|
Status |
Public on Dec 04, 2020 |
Title |
AMA1ChIPseq_wt_rep2 |
Sample type |
SRA |
|
|
Source name |
whole animal
|
Organism |
Caenorhabditis elegans |
Characteristics |
tissue: whole animal selection/treatment: AMA-1 antibody
|
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 |
genomic DNA |
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 |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina HiSeq 1500 |
|
|
Description |
ChIP-seq
|
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 05, 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 |
SAMN14656070 |
SRA |
SRX8151843 |