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Series GSE77709 Query DataSets for GSE77709
Status Public on Feb 09, 2016
Title High-throughput measurements of fitness effects of mutations in the yeast U3 snoRNA
Organisms Saccharomyces cerevisiae; synthetic construct
Experiment type Other
Summary We used a molecular barcoding approach to quantify the fitness of ~60,000 randomly mutated variants of the Saccharomyces cerevisiae U3 snoRNA (the data were further used to calculate a map of intragenic epistatic interactions within this RNA molecule, as descibed in Puchta et al. 2016)
 
Overall design We generated two independent mutant libraries ('Small' with ~3 and 'Big' with ~10 SNPs per allele) on centromeric plasmid, with 20nt random barcodes placed in a non-transcribed region downstream of the gene (PE Samples 30-37 - paired-end sequencing of: U3, 70nt linker and 20nt barcode); next we performed competition experiments in several conditions (E1-5) on populations of yeast cells transformed with both libraries and measured frequencies of mutated variants in time-points during the experiment by deep sequencing of barcodes (Samples 1-29).
 
Contributor(s) Kudla G, Puchta O
Citation(s) 27080103
Submission date Feb 08, 2016
Last update date May 15, 2019
Contact name Olga Anna Puchta
E-mail(s) olga.puchta@igmm.ed.ac.uk
Organization name University of Edinburgh
Department MRC Human Genetics Unit IGMM
Lab Greg's Kudla Lab
Street address Crewe Road
City Edinburgh
ZIP/Postal code EH4 2XU
Country United Kingdom
 
Platforms (3)
GPL17143 Illumina MiSeq (Saccharomyces cerevisiae)
GPL19604 Illumina HiSeq 2500 (synthetic construct)
GPL21440 Ion Torrent Proton (synthetic construct)
Samples (37)
GSM2056885 E1_G0
GSM2056886 E1_D1.25
GSM2056887 E1_D2.25
Relations
BioProject PRJNA311244
SRA SRP069793

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
GSE77709_E1_Small_1_30C_Glu.txt.gz 719.7 Kb (ftp)(http) TXT
GSE77709_E2_Small_2_37C_Glu.txt.gz 741.5 Kb (ftp)(http) TXT
GSE77709_E3_Small_3_30C_Glu.txt.gz 828.0 Kb (ftp)(http) TXT
GSE77709_E4_Small_3_30C_Gal.txt.gz 813.2 Kb (ftp)(http) TXT
GSE77709_E5_Big_1_30C_Glu.txt.gz 2.3 Mb (ftp)(http) TXT
GSE77709_big_library_sequences.txt.gz 3.0 Mb (ftp)(http) TXT
GSE77709_small_library_sequences.txt.gz 518.4 Kb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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