|
| Status |
Public on Jul 25, 2024 |
| Title |
frac_mef_ip_nuc_ctrl_2 |
| Sample type |
SRA |
| |
|
| Source name |
pMEF
|
| Organism |
Mus musculus |
| Characteristics |
cell line: pMEF
cell type: primary cells
library type: RNA-seq
|
| Growth protocol |
Mammalian cell lines were grown at 37°C and 5 % CO2 in DMEM (10% FBS, with Antibiotics Penn/Strep)
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Nucleozol total RNA extraction protocol according to the manufacturers protocol.
All libraries were conducted according to the libraray preparation protocol in Dierks et al. 2021. For RNA-seq, the protocol was performed as in Dierks 2021, excluding the m6A IP step, (performed as if only is the input sample.
m6A-seq2 & RNA-seq (m6A-seq2 protocol exluding the m6A IP section)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
mRNA samples from human and mouse were aligned to the mm9/hg19 genome using STAR v.2.5.3a with default settings (‘--alignIntronMax 1000000’) (Dobin et al., 2013). For gene expression (TPM) and read counts, rsem-calculate-expression (rsem/1.3.3) was employed (Li and Dewey, 2011). m6A-GI and m6A-SI metrics were derived using the bam2ReadEnds.R script (Garcia-Campos et al., 2019) as per Dierks et al. 2021, calculating m6A IP enrichment against input coverage.
Assembly: mm9 & hg19
Supplementary files format and content: RSEM hg19 counted reads and tpm tables
|
| |
|
| Submission date |
Jul 19, 2024 |
| Last update date |
Jul 25, 2024 |
| Contact name |
David Dierks |
| E-mail(s) |
david.dierks@weizmann.ac.il
|
| Organization name |
Weizmann Institute of Science
|
| Department |
Molecular Genetics
|
| Lab |
Schraga Schwartz
|
| Street address |
Herzl St 234, Weizmann Institute of Science to the Department of Biomolecular Sciences, Laboratory of Dr. Scherz-Shouval
|
| City |
Rehovot |
| State/province |
Central District |
| ZIP/Postal code |
7610001 |
| Country |
Israel |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE272629 |
Passive shaping of intra- and intercellular m6A dynamics via mRNA metabolism |
|
| Relations |
| BioSample |
SAMN42642281 |
| SRA |
SRX25386238 |
