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| Status |
Public on Dec 31, 2018 |
| Title |
MG-63_RNA_1 |
| Sample type |
SRA |
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| Source name |
Human osteosarcoma
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| Organism |
Homo sapiens |
| Characteristics |
cell type: osteoblast cell line
cell line: MG-63
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA library preparations were carried out on 500 ng of RNA from SaOS-2, U2OS, MG63 and HOS cells with RNA integrity number (RIN) > 7 using the Illumina TruSeq Stranded Total RNA Sample preparation kit, according to manufacturer's protocol.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
RNA-Seq: Raw reads were trimmed for quality (phred33 ≥ 30) and length (n ≥ 32), and Illumina adapters were clipped off using Trimmomatic v. 0.3564.
RNA-Seq: Filtered reads were aligned to the GRCh37 human reference using STAR v. 2.5.1b65.
RNA-Seq: Raw read counts of genes were obtained using HTseq-count v.0.6.166.
ATAC-Seq; DNAse-Seq: Illumina adapters were trimmed using Trimmomatic v. 0.3664.
ATAC-Seq; DNAse-Seq: Reads were aligned to the hg38 human reference using BWA v.0.7.15 65.
ATAC-Seq; DNAse-Seq: Peak calling was performed using hotspot2 with a cutoff of 1% FDR and converted to hg19 reference coordinates using UCSC liftOver.
Genome_build: hg19 (RNA-Seq); hg38 (ATAC-Seq; DNase-Seq)
Supplementary_files_format_and_content: bedGraph; Tab delimited peak files in starch format
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| Submission date |
Oct 02, 2018 |
| Last update date |
Dec 31, 2018 |
| Contact name |
John A Morris |
| E-mail(s) |
jmorris@nygenome.org
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| Organization name |
New York Genome Center
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| Street address |
101 Avenue of the Americas, 4th Floor
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| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10013 |
| Country |
USA |
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| Platform ID |
GPL20301 |
| Series (1) |
| GSE120755 |
An atlas of genetic influences on osteoporosis in humans and mice |
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| Relations |
| BioSample |
SAMN10166807 |
| SRA |
SRX4789666 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3414759_MG-63_RNA_1.forward.bedGraph.gz |
228.6 Mb |
(ftp)(http) |
BEDGRAPH |
| GSM3414759_MG-63_RNA_1.reverse.bedGraph.gz |
223.3 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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