|
| Status |
Public on Jan 06, 2023 |
| Title |
B2 |
| Sample type |
SRA |
| |
|
| Source name |
Testis
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Testis
strain: ICR mouse
treatment: Basal diet inclusion of DON at 12mg/kg
|
| Treatment protocol |
Mice in vehicle group were feed with basal diet; In DON group mice were fed basal diet supplemented with 12 mg/kg DON, which was orignated from DON contaminated corn.LF was dissolved in normal saline and mice were oral administrated with LF at 10mg per day. Mice in DON+LF group was co-treatment of DON and LF with same dose refered above.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The testis tissue RNA were isolated using Illumina Tru-Seq RNA Sample Prep Kit according to the instructions of the manufacturer.
The quality of libraries were validated with an Agilent Bioanalyzer, sequencing was performed on an Illumina HiSeq 2000 sequencer at BGI Tech
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Description |
bio rep DON 1
|
| Data processing |
The sequence data in FASTQ format was analyzed using a standard BWA–Bowtie-Cufflinks workflow
Sequence reads were mapped to mm9 assembly with BWA and Bowtie software
The Cufflinks package was used for transcripts assembly, quantification of normalized gene and isoform expression, and analysis of different expressions
Genes were ranked using the Gene Set Enrichment Analysis (GSEA v.4.1) based on the shrunken limma log2 fold changes.The GSEA tool was used in a ‘pre-ranked’ model with default parameters.
Gene Ontology (GO) analysis was performed using DAVID Bioinformatics Resources.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
|
| |
|
| Submission date |
Sep 19, 2022 |
| Last update date |
Jan 06, 2023 |
| Contact name |
Demin Cai |
| E-mail(s) |
demincai@yzu.edu.cn
|
| Organization name |
Yangzhou University
|
| Street address |
Daxue South Road 88
|
| City |
Yangzhou |
| ZIP/Postal code |
225009 |
| Country |
China |
| |
|
| Platform ID |
GPL23479 |
| Series (1) |
| GSE213641 |
Lactoferrin attenuated deoxynivalenol induced malfunction in mouse testis |
|
| Relations |
| BioSample |
SAMN30921480 |
| SRA |
SRX17625083 |
