|
| Status |
Public on May 09, 2024 |
| Title |
TDP-43 G298S unbound [21101506_506_unbound_S21] |
| Sample type |
SRA |
| |
|
| Source name |
Whole head
|
| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: Whole head
cell type: Mushroom body Kenyon cells
Sex: pooled male and female
time: Day 1 - 3
genotype: w; UAS TDP43G298S-YFP, UAS mCD8-RFP II (TDP-94)
developmental stage: adult
|
| Extracted molecule |
total RNA |
| Extraction protocol |
TRIzol RNA isolation was performed on three biological replicates of IPs from YFP, TDPWT YFP, and TDPG298S YFP from mushroom bodies. RNA was quantified by nanodrop to bring it within range for ribogreen quantification of 0.15625 and 10 ng/ul. RNA was also checked using Agilent Tapestation High Sensitivitiy RNA screentape. 1 ng total RNA was used for SMART Seq HT PLUS (Takara Bio USA, Inc. Cat #R400748) following manufacturer’s protocol. Determination of cDNA quality and quantity was determined via Agilent Tapestation High Sensitivity D5000 Screentape and Qubit dsDNA HS assay for input into library amplification.
Libraries were quantified by Agilent Tapestaion High Sensitivity D1000 Screentape and Kapa Library Quantification kit for Illumina platforms. Libraries were pooled equimolarly, pools were quantified by Agilent Tapestation High Sensitivity D1000 Screentape and Kapa Library Quantification kit and loaded on the NovaSeq 6000 S4 flowcell and sequenced to 101 x 11 x 11 x 101 cycles.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
50:50 males and females
21101506_506_unbound_S21
|
| Data processing |
fastq files were generated using bcl2fastq v2.19.1.403
Reads were trimmed with cutadapt v2.7
Trimmed fastqs were aligned to the Dmel genome with STAR v2.6.1d using the following parameters: --runMode alignReads --outSAMtype BAM Unsorted --outSAMmode Full --outSAMstrandField intronMotif --outFilterType BySJout --outSAMunmapped Within --outSAMmapqUnique 255 --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.1 --alignMatesGapMax 1000000 --seedSearchStartLmax 50 --alignIntronMin 20 --alignIntronMax 1000000 --alignSJoverhangMin 18 --alignSJDBoverhangMin 18 --chimSegmentMin 18 --chimJunctionOverhangMin 18 --outSJfilterOverhangMin 18 18 18 18 --alignTranscriptsPerReadNmax 50000
Aligned reads were counted with featureCounts v1.6.3 using the genome annotation dmel-6.27
.txt files produced for individual samples were aggregated into a single .txt file using python
Assembly: Dmel genome
Supplementary files format and content: A single tab delimited .txt file containing raw counts for each sample
|
| |
|
| Submission date |
Nov 03, 2022 |
| Last update date |
May 09, 2024 |
| Contact name |
Daniela Zarnescu |
| E-mail(s) |
dcz102@psu.edu
|
| Organization name |
Penn State College of Medicine
|
| Department |
Cellular and Molecular Physiology
|
| Street address |
500 University Drive Crescent Building C4605
|
| City |
Hershey |
| State/province |
PA |
| ZIP/Postal code |
17033 |
| Country |
USA |
| |
|
| Platform ID |
GPL25244 |
| Series (1) |
| GSE217213 |
Drosophila models of dementia uncover shared and specific targets of TDP-43 proteinopathy across ALS and FTD relevant circuits |
|
| Relations |
| BioSample |
SAMN31592141 |
| SRA |
SRX18158002 |
