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Series GSE242556

Query DataSets for GSE242556

Status

Public on Sep 21, 2023

Title

Simultaneous estimation of gene regulatory network structure and RNA kinetics from single cell gene expression

Organism

Saccharomyces cerevisiae

Experiment type

Expression profiling by high throughput sequencing

Summary

Cells respond to environmental and developmental stimuli by changing their transcriptomes through both regulation of transcription rate and regulated mRNA decay. These biophysical properties determine the transcriptional state of a cell, but measuring them requires metabolic RNA labeling (e.g. 4-thiouracil pulse-chase) to separate RNA decay from synthesis rates. We approach this problem by sequencing individual Saccharomyces cerevisiae cell transcriptomes by continuously sampling from a population without metabolic labeling. Using this continuous-sampling system, we measure expression in 180,000 individual cells both prior to and in response to rapamycin treatment. The rates of change for each transcript can be calculated on a per-cell basis to give smooth, biologically relevant, estimates of RNA velocity. We then train deep learning models to use this transcriptomic and velocity information to make time-dependent predictions about RNA biophysics, and to infer causal regulatory relationships between transcription factors and their genes.

Overall design

To minimize the interval between observed data points, we continually pump culture into excess saturated ammonium sulfate to collect cells, fixing transcriptomes at the time of collection. We use this system to quantify the transcriptomic response to rapamycin on a continuous basis, collecting 173,361 cells across 8 defined 10-minute time intervals, from two biological replicate experiments. Samples were collected continuously into 50 mL conicals containing 20 mL RNAlater. Sample collection conicals were changed every 10 minutes and the collected samples were placed on ice. After 20 minutes, 200 ng/mL rapamycin was added to the stirring culture. Sampling continued for 60 additional minutes, yielding 2 10-minute sample pools without rapamycin treatment and 6 10-minute sample pools with rapamycin treatment.

Contributor(s)

Jackson CA, Suresh I, Hickey A, Gresham D

Citation(s)

Submission date

Sep 07, 2023

Last update date

Jan 19, 2024

Contact name

Christopher Jackson

E-mail(s)

Organization name

New York University

Department

Center for Genomics and Systems Biology

Lab

Bonneau Lab

Street address

12 Waverly Place

City

New York

State/province

NY

ZIP/Postal code

10003

Country

USA

Platforms (1)

Illumina NovaSeq 6000 (Saccharomyces cerevisiae)

Samples (35)

More...

GSM7765995	scRNA-seq Rapamycin Time 1 (-20 to -10) Replicate 1
GSM7765996	scRNA-seq Rapamycin Time 2 (-10 to 0) Replicate 1
GSM7765997	scRNA-seq Rapamycin Time 3 (0 to 10) Replicate 1

GSM7765998	scRNA-seq Rapamycin Time 4 (10 to 20) Replicate 1
GSM7765999	scRNA-seq Rapamycin Time 5 (20 to 30) Replicate 1
GSM7766000	scRNA-seq Rapamycin Time 6 (30 to 40) Replicate 1
GSM7766001	scRNA-seq Rapamycin Time 7 (40 to 50) Replicate 1
GSM7766002	scRNA-seq Rapamycin Time 8 (50 to 60) Replicate 1
GSM7766003	scRNA-seq Genotype PCR Rapamycin Time 1 (-20 to -10) Replicate 1
GSM7766004	scRNA-seq Genotype PCR Rapamycin Time 2 (-10 to 0) Replicate 1
GSM7766005	scRNA-seq Genotype PCR Rapamycin Time 3 (0 to 10) Replicate 1
GSM7766006	scRNA-seq Genotype PCR Rapamycin Time 4 (10 to 20) Replicate 1
GSM7766007	scRNA-seq Genotype PCR Rapamycin Time 5 (20 to 30) Replicate 1
GSM7766008	scRNA-seq Genotype PCR Rapamycin Time 6 (30 to 40) Replicate 1
GSM7766009	scRNA-seq Genotype PCR Rapamycin Time 7 (40 to 50) Replicate 1
GSM7766010	scRNA-seq Genotype PCR Rapamycin Time 8 (50 to 60) Replicate 1
GSM7766011	scRNA-seq Rapamycin Time 1 (-20 to -10) Replicate 2
GSM7766012	scRNA-seq Rapamycin Time 2 (-10 to 0) Replicate 2
GSM7766013	scRNA-seq Rapamycin Time 3 (0 to 10) Replicate 2
GSM7766014	scRNA-seq Rapamycin Time 4 (10 to 20) Replicate 2
GSM7766015	scRNA-seq Rapamycin Time 5 (20 to 30) Replicate 2
GSM7766016	scRNA-seq Rapamycin Time 6 (30 to 40) Replicate 2
GSM7766017	scRNA-seq Rapamycin Time 7 (40 to 50) Replicate 2
GSM7766018	scRNA-seq Rapamycin Time 8 (50 to 60) Replicate 2
GSM7766019	scRNA-seq Genotype PCR Rapamycin Time 1 (-20 to -10) Replicate 2
GSM7766020	scRNA-seq Genotype PCR Rapamycin Time 2 (-10 to 0) Replicate 2
GSM7766021	scRNA-seq Genotype PCR Rapamycin Time 3 (0 to 10) Replicate 2
GSM7766022	scRNA-seq Genotype PCR Rapamycin Time 4 (10 to 20) Replicate 2
GSM7766023	scRNA-seq Genotype PCR Rapamycin Time 5 (20 to 30) Replicate 2
GSM7766024	scRNA-seq Genotype PCR Rapamycin Time 6 (30 to 40) Replicate 2
GSM7766025	scRNA-seq Genotype PCR Rapamycin Time 7 (40 to 50) Replicate 2
GSM7766026	scRNA-seq Genotype PCR Rapamycin Time 8 (50 to 60) Replicate 2
GSM7773175	Bulk RNA-seq Rapamycin Replicate 1
GSM7773176	Bulk RNA-seq Rapamycin Replicate 2
GSM7773177	Bulk RNA-seq Rapamycin Replicate 3

Relations

BioProject

Download family	Format
SOFT formatted family file(s)	SOFT
MINiML formatted family file(s)	MINiML
Series Matrix File(s)	TXT

Supplementary file	Size	Download	File type/resource
GSE242556_2021_RAPA_BULK_TIMECOURSE.tsv.gz	104.3 Kb	(ftp)(http)	TSV
GSE242556_2021_RAPA_TIMECOURSE.tsv.gz	231.8 Mb	(ftp)(http)	TSV
GSE242556_2021_RAPA_TIMECOURSE_EXTRA_METADATA.tsv.gz	1.1 Mb	(ftp)(http)	TSV
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