|
| Status |
Public on Jan 02, 2023 |
| Title |
cDNA_pLenti6_pool3_IP_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
NIH3T3
|
| Organism |
Homo sapiens |
| Characteristics |
sample type: mouse, human
cell line: NIH3T3
cell type: mouse fibroblast
treatment: Plasmid transfection with cDNA pLentli6 plasmid pool described in Table S1.
|
| Treatment protocol |
Cells were seeded on 60 mm plates 24 hours prior to transfection. Cells were transfected with pLenti cDNA constructs with Lipofectamine 2000 (Thermo Fisher Scientific) reagent according to the manufacturer’s protocol. A total of 33 different cDNA plasmids were transfected in pools of 12, in duplicates.
|
| Growth protocol |
NIH3T3 cells were cultured in DMEM (Gibco) supplemented with 10% FBS and 1% Penicillin and Streptomycin.
|
| 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 |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
NIH3T3 cells transfected with a pool of 12 cDNA pLenti6 plasmids.
cDNAExpV2IPpool3_AlignedReads.bam.txDT.rds
TableS1.xlsx
|
| Data processing |
Reads were mapped to mm9 genome and corresponding cDNA sequences (Table S1) using STAR/2.7.9a (Dobin et al., 2013).
Assembly: mm9
Supplementary files format and content: 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. Replicates of the same pool were merged together.
|
| |
|
| Submission date |
Sep 26, 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 |
GPL24676 |
| Series (1) |
| GSE204980 |
Exclusion of m6A from splice-site-proximal regions by the exon-junction complex dictates m6A topologies and mRNA stability |
|
| Relations |
| BioSample |
SAMN31022810 |
| SRA |
SRX17709838 |
