 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Sep 01, 2020 |
| Title |
Minimal rep A |
| Sample type |
SRA |
| |
|
| Source name |
Minimal_yeast cells
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: JGY2000
genotype: Wild-type RPO21-FRB
growth medium: Minimal
culture stage: log phase
|
| Treatment protocol |
none
|
| Growth protocol |
Growth in the specified culture medium to mid-log phase except for diauxic cells, which were cultured for approximately 72 hours
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Hot acid phenol RNA extraction followed by Qiagen RNeasy purification
3' READS starting with 25µg total RNA (Jin, Y. et al., 2015 Curr Protoc Mol Biol 110, 4.23.21-24.23.17)
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
3' READS library
|
| Data processing |
library strategy: 3' READS
Prep for mapping (removal of adapters, counting and removal of initial Ts, discarding reads with ambiguous base calls): python3
Mapping to yeast genome build Sac cer3 (first 17 non-A bases; accepting perfect matches and unique reads only): Bowtie (Langmead et al., 2009)
Discard mapped reads with fewer initial Ts than there are As in the adjacent genome: python3
Tally reads by UTR position if they map to the first 400nt after an ORF end: python3
Genome_build: Sac cer 3
Supplementary_files_format_and_content: tab-delimited text files with isoform expression percentages for every position in the first 400 nt after yeast genes
|
| |
|
| Submission date |
May 26, 2020 |
| Last update date |
Jan 11, 2022 |
| Contact name |
Zarmik Moqtaderi |
| Organization name |
Harvard Medical School
|
| Department |
BCMP
|
| Lab |
Struhl lab
|
| Street address |
240 Longwood Avenue C2-355
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL19756 |
| Series (1) |
| GSE151196 |
The transcriptional elongation rate regulates alternative polyadenylation in yeast |
|
| Relations |
| Reanalyzed by |
GSM5808424 |
| BioSample |
SAMN15016302 |
| SRA |
SRX8399842 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4568404_JGY2000_Minimal_ABmerged_RelCountsByPosition_1_to_400.txt.gz |
2.6 Mb |
(ftp)(http) |
TXT |
| GSM4568404_JGY2000_Minimal_RepA_RelCountsByPosition_1_to_400.txt.gz |
2.4 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
