|
| Status |
Public on May 07, 2015 |
| Title |
Huh7 U6 20 Cre 16 |
| Sample type |
RNA |
| |
|
| Source name |
Huh7 cell line, shmiRNA integration and miR-122 ko, passage 1
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Huh7
passage: 1
genotype/variation: integration of a an anti-HCV shmiRNA in the hcr locus of Huh7 wild type cells and knock out 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
|
| 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
|
| Label protocol |
Agilent protocol "miRNA Complete Labeling and Hyb Kit"
|
| |
|
| Hybridization protocol |
Labeled miRNA sample were hybridized for at least 20 hr at 55C on Agilent human miRNA Microarray Release 19.0, 8x60k.
|
| Scan protocol |
Gene Expression Microarrays were scanned using the Agilent Scanner G2505C.
|
| Description |
miRNA expression profile after integration of a an anti-HCV shmiRNA in the hcr locus of Huh7 wild type cells and knock out 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).
|
| |
|
| 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 |
|
