NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1964924 Query DataSets for GSM1964924
Status Public on Jan 08, 2016
Title # 3VHL/HIF1A Vhlh fl/fl w/ Adeno-Cre-GFP Cy5 and # 3VHL/HIF1A Vhlh fl/fl w/ Adeno-GFP. Control Cy3
Sample type RNA
 
Channel 1
Source name Animal 3; Primary kidney epithelial cells from Vhlh flox/flox, Hif1a flox/flox animal. Cells treated with Adeno-GFP virus. Control cell culture Cy3 labeled.
Organism Mus musculus
Characteristics Sex: female
cell type: primary kidney epithelial cell
age: 50 days (adult)
Treatment protocol After 5–6 days in culture, cells were infected with adenoviruses expressing GFP (Vector Biolabs, 1060) or Cre-GFP (Vector Biolabs, 1700). 
Growth protocol Kidneys were dissected from 2-month-old floxed mice. After removing the capsule under sterile conditions, kidneys were mashed with a razor blade on ice and digested in collagenase II (Gibco) and soya trypsin inhibitor (Gibco) solution at 37°C for 30 min. The cell suspension was filtered through a 70 µm cell strainer and washed in HBSS + 5% FCS. Erythrocytes were lysed for 1 min using standard ACK buffer. Cells were resuspended in complete K-1 culture medium [Dulbecco's modified Eagle's medium (DMEM):Hams F12] (50:50), supplemented with 0.5% foetal calf serum, hormone mix [5 µg/ml insulin, 1.25 ng/ml prostaglandin E1 (PGE1), 34 pg/ml triiodothyronine, 5 µg/ml Apo-transferrin, 1.73 ng/ml sodium selenite and 18 ng/ml of hydrocortisone] and 25 ng/ml epidermal growth factor (EGF). Cells were counted and seeded at a density of 1 × 106 cells on standard 100 mm plastic tissue culture plates.
Extracted molecule total RNA
Extraction protocol Machery Nagel Nucleospin RNA II according to producer instructions.
Label Cy3
Label protocol standard Agilent protocol
 
Channel 2
Source name Animal 3. Primary kidney epithelial cells from Vhlh flox/flox, Hif1a flox/flox animals. Cells treated with Adeno-Cre-GFP virus labeled with Cy5.
Organism Mus musculus
Characteristics Sex: female
cell type: primary kidney epithelial cell
age: 50 days (adult)
Treatment protocol After 5–6 days in culture, cells were infected with adenoviruses expressing GFP (Vector Biolabs, 1060) or Cre-GFP (Vector Biolabs, 1700). 
Growth protocol Kidneys were dissected from 2-month-old floxed mice. After removing the capsule under sterile conditions, kidneys were mashed with a razor blade on ice and digested in collagenase II (Gibco) and soya trypsin inhibitor (Gibco) solution at 37°C for 30 min. The cell suspension was filtered through a 70 µm cell strainer and washed in HBSS + 5% FCS. Erythrocytes were lysed for 1 min using standard ACK buffer. Cells were resuspended in complete K-1 culture medium [Dulbecco's modified Eagle's medium (DMEM):Hams F12] (50:50), supplemented with 0.5% foetal calf serum, hormone mix [5 µg/ml insulin, 1.25 ng/ml prostaglandin E1 (PGE1), 34 pg/ml triiodothyronine, 5 µg/ml Apo-transferrin, 1.73 ng/ml sodium selenite and 18 ng/ml of hydrocortisone] and 25 ng/ml epidermal growth factor (EGF). Cells were counted and seeded at a density of 1 × 106 cells on standard 100 mm plastic tissue culture plates.
Extracted molecule total RNA
Extraction protocol Machery Nagel Nucleospin RNA II according to producer instructions.
Label Cy5
Label protocol standard Agilent protocol
 
 
Hybridization protocol standard Agilent protocol
Scan protocol standard Agilent protocol
Description One of the biological replicates avaraged to obtain values for Vhlh-/-, Hif1a-/-_logRatio
mouse number 3VHL/HIF1A_primary kidney epithelial cells from Vhlh flox/flox infected with Adeno-Cre-GFP virus Cy5 labeled and mouse number_ 3VHL/HIF1A_primary kidney epithelial cells from Vhlh flox/flox infected with Adeno-GFP virus. Control cell culture Cy3 labeled.
Data processing Data were processed using R Bioconductor (limma). For the final analysis the gene expression levels were dye effect corrected and values for biological replicates were averaged to obtain a matrix with gene expression levels for 4 independent biological conditions (Vhlh-/-, Vhlh-/-/Hif1α-/-, Vhlh-/-/Hif2α-/- and Vhlh-/-/Hif1α-/-/Hif2α-/-).
normalized log2 ratio (Cy5/Cy3) representing values for primary kidney cells with defined alleles floxed infected either with CRE-GFP adenovirus (excision) or GFP adenovirus (control).
 
Submission date Dec 07, 2015
Last update date Jan 09, 2016
Contact name Michal Rajski
E-mail(s) rajski.michal@gmail.com
Organization name University of Zurich
Department Institute of Physiology
Lab 23K86
Street address Winterthurerstrasse 190
City Zurich
ZIP/Postal code CH - 8057
Country Switzerland
 
Platform ID GPL10333
Series (1)
GSE75745 Microarray characterization of Vhl; Vhl, Hif1a; Vhl, Hif2a and Vhl, Hif1a, Hif2a deficient primary kidney cells

Data table header descriptions
ID_REF
VALUE normalized log10 ratio Cy5/Cy3

Data table
ID_REF VALUE
1 -2.602198849e-001
2 0.000000000e+000
3 0.000000000e+000
4 0.000000000e+000
5 0.000000000e+000
6 0.000000000e+000
7 0.000000000e+000
8 0.000000000e+000
9 0.000000000e+000
10 0.000000000e+000
11 0.000000000e+000
12 -8.628407112e-002
13 0.000000000e+000
14 -8.518589691e-002
15 1.196476039e-001
16 5.167820243e-002
17 1.010799840e-001
18 0.000000000e+000
19 0.000000000e+000
20 1.232744408e-001

Total number of rows: 44397

Table truncated, full table size 1005 Kbytes.




Supplementary file Size Download File type/resource
GSM1964924_Vhlh_HIF1A_A3_GFP-Cy3--Vhlh_HIF1A_A3_CRE-Cy5.txt.gz 4.2 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data provided as supplementary file
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap