**6.1.1 Single strand conformation polymorphism (SSCP)**

Each of the samples was analysed for all the three markers in the tissue using blood as control. MSI positivity was indicated by *mobility* difference between blood, ectopic and eutopic tissue; presence of additional band or absence of bands.

MSI is defined as a difference in length due to insertion or deletion of the amplified microsatellite markers between the normal and ectopic tissue of the same individual. MSI in the ectopic tissues is assessed by the detection of alleles of novel size that are not present in the normal tissues of the same individuals. All microsatellite markers showing instability were analyzed. Samples lacking MSI were defined as Microsatellite stable (MSS).

#### **6.1.2 Differential display- reverse transcriptase-PCR (DD-RT-PCR)**

*RNA isolation and RT-PCR analysis:* Biopsy material obtained from the ectopic and eutopic endometrial tissue at the time of surgery was collected in sterile normal saline and transported to the lab for storage at minus 70°C. mRNA was isolated using mRNA direct isolation kit (Qiagen, Oligotex direct mRNA micro kit, Catalogue No. 72012) according to the manufacturer's instructions. mRNA was converted to cDNA by Reverse Transcriptase (RT) step which was followed by 45 cycles of 3-stage PCR with a specific annealing temperature for each primer set. DD RT-PCR allows identification of differentially expressed genes in various cell types and under defined physiologic conditions. DD was performed by the modified method of Hasan et al (2000). PCR was performed using selected primers to study the differential expression of the selected genes in the ectopic and eutopic endometrial tissues.

*cDNA DD PCR:* 5 sets of random exonic primers were used. DD-PCR was repeated with a different set of seven primers, which were selected arbitrarily.
