 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on May 01, 2022 |
| Title |
Nile rat Male 8 weeks |
| Sample type |
SRA |
| |
|
| Source name |
Olfactory epithelium
|
| Organism |
Arvicanthis niloticus |
| Characteristics |
tissue: olfactory epithelium
Sex: male
age: 8 weeks
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The olfactory epithelium was dissected out from the nasal cavity for each sample. The total RNA was isolated by TRIzol Reagent and subsequently purified with the RNeasy Mini Kit (Qiagen, Hilden, Germany). The quantity and purity of the isolated RNA were measured by NanoDrop ND-1000 Spectrophotometer before cDNA library construction.
The cDNA libearies were constructed by TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA, USA). Briefly, mRNA was purified from total RNA (1 μg) by oligo(dT)-coupled magnetic beads and fragmented into small pieces under elevated temperature. The first-strand cDNA was synthesized using reverse transcriptase and random primers. After the generation of double-strand cDNA and adenylation on 3’ ends of DNA fragments, the adaptors were ligated, and the samples were purified with AMPure XP system (Beckman Coulter, Beverly, USA). The quality of the libraries was assessed on the Agilent Bioanalyzer 2100 system and a Real-Time PCR system.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Illumina Real Time Analysis 3 (RTA3) software was used for basecalling
The bases with low quality and sequences from adapters in raw data were removed using program fastp (v.0.22.0)
Cleaned paired-end reads of FASTQ files derived from various tissue samples were analyzed using kallisto (v.0.46.1)
The kallisto index was built with default parameters from the reference transcriptome file for quantification in each organism.
kallisto computed the transcript abundances as TPMs (Transcripts Per Kilobase Million). The TPM value of the longest transcript was assigned to each gene.
genome build: GRCm39
genome build: mArvNil1.pat.X
processed data files format and content: tab-delimited text files include Ensembl Gene ID and normalized TPM values for each sample.
|
| |
|
| Submission date |
Apr 28, 2022 |
| Last update date |
Dec 15, 2022 |
| Contact name |
Ben-Yang Liao |
| E-mail(s) |
liaoby@nhri.edu.tw
|
| Organization name |
National Health Research Institutes
|
| Department |
Institute of Population Health Sciences
|
| Street address |
35 Keyan Rd.
|
| City |
Zhunan, Miaoli County |
| ZIP/Postal code |
350 |
| Country |
Taiwan |
| |
|
| Platform ID |
GPL32219 |
| Series (1) |
| GSE201761 |
Next Generation Sequencing and Quantitative Analysis of Mus musculus and Arvicanthis niloticus Olfactory Epithelium Transcriptomes |
|
| Relations |
| BioSample |
SAMN27926302 |
| SRA |
SRX15038463 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6070920_Anil_male_8w_normalized_TPM.txt.gz |
230.7 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
