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| Status |
Public on Jan 31, 2018 |
| Title |
GM12878 SALP-seq |
| Sample type |
SRA |
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| Source name |
GM12878
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| Organism |
Homo sapiens |
| Characteristics |
cell line: GM12878
cell type: lymphoblastoid cells
fragment method: Tagmentation
cell number: 100000
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| Growth protocol |
HeLa, HepG2 and 293T cells were grown in Dulbecco’s Modified Eagle’s Medium (DMEM, GIBCO), GM12878 cells were cultured in RPMI 1640, which were all supplemented with 10% fetal bovine serum (FBS, GIBCO) with 100 μg/mL streptomycin and 100 units/mL penicillin at 37°C in 5% CO2.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
The nuclei of 100,000 GM12878, HeLa, HepG2, and 293T cells, and various numbers of HepG2 cells (50,000, 10,000, 5,000, 2,500, and 500) were extracted.
Nuclei then tagmented by Tn5 transposome with different barcoded Tn5 adaptors.The denatured tagmented gDNA was ligated with variant single strand adaptors. Then elongated, purified with Ampure XP beads and amplified with Illumina compatible primers. The genome DNA of HepG2 were digested with Hind III and sonicated, and genome DNA libraries were constructed with SALP protocol.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
HiSeq X Ten |
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| Description |
100,000 GM12878, HeLa, HepG2, and 293T cells, and various numbers of HepG2 cells (50,000, 10,000, 5,000, 2,500, and 500) tagmented chromatin were pooled together.
This sample represents GM12878
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| Data processing |
The raw reads data were separated according to the barcode using a homemade Perl scripts.
All reads were cut to 30 bp and aligned to the human genome (hg19) using Bowtie program (version 1.1.2)
Peak calling was performed with macs2 with the following parameters: -f BEDPE –keep-dup=2.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig
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| Submission date |
Sep 22, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Jian Wu |
| E-mail(s) |
[email protected]
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| Organization name |
Southeast University
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| Street address |
Sipailou 2#, Sipailou 2#
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| City |
NanJing |
| State/province |
Jiangsu |
| ZIP/Postal code |
210096 |
| Country |
China |
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| Platform ID |
GPL20795 |
| Series (1) |
| GSE104162 |
SALP, a new NGS library construction method especially useful for the high-throughput characterization of chromatin openness states |
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| Relations |
| BioSample |
SAMN07689059 |
| SRA |
SRX3206843 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2790937_GM12878.bigWig |
1.8 Gb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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