m6Am-Exo-Seq mapping of MEL624 control and PCIF1 KO cells

We analyzed m6Am distribution by m6Am-Exo-Seq in order to determine the mRNAs marked by m6Am in human melanoma cells Overall design: The experiment was divided in two stages. In the first stage, mRNA from one clonal PCIF1 KO cell line and one control cell line was treated using the m6Am-Exo-Seq protocol and immunoprecipitated with 8 different m6A antibodies. RNA-Seq libraries for Illumina sequencing from Input and immunoprecipitated mRNA were prepared and sequenced in a NextSeq witn an average coverage of 15 million reads per sample. In the second stage, mRNA from three biological replicates from control and PCIF1 KOs was treated with the m6A-Exo-Seq protocol and immunoprecipitated with a single m6A antibody. RNA-seq libraries were prepared from input and immunoprecipitated mRNA and sequenced in a NextSeq with an average coverage of 35 Million reads for Inputs and 18 Million reads for IPs Here is the antibody information; Ab1: Monoclonal Rabbit antibody from the EpiMark N6-Methyladenosine Enrichment Kit Ab2: Mouse monoclonal, clone 80C9, gift of Synaptic Systems Ab3: Mouse monoclonal, clone 345E11, Synaptic Systems cat # 202 011 Ab4: Mouse monoclonal, clone 212B11, Synaptic Systems cat # 202 111 Ab5: Rabbit polyclonal, affinity purified, batch #8699, gift of Synaptic Systems Ab6: Rabbit polyclonal, affinity purified, batch #8700, gift of Synaptic Systems Ab7: Rabbit polyclonal, affinity purified, batch #8701, gift of Synaptic Systems Ab8: Rabbit polyclonal, affinity purified, batch #8702, gift of Synaptic Systems For the samples where antibody number is not specified, antibody 4 (Synaptic Systems cat # 202 111) was used.