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GEO Series: GSE37452

Title: RNA sequencing reveals diverse and dynamic repertoire of the Xenopus tropicalis transcriptome over development.

Summary

We report the application of paired-end RNA sequencing for high throughput profiling of the Xenopus transcriptome in 23 distinct developmental stages. In total, we obtained over 900 million reads and the deep coverage allowed us to examine the transcriptome in detail. First, we found that ~150 genes are transcribed before embryonic genome activation when transcription is generally thought to be repressed. Second, we discovered thousands of novel splice junctions, the majority of which modify existing gene structures. Third, we curated a confident set of 6686 non-coding transcripts in 3859 genomic loci. Many of these non-coding RNAs are also developmentally regulated, which suggests that they may play important roles during embryogenesis. Finally, we found hundreds of contigs that cannot be aligned to the reference genome, which indicates that the current genome (XenTro3) is still unfinished. Our results will aid in the full assembly and annotation of the Xenopus tropicalis genome.


Contributors: Kin Fai Au, Meng Tan, Kin Au, Arielle Yablonovitch, Andrea Wills, Julie Baker, Wing Wong, Jin Li

Experiment Type: Examination of the transcriptome of Xenopus tropicalis from a 2-cell fertilized embryo to a stage 45 feeding tapole

Article: XB-ART-45933, PubMed

Source: NCBI GEO, Xenbase FTP

Samples: (DEG = Differentially Expressed Genes; GSM = GEO Sample Number)
Sample View GSMs Assay Type
WE - NF10 GSM919923  GSM919945  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 10  
WE - NF11-12 GSM919924  GSM919925  GSM919946  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 11 to NF stage 12  
WE - NF13-14 GSM919947  GSM919948  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 13 to NF stage 14  
WE - NF15 GSM919926  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 15  
WE - NF16-18 GSM919927  GSM919949  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 16 to NF stage 18  
WE - NF19 GSM919928  GSM919929  GSM919950  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 19  
WE - NF2 GSM919938  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 2 (2-cell)  
WE - NF20-21 GSM919930  GSM919951  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 20 to NF stage 21  
WE - NF22-23 GSM919931  GSM919952  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 22 to NF stage 23  
WE - NF24-26 GSM919932  GSM919953  GSM919954  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 24 to NF stage 26  
WE - NF28 GSM919933  GSM919955  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 28  
WE - NF3 GSM919939  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 3 (4-cell)  
WE - NF31-32 GSM919934  GSM919956  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 31 to NF stage 32  
WE - NF33/34 GSM919935  GSM919957  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 33 and 34  
WE - NF37/38-39 GSM919958  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 37 and 38 to NF stage 39  
WE - NF4 GSM919940  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 4 (8-cell)  
WE - NF40 GSM919936  GSM919959  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 40  
WE - NF41-42 GSM919937  GSM919960  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 41 to NF stage 42  
WE - NF44-45 GSM919961  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 44 to NF stage 45  
WE - NF5 GSM919941  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 5 (16-cell)  
WE - NF6 GSM919942  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 6 (32-cell)  
WE - NF8 GSM919943  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 8  
WE - NF9 GSM919922  GSM919944  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 9  
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