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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Nov 22, 2018 |
| Title |
WT-3 |
| Sample type |
SRA |
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| Source name |
Human colon cancer cells
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| Organism |
Homo sapiens |
| Characteristics |
cell line: HCT116
genotype: WT
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| Growth protocol |
HCT116 cells were obtained from ATCC and maintained at 37℃ and 5% CO2 in DMEM supplemented with 10% (v/v) FBS, 100 U/mL penicillin, and 100 mg/mL streptomycin. All cell lines were tested for mycoplasma contamination and authenticated utilizing short tandem repeat profiling.
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Trizol reagent. 3 ug of total RNA is used for the construction of sequencing libraries.
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 4000 |
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| Data processing |
Normal sequence Hiseq 4000 PE150
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCH38 whole genome using hisat2 v2.1.0 with parameters hisat2 -p 8 --dta -x -1 -2 -S.
Transcript assembly and quantification with StringTie. Analysis of RNA-seq experiments requires accurate reconstructions of all the isoforms expressed from each gene, as well as estimates of the relative abundance of those isoforms. Use parameters as stringtie –e –B -p 8 -G -o.
Fragments per kilobase of transcript per million mapped reads (FPKM) were calculated using Ballgown from Pertea M et al., Nature Protocols, 2016. In short, differential expression analysis proceeds using a linear model. The FPKM values attached to transcripts are typically highly skewed; thus, to stabilize the variance, Ballgown’s builtin functions apply a log transformation and then fit standard linear models that can be used to test for differential expression.
Genome_build: GRCH38
Supplementary_files_format_and_content: text files include FPKM values for each Sample ...
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| Submission date |
Nov 20, 2018 |
| Last update date |
Nov 22, 2018 |
| Contact name |
Xin Yang |
| E-mail(s) |
xinyang2448@outlook.com
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| Organization name |
Columbia University
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| Department |
Institute for Cancer Genetics
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| Lab |
Wei Gu
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| Street address |
1130 Saint Nicholas Ave, ICRC building
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| City |
New York |
| ZIP/Postal code |
10032 |
| Country |
USA |
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| Platform ID |
GPL20301 |
| Series (1) |
| GSE122761 |
Acetylation of spliceosome protein PHF5A modulates stress responses and colorectal carcinogenesis through alternative splicing mediated upregulation of KDM3A |
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| Relations |
| BioSample |
SAMN10456647 |
| SRA |
SRX5035069 |
| 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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