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| Status |
Public on Mar 30, 2021 |
| Title |
SRSF6 KD+Bleomycin 1 |
| Sample type |
SRA |
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| Source name |
Mesothelial cells
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| Organism |
Homo sapiens |
| Characteristics |
tissue: mesothelium
cell type: epithelial virus transformed
transfection: SRSF6 siRNA for 48 h
treatment: incubated with bleomycin (0.2 µg/ml) for 24 h
cell line: Met-5A
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| Treatment protocol |
After transfection with SRSF6 siRNAs or negative control siRNAs, Met-5A were incubated with bleomycin (0.2 µg/ml) for 24 h.
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| Growth protocol |
The human PMC line Met-5A was obtained from the American Type Culture Collection (ATCC, Manassas, VA, USA). PMCs were cultured in RPMI 1640 medium (Gibco, Grand Island, NY, USA) supplemented with 10% fetal bovine serum (FBS).Culture media contained 100 U/ml penicillin and 100 μg/ml streptomycin and maintained at 37 °C in a humidified atmosphere containing 5% CO2. The cells were sub-cultured at 1:3 ratios, and culture medium was changed every 2 days.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s protocol. The samples were assessed with Agilent 2100 BioAnalyzer (Agilent Technologies, Santa Clara, CA, USA) and Qubit Fluorometer (Invitrogen).
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 NovaSeq 6000 |
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| Data processing |
The genome of human genome version of hg38 was used as reference. The sequencing quality were assessed with FastQC (v0.11.5) and then low quality data were filtered using NGSQC (v2.3.3).The clean reads were then aligned to the reference genome using HISAT2 (v2.1.0) with default parameters.
The processed reads from each sample were aligned using HISAT2 against the reference genome. The gene expression analyses were performed with StringTie (v1.3.3b). DESeq(v1.28.0) was used to analyze the DEGs between samples
Then a p-value was obtained, which was corrected by FDR method. And Corrected P-value (q-value) was calculated by correcting using BH method. p-value or q-value were used to conduct significance analysis. Parameters for classifying significantly DEGs are ≥2-fold differences (|log2FC|≥1, FC: the fold change of expressions) in the transcript abundance and p ≤ 0.05.
The annotation of the DEGs were perfomed based on the information obtained from the database of ENSEMBL, NCBI, Uniprot, GO, and KEGG.
Genome_build: Homo_sapiens.GRCh38.dna.toplevel.REF.fa
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample. Matrix table with raw gene counts for every gene and every sample.
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| Submission date |
Mar 09, 2021 |
| Last update date |
Mar 30, 2021 |
| Contact name |
Li-Mei Liang |
| E-mail(s) |
d201881384@sina.com
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| Organization name |
Huazhong University of Science and Technology
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| Department |
Department of Respiratory and Critical Care Medicine, Union Hospital
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| Lab |
Key Laboratory of Respiratory Diseases, Ministry of Health of China
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| Street address |
1277 JieFang Avenue
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| City |
Wuhan |
| State/province |
Hubei |
| ZIP/Postal code |
430030 |
| Country |
China |
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| Platform ID |
GPL27644 |
| Series (1) |
| GSE168578 |
Identification of SRSF6 downstream regulatory genes and its impact on pleural fibrosis progression |
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| Relations |
| BioSample |
SAMN18148002 |
| SRA |
SRX10243669 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5149186_SRSF6_KD+Bleomycin_1.txt.gz |
164.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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