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Series GSE211415 Query DataSets for GSE211415
Status Public on Aug 23, 2022
Title Comparison of RNA localization during oogenesis within Acipenser ruthenus and Xenopus laevis [Xenopus laevis]
Organism Xenopus laevis
Experiment type Expression profiling by high throughput sequencing
Summary In this study we analyzed the spatial and temporal localization of maternal transcripts during oogenesis in Xenopus laevis. The occurrence of transcript asymmetry in X. laevis has been described at a global level only in matured eggs, while the establishment of the asymmetry during oogenesis has been described only for a few transcripts. In this model it was discerned that there exist three pathways (early, intermediate, late) for the establishment of the vegetal gradient, while for the animal gradient not much is known for its production. In this study we assessed the temporal establishment of the transcript localization at a global level for Xenopus laevis. We were able to determine that there are many transcripts that show temporal variability in the establishment of their localization. We observed the previously described early, intermediate (predefined) and also late pathways but found more member transcripts within these groups. We also described, perhaps for the first time, an early, intermediate (predefined) and late pathway for the animal genes as well. Additionally, we showed that some maternal transcripts are dynamic during oogenesis with degradation and de novo production being observed. Our study showed that in additional to spatial orientation to the transcripts, there is a strong temporal factor. The discovery of these new temporal profiles should help to better understand the driving forces during embryogenesis.
 
Overall design Oocytes from Xenopus laevis females were extracted to create four groups: very small oocytes (n = 3; stage III, size 560-580µm); small oocytes (n = 5; stage IV, size 720-810µm); medium (n =2; stage V, size 1050µm); and big (n = 2; stage VI, size 1140-1200µm). Samples were oriented along their animal-vegetal axis and cryosectioned to produce 5 main sections (A (extreme animal) – E (extreme vegetal)). Each section was sequenced and the abundance of the transcript across the section and stages analyzed.
 
Contributor(s) Abaffy P, Iegorova V, Naraine R, Sindelka R
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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
Organization name Institute of Biotechnology, Czech Academy of Science, v.v.i.
Lab Laboratory of Gene Expression
Street address Průmyslová 595
City Vestec by Prague
ZIP/Postal code 25250
Country Czech Republic
 
Platforms (1)
GPL21248 Illumina NextSeq 500 (Xenopus laevis)
Samples (59)
GSM6469709 section A big oocyte rep 1 [X. laevis]
GSM6469710 section B big oocyte rep 1 [X. laevis]
GSM6469711 section C big oocyte rep 1 [X. laevis]
This SubSeries is part of SuperSeries:
GSE211416 Comparison of RNA localization during oogenesis within Acipenser ruthenus and Xenopus laevis
Relations
BioProject PRJNA870171

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SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE211415_xlaevis_alteration_between_the_sections_at_big_stage_normalized.xlsx 3.0 Mb (ftp)(http) XLSX
GSE211415_xlaevis_alteration_between_the_sections_at_medium_stage_normalized.xlsx 3.0 Mb (ftp)(http) XLSX
GSE211415_xlaevis_alteration_between_the_sections_at_small_stage_normalized.xlsx 7.4 Mb (ftp)(http) XLSX
GSE211415_xlaevis_alteration_between_the_sections_at_very_small_stage_normalized.xlsx 4.1 Mb (ftp)(http) XLSX
GSE211415_xlaevis_altered_magnitudes_per_section_and_stage_normalized.xlsx 17.9 Mb (ftp)(http) XLSX
GSE211415_xlaevis_non_normalized.xlsx 7.3 Mb (ftp)(http) XLSX
GSE211415_xlaevis_total_altered_counts_per_stage_non_normalized.xlsx 1.9 Mb (ftp)(http) XLSX
GSE211415_xlaevis_total_altered_counts_per_stage_normalized.xlsx 4.1 Mb (ftp)(http) XLSX
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