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Overlapping activities of ELAV/Hu family RNA binding proteins specify the extended neuronal 3' UTR landscape in Drosophila [L1 CNS RNA-seq]

UID: 10916

Author(s): Wei, Lu*, Lee, Seungjae*, Majumdar, Sonali*, Zhang, Binglong*, Sanfilippo, Piero*, Joseph, Brian*, Miura, Pedro*, Soller, Matthias, Lai, Eric C* * MSK affiliated

Description
Summary from GEO:

"The goals of this study are to perform quantitative comparison of whole transcriptome of Drosophila melanogaster 1st instar larvae central neural system (L1CNS) from three genotypes: Canton-S, elav5 single mutant, and elav5/fne double mutant; and the global 3'-end features of Drosophila melanogaster 1st instar larvae central neural system from three genotypes: Canton-S, elav5 single mutant. Total RNAs were extracted from dissected L1CNS of Drosophila melanogaster Canton-S, elav5 single mutant, and elav5/fne double mutant; total RNA-seq libraries were prepared using Illumina TruSeq Stranded Total RNA Sample Prep kit with replicates for each genotype; final cDNA libraries were sequenced on Illumina HiSeq-1000 sequencer with PE-100 mode. Total RNA-seq data were mapped to the corresponding UCSC genome assemblies: Drosophila melanogaster (dm6), HISAT2 aligner was used for the alignment with default parameters. We found that L1CNS from Canton-S expresses neural specific 3' UTR extensions like head, while in L1CNS from elav5 single mutant, global neural specific 3' UTR extensions are not significantly lost, but in elav5/fne double mutant L1CNS, there is a dramatic loss of neural specific 3' UTR extensions. We reported for the first time demonstration of trans-acting factors that globally maintain this very distinctive tissue-specific APA landscape."

Overall design from GEO:

"RNA-seq profiles from dissected Drosophila melanogaster 1st instar larvae central neural system from three genotypes: Canton-S (WT), elav5 single mutant, and elav5/fne double mutant. Elav5 and fne mutants are deletion KO alleles."
Subject of Study
Drosophila melanogaster
Subject(s)
3' Untranslated Regions
ELAV Proteins
RNA 3' End Processing
RNA-Binding Proteins
RNA-Seq
Access via GEO


Accession #: GSE155532

Access via BioProject


Accession #: PRJNA650191

Access via SRA


Accession #: SRP275490

Access Restrictions
Free to All
Access Instructions
The NCBI Gene Expression Omnibus, BioProject, and SRA databases provide open access to these files.
Associated Publications
Wei L, Lee S, Majumdar S, Zhang B, Sanfilippo P, Joseph B, Miura P, Soller M, Lai E. Overlapping activities of ELAV/Hu family RNA binding proteins specify the extended neuronal 3′ UTR landscape in drosophila. Molecular Cell. 2020; 80(1):140-155.e6.
Equipment Used
Illumina HiSeq 1000

High throughput sequencing system

Lexogen QuantSeq 3′ mRNA-Seq Library Prep Kit

All-in-one library preparation protocol designed to generate Illumina compatible libraries of sequences close to the 3’ end of polyadenylated RNA.

Dataset Format(s)
CSV, TAR, BW
Dataset Size
675.4 KB (CSV), 2.0 GB (TAR)
Data Catalog Record Updated
2023-10-10