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| Status |
Public on Oct 10, 2019 |
| Title |
sgP130_siP107_350_B |
| Sample type |
SRA |
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| Source name |
Human Foreskin Fibroblasts (HFF)
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| Organism |
Homo sapiens |
| Characteristics |
cell type: Human Foreskin Fibroblasts (HFF)
crispr-cas9 target: sgP130
sirna target: siP107
doxorubicin treatment: 350 nM
biological replicate: bio repeat B
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from HFFs using Qiagen RNeasy plus kit, treated with DNAse (Turbo DNA-free, Life Technologies), and quality control checked using Qubit, TapeStation, and qPCR.
Libraries were prepared using Kappa stranded mRNA Hyper Prep
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Reads were mapped to the Hg19 genome by STAR.
HTseq was used to generate count file with gene names(53).
R package DESeq2 was used to normalize counts (mean-ratio method), calculate total reads, and determine differential gene expression(54).
MA plots were generated to display differentially expressed genes.
Principal component analysis showed sufficient clustering of biological replicates.
Genome_build: hg19
Supplementary_files_format_and_content: DESeq2 normalized reads.
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| Submission date |
Aug 14, 2019 |
| Last update date |
Oct 10, 2019 |
| Contact name |
Amy E Schade |
| E-mail(s) |
[email protected]
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| Organization name |
Brigham and Women's Hospital
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| Department |
Medicine
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| Lab |
Karen Cichowski
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| Street address |
77 Avenue Louis Pasteur
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
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| Platform ID |
GPL18573 |
| Series (1) |
| GSE135842 |
RNA-seq of human foreskin fibroblast cells lacking RB, p130, and p107 treated with doxorubicin. |
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| Relations |
| BioSample |
SAMN12573849 |
| SRA |
SRX6716665 |
| 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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