|
| Status |
Public on Aug 07, 2023 |
| Title |
HeLa_polyA_ModSeq_GS_PRUNE1_Mg |
| Sample type |
SRA |
| |
|
| Source name |
HeLa cell line
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: cervical cancer
cell line: HeLa
|
| Growth protocol |
Human cell lines were grown in DMEM supplemented with 10% fetal bovine serum and 1X antimycotic-antibiotic at 37 deg C
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Trizol
cDNA was prepared from polyA-enriched RNA from each source using gene specific primers, along with MarathonRT enzyme in the presence of either Mg or Mn as enzymatic cofactors; gene-specific PCR was done to get targeted amplicons from each cDNA sample (target 1 = MALAT1 lncRNA, target 2 = PRUNE1 mRNA); library preparation was carried out from resulting dsDNA amplicons using the Nextera XT DNA kit
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
NextSeq 2000 |
| |
|
| Data processing |
ShapeMapper2 (Busan et al.2018)
Mg libraries = untreated samples; Mn libraries = modified samples; use ‘--output-counted-mutations’ flag to output counted mutations
Assembly: MALAT1 (NR_002819.4); PRUNE1 (NM_021222.3)
Supplementary files format and content: profile.txt files = csv containing calculated mutation rates for each nucleotide position in the reference sequence; mutation_counts.txt files = csv containing mutation rate compositions for each nucleotide position in the reference sequence
|
| |
|
| Submission date |
Mar 28, 2023 |
| Last update date |
Aug 07, 2023 |
| Contact name |
Rafael de Cesaris Araujo Tavares |
| E-mail(s) |
[email protected]
|
| Organization name |
Yale University
|
| Department |
Chemistry
|
| Lab |
Pyle
|
| Street address |
260 Whitney Ave
|
| City |
New Haven |
| State/province |
Connecticut |
| ZIP/Postal code |
06511 |
| Country |
USA |
| |
|
| Platform ID |
GPL30173 |
| Series (1) |
| GSE202160 |
MRT-ModSeq - Rapid detection of RNA modifications with MarathonRT |
|
| Relations |
| BioSample |
SAMN33948735 |
| SRA |
SRX19793407 |
