Search results for the GEO ID: GSE47643  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM1153941 | GPL1261 |
|
Group1: preB cells without induction_4
|
Grp1-4: preB cells without induction
|
strain: C57BL/6
tissue: fetal liver
cell type: preB-cells
induction of mir-221: 0 h
|
Grp1_C57B6_4_SCfl_mir221_0h_430_2
Gene expression profiles of un-induced preB cells prepared from tissue culture were compared using Affymetrix MG430Av2 GeneChip arrays. After total RNA extraction, reverse transcription, cDNA extraction, the biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized in triplicates for each of the four groups to the GeneChip arrays. Twelve chips in these four groups were hybridized and analyzed: Group1 are un-induced preB cells
|
| Sample_geo_accession | GSM1153941
| | Sample_status | Public on Jun 05 2013
| | Sample_submission_date | Jun 04 2013
| | Sample_last_update_date | Jun 07 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | Samples were obtained from the fetal liver of C57BL/6, CD45.1pos mice (MPIIB, Berlin, Germany)
| | Sample_treatment_protocol_ch1 | MiR-221 expression was induced by adding 1 mg/ml doxycycline to the cell culture media and samples were taken at 8, 16, or 24h after induction.
| | Sample_growth_protocol_ch1 | PreB cells derived from wild type fetal liver (C57BL/6, CD45.1pos) at day 18 of gestation were grown on a confluent layer of gamma-irradiated (30Gy) M-CSF-deficient OP9 stromal cells in IMDM medium (Gibco) supplemented with 2% FCS (Sigma-Aldrich), 0.03% Primatone-RL (Quest) and 1% mouse IL7 conditioned media as described by Rolink et al, 1991.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instruction, including the recommended DNase digest. The purity and integrity of RNA were assessed for each sample using an Agilent 2100 Bioanalyzer with the RNA 6000 Nano LabChip and amount was checked with a NanoDrop ND-1000 spectrophotometer. Contaminating genomic DNA was removed by an on-column DNA digestion step (Qiagen).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Labeling and hybridization of total RNA was performed using the GeneChip 3’ IVT Express Kit from Affymetrix according to the manufacturers instruction. Briefly, after total RNA extraction, 100 ng of total RNA from each cell sample was reverse transcribed, cDNA was extracted, biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized to each of the GeneChip arrays. The MG430Av2 GeneChip arrays were loaded with the hybridization cocktail, hybridized at 45 °C rotating for 16 h in a hybridization oven 640 (Affymetrix), washed and stained with streptavidin-phycoerythrin using the Affymetrix GeneChip Fluidics Workstation 400.
| | Sample_hyb_protocol | Labeling and hybridization of total RNA was performed using the GeneChip 3’ IVT Express Kit from Affymetrix according to the manufacturers instruction. Briefly, after total RNA extraction, 100 ng of total RNA from each cell sample was reverse transcribed, cDNA was extracted, biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized to each of the GeneChip arrays. The MG430Av2 GeneChip arrays were loaded with the hybridization cocktail, hybridized at 45 °C rotating for 16 h in a hybridization oven 640 (Affymetrix), washed and stained with streptavidin-phycoerythrin using the Affymetrix GeneChip Fluidics Workstation 400.
| | Sample_scan_protocol | Arrays were scanned with an Affymetrix GeneChip Scanner 3000, using the GCOS software from Affymetrix.
| | Sample_data_processing | Data were analyzed according to High Performance Chip Data Analysis (HPCDA, unpublished - Joachim R. Grün) with the Bioretis database (http://www.bioretis-analysis.de/) using the default filter parameters for decreased and increased gene lists (description of database c.f. open access paper Menssen et al., 2009; PubMedID: 19265543). Chip data included in the Bioretis database were analyzed using the GeneChip Operating Software (GCOS, Affymetrix), version 1.4. Microarrays were globally normalized and scaled to a trimmed mean expression value of 150. Quality checks were performed according to the manufacturer's recommendations. All 3 chips of one group were compared to each 3 chips of any other group (results, compared to 16h chips were ignored in this study), and the following parameters of absolute and comparative analysis were included in the Bioretis database: expression heights (Signals) and mean, median and standard deviation of Signals of both groups, call for presence of transcripts (Absent, A; Marginal, M; Present, P), p-value for presence or absence of transcripts, log2 value of fold change (Signal Log Ratio, SLR) and the fold change as mean values, call for the significance of differentially expression (Change Call: Increase, I; Marginal I, MI; Decrease, D; Marginal D, MD; No Change, NC), and the p value for that call. Additionally -- not calculated with GCOS -- t-tests of log Signals and SLRs were included in the database. For each present transcript the significance of differential expression between the groups of arrays was either calculated using strict Bonferroni corrected Welch t-tests between 9 SLR values of Experiment group vs. Baseline group and 12 SLR values within both groups (the latter 12 giving a mean SLR value of zero; p-value had to be <= 5.279E-08) or more than 50% of non-parametrically calculated Change calls (Mann-Whitney U test, GCOS) i.e. 5 or more of all 9 Change calls have to be in the same direction. Significantly differentially expressed genes, were filtered using both default parameter sets of filter criteria; these are a combination of four different queries. Filter criteria were developed with various data sets of GeneChips and validated with the Affymetrix Latin Square dataset as shown in Menssen et al., 2009. You can find these validation experiments in BioRetis without registering, using the public content and public login. Click on view single results, select any existing Analysis beginning with first 3 letters "SGU" and click on "Next". Click on "Chose an existing parameterset" and select "JRG_Increase" for increased or "JRG_Decrease" for decreased probesets and click on "Fill". At the bottom of the site check the box named "* use Bonferroni correction" and click on "Search only" to get the list of significantly changed increased or decreased probesets, respectively. The Affymetrix Latin Square dataset, consisting of 42 chips in 14 experiments with three replicates each were analyzed in BioRetis with all possible 3 vs. 3 chip comparisons (one direction).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Joachim,R.,Grün
| | Sample_contact_email | Gruen@DRFZ.de
| | Sample_contact_department | Bioinformatics
| | Sample_contact_institute | Deutsches Rheuma-Forschungszentrum (DRFZ)
| | Sample_contact_address | Charitéplatz 1
| | Sample_contact_city | Berlin
| | Sample_contact_zip/postal_code | D-10117
| | Sample_contact_country | Germany
| | Sample_contact_web_link | www.drfz.de
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1153nnn/GSM1153941/suppl/GSM1153941_Grp1_C57B6_4_SCfl_mir221_0h_430_2.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1153nnn/GSM1153941/suppl/GSM1153941_Grp1_C57B6_4_SCfl_mir221_0h_430_2.CHP.gz
| | Sample_series_id | GSE47643
| | Sample_data_row_count | 45101
| | |
|
GSM1153942 | GPL1261 |
|
Group1: preB cells without induction_5
|
Grp1-5: preB cells without induction
|
strain: C57BL/6
tissue: fetal liver
cell type: preB-cells
induction of mir-221: 0 h
|
Grp1_C57B6_5_SCfl_mir221_0h_430_2
Gene expression profiles of un-induced preB cells prepared from tissue culture were compared using Affymetrix MG430Av2 GeneChip arrays. After total RNA extraction, reverse transcription, cDNA extraction, the biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized in triplicates for each of the four groups to the GeneChip arrays. Twelve chips in these four groups were hybridized and analyzed: Group1 are un-induced preB cells
|
| Sample_geo_accession | GSM1153942
| | Sample_status | Public on Jun 05 2013
| | Sample_submission_date | Jun 04 2013
| | Sample_last_update_date | Jun 07 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | Samples were obtained from the fetal liver of C57BL/6, CD45.1pos mice (MPIIB, Berlin, Germany)
| | Sample_treatment_protocol_ch1 | MiR-221 expression was induced by adding 1 mg/ml doxycycline to the cell culture media and samples were taken at 8, 16, or 24h after induction.
| | Sample_growth_protocol_ch1 | PreB cells derived from wild type fetal liver (C57BL/6, CD45.1pos) at day 18 of gestation were grown on a confluent layer of gamma-irradiated (30Gy) M-CSF-deficient OP9 stromal cells in IMDM medium (Gibco) supplemented with 2% FCS (Sigma-Aldrich), 0.03% Primatone-RL (Quest) and 1% mouse IL7 conditioned media as described by Rolink et al, 1991.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instruction, including the recommended DNase digest. The purity and integrity of RNA were assessed for each sample using an Agilent 2100 Bioanalyzer with the RNA 6000 Nano LabChip and amount was checked with a NanoDrop ND-1000 spectrophotometer. Contaminating genomic DNA was removed by an on-column DNA digestion step (Qiagen).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Labeling and hybridization of total RNA was performed using the GeneChip 3’ IVT Express Kit from Affymetrix according to the manufacturers instruction. Briefly, after total RNA extraction, 100 ng of total RNA from each cell sample was reverse transcribed, cDNA was extracted, biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized to each of the GeneChip arrays. The MG430Av2 GeneChip arrays were loaded with the hybridization cocktail, hybridized at 45 °C rotating for 16 h in a hybridization oven 640 (Affymetrix), washed and stained with streptavidin-phycoerythrin using the Affymetrix GeneChip Fluidics Workstation 400.
| | Sample_hyb_protocol | Labeling and hybridization of total RNA was performed using the GeneChip 3’ IVT Express Kit from Affymetrix according to the manufacturers instruction. Briefly, after total RNA extraction, 100 ng of total RNA from each cell sample was reverse transcribed, cDNA was extracted, biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized to each of the GeneChip arrays. The MG430Av2 GeneChip arrays were loaded with the hybridization cocktail, hybridized at 45 °C rotating for 16 h in a hybridization oven 640 (Affymetrix), washed and stained with streptavidin-phycoerythrin using the Affymetrix GeneChip Fluidics Workstation 400.
| | Sample_scan_protocol | Arrays were scanned with an Affymetrix GeneChip Scanner 3000, using the GCOS software from Affymetrix.
| | Sample_data_processing | Data were analyzed according to High Performance Chip Data Analysis (HPCDA, unpublished - Joachim R. Grün) with the Bioretis database (http://www.bioretis-analysis.de/) using the default filter parameters for decreased and increased gene lists (description of database c.f. open access paper Menssen et al., 2009; PubMedID: 19265543). Chip data included in the Bioretis database were analyzed using the GeneChip Operating Software (GCOS, Affymetrix), version 1.4. Microarrays were globally normalized and scaled to a trimmed mean expression value of 150. Quality checks were performed according to the manufacturer's recommendations. All 3 chips of one group were compared to each 3 chips of any other group (results, compared to 16h chips were ignored in this study), and the following parameters of absolute and comparative analysis were included in the Bioretis database: expression heights (Signals) and mean, median and standard deviation of Signals of both groups, call for presence of transcripts (Absent, A; Marginal, M; Present, P), p-value for presence or absence of transcripts, log2 value of fold change (Signal Log Ratio, SLR) and the fold change as mean values, call for the significance of differentially expression (Change Call: Increase, I; Marginal I, MI; Decrease, D; Marginal D, MD; No Change, NC), and the p value for that call. Additionally -- not calculated with GCOS -- t-tests of log Signals and SLRs were included in the database. For each present transcript the significance of differential expression between the groups of arrays was either calculated using strict Bonferroni corrected Welch t-tests between 9 SLR values of Experiment group vs. Baseline group and 12 SLR values within both groups (the latter 12 giving a mean SLR value of zero; p-value had to be <= 5.279E-08) or more than 50% of non-parametrically calculated Change calls (Mann-Whitney U test, GCOS) i.e. 5 or more of all 9 Change calls have to be in the same direction. Significantly differentially expressed genes, were filtered using both default parameter sets of filter criteria; these are a combination of four different queries. Filter criteria were developed with various data sets of GeneChips and validated with the Affymetrix Latin Square dataset as shown in Menssen et al., 2009. You can find these validation experiments in BioRetis without registering, using the public content and public login. Click on view single results, select any existing Analysis beginning with first 3 letters "SGU" and click on "Next". Click on "Chose an existing parameterset" and select "JRG_Increase" for increased or "JRG_Decrease" for decreased probesets and click on "Fill". At the bottom of the site check the box named "* use Bonferroni correction" and click on "Search only" to get the list of significantly changed increased or decreased probesets, respectively. The Affymetrix Latin Square dataset, consisting of 42 chips in 14 experiments with three replicates each were analyzed in BioRetis with all possible 3 vs. 3 chip comparisons (one direction).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Joachim,R.,Grün
| | Sample_contact_email | Gruen@DRFZ.de
| | Sample_contact_department | Bioinformatics
| | Sample_contact_institute | Deutsches Rheuma-Forschungszentrum (DRFZ)
| | Sample_contact_address | Charitéplatz 1
| | Sample_contact_city | Berlin
| | Sample_contact_zip/postal_code | D-10117
| | Sample_contact_country | Germany
| | Sample_contact_web_link | www.drfz.de
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1153nnn/GSM1153942/suppl/GSM1153942_Grp1_C57B6_5_SCfl_mir221_0h_430_2.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1153nnn/GSM1153942/suppl/GSM1153942_Grp1_C57B6_5_SCfl_mir221_0h_430_2.CHP.gz
| | Sample_series_id | GSE47643
| | Sample_data_row_count | 45101
| | |
|
GSM1153943 | GPL1261 |
|
Group1: preB cells without induction_6
|
Grp1-6: preB cells without induction
|
strain: C57BL/6
tissue: fetal liver
cell type: preB-cells
induction of mir-221: 0 h
|
Grp1_C57B6_6_SCfl_mir221_0h_430_2
Gene expression profiles of un-induced preB cells prepared from tissue culture were compared using Affymetrix MG430Av2 GeneChip arrays. After total RNA extraction, reverse transcription, cDNA extraction, the biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized in triplicates for each of the four groups to the GeneChip arrays. Twelve chips in these four groups were hybridized and analyzed: Group1 are un-induced preB cells
|
| Sample_geo_accession | GSM1153943
| | Sample_status | Public on Jun 05 2013
| | Sample_submission_date | Jun 04 2013
| | Sample_last_update_date | Jun 07 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | Samples were obtained from the fetal liver of C57BL/6, CD45.1pos mice (MPIIB, Berlin, Germany)
| | Sample_treatment_protocol_ch1 | MiR-221 expression was induced by adding 1 mg/ml doxycycline to the cell culture media and samples were taken at 8, 16, or 24h after induction.
| | Sample_growth_protocol_ch1 | PreB cells derived from wild type fetal liver (C57BL/6, CD45.1pos) at day 18 of gestation were grown on a confluent layer of gamma-irradiated (30Gy) M-CSF-deficient OP9 stromal cells in IMDM medium (Gibco) supplemented with 2% FCS (Sigma-Aldrich), 0.03% Primatone-RL (Quest) and 1% mouse IL7 conditioned media as described by Rolink et al, 1991.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instruction, including the recommended DNase digest. The purity and integrity of RNA were assessed for each sample using an Agilent 2100 Bioanalyzer with the RNA 6000 Nano LabChip and amount was checked with a NanoDrop ND-1000 spectrophotometer. Contaminating genomic DNA was removed by an on-column DNA digestion step (Qiagen).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Labeling and hybridization of total RNA was performed using the GeneChip 3’ IVT Express Kit from Affymetrix according to the manufacturers instruction. Briefly, after total RNA extraction, 100 ng of total RNA from each cell sample was reverse transcribed, cDNA was extracted, biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized to each of the GeneChip arrays. The MG430Av2 GeneChip arrays were loaded with the hybridization cocktail, hybridized at 45 °C rotating for 16 h in a hybridization oven 640 (Affymetrix), washed and stained with streptavidin-phycoerythrin using the Affymetrix GeneChip Fluidics Workstation 400.
| | Sample_hyb_protocol | Labeling and hybridization of total RNA was performed using the GeneChip 3’ IVT Express Kit from Affymetrix according to the manufacturers instruction. Briefly, after total RNA extraction, 100 ng of total RNA from each cell sample was reverse transcribed, cDNA was extracted, biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized to each of the GeneChip arrays. The MG430Av2 GeneChip arrays were loaded with the hybridization cocktail, hybridized at 45 °C rotating for 16 h in a hybridization oven 640 (Affymetrix), washed and stained with streptavidin-phycoerythrin using the Affymetrix GeneChip Fluidics Workstation 400.
| | Sample_scan_protocol | Arrays were scanned with an Affymetrix GeneChip Scanner 3000, using the GCOS software from Affymetrix.
| | Sample_data_processing | Data were analyzed according to High Performance Chip Data Analysis (HPCDA, unpublished - Joachim R. Grün) with the Bioretis database (http://www.bioretis-analysis.de/) using the default filter parameters for decreased and increased gene lists (description of database c.f. open access paper Menssen et al., 2009; PubMedID: 19265543). Chip data included in the Bioretis database were analyzed using the GeneChip Operating Software (GCOS, Affymetrix), version 1.4. Microarrays were globally normalized and scaled to a trimmed mean expression value of 150. Quality checks were performed according to the manufacturer's recommendations. All 3 chips of one group were compared to each 3 chips of any other group (results, compared to 16h chips were ignored in this study), and the following parameters of absolute and comparative analysis were included in the Bioretis database: expression heights (Signals) and mean, median and standard deviation of Signals of both groups, call for presence of transcripts (Absent, A; Marginal, M; Present, P), p-value for presence or absence of transcripts, log2 value of fold change (Signal Log Ratio, SLR) and the fold change as mean values, call for the significance of differentially expression (Change Call: Increase, I; Marginal I, MI; Decrease, D; Marginal D, MD; No Change, NC), and the p value for that call. Additionally -- not calculated with GCOS -- t-tests of log Signals and SLRs were included in the database. For each present transcript the significance of differential expression between the groups of arrays was either calculated using strict Bonferroni corrected Welch t-tests between 9 SLR values of Experiment group vs. Baseline group and 12 SLR values within both groups (the latter 12 giving a mean SLR value of zero; p-value had to be <= 5.279E-08) or more than 50% of non-parametrically calculated Change calls (Mann-Whitney U test, GCOS) i.e. 5 or more of all 9 Change calls have to be in the same direction. Significantly differentially expressed genes, were filtered using both default parameter sets of filter criteria; these are a combination of four different queries. Filter criteria were developed with various data sets of GeneChips and validated with the Affymetrix Latin Square dataset as shown in Menssen et al., 2009. You can find these validation experiments in BioRetis without registering, using the public content and public login. Click on view single results, select any existing Analysis beginning with first 3 letters "SGU" and click on "Next". Click on "Chose an existing parameterset" and select "JRG_Increase" for increased or "JRG_Decrease" for decreased probesets and click on "Fill". At the bottom of the site check the box named "* use Bonferroni correction" and click on "Search only" to get the list of significantly changed increased or decreased probesets, respectively. The Affymetrix Latin Square dataset, consisting of 42 chips in 14 experiments with three replicates each were analyzed in BioRetis with all possible 3 vs. 3 chip comparisons (one direction).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Joachim,R.,Grün
| | Sample_contact_email | Gruen@DRFZ.de
| | Sample_contact_department | Bioinformatics
| | Sample_contact_institute | Deutsches Rheuma-Forschungszentrum (DRFZ)
| | Sample_contact_address | Charitéplatz 1
| | Sample_contact_city | Berlin
| | Sample_contact_zip/postal_code | D-10117
| | Sample_contact_country | Germany
| | Sample_contact_web_link | www.drfz.de
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1153nnn/GSM1153943/suppl/GSM1153943_Grp1_C57B6_6_SCfl_mir221_0h_430_2.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1153nnn/GSM1153943/suppl/GSM1153943_Grp1_C57B6_6_SCfl_mir221_0h_430_2.CHP.gz
| | Sample_series_id | GSE47643
| | Sample_data_row_count | 45101
| | |
|
GSM1153944 | GPL1261 |
|
Group2: preB cells after 8h induction with doxycycline_4
|
Grp2-4: preB cells after 8h induction for miR-221 expression with doxycycline
|
strain: C57BL/6
tissue: fetal liver
cell type: preB-cells
induction of mir-221: 8 h
|
Grp2_C57B6_4_SCfl_mir221_8h_430_2
Gene expression profiles of un-induced preB cells prepared from tissue culture were compared using Affymetrix MG430Av2 GeneChip arrays. After total RNA extraction, reverse transcription, cDNA extraction, the biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized in triplicates for each of the four groups to the GeneChip arrays. Twelve chips in these four groups were hybridized and analyzed: Group2 are preB cells induced for miR-221 expression after 8h
|
| Sample_geo_accession | GSM1153944
| | Sample_status | Public on Jun 05 2013
| | Sample_submission_date | Jun 04 2013
| | Sample_last_update_date | Jun 07 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | Samples were obtained from the fetal liver of C57BL/6, CD45.1pos mice (MPIIB, Berlin, Germany)
| | Sample_treatment_protocol_ch1 | MiR-221 expression was induced by adding 1 mg/ml doxycycline to the cell culture media and samples were taken at 8, 16, or 24h after induction.
| | Sample_growth_protocol_ch1 | PreB cells derived from wild type fetal liver (C57BL/6, CD45.1pos) at day 18 of gestation were grown on a confluent layer of gamma-irradiated (30Gy) M-CSF-deficient OP9 stromal cells in IMDM medium (Gibco) supplemented with 2% FCS (Sigma-Aldrich), 0.03% Primatone-RL (Quest) and 1% mouse IL7 conditioned media as described by Rolink et al, 1991.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instruction, including the recommended DNase digest. The purity and integrity of RNA were assessed for each sample using an Agilent 2100 Bioanalyzer with the RNA 6000 Nano LabChip and amount was checked with a NanoDrop ND-1000 spectrophotometer. Contaminating genomic DNA was removed by an on-column DNA digestion step (Qiagen).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Labeling and hybridization of total RNA was performed using the GeneChip 3’ IVT Express Kit from Affymetrix according to the manufacturers instruction. Briefly, after total RNA extraction, 100 ng of total RNA from each cell sample was reverse transcribed, cDNA was extracted, biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized to each of the GeneChip arrays. The MG430Av2 GeneChip arrays were loaded with the hybridization cocktail, hybridized at 45 °C rotating for 16 h in a hybridization oven 640 (Affymetrix), washed and stained with streptavidin-phycoerythrin using the Affymetrix GeneChip Fluidics Workstation 400.
| | Sample_hyb_protocol | Labeling and hybridization of total RNA was performed using the GeneChip 3’ IVT Express Kit from Affymetrix according to the manufacturers instruction. Briefly, after total RNA extraction, 100 ng of total RNA from each cell sample was reverse transcribed, cDNA was extracted, biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized to each of the GeneChip arrays. The MG430Av2 GeneChip arrays were loaded with the hybridization cocktail, hybridized at 45 °C rotating for 16 h in a hybridization oven 640 (Affymetrix), washed and stained with streptavidin-phycoerythrin using the Affymetrix GeneChip Fluidics Workstation 400.
| | Sample_scan_protocol | Arrays were scanned with an Affymetrix GeneChip Scanner 3000, using the GCOS software from Affymetrix.
| | Sample_data_processing | Data were analyzed according to High Performance Chip Data Analysis (HPCDA, unpublished - Joachim R. Grün) with the Bioretis database (http://www.bioretis-analysis.de/) using the default filter parameters for decreased and increased gene lists (description of database c.f. open access paper Menssen et al., 2009; PubMedID: 19265543). Chip data included in the Bioretis database were analyzed using the GeneChip Operating Software (GCOS, Affymetrix), version 1.4. Microarrays were globally normalized and scaled to a trimmed mean expression value of 150. Quality checks were performed according to the manufacturer's recommendations. All 3 chips of one group were compared to each 3 chips of any other group (results, compared to 16h chips were ignored in this study), and the following parameters of absolute and comparative analysis were included in the Bioretis database: expression heights (Signals) and mean, median and standard deviation of Signals of both groups, call for presence of transcripts (Absent, A; Marginal, M; Present, P), p-value for presence or absence of transcripts, log2 value of fold change (Signal Log Ratio, SLR) and the fold change as mean values, call for the significance of differentially expression (Change Call: Increase, I; Marginal I, MI; Decrease, D; Marginal D, MD; No Change, NC), and the p value for that call. Additionally -- not calculated with GCOS -- t-tests of log Signals and SLRs were included in the database. For each present transcript the significance of differential expression between the groups of arrays was either calculated using strict Bonferroni corrected Welch t-tests between 9 SLR values of Experiment group vs. Baseline group and 12 SLR values within both groups (the latter 12 giving a mean SLR value of zero; p-value had to be <= 5.279E-08) or more than 50% of non-parametrically calculated Change calls (Mann-Whitney U test, GCOS) i.e. 5 or more of all 9 Change calls have to be in the same direction. Significantly differentially expressed genes, were filtered using both default parameter sets of filter criteria; these are a combination of four different queries. Filter criteria were developed with various data sets of GeneChips and validated with the Affymetrix Latin Square dataset as shown in Menssen et al., 2009. You can find these validation experiments in BioRetis without registering, using the public content and public login. Click on view single results, select any existing Analysis beginning with first 3 letters "SGU" and click on "Next". Click on "Chose an existing parameterset" and select "JRG_Increase" for increased or "JRG_Decrease" for decreased probesets and click on "Fill". At the bottom of the site check the box named "* use Bonferroni correction" and click on "Search only" to get the list of significantly changed increased or decreased probesets, respectively. The Affymetrix Latin Square dataset, consisting of 42 chips in 14 experiments with three replicates each were analyzed in BioRetis with all possible 3 vs. 3 chip comparisons (one direction).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Joachim,R.,Grün
| | Sample_contact_email | Gruen@DRFZ.de
| | Sample_contact_department | Bioinformatics
| | Sample_contact_institute | Deutsches Rheuma-Forschungszentrum (DRFZ)
| | Sample_contact_address | Charitéplatz 1
| | Sample_contact_city | Berlin
| | Sample_contact_zip/postal_code | D-10117
| | Sample_contact_country | Germany
| | Sample_contact_web_link | www.drfz.de
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1153nnn/GSM1153944/suppl/GSM1153944_Grp2_C57B6_4_SCfl_mir221_8h_430_2.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1153nnn/GSM1153944/suppl/GSM1153944_Grp2_C57B6_4_SCfl_mir221_8h_430_2.CHP.gz
| | Sample_series_id | GSE47643
| | Sample_data_row_count | 45101
| | |
|
GSM1153945 | GPL1261 |
|
Group2: preB cells after 8h induction with doxycycline_5
|
Grp2-5: preB cells after 8h induction for miR-221 expression with doxycycline
|
strain: C57BL/6
tissue: fetal liver
cell type: preB-cells
induction of mir-221: 8 h
|
Grp2_C57B6_5_SCfl_mir221_8h_430_2
Gene expression profiles of un-induced preB cells prepared from tissue culture were compared using Affymetrix MG430Av2 GeneChip arrays. After total RNA extraction, reverse transcription, cDNA extraction, the biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized in triplicates for each of the four groups to the GeneChip arrays. Twelve chips in these four groups were hybridized and analyzed: Group2 are preB cells induced for miR-221 expression after 8h
|
| Sample_geo_accession | GSM1153945
| | Sample_status | Public on Jun 05 2013
| | Sample_submission_date | Jun 04 2013
| | Sample_last_update_date | Jun 07 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | Samples were obtained from the fetal liver of C57BL/6, CD45.1pos mice (MPIIB, Berlin, Germany)
| | Sample_treatment_protocol_ch1 | MiR-221 expression was induced by adding 1 mg/ml doxycycline to the cell culture media and samples were taken at 8, 16, or 24h after induction.
| | Sample_growth_protocol_ch1 | PreB cells derived from wild type fetal liver (C57BL/6, CD45.1pos) at day 18 of gestation were grown on a confluent layer of gamma-irradiated (30Gy) M-CSF-deficient OP9 stromal cells in IMDM medium (Gibco) supplemented with 2% FCS (Sigma-Aldrich), 0.03% Primatone-RL (Quest) and 1% mouse IL7 conditioned media as described by Rolink et al, 1991.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instruction, including the recommended DNase digest. The purity and integrity of RNA were assessed for each sample using an Agilent 2100 Bioanalyzer with the RNA 6000 Nano LabChip and amount was checked with a NanoDrop ND-1000 spectrophotometer. Contaminating genomic DNA was removed by an on-column DNA digestion step (Qiagen).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Labeling and hybridization of total RNA was performed using the GeneChip 3’ IVT Express Kit from Affymetrix according to the manufacturers instruction. Briefly, after total RNA extraction, 100 ng of total RNA from each cell sample was reverse transcribed, cDNA was extracted, biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized to each of the GeneChip arrays. The MG430Av2 GeneChip arrays were loaded with the hybridization cocktail, hybridized at 45 °C rotating for 16 h in a hybridization oven 640 (Affymetrix), washed and stained with streptavidin-phycoerythrin using the Affymetrix GeneChip Fluidics Workstation 400.
| | Sample_hyb_protocol | Labeling and hybridization of total RNA was performed using the GeneChip 3’ IVT Express Kit from Affymetrix according to the manufacturers instruction. Briefly, after total RNA extraction, 100 ng of total RNA from each cell sample was reverse transcribed, cDNA was extracted, biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized to each of the GeneChip arrays. The MG430Av2 GeneChip arrays were loaded with the hybridization cocktail, hybridized at 45 °C rotating for 16 h in a hybridization oven 640 (Affymetrix), washed and stained with streptavidin-phycoerythrin using the Affymetrix GeneChip Fluidics Workstation 400.
| | Sample_scan_protocol | Arrays were scanned with an Affymetrix GeneChip Scanner 3000, using the GCOS software from Affymetrix.
| | Sample_data_processing | Data were analyzed according to High Performance Chip Data Analysis (HPCDA, unpublished - Joachim R. Grün) with the Bioretis database (http://www.bioretis-analysis.de/) using the default filter parameters for decreased and increased gene lists (description of database c.f. open access paper Menssen et al., 2009; PubMedID: 19265543). Chip data included in the Bioretis database were analyzed using the GeneChip Operating Software (GCOS, Affymetrix), version 1.4. Microarrays were globally normalized and scaled to a trimmed mean expression value of 150. Quality checks were performed according to the manufacturer's recommendations. All 3 chips of one group were compared to each 3 chips of any other group (results, compared to 16h chips were ignored in this study), and the following parameters of absolute and comparative analysis were included in the Bioretis database: expression heights (Signals) and mean, median and standard deviation of Signals of both groups, call for presence of transcripts (Absent, A; Marginal, M; Present, P), p-value for presence or absence of transcripts, log2 value of fold change (Signal Log Ratio, SLR) and the fold change as mean values, call for the significance of differentially expression (Change Call: Increase, I; Marginal I, MI; Decrease, D; Marginal D, MD; No Change, NC), and the p value for that call. Additionally -- not calculated with GCOS -- t-tests of log Signals and SLRs were included in the database. For each present transcript the significance of differential expression between the groups of arrays was either calculated using strict Bonferroni corrected Welch t-tests between 9 SLR values of Experiment group vs. Baseline group and 12 SLR values within both groups (the latter 12 giving a mean SLR value of zero; p-value had to be <= 5.279E-08) or more than 50% of non-parametrically calculated Change calls (Mann-Whitney U test, GCOS) i.e. 5 or more of all 9 Change calls have to be in the same direction. Significantly differentially expressed genes, were filtered using both default parameter sets of filter criteria; these are a combination of four different queries. Filter criteria were developed with various data sets of GeneChips and validated with the Affymetrix Latin Square dataset as shown in Menssen et al., 2009. You can find these validation experiments in BioRetis without registering, using the public content and public login. Click on view single results, select any existing Analysis beginning with first 3 letters "SGU" and click on "Next". Click on "Chose an existing parameterset" and select "JRG_Increase" for increased or "JRG_Decrease" for decreased probesets and click on "Fill". At the bottom of the site check the box named "* use Bonferroni correction" and click on "Search only" to get the list of significantly changed increased or decreased probesets, respectively. The Affymetrix Latin Square dataset, consisting of 42 chips in 14 experiments with three replicates each were analyzed in BioRetis with all possible 3 vs. 3 chip comparisons (one direction).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Joachim,R.,Grün
| | Sample_contact_email | Gruen@DRFZ.de
| | Sample_contact_department | Bioinformatics
| | Sample_contact_institute | Deutsches Rheuma-Forschungszentrum (DRFZ)
| | Sample_contact_address | Charitéplatz 1
| | Sample_contact_city | Berlin
| | Sample_contact_zip/postal_code | D-10117
| | Sample_contact_country | Germany
| | Sample_contact_web_link | www.drfz.de
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1153nnn/GSM1153945/suppl/GSM1153945_Grp2_C57B6_5_SCfl_mir221_8h_430_2.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1153nnn/GSM1153945/suppl/GSM1153945_Grp2_C57B6_5_SCfl_mir221_8h_430_2.CHP.gz
| | Sample_series_id | GSE47643
| | Sample_data_row_count | 45101
| | |
|
GSM1153946 | GPL1261 |
|
Group2: preB cells after 8h induction with doxycycline_6
|
Grp2-6: preB cells after 8h induction for miR-221 expression with doxycycline
|
strain: C57BL/6
tissue: fetal liver
cell type: preB-cells
induction of mir-221: 8 h
|
Grp2_C57B6_6_SCfl_mir221_8h_430_2
Gene expression profiles of un-induced preB cells prepared from tissue culture were compared using Affymetrix MG430Av2 GeneChip arrays. After total RNA extraction, reverse transcription, cDNA extraction, the biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized in triplicates for each of the four groups to the GeneChip arrays. Twelve chips in these four groups were hybridized and analyzed: Group2 are preB cells induced for miR-221 expression after 8h
|
| Sample_geo_accession | GSM1153946
| | Sample_status | Public on Jun 05 2013
| | Sample_submission_date | Jun 04 2013
| | Sample_last_update_date | Jun 07 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | Samples were obtained from the fetal liver of C57BL/6, CD45.1pos mice (MPIIB, Berlin, Germany)
| | Sample_treatment_protocol_ch1 | MiR-221 expression was induced by adding 1 mg/ml doxycycline to the cell culture media and samples were taken at 8, 16, or 24h after induction.
| | Sample_growth_protocol_ch1 | PreB cells derived from wild type fetal liver (C57BL/6, CD45.1pos) at day 18 of gestation were grown on a confluent layer of gamma-irradiated (30Gy) M-CSF-deficient OP9 stromal cells in IMDM medium (Gibco) supplemented with 2% FCS (Sigma-Aldrich), 0.03% Primatone-RL (Quest) and 1% mouse IL7 conditioned media as described by Rolink et al, 1991.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instruction, including the recommended DNase digest. The purity and integrity of RNA were assessed for each sample using an Agilent 2100 Bioanalyzer with the RNA 6000 Nano LabChip and amount was checked with a NanoDrop ND-1000 spectrophotometer. Contaminating genomic DNA was removed by an on-column DNA digestion step (Qiagen).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Labeling and hybridization of total RNA was performed using the GeneChip 3’ IVT Express Kit from Affymetrix according to the manufacturers instruction. Briefly, after total RNA extraction, 100 ng of total RNA from each cell sample was reverse transcribed, cDNA was extracted, biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized to each of the GeneChip arrays. The MG430Av2 GeneChip arrays were loaded with the hybridization cocktail, hybridized at 45 °C rotating for 16 h in a hybridization oven 640 (Affymetrix), washed and stained with streptavidin-phycoerythrin using the Affymetrix GeneChip Fluidics Workstation 400.
| | Sample_hyb_protocol | Labeling and hybridization of total RNA was performed using the GeneChip 3’ IVT Express Kit from Affymetrix according to the manufacturers instruction. Briefly, after total RNA extraction, 100 ng of total RNA from each cell sample was reverse transcribed, cDNA was extracted, biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized to each of the GeneChip arrays. The MG430Av2 GeneChip arrays were loaded with the hybridization cocktail, hybridized at 45 °C rotating for 16 h in a hybridization oven 640 (Affymetrix), washed and stained with streptavidin-phycoerythrin using the Affymetrix GeneChip Fluidics Workstation 400.
| | Sample_scan_protocol | Arrays were scanned with an Affymetrix GeneChip Scanner 3000, using the GCOS software from Affymetrix.
| | Sample_data_processing | Data were analyzed according to High Performance Chip Data Analysis (HPCDA, unpublished - Joachim R. Grün) with the Bioretis database (http://www.bioretis-analysis.de/) using the default filter parameters for decreased and increased gene lists (description of database c.f. open access paper Menssen et al., 2009; PubMedID: 19265543). Chip data included in the Bioretis database were analyzed using the GeneChip Operating Software (GCOS, Affymetrix), version 1.4. Microarrays were globally normalized and scaled to a trimmed mean expression value of 150. Quality checks were performed according to the manufacturer's recommendations. All 3 chips of one group were compared to each 3 chips of any other group (results, compared to 16h chips were ignored in this study), and the following parameters of absolute and comparative analysis were included in the Bioretis database: expression heights (Signals) and mean, median and standard deviation of Signals of both groups, call for presence of transcripts (Absent, A; Marginal, M; Present, P), p-value for presence or absence of transcripts, log2 value of fold change (Signal Log Ratio, SLR) and the fold change as mean values, call for the significance of differentially expression (Change Call: Increase, I; Marginal I, MI; Decrease, D; Marginal D, MD; No Change, NC), and the p value for that call. Additionally -- not calculated with GCOS -- t-tests of log Signals and SLRs were included in the database. For each present transcript the significance of differential expression between the groups of arrays was either calculated using strict Bonferroni corrected Welch t-tests between 9 SLR values of Experiment group vs. Baseline group and 12 SLR values within both groups (the latter 12 giving a mean SLR value of zero; p-value had to be <= 5.279E-08) or more than 50% of non-parametrically calculated Change calls (Mann-Whitney U test, GCOS) i.e. 5 or more of all 9 Change calls have to be in the same direction. Significantly differentially expressed genes, were filtered using both default parameter sets of filter criteria; these are a combination of four different queries. Filter criteria were developed with various data sets of GeneChips and validated with the Affymetrix Latin Square dataset as shown in Menssen et al., 2009. You can find these validation experiments in BioRetis without registering, using the public content and public login. Click on view single results, select any existing Analysis beginning with first 3 letters "SGU" and click on "Next". Click on "Chose an existing parameterset" and select "JRG_Increase" for increased or "JRG_Decrease" for decreased probesets and click on "Fill". At the bottom of the site check the box named "* use Bonferroni correction" and click on "Search only" to get the list of significantly changed increased or decreased probesets, respectively. The Affymetrix Latin Square dataset, consisting of 42 chips in 14 experiments with three replicates each were analyzed in BioRetis with all possible 3 vs. 3 chip comparisons (one direction).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Joachim,R.,Grün
| | Sample_contact_email | Gruen@DRFZ.de
| | Sample_contact_department | Bioinformatics
| | Sample_contact_institute | Deutsches Rheuma-Forschungszentrum (DRFZ)
| | Sample_contact_address | Charitéplatz 1
| | Sample_contact_city | Berlin
| | Sample_contact_zip/postal_code | D-10117
| | Sample_contact_country | Germany
| | Sample_contact_web_link | www.drfz.de
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1153nnn/GSM1153946/suppl/GSM1153946_Grp2_C57B6_6_SCfl_mir221_8h_430_2.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1153nnn/GSM1153946/suppl/GSM1153946_Grp2_C57B6_6_SCfl_mir221_8h_430_2.CHP.gz
| | Sample_series_id | GSE47643
| | Sample_data_row_count | 45101
| | |
|
GSM1153947 | GPL1261 |
|
Group3: preB cells after 16h induction with doxycycline; not used in this publication_4
|
Grp3-4 preB cells after 16h induction for miR-221 expression with doxycycline
|
strain: C57BL/6
tissue: fetal liver
cell type: preB-cells
induction of mir-221: 16 h
|
Grp3_C57B6_4_SCfl_mir221_16h_430_2
Gene expression profiles of un-induced preB cells prepared from tissue culture were compared using Affymetrix MG430Av2 GeneChip arrays. After total RNA extraction, reverse transcription, cDNA extraction, the biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized in triplicates for each of the four groups to the GeneChip arrays. Twelve chips in these four groups were hybridized and analyzed: Group3 are preB cells induced for miR-221 expression after 16h. The 16h chips were not used in this publication, because miR-221 expression did not reach the maximum at this time point and so did not give us additional information.
|
| Sample_geo_accession | GSM1153947
| | Sample_status | Public on Jun 05 2013
| | Sample_submission_date | Jun 04 2013
| | Sample_last_update_date | Jun 07 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | Samples were obtained from the fetal liver of C57BL/6, CD45.1pos mice (MPIIB, Berlin, Germany)
| | Sample_treatment_protocol_ch1 | MiR-221 expression was induced by adding 1 mg/ml doxycycline to the cell culture media and samples were taken at 8, 16, or 24h after induction.
| | Sample_growth_protocol_ch1 | PreB cells derived from wild type fetal liver (C57BL/6, CD45.1pos) at day 18 of gestation were grown on a confluent layer of gamma-irradiated (30Gy) M-CSF-deficient OP9 stromal cells in IMDM medium (Gibco) supplemented with 2% FCS (Sigma-Aldrich), 0.03% Primatone-RL (Quest) and 1% mouse IL7 conditioned media as described by Rolink et al, 1991.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instruction, including the recommended DNase digest. The purity and integrity of RNA were assessed for each sample using an Agilent 2100 Bioanalyzer with the RNA 6000 Nano LabChip and amount was checked with a NanoDrop ND-1000 spectrophotometer. Contaminating genomic DNA was removed by an on-column DNA digestion step (Qiagen).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Labeling and hybridization of total RNA was performed using the GeneChip 3’ IVT Express Kit from Affymetrix according to the manufacturers instruction. Briefly, after total RNA extraction, 100 ng of total RNA from each cell sample was reverse transcribed, cDNA was extracted, biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized to each of the GeneChip arrays. The MG430Av2 GeneChip arrays were loaded with the hybridization cocktail, hybridized at 45 °C rotating for 16 h in a hybridization oven 640 (Affymetrix), washed and stained with streptavidin-phycoerythrin using the Affymetrix GeneChip Fluidics Workstation 400.
| | Sample_hyb_protocol | Labeling and hybridization of total RNA was performed using the GeneChip 3’ IVT Express Kit from Affymetrix according to the manufacturers instruction. Briefly, after total RNA extraction, 100 ng of total RNA from each cell sample was reverse transcribed, cDNA was extracted, biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized to each of the GeneChip arrays. The MG430Av2 GeneChip arrays were loaded with the hybridization cocktail, hybridized at 45 °C rotating for 16 h in a hybridization oven 640 (Affymetrix), washed and stained with streptavidin-phycoerythrin using the Affymetrix GeneChip Fluidics Workstation 400.
| | Sample_scan_protocol | Arrays were scanned with an Affymetrix GeneChip Scanner 3000, using the GCOS software from Affymetrix.
| | Sample_data_processing | Data were analyzed according to High Performance Chip Data Analysis (HPCDA, unpublished - Joachim R. Grün) with the Bioretis database (http://www.bioretis-analysis.de/) using the default filter parameters for decreased and increased gene lists (description of database c.f. open access paper Menssen et al., 2009; PubMedID: 19265543). Chip data included in the Bioretis database were analyzed using the GeneChip Operating Software (GCOS, Affymetrix), version 1.4. Microarrays were globally normalized and scaled to a trimmed mean expression value of 150. Quality checks were performed according to the manufacturer's recommendations. All 3 chips of one group were compared to each 3 chips of any other group (results, compared to 16h chips were ignored in this study), and the following parameters of absolute and comparative analysis were included in the Bioretis database: expression heights (Signals) and mean, median and standard deviation of Signals of both groups, call for presence of transcripts (Absent, A; Marginal, M; Present, P), p-value for presence or absence of transcripts, log2 value of fold change (Signal Log Ratio, SLR) and the fold change as mean values, call for the significance of differentially expression (Change Call: Increase, I; Marginal I, MI; Decrease, D; Marginal D, MD; No Change, NC), and the p value for that call. Additionally -- not calculated with GCOS -- t-tests of log Signals and SLRs were included in the database. For each present transcript the significance of differential expression between the groups of arrays was either calculated using strict Bonferroni corrected Welch t-tests between 9 SLR values of Experiment group vs. Baseline group and 12 SLR values within both groups (the latter 12 giving a mean SLR value of zero; p-value had to be <= 5.279E-08) or more than 50% of non-parametrically calculated Change calls (Mann-Whitney U test, GCOS) i.e. 5 or more of all 9 Change calls have to be in the same direction. Significantly differentially expressed genes, were filtered using both default parameter sets of filter criteria; these are a combination of four different queries. Filter criteria were developed with various data sets of GeneChips and validated with the Affymetrix Latin Square dataset as shown in Menssen et al., 2009. You can find these validation experiments in BioRetis without registering, using the public content and public login. Click on view single results, select any existing Analysis beginning with first 3 letters "SGU" and click on "Next". Click on "Chose an existing parameterset" and select "JRG_Increase" for increased or "JRG_Decrease" for decreased probesets and click on "Fill". At the bottom of the site check the box named "* use Bonferroni correction" and click on "Search only" to get the list of significantly changed increased or decreased probesets, respectively. The Affymetrix Latin Square dataset, consisting of 42 chips in 14 experiments with three replicates each were analyzed in BioRetis with all possible 3 vs. 3 chip comparisons (one direction).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Joachim,R.,Grün
| | Sample_contact_email | Gruen@DRFZ.de
| | Sample_contact_department | Bioinformatics
| | Sample_contact_institute | Deutsches Rheuma-Forschungszentrum (DRFZ)
| | Sample_contact_address | Charitéplatz 1
| | Sample_contact_city | Berlin
| | Sample_contact_zip/postal_code | D-10117
| | Sample_contact_country | Germany
| | Sample_contact_web_link | www.drfz.de
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1153nnn/GSM1153947/suppl/GSM1153947_Grp3_C57B6_4_SCfl_mir221_16h_430_2.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1153nnn/GSM1153947/suppl/GSM1153947_Grp3_C57B6_4_SCfl_mir221_16h_430_2.CHP.gz
| | Sample_series_id | GSE47643
| | Sample_data_row_count | 45101
| | |
|
GSM1153948 | GPL1261 |
|
Group3: preB cells after 16h induction with doxycycline; not used in this publication_5
|
Grp3-5 preB cells after 16h induction for miR-221 expression with doxycycline
|
strain: C57BL/6
tissue: fetal liver
cell type: preB-cells
induction of mir-221: 16 h
|
Grp3_C57B6_5_SCfl_mir221_16h_430_2
Gene expression profiles of un-induced preB cells prepared from tissue culture were compared using Affymetrix MG430Av2 GeneChip arrays. After total RNA extraction, reverse transcription, cDNA extraction, the biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized in triplicates for each of the four groups to the GeneChip arrays. Twelve chips in these four groups were hybridized and analyzed: Group3 are preB cells induced for miR-221 expression after 16h. The 16h chips were not used in this publication, because miR-221 expression did not reach the maximum at this time point and so did not give us additional information.
|
| Sample_geo_accession | GSM1153948
| | Sample_status | Public on Jun 05 2013
| | Sample_submission_date | Jun 04 2013
| | Sample_last_update_date | Jun 07 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | Samples were obtained from the fetal liver of C57BL/6, CD45.1pos mice (MPIIB, Berlin, Germany)
| | Sample_treatment_protocol_ch1 | MiR-221 expression was induced by adding 1 mg/ml doxycycline to the cell culture media and samples were taken at 8, 16, or 24h after induction.
| | Sample_growth_protocol_ch1 | PreB cells derived from wild type fetal liver (C57BL/6, CD45.1pos) at day 18 of gestation were grown on a confluent layer of gamma-irradiated (30Gy) M-CSF-deficient OP9 stromal cells in IMDM medium (Gibco) supplemented with 2% FCS (Sigma-Aldrich), 0.03% Primatone-RL (Quest) and 1% mouse IL7 conditioned media as described by Rolink et al, 1991.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instruction, including the recommended DNase digest. The purity and integrity of RNA were assessed for each sample using an Agilent 2100 Bioanalyzer with the RNA 6000 Nano LabChip and amount was checked with a NanoDrop ND-1000 spectrophotometer. Contaminating genomic DNA was removed by an on-column DNA digestion step (Qiagen).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Labeling and hybridization of total RNA was performed using the GeneChip 3’ IVT Express Kit from Affymetrix according to the manufacturers instruction. Briefly, after total RNA extraction, 100 ng of total RNA from each cell sample was reverse transcribed, cDNA was extracted, biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized to each of the GeneChip arrays. The MG430Av2 GeneChip arrays were loaded with the hybridization cocktail, hybridized at 45 °C rotating for 16 h in a hybridization oven 640 (Affymetrix), washed and stained with streptavidin-phycoerythrin using the Affymetrix GeneChip Fluidics Workstation 400.
| | Sample_hyb_protocol | Labeling and hybridization of total RNA was performed using the GeneChip 3’ IVT Express Kit from Affymetrix according to the manufacturers instruction. Briefly, after total RNA extraction, 100 ng of total RNA from each cell sample was reverse transcribed, cDNA was extracted, biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized to each of the GeneChip arrays. The MG430Av2 GeneChip arrays were loaded with the hybridization cocktail, hybridized at 45 °C rotating for 16 h in a hybridization oven 640 (Affymetrix), washed and stained with streptavidin-phycoerythrin using the Affymetrix GeneChip Fluidics Workstation 400.
| | Sample_scan_protocol | Arrays were scanned with an Affymetrix GeneChip Scanner 3000, using the GCOS software from Affymetrix.
| | Sample_data_processing | Data were analyzed according to High Performance Chip Data Analysis (HPCDA, unpublished - Joachim R. Grün) with the Bioretis database (http://www.bioretis-analysis.de/) using the default filter parameters for decreased and increased gene lists (description of database c.f. open access paper Menssen et al., 2009; PubMedID: 19265543). Chip data included in the Bioretis database were analyzed using the GeneChip Operating Software (GCOS, Affymetrix), version 1.4. Microarrays were globally normalized and scaled to a trimmed mean expression value of 150. Quality checks were performed according to the manufacturer's recommendations. All 3 chips of one group were compared to each 3 chips of any other group (results, compared to 16h chips were ignored in this study), and the following parameters of absolute and comparative analysis were included in the Bioretis database: expression heights (Signals) and mean, median and standard deviation of Signals of both groups, call for presence of transcripts (Absent, A; Marginal, M; Present, P), p-value for presence or absence of transcripts, log2 value of fold change (Signal Log Ratio, SLR) and the fold change as mean values, call for the significance of differentially expression (Change Call: Increase, I; Marginal I, MI; Decrease, D; Marginal D, MD; No Change, NC), and the p value for that call. Additionally -- not calculated with GCOS -- t-tests of log Signals and SLRs were included in the database. For each present transcript the significance of differential expression between the groups of arrays was either calculated using strict Bonferroni corrected Welch t-tests between 9 SLR values of Experiment group vs. Baseline group and 12 SLR values within both groups (the latter 12 giving a mean SLR value of zero; p-value had to be <= 5.279E-08) or more than 50% of non-parametrically calculated Change calls (Mann-Whitney U test, GCOS) i.e. 5 or more of all 9 Change calls have to be in the same direction. Significantly differentially expressed genes, were filtered using both default parameter sets of filter criteria; these are a combination of four different queries. Filter criteria were developed with various data sets of GeneChips and validated with the Affymetrix Latin Square dataset as shown in Menssen et al., 2009. You can find these validation experiments in BioRetis without registering, using the public content and public login. Click on view single results, select any existing Analysis beginning with first 3 letters "SGU" and click on "Next". Click on "Chose an existing parameterset" and select "JRG_Increase" for increased or "JRG_Decrease" for decreased probesets and click on "Fill". At the bottom of the site check the box named "* use Bonferroni correction" and click on "Search only" to get the list of significantly changed increased or decreased probesets, respectively. The Affymetrix Latin Square dataset, consisting of 42 chips in 14 experiments with three replicates each were analyzed in BioRetis with all possible 3 vs. 3 chip comparisons (one direction).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Joachim,R.,Grün
| | Sample_contact_email | Gruen@DRFZ.de
| | Sample_contact_department | Bioinformatics
| | Sample_contact_institute | Deutsches Rheuma-Forschungszentrum (DRFZ)
| | Sample_contact_address | Charitéplatz 1
| | Sample_contact_city | Berlin
| | Sample_contact_zip/postal_code | D-10117
| | Sample_contact_country | Germany
| | Sample_contact_web_link | www.drfz.de
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1153nnn/GSM1153948/suppl/GSM1153948_Grp3_C57B6_5_SCfl_mir221_16h_430_2.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1153nnn/GSM1153948/suppl/GSM1153948_Grp3_C57B6_5_SCfl_mir221_16h_430_2.CHP.gz
| | Sample_series_id | GSE47643
| | Sample_data_row_count | 45101
| | |
|
GSM1153949 | GPL1261 |
|
Group3: preB cells after 16h induction with doxycycline; not used in this publication_6
|
Grp3-6 preB cells after 16h induction for miR-221 expression with doxycycline
|
strain: C57BL/6
tissue: fetal liver
cell type: preB-cells
induction of mir-221: 16 h
|
Grp3_C57B6_6_SCfl_mir221_16h_430_2
Gene expression profiles of un-induced preB cells prepared from tissue culture were compared using Affymetrix MG430Av2 GeneChip arrays. After total RNA extraction, reverse transcription, cDNA extraction, the biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized in triplicates for each of the four groups to the GeneChip arrays. Twelve chips in these four groups were hybridized and analyzed: Group3 are preB cells induced for miR-221 expression after 16h. The 16h chips were not used in this publication, because miR-221 expression did not reach the maximum at this time point and so did not give us additional information.
|
| Sample_geo_accession | GSM1153949
| | Sample_status | Public on Jun 05 2013
| | Sample_submission_date | Jun 04 2013
| | Sample_last_update_date | Jun 07 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | Samples were obtained from the fetal liver of C57BL/6, CD45.1pos mice (MPIIB, Berlin, Germany)
| | Sample_treatment_protocol_ch1 | MiR-221 expression was induced by adding 1 mg/ml doxycycline to the cell culture media and samples were taken at 8, 16, or 24h after induction.
| | Sample_growth_protocol_ch1 | PreB cells derived from wild type fetal liver (C57BL/6, CD45.1pos) at day 18 of gestation were grown on a confluent layer of gamma-irradiated (30Gy) M-CSF-deficient OP9 stromal cells in IMDM medium (Gibco) supplemented with 2% FCS (Sigma-Aldrich), 0.03% Primatone-RL (Quest) and 1% mouse IL7 conditioned media as described by Rolink et al, 1991.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instruction, including the recommended DNase digest. The purity and integrity of RNA were assessed for each sample using an Agilent 2100 Bioanalyzer with the RNA 6000 Nano LabChip and amount was checked with a NanoDrop ND-1000 spectrophotometer. Contaminating genomic DNA was removed by an on-column DNA digestion step (Qiagen).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Labeling and hybridization of total RNA was performed using the GeneChip 3’ IVT Express Kit from Affymetrix according to the manufacturers instruction. Briefly, after total RNA extraction, 100 ng of total RNA from each cell sample was reverse transcribed, cDNA was extracted, biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized to each of the GeneChip arrays. The MG430Av2 GeneChip arrays were loaded with the hybridization cocktail, hybridized at 45 °C rotating for 16 h in a hybridization oven 640 (Affymetrix), washed and stained with streptavidin-phycoerythrin using the Affymetrix GeneChip Fluidics Workstation 400.
| | Sample_hyb_protocol | Labeling and hybridization of total RNA was performed using the GeneChip 3’ IVT Express Kit from Affymetrix according to the manufacturers instruction. Briefly, after total RNA extraction, 100 ng of total RNA from each cell sample was reverse transcribed, cDNA was extracted, biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized to each of the GeneChip arrays. The MG430Av2 GeneChip arrays were loaded with the hybridization cocktail, hybridized at 45 °C rotating for 16 h in a hybridization oven 640 (Affymetrix), washed and stained with streptavidin-phycoerythrin using the Affymetrix GeneChip Fluidics Workstation 400.
| | Sample_scan_protocol | Arrays were scanned with an Affymetrix GeneChip Scanner 3000, using the GCOS software from Affymetrix.
| | Sample_data_processing | Data were analyzed according to High Performance Chip Data Analysis (HPCDA, unpublished - Joachim R. Grün) with the Bioretis database (http://www.bioretis-analysis.de/) using the default filter parameters for decreased and increased gene lists (description of database c.f. open access paper Menssen et al., 2009; PubMedID: 19265543). Chip data included in the Bioretis database were analyzed using the GeneChip Operating Software (GCOS, Affymetrix), version 1.4. Microarrays were globally normalized and scaled to a trimmed mean expression value of 150. Quality checks were performed according to the manufacturer's recommendations. All 3 chips of one group were compared to each 3 chips of any other group (results, compared to 16h chips were ignored in this study), and the following parameters of absolute and comparative analysis were included in the Bioretis database: expression heights (Signals) and mean, median and standard deviation of Signals of both groups, call for presence of transcripts (Absent, A; Marginal, M; Present, P), p-value for presence or absence of transcripts, log2 value of fold change (Signal Log Ratio, SLR) and the fold change as mean values, call for the significance of differentially expression (Change Call: Increase, I; Marginal I, MI; Decrease, D; Marginal D, MD; No Change, NC), and the p value for that call. Additionally -- not calculated with GCOS -- t-tests of log Signals and SLRs were included in the database. For each present transcript the significance of differential expression between the groups of arrays was either calculated using strict Bonferroni corrected Welch t-tests between 9 SLR values of Experiment group vs. Baseline group and 12 SLR values within both groups (the latter 12 giving a mean SLR value of zero; p-value had to be <= 5.279E-08) or more than 50% of non-parametrically calculated Change calls (Mann-Whitney U test, GCOS) i.e. 5 or more of all 9 Change calls have to be in the same direction. Significantly differentially expressed genes, were filtered using both default parameter sets of filter criteria; these are a combination of four different queries. Filter criteria were developed with various data sets of GeneChips and validated with the Affymetrix Latin Square dataset as shown in Menssen et al., 2009. You can find these validation experiments in BioRetis without registering, using the public content and public login. Click on view single results, select any existing Analysis beginning with first 3 letters "SGU" and click on "Next". Click on "Chose an existing parameterset" and select "JRG_Increase" for increased or "JRG_Decrease" for decreased probesets and click on "Fill". At the bottom of the site check the box named "* use Bonferroni correction" and click on "Search only" to get the list of significantly changed increased or decreased probesets, respectively. The Affymetrix Latin Square dataset, consisting of 42 chips in 14 experiments with three replicates each were analyzed in BioRetis with all possible 3 vs. 3 chip comparisons (one direction).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Joachim,R.,Grün
| | Sample_contact_email | Gruen@DRFZ.de
| | Sample_contact_department | Bioinformatics
| | Sample_contact_institute | Deutsches Rheuma-Forschungszentrum (DRFZ)
| | Sample_contact_address | Charitéplatz 1
| | Sample_contact_city | Berlin
| | Sample_contact_zip/postal_code | D-10117
| | Sample_contact_country | Germany
| | Sample_contact_web_link | www.drfz.de
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1153nnn/GSM1153949/suppl/GSM1153949_Grp3_C57B6_6_SCfl_mir221_16h_430_2.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1153nnn/GSM1153949/suppl/GSM1153949_Grp3_C57B6_6_SCfl_mir221_16h_430_2.CHP.gz
| | Sample_series_id | GSE47643
| | Sample_data_row_count | 45101
| | |
|
GSM1153950 | GPL1261 |
|
Group4: preB cells after 24h induction with doxycycline_4
|
Grp4-4 preB cells after 24h induction for miR-221 expression with doxycycline
|
strain: C57BL/6
tissue: fetal liver
cell type: preB-cells
induction of mir-221: 24 h
|
Grp4_C57B6_4_SCfl_mir221_24h_430_2
Gene expression profiles of un-induced preB cells prepared from tissue culture were compared using Affymetrix MG430Av2 GeneChip arrays. After total RNA extraction, reverse transcription, cDNA extraction, the biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized in triplicates for each of the four groups to the GeneChip arrays. Twelve chips in these four groups were hybridized and analyzed: Group4 are preB cells induced for miR-221 expression after 24h
|
| Sample_geo_accession | GSM1153950
| | Sample_status | Public on Jun 05 2013
| | Sample_submission_date | Jun 04 2013
| | Sample_last_update_date | Jun 07 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | Samples were obtained from the fetal liver of C57BL/6, CD45.1pos mice (MPIIB, Berlin, Germany)
| | Sample_treatment_protocol_ch1 | MiR-221 expression was induced by adding 1 mg/ml doxycycline to the cell culture media and samples were taken at 8, 16, or 24h after induction.
| | Sample_growth_protocol_ch1 | PreB cells derived from wild type fetal liver (C57BL/6, CD45.1pos) at day 18 of gestation were grown on a confluent layer of gamma-irradiated (30Gy) M-CSF-deficient OP9 stromal cells in IMDM medium (Gibco) supplemented with 2% FCS (Sigma-Aldrich), 0.03% Primatone-RL (Quest) and 1% mouse IL7 conditioned media as described by Rolink et al, 1991.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instruction, including the recommended DNase digest. The purity and integrity of RNA were assessed for each sample using an Agilent 2100 Bioanalyzer with the RNA 6000 Nano LabChip and amount was checked with a NanoDrop ND-1000 spectrophotometer. Contaminating genomic DNA was removed by an on-column DNA digestion step (Qiagen).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Labeling and hybridization of total RNA was performed using the GeneChip 3’ IVT Express Kit from Affymetrix according to the manufacturers instruction. Briefly, after total RNA extraction, 100 ng of total RNA from each cell sample was reverse transcribed, cDNA was extracted, biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized to each of the GeneChip arrays. The MG430Av2 GeneChip arrays were loaded with the hybridization cocktail, hybridized at 45 °C rotating for 16 h in a hybridization oven 640 (Affymetrix), washed and stained with streptavidin-phycoerythrin using the Affymetrix GeneChip Fluidics Workstation 400.
| | Sample_hyb_protocol | Labeling and hybridization of total RNA was performed using the GeneChip 3’ IVT Express Kit from Affymetrix according to the manufacturers instruction. Briefly, after total RNA extraction, 100 ng of total RNA from each cell sample was reverse transcribed, cDNA was extracted, biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized to each of the GeneChip arrays. The MG430Av2 GeneChip arrays were loaded with the hybridization cocktail, hybridized at 45 °C rotating for 16 h in a hybridization oven 640 (Affymetrix), washed and stained with streptavidin-phycoerythrin using the Affymetrix GeneChip Fluidics Workstation 400.
| | Sample_scan_protocol | Arrays were scanned with an Affymetrix GeneChip Scanner 3000, using the GCOS software from Affymetrix.
| | Sample_data_processing | Data were analyzed according to High Performance Chip Data Analysis (HPCDA, unpublished - Joachim R. Grün) with the Bioretis database (http://www.bioretis-analysis.de/) using the default filter parameters for decreased and increased gene lists (description of database c.f. open access paper Menssen et al., 2009; PubMedID: 19265543). Chip data included in the Bioretis database were analyzed using the GeneChip Operating Software (GCOS, Affymetrix), version 1.4. Microarrays were globally normalized and scaled to a trimmed mean expression value of 150. Quality checks were performed according to the manufacturer's recommendations. All 3 chips of one group were compared to each 3 chips of any other group (results, compared to 16h chips were ignored in this study), and the following parameters of absolute and comparative analysis were included in the Bioretis database: expression heights (Signals) and mean, median and standard deviation of Signals of both groups, call for presence of transcripts (Absent, A; Marginal, M; Present, P), p-value for presence or absence of transcripts, log2 value of fold change (Signal Log Ratio, SLR) and the fold change as mean values, call for the significance of differentially expression (Change Call: Increase, I; Marginal I, MI; Decrease, D; Marginal D, MD; No Change, NC), and the p value for that call. Additionally -- not calculated with GCOS -- t-tests of log Signals and SLRs were included in the database. For each present transcript the significance of differential expression between the groups of arrays was either calculated using strict Bonferroni corrected Welch t-tests between 9 SLR values of Experiment group vs. Baseline group and 12 SLR values within both groups (the latter 12 giving a mean SLR value of zero; p-value had to be <= 5.279E-08) or more than 50% of non-parametrically calculated Change calls (Mann-Whitney U test, GCOS) i.e. 5 or more of all 9 Change calls have to be in the same direction. Significantly differentially expressed genes, were filtered using both default parameter sets of filter criteria; these are a combination of four different queries. Filter criteria were developed with various data sets of GeneChips and validated with the Affymetrix Latin Square dataset as shown in Menssen et al., 2009. You can find these validation experiments in BioRetis without registering, using the public content and public login. Click on view single results, select any existing Analysis beginning with first 3 letters "SGU" and click on "Next". Click on "Chose an existing parameterset" and select "JRG_Increase" for increased or "JRG_Decrease" for decreased probesets and click on "Fill". At the bottom of the site check the box named "* use Bonferroni correction" and click on "Search only" to get the list of significantly changed increased or decreased probesets, respectively. The Affymetrix Latin Square dataset, consisting of 42 chips in 14 experiments with three replicates each were analyzed in BioRetis with all possible 3 vs. 3 chip comparisons (one direction).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Joachim,R.,Grün
| | Sample_contact_email | Gruen@DRFZ.de
| | Sample_contact_department | Bioinformatics
| | Sample_contact_institute | Deutsches Rheuma-Forschungszentrum (DRFZ)
| | Sample_contact_address | Charitéplatz 1
| | Sample_contact_city | Berlin
| | Sample_contact_zip/postal_code | D-10117
| | Sample_contact_country | Germany
| | Sample_contact_web_link | www.drfz.de
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1153nnn/GSM1153950/suppl/GSM1153950_Grp4_C57B6_4_SCfl_mir221_24h_430_2.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1153nnn/GSM1153950/suppl/GSM1153950_Grp4_C57B6_4_SCfl_mir221_24h_430_2.CHP.gz
| | Sample_series_id | GSE47643
| | Sample_data_row_count | 45101
| | |
|
GSM1153951 | GPL1261 |
|
Group4: preB cells after 24h induction with doxycycline_5
|
Grp4-5 preB cells after 24h induction for miR-221 expression with doxycycline
|
strain: C57BL/6
tissue: fetal liver
cell type: preB-cells
induction of mir-221: 24 h
|
Grp4_C57B6_5_SCfl_mir221_24h_430_2
Gene expression profiles of un-induced preB cells prepared from tissue culture were compared using Affymetrix MG430Av2 GeneChip arrays. After total RNA extraction, reverse transcription, cDNA extraction, the biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized in triplicates for each of the four groups to the GeneChip arrays. Twelve chips in these four groups were hybridized and analyzed: Group4 are preB cells induced for miR-221 expression after 24h
|
| Sample_geo_accession | GSM1153951
| | Sample_status | Public on Jun 05 2013
| | Sample_submission_date | Jun 04 2013
| | Sample_last_update_date | Jun 07 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | Samples were obtained from the fetal liver of C57BL/6, CD45.1pos mice (MPIIB, Berlin, Germany)
| | Sample_treatment_protocol_ch1 | MiR-221 expression was induced by adding 1 mg/ml doxycycline to the cell culture media and samples were taken at 8, 16, or 24h after induction.
| | Sample_growth_protocol_ch1 | PreB cells derived from wild type fetal liver (C57BL/6, CD45.1pos) at day 18 of gestation were grown on a confluent layer of gamma-irradiated (30Gy) M-CSF-deficient OP9 stromal cells in IMDM medium (Gibco) supplemented with 2% FCS (Sigma-Aldrich), 0.03% Primatone-RL (Quest) and 1% mouse IL7 conditioned media as described by Rolink et al, 1991.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instruction, including the recommended DNase digest. The purity and integrity of RNA were assessed for each sample using an Agilent 2100 Bioanalyzer with the RNA 6000 Nano LabChip and amount was checked with a NanoDrop ND-1000 spectrophotometer. Contaminating genomic DNA was removed by an on-column DNA digestion step (Qiagen).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Labeling and hybridization of total RNA was performed using the GeneChip 3’ IVT Express Kit from Affymetrix according to the manufacturers instruction. Briefly, after total RNA extraction, 100 ng of total RNA from each cell sample was reverse transcribed, cDNA was extracted, biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized to each of the GeneChip arrays. The MG430Av2 GeneChip arrays were loaded with the hybridization cocktail, hybridized at 45 °C rotating for 16 h in a hybridization oven 640 (Affymetrix), washed and stained with streptavidin-phycoerythrin using the Affymetrix GeneChip Fluidics Workstation 400.
| | Sample_hyb_protocol | Labeling and hybridization of total RNA was performed using the GeneChip 3’ IVT Express Kit from Affymetrix according to the manufacturers instruction. Briefly, after total RNA extraction, 100 ng of total RNA from each cell sample was reverse transcribed, cDNA was extracted, biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized to each of the GeneChip arrays. The MG430Av2 GeneChip arrays were loaded with the hybridization cocktail, hybridized at 45 °C rotating for 16 h in a hybridization oven 640 (Affymetrix), washed and stained with streptavidin-phycoerythrin using the Affymetrix GeneChip Fluidics Workstation 400.
| | Sample_scan_protocol | Arrays were scanned with an Affymetrix GeneChip Scanner 3000, using the GCOS software from Affymetrix.
| | Sample_data_processing | Data were analyzed according to High Performance Chip Data Analysis (HPCDA, unpublished - Joachim R. Grün) with the Bioretis database (http://www.bioretis-analysis.de/) using the default filter parameters for decreased and increased gene lists (description of database c.f. open access paper Menssen et al., 2009; PubMedID: 19265543). Chip data included in the Bioretis database were analyzed using the GeneChip Operating Software (GCOS, Affymetrix), version 1.4. Microarrays were globally normalized and scaled to a trimmed mean expression value of 150. Quality checks were performed according to the manufacturer's recommendations. All 3 chips of one group were compared to each 3 chips of any other group (results, compared to 16h chips were ignored in this study), and the following parameters of absolute and comparative analysis were included in the Bioretis database: expression heights (Signals) and mean, median and standard deviation of Signals of both groups, call for presence of transcripts (Absent, A; Marginal, M; Present, P), p-value for presence or absence of transcripts, log2 value of fold change (Signal Log Ratio, SLR) and the fold change as mean values, call for the significance of differentially expression (Change Call: Increase, I; Marginal I, MI; Decrease, D; Marginal D, MD; No Change, NC), and the p value for that call. Additionally -- not calculated with GCOS -- t-tests of log Signals and SLRs were included in the database. For each present transcript the significance of differential expression between the groups of arrays was either calculated using strict Bonferroni corrected Welch t-tests between 9 SLR values of Experiment group vs. Baseline group and 12 SLR values within both groups (the latter 12 giving a mean SLR value of zero; p-value had to be <= 5.279E-08) or more than 50% of non-parametrically calculated Change calls (Mann-Whitney U test, GCOS) i.e. 5 or more of all 9 Change calls have to be in the same direction. Significantly differentially expressed genes, were filtered using both default parameter sets of filter criteria; these are a combination of four different queries. Filter criteria were developed with various data sets of GeneChips and validated with the Affymetrix Latin Square dataset as shown in Menssen et al., 2009. You can find these validation experiments in BioRetis without registering, using the public content and public login. Click on view single results, select any existing Analysis beginning with first 3 letters "SGU" and click on "Next". Click on "Chose an existing parameterset" and select "JRG_Increase" for increased or "JRG_Decrease" for decreased probesets and click on "Fill". At the bottom of the site check the box named "* use Bonferroni correction" and click on "Search only" to get the list of significantly changed increased or decreased probesets, respectively. The Affymetrix Latin Square dataset, consisting of 42 chips in 14 experiments with three replicates each were analyzed in BioRetis with all possible 3 vs. 3 chip comparisons (one direction).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Joachim,R.,Grün
| | Sample_contact_email | Gruen@DRFZ.de
| | Sample_contact_department | Bioinformatics
| | Sample_contact_institute | Deutsches Rheuma-Forschungszentrum (DRFZ)
| | Sample_contact_address | Charitéplatz 1
| | Sample_contact_city | Berlin
| | Sample_contact_zip/postal_code | D-10117
| | Sample_contact_country | Germany
| | Sample_contact_web_link | www.drfz.de
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1153nnn/GSM1153951/suppl/GSM1153951_Grp4_C57B6_5_SCfl_mir221_24h_430_2.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1153nnn/GSM1153951/suppl/GSM1153951_Grp4_C57B6_5_SCfl_mir221_24h_430_2.CHP.gz
| | Sample_series_id | GSE47643
| | Sample_data_row_count | 45101
| | |
|
GSM1153952 | GPL1261 |
|
Group4: preB cells after 24h induction with doxycycline_6
|
Grp4-6 preB cells after 24h induction for miR-221 expression with doxycycline
|
strain: C57BL/6
tissue: fetal liver
cell type: preB-cells
induction of mir-221: 24 h
|
Grp4_C57B6_6_SCfl_mir221_24h_430_2
Gene expression profiles of un-induced preB cells prepared from tissue culture were compared using Affymetrix MG430Av2 GeneChip arrays. After total RNA extraction, reverse transcription, cDNA extraction, the biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized in triplicates for each of the four groups to the GeneChip arrays. Twelve chips in these four groups were hybridized and analyzed: Group4 are preB cells induced for miR-221 expression after 24h
|
| Sample_geo_accession | GSM1153952
| | Sample_status | Public on Jun 05 2013
| | Sample_submission_date | Jun 04 2013
| | Sample_last_update_date | Jun 07 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | Samples were obtained from the fetal liver of C57BL/6, CD45.1pos mice (MPIIB, Berlin, Germany)
| | Sample_treatment_protocol_ch1 | MiR-221 expression was induced by adding 1 mg/ml doxycycline to the cell culture media and samples were taken at 8, 16, or 24h after induction.
| | Sample_growth_protocol_ch1 | PreB cells derived from wild type fetal liver (C57BL/6, CD45.1pos) at day 18 of gestation were grown on a confluent layer of gamma-irradiated (30Gy) M-CSF-deficient OP9 stromal cells in IMDM medium (Gibco) supplemented with 2% FCS (Sigma-Aldrich), 0.03% Primatone-RL (Quest) and 1% mouse IL7 conditioned media as described by Rolink et al, 1991.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instruction, including the recommended DNase digest. The purity and integrity of RNA were assessed for each sample using an Agilent 2100 Bioanalyzer with the RNA 6000 Nano LabChip and amount was checked with a NanoDrop ND-1000 spectrophotometer. Contaminating genomic DNA was removed by an on-column DNA digestion step (Qiagen).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Labeling and hybridization of total RNA was performed using the GeneChip 3’ IVT Express Kit from Affymetrix according to the manufacturers instruction. Briefly, after total RNA extraction, 100 ng of total RNA from each cell sample was reverse transcribed, cDNA was extracted, biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized to each of the GeneChip arrays. The MG430Av2 GeneChip arrays were loaded with the hybridization cocktail, hybridized at 45 °C rotating for 16 h in a hybridization oven 640 (Affymetrix), washed and stained with streptavidin-phycoerythrin using the Affymetrix GeneChip Fluidics Workstation 400.
| | Sample_hyb_protocol | Labeling and hybridization of total RNA was performed using the GeneChip 3’ IVT Express Kit from Affymetrix according to the manufacturers instruction. Briefly, after total RNA extraction, 100 ng of total RNA from each cell sample was reverse transcribed, cDNA was extracted, biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized to each of the GeneChip arrays. The MG430Av2 GeneChip arrays were loaded with the hybridization cocktail, hybridized at 45 °C rotating for 16 h in a hybridization oven 640 (Affymetrix), washed and stained with streptavidin-phycoerythrin using the Affymetrix GeneChip Fluidics Workstation 400.
| | Sample_scan_protocol | Arrays were scanned with an Affymetrix GeneChip Scanner 3000, using the GCOS software from Affymetrix.
| | Sample_data_processing | Data were analyzed according to High Performance Chip Data Analysis (HPCDA, unpublished - Joachim R. Grün) with the Bioretis database (http://www.bioretis-analysis.de/) using the default filter parameters for decreased and increased gene lists (description of database c.f. open access paper Menssen et al., 2009; PubMedID: 19265543). Chip data included in the Bioretis database were analyzed using the GeneChip Operating Software (GCOS, Affymetrix), version 1.4. Microarrays were globally normalized and scaled to a trimmed mean expression value of 150. Quality checks were performed according to the manufacturer's recommendations. All 3 chips of one group were compared to each 3 chips of any other group (results, compared to 16h chips were ignored in this study), and the following parameters of absolute and comparative analysis were included in the Bioretis database: expression heights (Signals) and mean, median and standard deviation of Signals of both groups, call for presence of transcripts (Absent, A; Marginal, M; Present, P), p-value for presence or absence of transcripts, log2 value of fold change (Signal Log Ratio, SLR) and the fold change as mean values, call for the significance of differentially expression (Change Call: Increase, I; Marginal I, MI; Decrease, D; Marginal D, MD; No Change, NC), and the p value for that call. Additionally -- not calculated with GCOS -- t-tests of log Signals and SLRs were included in the database. For each present transcript the significance of differential expression between the groups of arrays was either calculated using strict Bonferroni corrected Welch t-tests between 9 SLR values of Experiment group vs. Baseline group and 12 SLR values within both groups (the latter 12 giving a mean SLR value of zero; p-value had to be <= 5.279E-08) or more than 50% of non-parametrically calculated Change calls (Mann-Whitney U test, GCOS) i.e. 5 or more of all 9 Change calls have to be in the same direction. Significantly differentially expressed genes, were filtered using both default parameter sets of filter criteria; these are a combination of four different queries. Filter criteria were developed with various data sets of GeneChips and validated with the Affymetrix Latin Square dataset as shown in Menssen et al., 2009. You can find these validation experiments in BioRetis without registering, using the public content and public login. Click on view single results, select any existing Analysis beginning with first 3 letters "SGU" and click on "Next". Click on "Chose an existing parameterset" and select "JRG_Increase" for increased or "JRG_Decrease" for decreased probesets and click on "Fill". At the bottom of the site check the box named "* use Bonferroni correction" and click on "Search only" to get the list of significantly changed increased or decreased probesets, respectively. The Affymetrix Latin Square dataset, consisting of 42 chips in 14 experiments with three replicates each were analyzed in BioRetis with all possible 3 vs. 3 chip comparisons (one direction).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Joachim,R.,Grün
| | Sample_contact_email | Gruen@DRFZ.de
| | Sample_contact_department | Bioinformatics
| | Sample_contact_institute | Deutsches Rheuma-Forschungszentrum (DRFZ)
| | Sample_contact_address | Charitéplatz 1
| | Sample_contact_city | Berlin
| | Sample_contact_zip/postal_code | D-10117
| | Sample_contact_country | Germany
| | Sample_contact_web_link | www.drfz.de
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1153nnn/GSM1153952/suppl/GSM1153952_Grp4_C57B6_6_SCfl_mir221_24h_430_2.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1153nnn/GSM1153952/suppl/GSM1153952_Grp4_C57B6_6_SCfl_mir221_24h_430_2.CHP.gz
| | Sample_series_id | GSE47643
| | Sample_data_row_count | 45101
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