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 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.