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SRX5822695: GSM3762876: Dnttip1KO2_D1E6_rep2; Mus musculus; RNA-Seq
1 ILLUMINA (Illumina NovaSeq 6000) run: 81.5M spots, 16.5G bases, 2.4Gb downloads

Submitted by: NCBI (GEO)
Study: The histone deacetylase complex MiDAC regulates a neurodevelopmental gene expression to control neurite outgrowth [RNA-Seq]
show Abstracthide Abstract
Cell type diversity during neuro-ectodermal (NE) differentiation is achieved through selective activation and silencing of neurodevelopmental genes. Here, we show a key role for the histone deacetylase complex MiDAC during neuronal differentiation of mouse embryonic stem cells (mESCs) into NE. We demonstrate that MiDAC functions as a modulator of a neurodevelopmental gene expression program and binds to important regulators of neurite outgrowth. MiDAC mediates the removal of H4K20ac on the promoters and enhancers of pro-neural genes such as the axon guidance ligands Slit3 and Ntn1 while in parallel reducing H3K27ac on promoter-proximal and -distal elements of negative regulators of neurogenesis thereby upregulating and inhibiting gene expression, respectively. Furthermore, neurite outgrowth defects in MiDAC KO neurons can be rescued by restoring Slit3/Robo3-Ntn1/Unc5b signaling. Taken together, our work suggests a crucial role for MiDAC in regulating the secretome of the Slit3/Robo3-Ntn1/Unc5b signaling axes to ensure the proper integrity of neurite development. Overall design: RNA was isolated from 3 x 10e6 mESCs with the RNeasy Mini Kit (Qiagen, 74106) following the manufacturer's instructions from each genotype in duplicate. Genotypes: WT, Dnttip1 KO1 (D1E6), Dnttip1 KO2 (D2A7), Elmsan1 KO1 (E2E8) and Elmsan1 KO2 (E2G7).
Sample: Dnttip1KO2_D1E6_rep2
SAMN11632852 • SRS4751257 • All experiments • All runs
Organism: Mus musculus
Library:
Instrument: Illumina NovaSeq 6000
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: cDNA
Layout: PAIRED
Construction protocol: RNA was isolated from 3 x 10e6 cells with the RNeasy Mini Kit (Qiagen, 74106) following the manufacturer's instructions with the following alterations. Cells were resuspended in 600 μl RLT buffer (with 2-Mercaptoethanol) and the homogenate further passed through a QiaShredder column (Qiagen, 79656) by centrifugation in a table top centrifuge for 2 minutes at full speed at room temperature (RT). The optional step after the second wash with RPE buffer was applied to dry the membrane. RNA was eluted with 85 μl H2O and supplied with 10 μl 10x DNAase buffer and 5 μl DNAse I (NEB, M0303S), mixed and incubated at RT for 20 min. After incubation RNA was purified by following the “RNA Cleanup” protocol in the RNeasy Mini Handbook. The optional step after the second wash with RPE buffer was applied to dry the membrane. RNA was eluted in 50 μl H2O and concentration determined with a NanoDrop 8000 Spectrophotometer. RNA-seq Library Preparation and Sequencing:RNA was quantified using the Quant-iT RiboGreen RNA Assay Kit (Thermo Fisher Scientific, R11490) and quality checked with the RNA 6000 Nano Kit (Agilent, 5067-1511) on a 2100 Bioanalyzer (Agilent, G2939BA) or High Sensitivity RNA ScreenTape Assay (Agilent, 5067-5579, 5067-5580, 5067-5581) on a 4200 TapeStation (Agilent, G2991AA) prior to library generation. Libraries were prepared from total RNA with the TruSeq Stranded Total RNA Library Prep Gold Kit (Illumina, 20020599) according to the manufacturer's instructions. Libraries were analyzed for insert size distribution with the High Sensitivity DNA Kit (Agilent, 5067-4626) on a 2100 Bioanalyzer or the High Sensitivity D1000 ScreenTape Assay (Agilent, 5067-5584, 5067-5585, 5067-5587, 5067-5603) on a 4200 TapeStation. Libraries were quantified using the Quant-iT PicoGreen dsDNA Assay (Thermo Fisher Scientific, P11496). Paired end 100 cycle sequencing was performed on a HiSeq 2500, HiSeq 4000, or NovaSeq 6000 System (all from Illumina) according to the manufacturer's instructions.
Experiment attributes:
GEO Accession: GSM3762876
Links:
Runs: 1 run, 81.5M spots, 16.5G bases, 2.4Gb
Run# of Spots# of BasesSizePublished
SRR904615781,522,40716.5G2.4Gb2020-04-10

ID:
7828403

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