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| Status |
Public on Apr 11, 2016 |
| Title |
ATAC-Seq_Sample09_Fibroblast_Rep4 |
| Sample type |
SRA |
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| Source name |
Fibroblasts
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| Organism |
Homo sapiens |
| Characteristics |
cell type: fibroblast
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Sorted cells were lysed in 5 to 10 μl ice-cold ATAC lysis buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1 % IGEPAL CA-630) for 10 minutes. Without nuclear extraction step, samples were processed using transposase reaction mix of Nextera DNA sample preparation kit (Illumina), with incubation for 30 minutes at 37 ˚C. Indices were incorporated using Nextera Index Kit (Illumina) in amplification step.
ATAC-seq libraries were purified using Ampure XP beads (Beckman Coulter Genomics) to remove remaining adapters. Libraries were assessed for the quality and quantity using Agilent Bioanalyzer 2000 and the KAPA library quantification kit for Illumina (KAPA Biosystems).
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
Protocol: ATAC-Seq
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| Data processing |
Library strategy: ATAC-Seq
Basecalls performed using BCL2FASTQ version 1.8.4.
Mapping was performed by BWA (version 0.6.2) , allowing up to 2 mismatches, using the reference human genome, NCBI build 37 (hg19) .
PCR duplicated reads and multi-mapped reads were discarded using Samtools (version 0.1.19).
Peak detection was performed using Hotspot (version 4.1.0) with a false discovery rate (FDR) cut-off of 0.01
Genome_build: hg19
Supplementary_files_format_and_content: bed files which contain peak information were generated using Hotspot version 4.1.0.
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| Submission date |
Apr 20, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Koji Kitazawa |
| E-mail(s) |
kkitazaw@koto.kpu-m.ac.jp
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| Organization name |
Kyoto Prefectural University of Medicine
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| Department |
Ophthalmology
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| Street address |
465 Kajiicho Kamigyoku
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| City |
Kyoto |
| State/province |
Kyoto |
| ZIP/Postal code |
601-0841 |
| Country |
Japan |
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| Platform ID |
GPL16791 |
| Series (2) |
| GSE67823 |
Master transcription factors in corneal epithelial cells |
| GSE68069 |
Master transcription factors in corneal epithelial cells [ATAC-Seq] |
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| Relations |
| BioSample |
SAMN03492780 |
| SRA |
SRX1000988 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1662261_Sample12_Fibroblast_Rep4.fdr0.01.hot.bed.gz |
1.7 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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