GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
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
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
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
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap