Result

Search results for the GEO ID: GSE45997

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Title

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Description

Characteristics

GSM1121537

GPL1355

Todd 1I

ipsilateral hemi-brain

tissue: Brain age: 6.5-9 weeks weight: 290-300g strain: Sprague-Dawley treatment: traumatic brain injury

Gene expression data from ipsilateral hemi-brain after brain injury

Sample_geo_accession	GSM1121537
Sample_status	Public on Apr 12 2013
Sample_submission_date	Apr 11 2013
Sample_last_update_date	Apr 12 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_treatment_protocol_ch1	Under isoflurane anesthesia, rats received a unilateral controlled cortical impact (CCI/TBI) using the Pittsburgh Precision Instruments, Inc. device. A craniotomy was made with the center 4 mm posterior and 3-4 mm lateral to bregma using a 6 mm diameter trephan drill bit. The impact was done at an angle of 15° from vertical with a velocity of 3 m/s to a depth of 2 mm using a 5 mm diameter impact tip. The rats were sacrificed 24 h post-injury and the brains were removed for RNA isolation.
Sample_growth_protocol_ch1	All animals used in these studies were treated humanely and with regard for alleviation of suffering and pain and all protocols involving animals were approved by the IACUCs of Morehouse School of Medicine and/or The Georgia Institute of Technology prior to the initiation of experimentation. Adult male Sprague-Dawley rats (290-300g; Charles River Laboratories International, Inc., USA) were housed individually in standard plastic cages in a temperature-controlled room (22 ± 2C) on a 12 h reverse light-dark cycle. Food and water were provided ad libitum.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	The ipsilateral hemi-brain tissue at the site of the injury, the corresponding contralateral hemi-brain tissue, and naïve (control) brain tissue (n=3 for each) were used for RNA isolation. Total RNA was extracted with TRIzol Reagent (Life Technologies, Rockville, MD, USA) and cleaned (RNAqueous Kit, Ambion, Austin, TX, USA). The RNA was prepared for microarray hybridization with the GeneChip® 3’ IVT Express Kit (Affymetrix Inc., Santa Clara, CA, USA) aRNA amplification procedure. Briefly, total RNA was reverse transcribed to synthesize first-strand cDNA containing a T7 promoter sequence. The single-stranded cDNA was converted into a double-stranded DNA template for transcription. The reaction employed DNA polymerase and RNase H to simultaneously degrade the RNA and synthesize second-strand cDNA. In vitro transcription generated multiple copies of biotin-modified aRNA from the double-stranded cDNA templates (this was the amplification step). aRNA Purification removed unincorporated NTPs, salts, enzymes, and inorganic phosphate to improve the stability of the biotin-modified aRNA. Finally, the labeled aRNA was fragmented to prepare the target for hybridization to GeneChip® 3’ expression arrays
Sample_label_ch1	biotin
Sample_label_protocol_ch1	standard Affymetrix protocol
Sample_hyb_protocol	standard Affymetrix protocol
Sample_scan_protocol	standard Affymetrix protocol
Sample_data_processing	The data were analyzed with Affymetrix Expression Console using Affymetrix default analysis settings for MAS5
Sample_platform_id	GPL1355
Sample_contact_name	Benem-Orom,Andrew,Davids
Sample_contact_email	benemdavids@gmail.com
Sample_contact_laboratory	FordLab
Sample_contact_department	Neurobiology
Sample_contact_institute	Morehouse School of Medicine
Sample_contact_address	720 Westview Drive SW
Sample_contact_city	Atlanta
Sample_contact_state	ga
Sample_contact_zip/postal_code	30310-1495
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1121nnn/GSM1121537/suppl/GSM1121537_Todd_1I_A_Rat230_2_.CEL.gz
Sample_series_id	GSE45997
Sample_data_row_count	31099

GSM1121538

GPL1355

2I Todd

ipsilateral hemi-brain

tissue: Brain age: 6.5-9 weeks weight: 290-300g strain: Sprague-Dawley treatment: traumatic brain injury

Gene expression data from ipsilateral hemi-brain after brain injury

Sample_geo_accession	GSM1121538
Sample_status	Public on Apr 12 2013
Sample_submission_date	Apr 11 2013
Sample_last_update_date	Apr 12 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_treatment_protocol_ch1	Under isoflurane anesthesia, rats received a unilateral controlled cortical impact (CCI/TBI) using the Pittsburgh Precision Instruments, Inc. device. A craniotomy was made with the center 4 mm posterior and 3-4 mm lateral to bregma using a 6 mm diameter trephan drill bit. The impact was done at an angle of 15° from vertical with a velocity of 3 m/s to a depth of 2 mm using a 5 mm diameter impact tip. The rats were sacrificed 24 h post-injury and the brains were removed for RNA isolation.
Sample_growth_protocol_ch1	All animals used in these studies were treated humanely and with regard for alleviation of suffering and pain and all protocols involving animals were approved by the IACUCs of Morehouse School of Medicine and/or The Georgia Institute of Technology prior to the initiation of experimentation. Adult male Sprague-Dawley rats (290-300g; Charles River Laboratories International, Inc., USA) were housed individually in standard plastic cages in a temperature-controlled room (22 ± 2C) on a 12 h reverse light-dark cycle. Food and water were provided ad libitum.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	The ipsilateral hemi-brain tissue at the site of the injury, the corresponding contralateral hemi-brain tissue, and naïve (control) brain tissue (n=3 for each) were used for RNA isolation. Total RNA was extracted with TRIzol Reagent (Life Technologies, Rockville, MD, USA) and cleaned (RNAqueous Kit, Ambion, Austin, TX, USA). The RNA was prepared for microarray hybridization with the GeneChip® 3’ IVT Express Kit (Affymetrix Inc., Santa Clara, CA, USA) aRNA amplification procedure. Briefly, total RNA was reverse transcribed to synthesize first-strand cDNA containing a T7 promoter sequence. The single-stranded cDNA was converted into a double-stranded DNA template for transcription. The reaction employed DNA polymerase and RNase H to simultaneously degrade the RNA and synthesize second-strand cDNA. In vitro transcription generated multiple copies of biotin-modified aRNA from the double-stranded cDNA templates (this was the amplification step). aRNA Purification removed unincorporated NTPs, salts, enzymes, and inorganic phosphate to improve the stability of the biotin-modified aRNA. Finally, the labeled aRNA was fragmented to prepare the target for hybridization to GeneChip® 3’ expression arrays
Sample_label_ch1	biotin
Sample_label_protocol_ch1	standard Affymetrix protocol
Sample_hyb_protocol	standard Affymetrix protocol
Sample_scan_protocol	standard Affymetrix protocol
Sample_data_processing	The data were analyzed with Affymetrix Expression Console using Affymetrix default analysis settings for MAS5
Sample_platform_id	GPL1355
Sample_contact_name	Benem-Orom,Andrew,Davids
Sample_contact_email	benemdavids@gmail.com
Sample_contact_laboratory	FordLab
Sample_contact_department	Neurobiology
Sample_contact_institute	Morehouse School of Medicine
Sample_contact_address	720 Westview Drive SW
Sample_contact_city	Atlanta
Sample_contact_state	ga
Sample_contact_zip/postal_code	30310-1495
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1121nnn/GSM1121538/suppl/GSM1121538_2I_Todd_Rat230_2_.CEL.gz
Sample_series_id	GSE45997
Sample_data_row_count	31099

GSM1121539

GPL1355

Todd 3I

ipsilateral hemi-brain

tissue: Brain age: 6.5-9 weeks weight: 290-300g strain: Sprague-Dawley treatment: traumatic brain injury

Gene expression data from ipsilateral hemi-brain after brain injury

Sample_geo_accession	GSM1121539
Sample_status	Public on Apr 12 2013
Sample_submission_date	Apr 11 2013
Sample_last_update_date	Apr 12 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_treatment_protocol_ch1	Under isoflurane anesthesia, rats received a unilateral controlled cortical impact (CCI/TBI) using the Pittsburgh Precision Instruments, Inc. device. A craniotomy was made with the center 4 mm posterior and 3-4 mm lateral to bregma using a 6 mm diameter trephan drill bit. The impact was done at an angle of 15° from vertical with a velocity of 3 m/s to a depth of 2 mm using a 5 mm diameter impact tip. The rats were sacrificed 24 h post-injury and the brains were removed for RNA isolation.
Sample_growth_protocol_ch1	All animals used in these studies were treated humanely and with regard for alleviation of suffering and pain and all protocols involving animals were approved by the IACUCs of Morehouse School of Medicine and/or The Georgia Institute of Technology prior to the initiation of experimentation. Adult male Sprague-Dawley rats (290-300g; Charles River Laboratories International, Inc., USA) were housed individually in standard plastic cages in a temperature-controlled room (22 ± 2C) on a 12 h reverse light-dark cycle. Food and water were provided ad libitum.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	The ipsilateral hemi-brain tissue at the site of the injury, the corresponding contralateral hemi-brain tissue, and naïve (control) brain tissue (n=3 for each) were used for RNA isolation. Total RNA was extracted with TRIzol Reagent (Life Technologies, Rockville, MD, USA) and cleaned (RNAqueous Kit, Ambion, Austin, TX, USA). The RNA was prepared for microarray hybridization with the GeneChip® 3’ IVT Express Kit (Affymetrix Inc., Santa Clara, CA, USA) aRNA amplification procedure. Briefly, total RNA was reverse transcribed to synthesize first-strand cDNA containing a T7 promoter sequence. The single-stranded cDNA was converted into a double-stranded DNA template for transcription. The reaction employed DNA polymerase and RNase H to simultaneously degrade the RNA and synthesize second-strand cDNA. In vitro transcription generated multiple copies of biotin-modified aRNA from the double-stranded cDNA templates (this was the amplification step). aRNA Purification removed unincorporated NTPs, salts, enzymes, and inorganic phosphate to improve the stability of the biotin-modified aRNA. Finally, the labeled aRNA was fragmented to prepare the target for hybridization to GeneChip® 3’ expression arrays
Sample_label_ch1	biotin
Sample_label_protocol_ch1	standard Affymetrix protocol
Sample_hyb_protocol	standard Affymetrix protocol
Sample_scan_protocol	standard Affymetrix protocol
Sample_data_processing	The data were analyzed with Affymetrix Expression Console using Affymetrix default analysis settings for MAS5
Sample_platform_id	GPL1355
Sample_contact_name	Benem-Orom,Andrew,Davids
Sample_contact_email	benemdavids@gmail.com
Sample_contact_laboratory	FordLab
Sample_contact_department	Neurobiology
Sample_contact_institute	Morehouse School of Medicine
Sample_contact_address	720 Westview Drive SW
Sample_contact_city	Atlanta
Sample_contact_state	ga
Sample_contact_zip/postal_code	30310-1495
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1121nnn/GSM1121539/suppl/GSM1121539_Todd_3I-B_Rat230_2_.CEL.gz
Sample_series_id	GSE45997
Sample_data_row_count	31099

GSM1121540

GPL1355

Todd 1C

contralateral hemi-brain

tissue: Brain age: 6.5-9 weeks weight: 290-300g strain: Sprague-Dawley treatment: contralateral to traumatic brain injury

Gene expression data from contralateral hemi-brain after brain injury

Sample_geo_accession	GSM1121540
Sample_status	Public on Apr 12 2013
Sample_submission_date	Apr 11 2013
Sample_last_update_date	Apr 12 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_treatment_protocol_ch1	Under isoflurane anesthesia, rats received a unilateral controlled cortical impact (CCI/TBI) using the Pittsburgh Precision Instruments, Inc. device. A craniotomy was made with the center 4 mm posterior and 3-4 mm lateral to bregma using a 6 mm diameter trephan drill bit. The impact was done at an angle of 15° from vertical with a velocity of 3 m/s to a depth of 2 mm using a 5 mm diameter impact tip. The rats were sacrificed 24 h post-injury and the brains were removed for RNA isolation.
Sample_growth_protocol_ch1	All animals used in these studies were treated humanely and with regard for alleviation of suffering and pain and all protocols involving animals were approved by the IACUCs of Morehouse School of Medicine and/or The Georgia Institute of Technology prior to the initiation of experimentation. Adult male Sprague-Dawley rats (290-300g; Charles River Laboratories International, Inc., USA) were housed individually in standard plastic cages in a temperature-controlled room (22 ± 2C) on a 12 h reverse light-dark cycle. Food and water were provided ad libitum.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	The ipsilateral hemi-brain tissue at the site of the injury, the corresponding contralateral hemi-brain tissue, and naïve (control) brain tissue (n=3 for each) were used for RNA isolation. Total RNA was extracted with TRIzol Reagent (Life Technologies, Rockville, MD, USA) and cleaned (RNAqueous Kit, Ambion, Austin, TX, USA). The RNA was prepared for microarray hybridization with the GeneChip® 3’ IVT Express Kit (Affymetrix Inc., Santa Clara, CA, USA) aRNA amplification procedure. Briefly, total RNA was reverse transcribed to synthesize first-strand cDNA containing a T7 promoter sequence. The single-stranded cDNA was converted into a double-stranded DNA template for transcription. The reaction employed DNA polymerase and RNase H to simultaneously degrade the RNA and synthesize second-strand cDNA. In vitro transcription generated multiple copies of biotin-modified aRNA from the double-stranded cDNA templates (this was the amplification step). aRNA Purification removed unincorporated NTPs, salts, enzymes, and inorganic phosphate to improve the stability of the biotin-modified aRNA. Finally, the labeled aRNA was fragmented to prepare the target for hybridization to GeneChip® 3’ expression arrays
Sample_label_ch1	biotin
Sample_label_protocol_ch1	standard Affymetrix protocol
Sample_hyb_protocol	standard Affymetrix protocol
Sample_scan_protocol	standard Affymetrix protocol
Sample_data_processing	The data were analyzed with Affymetrix Expression Console using Affymetrix default analysis settings for MAS5
Sample_platform_id	GPL1355
Sample_contact_name	Benem-Orom,Andrew,Davids
Sample_contact_email	benemdavids@gmail.com
Sample_contact_laboratory	FordLab
Sample_contact_department	Neurobiology
Sample_contact_institute	Morehouse School of Medicine
Sample_contact_address	720 Westview Drive SW
Sample_contact_city	Atlanta
Sample_contact_state	ga
Sample_contact_zip/postal_code	30310-1495
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1121nnn/GSM1121540/suppl/GSM1121540_Todd_1C_C_Rat230_2_.CEL.gz
Sample_series_id	GSE45997
Sample_data_row_count	31099

GSM1121541

GPL1355

2C Todd

contralateral hemi-brain

tissue: Brain age: 6.5-9 weeks weight: 290-300g strain: Sprague-Dawley treatment: contralateral to traumatic brain injury

Gene expression data from contralateral hemi-brain after brain injury

Sample_geo_accession	GSM1121541
Sample_status	Public on Apr 12 2013
Sample_submission_date	Apr 11 2013
Sample_last_update_date	Apr 12 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_treatment_protocol_ch1	Under isoflurane anesthesia, rats received a unilateral controlled cortical impact (CCI/TBI) using the Pittsburgh Precision Instruments, Inc. device. A craniotomy was made with the center 4 mm posterior and 3-4 mm lateral to bregma using a 6 mm diameter trephan drill bit. The impact was done at an angle of 15° from vertical with a velocity of 3 m/s to a depth of 2 mm using a 5 mm diameter impact tip. The rats were sacrificed 24 h post-injury and the brains were removed for RNA isolation.
Sample_growth_protocol_ch1	All animals used in these studies were treated humanely and with regard for alleviation of suffering and pain and all protocols involving animals were approved by the IACUCs of Morehouse School of Medicine and/or The Georgia Institute of Technology prior to the initiation of experimentation. Adult male Sprague-Dawley rats (290-300g; Charles River Laboratories International, Inc., USA) were housed individually in standard plastic cages in a temperature-controlled room (22 ± 2C) on a 12 h reverse light-dark cycle. Food and water were provided ad libitum.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	The ipsilateral hemi-brain tissue at the site of the injury, the corresponding contralateral hemi-brain tissue, and naïve (control) brain tissue (n=3 for each) were used for RNA isolation. Total RNA was extracted with TRIzol Reagent (Life Technologies, Rockville, MD, USA) and cleaned (RNAqueous Kit, Ambion, Austin, TX, USA). The RNA was prepared for microarray hybridization with the GeneChip® 3’ IVT Express Kit (Affymetrix Inc., Santa Clara, CA, USA) aRNA amplification procedure. Briefly, total RNA was reverse transcribed to synthesize first-strand cDNA containing a T7 promoter sequence. The single-stranded cDNA was converted into a double-stranded DNA template for transcription. The reaction employed DNA polymerase and RNase H to simultaneously degrade the RNA and synthesize second-strand cDNA. In vitro transcription generated multiple copies of biotin-modified aRNA from the double-stranded cDNA templates (this was the amplification step). aRNA Purification removed unincorporated NTPs, salts, enzymes, and inorganic phosphate to improve the stability of the biotin-modified aRNA. Finally, the labeled aRNA was fragmented to prepare the target for hybridization to GeneChip® 3’ expression arrays
Sample_label_ch1	biotin
Sample_label_protocol_ch1	standard Affymetrix protocol
Sample_hyb_protocol	standard Affymetrix protocol
Sample_scan_protocol	standard Affymetrix protocol
Sample_data_processing	The data were analyzed with Affymetrix Expression Console using Affymetrix default analysis settings for MAS5
Sample_platform_id	GPL1355
Sample_contact_name	Benem-Orom,Andrew,Davids
Sample_contact_email	benemdavids@gmail.com
Sample_contact_laboratory	FordLab
Sample_contact_department	Neurobiology
Sample_contact_institute	Morehouse School of Medicine
Sample_contact_address	720 Westview Drive SW
Sample_contact_city	Atlanta
Sample_contact_state	ga
Sample_contact_zip/postal_code	30310-1495
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1121nnn/GSM1121541/suppl/GSM1121541_2C_Todd_Rat230_2_.CEL.gz
Sample_series_id	GSE45997
Sample_data_row_count	31099

GSM1121542

GPL1355

Todd 3C

contralateral hemi-brain

tissue: Brain age: 6.5-9 weeks weight: 290-300g strain: Sprague-Dawley treatment: contralateral to traumatic brain injury

Gene expression data from contralateral hemi-brain after brain injury

Sample_geo_accession	GSM1121542
Sample_status	Public on Apr 12 2013
Sample_submission_date	Apr 11 2013
Sample_last_update_date	Apr 12 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_treatment_protocol_ch1	Under isoflurane anesthesia, rats received a unilateral controlled cortical impact (CCI/TBI) using the Pittsburgh Precision Instruments, Inc. device. A craniotomy was made with the center 4 mm posterior and 3-4 mm lateral to bregma using a 6 mm diameter trephan drill bit. The impact was done at an angle of 15° from vertical with a velocity of 3 m/s to a depth of 2 mm using a 5 mm diameter impact tip. The rats were sacrificed 24 h post-injury and the brains were removed for RNA isolation.
Sample_growth_protocol_ch1	All animals used in these studies were treated humanely and with regard for alleviation of suffering and pain and all protocols involving animals were approved by the IACUCs of Morehouse School of Medicine and/or The Georgia Institute of Technology prior to the initiation of experimentation. Adult male Sprague-Dawley rats (290-300g; Charles River Laboratories International, Inc., USA) were housed individually in standard plastic cages in a temperature-controlled room (22 ± 2C) on a 12 h reverse light-dark cycle. Food and water were provided ad libitum.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	The ipsilateral hemi-brain tissue at the site of the injury, the corresponding contralateral hemi-brain tissue, and naïve (control) brain tissue (n=3 for each) were used for RNA isolation. Total RNA was extracted with TRIzol Reagent (Life Technologies, Rockville, MD, USA) and cleaned (RNAqueous Kit, Ambion, Austin, TX, USA). The RNA was prepared for microarray hybridization with the GeneChip® 3’ IVT Express Kit (Affymetrix Inc., Santa Clara, CA, USA) aRNA amplification procedure. Briefly, total RNA was reverse transcribed to synthesize first-strand cDNA containing a T7 promoter sequence. The single-stranded cDNA was converted into a double-stranded DNA template for transcription. The reaction employed DNA polymerase and RNase H to simultaneously degrade the RNA and synthesize second-strand cDNA. In vitro transcription generated multiple copies of biotin-modified aRNA from the double-stranded cDNA templates (this was the amplification step). aRNA Purification removed unincorporated NTPs, salts, enzymes, and inorganic phosphate to improve the stability of the biotin-modified aRNA. Finally, the labeled aRNA was fragmented to prepare the target for hybridization to GeneChip® 3’ expression arrays
Sample_label_ch1	biotin
Sample_label_protocol_ch1	standard Affymetrix protocol
Sample_hyb_protocol	standard Affymetrix protocol
Sample_scan_protocol	standard Affymetrix protocol
Sample_data_processing	The data were analyzed with Affymetrix Expression Console using Affymetrix default analysis settings for MAS5
Sample_platform_id	GPL1355
Sample_contact_name	Benem-Orom,Andrew,Davids
Sample_contact_email	benemdavids@gmail.com
Sample_contact_laboratory	FordLab
Sample_contact_department	Neurobiology
Sample_contact_institute	Morehouse School of Medicine
Sample_contact_address	720 Westview Drive SW
Sample_contact_city	Atlanta
Sample_contact_state	ga
Sample_contact_zip/postal_code	30310-1495
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1121nnn/GSM1121542/suppl/GSM1121542_Todd_3C_D_Rat230_2_.CEL.gz
Sample_series_id	GSE45997
Sample_data_row_count	31099

GSM1121543

GPL1355

Xu 13 control

naïve brain

tissue: Brain age: 6.5-9 weeks weight: 290-300g strain: Sprague-Dawley treatment: naïve

naïve brain

Sample_geo_accession	GSM1121543
Sample_status	Public on Apr 12 2013
Sample_submission_date	Apr 11 2013
Sample_last_update_date	Apr 12 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_treatment_protocol_ch1	Under isoflurane anesthesia, rats received a unilateral controlled cortical impact (CCI/TBI) using the Pittsburgh Precision Instruments, Inc. device. A craniotomy was made with the center 4 mm posterior and 3-4 mm lateral to bregma using a 6 mm diameter trephan drill bit. The impact was done at an angle of 15° from vertical with a velocity of 3 m/s to a depth of 2 mm using a 5 mm diameter impact tip. The rats were sacrificed 24 h post-injury and the brains were removed for RNA isolation.
Sample_growth_protocol_ch1	All animals used in these studies were treated humanely and with regard for alleviation of suffering and pain and all protocols involving animals were approved by the IACUCs of Morehouse School of Medicine and/or The Georgia Institute of Technology prior to the initiation of experimentation. Adult male Sprague-Dawley rats (290-300g; Charles River Laboratories International, Inc., USA) were housed individually in standard plastic cages in a temperature-controlled room (22 ± 2C) on a 12 h reverse light-dark cycle. Food and water were provided ad libitum.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	The ipsilateral hemi-brain tissue at the site of the injury, the corresponding contralateral hemi-brain tissue, and naïve (control) brain tissue (n=3 for each) were used for RNA isolation. Total RNA was extracted with TRIzol Reagent (Life Technologies, Rockville, MD, USA) and cleaned (RNAqueous Kit, Ambion, Austin, TX, USA). The RNA was prepared for microarray hybridization with the GeneChip® 3’ IVT Express Kit (Affymetrix Inc., Santa Clara, CA, USA) aRNA amplification procedure. Briefly, total RNA was reverse transcribed to synthesize first-strand cDNA containing a T7 promoter sequence. The single-stranded cDNA was converted into a double-stranded DNA template for transcription. The reaction employed DNA polymerase and RNase H to simultaneously degrade the RNA and synthesize second-strand cDNA. In vitro transcription generated multiple copies of biotin-modified aRNA from the double-stranded cDNA templates (this was the amplification step). aRNA Purification removed unincorporated NTPs, salts, enzymes, and inorganic phosphate to improve the stability of the biotin-modified aRNA. Finally, the labeled aRNA was fragmented to prepare the target for hybridization to GeneChip® 3’ expression arrays
Sample_label_ch1	biotin
Sample_label_protocol_ch1	standard Affymetrix protocol
Sample_hyb_protocol	standard Affymetrix protocol
Sample_scan_protocol	standard Affymetrix protocol
Sample_data_processing	The data were analyzed with Affymetrix Expression Console using Affymetrix default analysis settings for MAS5
Sample_platform_id	GPL1355
Sample_contact_name	Benem-Orom,Andrew,Davids
Sample_contact_email	benemdavids@gmail.com
Sample_contact_laboratory	FordLab
Sample_contact_department	Neurobiology
Sample_contact_institute	Morehouse School of Medicine
Sample_contact_address	720 Westview Drive SW
Sample_contact_city	Atlanta
Sample_contact_state	ga
Sample_contact_zip/postal_code	30310-1495
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1121nnn/GSM1121543/suppl/GSM1121543_Xu_13_control_Rat230_2_.CEL.gz
Sample_series_id	GSE45997
Sample_data_row_count	31099

GSM1121544

GPL1355

Xu 2 control

naïve brain

tissue: Brain age: 6.5-9 weeks weight: 290-300g strain: Sprague-Dawley treatment: naïve

naïve brain

Sample_geo_accession	GSM1121544
Sample_status	Public on Apr 12 2013
Sample_submission_date	Apr 11 2013
Sample_last_update_date	Apr 12 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_treatment_protocol_ch1	Under isoflurane anesthesia, rats received a unilateral controlled cortical impact (CCI/TBI) using the Pittsburgh Precision Instruments, Inc. device. A craniotomy was made with the center 4 mm posterior and 3-4 mm lateral to bregma using a 6 mm diameter trephan drill bit. The impact was done at an angle of 15° from vertical with a velocity of 3 m/s to a depth of 2 mm using a 5 mm diameter impact tip. The rats were sacrificed 24 h post-injury and the brains were removed for RNA isolation.
Sample_growth_protocol_ch1	All animals used in these studies were treated humanely and with regard for alleviation of suffering and pain and all protocols involving animals were approved by the IACUCs of Morehouse School of Medicine and/or The Georgia Institute of Technology prior to the initiation of experimentation. Adult male Sprague-Dawley rats (290-300g; Charles River Laboratories International, Inc., USA) were housed individually in standard plastic cages in a temperature-controlled room (22 ± 2C) on a 12 h reverse light-dark cycle. Food and water were provided ad libitum.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	The ipsilateral hemi-brain tissue at the site of the injury, the corresponding contralateral hemi-brain tissue, and naïve (control) brain tissue (n=3 for each) were used for RNA isolation. Total RNA was extracted with TRIzol Reagent (Life Technologies, Rockville, MD, USA) and cleaned (RNAqueous Kit, Ambion, Austin, TX, USA). The RNA was prepared for microarray hybridization with the GeneChip® 3’ IVT Express Kit (Affymetrix Inc., Santa Clara, CA, USA) aRNA amplification procedure. Briefly, total RNA was reverse transcribed to synthesize first-strand cDNA containing a T7 promoter sequence. The single-stranded cDNA was converted into a double-stranded DNA template for transcription. The reaction employed DNA polymerase and RNase H to simultaneously degrade the RNA and synthesize second-strand cDNA. In vitro transcription generated multiple copies of biotin-modified aRNA from the double-stranded cDNA templates (this was the amplification step). aRNA Purification removed unincorporated NTPs, salts, enzymes, and inorganic phosphate to improve the stability of the biotin-modified aRNA. Finally, the labeled aRNA was fragmented to prepare the target for hybridization to GeneChip® 3’ expression arrays
Sample_label_ch1	biotin
Sample_label_protocol_ch1	standard Affymetrix protocol
Sample_hyb_protocol	standard Affymetrix protocol
Sample_scan_protocol	standard Affymetrix protocol
Sample_data_processing	The data were analyzed with Affymetrix Expression Console using Affymetrix default analysis settings for MAS5
Sample_platform_id	GPL1355
Sample_contact_name	Benem-Orom,Andrew,Davids
Sample_contact_email	benemdavids@gmail.com
Sample_contact_laboratory	FordLab
Sample_contact_department	Neurobiology
Sample_contact_institute	Morehouse School of Medicine
Sample_contact_address	720 Westview Drive SW
Sample_contact_city	Atlanta
Sample_contact_state	ga
Sample_contact_zip/postal_code	30310-1495
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1121nnn/GSM1121544/suppl/GSM1121544_Xu_2_control_Rat230_2_.CEL.gz
Sample_series_id	GSE45997
Sample_data_row_count	31099

GSM1121545

GPL1355

Xu 6 control

naïve brain

tissue: Brain age: 6.5-9 weeks weight: 290-300g strain: Sprague-Dawley treatment: naïve

naïve brain

Sample_geo_accession	GSM1121545
Sample_status	Public on Apr 12 2013
Sample_submission_date	Apr 11 2013
Sample_last_update_date	Apr 12 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_treatment_protocol_ch1	Under isoflurane anesthesia, rats received a unilateral controlled cortical impact (CCI/TBI) using the Pittsburgh Precision Instruments, Inc. device. A craniotomy was made with the center 4 mm posterior and 3-4 mm lateral to bregma using a 6 mm diameter trephan drill bit. The impact was done at an angle of 15° from vertical with a velocity of 3 m/s to a depth of 2 mm using a 5 mm diameter impact tip. The rats were sacrificed 24 h post-injury and the brains were removed for RNA isolation.
Sample_growth_protocol_ch1	All animals used in these studies were treated humanely and with regard for alleviation of suffering and pain and all protocols involving animals were approved by the IACUCs of Morehouse School of Medicine and/or The Georgia Institute of Technology prior to the initiation of experimentation. Adult male Sprague-Dawley rats (290-300g; Charles River Laboratories International, Inc., USA) were housed individually in standard plastic cages in a temperature-controlled room (22 ± 2C) on a 12 h reverse light-dark cycle. Food and water were provided ad libitum.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	The ipsilateral hemi-brain tissue at the site of the injury, the corresponding contralateral hemi-brain tissue, and naïve (control) brain tissue (n=3 for each) were used for RNA isolation. Total RNA was extracted with TRIzol Reagent (Life Technologies, Rockville, MD, USA) and cleaned (RNAqueous Kit, Ambion, Austin, TX, USA). The RNA was prepared for microarray hybridization with the GeneChip® 3’ IVT Express Kit (Affymetrix Inc., Santa Clara, CA, USA) aRNA amplification procedure. Briefly, total RNA was reverse transcribed to synthesize first-strand cDNA containing a T7 promoter sequence. The single-stranded cDNA was converted into a double-stranded DNA template for transcription. The reaction employed DNA polymerase and RNase H to simultaneously degrade the RNA and synthesize second-strand cDNA. In vitro transcription generated multiple copies of biotin-modified aRNA from the double-stranded cDNA templates (this was the amplification step). aRNA Purification removed unincorporated NTPs, salts, enzymes, and inorganic phosphate to improve the stability of the biotin-modified aRNA. Finally, the labeled aRNA was fragmented to prepare the target for hybridization to GeneChip® 3’ expression arrays
Sample_label_ch1	biotin
Sample_label_protocol_ch1	standard Affymetrix protocol
Sample_hyb_protocol	standard Affymetrix protocol
Sample_scan_protocol	standard Affymetrix protocol
Sample_data_processing	The data were analyzed with Affymetrix Expression Console using Affymetrix default analysis settings for MAS5
Sample_platform_id	GPL1355
Sample_contact_name	Benem-Orom,Andrew,Davids
Sample_contact_email	benemdavids@gmail.com
Sample_contact_laboratory	FordLab
Sample_contact_department	Neurobiology
Sample_contact_institute	Morehouse School of Medicine
Sample_contact_address	720 Westview Drive SW
Sample_contact_city	Atlanta
Sample_contact_state	ga
Sample_contact_zip/postal_code	30310-1495
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1121nnn/GSM1121545/suppl/GSM1121545_Xu_6_control_Rat230_2_.CEL.gz
Sample_series_id	GSE45997
Sample_data_row_count	31099

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