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Status |
Public on Jul 25, 2024 |
Title |
frac_mef_ip_nuc_ctrl_1 |
Sample type |
SRA |
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Source name |
pMEF
|
Organism |
Mus musculus |
Characteristics |
cell line: pMEF cell type: primary cells library type: RNA-seq
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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)
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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
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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 |
SAMN42642282 |
SRA |
SRX25386237 |