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SRX8142330: GSM4486219: ATAC-seq_control-2; Rattus norvegicus; ATAC-seq
4 ILLUMINA (Illumina HiSeq 2500) runs: 28.5M spots, 2.4G bases, 908.4Mb downloads

Submitted by: NCBI (GEO)
Study: CTCF-dependent chromatin architecture and SUZ12/PRC2 complex recruitment are required for peripheral myelination and repair
show Abstracthide Abstract
Chromatin organization is critical for cell growth, differentiation, and disease development, however, its functions in peripheral myelination and myelin repair remain elusive. Here we observed a global diminution of chromatin accessibility during Schwann cell differentiation and demonstrated that the chromatin organizer CCCTC-binding factor (CTCF) is critical for Schwann cell myelination and myelin regeneration after nerve injury. Inhibition of Ctcf or its deletion blocked Schwann cell differentiation at the pre-myelinating stage, whereas overexpression of CTCF promoted the myelination program. CTCF establishes the chromatin interaction loop between promoters and regulatory elements to promote expression of key pro-myelinogenic factors such as EGR2. In addition, CTCF interacts with SUZ12, a component of polycomb-repressive-complex 2, to repress expression of immature Schwann cell-associated regulators including HES1, RSPO2, and CALCA. Together, our findings reveal the dual role of CTCF-dependent chromatin organization in promoting myelinogenic programs and recruiting chromatin-repressive complexes to block differentiation inhibitors to control peripheral myelination and myelin repair. Overall design: RNA-seq: 2 Control and 2 Ctcf cKO mouse sciatic nerves; 3 siControl and 3 siCtcf rat Schwann cell cultures. ChIP-seq: 1 proliferating and 1 differentiating samples for CTCF ChIP-seq; 1 siControl and 1 siCtcf samples for H3K27ac ChIP-seq. ATAC-seq: 2 siControl and 2 siCtcf samples.
Sample: ATAC-seq_control-2
SAMN14644427 • SRS6505282 • All experiments • All runs
Library:
Instrument: Illumina HiSeq 2500
Strategy: ATAC-seq
Source: GENOMIC
Selection: other
Layout: SINGLE
Construction protocol: DNA for ATAC-seq: We isolated nuclei of 50,000 cells from the siControl and siCtcf rat Schwann cells in a cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) by exclude GFP- and 7-AAD+ cells. After spinning down at 500 × g for 10 min at 4 °C, nuclei were resuspended in transposition mix containing TD (2× reaction buffer), TDE1 (Nextera Tn5 Transposase) at 37°C for 30 min. The samples were purified using a Qiagen MinElute kit. Transposed DNA fragments were subsequently amplified and purified using Qiagen MinElute PCR Purification Kit. Libraries were generated using the Ad1_noMX and Ad2.1-2.4 barcoded primers and were amplified for 11 total cycles. Libraries were purified with AMPure beads (Agencourt) to remove contaminating primer dimers. All libraries were sequenced on the Illumina HiSeq 2500 with 75 bp single-end reads. ATAC-seq libraries were purified with AMPure beads (Agencourt) to remove contaminating primer dimers. All libraries were sequenced on the Illumina HiSeq 2500 with 75 bp single-end reads.
Experiment attributes:
GEO Accession: GSM4486219
Links:
Runs: 4 runs, 28.5M spots, 2.4G bases, 908.4Mb
Run# of Spots# of BasesSizePublished
SRR115741297,210,159609.2M229.8Mb2020-06-22
SRR115741307,093,912599.4M225.1Mb2020-06-22
SRR115741317,185,891607.2M229.5Mb2020-06-22
SRR115741327,057,565596.4M224.1Mb2020-06-22

ID:
10619563

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