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Status |
Public on May 07, 2015 |
Title |
Huh7 TS 30 Cre 20 P2 |
Sample type |
RNA |
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|
Source name |
Huh7 cell line, shmiRNA integration and miR-122 mutation, passage 2
|
Organism |
Homo sapiens |
Characteristics |
cell line: Huh7 passage: 2 genotype/variation: integration of a an anti-HCV shmiRNA in the hcr locus of Huh7 wild type cells and mutation of miR-122 origin: Hepatocellular carcinoma gender: Male
|
Growth protocol |
Huh7 cells were culture with DMEM supplemented with 10% FCS, 1% P/S and 1% NEAA
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Extracted molecule |
total RNA |
Extraction protocol |
To extract the total RNA the cells were harvested from one confluent 10 cm dish and resuspended in 5 ml of QIAzol Lysis Reagent (QIAGEN, Hilden, Germany). The QIAzol RNA extraction protocol recommended by QIAGEN was used for RNA purification.
|
Label |
Cyanine 3-pCp
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Label protocol |
Agilent protocol "miRNA Complete Labeling and Hyb Kit"
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|
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Hybridization protocol |
Labeled miRNA sample were hybridized for at least 20 hr at 55C on Agilent human miRNA Microarray Release 19.0, 8x60k.
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Scan protocol |
Gene Expression Microarrays were scanned using the Agilent Scanner G2505C.
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Description |
miRNA expression profile after integration of a an anti-HCV shmiRNA in the hcr locus of Huh7 wild type cells and mutation of miR-122
|
Data processing |
Background correction was applied with "normexp"-method following quantile normalization on the probe level and log2-transformation. Probes were then averaged i) by duplicates ii) per gene target. Quantile normalization was re-applied (all Bioconductor software package limma), and finally ComBat batch-effect removal (Bioconductor package sva).
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|
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Submission date |
May 06, 2015 |
Last update date |
May 07, 2015 |
Contact name |
Tobias Bauer |
Organization name |
German Cancer Research Center
|
Department |
Theoretical Bioinformatics
|
Lab |
eilslabs
|
Street address |
Im Neuenheimer Feld 280
|
City |
Heidelberg |
ZIP/Postal code |
69120 |
Country |
Germany |
|
|
Platform ID |
GPL18044 |
Series (2) |
GSE68620 |
Engineering of a promoterless anti-viral RNAi hairpin into an endogenous miRNA locus [miRNA] |
GSE68638 |
Engineering of a promoterless anti-viral RNAi hairpin into an endogenous miRNA locus |
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