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Sample GSM7922761 Query DataSets for GSM7922761
Status Public on Jan 09, 2024
Title WT-1-Tail
Sample type SRA
 
Source name Skin - Tail
Organism Mus musculus
Characteristics tissue: Skin - Tail
genotype: Wild type IKBKB
Extracted molecule total RNA
Extraction protocol Skin from ears and tail of each mouse was taken and snap froze in liquid nitrogen. Samples were defrosted in RNA protect reagent, and mechanically cut into smaller pieces of 3-4 mm. We used Monarch total RNA extraction kit to isolate total RNA from the samples. Briefly: 300 ul of RNA protection samples added to each sample followed by 45ul of Prot K Reaction buffer plus Prot K and incubated at 55 C for 30 minutes. Samples were vortex and spun at 16000 xg for 2 minutes and supernatant transferred to fresh microfuge tubes. Equal volume of RNA Lysis buffer was added and transferred samples to gDNA removal column, spun at 16000xg for 1 minute. equal volume 95% ethanol was added to flow through and transferred to purification column and spun at 16000xg for 1 minute. discarded flow through, added 500 ul RNA wash buffer to the column and spun for 30 seconds, then 80 ul of DNases plus DNase I reaction buffer was added to the column and incubated for 15 minutes at room temperature. 500 ul RNA priming buffer was added and spun for 30 seconds, discarded flow through, and wash the column with 500ul of Wash buffer twice. added 40 ul Nuclease free water to the column and spun for 30 seconds to collect the total RNA in fresh nuclease-free microfuge tubes.
NEB Ultra II Directional RNA Prep kit was used for library preperation
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model NextSeq 2000
 
Data processing quality check with FastQC
alignment using HIsat2(v2.1.0)
alignment reads were sorted using samtools
aligned reads were assigned using FeatureCounts (v1.4) based on NCBI refseq gene models
differential gene expression analysis using limma_voom
Assembly: mm10
Supplementary files format and content: count matrix in txt format
 
Submission date Nov 29, 2023
Last update date Jan 09, 2024
Contact name Zhi-Ping Feng
E-mail(s) zhi-ping.feng@anu.edu.au
Phone 61 2 6125 2933
Organization name JCSMR
Street address 131 Garran Road, John Curtin School Of Medical Research Building (Level 3, Stage 1)
, The Australian National University

City Acton
State/province ACT
ZIP/Postal code 2600
Country Australia
 
Platform ID GPL30172
Series (1)
GSE248917 RNAseq analysis for tails, and ears from Ikbkb mut/mut and Ikbkb wt/wt mice
Relations
BioSample SAMN38498671
SRA SRX22677443

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA

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