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Search results for the GEO ID: GSE29316

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GSM ID

GPL ID

Select for analysis

Title

Source name

Description

Characteristics

GSM724521

GPL570

Untreated, replicate 1

CCD-18Co, untreated

cell line: CCD-18Co cell type: colon fibroblasts treatment: none

Sample_geo_accession	GSM724521
Sample_status	Public on May 17 2011
Sample_submission_date	May 16 2011
Sample_last_update_date	May 17 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Colon fibroblasts CCD-18Co were stimulated with SHH (1 ug/ml) for 72 h.
Sample_growth_protocol_ch1	Colon fibroblasts were cultured in media plus 0.1% BSA.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was extracted using the Qiagen RNeasy kit.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	The method for preparation of cRNA was provided by Affymetrix. Briefly, 5 ug of total RNA was converted into double-stranded cDNA using a cDNA synthesis kit SuperScript Choice and a T7-(dT)24 oligomer primer. Double-stranded cDNA was purified on an affinity resin and ethanol precipitation. Following second-strand cDNA synthesis, labeled cRNA was generated using a T7 RNA polymerase and biotin-labeled nucleotide in an in vitro transcription reaction (Enzo Diagnostics). The labeled cRNA was purified on an affinity resin.
Sample_hyb_protocol	The method for hybridization of the arrays was provided by Affymetrix. Twenty micrograms of cRNA was fragmented and then hybridized to the arrays at 45°C for 19 hours in a rotisserie oven set at 60 rpm. Arrays were washed and stained in a Fluidics station.
Sample_scan_protocol	The method for array scanning was provided by Affymetrix. Arrays were scanned on an Affymetrix scanner.
Sample_data_processing	Data analysis was performed using the Affymetrix GeneChip Analysis software.
Sample_platform_id	GPL570
Sample_contact_name	Weiwei,,Chen
Sample_contact_email	weiweic@gene.com
Sample_contact_institute	Genentech
Sample_contact_address	1st DNA Way
Sample_contact_city	SSF
Sample_contact_zip/postal_code	94080
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM724nnn/GSM724521/suppl/GSM724521.CEL.gz
Sample_series_id	GSE29316
Sample_data_row_count	54613

GSM724522

GPL570

Untreated, replicate 2

CCD-18Co, untreated

cell line: CCD-18Co cell type: colon fibroblasts treatment: none

Sample_geo_accession	GSM724522
Sample_status	Public on May 17 2011
Sample_submission_date	May 16 2011
Sample_last_update_date	May 17 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Colon fibroblasts CCD-18Co were stimulated with SHH (1 ug/ml) for 72 h.
Sample_growth_protocol_ch1	Colon fibroblasts were cultured in media plus 0.1% BSA.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was extracted using the Qiagen RNeasy kit.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	The method for preparation of cRNA was provided by Affymetrix. Briefly, 5 ug of total RNA was converted into double-stranded cDNA using a cDNA synthesis kit SuperScript Choice and a T7-(dT)24 oligomer primer. Double-stranded cDNA was purified on an affinity resin and ethanol precipitation. Following second-strand cDNA synthesis, labeled cRNA was generated using a T7 RNA polymerase and biotin-labeled nucleotide in an in vitro transcription reaction (Enzo Diagnostics). The labeled cRNA was purified on an affinity resin.
Sample_hyb_protocol	The method for hybridization of the arrays was provided by Affymetrix. Twenty micrograms of cRNA was fragmented and then hybridized to the arrays at 45°C for 19 hours in a rotisserie oven set at 60 rpm. Arrays were washed and stained in a Fluidics station.
Sample_scan_protocol	The method for array scanning was provided by Affymetrix. Arrays were scanned on an Affymetrix scanner.
Sample_data_processing	Data analysis was performed using the Affymetrix GeneChip Analysis software.
Sample_platform_id	GPL570
Sample_contact_name	Weiwei,,Chen
Sample_contact_email	weiweic@gene.com
Sample_contact_institute	Genentech
Sample_contact_address	1st DNA Way
Sample_contact_city	SSF
Sample_contact_zip/postal_code	94080
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM724nnn/GSM724522/suppl/GSM724522.CEL.gz
Sample_series_id	GSE29316
Sample_data_row_count	54613

GSM724523

GPL570

Untreated, replicate 3

CCD-18Co, untreated

cell line: CCD-18Co cell type: colon fibroblasts treatment: none

Sample_geo_accession	GSM724523
Sample_status	Public on May 17 2011
Sample_submission_date	May 16 2011
Sample_last_update_date	May 17 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Colon fibroblasts CCD-18Co were stimulated with SHH (1 ug/ml) for 72 h.
Sample_growth_protocol_ch1	Colon fibroblasts were cultured in media plus 0.1% BSA.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was extracted using the Qiagen RNeasy kit.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	The method for preparation of cRNA was provided by Affymetrix. Briefly, 5 ug of total RNA was converted into double-stranded cDNA using a cDNA synthesis kit SuperScript Choice and a T7-(dT)24 oligomer primer. Double-stranded cDNA was purified on an affinity resin and ethanol precipitation. Following second-strand cDNA synthesis, labeled cRNA was generated using a T7 RNA polymerase and biotin-labeled nucleotide in an in vitro transcription reaction (Enzo Diagnostics). The labeled cRNA was purified on an affinity resin.
Sample_hyb_protocol	The method for hybridization of the arrays was provided by Affymetrix. Twenty micrograms of cRNA was fragmented and then hybridized to the arrays at 45°C for 19 hours in a rotisserie oven set at 60 rpm. Arrays were washed and stained in a Fluidics station.
Sample_scan_protocol	The method for array scanning was provided by Affymetrix. Arrays were scanned on an Affymetrix scanner.
Sample_data_processing	Data analysis was performed using the Affymetrix GeneChip Analysis software.
Sample_platform_id	GPL570
Sample_contact_name	Weiwei,,Chen
Sample_contact_email	weiweic@gene.com
Sample_contact_institute	Genentech
Sample_contact_address	1st DNA Way
Sample_contact_city	SSF
Sample_contact_zip/postal_code	94080
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM724nnn/GSM724523/suppl/GSM724523.CEL.gz
Sample_series_id	GSE29316
Sample_data_row_count	54613

GSM724524

GPL570

SHH treated, replicate 1

CCD-18Co, SHH treated

cell line: CCD-18Co cell type: colon fibroblasts treatment: Sonic hedgehog homolog (SHH)

Sample_geo_accession	GSM724524
Sample_status	Public on May 17 2011
Sample_submission_date	May 16 2011
Sample_last_update_date	May 17 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Colon fibroblasts CCD-18Co were stimulated with SHH (1 ug/ml) for 72 h.
Sample_growth_protocol_ch1	Colon fibroblasts were cultured in media plus 0.1% BSA.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was extracted using the Qiagen RNeasy kit.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	The method for preparation of cRNA was provided by Affymetrix. Briefly, 5 ug of total RNA was converted into double-stranded cDNA using a cDNA synthesis kit SuperScript Choice and a T7-(dT)24 oligomer primer. Double-stranded cDNA was purified on an affinity resin and ethanol precipitation. Following second-strand cDNA synthesis, labeled cRNA was generated using a T7 RNA polymerase and biotin-labeled nucleotide in an in vitro transcription reaction (Enzo Diagnostics). The labeled cRNA was purified on an affinity resin.
Sample_hyb_protocol	The method for hybridization of the arrays was provided by Affymetrix. Twenty micrograms of cRNA was fragmented and then hybridized to the arrays at 45°C for 19 hours in a rotisserie oven set at 60 rpm. Arrays were washed and stained in a Fluidics station.
Sample_scan_protocol	The method for array scanning was provided by Affymetrix. Arrays were scanned on an Affymetrix scanner.
Sample_data_processing	Data analysis was performed using the Affymetrix GeneChip Analysis software.
Sample_platform_id	GPL570
Sample_contact_name	Weiwei,,Chen
Sample_contact_email	weiweic@gene.com
Sample_contact_institute	Genentech
Sample_contact_address	1st DNA Way
Sample_contact_city	SSF
Sample_contact_zip/postal_code	94080
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM724nnn/GSM724524/suppl/GSM724524.CEL.gz
Sample_series_id	GSE29316
Sample_data_row_count	54613

GSM724525

GPL570

SHH treated, replicate 2

CCD-18Co, SHH treated

cell line: CCD-18Co cell type: colon fibroblasts treatment: Sonic hedgehog homolog (SHH)

Sample_geo_accession	GSM724525
Sample_status	Public on May 17 2011
Sample_submission_date	May 16 2011
Sample_last_update_date	May 17 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Colon fibroblasts CCD-18Co were stimulated with SHH (1 ug/ml) for 72 h.
Sample_growth_protocol_ch1	Colon fibroblasts were cultured in media plus 0.1% BSA.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was extracted using the Qiagen RNeasy kit.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	The method for preparation of cRNA was provided by Affymetrix. Briefly, 5 ug of total RNA was converted into double-stranded cDNA using a cDNA synthesis kit SuperScript Choice and a T7-(dT)24 oligomer primer. Double-stranded cDNA was purified on an affinity resin and ethanol precipitation. Following second-strand cDNA synthesis, labeled cRNA was generated using a T7 RNA polymerase and biotin-labeled nucleotide in an in vitro transcription reaction (Enzo Diagnostics). The labeled cRNA was purified on an affinity resin.
Sample_hyb_protocol	The method for hybridization of the arrays was provided by Affymetrix. Twenty micrograms of cRNA was fragmented and then hybridized to the arrays at 45°C for 19 hours in a rotisserie oven set at 60 rpm. Arrays were washed and stained in a Fluidics station.
Sample_scan_protocol	The method for array scanning was provided by Affymetrix. Arrays were scanned on an Affymetrix scanner.
Sample_data_processing	Data analysis was performed using the Affymetrix GeneChip Analysis software.
Sample_platform_id	GPL570
Sample_contact_name	Weiwei,,Chen
Sample_contact_email	weiweic@gene.com
Sample_contact_institute	Genentech
Sample_contact_address	1st DNA Way
Sample_contact_city	SSF
Sample_contact_zip/postal_code	94080
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM724nnn/GSM724525/suppl/GSM724525.CEL.gz
Sample_series_id	GSE29316
Sample_data_row_count	54613

GSM724526

GPL570

SHH treated, replicate 3

CCD-18Co, SHH treated

cell line: CCD-18Co cell type: colon fibroblasts treatment: Sonic hedgehog homolog (SHH)

Sample_geo_accession	GSM724526
Sample_status	Public on May 17 2011
Sample_submission_date	May 16 2011
Sample_last_update_date	May 17 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Colon fibroblasts CCD-18Co were stimulated with SHH (1 ug/ml) for 72 h.
Sample_growth_protocol_ch1	Colon fibroblasts were cultured in media plus 0.1% BSA.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was extracted using the Qiagen RNeasy kit.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	The method for preparation of cRNA was provided by Affymetrix. Briefly, 5 ug of total RNA was converted into double-stranded cDNA using a cDNA synthesis kit SuperScript Choice and a T7-(dT)24 oligomer primer. Double-stranded cDNA was purified on an affinity resin and ethanol precipitation. Following second-strand cDNA synthesis, labeled cRNA was generated using a T7 RNA polymerase and biotin-labeled nucleotide in an in vitro transcription reaction (Enzo Diagnostics). The labeled cRNA was purified on an affinity resin.
Sample_hyb_protocol	The method for hybridization of the arrays was provided by Affymetrix. Twenty micrograms of cRNA was fragmented and then hybridized to the arrays at 45°C for 19 hours in a rotisserie oven set at 60 rpm. Arrays were washed and stained in a Fluidics station.
Sample_scan_protocol	The method for array scanning was provided by Affymetrix. Arrays were scanned on an Affymetrix scanner.
Sample_data_processing	Data analysis was performed using the Affymetrix GeneChip Analysis software.
Sample_platform_id	GPL570
Sample_contact_name	Weiwei,,Chen
Sample_contact_email	weiweic@gene.com
Sample_contact_institute	Genentech
Sample_contact_address	1st DNA Way
Sample_contact_city	SSF
Sample_contact_zip/postal_code	94080
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM724nnn/GSM724526/suppl/GSM724526.CEL.gz
Sample_series_id	GSE29316
Sample_data_row_count	54613

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