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E-GEOD-64551 - Occupancy and transcriptional profile of Prdm12 in posteriorized neural tissue

Status
Released on 4 November 2015, last updated on 1 December 2015
Organism
Xenopus laevis
Samples (14)
Protocols (3)
Description
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. 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 types
ChIP-seq, RNA-seq of coding RNA 
Contacts
Ian K Quigley <iquigley@salk.edu>, Chris Kintner, Claude Van Campenhout, Eric J Bellefroid, Kristine Henningfeld
Citation
Prdm12 specifies V1 interneurons through cross-repressive interactions with Dbx1 and Nkx6 genes in Xenopus. Th�lie A, Desiderio S, Hanotel J, Quigley I, Van Driessche B, Rodari A, Borromeo MD, Kricha S, Lahaye F, Croce J, Cerda-Moya G, Ordo�o Fernandez J, Bolle B, Lewis KE, Sander M, Pierani A, Schubert M, Johnson JE, Kintner CR, Pieler T, Van Lint C, Henningfeld KA, Bellefroid EJ, Van Campenhout C. , PMID:26443638
MINSEQE
Exp. designProtocolsVariablesProcessedSeq. reads
Files
Investigation descriptionE-GEOD-64551.idf.txt
Sample and data relationshipE-GEOD-64551.sdrf.txt
Additional data (1)E-GEOD-64551.additional.1.zip
Links