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Sample GSM7030555 Query DataSets for GSM7030555
Status Public on Mar 04, 2024
Title Healthy Control 3_2
Sample type RNA
 
Source name Human Skin Slit
Organism Mycobacterium leprae
Characteristics source: Human Skin Slit
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 Healthy Control 3_2
SBL 38_HC_2
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 1.2017207
GT_EA943_M.Leprae_Sense_NC_002677_10001 0.7856984
GT_EA943_M.Leprae_Sense_NC_002677_10005 0.21710348
GT_EA943_M.Leprae_Sense_NC_002677_10008 -0.1996541
GT_EA943_M.Leprae_Sense_NC_002677_100133 -0.27725458
GT_EA943_M.Leprae_Sense_NC_002677_100167 -0.75783396
GT_EA943_M.Leprae_Sense_NC_002677_100169 -1.020504
GT_EA943_M.Leprae_Sense_NC_002677_10023 0.09084749
GT_EA943_M.Leprae_Sense_NC_002677_100259 0.12799263
GT_EA943_M.Leprae_Sense_NC_002677_100261 -1.4513597
GT_EA943_M.Leprae_Sense_NC_002677_100270 1.1775503
GT_EA943_M.Leprae_Sense_NC_002677_100272 0.5044956
GT_EA943_M.Leprae_Sense_NC_002677_100275 -0.6039648
GT_EA943_M.Leprae_Sense_NC_002677_100280 0.28382397
GT_EA943_M.Leprae_Sense_NC_002677_10034 0.08820248
GT_EA943_M.Leprae_Sense_NC_002677_10035 0.06933117
GT_EA943_M.Leprae_Sense_NC_002677_10036 -0.35948944
GT_EA943_M.Leprae_Sense_NC_002677_100369 -0.6685009
GT_EA943_M.Leprae_Sense_NC_002677_10037 -0.6097684
GT_EA943_M.Leprae_Sense_NC_002677_10038 -0.19611454

Total number of rows: 10555

Table truncated, full table size 532 Kbytes.




Supplementary file Size Download File type/resource
GSM7030555_SG13134300_258476510003_S001_GE1_1105_Oct12_1_4.txt.gz 2.1 Mb (ftp)(http) TXT
Processed data included within Sample table
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