Result

Search results for the GEO ID: GSE31165

(Click on the check boxes provided under "Select for analysis", to initiate grouping)

(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

GSM772499

GPL1261

shCTL, biological replicate 1

knock-down ES stable cell line control

cell line: mouse Embryonic Stem (ES) cells

Gene expression data from mouse knock-down ES stable control clone Raw data file: shCTL 1.CEL

Sample_geo_accession	GSM772499
Sample_status	Public on Dec 13 2012
Sample_submission_date	Aug 03 2011
Sample_last_update_date	Dec 13 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	The stable knock-down cell line was generated by using the short-hairpin RNA strategy.
Sample_growth_protocol_ch1	The growth of each clone was performed in mouse ES standard conditions and the total RNA was extracted
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNAs from either undifferentiated ES cells were purified by QIAshredder (Qiagen spa, Milano, Italy, catalog no. 79656) and extracted with RNeasy Protect Mini Kit (Qiagen, catalog no. 74126) using standard conditions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	Biotinylated cRNAs were then generated, using the GeneChip IVT labelling kit (Affymetrix). 20µg of Biotinylated cRNA was fragmented and 10µg hybridised to the Affymetrix GeneChip Mouse Genome 430_2 array for 16hrs at 45°C using an Affymetrix GeneChip Fluidics Station 450 according to the manufacturer’ standard protocols.
Sample_scan_protocol	GeneChips were scanned using the GeneChip® Scanner 3000 .
Sample_data_processing	The data were analyzed with the Bioconductor package Affy using RMA method for normalizing and summarizing probe level intensity measurements.
Sample_platform_id	GPL1261
Sample_contact_name	Rossella,,De Cegli
Sample_contact_email	decegli@tigem.it
Sample_contact_institute	Tigem
Sample_contact_address	via Castellino
Sample_contact_city	Naples
Sample_contact_zip/postal_code	80131
Sample_contact_country	Italy
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM772nnn/GSM772499/suppl/GSM772499.CEL.gz
Sample_series_id	GSE31165
Sample_series_id	GSE31701
Sample_data_row_count	45101

GSM772500

GPL1261

shCTL, biological replicate 2

knock-down ES stable cell line control

cell line: mouse Embryonic Stem (ES) cells

Gene expression data from mouse knock-down ES stable control clone Raw data file: shCTL 2.CEL

Sample_geo_accession	GSM772500
Sample_status	Public on Dec 13 2012
Sample_submission_date	Aug 03 2011
Sample_last_update_date	Dec 13 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	The stable knock-down cell line was generated by using the short-hairpin RNA strategy.
Sample_growth_protocol_ch1	The growth of each clone was performed in mouse ES standard conditions and the total RNA was extracted
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNAs from either undifferentiated ES cells were purified by QIAshredder (Qiagen spa, Milano, Italy, catalog no. 79656) and extracted with RNeasy Protect Mini Kit (Qiagen, catalog no. 74126) using standard conditions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	Biotinylated cRNAs were then generated, using the GeneChip IVT labelling kit (Affymetrix). 20µg of Biotinylated cRNA was fragmented and 10µg hybridised to the Affymetrix GeneChip Mouse Genome 430_2 array for 16hrs at 45°C using an Affymetrix GeneChip Fluidics Station 450 according to the manufacturer’ standard protocols.
Sample_scan_protocol	GeneChips were scanned using the GeneChip® Scanner 3000 .
Sample_data_processing	The data were analyzed with the Bioconductor package Affy using RMA method for normalizing and summarizing probe level intensity measurements.
Sample_platform_id	GPL1261
Sample_contact_name	Rossella,,De Cegli
Sample_contact_email	decegli@tigem.it
Sample_contact_institute	Tigem
Sample_contact_address	via Castellino
Sample_contact_city	Naples
Sample_contact_zip/postal_code	80131
Sample_contact_country	Italy
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM772nnn/GSM772500/suppl/GSM772500.CEL.gz
Sample_series_id	GSE31165
Sample_series_id	GSE31701
Sample_data_row_count	45101

GSM772501

GPL1261

shE13, biological replicate1

specific gene knock-down ES cell line

cell line: mouse Embryonic Stem (ES) cells

Gene expression data from mouse specific gene knock-down ES stable clone Raw data file: shE13 1.CEL

Sample_geo_accession	GSM772501
Sample_status	Public on Dec 13 2012
Sample_submission_date	Aug 03 2011
Sample_last_update_date	Dec 13 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	The stable knock-down cell line was generated by using the short-hairpin RNA strategy.
Sample_growth_protocol_ch1	The growth of each clone was performed in mouse ES standard conditions and the total RNA was extracted
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNAs from either undifferentiated ES cells were purified by QIAshredder (Qiagen spa, Milano, Italy, catalog no. 79656) and extracted with RNeasy Protect Mini Kit (Qiagen, catalog no. 74126) using standard conditions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	Biotinylated cRNAs were then generated, using the GeneChip IVT labelling kit (Affymetrix). 20µg of Biotinylated cRNA was fragmented and 10µg hybridised to the Affymetrix GeneChip Mouse Genome 430_2 array for 16hrs at 45°C using an Affymetrix GeneChip Fluidics Station 450 according to the manufacturer’ standard protocols.
Sample_scan_protocol	GeneChips were scanned using the GeneChip® Scanner 3000 .
Sample_data_processing	The data were analyzed with the Bioconductor package Affy using RMA method for normalizing and summarizing probe level intensity measurements.
Sample_platform_id	GPL1261
Sample_contact_name	Rossella,,De Cegli
Sample_contact_email	decegli@tigem.it
Sample_contact_institute	Tigem
Sample_contact_address	via Castellino
Sample_contact_city	Naples
Sample_contact_zip/postal_code	80131
Sample_contact_country	Italy
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM772nnn/GSM772501/suppl/GSM772501.CEL.gz
Sample_series_id	GSE31165
Sample_series_id	GSE31701
Sample_data_row_count	45101

GSM772502

GPL1261

shE13, biological replicate2

specific gene knock-down ES cell line

cell line: mouse Embryonic Stem (ES) cells

Gene expression data from mouse specific gene knock-down ES stable clone Raw data file: shE13 2.CEL

Sample_geo_accession	GSM772502
Sample_status	Public on Dec 13 2012
Sample_submission_date	Aug 03 2011
Sample_last_update_date	Dec 13 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	The stable knock-down cell line was generated by using the short-hairpin RNA strategy.
Sample_growth_protocol_ch1	The growth of each clone was performed in mouse ES standard conditions and the total RNA was extracted
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNAs from either undifferentiated ES cells were purified by QIAshredder (Qiagen spa, Milano, Italy, catalog no. 79656) and extracted with RNeasy Protect Mini Kit (Qiagen, catalog no. 74126) using standard conditions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	Biotinylated cRNAs were then generated, using the GeneChip IVT labelling kit (Affymetrix). 20µg of Biotinylated cRNA was fragmented and 10µg hybridised to the Affymetrix GeneChip Mouse Genome 430_2 array for 16hrs at 45°C using an Affymetrix GeneChip Fluidics Station 450 according to the manufacturer’ standard protocols.
Sample_scan_protocol	GeneChips were scanned using the GeneChip® Scanner 3000 .
Sample_data_processing	The data were analyzed with the Bioconductor package Affy using RMA method for normalizing and summarizing probe level intensity measurements.
Sample_platform_id	GPL1261
Sample_contact_name	Rossella,,De Cegli
Sample_contact_email	decegli@tigem.it
Sample_contact_institute	Tigem
Sample_contact_address	via Castellino
Sample_contact_city	Naples
Sample_contact_zip/postal_code	80131
Sample_contact_country	Italy
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM772nnn/GSM772502/suppl/GSM772502.CEL.gz
Sample_series_id	GSE31165
Sample_series_id	GSE31701
Sample_data_row_count	45101

GSM772503

GPL1261

shE13, biological replicate 3

specific gene knock-down ES cell line

cell line: mouse Embryonic Stem (ES) cells

Gene expression data from mouse specific gene knock-down ES stable clone Raw data file: shE13 3.CEL

Sample_geo_accession	GSM772503
Sample_status	Public on Dec 13 2012
Sample_submission_date	Aug 03 2011
Sample_last_update_date	Dec 13 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	The stable knock-down cell line was generated by using the short-hairpin RNA strategy.
Sample_growth_protocol_ch1	The growth of each clone was performed in mouse ES standard conditions and the total RNA was extracted
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNAs from either undifferentiated ES cells were purified by QIAshredder (Qiagen spa, Milano, Italy, catalog no. 79656) and extracted with RNeasy Protect Mini Kit (Qiagen, catalog no. 74126) using standard conditions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	Biotinylated cRNAs were then generated, using the GeneChip IVT labelling kit (Affymetrix). 20µg of Biotinylated cRNA was fragmented and 10µg hybridised to the Affymetrix GeneChip Mouse Genome 430_2 array for 16hrs at 45°C using an Affymetrix GeneChip Fluidics Station 450 according to the manufacturer’ standard protocols.
Sample_scan_protocol	GeneChips were scanned using the GeneChip® Scanner 3000 .
Sample_data_processing	The data were analyzed with the Bioconductor package Affy using RMA method for normalizing and summarizing probe level intensity measurements.
Sample_platform_id	GPL1261
Sample_contact_name	Rossella,,De Cegli
Sample_contact_email	decegli@tigem.it
Sample_contact_institute	Tigem
Sample_contact_address	via Castellino
Sample_contact_city	Naples
Sample_contact_zip/postal_code	80131
Sample_contact_country	Italy
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM772nnn/GSM772503/suppl/GSM772503.CEL.gz
Sample_series_id	GSE31165
Sample_series_id	GSE31701
Sample_data_row_count	45101

Make groups for comparisons

(2 groups will be compared at a time)

Select GSMs and click on "Add groups"

Enter the group name here:

Select expression type

Transcripts profile based on;

A. Differential status (Up/Down regulation)

B. Absolute calls (Transcribed/Not-detected)

Filter results by number of probes