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| Status |
Public on Jun 29, 2017 |
| Title |
Circular RNA replicate 2 |
| Sample type |
SRA |
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| Source name |
Circular RNA, HeLa
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| Organism |
Homo sapiens |
| Characteristics |
cell line: HeLa
transfection: Circular RNA
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| Treatment protocol |
The RNA and Lipofectamine 2000 were diluted and mixed in Opti-MEM (Invitrogen, 31985-088), incubated for 5 min at rt, the nucleic acids and Lipofectamine 2000 were mixed together, incubated for 15 min at rt and then the nucleic acids-Lipofectamine 2000 complexes were applied to the monolayer cultures. (500 ng of nucleic acids was transfected into one well of a 24-well plate.)
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| Growth protocol |
Hela cells were grown in Dulbecco’s modified Eagle’s medium (DMEM, 11995-073) supplemented with 100 units/ml penicillin-streptomycin (Gibco, 15140-163), 10% (v/v) fetal bovine serum
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using TRIzol reagent, according to manufacturer’s instructions. Total RNA was subjected to rRNA depletion with Ribo Minus Kit.
RNA sequencing libraries were prepared as decribed in Flynn et al., 2015
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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 |
Sequenced reads were collapsed for PCR duplicates and trimmed for adaptor sequence. Reads mapping to rRNA and transfected RNA were removed. Remaining reads were mapped to hg19 genome assembly whole genome using sequence aligner STAR with parameters FilterMatchNminOverLread 0.4 --outFilterScoreMinOverLread 0.4
Reads matching each gene were calculated using HTSeq. Differential gene expression was calculated with DESeq2.
Genome_build: hg19
Supplementary_files_format_and_content: counts.txt files include counts calculated by HTSeq, and DGE.txt includes fold change and p-value calculated by DESeq2.
Supplementary_files_format_and_content: MolCell2017_DNA_plasmidseq.docx includes plasmid insert sequences.
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| Submission date |
May 11, 2016 |
| Last update date |
Apr 21, 2024 |
| Contact name |
Howard Y Chang |
| Organization name |
Stanford University
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| Department |
Dermatology
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| Lab |
Chang lab
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| Street address |
CCSR 2130, 269 Campus Drive
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| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
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| Platform ID |
GPL18573 |
| Series (1) |
| GSE81345 |
Sensing self and nonself circular RNAs |
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| Relations |
| BioSample |
SAMN04990200 |
| SRA |
SRX1756869 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2150851_Circ2A.counts.txt.gz |
93.0 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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