GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM7680862 Query DataSets for GSM7680862
Status Public on Dec 31, 2023
Title kidney, PND7, mCherry Glis3 WT, rep3
Sample type SRA
Source name kidney
Organism Mus musculus
Characteristics tissue: kidney
age: PND7
genotype: mCherry Glis3 WT
Extracted molecule total RNA
Extraction protocol Purelink RNA mini kit was used for RNA extraction
RNA libraries were prepared using TruSeq RNA library preparation kit from Illumina following manufacturer’s protocol.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
Data processing Read pairs were filtered to retain only those with mean base quality scores at least 20, then aligned via STAR v2.5 with parameters "--outSAMattrIHstart 0 --outFilterType BySJout --alignSJoverhangMin 8 --limitBAMsortRAM 55000000000 --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical".
Counts per gene were determined via featureCounts (Subread v1.5.0-p1) with parameters "-s0 -Sfr -p" for the unstranded PAX8-cre dataset and "-s2 -Sfr -p" for the reverse-stranded mCherry dataset.
Depth tracks were generated by STAR v2.5 with parameters "--outWigType bedGraph --outWigStrand {Unstranded,Stranded} --outWigNorm RPM", followed by conversion to bigWig format via UCSC utility bedGraphToBigWig.
Assembly: mm10
Supplementary files format and content: counts-per-gene matrix per dataset (tab-delimited text)
Supplementary files format and content: normalized depth tracks (bigWig)
Submission date Aug 04, 2023
Last update date Dec 31, 2023
Contact name Hong Soon Kang
Phone 984-287-3921
Organization name NIH/NIEHS
Department IIDL
Lab Cell Biology Group
Street address 111 T.W. Alexander Dr.
City Research Triangle Park
State/province NC
ZIP/Postal code 27709
Country USA
Platform ID GPL24247
Series (2)
GSE240071 Regulation of gene expression by GLIS3 during neonatal kidney development
GSE240074 GLIS3
BioSample SAMN36836701
SRA SRX21247541

Supplementary file Size Download File type/resource
GSM7680862_mCherry-P7-WT-rep3.depthRPM.minus.bigWig 34.8 Mb (ftp)(http) BIGWIG 35.5 Mb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap