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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jun 25, 2023 |
| Title |
SJSA-1 cells overexpressing scramble shRNA rep4 |
| Sample type |
SRA |
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| Source name |
SJSA-1 cell
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| Organism |
Homo sapiens |
| Characteristics |
cell type: human osteosarcoma cell
cell line: SJSA-1
knockdown: scramble shRNA
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using Trizol reagent.
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 NovaSeq 6000 |
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| Description |
shNC-4
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| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Homo_sapiens.GRCh38.87 whole genome
Fragments per kilobase per million mapped fragments (FPKM) were calculated using a protocol from Trapnell, C. et al, Nature biotechnology, 2010.
Genome_build: GRCh38
Supplementary_files_format_and_content: raw and normalized read count
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| Submission date |
Oct 04, 2020 |
| Last update date |
Jun 25, 2023 |
| Contact name |
Jianlin Zhou |
| E-mail(s) |
[email protected]
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| Phone |
+8613755191079
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| Organization name |
Hunan Normal University
|
| Department |
College of Life Science
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| Street address |
36 Lushan road
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| City |
Changsha |
| State/province |
Hunan |
| ZIP/Postal code |
410081 |
| Country |
China |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE158976 |
Datasets for the effects of RUNX2 silencing on transcriptomic and metabolomic profiles in SJSA-1 osteosarcoma cells |
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| Relations |
| BioSample |
SAMN16362513 |
| SRA |
SRX9239959 |
| 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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