|
| Status |
Public on Dec 04, 2020 |
| Title |
smallRNA_rpb9mj261_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
whole animal
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
tissue: whole animal
selection/treatment: pyrophosphatase treatment
|
| Treatment protocol |
For ChIP, extracts were fixed with 1% FA.
|
| Growth protocol |
animals were grown at 20C, on HB101 E. coli seeded NGM plates.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
All RNA samples were collected with Trizol and treated with Dnase I.
for polyA selected total RNA and ChIP-seq libraries, NEB-NEXT Ultra for Illumina was used. For, ribo-zero depleted total RNA libraries, NEB-NEXT Ultra II Directional for Illumina was used. For small-RNA-seq, Illumina TRU-SEQ was ued.
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Description |
5independent smalRNAs
|
| Data processing |
ChIP-seq data mapping was done with BWA. RNA-seq data setes were mapped via STAR.
ChIP peak calling was done with MACS2 and linear enrichment was obtained with MACS2 bdgcmp function.
RNA-seq counting over genes and transposons was done with featureCounts.
Differential analysis of genes was performed via DEseq2 in Rstudio.
Log2 and Z-score transformation of ChIP-seq data was performed via custom scripts in Rstudio.
Genome_build: ce11
Supplementary_files_format_and_content: bw: big wigle format contains log2 or Z-score for ChIP-seq libraries per replicate.
|
| |
|
| Submission date |
Apr 21, 2020 |
| Last update date |
Dec 04, 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) |
| GSE149071 |
The RNA Polymerase II subunit RPB-9 directs transcriptional elongation at piRNA loci in C. elegans |
|
| Relations |
| BioSample |
SAMN14656035 |
| SRA |
SRX8151862 |
