title: LCL, carrier mother, GM22011, low glucose

value: carrier mother


title: NOD2-L1007fsinsC_6h_MDP_biological replicate 3

status: Public on Jan 01 2013

type: RNA

city: Kiel

first: Susanne

last: Billmann

address: Schittenhelmstraße 12

country: Germany

institute: Institute of Clinical Molecular Biology Christian-Albrechts-Universität Kiel

description: RNA from cell culture with different NOD2 genotypes

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 Array in a Affymetrix Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner  3000.

data_processing: The data were analyzed with Gene Chip Operating Software 1.1. Represents the relative level of expression of a transcript. The median of the data is identified and each datum is weighted by how far it is from the median using One-step Tukey's Biweight Algorithm. A weighted mean is then calculated.

label: biotin

molecule: total RNA

organism: Homo sapiens

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: NOD2wt and NOD2-L1007fsinsC expressing cells were generated with the FLP-IN system (Invitrogen, Carlsbad, CA, USA). HEK 293 cells containing the recombination site were purchased from Invitrogen. Wildtype and mutated NOD2 were inserted to the genomic recombination site by FLP-recombinase enzyme. A control cell line was generated by transfecting an empty mock vector. All stable cell lines were selected for Hygromycin B resistance and consequently cultured in MEM + 10 % FCS + 1% Penicillin/Streptomycin + 50 μg/ml Hygromycin B (Invitrogen).

extract_protocol: RNA was isolated using the RNeasy Kit (Qiagen)

treatment_protocol: FLP-IN HEK 293-NOD2wt, HEK 293-NOD2L1007fsinsC and HEK 293mock cells were cultivated in medium without FCS for 7 h before stimulation with 10 µg/ml MDP for 0h, 2h and 6h. Cells were harvested simultaneously.

tag: cell line

tag: genotype

value: NOD2 L1007fsinsC

tag: stimulation

value: Muramyl-dipeptide (MDP) 10 µg/ml

tag: time point

value: 6 h


title: 288h_lwp_rep2

city: Dresden

first: Dunja

last: Knapp

address: Fetscherstraße 105

institute: DFG-Center for Regenerative Therapies Dresden

description: Gene expression in wound-healing limb, 288h after lateral injury

scan_protocol: Slides were scanned immediately after washing on the Agilent Technologies Scanner (G2505C US45102998) using one color scan setting for 1x44k array slides, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software from Agilent using default parameters (protocol GE1-v5_95_Feb07 and Grid: 019788_D_F_20080327 ) to obtain background subtracted and spatially detrended Processed Signal intensities.  Thus obtained values are termed raw [attached to the Series record as a supplementary file]. For expression analysis arrays have been quantile normalized using GeneSpring 10 and displayed as log2 values.

organism: Ambystoma mexicanum

source_name: wound-healing limb, 288h after lateral injury, replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.3 ug total RNA using the Quick Amp Labeling Kit (Agilent) according to the manufacturer's protocol.

extract_protocol: Total RNA was purified using Qiagen RNeasy midi kit.  RNA was then DNase-treated and then repurified using Qiagen RNeasy mini kit. RNA quality was confirmed using Agilent Bioanalyzer-  The RIN values were at least  9.4.

treatment_protocol: For both, amputation and lateral injury samples the first cut was done at ¼ stylopod length behind the wrist using animals at the size  40-50 mm from nose to cloaca. In amputated stumps protruding bones were trimmed (≈ 0.5 mm ).  For regenerating samples, for each timepoint all tissue between 2mm behind the amputation plane and the tip of the blastema was collected. For lateral wound samples an incision was made using scalpel through the posterior half of the lower arm such that ulna was cut through but radius was not. No tissue was removed. At the appropriate timepoint all tissue between 2mm proximal to the cut plane and 0.5 mm distal to the cut plane was collected. Collected tissue was frozen immediately in liquid nitrogen, for each sample tissue from four limbs was pooled together and kept at -80°C until further processing.   Limb bud samples were collected at mid-bud and notch stage from 1.5-1.7 cm long animals 6 and 12 days after hatching, respectively. 40-50 buds were collected per sample.

tag: time after injury (hours)

tag: type of injury

value: lateral wound

tag: tissue type

value: limb

tag: biological replicate


title: seborrheic keratosis from patient D

city: Seoul

first: Eun Young

last: Seo

address: Yongon-dong 28, Chongno-gu

department: Department of Dermatology

country: South Korea

institute: Seoul National University College of Medicine

hyb_protocol: Affymetrix protocol

scan_protocol: GeneChips were scanned using Affymetrix GeneChip® Scanner 3000 7G.

data_processing: The data were analyzed with Robust Multi-array Analysis (RMA) as normalization method using Affymetrix Expression Console 1.1 software. The trimmed mean intensity of each array was arbitrarily set to 100.

source_name: control skin

label_protocol: Affymetrix protocol

extract_protocol: Full thickness excisional skin biopsy was performed from skin with seborrheic keratosis and uninvolved skin. RNA was extracted using Trizol (Invitrogen, Carlsbad, CA) according to the manufacturer's instructions.

tag: tissue

value: skin

tag: patient identification

value: D

tag: condition

value: control skin


title: uninvolved skin from patient B

source_name: skin with seborrheic keratosis

value: B

value: seborrheic keratosis


title: LCl, PA 9 yo female, GM22018, low glucose

city: Washington

first: Kimberly

last: Chapman

state: DC

address: 111 Michigan Ave NW

department: Genetics and Metabolism

country: USA

institute: Children's National Medical Center

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Gene 1.0 ST array

scan_protocol: GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and Primary Component anylsis, Partek

source_name: LCL, low glucose

label_protocol: Biotinylated cRNA were created using GeneChip Whole transcripts sense target Labeling assay (Affymetrix) according to manufacturer's instructions

growth_protocol: Cells maintained in RPMI 1640 with 15% FBS, 2 mmol/L L-glutamine, 100 units/mL penicukkub-streptomycin

extract_protocol: Cells lysed using Quiashredder and total RNA isolated using Rneasy Purification kits

treatment_protocol: Cells switch to low glucose (RPMI 1640 with no glucose) +15% FBS +2 mM glutamine or RPMI 1640 +15%FBS +2 mM glutamine  24 hours prior to harvest and extraction

tag: gender

value: female

tag: age

value: 9  y

tag: disease state

value: Propionic acidemia

tag: treatment

value: low glucose


title: 168h_lwp_rep2

description: Gene expression in wound-healing limb, 168h after lateral injury

hyb_protocol: according to the manufacturer's protocol

source_name: wound-healing limb, 168h after lateral injury, replicate 2


title: LCL, Sibling, GM22020, normal

source_name: LCL, normal glucose

value: Sibling

value: normal glucose


title: seborrheic keratosis from patient B


title: 120h_lwp_rep2

description: Gene expression in wound-healing limb, 120h after lateral injury

source_name: wound-healing limb, 120h after lateral injury, replicate 2


title: MOCK_6h_MDP_biological replicate 1

value: control mock


title: NOD2-L1007fsinsC_6h_MDP_biological replicate 2

value: NOD2 L1007fsinsC


title: seborrheic keratosis from patient A

value: A


title: LCL, carrier mother, GM22011, normal

value: carrier mother


title: NOD2wt_6h_MDP_biological replicate 3

value: NOD2 wt

value: Muramyl-dipeptide (MDP) 10 µg/ml

value: 6 h


title: 52h_lwp_rep2

description: Gene expression in wound-healing limb, 52h after lateral injury

source_name: wound-healing limb, 52h after lateral injury, replicate 2

value: lateral wound

value: limb


title: NOD2-L1007fsinsC_6h_MDP_biological replicate 1


title: 72h_lwp_rep2

description: Gene expression in wound-healing limb, 72h after lateral injury

source_name: wound-healing limb, 72h after lateral injury, replicate 2


title: 36h_lwp_rep2

description: Gene expression in wound-healing limb, 36h after lateral injury

source_name: wound-healing limb, 36h after lateral injury, replicate 2


title: NOD2wt_6h_MDP_biological replicate 2


title: LCL, PA 7yo male, GM22010, low glucose

value: male

value: 7 y


title: 24h_lwp_rep2

description: Gene expression in wound-healing limb, 24h after lateral injury

source_name: wound-healing limb, 24h after lateral injury, replicate 2


title: MOCK_6h_MDP_biological replicate 3


title: NOD2wt_6h_MDP_biological replicate 1


title: MOCK_2h_MDP_biological replicate 3

value: 2 h


title: LCL, carrer father, GM22022,low glucose

value: carrer father


title: LCL, carrer father, GM22022, normal


title: LCL, PA 7yo male, GM22010, normal

value: Propionic acidemia


title: MOCK_2h_MDP_biological replicate 2


title: 9h_lwp_rep2

description: Gene expression in wound-healing limb, 9h after lateral injury

source_name: wound-healing limb, 9h after lateral injury, replicate 2


title: LCL, carrier father, GM22012, normal

value: carrier father


title: LCL, control, GM10858, low glucose

value: control

value: low glucose


title: NOD2-L1007fsinsC_2h_MDP_biological replicate 3


title: 3h_lwp_rep2

description: Gene expression in wound-healing limb, 3h after lateral injury

source_name: wound-healing limb, 3h after lateral injury, replicate 2


title: LCL, control GM12042, normal

value: normal glucose


title: 288h_amp_rep2

description: Gene expression in regenerating limb, 288h after amputation

source_name: regenerating limb, 288h after amputation, replicate 2

value: amputation


title: LCL, control GM12042, low glucose


title: LCL, carrier father, GM22012, low glucose


title: 72h_amp_rep2

description: Gene expression in regenerating limb, 72h after amputation

source_name: regenerating limb, 72h after amputation, replicate 2


title: LCL, control, GM10858, normal


title: 12h_lwp_rep2

description: Gene expression in wound-healing limb, 12h after lateral injury

source_name: wound-healing limb, 12h after lateral injury, replicate 2


title: 528h_amp_rep2

description: Gene expression in regenerating limb, 524h after amputation

source_name: regenerating limb, 524h after amputation, replicate 2


title: NOD2-L1007fsinsC_2h_MDP_biological replicate 2

value: NOD2 L1007fsinsC


title: NOD2wt_2h_MDP_biological replicate 2


title: MOCK_2h_MDP_biological replicate 1

value: control mock


title: 120h_amp_rep2

description: Gene expression in regenerating limb, 120h after amputation

source_name: regenerating limb, 120h after amputation, replicate 2


title: 52h_amp_rep2

description: Gene expression in regenerating limb, 52h after amputation

source_name: regenerating limb, 52h after amputation, replicate 2


title: NOD2wt_2h_MDP_biological replicate 3

value: NOD2 wt


title: NOD2wt_2h_MDP_biological replicate 1

value: Muramyl-dipeptide (MDP) 10 µg/ml


title: MOCK_0h_MDP_biological replicate 3

value: contol mock

value: 0 h


title: 168h_amp_rep2

description: Gene expression in regenerating limb, 168h after amputation

source_name: regenerating limb, 168h after amputation, replicate 2

value: limb


title: NOD2-L1007fsinsC_2h_MDP_biological replicate 1

description: RNA from cell culture with different NOD2 genotypes


title: 6h_lwp_rep2

description: Gene expression in wound-healing limb, 6h after lateral injury

source_name: wound-healing limb, 6h after lateral injury, replicate 2

value: lateral wound


title: MOCK_0h_MDP_biological replicate 2


title: LCL, control, GM10859, normal


title: LCL, control, GM10859, low glucose

source_name: LCL, low glucose


title: LCL, PA female 12y, GM22112,low glucose

value: female


title: NOD2-L1007fsinsC_0h_MDP_biological replicate 3


title: MOCK_0h_MDP_biological replicate 1


title: NOD2-L1007fsinsC_0h_MDP_biological replicate 2


title: 36h_amp_rep2

description: Gene expression in regenerating limb, 36h after amputation

source_name: regenerating limb, 36h after amputation, replicate 2


title: 9h_amp_rep2

description: Gene expression in regenerating limb, 9h after amputation

source_name: regenerating limb, 9h after amputation, replicate 2


title: LCL, carrier mother, GM22111, glucose

value: carrier mother


title: LCL, Carrier father, GM22110, normal

source_name: LCL, normal glucose

value: male

value: Carrier father


title: NOD2wt_0h_MDP_biological replicate 3


title: LCL, carrier mother, GM22111, normal


title: NOD2-L1007fsinsC_0h_MDP_biological replicate 1


title: LCL, PA female 12 y, GM22112, normal

value: Propionic acidemia


title: LCL, carrier father, GM22017, low glucose

value: carrier father


title: limb.bud_rep2

description: Gene expression in the developing limb bud

source_name: developing limb bud, replicate 2

value: limb bud


title: SID_59_hPL_AT_D9_Utre

city: Nijmegen

first: Ruurd

last: Torensma

address: GeertGrooteplein 28

department: Tumorimmunology

country: Netherlands

institute: Radboud University Nijmegen Medical Centre

description: Adipose tissue cells from donor D9 cultured with Human platelet lysate in Utrecht, and hybridized in batch B2

hyb_protocol: 17 hours at 45 degrees in Affymetrix hybridization oven at 60 rpm,washing and staining in  Fluidics station 450 using stain cocktails: SAPE and antibody solution, (protocol FS450_0001)

scan_protocol: GeneChip scanner 3000 7G

data_processing:
Quantile normalization, with RMA, GC correction and mean probeset summarization, log2 values from Partek Genomic Suite 6.4
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file:HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: Adipose tissue cells from donor D9

label_protocol: GeneChip WT Terminal Labeling Kit

growth_protocol: Cells were cultured as described in:Torensma et al., Stem Cells & Development 2012 in press

extract_protocol: Rneasy column purification

treatment_protocol: Cells were treated as described in: Torensma et al., Stem Cells & Development 2012 in press

tag: culture methodology

value: Human platelet lysate

tag: cell source

value: Adipose tissue

tag: donor

tag: culture location

value: Utrecht

tag: hybridization batch


title: mat_rep2

description: Gene expression in the mature limb

source_name: mature limb, replicate 2


title: NOD2wt_0h_MDP_biological replicate 1

tag: cell line

tag: genotype

tag: stimulation

tag: time point


title: LCL, Carrier father, GM22110, low glucose

value: low glucose


title: LCL, carrier father, GM22017, normal

value: normal glucose


title: 24h_amp_rep2

description: Gene expression in regenerating limb, 24h after amputation

source_name: regenerating limb, 24h after amputation, replicate 2

tag: time after injury (hours)

tag: type of injury

value: amputation

tag: tissue type

tag: biological replicate


title: NOD2wt_0h_MDP_biological replicate 2

value: NOD2 wt

value: Muramyl-dipeptide (MDP) 10 µg/ml


title: 288h_lwp_rep1

description: Gene expression in wound-healing limb, 288h after lateral injury

source_name: wound-healing limb, 288h after lateral injury, replicate 1

value: limb


title: 12h_amp_rep2

description: Gene expression in regenerating limb, 12h after amputation

source_name: regenerating limb, 12h after amputation, replicate 2


title: 3h_amp_rep2

description: Gene expression in regenerating limb, 3h after amputation

source_name: regenerating limb, 3h after amputation, replicate 2


title: SID_60_hPL_AT_D10_Utre

description: Adipose tissue cells from donor D10 cultured with Human platelet lysate in Utrecht, and hybridized in batch B3

source_name: Adipose tissue cells from donor D10


title: LCL, carrier mother, GM22016, low glucose

tag: gender


title: SID_58_hPL_AT_D8_Utre

description: Adipose tissue cells from donor D8 cultured with Human platelet lysate in Utrecht, and hybridized in batch B1

source_name: Adipose tissue cells from donor D8


title: 168h_lwp_rep1

description: Gene expression in wound-healing limb, 168h after lateral injury

source_name: wound-healing limb, 168h after lateral injury, replicate 1

value: lateral wound


title: LCL, carrier mother, GM22016, normal

value: female


title: 6h_amp_rep2

description: Gene expression in regenerating limb, 6h after amputation

source_name: regenerating limb, 6h after amputation, replicate 2


title: 528h_lwp_rep1

description: Gene expression in wound-healing limb, 524h after lateral injury

source_name: wound-healing limb, 524h after lateral injury, replicate 1


title: SID_57_hPL_AT_D7_Utre

description: Adipose tissue cells from donor D7 cultured with Human platelet lysate in Utrecht, and hybridized in batch B3

source_name: Adipose tissue cells from donor D7


title: SID_56_hPL_AT_D6_Utre

description: Adipose tissue cells from donor D6 cultured with Human platelet lysate in Utrecht, and hybridized in batch B2

source_name: Adipose tissue cells from donor D6


title: 120h_lwp_rep1

description: Gene expression in wound-healing limb, 120h after lateral injury

source_name: wound-healing limb, 120h after lateral injury, replicate 1


title: LCL, PA 2 y female, GM22208, normal

tag: age

value: 2 y


title: LCL, PA 30 y female, GM22013, low glucose

tag: disease state


title: 72h_lwp_rep1

description: Gene expression in wound-healing limb, 72h after lateral injury

source_name: wound-healing limb, 72h after lateral injury, replicate 1


title: 52h_lwp_rep1

description: Gene expression in wound-healing limb, 52h after lateral injury

source_name: wound-healing limb, 52h after lateral injury, replicate 1


title: SID_54_hPL_BM_D4_Utre

description: Bone marrow cells from donor D4 cultured with Human platelet lysate in Utrecht, and hybridized in batch B3

source_name: Bone marrow cells from donor D4

value: Bone marrow


title: LCL, PA 2 y female, GM22208, low glucose

source_name: LCL, low glucose

tag: treatment


title: SID_51_hPL_BM_D1_Utre

description: Bone marrow cells from donor D1 cultured with Human platelet lysate in Utrecht, and hybridized in batch B3

source_name: Bone marrow cells from donor D1

tag: culture methodology


title: 24h_lwp_rep1

description: Gene expression in wound-healing limb, 24h after lateral injury

source_name: wound-healing limb, 24h after lateral injury, replicate 1


title: 36h_lwp_rep1

description: Gene expression in wound-healing limb, 36h after lateral injury

source_name: wound-healing limb, 36h after lateral injury, replicate 1


title: LCL, PA 30 y female, GM22013, normal


title: SID_55_hPL_BM_D5_Utre

description: Bone marrow cells from donor D5 cultured with Human platelet lysate in Utrecht, and hybridized in batch B1

source_name: Bone marrow cells from donor D5

tag: cell source


title: SID_52_hPL_BM_D2_Utre

description: Bone marrow cells from donor D2 cultured with Human platelet lysate in Utrecht, and hybridized in batch B1

source_name: Bone marrow cells from donor D2

tag: donor


title: LCL, control GM11991, low glucose

value: control


title: LCL, PA 11 m female,  GM22366, normal

source_name: LCL, normal glucose

value: 11 mo

value: Propionic acidemia


title: LCL, control GM11991, normal


title: SID_53_hPL_BM_D3_Utre

description: Bone marrow cells from donor D3 cultured with Human platelet lysate in Utrecht, and hybridized in batch B2

source_name: Bone marrow cells from donor D3

tag: culture location


title: 12h_lwp_rep1

description: Gene expression in wound-healing limb, 12h after lateral injury

source_name: wound-healing limb, 12h after lateral injury, replicate 1


title: 9h_lwp_rep1

description: Gene expression in wound-healing limb, 9h after lateral injury

source_name: wound-healing limb, 9h after lateral injury, replicate 1


title: LCL, carrier mother, GM22367, low glucose

value: carrier mother


title: 3h_lwp_rep1

description: Gene expression in wound-healing limb, 3h after lateral injury

source_name: wound-healing limb, 3h after lateral injury, replicate 1


title: 6h_lwp_rep1

description: Gene expression in wound-healing limb, 6h after lateral injury

source_name: wound-healing limb, 6h after lateral injury, replicate 1


title: AML [5363_27nov08]

city: Rotterdam

first: Martin

middle: van

last: Vliet

address: Lichtenauerlaan 40

department: Bioinformatics

institute: SkylineDx

description: Not Applicable

hyb_protocol: As described in the AMLprofiler IFU (instructions for use), Hybridized for 17 hours, 45C at 60 rpm in Affymetrix Hybridization oven

scan_protocol: As described in the AMLprofiler IFU (instructions for use) on an Affymetrix GeneChip System 3000Dx v.2

data_processing: DM algorithm implemented in the Affymetrix Power Tools (APT 1.10.2).

label: Biotin

source_name: AML

label_protocol: We used 10 µg of total RNA to prepare antisense biotinylated RNA. Single-stranded complementary DNA (cDNA) and double-stranded cDNA were synthesized according to the manufacturer’s protocol (Invitrogen Life Technologies) with the use of the T7-(deoxythymidine)24-primer (Genset). In vitro transcription was performed with biotin-11-cytidine triphosphate and biotin-16-uridine triphosphate (Perkin–Elmer) and the MEGAScript T7 labeling kit (Ambion). Double-stranded cDNA and complementary RNA (cRNA) were purified and fragmented with the GeneChip Sample Cleanup Module (Affymetrix).

growth_protocol: Not Applicable

extract_protocol: After thawing, cells were washed once with Hanks’balanced-salt solution. High-quality total RNA was extracted by lysis with guanidinium thiocyanate followed by cesium chloride–gradient purification. RNA levels, quality, and purity were assessed with the use of the RNA 6000 Nano assay on the Agilent 2100 Bioanalyzer (Agilent). None of the samples showed RNA degradation (ratio of 28S ribosomal RNA to 18S ribosomal RNA of at least 2) or contamination by DNA.

treatment_protocol: Not Applicable

tag: cohort

value: Training

tag: npm1 status

value: NPM1 A


title: SID_49_FCD_AT_D9_Utre

description: Adipose tissue cells from donor D9 cultured with Fetal calf serum in Utrecht, and hybridized in batch B1

source_name: Adipose tissue cells from donor D9

value: Fetal calf serum

value: Adipose tissue

value: Utrecht

tag: hybridization batch


title: SID_50_FCD_AT_D10_Utre

description: Adipose tissue cells from donor D10 cultured with Fetal calf serum in Utrecht, and hybridized in batch B2

source_name: Adipose tissue cells from donor D10


title: AML [5364_27nov08]

description: Not Applicable

value: NPM1 wt


title: LCL, PA 11 mo female,  GM22366, low glucose

value: low glucose

tag: cell line


title: SID_48_FCD_AT_D8_Utre

description: Adipose tissue cells from donor D8 cultured with Fetal calf serum in Utrecht, and hybridized in batch B3

source_name: Adipose tissue cells from donor D8


title: AML [5362_27nov08]

description: Not Applicable


title: LCL, carrier mother, GM22367, normal

value: normal glucose


title: 528h_amp_rep1

description: Gene expression in regenerating limb, 524h after amputation

source_name: regenerating limb, 524h after amputation, replicate 1

value: amputation

value: limb


title: AML [5361_27nov08]

description: Not Applicable


title: AML [5360_27nov08]

description: Not Applicable


title: SID_47_FCD_AT_D7_Utre

description: Adipose tissue cells from donor D7 cultured with Fetal calf serum in Utrecht, and hybridized in batch B2

source_name: Adipose tissue cells from donor D7


title: LCL, control GM07029, normal

source_name: LCL, low glucose


title: LCL, control GM07029, low glucose


title: 288h_amp_rep1

description: Gene expression in regenerating limb, 288h after amputation

source_name: regenerating limb, 288h after amputation, replicate 1


title: 168h_amp_rep1

description: Gene expression in regenerating limb, 168h after amputation

source_name: regenerating limb, 168h after amputation, replicate 1


title: AML [5359_21oct08]

description: Not Applicable


title: SID_45_FCD_BM_D5_Utre

description: Bone marrow cells from donor D5 cultured with Fetal calf serum in Utrecht, and hybridized in batch B3

source_name: Bone marrow cells from donor D5


title: AML [5357_21oct08]

description: Not Applicable


title: AML [5358_27nov08]

description: Not Applicable


title: SID_46_FCD_AT_D6_Utre

description: Adipose tissue cells from donor D6 cultured with Fetal calf serum in Utrecht, and hybridized in batch B1

source_name: Adipose tissue cells from donor D6


title: LCL, control, GM06997, low glucose


title: LCL, control, GM06997, normal

source_name: LCL, normal glucose


title: SID_44_FCD_BM_D4_Utre

description: Bone marrow cells from donor D4 cultured with Fetal calf serum in Utrecht, and hybridized in batch B2

source_name: Bone marrow cells from donor D4


title: LCL, control GM12153, low


title: 72h_amp_rep1

description: Gene expression in regenerating limb, 72h after amputation

source_name: regenerating limb, 72h after amputation, replicate 1


title: AML [5356_27nov08]

description: Not Applicable


title: SID_42_FCD_BM_D2_Utre

description: Bone marrow cells from donor D2 cultured with Fetal calf serum in Utrecht, and hybridized in batch B3

source_name: Bone marrow cells from donor D2


title: SID_43_FCD_BM_D3_Utre

description: Bone marrow cells from donor D3 cultured with Fetal calf serum in Utrecht, and hybridized in batch B1

source_name: Bone marrow cells from donor D3


title: 36h_amp_rep1

description: Gene expression in regenerating limb, 36h after amputation

source_name: regenerating limb, 36h after amputation, replicate 1


title: 120h_amp_rep1

description: Gene expression in regenerating limb, 120h after amputation

source_name: regenerating limb, 120h after amputation, replicate 1


title: 52h_amp_rep1

description: Gene expression in regenerating limb, 52h after amputation

source_name: regenerating limb, 52h after amputation, replicate 1


title: AML [5354_27nov08]

description: Not Applicable

source_name: AML


title: SID_41_FCD_BM_D1_Utre

description: Bone marrow cells from donor D1 cultured with Fetal calf serum in Utrecht, and hybridized in batch B2

source_name: Bone marrow cells from donor D1


title: LCL, PA 23 y male,  GM22080, normal

value: male


title: LCL, PA 23 y male,  GM22080, low glucose


title: 9h_amp_rep1

description: Gene expression in regenerating limb, 9h after amputation

source_name: regenerating limb, 9h after amputation, replicate 1


title: 24h_amp_rep1

description: Gene expression in regenerating limb, 24h after amputation

source_name: regenerating limb, 24h after amputation, replicate 1


title: AML [5353_21oct08]

description: Not Applicable


title: AML [5355_27nov08]

description: Not Applicable


title: LCL, carrier father, GM22082, low glucose

source_name: LCL, low glucose

value: carrier father


title: 12h_amp_rep1

description: Gene expression in regenerating limb, 12h after amputation

source_name: regenerating limb, 12h after amputation, replicate 1


title: LCL, control GM12153, normal


title: AML [5352_27nov08]

description: Not Applicable


title: SID_40_hPL_AT_D10_Nijm

description: Adipose tissue cells from donor D10 cultured with Human platelet lysate in Nijmegen, and hybridized in batch B1

source_name: Adipose tissue cells from donor D10

value: Human platelet lysate

value: Nijmegen


title: AML [5351_27nov08]

description: Not Applicable


title: LCL, carrier father, GM22082, normal


title: SID_36_hPL_AT_D6_Nijm

description: Adipose tissue cells from donor D6 cultured with Human platelet lysate in Nijmegen, and hybridized in batch B3


title: AML [5349_27nov08]

description: Not Applicable


title: AML [5350_21oct08]

description: Not Applicable


title: SID_35_hPL_BM_D5_Nijm

description: Bone marrow cells from donor D5 cultured with Human platelet lysate in Nijmegen, and hybridized in batch B2

source_name: Bone marrow cells from donor D5

value: Bone marrow


title: SID_37_hPL_AT_D7_Nijm

description: Adipose tissue cells from donor D7 cultured with Human platelet lysate in Nijmegen, and hybridized in batch B1

source_name: Adipose tissue cells from donor D7


title: 6h_amp_rep1

description: Gene expression in regenerating limb, 6h after amputation

source_name: regenerating limb, 6h after amputation, replicate 1


title: SID_39_hPL_AT_D9_Nijm

description: Adipose tissue cells from donor D9 cultured with Human platelet lysate in Nijmegen, and hybridized in batch B3

source_name: Adipose tissue cells from donor D9


title: LCL, carrier mother, GM 22081, low glucose

value: female


title: SID_38_hPL_AT_D8_Nijm

description: Adipose tissue cells from donor D8 cultured with Human platelet lysate in Nijmegen, and hybridized in batch B2

source_name: Adipose tissue cells from donor D8


title: 3h_amp_rep1

description: Gene expression in regenerating limb, 3h after amputation

source_name: regenerating limb, 3h after amputation, replicate 1


title: LCL, carrier mother, GM 22081, normal

source_name: LCL, normal glucose

value: carrier mother


title: SID_34_hPL_BM_D4_Nijm

description: Bone marrow cells from donor D4 cultured with Human platelet lysate in Nijmegen, and hybridized in batch B1

source_name: Bone marrow cells from donor D4


title: LCL, control, GM06985, low glucose

value: control


title: LCL, control GM06985, normal


title: mat-2_rep1

description: Gene expression in the mature limb

source_name: mature limb, replicate 1


title: limb.bud_rep1

description: Gene expression in the developing limb bud

source_name: developing limb bud, replicate 1

value: limb bud


title: AML [5348_20jan09]

description: Not Applicable

source_name: AML

value: Training

value: NPM1 A


title: AML [5292_26nov08]

description: Not Applicable


title: AML [5291_26nov08]

description: Not Applicable


title: SID_33_hPL_BM_D3_Nijm

description: Bone marrow cells from donor D3 cultured with Human platelet lysate in Nijmegen, and hybridized in batch B3

source_name: Bone marrow cells from donor D3


title: SID_32_hPL_BM_D2_Nijm

description: Bone marrow cells from donor D2 cultured with Human platelet lysate in Nijmegen, and hybridized in batch B2

source_name: Bone marrow cells from donor D2


title: iPSCs derived from dermal skin fibroblasts of donor91 [SF91-iPS-A18]

city: kyoto

first: Junya

last: Toguchida

address: 53 kawahara-cho, shogoin

department: Center for iPS Cell Research and Application(CiRA)

country: Japan

institute: Kyoto University

hyb_protocol: Hybridisations were carried out with GeneChip® Hybridisation, Wash, and Stain Kit, with subsequent washing and staining of arrays on GeneChip® Fluid Station 450.

scan_protocol: Arrays were scanned using GeneChip Scanner 3000 7G

data_processing: Analysis was performed using GeneSpringGX software. Datas were normalized with RMA algorithms.

source_name: iPSCs

label_protocol: 500ng of total RNA from samples were reversed transcribed according to the Ambion® WT Expression Kit Protocol.  Synthesized cDNA was then Labeled with GeneChip® Terminal Labeling Kit.

growth_protocol: Cells were cultured in Primate ES Cell medium supplemented with 4ng/ml of bFGF on SNL feeder cells.

extract_protocol: Total RNA were extracted using RNeasy Mini Kit (QIAGEN) according to manufacture's instruction.

tag: cell type

value: iPSCs generated with Yamanaka 4factors by retrovisal transduction

tag: iPScs derived from

value: dermal skin fibroblasts


title: AML [5290_26nov08]

description: Not Applicable

value: NPM1 wt


title: iPSCs derived from dermal skin fibroblasts of donor91 [SF91-iPS-A11]


title: mat-1_rep1

description: Gene expression in the mature limb

tag: time after injury (hours)

tag: type of injury


title: SID_31_hPL_BM_D1_Nijm

description: Bone marrow cells from donor D1 cultured with Human platelet lysate in Nijmegen, and hybridized in batch B1

source_name: Bone marrow cells from donor D1


title: AML [5289_26nov08]

description: Not Applicable


title: AML [5288_21oct08]

description: Not Applicable


title: SID_30_FCD_AT_D10_Nijm

description: Adipose tissue cells from donor D10 cultured with Fetal calf serum in Nijmegen, and hybridized in batch B3

value: Fetal calf serum

value: Adipose tissue


title: FAST-5.2-REP3

city: Dublin

first: Padraig

last: Doolan

address: Glasnevin

country: Ireland

institute: Dublin City University

description: CHO gene expression data

hyb_protocol: 12.5 ug of fragmented and labelled cRNA for each sample was added to a hybridisation cocktail for 49 (Standard) format arrays as per manufacturer's instructions (http://media.affymetrix.com/support/downloads/manuals/3_ivt_express_kit_manual.pdf). Custom WyeHamster3a oligonucleotide microarrays were pre-hybridised in a Hybridization Oven 640 (Affymetrix) for 10 min at 45oC and 60 rpm with pre-hybridisation solution (#900720; GeneChip® Hybridization Wash and Stain Kit). The prehybridisation solution was removed and replaced with 200 ul hybridisation solution containing 0.025 ug/ul fragmented cRNA, making a total of 10 ug fragmented cRNA hybridised to each array. The arrays were hybridised for 17hrs at 45oC and 60 rpm. Arrays were subsequently washed and stained with Stain Cocktails 1 and 2 before being re-filled with array Holding Buffer (#900720; GeneChip® Hybridization Wash and Stain Kit) in a Fluidics Station 450 (Affymetrix) using Fluidics script EukGE_WS2v5_450 as per manufacturer's instructions.

scan_protocol: Wye3aHamster arrays were scanned on an GCS GeneChip GeneArray scanner (Affymetrix) as per manufacturer's instructions.

data_processing: All microarray data were pre-processed using the RMA algorithm in R (rma(AffyData))

organism: Cricetulus griseus

source_name: Suspension Cell Culture

label_protocol: 100 ng of Total RNA from each sample underwent cDNA synthesis, followed by cleanup and overnight IVT amplification and labeling using the GeneChip® 3' IVT Express Kit (#901229, Affymetrix) according to manufacturer's instructions (GeneChip® 3' IVT Express Kit User Manual: http://media.affymetrix.com/support/downloads/manuals/3_ivt_express_kit_manual.pdf). cRNA cleanup was carried out using the GeneChip® Sample Cleanup Module (#900371, Affymetrix) according to manufacturer's instructions (GeneChip® Expression Analysis Technical Manual: http://media.affymetrix.com/support/downloads/manuals/expression_analysis_technical_manual.pdf).

growth_protocol: All samples were from CHO K1 cell lines and were grown in replicate suspension cultures using identical proprietary chemically-defined culture media (AS1) at shake flask scale. Cultures were maintained at 37oC and 5% CO2 at a contant rotation speed of 130rpm in an orbital shaker.

extract_protocol: Total RNA was isolated using the mirVana miRNA Isolation Kit according (#AM1560; Invitrogen) to the manufacturer's instructions (mirVana™ miRNA Isolation Kit Protocol: http://tools.invitrogen.com/content/sfs/manuals/fm_1560.pdf). RNA quantity and purity were assessed at 260 nm and 280 nm using a Nanodrop (Labtech Int.). A Bioanalyser 2100 (Agilent Technologies) was used to qualitatively assess RNA after isolation, biotin-labeling and fragmentation.

treatment_protocol: Samples were taken down at discrete 72 hour intervals of culture. Typically, cell pellets of 2x10^6 cells were lysed in 1ml Lysis/Binding Solution buffer (mirVana miRNA Isolation Kit, Invitrogen), and stored at -80oC until required.

value: CHO K1

tag: group

value: fast grower

tag: growth rate

tag: cell viability

tag: cell density

tag: temperature


title: AML [5287_21oct08]

description: Not Applicable

value: NPM1 non-ABD


title: AML [5286_26nov08]

description: Not Applicable


title: FAST-5.16-REP3

description: CHO gene expression data


title: SID_28_FCD_AT_D8_Nijm

description: Adipose tissue cells from donor D8 cultured with Fetal calf serum in Nijmegen, and hybridized in batch B1

tag: culture methodology


title: iPSCs derived from dermal skin fibroblasts of donor91 [SF91-iPS-A1]


title: FAST-5.18-REP3

description: CHO gene expression data


title: SID_27_FCD_AT_D7_Nijm

description: Adipose tissue cells from donor D7 cultured with Fetal calf serum in Nijmegen, and hybridized in batch B3

tag: cell source


title: SID_26_FCD_AT_D6_Nijm

description: Adipose tissue cells from donor D6 cultured with Fetal calf serum in Nijmegen, and hybridized in batch B2

source_name: Adipose tissue cells from donor D6

tag: donor


title: iPSCs derived from dermal skin fibroblasts of donor91 [SF91-iPS-A5]


title: FAST-5.13-REP3

description: CHO gene expression data


title: SID_29_FCD_AT_D9_Nijm

description: Adipose tissue cells from donor D9 cultured with Fetal calf serum in Nijmegen, and hybridized in batch B2

tag: culture location


title: AML [5283_21oct08]

description: Not Applicable

tag: cohort


title: iPSCs derived from bone marrow stromal cells of donor91 [BM91-iPS-B17]

value: bone marrow stromal cells


title: FAST-5.2-REP2

description: CHO gene expression data


title: FAST-5.22-REP3

description: CHO gene expression data


title: iPSCs derived from dermal skin fibroblasts of donor90 [SF49_iPS_F2]


title: AML [5284_26nov08]

description: Not Applicable

tag: npm1 status


title: iPSCs derived from bone marrow stromal cells of donor91 [BM91-iPS-B14]


title: iPSCs derived from bone marrow stromal cells of donor91 [BM91-iPS-A15]


title: FAST-5.22-REP2

description: CHO gene expression data


title: SID_25_FCD_BM_D5_Nijm

description: Bone marrow cells from donor D5 cultured with Fetal calf serum in Nijmegen, and hybridized in batch B1

source_name: Bone marrow cells from donor D5

value: Nijmegen

tag: hybridization batch


title: iPSCs derived from bone marrow stromal cells of donor91 [BM91-iPS-A18]


title: AML [5285_26nov08]

description: Not Applicable


title: SID_24_FCD_BM_D4_Nijm

description: Bone marrow cells from donor D4 cultured with Fetal calf serum in Nijmegen, and hybridized in batch B3

value: Bone marrow


title: FAST-5.18-REP2

description: CHO gene expression data

tag: cell line


title: iPSCs derived from dermal skin fibroblasts of donor90 [SF49_iPS_B3]

tag: cell type


title: SID_23_FCD_BM_D3_Nijm

description: Bone marrow cells from donor D3 cultured with Fetal calf serum in Nijmegen, and hybridized in batch B2


title: FAST-5.16-REP2

description: CHO gene expression data


title: AML [4342_26nov08]

description: Not Applicable


title: iPSCs derived from bone marrow stromal cells of donor90 [BM90_iPS_A16]

tag: iPScs derived from


title: iPSCs derived from bone marrow stromal cells of donor90 [BM90_iPS_B6]


title: AML [4341_26nov08]

description: Not Applicable


title: SID_22_FCD_BM_D2_Nijm

description: Bone marrow cells from donor D2 cultured with Fetal calf serum in Nijmegen, and hybridized in batch B1


title: SID_20_hPL_AT_D10_Leid

description: Adipose tissue cells from donor D10 cultured with Human platelet lysate in Leiden, and hybridized in batch B2

source_name: Adipose tissue cells from donor D10

value: Human platelet lysate

value: Leiden


title: SID_21_FCD_BM_D1_Nijm

description: Bone marrow cells from donor D1 cultured with Fetal calf serum in Nijmegen, and hybridized in batch B3


title: FAST-5.2-REP1

description: CHO gene expression data


title: iPSCs derived from bone marrow stromal cells of donor90 [BM90_iPS_A12]


title: AML [4339_26nov08]

description: Not Applicable


title: iPSCs derived from bone marrow stromal cells of donor90 [BM90-iPS_A3]


title: AML [4340_26nov08]

description: Not Applicable


title: SID_18_hPL_AT_D8_Leid

description: Adipose tissue cells from donor D8 cultured with Human platelet lysate in Leiden, and hybridized in batch B3


title: AML [4337_26nov08]

description: Not Applicable


title: AML [4338_21oct08]

description: Not Applicable


title: FAST-5.22-REP1

description: CHO gene expression data


title: FAST-5.13-REP1

description: CHO gene expression data


title: FAST-5.16-REP1

description: CHO gene expression data


title: AML [4336_26nov08]

description: Not Applicable


title: SID_17_hPL_AT_D7_Leid

description: Adipose tissue cells from donor D7 cultured with Human platelet lysate in Leiden, and hybridized in batch B2

source_name: Adipose tissue cells from donor D7


title: FAST-5.13-REP2

description: CHO gene expression data


title: SID_15_hPL_BM_D5_Leid

description: Bone marrow cells from donor D5 cultured with Human platelet lysate in Leiden, and hybridized in batch B3


title: SLOW-11.1-REP3

description: CHO gene expression data

value: slow grower


title: SID_16_hPL_AT_D6_Leid

description: Adipose tissue cells from donor D6 cultured with Human platelet lysate in Leiden, and hybridized in batch B1


title: FAST-5.18-REP1

description: CHO gene expression data


title: AML [4335_26nov08]

description: Not Applicable


title: AML [3492_10jun08]

description: Not Applicable


title: SID_19_hPL_AT_D9_Leid

description: Adipose tissue cells from donor D9 cultured with Human platelet lysate in Leiden, and hybridized in batch B1

source_name: Adipose tissue cells from donor D9


title: Mouse corneal epithelium, postnatal day 28

city: Irvine

first: Denise

last: Stephens

state: CA

address: 250 Sprague Hall

department: Biological Chemistry

institute: University of California, Irvine

description:
sep E2 P28
Gene expression data from corneal epithelium, postnatal day 28.

hyb_protocol: 2.2 μg of the resulting fragmented, biotin-tagged cDNA was placed into a hybridization cocktail (220 μL), with 200 μL actually hybridized at 45°C with rotation for 18 hours (Affymetrix GeneChip Hybridization Oven 640) to probe sets present on an Affymetrix Mouse Gene 1.0 ST array. The GeneChip arrays were washed and then stained (SAPE, streptavidin-phycoerythrin) on an Affymetrix Fluidics Station 450 using the FS450_0004 fluidics protocol.

scan_protocol: Affymetrix GeneChip 3000 Scanner 7G.

data_processing: The results were quantified and analyzed using Expression Console ver.1.1 software (Affymetrix, Inc.) using the PLIER Algorithm default values (Quantification Scale: Linear; Quantification Type: Signal and Detection P-Value; Background: PM-GCBG; Normalization Method: Sketch-Quantile).

organism: Mus musculus

label_protocol: Using the NuGEN Ovation RNA Amplification System V2 (NuGEN Technologies, San Carlos, CA), first strand cDNA was synthesized from the poly(A)+ mRNA present within the isolated total RNA (20 ng total RNA starting material used in each sample reaction). Fragmentation of the mRNA within the resulting cDNA/mRNA complexes created priming sites for DNA polymerase to synthesize DNA complementary to the first strand cDNAs. The resulting ds cDNAs have a unique DNA/RNA heteroduplex at one end. These ds DNA templates were used to perform linear isothermal DNA amplification (SPIA, NuGEN Technologies, San Carlos, CA). 3.75 μg of the resulting amplified cDNA material for each sample was first fragmented and subsequently end-labeled using the NuGEN FL-Ovation cDNA Biotin Module V2 (NuGEN Technologies, San Carlos CA).

growth_protocol: Corneas from wildtype CB6 mice were collected at the respective ages.

extract_protocol: Whole eye globes were removed and corneas dissected, removing all surrounding tissues. Corneal epithelium was isolated by incubation of total cornea in dispase II for 2h at 37C. Total RNA was extracted with Trizol followed by clean-up with the RNeasy micro kit. Corneal stroma was isolated by embedding eye globes in OCT, sectioning at 8 um, and performing laser capture microdissection. Total RNA was isolated with the RNeasy micro kit.

tag: strain

tag: genotype

value: wildtype

tag: tissue

value: corneal epithelium

tag: age

value: postnatal day 28


title: Mouse corneal stroma, postnatal day 7

description:
sep Str 2 P7
Gene expression data from corneal stroma, postnatal day 7.

source_name: Mouse corneal stroma, postnatal day 7

value: corneal stroma

value: postnatal day 7


title: SLOW-10.2-REP3

description: CHO gene expression data

tag: group

tag: growth rate

tag: cell viability


title: Whole mouse cornea, 2 years of age, rep2

description:
Cornea 2Y4
Gene expression data from whole mouse cornea, 2 years of age.

source_name: Whole mouse cornea, 2 years of age

value: whole cornea

value: 2 years


title: SID_14_hPL_BM_D4_Leid

description: Bone marrow cells from donor D4 cultured with Human platelet lysate in Leiden, and hybridized in batch B2

tag: culture methodology


title: AML [3491_20jun08]

description: Not Applicable

value: Training

value: NPM1 wt


title: SID_13_hPL_BM_D3_Leid

description: Bone marrow cells from donor D3 cultured with Human platelet lysate in Leiden, and hybridized in batch B1

tag: cell source


title: AML [3489_19jun08]

description: Not Applicable

value: NPM1 B


title: AML [3490_22may08]

description: Not Applicable


title: Whole mouse cornea, 2 years of age, rep1

description:
Cornea 2Y1
Gene expression data from whole mouse cornea, 2 years of age.


title: SID_12_hPL_BM_D2_Leid

description: Bone marrow cells from donor D2 cultured with Human platelet lysate in Leiden, and hybridized in batch B3

tag: donor


title: Whole mouse cornea, 1 year of age, rep2

description:
Cornea 1YmB
Gene expression data from whole mouse cornea, 1 year of age.

source_name: Whole mouse cornea, 1 year of age

value: 1 year


title: AML [3488_20jun08]

description: Not Applicable


title: Whole mouse cornea, 1 year of age, rep1

description:
Cornea 1YmA
Gene expression data from whole mouse cornea, 1 year of age.


title: AML [3487_22may08]

description: Not Applicable


title: SID_11_hPL_BM_D1_Leid

description: Bone marrow cells from donor D1 cultured with Human platelet lysate in Leiden, and hybridized in batch B2

tag: culture location


title: SID_10_FCD_AT_D10_Leid

description: Adipose tissue cells from donor D10 cultured with Fetal calf serum in Leiden, and hybridized in batch B1

value: Fetal calf serum

value: Adipose tissue


title: AML [3485_22may08]

description: Not Applicable

tag: cohort


title: SLOW-5.1-REP3

description: CHO gene expression data

value: CHO K1

tag: cell density

tag: temperature


title: AML [3486_5jun08]

description: Not Applicable

tag: npm1 status

value: NPM1 A


title: Whole mouse cornea, 18 months of age, rep1

description:
Cornea 18moM2
Gene expression data from whole mouse cornea,18 months of age.

source_name: Whole mouse cornea, 18 months of age

value: 18 months


title: SLOW-7.7-REP3

description: CHO gene expression data

tag: cell line

value: slow grower


title: AML [3484_12jun08]

description: Not Applicable


title: SID_8_FCD_AT_D8_Leid

description: Adipose tissue cells from donor D8 cultured with Fetal calf serum in Leiden, and hybridized in batch B2

source_name: Adipose tissue cells from donor D8

value: Leiden

tag: hybridization batch


title: Whole mouse cornea, 2 months of age, rep3

description:
Cornea P60 1A
Gene expression data from whole mouse cornea, 2 months of age.

source_name: Whole mouse cornea, 2 months of age

tag: strain

value: wildtype

value: 2 months


title: Whole mouse cornea, 18 months of age, rep2

description:
Cornea 18moM3
Gene expression data from whole mouse cornea,18 months of age.

tag: genotype


title: SLOW-7.7-REP2

description: CHO gene expression data


title: SLOW-5.11-REP3

description: CHO gene expression data


title: SLOW-5.1-REP2

description: CHO gene expression data


title: SID_6_FCD_AT_D6_Leid

description: Adipose tissue cells from donor D6 cultured with Fetal calf serum in Leiden, and hybridized in batch B3


title: SLOW-5.11-REP2

description: CHO gene expression data


title: AML [5282_26nov08]

description: Not Applicable

source_name: AML


title: SLOW-10.2-REP2

description: CHO gene expression data


title: SID_7_FCD_AT_D7_Leid

description: Adipose tissue cells from donor D7 cultured with Fetal calf serum in Leiden, and hybridized in batch B1


title: SID_5_FCD_BM_D5_Leid

description: Bone marrow cells from donor D5 cultured with Fetal calf serum in Leiden, and hybridized in batch B2

value: Bone marrow


title: Whole mouse cornea, 2 months of age, rep2

description:
Cornea P60 1B
Gene expression data from whole mouse cornea, 2 months of age.

tag: tissue


title: AML [3482_07may08]

description: Not Applicable

value: NPM1 D


title: AML [3483_29may08]

description: Not Applicable


title: Whole mouse cornea, 2 months of age, rep1

description:
Cornea P60 3A
Gene expression data from whole mouse cornea, 2 months of age.

value: whole cornea

tag: age


title: SID_9_FCD_AT_D9_Leid

description: Adipose tissue cells from donor D9 cultured with Fetal calf serum in Leiden, and hybridized in batch B3


title: Whole mouse cornea, 6 months of age, rep1

description:
Cornea P180 C3
Gene expression data from whole mouse cornea, 6 months of age.

source_name: Whole mouse cornea, 6 months of age

value: 6 months


title: AML [3481_14may08]

description: Not Applicable

value: Training


title: Whole mouse cornea, postnatal day 28, rep2

description:
Cornea P28 7a
Gene expression data from whole mouse cornea, postnatal day 28.

source_name: Whole mouse cornea, postnatal day 28

value: postnatal day 28


title: SID_4_FCD_BM_D4_Leid

description: Bone marrow cells from donor D4 cultured with Fetal calf serum in Leiden, and hybridized in batch B1

source_name: Bone marrow cells from donor D4


title: SLOW-7.7-REP1

description: CHO gene expression data

tag: group


title: Whole mouse cornea, 6 months of age, rep2

description:
Cornea P180 C5
Gene expression data from whole mouse cornea, 6 months of age.


title: AML [3334_20jun08]

description: Not Applicable


title: SLOW-11.1-REP2

description: CHO gene expression data

tag: growth rate


title: SLOW-10.2-REP1

description: CHO gene expression data

tag: cell viability


title: SID_3_FCD_BM_D3_Leid

description: Bone marrow cells from donor D3 cultured with Fetal calf serum in Leiden, and hybridized in batch B3

source_name: Bone marrow cells from donor D3

tag: culture methodology


title: Whole mouse cornea, postnatal day 28, rep3

description:
Cornea P28 9a
Gene expression data from whole mouse cornea, postnatal day 28.


title: SLOW-11.1-REP1

description: CHO gene expression data

source_name: Suspension Cell Culture


title: SLOW-5.11-REP1

description: CHO gene expression data


title: SID_1_FCD_BM_D1_Leid

description: Bone marrow cells from donor D1 cultured with Fetal calf serum in Leiden, and hybridized in batch B1

source_name: Bone marrow cells from donor D1

tag: cell source


title: Whole mouse cornea, postnatal day 28, rep1

description:
Cornea P28 3a
Gene expression data from whole mouse cornea, postnatal day 28.


title: AML [3331_13jun08]

description: Not Applicable


title: AML [3332_22apr08]

description: Not Applicable

value: NPM1 wt


title: SID_2_FCD_BM_D2_Leid

description: Bone marrow cells from donor D2 cultured with Fetal calf serum in Leiden, and hybridized in batch B2

source_name: Bone marrow cells from donor D2

tag: donor


title: Whole mouse cornea, postnatal day 14, rep1

description:
Cornea P14 01a
Gene expression data from whole mouse cornea, postnatal day 14.

source_name: Whole mouse cornea, postnatal day 14

value: postnatal day 14


title: SLOW-5.1-REP1

description: CHO gene expression data


title: Whole mouse cornea, postnatal day 14, rep2

description:
Cornea P14 03b
Gene expression data from whole mouse cornea, postnatal day 14.


title: OSCC mRNA 575

city: Houston

first: Jiexin

last: Zhang

state: TX

address: 1515 Holcombe Blvd

department: Bioinformatics & Computational Biology

institute: UT MD Anderson Cancer Center

description: Alveolar

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing:
Used aroma.affymetrix package in R for data processing. We performed background correction using RMA and quantile normalization. Then we estimated the overall expression for the transcript using ExonRmaPlm function.
probe group file not applicable
HuEx-1_0-st-v2.na32.hg19.probeset.csv

source_name: OSCC

label_protocol: Standard Affymetrix protocol

extract_protocol: Tri-reagent (Sigma)

tag: gender

value: M

tag: source tissue

value: Alveolar

value: Oral cavity squamous cell carcinoma tumor

tag: case


title: RPE_16W_rep2

city: Harbin

first: Shaomin

last: Peng

address: 246 XueFu Road

country: China

institute: The Second Hospital of Harbin Medical University

description:
differental gene expression of RPE  in 16 weeks gastation
Treat-16W

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: Slides were scanned at 5 μm/pixel resolution using an Axon GenePix 4000B scanner (Molecular Devices Corporation) piloted by GenePix Pro 6.0 software (Axon). Scanned images (TIFF format) were then imported into NimbleScan software (version 2.5) for grid alignment and expression data analysis. Expression data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan software. NimbleScan software’s implementation of RMA offers quantile normalization and background correction. There are three steps of RMA: Firstly, background subtraction was performed using a local background estimator. Secondly, quantile normalization (Bioinformatics 2003; 19:185) at probe level was done to make the expression distributions the same for all arrays. Last, probe set summarization was performed using Robust Multichip Average (RMA) algorithm as described by Irizarry, et al (Nucleic Acids Res. 2003; 31:e15 and Biostatistics 2003; 4:249).  The Probe level (*_norm_RMA.pair) files and Gene level (*_RMA.calls) files were generated after normalization. All gene level files were imported into Agilent GeneSpring GX software (version 11.5.1) for further analysis. Differentially expressed genes were identified through Fold Change filtering. Hierarchical clustering was performed using the Agilent GeneSpring GX software (version 11.5.1). GO analysis and Pathway analysis were performed using the standard enrichment computation method.

source_name: human fetal RPE

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

extract_protocol: Equal amounts of RNA were pooled from the 3 independent replicates used for each time point of each group. RNA was extracted using TRIzol (Invitrogen, USA) and the RNeasy kit (Qiagen, Valencia, CA, USA) according to manufacturer’s instructions. Concentration and quality of RNA was determined using Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and/or Nano drop spectrophotometer (Wilmington, DE, USA). All samples had A (260)/A(280) ratios of the total RNA 2.0, and the ratio of 28S/18S ribosomal RNA bands was more than 1.8.

tag: developmental stage

value: fetus (16 weeks of gestation)

value: eye

tag: cell type

value: retinal pigment epithelium


title: OSCC mRNA 592

description: Tongue

value: Tongue


title: Whole mouse cornea, postnatal day 14, rep3

description:
Cornea P14 05a
Gene expression data from whole mouse cornea, postnatal day 14.

value: wildtype


title: Whole mouse cornea, postnatal day 7, rep1

description:
Cornea P7 4b
Gene expression data from whole mouse cornea, postnatal day 7.

source_name: Whole mouse cornea, postnatal day 7

value: postnatal day 7


title: Tennessee treatment-2

city: Bedford Park

first: Haiping

last: Li

state: IL

address: 6502 S. Archer Rd

department: CFSAN/OFS/Moffett Center

institute: Food and Drug Administration

description: stationary culture, 0h desiccation

hyb_protocol: 1 µg of purified cRNA was fragmented to uniform size and applied to a custom Agilent 4x44K microarrays (Agilent Technologies, Santa Clara, CA) in hybridization buffer. Arrays were hybridized at 65° C for 17 hrs. in a rotating incubator, and washed at 37° C for 1 min.

scan_protocol: Rinsed and dried arrays were scanned with an Agilent G2565 Microarray Scanner (Agilent Technologies, Santa Clara, CA) at 5 µm resolution.

data_processing: Agilent Feature Extraction software was used to process the scanned images from arrays (gridding and feature intensity extraction) and the data generated for each probe on the array was analyzed with GeneSpring GX v7.3.1 software (Agilent Technologies, Santa Clara, CA).

organism: Salmonella enterica subsp. enterica serovar Tennessee

source_name: S. Tennessee 20h culture stored at 11% ERH for 2h

label_protocol: First and second strand cDNA was prepared from the total RNA samples.  cRNA target was prepared from the DNA template and verified on the Bioanalyzer.  cRNA was fragmented to uniform size and verified on the Bioanalyzer.

growth_protocol: Salmonella Tennessee strain K4643 (Tennessee) and Typhimurium LT2 ATCC strain 19585 (LT2) were grown in Tryptic Soy Broth at 37ºC with orbital shaking for 20h.

extract_protocol: Total RNA was isolated (Rneasy Mini Kit, Qiagen Inc., CA) and confirmed for quality (Agilent 2100 Bioanalyzer, Agilent Technologies, Inc., Santa Clara, CA) following the manufacturers’ instructions.

treatment_protocol: For each strain approximately 8 log CFU in 0.1M PBS were added onto a sterile filter paper disc and stored in a desiccator at 11% equillibrated relative humidity  for 2 h.

value: Tennessee

tag: treatment

value: dessicated


title: Whole mouse cornea, postnatal day 7, rep3

description:
Cornea P7 10a
Gene expression data from whole mouse cornea, postnatal day 7.

value: whole cornea


title: RPE_13W_rep2

description:
differental gene expression of RPE  in 13 weeks gastation
Treat-13W

value: fetus (13 weeks of gestation)


title: Tennessee treatment-3

description: stationary culture, 0h desiccation


title: RPE_Adult_rep2

description:
differental gene expression of RPE  in adult
Control

source_name: human adult RPE

value: mature adult (40-60 years old)


title: Whole mouse cornea, postnatal day 7, rep2

description:
Cornea P7 7b
Gene expression data from whole mouse cornea, postnatal day 7.


title: AML [3330_22may08]

description: Not Applicable

tag: cohort

value: Training

tag: npm1 status


title: OSCC mRNA 530

description: FOM

value: FOM


title: Whole mouse cornea, postnatal day 3, rep3

description:
Cornea P3 9a
Gene expression data from whole mouse cornea, postnatal day 3.

source_name: Whole mouse cornea, postnatal day 3

tag: strain

tag: genotype

value: postnatal day 3


title: AML [3329_5jun08]

description: Not Applicable

value: NPM1 wt


title: AML [3328_29may08]

description: Not Applicable


title: OSCC mRNA 537

description: Buccal

value: M

value: Buccal

tag: tissue


title: OSCC mRNA 449

description: Tongue

value: Oral cavity squamous cell carcinoma tumor


title: Tennessee control-3

description: stationary culture, 2h desiccation

source_name: S. Tennessee 20h culture

value: control


title: Whole mouse cornea, postnatal day 3, rep2

description:
Cornea P3 7b
Gene expression data from whole mouse cornea, postnatal day 3.

tag: age


title: AML [3326_28may08]

description: Not Applicable


title: Whole mouse cornea, postnatal day 3, rep1

description:
Cornea P3 2a
Gene expression data from whole mouse cornea, postnatal day 3.


title: AML [3325_29may08]

description: Not Applicable

value: NPM1 B


title: OSCC mRNA 364

description: Alveolar

value: Alveolar


title: Tennessee treatment-1

description: stationary culture, 0h desiccation


title: Tennessee control-2

description: stationary culture, 2h desiccation


title: AML [3324_5jun08]

description: Not Applicable


title: AML [3323_29apr08]

description: Not Applicable


title: OSCC mRNA 394

description: FOM


title: OSCC mRNA 201

description: FOM


title: AML [3321_10jun08]

description: Not Applicable


title: Tennessee control-1

description: stationary culture, 2h desiccation


title: AML [3320_25apr08]

description: Not Applicable


title: OSCC mRNA 193

description: Buccal


title: OSCC mRNA 180

description: Tongue

value: F

value: Tongue


title: Whole mouse cornea, embryonic day 17.5, rep2

description:
Cornea E17_5 5R
Gene expression data from whole mouse cornea, embryonic day 17.5.

source_name: Whole mouse cornea, embryonic day 17.5

value: wildtype

value: embryonic day 17.5


title: Typhimurium LT2 treatment-2

description: stationary culture, 0h desiccation

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

source_name: S. Typhimurium LT2 20h culture stored at 11% ERH for 2h

value: Typhimurium LT2

value: dessicated


title: AML [3319_18jun08]

description: Not Applicable

source_name: AML


title: Whole mouse cornea, embryonic day 17.5, rep1

description:
Cornea E17_5 3L
Gene expression data from whole mouse cornea, embryonic day 17.5.

value: whole cornea


title: Whole mouse cornea, embryonic day 15.5, rep3

description:
Cornea E15_5 7b
Gene expression data from whole mouse cornea, embryonic day 15.5.

source_name: Whole mouse cornea, embryonic day 15.5

value: embryonic day 15.5


title: OSCC mRNA 169

description: FOM

value: FOM


title: Whole mouse cornea, embryonic day 17.5, rep3

description:
Cornea E17_5 6L
Gene expression data from whole mouse cornea, embryonic day 17.5.


title: Whole mouse cornea, embryonic day 15.5, rep1

description:
Cornea E15_5 1a
Gene expression data from whole mouse cornea, embryonic day 15.5.


title: Typhimurium LT2 treatment-1

description: stationary culture, 0h desiccation


title: AML [3322_5jun08]

description: Not Applicable

value: Training


title: Whole mouse cornea, embryonic day 14.5, rep3

description:
Cornea E14_5 13a
Gene expression data from whole mouse cornea, embryonic day 14.5.

source_name: Whole mouse cornea, embryonic day 14.5

value: embryonic day 14.5


title: Typhimurium LT2 control-2

description: stationary culture, 2h desiccation

source_name: S. Typhimurium LT2 20h culture


title: OSCC mRNA 281

description: Tongue

value: M


title: Typhimurium LT2 control-1

description: stationary culture, 2h desiccation


title: AML [3318_14may08]

description: Not Applicable

value: NPM1 wt


title: OSCC mRNA 562

description: Tongue

value: Oral cavity squamous cell carcinoma tumor


title: Whole mouse cornea, embryonic day 15.5, rep2

description:
Cornea E15_5 6a
Gene expression data from whole mouse cornea, embryonic day 15.5.


title: Whole mouse cornea, embryonic day 14.5, rep2

description:
Cornea E14_5 8a
Gene expression data from whole mouse cornea, embryonic day 14.5.


title: Typhimurium LT2 control-3

description: stationary culture, 2h desiccation

value: control


title: AML [3316_13jun08]

description: Not Applicable


title: AML [3315_22apr08]

description: Not Applicable


title: Whole mouse cornea, embryonic day 14.5, rep1

description:
Cornea E14_5 4a
Gene expression data from whole mouse cornea, embryonic day 14.5.


title: AML [3313_27may08]

description: Not Applicable


title: OSCC mRNA 288

description: Tongue


title: AML [3312_12jun08]

description: Not Applicable


title: OSCC mRNA 234

description: Tongue


title: AML [3317_29may08]

description: Not Applicable


title: OSCC mRNA 489

description: FOM


title: OSCC mRNA 298

description: Tongue


title: n.c. mimic rep 3

city: Bethesda

first: Aliaksandr

last: druz

state: MD

address: 14A Service Rd. Room 176

department: NIDDK

institute: NIH

description:
B/CMBA.ov cells transfected with negative control rep3
Mo_Gene1_0_ST_3_nc.

hyb_protocol: Biotin labeled samples were hybridized with Affymetrix Mouse Gene 1.0 ST arrays (Platform GPL6246) for 18 hours in hybridization oven at 45C rotating 60rpm (Affymetrix) . Arrays were hybridized, washed and stained using Affymetrix  kit and  processed in Affymetrix 450 Fluidic stations

scan_protocol: Chips were scanned with Affymetrix GeneChip scanner 3000 operated by  Affymetrix GeneChip Operating Software, version 1. 4 (GCOS 1.4).

data_processing: CEL files were generated using MAS 5.0 and processed using Expression console software using 'RMA sketch' to generate .CHP files.Partek Genomic Suite software was used for data processing. The  ANOVA and t-test analysis were carried out on the log2 normalized signals to compare sample groups. PCA analyses were used to identify the outliers

label_protocol: RNA from each sample was amplified to generate cDNA using NUGEN Applause WT-Amp ST system (NuGEN Technologies) and  cDNA was  fragmented and biotinylated  using  Encore Biotin module (NUGEN Technologies) according to the manufactures instructions

growth_protocol: B/CMBA.ov cells were seeded on 12-well plates 1 day prior transfection and grown at 37C in humidified incubator with 5%CO2

extract_protocol: RNA was extracted 48h after transfection using RNeasy Mini Kit (Qiagen)

treatment_protocol: B/CMBA.ov cells were transfected with miRIDIAN mmu-miR-15a-3p and negative control miRNA mimics (Dharmacon) at 20nM final concentration using RNAiMax (Life Tehcnologies)

value: Ovary

value: BALB/c

value: B/CMBA.ov cells

tag: transfection

value: negative control


title: IFNW_D4

city: London

first: Akul

last: Singhania

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

description: Interferon treated MDM at day 4 of IFNW experiment

hyb_protocol: Hybridization of labeled cRNA to the BeadChip, and washing and scanning were performed according to the Illumina BeadStation manual.

scan_protocol: The arrays were scanned on the Illumina BeadArray Reader.

data_processing: The data were normalised using quantile normalization of log2 transformed data. We used the bioconductor package lumi for R (version 2.10.1).

label_protocol: Biotinylated cRNA was prepared using the Illumina RNA Amplification Kit according to the manufacturer's directions.

extract_protocol: RNA was extracted with Trizol reagent from MDM.

tag: cell

value: monocyte derived macrophages (MDMs)

tag: experimental setup

value: Interferon treated

tag: type of ifn

value: IFNW


title: MDMW_D1

description: Untreated MDM control at day 1 of IFNW experiment

value: Untreated control


title: OSCC mRNA 513

description: Tongue

value: Tongue


title: AML [3310_03jun08]

description: Not Applicable

value: NPM1 A


title: AML [3327_14may08_2]

description: Not Applicable


title: OSCC mRNA 350

description: Tongue


title: IFNW_HIV_D8

description: Interferon treated and HIV infected MDM at day 8 of IFNW experiment

value: Interferon treated and HIV infected


title: OSCC mRNA 229

description: FOM

value: FOM


title: miR-15a-3p mimic rep 3

description:
B/CMBA.ov cells transfected with miR-15a-3p rep3
Mo_Gene1_0_ST_3_15-mimic


title: IFNW_HIV_D4

description: Interferon treated and HIV infected MDM at day 4 of IFNW experiment


title: miR-15a-3p mimic rep 2

description:
B/CMBA.ov cells transfected with miR-15a-3p rep2
Mo_Gene1_0_ST_2_15-mimic


title: AML [3308_20jun08]

description: Not Applicable

value: Training


title: OSCC mRNA 238

description: Tongue

value: F


title: HIVW_D4

description: HIV infected MDM at day 4 of IFNW experiment

value: HIV infected


title: MDMW_D8

description: Untreated MDM control at day 8 of IFNW experiment


title: miR-15a-3p mimic rep 1

description:
B/CMBA.ov cells transfected with miR-15a-3p rep1
Mo_Gene1_0_ST_1_15-mimic


title: OSCC mRNA 37

description: FOM

value: M

value: Oral cavity squamous cell carcinoma tumor


title: OSCC mRNA 481

description: Tongue


title: OSCC mRNA 331

description: FOM


title: IFNW_D8

description: Interferon treated MDM at day 8 of IFNW experiment


title: n.c. mimic rep 2

description:
B/CMBA.ov cells transfected with negative control rep2
Mo_Gene1_0_ST_2_nc.

value: Ovary


title: IFNW_D1

description: Interferon treated MDM at day 1 of IFNW experiment


title: HIVW_D8

description: HIV infected MDM at day 8 of IFNW experiment


title: AML [3301_22apr08]

description: Not Applicable

value: NPM1 wt


title: MDMW_D4

description: Untreated MDM control at day 4 of IFNW experiment


title: AML [3304_18apr08]

description: Not Applicable


title: AML [3295_13jun08]

description: Not Applicable


title: AML [3293_14may08]

description: Not Applicable


title: OSCC mRNA 600

description: Tongue


title: OSCC mRNA 392

description: Tongue


title: n.c. mimic rep 1

description:
B/CMBA.ov cells transfected with negative control rep1
Mo_Gene1_0_ST_1_nc.

value: BALB/c

value: B/CMBA.ov cells


title: AML [3289_20jun08]

description: Not Applicable


title: AML [3292_20may08]

description: Not Applicable


title: WT2

city: Cincinnati

first: Hee-Woong

last: Lim

state: Ohio

address: 3333 Burnet Ave. MLC 7024

department: Division of Biomedical Informatics

institute: Cincinnati Children's Hospital Medical Center

description: Hepatic gene expression data from normal mice

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: The array was read by GCS3000 laser scanner (Affymetrix).

data_processing: Data analysis was carried out using Partek Genomics Suite software (Copyright, Partek Inc.). Data were subjected to background subtraction, quantile normalization, log2 transformation and probeset summarization using RMA (Robust Multichip Average) algorithm. Only the probesets that interrogate genes were retained and those meant for QC and normalization purposes were excluded from further analysis.

source_name: Liver tissue

label_protocol: Each RNA sample (at least 50ng) was processed with the Ambion WT Expression Kit and the GeneChip WT Terminal Labeling and Controls Kit (Affymetrix). Single strand cDNA is labeled by terminal deoxynucleotidyl transferase (TdT) with the Affymetrix proprietary DNA Labeling Reagent that is covalently linked to biotin.

growth_protocol: Male WT C57Bl/6 mice grow in regular 12h light/ 12h dark cycles on normal chow.

extract_protocol: Total RNA was extracted >20mg mouse liver samples using Trizol extraction followed by QIAGEN Rneasy Kit according to the manufacture's instructions.

value: Liver

tag: time

tag: genotype/variation

value: WT


title: WT3


title: WT4


title: IFNW_HIV_D1

description: Interferon treated and HIV infected MDM at day 1 of IFNW experiment

value: monocyte derived macrophages (MDMs)

value: IFNW


title: AML [3286_17jun08]

description: Not Applicable


title: WT1


title: Typhimurium LT2 treatment-3

description: stationary culture, 0h desiccation

value: Typhimurium LT2

value: dessicated


title: HIVW_D1

description: HIV infected MDM at day 1 of IFNW experiment


title: IFNA2_HIV_D8

description: Interferon treated and HIV infected MDM at day 8 of IFNA2 experiment

value: Interferon treated and HIV infected


title: OSCC mRNA 327

description: Tongue

tag: gender

tag: source tissue

value: Tongue


title: OSCC mRNA 391

description: Tongue

tag: case


title: IFNA2_D4

description: Interferon treated MDM at day 4 of IFNA2 experiment

value: Interferon treated


title: AML [3279_03jun08]

description: Not Applicable

value: Training


title: NSDADm3

description: Hepatic gene expression data from mice with NCOR and SMRT DAD-mutation

value: NS-DADm


title: NSDADm1


title: AML [3278_27may08]

description: Not Applicable


title: OSCC mRNA 258

description: Tongue

value: F


title: AML [3285_18apr08]

description: Not Applicable


title: AML [3311_12jun08]

description: Not Applicable

value: NPM1 A


title: NSDADm2


title: OSCC mRNA 478

description: Tongue

value: Oral cavity squamous cell carcinoma tumor


title: AML [322_19jun08]

description: Not Applicable

value: NPM1 wt


title: MDMA2_D8

description: Untreated MDM control at day 8 of IFNA2 experiment

value: Untreated control


title: OSCC mRNA 353

description: Tongue

value: M


title: AML [2769_10jun08]

description: Not Applicable


title: AML [2767_14may08]

description: Not Applicable


title: OSCC mRNA 266

description: Tongue


title: IFNA2_D1

description: Interferon treated MDM at day 1 of IFNA2 experiment


title: EMT6.5 whole primary tumour mouse no. 3

city: East Melbourne

first: Cameron

middle: N

last: Johnstone

state: Vic

address: 2 St. Andrew's Place

department: Research Division

country: Australia

institute: Peter MacCallum Cancer Centre

hyb_protocol: Following fragmentation, 2.5 mg of cDNA were hybridized for 18 hr at 45oC on GeneChip Mouse Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: Data were processed using Partek Genomics Suite 6.6. Robust Multiarray Averaging (RMA) background correction were applied to probe intensities, gene level expression were quantile normalized.

source_name: EMT6.5 whole primary tumour mouse no. 3 in Balb/c mouse

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 200 ng total RNA ('NuGEN' Applause WT-Amp ST RNA Amplification System, Manual M01134 v2).

growth_protocol: Standard mouse barrier facility (SPF)

extract_protocol: Standard total RNA isolation using Trizol reagent with DNase I digestion

value: Balb/c

tag: tumour behaviour

value: metastatic

tag: tumour location

value: 4th inguinal mammary fat pad

value: 6-8 weeks

tag: Sex

value: female


title: IFNA2_HIV_D4

description: Interferon treated and HIV infected MDM at day 4 of IFNA2 experiment

value: monocyte derived macrophages (MDMs)


title: HIVA2_D8

description: HIV infected MDM at day 8 of IFNA2 experiment

value: HIV infected


title: EMT6.5 whole primary tumour mouse no. 1

source_name: EMT6.5 whole primary tumour mouse no. 1 in Balb/c mouse


title: EMT6.5 whole primary tumour mouse no. 2

source_name: EMT6.5 whole primary tumour mouse no. 2 in Balb/c mouse


title: AML [3115_22may08]

description: Not Applicable

tag: cohort

tag: npm1 status


title: OSCC mRNA 325

description: Tongue

source_name: OSCC

value: Tongue


title: IFNA2_D8

description: Interferon treated MDM at day 8 of IFNA2 experiment

value: Interferon treated


title: OSCC mRNA 385

description: Tongue


title: OSCC mRNA 43

description: Tongue


title: MDMA2_D4

description: Untreated MDM control at day 4 of IFNA2 experiment


title: EO771 whole primary tumour mouse no. 1

source_name: EO771 whole primary tumour mouse no. 1 in C57Bl/6 mouse

tag: strain

value: non-metastatic


title: EO771 whole primary tumour mouse no. 2

source_name: EO771 whole primary tumour mouse no. 2 in C57Bl/6 mouse


title: EO771 whole primary tumour mouse no. 3

source_name: EO771 whole primary tumour mouse no. 3 in C57Bl/6 mouse


source_name: EO771.LMB whole primary tumour mouse no. 3 in C57Bl/6 mouse


title: IFNA2_HIV_D1

description: Interferon treated and HIV infected MDM at day 1 of IFNA2 experiment

value: Interferon treated and HIV infected


title: OSCC mRNA 388

description: Tongue

value: F

tag: tissue


title: NSDADm4

value: Liver

value: NS-DADm


title: AML [2765_07may08]

description: Not Applicable

value: Training

value: NPM1 wt


title: AML [2764_22apr08]

description: Not Applicable


title: HIVA2_D4

description: HIV infected MDM at day 4 of IFNA2 experiment


source_name: EO771.LMB whole primary tumour mouse no. 2 in C57Bl/6 mouse

tag: age


title: OSCC mRNA 447

description: Tongue

value: M

value: Oral cavity squamous cell carcinoma tumor


title: HIVA2_D1

description: HIV infected MDM at day 1 of IFNA2 experiment


title: OSCC mRNA 578

description: Tongue


title: MDMA2_D1

description: Untreated MDM control at day 1 of IFNA2 experiment

value: Untreated control


title: OSCC mRNA 347

description: Tongue


source_name: EO771.LMB whole primary tumour mouse no. 1 in C57Bl/6 mouse

value: metastatic

value: 4th inguinal mammary fat pad


title: OSCC mRNA 91

description: Tongue


title: OSCC mRNA 367

description: Tongue


title: AML [2766_10jun08]

description: Not Applicable


title: AML [2754_18jun08]

description: Not Applicable

value: NPM1 B


title: OSCC mRNA 166

description: Tongue


title: AML [2762_28may08]

description: Not Applicable


title: AML [2756_19jun08]

description: Not Applicable

value: NPM1 A


title: AML [2757_10jun08]

description: Not Applicable


title: 4T1.2 whole primary tumour mouse no. 2

source_name: 4T1.2 whole primary tumour mouse no. 2 in Balb/c mouse

value: Balb/c

value: 6-8 weeks

value: female


title: OSCC mRNA 139

description: Tongue

value: Tongue


title: AML [2753_29may08]

description: Not Applicable


title: RNA from RKO cells treated with siRNA SRCAP and 5-AZA-CdR for 72hr rep2

city: Detroit

first: Houtan

last: Noushmehr

state: MI

address: 2799 W. Grand Blvd

institute: Henry Ford Health System

description:
Replicate 2
5067319030_F

hyb_protocol: According to Illumina protocol

scan_protocol: According to Illumina protocol

data_processing: The data was processed using BeadStudio 3.0.1 software. The summarized data for each bead type were processed using the lumi package in Bioconductor. The data are log2 transformed and normalized using Robust Spline Normalization (RSN) as implemented in the lumi package.

label_protocol: According to Illumina protocol

growth_protocol: RKO cell line is purchased from ATCC and cultured in MEM mediun with 10%FBS.

extract_protocol: not applicable

treatment_protocol: RKO cells are treated with non target or SRCAP siRNA 100nM for 24hrs and  followed by 1uM 5-Aza-CdR or PBS for 72hrs.

tag: cell line

value: RKO

tag: organ

value: colon

tag: disease state

value: carcinoma


title: AML [2752_04jun08]

description: Not Applicable


title: 67NR whole primary tumour mouse no. 3

source_name: 67NR whole primary tumour mouse no. 3 in Balb/c mouse

value: non-metastatic


title: 4T1.2 whole primary tumour mouse no. 3

source_name: 4T1.2 whole primary tumour mouse no. 3 in Balb/c mouse


title: AML [2751_07may08]

description: Not Applicable

source_name: AML

value: Training


title: RNA from RKO cells treated with siRNA SRCAP and PBS for 72hr rep1

description:
Replicate 1
5067319005_C


title: RNA from RKO cells treated with siRNA SRCAP and 5-AZA-CdR for 72hr rep1

description:
Replicate 1
5067319005_F


title: RNA from RKO cells treated with siRNA SRCAP and PBS for 72hr rep2

description:
Replicate 2
5067319030_E


title: 4T1.2 whole primary tumour mouse no. 1

source_name: 4T1.2 whole primary tumour mouse no. 1 in Balb/c mouse


title: AML [2750_11jun08]

description: Not Applicable

value: NPM1 wt


title: Nascent RNA sample of GM12813 biological replicate3 technical duplicate

city: Evanston

first: Jubao

last: Duan

address: 1001 University Place

department: Psychiatry and Behavioral Sciences

institute: Northshore University HealthSystem/University of Chicago

hyb_protocol: 5.5 µg fragmented/labeled cDNAs were used to hybridize with probes on the exon array at 45°C for 16-18 hr.

scan_protocol: Hybridized chips were washed and stained on a GeneChip Fluidics Station 450 and finally scanned on a GCS3000 Scanner (Affymetrix).

data_processing:
The Affymetrix Power Tools (APT) software package (Affymetrix) was used to normalize the probe intensities and summarize the expression values at at meta-probe set level (representing gene level expression). We removed ~597 K SNP-containing probes (based on dbSNP build 129){Duan, 2008 #4758} before array normalization. Hybridization intensities of the remaining probes on an array were normalized on a log scale using a quantile normalization method {Bolstad, 2003 ; Barbacioru, 2006}. Normalization was carried out for total RNA arrays and  nascent RNA arrays separately, because they represent different biology and therefore may show different gene expression patterns. “Detection Above Background” (DABG) algorithm implemented in APT was used to determine the reliability of the signal intensity of each probe set (core exon) and each meta-probe set (transcript cluster or gene) through deriving a detection P-value. We followed the recommended detection P-value of ≤0.01 (Affymetrix) as a cut-off for determining an expressed or detectable probe. Furthermore, only genes expressed in >95% samples and with log-scale expression values >6 in total RNA  arrays were considered for further expression analyses.
HuEx-1_0-st-v2.r2.pgf
HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: B-LCL Coriell Cell Repositories (http://ccr.coriell.org/), treated with 200 uM 4sU for 2 hr

label_protocol: Ribosome RNA reduction was performed with RiboMinus Transcriptome Isolation Kit  (Invitrogen) before cDNA sythesis. 100 ng of total RNAs were used in cDNA synthesis with GeneChip WT cDNA Synthesis Kit (Affymetrix). cDNAs were then fragmented and end-labeled with GeneChip WT terminal Labeling Kit (Affymetrix).

growth_protocol: We grew the cells in 15 ml RPMI 1640 media (from ATCC) supplemented with 15% fetal bovine serum (FBS) (from ATCC) in T-25 cell culture flasks, maintaining the cell density at ~5-6 x 105 cells/ml.

extract_protocol: We used TRIzol reagent (Invitrogen) to isolate total RNAs from ~7-9 x 106 LCL cells. The total RNAs were further purified by RNeasy Mini Kit (Qiagen). To separate the 4sU-labeled nascent RNAs from total RNAs, we followed the protocol developed by Dolken et al {Dolken, 2008).

treatment_protocol: Upon the cell growth reaching log phase (~5 days), we seeded the cells at a density of 2.5 x 105 cells/ml one day before harvesting cells. On the harvest day (cell density usually reached 5-6 x 105 cells/ml), we treated cells for two hours with 200µM 4sU

tag: sample type

value: Nascent RNA


title: AML [2749_18jun08]

description: Not Applicable


title: AML [2748_29may08]

description: Not Applicable


title: RNA from RKO cells treated with Non-target siRNA and 5-AZA-CdR for 72hr rep1

description:
Replicate 1
5067319005_D


title: RNA from RKO cells treated with Non-target siRNA and 5-AZA-CdR for 72hr rep2

description:
Replicate 2
5067319030_B


title: Nascent RNA sample of GM12813 biological replicate3


title: AML [2747_20jun08]

description: Not Applicable


title: Nascent RNA sample of GM12814


title: AML [2695_22may08]

description: Not Applicable


title: Nascent RNA sample of GM12815


title: AML [2704_12jun08]

description: Not Applicable


title: 67NR whole primary tumour mouse no. 2

source_name: 67NR whole primary tumour mouse no. 2 in Balb/c mouse


title: AML [2692_03jun08]

description: Not Applicable


title: Primary cultured Glioma cells 3531-20-O2-2

city: Minneapolis

first: Aaron

last: Sarver

state: MN

address: 425 East River Road

department: Masonic Cancer Center

institute: University of Minnesota

description: replicate 2

hyb_protocol: Biotinylated cDNA was hybridized to assay oligonucleotides, which were subsequently bound to streptavidin-conjugated paramagnetic particles. Oligos were extended and ligated, creating templates that were amplified with random, fluorescent primers.

scan_protocol: The fluorescently labeled products were bound to 24,631 oligonucleotide probes contained on each microarray of a Illumina HumanRef-8_V3 Expression BeadChip, and analyzed with laser  confocal microscopy.

data_processing: Array data were analyzed for quality control, quantile normalized, and multiple probes for each gene were averaged.

source_name: Primary cultured Glioma cells from 3531

label_protocol: Biotinylated cDNA was synthesized from 100 ng of total RNA from each sample using mixed poly-T and random nonamer primers.

growth_protocol: Total RNA was isolated from snap frozen tissue at time of  resection, and from cells grown in 5% and 20% O2 in neural stem cell media.

extract_protocol: Total RNA was isolated from snap frozen tissue at time of  resection, and from cells grown in 5% and 20% O2 using the RNEasy Plus Mini Kit (Qiagen, Valencia, CA) according to the manufacturer’s instructions.

treatment_protocol: Tumor cells were initially grown in 20% oxygen and then subsequently moved to 5% oxygen for a minimum of 30 days prior to experiments

tag: treatment

value: 20 percent oxygen

tag: cell type

value: glioma cell


title: Nascent RNA sample of GM12813 biological replicate2


title: Primary cultured Glioma cells 3531-20-O2-1

description: replicate 1


title: Nascent RNA sample of GM12813 biological replicate2 technical duplicate


title: Primary Glioma tumor 3531-Tissue-1

description: replicate 1

source_name: Primary Glioma tumor 3531

value: endogenous oxygen

value: glioma tumor


title: Primary Glioma tumor 3531-Tissue-3

description: replicate 3


title: Nascent RNA sample of GM12813 biological replicate1 technical duplicate


title: RNA from RKO cells treated with Non-target siRNA and PBS for 72hr rep1

description:
Replicate 1
5067319005_A


title: Primary Glioma tumor 3531-Tissue-2

description: replicate 2


title: RNA from RKO cells treated with Non-target siRNA and PBS for 72hr rep2

description:
Replicate 2
5067319030_A


title: Primary cultured Glioma cells 3531-20-O2-3

description: replicate 3


title: Nascent RNA sample of GM12812


title: Nascent RNA sample of GM10835 biological replicate 3


title: Primary cultured Glioma cells 3531-5-O2-3

description: replicate 3

value: 5 percent oxygen


title: AML [2690_28may08]

description: Not Applicable


title: AML [2689_20may08]

description: Not Applicable

value: NPM1 A


title: Nascent RNA sample of GM12813 biological replicate1


title: 67NR whole primary tumour mouse no. 1

source_name: 67NR whole primary tumour mouse no. 1 in Balb/c mouse

value: Balb/c

value: 4th inguinal mammary fat pad


title: AML [2688_12jun08]

description: Not Applicable


title: AML [2687_9may08]

description: Not Applicable


title: Primary cultured Glioma cells 3531-5-O2-2

description: replicate 2


title: Nascent RNA sample of GM10835 biological replicate 1


title: AML [2686_03jun08]

description: Not Applicable


title: AML [2682_20may08]

description: Not Applicable


title: AML [2685_22may08]

description: Not Applicable


title: AML [2683_28may08]

description: Not Applicable


title: Primary Glioma tumor BST001-Tissue-2

description: replicate 2

source_name: Primary Glioma tumor BST001


title: Nascent RNA sample of GM07029 biological replicate 3


title: Nascent RNA sample of GM10835 biological replicate 2


title: Primary cultured Glioma cells  BST001-20-O2-2

description: replicate 2

source_name: Primary cultured Glioma cells from BST001


title: Nascent RNA sample of GM07029 biological replicate 1


title: AML [2678_14may08]

description: Not Applicable


title: Primary Glioma tumor BST001-Tissue-3

description: replicate 3


title: AML [2679_14may08]

description: Not Applicable


title: Nascent RNA sample of GM07019


title: Total RNA sample of GM12813 biological replicate3 technical duplicate

value: total RNA


title: Total RNA sample of GM12815


title: Primary cultured Glioma cells 3531-5-O2-1

description: replicate 1


title: Total RNA sample of GM12813 biological replicate3


title: AML [2676_29apr08]

description: Not Applicable

value: NPM1 D


title: Primary cultured Glioma cells  BST001-20-O2-1

description: replicate 1


title: Primary cultured Glioma cells   BST001-5-O2-1

description: replicate 1


title: Primary Glioma tumor BST001-Tissue-1

description: replicate 1


title: Total RNA sample of GM12814


title: Nascent RNA sample of GM07029 biological replicate 2


title: Primary cultured Glioma cells  BST001-5-O2-2

description: replicate 2


title: Total RNA sample of GM12813 biological replicate2 technical duplicate


title: Total RNA sample of GM12813 biological replicate2


title: Sox17-GFP(+) from Nodal treatment

city: Cambridge

first: Alice

middle: E

last: Chen

state: Ma

address: 7 Divinity Avenue

department: Stem Cell and Regenerative Biology

institute: Harvard University

description: 3 replicates for each sample

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using cubic spline with Bead Studio v2.0

source_name: Sox17-GFP mESC_Nodal_7d

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: Mouse ES cells were maintained on gelatin-coated plates with MEFs in DMEM, 0.1mM NEAA, 1x Glutamax, 1x Penn/Strep (Invitrogen), 15% FBS (HyClone), 0.055mM 2-mercaptoethanol (βMe; Sigma), and 5x10^5 units LIF (Chemicon)

extract_protocol: Total RNA isolated using Qiashredder and RNAeasy Mini Kit. Biotinylated cRNA prepared from ≥100ng of RNA using Illumina TotalPrep RNA Amplification Kit.

treatment_protocol: Endoderm differentiation was induced for 6-8 days in DMEM, 5% FBS, 0.1mM NEAA, 1x Glutamax, 1x Penn/Strep, 0.055mM βMe, supplemented with 50 ng/ml recombinant human Activin A or 1000ng/ml recombinant mouse Nodal; media changed every other day.

tag: strain background

tag: genotype/variation

value: mESC


title: Total RNA sample of GM12813 biological replicate1 technical duplicate


title: Sox17-GFP(+) from Activin treatment

description: 2 replicates for each sample

source_name: Sox17-GFP mESC_Activin_7d


title: undifferentiated Sox17-GFP mES cells

description: 4 replicates for each sample

source_name: Sox17-GFP mESC_undifferentiated


title: AML [2671_03jun08]

description: Not Applicable


title: AML [2670_18apr08]

description: Not Applicable


title: Total RNA sample of GM12813 biological replicate1


title: AML [2672_18jun08]

description: Not Applicable


title: AML [2669_18jun08]

description: Not Applicable


title: AML [2666_18jun08]

description: Not Applicable


title: AML [2668_11jun08]

description: Not Applicable


title: AML [2665_25apr08]

description: Not Applicable


title: muscle_Sgms1_rep4

city: Neuherberg

last: Irmler

state: Bayern

address: Ingolstaedter Landstrasse 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum München GmbH

description:
SAMPLE 22
replicate 4

scan_protocol: Standard Illumina scanning protocol using HiScan

data_processing: The data were normalised using cubic spline normalisation with Illumina Genomestudio 2011.1

source_name: muscle

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up with QIAGEN RNeasy midi kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with gel electrophoreses.

value: muscle

value: Sgms1 mutant

value: 17 weeks

tag: mouse id


title: Total RNA sample of GM07029 biological replicate 3


title: Total RNA sample of GM10835 biological replicate 3


title: muscle_wt_rep3

description:
SAMPLE 18
replicate 3

value: wt


title: Total RNA sample of GM12812


title: muscle_Sgms1_rep2

description:
SAMPLE 20
replicate 2


title: muscle_wt_rep1

description:
SAMPLE 16
replicate 1


title: muscle_wt_rep2

description:
SAMPLE 17
replicate 2


title: muscle_Sgms1_rep1

description:
SAMPLE 19
replicate 1


title: AML [2664_5jun08]

description: Not Applicable

value: Training

value: NPM1 wt


title: AML [2647_28may08]

description: Not Applicable


title: Total RNA sample of GM10835 biological replicate 2


title: d/d-10w-KA, biological rep2

city: Fukuoka

first: Yusaku

last: Nakabeppu

state: Fukuoka

address: 3-1-1 Maidashi Higashi-ku

department: Department of Immunobiology and Neuroscience

institute: Medical Institute of Bioregulation, Kyushu University

hyb_protocol: Following fragmentation, 5.5 µg of cDNA were hybridized for 17 hr at 45℃ on Affymetrix Mouse Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip® Scanner 3000 7G.

data_processing: CEL files were imported into Affymetrix Expression Console Software, and CHP files were generated.

source_name: Hippocampus of d/d mouse treatment with Kainate acid

label_protocol: The Ambion WT Expression Kit and the GeneChip WT Terminal Labeling and Controls Kit (Affymetrix) were used to generate amplified and biotinylated sense-strand DNA targets from expressed transcripts (100 ng of total RNA).

growth_protocol: Each mouse was maintained in SPF condition and sacrificed at 14 months of age.

extract_protocol: Total RNA was isolated using a combination of Isogen (Nippon Gene) and the RNeasy Mini Kit (Qiagen), according to the manufacturers’ instructions.

treatment_protocol: Brains were removed from each mouse under pentobarbital anesthesia (i.p), with perfusion of 40 ml of saline via the left ventricle. Hippocampi were isolated and preserved at –80°C until RNA preparation.

value: Hippocampus

tag: genotype

value: d/d (lacking FosB protein)

value: 10 weeks

value: female

value: KA


title: AML [2658_9may08]

city: Rotterdam

last: Vliet

address: Lichtenauerlaan 40

institute: SkylineDx

description: Not Applicable

scan_protocol: As described in the AMLprofiler IFU (instructions for use) on an Affymetrix GeneChip System 3000Dx v.2

data_processing: DM algorithm implemented in the Affymetrix Power Tools (APT 1.10.2).

extract_protocol: After thawing, cells were washed once with Hanks’balanced-salt solution. High-quality total RNA was extracted by lysis with guanidinium thiocyanate followed by cesium chloride–gradient purification. RNA levels, quality, and purity were assessed with the use of the RNA 6000 Nano assay on the Agilent 2100 Bioanalyzer (Agilent). None of the samples showed RNA degradation (ratio of 28S ribosomal RNA to 18S ribosomal RNA of at least 2) or contamination by DNA.


title: Total RNA sample of GM10835 biological replicate 1


title: muscle_Sgms1_rep3

description:
SAMPLE 21
replicate 3


title: Total RNA sample of GM07029 biological replicate 2


title: G/G-10w-KA, biological rep3

source_name: Hippocampus of G/G mouse treatment with Kainate acid

value: G/G (fosB-null)


title: d/d-10w-KA, biological rep1


title: d/d-10w-KA, biological rep3


title: brain_Sgms1_rep4

description:
SAMPLE 15
replicate 4

source_name: brain

value: brain


title: G/G-10w-KA, biological rep2


title: AML [2551_25apr08]

description: Not Applicable


title: AML [2644_20jun08]

description: Not Applicable

value: NPM1 non-ABD


title: Total RNA sample of GM07029 biological replicate 1

value: total RNA


title: AML [2550_16may08]

description: Not Applicable


title: brain_Sgms1_rep3

description:
SAMPLE 14
replicate 3


title: brain_Sgms1_rep2

description:
SAMPLE 13
replicate 2


title: G/G-10w-KA, biological rep1


title: AML [2549_16may08]

description: Not Applicable


title: AML [2545_13jun08]

description: Not Applicable


title: brain_wt_rep1

description:
SAMPLE 9
replicate 1


title: wt-10w-KA, biological rep2

source_name: Hippocampus of wt mouse treatment with Kainate acid

value: wild type


title: Total RNA sample of GM07019


title: wt-10w-KA, biological rep1


title: brain_wt_rep2

description:
SAMPLE 10
replicate 2


title: RNA-UPPP-23

city: Baltimore

first: Michael

middle: F

last: Ochs

address: 550 North Broadway, Ste 1103

department: Oncology Biostatistics

institute: Johns Hopkins University

description:
Sample name: 27934
PHen-HNC-27934-1a-hsExon1_(HuEx-1_0-st-v2).CEL

hyb_protocol: The labeled sense strand DNA was hybridized to the Affymetrix GeneChip human Exon 1.0 ST arrays for 17hr at 45 C with constant rotation (60 rpm).  Affymetrix Fluidics Station 450 was used to wash and stain the Chips, removing the non-hybridized target and incubating with a streptavidin-phycoerythrin conjugate to stain the biotinilated cDNA.  The staining was further amplified using goat IgG as blocking reagent and biotinilated anti-streptavidin antibody (goat), followed by a second staining step with a streptavidin-phycoerythrin conjugate.

scan_protocol: Fluorescence was detected using the Affymetrix G3000 GeneArray Scanner and image analysis of each GeneChip was perfomed through the Affymetrix GeneChip Command Console version 3.4 (AGCC v3.4) software from Affymetrix.

data_processing:
Analysis was performed in R with the oligo package, RMA was used for normalization at both exon and gene levels
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.na30.hg19.transcript.csv

source_name: Ctrl 123

label_protocol: RNA from control and experimental samples were labeled using the Whole Transcript Sense Target Labeling protocol described by Affymetrix and reagent from Ambion and Affymetrix. Briefly, 100ng of total RNA was used to synthesize first strand cDNA using random oligonucleotides with T7 promoter as primer and the SuperScript Choice System (Invitrogen, Carlsbad, California).  Following the double stranded cDNA synthesis, the double strand cDNA was purified using magnetic beads, and cRNA was generated through in vitro transcription.  10 ug of cRNA was then used to generate sense strand cDNA using random primer, dNTP-dUTP mix, and Superscript II reverse transcriptase (Invitrogen, Carlsbad, California).  The resulting sense strand cDNA was then purified, fragmented using UDG and APE at 37C for 60 minutes, and terminal labeled with biotinylated nucleotide and terminal DNA transferase at 37C for 60 minutes.

growth_protocol: human HNSCC and UPPP surgical samples

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: human surgical specimens, flash frozen

tag: sample identifier

value: Ctrl 123

value: normal

value: control (UPPP)


title: RNA-UPPP-22

description:
Sample name: 27911
PHen-HNC-27911-1a-hsExon1_(HuEx-1_0-st-v2).CEL

source_name: Ctrl 122

value: Ctrl 122


title: wt-10w-KA, biological rep3

tag: Sex


title: brain_Sgms1_rep1

first: Martin

description:
SAMPLE 12
replicate 1

value: Sgms1 mutant

value: 17 weeks


title: brain_wt_rep3

description:
SAMPLE 11
replicate 3

value: wt


title: AML [2544_28may08]

description: Not Applicable

hyb_protocol: As described in the AMLprofiler IFU (instructions for use), Hybridized for 17 hours, 45C at 60 rpm in Affymetrix Hybridization oven

source_name: AML

label_protocol: We used 10 µg of total RNA to prepare antisense biotinylated RNA. Single-stranded complementary DNA (cDNA) and double-stranded cDNA were synthesized according to the manufacturer’s protocol (Invitrogen Life Technologies) with the use of the T7-(deoxythymidine)24-primer (Genset). In vitro transcription was performed with biotin-11-cytidine triphosphate and biotin-16-uridine triphosphate (Perkin–Elmer) and the MEGAScript T7 labeling kit (Ambion). Double-stranded cDNA and complementary RNA (cRNA) were purified and fragmented with the GeneChip Sample Cleanup Module (Affymetrix).

tag: cohort

value: Training

value: NPM1 wt


title: RNA-UPPP-25

description:
Sample name: 27901
PHen-HNC-27901-1a-hsExon1_(HuEx-1_0-st-v2).CEL

source_name: Ctrl 125

value: Ctrl 125


title: d/d-10w-sa, biological rep1

value: Hippocampus

value: d/d (lacking FosB protein)

value: 10 weeks

value: female

value: saline


title: testis_Sgms1_rep4

description:
SAMPLE 8
replicate 4

source_name: testis

value: testis

value: 27 weeks