title: MSC from healthy donor 6 +TNF/LT set 2

description: Gene expression from Healthy Donnor derived BM-MSC stimulated by TNFalpha and Lymphotoxin alpha1beta7

value: Female

tag: treatment


title: Subject THG EDTA, biological rep1

status: Public on Jan 26 2012

type: RNA

city: Vancouver

first: Scott

last: Tebbutt

state: BC

address: Room 166, 1081 Burrard Street

department: Medicine

country: Canada

institute: University of British Columbia

hyb_protocol: Affymetrix Human Gene 1.0 ST array (Affymetrix, Santa Clara, CA)

scan_protocol: standand Affymetrix protocol

data_processing:
Raw data normalization using the 'farms' package consisted of quantile normalization and  summarization of probe-level data.
Data filtering was also performed using the Informative vs. Non-Informative Calls function in the 'farms' package. Differential gene expression was determined using moderated t-tests in limma using an FDR cut-off of 5%.
All statistical analyses were performed in the statistical computing program R.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: whole blood Pre-challenged

label_protocol: standand Affymetrix protocol

extract_protocol:
Samples were stored at -80⁰C until RNA extraction
From PAXgene tube samples, total RNA was purified from 2.5 mL of whole blood using Rneasy mini kit (Qiagen, Chatsworth, CA, USA)
From EDTA tube samples, total RNA was purified from 3.0 mL of whole blood following modified TRIzol-based extraction method.
The yield and quality of RNA was assessed by NanoDrop 8000 Spectrophotometer (Thermo Scientific, Wilmington, DE, USA) and Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA)

tag: gender

value: F

tag: age

tag: site

value: McM

tag: allergen

value: Cat

tag: mch pc20 (mg/ml) at pre-challenge

tag: mch pc20 (mg/ml) at post-challenge

tag: % fall in fev1 (early)

tag: % fall in fev1 (late)

tag: rna integrity number

tag: tissue

value: whole blood


title: MSC from healthy donor 6 set 2

city: Rennes

first: Delphine

last: Rossille

address: 2 avenue du Pr. Léon Bernard

country: France

institute: INSERM U1236-MOBIDIC

description: Gene expression from Healthy Donnor derived BM-MSC

hyb_protocol: Following fragmentation, 12 µg of cARN were hybridized for 16h at 45°C and 60rpm on GeneChip Human U133Plus2 arrays

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

data_processing:
The data were normalized by the RMA algorithm using GC content from the Partek Genomics Suite software (Partek, St Louis, MO).
set 1: FL-MSC signaturethat includes the genes differentially expressed in FL-MSC compared with HD-MSC (GUILLOTON F et al., Blood, 2012, figure 1 and tableS3)
set 2: TNF/LT signature that includes the genes differentially expressed in HD-MSC+TNF/LT compared with HD-MSC (GUILLOTON F et al., Blood, 2012, figure 2 and tableS4).

source_name: In vitro expanded BM-MSC

label_protocol: Biotinylated cRNA were amplified according to the small sample labelling protocol (TwoCycle amplification kit, Affymetrix, Santa Clara, CA)

growth_protocol: MSC were expanded from bone marrow mononuclear cells until passage 1 in aphaMEM+10%FBS+FGF2 (1ng/mL)

extract_protocol: RNA was extracted using AllPrep ARN/ADN/protein kit (Qiagen, Valencia, CA)

tag: pathology

value: Healthy donor

tag: age (y)

tag: growth protocol

value: Untreated

tag: cell type

value: Bone-Marrow Mesenchymal Stromal Cells


title: MSC from healthy donor 3 +TNF/LT set 2

description: Gene expression from Healthy Donnor derived BM-MSC stimulated by TNFalpha and Lymphotoxin alpha1beta4

value: Male

value: Stimulated by TNF+LT for 3 days


title: MSC from healthy donor 3 set 2


title: Subject THG EDTA,  biological rep2

source_name: whole blood Post-challenged


title: CAFs_rep_1

city: Hefei

first: Wei

last: Lan

state: Anhui

address: 96#, Jinzhai Road

department: School of Life Science

country: China

institute: University of Science and Technology of China

description: Gene expression of oral CAFs

hyb_protocol: Hybridized to the chip at 65°C for 17 h according to Agilent protocol.

scan_protocol: After wash, the chip was scanned and visualized using the Agilent DNA microarray scanner. Probe set intensities were measured using Agilent Feature Extraction software.

data_processing: Raw data were normalized in the Agilent GeneSpring GX software using the Agilent FE one-color scenario (median normalization).

source_name: CAFs replicate 1

label_protocol: 1 μg total RNA pooled respectively from the CAFs and the NFs were reversed transcripted, labeled, and hybridized to the chip at 65°C for 17 h.

extract_protocol: TRIzol reagent (Invitrogen, USA) was used to extract total RNA and ultraviolet spectrophotometry was used to examine the quality of RNA samples.

treatment_protocol: The tissues were isolated, cultured, purified and identified using standard methods. The protocol was reviewed by the Institutional Ethics Committee of West China Hospital of Stomatology and informed consent was obtained from each subject. Briefly, tissues were washed thrice with phosphate-buffered saline (PBS) and antibiotics (100 U/ml penicillin and 100 μg/ml streptomycin). Then epithelial and adipose tissues were separated from surrounding stromal cells. The residual connective tissue was cut into small pieces (1 × 1 × 1 mm) that were maintained in Dulbecco’s modified Eagle’s medium (DMEM, Gibco, pH 7.2) containing 20% fetal calf serum at 37°C in an atmosphere containing 5% CO2. To purify the cells, we opted for a method of curettage combined with trypsinization, which was performed when cells fully covered the bottom of the culture bottle. Cultures at passage number three were used for the cellular identification of oral CAFs and NFs. A wide-spectrum a-cytokeratin antibody was used to confirm the absence of contaminating epithelial cells. Finally, antibodies against vimentin and smooth muscle actin (SMA) were used to confirm the myofibroblastic nature of these cells.

value: oral carcinoma-associated fibroblasts (CAFs)


title: Subject 102 EDTA, biological rep1


title: MSC from healthy donor 4 +TNF/LT set 2

description: Gene expression from Healthy Donnor derived BM-MSC stimulated by TNFalpha and Lymphotoxin alpha1beta5


title: MSC from healthy donor 4 set 2


title: Subject 105 EDTA,  biological rep2

source_name: Post

value: M

value: HDMDP


title: MSC from healthy donor 1  set 2


title: MSC from healthy donor 1 +TNF/LT set 2

description: Gene expression from Healthy Donnor derived BM-MSC stimulated by TNFalpha and Lymphotoxin alpha1beta2


title: Subject 012 EDTA,  biological rep2


title: 790T_NETs alone 3.1

type: protein

city: Stanford

first: Chih Long

last: Liu

state: CA

address: 269 Campus Drive

department: Medicine - Imm. & Rheum

country: USA

institute: Stanford University

description:
790T
Murine antiserum was obtained from blood collected from an individual Balb/c mouse (3) treated with 2 ug NETs at 1 month. A 1:250 dilution of this antiserum was then applied onto the Utz Lab Whole Protein Autoantigen Array (V2.0), labeled with a goat anti-mouse IgM secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.

hyb_protocol: Murine antiserum was probed on the antigen microarray at 1:250 dilution in 5% fetal bovine serum in phosphate-buffered saline with 0.1% Tween-20, and incubated for 1.25 hours at 4 degrees Celsius.

scan_protocol: Fluorescent array images were collected at 635 nm with a GenePix 4000B fluorescent scanner at 10 micron resolution and image intensity data were extracted and analyzed with GenePix Pro 6.1 analysis software.

data_processing: Data were background corrected and flagged values were removed.  The remaining replicate values were averaged.

label: DyLight-649-conjugated goat anti-mouse IgM antibody

molecule: protein

organism: Mus musculus

source_name: murine antiserum

label_protocol: Commercially available DyLight 649-conjugated goat anti-mouse antibody was added to the microarray at 1:2000 in 5% fetal bovine serum in phosphate-buffered saline with 0.1% Tween-20.

extract_protocol: Whole antiserum was obtained.

tag: strain

value: Balb/c

value: NETs


title: Subject 012 EDTA, biological rep1


title: Subject AKA EDTA,  biological rep2


title: MSC from follicular lymphoma patient 8 set 1

description: Gene expression from Follicular Lymphoma derived BM-MSC

value: Follicular Lymphoma patient


title: MSC from healthy donor 2 +TNF/LT set 2

description: Gene expression from Healthy Donnor derived BM-MSC stimulated by TNFalpha and Lymphotoxin alpha1beta3


title: MSC from follicular lymphoma patient 7 set 1


title: MSC from follicular lymphoma patient 10 set 1


title: MSC from healthy donor 2 set 2


title: Subject 105 EDTA, biological rep1


title: MSC from follicular lymphoma patient 9 set 1


title: MSC from healthy donor 5 set 2


title: 309B_NETs alone 2.2

description:
309B
Murine antiserum was obtained from blood collected from an individual Balb/c mouse (2) treated with 2 ug NETs at 2 months. A 1:250 dilution of this antiserum was then applied onto the Utz Lab Whole Protein Autoantigen Array (V2.0), labeled with a goat anti-mouse IgM secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.


title: 233T_NETs alone 3.0

description:
233T
Murine antiserum was obtained from blood collected from an individual Balb/c mouse (3) treated with 2 ug NETs at 0 months. A 1:250 dilution of this antiserum was then applied onto the Utz Lab Whole Protein Autoantigen Array (V2.0), labeled with a goat anti-mouse IgM secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.


title: 231B_NETs alone 2.1

description:
231B
Murine antiserum was obtained from blood collected from an individual Balb/c mouse (2) treated with 2 ug NETs at 1 month. A 1:250 dilution of this antiserum was then applied onto the Utz Lab Whole Protein Autoantigen Array (V2.0), labeled with a goat anti-mouse IgM secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.


title: 236B_NETs alone 2.0

description:
236B
Murine antiserum was obtained from blood collected from an individual Balb/c mouse (2) treated with 2 ug NETs at 0 months. A 1:250 dilution of this antiserum was then applied onto the Utz Lab Whole Protein Autoantigen Array (V2.0), labeled with a goat anti-mouse IgM secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.


title: 309T_NETs alone 1.2

description:
309T
Murine antiserum was obtained from blood collected from an individual Balb/c mouse (1) treated with 2 ug NETs at 2 months. A 1:250 dilution of this antiserum was then applied onto the Utz Lab Whole Protein Autoantigen Array (V2.0), labeled with a goat anti-mouse IgM secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.


title: 231T_NETs alone 1.1

description:
231T
Murine antiserum was obtained from blood collected from an individual Balb/c mouse (1) treated with 2 ug NETs at 1 month. A 1:250 dilution of this antiserum was then applied onto the Utz Lab Whole Protein Autoantigen Array (V2.0), labeled with a goat anti-mouse IgM secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.


title: Subject 026 PAX.NGR (reanalysis),  biological rep2


title: MSC from follicular lymphoma patient 6 set 1


title: Subject 005 PAX.NGR (reanalysis),  biological rep2

value: Van

value: Timothy Grass


title: MSC from follicular lymphoma patient 5 set 1


title: Subject 026 PAX.NGR (reanalysis), biological rep1

value: F


title: Subject 006 PAX.NGR (reanalysis), biological rep1

value: Orchard Grass


title: Subject 006 PAX.NGR (reanalysis),  biological rep2


title: MSC from follicular lymphoma patient 1 set 1


title: MSC from follicular lymphoma patient 4 set 1

value: Female


title: MSC from follicular lymphoma patient 3 set 1


title: MSC from follicular lymphoma patient 2 set 1


title: Subject 004 PAX.NGR (reanalysis),  biological rep2

value: whole blood


title: MSC from healthy donor 5 set 1

value: Healthy donor


title: Subject 005 PAX.NGR (reanalysis), biological rep1


title: MSC from healthy donor 6 set 1

value: Untreated


title: 236T_NETs alone 1.0

description:
236T
Murine antiserum was obtained from blood collected from an individual Balb/c mouse (1) treated with 2 ug NETs at 0 months. A 1:250 dilution of this antiserum was then applied onto the Utz Lab Whole Protein Autoantigen Array (V2.0), labeled with a goat anti-mouse IgM secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.


title: 310B_NETs + CRAMP 3.2

description:
310B
Murine antiserum was obtained from blood collected from an individual Balb/c mouse (3) treated with 2 ug NETs + 10 ug CRAMP at 2 months. A 1:250 dilution of this antiserum was then applied onto the Utz Lab Whole Protein Autoantigen Array (V2.0), labeled with a goat anti-mouse IgM secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.

value: NETs + CRAMP


title: 310T_NETs + CRAMP 2.2

description:
310T
Murine antiserum was obtained from blood collected from an individual Balb/c mouse (2) treated with 2 ug NETs + 10 ug CRAMP at 2 months. A 1:250 dilution of this antiserum was then applied onto the Utz Lab Whole Protein Autoantigen Array (V2.0), labeled with a goat anti-mouse IgM secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.


title: 234B_NETs + CRAMP 3.0

description:
234B
Murine antiserum was obtained from blood collected from an individual Balb/c mouse (3) treated with 2 ug NETs + 10 ug CRAMP at 0 months. A 1:250 dilution of this antiserum was then applied onto the Utz Lab Whole Protein Autoantigen Array (V2.0), labeled with a goat anti-mouse IgM secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.


title: 792B_NETs + CRAMP 3.1

description:
792B
Murine antiserum was obtained from blood collected from an individual Balb/c mouse (3) treated with 2 ug NETs + 10 ug CRAMP at 1 month. A 1:250 dilution of this antiserum was then applied onto the Utz Lab Whole Protein Autoantigen Array (V2.0), labeled with a goat anti-mouse IgM secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.


title: 792T_NETs + CRAMP 2.1

description:
792T
Murine antiserum was obtained from blood collected from an individual Balb/c mouse (2) treated with 2 ug NETs + 10 ug CRAMP at 1 month. A 1:250 dilution of this antiserum was then applied onto the Utz Lab Whole Protein Autoantigen Array (V2.0), labeled with a goat anti-mouse IgM secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.


title: 234T_NETs + CRAMP 2.0

description:
234T
Murine antiserum was obtained from blood collected from an individual Balb/c mouse (2) treated with 2 ug NETs + 10 ug CRAMP at 0 months. A 1:250 dilution of this antiserum was then applied onto the Utz Lab Whole Protein Autoantigen Array (V2.0), labeled with a goat anti-mouse IgM secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.


title: 306B_NETs + CRAMP 1.2

description:
306B
Murine antiserum was obtained from blood collected from an individual Balb/c mouse (1) treated with 2 ug NETs + 10 ug CRAMP at 2 months. A 1:250 dilution of this antiserum was then applied onto the Utz Lab Whole Protein Autoantigen Array (V2.0), labeled with a goat anti-mouse IgM secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.


title: 790B_NETs + CRAMP 1.1

description:
790B
Murine antiserum was obtained from blood collected from an individual Balb/c mouse (1) treated with 2 ug NETs + 10 ug CRAMP at 1 month. A 1:250 dilution of this antiserum was then applied onto the Utz Lab Whole Protein Autoantigen Array (V2.0), labeled with a goat anti-mouse IgM secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.


title: Subject 004 PAX.NGR (reanalysis), biological rep1


title: 233B_NETs + CRAMP 1.0

description:
233B
Murine antiserum was obtained from blood collected from an individual Balb/c mouse (1) treated with 2 ug NETs + 10 ug CRAMP at 0 months. A 1:250 dilution of this antiserum was then applied onto the Utz Lab Whole Protein Autoantigen Array (V2.0), labeled with a goat anti-mouse IgM secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.


title: Subject 026 PAX.NGR,  biological rep2

scan_protocol: standard Affymetrix protocol

label_protocol: standard Affymetrix protocol

extract_protocol:
The samples collected pre- and post-challenge were frozen and transported to the laboratory on dry ice, where they were stored at –80°C until RNA extraction.
From 8 PAXgene Blood RNA tubes (PreAnalytiX – Qiagen / BD, Valencia, CA, USA), total intracellular RNA was purified from 2.5 mL of whole-blood according to manufacturer protocols using the RNeasy mini kit (Qiagen, Chatsworth, CA, USA).
The yield and quality of RNA was assessed by NanoDrop 8000 Spectrophotometer (Thermo Scientific, Wilmington, DE, USA) and Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA)

value: McM


title: Subject 026 PAX.NGR, biological rep1


title: Subject 006 PAX.NGR,  biological rep2


title: Subject 005 PAX.NGR,  biological rep2


title: Subject 006 PAX.NGR, biological rep1


title: 833B_negative control

description:
833B
As a negative control, serum dilutent was applied onto the Utz Lab Whole Protein Autoantigen Array (V2.0), labeled with a goat anti-mouse IgG secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.

hyb_protocol: As a negative control, 5% fetal bovine serum in phosphate-buffered saline with 0.1% Tween-20 was incubated for 1.25 hours at 4 degrees Celsius.

source_name: Dilution buffer

value: negative control


title: Subject 005 PAX.NGR, biological rep1


title: 833T_MRL/lpr positive control

description:
833T
Murine antiserum was obtained from blood collected from an individual MLR/lpr mouse exhibiting lupus-like symptoms.  A 1:250 dilution of this antiserum was then applied onto the Utz Lab Whole Protein Autoantigen Array (V2.0), labeled with a goat anti-mouse IgG secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.

value: MRL/lpr

value: positive control


title: MSC from healthy donor 1  set 1

description: Gene expression from Healthy Donnor derived BM-MSC

value: Male

value: Bone-Marrow Mesenchymal Stromal Cells


title: Subject 026 PAX.GR, biological rep1

data_processing:
Raw data normalization using the 'farms' package consisted of quantile normalization and  summarization using factor analysis of probe-level data.
Data filtering was also performed using the Informative vs. Non-Informative Calls function in the 'farms' package. Differential gene expression was determined using moderated t-tests in limma using an FDR cut-off of 5%.
All statistical analyses were performed in the statistical computing program R.

extract_protocol:
The samples collected pre- and post-challenge were frozen and transported to the laboratory on dry ice, where they were stored at –80°C until RNA extraction.
From 8 PAXgene Blood RNA tubes (PreAnalytiX – Qiagen / BD, Valencia, CA, USA), total intracellular RNA was purified from 2.5 mL of whole-blood according to manufacturer protocols using the RNeasy mini kit (Qiagen, Chatsworth, CA, USA).
Aliquots of RNA isolated from PAXgene tube samples taken from the 4 individuals were subjected to globin transcript reduction processes using the GLOBINclear™ - Human kit (Ambion – AB, Austin, TX, USA).
The yield and quality of RNA was assessed by NanoDrop 8000 Spectrophotometer (Thermo Scientific, Wilmington, DE, USA) and Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA)

value: HDMDP


title: Subject 004 PAX.NGR, biological rep1

value: M


title: Subject 026 PAX.GR,  biological rep2


title: Subject 004 PAX.NGR,  biological rep2

value: Van


title: MSC from healthy donor 3 set 1


title: MSC from healthy donor 2 set 1


title: Subject 006 PAX.GR,  biological rep2


title: MSC from healthy donor 4 set 1


title: Endometrial Cancer Specimen, Progressive 2

city: Rotterdam

first: Paul

middle: H

last: van der Horst

address: PO box 2040

department: Obstetrics & Gynaecology

country: Netherlands

institute: Erasmus University Medical Center

description: Gene expression data from progressive endometrial cancer specimen.

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol.

data_processing: Using RMAexpress (Robust Multi-array Analysis), normalization of raw data was performed to be able to produce gene lists.

label: Biotin

source_name: Snap-frozen endometrial cancer specimen from progressive patient

label_protocol: Standard Affymetrix protocol.

extract_protocol: Patient tissue samples were sectioned (5 μm, cryostat) and every 10th section was HE stained and revised by the pathologist (PCE) to assess tumor load. Only sections containing >80% tumor were lysed in Trizol (Invitrogen) and sonified for 1 min. Phase separation was accomplished with 0.2 ml chloroform and centrifugation for 15 min. The supernatant was transferred and isopropanol was added for RNA precipitation. The precipitated RNA was washed with 75% ethanol. All RNA was cleaned with the RNeasy MinElute cleanup kit (Qiagen, Venlo, The Netherlands). Amount and quality of the RNA was assessed by using the Nanodrop (Nanodrop, Wilmington, DE, USA) and Bio-analyzer (Aligent, Santa Clara, CA, USA).

value: endometrial cancer

tag: progressive status

value: progressive (recurrence or metastasis)


title: Endometrial Cancer Specimen, Progressive 1


title: Endometrial Cancer Specimen, Progressive 4


title: Endometrial Cancer Specimen, Non-progressive 2

description: Gene expression data from non-progressive endometrial cancer specimen.

source_name: Snap-frozen endometrial cancer specimen from non-progressive patient

value: non-progressive (no recurrence or metastasis)


title: Endometrial Cancer Specimen, Non-progressive 4


title: Endometrial Cancer Specimen, Non-progressive 3


title: 839T_NETs alone 3.1

description:
839T
Murine antiserum was obtained from blood collected from an individual Balb/c mouse (3) treated with 2 ug NETs at 1 month. A 1:250 dilution of this antiserum was then applied onto the Utz Lab Whole Protein Autoantigen Array (V2.0), labeled with a goat anti-mouse IgG secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.

label: DyLight-649-conjugated goat anti-mouse IgG antibody

value: Balb/c

tag: treatment

value: NETs


title: Subject 006 PAX.GR, biological rep1

tag: gender

value: Orchard Grass

value: whole blood


title: Endometrial Cancer Specimen, Progressive 3


title: Endometrial Cancer Specimen, Non-progressive 1


title: Subject 005 PAX.GR,  biological rep2

value: F

tag: age

value: Timothy Grass


title: 834T_NETs alone 3.2

description:
834T
Murine antiserum was obtained from blood collected from an individual Balb/c mouse (3) treated with 2 ug NETs at 2 months. A 1:250 dilution of this antiserum was then applied onto the Utz Lab Whole Protein Autoantigen Array (V2.0), labeled with a goat anti-mouse IgG secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.


title: 837B_NETs alone 2.2

description:
837B
Murine antiserum was obtained from blood collected from an individual Balb/c mouse (2) treated with 2 ug NETs at 2 months. A 1:250 dilution of this antiserum was then applied onto the Utz Lab Whole Protein Autoantigen Array (V2.0), labeled with a goat anti-mouse IgG secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.


title: 570B_NETs alone 2.0

description:
570B
Murine antiserum was obtained from blood collected from an individual Balb/c mouse (2) treated with 2 ug NETs at 0 months. A 1:250 dilution of this antiserum was then applied onto the Utz Lab Whole Protein Autoantigen Array (V2.0), labeled with a goat anti-mouse IgG secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.


title: 575B_NETs alone 2.1

description:
575B
Murine antiserum was obtained from blood collected from an individual Balb/c mouse (2) treated with 2 ug NETs at 1 month. A 1:250 dilution of this antiserum was then applied onto the Utz Lab Whole Protein Autoantigen Array (V2.0), labeled with a goat anti-mouse IgG secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.


title: 575T_NETs alone 1.1

description:
575T
Murine antiserum was obtained from blood collected from an individual Balb/c mouse (1) treated with 2 ug NETs at 1 month. A 1:250 dilution of this antiserum was then applied onto the Utz Lab Whole Protein Autoantigen Array (V2.0), labeled with a goat anti-mouse IgG secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.


title: 571T_NETs alone 3.0

description:
571T
Murine antiserum was obtained from blood collected from an individual Balb/c mouse (3) treated with 2 ug NETs at 0 months. A 1:250 dilution of this antiserum was then applied onto the Utz Lab Whole Protein Autoantigen Array (V2.0), labeled with a goat anti-mouse IgG secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.


title: 836B_NETs + CRAMP 3.1

description:
836B
Murine antiserum was obtained from blood collected from an individual Balb/c mouse (3) treated with 2 ug NETs + 10 ug CRAMP at 1 month. A 1:250 dilution of this antiserum was then applied onto the Utz Lab Whole Protein Autoantigen Array (V2.0), labeled with a goat anti-mouse IgG secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.

value: NETs + CRAMP


title: BASC-Myc-depletion-1 [miRNA]

city: Rochester

first: Jie

last: Dong

state: MN

address: 200 1st SW

department: Thoracic Surgery

institute: Mayo Clinic

description:
Non-coding RNA profiling data from mouse bronchoalveolar stem cells
Method: real-time PCR

hyb_protocol: Not applicable.

scan_protocol: Not applicable.

data_processing:
The data were analyzed with RQ manager and Partek Genomics Suite 6.4.
Target gene Ct normalized to microRNA "MammU6" control gene Ct.

label: SYBR Green

source_name: bronchoalveolar stem cells

label_protocol: Running protocol: Quantitative 384 well TaqMan Low Density Array real-time PCR was run on the ABI PRISM 7900 System using the TaqMan Universal PCR Master Mix.

growth_protocol: BASCs were isolated from the lungs of 4-6 week old ICR mice. In brief, Mice were sacrificed, and their lungs were removed and cut into small pieces. Tissue dissociation was performed, then passing the lungs through a 70 μM filter to obtain a single cell suspension. After washing with PBS. cells were stained with Biotin-conjugated anti-CD31 and anti-CD45, APC-conjugated streptavidin, PE-conjugated anti-Scal, and FITC-conjugated anti-CD34. Cells were washed and sorted for CD31neg, CD45neg, CD34pos and ScaIpos cells on an Aria Flow Cytometry machine. Sorted BASCs were cultured onto irradiated MEF (mouse embryonic fibroblast) cells with BASC media.

extract_protocol:
miR VanaTM miRNA Isolation Kit (Ambion) was used for miRNA isolation in according ot manufacturer's instructions
Reverse Transcribe protocol: miRNA was reverse transcribed to cDNA using the Megaplex TM RT Todent Primers Pool and the TaqMan MicroRNA Reverse transcription Kit

treatment_protocol: We depleted c-Myc endogenous expression by transfecting lentivirus-delivered c-Myc shRNA into BASCs, After several generations of puromycin selection, stable c-Myc knock down cell lines were established and the degree of c-Myc reduction in both mRNA and protein level was confirmed

value: ICR

value: bronchoalveolar stem cells (BASC)

tag: genotype/variation

value: Myc-depleted

tag: c-myc depletion

value: Myc-depleted BASC cells


title: BASC-Myc-depletion-2 [miRNA]


title: 832T_NETs + CRAMP 2.2

description:
832T
Murine antiserum was obtained from blood collected from an individual Balb/c mouse (2) treated with 2 ug NETs + 10 ug CRAMP at 2 months. A 1:250 dilution of this antiserum was then applied onto the Utz Lab Whole Protein Autoantigen Array (V2.0), labeled with a goat anti-mouse IgG secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.


title: Subject 005 PAX.GR, biological rep1

tag: site

tag: allergen

tag: mch pc20 (mg/ml) at pre-challenge


title: 837T_NETs alone 1.2

description:
837T
Murine antiserum was obtained from blood collected from an individual Balb/c mouse (1) treated with 2 ug NETs at 2 months. A 1:250 dilution of this antiserum was then applied onto the Utz Lab Whole Protein Autoantigen Array (V2.0), labeled with a goat anti-mouse IgG secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.


title: Subject 004 PAX.GR, biological rep1

tag: mch pc20 (mg/ml) at post-challenge

tag: % fall in fev1 (early)

tag: % fall in fev1 (late)


title: 573B_NETs + CRAMP 3.0

description:
573B
Murine antiserum was obtained from blood collected from an individual Balb/c mouse (3) treated with 2 ug NETs + 10 ug CRAMP at 0 months. A 1:250 dilution of this antiserum was then applied onto the Utz Lab Whole Protein Autoantigen Array (V2.0), labeled with a goat anti-mouse IgG secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.


title: IKPRAB36, MPA 3

description: Gene expression data from IKPRAB36 cell line treated with 1nM MPA for 48 hours.

source_name: IKPRAB36 cell line cultured for 48 hours in presence of 1nm MPA

growth_protocol: For all assays, cells were cultured in DMEM/F12 Glutamax culture medium supplemented with penicillin and streptomycin (Invitrogen), containing 5% charcoal stripped FCS (Invitrogen) with addition of hygromycin and neomycin.

extract_protocol: The cells were placed on ice and lysed in Trizol (Invitrogen). Phase separation was accomplished with 0.2 ml chloroform and centrifugation for 15 min. The supernatant was transferred and isopropanol was added for RNA precipitation. The precipitated RNA was washed with 75% ethanol. All RNA was cleaned with the RNeasy MinElute cleanup kit (Qiagen, Venlo, The Netherlands). Amount and quality of the RNA was assessed by using the Nanodrop (Nanodrop, Wilmington, DE, USA) and Bio-analyzer (Aligent, Santa Clara, CA, USA).

treatment_protocol: The IKPRAB36 cell line was cultured for 48h in the absence or presence of 1nM MPA (n = 3).

tag: cell line

value: Ishikawa endometrial cancer cells expressing PRA and PRB

tag: treament

value: 1 nM medroxyprogesterone acetate (MPA)

tag: treament duration

value: 48 hours


title: 570T_NETs alone 1.0

description:
570T
Murine antiserum was obtained from blood collected from an individual Balb/c mouse (1) treated with 2 ug NETs at 0 months. A 1:250 dilution of this antiserum was then applied onto the Utz Lab Whole Protein Autoantigen Array (V2.0), labeled with a goat anti-mouse IgG secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.


title: BASC-Control-1 [miRNA]

tag: cell type

value: control

value: BASC cells


title: 832B_NETs + CRAMP 3.2

description:
832B
Murine antiserum was obtained from blood collected from an individual Balb/c mouse (3) treated with 2 ug NETs + 10 ug CRAMP at 2 months. A 1:250 dilution of this antiserum was then applied onto the Utz Lab Whole Protein Autoantigen Array (V2.0), labeled with a goat anti-mouse IgG secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.

tag: strain


title: IKPRAB36, MPA 1


title: IKPRAB36, MPA 2


title: IKPRAB36, Control 1

description: Gene expression data from IKPRAB36 cell line (Control).

source_name: IKPRAB36 cell line cultured for 48 hours in absence of 1nm MPA


title: UM1_Mut_rep1

city: Birmingham

first: Dongquan

last: Chen

state: AL

address: 1717 11th Ave South

institute: Univ of Alabama at Birmingham

description: Gene expression data from tumor tissue of cancer patient.

hyb_protocol: Hybridization of the GeneChips was carried out in the following the manufacturer’s protocol. Briefly, the fragmented biotin labeled cRNA was mixed with 0.05nM control oligonucleotide B2, 20X Eukaryotic hybridization controls (bioB, bioC, bioD, cre), 0.1 mg/mL herring sperm DNA, 0.5 mg/mL BSA, 2X hybridization buffer (1X 100mM MES/1M NaCl/20mM EDTA/0.01% Tween-20) and 10% DMSO.  The hybridization cocktail was incubated at 99oC for 5 minutes to denature the herring sperm DNA and any secondary structure on the cRNA.  The cocktail was then equilibrated to 45oC for 5 minutes prior to addition to the GeneChip.  Hybridiztion was carried out in the Affymetrix Hybridization Oven 640 at 45oC with rotation at 60rpm for 16 hours.  Following the hybridization step the GeneChips were washed and stained in the Affymetrix Fluidics Station 450 following Fluidics Protocol Mini_euk2v3 as recommended by the manufacturer for this Chip type.  The GeneChips were first washed in a non-stringent wash buffer of 6X SSPE/0.01% Tween-20 followed by stringent wash with 100mM MES/0.1M NaCl/0.01% Tween-20.  The first staining of the GeneChips was done in 2X stain buffer (1X 100mM MES/1M NaCl/0.05% Tween-20), 2mg/mL BSA, and 0.01 mg/mL Streptavidin Phycoerythrin (SAPE).  The GeneChips were washed in non-stringent wash buffer.  A second stain comprised of 2X staining buffer, 2mg/mL BSA, 0.1mg/mL Goat IgG, and 0.003mg/mL of biotinylated antibody was conducted immediately followed by a third stain comprised of the SAPE solution (see above).  Finally, the GeneChips were washed in non-stringent wash buffer prior to scanning.

scan_protocol: Scanning of the GeneChips was done using the Affymetrix 3000 7G scanner as described by the manufacturer. The Fluidics station and Scanner were controlled using Affymetrix GeneChip Command Console (AGCC).

data_processing: MAS 5.0

source_name: Tumor sample from patient with p53 mutant, replicate 1

label_protocol: The labeling of the RNA was done as per the manufacturers instructions (Affymetrix, Santa Clara, CA).  Briefly, One microgram of total RNA was reverse transcribed using an oligo dT-T7 primer under standard conditions.  The resulting first strand cDNA was incubated with RNAse H, E. coli DNA ligase, and E. coli DNA polymerase, dNTPs and buffer to produce second-stranded cDNA.  The cDNA was purified using spin columns following the manufacturer’s instructions (Qiagen).  The purified cDNA was then used in an in vitro transcription assay to produce the target biotin labeled cRNA for hybridization using the 3’ IVT kit from Affymetrix following the manufacturer’s instructions.  The cRNA was purified using a spin column following the kit’s instructions (Qiagen), and fragmented prior to hybridization onto the GeneChips.

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

treatment_protocol: The tumor sample were collected from cancer patients

tag: tissue

value: tumor tissue from cancer patients

tag: genotype

value: p53 mutant

tag: disease state

value: Microsatellite Stable Stage III Colorectal adenocarcinoma


title: UM2_Mtu_rep4

source_name: Tumor sample from patient with p53 mutant, replicate 4


title: 836T_NETs + CRAMP 2.1

description:
836T
Murine antiserum was obtained from blood collected from an individual Balb/c mouse (2) treated with 2 ug NETs + 10 ug CRAMP at 1 month. A 1:250 dilution of this antiserum was then applied onto the Utz Lab Whole Protein Autoantigen Array (V2.0), labeled with a goat anti-mouse IgG secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.

value: Balb/c

tag: treatment


title: UM17_Mtu_rep3

source_name: Tumor sample from patient with p53 mutant, replicate 3


title: Subject 004 PAX.GR,  biological rep2

tag: gender

value: M

tag: age

value: Van

tag: rna integrity number

value: whole blood


title: UM15_Mtu_rep2

source_name: Tumor sample from patient with p53 mutant, replicate 2


title: BASC-Control-2 [miRNA]

tag: genotype/variation

tag: c-myc depletion


title: IKPRAB36, Control 2


title: 839B_NETs + CRAMP 1.1

description:
839B
Murine antiserum was obtained from blood collected from an individual Balb/c mouse (1) treated with 2 ug NETs + 10 ug CRAMP at 1 month. A 1:250 dilution of this antiserum was then applied onto the Utz Lab Whole Protein Autoantigen Array (V2.0), labeled with a goat anti-mouse IgG secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.

value: NETs + CRAMP


title: 571B_NETs + CRAMP 1.0

description:
571B
Murine antiserum was obtained from blood collected from an individual Balb/c mouse (1) treated with 2 ug NETs + 10 ug CRAMP at 0 months. A 1:250 dilution of this antiserum was then applied onto the Utz Lab Whole Protein Autoantigen Array (V2.0), labeled with a goat anti-mouse IgG secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.


title: 834B_NETs + CRAMP 1.2

description:
834B
Murine antiserum was obtained from blood collected from an individual Balb/c mouse (1) treated with 2 ug NETs + 10 ug CRAMP at 2 months. A 1:250 dilution of this antiserum was then applied onto the Utz Lab Whole Protein Autoantigen Array (V2.0), labeled with a goat anti-mouse IgG secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.


title: UM25_Mtu_rep5

source_name: Tumor sample from patient with p53 mutant, replicate 5


title: UM3_Wt_rep5

source_name: Tumor sample from patient with p53 wild type, replicate 5

value: p53 wild type


title: IKPRAB36, Control 3


title: UM23_Wt_rep2

source_name: Tumor sample from patient with p53 wild type, replicate 2


title: UM13_Wt_rep1

source_name: Tumor sample from patient with p53 wild type, replicate 1


title: SCC6

status: Public on Jan 25 2012

type: genomic

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

institute: Vrije Universiteit Medical Center

description:
US22502676_251901510375_S01_CGH_105_Dec08_1_1.txt
Pooled DNA from 5 normal cervical FFPE biopsies was used as reference in the aCGH experiments; across array CGH comparisons were made as described by Buffart et al, Genes, Chromosomes & Cancer 2008, 47(11): 994-1004

hyb_protocol: Hybridization protocol available via www.agilent.com

scan_protocol: Slides were scanned using the Agilent G2505B micro-array scanner. Image data acquisition was performed in feature extraction software v9.5.1 (Agilent Technologies) using the Agilent CGH-v4_95 protocol with default settings

data_processing:
Median Signal intensity minus median Background intensity; excluding negative values. To overcome potential wave bias due to differences in GC-content of the different chromosomal regions, a smoothing algorithm was applied on our dataset as described by van de Wiel et al, Bioinformatics 2009; 25(9):1099-1104.
The data analysis method used employs across array CGH comparisons (as described in Buffart et al.). In short, using across array CGH it is possible to digitally swap dye channels, allowing one to hybridize 2 different samples to one array and use the reference in another array (either present on the same array slide or even on a different slide) for comparison. Therefore, some of the raw data files are duplicated between Samples, and the appendix (e.g. Cy3_test, Cy3_ref, Cy5_test, Cy5_ref) refers to the label and channel used in each raw data file..

molecule: genomic DNA

source_name: Cervical tissue, microdissected

label_protocol: DNA labeling protocol according to Enzo Life Sciences.

extract_protocol: Laser capture microdissection was performed on haematoxylin stained tissue section to obtain the dysplastic cells. Tissues were incubated overnight 37°C in 1M NaSCN. Subsequently, samples were treated with proteinase K for 5 days. DNA was extracted using the DNA Qiagen micro kit (Qiagen).

tag: Stage

value: squamous cell carcinoma of cervix

source_name: Amplified FFPE cervical DNA from 5 individuals

value: normal cervix


title: SCC2

description:
US22502676_251901510379_S01_CGH_105_Dec08_1_1.txt
Pooled DNA from 5 normal cervical FFPE biopsies was used as reference in the aCGH experiments; across array CGH comparisons were made as described by Buffart et al, Genes, Chromosomes & Cancer 2008, 47(11): 994-1004


title: SCC4.CIN3

description:
US22502676_251901512076_S01_CGH_105_Dec08_1_1.txt
Pooled DNA from 5 normal cervical FFPE biopsies was used as reference in the aCGH experiments; across array CGH comparisons were made as described by Buffart et al, Genes, Chromosomes & Cancer 2008, 47(11): 994-1004

value: cervical intraepithelial neoplasia grade 3 adjacent to squamous cell carcinoma


title: SCC4


title: UM9_Wt_rep4

source_name: Tumor sample from patient with p53 wild type, replicate 4


title: SCC1

description:
US22502676_251901510376_S01_CGH_105_Dec08_1_2.txt
Pooled DNA from 5 normal cervical FFPE biopsies was used as reference in the aCGH experiments; across array CGH comparisons were made as described by Buffart et al, Genes, Chromosomes & Cancer 2008, 47(11): 994-1004


title: UM30_Wt_rep3

source_name: Tumor sample from patient with p53 wild type, replicate 3


title: SCC5.CIN3

description:
US22502676_251901510374_S01_CGH_105_Dec08_1_2.txt
Pooled DNA from 5 normal cervical FFPE biopsies was used as reference in the aCGH experiments; across array CGH comparisons were made as described by Buffart et al, Genes, Chromosomes & Cancer 2008, 47(11): 994-1004


title: SCC6.CIN3


title: CIN3.2.20

description:
US22502676_251901510360_S01_CGH_105_Dec08_1_1.txt
Pooled DNA from 5 normal cervical FFPE biopsies was used as reference in the aCGH experiments; across array CGH comparisons were made as described by Buffart et al, Genes, Chromosomes & Cancer 2008, 47(11): 994-1004

value: cervical intraepithelial neoplasia grade 3, prevalent hrHPV infection


title: CIN3.2.18


title: SCC3.CIN3

description:
US22502676_251901512075_S01_CGH_105_Dec08_1_2.txt
Pooled DNA from 5 normal cervical FFPE biopsies was used as reference in the aCGH experiments; across array CGH comparisons were made as described by Buffart et al, Genes, Chromosomes & Cancer 2008, 47(11): 994-1004


title: SCC2.CIN3


title: CIN3.2.22

description:
US22502676_251901512077_S01_CGH_105_Dec08_1_2.txt
Pooled DNA from 5 normal cervical FFPE biopsies was used as reference in the aCGH experiments; across array CGH comparisons were made as described by Buffart et al, Genes, Chromosomes & Cancer 2008, 47(11): 994-1004


title: CIN3.2.15

description:
US22502676_251901510435_S01_CGH_105_Dec08_1_1.txt
Pooled DNA from 5 normal cervical FFPE biopsies was used as reference in the aCGH experiments; across array CGH comparisons were made as described by Buffart et al, Genes, Chromosomes & Cancer 2008, 47(11): 994-1004


title: CIN3.2.24

description:
US22502676_251901512133_S01_CGH_105_Dec08_1_1.txt
Pooled DNA from 5 normal cervical FFPE biopsies was used as reference in the aCGH experiments; across array CGH comparisons were made as described by Buffart et al, Genes, Chromosomes & Cancer 2008, 47(11): 994-1004


title: SCC5


title: CIN3.2.23


title: SCC3


title: SCC1.CIN3


title: CIN3.2.14

description:
MAF_251901510362_S01_CGH_105_Dec08_1_2.txt
Pooled DNA from 5 normal cervical FFPE biopsies was used as reference in the aCGH experiments; across array CGH comparisons were made as described by Buffart et al, Genes, Chromosomes & Cancer 2008, 47(11): 994-1004


title: CIN3.2.19

description:
US22502676_251901510383_S01_CGH_105_Dec08_1_2.txt
Pooled DNA from 5 normal cervical FFPE biopsies was used as reference in the aCGH experiments; across array CGH comparisons were made as described by Buffart et al, Genes, Chromosomes & Cancer 2008, 47(11): 994-1004


title: CIN3.2.17

description:
US22502676_251901510381_S01_CGH_105_Dec08_1_2.txt
Pooled DNA from 5 normal cervical FFPE biopsies was used as reference in the aCGH experiments; across array CGH comparisons were made as described by Buffart et al, Genes, Chromosomes & Cancer 2008, 47(11): 994-1004


title: CIN3.2.21

description:
MAF_251901510361_S01_CGH_105_Dec08_1_2.txt
Pooled DNA from 5 normal cervical FFPE biopsies was used as reference in the aCGH experiments; across array CGH comparisons were made as described by Buffart et al, Genes, Chromosomes & Cancer 2008, 47(11): 994-1004


title: CIN3.2.110

description:
US22502676_251901510434_S01_CGH_105_Dec08_1_1.txt
Pooled DNA from 5 normal cervical FFPE biopsies was used as reference in the aCGH experiments; across array CGH comparisons were made as described by Buffart et al, Genes, Chromosomes & Cancer 2008, 47(11): 994-1004


title: CIN3.2.13

description:
MAF_251901510362_S01_CGH_105_Dec08_1_1.txt
Pooled DNA from 5 normal cervical FFPE biopsies was used as reference in the aCGH experiments; across array CGH comparisons were made as described by Buffart et al, Genes, Chromosomes & Cancer 2008, 47(11): 994-1004


title: CIN3.2.8


title: CIN3.2.16

description:
US22502676_251901510359_S01_CGH_105_Dec08_1_2.txt
Pooled DNA from 5 normal cervical FFPE biopsies was used as reference in the aCGH experiments; across array CGH comparisons were made as described by Buffart et al, Genes, Chromosomes & Cancer 2008, 47(11): 994-1004


title: CIN3.2.6

description:
US22502676_251901510383_S01_CGH_105_Dec08_1_1.txt
Pooled DNA from 5 normal cervical FFPE biopsies was used as reference in the aCGH experiments; across array CGH comparisons were made as described by Buffart et al, Genes, Chromosomes & Cancer 2008, 47(11): 994-1004


title: CIN3.2.9

description:
MAL_251901510428_S01_CGH_105_Dec08_1_1.txt
Pooled DNA from 5 normal cervical FFPE biopsies was used as reference in the aCGH experiments; across array CGH comparisons were made as described by Buffart et al, Genes, Chromosomes & Cancer 2008, 47(11): 994-1004


title: CIN3.2.4

description:
MAL_251901510428_S01_CGH_105_Dec08_1_2.txt
Pooled DNA from 5 normal cervical FFPE biopsies was used as reference in the aCGH experiments; across array CGH comparisons were made as described by Buffart et al, Genes, Chromosomes & Cancer 2008, 47(11): 994-1004


title: CIN3.2.10

description:
US22502676_251901510434_S01_CGH_105_Dec08_1_2.txt
Pooled DNA from 5 normal cervical FFPE biopsies was used as reference in the aCGH experiments; across array CGH comparisons were made as described by Buffart et al, Genes, Chromosomes & Cancer 2008, 47(11): 994-1004


title: CIN3.2.1

description:
US22502676_251901510360_S01_CGH_105_Dec08_1_2.txt
Pooled DNA from 5 normal cervical FFPE biopsies was used as reference in the aCGH experiments; across array CGH comparisons were made as described by Buffart et al, Genes, Chromosomes & Cancer 2008, 47(11): 994-1004


title: CIN3.2.7

description:
MAL_251901510427_S01_CGH_105_Dec08_1_2.txt
Pooled DNA from 5 normal cervical FFPE biopsies was used as reference in the aCGH experiments; across array CGH comparisons were made as described by Buffart et al, Genes, Chromosomes & Cancer 2008, 47(11): 994-1004


title: CIN3.2.5

description:
US22502676_251901510435_S01_CGH_105_Dec08_1_2.txt
Pooled DNA from 5 normal cervical FFPE biopsies was used as reference in the aCGH experiments; across array CGH comparisons were made as described by Buffart et al, Genes, Chromosomes & Cancer 2008, 47(11): 994-1004


title: CIN3.1.14

description:
251901512376_251901512376_S01_CGH_105_Dec08_1_2.txt
Pooled DNA from 5 normal cervical FFPE biopsies was used as reference in the aCGH experiments; across array CGH comparisons were made as described by Buffart et al, Genes, Chromosomes & Cancer 2008, 47(11): 994-1004

value: cervical intraepithelial neoplasia grade 3, incident hrHPV infection [<5years preceding hrHPV infection]


title: CIN3.1.12

description:
251901512375_251901512375_S01_CGH_105_Dec08_1_2.txt
Pooled DNA from 5 normal cervical FFPE biopsies was used as reference in the aCGH experiments; across array CGH comparisons were made as described by Buffart et al, Genes, Chromosomes & Cancer 2008, 47(11): 994-1004


title: CIN3.2.3

description:
MAL_251901510134_S01_CGH_105_Dec08_1_1.txt
Pooled DNA from 5 normal cervical FFPE biopsies was used as reference in the aCGH experiments; across array CGH comparisons were made as described by Buffart et al, Genes, Chromosomes & Cancer 2008, 47(11): 994-1004


title: CIN3.1.5


title: CIN3.1.11

description:
251901512375_251901512375_S01_CGH_105_Dec08_1_1.txt
Pooled DNA from 5 normal cervical FFPE biopsies was used as reference in the aCGH experiments; across array CGH comparisons were made as described by Buffart et al, Genes, Chromosomes & Cancer 2008, 47(11): 994-1004


title: CIN3.1.6


title: CIN3.1.3


title: CIN1.4

description:
US22502676_251901510375_S01_CGH_105_Dec08_1_2.txt
Pooled DNA from 5 normal cervical FFPE biopsies was used as reference in the aCGH experiments; across array CGH comparisons were made as described by Buffart et al, Genes, Chromosomes & Cancer 2008, 47(11): 994-1004

value: cervical intraepithelial neoplasia grade 1


title: CIN3.1.1


title: CIN3.1.4

description:
MAL_251901510427_S01_CGH_105_Dec08_1_1.txt
Pooled DNA from 5 normal cervical FFPE biopsies was used as reference in the aCGH experiments; across array CGH comparisons were made as described by Buffart et al, Genes, Chromosomes & Cancer 2008, 47(11): 994-1004


title: CIN3.2.2

description:
MAF_251901510361_S01_CGH_105_Dec08_1_1.txt
Pooled DNA from 5 normal cervical FFPE biopsies was used as reference in the aCGH experiments; across array CGH comparisons were made as described by Buffart et al, Genes, Chromosomes & Cancer 2008, 47(11): 994-1004


title: CIN1.2

description:
US22502676_251901512076_S01_CGH_105_Dec08_1_2.txt
Pooled DNA from 5 normal cervical FFPE biopsies was used as reference in the aCGH experiments; across array CGH comparisons were made as described by Buffart et al, Genes, Chromosomes & Cancer 2008, 47(11): 994-1004


title: CIN3.1.8

description:
US22502676_251901510435_S01_CGH_105_Dec08_1_1.txt
Pooled DNA from 5 normal cervical FFPE biopsies was used as reference in the aCGH experiments; across array CGH comparisons were made as described by Buffart et al, Genes, Chromosomes & Cancer 2008, 47(11): 994-1004


title: CIN1.5

description:
US22502676_251901510376_S01_CGH_105_Dec08_1_1.txt
Pooled DNA from 5 normal cervical FFPE biopsies was used as reference in the aCGH experiments; across array CGH comparisons were made as described by Buffart et al, Genes, Chromosomes & Cancer 2008, 47(11): 994-1004


title: CIN3.1.2


title: CIN1.1

description:
US22502676_251901510379_S01_CGH_105_Dec08_1_2.txt
Pooled DNA from 5 normal cervical FFPE biopsies was used as reference in the aCGH experiments; across array CGH comparisons were made as described by Buffart et al, Genes, Chromosomes & Cancer 2008, 47(11): 994-1004


title: CIN1.6

description:
US22502676_251901510374_S01_CGH_105_Dec08_1_1.txt
Pooled DNA from 5 normal cervical FFPE biopsies was used as reference in the aCGH experiments; across array CGH comparisons were made as described by Buffart et al, Genes, Chromosomes & Cancer 2008, 47(11): 994-1004


title: CIN1.3

description:
US22502676_251901512075_S01_CGH_105_Dec08_1_1.txt
Pooled DNA from 5 normal cervical FFPE biopsies was used as reference in the aCGH experiments; across array CGH comparisons were made as described by Buffart et al, Genes, Chromosomes & Cancer 2008, 47(11): 994-1004


title: CIN3.2.12

description:
MAF_251901510362_S01_CGH_105_Dec08_1_1.txt
Pooled DNA from 5 normal cervical FFPE biopsies was used as reference in the aCGH experiments; across array CGH comparisons were made as described by Buffart et al, Genes, Chromosomes & Cancer 2008, 47(11): 994-1004


title: 573T_NETs + CRAMP 2.0

description:
573T
Murine antiserum was obtained from blood collected from an individual Balb/c mouse (2) treated with 2 ug NETs + 10 ug CRAMP at 0 months. A 1:250 dilution of this antiserum was then applied onto the Utz Lab Whole Protein Autoantigen Array (V2.0), labeled with a goat anti-mouse IgG secondary antibody conjugated to DyLight-649 (Jackson ImmunoResearch), and scanned with a GenePix 4000B scanner using GenePix Pro 6.1.

source_name: murine antiserum


title: D2_Granulocytes_(Gr1+)_rep1

city: Groningen

first: Leonid

last: Bystrykh

state: Groningen

address: A. Deusinglaan 1

department: European Research Institute for the Biology of Ageing - ERIBA

institute: University Medical Center Groningen

description: D2 Gr 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: GeneSpring GX 11.0-computed quantile normalized signal intensity. Non-normalized matrix: GenomeStudio-computed raw signal intensity.

label_protocol: Biotinylated cRNA was prepared using the Illumina TotalPrep RNA Amplification Kit (Ambion) according to the manufacturer’s specifications starting with 100 ng total RNA.

extract_protocol: Total RNA was isolated using the RNeasy Mini kit (Qiagen) in accordance with the manufacturer’s protocol.

value: primary bone marrow

value: myeloid Gr-1+ cells


title: D2_Granulocytes_(Gr1+)_rep2

description: D2 Gr 2


title: D2_Progenitors_(L-S-K+)_rep2

description: D2 Prog 2

value: committed LS−K+ cells


title: B6_Erythrocytes_(Ter119+)_rep2

description: B6 Ter 2

value: erythroid TER-119+ cells


title: D2_Erythrocytes_(Ter119+)_rep3

description: D2 Ter 3


title: VUB05 NSC P38

city: Evry

first: nathalie

last: lefort

address: 5 rue Henri Desbruères

institute: INSERM

hyb_protocol: After addition of tRNA (48 mg) plus a quantity of human Cot DNA (Invitrogen, Carlsbad, CA) equal to 50 times the mass of the labeled DNAs, the resulting products were concentrated by vacuum centrifugation, resuspended in 43 mL of hybridization solution (Ambion, Austin, TX) and deposited on the array under a coverslip. Hybridization in a sealed chamber (Corning Life Sciences, Acton, MA) was for 66 hours at 55_C, a post hybridization treatement was done.

scan_protocol: Slides were scanned (Agilent Technologies, Santa Clara, CA), data were extracted with GenePix 6 (Axon InstrumentseMolecular Devices, Sunnyvale, CA),

data_processing: All data is lowess normalized, ratio value is CY5/CY3. Copy number analysis was performed with GenoCensus (IntegraGen), which includes block Loess normalization

source_name: VUB05 NSC P38

label_protocol: A genomic DNA labeling kit (Enzo, Farmingdale, NY) was used to label the sample DNA with Cy5. The labeled products were purified with QiaQuick polymerase chain reaction (PCR) purification kits (Qiagen, Valencia, CA).

growth_protocol: The protocol used to obtain NSC from human ES cells has two steps. The first one is the production of neuro-epithelial cells (NEP) from human pluripotent and the second the production of NSC from NEP. NEP are obtained after 8-10 days of differentiation in N2B27 medium containing neurobasal, DMEM/F12, N2 supplement, B27 supplement, 0.55 mM b-mercaptoethanol complemented with human recombinant noggin (300ng/mL) and SB431542 (20µM). The medium is changed daily until the appearance of neural rosettes containing NEP after 8-10 days of differentiation. At this time, medium is replaced by the N2B27 medium supplemented by EGF (epidermal growth factor) (10ng/mL), hFGF2 (10ng/mL) and hBDNF (human brain-derived neurotrophic factor). NSC are cultured during 3 to 5 days until confluence and passed (dilution factor: ~1/3 to 1/5) using 0.05 tryspin/EDTA.

extract_protocol: Genomi DNA was extraxted from human NSC using the Wizard Genomic DNA purification kit (Promega, Charbonnières, France)

tag: passage

value: Neural Stem Cells derived human ES cells

source_name: Control genomic DNA

tag: reference

value: pool of 25 male genomic DNA from Coriell


title: D2_Progenitors_(L-S-K+)_rep1

description: D2 Prog 1


title: D2_Stem cells_(LSK)_rep3

description: D2 Stem 3

source_name: D2_Stem cells_(LSK)

value: LSK multilineage cell


title: D2_Granulocytes_(Gr1+)_rep3

description: D2 Gr 3


title: B6_Progenitors_(L-S-K+)_rep3

description: B6 Prog 3


title: D2_Erythrocytes_(Ter119+)_rep1

description: D2 Ter 1


title: SA001 NSC P34

source_name: SA01 NSC P34

tag: cell line


title: B6_Stem cells_(LSK)_rep3

description: B6 Stem 3

source_name: B6_Stem cells_(LSK)


title: D2_Progenitors_(L-S-K+)_rep3

description: D2 Prog 3


title: B6_Stem cells_(LSK)_rep2

description: B6 Stem 2


title: VUB05 NSC P32

source_name: VUB05 NSC P32


title: B6_Granulocytes_(Gr1+)_rep2

description: B6 Gr 2


title: B6_Granulocytes_(Gr1+)_rep3

description: B6 Gr 3


title: B6_Erythrocytes_(Ter119+)_rep1

description: B6 Ter 1


title: B6_Progenitors_(L-S-K+)_rep1

description: B6 Prog 1


title: D2_Erythrocytes_(Ter119+)_rep2

description: D2 Ter 2


title: B6_Erythrocytes_(Ter119+)_rep3

description: B6 Ter 3


title: D2_Stem cells_(LSK)_rep1

description: D2 Stem 1


title: B6_Progenitors_(L-S-K+)_rep2

description: B6 Prog 2


title: D2_Stem cells_(LSK)_rep2

description: D2 Stem 2


title: B6_Granulocytes_(Gr1+)_rep1

description: B6 Gr 1


title: B6_Stem cells_(LSK)_rep1

description: B6 Stem 1


title: CD161+CD8+ T cells, biological repeat 3

city: Oxford

first: Natasha

last: Sahgal

address: Old Road Campus

department: Ludwig Institute of Cancer Research

country: United Kingdom

institute: University of Oxford

description: Gene expression data from human cord blood CD161+CD8+ T cells

hyb_protocol: Following fragmentation, 5ug of biotinylated cDNA was hybridized to GeneChip Human Genome U133 Plus 2.0 arrays (Affymetrix) for 18 hrs at 45C and stained in the affymetrix  3 GeneChip® Fluidics Stations F450.

scan_protocol: GeneChip® Scanner 3000 7G with autoloader

data_processing: R and Bioconductor packages were used for processing and analysing raw data, to generate RMA normalised intensities

source_name: Cord blood Ex-vivo CD16+-CD8+ T cells

label_protocol: Biotinylated cDNA were prepared according to the Ovation Pico WTA system (Nugen) protocol.

extract_protocol: Total RNA was extracted using RNAeasy mini extraction kit (Qiagen) according to the manufacturers instructions.

value: CD8+ T cell

tag: cell subtype

value: CD16+-CD8+ T cells


title: WT mouse (WT_Tal4)

city: Göttingen

first: Nicolai

last: Miosge

address: Robert-Koch-Str. 40

department: Prothetik, Oral biology and Tissue regeneration

country: Germany

institute: University Göttingen

description:
wild type mice TMJ-cartilage
miosge_WT_Tal4_20110623_(MoGene-1_0-st-v1).rma-gene-default.chp
miosge_WT_Tal4_20110623_(MoGene-1_0-st-v1).CEL

hyb_protocol: using the genechip hybridisation, wash and stain kit

scan_protocol: Array washing and staining as described in chp 6 of above manual using the GeneChip Fluidics station 450 (fluidics script FS450-007). Arrays were scanned on a GeneChip scanner 3000 7G using default scanner settings. Affymetrix GeneChip® Command Console® (AGCC) was used to process all Affymetrix arrays through fluidics and scanning.

data_processing: Gene level probe set summarisation (signal value), calculation of QC metrics and CHP file generation were performed using GeneChip® Expression Console software using the Robust Multichip Analysis (RMA) algorithm

source_name: mouse TMJ-cartilage from wild type mouse WT_Tal4

label_protocol: GeneChip Whole Transcript (WT) sense target labeling assay manual, version 4 - starting with 300ng RNA and following the Total RNA labeling protocol to prepare targets for GeneChip gene 1.0 ST Arrays(omitting RiboMinus procedure).

growth_protocol: RNA was extracted directly of the madibular condyle cartilage

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

value: wild type

value: madibular condyle cartilage


title: HeLa cells 12h released, biological rep3

city: Boston

first: Subhashini

last: Sadasivam

state: MA

address: 450 Brookline Avenue

department: Medical Oncology

institute: Dana Farber Cancer Insitute

hyb_protocol: The cRNA was hybridized to a microarray chip.

scan_protocol: The bound cRNA was stained with fluorescent streptavidin.

data_processing: R Bioconductor Affy package was used to analyze the microarray files. After loading the raw CEL files in R, RMA (Robust Multi-Array Averaging) was used to subtract background, normalize intensities and summarize gene expression levels

source_name: HeLa cell line

label_protocol: RNA from each sample was converted into cDNA, then amplified and labeled with biotinylated nucleotides by in vitro transcription to produce biotinylated cRNA.

growth_protocol: RNA was purified from HeLa cells in double thymidine (0) and cells released into the cell cycle after washing out the thymidine. RNA was collected from cells at 2, 4, 6, 8 and 12 hours after washing out the thymidine.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. The RNA was then Dnase treated and purified using Qiagen Rneasy columns.

value: HeLa cells

tag: growth condition

value: 12h released


title: WT mouse (WT_Tal6)

description:
wild type mice TMJ-cartilage
miosge_WT_Tal6_20110623_(MoGene-1_0-st-v1).rma-gene-default.chp
miosge_WT_Tal6_20110623_(MoGene-1_0-st-v1).CEL

source_name: mouse TMJ-cartilage from wild type mouse WT_Tal6


title: WT mouse (WT_Tal3)

description:
wild type mice TMJ-cartilage
miosge_WT_Tal3_20110505_(MoGene-1_0-st-v1).rma-gene-default.chp
miosge_WT_Tal3_20110505_(MoGene-1_0-st-v1).CEL

source_name: mouse TMJ-cartilage from wild type mouse WT_Tal3


title: CD161-CD8+ T cells, biological repeat 3

description: Gene expression data from human cord blood CD161-CD8+ T cells

source_name: Cord blood Ex-vivo CD161-CD8+ T cells

value: CD161-CD8+ T cells


title: DDR-1-KO mouse (KO_Tal5)

description:
DDR-1-KO mice TMJ-cartilage
miosge_KO_Tal5_20110623_(MoGene-1_0-st-v1).rma-gene-default.chp
miosge_KO_Tal5_20110623_(MoGene-1_0-st-v1).CEL

source_name: mouse TMJ-cartilage from DDR-1-KO mouse KO_Tal5


title: DDR-1-KO mouse (KO_Tal2)

description:
DDR-1-KO mice TMJ-cartilage
miosge_KO_Tal2_20110505_(MoGene-1_0-st-v1).rma-gene-default.chp
miosge_KO_Tal2_20110505_(MoGene-1_0-st-v1).CEL

source_name: mouse TMJ-cartilage from DDR-1-KO mouse KO_Tal2


title: HeLa cells 12h released, biological rep2


title: C4-2B B-DIM 48h

city: Detroit

first: Fazlul

middle: H.

last: Sarkar

state: MI

address: 4100 John R

institute: Wayne State University School of Medicine

description:
gene expression data from B-DIM treated C4-2B cells
FS19-C4_B_48.CEL

hyb_protocol: Standard Affymetrix hybridization protocol was used.

scan_protocol: The arrays were scanned using standard Affymetrix scanning protocol.

data_processing: The data were analyzed with Microarray Suite using Affymetrix default analysis settings and global scaling as normalization method.

source_name: C4-2B cells treated with 25uM B-DIM for 48 hours

label_protocol: Biotinylated cRNA were prepared using Affymetrix standard protocol.

growth_protocol: C4-2B cells were cultured in RPMI 1640 medium supplemented with 10% FBS

extract_protocol: Total RNA was extracted with Trizol reagent followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Cells were treated with 25uM B-DIM or 25uM isoflavone (the concentrations of isoflavone we described refer to the concentration of genistein in isoflavone mixture).

value: C4-2B prostate cancer cells

tag: agent

value: B-DIM

tag: time

value: 48 hours


title: HeLa cells 8h released, biological rep3

value: 8h released


title: CD161++CD8+ T cells, biological repeat 3

description: Gene expression data from human cord blood CD161++CD8+ T cells

source_name: Cord blood Ex-vivo CD161++CD8+ T cells

tag: tissue

value: CD161++CD8+ T cells


title: C4-2B Isoflavone 72h

description:
gene expression data from isoflavone treated C4-2B cells
FS22-C4_S_72.CEL

source_name: C4-2B cells treated with 25uM isoflavone for 72 hours

value: isoflavone

value: 72 hours


title: CD161+CD8+ T cells, biological repeat 2

source_name: Cord blood Ex-vivo CD161+CD8+ T cells

value: CD161+CD8+ T cells


title: C4-2B B-DIM 6h

description:
gene expression data from B-DIM treated C4-2B cells
FS17-C4_B_6.CEL

source_name: C4-2B cells treated with 25uM B-DIM for 6 hours

value: 6 hours


title: CD161++CD8+ T cells, biological repeat 2


title: HeLa cells 12h released, biological rep1


title: HeLa cells 8h released, biological rep2


title: CD161-CD8+ T cells, biological repeat 2


title: C4-2B control

description:
Gene expression data from control C4-2B cells
FS16-C4_C.CEL

source_name: C4-2B cells treated with 0.1% DMSO (vericle control)

value: DMSO

value: control


title: C4-2B Isoflavone 6h

description:
gene expression data from isoflavone treated C4-2B cells
FS20-C4_S_6.CEL

source_name: C4-2B cells treated with 25uM isoflavone for 6 hours


title: CD161+CD8+ T cells, biological repeat 1

value: CD8+ T cell


title: HeLa cells 8h released, biological rep1


title: HeLa cells 4h released, biological rep2

value: 4h released


title: HeLa cells 4h released, biological rep1


title: CD161++CD8+ T cells, biological repeat 1


title: HeLa cells 6h released, biological rep2

value: 6h released


title: HeLa cells 6h released, biological rep3

value: HeLa cells


title: HeLa cells blocked, biological rep3

value: blocked


title: HeLa cells blocked, biological rep2


title: HeLa cells 4h released, biological rep3


title: HeLa cells 2h released, biological rep2

value: 2h released


title: HeLa cells 2h released, biological rep3


title: HeLa cells 6h released, biological rep1


title: SKBR3-P5, biological rep2

status: Public on Jan 24 2012

city: Bern

first: Ramin

last: Radpour

address: Murtenstrasse 35

department: Department for BioMedical Research

country: Switzerland

institute: University of Bern

description: Gene expression data at passage 5 follow-up at “drug holiday” condition

hyb_protocol: The labelled products were hybridized for 18 hr at 45C on Affymetrix Genome 133 Plus 2.0 GeneChips. GeneChips were washed and stained on GeneChip Fluidics 450 Workstations (Affymetrix Inc.).

scan_protocol: The arrays were scanned on GeneChip Scanner 3000 7G (Affymetrix Inc.)

data_processing: The expression signals were acquired using the Affymetrix GeneChip Command Console Software (AGCC). The system was used to generate the numerical values of the probe intensity (Signal). The differentially expressed mRNAs were defined using Partek Genomics Suite software v6.5 (Partek Incorporated, Missouri, USA) and and RMA normalization.

source_name: SKBR3 Passage 5

label_protocol: Biotinylated mRNAs were prepared according to the FlashTag Biotin HSR RNA Labeling protocol (Genisphere) using 100ng total RNA.

growth_protocol: HB2 cell line was cultured in DMEM, 10% FBS, Insulin (0.01 mg/ml, hydrocortisone (500 ng/ml). MDA-MB231 cell line was cultured in DMEM, 10% FBS. SKBR3 cell line was cultured in McCoys 5A, 10% FBS.

extract_protocol: Total RNA was extracted using AllPrep DNA/RNA/Protein Mini Kit (QIAGEN AG) according to the manufacturer's instructions.

treatment_protocol: Cells were seeded (2 X l0^5 cells / T75 flasks) for 24h then media were removed and cells were freshly exposed to the 5-aza-2’-deoxycytidine (DAC) (Sigma Chemical Co.) at concentrations of l00nM in suspension culture every 24h until cultured cells reached 80-85 % confluence (~5 days). The cells were split for 10 follow-up passages at “drug holiday” condition.


title: SKBR3-P7, biological rep2

description: Gene expression data at passage 7 follow-up at “drug holiday” condition

source_name: SKBR3 Passage 7


title: SKBR3-P10, biological rep1

description: Gene expression data at passage 10 follow-up at “drug holiday” condition

source_name: SKBR3 Passage 10


title: HeLa cells 2h released, biological rep1


title: SKBR3-P7, biological rep1

value: passage 7 follow-up at “drug holiday” condition


title: SKBR3-P10, biological rep2

value: passage 10 follow-up at “drug holiday” condition


title: HeLa cells blocked, biological rep1


title: SAS_HAI-1knockdown_Ex2

city: Miyazaki

first: Tsuyoshi

last: Fukushima

address: 5200 Kihara, Kiyotake

country: Japan

institute: University of Miyazaki

description: Gene expression data from HAI-1 knockdown SAS cells

hyb_protocol: Affymetrix standard procedure for HG U133 plus 2.0 array

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 (Affymetrix)

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: oral squamous cell carcinoma cell line, SAS with HAI-1 silencing

label_protocol: Biotinylated cRNA were prepared using One-cycle target labeling kit according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: The cells were cultured in RPMI1640 containing 10% FBS at 37°C in a humidified atmosphere containing 5%CO2.

extract_protocol: Total RNAs were extracted with Trizol reagent and PureLink RNA Micro Kit (Invitrogen).

treatment_protocol: Silencing of HAI-1 was performed by retroviral infection. The knockdown vector was constructed using the short hairpin RNA (shRNA) expression retroviral vector pSINsi-hU6 (Takara Bio). The target sequence of the SPINT1 (HAI-1) gene was 5’-GGGCAGGCATAGACTTGAAGG-3'. Control retroviral infection was also performed. The control vector was constructed using the short hairpin RNA (shRNA) expression retroviral vector pSINsi-hU6 (Takara Bio). The control sequence is 5’-GGGACGGAGATTTCACGAGGA-3', that is, the scrambled form of knockdown sequence of the SPINT1 (HAI-1) (5’-GGGCAGGCATAGACTTGAAGG-3').

tag: cell type

value: human oral squamous cell carcinoma cell line

value: SAS


title: SAS_HAI-1control_Ex1

description: Gene expression data from control SAS cells

source_name: oral squamous cell carcinoma cell line, SAS with control shRNA expressing


title: SKBR3-P5, biological rep1

value: passage 5 follow-up at “drug holiday” condition


title: SAS_HAI-1knockdown_Ex1


title: SAS_HAI-1control_Ex2


title: CD161-CD8+ T cells, biological repeat 1

value: CD161-CD8+ T cells


title: Nelore_WG

city: Beltsville

first: George

state: MD

address: 10300 Baltimore Ave

institute: United States Department of Agriculture

description: Hybridization of test sample Nelore_WG and reference sample Dominette

hyb_protocol: Performed by NimbleGen standard protocol

data_processing: Spacial corrected and normalized by standard NimbleGen methods

organism: Bos taurus

source_name: semen from Nelore_WG

label_protocol: Labeled by NimbleGen

extract_protocol: Qiagen QIAamp DNA Mini Kit

tag: breed

value: Nelore

value: Male

value: semen

source_name: whole blood from Hereford L1 Dominette 01449

extract_protocol: Qiagen QIAamp DNA Blood Maxi Kit

value: Hereford L1 Dominette 01449

value: Female

value: whole blood


title: CIN3.1.9

description:
US22502676_251901510381_S01_CGH_105_Dec08_1_1.txt
Pooled DNA from 5 normal cervical FFPE biopsies was used as reference in the aCGH experiments; across array CGH comparisons were made as described by Buffart et al, Genes, Chromosomes & Cancer 2008, 47(11): 994-1004

source_name: Cervical tissue, microdissected

value: cervical intraepithelial neoplasia grade 3, incident hrHPV infection [<5years preceding hrHPV infection]

source_name: Amplified FFPE cervical DNA from 5 individuals

value: normal cervix


title: Holstein_WG

description: Hybridization of test sample Holstein_WG and reference sample Dominette

scan_protocol: Performed by NimbleGen standard protocol

source_name: semen from Holstein_WG

value: Holstein


title: SKBR3-P3, biological rep1

description: Gene expression data at passage 3 follow-up at “drug holiday” condition

source_name: SKBR3 Passage 3

tag: treatment


title: SKBR3-P1, biological rep2

description: Gene expression data at passage 1 follow-up at “drug holiday” condition

source_name: SKBR3 Passage 1


title: MDA-P10, biological rep1

source_name: MDA-MB231 Passage 10


title: MDA-P10, biological rep2


title: SKBR3-UT, biological rep1

description: Gene expression data before treatment with DAC

source_name: SKBR3 Un-treated


title: SKBR3-P1, biological rep1

value: passage 1 follow-up at “drug holiday” condition


title: MDA-P3, biological rep2

source_name: MDA-MB231 Passage 3

value: passage 3 follow-up at “drug holiday” condition


title: MDA-T, biological rep2

description: Gene expression data directly after treatment with DAC

source_name: MDA-MB231 Treated

value: treatment with DAC


title: MDA-P7, biological rep1

source_name: MDA-MB231 Passage 7

value: passage 7 follow-up at “drug holiday” condition


title: MDA-P3, biological rep1


title: SKBR3-T, biological rep1

source_name: SKBR3 Treated


title: SKBR3-T, biological rep2


title: SKBR3-UT, biological rep2


title: MDA-P1, biological rep2

source_name: MDA-MB231 Passage 1


title: MDA-P5, biological rep1

source_name: MDA-MB231 Passage 5


title: MDA-P5, biological rep2


title: SKBR3-P3, biological rep2


title: MDA-T, biological rep1


title: Angus2_WG

description: Hybridization of test sample Angus2_WG and reference sample Dominette

source_name: semen from Angus2_WG

value: Angus

tag: gender


title: MDA-P7, biological rep2


title: HB2-P10, biological rep2

source_name: HB2 Passage 10

value: passage 10 follow-up at “drug holiday” condition


title: HB2-P10, biological rep1


title: MDA-UT, biological rep1

source_name: MDA-MB231 Un-treated


title: MDA-UT, biological rep2


title: MDA-P1, biological rep1


title: Angus1_WG

description: Hybridization of test sample Angus1_WG and reference sample Dominette

source_name: semen from Angus1_WG

source_name: whole blood from Hereford L1 Dominette 01449


title: HB2-P7, biological rep2

source_name: HB2 Passage 7


title: HB2-P7, biological rep1


title: HB2-P5, biological rep1

source_name: HB2 Passage 5

value: passage 5 follow-up at “drug holiday” condition


title: HB2-P5, biological rep2


title: HB2-P3, biological rep1

source_name: HB2 Passage 3


title: HB2-T, biological rep1

source_name: HB2 Treated


title: HB2-UT, biological rep1

source_name: HB2 Un-treated


title: HB2-P1, biological rep2

source_name: HB2 Passage 1


title: HB2-UT, biological rep2


title: HB2-T, biological rep2


title: HB2-P1, biological rep1


title: KAT1

city: Kfar Yona

first: Dalit

last: Roth

address: Turmus 199

department: Microbiology

country: Israel

institute: Tel Aviv University

description: P. vortex after 18h incubation in the presence of 10ug/ml kanamycin. Biological replicate of KCT1

hyb_protocol: The cDNA samples were hybridized to Agilent P.vortex 8x15k Array using the Agilent In situ Hybridization kit 5188-5244.

scan_protocol: Agilent scanner.

data_processing: Data analysis has been done using GeneSpring GX version 10.0 and Microsoft Excel. The normalization was done using GeneSpring GX 10 Software. The normalization was done for samples labeled with Cy3 and samples labeled with Cy5 separately (normalized data for Cy5 channel has not been included in this submission because it is not relevant to the publication analysis).

organism: Paenibacillus vortex

label_protocol: Samples were labeled using the Agilent’s Quick-Amp labeling Kit (p/n5190-0444).

growth_protocol: Cells were incubated in LB broth for 8 hours (mid log phase) then transferred into a fresh LB medium for 18 hours at 37C.

extract_protocol: For preservation of the RNA 0.5ml of RNAlater (Ambion) was added into the harvested samples. RNA from samples was extracted using Qiagen’s RNeasy minikit Cat#74104.

treatment_protocol: 10ug/ml kanamycin was added into the medium prior to bacteria inoculation and incubation of 18 hours.

tag: incubation

value: 18 hours


title: KCT1

description: P. vortex after 18h incubation in the presence of 10ug/ml kanamycin. Biological replicate of KAT1


title: CAT1

description: P. vortex after 18h incubation. Biological replicate of CBT1


title: CBT1

description: P. vortex after 18h incubation. Biological replicate of CAT1


title: MZL_043

city: Scottsdale

first: Esteban

last: Braggio

state: AZ

address: 13400 E. Shea Blvd, MCCRB-300

institute: Mayo Clinic Arizona

hyb_protocol: Aliquouts of agilent Oligo aCGH hybridization kit were added to the samples as recommended by the manafacture. Samples were heat at 95C for 3 minutes, then 37C for 30 minutes. Samples were dispense in the arrays and hybridized at 65C for 40 hours in a hybrization oven at 20rpm.

scan_protocol: Scanned on DNA Microarray Scanner (Agilent Technologies). Images were quantified using Agilent Feature Extraction Software (version 9.5).

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Agilent software was used.

source_name: Nodal marginal zone lymphoma

label_protocol: 1ug of tumor and reference DNA were independently labeled with Bioprime labeling kit from Invitrogen with CY dyes from Amersham as recommended by the manafacture. Cy5 dye was used to label tumor DNA samples and Cy3 to label reference DNA samples. Next, labeled genomic reactions were cleaned-up with Microcon YM-30 columns

extract_protocol: Genomic DNA was obtained from frozen tumors using the Puregene Core A kit (Qiagen) according to manufacturer’s recommendations.

tag: pathology

value: Nodal marginal zone lymphoma

value: F

tag: organ

value: LN

source_name: Female reference DNA sample

tag: sample type

value: reference


title: MZL_055


title: MZL_079


title: MZL_091

value: M


title: MZL_063


title: MZL_059


title: MZL_051


title: MZL_047


title: MZL_031


title: MZL_083


title: MZL_087


title: MZL_071


title: MZL_139

source_name: MALT lymphoma

value: MALT lymphoma

value: Lacrimal gland


title: MZL_005


title: MZL_027


title: MZL_011


title: MZL_023


title: MZL_039


title: MZL_017


title: MZL_140


title: MZL_138


title: MZL_136

value: Lung


title: MZL_134


title: MZL_130


title: MZL_131


title: MZL_099


title: MZL_137


title: MZL_129


title: MZL_128


title: MZL_141


title: MZL_127


title: MZL_124


title: MZL_132


title: MZL_126


title: MZL_133


title: HB2-P3, biological rep2


title: MZL_135


title: MZL_121


title: MZL_125


title: MZL_122


title: MZL_120


title: MZL_119


title: MZL_117


title: MZL_105

value: Salivary gland


title: MZL_118


title: MZL_090


title: MZL_123


title: MZL_082


title: MZL_078


title: MZL_094

value: Stomach


title: MZL_067


title: MZL_074


title: MZL_054


title: MZL_030


title: Herford_WG

description: Hybridization of test sample Herford_WG and reference sample Dominette

source_name: whole blood from Herford_WG

value: Herford

value: Female

value: whole blood

value: Hereford L1 Dominette 01449


title: MZL_077

source_name: Lymphoplasmacytic lymphoma

value: Lymphoplasmacytic lymphoma


title: MZL_085


title: MZL_016


title: MZL_050

value: Bowel


title: MZL_038

value: Salivary gland + BR


title: MZL_034


title: MZL_069


title: MZL_004


title: MZL_065


title: MZL_045


title: MZL_073


title: MZL_033


title: MZL_037


title: MZL_062


title: MZL_022

value: Parotid


title: MZL_015


title: MZL_003


title: MZL_049

value: F


title: MZL_070


title: MZL_058

value: Colon


title: MZL_029

value: LN

value: reference


title: MZL_066

value: MALT lymphoma

value: Illeum


title: MZL_010


title: MZL_116

source_name: SMZL

value: SMZL

value: Spleen


title: MZL_046

value: Salivary gland


title: MZL_113


title: MZL_115


title: MZL_111


title: MZL_114


title: MZL_009

value: M


title: MZL_109


title: MZL_112


title: MZL_108


title: MZL_092


title: MZL_110


title: pancreas normal, Kras-Pdx1-cre-IKK2, biological rep1

city: Houston

middle: J

last: Chiao

state: Texas

address: 1515 Holcombe Blvd

department: Department of Molecular and Cellular Oncology

institute: The University of Texas M. D. Anderson Cancer Center

description:
10_Kras-Pdx1-cre-IKK2-N-1
Gene expression data; Pdx1-cre;KrasLSL-G12D;IKK2/b 1

hyb_protocol: Hybridization was according to the Affymetrx protocol.

scan_protocol: The images were scanned using the Hewlett-Packard Gene Array scanner G2500A.

data_processing: The data were normalized using RMA and analyzed by using Significance Analysis of Microarray (SAM).

label_protocol: cDNA were labeled according to the Affymetrix protocol.

growth_protocol: The mice were maintained at the conventional conditions at the animal core facility at MD Anderson Cancer Center.

extract_protocol: Total RNA from pancreas was isolated by Trizol.

treatment_protocol: Pancreas was directly taken out after the mice were sacrificed.

tag: strain

tag: genotype

tag: age

value: 6-8 months

value: male

value: pancreas


title: MZL_098

value: Stomach


title: MZL_107


title: pancreas normal, Kras-Pdx1-cre-IKK2, biological rep3

description:
12_Kras-Pdx1-cre-IKK2-N-3
Gene expression data; Pdx1-cre;KrasLSL-G12D;IKK2/b 3


title: pancreas normal, Kras-Pdx1-cre-IKK2, biological rep2

description:
11_Kras-Pdx1-cre-IKK2-N-2
Gene expression data; Pdx1-cre;KrasLSL-G12D;IKK2/b 2


title: PDAC, Kras-Pdx1-cre, biological rep3

description:
9_Kras-Pdx1-cre-PDAC-3
Gene expression data; Pdx1-cre;KrasLSL-G12D 3

source_name: pancreas, Pdx1-cre;KrasLSL-G12D, PDAC

value: pancreatic ductal adenocarcinoma (PDAC)


title: MZL_072


title: MZL_084


title: MZL_080


title: MZL_104


title: MZL_106


title: MZL_068


title: PanIN, Kras-Pdx1-cre, biological rep3

description:
6-Kras-Pdx1-cre-painIN-3
Gene expression data; Pdx1-cre;KrasLSL-G12D 3

source_name: pancreas, Pdx1-cre;KrasLSL-G12D, panIN

value: pancreatic intraepithelial neoplasia (PanIN)


title: PDAC, Kras-Pdx1-cre, biological rep1

description:
7_Kras-Pdx1-cre-PDAC-1
Gene expression data; Pdx1-cre;KrasLSL-G12D 1


title: MZL_100


title: MZL_076


title: PDAC, Kras-Pdx1-cre, biological rep2

description:
8_Kras-Pdx1-cre-PDAC-2
Gene expression data; Pdx1-cre;KrasLSL-G12D 2


title: MZL_096


title: Normal pancreas, Kras-Pdx1-cre, biological rep1

description:
1_Kras-Pdx1-cre-N
Gene expression data; Pdx1-cre;KrasLSL-G12D 1

source_name: pancreas, Pdx1-cre;KrasLSL-G12D, normal


title: PanIN, Kras-Pdx1-cre, biological rep1

description:
4-Kras-Pdx1-cre-painIN-1
Gene expression data; Pdx1-cre;KrasLSL-G12D 1


title: MZL_064


title: PanIN, Kras-Pdx1-cre, biological rep2

description:
5-Kras-Pdx1-cre-painIN-2
Gene expression data; Pdx1-cre;KrasLSL-G12D 2


title: Normal pancreas, Kras-Pdx1-cre, biological rep2

description:
2_Kras-Pdx1-cre-N
Gene expression data; Pdx1-cre;KrasLSL-G12D 2


title: Normal pancreas, Kras-Pdx1-cre, biological rep3

description:
3_Kras-Pdx1-cre-N
Gene expression data; Pdx1-cre;KrasLSL-G12D 3


title: MZL_044


title: MZL_048


title: MZL_056


title: MZL_088


title: MZL_040


title: Kidney 25 days

city: Lugo

first: Adrian

middle: Millan

last: Perez

state: Lugo

address: Facultad Veterinaria, Campus Universitario Pabellon IV 2 superior

department: Acuigen

country: Spain

institute: Universidad Santiago Compostela

description: Gene expression after challenging with Philasterides dicentrarchi

hyb_protocol: 0,6 ug of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul adding 1ul 25x Agilent fragmentation buffer and 5 ul 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction 25 ul 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to the turbot custom oligo-microarray for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x15k array slides (Scan Area 61x21.6 mm, Scan resolution 5 um).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters (protocol GE1-v5_95 and Grid:016528_D_F_20070525) to obtain Processed Signal intensities.  Those microarrays having an average coefficient of variation (CV) across Spike-In and non-Spike-In probes below 10% were considered for further analysis. Secondly, the following features and/or genes which did not conform to the established quality criteria were filtered: i) non-uniform pixel distributed outliers and population replicate outliers according to the default Agilent feature extraction criteria; ii) features whose ratio between processed signal and its error was below 2; iii) spots not differentiated from background signal (as estimated for each spot); iv) features below the limit where the linear relationship between concentration and intensity was lost according to Spike-In information; v) genes which did not show at least 3 quality replicates out of 5 and/or a coefficient of variation (CV) across replicates >10%.

organism: Scophthalmus maximus

source_name: Kidney 25 days

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Microarray-Based Gene Expression Analysis (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: 150 individuals of ~ 30g from 20 equally represented families from a turbot company (Alrogal SA) were transported to CETGA (Centro Tecnológico Gallego de Acuicultura; NW Spain) facilities. Prior to challenge, fry were maintained during 10 days at standard culture conditions to cut down on transport stress and to check if they were free from diseases.

extract_protocol: Total RNA was extracted from pooled tissues of control and infected fish using TRIZOL Reagent (Life Technologies) according to manufacturer’s recommendations. All extractions were performed by the same researcher.

treatment_protocol: Fish were injected intracelomically (i.p.) with 0.1 ml of a parasite suspension of 2.5x10^6 parasites/mL. The presence of P. dicentrarchi in infected fish was checked by plating drops of the ascitic fluid and blood that were impregnated with ammoniacal pyridinated silver carbonate, and biometric measurements of taxonomically important characters were made under an optical microscope (Budiño et al., 2011b). The challenges were performed at the CETGA facilities in quarantine tanks. All fish used in the experiment were anaesthetized with benzocaine (50 mg/ml) and sacrificed by decapitation. Equal amounts of spleen, liver and head kidney were sampled from each fish, pooled per organ at each sampling point and immediately stored in liquid nitrogen.

tag: infection agent

value: 0.1 ml of 2.5x10^6 P. dicentrarchi/mL suspension

tag: time point

value: 25 day post-challenging

value: kidney


title: Kidney 7 days

source_name: Kidney 7 days

value: 7 day post-challenging


title: MZL_036

value: reference


title: Kidney 3 days

source_name: Kidney 3 days

value: 3 day post-challenging


title: MZL_060


title: Pol II_met-1_rep1

city: Santa Cruz

first: Susan

last: Strome

address: 1156 High St

department: MCD Biology

institute: UC Santa Cruz

description: ChIP-chip of Pol II in met-1 EEMB; channel ch1 is ChIP DNA; ChIP-chip of CENP-A/HCP-3 in met-1 EEMB; channel ch1 is ChIP DNA; Antibody information: official name: ABAB817 8WG16;target name: RNA polII CTD domain unphosophorylated;host: Mouse;antigen: Native RNA Polymerase II purified from wheat germ;clonal: Monoclonal;purified: Size;company: Covance;catalog: Covance (MMS126R);short description: A mouse monoclonal antibody which recognizes primarily the unphosphorylated RNA Pol II CTD (8WG16) obtained from Covance (MMS126R) was used for ChIP; channel ch2 is Input DNA;

hyb_protocol: ChIP-chip_label_hyb_nimblegen_v1. DNA was labeled and hybridized to C. elegans tiling array by Roche NimbleGen according to the protocol described in chapter 3 and 4 of the NimbleGen Arrays User?s Guide ChIP-chip Analysis, Version 3.1, 27 May 2008. Briefly, Amplified IP or input DNA was either labeled with Cy5 or Cy3 in the presence of Klenow fragment. The reaction was stopped by the addition of EDTA. Labeled DNA was recovered by isopropanol precipitation, and dried. The labeled DNA was hybridized to C. elegans tiling array for 16 - 20 hours at 42°C.

scan_protocol: ChIP-chip_scanning_nimblegen_v1. Array scanning and raw data extraction were performed at Roche NimbleGen, according to the protocol described in chapter 5 and 6 of the NimbleGen Arrays Users Guide ChIP-chip Analysis, Version 3.1, 27 May 2008. Briefly, array signal was scanned by using a GenePix 4000B Scanner with associated software and saved as .tif files of the 532nm and 635nm images individually. Raw signal intensities of the images were extracted and saved as .pair files by using NimbleScan software according to the NimbleScan v2.4 User?s Guide.

data_processing: ChIP-chip normalization standard nimblegen:JL:1 protocol.  The log2-ratio ratio of intensity from sample/reference channel was scaled to center the ratio data around zero by subtracting the bi-weight mean for the log2-ratio values for all features on the array from each log2-ratio value (results in linked .gff files). This was performed using NimbleScan software according to the NimbleScan v2.4 User's Guide and chapter 6 of the NimbleGen Arrays User's Guide ChIP-chip Analysis (version 3.1, 27 May 2008) at Roche NimbleGen. Processed data are obtained using following parameters: genome version is WS180

organism: Caenorhabditis elegans

source_name: Pol II ChIP DNA for met-1 EEMB

label_protocol: ChIP-chip_label_hyb_nimblegen_v1. DNA was labeled and hybridized to C. elegans tiling array by Roche NimbleGen according to the protocol described in chapter 3 and 4 of the NimbleGen Arrays Users Guide ChIP-chip Analysis, Version 3.1, 27 May 2008. Briefly, Amplified IP or input DNA was either labeled with Cy5 or Cy3 in the presence of Klenow fragment. The reaction was stopped by the addition of EDTA. Labeled DNA was recovered by isopropanol precipitation, and dried. The labeled DNA was hybridized to C. elegans tiling array for 16 - 20 hours at 42°C.

growth_protocol: Worm_embryo_growth_and_harvest_vSS3. Embryos were prepared by bleaching from gravid met-1 adults grown in standard S-basal media liquid culture. Live embryos were cross-linked in M9 + 1.85 % formaldehyde for 30 minutes at room temperature. Embryos were then washed twice with M9 Buffer, once with 100 mM Tris-HCl pH 7.5 and once with FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 150 mM NaCl). Pellets were frozen at -80C.

extract_protocol: Worm_embryo_extraction_vSS5. Embryos were resuspended in FA buffer (50 mM HEPES/KOH pH 7.5, 1mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate; 150 mM NaCl) + protease inhibitors. Sample was dounced 30 times using tight pestle at 4ºC, then sonicated in ice water bath using a Diagenode Bioruptor at the highest setting for 14 pulses 30 seconds long with 1 minute pauses. Cell debris was removed by centrifuging at 13,000 rpm for 15 minutes at 4ºC and taking the supernatant. Supernatants were filtered through Millipore Ultrafree-MC 0.45 um filter units (cat. UFC30HV0S) at 13,000 rpm, 4°C for 1 minute to remove lipids. Protein concentration was determined, and extracts were aliquoted and stored at -80ºC.   Worm_chromatin_immunoprecipitation_vSS4. 0.3-3 mg extract + 1% sarkosyl was used for each ChIP with 10% taken as input directly into elution buffer (1% SDS in TE, 250 mM NaCl). Antibody was added to each IP sample and incubated overnight at 4ºC. Immune complexes were incubated (2 hrs at 4ºC) with 50 ul of IgG dynabeads (Dyna), and washed 5 minutes with 1.5 mL of each of the following solutions: ChIP Buffer, ChIP Buffer + 1 M NaCl, ChIP Buffer + 500 mM NaCl, TEL Buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA), and 2X TE (10 mM Tris-HCl pH 8.0, 1 mM EDTA). Samples were eluted twice with 150 uL elution buffer for 15 minutes at 65ºC. Samples were treated with RNAse for 30 minutes at 37ºC. Samples were treated with proteinase K at 55ºC for 1-2 hrs then transfer to 65ºC overnight to reverse crosslinks. DNA was cleaned up using Zymo kit.   Worm_LM-PCR_Amplification_for_ChIP-chip_vSS2. ChIP DNA was amplified with a modified ligation mediated PCR (LM-PCR) protocol derived from FlyChip protocol version 1.2 from R. Auburn: http://www.flychip.org.uk/protocols/chip/lm_pcr.php.  For more details see www.modencode.org

tag: developmental stage

value: Early Embryo

tag: chip antibody

value: Pol II

tag: Sex

value: population predominantly Hermaphrodites perhaps with some Males

source_name: Input DNA for met-1 EEMB

value: none, Input DNA


title: MZL_028

value: SMZL

value: F

value: Spleen + hilar + portal LN


title: MZL_018

value: M

value: Spleen


title: Kidney 15 days

source_name: Kidney 15 days

value: 15 day post-challenging

tag: tissue


title: Kidney control

source_name: Kidney control

value: time 0; non-injected


title: PVN_sham_2h_rep2

city: Tokyo

first: Eri

last: Segi-Nishida

state: Tokyo

address: Niijuku 6-3-1

institute: Tokyo University of Science

description: Gene expression data from sham-treated mouse PVN

hyb_protocol: Following fragmentation, 5 ug of cDNA were hybridized for 16 hr at 45C on GeneChip® Mouse Genome 430A 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned by GeneChip Scanner 3000.

label_protocol: RNA amplification reaction was carried out using 2 ng of total RNA by Ovation Pico WTA System (NuGEN Technologies, San Carlos, CA), and amplified cDNA products were fragmented and labeled to generate biotinylated cDNA targets by Ovation biotylation kit. Then 5 µg of labeled cDNA was used for subsequent microarray analysis.

extract_protocol: Cryocut sections (7 μm thickness) were placed non-coated glass slides (Jung CM3000 cryostat; Leica Microsystems, Wetzlar, Germany), fixed, stained and dehydrated using the following protocol: 75% of ethanol for 30 sec, RNase-free water for 30 sec, staining using Histogene (Applied Biosystems, Carlsbad, CA) for 20 sec, RNase-free water for 30 sec, 75% of ethanol for 30 sec, 95% of ethanol for 30 sec, 100% of ethanol for 30 sec twice, xylene for 5 min; then sections were vacuumed for 15 min to dry. Laser microdissection was carried out on the Pixell Ile Laser Capture Microdissection System (Applied Biosystems). Immediately after microdissection, samples were dissolved in denaturing buffer and total RNA was isolated using an RNeasy Micro Kit (Qiagen).

treatment_protocol: Bilateral ECS was administered via moistened spring-loaded ear clip electrodes to isoflurane-anesthetized mice using a pulse generator (ECT Unit; Ugo Basile, Comeria, Italy) (current, 25 mA; shock duration, 1 sec; frequency, 100 pulse/sec; pulse width, 0.5 msec). ECS-treated animals received one shock and tissue was collected at 2 or 6 h after shock. Sham-treated animals were handled the same fashion as ECS-treated animals, but no shock was delivered. Tissue of sham-treated animals was collected at 2 h after treatment. For microdissection from brain sections, the whole brains were quickly removed and rapidly frozen on dry ice, then stored at -20°C until microdissection.

value: paraventricular hypothalamus

value: sham


title: Pol II_met-1_rep2


title: PVN_ECS_2h_rep1

description: Gene expression data from mouse PVN  at 2 h after ECS

value: electroconvulsive seizure


title: MZL_012


title: MZL_024


title: CENP-A_met-1_rep2

description: ChIP-chip of CENP-A/HCP-3 in met-1 EEMB; channel ch1 is ChIP DNA; Antibody information: official name: OD79 HCP3;target name: HCP-3;host: Rabbit;antigen: N-terminal histone tail of HCP-3;clonal: Polyclonal;purified: Affinity;company: Other;catalog: Desai Lab;reference: Monen et al. (2005) Nat Cell Biol 7: 1248-55; channel ch2 is Input DNA

source_name: CENP-A ChIP DNA for met-1 EEMB


title: MZL_006


title: CENP-A_met-1_rep1


title: PVN_sham_2h_rep1


title: PVN_ECS_2h_rep2


title: PVN_ECS_6h_rep2

description: Gene expression data from mouse PVN  at 6 h after ECS


title: Kidney 1 day

source_name: Kidney 1 day

value: 0.1 ml of 2.5x10^6 P. dicentrarchi/mL suspension

value: 1 day post-challenging

value: kidney


title: MZL_032

source_name: Female reference DNA sample

value: reference


title: Liver 25 days

source_name: Liver 25 days

value: 25 day post-challenging

value: liver


title: H3K36me3_met1_rep1

description: ChIP-chip of H3K36me3 in met-1 EEMB; channel ch1 is ChIP DNA; Antibody information: HK00001 H3K36me3:13C9;target name: H3K36me3;host: Mouse;antigen: KSAPATGGV(me3-K)KPHRYRPGTC;clonal: Monoclonal;purified: Protein A/G;company: Other;catalog: HK00001;short description: A protein G purified mouse monoclonal antibody to H3K36me3 (clone 13C9) obtained from Hiroshi Kimura. Used for ChIP; channel ch2 is Input DNA

source_name: H3K36me3 ChIP DNA for met-1 EEMB

value: Early Embryo

value: population predominantly Hermaphrodites perhaps with some Males

value: none, Input DNA


title: Liver 3 days

source_name: Liver 3 days

value: 3 day post-challenging