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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jan 18, 2023 |
| Title |
UB cells,cKO,E16.5,biol rep 2 [B_2] |
| Sample type |
SRA |
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| Source name |
ureteric bud,FACS-sorted,E16.5
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| Organism |
Mus musculus |
| Characteristics |
tissue: ureteric bud,FACS-sorted,E16.5
cell type: intermediate mesoderm epithelial cells
genotype: Hoxb7Cre-GFP+,Ash2l F/F
treatment: no treatment
age: E16.5
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using mirVana miRNA Isolation Kit (Ambion).
RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Then the libraries were constructed using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions. The transcriptome sequencing and analysis were conducted by OE Biotech Co., Ltd. (Shanghai, China).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
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| Data processing |
The clean reads were mapped to the mouse genome (GRCm39) using HISAT2 . FPKM of each gene was calculated using Cufflinks , and the read counts of each gene were obtained by HTSeq_x0002_count. Differential expression analysis was performed using the DESeq (2012) R package. P value < 0.05 and foldchange > 1.5 or foldchange < 0.67 was set as the threshold for significantly differential expression. Hierarchical cluster analysis of differentially expressed genes (DEGs) was performed to demonstrate the expression pattern of genes in different groups and samples. GO enrichment and KEGG pathway enrichment analysis of DEGs were performed respectively using R based on the hypergeometric distribution.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
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| Submission date |
Jul 15, 2022 |
| Last update date |
Jan 18, 2023 |
| Contact name |
Ziyi Zhao |
| E-mail(s) |
nephox@sjtu.edu.cn
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| Organization name |
Shanghai jiaotong university school of medicine
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| Street address |
320 Yueyang Road
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| City |
Shanghai |
| ZIP/Postal code |
200031 |
| Country |
China |
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| Platform ID |
GPL21273 |
| Series (2) |
| GSE208274 |
ASH2L controls ureteric bud morphogenesis via regulation of RET/GFRA1 signaling activity [RNA-seq] |
| GSE208275 |
ASH2L controls ureteric bud morphogenesis via regulation of RET/GFRA1 signaling activity |
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| Relations |
| BioSample |
SAMN29765766 |
| SRA |
SRX16252989 |
| 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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