Transcriptomics

Dataset Information

0

RNA-seq of human iPSCs derived neural crest stem cells (NCSCs) upon knock-down of BAZ1B (WSTF), including 3 williams beuren syndrome lines, 1 atypical deletion line, and 3 individuals with 7q11.23 duplication syndrome. Each line has been infected with a scramble, or at least one of two short-hairpins (as described in the coupled paper).


ABSTRACT: In order to dissect the role of BAZ1B in the paradigmatic craniofacial dysmorphisms that characterize Williams Beuren Syndrome and the simmetrical genetically opposite 7q11.23 duplication syndrome(7dupASD), we selected a large cohort of NCSCs lines (4 from WBS patients, 3 from 7dupASD patients and 4 from control individuals) to perform transcriptomic profiling. These lines show a clear cranial identity signatures which is crucial to pinpoint the disease pathogenesis, We then knocked-down (KD) BAZ1B via RNA interference in all lines across the three genetic conditions, including also NCSCs derived from a particularly informative atypical WBS patient (atWBS) bearing a partial deletion of the region that spares BAZ1B and six additional genes (see paper). In order to establish a high-resolution gradient of BAZ1B dosages, we selected two distinct shRNA against BAZ1B (i.e., sh1 and sh2) along with a scrambled shRNA sequence (hereafter scr) as negative control, for a total of 32 NCSC lines. KD efficiency was evaluated both at the RNA level by quantitative PCR (qPCR), confirming the attainment of the desired gradient with an overall reduction of about 40% for sh1 and 70% for sh2, as well as reduction at the protein level, as detected by Western blot (see the coupled paper).

INSTRUMENT(S): Illumina Hiseq 2500

ORGANISM(S): Homo sapiens  

SUBMITTER: Giuseppe Testa   Alessandro Vitriolo  

PROVIDER: E-MTAB-8455 | ArrayExpress | 2020-02-29

SECONDARY ACCESSION(S): ERP118000

REPOSITORIES: ArrayExpress, ENA

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