|
| Status |
Public on Mar 09, 2020 |
| Title |
EE_nipnip2_3_input |
| Sample type |
SRA |
| |
|
| Source name |
early embyo mixed stage
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
age: embryo
ip tag: FLAG
antibody: anti-FLAG M2
|
| Growth protocol |
C. elegans was grown at 20C, with HB101 bacteria on agar plates.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol-Dnase
Illumina TruSeq small RNA
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Description |
5` independent small RNA-seq
NRDE3:FLAG_IP
input_embryo_rawcounts.csv
input_embryo_rawcounts_TE.csv
|
| Data processing |
Reads were trimmed with CutAdapt.
Trimmed reads were aligned to ce11 reference genome using the STAR aligner with multipmapping options.
Read counts on exons was extracted using the FeatureCounts with --fraction option.
data was normalized with unique reads per million or with DeSEQ2.
heatmaps and volcano plots were generated with a custom script on Rstudio.
Genome_build: ce11
Supplementary_files_format_and_content: csv
|
| |
|
| Submission date |
Feb 11, 2019 |
| Last update date |
Mar 09, 2020 |
| Contact name |
Eric Miska |
| E-mail(s) |
eam29@cam.ac.uk
|
| Organization name |
University of Cambridge
|
| Department |
The Gurdon Institute
|
| Lab |
Eric Miska Lab
|
| Street address |
tennis court road
|
| City |
cambridge |
| ZIP/Postal code |
CB2 1QN |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL18730 |
| Series (1) |
| GSE126377 |
RNA memories: trans-generational epigenetic inheritance of RNA-mediated gene silencing |
|
| Relations |
| BioSample |
SAMN10909827 |
| SRA |
SRX5358447 |
