|
|
GEO help: Mouse over screen elements for information. |
|
Status |
Public on Jul 13, 2024 |
Title |
Prog-Tg endothelial cells, microRNA, replicate 3 |
Sample type |
SRA |
|
|
Source name |
Lung, (age 10-15 days)
|
Organism |
Mus musculus |
Characteristics |
tissue: Lung, (age 10-15 days) cell line: primary endothelial cells cell type: endothelial cells genotype: Prog-Tg treatment: Cdh5TA+TetOp-LAG608G minigene molecule subtype: small RNA
|
Treatment protocol |
no treatment
|
Growth protocol |
Endothelial cells were cultured in DMEM supplemented with 20% FCS, EC growth supplement (CellBiologics Catalog No 1166), 25 mM HEPES, 50 U/ml penicillin, 50 μg/ml streptomycin, 2 mM L-glutamine, 1 mM nonessential amino acids, 1 mM sodium pyruvate, and 139 μg/ml heparin (complete culture medium) and were used at passage 3 forpreparation of RNA extracts.
|
Extracted molecule |
other |
Extraction protocol |
RNA extracts were prepared using miRNeasy Mini Kit (Qiagen 217084) For mRNA (with parallel isolation of microRNA libraries) from endothelial cells polyA enrichment was performed for mRNAs from 100 ng total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module according to the manufacturer's instructions. Library preparation of polyA+ enriched RNA was performed with the NEBNext UltraII Directional RNA library Kit from Illumina. microRNA libraries from endothelial cells were prepared from 100 ng total RNA with the QIAseq miRNA library Kit according to the manufacturer's instructions small RNA libraries from supernatants of endothelial cells and mouse plasma were prepared using CleanTag™ Small RNA Library Preparation Kit Catalog # L-3206.
|
|
|
Library strategy |
miRNA-Seq |
Library source |
other |
Library selection |
size fractionation |
Instrument model |
Illumina HiSeq 2000 |
|
|
Description |
54374 Counts_miRNA.xlsx miRNA_Pr_vs_WT.xlsx
|
Data processing |
Sequencing reads were aligned against the mus musculus reference genome (GRCm38 release) (https://doi.org/10.1093/nar/gkx1098) with STAR (https://doi.org/10.1093/bioinformatics/bts635), version 2.5.1b using 2-pass alignment mode. Gencode v4 annotation was used in the alignment. TMM normalisation method of the edgeR (https://doi.org/10.1093/bioinformatics/btp616), R/Bioconductor package (R version 3.3.2, Bioconductor version 2.12) was applied. The short sequencing reads were aligned against the reference genome using Gencode v4 annotation with 2-pass alignment mode of STAR v2.5.1b. After alignment, the short reads were associated with known genes, and the number of reads aligned within each gene was counted using HTSeq v0.5.4p3. The data was normalised to remove variation between samples caused by non-biological reasons and to make the values comparable across the sample set using the TMM normalisation method of the edgeR. For differential expression analyses, the data were further log transformed using the voom approach, and the R package limma was used to perform the statistical testing. Assembly: mus musculus reference genome (GRCm38 release) (https://doi.org/10.1093/nar/gkx1098) Supplementary files format and content: Excel files starting with Counts contains the number of raw counts for each gene for each sample. Supplementary files format and content: The rest of the Excel files (which do not start with Counts) contain differential expression results between each comparison pair using 3 replicates of each sample versus Wild Type.
|
|
|
Submission date |
Jul 13, 2024 |
Last update date |
Jul 13, 2024 |
Contact name |
Roland Foisner |
Organization name |
Max Perutz Labs, Medical University of Vienna
|
Department |
Center for Medical Biochemistry
|
Lab |
Roland Foisner
|
Street address |
Dr.-Bohr-Gasse 9
|
City |
Vienna |
ZIP/Postal code |
1030 |
Country |
Austria |
|
|
Platform ID |
GPL13112 |
Series (1) |
GSE272195 |
Endothelial and systemic upregulation of miR-34a-5p fine-tunes senescence in progeria |
|
Relations |
BioSample |
SAMN42484151 |
SRA |
SRX25319437 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
|
|
|
|
|