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| Status |
Public on Jan 09, 2024 |
| Title |
WT-1-Ears |
| Sample type |
SRA |
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| Source name |
Skin - Ears
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| Organism |
Mus musculus |
| Characteristics |
tissue: Skin - Ears
genotype: Wild type IKBKB
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| 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
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
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| 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
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| 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
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| Phone |
61 2 6125 2933
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| Organization name |
JCSMR
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| Street address |
131 Garran Road, John Curtin School Of Medical Research Building (Level 3, Stage 1)
, The Australian National University
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| City |
Acton |
| State/province |
ACT |
| ZIP/Postal code |
2600 |
| Country |
Australia |
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| Platform ID |
GPL30172 |
| Series (1) |
| GSE248917 |
RNAseq analysis for tails, and ears from Ikbkb mut/mut and Ikbkb wt/wt mice |
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| Relations |
| BioSample |
SAMN38498672 |
| SRA |
SRX22677442 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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