Search results for the GEO ID: GSE15566 |
(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 |
GSM389589 | GPL1261 |
|
Single cell profile of P0 peripheral cell E8
|
P0 single ciliary body cell E8
|
strain: CD1
developmental stage: postnatal day 0 (P0)
tissue: retina
cell type: ciliary body
|
Single cells were harvested from a dissociated CD1 mouse retina at postnatal day 0 (P0). The isolated single cells were lysed, the RNA reverse transcribed, and the resulting cDNAs subjected to a 35 cycle RT-PCR based protocol that was previously shown to generate a sufficient amount of cDNA (10-20 ug) for hybridization on Affymetrix microarrays.
|
Sample_geo_accession | GSM389589
| Sample_status | Public on May 01 2009
| Sample_submission_date | Apr 06 2009
| Sample_last_update_date | Apr 10 2009
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Mus musculus
| Sample_taxid_ch1 | 10090
| Sample_treatment_protocol_ch1 | Retinas were dissociated to individual cells using papain and single cells were harvested using a capillary pipette drawn into a fine needle.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | The isolated single cells were lysed, their mRNAs were reverse transcribed, and the resulting cDNAs were PCR amplified. Individual retinal cells were harvested using a mouth pipette and were expelled into cold lysis buffer (10 mM Tris-HCl [pH 8.3], 50 mM KCl, 1.5 mM MgCl2, 5 mM DTT, 0.5% NP-40). The total single cell RNA was reverse transcribed using Superscript II (Invitrogen) combined with an oligo dT primer. This first strand cDNA product was tailed with A’s using terminal deoxynucleotidyl transferase (TdT) and PCR amplified for 35 cycles using the same oligo dT primer.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Ten micrograms of each single cell cDNA was digested with DNase I for 13 minutes at 37C, heated to 99C for 15 minutes and biotin labeled using Biotin N6 ddATP (Enzo Biosciences) and TdT (Roche) at 37C for 1.5 hours.
| Sample_hyb_protocol | Affymetrix
| Sample_scan_protocol | Affymetrix
| Sample_data_processing | The MAS5.0 algorithm was used with the data normalized by scaling all probe sets to 500.
| Sample_platform_id | GPL1261
| Sample_contact_name | jeffrey,,trimarchi
| Sample_contact_email | jtrimarc@receptor.med.harvard.edu
| Sample_contact_laboratory | Cepko
| Sample_contact_department | Genetics
| Sample_contact_institute | Harvard Medical School
| Sample_contact_address | 77 Avenue Louis Pasteur
| Sample_contact_city | Boston
| Sample_contact_state | MA
| Sample_contact_zip/postal_code | 02115
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM389nnn/GSM389589/suppl/GSM389589.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM389nnn/GSM389589/suppl/GSM389589.CHP.gz
| Sample_series_id | GSE15566
| Sample_data_row_count | 45101
| |
|
GSM389591 | GPL1261 |
|
Single cell profile of E12.5 peripheral cell A6
|
E12.5 single developing ciliary body cell A6
|
strain: CD1
developmental stage: embryonic day 12.5 (E12.5)
tissue: retina
cell type: ciliary body
|
Single cells were harvested from a dissociated CD1 mouse retina at embryonic day 12.5 (E12.5). The isolated single cells were lysed, the RNA reverse transcribed, and the resulting cDNAs subjected to a 35 cycle RT-PCR based protocol that was previously shown to generate a sufficient amount of cDNA (10-20 ug) for hybridization on Affymetrix microarrays.
|
Sample_geo_accession | GSM389591
| Sample_status | Public on May 01 2009
| Sample_submission_date | Apr 06 2009
| Sample_last_update_date | Apr 10 2009
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Mus musculus
| Sample_taxid_ch1 | 10090
| Sample_treatment_protocol_ch1 | Retinas were dissociated to individual cells using papain and single cells were harvested using a capillary pipette drawn into a fine needle.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | The isolated single cells were lysed, their mRNAs were reverse transcribed, and the resulting cDNAs were PCR amplified. Individual retinal cells were harvested using a mouth pipette and were expelled into cold lysis buffer (10 mM Tris-HCl [pH 8.3], 50 mM KCl, 1.5 mM MgCl2, 5 mM DTT, 0.5% NP-40). The total single cell RNA was reverse transcribed using Superscript II (Invitrogen) combined with an oligo dT primer. This first strand cDNA product was tailed with A’s using terminal deoxynucleotidyl transferase (TdT) and PCR amplified for 35 cycles using the same oligo dT primer.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Ten micrograms of each single cell cDNA was digested with DNase I for 13 minutes at 37C, heated to 99C for 15 minutes and biotin labeled using Biotin N6 ddATP (Enzo Biosciences) and TdT (Roche) at 37C for 1.5 hours.
| Sample_hyb_protocol | Affymetrix
| Sample_scan_protocol | Affymetrix
| Sample_data_processing | The MAS5.0 algorithm was used with the data normalized by scaling all probe sets to 500.
| Sample_platform_id | GPL1261
| Sample_contact_name | jeffrey,,trimarchi
| Sample_contact_email | jtrimarc@receptor.med.harvard.edu
| Sample_contact_laboratory | Cepko
| Sample_contact_department | Genetics
| Sample_contact_institute | Harvard Medical School
| Sample_contact_address | 77 Avenue Louis Pasteur
| Sample_contact_city | Boston
| Sample_contact_state | MA
| Sample_contact_zip/postal_code | 02115
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM389nnn/GSM389591/suppl/GSM389591.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM389nnn/GSM389591/suppl/GSM389591.CHP.gz
| Sample_series_id | GSE15566
| Sample_data_row_count | 45101
| |
|
|
|
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 |
|
|