GSE136999
Genome-wide binding of Lola in S2 cells
Purpose: The transcription fact Lola is identified as a conponent acting downstream of Hippo signaling to restrict ISC proliferation and regulate midgut homeostasis. To further elucidate the mechanism of Lola regulating ISC proliferation and midgut homeostasis,Chromatin immunoprecipitation assay followed by sequencing (ChIP-seq) was performed to identify genes suppressed directly by Lola. Methods: Chromatin lysates were clarified from homogenized and sonicated S2 cells; protein-DNA complexes were isolated with antibody. Genomic DNA fragments were purified with a DNA purification kit (QIAGEN) and subjected to high throughput sequencing using  Illumina HiSeq2500. Process: After the genomic DNA segments were sequenced using Illumina HiSeq2500. After quality control with fastqc (version 0.11.8), we built genome index from Drosophila melanogaster genome(BDGP6)with bowtie2-build. Reads were aligned to Drosophila genome BDGP6 index with bowtie2. Then we converted sam files to bam files with samtools. Peaks were called from the aligned reads using MACS2 callpeak, and peaks annotation using R package ChIPseeker. Conclusion: Thousands of Lola-associated chromatin binding sites were identified in cultured S2 cells. Analysis of the Lola binding profiles revealed that Lola mainly binds to the regions around transcription start sites (TSS) and promoters. Overall design: Identification of the transcription factor Lola binding region in S2 cells.