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Sample GSM1908747 Query DataSets for GSM1908747
Status Public on Oct 25, 2016
Title HF_C
Sample type RNA
 
Source name macrophages cells
Organism Bos primigenius
Characteristics tissue: Blood
time point: 24 hr infection
infection: Mycobacterium bovis
Treatment protocol Monocyte cells were harvested for treatments of M.Bovis 6 h post stimulation and stored at -80 0C in 1 ml of Trizol1 reagent (Invitrogen Ltd.).
Growth protocol Blood from the jugular vein was collected into lithium heparin and in 15 ml clean centrifuge tube, equal amount of blood and Histopaque 1077 (Sigma-Aldrich Ireland Ltd., Dublin, Ireland) centri. at 850 × g for 20 min., buffy coats were harvested, diluted 1:3 in PBS, centri. at 1200 × g for 30 min. PBMC were then washed twice in PBS at 500 × g for 10 min and in RPMI 1640 with 10% foetal calf serum and penicillin/streptomycin) placed at 5 × 106 PBMC in 50 ml teflon flasks. Non-adherent cells were removed by washes with pre-warmed PBS, and adhered monocyte cells were cultured for 6 days at 370C, with 5% CO2 to obtain MDMs.
Extracted molecule total RNA
Extraction protocol RNA isolation was performed using Qiagen RNeasy Mini Kit (CAT# 74106 ) following the manufacturer's recommendations.
Label Cy3
Label protocol The samples were labeled using Agilent Quick-Amp labeling kit (Part number: 5190-0442). 500ng of total RNA was reverse transcribed using oligo dT based method. mRNA was primed with oligo dT primer tagged to T7 promoter sequence and converted into double stranded cDNA using MMLV-RT reverse transcriptase. Further, in the same reaction cDNA was in-vitro transcribed to cRNA using T7 RNA polymerase enzyme. During cRNA synthesis, Cy3 labeled Cytosine nucleotide was incorporated into the newly synthesized strands. Labeled cRNA thus obtained was cleaned up using Qiagen RNeasy columns (Qiagen, Cat No: 74106). Concentration and amount of dye incorporated were determined using Nanodrop ND-1000.
 
Hybridization protocol Samples that pass the QC for specific activity were taken for hybridization. 600ng of labeled cRNA were hybridized on the array (AMADID: 29411) using the Gene Expression Hybridization kit (Part Number 5190-0404; Agilent) in Sure hybridization Chambers (Agilent) at 65ºC for 16 hours. Hybridized slides were washed using wash buffers (Part No: 5188-5327; Agilent)
Scan protocol scanned using the Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D)
Description Gene Expression after 24 hr infection of M.Bovis in cattle blood
Data processing Images were quantified using Feature Extraction Software ( Agilent). Feature extracted raw data was analyzed using GeneSpring GX Version software from Agilent. Normalization of the data was done in GeneSpring GX using the 75th percentile shift
 
Submission date Oct 15, 2015
Last update date Oct 25, 2016
Contact name SANJEEV KUMAR SHUKLA
E-mail(s) sanjeevcloning@gmail.com
Phone +919457273980
Organization name Indian Veterinary Research Institute
Department Division of Animal Genetics
Lab Blood Biochemical Polymorphism Laboratory
Street address IZATNAGAR
City Bareillly
State/province UTTAR PRADESH
ZIP/Postal code 243122
Country India
 
Platform ID GPL21036
Series (1)
GSE74050 Developing gene signature against Mycobacterium bovis infection in Cattle

Data table header descriptions
ID_REF
VALUE Log base 2

Data table
ID_REF VALUE
MARCH1 -0.5046189
MARCH2 3.4791288
MARCH3 1.683764
MARCH4 -3.1484752
MARCH5 4.1208916
MARCH6 5.3330784
MARCH7 5.671069
MARCH8 1.1987686
MARCH9 2.0458713
MARCH10 -2.7994056
MARCH11 -1.0416939
SEPT1 6.334547
SEPT2 6.1744776
SEPT3 -3.064557
SEPT4 1.5255489
SEPT5 2.8060455
SEPT6 5.03454
SEPT7 5.8665447
SEPT8 0.18840313
SEPT9 5.6039057

Total number of rows: 32429

Table truncated, full table size 624 Kbytes.




Supplementary file Size Download File type/resource
GSM1908747_SG13134300_252941110012_S001_GE1_1105_Oct12_1_1.txt.gz 12.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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