title: Control Shoot

city: Varanasi

first: Sudhakar

last: Srivastava

address: Lanka

department: INSTT. OF ENV.  AND SUST. DEV.

country: India

institute: Banaras Hindu University

hyb_protocol: With the use of Agilent’s Gene Expression Hybridization Kit, 1.65 µg of cyanine 3-labeled linearly amplified cRNA was added to a hybridization cocktail and then fragmented. The hybridization cocktail was then dispensed into the wells of gasket slides on top of which a Brassica 4x44K Gene Expression Microarray was placed. This microarray “sandwich” was then sealed in a hybridization chamber. The microarrays were hybridized at 65°C rotating at 10 RPMs for 17 hours. Slides were washed in Agilent’s Gene Expression Wash Buffers according to manufacturer specifications.

scan_protocol: The microarrays were scanned on the Agilent Microarray Scanner. Scanner data extraction and analysis was performed using Agilent Technologies Feature Extraction software version 10.7.3.1.

data_processing: Microarray data quality was evaluated by reviewing ten standard QC metrics generated by the Feature Extraction Software [Consult the Agilent Technologies Feature Extraction Software version 10.7.3.1 reference guide for a full explanation of the QC metrics]. The intensity values obtained from Agilent Feature Extraction software were background corrected, and were normalized by using Quantile Normalization.

organism: Brassica juncea

source_name: Shoot of control treatment

label_protocol: With the use of Agilent’s 1-Color Quick Amp Labeling Kit, 500 ng of high quality total RNA was denatured in the presence of a T7 promoter primer and a 1-Color RNA Spike-In Kit. Reverse transcriptase was used to reverse-transcribe the mRNA. cDNA was used as a template for in vitro transcription where a T7 RNA polymerase simultaneously amplified target material and incorporated cyanine 3-labeled CTP.

growth_protocol: Seeds were sterilized and grown in a Plant Growth Chamber (Sanyo, Japan) in Hoaglands nutrient medium

extract_protocol: The DNA-free total RNA was extracted using a mirVANA kit (AM1560, Ambion). The quantity and purity of the RNA was determined by absorbance at 260 nm and 260/280 absorbance ratio respectively.  Each of the total RNA preparations was individually assessed for RNA quality based on the 28S/18S ratio and RIN measured on an Agilent 2100 Bioanalyzer system using the RNA 6000 Nano LabChip Kit .

treatment_protocol: After 12 d, seedlings were exposed to 500 μM arsenate (AsV; as Na2HAsO4) for 96 h. Seedlings were harvested for conducting microarray analysis at 4, 24 and 96 h and roots and shoots were separated.

value: Whole shoot

value: control

tag: time


title: Head and neck Squamous cell carcinomas_OROPHARYNX_70

status: Public on Mar 04 2015

type: RNA

city: chicago

first: Tanguy

last: Seiwert

state: IL

address: 900 E. 57th street

country: USA

institute: University of Chicago

hyb_protocol: Expression arrays were performed at the Argonne National Laboratory in an ozone-controlled atmosphere.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1. Raw data were background corrected, quantile normalized and log2 transformed.

molecule: total RNA

organism: Homo sapiens

source_name: Head and neck Squamous cell carcinomas_OROPHARYNX_pretreatmeant_70

label_protocol: Labeling for Agilent 4x44K v2 expression arrays was done using a Quick Amp Labeling Kit one-color according to the manufacturer’s protocol using 200ng of starting material.

extract_protocol: Guided by H&E stained slides, the region with the highest tumor content was cut from OCT blocks, pulverized using CryoPrep (Covaris, Woburn, MA) and homogenized in a lysis buffer from an AllPrepRNA/DNA/Protein Mini kit (Qiagen, Valencia, CA) or from a RNA/DNA/Protein Purification Kit (Norgen Biotek, Thorold, Canada) using an Ultrasonicator (Covaris, Woburn, MA). DNA, RNA and protein were isolated from each sample using the respective kit and following manufacturer’s protocol. RNA integrity was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA). If DNA contamination was seen, RNAs were treated with TURBO DNA-free (Ambion, CA) to remove genomic DNA, and subsequently quantitated using a spectrophotometer. Only RNAs with integrity number (RIN) ≥7.5, a 260/280 ratio ≥1.8 and a 260/230 ratio ≥1.8 (≥1.1 for a few RNAs) were labeled for expression arrays.

treatment_protocol: All the patients were treated with concurrent chemoradiotherapy. Samples with microscopic tumor or tumor content <60% were excluded from further analysis.

tag: tissue type

value: head and neck squamous cell carcinoma (HNSCC)

tag: anatomic site

value: OROPHARYNX

tag: gender

value: M

tag: hpv status

value: pos


title: Control Root

source_name: Root of control treatment

tag: tissue

value: Whole root

tag: treatment


title: 4 h_Root

source_name: Root of As exposed plants at 4 h

value: Whole Root

value: arsenate

value: 4 h


title: 96 h_Root

source_name: Root of As exposed plants at 96 h


title: 24 h_Root

source_name: Root of As exposed plants at 24 h


title: Head and neck Squamous cell carcinomas_OROPHARYNX_72

scan_protocol: Expression arrays were performed at the Argonne National Laboratory in an ozone-controlled atmosphere.

source_name: Head and neck Squamous cell carcinomas_OROPHARYNX_pretreatmeant_72

value: neg


title: 96 h_Shoot

source_name: Shoot of As exposed plants at 96 h


title: 24 h_Shoot

source_name: Shoot of As exposed plants at 24 h


title: Head and neck Squamous cell carcinomas_HYPOPHARYNX_69

source_name: Head and neck Squamous cell carcinomas_HYPOPHARYNX_pretreatmeant_69

value: HYPOPHARYNX


title: Head and neck Squamous cell carcinomas_OROPHARYNX_67

source_name: Head and neck Squamous cell carcinomas_OROPHARYNX_pretreatmeant_67


title: Head and neck Squamous cell carcinomas_ORAL CAVITY_68

source_name: Head and neck Squamous cell carcinomas_ORAL CAVITY_pretreatmeant_68

value: ORAL CAVITY


title: C-3-24h

city: Yangzhou

first: Jiao

last: Hu

address: 48 Wenhui Road

country: China

institute: Yangzhou University

description: Gene expression data of lung from mock-infected chicken

hyb_protocol: After fragmentation, 12.5 ug of aRNA were hybridized at 45 ℃ for 16 hr on Affymetrix  Genome GeneChip. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

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.

label: biotin

organism: Gallus gallus

source_name: lung from mock-infected chicken

label_protocol: Biotinylated aRNA were prepared using Genechip IVT Express Kit according to the standard Affymetrix protocol from 1 ug total RNA.

extract_protocol: Total tissue RNA was extracted using the TRIZOL reagent and purified using QIAGEN RNeasy Mini kit according to the manufacturer's instructions.

value: lung


title: Head and neck Squamous cell carcinomas_ORAL CAVITY_63

source_name: Head and neck Squamous cell carcinomas_ORAL CAVITY_pretreatmeant_63


title: Head and neck Squamous cell carcinomas_OROPHARYNX_65

source_name: Head and neck Squamous cell carcinomas_OROPHARYNX_pretreatmeant_65


title: Empty D2

city: meguro-ku

first: Takeshi

last: Inagaki

state: Tokyo

address: 4-6-1 Komaba

country: Japan

institute: Univ of Tokyo

description: Day 2 of differentiation

hyb_protocol: biotinylated cRNA were prepared according to the standard Affymetrix protocol

scan_protocol: scanned by Affymetrix GeneChip scanner 3000 (Affymetrix).

data_processing: GeneChip Analysis Suite software version 5.0 was used (Affymetrix)

organism: Mus musculus

source_name: 3T3-L1 cells tranduced empty vector

growth_protocol: cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum at 37°C in 5% CO2.  For adipocyte differentiation, two days after reaching confluence (day 0), 3T3-L1 preadipocytes were treated with differentiation medium containing insulin (1 ug/ml), 0.25 μM dexamethasone, and 0.5 mM isobutylmethylxanthine (MDI cocktail)

extract_protocol: RNA was extracted using ISOGEN following manufacturer's protocol

treatment_protocol: To construct retroviral expression vectors, Fbxl10 sequence was cloned into EcoRI/NotI site of pMXs-puro vector driven by weak LTR promoter (a kind gift from Dr. Toshio Kitamura, The University of Tokyo)

tag: cell line

value: 3T3-L1 cells

value: empty vector


title: Fbxl10 D2

description: Day 2 of differentiation

source_name: 3T3-L1 cells overexpressing Fbxl10

label_protocol: prepared according to the standard Affymetrix protocol

value: Fbxl10 overexpression


title: C-1-24h


title: Head and neck Squamous cell carcinomas_ORAL CAVITY_61

source_name: Head and neck Squamous cell carcinomas_ORAL CAVITY_pretreatmeant_61


title: Head and neck Squamous cell carcinomas_OROPHARYNX_62

source_name: Head and neck Squamous cell carcinomas_OROPHARYNX_pretreatmeant_62


title: Head and neck Squamous cell carcinomas_SUPRAGLOTTIC_60

source_name: Head and neck Squamous cell carcinomas_SUPRAGLOTTIC_pretreatmeant_60

value: SUPRAGLOTTIC


title: Head and neck Squamous cell carcinomas_HYPOPHARYNX_58

source_name: Head and neck Squamous cell carcinomas_HYPOPHARYNX_pretreatmeant_58


title: Head and neck Squamous cell carcinomas_OROPHARYNX_66

source_name: Head and neck Squamous cell carcinomas_OROPHARYNX_pretreatmeant_66


title: Head and neck Squamous cell carcinomas_SUPRAGLOTTIC_64

source_name: Head and neck Squamous cell carcinomas_SUPRAGLOTTIC_pretreatmeant_64


title: Head and neck Squamous cell carcinomas_HYPOPHARYNX_59

source_name: Head and neck Squamous cell carcinomas_HYPOPHARYNX_pretreatmeant_59


title: Head and neck Squamous cell carcinomas_SUPRAGLOTTIC_57

source_name: Head and neck Squamous cell carcinomas_SUPRAGLOTTIC_pretreatmeant_57


title: C-2-24h


title: CK-PAX3-1-24h

description: Gene expression data of lung from CK-PAX3-infected chicken

source_name: lung from CK-PAX3-infected chicken, 24 hours post infection


title: Head and neck Squamous cell carcinomas_ORAL CAVITY_54

source_name: Head and neck Squamous cell carcinomas_ORAL CAVITY_pretreatmeant_54


title: C-3-12h


title: Head and neck Squamous cell carcinomas_SUPRAGLOTTIC_53

source_name: Head and neck Squamous cell carcinomas_SUPRAGLOTTIC_pretreatmeant_53

value: F


title: Head and neck Squamous cell carcinomas_OROPHARYNX_55

source_name: Head and neck Squamous cell carcinomas_OROPHARYNX_pretreatmeant_55

value: head and neck squamous cell carcinoma (HNSCC)


title: CK-PAX3-3-24h


title: C-2-12h

source_name: lung from mock-infected chicken


title: CK10-2-24h

description: Gene expression data of lung from CK10-infected chicken

source_name: lung from CK10-infected chicken, 24 hours post infection


title: Head and neck Squamous cell carcinomas_OROPHARYNX_56

source_name: Head and neck Squamous cell carcinomas_OROPHARYNX_pretreatmeant_56

value: OROPHARYNX


title: CK10-3-24h


title: CK-PAX3-2-24h


title: CK10-1-24h


title: CK-PAX3-1-12h

source_name: lung from CK-PAX3-infected chicken, 12 hours post infection


title: CK-PAX3-3-12h


title: CK-PAX3-2-12h


title: Head and neck Squamous cell carcinomas_OROPHARYNX_52

source_name: Head and neck Squamous cell carcinomas_OROPHARYNX_pretreatmeant_52


title: C-1-12h


title: CK10-3-12h

source_name: lung from CK10-infected chicken, 12 hours post infection


title: CK10-2-12h


title: Head and neck Squamous cell carcinomas_OROPHARYNX_48

source_name: Head and neck Squamous cell carcinomas_OROPHARYNX_pretreatmeant_48

value: M


title: Head and neck Squamous cell carcinomas_OROPHARYNX_47

source_name: Head and neck Squamous cell carcinomas_OROPHARYNX_pretreatmeant_47

value: pos


title: Head and neck Squamous cell carcinomas_OROPHARYNX_49

source_name: Head and neck Squamous cell carcinomas_OROPHARYNX_pretreatmeant_49


title: Head and neck Squamous cell carcinomas_OROPHARYNX_51

source_name: Head and neck Squamous cell carcinomas_OROPHARYNX_pretreatmeant_51


title: Head and neck Squamous cell carcinomas_OROPHARYNX_50

source_name: Head and neck Squamous cell carcinomas_OROPHARYNX_pretreatmeant_50


title: TAKO-CD45+EpCAM-

city: Nankoku

first: Taro

last: Fukazawa

state: Kochi

address: Kohasu, Oko-cho

department: Department of Immunology

institute: Kochi Medical School

hyb_protocol: 1.5 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x GE Hybridization Buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Microarray 4x44K v2 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.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: TAKO, CD45+EpCAM- thymic stroma

label_protocol: Low Input Quick Amp Labeling Kit, one-color (Agilent Technologies) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).

extract_protocol: Total RNA was extracted from pooled cells by using TRIzol reagent. The quality of the RNA was checked with an Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA, USA) and an RNA 6000 Pico kit (Agilent Technologies).

tag: genotype/variation

value: TNFalpha and RelA double KO

tag: cell type

value: CD45+EpCAM- thymic stroma

tag: strain


title: CK10-1-12h


title: Head and neck Squamous cell carcinomas_OROPHARYNX_41

source_name: Head and neck Squamous cell carcinomas_OROPHARYNX_pretreatmeant_41


title: Head and neck Squamous cell carcinomas_OROPHARYNX_43

source_name: Head and neck Squamous cell carcinomas_OROPHARYNX_pretreatmeant_43


title: Head and neck Squamous cell carcinomas_OROPHARYNX_46

source_name: Head and neck Squamous cell carcinomas_OROPHARYNX_pretreatmeant_46


title: TKO-CD45-EpCAM+

source_name: TKO, CD45-EpCAM+ thymic epithelial cells

value: TNFalpha-KO

value: CD45-EpCAM+ thymic epithelial cells


title: TKO-CD45+EpCAM-

source_name: TKO, CD45+EpCAM- thymic stroma


title: Head and neck Squamous cell carcinomas_OROPHARYNX_40

source_name: Head and neck Squamous cell carcinomas_OROPHARYNX_pretreatmeant_40


title: TAKO-CD45-EpCAM+

source_name: TAKO, CD45-EpCAM+ thymic epithelial cells


title: Head and neck Squamous cell carcinomas_OROPHARYNX_38

source_name: Head and neck Squamous cell carcinomas_OROPHARYNX_pretreatmeant_38


title: Head and neck Squamous cell carcinomas_OROPHARYNX_44

source_name: Head and neck Squamous cell carcinomas_OROPHARYNX_pretreatmeant_44


title: Head and neck Squamous cell carcinomas_OROPHARYNX_42

source_name: Head and neck Squamous cell carcinomas_OROPHARYNX_pretreatmeant_42


title: Head and neck Squamous cell carcinomas_OROPHARYNX_39

source_name: Head and neck Squamous cell carcinomas_OROPHARYNX_pretreatmeant_39


title: Head and neck Squamous cell carcinomas_OROPHARYNX_45

source_name: Head and neck Squamous cell carcinomas_OROPHARYNX_pretreatmeant_45


title: TKO-CD4+CD25hi

source_name: TKO, CD4+CD25hi thymocytes

value: CD4+CD25hi thymocytes


title: TAKO-CD4+CD25hi

source_name: TAKO, CD4+CD25hi thymocytes


title: AM14 TLR7 TLR9 KO PL2-3 Treated - 42 hours - mAdbID:123219

city: Bethesda

first: Louis

middle: M.

last: Staudt

state: MD

address: 9000 Rockville Pike, Bldg 10, Rm 4N114

department: Lymphoid Malignancies Branch

institute: National Cancer Institute

description: mAdb experiment ID: 123219

hyb_protocol: Agilent Hybridization Other: According to the manufacture's recommended protocol (Two-Color Microarray-Based Gene Expression Analysis, Agilent).

scan_protocol: Scan_MicronsPerPixelX: 3 Scan_MicronsPerPixelY: 3 Scan_ScannerName: Agilent Technologies Scanner G2505C US45102888

data_processing:
Agilent Data Processing Protocol
Calculation Method: Images were auto gridded, analyzed and data extracted using Agilent Feature Extraction Software. Spot values were normalized using the default linear-lowess normalization.
FeatureExtractor_Version: 10.1.1.1
Protocol_Name: GE2-v5_10_Apr08 (Read Only)

source_name: Unstimulated Pooled B-cell Control

label_protocol:
Agilent Labeling-Cy3
Other: Total RNA was reverse transcribed to cDNA using T7 Promoter Primer and MMLV-RT. Then the cDNA was converted to aRNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3- or cyanine 5-labeled CTP (Two-Color Microarray-Based Gene Expression Analysis Protocol, Agilent).

extract_protocol:
Trizol Extraction Protocol
Other: Total RNA was prepared by the Trizol method (Invitrogen) and purified using RNeasy Mini columns (Qiagen).

value: spleen

value: B cells

value: gene knock out

tag: other

value: Sample Pooling Protocol:Pool of unstimulated AM14 B cell RNAs from all genotypes (WT, Tlr7-/-, Tlr9-/- and Tlr7/9-/-).

label_protocol:
Agilent Labeling-Cy5
Other: Total RNA was reverse transcribed to cDNA using T7 Promoter Primer and MMLV-RT. Then the cDNA was converted to aRNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3- or cyanine 5-labeled CTP (Two-Color Microarray-Based Gene Expression Analysis Protocol, Agilent).

treatment_protocol:
Agent: Monoclonal autoantibody PL2-3
Treatment time: 42 hours
In-vitro treatment: The monoclonal autoantibody, PL2-3, was added to wild-type (WT), TLR7-deficient (Tlr7-/-), TLR9-deficient (Tlr9-/-) and TLR7/9 double-deficient (Tlr7/9-/-) AM14 B cells for 42 hours.

value: Tlr7/9-/- gene knock out

value: 42 hours


title: AM14 TLR7 TLR9 KO PL2-3 Treated - 24 hours - mAdbID:123218

description: mAdb experiment ID: 123218

treatment_protocol:
Agent: Monoclonal autoantibody PL2-3
Treatment time: 24 hours
In-vitro treatment: The monoclonal autoantibody, PL2-3, was added to wild-type (WT), TLR7-deficient (Tlr7-/-), TLR9-deficient (Tlr9-/-) and TLR7/9 double-deficient (Tlr7/9-/-) AM14 B cells for 24 hours.

value: 24 hours


title: AM14 TLR7 TLR9 KO Untreated - 0 hour - mAdbID:123216

description: mAdb experiment ID: 123216

source_name: Unstimulated AM14 TLR7 TLR9 KO - 0 hour

value: Unstimulated

value: 0 hour


title: AM14 TLR7 TLR9 KO PL2-3 Treated - 6 hours - mAdbID:123217

description: mAdb experiment ID: 123217

treatment_protocol:
Agent: Monoclonal autoantibody PL2-3
Treatment time: 6 hours
In-vitro treatment: The monoclonal autoantibody, PL2-3, was added to wild-type (WT), TLR7-deficient (Tlr7-/-), TLR9-deficient (Tlr9-/-) and TLR7/9 double-deficient (Tlr7/9-/-) AM14 B cells for 6 hours.

value: 6 hours


title: Head and neck Squamous cell carcinomas_OROPHARYNX_37

source_name: Head and neck Squamous cell carcinomas_OROPHARYNX_pretreatmeant_37

value: head and neck squamous cell carcinoma (HNSCC)

value: OROPHARYNX

value: M


title: AM14 TLR9 KO PL2-3 Treated - 6 hours - mAdbID:123213

description: mAdb experiment ID: 123213

source_name: AM14 TLR9 KO PL2-3 Treated - 6 hours

value: Tlr9-/- gene knock out


title: Head and neck Squamous cell carcinomas_OROPHARYNX_36

source_name: Head and neck Squamous cell carcinomas_OROPHARYNX_pretreatmeant_36

value: pos


title: AM14 TLR9 KO PL2-3 Treated - 24 hours - mAdbID:123214

description: mAdb experiment ID: 123214

source_name: AM14 TLR9 KO PL2-3 Treated - 24 hours


title: Head and neck Squamous cell carcinomas_ORAL CAVITY_33

source_name: Head and neck Squamous cell carcinomas_ORAL CAVITY_pretreatmeant_33

value: ORAL CAVITY

value: neg


title: Head and neck Squamous cell carcinomas_ORAL CAVITY_30

source_name: Head and neck Squamous cell carcinomas_ORAL CAVITY_pretreatmeant_30

value: F


title: AM14 TLR9 KO Untreated - 0 hour - mAdbID:123212

description: mAdb experiment ID: 123212

value: spleen

value: B cells

source_name: Unstimulated AM14 TLR9 KO - 0 hour


title: Head and neck Squamous cell carcinomas_ORAL CAVITY_29

source_name: Head and neck Squamous cell carcinomas_ORAL CAVITY_pretreatmeant_29


title: Head and neck Squamous cell carcinomas_OROPHARYNX_35

source_name: Head and neck Squamous cell carcinomas_OROPHARYNX_pretreatmeant_35


title: Head and neck Squamous cell carcinomas_ORAL CAVITY_34

source_name: Head and neck Squamous cell carcinomas_ORAL CAVITY_pretreatmeant_34


title: AM14 TLR7 KO Untreated - 0 hour - mAdbID:123208

description: mAdb experiment ID: 123208

value: gene knock out

value: Sample Pooling Protocol:Pool of unstimulated AM14 B cell RNAs from all genotypes (WT, Tlr7-/-, Tlr9-/- and Tlr7/9-/-).

source_name: Unstimulated AM14 TLR7 KO - 0 hour

value: Tlr7-/- gene knock out


title: Head and neck Squamous cell carcinomas_ORAL CAVITY_31

source_name: Head and neck Squamous cell carcinomas_ORAL CAVITY_pretreatmeant_31


title: Head and neck Squamous cell carcinomas_ORAL CAVITY_27

source_name: Head and neck Squamous cell carcinomas_ORAL CAVITY_pretreatmeant_27


title: Head and neck Squamous cell carcinomas_SUPRAGLOTTIC_22

source_name: Head and neck Squamous cell carcinomas_SUPRAGLOTTIC_pretreatmeant_22

value: SUPRAGLOTTIC


title: AM14 TLR7 KO PL2-3 Treated - 24 hours - mAdbID:123210

description: mAdb experiment ID: 123210

source_name: AM14 TLR7 KO PL2-3 Treated - 24 hours

value: 24 hours


title: AM14 TLR7 KO PL2-3 Treated - 6 hours - mAdbID:123209

description: mAdb experiment ID: 123209

source_name: Unstimulated Pooled B-cell Control

source_name: AM14 TLR7 KO PL2-3 Treated - 6 hours


title: AM14 WT PL2-3 Treated - 24 hours - mAdbID:123206

description: mAdb experiment ID: 123206

source_name: AM14 WT PL2-3 Treated - 24 hours

value: WT


title: Head and neck Squamous cell carcinomas_OROPHARYNX_32

source_name: Head and neck Squamous cell carcinomas_OROPHARYNX_pretreatmeant_32


title: Head and neck Squamous cell carcinomas_ORAL CAVITY_21

source_name: Head and neck Squamous cell carcinomas_ORAL CAVITY_pretreatmeant_21


title: Head and neck Squamous cell carcinomas_OROPHARYNX_25

source_name: Head and neck Squamous cell carcinomas_OROPHARYNX_pretreatmeant_25


title: AM14 WT PL2-3 Treated - 6 hours - mAdbID:123205

description: mAdb experiment ID: 123205

source_name: AM14 WT PL2-3 Treated - 6 hours

value: 6 hours


title: Head and neck Squamous cell carcinomas_ORAL CAVITY_20

source_name: Head and neck Squamous cell carcinomas_ORAL CAVITY_pretreatmeant_20

value: head and neck squamous cell carcinoma (HNSCC)


title: Head and neck Squamous cell carcinomas_OROPHARYNX_26

source_name: Head and neck Squamous cell carcinomas_OROPHARYNX_pretreatmeant_26

value: OROPHARYNX


title: Head and neck Squamous cell carcinomas_OROPHARYNX_24

source_name: Head and neck Squamous cell carcinomas_OROPHARYNX_pretreatmeant_24

value: M


title: AM14 TLR9 KO PL2-3 Treated - 42 hours - mAdbID:123215

description: mAdb experiment ID: 123215

source_name: AM14 TLR9 KO PL2-3 Treated - 42 hours

value: Tlr9-/- gene knock out

value: 42 hours


title: Head and neck Squamous cell carcinomas_SUPRAGLOTTIC_19

source_name: Head and neck Squamous cell carcinomas_SUPRAGLOTTIC_pretreatmeant_19


title: AM14 WT PL2-3 Treated - 42 hours - mAdbID:123207

description: mAdb experiment ID: 123207

source_name: AM14 WT PL2-3 Treated - 42 hours


title: Head and neck Squamous cell carcinomas_OTHER_28

source_name: Head and neck Squamous cell carcinomas_OTHER_pretreatmeant_28

value: OTHER

value: pos


title: AM14 TLR7 KO PL2-3 Treated - 42 hours - mAdbID:123211

description: mAdb experiment ID: 123211

source_name: AM14 TLR7 KO PL2-3 Treated - 42 hours


title: Head and neck Squamous cell carcinomas_SUPRAGLOTTIC_23

source_name: Head and neck Squamous cell carcinomas_SUPRAGLOTTIC_pretreatmeant_23

value: neg


title: AM14 WT Untreated - 0 hour - mAdbID:123204

description: mAdb experiment ID: 123204

value: spleen

source_name: Unstimulated AM14 WT - 0 hour

value: Unstimulated

value: 0 hour


title: Head and neck Squamous cell carcinomas_OROPHARYNX_18

source_name: Head and neck Squamous cell carcinomas_OROPHARYNX_pretreatmeant_18


title: Head and neck Squamous cell carcinomas_ORAL CAVITY_17

source_name: Head and neck Squamous cell carcinomas_ORAL CAVITY_pretreatmeant_17

value: ORAL CAVITY

value: F


title: Head and neck Squamous cell carcinomas_SUPRAGLOTTIC_14

source_name: Head and neck Squamous cell carcinomas_SUPRAGLOTTIC_pretreatmeant_14

value: SUPRAGLOTTIC


title: Head and neck Squamous cell carcinomas_ORAL CAVITY_16

source_name: Head and neck Squamous cell carcinomas_ORAL CAVITY_pretreatmeant_16


title: Head and neck Squamous cell carcinomas_ORAL CAVITY_13

source_name: Head and neck Squamous cell carcinomas_ORAL CAVITY_pretreatmeant_13


title: Head and neck Squamous cell carcinomas_ORAL CAVITY_9

source_name: Head and neck Squamous cell carcinomas_ORAL CAVITY_pretreatmeant_9


title: Head and neck Squamous cell carcinomas_GLOTTIC LARYNX_11

source_name: Head and neck Squamous cell carcinomas_GLOTTIC LARYNX_pretreatmeant_11

value: GLOTTIC LARYNX


title: Head and neck Squamous cell carcinomas_SUPRAGLOTTIC_8

source_name: Head and neck Squamous cell carcinomas_SUPRAGLOTTIC_pretreatmeant_8


title: Head and neck Squamous cell carcinomas_SUPRAGLOTTIC_12

source_name: Head and neck Squamous cell carcinomas_SUPRAGLOTTIC_pretreatmeant_12


title: Head and neck Squamous cell carcinomas_HYPOPHARYNX_15

source_name: Head and neck Squamous cell carcinomas_HYPOPHARYNX_pretreatmeant_15

value: HYPOPHARYNX


title: Head and neck Squamous cell carcinomas_OROPHARYNX_6

source_name: Head and neck Squamous cell carcinomas_OROPHARYNX_pretreatmeant_6


title: Head and neck Squamous cell carcinomas_HYPOPHARYNX_10

source_name: Head and neck Squamous cell carcinomas_HYPOPHARYNX_pretreatmeant_10


title: Head and neck Squamous cell carcinomas_OROPHARYNX_5

source_name: Head and neck Squamous cell carcinomas_OROPHARYNX_pretreatmeant_5


title: Head and neck Squamous cell carcinomas_ORAL CAVITY_7

source_name: Head and neck Squamous cell carcinomas_ORAL CAVITY_pretreatmeant_7


title: Head and neck Squamous cell carcinomas_ORAL CAVITY_4

source_name: Head and neck Squamous cell carcinomas_ORAL CAVITY_pretreatmeant_4


title: Head and neck Squamous cell carcinomas_OROPHARYNX_2

source_name: Head and neck Squamous cell carcinomas_OROPHARYNX_pretreatmeant_2


title: Head and neck Squamous cell carcinomas_OROPHARYNX_1

source_name: Head and neck Squamous cell carcinomas_OROPHARYNX_pretreatmeant_1


title: Head and neck Squamous cell carcinomas_OROPHARYNX_3

source_name: Head and neck Squamous cell carcinomas_OROPHARYNX_pretreatmeant_3


title: p-79-stimulated BDC, repl. 1

city: Hershey

first: Hanspeter

last: Waldner

address: 500 University Dr.

institute: PSU College of Medicine

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using average normalization

source_name: mouse CD4+TCRVβ4+ T cell

label_protocol: Biotinylated cRNA were prepared with the Ambion TotalPrep Amplification kit

extract_protocol: RNA was extracted with QIAGEN RNeasy kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: p-79-stimulated CD4+TCRVβ4+ T cell

tag: sample id

value: BDC2.5 TCR transgenic NOD

tag: age

value: 6-9 weeks


title: p-79-stimulated BDC-Idd9, repl. 2

description: replicate 2

value: BDC2.5 TCR transgenic NOD.B10 Idd9


title: p-79-stimulated BDC, repl. 2

description: replicate 2


title: p-79-stimulated BDC-Idd9, repl. 3

description: replicate 3


title: ex-vivo BDC-Idd9, repl. 2

description: replicate 2

value: ex-vivo CD4+TCRVβ4+ T cell


title: ex-vivo BDC, repl. 2

description: replicate 2


title: ex-vivo BDC, repl. 3

description: replicate 3


title: p-79-stimulated BDC-Idd9, repl. 1

description: replicate 1


title: p-79-stimulated BDC, repl. 3

description: replicate 3


title: Ifnar1-/- BMDM infected with Francisella, rep 1

city: Memphis

first: Geoffrey

last: Neale

state: TN

address: 262 Danny Thomas Place

department: Hartwell Center

institute: St Jude Childrens Research Hospital

description:
SMM007
Ifnar1-/- mouse backcrossed to the C57BL/6 background.

hyb_protocol: Five micrograms of cDNA was hybridized for 16h at 45C on a Mouse Gene 2.0 ST GeneChip array.

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

data_processing: Probe signals were quantile normalized and summarized by the RMA algorithm using Partek Genomics Suite software v6.5.

source_name: bone marrow-derived macrophages infected for 8 hour with Francisella novicida, Ifnar1-/-

label_protocol: Sense target cDNA was prepared from 200ng of total RNA using the Ambion® WT Expression Kit (Life Technologies P/N 4411973). cDNA was fragmented and biotin-labeled using the Affymetrix® GeneChip® WT Terminal Labeling Kit (Affymetrix P/N 900671).

growth_protocol: Primary BMDMs were grown for 5-6 days in IMDM (Gibco) supplemented with 1% non-essential amino acids (Gibco), 10% FBS (Atlanta Biologicals), 30% medium conditioned by L929 mouse fibroblasts, and 1% penicillin and streptomycin (Sigma). F. novicida strain U112 was grown overnight under aerobic conditions at 37 °C in BBL Trypticase Soy Broth (211768; BD) supplemented with 0.2% l-cysteine (Fisher).

extract_protocol: Total RNA was extracted using the Qiagen RNeasy protocol according to the manufacturer's recommended methods.

treatment_protocol: BMDMs in antibiotic-free medium were seeded onto 12-well plates at a density of 1 x 10^6 cells per well, followed by incubation overnight. Cells were then infected at an MOI of 100 with Francisella novicida strain U112 and cultured for an additional 8 hours before extracting total RNA.

tag: strain/background

value: bone marrow-derived macrophages

value: infected with Francisella novicida strain U112 for 8 hours


title: ex-vivo BDC-Idd9, repl. 3

description: replicate 3


title: ex-vivo BDC-Idd9, repl. 1

description: replicate 1


title: PI 567516C-SCN-8dpi-rep1

city: Columbia

first: Henry

middle: T.

last: Nguyen

state: Missouri

address: Hitt Street

department: Plant Sciences

institute: University of Missouri

hyb_protocol: Hybridizations were conducted at the DNA Core Facility, University of Missouri (http://www.biotech.rnet.missouri.edu/dnacore), following the standard Affymetrix procedures (Affymetrix, Santa Clara, CA).

scan_protocol: The arrays were scanned with a GeneChip 7G Plus high-resolution scanner.

data_processing: Gene expression values were summarized by Robust Multi-Array Average (RMA) algorithm by using Expressionist Refiner 6.1 (GeneData). Briefly, the signal intensity CEL files from scanner were analyzed by a workflow with GC background subtraction, quantile normalization, and Median-Polish. The gene expression values from different samples were further used for gene differential statistical analysis.

label: Biotin

organism: Glycine max

source_name: 11-day-old roots collected 8 days after SCN treatment from PI 567516C

label_protocol: Approximately 500 ng of gDNA-free RNA were used to produce fragmented and biotin-labeled cDNA using the Ambion WT Expression Kit (Affymetrix, Santa Clara, CA) and the Affymetrix WT Terminal Labeling and Hybridization Kit (Affymetrix, Santa Clara, CA) following the manufacturer’s instructions. The integrity of total RNA and fragmented biotin-labeled cRNA were examined with RNA6000 Nano Assay using the Agilent 2100 BioanalyzerTM (Agilent Technologies, Palo Alto, CA).

growth_protocol: Seeds of these soybean genotypes were germinated in germination paper pouches in the dark for 3-4 days. Each normal seedling was then transplanted into a micropot filled with steam-pasteurized sand. Seedling-containing micropots were pre-arranged in buckets, which were placed in a water bath tank with temperature maintained at 27±1 oC as previously described.

extract_protocol: Frozen root tissue was ground to a fine powder using mortar and pestle pre-chilled in liquid nitrogen. Total RNA isolation was performed using Trizol Reagent (Invitrogen, Carlsbad, CA) following the manufacturer’s instructions. Subsequently, contaminating genomic DNA (gDNA) was removed from each sample using TURBO™ DNase following the manufacturer’s instructions (Life Technologies, Grand Island, NY).

treatment_protocol: A homogenous nematode population of HG type 0 (PA 3) [10] has been maintained at the University of Missouri for more than 30 generations. Eggs from females of this SCN population were incubated in 1% water agar and shaken at 25 rpm at 27oC on a rotary shaker for two days to promote hatching. Juvenile nematodes (J2) were then collected in fresh distilled water and checked for the density. For inoculation, two days after transplantation, each seedling was inoculated with 1 mL of J2 inoculum at a density of 2,000 J2/mL. In parallel, mock-inoculation with distilled water was also performed for each line as the control. Seedlings were watered daily to maintain soil moisture to facilitate uniform infection throughout the root system. Both SCN-inoculated and mock-inoculated root samples were harvested at 0, 3, and 8 days post inoculation (dpi), frozen in liquid nitrogen, and then stored at -80oC until RNA isolation.

tag: cultivar

value: Root


title: Ifnar1-/- BMDM infected with Francisella, rep 2

description:
SMM008
Ifnar1-/- mouse backcrossed to the C57BL/6 background.


title: ex-vivo BDC, repl. 1

description: replicate 1


title: Wild-type BMDM infected with Fancisella, rep 2

description:
SMM002
C57BL/6 wild-type mouse.

source_name: bone marrow-derived macrophages infected for 8 hour with Francisella novicida, wild-type

value: wild-type


title: Irf1-/- BMDM infected with Francisella, rep 2

description:
SMM004
Irf1-/- mouse backcrossed to the C57BL/6 background.

source_name: bone marrow-derived macrophages infected for 8 hour with Francisella novicida, Irf1-/-


title: Irf1-/- BMDM infected with Francisella, rep 1

description:
SMM003
Irf1-/- mouse backcrossed to the C57BL/6 background.


title: PI 437654-SCN-8dpi-rep2

source_name: 11-day-old roots collected 8 days after SCN treatment from PI 437654


title: Aim2-/- BMDM infected with Francisella, rep 1

description:
SMM005
Aim2-/- mouse backcrossed to the C57BL/6 background.

source_name: bone marrow-derived macrophages infected for 8 hour with Francisella novicida, Aim2-/-


title: Wild-type BMDM infected with Fancisella, rep 1

description:
SMM001
C57BL/6 wild-type mouse.


title: Magellen-SCN-8dpi-rep2

source_name: 11-day-old roots collected 8 days after SCN treatment from Magellan

value: Magellan


title: Medial habenula of nicotine self-administraion 2 (mRNA)

city: Seongbuk-gu, Seoul

first: Heh-In

last: Im

address: 5, Hwarang-ro 14-gil

country: South Korea

institute: Korea Institute of Science and Technology

description: mRNA

hyb_protocol: Fragmented end-labeled cDNA was  hybridized to the GeneChip® Mouse Gene 1.0 ST arrays for 16 hours at 45 “C and 60 rpm as described in the Gene Chip Whole Transcript (WT) Sense Target Labeling Assay Manual (Affymetrix).

scan_protocol: After hybridization, the chips were stained and washed in a Genechip Fluidics Station 450(Affymetrix) and scanned by using a Genechip Array scanner 3000 7G (Affymetrix).

data_processing: Expression data were generated by Affymetrix Expression Console software version1.1. For the normalization, RMA (Robust Multi-Average) algorithm implemented in Affymetrix Expression Console software was used.

source_name: Mus musculus after nicotine self-administraion experiment

label_protocol: 300 ng of total RNA from each sample was converted to double-strand cDNA Using a random hexamer incorporating a T7 promoter, amplified RNA( cRNA) was generated from the double-stranded cDNA template though an IVT( in-vitro transcription) reaction and purified with the Affymetrix sample cleanup module. cDNA was regenerated through a random-primed reverse transcription using a dNTP mix containing dUTP. The cDNA was then fragmented by UDG and APE 1 restriction endonucleases and end-labeled by terminal transferase reaction incorporating a biotinylated dideoxynucleotide.

growth_protocol: C57BL/6 mice were individually housed for 12 hours with a reversed light-dark cycle in a laboratory breeding room.

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

treatment_protocol: Nicotine self-administration (intravenous infusion, 0.01, 0.03, 0.1, 0.25, 0.4 mg/kg/infusion), using an operant self-administration chamber, was conducted in the sound attenuating cubicle (Med Associates, Inc.) in the dark room.

value: Medial habenula (MHb)


title: PI 567516C-SCN-8dpi-rep2


title: Aim2-/- BMDM infected with Francisella, rep 2

description:
SMM006
Aim2-/- mouse backcrossed to the C57BL/6 background.


title: PI 437654-SCN-8dpi-rep3


title: PI 437654-SCN-8dpi-rep1


title: Magellen-SCN-8dpi-rep1


title: PI 567516C-SCN-8dpi-rep3


title: Magellen-SCN-8dpi-rep3


title: Medial habenula of control 2 (mRNA)

description: mRNA

source_name: Mus musculus


title: Lateral habenula of nicotine self-administraion 1 (microRNA)

description: miRNA

hyb_protocol: Labeled miRNA was hybridized to the array for 16 hours at 48 “C and 60 rpm as described in the protocol.

data_processing: The scan image data was extracted through Affymetrix Commnad Console software1.1. The raw .cel file generated through above procedure meant expression intensity data and was used for the next step. Expression data were generated by Affymetrix Expression Console software version1.1. For the normalization, RMA (Robust Multi-Average) algorithm implemented in Affymetrix Expression Console software was used. Affymetrix miRNA-4 Array contains multispecies. The data of Mus musculus was analysed in this study.

label_protocol: Per RNA sample, 1 ug were used as input into the procedure as recommended by protocol (Genisphere FlashTagTM Biotin RNA Labeling for Affymetrix GeneChip miRNA arrays). 1 ug of total RNA was used as input into the labeling reaction.

extract_protocol: Total RNA was isolated using TriZol as described by the manufacturer (Ambion). RNA quality was assessed by Agilent 2100 bioanalyser using the RNA 6000 Nano Chip (Agilent Technologies, Amstelveen, The Netherlands), and quantity was determined by ND-1000 Spectrophotometer (NanoDrop Technologies, Inc., DE, USA).

value: Lateral habenula (LHb)


title: Medial habenula of control 2 (microRNA)

description: miRNA


title: PI 567516C-SCN-3dpi-rep3

source_name: 6-day-old roots collected  3 days after SCN treatment from PI 567516C


title: Lateral habenula of control 1 (microRNA)

description: miRNA


title: Magellen-water-8dpi-rep1

source_name: 11-day-old roots collected 8 days after water treatment from Magellan


title: PI 437654-water-8dpi-rep2

source_name: 11-day-old roots collected 8 days after water treatment from PI 437654


title: Lateral habenula of nicotine self-administraion 1 (mRNA)

description: mRNA


title: Lateral habenula of control 1 (mRNA)

description: mRNA


title: PI 437654-water-8dpi-rep3


title: PI 567516C-SCN-3dpi-rep2


title: Magellen-water-8dpi-rep2


title: PI 567516C-water-8dpi-rep3

source_name: 11-day-old roots collected 8 days after water treatment from PI 567516C


title: PI 567516C-SCN-3dpi-rep1


title: PI 437654-water-8dpi-rep1


title: PI 437654-SCN-3dpi-rep2

source_name: 6-day-old roots collected  3 days after SCN treatment from PI 437654


title: Magellen-SCN-3dpi-rep3

source_name: 6-day-old roots collected 3 days after SCN treatment from Magellan


title: PI 567516C-water-8dpi-rep1


title: Magellen-water-8dpi-rep3


title: PI 437654-SCN-3dpi-rep3


title: Magellen-SCN-3dpi-rep2


title: PI 567516C-water-8dpi-rep2


title: PI 437654-SCN-3dpi-rep1


title: Magellen-SCN-3dpi-rep1


title: PI 567516C-water-3dpi-rep3

source_name: 6-day-old roots collected  3 days after water treatment from PI 567516C


title: PI 437654-water-3dpi-rep3

source_name: 6-day-old roots collected  3 days after water treatment from PI 437654


title: Medial habenula of nicotine self-administraion 2 (microRNA)

description: miRNA


title: WP3ΔSW1-20MPa and 4°C rep4

city: Shanghai

first: Huahua

last: Jian

address: No.800 Dongchuan Road

institute: Shanghai Jiao Tong University

description:
8199 WP3cy5+SW1cy3.LSR
WP3ΔSW1 cDNA was labled with Cy3 and WP3 wild-type cDNA was labled with Cy5

hyb_protocol: Klenow enzyme labeling strategy was adopted after reverse transcription. Briefly, 20 μg amplified RNA was mixed with 4 μl random hexamers, denatured at 70°C for 5 min, and cooled on ice. Then, 4 μl of first-strand buffer, 2 μl of 0.1M DTT, 1 μl 10mM dNTP, and 1.5 μl SuperScipt Ⅱ (Invitrogen) were added. The mixtures were incubated for 10 min at 25°C, then for 90 min at 42°C. The cDNA products were purified using the PCR purification kit and vacuum evaporated to 10 μl, and then it was mixed with 4 μg random nanomer, heated to 95°C for 3 min, and snap cooled on ice. After that, 10 μl buffer, dNTP, and Cy5-dCTP or Cy3-dCTP (Amersham Biosciences) were added to final concentrations of 120 mM dATP, dGTP, dTTP and 60 mM dCTP, and 40mM Cy-dye. Klenow enzyme (Takara, Japan) was then added, and the reaction was performed for 90 min at 37°C. Labeled cDNA was purified with the PCR purification kit and resuspended in elution buffer.

scan_protocol: All microarrays were scanned with a LuxScan 10K canner using microarray scanner 2.3 software (CapitalBio, Beijing, China). We quantified signal intensites of individual spot from the 24-bit TIFF images using SpotData Pro 2.2 (CapitalBio, Beijing, China).

data_processing: S-plus software was used for the normalization of microarray data. A spatial and intensity-dependent normalization based on a LOWESS program were used. Normalized data was log transformed and loaded into MAANOVA under R environment for multiple testing, by fitting a mixed effects ANOVA model

organism: Shewanella piezotolerans WP3

source_name: WP3 cells at mid-exponential phase

label_protocol: The retro-transcription of the 20 μg total RNA was accorded with the Invitrogen manufacturer’s instruction. cDNA labeled with a fluorescent dye (Cy5 and Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction.

growth_protocol: Shewanella strains were cultured in modified marine medium 2216E (5 g/l tryptone, 1 g/l yeast extract, 0.1 g/l FePO4, 34 g/l NaCl) at 20MPa and 4°C

value: WP3 cells were cultured at 20MPa and 4℃ in 2216E medium

tag: genotype

value: wild type

value: delta SW1


title: WP3ΔSW1-20MPa and 4°C rep6


title: PI 567516C-water-3dpi-rep1


title: PI 567516C-water-3dpi-rep2


title: WP3ΔSW1-20MPa and 4°C rep3

description:
8200 WP3cy3+SW1cy5.LSR
WP3ΔSW1 cDNA was labled with Cy5 and WP3 wild-type cDNA was labled with Cy3


title: WP3ΔSW1-20MPa and 4°C rep5


title: PI 437654-water-3dpi-rep2


title: stomach_MNU+HP cancer

city: Hong Kong

first: Jing

last: Shen

address: Lo Kwee-Seong Integrated Biomedical Sciences Building, cuhk, Shatin NT

department: sbs

country: Hong Kong

institute: The Chinese University of Hong Kong

description: miRNA expression in mice stomach after treatment for 12 months

hyb_protocol: Completely dry the samples and resuspend the dried sample in 17 μL of nuclease-free water. Add 4.5 μL of the 10X GE Blocking Agent and 22.5 μL of 2X Hi-RPM Hybridization Buffer to each sample and mix well. Incubate at 100°C for 5 minutes. Hybridize all of the volume of the hybridization sample to the Agilent mouse whole genome miRNA array at 55°C for 20 hours in a hybridization oven.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (Surescan) using one color scan setting for 8x15K array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: stomach, 12 months, treated with H. pylori plus MNU

label_protocol: Dilute total RNA sample to 50 ng/μL. Add 2 μL of the CIP Master Mix to 2 μL sample and dephosphorylate the sample by incubating at 37°C for 30 min. Add 2.8 μL of 100% DMSO to each sample and incubate samples at 100°C in for 5 minutes. Immediately add 4.5 μL of the Ligation Master Mix to each sample and incubate at 16°C for 2 hours.

extract_protocol: Total RNA was isolated using TRIzol reagent

treatment_protocol: MNU was given in drinking water starting from 7 week of age for a total 5 cycles of 1-week regimen followed by 1-week pause. Mice were inoculated with H. pylori every other day for totally 3 times starting from 18 weeks of age.

value: stomach

tag: histology

value: cancer


title: WP3ΔSW1-20MPa and 4°C rep2


title: PI 437654-water-3dpi-rep1


title: Magellen-water-3dpi-rep3

source_name: 6-day-old roots collected 3 days after water treatment from Magellan


title: WP3ΔSW1-20MPa and 4°C rep1


title: Magellen-water-3dpi-rep2


title: stomach_Hp

source_name: stomach, 12 months, treated with H. pylori

value: inflammation


title: Magellen-water-3dpi-rep1


title: PI 567516C-water-0dpi-rep1

source_name: 3-day-old roots collected  immediately after water treatment from PI 567516C


title: stomach_MNU+HP IM

value: intestinal metaplasia


title: stomach_ctrl

source_name: stomach, 12 months, treated with broth control

value: normal


title: PI 437654-water-0dpi-rep1

source_name: 3-day-old roots collected  immediately after water treatment from PI 437654


title: PI 567516C-water-0dpi-rep2


title: PF-04691502-regulated genes

city: Shimotsuke

first: Yusuke

last: Furukawa

state: Tochigi

address: 3311-1 Yakushiji

department: Center for Molecular Medicine

institute: Jichi Medical University

hyb_protocol: Labeled cRNAs were hybridized with SurePrint G3 Human Gene Expression 8x60K v2 Microarray in Agilent In Situ Hybridization buffer Kit Plus) enclosed in Agilent SureHyb-enabled hybridization chambers.

scan_protocol: Arrays were scanned on an Agilent G2565AA scanner.  Images were quantified using the Agilent Feature Extraction Software (version 10.7.3.1).

data_processing: Agilent Feature Extraction Software (version 10.7.3.1) was used for background subtraction and LOWESS normalization.

source_name: RPMI8226 cells

label_protocol: RNA samples (50 ng) were primed with T7 primer at 70°C for 10 min and reversed transcribed at 40°C for 2 h in the presence of AffinityScript,followed by T7 transcription in the presence of  Cy3- or Cy5-CTP.

growth_protocol: We cultured RPMI8226 cells in RPMI1640 medium supplemented with 10% fetal bovine serum.

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

treatment_protocol: RPMI8226 cells were cultured in the absence or presence of UBE6T-7 stroma cell line, or with or without 1 μM PF-04691502 for 24 hours for RNA extraction.

value: Untreated control

value: Treated with PF-04691502


title: Cell adhesion-regulated genes

value: Adhesion to stromal cells


title: PI 437654-water-0dpi-rep2


title: Magellen-water-0dpi-rep2

source_name: 3-day-old roots collected  immediately after water treatment from Magellan


title: Magellen-water-0dpi-rep1


title: Old LLC tumor Replicate 8

status: Public on Mar 03 2015

city: Mountain View

first: Afshin

last: Beheshti

state: CA

address: Moffett Blvd

institute: NASA Ames Research Center

description: Old LLC tumor Replicate 8

data_processing: The data were corrected with normalization to housekeeping genes and then quantile normalisation with GenePattern Illumina Normalizer Module

source_name: LLC tumor in mouse

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

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: C57BL/6 Male Mouse

value: 736 days old

value: LLC Tumor


title: Old LLC tumor Replicate 12

description: Old LLC tumor Replicate 12


title: Old LLC tumor Replicate 15

description: Old LLC tumor Replicate 15


title: Old LLC tumor Replicate 1

description: Old LLC tumor Replicate 1


title: Old LLC tumor Replicate 11

description: Old LLC tumor Replicate 11


title: Old LLC tumor Replicate 17

description: Old LLC tumor Replicate 17


title: Old LLC tumor Replicate 4

description: Old LLC tumor Replicate 4


title: Old LLC tumor Replicate 6

description: Old LLC tumor Replicate 6


title: Old LLC tumor Replicate 3

description: Old LLC tumor Replicate 3


title: Old LLC tumor Replicate 13

description: Old LLC tumor Replicate 13


title: Old LLC tumor Replicate 9

description: Old LLC tumor Replicate 9


title: Old LLC tumor Replicate 16

description: Old LLC tumor Replicate 16


title: Old LLC tumor Replicate 19

description: Old LLC tumor Replicate 19


title: Old LLC tumor Replicate 7

description: Old LLC tumor Replicate 7


title: Old LLC tumor Replicate 2

description: Old LLC tumor Replicate 2


title: Old LLC tumor Replicate 10

description: Old LLC tumor Replicate 10


title: Old LLC tumor Replicate 18

description: Old LLC tumor Replicate 18


title: Old LLC tumor Replicate 14

description: Old LLC tumor Replicate 14


title: Middle Aged LLC tumor Replicate 7

description: Middle Aged LLC tumor Replicate 7

value: 551 days old


title: Middle Aged LLC tumor Replicate 2

description: Middle Aged LLC tumor Replicate 2


title: Young Adult LLC tumor Replicate 9

description: Young Adult LLC tumor Replicate 9

value: 143 days old


title: Young Adult LLC tumor Replicate 10

description: Young Adult LLC tumor Replicate 10


title: Middle Aged LLC tumor Replicate 6

description: Middle Aged LLC tumor Replicate 6


title: Middle Aged LLC tumor Replicate 4

description: Middle Aged LLC tumor Replicate 4


title: Young Adult LLC tumor Replicate 6

description: Young Adult LLC tumor Replicate 6


title: Middle Aged LLC tumor Replicate 3

description: Middle Aged LLC tumor Replicate 3


title: Young Adult LLC tumor Replicate 8

description: Young Adult LLC tumor Replicate 8


title: Middle Aged LLC tumor Replicate 1

description: Middle Aged LLC tumor Replicate 1


title: Young Adult LLC tumor Replicate 4

description: Young Adult LLC tumor Replicate 4


title: Old LLC tumor Replicate 5

description: Old LLC tumor Replicate 5


title: Young Adult LLC tumor Replicate 1

description: Young Adult LLC tumor Replicate 1


title: Young Adult LLC tumor Replicate 2

description: Young Adult LLC tumor Replicate 2


title: Young Adult LLC tumor Replicate 7

description: Young Adult LLC tumor Replicate 7


title: Adolescent LLC tumor Replicate 18

description: Adolescent LLC tumor Replicate 18

value: 68 days old


title: Adolescent LLC tumor Replicate 17

description: Adolescent LLC tumor Replicate 17


title: Adolescent LLC tumor Replicate 4

description: Adolescent LLC tumor Replicate 4


title: Adolescent LLC tumor Replicate 16

description: Adolescent LLC tumor Replicate 16


title: Adolescent LLC tumor Replicate 5

description: Adolescent LLC tumor Replicate 5


title: Adolescent LLC tumor Replicate 10

description: Adolescent LLC tumor Replicate 10


title: Adolescent LLC tumor Replicate 3

description: Adolescent LLC tumor Replicate 3


title: Adolescent LLC tumor Replicate 13

description: Adolescent LLC tumor Replicate 13


title: Adolescent LLC tumor Replicate 11

description: Adolescent LLC tumor Replicate 11


title: Adolescent LLC tumor Replicate 6

description: Adolescent LLC tumor Replicate 6


title: Adolescent LLC tumor Replicate 12

description: Adolescent LLC tumor Replicate 12


title: Adolescent LLC tumor Replicate 9

description: Adolescent LLC tumor Replicate 9


title: Adolescent LLC tumor Replicate 7

description: Adolescent LLC tumor Replicate 7


title: Adolescent LLC tumor Replicate 15

description: Adolescent LLC tumor Replicate 15


title: Middle Aged LLC tumor Replicate 5

description: Middle Aged LLC tumor Replicate 5


title: CHIP_001961_CytoscanHD

type: genomic

city: Nijmegen

first: Rolph

last: Pfundt

address: Geert Grooteplein Zuid 6

department: Genetics

country: Netherlands

institute: RUNMC

description: Hybridized to CytoscanHD

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
The array image was acquired using Affymetrix Command Console. Copy number values for probesets were extracted and converted from CEL files into signal intensities and SNP calls.
Data for visualisation of copynumber states and SNP calls

molecule: genomic DNA

source_name: Amniotic fluid

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: No culture but direct isolation in case of DNA from peripheral blood / Amniotic fluid was cultured before DNA isolation

extract_protocol: Genomic DNA was isloated with a Chemagen/Hamilton magnetic bead DNA isolation robot

value: female

tag: case id

value: patient chromosome 14 case


title: SK-N-SH

city: Essen

first: Sven

last: Lindner

address: Hufelandstraße 55

country: Germany

institute: University Hospital Essen

data_processing: Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

source_name: Human neuroblastoma cell line SK-N-SH

label_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

growth_protocol: Cell lines were grown according to standard conditions.

extract_protocol: Genomic DNA was extracted from cell lines  the Qiagen DNA Blood & Tissue Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer.

value: SK-N-SH


title: PN01-0918

description: Hybridized to CytoscanHD

source_name: peripheral (EDTA) blood

value: mother chromosome 9 case


title: WT committed progenitor cells 606

city: NEW YORK

first: WENHUO

last: HU

email: huwenhuo@gmail.com, huw@mskcc.org

state: NEW YORK

address: 1275 YORK AVENUE

department: HOPP

institute: MEMORIAL SLOAN KETTERING CANCER CENTER

description: replicate 1

data_processing: The data were normalised using quantile normalisation with package 'lumi' in R

source_name: mouse bone marrow cells

extract_protocol: Total RNA are extracted from these cells using an RNeasy Mini Kit (Qiagen). Nugen Ovation Pico WTA is used for pre-amplification of RNA samples before hybridized to Illumina Mouse 6 arrays using standard protocols.

value: 3 months

value: bone marrow

value: WT

tag: cell population


title: Nm dCas9-LSD1 + sgCtrl 2

city: Worcester

first: Barbara

last: Tabak

state: MA

address: 55 Lake Avenue North

department: Molecular Medicine

institute: University of Massachusetts Medical School

hyb_protocol: Standard Illumina protocol

scan_protocol: Standard Illumina protocol

data_processing: The data were normalized using quantile normalization with limma in R

source_name: mESC

label_protocol: 250ng of total RNA was amplified to generate labeled cRNA using the Illumina Total Prep RNA Amplification Kit (Ambion, AMIL 1791).

growth_protocol: Cells were maintained in ESC-Media (KnockOUT DMEM [GIBCO, 10829] supplemented with 15% Hyclone FBS [Thermo Scientific, SH30070.03], 1% Glutamax [GIBCO, 35050079], 1% NEAA [Cellgro, 25-025-CI], 100µM β-mercaptoethanol [Invitrogen, 21985023], and 1x103 U/mL LIF)supplemented with 2i (1uM PD0325901 [Tocris, 4192], and 3uM CHIR99021 [Tocris, 4423]).

extract_protocol: RNA was extracted using Trizol reageant (Invitrogen, 15596-018) according to the manufacturer’s instructions.

treatment_protocol: ES cells were washed once with PBS and split with 0.25% trypsin (GIBCO, 25200114). Cells were MEF-depleted on 0.1% gelatinized plates for 30 minutes, then collected and counted. Cells were incubated with sgRNA lentivirus on low attachment plates for 3 hours in 2i media (ESC-media supplemented with 1uM PD0325901 [Tocris, 4192], and 3uM CHIR99021 [Tocris, 4423]), then plated onto 0.1% gelatin coated plates at 12.5x104 cells/cm2. After 48 hours, cells were split using 0.25% trypsin and plated in 2i media supplemented with 1uM puromycin to select for cells expressing the sgRNA. Transduced cells were maintained in 2i media with 1uM puromycin and split every 3 days.

value: Nm dCas9-LSD1

value: sgCtrl

tag: rna preparation

value: Direct RNA extraction


title: Adolescent LLC tumor Replicate 2

description: Adolescent LLC tumor Replicate 2


title: Adolescent LLC tumor Replicate 1

description: Adolescent LLC tumor Replicate 1


title: WT committed progenitor cells 477

description: replicate 3


title: WT committed progenitor cells 611

description: replicate 2


title: KO committed progenitor cells 419

description: replicate 3

value: KO


title: KO committed progenitor cells 604

description: replicate 1


title: KO HSC cells 419

description: replicate 2


title: Nm dCas9-LSD1 + sgOct4-DE


title: Adolescent LLC tumor Replicate 8

description: Adolescent LLC tumor Replicate 8

value: C57BL/6 Male Mouse


title: WT HSC cells 606

description: replicate 3


title: Young Adult LLC tumor Replicate 5

description: Young Adult LLC tumor Replicate 5


title: PN01-0916

description: Hybridized to CytoscanHD

tag: gender

value: patient chromosome 9 case


title: Young Adult LLC tumor Replicate 3

description: Young Adult LLC tumor Replicate 3

tag: tissue

value: LLC Tumor


title: Human HC3 Male3

city: Kahoku

first: Akio

last: Nakajima

state: Ishikawa

address: 1-1 Daigaku Uchinada

department: Immunology and Hematotology

institute: kanazawa-med

hyb_protocol: Following fragmentad labered DNA were hybridized for 16 hr at 45C on GeneChip Human Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using the GeneArray Scanner.

data_processing: The data were analyzed with genespring version 11.0 using Affymetrix default analysis settings and global scaling as normalization method.

source_name: Healthy control

label_protocol: Biotinylated DNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Immediately after blood collection, PBMCs were separated using Lymphoprep® (Axis-Shield, Oslo, Norway), according to the manufacturer’s instructions. Total RNA was extracted using RNeasy Plus Mini® kits (Qiagen, Hilden, Germany), according to the manufacturer’s protocol.

extract_protocol: Total RNA was extracted according to the manufacturer's instructions.

treatment_protocol: Initial steroid therapy for IgG4-RD consisted of prednisolone (0.6 mg/kg body weight per day),  with this dose reduced 10% every 2 weeks.

tag: disease state

value: healthy control

tag: ethnicity

value: Japanese

value: male

tag: individual

tag: treatment

tag: time


title: Nm dCas9-LSD1 + sgOct4-PP

tag: cell line


title: Nm dCas9-KRAB + sgOct4-PP

value: Nm dCas9-KRAB


title: Human HC2 Male2


title: Human IgG4 RD before treatment Male 2

source_name: IgG4 RD before treatment

value: control (before treatment)


title: Nm dCas9-KRAB + sgOct4-DE


title: Nm dCas9-KRAB + sgCtrl 2


title: Human HC1 Male1


title: WT HSC cells 611

description: replicate 1

tag: strain


title: Nm dCas9-BAT + sgOct4-PP

value: Nm dCas9-BAT


title: WT HSC cells 609

description: replicate 2

tag: age


title: Adolescent LLC tumor Replicate 14

description: Adolescent LLC tumor Replicate 14

value: 68 days old


title: Human HC4 Male4


title: Human IgG4 RD after treatment Male 1

source_name: IgG4 RD after treatment

value: prednisolone


title: Human IgG4 RD after treatment Male 2


title: PN11-4461

description: Hybridized to CytoscanHD

value: female

value: patient chromosome 10 case


title: SH-EP

source_name: Human neuroblastoma cell line SH-EP

value: SH-EP


title: PN12-1020

description: Hybridized to CytoscanHD

value: father chromosome 10 case


title: Nm dCas9-KRAB + sgTbx3-DE

value: RNA extraction post trypsinization


title: Nm dCas9-KRAB + sgTbx3-PP


title: Nm dCas9-BAT + sgOct4-DE

value: Direct RNA extraction


title: Nm dCas9-KRAB + sgCtrl 1

value: sgCtrl


title: PN12-0755

description: Hybridized to CytoscanHD

value: mother chromosome 10 case


title: SH-SY5Y

source_name: Human neuroblastoma cell line SH-SY5Y


title: Human IgG4 RD before treatment Male 1


title: Nm dCas9-LSD1 + sgCtrl 1

value: Nm dCas9-LSD1


title: KO HSC cells 469

description: replicate 3

value: 3 months

value: bone marrow

value: KO


title: Nm dCas9-LSD1 + sgTbx3-PP


title: PN10-4297_CytoscanHD

description: Hybridized to CytoscanHD

value: male

value: patient chromosome 6 case


title: cancer stem cells_sample 3_rep 3

city: Kepala Batas

first: Badrul

middle: Hisham

last: Yahaya

state: Penang

address: Bertam, Kepala Batas

department: Advanced Medical & Dental Institute

country: Malaysia

institute: Advanced Medical and Dental Institute

description: RMA expression value derived from Expression Console software; core-exon analysis

hyb_protocol: Samples were hybridized to GeneChip Human Exon 1.0 ST Arrays (Affymetrix) for 17 hours at 45 ˚C. The arrays were stained and washed using GeneChip® hybridisation wash and stain kit (Affymetrix) on the Affymetrix Fluidics Station FS450

scan_protocol: The arrays were scanned on Affymetrix Scanner 3000

data_processing: The normalisation and signal summarisation of the array raw data were performed on Affymetrix Expression Console. The data analysis and statististical analysis was performed on GeneSpring GX 7.3.1 software (Agilent Technology, Santa Clara, USA)

source_name: putative cancer stem cells NCI-H2170

label_protocol: Single stranded ST-cDNA were generated from 1.5 µg of total RNA using ApplauseTM WT-Amp ST System (Nugen Technologies, Inc., San Carlos, USA) and purified using MinElute Reaction Cleanup kit (Qiagen, Limburg, Netherlands). Then, 2.25 µg purified-ST-cDNA fragmented and labelled with Encore Biotin Module (Nugen Technologies, Inc., San Carlos, USA).

growth_protocol: The normal primary human bronchial trachial epithelial cells (ATCC) were cultured in specific airway epithelial cell media from ATCC and the cancer cell lines, A549 and H2170 (ATCC) were cultured in RPMI-1640 media supplemented with 10% FBS and 1% Penicillin/Streptomycin. All cells were incubated in a humidified incubator at the 37 ˚C supplied with 5% carbon dioxide.

extract_protocol: Total RNA (1.5 µg) was extracted from up to 1 millions CD166+/CD44+ and CD166+/EpCAM+ cells of PHBEC, A549 and H2170 cells using Qiagen AllPrep DNA/RNA isolation kit (Qiagen, Limburg, Netherlands)

treatment_protocol: The normal and cancer cells were trypsinized and labelled with antibody CD166-PE, CD44-FITC and EpCAM-FITC. The labelled cells were analysed and double positive cell population were sorted using FACSAria III

tag: cell type

value: lung squamous cell carcinoma cell line


title: PN01-0917

description: Hybridized to CytoscanHD

value: father chromosome 9 case


title: cancer stem cells_sample 2_rep 2

source_name: putative cancer stem cells A549

value: lung adenocarcinoma cell line


title: cancer stem cells_sample 3_rep 1


title: Nm dCas9-BAT + sgTbx3-DE

value: Nm dCas9-BAT


title: normal stem cells_sample 2_rep 3

source_name: Normal putative stem cells

value: normal lung epithelial cell line


title: normal stem cells_sample 2_rep 1


title: cancer stem cells_sample 1_rep 2


title: normal stem cells_sample 2_rep 2


title: Nm dCas9-BAT + sgTbx3-PP


title: Nm dCas9-LSD1 + sgTbx3-DE


title: KO HSC cells 610

description: replicate 1


title: cancer stem cells_sample 2_rep 1


title: cancer stem cells_sample 2_rep 3


title: cancer stem cells_sample 3_rep 2


title: cancer stem cells_sample 1_rep 1


title: normal stem cells_sample 1_rep 3


title: KO committed progenitor cells 431

description: replicate 2


title: cancer stem cells_sample 1_rep 3


title: normal stem cells_sample 1_rep 2


title: genomic DNA from peripheral blood, mother of a subject affected by Down syndrome, 2018

city: Bologna

first: Maria Giulia

last: Bacalini

address: Via Altura 3

department: Brain Aging Laboratory

country: Italy

institute: IRCCS Istituto delle Scienze Neurologiche di Bologna

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
GenomeStudio (2010.3) Methylation module (1.8.5) software
raw_data.txt includes Unmethylated and methylated signal intensities

label: Cy5 and Cy3

source_name: peripheral whole blood, subject  2018

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted and purified from peripheral whole blood using the QIAamp 96 DNA Blood Kit (QIAGEN)

tag: group

value: mother of a subject affected by Down syndrome (DSS)

value: healthy

tag: family

value: Female

value: peripheral whole blood


title: CD2AP wild type podocyte 18

city: Cincinnati

first: Steven

last: Potter

state: OH

address: 3333 Burnet Ave.

department: Developmental Biology

institute: Children's hospital Medical Center

description: RMA expression value derived from Expression Console software; gene level analysis

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials and standard protocols •  Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Data were processed using GeneBASE software. MAT background correction were applied to probe intensities, gene level expression were summarized from the corrected intensities and then quantile normalized.

source_name: wild type podocyte

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

extract_protocol: RNA was purified using Qiagen Rneasy Micro Kit #74004

value: podocyte

tag: genotype

value: wildtype

value: five weeks


title: CD2AP mutant podocyte 13

source_name: mutant podocyte


title: CD2AP mutant podocyte 14


title: CD2AP wild type podocyte 17


title: CD2AP control mesangial 12

source_name: control mesangial

value: mesangial


title: CD2AP wild type podocytel 16


title: normal stem cells_sample 1_rep 1


title: CD2AP control mesangiall 11


title: CD2AP mutant podocytel 15


title: CD2AP control mesangiall 10


title: genomic DNA from peripheral blood, mother of a subject affected by Down syndrome, 2029

source_name: peripheral whole blood, subject  2029


title: CD2AP mutant mesangiall 9

source_name: mutant mesangial


title: genomic DNA from peripheral blood, mother of a subject affected by Down syndrome, 2043

source_name: peripheral whole blood, subject  2043


title: genomic DNA from peripheral blood, mother of a subject affected by Down syndrome, 2014

source_name: peripheral whole blood, subject  2014


title: genomic DNA from peripheral blood, mother of a subject affected by Down syndrome, 2030

source_name: peripheral whole blood, subject  2030


title: CD2AP mutant mesangial 8


title: CD2AP mutant mesangiall 7


title: CD2AP wild type endothelial 6

source_name: wild type endothelial

value: endothelial


title: genomic DNA from peripheral blood, mother of a subject affected by Down syndrome, 2037

source_name: peripheral whole blood, subject  2037


title: genomic DNA from peripheral blood, mother of a subject affected by Down syndrome, 2022

source_name: peripheral whole blood, subject  2022


title: genomic DNA from peripheral blood, mother of a subject affected by Down syndrome, 2005

source_name: peripheral whole blood, subject  2005


title: genomic DNA from peripheral blood, mother of a subject affected by Down syndrome, 2021

source_name: peripheral whole blood, subject  2021


title: genomic DNA from peripheral blood, mother of a subject affected by Down syndrome, 2016

source_name: peripheral whole blood, subject  2016


title: genomic DNA from peripheral blood, mother of a subject affected by Down syndrome, 2046

source_name: peripheral whole blood, subject  2046


title: genomic DNA from peripheral blood, mother of a subject affected by Down syndrome, 2042

source_name: peripheral whole blood, subject  2042


title: genomic DNA from peripheral blood, mother of a subject affected by Down syndrome, 2026

source_name: peripheral whole blood, subject  2026


title: genomic DNA from peripheral blood, mother of a subject affected by Down syndrome, 2002

source_name: peripheral whole blood, subject  2002


title: genomic DNA from peripheral blood, mother of a subject affected by Down syndrome, 2006

source_name: peripheral whole blood, subject  2006


title: CD2AP wild type endothelial 4


title: CD2AP mutant endothelial 3

source_name: mutant endothelial


title: CD2AP wild typet endothelial 5


title: genomic DNA from peripheral blood, mother of a subject affected by Down syndrome, 2038

source_name: peripheral whole blood, subject  2038


title: genomic DNA from peripheral blood, mother of a subject affected by Down syndrome, 2028

source_name: peripheral whole blood, subject  2028


title: CD2AP mutant endothelial 2


title: genomic DNA from peripheral blood, mother of a subject affected by Down syndrome, 2052

source_name: peripheral whole blood, subject  2052


title: genomic DNA from peripheral blood, mother of a subject affected by Down syndrome, 2019

source_name: peripheral whole blood, subject  2019


title: CD2AP mutant endothelial 1


title: genomic DNA from peripheral blood, mother of a subject affected by Down syndrome, 2023

source_name: peripheral whole blood, subject  2023


title: genomic DNA from peripheral blood, mother of a subject affected by Down syndrome, 2013

source_name: peripheral whole blood, subject  2013


title: genomic DNA from peripheral blood, mother of a subject affected by Down syndrome, 2036

source_name: peripheral whole blood, subject  2036


title: genomic DNA from peripheral blood, mother of a subject affected by Down syndrome, 2020

source_name: peripheral whole blood, subject  2020


title: Air-exposed_control rep 4

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description:
Sample name: 14822_576_E2_2RD_CTL_Rep_4
gene expression in control bronchi

hyb_protocol: 5 ug of amplified biotin aRNAs were fragemented and hybridized to each array for 18hr at 45C. Slides were stained with streptavidin/phycoerythrin using a double antibody staining procedure, washed for antibody amplification according to the GeneChip Hybridization, Wash and Stain Kit user manual.

scan_protocol: Slides were scanned in an Affymetrix Scanner, model 3000.

data_processing: Raw data was obtained using the Affymetrix GeneChip Command Console Software (AGCC; version 1.1) using the MAS5 normalization algorithm to generate .CHP files.

organism: Rattus norvegicus

source_name: Lung, right diaphragmatic lobe

label_protocol: 20 ng total RNA was amplified and labeled using the Nugen WT-Ovation Pico RNA Amplification and Encore Biotin Module protocols

extract_protocol: RNA was isolated using the PicoPure Isolation kit adapted for use with CapSure laser capture microdissection Caps

treatment_protocol: Rats exposed by inhalation to air (control) or 200 ppm 2,3-pentanedione

value: normal bronchial wall

value: Wistar

value: air


title: Air-exposed_control rep 6

description:
Sample name: 14824_576_E2_4RD_CTL_Rep_6
gene expression in control bronchi

value: male


title: genomic DNA from peripheral blood, mother of a subject affected by Down syndrome, 2009

source_name: peripheral whole blood, subject  2009


title: PD exposed-fibrotic rep 7

description: gene expression in exposed fibrotic bronchi

value: fibrotic bronchial wall

value: 2,3-pentanedione for 2 wks


title: Air-exposed_control rep 3

description:
Sample name: 14821_576_E2_1RD_CTL_Rep_3
gene expression in control bronchi


title: PD exposed-fibrotic rep 9


title: PD exposed-fibrotic rep 3


title: PD exposed-nonfibrotic rep 8

description: gene expression in exposed nonfibrotic bronchi

value: nonfibrotic bronochial wall


title: genomic DNA from peripheral blood, mother of a subject affected by Down syndrome, 2010

source_name: peripheral whole blood, subject  2010


title: PD exposed-nonfibrotic rep 10


title: genomic DNA from peripheral blood, sibling of a subject affected by Down syndrome, 3018

source_name: peripheral whole blood, subject  3018

value: sibling of a subject affected by Down syndrome (DSS)


title: Air-exposed_control rep 5

description:
Sample name: 14823_576_E2_3RD_CTL_Rep_5
gene expression in control bronchi


title: Air-exposed_control rep 1

description: gene expression in control bronchi


title: Air-exposed_control rep 2

description: gene expression in control bronchi


title: genomic DNA from peripheral blood, sibling of a subject affected by Down syndrome, 3037

source_name: peripheral whole blood, subject  3037


title: genomic DNA from peripheral blood, mother of a subject affected by Down syndrome, 2007

source_name: peripheral whole blood, subject  2007

value: mother of a subject affected by Down syndrome (DSS)


title: PLN_autoantibodies_6167_rep2

city: Stanford

first: Keiichi

last: Kodama

address: 269 Campus Drive, Room 2225

department: Department of Medicine, Division of Immunology & Rheumatology

institute: Stanford Univeristy School of Medicine

hyb_protocol: Using the Agilent Microarray-Based Gene Expression Analysis protocol, the fragmentation mix consisting of 750ng of cyanine 3 labeled amplified cRNA, 50μ of 10X blocking agent (Gene Expression Hybridization Kit; Agilent Technologies), 10μl of 25X fragmentation buffer (Agilent Technologies) and nuclease free water to a total volume of 250μl, was incubated for 30 minutes at 60 degree Celsius and then 250 μl of 2X hybridization buffer was added to stop the fragmentation reaction.  The 500μl solution was then pipetted onto the microarray and incubated in an oven rotator at 60 degree Celsius for 17 hours.    Due to a high level of ozone in the lab, the Agilent Stabilization and Drying Solution protocol was used.  Washing conditions include 1st, 2nd, Acetonitrile for 1 minute each and the 3rd wash for 30 seconds on a magnetic stir plate.

scan_protocol: The arrays were then scanned using an Agilent Microarray Scanner laser based detection system.  Background subtracted signal data (BGSub Signal: raw spot signal – background signal) and processed signal were obtained from images using the Agilent Feature Extraction software version 8.5.

data_processing: Gene expression data were processed (cy3) and presented as normalized log2 (processed signal) using the limma package and ComBat, available through the Bioconductor project for use with R statistical software.

label_protocol: cRNA amplification and fluorescence labeling was performed using the Agilent Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies). The cRNA synthesis involved a single amplification for one-color labeling, to create ample cyanine 3 (cy3) labeled cRNA. In this technique a primer that contains poly dT, and a T7 polymerase promoter is annealed to the poly A+ RNA (mRNA).  Reverse transcriptase is added to the reaction to synthesize the first and second strands of cDNA (to create double stranded DNA).  Fluorescence labeled anti-sense cRNA is next synthesized with T7 Polymerase, which simultaneously incorporates cy3-labeled cytidine triphosphate (CTP).

extract_protocol: Total RNA was extracted using Trizol reagent and the Qiagen RNeasy mini kit.

value: pancreatic lymph nodes

tag: phenotype

value: at-risk autoantibody-positive

tag: tag


title: PLN_healthy_6097

source_name: Pancreatic lymph nodes_healthy-control

value: healthy

value: female


title: genomic DNA from peripheral blood, sibling of a subject affected by Down syndrome, 3030

source_name: peripheral whole blood, subject  3030

value: Female

value: peripheral whole blood


title: genomic DNA from peripheral blood, mother of a subject affected by Down syndrome, 2011

source_name: peripheral whole blood, subject  2011


title: genomic DNA from peripheral blood, mother of a subject affected by Down syndrome, 2003

source_name: peripheral whole blood, subject  2003


title: genomic DNA from peripheral blood, sibling of a subject affected by Down syndrome, 3022

source_name: peripheral whole blood, subject  3022

value: Male


title: PD exposed-nonfibrotic rep 4


title: genomic DNA from peripheral blood, sibling of a subject affected by Down syndrome, 3016

source_name: peripheral whole blood, subject  3016


title: genomic DNA from peripheral blood, sibling of a subject affected by Down syndrome, 3026

source_name: peripheral whole blood, subject  3026


title: genomic DNA from peripheral blood, sibling of a subject affected by Down syndrome, 3043

source_name: peripheral whole blood, subject  3043


title: PLN_autoantibodies_6147


title: genomic DNA from peripheral blood, sibling of a subject affected by Down syndrome, 3029

source_name: peripheral whole blood, subject  3029


title: PLN_autoantibodies_6156


title: genomic DNA from peripheral blood, sibling of a subject affected by Down syndrome, 3014

source_name: peripheral whole blood, subject  3014


title: PLN_autoantibodies_6181_rep2


title: genomic DNA from peripheral blood, mother of a subject affected by Down syndrome, 2001

source_name: peripheral whole blood, subject  2001


title: PLN_autoantibodies_6170_rep2


title: genomic DNA from peripheral blood, sibling of a subject affected by Down syndrome, 3019

source_name: peripheral whole blood, subject  3019


title: genomic DNA from peripheral blood, sibling of a subject affected by Down syndrome, 3006

source_name: peripheral whole blood, subject  3006


title: genomic DNA from peripheral blood, sibling of a subject affected by Down syndrome, 3021

source_name: peripheral whole blood, subject  3021


title: PLN_autoantibodies_6027


title: genomic DNA from peripheral blood, sibling of a subject affected by Down syndrome, 3002

source_name: peripheral whole blood, subject  3002


title: genomic DNA from peripheral blood, sibling of a subject affected by Down syndrome, 3042

source_name: peripheral whole blood, subject  3042


title: genomic DNA from peripheral blood, sibling of a subject affected by Down syndrome, 3046

source_name: peripheral whole blood, subject  3046


title: genomic DNA from peripheral blood, sibling of a subject affected by Down syndrome, 3052

source_name: peripheral whole blood, subject  3052


title: PLN_healthy_6029

source_name: Pancreatic lymph nodes_healthy-control


title: PLN_autoantibodies_6197


title: PLN_healthy_6060


title: PLN_healthy_6048


title: PLN_autoantibodies_6184


title: PLN_healthy_6034


title: PLN_autoantibodies_6181_rep1


title: PLN_autoantibodies_6170_rep1


title: PLN_autoantibodies_6213


title: genomic DNA from peripheral blood, sibling of a subject affected by Down syndrome, 3005

source_name: peripheral whole blood, subject  3005


title: genomic DNA from peripheral blood, sibling of a subject affected by Down syndrome, 3038

source_name: peripheral whole blood, subject  3038


title: PLN_healthy_6057


title: PLN_healthy_6058


title: genomic DNA from peripheral blood, sibling of a subject affected by Down syndrome, 3036

source_name: peripheral whole blood, subject  3036


title: PLN_autoantibodies_6171


title: PLN_autoantibodies_6158


title: genomic DNA from peripheral blood, sibling of a subject affected by Down syndrome, 3028

source_name: peripheral whole blood, subject  3028


title: PLN_autoantibodies_6044


title: genomic DNA from peripheral blood, sibling of a subject affected by Down syndrome, 3023

source_name: peripheral whole blood, subject  3023


title: PLN_autoantibodies_6080


title: PLN_autoantibodies_6167_rep1


title: Lean 1 Visceral

city: Washington

first: Robert

last: Freishtat

state: DC

address: 111 Michigan Avenue NW

department: Center for Genetic Medicine

institute: Children's National Medical Center

description: Lean visceral fat was promplty cultured after surgery for 60 minutes. Cell culture supernatant was used to isolate exosomes.

hyb_protocol: For hybridization, we followed Affymetrix Gene Chip miRNA Array Procedure for Affymetrix miRNA 3.0 arrays to hybridize biotin-labeled sample.

scan_protocol: We scanned the Affymetrix miRNA 3.0 arrays following the Affymetrix Command Console User Manual Instructions.

data_processing: We analyzed the resulting data in Expression Console using RMA+DMBG (Affymetrix) and then exported it to Partek Genomics Suite for analyses. We used three-factor ANCOVA (ID*group (lean vs. obese)*adipose depot; age covariate) to compare miRNA expression, using unadjusted p ≤ 0.05 and fold change ≥ |1.2| as filters. We generated main effects for group (obesity-state) and tissue depot along with their interaction term. As a part of the overall ANCOVA, we used specific within-group (depot effects within obese or lean) and within-tissue (obesity effects within depot) contrasts. No corrections were made for multiple testing, as the primary purpose of list generation was to power pathway analysis, which mitigates false positive discovery risks.

source_name: Lean 1 Visceral Adipose

label_protocol: We used Affymetrix FlashTag Biotin HSR RNA Labeling Kit to label 1000 ng of cRNA from each sample.

growth_protocol: Human obese and lean visceral and subcutaneous fat were surgically acquired, dissected, and promptly cultured for 60 minutes.

extract_protocol: To isolate exosomes, we used the cell culture supernatant from the adipose tissue cultures and used ExoQuick-TC precipitation solution, according to ExoQuick-TC protocol. Total RNA was isolated following mirVana's total RNA Isolation kit.

treatment_protocol: No Treatment

value: Adipose

value: Lean

tag: bmi

tag: race

value: AF

tag: Sex


title: Lean 3 Visceral

source_name: Lean 3 Visceral Adipose

tag: tissue

tag: disease state


title: genomic DNA from peripheral blood, sibling of a subject affected by Down syndrome, 3010

source_name: peripheral whole blood, subject  3010

tag: gender


title: Lean 5 Visceral

source_name: Lean 5 Visceral Adipose

value: Mexican


title: genomic DNA from peripheral blood, sibling of a subject affected by Down syndrome, 3009

source_name: peripheral whole blood, subject  3009


title: Obese 8 Visceral

description: Obese visceral fat was promplty cultured after surgery for 60 minutes. Cell culture supernatant was used to isolate exosomes.

source_name: Obese 8 Visceral Adipose

value: Obese

value: Hispanic


title: genomic DNA from peripheral blood, sibling of a subject affected by Down syndrome, 3020

source_name: peripheral whole blood, subject  3020


title: Obese 9 Visceral

source_name: Obese 9 Visceral Adipose

value: Caucasian


title: Lean 6 Visceral

source_name: Lean 6 Visceral Adipose


title: genomic DNA from peripheral blood, sibling of a subject affected by Down syndrome, 3001

source_name: peripheral whole blood, subject  3001


title: genomic DNA from peripheral blood, sibling of a subject affected by Down syndrome, 3011

source_name: peripheral whole blood, subject  3011


title: Obese 4 Visceral

source_name: Obese 4 VisceralAdipose


title: genomic DNA from peripheral blood, sibling of a subject affected by Down syndrome, 3003

source_name: peripheral whole blood, subject  3003


title: Obese 2 Visceral

source_name: Obese 2 Visceral Adipose


title: Obese 6 Visceral

source_name: Obese 6 Visceral Adipose

value: Dominican/Nicaraguan


title: genomic DNA from peripheral blood, subject affected by Down syndrome, 1030

source_name: peripheral whole blood, subject  1030

value: subject affected by Down syndrome (DS)

value: Down syndrome


title: genomic DNA from peripheral blood, subject affected by Down syndrome, 1043

source_name: peripheral whole blood, subject  1043


title: Obese 1 Visceral

source_name: Obese 1 Visceral Adipose


title: Obese 3 Visceral

source_name: Obese 3 Visceral Adipose


title: genomic DNA from peripheral blood, subject affected by Down syndrome, 1018

source_name: peripheral whole blood, subject  1018


title: genomic DNA from peripheral blood, sibling of a subject affected by Down syndrome, 3007

source_name: peripheral whole blood, subject  3007

value: sibling of a subject affected by Down syndrome (DSS)


title: genomic DNA from peripheral blood, subject affected by Down syndrome, 1026

source_name: peripheral whole blood, subject  1026


title: genomic DNA from peripheral blood, subject affected by Down syndrome, 1037

source_name: peripheral whole blood, subject  1037


title: genomic DNA from peripheral blood, sibling of a subject affected by Down syndrome, 3013

source_name: peripheral whole blood, subject  3013


title: Lean 4 Visceral

source_name: Lean 4 Visceral Adipose


title: genomic DNA from peripheral blood, subject affected by Down syndrome, 1019

source_name: peripheral whole blood, subject  1019


title: genomic DNA from peripheral blood, subject affected by Down syndrome, 1016

source_name: peripheral whole blood, subject  1016


title: S11697 -T cell lymphoma compared to sex-matched ear DNA reference

city: Inage-ku

first: Benjamin

middle: John

last: Blyth

state: Chiba

address: 4-9-1 Anagawa

department: Centre for Radiation Protection

institute: National Institute of Radiological Sciences

hyb_protocol: Labelled DNA was hybridised in 1X Agilent Blocking Agent/Hi-RPM Buffer at 65°C for 24 h in a rotating hybridisation oven, then the slides were washed in Oligo aCGH Wash Buffer 1 and 2

scan_protocol: The slides were scanned in an Agilent DNA Microarray scanner (G2565CA)

data_processing:
Agilent Feature Extraction Software (10.7.3.1) was used for computing ratios
Normalised log2 ratio [T-cell lymphoma (test)/Ear (reference)] either Cy3/Cy5 or Cy5/Cy3 depending on the array slide

source_name: S11697- T cell lymphoma

label_protocol: 250 ng of purified DNA was digested with Alu I and Rsa I restriction enzymes for 2 h at 37°C, then fluorescently labelled with Cy3/Cy5 using the Agilent SureTag Complete DNA labelling kit using the 'half-volume' protocol for use with 8-pack array slides

extract_protocol: DNA was extracted from T cell lymphoma cells or sex-matched mouse ear tissue using an automated Maxwell-16 DNA Purification kit, then 2-3 μg of DNA was further purified by RNase treatment followed by phenol/chloroform re-extraction

treatment_protocol: Ear tissue or T cell lymphoma cell suspensions stored frozen at -80°C since autopsy were used to extract genomic DNA

tag: dose group

value: Gamma-1 x 4 Gy

value: Carbon-4 x 1 Gy


title: genomic DNA from peripheral blood, subject affected by Down syndrome, 1029

source_name: peripheral whole blood, subject  1029


title: genomic DNA from peripheral blood, subject affected by Down syndrome, 1021

source_name: peripheral whole blood, subject  1021


title: genomic DNA from peripheral blood, subject affected by Down syndrome, 1014

source_name: peripheral whole blood, subject  1014


title: S11534 -T cell lymphoma compared to sex-matched ear DNA reference

source_name: S11534- T cell lymphoma


title: S11498 -T cell lymphoma compared to sex-matched ear DNA reference

source_name: S11498- T cell lymphoma


title: S12077 -T cell lymphoma compared to sex-matched ear DNA reference

source_name: S12077- T cell lymphoma


title: S10910 -T cell lymphoma compared to sex-matched ear DNA reference

source_name: S10910- T cell lymphoma


title: genomic DNA from peripheral blood, subject affected by Down syndrome, 1022

source_name: peripheral whole blood, subject  1022


title: genomic DNA from peripheral blood, subject affected by Down syndrome, 1002

source_name: peripheral whole blood, subject  1002


title: genomic DNA from peripheral blood, subject affected by Down syndrome, 1006

source_name: peripheral whole blood, subject  1006


title: genomic DNA from peripheral blood, subject affected by Down syndrome, 1052

source_name: peripheral whole blood, subject  1052


title: genomic DNA from peripheral blood, subject affected by Down syndrome, 1046

source_name: peripheral whole blood, subject  1046


title: genomic DNA from peripheral blood, subject affected by Down syndrome, 1038

source_name: peripheral whole blood, subject  1038


title: S11463 -T cell lymphoma compared to sex-matched ear DNA reference

source_name: S11463- T cell lymphoma


title: genomic DNA from peripheral blood, subject affected by Down syndrome, 1013

source_name: peripheral whole blood, subject  1013


title: S23473 -T cell lymphoma compared to sex-matched ear DNA reference

source_name: S23473-T cell lymphoma

value: Carbon-1 x 4 Gy


title: genomic DNA from peripheral blood, subject affected by Down syndrome, 1010

source_name: peripheral whole blood, subject  1010


title: genomic DNA from peripheral blood, subject affected by Down syndrome, 1009

source_name: peripheral whole blood, subject  1009


title: genomic DNA from peripheral blood, subject affected by Down syndrome, 1028

source_name: peripheral whole blood, subject  1028


title: S23584 -T cell lymphoma compared to sex-matched ear DNA reference

source_name: S23584-T cell lymphoma

value: Female

value: Carbon-1 x 4.8 Gy


title: S23364 -T cell lymphoma compared to sex-matched ear DNA reference

source_name: S23364-T cell lymphoma

value: Male

value: Carbon-4 x 1.2 Gy


title: S10989 -T cell lymphoma compared to sex-matched ear DNA reference

source_name: S10989- T cell lymphoma


title: S23500 -T cell lymphoma compared to sex-matched ear DNA reference

source_name: S23500-T cell lymphoma


title: genomic DNA from peripheral blood, subject affected by Down syndrome, 1023

source_name: peripheral whole blood, subject  1023

value: peripheral whole blood


title: genomic DNA from peripheral blood, subject affected by Down syndrome, 1042

source_name: peripheral whole blood, subject  1042


title: genomic DNA from peripheral blood, subject affected by Down syndrome, 1020

source_name: peripheral whole blood, subject  1020


title: genomic DNA from peripheral blood, subject affected by Down syndrome, 1036

source_name: peripheral whole blood, subject  1036


title: genomic DNA from peripheral blood, subject affected by Down syndrome, 1003

source_name: peripheral whole blood, subject  1003


title: S23291 -T cell lymphoma compared to sex-matched ear DNA reference

source_name: S23291-T cell lymphoma


title: S23741 -T cell lymphoma compared to sex-matched ear DNA reference

source_name: S23741-T cell lymphoma


title: S23721 -T cell lymphoma compared to sex-matched ear DNA reference

source_name: S23721-T cell lymphoma


title: S23476 -T cell lymphoma compared to sex-matched ear DNA reference

source_name: S23476-T cell lymphoma


title: S23362 -T cell lymphoma compared to sex-matched ear DNA reference

source_name: S23362-T cell lymphoma


title: genomic DNA from peripheral blood, subject affected by Down syndrome, 1011

source_name: peripheral whole blood, subject  1011


title: S22803 -T cell lymphoma compared to sex-matched ear DNA reference

source_name: S22803-T cell lymphoma


title: genomic DNA from peripheral blood, subject affected by Down syndrome, 1005

source_name: peripheral whole blood, subject  1005


title: genomic DNA from peripheral blood, subject affected by Down syndrome, 1007

source_name: peripheral whole blood, subject  1007


title: S22717 -T cell lymphoma compared to sex-matched ear DNA reference

source_name: S22717-T cell lymphoma


title: genomic DNA from peripheral blood, subject affected by Down syndrome, 1001

source_name: peripheral whole blood, subject 1001


title: S10691 -T cell lymphoma compared to sex-matched ear DNA reference

source_name: S10691- T cell lymphoma


title: S22705 -T cell lymphoma compared to sex-matched ear DNA reference

source_name: S22705-T cell lymphoma


title: S22708 -T cell lymphoma compared to sex-matched ear DNA reference

source_name: S22708-T cell lymphoma


title: IRAKM_C

city: Boston

first: M. Simo

last: Arredouani

address: 330 Brookline Ave.

department: Surgery

institute: Beth Israel Deaconess Medical Center

hyb_protocol: cRNA (15 μg) was fragmented and hybridized to arrays according to the manufacturer's (Ambion® | Life Technologies) protocols.

scan_protocol: Arrays were scanned with the GeneChip Scanner 3000 and GeneChip Operating Software acquired raw fluorescence signal.

data_processing: Scanned array images and CEL file data were analyzed and normalized  using RMAexpress.

source_name: DC2.4 cell line

label_protocol: Biotin-UTP was incorporated during the overnight in vitro transcription step according to the manufacturer's (Ambion® | Life Technologies) protocol.

growth_protocol: Genetically modified DC2.4 cells were grown overnight in RMPI 10% complete medium

extract_protocol: Total RNA was extracted using Trizol.

treatment_protocol: Virally induced PLKO, shIRAKM and IRAKM-transfected DC2.4 cells were treated with IL-33 or vehicle overnight before RNA extraction

value: C57BL/6 bone marrow-derived dendritic cell line


title: S12118 -T cell lymphoma compared to sex-matched ear DNA reference

source_name: S12118-T cell lymphoma


title: S22578 -T cell lymphoma compared to sex-matched ear DNA reference

source_name: S22578-T cell lymphoma


title: shIRAKM +IL33

description: shIRAKM +IL33

value: shIRAKM +IL33


title: IRAKM + IL33

description: IRAKM + IL33

value: IRAKM + IL33


title: PLKO +IL33

description: PLKO +IL33

value: PLKO +IL33


title: S22544 -T cell lymphoma compared to sex-matched ear DNA reference

source_name: S22544-T cell lymphoma


title: PLKO_C


title: shIRAKM_C


title: S22533 -T cell lymphoma compared to sex-matched ear DNA reference

source_name: S22533-T cell lymphoma


title: S22570 -T cell lymphoma compared to sex-matched ear DNA reference

source_name: S22570-T cell lymphoma


title: S11478 -T cell lymphoma compared to sex-matched ear DNA reference

source_name: S11478-T cell lymphoma


title: S11360 -T cell lymphoma compared to sex-matched ear DNA reference

source_name: S11360-T cell lymphoma


title: SM01R071

status: Public on Mar 02 2015

first: Gabriel

last: Gruionu

address: 149 13th Street, Room 3316

department: Radiation Oncology

institute: Massachusetts General Hospital

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 17 hr at 45C on RG*34A Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using the standard Affymetrix protocol.

data_processing: The data were analyzed with Affymetrix Gene Chip Operating Software (GCOS) using the MAS 5.0 algorithm using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 1000.

source_name: thoracic artery, BN, 6 mo.

label_protocol: Biotinylated cRNA were prepared from <1ug of total RNA,  see McClintick, J. N., R. E. Jerome, et al. (2003). "Reproducibility of oligonucleotide arrays using small samples." BMC Genomics 4(1): 4.

extract_protocol: Total RNA was purified by using an RNeasy Fibrous Tissue Mini Kit (Qiagen, Valencia, CA).

treatment_protocol: Collateral artery model created by adjacent arterial occlusion, see Unthank JL, Fath SW, et al. (1996). "Wall remodeling during luminal expansion of mesenteric arterial collaterals in the rat." Circulation Research 79: 1015.

value: Brown Norway

value: thoracic artery

tag: age in months

tag: mass (mg)


title: S10976 -T cell lymphoma compared to sex-matched ear DNA reference

source_name: S10976-T cell lymphoma


title: SM01R072

tag: strain


title: S22490 -T cell lymphoma compared to sex-matched ear DNA reference

source_name: S22490-T cell lymphoma


title: SM01R070


title: SM01R068


title: SM01R064

source_name: thoracic artery, BN, 24 mo.


title: SM01R066


title: SM01R055

source_name: thoracic artery, BN, 15 mo.


title: SM01R059


title: SM01R065


title: SM01R052

source_name: thoracic artery, F344xBN, 24 mo.

value: Fischer344 x Brown Norway


title: S23265 -T cell lymphoma compared to sex-matched ear DNA reference

source_name: S23265-T cell lymphoma


title: SM01R061


title: SM01R063


title: SM01R056


title: SM01R060


title: SM01R062


title: S22767 -T cell lymphoma compared to sex-matched ear DNA reference

source_name: S22767-T cell lymphoma


title: SM01R067


title: SM01R053


title: SM01R058


title: SM01R048

source_name: thoracic artery, F344xBN, 15 mo.


title: SM01R069


title: SM01R054


title: SM01R051


title: SM01R049


title: SM01R050


title: SM01R047


title: SM01R046


title: PN10-5118

description: Hybridized to 250K array

source_name: peripheral (EDTA) blood

value: female

tag: case id

value: mother chromosome 6 case


title: SM01R041

source_name: thoracic artery, F344xBN, 6 mo.


title: PN10-5117

description: Hybridized to 250K array

value: male

value: father chromosome 6 case


title: CHIP_002003

description: Hybridized to 250K array

value: mother chromosome 14 case


title: CHIP_001961

description: Hybridized to 250K array

source_name: Amniotic fluid

value: patient chromosome 14 case


title: SM01R044


title: SM01R039


title: SM01R043


title: SM01R034

source_name: mesenteric artery, BN, 6 mo.

value: mesenteric artery


title: SM01R029

source_name: mesenteric artery, BN, 24 mo.


title: SM01R037


title: SM01R028


title: SM01R031


title: SM01R045


title: CHIP_002002

description: Hybridized to 250K array

value: father chromosome 14 case


title: SM01R036


title: SM01R026


title: SM01R030


title: SM01R027


title: SM01R035


title: SM01R038


title: SM01R040


title: SM01R025


title: SM01R032


title: SM01R024

source_name: mesenteric artery, BN, 15 mo.


title: SM01R021


title: SM01R042


title: SM01R022


title: SM01R023


title: PN10-4297

description: Hybridized to 250K array

value: patient chromosome 6 case


title: SM01R017

source_name: mesenteric artery, F344xBN, 24 mo.


title: SM01R019