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Series GSE64551 Query DataSets for GSE64551
Status Public on Nov 04, 2015
Title Occupancy and transcriptional profile of Prdm12 in posteriorized neural tissue
Organism Xenopus laevis
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
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.
Overall design 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.
Contributor(s) Quigley IK, Henningfeld K, Kintner C, Bellefroid EJ, Van Campenhout C
Citation(s) 26443638
Submission date Dec 29, 2014
Last update date May 15, 2019
Contact name Ian K Quigley
Phone 858-453-4100
Organization name Salk Institute
Department Molecular Neurobiology Lab
Lab Kintner
Street address 10010 North Torrey Pines Road
City La Jolla
State/province CA
ZIP/Postal code 92037
Country USA
Platforms (2)
GPL17682 Illumina HiSeq 2000 (Xenopus laevis)
GPL18936 Illumina HiSeq 2500 (Xenopus laevis)
Samples (14)
GSM1574071 wt_RNAseq_rep_1
GSM1574072 wt_RNAseq_rep_2
GSM1574073 noggin_RNAseq_rep_1
BioProject PRJNA271289
SRA SRP051597

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Supplementary file Size Download File type/resource
GSE64551_RNAseq_normalized.txt.gz 1.3 Mb (ftp)(http) TXT
GSE64551_prdm12_FLAG_ChIPseq.bed.gz 503.9 Kb (ftp)(http) BED
GSE64551_prdm12_FLAG_noggin_RA_ChIPseq.bed.gz 553.4 Kb (ftp)(http) BED
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