Search results for the GEO ID: GSE17645  |
(Click on the check boxes provided under "Select for analysis", to initiate grouping) |
(Once the selection is made, click on "Add groups" in "Make groups for comparison", to make a group. Scroll down) |
|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM440299 | GPL96 |
|
Primary human fetal neuronal cell culture
|
Human fetal material, 8-12 weeks, from legal abortions
|
cell type: primary human fetal neuronal cell culture
|
Primary neuronal cell cultures were established from human brain tissue, which was obtained from 8-12 weeks old fetuses at legal abortion after informed consent from the patients. A total of 28 tissue samples yielding 10 cell cultures were used in this experiment. The cells were harvested after 8 days of culturing for RNA extraction.
|
| Sample_geo_accession | GSM440299
| | Sample_status | Public on Dec 01 2009
| | Sample_submission_date | Aug 14 2009
| | Sample_last_update_date | Aug 28 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Karolinska University Hospital, Stockholm, Sweden (anonymous donors)
| | Sample_growth_protocol_ch1 | Primary neuronal cell cultures were established from human brain tissue, which was obtained from 8-12 weeks old fetuses at legal abortion after informed consent from the patients. Procedures were approved by the local Ethics committee at the Karolinska University Hospital, Stockholm. The cells were grown on Poly-D-lysine in Neurobasal medium supplemented with 2% B27 supplement, L-Glutamine and Antibiotic-antimycotic. The cells were grown for 8 days.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using Qiagen RNeasy Mini Kit, followed by further cleaning and concentration by using RNeasy MinElute Cleanup Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | We used GeneChip® One-Cycle Target Labeling and Control Reagents according to the manufacturer's recommended protocols.
| | Sample_hyb_protocol | Hybridization was performed at the Cancer Centre Karolinska Microarray Core Facility at the Karolinska University Hospital in Solna according to the manufactureres protocol.
| | Sample_scan_protocol | Scanning was performed according to the manufacturer's recommended protocols with Agilent Probe Array Scan.
| | Sample_data_processing | Raw data was analysed with the MAS5 method using Affymetrix GeneChip Operating Software (GCOS). Transcripts with signal intensities <100 in both samples were excluded.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Linda,Alexandra Csöregh,Nord
| | Sample_contact_email | linda.csoregh@ki.se
| | Sample_contact_department | Dept. of Women's and Children's Health
| | Sample_contact_institute | Karolinska Institute
| | Sample_contact_address | Karolinska University Hospital, Solna, C4:U1
| | Sample_contact_city | Stockholm
| | Sample_contact_zip/postal_code | 171 76
| | Sample_contact_country | Sweden
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM440nnn/GSM440299/suppl/GSM440299.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM440nnn/GSM440299/suppl/GSM440299.CHP.gz
| | Sample_series_id | GSE17645
| | Sample_data_row_count | 22283
| | |
|
GSM440300 | GPL96 |
|
Oestrogen treated primary human fetal neuronal cell culture
|
Human fetal material, 8-12 weeks, from legal abortions
|
cell type: primary human fetal neuronal cell culture
agent: oestrogen
|
Primary neuronal cell cultures were established from human brain tissue, which was obtained from 8-12 weeks old fetuses at legal abortion after informed consent from the patients. A total of 28 tissue samples yielding 10 cell cultures were used in this experiment. Half of the cell cultures were treated with β-oestradiol the day after seeding. The duration of the oestrogen treatment was 7 days and the cells were harvested after 8 days of culturing for RNA extraction.
|
| Sample_geo_accession | GSM440300
| | Sample_status | Public on Dec 01 2009
| | Sample_submission_date | Aug 14 2009
| | Sample_last_update_date | Aug 28 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Karolinska University Hospital, Stockholm, Sweden (anonymous donors)
| | Sample_treatment_protocol_ch1 | The cell cultures were treated with 2µM β-oestradiol, the day after seeding. Medium was not changed during the culture period. The duration of oestrogen treatment was 7 days and then cells were harvested for RNA extraction.
| | Sample_growth_protocol_ch1 | Primary neuronal cell cultures were established from human brain tissue, which was obtained from 8-12 weeks old fetuses at legal abortion after informed consent from the patients. Procedures were approved by the local Ethics committee at the Karolinska University Hospital, Stockholm. The cells were grown on Poly-D-lysine in Neurobasal medium supplemented with 2% B27 supplement, L-Glutamine and Antibiotic-antimycotic. The cells were grown for 8 days.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using Qiagen RNeasy Mini Kit, followed by further cleaning and concentration by using RNeasy MinElute Cleanup Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | We used GeneChip® One-Cycle Target Labeling and Control Reagents according to the manufacturer's recommended protocols.
| | Sample_hyb_protocol | Hybridization was performed at the Cancer Centre Karolinska Microarray Core Facility at the Karolinska University Hospital in Solna according to the manufactureres protocol.
| | Sample_scan_protocol | Scanning was performed according to the manufacturer's recommended protocols with Agilent Probe Array Scan.
| | Sample_data_processing | Raw data was analysed with the MAS5 method using Affymetrix GeneChip Operating Software (GCOS). Transcripts with signal intensities <100 in both samples were excluded.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Linda,Alexandra Csöregh,Nord
| | Sample_contact_email | linda.csoregh@ki.se
| | Sample_contact_department | Dept. of Women's and Children's Health
| | Sample_contact_institute | Karolinska Institute
| | Sample_contact_address | Karolinska University Hospital, Solna, C4:U1
| | Sample_contact_city | Stockholm
| | Sample_contact_zip/postal_code | 171 76
| | Sample_contact_country | Sweden
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM440nnn/GSM440300/suppl/GSM440300.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM440nnn/GSM440300/suppl/GSM440300.CHP.gz
| | Sample_series_id | GSE17645
| | Sample_data_row_count | 22283
| | |
|
| |
| |
Make groups for comparisons |
(2 groups will be compared at a time) |
|
| Select GSMs and click on "Add groups" |
Enter the group name here: |
|
|
|
Select expression type |
| Transcripts profile based on; |
A. Differential status (Up/Down regulation) |
|
|
Regulation type |
|
Fold change |
|
p-value |
|
|
|
B. Absolute calls (Transcribed/Not-detected) |
|
|
| Derive calls within/across groups |
Within groups |
|
|
Detection status |
|
Percentage detection |
|
|
Across groups |
|
|
Detection status |
First group: |
- |
Second group:
|
Percentage detection |
First group: |
- |
Second group:
|
|
|
| |
Filter results by number of probes |
|
|
