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GEO Series: GSE64551

Title: Occupancy and transcriptional profile of Prdm12 in posteriorized neural tissue

Summary

V1 interneurons are a class of inhibitory neurons that play an essential role in vertebrate locomotion; however, the factors contributing to their specification are poorly understood. Morphological and molecular evidence suggest that the zinc finger transcription factor Prdm12 may play a role in promoting V1 interneurons while repressing V2 and V0 fates. Here, we performed RNAseq on Xenopus laevis ectoderm converted to posteriorized neural tissue (with noggin and retinoic acid) in the presence or absence of a series of Prdm12 constructs (wild-type Prdm12, Prdm12-VP16, and Prdm12-engrailed-repressor). We also performed ChIPseq on a Prdm12-FLAG in wild-type or posteriorized neuralized (with noggin and retinoic acid) X. laevis ectoderm. Taken together, these data demonstrate Prdm12's genomic targets and their downstream transcription.


Contributors: Ian Quigley, Kristine Henningfeld, Chris Kintner, Eric Bellefroid, Claude Van Campenhout

Experiment Type: X. laevis embryos were injected with mRNAs encoding prdm12 constructs, along with the bmp inhibitor noggin. Presumptive ectoderm (neuralized by noggin) was dissected and treated with retinoic acid. Samples were then processed into RNAseq libraries or prdm12-FLAG was immunoprecipitated and its targets sequenced. Background was input prior to IP.

Experiment Reagents: nog.L, Retinoic acid, Tg(Flag-Mmu.prdm12),

Article: Xenbase, PubMed

Source: NCBI GEO, Xenbase FTP

Samples: (DEG = Differentially Expressed Genes; GSM = GEO Sample Number)
Sample View GSMs Assay Type
input animal cap + nog + RA - NF28 GSM1574084  ChIP-Seq
Background: Xla.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
mRNA injection nog.L nog.L NF stage 3 (4-cell) animal blastomere
mRNA injection Tg(Flag-Mmu.prdm12) prdm12.L NF stage 3 (4-cell) animal blastomere
chemical Retinoic acid NF stage 10 animal cap
explant   NF stage 10 animal cap
Conditions:
Tissue Assay Stages ChIP Antibody
animal cap NF stage 28  
   prdm12 animal cap + nog + RA - NF28 GSM1574082  ChIP-Seq
Background: Xla.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
mRNA injection nog.L nog.L NF stage 3 (4-cell) animal blastomere
mRNA injection Tg(Flag-Mmu.prdm12) prdm12.L NF stage 3 (4-cell) animal blastomere
chemical Retinoic acid NF stage 10 animal cap
explant   NF stage 10 animal cap
Conditions:
Tissue Assay Stages ChIP Antibody
animal cap NF stage 28 FLAG Ab3
input animal cap - NF28 GSM1574083  ChIP-Seq
Background: Xla.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
mRNA injection Tg(Flag-Mmu.prdm12) prdm12.L NF stage 3 (4-cell) animal blastomere
explant   NF stage 10 animal cap
Conditions:
Tissue Assay Stages ChIP Antibody
animal cap NF stage 28  
   prdm12 animal cap - NF28 GSM1574081  ChIP-Seq
Background: Xla.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
mRNA injection Tg(Flag-Mmu.prdm12) prdm12.L NF stage 3 (4-cell) animal blastomere
explant   NF stage 10 animal cap
Conditions:
Tissue Assay Stages ChIP Antibody
animal cap NF stage 28 FLAG Ab3
animal cap - NF28 GSM1574071  GSM1574072  RNA-Seq
Background: Xla.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
explant   NF stage 10 animal cap
Conditions:
Tissue Assay Stages ChIP Antibody
animal cap NF stage 28  
   animal cap + EnR-prdm12 - NF28 DEG GSM1574079  GSM1574080  RNA-Seq
Background: Xla.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
mRNA injection Tg(prdm12-EnR-Flag) prdm12.L NF stage 3 (4-cell) animal blastomere
explant   NF stage 10 animal cap
Conditions:
Tissue Assay Stages ChIP Antibody
animal cap NF stage 28  
   animal cap + nog - NF28 DEG GSM1574073  GSM1574074  RNA-Seq
Background: Xla.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
mRNA injection nog.L nog.L NF stage 3 (4-cell) animal blastomere
explant   NF stage 10 animal cap
Conditions:
Tissue Assay Stages ChIP Antibody
animal cap NF stage 28  
   animal cap + prdm12 - NF28 DEG GSM1574075  GSM1574076  RNA-Seq
Background: Xla.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
mRNA injection Tg(Flag-Mmu.prdm12) prdm12.L NF stage 3 (4-cell) animal blastomere
explant   NF stage 10 animal cap
Conditions:
Tissue Assay Stages ChIP Antibody
animal cap NF stage 28  
   animal cap + prdm12-VP16 - NF28 DEG GSM1574077  GSM1574078  RNA-Seq
Background: Xla.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
mRNA injection Tg(VP16-Flag-prdm12) prdm12.L NF stage 3 (4-cell) animal blastomere
explant   NF stage 10 animal cap
Conditions:
Tissue Assay Stages ChIP Antibody
animal cap NF stage 28  
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