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Search results for the GEO ID: GSE29798

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GSM738385

GPL1261

Oct4GipES_Panct1_esiRNA_72h_rep1

Oct4-Gip ES cells, Panct1 RNAi, 72h post transfection

cell type: Oct4-Gip ES RNAi: Panct1 treatment time: 72h

Gene expression data from Oct4-Gip ES cells 72h after Panct1-esiRNA treatment.

Sample_geo_accession	GSM738385
Sample_status	Public on Feb 15 2012
Sample_submission_date	Jun 07 2011
Sample_last_update_date	Feb 16 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Oct4-Gip ES cells (60,000 cells in 2ml media) were reverse transfected in 6 well plates with 800ng esiRNAs, 2ul lipofectamine (Invitrogen) and 200ul Opti-MEM (Invitrogen). 72 hours after transfection, RNA was extracted as described above. In total, 6 arrays including 3 replicates of control (Luc) and 3 replicates of experiment (Panct1 knockdown) were processed and hybridized on the Mouse 430 version 2 Array (Affymetrix).
Sample_growth_protocol_ch1	ES cells (E14TG2a, R1/E, Oct4-Gip34) were cultured in Dulbecco’s Modified Eagle Medium (Invitrogen) supplemented with 4.5 g/l D Glucose and pyruvate, 10% fetal bovine Serum (Pan Sera), 30 uM 2-mercaptoethanol, 0.6X NEAA (Invitrogen), 300 units of Penicillin/Streptomycin (Invitrogen) and 8ng LIF (prepared in-house). Media was changed every day and ES cells were detached by treatment with Trypsin-EDTA (Invitrogen) and split every 2 days.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA from ES cells was extracted using RNeasy Mini Kit (QIAGEN) with DNAse I treatment. 1.5 ug of total RNA was reverse transcribed using Superscript III Reverse Transcriptase (Invitrogen) and a 1:1 mix of oligo(dT)12-18 primer (Invitrogen) and Random Hexamers (Applied Biosystems) according to manufacturer’s instructions. cDNA was diluted 1:5 in water and qPCR was performed with the SYBR Green qPCR kit (Abgene) on an MX P3000 qPCR machine (Stratagene). Dilution curves for primer efficiency were plotted and products were run on gel and sequence verified for the lncRNAs obtained as screen hits. For all qPCR measurements, Beta-2-microglobulin or GAPDH mRNA were used as housekeeping markers and all measurements were normalized to these controls.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA was synthesized with Perkin-Elmer's nucleotide analogs using the MEGAScript T7 kit (Ambion).
Sample_hyb_protocol	After fragmenting of the cRNA for target preparation using the standard Affymetrix protocol 15 µg fragmented cRNA was hybridized for 16 h at 45 °C to Mouse Genome 430 v. 2 array.
Sample_scan_protocol	Arrays were washed and stained with streptavidin-phycoerythrin in the Affymetrix Fluidics Station 400 and further scanned using the AFFYMETRIX GeneChip Scanner 3000 7G.
Sample_data_processing	The image data were analyzed with GCOS 1.4 using Affymetrix default analysis settings. Arrays have been quantile-normalize using the RMA algorithm.
Sample_platform_id	GPL1261
Sample_contact_name	Maciej,,Paszkowski-Rogacz
Sample_contact_laboratory	Buchholz
Sample_contact_institute	MPI-CBG
Sample_contact_address	Pfotenhauerstr. 108
Sample_contact_city	Dresden
Sample_contact_zip/postal_code	01307
Sample_contact_country	Germany
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM738nnn/GSM738385/suppl/GSM738385.CEL.gz
Sample_series_id	GSE29798
Sample_data_row_count	45101

GSM738386

GPL1261

Oct4GipES_Panct1_esiRNA_72h_rep2

Oct4-Gip ES cells, Panct1 RNAi, 72h post transfection

cell type: Oct4-Gip ES RNAi: Panct1 treatment time: 72h

Gene expression data from Oct4-Gip ES cells 72h after Panct1-esiRNA treatment.

Sample_geo_accession	GSM738386
Sample_status	Public on Feb 15 2012
Sample_submission_date	Jun 07 2011
Sample_last_update_date	Feb 16 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Oct4-Gip ES cells (60,000 cells in 2ml media) were reverse transfected in 6 well plates with 800ng esiRNAs, 2ul lipofectamine (Invitrogen) and 200ul Opti-MEM (Invitrogen). 72 hours after transfection, RNA was extracted as described above. In total, 6 arrays including 3 replicates of control (Luc) and 3 replicates of experiment (Panct1 knockdown) were processed and hybridized on the Mouse 430 version 2 Array (Affymetrix).
Sample_growth_protocol_ch1	ES cells (E14TG2a, R1/E, Oct4-Gip34) were cultured in Dulbecco’s Modified Eagle Medium (Invitrogen) supplemented with 4.5 g/l D Glucose and pyruvate, 10% fetal bovine Serum (Pan Sera), 30 uM 2-mercaptoethanol, 0.6X NEAA (Invitrogen), 300 units of Penicillin/Streptomycin (Invitrogen) and 8ng LIF (prepared in-house). Media was changed every day and ES cells were detached by treatment with Trypsin-EDTA (Invitrogen) and split every 2 days.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA from ES cells was extracted using RNeasy Mini Kit (QIAGEN) with DNAse I treatment. 1.5 ug of total RNA was reverse transcribed using Superscript III Reverse Transcriptase (Invitrogen) and a 1:1 mix of oligo(dT)12-18 primer (Invitrogen) and Random Hexamers (Applied Biosystems) according to manufacturer’s instructions. cDNA was diluted 1:5 in water and qPCR was performed with the SYBR Green qPCR kit (Abgene) on an MX P3000 qPCR machine (Stratagene). Dilution curves for primer efficiency were plotted and products were run on gel and sequence verified for the lncRNAs obtained as screen hits. For all qPCR measurements, Beta-2-microglobulin or GAPDH mRNA were used as housekeeping markers and all measurements were normalized to these controls.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA was synthesized with Perkin-Elmer's nucleotide analogs using the MEGAScript T7 kit (Ambion).
Sample_hyb_protocol	After fragmenting of the cRNA for target preparation using the standard Affymetrix protocol 15 µg fragmented cRNA was hybridized for 16 h at 45 °C to Mouse Genome 430 v. 2 array.
Sample_scan_protocol	Arrays were washed and stained with streptavidin-phycoerythrin in the Affymetrix Fluidics Station 400 and further scanned using the AFFYMETRIX GeneChip Scanner 3000 7G.
Sample_data_processing	The image data were analyzed with GCOS 1.4 using Affymetrix default analysis settings. Arrays have been quantile-normalize using the RMA algorithm.
Sample_platform_id	GPL1261
Sample_contact_name	Maciej,,Paszkowski-Rogacz
Sample_contact_laboratory	Buchholz
Sample_contact_institute	MPI-CBG
Sample_contact_address	Pfotenhauerstr. 108
Sample_contact_city	Dresden
Sample_contact_zip/postal_code	01307
Sample_contact_country	Germany
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM738nnn/GSM738386/suppl/GSM738386.CEL.gz
Sample_series_id	GSE29798
Sample_data_row_count	45101

GSM738387

GPL1261

Oct4GipES_Panct1_esiRNA_72h_rep3

Oct4-Gip ES cells, Panct1 RNAi, 72h post transfection

cell type: Oct4-Gip ES RNAi: Panct1 treatment time: 72h

Gene expression data from Oct4-Gip ES cells 72h after Panct1-esiRNA treatment.

Sample_geo_accession	GSM738387
Sample_status	Public on Feb 15 2012
Sample_submission_date	Jun 07 2011
Sample_last_update_date	Feb 16 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Oct4-Gip ES cells (60,000 cells in 2ml media) were reverse transfected in 6 well plates with 800ng esiRNAs, 2ul lipofectamine (Invitrogen) and 200ul Opti-MEM (Invitrogen). 72 hours after transfection, RNA was extracted as described above. In total, 6 arrays including 3 replicates of control (Luc) and 3 replicates of experiment (Panct1 knockdown) were processed and hybridized on the Mouse 430 version 2 Array (Affymetrix).
Sample_growth_protocol_ch1	ES cells (E14TG2a, R1/E, Oct4-Gip34) were cultured in Dulbecco’s Modified Eagle Medium (Invitrogen) supplemented with 4.5 g/l D Glucose and pyruvate, 10% fetal bovine Serum (Pan Sera), 30 uM 2-mercaptoethanol, 0.6X NEAA (Invitrogen), 300 units of Penicillin/Streptomycin (Invitrogen) and 8ng LIF (prepared in-house). Media was changed every day and ES cells were detached by treatment with Trypsin-EDTA (Invitrogen) and split every 2 days.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA from ES cells was extracted using RNeasy Mini Kit (QIAGEN) with DNAse I treatment. 1.5 ug of total RNA was reverse transcribed using Superscript III Reverse Transcriptase (Invitrogen) and a 1:1 mix of oligo(dT)12-18 primer (Invitrogen) and Random Hexamers (Applied Biosystems) according to manufacturer’s instructions. cDNA was diluted 1:5 in water and qPCR was performed with the SYBR Green qPCR kit (Abgene) on an MX P3000 qPCR machine (Stratagene). Dilution curves for primer efficiency were plotted and products were run on gel and sequence verified for the lncRNAs obtained as screen hits. For all qPCR measurements, Beta-2-microglobulin or GAPDH mRNA were used as housekeeping markers and all measurements were normalized to these controls.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA was synthesized with Perkin-Elmer's nucleotide analogs using the MEGAScript T7 kit (Ambion).
Sample_hyb_protocol	After fragmenting of the cRNA for target preparation using the standard Affymetrix protocol 15 µg fragmented cRNA was hybridized for 16 h at 45 °C to Mouse Genome 430 v. 2 array.
Sample_scan_protocol	Arrays were washed and stained with streptavidin-phycoerythrin in the Affymetrix Fluidics Station 400 and further scanned using the AFFYMETRIX GeneChip Scanner 3000 7G.
Sample_data_processing	The image data were analyzed with GCOS 1.4 using Affymetrix default analysis settings. Arrays have been quantile-normalize using the RMA algorithm.
Sample_platform_id	GPL1261
Sample_contact_name	Maciej,,Paszkowski-Rogacz
Sample_contact_laboratory	Buchholz
Sample_contact_institute	MPI-CBG
Sample_contact_address	Pfotenhauerstr. 108
Sample_contact_city	Dresden
Sample_contact_zip/postal_code	01307
Sample_contact_country	Germany
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM738nnn/GSM738387/suppl/GSM738387.CEL.gz
Sample_series_id	GSE29798
Sample_data_row_count	45101

GSM738388

GPL1261

Oct4GipES_Luc_esiRNA_72h_rep1

Oct4-Gip ES cells, Luc RNAi, 72h post transfection

cell type: Oct4-Gip ES RNAi: Luciferase treatment time: 72h

Gene expression data from Oct4-Gip ES cells 72h after Luc-esiRNA (negative control) treatment.

Sample_geo_accession	GSM738388
Sample_status	Public on Feb 15 2012
Sample_submission_date	Jun 07 2011
Sample_last_update_date	Feb 16 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Oct4-Gip ES cells (60,000 cells in 2ml media) were reverse transfected in 6 well plates with 800ng esiRNAs, 2ul lipofectamine (Invitrogen) and 200ul Opti-MEM (Invitrogen). 72 hours after transfection, RNA was extracted as described above. In total, 6 arrays including 3 replicates of control (Luc) and 3 replicates of experiment (Panct1 knockdown) were processed and hybridized on the Mouse 430 version 2 Array (Affymetrix).
Sample_growth_protocol_ch1	ES cells (E14TG2a, R1/E, Oct4-Gip34) were cultured in Dulbecco’s Modified Eagle Medium (Invitrogen) supplemented with 4.5 g/l D Glucose and pyruvate, 10% fetal bovine Serum (Pan Sera), 30 uM 2-mercaptoethanol, 0.6X NEAA (Invitrogen), 300 units of Penicillin/Streptomycin (Invitrogen) and 8ng LIF (prepared in-house). Media was changed every day and ES cells were detached by treatment with Trypsin-EDTA (Invitrogen) and split every 2 days.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA from ES cells was extracted using RNeasy Mini Kit (QIAGEN) with DNAse I treatment. 1.5 ug of total RNA was reverse transcribed using Superscript III Reverse Transcriptase (Invitrogen) and a 1:1 mix of oligo(dT)12-18 primer (Invitrogen) and Random Hexamers (Applied Biosystems) according to manufacturer’s instructions. cDNA was diluted 1:5 in water and qPCR was performed with the SYBR Green qPCR kit (Abgene) on an MX P3000 qPCR machine (Stratagene). Dilution curves for primer efficiency were plotted and products were run on gel and sequence verified for the lncRNAs obtained as screen hits. For all qPCR measurements, Beta-2-microglobulin or GAPDH mRNA were used as housekeeping markers and all measurements were normalized to these controls.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA was synthesized with Perkin-Elmer's nucleotide analogs using the MEGAScript T7 kit (Ambion).
Sample_hyb_protocol	After fragmenting of the cRNA for target preparation using the standard Affymetrix protocol 15 µg fragmented cRNA was hybridized for 16 h at 45 °C to Mouse Genome 430 v. 2 array.
Sample_scan_protocol	Arrays were washed and stained with streptavidin-phycoerythrin in the Affymetrix Fluidics Station 400 and further scanned using the AFFYMETRIX GeneChip Scanner 3000 7G.
Sample_data_processing	The image data were analyzed with GCOS 1.4 using Affymetrix default analysis settings. Arrays have been quantile-normalize using the RMA algorithm.
Sample_platform_id	GPL1261
Sample_contact_name	Maciej,,Paszkowski-Rogacz
Sample_contact_laboratory	Buchholz
Sample_contact_institute	MPI-CBG
Sample_contact_address	Pfotenhauerstr. 108
Sample_contact_city	Dresden
Sample_contact_zip/postal_code	01307
Sample_contact_country	Germany
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM738nnn/GSM738388/suppl/GSM738388.CEL.gz
Sample_series_id	GSE29798
Sample_data_row_count	45101

GSM738389

GPL1261

Oct4GipES_Luc_esiRNA_72h_rep2

Oct4-Gip ES cells, Luc RNAi, 72h post transfection

cell type: Oct4-Gip ES RNAi: Luciferase treatment time: 72h

Gene expression data from Oct4-Gip ES cells 72h after Luc-esiRNA (negative control) treatment.

Sample_geo_accession	GSM738389
Sample_status	Public on Feb 15 2012
Sample_submission_date	Jun 07 2011
Sample_last_update_date	Feb 16 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Oct4-Gip ES cells (60,000 cells in 2ml media) were reverse transfected in 6 well plates with 800ng esiRNAs, 2ul lipofectamine (Invitrogen) and 200ul Opti-MEM (Invitrogen). 72 hours after transfection, RNA was extracted as described above. In total, 6 arrays including 3 replicates of control (Luc) and 3 replicates of experiment (Panct1 knockdown) were processed and hybridized on the Mouse 430 version 2 Array (Affymetrix).
Sample_growth_protocol_ch1	ES cells (E14TG2a, R1/E, Oct4-Gip34) were cultured in Dulbecco’s Modified Eagle Medium (Invitrogen) supplemented with 4.5 g/l D Glucose and pyruvate, 10% fetal bovine Serum (Pan Sera), 30 uM 2-mercaptoethanol, 0.6X NEAA (Invitrogen), 300 units of Penicillin/Streptomycin (Invitrogen) and 8ng LIF (prepared in-house). Media was changed every day and ES cells were detached by treatment with Trypsin-EDTA (Invitrogen) and split every 2 days.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA from ES cells was extracted using RNeasy Mini Kit (QIAGEN) with DNAse I treatment. 1.5 ug of total RNA was reverse transcribed using Superscript III Reverse Transcriptase (Invitrogen) and a 1:1 mix of oligo(dT)12-18 primer (Invitrogen) and Random Hexamers (Applied Biosystems) according to manufacturer’s instructions. cDNA was diluted 1:5 in water and qPCR was performed with the SYBR Green qPCR kit (Abgene) on an MX P3000 qPCR machine (Stratagene). Dilution curves for primer efficiency were plotted and products were run on gel and sequence verified for the lncRNAs obtained as screen hits. For all qPCR measurements, Beta-2-microglobulin or GAPDH mRNA were used as housekeeping markers and all measurements were normalized to these controls.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA was synthesized with Perkin-Elmer's nucleotide analogs using the MEGAScript T7 kit (Ambion).
Sample_hyb_protocol	After fragmenting of the cRNA for target preparation using the standard Affymetrix protocol 15 µg fragmented cRNA was hybridized for 16 h at 45 °C to Mouse Genome 430 v. 2 array.
Sample_scan_protocol	Arrays were washed and stained with streptavidin-phycoerythrin in the Affymetrix Fluidics Station 400 and further scanned using the AFFYMETRIX GeneChip Scanner 3000 7G.
Sample_data_processing	The image data were analyzed with GCOS 1.4 using Affymetrix default analysis settings. Arrays have been quantile-normalize using the RMA algorithm.
Sample_platform_id	GPL1261
Sample_contact_name	Maciej,,Paszkowski-Rogacz
Sample_contact_laboratory	Buchholz
Sample_contact_institute	MPI-CBG
Sample_contact_address	Pfotenhauerstr. 108
Sample_contact_city	Dresden
Sample_contact_zip/postal_code	01307
Sample_contact_country	Germany
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM738nnn/GSM738389/suppl/GSM738389.CEL.gz
Sample_series_id	GSE29798
Sample_data_row_count	45101

GSM738390

GPL1261

Oct4GipES_Luc_esiRNA_72h_rep3

Oct4-Gip ES cells, Luc RNAi, 72h post transfection

cell type: Oct4-Gip ES RNAi: Luciferase treatment time: 72h

Gene expression data from Oct4-Gip ES cells 72h after Luc-esiRNA (negative control) treatment.

Sample_geo_accession	GSM738390
Sample_status	Public on Feb 15 2012
Sample_submission_date	Jun 07 2011
Sample_last_update_date	Feb 16 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Oct4-Gip ES cells (60,000 cells in 2ml media) were reverse transfected in 6 well plates with 800ng esiRNAs, 2ul lipofectamine (Invitrogen) and 200ul Opti-MEM (Invitrogen). 72 hours after transfection, RNA was extracted as described above. In total, 6 arrays including 3 replicates of control (Luc) and 3 replicates of experiment (Panct1 knockdown) were processed and hybridized on the Mouse 430 version 2 Array (Affymetrix).
Sample_growth_protocol_ch1	ES cells (E14TG2a, R1/E, Oct4-Gip34) were cultured in Dulbecco’s Modified Eagle Medium (Invitrogen) supplemented with 4.5 g/l D Glucose and pyruvate, 10% fetal bovine Serum (Pan Sera), 30 uM 2-mercaptoethanol, 0.6X NEAA (Invitrogen), 300 units of Penicillin/Streptomycin (Invitrogen) and 8ng LIF (prepared in-house). Media was changed every day and ES cells were detached by treatment with Trypsin-EDTA (Invitrogen) and split every 2 days.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA from ES cells was extracted using RNeasy Mini Kit (QIAGEN) with DNAse I treatment. 1.5 ug of total RNA was reverse transcribed using Superscript III Reverse Transcriptase (Invitrogen) and a 1:1 mix of oligo(dT)12-18 primer (Invitrogen) and Random Hexamers (Applied Biosystems) according to manufacturer’s instructions. cDNA was diluted 1:5 in water and qPCR was performed with the SYBR Green qPCR kit (Abgene) on an MX P3000 qPCR machine (Stratagene). Dilution curves for primer efficiency were plotted and products were run on gel and sequence verified for the lncRNAs obtained as screen hits. For all qPCR measurements, Beta-2-microglobulin or GAPDH mRNA were used as housekeeping markers and all measurements were normalized to these controls.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA was synthesized with Perkin-Elmer's nucleotide analogs using the MEGAScript T7 kit (Ambion).
Sample_hyb_protocol	After fragmenting of the cRNA for target preparation using the standard Affymetrix protocol 15 µg fragmented cRNA was hybridized for 16 h at 45 °C to Mouse Genome 430 v. 2 array.
Sample_scan_protocol	Arrays were washed and stained with streptavidin-phycoerythrin in the Affymetrix Fluidics Station 400 and further scanned using the AFFYMETRIX GeneChip Scanner 3000 7G.
Sample_data_processing	The image data were analyzed with GCOS 1.4 using Affymetrix default analysis settings. Arrays have been quantile-normalize using the RMA algorithm.
Sample_platform_id	GPL1261
Sample_contact_name	Maciej,,Paszkowski-Rogacz
Sample_contact_laboratory	Buchholz
Sample_contact_institute	MPI-CBG
Sample_contact_address	Pfotenhauerstr. 108
Sample_contact_city	Dresden
Sample_contact_zip/postal_code	01307
Sample_contact_country	Germany
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM738nnn/GSM738390/suppl/GSM738390.CEL.gz
Sample_series_id	GSE29798
Sample_data_row_count	45101

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