Search results for the GEO ID: GSE12621  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM315989 | GPL570 |
|
retina_macula_rep1
|
19-20 weeks' gestation human retina, macula biopsy
|
Gestational age: 19-20 weeks' gestation
Tissue: retina
|
biological replicate: Macula1_human, Nasal1_human, Surround1_human
|
| Sample_geo_accession | GSM315989
| | Sample_status | Public on Dec 30 2008
| | Sample_submission_date | Aug 29 2008
| | Sample_last_update_date | Dec 30 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Retinal tissue was not subjected to any pre-treatment prior to RNA extraction which commenced 90-120 minutes after surgery to terminate pregnancy.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from each retinal biopsy using Trizol and chloroform to separate the RNA from other cell components. The RNA was then purified and isolated using RNAqueous-Micro RNA isolation kit (Ambion, Inc., Austin, TX). In some cases where genomic DNA contamination was a concern, the RNA was DNAse treated.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotin-labeled cRNA was prepared according to the standard Affymetrix protocol from 5 ug total RNA (GeneChip Expression Analysis Technical Manual, 2003, Affymetrix, Inc.).
| | Sample_hyb_protocol | The target cRNAs were fragmented, combined with poly-A sense RNA labeling controls and cRNA hybridisation controls, then hybridized to the HG-U133 Plus 2.0 GeneChip microarrays for 16 hr at 45 deg C according to the standard Affymetrix protocol (GeneChip Expression Analysis Technical Manual, 2003, Affymetrix, Inc.). GeneChips were washed and stained with streptavidin phycoerythrin conjugate in the Affymetrix GeneChip Fluidics Station 450.
| | Sample_scan_protocol | Microarrays were scanned with an Affymetrix GeneChip Scanner 3000 using a 570 nm excitation wavelength laser.
| | Sample_data_processing | Probe-level data was analyzed with GC-RMA (robust multi-array average (RMA) analysis adjusted for probe sequence and GC content). GC-RMA adjusts for background noise on each array using only perfect match probe intensities. Subsequent data normalisation was performed across all arrays using quantile normalization. The background-adjusted, normalized PM values were then compiled, or summarised, within each probe set using the median polish technique, to generate a single measure of expression. These expression measures were then log transformed, base 2.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Peter,,Kozulin
| | Sample_contact_email | peter.kozulin@anu.edu.au
| | Sample_contact_phone | +61261251378
| | Sample_contact_fax | +61261254891
| | Sample_contact_laboratory | Visual Sciences
| | Sample_contact_department | Research School of Biological Sciences
| | Sample_contact_institute | ANU
| | Sample_contact_address | Building 46, Sullivan's Creek Road
| | Sample_contact_city | Canberra
| | Sample_contact_state | ACT
| | Sample_contact_zip/postal_code | 2601
| | Sample_contact_country | Australia
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM315nnn/GSM315989/suppl/GSM315989.CEL.gz
| | Sample_series_id | GSE12621
| | Sample_data_row_count | 54613
| | |
|
GSM315990 | GPL570 |
|
retina_macula_rep2
|
19-20 weeks' gestation human retina, macula biopsy
|
Gestational age: 19-20 weeks' gestation
Tissue: retina
|
biological replicate: Macula2_human, Nasal2_human, Surround2_human
|
| Sample_geo_accession | GSM315990
| | Sample_status | Public on Dec 30 2008
| | Sample_submission_date | Aug 29 2008
| | Sample_last_update_date | Dec 30 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Retinal tissue was not subjected to any pre-treatment prior to RNA extraction which commenced 90-120 minutes after surgery to terminate pregnancy.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from each retinal biopsy using Trizol and chloroform to separate the RNA from other cell components. The RNA was then purified and isolated using RNAqueous-Micro RNA isolation kit (Ambion, Inc., Austin, TX). In some cases where genomic DNA contamination was a concern, the RNA was DNAse treated.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotin-labeled cRNA was prepared according to the standard Affymetrix protocol from 5 ug total RNA (GeneChip Expression Analysis Technical Manual, 2003, Affymetrix, Inc.).
| | Sample_hyb_protocol | The target cRNAs were fragmented, combined with poly-A sense RNA labeling controls and cRNA hybridisation controls, then hybridized to the HG-U133 Plus 2.0 GeneChip microarrays for 16 hr at 45 deg C according to the standard Affymetrix protocol (GeneChip Expression Analysis Technical Manual, 2003, Affymetrix, Inc.). GeneChips were washed and stained with streptavidin phycoerythrin conjugate in the Affymetrix GeneChip Fluidics Station 450.
| | Sample_scan_protocol | Microarrays were scanned with an Affymetrix GeneChip Scanner 3000 using a 570 nm excitation wavelength laser.
| | Sample_data_processing | Probe-level data was analyzed with GC-RMA (robust multi-array average (RMA) analysis adjusted for probe sequence and GC content). GC-RMA adjusts for background noise on each array using only perfect match probe intensities. Subsequent data normalisation was performed across all arrays using quantile normalization. The background-adjusted, normalized PM values were then compiled, or summarised, within each probe set using the median polish technique, to generate a single measure of expression. These expression measures were then log transformed, base 2.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Peter,,Kozulin
| | Sample_contact_email | peter.kozulin@anu.edu.au
| | Sample_contact_phone | +61261251378
| | Sample_contact_fax | +61261254891
| | Sample_contact_laboratory | Visual Sciences
| | Sample_contact_department | Research School of Biological Sciences
| | Sample_contact_institute | ANU
| | Sample_contact_address | Building 46, Sullivan's Creek Road
| | Sample_contact_city | Canberra
| | Sample_contact_state | ACT
| | Sample_contact_zip/postal_code | 2601
| | Sample_contact_country | Australia
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM315nnn/GSM315990/suppl/GSM315990.CEL.gz
| | Sample_series_id | GSE12621
| | Sample_data_row_count | 54613
| | |
|
GSM315991 | GPL570 |
|
retina_macula_rep3
|
19-20 weeks' gestation human retina, macula biopsy
|
Gestational age: 19-20 weeks' gestation
Tissue: retina
|
biological replicate: Macula3_human, Nasal3_human, Surround3_human
|
| Sample_geo_accession | GSM315991
| | Sample_status | Public on Dec 30 2008
| | Sample_submission_date | Aug 29 2008
| | Sample_last_update_date | Dec 30 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Retinal tissue was not subjected to any pre-treatment prior to RNA extraction which commenced 90-120 minutes after surgery to terminate pregnancy.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from each retinal biopsy using Trizol and chloroform to separate the RNA from other cell components. The RNA was then purified and isolated using RNAqueous-Micro RNA isolation kit (Ambion, Inc., Austin, TX). In some cases where genomic DNA contamination was a concern, the RNA was DNAse treated.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotin-labeled cRNA was prepared according to the standard Affymetrix protocol from 5 ug total RNA (GeneChip Expression Analysis Technical Manual, 2003, Affymetrix, Inc.).
| | Sample_hyb_protocol | The target cRNAs were fragmented, combined with poly-A sense RNA labeling controls and cRNA hybridisation controls, then hybridized to the HG-U133 Plus 2.0 GeneChip microarrays for 16 hr at 45 deg C according to the standard Affymetrix protocol (GeneChip Expression Analysis Technical Manual, 2003, Affymetrix, Inc.). GeneChips were washed and stained with streptavidin phycoerythrin conjugate in the Affymetrix GeneChip Fluidics Station 450.
| | Sample_scan_protocol | Microarrays were scanned with an Affymetrix GeneChip Scanner 3000 using a 570 nm excitation wavelength laser.
| | Sample_data_processing | Probe-level data was analyzed with GC-RMA (robust multi-array average (RMA) analysis adjusted for probe sequence and GC content). GC-RMA adjusts for background noise on each array using only perfect match probe intensities. Subsequent data normalisation was performed across all arrays using quantile normalization. The background-adjusted, normalized PM values were then compiled, or summarised, within each probe set using the median polish technique, to generate a single measure of expression. These expression measures were then log transformed, base 2.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Peter,,Kozulin
| | Sample_contact_email | peter.kozulin@anu.edu.au
| | Sample_contact_phone | +61261251378
| | Sample_contact_fax | +61261254891
| | Sample_contact_laboratory | Visual Sciences
| | Sample_contact_department | Research School of Biological Sciences
| | Sample_contact_institute | ANU
| | Sample_contact_address | Building 46, Sullivan's Creek Road
| | Sample_contact_city | Canberra
| | Sample_contact_state | ACT
| | Sample_contact_zip/postal_code | 2601
| | Sample_contact_country | Australia
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM315nnn/GSM315991/suppl/GSM315991.CEL.gz
| | Sample_series_id | GSE12621
| | Sample_data_row_count | 54613
| | |
|
GSM315992 | GPL570 |
|
retina_macula_rep4
|
19-20 weeks' gestation human retina, macula biopsy
|
Gestational age: 19-20 weeks' gestation
Tissue: retina
|
biological replicate: Macula4_human, Nasal4_human, Surround4_human
|
| Sample_geo_accession | GSM315992
| | Sample_status | Public on Dec 30 2008
| | Sample_submission_date | Aug 29 2008
| | Sample_last_update_date | Dec 30 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Retinal tissue was not subjected to any pre-treatment prior to RNA extraction which commenced 90-120 minutes after surgery to terminate pregnancy.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from each retinal biopsy using Trizol and chloroform to separate the RNA from other cell components. The RNA was then purified and isolated using RNAqueous-Micro RNA isolation kit (Ambion, Inc., Austin, TX). In some cases where genomic DNA contamination was a concern, the RNA was DNAse treated.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotin-labeled cRNA was prepared according to the standard Affymetrix protocol from 5 ug total RNA (GeneChip Expression Analysis Technical Manual, 2003, Affymetrix, Inc.).
| | Sample_hyb_protocol | The target cRNAs were fragmented, combined with poly-A sense RNA labeling controls and cRNA hybridisation controls, then hybridized to the HG-U133 Plus 2.0 GeneChip microarrays for 16 hr at 45 deg C according to the standard Affymetrix protocol (GeneChip Expression Analysis Technical Manual, 2003, Affymetrix, Inc.). GeneChips were washed and stained with streptavidin phycoerythrin conjugate in the Affymetrix GeneChip Fluidics Station 450.
| | Sample_scan_protocol | Microarrays were scanned with an Affymetrix GeneChip Scanner 3000 using a 570 nm excitation wavelength laser.
| | Sample_data_processing | Probe-level data was analyzed with GC-RMA (robust multi-array average (RMA) analysis adjusted for probe sequence and GC content). GC-RMA adjusts for background noise on each array using only perfect match probe intensities. Subsequent data normalisation was performed across all arrays using quantile normalization. The background-adjusted, normalized PM values were then compiled, or summarised, within each probe set using the median polish technique, to generate a single measure of expression. These expression measures were then log transformed, base 2.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Peter,,Kozulin
| | Sample_contact_email | peter.kozulin@anu.edu.au
| | Sample_contact_phone | +61261251378
| | Sample_contact_fax | +61261254891
| | Sample_contact_laboratory | Visual Sciences
| | Sample_contact_department | Research School of Biological Sciences
| | Sample_contact_institute | ANU
| | Sample_contact_address | Building 46, Sullivan's Creek Road
| | Sample_contact_city | Canberra
| | Sample_contact_state | ACT
| | Sample_contact_zip/postal_code | 2601
| | Sample_contact_country | Australia
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM315nnn/GSM315992/suppl/GSM315992.CEL.gz
| | Sample_series_id | GSE12621
| | Sample_data_row_count | 54613
| | |
|
GSM315993 | GPL570 |
|
retina_nasal_rep1
|
19-20 weeks' gestation human retina, nasal biopsy
|
Gestational age: 19-20 weeks' gestation
Tissue: retina
|
biological replicate: Macula1_human, Nasal1_human, Surround1_human
|
| Sample_geo_accession | GSM315993
| | Sample_status | Public on Dec 30 2008
| | Sample_submission_date | Aug 29 2008
| | Sample_last_update_date | Dec 30 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Retinal tissue was not subjected to any pre-treatment prior to RNA extraction which commenced 90-120 minutes after surgery to terminate pregnancy.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from each retinal biopsy using Trizol and chloroform to separate the RNA from other cell components. The RNA was then purified and isolated using RNAqueous-Micro RNA isolation kit (Ambion, Inc., Austin, TX). In some cases where genomic DNA contamination was a concern, the RNA was DNAse treated.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotin-labeled cRNA was prepared according to the standard Affymetrix protocol from 5 ug total RNA (GeneChip Expression Analysis Technical Manual, 2003, Affymetrix, Inc.).
| | Sample_hyb_protocol | The target cRNAs were fragmented, combined with poly-A sense RNA labeling controls and cRNA hybridisation controls, then hybridized to the HG-U133 Plus 2.0 GeneChip microarrays for 16 hr at 45 deg C according to the standard Affymetrix protocol (GeneChip Expression Analysis Technical Manual, 2003, Affymetrix, Inc.). GeneChips were washed and stained with streptavidin phycoerythrin conjugate in the Affymetrix GeneChip Fluidics Station 450.
| | Sample_scan_protocol | Microarrays were scanned with an Affymetrix GeneChip Scanner 3000 using a 570 nm excitation wavelength laser.
| | Sample_data_processing | Probe-level data was analyzed with GC-RMA (robust multi-array average (RMA) analysis adjusted for probe sequence and GC content). GC-RMA adjusts for background noise on each array using only perfect match probe intensities. Subsequent data normalisation was performed across all arrays using quantile normalization. The background-adjusted, normalized PM values were then compiled, or summarised, within each probe set using the median polish technique, to generate a single measure of expression. These expression measures were then log transformed, base 2.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Peter,,Kozulin
| | Sample_contact_email | peter.kozulin@anu.edu.au
| | Sample_contact_phone | +61261251378
| | Sample_contact_fax | +61261254891
| | Sample_contact_laboratory | Visual Sciences
| | Sample_contact_department | Research School of Biological Sciences
| | Sample_contact_institute | ANU
| | Sample_contact_address | Building 46, Sullivan's Creek Road
| | Sample_contact_city | Canberra
| | Sample_contact_state | ACT
| | Sample_contact_zip/postal_code | 2601
| | Sample_contact_country | Australia
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM315nnn/GSM315993/suppl/GSM315993.CEL.gz
| | Sample_series_id | GSE12621
| | Sample_data_row_count | 54613
| | |
|
GSM315994 | GPL570 |
|
retina_nasal_rep2
|
19-20 weeks' gestation human retina, nasal biopsy
|
Gestational age: 19-20 weeks' gestation
Tissue: retina
|
biological replicate: Macula2_human, Nasal2_human, Surround2_human
|
| Sample_geo_accession | GSM315994
| | Sample_status | Public on Dec 30 2008
| | Sample_submission_date | Aug 29 2008
| | Sample_last_update_date | Dec 30 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Retinal tissue was not subjected to any pre-treatment prior to RNA extraction which commenced 90-120 minutes after surgery to terminate pregnancy.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from each retinal biopsy using Trizol and chloroform to separate the RNA from other cell components. The RNA was then purified and isolated using RNAqueous-Micro RNA isolation kit (Ambion, Inc., Austin, TX). In some cases where genomic DNA contamination was a concern, the RNA was DNAse treated.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotin-labeled cRNA was prepared according to the standard Affymetrix protocol from 5 ug total RNA (GeneChip Expression Analysis Technical Manual, 2003, Affymetrix, Inc.).
| | Sample_hyb_protocol | The target cRNAs were fragmented, combined with poly-A sense RNA labeling controls and cRNA hybridisation controls, then hybridized to the HG-U133 Plus 2.0 GeneChip microarrays for 16 hr at 45 deg C according to the standard Affymetrix protocol (GeneChip Expression Analysis Technical Manual, 2003, Affymetrix, Inc.). GeneChips were washed and stained with streptavidin phycoerythrin conjugate in the Affymetrix GeneChip Fluidics Station 450.
| | Sample_scan_protocol | Microarrays were scanned with an Affymetrix GeneChip Scanner 3000 using a 570 nm excitation wavelength laser.
| | Sample_data_processing | Probe-level data was analyzed with GC-RMA (robust multi-array average (RMA) analysis adjusted for probe sequence and GC content). GC-RMA adjusts for background noise on each array using only perfect match probe intensities. Subsequent data normalisation was performed across all arrays using quantile normalization. The background-adjusted, normalized PM values were then compiled, or summarised, within each probe set using the median polish technique, to generate a single measure of expression. These expression measures were then log transformed, base 2.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Peter,,Kozulin
| | Sample_contact_email | peter.kozulin@anu.edu.au
| | Sample_contact_phone | +61261251378
| | Sample_contact_fax | +61261254891
| | Sample_contact_laboratory | Visual Sciences
| | Sample_contact_department | Research School of Biological Sciences
| | Sample_contact_institute | ANU
| | Sample_contact_address | Building 46, Sullivan's Creek Road
| | Sample_contact_city | Canberra
| | Sample_contact_state | ACT
| | Sample_contact_zip/postal_code | 2601
| | Sample_contact_country | Australia
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM315nnn/GSM315994/suppl/GSM315994.CEL.gz
| | Sample_series_id | GSE12621
| | Sample_data_row_count | 54613
| | |
|
GSM315995 | GPL570 |
|
retina_nasal_rep3
|
19-20 weeks' gestation human retina, nasal biopsy
|
Gestational age: 19-20 weeks' gestation
Tissue: retina
|
biological replicate: Macula3_human, Nasal3_human, Surround3_human
|
| Sample_geo_accession | GSM315995
| | Sample_status | Public on Dec 30 2008
| | Sample_submission_date | Aug 29 2008
| | Sample_last_update_date | Dec 30 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Retinal tissue was not subjected to any pre-treatment prior to RNA extraction which commenced 90-120 minutes after surgery to terminate pregnancy.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from each retinal biopsy using Trizol and chloroform to separate the RNA from other cell components. The RNA was then purified and isolated using RNAqueous-Micro RNA isolation kit (Ambion, Inc., Austin, TX). In some cases where genomic DNA contamination was a concern, the RNA was DNAse treated.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotin-labeled cRNA was prepared according to the standard Affymetrix protocol from 5 ug total RNA (GeneChip Expression Analysis Technical Manual, 2003, Affymetrix, Inc.).
| | Sample_hyb_protocol | The target cRNAs were fragmented, combined with poly-A sense RNA labeling controls and cRNA hybridisation controls, then hybridized to the HG-U133 Plus 2.0 GeneChip microarrays for 16 hr at 45 deg C according to the standard Affymetrix protocol (GeneChip Expression Analysis Technical Manual, 2003, Affymetrix, Inc.). GeneChips were washed and stained with streptavidin phycoerythrin conjugate in the Affymetrix GeneChip Fluidics Station 450.
| | Sample_scan_protocol | Microarrays were scanned with an Affymetrix GeneChip Scanner 3000 using a 570 nm excitation wavelength laser.
| | Sample_data_processing | Probe-level data was analyzed with GC-RMA (robust multi-array average (RMA) analysis adjusted for probe sequence and GC content). GC-RMA adjusts for background noise on each array using only perfect match probe intensities. Subsequent data normalisation was performed across all arrays using quantile normalization. The background-adjusted, normalized PM values were then compiled, or summarised, within each probe set using the median polish technique, to generate a single measure of expression. These expression measures were then log transformed, base 2.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Peter,,Kozulin
| | Sample_contact_email | peter.kozulin@anu.edu.au
| | Sample_contact_phone | +61261251378
| | Sample_contact_fax | +61261254891
| | Sample_contact_laboratory | Visual Sciences
| | Sample_contact_department | Research School of Biological Sciences
| | Sample_contact_institute | ANU
| | Sample_contact_address | Building 46, Sullivan's Creek Road
| | Sample_contact_city | Canberra
| | Sample_contact_state | ACT
| | Sample_contact_zip/postal_code | 2601
| | Sample_contact_country | Australia
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM315nnn/GSM315995/suppl/GSM315995.CEL.gz
| | Sample_series_id | GSE12621
| | Sample_data_row_count | 54613
| | |
|
GSM315996 | GPL570 |
|
retina_nasal_rep4
|
19-20 weeks' gestation human retina, nasal biopsy
|
Gestational age: 19-20 weeks' gestation
Tissue: retina
|
biological replicate: Macula4_human, Nasal4_human, Surround4_human
|
| Sample_geo_accession | GSM315996
| | Sample_status | Public on Dec 30 2008
| | Sample_submission_date | Aug 29 2008
| | Sample_last_update_date | Dec 30 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Retinal tissue was not subjected to any pre-treatment prior to RNA extraction which commenced 90-120 minutes after surgery to terminate pregnancy.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from each retinal biopsy using Trizol and chloroform to separate the RNA from other cell components. The RNA was then purified and isolated using RNAqueous-Micro RNA isolation kit (Ambion, Inc., Austin, TX). In some cases where genomic DNA contamination was a concern, the RNA was DNAse treated.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotin-labeled cRNA was prepared according to the standard Affymetrix protocol from 5 ug total RNA (GeneChip Expression Analysis Technical Manual, 2003, Affymetrix, Inc.).
| | Sample_hyb_protocol | The target cRNAs were fragmented, combined with poly-A sense RNA labeling controls and cRNA hybridisation controls, then hybridized to the HG-U133 Plus 2.0 GeneChip microarrays for 16 hr at 45 deg C according to the standard Affymetrix protocol (GeneChip Expression Analysis Technical Manual, 2003, Affymetrix, Inc.). GeneChips were washed and stained with streptavidin phycoerythrin conjugate in the Affymetrix GeneChip Fluidics Station 450.
| | Sample_scan_protocol | Microarrays were scanned with an Affymetrix GeneChip Scanner 3000 using a 570 nm excitation wavelength laser.
| | Sample_data_processing | Probe-level data was analyzed with GC-RMA (robust multi-array average (RMA) analysis adjusted for probe sequence and GC content). GC-RMA adjusts for background noise on each array using only perfect match probe intensities. Subsequent data normalisation was performed across all arrays using quantile normalization. The background-adjusted, normalized PM values were then compiled, or summarised, within each probe set using the median polish technique, to generate a single measure of expression. These expression measures were then log transformed, base 2.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Peter,,Kozulin
| | Sample_contact_email | peter.kozulin@anu.edu.au
| | Sample_contact_phone | +61261251378
| | Sample_contact_fax | +61261254891
| | Sample_contact_laboratory | Visual Sciences
| | Sample_contact_department | Research School of Biological Sciences
| | Sample_contact_institute | ANU
| | Sample_contact_address | Building 46, Sullivan's Creek Road
| | Sample_contact_city | Canberra
| | Sample_contact_state | ACT
| | Sample_contact_zip/postal_code | 2601
| | Sample_contact_country | Australia
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM315nnn/GSM315996/suppl/GSM315996.CEL.gz
| | Sample_series_id | GSE12621
| | Sample_data_row_count | 54613
| | |
|
GSM315997 | GPL570 |
|
retina_surround_rep1
|
19-20 weeks' gestation human retina, surround biopsy (remaining retina after macula and nasal biopsies)
|
Gestational age: 19-20 weeks' gestation
Tissue: retina
|
biological replicate: Macula1_human, Nasal1_human, Surround1_human
|
| Sample_geo_accession | GSM315997
| | Sample_status | Public on Dec 30 2008
| | Sample_submission_date | Aug 29 2008
| | Sample_last_update_date | Dec 30 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Retinal tissue was not subjected to any pre-treatment prior to RNA extraction which commenced 90-120 minutes after surgery to terminate pregnancy.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from each retinal biopsy using Trizol and chloroform to separate the RNA from other cell components. The RNA was then purified and isolated using RNAqueous-Micro RNA isolation kit (Ambion, Inc., Austin, TX). In some cases where genomic DNA contamination was a concern, the RNA was DNAse treated.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotin-labeled cRNA was prepared according to the standard Affymetrix protocol from 5 ug total RNA (GeneChip Expression Analysis Technical Manual, 2003, Affymetrix, Inc.).
| | Sample_hyb_protocol | The target cRNAs were fragmented, combined with poly-A sense RNA labeling controls and cRNA hybridisation controls, then hybridized to the HG-U133 Plus 2.0 GeneChip microarrays for 16 hr at 45 deg C according to the standard Affymetrix protocol (GeneChip Expression Analysis Technical Manual, 2003, Affymetrix, Inc.). GeneChips were washed and stained with streptavidin phycoerythrin conjugate in the Affymetrix GeneChip Fluidics Station 450.
| | Sample_scan_protocol | Microarrays were scanned with an Affymetrix GeneChip Scanner 3000 using a 570 nm excitation wavelength laser.
| | Sample_data_processing | Probe-level data was analyzed with GC-RMA (robust multi-array average (RMA) analysis adjusted for probe sequence and GC content). GC-RMA adjusts for background noise on each array using only perfect match probe intensities. Subsequent data normalisation was performed across all arrays using quantile normalization. The background-adjusted, normalized PM values were then compiled, or summarised, within each probe set using the median polish technique, to generate a single measure of expression. These expression measures were then log transformed, base 2.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Peter,,Kozulin
| | Sample_contact_email | peter.kozulin@anu.edu.au
| | Sample_contact_phone | +61261251378
| | Sample_contact_fax | +61261254891
| | Sample_contact_laboratory | Visual Sciences
| | Sample_contact_department | Research School of Biological Sciences
| | Sample_contact_institute | ANU
| | Sample_contact_address | Building 46, Sullivan's Creek Road
| | Sample_contact_city | Canberra
| | Sample_contact_state | ACT
| | Sample_contact_zip/postal_code | 2601
| | Sample_contact_country | Australia
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM315nnn/GSM315997/suppl/GSM315997.CEL.gz
| | Sample_series_id | GSE12621
| | Sample_data_row_count | 54613
| | |
|
GSM315998 | GPL570 |
|
retina_surround_rep2
|
19-20 weeks' gestation human retina, surround biopsy (remaining retina after macula and nasal biopsies)
|
Gestational age: 19-20 weeks' gestation
Tissue: retina
|
biological replicate: Macula2_human, Nasal2_human, Surround2_human
|
| Sample_geo_accession | GSM315998
| | Sample_status | Public on Dec 30 2008
| | Sample_submission_date | Aug 29 2008
| | Sample_last_update_date | Dec 30 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Retinal tissue was not subjected to any pre-treatment prior to RNA extraction which commenced 90-120 minutes after surgery to terminate pregnancy.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from each retinal biopsy using Trizol and chloroform to separate the RNA from other cell components. The RNA was then purified and isolated using RNAqueous-Micro RNA isolation kit (Ambion, Inc., Austin, TX). In some cases where genomic DNA contamination was a concern, the RNA was DNAse treated.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotin-labeled cRNA was prepared according to the standard Affymetrix protocol from 5 ug total RNA (GeneChip Expression Analysis Technical Manual, 2003, Affymetrix, Inc.).
| | Sample_hyb_protocol | The target cRNAs were fragmented, combined with poly-A sense RNA labeling controls and cRNA hybridisation controls, then hybridized to the HG-U133 Plus 2.0 GeneChip microarrays for 16 hr at 45 deg C according to the standard Affymetrix protocol (GeneChip Expression Analysis Technical Manual, 2003, Affymetrix, Inc.). GeneChips were washed and stained with streptavidin phycoerythrin conjugate in the Affymetrix GeneChip Fluidics Station 450.
| | Sample_scan_protocol | Microarrays were scanned with an Affymetrix GeneChip Scanner 3000 using a 570 nm excitation wavelength laser.
| | Sample_data_processing | Probe-level data was analyzed with GC-RMA (robust multi-array average (RMA) analysis adjusted for probe sequence and GC content). GC-RMA adjusts for background noise on each array using only perfect match probe intensities. Subsequent data normalisation was performed across all arrays using quantile normalization. The background-adjusted, normalized PM values were then compiled, or summarised, within each probe set using the median polish technique, to generate a single measure of expression. These expression measures were then log transformed, base 2.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Peter,,Kozulin
| | Sample_contact_email | peter.kozulin@anu.edu.au
| | Sample_contact_phone | +61261251378
| | Sample_contact_fax | +61261254891
| | Sample_contact_laboratory | Visual Sciences
| | Sample_contact_department | Research School of Biological Sciences
| | Sample_contact_institute | ANU
| | Sample_contact_address | Building 46, Sullivan's Creek Road
| | Sample_contact_city | Canberra
| | Sample_contact_state | ACT
| | Sample_contact_zip/postal_code | 2601
| | Sample_contact_country | Australia
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM315nnn/GSM315998/suppl/GSM315998.CEL.gz
| | Sample_series_id | GSE12621
| | Sample_data_row_count | 54613
| | |
|
GSM315999 | GPL570 |
|
retina_surround_rep3
|
19-20 weeks' gestation human retina, surround biopsy (remaining retina after macula and nasal biopsies)
|
Gestational age: 19-20 weeks' gestation
Tissue: retina
|
biological replicate: Macula3_human, Nasal3_human, Surround3_human
|
| Sample_geo_accession | GSM315999
| | Sample_status | Public on Dec 30 2008
| | Sample_submission_date | Aug 29 2008
| | Sample_last_update_date | Dec 30 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Retinal tissue was not subjected to any pre-treatment prior to RNA extraction which commenced 90-120 minutes after surgery to terminate pregnancy.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from each retinal biopsy using Trizol and chloroform to separate the RNA from other cell components. The RNA was then purified and isolated using RNAqueous-Micro RNA isolation kit (Ambion, Inc., Austin, TX). In some cases where genomic DNA contamination was a concern, the RNA was DNAse treated.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotin-labeled cRNA was prepared according to the standard Affymetrix protocol from 5 ug total RNA (GeneChip Expression Analysis Technical Manual, 2003, Affymetrix, Inc.).
| | Sample_hyb_protocol | The target cRNAs were fragmented, combined with poly-A sense RNA labeling controls and cRNA hybridisation controls, then hybridized to the HG-U133 Plus 2.0 GeneChip microarrays for 16 hr at 45 deg C according to the standard Affymetrix protocol (GeneChip Expression Analysis Technical Manual, 2003, Affymetrix, Inc.). GeneChips were washed and stained with streptavidin phycoerythrin conjugate in the Affymetrix GeneChip Fluidics Station 450.
| | Sample_scan_protocol | Microarrays were scanned with an Affymetrix GeneChip Scanner 3000 using a 570 nm excitation wavelength laser.
| | Sample_data_processing | Probe-level data was analyzed with GC-RMA (robust multi-array average (RMA) analysis adjusted for probe sequence and GC content). GC-RMA adjusts for background noise on each array using only perfect match probe intensities. Subsequent data normalisation was performed across all arrays using quantile normalization. The background-adjusted, normalized PM values were then compiled, or summarised, within each probe set using the median polish technique, to generate a single measure of expression. These expression measures were then log transformed, base 2.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Peter,,Kozulin
| | Sample_contact_email | peter.kozulin@anu.edu.au
| | Sample_contact_phone | +61261251378
| | Sample_contact_fax | +61261254891
| | Sample_contact_laboratory | Visual Sciences
| | Sample_contact_department | Research School of Biological Sciences
| | Sample_contact_institute | ANU
| | Sample_contact_address | Building 46, Sullivan's Creek Road
| | Sample_contact_city | Canberra
| | Sample_contact_state | ACT
| | Sample_contact_zip/postal_code | 2601
| | Sample_contact_country | Australia
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM315nnn/GSM315999/suppl/GSM315999.CEL.gz
| | Sample_series_id | GSE12621
| | Sample_data_row_count | 54613
| | |
|
GSM316000 | GPL570 |
|
retina_surround_rep4
|
19-20 weeks' gestation human retina, surround biopsy (remaining retina after macula and nasal biopsies)
|
Gestational age: 19-20 weeks' gestation
Tissue: retina
|
biological replicate: Macula4_human, Nasal4_human, Surround4_human
|
| Sample_geo_accession | GSM316000
| | Sample_status | Public on Dec 30 2008
| | Sample_submission_date | Aug 29 2008
| | Sample_last_update_date | Dec 30 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Retinal tissue was not subjected to any pre-treatment prior to RNA extraction which commenced 90-120 minutes after surgery to terminate pregnancy.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from each retinal biopsy using Trizol and chloroform to separate the RNA from other cell components. The RNA was then purified and isolated using RNAqueous-Micro RNA isolation kit (Ambion, Inc., Austin, TX). In some cases where genomic DNA contamination was a concern, the RNA was DNAse treated.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotin-labeled cRNA was prepared according to the standard Affymetrix protocol from 5 ug total RNA (GeneChip Expression Analysis Technical Manual, 2003, Affymetrix, Inc.).
| | Sample_hyb_protocol | The target cRNAs were fragmented, combined with poly-A sense RNA labeling controls and cRNA hybridisation controls, then hybridized to the HG-U133 Plus 2.0 GeneChip microarrays for 16 hr at 45 deg C according to the standard Affymetrix protocol (GeneChip Expression Analysis Technical Manual, 2003, Affymetrix, Inc.). GeneChips were washed and stained with streptavidin phycoerythrin conjugate in the Affymetrix GeneChip Fluidics Station 450.
| | Sample_scan_protocol | Microarrays were scanned with an Affymetrix GeneChip Scanner 3000 using a 570 nm excitation wavelength laser.
| | Sample_data_processing | Probe-level data was analyzed with GC-RMA (robust multi-array average (RMA) analysis adjusted for probe sequence and GC content). GC-RMA adjusts for background noise on each array using only perfect match probe intensities. Subsequent data normalisation was performed across all arrays using quantile normalization. The background-adjusted, normalized PM values were then compiled, or summarised, within each probe set using the median polish technique, to generate a single measure of expression. These expression measures were then log transformed, base 2.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Peter,,Kozulin
| | Sample_contact_email | peter.kozulin@anu.edu.au
| | Sample_contact_phone | +61261251378
| | Sample_contact_fax | +61261254891
| | Sample_contact_laboratory | Visual Sciences
| | Sample_contact_department | Research School of Biological Sciences
| | Sample_contact_institute | ANU
| | Sample_contact_address | Building 46, Sullivan's Creek Road
| | Sample_contact_city | Canberra
| | Sample_contact_state | ACT
| | Sample_contact_zip/postal_code | 2601
| | Sample_contact_country | Australia
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM316nnn/GSM316000/suppl/GSM316000.CEL.gz
| | Sample_series_id | GSE12621
| | Sample_data_row_count | 54613
| | |
|
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