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Search results for the GEO ID: GSE43881

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GSM ID

GPL ID

Select for analysis

Title

Source name

Description

Characteristics

GSM1072825

GPL570

LNCaP-abl_siHIPK2_2

cell culture

cell line: LNCaP-abl transfection: siHIPK2

Sample_geo_accession	GSM1072825
Sample_status	Public on Jan 30 2013
Sample_submission_date	Jan 29 2013
Sample_last_update_date	Jan 30 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Three individual siRNAs (Silencer Select, Ambion; Life Technologies, Grand Island, NY) were pooled and transfected into cells using the HiPerFect transfection reagent (Qiagen, Valencia, CA) following manufacturer’s instructions. Non-silencing siRNAs were used as controls. siRNAs were used at a final concentration of 30nM per individual siRNA
Sample_growth_protocol_ch1	LNCaP-abl cells were cultured in RPMI-1640 without phenol red media (Cellgro, Mediatech, Inc. Manassas, VA) supplemented with 10% Charcoal-stripped fetal bovine serum (cFBS), 1% penicillin-streptomycin and 1% L-Glutamine
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was isolated from cells using RNeasy Mini Kit (Qiagen, Valencia, CA)
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA
Sample_hyb_protocol	Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Sample_scan_protocol	GeneChips were scanned using the Affymetrix 3000 7G Scanner.
Sample_data_processing	Robust Median Averaging, and quantile normalization using the espresso function form the affy package of R bioconductor
Sample_platform_id	GPL570
Sample_contact_name	Michael,,Garabedian
Sample_contact_email	michael.garabedian@nyumc.org
Sample_contact_phone	212 263-7662
Sample_contact_fax	212 263-8276
Sample_contact_department	Microbiology
Sample_contact_institute	NYU School of Medicine
Sample_contact_address	550 First Avenue
Sample_contact_city	New York
Sample_contact_state	NY
Sample_contact_zip/postal_code	10016
Sample_contact_country	USA
Sample_contact_web_link	http://microbiology-parasitology.med.nyu.edu/node/122
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1072nnn/GSM1072825/suppl/GSM1072825_KI_SiHIPK22_HGU133_Plus_2.CEL.gz
Sample_series_id	GSE43881
Sample_data_row_count	54675

GSM1072826

GPL570

LNCaP-abl_siControl_1

cell culture

cell line: LNCaP-abl transfection: siControl

Sample_geo_accession	GSM1072826
Sample_status	Public on Jan 30 2013
Sample_submission_date	Jan 29 2013
Sample_last_update_date	Jan 30 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Three individual siRNAs (Silencer Select, Ambion; Life Technologies, Grand Island, NY) were pooled and transfected into cells using the HiPerFect transfection reagent (Qiagen, Valencia, CA) following manufacturer’s instructions. Non-silencing siRNAs were used as controls. siRNAs were used at a final concentration of 30nM per individual siRNA
Sample_growth_protocol_ch1	LNCaP-abl cells were cultured in RPMI-1640 without phenol red media (Cellgro, Mediatech, Inc. Manassas, VA) supplemented with 10% Charcoal-stripped fetal bovine serum (cFBS), 1% penicillin-streptomycin and 1% L-Glutamine
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was isolated from cells using RNeasy Mini Kit (Qiagen, Valencia, CA)
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA
Sample_hyb_protocol	Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Sample_scan_protocol	GeneChips were scanned using the Affymetrix 3000 7G Scanner.
Sample_data_processing	Robust Median Averaging, and quantile normalization using the espresso function form the affy package of R bioconductor
Sample_platform_id	GPL570
Sample_contact_name	Michael,,Garabedian
Sample_contact_email	michael.garabedian@nyumc.org
Sample_contact_phone	212 263-7662
Sample_contact_fax	212 263-8276
Sample_contact_department	Microbiology
Sample_contact_institute	NYU School of Medicine
Sample_contact_address	550 First Avenue
Sample_contact_city	New York
Sample_contact_state	NY
Sample_contact_zip/postal_code	10016
Sample_contact_country	USA
Sample_contact_web_link	http://microbiology-parasitology.med.nyu.edu/node/122
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1072nnn/GSM1072826/suppl/GSM1072826_KI_SiCon1_HGU133_Plus_2.CEL.gz
Sample_series_id	GSE43881
Sample_data_row_count	54675

GSM1072827

GPL570

LNCaP-abl_siControl_2

cell culture

cell line: LNCaP-abl transfection: siControl

Sample_geo_accession	GSM1072827
Sample_status	Public on Jan 30 2013
Sample_submission_date	Jan 29 2013
Sample_last_update_date	Jan 30 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Three individual siRNAs (Silencer Select, Ambion; Life Technologies, Grand Island, NY) were pooled and transfected into cells using the HiPerFect transfection reagent (Qiagen, Valencia, CA) following manufacturer’s instructions. Non-silencing siRNAs were used as controls. siRNAs were used at a final concentration of 30nM per individual siRNA
Sample_growth_protocol_ch1	LNCaP-abl cells were cultured in RPMI-1640 without phenol red media (Cellgro, Mediatech, Inc. Manassas, VA) supplemented with 10% Charcoal-stripped fetal bovine serum (cFBS), 1% penicillin-streptomycin and 1% L-Glutamine
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was isolated from cells using RNeasy Mini Kit (Qiagen, Valencia, CA)
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA
Sample_hyb_protocol	Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Sample_scan_protocol	GeneChips were scanned using the Affymetrix 3000 7G Scanner.
Sample_data_processing	Robust Median Averaging, and quantile normalization using the espresso function form the affy package of R bioconductor
Sample_platform_id	GPL570
Sample_contact_name	Michael,,Garabedian
Sample_contact_email	michael.garabedian@nyumc.org
Sample_contact_phone	212 263-7662
Sample_contact_fax	212 263-8276
Sample_contact_department	Microbiology
Sample_contact_institute	NYU School of Medicine
Sample_contact_address	550 First Avenue
Sample_contact_city	New York
Sample_contact_state	NY
Sample_contact_zip/postal_code	10016
Sample_contact_country	USA
Sample_contact_web_link	http://microbiology-parasitology.med.nyu.edu/node/122
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1072nnn/GSM1072827/suppl/GSM1072827_KI_SiCon2_HGU133_Plus_2.CEL.gz
Sample_series_id	GSE43881
Sample_data_row_count	54675

GSM1072828

GPL570

LNCaP-abl_siHIPK2_1

cell culture

cell line: LNCaP-abl transfection: siHIPK2

Sample_geo_accession	GSM1072828
Sample_status	Public on Jan 30 2013
Sample_submission_date	Jan 29 2013
Sample_last_update_date	Jan 30 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Three individual siRNAs (Silencer Select, Ambion; Life Technologies, Grand Island, NY) were pooled and transfected into cells using the HiPerFect transfection reagent (Qiagen, Valencia, CA) following manufacturer’s instructions. Non-silencing siRNAs were used as controls. siRNAs were used at a final concentration of 30nM per individual siRNA
Sample_growth_protocol_ch1	LNCaP-abl cells were cultured in RPMI-1640 without phenol red media (Cellgro, Mediatech, Inc. Manassas, VA) supplemented with 10% Charcoal-stripped fetal bovine serum (cFBS), 1% penicillin-streptomycin and 1% L-Glutamine
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was isolated from cells using RNeasy Mini Kit (Qiagen, Valencia, CA)
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA
Sample_hyb_protocol	Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Sample_scan_protocol	GeneChips were scanned using the Affymetrix 3000 7G Scanner.
Sample_data_processing	Robust Median Averaging, and quantile normalization using the espresso function form the affy package of R bioconductor
Sample_platform_id	GPL570
Sample_contact_name	Michael,,Garabedian
Sample_contact_email	michael.garabedian@nyumc.org
Sample_contact_phone	212 263-7662
Sample_contact_fax	212 263-8276
Sample_contact_department	Microbiology
Sample_contact_institute	NYU School of Medicine
Sample_contact_address	550 First Avenue
Sample_contact_city	New York
Sample_contact_state	NY
Sample_contact_zip/postal_code	10016
Sample_contact_country	USA
Sample_contact_web_link	http://microbiology-parasitology.med.nyu.edu/node/122
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1072nnn/GSM1072828/suppl/GSM1072828_KI_SiHIPK21_HGU133_Plus_2.CEL.gz
Sample_series_id	GSE43881
Sample_data_row_count	54675

GSM1072829

GPL570

LNCaP-abl_siMED19_1

cell culture

cell line: LNCaP-abl transfection: siMED19

Sample_geo_accession	GSM1072829
Sample_status	Public on Jan 30 2013
Sample_submission_date	Jan 29 2013
Sample_last_update_date	Jan 30 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Three individual siRNAs (Silencer Select, Ambion; Life Technologies, Grand Island, NY) were pooled and transfected into cells using the HiPerFect transfection reagent (Qiagen, Valencia, CA) following manufacturer’s instructions. Non-silencing siRNAs were used as controls. siRNAs were used at a final concentration of 30nM per individual siRNA
Sample_growth_protocol_ch1	LNCaP-abl cells were cultured in RPMI-1640 without phenol red media (Cellgro, Mediatech, Inc. Manassas, VA) supplemented with 10% Charcoal-stripped fetal bovine serum (cFBS), 1% penicillin-streptomycin and 1% L-Glutamine
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was isolated from cells using RNeasy Mini Kit (Qiagen, Valencia, CA)
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA
Sample_hyb_protocol	Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Sample_scan_protocol	GeneChips were scanned using the Affymetrix 3000 7G Scanner.
Sample_data_processing	Robust Median Averaging, and quantile normalization using the espresso function form the affy package of R bioconductor
Sample_platform_id	GPL570
Sample_contact_name	Michael,,Garabedian
Sample_contact_email	michael.garabedian@nyumc.org
Sample_contact_phone	212 263-7662
Sample_contact_fax	212 263-8276
Sample_contact_department	Microbiology
Sample_contact_institute	NYU School of Medicine
Sample_contact_address	550 First Avenue
Sample_contact_city	New York
Sample_contact_state	NY
Sample_contact_zip/postal_code	10016
Sample_contact_country	USA
Sample_contact_web_link	http://microbiology-parasitology.med.nyu.edu/node/122
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1072nnn/GSM1072829/suppl/GSM1072829_KI_SiMED191_HGU133_Plus_2.CEL.gz
Sample_series_id	GSE43881
Sample_data_row_count	54675

GSM1072830

GPL570

LNCaP-abl_siMED19_2

cell culture

cell line: LNCaP-abl transfection: siMED19

Sample_geo_accession	GSM1072830
Sample_status	Public on Jan 30 2013
Sample_submission_date	Jan 29 2013
Sample_last_update_date	Jan 30 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Three individual siRNAs (Silencer Select, Ambion; Life Technologies, Grand Island, NY) were pooled and transfected into cells using the HiPerFect transfection reagent (Qiagen, Valencia, CA) following manufacturer’s instructions. Non-silencing siRNAs were used as controls. siRNAs were used at a final concentration of 30nM per individual siRNA
Sample_growth_protocol_ch1	LNCaP-abl cells were cultured in RPMI-1640 without phenol red media (Cellgro, Mediatech, Inc. Manassas, VA) supplemented with 10% Charcoal-stripped fetal bovine serum (cFBS), 1% penicillin-streptomycin and 1% L-Glutamine
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was isolated from cells using RNeasy Mini Kit (Qiagen, Valencia, CA)
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA
Sample_hyb_protocol	Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Sample_scan_protocol	GeneChips were scanned using the Affymetrix 3000 7G Scanner.
Sample_data_processing	Robust Median Averaging, and quantile normalization using the espresso function form the affy package of R bioconductor
Sample_platform_id	GPL570
Sample_contact_name	Michael,,Garabedian
Sample_contact_email	michael.garabedian@nyumc.org
Sample_contact_phone	212 263-7662
Sample_contact_fax	212 263-8276
Sample_contact_department	Microbiology
Sample_contact_institute	NYU School of Medicine
Sample_contact_address	550 First Avenue
Sample_contact_city	New York
Sample_contact_state	NY
Sample_contact_zip/postal_code	10016
Sample_contact_country	USA
Sample_contact_web_link	http://microbiology-parasitology.med.nyu.edu/node/122
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1072nnn/GSM1072830/suppl/GSM1072830_KI_SiMED192_HGU133_Plus_2.CEL.gz
Sample_series_id	GSE43881
Sample_data_row_count	54675

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