Result

Search results for the GEO ID: GSE49118

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GSM ID

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Title

Source name

Description

Characteristics

GSM1193989

GPL1261

BMT-ASXL1Mt-1

Myeloid BM cells derived from ASXL1-MT-transplanted mice (myelodysplastic symdrome-like disease)

cell type: myeloid BM cells

Sample_geo_accession	GSM1193989
Sample_status	Public on Jul 31 2013
Sample_submission_date	Jul 23 2013
Sample_last_update_date	Jul 31 2013
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 RNAs were extracted using TRIzol (Invitrogen, Carlsbad, CA). 3 micrograms of total RNA was reverse transcribed using the SuperScript III system for cDNA synthesis (Invitrogen) according to the protocol recommended by Affymetrix. The oligonucleotide used for priming was 5'-ggccagtgaattgtaatacgactcactatagggaggcgg-(t)24-3' (Invitrogen). Double-stranded cDNA was cleaned by phenol:chloroform extraction and the aqueous phase removed by centrifugation through Phase-lock Gel (Eppendorf).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	In vitro transcription was performed on 1 microgram of cDNA using the Enzo BioArray High Yield RNA transcript labelling kit (Enzo Diagnostics). The cRNA was cleaned using RNAeasy clean-up columns (Qiagen). The cRNA was fragmented by heating in 40 mM Tris-acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc.
Sample_hyb_protocol	10 micrograms of fragmented cRNA were hybridised (45degree CelsiusC, 16 hours). Hybridization was controled by use of the GeneChip Eukaryotic Hybridization Control Kit (Affymetrix). Washing and staining was performed in a Fluidics Station 450 (Affymetrix) using the protocol EukGE-WS2v4.
Sample_scan_protocol	Scanning was performed in an Affymetrix GeneChip scanner 3000 7G.
Sample_data_processing	Genechip analysis was performed using the Affymetrix GeneChip Operating Software v1.3. Signal value was calculated using MAS5 algorithm.
Sample_platform_id	GPL1261
Sample_contact_name	Daichi,,Inoue
Sample_contact_email	daichi-i@hotmail.co.jp
Sample_contact_institute	Division of Cellular Therapy, Advanced Clinical Research Center, The Institute of Medical Science, The University of Tokyo
Sample_contact_address	4-6-1 Shirokanedai, Minato-ku
Sample_contact_city	Tokyo
Sample_contact_zip/postal_code	108-8639
Sample_contact_country	Japan
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1193nnn/GSM1193989/suppl/GSM1193989_BMT_ASXL1Mt_1.CEL.gz
Sample_series_id	GSE49118
Sample_data_row_count	45037

GSM1193990

GPL1261

BMT-ASXL1Mt-2

Myeloid BM cells derived from ASXL1-MT-transplanted mice (myelodysplastic symdrome-like disease)

cell type: myeloid BM cells

Sample_geo_accession	GSM1193990
Sample_status	Public on Jul 31 2013
Sample_submission_date	Jul 23 2013
Sample_last_update_date	Jul 31 2013
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 RNAs were extracted using TRIzol (Invitrogen, Carlsbad, CA). 3 micrograms of total RNA was reverse transcribed using the SuperScript III system for cDNA synthesis (Invitrogen) according to the protocol recommended by Affymetrix. The oligonucleotide used for priming was 5'-ggccagtgaattgtaatacgactcactatagggaggcgg-(t)24-3' (Invitrogen). Double-stranded cDNA was cleaned by phenol:chloroform extraction and the aqueous phase removed by centrifugation through Phase-lock Gel (Eppendorf).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	In vitro transcription was performed on 1 microgram of cDNA using the Enzo BioArray High Yield RNA transcript labelling kit (Enzo Diagnostics). The cRNA was cleaned using RNAeasy clean-up columns (Qiagen). The cRNA was fragmented by heating in 40 mM Tris-acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc.
Sample_hyb_protocol	10 micrograms of fragmented cRNA were hybridised (45degree CelsiusC, 16 hours). Hybridization was controled by use of the GeneChip Eukaryotic Hybridization Control Kit (Affymetrix). Washing and staining was performed in a Fluidics Station 450 (Affymetrix) using the protocol EukGE-WS2v4.
Sample_scan_protocol	Scanning was performed in an Affymetrix GeneChip scanner 3000 7G.
Sample_data_processing	Genechip analysis was performed using the Affymetrix GeneChip Operating Software v1.3. Signal value was calculated using MAS5 algorithm.
Sample_platform_id	GPL1261
Sample_contact_name	Daichi,,Inoue
Sample_contact_email	daichi-i@hotmail.co.jp
Sample_contact_institute	Division of Cellular Therapy, Advanced Clinical Research Center, The Institute of Medical Science, The University of Tokyo
Sample_contact_address	4-6-1 Shirokanedai, Minato-ku
Sample_contact_city	Tokyo
Sample_contact_zip/postal_code	108-8639
Sample_contact_country	Japan
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1193nnn/GSM1193990/suppl/GSM1193990_BMT_ASXL1Mt_2.CEL.gz
Sample_series_id	GSE49118
Sample_data_row_count	45037

GSM1193991

GPL1261

BMT-ASXL1Mt-3

Myeloid BM cells derived from ASXL1-MT-transplanted mice (myelodysplastic symdrome-like disease)

cell type: myeloid BM cells

Sample_geo_accession	GSM1193991
Sample_status	Public on Jul 31 2013
Sample_submission_date	Jul 23 2013
Sample_last_update_date	Jul 31 2013
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 RNAs were extracted using TRIzol (Invitrogen, Carlsbad, CA). 3 micrograms of total RNA was reverse transcribed using the SuperScript III system for cDNA synthesis (Invitrogen) according to the protocol recommended by Affymetrix. The oligonucleotide used for priming was 5'-ggccagtgaattgtaatacgactcactatagggaggcgg-(t)24-3' (Invitrogen). Double-stranded cDNA was cleaned by phenol:chloroform extraction and the aqueous phase removed by centrifugation through Phase-lock Gel (Eppendorf).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	In vitro transcription was performed on 1 microgram of cDNA using the Enzo BioArray High Yield RNA transcript labelling kit (Enzo Diagnostics). The cRNA was cleaned using RNAeasy clean-up columns (Qiagen). The cRNA was fragmented by heating in 40 mM Tris-acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc.
Sample_hyb_protocol	10 micrograms of fragmented cRNA were hybridised (45degree CelsiusC, 16 hours). Hybridization was controled by use of the GeneChip Eukaryotic Hybridization Control Kit (Affymetrix). Washing and staining was performed in a Fluidics Station 450 (Affymetrix) using the protocol EukGE-WS2v4.
Sample_scan_protocol	Scanning was performed in an Affymetrix GeneChip scanner 3000 7G.
Sample_data_processing	Genechip analysis was performed using the Affymetrix GeneChip Operating Software v1.3. Signal value was calculated using MAS5 algorithm.
Sample_platform_id	GPL1261
Sample_contact_name	Daichi,,Inoue
Sample_contact_email	daichi-i@hotmail.co.jp
Sample_contact_institute	Division of Cellular Therapy, Advanced Clinical Research Center, The Institute of Medical Science, The University of Tokyo
Sample_contact_address	4-6-1 Shirokanedai, Minato-ku
Sample_contact_city	Tokyo
Sample_contact_zip/postal_code	108-8639
Sample_contact_country	Japan
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1193nnn/GSM1193991/suppl/GSM1193991_BMT_ASXL1Mt_3.CEL.gz
Sample_series_id	GSE49118
Sample_data_row_count	45037

GSM1193992

GPL1261

BMT-mock-1

CD3-B220-Ter119- Myeloid BM cells derived from mock-transplanted mice (normal control)

cell type: myeloid BM cells

Sample_geo_accession	GSM1193992
Sample_status	Public on Jul 31 2013
Sample_submission_date	Jul 23 2013
Sample_last_update_date	Jul 31 2013
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 RNAs were extracted using TRIzol (Invitrogen, Carlsbad, CA). 3 micrograms of total RNA was reverse transcribed using the SuperScript III system for cDNA synthesis (Invitrogen) according to the protocol recommended by Affymetrix. The oligonucleotide used for priming was 5'-ggccagtgaattgtaatacgactcactatagggaggcgg-(t)24-3' (Invitrogen). Double-stranded cDNA was cleaned by phenol:chloroform extraction and the aqueous phase removed by centrifugation through Phase-lock Gel (Eppendorf).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	In vitro transcription was performed on 1 microgram of cDNA using the Enzo BioArray High Yield RNA transcript labelling kit (Enzo Diagnostics). The cRNA was cleaned using RNAeasy clean-up columns (Qiagen). The cRNA was fragmented by heating in 40 mM Tris-acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc.
Sample_hyb_protocol	10 micrograms of fragmented cRNA were hybridised (45degree CelsiusC, 16 hours). Hybridization was controled by use of the GeneChip Eukaryotic Hybridization Control Kit (Affymetrix). Washing and staining was performed in a Fluidics Station 450 (Affymetrix) using the protocol EukGE-WS2v4.
Sample_scan_protocol	Scanning was performed in an Affymetrix GeneChip scanner 3000 7G.
Sample_data_processing	Genechip analysis was performed using the Affymetrix GeneChip Operating Software v1.3. Signal value was calculated using MAS5 algorithm.
Sample_platform_id	GPL1261
Sample_contact_name	Daichi,,Inoue
Sample_contact_email	daichi-i@hotmail.co.jp
Sample_contact_institute	Division of Cellular Therapy, Advanced Clinical Research Center, The Institute of Medical Science, The University of Tokyo
Sample_contact_address	4-6-1 Shirokanedai, Minato-ku
Sample_contact_city	Tokyo
Sample_contact_zip/postal_code	108-8639
Sample_contact_country	Japan
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1193nnn/GSM1193992/suppl/GSM1193992_BMT_mock_1.CEL.gz
Sample_series_id	GSE49118
Sample_data_row_count	45037

GSM1193993

GPL1261

BMT-mock-2

CD3-B220-Ter119- Myeloid BM cells derived from mock-transplanted mice (normal control)

cell type: myeloid BM cells

Sample_geo_accession	GSM1193993
Sample_status	Public on Jul 31 2013
Sample_submission_date	Jul 23 2013
Sample_last_update_date	Jul 31 2013
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 RNAs were extracted using TRIzol (Invitrogen, Carlsbad, CA). 3 micrograms of total RNA was reverse transcribed using the SuperScript III system for cDNA synthesis (Invitrogen) according to the protocol recommended by Affymetrix. The oligonucleotide used for priming was 5'-ggccagtgaattgtaatacgactcactatagggaggcgg-(t)24-3' (Invitrogen). Double-stranded cDNA was cleaned by phenol:chloroform extraction and the aqueous phase removed by centrifugation through Phase-lock Gel (Eppendorf).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	In vitro transcription was performed on 1 microgram of cDNA using the Enzo BioArray High Yield RNA transcript labelling kit (Enzo Diagnostics). The cRNA was cleaned using RNAeasy clean-up columns (Qiagen). The cRNA was fragmented by heating in 40 mM Tris-acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc.
Sample_hyb_protocol	10 micrograms of fragmented cRNA were hybridised (45degree CelsiusC, 16 hours). Hybridization was controled by use of the GeneChip Eukaryotic Hybridization Control Kit (Affymetrix). Washing and staining was performed in a Fluidics Station 450 (Affymetrix) using the protocol EukGE-WS2v4.
Sample_scan_protocol	Scanning was performed in an Affymetrix GeneChip scanner 3000 7G.
Sample_data_processing	Genechip analysis was performed using the Affymetrix GeneChip Operating Software v1.3. Signal value was calculated using MAS5 algorithm.
Sample_platform_id	GPL1261
Sample_contact_name	Daichi,,Inoue
Sample_contact_email	daichi-i@hotmail.co.jp
Sample_contact_institute	Division of Cellular Therapy, Advanced Clinical Research Center, The Institute of Medical Science, The University of Tokyo
Sample_contact_address	4-6-1 Shirokanedai, Minato-ku
Sample_contact_city	Tokyo
Sample_contact_zip/postal_code	108-8639
Sample_contact_country	Japan
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1193nnn/GSM1193993/suppl/GSM1193993_BMT_mock_2_430.CEL.gz
Sample_series_id	GSE49118
Sample_data_row_count	45037

GSM1193994

GPL1261

BMT-mock-3

CD3-B220-Ter119- Myeloid BM cells derived from mock-transplanted mice (normal control)

cell type: myeloid BM cells

Sample_geo_accession	GSM1193994
Sample_status	Public on Jul 31 2013
Sample_submission_date	Jul 23 2013
Sample_last_update_date	Jul 31 2013
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 RNAs were extracted using TRIzol (Invitrogen, Carlsbad, CA). 3 micrograms of total RNA was reverse transcribed using the SuperScript III system for cDNA synthesis (Invitrogen) according to the protocol recommended by Affymetrix. The oligonucleotide used for priming was 5'-ggccagtgaattgtaatacgactcactatagggaggcgg-(t)24-3' (Invitrogen). Double-stranded cDNA was cleaned by phenol:chloroform extraction and the aqueous phase removed by centrifugation through Phase-lock Gel (Eppendorf).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	In vitro transcription was performed on 1 microgram of cDNA using the Enzo BioArray High Yield RNA transcript labelling kit (Enzo Diagnostics). The cRNA was cleaned using RNAeasy clean-up columns (Qiagen). The cRNA was fragmented by heating in 40 mM Tris-acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc.
Sample_hyb_protocol	10 micrograms of fragmented cRNA were hybridised (45degree CelsiusC, 16 hours). Hybridization was controled by use of the GeneChip Eukaryotic Hybridization Control Kit (Affymetrix). Washing and staining was performed in a Fluidics Station 450 (Affymetrix) using the protocol EukGE-WS2v4.
Sample_scan_protocol	Scanning was performed in an Affymetrix GeneChip scanner 3000 7G.
Sample_data_processing	Genechip analysis was performed using the Affymetrix GeneChip Operating Software v1.3. Signal value was calculated using MAS5 algorithm.
Sample_platform_id	GPL1261
Sample_contact_name	Daichi,,Inoue
Sample_contact_email	daichi-i@hotmail.co.jp
Sample_contact_institute	Division of Cellular Therapy, Advanced Clinical Research Center, The Institute of Medical Science, The University of Tokyo
Sample_contact_address	4-6-1 Shirokanedai, Minato-ku
Sample_contact_city	Tokyo
Sample_contact_zip/postal_code	108-8639
Sample_contact_country	Japan
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1193nnn/GSM1193994/suppl/GSM1193994_BMT_mock_3_430.CEL.gz
Sample_series_id	GSE49118
Sample_data_row_count	45037

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