|
| Status |
Public on Jan 09, 2024 |
| Title |
1.5% DMS treated lncRNA Panda + ASO1 |
| Sample type |
SRA |
| |
|
| Source name |
Human olido-dt cDNA
|
| Organism |
synthetic construct |
| Characteristics |
tissue: Brain
cell line: N/A
cell type: N/A
treatment: 1.5% DMS + ASO1
|
| Extracted molecule |
other |
| Extraction protocol |
All RNA was acquired from in-vitro transcription of PCR amplified cDNA or gene-blockes.
The libraies for the HIV-1 RRE were prepared using the NEBnext RNA library prep kit. The libraries for the lncRNA PANDA were prepared using the Broad range RNA Xgen kit form IDT. The reverse transcriptase was changed to the Induro RT from NEB for the purposes of our experiment.
|
| |
|
| Library strategy |
OTHER |
| Library source |
other |
| Library selection |
other |
| Instrument model |
NextSeq 1000 |
| |
|
| Data processing |
Data was processed using the DREEM software (https://github.com/rouskinlab/DREEM) .
Assembly: For PANDA the NCBI Reference Sequence is NR_109836.1. For the RRE the GenBank accession number is MN989412.1
Supplementary files format and content: The filw format is a .csv file that can be opened as a data table using excell. It provides the number of mutations per position of the entire population of RNA molecules that aligned to the referecne sequence.
Library strategy: DMS-MaPseq
|
| |
|
| Submission date |
Dec 15, 2023 |
| Last update date |
Jan 09, 2024 |
| Contact name |
Gabriel A Romero Agosto |
| E-mail(s) |
gabrielromeroagosto@g.harvard.edu
|
| Organization name |
Harvard Medical School
|
| Street address |
77 Avenue Louis Pasteur
|
| City |
Boston |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL34014 |
| Series (1) |
| GSE250290 |
DMS-MapSeq Analysis of Antisense Oligonucleotide Binding to lncRNA PANDA |
|
| Relations |
| BioSample |
SAMN38859694 |
| SRA |
SRX22906852 |
