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| Status |
Public on Apr 30, 2019 |
| Title |
Day5_CPC_ATAC-seq-Rep2 |
| Sample type |
SRA |
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| Source name |
Cardiac progenitors
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| Organism |
Mus musculus |
| Characteristics |
cell type: ES cell derived cardiac progenitor cells
passages: 16-20
strain: C57BL/6
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| Treatment protocol |
N/A
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| Growth protocol |
E14 Tg(Nkx2–5-EmGFP) ES cells were maintained on mitomycin treated MEF in Knockout DMEM medium containing 4.5 mg/ml D-glucose, supplemented with 10% serum replacement, 2 mM L-Glutamine, 0.1 mM 2-mercaptoethanol, 1 mM sodium pyruvate, and 1,000 U/ml of leukemia inhibitory factor. For directed cardiomyocyte differentiation, ES cells were grown on gelatin in Neurobasal medium: DMEM/F12 (1:1) medium supplemented with 2,000 U/ml LIF and 10 ng/ml BMP4 for 2 days and differentiated by aggregation in low attachment bacterial dishes at a cell density of 75000 cells/ml in IMDM: F12 medium (3:1). After 48h aggregates were dissociated and re-aggregated in the presence of 5 ng/ml Activin A, 5ng/ml VEGF and 0.2ng/ml BMP4. 40h following the second aggregation, aggregates were dissociated and plated as a monolayer in Stempro-34 medium supplemented with Stempro34 nutrient supplement, L-Ascorbic Acid and 5ng/ml VEGF, 10ng/ml bFGF, and 25ng/ml FGF10 growth factors.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
ES cell derived cardiac progenitors were trypsinized and washed in PBS. 100,000 cells were resuspended in 50 uL cold lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Igepal CA-630) and used for ATAC Library preparation using Tn5 Transposase from Nextera DNA Library Prep Kit (Illumina #15028211). After centrifugation (10 min, 500 g at 4 °C), cell pellet was resuspended in transposition reaction mix (25 µl TD-Buffer, 2.5 µl Tn5, 22.5 µl water) and incubated for 30 min at 37 °C with gentle mixing. Immediately following the transposition reaction, purification was carried out using MinElute PCR Purification Kit (Qiagen #28004).
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Ion Torrent Proton |
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| Data processing |
Library strategy: ATAC-Seq
ATAC-Seq reads were mapped with bowtie2 to mm9 mouse genome. Samtools view (-F 1804 -f2) was used to remove unmapped, mate unmapped, not primary aligned reads. The MarkDuplicates.jar from Picard 1.136 was use to remove PCR artefacts. Peaks calling was performed with MACS14 60 (p1e5 --nomodel and --shiftsize 100), and peaks overlapping blacklist defined by ENCODE with the help of Bedtools v2.15 (intersect -wa)
Genome_build: mm9
Supplementary_files_format_and_content: Day5_CPC_Isl1_control_ATAC_Seq_merge.bw
Supplementary_files_format_and_content: Day5_CPC_control_ATAC_seq_peaks_annot.bed: Peaks file.
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| Submission date |
May 24, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Gergana Dobreva |
| E-mail(s) |
Gergana.Dobreva@medma.uni-heidelberg.de
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| Organization name |
Medical Faculty Mannheim/University of Heidelberg
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| Department |
Cardiovascular Genomics and Epigenomics
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| Lab |
AG Dobreva
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| Street address |
Ludolf-Krehl-Str. 7-11
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| City |
Mannheim |
| State/province |
Baden Württemberg |
| ZIP/Postal code |
68167 |
| Country |
Germany |
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| Platform ID |
GPL18635 |
| Series (2) |
| GSE80383 |
Pioneering function of Isl1 in the epigenetic control of cardiomyocyte cell fate |
| GSE81815 |
Pioneering function of Isl1 in the epigenetic control of cardiomyocyte cell fate [CPC_ATAC-seq] |
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| Relations |
| BioSample |
SAMN05171464 |
| SRA |
SRX1797666 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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