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| Status |
Public on Aug 01, 2012 |
| Title |
HepG2.2.15_DGE |
| Sample type |
SRA |
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| Source name |
HepG2.2.15 cells
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| Organism |
Homo sapiens |
| Characteristics |
cell line: HepG2.2.15
cell type: human hepatocellular liver carcinoma cells
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| Growth protocol |
HepG2.2.15 cells and HepG2 cells were maintained in Dulbecco's Modified Eagle’s Medium (DMEM) supplemented with 10% (v/v) foetal bovine serum (all from Gibco, USA) at 37 ℃, in an atmosphere of 5% CO2; 380µg/mL G418 was added to the HepG2.2.15 cell culture.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from HepG2 and HepG2.2.15 cells using TRIzol® Reagent (Invitrogen, USA), treated with DNase I (Roche, Germany) and converted to double-stranded cDNA using Oligo dT beads. Subsequently, the cDNA samples were digested using the restriction enzyme NlaIII, which recognizes and cuts the most 3' "CATG". Once digested into fragments, cDNA samples were ligated to Illumina specific adapter A, which contains a recognition site for enzyme MmeI. The Illumina specific adapter B was ligated after MmeI digestion (Illumina, USA). Using this technique, two DGE libraries from the two cells were constructed such that each molecule in the library is a 21 bp tag derived from a single transcript with Illumina specific adapters attached to both ends. Next, the 21 bp tags were enriched using PCR primers that anneal to the adaptors, and clusters were created on a flow cell using a Solexa Cluster Station following the manufacturer's instructions (Illumina, USA). Finally, massively parallel sequencing by synthesis was performed on the Illumina HiSeq™ 2000. Image analysis, base calling, extraction of 21 bp tags, and tag counting were performed using the Illumina pipeline. The number of times that a unique tag sequence is detected represents the quantitative expression level of the corresponding transcript in the cell type.
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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 |
Counts: All distinct tags were mapped to the University of California, Santa Cruz (UCSC) human genome (hg18) by SOAP2, which allowed a uniquely aligned tag to have up to one mismatching base. Tags that matched to more than one gene were not used in analyzing differential expression among the libraries. The number of normalized sequence tags of a gene locus=(the number of tags in the gene locus/ the total number of sequence tags of the whole genome)×1,000,000.
Genome Build:
HepG2.2.15_TagSeq.txt: UCSC hg18
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| Submission date |
Jan 31, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Ni Bing |
| E-mail(s) |
nibingxi@yahoo.com
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| Phone |
+86-23-68772348
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| Fax |
+86-23-68772348
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| Organization name |
PLA, Third Military Medical University
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| Department |
Institute of Immunology
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| Street address |
PLA, Third Military Medical University
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| City |
Chongqing |
| ZIP/Postal code |
400038 |
| Country |
China |
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| Platform ID |
GPL11154 |
| Series (2) |
| GSE35464 |
Genome-wide analysis of histone methylation reveals chromatin state-based regulation of host cellular gene expression induced by hepatitis B viruses (DGE dataset) |
| GSE35465 |
Genome-wide analysis of histone methylation reveals chromatin state-based regulation of host cellular gene expression induced by hepatitis B viruses |
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| Relations |
| SRA |
SRX118248 |
| BioSample |
SAMN00779879 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM869016_HepG2.2.15_TagSeq.txt.gz |
786.0 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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