description:
EQUIVALENCE STUDY::Specimen-0222T;RNALater    ;'Rep.1 (S0867F0001.1)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.


status: Public on Nov 06 2014

type: RNA

city: Pittsburgh

first: Victoria

last: Plamadeala

state: Pennsylvania

address: 2516 Jane St

country: USA

institute: Precision Therapeutics

description:
ACCURACY STUDY::Specimen-S0867F0099.2.Lab 1 (S0867F0099.2.Lab 1)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.

hyb_protocol: Fragmented and labelled cDNA was hybridized to HG-U133 Plus 2.0 microarray (Affymetrix) at 45C for 18 hours at a rotation speed of 60rpm. Arrays were washed and stained using the Affymetrix GeneChip Hybridization, Wash & Stain kit in the Affymetrix FS450Dx2 Fluidics Station.

scan_protocol: Arrays were scanned on the GeneChip System 3000Dx v.2 (Affymetrix) using the HG-U133+2.0 protocol.

data_processing: RefRMA

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Lung

label_protocol: Extracted total RNA was amplified using the Ovation Pico WTA System V2 (NuGEN Technologies, Inc.) and then fragmented and labelled with the Encore Biotin Module (NuGEN Technologies, Inc.).

growth_protocol: Immediately upon surgical extraction, specimens were either flash frozen and stored at -80C or placed in RNAL. Specimens were not subjected to any type of growth environment between surgical extraction and total RNA extraction.

extract_protocol: Total RNA was extracted from each specimen via a phenol-chloroform protocol.

treatment_protocol: Specimens were treated in 2 different ways to ensure stabilization of genomic material, notably total RNA.  Specimens were either flash frozen and then stored at -80C or placed immediately in RNAL.

tag: study

value: ACCURACY STUDY

tag: tissue

value: non-small-cell lung carcinoma

tag: specimen

tag: lab


description:
ACCURACY STUDY::Specimen-S0867F0100.1.Lab 1 (S0867F0100.1.Lab 1)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.


description:
ACCURACY STUDY::Specimen-S0867F0099.1.Lab 2 (S0867F0099.1.Lab 2)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.


description:
ACCURACY STUDY::Specimen-S0867F0099.2.Lab 2 (S0867F0099.2.Lab 2)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.


description:
ACCURACY STUDY::Specimen-S0867F0099.1.Lab 1 (S0867F0099.1.Lab 1)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.


description:
ACCURACY STUDY::Specimen-S0867F0089.1.Lab 2 (S0867F0089.1.Lab 2)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.


description:
ACCURACY STUDY::Specimen-S0867F0095.2.Lab 2 (S0867F0095.2.Lab 2)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.


description:
ACCURACY STUDY::Specimen-S0867F0089.2.Lab 2 (S0867F0089.2.Lab 2)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.


description:
ACCURACY STUDY::Specimen-S0867F0100.1.Lab 2 (S0867F0100.1.Lab 2)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.


description:
ACCURACY STUDY::Specimen-S0867F0095.1.Lab 2 (S0867F0095.1.Lab 2)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.


description:
ACCURACY STUDY::Specimen-S0867F0087.2.Lab 2 (S0867F0087.2.Lab 2)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.


description:
ACCURACY STUDY::Specimen-S0867F0086.1.Lab 2 (S0867F0086.1.Lab 2)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.


description:
ACCURACY STUDY::Specimen-S0867F0087.1.Lab 2 (S0867F0087.1.Lab 2)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.


description:
ACCURACY STUDY::Specimen-S0867F0087.1.Lab 1 (S0867F0087.1.Lab 1)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.


description:
ACCURACY STUDY::Specimen-S0867F0086.2.Lab 2 (S0867F0086.2.Lab 2)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.


description:
ACCURACY STUDY::Specimen-S0867F0087.2.Lab 1 (S0867F0087.2.Lab 1)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.


description:
ACCURACY STUDY::Specimen-S0867F0084.2.Lab 2 (S0867F0084.2.Lab 2)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.


description:
ACCURACY STUDY::Specimen-S0867F0086.2.Lab 1 (S0867F0086.2.Lab 1)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.


description:
ACCURACY STUDY::Specimen-S0867F0086.1.Lab 1 (S0867F0086.1.Lab 1)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.


description:
ACCURACY STUDY::Specimen-S0867F0089.2.Lab 1 (S0867F0089.2.Lab 1)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.


description:
ACCURACY STUDY::Specimen-S0867F0084.2.Lab 1 (S0867F0084.2.Lab 1)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.


description:
ACCURACY STUDY::Specimen-S0867F0095.2.Lab 1 (S0867F0095.2.Lab 1)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.


title: adult progenitor of oligodendrocytes from control brains_rep3

city: New York

first: Sarah

last: Moyon

state: NY

address: 85 St Nicholas Terrace

department: Neuroscience

institute: CUNY ASRC

hyb_protocol: Five hundred nanogams of each Cy3-cRNA were hybridized overnight at 65°C on Whole Mouse Genome Microarray 4x44K v2 (Agilent Technologies) according to the manufacturer’s instructions.

scan_protocol: Microarrays data were acquired on an InnoScan 900 (Innopsys, France) with a resolution of 5 µm

data_processing:
We scanned the chips using Nimbile Gem MS 200 (Roche).
Raw data were obtained with Mapix 5.0.0 software (Innopsys, France). For each sample, raw data consisted of the Median Feature Intensity – Median Background Intensity (F-B) at wavelength 532nm.
We then used R to normalize our data.

organism: Mus musculus

label_protocol: Ten nanograms of each RNA were amplified by IVT and labeled with Cy3 using the Low Imput Quick Amp labeling kit (Agilent Technologies) according to the manufacturer’s instructions.

extract_protocol: Total RNAs were obtained from FAC-sorted neonatal or 2-month-old progenitors of oligodendrocytes or oligodendrocytes, isolated from mice treated or not with cuprizone for 5 weeks. We used Nucleospin RNA XS kit (Macherey Nagel, France) in accordance with the manufacturer’s protocol. The quality and quantity of each RNA preparation was assessed on the Agilent 2100 Bioanalyzer with RNA 6000 PicoChips (Agilent Technologies).

tag: strain

tag: cell type

value: Primary FAC-sorted adult OPCs

tag: treatment

value: Control


description:
ACCURACY STUDY::Specimen-S0867F0095.1.Lab 1 (S0867F0095.1.Lab 1)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.


description:
ACCURACY STUDY::Specimen-S0867F0084.1.Lab 2 (S0867F0084.1.Lab 2)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.


description:
ACCURACY STUDY::Specimen-S0867F0084.1.Lab 1 (S0867F0084.1.Lab 1)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.


description:
ACCURACY STUDY::Specimen-S0867F0089.1.Lab 1 (S0867F0089.1.Lab 1)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.


title: adult progenitor of oligodendrocytes from control brains_rep2


description:
ACCURACY STUDY::Specimen-S0867F0036.2.Lab 2 (S0867F0036.2.Lab 2)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.


description:
ACCURACY STUDY::Specimen-S0867F0036.2.Lab 1 (S0867F0036.2.Lab 1)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.


title: adult progenitor of oligodendrocytes from cuprizone-treated brains_rep4

value: Cuprizone-treated


title: adult progenitor of oligodendrocytes from cuprizone-treated brains_rep3


description:
ACCURACY STUDY::Specimen-S0867F0028.2.Lab 2 (S0867F0028.2.Lab 2)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.


description:
ACCURACY STUDY::Specimen-S0867F0028.2.Lab 1 (S0867F0028.2.Lab 1)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.


title: adult oligodendrocytes_rep4

source_name: adult oligodendrocytes

value: Primary FAC-sorted adult OLs


title: adult progenitor of oligodendrocytes from control brains_rep1


title: adult oligodendrocytes_rep3


title: adult oligodendrocytes_rep1


title: adult progenitor of oligodendrocytes from cuprizone-treated brains_rep2


description:
ACCURACY STUDY::Specimen-S0867F0028.1.Lab 1 (S0867F0028.1.Lab 1)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.


description:
ACCURACY STUDY::Specimen-S0867F0036.1.Lab 2 (S0867F0036.1.Lab 2)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.


description:
ACCURACY STUDY::Specimen-S0867F0028.1.Lab 2 (S0867F0028.1.Lab 2)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.


title: adult progenitor of oligodendrocytes from cuprizone-treated brains_rep1


title: adult oligodendrocytes_rep2


title: neonatal progenitor of oligodendrocytes_rep3

source_name: neonatal progenitor of oligodendrocytes

value: Primary FAC-sorted neonatal OPCs


description:
ACCURACY STUDY::Specimen-S0867F0023.2.Lab 2 (S0867F0023.2.Lab 2)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.


title: neonatal progenitor of oligodendrocytes_rep2


description:
ACCURACY STUDY::Specimen-S0867F0023.2.Lab 1 (S0867F0023.2.Lab 1)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.


description:
ACCURACY STUDY::Specimen-S0867F0023.1.Lab 2 (S0867F0023.1.Lab 2)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.


title: neonatal progenitor of oligodendrocytes_rep1


description:
ACCURACY STUDY::Specimen-S0867F0019.2.Lab 2 (S0867F0019.2.Lab 2)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.


description:
ACCURACY STUDY::Specimen-S0867F0036.1.Lab 1 (S0867F0036.1.Lab 1)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.


title: adult progenitor of oligodendrocytes_rep4

source_name: adult progenitor of oligodendrocytes


title: adult progenitor of oligodendrocytes_rep2


description:
ACCURACY STUDY::Specimen-S0867F0023.1.Lab 1 (S0867F0023.1.Lab 1)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.


title: adult progenitor of oligodendrocytes_rep3


description:
ACCURACY STUDY::Specimen-S0867F0019.1.Lab 2 (S0867F0019.1.Lab 2)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.


description:
ACCURACY STUDY::Specimen-S0867F0019.2.Lab 1 (S0867F0019.2.Lab 1)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.


description:
ACCURACY STUDY::Specimen-S0867F0013.2.Lab 2 (S0867F0013.2.Lab 2)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.


description:
ACCURACY STUDY::Specimen-S0867F0019.1.Lab 1 (S0867F0019.1.Lab 1)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.


title: RNA_24hours_subjectV

city: Cambridge

first: Emma

middle: Elisabeth

last: Davenport

state: Cambridgeshire

address: Hinxton

country: United Kingdom

institute: Wellcome Sanger Institute

hyb_protocol: The amplified biotin-labeled cRNA were used for hybridisation with the Illumina HumanHT-12 V4.0 Expression Beadchip.

scan_protocol: The hybridised Illumina arrays were scanned using Illumina iScan scanner.

data_processing: Background signals were subtracted. Two samples were identified as outliers and removed (F_t12 and U_t24).  11,158 low expression probes (detection value < 0.95) were removed. The raw data were transformed and normalised using the Variance Stabilization and Normalization method in R.

label: Biotin

source_name: Peripheral blood RNA, 24 hours post influenza challenge

label_protocol: Biotin-labeled cRNA were generated using the Illumina TotalPrep-96 Amplification Kit.

extract_protocol: Total RNA was extracted from whole blood using the PAXgene Blood RNA Kit. Globin depletion was carried out using the GLOBINclear Human kit.

tag: timepoint

value: 24 hours post-challenge

tag: vaccination status

tag: symptom severity

value: Mild

tag: seroconversion

value: Positive

tag: viral shedding

value: Negative


title: RNA_0hours_subjectU

source_name: Peripheral blood RNA, pre influenza challenge

value: Pre-challenge


title: RNA_12hours_subjectV

source_name: Peripheral blood RNA, 12 hours post influenza challenge

value: 12 hours post-challenge


title: RNA_24hours_subjectU


title: RNA_48hours_subjectV

source_name: Peripheral blood RNA, 48 hours post influenza challenge

value: 48 hours post-challenge


description:
ACCURACY STUDY::Specimen-S0867F0013.2.Lab 1 (S0867F0013.2.Lab 1)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.


title: RNA_12hours_subjectU


title: RNA_48hours_subjectU


description:
ACCURACY STUDY::Specimen-S0867F0007.2.Lab 2 (S0867F0007.2.Lab 2)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.


title: RNA_0hours_subjectV


description:
ACCURACY STUDY::Specimen-S0867F0013.1.Lab 2 (S0867F0013.1.Lab 2)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.


description:
ACCURACY STUDY::Specimen-S0867F0007.2.Lab 1 (S0867F0007.2.Lab 1)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.


title: RNA_0hours_subjectT

value: Moderate/severe


title: RNA_48hours_subjectT


description:
ACCURACY STUDY::Specimen-S0867F0013.1.Lab 1 (S0867F0013.1.Lab 1)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.


title: RNA_24hours_subjectT


description:
ACCURACY STUDY::Specimen-S0867F0007.1.Lab 2 (S0867F0007.1.Lab 2)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.


title: adult progenitor of oligodendrocytes_rep1


title: RNA_24hours_subjectS


title: RNA_48hours_subjectS


title: RNA_12hours_subjectT


title: RNA_12hours_subjectS


title: RNA_0hours_subjectR


description:
ACCURACY STUDY::Specimen-S0867F0005.2.Lab 2 (S0867F0005.2.Lab 2)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.


title: RNA_0hours_subjectS


title: RNA_48hours_subjectR


title: RNA_48hours_subjectQ


title: RNA_12hours_subjectQ


description:
ACCURACY STUDY::Specimen-S0867F0005.2.Lab 1 (S0867F0005.2.Lab 1)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.


title: RNA_24hours_subjectQ


description:
ACCURACY STUDY::Specimen-S0867F0005.1.Lab 1 (S0867F0005.1.Lab 1)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.


description:
ACCURACY STUDY::Specimen-S0867F0100.2.Lab 2 (S0867F0100.2.Lab 2)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.


title: RNA_48hours_subjectP


description:
ACCURACY STUDY::Specimen-S0867F0004.2.Lab 2 (S0867F0004.2.Lab 2)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.


title: IκBα-deficient animal, biological repeat 3

city: Houston

first: Hui

last: Zheng

state: TEXAS

address: one baylor plaza

department: Huffington Center on Aging

institute: Baylor College of Medicine

hyb_protocol: Procedures were performed following the protocol of the microarray Genomic and RNA Profiling Core in Baylor College of Medicine

data_processing: Raw data were analyzed by Bio-conductor, RMA method was used for normalization

source_name: 2-3 month old animal with brain-specific IκBα deletion ( IκBαfl/-;Nestin-Cre)

growth_protocol: Mice were maintained in the pathogen-free mouse facility until sacrifice.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Mice were anesthetized by isofluorane. Mouse brains were briefly rinsed with PBS after dissection and hippocampi tissues were collected for RNA extraction

value: Hippocampus

tag: age

value: 2-3 months

tag: genotype/variation

value: IκBαfl/-;Nestin-Cre


title: Control animal, biological repeat 3

scan_protocol: Procedures were performed following the protocol of the microarray Genomic and RNA Profiling Core in Baylor College of Medicine

source_name: 2-3 month old littermate control animal (IκBαfl/-)

value: IκBαfl/-


title: RNA_12hours_subjectP


description:
ACCURACY STUDY::Specimen-S0867F0004.1.Lab 2 (S0867F0004.1.Lab 2)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.

value: ACCURACY STUDY

value: non-small-cell lung carcinoma


title: RNA_0hours_subjectQ

value: Control


title: Control animal, biological repeat 1

label_protocol: Procedures were performed following the protocol of the microarray Genomic and RNA Profiling Core in Baylor College of Medicine


description:
ACCURACY STUDY::Specimen-S0867F0007.1.Lab 1 (S0867F0007.1.Lab 1)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.


title: IκBα-deficient animal, biological repeat 1


title: RNA_24hours_subjectP


title: RNA_0hours_subjectP


title: RNA_24hours_subjectO


description:
ACCURACY STUDY::Specimen-S0867F0004.1.Lab 1 (S0867F0004.1.Lab 1)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.


description:
ACCURACY STUDY::Specimen-S0867F0005.1.Lab 2 (S0867F0005.1.Lab 2)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.


description:
ACCURACY STUDY::Specimen-S0867F0004.2.Lab 1 (S0867F0004.2.Lab 1)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.


title: RNA_12hours_subjectO


title: Control animal, biological repeat 2


title: IκBα-deficient animal, biological repeat 2


title: RNA_24hours_subjectR


title: Bonemarrow_KO_Dusp5_rep5

city: South San Francisco

first: Derek

middle: A

last: Holmes

state: CA

address: 1 DNA Way

institute: Genentech Inc

description: GeneExpressionData_Bonemarrow_KO_Dusp5_rep5

hyb_protocol: 12.5 micrograms of cRNA was fragmented and hybridized to Mouse Genome 430 2.0 arrays at 45°C for 19 hours in a rotisserie oven set at 60 rpm.

scan_protocol: Arrays were washed and stained using Affymrtrix HWS kit using their Fluidics station and then scanned on GeneChip scanner 3000.

data_processing: Data analysis was performed using the Affymetrix GeneChip operating system and analysis software.

source_name: Bone marrow derived eosinophil

label_protocol: Preparation of cRNA was done using Affymetrix 3'IVT Express kit and protocol provided by Affymetrix. Briefly, 0.5 ug of total RNA was converted into double-stranded cDNA and used to generate biotin labeled cRNA which was then purified.

growth_protocol: Bone marrow derived eosinophils from WT and KO mice.

extract_protocol: Treated cells were washed with ice cold PBS and cell pellets were directly lysed in RLT buffer (Qiagen) followed by immediate RNA isolation (RNEasy plus mini kit with genomic DNA eliminator columns).

treatment_protocol: Day 12 bone marrow derived eosinophils from WT and KO were left untreated (media only) or IL-33 (25ng/ml) stimulated for 4 hours.

value: bone marrow

value: eosinophils

tag: genotype

value: KO (Dusp5-/-)


description:
ACCURACY STUDY::Specimen-S0867F0002.2.Lab 2 (S0867F0002.2.Lab 2)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.


title: RNA_48hours_subjectN


title: Bonemarrow_KO_Dusp5_rep3

description: GeneExpressionData_Bonemarrow_KO_Dusp5_rep3


title: RNA_12hours_subjectN


description:
ACCURACY STUDY::Specimen-S0867F0002.1.Lab 2 (S0867F0002.1.Lab 2)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.


description:
ACCURACY STUDY::Specimen-S0867F0002.2.Lab 1 (S0867F0002.2.Lab 1)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.


description:
ACCURACY STUDY::Specimen-S0867F0002.1.Lab 1 (S0867F0002.1.Lab 1)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.


title: RNA_48hours_subjectO


title: Bonemarrow_KO_Dusp5_rep2

description: GeneExpressionData_Bonemarrow_KO_Dusp5_rep2


title: Bonemarrow_WT_Dusp5_rep5

description: GeneExpressionData_Bonemarrow_WT_Dusp5_rep5

value: WT (Dusp5+/+)


title: RNA_0hours_subjectO

value: Positive


title: siCtrl rep2

city: Bridgewater

first: Wencheng

last: Li

state: NJ - New Jersey

institute: PTC Therapeutics

hyb_protocol: RNA was hybridized to GeneChip Exon 1.0 ST arrays (Affymetrix) according to standard protocols.

scan_protocol: Standard Affymetrix protocol

data_processing:
Raw data from the Affymetrix GeneChip Human Exon 1.0 ST array were normalized by the RMA method in the Affymetrix Power Tools (APT) program, and probe sets with detection above background (DABG) P-value < 0.05 in at least one sample group were used for further analysis. To eliminate the potential effect of APA in 3′ UTRs on expression analysis of a gene, we used only probe sets mapped to the coding sequence (CDS) to represent the expression level of a gene.
HuEx-1_0-st-v2.r2.pgf

source_name: MCF7 cells

label_protocol: The GeneChip wild-type terminal labeling and control kit combined with the Ambion wild-type expression kit were then used.

growth_protocol: MCF-7 cells were cultured in DMEM with 10% fetal bovine serum.

extract_protocol: RNA was purified using the RNeasy kit (Qiagen) followed by on-column DNase treatment (Qiagen).

treatment_protocol: siRNA (50 nM) against RBBP6 (CGAAAGAAGAAUAUACUGA) or nontargeting control was transfected with Lipofectamine RNAimax (Invitrogen), and NEs were made 72 h post-transfection (as described in Kleiman and Manley 2001).

tag: cell line

value: MCF7 breast cancer cell line

value: siRNA control


title: RNA_48hours_subjectM

value: Mild

value: Negative


title: RNA_24hours_subjectN

value: 24 hours post-challenge

value: Moderate/severe


description:
ACCURACY STUDY::Specimen-S0867F0001.2.Lab 1 (S0867F0001.2.Lab 1)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.


title: Bonemarrow_KO_Dusp5_rep1

description: GeneExpressionData_Bonemarrow_KO_Dusp5_rep1


title: RNA_0hours_subjectN

value: Pre-challenge


description:
ACCURACY STUDY::Specimen-S0867F0001.1.Lab 2 (S0867F0001.1.Lab 2)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.


title: Bonemarrow_WT_Dusp5_rep4

description: GeneExpressionData_Bonemarrow_WT_Dusp5_rep4


title: RNA_24hours_subjectM


description:
ACCURACY STUDY::Specimen-S0867F0001.2.Lab 2 (S0867F0001.2.Lab 2)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.


title: siRBBP6 rep1

value: knockdown RBBP6


title: siRBBP6 rep2


title: Bonemarrow_WT_Dusp5_rep3

description: GeneExpressionData_Bonemarrow_WT_Dusp5_rep3


title: siCtrl rep1


title: RNA_12hours_subjectR

value: 12 hours post-challenge


title: RNA_12hours_subjectL


title: Bonemarrow_KO_Untreated_rep5

description: GeneExpressionData_Bonemarrow_KO_Untreated_rep5

value: Untreated


title: Bonemarrow_KO_Untreated_rep4

description: GeneExpressionData_Bonemarrow_KO_Untreated_rep4


title: Bonemarrow_WT_Dusp5_rep2

description: GeneExpressionData_Bonemarrow_WT_Dusp5_rep2


title: Bonemarrow_WT_Dusp5_rep1

description: GeneExpressionData_Bonemarrow_WT_Dusp5_rep1


title: RNA_24hours_subjectL


description:
SENSITIVITY STUDY::Concentration-14.5 ng/ul;'Rep.E (M34F003E)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.

value: SENSITIVITY STUDY

value: non-small-cell lung carcinoma

tag: agent

value: total extracted RNA concentration-14.5 ng/ul


title: RNA_0hours_subjectM

value: Control


title: RNA_48hours_subjectL

value: 48 hours post-challenge


title: B220-ES

type: genomic

city: Jerusalem

first: Ido

last: Sagi

address: Givat Ram

department: Genetics

country: Israel

institute: The Hebrew University of Jerusalem

hyb_protocol: Standard Illumina protocol

scan_protocol: HumanMethylation450 BeadChips were scanned with Illumina's iScan System

data_processing: IDAT files were processed and normalized by subset-quantile within array normalization (SWAN) and adjusted for batch effects using the R package ChAMP (version 1.2.7)

label: Cy5 and Cy3

molecule: genomic DNA

source_name: Embryonic stem cell line

label_protocol: Standard Illumina protocol

extract_protocol: Genomic DNA was isolated (High Pure PCR Template Preparation Kit, Roche) and bisulfite converted (EZDNA Methylation Kit, Zymo Research) according to the manufacturers' protocol

value: Embryonic stem cell line

value: Undifferentiated embryonic stem cells


description:
ACCURACY STUDY::Specimen-S0867F0001.1.Lab 1 (S0867F0001.1.Lab 1)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.

tag: study

value: ACCURACY STUDY


title: B312-ES


description:
SENSITIVITY STUDY::Concentration-14.5 ng/ul;'Rep.C (M34F003C)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.

tag: tissue


title: Bonemarrow_KO_Dusp5_rep4

description: GeneExpressionData_Bonemarrow_KO_Dusp5_rep4

value: bone marrow

value: eosinophils

value: KO (Dusp5-/-)


description:
SENSITIVITY STUDY::Concentration-14.5 ng/ul;'Rep.A (M34F003A)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.


description:
SENSITIVITY STUDY::Concentration-14.5 ng/ul;'Rep.B (M34F003B)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.


title: RNA_0hours_subjectL

value: Positive

value: Negative


description:
SENSITIVITY STUDY::Concentration-12.5 ng/ul;'Rep.E (M34F002E)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.

value: total extracted RNA concentration-12.5 ng/ul


description:
SENSITIVITY STUDY::Concentration-12.5 ng/ul;'Rep.D (M34F002D)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.


title: B209-ES


title: B160-ES


title: RNA_12hours_subjectK

value: Vaccinee


description:
SENSITIVITY STUDY::Concentration-14.5 ng/ul;'Rep.D (M34F003D)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.


title: Bonemarrow_WT_Untreated_rep5

description: GeneExpressionData_Bonemarrow_WT_Untreated_rep5

value: WT (Dusp5+/+)


title: Bonemarrow_KO_Untreated_rep2

description: GeneExpressionData_Bonemarrow_KO_Untreated_rep2

value: Untreated


title: RNA_24hours_subjectK

value: 24 hours post-challenge


title: Bonemarrow_KO_Untreated_rep1

description: GeneExpressionData_Bonemarrow_KO_Untreated_rep1


description:
SENSITIVITY STUDY::Concentration-12.5 ng/ul;'Rep.C (M34F002C)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.

value: SENSITIVITY STUDY

value: non-small-cell lung carcinoma


title: Bonemarrow_WT_Untreated_rep4

description: GeneExpressionData_Bonemarrow_WT_Untreated_rep4


description:
SENSITIVITY STUDY::Concentration-12.5 ng/ul;'Rep.B (M34F002B)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.


title: B105-ES


title: 1018-iPS-F

source_name: RNA-reprogrammed induced pluripotent stem cell line from adult fibroblasts of a type 1 diabetic subject (ID 1018), clone F

value: Undifferentiated induced pluripotent stem cells


title: RNA_12hours_subjectM

value: 12 hours post-challenge

value: Control

value: Mild


title: Bonemarrow_WT_Untreated_rep3

description: GeneExpressionData_Bonemarrow_WT_Untreated_rep3


title: RNA_48hours_subjectK

value: 48 hours post-challenge


title: RNA_0hours_subjectK

value: Pre-challenge


title: RNA_48hours_subjectJ


title: 1018-iPS-E

source_name: RNA-reprogrammed induced pluripotent stem cell line from adult fibroblasts of a type 1 diabetic subject (ID 1018), clone E


description:
SENSITIVITY STUDY::Concentration-12.5 ng/ul;'Rep.A (M34F002A)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.


description:
SENSITIVITY STUDY::Concentration-10.5 ng/ul;'Rep.E (M34F001E)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.

value: total extracted RNA concentration-10.5 ng/ul


title: RNA_12hours_subjectJ


title: Bonemarrow_WT_Untreated_rep2

description: GeneExpressionData_Bonemarrow_WT_Untreated_rep2

value: bone marrow

value: eosinophils


title: 1018-iPS-D

source_name: RNA-reprogrammed induced pluripotent stem cell line from adult fibroblasts of a type 1 diabetic subject (ID 1018), clone D


title: Bonemarrow_WT_Untreated_rep1

description: GeneExpressionData_Bonemarrow_WT_Untreated_rep1


description:
SENSITIVITY STUDY::Concentration-10.5 ng/ul;'Rep.D (M34F001D)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.


title: Bonemarrow_KO_Untreated_rep3

description: GeneExpressionData_Bonemarrow_KO_Untreated_rep3

value: KO (Dusp5-/-)


title: RNA_24hours_subjectI

value: Negative


title: 1018-iPS-A

source_name: RNA-reprogrammed induced pluripotent stem cell line from adult fibroblasts of a type 1 diabetic subject (ID 1018), clone A


description:
SENSITIVITY STUDY::Concentration-10.5 ng/ul;'Rep.C (M34F001C)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.

source_name: Lung


title: RNA_48hours_subjectI

value: Vaccinee


title: Normal_rep5

first: Josh

last: Kaminker

department: Bioinformatics and Computational Biology

institute: Genentech

description:
Sample name: BIO116257
Gene expression of lung, Normal_rep5

hyb_protocol: The method for hybridization of the arrays was provided by Affymetrix. Fifteen micrograms of cRNA was fragmented and hybridized to Mouse430v2 arrays at 45°C for 19 hours in a rotisserie oven set at 60 rpm.

scan_protocol: Arrays were washed and stained in the Affymetrix Fluidics station and scanned on GeneChip scanner 3000.

source_name: Lung, Normal_rep5

label_protocol: The method for prepartation of cRNA was provided by Affymetrix. Briefly, 3 ug of total RNA was converted into double-stranded cDNA using a cDNA synthesis kit SuperScript Choice (Invitrogen) and a T7-(dT) primer (Biosearch Technologies, Inc.). cDNA was purified using Sample Cleanup Module Kit (Affymetrix) and used to generate biotin labeled cRNA using an in vitro transcription kit (Enzo Diagnostics, Inc.,).  The labeled cRNA was purified using Sample Cleanup Module Kit (Affymterix).

growth_protocol: BALB/c mice were injected with nonmetastatic 67NR or metastatic 4T1 cells. Control (naïve) mice received PBS only.

extract_protocol: Total DNA-free RNA was prepared from PBS-perfused lungs with the RNeasy kit (Qiagen) according to the manufacturer’s protocol

treatment_protocol: Six days after tumor cell inoculation (or when tumors reached about 50 mm3), mice were euthanized, and lungs were perfused with PBS to completely remove blood from the lung vasculature. Cleaned lung lobes were immersed in RNAlater (Qiagen) to stabilize RNA.

value: BALB/c

value: PBS control

value: Lung, Normal


title: Normal_rep4

description:
Sample name: BIO116256
Gene expression of lung, Normal_rep4

source_name: Lung, Normal_rep4


title: RNA_24hours_subjectJ

value: 24 hours post-challenge

value: Positive


title: NYSCF1-ES

value: Embryonic stem cell line

value: Undifferentiated embryonic stem cells


title: Normal_rep3

description:
Sample name: BIO116255
Gene expression of lung, Normal_rep3

source_name: Lung, Normal_rep3


title: BJ-iPS-O

source_name: RNA-reprogrammed induced pluripotent stem cell line derived from neonatal BJ fibroblasts, clone O

value: Undifferentiated induced pluripotent stem cells


description:
SENSITIVITY STUDY::Concentration-10.5 ng/ul;'Rep.B (M34F001B)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.

value: SENSITIVITY STUDY

value: non-small-cell lung carcinoma


title: RNA_0hours_subjectJ

source_name: Peripheral blood RNA, pre influenza challenge

value: Pre-challenge


title: RNA_12hours_subjectI

source_name: Peripheral blood RNA, 12 hours post influenza challenge

value: 12 hours post-challenge


title: 1018-iPS-C

source_name: RNA-reprogrammed induced pluripotent stem cell line from adult fibroblasts of a type 1 diabetic subject (ID 1018), clone C


title: B152-ES


description:
SENSITIVITY STUDY::Concentration-10.5 ng/ul;'Rep.A (M34F001A)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.

value: total extracted RNA concentration-10.5 ng/ul


title: Normal_rep2

description:
Sample name: BIO116254
Gene expression of lung, Normal_rep2

source_name: Lung, Normal_rep2


title: BJ-iPS-M

source_name: RNA-reprogrammed induced pluripotent stem cell line derived from neonatal BJ fibroblasts, clone M


title: 1018-NT-ES

source_name: Nuclear-transfer embryonic stem cell line derived from adult fibroblasts of a type 1 diabetic subject (ID 1018)

value: Undifferentiated nuclear-transfer embryonic stem cells


title: 1018-iPS-B

source_name: RNA-reprogrammed induced pluripotent stem cell line from adult fibroblasts of a type 1 diabetic subject (ID 1018), clone B


description:
SPECIFICITY STUDY::Concentration-1X   ;Risk-Low    ;Rep.5 (M36F005.1X.5)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.

value: SPECIFICITY STUDY

value: genomic DNA concentration-1X

tag: risk

value: low


title: BJ-NT-ES-8

source_name: Nuclear-transfer embryonic stem cell line derived from neonatal BJ fibroblasts, clone 8


title: Normal_rep1

description:
Sample name: BIO116253
Gene expression of lung, Normal_rep1

source_name: Lung, Normal_rep1

value: BALB/c


title: 25_pRCC2

city: NICE

first: Thibault

last: FABAS

address: 28 av Valombrose

country: France

institute: CHU Nice

hyb_protocol: DNA was hybridized with the hybridization kit according the Agilent protocol

scan_protocol: We used a Surescan provided by Agilent and controled by SureScan Software

data_processing: the data was processed on Cytogenomics 2.9.1.3 using the Default Analysis Method - CGH v2 proposed by Agilent

source_name: Renal Cells Tumor

label_protocol: DNA was labeled with the sureTag labeling kit accirding the agilent protocol

extract_protocol: DNA was extracted from fresh, frozen or formol fixed-paraffin embedded fragments using Qiamp DNA mini kit.

value: Papillary renal cell carcinoma (pRCC)

tag: rcc type

value: type 2

source_name: commercial reference DNA from cell lines

tag: sample type

value: Male/Female DNA control provided in SureTag Labeling Kit


title: BJ-NT-ES-6

source_name: Nuclear-transfer embryonic stem cell line derived from neonatal BJ fibroblasts, clone 6

tag: cell type


title: Non-metastatic_rep5

description:
Sample name: BIO116262
Gene expression of lung, Non-metastatic_rep5

source_name: Lung, Non-metastatic_rep5

tag: strain

tag: treatment

value: 67NR mouse breast carcinoma cell line injected into fourth mammary fat pad of BALB/c mouse

value: Lung, Non-metastatic


title: RNA_24hours_subjectH

source_name: Peripheral blood RNA, 24 hours post influenza challenge

tag: timepoint

value: 24 hours post-challenge

tag: vaccination status

value: Vaccinee

value: Positive

value: Negative


description:
SPECIFICITY STUDY::Concentration-1X   ;Risk-Low    ;Rep.1 (M36F005.1X.1)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.

source_name: Lung

value: non-small-cell lung carcinoma


title: RNA_12hours_subjectH

value: 12 hours post-challenge

tag: symptom severity

tag: seroconversion


title: Non-metastatic_rep4

description:
Sample name: BIO116260
Gene expression of lung, Non-metastatic_rep4

source_name: Lung, Non-metastatic_rep4


description:
SPECIFICITY STUDY::Concentration-1X   ;Risk-Low    ;Rep.3 (M36F005.1X.3)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.


title: Non-metastatic_rep2

description:
Sample name: BIO116261
Gene expression of lung, Non-metastatic_rep2

source_name: Lung, Non-metastatic_rep2


title: RNA_0hours_subjectI

source_name: Peripheral blood RNA, pre influenza challenge

value: Pre-challenge

tag: viral shedding


title: BJ-NT-ES-5

source_name: Nuclear-transfer embryonic stem cell line derived from neonatal BJ fibroblasts, clone 5

value: Undifferentiated nuclear-transfer embryonic stem cells


title: RNA_48hours_subjectH

source_name: Peripheral blood RNA, 48 hours post influenza challenge

value: 48 hours post-challenge


title: RNA_0hours_subjectH


description:
SPECIFICITY STUDY::Concentration-1X   ;Risk-Low    ;Rep.2 (M36F005.1X.2)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.

value: SPECIFICITY STUDY

value: genomic DNA concentration-1X


description:
SPECIFICITY STUDY::Concentration-1X   ;Risk-Low    ;Rep.4 (M36F005.1X.4)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.

value: low


title: 18_pRCC2

value: Papillary renal cell carcinoma (pRCC)


title: Non-metastatic_rep3

description:
Sample name: BIO116258
Gene expression of lung, Non-metastatic_rep3

source_name: Lung, Non-metastatic_rep3

value: BALB/c


title: 33_uRCC

value: unclassified renal cell carcinoma (uRCC)

value: unclassified

value: Male/Female DNA control provided in SureTag Labeling Kit


title: 30_pRCC2

value: type 2


title: 36_uRCC


title: BJ fibroblasts

source_name: BJ fibroblast cell line

value: BJ fibroblast cell line

value: Fibroblasts


title: RNA_48hours_subjectG

value: Vaccinee

value: Mild

value: Positive


title: DNA_38_TFE-RCC

hyb_protocol: DNA was hybridizated with the Perkin Elmer hybridization Kit according its recommendations

scan_protocol: Slide was scaned on an Innopsys 700 scanner

data_processing: Data were analysed with SpectralWare software supplied by Perkin Elmer (unknown default parameters)

label_protocol: DNA was labeled with the Perkin Elmer labeling Kit according its recommendations

extract_protocol: Dna was extcracted from fresh or frozen fragment with the QIAmp DNA Mini Kit

value: TFE translocation renal cell carcinoma

source_name: Promega Human Genommic DNA (G1471/G1521)

value: reference


title: 1018 fibroblasts

source_name: ID 1018 fibroblast cell line

value: ID 1018 fibroblast cell line


description:
SPECIFICITY STUDY::Concentration-1/2X ;Risk-Low    ;Rep.4 (M36F005.0.5X.4)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.

value: SPECIFICITY STUDY

value: non-small-cell lung carcinoma

value: genomic DNA concentration-1/2X


title: DNA_37_TFE-RCC


title: Metastatic_rep1

description:
Sample name: BIO116263
Gene expression of lung, Metastatic_rep1

source_name: Lung, Metastatic_rep1

value: 4T1 mouse breast carcinoma cell line injected into fourth mammary fat pad of BALB/c mouse

value: Lung, Metastatic


title: RNA_12hours_subjectG

source_name: Peripheral blood RNA, 12 hours post influenza challenge

value: 12 hours post-challenge


title: Metastatic_rep2

description:
Sample name: BIO116265
Gene expression of lung, Metastatic_rep2

source_name: Lung, Metastatic_rep2

value: BALB/c


title: 15_pRCC1

source_name: Renal Cells Tumor

value: Papillary renal cell carcinoma (pRCC)

value: type 1

source_name: commercial reference DNA from cell lines

value: Male/Female DNA control provided in SureTag Labeling Kit


title: 13_pRCC1


title: Metastatic_rep3

description:
Sample name: BIO116267
Gene expression of lung, Metastatic_rep3

source_name: Lung, Metastatic_rep3


title: DNA_32_uRCC

value: unclassified renal cell carcinoma (uRCC)

value: unclassified


title: RNA_24hours_subjectG

source_name: Peripheral blood RNA, 24 hours post influenza challenge

value: 24 hours post-challenge

value: Vaccinee

value: Mild


title: 5_pRCC1


description:
SPECIFICITY STUDY::Concentration-1/2X ;Risk-Low    ;Rep.3 (M36F005.0.5X.3)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.

source_name: Lung

value: low


title: DNA_31_pRCC2

value: type 2

value: reference


title: 2_pRCC1


description:
SPECIFICITY STUDY::Concentration-1/2X ;Risk-Low    ;Rep.1 (M36F005.0.5X.1)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.

value: SPECIFICITY STUDY

value: non-small-cell lung carcinoma


title: Non-metastatic_rep1

description:
Sample name: BIO116259
Gene expression of lung, Non-metastatic_rep1

source_name: Lung, Non-metastatic_rep1

value: 67NR mouse breast carcinoma cell line injected into fourth mammary fat pad of BALB/c mouse

value: Lung, Non-metastatic


title: RNA_0hours_subjectG

value: Pre-challenge

value: Positive


title: RNA_48hours_subjectF

value: 48 hours post-challenge

value: Negative