|
| Status |
Public on Dec 13, 2024 |
| Title |
Wild type, in vitro DMS experiment, DMS-treated, replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
in vitro
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: in vitro
genotype: wild type
treatment: DMS
|
| Growth protocol |
For in-cell probing (library names include "DMSic") HeLa cells (ATCC number CCL 2) were cultured in high glucose DMEM (Gibco) supplemented with10% fetal bovine serum (Sigma) and 0.5 % pen/strep (Gibco). Cells were maintained at 37° C and 5% CO2. Plasmid constructs were transfected into cells, and cells were later DMS probed
|
| Extracted molecule |
other |
| Extraction protocol |
For in-cell probing, RNA was isolated with Trizol reagent. For in vitro probing, RNA was generated by in vitro transcription with NEB HiScribe T7 High Yield RNA Synthesis kit
For MaP RT, superscript II was used to generate cDNA. For JuMP, C8 enzyme was used to perform RT. In-cell and SHAPE-JuMP libraries were constructed with two rounds of PCR to add Illumina adaptor sequences and barcodes. In vitro MaP libraries were prepared using the NEBNext Ultra II FS DNA Library Prep kit for Illumina
|
| |
|
| Library strategy |
OTHER |
| Library source |
other |
| Library selection |
other |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
Library name: WT_DMSiv_DMS_rep1
MaP_profiles.tar.gz
|
| Data processing |
Shapemapper2 v2.1.5
ShapeJumper v1.0
JuMP filtering: SHAPE-JuMP frequencies were calculated with using the data from normalizeDeletionRates.py in the ShapeJumper package, with low count (<20) JuMP events omitted. Low count JuMP events were omitted because they can be artificially high in this system due to both a low JuMP count and a low read depth (i.e., 1 event in 1 read is a 100% frequency), where the low read depth occurs on JuMPs deep into the read from the poor processivity of the reverse transcriptase. Differences are taken as the AMT-treated minus the untreated values.
Assembly: GRCh38/hg38
Supplementary files format and content: MaP_profiles.tar.gz contains files of the format _profile.txt from ShapeMapper v2.1.5. Each row in these tables describes per-nucleotide mutation rates and normalized reactivity profiles
Supplementary files format and content: JuMP_data.tar.gz contain csv files of processed -JuMP data. These files contain position information for each deletion recorded (nucleotide_position_i, and nucleotide_position_j), as well as information on the counts and read-depth normalized frequencies of deletions in AMT-treated and untreated conditions
|
| |
|
| Submission date |
Dec 06, 2024 |
| Last update date |
Dec 13, 2024 |
| Contact name |
Justin Waldern |
| E-mail(s) |
jwaldern@unc.edu
|
| Organization name |
The University of North Carolina at Chapel Hill
|
| Department |
Biology
|
| Lab |
Alain Laederach
|
| Street address |
250 Bell Tower Dr
|
| City |
Chapel Hill |
| State/province |
NC |
| ZIP/Postal code |
27599 |
| Country |
USA |
| |
|
| Platform ID |
GPL15520 |
| Series (1) |
| GSE283716 |
Structural determinants of inverted Alu-mediated backsplicing revealed by -MaP and -JuMP |
|
| Relations |
| BioSample |
SAMN45210046 |
| SRA |
SRX26999138 |
