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| Status |
Public on Jul 11, 2020 |
| Title |
NC_Rep3 |
| Sample type |
SRA |
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| Source name |
Human myofibroblasts
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| Organism |
Homo sapiens |
| Characteristics |
strain: Lung of Idiopathic pulmonary fibrosis patient
tissue: Lung
cell type: myofibroblasts
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| Treatment protocol |
Expanded myofibroblasts at passage 5 were used for the following experiments. After 24 h of serum deprivation in DMEM containing 0.2% fat-free bovine serum albumin, myofibroblasts were treated with or without JQ1 (1 µM) for a further 48 h.
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| Growth protocol |
Lung tissue from a 46-y old male patient who underwent lung transplantation by reason of severe IPF (usual interstitial pneumonia pattern) was obtained after surgery. The patient provided informed consent, and the study was approved by the Ethics Committee of Chiba University, Graduate School of Medicine and Hospital, Japan. Lung tissue was minced into small pieces, and then were incubated in DMEM supplemented with 1 mg/ml collagenase type I, 0.5 mg/ml dispase, 2 U/ml DNase, 0.1 mg/ml streptomycin, and 100 U/ml penicillin at 37°C for 15 min with gentle shaking. After washing twice with DMEM, the resulting pieces were transferred to a 90 mm-culture dish and were dipped with culture medium (10% FBS in DMEM supplemented with streptomycin and penicillin) and cultured at 37°C and 5% CO2. Outgrowth of cells was monitored daily with changing the culture medium every 4 d. When the dish reached confluence (about 14 days in vitro), outgrown cells were harvested as cells at passage 0. Expanded cells at passage 3 were subjected to the immunofluorescent study to verify population of α-SMAhighED-A-FN+S100A4- cells as myofibroblasts. More than 90% of the cells were myofibroblasts.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA of the cells was extracted using ISOGEN plus (Nippon Gene, Toyama, Japan) according to manufacturer instructions. 500 ng of total RNA were ribosomal RNA-depleted using NEBNext rRNA Depletion Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Reads were mapped on hg19 human reference genome and quantified using CLC Genomics Workbench version 10.1.1 (Qiagen).
Read counts were normalized by calculating number of reads per kilobase per million (RPKM) for each transcript in individual samples using the CLC Genomic Workbench software version 12.0. (Qiagen).
Filtering characteristics of fold-change -2 to 2 (false discovery rate (FDR) at P < 0.05) were used to identify the DEGs.
Genome_build: hg19
Supplementary_files_format_and_content: Excel file includes raw read counts and RPKM normalized values for all genes from each sample.
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| Submission date |
Nov 15, 2019 |
| Last update date |
Jul 11, 2020 |
| Contact name |
Yoshitoshi Kasuya |
| Organization name |
Chiba Univ.
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| Department |
Grad. Sch. Med
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| Lab |
Biomedical Sci.
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| Street address |
1-8-1 Inohana Chuo-ku
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| City |
Chiba |
| ZIP/Postal code |
260-8670 |
| Country |
Japan |
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| Platform ID |
GPL18573 |
| Series (2) |
| GSE140476 |
Comprehensive transcriptome analysis of human myofibroblasts with/without the JQ-1 treatment [mRNA] |
| GSE140477 |
Comprehensive transcriptome analysis of human myofibroblasts with/without the JQ-1 treatment |
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| Relations |
| BioSample |
SAMN13293089 |
| SRA |
SRX7157011 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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