Basic Information
| Dataset | GSE199254 |
|---|---|
| Status | 2022-12-13 |
| Species | Xenopus laevis |
| Source | NCBI GEO |
| Subcellular Localization | Cytosol|Endoplasmic Reticulum (ER)|Pellet |
| PMID | 36516762 |
| Title | Transcriptome profiling of cytosol, endoplasmic reticulum (ER), and pellet fraction from the Xenopus laevis oocyte and mature egg |
| Citation | Hwang H, Yun S, Arcanjo RB, Divyanshi et al. Regulation of RNA localization during oocyte maturation by dynamic RNA-ER association and remodeling of the ER. Cell Rep 2022 Dec 13;41(11):111802. |
| Experimental Design | Three biological replicates were assigned for each group. Before RNA extraction, a mixture of spike-in RNAs (egfp, mCherry, mRuby2, firefly, renilla) was added to each fraction. Total RNA was extracted from the cytosol, ER, and pellet fraction in the four oocytes or four mature eggs using TRIzol reagent. Ribosomal RNA was removed with the Ribozero HMR kit (Illumina), and the RNA libraries were prepared using the TruSeq Stranded mRNAseq Sample Prep kit (Illumina). The libraries were quantitated by qPCR and sequenced on one lane for 101 cycles from each end of the fragments on a NovaSeq 6000 using a NovaSeq S1reagent kit. Fastq files were generated and demultiplexed with the bcl2fastq v2.20 Conversion Software (Illumina). Transcript abundance (TPM) was quantified by Kallisto, and the TPM of each RNA-seq data was converted to absolute attomolar concentration (aM) through the regression estimation with five spike-in RNAs. |
Sample Information
| BioProject | Sample Name | Localization | Develop Stage | Source | Label |
|---|---|---|---|---|---|
| PRJNA819062 | GSM5968168 | Pellet | Germinal Vesicle Breakdown (GVBD) | Mature egg | Egg_Pellet_Rep 3 |
| PRJNA819062 | GSM5968167 | Pellet | Germinal Vesicle Breakdown (GVBD) | Mature egg | Egg_Pellet_Rep 2 |
| PRJNA819062 | GSM5968166 | Pellet | Germinal Vesicle Breakdown (GVBD) | Mature egg | Egg_Pellet_Rep 1 |
| PRJNA819062 | GSM5968165 | Endoplasmic Reticulum (ER) | Germinal Vesicle Breakdown (GVBD) | Mature egg | Egg_ER_Rep 3 |
| PRJNA819062 | GSM5968164 | Endoplasmic Reticulum (ER) | Germinal Vesicle Breakdown (GVBD) | Mature egg | Egg_ER_Rep 2 |
| PRJNA819062 | GSM5968163 | Endoplasmic Reticulum (ER) | Germinal Vesicle Breakdown (GVBD) | Mature egg | Egg_ER_Rep 1 |
| PRJNA819062 | GSM5968162 | Cytosol | Germinal Vesicle Breakdown (GVBD) | Mature egg | Egg_Cytosol_Rep 3 |
| PRJNA819062 | GSM5968161 | Cytosol | Germinal Vesicle Breakdown (GVBD) | Mature egg | Egg_Cytosol_Rep 2 |
| PRJNA819062 | GSM5968160 | Cytosol | Germinal Vesicle Breakdown (GVBD) | Mature egg | Egg_Cytosol_Rep 1 |
| PRJNA819062 | GSM5968159 | Pellet | Stage VI Oocyte | Oocyte | Oocyte_Pellet_Rep 3 |
| PRJNA819062 | GSM5968158 | Pellet | Stage VI Oocyte | Oocyte | Oocyte_Pellet_Rep 2 |
| PRJNA819062 | GSM5968157 | Pellet | Stage VI Oocyte | Oocyte | Oocyte_Pellet_Rep 1 |
| PRJNA819062 | GSM5968156 | Endoplasmic Reticulum (ER) | Stage VI Oocyte | Oocyte | Oocyte_ER_Rep 3 |
| PRJNA819062 | GSM5968155 | Endoplasmic Reticulum (ER) | Stage VI Oocyte | Oocyte | Oocyte_ER_Rep 2 |
| PRJNA819062 | GSM5968154 | Endoplasmic Reticulum (ER) | Stage VI Oocyte | Oocyte | Oocyte_ER_Rep 1 |
| PRJNA819062 | GSM5968153 | Cytosol | Stage VI Oocyte | Oocyte | Oocyte_Cytosol_Rep 3 |
| PRJNA819062 | GSM5968152 | Cytosol | Stage VI Oocyte | Oocyte | Oocyte_Cytosol_Rep 2 |
| PRJNA819062 | GSM5968151 | Cytosol | Stage VI Oocyte | Oocyte | Oocyte_Cytosol_Rep 1 |
Subcellular Localization Number
RNA Type:
Condition:
Localization Differential Analysis
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Specific Subcellular Localization
RNA Type:
Method:
Dynamic RNA Localization
RNA Type:
Method:
Specific Enrichment Analysis
RNA Type:
Localization:
Condition:
Method:
Enrichment:
Specific RNA Ratio
RNA Type:
RNA Symbol:
TPM:
