title: TGFbeta MCT 1

city: Tokyo

first: Ryuji

last: Morizane

address: 35 shinanomachi, shinjukuku

department: Internal Medicine

institute: Keio University School of Medicine

description: SAMPLE 4

hyb_protocol: 18ul of Cy3-labelled miRNA was fragmented following the manufacturers instructions. On completion of the fragmentation reaction, 4.5ul of 10x GE Block and 22.5ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Mouse miRNA Microarray Kit (V2), 8x15K (Based on Sanger miRBase release 12.0)ver2(G4471A) for 20 hours at 55℃,20RPM in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 5 minute at room temperature with GE Wash Buffer 1 (Agilent) and 5 minute at 37℃  GE Wash buffer 2 (Agilent), then dried immediately by air spray

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 8x15k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to XDR Hi 100% and XDR Lo 5% ).

data_processing: The scanned images were analyzed with Feature Extraction software Ver 10.1.1(Agilent).

label_protocol: pCp Cyanine-3 (Cy3) labeled miRNA was prepared from 100ng total RNA using the miRNA Complete Labeling Kit(Agilent) according to the manufacturer's instructions.After labering reaction,completely dray the samples.Use a vacuum concentrator at the midium-high heat setting.. Resuspend the dried sample in 18ul of nuclease-free water.

growth_protocol: A mouse renal tubular cell line, MCT was maintained in Dulbecco's modified Eagles's medium (DMEM) and 10% fetal calf serum (FCS). Prior to TGF-β stimulation, the medium was changed to DMEM supplemented with 0.5% FCS, and TGF-β was subsequently added to the medium at 3 ng/ml on the next day.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.And RNA was prepared using the , miRNAeasy mini (QIAGEN, Valencia, CA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Prior to TGF-β stimulation, the medium was changed to DMEM supplemented with 0.5% FCS, and TGF-β was subsequently added to the medium at 3 ng/ml on the next day. Cells were treated with TGF-βfor three days.

tag: strain background

value: SJL H-2S

value: Mouse renal tubular cells (MCT)

tag: stimulated with

value: GFbeta 3ng/ml for 72 hrs

tag: molecule subtype

value: miRNA


title: control MCT 3

status: Public on Dec 05 2012

type: RNA

country: Japan

description: SAMPLE 3

molecule: total RNA

organism: Mus musculus

tag: cell type


title: TGFbeta MCT 3

description: SAMPLE 6


title: TGFbeta MCT 2

description: SAMPLE 5


title: control MCT 2

description: SAMPLE 2


title: OVX+E2+ICI

city: Quebec

first: Ezequiel

middle: L

last: Calvo

state: Quebec

address: 2705 Boul. Laurier

department: Molecular Endocrinilogy

country: Canada

institute: CRCHUL

description: Raw data file: R136-03FX7A05C1.CEL

hyb_protocol: Fragmented cRNA (15 ug) was incubated with 1x hybridization buffer (0.1 mg/ml herring sperm DNA, 0.5 mg/ml acetylated BSA, 5 nM control oligonucleotide B2) and 1x eukaryotic hybridization control solution (1.5 pM BioB, 5 pM BioC, 25 pm BioD, and 100 pM cre), for 16h at 45°C with constant rotation (60 rpm). Microarrays were processed using an Affymetrix GeneChip Fluidic Station 400 (protocol EukGE-WS2Av4). Staining was performed with streptavidin-conjugated phycoerythrin (SAPE) followed by amplification with a biotinylated anti-streptavidin antibody and by a second round of SAPE solution.

scan_protocol: GeneChips were scanned using an Agilent GeneArray Scanner (Agilent Technologies).

data_processing: RMA

label: biotin

source_name: Mammary gland of OVX mice, treated with estradiol plus fulvestrant

label_protocol: Total mRNA (20 ug) was converted to cDNA by incubation with 400 U SuperScript II reverse transcriptase (Invitrogen) using a T7- oligo-(dt)24 primer [5‑GGCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGG-(dt)24-3_] 1‑first‑strand buffer (50 mM Tris‑HCl pH 8.3, 75 mM KCl, 3 mM MgCl2, 10 mM DTT) and 0.5 mM dNTPs at 42°C for 1h. Second-strand synthesis was performed using 40 U DNA polymerase I (Invitrogen), 10 U Escherichia coli DNA ligase (Invitrogen), 2 U RNase H (Invitrogen), reaction buffer [18.8 mM Tris‑HCl pH 8.3, 90.6 mM KCl, 4.6 mM MgCl2, 3.8 mM DTT, 0.15 mM NAD, 10 mM (NH4)2SO4] and 0.2 mM dNTPs at 16°C for 2 h. cDNAs were blunt-ended with 10 U of T4 DNA polymerase (Invitrogen) incubated 5 min at 16°C. cDNA was extracted with phenol-chloroform using phase lock gels (Brinkman, Mississauga, Ontario, Canada), ethanol precipitated, and resuspended in 10 µl of DEPC-treated H2O. cDNA was in vitro transcribed using a T7 BioArray High Yield RNA Transcript Labeling Kit (Enzo Diagnostics, Farmingdale, NY) to produce biotinylated cRNA. The mixture (20 µl final volume) was incubated at 37°C for 5h, with gentle mixing every 30 min. Labeled cRNA was purified with an RNeasy Mini Kit (Qiagen, Valencia, CA) according to the manufacturer’s protocol. Purified cRNA was fragmented to 30–200 mer using a fragmentation buffer (100 mM potassium acetate, 30 mM magnesium acetate, 40 mM Tris-acetate pH 8.1), for 20 min at 94°C.

growth_protocol: Eleven to twelve week-old female C57BL6 mice obtained from Harlan Sprague Dawley (Indianapolis, IN) were allowed to acclimatate for 1 week after their arrival. Animals weighing between 17 to 23 g (average of 20g) were randomized according to their body weights and were assigned to experimental groups of 8 animals each. Ovariectomy was performed under isoflurane-induced anesthesia 7 days prior to treatment.

extract_protocol: Mammary glands from all mice of the same group were collected, rapidly trimmed, snap-frozen in liquid nitrogen and stored at -80°C until mRNA extraction. Total mRNA was isolated with TRIzol (Invitrogen, Burlington, Ontario) following the manufacturer’s protocol.

treatment_protocol: EM-652.HCl (acolbifene), tamoxifen citrate, raloxifene or ICI 182780 (fulvestrant), were administered to ovariectomized (OVX) mice or to OVX mice simultaneously treated with 17b-estradiol (E2; 0.05 mg/mouse; single sc injection). Mice from the OVX control group received an injection of the vehicle alone. All animals were sacrificed 3h after treatment.

tag: strain

tag: treatment

value: estradiol plus fulvestrant

tag: tissue

value: Mammary gland


title: OVX-rep1

description: Raw data file: R137-03F02D05C2-R1.CEL

source_name: Mammary gland of OVX mice, treated with vehicle

value: vehicle


title: control MCT 1

description: SAMPLE 1


title: ES Activin (+) 2

description: SAMPLE 5

source_name: EB3_differentiated with Activin

growth_protocol: Mouse ES cells were differentiated through 3 days formation of embryoid bodies with Activin 10ng/ml.  After embryoid body formation, embryoid bodies were transfeterd onto cell culture dishes coated with gelatin.  Cells were subsequently cultured with Activin 10ng/ml for additionally 15 days.

treatment_protocol: Mouse ES cells were treated with Activin 10ng/ml for 18 days.

tag: cell line

value: embryonic stem cells


title: ES Activin (+) 1

description: SAMPLE 4


title: Osteosarcoma cell line IOR/SARG [copy number]

status: Public on Dec 06 2012

type: genomic

city: Oslo

first: Leonardo

middle: A.

last: Meza-Zepeda

address: Ullernchausseen 70

department: Dept. of Tumor Biology

country: Norway

institute: The Norwegian Radium Hospital

description: Osteosarcoma cell line IOR/SARG Affymetrix SNP 6

hyb_protocol: Standard Affymetrix hyb protocol

scan_protocol: Standard Affymetrix scan protocol

data_processing: Quality control was performed using the Genotyping Console v3.0.1 software (Affymetrix), applying the contrast quality control (CQC) algorithm with a minimal call rate of > 86 %. DNA copy number analysis was performed using the Nexus software (BioDiscovery, California, USA), with the SNPRank segmentation algorithm using default settings (threshold of 0.6 for high copy gain, 0.2 for gain, -0.2 for loss and -1.0 for homozygous loss).

label: Biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: Osteosarcoma cell line IOR/SARG

label_protocol: Standard Affymetrix label protocol

growth_protocol: The osteosarcoma cells were grown in RPMI1640 (Lonza, Basel, Switzerland) or DMEM (Lonza) supplemented with 10 % foetal calf serum (PAA Laboratories GmbH, Pasching, Austria), GlutaMAX (Invitrogen, California, USA) and penicillin/streptomycin (Lonza), at 37°C with 5 % CO2. All cells were split when reaching 80 % confluency. The osteoblast cells were maintained in medium provided by the manufacturer, split when reaching 80 % confluency, and harvested when enough cells for DNA and RNA isolation were obtained.

extract_protocol: DNA was isolated using the Wizard Genomic DNA Purification Kit (Promega, Madison, USA).

value: IOR/SARG

value: Osteosarcoma

tag: sample origin

value: Primary tumour

tag: gender

value: male

tag: age (yrs)


title: Osteosarcoma cell line OHS [copy number]

description: Osteosarcoma cell line OHS Affymetrix SNP 6

source_name: Osteosarcoma cell line OHS

value: OHS


title: ES Activin (-) 3

description: SAMPLE 3


title: ES Activin (-) 2

description: SAMPLE 2


title: Osteosarcoma cell line MG-63 [copy number]

description: Osteosarcoma cell line MG-63 Affymetrix SNP 6

source_name: Osteosarcoma cell line MG-63

value: Not available

tag: atcc number


title: ES Activin (-) 1

description: SAMPLE 1


title: UUO kindey 3

description: SAMPLE 7

source_name: ureteral obstruction

growth_protocol: Mice, ICR were anesthetized, and their unilateral ureter was ligated. After 7 days, mice were sacrificed, and kidneys were harvested.

treatment_protocol: Unilateral ureter was ligated for 7 days.

value: ICR

value: kidneys with ureteral obstruction


title: Osteosarcoma cell line OSA [copy number]

description: Osteosarcoma cell line OSA Affymetrix SNP 6

source_name: Osteosarcoma cell line OSA

value: OSA


title: UUO kidney 2

description: SAMPLE 6


title: Osteosarcoma cell line IOR/OS10 [copy number]

description: Osteosarcoma cell line IOR/OS10 Affymetrix SNP 6

source_name: Osteosarcoma cell line IOR/OS10

value: female


title: Osteosarcoma cell line MHM [copy number]

description: Osteosarcoma cell line MHM Affymetrix SNP 6

source_name: Osteosarcoma cell line MHM

value: MHM

value: Metastasis


title: Osteosarcoma cell lineI OR/MOS [copy number]

description: Osteosarcoma cell lineI OR/MOS Affymetrix SNP 6

source_name: Osteosarcoma cell lineI OR/MOS

value: IOR/MOS


title: ES Activin (+) 3

description: SAMPLE 6

value: miRNA


title: control kidney 1

description: SAMPLE 1

source_name: control

value: contralateral kidneys without ureteral obstruction


title: CI7d_cellline3_rep2

city: Princeton

first: Eric

middle: Jungwoo

last: Suh

state: NJ

address: 14 Washington Rd

department: Molecular Biology

country: USA

institute: Princeton University

description: Contact inhibited 7d, cell line 3

hyb_protocol: End-labeled samples hybridized and washed on arrays according to manufacturer's protocol.

scan_protocol: Scanned using Agilent G2505B array scanner according to manufacturer's protocol.

data_processing:
Probe intensities were filtered to eliminate any probes that, for any sample, had signals that were flagged as saturated or below background by Feature Extractor. Intensities of probes to identical microRNAs were averaged and then log2 transformed. The log2 transformed signals for each microRNA were then individually normalized and analyzed using multiple linear regression on the experimental design and surrogate variable analysis. Experimental design variables included in the regression were cell line identity, slide on which array was hybridized, cell proliferation state, serum concentration state, and mean sample intensity. Values represented in data matrix are the sum contributions of residual error, cell proliferation state, and serum concentration state, i.e. the biological variables of interest.
log2 transformed sum changes normalized for cell line, overall signal intensity, date of hybridization, and date of sample collection

source_name: Contact inhibited 7d, cell line 3

label_protocol: microRNAs end labled with Cy3-ppCpp using the Agilent labeling kit as described in the manufacturer's protocol

extract_protocol: Total RNA isolated using mirVana total RNA isolation kit and procedure.

value: Male

value: Fibroblast


title: UUO kidney 1

description: SAMPLE 5


title: control kidney 3

description: SAMPLE 3


title: P_cellline3_rep2

description: Proliferating, cell line 3

source_name: Proliferating, cell line 3


title: SS4d_cellline3_rep1

description: Serum starved 4d, cell line 3

source_name: Serum starved 4d, cell line 3


title: Osteosarcoma cell line IOR/OS18 [copy number]

description: Osteosarcoma cell line IOR/OS18 Affymetrix SNP 6

source_name: Osteosarcoma cell line IOR/OS18


title: control kindey 4

description: SAMPLE 4


title: control kidney 2

description: SAMPLE 2


title: Osteosarcoma cell line MNNG/HOS [copy number]

description: Osteosarcoma cell line MNNG/HOS Affymetrix SNP 6

source_name: Osteosarcoma cell line MNNG/HOS

value: MNNG/HOS


title: P_cellline2_rep2

description: Proliferating, cell line 2

source_name: Proliferating, cell line 2


title: SS4d_cellline2_rep2

description: Serum starved 4d, cell line 2

source_name: Serum starved 4d, cell line 2


title: SS4d_cellline2_rep1

description: Serum starved 4d, cell line 2


title: CI7d_cellline3_rep1

description: Contact inhibited 7d, cell line 3


title: CI7d_cellline2_rep1

description: Contact inhibited 7d, cell line 2

source_name: Contact inhibited 7d, cell line 2


title: Osteosarcoma cell line KPD [copy number]

description: Osteosarcoma cell line KPD Affymetrix SNP 6

source_name: Osteosarcoma cell line KPD

value: KPD

value: Osteosarcoma


title: SS4d_cellline3_rep2

description: Serum starved 4d, cell line 3


title: Osteosarcoma cell line HAL [copy number]

description: Osteosarcoma cell line HAL Affymetrix SNP 6

source_name: Osteosarcoma cell line HAL

value: HAL

value: Bone marrow

value: male


title: Osteosarcoma cell line IOR/OS15 [copy number]

description: Osteosarcoma cell line IOR/OS15 Affymetrix SNP 6

source_name: Osteosarcoma cell line IOR/OS15

value: Primary tumour


title: Osteosarcoma cell line IOR/OS9 [copy number]

description: Osteosarcoma cell line IOR/OS9 Affymetrix SNP 6

source_name: Osteosarcoma cell line IOR/OS9


title: CI7d_cellline1_rep1

description: Contact inhibited 7d, cell line 1

source_name: Contact inhibited 7d, cell line 1


title: P_cellline1_rep2

description: Proliferating, cell line 1

source_name: Proliferating, cell line 1


title: CI7d_cellline1_rep2

description: Contact inhibited 7d, cell line 1


title: P_cellline3_rep1

description: Proliferating, cell line 3


title: SS4d_cellline1_rep2

description: Serum starved 4d, cell line 1

source_name: Serum starved 4d, cell line 1


title: SS4d_cellline1_rep1

description: Serum starved 4d, cell line 1


title: Osteosarcoma cell line HOS [copy number]

description: Osteosarcoma cell line HOS Affymetrix SNP 6

source_name: Osteosarcoma cell line HOS

value: HOS

value: Not available


title: P_cellline1_rep1

description: Proliferating, cell line 1


title: CI7d_cellline2_rep2

description: Contact inhibited 7d, cell line 2


title: UUO kindey 4

description: SAMPLE 8

source_name: ureteral obstruction

value: ICR

value: kidneys with ureteral obstruction


title: Steroid-requiring asthma (X37MASTBA.B5)

city: San Francisco

first: Andrea

middle: J

last: Barczak

state: CA

address: 1550 4th St Rock Hall 545

institute: UCSF Sandler Center Functional Genomics Core Facility

description:
Raw data fiile:
253105210008_S01_GE1_107_Sep09_1_4.txt
FEV1 = the volume of air exhaled in the first second of a forced expiratory maneuver
FVC =  the total volume of air exhaled in a forced expiratory maneuver
PC20 =  the provocative concentration of methacholine required to decrease the FEV1 by 20%

hyb_protocol: Cy3-labelled RNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent UCSF custom 8x15K miRNA arrays for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned on the Agilent scanner immediately after washing.

data_processing:
The scanned images were analyzed with Feature Extraction Software 10.6 (Agilent) using default parameters. The data in this study are comprised from 3 different custom designs. The processed data were collapsed to include only probe IDs from one of the designs, and the raw data files have different Agilent design numbers (023723, 025771, 031052). See Platform GPL15016 for a Core Annotation file that shows relationships among the probeIDs across the 3 array designs.
Data filtering was done based on the number of human microRNA probsets common across the three designs used in this study. Non- human and non miRNA probes were excluded from the list.

source_name: human airway epithelial bronchoscopy brushing

label_protocol: Total RNA was labeled with Cy3-CTP using the miRCURY LNA microRNA power labeling kit (Exiqon, Inc, Woburn, MA), according to manufacturers protocol

extract_protocol: Total RNA was purified from airway epithelial brushings using TRIzol reagent (Invitrogen Life Technologies, Carlsbad Ca), and the quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA) and Nanodrop ND-8000 (Nanodrop Technologies, Inc., Wilmington DE).

treatment_protocol: We obtained airway epithelial cells by bronchoscopic brushing from three groups of subjects. The first group consisted of non-asthmatic healthy controls without lung disease. The second group consisted of subjects with asthma who were not judged by their treating physician to require ICS for asthma control. These subjects were studied at baseline and again after eight weeks of treatment with budesonide 200mcg bid. The third group consisted of subjects with asthma who required ICS for asthma control. These subjects underwent bronchoscopy after standardizing their ICS regimen to budesonide 200mcg bid for eight weeks

tag: group

value: MASTC A2

tag: age

value: Female

tag: disease state

value: Steroid-requiring asthma

value: airway epithelial cells

tag: fvc

tag: fvc(%pred)


title: Steroid-requiring asthma (X35MASTBA2.B5)

description:
Raw data fiile:
253105210008_S01_GE1_107_Sep09_1_2.txt
FEV1 = the volume of air exhaled in the first second of a forced expiratory maneuver
FVC =  the total volume of air exhaled in a forced expiratory maneuver
PC20 =  the provocative concentration of methacholine required to decrease the FEV1 by 20%

value: Male


title: Steroid-requiring asthma (X34MASTBA2.B5)

description:
Raw data fiile:
253105210008_S01_GE1_107_Sep09_2_3.txt
FEV1 = the volume of air exhaled in the first second of a forced expiratory maneuver
FVC =  the total volume of air exhaled in a forced expiratory maneuver
PC20 =  the provocative concentration of methacholine required to decrease the FEV1 by 20%


title: Steroid-requiring asthma (X36MASTBA.B5)

description:
Raw data fiile:
253105210008_S01_GE1_107_Sep09_2_1.txt
FEV1 = the volume of air exhaled in the first second of a forced expiratory maneuver
FVC =  the total volume of air exhaled in a forced expiratory maneuver
PC20 =  the provocative concentration of methacholine required to decrease the FEV1 by 20%


title: Steroid-requiring asthma (X36MASTBA2.B5)

description:
Raw data fiile:
253105210008_S01_GE1_107_Sep09_2_4.txt
FEV1 = the volume of air exhaled in the first second of a forced expiratory maneuver
FVC =  the total volume of air exhaled in a forced expiratory maneuver
PC20 =  the provocative concentration of methacholine required to decrease the FEV1 by 20%


title: Steroid-requiring asthma (X23MASTAH.B5)

description:
Raw data fiile:
253105210008_S01_GE1_107_Sep09_1_3.txt
FEV1 = the volume of air exhaled in the first second of a forced expiratory maneuver
FVC =  the total volume of air exhaled in a forced expiratory maneuver
PC20 =  the provocative concentration of methacholine required to decrease the FEV1 by 20%


title: Steroid-naive asthma (X22MASTAH.B5)

description:
Raw data fiile:
253105210008_S01_GE1_107_Sep09_2_2.txt
FEV1 = the volume of air exhaled in the first second of a forced expiratory maneuver
FVC =  the total volume of air exhaled in a forced expiratory maneuver
PC20 =  the provocative concentration of methacholine required to decrease the FEV1 by 20%

value: MASTB A

value: Steroid-naive asthma (baseline)


title: Steroid-requiring asthma (X21MASTAH.B5)

description:
Raw data fiile:
253105210008_S01_GE1_107_Sep09_1_1.txt
FEV1 = the volume of air exhaled in the first second of a forced expiratory maneuver
FVC =  the total volume of air exhaled in a forced expiratory maneuver
PC20 =  the provocative concentration of methacholine required to decrease the FEV1 by 20%


title: Post-steroid asthma (X51MASTCA2.B4)

description:
Raw data fiile:
252577110031_S01_miRNA_105_Jan09_2_2.txt
FEV1 = the volume of air exhaled in the first second of a forced expiratory maneuver
FVC =  the total volume of air exhaled in a forced expiratory maneuver
PC20 =  the provocative concentration of methacholine required to decrease the FEV1 by 20%

value: MASTB A2

value: Post-steroid asthma (ie, Steroid-naive asthma after 8wks treatment)


title: Osteosarcoma cell line 143B [copy number]

description: Osteosarcoma cell line 143B Affymetrix SNP 6

source_name: Osteosarcoma cell line 143B

value: Osteosarcoma

value: female


title: Post-steroid asthma (X34MASTBA.B4)

description:
Raw data fiile:
252577110030_S01_miRNA_105_Jan09_2_3.txt
FEV1 = the volume of air exhaled in the first second of a forced expiratory maneuver
FVC =  the total volume of air exhaled in a forced expiratory maneuver
PC20 =  the provocative concentration of methacholine required to decrease the FEV1 by 20%


title: Post-steroid asthma (X41MASTCA2.B4)

description:
Raw data fiile:
252577110029_S01_miRNA_105_Jan09_2_4.txt
FEV1 = the volume of air exhaled in the first second of a forced expiratory maneuver
FVC =  the total volume of air exhaled in a forced expiratory maneuver
PC20 =  the provocative concentration of methacholine required to decrease the FEV1 by 20%


title: Steroid-requiring asthma (X46MASTCA2.B4)

description:
Raw data fiile:
252577110029_S01_miRNA_105_Jan09_1_3.txt
FEV1 = the volume of air exhaled in the first second of a forced expiratory maneuver
FVC =  the total volume of air exhaled in a forced expiratory maneuver
PC20 =  the provocative concentration of methacholine required to decrease the FEV1 by 20%


title: Osteosarcoma cell line IOR/OS14 [copy number]

description: Osteosarcoma cell line IOR/OS14 Affymetrix SNP 6

source_name: Osteosarcoma cell line IOR/OS14

value: male


title: Steroid-naive asthma (X47MASTCA2.B4)

description:
Raw data fiile:
252577110030_S01_miRNA_105_Jan09_1_1.txt
FEV1 = the volume of air exhaled in the first second of a forced expiratory maneuver
FVC =  the total volume of air exhaled in a forced expiratory maneuver
PC20 =  the provocative concentration of methacholine required to decrease the FEV1 by 20%


title: Steroid-requiring asthma (X35MASTBA.B4)

description:
Raw data fiile:
252577110030_S01_miRNA_105_Jan09_2_1.txt
FEV1 = the volume of air exhaled in the first second of a forced expiratory maneuver
FVC =  the total volume of air exhaled in a forced expiratory maneuver
PC20 =  the provocative concentration of methacholine required to decrease the FEV1 by 20%


title: Steroid-naive asthma (X40MASTCA2.B4)

description:
Raw data fiile:
252577110031_S01_miRNA_105_Jan09_1_3.txt
FEV1 = the volume of air exhaled in the first second of a forced expiratory maneuver
FVC =  the total volume of air exhaled in a forced expiratory maneuver
PC20 =  the provocative concentration of methacholine required to decrease the FEV1 by 20%


title: Steroid-requiring asthma (X32MASTBA.B4)

description:
Raw data fiile:
252577110031_S01_miRNA_105_Jan09_1_4.txt
FEV1 = the volume of air exhaled in the first second of a forced expiratory maneuver
FVC =  the total volume of air exhaled in a forced expiratory maneuver
PC20 =  the provocative concentration of methacholine required to decrease the FEV1 by 20%


title: Post-steroid asthma (X31MASTBA2.B4)

description:
Raw data fiile:
252577110031_S01_miRNA_105_Jan09_1_2.txt
FEV1 = the volume of air exhaled in the first second of a forced expiratory maneuver
FVC =  the total volume of air exhaled in a forced expiratory maneuver
PC20 =  the provocative concentration of methacholine required to decrease the FEV1 by 20%


title: Steroid-naive asthma (X32MASTBA2.B4)

description:
Raw data fiile:
252577110029_S01_miRNA_105_Jan09_2_1.txt
FEV1 = the volume of air exhaled in the first second of a forced expiratory maneuver
FVC =  the total volume of air exhaled in a forced expiratory maneuver
PC20 =  the provocative concentration of methacholine required to decrease the FEV1 by 20%


title: Steroid-naive asthma (X35MASTCA2.B2)

description:
Raw data fiile:
252577110008_SLOT02_S01_miRNA_105_Jan09_2_2.txt
FEV1 = the volume of air exhaled in the first second of a forced expiratory maneuver
FVC =  the total volume of air exhaled in a forced expiratory maneuver
PC20 =  the provocative concentration of methacholine required to decrease the FEV1 by 20%


title: Post-steroid asthma (X36MASTCA2.B2)

description:
Raw data fiile:
252577110008_SLOT02_S01_miRNA_105_Jan09_1_3.txt
FEV1 = the volume of air exhaled in the first second of a forced expiratory maneuver
FVC =  the total volume of air exhaled in a forced expiratory maneuver
PC20 =  the provocative concentration of methacholine required to decrease the FEV1 by 20%


title: Steroid-requiring asthma (X38MASTCA2.B2)

description:
Raw data fiile:
252577110007_SLOT03_S01_miRNA_105_Jan09_1_1.txt
FEV1 = the volume of air exhaled in the first second of a forced expiratory maneuver
FVC =  the total volume of air exhaled in a forced expiratory maneuver
PC20 =  the provocative concentration of methacholine required to decrease the FEV1 by 20%


title: Steroid-naive asthma (X25MASTBA.B4)

description:
Raw data fiile:
252577110030_S01_miRNA_105_Jan09_1_2.txt
FEV1 = the volume of air exhaled in the first second of a forced expiratory maneuver
FVC =  the total volume of air exhaled in a forced expiratory maneuver
PC20 =  the provocative concentration of methacholine required to decrease the FEV1 by 20%


title: Post-steroid asthma (X25MASTBA2.B4)

description:
Raw data fiile:
252577110031_S01_miRNA_105_Jan09_2_3.txt
FEV1 = the volume of air exhaled in the first second of a forced expiratory maneuver
FVC =  the total volume of air exhaled in a forced expiratory maneuver
PC20 =  the provocative concentration of methacholine required to decrease the FEV1 by 20%


title: Steroid-naive asthma (X31MASTBA.B4)

description:
Raw data fiile:
252577110029_S01_miRNA_105_Jan09_1_2.txt
FEV1 = the volume of air exhaled in the first second of a forced expiratory maneuver
FVC =  the total volume of air exhaled in a forced expiratory maneuver
PC20 =  the provocative concentration of methacholine required to decrease the FEV1 by 20%


title: Steroid-requiring asthma (X20MASTAH.B4)

description:
Raw data fiile:
252577110031_S01_miRNA_105_Jan09_2_1.txt
FEV1 = the volume of air exhaled in the first second of a forced expiratory maneuver
FVC =  the total volume of air exhaled in a forced expiratory maneuver
PC20 =  the provocative concentration of methacholine required to decrease the FEV1 by 20%


title: Steroid-naive asthma (X07MASTAH.B4)

description:
Raw data fiile:
252577110030_S01_miRNA_105_Jan09_1_4.txt
FEV1 = the volume of air exhaled in the first second of a forced expiratory maneuver
FVC =  the total volume of air exhaled in a forced expiratory maneuver
PC20 =  the provocative concentration of methacholine required to decrease the FEV1 by 20%


title: Healthy control (X27MASTBA2.B2)

description:
Raw data fiile:
252577110007_SLOT03_S01_miRNA_105_Jan09_2_3.txt
FEV1 = the volume of air exhaled in the first second of a forced expiratory maneuver
FVC =  the total volume of air exhaled in a forced expiratory maneuver
PC20 =  the provocative concentration of methacholine required to decrease the FEV1 by 20%

value: MASTA H

value: Healthy control (non-asthmatic)


title: Healthy control (X33MASTCA2.B2)

description:
Raw data fiile:
252577110008_SLOT02_S01_miRNA_105_Jan09_2_4.txt
FEV1 = the volume of air exhaled in the first second of a forced expiratory maneuver
FVC =  the total volume of air exhaled in a forced expiratory maneuver
PC20 =  the provocative concentration of methacholine required to decrease the FEV1 by 20%


title: Steroid-requiring asthma (X29MASTCA2.B2)

description:
Raw data fiile:
252577110008_SLOT02_S01_miRNA_105_Jan09_1_2.txt
FEV1 = the volume of air exhaled in the first second of a forced expiratory maneuver
FVC =  the total volume of air exhaled in a forced expiratory maneuver
PC20 =  the provocative concentration of methacholine required to decrease the FEV1 by 20%


title: Post-steroid asthma (X19MASTAH.B4)

description:
Raw data fiile:
252577110029_S01_miRNA_105_Jan09_1_1.txt
FEV1 = the volume of air exhaled in the first second of a forced expiratory maneuver
FVC =  the total volume of air exhaled in a forced expiratory maneuver
PC20 =  the provocative concentration of methacholine required to decrease the FEV1 by 20%


title: Post-steroid asthma (X23MASTBA.B2)

description:
Raw data fiile:
252577110006_SLOT04_S01_miRNA_105_Jan09_2_3.txt
FEV1 = the volume of air exhaled in the first second of a forced expiratory maneuver
FVC =  the total volume of air exhaled in a forced expiratory maneuver
PC20 =  the provocative concentration of methacholine required to decrease the FEV1 by 20%


title: Steroid-requiring asthma (X27MASTBA.B2)

description:
Raw data fiile:
252577110007_SLOT03_S01_miRNA_105_Jan09_1_2.txt
FEV1 = the volume of air exhaled in the first second of a forced expiratory maneuver
FVC =  the total volume of air exhaled in a forced expiratory maneuver
PC20 =  the provocative concentration of methacholine required to decrease the FEV1 by 20%


title: Healthy control (X21MASTBA.B2)

description:
Raw data fiile:
252577110008_SLOT02_S01_miRNA_105_Jan09_1_1.txt
FEV1 = the volume of air exhaled in the first second of a forced expiratory maneuver
FVC =  the total volume of air exhaled in a forced expiratory maneuver
PC20 =  the provocative concentration of methacholine required to decrease the FEV1 by 20%


title: Steroid-naive asthma (X21MASTBA2.B2)

description:
Raw data fiile:
252577110008_SLOT02_S01_miRNA_105_Jan09_2_3.txt
FEV1 = the volume of air exhaled in the first second of a forced expiratory maneuver
FVC =  the total volume of air exhaled in a forced expiratory maneuver
PC20 =  the provocative concentration of methacholine required to decrease the FEV1 by 20%


title: Steroid-naive asthma (X20MASTBA.B2)

description:
Raw data fiile:
252577110006_SLOT04_S01_miRNA_105_Jan09_1_3.txt
FEV1 = the volume of air exhaled in the first second of a forced expiratory maneuver
FVC =  the total volume of air exhaled in a forced expiratory maneuver
PC20 =  the provocative concentration of methacholine required to decrease the FEV1 by 20%


title: Healthy control (X19MASTBA2.B2)

description:
Raw data fiile:
252577110007_SLOT03_S01_miRNA_105_Jan09_1_3.txt
FEV1 = the volume of air exhaled in the first second of a forced expiratory maneuver
FVC =  the total volume of air exhaled in a forced expiratory maneuver
PC20 =  the provocative concentration of methacholine required to decrease the FEV1 by 20%


title: Post-steroid asthma (X20MASTBA2.B2)

description:
Raw data fiile:
252577110007_SLOT03_S01_miRNA_105_Jan09_2_4.txt
FEV1 = the volume of air exhaled in the first second of a forced expiratory maneuver
FVC =  the total volume of air exhaled in a forced expiratory maneuver
PC20 =  the provocative concentration of methacholine required to decrease the FEV1 by 20%


title: Post-steroid asthma (X19MASTBA.B2)

description:
Raw data fiile:
252577110006_SLOT04_S01_miRNA_105_Jan09_2_2.txt
FEV1 = the volume of air exhaled in the first second of a forced expiratory maneuver
FVC =  the total volume of air exhaled in a forced expiratory maneuver
PC20 =  the provocative concentration of methacholine required to decrease the FEV1 by 20%


title: Steroid-naive asthma (X17MASTBA2.B2)

description:
Raw data fiile:
252577110006_SLOT04_S01_miRNA_105_Jan09_1_2.txt
FEV1 = the volume of air exhaled in the first second of a forced expiratory maneuver
FVC =  the total volume of air exhaled in a forced expiratory maneuver
PC20 =  the provocative concentration of methacholine required to decrease the FEV1 by 20%


title: Steroid-requiring asthma (X15MASTBA2.B2)

description:
Raw data fiile:
252577110006_SLOT04_S01_miRNA_105_Jan09_1_1.txt
FEV1 = the volume of air exhaled in the first second of a forced expiratory maneuver
FVC =  the total volume of air exhaled in a forced expiratory maneuver
PC20 =  the provocative concentration of methacholine required to decrease the FEV1 by 20%


title: Steroid-naive asthma (X34MASTCA2.B2)

description:
Raw data fiile:
252577110008_SLOT02_S01_miRNA_105_Jan09_2_1.txt
FEV1 = the volume of air exhaled in the first second of a forced expiratory maneuver
FVC =  the total volume of air exhaled in a forced expiratory maneuver
PC20 =  the provocative concentration of methacholine required to decrease the FEV1 by 20%


title: Post-steroid asthma (X08MASTAH.B2)

description:
Raw data fiile:
252577110006_SLOT04_S01_miRNA_105_Jan09_2_4.txt
FEV1 = the volume of air exhaled in the first second of a forced expiratory maneuver
FVC =  the total volume of air exhaled in a forced expiratory maneuver
PC20 =  the provocative concentration of methacholine required to decrease the FEV1 by 20%


title: Steroid-requiring asthma (X14MASTAH.B2)

description:
Raw data fiile:
252577110007_SLOT03_S01_miRNA_105_Jan09_2_2.txt
FEV1 = the volume of air exhaled in the first second of a forced expiratory maneuver
FVC =  the total volume of air exhaled in a forced expiratory maneuver
PC20 =  the provocative concentration of methacholine required to decrease the FEV1 by 20%


title: Steroid-naive asthma (X26MASTCA2.B1)

description:
Raw data fiile:
252372310000_S01_miRNA_105_Dec08_2_2.txt
FEV1 = the volume of air exhaled in the first second of a forced expiratory maneuver
FVC =  the total volume of air exhaled in a forced expiratory maneuver
PC20 =  the provocative concentration of methacholine required to decrease the FEV1 by 20%


title: Healthy control (X17MASTBA.B2)

description:
Raw data fiile:
252577110007_SLOT03_S01_miRNA_105_Jan09_2_1.txt
FEV1 = the volume of air exhaled in the first second of a forced expiratory maneuver
FVC =  the total volume of air exhaled in a forced expiratory maneuver
PC20 =  the provocative concentration of methacholine required to decrease the FEV1 by 20%


title: Steroid-naive asthma (X18MASTCA2.B1)

description:
Raw data fiile:
252372310000_S01_miRNA_105_Dec08_2_4.txt
FEV1 = the volume of air exhaled in the first second of a forced expiratory maneuver
FVC =  the total volume of air exhaled in a forced expiratory maneuver
PC20 =  the provocative concentration of methacholine required to decrease the FEV1 by 20%


title: Post-steroid asthma (X21MASTCA2.B1)

description:
Raw data fiile:
252372310002_S01_miRNA_105_Dec08_2_2.txt
FEV1 = the volume of air exhaled in the first second of a forced expiratory maneuver
FVC =  the total volume of air exhaled in a forced expiratory maneuver
PC20 =  the provocative concentration of methacholine required to decrease the FEV1 by 20%


title: Healthy control (X16MASTCA2.B1)

description:
Raw data fiile:
252372310001_S01_miRNA_105_Dec08_1_3.txt
FEV1 = the volume of air exhaled in the first second of a forced expiratory maneuver
FVC =  the total volume of air exhaled in a forced expiratory maneuver
PC20 =  the provocative concentration of methacholine required to decrease the FEV1 by 20%


title: Post-steroid asthma (X17MASTCA2.B1)

description:
Raw data fiile:
252372310001_S01_miRNA_105_Dec08_2_1.txt
FEV1 = the volume of air exhaled in the first second of a forced expiratory maneuver
FVC =  the total volume of air exhaled in a forced expiratory maneuver
PC20 =  the provocative concentration of methacholine required to decrease the FEV1 by 20%


title: Post-steroid asthma (X10MASTCA2.B1)

description:
Raw data fiile:
252372310000_S01_miRNA_105_Dec08_1_3.txt
FEV1 = the volume of air exhaled in the first second of a forced expiratory maneuver
FVC =  the total volume of air exhaled in a forced expiratory maneuver
PC20 =  the provocative concentration of methacholine required to decrease the FEV1 by 20%


title: Steroid-requiring asthma (X22MASTCA2.B1)

description:
Raw data fiile:
252372310001_S01_miRNA_105_Dec08_2_3.txt
FEV1 = the volume of air exhaled in the first second of a forced expiratory maneuver
FVC =  the total volume of air exhaled in a forced expiratory maneuver
PC20 =  the provocative concentration of methacholine required to decrease the FEV1 by 20%


title: Steroid-naive asthma (X12MASTBA.B1)

description:
Raw data fiile:
252372310001_S01_miRNA_105_Dec08_1_1.txt
FEV1 = the volume of air exhaled in the first second of a forced expiratory maneuver
FVC =  the total volume of air exhaled in a forced expiratory maneuver
PC20 =  the provocative concentration of methacholine required to decrease the FEV1 by 20%


title: Healthy control (X15MASTBA.B1)

description:
Raw data fiile:
252372310001_S01_miRNA_105_Dec08_2_4.txt
FEV1 = the volume of air exhaled in the first second of a forced expiratory maneuver
FVC =  the total volume of air exhaled in a forced expiratory maneuver
PC20 =  the provocative concentration of methacholine required to decrease the FEV1 by 20%


title: Steroid-naive asthma (X05MASTCA2.B1)

description:
Raw data fiile:
252372310002_S01_miRNA_105_Dec08_1_1.txt
FEV1 = the volume of air exhaled in the first second of a forced expiratory maneuver
FVC =  the total volume of air exhaled in a forced expiratory maneuver
PC20 =  the provocative concentration of methacholine required to decrease the FEV1 by 20%


title: Steroid-requiring asthma (X14MASTBA2.B1)

description:
Raw data fiile:
252372310000_S01_miRNA_105_Dec08_2_3.txt
FEV1 = the volume of air exhaled in the first second of a forced expiratory maneuver
FVC =  the total volume of air exhaled in a forced expiratory maneuver
PC20 =  the provocative concentration of methacholine required to decrease the FEV1 by 20%


title: Post-steroid asthma (X12MASTBA2.B1)

description:
Raw data fiile:
252372310001_S01_miRNA_105_Dec08_1_4.txt
FEV1 = the volume of air exhaled in the first second of a forced expiratory maneuver
FVC =  the total volume of air exhaled in a forced expiratory maneuver
PC20 =  the provocative concentration of methacholine required to decrease the FEV1 by 20%


title: Healthy control (X10MASTBA2.B1)

description:
Raw data fiile:
252372310002_S01_miRNA_105_Dec08_2_3.txt
FEV1 = the volume of air exhaled in the first second of a forced expiratory maneuver
FVC =  the total volume of air exhaled in a forced expiratory maneuver
PC20 =  the provocative concentration of methacholine required to decrease the FEV1 by 20%


title: Healthy control (X06MASTAH.B1)

description:
Raw data fiile:
252372310000_S01_miRNA_105_Dec08_1_1.txt
FEV1 = the volume of air exhaled in the first second of a forced expiratory maneuver
FVC =  the total volume of air exhaled in a forced expiratory maneuver
PC20 =  the provocative concentration of methacholine required to decrease the FEV1 by 20%


title: Healthy control (X03MASTBA2.B1)

description:
Raw data fiile:
252372310002_S01_miRNA_105_Dec08_1_4.txt
FEV1 = the volume of air exhaled in the first second of a forced expiratory maneuver
FVC =  the total volume of air exhaled in a forced expiratory maneuver
PC20 =  the provocative concentration of methacholine required to decrease the FEV1 by 20%


title: Healthy control (X10MASTBA.B1)

description:
Raw data fiile:
252372310000_S01_miRNA_105_Dec08_1_2.txt
FEV1 = the volume of air exhaled in the first second of a forced expiratory maneuver
FVC =  the total volume of air exhaled in a forced expiratory maneuver
PC20 =  the provocative concentration of methacholine required to decrease the FEV1 by 20%


title: Post-steroid asthma (X05MASTAH.B1)

description:
Raw data fiile:
252372310002_S01_miRNA_105_Dec08_1_3.txt
FEV1 = the volume of air exhaled in the first second of a forced expiratory maneuver
FVC =  the total volume of air exhaled in a forced expiratory maneuver
PC20 =  the provocative concentration of methacholine required to decrease the FEV1 by 20%


title: Healthy control (X02MASTAH.B1)

description:
Raw data fiile:
252372310002_S01_miRNA_105_Dec08_2_4.txt
Descriptions of abbreviated clinical characteristics:
FEV1 = the volume of air exhaled in the first second of a forced expiratory maneuver
FVC =  the total volume of air exhaled in a forced expiratory maneuver
PC20 =  the provocative concentration of methacholine required to decrease the FEV1 by 20%


title: neuron-differentiated hMSCs (1 of 2)

city: Taichung

first: chanshiou

last: Wu

address: No6,Hsueh-shih road

country: Taiwan

institute: china medical university

description: Chip-chip neuron-differentiated 3A6 cells EZH2

hyb_protocol: standard Nimblegen hybridization kits and protocols were used.

scan_protocol: arrays were scanned with Axon scanner at 5 um resolution according to standard Nimblegen protocols.

data_processing: Signal intensity data is extracted from the scanned images of each array using NimbleScan (version 2.3.78), a NimbleGen's data extraction software. Arrays were scanned with Axon scanner at 5 um resolution according to standard NimbleGen protocols.Log2 ChIP/input ratios were created from the two raw pair files. Each feature on the array has a corresponding scaled log2-ratio. This is the ratio of the input signals for the experimental and test samples that were co-hybridized to the array. The log2-ratio is computed and scaled to center the ratio data around zero. Using NimbleScan, peak data files are generated from the scaled log2-ratio data. The ratio data is then randomized 20 times to evaluate the probability of false positives. Each peak is then assigned a false discovery rate (FDR) score based on the randomization. NimbleScan searches for peaks that appear in a specified promoter region around the transcription start site (TSS). Lists all peaks with an FDR 0.2 and maps them to promoter regions. Each row in the report lists a peak-transcript pair. For each transcript, if more than one peak lies within the promoter region, there will be multiple rows for that transcript.

source_name: EZH2 ChIP DNA from neuron-differentiated 3A6 cells

label_protocol: standard Nimblegen ChIP labeling protocol (1 ug of Amplified ChIP DNA, direct incorporation of cy labeled primers with klenow extension).

growth_protocol: The 3A6 cells were grown in DMEM-LG with 10% FBS.

extract_protocol: cell lines were cross-linked with formaldehyde and the chromatin extracts were sonicated (Misonix Sonicater 3000). Following immunoprecipitation with anti-mouse EZH2 antibody (Cell Signaling, #3147, lot 4), DNAs were purified from ChIP samples and input control samples. Purified DNAs were blunt ended, ligated with linkers and amplified by PCR.

treatment_protocol: The 3A6 were treated with DMEM-HG neuronal induction medium (NIM) containing 10-7 M dexamethasone, 50 μg/ml ascorbic acid-2-phosphate, 50 μM indomethacin, 10 μg/ml insulin, and 0.45 mM 3-isobutyl-1-methyl-xanthine for 5 days.

value: neuron-differentiated hMSCs

tag: chip antibody

value: anti-EZH2 mouse antibody

tag: chip antibody vendor

value: Cell Signaling

tag: chip antibody cat. #

tag: chip antibody lot #

source_name: Input DNA from neuron-differentiated 3A6 cells

tag: sample type

value: Input DNA


title: undifferentiated hMSCs (1 of 2)

description: Chip-chip undifferentiated 3A6 cells EZH2

source_name: EZH2 ChIP DNA from 3A6 cells

growth_protocol: The 3A6 cells were grown in Dulbecco’s modified Eagle’s medium-low glucose (DMEM-LG) with 10% fetal bovine serum (FBS).

tag: cell type

value: undifferentiated hMSCs

source_name: Input DNA from undifferentiated 3A6 cells

treatment_protocol: no special treatment


title: m_DCs_PolyIC3

city: Seattle

first: Aderem

last: Lab

state: WA

address: 307 Westlake Avenue North, Suite 500

institute: Seattle Children's Research Institute

description: Biological replicate 3 of 3, PolyI:C 30 ug/mL, 8 hours.

hyb_protocol: The Hy3™-labeled samples and a Hy5™-labeled reference RNA sample were mixed pair-wise and hybridized to the miRCURY™ LNA array version 10.0 (Exiqon, Denmark), which contains capture probes targeting all miRNAs for all species registered in the miRBASE version 11.0 at the Sanger Institute. The hybridization was performed according to the miRCURY™ LNA array manual using a Tecan HS4800 hybridization station (Tecan, Austria). After hybridization the microarray slides were scanned and stored in an ozone free environment (ozone level below 2.0 ppb) in order to prevent potential bleaching of the fluorescent dyes.

scan_protocol: The miRCURY™ LNA array microarray slides were scanned using the Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA) and the image analysis was carried out using the ImaGene 8.0 software (BioDiscovery, Inc., USA).

data_processing: The quantified signals were normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm.  The genes were selected based on two-tailed T-test calculated between the two sample groups with p-values lower than 0.001, and some of the genes were selected with further Bonferroni correction.

source_name: Splenic dendritic cell, polyI:C-stimulated, 8 hours

label_protocol: One µg total RNA from sample and reference were labeled with Hy3™ and Hy5™ fluorescent label, respectively, using the miRCURY™ LNA Array power labeling kit (Exiqon, Denmark) following the procedure described by the manufacturer

growth_protocol: C57Bl/6 mice were injected subcutaneously between the shoulder blades with 6x106 B6-melanoma cells expressing Flt3L to expand the dendritic cell compartment.  After 2 weeks, spleens were isolated, enzymatically dissociated using Liberase Blendzyme III and dendritic cells isolated by autoMACS magnetic bead purification using pan-DC beads.  Cell purity was measured by flow cytometry of CD11c expression and was >95% in each experiment.  This purification scheme yielded a mixture of conventional CD11chi dendritic cells as well as PDCA1+ plasmacytoid cells, and the ratio of these two populations was consistent between experiments.

extract_protocol: RNA extraction using Trizol. The quality of the total RNA was verified by an Agilent 2100 Bioanalyzer profile.

treatment_protocol: Cells were infected with H1N1 influenza A/Puerto Rico/8/34 at an MOI=10, stimulated with 30 ug/mL polyI:C, or cultured in media alone for 8 h (RPMI-1640, 10% heat-inactivated FBS, 2 mM L-glutamine, penicillin, streptomycin, 100 μM β-mercaptoethanol).

tag: strain

value: splenic dendritic cell, Flt3L expanded in vivo

tag: treatment

value: In vitro polyI:C stimulation, 8 hours

source_name: Common reference RNA, equal mixture of all 9 dendritic cell RNA study samples

value: reference


title: Steroid-requiring asthma (X11MASTAH.B1)

description:
Raw data fiile:
252372310001_S01_miRNA_105_Dec08_2_2.txt
FEV1 = the volume of air exhaled in the first second of a forced expiratory maneuver
FVC =  the total volume of air exhaled in a forced expiratory maneuver
PC20 =  the provocative concentration of methacholine required to decrease the FEV1 by 20%

value: MASTC A2

value: Male

value: Steroid-requiring asthma

value: airway epithelial cells


title: m_DCs_PolyIC2

description: Biological replicate 2 of 3, PolyI:C 30 ug/mL, 8 hours.


title: S.cerevisiae_H3_wild_type_1

city: Daejeon

first: Inkyung

last: Jung

address: KAIST, 291 Daehak-ro, Yuseong-gu

department: Biological Sciences

country: South Korea

institute: KAIST

description: log2 ratio (mut / WT) data after VSN normalization and removing batch effect using Combat provided as supplementary file.

hyb_protocol: The fragmented, labelled complementary RNA was hybridized to oligonucleotide Nimblegen 135K microarrays 42°C for 16-20h according to Nimblegen 12X135K kit protocol.

scan_protocol: Microarrays were scanned using NimbleScan 2.5.26(Roche NimbleGen).

data_processing: The raw data generated from microarray was normalized by using VSN (Variance Stabilization and Normalization) algorithm. After pre-processing microarray data we removed batch effect by using Combat algorithm.

organism: Saccharomyces cerevisiae

label_protocol: Fluorescence-labelled RNA was generated by carrying out an in vitro transcription reaction (Double-stranded cDNA in Nuclease-free water 16ul, T7 rNTP mix 16ul, T7 10X Reaction Buffer 4ul, and T7 Enzyme Mix) at 37°C for 16h.

growth_protocol:
The 2ml glycerol stocks of selected mutants and H3/H4 wild-types were cultured in SD-ura medium for 22h at 25C.
After streaking on YPD plate at 25C, single colony was cultured in 2ml SD-ura medium for 22h at 25C. Again, 500ul of this culture solution was cultured 10ml SD-ura medium for 22h at 25C.

extract_protocol: RNA was prepared from yeast pellet using the RNeasy Mini Kit according to the manufacturer's instructions (Qiagen).

tag: mutant collection

value: Histone H3 & H4 Mutant Collection

tag: genotype/variation


title: S.cerevisiae_H4S64A_mutant


title: m_DCs_PolyIC1

description: Biological replicate 1 of 3, PolyI:C 30 ug/mL, 8 hours.


title: S.cerevisiae_H3K56Q_mutant


title: S.cerevisiae_H4K16R_mutant


title: MGC-803_cells_synbindin_rep2

city: Shanghai

first: Jie

last: Xu

address: Shandong Rd 145

department: Shanghai Renji Hospital

country: China

institute: Shanghai Institute for Digestive Diseases

description:
synbindin_2
Gene expression after synbindin adenovirus infection.

hyb_protocol: The labeled cRNAs were hybridized onto the Whole Human Genome Oligo Microarray (4 x 44K, Agilent Technologies).

scan_protocol: After washing, the arrays were scanned by the Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v11.5.1 software package (Agilent Technologies).

source_name: MGC-803 cells infected with synbindin adenoviruses

label_protocol: The Agilent Quick Amp Labeling Kit was used for sample labeling. Briefly, total RNA from each sample was amplified and transcribed into fluorescent cRNA using Agilent's Quick Amp Labeling protocol (version 5.7, Agilent Technologies).

growth_protocol: MGC-803 cells were maintained at 37 °C in an atmosphere of 5% CO2 in RPMI-1640 medium (Invitrogen) supplemented with 10% fetal bovine serum, penicillin and streptomycin (Invitrogen) in 25-ml culture flasks.

extract_protocol: Forty-eight hours after treatment, total RNA from each sample was isolated and quantified. Integrity and concentration of RNA were assessed after RNA extraction and prior to sample labeling.

treatment_protocol: MGC-803 cells were treated with adenoviruses carrying synbindin or control viruses carrying GFP.

tag: cell line

value: gastric cancer cell line

value: synbindin adenoviruses


title: S.cerevisiae_H3_wild_type_2


title: m_DCs_Virus1

description: Biological replicate 1 of 3, Influenza A/PR/8/34 MOI=10, 8 hours.

source_name: Splenic dendritic cell, influenza-infected, 8 hours

value: In vitro influenza infection, 8 hours


title: m_DCs_Virus2

description: Biological replicate 2 of 3, Influenza A/PR/8/34 MOI=10, 8 hours.


title: S.cerevisiae_H3K56R_mutant


title: S.cerevisiae_H4_wild_type_2


title: S.cerevisiae_H3K37A_mutant


title: MGC-803_cells_neg_rep2

description:
Control_2
Gene expression after GFP adenovirus infection.

source_name: MGC-803 cells infected with GFP adenoviruses

value: GFP adenoviruses


title: MGC-803_cells_synbindin_rep1

description:
synbindin_1
Gene expression after synbindin adenovirus infection.


title: MGC-803_cells_synbindin_rep3

description:
synbindin_3
Gene expression after synbindin adenovirus infection.


title: MGC-803_cells_neg_rep1

description:
Control_1
Gene expression after GFP adenovirus infection.


title: MGC-803_cells_neg_rep3

description:
Control_3
Gene expression after GFP adenovirus infection.


title: m_DCs_Mock2

description: Biological replicate 2 of 3, Mock, 8 hours.

source_name: Splenic dendritic cell, mock, 8 hours

value: In vitro culture, 8 hours


title: m_DCs_Virus3

description: Biological replicate 3 of 3, Influenza A/PR/8/34 MOI=10, 8 hours.


title: S.cerevisiae_H3K23A_mutant


title: S.cerevisiae_H3K27A_mutant


title: P_cellline2_rep1

description: Proliferating, cell line 2

source_name: Proliferating, cell line 2

tag: gender

value: Fibroblast


title: S.cerevisiae_H4G9A_mutant


title: S.cerevisiae_H4A38S_mutant


title: CD16 vs CDH16 (dye swap reps)

city: Duarte

first: Xiwei

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

description:
Infected vs. control at day 16
Infected vs. control dye Swap at day 16
US45102989_13730770_S01_crop_Exiqon_KBB3.txt: CD16_Hy3vsCDH16_Hy5
US45102989_13730771_S01_crop_Exiqon_KBB3.txt: CDH16_Hy3vsCD16_Hy5

hyb_protocol: The samples were hybridized on the miRCURY™ LNA Array (v.9.2) as per Exiqons protocols.

scan_protocol: Arrays were scanned by Agilent Scanner as per Agilent's default protocol

data_processing:
When the array was scanned, a GAL file specially designed for human was provided by the manufacturer and it was used to extract intensities from the array. The GAL file does not have any spots other than human miRNAs. Therefore, the non-human miRNAs (not useful for this study) are never reported by the scanner.
Log ratios between the Hy3/Hy5 have been provided along with the normalized independent Hy3 and Hy5 signals. The quantified signals (background correction) were normalized using the global Lowess method.
LOWESS normalized log ratio (infected/untreated) using Limma package. When dye swap is present, it is the mean of the two replicates.

label: Hy3, Hy5

label_protocol: The samples were labeled using the miRCURY™ Hy3™/Hy5™ power labeling kit

growth_protocol: Cultured in ActiCyte -TC media

extract_protocol: Total RNA was extracted with RNA STAT-60

treatment_protocol: untreated versus infected by HIV-1 at MOI=0.01, RNA was extracted at different days post infection

value: CD4+CD8- cells from pooled plasma

tag: infection

value: untreated

tag: time (days post-infection)

value: HIV1 infected


title: m_DCs_Mock3

description: Biological replicate 3 of 3, Mock, 8 hours.

value: splenic dendritic cell, Flt3L expanded in vivo


title: CD15 vs CDH15

description: Infected vs. control at day 15


title: CD10 vs CDH10 (dye swap reps)

description:
Infected vs. control at day 10
Infected vs. control dye swap at day 10
US45102989_13730768_crop_Exiqon_KBB3.txt: CD10_Hy3vsCDH10_Hy5
US45102989_13730769_S01_Cropped_Exiqon_KBB3.txt: CDH10_Hy3vsCD10_Hy5


title: CD12 vs CDH12

description: Infected vs. control at day 12


title: MDA-HNS-133

city: Stanford

first: Floyd

middle: Christopher

last: Holsinger

address: 875 Blake Wilbur Drive, CC-2227

department: Head and Neck srugery

institute: Stanford University School of Medicine, Stanford Cancer Center

description:
*  Treatment Modality:
s= surgery
IC=induction chemotherapy
R=radiation therapy
cRT=chemoradiation

hyb_protocol: Fragmented cRNA was used for hybridization to the U133 plus 2.0 chips at 42 °C for 16 hrs.

scan_protocol: U133+2.0 chips were washed and stained with Affymetrix GeneChip Fluid, then scanned and visualized with a GeneArray Scanner (Hewlett-Packard, Palo Alto, CA)

data_processing: No expression profiles are generated here, as these .cel files were provided as a validation set for a signature developed by Eduardo Mendez <edmendez@u.washington.edu> and Lohavanichbutr, Pawadee <plohavan@fhcrc.org>

source_name: cancer

label_protocol: 200 ng of total RNA were used to prepare antisense biotinylated RNA and single-stranded cDNA was synthesized using a T7-Oligo(dT) promoter primer (GenSet, San Diego, California) followed by RNase H–facilitated second-strand cDNA synthesis, which was purified and served as a template in the subsequent in vitro transcription (IVT). In vitro transcription reaction was carried out in the presence of T7 RNA polymerase (MEGAscript® T7 Kit, Ambion, Austin, Tx) and a biotinylated nucleotide analogue/ribonucleotide mix (ENZO Life Sciences, Farmingdale, NY) for cRNA.  A second cycle (double IVT) was used systematically for all samples to increase yield. The biotinylated cRNA targets were then cleaned and fragmented.

growth_protocol: Archival human sample, not applicable

extract_protocol: RNA extracted using RNeasy Kit (Qiagen, Valencia, CA)

treatment_protocol: Archival human sample, not applicable

tag: tu-vs-nl

value: cancer

tag: smoking status

value: Current

tag: oc vs. op

value: Oral cavity

tag: t stage

tag: cn stage

tag: pn stage

tag: dm?

tag: ecs

value: N

tag: treatment*

value: S, cRT

tag: dxdate

tag: txdate

tag: localrecur

tag: nodalrecur

tag: survivallastfollowup

value: Dead with Disease

tag: vital

value: Dead-OSCC

tag: lastfudt

tag: futime

tag: osccdeath

tag: alldeath


title: MDA-HNS-134

tag: tu-vs-nl

tag: gender

value: Female

tag: smoking status

value: Former

tag: oc vs. op

value: Y

value: Dead, other cause

value: Dead-other


title: S.cerevisiae_H4_wild_type_1

tag: mutant collection

value: Histone H3 & H4 Mutant Collection

tag: genotype/variation


title: MDA-HNS-131

value: Male

value: Oropharynx

tag: t stage

tag: cn stage

tag: pn stage

tag: dm?

tag: ecs

tag: treatment*

value: S


title: S.cerevisiae_H4K8A_mutant


title: MDA-HNS-129

value: NeverSmoker

tag: dxdate

tag: txdate

tag: localrecur

tag: nodalrecur

tag: survivallastfollowup

value: Living NED

tag: vital

value: Alive


title: CD3 vs CDH3

description: Infected vs. control at day 3

tag: cell type

value: CD4+CD8- cells from pooled plasma

tag: infection

value: untreated

tag: time (days post-infection)

value: HIV1 infected


title: m_DCs_Mock1

description: Biological replicate 1 of 3, Mock, 8 hours.

tag: strain

value: splenic dendritic cell, Flt3L expanded in vivo

tag: treatment

value: In vitro culture, 8 hours

tag: sample type

value: reference


title: MDA-HNS-130

tag: tu-vs-nl

value: cancer

tag: gender

tag: smoking status

value: Former

tag: oc vs. op

value: Oral cavity

tag: t stage

tag: cn stage

value: N

tag: lastfudt

tag: futime

tag: osccdeath

tag: alldeath


title: MDA-HNS-126

value: Current

tag: pn stage

tag: dm?

tag: ecs

value: Y

tag: treatment*

value: IC, S, RT

tag: dxdate

tag: txdate

tag: localrecur

tag: nodalrecur

tag: nodrecurdt

tag: survivallastfollowup

value: Dead with Disease

tag: vital

value: Dead-OSCC


title: S.cerevisiae_H3R128A_mutant

description: log2 ratio (mut / WT) data after VSN normalization and removing batch effect using Combat provided as supplementary file.

tag: mutant collection

value: Histone H3 & H4 Mutant Collection

tag: genotype/variation


title: S.cerevisiae_H3K122A_mutant


title: S.cerevisiae_H4K5A_mutant


title: S.cerevisiae_H3F78A_mutant


title: S.cerevisiae_H3K125A_mutant


title: S.cerevisiae_H4G7A_mutant


title: S.cerevisiae_H3R131A_mutant


title: MDA-HNS-122

tag: tu-vs-nl

tag: gender

value: Female

tag: smoking status

tag: oc vs. op

tag: t stage

tag: cn stage

value: S, RT

value: Dead

tag: lastfudt


title: MDA-HNS-123

value: Male

value: Oropharynx

tag: pn stage

tag: dm?

tag: ecs

tag: treatment*

value: Living NED

value: Alive

tag: futime

tag: osccdeath

tag: alldeath


title: MDA-HNS-119

value: cancer

tag: dxdate

tag: txdate

tag: localrecur

tag: nodalrecur

tag: survivallastfollowup

tag: vital


title: MDA-HNS-128

tag: tu-vs-nl

tag: gender

tag: smoking status

value: Former

tag: oc vs. op


title: S.cerevisiae_H4S1A_mutant

tag: mutant collection

tag: genotype/variation


title: MDA-HNS-116

value: Oral cavity

tag: t stage

tag: cn stage

tag: pn stage

tag: dm?

tag: ecs

tag: lastfudt


title: S.cerevisiae_H4K16Q_mutant


title: S.cerevisiae_H3Q76A_mutant


title: S.cerevisiae_H3D77A_mutant


title: S.cerevisiae_H3R72A_mutant


title: S.cerevisiae_H3V71A_mutant


title: MDA-HNS-125

value: N

tag: treatment*

tag: dxdate

tag: txdate

value: Dead, no disease

value: Dead-other

tag: futime

tag: osccdeath

tag: alldeath


title: MDA-HNS-114

tag: tu-vs-nl

tag: gender

value: S

tag: localrecur

tag: nodalrecur

tag: survivallastfollowup

tag: vital


title: MDA-HNS-113

source_name: normal

value: normal

tag: smoking status

value: NeverSmoker

tag: oc vs. op

tag: t stage

tag: cn stage


title: S.cerevisiae_H3E73A_mutant

tag: mutant collection

value: Histone H3 & H4 Mutant Collection

tag: genotype/variation


title: S.cerevisiae_H3L70A_mutant


title: S.cerevisiae_H3K64A_mutant


title: MDA-HNS-112

value: Female

value: Current

tag: pn stage

tag: dm?

tag: ecs

tag: treatment*

tag: dxdate

tag: lastfudt


title: S.cerevisiae_H3R69A_mutant


title: MDA-HNS-117

tag: tu-vs-nl

tag: gender

value: Y

value: S, RT

tag: txdate

tag: futime

tag: osccdeath

tag: alldeath


title: S.cerevisiae_H3L60A_mutant


title: S.cerevisiae_H3L20A_mutant


title: MDA-HNS-115

tag: smoking status

tag: oc vs. op

tag: localrecur

tag: nodalrecur

tag: survivallastfollowup

tag: vital


title: MDA-HNS-107

tag: t stage

tag: cn stage

tag: pn stage

tag: dm?

value: Dead


title: MDA-HNS-111

value: Male

tag: ecs

tag: treatment*

tag: dxdate

value: Living NED

tag: lastfudt


title: MDA-HNS-108

tag: tu-vs-nl

tag: gender

tag: txdate

tag: futime


title: MDA-HNS-110

tag: smoking status

tag: oc vs. op

tag: locrecurdt

tag: nodrecurdt

tag: dm date?

value: Dead with Disease

tag: osccdeath

tag: alldeath


title: MDA-HNS-106

tag: t stage

tag: cn stage

tag: pn stage

tag: localrecur

tag: nodalrecur

tag: survivallastfollowup

tag: vital


title: MDA-HNS-105

tag: tu-vs-nl

value: cancer

tag: gender

tag: dm?

tag: ecs

tag: treatment*

tag: dxdate

tag: lastfudt


title: MDA-HNS-109

tag: smoking status

tag: oc vs. op

value: Oral cavity

tag: txdate

value: Alive

tag: futime


title: MDA-HNS-104

tag: t stage

tag: cn stage

value: N

tag: locrecurdt

tag: osccdeath

tag: alldeath


title: S.cerevisiae_H3Q68A_mutant

tag: mutant collection

tag: genotype/variation


title: S.cerevisiae_H3R17A_mutant


title: S.cerevisiae_H3K18A_mutant


title: S.cerevisiae_H3L61A_mutant


title: S.cerevisiae_H3K14A_mutant


title: MDA-HNS-101

tag: tu-vs-nl

tag: gender

tag: pn stage

tag: localrecur

tag: nodalrecur

tag: survivallastfollowup

value: Dead, unknown disease status

tag: vital


title: S.cerevisiae_H3K4A_mutant


title: MDA-HNS-102

tag: smoking status

tag: oc vs. op

tag: dm?

tag: ecs

tag: treatment*

tag: dxdate

value: Dead-unknown

tag: lastfudt


title: MDA-HNS-100

value: normal

tag: t stage

tag: cn stage

value: S

tag: txdate

tag: futime

tag: osccdeath

tag: alldeath


title: S.cerevisiae_H3T11A_mutant

tag: mutant collection

value: Histone H3 & H4 Mutant Collection

tag: genotype/variation


title: S.cerevisiae_H3T3A_mutant


title: MDA-HNS-098

tag: tu-vs-nl

tag: gender

value: Former

tag: pn stage

tag: localrecur

tag: nodalrecur

tag: survivallastfollowup


title: MDA-HNS-097

tag: smoking status

value: Current

tag: oc vs. op

tag: dm?

tag: ecs

tag: treatment*

tag: locrecurdt

tag: vital


title: MDA-HNS-095

value: Female

value: NeverSmoker

tag: t stage

tag: cn stage

tag: dxdate

tag: txdate

tag: lastfudt

tag: futime

tag: osccdeath


title: S.cerevisiae_H3R8A_mutant

tag: mutant collection

tag: genotype/variation


title: MDA-HNS-103

tag: tu-vs-nl

tag: gender

tag: pn stage

tag: localrecur

tag: nodalrecur

tag: survivallastfollowup

tag: alldeath


title: MDA-HNS-094

tag: smoking status

tag: oc vs. op

tag: dm?

tag: ecs

value: Y

tag: treatment*

value: S, RT

tag: nodrecurdt

tag: vital

value: Dead-OSCC


title: S.cerevisiae_H4G99A_mutant


title: S.cerevisiae_H3Q5A_mutant


title: S.cerevisiae_H3K9A_mutant


title: S.cerevisiae_H4S47A_mutant


title: S.cerevisiae_H3R2A_mutant


title: S.cerevisiae_H4K44A_mutant


title: S.cerevisiae_H4I46A_mutant


title: S.cerevisiae_H4G48A_mutant


title: S.cerevisiae_H4Y98A_mutant


title: MDA-HNS-099

value: Male

tag: t stage

tag: cn stage

tag: dxdate

tag: txdate

value: Living NED

tag: lastfudt

tag: futime

tag: osccdeath


title: MDA-HNS-092

tag: tu-vs-nl

value: cancer

tag: gender

value: Oral cavity

tag: pn stage

tag: localrecur

tag: locrecurdt

tag: nodalrecur

value: Dead with Disease


title: MDA-HNS-096

tag: smoking status

tag: oc vs. op

tag: dm?

tag: ecs

value: N

tag: survivallastfollowup

value: Alive

tag: alldeath


title: MDA-HNS-089

value: normal

tag: t stage

tag: cn stage

tag: treatment*

tag: dxdate

tag: vital


title: MDA-HNS-090

tag: tu-vs-nl

tag: txdate

tag: lastfudt

tag: futime

tag: osccdeath


title: MDA-HNS-091

tag: gender

tag: pn stage

tag: localrecur

tag: locrecurdt

tag: nodalrecur


title: MDA-HNS-088

tag: smoking status

tag: oc vs. op

tag: dm?

tag: ecs

tag: survivallastfollowup


title: S.cerevisiae_H4R36A_mutant

tag: mutant collection

tag: genotype/variation


title: S.cerevisiae_H4F100A_mutant


title: MDA-HNS-087

tag: tu-vs-nl

tag: t stage

tag: cn stage

tag: treatment*

tag: dxdate

tag: vital

tag: alldeath


title: MDA-HNS-086

tag: gender

tag: pn stage

tag: txdate

tag: localrecur

tag: lastfudt

tag: futime

tag: osccdeath


title: S.cerevisiae_H4G41A_mutant


title: S.cerevisiae_H4L37A_mutant


title: MDA-HNS-093

tag: smoking status

tag: oc vs. op

tag: dm?

tag: ecs

value: S

tag: nodalrecur

tag: survivallastfollowup


title: S.cerevisiae_H4T73A_mutant

tag: mutant collection

value: Histone H3 & H4 Mutant Collection

tag: genotype/variation


title: S.cerevisiae_H4E74A_mutant


title: MDA-HNS-085

tag: tu-vs-nl

tag: t stage

tag: cn stage

tag: treatment*

tag: dxdate

tag: vital


title: MDA-HNS-084

tag: gender

tag: pn stage

tag: txdate

tag: localrecur

tag: nodrecurdt

value: Dead, unknown disease status

value: Dead-unknown

tag: lastfudt

tag: alldeath


title: MDA-HNS-083

tag: smoking status

tag: oc vs. op

tag: dm?

tag: ecs

tag: nodalrecur

tag: futime

tag: osccdeath


title: S.cerevisiae_H4R67A_mutant

tag: mutant collection

tag: genotype/variation


title: S.cerevisiae_H4I66A_mutant


title: S.cerevisiae_H4L97A_mutant


title: MDA-HNS-081

tag: tu-vs-nl

value: Former

tag: t stage

tag: cn stage

tag: treatment*

tag: dxdate

tag: survivallastfollowup

value: Died, due to treatment of disease

tag: vital

value: Dead-other


title: MDA-HNS-080

tag: gender

tag: pn stage

value: S, RT

tag: txdate

tag: localrecur

tag: lastfudt

tag: alldeath


title: MDA-HNS-078

tag: smoking status

tag: oc vs. op

tag: dm?

tag: ecs

value: Y

value: Surgery

tag: nodalrecur

tag: futime


title: MDA-HNS-079

tag: tu-vs-nl

value: Male

tag: t stage

tag: cn stage

tag: osccdeath


title: S.cerevisiae_H4V65A_mutant

tag: mutant collection

tag: genotype/variation


title: S.cerevisiae_H4K77A_mutant


title: S.cerevisiae_H4K12A_mutant


title: S.cerevisiae_H4V57A_mutant


title: S.cerevisiae_H4Y51A_mutant


title: S.cerevisiae_H3S10A_mutant


title: S.cerevisiae_H4I29A_mutant


title: S.cerevisiae_H3V117A_mutant


title: MDA-HNS-077

tag: gender

tag: pn stage

tag: treatment*

tag: dxdate

tag: survivallastfollowup

value: Dead, no disease

tag: vital


title: MDA-HNS-076

value: cancer

tag: smoking status

tag: oc vs. op

value: Oral cavity

tag: txdate

tag: localrecur

tag: lastfudt

tag: alldeath


title: MDA-HNS-082

tag: tu-vs-nl

value: NeverSmoker

tag: t stage

tag: dm?

tag: ecs

value: N

tag: nodalrecur

tag: nodrecurdt

value: Dead with Disease

tag: futime


title: MDA-HNS-074

value: normal

tag: gender

value: Female

tag: cn stage

tag: pn stage

tag: treatment*

value: S

tag: dm date?

tag: osccdeath


title: MDA-HNS-071

tag: smoking status

value: Current

tag: oc vs. op

tag: dxdate

tag: txdate

tag: survivallastfollowup

value: Living NED

tag: vital

value: Alive


title: MDA-HNS-072

tag: tu-vs-nl

value: Former

tag: t stage

tag: dm?

tag: localrecur

value: Dead-OSCC

tag: lastfudt

tag: alldeath


title: MDA-HNS-073

tag: gender

tag: cn stage

tag: ecs

value: Y

value: S, RT

tag: nodalrecur

tag: futime


title: MDA-HNS-070

value: Male

tag: smoking status

tag: pn stage

tag: treatment*

tag: osccdeath


title: S.cerevisiae_H4R23A_mutant

tag: mutant collection

value: Histone H3 & H4 Mutant Collection

tag: genotype/variation


title: S.cerevisiae_H4R19A_mutant


title: S.cerevisiae_H4K20A_mutant


title: S.cerevisiae_H4I21A_mutant


title: MDA-HNS-069

tag: tu-vs-nl

value: cancer

tag: oc vs. op

tag: dxdate

tag: txdate

tag: survivallastfollowup

tag: vital


title: MDA-HNS-068

tag: gender

value: Oral cavity

tag: t stage

tag: dm?

tag: localrecur

value: Dead, unknown disease status

value: Dead-unknown

tag: lastfudt

tag: alldeath


title: S.cerevisiae_H4K16A_mutant


title: S.cerevisiae_H4R17A_mutant


title: MDA-HNS-064

tag: smoking status

tag: cn stage

tag: pn stage

tag: ecs

value: N

tag: nodalrecur

value: Dead with Disease

tag: futime


title: MDA-HNS-067

tag: tu-vs-nl

tag: oc vs. op

tag: treatment*

tag: nodrecurdt

tag: osccdeath


title: MDA-HNS-065

value: normal

tag: gender

tag: dxdate

tag: txdate

tag: survivallastfollowup

tag: vital


title: MDA-HNS-066

tag: t stage

tag: dm?

tag: localrecur

tag: lastfudt

tag: alldeath


title: MDA-HNS-075

value: Female

tag: smoking status

tag: cn stage

tag: pn stage

tag: ecs

value: S

tag: nodalrecur

tag: dm date?


title: MDA-HNS-062

tag: tu-vs-nl

tag: oc vs. op

tag: treatment*

value: Living NED

tag: futime

tag: osccdeath


title: S.cerevisiae_H4G14A_mutant

tag: mutant collection

tag: genotype/variation


title: S.cerevisiae_H4G28A_mutant


title: S.cerevisiae_H4N25A_mutant


title: S.cerevisiae_H4G13A_mutant


title: S.cerevisiae_H3L109A_mutant


title: S.cerevisiae_H3A110S_mutant


title: S.cerevisiae_H3A111S_mutant


title: MDA-HNS-061

tag: gender

tag: t stage

tag: dm?

tag: dxdate

tag: txdate

tag: survivallastfollowup

tag: vital


title: S.cerevisiae_H4H18A_mutant


title: S.cerevisiae_H3T107A_mutant


title: MDA-HNS-059

tag: smoking status

tag: cn stage

tag: pn stage

tag: ecs

tag: localrecur

value: Died, due to treatment of disease

tag: lastfudt

tag: alldeath


title: MDA-HNS-060

tag: tu-vs-nl

value: Former

tag: oc vs. op

tag: treatment*

tag: nodalrecur

value: Alive

tag: futime

tag: osccdeath


title: MDA-HNS-058

tag: gender

tag: t stage

tag: dm?

tag: dxdate


title: S.cerevisiae_H3D106A_mutant

tag: mutant collection

tag: genotype/variation


title: S.cerevisiae_H3T58A_mutant


title: MDA-HNS-057

tag: smoking status

tag: cn stage

tag: pn stage

tag: txdate

tag: survivallastfollowup

tag: vital


title: S.cerevisiae_H3K56A_mutant


title: MDA-HNS-056

tag: tu-vs-nl

value: NeverSmoker

tag: oc vs. op

tag: ecs

tag: localrecur

tag: nodrecurdt

tag: dm date?

value: Dead, due to disease

tag: lastfudt

tag: alldeath


title: MDA-HNS-055

tag: gender

value: Male

tag: t stage

tag: dm?

tag: treatment*

value: S, RT

tag: dxdate

tag: nodalrecur

value: Dead-OSCC

tag: futime

tag: osccdeath


title: S.cerevisiae_H3E105A_mutant

tag: mutant collection

value: Histone H3 & H4 Mutant Collection

tag: genotype/variation


title: MDA-HNS-054

tag: tu-vs-nl

tag: smoking status

tag: oc vs. op

value: Oral cavity

tag: cn stage

tag: pn stage

tag: txdate

tag: locrecurdt

tag: survivallastfollowup

tag: vital


title: S.cerevisiae_H3E59A_mutant


title: MDA-HNS-053

value: cancer

tag: gender

tag: t stage

tag: dm?

tag: ecs

tag: localrecur

tag: nodrecurdt

tag: lastfudt

tag: alldeath


title: MDA-HNS-051

tag: tu-vs-nl

value: N

tag: treatment*

tag: dxdate

tag: nodalrecur

tag: futime

tag: osccdeath


title: MDA-HNS-052

tag: smoking status

tag: oc vs. op

tag: cn stage

tag: pn stage

tag: txdate


title: S.cerevisiae_H3E50A_mutant

tag: mutant collection

tag: genotype/variation


title: MDA-HNS-049

tag: gender

value: Current

tag: t stage

tag: dm?

tag: ecs

value: Y

value: S, cRT

tag: localrecur

tag: survivallastfollowup

tag: vital


title: MDA-HNS-050

tag: tu-vs-nl

value: Female

tag: treatment*

value: S

tag: dxdate

tag: locrecurdt

tag: nodalrecur

tag: nodrecurdt

tag: dm date?

value: Dead with Disease

tag: lastfudt

tag: alldeath


title: MDA-HNS-048

tag: smoking status

tag: oc vs. op

tag: cn stage

tag: pn stage

tag: txdate

value: Living NED

tag: futime

tag: osccdeath


title: MDA-HNS-047

tag: gender

tag: t stage

tag: dm?

tag: ecs

value: IC, S, RT

tag: localrecur

tag: survivallastfollowup

tag: vital


title: S.cerevisiae_H3V46A_mutant

tag: mutant collection

tag: genotype/variation


title: S.cerevisiae_H3R49A_mutant


title: MDA-HNS-046

tag: tu-vs-nl

value: Former

tag: treatment*

value: IC, S, cRT

tag: dxdate

tag: nodalrecur

tag: lastfudt

tag: alldeath


title: S.cerevisiae_H3F104A_mutant


title: S.cerevisiae_H3K36A_mutant


title: MDA-HNS-045

value: Male

tag: smoking status

tag: oc vs. op

tag: cn stage

tag: pn stage

tag: txdate

value: Alive

tag: futime


title: MDA-HNS-044

tag: gender

tag: t stage

tag: dm?

tag: ecs

tag: localrecur

tag: osccdeath


title: MDA-HNS-043

tag: tu-vs-nl

tag: treatment*

tag: survivallastfollowup

value: Dead, unknown disease status

tag: vital

value: Dead-unknown


title: S.cerevisiae_H3H39A_mutant

tag: mutant collection

value: Histone H3 & H4 Mutant Collection

tag: genotype/variation


title: S.cerevisiae_H3R26A_mutant


title: MDA-HNS-042

value: cancer

tag: smoking status

tag: oc vs. op

value: Oral cavity

tag: dxdate

tag: nodalrecur

tag: lastfudt

tag: alldeath


title: S.cerevisiae_H3K42A_mutant


title: S.cerevisiae_H3Q120A_mutant


title: S.cerevisiae_H3R40A_mutant


title: MDA-HNS-040

tag: gender

value: NeverSmoker

tag: t stage

tag: cn stage

tag: pn stage

value: S, RT

tag: txdate

tag: futime


title: MDA-HNS-041

tag: tu-vs-nl

value: Current

tag: dm?

tag: ecs

value: N

tag: treatment*

tag: localrecur

tag: osccdeath


title: S.cerevisiae_H3K115A_mutant

tag: mutant collection

tag: genotype/variation


title: S.cerevisiae_H3G44A_mutant


title: S.cerevisiae_H3E94A_mutant


title: S.cerevisiae_H3S86A_mutant


title: S.cerevisiae_H3I89A_mutant


title: MDA-HNS-039

tag: smoking status

tag: oc vs. op

value: Y

value: S, cRT

tag: dxdate

tag: nodalrecur

tag: survivallastfollowup

tag: vital


title: MDA-HNS-038

tag: gender

tag: t stage

tag: cn stage

tag: pn stage

value: Living NED

tag: lastfudt

tag: alldeath


title: MDA-HNS-037

tag: tu-vs-nl

tag: dm?

tag: ecs

tag: treatment*

value: S, IC, S, cRT

tag: txdate

tag: dm date?

value: Dead, due to disease

value: Dead-OSCC

tag: futime


title: S.cerevisiae_H3A91S_mutant

tag: mutant collection

tag: genotype/variation


title: S.cerevisiae_H3G90A_mutant


title: MDA-HNS-036

value: Male

tag: smoking status

value: Former

tag: oc vs. op

value: S

tag: dxdate

tag: localrecur

tag: nodalrecur

tag: survivallastfollowup

value: Dead, other cause

value: Dead-other

tag: osccdeath


title: MDA-HNS-035

value: cancer

tag: gender

tag: t stage

tag: cn stage

tag: pn stage

value: IC, S

tag: locrecurdt

tag: nodrecurdt

tag: vital

tag: lastfudt

tag: alldeath


title: MDA-HNS-034

tag: tu-vs-nl

value: Female

value: NeverSmoker

value: Oral cavity

tag: dm?

tag: ecs

tag: treatment*

tag: txdate

value: Died, due to treatment of disease

tag: futime


title: S.cerevisiae_H4Q93A_mutant

tag: mutant collection

value: Histone H3 & H4 Mutant Collection

tag: genotype/variation


title: S.cerevisiae_H4R95A_mutant


title: MDA-HNS-033

tag: gender

tag: smoking status

tag: oc vs. op

value: N

tag: dxdate

tag: localrecur

tag: nodalrecur

tag: survivallastfollowup

tag: osccdeath


title: S.cerevisiae_H3T80A_mutant


title: ReninCortic_B

city: Edinburgh

first: GUDMAP

last: Developers

address: Crewe Road

country: United Kingdom

institute: IGMM MRC Human Genetics Unit

description:
Amplification protocol
Target Amplified manufacturer/kit: WT-Ovation™ Pico RNA Amplification System (NuGEN)
Target Amplified protocol: NuGEN
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:20741

hyb_protocol: Affymetrix Standard Protocol. The arrays were washed and stained using a Fluidics Station 450 (Affymetrix) utilising the fluidics protocol FS450-0007. Amount labeled  target hybridization to array: 2.5 µg

scan_protocol: Probe arrays were scanned using an Affymetrix GeneChip Scanner 3000 7G and Affymetrix scanning software Genechip Operating Software Version 1.4.

data_processing: Analysis method: Affymetrix Expression Console and GeneSpring 10.

source_name: Adult Renal Cortex, mixed cell types, standard labeled

label_protocol: FL-Ovation cDNA Biotin Module V2 (NuGEN)

extract_protocol: Potter protocol: 'RNA purification'

treatment_protocol:
Pooled sample: No
Dissection method: The cortical region of the kidney was isolated using a scalpel.
Experimental design: Adult Renin-YFP male mice were euthanized by standard carbon dioxide asphyxiation.  The kidneys were isolated and placed in ice-cold PBS.  The medullary region of the kidney was removed and the remaining cortex region was sampled in a limited area to obtain a tissue area that contained various cells.  These were lysed and labeled by standard NuGEN pico technique to be compared to that from JGA cells that were FACS-separated based on Ren1-YFP expression.

tag: gene reported

tag: strain

value: unspecified

tag: Sex

tag: developmental stage

value: Adult

tag: theiler stage

tag: developmental landmark


title: ReninSS_scamp6

description:
Amplification protocol
Target Amplified manufacturer/kit: NA
Target Amplified protocol: SCAMP-Brunskill/Potter
Rounds of amplification: 32
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:20745

source_name: Adult Juxtaglomerular Complex, single cell amplified

label_protocol: SCAMP labeling-Brunskil/Potter

extract_protocol: Individual cells were isolated, placed directly into 5ul of RT-Lysis Buffer and quick frozen in dry-ice

treatment_protocol:
Pooled sample: No
Dissection method: The cells of the juxtaglomerular complex (JGA) were isolated by using Ren1d GFP transgenic mice. The JGA cells were isolated by a combination of mirodissection, collagenase A and trypsin digestion, and filtration. Single JGA cells were isolated by using a fluorescent microscope and pulled glass needles.
Experimental design: Adult Renin-YFP male mice were euthanized by standard carbon dioxide asphyxiation. The kidneys were isolated and placed in ice-cold PBS.  The medullary region of the kidney was removed and the YFP-positive JGA cells directly adjacent to glomeruli were isolated using collagenase A and trypsin treatment. Single JGA cells were isolated using pulled glass needles and lysed in preparation for the single cell amplification technique to be compared to that from mixed non JGA cortical cells identically lysed and labeled.


title: ReninCortic_A

description:
Amplification protocol
Target Amplified manufacturer/kit: WT-Ovation™ Pico RNA Amplification System (NuGEN)
Target Amplified protocol: NuGEN
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:20740


title: ReninSS_scamp5

description:
Amplification protocol
Target Amplified manufacturer/kit: NA
Target Amplified protocol: SCAMP-Brunskill/Potter
Rounds of amplification: 32
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:20744


title: ReninSS_scamp4

description:
Amplification protocol
Target Amplified manufacturer/kit: NA
Target Amplified protocol: SCAMP-Brunskill/Potter
Rounds of amplification: 32
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:20743


title: ReninCortic_C

description:
Amplification protocol
Target Amplified manufacturer/kit: WT-Ovation™ Pico RNA Amplification System (NuGEN)
Target Amplified protocol: NuGEN
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:20742


title: S.cerevisiae_H3K79A_mutant


title: E11.5_mm_16_MoGene_1_0_st_v1

description:
Amplification protocol
Target Amplified manufacturer/kit: NA
Target Amplified protocol: SCAMP-Brunskill/Potter
Rounds of amplification: 32
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:20738

source_name: E11.5 metanephric mesenchyme, single cell amplified

treatment_protocol:
Pooled sample: No
Dissection method: The cells of the metanephric mesenchyme were isolated from Crym-GFP transgenic mice.  E11.5 metaneprhic mesenchyme (MM) was microdissected followed by trituration.  Single MM cells were isolated by using a fluorescent microscope and pulled glass needles.
Experimental design: E11.5 metanephric mesenchyme single cells were isolated from Crym-GFP transgenic mice.  The cells of the metanephric mesenchyme were isolated by microdissection followed by trituration.  Individual cells were isolated using pulled glass needles and subjected to RNA amplification.

value: Unknown


title: E11.5_mm_15_MoGene_1_0_st_v1

description:
Amplification protocol
Target Amplified manufacturer/kit: NA
Target Amplified protocol: SCAMP-Brunskill/Potter
Rounds of amplification: 32
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:20737


title: S.cerevisiae_H4R92A_mutant


title: Renin_scampCortical_A_2

description:
Amplification protocol
Target Amplified manufacturer/kit: NA
Target Amplified protocol: SCAMP-Brunskill/Potter
Rounds of amplification: 32
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:20748

source_name: Adult Renal Cortex, mixed cell types, single cell amplified

treatment_protocol:
Pooled sample: No
Dissection method: The cortical region of the kidney was isolated using a scalpel and total RNA was isolated from the cortical region using standard protocols.
Experimental design: Adult Renin-YFP male mice were euthanized by standard carbon dioxide asphyxiation. The kidneys were isolated and placed in ice-cold PBS.  The medullary region of the kidney was removed and the remaining cortex region was sampled in a limited area to obtain a tissue area that contained various cells. These were lysed and diluted to provide an expression profile via the single cell amplification technique to be compared to that from JGA cells identically labeled.


title: Renin_scampCortical_C

description:
Amplification protocol
Target Amplified manufacturer/kit: NA
Target Amplified protocol: SCAMP-Brunskill/Potter
Rounds of amplification: 32
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:20750


title: E11.5_mm_19_MoGene_1_0_st_v1

description:
Amplification protocol
Target Amplified manufacturer/kit: NA
Target Amplified protocol: SCAMP-Brunskill/Potter
Rounds of amplification: 32
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:20739


title: S.cerevisiae_H4K91A_mutant


title: MDA-HNS-032

tag: tu-vs-nl

tag: t stage

tag: cn stage

tag: pn stage

tag: dm?

tag: ecs

tag: treatment*

value: S, RT

tag: txdate

value: Dead with Disease

tag: vital

value: Dead-OSCC

tag: lastfudt

tag: futime

tag: alldeath


title: S.cerevisiae_H4A89S_mutant

tag: mutant collection

tag: genotype/variation


title: S.cerevisiae_H3R83A_mutant


title: ReninSS_scamp7

description:
Amplification protocol
Target Amplified manufacturer/kit: NA
Target Amplified protocol: SCAMP-Brunskill/Potter
Rounds of amplification: 32
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:20746

tag: gene reported

tag: strain

tag: Sex

value: Male

tag: developmental stage


title: ReninSS_scamp8

description:
Amplification protocol
Target Amplified manufacturer/kit: NA
Target Amplified protocol: SCAMP-Brunskill/Potter
Rounds of amplification: 32
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:20747

tag: theiler stage

tag: developmental landmark


title: S.cerevisiae_H3D81A_mutant


title: S.cerevisiae_H3L82A_mutant


title: Renin_scampCortical_B

description:
Amplification protocol
Target Amplified manufacturer/kit: NA
Target Amplified protocol: SCAMP-Brunskill/Potter
Rounds of amplification: 32
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:20749


title: E11.5_mm_14_MoGene_1_0_st_v1

description:
Amplification protocol
Target Amplified manufacturer/kit: NA
Target Amplified protocol: SCAMP-Brunskill/Potter
Rounds of amplification: 32
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:20736


title: MDA-HNS-031

description:
*  Treatment Modality:
s= surgery
IC=induction chemotherapy
R=radiation therapy
cRT=chemoradiation

tag: tu-vs-nl

tag: gender

tag: smoking status

tag: oc vs. op

tag: t stage

tag: cn stage

tag: pn stage

tag: dxdate

tag: localrecur

tag: nodalrecur

tag: survivallastfollowup

tag: osccdeath


title: MDA-HNS-030

value: Current

tag: dm?

tag: ecs

value: Y

tag: treatment*

tag: txdate

value: Dead, other cause

tag: vital

tag: lastfudt

tag: futime

tag: alldeath


title: MDA-HNS-026

tag: tu-vs-nl

value: cancer

tag: gender

tag: smoking status

value: Former

tag: oc vs. op

value: cRT, surgery

value: Living NED

value: Alive


title: MDA-HNS-029

value: Oral cavity

tag: t stage

tag: cn stage

tag: pn stage

tag: dxdate


title: S.cerevisiae_H4V86A_mutant

description: log2 ratio (mut / WT) data after VSN normalization and removing batch effect using Combat provided as supplementary file.

tag: mutant collection

value: Histone H3 & H4 Mutant Collection

tag: genotype/variation


title: MDA-HNS-027

tag: dm?

tag: ecs

tag: localrecur

tag: nodalrecur

tag: nodrecurdt

tag: survivallastfollowup

tag: osccdeath


title: MDA-HNS-025

tag: tu-vs-nl

value: N

tag: treatment*

value: S

tag: txdate

tag: vital

tag: lastfudt

tag: futime

tag: alldeath


title: MDA-HNS-024

tag: gender

tag: smoking status

tag: oc vs. op

tag: t stage

tag: cn stage

tag: pn stage

value: S, cRT

tag: dxdate

value: Dead, unknown disease status

value: Dead-unknown


title: Liver set 3

city: Norfolk

first: yumi

last: imai

state: VA

address: 799W Olney Road, LH 2156

institute: Eastern Virginia Medical School

description:
572_3
Biological replicate 3 of 4. Liver from control oligo- and Plin2-ASO-treated mice.

hyb_protocol: The Cy3- and Cy5-coupled samples were combined and purified using the MinElute PCR Purification Kit (Qiagen, CA). After purification, samples were combined with hybridization buffer, denatured, applied to the array and hybridized overnight at 65 °C.

scan_protocol: Agilent G2565BA Microarray Scanner was used to scan the microarray slides.

data_processing: Images were analyzed with GenePix 5.0 software (Axon Instruments) setting background as zero and using LOWESS for data normalization.

source_name: Cont liver 4

label_protocol: Approximately 50 ng of total RNA was amplified using the Ovation™ Aminoallyl RNA Amplification and Labeling System (Nugen Inc, CA). Amplified cDNA was purified using the QIAquick PCR Purification Kit (Qiagen, CA) and then eluted in coupling buffer (0.1M Sodium Bicarbonate, pH 9). 2 μg of each cDNA was coupled with Cy3 or Cy5 fluorescent label using Cy™Dye from Amersham Pharmacia Biotech Ltd, NJ).

growth_protocol: Male C57BL/6 mice were fed on high-fat diet with ad libitum food and water access.

extract_protocol: Total RNA was extracted from liver using Trizol (Invitrogen).

treatment_protocol: Mice were treated twice a week with an intraperitoneal injection of Plin2 ASO or a control ASO, 25 mg/kg body weight, for 4 weeks.

tag: strain/background

tag: tissue

value: liver

value: male

tag: diet

value: high fat

tag: oligo treatment

value: scrambled control

source_name: Plin2-ASO liver 9


title: Adult_Captopril_5

description:
Amplification protocol
Target Amplified manufacturer/kit: OvationPico WTA System v2 (Cat.# 3302) & WT-Ovation™ Exon Module (Cat.# 2000).
Target Amplified protocol: NuGEN
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:20735

hyb_protocol: Affymetrix Standard Protocol. The arrays were washed and stained using a Fluidics Station 450 (Affymetrix) utilising the fluidics protocol FS450-0007. Amount labeled  target hybridization to array: 2.5µg

source_name: Adult juxtaglomerular complex (captopril treated animals)

label_protocol: EncoreTM Biotin Module (Cat.# 4200)

treatment_protocol:
Pooled sample: No
Dissection method: Ren1c-YFP transgenic mice were treated with Captopril.  The cells of the Juxtaglomerular apparatus were isolated using a combination of collagenase A digestion and sieving followed by FACS.
Experimental design: Adult Ren1c-YFP male mice treated with captopril, which was provided in the drinking water at a concentration of 0.5mg/ml.  In addition, mice were given low-salt chow.  Mice were treated for two weeks before they were euthanized by standard carbon dioxide asphyxiation.  The kidneys were isolated and placed in ice-cold PBS.  The medullary region of the kidney was removed and the remaining cortex region was minced with a razor blade and incubated in the presence of 500 µl of 0.5% Collagenase A for 15 minutes at 37°C.  After incubation, the kidneys were further dissociated by titurating in the presence of 600 µl of ice-cold 10% FBS/PBS and then pelleted at 5000 rpm, 4°C for 5 minutes.  The cells were resuspended in 200 µl of ice-cold 2% FBS/PBS and filtered using a 70 micron mesh. The YFP positive cells were isolated using FACS.

tag: gene reported

tag: strain

value: unspecified

tag: Sex

value: Male

tag: developmental stage

value: Adult

tag: theiler stage

tag: developmental landmark


title: S.cerevisiae_H4D85A_mutant

tag: mutant collection

tag: genotype/variation


title: S.cerevisiae_H4T80A_mutant


title: S.cerevisiae_H4V81A_mutant


title: Liver set 4

description:
572_4
Biological replicate 4 of 4. Liver from control oligo- and Plin2-ASO-treated mice.

source_name: Cont liver 5

tag: gender

source_name: Plin2-ASO liver 10


title: Adult_Captopril_4

description:
Amplification protocol
Target Amplified manufacturer/kit: OvationPico WTA System v2 (Cat.# 3302) & WT-Ovation™ Exon Module (Cat.# 2000).
Target Amplified protocol: NuGEN
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:20734


title: Adult_Captopril_2

description:
Amplification protocol
Target Amplified manufacturer/kit: OvationPico WTA System v2 (Cat.# 3302) & WT-Ovation™ Exon Module (Cat.# 2000).
Target Amplified protocol: NuGEN
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:20733


title: S.cerevisiae_H4K79A_mutant


title: S.cerevisiae_H4V70A_mutant


title: Bcl6 KO 2 sample B

city: Indianapolis

first: Alexander

last: Dent

state: IN

address: 950 W. Walnut St. R2 302, Walther Oncology Center

institute: Alexander Dent

hyb_protocol: Labeled DNA were hybridized for 17 hr at 45C on Mouse Gene 1.0 St Genechips. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Scanned using Affymetrix GeneChip® Scanner 3000 7G

data_processing: The data were analyzed with Partek Genomics Suite to produce RMA

source_name: Treg cell

label_protocol: Biotinylated DNA were prepared according to the Affymetrix standard WT protocol using 100ng of total RNA (not pretreated with Ribominus (Invitrogen))

extract_protocol: standard RNA isolation method-- Qiagen Rneasy

treatment_protocol: Tregs were stimulated with anti-CD3 nd anti-CD28 for 16 hours prior to RNA extraction

tag: genotype

value: Bcl6 knock-out

tag: cell type

value: FoxP3+ Treg


title: WT 2 sample A

value: wild type


title: TimKO rep3

city: Beijing

first: Gencheng

last: HAN

address: 27 Taiping Road, Haidian District

department: Department of Immunology

institute: Beijing Institute of Basic Medical Sciences

description: This sample is of Tim-3-siRNA transfected RAW264.7 cells. It is the third of three Tim-3 knockdown biological replicates used in this experiment, each from separate cultures.

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.5 (Roche NimbleGen, Inc.). All gene level files were imported into Agilent GeneSpring GX software(version 11.5.1) for further analysis. Genes that at least 3 out of 6 samples have values greater than or equal to lower cut-off: 100.0 were chosen for differentially expressed gene screening.

source_name: Tim-3 knockdown

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Tim-3 knockdown and control RAW264.7 cells were maintained in DMEM supplemented with 10% heat-inactivated FBS, 100 units/ml of penicillin, and 100 units/ml of streptomycin in a humidified 5% CO2 atmosphere at 37 °C.

extract_protocol: Total RNA from each sample was quantified by the NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

treatment_protocol: RAW264.7 cells were transfected with pRNAi-U6H1vector containing Tim-3 siRNA or control siRNA. The siRNA duplex giving maximal knockdown was selected. Raw264.7 cell clones stably express Tim-3 SiRNA were selected after continued culture with selecting drugs (G418, Sigma-Aldrich), and were analyzed for Tim-3 expression.

tag: treatment

value: Tim-3 knockdown

tag: cell line


title: NC rep3

description: This sample is of control siRNA transfected RAW264.7 cells. It is the third of three negative control (NC) biological replicates used in this experiment, each from separate cultures.

source_name: control

value: control


title: Liver set 1

description:
572_1
Biological replicate 1 of 4. Liver from control oligo- and Plin2-ASO-treated mice.

source_name: Cont liver 1

tag: strain/background

source_name: Plin2-ASO liver 6


title: Liver set 2

description:
572_2
Biological replicate 2 of 4. Liver from control oligo- and Plin2-ASO-treated mice.

source_name: Cont liver 2

tag: tissue

source_name: Plin2-ASO liver 7


title: WT 2 sample B


title: S.cerevisiae_H4H75A_mutant

value: Histone H3 & H4 Mutant Collection


title: NC rep1

description: This sample is of control siRNA transfected RAW264.7 cells. It is the first of three negative control (NC) biological replicates used in this experiment, each from separate cultures.


title: S.cerevisiae_H3L100A_mutant


title: S.cerevisiae_H4L62A_mutant


title: NC rep2

description: This sample is of control siRNA transfected RAW264.7 cells. It is the second of three negative control (NC) biological replicates used in this experiment, each from separate cultures.


title: S.cerevisiae_H4S60A_mutant


title: WT 1 sample B


title: WT 1 sample A


title: Bcl6 KO 2 sample A


title: TimKO rep1

description: This sample is of Tim-3-siRNA transfected RAW264.7 cells. It is the first of three Tim-3 knockdown biological replicates used in this experiment, each from separate cultures.


title: S.cerevisiae_H4K59A_mutant


title: S.cerevisiae_H4R55A_mutant


title: Bcl6 KO 1 sample B


title: Bcl6 KO 1 sample A


title: cellline3_rep1

hyb_protocol: Labeled cRNA were hybridized to arrays according to Agilent's manufacturer's protocol

data_processing: Probes were filtered to eliminate those with either a signal intensity below 350 or flagged by Feature Extractor for saturation or no signal above background in any hybridization. Replicated signals from identical sequence-probes were averaged. For each array, the ratio of Cy5 to Cy3 (red to green) was log2 transformed and zero-centered.

source_name: miR-29b transfected cell line 3

label_protocol: Total RNA extracts were cRNA labeled using the Agilent Low RNA Input Fluorescent Labeling Kit according to the manufacturer's protocol

extract_protocol: Total RNA isolated from fibroblasts 48 hours post-transfection using mirVana total RNA isolation kit and procedure.

treatment_protocol: Asynchronously proliferating fibroblasts were reverse transfected with either miR-29b or a microRNA negative control Pre-miR from Ambion.

value: Fibroblast

source_name: Negative control transfected cell line 3


title: cellline2_rep1

source_name: miR-29b transfected cell line 2

source_name: Negative control transfected cell line 2


title: 786_O_SUZ12sh2_2

city: Helsinki

first: Sakari

last: Vanharanta

address: Haartmaninkatu 8

department: Translational Cancer Medicine Program

country: Finland

institute: University of Helsinki

description: 786-O cells transduced with SUZ12sh2

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: GCRMA as implemented in the R-package gcrma using the default settings and the custom Brain Array CDF-file hs133phsentrezgcdf version 10 (http://brainarray.mbni.med.umich.edu/).

label_protocol: Standard Affymetrix protocol

growth_protocol: Standard tissue culture conditions.

extract_protocol: PrepEase RNA spin kit (USB)

value: 786-O renal cell carcinoma cell line

tag: tranduced with


title: 786_O_SUZ12sh2_1

description: 786-O cells transduced with SUZ12sh2


title: cellline1_rep2

source_name: miR-29b transfected cell line 1

source_name: Negative control transfected cell line 1


title: 786_O_SUZ12sh1_1

description: 786-O cells transduced with SUZ12sh1


title: 786_O_SUZ12sh1_2

description: 786-O cells transduced with SUZ12sh1