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Sample GSM7892711

Query DataSets for GSM7892711

Status

Public on Nov 15, 2023

Title

cf-s-12-2

Sample type

SRA

Source name

primary neonatal mouse fibroblasts

Organism

Mus musculus

Characteristics

cell type: primary neonatal mouse fibroblasts
treatment: NC-12h

Extracted molecule

total RNA

Extraction protocol

Pulse labeling: Seed cells the day before the labelling experiment in a density that allows exponential growth for the duration of the experiment.Pulse/chase labeling: After pulse labeling, remove s4U -containing media from the cells. IAA treatment (Protect samples from light) .
RNA libraries were prepared for sequencing using standard Illumina protocols

Library strategy

OTHER

Library source

transcriptomic

Library selection

other

Instrument model

Illumina NovaSeq 6000

Data processing

Cutadapt (v2.5) was used to trim adapters and filter for sequences.
Slam-seq:The flow ofslamdunkis to first map your reads, filter your alignments, call variants on your final alignments and use these to calculate conversion rates, counts and various statistics for your 3’UTRs.
Slam-seq:SLAM-DUNK was used to map reads, filter alignments, call variants on final alignments and use these to calculate conversion rates, counts and various statistics for 3’UTRs.Extract and summarize the count results of tcount files into a count table.
Slam-seq:Differential gene expression analysis was performed using the DESeq2 R-package.
Slam-seq:GO and KEGG analysis were performed using clusterProfiler R package (v3.6.0).
Assembly: mm10
Supplementary files format and content: TcReadfpkm.xls
Library strategy: Slam-seq

Submission date

Nov 12, 2023

Last update date

Nov 15, 2023

Contact name

Chuanxi Yang

E-mail(s)

2205515@tongji.edu.cn

Organization name

School of Medicine, Southeast University

Department

Department of Cardiology