ASC-J9 blocks STAT3 signaling, cell proliferation, collagen synthesis, inflammation, and ROS generation in keloid fibroblasts
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE198095 | GEO | 2022/06/01
REPOSITORIES: GEO
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2020-03-09 | GSE139505 | GEO
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2017-12-01 | GSE101928 | GEO
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2017-07-12 | GSE98034 | GEO
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2017-12-19 | E-MTAB-4182 | biostudies-arrayexpress
Project description:RNAseq analysis between control (normoxia) and hypoxic mice +/- bacterial infection. Murine peripheral blood leukocytes (1x10^6/condition) were lysed and RNA extracted using Qiagen mini total RNA isolation protocols (Qiagen, Germany). Samples were treated with DNase (Ambion), and sample integrity verified on the Agilent Bioanalyser with the RNA Nano chip. Illumina Tru-seq paired end strand specific sequencing (Illumina, USA) was carried out by on a NextSeq-550 sequencer (Edinburgh Clinical Research Facility, Western General Hospital, Edinburgh, Scotland, UK). 500ng of Total RNA underwent ribosomal RNA depletion (rRNA) prior to purification, fragmentation, random hexamer cDNA generation and purification with AMPure XP beads (Beckman-Coulter, USA). Multiple indexing adapters were ligated to ds cDNA with subsequent hybridisation onto flow cells, and DNA fragment enrichment by 15 cycle PCR for sequencing. Completed libraries were quantified by qPCR using the KAPA Illumina Library Quantification Kit (Illumina, USA) before multiplexing in two equimolar pools and running on two flow cells on the Illumina NextSeq 550. The resulting FastQ files were mapped to the reference genome (mm9) using the Tophat alignment tool (V1) on Illumina Basespace software and reads per kilobase per million (RPKM) scores calculated.
2017-03-22 | GSE79484 | GEO
Project description:Purpose: Circulating hematopoietic stem/progenitor cells (cHSPCs) are rare in normal human peripheral blood (PB) without mobilization. We apply a novel three-dimension culture system (3DCS) seeded with no mobilized PB monocytes (PBMNCs), to expand cHSPCs. Two-dimension culture system (2DCS), primary PBMNCs and CD34+ HSPCs derived from bone marrow serves as system, negative and positive control groups respectively. Bulk RNA sequencing analysis is performed to dissect the function and molecular mechanism for cHSPCs. Methods: Four groups are designed in the study including the samples cultured in 2DCS, cultured in 3DCS, normal primary PBMNCs and CD34+ HSPCs derived from mobilized peripheral blood. Total RNA was extracted from the cells followed by mRNA enrichment with poly-T oligo-attached magnetic beads. Cells from 2DCS and normal primary PBMNCs served as controls (the number of repetitions for the groups, n = 3). Mobilized bone marrow-derived CD34+ HSPCs were purified with EasySep Human CD34 Positive Selection Kit (StemCell Technologies) serving as positive control (n = 4). Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit (NEB, Illumina®, USA) following manufacturer’s recommendations. Index codes were added to attribute sequences to each sample. Preferential 150~200 bp in length of cDNA fragments were selected and purified with AMPure XP system (Beckman Coulter, Beverly, USA). PCR was performed with Phusion High-Fidelity DNA polymerase, universal PCR primers and index (X) Primer after adaptor of cDNA being ligated with USER Enzyme (NEB, USA). At last, PCR products were purified with AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded products was carried out on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufacturer’s instructions. Sequencing raw data were generated using the Illumina HiSeqTM platform, and 125 bp/150 bp paired-end reads were selected. Results: Bulk RNA sequencing analysis reveals that the samples in 3DCS have more similarity expression pattern with CD34+ hematopoietic stem/progenitor cells (HSPCs) than ones in 2DCS and PBMNCs, for their expression higher level of the specific hematopoietic stem signatures including core stem transcription factors (TFs) as Runx1, HoxA9, HoxB4 and GATA2, self-renewal genes, surface epitopes, and some signaling pathways essential for HSPC fate determination. This study provides a novel culture system to expand rare cHSPC in normal PB, and the underlying molecular and functional signatures are dissected. Conclusions: Our study demonstrates the first detailed analysis of normal peripheral blood-derived cHSPC transcriptomes based on RNA-seq technology. Our results show that 3DCS facilitates to expand the rare circulating HSPCs with repopulating capacity. The underlying molecular and functional signatures of cHSPCs are dissected. The study provides a platform for normal PB further clinical applications in cell transplantation and personalized precision medicine.
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2017-09-08 | GSE98074 | GEO
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2018-10-29 | GSE111881 | GEO
Project description:The goal of this study is to investigate the differential transcripted genes affected by CRISPR induced endoglin knockout in PASMC cells. Total RNA was purified from NTC or ENG-/- PASMC cells using RNeasy Mini Kit (Qiagen, Hilden, Germany). RNA quality and concentration were assessed with Agilent Tapestation 200 (Agilent Technologies) and Qubit 2.0 (ThermoFisher Scientific). ~250-500 ng RNA were used for library construction. The NGS libraries were constructed using the KAPA Stranded mRNA-Seq Kits (KapaBioSystems). mRNA was captured using magnetic oligo-dT beads and 1st strand cDNA was synthesized using random priming. In order to preserve strand-specificity, 2nd strand synthesis, which converts the cDNA:RNA hybrid to double-stranded cDNA (dscDNA), was marked by dUTP incorporation. cDNA framents were A-tailed by adding dAMP to the 3'-ends of the dscDNA library fragments. dsDNA Illumina TruSeq "forkedâ adapters 3'-dTMP overhangs were then ligated to A-tailed library insert fragments. Each of the six libraries were ligated with a unique Truseq 6bp barcode. Library fragments were amplified using the KAPA HiFi HotStart polymerase. The strand marked with dUTP was not amplified, allowing strand-specific sequencing. Fragment length and library quality was assessed on a 2100 Bioanalyzer using the High Sensitivity DNA Kit (Agilent Technologies). Libraries were diluted to 10nM and pooled at equimolar ratios. The pool was then diluted to 2nM and denatured in NaOH following Illumina recommendations. 10pM of denatured library pool was loaded in one HiSeq lane and flowcell was clustered on the Illumina C-bot. 5% PhiX control was spiked-in. The flowcell was sequenced on a HiSeq 2500 V4 chemistry with 50bp Single read protocol. Data was demultiplexed and Fastq files were generated using BcptoFastq 1.8.4 script provided by Illumina.
2017-05-16 | E-GEOD-78271 | biostudies-arrayexpress