Result

Search results for the GEO ID: GSE10912

(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

GSM276683

GPL1261

Vector_1

HSC transfected with empty vector

Transfected with empty vector

HSC transfected with empty vector.

Sample_geo_accession	GSM276683
Sample_status	Public on Mar 22 2008
Sample_submission_date	Mar 20 2008
Sample_last_update_date	Mar 21 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA is isolated by following the protocol for the RNeasy Micro Kit, and quality is assessed using a 2100 Bioanalyzer instrument and RNA 6000 Pico LabChip assay (Agilent Technologies, Palo Alto, CA).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Utilizing the GeneChip Whole Transcript Sense Target Labeling Assay kit (Affymetrix, Santa Clara, CA.) between 100-300ng of total RNA undergoes reverse transcription with random hexamers tagged with T7 sequence. The double stranded cDNA that is generated is then amplified by T7 RNA polymerase to produce cRNA. Second cycle first strand cDNA synthesis then takes place incorporating dUTP which is later used as sites where fragmentation occurs by utilizing an uracil DNA glycosylase and apurinic/apyrimidinic endonuclease 1 enzyme mix. The fragmented cDNA is then labeled by terminal transferase attaching a biotin molecule using Affymetrix proprietary DNA labeling Reagent.
Sample_hyb_protocol	Approximately 2.0µg of fragmented and biotin-labeled cDNA is then hybridized onto a Mouse Gene ST 1.0 Array (Affymetrix, Santa Clara, CA.) for 16 hours at 45°C. Post-hybridization staining and washing are performed according to manufacturer's protocols using the Fluidics Station 450 instrument (Affymetrix).
Sample_scan_protocol	The arrays are scanned with a GeneChip Scanner 3000. Images are acquired and cel files generated which are then used for analysis.
Sample_data_processing	Affymetrix Expression Console, MAS5 algorithm
Sample_platform_id	GPL1261
Sample_contact_name	Shaoguang,,Li
Sample_contact_email	shaoguang.li@jax.org
Sample_contact_phone	207-288-6000
Sample_contact_institute	The Jackson Laboratory
Sample_contact_address	600 Main Street
Sample_contact_city	Bar Harbor
Sample_contact_state	ME
Sample_contact_zip/postal_code	04609
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM276nnn/GSM276683/suppl/GSM276683.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM276nnn/GSM276683/suppl/GSM276683.CHP.gz
Sample_series_id	GSE10912
Sample_data_row_count	45101

GSM276684

GPL1261

BCR/ABL_1

BCR/ABL transduced HSC

Transfected with BCR/ABL

HSC transfected with BCR/ABL.

Sample_geo_accession	GSM276684
Sample_status	Public on Mar 22 2008
Sample_submission_date	Mar 20 2008
Sample_last_update_date	Mar 21 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA is isolated by following the protocol for the RNeasy Micro Kit, and quality is assessed using a 2100 Bioanalyzer instrument and RNA 6000 Pico LabChip assay (Agilent Technologies, Palo Alto, CA).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Utilizing the GeneChip Whole Transcript Sense Target Labeling Assay kit (Affymetrix, Santa Clara, CA.) between 100-300ng of total RNA undergoes reverse transcription with random hexamers tagged with T7 sequence. The double stranded cDNA that is generated is then amplified by T7 RNA polymerase to produce cRNA. Second cycle first strand cDNA synthesis then takes place incorporating dUTP which is later used as sites where fragmentation occurs by utilizing an uracil DNA glycosylase and apurinic/apyrimidinic endonuclease 1 enzyme mix. The fragmented cDNA is then labeled by terminal transferase attaching a biotin molecule using Affymetrix proprietary DNA labeling Reagent.
Sample_hyb_protocol	Approximately 2.0µg of fragmented and biotin-labeled cDNA is then hybridized onto a Mouse Gene ST 1.0 Array (Affymetrix, Santa Clara, CA.) for 16 hours at 45°C. Post-hybridization staining and washing are performed according to manufacturer's protocols using the Fluidics Station 450 instrument (Affymetrix).
Sample_scan_protocol	The arrays are scanned with a GeneChip Scanner 3000. Images are acquired and cel files generated which are then used for analysis.
Sample_data_processing	Affymetrix Expression Console, MAS5 algorithm
Sample_platform_id	GPL1261
Sample_contact_name	Shaoguang,,Li
Sample_contact_email	shaoguang.li@jax.org
Sample_contact_phone	207-288-6000
Sample_contact_institute	The Jackson Laboratory
Sample_contact_address	600 Main Street
Sample_contact_city	Bar Harbor
Sample_contact_state	ME
Sample_contact_zip/postal_code	04609
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM276nnn/GSM276684/suppl/GSM276684.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM276nnn/GSM276684/suppl/GSM276684.CHP.gz
Sample_series_id	GSE10912
Sample_data_row_count	45101

GSM276686

GPL1261

BCR/ABL_treated_1

BCR/ABL transduced HSC treated with imatinib

Transfected with BCR/ABL and treated

HSC transfected with BCR/ABL and treated.

Sample_geo_accession	GSM276686
Sample_status	Public on Mar 22 2008
Sample_submission_date	Mar 20 2008
Sample_last_update_date	Mar 21 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA is isolated by following the protocol for the RNeasy Micro Kit, and quality is assessed using a 2100 Bioanalyzer instrument and RNA 6000 Pico LabChip assay (Agilent Technologies, Palo Alto, CA).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Utilizing the GeneChip Whole Transcript Sense Target Labeling Assay kit (Affymetrix, Santa Clara, CA.) between 100-300ng of total RNA undergoes reverse transcription with random hexamers tagged with T7 sequence. The double stranded cDNA that is generated is then amplified by T7 RNA polymerase to produce cRNA. Second cycle first strand cDNA synthesis then takes place incorporating dUTP which is later used as sites where fragmentation occurs by utilizing an uracil DNA glycosylase and apurinic/apyrimidinic endonuclease 1 enzyme mix. The fragmented cDNA is then labeled by terminal transferase attaching a biotin molecule using Affymetrix proprietary DNA labeling Reagent.
Sample_hyb_protocol	Approximately 2.0µg of fragmented and biotin-labeled cDNA is then hybridized onto a Mouse Gene ST 1.0 Array (Affymetrix, Santa Clara, CA.) for 16 hours at 45°C. Post-hybridization staining and washing are performed according to manufacturer's protocols using the Fluidics Station 450 instrument (Affymetrix).
Sample_scan_protocol	The arrays are scanned with a GeneChip Scanner 3000. Images are acquired and cel files generated which are then used for analysis.
Sample_data_processing	Affymetrix Expression Console, MAS5 algorithm
Sample_platform_id	GPL1261
Sample_contact_name	Shaoguang,,Li
Sample_contact_email	shaoguang.li@jax.org
Sample_contact_phone	207-288-6000
Sample_contact_institute	The Jackson Laboratory
Sample_contact_address	600 Main Street
Sample_contact_city	Bar Harbor
Sample_contact_state	ME
Sample_contact_zip/postal_code	04609
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM276nnn/GSM276686/suppl/GSM276686.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM276nnn/GSM276686/suppl/GSM276686.CHP.gz
Sample_series_id	GSE10912
Sample_data_row_count	45101

GSM276687

GPL1261

Vector_2

HSC transfected with empty vector

Transfected with empty vector

HSC transfected with empty vector.

Sample_geo_accession	GSM276687
Sample_status	Public on Mar 22 2008
Sample_submission_date	Mar 20 2008
Sample_last_update_date	Mar 21 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA is isolated by following the protocol for the RNeasy Micro Kit, and quality is assessed using a 2100 Bioanalyzer instrument and RNA 6000 Pico LabChip assay (Agilent Technologies, Palo Alto, CA).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Utilizing the GeneChip Whole Transcript Sense Target Labeling Assay kit (Affymetrix, Santa Clara, CA.) between 100-300ng of total RNA undergoes reverse transcription with random hexamers tagged with T7 sequence. The double stranded cDNA that is generated is then amplified by T7 RNA polymerase to produce cRNA. Second cycle first strand cDNA synthesis then takes place incorporating dUTP which is later used as sites where fragmentation occurs by utilizing an uracil DNA glycosylase and apurinic/apyrimidinic endonuclease 1 enzyme mix. The fragmented cDNA is then labeled by terminal transferase attaching a biotin molecule using Affymetrix proprietary DNA labeling Reagent.
Sample_hyb_protocol	Approximately 2.0µg of fragmented and biotin-labeled cDNA is then hybridized onto a Mouse Gene ST 1.0 Array (Affymetrix, Santa Clara, CA.) for 16 hours at 45°C. Post-hybridization staining and washing are performed according to manufacturer's protocols using the Fluidics Station 450 instrument (Affymetrix).
Sample_scan_protocol	The arrays are scanned with a GeneChip Scanner 3000. Images are acquired and cel files generated which are then used for analysis.
Sample_data_processing	Affymetrix Expression Console, MAS5 algorithm
Sample_platform_id	GPL1261
Sample_contact_name	Shaoguang,,Li
Sample_contact_email	shaoguang.li@jax.org
Sample_contact_phone	207-288-6000
Sample_contact_institute	The Jackson Laboratory
Sample_contact_address	600 Main Street
Sample_contact_city	Bar Harbor
Sample_contact_state	ME
Sample_contact_zip/postal_code	04609
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM276nnn/GSM276687/suppl/GSM276687.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM276nnn/GSM276687/suppl/GSM276687.CHP.gz
Sample_series_id	GSE10912
Sample_data_row_count	45101

GSM276688

GPL1261

BCR/ABL_2

HSC transduced with BCR/ABL

HSC transfected with BCR/ABL.

Sample_geo_accession	GSM276688
Sample_status	Public on Mar 22 2008
Sample_submission_date	Mar 20 2008
Sample_last_update_date	Mar 21 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA is isolated by following the protocol for the RNeasy Micro Kit, and quality is assessed using a 2100 Bioanalyzer instrument and RNA 6000 Pico LabChip assay (Agilent Technologies, Palo Alto, CA).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Utilizing the GeneChip Whole Transcript Sense Target Labeling Assay kit (Affymetrix, Santa Clara, CA.) between 100-300ng of total RNA undergoes reverse transcription with random hexamers tagged with T7 sequence. The double stranded cDNA that is generated is then amplified by T7 RNA polymerase to produce cRNA. Second cycle first strand cDNA synthesis then takes place incorporating dUTP which is later used as sites where fragmentation occurs by utilizing an uracil DNA glycosylase and apurinic/apyrimidinic endonuclease 1 enzyme mix. The fragmented cDNA is then labeled by terminal transferase attaching a biotin molecule using Affymetrix proprietary DNA labeling Reagent.
Sample_hyb_protocol	Approximately 2.0µg of fragmented and biotin-labeled cDNA is then hybridized onto a Mouse Gene ST 1.0 Array (Affymetrix, Santa Clara, CA.) for 16 hours at 45°C. Post-hybridization staining and washing are performed according to manufacturer's protocols using the Fluidics Station 450 instrument (Affymetrix).
Sample_scan_protocol	The arrays are scanned with a GeneChip Scanner 3000. Images are acquired and cel files generated which are then used for analysis.
Sample_data_processing	Affymetrix Expression Console, MAS5 algorithm
Sample_platform_id	GPL1261
Sample_contact_name	Shaoguang,,Li
Sample_contact_email	shaoguang.li@jax.org
Sample_contact_phone	207-288-6000
Sample_contact_institute	The Jackson Laboratory
Sample_contact_address	600 Main Street
Sample_contact_city	Bar Harbor
Sample_contact_state	ME
Sample_contact_zip/postal_code	04609
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM276nnn/GSM276688/suppl/GSM276688.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM276nnn/GSM276688/suppl/GSM276688.CHP.gz
Sample_series_id	GSE10912
Sample_data_row_count	45101

GSM276689

GPL1261

BCR/ABL_treated_2

BCR/ABL transduced HSC treated with imatinib

Transfected with BCR/ABL and treated

HSC transfected with BCR/ABL and treated.

Sample_geo_accession	GSM276689
Sample_status	Public on Mar 22 2008
Sample_submission_date	Mar 20 2008
Sample_last_update_date	Mar 21 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA is isolated by following the protocol for the RNeasy Micro Kit, and quality is assessed using a 2100 Bioanalyzer instrument and RNA 6000 Pico LabChip assay (Agilent Technologies, Palo Alto, CA).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Utilizing the GeneChip Whole Transcript Sense Target Labeling Assay kit (Affymetrix, Santa Clara, CA.) between 100-300ng of total RNA undergoes reverse transcription with random hexamers tagged with T7 sequence. The double stranded cDNA that is generated is then amplified by T7 RNA polymerase to produce cRNA. Second cycle first strand cDNA synthesis then takes place incorporating dUTP which is later used as sites where fragmentation occurs by utilizing an uracil DNA glycosylase and apurinic/apyrimidinic endonuclease 1 enzyme mix. The fragmented cDNA is then labeled by terminal transferase attaching a biotin molecule using Affymetrix proprietary DNA labeling Reagent.
Sample_hyb_protocol	Approximately 2.0µg of fragmented and biotin-labeled cDNA is then hybridized onto a Mouse Gene ST 1.0 Array (Affymetrix, Santa Clara, CA.) for 16 hours at 45°C. Post-hybridization staining and washing are performed according to manufacturer's protocols using the Fluidics Station 450 instrument (Affymetrix).
Sample_scan_protocol	The arrays are scanned with a GeneChip Scanner 3000. Images are acquired and cel files generated which are then used for analysis.
Sample_data_processing	Affymetrix Expression Console, MAS5 algorithm
Sample_platform_id	GPL1261
Sample_contact_name	Shaoguang,,Li
Sample_contact_email	shaoguang.li@jax.org
Sample_contact_phone	207-288-6000
Sample_contact_institute	The Jackson Laboratory
Sample_contact_address	600 Main Street
Sample_contact_city	Bar Harbor
Sample_contact_state	ME
Sample_contact_zip/postal_code	04609
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM276nnn/GSM276689/suppl/GSM276689.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM276nnn/GSM276689/suppl/GSM276689.CHP.gz
Sample_series_id	GSE10912
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