|
| Status |
Public on Feb 05, 2024 |
| Title |
Dlx5_D1_Dox_remv |
| Sample type |
SRA |
| |
|
| Source name |
pre-implantation embryo
|
| Organism |
Mus musculus |
| Characteristics |
tissue: pre-implantation embryo
cell line: J1
cell type: mouse embryonic stem (ES) cells
genotype: Dlx5 SBFB
treatment: 1 day of doxycycline treatment (500ng/ml) and then the doxycycline was removed. The cells were maintained to day 7.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from cells using the RNeasy Plus Mini Kit (Qiagen) (74136). The mRNA was enriched using the NEBNext® Poly(A) mRNA Magnetic Isolation Module kit (E7490L).
The RNAs-seq libraries were constructed using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina (E7770L) and NEBNext Multiplex Oligos for Illumina (E7600S) following the manufacturer’s protocol. RNA-seq was then performed with paired-end 150bp on the NovaSeq 6000 (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
processed data file: TPM_table.txt
|
| Data processing |
Adapter/quality trimming was done with Trim Galore v0.6.10 (Babraham Bioinformatics, https://github.com/FelixKrueger/TrimGalore)
Quantification of transcript expressions was done using Salmon v1.10.2 (PMID: 28263959) based on the mm10 reference, and the data were aggregated to the gene level using the R package tximport v1.22.0 (PMID: 26925227).
Assembly: mm10
Supplementary files format and content: TPM_table.txt, length-scaled TPM values of genes (rows) from each sample (column)
|
| |
|
| Submission date |
Nov 29, 2023 |
| Last update date |
Feb 05, 2024 |
| Contact name |
Muyoung Lee |
| E-mail(s) |
ml49649@utexas.edu
|
| Organization name |
University of Texas at Austin
|
| Department |
Molecular Biosciences
|
| Street address |
2506 Speedway
|
| City |
Austin |
| State/province |
TX |
| ZIP/Postal code |
78712 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE218628 |
Systematic mapping of TF-mediated cell fate changes by a pooled induction coupled with scRNA-seq and multi-omics approaches |
|
| Relations |
| BioSample |
SAMN38504696 |
| SRA |
SRX22684382 |
