|
| Status |
Public on Aug 31, 2020 |
| Title |
TSS_2018_A_RNA |
| Sample type |
SRA |
| |
|
| Source name |
Synthetic DNA oligo library with barcodes
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
treatment: TSS library
strain: S288C
treatment: RNA
|
| Growth protocol |
Yeast were grown to late log phase in YNB (MSG) + glucose + G418 at 30˚C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For DNA, plasmids were isolated using Qiagen kits (Qiaprep Spin Miniprep #27106, or Plasmid Plus Midi). Total RNA was extracted using a Zymo Research Fungal/Bacterial RNA Miniprep kit (ZR, #R2014) or a Qiagen RNeasy Maxi Kit. For some samples, polyA-RNA was isolated using an mRNA Purification kit (Ambion #61006).
Sequencing libraries were constructed by PCR targeted at the barcodes. For RNA samples, 1st-strand cDNA was created using a targeted primer and used as the template for the PCR.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
processed data file:
TSS_countedMappedBarcodes_200806.txt.gz
TSS_countedBarcodesMappedToDesign_200806.txt.gz
|
| Data processing |
library strategy: amplicon sequencing of barcoded library
Barcodes with perfect matches in the annotation runs were counted
Genome_build: Annotation runs performed for this study; custom synthetic oligo design was based on sacCer3
Supplementary_files_format_and_content: The processed annotation files are tab separated txt files. There are two files for the TSS and Upstream libraries, respectively. Processed files named "countedMappedBarcodes" give the counts from each sample for every detected barcode (one row per barcode). Processed files named "countedBarcodesMappedToDesign" have the same format but only include barcodes mapped to oligos that matched the designed oligos perfectly (i.e., had no synthesis errors), along with their given oligo ID as provided in the oligo design given in the associated publication.
|
| |
|
| Submission date |
Aug 09, 2020 |
| Last update date |
Aug 31, 2020 |
| Contact name |
Frank Wolfgang Albert |
| E-mail(s) |
falbert@umn.edu
|
| Phone |
6123011243
|
| Organization name |
University of Minnesota
|
| Department |
Department of Genetics, Cell Biology, & Development
|
| Street address |
6-160 Jackson Hall, 321 Church St SE
|
| City |
Minneapolis |
| State/province |
MN |
| ZIP/Postal code |
55455 |
| Country |
USA |
| |
|
| Platform ID |
GPL17342 |
| Series (2) |
| GSE155943 |
Massively parallel identification of cis-regulatory variants in yeast promoters - Experimental measurements |
| GSE155944 |
Massively parallel identification of cis-regulatory variants in yeast promoters |
|
| Relations |
| BioSample |
SAMN15769585 |
| SRA |
SRX8913856 |
