NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM7030565 Query DataSets for GSM7030565
Status Public on Mar 04, 2024
Title Lepromatous leprosy 5
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 Lepromatous leprosy 5
SBL 9_LL
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 2.4653864
GT_EA943_M.Leprae_Sense_NC_002677_10001 2.3979726
GT_EA943_M.Leprae_Sense_NC_002677_10005 4.5321426
GT_EA943_M.Leprae_Sense_NC_002677_10008 5.1799707
GT_EA943_M.Leprae_Sense_NC_002677_100133 1.6507239
GT_EA943_M.Leprae_Sense_NC_002677_100167 -1.4186566
GT_EA943_M.Leprae_Sense_NC_002677_100169 -1.541558
GT_EA943_M.Leprae_Sense_NC_002677_10023 0.6699662
GT_EA943_M.Leprae_Sense_NC_002677_100259 -0.76194
GT_EA943_M.Leprae_Sense_NC_002677_100261 -0.7401881
GT_EA943_M.Leprae_Sense_NC_002677_100270 0.15770483
GT_EA943_M.Leprae_Sense_NC_002677_100272 -0.33907604
GT_EA943_M.Leprae_Sense_NC_002677_100275 -1.3589721
GT_EA943_M.Leprae_Sense_NC_002677_100280 -1.3054171
GT_EA943_M.Leprae_Sense_NC_002677_10034 -1.320138
GT_EA943_M.Leprae_Sense_NC_002677_10035 -1.2098994
GT_EA943_M.Leprae_Sense_NC_002677_10036 -1.2367227
GT_EA943_M.Leprae_Sense_NC_002677_100369 -3.340167
GT_EA943_M.Leprae_Sense_NC_002677_10037 -1.959975
GT_EA943_M.Leprae_Sense_NC_002677_10038 -0.3180561

Total number of rows: 10555

Table truncated, full table size 528 Kbytes.




Supplementary file Size Download File type/resource
GSM7030565_SG13134300_258476510002_S001_GE1_1105_Oct12_1_3.txt.gz 2.2 Mb (ftp)(http) TXT
Processed data included within Sample table
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap