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RNA-seq profiling of fibroblasts isolated from two distinct lung metastases stages and from normal lungs

ABSTRACT: RNA-seq profiling of fibroblasts isolated from two distinct lung metastases stages and from normal lungs

PROVIDER: PRJNA529667 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8799800.fastq.gz	Fastqsanger.gz
	SRR8799801.fastq.gz	Fastqsanger.gz
	SRR8799802.fastq.gz	Fastqsanger.gz
	SRR8799803.fastq.gz	Fastqsanger.gz
	SRR8799804.fastq.gz	Fastqsanger.gz

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RNA-seq profiling of fibroblasts isolated from two distinct lung metastases stages and from normal lungs

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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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Mesenchymal–Epithelial Transition in fibroblasts of human normal lungs and interstitial lung diseases

Project description:To evaluate the possible occurrence of MET, fibroblasts from normal lungs and from interstitial lung diseases were cultured under standard conditions. When was observed an unusual epithelial-like phenotypic change gene expression was evaluated by complete transcriptome microarrays.

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