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| Status |
Public on Mar 09, 2022 |
| Title |
0h rep2, PCAT2 KI |
| Sample type |
SRA |
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| Source name |
SW480 colon cancer cells
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| Organism |
Homo sapiens |
| Characteristics |
cell tyep: SW480 knocked-in with PCAT2 gene
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using TRIzol methods and treated with DNAse.
Sequencing libraries were generated using Illumina TruSeq V3 protocol and subject to 101 bp paired-end sequencing on Illumina HiSeq2000.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Base-calling with Illumina run time analysis software 1.12.4.2
Alignment to mm9 using Casava Eland extended
Transcript levels were quantified using Tophat and Cufflinks.
Genome_build: hg38
Supplementary_files_format_and_content: FPKM
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| Submission date |
Jul 27, 2021 |
| Last update date |
Mar 09, 2022 |
| Contact name |
Songjoon Baek |
| Organization name |
NCI / NIH
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| Department |
CCR
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| Lab |
LRBGE
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| Street address |
41 Library Drive
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| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
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| Platform ID |
GPL11154 |
| Series (2) |
| GSE180923 |
Oncogenic lncRNAs alter epigenetic memory at a fragile chromosomal site in human cancer cells [RNA-seq] |
| GSE180959 |
Oncogenic lncRNAs alter epigenetic memory at a fragile chromosomal site in human cancer cells |
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| Relations |
| BioSample |
SAMN20434875 |
| SRA |
SRX11569463 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5478535_2_SW480_PCAT2_KI_2_rsem.genes.results.gz |
2.4 Mb |
(ftp)(http) |
RESULTS |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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