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| Status |
Public on Jun 22, 2020 |
| Title |
ATAC-seq_siCtcf-1 |
| Sample type |
SRA |
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| Source name |
rat Schwann cell
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| Organism |
Rattus norvegicus |
| Characteristics |
tissue: Schwann cell
genotype: siCtcf
developmental stage: differentiation for 9h
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| Growth protocol |
Rat Schwann cells from sciatic nerves of newborn rats (1–2 days-old) were isolated. Schwann cells were grown routinely in DMEM/10% FBS (Life Technologies), supplemented with 10 ng/ml Neuregulin 1 (Nrg1; R&D Systems), and 5 μM forskolin (Sigma), plus L-glutamine and penicillin/streptomycin, hereafter denoted as SC proliferation medium. Cells between passages 2 and 6 were used in all experiments. >95% SC purity was achieved, assessed by positive SOX10 and S100β immunoreactivity.
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| Extracted molecule |
genomic DNA |
| Extraction 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.
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence.
ATAC-seq: Reads mapped to rn5 whole genome by Bowtie2 with default options.
ATAC-seq: Peak calling was performed using Model-based analysis of MACS with special parameter: --shift -75 --extsize 150 --nomodel --call-summits --nolambda --keep-dup all -p 0.01, to call peak.
Genome_build: rn5
Supplementary_files_format_and_content: wig files were generated by MACS
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| Submission date |
Sep 30, 2019 |
| Last update date |
Jun 22, 2020 |
| Contact name |
Richard Lu |
| Organization name |
Cincinnati Children's Hospital Medical Center
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| Department |
CBDI
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| Lab |
Lu Lab,T6.525
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| Street address |
3333 Burnet Ave
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| City |
Cincinnati |
| State/province |
OH |
| ZIP/Postal code |
45229 |
| Country |
USA |
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| Platform ID |
GPL18694 |
| Series (1) |
| GSE138117 |
CTCF-dependent chromatin architecture and SUZ12/PRC2 complex recruitment are required for peripheral myelination and repair |
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| Relations |
| BioSample |
SAMN12873000 |
| SRA |
SRX6922980 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4101156_jincheng-rSC-siCTCF-ATAC.wig_temp.wig.gz |
60.2 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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