Search results for the GEO ID: GSE15737  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM393924 | GPL1355 |
|
EOM 15 fiber
|
extraocular muscle fiber
|
tissue: rectus extraocular muscle
cellular location: non-neuromuscular junction
|
EOM fiber was captured by LCM.
|
| Sample_geo_accession | GSM393924
| | Sample_status | Public on Apr 16 2010
| | Sample_submission_date | Apr 18 2009
| | Sample_last_update_date | Apr 23 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated and purified from each captured set by RNeasy micro kit (Qiagen, Valencia, CA) as described by manufacturer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | All total RNAs from EOM and TA synapse as well as EOM and TA fiber were used to generate double-stranded cDNA with the T7-oligo (dT) primer according to the GeneChip® Two cycle target labeling protocol (Affymetrix Inc., Santa Clara, CA, USA) as described by the manufacturer. At the end of the first cycle linear amplification, all amplified RNAs (i.e, aRNAs) were normalized to 600 ng (260/280 ratio ranging from 2.0-2.3) for the next amplification and labeling steps. Two rounds of in vitro transcription were performed as described by manufacturer. Labeled cRNA yield and purity were determined by measuring the absorbance at 260 and 280 nm using Nanodrop ND-1000 spectrophotometer.
| | Sample_hyb_protocol | Fifteen micrograms of labeled cRNA from EOM fiber was fragmented, and 10μg was hybridized to Affymetrix® Rat 230 ver 2.0 GeneChip arrays for 18–24h (Affymetrix Inc.). Genechip was washed and stained with streptavidin–phycoerythrin.
| | Sample_scan_protocol | The chip was scanned at a 6μm resolution with Agilent model G2500A GeneArray scanner. A visual quality control measurement was performed to ensure proper hybridization after each chip was scanned.
| | Sample_data_processing | Quality control parameters such as scaling factors used to normalize the chips, average background, and noise were also evaluated. In addition, raw intensities for each probe set were stored in electronic formats by the GeneChip Operating System version 1.1 (GCOS1.1, Affymetrix Inc.).
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Murat,T,Budak
| | Sample_contact_email | mtbudak@mail.med.upenn.edu
| | Sample_contact_phone | 215-8989726
| | Sample_contact_laboratory | Rubinstein and Khurana Labs
| | Sample_contact_department |
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address |
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM393nnn/GSM393924/suppl/GSM393924.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM393nnn/GSM393924/suppl/GSM393924.CHP.gz
| | Sample_series_id | GSE15737
| | Sample_data_row_count | 31099
| | |
|
GSM393925 | GPL1355 |
|
EOM 25 fiber
|
extraocular muscle fiber
|
tissue: rectus extraocular muscle
cellular location: non-neuromuscular junction
|
EOM fiber was captured by LCM.
|
| Sample_geo_accession | GSM393925
| | Sample_status | Public on Apr 16 2010
| | Sample_submission_date | Apr 18 2009
| | Sample_last_update_date | Apr 23 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated and purified from each captured set by RNeasy micro kit (Qiagen, Valencia, CA) as described by manufacturer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | All total RNAs from EOM and TA synapse as well as EOM and TA fiber were used to generate double-stranded cDNA with the T7-oligo (dT) primer according to the GeneChip® Two cycle target labeling protocol (Affymetrix Inc., Santa Clara, CA, USA) as described by the manufacturer. At the end of the first cycle linear amplification, all amplified RNAs (i.e, aRNAs) were normalized to 600 ng (260/280 ratio ranging from 2.0-2.3) for the next amplification and labeling steps. Two rounds of in vitro transcription were performed as described by manufacturer. Labeled cRNA yield and purity were determined by measuring the absorbance at 260 and 280 nm using Nanodrop ND-1000 spectrophotometer.
| | Sample_hyb_protocol | Fifteen micrograms of labeled cRNA from EOM fiber was fragmented, and 10μg was hybridized to Affymetrix® Rat 230 ver 2.0 GeneChip arrays for 18–24h (Affymetrix Inc.). Genechip was washed and stained with streptavidin–phycoerythrin.
| | Sample_scan_protocol | The chip was scanned at a 6μm resolution with Agilent model G2500A GeneArray scanner. A visual quality control measurement was performed to ensure proper hybridization after each chip was scanned.
| | Sample_data_processing | Quality control parameters such as scaling factors used to normalize the chips, average background, and noise were also evaluated. In addition, raw intensities for each probe set were stored in electronic formats by the GeneChip Operating System version 1.1 (GCOS1.1, Affymetrix Inc.).
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Murat,T,Budak
| | Sample_contact_email | mtbudak@mail.med.upenn.edu
| | Sample_contact_phone | 215-8989726
| | Sample_contact_laboratory | Rubinstein and Khurana Labs
| | Sample_contact_department |
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address |
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM393nnn/GSM393925/suppl/GSM393925.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM393nnn/GSM393925/suppl/GSM393925.CHP.gz
| | Sample_series_id | GSE15737
| | Sample_data_row_count | 31099
| | |
|
GSM393926 | GPL1355 |
|
EOM 27 fiber
|
extraocular muscle fiber
|
tissue: rectus extraocular muscle
cellular location: non-neuromuscular junction
|
EOM fiber was captured by LCM.
|
| Sample_geo_accession | GSM393926
| | Sample_status | Public on Apr 16 2010
| | Sample_submission_date | Apr 18 2009
| | Sample_last_update_date | Apr 23 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated and purified from each captured set by RNeasy micro kit (Qiagen, Valencia, CA) as described by manufacturer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | All total RNAs from EOM and TA synapse as well as EOM and TA fiber were used to generate double-stranded cDNA with the T7-oligo (dT) primer according to the GeneChip® Two cycle target labeling protocol (Affymetrix Inc., Santa Clara, CA, USA) as described by the manufacturer. At the end of the first cycle linear amplification, all amplified RNAs (i.e, aRNAs) were normalized to 600 ng (260/280 ratio ranging from 2.0-2.3) for the next amplification and labeling steps. Two rounds of in vitro transcription were performed as described by manufacturer. Labeled cRNA yield and purity were determined by measuring the absorbance at 260 and 280 nm using Nanodrop ND-1000 spectrophotometer.
| | Sample_hyb_protocol | Fifteen micrograms of labeled cRNA from EOM fiber was fragmented, and 10μg was hybridized to Affymetrix® Rat 230 ver 2.0 GeneChip arrays for 18–24h (Affymetrix Inc.). Genechip was washed and stained with streptavidin–phycoerythrin.
| | Sample_scan_protocol | The chip was scanned at a 6μm resolution with Agilent model G2500A GeneArray scanner. A visual quality control measurement was performed to ensure proper hybridization after each chip was scanned.
| | Sample_data_processing | Quality control parameters such as scaling factors used to normalize the chips, average background, and noise were also evaluated. In addition, raw intensities for each probe set were stored in electronic formats by the GeneChip Operating System version 1.1 (GCOS1.1, Affymetrix Inc.).
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Murat,T,Budak
| | Sample_contact_email | mtbudak@mail.med.upenn.edu
| | Sample_contact_phone | 215-8989726
| | Sample_contact_laboratory | Rubinstein and Khurana Labs
| | Sample_contact_department |
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address |
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM393nnn/GSM393926/suppl/GSM393926.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM393nnn/GSM393926/suppl/GSM393926.CHP.gz
| | Sample_series_id | GSE15737
| | Sample_data_row_count | 31099
| | |
|
GSM393927 | GPL1355 |
|
EOM 29 fiber
|
extraocular muscle fiber
|
tissue: rectus extraocular muscle
cellular location: non-neuromuscular junction
|
EOM fiber was captured by LCM.
|
| Sample_geo_accession | GSM393927
| | Sample_status | Public on Apr 16 2010
| | Sample_submission_date | Apr 18 2009
| | Sample_last_update_date | Apr 23 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated and purified from each captured set by RNeasy micro kit (Qiagen, Valencia, CA) as described by manufacturer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | All total RNAs from EOM and TA synapse as well as EOM and TA fiber were used to generate double-stranded cDNA with the T7-oligo (dT) primer according to the GeneChip® Two cycle target labeling protocol (Affymetrix Inc., Santa Clara, CA, USA) as described by the manufacturer. At the end of the first cycle linear amplification, all amplified RNAs (i.e, aRNAs) were normalized to 600 ng (260/280 ratio ranging from 2.0-2.3) for the next amplification and labeling steps. Two rounds of in vitro transcription were performed as described by manufacturer. Labeled cRNA yield and purity were determined by measuring the absorbance at 260 and 280 nm using Nanodrop ND-1000 spectrophotometer.
| | Sample_hyb_protocol | Fifteen micrograms of labeled cRNA from EOM fiber was fragmented, and 10μg was hybridized to Affymetrix® Rat 230 ver 2.0 GeneChip arrays for 18–24h (Affymetrix Inc.). Genechip was washed and stained with streptavidin–phycoerythrin.
| | Sample_scan_protocol | The chip was scanned at a 6μm resolution with Agilent model G2500A GeneArray scanner. A visual quality control measurement was performed to ensure proper hybridization after each chip was scanned.
| | Sample_data_processing | Quality control parameters such as scaling factors used to normalize the chips, average background, and noise were also evaluated. In addition, raw intensities for each probe set were stored in electronic formats by the GeneChip Operating System version 1.1 (GCOS1.1, Affymetrix Inc.).
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Murat,T,Budak
| | Sample_contact_email | mtbudak@mail.med.upenn.edu
| | Sample_contact_phone | 215-8989726
| | Sample_contact_laboratory | Rubinstein and Khurana Labs
| | Sample_contact_department |
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address |
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM393nnn/GSM393927/suppl/GSM393927.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM393nnn/GSM393927/suppl/GSM393927.CHP.gz
| | Sample_series_id | GSE15737
| | Sample_data_row_count | 31099
| | |
|
GSM393928 | GPL1355 |
|
TA 15 fiber
|
tibialis anterior muscle fiber
|
tissue: tibialis anterior muscle
cellular location: non-neuromuscular junction
|
TA fiber was captured by LCM.
|
| Sample_geo_accession | GSM393928
| | Sample_status | Public on Apr 16 2010
| | Sample_submission_date | Apr 18 2009
| | Sample_last_update_date | Apr 23 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated and purified from each captured set by RNeasy micro kit (Qiagen, Valencia, CA) as described by manufacturer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | All total RNAs from EOM and TA synapse as well as EOM and TA fiber were used to generate double-stranded cDNA with the T7-oligo (dT) primer according to the GeneChip® Two cycle target labeling protocol (Affymetrix Inc., Santa Clara, CA, USA) as described by the manufacturer. At the end of the first cycle linear amplification, all amplified RNAs (i.e, aRNAs) were normalized to 600 ng (260/280 ratio ranging from 2.0-2.3) for the next amplification and labeling steps. Two rounds of in vitro transcription were performed as described by manufacturer. Labeled cRNA yield and purity were determined by measuring the absorbance at 260 and 280 nm using Nanodrop ND-1000 spectrophotometer.
| | Sample_hyb_protocol | Fifteen micrograms of labeled cRNA from TA fiber was fragmented, and 10μg was hybridized to Affymetrix® Rat 230 ver 2.0 GeneChip arrays for 18–24h (Affymetrix Inc.). Genechip was washed and stained with streptavidin–phycoerythrin.
| | Sample_scan_protocol | The chip was scanned at a 6μm resolution with Agilent model G2500A GeneArray scanner. A visual quality control measurement was performed to ensure proper hybridization after each chip was scanned.
| | Sample_data_processing | Quality control parameters such as scaling factors used to normalize the chips, average background, and noise were also evaluated. In addition, raw intensities for each probe set were stored in electronic formats by the GeneChip Operating System version 1.1 (GCOS1.1, Affymetrix Inc.).
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Murat,T,Budak
| | Sample_contact_email | mtbudak@mail.med.upenn.edu
| | Sample_contact_phone | 215-8989726
| | Sample_contact_laboratory | Rubinstein and Khurana Labs
| | Sample_contact_department |
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address |
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM393nnn/GSM393928/suppl/GSM393928.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM393nnn/GSM393928/suppl/GSM393928.CHP.gz
| | Sample_series_id | GSE15737
| | Sample_data_row_count | 31099
| | |
|
GSM393929 | GPL1355 |
|
TA 25 fiber
|
tibialis anterior muscle fiber
|
tissue: tibialis anterior muscle
cellular location: non-neuromuscular junction
|
TA fiber was captured by LCM.
|
| Sample_geo_accession | GSM393929
| | Sample_status | Public on Apr 16 2010
| | Sample_submission_date | Apr 18 2009
| | Sample_last_update_date | Apr 23 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated and purified from each captured set by RNeasy micro kit (Qiagen, Valencia, CA) as described by manufacturer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | All total RNAs from EOM and TA synapse as well as EOM and TA fiber were used to generate double-stranded cDNA with the T7-oligo (dT) primer according to the GeneChip® Two cycle target labeling protocol (Affymetrix Inc., Santa Clara, CA, USA) as described by the manufacturer. At the end of the first cycle linear amplification, all amplified RNAs (i.e, aRNAs) were normalized to 600 ng (260/280 ratio ranging from 2.0-2.3) for the next amplification and labeling steps. Two rounds of in vitro transcription were performed as described by manufacturer. Labeled cRNA yield and purity were determined by measuring the absorbance at 260 and 280 nm using Nanodrop ND-1000 spectrophotometer.
| | Sample_hyb_protocol | Fifteen micrograms of labeled cRNA from TA fiber was fragmented, and 10μg was hybridized to Affymetrix® Rat 230 ver 2.0 GeneChip arrays for 18–24h (Affymetrix Inc.). Genechip was washed and stained with streptavidin–phycoerythrin.
| | Sample_scan_protocol | The chip was scanned at a 6μm resolution with Agilent model G2500A GeneArray scanner. A visual quality control measurement was performed to ensure proper hybridization after each chip was scanned.
| | Sample_data_processing | Quality control parameters such as scaling factors used to normalize the chips, average background, and noise were also evaluated. In addition, raw intensities for each probe set were stored in electronic formats by the GeneChip Operating System version 1.1 (GCOS1.1, Affymetrix Inc.).
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Murat,T,Budak
| | Sample_contact_email | mtbudak@mail.med.upenn.edu
| | Sample_contact_phone | 215-8989726
| | Sample_contact_laboratory | Rubinstein and Khurana Labs
| | Sample_contact_department |
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address |
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM393nnn/GSM393929/suppl/GSM393929.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM393nnn/GSM393929/suppl/GSM393929.CHP.gz
| | Sample_series_id | GSE15737
| | Sample_data_row_count | 31099
| | |
|
GSM393930 | GPL1355 |
|
TA 27 fiber
|
tibialis anterior muscle fiber
|
tissue: tibialis anterior muscle
cellular location: non-neuromuscular junction
|
TA fiber was captured by LCM.
|
| Sample_geo_accession | GSM393930
| | Sample_status | Public on Apr 16 2010
| | Sample_submission_date | Apr 18 2009
| | Sample_last_update_date | Apr 23 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated and purified from each captured set by RNeasy micro kit (Qiagen, Valencia, CA) as described by manufacturer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | All total RNAs from EOM and TA synapse as well as EOM and TA fiber were used to generate double-stranded cDNA with the T7-oligo (dT) primer according to the GeneChip® Two cycle target labeling protocol (Affymetrix Inc., Santa Clara, CA, USA) as described by the manufacturer. At the end of the first cycle linear amplification, all amplified RNAs (i.e, aRNAs) were normalized to 600 ng (260/280 ratio ranging from 2.0-2.3) for the next amplification and labeling steps. Two rounds of in vitro transcription were performed as described by manufacturer. Labeled cRNA yield and purity were determined by measuring the absorbance at 260 and 280 nm using Nanodrop ND-1000 spectrophotometer.
| | Sample_hyb_protocol | Fifteen micrograms of labeled cRNA from TA fiber was fragmented, and 10μg was hybridized to Affymetrix® Rat 230 ver 2.0 GeneChip arrays for 18–24h (Affymetrix Inc.). Genechip was washed and stained with streptavidin–phycoerythrin.
| | Sample_scan_protocol | The chip was scanned at a 6μm resolution with Agilent model G2500A GeneArray scanner. A visual quality control measurement was performed to ensure proper hybridization after each chip was scanned.
| | Sample_data_processing | Quality control parameters such as scaling factors used to normalize the chips, average background, and noise were also evaluated. In addition, raw intensities for each probe set were stored in electronic formats by the GeneChip Operating System version 1.1 (GCOS1.1, Affymetrix Inc.).
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Murat,T,Budak
| | Sample_contact_email | mtbudak@mail.med.upenn.edu
| | Sample_contact_phone | 215-8989726
| | Sample_contact_laboratory | Rubinstein and Khurana Labs
| | Sample_contact_department |
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address |
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM393nnn/GSM393930/suppl/GSM393930.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM393nnn/GSM393930/suppl/GSM393930.CHP.gz
| | Sample_series_id | GSE15737
| | Sample_data_row_count | 31099
| | |
|
GSM393931 | GPL1355 |
|
TA 29 fiber
|
tibialis anterior muscle fiber
|
tissue: tibialis anterior muscle
cellular location: non-neuromuscular junction
|
TA fiber was captured by LCM.
|
| Sample_geo_accession | GSM393931
| | Sample_status | Public on Apr 16 2010
| | Sample_submission_date | Apr 18 2009
| | Sample_last_update_date | Apr 23 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated and purified from each captured set by RNeasy micro kit (Qiagen, Valencia, CA) as described by manufacturer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | All total RNAs from EOM and TA synapse as well as EOM and TA fiber were used to generate double-stranded cDNA with the T7-oligo (dT) primer according to the GeneChip® Two cycle target labeling protocol (Affymetrix Inc., Santa Clara, CA, USA) as described by the manufacturer. At the end of the first cycle linear amplification, all amplified RNAs (i.e, aRNAs) were normalized to 600 ng (260/280 ratio ranging from 2.0-2.3) for the next amplification and labeling steps. Two rounds of in vitro transcription were performed as described by manufacturer. Labeled cRNA yield and purity were determined by measuring the absorbance at 260 and 280 nm using Nanodrop ND-1000 spectrophotometer.
| | Sample_hyb_protocol | Fifteen micrograms of labeled cRNA from TA fiber was fragmented, and 10μg was hybridized to Affymetrix® Rat 230 ver 2.0 GeneChip arrays for 18–24h (Affymetrix Inc.). Genechip was washed and stained with streptavidin–phycoerythrin.
| | Sample_scan_protocol | The chip was scanned at a 6μm resolution with Agilent model G2500A GeneArray scanner. A visual quality control measurement was performed to ensure proper hybridization after each chip was scanned.
| | Sample_data_processing | Quality control parameters such as scaling factors used to normalize the chips, average background, and noise were also evaluated. In addition, raw intensities for each probe set were stored in electronic formats by the GeneChip Operating System version 1.1 (GCOS1.1, Affymetrix Inc.).
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Murat,T,Budak
| | Sample_contact_email | mtbudak@mail.med.upenn.edu
| | Sample_contact_phone | 215-8989726
| | Sample_contact_laboratory | Rubinstein and Khurana Labs
| | Sample_contact_department |
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address |
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM393nnn/GSM393931/suppl/GSM393931.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM393nnn/GSM393931/suppl/GSM393931.CHP.gz
| | Sample_series_id | GSE15737
| | Sample_data_row_count | 31099
| | |
|
GSM393932 | GPL1355 |
|
EOM 15 synapse
|
extraocular muscle synapse
|
tissue: rectus extraocular muscle
cellular location: neuromuscular junction
|
EOM synapse was captured by LCM.
|
| Sample_geo_accession | GSM393932
| | Sample_status | Public on Apr 16 2010
| | Sample_submission_date | Apr 18 2009
| | Sample_last_update_date | Apr 23 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated and purified from each captured set by RNeasy micro kit (Qiagen, Valencia, CA) as described by manufacturer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | All total RNAs from EOM and TA synapse as well as EOM and TA fiber were used to generate double-stranded cDNA with the T7-oligo (dT) primer according to the GeneChip® Two cycle target labeling protocol (Affymetrix Inc., Santa Clara, CA, USA) as described by the manufacturer. At the end of the first cycle linear amplification, all amplified RNAs (i.e, aRNAs) were normalized to 600 ng (260/280 ratio ranging from 2.0-2.3) for the next amplification and labeling steps. Two rounds of in vitro transcription were performed as described by manufacturer. Labeled cRNA yield and purity were determined by measuring the absorbance at 260 and 280 nm using Nanodrop ND-1000 spectrophotometer.
| | Sample_hyb_protocol | Fifteen micrograms of labeled cRNA from EOM synapse was fragmented, and 10μg was hybridized to Affymetrix® Rat 230 ver 2.0 GeneChip arrays for 18–24h (Affymetrix Inc.). Genechip was washed and stained with streptavidin–phycoerythrin.
| | Sample_scan_protocol | The chip was scanned at a 6μm resolution with Agilent model G2500A GeneArray scanner. A visual quality control measurement was performed to ensure proper hybridization after each chip was scanned.
| | Sample_data_processing | Quality control parameters such as scaling factors used to normalize the chips, average background, and noise were also evaluated. In addition, raw intensities for each probe set were stored in electronic formats by the GeneChip Operating System version 1.1 (GCOS1.1, Affymetrix Inc.).
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Murat,T,Budak
| | Sample_contact_email | mtbudak@mail.med.upenn.edu
| | Sample_contact_phone | 215-8989726
| | Sample_contact_laboratory | Rubinstein and Khurana Labs
| | Sample_contact_department |
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address |
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM393nnn/GSM393932/suppl/GSM393932.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM393nnn/GSM393932/suppl/GSM393932.CHP.gz
| | Sample_series_id | GSE15737
| | Sample_data_row_count | 31099
| | |
|
GSM393933 | GPL1355 |
|
EOM 25 synapse
|
extraocular muscle synapse
|
tissue: rectus extraocular muscle
cellular location: neuromuscular junction
|
EOM synapse was captured by LCM.
|
| Sample_geo_accession | GSM393933
| | Sample_status | Public on Apr 16 2010
| | Sample_submission_date | Apr 18 2009
| | Sample_last_update_date | Apr 23 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated and purified from each captured set by RNeasy micro kit (Qiagen, Valencia, CA) as described by manufacturer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | All total RNAs from EOM and TA synapse as well as EOM and TA fiber were used to generate double-stranded cDNA with the T7-oligo (dT) primer according to the GeneChip® Two cycle target labeling protocol (Affymetrix Inc., Santa Clara, CA, USA) as described by the manufacturer. At the end of the first cycle linear amplification, all amplified RNAs (i.e, aRNAs) were normalized to 600 ng (260/280 ratio ranging from 2.0-2.3) for the next amplification and labeling steps. Two rounds of in vitro transcription were performed as described by manufacturer. Labeled cRNA yield and purity were determined by measuring the absorbance at 260 and 280 nm using Nanodrop ND-1000 spectrophotometer.
| | Sample_hyb_protocol | Fifteen micrograms of labeled cRNA from EOM synapse was fragmented, and 10μg was hybridized to Affymetrix® Rat 230 ver 2.0 GeneChip arrays for 18–24h (Affymetrix Inc.). Genechip was washed and stained with streptavidin–phycoerythrin.
| | Sample_scan_protocol | The chip was scanned at a 6μm resolution with Agilent model G2500A GeneArray scanner. A visual quality control measurement was performed to ensure proper hybridization after each chip was scanned.
| | Sample_data_processing | Quality control parameters such as scaling factors used to normalize the chips, average background, and noise were also evaluated. In addition, raw intensities for each probe set were stored in electronic formats by the GeneChip Operating System version 1.1 (GCOS1.1, Affymetrix Inc.).
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Murat,T,Budak
| | Sample_contact_email | mtbudak@mail.med.upenn.edu
| | Sample_contact_phone | 215-8989726
| | Sample_contact_laboratory | Rubinstein and Khurana Labs
| | Sample_contact_department |
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address |
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM393nnn/GSM393933/suppl/GSM393933.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM393nnn/GSM393933/suppl/GSM393933.CHP.gz
| | Sample_series_id | GSE15737
| | Sample_data_row_count | 31099
| | |
|
GSM393934 | GPL1355 |
|
EOM 27 synapse
|
extraocular muscle synapse
|
tissue: rectus extraocular muscle
cellular location: neuromuscular junction
|
EOM synapse was captured by LCM.
|
| Sample_geo_accession | GSM393934
| | Sample_status | Public on Apr 16 2010
| | Sample_submission_date | Apr 18 2009
| | Sample_last_update_date | Apr 23 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated and purified from each captured set by RNeasy micro kit (Qiagen, Valencia, CA) as described by manufacturer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | All total RNAs from EOM and TA synapse as well as EOM and TA fiber were used to generate double-stranded cDNA with the T7-oligo (dT) primer according to the GeneChip® Two cycle target labeling protocol (Affymetrix Inc., Santa Clara, CA, USA) as described by the manufacturer. At the end of the first cycle linear amplification, all amplified RNAs (i.e, aRNAs) were normalized to 600 ng (260/280 ratio ranging from 2.0-2.3) for the next amplification and labeling steps. Two rounds of in vitro transcription were performed as described by manufacturer. Labeled cRNA yield and purity were determined by measuring the absorbance at 260 and 280 nm using Nanodrop ND-1000 spectrophotometer.
| | Sample_hyb_protocol | Fifteen micrograms of labeled cRNA from EOM synapse was fragmented, and 10μg was hybridized to Affymetrix® Rat 230 ver 2.0 GeneChip arrays for 18–24h (Affymetrix Inc.). Genechip was washed and stained with streptavidin–phycoerythrin.
| | Sample_scan_protocol | The chip was scanned at a 6μm resolution with Agilent model G2500A GeneArray scanner. A visual quality control measurement was performed to ensure proper hybridization after each chip was scanned.
| | Sample_data_processing | Quality control parameters such as scaling factors used to normalize the chips, average background, and noise were also evaluated. In addition, raw intensities for each probe set were stored in electronic formats by the GeneChip Operating System version 1.1 (GCOS1.1, Affymetrix Inc.).
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Murat,T,Budak
| | Sample_contact_email | mtbudak@mail.med.upenn.edu
| | Sample_contact_phone | 215-8989726
| | Sample_contact_laboratory | Rubinstein and Khurana Labs
| | Sample_contact_department |
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address |
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM393nnn/GSM393934/suppl/GSM393934.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM393nnn/GSM393934/suppl/GSM393934.CHP.gz
| | Sample_series_id | GSE15737
| | Sample_data_row_count | 31099
| | |
|
GSM393935 | GPL1355 |
|
EOM 29 synapse
|
extraocular muscle synapse
|
tissue: rectus extraocular muscle
cellular location: neuromuscular junction
|
EOM synapse was captured by LCM.
|
| Sample_geo_accession | GSM393935
| | Sample_status | Public on Apr 16 2010
| | Sample_submission_date | Apr 18 2009
| | Sample_last_update_date | Apr 23 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated and purified from each captured set by RNeasy micro kit (Qiagen, Valencia, CA) as described by manufacturer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | All total RNAs from EOM and TA synapse as well as EOM and TA fiber were used to generate double-stranded cDNA with the T7-oligo (dT) primer according to the GeneChip® Two cycle target labeling protocol (Affymetrix Inc., Santa Clara, CA, USA) as described by the manufacturer. At the end of the first cycle linear amplification, all amplified RNAs (i.e, aRNAs) were normalized to 600 ng (260/280 ratio ranging from 2.0-2.3) for the next amplification and labeling steps. Two rounds of in vitro transcription were performed as described by manufacturer. Labeled cRNA yield and purity were determined by measuring the absorbance at 260 and 280 nm using Nanodrop ND-1000 spectrophotometer.
| | Sample_hyb_protocol | Fifteen micrograms of labeled cRNA from EOM synapse was fragmented, and 10μg was hybridized to Affymetrix® Rat 230 ver 2.0 GeneChip arrays for 18–24h (Affymetrix Inc.). Genechip was washed and stained with streptavidin–phycoerythrin.
| | Sample_scan_protocol | The chip was scanned at a 6μm resolution with Agilent model G2500A GeneArray scanner. A visual quality control measurement was performed to ensure proper hybridization after each chip was scanned.
| | Sample_data_processing | Quality control parameters such as scaling factors used to normalize the chips, average background, and noise were also evaluated. In addition, raw intensities for each probe set were stored in electronic formats by the GeneChip Operating System version 1.1 (GCOS1.1, Affymetrix Inc.).
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Murat,T,Budak
| | Sample_contact_email | mtbudak@mail.med.upenn.edu
| | Sample_contact_phone | 215-8989726
| | Sample_contact_laboratory | Rubinstein and Khurana Labs
| | Sample_contact_department |
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address |
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM393nnn/GSM393935/suppl/GSM393935.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM393nnn/GSM393935/suppl/GSM393935.CHP.gz
| | Sample_series_id | GSE15737
| | Sample_data_row_count | 31099
| | |
|
GSM393936 | GPL1355 |
|
TA 15 synapse
|
tibialis anterior muscle synapse
|
tissue: tibialis anterior muscle
cellular location: neuromuscular junction
|
TA synapse was captured by LCM.
|
| Sample_geo_accession | GSM393936
| | Sample_status | Public on Apr 16 2010
| | Sample_submission_date | Apr 18 2009
| | Sample_last_update_date | Apr 23 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated and purified from each captured set by RNeasy micro kit (Qiagen, Valencia, CA) as described by manufacturer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | All total RNAs from EOM and TA synapse as well as EOM and TA fiber were used to generate double-stranded cDNA with the T7-oligo (dT) primer according to the GeneChip® Two cycle target labeling protocol (Affymetrix Inc., Santa Clara, CA, USA) as described by the manufacturer. At the end of the first cycle linear amplification, all amplified RNAs (i.e, aRNAs) were normalized to 600 ng (260/280 ratio ranging from 2.0-2.3) for the next amplification and labeling steps. Two rounds of in vitro transcription were performed as described by manufacturer. Labeled cRNA yield and purity were determined by measuring the absorbance at 260 and 280 nm using Nanodrop ND-1000 spectrophotometer.
| | Sample_hyb_protocol | Fifteen micrograms of labeled cRNA from TA synapse was fragmented, and 10μg was hybridized to Affymetrix® Rat 230 ver 2.0 GeneChip arrays for 18–24h (Affymetrix Inc.). Genechip was washed and stained with streptavidin–phycoerythrin.
| | Sample_scan_protocol | The chip was scanned at a 6μm resolution with Agilent model G2500A GeneArray scanner. A visual quality control measurement was performed to ensure proper hybridization after each chip was scanned.
| | Sample_data_processing | Quality control parameters such as scaling factors used to normalize the chips, average background, and noise were also evaluated. In addition, raw intensities for each probe set were stored in electronic formats by the GeneChip Operating System version 1.1 (GCOS1.1, Affymetrix Inc.).
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Murat,T,Budak
| | Sample_contact_email | mtbudak@mail.med.upenn.edu
| | Sample_contact_phone | 215-8989726
| | Sample_contact_laboratory | Rubinstein and Khurana Labs
| | Sample_contact_department |
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address |
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM393nnn/GSM393936/suppl/GSM393936.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM393nnn/GSM393936/suppl/GSM393936.CHP.gz
| | Sample_series_id | GSE15737
| | Sample_data_row_count | 31099
| | |
|
GSM393937 | GPL1355 |
|
TA 25 synapse
|
tibialis anterior muscle synapse
|
tissue: tibialis anterior muscle
cellular location: neuromuscular junction
|
TA synapse was captured by LCM.
|
| Sample_geo_accession | GSM393937
| | Sample_status | Public on Apr 16 2010
| | Sample_submission_date | Apr 18 2009
| | Sample_last_update_date | Apr 23 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated and purified from each captured set by RNeasy micro kit (Qiagen, Valencia, CA) as described by manufacturer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | All total RNAs from EOM and TA synapse as well as EOM and TA fiber were used to generate double-stranded cDNA with the T7-oligo (dT) primer according to the GeneChip® Two cycle target labeling protocol (Affymetrix Inc., Santa Clara, CA, USA) as described by the manufacturer. At the end of the first cycle linear amplification, all amplified RNAs (i.e, aRNAs) were normalized to 600 ng (260/280 ratio ranging from 2.0-2.3) for the next amplification and labeling steps. Two rounds of in vitro transcription were performed as described by manufacturer. Labeled cRNA yield and purity were determined by measuring the absorbance at 260 and 280 nm using Nanodrop ND-1000 spectrophotometer.
| | Sample_hyb_protocol | Fifteen micrograms of labeled cRNA from TA synapse was fragmented, and 10μg was hybridized to Affymetrix® Rat 230 ver 2.0 GeneChip arrays for 18–24h (Affymetrix Inc.). Genechip was washed and stained with streptavidin–phycoerythrin.
| | Sample_scan_protocol | The chip was scanned at a 6μm resolution with Agilent model G2500A GeneArray scanner. A visual quality control measurement was performed to ensure proper hybridization after each chip was scanned.
| | Sample_data_processing | Quality control parameters such as scaling factors used to normalize the chips, average background, and noise were also evaluated. In addition, raw intensities for each probe set were stored in electronic formats by the GeneChip Operating System version 1.1 (GCOS1.1, Affymetrix Inc.).
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Murat,T,Budak
| | Sample_contact_email | mtbudak@mail.med.upenn.edu
| | Sample_contact_phone | 215-8989726
| | Sample_contact_laboratory | Rubinstein and Khurana Labs
| | Sample_contact_department |
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address |
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM393nnn/GSM393937/suppl/GSM393937.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM393nnn/GSM393937/suppl/GSM393937.CHP.gz
| | Sample_series_id | GSE15737
| | Sample_data_row_count | 31099
| | |
|
GSM393938 | GPL1355 |
|
TA 27 synapse
|
tibialis anterior muscle synapse
|
tissue: tibialis anterior muscle
cellular location: neuromuscular junction
|
TA synapse was captured by LCM.
|
| Sample_geo_accession | GSM393938
| | Sample_status | Public on Apr 16 2010
| | Sample_submission_date | Apr 18 2009
| | Sample_last_update_date | Apr 23 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated and purified from each captured set by RNeasy micro kit (Qiagen, Valencia, CA) as described by manufacturer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | All total RNAs from EOM and TA synapse as well as EOM and TA fiber were used to generate double-stranded cDNA with the T7-oligo (dT) primer according to the GeneChip® Two cycle target labeling protocol (Affymetrix Inc., Santa Clara, CA, USA) as described by the manufacturer. At the end of the first cycle linear amplification, all amplified RNAs (i.e, aRNAs) were normalized to 600 ng (260/280 ratio ranging from 2.0-2.3) for the next amplification and labeling steps. Two rounds of in vitro transcription were performed as described by manufacturer. Labeled cRNA yield and purity were determined by measuring the absorbance at 260 and 280 nm using Nanodrop ND-1000 spectrophotometer.
| | Sample_hyb_protocol | Fifteen micrograms of labeled cRNA from TA synapse was fragmented, and 10μg was hybridized to Affymetrix® Rat 230 ver 2.0 GeneChip arrays for 18–24h (Affymetrix Inc.). Genechip was washed and stained with streptavidin–phycoerythrin.
| | Sample_scan_protocol | The chip was scanned at a 6μm resolution with Agilent model G2500A GeneArray scanner. A visual quality control measurement was performed to ensure proper hybridization after each chip was scanned.
| | Sample_data_processing | Quality control parameters such as scaling factors used to normalize the chips, average background, and noise were also evaluated. In addition, raw intensities for each probe set were stored in electronic formats by the GeneChip Operating System version 1.1 (GCOS1.1, Affymetrix Inc.).
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Murat,T,Budak
| | Sample_contact_email | mtbudak@mail.med.upenn.edu
| | Sample_contact_phone | 215-8989726
| | Sample_contact_laboratory | Rubinstein and Khurana Labs
| | Sample_contact_department |
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address |
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM393nnn/GSM393938/suppl/GSM393938.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM393nnn/GSM393938/suppl/GSM393938.CHP.gz
| | Sample_series_id | GSE15737
| | Sample_data_row_count | 31099
| | |
|
GSM393939 | GPL1355 |
|
TA 29 synapse
|
tibialis anterior muscle synapse
|
tissue: tibialis anterior muscle
cellular location: neuromuscular junction
|
TA synapse was captured by LCM.
|
| Sample_geo_accession | GSM393939
| | Sample_status | Public on Apr 16 2010
| | Sample_submission_date | Apr 18 2009
| | Sample_last_update_date | Apr 23 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated and purified from each captured set by RNeasy micro kit (Qiagen, Valencia, CA) as described by manufacturer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | All total RNAs from EOM and TA synapse as well as EOM and TA fiber were used to generate double-stranded cDNA with the T7-oligo (dT) primer according to the GeneChip® Two cycle target labeling protocol (Affymetrix Inc., Santa Clara, CA, USA) as described by the manufacturer. At the end of the first cycle linear amplification, all amplified RNAs (i.e, aRNAs) were normalized to 600 ng (260/280 ratio ranging from 2.0-2.3) for the next amplification and labeling steps. Two rounds of in vitro transcription were performed as described by manufacturer. Labeled cRNA yield and purity were determined by measuring the absorbance at 260 and 280 nm using Nanodrop ND-1000 spectrophotometer.
| | Sample_hyb_protocol | Fifteen micrograms of labeled cRNA from TA synapse was fragmented, and 10μg was hybridized to Affymetrix® Rat 230 ver 2.0 GeneChip arrays for 18–24h (Affymetrix Inc.). Genechip was washed and stained with streptavidin–phycoerythrin.
| | Sample_scan_protocol | The chip was scanned at a 6μm resolution with Agilent model G2500A GeneArray scanner. A visual quality control measurement was performed to ensure proper hybridization after each chip was scanned.
| | Sample_data_processing | Quality control parameters such as scaling factors used to normalize the chips, average background, and noise were also evaluated. In addition, raw intensities for each probe set were stored in electronic formats by the GeneChip Operating System version 1.1 (GCOS1.1, Affymetrix Inc.).
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Murat,T,Budak
| | Sample_contact_email | mtbudak@mail.med.upenn.edu
| | Sample_contact_phone | 215-8989726
| | Sample_contact_laboratory | Rubinstein and Khurana Labs
| | Sample_contact_department |
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address |
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM393nnn/GSM393939/suppl/GSM393939.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM393nnn/GSM393939/suppl/GSM393939.CHP.gz
| | Sample_series_id | GSE15737
| | Sample_data_row_count | 31099
| | |
|
| |
| |
Make groups for comparisons |
(2 groups will be compared at a time) |
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| Select GSMs and click on "Add groups" |
Enter the group name here: |
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