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Sample GSM7030575 Query DataSets for GSM7030575
Status Public on Mar 04, 2024
Title Reaction_I_2_1
Sample type RNA
 
Source name Human skin biopsy
Organism Mycobacterium leprae
Characteristics source: Human skin biopsy
Extracted molecule total RNA
Extraction protocol RNA was prepared using the TRIzol following the manufacturer's recommendations. The concentration and purity of the RNA was evaluated using the Nanodrop Spectrophotometer (Thermo Scientific; 2000). The integrity of the RNA was analyzed on the Bioanalyzer (Agilent; 2100 expert). We considered RNA to be of good quality based on the 260/280 values (Nanodrop) and optimal RNA integrity profile in Bioanalyzer.
Label Cy3
Label protocol The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0424). The total RNA were reverse transcribed at 40°C using oligo dT primer tagged to a T7 polymerase promoter and converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNeasy columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-2000
 
Hybridization protocol Labeled cRNA sample were fragmented at 60ºC and hybridized on to a Agilent Mycobacterium leprae Gene Expression Microarray 8X15K. Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of (Agilent Technologies, In situ Hybridization kit, Part Number 5188-5242). Hybridization was carried out in Agilent’s Hybridization oven at 65ºC for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Agilent Technologies, Part Number 5188-5325 and 5188-5326)
Scan protocol Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D).
Description Reaction_I_2_1
SBL 29_R_I_1
Data processing Images were quantified using Feature Extraction Software ( Agilent). Feature extracted raw data was analyzed using GeneSpring GX software from Agilent. Normalization of the data was done in GeneSpring GX using the 75th percentile shift
 
Submission date Feb 07, 2023
Last update date Mar 04, 2024
Contact name Genotypic technology
E-mail(s) sudha.rao@genotypic.co.in
Organization name Genotypic Technology
Street address 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE
City Bangalore
State/province Karnataka
ZIP/Postal code 560094
Country India
 
Platform ID GPL33105
Series (1)
GSE224736 Development of gene expression signatures in whole spectrum of leprosy

Data table header descriptions
ID_REF
VALUE Normalized signal intensity (log base2)

Data table
ID_REF VALUE
GT_EA943_M.Leprae_Sense_NC_002677_10000 1.5179472
GT_EA943_M.Leprae_Sense_NC_002677_10001 1.9300094
GT_EA943_M.Leprae_Sense_NC_002677_10005 1.9176941
GT_EA943_M.Leprae_Sense_NC_002677_10008 2.5954027
GT_EA943_M.Leprae_Sense_NC_002677_100133 -0.35373402
GT_EA943_M.Leprae_Sense_NC_002677_100167 -1.7056046
GT_EA943_M.Leprae_Sense_NC_002677_100169 -2.130234
GT_EA943_M.Leprae_Sense_NC_002677_10023 0.07504463
GT_EA943_M.Leprae_Sense_NC_002677_100259 -1.3105841
GT_EA943_M.Leprae_Sense_NC_002677_100261 -1.3845325
GT_EA943_M.Leprae_Sense_NC_002677_100270 -0.3462305
GT_EA943_M.Leprae_Sense_NC_002677_100272 0.298707
GT_EA943_M.Leprae_Sense_NC_002677_100275 -0.8530302
GT_EA943_M.Leprae_Sense_NC_002677_100280 -1.944732
GT_EA943_M.Leprae_Sense_NC_002677_10034 -0.5218587
GT_EA943_M.Leprae_Sense_NC_002677_10035 0.38940477
GT_EA943_M.Leprae_Sense_NC_002677_10036 -0.35778666
GT_EA943_M.Leprae_Sense_NC_002677_100369 -2.5463784
GT_EA943_M.Leprae_Sense_NC_002677_10037 -0.24392557
GT_EA943_M.Leprae_Sense_NC_002677_10038 -0.100066185

Total number of rows: 10555

Table truncated, full table size 529 Kbytes.




Supplementary file Size Download File type/resource
GSM7030575_SG13134300_258476510005_S001_GE1_1105_Oct12_2_2.txt.gz 2.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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