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| Status |
Public on Dec 31, 2019 |
| Title |
siRNA-PiHL_rep3 |
| Sample type |
SRA |
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| Source name |
Colon cancer
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| Organism |
Homo sapiens |
| Characteristics |
cell line: HCT116
genotype/variation: siRNA-PiHL treatment
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| Treatment protocol |
HCT116 cells were treated with siRNA-NC or siRNA-PiHL
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| Growth protocol |
HCT116 cells were maintained at 37 °C in a humidified incubator containing 5% CO2 in Dulbecco’s modified Eagle medium (DMEM) (Gibco, Grand Island, NY, USA) supplemented with 10% fetal bovine serum (Gibco).
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from each sample was extracted using Trizol reagent (Life Technologies, Carlsbad, CA, USA) according to the manufacturer’s protocol. RNA purity was assessed by using an ND-1000 NanoDrop (Thermo Scientific, Wilmington, DE, USA). Each RNA sample had an A260:A280 ratio above 1.8 and an A260:A230 ratio above 2.0. RNA integrity was evaluated using the Agilent 2200 Tape Station (Agilent Technologies, Santa Clara, CA, USA), and all samples had an RNA integrity value above 7.0.
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 3000 |
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| Description |
siRNA-NC_rep3 vs. siRNA-PiHL_rep3
siRNA-PiHL treated HCT116 cells, replicate 3
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| Data processing |
HiSeq 3000 software was used for basecalling
Sequenced reads were mapped human transcriptome hg19 using TopHat 2.0.2 module
Transcripts were assembled and tested for abundance using Cufflinks 2.0.2 module
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM value for each sample
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| Submission date |
Jan 01, 2019 |
| Last update date |
Dec 31, 2019 |
| Contact name |
Xuan Deng |
| E-mail(s) |
16111220036@fudan.edu.cn
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| Organization name |
Huashan Hospital
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| Street address |
No.512 Huashan Road
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| City |
shanghai |
| ZIP/Postal code |
200040 |
| Country |
China |
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| Platform ID |
GPL21290 |
| Series (1) |
| GSE124526 |
A recurrently amplified long noncoding RNA in colorectal cancer regulates p53 protein stability through GRWD1/RPL11/MDM2 axis [RNA-seq] |
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| Relations |
| BioSample |
SAMN10666583 |
| SRA |
SRX5192121 |
| 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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