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Single cell RNAseq reconstruct normal and IPF lung epithelium

ABSTRACT: Single cell RNAseq reconstruct normal and IPF lung epithelium

PROVIDER: PRJNA612553 | ENA |

REPOSITORIES: ENA

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	SRR11306531.fastq.gz	Fastqsanger.gz

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Single cell RNAseq reconstruct normal and IPF lung epithelium

Project description:Tissue fibrosis is a common pathological outcome of chronic disease that markedly impairs organ function leading to morbidity and mortality. In the lung, idiopathic pulmonary fibrosis (IPF) is an insidious and fatal interstitial lung disease associated with declining pulmonary function. Single cell RNA sequencing was used to map epithelial cell types of the normal human airway and alveolaor as well as IPF explant tissue.

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Project description:Genome wide DNA methylation profiling of normal and IPF lung samples. The Illumina human methylation 27 Beadchip was used to obtain DNA methylation profiles across approximately 27,000 CpGs samples. 2 normal samples, and 4 IPF samples Bisulphite converted DNA from the 12 samples were hybridised to the Illumina Infinium 27k Human Methylation Beadchip v1.2

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Project description:Idiopathic pulmonary fibrosis (IPF) is a progressive lethal interstitial lung disease of unkown etiology with limited effective therapies. The pathogenic mechanisms of IPF remain unkown. Emerging evidences indicate that abnormal behaviors of fibroblasts in IPF are associated with a variety of genetic alterations and aberrant reactivation of developmental signaling pathways. We compared gene expression profiles in fibrotic lung tissues from IPF patients and normal lung tissues from patients with primary spontaneous pneumothorax using cDNA microarray to examine the mechnisms involved in the pathogenesis of IPF.

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Project description:Objective: To evaluate the characteristics of IPF lungs in fibroblasts, we performed RNA-Sequencing of fibroblasts derived from normal and IPF lungs Method:　NHLF（Normal human lung fibroblast）　and DHLF-IPF (DIPF; Diseased human lung fibroblasts derived from idiopathic pulmonary fibrosis)　were purchased from Lonza (Walkersville, MD, USA) .Total RNA was extracted from fibroblasts (NHLF and DIPF) using an RNeasy® Mini Kit (#74106; Qiagen, Valencia, CA, USA). Preparation of a next-generation sequencing library was performed using a SMARTer® Stranded Total RNA Sample Prep Kit–Pico Input Mammalian (TaKaRa, Shiga, Japan). Sequencing was performed on an Illumina HiSeq 2500 platform in 75-base single-end mode with Illumina Casava 1.8.2 software for base calling. Sequenced reads were mapped to the human reference genome sequence (hg19) using TopHat v.2.0.13 software, in combination with Bowtie 2 v.2.2.3 and SAMtools v.0.1.19. Result: Of the 26,257 genes analyzed, for NHLF and DHLF-IPF (DIPF), FPKM was required to be greater than or equal to 0.3. Under these conditions, 764 genes were up regulated inDHLF-IPF (DIPF) and 691 genes were down regulated.

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