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GEO Series: GSE74919

Title: Whole transcriptome target sequencing: profiling gene expression and alternative polyadenylation with one pipeline.

Summary

We have developed a deep sequencing method called Whole Transcriptome Target Sequencing (WTTS), which sequences the 3’ ends of polyA+ RNA. This method can simultaneously profile gene expression and alternative polyadenylation.


Contributors: Zhihua Jiang, Xiang Zhou, Rui Li, Jennifer Michal, Richard Harland

Experiment Type: A pooled total RNA sample derived from three male and three female adult frogs was used in seven trials to develop the WTTS assay. The same sample was sequenced using RNA-seq as control. Technical replicates of the same female adult frog were analyzed using the finalized WTTS library preparation method. Biological replicates, which included 10 embryo pools collected from two families at stages 6, 8, 11, 15 and 28 were subsequently analyzed to validate the finalized WTTS method. Six embryo samples collected at stages of 6, 8 and 11 were also sequenced using RNA-seq. Therefore, this submission involved a total of 26 libraries.

Article: Xenbase, PubMed

Source: NCBI GEO, Xenbase FTP

Samples: (DEG = Differentially Expressed Genes; GSM = GEO Sample Number)
Sample View GSMs Assay Type
WE (female) - adult GSM1937550  GSM1937551  WTTS-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
whole organism adult frog stage  
WE - NF11 GSM1937567  GSM1937568  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 11  
WE - NF11 (WTTS-Seq) GSM1937556  GSM1937557  WTTS-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 11  
WE - NF15 GSM1937558  GSM1937559  WTTS-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 15  
WE - NF28 GSM1937560  GSM1937561  WTTS-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 28  
WE - NF6 GSM1937563  GSM1937564  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 6 (32-cell)  
WE - NF6 (WTTS-Seq) GSM1937552  GSM1937553  WTTS-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 6 (32-cell)  
WE - NF8 GSM1937565  GSM1937566  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 8  
WE - NF8 (WTTS-Seq) GSM1937554  GSM1937555  WTTS-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 8  
WE - adult GSM1937562  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
whole organism adult frog stage  
WE - adult - Trial 1 GSM1937543  WTTS-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
whole organism adult frog stage  
WE - adult - Trial 2 GSM1937544  WTTS-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
whole organism adult frog stage  
WE - adult - Trial 3 GSM1937545  WTTS-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
whole organism adult frog stage  
WE - adult - Trial 4 GSM1937546  WTTS-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
whole organism adult frog stage  
WE - adult - Trial 5 GSM1937547  WTTS-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
whole organism adult frog stage  
WE - adult - Trial 6 GSM1937548  WTTS-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
whole organism adult frog stage  
WE - adult - Trial 7 GSM1937549  WTTS-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
whole organism adult frog stage  
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