|
| Status |
Public on Mar 10, 2023 |
| Title |
Emx1-cre(+/-)::MDMD::Axin2(-/-) cell et E11.5_rep6 |
| Sample type |
SRA |
| |
|
| Source name |
Neural progenitor cells
|
| Organism |
Mus musculus |
| Characteristics |
genotype: Emx1-cre(+/-)::MDMD::Axin2(-/-)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Emx1-CreERT2::MADM-11::Axin2LacZ/+ mice were breed and medial cortex were dissociated at E11.5.Axin2+/+ and Axin2-/- cells were separated for single cell rna-seq.Dosal diencephalon and ventral diencephalon were collected for Bulk RNA-seq at E10.5 wild type mice.
RNA libraries were prepared for sequencing using standard Illumina protocols and smart-seq2 protocals
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Description |
Green1_R6
|
| Data processing |
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using STAR(2.7.0a) with with default parameter settings.
Fastq reads were filtered using Trimmomatic to discard low-quality reads and trim poor-quality bases.The remaining clean reads were aligned to GRCm38 (mm10) genome. STAR with default parameter settings was used for alignment to generate BAM files. Gene-counting tools, featureCounts were used to generate TPM(transcripts per million) gene counts per cell/sample.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with gene TPM for every gene and every sample
|
| |
|
| Submission date |
Jun 20, 2021 |
| Last update date |
Mar 10, 2023 |
| Contact name |
Zhenhua Chen |
| E-mail(s) |
czh@genetics.ac.cn
|
| Organization name |
Institute of Genetics and Developmental Biology, Chinese Academy of Sciences
|
| Department |
State Key Laboratory of Molecular Development Biology
|
| Lab |
Wu
|
| Street address |
West Beichen Road, Olympic Village, Beijing
|
| City |
Beijing |
| State/province |
China |
| ZIP/Postal code |
100000 |
| Country |
China |
| |
|
| Platform ID |
GPL18480 |
| Series (1) |
| GSE178509 |
Axin2 mediates stem cell competition in developing brain |
|
| Relations |
| BioSample |
SAMN19789239 |
| SRA |
SRX11185186 |
