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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Feb 27, 2024 |
| Title |
Kidney, Foxp1-deficient 2 |
| Sample type |
SRA |
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| Source name |
Kidney
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| Organism |
Mus musculus |
| Characteristics |
tissue: Kidney
cell line: Cdh16-cre
cell type: kidney tubular cells
genotype: Foxp1_KO
treatment: chronic acid load
rip antibody: anti-HA antibody
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| Treatment protocol |
Samples were then centrifuged at 10,000g for 10 min to collect a post-mitochondrial supernatant. 25μl of washed anti-HA antibody-conjugated magnetic beads (Thermo ScientificTM; 88836) was added to the supernatant and incubated on an orbital shaker at 4°C overnight. The following day, samples were washed four times for 5 min in high salt buffer (50 mM Tris, pH 7.5, 300 mM KCl, 12 mM MgCl2, 1% Nonidet P-40, 1 mM DTT, 100 μg/mL cycloheximide) in a magnet on ice. After washing, the beads were resuspended in 500ul TRIzol® Reagent for total RNA isolation according the manufacturer’s instructions (Invitrogen).
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| Growth protocol |
Neonatal littermate control (Cdh16Cre;Foxp1fl/+;RiboTag) and Foxp1-deficient (Cdh16Cre;Foxp1fl/fl;RiboTag) animals were used for polysomes isolation analysis. Mice after hypothermic anaesthesia were perfused with PBS. The kidneys were quickly removed, homogenized in 400μl polysome buffer (50mM Tris, pH 7.5, 100mM KCl, 12mM MgCl2, 1% Nonidet P-40, 1mM DTT, 200U/ml RNasin (N2615; Promega), 1 mg/ml heparin, 100μg/ml cyclohexamide, and 1 x protease inhibitor (Roche; 04693132001)) using pellet pestles.
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| Extracted molecule |
total RNA |
| Extraction protocol |
The total RNA quality was determined by 2100 Bioanalyzer (Agilent) and quantified using the ND-2000 (NanoDrop Technologies).
RNA-seq transcriptome library was prepared following TruSeqTM RNA sample preparation Kit from Illumina (San Diego, CA) according to the manufacturer’s instructions.
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| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Illumina HiSeq xten/NovaSeq 6000 sequencer
The raw paired-end reads were quality checked by FastQC (https://github.com/s-andrews/FastQC) and trimmed to remove adaptor sequences and low-quality reads using Trimmomatic with the default setting.
Then clean reads were mapped to the mouse reference genome GRCm38.86 using the STAR aligner. Only uniquely mapped reads were selected by SAMtools to minimize the rate of false positives.
Deeptools was used to generate a bigwig format to facilitate visualization of the reads coverage and comparison among different samples.
To identify differential expression genes (DEGs) between two different conditions, the raw read count file generated by featureCounts was used as an input for DESeq2, followed by standard differential expression analysis. Genes with Q value≤ 0.05 and |log2FC|>1 (DESeq2) were considered to be significantly different expressed genes.
Gene Ontology (GO) functional-enrichment analysis was performed using the R package clusterProfiler to identify which DEGs were significantly enriched in GO terms and metabolic pathways at Bonferroni-corrected P-value ≤0.05 compared with all the expressed genes as background.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes the raw read count file generated by featureCounts
Supplementary files format and content: bigwig files to view the data
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| Submission date |
Jul 26, 2023 |
| Last update date |
Feb 27, 2024 |
| Contact name |
RENHUA SONG |
| E-mail(s) |
Renhua.song1989@gmail.com
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| Phone |
61452667663
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| Organization name |
Centenary Institute
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| Lab |
Epigenetics and RNA Biology Program
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| Street address |
Charles Perkins Centre - D17, Level 4 West. The University of Sydney Johns Hopkins Drive
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| City |
Camperdown |
| State/province |
NSW |
| ZIP/Postal code |
2050 |
| Country |
Australia |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE238266 |
Identification of expression patterns of FoxP1 in the kidneys using RiboTag mice and RNA sequencing |
| GSE238268 |
Foxp1 is required for renal intercalated cell differentiation and acid-base regulation |
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| Relations |
| BioSample |
SAMN36708620 |
| SRA |
SRX21159269 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7661287_KO2.bw |
12.5 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
| Processed data provided as supplementary file |
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