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Series GSE141269 Query DataSets for GSE141269
Status Public on Dec 15, 2020
Title An alternative transcriptome shapes cell fate transitions in yeast (TIF-seq)
Organism Saccharomyces cerevisiae
Experiment type Expression profiling by high throughput sequencing
Other
Summary Alternative mRNA isoforms and long noncoding RNAs (lncRNA) make up a large fraction of the transcriptome and play key functions in cell-fate programming. These transcripts often initiate upstream of coding gene promoters from alternative transcription start sites (TSS) where they can regulate gene expression in cis through transcription-coupled chromatin alterations. How, when and where transcription of alternative cis-acting RNAs regulates local gene expression remains poorly understood. Here, we use a high-resolution quantitative approach to study alternative TSS and transcript end site (TES) usage during three different cell fate transitions in yeast: entry into gametogenesis, commitment to meiotic divisions and return to vegetative growth. We propose that an alternative transcriptome of mRNA isoforms and lncRNAs shapes local gene expression during cell fate transitions. Hence, changes in the types and proportions of different RNAs transcribed at a locus are important inputs for gene expression at distinct stages of development.
 
Overall design Transcript Isoform sequencing (TIF) analysis of Saccharomyces cerevisiae SK1 strains. All strains used in this study harbor the IME1gene controlled by a copper inducible promoter (pCUP1), the NDT80 gene controlled by a galactose inducible promoter (pGAL) and a constitutively expressed Gal4 transcription factor fused to the hormone binding domain of the estrogen receptor (Gal4-ER). For the sporulation time course, cells were grown overnight in YPD medium, diluted, and shifted to sporulation media (SPO). IME1 was induced after 2h in Spo by adding 50 μM CuSO4. Time points for each cell fate transition were pooled in equal proportions for library construction and sequencing. Two independent replicates were sequenced.. Details for library preparation are described below.
 
Contributor(s) Chia M, Li C, van Werven F, Marques S, Pelechano V
Citation(s) 33446241
Submission date Dec 02, 2019
Last update date Jan 19, 2021
Contact name Folkert van Werven
E-mail(s) Folkert.vanWerven@crick.ac.uk
Organization name Francis Crick Institute
Street address 1 Midland Road
City London
ZIP/Postal code NW1 1AT
Country United Kingdom
 
Platforms (1)
GPL19756 Illumina NextSeq 500 (Saccharomyces cerevisiae)
Samples (8)
GSM4200179 Wild-type TIFseq premeiotic replicate 1
GSM4200180 Wild-type TIFseq premeiotic replicate 2
GSM4200181 Wild-type TIFseq early meiotic replicate 1
This SubSeries is part of SuperSeries:
GSE137711 High-resolution analysis of cell-state transitions in yeast suggests widespread transcriptional tuning by alternative starts
Relations
BioProject PRJNA592981
SRA SRP234421

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE141269_RAW.tar 148.0 Mb (http)(custom) TAR (of BEDPE)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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