Result

Search results for the GEO ID: GSE28882

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Description

Characteristics

GSM715468

GPL570

IP-DZIP1 technical 1

IP-DZIP

cell line: HeLa ip antibody: rabbit anti-DZIP1 polyclonal antibody vendor: Santa Cruz Biotechnology antibody catalog number: SC-84091 antibody lot number: L2308

mRNAs associated with human DZIP1 protein

Sample_geo_accession	GSM715468
Sample_status	Public on Nov 01 2011
Sample_submission_date	Apr 27 2011
Sample_last_update_date	Nov 01 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Immunoprecipitation (IP) reactions were performed with 2 µg of anti-DZIP1 antibody (SC-84091 -lot# L2308, rabbit polyclonal, Santa Cruz Biotechnology, CA, USA) bound to protein A-agarose beads (Sigma, Deisenhofen, Germany). MSCs were lysed in polysome lysis buffer (Tris-HCl pH 7,4 15mM, MgCl2 15 mM, NaCl 0,3 M, 1% Triton X-100, 1 mM DTT, 100 U / ml RNase Out, PMSF 1mM and E64 10uM) for 1 hat 4°C. Beads were washed, then buffer and cell lysate were added, and the reaction mixtures were tumbled for 2 h at 4°C. After this incubation, the beads were thoroughly washed again with polysome lysis buffer and then their RNA extracted for microarray and RT-PCR experiments. Identical IPs were performed with beads precoated with rabbit IgG as a negative control.
Sample_growth_protocol_ch1	HeLa cells were cultivated in T75 culture flasks in RPMI (Gibco Invitrogen) supplemented with 10% FCS, penicillin (100 units/ml), and streptomycin (100 lg/ml). The culture medium was then replaced twice each week.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA was extracted using the RNeasy kit (Qiagen) according to the manufacturer's instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	cDNA was synthesized from immunoprecipitated RNA using reverse transcriptase followed by second-strand synthesis to generate double-stranded cDNA. An in vitro transcription reaction was used to generate biotinylated cRNA from 100 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	RNA was processed for hybridization with GeneChip 3’ IVT Express (Affymetrix - Santa Clara, USA), in accordance with the manufacturer’s instructions. After purification and fragmentation, cRNA (1µg) was hybridized for 16 hr at 45C on GeneChip Affymetrix Human Genome U133 Plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix.
Sample_scan_protocol	Post-hybridization washes were preformed on an Affymetrix GeneChip® Fluidics Station 450. Arrays were scanned on an Affymetrix GeneChip® Scanner 3000.
Sample_data_processing	Data was imported into Partek software using GCRMA protocol (Partek Incorporated. St. Louis, MO). Differentially enriched RNAs were found comparing immunoprecipitated samples against control samples.
Sample_platform_id	GPL570
Sample_contact_name	PATRICIA ,,SHIGUNOV
Sample_contact_email	shigunov@tecpar.br
Sample_contact_phone	55 41 3316-3231
Sample_contact_fax	55 41 3316-3238
Sample_contact_laboratory	LABCET - Laboratório de Biologia Básica de Células-Tronco
Sample_contact_institute	Instituto Carlos Chagas - FIOCRUZ-PR
Sample_contact_address	Rua Prof. Algacyr Munhoz Mader, 3775
Sample_contact_city	Curitiba
Sample_contact_state	Paraná
Sample_contact_zip/postal_code	81350010
Sample_contact_country	Brazil
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM715nnn/GSM715468/suppl/GSM715468.CEL.gz
Sample_series_id	GSE28882
Sample_data_row_count	54675

GSM715469

GPL570

IP-DZIP1 technical 2

IP-DZIP

cell line: HeLa ip antibody: rabbit anti-DZIP1 polyclonal antibody vendor: Santa Cruz Biotechnology antibody catalog number: SC-84091 antibody lot number: L2308

mRNAs associated with human DZIP1 protein

Sample_geo_accession	GSM715469
Sample_status	Public on Nov 01 2011
Sample_submission_date	Apr 27 2011
Sample_last_update_date	Nov 01 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Immunoprecipitation (IP) reactions were performed with 2 µg of anti-DZIP1 antibody (SC-84091 -lot# L2308, rabbit polyclonal, Santa Cruz Biotechnology, CA, USA) bound to protein A-agarose beads (Sigma, Deisenhofen, Germany). MSCs were lysed in polysome lysis buffer (Tris-HCl pH 7,4 15mM, MgCl2 15 mM, NaCl 0,3 M, 1% Triton X-100, 1 mM DTT, 100 U / ml RNase Out, PMSF 1mM and E64 10uM) for 1 hat 4°C. Beads were washed, then buffer and cell lysate were added, and the reaction mixtures were tumbled for 2 h at 4°C. After this incubation, the beads were thoroughly washed again with polysome lysis buffer and then their RNA extracted for microarray and RT-PCR experiments. Identical IPs were performed with beads precoated with rabbit IgG as a negative control.
Sample_growth_protocol_ch1	HeLa cells were cultivated in T75 culture flasks in RPMI (Gibco Invitrogen) supplemented with 10% FCS, penicillin (100 units/ml), and streptomycin (100 lg/ml). The culture medium was then replaced twice each week.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA was extracted using the RNeasy kit (Qiagen) according to the manufacturer's instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	cDNA was synthesized from immunoprecipitated RNA using reverse transcriptase followed by second-strand synthesis to generate double-stranded cDNA. An in vitro transcription reaction was used to generate biotinylated cRNA from 100 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	RNA was processed for hybridization with GeneChip 3’ IVT Express (Affymetrix - Santa Clara, USA), in accordance with the manufacturer’s instructions. After purification and fragmentation, cRNA (1µg) was hybridized for 16 hr at 45C on GeneChip Affymetrix Human Genome U133 Plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix.
Sample_scan_protocol	Post-hybridization washes were preformed on an Affymetrix GeneChip® Fluidics Station 450. Arrays were scanned on an Affymetrix GeneChip® Scanner 3000.
Sample_data_processing	Data was imported into Partek software using GCRMA protocol (Partek Incorporated. St. Louis, MO). Differentially enriched RNAs were found comparing immunoprecipitated samples against control samples.
Sample_platform_id	GPL570
Sample_contact_name	PATRICIA ,,SHIGUNOV
Sample_contact_email	shigunov@tecpar.br
Sample_contact_phone	55 41 3316-3231
Sample_contact_fax	55 41 3316-3238
Sample_contact_laboratory	LABCET - Laboratório de Biologia Básica de Células-Tronco
Sample_contact_institute	Instituto Carlos Chagas - FIOCRUZ-PR
Sample_contact_address	Rua Prof. Algacyr Munhoz Mader, 3775
Sample_contact_city	Curitiba
Sample_contact_state	Paraná
Sample_contact_zip/postal_code	81350010
Sample_contact_country	Brazil
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM715nnn/GSM715469/suppl/GSM715469.CEL.gz
Sample_series_id	GSE28882
Sample_data_row_count	54675

GSM715471

GPL570

IP-DZIP1 technical 3

IP-DZIP

cell line: HeLa ip antibody: rabbit anti-DZIP1 polyclonal antibody vendor: Santa Cruz Biotechnology antibody catalog number: SC-84091 antibody lot number: L2308

mRNAs associated with human DZIP1 protein

Sample_geo_accession	GSM715471
Sample_status	Public on Nov 01 2011
Sample_submission_date	Apr 27 2011
Sample_last_update_date	Nov 01 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Immunoprecipitation (IP) reactions were performed with 2 µg of anti-DZIP1 antibody (SC-84091 -lot# L2308, rabbit polyclonal, Santa Cruz Biotechnology, CA, USA) bound to protein A-agarose beads (Sigma, Deisenhofen, Germany). MSCs were lysed in polysome lysis buffer (Tris-HCl pH 7,4 15mM, MgCl2 15 mM, NaCl 0,3 M, 1% Triton X-100, 1 mM DTT, 100 U / ml RNase Out, PMSF 1mM and E64 10uM) for 1 hat 4°C. Beads were washed, then buffer and cell lysate were added, and the reaction mixtures were tumbled for 2 h at 4°C. After this incubation, the beads were thoroughly washed again with polysome lysis buffer and then their RNA extracted for microarray and RT-PCR experiments. Identical IPs were performed with beads precoated with rabbit IgG as a negative control.
Sample_growth_protocol_ch1	HeLa cells were cultivated in T75 culture flasks in RPMI (Gibco Invitrogen) supplemented with 10% FCS, penicillin (100 units/ml), and streptomycin (100 lg/ml). The culture medium was then replaced twice each week.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA was extracted using the RNeasy kit (Qiagen) according to the manufacturer's instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	cDNA was synthesized from immunoprecipitated RNA using reverse transcriptase followed by second-strand synthesis to generate double-stranded cDNA. An in vitro transcription reaction was used to generate biotinylated cRNA from 100 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	RNA was processed for hybridization with GeneChip 3’ IVT Express (Affymetrix - Santa Clara, USA), in accordance with the manufacturer’s instructions. After purification and fragmentation, cRNA (1µg) was hybridized for 16 hr at 45C on GeneChip Affymetrix Human Genome U133 Plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix.
Sample_scan_protocol	Post-hybridization washes were preformed on an Affymetrix GeneChip® Fluidics Station 450. Arrays were scanned on an Affymetrix GeneChip® Scanner 3000.
Sample_data_processing	Data was imported into Partek software using GCRMA protocol (Partek Incorporated. St. Louis, MO). Differentially enriched RNAs were found comparing immunoprecipitated samples against control samples.
Sample_platform_id	GPL570
Sample_contact_name	PATRICIA ,,SHIGUNOV
Sample_contact_email	shigunov@tecpar.br
Sample_contact_phone	55 41 3316-3231
Sample_contact_fax	55 41 3316-3238
Sample_contact_laboratory	LABCET - Laboratório de Biologia Básica de Células-Tronco
Sample_contact_institute	Instituto Carlos Chagas - FIOCRUZ-PR
Sample_contact_address	Rua Prof. Algacyr Munhoz Mader, 3775
Sample_contact_city	Curitiba
Sample_contact_state	Paraná
Sample_contact_zip/postal_code	81350010
Sample_contact_country	Brazil
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM715nnn/GSM715471/suppl/GSM715471.CEL.gz
Sample_series_id	GSE28882
Sample_data_row_count	54675

GSM715473

GPL570

IP-control technical 1

IP-control

cell line: HeLa ip antibody: rabbit IgG

non-specifically enriched RNAs

Sample_geo_accession	GSM715473
Sample_status	Public on Nov 01 2011
Sample_submission_date	Apr 27 2011
Sample_last_update_date	Nov 01 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Immunoprecipitation (IP) reactions were performed with 2 µg of anti-DZIP1 antibody (SC-84091 -lot# L2308, rabbit polyclonal, Santa Cruz Biotechnology, CA, USA) bound to protein A-agarose beads (Sigma, Deisenhofen, Germany). MSCs were lysed in polysome lysis buffer (Tris-HCl pH 7,4 15mM, MgCl2 15 mM, NaCl 0,3 M, 1% Triton X-100, 1 mM DTT, 100 U / ml RNase Out, PMSF 1mM and E64 10uM) for 1 hat 4°C. Beads were washed, then buffer and cell lysate were added, and the reaction mixtures were tumbled for 2 h at 4°C. After this incubation, the beads were thoroughly washed again with polysome lysis buffer and then their RNA extracted for microarray and RT-PCR experiments. Identical IPs were performed with beads precoated with rabbit IgG as a negative control.
Sample_growth_protocol_ch1	HeLa cells were cultivated in T75 culture flasks in RPMI (Gibco Invitrogen) supplemented with 10% FCS, penicillin (100 units/ml), and streptomycin (100 lg/ml). The culture medium was then replaced twice each week.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA was extracted using the RNeasy kit (Qiagen) according to the manufacturer's instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	cDNA was synthesized from immunoprecipitated RNA using reverse transcriptase followed by second-strand synthesis to generate double-stranded cDNA. An in vitro transcription reaction was used to generate biotinylated cRNA from 100 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	RNA was processed for hybridization with GeneChip 3’ IVT Express (Affymetrix - Santa Clara, USA), in accordance with the manufacturer’s instructions. After purification and fragmentation, cRNA (1µg) was hybridized for 16 hr at 45C on GeneChip Affymetrix Human Genome U133 Plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix.
Sample_scan_protocol	Post-hybridization washes were preformed on an Affymetrix GeneChip® Fluidics Station 450. Arrays were scanned on an Affymetrix GeneChip® Scanner 3000.
Sample_data_processing	Data was imported into Partek software using GCRMA protocol (Partek Incorporated. St. Louis, MO). Differentially enriched RNAs were found comparing immunoprecipitated samples against control samples.
Sample_platform_id	GPL570
Sample_contact_name	PATRICIA ,,SHIGUNOV
Sample_contact_email	shigunov@tecpar.br
Sample_contact_phone	55 41 3316-3231
Sample_contact_fax	55 41 3316-3238
Sample_contact_laboratory	LABCET - Laboratório de Biologia Básica de Células-Tronco
Sample_contact_institute	Instituto Carlos Chagas - FIOCRUZ-PR
Sample_contact_address	Rua Prof. Algacyr Munhoz Mader, 3775
Sample_contact_city	Curitiba
Sample_contact_state	Paraná
Sample_contact_zip/postal_code	81350010
Sample_contact_country	Brazil
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM715nnn/GSM715473/suppl/GSM715473.CEL.gz
Sample_series_id	GSE28882
Sample_data_row_count	54675

GSM715474

GPL570

IP-control technical 2

IP-control

cell line: HeLa ip antibody: rabbit IgG

non-specifically enriched RNAs

Sample_geo_accession	GSM715474
Sample_status	Public on Nov 01 2011
Sample_submission_date	Apr 27 2011
Sample_last_update_date	Nov 01 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Immunoprecipitation (IP) reactions were performed with 2 µg of anti-DZIP1 antibody (SC-84091 -lot# L2308, rabbit polyclonal, Santa Cruz Biotechnology, CA, USA) bound to protein A-agarose beads (Sigma, Deisenhofen, Germany). MSCs were lysed in polysome lysis buffer (Tris-HCl pH 7,4 15mM, MgCl2 15 mM, NaCl 0,3 M, 1% Triton X-100, 1 mM DTT, 100 U / ml RNase Out, PMSF 1mM and E64 10uM) for 1 hat 4°C. Beads were washed, then buffer and cell lysate were added, and the reaction mixtures were tumbled for 2 h at 4°C. After this incubation, the beads were thoroughly washed again with polysome lysis buffer and then their RNA extracted for microarray and RT-PCR experiments. Identical IPs were performed with beads precoated with rabbit IgG as a negative control.
Sample_growth_protocol_ch1	HeLa cells were cultivated in T75 culture flasks in RPMI (Gibco Invitrogen) supplemented with 10% FCS, penicillin (100 units/ml), and streptomycin (100 lg/ml). The culture medium was then replaced twice each week.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA was extracted using the RNeasy kit (Qiagen) according to the manufacturer's instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	cDNA was synthesized from immunoprecipitated RNA using reverse transcriptase followed by second-strand synthesis to generate double-stranded cDNA. An in vitro transcription reaction was used to generate biotinylated cRNA from 100 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	RNA was processed for hybridization with GeneChip 3’ IVT Express (Affymetrix - Santa Clara, USA), in accordance with the manufacturer’s instructions. After purification and fragmentation, cRNA (1µg) was hybridized for 16 hr at 45C on GeneChip Affymetrix Human Genome U133 Plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix.
Sample_scan_protocol	Post-hybridization washes were preformed on an Affymetrix GeneChip® Fluidics Station 450. Arrays were scanned on an Affymetrix GeneChip® Scanner 3000.
Sample_data_processing	Data was imported into Partek software using GCRMA protocol (Partek Incorporated. St. Louis, MO). Differentially enriched RNAs were found comparing immunoprecipitated samples against control samples.
Sample_platform_id	GPL570
Sample_contact_name	PATRICIA ,,SHIGUNOV
Sample_contact_email	shigunov@tecpar.br
Sample_contact_phone	55 41 3316-3231
Sample_contact_fax	55 41 3316-3238
Sample_contact_laboratory	LABCET - Laboratório de Biologia Básica de Células-Tronco
Sample_contact_institute	Instituto Carlos Chagas - FIOCRUZ-PR
Sample_contact_address	Rua Prof. Algacyr Munhoz Mader, 3775
Sample_contact_city	Curitiba
Sample_contact_state	Paraná
Sample_contact_zip/postal_code	81350010
Sample_contact_country	Brazil
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM715nnn/GSM715474/suppl/GSM715474.CEL.gz
Sample_series_id	GSE28882
Sample_data_row_count	54675

GSM715476

GPL570

IP-control technical 3

IP-control

cell line: HeLa ip antibody: rabbit IgG

non-specifically enriched RNAs

Sample_geo_accession	GSM715476
Sample_status	Public on Nov 01 2011
Sample_submission_date	Apr 27 2011
Sample_last_update_date	Nov 01 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Immunoprecipitation (IP) reactions were performed with 2 µg of anti-DZIP1 antibody (SC-84091 -lot# L2308, rabbit polyclonal, Santa Cruz Biotechnology, CA, USA) bound to protein A-agarose beads (Sigma, Deisenhofen, Germany). MSCs were lysed in polysome lysis buffer (Tris-HCl pH 7,4 15mM, MgCl2 15 mM, NaCl 0,3 M, 1% Triton X-100, 1 mM DTT, 100 U / ml RNase Out, PMSF 1mM and E64 10uM) for 1 hat 4°C. Beads were washed, then buffer and cell lysate were added, and the reaction mixtures were tumbled for 2 h at 4°C. After this incubation, the beads were thoroughly washed again with polysome lysis buffer and then their RNA extracted for microarray and RT-PCR experiments. Identical IPs were performed with beads precoated with rabbit IgG as a negative control.
Sample_growth_protocol_ch1	HeLa cells were cultivated in T75 culture flasks in RPMI (Gibco Invitrogen) supplemented with 10% FCS, penicillin (100 units/ml), and streptomycin (100 lg/ml). The culture medium was then replaced twice each week.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA was extracted using the RNeasy kit (Qiagen) according to the manufacturer's instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	cDNA was synthesized from immunoprecipitated RNA using reverse transcriptase followed by second-strand synthesis to generate double-stranded cDNA. An in vitro transcription reaction was used to generate biotinylated cRNA from 100 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	RNA was processed for hybridization with GeneChip 3’ IVT Express (Affymetrix - Santa Clara, USA), in accordance with the manufacturer’s instructions. After purification and fragmentation, cRNA (1µg) was hybridized for 16 hr at 45C on GeneChip Affymetrix Human Genome U133 Plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix.
Sample_scan_protocol	Post-hybridization washes were preformed on an Affymetrix GeneChip® Fluidics Station 450. Arrays were scanned on an Affymetrix GeneChip® Scanner 3000.
Sample_data_processing	Data was imported into Partek software using GCRMA protocol (Partek Incorporated. St. Louis, MO). Differentially enriched RNAs were found comparing immunoprecipitated samples against control samples.
Sample_platform_id	GPL570
Sample_contact_name	PATRICIA ,,SHIGUNOV
Sample_contact_email	shigunov@tecpar.br
Sample_contact_phone	55 41 3316-3231
Sample_contact_fax	55 41 3316-3238
Sample_contact_laboratory	LABCET - Laboratório de Biologia Básica de Células-Tronco
Sample_contact_institute	Instituto Carlos Chagas - FIOCRUZ-PR
Sample_contact_address	Rua Prof. Algacyr Munhoz Mader, 3775
Sample_contact_city	Curitiba
Sample_contact_state	Paraná
Sample_contact_zip/postal_code	81350010
Sample_contact_country	Brazil
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM715nnn/GSM715476/suppl/GSM715476.CEL.gz
Sample_series_id	GSE28882
Sample_data_row_count	54675

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