Result

Search results for the GEO ID: GSE29885

(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

GSM740103

GPL1355

Amoeboid microglia from 5-day rat brain biological rep1

Amoeboid microglia from 5-day rat brain

age: Postnatal day 5 tissue origin: brain tissue type: corpus callosum cell type: Microglia cell morphology: Amoeboid (AMC)

Gene expression data from amoedboid microglia isolated from corpus callosum of 5-day rat brain

Sample_geo_accession	GSM740103
Sample_status	Public on Jun 11 2011
Sample_submission_date	Jun 10 2011
Sample_last_update_date	Jun 11 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was extracted from 600 microglia cells isolated by Laser-capture microdissection using RNeasy micro kit according to the manufacturer's instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Total RNA (15ng) was reverse transcripted into the first-strand cDNA using a T7-Oligo (dT) Primer (Two-Cycle Target Labeling and Control Reagent package, Affymetrix, CA, USA). After second-strand cDNA synthesis, the double-stranded cDNA was purified and served as a template in the first cycle of in vitro transcription (IVT) reaction. The unlabeled cRNA was then reverse transcripted into the first-strand cDNA of the second cycle using random primers. Subsequently, the T7-Oligo(dT) Promoter Primer was used in the second-strand cDNA synthesis to generate double-stranded cDNA template containing T7 promoter sequences. Then the double-stranded cDNA was amplified and labeled using a biotinylated nucleotide analog/ribonucleotide mix in the second IVT reaction.
Sample_hyb_protocol	The labeled cRNA was then cleaned up, fragmented, and hybridized to Rat Genome 230 2.0 Array (Cat. No. 900506, Affymetrix, CA, USA).
Sample_scan_protocol	The arrays were stained according to the manufacturer's protocols and then scanned with the Genechip scanner (Affymetrix, CA, USA).
Sample_data_processing	CEL files were exported to Affymetrix Expression Console Version 1.1 and RMA normalization was carried out. [The data were also analyzed with Microarray Suite version 5.0 (MAS5.0)using GeneChip Operating Software (GCOS, Affymetrix, CA, USA). For absolute analysis, each chip was normalized to a target intensity of 500, and probe sets were assigned a signal intensity and detection call of Present, Marginal or Absent (See MAS5_GCOS_analyzed.txt on GSE29885)]
Sample_platform_id	GPL1355
Sample_contact_name	S Thameem,,Dheen
Sample_contact_email	antstd@nus.edu.sg
Sample_contact_institute	National University of Singapore
Sample_contact_address	Medical Drive 10
Sample_contact_city	Singapore
Sample_contact_zip/postal_code	117597
Sample_contact_country	Singapore
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM740nnn/GSM740103/suppl/GSM740103.CEL.gz
Sample_series_id	GSE29885
Sample_data_row_count	31097

GSM740104

GPL1355

Amoeboid microglia from 5-day rat brain biological rep2

Amoeboid microglia from 5-day rat brain

age: Postnatal day 5 tissue origin: brain tissue type: corpus callosum cell type: Microglia cell morphology: Amoeboid (AMC)

Gene expression data from amoedboid microglia isolated from corpus callosum of 5-day rat brain

Sample_geo_accession	GSM740104
Sample_status	Public on Jun 11 2011
Sample_submission_date	Jun 10 2011
Sample_last_update_date	Jun 11 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was extracted from 600 microglia cells isolated by Laser-capture microdissection using RNeasy micro kit according to the manufacturer's instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Total RNA (15ng) was reverse transcripted into the first-strand cDNA using a T7-Oligo (dT) Primer (Two-Cycle Target Labeling and Control Reagent package, Affymetrix, CA, USA). After second-strand cDNA synthesis, the double-stranded cDNA was purified and served as a template in the first cycle of in vitro transcription (IVT) reaction. The unlabeled cRNA was then reverse transcripted into the first-strand cDNA of the second cycle using random primers. Subsequently, the T7-Oligo(dT) Promoter Primer was used in the second-strand cDNA synthesis to generate double-stranded cDNA template containing T7 promoter sequences. Then the double-stranded cDNA was amplified and labeled using a biotinylated nucleotide analog/ribonucleotide mix in the second IVT reaction.
Sample_hyb_protocol	The labeled cRNA was then cleaned up, fragmented, and hybridized to Rat Genome 230 2.0 Array (Cat. No. 900506, Affymetrix, CA, USA).
Sample_scan_protocol	The arrays were stained according to the manufacturer's protocols and then scanned with the Genechip scanner (Affymetrix, CA, USA).
Sample_data_processing	CEL files were exported to Affymetrix Expression Console Version 1.1 and RMA normalization was carried out. [The data were also analyzed with Microarray Suite version 5.0 (MAS 5.0) using GeneChip Operating Software (GCOS, Affymetrix, CA, USA). For absolute analysis, each chip was normalized to a target intensity of 500, and probe sets were assigned a signal intensity and detection call of Present, Marginal or Absent (See MAS5_GCOS_analyzed.txt on GSE29885)]
Sample_platform_id	GPL1355
Sample_contact_name	S Thameem,,Dheen
Sample_contact_email	antstd@nus.edu.sg
Sample_contact_institute	National University of Singapore
Sample_contact_address	Medical Drive 10
Sample_contact_city	Singapore
Sample_contact_zip/postal_code	117597
Sample_contact_country	Singapore
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM740nnn/GSM740104/suppl/GSM740104.CEL.gz
Sample_series_id	GSE29885
Sample_data_row_count	31097

GSM740105

GPL1355

Amoeboid microglia from 5-day rat brain biological rep3

Amoeboid microglia from 5-day rat brain

age: Postnatal day 5 tissue origin: brain tissue type: corpus callosum cell type: Microglia cell morphology: Amoeboid (AMC)

Gene expression data from amoedboid microglia isolated from corpus callosum of 5-day rat brain

Sample_geo_accession	GSM740105
Sample_status	Public on Jun 11 2011
Sample_submission_date	Jun 10 2011
Sample_last_update_date	Jun 11 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was extracted from 600 microglia cells isolated by Laser-capture microdissection using RNeasy micro kit according to the manufacturer's instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Total RNA (15ng) was reverse transcripted into the first-strand cDNA using a T7-Oligo (dT) Primer (Two-Cycle Target Labeling and Control Reagent package, Affymetrix, CA, USA). After second-strand cDNA synthesis, the double-stranded cDNA was purified and served as a template in the first cycle of in vitro transcription (IVT) reaction. The unlabeled cRNA was then reverse transcripted into the first-strand cDNA of the second cycle using random primers. Subsequently, the T7-Oligo(dT) Promoter Primer was used in the second-strand cDNA synthesis to generate double-stranded cDNA template containing T7 promoter sequences. Then the double-stranded cDNA was amplified and labeled using a biotinylated nucleotide analog/ribonucleotide mix in the second IVT reaction.
Sample_hyb_protocol	The labeled cRNA was then cleaned up, fragmented, and hybridized to Rat Genome 230 2.0 Array (Cat. No. 900506, Affymetrix, CA, USA).
Sample_scan_protocol	The arrays were stained according to the manufacturer's protocols and then scanned with the Genechip scanner (Affymetrix, CA, USA).
Sample_data_processing	CEL files were exported to Affymetrix Expression Console Version 1.1 and RMA normalization was carried out. [The data were also analyzed with Microarray Suite version 5.0 (MAS 5.0) using GeneChip Operating Software (GCOS, Affymetrix, CA, USA). For absolute analysis, each chip was normalized to a target intensity of 500, and probe sets were assigned a signal intensity and detection call of Present, Marginal or Absent (See MAS5_GCOS_analyzed.txt on GSE29885)]
Sample_platform_id	GPL1355
Sample_contact_name	S Thameem,,Dheen
Sample_contact_email	antstd@nus.edu.sg
Sample_contact_institute	National University of Singapore
Sample_contact_address	Medical Drive 10
Sample_contact_city	Singapore
Sample_contact_zip/postal_code	117597
Sample_contact_country	Singapore
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM740nnn/GSM740105/suppl/GSM740105.CEL.gz
Sample_series_id	GSE29885
Sample_data_row_count	31097

GSM740106

GPL1355

Ramified microglia from 4-week rat brain biological rep1

Ramified microglia from 4-week rat brain

age: Postnatal day 28 tissue origin: brain tissue type: corpus callosum cell type: Microglia cell morphology: Ramified (RMC)

Gene expression data from ramified microglia isolated from corpus callosum of 4-week rat brain

Sample_geo_accession	GSM740106
Sample_status	Public on Jun 11 2011
Sample_submission_date	Jun 10 2011
Sample_last_update_date	Jun 11 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was extracted from 600 microglia cells isolated by Laser-capture microdissection using RNeasy micro kit according to the manufacturer's instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Total RNA (15ng) was reverse transcripted into the first-strand cDNA using a T7-Oligo (dT) Primer (Two-Cycle Target Labeling and Control Reagent package, Affymetrix, CA, USA). After second-strand cDNA synthesis, the double-stranded cDNA was purified and served as a template in the first cycle of in vitro transcription (IVT) reaction. The unlabeled cRNA was then reverse transcripted into the first-strand cDNA of the second cycle using random primers. Subsequently, the T7-Oligo(dT) Promoter Primer was used in the second-strand cDNA synthesis to generate double-stranded cDNA template containing T7 promoter sequences. Then the double-stranded cDNA was amplified and labeled using a biotinylated nucleotide analog/ribonucleotide mix in the second IVT reaction.
Sample_hyb_protocol	The labeled cRNA was then cleaned up, fragmented, and hybridized to Rat Genome 230 2.0 Array (Cat. No. 900506, Affymetrix, CA, USA).
Sample_scan_protocol	The arrays were stained according to the manufacturer's protocols and then scanned with the Genechip scanner (Affymetrix, CA, USA).
Sample_data_processing	CEL files were exported to Affymetrix Expression Console Version 1.1 and RMA normalization was carried out. [The data were also analyzed with Microarray Suite version 5.0 (MAS 5.0) using GeneChip Operating Software (GCOS, Affymetrix, CA, USA). For absolute analysis, each chip was normalized to a target intensity of 500, and probe sets were assigned a signal intensity and detection call of Present, Marginal or Absent (See MAS5_GCOS_analyzed.txt on GSE29885)]
Sample_platform_id	GPL1355
Sample_contact_name	S Thameem,,Dheen
Sample_contact_email	antstd@nus.edu.sg
Sample_contact_institute	National University of Singapore
Sample_contact_address	Medical Drive 10
Sample_contact_city	Singapore
Sample_contact_zip/postal_code	117597
Sample_contact_country	Singapore
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM740nnn/GSM740106/suppl/GSM740106.CEL.gz
Sample_series_id	GSE29885
Sample_data_row_count	31097

GSM740107

GPL1355

Ramified microglia from 4-week rat brain biological rep2

Ramified microglia from 4-week rat brain

age: Postnatal day 28 tissue origin: brain tissue type: corpus callosum cell type: Microglia cell morphology: Ramified (RMC)

Gene expression data from ramified microglia isolated from corpus callosum of 4-week rat brain

Sample_geo_accession	GSM740107
Sample_status	Public on Jun 11 2011
Sample_submission_date	Jun 10 2011
Sample_last_update_date	Jun 11 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was extracted from 600 microglia cells isolated by Laser-capture microdissection using RNeasy micro kit according to the manufacturer's instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Total RNA (15ng) was reverse transcripted into the first-strand cDNA using a T7-Oligo (dT) Primer (Two-Cycle Target Labeling and Control Reagent package, Affymetrix, CA, USA). After second-strand cDNA synthesis, the double-stranded cDNA was purified and served as a template in the first cycle of in vitro transcription (IVT) reaction. The unlabeled cRNA was then reverse transcripted into the first-strand cDNA of the second cycle using random primers. Subsequently, the T7-Oligo(dT) Promoter Primer was used in the second-strand cDNA synthesis to generate double-stranded cDNA template containing T7 promoter sequences. Then the double-stranded cDNA was amplified and labeled using a biotinylated nucleotide analog/ribonucleotide mix in the second IVT reaction.
Sample_hyb_protocol	The labeled cRNA was then cleaned up, fragmented, and hybridized to Rat Genome 230 2.0 Array (Cat. No. 900506, Affymetrix, CA, USA).
Sample_scan_protocol	The arrays were stained according to the manufacturer's protocols and then scanned with the Genechip scanner (Affymetrix, CA, USA).
Sample_data_processing	CEL files were exported to Affymetrix Expression Console Version 1.1 and RMA normalization was carried out. [The data were also analyzed with Microarray Suite version 5.0 (MAS 5.0) using GeneChip Operating Software (GCOS, Affymetrix, CA, USA). For absolute analysis, each chip was normalized to a target intensity of 500, and probe sets were assigned a signal intensity and detection call of Present, Marginal or Absent (See MAS5_GCOS_analyzed.txt on GSE29885)]
Sample_platform_id	GPL1355
Sample_contact_name	S Thameem,,Dheen
Sample_contact_email	antstd@nus.edu.sg
Sample_contact_institute	National University of Singapore
Sample_contact_address	Medical Drive 10
Sample_contact_city	Singapore
Sample_contact_zip/postal_code	117597
Sample_contact_country	Singapore
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM740nnn/GSM740107/suppl/GSM740107.CEL.gz
Sample_series_id	GSE29885
Sample_data_row_count	31097

GSM740108

GPL1355

Ramified microglia from 4-week rat brain biological rep3

Ramified microglia from 4-week rat brain

age: Postnatal day 28 tissue origin: brain tissue type: corpus callosum cell type: Microglia cell morphology: Ramified (RMC)

Gene expression data from ramified microglia isolated from corpus callosum of 4-week rat brain

Sample_geo_accession	GSM740108
Sample_status	Public on Jun 11 2011
Sample_submission_date	Jun 10 2011
Sample_last_update_date	Jun 11 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was extracted from 600 microglia cells isolated by Laser-capture microdissection using RNeasy micro kit according to the manufacturer's instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Total RNA (15ng) was reverse transcripted into the first-strand cDNA using a T7-Oligo (dT) Primer (Two-Cycle Target Labeling and Control Reagent package, Affymetrix, CA, USA). After second-strand cDNA synthesis, the double-stranded cDNA was purified and served as a template in the first cycle of in vitro transcription (IVT) reaction. The unlabeled cRNA was then reverse transcripted into the first-strand cDNA of the second cycle using random primers. Subsequently, the T7-Oligo(dT) Promoter Primer was used in the second-strand cDNA synthesis to generate double-stranded cDNA template containing T7 promoter sequences. Then the double-stranded cDNA was amplified and labeled using a biotinylated nucleotide analog/ribonucleotide mix in the second IVT reaction.
Sample_hyb_protocol	The labeled cRNA was then cleaned up, fragmented, and hybridized to Rat Genome 230 2.0 Array (Cat. No. 900506, Affymetrix, CA, USA).
Sample_scan_protocol	The arrays were stained according to the manufacturer's protocols and then scanned with the Genechip scanner (Affymetrix, CA, USA).
Sample_data_processing	CEL files were exported to Affymetrix Expression Console Version 1.1 and RMA normalization was carried out. [The data were also analyzed with Microarray Suite version 5.0 (MAS 5.0) using GeneChip Operating Software (GCOS, Affymetrix, CA, USA). For absolute analysis, each chip was normalized to a target intensity of 500, and probe sets were assigned a signal intensity and detection call of Present, Marginal or Absent (See MAS5_GCOS_analyzed.txt on GSE29885)]
Sample_platform_id	GPL1355
Sample_contact_name	S Thameem,,Dheen
Sample_contact_email	antstd@nus.edu.sg
Sample_contact_institute	National University of Singapore
Sample_contact_address	Medical Drive 10
Sample_contact_city	Singapore
Sample_contact_zip/postal_code	117597
Sample_contact_country	Singapore
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM740nnn/GSM740108/suppl/GSM740108.CEL.gz
Sample_series_id	GSE29885
Sample_data_row_count	31097

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