Search results for the GEO ID: GSE45534  |
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GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM1108136 | GPL1261 |
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HT22 cells plus DMSO vehicle at 1 hour exposure
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HT22 is a nerve cell line derived from mouse brain and is widely used to study nerve cell physiology.
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cell line: HT22
treatment: untreated
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HT22 is a nerve cell line derived from mouse brain. Tissues were not examined via microarray.
Gene expression data from hippocampal cell line HT22-untreated.
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| Sample_geo_accession | GSM1108136
| | Sample_status | Public on Mar 28 2013
| | Sample_submission_date | Mar 27 2013
| | Sample_last_update_date | Mar 28 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | The next day after plating, the cells were treated with 10mM J147 for 1 hr before RNA isolation.
| | Sample_growth_protocol_ch1 | HT22 cells were plated in DMEM plus 10% FCS and placed in a 37C incubator overnight.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated with the use of RNeasy Mini kit (Qiagen, #74104; Valencia, CA, USA) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | After RNA isolation for each sample, double stranded cDNA was synthesized from 500 ng total RNA and biotin-labeled using the GeneChip 3’ IVT Express Kit (Affymetrix, #901228-A) per the manufacturer’s instructions and protocol.
| | Sample_hyb_protocol | The hybridization and processing of the GeneChips were conducted by Salk Institute’s Functional Genomics Core Facility using the following systems: GeneChip® Hybridization Oven 640 and GeneChip® Fluidics Station 450 to the wash and stain operation of Affymetrix GeneChip® arrays.
| | Sample_scan_protocol | GeneChip® Scanner 3000 7G
| | Sample_data_processing | Affymetrix Expression Console Software (version 1.0) was used to perform quality assessment of the microarray scan/experiments. Array data were normalized via scaling to adjust the average intensity of each array to be similar. GeneChips were analyzed by the GeneChip Operating Software (Affymetrix, Santa Clara, CA, USA) with the default settings except that the target signal was set to 200 for GeneChip quality control. Raw data were analyzed through the gcRMA-algorithm using the Affymetrix package in R software for statistical computing and graphics. The median microarray intensity for all microarrays was normalized to 100.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Jennifer,Lynn,Ehren
| | Sample_contact_email | jehren@salk.edu
| | Sample_contact_fax | 858-535-9062
| | Sample_contact_department | Cellular Neurobiology
| | Sample_contact_institute | Salk Institute
| | Sample_contact_address | 10010 N Torrey Pines Road
| | Sample_contact_city | La Jolla
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 92037
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1108nnn/GSM1108136/suppl/GSM1108136_JE11060101.CEL.gz
| | Sample_series_id | GSE45534
| | Sample_data_row_count | 45101
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GSM1108137 | GPL1261 |
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HT22 cells plus J147 compound at 1 hour exposure
|
HT22 is a nerve cell line derived from mouse brain and is widely used to study nerve cell physiology.
|
cell line: HT22
treatment: J147
|
HT22 is a nerve cell line derived from mouse brain. Tissues were not examined via microarray.
Gene expression data from hippocampal cell line HT22-treated with J147 compound for 1 hour.
|
| Sample_geo_accession | GSM1108137
| | Sample_status | Public on Mar 28 2013
| | Sample_submission_date | Mar 27 2013
| | Sample_last_update_date | Mar 28 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | The next day after plating, the cells were treated with 10mM J147 for 1 hr before RNA isolation.
| | Sample_growth_protocol_ch1 | HT22 cells were plated in DMEM plus 10% FCS and placed in a 37C incubator overnight.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated with the use of RNeasy Mini kit (Qiagen, #74104; Valencia, CA, USA) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | After RNA isolation for each sample, double stranded cDNA was synthesized from 500 ng total RNA and biotin-labeled using the GeneChip 3’ IVT Express Kit (Affymetrix, #901228-A) per the manufacturer’s instructions and protocol.
| | Sample_hyb_protocol | The hybridization and processing of the GeneChips were conducted by Salk Institute’s Functional Genomics Core Facility using the following systems: GeneChip® Hybridization Oven 640 and GeneChip® Fluidics Station 450 to the wash and stain operation of Affymetrix GeneChip® arrays.
| | Sample_scan_protocol | GeneChip® Scanner 3000 7G
| | Sample_data_processing | Affymetrix Expression Console Software (version 1.0) was used to perform quality assessment of the microarray scan/experiments. Array data were normalized via scaling to adjust the average intensity of each array to be similar. GeneChips were analyzed by the GeneChip Operating Software (Affymetrix, Santa Clara, CA, USA) with the default settings except that the target signal was set to 200 for GeneChip quality control. Raw data were analyzed through the gcRMA-algorithm using the Affymetrix package in R software for statistical computing and graphics. The median microarray intensity for all microarrays was normalized to 100.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Jennifer,Lynn,Ehren
| | Sample_contact_email | jehren@salk.edu
| | Sample_contact_fax | 858-535-9062
| | Sample_contact_department | Cellular Neurobiology
| | Sample_contact_institute | Salk Institute
| | Sample_contact_address | 10010 N Torrey Pines Road
| | Sample_contact_city | La Jolla
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 92037
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1108nnn/GSM1108137/suppl/GSM1108137_JE11060103.CEL.gz
| | Sample_series_id | GSE45534
| | Sample_data_row_count | 45101
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