 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Dec 13, 2022 |
| Title |
Egg_ER_Rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
Mature egg
|
| Organism |
Xenopus laevis |
| Characteristics |
developmental stage: Germinal Vesicle Breakdown (GVBD)
cell fraction: Endoplasmic Reticulum (ER)
cell type: Mature egg
|
| Growth protocol |
Defolliculated stage VI oocytes were cultured in the oocyte culture medium, or oocyte culture medium containing 2µM progesterone to induce oocyte maturation. All cells were incubated at 18 ℃.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Oocytes and mature eggs were fractionated into the cytosolic, ER, and pellet fractions. Spike mixture was added into each fraction. Total RNAs were extracted using the TRIzol reagent. Before library construction, Ribosomal RNAs was removed with the Ribozero HMR kit (Illumina).
The RNAseq libraries were prepared with Illumina's 'TruSeq Stranded mRNAseq Sample Prep kit' (Illumina). Reads are 100 nt in length.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Fastq files were generated and demultiplexed with the bcl2fastq v2.20 Conversion Software (Illumina).
Adaptors were trimmed from the 3'-end of the reads. The quality-scores line in fastq files uses an ASCII offset of 33 known as Sanger scores.
Transcripts per million (TPM) were quantified using Kallisto (v 0.46.2) and the Xenopus laevis transcriptome (v 9.2) from the XenBase (http://www.xenbase.org) was used as the reference sequence.
TPM was converted to the absolute concentration by the regression estimation with five spike-in RNAs (egfp, mCherry, mRuby2, firefly, renilla).
Assembly: XENLA_9.2_genome.fa.gz (Xenopus laevis transcriptome)
Supplementary files format and content: tsv files were generated from Kallisto and included TPM values.
Supplementary files format and content: xlsx files contained the absolute concentration, FC, qvalue and proportion of all genes in each fraction.
|
| |
|
| Submission date |
Mar 23, 2022 |
| Last update date |
Dec 13, 2022 |
| Contact name |
Jing Yang |
| E-mail(s) |
yangj@illinois.edu
|
| Organization name |
University of Illinois Urbana Champaign
|
| Department |
Comparative Biosciences
|
| Lab |
Yang Laboratory
|
| Street address |
2001 South Lincoln Avenue
|
| City |
Urbana |
| State/province |
Illinois |
| ZIP/Postal code |
61802 |
| Country |
USA |
| |
|
| Platform ID |
GPL28901 |
| Series (1) |
| GSE199254 |
Transcriptome profiling of cytosol, endoplasmic reticulum (ER), and pellet fraction from the Xenopus laevis oocyte and mature egg |
|
| Relations |
| BioSample |
SAMN26897508 |
| SRA |
SRX14587635 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5968163_Egg_ER_Rep_1.tsv.gz |
833.2 Kb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
|
|
|
|
 |
