|
| Status |
Public on Jan 26, 2019 |
| Title |
ztf-11_03 |
| Sample type |
SRA |
| |
|
| Source name |
Embryo
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
strain: TV23837
tissue: mixed
developmental stage: embryo
treatment: treated with feeding RNAi clone expressing dsRNA against ztf-11
|
| Treatment protocol |
Knockdown by feeding RNAi. In brief, synchronized L1 animals were grown on a lawn of bacterial clone expressing dsRNA against ztf-11 or control for 64 hours in 20℃. Each bacterial lawn were innoculated onto 10cm NGM plates containing IPTG (1mM) 3 days prior to each experiment.
|
| Growth protocol |
Standard C. elegans growing protocols
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Embryos were isolated using bleaching and then incubated in M9 for three hours. Egg shells were disturbed with chymotrypsin/chitinase treatment. Embryonic cells were then homogenized by qiaShredder columns (Qiagen) following manufacturer's instructions. RNA was extracted using RNeasy micro plus kit (Qiagen) followng manufacturer's instructions.
mRNA libraries were prepared by Stanford Genome Sequencing Center using TruSeq Stranded mRNA Library Preparation kit (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Transcriptome of embryos prepped from hermaphrodite animals treated with feeding RNAi clone expressing dsRNA against ztf-11. 3 of 4 biological replicates.
|
| Data processing |
Raw reads were trimmed of adaptor sequences using fastx (http://hannonlab.cshl.edu/fastx_toolkit/)
Mapped using Tophat2 and featureCounts.
Differential expression analysis was performed using DeSeq2
Genome_build: ce10
Supplementary_files_format_and_content: Excel spreadsheet file containing DESeq2 output results
|
| |
|
| Submission date |
Jan 25, 2019 |
| Last update date |
Jan 26, 2019 |
| Contact name |
Kang Shen |
| E-mail(s) |
kangshen@stanford.edu
|
| Phone |
6507247975
|
| Organization name |
Stanford University
|
| Street address |
385 Serra Mall, Herrin lab 144
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL22765 |
| Series (1) |
| GSE125694 |
A Myt1 family transcription factor defines neuronal fate by repressing non-neuronal genes |
|
| Relations |
| BioSample |
SAMN10822040 |
| SRA |
SRX5294353 |
