Project description:This study presents a comparison of small RNA sequencing libraries generated from the same cell lines but using different sequencing platforms and protocols. The samples were analyzed and compared at the level of miRNAs expression and as a population of small RNAs derived from repetitive elements. Despite a good correlation between sequencing platforms, there are qualitative and quantitative variations in the results depending on the protocol used.
Project description:Deep whole genome sequencing of Drosophila melanogaster inbred lines: DGRP-28, DGRP-307, DGRP-399, DGRP-57, DGRP-639, DGRP-712, DGRP-714, DGRP-852 and Virginizer (VGN). The lines were sequenced deeply giving between 54M and 92M reads to achieve a whole genome coverage that ranged between 74X and 125X. The sequencing was used for de novo genotyping.
Project description:Purpose: Gene expression analysis of knockdown and overexpression of LBH (Limb-Bud-and-Heart) in human breast cancer cell lines using RNA-Seq Methods: RNA was collected and analyzed from three biological replicates of each condition (LBH vs vector) for LBH overexpression (OE) in two human breast cancer cell lines (BT549, MCF7). Additionally, RNA was collected and analyzed from three biological replicates of each condition (siLBH vs non-target/NT siRNA) for LBH knockdown (KD) in two human triple negative breast cancer cells lines (HCC1395, MDA-MB-231). High-throughput sequencing used Illumina platforms. Results: Using an optimized data analysis workflow, we mapped about 60 million sequence reads per sample to the human genome (build hg19). Conclusions: Our study represents the first gene profiling analysis of LBH transcriptomes in human breast cancer cell lines, with biologic replicates, generated by RNA-seq technology.
Project description:P53 mutation is closely associated with the occurrence and progression of colon cancer. In this project, we did crotonylomics sequencing by using human colon cancer homologous cell line pair-HCT116+/+(with wild type p53) and HCT116-/- (with null p53). Crotonylomics sequencing results showed that p53 deficiency regulated crotonylation of non-histone proteins.
Project description:This study presents a comparison of small RNA sequencing libraries generated from the same cell lines but using different sequencing platforms and protocols. The samples were analyzed and compared at the level of miRNAs expression and as a population of small RNAs derived from repetitive elements. Despite a good correlation between sequencing platforms, there are qualitative and quantitative variations in the results depending on the protocol used. 10 samples were examined: 6 from the ES E14 XY cell type: 1 454, 2 SOLiD from 2 technological versions, and 3 SOLEXA from 3 different protocols, and 4 samples from ES PGK XX cells: 1 454 and 1 SOLEXA sample, and 2 SOLiD samples from 2 technological versions.