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. Author manuscript; available in PMC: 2024 Dec 7.
Published in final edited form as: Mol Cell. 2023 Dec 7;83(23):4239–4254.e10. doi: 10.1016/j.molcel.2023.11.003

KEY RESOURCES TABLE

REAGENT or RESOURCE SOURCE IDENTIFIER
Antibodies
Rabbit monoclonal anti-m5C (for RNA dot bot) Abcam Cat# ab214727; RRID: AB_2802117
Mouse monoclonal anti-m5C (for RNA m5C MeRIP) Diagenode Cat# C15200003
Mouse monoclonal anti-Flag Sigma-Aldrich Cat# F3165; RRID: AB_259529
Mouse monoclonal anti-His Abcam Cat# ab18184; RRID: AB_444306
Mouse monoclonal anti-Myc Cell Signaling Cat# 2276; RRID: AB_2148465
Rabbit polyclonal anti-NSUN2 Proteintech Cat# 20854-1-AP; RRID: AB_10693629
Mouse monoclonal anti-ACTIN Sigma-Aldrich Cat# A5316; RRID: AB_476743
anti-Mouse IgG, HRP-linked secondary antibody GE Healthcare Cat# NXA931V; RRID: AB_2721110
anti-Rabbit IgG, HRP-linked secondary antibody GE Healthcare Cat# NA934V; RRID: AB_772191
Bacterial and virus strains
BL21(DE3) Competent E. coli NEB Cat# C2530H
Chemicals, peptides, and recombinant proteins
Acid-Phenol:Chloroform Thermo Fisher Cat# AM9722
TURBO™ Dnase Thermo Fisher Cat# AM2239
RNasin Promega Cat# N251B
4-thiouridine Sigma-Aldrich Cat# T4509
Protease inhibitor cocktail Sigma-Aldrich Cat# P8340
Protease K Sigma-Aldrich Cat# P2308
RNase T1 Fermentas Cat# EN0542
T4 Polynucleotide Kinase (T4 PNK) NEB Cat# M0201L
Adenosine 5′-Triphosphate (ATP) NEB Cat# P0756S
Alkaline Phosphatase, Calf Intestinal (CIP) NEB Cat# M0290L
SuperScript™ II Reverse Transcriptase Invitrogen Cat# 18064014
LightCycler® 480 SYBR Green Roche Cat# 4887352001
Chemiluminescent Nucleic Acid Detection Module Thermo Fisher Cat# 89880
Dynabeads Protein A beads Invitrogen Cat# 10001D
Streptavidin Magnetic Beads NEB Cat# S1420S
Anti-FLAG® M2 Magnetic Beads Millipore Cat# M8823
Critical commercial assays
QuikChange™ site-directed mutagenesis kit Stratagene Cat# 200518
NEBNext® Multiplex Small RNA Library Prep Set for Illumina NEB Cat# E7300S
SMARTer smRNA-seq Kit for Illumina Takara Cat# 635030
RNA 3’ end biotinylation kit Thermo Fisher Cat# 20160
Deposited data
Raw and processed high-throughput sequencing data This paper GEO: GSE207643
The original imaging data and source dataset deposited in Mendeley Data This paper Mendeley Data: https://doi.org/10.17632/zv3fyzh4tr.1
m5C RNA-BisSeq data in HeLa cells Yang et al.9 GEO: GSE93749
SRSF1 and SRSF3 PAR-CLIP-seq data Xiao et al.52 GEO: GSE71096
SRSF3 and SRSF10 RNA-seq data Xiao et al.52 GEO: GSE71095
Polysome profiling sequencing data in HeLa Choe et al.53 GEO: GSE117299
Polysome profiling sequencing data in K562 Karmakar et al.54 https://academic.oup.com/narcancer/article/4/2/zcac015/6576546#supplementary-data
AML cohort: Bamopoulos et al. Bamopoulos et al.35 GEO: GSE146173
AML cohort: Beat AML Tyner et al.36 http://www.vizome.org/
CMML cohort: Franzini et al. Franzini et al.34 GEO: GSE135902
CMML cohort: Pronier et al. Pronier et al.55 GEO: GSE165305, GSE188624
Leukemia gene and literature (LGL) database Liu et al.56 http://soft.bioinfo-minzhao.org/lgl/
Experimental models: Cell lines
Human: K562 cells This paper N/A
Human: HeLa cells ATCC RRID: CVCL_0030
Human: HEK293GP cells ATCC RRID: CVCL_E072
Oligonucleotides
RNA sequences used for biotinylated pull-down assays and NanoBRET assays, see Table S1 This paper N/A
Primers for RT-qPCR, MeRIP-RT-qPCR, RIP-qPCR, see Table S7 This paper N/A
siRNA/shRNA sequence, see Table S7 This paper N/A
Recombinant DNA
Plasmid: pcDNA3.1-Myc-His-SRSF2 Addgene Cat# 44721
Plasmid: pcDNA3.1-Myc-His-SRSF2P95H This paper N/A
Plasmid: pcDNA3.1-Myc-His-SRSF2T51A This paper N/A
Plasmid: pcDNA3.1-Myc-His-SRSF2K52A This paper N/A
Plasmid: pcDNA3.1-Myc-His-SRSF2H99A This paper N/A
Plasmid: pcDNA3.1-Myc-His-SRSF2P107H This paper N/A
Plasmid: pET30a(+)-His-SRSF2 This paper N/A
Plasmid: pET30a(+)-His-SRSF2-N (1-115) This paper N/A
Plasmid: pET30a(+)-His-SRSF2-C (115-221) This paper N/A
Plasmid: pCMV-Flag-SRSF2 This paper N/A
Plasmid: pCMV-Flag-SRSF2P95H This paper N/A
Plasmid: pCMV-Myc-SRSF2 This paper N/A
Plasmid: pCMV-Myc-SRSF2P95H This paper N/A
Software and algorithms
FastQC v0.11.5 Andrews57 https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
Cutadapt v1.9.1 Martin58 https://cutadapt.readthedocs.io/en/stable/
Trimmomatic v0.33 Bolger et al.59 http://www.usadellab.org/cms/index.php?page=trimmomatic
Bowtie v2.3.4,1 Langmead and Salzberg60 http://bowtie-bio.sf.net.
STAR v2.6.1d Dobin et al.61 https://github.com/alexdobin/STAR
Bedtools v2.25.0 Quinlan and Hall62 https://bedtools.readthedocs.io/en/latest/
PARalyzer v1.5 Corcoran et al.63 https://ohlerlab.mdc-berlin.de/software/PARalyzer_85/
IGV v2.9.4 Thorvaldsdóttir et al.64 https://software.broadinstitute.org/software/igv/
MEME (Web-based) Bailey et al.65 http://meme-suite.org/tools/meme
DAVID v2021q4 (Web-based) Sherman et al.66 and Huang et al.67 https://david.ncifcrf.gov
rMARTs v4.1.2 Shen et al.68 https://github.com/Xinglab/rmats-turbo
rmats2sashimiplot v2.0.4 Xing Lab https://github.com/Xinglab/rmats2sashimiplot
Python v2.7 Python Software Foundation https://www.python.org
R v4.0.4 The R Foundation https://www.r-project.org
GraphPad Prism 9 GraphPad Software, Inc. https://www.graphpad.com/scientific-software/prism/
AfterQC v0.9.6 Chen et al.69 https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-017-1469-3
HTSeq count v0.9.1 Anders et al.70 https://academic.oup.com/bioinformatics/article/31/2/166/2366196
m6aViewer v1.6.1 Antanaviciute et al.71 https://pubmed.ncbi.nlm.nih.gov/28724534/
meRanTK v1.2.1b Rieder et al.72 https://icbi.i-med.ac.at/software/meRanTK/
Biorender Biorender https://biorender.com
Other
NanoBRET assay Promega https://www.promega.com
Mass spectrometry Promega https://www.promega.com