Search results for the GEO ID: GSE20430  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM512409 | GPL201 |
|
Tarsal conjunctiva, GAR_01
|
Swab, tarsal conjunctiva, T0
|
tissue: tarsal conjunctiva
gender: Male
age (years): 9
ethnicity: Manjago
fpc trachoma score: F1/P1/C0
equivalent who simplified trachoma grade: --
roche ct/ng amplicor pcr value: NEG
ompa copies per swab: 0
disease: normal
|
GAR_01
|
| Sample_geo_accession | GSM512409
| | Sample_status | Public on Sep 03 2010
| | Sample_submission_date | Feb 19 2010
| | Sample_last_update_date | Sep 03 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Swabs from the tarsal conjunctiva of participants with clinical signs (test) and without (control) of acute trachoma were collected into RNA preservative (RNAlater, Ambion, Inc).
| | Sample_growth_protocol_ch1 | N/A
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Upper tarsal conjunctival swab total RNA was extracted and purified with the RNeasy Micro-kit (Qiagen Ltd, Crawley, UK).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | cRNA probes were prepared from 100 microg total RNA using two-rounds in vitro transcription with biotin-labeled nucleotides (Affymetrix RNA transcript labelling kits (Affymetrix, Santa Clara, CA)).
| | Sample_hyb_protocol | Biotinylated complementary RNA (cRNA) targets were purified using the Sample Cleanup Module (Affymetrix, Santa Clara, CA) and subsequently 10ug of Fragmented biotinylated cRNA was hybridized, according to the manufacturer’s standard protocols, for 16hrs at 45oC.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix confocal laser scanner 3000.
| | Sample_data_processing | Data was subjected to QC analysis followed by RMA and is provided as RMA-normalised natural-scale data. RMA was performed using function rmasummary in Bioinformatics Toolbox version 3.4, Matlab version R2009b.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Martin,James,Holland
| | Sample_contact_email | Martin.Holland@lshtm.ac.uk
| | Sample_contact_phone | +442079272295
| | Sample_contact_laboratory | Clinical Research
| | Sample_contact_department | Infectious and Tropical Diseases
| | Sample_contact_institute | London School of Hygiene and Tropical Medicine
| | Sample_contact_address | Keppel Street
| | Sample_contact_city | London
| | Sample_contact_zip/postal_code | WC1E 7HT
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM512nnn/GSM512409/suppl/GSM512409.CEL.gz
| | Sample_series_id | GSE20430
| | Sample_data_row_count | 8793
| | |
|
GSM512410 | GPL201 |
|
Tarsal conjunctiva, GAR_04
|
Swab, tarsal conjunctiva, N
|
tissue: tarsal conjunctiva
gender: Female
age (years): 4
ethnicity: Manjago
fpc trachoma score: F0/P0/C0
equivalent who simplified trachoma grade: --
roche ct/ng amplicor pcr value: NEG
ompa copies per swab: 0
disease: normal
|
GAR_04
|
| Sample_geo_accession | GSM512410
| | Sample_status | Public on Sep 03 2010
| | Sample_submission_date | Feb 19 2010
| | Sample_last_update_date | Sep 03 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Swabs from the tarsal conjunctiva of participants with clinical signs (test) and without (control) of acute trachoma were collected into RNA preservative (RNAlater, Ambion, Inc).
| | Sample_growth_protocol_ch1 | N/A
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Upper tarsal conjunctival swab total RNA was extracted and purified with the RNeasy Micro-kit (Qiagen Ltd, Crawley, UK).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | cRNA probes were prepared from 100 microg total RNA using two-rounds in vitro transcription with biotin-labeled nucleotides (Affymetrix RNA transcript labelling kits (Affymetrix, Santa Clara, CA)).
| | Sample_hyb_protocol | Biotinylated complementary RNA (cRNA) targets were purified using the Sample Cleanup Module (Affymetrix, Santa Clara, CA) and subsequently 10ug of Fragmented biotinylated cRNA was hybridized, according to the manufacturer’s standard protocols, for 16hrs at 45oC.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix confocal laser scanner 3000.
| | Sample_data_processing | Data was subjected to QC analysis followed by RMA and is provided as RMA-normalised natural-scale data. RMA was performed using function rmasummary in Bioinformatics Toolbox version 3.4, Matlab version R2009b.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Martin,James,Holland
| | Sample_contact_email | Martin.Holland@lshtm.ac.uk
| | Sample_contact_phone | +442079272295
| | Sample_contact_laboratory | Clinical Research
| | Sample_contact_department | Infectious and Tropical Diseases
| | Sample_contact_institute | London School of Hygiene and Tropical Medicine
| | Sample_contact_address | Keppel Street
| | Sample_contact_city | London
| | Sample_contact_zip/postal_code | WC1E 7HT
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM512nnn/GSM512410/suppl/GSM512410.CEL.gz
| | Sample_series_id | GSE20430
| | Sample_data_row_count | 8793
| | |
|
GSM512411 | GPL201 |
|
Tarsal conjunctiva, GAR_12
|
Swab, tarsal conjunctiva, TF
|
tissue: tarsal conjunctiva
gender: Female
age (years): 3
ethnicity: Manjago
fpc trachoma score: F2/P1/C0
equivalent who simplified trachoma grade: TF
roche ct/ng amplicor pcr value: POS
ompa copies per swab: 96
disease: trachoma
|
GAR_12
|
| Sample_geo_accession | GSM512411
| | Sample_status | Public on Sep 03 2010
| | Sample_submission_date | Feb 19 2010
| | Sample_last_update_date | Sep 03 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Swabs from the tarsal conjunctiva of participants with clinical signs (test) and without (control) of acute trachoma were collected into RNA preservative (RNAlater, Ambion, Inc).
| | Sample_growth_protocol_ch1 | N/A
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Upper tarsal conjunctival swab total RNA was extracted and purified with the RNeasy Micro-kit (Qiagen Ltd, Crawley, UK).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | cRNA probes were prepared from 100 microg total RNA using two-rounds in vitro transcription with biotin-labeled nucleotides (Affymetrix RNA transcript labelling kits (Affymetrix, Santa Clara, CA)).
| | Sample_hyb_protocol | Biotinylated complementary RNA (cRNA) targets were purified using the Sample Cleanup Module (Affymetrix, Santa Clara, CA) and subsequently 10ug of Fragmented biotinylated cRNA was hybridized, according to the manufacturer’s standard protocols, for 16hrs at 45oC.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix confocal laser scanner 3000.
| | Sample_data_processing | Data was subjected to QC analysis followed by RMA and is provided as RMA-normalised natural-scale data. RMA was performed using function rmasummary in Bioinformatics Toolbox version 3.4, Matlab version R2009b.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Martin,James,Holland
| | Sample_contact_email | Martin.Holland@lshtm.ac.uk
| | Sample_contact_phone | +442079272295
| | Sample_contact_laboratory | Clinical Research
| | Sample_contact_department | Infectious and Tropical Diseases
| | Sample_contact_institute | London School of Hygiene and Tropical Medicine
| | Sample_contact_address | Keppel Street
| | Sample_contact_city | London
| | Sample_contact_zip/postal_code | WC1E 7HT
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM512nnn/GSM512411/suppl/GSM512411.CEL.gz
| | Sample_series_id | GSE20430
| | Sample_data_row_count | 8793
| | |
|
GSM512412 | GPL201 |
|
Tarsal conjunctiva, GAR_14
|
Swab, tarsal conjunctiva, N
|
tissue: tarsal conjunctiva
gender: Female
age (years): 7
ethnicity: Manjago
fpc trachoma score: F0/P0/C0
equivalent who simplified trachoma grade: --
roche ct/ng amplicor pcr value: POS
ompa copies per swab: 0
disease: normal
|
GAR_14
|
| Sample_geo_accession | GSM512412
| | Sample_status | Public on Sep 03 2010
| | Sample_submission_date | Feb 19 2010
| | Sample_last_update_date | Sep 03 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Swabs from the tarsal conjunctiva of participants with clinical signs (test) and without (control) of acute trachoma were collected into RNA preservative (RNAlater, Ambion, Inc).
| | Sample_growth_protocol_ch1 | N/A
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Upper tarsal conjunctival swab total RNA was extracted and purified with the RNeasy Micro-kit (Qiagen Ltd, Crawley, UK).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | cRNA probes were prepared from 100 microg total RNA using two-rounds in vitro transcription with biotin-labeled nucleotides (Affymetrix RNA transcript labelling kits (Affymetrix, Santa Clara, CA)).
| | Sample_hyb_protocol | Biotinylated complementary RNA (cRNA) targets were purified using the Sample Cleanup Module (Affymetrix, Santa Clara, CA) and subsequently 10ug of Fragmented biotinylated cRNA was hybridized, according to the manufacturer’s standard protocols, for 16hrs at 45oC.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix confocal laser scanner 3000.
| | Sample_data_processing | Data was subjected to QC analysis followed by RMA and is provided as RMA-normalised natural-scale data. RMA was performed using function rmasummary in Bioinformatics Toolbox version 3.4, Matlab version R2009b.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Martin,James,Holland
| | Sample_contact_email | Martin.Holland@lshtm.ac.uk
| | Sample_contact_phone | +442079272295
| | Sample_contact_laboratory | Clinical Research
| | Sample_contact_department | Infectious and Tropical Diseases
| | Sample_contact_institute | London School of Hygiene and Tropical Medicine
| | Sample_contact_address | Keppel Street
| | Sample_contact_city | London
| | Sample_contact_zip/postal_code | WC1E 7HT
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM512nnn/GSM512412/suppl/GSM512412.CEL.gz
| | Sample_series_id | GSE20430
| | Sample_data_row_count | 8793
| | |
|
GSM512413 | GPL201 |
|
Tarsal conjunctiva, GAR_15
|
Swab, tarsal conjunctiva, N
|
tissue: tarsal conjunctiva
gender: Female
age (years): 6
ethnicity: Manjago
fpc trachoma score: F0/P0/C0
equivalent who simplified trachoma grade: --
roche ct/ng amplicor pcr value: POS
ompa copies per swab: 19
disease: normal
|
GAR_15
|
| Sample_geo_accession | GSM512413
| | Sample_status | Public on Sep 03 2010
| | Sample_submission_date | Feb 19 2010
| | Sample_last_update_date | Sep 03 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Swabs from the tarsal conjunctiva of participants with clinical signs (test) and without (control) of acute trachoma were collected into RNA preservative (RNAlater, Ambion, Inc).
| | Sample_growth_protocol_ch1 | N/A
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Upper tarsal conjunctival swab total RNA was extracted and purified with the RNeasy Micro-kit (Qiagen Ltd, Crawley, UK).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | cRNA probes were prepared from 100 microg total RNA using two-rounds in vitro transcription with biotin-labeled nucleotides (Affymetrix RNA transcript labelling kits (Affymetrix, Santa Clara, CA)).
| | Sample_hyb_protocol | Biotinylated complementary RNA (cRNA) targets were purified using the Sample Cleanup Module (Affymetrix, Santa Clara, CA) and subsequently 10ug of Fragmented biotinylated cRNA was hybridized, according to the manufacturer’s standard protocols, for 16hrs at 45oC.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix confocal laser scanner 3000.
| | Sample_data_processing | Data was subjected to QC analysis followed by RMA and is provided as RMA-normalised natural-scale data. RMA was performed using function rmasummary in Bioinformatics Toolbox version 3.4, Matlab version R2009b.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Martin,James,Holland
| | Sample_contact_email | Martin.Holland@lshtm.ac.uk
| | Sample_contact_phone | +442079272295
| | Sample_contact_laboratory | Clinical Research
| | Sample_contact_department | Infectious and Tropical Diseases
| | Sample_contact_institute | London School of Hygiene and Tropical Medicine
| | Sample_contact_address | Keppel Street
| | Sample_contact_city | London
| | Sample_contact_zip/postal_code | WC1E 7HT
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM512nnn/GSM512413/suppl/GSM512413.CEL.gz
| | Sample_series_id | GSE20430
| | Sample_data_row_count | 8793
| | |
|
GSM512414 | GPL201 |
|
Tarsal conjunctiva, GAR_16
|
Swab, tarsal conjunctiva, N
|
tissue: tarsal conjunctiva
gender: Male
age (years): <1
ethnicity: Manjago
fpc trachoma score: F0/P0/C0
equivalent who simplified trachoma grade: --
roche ct/ng amplicor pcr value: POS
ompa copies per swab: 19
disease: normal
|
GAR_16
|
| Sample_geo_accession | GSM512414
| | Sample_status | Public on Sep 03 2010
| | Sample_submission_date | Feb 19 2010
| | Sample_last_update_date | Sep 03 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Swabs from the tarsal conjunctiva of participants with clinical signs (test) and without (control) of acute trachoma were collected into RNA preservative (RNAlater, Ambion, Inc).
| | Sample_growth_protocol_ch1 | N/A
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Upper tarsal conjunctival swab total RNA was extracted and purified with the RNeasy Micro-kit (Qiagen Ltd, Crawley, UK).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | cRNA probes were prepared from 100 microg total RNA using two-rounds in vitro transcription with biotin-labeled nucleotides (Affymetrix RNA transcript labelling kits (Affymetrix, Santa Clara, CA)).
| | Sample_hyb_protocol | Biotinylated complementary RNA (cRNA) targets were purified using the Sample Cleanup Module (Affymetrix, Santa Clara, CA) and subsequently 10ug of Fragmented biotinylated cRNA was hybridized, according to the manufacturer’s standard protocols, for 16hrs at 45oC.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix confocal laser scanner 3000.
| | Sample_data_processing | Data was subjected to QC analysis followed by RMA and is provided as RMA-normalised natural-scale data. RMA was performed using function rmasummary in Bioinformatics Toolbox version 3.4, Matlab version R2009b.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Martin,James,Holland
| | Sample_contact_email | Martin.Holland@lshtm.ac.uk
| | Sample_contact_phone | +442079272295
| | Sample_contact_laboratory | Clinical Research
| | Sample_contact_department | Infectious and Tropical Diseases
| | Sample_contact_institute | London School of Hygiene and Tropical Medicine
| | Sample_contact_address | Keppel Street
| | Sample_contact_city | London
| | Sample_contact_zip/postal_code | WC1E 7HT
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM512nnn/GSM512414/suppl/GSM512414.CEL.gz
| | Sample_series_id | GSE20430
| | Sample_data_row_count | 8793
| | |
|
GSM512415 | GPL201 |
|
Tarsal conjunctiva, GAR_17
|
Swab, tarsal conjunctiva, N
|
tissue: tarsal conjunctiva
gender: Male
age (years): 8
ethnicity: Manjago
fpc trachoma score: F0/P0/C0
equivalent who simplified trachoma grade: --
roche ct/ng amplicor pcr value: NEG
ompa copies per swab: 0
disease: normal
|
GAR_17
|
| Sample_geo_accession | GSM512415
| | Sample_status | Public on Sep 03 2010
| | Sample_submission_date | Feb 19 2010
| | Sample_last_update_date | Sep 03 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Swabs from the tarsal conjunctiva of participants with clinical signs (test) and without (control) of acute trachoma were collected into RNA preservative (RNAlater, Ambion, Inc).
| | Sample_growth_protocol_ch1 | N/A
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Upper tarsal conjunctival swab total RNA was extracted and purified with the RNeasy Micro-kit (Qiagen Ltd, Crawley, UK).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | cRNA probes were prepared from 100 microg total RNA using two-rounds in vitro transcription with biotin-labeled nucleotides (Affymetrix RNA transcript labelling kits (Affymetrix, Santa Clara, CA)).
| | Sample_hyb_protocol | Biotinylated complementary RNA (cRNA) targets were purified using the Sample Cleanup Module (Affymetrix, Santa Clara, CA) and subsequently 10ug of Fragmented biotinylated cRNA was hybridized, according to the manufacturer’s standard protocols, for 16hrs at 45oC.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix confocal laser scanner 3000.
| | Sample_data_processing | Data was subjected to QC analysis followed by RMA and is provided as RMA-normalised natural-scale data. RMA was performed using function rmasummary in Bioinformatics Toolbox version 3.4, Matlab version R2009b.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Martin,James,Holland
| | Sample_contact_email | Martin.Holland@lshtm.ac.uk
| | Sample_contact_phone | +442079272295
| | Sample_contact_laboratory | Clinical Research
| | Sample_contact_department | Infectious and Tropical Diseases
| | Sample_contact_institute | London School of Hygiene and Tropical Medicine
| | Sample_contact_address | Keppel Street
| | Sample_contact_city | London
| | Sample_contact_zip/postal_code | WC1E 7HT
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM512nnn/GSM512415/suppl/GSM512415.CEL.gz
| | Sample_series_id | GSE20430
| | Sample_data_row_count | 8793
| | |
|
GSM512416 | GPL201 |
|
Tarsal conjunctiva, GAR_20
|
Swab, tarsal conjunctiva, N
|
tissue: tarsal conjunctiva
gender: Male
age (years): <1
ethnicity: Manjago
fpc trachoma score: F0/P0/C0
equivalent who simplified trachoma grade: --
roche ct/ng amplicor pcr value: POS
ompa copies per swab: 0
disease: normal
|
GAR_20
|
| Sample_geo_accession | GSM512416
| | Sample_status | Public on Sep 03 2010
| | Sample_submission_date | Feb 19 2010
| | Sample_last_update_date | Sep 03 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Swabs from the tarsal conjunctiva of participants with clinical signs (test) and without (control) of acute trachoma were collected into RNA preservative (RNAlater, Ambion, Inc).
| | Sample_growth_protocol_ch1 | N/A
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Upper tarsal conjunctival swab total RNA was extracted and purified with the RNeasy Micro-kit (Qiagen Ltd, Crawley, UK).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | cRNA probes were prepared from 100 microg total RNA using two-rounds in vitro transcription with biotin-labeled nucleotides (Affymetrix RNA transcript labelling kits (Affymetrix, Santa Clara, CA)).
| | Sample_hyb_protocol | Biotinylated complementary RNA (cRNA) targets were purified using the Sample Cleanup Module (Affymetrix, Santa Clara, CA) and subsequently 10ug of Fragmented biotinylated cRNA was hybridized, according to the manufacturer’s standard protocols, for 16hrs at 45oC.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix confocal laser scanner 3000.
| | Sample_data_processing | Data was subjected to QC analysis followed by RMA and is provided as RMA-normalised natural-scale data. RMA was performed using function rmasummary in Bioinformatics Toolbox version 3.4, Matlab version R2009b.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Martin,James,Holland
| | Sample_contact_email | Martin.Holland@lshtm.ac.uk
| | Sample_contact_phone | +442079272295
| | Sample_contact_laboratory | Clinical Research
| | Sample_contact_department | Infectious and Tropical Diseases
| | Sample_contact_institute | London School of Hygiene and Tropical Medicine
| | Sample_contact_address | Keppel Street
| | Sample_contact_city | London
| | Sample_contact_zip/postal_code | WC1E 7HT
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM512nnn/GSM512416/suppl/GSM512416.CEL.gz
| | Sample_series_id | GSE20430
| | Sample_data_row_count | 8793
| | |
|
GSM512417 | GPL201 |
|
Tarsal conjunctiva, GAR_23
|
Swab, tarsal conjunctiva, TF
|
tissue: tarsal conjunctiva
gender: Female
age (years): 5
ethnicity: Manjago
fpc trachoma score: F2/P1/C0
equivalent who simplified trachoma grade: TF
roche ct/ng amplicor pcr value: NEG
ompa copies per swab: 0
disease: trachoma
|
GAR_23
|
| Sample_geo_accession | GSM512417
| | Sample_status | Public on Sep 03 2010
| | Sample_submission_date | Feb 19 2010
| | Sample_last_update_date | Sep 03 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Swabs from the tarsal conjunctiva of participants with clinical signs (test) and without (control) of acute trachoma were collected into RNA preservative (RNAlater, Ambion, Inc).
| | Sample_growth_protocol_ch1 | N/A
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Upper tarsal conjunctival swab total RNA was extracted and purified with the RNeasy Micro-kit (Qiagen Ltd, Crawley, UK).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | cRNA probes were prepared from 100 microg total RNA using two-rounds in vitro transcription with biotin-labeled nucleotides (Affymetrix RNA transcript labelling kits (Affymetrix, Santa Clara, CA)).
| | Sample_hyb_protocol | Biotinylated complementary RNA (cRNA) targets were purified using the Sample Cleanup Module (Affymetrix, Santa Clara, CA) and subsequently 10ug of Fragmented biotinylated cRNA was hybridized, according to the manufacturer’s standard protocols, for 16hrs at 45oC.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix confocal laser scanner 3000.
| | Sample_data_processing | Data was subjected to QC analysis followed by RMA and is provided as RMA-normalised natural-scale data. RMA was performed using function rmasummary in Bioinformatics Toolbox version 3.4, Matlab version R2009b.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Martin,James,Holland
| | Sample_contact_email | Martin.Holland@lshtm.ac.uk
| | Sample_contact_phone | +442079272295
| | Sample_contact_laboratory | Clinical Research
| | Sample_contact_department | Infectious and Tropical Diseases
| | Sample_contact_institute | London School of Hygiene and Tropical Medicine
| | Sample_contact_address | Keppel Street
| | Sample_contact_city | London
| | Sample_contact_zip/postal_code | WC1E 7HT
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM512nnn/GSM512417/suppl/GSM512417.CEL.gz
| | Sample_series_id | GSE20430
| | Sample_data_row_count | 8793
| | |
|
GSM512418 | GPL201 |
|
Tarsal conjunctiva, GAR_24
|
Swab, tarsal conjunctiva, N
|
tissue: tarsal conjunctiva
gender: Male
age (years): 7
ethnicity: Manjago
fpc trachoma score: F0/P0/C0
equivalent who simplified trachoma grade: --
roche ct/ng amplicor pcr value: NEG
ompa copies per swab: 0
disease: normal
|
GAR_24
|
| Sample_geo_accession | GSM512418
| | Sample_status | Public on Sep 03 2010
| | Sample_submission_date | Feb 19 2010
| | Sample_last_update_date | Sep 03 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Swabs from the tarsal conjunctiva of participants with clinical signs (test) and without (control) of acute trachoma were collected into RNA preservative (RNAlater, Ambion, Inc).
| | Sample_growth_protocol_ch1 | N/A
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Upper tarsal conjunctival swab total RNA was extracted and purified with the RNeasy Micro-kit (Qiagen Ltd, Crawley, UK).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | cRNA probes were prepared from 100 microg total RNA using two-rounds in vitro transcription with biotin-labeled nucleotides (Affymetrix RNA transcript labelling kits (Affymetrix, Santa Clara, CA)).
| | Sample_hyb_protocol | Biotinylated complementary RNA (cRNA) targets were purified using the Sample Cleanup Module (Affymetrix, Santa Clara, CA) and subsequently 10ug of Fragmented biotinylated cRNA was hybridized, according to the manufacturer’s standard protocols, for 16hrs at 45oC.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix confocal laser scanner 3000.
| | Sample_data_processing | Data was subjected to QC analysis followed by RMA and is provided as RMA-normalised natural-scale data. RMA was performed using function rmasummary in Bioinformatics Toolbox version 3.4, Matlab version R2009b.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Martin,James,Holland
| | Sample_contact_email | Martin.Holland@lshtm.ac.uk
| | Sample_contact_phone | +442079272295
| | Sample_contact_laboratory | Clinical Research
| | Sample_contact_department | Infectious and Tropical Diseases
| | Sample_contact_institute | London School of Hygiene and Tropical Medicine
| | Sample_contact_address | Keppel Street
| | Sample_contact_city | London
| | Sample_contact_zip/postal_code | WC1E 7HT
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM512nnn/GSM512418/suppl/GSM512418.CEL.gz
| | Sample_series_id | GSE20430
| | Sample_data_row_count | 8793
| | |
|
GSM512419 | GPL201 |
|
Tarsal conjunctiva, GAR_25
|
Swab, tarsal conjunctiva, N
|
tissue: tarsal conjunctiva
gender: Female
age (years): 6
ethnicity: Manjago
fpc trachoma score: F0/P0/C0
equivalent who simplified trachoma grade: --
roche ct/ng amplicor pcr value: NEG
ompa copies per swab: 0
disease: normal
|
GAR_25
|
| Sample_geo_accession | GSM512419
| | Sample_status | Public on Sep 03 2010
| | Sample_submission_date | Feb 19 2010
| | Sample_last_update_date | Sep 03 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Swabs from the tarsal conjunctiva of participants with clinical signs (test) and without (control) of acute trachoma were collected into RNA preservative (RNAlater, Ambion, Inc).
| | Sample_growth_protocol_ch1 | N/A
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Upper tarsal conjunctival swab total RNA was extracted and purified with the RNeasy Micro-kit (Qiagen Ltd, Crawley, UK).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | cRNA probes were prepared from 100 microg total RNA using two-rounds in vitro transcription with biotin-labeled nucleotides (Affymetrix RNA transcript labelling kits (Affymetrix, Santa Clara, CA)).
| | Sample_hyb_protocol | Biotinylated complementary RNA (cRNA) targets were purified using the Sample Cleanup Module (Affymetrix, Santa Clara, CA) and subsequently 10ug of Fragmented biotinylated cRNA was hybridized, according to the manufacturer’s standard protocols, for 16hrs at 45oC.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix confocal laser scanner 3000.
| | Sample_data_processing | Data was subjected to QC analysis followed by RMA and is provided as RMA-normalised natural-scale data. RMA was performed using function rmasummary in Bioinformatics Toolbox version 3.4, Matlab version R2009b.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Martin,James,Holland
| | Sample_contact_email | Martin.Holland@lshtm.ac.uk
| | Sample_contact_phone | +442079272295
| | Sample_contact_laboratory | Clinical Research
| | Sample_contact_department | Infectious and Tropical Diseases
| | Sample_contact_institute | London School of Hygiene and Tropical Medicine
| | Sample_contact_address | Keppel Street
| | Sample_contact_city | London
| | Sample_contact_zip/postal_code | WC1E 7HT
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM512nnn/GSM512419/suppl/GSM512419.CEL.gz
| | Sample_series_id | GSE20430
| | Sample_data_row_count | 8793
| | |
|
GSM512420 | GPL201 |
|
Tarsal conjunctiva, GAR_26
|
Swab, tarsal conjunctiva, TF
|
tissue: tarsal conjunctiva
gender: Male
age (years): 5
ethnicity: Manjago
fpc trachoma score: F2/P1/C0
equivalent who simplified trachoma grade: TF
roche ct/ng amplicor pcr value: NEG
ompa copies per swab: 0
disease: trachoma
|
GAR_26
|
| Sample_geo_accession | GSM512420
| | Sample_status | Public on Sep 03 2010
| | Sample_submission_date | Feb 19 2010
| | Sample_last_update_date | Sep 03 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Swabs from the tarsal conjunctiva of participants with clinical signs (test) and without (control) of acute trachoma were collected into RNA preservative (RNAlater, Ambion, Inc).
| | Sample_growth_protocol_ch1 | N/A
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Upper tarsal conjunctival swab total RNA was extracted and purified with the RNeasy Micro-kit (Qiagen Ltd, Crawley, UK).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | cRNA probes were prepared from 100 microg total RNA using two-rounds in vitro transcription with biotin-labeled nucleotides (Affymetrix RNA transcript labelling kits (Affymetrix, Santa Clara, CA)).
| | Sample_hyb_protocol | Biotinylated complementary RNA (cRNA) targets were purified using the Sample Cleanup Module (Affymetrix, Santa Clara, CA) and subsequently 10ug of Fragmented biotinylated cRNA was hybridized, according to the manufacturer’s standard protocols, for 16hrs at 45oC.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix confocal laser scanner 3000.
| | Sample_data_processing | Data was subjected to QC analysis followed by RMA and is provided as RMA-normalised natural-scale data. RMA was performed using function rmasummary in Bioinformatics Toolbox version 3.4, Matlab version R2009b.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Martin,James,Holland
| | Sample_contact_email | Martin.Holland@lshtm.ac.uk
| | Sample_contact_phone | +442079272295
| | Sample_contact_laboratory | Clinical Research
| | Sample_contact_department | Infectious and Tropical Diseases
| | Sample_contact_institute | London School of Hygiene and Tropical Medicine
| | Sample_contact_address | Keppel Street
| | Sample_contact_city | London
| | Sample_contact_zip/postal_code | WC1E 7HT
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM512nnn/GSM512420/suppl/GSM512420.CEL.gz
| | Sample_series_id | GSE20430
| | Sample_data_row_count | 8793
| | |
|
GSM512421 | GPL201 |
|
Tarsal conjunctiva, GAR_27
|
Swab, tarsal conjunctiva, TF
|
tissue: tarsal conjunctiva
gender: Male
age (years): 5
ethnicity: Manjago
fpc trachoma score: F2/P1/C0
equivalent who simplified trachoma grade: TF
roche ct/ng amplicor pcr value: NEG
ompa copies per swab: 0
disease: trachoma
|
GAR_27
|
| Sample_geo_accession | GSM512421
| | Sample_status | Public on Sep 03 2010
| | Sample_submission_date | Feb 19 2010
| | Sample_last_update_date | Sep 03 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Swabs from the tarsal conjunctiva of participants with clinical signs (test) and without (control) of acute trachoma were collected into RNA preservative (RNAlater, Ambion, Inc).
| | Sample_growth_protocol_ch1 | N/A
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Upper tarsal conjunctival swab total RNA was extracted and purified with the RNeasy Micro-kit (Qiagen Ltd, Crawley, UK).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | cRNA probes were prepared from 100 microg total RNA using two-rounds in vitro transcription with biotin-labeled nucleotides (Affymetrix RNA transcript labelling kits (Affymetrix, Santa Clara, CA)).
| | Sample_hyb_protocol | Biotinylated complementary RNA (cRNA) targets were purified using the Sample Cleanup Module (Affymetrix, Santa Clara, CA) and subsequently 10ug of Fragmented biotinylated cRNA was hybridized, according to the manufacturer’s standard protocols, for 16hrs at 45oC.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix confocal laser scanner 3000.
| | Sample_data_processing | Data was subjected to QC analysis followed by RMA and is provided as RMA-normalised natural-scale data. RMA was performed using function rmasummary in Bioinformatics Toolbox version 3.4, Matlab version R2009b.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Martin,James,Holland
| | Sample_contact_email | Martin.Holland@lshtm.ac.uk
| | Sample_contact_phone | +442079272295
| | Sample_contact_laboratory | Clinical Research
| | Sample_contact_department | Infectious and Tropical Diseases
| | Sample_contact_institute | London School of Hygiene and Tropical Medicine
| | Sample_contact_address | Keppel Street
| | Sample_contact_city | London
| | Sample_contact_zip/postal_code | WC1E 7HT
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM512nnn/GSM512421/suppl/GSM512421.CEL.gz
| | Sample_series_id | GSE20430
| | Sample_data_row_count | 8793
| | |
|
GSM512422 | GPL201 |
|
Tarsal conjunctiva, GAR_28
|
Swab, tarsal conjunctiva, TF
|
tissue: tarsal conjunctiva
gender: Male
age (years): 2
ethnicity: Manjago
fpc trachoma score: F2/P1/C0
equivalent who simplified trachoma grade: TF
roche ct/ng amplicor pcr value: POS
ompa copies per swab: 0
disease: trachoma
|
GAR_28
|
| Sample_geo_accession | GSM512422
| | Sample_status | Public on Sep 03 2010
| | Sample_submission_date | Feb 19 2010
| | Sample_last_update_date | Sep 03 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Swabs from the tarsal conjunctiva of participants with clinical signs (test) and without (control) of acute trachoma were collected into RNA preservative (RNAlater, Ambion, Inc).
| | Sample_growth_protocol_ch1 | N/A
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Upper tarsal conjunctival swab total RNA was extracted and purified with the RNeasy Micro-kit (Qiagen Ltd, Crawley, UK).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | cRNA probes were prepared from 100 microg total RNA using two-rounds in vitro transcription with biotin-labeled nucleotides (Affymetrix RNA transcript labelling kits (Affymetrix, Santa Clara, CA)).
| | Sample_hyb_protocol | Biotinylated complementary RNA (cRNA) targets were purified using the Sample Cleanup Module (Affymetrix, Santa Clara, CA) and subsequently 10ug of Fragmented biotinylated cRNA was hybridized, according to the manufacturer’s standard protocols, for 16hrs at 45oC.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix confocal laser scanner 3000.
| | Sample_data_processing | Data was subjected to QC analysis followed by RMA and is provided as RMA-normalised natural-scale data. RMA was performed using function rmasummary in Bioinformatics Toolbox version 3.4, Matlab version R2009b.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Martin,James,Holland
| | Sample_contact_email | Martin.Holland@lshtm.ac.uk
| | Sample_contact_phone | +442079272295
| | Sample_contact_laboratory | Clinical Research
| | Sample_contact_department | Infectious and Tropical Diseases
| | Sample_contact_institute | London School of Hygiene and Tropical Medicine
| | Sample_contact_address | Keppel Street
| | Sample_contact_city | London
| | Sample_contact_zip/postal_code | WC1E 7HT
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM512nnn/GSM512422/suppl/GSM512422.CEL.gz
| | Sample_series_id | GSE20430
| | Sample_data_row_count | 8793
| | |
|
GSM512423 | GPL201 |
|
Tarsal conjunctiva, GAR_29
|
Swab, tarsal conjunctiva, TF
|
tissue: tarsal conjunctiva
gender: Female
age (years): 2
ethnicity: Manjago
fpc trachoma score: F2/P1/C0
equivalent who simplified trachoma grade: TF
roche ct/ng amplicor pcr value: POS
ompa copies per swab: 0
disease: trachoma
|
GAR_29
|
| Sample_geo_accession | GSM512423
| | Sample_status | Public on Sep 03 2010
| | Sample_submission_date | Feb 19 2010
| | Sample_last_update_date | Sep 03 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Swabs from the tarsal conjunctiva of participants with clinical signs (test) and without (control) of acute trachoma were collected into RNA preservative (RNAlater, Ambion, Inc).
| | Sample_growth_protocol_ch1 | N/A
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Upper tarsal conjunctival swab total RNA was extracted and purified with the RNeasy Micro-kit (Qiagen Ltd, Crawley, UK).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | cRNA probes were prepared from 100 microg total RNA using two-rounds in vitro transcription with biotin-labeled nucleotides (Affymetrix RNA transcript labelling kits (Affymetrix, Santa Clara, CA)).
| | Sample_hyb_protocol | Biotinylated complementary RNA (cRNA) targets were purified using the Sample Cleanup Module (Affymetrix, Santa Clara, CA) and subsequently 10ug of Fragmented biotinylated cRNA was hybridized, according to the manufacturer’s standard protocols, for 16hrs at 45oC.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix confocal laser scanner 3000.
| | Sample_data_processing | Data was subjected to QC analysis followed by RMA and is provided as RMA-normalised natural-scale data. RMA was performed using function rmasummary in Bioinformatics Toolbox version 3.4, Matlab version R2009b.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Martin,James,Holland
| | Sample_contact_email | Martin.Holland@lshtm.ac.uk
| | Sample_contact_phone | +442079272295
| | Sample_contact_laboratory | Clinical Research
| | Sample_contact_department | Infectious and Tropical Diseases
| | Sample_contact_institute | London School of Hygiene and Tropical Medicine
| | Sample_contact_address | Keppel Street
| | Sample_contact_city | London
| | Sample_contact_zip/postal_code | WC1E 7HT
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM512nnn/GSM512423/suppl/GSM512423.CEL.gz
| | Sample_series_id | GSE20430
| | Sample_data_row_count | 8793
| | |
|
GSM512424 | GPL201 |
|
Tarsal conjunctiva, GAR_30
|
Swab, tarsal conjunctiva, TF
|
tissue: tarsal conjunctiva
gender: Male
age (years): 6
ethnicity: Serer
fpc trachoma score: F2/P1/C0
equivalent who simplified trachoma grade: TF
roche ct/ng amplicor pcr value: NEG
ompa copies per swab: 0
disease: trachoma
|
GAR_30
|
| Sample_geo_accession | GSM512424
| | Sample_status | Public on Sep 03 2010
| | Sample_submission_date | Feb 19 2010
| | Sample_last_update_date | Sep 03 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Swabs from the tarsal conjunctiva of participants with clinical signs (test) and without (control) of acute trachoma were collected into RNA preservative (RNAlater, Ambion, Inc).
| | Sample_growth_protocol_ch1 | N/A
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Upper tarsal conjunctival swab total RNA was extracted and purified with the RNeasy Micro-kit (Qiagen Ltd, Crawley, UK).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | cRNA probes were prepared from 100 microg total RNA using two-rounds in vitro transcription with biotin-labeled nucleotides (Affymetrix RNA transcript labelling kits (Affymetrix, Santa Clara, CA)).
| | Sample_hyb_protocol | Biotinylated complementary RNA (cRNA) targets were purified using the Sample Cleanup Module (Affymetrix, Santa Clara, CA) and subsequently 10ug of Fragmented biotinylated cRNA was hybridized, according to the manufacturer’s standard protocols, for 16hrs at 45oC.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix confocal laser scanner 3000.
| | Sample_data_processing | Data was subjected to QC analysis followed by RMA and is provided as RMA-normalised natural-scale data. RMA was performed using function rmasummary in Bioinformatics Toolbox version 3.4, Matlab version R2009b.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Martin,James,Holland
| | Sample_contact_email | Martin.Holland@lshtm.ac.uk
| | Sample_contact_phone | +442079272295
| | Sample_contact_laboratory | Clinical Research
| | Sample_contact_department | Infectious and Tropical Diseases
| | Sample_contact_institute | London School of Hygiene and Tropical Medicine
| | Sample_contact_address | Keppel Street
| | Sample_contact_city | London
| | Sample_contact_zip/postal_code | WC1E 7HT
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM512nnn/GSM512424/suppl/GSM512424.CEL.gz
| | Sample_series_id | GSE20430
| | Sample_data_row_count | 8793
| | |
|
GSM512425 | GPL201 |
|
Tarsal conjunctiva, GAR_31
|
Swab, tarsal conjunctiva, TF
|
tissue: tarsal conjunctiva
gender: Male
age (years): 10
ethnicity: Manjago
fpc trachoma score: F2/P1/C0
equivalent who simplified trachoma grade: TF
roche ct/ng amplicor pcr value: POS
ompa copies per swab: 0
disease: trachoma
|
GAR_31
|
| Sample_geo_accession | GSM512425
| | Sample_status | Public on Sep 03 2010
| | Sample_submission_date | Feb 19 2010
| | Sample_last_update_date | Sep 03 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Swabs from the tarsal conjunctiva of participants with clinical signs (test) and without (control) of acute trachoma were collected into RNA preservative (RNAlater, Ambion, Inc).
| | Sample_growth_protocol_ch1 | N/A
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Upper tarsal conjunctival swab total RNA was extracted and purified with the RNeasy Micro-kit (Qiagen Ltd, Crawley, UK).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | cRNA probes were prepared from 100 microg total RNA using two-rounds in vitro transcription with biotin-labeled nucleotides (Affymetrix RNA transcript labelling kits (Affymetrix, Santa Clara, CA)).
| | Sample_hyb_protocol | Biotinylated complementary RNA (cRNA) targets were purified using the Sample Cleanup Module (Affymetrix, Santa Clara, CA) and subsequently 10ug of Fragmented biotinylated cRNA was hybridized, according to the manufacturer’s standard protocols, for 16hrs at 45oC.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix confocal laser scanner 3000.
| | Sample_data_processing | Data was subjected to QC analysis followed by RMA and is provided as RMA-normalised natural-scale data. RMA was performed using function rmasummary in Bioinformatics Toolbox version 3.4, Matlab version R2009b.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Martin,James,Holland
| | Sample_contact_email | Martin.Holland@lshtm.ac.uk
| | Sample_contact_phone | +442079272295
| | Sample_contact_laboratory | Clinical Research
| | Sample_contact_department | Infectious and Tropical Diseases
| | Sample_contact_institute | London School of Hygiene and Tropical Medicine
| | Sample_contact_address | Keppel Street
| | Sample_contact_city | London
| | Sample_contact_zip/postal_code | WC1E 7HT
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM512nnn/GSM512425/suppl/GSM512425.CEL.gz
| | Sample_series_id | GSE20430
| | Sample_data_row_count | 8793
| | |
|
GSM512426 | GPL201 |
|
Tarsal conjunctiva, GAR_33
|
Swab, tarsal conjunctiva, TF
|
tissue: tarsal conjunctiva
gender: Male
age (years): 4
ethnicity: Manjago
fpc trachoma score: F2/P1/C0
equivalent who simplified trachoma grade: TF
roche ct/ng amplicor pcr value: POS
ompa copies per swab: 0
disease: trachoma
|
GAR_33
|
| Sample_geo_accession | GSM512426
| | Sample_status | Public on Sep 03 2010
| | Sample_submission_date | Feb 19 2010
| | Sample_last_update_date | Sep 03 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Swabs from the tarsal conjunctiva of participants with clinical signs (test) and without (control) of acute trachoma were collected into RNA preservative (RNAlater, Ambion, Inc).
| | Sample_growth_protocol_ch1 | N/A
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Upper tarsal conjunctival swab total RNA was extracted and purified with the RNeasy Micro-kit (Qiagen Ltd, Crawley, UK).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | cRNA probes were prepared from 100 microg total RNA using two-rounds in vitro transcription with biotin-labeled nucleotides (Affymetrix RNA transcript labelling kits (Affymetrix, Santa Clara, CA)).
| | Sample_hyb_protocol | Biotinylated complementary RNA (cRNA) targets were purified using the Sample Cleanup Module (Affymetrix, Santa Clara, CA) and subsequently 10ug of Fragmented biotinylated cRNA was hybridized, according to the manufacturer’s standard protocols, for 16hrs at 45oC.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix confocal laser scanner 3000.
| | Sample_data_processing | Data was subjected to QC analysis followed by RMA and is provided as RMA-normalised natural-scale data. RMA was performed using function rmasummary in Bioinformatics Toolbox version 3.4, Matlab version R2009b.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Martin,James,Holland
| | Sample_contact_email | Martin.Holland@lshtm.ac.uk
| | Sample_contact_phone | +442079272295
| | Sample_contact_laboratory | Clinical Research
| | Sample_contact_department | Infectious and Tropical Diseases
| | Sample_contact_institute | London School of Hygiene and Tropical Medicine
| | Sample_contact_address | Keppel Street
| | Sample_contact_city | London
| | Sample_contact_zip/postal_code | WC1E 7HT
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM512nnn/GSM512426/suppl/GSM512426.CEL.gz
| | Sample_series_id | GSE20430
| | Sample_data_row_count | 8793
| | |
|
GSM512427 | GPL201 |
|
Tarsal conjunctiva, GAR_34
|
Swab, tarsal conjunctiva, TF
|
tissue: tarsal conjunctiva
gender: Female
age (years): 3
ethnicity: Manjago
fpc trachoma score: F2/P1/C0
equivalent who simplified trachoma grade: TF
roche ct/ng amplicor pcr value: NEG
ompa copies per swab: 0
disease: trachoma
|
GAR_34
|
| Sample_geo_accession | GSM512427
| | Sample_status | Public on Sep 03 2010
| | Sample_submission_date | Feb 19 2010
| | Sample_last_update_date | Sep 03 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Swabs from the tarsal conjunctiva of participants with clinical signs (test) and without (control) of acute trachoma were collected into RNA preservative (RNAlater, Ambion, Inc).
| | Sample_growth_protocol_ch1 | N/A
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Upper tarsal conjunctival swab total RNA was extracted and purified with the RNeasy Micro-kit (Qiagen Ltd, Crawley, UK).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | cRNA probes were prepared from 100 microg total RNA using two-rounds in vitro transcription with biotin-labeled nucleotides (Affymetrix RNA transcript labelling kits (Affymetrix, Santa Clara, CA)).
| | Sample_hyb_protocol | Biotinylated complementary RNA (cRNA) targets were purified using the Sample Cleanup Module (Affymetrix, Santa Clara, CA) and subsequently 10ug of Fragmented biotinylated cRNA was hybridized, according to the manufacturer’s standard protocols, for 16hrs at 45oC.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix confocal laser scanner 3000.
| | Sample_data_processing | Data was subjected to QC analysis followed by RMA and is provided as RMA-normalised natural-scale data. RMA was performed using function rmasummary in Bioinformatics Toolbox version 3.4, Matlab version R2009b.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Martin,James,Holland
| | Sample_contact_email | Martin.Holland@lshtm.ac.uk
| | Sample_contact_phone | +442079272295
| | Sample_contact_laboratory | Clinical Research
| | Sample_contact_department | Infectious and Tropical Diseases
| | Sample_contact_institute | London School of Hygiene and Tropical Medicine
| | Sample_contact_address | Keppel Street
| | Sample_contact_city | London
| | Sample_contact_zip/postal_code | WC1E 7HT
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM512nnn/GSM512427/suppl/GSM512427.CEL.gz
| | Sample_series_id | GSE20430
| | Sample_data_row_count | 8793
| | |
|
GSM512428 | GPL201 |
|
Tarsal conjunctiva, GAR_35
|
Swab, tarsal conjunctiva, TF
|
tissue: tarsal conjunctiva
gender: Male
age (years): 14
ethnicity: Manjago
fpc trachoma score: F2/P1/C0
equivalent who simplified trachoma grade: TF
roche ct/ng amplicor pcr value: NEG
ompa copies per swab: 0
disease: trachoma
|
GAR_35
|
| Sample_geo_accession | GSM512428
| | Sample_status | Public on Sep 03 2010
| | Sample_submission_date | Feb 19 2010
| | Sample_last_update_date | Sep 03 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Swabs from the tarsal conjunctiva of participants with clinical signs (test) and without (control) of acute trachoma were collected into RNA preservative (RNAlater, Ambion, Inc).
| | Sample_growth_protocol_ch1 | N/A
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Upper tarsal conjunctival swab total RNA was extracted and purified with the RNeasy Micro-kit (Qiagen Ltd, Crawley, UK).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | cRNA probes were prepared from 100 microg total RNA using two-rounds in vitro transcription with biotin-labeled nucleotides (Affymetrix RNA transcript labelling kits (Affymetrix, Santa Clara, CA)).
| | Sample_hyb_protocol | Biotinylated complementary RNA (cRNA) targets were purified using the Sample Cleanup Module (Affymetrix, Santa Clara, CA) and subsequently 10ug of Fragmented biotinylated cRNA was hybridized, according to the manufacturer’s standard protocols, for 16hrs at 45oC.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix confocal laser scanner 3000.
| | Sample_data_processing | Data was subjected to QC analysis followed by RMA and is provided as RMA-normalised natural-scale data. RMA was performed using function rmasummary in Bioinformatics Toolbox version 3.4, Matlab version R2009b.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Martin,James,Holland
| | Sample_contact_email | Martin.Holland@lshtm.ac.uk
| | Sample_contact_phone | +442079272295
| | Sample_contact_laboratory | Clinical Research
| | Sample_contact_department | Infectious and Tropical Diseases
| | Sample_contact_institute | London School of Hygiene and Tropical Medicine
| | Sample_contact_address | Keppel Street
| | Sample_contact_city | London
| | Sample_contact_zip/postal_code | WC1E 7HT
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM512nnn/GSM512428/suppl/GSM512428.CEL.gz
| | Sample_series_id | GSE20430
| | Sample_data_row_count | 8793
| | |
|
GSM512429 | GPL201 |
|
Tarsal conjunctiva, GAR_37
|
Swab, tarsal conjunctiva, TF
|
tissue: tarsal conjunctiva
gender: Male
age (years): 5
ethnicity: Manjago
fpc trachoma score: F2/P1/C0
equivalent who simplified trachoma grade: TF
roche ct/ng amplicor pcr value: NEG
ompa copies per swab: 0
disease: trachoma
|
GAR_37
|
| Sample_geo_accession | GSM512429
| | Sample_status | Public on Sep 03 2010
| | Sample_submission_date | Feb 19 2010
| | Sample_last_update_date | Sep 03 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Swabs from the tarsal conjunctiva of participants with clinical signs (test) and without (control) of acute trachoma were collected into RNA preservative (RNAlater, Ambion, Inc).
| | Sample_growth_protocol_ch1 | N/A
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Upper tarsal conjunctival swab total RNA was extracted and purified with the RNeasy Micro-kit (Qiagen Ltd, Crawley, UK).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | cRNA probes were prepared from 100 microg total RNA using two-rounds in vitro transcription with biotin-labeled nucleotides (Affymetrix RNA transcript labelling kits (Affymetrix, Santa Clara, CA)).
| | Sample_hyb_protocol | Biotinylated complementary RNA (cRNA) targets were purified using the Sample Cleanup Module (Affymetrix, Santa Clara, CA) and subsequently 10ug of Fragmented biotinylated cRNA was hybridized, according to the manufacturer’s standard protocols, for 16hrs at 45oC.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix confocal laser scanner 3000.
| | Sample_data_processing | Data was subjected to QC analysis followed by RMA and is provided as RMA-normalised natural-scale data. RMA was performed using function rmasummary in Bioinformatics Toolbox version 3.4, Matlab version R2009b.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Martin,James,Holland
| | Sample_contact_email | Martin.Holland@lshtm.ac.uk
| | Sample_contact_phone | +442079272295
| | Sample_contact_laboratory | Clinical Research
| | Sample_contact_department | Infectious and Tropical Diseases
| | Sample_contact_institute | London School of Hygiene and Tropical Medicine
| | Sample_contact_address | Keppel Street
| | Sample_contact_city | London
| | Sample_contact_zip/postal_code | WC1E 7HT
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM512nnn/GSM512429/suppl/GSM512429.CEL.gz
| | Sample_series_id | GSE20430
| | Sample_data_row_count | 8793
| | |
|
GSM512430 | GPL201 |
|
Tarsal conjunctiva, GAR_38
|
Swab, tarsal conjunctiva, TF
|
tissue: tarsal conjunctiva
gender: Female
age (years): 2
ethnicity: Manjago
fpc trachoma score: F2/P1/C0
equivalent who simplified trachoma grade: TF
roche ct/ng amplicor pcr value: NEG
ompa copies per swab: 0
disease: trachoma
|
GAR_38
|
| Sample_geo_accession | GSM512430
| | Sample_status | Public on Sep 03 2010
| | Sample_submission_date | Feb 19 2010
| | Sample_last_update_date | Sep 03 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Swabs from the tarsal conjunctiva of participants with clinical signs (test) and without (control) of acute trachoma were collected into RNA preservative (RNAlater, Ambion, Inc).
| | Sample_growth_protocol_ch1 | N/A
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Upper tarsal conjunctival swab total RNA was extracted and purified with the RNeasy Micro-kit (Qiagen Ltd, Crawley, UK).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | cRNA probes were prepared from 100 microg total RNA using two-rounds in vitro transcription with biotin-labeled nucleotides (Affymetrix RNA transcript labelling kits (Affymetrix, Santa Clara, CA)).
| | Sample_hyb_protocol | Biotinylated complementary RNA (cRNA) targets were purified using the Sample Cleanup Module (Affymetrix, Santa Clara, CA) and subsequently 10ug of Fragmented biotinylated cRNA was hybridized, according to the manufacturer’s standard protocols, for 16hrs at 45oC.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix confocal laser scanner 3000.
| | Sample_data_processing | Data was subjected to QC analysis followed by RMA and is provided as RMA-normalised natural-scale data. RMA was performed using function rmasummary in Bioinformatics Toolbox version 3.4, Matlab version R2009b.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Martin,James,Holland
| | Sample_contact_email | Martin.Holland@lshtm.ac.uk
| | Sample_contact_phone | +442079272295
| | Sample_contact_laboratory | Clinical Research
| | Sample_contact_department | Infectious and Tropical Diseases
| | Sample_contact_institute | London School of Hygiene and Tropical Medicine
| | Sample_contact_address | Keppel Street
| | Sample_contact_city | London
| | Sample_contact_zip/postal_code | WC1E 7HT
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM512nnn/GSM512430/suppl/GSM512430.CEL.gz
| | Sample_series_id | GSE20430
| | Sample_data_row_count | 8793
| | |
|
GSM512431 | GPL201 |
|
Tarsal conjunctiva, GAR_44
|
Swab, tarsal conjunctiva, TF
|
tissue: tarsal conjunctiva
gender: Male
age (years): 3
ethnicity: Wolof
fpc trachoma score: F3/P2/C0
equivalent who simplified trachoma grade: TF
roche ct/ng amplicor pcr value: POS
ompa copies per swab: 0
disease: trachoma
|
GAR_44
|
| Sample_geo_accession | GSM512431
| | Sample_status | Public on Sep 03 2010
| | Sample_submission_date | Feb 19 2010
| | Sample_last_update_date | Sep 03 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Swabs from the tarsal conjunctiva of participants with clinical signs (test) and without (control) of acute trachoma were collected into RNA preservative (RNAlater, Ambion, Inc).
| | Sample_growth_protocol_ch1 | N/A
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Upper tarsal conjunctival swab total RNA was extracted and purified with the RNeasy Micro-kit (Qiagen Ltd, Crawley, UK).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | cRNA probes were prepared from 100 microg total RNA using two-rounds in vitro transcription with biotin-labeled nucleotides (Affymetrix RNA transcript labelling kits (Affymetrix, Santa Clara, CA)).
| | Sample_hyb_protocol | Biotinylated complementary RNA (cRNA) targets were purified using the Sample Cleanup Module (Affymetrix, Santa Clara, CA) and subsequently 10ug of Fragmented biotinylated cRNA was hybridized, according to the manufacturer’s standard protocols, for 16hrs at 45oC.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix confocal laser scanner 3000.
| | Sample_data_processing | Data was subjected to QC analysis followed by RMA and is provided as RMA-normalised natural-scale data. RMA was performed using function rmasummary in Bioinformatics Toolbox version 3.4, Matlab version R2009b.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Martin,James,Holland
| | Sample_contact_email | Martin.Holland@lshtm.ac.uk
| | Sample_contact_phone | +442079272295
| | Sample_contact_laboratory | Clinical Research
| | Sample_contact_department | Infectious and Tropical Diseases
| | Sample_contact_institute | London School of Hygiene and Tropical Medicine
| | Sample_contact_address | Keppel Street
| | Sample_contact_city | London
| | Sample_contact_zip/postal_code | WC1E 7HT
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM512nnn/GSM512431/suppl/GSM512431.CEL.gz
| | Sample_series_id | GSE20430
| | Sample_data_row_count | 8793
| | |
|
GSM512432 | GPL201 |
|
Tarsal conjunctiva, GAR_51
|
Swab, tarsal conjunctiva, TF/TI
|
tissue: tarsal conjunctiva
gender: Male
age (years): 1
ethnicity: Wolof
fpc trachoma score: F3/P3/C0
equivalent who simplified trachoma grade: TF/TI
roche ct/ng amplicor pcr value: NEG
ompa copies per swab: 0
disease: trachoma
|
GAR_51
|
| Sample_geo_accession | GSM512432
| | Sample_status | Public on Sep 03 2010
| | Sample_submission_date | Feb 19 2010
| | Sample_last_update_date | Sep 03 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Swabs from the tarsal conjunctiva of participants with clinical signs (test) and without (control) of acute trachoma were collected into RNA preservative (RNAlater, Ambion, Inc).
| | Sample_growth_protocol_ch1 | N/A
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Upper tarsal conjunctival swab total RNA was extracted and purified with the RNeasy Micro-kit (Qiagen Ltd, Crawley, UK).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | cRNA probes were prepared from 100 microg total RNA using two-rounds in vitro transcription with biotin-labeled nucleotides (Affymetrix RNA transcript labelling kits (Affymetrix, Santa Clara, CA)).
| | Sample_hyb_protocol | Biotinylated complementary RNA (cRNA) targets were purified using the Sample Cleanup Module (Affymetrix, Santa Clara, CA) and subsequently 10ug of Fragmented biotinylated cRNA was hybridized, according to the manufacturer’s standard protocols, for 16hrs at 45oC.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix confocal laser scanner 3000.
| | Sample_data_processing | Data was subjected to QC analysis followed by RMA and is provided as RMA-normalised natural-scale data. RMA was performed using function rmasummary in Bioinformatics Toolbox version 3.4, Matlab version R2009b.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Martin,James,Holland
| | Sample_contact_email | Martin.Holland@lshtm.ac.uk
| | Sample_contact_phone | +442079272295
| | Sample_contact_laboratory | Clinical Research
| | Sample_contact_department | Infectious and Tropical Diseases
| | Sample_contact_institute | London School of Hygiene and Tropical Medicine
| | Sample_contact_address | Keppel Street
| | Sample_contact_city | London
| | Sample_contact_zip/postal_code | WC1E 7HT
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM512nnn/GSM512432/suppl/GSM512432.CEL.gz
| | Sample_series_id | GSE20430
| | Sample_data_row_count | 8793
| | |
|
GSM512433 | GPL201 |
|
Tarsal conjunctiva, GAR_55
|
Swab, tarsal conjunctiva, N
|
tissue: tarsal conjunctiva
gender: Male
age (years): 4
ethnicity: Wolof
fpc trachoma score: F0/P0/C0
equivalent who simplified trachoma grade: --
roche ct/ng amplicor pcr value: NEG
ompa copies per swab: 0
disease: normal
|
GAR_55
|
| Sample_geo_accession | GSM512433
| | Sample_status | Public on Sep 03 2010
| | Sample_submission_date | Feb 19 2010
| | Sample_last_update_date | Sep 03 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Swabs from the tarsal conjunctiva of participants with clinical signs (test) and without (control) of acute trachoma were collected into RNA preservative (RNAlater, Ambion, Inc).
| | Sample_growth_protocol_ch1 | N/A
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Upper tarsal conjunctival swab total RNA was extracted and purified with the RNeasy Micro-kit (Qiagen Ltd, Crawley, UK).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | cRNA probes were prepared from 100 microg total RNA using two-rounds in vitro transcription with biotin-labeled nucleotides (Affymetrix RNA transcript labelling kits (Affymetrix, Santa Clara, CA)).
| | Sample_hyb_protocol | Biotinylated complementary RNA (cRNA) targets were purified using the Sample Cleanup Module (Affymetrix, Santa Clara, CA) and subsequently 10ug of Fragmented biotinylated cRNA was hybridized, according to the manufacturer’s standard protocols, for 16hrs at 45oC.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix confocal laser scanner 3000.
| | Sample_data_processing | Data was subjected to QC analysis followed by RMA and is provided as RMA-normalised natural-scale data. RMA was performed using function rmasummary in Bioinformatics Toolbox version 3.4, Matlab version R2009b.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Martin,James,Holland
| | Sample_contact_email | Martin.Holland@lshtm.ac.uk
| | Sample_contact_phone | +442079272295
| | Sample_contact_laboratory | Clinical Research
| | Sample_contact_department | Infectious and Tropical Diseases
| | Sample_contact_institute | London School of Hygiene and Tropical Medicine
| | Sample_contact_address | Keppel Street
| | Sample_contact_city | London
| | Sample_contact_zip/postal_code | WC1E 7HT
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM512nnn/GSM512433/suppl/GSM512433.CEL.gz
| | Sample_series_id | GSE20430
| | Sample_data_row_count | 8793
| | |
|
GSM512434 | GPL201 |
|
Tarsal conjunctiva, GAR_57
|
Swab, tarsal conjunctiva, N
|
tissue: tarsal conjunctiva
gender: Female
age (years): 9
ethnicity: Wolof
fpc trachoma score: F0/P0/C0
equivalent who simplified trachoma grade: --
roche ct/ng amplicor pcr value: NEG
ompa copies per swab: 0
disease: normal
|
GAR_57
|
| Sample_geo_accession | GSM512434
| | Sample_status | Public on Sep 03 2010
| | Sample_submission_date | Feb 19 2010
| | Sample_last_update_date | Sep 03 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Swabs from the tarsal conjunctiva of participants with clinical signs (test) and without (control) of acute trachoma were collected into RNA preservative (RNAlater, Ambion, Inc).
| | Sample_growth_protocol_ch1 | N/A
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Upper tarsal conjunctival swab total RNA was extracted and purified with the RNeasy Micro-kit (Qiagen Ltd, Crawley, UK).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | cRNA probes were prepared from 100 microg total RNA using two-rounds in vitro transcription with biotin-labeled nucleotides (Affymetrix RNA transcript labelling kits (Affymetrix, Santa Clara, CA)).
| | Sample_hyb_protocol | Biotinylated complementary RNA (cRNA) targets were purified using the Sample Cleanup Module (Affymetrix, Santa Clara, CA) and subsequently 10ug of Fragmented biotinylated cRNA was hybridized, according to the manufacturer’s standard protocols, for 16hrs at 45oC.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix confocal laser scanner 3000.
| | Sample_data_processing | Data was subjected to QC analysis followed by RMA and is provided as RMA-normalised natural-scale data. RMA was performed using function rmasummary in Bioinformatics Toolbox version 3.4, Matlab version R2009b.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Martin,James,Holland
| | Sample_contact_email | Martin.Holland@lshtm.ac.uk
| | Sample_contact_phone | +442079272295
| | Sample_contact_laboratory | Clinical Research
| | Sample_contact_department | Infectious and Tropical Diseases
| | Sample_contact_institute | London School of Hygiene and Tropical Medicine
| | Sample_contact_address | Keppel Street
| | Sample_contact_city | London
| | Sample_contact_zip/postal_code | WC1E 7HT
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM512nnn/GSM512434/suppl/GSM512434.CEL.gz
| | Sample_series_id | GSE20430
| | Sample_data_row_count | 8793
| | |
|
GSM512435 | GPL201 |
|
Tarsal conjunctiva, GAR_73A
|
Swab, tarsal conjunctiva, TF
|
tissue: tarsal conjunctiva
gender: Female
age (years): 2
ethnicity: Fula
fpc trachoma score: F3/P0/C0
equivalent who simplified trachoma grade: TF
roche ct/ng amplicor pcr value: POS
ompa copies per swab: 185270
disease: trachoma
|
GAR_73A
|
| Sample_geo_accession | GSM512435
| | Sample_status | Public on Sep 03 2010
| | Sample_submission_date | Feb 19 2010
| | Sample_last_update_date | Sep 03 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Swabs from the tarsal conjunctiva of participants with clinical signs (test) and without (control) of acute trachoma were collected into RNA preservative (RNAlater, Ambion, Inc).
| | Sample_growth_protocol_ch1 | N/A
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Upper tarsal conjunctival swab total RNA was extracted and purified with the RNeasy Micro-kit (Qiagen Ltd, Crawley, UK).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | cRNA probes were prepared from 100 microg total RNA using two-rounds in vitro transcription with biotin-labeled nucleotides (Affymetrix RNA transcript labelling kits (Affymetrix, Santa Clara, CA)).
| | Sample_hyb_protocol | Biotinylated complementary RNA (cRNA) targets were purified using the Sample Cleanup Module (Affymetrix, Santa Clara, CA) and subsequently 10ug of Fragmented biotinylated cRNA was hybridized, according to the manufacturer’s standard protocols, for 16hrs at 45oC.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix confocal laser scanner 3000.
| | Sample_data_processing | Data was subjected to QC analysis followed by RMA and is provided as RMA-normalised natural-scale data. RMA was performed using function rmasummary in Bioinformatics Toolbox version 3.4, Matlab version R2009b.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Martin,James,Holland
| | Sample_contact_email | Martin.Holland@lshtm.ac.uk
| | Sample_contact_phone | +442079272295
| | Sample_contact_laboratory | Clinical Research
| | Sample_contact_department | Infectious and Tropical Diseases
| | Sample_contact_institute | London School of Hygiene and Tropical Medicine
| | Sample_contact_address | Keppel Street
| | Sample_contact_city | London
| | Sample_contact_zip/postal_code | WC1E 7HT
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM512nnn/GSM512435/suppl/GSM512435.CEL.gz
| | Sample_series_id | GSE20430
| | Sample_data_row_count | 8793
| | |
|
GSM512436 | GPL201 |
|
Tarsal conjunctiva, GAR_74
|
Swab, tarsal conjunctiva, N
|
tissue: tarsal conjunctiva
gender: Female
age (years): 11
ethnicity: Fula
fpc trachoma score: F0/P0/C0
equivalent who simplified trachoma grade: --
roche ct/ng amplicor pcr value: NEG
ompa copies per swab: 0
disease: normal
|
GAR_74
|
| Sample_geo_accession | GSM512436
| | Sample_status | Public on Sep 03 2010
| | Sample_submission_date | Feb 19 2010
| | Sample_last_update_date | Sep 03 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Swabs from the tarsal conjunctiva of participants with clinical signs (test) and without (control) of acute trachoma were collected into RNA preservative (RNAlater, Ambion, Inc).
| | Sample_growth_protocol_ch1 | N/A
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Upper tarsal conjunctival swab total RNA was extracted and purified with the RNeasy Micro-kit (Qiagen Ltd, Crawley, UK).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | cRNA probes were prepared from 100 microg total RNA using two-rounds in vitro transcription with biotin-labeled nucleotides (Affymetrix RNA transcript labelling kits (Affymetrix, Santa Clara, CA)).
| | Sample_hyb_protocol | Biotinylated complementary RNA (cRNA) targets were purified using the Sample Cleanup Module (Affymetrix, Santa Clara, CA) and subsequently 10ug of Fragmented biotinylated cRNA was hybridized, according to the manufacturer’s standard protocols, for 16hrs at 45oC.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix confocal laser scanner 3000.
| | Sample_data_processing | Data was subjected to QC analysis followed by RMA and is provided as RMA-normalised natural-scale data. RMA was performed using function rmasummary in Bioinformatics Toolbox version 3.4, Matlab version R2009b.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Martin,James,Holland
| | Sample_contact_email | Martin.Holland@lshtm.ac.uk
| | Sample_contact_phone | +442079272295
| | Sample_contact_laboratory | Clinical Research
| | Sample_contact_department | Infectious and Tropical Diseases
| | Sample_contact_institute | London School of Hygiene and Tropical Medicine
| | Sample_contact_address | Keppel Street
| | Sample_contact_city | London
| | Sample_contact_zip/postal_code | WC1E 7HT
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM512nnn/GSM512436/suppl/GSM512436.CEL.gz
| | Sample_series_id | GSE20430
| | Sample_data_row_count | 8793
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GSM512437 | GPL201 |
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Tarsal conjunctiva, GAR_78
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Swab, tarsal conjunctiva, TF
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tissue: tarsal conjunctiva
gender: Male
age (years): 4
ethnicity: Fula
fpc trachoma score: F3/P1/C0
equivalent who simplified trachoma grade: TF
roche ct/ng amplicor pcr value: NEG
ompa copies per swab: 0
disease: trachoma
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GAR_78
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| Sample_geo_accession | GSM512437
| | Sample_status | Public on Sep 03 2010
| | Sample_submission_date | Feb 19 2010
| | Sample_last_update_date | Sep 03 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Swabs from the tarsal conjunctiva of participants with clinical signs (test) and without (control) of acute trachoma were collected into RNA preservative (RNAlater, Ambion, Inc).
| | Sample_growth_protocol_ch1 | N/A
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Upper tarsal conjunctival swab total RNA was extracted and purified with the RNeasy Micro-kit (Qiagen Ltd, Crawley, UK).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | cRNA probes were prepared from 100 microg total RNA using two-rounds in vitro transcription with biotin-labeled nucleotides (Affymetrix RNA transcript labelling kits (Affymetrix, Santa Clara, CA)).
| | Sample_hyb_protocol | Biotinylated complementary RNA (cRNA) targets were purified using the Sample Cleanup Module (Affymetrix, Santa Clara, CA) and subsequently 10ug of Fragmented biotinylated cRNA was hybridized, according to the manufacturer’s standard protocols, for 16hrs at 45oC.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix confocal laser scanner 3000.
| | Sample_data_processing | Data was subjected to QC analysis followed by RMA and is provided as RMA-normalised natural-scale data. RMA was performed using function rmasummary in Bioinformatics Toolbox version 3.4, Matlab version R2009b.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Martin,James,Holland
| | Sample_contact_email | Martin.Holland@lshtm.ac.uk
| | Sample_contact_phone | +442079272295
| | Sample_contact_laboratory | Clinical Research
| | Sample_contact_department | Infectious and Tropical Diseases
| | Sample_contact_institute | London School of Hygiene and Tropical Medicine
| | Sample_contact_address | Keppel Street
| | Sample_contact_city | London
| | Sample_contact_zip/postal_code | WC1E 7HT
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM512nnn/GSM512437/suppl/GSM512437.CEL.gz
| | Sample_series_id | GSE20430
| | Sample_data_row_count | 8793
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