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Status |
Public on Jan 02, 2023 |
Title |
MCF7_MR32MR33MR34_input_rep1 |
Sample type |
SRA |
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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.
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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.
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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.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
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Description |
MCF7 cells transfected with MR32, MR33 and MR34, m6A input sample, replicate 1, part of experiment 2
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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) hg19 and the transfected 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 |
GPL24676 |
Series (1) |
GSE204980 |
Exclusion of m6A from splice-site-proximal regions by the exon-junction complex dictates m6A topologies and mRNA stability |
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Relations |
BioSample |
SAMN28697667 |
SRA |
SRX15483291 |