Search results for the GEO ID: GSE44723  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM1089614 | GPL570 |
|
fibroblast_Rapid_D10_Media_13
|
Rapid progressing fibrosis
|
status: Rapid
age: 48
gender: male
tissue: cultured human fibroblasts
|
|
| Sample_geo_accession | GSM1089614
| | Sample_status | Public on Apr 10 2013
| | Sample_submission_date | Feb 27 2013
| | Sample_last_update_date | Apr 11 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | No additional treatments were applied to the cultured cell lines
| | Sample_growth_protocol_ch1 = Primary cultures of LFs were isolated from the distal parenchyma of patients from unaffected donor controls (lung cancer patients) and patients with IPF as previously described [Hogaboam CM, Carpenter KJ, Evanoff H, Kunkel SL (2005), Pechkovsky DV, Prele CM, Wong J, Hogaboam CM, McAnulty RJ, et al. (2012)]. All fibroblast cell lines were completely de-identified from the patients they were grown from prior to characterization in this study. The IPF lung tissue was obtained and the diagnosis of Usual Interstitial Pneumonia (UIP) / IPF achieved as previously outlined [Pechkovsky DV, Prele CM, Wong J, Hogaboam CM, McAnulty RJ, et al. (2012)]. Normal human lung tissue was obtained from macroscopically tumor-free lung resections of patients with lung cancer. The human lung tissue collection was approved by the ethics committees of all institutions involved. In this study we characterized fibroblasts cell lines originated from 14 donors across 3 phenotypes: non-IPF control (n = 4), stable IPF (n = 6), and rapidly progressing IPF (n | 4) subjects. Cells from these lines were plated and passaged (up to the 11th passage).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated and homogenized in QIAzol reagent. Purified RNA was then amplified and labeled using NuGen Ovation kits
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Purified total RNA was amplified and labeled using NuGen Ovation kits (NuGEN Technologies, Inc., San Carlos, CA) and RNA from samples was hybridized to Affymetrix HG-U133 plus 2.0 arrays.
| | Sample_hyb_protocol | Array washing, staining and scanning was performed according to standard Affymetrix protocols .
| | Sample_scan_protocol | Array washing, staining and scanning was performed according to standard Affymetrix protocols .
| | Sample_data_processing | Probe level data was curated by first mapping individual probe sequences to their most current genome sequences. Probes which were non-uniquely mapped to specific genes or contained outdated mappings were discarded, and the remaining probes were summarized into probesets and normalized using Robust Multi-array Average (RMA). Probes expressed at low levels across all samples were subsequently discarded.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sriram,,Sridhar
| | Sample_contact_email | ssridhar21@gmail.com
| | Sample_contact_phone | 6178771485
| | Sample_contact_department | Translational Research Sciences
| | Sample_contact_institute | Hoffmann-La Roche, Inc.
| | Sample_contact_address | 340 Kingsland St.
| | Sample_contact_city | Nutley
| | Sample_contact_state | NJ
| | Sample_contact_zip/postal_code | 07110
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1089nnn/GSM1089614/suppl/GSM1089614_LargeRNA_Donor10_Media_13.CEL.gz
| | Sample_series_id | GSE44723
| | Sample_data_row_count | 21095
| | |
|
GSM1089615 | GPL570 |
|
fibroblast_Slow_D123_Media_10
|
Slow progressing fibrosis
|
status: Slow
age: 71
gender: male
tissue: cultured human fibroblasts
|
|
| Sample_geo_accession | GSM1089615
| | Sample_status | Public on Apr 10 2013
| | Sample_submission_date | Feb 27 2013
| | Sample_last_update_date | Apr 11 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | No additional treatments were applied to the cultured cell lines
| | Sample_growth_protocol_ch1 = Primary cultures of LFs were isolated from the distal parenchyma of patients from unaffected donor controls (lung cancer patients) and patients with IPF as previously described [Hogaboam CM, Carpenter KJ, Evanoff H, Kunkel SL (2005), Pechkovsky DV, Prele CM, Wong J, Hogaboam CM, McAnulty RJ, et al. (2012)]. All fibroblast cell lines were completely de-identified from the patients they were grown from prior to characterization in this study. The IPF lung tissue was obtained and the diagnosis of Usual Interstitial Pneumonia (UIP) / IPF achieved as previously outlined [Pechkovsky DV, Prele CM, Wong J, Hogaboam CM, McAnulty RJ, et al. (2012)]. Normal human lung tissue was obtained from macroscopically tumor-free lung resections of patients with lung cancer. The human lung tissue collection was approved by the ethics committees of all institutions involved. In this study we characterized fibroblasts cell lines originated from 14 donors across 3 phenotypes: non-IPF control (n = 4), stable IPF (n = 6), and rapidly progressing IPF (n | 4) subjects. Cells from these lines were plated and passaged (up to the 11th passage).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated and homogenized in QIAzol reagent. Purified RNA was then amplified and labeled using NuGen Ovation kits
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Purified total RNA was amplified and labeled using NuGen Ovation kits (NuGEN Technologies, Inc., San Carlos, CA) and RNA from samples was hybridized to Affymetrix HG-U133 plus 2.0 arrays.
| | Sample_hyb_protocol | Array washing, staining and scanning was performed according to standard Affymetrix protocols .
| | Sample_scan_protocol | Array washing, staining and scanning was performed according to standard Affymetrix protocols .
| | Sample_data_processing | Probe level data was curated by first mapping individual probe sequences to their most current genome sequences. Probes which were non-uniquely mapped to specific genes or contained outdated mappings were discarded, and the remaining probes were summarized into probesets and normalized using Robust Multi-array Average (RMA). Probes expressed at low levels across all samples were subsequently discarded.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sriram,,Sridhar
| | Sample_contact_email | ssridhar21@gmail.com
| | Sample_contact_phone | 6178771485
| | Sample_contact_department | Translational Research Sciences
| | Sample_contact_institute | Hoffmann-La Roche, Inc.
| | Sample_contact_address | 340 Kingsland St.
| | Sample_contact_city | Nutley
| | Sample_contact_state | NJ
| | Sample_contact_zip/postal_code | 07110
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1089nnn/GSM1089615/suppl/GSM1089615_LargeRNA_Donor123_Media_10.CEL.gz
| | Sample_series_id | GSE44723
| | Sample_data_row_count | 21095
| | |
|
GSM1089616 | GPL570 |
|
fibroblast_Normal_D133_Media_3
|
Normal - no fibrosis
|
status: Normal
age: 75
gender: male
tissue: cultured human fibroblasts
|
|
| Sample_geo_accession | GSM1089616
| | Sample_status | Public on Apr 10 2013
| | Sample_submission_date | Feb 27 2013
| | Sample_last_update_date | Apr 11 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | No additional treatments were applied to the cultured cell lines
| | Sample_growth_protocol_ch1 = Primary cultures of LFs were isolated from the distal parenchyma of patients from unaffected donor controls (lung cancer patients) and patients with IPF as previously described [Hogaboam CM, Carpenter KJ, Evanoff H, Kunkel SL (2005), Pechkovsky DV, Prele CM, Wong J, Hogaboam CM, McAnulty RJ, et al. (2012)]. All fibroblast cell lines were completely de-identified from the patients they were grown from prior to characterization in this study. The IPF lung tissue was obtained and the diagnosis of Usual Interstitial Pneumonia (UIP) / IPF achieved as previously outlined [Pechkovsky DV, Prele CM, Wong J, Hogaboam CM, McAnulty RJ, et al. (2012)]. Normal human lung tissue was obtained from macroscopically tumor-free lung resections of patients with lung cancer. The human lung tissue collection was approved by the ethics committees of all institutions involved. In this study we characterized fibroblasts cell lines originated from 14 donors across 3 phenotypes: non-IPF control (n = 4), stable IPF (n = 6), and rapidly progressing IPF (n | 4) subjects. Cells from these lines were plated and passaged (up to the 11th passage).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated and homogenized in QIAzol reagent. Purified RNA was then amplified and labeled using NuGen Ovation kits
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Purified total RNA was amplified and labeled using NuGen Ovation kits (NuGEN Technologies, Inc., San Carlos, CA) and RNA from samples was hybridized to Affymetrix HG-U133 plus 2.0 arrays.
| | Sample_hyb_protocol | Array washing, staining and scanning was performed according to standard Affymetrix protocols .
| | Sample_scan_protocol | Array washing, staining and scanning was performed according to standard Affymetrix protocols .
| | Sample_data_processing | Probe level data was curated by first mapping individual probe sequences to their most current genome sequences. Probes which were non-uniquely mapped to specific genes or contained outdated mappings were discarded, and the remaining probes were summarized into probesets and normalized using Robust Multi-array Average (RMA). Probes expressed at low levels across all samples were subsequently discarded.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sriram,,Sridhar
| | Sample_contact_email | ssridhar21@gmail.com
| | Sample_contact_phone | 6178771485
| | Sample_contact_department | Translational Research Sciences
| | Sample_contact_institute | Hoffmann-La Roche, Inc.
| | Sample_contact_address | 340 Kingsland St.
| | Sample_contact_city | Nutley
| | Sample_contact_state | NJ
| | Sample_contact_zip/postal_code | 07110
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1089nnn/GSM1089616/suppl/GSM1089616_LargeRNA_Donor133_Media_3.CEL.gz
| | Sample_series_id | GSE44723
| | Sample_data_row_count | 21095
| | |
|
GSM1089617 | GPL570 |
|
fibroblast_Normal_D139_Media_4
|
Normal - no fibrosis
|
status: Normal
age: 64
gender: female
tissue: cultured human fibroblasts
|
|
| Sample_geo_accession | GSM1089617
| | Sample_status | Public on Apr 10 2013
| | Sample_submission_date | Feb 27 2013
| | Sample_last_update_date | Apr 11 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | No additional treatments were applied to the cultured cell lines
| | Sample_growth_protocol_ch1 = Primary cultures of LFs were isolated from the distal parenchyma of patients from unaffected donor controls (lung cancer patients) and patients with IPF as previously described [Hogaboam CM, Carpenter KJ, Evanoff H, Kunkel SL (2005), Pechkovsky DV, Prele CM, Wong J, Hogaboam CM, McAnulty RJ, et al. (2012)]. All fibroblast cell lines were completely de-identified from the patients they were grown from prior to characterization in this study. The IPF lung tissue was obtained and the diagnosis of Usual Interstitial Pneumonia (UIP) / IPF achieved as previously outlined [Pechkovsky DV, Prele CM, Wong J, Hogaboam CM, McAnulty RJ, et al. (2012)]. Normal human lung tissue was obtained from macroscopically tumor-free lung resections of patients with lung cancer. The human lung tissue collection was approved by the ethics committees of all institutions involved. In this study we characterized fibroblasts cell lines originated from 14 donors across 3 phenotypes: non-IPF control (n = 4), stable IPF (n = 6), and rapidly progressing IPF (n | 4) subjects. Cells from these lines were plated and passaged (up to the 11th passage).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated and homogenized in QIAzol reagent. Purified RNA was then amplified and labeled using NuGen Ovation kits
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Purified total RNA was amplified and labeled using NuGen Ovation kits (NuGEN Technologies, Inc., San Carlos, CA) and RNA from samples was hybridized to Affymetrix HG-U133 plus 2.0 arrays.
| | Sample_hyb_protocol | Array washing, staining and scanning was performed according to standard Affymetrix protocols .
| | Sample_scan_protocol | Array washing, staining and scanning was performed according to standard Affymetrix protocols .
| | Sample_data_processing | Probe level data was curated by first mapping individual probe sequences to their most current genome sequences. Probes which were non-uniquely mapped to specific genes or contained outdated mappings were discarded, and the remaining probes were summarized into probesets and normalized using Robust Multi-array Average (RMA). Probes expressed at low levels across all samples were subsequently discarded.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sriram,,Sridhar
| | Sample_contact_email | ssridhar21@gmail.com
| | Sample_contact_phone | 6178771485
| | Sample_contact_department | Translational Research Sciences
| | Sample_contact_institute | Hoffmann-La Roche, Inc.
| | Sample_contact_address | 340 Kingsland St.
| | Sample_contact_city | Nutley
| | Sample_contact_state | NJ
| | Sample_contact_zip/postal_code | 07110
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1089nnn/GSM1089617/suppl/GSM1089617_LargeRNA_Donor139_Media_4.CEL.gz
| | Sample_series_id | GSE44723
| | Sample_data_row_count | 21095
| | |
|
GSM1089618 | GPL570 |
|
fibroblast_Normal_D160_Media_5
|
Normal - no fibrosis
|
status: Normal
age: 59
gender: female
tissue: cultured human fibroblasts
|
|
| Sample_geo_accession | GSM1089618
| | Sample_status | Public on Apr 10 2013
| | Sample_submission_date | Feb 27 2013
| | Sample_last_update_date | Apr 11 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | No additional treatments were applied to the cultured cell lines
| | Sample_growth_protocol_ch1 = Primary cultures of LFs were isolated from the distal parenchyma of patients from unaffected donor controls (lung cancer patients) and patients with IPF as previously described [Hogaboam CM, Carpenter KJ, Evanoff H, Kunkel SL (2005), Pechkovsky DV, Prele CM, Wong J, Hogaboam CM, McAnulty RJ, et al. (2012)]. All fibroblast cell lines were completely de-identified from the patients they were grown from prior to characterization in this study. The IPF lung tissue was obtained and the diagnosis of Usual Interstitial Pneumonia (UIP) / IPF achieved as previously outlined [Pechkovsky DV, Prele CM, Wong J, Hogaboam CM, McAnulty RJ, et al. (2012)]. Normal human lung tissue was obtained from macroscopically tumor-free lung resections of patients with lung cancer. The human lung tissue collection was approved by the ethics committees of all institutions involved. In this study we characterized fibroblasts cell lines originated from 14 donors across 3 phenotypes: non-IPF control (n = 4), stable IPF (n = 6), and rapidly progressing IPF (n | 4) subjects. Cells from these lines were plated and passaged (up to the 11th passage).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated and homogenized in QIAzol reagent. Purified RNA was then amplified and labeled using NuGen Ovation kits
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Purified total RNA was amplified and labeled using NuGen Ovation kits (NuGEN Technologies, Inc., San Carlos, CA) and RNA from samples was hybridized to Affymetrix HG-U133 plus 2.0 arrays.
| | Sample_hyb_protocol | Array washing, staining and scanning was performed according to standard Affymetrix protocols .
| | Sample_scan_protocol | Array washing, staining and scanning was performed according to standard Affymetrix protocols .
| | Sample_data_processing | Probe level data was curated by first mapping individual probe sequences to their most current genome sequences. Probes which were non-uniquely mapped to specific genes or contained outdated mappings were discarded, and the remaining probes were summarized into probesets and normalized using Robust Multi-array Average (RMA). Probes expressed at low levels across all samples were subsequently discarded.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sriram,,Sridhar
| | Sample_contact_email | ssridhar21@gmail.com
| | Sample_contact_phone | 6178771485
| | Sample_contact_department | Translational Research Sciences
| | Sample_contact_institute | Hoffmann-La Roche, Inc.
| | Sample_contact_address | 340 Kingsland St.
| | Sample_contact_city | Nutley
| | Sample_contact_state | NJ
| | Sample_contact_zip/postal_code | 07110
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1089nnn/GSM1089618/suppl/GSM1089618_LargeRNA_Donor160_Media_5.CEL.gz
| | Sample_series_id | GSE44723
| | Sample_data_row_count | 21095
| | |
|
GSM1089619 | GPL570 |
|
fibroblast_Rapid_D200_Media_14
|
Rapid progressing fibrosis
|
status: Rapid
age: 66
gender: male
tissue: cultured human fibroblasts
|
|
| Sample_geo_accession | GSM1089619
| | Sample_status | Public on Apr 10 2013
| | Sample_submission_date | Feb 27 2013
| | Sample_last_update_date | Apr 11 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | No additional treatments were applied to the cultured cell lines
| | Sample_growth_protocol_ch1 = Primary cultures of LFs were isolated from the distal parenchyma of patients from unaffected donor controls (lung cancer patients) and patients with IPF as previously described [Hogaboam CM, Carpenter KJ, Evanoff H, Kunkel SL (2005), Pechkovsky DV, Prele CM, Wong J, Hogaboam CM, McAnulty RJ, et al. (2012)]. All fibroblast cell lines were completely de-identified from the patients they were grown from prior to characterization in this study. The IPF lung tissue was obtained and the diagnosis of Usual Interstitial Pneumonia (UIP) / IPF achieved as previously outlined [Pechkovsky DV, Prele CM, Wong J, Hogaboam CM, McAnulty RJ, et al. (2012)]. Normal human lung tissue was obtained from macroscopically tumor-free lung resections of patients with lung cancer. The human lung tissue collection was approved by the ethics committees of all institutions involved. In this study we characterized fibroblasts cell lines originated from 14 donors across 3 phenotypes: non-IPF control (n = 4), stable IPF (n = 6), and rapidly progressing IPF (n | 4) subjects. Cells from these lines were plated and passaged (up to the 11th passage).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated and homogenized in QIAzol reagent. Purified RNA was then amplified and labeled using NuGen Ovation kits
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Purified total RNA was amplified and labeled using NuGen Ovation kits (NuGEN Technologies, Inc., San Carlos, CA) and RNA from samples was hybridized to Affymetrix HG-U133 plus 2.0 arrays.
| | Sample_hyb_protocol | Array washing, staining and scanning was performed according to standard Affymetrix protocols .
| | Sample_scan_protocol | Array washing, staining and scanning was performed according to standard Affymetrix protocols .
| | Sample_data_processing | Probe level data was curated by first mapping individual probe sequences to their most current genome sequences. Probes which were non-uniquely mapped to specific genes or contained outdated mappings were discarded, and the remaining probes were summarized into probesets and normalized using Robust Multi-array Average (RMA). Probes expressed at low levels across all samples were subsequently discarded.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sriram,,Sridhar
| | Sample_contact_email | ssridhar21@gmail.com
| | Sample_contact_phone | 6178771485
| | Sample_contact_department | Translational Research Sciences
| | Sample_contact_institute | Hoffmann-La Roche, Inc.
| | Sample_contact_address | 340 Kingsland St.
| | Sample_contact_city | Nutley
| | Sample_contact_state | NJ
| | Sample_contact_zip/postal_code | 07110
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1089nnn/GSM1089619/suppl/GSM1089619_LargeRNA_Donor200_Media_14.CEL.gz
| | Sample_series_id | GSE44723
| | Sample_data_row_count | 21095
| | |
|
GSM1089620 | GPL570 |
|
fibroblast_Normal_D207_Media_6
|
Normal - no fibrosis
|
status: Normal
age: 58
gender: female
tissue: cultured human fibroblasts
|
|
| Sample_geo_accession | GSM1089620
| | Sample_status | Public on Apr 10 2013
| | Sample_submission_date | Feb 27 2013
| | Sample_last_update_date | Apr 11 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | No additional treatments were applied to the cultured cell lines
| | Sample_growth_protocol_ch1 = Primary cultures of LFs were isolated from the distal parenchyma of patients from unaffected donor controls (lung cancer patients) and patients with IPF as previously described [Hogaboam CM, Carpenter KJ, Evanoff H, Kunkel SL (2005), Pechkovsky DV, Prele CM, Wong J, Hogaboam CM, McAnulty RJ, et al. (2012)]. All fibroblast cell lines were completely de-identified from the patients they were grown from prior to characterization in this study. The IPF lung tissue was obtained and the diagnosis of Usual Interstitial Pneumonia (UIP) / IPF achieved as previously outlined [Pechkovsky DV, Prele CM, Wong J, Hogaboam CM, McAnulty RJ, et al. (2012)]. Normal human lung tissue was obtained from macroscopically tumor-free lung resections of patients with lung cancer. The human lung tissue collection was approved by the ethics committees of all institutions involved. In this study we characterized fibroblasts cell lines originated from 14 donors across 3 phenotypes: non-IPF control (n = 4), stable IPF (n = 6), and rapidly progressing IPF (n | 4) subjects. Cells from these lines were plated and passaged (up to the 11th passage).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated and homogenized in QIAzol reagent. Purified RNA was then amplified and labeled using NuGen Ovation kits
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Purified total RNA was amplified and labeled using NuGen Ovation kits (NuGEN Technologies, Inc., San Carlos, CA) and RNA from samples was hybridized to Affymetrix HG-U133 plus 2.0 arrays.
| | Sample_hyb_protocol | Array washing, staining and scanning was performed according to standard Affymetrix protocols .
| | Sample_scan_protocol | Array washing, staining and scanning was performed according to standard Affymetrix protocols .
| | Sample_data_processing | Probe level data was curated by first mapping individual probe sequences to their most current genome sequences. Probes which were non-uniquely mapped to specific genes or contained outdated mappings were discarded, and the remaining probes were summarized into probesets and normalized using Robust Multi-array Average (RMA). Probes expressed at low levels across all samples were subsequently discarded.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sriram,,Sridhar
| | Sample_contact_email | ssridhar21@gmail.com
| | Sample_contact_phone | 6178771485
| | Sample_contact_department | Translational Research Sciences
| | Sample_contact_institute | Hoffmann-La Roche, Inc.
| | Sample_contact_address | 340 Kingsland St.
| | Sample_contact_city | Nutley
| | Sample_contact_state | NJ
| | Sample_contact_zip/postal_code | 07110
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1089nnn/GSM1089620/suppl/GSM1089620_LargeRNA_Donor207_Media_6.CEL.gz
| | Sample_series_id | GSE44723
| | Sample_data_row_count | 21095
| | |
|
GSM1089621 | GPL570 |
|
fibroblast_Slow_D223_Media_12
|
Slow progressing fibrosis
|
status: Slow
age: 72
gender: female
tissue: cultured human fibroblasts
|
|
| Sample_geo_accession | GSM1089621
| | Sample_status | Public on Apr 10 2013
| | Sample_submission_date | Feb 27 2013
| | Sample_last_update_date | Apr 11 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | No additional treatments were applied to the cultured cell lines
| | Sample_growth_protocol_ch1 = Primary cultures of LFs were isolated from the distal parenchyma of patients from unaffected donor controls (lung cancer patients) and patients with IPF as previously described [Hogaboam CM, Carpenter KJ, Evanoff H, Kunkel SL (2005), Pechkovsky DV, Prele CM, Wong J, Hogaboam CM, McAnulty RJ, et al. (2012)]. All fibroblast cell lines were completely de-identified from the patients they were grown from prior to characterization in this study. The IPF lung tissue was obtained and the diagnosis of Usual Interstitial Pneumonia (UIP) / IPF achieved as previously outlined [Pechkovsky DV, Prele CM, Wong J, Hogaboam CM, McAnulty RJ, et al. (2012)]. Normal human lung tissue was obtained from macroscopically tumor-free lung resections of patients with lung cancer. The human lung tissue collection was approved by the ethics committees of all institutions involved. In this study we characterized fibroblasts cell lines originated from 14 donors across 3 phenotypes: non-IPF control (n = 4), stable IPF (n = 6), and rapidly progressing IPF (n | 4) subjects. Cells from these lines were plated and passaged (up to the 11th passage).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated and homogenized in QIAzol reagent. Purified RNA was then amplified and labeled using NuGen Ovation kits
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Purified total RNA was amplified and labeled using NuGen Ovation kits (NuGEN Technologies, Inc., San Carlos, CA) and RNA from samples was hybridized to Affymetrix HG-U133 plus 2.0 arrays.
| | Sample_hyb_protocol | Array washing, staining and scanning was performed according to standard Affymetrix protocols .
| | Sample_scan_protocol | Array washing, staining and scanning was performed according to standard Affymetrix protocols .
| | Sample_data_processing | Probe level data was curated by first mapping individual probe sequences to their most current genome sequences. Probes which were non-uniquely mapped to specific genes or contained outdated mappings were discarded, and the remaining probes were summarized into probesets and normalized using Robust Multi-array Average (RMA). Probes expressed at low levels across all samples were subsequently discarded.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sriram,,Sridhar
| | Sample_contact_email | ssridhar21@gmail.com
| | Sample_contact_phone | 6178771485
| | Sample_contact_department | Translational Research Sciences
| | Sample_contact_institute | Hoffmann-La Roche, Inc.
| | Sample_contact_address | 340 Kingsland St.
| | Sample_contact_city | Nutley
| | Sample_contact_state | NJ
| | Sample_contact_zip/postal_code | 07110
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1089nnn/GSM1089621/suppl/GSM1089621_LargeRNA_Donor223_Media_12.CEL.gz
| | Sample_series_id | GSE44723
| | Sample_data_row_count | 21095
| | |
|
GSM1089622 | GPL570 |
|
fibroblast_Rapid_D26_Media_15
|
Rapid progressing fibrosis
|
status: Rapid
age: 49
gender: male
tissue: cultured human fibroblasts
|
|
| Sample_geo_accession | GSM1089622
| | Sample_status | Public on Apr 10 2013
| | Sample_submission_date | Feb 27 2013
| | Sample_last_update_date | Apr 11 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | No additional treatments were applied to the cultured cell lines
| | Sample_growth_protocol_ch1 = Primary cultures of LFs were isolated from the distal parenchyma of patients from unaffected donor controls (lung cancer patients) and patients with IPF as previously described [Hogaboam CM, Carpenter KJ, Evanoff H, Kunkel SL (2005), Pechkovsky DV, Prele CM, Wong J, Hogaboam CM, McAnulty RJ, et al. (2012)]. All fibroblast cell lines were completely de-identified from the patients they were grown from prior to characterization in this study. The IPF lung tissue was obtained and the diagnosis of Usual Interstitial Pneumonia (UIP) / IPF achieved as previously outlined [Pechkovsky DV, Prele CM, Wong J, Hogaboam CM, McAnulty RJ, et al. (2012)]. Normal human lung tissue was obtained from macroscopically tumor-free lung resections of patients with lung cancer. The human lung tissue collection was approved by the ethics committees of all institutions involved. In this study we characterized fibroblasts cell lines originated from 14 donors across 3 phenotypes: non-IPF control (n = 4), stable IPF (n = 6), and rapidly progressing IPF (n | 4) subjects. Cells from these lines were plated and passaged (up to the 11th passage).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated and homogenized in QIAzol reagent. Purified RNA was then amplified and labeled using NuGen Ovation kits
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Purified total RNA was amplified and labeled using NuGen Ovation kits (NuGEN Technologies, Inc., San Carlos, CA) and RNA from samples was hybridized to Affymetrix HG-U133 plus 2.0 arrays.
| | Sample_hyb_protocol | Array washing, staining and scanning was performed according to standard Affymetrix protocols .
| | Sample_scan_protocol | Array washing, staining and scanning was performed according to standard Affymetrix protocols .
| | Sample_data_processing | Probe level data was curated by first mapping individual probe sequences to their most current genome sequences. Probes which were non-uniquely mapped to specific genes or contained outdated mappings were discarded, and the remaining probes were summarized into probesets and normalized using Robust Multi-array Average (RMA). Probes expressed at low levels across all samples were subsequently discarded.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sriram,,Sridhar
| | Sample_contact_email | ssridhar21@gmail.com
| | Sample_contact_phone | 6178771485
| | Sample_contact_department | Translational Research Sciences
| | Sample_contact_institute | Hoffmann-La Roche, Inc.
| | Sample_contact_address | 340 Kingsland St.
| | Sample_contact_city | Nutley
| | Sample_contact_state | NJ
| | Sample_contact_zip/postal_code | 07110
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1089nnn/GSM1089622/suppl/GSM1089622_LargeRNA_Donor26_Media_15.CEL.gz
| | Sample_series_id | GSE44723
| | Sample_data_row_count | 21095
| | |
|
GSM1089623 | GPL570 |
|
fibroblast_Rapid_D56_Media_16
|
Rapid progressing fibrosis
|
status: Rapid
age: 68
gender: male
tissue: cultured human fibroblasts
|
|
| Sample_geo_accession | GSM1089623
| | Sample_status | Public on Apr 10 2013
| | Sample_submission_date | Feb 27 2013
| | Sample_last_update_date | Apr 11 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | No additional treatments were applied to the cultured cell lines
| | Sample_growth_protocol_ch1 = Primary cultures of LFs were isolated from the distal parenchyma of patients from unaffected donor controls (lung cancer patients) and patients with IPF as previously described [Hogaboam CM, Carpenter KJ, Evanoff H, Kunkel SL (2005), Pechkovsky DV, Prele CM, Wong J, Hogaboam CM, McAnulty RJ, et al. (2012)]. All fibroblast cell lines were completely de-identified from the patients they were grown from prior to characterization in this study. The IPF lung tissue was obtained and the diagnosis of Usual Interstitial Pneumonia (UIP) / IPF achieved as previously outlined [Pechkovsky DV, Prele CM, Wong J, Hogaboam CM, McAnulty RJ, et al. (2012)]. Normal human lung tissue was obtained from macroscopically tumor-free lung resections of patients with lung cancer. The human lung tissue collection was approved by the ethics committees of all institutions involved. In this study we characterized fibroblasts cell lines originated from 14 donors across 3 phenotypes: non-IPF control (n = 4), stable IPF (n = 6), and rapidly progressing IPF (n | 4) subjects. Cells from these lines were plated and passaged (up to the 11th passage).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated and homogenized in QIAzol reagent. Purified RNA was then amplified and labeled using NuGen Ovation kits
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Purified total RNA was amplified and labeled using NuGen Ovation kits (NuGEN Technologies, Inc., San Carlos, CA) and RNA from samples was hybridized to Affymetrix HG-U133 plus 2.0 arrays.
| | Sample_hyb_protocol | Array washing, staining and scanning was performed according to standard Affymetrix protocols .
| | Sample_scan_protocol | Array washing, staining and scanning was performed according to standard Affymetrix protocols .
| | Sample_data_processing | Probe level data was curated by first mapping individual probe sequences to their most current genome sequences. Probes which were non-uniquely mapped to specific genes or contained outdated mappings were discarded, and the remaining probes were summarized into probesets and normalized using Robust Multi-array Average (RMA). Probes expressed at low levels across all samples were subsequently discarded.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sriram,,Sridhar
| | Sample_contact_email | ssridhar21@gmail.com
| | Sample_contact_phone | 6178771485
| | Sample_contact_department | Translational Research Sciences
| | Sample_contact_institute | Hoffmann-La Roche, Inc.
| | Sample_contact_address | 340 Kingsland St.
| | Sample_contact_city | Nutley
| | Sample_contact_state | NJ
| | Sample_contact_zip/postal_code | 07110
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1089nnn/GSM1089623/suppl/GSM1089623_LargeRNA_Donor56_Media_16.CEL.gz
| | Sample_series_id | GSE44723
| | Sample_data_row_count | 21095
| | |
|
GSM1089624 | GPL570 |
|
fibroblast_Slow_D69_Media_7
|
Slow progressing fibrosis
|
status: Slow
age: 64
gender: female
tissue: cultured human fibroblasts
|
|
| Sample_geo_accession | GSM1089624
| | Sample_status | Public on Apr 10 2013
| | Sample_submission_date | Feb 27 2013
| | Sample_last_update_date | Apr 11 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | No additional treatments were applied to the cultured cell lines
| | Sample_growth_protocol_ch1 = Primary cultures of LFs were isolated from the distal parenchyma of patients from unaffected donor controls (lung cancer patients) and patients with IPF as previously described [Hogaboam CM, Carpenter KJ, Evanoff H, Kunkel SL (2005), Pechkovsky DV, Prele CM, Wong J, Hogaboam CM, McAnulty RJ, et al. (2012)]. All fibroblast cell lines were completely de-identified from the patients they were grown from prior to characterization in this study. The IPF lung tissue was obtained and the diagnosis of Usual Interstitial Pneumonia (UIP) / IPF achieved as previously outlined [Pechkovsky DV, Prele CM, Wong J, Hogaboam CM, McAnulty RJ, et al. (2012)]. Normal human lung tissue was obtained from macroscopically tumor-free lung resections of patients with lung cancer. The human lung tissue collection was approved by the ethics committees of all institutions involved. In this study we characterized fibroblasts cell lines originated from 14 donors across 3 phenotypes: non-IPF control (n = 4), stable IPF (n = 6), and rapidly progressing IPF (n | 4) subjects. Cells from these lines were plated and passaged (up to the 11th passage).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated and homogenized in QIAzol reagent. Purified RNA was then amplified and labeled using NuGen Ovation kits
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Purified total RNA was amplified and labeled using NuGen Ovation kits (NuGEN Technologies, Inc., San Carlos, CA) and RNA from samples was hybridized to Affymetrix HG-U133 plus 2.0 arrays.
| | Sample_hyb_protocol | Array washing, staining and scanning was performed according to standard Affymetrix protocols .
| | Sample_scan_protocol | Array washing, staining and scanning was performed according to standard Affymetrix protocols .
| | Sample_data_processing | Probe level data was curated by first mapping individual probe sequences to their most current genome sequences. Probes which were non-uniquely mapped to specific genes or contained outdated mappings were discarded, and the remaining probes were summarized into probesets and normalized using Robust Multi-array Average (RMA). Probes expressed at low levels across all samples were subsequently discarded.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sriram,,Sridhar
| | Sample_contact_email | ssridhar21@gmail.com
| | Sample_contact_phone | 6178771485
| | Sample_contact_department | Translational Research Sciences
| | Sample_contact_institute | Hoffmann-La Roche, Inc.
| | Sample_contact_address | 340 Kingsland St.
| | Sample_contact_city | Nutley
| | Sample_contact_state | NJ
| | Sample_contact_zip/postal_code | 07110
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1089nnn/GSM1089624/suppl/GSM1089624_LargeRNA_Donor69_Media_7.CEL.gz
| | Sample_series_id | GSE44723
| | Sample_data_row_count | 21095
| | |
|
GSM1089625 | GPL570 |
|
fibroblast_Slow_D72_Media_8
|
Slow progressing fibrosis
|
status: Slow
age: 68
gender: female
tissue: cultured human fibroblasts
|
|
| Sample_geo_accession | GSM1089625
| | Sample_status | Public on Apr 10 2013
| | Sample_submission_date | Feb 27 2013
| | Sample_last_update_date | Apr 11 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | No additional treatments were applied to the cultured cell lines
| | Sample_growth_protocol_ch1 = Primary cultures of LFs were isolated from the distal parenchyma of patients from unaffected donor controls (lung cancer patients) and patients with IPF as previously described [Hogaboam CM, Carpenter KJ, Evanoff H, Kunkel SL (2005), Pechkovsky DV, Prele CM, Wong J, Hogaboam CM, McAnulty RJ, et al. (2012)]. All fibroblast cell lines were completely de-identified from the patients they were grown from prior to characterization in this study. The IPF lung tissue was obtained and the diagnosis of Usual Interstitial Pneumonia (UIP) / IPF achieved as previously outlined [Pechkovsky DV, Prele CM, Wong J, Hogaboam CM, McAnulty RJ, et al. (2012)]. Normal human lung tissue was obtained from macroscopically tumor-free lung resections of patients with lung cancer. The human lung tissue collection was approved by the ethics committees of all institutions involved. In this study we characterized fibroblasts cell lines originated from 14 donors across 3 phenotypes: non-IPF control (n = 4), stable IPF (n = 6), and rapidly progressing IPF (n | 4) subjects. Cells from these lines were plated and passaged (up to the 11th passage).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated and homogenized in QIAzol reagent. Purified RNA was then amplified and labeled using NuGen Ovation kits
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Purified total RNA was amplified and labeled using NuGen Ovation kits (NuGEN Technologies, Inc., San Carlos, CA) and RNA from samples was hybridized to Affymetrix HG-U133 plus 2.0 arrays.
| | Sample_hyb_protocol | Array washing, staining and scanning was performed according to standard Affymetrix protocols .
| | Sample_scan_protocol | Array washing, staining and scanning was performed according to standard Affymetrix protocols .
| | Sample_data_processing | Probe level data was curated by first mapping individual probe sequences to their most current genome sequences. Probes which were non-uniquely mapped to specific genes or contained outdated mappings were discarded, and the remaining probes were summarized into probesets and normalized using Robust Multi-array Average (RMA). Probes expressed at low levels across all samples were subsequently discarded.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sriram,,Sridhar
| | Sample_contact_email | ssridhar21@gmail.com
| | Sample_contact_phone | 6178771485
| | Sample_contact_department | Translational Research Sciences
| | Sample_contact_institute | Hoffmann-La Roche, Inc.
| | Sample_contact_address | 340 Kingsland St.
| | Sample_contact_city | Nutley
| | Sample_contact_state | NJ
| | Sample_contact_zip/postal_code | 07110
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1089nnn/GSM1089625/suppl/GSM1089625_LargeRNA_Donor72_Media_8.CEL.gz
| | Sample_series_id | GSE44723
| | Sample_data_row_count | 21095
| | |
|
GSM1089626 | GPL570 |
|
fibroblast_Slow_D76_Media_9
|
Slow progressing fibrosis
|
status: Slow
age: 54
gender: female
tissue: cultured human fibroblasts
|
|
| Sample_geo_accession | GSM1089626
| | Sample_status | Public on Apr 10 2013
| | Sample_submission_date | Feb 27 2013
| | Sample_last_update_date | Apr 11 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | No additional treatments were applied to the cultured cell lines
| | Sample_growth_protocol_ch1 = Primary cultures of LFs were isolated from the distal parenchyma of patients from unaffected donor controls (lung cancer patients) and patients with IPF as previously described [Hogaboam CM, Carpenter KJ, Evanoff H, Kunkel SL (2005), Pechkovsky DV, Prele CM, Wong J, Hogaboam CM, McAnulty RJ, et al. (2012)]. All fibroblast cell lines were completely de-identified from the patients they were grown from prior to characterization in this study. The IPF lung tissue was obtained and the diagnosis of Usual Interstitial Pneumonia (UIP) / IPF achieved as previously outlined [Pechkovsky DV, Prele CM, Wong J, Hogaboam CM, McAnulty RJ, et al. (2012)]. Normal human lung tissue was obtained from macroscopically tumor-free lung resections of patients with lung cancer. The human lung tissue collection was approved by the ethics committees of all institutions involved. In this study we characterized fibroblasts cell lines originated from 14 donors across 3 phenotypes: non-IPF control (n = 4), stable IPF (n = 6), and rapidly progressing IPF (n | 4) subjects. Cells from these lines were plated and passaged (up to the 11th passage).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated and homogenized in QIAzol reagent. Purified RNA was then amplified and labeled using NuGen Ovation kits
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Purified total RNA was amplified and labeled using NuGen Ovation kits (NuGEN Technologies, Inc., San Carlos, CA) and RNA from samples was hybridized to Affymetrix HG-U133 plus 2.0 arrays.
| | Sample_hyb_protocol | Array washing, staining and scanning was performed according to standard Affymetrix protocols .
| | Sample_scan_protocol | Array washing, staining and scanning was performed according to standard Affymetrix protocols .
| | Sample_data_processing | Probe level data was curated by first mapping individual probe sequences to their most current genome sequences. Probes which were non-uniquely mapped to specific genes or contained outdated mappings were discarded, and the remaining probes were summarized into probesets and normalized using Robust Multi-array Average (RMA). Probes expressed at low levels across all samples were subsequently discarded.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sriram,,Sridhar
| | Sample_contact_email | ssridhar21@gmail.com
| | Sample_contact_phone | 6178771485
| | Sample_contact_department | Translational Research Sciences
| | Sample_contact_institute | Hoffmann-La Roche, Inc.
| | Sample_contact_address | 340 Kingsland St.
| | Sample_contact_city | Nutley
| | Sample_contact_state | NJ
| | Sample_contact_zip/postal_code | 07110
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1089nnn/GSM1089626/suppl/GSM1089626_LargeRNA_Donor76_Media_9.CEL.gz
| | Sample_series_id | GSE44723
| | Sample_data_row_count | 21095
| | |
|
GSM1089627 | GPL570 |
|
fibroblast_Slow_D98_Media_11
|
Slow progressing fibrosis
|
status: Slow
age: 73
gender: male
tissue: cultured human fibroblasts
|
|
| Sample_geo_accession | GSM1089627
| | Sample_status | Public on Apr 10 2013
| | Sample_submission_date | Feb 27 2013
| | Sample_last_update_date | Apr 11 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | No additional treatments were applied to the cultured cell lines
| | Sample_growth_protocol_ch1 = Primary cultures of LFs were isolated from the distal parenchyma of patients from unaffected donor controls (lung cancer patients) and patients with IPF as previously described [Hogaboam CM, Carpenter KJ, Evanoff H, Kunkel SL (2005), Pechkovsky DV, Prele CM, Wong J, Hogaboam CM, McAnulty RJ, et al. (2012)]. All fibroblast cell lines were completely de-identified from the patients they were grown from prior to characterization in this study. The IPF lung tissue was obtained and the diagnosis of Usual Interstitial Pneumonia (UIP) / IPF achieved as previously outlined [Pechkovsky DV, Prele CM, Wong J, Hogaboam CM, McAnulty RJ, et al. (2012)]. Normal human lung tissue was obtained from macroscopically tumor-free lung resections of patients with lung cancer. The human lung tissue collection was approved by the ethics committees of all institutions involved. In this study we characterized fibroblasts cell lines originated from 14 donors across 3 phenotypes: non-IPF control (n = 4), stable IPF (n = 6), and rapidly progressing IPF (n | 4) subjects. Cells from these lines were plated and passaged (up to the 11th passage).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated and homogenized in QIAzol reagent. Purified RNA was then amplified and labeled using NuGen Ovation kits
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Purified total RNA was amplified and labeled using NuGen Ovation kits (NuGEN Technologies, Inc., San Carlos, CA) and RNA from samples was hybridized to Affymetrix HG-U133 plus 2.0 arrays.
| | Sample_hyb_protocol | Array washing, staining and scanning was performed according to standard Affymetrix protocols .
| | Sample_scan_protocol | Array washing, staining and scanning was performed according to standard Affymetrix protocols .
| | Sample_data_processing | Probe level data was curated by first mapping individual probe sequences to their most current genome sequences. Probes which were non-uniquely mapped to specific genes or contained outdated mappings were discarded, and the remaining probes were summarized into probesets and normalized using Robust Multi-array Average (RMA). Probes expressed at low levels across all samples were subsequently discarded.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sriram,,Sridhar
| | Sample_contact_email | ssridhar21@gmail.com
| | Sample_contact_phone | 6178771485
| | Sample_contact_department | Translational Research Sciences
| | Sample_contact_institute | Hoffmann-La Roche, Inc.
| | Sample_contact_address | 340 Kingsland St.
| | Sample_contact_city | Nutley
| | Sample_contact_state | NJ
| | Sample_contact_zip/postal_code | 07110
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1089nnn/GSM1089627/suppl/GSM1089627_LargeRNA_Donor98_Media_11.CEL.gz
| | Sample_series_id | GSE44723
| | Sample_data_row_count | 21095
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