Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Effect of TUC-seq protocol versus SLAM-seq on quantification bias in nucleotide conversion RNA-seq data

ABSTRACT: To investigate the effect of TUC-seq versus SLAM-seq on quantification bias in nucleotide conversion RNA-seq, we performed SLAM-seq and TUC-seq on NIH cells. We then measured 4sU dropout in 4sU samples compared to 4sU naive samples.

ORGANISM(S): Mus musculus

PROVIDER: GSE253169 | GEO | 2024/02/06

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Effect of 4sU labeling durations on quantification bias in nucleotide conversion RNA-seq data

Project description:To investigate the effect of labeling durations on quantification bias in nucleotide conversion RNA-seq, we labeled NIH cells with 4sU. We then measured 4sU dropout in 4sU samples compared to 4sU naive samples.

2024-02-06 | GSE229506 | GEO

Effect of performing SLAM-seq chemistry in methanol fixed cells versus standard tube processing on quantification bias in nucleotide conversion RNA-seq data

Project description:To investigate the occuring 4sU dropout during library preparation we performed SLAM conversion either in intact, methanol fixed cells or in tubes

2024-02-06 | GSE253370 | GEO

Effect of 4sU labeling concentrations on quantification bias in nucleotide conversion RNA-seq data

Project description:To investigate the effect of increasing 4sU labeling concentrations on quantification bias in nucleotide conversion RNA-seq, we labeled 3 different cell lines with increasing concentrations of 4sU. We then measured 4sU dropout in 4sU samples compared to 4sU naive samples.

2024-02-06 | GSE229504 | GEO

SLAM-Seq analysis of Ythdf2-deficient pre-leukemic cells

Project description:The mRNA m6A reader YTHDF2 is overexpressed in a broad spectrum of human acute myeloid leukemias (AML). To study the role of YTHDF2 on mRNA decay rates in leukemia, c-Kit+ cells from foetal livers of Ythdf2fl/fl; Vav-iCre (Ythdf2CKO) and Ythdf2fl/fl (Ythdf2CTL) 14.5 dpc embryos were transduced with Meis1 and Hoxa9 oncogenes and serially re-plated to generate pre-leukemic cells. Medium with 4SU was used for pre-leukemic cells labelling for 12 hours and was later replaced with 4SU-free medium (time 0). Cells were collected immediately after medium change and at 1, 3 and 9 hours for library generation. RNA from Ythdf2CKO (n=3 biological replicates) and Ythdf2CTL (n=3 biological replicates) pre-leukemic cells were used for SLAM-seq library generation.

2019-04-05 | E-MTAB-7784 | biostudies-arrayexpress

Effect of TUC-seq protocol versus SLAM-seq on quantification bias in nucleotide conversion RNA-seq data

Project description:Effect of TUC-seq protocol versus SLAM-seq on quantification bias in nucleotide conversion RNA-seq data

| PRJNA1064143 | ENA

dSLAM-seq of MCMV

Project description:Swiss murine embryonic fibroblasts (NIH-3T3) were infected with wild-type Smith strain mouse cytomegalovirus (MCMV) at a multiplicity of infection (MOI) of 10. Metabolic RNA labelling was performed using 400µM 4sU for one hour prior to cell lysis. Total RNA was isolated using the Trizol protocol and U-to-C conversions were induced by IAA treatment according to the SLAM-seq protocol (Herzog et al., Nature Methods 2017). Sequencing libraries were prepared using the dRNA-seq protocol from the indicated time points of infection as described by Whisnant A.W. et al, Nat. Commun (2020).

2023-04-26 | GSE212286 | GEO

SLAM-seq ML-792

Project description:SLAM-seq ML-792

| PRJNA703953 | ENA

PHF3 binds RNA polymerase II via the SPOC domain and regulates transcription of neuronal genes - SLAM - seq

Project description:Pulse-chase experiment using SLAM-seq in WT, PHF3KO, and dSPOC, HEK293 cells

2021-09-07 | E-MTAB-7898 | biostudies-arrayexpress

PHF3 binds RNA polymerase II via the SPOC domain and regulates transcription of neuronal genes - Targeted SLAM-seq

Project description:Tergeted SLAM seq of WT, PHF3 KO and dSPOC, HEK293 cells

2021-09-07 | E-MTAB-7899 | biostudies-arrayexpress

SLAM-seq on INTS11-degron cells

Project description:SLAM-seq on INTS11-degron cells