|
| Status |
Public on Mar 27, 2017 |
| Title |
HWT Start-seq mixed MiSeq rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Whole 3rd Instar Larvae
|
| Organism |
Drosophila melanogaster |
| Characteristics |
developmental stage: 3rd instar larvae
tissue: Whole larvae
Sex: Mixed
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 |
SAMN06627585 |
| SRA |
SRX2661660 |
