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| Status |
Public on Dec 06, 2016 |
| Title |
Vitamin D, KD, rep1 |
| Sample type |
SRA |
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| Source name |
Human MG63 osteosarcoma cells
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Bone
age: 14 years old
cell line: MG63 osteosarcoma cells
genotype/variation: HNRNPC KD
agent: 1,25D
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| Extracted molecule |
total RNA |
| Extraction protocol |
Human MG63 osteosarcoma cells (American Type Culture Collection, CRL-1427) were cultured in Dulbecco’s modified Eagle medium (DMEM, high glucose, Gibco, 11995-065) supplemented with 10% Fetal Bovine Serum (FBS) cultured at 37oC with 5% CO2. Crystalline 1,25-dihydroxyvitamin D3 (1,25(OH)2D3, Enzo Life Sciences, BML-DM200-0050) was reconstituted in ethanol. Ethanol (0.1%) was used as vehicle treatment.
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
D.KD-1
yes vitamin D treatment, yes HNRNPC knockdown
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| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were mapped to Ensembl transcript (release 72) then hg19 whole genome using tophat v1.4.1 with parameters -a 8 -m 0 -I 300000 -p 8 -g 20 --library-type fr-unstranded --initial-read-mismatches 3 --segment-mismatches 2
Fragments Per Kilobase of exon per Million fragments mapped (FPKM) were calculated using cufflinks v2.0.2 with uniquely and properly mapped pairs.
Genome_build: hg19
Supplementary_files_format_and_content: The .txt file reports FPKMs for all samples.
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| Submission date |
Nov 07, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Yi Xing |
| Organization name |
UCLA
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| Department |
Department of Microbiology, Immunology, & Molecular Genetics
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| Street address |
650 Charles E. Young Dr. South
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| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095-7278 |
| Country |
USA |
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| Platform ID |
GPL16791 |
| Series (1) |
| GSE63086 |
Heterogeneous nuclear ribonucleoprotein C1/C2 links transcriptional and splicing actions of 1,25-dihydroxyvitamin D |
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| Relations |
| BioSample |
SAMN03167934 |
| SRA |
SRX753526 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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