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| Status |
Public on Mar 31, 2017 |
| Title |
ATACseq_E10.5-Md_1 |
| Sample type |
SRA |
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| Source name |
Cranial neural crest cells
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| Organism |
Mus musculus |
| Characteristics |
cell type: Cranial neural crest cells
cell subpopulation: Md
age: E10.5
genotype: WT
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
To profile for open chromatin, we used the Assay for Transposase Accessible Chromatin (ATACseq) protocol, performed according to Buenrostro et al., 2015 with minor modifications. The dissected samples were incubated in trypsin 0.5%/EDTA 1X at 37 °C for 10 minutes and rinsed in DMEM 1X/ FBS 10%. Cranial neural crest cells (CNCCs) were then dissociated with a pipette, filtered and collected by FACS. 50.000 CNCCs were used per transposition reaction. After sorting, CNCCs were pelleted by centrifugation (500 g for 5 minutes at 4°C), washed with cold 1X PBS buffer and pelleted again by centrifugation (500 g for 5 minutes at 4°C). They were then re-suspended in cold lysis buffer (10mM Tris-HCl pH 8.0; 10mM NaCl; 3mM MgCl2; 0.5% NP40) and pelleted by centrifugation (5 minutes, 500 g at 4°C). The supernatant was discarded.
The transposition reaction was performed as reported in Buenrostro et al., 2015, steps 6 – 12, using the Nextera Sample preparation kit from Illumina. PCR Amplification was done according to Buenrostro et al., 2015, steps 13 – 18. The indexing PCR primers mentioned in the supplemental material from Buenrostro et al., 2013 were used. Amplified libraries were cleaned up using AMPure XP beads in a DNA / beads ratio of 1 / 1.8. The Quality of the libraries and size distribution was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies). Sequencing was performed on an Illumina HiSeq 2500 machine (50 bp read length, paired-end) according to Illumina standards.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Library strategy: ATAC-Seq
Illumina RTA 1.18.64 and bcl2fastq2 v2.17 was used for basecalling and demultiplexing.
Read pairs were aligned to the GRCm38/mm10 reference genome using the QuasR Bioconductor package (PMID: 25417205, version 1.12.0) by the qAlign function with parameters maxHits=10 (allowing up to 10 hits per read, reporting one randomly), which internally uses bowtie (version 1.1.1, PMID: 19261174).
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: wig files were generated using the qExportWig function from the QuasR package with default parameters except scaling=1e6 and binsize=100. The scores in the wig file therefore represent the number of alignment pairs per 100bp window and per million reads in the library.
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| Submission date |
Nov 02, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Filippo M. RIJLI |
| Organization name |
Friedrich Miescher Institute for Biomedical Research
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| Street address |
Maulbeerstrasse 66
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| City |
Basel |
| ZIP/Postal code |
4058 |
| Country |
Switzerland |
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| Platform ID |
GPL17021 |
| Series (2) |
| GSE89436 |
Gene bivalency at Polycomb domains regulates cranial neural crest positional identity [ATAC-seq] |
| GSE89437 |
Gene bivalency at Polycomb domains regulates cranial neural crest positional identity |
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| Relations |
| BioSample |
SAMN05967824 |
| SRA |
SRX2320603 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2371734_ATACseq_E10.5-Md_1.scaled_0100.wig.gz |
9.9 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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