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Sample GSM3825519 Query DataSets for GSM3825519
Status Public on Sep 14, 2021
Title ZT4RL
Sample type SRA
 
Source name kidney
Organism Mus musculus
Characteristics diagnosis: Young
time: ZT4
tissue: kidney
strain: NZB/W F1
Extracted molecule total RNA
Extraction protocol Paired-end sequencing at 150bp read length was performed on a HiSeq 4000 (Illumina, San Diego CA)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Data processing The reads with good quality were firstly aligned to several mouse reference databases including mm10 mouse genome, exon, splicing junction segment and contamination database including ribosome and mitochondria sequences using HISAT alignment algorithm. After filtering reads mapped to contamination database, the reads that are uniquely aligned to the exon and splicing-junction segments with a maximal 2 mis-matches for each transcript were then counted as expression level for corresponding transcript. After filtering out of the transcripts with low read (<100) across all samples, the read counts were log2 transformed and quantile-normalized at an equal global median value in order to compare transcription level across samples.
Genome_build: mm10
Supplementary_files_format_and_content: txt files with read counts
 
Submission date May 29, 2019
Last update date Sep 14, 2021
Contact name Weijia Zhang
E-mail(s) weijia.zhang@mssm.edu
Organization name Icahn School of Medicine at Mount Sinai
Department Renal
Lab Bioinfomatics
Street address 1 Gustave L. Levy Pl
City New York
State/province NY
ZIP/Postal code 10029
Country USA
 
Platform ID GPL21103
Series (2)
GSE131893 Renal circadian rhythm dysregulation in lupus nephritis [RNA-seq]
GSE131894 Renal circadian rhythm dysregulation in lupus nephritis
Relations
BioSample SAMN11879796
SRA SRX5914635

Supplementary file Size Download File type/resource
GSM3825519_ZT4RL.txt.gz 103.1 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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