H3K4me3 ChIP-seq of hsa-miR-96-5p Overexpressing Cells

H3K4me3 ChIP-seq of hsa-miR-96-5p Overexpressing IMR-90 Human Lung Fibroblasts. Compressed FASTQ archives of Control (C2 and C3) and miR-96-5p overexpressing IMR-90 cells (M2 and M3), forward (R1) and reverse (R2) strands. METHOD. Chromatin Immunoprecipitation and Analysis. Cell cultures for each condition were grown in T-175 flasks, treated as indicated, and processed according to instructions for ChIP-PCR workflows (SimpleChIP® Plus Enzymatic Chromatin IP Kit Agarose Beads #9004) and ChIP-seq workflows (SimpleChIP® Plus Enzymatic Chromatin IP Kit Magnetic Beads #9005). ChIP-PCR primers sequences (5’→3’) are: p16 prom 1 up-TCCTAGTTGTGAGAGCCCCA; p16 prom 1 dn-CCGCGCTCCTGAAAATCAAG; p16 prom 2 up-CAAATCCTCTGGAGGGACCG; p16 prom 2 dn-TGCCACATTCGCTAAGTGCT; p16 prom 3 up-TCGAAGCGCTACCTGATTCC; p16 prom 3 dn-ATCCAGGTGGGTAGAGGGTC; p21 prom 1 up-CTCCATCCCTATGCTGCCTG; p21 prom 1 dn-TTGGGACATGTTCCTGACGG; p21 prom 2 up-ATACGGGCTATGTGGGGAGT; p21 prom 2 dn-TGGTTGCAGCAGCTTTGTTG; p21 prom 3 up-CGTTCACAGGTGTTTCTGCG; p21 prom 3 dn-CACATCCCGACTCTCGTCAC; p21 prom 4 up-CTCTCCGAAAGCTACAGGGC; p21 prom 4 dn-TTTTCCTCACGAAGAGGGCG; p21 prom 5 up-CCGAGATCAACCCCTATGCC; p21 prom 5 dn-TTGGCCTTCCTGCCTTAGAC; IL1b prom 1 up-GAGGGTGTGGGTCTCTACCT; IL1b prom 1 dn-CCCCAGCCAAGAAAGGTCAA; IL1b prom 2 up-CATCCAGTGCATGGCAGTCA;
IL1b prom 2 dn-CCTCTGCTCCAGCTCTCCTA; IL1b prom 3 up-GAGGCTAGGGGAGGCTATCA; IL1b prom 3 dn-GCTAGGTCAGTTGTGCAGGT; IL1b prom 4 up-TTTGGCTACTGTGGCACGAT; IL1b prom 4 dn-ATTTTACCGCCCAGCAGGAA;IL6 prom 1 up-AGGATTCCCAAGGGGTCACT; IL6 prom 1 dn-GTCTCCAGGTGGAGTGTGTG; IL6 prom 2 up-TAGATTTGAGGCCAACGGGG; IL6 prom 2 dn-GGAACTTCCTGACACCAGCA; IL6 prom 3 up-ACCAACTTGTCGCACTCACT; IL6 prom 3 dn-ACCCACTTTTTGTTGCTGCC. Immunoprecipitations were done with Tri-Methyl-Histone H3 (Lys27) (C36B11) Rabbit mAb #9733 (Cell Signaling) and Tri-Methyl-Histone H3 (Lys4) (C42D8) Rabbit mAb #9751 (Cell Signaling). For ChIP-PCR immunoprecipitations were done with ChIP-seq libraries were sequenced with ThruPLEX® DNA-Seq Kit (Takara Bio) and sequenced the pooled libraries on a NextSeq 2K P3 2x100-bp run, generating > 1 billion reads. Output FASTQ files were processed with FastQC; Genome Analysis Toolkit (GATK; Broad Institute) was used clean FASTQ files which were then aligned to hg38 with (Burrows-Wheeler Aligner) BWA. The Galaxy Platform (Galaxy Community, 2022) was used for narrow and broad peak calling (MACS2) and differential peak calling (DiffBind).