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Sample GSM3554070 Query DataSets for GSM3554070
Status Public on Apr 08, 2019
Title Ctrl_IPF
Sample type SRA
 
Source name Fibroblasts
Organism Homo sapiens
Characteristics source subject age: 83-year-old
gender: male
tissue: Lung
cell line: Diseased Human Lung Fibroblasts, Idiopathic Pulmonary Fibrosis (DHLF-IPF)
treatment: none (control)
Treatment protocol Nintedanib (BIBF1120, Catalog No. S1010), purchased from Selleckchem (Houston, TX, USA), was dissolved in dimethyl sulfoxide (DMSO) (Sigma Chemical Co., St. Louis, MO, USA) to obtain various concentrations. The reagents were stored at -20°C until use in the experiments. In nintedanib-treated cultures, cells were treated with 1 μM, 2 μM, and 4 μM nintedanib for 24 h, 48 h, and 72 h. In control cultures, cells were treated with the carrier solvent (0.1% DMSO).
Growth protocol Human IPF lung fibroblasts (Disease Human Lung Fibroblasts, Idiopathic Pulmonary Fibrosis. Catalog No. CC-7231), purchased from Lonza Inc. (Walkersville, MD, USA), were incubated at 37°C in a 5% CO2-containing incubator in FGM™-2 Fibroblast Growth Medium-2 Bulletkit™ (Lonza, Catalog No. CC-3132) containing 0.5 mL human fibroblast growth factor-basic (hFGF-B), 0.5 mL insulin, 10 mL fetal bovine serum, and 0.5 mL GA-1000. The medium was changed every 2-3 days and the cells were passaged at 80-90% confluence for the following experiments.
Extracted molecule total RNA
Extraction protocol total RNAs from Ctrl_IPF fibroblasts, Nintedanib_2uM_IPF fibroblasts and Nintedanib_4uM_IPF fibroblasts were extracted by Trizol Reagent according to the manufacturer’s instructions.
All RNA Sample preparation procedures were carried out according to the official Illumina protocol. Agilent's SureSelect Strand-Specific RNA Library Preparation Kitwere used for library construction followed by AMPure XP Beads size selection. The sequence was directly determined using Illumina's sequencing-by-synthesis (SBS) technology. Sequencing data (FASTQ files) were generated by Welgene's pipeline based on Illumina's basecalling program bcl2fastq v2.2.0.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing Illumina official tool, BCL2FASTQ conversion Software v2.20 was used to convert BCL files from the Illumina sequencing platform.
TRIMMOMATIC v0.36 was used to remove adaptors and trim low quality bases.
Trimmed reads were aligned to the reference genome sequence using HISAT2 v2.1.0 aligner to produce SAM file and then converted to sorted BAM files using SAMTOOLS v1.2.
Differential expression analysis was performed using CUFFDIFF of CUFFLINKS package v2.2.1 to produce gene/transcript read count and FPKM profiles for each group of samples, then functional enrichment assay was performed using clusterProfiler v3.6.
Genome_build: GRCh38.p10
Supplementary_files_format_and_content: excel files include gene ID, gene type, gene name, EntrezGene ID, locus and FPKM values for each samples
 
Submission date Jan 08, 2019
Last update date Apr 08, 2019
Contact name Wei An Chang
E-mail(s) 960215kmuh@gmail.com
Phone +886-982202456
Organization name Kaohsiung Medical University
Street address No.100, Shihcyuan 1st Rd., Sanmin Dist., Kaohsiung City 80708, Taiwan (R.O.C.)
City Kaohsiung
ZIP/Postal code 80708
Country Taiwan
 
Platform ID GPL24676
Series (2)
GSE124786 Gene Expression Changes Associated with Nintedanib Treatment in Idiopathic Pulmonary Fibrosis Fibroblasts [RNA-seq]
GSE124788 Gene Expression Changes Associated with Nintedanib Treatment in Idiopathic Pulmonary Fibrosis Fibroblasts
Relations
BioSample SAMN10713577
SRA SRX5226958

Supplementary file Size Download File type/resource
GSM3554070_Ctrl_IPF_fibroblasts_mRNA.xlsx 3.1 Mb (ftp)(http) XLSX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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