|
| Status |
Public on Feb 03, 2024 |
| Title |
RNA-seq PGC rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Primordial germ cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Primordial germ cells
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Cells were lysed in TRI reagent and total RNA was extracted using a Zymo Direct-zol RNA Miniprep kit. Total RNA was then incubated with RQ1 DNase to remove contaminating genomic DNA and was then re-purified using Zymo RNA Clean & Concentrator-5 kit according to the manufacturers instructions.
About 50 ng of total RNA from each sample was used for synthesis and amplification of cDNA. cDNA synthesis was performed by the UTSA Genomics Core using the QuantSeq 3' mRNA-Seq Library Prep Kit FWD from Illumina (LEXOGEN).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
fc_all_counts.txt
|
| Data processing |
All reads from the QuantSeq sequencing datasets were processed with cutadapt v1.18 to remove adaptors and poly-A sequences. Reads of 30-bp or longer were mapped to the GRCm39 version of the mouse reference genome using Rsubread v2.10.1.. All RNA-seq datasets were processed using the R software (version 4.1.1) packages edgeR v3.38.1 and DESeq2 v1.36 with default settings to detect differential gene expression levels, including <5% for false discovery rate and p <0.05. Data from biological replicates was averaged and differentially expressed genes were defined as those with a ≥1.5-fold difference in expression levels between the control ESC line and each set of iPSC lines produced in this study. Hierarchical clustering was performed using the hclust function and principal component analysis (PCA) was performed using the autoplot and prcomp function without scaling.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
|
| |
|
| Submission date |
Jan 29, 2024 |
| Last update date |
Feb 03, 2024 |
| Contact name |
Yu-Huey Lin |
| E-mail(s) |
[email protected]
|
| Organization name |
The University of Texas at San Antonio
|
| Department |
The Department of Neuroscience, Developmental and Regenerative Biology
|
| Street address |
One UTSA Circle,
|
| City |
San Antonio |
| State/province |
Texas |
| ZIP/Postal code |
78249 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE254454 |
Source cell-type epigenetic memory persists in induced pluripotent cells but is lost in subsequently derived germline cells [RNA-seq] |
| GSE254465 |
Source cell-type epigenetic memory persists in induced pluripotent cells but is lost in subsequently derived germline cells |
|
| Relations |
| BioSample |
SAMN38334516 |
| SRA |
SRX22585356 |
