Return to search results 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:

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 Xla   [-] [+] 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 Xla   [-] [+] 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 Xla   [-] [+] 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 Xla   [-] [+] 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 Xla   [-] [+] 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 Xla   [-] [+] 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 Xla   [-] [+] 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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