|
| Status |
Public on Jan 02, 2023 |
| Title |
Calm3_distToPolyA_25_IP_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
MCF7
|
| Organism |
Homo sapiens |
| Characteristics |
sample type: human cell line, plasmid with mouse sequence
cell line: MCF7
cell type: human breast cancer
treatment: Plasmid transfection with an insert described in the 'description'. Insert sequences are in TableS1.xlsx.
|
| Treatment protocol |
Transfections were done with JetPrime (Polyplus) reagent, according to the supplier’s instructions. Typically, the cells were seeded in 6-cm dishes (Corning) and on the next day transfected with 1-2µg of plasmids. The cells were harvested after additional 24 hours by scraping and subjected to RNA extraction.
|
| Growth protocol |
MCF7 cells (ATCC) were maintained in DMEM (GIBCO) supplemented with 10% FBS and 1% Penicillin and Streptomycin.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted with BIO TRI RNA reagent (Bio-lab)
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 |
MCF7 cells transfected with Calm3 contruct with 25nt distance between the DRACH motif and polyA site, IP, rep1
TableS1.xlsx
|
| Data processing |
Reads were mapped to hg19 genome assembly and the transfected plasmid sequences with STAR/2.7.9a (Dobin et al., 2013). Per-base read coverages were obtained with txtools (https://github.com/AngelCampos/txtools)
Assembly: hg19 and the transfected plasmid (See TableS1 for sequence)
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.
|
| |
|
| 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 |
SAMN31022795 |
| SRA |
SRX17709853 |
