Search results for the GEO ID: GSE34179  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM843532 | GPL1261 |
|
hd/hd NKT-A
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sorted Va14i NKT cells from three hd/hd mutant mice
|
background strain: C57Bl/6
genotype/variation: hd/hd
|
|
| Sample_geo_accession | GSM843532
| | Sample_status | Public on Dec 01 2012
| | Sample_submission_date | Dec 06 2011
| | Sample_last_update_date | Dec 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | NKT cells were enriched by magnetic depletion of CD19+, TER-119+, CD11b+ and CD62L+ cells with LS columns and supplied reagents and protocols from Miltenyi, stained with PBS57-loaded CD1d-Streptavidin-PE tetramers and anti TCR beta antibodies, and sorted using a FACS ARIA. ~1 to 2 million Va14i NKT cells were collected.
| | Sample_growth_protocol_ch1 | Perfused livers from hd/hd and control (hd/+ or +/+) mice (three of each genotype, ~two months old) were harvested. Hemopoietic cells were isolated by Percoll gradient, and RBCs were lysed with KCl solution.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from sorted cells was prepared using an Rneasy mini kit (Qiagen). In some cases RNA was further concentrated and purified using an Rneasy MinElute Cleanup kit (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200 ng total RNA (Expression Analysis Technical Manual, 2006, Affymetrix).
| | Sample_hyb_protocol | Microarray chips were hybridized to fragmented cRNA in an Affymetrix Hybridization Oven 320 and washed using an Affymetrix GeneChip Fluidics Station 450, according to the Expression Analysis Technical Manual, 2006, Affymetrix.
| | Sample_scan_protocol | Microarrays were scanned using the Affymetrix GeneChip Scanner 3000 according to the Expression Analysis Technical Manual, 2006 (Affymetrix).
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. Tables with pairwise comparison of samples hd/hd NKT-A and hd/+ NKT and samples hd/hd NKT-B and +/+ NKT were generated using VAMPIRE software (Subramanian lab, UCSD).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Mitch,,Kronenberg
| | Sample_contact_email | mitch@liai.org
| | Sample_contact_institute | LIAI
| | Sample_contact_address | 9420 Athena Circle
| | Sample_contact_city | La Jolla
| | Sample_contact_zip/postal_code | 92037
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM843nnn/GSM843532/suppl/GSM843532_8755.Kronenberg.hd-hd.as.CEL.gz
| | Sample_series_id | GSE34179
| | Sample_data_row_count | 45101
| | |
|
GSM843533 | GPL1261 |
|
hd/+ NKT
|
sorted Va14i NKT cells from three hd/+ mice (age-matched with hd/hd NKT-A)
|
background strain: C57Bl/6
genotype/variation: hd/+
|
|
| Sample_geo_accession | GSM843533
| | Sample_status | Public on Dec 01 2012
| | Sample_submission_date | Dec 06 2011
| | Sample_last_update_date | Dec 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | NKT cells were enriched by magnetic depletion of CD19+, TER-119+, CD11b+ and CD62L+ cells with LS columns and supplied reagents and protocols from Miltenyi, stained with PBS57-loaded CD1d-Streptavidin-PE tetramers and anti TCR beta antibodies, and sorted using a FACS ARIA. ~1 to 2 million Va14i NKT cells were collected.
| | Sample_growth_protocol_ch1 | Perfused livers from hd/hd and control (hd/+ or +/+) mice (three of each genotype, ~two months old) were harvested. Hemopoietic cells were isolated by Percoll gradient, and RBCs were lysed with KCl solution.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from sorted cells was prepared using an Rneasy mini kit (Qiagen). In some cases RNA was further concentrated and purified using an Rneasy MinElute Cleanup kit (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200 ng total RNA (Expression Analysis Technical Manual, 2006, Affymetrix).
| | Sample_hyb_protocol | Microarray chips were hybridized to fragmented cRNA in an Affymetrix Hybridization Oven 320 and washed using an Affymetrix GeneChip Fluidics Station 450, according to the Expression Analysis Technical Manual, 2006, Affymetrix.
| | Sample_scan_protocol | Microarrays were scanned using the Affymetrix GeneChip Scanner 3000 according to the Expression Analysis Technical Manual, 2006 (Affymetrix).
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. Tables with pairwise comparison of samples hd/hd NKT-A and hd/+ NKT and samples hd/hd NKT-B and +/+ NKT were generated using VAMPIRE software (Subramanian lab, UCSD).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Mitch,,Kronenberg
| | Sample_contact_email | mitch@liai.org
| | Sample_contact_institute | LIAI
| | Sample_contact_address | 9420 Athena Circle
| | Sample_contact_city | La Jolla
| | Sample_contact_zip/postal_code | 92037
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM843nnn/GSM843533/suppl/GSM843533_8756.Kronenberg.hd-+.as.CEL.gz
| | Sample_series_id | GSE34179
| | Sample_data_row_count | 45101
| | |
|
GSM843534 | GPL1261 |
|
hd/hd NKT-B
|
sorted Va14i NKT cells from three hd/hd mutant mice
|
background strain: C57Bl/6
genotype/variation: hd/hd
|
|
| Sample_geo_accession | GSM843534
| | Sample_status | Public on Dec 01 2012
| | Sample_submission_date | Dec 06 2011
| | Sample_last_update_date | Dec 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | NKT cells were enriched by magnetic depletion of CD19+, TER-119+, CD11b+ and CD62L+ cells with LS columns and supplied reagents and protocols from Miltenyi, stained with PBS57-loaded CD1d-Streptavidin-PE tetramers and anti TCR beta antibodies, and sorted using a FACS ARIA. ~1 to 2 million Va14i NKT cells were collected.
| | Sample_growth_protocol_ch1 | Perfused livers from hd/hd and control (hd/+ or +/+) mice (three of each genotype, ~two months old) were harvested. Hemopoietic cells were isolated by Percoll gradient, and RBCs were lysed with KCl solution.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from sorted cells was prepared using an Rneasy mini kit (Qiagen). In some cases RNA was further concentrated and purified using an Rneasy MinElute Cleanup kit (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200 ng total RNA (Expression Analysis Technical Manual, 2006, Affymetrix).
| | Sample_hyb_protocol | Microarray chips were hybridized to fragmented cRNA in an Affymetrix Hybridization Oven 320 and washed using an Affymetrix GeneChip Fluidics Station 450, according to the Expression Analysis Technical Manual, 2006, Affymetrix.
| | Sample_scan_protocol | Microarrays were scanned using the Affymetrix GeneChip Scanner 3000 according to the Expression Analysis Technical Manual, 2006 (Affymetrix).
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. Tables with pairwise comparison of samples hd/hd NKT-A and hd/+ NKT and samples hd/hd NKT-B and +/+ NKT were generated using VAMPIRE software (Subramanian lab, UCSD).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Mitch,,Kronenberg
| | Sample_contact_email | mitch@liai.org
| | Sample_contact_institute | LIAI
| | Sample_contact_address | 9420 Athena Circle
| | Sample_contact_city | La Jolla
| | Sample_contact_zip/postal_code | 92037
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM843nnn/GSM843534/suppl/GSM843534_8786.Kronenberg.hd-hd_NKT.as.CEL.gz
| | Sample_series_id | GSE34179
| | Sample_data_row_count | 45101
| | |
|
GSM843535 | GPL1261 |
|
+/+ NKT
|
sorted Va14i NKT cells from three +/+ mice (age-matched with hd/hd NKT-B)
|
background strain: C57Bl/6
genotype/variation: +/+
|
|
| Sample_geo_accession | GSM843535
| | Sample_status | Public on Dec 01 2012
| | Sample_submission_date | Dec 06 2011
| | Sample_last_update_date | Dec 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | NKT cells were enriched by magnetic depletion of CD19+, TER-119+, CD11b+ and CD62L+ cells with LS columns and supplied reagents and protocols from Miltenyi, stained with PBS57-loaded CD1d-Streptavidin-PE tetramers and anti TCR beta antibodies, and sorted using a FACS ARIA. ~1 to 2 million Va14i NKT cells were collected.
| | Sample_growth_protocol_ch1 | Perfused livers from hd/hd and control (hd/+ or +/+) mice (three of each genotype, ~two months old) were harvested. Hemopoietic cells were isolated by Percoll gradient, and RBCs were lysed with KCl solution.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from sorted cells was prepared using an Rneasy mini kit (Qiagen). In some cases RNA was further concentrated and purified using an Rneasy MinElute Cleanup kit (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200 ng total RNA (Expression Analysis Technical Manual, 2006, Affymetrix).
| | Sample_hyb_protocol | Microarray chips were hybridized to fragmented cRNA in an Affymetrix Hybridization Oven 320 and washed using an Affymetrix GeneChip Fluidics Station 450, according to the Expression Analysis Technical Manual, 2006, Affymetrix.
| | Sample_scan_protocol | Microarrays were scanned using the Affymetrix GeneChip Scanner 3000 according to the Expression Analysis Technical Manual, 2006 (Affymetrix).
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. Tables with pairwise comparison of samples hd/hd NKT-A and hd/+ NKT and samples hd/hd NKT-B and +/+ NKT were generated using VAMPIRE software (Subramanian lab, UCSD).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Mitch,,Kronenberg
| | Sample_contact_email | mitch@liai.org
| | Sample_contact_institute | LIAI
| | Sample_contact_address | 9420 Athena Circle
| | Sample_contact_city | La Jolla
| | Sample_contact_zip/postal_code | 92037
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM843nnn/GSM843535/suppl/GSM843535_8787.Kronenberg.+-+_NKT.as.CEL.gz
| | Sample_series_id | GSE34179
| | Sample_data_row_count | 45101
| | |
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