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SRX15377602: GSM6170878: heads_FLAMseq_1; Drosophila melanogaster; OTHER
1 PACBIO_SMRT (Sequel) run: 846,411 spots, 1.1G bases, 453.6Mb downloads

External Id: GSM6170878_r1
Submitted by: MPI of Immunobiology and Epigenetics
Study: Sites of transcription initiation drive mRNA isoform selection [FLAMseq]
show Abstracthide Abstract
The generation of distinct messenger RNA isoforms through alternative splicing and alternative 3' end formation influences the expression and function of genes, often in a cell-type specific manner. Here, we quantitatively assess the regulatory relationships between transcription initiation and co-transcriptional processing steps, particularly 3' end formation. Applying multiple long-read-sequencing approaches to obtain an assembly accurately representing even the longest mRNA isoforms from end-to-end, we quantify mRNA isoform choice in Drosophila and human tissues, including the transcriptionally complex nervous system. We find that in Drosophila brains as well as in human cerebral organoids, 3' end site choice is globally influenced by the site of transcription start. We define a subset of TSSs, “dominant promoters” that impose a transcriptional constraint to predetermine splice and polyadenylation variants, which are characterized by specific epigenetic signatures. In vivo deletion or overexpression of dominant promoters disrupted the 3' end expression landscape. Our study demonstrates the crucial impact of transcription initiation site choice on the regulation of transcript diversity and tissue identity. Overall design: FLAM-sequencing of wild type (w1118) Drosophila melanogaster heads, 3 replicates
Sample: heads_FLAMseq_1
SAMN28550002 • SRS13106508 • All experiments • All runs
Library:
Name: GSM6170878
Instrument: Sequel
Strategy: OTHER
Source: TRANSCRIPTOMIC
Selection: other
Layout: SINGLE
Construction protocol: For head transcriptomes, 3-day-old w1118 flies were collected and flash-frozen in liquid nitrogen and heads were used for RNA extraction. FLAM-seq libraries were prepared as described in (Legnini, I, et al., 2019) (extended protocol available at 10.21203/rs.2.10045/v1) using 4µg total RNA from 3-day-old w1118 fly heads and 14-16h AEL embryos. After SMRTbell adapter addition, libraries were sequenced on 3 SMRTcells on a Sequel I PacBio sequencer. Three replicates were performed for each tissue. Reads were processed using the FLAMAnalysis pipeline described in (Legnini, I, et al., 2019, https://github.com/rajewsky-lab/FLAMAnalysis)
Runs: 1 run, 846,411 spots, 1.1G bases, 453.6Mb
Run# of Spots# of BasesSizePublished
SRR19317537846,4111.1G453.6Mb2023-05-10

ID:
21916125

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