|
| Status |
Public on Sep 05, 2014 |
| Title |
-CMC 100-115nt long RT fragments |
| Sample type |
SRA |
| |
|
| Source name |
YWG11
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: YWG11
rna: Total RNA
od: exponential
cmc use: -
rt enzyme: SuperScript III
|
| Treatment protocol |
Yeast: Cells were poured over ice, harvested by centrifugation, and cell pellets were frozen in liquid nitrogen.
|
| Growth protocol |
Yeast: Yeast were grown to mid log phase (OD~1.0) or high density (OD~12-15) in YPD at 30°C
HeLa: Cells were grown at 37°C with 5% CO2 under standard laboratory conditions. For serum starvation cells were plated at a density of 5 x 106 per 150 mm plate in DMEM+10% FBS, 24h prior to the experiment. Cells were then washed three times in PBS, before the addition of either serum-free medium (DMEM, no FBS) or full medium containing FBS (DMEM+10% FBS) for 24h.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Yeast: Cells were lysed using hot-acid phenol as described in the text
HeLa: HeLa total RNA was isolated using QIAzol and mechanical distruption with a syringe
OTHER: As described in text.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
RNA was fragmented, treated with CMC as indicated, and captured by 3' adaptor ligation. RT was perfromed with enzyme indicated, and truncated CD fragments were selected on a gel, circularized, PCR amplified, and sequenced.
|
| Data processing |
Reads were trimmed of adapter sequence
Yeast: Reads were mapped to SacCer3 downloaded from UCSC on 9/2/2011 using TopHat allowing multiply mapping reads
HeLa: Reads were mapped to spliced transcripts (see text) of hg19 downloaded from UCSC on 1/8/2012 using bowtie1 requiring uniquely mapping data
Mapped reads were processed using custom bash and python scripts (see text)
Ψ's were identified using custom python scripts (see text)
Genome_build: SacCer3 (9/2/2011), hg19 (1/8/2012)
Supplementary_files_format_and_content: USCS wiggle files, and tab delimited text files for rpkms
|
| |
|
| Submission date |
Jun 03, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Thomas M Carlile |
| E-mail(s) |
[email protected]
|
| Phone |
6172533707
|
| Organization name |
MIT
|
| Department |
Biology
|
| Lab |
Gilbert
|
| Street address |
77 Massachusetts Ave
|
| City |
Cambridge |
| State/province |
Massachusetts |
| ZIP/Postal code |
02139 |
| Country |
USA |
| |
|
| Platform ID |
GPL13821 |
| Series (1) |
| GSE58200 |
Pseudouridine profiling reveals widespread regulated mRNA pseudouridylation in yeast and human cells |
|
| Relations |
| BioSample |
SAMN02836993 |
| SRA |
SRX566309 |
