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Sample GSM2545933 Query DataSets for GSM2545933
Status Public on Mar 27, 2017
Title HWT Start-seq females MiSeq rep1
Sample type SRA
 
Source name Whole 3rd Instar Larvae
Organism Drosophila melanogaster
Characteristics developmental stage: 3rd instar larvae
tissue: Whole larvae
Sex: Female
genotype: HWT
target molecule: Short nascent capped RNA
Growth protocol 3rd instar larvae were staged by wandering behavior and collected for extraction
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from isolated nuclei using TRIzol reagent (Thermo Fisher) using manufacturer's protocols.
Start-seq libraries were prepared as previously described (Henriques et al., 2013; Nechaev et al., 2010).
 
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina MiSeq
 
Description HWT vs. K36R Start-seq
processed file: obsTSS_calls.full.bed
processed file: nuTSS_calls.full.header.bed
Data processing Library strategy: Start-seq (Nechaev et al. 2010, Henriques et al. 2013)
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 GPL16479
Series (1)
GSE96922 Histone gene replacement reveals a post-transcriptional role for H3K36 in maintaining metazoan transcriptome fidelity
Relations
BioSample SAMN06627571
SRA SRX2661665

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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