|
| Status |
Public on Feb 09, 2016 |
| Title |
E4_G0.25 |
| Sample type |
SRA |
| |
|
| Source name |
E4_Small_3_30C_Gal
|
| 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 |
E4_Small_3_30C_Gal.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 |
| 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 |
| |
|
| Platform ID |
GPL19604 |
| Series (1) |
| GSE77709 |
High-throughput measurements of fitness effects of mutations in the yeast U3 snoRNA |
|
| Relations |
| BioSample |
SAMN04481053 |
| SRA |
SRX1566694 |
