Search results for the GEO ID: GSE20666  |
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GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM518492 | GPL570 |
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DLBCL_CH1_Ctrl
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Diffuse large B-cell lymphoma line CH1, non-treated
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cell line: B-cell lymphoma CH1
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The formation of aberrant heterochromatic foci, coupled to abnormal enrichment of adjacent 2p sequences in repressive heterochromatin marks (H4K20me3, H3K9me3 and HP1), delayed replication and repositioning of the rearranged chromosome 2 to the nuclear periphery, could be associated to altered gene expression of at least those genes brought into close proximity to heterochromatin. To assess this question, global gene expression profiling was performed in the lymphoma B cells presenting the aberrant heterochromatin foci (CH1), treated or not with the histone deacetylase inhibitor, trichostatin A.
This control DLBCL_CH1 sample was compared to a Trichostatin A treated sample.
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| Sample_geo_accession | GSM518492
| | Sample_status | Public on Mar 10 2010
| | Sample_submission_date | Mar 06 2010
| | Sample_last_update_date | Mar 09 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | No treatment
| | Sample_growth_protocol_ch1 | The diffuse large B-cell lymphoma line CH1was cultivated at 37°C in a humidified 5% CO2 atmosphere, in RPMI 1640 medium supplemented with 10% human AB+ serum, 100 µg/ml penicillin-streptomycin, 1.4 mM sodium pyruvate and 1.4 mM non-essential amino acids (Life Technologies, Grand Island, NY, USA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the TRIzol reagent (Invitrogen Life Technologies), quality controlled by using the Agilent Bioanalyzer system and quantified, prior to labelling, by NanoDrop (Thermo Scientific).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was amplified with double in vitro transcription and hybridized to the Affymetrix HG U133 Plus 2.0 microarrays, according to the manufacturer’s instructions (Affymetrix, Santa Clara, CA, USA).
| | Sample_hyb_protocol | Hybridization and washing was carried out on a GeneChip (Affymetrix) station, washing according to the manufacturer’s protocol.
| | Sample_scan_protocol | Scann carried out on a GeneChip (Affymetrix) station (7G Scanner) according to the manufacturer’s protocol.
| | Sample_data_processing | Data were analyzed with the GCOS 1.2 software (Affymetrix), using the default analysis settings and global scaling as normalization method, with a trimmed mean target intensity value (TGT) of each array arbitrarily set to 100.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Mary,Bridgid,Callanan
| | Sample_contact_email | mary.callanan@ujf-grenoble.fr
| | Sample_contact_laboratory | Team 7 "Oncogenic pathways in the hematological malignancies"
| | Sample_contact_department | Cell differentiation and transformation
| | Sample_contact_institute | INSERM-UJF U823, Institut Albert Bonniot
| | Sample_contact_address | Rond point de la Chantourne, La Tronche
| | Sample_contact_city | Grenoble
| | Sample_contact_zip/postal_code | F-38706
| | Sample_contact_country | France
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM518nnn/GSM518492/suppl/GSM518492.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM518nnn/GSM518492/suppl/GSM518492.CHP.gz
| | Sample_series_id | GSE20666
| | Sample_data_row_count | 54675
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GSM518493 | GPL570 |
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DLBCL_CH1_TSA
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Diffuse large B-cell lymphoma line CH1, Trichostatin A-treated
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cell line: B-cell lymphoma CH1
|
The formation of aberrant heterochromatic foci, coupled to abnormal enrichment of adjacent 2p sequences in repressive heterochromatin marks (H4K20me3, H3K9me3 and HP1), delayed replication and repositioning of the rearranged chromosome 2 to the nuclear periphery, could be associated to altered gene expression of at least those genes brought into close proximity to heterochromatin. To assess this question, global gene expression profiling was performed in the lymphoma B cells presenting the aberrant heterochromatin foci (CH1), treated or not with the histone deacetylase inhibitor, trichostatin A.
This TSA-treated DLBCL_CH1 sample was compared to a non-treated sample.
|
| Sample_geo_accession | GSM518493
| | Sample_status | Public on Mar 10 2010
| | Sample_submission_date | Mar 06 2010
| | Sample_last_update_date | Mar 09 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Trichostatin A-treated: 50 ng/mL during 6 hours
| | Sample_growth_protocol_ch1 | The diffuse large B-cell lymphoma line CH1was cultivated at 37°C in a humidified 5% CO2 atmosphere, in RPMI 1640 medium supplemented with 10% human AB+ serum, 100 µg/ml penicillin-streptomycin, 1.4 mM sodium pyruvate and 1.4 mM non-essential amino acids (Life Technologies, Grand Island, NY, USA). Six hours before lysing the cells, trichostatin A was added to the culture medium at a concentration of 50 ng/mL.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the TRIzol reagent (Invitrogen Life Technologies), quality controlled by using the Agilent Bioanalyzer system and quantified, prior to labelling, by NanoDrop (Thermo Scientific).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was amplified with double in vitro transcription and hybridized to the Affymetrix HG U133 Plus 2.0 microarrays, according to the manufacturer’s instructions (Affymetrix, Santa Clara, CA, USA).
| | Sample_hyb_protocol | Hybridization and washing was carried out on a GeneChip (Affymetrix) station, washing according to the manufacturer’s protocol.
| | Sample_scan_protocol | Scann carried out on a GeneChip (Affymetrix) station (7G Scanner) according to the manufacturer’s protocol.
| | Sample_data_processing | Data were analyzed with the GCOS 1.2 software (Affymetrix), using the default analysis settings and global scaling as normalization method, with a trimmed mean target intensity value (TGT) of each array arbitrarily set to 100.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Mary,Bridgid,Callanan
| | Sample_contact_email | mary.callanan@ujf-grenoble.fr
| | Sample_contact_laboratory | Team 7 "Oncogenic pathways in the hematological malignancies"
| | Sample_contact_department | Cell differentiation and transformation
| | Sample_contact_institute | INSERM-UJF U823, Institut Albert Bonniot
| | Sample_contact_address | Rond point de la Chantourne, La Tronche
| | Sample_contact_city | Grenoble
| | Sample_contact_zip/postal_code | F-38706
| | Sample_contact_country | France
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM518nnn/GSM518493/suppl/GSM518493.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM518nnn/GSM518493/suppl/GSM518493.CHP.gz
| | Sample_series_id | GSE20666
| | Sample_data_row_count | 54675
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