Project description:We measured 720 HeLa-CCL2 cells (288 from the 9th passage, 288 from the 14th passage and 144 from the 20th passage) in this work on an Illumina HiSeq 4000 platform (sequenced by Novogene, China) for 150 bp paired-end sequencing. The protocol was based on Tang’s modification on SMART-Seq2. Single cells were captured by mouth pipette under the stereomicroscope(Nikon SZM745)and followed by the protocol. Every cell was assigned with 250 M raw data on average.
Project description:1.Comparison of chromatin occupancy of H2BUb and RNA Polymerase II in SHP-1 WT and KO MCF7 cells. Paired end sequencing (2X100 bp) was performed on the Illumina HiSeq X ten. 2.Identification of the SHP-1 binding site in MCF7 cells using ChIP Seq. Paired end sequencing (2X100 bp) was performed on the Illumina Nextseq 2000 platform.
Project description:RNA sequencing was performed on bladder tumor and normal urothelial tissues to investigate gene expression differences between the two groups. A total of 22 samples (11 tumor and 11 normal samples) were included. Libraries were prepared and sequenced using the Illumina NovaseqTM 6000 platform with paired-end sequencing.
Project description:Purpose:The goals of this study are to MS (mechanical stress) how to change the cellular pathway of hLFSCs (human ligament flavum stem cells). Methods: Extract hLFSCs from the ligament flavum of patients.Treat the cells with and without (in control)MS.Total RNA was extracted from cells with Tripure Isolation Reagent.Subsequently, RNA was purified through rRNA depletion and then subjected to cDNA synthesis and RNA amplification. Next, random hexamer primer cDNA libraries were evaluated using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) and sequenced on Illumina Hiseq 4000 sequencing platform (Illumina, San Diego, California, USA) following the manufacturer’s instructions for paired-end 150 bp reads (Lifegenes, Shanghai, China).
2021-10-13 | GSE185614 | GEO
Project description:Illumina NextSeq 500 paired end sequencing
Project description:We sought to explore the underlying mechanisms by which MCUR1 promotes erythropoiesis. Total RNAs were extracted from cultured human CD34+ HPCs stably expressing sh-MCUR1 or sh-Ctrl under hypoxia (1% O2) following 2 days of EPO stimulation, using TRIZOL Reagent (Invitrogen, CA, USA). RNA sequencing (RNA-seq) was performed using Illumina NovaSeq6000 at Berry Genomics Co. Ltd. (Beijing, China), and a mean of 40 million paired-end reads per sample was obtained.
Project description:Next-Generation-Sequencing (NGS) technologies have led to important improvement in the detection of new or unrecognized infective agents, related to infectious diseases. In this context, NGS high-throughput technology can be used to achieve a comprehensive and unbiased sequencing of the nucleic acids present in a clinical sample (i.e. tissues). Metagenomic shotgun sequencing has emerged as powerful high-throughput approaches to analyze and survey microbial composition in the field of infectious diseases. By directly sequencing millions of nucleic acid molecules in a sample and matching the sequences to those available in databases, pathogens of an infectious disease can be inferred. Despite the large amount of metagenomic shotgun data produced, there is a lack of a comprehensive and easy-use pipeline for data analysis that avoid annoying and complicated bioinformatics steps. Here we present HOME-BIO, a modular and exhaustive pipeline for analysis of biological entity estimation, specific designed for shotgun sequenced clinical samples. HOME-BIO analysis provides comprehensive taxonomy classification by querying different source database and carry out main steps in metagenomic investigation. HOME-BIO is a powerful tool in the hand of biologist without computational experience, which are focused on metagenomic analysis. Its easy-to-use intrinsic characteristic allows users to simply import raw sequenced reads file and obtain taxonomy profile of their samples.