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| Status |
Public on Aug 23, 2022 |
| Title |
section C medium oocyte rep 2 [X. laevis] |
| Sample type |
SRA |
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| Source name |
oocyte
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| Organism |
Xenopus laevis |
| Characteristics |
cell type: oocyte
treatment: None
Sex: female
source female: 1
oocyte stage: medium
oocyte size: 1050
section: C
biological replicate: 4
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Qiagen RNeasy Minikit according to the manufacturer’s instructions. The concentration of total RNA was measured using a spectrophotometer (Nanodrop 2000, Thermo Scientific), and the quality of RNA was assessed using a Fragment Analyzer (AATI, Standard Sensitivity RNA analysis kit, DNF-471).
Samples were depleted using RiboCop rRNA Depletion kit (Lexogen) and libraries were prepared using SureSelect XT (Agilent). Library qualities were assessed using the Fragment Analyzer (AATI, NGS High Sensitivity kit (DNF-474) and the concentrations were determined by the Qubit 4 Fluorometer (ThermoFisher Scientific). Equimolar library pools were prepared and sequenced using two 2x80bp, NextSeq 500 runs.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Low quality reads and adaptor sequences were removed using Trimmomatic PE (v. 0.36) . Ribosomal RNA sequences were removed using sortmerna (v. 2.1b) and the SILVA rRNA database (version 119). The X. laevis reads were then aligned to the X. laevis v9.1 genome Xenbase (http://www.xenbase.org/, RRID:SCR_003280; Fortriede et al., 2020) using STAR v2.5.2b (Dobin et al., 2013) and counted using htseq-count.
Normalized number of reads was generated using DESeq2.
Transcripts were removed that had zero counts in all samples.
Assembly: X. laevis v9.1 genome
Supplementary files format and content: Excel files include non-normalized number of reads for each sample and normalized number of reads with name of the sample in first row of each column. "xlaevis_non_normalized.xlsx" contains the non-normalized reads while "xlaevis_altered_magnitudes_per_section_and_stage_normalized.xlsx" contains the normalized reads for all samples (all oocyte sections). "xlaevis_total_altered_counts_per_stage_non_normalized.xlsx" contains the non-normalized reads while "xlaevis_total_altered_counts_per_stage_normalized.xlsx" the normalized reads for the total transcripts within the whole oocyte. "xlaevis_alteration_between_the_sections_at_big_stage_normalized.xlsx", "xlaevis_alteration_between_the_sections_at_medium_stage_normalized.xlsx", "xlaevis_alteration_between_the_sections_at_small_stage_normalized.xlsx", and "xlaevis_alteration_between_the_sections_at_very_small_stage_normalized.xlsx" contain the normalized reads at a given oocyte stage.
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| Submission date |
Aug 16, 2022 |
| Last update date |
Aug 23, 2022 |
| Contact name |
Radek Sindelka |
| E-mail(s) |
Radek.Sindelka@ibt.cas.cz
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| Organization name |
Institute of Biotechnology, Czech Academy of Science, v.v.i.
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| Lab |
Laboratory of Gene Expression
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| Street address |
Průmyslová 595
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| City |
Vestec by Prague |
| ZIP/Postal code |
25250 |
| Country |
Czech Republic |
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| Platform ID |
GPL21248 |
| Series (2) |
| GSE211415 |
Comparison of RNA localization during oogenesis within Acipenser ruthenus and Xenopus laevis [Xenopus laevis] |
| GSE211416 |
Comparison of RNA localization during oogenesis within Acipenser ruthenus and Xenopus laevis |
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| Relations |
| BioSample |
SAMN30353881 |
| SRA |
SRX17109657 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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