Search results for the GEO ID: GSE47694  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM1155018 | GPL1261 |
|
E16.5_WT_sample_1
|
Whole lens of mouse
|
age: Embryonic day 16.5
tissue: lens
genotype: wild type
|
|
| Sample_geo_accession | GSM1155018
| | Sample_status | Public on Jul 01 2013
| | Sample_submission_date | Jun 06 2013
| | Sample_last_update_date | Jul 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Three independent preparations each used lens pooled from five embryos (E16.5) and two independent preparations each used lens pooled from 3 young adult mice (PN56).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from dissected lenses using the appropriate RNeasy kit (Qiagen, Valencia, CA)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNAs were amplified and labeled using a 3' IVT Express Kit (Affymetrix Inc., Santa Clara, CA)
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | Sample_data_processing = The raw data obtained from microarray analysis were processed using Affymetrix GeneChip Operating Software (GCOS v 1.4) using software defaults, to assess the presence or absence of each transcript target sequence, its expression level, and then to make all relevant pair-wise statistical comparisons among samples. Expression levels were scaled to a target value of 500 using the software default (2% trimmed mean). Prior to scaling, E16.5 lenses were 311 ± 27 and 329 ± 8 for WT and Klf4CN samples respectively (mean ± SD, n | 3). The equivalent signals for the PN56 lenses were 95 and 84 (mean 90) for WT samples; and 127 and 142 (mean 135) for Klf4CN samples. After scaling, rhree redundant panels measuring GAPDH showed coefficients of variation of 7.3% ± 1.0% and 7.5% ± 2.4% for E16.5 and PN56 samples, respectively.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Stephen,Alan Kenneth,Harvey
| | Sample_contact_email | harveysa@upmc.edu
| | Sample_contact_laboratory | EEINS 1014
| | Sample_contact_department | Ophthalmology
| | Sample_contact_institute | University of Pittsburgh School of Medicine
| | Sample_contact_address | 203 Lothrop St
| | Sample_contact_city | Pittsburgh
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 15213-2588
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1155nnn/GSM1155018/suppl/GSM1155018_E16.5_WT_sample_1.CEL.gz
| | Sample_series_id | GSE47694
| | Sample_data_row_count | 45101
| | |
|
GSM1155019 | GPL1261 |
|
E16.5_WT_sample_2
|
Whole lens of mouse
|
age: Embryonic day 16.5
tissue: lens
genotype: wild type
|
|
| Sample_geo_accession | GSM1155019
| | Sample_status | Public on Jul 01 2013
| | Sample_submission_date | Jun 06 2013
| | Sample_last_update_date | Jul 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Three independent preparations each used lens pooled from five embryos (E16.5) and two independent preparations each used lens pooled from 3 young adult mice (PN56).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from dissected lenses using the appropriate RNeasy kit (Qiagen, Valencia, CA)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNAs were amplified and labeled using a 3' IVT Express Kit (Affymetrix Inc., Santa Clara, CA)
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | Sample_data_processing = The raw data obtained from microarray analysis were processed using Affymetrix GeneChip Operating Software (GCOS v 1.4) using software defaults, to assess the presence or absence of each transcript target sequence, its expression level, and then to make all relevant pair-wise statistical comparisons among samples. Expression levels were scaled to a target value of 500 using the software default (2% trimmed mean). Prior to scaling, E16.5 lenses were 311 ± 27 and 329 ± 8 for WT and Klf4CN samples respectively (mean ± SD, n | 3). The equivalent signals for the PN56 lenses were 95 and 84 (mean 90) for WT samples; and 127 and 142 (mean 135) for Klf4CN samples. After scaling, rhree redundant panels measuring GAPDH showed coefficients of variation of 7.3% ± 1.0% and 7.5% ± 2.4% for E16.5 and PN56 samples, respectively.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Stephen,Alan Kenneth,Harvey
| | Sample_contact_email | harveysa@upmc.edu
| | Sample_contact_laboratory | EEINS 1014
| | Sample_contact_department | Ophthalmology
| | Sample_contact_institute | University of Pittsburgh School of Medicine
| | Sample_contact_address | 203 Lothrop St
| | Sample_contact_city | Pittsburgh
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 15213-2588
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1155nnn/GSM1155019/suppl/GSM1155019_E16.5_WT_sample_2.CEL.gz
| | Sample_series_id | GSE47694
| | Sample_data_row_count | 45101
| | |
|
GSM1155020 | GPL1261 |
|
E16.5_WT_sample_3
|
Whole lens of mouse
|
age: Embryonic day 16.5
tissue: lens
genotype: wild type
|
|
| Sample_geo_accession | GSM1155020
| | Sample_status | Public on Jul 01 2013
| | Sample_submission_date | Jun 06 2013
| | Sample_last_update_date | Jul 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Three independent preparations each used lens pooled from five embryos (E16.5) and two independent preparations each used lens pooled from 3 young adult mice (PN56).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from dissected lenses using the appropriate RNeasy kit (Qiagen, Valencia, CA)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNAs were amplified and labeled using a 3' IVT Express Kit (Affymetrix Inc., Santa Clara, CA)
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | Sample_data_processing = The raw data obtained from microarray analysis were processed using Affymetrix GeneChip Operating Software (GCOS v 1.4) using software defaults, to assess the presence or absence of each transcript target sequence, its expression level, and then to make all relevant pair-wise statistical comparisons among samples. Expression levels were scaled to a target value of 500 using the software default (2% trimmed mean). Prior to scaling, E16.5 lenses were 311 ± 27 and 329 ± 8 for WT and Klf4CN samples respectively (mean ± SD, n | 3). The equivalent signals for the PN56 lenses were 95 and 84 (mean 90) for WT samples; and 127 and 142 (mean 135) for Klf4CN samples. After scaling, rhree redundant panels measuring GAPDH showed coefficients of variation of 7.3% ± 1.0% and 7.5% ± 2.4% for E16.5 and PN56 samples, respectively.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Stephen,Alan Kenneth,Harvey
| | Sample_contact_email | harveysa@upmc.edu
| | Sample_contact_laboratory | EEINS 1014
| | Sample_contact_department | Ophthalmology
| | Sample_contact_institute | University of Pittsburgh School of Medicine
| | Sample_contact_address | 203 Lothrop St
| | Sample_contact_city | Pittsburgh
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 15213-2588
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1155nnn/GSM1155020/suppl/GSM1155020_E16.5_WT_sample_3.CEL.gz
| | Sample_series_id | GSE47694
| | Sample_data_row_count | 45101
| | |
|
GSM1155021 | GPL1261 |
|
E16.5_Klf4CN_sample_1
|
Whole lens of mouse
|
age: Embryonic day 16.5
tissue: lens
genotype: Klf4-conditional null
|
|
| Sample_geo_accession | GSM1155021
| | Sample_status | Public on Jul 01 2013
| | Sample_submission_date | Jun 06 2013
| | Sample_last_update_date | Jul 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Three independent preparations each used lens pooled from five embryos (E16.5) and two independent preparations each used lens pooled from 3 young adult mice (PN56).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from dissected lenses using the appropriate RNeasy kit (Qiagen, Valencia, CA)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNAs were amplified and labeled using a 3' IVT Express Kit (Affymetrix Inc., Santa Clara, CA)
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | Sample_data_processing = The raw data obtained from microarray analysis were processed using Affymetrix GeneChip Operating Software (GCOS v 1.4) using software defaults, to assess the presence or absence of each transcript target sequence, its expression level, and then to make all relevant pair-wise statistical comparisons among samples. Expression levels were scaled to a target value of 500 using the software default (2% trimmed mean). Prior to scaling, E16.5 lenses were 311 ± 27 and 329 ± 8 for WT and Klf4CN samples respectively (mean ± SD, n | 3). The equivalent signals for the PN56 lenses were 95 and 84 (mean 90) for WT samples; and 127 and 142 (mean 135) for Klf4CN samples. After scaling, rhree redundant panels measuring GAPDH showed coefficients of variation of 7.3% ± 1.0% and 7.5% ± 2.4% for E16.5 and PN56 samples, respectively.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Stephen,Alan Kenneth,Harvey
| | Sample_contact_email | harveysa@upmc.edu
| | Sample_contact_laboratory | EEINS 1014
| | Sample_contact_department | Ophthalmology
| | Sample_contact_institute | University of Pittsburgh School of Medicine
| | Sample_contact_address | 203 Lothrop St
| | Sample_contact_city | Pittsburgh
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 15213-2588
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1155nnn/GSM1155021/suppl/GSM1155021_E16.5_Klf4CN_sample_1.CEL.gz
| | Sample_series_id | GSE47694
| | Sample_data_row_count | 45101
| | |
|
GSM1155022 | GPL1261 |
|
E16.5_Klf4CN_sample_2
|
Whole lens of mouse
|
age: Embryonic day 16.5
tissue: lens
genotype: Klf4-conditional null
|
|
| Sample_geo_accession | GSM1155022
| | Sample_status | Public on Jul 01 2013
| | Sample_submission_date | Jun 06 2013
| | Sample_last_update_date | Jul 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Three independent preparations each used lens pooled from five embryos (E16.5) and two independent preparations each used lens pooled from 3 young adult mice (PN56).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from dissected lenses using the appropriate RNeasy kit (Qiagen, Valencia, CA)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNAs were amplified and labeled using a 3' IVT Express Kit (Affymetrix Inc., Santa Clara, CA)
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | Sample_data_processing = The raw data obtained from microarray analysis were processed using Affymetrix GeneChip Operating Software (GCOS v 1.4) using software defaults, to assess the presence or absence of each transcript target sequence, its expression level, and then to make all relevant pair-wise statistical comparisons among samples. Expression levels were scaled to a target value of 500 using the software default (2% trimmed mean). Prior to scaling, E16.5 lenses were 311 ± 27 and 329 ± 8 for WT and Klf4CN samples respectively (mean ± SD, n | 3). The equivalent signals for the PN56 lenses were 95 and 84 (mean 90) for WT samples; and 127 and 142 (mean 135) for Klf4CN samples. After scaling, rhree redundant panels measuring GAPDH showed coefficients of variation of 7.3% ± 1.0% and 7.5% ± 2.4% for E16.5 and PN56 samples, respectively.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Stephen,Alan Kenneth,Harvey
| | Sample_contact_email | harveysa@upmc.edu
| | Sample_contact_laboratory | EEINS 1014
| | Sample_contact_department | Ophthalmology
| | Sample_contact_institute | University of Pittsburgh School of Medicine
| | Sample_contact_address | 203 Lothrop St
| | Sample_contact_city | Pittsburgh
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 15213-2588
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1155nnn/GSM1155022/suppl/GSM1155022_E16.5_Klf4CN_sample_2.CEL.gz
| | Sample_series_id | GSE47694
| | Sample_data_row_count | 45101
| | |
|
GSM1155023 | GPL1261 |
|
E16.5_Klf4CN_sample_3
|
Whole lens of mouse
|
age: Embryonic day 16.5
tissue: lens
genotype: Klf4-conditional null
|
|
| Sample_geo_accession | GSM1155023
| | Sample_status | Public on Jul 01 2013
| | Sample_submission_date | Jun 06 2013
| | Sample_last_update_date | Jul 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Three independent preparations each used lens pooled from five embryos (E16.5) and two independent preparations each used lens pooled from 3 young adult mice (PN56).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from dissected lenses using the appropriate RNeasy kit (Qiagen, Valencia, CA)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNAs were amplified and labeled using a 3' IVT Express Kit (Affymetrix Inc., Santa Clara, CA)
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | Sample_data_processing = The raw data obtained from microarray analysis were processed using Affymetrix GeneChip Operating Software (GCOS v 1.4) using software defaults, to assess the presence or absence of each transcript target sequence, its expression level, and then to make all relevant pair-wise statistical comparisons among samples. Expression levels were scaled to a target value of 500 using the software default (2% trimmed mean). Prior to scaling, E16.5 lenses were 311 ± 27 and 329 ± 8 for WT and Klf4CN samples respectively (mean ± SD, n | 3). The equivalent signals for the PN56 lenses were 95 and 84 (mean 90) for WT samples; and 127 and 142 (mean 135) for Klf4CN samples. After scaling, rhree redundant panels measuring GAPDH showed coefficients of variation of 7.3% ± 1.0% and 7.5% ± 2.4% for E16.5 and PN56 samples, respectively.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Stephen,Alan Kenneth,Harvey
| | Sample_contact_email | harveysa@upmc.edu
| | Sample_contact_laboratory | EEINS 1014
| | Sample_contact_department | Ophthalmology
| | Sample_contact_institute | University of Pittsburgh School of Medicine
| | Sample_contact_address | 203 Lothrop St
| | Sample_contact_city | Pittsburgh
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 15213-2588
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1155nnn/GSM1155023/suppl/GSM1155023_E16.5_Klf4CN_sample_3.CEL.gz
| | Sample_series_id | GSE47694
| | Sample_data_row_count | 45101
| | |
|
GSM1155024 | GPL1261 |
|
PN56_WT_sample_1
|
Whole lens of mouse
|
age: Postnatal day 56
tissue: lens
genotype: wild type
|
|
| Sample_geo_accession | GSM1155024
| | Sample_status | Public on Jul 01 2013
| | Sample_submission_date | Jun 06 2013
| | Sample_last_update_date | Jul 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Three independent preparations each used lens pooled from five embryos (E16.5) and two independent preparations each used lens pooled from 3 young adult mice (PN56).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from dissected lenses using the appropriate RNeasy kit (Qiagen, Valencia, CA)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNAs were amplified and labeled using a 3' IVT Express Kit (Affymetrix Inc., Santa Clara, CA)
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | Sample_data_processing = The raw data obtained from microarray analysis were processed using Affymetrix GeneChip Operating Software (GCOS v 1.4) using software defaults, to assess the presence or absence of each transcript target sequence, its expression level, and then to make all relevant pair-wise statistical comparisons among samples. Expression levels were scaled to a target value of 500 using the software default (2% trimmed mean). Prior to scaling, E16.5 lenses were 311 ± 27 and 329 ± 8 for WT and Klf4CN samples respectively (mean ± SD, n | 3). The equivalent signals for the PN56 lenses were 95 and 84 (mean 90) for WT samples; and 127 and 142 (mean 135) for Klf4CN samples. After scaling, rhree redundant panels measuring GAPDH showed coefficients of variation of 7.3% ± 1.0% and 7.5% ± 2.4% for E16.5 and PN56 samples, respectively.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Stephen,Alan Kenneth,Harvey
| | Sample_contact_email | harveysa@upmc.edu
| | Sample_contact_laboratory | EEINS 1014
| | Sample_contact_department | Ophthalmology
| | Sample_contact_institute | University of Pittsburgh School of Medicine
| | Sample_contact_address | 203 Lothrop St
| | Sample_contact_city | Pittsburgh
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 15213-2588
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1155nnn/GSM1155024/suppl/GSM1155024_PN56_WT_sample_1.CEL.gz
| | Sample_series_id | GSE47694
| | Sample_data_row_count | 45101
| | |
|
GSM1155025 | GPL1261 |
|
PN56_WT_sample_2
|
Whole lens of mouse
|
age: Postnatal day 56
tissue: lens
genotype: wild type
|
|
| Sample_geo_accession | GSM1155025
| | Sample_status | Public on Jul 01 2013
| | Sample_submission_date | Jun 06 2013
| | Sample_last_update_date | Jul 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Three independent preparations each used lens pooled from five embryos (E16.5) and two independent preparations each used lens pooled from 3 young adult mice (PN56).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from dissected lenses using the appropriate RNeasy kit (Qiagen, Valencia, CA)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNAs were amplified and labeled using a 3' IVT Express Kit (Affymetrix Inc., Santa Clara, CA)
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | Sample_data_processing = The raw data obtained from microarray analysis were processed using Affymetrix GeneChip Operating Software (GCOS v 1.4) using software defaults, to assess the presence or absence of each transcript target sequence, its expression level, and then to make all relevant pair-wise statistical comparisons among samples. Expression levels were scaled to a target value of 500 using the software default (2% trimmed mean). Prior to scaling, E16.5 lenses were 311 ± 27 and 329 ± 8 for WT and Klf4CN samples respectively (mean ± SD, n | 3). The equivalent signals for the PN56 lenses were 95 and 84 (mean 90) for WT samples; and 127 and 142 (mean 135) for Klf4CN samples. After scaling, rhree redundant panels measuring GAPDH showed coefficients of variation of 7.3% ± 1.0% and 7.5% ± 2.4% for E16.5 and PN56 samples, respectively.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Stephen,Alan Kenneth,Harvey
| | Sample_contact_email | harveysa@upmc.edu
| | Sample_contact_laboratory | EEINS 1014
| | Sample_contact_department | Ophthalmology
| | Sample_contact_institute | University of Pittsburgh School of Medicine
| | Sample_contact_address | 203 Lothrop St
| | Sample_contact_city | Pittsburgh
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 15213-2588
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1155nnn/GSM1155025/suppl/GSM1155025_PN56_WT_sample_2.CEL.gz
| | Sample_series_id | GSE47694
| | Sample_data_row_count | 45101
| | |
|
GSM1155026 | GPL1261 |
|
PN56_Klf4CN_sample_1
|
Whole lens of mouse
|
age: Postnatal day 56
tissue: lens
genotype: Klf4-conditional null
|
|
| Sample_geo_accession | GSM1155026
| | Sample_status | Public on Jul 01 2013
| | Sample_submission_date | Jun 06 2013
| | Sample_last_update_date | Jul 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Three independent preparations each used lens pooled from five embryos (E16.5) and two independent preparations each used lens pooled from 3 young adult mice (PN56).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from dissected lenses using the appropriate RNeasy kit (Qiagen, Valencia, CA)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNAs were amplified and labeled using a 3' IVT Express Kit (Affymetrix Inc., Santa Clara, CA)
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | Sample_data_processing = The raw data obtained from microarray analysis were processed using Affymetrix GeneChip Operating Software (GCOS v 1.4) using software defaults, to assess the presence or absence of each transcript target sequence, its expression level, and then to make all relevant pair-wise statistical comparisons among samples. Expression levels were scaled to a target value of 500 using the software default (2% trimmed mean). Prior to scaling, E16.5 lenses were 311 ± 27 and 329 ± 8 for WT and Klf4CN samples respectively (mean ± SD, n | 3). The equivalent signals for the PN56 lenses were 95 and 84 (mean 90) for WT samples; and 127 and 142 (mean 135) for Klf4CN samples. After scaling, rhree redundant panels measuring GAPDH showed coefficients of variation of 7.3% ± 1.0% and 7.5% ± 2.4% for E16.5 and PN56 samples, respectively.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Stephen,Alan Kenneth,Harvey
| | Sample_contact_email | harveysa@upmc.edu
| | Sample_contact_laboratory | EEINS 1014
| | Sample_contact_department | Ophthalmology
| | Sample_contact_institute | University of Pittsburgh School of Medicine
| | Sample_contact_address | 203 Lothrop St
| | Sample_contact_city | Pittsburgh
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 15213-2588
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1155nnn/GSM1155026/suppl/GSM1155026_PN56_Klf4CN_sample_1.CEL.gz
| | Sample_series_id | GSE47694
| | Sample_data_row_count | 45101
| | |
|
GSM1155027 | GPL1261 |
|
PN56_Klf4CN_sample_2
|
Whole lens of mouse
|
age: Postnatal day 56
tissue: lens
genotype: Klf4-conditional null
|
|
| Sample_geo_accession | GSM1155027
| | Sample_status | Public on Jul 01 2013
| | Sample_submission_date | Jun 06 2013
| | Sample_last_update_date | Jul 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Three independent preparations each used lens pooled from five embryos (E16.5) and two independent preparations each used lens pooled from 3 young adult mice (PN56).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from dissected lenses using the appropriate RNeasy kit (Qiagen, Valencia, CA)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNAs were amplified and labeled using a 3' IVT Express Kit (Affymetrix Inc., Santa Clara, CA)
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | Sample_data_processing = The raw data obtained from microarray analysis were processed using Affymetrix GeneChip Operating Software (GCOS v 1.4) using software defaults, to assess the presence or absence of each transcript target sequence, its expression level, and then to make all relevant pair-wise statistical comparisons among samples. Expression levels were scaled to a target value of 500 using the software default (2% trimmed mean). Prior to scaling, E16.5 lenses were 311 ± 27 and 329 ± 8 for WT and Klf4CN samples respectively (mean ± SD, n | 3). The equivalent signals for the PN56 lenses were 95 and 84 (mean 90) for WT samples; and 127 and 142 (mean 135) for Klf4CN samples. After scaling, rhree redundant panels measuring GAPDH showed coefficients of variation of 7.3% ± 1.0% and 7.5% ± 2.4% for E16.5 and PN56 samples, respectively.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Stephen,Alan Kenneth,Harvey
| | Sample_contact_email | harveysa@upmc.edu
| | Sample_contact_laboratory | EEINS 1014
| | Sample_contact_department | Ophthalmology
| | Sample_contact_institute | University of Pittsburgh School of Medicine
| | Sample_contact_address | 203 Lothrop St
| | Sample_contact_city | Pittsburgh
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 15213-2588
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1155nnn/GSM1155027/suppl/GSM1155027_PN56_Klf4CN_sample_2.CEL.gz
| | Sample_series_id | GSE47694
| | Sample_data_row_count | 45101
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