Result

Search results for the GEO ID: GSE43957

(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

GSM1075009

GPL1261

Th0_Ctrl1

Th17 cells

treatment: Th0 cell type: Th17

Sample_geo_accession	GSM1075009
Sample_status	Public on Mar 07 2013
Sample_submission_date	Jan 31 2013
Sample_last_update_date	Mar 07 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Naïve T cells were isolated from WT mice, and cultured under Th0 condition with or without 40mM NaCl for 72 h.
Sample_growth_protocol_ch1	Cd4+ T cells were purified from spleen and lymph nodes using anti-CD4 microbeads (Miltenyi Biotech) then stained in PBS with 1% FCS for 20 min at room temperature with anti-Cd4-PerCP, anti-Cd62l-APC, and anti-Cd44-PE antibodies (all Biolegend, CA). Naïve Cd4+ Cd62lhigh Cd44low T cells were sorted using the BD FACSAria cell sorter. Sorted cells were activated with plate bound anti-Cd3 (2μg/ml) and anti-Cd28 (2μg/ml) in the presence of cytokines.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Extraction of total RNA was performed according to the RNeasy Mini Kit (Qiagen) manufacturer's instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (3' IVT Express Kit, Affymetrix).
Sample_hyb_protocol	Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Mouse 430 2.0 microarrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Sample_scan_protocol	GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G
Sample_data_processing	Expression data was preprocessed using the RMA algorithm followed by quantile normalization, with the parameters in the ExpressionFileCreator module of the GenePattern suite set to default
Sample_platform_id	GPL1261
Sample_contact_name	Nir,,Yosef
Sample_contact_email	nir@broadinstitute.org
Sample_contact_phone	(617) 714-7734
Sample_contact_laboratory	Regev
Sample_contact_institute	Broad
Sample_contact_address	7 Cambridge center
Sample_contact_city	Cambridge
Sample_contact_state	MA
Sample_contact_zip/postal_code	02142
Sample_contact_country	USA
Sample_contact_web_link	http://www.broadinstitute.org/~nir/
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1075nnn/GSM1075009/suppl/GSM1075009_Th0_Ctrl1.CEL.gz
Sample_series_id	GSE43957
Sample_series_id	GSE43970
Sample_data_row_count	45101

GSM1075010

GPL1261

Th0_Ctrl2

Th17 cells

treatment: Th0 cell type: Th17

Sample_geo_accession	GSM1075010
Sample_status	Public on Mar 07 2013
Sample_submission_date	Jan 31 2013
Sample_last_update_date	Mar 07 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Naïve T cells were isolated from WT mice, and cultured under Th0 condition with or without 40mM NaCl for 72 h.
Sample_growth_protocol_ch1	Cd4+ T cells were purified from spleen and lymph nodes using anti-CD4 microbeads (Miltenyi Biotech) then stained in PBS with 1% FCS for 20 min at room temperature with anti-Cd4-PerCP, anti-Cd62l-APC, and anti-Cd44-PE antibodies (all Biolegend, CA). Naïve Cd4+ Cd62lhigh Cd44low T cells were sorted using the BD FACSAria cell sorter. Sorted cells were activated with plate bound anti-Cd3 (2μg/ml) and anti-Cd28 (2μg/ml) in the presence of cytokines.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Extraction of total RNA was performed according to the RNeasy Mini Kit (Qiagen) manufacturer's instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (3' IVT Express Kit, Affymetrix).
Sample_hyb_protocol	Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Mouse 430 2.0 microarrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Sample_scan_protocol	GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G
Sample_data_processing	Expression data was preprocessed using the RMA algorithm followed by quantile normalization, with the parameters in the ExpressionFileCreator module of the GenePattern suite set to default
Sample_platform_id	GPL1261
Sample_contact_name	Nir,,Yosef
Sample_contact_email	nir@broadinstitute.org
Sample_contact_phone	(617) 714-7734
Sample_contact_laboratory	Regev
Sample_contact_institute	Broad
Sample_contact_address	7 Cambridge center
Sample_contact_city	Cambridge
Sample_contact_state	MA
Sample_contact_zip/postal_code	02142
Sample_contact_country	USA
Sample_contact_web_link	http://www.broadinstitute.org/~nir/
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1075nnn/GSM1075010/suppl/GSM1075010_Th0_Ctrl2.CEL.gz
Sample_series_id	GSE43957
Sample_series_id	GSE43970
Sample_data_row_count	45101

GSM1075011

GPL1261

Th0_NaCl1

Th17 cells

treatment: Th0+NaCl cell type: Th17

Sample_geo_accession	GSM1075011
Sample_status	Public on Mar 07 2013
Sample_submission_date	Jan 31 2013
Sample_last_update_date	Mar 07 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Naïve T cells were isolated from WT mice, and cultured under Th0 condition with or without 40mM NaCl for 72 h.
Sample_growth_protocol_ch1	Cd4+ T cells were purified from spleen and lymph nodes using anti-CD4 microbeads (Miltenyi Biotech) then stained in PBS with 1% FCS for 20 min at room temperature with anti-Cd4-PerCP, anti-Cd62l-APC, and anti-Cd44-PE antibodies (all Biolegend, CA). Naïve Cd4+ Cd62lhigh Cd44low T cells were sorted using the BD FACSAria cell sorter. Sorted cells were activated with plate bound anti-Cd3 (2μg/ml) and anti-Cd28 (2μg/ml) in the presence of cytokines.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Extraction of total RNA was performed according to the RNeasy Mini Kit (Qiagen) manufacturer's instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (3' IVT Express Kit, Affymetrix).
Sample_hyb_protocol	Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Mouse 430 2.0 microarrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Sample_scan_protocol	GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G
Sample_data_processing	Expression data was preprocessed using the RMA algorithm followed by quantile normalization, with the parameters in the ExpressionFileCreator module of the GenePattern suite set to default
Sample_platform_id	GPL1261
Sample_contact_name	Nir,,Yosef
Sample_contact_email	nir@broadinstitute.org
Sample_contact_phone	(617) 714-7734
Sample_contact_laboratory	Regev
Sample_contact_institute	Broad
Sample_contact_address	7 Cambridge center
Sample_contact_city	Cambridge
Sample_contact_state	MA
Sample_contact_zip/postal_code	02142
Sample_contact_country	USA
Sample_contact_web_link	http://www.broadinstitute.org/~nir/
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1075nnn/GSM1075011/suppl/GSM1075011_Th0_NaCl1.CEL.gz
Sample_series_id	GSE43957
Sample_series_id	GSE43970
Sample_data_row_count	45101

GSM1075012

GPL1261

Th0_NaCl2

Th17 cells

treatment: Th0+NaCl cell type: Th17

Sample_geo_accession	GSM1075012
Sample_status	Public on Mar 07 2013
Sample_submission_date	Jan 31 2013
Sample_last_update_date	Mar 07 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Naïve T cells were isolated from WT mice, and cultured under Th0 condition with or without 40mM NaCl for 72 h.
Sample_growth_protocol_ch1	Cd4+ T cells were purified from spleen and lymph nodes using anti-CD4 microbeads (Miltenyi Biotech) then stained in PBS with 1% FCS for 20 min at room temperature with anti-Cd4-PerCP, anti-Cd62l-APC, and anti-Cd44-PE antibodies (all Biolegend, CA). Naïve Cd4+ Cd62lhigh Cd44low T cells were sorted using the BD FACSAria cell sorter. Sorted cells were activated with plate bound anti-Cd3 (2μg/ml) and anti-Cd28 (2μg/ml) in the presence of cytokines.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Extraction of total RNA was performed according to the RNeasy Mini Kit (Qiagen) manufacturer's instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (3' IVT Express Kit, Affymetrix).
Sample_hyb_protocol	Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Mouse 430 2.0 microarrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Sample_scan_protocol	GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G
Sample_data_processing	Expression data was preprocessed using the RMA algorithm followed by quantile normalization, with the parameters in the ExpressionFileCreator module of the GenePattern suite set to default
Sample_platform_id	GPL1261
Sample_contact_name	Nir,,Yosef
Sample_contact_email	nir@broadinstitute.org
Sample_contact_phone	(617) 714-7734
Sample_contact_laboratory	Regev
Sample_contact_institute	Broad
Sample_contact_address	7 Cambridge center
Sample_contact_city	Cambridge
Sample_contact_state	MA
Sample_contact_zip/postal_code	02142
Sample_contact_country	USA
Sample_contact_web_link	http://www.broadinstitute.org/~nir/
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1075nnn/GSM1075012/suppl/GSM1075012_Th0_NaCl2.CEL.gz
Sample_series_id	GSE43957
Sample_series_id	GSE43970
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