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| Status |
Public on Jun 01, 2019 |
| Title |
MHCC97H_RNA-seq |
| Sample type |
SRA |
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| Source name |
hepatocellular carcinoma cell line
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| Organism |
Homo sapiens |
| Characteristics |
cell line: MHCC97H
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA of MHCC97H, MHCCLM3 and MHCCLM6 were extracted using standard Trizol protocol. MHCCLM6 was washed by pre-chilled phosphate buffered saline twice and addition of 2ml cell lysis buffer [1% Triton X-100 in ribosome buffer (RB buffer) [20 mM HEPES-KOH (pH 7.4), 15 mM MgCl2, 200mM KCl, 100 mg/ml cycloheximide and 2mM dithiothreitol]. After 30-min ice-bath, cell lysates were scraped and transferred to pre-chilled 1.5 ml tubes. Cell debris was removed by centrifuging at 16 200 g for 10 min at 4C. Supernatants were transferred on the surface of 20 ml of sucrose buffer (30% sucrose in RB buffer). RNCs were pelleted after ultra-centrifugation at 185000 g for 5h at 4C. Then RNC-RNA were isolated by using standard TRIzol protocol.
PolyA+ mRNA was extracted from the Total RNA and RNC-RNA using RNA purification beads (Illumina). Then the library construction was performed using Vazyme mRNA-seq v2 Library Kit with the insert size 200~300bp. mRNA and RNC-mRNA libraries were sequenced in an Illumina HiSeq X Ten sequencer under PE150 mode.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
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| Description |
MHCC97H
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| Data processing |
Illumina basecalling
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
Genome_build: GRCh38
Supplementary_files_format_and_content: excel files include log2(rpkm) for each sample.
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| Submission date |
Oct 09, 2018 |
| Last update date |
Jun 02, 2019 |
| Contact name |
Zhibiao Mai |
| E-mail(s) |
[email protected]
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| Organization name |
Jinan University
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| Department |
Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering
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| Lab |
920
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| Street address |
Huang-Pu Avenue West 601
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| City |
Guangzhou |
| State/province |
Guangdong |
| ZIP/Postal code |
510632 |
| Country |
China |
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| Platform ID |
GPL20795 |
| Series (1) |
| GSE121013 |
De novo assembled individual genome does not show advantage against standard reference genome: a demonstration of Chinese Han Population |
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| Relations |
| BioSample |
SAMN10222230 |
| SRA |
SRX4818265 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3423946_97HRNA_quant.xlsx |
1005.8 Kb |
(ftp)(http) |
XLSX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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