 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Apr 26, 2022 |
| Title |
Young skin |
| Sample type |
SRA |
| |
|
| Source name |
NMR Dorsal skin
|
| Organism |
Heterocephalus glaber |
| Characteristics |
tissue: full-thickness skin
age: 4 year-old
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from full-thickness dorsal skin samples obtained from young and old animals and purified using Direct-zol RNA purification kit (Zymo Research; Irvine, CA) following by DNAse treatment. Integrity of RNA was assessed on 2100 Bioanalyzer Instrument (Agilent Technologies, Inc.), only samples with RIN factor above 7.5 were used for NGS library preparation.
For RNA sequencing, approximately 10 ug of total RNA was used to remove ribosomal RNA according to the manuscript of the Epicentre Ribo-Zero Gold Kit (Illumina, San Diego, USA). The pair-end 2×150bp sequencing was performed on an Illumina Hiseq 4000 platform in the LC Sciences (Houston, TX).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
The bioinformatics analysis of the RNAseq data was performed by the LC Sciences (Houston, TX). Firstly, Cutadapt (Martin, 2011) and Perl scripts were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases. Then, sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Bowtie2 (Langmead and Salzberg, 2012) and Tophat2 (Kim et al., 2013) were used to map reads to the genome of Heterocephalus glaber (https://useast.ensembl.org/Heterocephalus_glaber_female/Info/Index). The differentially expressed mRNAs were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with parametric F-test comparing nested linear models (p value < 0.05) by R package Ballgown. Ballgown was used to generate a list and heatmaps of differentially expressed genes, and in-house generated Perl scripts (LC Science, Houston, TX) were used for Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses.
Assembly: Naked Mole-Rat genome (version Ensemble 104.1)
Supplementary files format and content: Excel files include FPKM values for each Sample. *Sample1.xlsx contains data from only the R1 read. *Sample2.xlsx contains data from only the R2 read.
|
| |
|
| Submission date |
Apr 13, 2022 |
| Last update date |
Apr 26, 2022 |
| Contact name |
Vladimir Botchkarev |
| E-mail(s) |
vladbotc@bu.edu
|
| Organization name |
Boston University
|
| Street address |
609 Albany Street
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02118 |
| Country |
USA |
| |
|
| Platform ID |
GPL26775 |
| Series (1) |
| GSE200736 |
Age-associated changes in the skin transcriptome in Naked mole-rats |
|
| Relations |
| BioSample |
SAMN27565399 |
| SRA |
SRX14842824 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6042915_YoungSkinSample1.xlsx |
4.0 Mb |
(ftp)(http) |
XLSX |
| GSM6042915_YoungSkinSample2.xlsx |
4.0 Mb |
(ftp)(http) |
XLSX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
