|
| Status |
Public on Jan 02, 2023 |
| Title |
mESC_SLC25A3_mutAll_IP |
| Sample type |
SRA |
| |
|
| Source name |
mESC
|
| Organism |
Mus musculus |
| Characteristics |
sample type: mouse cell line, plasmid with human sequence
cell line: mESC
cell type: V6.5 mouse embryonic stem cell
treatment: Plasmid transfection with an insert described in the 'description'. Insert sequences are in TableS1.xlsx.
|
| Treatment protocol |
Cells were seeded on gelatin-covered 6-well plates (without MEF feeder cells) for transfection. GFP-SLC25A3 plasmid was transfected with the TransIT-X2 reagent (Mirus) according to the manufacturer’s instructions. Cells were collected 24 hours post-transfection.
|
| Growth protocol |
V6.5 mESC line was kept in DMEM (Gibco) supplemented with 1% Penicillin-Streptomycin, 1 mM L-glutamine, 1% non-essential amino acids, 20% high-grade fetal bovine serum (Biological Industries), beta-mercaptoethanol and 10 µg recombinant leukemia inhibiting factor. Cells were kept on tissue culture plates covered by gelatin (0.2%), in co-culture with in-house generated, radiation-inactivated mouse embryonic fibroblasts.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted with NucleoZOL (Macherey-Nagel)
RNA was poly-A selected with oligo dT-beads (Dynabeads® mRNA DIRECT™ Kit life tech) and subjected to m6Aseq2 according to Dierks et al, 2021 Nature Methods.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
mESC cells transfected with SLC25A mut-all, m6A IP
|
| Data processing |
Reads were mapped to mm9 (mESC) genome assembly and the transfected GFP-SLC25A3 plasmid with STAR/2.7.9a (Dobin et al., 2013). Per-base read coverages were obtained with txtools (https://github.com/AngelCampos/txtools)
mm9, transfected GFP-SLC25A3 plasmid (See TableS1 for sequence)
R data table (rds) file output from txtools https://github.com/AngelCampos/txtools. In addition, the TableS1.xlsx excel file contains the tranfected plasmid sequences.
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| |
|
| Submission date |
May 27, 2022 |
| Last update date |
Jan 02, 2023 |
| Contact name |
Anna Uzonyi |
| E-mail(s) |
uzonyianna@gmail.com
|
| Organization name |
Weizmann Institute of Science
|
| Department |
Department of Molecular Genetics
|
| Lab |
Schraga Schwartz
|
| Street address |
234 Herzl street
|
| City |
Rehovot |
| ZIP/Postal code |
7610001 |
| Country |
Israel |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE204980 |
Exclusion of m6A from splice-site-proximal regions by the exon-junction complex dictates m6A topologies and mRNA stability |
|
| Relations |
| BioSample |
SAMN28697630 |
| SRA |
SRX15483250 |
