Search results for the GEO ID: GSE15041  |
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GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM375686 | GPL1355 |
|
2 months, sham group, biological replicate 1
|
L4/L5 dorsal root ganglia from adult rats (2 months old) 7 days after sham surgery
|
strain: Sprague-Dawley
tissue: Dorsal root ganglia
postnatal age: 2 months
surgery type: Sham
experimetal group: Adult Sham
|
The L4/L5 dorsal root ganglia in the sham group are those ganglia ipsilateral to the surgery
|
| Sample_geo_accession | GSM375686
| | Sample_status | Public on Dec 18 2009
| | Sample_submission_date | Feb 27 2009
| | Sample_last_update_date | Dec 18 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Experiments were performed on adult (2 months old) male Sprague–Dawley rats and rat pups (10 days postnatal age, P10) and carried out in accordance with the United Kingdom Animal (Scientific Procedures) Act 1986. Spared nerve injury and sham surgery were performed under halothane general anaesthesia with antiseptic conditions. After skin preparation, the sciatic nerve and its three terminal branches were exposed in the upper lateral thigh. Axotomy and ligation of the common peroneal and tibial branches was performed under direct vision, leaving the sural nerve intact. Muscle and skin were closed in two layers. In the sham operation, the procedures were the same but the nerves were only exposed and not cut or ligated. In all cases great care was taken not to stretch the nerve, or its branches, nor to damage the intact nerves.
| | Sample_growth_protocol_ch1 | After the surgery, the animals were returned to their cages and litters and maintained on a 12 hour light/dark cycle at constant ambient temperature in the Biological Services Unit with free access to food and water for 7 days post surgery (ps) until DRGs collection.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Seven days post surgery, animals were sacrificed with 0.1 mL of Euthanal®, the fresh DRGs were snap frozen on liquid nitrogen and stored at –80o C until RNA extraction. L4 and L5 DRGs ipsilateral to the lesion were collected and pooled from 3 animals per adult experimental group and 4 animals per P10 group, (i.e. n= 6 DRGs per adult sample , n=8 per P10 sample) to minimise inter-animal differences. RNA was extracted using Trizol® reagent (Invitrogen®) and QIAshredder column (Qiagen®) for homogenisation according to manufacturer’s protocols. Additionally, the RNA was cleaned by ”RNA purification column” (Qiagen®) and a final volume of 50 uL obtained according to manufacturer protocol. The amount of RNA was measured with a NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies, Inc.) and its quality assessed with Experion RNA HighSens StdSens analysis kit (Bio-Rad®). Then, the RNA was precipitated and dissolved to obtain a final concentration of 1 µg/µL and stored at -80°C until for cRNA synthesis or amplification by quantitative real-time polymerase chain reaction (qPCR).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA synthesis First strand cDNA synthesis; 2 g (for qPCR) or 10 ug (microarray analysis) of total RNA and 100 pmol/uL of the T7(dT)24 primer (5’-GGCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGGTTTTTTTTTTTTTTTTTTTTTTTT-3’) were combined for annealing at 70o C for 10mins and chilled on ice for 2mins. Then, the SuperScript III kit (Invitrogen®) was added according to manufacturer indications to synthesize the cDNA. Second strand cDNA synthesis; the whole amount of the cDNA produced was used as template for the second strand synthesis plus 10 units of E. coli DNA ligase, 40 units of E. coli DNA polymerase (Invitrogen®), 3uL of 10 mM dNTPs and 2 units of Rnase H (Invitrogen®). The reaction was stopped by addition of 10 uL of 0.5M EDTA. The double stranded cDNA was then purified and precipitated and the resuspended in 10uL of nuclease free water. Synthesis of biotin-labelled cRNA; we used the Enzo-Bioarray kit (Enzo Life Sciences, Inc) for synthesis of the cRNA according to manufacturer protocol. The resulting cRNA was purified with Rneasy kit (Qiagen®). The concentration was measured on a spectrophotometer and 20 µg of each sample was fragmented in 200 mM tris-acetate (pH= 8.1), 500mM potassium acetate and 150 mM magnesium acetate for 35mins at 95°C, then chilled on ice and stored at -80°C until microarray hybridisation
| | Sample_hyb_protocol | For the mRNA high-throughput screening we used the GeneChip ® Rat expression 230 version 2.0 arrays and the GeneChip® Hybridization, Wash and stain kit from Affymetrix®. The protocol of hybridisation, according to manufactured indications was the 49/64 formats, which corresponds to the selected type of array. The control oligonucleotides were: B2 and the Eukaryotic bioB, bioC, bioD and cre. Then, the samples were washed and stained on the Fluidics Station 450 (Affymetrix®) monitored with the GeneChip® Operating Software (Affymetrix®) according to manufactured instructions (using the protocol FS450_003 which corresponds to rat 230 v2.0 array).
| | Sample_scan_protocol | We used GeneChip Scanner 3000 (Affymetrix®).
| | Sample_data_processing | The data were analyzed with 'R software' loaded with the 'Bioconductor' platform using GC-RMA normalisation and Limma test to contrast the experimental groups.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | David,,Vega-Avelaira
| | Sample_contact_email | david.vega74@gmail.com
| | Sample_contact_institute | University College of London
| | Sample_contact_address | Gower street
| | Sample_contact_city | Lonndon
| | Sample_contact_zip/postal_code | wc1e 6bt
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM375nnn/GSM375686/suppl/GSM375686.CEL.gz
| | Sample_series_id | GSE15041
| | Sample_data_row_count | 31099
| | |
|
GSM375687 | GPL1355 |
|
2 months, sham group, biological replicate 2
|
L4/L5 dorsal root ganglia from adult rats (2 months old) 7 days after sham surgery
|
strain: Sprague-Dawley
tissue: Dorsal root ganglia
postnatal age: 2 months
surgery type: Sham
experimetal group: Adult Sham
|
The L4/L5 dorsal root ganglia in the sham group are those ganglia ipsilateral to the surgery
|
| Sample_geo_accession | GSM375687
| | Sample_status | Public on Dec 18 2009
| | Sample_submission_date | Feb 27 2009
| | Sample_last_update_date | Dec 18 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Experiments were performed on adult (2 months old) male Sprague–Dawley rats and rat pups (10 days postnatal age, P10) and carried out in accordance with the United Kingdom Animal (Scientific Procedures) Act 1986. Spared nerve injury and sham surgery were performed under halothane general anaesthesia with antiseptic conditions. After skin preparation, the sciatic nerve and its three terminal branches were exposed in the upper lateral thigh. Axotomy and ligation of the common peroneal and tibial branches was performed under direct vision, leaving the sural nerve intact. Muscle and skin were closed in two layers. In the sham operation, the procedures were the same but the nerves were only exposed and not cut or ligated. In all cases great care was taken not to stretch the nerve, or its branches, nor to damage the intact nerves.
| | Sample_growth_protocol_ch1 | After the surgery, the animals were returned to their cages and litters and maintained on a 12 hour light/dark cycle at constant ambient temperature in the Biological Services Unit with free access to food and water for 7 days post surgery (ps) until DRGs collection.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Seven days post surgery, animals were sacrificed with 0.1 mL of Euthanal®, the fresh DRGs were snap frozen on liquid nitrogen and stored at –80o C until RNA extraction. L4 and L5 DRGs ipsilateral to the lesion were collected and pooled from 3 animals per adult experimental group and 4 animals per P10 group, (i.e. n= 6 DRGs per adult sample , n=8 per P10 sample) to minimise inter-animal differences. RNA was extracted using Trizol® reagent (Invitrogen®) and QIAshredder column (Qiagen®) for homogenisation according to manufacturer’s protocols. Additionally, the RNA was cleaned by ”RNA purification column” (Qiagen®) and a final volume of 50 uL obtained according to manufacturer protocol. The amount of RNA was measured with a NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies, Inc.) and its quality assessed with Experion RNA HighSens StdSens analysis kit (Bio-Rad®). Then, the RNA was precipitated and dissolved to obtain a final concentration of 1 µg/µL and stored at -80°C until for cRNA synthesis or amplification by quantitative real-time polymerase chain reaction (qPCR).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA synthesis First strand cDNA synthesis; 2 g (for qPCR) or 10 ug (microarray analysis) of total RNA and 100 pmol/uL of the T7(dT)24 primer (5’-GGCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGGTTTTTTTTTTTTTTTTTTTTTTTT-3’) were combined for annealing at 70o C for 10mins and chilled on ice for 2mins. Then, the SuperScript III kit (Invitrogen®) was added according to manufacturer indications to synthesize the cDNA. Second strand cDNA synthesis; the whole amount of the cDNA produced was used as template for the second strand synthesis plus 10 units of E. coli DNA ligase, 40 units of E. coli DNA polymerase (Invitrogen®), 3uL of 10 mM dNTPs and 2 units of Rnase H (Invitrogen®). The reaction was stopped by addition of 10 uL of 0.5M EDTA. The double stranded cDNA was then purified and precipitated and the resuspended in 10uL of nuclease free water. Synthesis of biotin-labelled cRNA; we used the Enzo-Bioarray kit (Enzo Life Sciences, Inc) for synthesis of the cRNA according to manufacturer protocol. The resulting cRNA was purified with Rneasy kit (Qiagen®). The concentration was measured on a spectrophotometer and 20 µg of each sample was fragmented in 200 mM tris-acetate (pH= 8.1), 500mM potassium acetate and 150 mM magnesium acetate for 35mins at 95°C, then chilled on ice and stored at -80°C until microarray hybridisation
| | Sample_hyb_protocol | For the mRNA high-throughput screening we used the GeneChip ® Rat expression 230 version 2.0 arrays and the GeneChip® Hybridization, Wash and stain kit from Affymetrix®. The protocol of hybridisation, according to manufactured indications was the 49/64 formats, which corresponds to the selected type of array. The control oligonucleotides were: B2 and the Eukaryotic bioB, bioC, bioD and cre. Then, the samples were washed and stained on the Fluidics Station 450 (Affymetrix®) monitored with the GeneChip® Operating Software (Affymetrix®) according to manufactured instructions (using the protocol FS450_003 which corresponds to rat 230 v2.0 array).
| | Sample_scan_protocol | We used GeneChip Scanner 3000 (Affymetrix®).
| | Sample_data_processing | The data were analyzed with 'R software' loaded with the 'Bioconductor' platform using GC-RMA normalisation and Limma test to contrast the experimental groups.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | David,,Vega-Avelaira
| | Sample_contact_email | david.vega74@gmail.com
| | Sample_contact_institute | University College of London
| | Sample_contact_address | Gower street
| | Sample_contact_city | Lonndon
| | Sample_contact_zip/postal_code | wc1e 6bt
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM375nnn/GSM375687/suppl/GSM375687.CEL.gz
| | Sample_series_id | GSE15041
| | Sample_data_row_count | 31099
| | |
|
GSM375688 | GPL1355 |
|
2 months, sham group, biological replicate 3
|
L4/L5 dorsal root ganglia from adult rats (2 months old) 7 days after sham surgery
|
strain: Sprague-Dawley
tissue: Dorsal root ganglia
postnatal age: 2 months
surgery type: Sham
experimetal group: Adult Sham
|
The L4/L5 dorsal root ganglia in the sham group are those ganglia ipsilateral to the surgery
|
| Sample_geo_accession | GSM375688
| | Sample_status | Public on Dec 18 2009
| | Sample_submission_date | Feb 27 2009
| | Sample_last_update_date | Dec 18 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Experiments were performed on adult (2 months old) male Sprague–Dawley rats and rat pups (10 days postnatal age, P10) and carried out in accordance with the United Kingdom Animal (Scientific Procedures) Act 1986. Spared nerve injury and sham surgery were performed under halothane general anaesthesia with antiseptic conditions. After skin preparation, the sciatic nerve and its three terminal branches were exposed in the upper lateral thigh. Axotomy and ligation of the common peroneal and tibial branches was performed under direct vision, leaving the sural nerve intact. Muscle and skin were closed in two layers. In the sham operation, the procedures were the same but the nerves were only exposed and not cut or ligated. In all cases great care was taken not to stretch the nerve, or its branches, nor to damage the intact nerves.
| | Sample_growth_protocol_ch1 | After the surgery, the animals were returned to their cages and litters and maintained on a 12 hour light/dark cycle at constant ambient temperature in the Biological Services Unit with free access to food and water for 7 days post surgery (ps) until DRGs collection.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Seven days post surgery, animals were sacrificed with 0.1 mL of Euthanal®, the fresh DRGs were snap frozen on liquid nitrogen and stored at –80o C until RNA extraction. L4 and L5 DRGs ipsilateral to the lesion were collected and pooled from 3 animals per adult experimental group and 4 animals per P10 group, (i.e. n= 6 DRGs per adult sample , n=8 per P10 sample) to minimise inter-animal differences. RNA was extracted using Trizol® reagent (Invitrogen®) and QIAshredder column (Qiagen®) for homogenisation according to manufacturer’s protocols. Additionally, the RNA was cleaned by ”RNA purification column” (Qiagen®) and a final volume of 50 uL obtained according to manufacturer protocol. The amount of RNA was measured with a NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies, Inc.) and its quality assessed with Experion RNA HighSens StdSens analysis kit (Bio-Rad®). Then, the RNA was precipitated and dissolved to obtain a final concentration of 1 µg/µL and stored at -80°C until for cRNA synthesis or amplification by quantitative real-time polymerase chain reaction (qPCR).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA synthesis First strand cDNA synthesis; 2 g (for qPCR) or 10 ug (microarray analysis) of total RNA and 100 pmol/uL of the T7(dT)24 primer (5’-GGCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGGTTTTTTTTTTTTTTTTTTTTTTTT-3’) were combined for annealing at 70o C for 10mins and chilled on ice for 2mins. Then, the SuperScript III kit (Invitrogen®) was added according to manufacturer indications to synthesize the cDNA. Second strand cDNA synthesis; the whole amount of the cDNA produced was used as template for the second strand synthesis plus 10 units of E. coli DNA ligase, 40 units of E. coli DNA polymerase (Invitrogen®), 3uL of 10 mM dNTPs and 2 units of Rnase H (Invitrogen®). The reaction was stopped by addition of 10 uL of 0.5M EDTA. The double stranded cDNA was then purified and precipitated and the resuspended in 10uL of nuclease free water. Synthesis of biotin-labelled cRNA; we used the Enzo-Bioarray kit (Enzo Life Sciences, Inc) for synthesis of the cRNA according to manufacturer protocol. The resulting cRNA was purified with Rneasy kit (Qiagen®). The concentration was measured on a spectrophotometer and 20 µg of each sample was fragmented in 200 mM tris-acetate (pH= 8.1), 500mM potassium acetate and 150 mM magnesium acetate for 35mins at 95°C, then chilled on ice and stored at -80°C until microarray hybridisation
| | Sample_hyb_protocol | For the mRNA high-throughput screening we used the GeneChip ® Rat expression 230 version 2.0 arrays and the GeneChip® Hybridization, Wash and stain kit from Affymetrix®. The protocol of hybridisation, according to manufactured indications was the 49/64 formats, which corresponds to the selected type of array. The control oligonucleotides were: B2 and the Eukaryotic bioB, bioC, bioD and cre. Then, the samples were washed and stained on the Fluidics Station 450 (Affymetrix®) monitored with the GeneChip® Operating Software (Affymetrix®) according to manufactured instructions (using the protocol FS450_003 which corresponds to rat 230 v2.0 array).
| | Sample_scan_protocol | We used GeneChip Scanner 3000 (Affymetrix®).
| | Sample_data_processing | The data were analyzed with 'R software' loaded with the 'Bioconductor' platform using GC-RMA normalisation and Limma test to contrast the experimental groups.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | David,,Vega-Avelaira
| | Sample_contact_email | david.vega74@gmail.com
| | Sample_contact_institute | University College of London
| | Sample_contact_address | Gower street
| | Sample_contact_city | Lonndon
| | Sample_contact_zip/postal_code | wc1e 6bt
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM375nnn/GSM375688/suppl/GSM375688.CEL.gz
| | Sample_series_id | GSE15041
| | Sample_data_row_count | 31099
| | |
|
GSM375689 | GPL1355 |
|
2 months, contralateral group, biological replicate 1
|
L4/L5 dorsal root ganglia from adult rats (2 months old) 7 days after SNI surgery
|
strain: Sprague-Dawley
tissue: Dorsal root ganglia
postnatal age: 2 months
surgery type: Spare nerve injury
experimetal group: Adult Contralateral
|
The L4/L5 dorsal root ganglia in the contralateral group are those ganglia contralateral to the surgery in the spare nerve injury group
|
| Sample_geo_accession | GSM375689
| | Sample_status | Public on Dec 18 2009
| | Sample_submission_date | Feb 27 2009
| | Sample_last_update_date | Dec 18 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Experiments were performed on adult (2 months old) male Sprague–Dawley rats and rat pups (10 days postnatal age, P10) and carried out in accordance with the United Kingdom Animal (Scientific Procedures) Act 1986. Spared nerve injury and sham surgery were performed under halothane general anaesthesia with antiseptic conditions. After skin preparation, the sciatic nerve and its three terminal branches were exposed in the upper lateral thigh. Axotomy and ligation of the common peroneal and tibial branches was performed under direct vision, leaving the sural nerve intact. Muscle and skin were closed in two layers. In the sham operation, the procedures were the same but the nerves were only exposed and not cut or ligated. In all cases great care was taken not to stretch the nerve, or its branches, nor to damage the intact nerves.
| | Sample_growth_protocol_ch1 | After the surgery, the animals were returned to their cages and litters and maintained on a 12 hour light/dark cycle at constant ambient temperature in the Biological Services Unit with free access to food and water for 7 days post surgery (ps) until DRGs collection.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Seven days post surgery, animals were sacrificed with 0.1 mL of Euthanal®, the fresh DRGs were snap frozen on liquid nitrogen and stored at –80o C until RNA extraction. L4 and L5 DRGs ipsilateral to the lesion were collected and pooled from 3 animals per adult experimental group and 4 animals per P10 group, (i.e. n= 6 DRGs per adult sample , n=8 per P10 sample) to minimise inter-animal differences. RNA was extracted using Trizol® reagent (Invitrogen®) and QIAshredder column (Qiagen®) for homogenisation according to manufacturer’s protocols. Additionally, the RNA was cleaned by ”RNA purification column” (Qiagen®) and a final volume of 50 uL obtained according to manufacturer protocol. The amount of RNA was measured with a NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies, Inc.) and its quality assessed with Experion RNA HighSens StdSens analysis kit (Bio-Rad®). Then, the RNA was precipitated and dissolved to obtain a final concentration of 1 µg/µL and stored at -80°C until for cRNA synthesis or amplification by quantitative real-time polymerase chain reaction (qPCR).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA synthesis First strand cDNA synthesis; 2 g (for qPCR) or 10 ug (microarray analysis) of total RNA and 100 pmol/uL of the T7(dT)24 primer (5’-GGCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGGTTTTTTTTTTTTTTTTTTTTTTTT-3’) were combined for annealing at 70o C for 10mins and chilled on ice for 2mins. Then, the SuperScript III kit (Invitrogen®) was added according to manufacturer indications to synthesize the cDNA. Second strand cDNA synthesis; the whole amount of the cDNA produced was used as template for the second strand synthesis plus 10 units of E. coli DNA ligase, 40 units of E. coli DNA polymerase (Invitrogen®), 3uL of 10 mM dNTPs and 2 units of Rnase H (Invitrogen®). The reaction was stopped by addition of 10 uL of 0.5M EDTA. The double stranded cDNA was then purified and precipitated and the resuspended in 10uL of nuclease free water. Synthesis of biotin-labelled cRNA; we used the Enzo-Bioarray kit (Enzo Life Sciences, Inc) for synthesis of the cRNA according to manufacturer protocol. The resulting cRNA was purified with Rneasy kit (Qiagen®). The concentration was measured on a spectrophotometer and 20 µg of each sample was fragmented in 200 mM tris-acetate (pH= 8.1), 500mM potassium acetate and 150 mM magnesium acetate for 35mins at 95°C, then chilled on ice and stored at -80°C until microarray hybridisation
| | Sample_hyb_protocol | For the mRNA high-throughput screening we used the GeneChip ® Rat expression 230 version 2.0 arrays and the GeneChip® Hybridization, Wash and stain kit from Affymetrix®. The protocol of hybridisation, according to manufactured indications was the 49/64 formats, which corresponds to the selected type of array. The control oligonucleotides were: B2 and the Eukaryotic bioB, bioC, bioD and cre. Then, the samples were washed and stained on the Fluidics Station 450 (Affymetrix®) monitored with the GeneChip® Operating Software (Affymetrix®) according to manufactured instructions (using the protocol FS450_003 which corresponds to rat 230 v2.0 array).
| | Sample_scan_protocol | We used GeneChip Scanner 3000 (Affymetrix®).
| | Sample_data_processing | The data were analyzed with 'R software' loaded with the 'Bioconductor' platform using GC-RMA normalisation and Limma test to contrast the experimental groups.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | David,,Vega-Avelaira
| | Sample_contact_email | david.vega74@gmail.com
| | Sample_contact_institute | University College of London
| | Sample_contact_address | Gower street
| | Sample_contact_city | Lonndon
| | Sample_contact_zip/postal_code | wc1e 6bt
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM375nnn/GSM375689/suppl/GSM375689.CEL.gz
| | Sample_series_id | GSE15041
| | Sample_data_row_count | 31099
| | |
|
GSM375690 | GPL1355 |
|
2 months, contralateral group, biological replicate 2
|
L4/L5 dorsal root ganglia from adult rats (2 months old) 7 days after SNI surgery
|
strain: Sprague-Dawley
tissue: Dorsal root ganglia
postnatal age: 2 months
surgery type: Spare nerve injury
experimetal group: Adult Contralateral
|
The L4/L5 dorsal root ganglia in the contralateral group are those ganglia contralateral to the surgery in the spare nerve injury group
|
| Sample_geo_accession | GSM375690
| | Sample_status | Public on Dec 18 2009
| | Sample_submission_date | Feb 27 2009
| | Sample_last_update_date | Dec 18 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Experiments were performed on adult (2 months old) male Sprague–Dawley rats and rat pups (10 days postnatal age, P10) and carried out in accordance with the United Kingdom Animal (Scientific Procedures) Act 1986. Spared nerve injury and sham surgery were performed under halothane general anaesthesia with antiseptic conditions. After skin preparation, the sciatic nerve and its three terminal branches were exposed in the upper lateral thigh. Axotomy and ligation of the common peroneal and tibial branches was performed under direct vision, leaving the sural nerve intact. Muscle and skin were closed in two layers. In the sham operation, the procedures were the same but the nerves were only exposed and not cut or ligated. In all cases great care was taken not to stretch the nerve, or its branches, nor to damage the intact nerves.
| | Sample_growth_protocol_ch1 | After the surgery, the animals were returned to their cages and litters and maintained on a 12 hour light/dark cycle at constant ambient temperature in the Biological Services Unit with free access to food and water for 7 days post surgery (ps) until DRGs collection.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Seven days post surgery, animals were sacrificed with 0.1 mL of Euthanal®, the fresh DRGs were snap frozen on liquid nitrogen and stored at –80o C until RNA extraction. L4 and L5 DRGs ipsilateral to the lesion were collected and pooled from 3 animals per adult experimental group and 4 animals per P10 group, (i.e. n= 6 DRGs per adult sample , n=8 per P10 sample) to minimise inter-animal differences. RNA was extracted using Trizol® reagent (Invitrogen®) and QIAshredder column (Qiagen®) for homogenisation according to manufacturer’s protocols. Additionally, the RNA was cleaned by ”RNA purification column” (Qiagen®) and a final volume of 50 uL obtained according to manufacturer protocol. The amount of RNA was measured with a NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies, Inc.) and its quality assessed with Experion RNA HighSens StdSens analysis kit (Bio-Rad®). Then, the RNA was precipitated and dissolved to obtain a final concentration of 1 µg/µL and stored at -80°C until for cRNA synthesis or amplification by quantitative real-time polymerase chain reaction (qPCR).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA synthesis First strand cDNA synthesis; 2 g (for qPCR) or 10 ug (microarray analysis) of total RNA and 100 pmol/uL of the T7(dT)24 primer (5’-GGCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGGTTTTTTTTTTTTTTTTTTTTTTTT-3’) were combined for annealing at 70o C for 10mins and chilled on ice for 2mins. Then, the SuperScript III kit (Invitrogen®) was added according to manufacturer indications to synthesize the cDNA. Second strand cDNA synthesis; the whole amount of the cDNA produced was used as template for the second strand synthesis plus 10 units of E. coli DNA ligase, 40 units of E. coli DNA polymerase (Invitrogen®), 3uL of 10 mM dNTPs and 2 units of Rnase H (Invitrogen®). The reaction was stopped by addition of 10 uL of 0.5M EDTA. The double stranded cDNA was then purified and precipitated and the resuspended in 10uL of nuclease free water. Synthesis of biotin-labelled cRNA; we used the Enzo-Bioarray kit (Enzo Life Sciences, Inc) for synthesis of the cRNA according to manufacturer protocol. The resulting cRNA was purified with Rneasy kit (Qiagen®). The concentration was measured on a spectrophotometer and 20 µg of each sample was fragmented in 200 mM tris-acetate (pH= 8.1), 500mM potassium acetate and 150 mM magnesium acetate for 35mins at 95°C, then chilled on ice and stored at -80°C until microarray hybridisation
| | Sample_hyb_protocol | For the mRNA high-throughput screening we used the GeneChip ® Rat expression 230 version 2.0 arrays and the GeneChip® Hybridization, Wash and stain kit from Affymetrix®. The protocol of hybridisation, according to manufactured indications was the 49/64 formats, which corresponds to the selected type of array. The control oligonucleotides were: B2 and the Eukaryotic bioB, bioC, bioD and cre. Then, the samples were washed and stained on the Fluidics Station 450 (Affymetrix®) monitored with the GeneChip® Operating Software (Affymetrix®) according to manufactured instructions (using the protocol FS450_003 which corresponds to rat 230 v2.0 array).
| | Sample_scan_protocol | We used GeneChip Scanner 3000 (Affymetrix®).
| | Sample_data_processing | The data were analyzed with 'R software' loaded with the 'Bioconductor' platform using GC-RMA normalisation and Limma test to contrast the experimental groups.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | David,,Vega-Avelaira
| | Sample_contact_email | david.vega74@gmail.com
| | Sample_contact_institute | University College of London
| | Sample_contact_address | Gower street
| | Sample_contact_city | Lonndon
| | Sample_contact_zip/postal_code | wc1e 6bt
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM375nnn/GSM375690/suppl/GSM375690.CEL.gz
| | Sample_series_id | GSE15041
| | Sample_data_row_count | 31099
| | |
|
GSM375691 | GPL1355 |
|
2 months, contralateral group, biological replicate 3
|
L4/L5 dorsal root ganglia from adult rats (2 months old) 7 days after SNI surgery
|
strain: Sprague-Dawley
tissue: Dorsal root ganglia
postnatal age: 2 months
surgery type: Spare nerve injury
experimetal group: Adult Contralateral
|
The L4/L5 dorsal root ganglia in the contralateral group are those ganglia contralateral to the surgery in the spare nerve injury group
|
| Sample_geo_accession | GSM375691
| | Sample_status | Public on Dec 18 2009
| | Sample_submission_date | Feb 27 2009
| | Sample_last_update_date | Dec 18 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Experiments were performed on adult (2 months old) male Sprague–Dawley rats and rat pups (10 days postnatal age, P10) and carried out in accordance with the United Kingdom Animal (Scientific Procedures) Act 1986. Spared nerve injury and sham surgery were performed under halothane general anaesthesia with antiseptic conditions. After skin preparation, the sciatic nerve and its three terminal branches were exposed in the upper lateral thigh. Axotomy and ligation of the common peroneal and tibial branches was performed under direct vision, leaving the sural nerve intact. Muscle and skin were closed in two layers. In the sham operation, the procedures were the same but the nerves were only exposed and not cut or ligated. In all cases great care was taken not to stretch the nerve, or its branches, nor to damage the intact nerves.
| | Sample_growth_protocol_ch1 | After the surgery, the animals were returned to their cages and litters and maintained on a 12 hour light/dark cycle at constant ambient temperature in the Biological Services Unit with free access to food and water for 7 days post surgery (ps) until DRGs collection.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Seven days post surgery, animals were sacrificed with 0.1 mL of Euthanal®, the fresh DRGs were snap frozen on liquid nitrogen and stored at –80o C until RNA extraction. L4 and L5 DRGs ipsilateral to the lesion were collected and pooled from 3 animals per adult experimental group and 4 animals per P10 group, (i.e. n= 6 DRGs per adult sample , n=8 per P10 sample) to minimise inter-animal differences. RNA was extracted using Trizol® reagent (Invitrogen®) and QIAshredder column (Qiagen®) for homogenisation according to manufacturer’s protocols. Additionally, the RNA was cleaned by ”RNA purification column” (Qiagen®) and a final volume of 50 uL obtained according to manufacturer protocol. The amount of RNA was measured with a NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies, Inc.) and its quality assessed with Experion RNA HighSens StdSens analysis kit (Bio-Rad®). Then, the RNA was precipitated and dissolved to obtain a final concentration of 1 µg/µL and stored at -80°C until for cRNA synthesis or amplification by quantitative real-time polymerase chain reaction (qPCR).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA synthesis First strand cDNA synthesis; 2 g (for qPCR) or 10 ug (microarray analysis) of total RNA and 100 pmol/uL of the T7(dT)24 primer (5’-GGCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGGTTTTTTTTTTTTTTTTTTTTTTTT-3’) were combined for annealing at 70o C for 10mins and chilled on ice for 2mins. Then, the SuperScript III kit (Invitrogen®) was added according to manufacturer indications to synthesize the cDNA. Second strand cDNA synthesis; the whole amount of the cDNA produced was used as template for the second strand synthesis plus 10 units of E. coli DNA ligase, 40 units of E. coli DNA polymerase (Invitrogen®), 3uL of 10 mM dNTPs and 2 units of Rnase H (Invitrogen®). The reaction was stopped by addition of 10 uL of 0.5M EDTA. The double stranded cDNA was then purified and precipitated and the resuspended in 10uL of nuclease free water. Synthesis of biotin-labelled cRNA; we used the Enzo-Bioarray kit (Enzo Life Sciences, Inc) for synthesis of the cRNA according to manufacturer protocol. The resulting cRNA was purified with Rneasy kit (Qiagen®). The concentration was measured on a spectrophotometer and 20 µg of each sample was fragmented in 200 mM tris-acetate (pH= 8.1), 500mM potassium acetate and 150 mM magnesium acetate for 35mins at 95°C, then chilled on ice and stored at -80°C until microarray hybridisation
| | Sample_hyb_protocol | For the mRNA high-throughput screening we used the GeneChip ® Rat expression 230 version 2.0 arrays and the GeneChip® Hybridization, Wash and stain kit from Affymetrix®. The protocol of hybridisation, according to manufactured indications was the 49/64 formats, which corresponds to the selected type of array. The control oligonucleotides were: B2 and the Eukaryotic bioB, bioC, bioD and cre. Then, the samples were washed and stained on the Fluidics Station 450 (Affymetrix®) monitored with the GeneChip® Operating Software (Affymetrix®) according to manufactured instructions (using the protocol FS450_003 which corresponds to rat 230 v2.0 array).
| | Sample_scan_protocol | We used GeneChip Scanner 3000 (Affymetrix®).
| | Sample_data_processing | The data were analyzed with 'R software' loaded with the 'Bioconductor' platform using GC-RMA normalisation and Limma test to contrast the experimental groups.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | David,,Vega-Avelaira
| | Sample_contact_email | david.vega74@gmail.com
| | Sample_contact_institute | University College of London
| | Sample_contact_address | Gower street
| | Sample_contact_city | Lonndon
| | Sample_contact_zip/postal_code | wc1e 6bt
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM375nnn/GSM375691/suppl/GSM375691.CEL.gz
| | Sample_series_id | GSE15041
| | Sample_data_row_count | 31099
| | |
|
GSM375692 | GPL1355 |
|
2 months, ipsilateral group, biological replicate 1
|
L4/L5 dorsal root ganglia from adult rats (2 months old) 7 days after SNI surgery
|
strain: Sprague-Dawley
tissue: Dorsal root ganglia
postnatal age: 2 months
surgery type: Spare nerve injury
experimetal group: Adult Ipsilateral
|
The L4/L5 dorsal root ganglia in the ipsilateral group are those ganglia ipsilateral to the surgery in the spare nerve injury group
|
| Sample_geo_accession | GSM375692
| | Sample_status | Public on Dec 18 2009
| | Sample_submission_date | Feb 27 2009
| | Sample_last_update_date | Dec 18 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Experiments were performed on adult (2 months old) male Sprague–Dawley rats and rat pups (10 days postnatal age, P10) and carried out in accordance with the United Kingdom Animal (Scientific Procedures) Act 1986. Spared nerve injury and sham surgery were performed under halothane general anaesthesia with antiseptic conditions. After skin preparation, the sciatic nerve and its three terminal branches were exposed in the upper lateral thigh. Axotomy and ligation of the common peroneal and tibial branches was performed under direct vision, leaving the sural nerve intact. Muscle and skin were closed in two layers. In the sham operation, the procedures were the same but the nerves were only exposed and not cut or ligated. In all cases great care was taken not to stretch the nerve, or its branches, nor to damage the intact nerves.
| | Sample_growth_protocol_ch1 | After the surgery, the animals were returned to their cages and litters and maintained on a 12 hour light/dark cycle at constant ambient temperature in the Biological Services Unit with free access to food and water for 7 days post surgery (ps) until DRGs collection.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Seven days post surgery, animals were sacrificed with 0.1 mL of Euthanal®, the fresh DRGs were snap frozen on liquid nitrogen and stored at –80o C until RNA extraction. L4 and L5 DRGs ipsilateral to the lesion were collected and pooled from 3 animals per adult experimental group and 4 animals per P10 group, (i.e. n= 6 DRGs per adult sample , n=8 per P10 sample) to minimise inter-animal differences. RNA was extracted using Trizol® reagent (Invitrogen®) and QIAshredder column (Qiagen®) for homogenisation according to manufacturer’s protocols. Additionally, the RNA was cleaned by ”RNA purification column” (Qiagen®) and a final volume of 50 uL obtained according to manufacturer protocol. The amount of RNA was measured with a NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies, Inc.) and its quality assessed with Experion RNA HighSens StdSens analysis kit (Bio-Rad®). Then, the RNA was precipitated and dissolved to obtain a final concentration of 1 µg/µL and stored at -80°C until for cRNA synthesis or amplification by quantitative real-time polymerase chain reaction (qPCR).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA synthesis First strand cDNA synthesis; 2 g (for qPCR) or 10 ug (microarray analysis) of total RNA and 100 pmol/uL of the T7(dT)24 primer (5’-GGCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGGTTTTTTTTTTTTTTTTTTTTTTTT-3’) were combined for annealing at 70o C for 10mins and chilled on ice for 2mins. Then, the SuperScript III kit (Invitrogen®) was added according to manufacturer indications to synthesize the cDNA. Second strand cDNA synthesis; the whole amount of the cDNA produced was used as template for the second strand synthesis plus 10 units of E. coli DNA ligase, 40 units of E. coli DNA polymerase (Invitrogen®), 3uL of 10 mM dNTPs and 2 units of Rnase H (Invitrogen®). The reaction was stopped by addition of 10 uL of 0.5M EDTA. The double stranded cDNA was then purified and precipitated and the resuspended in 10uL of nuclease free water. Synthesis of biotin-labelled cRNA; we used the Enzo-Bioarray kit (Enzo Life Sciences, Inc) for synthesis of the cRNA according to manufacturer protocol. The resulting cRNA was purified with Rneasy kit (Qiagen®). The concentration was measured on a spectrophotometer and 20 µg of each sample was fragmented in 200 mM tris-acetate (pH= 8.1), 500mM potassium acetate and 150 mM magnesium acetate for 35mins at 95°C, then chilled on ice and stored at -80°C until microarray hybridisation
| | Sample_hyb_protocol | For the mRNA high-throughput screening we used the GeneChip ® Rat expression 230 version 2.0 arrays and the GeneChip® Hybridization, Wash and stain kit from Affymetrix®. The protocol of hybridisation, according to manufactured indications was the 49/64 formats, which corresponds to the selected type of array. The control oligonucleotides were: B2 and the Eukaryotic bioB, bioC, bioD and cre. Then, the samples were washed and stained on the Fluidics Station 450 (Affymetrix®) monitored with the GeneChip® Operating Software (Affymetrix®) according to manufactured instructions (using the protocol FS450_003 which corresponds to rat 230 v2.0 array).
| | Sample_scan_protocol | We used GeneChip Scanner 3000 (Affymetrix®).
| | Sample_data_processing | The data were analyzed with 'R software' loaded with the 'Bioconductor' platform using GC-RMA normalisation and Limma test to contrast the experimental groups.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | David,,Vega-Avelaira
| | Sample_contact_email | david.vega74@gmail.com
| | Sample_contact_institute | University College of London
| | Sample_contact_address | Gower street
| | Sample_contact_city | Lonndon
| | Sample_contact_zip/postal_code | wc1e 6bt
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM375nnn/GSM375692/suppl/GSM375692.CEL.gz
| | Sample_series_id | GSE15041
| | Sample_data_row_count | 31099
| | |
|
GSM375693 | GPL1355 |
|
2 months, ipsilateral group, biological replicate 2
|
L4/L5 dorsal root ganglia from adult rats (2 months old) 7 days after SNI surgery
|
strain: Sprague-Dawley
tissue: Dorsal root ganglia
postnatal age: 2 months
surgery type: Spare nerve injury
experimetal group: Adult Ipsilateral
|
The L4/L5 dorsal root ganglia in the ipsilateral group are those ganglia ipsilateral to the surgery in the spare nerve injury group
|
| Sample_geo_accession | GSM375693
| | Sample_status | Public on Dec 18 2009
| | Sample_submission_date | Feb 27 2009
| | Sample_last_update_date | Dec 18 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Experiments were performed on adult (2 months old) male Sprague–Dawley rats and rat pups (10 days postnatal age, P10) and carried out in accordance with the United Kingdom Animal (Scientific Procedures) Act 1986. Spared nerve injury and sham surgery were performed under halothane general anaesthesia with antiseptic conditions. After skin preparation, the sciatic nerve and its three terminal branches were exposed in the upper lateral thigh. Axotomy and ligation of the common peroneal and tibial branches was performed under direct vision, leaving the sural nerve intact. Muscle and skin were closed in two layers. In the sham operation, the procedures were the same but the nerves were only exposed and not cut or ligated. In all cases great care was taken not to stretch the nerve, or its branches, nor to damage the intact nerves.
| | Sample_growth_protocol_ch1 | After the surgery, the animals were returned to their cages and litters and maintained on a 12 hour light/dark cycle at constant ambient temperature in the Biological Services Unit with free access to food and water for 7 days post surgery (ps) until DRGs collection.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Seven days post surgery, animals were sacrificed with 0.1 mL of Euthanal®, the fresh DRGs were snap frozen on liquid nitrogen and stored at –80o C until RNA extraction. L4 and L5 DRGs ipsilateral to the lesion were collected and pooled from 3 animals per adult experimental group and 4 animals per P10 group, (i.e. n= 6 DRGs per adult sample , n=8 per P10 sample) to minimise inter-animal differences. RNA was extracted using Trizol® reagent (Invitrogen®) and QIAshredder column (Qiagen®) for homogenisation according to manufacturer’s protocols. Additionally, the RNA was cleaned by ”RNA purification column” (Qiagen®) and a final volume of 50 uL obtained according to manufacturer protocol. The amount of RNA was measured with a NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies, Inc.) and its quality assessed with Experion RNA HighSens StdSens analysis kit (Bio-Rad®). Then, the RNA was precipitated and dissolved to obtain a final concentration of 1 µg/µL and stored at -80°C until for cRNA synthesis or amplification by quantitative real-time polymerase chain reaction (qPCR).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA synthesis First strand cDNA synthesis; 2 g (for qPCR) or 10 ug (microarray analysis) of total RNA and 100 pmol/uL of the T7(dT)24 primer (5’-GGCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGGTTTTTTTTTTTTTTTTTTTTTTTT-3’) were combined for annealing at 70o C for 10mins and chilled on ice for 2mins. Then, the SuperScript III kit (Invitrogen®) was added according to manufacturer indications to synthesize the cDNA. Second strand cDNA synthesis; the whole amount of the cDNA produced was used as template for the second strand synthesis plus 10 units of E. coli DNA ligase, 40 units of E. coli DNA polymerase (Invitrogen®), 3uL of 10 mM dNTPs and 2 units of Rnase H (Invitrogen®). The reaction was stopped by addition of 10 uL of 0.5M EDTA. The double stranded cDNA was then purified and precipitated and the resuspended in 10uL of nuclease free water. Synthesis of biotin-labelled cRNA; we used the Enzo-Bioarray kit (Enzo Life Sciences, Inc) for synthesis of the cRNA according to manufacturer protocol. The resulting cRNA was purified with Rneasy kit (Qiagen®). The concentration was measured on a spectrophotometer and 20 µg of each sample was fragmented in 200 mM tris-acetate (pH= 8.1), 500mM potassium acetate and 150 mM magnesium acetate for 35mins at 95°C, then chilled on ice and stored at -80°C until microarray hybridisation
| | Sample_hyb_protocol | For the mRNA high-throughput screening we used the GeneChip ® Rat expression 230 version 2.0 arrays and the GeneChip® Hybridization, Wash and stain kit from Affymetrix®. The protocol of hybridisation, according to manufactured indications was the 49/64 formats, which corresponds to the selected type of array. The control oligonucleotides were: B2 and the Eukaryotic bioB, bioC, bioD and cre. Then, the samples were washed and stained on the Fluidics Station 450 (Affymetrix®) monitored with the GeneChip® Operating Software (Affymetrix®) according to manufactured instructions (using the protocol FS450_003 which corresponds to rat 230 v2.0 array).
| | Sample_scan_protocol | We used GeneChip Scanner 3000 (Affymetrix®).
| | Sample_data_processing | The data were analyzed with 'R software' loaded with the 'Bioconductor' platform using GC-RMA normalisation and Limma test to contrast the experimental groups.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | David,,Vega-Avelaira
| | Sample_contact_email | david.vega74@gmail.com
| | Sample_contact_institute | University College of London
| | Sample_contact_address | Gower street
| | Sample_contact_city | Lonndon
| | Sample_contact_zip/postal_code | wc1e 6bt
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM375nnn/GSM375693/suppl/GSM375693.CEL.gz
| | Sample_series_id | GSE15041
| | Sample_data_row_count | 31099
| | |
|
GSM375694 | GPL1355 |
|
2 months, ipsilateral group, biological replicate 3
|
L4/L5 dorsal root ganglia from adult rats (2 months old) 7 days after SNI surgery
|
strain: Sprague-Dawley
tissue: Dorsal root ganglia
postnatal age: 2 months
surgery type: Spare nerve injury
experimetal group: Adult Ipsilateral
|
The L4/L5 dorsal root ganglia in the ipsilateral group are those ganglia ipsilateral to the surgery in the spare nerve injury group
|
| Sample_geo_accession | GSM375694
| | Sample_status | Public on Dec 18 2009
| | Sample_submission_date | Feb 27 2009
| | Sample_last_update_date | Dec 18 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Experiments were performed on adult (2 months old) male Sprague–Dawley rats and rat pups (10 days postnatal age, P10) and carried out in accordance with the United Kingdom Animal (Scientific Procedures) Act 1986. Spared nerve injury and sham surgery were performed under halothane general anaesthesia with antiseptic conditions. After skin preparation, the sciatic nerve and its three terminal branches were exposed in the upper lateral thigh. Axotomy and ligation of the common peroneal and tibial branches was performed under direct vision, leaving the sural nerve intact. Muscle and skin were closed in two layers. In the sham operation, the procedures were the same but the nerves were only exposed and not cut or ligated. In all cases great care was taken not to stretch the nerve, or its branches, nor to damage the intact nerves.
| | Sample_growth_protocol_ch1 | After the surgery, the animals were returned to their cages and litters and maintained on a 12 hour light/dark cycle at constant ambient temperature in the Biological Services Unit with free access to food and water for 7 days post surgery (ps) until DRGs collection.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Seven days post surgery, animals were sacrificed with 0.1 mL of Euthanal®, the fresh DRGs were snap frozen on liquid nitrogen and stored at –80o C until RNA extraction. L4 and L5 DRGs ipsilateral to the lesion were collected and pooled from 3 animals per adult experimental group and 4 animals per P10 group, (i.e. n= 6 DRGs per adult sample , n=8 per P10 sample) to minimise inter-animal differences. RNA was extracted using Trizol® reagent (Invitrogen®) and QIAshredder column (Qiagen®) for homogenisation according to manufacturer’s protocols. Additionally, the RNA was cleaned by ”RNA purification column” (Qiagen®) and a final volume of 50 uL obtained according to manufacturer protocol. The amount of RNA was measured with a NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies, Inc.) and its quality assessed with Experion RNA HighSens StdSens analysis kit (Bio-Rad®). Then, the RNA was precipitated and dissolved to obtain a final concentration of 1 µg/µL and stored at -80°C until for cRNA synthesis or amplification by quantitative real-time polymerase chain reaction (qPCR).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA synthesis First strand cDNA synthesis; 2 g (for qPCR) or 10 ug (microarray analysis) of total RNA and 100 pmol/uL of the T7(dT)24 primer (5’-GGCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGGTTTTTTTTTTTTTTTTTTTTTTTT-3’) were combined for annealing at 70o C for 10mins and chilled on ice for 2mins. Then, the SuperScript III kit (Invitrogen®) was added according to manufacturer indications to synthesize the cDNA. Second strand cDNA synthesis; the whole amount of the cDNA produced was used as template for the second strand synthesis plus 10 units of E. coli DNA ligase, 40 units of E. coli DNA polymerase (Invitrogen®), 3uL of 10 mM dNTPs and 2 units of Rnase H (Invitrogen®). The reaction was stopped by addition of 10 uL of 0.5M EDTA. The double stranded cDNA was then purified and precipitated and the resuspended in 10uL of nuclease free water. Synthesis of biotin-labelled cRNA; we used the Enzo-Bioarray kit (Enzo Life Sciences, Inc) for synthesis of the cRNA according to manufacturer protocol. The resulting cRNA was purified with Rneasy kit (Qiagen®). The concentration was measured on a spectrophotometer and 20 µg of each sample was fragmented in 200 mM tris-acetate (pH= 8.1), 500mM potassium acetate and 150 mM magnesium acetate for 35mins at 95°C, then chilled on ice and stored at -80°C until microarray hybridisation
| | Sample_hyb_protocol | For the mRNA high-throughput screening we used the GeneChip ® Rat expression 230 version 2.0 arrays and the GeneChip® Hybridization, Wash and stain kit from Affymetrix®. The protocol of hybridisation, according to manufactured indications was the 49/64 formats, which corresponds to the selected type of array. The control oligonucleotides were: B2 and the Eukaryotic bioB, bioC, bioD and cre. Then, the samples were washed and stained on the Fluidics Station 450 (Affymetrix®) monitored with the GeneChip® Operating Software (Affymetrix®) according to manufactured instructions (using the protocol FS450_003 which corresponds to rat 230 v2.0 array).
| | Sample_scan_protocol | We used GeneChip Scanner 3000 (Affymetrix®).
| | Sample_data_processing | The data were analyzed with 'R software' loaded with the 'Bioconductor' platform using GC-RMA normalisation and Limma test to contrast the experimental groups.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | David,,Vega-Avelaira
| | Sample_contact_email | david.vega74@gmail.com
| | Sample_contact_institute | University College of London
| | Sample_contact_address | Gower street
| | Sample_contact_city | Lonndon
| | Sample_contact_zip/postal_code | wc1e 6bt
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM375nnn/GSM375694/suppl/GSM375694.CEL.gz
| | Sample_series_id | GSE15041
| | Sample_data_row_count | 31099
| | |
|
GSM375695 | GPL1355 |
|
17 days, sham group, biological replicate 1
|
L4/L5 dorsal root ganglia from young rats (10 days old) 7 days after sham surgery
|
strain: Sprague-Dawley
tissue: Dorsal root ganglia
postnatal age: 17 days
surgery type: Sham
experimetal group: Young Sham
|
The L4/L5 dorsal root ganglia in the sham group are those ganglia ipsilateral to the surgery
|
| Sample_geo_accession | GSM375695
| | Sample_status | Public on Dec 18 2009
| | Sample_submission_date | Feb 27 2009
| | Sample_last_update_date | Dec 18 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Experiments were performed on adult (2 months old) male Sprague–Dawley rats and rat pups (10 days postnatal age, P10) and carried out in accordance with the United Kingdom Animal (Scientific Procedures) Act 1986. Spared nerve injury and sham surgery were performed under halothane general anaesthesia with antiseptic conditions. After skin preparation, the sciatic nerve and its three terminal branches were exposed in the upper lateral thigh. Axotomy and ligation of the common peroneal and tibial branches was performed under direct vision, leaving the sural nerve intact. Muscle and skin were closed in two layers. In the sham operation, the procedures were the same but the nerves were only exposed and not cut or ligated. In all cases great care was taken not to stretch the nerve, or its branches, nor to damage the intact nerves.
| | Sample_growth_protocol_ch1 | After the surgery, the animals were returned to their cages and litters and maintained on a 12 hour light/dark cycle at constant ambient temperature in the Biological Services Unit with free access to food and water for 7 days post surgery (ps) until DRGs collection.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Seven days post surgery, animals were sacrificed with 0.1 mL of Euthanal®, the fresh DRGs were snap frozen on liquid nitrogen and stored at –80o C until RNA extraction. L4 and L5 DRGs ipsilateral to the lesion were collected and pooled from 3 animals per adult experimental group and 4 animals per P10 group, (i.e. n= 6 DRGs per adult sample , n=8 per P10 sample) to minimise inter-animal differences. RNA was extracted using Trizol® reagent (Invitrogen®) and QIAshredder column (Qiagen®) for homogenisation according to manufacturer’s protocols. Additionally, the RNA was cleaned by ”RNA purification column” (Qiagen®) and a final volume of 50 uL obtained according to manufacturer protocol. The amount of RNA was measured with a NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies, Inc.) and its quality assessed with Experion RNA HighSens StdSens analysis kit (Bio-Rad®). Then, the RNA was precipitated and dissolved to obtain a final concentration of 1 µg/µL and stored at -80°C until for cRNA synthesis or amplification by quantitative real-time polymerase chain reaction (qPCR).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA synthesis First strand cDNA synthesis; 2 g (for qPCR) or 10 ug (microarray analysis) of total RNA and 100 pmol/uL of the T7(dT)24 primer (5’-GGCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGGTTTTTTTTTTTTTTTTTTTTTTTT-3’) were combined for annealing at 70o C for 10mins and chilled on ice for 2mins. Then, the SuperScript III kit (Invitrogen®) was added according to manufacturer indications to synthesize the cDNA. Second strand cDNA synthesis; the whole amount of the cDNA produced was used as template for the second strand synthesis plus 10 units of E. coli DNA ligase, 40 units of E. coli DNA polymerase (Invitrogen®), 3uL of 10 mM dNTPs and 2 units of Rnase H (Invitrogen®). The reaction was stopped by addition of 10 uL of 0.5M EDTA. The double stranded cDNA was then purified and precipitated and the resuspended in 10uL of nuclease free water. Synthesis of biotin-labelled cRNA; we used the Enzo-Bioarray kit (Enzo Life Sciences, Inc) for synthesis of the cRNA according to manufacturer protocol. The resulting cRNA was purified with Rneasy kit (Qiagen®). The concentration was measured on a spectrophotometer and 20 µg of each sample was fragmented in 200 mM tris-acetate (pH= 8.1), 500mM potassium acetate and 150 mM magnesium acetate for 35mins at 95°C, then chilled on ice and stored at -80°C until microarray hybridisation
| | Sample_hyb_protocol | For the mRNA high-throughput screening we used the GeneChip ® Rat expression 230 version 2.0 arrays and the GeneChip® Hybridization, Wash and stain kit from Affymetrix®. The protocol of hybridisation, according to manufactured indications was the 49/64 formats, which corresponds to the selected type of array. The control oligonucleotides were: B2 and the Eukaryotic bioB, bioC, bioD and cre. Then, the samples were washed and stained on the Fluidics Station 450 (Affymetrix®) monitored with the GeneChip® Operating Software (Affymetrix®) according to manufactured instructions (using the protocol FS450_003 which corresponds to rat 230 v2.0 array).
| | Sample_scan_protocol | We used GeneChip Scanner 3000 (Affymetrix®).
| | Sample_data_processing | The data were analyzed with 'R software' loaded with the 'Bioconductor' platform using GC-RMA normalisation and Limma test to contrast the experimental groups.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | David,,Vega-Avelaira
| | Sample_contact_email | david.vega74@gmail.com
| | Sample_contact_institute | University College of London
| | Sample_contact_address | Gower street
| | Sample_contact_city | Lonndon
| | Sample_contact_zip/postal_code | wc1e 6bt
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM375nnn/GSM375695/suppl/GSM375695.CEL.gz
| | Sample_series_id | GSE15041
| | Sample_data_row_count | 31099
| | |
|
GSM375696 | GPL1355 |
|
17 days, sham group, biological replicate 2
|
L4/L5 dorsal root ganglia from young rats (10 days old) 7 days after sham surgery
|
strain: Sprague-Dawley
tissue: Dorsal root ganglia
postnatal age: 17 days
surgery type: Sham
experimetal group: Young Sham
|
The L4/L5 dorsal root ganglia in the sham group are those ganglia ipsilateral to the surgery
|
| Sample_geo_accession | GSM375696
| | Sample_status | Public on Dec 18 2009
| | Sample_submission_date | Feb 27 2009
| | Sample_last_update_date | Dec 18 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Experiments were performed on adult (2 months old) male Sprague–Dawley rats and rat pups (10 days postnatal age, P10) and carried out in accordance with the United Kingdom Animal (Scientific Procedures) Act 1986. Spared nerve injury and sham surgery were performed under halothane general anaesthesia with antiseptic conditions. After skin preparation, the sciatic nerve and its three terminal branches were exposed in the upper lateral thigh. Axotomy and ligation of the common peroneal and tibial branches was performed under direct vision, leaving the sural nerve intact. Muscle and skin were closed in two layers. In the sham operation, the procedures were the same but the nerves were only exposed and not cut or ligated. In all cases great care was taken not to stretch the nerve, or its branches, nor to damage the intact nerves.
| | Sample_growth_protocol_ch1 | After the surgery, the animals were returned to their cages and litters and maintained on a 12 hour light/dark cycle at constant ambient temperature in the Biological Services Unit with free access to food and water for 7 days post surgery (ps) until DRGs collection.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Seven days post surgery, animals were sacrificed with 0.1 mL of Euthanal®, the fresh DRGs were snap frozen on liquid nitrogen and stored at –80o C until RNA extraction. L4 and L5 DRGs ipsilateral to the lesion were collected and pooled from 3 animals per adult experimental group and 4 animals per P10 group, (i.e. n= 6 DRGs per adult sample , n=8 per P10 sample) to minimise inter-animal differences. RNA was extracted using Trizol® reagent (Invitrogen®) and QIAshredder column (Qiagen®) for homogenisation according to manufacturer’s protocols. Additionally, the RNA was cleaned by ”RNA purification column” (Qiagen®) and a final volume of 50 uL obtained according to manufacturer protocol. The amount of RNA was measured with a NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies, Inc.) and its quality assessed with Experion RNA HighSens StdSens analysis kit (Bio-Rad®). Then, the RNA was precipitated and dissolved to obtain a final concentration of 1 µg/µL and stored at -80°C until for cRNA synthesis or amplification by quantitative real-time polymerase chain reaction (qPCR).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA synthesis First strand cDNA synthesis; 2 g (for qPCR) or 10 ug (microarray analysis) of total RNA and 100 pmol/uL of the T7(dT)24 primer (5’-GGCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGGTTTTTTTTTTTTTTTTTTTTTTTT-3’) were combined for annealing at 70o C for 10mins and chilled on ice for 2mins. Then, the SuperScript III kit (Invitrogen®) was added according to manufacturer indications to synthesize the cDNA. Second strand cDNA synthesis; the whole amount of the cDNA produced was used as template for the second strand synthesis plus 10 units of E. coli DNA ligase, 40 units of E. coli DNA polymerase (Invitrogen®), 3uL of 10 mM dNTPs and 2 units of Rnase H (Invitrogen®). The reaction was stopped by addition of 10 uL of 0.5M EDTA. The double stranded cDNA was then purified and precipitated and the resuspended in 10uL of nuclease free water. Synthesis of biotin-labelled cRNA; we used the Enzo-Bioarray kit (Enzo Life Sciences, Inc) for synthesis of the cRNA according to manufacturer protocol. The resulting cRNA was purified with Rneasy kit (Qiagen®). The concentration was measured on a spectrophotometer and 20 µg of each sample was fragmented in 200 mM tris-acetate (pH= 8.1), 500mM potassium acetate and 150 mM magnesium acetate for 35mins at 95°C, then chilled on ice and stored at -80°C until microarray hybridisation
| | Sample_hyb_protocol | For the mRNA high-throughput screening we used the GeneChip ® Rat expression 230 version 2.0 arrays and the GeneChip® Hybridization, Wash and stain kit from Affymetrix®. The protocol of hybridisation, according to manufactured indications was the 49/64 formats, which corresponds to the selected type of array. The control oligonucleotides were: B2 and the Eukaryotic bioB, bioC, bioD and cre. Then, the samples were washed and stained on the Fluidics Station 450 (Affymetrix®) monitored with the GeneChip® Operating Software (Affymetrix®) according to manufactured instructions (using the protocol FS450_003 which corresponds to rat 230 v2.0 array).
| | Sample_scan_protocol | We used GeneChip Scanner 3000 (Affymetrix®).
| | Sample_data_processing | The data were analyzed with 'R software' loaded with the 'Bioconductor' platform using GC-RMA normalisation and Limma test to contrast the experimental groups.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | David,,Vega-Avelaira
| | Sample_contact_email | david.vega74@gmail.com
| | Sample_contact_institute | University College of London
| | Sample_contact_address | Gower street
| | Sample_contact_city | Lonndon
| | Sample_contact_zip/postal_code | wc1e 6bt
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM375nnn/GSM375696/suppl/GSM375696.CEL.gz
| | Sample_series_id | GSE15041
| | Sample_data_row_count | 31099
| | |
|
GSM375697 | GPL1355 |
|
17 days, sham group, biological replicate 3
|
L4/L5 dorsal root ganglia from young rats (10 days old) 7 days after sham surgery
|
strain: Sprague-Dawley
tissue: Dorsal root ganglia
postnatal age: 17 days
surgery type: Sham
experimetal group: Young Sham
|
The L4/L5 dorsal root ganglia in the sham group are those ganglia ipsilateral to the surgery
|
| Sample_geo_accession | GSM375697
| | Sample_status | Public on Dec 18 2009
| | Sample_submission_date | Feb 27 2009
| | Sample_last_update_date | Dec 18 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Experiments were performed on adult (2 months old) male Sprague–Dawley rats and rat pups (10 days postnatal age, P10) and carried out in accordance with the United Kingdom Animal (Scientific Procedures) Act 1986. Spared nerve injury and sham surgery were performed under halothane general anaesthesia with antiseptic conditions. After skin preparation, the sciatic nerve and its three terminal branches were exposed in the upper lateral thigh. Axotomy and ligation of the common peroneal and tibial branches was performed under direct vision, leaving the sural nerve intact. Muscle and skin were closed in two layers. In the sham operation, the procedures were the same but the nerves were only exposed and not cut or ligated. In all cases great care was taken not to stretch the nerve, or its branches, nor to damage the intact nerves.
| | Sample_growth_protocol_ch1 | After the surgery, the animals were returned to their cages and litters and maintained on a 12 hour light/dark cycle at constant ambient temperature in the Biological Services Unit with free access to food and water for 7 days post surgery (ps) until DRGs collection.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Seven days post surgery, animals were sacrificed with 0.1 mL of Euthanal®, the fresh DRGs were snap frozen on liquid nitrogen and stored at –80o C until RNA extraction. L4 and L5 DRGs ipsilateral to the lesion were collected and pooled from 3 animals per adult experimental group and 4 animals per P10 group, (i.e. n= 6 DRGs per adult sample , n=8 per P10 sample) to minimise inter-animal differences. RNA was extracted using Trizol® reagent (Invitrogen®) and QIAshredder column (Qiagen®) for homogenisation according to manufacturer’s protocols. Additionally, the RNA was cleaned by ”RNA purification column” (Qiagen®) and a final volume of 50 uL obtained according to manufacturer protocol. The amount of RNA was measured with a NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies, Inc.) and its quality assessed with Experion RNA HighSens StdSens analysis kit (Bio-Rad®). Then, the RNA was precipitated and dissolved to obtain a final concentration of 1 µg/µL and stored at -80°C until for cRNA synthesis or amplification by quantitative real-time polymerase chain reaction (qPCR).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA synthesis First strand cDNA synthesis; 2 g (for qPCR) or 10 ug (microarray analysis) of total RNA and 100 pmol/uL of the T7(dT)24 primer (5’-GGCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGGTTTTTTTTTTTTTTTTTTTTTTTT-3’) were combined for annealing at 70o C for 10mins and chilled on ice for 2mins. Then, the SuperScript III kit (Invitrogen®) was added according to manufacturer indications to synthesize the cDNA. Second strand cDNA synthesis; the whole amount of the cDNA produced was used as template for the second strand synthesis plus 10 units of E. coli DNA ligase, 40 units of E. coli DNA polymerase (Invitrogen®), 3uL of 10 mM dNTPs and 2 units of Rnase H (Invitrogen®). The reaction was stopped by addition of 10 uL of 0.5M EDTA. The double stranded cDNA was then purified and precipitated and the resuspended in 10uL of nuclease free water. Synthesis of biotin-labelled cRNA; we used the Enzo-Bioarray kit (Enzo Life Sciences, Inc) for synthesis of the cRNA according to manufacturer protocol. The resulting cRNA was purified with Rneasy kit (Qiagen®). The concentration was measured on a spectrophotometer and 20 µg of each sample was fragmented in 200 mM tris-acetate (pH= 8.1), 500mM potassium acetate and 150 mM magnesium acetate for 35mins at 95°C, then chilled on ice and stored at -80°C until microarray hybridisation
| | Sample_hyb_protocol | For the mRNA high-throughput screening we used the GeneChip ® Rat expression 230 version 2.0 arrays and the GeneChip® Hybridization, Wash and stain kit from Affymetrix®. The protocol of hybridisation, according to manufactured indications was the 49/64 formats, which corresponds to the selected type of array. The control oligonucleotides were: B2 and the Eukaryotic bioB, bioC, bioD and cre. Then, the samples were washed and stained on the Fluidics Station 450 (Affymetrix®) monitored with the GeneChip® Operating Software (Affymetrix®) according to manufactured instructions (using the protocol FS450_003 which corresponds to rat 230 v2.0 array).
| | Sample_scan_protocol | We used GeneChip Scanner 3000 (Affymetrix®).
| | Sample_data_processing | The data were analyzed with 'R software' loaded with the 'Bioconductor' platform using GC-RMA normalisation and Limma test to contrast the experimental groups.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | David,,Vega-Avelaira
| | Sample_contact_email | david.vega74@gmail.com
| | Sample_contact_institute | University College of London
| | Sample_contact_address | Gower street
| | Sample_contact_city | Lonndon
| | Sample_contact_zip/postal_code | wc1e 6bt
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM375nnn/GSM375697/suppl/GSM375697.CEL.gz
| | Sample_series_id | GSE15041
| | Sample_data_row_count | 31099
| | |
|
GSM375698 | GPL1355 |
|
17 days, contralateral group, biological replicate 1
|
L4/L5 dorsal root ganglia from young rats (10 days old) 7 days after SNI surgery
|
strain: Sprague-Dawley
tissue: Dorsal root ganglia
postnatal age: 17 days
surgery type: Spare nerve injury
experimetal group: Young Contralateral
|
The L4/L5 dorsal root ganglia in the contralateral group are those ganglia contralateral to the surgery in the spare nerve injury group
|
| Sample_geo_accession | GSM375698
| | Sample_status | Public on Dec 18 2009
| | Sample_submission_date | Feb 27 2009
| | Sample_last_update_date | Dec 18 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Experiments were performed on adult (2 months old) male Sprague–Dawley rats and rat pups (10 days postnatal age, P10) and carried out in accordance with the United Kingdom Animal (Scientific Procedures) Act 1986. Spared nerve injury and sham surgery were performed under halothane general anaesthesia with antiseptic conditions. After skin preparation, the sciatic nerve and its three terminal branches were exposed in the upper lateral thigh. Axotomy and ligation of the common peroneal and tibial branches was performed under direct vision, leaving the sural nerve intact. Muscle and skin were closed in two layers. In the sham operation, the procedures were the same but the nerves were only exposed and not cut or ligated. In all cases great care was taken not to stretch the nerve, or its branches, nor to damage the intact nerves.
| | Sample_growth_protocol_ch1 | After the surgery, the animals were returned to their cages and litters and maintained on a 12 hour light/dark cycle at constant ambient temperature in the Biological Services Unit with free access to food and water for 7 days post surgery (ps) until DRGs collection.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Seven days post surgery, animals were sacrificed with 0.1 mL of Euthanal®, the fresh DRGs were snap frozen on liquid nitrogen and stored at –80o C until RNA extraction. L4 and L5 DRGs ipsilateral to the lesion were collected and pooled from 3 animals per adult experimental group and 4 animals per P10 group, (i.e. n= 6 DRGs per adult sample , n=8 per P10 sample) to minimise inter-animal differences. RNA was extracted using Trizol® reagent (Invitrogen®) and QIAshredder column (Qiagen®) for homogenisation according to manufacturer’s protocols. Additionally, the RNA was cleaned by ”RNA purification column” (Qiagen®) and a final volume of 50 uL obtained according to manufacturer protocol. The amount of RNA was measured with a NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies, Inc.) and its quality assessed with Experion RNA HighSens StdSens analysis kit (Bio-Rad®). Then, the RNA was precipitated and dissolved to obtain a final concentration of 1 µg/µL and stored at -80°C until for cRNA synthesis or amplification by quantitative real-time polymerase chain reaction (qPCR).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA synthesis First strand cDNA synthesis; 2 g (for qPCR) or 10 ug (microarray analysis) of total RNA and 100 pmol/uL of the T7(dT)24 primer (5’-GGCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGGTTTTTTTTTTTTTTTTTTTTTTTT-3’) were combined for annealing at 70o C for 10mins and chilled on ice for 2mins. Then, the SuperScript III kit (Invitrogen®) was added according to manufacturer indications to synthesize the cDNA. Second strand cDNA synthesis; the whole amount of the cDNA produced was used as template for the second strand synthesis plus 10 units of E. coli DNA ligase, 40 units of E. coli DNA polymerase (Invitrogen®), 3uL of 10 mM dNTPs and 2 units of Rnase H (Invitrogen®). The reaction was stopped by addition of 10 uL of 0.5M EDTA. The double stranded cDNA was then purified and precipitated and the resuspended in 10uL of nuclease free water. Synthesis of biotin-labelled cRNA; we used the Enzo-Bioarray kit (Enzo Life Sciences, Inc) for synthesis of the cRNA according to manufacturer protocol. The resulting cRNA was purified with Rneasy kit (Qiagen®). The concentration was measured on a spectrophotometer and 20 µg of each sample was fragmented in 200 mM tris-acetate (pH= 8.1), 500mM potassium acetate and 150 mM magnesium acetate for 35mins at 95°C, then chilled on ice and stored at -80°C until microarray hybridisation
| | Sample_hyb_protocol | For the mRNA high-throughput screening we used the GeneChip ® Rat expression 230 version 2.0 arrays and the GeneChip® Hybridization, Wash and stain kit from Affymetrix®. The protocol of hybridisation, according to manufactured indications was the 49/64 formats, which corresponds to the selected type of array. The control oligonucleotides were: B2 and the Eukaryotic bioB, bioC, bioD and cre. Then, the samples were washed and stained on the Fluidics Station 450 (Affymetrix®) monitored with the GeneChip® Operating Software (Affymetrix®) according to manufactured instructions (using the protocol FS450_003 which corresponds to rat 230 v2.0 array).
| | Sample_scan_protocol | We used GeneChip Scanner 3000 (Affymetrix®).
| | Sample_data_processing | The data were analyzed with 'R software' loaded with the 'Bioconductor' platform using GC-RMA normalisation and Limma test to contrast the experimental groups.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | David,,Vega-Avelaira
| | Sample_contact_email | david.vega74@gmail.com
| | Sample_contact_institute | University College of London
| | Sample_contact_address | Gower street
| | Sample_contact_city | Lonndon
| | Sample_contact_zip/postal_code | wc1e 6bt
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM375nnn/GSM375698/suppl/GSM375698.CEL.gz
| | Sample_series_id | GSE15041
| | Sample_data_row_count | 31099
| | |
|
GSM375699 | GPL1355 |
|
17 days, contralateral group, biological replicate 2
|
L4/L5 dorsal root ganglia from young rats (10 days old) 7 days after SNI surgery
|
strain: Sprague-Dawley
tissue: Dorsal root ganglia
postnatal age: 17 days
surgery type: Spare nerve injury
experimetal group: Young Contralateral
|
The L4/L5 dorsal root ganglia in the contralateral group are those ganglia contralateral to the surgery in the spare nerve injury group
|
| Sample_geo_accession | GSM375699
| | Sample_status | Public on Dec 18 2009
| | Sample_submission_date | Feb 27 2009
| | Sample_last_update_date | Dec 18 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Experiments were performed on adult (2 months old) male Sprague–Dawley rats and rat pups (10 days postnatal age, P10) and carried out in accordance with the United Kingdom Animal (Scientific Procedures) Act 1986. Spared nerve injury and sham surgery were performed under halothane general anaesthesia with antiseptic conditions. After skin preparation, the sciatic nerve and its three terminal branches were exposed in the upper lateral thigh. Axotomy and ligation of the common peroneal and tibial branches was performed under direct vision, leaving the sural nerve intact. Muscle and skin were closed in two layers. In the sham operation, the procedures were the same but the nerves were only exposed and not cut or ligated. In all cases great care was taken not to stretch the nerve, or its branches, nor to damage the intact nerves.
| | Sample_growth_protocol_ch1 | After the surgery, the animals were returned to their cages and litters and maintained on a 12 hour light/dark cycle at constant ambient temperature in the Biological Services Unit with free access to food and water for 7 days post surgery (ps) until DRGs collection.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Seven days post surgery, animals were sacrificed with 0.1 mL of Euthanal®, the fresh DRGs were snap frozen on liquid nitrogen and stored at –80o C until RNA extraction. L4 and L5 DRGs ipsilateral to the lesion were collected and pooled from 3 animals per adult experimental group and 4 animals per P10 group, (i.e. n= 6 DRGs per adult sample , n=8 per P10 sample) to minimise inter-animal differences. RNA was extracted using Trizol® reagent (Invitrogen®) and QIAshredder column (Qiagen®) for homogenisation according to manufacturer’s protocols. Additionally, the RNA was cleaned by ”RNA purification column” (Qiagen®) and a final volume of 50 uL obtained according to manufacturer protocol. The amount of RNA was measured with a NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies, Inc.) and its quality assessed with Experion RNA HighSens StdSens analysis kit (Bio-Rad®). Then, the RNA was precipitated and dissolved to obtain a final concentration of 1 µg/µL and stored at -80°C until for cRNA synthesis or amplification by quantitative real-time polymerase chain reaction (qPCR).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA synthesis First strand cDNA synthesis; 2 g (for qPCR) or 10 ug (microarray analysis) of total RNA and 100 pmol/uL of the T7(dT)24 primer (5’-GGCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGGTTTTTTTTTTTTTTTTTTTTTTTT-3’) were combined for annealing at 70o C for 10mins and chilled on ice for 2mins. Then, the SuperScript III kit (Invitrogen®) was added according to manufacturer indications to synthesize the cDNA. Second strand cDNA synthesis; the whole amount of the cDNA produced was used as template for the second strand synthesis plus 10 units of E. coli DNA ligase, 40 units of E. coli DNA polymerase (Invitrogen®), 3uL of 10 mM dNTPs and 2 units of Rnase H (Invitrogen®). The reaction was stopped by addition of 10 uL of 0.5M EDTA. The double stranded cDNA was then purified and precipitated and the resuspended in 10uL of nuclease free water. Synthesis of biotin-labelled cRNA; we used the Enzo-Bioarray kit (Enzo Life Sciences, Inc) for synthesis of the cRNA according to manufacturer protocol. The resulting cRNA was purified with Rneasy kit (Qiagen®). The concentration was measured on a spectrophotometer and 20 µg of each sample was fragmented in 200 mM tris-acetate (pH= 8.1), 500mM potassium acetate and 150 mM magnesium acetate for 35mins at 95°C, then chilled on ice and stored at -80°C until microarray hybridisation
| | Sample_hyb_protocol | For the mRNA high-throughput screening we used the GeneChip ® Rat expression 230 version 2.0 arrays and the GeneChip® Hybridization, Wash and stain kit from Affymetrix®. The protocol of hybridisation, according to manufactured indications was the 49/64 formats, which corresponds to the selected type of array. The control oligonucleotides were: B2 and the Eukaryotic bioB, bioC, bioD and cre. Then, the samples were washed and stained on the Fluidics Station 450 (Affymetrix®) monitored with the GeneChip® Operating Software (Affymetrix®) according to manufactured instructions (using the protocol FS450_003 which corresponds to rat 230 v2.0 array).
| | Sample_scan_protocol | We used GeneChip Scanner 3000 (Affymetrix®).
| | Sample_data_processing | The data were analyzed with 'R software' loaded with the 'Bioconductor' platform using GC-RMA normalisation and Limma test to contrast the experimental groups.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | David,,Vega-Avelaira
| | Sample_contact_email | david.vega74@gmail.com
| | Sample_contact_institute | University College of London
| | Sample_contact_address | Gower street
| | Sample_contact_city | Lonndon
| | Sample_contact_zip/postal_code | wc1e 6bt
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM375nnn/GSM375699/suppl/GSM375699.CEL.gz
| | Sample_series_id | GSE15041
| | Sample_data_row_count | 31099
| | |
|
GSM375700 | GPL1355 |
|
17 days, ipsilateral group, biological replicate 1
|
L4/L5 dorsal root ganglia from young rats (10 days old) 7 days after SNI surgery
|
strain: Sprague-Dawley
tissue: Dorsal root ganglia
postnatal age: 17 days
surgery type: Spare nerve injury
experimetal group: Young Ipsilateral
|
The L4/L5 dorsal root ganglia in the ipsilateral group are those ganglia ipsilateral to the surgery in the spare nerve injury group
|
| Sample_geo_accession | GSM375700
| | Sample_status | Public on Dec 18 2009
| | Sample_submission_date | Feb 27 2009
| | Sample_last_update_date | Dec 18 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Experiments were performed on adult (2 months old) male Sprague–Dawley rats and rat pups (10 days postnatal age, P10) and carried out in accordance with the United Kingdom Animal (Scientific Procedures) Act 1986. Spared nerve injury and sham surgery were performed under halothane general anaesthesia with antiseptic conditions. After skin preparation, the sciatic nerve and its three terminal branches were exposed in the upper lateral thigh. Axotomy and ligation of the common peroneal and tibial branches was performed under direct vision, leaving the sural nerve intact. Muscle and skin were closed in two layers. In the sham operation, the procedures were the same but the nerves were only exposed and not cut or ligated. In all cases great care was taken not to stretch the nerve, or its branches, nor to damage the intact nerves.
| | Sample_growth_protocol_ch1 | After the surgery, the animals were returned to their cages and litters and maintained on a 12 hour light/dark cycle at constant ambient temperature in the Biological Services Unit with free access to food and water for 7 days post surgery (ps) until DRGs collection.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Seven days post surgery, animals were sacrificed with 0.1 mL of Euthanal®, the fresh DRGs were snap frozen on liquid nitrogen and stored at –80o C until RNA extraction. L4 and L5 DRGs ipsilateral to the lesion were collected and pooled from 3 animals per adult experimental group and 4 animals per P10 group, (i.e. n= 6 DRGs per adult sample , n=8 per P10 sample) to minimise inter-animal differences. RNA was extracted using Trizol® reagent (Invitrogen®) and QIAshredder column (Qiagen®) for homogenisation according to manufacturer’s protocols. Additionally, the RNA was cleaned by ”RNA purification column” (Qiagen®) and a final volume of 50 uL obtained according to manufacturer protocol. The amount of RNA was measured with a NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies, Inc.) and its quality assessed with Experion RNA HighSens StdSens analysis kit (Bio-Rad®). Then, the RNA was precipitated and dissolved to obtain a final concentration of 1 µg/µL and stored at -80°C until for cRNA synthesis or amplification by quantitative real-time polymerase chain reaction (qPCR).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA synthesis First strand cDNA synthesis; 2 g (for qPCR) or 10 ug (microarray analysis) of total RNA and 100 pmol/uL of the T7(dT)24 primer (5’-GGCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGGTTTTTTTTTTTTTTTTTTTTTTTT-3’) were combined for annealing at 70o C for 10mins and chilled on ice for 2mins. Then, the SuperScript III kit (Invitrogen®) was added according to manufacturer indications to synthesize the cDNA. Second strand cDNA synthesis; the whole amount of the cDNA produced was used as template for the second strand synthesis plus 10 units of E. coli DNA ligase, 40 units of E. coli DNA polymerase (Invitrogen®), 3uL of 10 mM dNTPs and 2 units of Rnase H (Invitrogen®). The reaction was stopped by addition of 10 uL of 0.5M EDTA. The double stranded cDNA was then purified and precipitated and the resuspended in 10uL of nuclease free water. Synthesis of biotin-labelled cRNA; we used the Enzo-Bioarray kit (Enzo Life Sciences, Inc) for synthesis of the cRNA according to manufacturer protocol. The resulting cRNA was purified with Rneasy kit (Qiagen®). The concentration was measured on a spectrophotometer and 20 µg of each sample was fragmented in 200 mM tris-acetate (pH= 8.1), 500mM potassium acetate and 150 mM magnesium acetate for 35mins at 95°C, then chilled on ice and stored at -80°C until microarray hybridisation
| | Sample_hyb_protocol | For the mRNA high-throughput screening we used the GeneChip ® Rat expression 230 version 2.0 arrays and the GeneChip® Hybridization, Wash and stain kit from Affymetrix®. The protocol of hybridisation, according to manufactured indications was the 49/64 formats, which corresponds to the selected type of array. The control oligonucleotides were: B2 and the Eukaryotic bioB, bioC, bioD and cre. Then, the samples were washed and stained on the Fluidics Station 450 (Affymetrix®) monitored with the GeneChip® Operating Software (Affymetrix®) according to manufactured instructions (using the protocol FS450_003 which corresponds to rat 230 v2.0 array).
| | Sample_scan_protocol | We used GeneChip Scanner 3000 (Affymetrix®).
| | Sample_data_processing | The data were analyzed with 'R software' loaded with the 'Bioconductor' platform using GC-RMA normalisation and Limma test to contrast the experimental groups.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | David,,Vega-Avelaira
| | Sample_contact_email | david.vega74@gmail.com
| | Sample_contact_institute | University College of London
| | Sample_contact_address | Gower street
| | Sample_contact_city | Lonndon
| | Sample_contact_zip/postal_code | wc1e 6bt
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM375nnn/GSM375700/suppl/GSM375700.CEL.gz
| | Sample_series_id | GSE15041
| | Sample_data_row_count | 31099
| | |
|
GSM375701 | GPL1355 |
|
17 days, ipsilateral group, biological replicate 2
|
L4/L5 dorsal root ganglia from young rats (10 days old) 7 days after SNI surgery
|
strain: Sprague-Dawley
tissue: Dorsal root ganglia
postnatal age: 17 days
surgery type: Spare nerve injury
experimetal group: Young Ipsilateral
|
The L4/L5 dorsal root ganglia in the ipsilateral group are those ganglia ipsilateral to the surgery in the spare nerve injury group
|
| Sample_geo_accession | GSM375701
| | Sample_status | Public on Dec 18 2009
| | Sample_submission_date | Feb 27 2009
| | Sample_last_update_date | Dec 18 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Experiments were performed on adult (2 months old) male Sprague–Dawley rats and rat pups (10 days postnatal age, P10) and carried out in accordance with the United Kingdom Animal (Scientific Procedures) Act 1986. Spared nerve injury and sham surgery were performed under halothane general anaesthesia with antiseptic conditions. After skin preparation, the sciatic nerve and its three terminal branches were exposed in the upper lateral thigh. Axotomy and ligation of the common peroneal and tibial branches was performed under direct vision, leaving the sural nerve intact. Muscle and skin were closed in two layers. In the sham operation, the procedures were the same but the nerves were only exposed and not cut or ligated. In all cases great care was taken not to stretch the nerve, or its branches, nor to damage the intact nerves.
| | Sample_growth_protocol_ch1 | After the surgery, the animals were returned to their cages and litters and maintained on a 12 hour light/dark cycle at constant ambient temperature in the Biological Services Unit with free access to food and water for 7 days post surgery (ps) until DRGs collection.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Seven days post surgery, animals were sacrificed with 0.1 mL of Euthanal®, the fresh DRGs were snap frozen on liquid nitrogen and stored at –80o C until RNA extraction. L4 and L5 DRGs ipsilateral to the lesion were collected and pooled from 3 animals per adult experimental group and 4 animals per P10 group, (i.e. n= 6 DRGs per adult sample , n=8 per P10 sample) to minimise inter-animal differences. RNA was extracted using Trizol® reagent (Invitrogen®) and QIAshredder column (Qiagen®) for homogenisation according to manufacturer’s protocols. Additionally, the RNA was cleaned by ”RNA purification column” (Qiagen®) and a final volume of 50 uL obtained according to manufacturer protocol. The amount of RNA was measured with a NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies, Inc.) and its quality assessed with Experion RNA HighSens StdSens analysis kit (Bio-Rad®). Then, the RNA was precipitated and dissolved to obtain a final concentration of 1 µg/µL and stored at -80°C until for cRNA synthesis or amplification by quantitative real-time polymerase chain reaction (qPCR).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA synthesis First strand cDNA synthesis; 2 g (for qPCR) or 10 ug (microarray analysis) of total RNA and 100 pmol/uL of the T7(dT)24 primer (5’-GGCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGGTTTTTTTTTTTTTTTTTTTTTTTT-3’) were combined for annealing at 70o C for 10mins and chilled on ice for 2mins. Then, the SuperScript III kit (Invitrogen®) was added according to manufacturer indications to synthesize the cDNA. Second strand cDNA synthesis; the whole amount of the cDNA produced was used as template for the second strand synthesis plus 10 units of E. coli DNA ligase, 40 units of E. coli DNA polymerase (Invitrogen®), 3uL of 10 mM dNTPs and 2 units of Rnase H (Invitrogen®). The reaction was stopped by addition of 10 uL of 0.5M EDTA. The double stranded cDNA was then purified and precipitated and the resuspended in 10uL of nuclease free water. Synthesis of biotin-labelled cRNA; we used the Enzo-Bioarray kit (Enzo Life Sciences, Inc) for synthesis of the cRNA according to manufacturer protocol. The resulting cRNA was purified with Rneasy kit (Qiagen®). The concentration was measured on a spectrophotometer and 20 µg of each sample was fragmented in 200 mM tris-acetate (pH= 8.1), 500mM potassium acetate and 150 mM magnesium acetate for 35mins at 95°C, then chilled on ice and stored at -80°C until microarray hybridisation
| | Sample_hyb_protocol | For the mRNA high-throughput screening we used the GeneChip ® Rat expression 230 version 2.0 arrays and the GeneChip® Hybridization, Wash and stain kit from Affymetrix®. The protocol of hybridisation, according to manufactured indications was the 49/64 formats, which corresponds to the selected type of array. The control oligonucleotides were: B2 and the Eukaryotic bioB, bioC, bioD and cre. Then, the samples were washed and stained on the Fluidics Station 450 (Affymetrix®) monitored with the GeneChip® Operating Software (Affymetrix®) according to manufactured instructions (using the protocol FS450_003 which corresponds to rat 230 v2.0 array).
| | Sample_scan_protocol | We used GeneChip Scanner 3000 (Affymetrix®).
| | Sample_data_processing | The data were analyzed with 'R software' loaded with the 'Bioconductor' platform using GC-RMA normalisation and Limma test to contrast the experimental groups.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | David,,Vega-Avelaira
| | Sample_contact_email | david.vega74@gmail.com
| | Sample_contact_institute | University College of London
| | Sample_contact_address | Gower street
| | Sample_contact_city | Lonndon
| | Sample_contact_zip/postal_code | wc1e 6bt
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM375nnn/GSM375701/suppl/GSM375701.CEL.gz
| | Sample_series_id | GSE15041
| | Sample_data_row_count | 31099
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