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Sample GSM4489576 Query DataSets for GSM4489576
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

Supplementary file Size Download File type/resource
GSM4489576_SX1316_rep2_Zscore.bw 170.7 Mb (ftp)(http) BW
GSM4489576_SX1316_rep2_log2.bw 170.7 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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