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Sample GSM5968153 Query DataSets for GSM5968153
Status Public on Dec 13, 2022
Title Oocyte_Cytosol_Rep 3
Sample type SRA
 
Source name Oocyte
Organism Xenopus laevis
Characteristics developmental stage: Stage VI Oocyte
cell fraction: Cytosol
cell type: Oocyte
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 SAMN26897518
SRA SRX14587625

Supplementary file Size Download File type/resource
GSM5968153_Oocyte_Cytosol_Rep_3.tsv.gz 845.0 Kb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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