|
| Status |
Public on Nov 27, 2019 |
| Title |
Adelman_Dmel_DL1_PRO-seq_Bgal |
| Sample type |
SRA |
| |
|
| Source name |
Adelman_Dmel_DL1_PRO-seq_Bgal
|
| Organism |
Drosophila melanogaster |
| Characteristics |
cell line: DL1
treatment: Bgal RNAi treatment
molecule subtype: biotin labeled nascent RNA
|
| Treatment protocol |
Drosophila DL1 cells treated with Bgal dsRNA for 3 days without CuSO4 induction
|
| Extracted molecule |
total RNA |
| Extraction protocol |
nascent biotin-labeled RNA was isolated from permeabilized cells using Total RNA Purification kit (Norgen Biotek Corp.)
Custom library preparation
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
biotin labeled nascent RNA isolated from Drosophila DL1 permeabilized cells
small RNA-seq (hidrolysis fractionation)
BgalA_PROseq
|
| Data processing |
Base calling and generation of FASTQ files performed using standard CASAVA pipeline for HiSeq runs, bcl2fastq2 for NextSeq
RNAseq read pairs containing one or more members with mean quality score <20 filtered and trimmed to 50nt; PRO-seq read pairs containing one or more members with mean quality score <20 filtered and trimmed to 50nt, for adapter using cutadapt 1.14, pairs containing reads trimmed shorter than 20 nt filtered
RNAseq mapped to reference using STAR 2.5.2b, in a strand-specific manner; PRO-seq mapped to index composed of spike-in genome (mm10), successfully aligned pairs filtered, remaining mapped to reference (dm3) using bowtie 1.2.2 retaining uniquely mappable pairs only, allowing 2 mismatches; ChIP-seq mapped using bowtie 1.1.1 retaining uniquely mapped pairs only, allowing 2 mismatches
RNAseq strand-specific coverage tracks were normalized with custom scripts using factors determined by DESeq2 v1.18.1 based on DESeq2 normalization factors and combined with unionBedGraphs and custom scripts (mean count); PROseq strand-specific bedGraphs generated using custom scripts based on 3' mapping location of end 1 reads only, with all replicates combined; ChIP-seq bedGraphs were generated by filtering fragments of length <75 and >350, and determining counts of fragment centers in 25 nt bins tiling the genome, using custom scripts
Genome_build: dm3 (RNA-seq, ChIP-seq, PRO-seq)
Supplementary_files_format_and_content: RNAseq: bigWig containing combined mean normalized coverage of all replicates for a given treatment; PRO-seq: bedGraph containing combined count of end 1 3' mapping locations for all replicates for a given treatment; ChIP-seq: bedGraph containing combined count of fragment centers for all replicates
|
| |
|
| Submission date |
Nov 21, 2018 |
| Last update date |
Nov 28, 2019 |
| Contact name |
Karen Adelman |
| E-mail(s) |
karen_adelman@hms.harvard.edu
|
| Organization name |
Harvard Medical School
|
| Department |
Biological Chemistry and Molecular Pharmacology
|
| Street address |
45 Shattuck St. LHRRB-201a
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL19132 |
| Series (1) |
| GSE114467 |
The Integrator complex terminates promoter-proximal transcription at protein-coding genes |
|
| Relations |
| BioSample |
SAMN10460050 |
| SRA |
SRX5053368 |
