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| Status |
Public on May 27, 2020 |
| Title |
Sample_kidney_SHAM_veh_d2_rep2 |
| Sample type |
SRA |
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| Source name |
Kidney Cortex
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
agent: Sham
genotype: wild-type
tissue: Kidney Cortex
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| Treatment protocol |
Male C57bl/6 mice, 10-12 weeks old, were randomly assigned to vehicle and JQ1 treatment before SHAM surgery, kidney cortex were harvested 48 hours after surgery
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from kidney cortex samples with the PureLink RNA Mini Kit (Thermo Fisher Scientific, 12183018A), Libraries for next generation sequencing were prepared with Kit, TruSeq RNA SMP Prep Kit-v2 (Illumina, RS-122-2001) and sequenced on HiSeq 3000 machine (Illumina).
Libraries for sequencing were prepared using standard Illumina protocols.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
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| Data processing |
RNA-seq data were trimmed using trimmomatic (Bolger et al., Bioinformatics, 2014) and subsequently aligned to the reference genome mm10 applying STAR RNA-seq aligner (Dobin et al., Bioinformatics, 2013). HTSeq(Anders et al., Bioinformatics, 2015) was applied for obtain HTSeq counts.
Genome_build: mm10
Supplementary_files_format_and_content: HTSeq counts from RNA-seq samples
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| Submission date |
Jan 14, 2019 |
| Last update date |
May 27, 2020 |
| Contact name |
Michaela Willi |
| Organization name |
NIH
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| Department |
NIDDK
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| Street address |
9000 Rockville Pike
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| City |
Bethesda |
| ZIP/Postal code |
20814 |
| Country |
USA |
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| Platform ID |
GPL21493 |
| Series (2) |
| GSE114294 |
Enhancer Regulation in Kidney Repair |
| GSE125056 |
Enhancer Regulation in Kidney Repair [RNA-Seq 2] |
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| Relations |
| BioSample |
SAMN10741723 |
| SRA |
SRX5248060 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3562000_Sample_kidney_SHAM_veh_d2_rep2.txt.gz |
101.6 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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