GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM7964195 Query DataSets for GSM7964195
Status Public on May 17, 2024
Title TA_FP_1
Sample type SRA
Source name Fore footpad skin 3 months old Eda mutant Tabby mouse
Organism Mus musculus
Characteristics strain: Tabby
Sex: Male
age: 3 months
tissue: Fore footpad skin
genotype: Eda mutant
Extracted molecule total RNA
Extraction protocol Footpad skin from fore paws of 3 months old Eda mutant Tabby male mice and age and sex matched C57BL/6J control mice was collected under a dissection microscope. Total RNA was isolated using Qiagen RNeasy Fibrous Tissue Mini Kit (Qiagen Cat# 74704). The quality and quantity of RNA were checked with Agilent Bioanalyzer using RNA 6000 Nano Kit (Agilent Cat# 5067-1511).
Total RNA was used for sequencing library prep using Illumina TruSeq Stranded mRNA Library prep kit (Illumina Cat# 20020594). Briefly, the Poly-A containing mRNA was isolated first by using Poly-T oligo attached magnetic beads. After cDNA synthesis, the cDNAs were subjected to the 3’ End Adenylation, the Adapter Ligation, and purified with AMPure beads (Beckman, Cat#A63881). The products were size selected with SPRIselect beads (Beckman, Cat#B23318). Then selected cDNAs were enriched by PCR and purified again with SPRIselect beads to generate final libraries. The quality and quantity of sequencing libraries were checked using Agilent DNA 1000 Screen Tape on the Agilent Tapestation.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
Data processing BCL files were de-multiplexed and converted to FASTQ files using bcl2fastq program (v2.20.0.422).
FASTQ files were trimmed for adapter sequences using Cutadapt version v1.18 and aligned to mouse genome mm10, Ensembl v89 using STAR software v2.4.0j.
featureCounts (v1.6.4) were used to generate gene counts
Differential expression analysis of gene counts was performed using the DESeq2
Assembly: mm10
Supplementary files format and content: text files containing counts
Submission date Dec 08, 2023
Last update date May 17, 2024
Contact name Supriyo De
Organization name NIA-IRP, NIH
Department Laboratory of Genetics and Genomics
Lab Computational Biology & Genomics Core
Street address 251 Bayview Blvd
City Baltimore
State/province Maryland
ZIP/Postal code 21224
Country USA
Platform ID GPL24247
Series (2)
GSE249782 Characterization of age-associated gene expression changes in mouse sweat glands [FP_WT_TA]
GSE249784 Characterization of age-associated gene expression changes in mouse sweat glands
BioSample SAMN38735607
SRA SRX22836217

Supplementary file Size Download File type/resource
GSM7964195_CC1_16_TA_FP_1_S6_geneCOUNT.txt.gz 193.4 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA

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