title: TB mouse liver, ZT 4, replicate 2

description:
TB 4-7
Gene expression data from mouse liver at indicated ZT.

source_name: TB mouse liver, ZT 4

value: ZT 4


title: FAIC_2

status: Public on Apr 01 2016

type: RNA

city: Pamplona

first: Jose

last: Hermida

address: Pio XII, 55

country: Spain

institute: CIMA

description: Gene expression data from AF patient with stroke

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: Data were normalized with Bioconductor software using RMA algorithm.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Peripheral blood cells of a patient with AF and stroke

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 synthezising the cRNA using the IVT labeling kit (Affymetrix). The synthezised cRNA was purified with the GeneChip Sample Cleanup Module (Affymetrix).

growth_protocol: It does not applied

extract_protocol: Whole blood (2.5 mL) was collected from each subject into a PAXgene tube (BD). PAXgene tubes were frozen at -80ºC after 2 hours at room temperature. Total RNA was isolated according to the manufacturer´s protocol using the PAXgene blood RNA kit (Pre-AnalytiX).

treatment_protocol: Whole blood from stroke (n=8) and non-stroke (n=8) atrial fibrillation patients

tag: cell type

value: peripheral blood cells


title: TB mouse liver, ZT 4, replicate 1

city: Irvine

first: Paolo

last: Sassone-Corsi

state: CALIFORNIA

address: Sprague Hall

country: USA

institute: University of California, Irvine

description:
TB 4-6
Gene expression data from mouse liver at indicated ZT.

hyb_protocol: 3.3ug of the labeled, fragmented single-stranded cDNA is hybridized at 45oC with rotation for 17 hours (Affymetrix GeneChip Hybridization Oven 640) to probe sets present on an Affymetrix Mouse GeneChip 2.0 ST array.

scan_protocol: Arrays were scanned using GeneChip Scanner 3000 7G and Command Console Software v. 3.2.3 to produce .CEL intensity files.

data_processing:
The probe cell intensity files (*.CEL) were analyzed in Affymetrix Expression Console software v1.1.1 using the PLIER algorithm to generate probe level summarization files (*.CHP).
The settings used were algorithm-PLIER v2.0; quantification scale-Linear; quantification type-signal and detection p-value; background-PM-GCBG; normalization method-sketch-quantile.

label: Biotin

organism: Mus musculus

label_protocol: Labeling using a recombinant terminal deoxynucleotidyl transferase (TdT) and an Affymetrix proprietary DNA labeling reagent was done to covalently link to biotin.

growth_protocol: Animals were housed in 12 hour Light/Dark conditions and harvested over the circadian cycle.

extract_protocol: Total RNA was prepared by Trizol extraction, and RNA was cleaned-up prior to array analysis with Qiagen RNeasy clean-up kit.

treatment_protocol: WT and TB mice were harvested every 4 hours over the circadian cycle and livers were flash frozen in liquid nitrogen after sacrifice.

tag: strain/background

tag: genotype/variation

tag: disease status

value: lung adenocarcinoma

tag: tissue

value: liver

tag: circadian cycle time point


title: T1D-2-PH-REPLICATE1

city: Cambridge

first: Jeffrey

middle: Robert

last: Millman

state: Massachusetts

address: 7 Divinity Ave

department: HSCRB

institute: Harvard University

hyb_protocol: 750 ng cRNA from each sample was hybridized to Human HT-12 Expression BeadChips (Illumina). The Whole- Genome Expression Direct Hybridization kit (Illumina) was used according to manufacturer's instructions.

scan_protocol: Illumina Beadstation 500

data_processing: GenomeStudio (Illumina, V2011.1). Raw data were adjusted by background subtraction and quantile normalization. The p- values for differences between mean signals were calculated in GenomeStudio by t-test and corrected for multiple hypotheses testing by the Benjamini-Hochberg method in combination with the Illumina custom false discovery rate (FDR) model.

label_protocol: The Illumina TotalPrep RNA Amplification kit (Ambion) was using according to manufacturer's instructions.

growth_protocol: hiPS cells were grown in suspension in mTesr prior to differentiation.

extract_protocol: MARIS was used to extract total RNA after flow cytometry sorting. Detailed protocol is described in the paper: Generation of functional human pancreatic β cells in vitro

treatment_protocol: Differentiation methods are available in the paper: Generation of functional human pancreatic β cells in vitro

tag: disease status of patient source

value: Type 1 diabetic

value: PH INS+ cells


title: FAIC_1


title: T1D-1-PH-REPLICATE1


title: WT mouse liver, ZT 20, replicate 3

description:
WT 20-5
Gene expression data from mouse liver at indicated ZT.

source_name: WT mouse liver, ZT 20

value: WT

value: ZT 20


title: ND-3-SC-B-REPLICATE1

value: non-diabetic

value: stage 6 Nkx6.1+/Ins+ cells


title: TB mouse liver, ZT 0, replicate 2

description:
TB 0-7
Gene expression data from mouse liver at indicated ZT.

source_name: TB mouse liver, ZT 0

value: ZT 0


title: TB mouse liver, ZT 4, replicate 3

description:
TB 4-8
Gene expression data from mouse liver at indicated ZT.


title: TB mouse liver, ZT 0, replicate 1

description:
TB 0-6
Gene expression data from mouse liver at indicated ZT.


title: ND-2-SC-B-REPLICATE2


title: T1D-1-SC-B-REPLICATE1


title: WT mouse liver, ZT 16, replicate 1

description:
WT 16-3
Gene expression data from mouse liver at indicated ZT.

source_name: WT mouse liver, ZT 16

value: ZT 16


title: WT mouse liver, ZT 12, replicate 3

description:
WT 12-5
Gene expression data from mouse liver at indicated ZT.

source_name: WT mouse liver, ZT 12

value: ZT 12


title: WT mouse liver, ZT 16, replicate 3

description:
WT 16-5
Gene expression data from mouse liver at indicated ZT.


title: ND-3-PH-REPLICATE2


title: T1D-1-PH-REPLICATE2


title: ND-3-PH-REPLICATE1


title: T1D-1-SC-B-REPLICATE2


title: ND-2-SC-B-REPLICATE3


title: WT mouse liver, ZT 16, replicate 2

description:
WT 16-4
Gene expression data from mouse liver at indicated ZT.


title: TB mouse liver, ZT 0, replicate 3

description:
TB 0-8
Gene expression data from mouse liver at indicated ZT.


title: WT mouse liver, ZT 20, replicate 1

description:
WT 20-3
Gene expression data from mouse liver at indicated ZT.


title: WT mouse liver, ZT 20, replicate 2

description:
WT 20-4
Gene expression data from mouse liver at indicated ZT.


title: ND-2-PH-REPLICATE2


title: ND-2-SC-B-REPLICATE1


title: Leaf_8 day_GFAS_vandana

city: Kharagpur

first: ALPGE

last: IITKGP

state: West Bengal

address: Formerly BREF Biotech

department: Advanced Technology Development Centre

country: India

institute: Indian Institute of Technology, Kharagpur

description:
Gene expression after 8 day of stress
Vand_GF_AS_Y

hyb_protocol: 1650 ng of labeled cRNA were hybridized on the array (AMADID 15241) using the Gene Expression Hybridization kit (Part Number 5190-0404; Agilent) in Sure hybridization Chambers (Agilent) at 65º C for 16 hours. Hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327).  The hybridized, washed microarray slides were then scanned on a G2505C scanner (Agilent Technologies)

scan_protocol: Scannedusing  Agilent Technologies G2505C scanner

data_processing: Images were quantified using Feature Extraction Software ( Agilent). Feature extracted raw data was analyzed using GeneSpring GX Version  software from Agilent. Normalization of the data was done in GeneSpring GX using the 75th percentile shift

organism: Oryza sativa

source_name: leaf_after 8 day of stress

label_protocol: The samples were labeled using Agilent Quick Amp Kit (Part number: 5190-0424). 500ng of total RNA was reverse transcribed using oligodT primer tagged to T7 promoter sequence. cDNA thus obtained was converted to double stranded cDNA in the same reaction. Further the cDNA was converted to cRNA in the in-vitro transcription step using T7 RNA polymerase enzyme and Cy3 dye was added into the reaction mix. During cRNA synthesis Cy3 dye was incorporated into the newly synthesized strands. cRNA obtained was cleaned up using Qiagen RNeasy columns(Qiagen, Cat No: 74106). Concentration and amount of dye incorporated was determined using Nanodrop. Samples that pass the QC for specific activity were taken for hybridization.

extract_protocol: RNA extraction was done by using protocol of QIAGEN RNeasy® Plant Mini Kit

treatment_protocol: Rice leaf samples were collected from two different stages of rice viz. Vegetative and Grainfilling, first sample collection is before stress (0 day), second sample collection after soil water stress treatment of 8 days and third sample collection after recovery of 2 days.

tag: variety

value: Vandana

tag: phenotype

value: tolerant under SWS condition

tag: developmental stage

value: Grainfilling

tag: time point

value: After Stress (AS; 8 days of soil water stress)

value: leaf


title: WT mouse liver, ZT 12, replicate 2

description:
WT 12-4
Gene expression data from mouse liver at indicated ZT.


title: Leaf_2 day_GFAR_vandana

description:
Gene expression after 2 day of recovery
Vand_GF_AR_Z

source_name: leaf_after 2 day of recovery

value: After Recovery (AR; recovery of 2 days)


title: WT mouse liver, ZT 8, replicate 3

description:
WT 8-3
Gene expression data from mouse liver at indicated ZT.

source_name: WT mouse liver, ZT 8

value: ZT 8


title: WT mouse liver, ZT 8, replicate 2

description:
WT 8-2
Gene expression data from mouse liver at indicated ZT.

value: liver


title: WT mouse liver, ZT 4, replicate 3

description:
WT 4-3
Gene expression data from mouse liver at indicated ZT.

source_name: WT mouse liver, ZT 4

value: ZT 4


title: WT mouse liver, ZT 4, replicate 2

description:
WT 4-2
Gene expression data from mouse liver at indicated ZT.


title: Leaf_8 day_VAS_vandana

description:
Gene expression after 8 day of stress
Vand_Veg_AS_U

value: Vegetative


title: WT mouse liver, ZT 12, replicate 1

description:
WT 12-3
Gene expression data from mouse liver at indicated ZT.

value: WT


title: ND-2-PH-REPLICATE1

value: PH INS+ cells


title: Leaf_0 day_VBS_vandana

description:
Gene expression after 0 day of stress
Vand_Veg_BS_R

source_name: leaf_after 0 day of stress

value: Before Stress (BS; 0 day)


title: Leaf_2 day_VAR_vandana

description:
Gene expression after 2 day of recovery
Vand_Veg_AR_Q


title: WT mouse liver, ZT 8, replicate 1

description:
WT 8-1
Gene expression data from mouse liver at indicated ZT.


title: Leaf_2 day_VAR_IR20

description:
Gene expression after 2 day of recovery
IR20_Veg_AR_T

value: susceptible under SWS condition


title: WT mouse liver, ZT 0, replicate 3

description:
WT 0-3
Gene expression data from mouse liver at indicated ZT.

source_name: WT mouse liver, ZT 0

value: ZT 0


title: Lame073 Array4 Data

city: Québec City

first: Marc-André

last: Sirard

state: Quebec

address: Offfice 2732, 2440 Hochelaga Blvd.

department: Sciences Animales

country: Canada

institute: Université Laval

description:
Biological replicats 3 of 3. Cumulus cells at 44 hours of coasting compare 20 hours of coasting.
Lame073 Array4 Data

hyb_protocol: The hybridization of microarray slides 4x44K printed with oligonucleotides by Agilent for all EmbryoGENE related projects using the expression array protocol.

scan_protocol: Scan on a PowerScanner (Tecan) using the autogain function. Images were quantified using ArrayPro version 6.3 (MediaCybernetics)

data_processing: Background subtracted, Loess and Quantile normalized data obtained from log2 of processed Red signal/processed Green signal. Flexarray software used.

organism: Bos taurus

label_protocol: The labelling aRNA was done using  the Universal Linkage System (ULS) by Kreatech for Gene Expression studies using microarray slides from Agilent. ULS is a non-enzymatic protocol that allows direct labeling of unmodified, amplified RNA. ULS will react with unmodified, amplified RNA and label it by formation of a coordinative bond on the N7 position of guanine. Fluorophore Cy3 and Cy5 are linked via a spacer to the ULS molecule.

growth_protocol: Cumulus are separated from oocyte with vortexing. Rince 3 times in sterile PBS, centrifuge at 4000 rpm for 4 minutes.  Snap freeze in liquid nitrogen and store at -80°C.

extract_protocol:
Total RNA extraction using the PicoPure RNA Isolation Kit from Molecular Devices. The PicoPure RNA Isolation Kit enables to recover total cellular RNA from pico-scale samples. Researchers can obtain high recoveries of total cellular RNA from as little as a single cell to samples with up to 100 ug of RNA.
Total RNA was amplified using the RiboAmp HSPlus RNA Amplification kit (Life Technologies) for 2 rounds according to the recommendations. aRNA was quantify using a Nanodrop (ThermoFisher).

treatment_protocol: Each animal (6 commercial milking cycling Bos taurus Holstein cows, 4 years old on average, 3.04+/-0.2 years old on average at calving) was exposed in a randomized scheme to the 4 conditions with at least one complete regular sexual cycle between 2 treatments and served as its own control. Each animal was treated during luteal phase to prevent spontaneous ovulation. Hormonal synchronisation was not performed; FSH application and OPU were done using natural di-estrus. We performed P4 serum assays showing no significant differences between coasting durations. The P4 level permitted to determine that there was a corpus luteum. We performed E2 serum assays; there was no significant difference between traitments in term of E2/P4. We could indirectly confirm that LH level was basal. The mean duration between calving and OPUs is 271.8+/-28.9 days. There isn’t correlation between order of OPUs and efficiency; there aren’t significant differences between cows in term of duration between 2 OPUs. There aren’t correlations between blastocyst rate and duration between calving and OPUs, or between coasting duration and duration between calving and OPUs, or between the efficiency to collect COCs and the duration between calving and OPUs. The efficiency to collect COCs (76% on average) is not significantly different from the beginning to the end of the protocol. There isn’t correlation between coasting duration and efficiency. There is no significant difference between cows in term of duration between calving and OPUs. The milk production mean was 8630.17 L +/-  771.1. The energy balance of the cows was positive. The cows were part of the same herd. The dominant follicle was aspirated 36 hours before administration of 229 hormones. Cows were  stimulated for 3 days with FSH (6 X 40 mg NIH Folltropin-V, Bioniche Animal Health, Belleville, ON,  Canada, given at 12-hour intervals), followed by a coasting (no FSH) period of four different durations (20, 44, 68, or 92 hours). Using transvaginal ultrasonography, follicular diameters were measured and cumulus-oocyte complexes (COCs) were collected by transvaginal puncture (PTV), under epidural, with  a 18G needle and COOK aspiration unit (COOK Medical, Bloomington, IN). COCs and granulosa cells were collected in warm HEPES-buffered Tyrode’s medium (TLH) containing Hepalean (10 UI/ml) and transferred to lab for in vitro maturation (half of the COCs) or treated (oocytes, cumulus, granulosa cells) for further studies.

value: cumulus cells

tag: follicular size

tag: time

value: 44 hours

value: 20 hours


title: WT mouse liver, ZT 4, replicate 1

description:
WT 4-1
Gene expression data from mouse liver at indicated ZT.


title: Leaf_0 day_VBS_IR20

description:
Gene expression after 0 day of stress
IR20_Veg_BS_G


title: Leaf_8 day_GFAS_N22

description: Gene expression after 8 day of stress

source_name: leaf

extract_protocol: RNA extraction was done by using protocol of PowerLyzer™ UltraClean® Plant RNA Isolation Kit

treatment_protocol: Rice leaf sample were collected from two different stages of rice viz. Vegetative and Grainfilling, first sample collection is before stress (0 day), second sample collection after soil moisture stress treatment of 8 days and third sample collection after recovery of 2 days.

value: cultivar

tag: collection time point

value: 8 day of stress


title: Lame073 Array2 Data

description:
Biological replicats 1 of 3. Cumulus cells at 44 hours of coasting compare 20 hours of coasting.
Lame073 Array2 Data


title: Leaf_0 day_GFBS_vandana

description:
Gene expression after 0 day of stress
Vand_GF_BS_X

value: Vandana

value: tolerant under SWS condition

value: Grainfilling


title: Lame073 Array3 Data

description:
Biological replicats 2 of 3. Cumulus cells at 44 hours of coasting compare 20 hours of coasting.
Lame073 Array3 Data


title: WT mouse liver, ZT 0, replicate 1

description:
WT 0-1
Gene expression data from mouse liver at indicated ZT.


title: Leaf_8 day_VAS_IR20

description:
Gene expression after 8 day of stress
IR20_Veg_AS_S

value: After Stress (AS; 8 days of soil water stress)

value: leaf


title: Lame073 Array1 Data

description:
Biological replicats 3 of 3. Cumulus cells at 68 hours of coasting compare 20 hours of coasting.
Lame073 Array1 Data

value: 68 hours


title: Leaf_8 day_GFAS_IR20

description:
Gene expression after 8 day of stress
IR20_GF_AS_I


title: WT mouse liver, ZT 0, replicate 2

description:
WT 0-2
Gene expression data from mouse liver at indicated ZT.

value: liver


title: Leaf_0 day_GFBS_N22

description: Gene expression after 0 day of stress

value: 0 day of stress


title: Lame072 Array1 Data

description:
Biological replicats 3 of 3. Cumulus cells at 20 hours of coasting compare 68 hours of coasting.
Lame072 Array1 Data


title: Leaf_0 day_GFBS_IR20

description:
Gene expression after 0 day of stress
IR20_GF_BS_H


title: Lame072 Array3 Data

description:
Biological replicats 2 of 3. Cumulus cells at 20 hours of coasting compare 44 hours of coasting.
Lame072 Array3 Data


title: Leaf_2 day_GFAR_rufipogan

description: Gene expression after 2 day of recovery

tag: genotype

value: rufipogan

value: wild

value: 2 day of recovery


title: Leaf_8 day_GFAS_rufipogan

description: Gene expression after 8 day of stress


title: Lame072 Array4 Data

description:
Biological replicats 3 of 3. Cumulus cells at 20 hours of coasting compare 44 hours of coasting.
Lame072 Array4 Data


title: Leaf_8 day_VAS_rufipogan

description: Gene expression after 8 day of stress

value: Vegetative


title: Lame071 Array4 Data

description:
Biological replicats 2 of 3. Cumulus cells at 20 hours of coasting compare 68 hours of coasting.
Lame071 Array4 Data

value: cumulus cells


title: Leaf_2 day_GFAR_IR20

description:
Gene expression after 2 day of recovery
IR20_GF_AR_J

value: susceptible under SWS condition

value: After Recovery (AR; recovery of 2 days)


title: Lame071 Array2 Data

description:
Biological replicats 1 of 3. Cumulus cells at 20 hours of coasting compare 68 hours of coasting.
Lame071 Array2 Data

value: 20 hours


title: Lame072 Array2 Data

description:
Biological replicats 1 of 3. Cumulus cells at 20 hours of coasting compare 44 hours of coasting.
Lame072 Array2 Data

value: 44 hours


title: Lame071 Array1 Data

description:
Biological replicats 1 of 3. Cumulus cells at 68 hours of coasting compare 20 hours of coasting.
Lame071 Array1 Data


title: Leaf_0 day_GFBS_rufipogan

description: Gene expression after 0 day of stress


title: Leaf_2 day_VAR_rufipogan

description: Gene expression after 2 day of recovery


title: Leaf_2 day_VAR_nivara

description: Gene expression after 2 day of recovery

value: nivara


title: ΔcstA1_LL_LB_2

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

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

institute: Genotypic Technology

description: Single knockout

hyb_protocol: 2000ng of labeled cRNA sample were fragmented at 60 º C and hybridized on to a Genotypic designed Agilent Custom Salmonella Typhimurium 8x15k arrays (AMADID No: 046639) . Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). 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 (Agilent Technologies, Part Number 5188-5327)

scan_protocol: Scanned using the Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D) at 5 micron resolution.

data_processing: Images were quantified using Feature Extraction Software ( Agilent). Feature extracted raw data was analyzed using GeneSpring GX software from Agilent. Normalization of the data was done in GeneSpring GX using the 75th percentile shift

organism: Salmonella enterica subsp. enterica serovar Typhimurium

source_name: LB medium_cstA

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-2331). 25ng each of total RNA were reverse transcribed at 40°C using WT primer with a T7 polymerase promoter converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNesay columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

growth_protocol: Overnight cultures in LB broth were subcultured in 5 ml LB with 100 fold dilution and incubated at 37 ⁰C under shaking condition. Duplicates for each strain were used.

extract_protocol: RNA was extracted by phase separation method using TRIzol (Sigma) reagent.

value: Single knockout (cstA)

tag: growth phase

value: late log phase


title: Leaf_8 day_GFAS_nivara

description: Gene expression after 8 day of stress

value: Grainfilling

value: 8 day of stress


title: Lame070 Array4 Data

description:
Biological replicats 3 of 3. Cumulus cells at 92 hours of coasting compare 20 hours of coasting.
Lame070 Array4 Data

value: > 8 mm

value: 92 hours


title: Leaf_0 day_VBS_rufipogan

description: Gene expression after 0 day of stress

value: 0 day of stress


title: Lame071 Array3 Data

description:
Biological replicats 2 of 3. Cumulus cells at 68 hours of coasting compare 20 hours of coasting.
Lame071 Array3 Data

value: 68 hours


title: Lame070 Array2 Data

description:
Biological replicats 1 of 3. Cumulus cells at 92 hours of coasting compare 20 hours of coasting.
Lame070 Array2 Data


title: ΔcstA1_LL_LB_1

description: Single knockout


title: ΔyjiY1_LL_LB_2

description: Single knockout

source_name: LB medium_yjiY

value: Single knockout (yjiY)


title: Leaf_2 day_GFAR_nivara

description: Gene expression after 2 day of recovery

value: wild

value: 2 day of recovery


title: Leaf_0 day_GFBS_nivara

description: Gene expression after 0 day of stress


title: Lame069 Array4 Data

description:
Biological replicats 3 of 3. Cumulus cells at 20 hours of coasting compare 92 hours of coasting.
Lame069 Array4 Data

value: cumulus cells


title: Lame070 Array3 Data

description:
Biological replicats 2 of 3. Cumulus cells at 92 hours of coasting compare 20 hours of coasting.
Lame070 Array3 Data


title: ΔΔ1_LL_LB_2

description: Double knockout

source_name: LB medium_double_knockout

value: Double knockout (cstA and yjiY)


title: WT1_LL_LB_1

description: Wild type

source_name: LB medium_wildtype

value: Wild type


title: ΔyjiY1_LL_LB_1

description: Single knockout


title: WT1_LL_LB_2

description: Wild type


title: ΔΔ1_LL_LB_1

description: Double knockout


title: Lame069 Array3 Data

description:
Biological replicats 2 of 3. Cumulus cells at 20 hours of coasting compare 92 hours of coasting.
Lame069 Array3 Data

value: 20 hours


title: RBcellLine-RB381

status: Public on Mar 31 2016

city: Amsterdam

first: Irsan

last: Kooi

state: Noord-Holland

address: van der Boechorstraat 7

department: Clininical Genetics

country: Netherlands

institute: VU university medical centre

hyb_protocol: Per sample, 7.5 µg cRNA of the obtained biotinylated cRNA samples was fragmented and hybridized in a final concentration of 0.0375 µg/µl on the Affymetrix [HT HG U133 + PM96] (Affymetrix, Santa Clara, CA, U.S.A.). After an automated process of washing and staining by the GeneTitan machine (Affymetrix, Santa Clara, CA, U.S.A) using the Affymetrix HWS Kit for GeneTitan (part nr. 901530), absolute values of expression were calculated from the scanned array using the Affymetrix Command Console v3.2 software.

scan_protocol: GeneChips were scanned using the Affymetrix GeneTitan system

data_processing:
Data were background adjusted, normalized and summarized by the RMA method. The affy package from Bioconductor was used for this analysis.
Affy: 1.46.1
BiocIntaller: 1.18.5

source_name: retinoblastoma cell line

label_protocol: Biotinylated cRNA was prepared using the Affymetrix 3’ IVT Express Kit (Affymetrix, Santa Clara, CA, USA) according to the manufacturer’s specifications with an input of 100 ng of total RNA

growth_protocol: Cell lines were cultured in Iscove’s MDM (Invitrogen) with 10% FBS Gold (PAA Laboratories), 10 mg/L insulin (SigmaAldrich) and 0.0004% (v/v) β-mercaptoethanol. Culture medium was supplemented with 100 U/ml penicillin and 0.1 mg/ml streptomycin (Invitrogen) and cells were grown in a humidified 37°C incubator with 5% CO2

extract_protocol: TRIzol extracted RNA was treated with rDNase (Macherey-Nagel, Düren, Germany) to digest any contaminating DNA and subsequently purified with the NucleoSpin RNA Clean-up XS kit (Macherey-Nagel). Quality control, RNA labeling, hybridization and data extraction were performed at ServiceXS B.V. RNA concentration was measured using the Nanodrop ND-1000 spectrophotometer (Nanodrop Technologies). The RNA quality and integrity were determined using Lab-on-chip analysis on the Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA, U.S.A.) and on the Shimadzu MultiNA RNA analysis chips (Shimadzu Corporation, Kyoto, Japan). Only RNA samples that passed the quality criteria of an OD 260/280 ratio of ≥ 1.8 and an RNA Integrity number (RIN) of ≥ 7 were processed for expression profiling.

treatment_protocol: No treatment was given

tag: cell line

value: Retinoblastoma cell line

tag: snp array id of tumor at ega


title: RBcellLine-VUMC-RB-26-iso2

tag: cell type


title: RBcellLine-Y79


title: RBcellLine-VUMC-RB-26-iso3


title: RBcellLine-VUMC-RB-26-iso1


title: liver, MC71-TT infection

city: Povo

first: Toma

last: Tebaldi

state: Trento

address: via Sommarive n. 9

department: Centre for Integrative Biology

country: Italy

institute: University of Trento

description:
Liver tissue collected from mice infected with S. Typhimurium (MC71-TT strain, expressing a functional typhoid toxin) for 60 days
LIV.TT

hyb_protocol: The samples were hybridized to the Affymetrix GeneChip Mouse Gene 2.0 ST array (Affymetrix, Santa Clara, CA, USA). The arrays were washed and stained with phycoerythrin-conjugated streptavidin using the Affymetrix Fluidics Station 450

scan_protocol: Arrays were scanned in the Affymetrix GeneArray 3000 7G scanner.

data_processing: CEL files  were analyzed with the R software environment for statistical computing (http://www.r-project.org/) and the Bioconductor library of biostatistical packages (http://www.bioconductor.org/). Raw data were preprocessed and normalized with the RMA method using the “oligo” package. Probe sets were mapped to transcripts using the Affymetrix mogene20 annotation data contained in the “mogene20sttranscriptcluster.db” package.

source_name: liver, MC71-TT infection

label_protocol: The RNA samples were amplified using the Ovation Pico WTA v.2 RNA Amplification System (NuGEN, San Carlos, CA, USA) and biotin labeled with the Encore Biotin Module (NuGEN) in accordance with the manufacturer’s instructions

growth_protocol: Female 129S6/SvEvTac mice 6- to 8-weeks-old, kept in a pathogen-free facility, were obtained from Taconic Biosciences Inc. (Bomholt, Denmark). Animal procedures were conducted following the institution guidelines under the Ethical permit N133/13 granted by the Northern Stockholm Experimental Animal Ethical Committee.

extract_protocol: Tissues from infected and control mice was harvested and preserved in RNAlater. Tissues were homogenised in RLT buffer (+beta-mercapto), extraction performed with RNAeasy QIAGEN kit with DNAse step

treatment_protocol: Mice were infected orally with 108 bacteria per mouse, and euthanized 60 days post-infection (p.i.)

tag: host strain

tag: infection

tag: host tissue

value: liver


title: coronal pulp-3

city: Seoul

first: Seong-Oh

last: Kim

address: 250 Seongsanno, Seodaemun-gu

department: Pediatric dentistry

country: South Korea

institute: Yonsei University College of Dentistry

hyb_protocol: Following fragmentation, fragmented cDNA were hybridized for 16 hr at 45C on Affymetrix GeneChip® Human Gene 1.0 ST Array. The GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The Robust Multiarray Average (RMA) algorithm implemented in Affymetrix Expression Console software (version1.3.1) was used to normalize the raw data. Highly expressed genes that showed over 2-fold difference between the signal values of control and test samples were selected for further study.

source_name: coronal pulp tissue

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 300  ng total RNA (GeneChip® WT Terminal Labeling and Controls Kit P/N 901525 1, Affymetrix).

growth_protocol: Coronal pulp tissues were obtained from 18 healthy subjects.

extract_protocol: Coronal pulp tissues were homogenized using a homogenizer. The Rneasy Fibrous Mini kit (Qiagen) was then used to extract total RNA from coronal pulp tissues, according to the manufacturer's instructions.

treatment_protocol: We combined three or four coronal pulp tissues into one sample to reduce sample vias.

tag: tissue

value: coronal pulp


title: RBcellLine-WERI-RB1


title: jejunum, uninfected

description:
Jejunum tissue collected from uninfected mice
JEJ.uninf

source_name: jejunum, uninfected

value: uninfected

value: jejunum


title: apical pulp complex-2

source_name: apical pulp complex tissue

value: apical pulp complex


title: apical pulp complex-1


title: jejunum, MC71-TT infection

description:
Jejunum tissue collected from mice infected with S. Typhimurium (MC71-TT strain, expressing a functional typhoid toxin) for 60 days
JEJ.TT

source_name: jejunum, MC71-TT infection


title: liver, MC71-DcdtB infection

description:
Liver tissue collected from mice infected with S. Typhimurium (MC71-DcdtB strain, expressing an inactive typhoid toxin) for 60 days
LIV.DcdtB

source_name: liver, MC71-DcdtB infection


title: RBcellLine-RB247


title: jejunum, MC71-DcdtB infection

description:
Jejunum tissue collected from mice infected with S. Typhimurium (MC71-DcdtB strain, expressing an inactive typhoid toxin) for 60 days
JEJ.DcdtB

source_name: jejunum, MC71-DcdtB infection


title: ileum, MC71-TT infection

description:
Ileum tissue collected from mice infected with S. Typhimurium (MC71-TT strain, expressing a functional typhoid toxin) for 60 days
ILE.TT

source_name: ileum, MC71-TT infection

value: ileum


title: Lame069 Array2 Data

description:
Biological replicats 1 of 3. Cumulus cells at 20 hours of coasting compare 92 hours of coasting.
Lame069 Array2 Data

value: > 8 mm

value: 92 hours


title: RBcellLine-RB383


title: RBcellLine-RB176


title: apical pulp complex-3


title: coronal pulp-1


title: coronal pulp-2


title: ileum, uninfected

description:
Ileum tissue collected from uninfected mice
ILE.uninf

source_name: ileum, uninfected


title: liver, uninfected

description:
Liver tissue collected from uninfected mice
LIV.uninf

source_name: liver, uninfected


title: Humanhair_postflight_12p_6

city: Tsukuba

first: Masaya

last: Seki

state: Ibaraki

address: Sengen 2-1-1

department: JEM Utilization Center

country: Japan

institute: Japan Aerospace Exploration agency

description:
Gene expression in post-flight human hair follicles
12p6

hyb_protocol: An 1.5 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 0.1ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 0.1 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Human Gene Expression 4x44K v2 Microarray Kit (G4845A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned on the Agilent DNA Microarray Scanner (G2505B)

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

source_name: hair follicles, Post-flight, astronaut12

label_protocol: Cyanine-3 (Cy3) labeled aRNA was prepared from RNA using the MessageAmp aRNA kit (Thermo Fisher Scientific, MA) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: A hair root was cut into ~15 fragments by using knife under a stereoscopic microscope. Collected fragments were immersed of ISOGEN (TakaraBio, Kyoto, Japan) in tube and stirred using the Bioruptor UCD250 (Cosmo Bio, Tokyo, Japan). Next, Total RNA was purified from hair lysates by using the ISOGEN as manufacutuerer's recommendation. Total RNA was amplified using the Ambion MessageAmp aRNA kit (Thermo Fisher Scientific, MA). Each RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: In sampling day, two astronauts were paired and plucked another hair sample using tweezer in the direction of hair growth without damaging the hair roots. These plucked samples were stored at -80°C until analysis.

tag: individual

tag: gender

value: male

value: Post-flight

value: hair follicles


title: ileum, MC71-DcdtB infection

description:
Ileum tissue collected from mice infected with S. Typhimurium (MC71-DcdtB strain, expressing an inactive typhoid toxin) for 60 days
ILE.DcdtB

source_name: ileum, MC71-DcdtB infection


title: colon, uninfected

description:
Colon tissue collected from uninfected mice
COL.uninf

source_name: colon, uninfected

value: colon


title: Humanhair_postflight_12p_5

description:
Gene expression in post-flight human hair follicles
12p5


title: colon, MC71-TT infection

description:
Colon tissue collected from mice infected with S. Typhimurium (MC71-TT strain, expressing a functional typhoid toxin) for 60 days
COL.TT

source_name: colon, MC71-TT infection


title: Humanhair_preflight_12p_2

description:
Gene expression in Pre-flight human hair follicles
12p2

source_name: hair follicles, Pre-flight, astronaut12

value: Pre-flight


title: Humanhair_preflight_12p_1

description:
Gene expression in Pre-flight human hair follicles
12p1


title: Humanhair_inflight_12p_3

description:
Gene expression in in-flight human hair follicles
12p3

source_name: hair follicles, in-flight, astronaut12

value: in-flight


title: Humanhair_postflight_11p_5

description:
Gene expression in post-flight human hair follicles
11p5

source_name: hair follicles, Post-flight, astronaut11


title: Humanhair_postflight_10p_5

description:
Gene expression in post-flight human hair follicles
10p5

source_name: hair follicles, Post-flight, astronaut10


title: Humanhair_postflight_9p_6

description:
Gene expression in post-flight human hair follicles
9p6

source_name: hair follicles, Post-flight, astronaut9


title: Humanhair_inflight_10p_4

description:
Gene expression in in-flight human hair follicles
10p4

source_name: hair follicles, in-flight, astronaut10


title: Humanhair_postflight_8p_5

description:
Gene expression in post-flight human hair follicles
8p5

source_name: hair follicles, Post-flight, astronaut8


title: Humanhair_postflight_10p_6

description:
Gene expression in post-flight human hair follicles
10p6


title: Humanhair_preflight_9p_2

description:
Gene expression in Pre-flight human hair follicles
9p2

source_name: hair follicles, Pre-flight, astronaut9


title: Humanhair_postflight_9p_5

description:
Gene expression in post-flight human hair follicles
9p5


title: Humanhair_inflight_10p_3

description:
Gene expression in in-flight human hair follicles
10p3


title: colon, MC71-DcdtB infection

description:
Colon tissue collected from mice infected with S. Typhimurium (MC71-DcdtB strain, expressing an inactive typhoid toxin) for 60 days
COL.DcdtB

source_name: colon, MC71-DcdtB infection


title: Humanhair_inflight_11p_3

description:
Gene expression in in-flight human hair follicles
11p3

source_name: hair follicles, in-flight, astronaut11


title: Humanhair_preflight_11p_1

description:
Gene expression in Pre-flight human hair follicles
11p1

source_name: hair follicles, Pre-flight, astronaut11


title: Humanhair_preflight_10p_1

description:
Gene expression in Pre-flight human hair follicles
10p1

source_name: hair follicles, Pre-flight, astronaut10


title: Humanhair_inflight_9p_4

description:
Gene expression in in-flight human hair follicles
9p4

source_name: hair follicles, in-flight, astronaut9


title: Humanhair_inflight_11p_4

description:
Gene expression in in-flight human hair follicles
11p4


title: Humanhair_inflight_8p_4

description:
Gene expression in in-flight human hair follicles
8p4

source_name: hair follicles, in-flight, astronaut8


title: Humanhair_inflight_12p_4

description:
Gene expression in in-flight human hair follicles
12p4


title: Humanhair_inflight_9p_3

description:
Gene expression in in-flight human hair follicles
9p3


title: Humanhair_postflight_11p_6

description:
Gene expression in post-flight human hair follicles
11p6


title: Humanhair_preflight_10p_2

description:
Gene expression in Pre-flight human hair follicles
10p2


title: Humanhair_preflight_11p_2

description:
Gene expression in Pre-flight human hair follicles
11p2


title: Humanhair_postflight_8p_6

description:
Gene expression in post-flight human hair follicles
8p6


title: Humanhair_preflight_9p_1

description:
Gene expression in Pre-flight human hair follicles
9p1


title: Humanhair_postflight_7p_6

description:
Gene expression in post-flight human hair follicles
7p6

source_name: hair follicles, Post-flight, astronaut7


title: Humanhair_inflight_8p_3

description:
Gene expression in in-flight human hair follicles
8p3


title: Humanhair_preflight_7p_1

description:
Gene expression in Pre-flight human hair follicles
7p1

source_name: hair follicles, Pre-flight, astronaut7


title: Humanhair_postflight_7p_5

description:
Gene expression in post-flight human hair follicles
7p5


title: Humanhair_preflight_8p_1

description:
Gene expression in Pre-flight human hair follicles
8p1

source_name: hair follicles, Pre-flight, astronaut8


title: Humanhair_preflight_6p_1

description:
Gene expression in Pre-flight human hair follicles
6p1

source_name: hair follicles, Pre-flight, astronaut6

value: female


title: Humanhair_preflight_7p_2

description:
Gene expression in Pre-flight human hair follicles
7p2


title: Humanhair_postflight_6p_5

description:
Gene expression in post-flight human hair follicles
6p5

source_name: hair follicles, Post-flight, astronaut6


title: Humanhair_preflight_3p_2

description:
Gene expression in Pre-flight human hair follicles
3p2

source_name: hair follicles, Pre-flight, astronaut3


title: Humanhair_postflight_4p_5

description:
Gene expression in post-flight human hair follicles
4p5

source_name: hair follicles, Post-flight, astronaut4


title: Humanhair_preflight_4p_1

description:
Gene expression in Pre-flight human hair follicles
4p1

source_name: hair follicles, Pre-flight, astronaut4


title: Humanhair_postflight_6p_6

description:
Gene expression in post-flight human hair follicles
6p6


title: Humanhair_preflight_4p_2

description:
Gene expression in Pre-flight human hair follicles
4p2


title: Humanhair_inflight_7p_4

description:
Gene expression in in-flight human hair follicles
7p4

source_name: hair follicles, in-flight, astronaut7


title: Humanhair_preflight_3p_1

description:
Gene expression in Pre-flight human hair follicles
3p1


title: Humanhair_inflight_3p_3

description:
Gene expression in in-flight human hair follicles
3p3

source_name: hair follicles, in-flight, astronaut3


title: Humanhair_inflight_7p_3

description:
Gene expression in in-flight human hair follicles
7p3


title: Humanhair_postflight_4p_6

description:
Gene expression in post-flight human hair follicles
4p6


title: Humanhair_preflight_6p_2

description:
Gene expression in Pre-flight human hair follicles
6p2


title: Humanhair_inflight_3p_4

description:
Gene expression in in-flight human hair follicles
3p4


title: Humanhair_preflight_8p_2

description:
Gene expression in Pre-flight human hair follicles
8p2


title: Humanhair_postflight_3p_5

description:
Gene expression in post-flight human hair follicles
3p5

source_name: hair follicles, Post-flight, astronaut3


title: Humanhair_inflight_6p_3

description:
Gene expression in in-flight human hair follicles
6p3

source_name: hair follicles, in-flight, astronaut6


title: Humanhair_inflight_1p_4

description:
Gene expression in in-flight human hair follicles
1p4

source_name: hair follicles, in-flight, astronaut1


title: Humanhair_postflight_1p_5

description:
Gene expression in post-flight human hair follicles
1p5

source_name: hair follicles, Post-flight, astronaut1


title: Humanhair_inflight_4p_4

description:
Gene expression in in-flight human hair follicles
4p4

source_name: hair follicles, in-flight, astronaut4


title: Humanhair_inflight_4p_3

description:
Gene expression in in-flight human hair follicles
4p3


title: Humanhair_postflight_3p_6

description:
Gene expression in post-flight human hair follicles
3p6


title: Humanhair_postflight_1p_6

description:
Gene expression in post-flight human hair follicles
1p6


title: Humanhair_inflight_6p_4

description:
Gene expression in in-flight human hair follicles
6p4


title: Humanhair_inflight_1p_3

description:
Gene expression in in-flight human hair follicles
1p3


title: Humanhair_preflight_1p_1

description:
Gene expression in Pre-flight human hair follicles
1p1

source_name: hair follicles, Pre-flight, astronaut1


title: Humanhair_preflight_1p_2

description:
Gene expression in Pre-flight human hair follicles
1p2


title: human_blood_H07_sample1

city: Jena

first: Andreas

last: Dix

address: Beutenbergstraße 11a

country: Germany

institute: Hans-Knöll-Institut

hyb_protocol: standard Affymetrix hybridisation protocol

scan_protocol: standard Affymetrix GeneTitan Scanner protocol

data_processing: Using the R package “affy”, the data was background corrected, log2-transformed and quantile normalized according to RMA. For probe-to-gene mapping, a custon chip definition file (version 19, “Entrez Gene”) from brainarray was used (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/19.0.0/entrezg.asp).

label_protocol: standard Affymetrix 3´-IVT Express Kit protocol

extract_protocol: standard Tempus™ Spin RNA Isolation Kit

tag: eortc classification

value: healthy

value: blood


title: human_blood_H03_sample1


title: human_blood_H01_sample1


title: human_blood_H01_sample2


title: human_blood_H05_sample1


title: human_blood_P13_unclass_sample1

value: unclassified


title: human_blood_P14_unclass_sample2


title: human_blood_H02_sample1


title: human_blood_H08_sample1


title: human_blood_P15_unclass_sample1


title: human_blood_P09_unclass_sample1


title: human_blood_P09_unclass_sample2


title: human_blood_P12_unclass_sample2


title: human_blood_H04_sample1


title: human_blood_P10_unclass_sample1


title: human_blood_P16_unclass_sample2


title: human_blood_P12_unclass_sample1


title: KYSE180_total_1

city: Tokushima

first: Kiyoshi

last: Masuda

address: 3-18-15 Kuramoto-cho

department: Department of Human Genetics

institute: Institute of Biomedical Sciences, Tokushima University Graduate School

description: total RNA (input)

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >20.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 μl containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE Oligo Microarrays (G4851B) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) 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 Feature Extraction Software 10.7 (Agilent) using default parameters (protocol GE1-107_Sep09 and Grid: 039494_D_F_20120628) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: KYSE180 esophageal squamous cell carcinoma 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the Low Input Quick Amp Labeling Kit, One-Color (Agilent, 5190-2305) according to the manufacturer's instructions. Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the RNeasy Mini Kit (Qiagen, Valencia, CA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (G2938C, Agilent Technologies, Santa Clara, CA).

value: esophageal squamous cell carcinoma


title: human_blood_P08_IA_sample3

source_name: probable IA_blood

value: probable IA


title: human_blood_P16_unclass_sample1


title: KYSE180_total_2

description: total RNA (input)

source_name: KYSE180 esophageal squamous cell carcinoma 2


title: human_blood_H06_sample1


title: human_blood_P08_IA_sample2


title: human_blood_P11_IFD_sample1

source_name: possible IFD_blood

value: possible IFD


title: KYSE180_TIA1_RIP_2

description:
RNA Immunoprecipitation
Antibody: anti-TIA1, Medical & Biological Laboratories (Nagoya, Japan), Catalog number RN014P, Lot number 001

source_name: KYSE180 esophageal squamous cell carcinoma, TIA1 Ab RIP 2


title: human_blood_P08_IA_sample1


title: KYSE180_TIA1_RIP_1

source_name: KYSE180 esophageal squamous cell carcinoma, TIA1 Ab RIP 1


title: human_blood_P07_IA_sample3


title: human_blood_P11_IFD_sample2


title: human_blood_P07_IA_sample2


title: human_blood_P06_IA_sample2


title: human_blood_P05_IA_sample2


title: human_blood_P04_IA_sample3


title: human_blood_P06_IA_sample1


title: human_blood_P04_IA_sample1


title: human_blood_P03_IA_sample3


title: human_blood_P07_IA_sample1


title: human_blood_P01_IA_sample2


title: human_blood_P04_IA_sample2


title: human_blood_P04_IA_sample4


title: human_blood_P02_IA_sample3


title: human_blood_P04_IA_sample5


title: Batch3_Mouse-11.5 D_Maxilla_Rep3

status: Public on Mar 24 2016

city: Los Angeles

first: Vasu

last: Punj

state: CA

address: Biggy Street

institute: USC

description: Gene expression

hyb_protocol: Following fragmentation, 12 µg of cRNA were hybridized for 16hr on Affymetrix Mouse 430_2 (gene version)  as recommended by manufacturer

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000A.

data_processing: RMA (Roboust Multi_array average) normalization was used

source_name: mouse embryo stage E11.5

label_protocol: Starting from 3 µg total RNA, labeled cRNA was prepared using the Qiagen Microarray cDNA Synthesis, Microarray RNA Target Synthesis (T7) and Microarray Target Purification Kit, according to the manufacturer's instructions

extract_protocol: RNA was extracted from tissues using  RNeasy mini kit (Qiagen Valenica, CA)

tag: strain

value: Distal bone

tag: developmental stage

value: embryo

tag: age


title: human_blood_P03_IA_sample2


title: Batch3_Mouse-11.5 P_Maxilla_Rep2

description: Gene expression

value: Proximal bone


title: Batch3_Mouse-11.5 P_Maxilla_Rep1

description: Gene expression


title: Batch3_Mouse-11.5 P_Mandible_Rep2

description: Gene expression


title: human_blood_P05_IA_sample1


title: Batch3_Mouse-11.5 P_Maxilla_Rep3

description: Gene expression


title: human_blood_P02_IA_sample1


title: human_blood_P01_IA_sample1


title: human_blood_P14_unclass_sample1


title: human_blood_P03_IA_sample1


title: human_blood_P02_IA_sample2


title: Batch3_Mouse-11.5 D_Mandible_Rep3

description: Gene expression


title: Batch3_Mouse-11.5 D_Mandible_Rep2

description: Gene expression


title: Batch3_Mouse-10.5 P_Mandible_Rep2

description: Gene expression

source_name: mouse embryo stage E10.5


title: Batch3_Mouse-10.5 D_Mandible_Rep3

description: Gene expression


title: Batch3_Mouse-10.5 P_Mandible_Rep1

description: Gene expression


title: Batch3_Mouse-10.5 P_Mandible_Rep3

description: Gene expression


title: Batch3_Mouse-10.5 D_Mandible_Rep1

description: Gene expression


title: Batch3_Mouse-11.5 D_Maxilla_Rep2

description: Gene expression


title: Batch3_Mouse-11.5 P_Mandible_Rep1

description: Gene expression


title: Batch3_Mouse-10.5 D_Mandible_Rep2

description: Gene expression


title: Batch3_Mouse-11.5 D_Mandible_Rep1

description: Gene expression


title: Batch3_Mouse-11.5 P_Mandible_Rep3

description: Gene expression


title: Batch2_Mouse-14.5 P_Maxilla_Rep3

description: Gene expression

source_name: mouse embryo stage E14.5


title: Batch2_Mouse-14.5 D_Maxilla_Rep3

description: Gene expression


title: Batch2_Mouse-14.5 D_Maxilla_Rep1

description: Gene expression


title: Batch2_Mouse-13.5 P_Maxilla_Rep1

description: Gene expression

source_name: mouse embryo stage E13.5


title: Batch2_Mouse-12.5 P_Mandible_Rep3

description: Gene expression

source_name: mouse embryo stage E12.5


title: Batch2_Mouse-14.5 D_Maxilla_Rep2

description: Gene expression


title: Batch2_Mouse-13.5 D_Maxilla_Rep2

description: Gene expression


title: Batch2_Mouse-13.5 D_Maxilla_Rep1

description: Gene expression


title: Batch2_Mouse-12.5 P_Mandible_Rep2

description: Gene expression


title: Batch2_Mouse-12.5 D_Mandible_Rep3

description: Gene expression


title: Batch2_Mouse-14.5 P_Maxilla_Rep1

description: Gene expression


title: Batch2_Mouse-12.5 D_Mandible_Rep1

description: Gene expression


title: Batch2_Mouse-13.5 P_Maxilla_Rep3

description: Gene expression


title: Batch2_Mouse-13.5 D_Maxilla_Rep3

description: Gene expression


title: Batch2_Mouse-12.5 P_Mandible_Rep1

description: Gene expression


title: Batch2_Mouse-14.5 P_Maxilla_Rep2

description: Gene expression


title: Batch2_Mouse-13.5 P_Maxilla_Rep2

description: Gene expression


title: Batch2_Mouse-12.5 P_Maxilla_Rep3

description: Gene expression


title: Batch2_Mouse-12.5 P_Maxilla_Rep1

description: Gene expression


title: Batch1_Mouse-14.5 P_Mandible_Rep3

description: Gene expression


title: Batch2_Mouse-12.5 D_Mandible_Rep2

description: Gene expression


title: Batch1_Mouse-14.5 P_Mandible_Rep2

description: Gene expression


title: Batch2_Mouse-12.5 D_Maxilla_Rep3

description: Gene expression


title: Batch2_Mouse-12.5 D_Maxilla_Rep2

description: Gene expression


title: Batch1_Mouse-14.5 D_Mandible_Rep2

description: Gene expression


title: Batch1_Mouse-14.5 P_Mandible_Rep1

description: Gene expression


title: Batch1_Mouse-14.5 D_Mandible_Rep3

description: Gene expression


title: Batch1_Mouse-14.5 D_Mandible_Rep1

description: Gene expression


title: Batch2_Mouse-12.5 P_Maxilla_Rep2

description: Gene expression


title: Batch2_Mouse-12.5 D_Maxilla_Rep1

description: Gene expression


title: Batch1_Mouse-13.5 P_Mandible_Rep2

description: Gene expression


title: Batch1_Mouse-13.5 D_Mandible_Rep3

description: Gene expression


title: Batch1_Mouse-13.5 P_Mandible_Rep1

description: Gene expression


title: Batch1_Mouse-13.5 P_Mandible_Rep3

description: Gene expression


title: Batch1_Mouse-13.5 D_Mandible_Rep2

description: Gene expression


title: Bcells RNA-Seq Control #2

status: Public on Jan 08 2016

type: SRA

city: Cincinnati

first: Mathieu

last: Sertorio

state: OH

address: 3333 Burnett Avenue

department: Exp Hem and Cancer Bio

institute: Cincinnati Children's Hospital Medical center

library_source: transcriptomic

data_processing:
Samples were sequenced at the CCHMC DNA core, on an Illumina HiSeq2500 using a TopHat/Cufflinks pipeline. Refence annotation is based on UCSC known genes table.
BAM files from RNA-Seq were imported into GeneSpring NGS software (v12.6) and aligned to mm9 reference genome. Reference annotations produced by Emsembl. Aligned reads were filtered on base quality >=50.
Aligned read couts quantified and normalized using TMM algorithm. Filtrations removed all genes with fewer than 1 reads in at least one sample of a condition.
Fold change was calculated as FancCKo/WT with a cut-off of 1.5 average fold change.
Genome_build: mm9
Supplementary_files_format_and_content: TXT files exported into Excel containing WT and FancC deficient B cells normalized values, gene symbols, and fold change

source_name: mature mouse B cells

extract_protocol:
RNA was extracted with the Rneasy plus mini kit. This included genomic DNA cleaning on spin column.  Final RNA was aliquoted and submitted for quality control and RNA-Sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols. WT and Ko samples were sequenced in 2 independent experiments, each one containing a WT and a Ko samples to test the reproductibility of results

treatment_protocol: B cellspurified from mouse total splenocytes by anti-CD43 magnetic beads purification (Miltenyi)  after Red blood cells lysis treatment.

tag: fanc status

value: Control

tag: genetic background


title: GFP+ colonies, biological rep2

status: Public on Mar 21 2016

city: tian jin

first: hongyan

last: zhang

state: Other(国外)

address: nanjing road 288

department: SKLEH

country: China

institute: PUMC

description: Gene expression data from GFP+ colonies

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Gene 1.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000 7G.

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: Partially reprogrammed colonies

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: iPS cells were cultured in mES medium.

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

value: colonies from the leukemia cells

tag: mouse genotype

tag: cell marker

value: GFP+


title: Notch-1 ips, biological rep3

description: Gene expression data from Notch-1 ips

source_name: Established iPS cells


title: Notch-1 leukemia-1, biological rep3

description: Gene expression data from Notch-1 leukemia

source_name: Leukemia cells

value: leukemia cells

value: spleen


title: Notch-1 leukemia-1, biological rep2


title: Notch-1 ips, biological rep1

description: Gene expression data from Notch-1 ips


title: GFP+ colonies, biological rep3

description: Gene expression data from GFP+ colonies


title: GFP+ colonies, biological rep1

description: Gene expression data from GFP+ colonies


title: Notch-1 leukemia-1, biological rep1


title: GFP- colonies, biological rep1

description: Gene expression data from GFP- colonies

source_name: Reprogrammed colonies

value: GFP-


title: Notch-1 ips, biological rep2

description: Gene expression data from Notch-1 ips


title: GFP- colonies, biological rep3

description: Gene expression data from GFP- colonies


title: GFP- colonies, biological rep2

description: Gene expression data from GFP- colonies


title: Batch1_Mouse-13.5 D_Mandible_Rep1

description: Gene expression


title: prz1-HA + Calcium ChIP-chip Replicate 1

status: Public on Feb 10 2016

type: genomic

city: Calgary

first: Gordon

last: Chua

state: Alberta

address: 2500 University Drive NW

department: Biological Sciences

institute: University of Calgary

description:
prz1 + calcium chIP-rep1
Treated with 0.5 M calcium.

hyb_protocol: Hybridization was performed according to the manufacturer's instruction (Agilent Technology). Microarray was washed in 6X SSPE/0.005% sodium N-lauroylsarcosine at room temperature for 5 min, followed by a second wash in pre-heated 42°C 0.6X SSPE for 2 min.

scan_protocol: Microarrays were scanned on a GenePix 4200A instrument with GenePix 3.0 software.

data_processing: The raw data was lowess normalized and the average log2 ratios with the corresponding t-test p values from the dye-swap experiments were obtained using the R Bioconductor Limma package. The significant spots were selected with chIPOTle.

molecule: genomic DNA

organism: Schizosaccharomyces pombe

source_name: prz1 HA-tagged auxotrophic strain, calcium, ChIP

label_protocol: The linker-ligated DNA was PCR-amplified by adding 15 µl of labeling mix (2 µl aa-dUTP dNTP mix containing 5 mM each dATP, dCTP and dGTP, 3 mM dTTP, and 2 mM aminoallyl-dUTP (Sigma)), 1.25 µl 40 µM Oligo #1 (5’-GCGGTGACCCGGGAGATCTGAATTC-3’), and 5 and 0.001 units of GoTaq DNA polymerase (Promega) and Pfu Turbo DNA polymerase (Stratagene), respectively, and using the following program: one cycle of 55°C (4 min); 72°C (5 min); 95°C (2 min) and 30 cycles of 95°C (30 sec); 55°C (30 sec); 72°C (1 min), followed by a final extension at 72°C (4 min). Equal amounts of PCR product (3-5 mg) from immunoprecipitated and corresponding input samples were coupled to Cy3 and Cy5 dyes (GE Healthcare), and combined for QIAquick purification (QIAGEN).

growth_protocol: S. pombe yeast cells were inoculated in YES+ALU media and cultured for 16-20hr. The ch1 and ch2 samples were exposed to 0.15 M calcium for the last 30 minutes.

extract_protocol: Cells were fixed and quenched in 1% formaldehyde and 125 mM glycine, respectively, followed by 30 minute room temperature agitation and lysis by bead-beating. The cell lysate was sonicated to generate 100 bp-1 kb DNA fragments. The chromatin-bound transcription factor was immunoprecipitated with 100-200 µl of Dynabeads® conjugated with sheep anti-mouse IgG (Invitrogen) and 5 µg of anti-HA F-7 antibody (Santa Cruz Biotechnology). Both immunoprecipitated and input cell lysates were incubated at 65°C overnight to reverse the DNA-protein cross-linking, and DNA was then extracted by phenol-chloroform. Blunt ends were generated in the entire immunoprecipitate and input DNA samples with 1 unit of T4 DNA Polymerase (Invitrogen), and 200 pmol of annealed linker (linker generated with Oligo #1: 5'-GCGGTGACCCGGGAGATCTGAATTC-3' and Oligo #2: 5'-GAATTCAGATC-3') was ligated with 1000 units of T4 DNA Ligase (NEB).

tag: strain/background

tag: genotype/variation

tag: treatment

value: calcium

tag: chip antibody

value: anti-HA F-7 antibody (Santa Cruz Biotechnology, catalogue sc-7392, lot E0610)

source_name: prz1 HA-tagged auxotrophic strain, calcium, input


title: prz1-HA + Calcium ChIP-chip Replicate 2

description:
prz1 + calcium chIP-rep2
Treated with 0.5 M calcium.


title: es_hey1_-dox_array

status: Public on Jan 01 2016

city: Wuerzburg

first: Manfred

last: Gessler

address: Am Hubland

department: Developmental Biochemistry

institute: Biocenter, University of Wuerzburg

hyb_protocol: Hybridization was performed according to the standrd Affymetrix protocol.

scan_protocol: The arrays were scanned using a GeneChip Scanner 3000 (Affymetrix)

data_processing: Data analysis and quality control was done using different R packages from the Bioconductor project. Probe sets were summarized using the RMA algorithm and resulting signal intensities were normalized by variance stabilization normalization.

source_name: murine embryonic stem cells (CM7/1)

label_protocol: Labeling was performed according to the standrd Affymetrix protocol.

extract_protocol: total RNA was isolated using the Qiagen RNeasy Mini Kit according to manufactures recomendations

tag: induction

value: control

tag: overexpression


title: es_hey2_+dox_array

value: 1000ng/ml doxycycline for 48h


title: es_hey1_+dox_array


title: es_hey2_-dox_array


title: prz1-HA + Tunicamycin ChIP-chip Replicate 2

description:
prz1 + tunicamycin chIP-rep2
Treated with 2.5 µg/mL tunicamycin.

source_name: prz1 HA-tagged auxotrophic strain, tunicamycin, ChIP

growth_protocol: S. pombe yeast cells were inoculated in YES+ALU media and cultured for 16-20hr. The ch1 and ch2 samples were exposed to 2.5 µg/mL tunicamycin for the last 1.5 hours.

value: tunicamycin

source_name: prz1 HA-tagged auxotrophic strain, tunicamycin, input


title: prz1-HA + Tunicamycin ChIP-chip Replicate 1

description:
prz1 + tunicamycin chIP-rep1
Treated with 2.5 µg/mL tunicamycin.


title: Batch3_Mouse-11.5 D_Maxilla_Rep1

description: Gene expression

tag: tissue


title: Buffy_FA/vB12_Baseline_Subject_87

status: Public on Nov 16 2015

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

hyb_protocol: Bisulfite-converted DNA was amplified, fragmented and hybridized to Illumina Infinium HumanMethylation450 BeadChip using the standard Infinium HD Methylation Assay protocols.

scan_protocol: Scanning was done according to the standard Infinium HD Methylation Assay protocols.

data_processing: SWAN normalization on IDAT files using minfi (1.12.0) in R (3.1.2).

label: Cy3 and Cy5

source_name: Buffy coat, FA/vB12, baseline

label_protocol: Labelling was done according to the standard Infinium HD Methylation Assay protocols.

growth_protocol: The current study was part of a double-blind, randomized and placebo-controlled trial on the effects of supplemental intake of folic acid and vitamin B12 on fracture incidence (B-PROOF: B-Vitamins for the PRevention Of Osteoporotic Fractures) in the Netherlands (PMID: 22136481 and PMID: 25411293; registered at clinicaltrials.gov with identifier NCT00696514). For the current study, a subgroup of participants was selected from the B-PROOF study cohort. From the 331 participants, who were among the first who completed the study, 92 participants were selected for DNA methylation analyses. In order to obtain a relatively homogenous study population, predefined selection criteria were included: age between 65 and 75 years and no reported changes in use of dietary supplements containing folic acid or vitamin B12 during the study. Levels of the C-reactive protein (CRP) at baseline should be ≤10 mg/L, because elevated levels of CRP as a consequence of inflammation may indicate aberrant leukocyte counts. Furthermore, participants who were current smokers, or excessive alcohol users (at least once a week ≥6 glasses of alcohol or 5-7 days/week ≥4 glasses of alcohol) at baseline were not selected for the current study. All participants had elevated homocysteine levels (12-50 µmol/L), which is in line with inclusion criteria of the B-PROOF study. Given the essential role of methylenetetrahydrofolate reductase (MTHFR) in folate-mediated one-carbon metabolism, the functional C677T single nucleotide polymorphism (SNP) of the MTHFR gene was considered as well for the selection procedure. Participants with the MTHFR (C677T) CC or TT genotype were equally and exclusively represented in the current study. Serum levels of folate and vitamin B12 were determined using electrochemiluminescence immunoassays (Elecsys 2010, Roche, Almere, The Netherlands). Depending on the study center, plasma levels of homocysteine were measured using the Architect i2000 RS analyzer (VU University Medical Center, Amsterdam), HPLC (Wageningen University, Wageningen) or LC-MS/MS method (Erasmus MC, Rotterdam). All participants provided written informed consent and the study protocol was approved by the institutional Medical Ethics Committee.

extract_protocol: In total, 500 ng of genomic DNA (extracted from buffy coat) was bisulfite converted using the EZ DNA Methylation Kit according to the manufacturer instructions (Zymo Research, Freiburg, Germany). Bisulfite-converted DNA was used for the genome-wide DNA methylation analyses.

treatment_protocol: Participants with mildly elevated homocysteine levels, aged 65-75 years, were randomly assigned to take 400 µg folic acid and 500 µg vitamin B12 (FA/vB12; Orthica, Almere, the Netherlands) per day or a placebo (Orthica, Almere, The Netherlands) during an intervention period of two years. Moreover, all participants received a daily dose of 15 µg vitamin D3, in the same tablet as the placebo or B-vitamins, to ensure a normal vitamin D status. Peripheral blood samples were collected before (baseline) and after the intervention (follow-up).

tag: subject

value: buffy coat

tag: intervention

value: folic acid / vitamin B12

tag: time point

value: baseline

value: female

tag: age at baseline

tag: bisulfite plate

tag: mthfr c677t genotype

value: TT

tag: serum folate levels (nm/l)

tag: serum vitamin b12 levels (pm/l)

tag: plasma homocysteine levels (µm/l)


title: Buffy_FA/vB12_Follow-up_Subject_84

source_name: Buffy coat, FA/vB12, follow-up

value: follow-up

tag: gender


title: Buffy_FA/vB12_Follow-up_Subject_87


title: Buffy_FA/vB12_Baseline_Subject_81

value: male


title: Buffy_FA/vB12_Follow-up_Subject_86


title: Buffy_FA/vB12_Baseline_Subject_85


title: Buffy_FA/vB12_Follow-up_Subject_85


title: Buffy_FA/vB12_Follow-up_Subject_81


title: Buffy_FA/vB12_Baseline_Subject_86


title: Buffy_FA/vB12_Baseline_Subject_83


title: Buffy_FA/vB12_Baseline_Subject_80


title: Buffy_FA/vB12_Baseline_Subject_84


title: Buffy_FA/vB12_Follow-up_Subject_82


title: Buffy_FA/vB12_Follow-up_Subject_77

value: CC


title: Buffy_FA/vB12_Baseline_Subject_74


title: Buffy_FA/vB12_Baseline_Subject_79


title: Buffy_FA/vB12_Baseline_Subject_78


title: Buffy_FA/vB12_Follow-up_Subject_79


title: Buffy_FA/vB12_Baseline_Subject_77


title: Buffy_FA/vB12_Follow-up_Subject_83


title: Buffy_FA/vB12_Follow-up_Subject_74


title: Buffy_FA/vB12_Follow-up_Subject_70


title: Buffy_FA/vB12_Follow-up_Subject_76


title: Buffy_FA/vB12_Baseline_Subject_70


title: Buffy_FA/vB12_Follow-up_Subject_75


title: Buffy_FA/vB12_Baseline_Subject_76


title: Buffy_FA/vB12_Baseline_Subject_82


title: Buffy_FA/vB12_Follow-up_Subject_80


title: Buffy_FA/vB12_Baseline_Subject_69


title: Buffy_FA/vB12_Baseline_Subject_71


title: Buffy_FA/vB12_Follow-up_Subject_67


title: Buffy_FA/vB12_Baseline_Subject_67


title: Buffy_FA/vB12_Baseline_Subject_68


title: Buffy_FA/vB12_Baseline_Subject_72


title: Buffy_FA/vB12_Baseline_Subject_75


title: Buffy_FA/vB12_Follow-up_Subject_72


title: Buffy_FA/vB12_Baseline_Subject_73


title: Buffy_FA/vB12_Follow-up_Subject_65


title: Buffy_FA/vB12_Follow-up_Subject_68


title: Buffy_FA/vB12_Follow-up_Subject_66


title: Buffy_FA/vB12_Baseline_Subject_66


title: Buffy_FA/vB12_Follow-up_Subject_73


title: Buffy_FA/vB12_Follow-up_Subject_63


title: Buffy_FA/vB12_Baseline_Subject_60


title: Buffy_FA/vB12_Follow-up_Subject_62


title: Buffy_FA/vB12_Baseline_Subject_62


title: Buffy_FA/vB12_Baseline_Subject_64


title: Buffy_FA/vB12_Follow-up_Subject_59


title: Buffy_FA/vB12_Follow-up_Subject_58


title: Buffy_FA/vB12_Baseline_Subject_59


title: Buffy_FA/vB12_Baseline_Subject_58


title: Buffy_FA/vB12_Follow-up_Subject_61


title: Buffy_FA/vB12_Follow-up_Subject_60


title: Buffy_FA/vB12_Follow-up_Subject_56


title: Buffy_FA/vB12_Baseline_Subject_56


title: Buffy_FA/vB12_Baseline_Subject_57


title: Buffy_FA/vB12_Follow-up_Subject_69


title: Buffy_FA/vB12_Baseline_Subject_61


title: Buffy_FA/vB12_Follow-up_Subject_71


title: Buffy_FA/vB12_Follow-up_Subject_54


title: Buffy_FA/vB12_Baseline_Subject_54


title: Buffy_FA/vB12_Follow-up_Subject_52


title: Buffy_FA/vB12_Baseline_Subject_52


title: Buffy_FA/vB12_Follow-up_Subject_57


title: Buffy_FA/vB12_Follow-up_Subject_51


title: Buffy_FA/vB12_Follow-up_Subject_78


title: Buffy_FA/vB12_Follow-up_Subject_49


title: Buffy_FA/vB12_Baseline_Subject_51


title: Buffy_FA/vB12_Follow-up_Subject_48


title: Buffy_FA/vB12_Baseline_Subject_50


title: Buffy_FA/vB12_Baseline_Subject_49


title: Buffy_FA/vB12_Follow-up_Subject_47


title: Buffy_FA/vB12_Follow-up_Subject_50


title: Buffy_FA/vB12_Follow-up_Subject_53


title: Buffy_FA/vB12_Baseline_Subject_48


title: Buffy_FA/vB12_Baseline_Subject_47


title: Buffy_FA/vB12_Baseline_Subject_55


title: Buffy_FA/vB12_Baseline_Subject_46


title: Buffy_FA/vB12_Baseline_Subject_63


title: Buffy_FA/vB12_Follow-up_Subject_55


title: Buffy_FA/vB12_Follow-up_Subject_45


title: Buffy_FA/vB12_Follow-up_Subject_64


title: Buffy_FA/vB12_Follow-up_Subject_44


title: Buffy_FA/vB12_Baseline_Subject_65


title: Buffy_FA/vB12_Baseline_Subject_53


title: Buffy_Placebo_Follow-up_Subject_43

source_name: Buffy coat, placebo, follow-up

value: placebo


title: Buffy_Placebo_Baseline_Subject_43

source_name: Buffy coat, placebo, baseline


title: Buffy_FA/vB12_Baseline_Subject_45


title: Buffy_FA/vB12_Baseline_Subject_44


title: Buffy_Placebo_Follow-up_Subject_41


title: Buffy_Placebo_Follow-up_Subject_38


title: Buffy_Placebo_Baseline_Subject_40


title: Buffy_Placebo_Baseline_Subject_39


title: Buffy_Placebo_Follow-up_Subject_39


title: Buffy_Placebo_Follow-up_Subject_42


title: Buffy_Placebo_Baseline_Subject_42


title: Buffy_Placebo_Baseline_Subject_37


title: Buffy_Placebo_Follow-up_Subject_40


title: Buffy_Placebo_Follow-up_Subject_35


title: Buffy_Placebo_Baseline_Subject_38


title: Buffy_Placebo_Baseline_Subject_34


title: Buffy_Placebo_Baseline_Subject_35


title: Buffy_Placebo_Follow-up_Subject_34


title: Buffy_Placebo_Baseline_Subject_36


title: Buffy_Placebo_Follow-up_Subject_36


title: Buffy_Placebo_Follow-up_Subject_33


title: Buffy_Placebo_Follow-up_Subject_37


title: Buffy_Placebo_Baseline_Subject_33


title: Buffy_Placebo_Follow-up_Subject_31


title: Buffy_Placebo_Follow-up_Subject_32


title: Buffy_Placebo_Baseline_Subject_30


title: Buffy_Placebo_Baseline_Subject_41


title: Buffy_Placebo_Baseline_Subject_31


title: Buffy_Placebo_Baseline_Subject_29


title: Buffy_Placebo_Follow-up_Subject_29


title: Buffy_Placebo_Follow-up_Subject_30


title: Buffy_Placebo_Follow-up_Subject_28


title: Buffy_Placebo_Follow-up_Subject_27


title: Buffy_Placebo_Baseline_Subject_32


title: Buffy_Placebo_Baseline_Subject_26


title: Buffy_Placebo_Follow-up_Subject_26


title: Buffy_Placebo_Follow-up_Subject_25


title: Buffy_Placebo_Baseline_Subject_25


title: Buffy_Placebo_Follow-up_Subject_23


title: Buffy_Placebo_Baseline_Subject_28


title: Buffy_Placebo_Baseline_Subject_22


title: Buffy_Placebo_Baseline_Subject_24


title: Buffy_Placebo_Baseline_Subject_27


title: Buffy_Placebo_Follow-up_Subject_19


title: Buffy_Placebo_Baseline_Subject_21


title: Buffy_Placebo_Follow-up_Subject_24


title: Buffy_Placebo_Follow-up_Subject_22


title: Buffy_Placebo_Baseline_Subject_19


title: Buffy_Placebo_Baseline_Subject_17


title: Buffy_Placebo_Follow-up_Subject_16


title: Buffy_Placebo_Follow-up_Subject_17


title: Buffy_Placebo_Follow-up_Subject_21


title: Buffy_Placebo_Baseline_Subject_18


title: Buffy_Placebo_Follow-up_Subject_15


title: Buffy_Placebo_Baseline_Subject_16


title: Buffy_Placebo_Follow-up_Subject_18


title: Buffy_Placebo_Follow-up_Subject_20


title: Buffy_FA/vB12_Follow-up_Subject_46


title: Buffy_Placebo_Follow-up_Subject_13


title: Buffy_Placebo_Baseline_Subject_15


title: Buffy_Placebo_Follow-up_Subject_14


title: Buffy_Placebo_Baseline_Subject_14


title: NK.CD127-.SI#3

status: Public on Jan 15 2015

city: Boston

first: Liang

last: Yang

state: MA

address: 77 Avenue Louis Pasteur

department: Pathology

institute: Harvard Medical School

hyb_protocol: Ambion WT Expression Kit

scan_protocol: Affymetrix GeneChip Scanner

data_processing: The datasets was 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, quantile normalization, median polish probeset summarization). Output on 2^ scale.

source_name: Small Intestine (Lamina Propria)

label_protocol: Affymetrix GeneChip WT Terminal Labeling and Controls Kit

extract_protocol: TriZol

tag: age

value: 46 Days Old

tag: exclusion markers

tag: genetic background

value: B6 RORgt-GFP

tag: phenotype markers

tag: separation method

value: FACSAria

tag: Sex

value: Male


title: Buffy_Placebo_Baseline_Subject_12

tag: tissue


title: Buffy_Placebo_Follow-up_Subject_11

tag: subject


title: Buffy_Placebo_Follow-up_Subject_12

tag: intervention


title: Buffy_Placebo_Baseline_Subject_13

tag: time point


title: Buffy_Placebo_Baseline_Subject_11

tag: age at baseline


title: NK.CD127-.SI#1

value: 52 Days Old


title: Buffy_Placebo_Follow-up_Subject_10

tag: bisulfite plate


title: Buffy_Placebo_Baseline_Subject_23

tag: mthfr c677t genotype


title: Buffy_Placebo_Follow-up_Subject_7

tag: serum folate levels (nm/l)


title: Buffy_Placebo_Baseline_Subject_5

tag: serum vitamin b12 levels (pm/l)


title: Buffy_Placebo_Baseline_Subject_9

tag: plasma homocysteine levels (µm/l)


title: Buffy_Placebo_Follow-up_Subject_8

tag: gender


title: NK.CD49b+.Lv#2

source_name: Liver

tag: age

value: 9 Weeks Old

value: CD3, CD19, 7-AAD

value: CD45+ CD3- CD19- NKp46+ NK1.1+ DX5+ TRAIL-


title: Buffy_Placebo_Baseline_Subject_4

value: buffy coat


title: Buffy_Placebo_Follow-up_Subject_4


title: Buffy_Placebo_Baseline_Subject_10


title: Buffy_Placebo_Baseline_Subject_6


title: Buffy_Placebo_Follow-up_Subject_3


title: Buffy_Placebo_Baseline_Subject_7


title: Buffy_Placebo_Follow-up_Subject_6


title: NK.CD49b+.Lv#3

value: 10 Weeks Old

tag: exclusion markers


title: NK.CD49b+.Lv#1

tag: genetic background


title: NK.CD127-.Sp#3

source_name: Spleen

value: 7 Weeks Old

tag: phenotype markers


title: Buffy_Placebo_Follow-up_Subject_1

value: female


title: ILC3.NKp46-.4-.SI#6

value: 8 Weeks Old

value: NKp46- CD4-

tag: separation method


title: Buffy_Placebo_Baseline_Subject_8

value: baseline

value: TT


title: ILC3.NKp46-.4+.SI#1

value: NKp46- CD4+

tag: Sex


title: Buffy_Placebo_Baseline_Subject_2

tag: tissue

value: placebo

value: male

value: CC


title: Buffy_Placebo_Baseline_Subject_3

tag: subject


title: ILC3.NKp46-.4+.SI#4

value: FACSAria

value: Male


title: Buffy_Placebo_Follow-up_Subject_9

tag: intervention

value: follow-up


title: Buffy_Placebo_Baseline_Subject_20

tag: time point


title: ILC3.NKp46-.4-.SI#5


title: Buffy_Placebo_Follow-up_Subject_2

tag: age at baseline


title: ILC3.NKp46-.4-.SI#4


title: Buffy_Placebo_Baseline_Subject_1

tag: bisulfite plate


title: ILC3.NKp46+.Rorgthi.SI#1

value: 52 Days Old

value: B6 RORgt-GFP

value: CD45+ NKp46+ RORgthi


title: ILC2.SI#3

value: CD3, CD19, 7-AAD


title: ILC2.SI#2

value: 7 Weeks Old


title: ILC3.NKp46+.Rorgthi.SI#2


title: ILC1.CD49b-.Lv#3

value: 10 Weeks Old

value: CD45+ CD3- CD19- NKp46+ NK1.1+ DX5- TRAIL+


title: ILC1.CD127+.SI#3

value: 46 Days Old


title: ILC1.CD49b-.Lv#2

value: 9 Weeks Old


title: ILC1.CD127+.Sp#3


title: ILC1.CD127+.Sp#1


title: ILC1.CD49b-.Lv#1


title: ILC3.NKp46+.Rorgthi.SI#3


title: ILC1.CD127+.Sp#2


title: Mo.Lu#1

status: Public on May 23 2014

source_name: Lung

value: 6 Weeks

value: MertK- CD11cint/lo CD11b+ CD64+ Ly6C+ MHCII+

value: lung


title: CD8.96h.LN#1

status: Public on Mar 28 2014

source_name: Lymph Node

value: 6 Weeks OLD

tag: cell treatment

value: Cultured with antiCD3 CD28 beads and collected at various time points

value: CD8+ CD4- TCR+ CD25- CD62Lhi CD44 Lo

value: Dissection / Trimming


title: Gen2.2 replicate 2

status: Public on Jul 30 2014

city: Granada

first: Pedro

last: Carmona

address: Avda. de la Ilustración 114

institute: GENYO

description: replicate 2

hyb_protocol: Standard Illumina Human-HT12 Version 4

scan_protocol: Standard Illumina Genome Studio

data_processing: The data were background corrected and normalized using the neqc function from the Limma package

source_name: Gen2.2 cell culture

label_protocol: Illumina TotalPrep RNA Amplification Kit

growth_protocol: Cells were mantained in RPMI 1640 supplemented with 10% FBS

extract_protocol: RNA was extracted high pure RNA isolation kit from Roche, in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Cultured cells at log phase

tag: cell line

tag: cell type

value: pDC leukemia

tag: treatment


title: Gen2.2 replicate 1

description: replicate 1


title: Mo.Lu#3

value: FACSAria

value: Male


title: CD8.24h.LN#2


title: NK.CD127-.Sp#1


title: CD8.5h.LN#2


title: CD8.CTR.LN#2


title: Gen2.2 replicate 3

description: replicate 3


title: Buffy_Placebo_Follow-up_Subject_5

value: buffy coat

value: placebo

value: follow-up

tag: gender

value: female

tag: mthfr c677t genotype

value: CC

tag: serum folate levels (nm/l)

tag: serum vitamin b12 levels (pm/l)

tag: plasma homocysteine levels (µm/l)


title: CD8.48h.LN#2

tag: age

tag: exclusion markers

tag: genetic background

tag: phenotype markers

tag: separation method


title: CD8.5h.LN#1

tag: Sex


title: CD8.48h.LN#1


title: CD8.CTR.LN#1


title: CD4.CTR.LN#2

value: CD4+ CD8- TCR+ CD25- CD62Lhi CD44 Lo


title: CD8.1h.LN#1


title: CD4.96h.LN#1


title: CD8.1h.LN#2


title: CD4.5h.LN#2


title: CD4.48h.LN#1


title: CD4.5h.LN#1


title: CD8.24h.LN#1


title: CD4.CTR.LN#1


title: Mo.Lu#2

tag: tissue


title: CD4.48h.LN#2


title: CD4.24h.LN#1


title: CD4.24h.LN#2


title: MF.F480hi.ctrl.PC#1

status: Public on Jan 16 2014

description: Macrophage, mixed background

source_name: Peritoneal Cavity

tag: genotype/variation

value: ctrl

tag: ageunit

value: Weeks

value: mixed background

value: F4/80hi ICAM2hi CD11bhi


title: CD4.1h.LN#2

value: 6 Weeks OLD

tag: cell treatment


title: ILC1.CD127+.SI#1

value: 52 Days Old

value: B6 RORgt-GFP


title: CD4.1h.LN#1

value: Cultured with antiCD3 CD28 beads and collected at various time points

value: Dissection / Trimming


title: MF.F480hi.Gata6ko.PC#3

description: Macrophage, mixed background

value: FACSAria


title: MF.F480hi.Gata6ko.PC#1

description: Macrophage, mixed background

value: Male


title: MF.F480hi.ctrl.PC#2

description: Macrophage, mixed background


title: T.DP69+.Th.v2#3

status: Public on Dec 07 2013

description: abT Cell

source_name: Thymus

value: 6 Weeks


title: T.DP69+.Th.v2#1

description: abT Cell


title: LEC.SLN.v2#1

description: Stromal Cell, C57BL/6J

source_name: Lymph Node (Subcutaneous)


title: MF.AT.v2#1

description: Macrophage, C57BL/6J

source_name: Fat (Visceral)

value: 45 Days

value: B220 SiglecF

value: CD45+ CD64+ Mertk+


title: T.DP.Th.v2#1

description: abT Cell


title: MF.AT.v2#3

description: Macrophage, C57BL/6J

value: 50 Days


title: T.DP69+.Th.v2#2

description: abT Cell


title: MF.F480hi.ctrl.PC#3

description: Macrophage, mixed background


title: T.DP.69-.e17.Th.v2#1

description: abT Cell, C57BL/6J

value: 5 Weeks

value: Mixed


title: LEC.SLN.CFA.d6.v2#2

description: Stromal Cell, C57BL/6J


title: GN.Bl.v2#6

description: Neutrophil, C57Bl/6J

source_name: Blood

value: 43 Days

value: SSChi Ly6Ghi


title: MF.F480hi.Gata6ko.PC#2

description: Macrophage, mixed background

value: Weeks

value: mixed background

value: F4/80hi ICAM2hi CD11bhi


title: T.DP.69-.e17.Th.v2#2

description: abT Cell, C57BL/6J


title: T.DP.69-.e17.Th.v2#3

description: abT Cell, C57BL/6J


title: MF.AT.v2#4

description: Macrophage, C57BL/6J

value: 52 Days


title: T.DP.Th.v2#3

description: abT Cell


title: GN.Bl.v2#5

description: Neutrophil, C57Bl/6J


title: NK.CD127-.Sp#2

value: 9 Weeks Old

value: CD3, CD19, 7-AAD


title: GN.Bl.v2#4

description: Neutrophil, C57Bl/6J

value: 7 Weeks

value: FACSAria


title: T.DP.Th.v2#2

description: abT Cell

value: 6 Weeks

tag: exclusion markers:

value: Male


title: FRC.SLN.v2#2

description: Stromal Cell, C57BL/6J

value: Dissection / Trimming


title: FRC.SLN.CFA.d6.v2#1

description: Stromal Cell, C57BL/6J


title: Eo.BL.v2#5

description: Eosinophil, C57BL/6

value: SSChi SiglecF+


title: FRC.Cad11.WT.v2#1

description: Stromal Cell, C57BL/6J 129SJL Cadherin 11 WT

value: C57BL/6J 129SJL Cadherin 11 WT


title: LEC.SLN.v2#2

description: Stromal Cell, C57BL/6J


title: GN.Bl.v2#7

description: Neutrophil, C57Bl/6J

value: 48 Days


title: FRC.SLN.CFA.d6.v2#2

description: Stromal Cell, C57BL/6J


title: Eo.BL.v2#3

description: Eosinophil, C57BL/6J

value: MHCII, CD4, B220


title: DN.SLN.v2#2

description: Stromal Cell, C57BL/6J


title: EO.AT.v2#1

description: Eosinophil, C57BL/6J

value: 45 Days

value: FSC B220

value: CD11b+ SiglecF+


title: DN.SLN.CFA.d6.v2#2

description: Stromal Cell, C57BL/6J


title: DN.SLN.v2#1

description: Stromal Cell, C57BL/6J


title: Eo.BL.v2#2

description: Eosinophil, C57BL/6J

value: 44 Days


title: FRC.SLN.v2#1

description: Stromal Cell, C57BL/6J


title: DN.SLN.CFA.d6.v2#1

description: Stromal Cell, C57BL/6J


title: Mo.6+2+.MLN#1

status: Public on May 09 2013

source_name: Lymph Node (Mesenteric)

value: 6 weeks

value: male

value: CD11b+ Ly6C+ MHCII+ CD64+ CD11cint/lo


title: DC.11b+.AT.v2#4

description: Dendritic Cell, N/A

value: 52 Days

value: B220 SiglecF CD64 Mertk

value: CD45+ MHCIIhi CD11c+ CD11b+


title: Mo.6+2+.SLN#1

source_name: Lymph Node (Skin-Draining)

value: CD11b+ CD64+ Ly6C+ MHCII+ CD11cint/lo

value: FACSAria


title: B.Mem.Sp.v2#1

description: B Cell, C57BL/6J

value: 15 Weeks

value: CD3, Ter119, Ly6c, CD11b, GR-1

value: Dissection / Trimming

value: Male


title: DC.11b-.AT.v2#1

description: Dendritic Cell, C57BL/6J

value: CD45+ MHCIIhi CD11c+


title: Mo.6+2-.BL#2

value: CD115+ Ly6C+ MHCII+

value: Dissection/trimming


title: DC.11b+.AT.v2#3

description: Dendritic Cell, N/A

value: 50 Days


title: Mo.6+2+.SLN#2


title: DC.11b-.AT.v2#3

description: Dendritic Cell, C57BL/6J


title: MF.Alv.Lu#3

value: MertK+ CD64+ CD11c+ CD11b-


title: Mo.6+2+.SLN#3

value: 6 weeks


title: DC.11b+.AT.v2#2

description: Dendritic Cell

value: 48 Days


title: B.Mem.Sp.v2#3

description: B Cell, C57BL/6J


title: MF.Alv.Lu#2

value: male


title: MF.11c-11b+.Lu#1

value: MertK+ CD64+ CD11c- CD11b+


title: MF.Alv.Lu#1


title: B1a.Sp.v2#6

description: B Cell

value: 9 Weeks


title: MF.11c-11b+.Lu#2


title: MF.11c-11b+.Lu#3


title: Mo.6+2-.BL#3


title: Mo.6+2+.BL#1


title: Bisulfite-Seq analysis of WGBS_Lib 11 derived from human liver cells; WGBS_Lib 11

status: Public on Sep 13 2012

city: Cambridge

first: BROAD

last: INSTITUTE

institute: Broad Institute

description:
sample_term_id: UBERON_0002107
assay_term_id: OBI_0001863
nucleic_acid_term_id: SO_0000352
Design description: WGBS REMC Sequencing on Illumina
Library name: WGBS_Lib 11
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.11648
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5941
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

library_source: genomic

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM916049_BI.Adult_Liver.Bisulfite-Seq.3.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: WGBS_Lib 11.hg19.level.2.release.8
ANALYSIS TITLE: Methylation Proportion Graphs of Adult Liver Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from Adult Liver, Donor 3 were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads. Reads from the + and - strands were combined for methylation proportion calculations.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13769
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 8
BROWSER_TRACK_NAME: AL BS 3 11
BROWSER_TRACK_DESCRIPTION: BI Adult Liver Bisulfite-Seq Donor 3 Library WGBS_Lib 11 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 1,565,245,097
NUMBER_OF_Bisulfite-Seq_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 6
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.47
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 50
MAXIMUM_REPLICATE_CORRELATION: NA

**********************************************************************

source_name: normal adult liver; WGBS_Lib 11

extract_protocol: Library construction protocol: Genomic DNA (1.5~5µg) was fragmented to 100-500 bp using a Covaris S2. Purified DNA fragments were end-repaired. After A-tailing, the DNA fragments were ligated with methylated paired-end adapters. Adapter-attached DNA fragments of 300-400 bp, which contain 150-250 bp genomic DNA inserts, were gel-purified. The purified DNA fragments were subjected to two cycles of sodium bisulfite conversion using the EpiTect Bisulfite kit (Qiagen). Adapter-attached, bisulfite-converted DNA molecules were enriched by PCR using PfuTurboCx Hotstart DNA polymerase (Stratagene). The PCR amplified DNA fragments were subjected to a second gel size selection to remove PCR primers and adapter dimers. The enriched library was quantified using a Qubit fluorometer and Quant-iT dsDNA HS Assay Kit. Library sequencing was performed using 101 BP PE Illumina technology.

tag: sample alias

tag: sample common name

value: Adult Liver

value: surgery

tag: molecule

value: genomic DNA

tag: disease

value: Unknown

value: Primary Tissue

value: liver

value: MGH Pathology

value: 2x5hrs Epitect Kit

value: 5 ug

value: Covaris shearing, duty cycle 5%, intensity 5, cycles / burst 200, duration 9 minutes

value: T4 Ligase (2,000U/ul) 16C o/n

value: Illumina paired end adapter

value: Standard Protocol (Smith et al., Methods 48, 226-232)

value: DNA Methylation

value: Smith et al., Methods 48, 226-232

value: SPRI Beads

value: Pfu Turbo Cx hot start

value: Covaris S2 (TM)


title: dsGFP treated worker light brown-eyed pupae vs. control

status: Public on Jan 10 2013

city: Piracicaba

first: Ana

middle: Durvalina

last: Bomtorin

state: São Paulo

address: R Ajudante Albano 847

country: Brazil

institute: Universidade de Sao Paulo

hyb_protocol: For hybridization, probes [in 44µL of hybridization solution (27.5ul of formamide hyb. buffer, 13.75ul KREAblock; 2.75ul Nuclease-free water] were incubated at 80°C for 10 min and incubated at 42oC until samples were loaded onto microarrays. Microarrays slides were placed in single slide hybridization chambers in MAUI Mixer A4 Hybridization Chambers (BioMicro Systems, Inc.) for 15-17 hours, at (42oC) under controlled humidity. Washing procedure included three washes, the first one : 100ml SSC 2X, 20ml 10% SDS and 880ml MilliQ water; the second wash: 100ml 20x SSC and 900 ml MilliQ water; and the last wash: 10ml 20x SSC and 990 ml MilliQ water. The washes were made at room-temperature with shaking for 10 minutes, and centrifuged 500g for 2 minutes.

scan_protocol: Slides were scanned by using  Axon GenePix 4000B, using the following parameters: ratio of signal to background >2-3, median intensity of each dye >1000. GenePix auto-pmt default is 0,05%, we changed it to 0.1%.

data_processing:
Each spot showing  an intensity less than the median array background intensity (300) were removed from the analysis. Spots with less than 14 measures, out of a possible 16, were also removed from the analysis. The data that pass through those criteria were transformed in log and analyzed by an ANOVA mixed-model approach in the SAS software (SAS® 9.2 Software - http://www.sas.com/software/sas9/) (Wolfinger et al. 2001, Ayroles & Gibson, 2006; Kocher et al., 2008). P-values were corrected using multiple tests to adjust the False Discovery Rate (FDR). FDR used were 0.05 (FDR05), supposing that only 5% of significantly differentially expressed transcripts were false positives
All data were log-transformed, and subsequently normalized using a mixed-model ANOVA.

label: Cy5, Cy3

organism: Apis mellifera

source_name: untreated (control) worker light brown-eyed pupae

label_protocol: RNA amplification (from 750 ng of total RNA) and probe synthesis (from 4μg of amplified RNA) were done with and according to Amino Allyl MessageAmp™ II aRNA Amplification Kit (Ambion).

growth_protocol: Bees were obtained from the Experimental Apiary of the Chemical Ecology Lab - State College - Pennsylvania State University

extract_protocol: Total RNA was extracted using Trizol (Invitrogen) following Invitrogen’s protocol and purified using RNeasy Mini Kit (QIAGEN).

treatment_protocol: L2 workers were treated with 1ul of dsGFP (5ug/ul) eluted in Rnase-Free water and collected in pre-pupal or in light brown-eyed pupal stages

tag: treatment

value: control

value: dsRNA-GFP


title: Tgd.vg4+24alo.e17.Th#1

status: Public on Apr 24 2012

description: Tgd.vg4+24alo.e17.Th#1, Thymus B6 E17 TCRgammadelta Vg3- Vg2- Vg1.1- Vg5- CD24lo

source_name: thymus

extract_protocol: Glass Tissue Grinder, ACK Lysis Buffer, Flow Sorting, TriZol

value: 5 weeks

value: TCRd+ CD24lo

value: Dissection/trimming

tag: gender

value: male

tag: cell type


title: Tgd.vg4+24alo.e17.Th#2

description: Tgd.vg4+24alo.e17.Th#2, Thymus B6 E17 TCRgammadelta Vg3- Vg2- Vg1.1- Vg5- CD24lo

tag: age

tag: exclusion markers


title: Tgd.vg2+24ahi.e17.Th.v2#3

description: Tgd.vg2+24ahi.e17.Th#3, Thymus B6 E17 TCRgammadelta Vg2+ CD24hi

tag: genetic background

tag: phenotype markers

value: TCRd+ Vg2+ CD24hi


title: Tgd.vg4+24ahi.e17.Th#2

description: Tgd.vg4+24ahi.e17.Th#2, Thymus B6 E17 TCRgammadelta Vg3- Vg2- Vg1.1- Vg5- CD24hi

value: TCRd+ CD24hi

tag: separation method


title: Tgd.vg4+24ahi.e17.Th#3

description: Tgd.vg4+24ahi.e17.Th#3, Thymus B6 E17 TCRgammadelta Vg3- Vg2- Vg1.1- Vg5- CD24hi


title: Non-treated vs dsRNA-GFP-treated honey bee larvae

hyb_protocol: For hybridization, probes [in 40µL of hybridization solution (0.98mL of formamide, 0.98mL SSC 20X, 39.2µLSDS 10%)] were pre-heated at 55°C during at 3 min and placed on microarrays under lifter-slip cover glasses (22x60, 31.25µL). Microarrays slides were placed in single slide hybridization chambers which were incubated in a water bath for hybridization for 22h, at 42°C. Washing procedure included twice the following steps: SSC 2X, SDS 0,1%; SSC 0,5X, SDS 0,01%; SSC 2X; SSC 0,1X; deionized water, shaking manually for 30s and for the last incubated in isopropanol before centrifuging for 3min at 2000rpm.

scan_protocol: Slides were scanned and images quantified by using Axon GenePix 4000B at default parameters.

data_processing: Background correction was performed in a manner we could avoid the correction of negative or zero intensities (offset correction) by adding to the background-corrected intensities a positive constant (=50). It restrains spurious variation in log-ratios, particularly at low intensity spots. The “loess” normalization was used to correct for within-array dye and spatial effects and single channel normalization was used to facilitate comparison between arrays. After normalization we determined a log2 ratio (dsRNA-Vg sample intensity/dsRNA-GFP sample intensity), for each probe on each array. The fold-change in expression and its standard error for each gene were calculated by fitting a linear regression to the normalized expression data. A Bayesian smoothing procedure was used to shrink the estimated standard errors, with which we calculated the moderated t-statistic for each gene.

source_name: dsRNA-GFP

label_protocol: RNA amplification (from 1μg of total RNA) and probe synthesis (from 20μg of amplified RNA) were done with and according to Amino Allyl MessageAmp™ II aRNA Amplification Kit (Ambion).

tag: developmental stages

value: 5th instar spinning phase worker larvae (L5S2)

tag: bee type

value: worker treated with dsRNA-GFP

tag: tissue

value: whole larval body

source_name: Control

value: worker non-treated (control)


title: Tgd.vg2+24ahi.e17.Th.v2#2

description: Tgd.vg2+24ahi.e17.Th#2, Thymus B6 E17 TCRgammadelta Vg2+ CD24hi


title: Tgd.vg2+24ahi.e17.Th.v2#1

description: Tgd.vg2+24ahi.e17.Th#1, Thymus B6 E17 TCRgammadelta Vg2+ CD24hi


title: dsRNA-GFP vs non-treated control fat body analysis

scan_protocol: Slides were scanned and images quantified by using  Axon GenePix 4000B at default parameters.

data_processing: Background correction was performed in a manner we could avoid the correction of negative or zero intensities (offset correction) by adding to the background-corrected intensities a positive constant (=50). It restrains spurious variation in log-ratios, particularly at low intensity spots. The “loess” normalization was used to correct for within-array dye and spatial effects and single channel normalization was used to facilitate comparison between arrays. After normalization we determined a log2 ratio (dsRNA-GFP sample intensity/control sample intensity), for each probe on each array. The fold-change in expression and its standard error for each gene were calculated by fitting a linear regression to the normalized expression data. A Bayesian smoothing procedure was used to shrink the estimated standard errors, with which we calculated the moderated t-statistic for each gene.

value: 7 day-old adult worker

value: fat body

value: worker with no treatment


title: dsRNA-Vg/dsRNA-GFP fat body analysis

value: adult

source_name: dsRNA-Vg

value: worker treated with dsRNA-Vg


title: Tgd.vg4+24ahi.e17.Th#1

description: Tgd.vg4+24ahi.e17.Th#1, Thymus B6 E17 TCRgammadelta Vg3- Vg2- Vg1.1- Vg5- CD24hi


title: CD4-430-D

status: Public on Mar 03 2012

city: Newcastle

first: Simon

last: Cockell

address: Framlington Place

country: United Kingdom

institute: Newcastle University

hyb_protocol: cRNA was hybridized to the Illumina Whole Genome 6 (version 3) BeadChip (Illumina, San Diego, non-RA inflammatory arthritisA), following the manufacturer’s protocol.

scan_protocol: Each BeadChip measured the expression of 48,804 genes (annotation file at http://www.illumina.com/support/annotation_files.ilmn) and was imaged using the Illumina BeadArray Reader.

data_processing:
Phases 1 and 2 of the study were independently normalized in 2 steps: each probe measurement was first divided by the 50th percentile of all measurements in its array, before being centred around its own median expression measurement accross all samples in the phase. The within-phase batch-effect related to RNA labelling was corrected in the R statistical computing environment (http://www.r-project.org/) using the empirical Bayes method of Johnston et al. (2007) before phases were combined.  Phases were then combined and residual between-phase batch effect corrected by the same method.

Non-normalized data is available in 'GSE20098_non-normalized.txt', which is linked to the Series GSE20098 record as a supplementary file.

source_name: ex-vivo peripheral blood CD4 T-cells, non-RA/non-inflammatory arthritis

label_protocol: 250ng RNA was reverse transcribed into cRNA, and biotin-UTP labeled, using the Illumina TotalPrep RNA Amplification Kit (Ambion, Texas).

extract_protocol: Monocytes were first depleted by immunorosetting (Rosettesep Human Monocyte depletion cocktail, Stemcell Technologies Inc., Vancouver, non-RA inflammatory arthritisanada), and remaining cells underwent positive selection using Easisep whole blood CD4+ positive selection kit reagents in conjunction with the Robosep automated cell separator (Stemcell). CD4+ T-cell purity was determined using standard flow cytometry techniques; FITC-conjugated anti-CD4 and PE-conjugated anti-CD14 antibodies were used (Beckton Dickinson, New Jersey, USA). RNA was immediately extracted from CD4+ T-cell isolates using RNeasy MINI kits (Qiagen GmbH, Germany), incorporating an “on-column” DNA digestion step.

treatment_protocol: Between 1300hrs and 1630hrs during the clinic appointment, 15ml peripheral whole blood was drawn into EDTA tubes (Greiner Bio-One, ACPA- RAustria) and stored at room temperature for a maximum of 4 hours before processing.

value: peripheral blood

value: CD4+ T-cells

tag: outcome

value: D

tag: classification

value: UA

tag: phase batch

tag: labelling batch


title: CD4-392-D


title: CD4-397-A

source_name: ex-vivo peripheral blood CD4 T-cells, ACPA- RA

value: A


title: CD4-142-A

value: training


title: CD4-433-D


title: CD4-378-B

source_name: ex-vivo peripheral blood CD4 T-cells, ACPA+ RA

value: B


title: CD4-431-C

source_name: ex-vivo peripheral blood CD4 T-cells, non-RA inflammatory arthritis

value: C


title: CD4-412-C