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| Status |
Public on Jun 19, 2023 |
| Title |
Flies, park , Rep3 |
| Sample type |
SRA |
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| Source name |
Entire fly lysate - 10 flies
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| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: Entire fly lysate - 10 flies
age: 4-5 days p. eclosion
developmental stage: Adult
genotype: park[25]
Sex: male
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| Treatment protocol |
n/a
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| Growth protocol |
Flies were raised in identifcal conditions (25°C normal L:D cycle) for 4 days following eclosion
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| Extracted molecule |
total RNA |
| Extraction protocol |
Direct-zol RNA Miniprep kit (Zymo Research P/N R2050), with DNAseI on column treatment
Zymo-Seq RiboFree Total RNA Library Kit- After extraction, all steps, including ribosomal RNA depletion, were performed by Zymo Research Services, using their Total-RNA-Seq protocol
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
in "merged_gene_counts.txt" Column 7
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| Data processing |
Seq pipeline was originally adapted from nf-core/rnaseq pipeline v1.4.2 (https://github.com/nf-core/rnaseq).
Quality control of reads performed with FastQC v0.11.9
Adapter and low-quality sequences were trimmed from raw reads using Trim Galore! v0.6.6
Trimmed reads were aligned to the reference genome using STAR v2.6.1d
BAM file filtering and indexing was carried out using SAMtools v1.9
RNAseq library quality control was implemented using RSeQC v4.0. and QualiMap v2.2.2-dev
Duplicate reads were marked using Picard tools v2.23.9
Library complexity was estimated using Preseq v2.0.3
Duplication rate quality control was performed using dupRadar v1.18.0
Reads were assigned to genes using featureCounts v2.0.1
Quality control and analysis results plots were visualized using MultiQC v1.9
Differential gene expression analysis was completed using DESeq2 v1.28.0 DESeq2 v1.28.0 ; DESeq2 FDR cutoff 0.05; DESeq2 Log2FC cutoff 0.585
Assembly: BDGP6 (GCA_000001215.4)
Supplementary files format and content: "merged_gene_counts.txt" ; matrix file containing raw read counts. Columns are indicated above
Supplementary files format and content: "zr6381_AM_Processed Data.xlsx" : Contains normalized read counts for all samples as well as the results of DESeq2 analyses on multiple spreadsheet pages: 1: "Normalized Counts", 2: "DESeq WT vs Park", 3: "DESeq WT vs Sting", 4: "DESeq WT vs Double", 5: "DESeq Sting vs Double", 6: "DESeq Park vs Double",
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| Submission date |
May 19, 2023 |
| Last update date |
Jun 19, 2023 |
| Contact name |
Richard Youle |
| E-mail(s) |
youle@helix.nih.gov
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| Organization name |
National Institute of Neurological Disorders and Stroke, NIH
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| Department |
Surgical Neurology Branch
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| Lab |
Biochemistry Section
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| Street address |
35 Convent Drive, 2C917
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| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
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| Platform ID |
GPL25244 |
| Series (1) |
| GSE232950 |
Transcriptomic profiling reveals a role for pro-survival and stress responsive genes in suppressing fly parkin phenotypes. |
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| Relations |
| BioSample |
SAMN35219149 |
| SRA |
SRX20447581 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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