE85445 |
HTS comparison of sig-7 (RNAi) vs WT C. elegans early stage embryos |
|
| Relations |
| BioSample |
SAMN05559054 |
| SRA |
SRX2011754 |
