|
| Status |
Public on Feb 04, 2014 |
| Title |
SMORE-seq_WT_TAP-_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
SMORE-seq_WT_TAP-
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: BY4741
genotype/variation: wild type
replicate: replicate2
|
| Growth protocol |
Cells were grown in yeast extract-peptone-dextrose (YPD) at 30°C to an A600 OD of 0.8. We harvested the cells by centrifugation at 3000 rcf for 5 min, and the cell pellets were frozen in liquid nitrogen after discarding supernatant
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Hot phenol total RNA extraction
Poly(A)+ RNA was purified and mixed with 5 units (1 μl) Tobacco Acid Pyrophosphatase (TAP). A parallel reaction without TAP enzyme was also performed. The RNA was combined with 5’ SR Adaptor (NEBNext Small RNA Library Prep Set for Illumina). This RNA was fragmented for 4 minutes at 94C using NEB fragmentation reagent. The RNA was then ligated to a 3’ sequencing adapter followed by reverse transcription and 10 cycles of PCR. PCR products of ~250 bp were selected and subjected to another 8 cycles of PCR
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Sample 4
|
| Data processing |
The 100 bp read sequences were trimmed to 50 bp before alignment.
Alignment of sequencing reads was performed with bwa (version 0.6.2) using default options
Three TAP+ and TAP- replicates were merged, respectively, using samtools (version 0.1.18)
Reads that mapped to snRNA and rRNA were removed.
Gaussian kernel density estimation was utilized for peak calling, and a bandwidth of 5 and a read threshold of 2 were applied.
When TAP+ peaks were present within ±50bp of TAP- peaks, the peaks were corrected.
The base position with the highest read stack within the highest corrected peak was called as the TSS and PAS.
Genome_build: sacCer3
Supplementary_files_format_and_content: 1-based TSS and PAS coordinates
|
| |
|
| Submission date |
Jul 18, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Vishy Iyer |
| E-mail(s) |
[email protected]
|
| Phone |
5122327833
|
| Organization name |
University of Texas at Austin
|
| Department |
Molecular Biosciences
|
| Street address |
2500 Speedway Dr. MBB 3.212
|
| City |
Austin |
| State/province |
TX |
| ZIP/Postal code |
78712 |
| Country |
USA |
| |
|
| Platform ID |
GPL13821 |
| Series (1) |
| GSE49026 |
SMORE-seq maps both ends of transcripts and identifies widespread promoter-associated non-coding RNA governed by TATA elements. |
|
| Relations |
| BioSample |
SAMN02260432 |
| SRA |
SRX326589 |
