|
| Status |
Public on Nov 08, 2023 |
| Title |
Ribo-Seq KDM5 Knockdown IP 3 |
| Sample type |
SRA |
| |
|
| Source name |
heads
|
| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: heads
cell type: neurons
genotype: elav;RPL3-FLAG;kdm5RNAI
|
| Growth protocol |
Flies were kept at 25℃ with a 12-hour light/dark cycle and 50% humidity. All flies were collected or harvested 1-5 days after eclosion from 9AM-12PM
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol/chloroform followed by precipitation using isopropanol
TruSeq Stranded mRNA Library Preparation Kit.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Ribo-Seq_Pshifted_Transcripts.xlsx
|
| Data processing |
R
Reads were trimmed using fastp
Reads were aligned using Rsubread (RNA-Seq) or RNA-STAR (Ribo-Seq)
Counts were obtained using featureCounts (RNA-Seq) or ORFik (Ribo-Seq)
Differential expression analysis was performed with DESeq2
Assembly: dm6
Supplementary files format and content: RNA-Seq comma separated values (csv) of raw counts
Supplementary files format and content: Ribo-Seq differential expression analyses using the R package ORFik.
Library strategy: Ribo-Seq
|
| |
|
| Submission date |
Oct 13, 2023 |
| Last update date |
Nov 08, 2023 |
| Contact name |
Matanel Yheskel |
| E-mail(s) |
matanel.yheskel@einsteinmed.edu
|
| Organization name |
Albert Einstein College of Medicine
|
| Department |
Genetics
|
| Lab |
Julie Secombe
|
| Street address |
1300 Morris Park
|
| City |
Bronx |
| State/province |
NY |
| ZIP/Postal code |
10461 |
| Country |
USA |
| |
|
| Platform ID |
GPL17275 |
| Series (1) |
| GSE245380 |
KDM5-mediated transcriptional activation of ribosomal protein genes alters translation efficiency to regulate mitochondrial metabolism. |
|
| Relations |
| BioSample |
SAMN37810141 |
| SRA |
SRX22111273 |
