|
| Status |
Public on Nov 21, 2023 |
| Title |
TMSC-blastocyst-14h-1 |
| Sample type |
SRA |
| |
|
| Source name |
Mouse blastocysts injected with T-MSCs for 14 h-1
|
| Organisms |
Homo sapiens; Mus musculus |
| Characteristics |
cell type: Mouse blastocysts injected with T-MSCs
strain: ENVY cell line and C57/BL6J mouse blastocyst
genotype: Wildtype
|
| Growth protocol |
MSCs were cultured in α-MEM with 20%FBS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Bulk mRNA was extracted using RNeasy mini kit (QIAGEN). Smart-seq samples were lysed in lysis buffer containing Triton X-100, RNase inhibitor, dNTPs and miliQ H2O preparing for expansion. Single cell mRNA was captured in Nadia platform (Dolomite) using ChemGenes Barcoded beads for Drop-seq (Macosko-2011-10)
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Bulk RNA sequenced reads were trimmed for short or low-quality sequence, then mapped to hg38 whole genome using hisat2 with defalut parameters
Single-cell squenced reads were analyzed using Drop-seq pipeline with parameters NUM_CORE_BARCODES=10000
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include read counts for each sample of bulk RNA-seq,
|
| |
|
| Submission date |
Jan 27, 2022 |
| Last update date |
Nov 21, 2023 |
| Contact name |
Ren-He Xu |
| E-mail(s) |
renhexu@um.edu.mo
|
| Organization name |
University of Macau
|
| Department |
Faculty of Health Sciences
|
| Street address |
N22 Research Building, University of Macau, Taipa
|
| City |
Macau |
| State/province |
Macau |
| ZIP/Postal code |
999078 |
| Country |
China |
| |
|
| Platform ID |
GPL19415 |
| Series (1) |
| GSE195573 |
Microinjection of human mesenchymal stem cells to mouse blastocysts |
|
| Relations |
| BioSample |
SAMN25337501 |
| SRA |
SRX13951109 |
