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Sample GSM2056901 Query DataSets for GSM2056901
Status Public on Feb 09, 2016
Title E3_D2.25
Sample type SRA
Source name E3_Small_3_30C_Glu
Organism synthetic construct
Characteristics sample type: 20nt random barcode (seqID)
Treatment protocol ~500 000 000 cells were transferred into fresh medium every 12 hours
Growth protocol Cells were grown at 30C (E1 and E3-5) or 37C (E2) and 230 RPM in liquid medium supplemented with 2% glucose in competition experiments (E1-3 and E5) or 2% galactose in control conditions (E2)
Extracted molecule other
Extraction protocol Yeast cells collected at each time point were treated with zymolyase to remove the cell wall, and plasmid DNA was isolated from remaining spheroplasts using Qiagen MAXIprep
Illumina / Ion Torrent adapters were added in a 25-cycles PCR reaction
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina HiSeq 2500
Description E3_Small_3_30C_Glu.txt.gz
Data processing (PE) candidate barcode sequences were extracted from between flanking sequences using blastall;
(PE) next we used bedtools programs and bowtie2 and samtools to map all reads with each barcode to wild type U3 to identify the consensus U3 sequence corresponding to each random barcode
(PE) to create a final 'filtered list' we discarded all barcodes for which we found any mutation in U3 present in between 20-79% of reads, or the linker sequence between U3 and the barcode was mutated or U3 sequence was not totally covered by reads
(E1-5) we used blast and bedtools to localise and remove the flanking sequences from reads and we counted unique barcodes;
(E1-5) next we recovered barcode sequences that could be uniquely matched to exactly one of the barcode sequences from the filtered list, allowing at most two sequencing errors per barcode
Supplementary_files_format_and_content: processed data files are in the custom format
Supplementary_files_format_and_content: column
Supplementary_files_format_and_content: 1 - barcode
Supplementary_files_format_and_content: 2 - sequence of U3 variant assigned to given barcode
Supplementary_files_format_and_content: 3 up to 9 - number of reads for given barcode in subsequent-time points of the experiment
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
Platform ID GPL19604
Series (1)
GSE77709 High-throughput measurements of fitness effects of mutations in the yeast U3 snoRNA
BioSample SAMN04481049
SRA SRX1566690

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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