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| Status |
Public on Nov 01, 2024 |
| Title |
Next generation sequencing for quantitative analysis of double-negative (DN) thymocyte transcriptomes from Toxf/f and Toxf/fCd4Cre mice. |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare the difference of NGS-derived transcriptome profiling between DN thymocytes from Toxf/f and Toxf/fCd4Cre mice.
Methods: mRNA profiles of DN thymocytes sorted by FACS from 3-4-week-old Toxf/f and Toxf/fCd4Cre mice were generated by deep sequencing, in triplicate, using Illumina Novaseq6000. The sequence reads that passed quality filters were analyzed at the transcript level with qRT–PCR using TaqMan and SYBR Green assays.
Results: Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample to the mouse genome (Build Ensembl_release100) and identified 19,045 transcripts in the DN thymocytes of Toxf/f and Toxf/fCd4Cre mice with BWA workflow. RNA-seq data showed approximately 1.1% of the transcripts which were differentially expressed between the DN thymocytes from Toxf/f and Toxf/fCd4Cre mice, with the parameter of false discovery rate (FDR) < 0.05 and absolute fold change ≥ 2.
Conclusions: Our study exhibits the detailed analysis of DN thymocyte transcriptomes with biologic replicates, generated by RNA-seq technology. The optimized data analysis here provides a framework for comparative investigations of expression profiles. The RNA-seq data allow researchers to identify the transcripts affected by TOX and to better understand the role of TOX in the development of thymocytes.
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| Overall design |
mRNA profiles of DN thymocytes from 3-4-week-old Toxf/f and Toxf/fCd4Cre mice
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| Contributor(s) |
He Q, Lu Y, Jiang R, Sun B |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| |
| Submission date |
Nov 03, 2021 |
| Last update date |
Nov 01, 2024 |
| Contact name |
qifeng he |
| E-mail(s) |
heqf@smail.nju.edu.cn
|
| Organization name |
nanjing university
|
| Department |
general surgery
|
| Lab |
Central laboratory of hepatobiliary and pancreatic disease
|
| Street address |
zhongshan Road
|
| City |
Nanjing |
| State/province |
JIANGSU |
| ZIP/Postal code |
211000 |
| Country |
China |
| |
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| Platforms (1) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
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| Samples (6)
|
| GSM5668682 |
DN thymocytes Toxf/f (Cd4 control) rep1 |
| GSM5668683 |
DN thymocytes Toxf/f (Cd4 control) rep2 |
| GSM5668684 |
DN thymocytes Toxf/f (Cd4 control) rep3 |
|
| Relations |
| BioProject |
PRJNA777592 |
| SRA |
SRP344408 |
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