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Sample GSM1662254 Query DataSets for GSM1662254
Status Public on Apr 11, 2016
Title ATAC-Seq_Sample05_CEC_Rep1
Sample type SRA
 
Source name CEC, Donor B, passage 2
Organism Homo sapiens
Characteristics cell type: corneal epithelium
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).
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina HiSeq 2500
 
Description Protocol: ATAC-Seq
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.
 
Submission date Apr 20, 2015
Last update date May 15, 2019
Contact name Koji Kitazawa
E-mail(s) kkitazaw@koto.kpu-m.ac.jp
Organization name Kyoto Prefectural University of Medicine
Department Ophthalmology
Street address 465 Kajiicho Kamigyoku
City Kyoto
State/province Kyoto
ZIP/Postal code 601-0841
Country Japan
 
Platform ID GPL16791
Series (2)
GSE67823 Master transcription factors in corneal epithelial cells
GSE68069 Master transcription factors in corneal epithelial cells [ATAC-Seq]
Relations
BioSample SAMN03492773
SRA SRX1000981

Supplementary file Size Download File type/resource
GSM1662254_Sample05_CEC_Rep1.fdr0.01.hot.bed.gz 1.6 Mb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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