Result

Search results for the GEO ID: GSE11862

(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

GSM299566

GPL1261

Noninjured eye 1

Retinal ganglion cell layer

C57BL/6J, Gender:Male,Age:60-120days

Control1

Sample_geo_accession	GSM299566
Sample_status	Public on Sep 01 2008
Sample_submission_date	Jun 23 2008
Sample_last_update_date	Jun 23 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Frozen sections, mounted on special membrane-coated slides (P.A.L.M. Microbeam) were briefly (1 min) stained with hematoxylin (HistoGeneTM; Arcturus, Mountain View, CA). Retinal ganglion cells to be isolated were outlined with a light pen to define the area that would be cut and catapulted intact into a Capsure Macro LCM cap (Molecular Devices, Sunnyvale, CA). In this manner, 6000 retinal ganglion cells were isolated from each eye yielding about 60 ng of total cellular RNA.
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	Briefly, 1.5 rounds of cRNA amplification were accomplished using a Ribo-AmpÂ® OA RNA amplification protocol (Arcturus). First strand cDNA was generated by reverse transcription using the total RNA. After the second strand cDNA was synthesized, a T7 RNA polymerase-driven cRNA synthesis was performed to obtain the first round of cRNA amplification. A second double strand cDNA synthesis was performed followed by a second round of cRNA amplification. A BioArrayTM HighYieldTM RNA transcript labeling protocol (T7) (Enzo Life Sciences, Famingdale, NY) was employed for the second round of amplification to biotinylate the cRNAs.
Sample_hyb_protocol	Labeled cRNA (8 Âµg) was subjected to in invitro transcription and hybridized to Affymetrix (Santa Clara, CA) Mu430 v2.0 chips as recommended by the manufacturer. Chips were hybridized for 16 hr at 45 deg in an Affymetrix 640 hybridization oven.
Sample_scan_protocol	Preparation of microarrays for scanning was carried out with Affymetrix wash protocols matched to the specific chip type on a Model 450 Fluidics station. Affymetrix GeneChip Operating Software (GCOS) operating system controls the Fluidics station process.
Sample_data_processing	For each dataset, invariant set normalization was performed using the PM/MM model for calculating signal intensities in dChip
Sample_platform_id	GPL1261
Sample_contact_name	Thomas,J,Lukas
Sample_contact_email	t-lukas@northwestern.edu
Sample_contact_phone	312-503-0847
Sample_contact_department	MPBC
Sample_contact_institute	Northwestern University
Sample_contact_address	303 E. Chicago Ave
Sample_contact_city	Chicago
Sample_contact_state	IL
Sample_contact_zip/postal_code	60611
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM299nnn/GSM299566/suppl/GSM299566.CEL.gz
Sample_series_id	GSE11862
Sample_data_row_count	45101

GSM299567

GPL1261

Eye with optic nerve crush 1

Retinal ganglion cell layer

C57BL/6J, Gender:Male,Age:60-120days

Crush1

Sample_geo_accession	GSM299567
Sample_status	Public on Sep 01 2008
Sample_submission_date	Jun 23 2008
Sample_last_update_date	Jun 23 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Frozen sections, mounted on special membrane-coated slides (P.A.L.M. Microbeam) were briefly (1 min) stained with hematoxylin (HistoGeneTM; Arcturus, Mountain View, CA). Retinal ganglion cells to be isolated were outlined with a light pen to define the area that would be cut and catapulted intact into a Capsure Macro LCM cap (Molecular Devices, Sunnyvale, CA). In this manner, 6000 retinal ganglion cells were isolated from each eye yielding about 60 ng of total cellular RNA.
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	Briefly, 1.5 rounds of cRNA amplification were accomplished using a Ribo-AmpÂ® OA RNA amplification protocol (Arcturus). First strand cDNA was generated by reverse transcription using the total RNA. After the second strand cDNA was synthesized, a T7 RNA polymerase-driven cRNA synthesis was performed to obtain the first round of cRNA amplification. A second double strand cDNA synthesis was performed followed by a second round of cRNA amplification. A BioArrayTM HighYieldTM RNA transcript labeling protocol (T7) (Enzo Life Sciences, Famingdale, NY) was employed for the second round of amplification to biotinylate the cRNAs.
Sample_hyb_protocol	Labeled cRNA (8 Âµg) was subjected to in invitro transcription and hybridized to Affymetrix (Santa Clara, CA) Mu430 v2.0 chips as recommended by the manufacturer. Chips were hybridized for 16 hr at 45 deg in an Affymetrix 640 hybridization oven.
Sample_scan_protocol	Preparation of microarrays for scanning was carried out with Affymetrix wash protocols matched to the specific chip type on a Model 450 Fluidics station. Affymetrix GeneChip Operating Software (GCOS) operating system controls the Fluidics station process.
Sample_data_processing	For each dataset, invariant set normalization was performed using the PM/MM model for calculating signal intensities in dChip
Sample_platform_id	GPL1261
Sample_contact_name	Thomas,J,Lukas
Sample_contact_email	t-lukas@northwestern.edu
Sample_contact_phone	312-503-0847
Sample_contact_department	MPBC
Sample_contact_institute	Northwestern University
Sample_contact_address	303 E. Chicago Ave
Sample_contact_city	Chicago
Sample_contact_state	IL
Sample_contact_zip/postal_code	60611
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM299nnn/GSM299567/suppl/GSM299567.CEL.gz
Sample_series_id	GSE11862
Sample_data_row_count	45101

GSM299568

GPL1261

Noninjured eye 2

Retinal ganglion cell layer

C57BL/6J, Gender:Male,Age:60-120days

Control 2

Sample_geo_accession	GSM299568
Sample_status	Public on Sep 01 2008
Sample_submission_date	Jun 23 2008
Sample_last_update_date	Jun 23 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Frozen sections, mounted on special membrane-coated slides (P.A.L.M. Microbeam) were briefly (1 min) stained with hematoxylin (HistoGeneTM; Arcturus, Mountain View, CA). Retinal ganglion cells to be isolated were outlined with a light pen to define the area that would be cut and catapulted intact into a Capsure Macro LCM cap (Molecular Devices, Sunnyvale, CA). In this manner, 6000 retinal ganglion cells were isolated from each eye yielding about 60 ng of total cellular RNA.
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	Briefly, 1.5 rounds of cRNA amplification were accomplished using a Ribo-AmpÂ® OA RNA amplification protocol (Arcturus). First strand cDNA was generated by reverse transcription using the total RNA. After the second strand cDNA was synthesized, a T7 RNA polymerase-driven cRNA synthesis was performed to obtain the first round of cRNA amplification. A second double strand cDNA synthesis was performed followed by a second round of cRNA amplification. A BioArrayTM HighYieldTM RNA transcript labeling protocol (T7) (Enzo Life Sciences, Famingdale, NY) was employed for the second round of amplification to biotinylate the cRNAs.
Sample_hyb_protocol	Labeled cRNA (8 Âµg) was subjected to in invitro transcription and hybridized to Affymetrix (Santa Clara, CA) Mu430 v2.0 chips as recommended by the manufacturer. Chips were hybridized for 16 hr at 45 deg in an Affymetrix 640 hybridization oven.
Sample_scan_protocol	Preparation of microarrays for scanning was carried out with Affymetrix wash protocols matched to the specific chip type on a Model 450 Fluidics station. Affymetrix GeneChip Operating Software (GCOS) operating system controls the Fluidics station process.
Sample_data_processing	For each dataset, invariant set normalization was performed using the PM/MM model for calculating signal intensities in dChip
Sample_platform_id	GPL1261
Sample_contact_name	Thomas,J,Lukas
Sample_contact_email	t-lukas@northwestern.edu
Sample_contact_phone	312-503-0847
Sample_contact_department	MPBC
Sample_contact_institute	Northwestern University
Sample_contact_address	303 E. Chicago Ave
Sample_contact_city	Chicago
Sample_contact_state	IL
Sample_contact_zip/postal_code	60611
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM299nnn/GSM299568/suppl/GSM299568.CEL.gz
Sample_series_id	GSE11862
Sample_data_row_count	45101

GSM299569

GPL1261

Eye with optic nerve crush 2

Retinal ganglion cell layer

C57BL/6J, Gender:Male,Age:60-120days

Crush 2

Sample_geo_accession	GSM299569
Sample_status	Public on Sep 01 2008
Sample_submission_date	Jun 23 2008
Sample_last_update_date	Jun 23 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Frozen sections, mounted on special membrane-coated slides (P.A.L.M. Microbeam) were briefly (1 min) stained with hematoxylin (HistoGeneTM; Arcturus, Mountain View, CA). Retinal ganglion cells to be isolated were outlined with a light pen to define the area that would be cut and catapulted intact into a Capsure Macro LCM cap (Molecular Devices, Sunnyvale, CA). In this manner, 6000 retinal ganglion cells were isolated from each eye yielding about 60 ng of total cellular RNA.
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	Briefly, 1.5 rounds of cRNA amplification were accomplished using a Ribo-AmpÂ® OA RNA amplification protocol (Arcturus). First strand cDNA was generated by reverse transcription using the total RNA. After the second strand cDNA was synthesized, a T7 RNA polymerase-driven cRNA synthesis was performed to obtain the first round of cRNA amplification. A second double strand cDNA synthesis was performed followed by a second round of cRNA amplification. A BioArrayTM HighYieldTM RNA transcript labeling protocol (T7) (Enzo Life Sciences, Famingdale, NY) was employed for the second round of amplification to biotinylate the cRNAs.
Sample_hyb_protocol	Labeled cRNA (8 Âµg) was subjected to in invitro transcription and hybridized to Affymetrix (Santa Clara, CA) Mu430 v2.0 chips as recommended by the manufacturer. Chips were hybridized for 16 hr at 45 deg in an Affymetrix 640 hybridization oven.
Sample_scan_protocol	Preparation of microarrays for scanning was carried out with Affymetrix wash protocols matched to the specific chip type on a Model 450 Fluidics station. Affymetrix GeneChip Operating Software (GCOS) operating system controls the Fluidics station process.
Sample_data_processing	For each dataset, invariant set normalization was performed using the PM/MM model for calculating signal intensities in dChip
Sample_platform_id	GPL1261
Sample_contact_name	Thomas,J,Lukas
Sample_contact_email	t-lukas@northwestern.edu
Sample_contact_phone	312-503-0847
Sample_contact_department	MPBC
Sample_contact_institute	Northwestern University
Sample_contact_address	303 E. Chicago Ave
Sample_contact_city	Chicago
Sample_contact_state	IL
Sample_contact_zip/postal_code	60611
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM299nnn/GSM299569/suppl/GSM299569.CEL.gz
Sample_series_id	GSE11862
Sample_data_row_count	45101

GSM299570

GPL1261

Noninjured eye 3

Retinal ganglion cell layer

C57BL/6J, Gender:Male,Age:60-120days

Control 3

Sample_geo_accession	GSM299570
Sample_status	Public on Sep 01 2008
Sample_submission_date	Jun 23 2008
Sample_last_update_date	Jun 23 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Frozen sections, mounted on special membrane-coated slides (P.A.L.M. Microbeam) were briefly (1 min) stained with hematoxylin (HistoGeneTM; Arcturus, Mountain View, CA). Retinal ganglion cells to be isolated were outlined with a light pen to define the area that would be cut and catapulted intact into a Capsure Macro LCM cap (Molecular Devices, Sunnyvale, CA). In this manner, 6000 retinal ganglion cells were isolated from each eye yielding about 60 ng of total cellular RNA.
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	Briefly, 1.5 rounds of cRNA amplification were accomplished using a Ribo-AmpÂ® OA RNA amplification protocol (Arcturus). First strand cDNA was generated by reverse transcription using the total RNA. After the second strand cDNA was synthesized, a T7 RNA polymerase-driven cRNA synthesis was performed to obtain the first round of cRNA amplification. A second double strand cDNA synthesis was performed followed by a second round of cRNA amplification. A BioArrayTM HighYieldTM RNA transcript labeling protocol (T7) (Enzo Life Sciences, Famingdale, NY) was employed for the second round of amplification to biotinylate the cRNAs.
Sample_hyb_protocol	Labeled cRNA (8 Âµg) was subjected to in invitro transcription and hybridized to Affymetrix (Santa Clara, CA) Mu430 v2.0 chips as recommended by the manufacturer. Chips were hybridized for 16 hr at 45 deg in an Affymetrix 640 hybridization oven.
Sample_scan_protocol	Preparation of microarrays for scanning was carried out with Affymetrix wash protocols matched to the specific chip type on a Model 450 Fluidics station. Affymetrix GeneChip Operating Software (GCOS) operating system controls the Fluidics station process.
Sample_data_processing	For each dataset, invariant set normalization was performed using the PM/MM model for calculating signal intensities in dChip
Sample_platform_id	GPL1261
Sample_contact_name	Thomas,J,Lukas
Sample_contact_email	t-lukas@northwestern.edu
Sample_contact_phone	312-503-0847
Sample_contact_department	MPBC
Sample_contact_institute	Northwestern University
Sample_contact_address	303 E. Chicago Ave
Sample_contact_city	Chicago
Sample_contact_state	IL
Sample_contact_zip/postal_code	60611
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM299nnn/GSM299570/suppl/GSM299570.CEL.gz
Sample_series_id	GSE11862
Sample_data_row_count	45101

GSM299571

GPL1261

Eye with optic nerve crush 3

Retinal ganglion cell layer

C57BL/6J, Gender:Male,Age:60-120days

Crush 3

Sample_geo_accession	GSM299571
Sample_status	Public on Sep 01 2008
Sample_submission_date	Jun 23 2008
Sample_last_update_date	Jun 23 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Frozen sections, mounted on special membrane-coated slides (P.A.L.M. Microbeam) were briefly (1 min) stained with hematoxylin (HistoGeneTM; Arcturus, Mountain View, CA). Retinal ganglion cells to be isolated were outlined with a light pen to define the area that would be cut and catapulted intact into a Capsure Macro LCM cap (Molecular Devices, Sunnyvale, CA). In this manner, 6000 retinal ganglion cells were isolated from each eye yielding about 60 ng of total cellular RNA.
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	Briefly, 1.5 rounds of cRNA amplification were accomplished using a Ribo-AmpÂ® OA RNA amplification protocol (Arcturus). First strand cDNA was generated by reverse transcription using the total RNA. After the second strand cDNA was synthesized, a T7 RNA polymerase-driven cRNA synthesis was performed to obtain the first round of cRNA amplification. A second double strand cDNA synthesis was performed followed by a second round of cRNA amplification. A BioArrayTM HighYieldTM RNA transcript labeling protocol (T7) (Enzo Life Sciences, Famingdale, NY) was employed for the second round of amplification to biotinylate the cRNAs.
Sample_hyb_protocol	Labeled cRNA (8 Âµg) was subjected to in invitro transcription and hybridized to Affymetrix (Santa Clara, CA) Mu430 v2.0 chips as recommended by the manufacturer. Chips were hybridized for 16 hr at 45 deg in an Affymetrix 640 hybridization oven.
Sample_scan_protocol	Preparation of microarrays for scanning was carried out with Affymetrix wash protocols matched to the specific chip type on a Model 450 Fluidics station. Affymetrix GeneChip Operating Software (GCOS) operating system controls the Fluidics station process.
Sample_data_processing	For each dataset, invariant set normalization was performed using the PM/MM model for calculating signal intensities in dChip
Sample_platform_id	GPL1261
Sample_contact_name	Thomas,J,Lukas
Sample_contact_email	t-lukas@northwestern.edu
Sample_contact_phone	312-503-0847
Sample_contact_department	MPBC
Sample_contact_institute	Northwestern University
Sample_contact_address	303 E. Chicago Ave
Sample_contact_city	Chicago
Sample_contact_state	IL
Sample_contact_zip/postal_code	60611
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM299nnn/GSM299571/suppl/GSM299571.CEL.gz
Sample_series_id	GSE11862
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)

B. Absolute calls (Transcribed/Not-detected)

Filter results by number of probes