|
| Status |
Public on Jan 21, 2022 |
| Title |
C2C12-Mm-MUNC-spliced-CF-Rep2-DMSO |
| Sample type |
SRA |
| |
|
| Source name |
Murine myoblasts C2C12
|
| Organism |
Mus musculus |
| Characteristics |
cell line: C2C12
genotype/variation: MUNC spliced overexpressing
cell type: Myoblasts
molecule subtype: reverse transcribed RNA
treatment: DMSO
treatment type: Extracted RNA
|
| Growth protocol |
C2C12 PAX7 NEG cells were maintained in HyClone Dulbecco’s High Glucose Modified Eagles Medium (GE #SH30081.01) with 20% FBS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were grown to ~80% confluency and washed briefly twice with ice-cold PBS. Total RNA for in-cell treatments was extracted by Trizol reagent (Invitrogen #15596018) and purified with column-based Direct-zol RNA Miniprep kit (Zymo Research #R2051), while cell-free samples were prepared according to SHAPE-MaP protocol.
MUNC amplicons were generated by gene-specific MaP reverse transcription and PCR. cDNA products were converted to libraries using Illumina Nextera XT library prep kit and sequenced on an Illumina MiSeq instrument.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
Input fasta file: Mn_MUNC_spliced_ncRNA.fa
processed data file:
C2C12_Mm_MUNC_spliced_CellFree_Rep2_SHAPE_profile.txt
C2C12_Mm_MUNC_spliced_CellFree_Rep2_SHAPE_MAP.map
C2C12_Mm_MUNC_spliced_CellFree_Rep2_SHAPE_pairing_prob.dp
C2C12_Mm_MUNC_spliced_CellFree_JoinedReps_SHAPE_MAP.map
C2C12_Mm_MUNC_spliced_CellFree_JoinedReps_SHAPE_pairing_prob.dp
|
| Data processing |
library strategy: SHAPE-MaP
Adduct locations identified by Shapemapper2 software
RNA structure models were generated from SHAPE data using SuperFold software
Supplementary_files_format_and_content: Shapemapper2 MAP file for Superfold; Superfold output pairing probabilities; Cell-free In-cell difference file
|
| |
|
| Submission date |
May 11, 2021 |
| Last update date |
Jan 21, 2022 |
| Contact name |
Roza Kamila Przanowska |
| Organization name |
University of Virginia
|
| Department |
Biochemistry and Molecular Genetics
|
| Street address |
1340 JPA
|
| City |
Charlottesville |
| State/province |
Virginia |
| ZIP/Postal code |
22908 |
| Country |
USA |
| |
|
| Platform ID |
GPL16417 |
| Series (2) |
| GSE174217 |
Distinct MUNC lncRNA structural domains regulate transcription of different promyogenic factors [SHAPE-MaP] |
| GSE174218 |
Distinct MUNC lncRNA structural domains regulate transcription of different promyogenic factors |
|
| Relations |
| BioSample |
SAMN19105214 |
| SRA |
SRX10841801 |
