|
| Status |
Public on Jan 05, 2023 |
| Title |
Bdp1_16-18_BS2 |
| Sample type |
SRA |
| |
|
| Source name |
embryos
|
| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: embryos
treatment: shBdp1
timepoint: 16-18 hours
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Frozen embryos were homogenized using the Pellet Pestle Cordless Motor (Kimble Cat. No. 749540-0000; Pellet Pestles Sigma Cat. No. Z359947). RNA was extracted from the homogenate using TRIzol Reagent (Thermo Fisher, Cat. No. 15596026), chloroform extraction and isopropanol precipitation. RNA was resuspended in Nuclease Free Water (Ambion AM9930) and incubated over night before purification using the RNeasy Mini Kit (QIAGEN Cat. No. 74106). After Qiagen clean up, RNA was quantified using NanoDrop ND1000v 3.5.2.
Libraries for sequencing were made using TruSeq Stranded mRNA Library Prep (llumina 20020594).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Drosophila embryos RNAi, shBdp1, replicate 2, 16-18 hours
|
| Data processing |
Raw FASTQ files were aligned to the Drosophila melanogaster reference genome (Release 6) using STAR aligner 2.7.3a with default settings and up to 20 multiple alignments to produce BAM files.
HTSeq htseq-count v0.12.4 was used to determine read counts overlapping genes.
Differential gene expression in the RNAi experimental samples compared to the mCherry controls was determined using DESeq2 1.24.0.
bigWig files were created using a custom tool called bam2bedgraph to convert bam files into bedgraph files, then UCSC's bedGraphToBigWig to convert the bedgraph files to bigWig format.
Assembly: dm6
Supplementary files format and content: BAM alignment files aligning FASTQ read files to dm6 assembly using STAR 2.7.3a.
Supplementary files format and content: HTSeq htseq-count files produced with HTSeq v0.12.4
Supplementary files format and content: DESeq csv files produced using DESeq2 v1.24.0
Supplementary files format and content: bigWig files produced using custom bam2bedgraph script and UCSC bedGraphToBigWig tool
|
| |
|
| Submission date |
Aug 18, 2022 |
| Last update date |
Jan 06, 2023 |
| Contact name |
Benjamin Wendell Booth |
| E-mail(s) |
[email protected]
|
| Organization name |
Lawrence Berkeley National Laboratory
|
| Department |
BioSciences
|
| Lab |
Celniker
|
| Street address |
1 Cyclotron Road
|
| City |
Berkeley |
| State/province |
CA |
| ZIP/Postal code |
94720 |
| Country |
USA |
| |
|
| Platform ID |
GPL19132 |
| Series (1) |
| GSE211573 |
A modERN Resource: Identification of Drosophila Transcription Factor candidate target genes using RNAi |
|
| Relations |
| BioSample |
SAMN30392455 |
| SRA |
SRX17137980 |
