|
| Status |
Public on Feb 28, 2018 |
| Title |
DI5 |
| Sample type |
RNA |
| |
|
| Source name |
Human Tarsal Conjunctiva
|
| Organism |
Homo sapiens |
| Characteristics |
gender: male
age: 6 years old
phenotype: ocular Chlamydia trachomatis (Ct) infection and trachomatous inflammation-follicular (TF)
tissue: conjunctiva
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from each sample was extracted using Qiagen AllPrep Mini protocol. 25uL cDNA was generated from RNA template using NuGEN Ovation Pico WTA System V2 protocol
|
| Label |
biotin
|
| Label protocol |
cDNA fragmentation and labelling was performed according to FL-Ovation cDNA Biotin Module V2 protocol using fragmentation enzyme and biotin for cDNA labelling. The final volume obtained was 50µL of cDNA per sample.
|
| |
|
| Hybridization protocol |
cDNA was hybridised to GeneChip HTA 2.0 microarrays according to the NuGEN Hybridization, Cocktail Assembly and Fluidics Protocol
|
| Scan protocol |
GeneChip scanner was used for signal detection. Obtained probe sets hybridization intensities row data for each sample was stored in CEL files, using Affimetrix Launcher
|
| Description |
Solomon Islands child
SB002563
Conjunctival gene expression data from Solomon Islands children with TF and Ct
|
| Data processing |
Raw hybridisation intensities were normalised using RMA algorithm and annotated with GENBANK accession numbers using Affimetrix hta20 annotation. Probe sets lacking hybridization intensities and/or accession number, those redundent per gene and GeneChip endogenous controls, were discarted from overal data. Probe sets with interquirtile range lower than 0.1log2 were discarded.
|
| |
|
| Submission date |
Nov 15, 2017 |
| Last update date |
Feb 28, 2018 |
| Contact name |
Hristina Chavdarova Vasileva |
| E-mail(s) |
[email protected]
|
| Phone |
0207 927 2195
|
| Organization name |
LSHTM
|
| Department |
CRD
|
| Lab |
Keppel street 246
|
| Street address |
Keppel Street
|
| City |
London |
| State/province |
London |
| ZIP/Postal code |
WC1E 7HT |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL17586 |
| Series (1) |
| GSE106961 |
Conjunctival transcriptome profiling of Solomon Islanders with active trachoma but without ocular Chlamydia trachomatis infection. |
|
