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Search results for the GEO ID: GSE40215

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(Once the selection is made, click on "Add groups" in "Make groups for comparison", to make a group. Scroll down)

GSM ID

GPL ID

Select for analysis

Title

Source name

Description

Characteristics

GSM988481

GPL570

shNFYA, replicate 1

HeLaS3 cells

cell line: HeLaS3 treatment: shNFYA genotype/variation: NF-YA knockdown

HeLaS3 cells treated with shNF-YA

Sample_geo_accession	GSM988481
Sample_status	Public on Dec 31 2012
Sample_submission_date	Aug 20 2012
Sample_last_update_date	Dec 31 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	HeLaS3 cells were transduced with shSCM (control) or shNF-YA viral supernatants, in triplicate, and cells collected after 48 hr of incubation.
Sample_growth_protocol_ch1	HeLaS3 cells were grown as adherent cells in alpha-MEM media supplemented with 5% fetal bovin serum with penn/strep.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Trizol extraction and Qiagen RNeasy kit purification performed according to the manufacturer's instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated aRNA were prepared using the 3’ IVT Express Kit (Affymetrix, USA).
Sample_hyb_protocol	Following fragmentation, 12.5 ug of fragmented aRNA was hybridized as per manufacturer's protocol for the U133 plus 2.0 arrays. Intruments used were Affymetrix GeneChip Fluidics Station 450, Affymetrix GeneChip Hybridization Oven 640.
Sample_scan_protocol	GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
Sample_data_processing	Arrays were RMA normalized (Irizarry et al. 2003), gene expression levels calculated, differential expression determined using the following R packages from the Bioconductor project: affy (Gautier et al. 2004), limma (Smyth 2004).
Sample_platform_id	GPL570
Sample_contact_name	Joseph,Daniel,Fleming
Sample_contact_email	jfleming@hms.harvard.edu
Sample_contact_phone	617-432-3771
Sample_contact_laboratory	Struhl, Kevin
Sample_contact_department	Biological Chemistry and Molecular Pharmacology
Sample_contact_institute	Harvard Medical School
Sample_contact_address	240 Longwood Ave
Sample_contact_city	Boston
Sample_contact_state	MA
Sample_contact_zip/postal_code	02115
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM988nnn/GSM988481/suppl/GSM988481_shNFYA_repA.CEL.gz
Sample_series_id	GSE40215
Sample_data_row_count	54675

GSM988482

GPL570

shNFYA, replicate 2

HeLaS3 cells

cell line: HeLaS3 treatment: shNFYA genotype/variation: NF-YA knockdown

HeLaS3 cells treated with shNF-YA

Sample_geo_accession	GSM988482
Sample_status	Public on Dec 31 2012
Sample_submission_date	Aug 20 2012
Sample_last_update_date	Dec 31 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	HeLaS3 cells were transduced with shSCM (control) or shNF-YA viral supernatants, in triplicate, and cells collected after 48 hr of incubation.
Sample_growth_protocol_ch1	HeLaS3 cells were grown as adherent cells in alpha-MEM media supplemented with 5% fetal bovin serum with penn/strep.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Trizol extraction and Qiagen RNeasy kit purification performed according to the manufacturer's instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated aRNA were prepared using the 3’ IVT Express Kit (Affymetrix, USA).
Sample_hyb_protocol	Following fragmentation, 12.5 ug of fragmented aRNA was hybridized as per manufacturer's protocol for the U133 plus 2.0 arrays. Intruments used were Affymetrix GeneChip Fluidics Station 450, Affymetrix GeneChip Hybridization Oven 640.
Sample_scan_protocol	GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
Sample_data_processing	Arrays were RMA normalized (Irizarry et al. 2003), gene expression levels calculated, differential expression determined using the following R packages from the Bioconductor project: affy (Gautier et al. 2004), limma (Smyth 2004).
Sample_platform_id	GPL570
Sample_contact_name	Joseph,Daniel,Fleming
Sample_contact_email	jfleming@hms.harvard.edu
Sample_contact_phone	617-432-3771
Sample_contact_laboratory	Struhl, Kevin
Sample_contact_department	Biological Chemistry and Molecular Pharmacology
Sample_contact_institute	Harvard Medical School
Sample_contact_address	240 Longwood Ave
Sample_contact_city	Boston
Sample_contact_state	MA
Sample_contact_zip/postal_code	02115
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM988nnn/GSM988482/suppl/GSM988482_shNFYA_repB.CEL.gz
Sample_series_id	GSE40215
Sample_data_row_count	54675

GSM988483

GPL570

shNFYA, replicate 3

HeLaS3 cells

cell line: HeLaS3 treatment: shNFYA genotype/variation: NF-YA knockdown

HeLaS3 cells treated with shNF-YA

Sample_geo_accession	GSM988483
Sample_status	Public on Dec 31 2012
Sample_submission_date	Aug 20 2012
Sample_last_update_date	Dec 31 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	HeLaS3 cells were transduced with shSCM (control) or shNF-YA viral supernatants, in triplicate, and cells collected after 48 hr of incubation.
Sample_growth_protocol_ch1	HeLaS3 cells were grown as adherent cells in alpha-MEM media supplemented with 5% fetal bovin serum with penn/strep.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Trizol extraction and Qiagen RNeasy kit purification performed according to the manufacturer's instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated aRNA were prepared using the 3’ IVT Express Kit (Affymetrix, USA).
Sample_hyb_protocol	Following fragmentation, 12.5 ug of fragmented aRNA was hybridized as per manufacturer's protocol for the U133 plus 2.0 arrays. Intruments used were Affymetrix GeneChip Fluidics Station 450, Affymetrix GeneChip Hybridization Oven 640.
Sample_scan_protocol	GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
Sample_data_processing	Arrays were RMA normalized (Irizarry et al. 2003), gene expression levels calculated, differential expression determined using the following R packages from the Bioconductor project: affy (Gautier et al. 2004), limma (Smyth 2004).
Sample_platform_id	GPL570
Sample_contact_name	Joseph,Daniel,Fleming
Sample_contact_email	jfleming@hms.harvard.edu
Sample_contact_phone	617-432-3771
Sample_contact_laboratory	Struhl, Kevin
Sample_contact_department	Biological Chemistry and Molecular Pharmacology
Sample_contact_institute	Harvard Medical School
Sample_contact_address	240 Longwood Ave
Sample_contact_city	Boston
Sample_contact_state	MA
Sample_contact_zip/postal_code	02115
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM988nnn/GSM988483/suppl/GSM988483_shNFYA_repC.CEL.gz
Sample_series_id	GSE40215
Sample_data_row_count	54675

GSM988484

GPL570

shSCM, replicate 1

HeLaS3 cells

cell line: HeLaS3 treatment: shSCM genotype/variation: control

HeLaS3 cells treated with shSCM (control)

Sample_geo_accession	GSM988484
Sample_status	Public on Dec 31 2012
Sample_submission_date	Aug 20 2012
Sample_last_update_date	Dec 31 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	HeLaS3 cells were transduced with shSCM (control) or shNF-YA viral supernatants, in triplicate, and cells collected after 48 hr of incubation.
Sample_growth_protocol_ch1	HeLaS3 cells were grown as adherent cells in alpha-MEM media supplemented with 5% fetal bovin serum with penn/strep.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Trizol extraction and Qiagen RNeasy kit purification performed according to the manufacturer's instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated aRNA were prepared using the 3’ IVT Express Kit (Affymetrix, USA).
Sample_hyb_protocol	Following fragmentation, 12.5 ug of fragmented aRNA was hybridized as per manufacturer's protocol for the U133 plus 2.0 arrays. Intruments used were Affymetrix GeneChip Fluidics Station 450, Affymetrix GeneChip Hybridization Oven 640.
Sample_scan_protocol	GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
Sample_data_processing	Arrays were RMA normalized (Irizarry et al. 2003), gene expression levels calculated, differential expression determined using the following R packages from the Bioconductor project: affy (Gautier et al. 2004), limma (Smyth 2004).
Sample_platform_id	GPL570
Sample_contact_name	Joseph,Daniel,Fleming
Sample_contact_email	jfleming@hms.harvard.edu
Sample_contact_phone	617-432-3771
Sample_contact_laboratory	Struhl, Kevin
Sample_contact_department	Biological Chemistry and Molecular Pharmacology
Sample_contact_institute	Harvard Medical School
Sample_contact_address	240 Longwood Ave
Sample_contact_city	Boston
Sample_contact_state	MA
Sample_contact_zip/postal_code	02115
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM988nnn/GSM988484/suppl/GSM988484_shSCM_repA.CEL.gz
Sample_series_id	GSE40215
Sample_data_row_count	54675

GSM988485

GPL570

shSCM, replicate 2

HeLaS3 cells

cell line: HeLaS3 treatment: shSCM genotype/variation: control

HeLaS3 cells treated with shSCM (control)

Sample_geo_accession	GSM988485
Sample_status	Public on Dec 31 2012
Sample_submission_date	Aug 20 2012
Sample_last_update_date	Dec 31 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	HeLaS3 cells were transduced with shSCM (control) or shNF-YA viral supernatants, in triplicate, and cells collected after 48 hr of incubation.
Sample_growth_protocol_ch1	HeLaS3 cells were grown as adherent cells in alpha-MEM media supplemented with 5% fetal bovin serum with penn/strep.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Trizol extraction and Qiagen RNeasy kit purification performed according to the manufacturer's instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated aRNA were prepared using the 3’ IVT Express Kit (Affymetrix, USA).
Sample_hyb_protocol	Following fragmentation, 12.5 ug of fragmented aRNA was hybridized as per manufacturer's protocol for the U133 plus 2.0 arrays. Intruments used were Affymetrix GeneChip Fluidics Station 450, Affymetrix GeneChip Hybridization Oven 640.
Sample_scan_protocol	GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
Sample_data_processing	Arrays were RMA normalized (Irizarry et al. 2003), gene expression levels calculated, differential expression determined using the following R packages from the Bioconductor project: affy (Gautier et al. 2004), limma (Smyth 2004).
Sample_platform_id	GPL570
Sample_contact_name	Joseph,Daniel,Fleming
Sample_contact_email	jfleming@hms.harvard.edu
Sample_contact_phone	617-432-3771
Sample_contact_laboratory	Struhl, Kevin
Sample_contact_department	Biological Chemistry and Molecular Pharmacology
Sample_contact_institute	Harvard Medical School
Sample_contact_address	240 Longwood Ave
Sample_contact_city	Boston
Sample_contact_state	MA
Sample_contact_zip/postal_code	02115
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM988nnn/GSM988485/suppl/GSM988485_shSCM_repB.CEL.gz
Sample_series_id	GSE40215
Sample_data_row_count	54675

GSM988486

GPL570

shSCM, replicate 3

HeLaS3 cells

cell line: HeLaS3 treatment: shSCM genotype/variation: control

HeLaS3 cells treated with shSCM (control)

Sample_geo_accession	GSM988486
Sample_status	Public on Dec 31 2012
Sample_submission_date	Aug 20 2012
Sample_last_update_date	Dec 31 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	HeLaS3 cells were transduced with shSCM (control) or shNF-YA viral supernatants, in triplicate, and cells collected after 48 hr of incubation.
Sample_growth_protocol_ch1	HeLaS3 cells were grown as adherent cells in alpha-MEM media supplemented with 5% fetal bovin serum with penn/strep.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Trizol extraction and Qiagen RNeasy kit purification performed according to the manufacturer's instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated aRNA were prepared using the 3’ IVT Express Kit (Affymetrix, USA).
Sample_hyb_protocol	Following fragmentation, 12.5 ug of fragmented aRNA was hybridized as per manufacturer's protocol for the U133 plus 2.0 arrays. Intruments used were Affymetrix GeneChip Fluidics Station 450, Affymetrix GeneChip Hybridization Oven 640.
Sample_scan_protocol	GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
Sample_data_processing	Arrays were RMA normalized (Irizarry et al. 2003), gene expression levels calculated, differential expression determined using the following R packages from the Bioconductor project: affy (Gautier et al. 2004), limma (Smyth 2004).
Sample_platform_id	GPL570
Sample_contact_name	Joseph,Daniel,Fleming
Sample_contact_email	jfleming@hms.harvard.edu
Sample_contact_phone	617-432-3771
Sample_contact_laboratory	Struhl, Kevin
Sample_contact_department	Biological Chemistry and Molecular Pharmacology
Sample_contact_institute	Harvard Medical School
Sample_contact_address	240 Longwood Ave
Sample_contact_city	Boston
Sample_contact_state	MA
Sample_contact_zip/postal_code	02115
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM988nnn/GSM988486/suppl/GSM988486_shSCM_repC.CEL.gz
Sample_series_id	GSE40215
Sample_data_row_count	54675

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