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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jul 26, 2019 |
| Title |
ATAC.d3F.r2 |
| Sample type |
SRA |
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| Source name |
mesendoderm cells
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| Organism |
Mus musculus |
| Characteristics |
cell line: double knock-in (DKI) mouse ES cell line carrying Foxa2-Venus and Sox17-Cherry gene fusions
genotype/variation: Foxa2-Venus heterozygous;Sox17-Cherry homozygous
facs sorting markers: Foxa2-Venus-pos/Sox17-Cherry-neg
time point: d3
antibody: none
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| Growth protocol |
The cells were cultured for few consecutive passages on gelatine and ES medium. On the day of differentiation, mESCs were seeded on 10 cm gelatine coated dishes directly in endoderm differentiation medium (EDM) supplemented with 1 ng/ml of murine Wnt3a and 10 ng/ml of Activin A. Freshly prepared EDM supplemented with Wnt3a and Activin A was added every day. Cells were collected on day0, day3 and day5 for FACS isolation.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
ATAC-seq was done as previously described (Buenrostro et al., 2013). Briefly, 50000 FACS sorted cells were washed in 1xPBS, re-suspended in 50 ul of lysis buffer (10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40,) and spun at 500g for 10 min at 4 °C to collect nuclei. Nuclei were subsequently re-suspended in 50 µl Transposase reaction containing 25µL 2x tagmentation buffer, 22.5 µl water, 2.5 µl Tn5 Transposase (Illumina Nextera DNA Library Preparation Kit, cat. FC-121-1030). Reactions were incubated for 30 min at 37° C in a thermomixer shaking at 300 rpm and DNA purified using Qiagen PCR clean-up MinElute kit (Qiagen).
The transposed DNA was subsequently amplified in 50µl reactions with custom primers as described (Buenrostro et al., 2013). After 4 cycles, libraries were then monitored with qPCR: 5 µl PCR sample in a 15 µl reaction with the same primers. qPCR output was monitored for the ΔRN; 0.25 ΔRN cycle number was used to estimate the number of additional cycles of the PCR reaction needed for the remaining PCR samples. Amplified libraries were purified with the Qiagen PCR clean-up MinElute kit (Qiagen) and size selected for fragments less than 600 bp using the Agencourt AMPure XP beads (Beckman Coulter). Libraries were quality controlled by Qubit and Agilent DNA Bioanalyzer analysis.
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 1500 |
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| Data processing |
Reads were mapped to the mouse genome (mm10) using bowtie (Langmead et al., 2009).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bigWig files were generated from Homer tag directories using makeBigWig.pl.
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| Submission date |
Jun 25, 2018 |
| Last update date |
Jul 26, 2019 |
| Contact name |
Filippo M. Cernilogar |
| E-mail(s) |
filippo.cernilogar@med.uni-muenchen.de
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| Organization name |
LMU Munich
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| Department |
Biomedical Center
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| Street address |
Grosshaderner Strasse 9
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| City |
Planegg-Martinsried |
| ZIP/Postal code |
82152 |
| Country |
Germany |
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| Platform ID |
GPL18480 |
| Series (2) |
| GSE116255 |
Pre-marked chromatin and transcription factor co-binding shape the pioneering activity of Foxa2 [ATAC-seq] |
| GSE116262 |
Pre-marked chromatin and transcription factor co-binding shape the pioneering activity of Foxa2 |
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| Relations |
| BioSample |
SAMN09486861 |
| SRA |
SRX4298266 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3223247_ATAC.d3F.r2_m1.ucsc.bigWig |
223.6 Mb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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