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| Status |
Public on Jul 10, 2017 |
| Title |
C15_0_1_ATAC-seq |
| Sample type |
SRA |
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| Source name |
hiPSC
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| Organism |
Homo sapiens |
| Characteristics |
cell type: hiPS cell
cell line: C15
differentiation time (days): 0
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| Treatment protocol |
The cardiomyocyte differentiation was initiated using a monolayer differentiation method with PSC Cardiomyocyte Differentiation kit (Thermo Fisher Scientific).
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| Growth protocol |
Both hESCs and hiPSCs were grown in Matrigel (Corning)-coated 12-well plates with Essential 8™ Medium (Thermo Fisher Scientific).
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
About 50,000 cells were collected and pelleted by centrifugation for 15 min at 500 g and 4°C. Cell pellets were washed once with ice-cold 1x PBS and then pelleted again by centrifugation at the previous settings. Cell pellets were re-suspended in 25 μl of ice-cold lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Igepal CA-630), and nuclei were pelleted by centrifugation for 30 min at 500g, 4°C
The nuclei were re-suspended in 50 μl reaction buffer (2 μl of Tn5 transposase and 12.5 μl of TD buffer from a Nextera DNA Library Prep Kit from Illumina, and 22.5 μl nuclease-free H2O). The reaction was incubated at 37°C for 30 min, and subsequently the reaction mixture was purified using MinElute PCR Purification Kit (Qiagen). The purified transposed DNA was amplified with NEBNext High-Fidelity 2 X PCR Master Mix (New England Biolabs) and custom-designed primers with barcodes (Buenrostro et al. 2013). Gel electrophoresis was used to remove primer dimers from the PCR products with 2% E-Gel EX Agarose Gels (Thermo Fisher Scientific), and then the PCR products were purified using QIAquick PCR Purification Kit (Qiagen). DNA concentration was measured with a Qubit Fluorometer (Thermo Fisher Scientific) and library sizes were determined using Agilent High Sensitivity DNA kit on Agilent 2100 Bioanalyzer. The ATAC-seq libraries were sequenced with a HiSeq 2000 sequencer (Illumina) with 2 X101 cycles.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
biological replicate 1
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| Data processing |
Library strategy: ATAC-seq
The raw data was then trimmed to remove the adapter sequences (CTGTCTCTTATACACATCT) with in house script. The trimmed files were mapped to the human genome (hg19 GRCh37) using Bowtie2 (2.1.0) with default parameters. Read pairs, which aligned concordantly to the genome and had a mapping quality greater than 10, were kept for following analysis. Read pairs mapped to mitochondria DNA were discarded. Redundancy read pairs from PCR amplification were also removed afterward using Picard tools (version 1.79). The finally filtered bam files were converted into normalized BigWig files using Bedtools (2.25.0) for visualization of the peaks.
To estimate global enrichment of open accessible-regions of the ATAC-seq data, the ATAC-seq signal around 2KB of transcription start sties of RefGenes (UCSC hg19) was compared to an upstream 4KB window. The maximum enrichment sites were taken as the enrichment score for each library and used to represent the quality of ATAC-seq library.
Open accessible-regions for each library were defined by the peaks called by MACS2 (2.1.0) with the parameters “-g hs --nomodel --shift 0 –q 0.01”. Peaks located at blacklist genomics regions were removed using bedtools (2.25.0).
Genome_build: hg19
Supplementary_files_format_and_content: bed file
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| Submission date |
Aug 08, 2016 |
| Last update date |
Oct 11, 2022 |
| Contact name |
Qing Liu |
| E-mail(s) |
liuqingcell@gmail.com
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| Organization name |
Clemson University
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| Department |
Biological Sciences
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| Lab |
Qing Liu
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| Street address |
Jordan Hall
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| City |
Clemson |
| State/province |
SC |
| ZIP/Postal code |
29634 |
| Country |
USA |
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| Platform ID |
GPL11154 |
| Series (2) |
| GSE85330 |
Genome-wide chromatin accessibility profiling of cardiomyocyte differentiation from human embryonic stem cells and iPS cells (ATAC-seq) |
| GSE85332 |
Genome-wide transcriptomic analysis and chromatin accessibility profiling of cardiomyocyte differentiation from human embryonic stem cells and iPS cells |
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| Relations |
| BioSample |
SAMN05525666 |
| SRA |
SRX2008161 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2264802_C15_0_1.filterBL.bed.gz |
1.6 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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