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Sample GSM3562000 Query DataSets for GSM3562000
Status Public on May 27, 2020
Title Sample_kidney_SHAM_veh_d2_rep2
Sample type SRA
Source name Kidney Cortex
Organism Mus musculus
Characteristics strain: C57BL/6
agent: Sham
genotype: wild-type
tissue: Kidney Cortex
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
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.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
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
Submission date Jan 14, 2019
Last update date May 27, 2020
Contact name Michaela Willi
Organization name NIH
Department NIDDK
Street address 9000 Rockville Pike
City Bethesda
ZIP/Postal code 20814
Country USA
Platform ID GPL21493
Series (2)
GSE114294 Enhancer Regulation in Kidney Repair
GSE125056 Enhancer Regulation in Kidney Repair [RNA-Seq 2]
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 SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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