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| Status |
Public on Jan 01, 2024 |
| Title |
mESC Tbxt delE6/delE6 rep2 |
| Sample type |
SRA |
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| Source name |
mESC
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| Organism |
Mus musculus |
| Characteristics |
cell type: mESC
genotype: Tbxt delE6/delE6
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA from each genotype was extracted using RNeasy Plus Mini Kit (QIAGEN, ID: 74134). mRNA was enriched using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, Cat. No. E7490L).
RNA-seq libraries were prepared using NEBNext Ultra II Directional RNA Library Prep Kit (NEB, Cat. No. 759 E7765L) and sequenced on one lane of NovaSeq X Plus 10B 2*150.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
23022FL-07-01-11_S11_L008
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| Data processing |
Raw sequencing reads were mapped to the mouse genome (mm10) with STAR 2.7.2a aligner. The resultant strand-specific read counts of all samples were integrated into a matrix for downstream analysis. Differentially expressed genes (DEGs) were detected by DESeq2 1.40.2 with the cutoff of log2 fold expression change >0.5 and p.adj < 0.05. The top 500 variable genes from DESeq2 across all samples were used to perform principal component analysis. The Tbxt-target genes were collected from Lolas et al. (2014), defined by significant Tbxt ChIP-seq signal in in vitro differentiated mESCs. The set of Tbxt-target genes was intersected with the significant DE genes identified in each mutant sample compared to the wild type controls, and these were aggregated to generate the overall set of differentially expressed Tbxt-target genes across the analyzed mESC lines. These differentially expressed Tbxt-target genes were visualized through a heatmap, with the log10-transformed normalized transcript matrix followed by z-score standardization across samples.
Assembly: mm10
Supplementary files format and content: *.tab: The processed data files generated by STAR2 after mapping to mm10 reference genome contain 4 columns: The first column corresponds to the Ensembl gene ID. Columns 2, 3, and 4 correspond to the number of reads mapped to each gene. The fourth column from each file was merged to a new datasheet and used for downstream analysis. The difference between columns 2, 3, and 4 is the strandedness. If an unstranded library prep kit was used, column 2 should be selected. If a stranded library prep kit was used, we must choose from column 3 or 4. The information from which strand the mRNA originated from is retained. Column 3 corresponds to the first read strand aligned, and column 4 corresponds to the second read strand aligned.
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| Submission date |
Dec 28, 2023 |
| Last update date |
Jan 01, 2024 |
| Contact name |
Bo Xia |
| E-mail(s) |
[email protected]
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| Organization name |
Broad institute
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| Street address |
415 Main Street
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| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02141 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE252196 |
On the genetic basis of tail-loss evolution in humans and apes [RNA-seq] |
| GSE252279 |
On the genetic basis of tail-loss evolution in humans and apes |
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| Relations |
| BioSample |
SAMN39181149 |
| SRA |
SRX23051153 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7996444_23022FL-07-01-11_S11_L008ReadsPerGene.out.tab.gz |
307.7 Kb |
(ftp)(http) |
TAB |
SRA Run Selector |
| Raw data are available in SRA |
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