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Status |
Public on Sep 14, 2021 |
Title |
ZT16LL |
Sample type |
SRA |
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Source name |
kidney
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Organism |
Mus musculus |
Characteristics |
diagnosis: Young time: ZT16 tissue: kidney strain: NZB/W F1
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Extracted molecule |
total RNA |
Extraction protocol |
Paired-end sequencing at 150bp read length was performed on a HiSeq 4000 (Illumina, San Diego CA)
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 4000 |
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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
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Submission date |
May 29, 2019 |
Last update date |
Sep 14, 2021 |
Contact name |
Weijia Zhang |
E-mail(s) |
weijia.zhang@mssm.edu
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Organization name |
Icahn School of Medicine at Mount Sinai
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Department |
Renal
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Lab |
Bioinfomatics
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Street address |
1 Gustave L. Levy Pl
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City |
New York |
State/province |
NY |
ZIP/Postal code |
10029 |
Country |
USA |
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Platform ID |
GPL21103 |
Series (2) |
GSE131893 |
Renal circadian rhythm dysregulation in lupus nephritis [RNA-seq] |
GSE131894 |
Renal circadian rhythm dysregulation in lupus nephritis |
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Relations |
BioSample |
SAMN11879783 |
SRA |
SRX5914648 |
Supplementary file |
Size |
Download |
File type/resource |
GSM3825532_ZT16LL.txt.gz |
102.9 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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