|
Status |
Public on Mar 27, 2017 |
Title |
K36R ATAC-seq rep1 |
Sample type |
SRA |
|
|
Source name |
Whole 3rd Instar Larvae
|
Organism |
Drosophila melanogaster |
Characteristics |
developmental stage: 3rd instar larvae tissue: Whole larvae Sex: Mixed genotype: K36R target molecule: genomic DNA
|
Growth protocol |
3rd instar larvae were staged by wandering behavior and collected for extraction
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Nuclei were isolated from whole larvae and incubated with Tn5 transposase from Nextera DNA Library Prep Kit (Illumina) according to manufacturer's protocols and standard ATAC-seq protocol (Buenrostro et al. 2013) Libraries were prepared according to Illumina Nextera DNA Library Prep Kit protocol
|
|
|
Library strategy |
ATAC-seq |
Library source |
genomic |
Library selection |
other |
Instrument model |
Illumina HiSeq 2000 |
|
|
Description |
K36R ATAC-seq processed file: K36R.ATAC.accepted_hits.sorted.hiquality.RPKM.bw
|
Data processing |
Alignment to reference genome using Tophat2 (RNA-seq) or Bowtie2 (Start-seq, ATAC-seq) Generation of count tables for RNA-seq using htseq-count Differential expression analysis of RNA-seq using DESeq2 or Cufflinks Assignment of nucleotide position for Start-seq peaks using custom scripts Generation of BigWig files for ATAC-seq samples using Deeptools Analysis of meta-TSS profiles for ATAC-seq samples using Deeptools Genome_build: dm3
|
|
|
Submission date |
Mar 22, 2017 |
Last update date |
May 15, 2019 |
Contact name |
Michael Meers |
E-mail(s) |
mpmeers@email.unc.edu
|
Organization name |
UNC Chapel Hill
|
Street address |
250 Bell Tower Dr.
|
City |
Chapel Hill |
State/province |
NC |
ZIP/Postal code |
27599 |
Country |
USA |
|
|
Platform ID |
GPL13304 |
Series (1) |
GSE96922 |
Histone gene replacement reveals a post-transcriptional role for H3K36 in maintaining metazoan transcriptome fidelity |
|
Relations |
BioSample |
SAMN06627554 |
SRA |
SRX2661684 |