title: Premalignant preB cell_Smchd1 null_Rep 1

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

description: HOMO 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Un-normalized summary probe profiles were exported from BeadStudio and analysed using the limma package version 3.12.1 (http://www.bioconductor.org) for R 2.15.1 (http://www.r-project.org). Raw intensities were neqc background corrected, normalized and log2-transformed with offset 16.

organism: Mus musculus

source_name: Premalignant preB cell, Smchd1 null

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

growth_protocol: All  samples were harvested fresh from mice and purified by cell sorting.

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

treatment_protocol: Tissue was stored in in buffer RLT (Qiagen) at -80 degrees until processing with an RNEasy kit.

tag: strain

tag: genotype/variation

value: Smchd1 null

value: Premalignant preB cell

tag: beadchip barcode

tag: beadchip section

value: E


title: Patient_#226_C3

status: Public on Sep 30 2012

type: other

city: Budapest

first: Krisztian

last: Papp

address: 1/C Pazmany P.

country: Hungary

institute: MTA-ELTE Immunology Research Group

hyb_protocol: Probe: Alexa647-conjugated  F(ab')2 fragment goat anti-human C3 antibody

scan_protocol: Arrays were scanned on Typhoon Trio+ imager (Amersham Bioscience) (Excitation:633nm ; Emission: 670BP, PMT:420 Mode:Fluorescence, Sensitivity:Normal, FocalPlane=+3 mm). Data were analyzed with GenePix Pro 6 software (Molecular Devices, Sunnyvale, CA, USA).

data_processing:
Local background of spot was substracted from the value of signal. The value of signal is set to zero if it is lower than 2*SD of local backgrounds on the given chip. For interassay comparison, data were normalized to the mean of 5 times diluted Protein G control material (ID_REF: #52, #53, #54).
Normalization procedure was carried out with Microsoft Office Exel software

molecule: other

organism: Homo sapiens

source_name: serum

label_protocol: Antigens were spotted onto nitrocellulose-covered FAST slides  (GE Healthcare) using BioOdyssey Calligrapher miniarrayer (BioRad). Features were printed in triplicates of 1:5 serial dilutions then stored at 4°C in sealed bags. Dried arrays were rinsed in PBS for 15 minutes before use, then incubated with diluted serum at 37°C for 1 hour, providing suitable conditions for complement activation. For each patient 5- times diluted serum was used in two different arrays for the detection of bound C3-IgM and IgG-C4. Sera were diluted in 5% BSA, 0.05% Tween 20, Ca and Mg supplemented Veronal buffer. Serum treated slides were washed with 0.05% Tween 20 containing PBS, then incubated in the mixture of 1:5000 diluted Alexa647-conjugated  F(ab')2 fragment goat anti-human C3 antibody (Cappel) and 1:5000 diluted Cy3-conjugated F(ab')2 fragment goat anti-human IgM (mu chain speific) (Jackson ImmunoResearch) or 1:2500 diluted FITC-conjugated goat anti-human C4 (Cappel) and 1:2500 diluted APC-conjugated F(ab')2 fragment goat anti-human IgG (gamma chain specific) (Jackson ImmunoResearch).Labeling with fluorescent antibodies was carried out at room temperature for 30 min in 5% BSA and 0.05% Tween 20 containing PBS. Following washing in 0.05% Tween 20 containing PBS, arrays were dried and scanned.

extract_protocol: Serum sample was centrifuged for 6min at 15000g for removing particles

treatment_protocol: Serum samples were stored at -70C

tag: Sex

value: Female

tag: sle (yes/no)

value: No


title: Premalignant preB cell_Smchd1 wildtype_Rep 6

type: RNA

description: WT 6

molecule: total RNA

source_name: Premalignant preB cell, Smchd1 wildtype

value: Smchd1 wildtype

tag: cell type

value: F


title: 11202.p1/NA18507

type: genomic

city: Seattle

first: Megan

middle: Y

last: Dennis

state: WA

address: 3720 15th Ave NE

department: Department of Genome Sciences

country: USA

institute: University of Washington

hyb_protocol: The hybridization protocol was performed per Agilent protocols (http://www.chem.agilent.com/Library/usermanuals/Public/G4410-90020_CGH_ULS_Protocol_v.3.1.pdf) with 10 ug of labelled test sample and 10 ug of labelled reference sample

scan_protocol: The scan protocol was performed using the Agilent Scanner per Agilent protocols (http://www.chem.agilent.com/Library/usermanuals/Public/G4410-90020_CGH_ULS_Protocol_v.3.1.pdf).

data_processing: The data were processed using the Agilent Feature Extraction software 10.5.1.1 using program defaults (http://www.chem.agilent.com/Library/usermanuals/Public/G4410-90020_CGH_ULS_Protocol_v.3.1.pdf)

molecule: genomic DNA

source_name: whole blood DNA

label_protocol: 250 ng of genomic DNA (unsonicated) was labeled by Klenow using random priming with Cy3/Cy5 nonamers (for test and reference samples, respectively) using Nimblegen labelling kit but with the following changes: reagents were scaled to the smaller amount of input DNA and with DNA labeling occurring overnight.

extract_protocol: unsonicated genomic DNA

tag: group

tag: gender

value: male

tag: family status

value: proband

tag: ndar guid

tag: tissue

value: whole blood

source_name: lymphoblast cell line DNA

tag: cell line


title: Cell line 10

city: Toon

first: Koh-ichi

last: Nakashiro

state: Ehime

address: 454 Shitsukawa

department: Oral and Maxillofacial Surgery

country: Japan

institute: Ehime University Graduate School of Medicine

hyb_protocol: Ten mg of labelled cRNA was hybridized to each pre-hybed microarray at 55℃ for 16 hours.

scan_protocol: After Chemiluminescence detection using Applied Biosystems Chemiluminescence Detection Kit, images were collected by the AB1700 Chemiluminescent Microarray Aanalyzer.

data_processing: The robust multichip average (RMA) method was used background correction and normalization.

label: digoxigenin

source_name: oral squamous cell carcinoma cell lines

label_protocol: Digoxigenin-UTP-labelled cRNA was generated and amplified from 1 mg of total RNA using Applied Biosystems Chemiluminescent RT-IVT Labelling Kit.

extract_protocol: After fresh tissues were homogenized by TissueLyser, total RNA was extracted by ISOGEN.

value: oral squamous cell carcinoma


title: Patient 11

source_name: normal oral mucosa

value: normal oral mucosa


title: Premalignant preB cell_Smchd1 wildtype_Rep 5

description: WT 5

value: C


title: Premalignant preB cell_Smchd1 wildtype_Rep 4

description: WT 4

value: B


title: Premalignant preB cell_Smchd1 null_Rep 3

description: HOMO 3

value: A


title: Premalignant preB cell_Smchd1 null_Rep 4

description: HOMO 4


title: Patient_#225_C3


title: 11200.p1/NA12878

value: female


title: Premalignant preB cell_Smchd1 wildtype_Rep 3

description: WT 3


title: Patient_#224_C3


title: Patient 2


title: Premalignant preB cell_Smchd1 wildtype_Rep 2

description: WT 2

value: D


title: Patient_#223_C3


title: Premalignant preB cell_Smchd1 null_Rep 5

description: HOMO 5

value: Smchd1 null


title: Patient_#222_C3


title: 11199.p1/NA12878


title: Premalignant preB cell_Smchd1 wildtype_Rep 1

description: WT 1

value: Premalignant preB cell


title: 11201.p1/NA18507


title: Lymphomas_Smchd1 wildtype_Rep 6

description: WT 6

data_processing: Un-normalized summary probe profiles were output from BeadStudio and analysed using the limma package version 3.12.1 (http://www.bioconductor.org) for R 2.15.1 (http://www.r-project.org). Raw intensities were neqc background corrected, normalized and log2-transformed with offset 16.

source_name: Lymphomas, Smchd1 wildtype

value: Lymphomas


title: Patient_#221_C3

value: Female


title: Lymphomas_Smchd1 null_Rep 1

description: HOMO 1

source_name: Lymphomas, Smchd1 null

value: E


title: Patient_#220_C3

value: No


title: Lymphomas_Smchd1 null_Rep 2

description: HOMO 2


title: 11198.p1/NA12878


title: Lymphomas_Smchd1 wildtype_Rep 4

description: WT 4

value: Smchd1 wildtype


title: 11198.mo/NA12878

value: mother


title: Patient_#219_C3


title: Patient_#218_C3


title: Lymphomas_Smchd1 wildtype_Rep 5

description: WT 5


title: Lymphomas_Smchd1 null_Rep 4

description: HOMO 4

value: F


title: 11198.fa/NA18507

value: male

value: father

value: whole blood


title: Premalignant preB cell_Smchd1 null_Rep 2

description: HOMO 2


title: 11227.p1/NA12878

value: proband


title: Lymphomas_Smchd1 wildtype_Rep 3

description: WT 3


title: Lymphomas_Smchd1 null_Rep 3

description: HOMO 3


title: 11197.mo/NA12878


title: 11196.p1/NA18507


title: Lymphomas_Smchd1 wildtype_Rep 2

description: WT 2


title: 11197.fa/NA18507


title: Lymphomas_Smchd1 null_Rep 6

description: HOMO 6

value: B


title: E17.5 preB cells_Smchd1 null_Rep 3

data_processing: Un-normalized summary probe profiles were output from BeadStudio and analysed using the limma package version 3.12.1 (http://www.bioconductor.org) for R 2.15.1 (http://www.r-project.org). Raw intensities were neqc background corrected and normalized with offset 16.

source_name: E17.5 preB cells, Smchd1 null

growth_protocol: All  samples were harvested fresh from embryos at E17.5 and purified by cell sorting.

tag: developmental stage

value: preB cells


title: E17.5 preB cells_Smchd1 wildtype_Rep 3

source_name: E17.5 preB cells, Smchd1 wildtype


title: 11205.p1/NA12878

value: female


title: 11214.p1/NA12878


title: Lymphomas_Smchd1 null_Rep 5

description: HOMO 5

value: C


title: Premalignant preB cell_Smchd1 null_Rep 6

description: HOMO 6

value: Smchd1 null


title: Lymphomas_Smchd1 wildtype_Rep 1

description: WT 1

value: A


title: Patient_#214_C3


title: Patient_#215_C3


title: E17.5 preB cells_Smchd1 wildtype_Rep 2


title: Patient_#212_C3


title: Patient_#217_C3


title: Patient_#211_C3


title: 11195.mo/NA12878


title: E17.5 preB cells_Smchd1 null_Rep 1


title: E17.5 preB cells_Smchd1 wildtype_Rep 1


title: 11194.p1/NA12878


title: Patient_#213_C3


title: E17.5 preB cells_Smchd1 null_Rep 2

value: D


title: 11195.fa/NA18507


title: Tumour derived from transformed MEF_Smchd1 wildtype_recipient 3_Rep 3

data_processing: Un-normalized summary probe profiles were output from BeadStudio and analysed using the limma package version 3.12.1 (http://www.bioconductor.org) for R 2.15.1 (http://www.r-project.org). Raw intensities were neqc background corrected with offset 50. Background correct intensities were quantile normalized in three batches, one for each cell type, then log2-transformed.

source_name: Tumour derived from transformed MEF, Smchd1 wildtype, recipient 3

growth_protocol: Growth protocols varied depending on the samples. Primary MEFs were passaged in culture for 2-3 passages before harvesting. Transformed MEFs were harvested 2 weeks post transformation with p53 knockdown and HRasv12 overexpression. All other samples were harvested fresh from mice.

tag: genotype

value: tumour derived from transformed MEF

tag: nude tumour recipient


title: Tumour derived from transformed MEF_Smchd1 null_recipient 4_Rep 3

source_name: Tumour derived from transformed MEF, Smchd1 null, recipient 4


title: Tumour derived from transformed MEF_Smchd1 null_recipient 6_Rep 3

source_name: Tumour derived from transformed MEF, Smchd1 null, recipient 6

value: E


title: Tumour derived from transformed MEF_Smchd1 wildtype_recipient 2_Rep 3

source_name: Tumour derived from transformed MEF, Smchd1 wildtype, recipient 2


title: Tumour derived from transformed MEF_Smchd1 null_recipient 5_Rep 3

source_name: Tumour derived from transformed MEF, Smchd1 null, recipient 5


title: Tumour derived from transformed MEF_Smchd1 wildtype_recipient 1_Rep 3

source_name: Tumour derived from transformed MEF, Smchd1 wildtype, recipient 1


title: Tumour derived from transformed MEF_Smchd1 wildtype_recipient 3_Rep 2


title: Tumour derived from transformed MEF_Smchd1 null_recipient 6_Rep 2


title: 11193.p1/NA18507


title: Patient_#209_C3

value: Female

value: No


title: Patient_#210_C3


title: 11193.mo/NA12878

value: mother


title: Tumour derived from transformed MEF_Smchd1 null_recipient 4_Rep 2


title: Patient_#216_C3


title: Tumour derived from transformed MEF_Smchd1 null_recipient 5_Rep 2


title: 11190.p1/NA12878


title: Patient_#208_C3


title: Patient_#207_C3


title: Tumour derived from transformed MEF_Smchd1 wildtype_recipient 3_Rep 1

value: Smchd1 wildtype


title: Patient_#206_C3


title: Tumour derived from transformed MEF_Smchd1 null_recipient 6_Rep 1

value: F


title: Tumour derived from transformed MEF_Smchd1 null_recipient 5_Rep 1


title: Tumour derived from transformed MEF_Smchd1 wildtype_recipient 1_Rep 2


title: Tumour derived from transformed MEF_Smchd1 wildtype_recipient 2_Rep 2


title: 11190.fa/NA18507

value: male

value: father


title: Tumour derived from transformed MEF_Smchd1 null_recipient 4_Rep 1


title: 11193.fa/NA18507

value: whole blood


title: Patient_#205_C3


title: 11190.mo/NA12878


title: Tumour derived from transformed MEF_Smchd1 wildtype_recipient 1_Rep 1


title: Transformed MEF_Smchd1 wildtype_Rep 2

source_name: Transformed MEF, Smchd1 wildtype

value: transformed MEF


title: Transformed MEF_Smchd1 wildtype_Rep 3


title: Transformed MEF_Smchd1 null_Rep 3

source_name: Transformed MEF, Smchd1 null


title: 11188.p1/NA18507

value: proband


title: 11189.p1/NA12878

value: female


title: Tumour derived from transformed MEF_Smchd1 wildtype_recipient 2_Rep 1

value: C


title: 11187.p1/NA12878


title: Patient_#203_C3

source_name: serum


title: Patient_#202_C3


title: Patient_#204_C3


title: Patient_#201_C3


title: Transformed MEF_Smchd1 wildtype_Rep 1

value: B


title: Transformed MEF_Smchd1 null_Rep 2

value: Smchd1 null


title: Transformed MEF_Smchd1 null_Rep 1

value: A


title: 11184.p1/NA12878

source_name: whole blood DNA


title: Primary MEF_Smchd1 null_Rep 3

source_name: Primary MEF, Smchd1 null

value: primary MEF


title: Primary MEF_Smchd1 null_Rep 2

value: D


title: Patient_#200_C3

value: Male


title: Primary MEF_Smchd1 wildtype_Rep 3

source_name: Primary MEF, Smchd1 wildtype

value: E


title: Patient_#80_C3

value: Female

value: Yes


title: 11184.fa/NA18507

source_name: lymphoblast cell line DNA


title: Foxp3-GFPxAPCΔ468 small intestine polyp Treg, biological rep 3

city: Chicago

first: Nichole

last: Blatner

state: IL

address: 303 East Superior Street, Lurie 3-250

department: Robert H. Lurie Comprehensive Cancer Center

institute: Northwestern University

hyb_protocol: Affymetrix GeneChip WT cDNA Synthesis and Amplification Kits

scan_protocol: Affymetrix GeneChip Scanner

data_processing: The datasets were pre-filtered to keep only those probesets for which a gene symbol could be found in the affymetrix annotation. CEL files were normalized using Affymetrix Power tools on the predefined probeset ID list mentioned above, and using the standard RMA workflow (background adjustment, quantiile normalization, median polish probeset summarization).

label: biotin

source_name: small intestine polyp infiltrating Treg

label_protocol: Affymetrix GeneChip WT Sense Target Labeling and Control Reagents

extract_protocol: Trizol

treatment_protocol: Mice were sacraficed and organs were harvested. For polyp-ridden APC mice, small intestine polyps were microdisected from health surrounding tissue; both parts were used as a source of mononuclear cells. Mononuclear cells from small intestine tissue were isolated by collengenase IV digestion and precoll gradient centrifugation. Cells from spleen and mesenteric lymph nodes were isolated by gentlely teasing between frosted glass slides. Spleen cells were subjected to red blood cell lysis. Negative selection with T-cell negative selection kit (Dynal beads; Invitrogen) was used to pre-purify cells. Cells were Pc blocked and then stained with CD4 antibody. PI was used to exclude dead cells during FACS sorting. Cells were then double sorted on a MoFlo sorter. A doublet exclusion gate was included. Cells were then gated on PI negative, CD4+ cells. Two populations were then collected directly into Trizol: CD4+Foxpe-GFP- and CD4+Foxp3-GFP+. Cell isolation and sorting were performed according to immgen.org SOP.

value: small intestine polyp

tag: genetic background

tag: age

value: 4 months old


title: Foxp3-GFPxAPCΔ468 small intestine polyp CD4+ non-Treg, biological rep 3

source_name: small intestine polyp infiltrating CD4+ non-Treg

value: male


title: Primary MEF_Smchd1 null_Rep 1


title: Foxp3-GFPxAPCΔ468 spleen CD4+ non-Treg, biological rep 3

source_name: spleen CD4+ non-Treg from polyp ridden mice

value: spleen


title: Foxp3-GFPxAPCΔ468 small intestine tissue surrounding polyps CD4+ non-Treg, biological rep 2

source_name: CD4+ non-Treg from small intestine tissue surrounding polyps in polyp-ridden mice

value: small intestine


title: 11181.p1/NA12878

value: proband

value: whole blood


title: 11180.p1/NA12878

value: female


title: 11184.mo/NA12878

value: mother


title: 11177.p1/NA12878


title: Patient_#79_C3


title: Foxp3-GFPxAPCΔ468 spleen Treg, biological rep 3

source_name: spleen Treg from polyp ridden mice


title: Patient_#77_C3


title: 11195.p1/NA18507


title: Primary MEF_Smchd1 wildtype_Rep 2

value: Smchd1 wildtype

value: C


title: 11176.p1/NA12878


title: Foxp3-GFPxAPCΔ468 mesenteric lymph node CD4+ non-Treg, biological rep 3

source_name: mesenteric lymph node CD4+ non-Treg from polyp ridden mice

value: Mesenteric lymph node


title: 11197.p1/NA18507


title: Foxp3-GFPxAPCΔ468 mesenteric lymph node Treg, biological rep 3

source_name: mesenteric lymph node Treg from polyp ridden mice


title: Foxp3-GFP small intestine Treg, biological rep 3

source_name: healthy small intestine Treg


title: Patient_#75_C3


title: 11178.p1/NA18507


title: Patient_#74_C3


title: Patient_#78_C3


title: 11173.p1/NA18507


title: Patient_#73_C3


title: Patient_#76_C3


title: Foxp3-GFPxAPCΔ468 small intestine tissue surrounding polyps Treg, biological rep 3

source_name: Treg from small intestine tissue surrounding polyps in polyp-ridden mice


title: 11172.p1/NA12878


title: Patient_#71_C3


title: Patient_#72_C3


title: Patient_#70_C3


title: 11172.mo/NA12878


title: Primary MEF_Smchd1 wildtype_Rep 1

value: primary MEF

value: A


title: Foxp3-GFP small intestine CD4+ non-Treg, biological rep 7

source_name: healthy small intestine CD4+ non-Treg


title: 11172.fa/NA18507

value: father


title: Patient_#68_C3

value: Female


title: Foxp3-GFP spleen CD4+ non-Treg, biological rep 2

source_name: healthy spleen CD4+ non-Treg


title: Foxp3-GFP small intestine CD4+ non-Treg, biological rep 6


title: 11168.p1/NA12878


title: Foxp3-GFP mesenteric lymph node Treg, bilogical rep 3

source_name: healthy mesenteric lymph node Treg


title: Foxp3-GFP mesenteric lymph node CD4+ non-Treg, biological rep 2

source_name: healthy mesenteric lymph node CD4+ non-Treg


title: Foxp3-GFPxAPCΔ468 small intestine polyp Treg, biological rep 2


title: Foxp3-GFPxAPCΔ468 small intestine tissue surrounding polyps Treg, biological rep 2


title: Foxp3-GFPxAPCΔ468 spleen CD4+ non-Treg, biological rep 2


title: 11169.p1/NA12878

source_name: whole blood DNA


title: Foxp3-GFP mesenteric lymph node CD4+ non-Treg, biological rep 3


title: Foxp3-GFPxAPCΔ468 spleen Treg, biological rep 2


title: Foxp3-GFP spleen CD4+ non-Treg, biological rep 3


title: Foxp3-GFPxAPCΔ468 small intestine polyp CD4+ non-Treg, biological rep 2


title: Patient_#69_C3

source_name: serum

value: Yes


title: Foxp3-GFP spleen Treg, biological rep 2

source_name: healthy spleen Treg


title: Foxp3-GFPxAPCΔ468 small intestine tissue surrounding polyps CD4+ non-Treg, biological rep 1


title: Foxp3-GFPxAPCΔ468 mesenteric lymph node Treg, biological rep 2


title: 11174.p1/NA18507

value: unknown

source_name: lymphoblast cell line DNA


title: Foxp3-GFPxAPCΔ468 mesenteric lymph node CD4+ non-Treg, biological rep 2

value: 4 months old


title: Patient_#67_C3


title: Patient_#66_C3


title: Foxp3-GFP small intestine CD4+ non-Treg, biological rep 5

value: male


title: 11167.p1/NA12878


title: Patient_#65_C3


title: Patient_#64_C3


title: Patient_#63_C3


title: Patient_#62_C3


title: Foxp3-GFP mesenteric lymph node Treg, bilogical rep 2


title: Foxp3-GFP small intestine CD4+ non-Treg, biological rep 4


title: Foxp3-GFP spleen Treg, biological rep 1

value: spleen


title: Foxp3-GFP spleen CD4+ non-Treg, biological rep 1


title: Diapause induced vs non-diapause at 30 hours of post oviposition - replicate 1

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

hyb_protocol: The labeled cRNA samples were hybridized on to a Genotypic designed Custom Bombyx mori 4x44k (AMADID No: 034793). 825ng each of cy3 and Cy5 labeled samples were fragmented and hybridized. Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5188-5242). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327)

scan_protocol: The arrays were scanned on an Agilent G2505C scanner and Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1)

data_processing: Analysis was performed using Lowesss Normalization.Software used: Agilent GeneSpring GX v11.5

organism: Bombyx mori

source_name: Diapause induced silkworm eggs at 30 hours of Oviposition

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0444). Five hundred nanograms each of the Control and test samples were incubated with reverse trancription mix at 40°C and converted to double stranded cDNA primed by oligodT with a T7 polymerase promoter. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(control) and Cy5 CTP(treated) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up and quality assessed for yields and specific activity.

growth_protocol: The silkworm eggs of M13 race were incubated for hatching at 25 ºC, 80% relative humidity, with photoperiod of 16h L : 18h D. The first to third instar silkworms were reared under 26 ºC and 80% relative humidity with 12h L : 12h D.

extract_protocol: After oviposition, the diapause and non-diapause egg samples were collected from 6 to 48h at every 6h time interval. Total RNA was extracted from the diapause and non-diapause eggs using TRIzol reagent (Invitrogen) using manufacturer’s instructions.

treatment_protocol: Subsequently, the fourth and fifth instar silkworms were reared at 18 ºC to 20 ºC with 6h L : 18h D to obtain diapausing eggs.

tag: race


title: Diapause induced vs non-diapause at 30 hours of post oviposition - replicate 2


title: Diapause induced vs non-diapause at 18 hours of post oviposition - replicate 1

source_name: Diapause induced silkworm eggs at 18 hours of Oviposition


title: Foxp3-GFP small intestine CD4+ non-Treg, biological rep 3

value: small intestine


title: 11161.p1/NA12878

value: proband


title: Diapause induced vs non-diapause at 18 hours of post oviposition - replicate 2


title: Patient_#61_C3


title: 11160.p1/NA12878

value: whole blood


title: Foxp3-GFPxAPCΔ468 small intestine tissue surrounding polyps Treg, biological rep 1


title: Patient_#59_C3


title: Patient_#60_C3


title: 11167.mo/NA12878

value: female


title: Insulinoma_frozen_pancreas_rep3_C#18

city: Odense C

first: Nete

middle: Vinstrup

last: Michelsen

address: Sdr Boulevard 29

department: Dept of Clinical Genetics

country: Denmark

institute: Odense University Hospital

description: Cells were grown according to ATCC for several passages, total RNA extracted and total RNA for all cell lines was pooled. The pooled total RNA was aliquotted and used for all slides as reference RNA.

hyb_protocol: Hybridization of samples and reference aaRNA and the subsequent microarray washes were performed using an Agilent Gene Expression Hybridization Kit according to the manufacturer’s protocol.

scan_protocol: Slides were scanned using an Agilent G2565BA microarray scanner (Agilent Technology).

data_processing: Spot intensities measured for references and samples were corrected for local background intensities. Data analysis was performed using the variance stabilization normalization procedure (vsn) implemented in the R-based Bioconductor package (http://www.bioconductor.org). A ratio of the normalized intensities was calculated for each spot. Finally, a geometric mean was calculated for the ratios of each pair of spot duplicates and was used as the gene expression measurement.

source_name: Insulinoma frozen pancreas

label_protocol: Amplification and labeling of DNase- treated samples and reference RNA was performed using an Amino Allyl MessageAmpTM aRNA kit (Ambion, Austin, TX, USA).

extract_protocol: RNA from frozen pancreatic samples was extracted from 50-100 mg of tissue. The tissue was homogenized and total RNA was extracted using TRIzol® Reagent.

tag: inclusion criteria

value: no disease-causing mutations found in MEN1 gene

tag: storage

value: frozen at -80⁰C

tag: amplification

value: subjected to two rounds of amplification

tag: hybridization

value: 2 µg of labeled pancreatic aaRNA, corresponding to approximately 200 pmol of incorporated dye Cy5 was hybridized.

source_name: Pooled total RNA from cancer cell lines.

extract_protocol: Total RNA was extracted using an RNeasy® Midi Kit (Qiagen, MD, USA).

tag: cell lines

value: HeLa (cervical epithelium), SK-BR-3 (mammary gland), HT29 (colon), A431 (skin)

value: subjected to one round of amplification

value: 1 µg of reference aaRNA, corresponding to approximately 100 pmol incorporated dye Cy3 was hybridized.


title: Foxp3-GFPxAPCΔ468 small intestine polyp CD4+ non-Treg, biological rep 1

source_name: small intestine polyp infiltrating CD4+ non-Treg

value: small intestine polyp


title: 11154.p1/NA12878

tag: group


title: Patient_#58_C3

tag: Sex

value: Female

tag: sle (yes/no)

value: Yes


title: Insulinoma_FFPE_pancreas_rep1_C#16

source_name: Insulinoma FFPE pancreas

extract_protocol: Paraffin blocks of FFPE pancreatic samples were cut in two 10µm sections. To extract RNA from FFPE pancreatic sections, paraffin was solubilized with xylene and centrifuged to pellet tissue from the solution. Residual xylene was removed by two ethanol rinses, and the tissue pellet was air-dried. The pellet was digested with Proteinase K overnight in digestion buffer. TRIzol® Reagent (Carlsbad, CA, USA) was used to isolate RNA. The final pellets were resuspended in 15 µl of nuclease free water.

value: routinely formalin-fixed and paraffin-embedded


title: Foxp3-GFPxAPCΔ468 small intestine polyp Treg, biological rep 1

source_name: small intestine polyp infiltrating Treg

value: 4 months old

tag: gender

value: male


title: Control_FFPE_pancreas_C#14

source_name: Control FFPE pancreas

value: death was not pancreas-related


title: 11164.p1/NA12878

tag: family status

value: proband

tag: ndar guid

tag: tissue


title: 11165.p1/NA18507

value: whole blood

tag: cell line


title: 11158.p1/NA12878

value: female


title: Foxp3-GFPxAPCΔ468 spleen CD4+ non-Treg, biological rep 1

source_name: spleen CD4+ non-Treg from polyp ridden mice

value: spleen

tag: genotype


title: Patient_#57_C3


title: Control_FFPE_pancreas_C#15


title: Foxp3-GFPxAPCΔ468 spleen Treg, biological rep 1

source_name: spleen Treg from polyp ridden mice

tag: genetic background


title: Patient_#56_C3


title: 11152.p1/NA12878


title: 11150.p1/NA18507


title: Control_FFPE_pancreas_C#12


title: Patient_#55_C3


title: Patient_#54_C3


title: Insulinoma_FFPE_pancreas_rep2_C#17

value: no disease-causing mutations found in MEN1 gene


title: CHI_frozen_pancreas_CHI#6

source_name: CHI frozen pancreas

value: no disease-causing mutations found in genes KCNJ11 and ABCC13

value: frozen at -80⁰C

value: subjected to two rounds of amplification


title: Foxp3-GFPxAPCΔ468 mesenteric lymph node CD4+ non-Treg, biological rep 1

source_name: mesenteric lymph node CD4+ non-Treg from polyp ridden mice

value: Mesenteric lymph node

tag: age


title: CHI_frozen_pancreas_CHI#7

value: no disease-causing mutations found in genes KCNJ11 and ABCC14

value: 2 µg of labeled pancreatic aaRNA, corresponding to approximately 200 pmol of incorporated dye Cy5 was hybridized.

value: HeLa (cervical epithelium), SK-BR-3 (mammary gland), HT29 (colon), A431 (skin)

value: subjected to one round of amplification

value: 1 µg of reference aaRNA, corresponding to approximately 100 pmol incorporated dye Cy3 was hybridized.


title: Foxp3-GFP small intestine CD4+ non-Treg, biological rep 2

source_name: healthy small intestine CD4+ non-Treg

value: small intestine

value: 4 months old


title: Control_FFPE_pancreas_C#13

value: death was not pancreas-related

value: routinely formalin-fixed and paraffin-embedded


title: Foxp3-GFPxAPCΔ468 mesenteric lymph node Treg, biological rep 1

source_name: mesenteric lymph node Treg from polyp ridden mice

value: male


title: Patient_#53_C3

source_name: serum

value: Male

value: Yes


title: 11148.p1/NA12878

source_name: whole blood DNA

value: proband

value: whole blood

value: female


title: Control_FFPE_pancreas_C#11

value: subjected to two rounds of amplification


title: 11146.p1/NA12878

source_name: lymphoblast cell line DNA


title: CHI_FFPE_pancreas_CHI#5

source_name: CHI FFPE pancreas

value: no disease-causing mutations found in genes KCNJ11 and ABCC12


title: 11141.mo/NA12878

value: mother


title: 11142.p1/NA12878


title: Patient_#52_C3


title: Patient_#51_C3

value: Female


title: 11148.mo/NA12878


title: 11145.p1/NA18507


title: Patient_#50_C3


title: Patient_#49_C3


title: 11141.p1/NA18507


title: Foxp3-GFP mesenteric lymph node CD4+ non-Treg, biological rep 1

source_name: healthy mesenteric lymph node CD4+ non-Treg

value: Mesenteric lymph node


title: Foxp3-GFP small intestine Treg, biological rep 1

source_name: healthy small intestine Treg


title: CHI_FFPE_pancreas_CHI#3

value: no disease-causing mutations found in genes KCNJ11 and ABCC10

value: 2 µg of labeled pancreatic aaRNA, corresponding to approximately 200 pmol of incorporated dye Cy5 was hybridized.

source_name: Pooled total RNA from cancer cell lines.

value: HeLa (cervical epithelium), SK-BR-3 (mammary gland), HT29 (colon), A431 (skin)

value: subjected to one round of amplification


title: CHI_FFPE_pancreas_CHI#1

value: no disease-causing mutations found in genes KCNJ11 and ABCC8

value: 1 µg of reference aaRNA, corresponding to approximately 100 pmol incorporated dye Cy3 was hybridized.


title: Foxp3-GFP mesenteric lymph node Treg, biological rep 1

source_name: healthy mesenteric lymph node Treg

value: 4 months old

value: male


title: Foxp3-GFP small intestine Treg, biological rep 2

value: small intestine


title: Patient_#48_C3

value: Male

value: Yes


title: 11156.p1/NA12878

value: proband

value: whole blood

value: female


title: Patient_#47_C3


title: 11148.fa/NA18507

value: father


title: CHI_FFPE_pancreas_CHI#2

value: no disease-causing mutations found in genes KCNJ11 and ABCC9

value: routinely formalin-fixed and paraffin-embedded

value: subjected to two rounds of amplification


title: CHI_FFPE_pancreas_CHI#4

value: no disease-causing mutations found in genes KCNJ11 and ABCC11

value: 2 µg of labeled pancreatic aaRNA, corresponding to approximately 200 pmol of incorporated dye Cy5 was hybridized.


title: GFP-positive liver cells, biological rep2

city: Jerusalem

first: Amir

last: Eden

address: Givat Ram

department: Cell & Developmental Biology

country: Israel

institute: Hebrew University

hyb_protocol: The labeled samples were hybridized to the Mouse gene1.0ST GeneChip array (Affymetrix, Santa Clara, CA, USA). The arrays were washed and stained with phycoerytrin conjugated streptavidin (SAPE) using the Affymetrix Fluidics Station® 450.

scan_protocol: The arrays were scanned in the Affymetrix GeneArray® 3000 scanner to generate fluorescent images, as described in the Affymetrix GeneChip® protocol.

data_processing: Gene expression profiles were processed with RMA (Robust Multichip Average) using the RMAExpress implementation.

source_name: Mouse liver replicating (GFP-positive) cells

label_protocol: 10 ng of total RNA from each sample was amplifyed using the WT-Ovation Pico RNA Amplification System (Nugen, San Carlos, CA, USA). Double-stranded cDNA was generated using the WT-Ovation Exon module(Nugen) followed by biotin labeling with the FL-Ovation cDNA Biotin Module V2(Nugen).

extract_protocol: total RNA was prepared using Qiagen RNeasy microkit according to the manufacturer's protocol.

treatment_protocol: Liver from CyclinB1-GFP mice was perfused and GFP-negative and positive cells were FACS-sorted in Tri-Reagent (SIGMA).

value: Liver

value: 3.5 week old

tag: strain

value: CyclinB1-GFP transgenic mice


title: GFP-positive liver cells, biological rep3


title: Patient_#46_C3

value: Female


title: Patient_#45_C3


title: FarRed_rep2

city: Iizuka

first: Kousuke

last: Hanada

state: Fukuoka

address: 680-4 Kawazu

department: Department of Bioscience and Bioinformatics

institute: Kyushu Institute Technology

hyb_protocol: Hybridization was performed using the in situ Hybridization Kit Plus (Agilent Technologies, Tokyo, Japan)

scan_protocol: Hybridized and washed material on each glass slide was scanned by an Agilent G2505 B DNA microarray scanner (Agilent Technologies)

data_processing: Data analysis was performed by Feature Extraction and Image Analysis software (Agilent Technologies, Tokyo, Japan). The array intensities were processed using the Bioconductor (www.bioconductor.org) affy package in the R software environment (www.r-project.org). Hybridization intensities in our arrays were simply normalized among different arrays by quantile normalization.

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: FarRed

label_protocol: cRNA amplification and fluorescence labeling were performed using the Agilent Low RNA Input Linear Amplification Kit (Agilent Technology, Tokyo, Japan) according to the manufacturer's protocol. A primer containing poly dT and a T7 polymerase promoter was annealed to the poly A+ RNA. First and second strands of cDNA were reverse transcribed from 500 ng total RNA using MMLV-RT enzyme. Cyanine 3- labeled cRNA was synthesized using T7 RNA polymerase. Labeled cRNA was purified by RNeasy Mini Kit (Qiagen, Tokyo, Japan).

extract_protocol: Approximately 500 μg of total RNA was three times extracted from each sample using TRIzol (Invitrogen).

tag: treatment group

value: light condition


title: FarRed_rep3


title: 11134.p1/NA18507

value: male


title: GFP-negative liver cells, biological rep3

source_name: Mouse liver quiescent (GFP-negative) cells


title: 11133.p1/NA18507


title: GFP-positive liver cells, biological rep1


title: FarRed_rep1


title: Patient_#44_C3


title: Patient_#43_C3


title: Blue_rep3

source_name: Blue


title: 11132.p1/NA12878


title: Patient_#42_C3


title: GFP-negative liver cells, biological rep2


title: 11141.fa/NA18507


title: Blue_rep1


title: 11129.p1/NA12878


title: Patient_#41_C3


title: Patient_#21_C3


title: 11124.p1/NA12878


title: Bin2 x lon end biol rep 3

city: Monrovia

first: Nora

last: Heisterkamp

state: CA

address: 1218 S Fifth Avenue

department: Department of Systems Biology

institute: Beckman Research Institute City of Hope

description: N147-A-MoGene-1_0-st-v1-01-1 (Bin2_FTI_end_c)

hyb_protocol: Automatically washed and stained with streptavidin-phycoerythrin using a fluidics system.

scan_protocol: Scanned using a Hewlett-Packard GeneArray Scanner.

data_processing: Results were analyzed using Partek and Ingenuity Systems (version 7.1) software

source_name: t=d30, lonafarnib

label_protocol: Converted to biotinylated cRNA with an Enzo High Yield RNA transcript labeling kit.

growth_protocol: Mouse preB ALL cells were grown on irradiated mouse embryonic fibroblast feeder layers in McCoy's 5A medium supplemented with 15% FCS, 110 mg/L sodium pyruvate, L-glutamine, penn/strep, 10 ng/ml recombinant IL-3 and 50 uM beta-mercaptoethanol.

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

treatment_protocol: 8093 cells were treated for 20 days with 20 nM nilotinib, or for 26 days with 1 uM lonafarnib. Bin-2 cells were treated for 21 days with 50 nM nilotinib, or for 30 days with 0.25 uM lonafarnib. These drug concentrations were earlier determined in pilot experiments to cause most of the leukemia cells to die, but allow a small percentage to grow out at the end of the treatment period as cells that had become drug-tolerant to the concentration of that drug used. Fresh drug was added with changes of fresh medium, generally every second day. For isolation of RNA at the t= 0 and t= end/resistance points we used a 10-cm dish per biological replicate. For the t= midpoint one 15-cm dish or two pooled 10-cm dishes were used to obtain sufficient cells.

tag: cell type

value: pre-B ALL Bin2

tag: treatment

value: lonafarnib

tag: time


title: Bin2 x lon end biol rep 1

description: N145-A-MoGene-1_0-st-v1-01-1 (Bin2_FTI_end_a)


title: Foxp3-GFP small intestine CD4+ non-Treg, biological rep 1

value: small intestine

value: 4 months old


title: GFP-negative liver cells, biological rep1


title: Red_rep3

source_name: Red


title: Bin2 x lon end biol rep 2

description: N146-A-MoGene-1_0-st-v1-01-1 (Bin2_FTI_end_b)


title: 11128.p1/NA18507

value: proband

value: whole blood


title: 11124.mo/NA12878

value: female

value: mother


title: Patient_#20_C3

value: Yes


title: 11124.fa/NA18507

value: father


title: Bin2 x lon mid biol rep 2

description: N143-A-MoGene-1_0-st-v1-01-1 (Bin2_FTI_mid_b)

source_name: t=d3, lonafarnib


title: Bin2 x lon mid biol rep 3

description: N144-A-MoGene-1_0-st-v1-01-1 (Bin2_FTI_mid_c)


title: Patient_#18_C3


title: 11131.p1/NA12878


title: 11122.p1/NA12878


title: Patient_#17_C3


title: 11120.p1/NA12878


title: 11121.p1/NA12878


title: Patient_#16_C3


title: 11120.mo/NA12878


title: Dark_rep2

source_name: Dark


title: Bin2 x lon mid biol rep 1

description: N142-A-MoGene-1_0-st-v1-01-1 (Bin2_FTI_mid_a)


title: Dark_rep1


title: Dark_rep3


title: Patient_#15_C3


title: Bin2 x lon start biol rep 2

description: N140-A-MoGene-1_0-st-v1-01-1 (Bin2_FTI_start_b)

source_name: t=0, lonafarnib


title: Bin2 x lon start biol rep 3

description: N141-A-MoGene-1_0-st-v1-01-1 (Bin2_FTI_start_c)


title: Light24h.2


title: Light24h.3


title: 11118.p1/NA12878


title: Blue_rep2


title: Patient_#14_C3

source_name: serum


title: Bin2 x lon start biol rep 1

description: N139-A-MoGene-1_0-st-v1-01-1 (Bin2_FTI_start_a)


title: Light24h.1


title: Bin2 x nil end biol rep 3

description: N138-A-MoGene-1_0-st-v1-01-1 (Bin2_AMN_end_c)

source_name: t=d21, nilotinib

value: nilotinib


title: Patient_#13_C3


title: Patient_#12_C3


title: Red_rep2


title: Light6h_rep3


title: Patient_#11_C3


title: Bin2 x nil end biol rep 2

description: N137-A-MoGene-1_0-st-v1-01-1 (Bin2_AMN_end_b)


title: 11116.p1/NA12878

source_name: whole blood DNA

source_name: lymphoblast cell line DNA


title: Red_rep1


title: 11115.p1/NA12878


title: Light6h_rep2


title: Light6h_rep1


title: Bin2 x nil end biol rep 1

description: N136-A-MoGene-1_0-st-v1-01-1 (Bin2_AMN_end_a)


title: Patient_#10_C3


title: Bin2 x nil mid biol rep 3

description: N135-A-MoGene-1_0-st-v1-01-1 (Bin2_AMN_mid_c)

source_name: t=d3, nilotinib


title: Light1h_rep3


title: Light1h_rep2


title: Bin2 x nil mid biol rep 2

description: N134-A-MoGene-1_0-st-v1-01-1 (Bin2_AMN_mid_b)


title: Bin2 x nil  mid biol rep 1

description: N133-A-MoGene-1_0-st-v1-01-1 (Bin2_AMN_mid_a)


title: 11111.p1/NA18507


title: 11113.p1/NA12878


title: Light1h_rep1


title: Patient_#9_C3


title: Patient_#8_C3


title: Bin2 x nil start biol rep 3

description: N132-A-MoGene-1_0-st-v1-01-1 (Bin2_AMN_start_c)

source_name: t=0, nilotinib


title: Patient_#7_C3

value: Male


title: Bin2 x nil start biol rep 2

description: N131-A-MoGene-1_0-st-v1-01-1 (Bin2_AMN_start_b)


title: Patient_#6_C3


title: Bin2 x nil start biol rep 1

description: N130-A-MoGene-1_0-st-v1-01-1 (Bin2_AMN_start_a)


title: Patient_#5_C3


title: Light0h_rep3


title: Light0h_rep2


title: Light0h_rep1


title: Patient_#19_C3


title: Callus_rep3

source_name: Callus

value: tissue


title: 8093 x lon end biol rep 2

description: N129-A-MoGene-1_0-st-v1-01-1 (8093_FTI_end_c)

source_name: t=d26, lonafarnib

value: pre-B ALL 8093


title: Patient_#4_C3

value: Female


title: 11109.p1/NA12878


title: Patient_#3_C3


title: Patient_#2_C3


title: Callus_rep2


title: 8093 x lon mid biol rep 3

description: N126-A-MoGene-1_0-st-v1-01-1 (8093_FTI_mid_c)

source_name: t=d4, lonafarnib


title: 11107.p1/NA18507


title: 11109.fa/NA18507


title: seed48h_rep3


title: 11117.p1/NA12878


title: 8093 x lon mid biol rep 1

description: N124-A-MoGene-1_0-st-v1-01-1 (8093_FTI_mid_a)


title: 8093 x lon start biol rep3

description: N123-A-MoGene-1_0-st-v1-01-1 (8093_FTI_start_c)


title: seed48h_rep2


title: 8093 x lon end biol rep 1

description: N127-A-MoGene-1_0-st-v1-01-1 (8093_FTI_end_a)


title: 11101.p1/NA12878


title: Callus_rep1


title: Patient_#230_IgG

hyb_protocol: Probe: APC-conjugated F(ab')2 fragment goat anti-human IgG

data_processing:
Local background of spot was substracted from the value of signal. The value of signal is set to zero if it is lower than 2*SD of local backgrounds on the given chip. For interassay comparison, data were normalized to the mean of 5 times diluted human IgG control material (ID_REF: #388, #389, #390).
Normalization procedure was carried out with Microsoft Office Exel software

label: APC

value: No


title: 11110.p1/NA12878

value: male


title: 11106.p1/NA12878


title: 11109.mo/NA12878


title: 11114.p1/NA12878


title: 11099.p1/NA18507


title: Patient_#228_IgG


title: Patient_#226_IgG


title: Patient_#227_IgG


title: 11120.fa/NA18507


title: 11098.mo/NA12878


title: Patient_#1_C3


title: 11098.p1/NA12878


title: Patient_#229_IgG


title: seed24h_rep2


title: Patient_#225_IgG


title: 8093 x lon start biol rep 1

description: N121-A-MoGene-1_0-st-v1-01-1 (8093_FTI_start_a)


title: 11108.p1/NA18507


title: 8093 x nil end biol rep 1

description: N119-A-MoGene-1_0-st-v1-01-1 (8093_AMN_end_b)

source_name: t=d20, nilotinib


title: 8093 x nil end biol rep 2

description: N120-A-MoGene-1_0-st-v1-01-1 (8093_AMN_end_c)


title: 11097.p1/NA18507


title: 8093 x lon mid biol rep 2

description: N125-A-MoGene-1_0-st-v1-01-1 (8093_FTI_mid_b)


title: seed48h_rep1


title: seed24h_rep3


title: dryseed_rep3

source_name: dryseed


title: seed24h_rep1


title: 11098.fa/NA18507


title: 11096.fa/NA18507


title: 11096.mo/NA12878


title: Patient_#223_IgG


title: 8093 x nil mid biol rep 3

description: N117-A-MoGene-1_0-st-v1-01-1 (8093_AMN_mid_c)


title: Patient_#221_IgG


title: Patient_#222_IgG


title: 8093 x nil start biol rep 3

description: N114-A-MoGene-1_0-st-v1-01-1 (8093_AMN_start_c)


title: Patient_#220_IgG


title: 8093 x nil start biol rep 2

description: N113-A-MoGene-1_0-st-v1-01-1 (8093_AMN_start_b)


title: 8093 x nil mid biol rep 2

description: N116-A-MoGene-1_0-st-v1-01-1 (8093_AMN_mid_b)


title: dryseed_rep2


title: Patient_#219_IgG


title: dryseed_rep1


title: 8093 x nil mid biol rep 1

description: N115-A-MoGene-1_0-st-v1-01-1 (8093_AMN_mid_a)


title: 11096.p1/NA12878


title: Cold6h_rep3

value: abiotic stress


title: Cold6h_rep1


title: Cold2h_rep3


title: 11093.p1/NA12878


title: Cold6h_rep2


title: 8093 x nil start biol rep 1

description: N112-A-MoGene-1_0-st-v1-01-1 (8093_AMN_start_a)


title: monocyte-derived macrophages, C_7days_rep4

city: Birmingham

first: Geeta

last: Datta

address: 1808 7th Ave S

institute: University of Alabama at Birmingham

hyb_protocol: The arrays were hybridized overnight per Affymetrix protocol at 45C, and then washed, stained, and scanned the next day.

scan_protocol: GeneChips were scanned on an Affymetrix 3000 7G scanner with an autoloader.

data_processing: The data were analyzed using GeneSpring GX version 11.0.2 software using Affymetrix Exon Expression default settings using RMA16. A baseline transformation to the mean of the Control Samples (GD-C1, GD-C2, GD-C3, and GD-C4) was performed.

source_name: monocyte-derived macrophages, Control, 7 days

label_protocol: cRNA was generated by standard methods (Affymetrix) followed by ssDNA fragmentation, end label biotinylation and preparation of hybridization cocktail.

growth_protocol: Primary human monocytes were grown in RPMI medium for 7 days with/without treatment.

extract_protocol: RNA was isolated from the monocyte-derived macrophages using the Ambion mirVANA RNA isolation kit.

treatment_protocol: Cells were treated with 4F (50ug/million cells) for 7 days. Controls were treated with medium alone for 7 days. On day 7, cells were treated with LPS (1ug/mL) for an additional 18 hrs.

value: monocyte-derived macrophages (MDMs)

value: control


title: 11092.p1/NA18507


title: Patient_#218_IgG


title: Patient_#217_IgG


title: Cold2h_rep2


title: Patient_#216_IgG


title: 8093 x lon start biol rep 2

description: N122-A-MoGene-1_0-st-v1-01-1 (8093_FTI_start_b)

value: lonafarnib


title: Patient_#215_IgG


title: 11093.mo/NA12878


title: 11094.p1/NA12878

value: proband


title: monocyte-derived macrophages, C_7days_rep3


title: monocyte-derived macrophages, C_7days_rep1


title: Heat6h_rep3


title: Patient_#224_IgG


title: Heat6h_rep2


title: Cold2h_rep1


title: Patient_#214_IgG


title: monocyte-derived macrophages, C_7days_rep2


title: Heat6h_rep1


title: monocyte-derived macrophages, C+LPS_7days_rep3

source_name: monocyte-derived macrophages, Control+LPS, 7 days

value: control + lipopolysaccharides (LPS)


title: Patient_#213_IgG


title: monocyte-derived macrophages, C+LPS_7days_rep4


title: Patient_#212_IgG


title: 11090.p1/NA12878

value: whole blood

value: female


title: 11093.fa/NA18507


title: Heat2h_rep3


title: monocyte-derived macrophages, C+LPS_7days_rep2


title: Heat2h_rep2


title: Patient_#211_IgG


title: 11083.mo/NA12878

value: mother


title: monocyte-derived macrophages, C+LPS_7days_rep1


title: Heat2h_rep1


title: 11085.p1/NA12878


title: monocyte-derived macrophages, 4F_7days_rep4

source_name: monocyte-derived macrophages, 4F, 7 days


title: Salt6h_rep3


title: 11083.p1/NA12878


title: monocyte-derived macrophages, 4F_7days_rep3


title: 11086.p1/NA12878


title: Patient_#209_IgG


title: monocyte-derived macrophages, 4F_7days_rep2


title: 11083.fa/NA18507

value: father


title: Patient_#207_IgG


title: 11089.p1/NA12878


title: 11079.p1/NA18507


title: monocyte-derived macrophages, 4F+LPS_7days_rep4

source_name: monocyte-derived macrophages, 4F+LPS, 7 days

value: 4F + lipopolysaccharides (LPS)


title: monocyte-derived macrophages, 4F_7days_rep1


title: Salt2h_rep3


title: Patient_#206_IgG


title: Patient_#205_IgG


title: Salt2h_rep2


title: 11080.p1/NA12878


title: monocyte-derived macrophages, 4F+LPS_7days_rep3


title: monocyte-derived macrophages, 4F+LPS_7days_rep2


title: Patient_#210_IgG


title: Patient_#204_IgG


title: Patient_#203_IgG


title: dry6h_rep3


title: 11074.p1/NA12878


title: 11078.p1/NA18507


title: dry6h_rep2


title: Salt2h_rep1


title: Lo MTX biological replicate 3

city: Philadelphia

first: Alexander

middle: Steven

last: Whitehead

state: PA

address: 421 Curie Blvd, 8th floor BRB

department: Pharmacology

institute: University of Pennsylvania

hyb_protocol: Hybridization was for 16-18 hours overnight at 45°C. Washing and staining was done on an Affymetrix 450 series fluidics machine.

scan_protocol: Chips were scanned in an Affymetrix Gene Chip Scanner 3000

data_processing: Cel files were imported into Partek Genomics Suite v6.5 where RMA was applied

source_name: EA.hy 926 cells in Lo media

label_protocol: Affymetrix Terminal Labeling kit from Ambion

growth_protocol: EA.hy 926 cells were adapted to growth under low folate conditions (Lo cells) in Medium 199, which contains 23nM of folic acid, supplemented with 10% FCS, non-essential amino acids, gentamycin, penicillin G, and fungizone. Parallel cultures of EA.hy 926 cells were grown under standard folate concentrations for that cell line (Hi cells) in Medium 199 supplemented with 4mg/L (9uM) folic acid and supplemented as above

extract_protocol: Total RNA was isolated with the RNeasy kit from Qiagen

treatment_protocol: Cells were grown to confluence, the media was changed and 24 hours later cells were treated with vehicle or 0.5uM MTX for 48 hours

tag: medium

value: Methotrexate


title: Patient_#202_IgG


title: 11073.p1/NA12878

tag: group


title: dry6h_rep1


title: Patient_#201_IgG

tag: Sex


title: 11069.p1/NA12878


title: Patient_#200_IgG

value: Male

tag: sle (yes/no)


title: monocyte-derived macrophages, 4F+LPS_7days_rep1

data_processing: The data were analyzed using GeneSpring GX version 11.0.2 software using Affymetrix Exon Expression default settings using RMA16. A baseline transformation to the mean of the Control Samples (GD-C1, GD-C2, GD-C3, and GD-C4) was performed. A baseline transformation to the mean of the Control Samples (GD-C1, GD-C2, GD-C3, and GD-C4) was performed.


title: 11069.mo/NA12878

tag: gender


title: Lo Control biological replicate 3

value: Control


title: Lo MTX biological replicate 2


title: Patient_#80_IgG

value: Female

value: Yes


title: 11075.p1/NA18507

value: male

tag: family status


title: dry2h_rep3

value: abiotic stress


title: dry2h_rep1


title: Patient_#79_IgG


title: 11069.fa/NA18507

tag: ndar guid


title: 11071.p1/NA12878

tag: tissue


title: Patient_#208_IgG

value: No


title: Lo MTX biological replicate 1


title: Control_rep2

source_name: Control


title: Lo Control biological replicate 2


title: Lo Control biological replicate 1


title: Salt6h_rep1


title: 11067.p1/NA12878

tag: cell line


title: Hi MTX biological replicate 3

source_name: EA.hy 926 cells in Hi media

value: M199 with folate added


title: Salt6h_rep2


title: 11066.p1/NA18507


title: Patient_#76_IgG

source_name: serum


title: Patient_#77_IgG


title: Young_Silique_rep3

value: tissue


title: 11064.p1/NA12878

source_name: whole blood DNA

value: proband


title: Patient_#75_IgG


title: dry2h_rep2


title: Hi MTX biological replicate 2


title: 11064.fa/NA18507

source_name: lymphoblast cell line DNA


title: Control_rep1


title: Control_rep3


title: Patient_#74_IgG


title: Hi MTX biological replicate 1


title: Young_Silique_rep2


title: Patient_#73_IgG


title: 11063.p1/NA12878


title: Hi Control biological replicate 2

value: control


title: Young_Silique_rep1


title: 11064.mo/NA12878

value: whole blood


title: 11060.p1/NA12878

value: female


title: Hi Control biological replicate 1


title: Hi Control biological replicate 3


title: Patient_#72_IgG


title: 11059.p1/NA18507


title: Old_Rosette_rep3


title: 11077.p1/NA12878


title: Patient_#71_IgG


title: Patient_#70_IgG


title: 11057.p1/NA12878


title: Patient_#69_IgG


title: Endomnetrioma_Ectopic_Proliferative_stage3_5

city: New Delhi

first: Meraj

middle: Alam

last: Khan

state: Delhi

address: Room No.2029

department: Physiology

institute: All India Institute of Medical Sciences

description:
E75_EC
This tissuewas ectopic endometrium obtained from endometrioma subject_E75.

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction,  55 µl of 2x Agilent hybridization buffer (GEx Hyb) was added to the fragmentation mixture to stop the fragmentation reaction. 100 µl hybridization mixture were loaded onto the Agilent Whole Human Genome Oligo Microarrays (G4112F) having 4X44K probes for 17 hours at 65° C in a rotating Agilent hybridization oven (G2545A).  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37° C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Immediately after washing slides were scanned on the Agilent microarray Scanner (G2505B) using one color scan setting (Profile AgilentHD_GX_1Color) for 4x44k array slides (Scan Area 61 x 21.6 mm, Scan resolution 5 um, Dye channel is set to Green and Green PMT is set to 100%). The produced separate 20-bit TIFF images for each array by collecting the fluorescence intensities from fluorescence labeled cRNA signals were archived for feature extractions.

data_processing: Scanned images of hybridized signals for all eutopic and ectopic endometrial samples were used for feature extraction and data acquisition (signal quantification) by using Feature Extraction software 10.7.3.1 (Agilent technology). For Agilent one-color microarrays, GE1-107_Sep09 (in FE 10.7) protocol was used, which automatically distinguished the formats for further processing of the data. Median normalization

label_protocol: Microarray experiments with individual tissue samples were performed according to manufacturer’s recommendations. RNA with RIN score >8.0 was used for cDNA synthesis and in vito transcription. Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy mini spin columns (QIAGEN, Colonge, Germany).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer. See  http://www.agilent.com for protocol and other details.

extract_protocol: Autologous eutopic and ectopic endometrial samples were collected during surgery of women diagnosed with endometrioma in sterile ice-cold phosphate buffered saline (PBS, pH 7.4). The tissue samples were quickly washed in ice-cold PBS to remove blood and debris. The total RNA was extracted using Trizol (Agilent Technologies Singapore Pvt. Ltd., Shung Avenue, Singapore) and cleaned up with DNase I (Sigma Chemical Co., St. Louis, Missouri, USA) and subjected to re-extraction when it was necessary. The yield and purity of the extracted RNA was checked using standard spectrophotometric method (NanoDrop-1000 spectrophotometer) and 1% agarose gel electrophoresis. Furthermore, RIN score of individual sample was determined using Bioanalyze-2100, RNA Chip kit and software from Agilent Technologies (Santa Clara, CA, USA).

tag: age (y)

value: female (fertile)

tag: subject id

tag: menstrual phase

value: Proliferative

tag: endometrioma severity stage

value: Moderate (stage 3)

tag: parity

value: Pregnancy_2; live offspriing_1


title: Patient_#78_IgG

value: Male


title: 11056.p1/NA12878


title: Patient_#68_IgG


title: Old_Rosette_rep1

tag: treatment group


title: Patient_#67_IgG


title: Endomnetrioma_Ectopic_Proliferative_stage4_8

description:
E73_EC
This tissue was ectopic endometrium obtained from endometrioma subject_E73.

value: Severe (stage 4)

value: Pregnancy_1; live offspriing_1


title: Endomnetrioma_Eutopic_Proliferative_stage4_8

description:
E73_EU
This tissue was eutopic endometrium obtained from endometrioma subject_E73.


title: Root_rep3

source_name: Root


title: Old_Rosette_rep2


title: Root_rep2


title: Endomnetrioma_Ectopic_Secretory_stage3_3

description:
E68_EC
This tissue was ectopic endometrium obtained from endometrioma subject_E68.

value: Secretory


title: 11056.mo/NA12878

value: mother


title: 11055.mo/NA12878


title: Endomnetrioma_Eutopic_Secretory_stage4_2

description:
E70_EU
This tissue was eutopic endometrium obtained from endometrioma subject_E70.

value: Pregnancy_2; live offspriing_2


title: Bud_rep3

source_name: Bud


title: Root_rep1


title: 11055.p1/NA12878

value: male


title: 11056.fa/NA18507

value: father


title: Bud_rep2

value: tissue


title: OCT_4

city: Torrance

first: Robert

last: Gelfand

address: 1124 W. Carson St

department: surgery

institute: LABiomed at Harbor UCLA,  and Charles Drew Univ

description: hind limb muscle tissue subjected to preplating procedure to isolate muscle derived stem cells

hyb_protocol: cRNAs were hybridized to 60-mer probes attached to nylon membrane, washed, and viewed for signal as described in the manual (see label protocol).

scan_protocol: See the manual described under label protocol:

data_processing: GEArray Expression Analysis Suite (SuperArray BioScience Corp., Frederick, MD)

source_name: transgenic Oct4 mouse

label_protocol: Labeling was carried out by SABiosciences according to their protocols for the oligo array EMM405, by synthesizing labeled cRNA. See http://www.sabiosciences.com/manuals/DNAMicroarrays.pdf

growth_protocol: Cells were grown in 25 ml flasks in the presence of DMEM plus 20% fetal bovine serum in the presence of penicillin, streptomycin, and amphotericin B until nearly confluent.

extract_protocol: RNA was extracted using Trizol according to the manufacturer's recommendations, followed by additional purification by the RNeasy procedure (Qiagen).

tag: background strain

tag: genotype/variation

value: Oct_4 transgenic

value: hind limb muscle tissue

tag: cell type

value: muscle derived stem cells


title: 11055.fa/NA18507

data_processing: The data were processed using the Agilent Feature Extraction software 10.5.1.1 using program defaults (http://www.chem.agilent.com/Library/usermanuals/Public/G4410-90020_CGH_ULS_Protocol_v.3.1.pdf)

tag: group

value: whole blood


title: Endomnetrioma_Ectopic_Secretory_stage3_2

description:
E57_EC
This tissue was ectopic endometrium obtained from endometrioma subject_E57.

value: female (fertile)

value: Pregnancy_4; live offspriing_4


title: KO

source_name: myostatin knockout mouse

value: Mst-/- (myostatin knockout)


title: Bud_rep1


title: 11054.p1/NA12878

value: proband

value: female


title: Young_Bud_rep2


title: Endomnetrioma_Eutopic_Secretory_stage3_3

description:
E68_EU
This tissue was eutopic endometrium obtained from endometrioma subject_E68.

value: Moderate (stage 3)


title: WT

source_name: wild type mouse

value: wild type


title: Young_Bud_rep1


title: Endomnetrioma_Ectopic_Proliferative_stage4_7

description:
E56_EC
This tissue was ectopic endometrium obtained from endometrioma subject_E56.

value: Proliferative

value: Severe (stage 4)

value: Pregnancy_1; live offspriing_1


title: Young_Rosette_rep3


title: Endomnetrioma_Ectopic_Secretory_stage4_2

description:
E70_EC
This tissue was ectopic endometrium obtained from endometrioma subject_E70.

value: Secretory

value: Pregnancy_2; live offspriing_2


title: Endomnetrioma_Eutopic_Secretory_stage3_2

description:
E57_EU
This tissue was eutopic endometrium obtained from endometrioma subject_E57.


title: Young_Bud_rep3

value: tissue


title: MDX

source_name: mdx mouse

value: male

value: 10ScSn-Dmdmdx (mdx)


title: Young_Rosette_rep2


title: Endomnetrioma_Eutopic_Proliferative_stage3_5

description:
E75_EU
This tissue was eutopic endometrium obtained from endometrioma subject_E75.

value: Pregnancy_2; live offspriing_1


title: Endomnetrioma_Eutopic_Proliferative_stage4_7

description:
E56_EU
This tissue was eutopic endometrium obtained from endometrioma subject_E56.


title: 11053.p1/NA12878

value: whole blood


title: Young_Rosette_rep1


title: SUB15

city: Fribourg

first: Pierre

last: Lavenex

address: Chemin du Musée 5

department: Medicine

country: Switzerland

institute: University of Fribourg

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on the Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: Analyses of gene expression levels were performed with ArrayAssist® Expression Software 4.0

organism: Macaca mulatta

source_name: Sub, newborn

label_protocol: Biotinylated cRNA were prepared from 50ng of total RNA according to Affymetrix's Two-Cycle Target Labeling  protocol (Expression Analysis Technical Manual, 2001, Affymetrix).

value: hippocampal formation

tag: age

value: newborn

tag: region

value: Sub


title: SUB16


title: 11051.p1/NA12878

tag: gender

value: proband


title: Endomnetrioma_Eutopic_Proliferative_stage4_6

description:
E52_EU
This tissue was eutopic endometrium obtained from endometrioma subject_E52.

value: female (fertile)

value: Pregnancy_4; live offspriing_2


title: Endomnetrioma_Ectopic_Proliferative_stage4_6

description:
E52_EC
This tissue was ectopicendometrium obtained from endometrioma subject_E52.


title: SUB14


title: 11049.p1/NA12878

tag: family status

value: female


title: Cauline_leaves_rep3


title: Endomnetrioma_Ectopic_Secretory_stage3_1

description:
E49_EC
This tissue was ectopic endometrium obtained from endometrioma subject_E49.

value: Moderate (stage 3)


title: 11052.p1/NA18507

tag: ndar guid


title: 11046.p1/NA12878

tag: tissue


title: 11050.p1/NA12878

tag: cell line


title: SUB12

source_name: Sub, six months

value: six months


title: 11048.p1/NA12878


title: SUB13


title: SUB11


title: Cauline_leaves_rep1


title: 11047.p1/NA12878


title: 11045.p1/NA12878


title: Endomnetrioma_Ectopic_Proliferative_stage4_4

description:
E40_EC
This tissue was ectopic endometrium obtained from endometrioma subject_E40.

tag: age (y)

value: Proliferative

value: Severe (stage 4)


title: 11044.mo/NA12878

value: mother


title: Endomnetrioma_Ectopic_Proliferative_stage4_5

description:
E48_EC
This tissue was ectopic endometrium obtained from endometrioma subject_E48.

tag: subject id

value: Pregnancy_1; live offspriing_1


title: 11044.p1/NA18507

value: male


title: Endomnetrioma_Eutopic_Secretory_stage3_1

description:
E49_EU
This tissue was eutopic endometrium obtained from endometrioma subject_E49.

tag: menstrual phase

value: Secretory

value: Pregnancy_2; live offspriing_2


title: Cauline_leaves_rep2

value: tissue


title: Stem_rep3

source_name: Stem


title: Stem_rep2


title: Rosette_rep2

source_name: Rosette


title: Endomnetrioma_Eutopic_Proliferative_stage3_4

description:
E43_EU
This tissue was eutopic endometrium obtained from endometrioma subject_E43.

tag: endometrioma severity stage


title: SUB06

source_name: Sub, one year

value: hippocampal formation

value: one year


title: Rosette_rep3


title: SUB09

value: Sub


title: 11043.p1/NA12878

value: proband

value: whole blood


title: Endomnetrioma_Ectopic_Proliferative_stage3_4

description:
E43_EC
This tissue was ectopic endometrium obtained from endometrioma subject_E43.

value: female (fertile)

tag: parity


title: SUB08


title: Endomnetrioma_Eutopic_Proliferative_stage4_5

description:
E48_EU
This tissue was eutopic endometrium obtained from endometrioma subject_E48.


title: SUB10


title: SUB07


title: Endomnetrioma_Eutopic_Proliferative_stage4_4

description:
E40_EU
This tissuewas eutopic endometrium obtained from endometrioma subject_E40.

value: Pregnancy_4; live offspriing_2


title: 11043.mo/NA12878

value: female


title: Rosette_rep1

tag: treatment group


title: 11044.fa/NA18507

value: father


title: SUB05


title: Endomnetrioma_Eutopic_Secretory_stage4_1

description:
E33_EU
This tissue was eutopic endometrium obtained from endometrioma subject_E33.

value: Pregnancy_2; live offspriing_1


title: Endomnetrioma_Ectopic_Secretory_stage4_1

description:
E33_EC
This tissue was ectopic endometrium obtained from endometrioma subject_E33.

value: Severe (stage 4)


title: SUB04

source_name: Sub, adult

value: adult


title: Flower_rep2

source_name: Flower


title: Flower_rep3


title: Endomnetrioma_Ectopic_Proliferative_stage3_3

description:
E32_EC
This tissue was ectopic endometrium obtained from endometrioma subject_E32.

value: Proliferative

value: Moderate (stage 3)

value: Pregnancy_3; live offspriing_2


title: Stem_rep1


title: Flower_rep1


title: SUB03


title: SUB02


title: Endomnetrioma_Eutopic_Proliferative_stage3_3

description:
E32_EU
This tissue was eutopic endometrium obtained from endometrioma subject_E32.


title: 11042.p1/NA18507

value: male


title: SUB01


title: Old_Silique_rep3

value: tissue


title: Old_Silique_rep2


title: 11038.p1/NA12878


title: 11043.fa/NA18507


title: EC16

source_name: EC, newborn

value: hippocampal formation

value: newborn

value: EC


title: 11040.p1/NA12878

value: proband


title: EC15


title: 11041.p1/NA12878

value: whole blood


title: 11039.p1/NA18507


title: Endomnetrioma_Eutopic_Proliferative_stage3_2

description:
E31_EU
This tissue was eutopic endometrium obtained from endometrioma subject_E31.

value: female (fertile)

value: Pregnancy_1; live offspriing_1


title: Endomnetrioma_Ectopic_Proliferative_stage3_1

description:
E26_EC
This tissue was ectopic endometrium obtained from endometrioma subject_E26.

value: Pregnancy_3; live offspriing_3


title: Endomnetrioma_Ectopic_Proliferative_stage3_2

description:
E31_EC
This tissue was ectopic endometrium obtained from endometrioma subject_E31.


title: 11037.p1/NA18507


title: Silique_rep3

source_name: Silique


title: EC13


title: Endomnetrioma_Ectopic_Proliferative_stage4_3

description:
E23_EC
This tissue was ectopic endometrium obtained from endometrioma subject_E23.


title: Silique_rep2


title: EC12

source_name: EC, six months

value: six months


title: Endomnetrioma_Eutopic_Proliferative_stage3_1

description:
E26_EU
This tissue was eutopic endometrium obtained from endometrioma subject_E26.


title: EC14


title: EC11


title: 11031.p1/NA12878

source_name: whole blood DNA

source_name: lymphoblast cell line DNA

value: female


title: 11030.p1/NA12878


title: Endomnetrioma_Ectopic_Proliferative_stage4_2

description:
E20_EC
This tissue was ectopic endometrium obtained from endometrioma subject_E20.

value: Severe (stage 4)

value: Pregnancy_6; live offspriing_6


title: Silique_rep1


title: 11030.mo/NA12878

value: mother


title: EC10


title: Endomnetrioma_Eutopic_Proliferative_stage4_3

description:
E23_EU
This tissue was eutopic endometrium obtained from endometrioma subject_E23.

value: Proliferative


title: EC09


title: Endomnetrioma_Eutopic_Proliferative_stage4_2

description:
E20_EU
This tissue was eutopic endometrium obtained from endometrioma subject_E20.


title: 11030.fa/NA18507

value: father


title: Endomnetrioma_Ectopic_Proliferative_stage4_1

description:
E17_EC
This tissue was ectopic endometrium obtained from endometrioma subject_E17.


title: EC07

source_name: EC, one year

value: one year


title: EC08


title: 11029.fa/NA18507

value: male


title: 11032.p1/NA18507


title: Old_Silique_rep1

value: tissue


title: Endomnetrioma_Eutopic_Proliferative_stage4_1

description:
E17_EU
This tissue was eutopic endometrium obtained from endometrioma subject_E17.


title: control knockout rep1

city: La Jolla

first: Gene

last: Yeo

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

hyb_protocol: Hybridization cocktails containing ~5.5 ug of fragmented and labeled DNA target were prepared and applied to GeneChip Human Splice Junction arrays. Hybridization was performed for 16 hours using the Fluidics 450 station.

scan_protocol: Arrays were scanned using the Affymetrix 3000 7G scanner and GeneChip Operating Software version 1.4 to produce .CEL intensity files.

data_processing: Data processed using Affymetrix package (Affy Power Tools) apt-probeset-summarize. Iter-plier algorithm used to quantify probesets.

source_name: Embryonic brain

label_protocol: WT Terminal Labeling Kit, Affymetrix

extract_protocol: Trizol extraction of RNA and protein was performed according to the manufacturer’s instructions. In summary, tissues were homogenized in Trizol using a Polytron homogenizer (Company) for 15 sec. Homogenates were then incubated at room temperature for 5min. Chloroform was added to the homogenates (200 l per 1 mL of Trizol) and tubes were shaken vigorously for 15 sec. After incubation at room temperature for 2-10 min, samples were centrifuged at 12,000 g for 15 min at 4oC. The RNA-containing aqueous phase was transferred to fresh tubes and after the addition of glycogen and isopropanol, RNA was precipitated at -20oC overnight. The next day, samples were centrifuged for 10 mins at maximum speed in a microcentrifuge at 4oC. RNA pellets were washed with 75% Ethanol twice, dried at room temperature and reconstituted in DEPC-treated water.

treatment_protocol: 8-10 week old female C57Bl/6 mice were anesthetized with 2.5-3% isofluorane, and a midline incision of approximately 1cm was made on their heads. Using stereotaxic guides, 3 mL of antisense oligonucleotide (ASO) solution targeting Tdp-43 or a control – corresponding to a total of 75 mg or 100 mg ASOs – or saline buffer was injected using a Hamilton syringe directly into their striatum. The incision was closed with sutures and the mice were allowed to recover in their cages. They were monitored for any adverse effects for the next two weeks until they were sacrificed. The striatum and adjacent cortex area were dissected, placed in separate tubes containing 1 mL Trizol (Invitrogen) and were frozen at -80oC until use.

value: embryonic brain

tag: genetic background

tag: genotype

value: control knockout


title: control knockout rep3


title: OsWRKY28 over-expressing rice leaves 48 h after warter treatment replicate 3

city: Tokyo

first: Kazunori

last: Okada

address: 1-1-1, Yayoi, Bunkyo-ku

department: Biotechnology Research Center

institute: The University of Tokyo

description:
OsWRKY28 over-expressing rice leaves treated with water
Biological replicate 3 of 3.

hyb_protocol: Agilent protocol G4140-90040

scan_protocol: Agilent scanner model G2565

data_processing: After data was analyzed by Fearure Extraction software (version 11, Agilent), data normalization was performed using Partek Genomics Suite software (ver. 6.5; Partek software) by quantile normalization method.

organism: Oryza sativa

label_protocol: Low RNA input Linear Amplification/Labeling Kit (Agilent)

growth_protocol: Rice plants were grown in a chamber under a 14-h-light (28℃) and 10-h-dark (24℃) cycle in hydroponic culture.

extract_protocol: RNeasy Plant Mini Kit (Qiagen)

treatment_protocol: WT and OsWRKY28-overexpressing rice plants were infected with M. oryzae strain Ina86-137 or treated with water at the four-leaf stage and then fourth leaves were harvested from three plants for each samples at 48 h after treatments.

tag: genotype/variation

value: OsWRKY28 over-expression

tag: infection

value: control

value: leaf


title: 11033.p1/NA12878

tag: group

value: proband

value: whole blood


title: OsWRKY28 over-expressing rice leaves 48 h after M.Oryzae infection replicate 3

description:
OsWRKY28 over-expressing rice leaves infected with M.Oryzae
Biological replicate 3 of 3.

value: M. oryzae


title: control knockout rep2

tag: age


title: 11029.mo/NA12878

tag: gender

value: female


title: EC04

source_name: EC, adult

value: hippocampal formation

value: adult

tag: region

value: EC


title: EC05


title: Fus/Tls knockout rep2

value: Fus/Tls knockout


title: EC03


title: Wild-type rice leaves 48 h after warter treatment replicate 3

description:
Wild-type rice leaves treated with water
Biological replicate 3 of 3.

value: Wild-type


title: EC06

value: one year


title: Wild-type rice leaves 48 h after M.Oryzae infection replicate 3

description:
Wild-type rice leaves infected with M.Oryzae
Biological replicate 3 of 3.


title: OsWRKY28 over-expressing rice leaves 48 h after M.Oryzae infection replicate 2

description:
OsWRKY28 over-expressing rice leaves infected with M.Oryzae
Biological replicate 2 of 3.


title: EC02


title: Fus/Tls knockout rep1


title: 11028.p1/NA12878

value: male

tag: family status

tag: ndar guid


title: Fus/Tls anti-sense oligo rep3

source_name: Striatum

tag: tissue

value: brain striatum

value: 8-10 weeks

tag: treatment

value: Fus/Tls anti-sense oligo


title: EC01


title: 11029.p1/NA12878

tag: cell line


title: OsWRKY28 over-expressing rice leaves 48 h after warter treatment replicate 2

description:
OsWRKY28 over-expressing rice leaves treated with water
Biological replicate 2 of 3.

value: OsWRKY28 over-expression


title: 11025.p1/NA12878


title: Fus/Tls anti-sense oligo rep1


title: Wild-type rice leaves 48 h after warter treatment replicate 2

description:
Wild-type rice leaves treated with water
Biological replicate 2 of 3.

value: control


title: DG15

source_name: DG, newborn

value: newborn

value: DG


title: Fus/Tls anti-sense oligo rep2


title: 11027.p1/NA12878

value: proband

value: whole blood


title: OsWRKY28 over-expressing rice leaves 48 h after M.Oryzae infection replicate 1

description:
OsWRKY28 over-expressing rice leaves infected with M.Oryzae
Biological replicate 1 of 3.

value: M. oryzae

value: leaf


title: 11024.mo/NA12878

value: female

value: mother


title: 11026.p1/NA12878


title: 11026.fa/NA18507

value: father


title: 11024.p1/NA18507


title: DG14

value: hippocampal formation


title: control anti-sense oligo rep1

value: control anti-sense oligo


title: Wild-type rice leaves 48 h after M.Oryzae infection replicate 2

description:
Wild-type rice leaves infected with M.Oryzae
Biological replicate 2 of 3.

value: Wild-type


title: DG16


title: control anti-sense oligo rep3

value: brain striatum


title: 11024.fa/NA18507

value: male


title: control anti-sense oligo rep2

value: 8-10 weeks


title: Wild-type rice leaves 48 h after M.Oryzae infection replicate 1

description:
Wild-type rice leaves infected with M.Oryzae
Biological replicate 1 of 3.


title: 11026.mo/NA12878


title: DG13


title: DG10

source_name: DG, six months

value: six months


title: Wild-type rice leaves 48 h after warter treatment replicate 1

description:
Wild-type rice leaves treated with water
Biological replicate 1 of 3.

value: control


title: 11023.p1/NA18507


title: DG09


title: DG11


title: DG06

source_name: DG, one year

value: one year


title: DG08

value: DG


title: DG05


title: DG12


title: DG07


title: DG04

source_name: DG, adult

value: adult


title: Mock_6h_rep3

city: Obihiro

first: Ryo

last: Takano

state: Hokkaido

address: Inada-cho

department: National Research Center for Protozoan Diseases

institute: Obihiro University of Agriculture and Veterinary Medicine

description:
Gene expression after 6hr in mock-infected human macrophages.
Replicate 3 of 3.

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent GE hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE 8x60K Microarrays (G4851) for 17 hours at 65 °C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37 °C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned with an Agilent's High-Resolution Microarray Scanner using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green).

data_processing: The scanned images were analyzed with Agilent Feature Extraction Software ver. 10.7.3.1. using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Monocyte-derived macrophages, not infected, 6hpi

label_protocol: Cy3-labeled cRNA probe synthesis was initiated with 50 ng of total RNAs by using the Agilent Low Input Quick Amp Labeling kit, one color (Agilent Technologies).

growth_protocol: Peripheral blood mononuclear cells were independently separated from the buffy coat of healthy donors. Monocytes were purified by adherence and were allowed to differentiate for 14 days in RPMI 1640 medium supplemented with 5 ng/ml of recombinant human GM-CSF and 10% human serum derived from the corresponding blood donors. Cells were incubated at 37 °C in 5% CO2.

extract_protocol: At 6 hpi, the cells were lysed with TRIzol Reagent (Invitrogen) and chloroform-isoamyl alchol (5:1) was added. The cells were then vortexed and centrifuged for 15 min at 12,000 g at 4 °C. The resulting aqueous layer was subjected to RNA extraction by using RNeasy Mini Kit columns (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Human monocyte-derived macrophages were mock-infected, or infected with IDN3006, VN3028IIcl2, or IDN3006/cl2PA at an MOI of 2. The virus inoculum was removed, and the cells were washed three times and then incubated in serum-free RPMI 1640 medium supplemented with 0.3% BSA.

tag: cell type

value: monocyte-derived macrophages

value: mock

tag: time post-infection

value: 6 hrs


title: 11017.p1/NA12878

hyb_protocol: The hybridization protocol was performed per Agilent protocols (http://www.chem.agilent.com/Library/usermanuals/Public/G4410-90020_CGH_ULS_Protocol_v.3.1.pdf) with 10 ug of labelled test sample and 10 ug of labelled reference sample

extract_protocol: unsonicated genomic DNA

value: proband

value: whole blood

value: female


title: 11013.p1/NA12878


title: Mock_6h_rep2

description:
Gene expression after 6hr in mock-infected human macrophages.
Replicate 2 of 3.


title: 11023.fa/NA18507

value: father


title: 11018.p1/NA18507


title: DG03

value: hippocampal formation


title: OsWRKY28 over-expressing rice leaves 48 h after warter treatment replicate 1

description:
OsWRKY28 over-expressing rice leaves treated with water
Biological replicate 1 of 3.

value: OsWRKY28 over-expression

value: leaf


title: IDN3006/cl2PA_6h_rep1

description:
Gene expression after 6hr in IDN3006/cl2PA-infected human macrophages.
Replicate 1 of 3.

source_name: Monocyte-derived macrophages, IDN3006/cl2PA, 6hpi


title: Mock_6h_rep1

description:
Gene expression after 6hr in mock-infected human macrophages.
Replicate 1 of 3.


title: IDN3006/cl2PA_6h_rep2

description:
Gene expression after 6hr in IDN3006/cl2PA-infected human macrophages.
Replicate 2 of 3.


title: DG01


title: CA316

source_name: CA3, newborn

value: newborn


title: DG02


title: IDN3006/cl2PA_6h_rep3

description:
Gene expression after 6hr in IDN3006/cl2PA-infected human macrophages.
Replicate 3 of 3.


title: 11013.mo/NA12878

value: mother


title: CA315


title: VN3028IIcl2_6h_rep3

description:
Gene expression after 6hr in VN3028IIcl2-infected human macrophages.
Replicate 3 of 3.

source_name: Monocyte-derived macrophages, VN3028IIcl2, 6hpi


title: 11013.fa/NA18507

value: male


title: VN3028IIcl2_6h_rep2

description:
Gene expression after 6hr in VN3028IIcl2-infected human macrophages.
Replicate 2 of 3.


title: CA314


title: 11009.mo/NA12878


title: 11012.p1/NA12878


title: 11010.p1/NA18507


title: 11023.mo/NA12878


title: 11011.p1/NA12878


title: IDN3006_6h_rep2

description:
Gene expression after 6hr in IDN3006-infected human macrophages.
Replicate 2 of 3.

source_name: Monocyte-derived macrophages, IDN3006, 6hpi


title: CA313


title: Bacteroides fragilis_mid log phase_MM-HMO_rep2

city: Davis

first: Bart

middle: C.

last: Weimer

address: 1 Shields Ave

department: Population Health and Reproduction

institute: University of California, Davis

description: Sample name: BFMMHMO_2

hyb_protocol: Affymetrix

scan_protocol: Affymetrix

data_processing: The raw data were RMA-MS normalized using R-2.9.1. and log2 transformed, excluding other species present on chip.

label: Biotin

organism: Bacteroides fragilis NCTC 9343

label_protocol: Enzo Biochemicals Bioarray terminal labeling kit

growth_protocol: 2 ml minimal medium HMO (1.5%) culture of  B.fragilis NCTC9343; grown to mid-log phase; replicate 2 of 2

extract_protocol: Qiagen Rneasy mini column extraction, Ambion DNA free treatment

tag: strain


title: 11009.fa/NA18507

city: Seattle

first: Megan

last: Dennis

address: 3720 15th Ave NE

institute: University of Washington

scan_protocol: The scan protocol was performed using the Agilent Scanner per Agilent protocols (http://www.chem.agilent.com/Library/usermanuals/Public/G4410-90020_CGH_ULS_Protocol_v.3.1.pdf).

label_protocol: 250 ng of genomic DNA (unsonicated) was labeled by Klenow using random priming with Cy3/Cy5 nonamers (for test and reference samples, respectively) using Nimblegen labelling kit but with the following changes: reagents were scaled to the smaller amount of input DNA and with DNA labeling occurring overnight.


title: VN3028IIcl2_6h_rep1

description:
Gene expression after 6hr in VN3028IIcl2-infected human macrophages.
Replicate 1 of 3.


title: CA312

source_name: CA3, six months

value: six months


title: Bacteroides fragilis_mid log phase_MM-HMO_rep1

description: Sample name: BFMMHMO_1

growth_protocol: 2 ml minimal medium HMO (1.5%) culture of  B.fragilis NCTC9343; grown to mid-log phase; replicate 1 of 2


title: CA311


title: Bacteroides fragilis_mid log phase_MM-Glucose_rep2

description: Sample name: BFMMGlu_2

growth_protocol: 2 ml minimal medium glucose (0.5%) culture of  B.fragilis NCTC9343; grown to mid-log phase; replicate 2 of 2


title: CA310


title: IDN3006_6h_rep3

description:
Gene expression after 6hr in IDN3006-infected human macrophages.
Replicate 3 of 3.


title: IDN3006_6h_rep1

description:
Gene expression after 6hr in IDN3006-infected human macrophages.
Replicate 1 of 3.


title: Bacteroides fragilis_mid log phase_MM-Glucose_rep1

description: Sample name: BFMMGlu_1

growth_protocol: 2 ml minimal medium glucose (0.5%) culture of  B.fragilis NCTC9343; grown to mid-log phase; replicate 1 of 2


title: CA308

source_name: CA3, one year

value: one year


title: 11006.mo/NA12878

source_name: whole blood DNA


title: 11006.fa/NA18507

source_name: lymphoblast cell line DNA


title: CA306


title: 11004.p1/NA18507


title: CA305


title: 11008.p1/NA18507


title: CA307


title: CA309


title: CA303

source_name: CA3, adult


title: 11014.p1/NA12878


title: CA301


title: CA114

source_name: CA1, newborn


title: CA113


title: CA302


title: CA111

source_name: CA1, six months


title: CA115


title: CA109


title: CA110


title: CA107

source_name: CA1, one year


title: 11009.p1/NA12878


title: Cell line 7

city: Toon

first: Koh-ichi

last: Nakashiro

address: 454 Shitsukawa

institute: Ehime University Graduate School of Medicine

hyb_protocol: Ten mg of labelled cRNA was hybridized to each pre-hybed microarray at 55℃ for 16 hours.

scan_protocol: After Chemiluminescence detection using Applied Biosystems Chemiluminescence Detection Kit, images were collected by the AB1700 Chemiluminescent Microarray Aanalyzer.

data_processing: The robust multichip average (RMA) method was used background correction and normalization.

source_name: oral squamous cell carcinoma cell lines

label_protocol: Digoxigenin-UTP-labelled cRNA was generated and amplified from 1 mg of total RNA using Applied Biosystems Chemiluminescent RT-IVT Labelling Kit.

extract_protocol: After fresh tissues were homogenized by TissueLyser, total RNA was extracted by ISOGEN.

value: oral squamous cell carcinoma


title: CA304

value: adult


title: 11003.p1/NA12878


title: CA104

source_name: CA1, adult


title: CA112


title: 11002.mo/NA12878


title: Cell line 8


title: 11001.p1/NA18507


title: 11002.fa/NA18507


title: CA116


title: Cell line 5

description: KB

value: KB


title: Kas_-Fe_48h_Roots_r3

city: Columbia

first: Samuel

middle: Alonzo

last: McInturf

state: Missouri

address: 1201 Rollins Street

department: Plant Sciences

institute: University of Missouri - Columbia

description: gene expression data from Kas roots on minus iron media for 48h

hyb_protocol: Done according the manufacturer’s protocol

data_processing: R/Bioconductor.  Normalized with rma

source_name: Kas roots on minus iron media for 48h

growth_protocol: Seeds of Arabidopsis thaliana ecotypes Kas-1 and Tsu-1 were imbibed in 0.1% agar at 4°C for 72 h, planted onto rockwool, and grown on hydroponic solution. Lighting was provided at a photoperiod of 16 h of 150 µmol m-2 s-1  4,100K fluorescent light. The ecotypes used are Kas-1 and Tsu-1 for our study, the citation of Schuler (2011) used Columbia-0.

extract_protocol: Total RNA was isolated from whole rosettes using the RNeasy Plant Kit (Qiagen), and quality was assessed using the Agilent Bioanalyzer 2100.

treatment_protocol: 24 d old plants were transferred to treatments of +Fe (50 µM Fe(III)-EDDHA) or -Fe for 24 or 48 h.

value: Kas

tag: time

tag: iron

value: Minus


title: Cell line 6


title: CA106


title: Kas_-Fe_24h_Roots_r2

description: gene expression data from Kas roots on minus iron media for 24h

scan_protocol: Done according the manufacturer’s protocol

source_name: Kas roots on minus iron media for 24h

tag: genotype


title: CA108


title: CA101


title: Cell line 2


title: Cell line 4


title: Cell line 3


title: Kas_-Fe_48h_Roots_r2

label_protocol: Done according the manufacturer’s protocol


title: CA102


title: Kas_-Fe_24h_Roots_r1


title: CA103


title: 11002.p1/NA12878

value: proband


title: 11006.p1/NA12878

value: whole blood


title: Cell line 1

description: HaCaT

source_name: non-neoplastic keratinocyte

value: HaCaT

value: non-neoplastic keratinocyte


title: 11022.p1/NA12878

value: female


title: Kas_-Fe_24h_Roots_r3


title: Kas_+Fe_24h_Roots_r2

description: gene expression data from Kas roots on complete media for 24h

source_name: Kas roots on complete media for 24h

value: Plus


title: TF1_controlsiRNA_3

city: Pamplona

first: Maria

middle: D

last: Odero

address: Pio XII, 55

country: Spain

institute: University of Navarra

description: Replicate 3 of 3.

hyb_protocol: Following fragmentation, 15 microg of cRNA were hybridized to the Affymetrix HG-U133Plus2 chip according to the protocols provided by the manufacturer.

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

data_processing: RMA normalization.

source_name: Myeloid cell line, control siRNA

label_protocol: The cDNA was prepared from 2 microg total RNA using the One –Cycle cDNA Synthesis kit from Affymetrix. This cDNA was used for synthesizing the cRNA using the IVT labeling kit (Affymetrix). The synthesized cRNA was purified with the GeneChip Sample Cleanup Module (Affymetrix).

growth_protocol: Cells were cultured in RPMI-1640 medium supplemented with 10% FBS in the case of HTB-58 cells or with 20% FBS and 5-10 ng/ml recombinant GM-CSF in the case of TF-1.

extract_protocol: The cells were harvested with TRIzol Reagent (Invitrogen)  and the RNA was extracted according to the manufacturer's instructions. As a last step of the extraction procedure, the RNA was purified with the RNeasy Mini-kit (Qiagen, Hilden, Germany).

treatment_protocol: Cell lines were transfected with 1 μg/μl (75 μM) of chemically synthesized anti-EVI1 siRNA or control siRNA.

value: 35 years

tag: disease

value: erythroleukemia (AML M6)

tag: sirna

value: control


title: Kas_+Fe_24h_Roots_r3


title: TF1_controlsiRNA_2

description: Replicate 2 of 3.

value: male


title: CA105

value: hippocampal formation


title: Kas_-Fe_48h_Roots_r1


title: TF1_controlsiRNA_1

description: Replicate 1 of 3.


title: KOCD8aDC

city: St. Louis

first: Kenneth

middle: M

last: Murphy

address: 660 S. Euclid

department: Pathology and Immunology

institute: Wustl/HHMI

hyb_protocol: Hybed onto Mouse 430 2.0 (Affymetrix)

scan_protocol: Standard Affymetrix protocol

data_processing: Data was analyzed using Arraystar software (DNASTAR) with Quantile RMA normalization

label_protocol: 3' IVT Express Kit (Affymetrix)

growth_protocol: Mice were analyzed at steady-state. Cells were harvested from spleens following digestion with Collagenase B (Roche) and Dnase I (Sigma-Aldrich). Dendritic cells were then positively selected with CD11c MicroBeads (Miltenyi). All enriched samples were sorted to >90% purity on BD FACSAria II.

extract_protocol: Total RNA was extracted with NucleoSpin RNA XS kit (Macherey-Nagel) according to manufacturer's instructions.

tag: genotype/variation

value: CD8alpha dendritic cells


title: WTCD8aDC_IL12

value: wild-type


title: AscarisSuum_MaleTestis_AvgAcross2rep

first: Makedonka

last: Mitreva

address: 4444 Forest Park Ave

institute: The Genome Institute

hyb_protocol: Each cDNA sample was paired and balanced with the common reference, and applied to a single plex of the custom array. Hybridization was carried out at 65 ºC for 20 hours. Washing procedures were carried out according to the Agilent protocols.

scan_protocol: Slides were scanned with an Axon 4000B scanner for the detection of fluorescent signals. Laser power was kept constant and PMT was varied for each slide to ensure optimal signal intensities while maintaining saturation below 0.1%. Images were processed using GenePix v6.1 (Axon) to generate gpr files containing raw intensities, gene information, etc.

data_processing:
Scanned GPR files were first inspected for quality control (QC) using built-in QC tools from the Bioconductor package of R. Inspected microarrays were then analyzed using LIMMA of Bioconductor. After background correction and normalization, gene expression was detected through a linear model fitting which considers both the dye effect and the variation among replications. Differentially expressed genes were defined based on the F test of the linear model fitting. To control the problem of multiple tests, we used false discovery rate (FDR) of 0.01 as a cutoff. The resulting differentially expressed gene set with corrected F-test and FDR was exported for further analysis.
Gene over- and under-expression was determined using the “2 fold” rule based on the linear modeling fitting results. For each gene, if the fitted effect coefficient for one tissue was more than 1 (log-ratio compared with the signal of pooled references), it was recorded as relatively over-expressed in this tissue; if the coefficient was less than -1, it was recorded as relatively under-expressed in that tissue. By this way, each tissue was assessed for its complement of over or under- expressed genes. We further examined the functions of predicted proteins encoded by the genes that were exclusively over-expressed in a specific tissue by GO term enrichment analysis using the Func program.

label: Alexa Fluor 555 succinimidyl ester, Alexa Fluor 647 succinimidyl ester

organism: Ascaris suum

source_name: Tissue from worm Testis

label_protocol: Fluorescence labeled cDNA was prepared from ~10 ug of total RNA using Superscript Plus Indirect labeling system (Invitrogen), with slight modifications. In brief, The anchored oligo(dT)20 primer is a mixture of 12 primers, each consisting of a string of 20 deoxythymidylic acid (dT) residues followed by two additional nucleotides represented by VN, where V is dA, dC, or dG, and N is dA, dC, dG, or dT. The VN “anchor” allows the primer to anneal preferentially at the 5´ end of the poly(A) tail of mRNA, ensuring high specificity, high yields, and longer lengths of cDNA. Two aminoallyl-modified nucleotides were used together with other dNTPs in reverse transcription, for incorporation into the cDNA. After RNA hydrolysis, neutralization, and column purification, the amino-modified cDNA is coupled with a monoreactive, N-hydroxysuccinimide (NHS)-ester fluorescent dye, either Alexa Fluor 555 succinimidyl ester or Alexa Fluor 647 succinimidyl ester. The Alexa dyes provide higher correlation coefficients, signal intensities, and single-to-background ratios. After the final column purification, the fluorescence labeled single-strand cDNA samples are quantified via spectrophotometer.

extract_protocol: Adult worms were collected from infected pigs, and fresh tissues were dissected and snap frozen in liquid nitrogen for subsequent storage at -80 °C. Total RNA of each individual tissue was prepared using TRIzol (Invitrogen) according to the manufacturer’s instruction and treated with Ambion Turbo DNase (Ambion/Applied Biosystems, Austin, TX).  RNA quality and quantity were assessed by Agilent 2100 Bioanalyzer (Agilent Technologies, Cedar Creek, Texas), and the yield determined using the NanoDrop ND-1000 UV-VIS spectrophotometer v.3.2.1 (NanoDrop Technologies, Wilmington, DE).

tag: species

value: Ascaris suum

value: Testis

value: Male

source_name: Pooled worm tissue

value: Pooled tissues

value: Pooled genders


title: TF1_antiEvi1siRNA_1

description: Replicate 1 of 3.

source_name: Myeloid cell line, anti-Evi1 siRNA

tag: gender

tag: age


title: Kas_+Fe_24h_Roots_r1

value: Kas


title: Tsu_-Fe_48h_Roots_r1

description: gene expression data from Tsu roots on minus iron media for 48h

source_name: Tsu roots on minus iron media for 48h

value: Tsu

value: Minus


title: Tsu_-Fe_48h_Roots_r2


title: Tsu_-Fe_24h_Roots_r3

description: gene expression data from Tsu roots on minus iron media for 24h

source_name: Tsu roots on minus iron media for 24h


title: 11000.p1/NA12878

source_name: whole blood DNA

tag: group

tag: family status

value: proband

value: whole blood

source_name: lymphoblast cell line DNA

value: female


title: TF1_antiEvi1siRNA_2

description: Replicate 2 of 3.

value: 35 years

value: erythroleukemia (AML M6)


title: TF1_antiEvi1siRNA_3

description: Replicate 3 of 3.

value: male


title: AscarisSuum_MaleSeminalVesicle_AvgAcross2rep

source_name: Seminal vesicle tissue from the worm

tag: tissue

value: Seminal vesicle


title: Tsu_-Fe_24h_Roots_r2


title: AscarisSuum_MaleIntestine_AvgAcross3rep

source_name: Tissue from worm intestine

value: Intestine


title: HTB58_controlsiRNA_2

description: Replicate 2 of 3.

source_name: Adherent lung cancer cell line, control siRNA

value: 65 years

tag: race

value: Caucasian

value: squamous cell carcinoma of the lung

value: control


title: HTB58_controlsiRNA_1

description: Replicate 1 of 3.

tag: cell line


title: HTB58_controlsiRNA_3

description: Replicate 3 of 3.


title: Tsu_-Fe_48h_Roots_r3


title: KOCD8aDC_IL12

tag: cell type

value: CD8alpha dendritic cells


title: Tsu_-Fe_24h_Roots_r1


title: WTCD8aDC

value: wild-type


title: AscarisSuum_FemalePharynx_AvgAcross3rep

source_name: Tissue from the pharynx of the worm

value: Ascaris suum

value: Pharynx

value: Female

value: Pooled tissues

value: Pooled genders


title: AscarisSuum_MalePharynx_AvgAcross3rep

value: Male


title: HTB58_antiEvi1siRNA_3

description: Replicate 3 of 3.

source_name: Adherent lung cancer cell line, anti-Evi1 siRNA


title: AscarisSuum_FemaleOvary_AvgAcross2rep

source_name: Tissue from the ovary of the worm

value: Ovary


title: AscarisSuum_MaleHead_AvgAcross3rep

source_name: Tissue from the head of the worm

value: Head


title: Tsu_+Fe_24h_Roots_r3

description: gene expression data from Tsu roots on complete media for 24h

source_name: Tsu roots on complete media for 24h

value: Tsu

value: Plus


title: Tsu_+Fe_24h_Roots_r2


title: HTB58_antiEvi1siRNA_2

description: Replicate 2 of 3.

value: male


title: AscarisSuum_FemaleIntestine_AvgAcross3rep

value: Intestine


title: AscarisSuum_FemaleHead_AvgAcross3rep


title: Seedlings_cbp2080_replicate1

status: Public on Sep 29 2012

city: No.12 Zhongguancun South Street, Haidian

first: Jun

last: Liu

state: Beijing

address: 1230 York Avenue

department: Chinese Academy of Agricultural Sciences

country: China

institute: Institute of Crop Science

description: Expression profiling of lincRNA in cbp20,80 double mutant

hyb_protocol: 1.5 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to ATH lincRNA v1 array for 17 hours at 65Â°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 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 8x15k array slides.

data_processing: Raw data of processed signal intensities are obtained by analysis using Feature Extraction Software (Agilent) with default parameters. Standard QC analysis, background normalization and quantile normalization were performed using GeneSpring GX Software (Agilent) with default parameters. We used eBays ANOVA to estimate possibility of differential expression of lincRNA between mutant and WT.

label_protocol: We performed RNA labeling, hybridization and scaning using protocols according to the Agilent's instructions. Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent).

growth_protocol: Seedling samples were collected from 2-week-old WT(Col-0) , se-2 and cbp20/cbp80 plants grown on solid MS medium under long-day conditions.

extract_protocol: Total RNA was extracted and treated with DNase I using RNeasy Plant mini kit (Qiagen).

value: 2-week-old Seedlings


title: Seedlings_cbp2080_replicate3


title: Seedlings_se_replicate2

description: Expression profiling of lincRNA in se-2