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| Status |
Public on May 08, 2020 |
| Title |
HGADFN188 |
| Sample type |
SRA |
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| Source name |
skin
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| Organism |
Homo sapiens |
| Characteristics |
cell type: fibroblasts
patient status: young
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
50,000 cells were washed with ice cold 1x PBS and resuspended in 50 μl lysis buffer (10 mM TRIS-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630). The lysis reaction was carried out while spinning down the samples at 500 g for 10 minutes at 4°C. Samples were then resuspended in transposition buffer (25 μl 2x TD buffer (Illumina), 2.5 μl TDEI (Tagment DNA Enzyme, Illumina) and 22.5 μl ddH2O) and incubated for 30 minutes at 37°C.
Samples were purified using the MinElute PCR Purification kit (Qiagen). Final libraries were then PCR-amplified, purified once again with the same kit and subjected to paired-end sequencing on a HiSeq 4000 platform (Illumina).
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
HGPS_control_young_peaks.xls
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| Data processing |
Illumina Casava1.8.1 software used for basecalling.
Preprocessing, read trimming and quality filtering: Trimmomatic 0.39
Read mapping: Bowtie2
Peak calling: MACS2
Genome_build: hg19
Supplementary_files_format_and_content: output of MACS2 peak calling
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| Submission date |
May 08, 2020 |
| Last update date |
May 10, 2020 |
| Contact name |
Guenter Raddatz |
| Organization name |
German Center for Cancer Research
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| Street address |
Im Neuenheimer Feld 580
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| City |
Heidelberg |
| ZIP/Postal code |
69120 |
| Country |
Germany |
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| Platform ID |
GPL20301 |
| Series (2) |
| GSE150136 |
Epigenetic deregulation of lamina-associated domains in Hutchinson-Gilford Progeria Syndrome (ATAC-Seq) |
| GSE150138 |
Epigenetic deregulation of lamina-associated domains in Hutchinson-Gilford Progeria Syndrome |
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| Relations |
| BioSample |
SAMN14856566 |
| SRA |
SRX8294587 |
| 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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