 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Nov 01, 2021 |
| Title |
Next Generation Sequencing Facilitates Quantitative Analysis of tetracycline (Tet) inducible Scl/tTA-BCR/ABL (BA) transgenic mouse hematopoietic stem-progenitor cells Transcriptomes |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Purpose: The goals of this study are to further clarify the regulation mechanism after BCR/ABL expression was induced for three weeks in Scl/tTA-BCR/ABL trangenic mouse hematopoietic stem-progenitor cells. Moreover, integrated analysis of miRNA-mRNA regulatory network was built by combining the transcriptomic data with miRNA microarray data.
Methods: Hematopoietic stem-progenitor cells mRNA profiles of BA mice after BCR/ABL expression induced for 0 week and 3 weeks were generated by deep sequencing, using Illumina Hiseq 2500, hematopoietic stem-progenitor cells of 3 mice were mixed in each group. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by edgeR. qRT–PCR validation was performed using SYBR Green assays.
Results: Using an optimized data analysis workflow, we investigated the regulation of mRNAs in BM LSKs during murine CML progression, GSEA and GO analysis were taken for the RNA-seq data, revealing that apoptosis pathway was downregulated while cell cycle was upregulated. Then, we comblined RNA-seq data with miRNA microarray data and identified integrated regulatory networks. To validate the analysis results, functional assays were performed with BM LSKs of BA mice and 32D-BCR/ABL cell line.
Conclusions: Our study represents mRNA expression profiles bone marrow (BM) LSKs (Lin-Sca-1+C-kit+) at 0 and 3 weeks after doxycyline withdrawal of BA mice, the analysis identified that several pathways including cell cycle, apoptosis, myeloid differentiation and DNA damage were influenced by BCR/ABL expression.
|
| |
|
| Overall design |
Hematopoietic stem-progenitor cells (lin-c-kit+sca1+, LSK) mRNA profiles of BA mice after BCR/ABL expression inducing for 0 week and 3 weeks were generated by deep sequencing, using Illumina Hiseq 2500, LSK cells from three mice were mixed in each group ,
|
| |
|
| Contributor(s) |
Chen Z, Huang Q |
| Citation(s) |
34386429 |
| |
| Submission date |
Nov 06, 2018 |
| Last update date |
Nov 03, 2021 |
| Contact name |
Zhiwei Chen |
| E-mail(s) |
chenzhiweimilan@163.com
|
| Organization name |
Shanghai Jiao Tong Universtiy School of Medicine
|
| Department |
Shanghai Institute Of Hematology
|
| Street address |
Room 807, Research and Education Plaza, 197 Ruijin 2nd Road, Luwan District, Shanghai, PRC
|
| City |
Shanghai |
| ZIP/Postal code |
200025 |
| Country |
China |
| |
|
| Platforms (1) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
|
| Samples (2) |
|
| Relations |
| BioProject |
PRJNA503993 |
| SRA |
SRP167948 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE122213_RAW.tar |
19.4 Mb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
