Search results for the GEO ID: GSE31776  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM788372 | GPL1261 |
|
LLC-TDAG8 cells before treatment
|
Lewis lung carcinoma (LLC) cells
|
strain: C57BL/6
cell type: TDAG8-LLC
ph: n/a
time point: 0
|
|
| Sample_geo_accession | GSM788372
| | Sample_status | Public on Nov 01 2012
| | Sample_submission_date | Aug 31 2011
| | Sample_last_update_date | Nov 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | After 12-h serum starvation, cells were treated with 0.1% BSA/DMEM at pH 6.4 or 7.4 for 4 or 12 h.
| | Sample_growth_protocol_ch1 | TDAG8-LLC or control LLC cells were seeded onto 6-cm dishes at 5 × 10e5 cells/dish. On the next day, the medium was replaced with 0.1% BSA/DMEM at pH 7.4.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA samples were extracted using RNeasy kit (QIAGEN) according to the manufacturer’s instructions
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | 2 µg of total RNA was reverse transcribed using the SuperScript II system for cDNA synthesis (Invitrogen) according to the protocol recommended by Affymetrix. The oligonucleotide used for priming was 5’-ggccagtgaattgtaatacgactcactatagggaggcgg-(t)24-3’ (Affymetrix). Double-stranded cDNA was cleaned up by using the GeneChip® Sample Cleanup Module (Affymetrix). In vitro transcription was performed on all of cDNA using the GeneChip® IVT Labeling Kit (Affymetrix). The cRNA was cleaned up by using RNeasy Mini spin column (QIAGEN). The cRNA was fragmented by heating in 40 mM Tris-acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc.
| | Sample_hyb_protocol | 10 µg of fragmented cRNA were hybridized (45°C, 16 hours). Hybridization was controled by adding cRNA cocktail (BioC, BioD, Cre) mixed as described in previous versions of the Expression Analysis Technical Manual. Washing and staining was performed in a Fluidics Station 450 (Affymetrix) using the protocol EukGE-WS2v5.
| | Sample_scan_protocol | Scanning was performed in an Affymetrix GeneChip® Scanner 3000.
| | Sample_data_processing | Global Normalization and Scaling have been applied by the Affymetrix GeneChip® Operating Software v1.4.
| | Sample_data_processing | The scan values were normalized to make its average equal to 100.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Satoshi,,Ishii
| | Sample_contact_email | mame@m.u-tokyo.ac.jp
| | Sample_contact_phone | +81-3-5082-2925
| | Sample_contact_fax | +81-3-3813-8732
| | Sample_contact_department | Department of Biochem. & Mol. Biol.
| | Sample_contact_institute | The University of Tokyo
| | Sample_contact_address | 7-3-1 Hongo, Bunkyo
| | Sample_contact_city | Tokyo
| | Sample_contact_zip/postal_code | 113-0033
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM788nnn/GSM788372/suppl/GSM788372.CEL.gz
| | Sample_series_id | GSE31776
| | Sample_data_row_count | 45101
| | |
|
GSM788373 | GPL1261 |
|
LLC-TDAG8 cells at pH 6.4 for 4 hr
|
Lewis lung carcinoma (LLC) cells
|
strain: C57BL/6
cell type: TDAG8-LLC
ph: at pH 6.4
time point: 4 hr
|
|
| Sample_geo_accession | GSM788373
| | Sample_status | Public on Nov 01 2012
| | Sample_submission_date | Aug 31 2011
| | Sample_last_update_date | Nov 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | After 12-h serum starvation, cells were treated with 0.1% BSA/DMEM at pH 6.4 or 7.4 for 4 or 12 h.
| | Sample_growth_protocol_ch1 | TDAG8-LLC or control LLC cells were seeded onto 6-cm dishes at 5 × 10e5 cells/dish. On the next day, the medium was replaced with 0.1% BSA/DMEM at pH 7.4.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA samples were extracted using RNeasy kit (QIAGEN) according to the manufacturer’s instructions
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | 2 µg of total RNA was reverse transcribed using the SuperScript II system for cDNA synthesis (Invitrogen) according to the protocol recommended by Affymetrix. The oligonucleotide used for priming was 5’-ggccagtgaattgtaatacgactcactatagggaggcgg-(t)24-3’ (Affymetrix). Double-stranded cDNA was cleaned up by using the GeneChip® Sample Cleanup Module (Affymetrix). In vitro transcription was performed on all of cDNA using the GeneChip® IVT Labeling Kit (Affymetrix). The cRNA was cleaned up by using RNeasy Mini spin column (QIAGEN). The cRNA was fragmented by heating in 40 mM Tris-acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc.
| | Sample_hyb_protocol | 10 µg of fragmented cRNA were hybridized (45°C, 16 hours). Hybridization was controled by adding cRNA cocktail (BioC, BioD, Cre) mixed as described in previous versions of the Expression Analysis Technical Manual. Washing and staining was performed in a Fluidics Station 450 (Affymetrix) using the protocol EukGE-WS2v5.
| | Sample_scan_protocol | Scanning was performed in an Affymetrix GeneChip® Scanner 3000.
| | Sample_data_processing | Global Normalization and Scaling have been applied by the Affymetrix GeneChip® Operating Software v1.4.
| | Sample_data_processing | The scan values were normalized to make its average equal to 100.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Satoshi,,Ishii
| | Sample_contact_email | mame@m.u-tokyo.ac.jp
| | Sample_contact_phone | +81-3-5082-2925
| | Sample_contact_fax | +81-3-3813-8732
| | Sample_contact_department | Department of Biochem. & Mol. Biol.
| | Sample_contact_institute | The University of Tokyo
| | Sample_contact_address | 7-3-1 Hongo, Bunkyo
| | Sample_contact_city | Tokyo
| | Sample_contact_zip/postal_code | 113-0033
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM788nnn/GSM788373/suppl/GSM788373.CEL.gz
| | Sample_series_id | GSE31776
| | Sample_data_row_count | 45101
| | |
|
GSM788374 | GPL1261 |
|
LLC-TDAG8 cells at pH 6.4 for 12 hr
|
Lewis lung carcinoma (LLC) cells
|
strain: C57BL/6
cell type: TDAG8-LLC
ph: at pH 6.4
time point: 12 hr
|
|
| Sample_geo_accession | GSM788374
| | Sample_status | Public on Nov 01 2012
| | Sample_submission_date | Aug 31 2011
| | Sample_last_update_date | Nov 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | After 12-h serum starvation, cells were treated with 0.1% BSA/DMEM at pH 6.4 or 7.4 for 4 or 12 h.
| | Sample_growth_protocol_ch1 | TDAG8-LLC or control LLC cells were seeded onto 6-cm dishes at 5 × 10e5 cells/dish. On the next day, the medium was replaced with 0.1% BSA/DMEM at pH 7.4.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA samples were extracted using RNeasy kit (QIAGEN) according to the manufacturer’s instructions
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | 2 µg of total RNA was reverse transcribed using the SuperScript II system for cDNA synthesis (Invitrogen) according to the protocol recommended by Affymetrix. The oligonucleotide used for priming was 5’-ggccagtgaattgtaatacgactcactatagggaggcgg-(t)24-3’ (Affymetrix). Double-stranded cDNA was cleaned up by using the GeneChip® Sample Cleanup Module (Affymetrix). In vitro transcription was performed on all of cDNA using the GeneChip® IVT Labeling Kit (Affymetrix). The cRNA was cleaned up by using RNeasy Mini spin column (QIAGEN). The cRNA was fragmented by heating in 40 mM Tris-acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc.
| | Sample_hyb_protocol | 10 µg of fragmented cRNA were hybridized (45°C, 16 hours). Hybridization was controled by adding cRNA cocktail (BioC, BioD, Cre) mixed as described in previous versions of the Expression Analysis Technical Manual. Washing and staining was performed in a Fluidics Station 450 (Affymetrix) using the protocol EukGE-WS2v5.
| | Sample_scan_protocol | Scanning was performed in an Affymetrix GeneChip® Scanner 3000.
| | Sample_data_processing | Global Normalization and Scaling have been applied by the Affymetrix GeneChip® Operating Software v1.4.
| | Sample_data_processing | The scan values were normalized to make its average equal to 100.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Satoshi,,Ishii
| | Sample_contact_email | mame@m.u-tokyo.ac.jp
| | Sample_contact_phone | +81-3-5082-2925
| | Sample_contact_fax | +81-3-3813-8732
| | Sample_contact_department | Department of Biochem. & Mol. Biol.
| | Sample_contact_institute | The University of Tokyo
| | Sample_contact_address | 7-3-1 Hongo, Bunkyo
| | Sample_contact_city | Tokyo
| | Sample_contact_zip/postal_code | 113-0033
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM788nnn/GSM788374/suppl/GSM788374.CEL.gz
| | Sample_series_id | GSE31776
| | Sample_data_row_count | 45101
| | |
|
GSM788375 | GPL1261 |
|
LLC-TDAG8 cells at pH 7.4 for 4 hr
|
Lewis lung carcinoma (LLC) cells
|
strain: C57BL/6
cell type: TDAG8-LLC
ph: at pH 7.4
time point: 4 hr
|
|
| Sample_geo_accession | GSM788375
| | Sample_status | Public on Nov 01 2012
| | Sample_submission_date | Aug 31 2011
| | Sample_last_update_date | Nov 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | After 12-h serum starvation, cells were treated with 0.1% BSA/DMEM at pH 6.4 or 7.4 for 4 or 12 h.
| | Sample_growth_protocol_ch1 | TDAG8-LLC or control LLC cells were seeded onto 6-cm dishes at 5 × 10e5 cells/dish. On the next day, the medium was replaced with 0.1% BSA/DMEM at pH 7.4.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA samples were extracted using RNeasy kit (QIAGEN) according to the manufacturer’s instructions
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | 2 µg of total RNA was reverse transcribed using the SuperScript II system for cDNA synthesis (Invitrogen) according to the protocol recommended by Affymetrix. The oligonucleotide used for priming was 5’-ggccagtgaattgtaatacgactcactatagggaggcgg-(t)24-3’ (Affymetrix). Double-stranded cDNA was cleaned up by using the GeneChip® Sample Cleanup Module (Affymetrix). In vitro transcription was performed on all of cDNA using the GeneChip® IVT Labeling Kit (Affymetrix). The cRNA was cleaned up by using RNeasy Mini spin column (QIAGEN). The cRNA was fragmented by heating in 40 mM Tris-acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc.
| | Sample_hyb_protocol | 10 µg of fragmented cRNA were hybridized (45°C, 16 hours). Hybridization was controled by adding cRNA cocktail (BioC, BioD, Cre) mixed as described in previous versions of the Expression Analysis Technical Manual. Washing and staining was performed in a Fluidics Station 450 (Affymetrix) using the protocol EukGE-WS2v5.
| | Sample_scan_protocol | Scanning was performed in an Affymetrix GeneChip® Scanner 3000.
| | Sample_data_processing | Global Normalization and Scaling have been applied by the Affymetrix GeneChip® Operating Software v1.4.
| | Sample_data_processing | The scan values were normalized to make its average equal to 100.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Satoshi,,Ishii
| | Sample_contact_email | mame@m.u-tokyo.ac.jp
| | Sample_contact_phone | +81-3-5082-2925
| | Sample_contact_fax | +81-3-3813-8732
| | Sample_contact_department | Department of Biochem. & Mol. Biol.
| | Sample_contact_institute | The University of Tokyo
| | Sample_contact_address | 7-3-1 Hongo, Bunkyo
| | Sample_contact_city | Tokyo
| | Sample_contact_zip/postal_code | 113-0033
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM788nnn/GSM788375/suppl/GSM788375.CEL.gz
| | Sample_series_id | GSE31776
| | Sample_data_row_count | 45101
| | |
|
GSM788376 | GPL1261 |
|
LLC-TDAG8 cells at pH 7.4 for 12 hr
|
Lewis lung carcinoma (LLC) cells
|
strain: C57BL/6
cell type: TDAG8-LLC
ph: at pH 7.4
time point: 12 hr
|
|
| Sample_geo_accession | GSM788376
| | Sample_status | Public on Nov 01 2012
| | Sample_submission_date | Aug 31 2011
| | Sample_last_update_date | Nov 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | After 12-h serum starvation, cells were treated with 0.1% BSA/DMEM at pH 6.4 or 7.4 for 4 or 12 h.
| | Sample_growth_protocol_ch1 | TDAG8-LLC or control LLC cells were seeded onto 6-cm dishes at 5 × 10e5 cells/dish. On the next day, the medium was replaced with 0.1% BSA/DMEM at pH 7.4.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA samples were extracted using RNeasy kit (QIAGEN) according to the manufacturer’s instructions
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | 2 µg of total RNA was reverse transcribed using the SuperScript II system for cDNA synthesis (Invitrogen) according to the protocol recommended by Affymetrix. The oligonucleotide used for priming was 5’-ggccagtgaattgtaatacgactcactatagggaggcgg-(t)24-3’ (Affymetrix). Double-stranded cDNA was cleaned up by using the GeneChip® Sample Cleanup Module (Affymetrix). In vitro transcription was performed on all of cDNA using the GeneChip® IVT Labeling Kit (Affymetrix). The cRNA was cleaned up by using RNeasy Mini spin column (QIAGEN). The cRNA was fragmented by heating in 40 mM Tris-acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc.
| | Sample_hyb_protocol | 10 µg of fragmented cRNA were hybridized (45°C, 16 hours). Hybridization was controled by adding cRNA cocktail (BioC, BioD, Cre) mixed as described in previous versions of the Expression Analysis Technical Manual. Washing and staining was performed in a Fluidics Station 450 (Affymetrix) using the protocol EukGE-WS2v5.
| | Sample_scan_protocol | Scanning was performed in an Affymetrix GeneChip® Scanner 3000.
| | Sample_data_processing | Global Normalization and Scaling have been applied by the Affymetrix GeneChip® Operating Software v1.4.
| | Sample_data_processing | The scan values were normalized to make its average equal to 100.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Satoshi,,Ishii
| | Sample_contact_email | mame@m.u-tokyo.ac.jp
| | Sample_contact_phone | +81-3-5082-2925
| | Sample_contact_fax | +81-3-3813-8732
| | Sample_contact_department | Department of Biochem. & Mol. Biol.
| | Sample_contact_institute | The University of Tokyo
| | Sample_contact_address | 7-3-1 Hongo, Bunkyo
| | Sample_contact_city | Tokyo
| | Sample_contact_zip/postal_code | 113-0033
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM788nnn/GSM788376/suppl/GSM788376.CEL.gz
| | Sample_series_id | GSE31776
| | Sample_data_row_count | 45101
| | |
|
GSM788377 | GPL1261 |
|
Control LLC cells before treatment
|
Lewis lung carcinoma (LLC) cells
|
strain: C57BL/6
cell type: control LLC
ph: n/a
time point: 0
|
|
| Sample_geo_accession | GSM788377
| | Sample_status | Public on Nov 01 2012
| | Sample_submission_date | Aug 31 2011
| | Sample_last_update_date | Nov 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | After 12-h serum starvation, cells were treated with 0.1% BSA/DMEM at pH 6.4 or 7.4 for 4 or 12 h.
| | Sample_growth_protocol_ch1 | TDAG8-LLC or control LLC cells were seeded onto 6-cm dishes at 5 × 10e5 cells/dish. On the next day, the medium was replaced with 0.1% BSA/DMEM at pH 7.4.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA samples were extracted using RNeasy kit (QIAGEN) according to the manufacturer’s instructions
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | 2 µg of total RNA was reverse transcribed using the SuperScript II system for cDNA synthesis (Invitrogen) according to the protocol recommended by Affymetrix. The oligonucleotide used for priming was 5’-ggccagtgaattgtaatacgactcactatagggaggcgg-(t)24-3’ (Affymetrix). Double-stranded cDNA was cleaned up by using the GeneChip® Sample Cleanup Module (Affymetrix). In vitro transcription was performed on all of cDNA using the GeneChip® IVT Labeling Kit (Affymetrix). The cRNA was cleaned up by using RNeasy Mini spin column (QIAGEN). The cRNA was fragmented by heating in 40 mM Tris-acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc.
| | Sample_hyb_protocol | 10 µg of fragmented cRNA were hybridized (45°C, 16 hours). Hybridization was controled by adding cRNA cocktail (BioC, BioD, Cre) mixed as described in previous versions of the Expression Analysis Technical Manual. Washing and staining was performed in a Fluidics Station 450 (Affymetrix) using the protocol EukGE-WS2v5.
| | Sample_scan_protocol | Scanning was performed in an Affymetrix GeneChip® Scanner 3000.
| | Sample_data_processing | Global Normalization and Scaling have been applied by the Affymetrix GeneChip® Operating Software v1.4.
| | Sample_data_processing | The scan values were normalized to make its average equal to 100.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Satoshi,,Ishii
| | Sample_contact_email | mame@m.u-tokyo.ac.jp
| | Sample_contact_phone | +81-3-5082-2925
| | Sample_contact_fax | +81-3-3813-8732
| | Sample_contact_department | Department of Biochem. & Mol. Biol.
| | Sample_contact_institute | The University of Tokyo
| | Sample_contact_address | 7-3-1 Hongo, Bunkyo
| | Sample_contact_city | Tokyo
| | Sample_contact_zip/postal_code | 113-0033
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM788nnn/GSM788377/suppl/GSM788377.CEL.gz
| | Sample_series_id | GSE31776
| | Sample_data_row_count | 45101
| | |
|
GSM788378 | GPL1261 |
|
Control LLC cells at pH 6.4 for 4 hr
|
Lewis lung carcinoma (LLC) cells
|
strain: C57BL/6
cell type: control LLC
ph: at pH 6.4
time point: 4 hr
|
|
| Sample_geo_accession | GSM788378
| | Sample_status | Public on Nov 01 2012
| | Sample_submission_date | Aug 31 2011
| | Sample_last_update_date | Nov 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | After 12-h serum starvation, cells were treated with 0.1% BSA/DMEM at pH 6.4 or 7.4 for 4 or 12 h.
| | Sample_growth_protocol_ch1 | TDAG8-LLC or control LLC cells were seeded onto 6-cm dishes at 5 × 10e5 cells/dish. On the next day, the medium was replaced with 0.1% BSA/DMEM at pH 7.4.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA samples were extracted using RNeasy kit (QIAGEN) according to the manufacturer’s instructions
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | 2 µg of total RNA was reverse transcribed using the SuperScript II system for cDNA synthesis (Invitrogen) according to the protocol recommended by Affymetrix. The oligonucleotide used for priming was 5’-ggccagtgaattgtaatacgactcactatagggaggcgg-(t)24-3’ (Affymetrix). Double-stranded cDNA was cleaned up by using the GeneChip® Sample Cleanup Module (Affymetrix). In vitro transcription was performed on all of cDNA using the GeneChip® IVT Labeling Kit (Affymetrix). The cRNA was cleaned up by using RNeasy Mini spin column (QIAGEN). The cRNA was fragmented by heating in 40 mM Tris-acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc.
| | Sample_hyb_protocol | 10 µg of fragmented cRNA were hybridized (45°C, 16 hours). Hybridization was controled by adding cRNA cocktail (BioC, BioD, Cre) mixed as described in previous versions of the Expression Analysis Technical Manual. Washing and staining was performed in a Fluidics Station 450 (Affymetrix) using the protocol EukGE-WS2v5.
| | Sample_scan_protocol | Scanning was performed in an Affymetrix GeneChip® Scanner 3000.
| | Sample_data_processing | Global Normalization and Scaling have been applied by the Affymetrix GeneChip® Operating Software v1.4.
| | Sample_data_processing | The scan values were normalized to make its average equal to 100.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Satoshi,,Ishii
| | Sample_contact_email | mame@m.u-tokyo.ac.jp
| | Sample_contact_phone | +81-3-5082-2925
| | Sample_contact_fax | +81-3-3813-8732
| | Sample_contact_department | Department of Biochem. & Mol. Biol.
| | Sample_contact_institute | The University of Tokyo
| | Sample_contact_address | 7-3-1 Hongo, Bunkyo
| | Sample_contact_city | Tokyo
| | Sample_contact_zip/postal_code | 113-0033
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM788nnn/GSM788378/suppl/GSM788378.CEL.gz
| | Sample_series_id | GSE31776
| | Sample_data_row_count | 45101
| | |
|
GSM788379 | GPL1261 |
|
Control LLC cells at pH 6.4 for 12 hr
|
Lewis lung carcinoma (LLC) cells
|
strain: C57BL/6
cell type: control LLC
ph: at pH 6.4
time point: 12 hr
|
|
| Sample_geo_accession | GSM788379
| | Sample_status | Public on Nov 01 2012
| | Sample_submission_date | Aug 31 2011
| | Sample_last_update_date | Nov 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | After 12-h serum starvation, cells were treated with 0.1% BSA/DMEM at pH 6.4 or 7.4 for 4 or 12 h.
| | Sample_growth_protocol_ch1 | TDAG8-LLC or control LLC cells were seeded onto 6-cm dishes at 5 × 10e5 cells/dish. On the next day, the medium was replaced with 0.1% BSA/DMEM at pH 7.4.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA samples were extracted using RNeasy kit (QIAGEN) according to the manufacturer’s instructions
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | 2 µg of total RNA was reverse transcribed using the SuperScript II system for cDNA synthesis (Invitrogen) according to the protocol recommended by Affymetrix. The oligonucleotide used for priming was 5’-ggccagtgaattgtaatacgactcactatagggaggcgg-(t)24-3’ (Affymetrix). Double-stranded cDNA was cleaned up by using the GeneChip® Sample Cleanup Module (Affymetrix). In vitro transcription was performed on all of cDNA using the GeneChip® IVT Labeling Kit (Affymetrix). The cRNA was cleaned up by using RNeasy Mini spin column (QIAGEN). The cRNA was fragmented by heating in 40 mM Tris-acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc.
| | Sample_hyb_protocol | 10 µg of fragmented cRNA were hybridized (45°C, 16 hours). Hybridization was controled by adding cRNA cocktail (BioC, BioD, Cre) mixed as described in previous versions of the Expression Analysis Technical Manual. Washing and staining was performed in a Fluidics Station 450 (Affymetrix) using the protocol EukGE-WS2v5.
| | Sample_scan_protocol | Scanning was performed in an Affymetrix GeneChip® Scanner 3000.
| | Sample_data_processing | Global Normalization and Scaling have been applied by the Affymetrix GeneChip® Operating Software v1.4.
| | Sample_data_processing | The scan values were normalized to make its average equal to 100.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Satoshi,,Ishii
| | Sample_contact_email | mame@m.u-tokyo.ac.jp
| | Sample_contact_phone | +81-3-5082-2925
| | Sample_contact_fax | +81-3-3813-8732
| | Sample_contact_department | Department of Biochem. & Mol. Biol.
| | Sample_contact_institute | The University of Tokyo
| | Sample_contact_address | 7-3-1 Hongo, Bunkyo
| | Sample_contact_city | Tokyo
| | Sample_contact_zip/postal_code | 113-0033
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM788nnn/GSM788379/suppl/GSM788379.CEL.gz
| | Sample_series_id | GSE31776
| | Sample_data_row_count | 45101
| | |
|
GSM788380 | GPL1261 |
|
Control LLC cells at pH 7.4 for 4 hr
|
Lewis lung carcinoma (LLC) cells
|
strain: C57BL/6
cell type: control LLC
ph: at pH 7.4
time point: 4 hr
|
|
| Sample_geo_accession | GSM788380
| | Sample_status | Public on Nov 01 2012
| | Sample_submission_date | Aug 31 2011
| | Sample_last_update_date | Nov 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | After 12-h serum starvation, cells were treated with 0.1% BSA/DMEM at pH 6.4 or 7.4 for 4 or 12 h.
| | Sample_growth_protocol_ch1 | TDAG8-LLC or control LLC cells were seeded onto 6-cm dishes at 5 × 10e5 cells/dish. On the next day, the medium was replaced with 0.1% BSA/DMEM at pH 7.4.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA samples were extracted using RNeasy kit (QIAGEN) according to the manufacturer’s instructions
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | 2 µg of total RNA was reverse transcribed using the SuperScript II system for cDNA synthesis (Invitrogen) according to the protocol recommended by Affymetrix. The oligonucleotide used for priming was 5’-ggccagtgaattgtaatacgactcactatagggaggcgg-(t)24-3’ (Affymetrix). Double-stranded cDNA was cleaned up by using the GeneChip® Sample Cleanup Module (Affymetrix). In vitro transcription was performed on all of cDNA using the GeneChip® IVT Labeling Kit (Affymetrix). The cRNA was cleaned up by using RNeasy Mini spin column (QIAGEN). The cRNA was fragmented by heating in 40 mM Tris-acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc.
| | Sample_hyb_protocol | 10 µg of fragmented cRNA were hybridized (45°C, 16 hours). Hybridization was controled by adding cRNA cocktail (BioC, BioD, Cre) mixed as described in previous versions of the Expression Analysis Technical Manual. Washing and staining was performed in a Fluidics Station 450 (Affymetrix) using the protocol EukGE-WS2v5.
| | Sample_scan_protocol | Scanning was performed in an Affymetrix GeneChip® Scanner 3000.
| | Sample_data_processing | Global Normalization and Scaling have been applied by the Affymetrix GeneChip® Operating Software v1.4.
| | Sample_data_processing | The scan values were normalized to make its average equal to 100.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Satoshi,,Ishii
| | Sample_contact_email | mame@m.u-tokyo.ac.jp
| | Sample_contact_phone | +81-3-5082-2925
| | Sample_contact_fax | +81-3-3813-8732
| | Sample_contact_department | Department of Biochem. & Mol. Biol.
| | Sample_contact_institute | The University of Tokyo
| | Sample_contact_address | 7-3-1 Hongo, Bunkyo
| | Sample_contact_city | Tokyo
| | Sample_contact_zip/postal_code | 113-0033
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM788nnn/GSM788380/suppl/GSM788380.CEL.gz
| | Sample_series_id | GSE31776
| | Sample_data_row_count | 45101
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GSM788381 | GPL1261 |
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Control LLC cells at pH 7.4 for 12 hr
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Lewis lung carcinoma (LLC) cells
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strain: C57BL/6
cell type: control LLC
ph: at pH 7.4
time point: 12 hr
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|
| Sample_geo_accession | GSM788381
| | Sample_status | Public on Nov 01 2012
| | Sample_submission_date | Aug 31 2011
| | Sample_last_update_date | Nov 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | After 12-h serum starvation, cells were treated with 0.1% BSA/DMEM at pH 6.4 or 7.4 for 4 or 12 h.
| | Sample_growth_protocol_ch1 | TDAG8-LLC or control LLC cells were seeded onto 6-cm dishes at 5 × 10e5 cells/dish. On the next day, the medium was replaced with 0.1% BSA/DMEM at pH 7.4.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA samples were extracted using RNeasy kit (QIAGEN) according to the manufacturer’s instructions
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | 2 µg of total RNA was reverse transcribed using the SuperScript II system for cDNA synthesis (Invitrogen) according to the protocol recommended by Affymetrix. The oligonucleotide used for priming was 5’-ggccagtgaattgtaatacgactcactatagggaggcgg-(t)24-3’ (Affymetrix). Double-stranded cDNA was cleaned up by using the GeneChip® Sample Cleanup Module (Affymetrix). In vitro transcription was performed on all of cDNA using the GeneChip® IVT Labeling Kit (Affymetrix). The cRNA was cleaned up by using RNeasy Mini spin column (QIAGEN). The cRNA was fragmented by heating in 40 mM Tris-acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc.
| | Sample_hyb_protocol | 10 µg of fragmented cRNA were hybridized (45°C, 16 hours). Hybridization was controled by adding cRNA cocktail (BioC, BioD, Cre) mixed as described in previous versions of the Expression Analysis Technical Manual. Washing and staining was performed in a Fluidics Station 450 (Affymetrix) using the protocol EukGE-WS2v5.
| | Sample_scan_protocol | Scanning was performed in an Affymetrix GeneChip® Scanner 3000.
| | Sample_data_processing | Global Normalization and Scaling have been applied by the Affymetrix GeneChip® Operating Software v1.4.
| | Sample_data_processing | The scan values were normalized to make its average equal to 100.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Satoshi,,Ishii
| | Sample_contact_email | mame@m.u-tokyo.ac.jp
| | Sample_contact_phone | +81-3-5082-2925
| | Sample_contact_fax | +81-3-3813-8732
| | Sample_contact_department | Department of Biochem. & Mol. Biol.
| | Sample_contact_institute | The University of Tokyo
| | Sample_contact_address | 7-3-1 Hongo, Bunkyo
| | Sample_contact_city | Tokyo
| | Sample_contact_zip/postal_code | 113-0033
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM788nnn/GSM788381/suppl/GSM788381.CEL.gz
| | Sample_series_id | GSE31776
| | Sample_data_row_count | 45101
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