Result

Search results for the GEO ID: GSE12588

(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

GSM315666

GPL1261

Six2_1

Cap mesenchyme

gene reported: Tg(Six2-EGFP/cre)1Amc / MGI:3845228 strain: CD-1 sex: unknown developmental stage: E15.5 theiler stage: 23 somite count: NA developmental landmark: NA

>> Amplification protocol << Target Amplified manufacturer/kit: TargetAmp 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies) Target Amplified protocol: Potter protocols Rounds of amplification: 2 URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:10720

Sample_geo_accession	GSM315666
Sample_status	Public on Jan 16 2009
Sample_submission_date	Aug 27 2008
Sample_last_update_date	Dec 30 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	pool size: approx 5-10 E15.5 kidneys
Sample_treatment_protocol_ch1	Pooled sample: Yes
Sample_treatment_protocol_ch1	Dissection Method: Trypsinization & FACS
Sample_treatment_protocol_ch1	Six2 transgenic mice are time-mated. Pregnant Six2 transgenic mice are euthanized by standard carbon dioxide asphyxiation. All fetuses are killed by decapitation with a scalpel. Fetal kidneys are dissected from fetuses and placed in ice-cold PBS. Embryonic kidneys are incubated in the presence of 300ul of trypsin for 5 minutes at 37 ºC. Kidneys are then dissociated by titurating in the presence of 600ul of ice-cold 10%FBS/PBS. The kidneys are pelleted at 5000 rpm, 4 ºC for 5 minutes. The media is aspirated and the cell pellet is resuspended in 200ul of ice-cold 2%FBS/PBS. Filter cells through 70 micron mesh filter and proceed with FACS.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Potter protocol: 'RNA purification'
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	Biotin-X-X-NHS (EPICENTRE Biotechnologies)
Sample_hyb_protocol	Affymetrix standard protocol
Sample_hyb_protocol	Amount labeled target hybridization to array: 5ug
Sample_scan_protocol	Affymetrix standard protocol
Sample_data_processing	Analysis method: Affymetrix GCOS, Gene Spring and Avadis programs.
Sample_data_processing	GCOS Tgt value: 1500
Sample_platform_id	GPL1261
Sample_contact_name	GUDMAP,,Developers
Sample_contact_email	gudmap-editors@gudmap.org
Sample_contact_phone	+44 131 3322471
Sample_contact_laboratory	GUDMAP Database Group
Sample_contact_institute	MRC Human Genetics Unit
Sample_contact_address	Crewe Road
Sample_contact_city	Edinburgh
Sample_contact_zip/postal_code	EH4 2XU
Sample_contact_country	United Kingdom
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM315nnn/GSM315666/suppl/GSM315666.CEL.gz
Sample_series_id	GSE12588
Sample_data_row_count	45101

GSM315667

GPL1261

Six2_2

Cap mesenchyme

gene reported: Tg(Six2-EGFP/cre)1Amc / MGI:3845228 strain: CD-1 sex: unknown developmental stage: E15.5 theiler stage: 23 somite count: NA developmental landmark: NA

Sample_geo_accession	GSM315667
Sample_status	Public on Jan 16 2009
Sample_submission_date	Aug 27 2008
Sample_last_update_date	Dec 30 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	pool size: approx 5-10 E15.5 kidneys
Sample_treatment_protocol_ch1	Pooled sample: Yes
Sample_treatment_protocol_ch1	Dissection Method: Trypsinization & FACS
Sample_treatment_protocol_ch1	Six2 transgenic mice are time-mated. Pregnant Six2 transgenic mice are euthanized by standard carbon dioxide asphyxiation. All fetuses are killed by decapitation with a scalpel. Fetal kidneys are dissected from fetuses and placed in ice-cold PBS. Embryonic kidneys are incubated in the presence of 300ul of trypsin for 5 minutes at 37 ºC. Kidneys are then dissociated by titurating in the presence of 600ul of ice-cold 10%FBS/PBS. The kidneys are pelleted at 5000 rpm, 4 ºC for 5 minutes. The media is aspirated and the cell pellet is resuspended in 200ul of ice-cold 2%FBS/PBS. Filter cells through 70 micron mesh filter and proceed with FACS.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Potter protocol: 'RNA purification'
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	Biotin-X-X-NHS (EPICENTRE Biotechnologies)
Sample_hyb_protocol	Affymetrix standard protocol
Sample_hyb_protocol	Amount labeled target hybridization to array: 5ug
Sample_scan_protocol	Affymetrix standard protocol
Sample_data_processing	Analysis method: Affymetrix GCOS, Gene Spring and Avadis programs.
Sample_data_processing	GCOS Tgt value: 1500
Sample_platform_id	GPL1261
Sample_contact_name	GUDMAP,,Developers
Sample_contact_email	gudmap-editors@gudmap.org
Sample_contact_phone	+44 131 3322471
Sample_contact_laboratory	GUDMAP Database Group
Sample_contact_institute	MRC Human Genetics Unit
Sample_contact_address	Crewe Road
Sample_contact_city	Edinburgh
Sample_contact_zip/postal_code	EH4 2XU
Sample_contact_country	United Kingdom
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM315nnn/GSM315667/suppl/GSM315667.CEL.gz
Sample_series_id	GSE12588
Sample_data_row_count	45101

GSM315668

GPL1261

Six2_3

Cap mesenchyme

gene reported: Tg(Six2-EGFP/cre)1Amc / MGI:3845228 strain: CD-1 sex: unknown developmental stage: E15.5 theiler stage: 23 somite count: NA developmental landmark: NA

Sample_geo_accession	GSM315668
Sample_status	Public on Jan 16 2009
Sample_submission_date	Aug 27 2008
Sample_last_update_date	Dec 30 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	pool size: approx 5-10 E15.5 kidneys
Sample_treatment_protocol_ch1	Pooled sample: Yes
Sample_treatment_protocol_ch1	Dissection Method: Trypsinization & FACS
Sample_treatment_protocol_ch1	Six2 transgenic mice are time-mated. Pregnant Six2 transgenic mice are euthanized by standard carbon dioxide asphyxiation. All fetuses are killed by decapitation with a scalpel. Fetal kidneys are dissected from fetuses and placed in ice-cold PBS. Embryonic kidneys are incubated in the presence of 300ul of trypsin for 5 minutes at 37 ºC. Kidneys are then dissociated by titurating in the presence of 600ul of ice-cold 10%FBS/PBS. The kidneys are pelleted at 5000 rpm, 4 ºC for 5 minutes. The media is aspirated and the cell pellet is resuspended in 200ul of ice-cold 2%FBS/PBS. Filter cells through 70 micron mesh filter and proceed with FACS.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Potter protocol: 'RNA purification'
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	Biotin-X-X-NHS (EPICENTRE Biotechnologies)
Sample_hyb_protocol	Affymetrix standard protocol
Sample_hyb_protocol	Amount labeled target hybridization to array: 5ug
Sample_scan_protocol	Affymetrix standard protocol
Sample_data_processing	Analysis method: Affymetrix GCOS, Gene Spring and Avadis programs.
Sample_data_processing	GCOS Tgt value: 1500
Sample_platform_id	GPL1261
Sample_contact_name	GUDMAP,,Developers
Sample_contact_email	gudmap-editors@gudmap.org
Sample_contact_phone	+44 131 3322471
Sample_contact_laboratory	GUDMAP Database Group
Sample_contact_institute	MRC Human Genetics Unit
Sample_contact_address	Crewe Road
Sample_contact_city	Edinburgh
Sample_contact_zip/postal_code	EH4 2XU
Sample_contact_country	United Kingdom
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM315nnn/GSM315668/suppl/GSM315668.CEL.gz
Sample_series_id	GSE12588
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