title: 12N-UC-Normal-Cecum-3

value: Cecum


title: 15N-UC-Inactive-Transverse-6

status: Public on Nov 11 2017

type: RNA

city: Saint Louis

first: Mei San

last: Tang

state: MO

address: 660 S Euclid, Campus Box 8118

department: Pathology & Immunology

country: USA

institute: Washington University in St Louis

hyb_protocol: Equal amount of Cy3 labeled target was hybridized to Sureprint G3 Human GE 8x60k array (Agilent) for 15 hours according to the manufacturers protocol

scan_protocol: Arrays were scanned using Agilent microarray scanner

data_processing: Raw signal intensities were extracted with feature extraction v11.5 software

molecule: total RNA

organism: Homo sapiens

source_name: Intestinal mucosa pinch biopsy

label_protocol: Labeling was performed with Cy3 according to the manufacturer protoocl for one color microarray based gene expression analysis (Agilent)

extract_protocol: Pinch biopsies were obtained at colonoscopy using sterile cold biopsy forceps and snap-frozen for RNA extraction in Trizol reagent (Invitrogen). RNA was isolated using chloroform purification and isopropanol extraction and purified using QIAgen Rneasy Mini Kit.

tag: disease (uc = ulcerative colitis; cd = crohn's disease)

value: UC

tag: inflammation

value: Inactive

tag: intestinal region

value: Transverse


title: 11I-CD-Active-Sigmoid-2

value: CD

value: Active

value: Sigmoid


title: 10I-CD-Active-Ileum-1

value: Ileum


title: 17N-CD-Normal-Descending-7

value: Normal

value: Descending


title: LS174T_Ctl_3

status: Public on Nov 10 2017

city: Lübeck

first: Hauke

last: Busch

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: Lübeck Institute of Experimental Dermatology

country: Germany

institute: University of Lübeck

description:
C_3
Array ID: 200739030022

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: All arrays were normalized together using the quantile normalization algorithm without background subtraction using the R Bioconductor beadarray package

label: Biotin

source_name: LS174T cell clone (1C6),CRISPR/Cas9 treated, FOXA1 locus WT

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

growth_protocol: LS174T cells were purchased from the Cell Line Service culture collection (CLS #300392, DKFZ, Heidelberg). Cell lines were maintained in growth medium consisting of DMEM supplemented with 10% FCS, 10 mM Hepes, 1/100 MEM non-essential amino acid solution and 1/100 penicillin/streptomycin

extract_protocol: Total RNA was isolated from LS174T cells using the PeqGOLD total RNA Kit (#732-2871, Peqlab/VWR Life Science)

treatment_protocol: LS174T cells were subjected to CRISPR/Cas9 genome editing using a guide RNA targeting exon 2 of the FOXA1 locus, followed by single cell cloning.

tag: cell line

tag: replicate

tag: genotype

value: WT

tag: treatment

value: transfected


title: LS174T_WT_3

description:
WT_3
Array ID: 200739030022

source_name: LS174T parental

value: untransfected


title: 5N-CD-Inactive-Transverse-22


title: LS174T_K1_2

description:
K1_2
Array ID: 200739030022

source_name: LS174T cell clone (2F8),CRISPR/Cas9 treated, FOXA1 Knock-out

value: FOXA1 Knockout


title: LS174T_Ctl_2

description:
C_2
Array ID: 200739030022


title: OSK-A549-SN-1 (P106)

status: Public on Nov 09 2017

city: Kobe City

first: Michiyo

last: Koyanagi-Aoi

address: Chuo-ku, Kusunoki-cho 7-5-1

country: Japan

institute: Kobe University

description: AR2166 05 a OSK A549 SN-1 (P106)

hyb_protocol: Agilent standard protocol

scan_protocol: Agilent standard protocol

data_processing: The data were analyzed using the Gene Spring GX 13.1.1 software program (Agilent Technologies).The data processing was performed as follows; (i) Threshold raw signals were set to 1.0, (ii) Log base 2 transformation was performed, (iii) 75th percentile normalization was chosen as the normalized algorithm.

label_protocol: Agilent standard protocol

extract_protocol: Total RNA was isolated by Trizol reagent (Life Technologies) according to the manufacturer's instruction.

tag: cell line background

tag: cell type

value: lung cancer cell line

tag: cell subtype

value: differentiated non lung cancer stem like cells (OSK-A549-SN)

tag: tranduced with

value: OSK via retrovirus


title: OSK-A549-Colony-2 (P107)

description: AR2166 06 a OSK A549 Colony-2 (P107)

value: induced lung cancer stem like cells (OSK-A549-Colony)


title: LS174T_K1_1

description:
K1_1
Array ID: 200739030022


title: OSK-A549-Colony-3 (P106)

description: AR2166 08 a OSK A549 Colony-3 (P106)


title: LS174T_K2_3

description:
K2_3
Array ID: 200739030022

source_name: LS174T cell clone (2F12),CRISPR/Cas9 treated, FOXA1 Knock-out


title: OSK-A549-Colony-1 (P106)

description: AR2166 04 a OSK A549 Colony-1 (P106)


title: LS174T_Ctl_1

description:
C_1
Array ID: 200739030022


title: LS174T_K2_2

description:
K2_2
Array ID: 200739030022


title: OSK-A549-SN-2 (P107)

description: AR2166 07 a OSK A549 SN-2 (P107)


title: A549-2 (P98)

description: AR2166 02 a A549-2 (P98)

source_name: parental A549

value: parental A549


title: LS174T_WT_2

description:
WT_2
Array ID: 200739030022


title: LS174T_K1_3

description:
K1_3
Array ID: 200739030022


title: OSK-A549-SN-3 (P106)

description: AR2166 09 a OSK A549 SN-3 (P106)


title: LS174T_WT_1

description:
WT_1
Array ID: 200739030022


title: A549-1 (P98)

description: AR2166 01 a A549-1 (P98)


title: A549-3 (P99)

description: AR2166 03 a A549-3 (P99)


title: AN24h2_HZ

city: Madrid

first: Sara

last: Pulido

address: Arturo Duperier, 4.

department: Department of Endocrine and Nervous Systems Pathophysiology

country: Spain

institute: Alberto Sols Biomedical Research Institute (Spanish National Research Council - Autonomous University of Madrid)

data_processing:
The open source NormFinder  v.5 software was used to identify a pair of stable genes, which were Il18 and Trf6, used as reference genes for the normalization of the data. Normalization was performed using the geometric mean normalization method and the data subsequently  filtered to discard the genes whose expression was undetermined (Ct values > 35) in at least 90 % of the samples in the dataset.
Fold Chages in log scale report of comparisons between conditions
Delta Ct values of relative quantification of expression against endogenous.

organism: Mus musculus

source_name: HZ mice cochlea -24 hours post-noise exposure

label_protocol: Genes involved in inflammasome were studied with the “Mouse Inflammasomes RT² Profiler PCR Array” (PAMM-097ZA, SABiosciences Corp., Frederick, MD, USA). It includes a panel of 84 target genes and 5 housekeeping genes. First-strand cDNA was synthesised using the RT2 first strand kit (C-03, SABiosciences Corp.) and PCR arrays were then processed on an Applied Biosystems 7900HT Real-Time PCR System, to obtain the Ct values.

extract_protocol: Total RNA was extracted using the Qiagen RNeasy Micro Kit after cochleae homogenisation.

treatment_protocol: Six month-old wild type and Igf1 heterozygous mice were exposed to a violet swept sine noise (frequency range 2–20 kHz) at 110 dB SPL for 30 minutes.

tag: tissue

value: Cochlea

value: Igf1 heterozygous

tag: noise insult

value: 24 hours post-noise exposure


title: AN24h1_WT

source_name: WT mice cochlea -24 hours post-noise exposure

value: wild type


title: AN2h3_HZ

source_name: HZ mice cochlea -2 hours post-noise exposure

value: 2 hours post-noise exposure


title: AN2h2_HZ


title: AN24h2_WT


title: AN2h2_WT

source_name: WT mice cochlea -2 hours post-noise exposure


title: AN2h3_WT


title: AN2h1_HZ


title: LS174T_K2_1

description:
K2_1
Array ID: 200739030022


title: AN24h1_HZ


title: AN2h1_WT


title: C3HZ

description: control

source_name: HZ mice cochlea - without noise exposure

value: without noise exposure


title: C2HZ

description: control


title: C3WT

description: control

source_name: WT mice cochlea - without noise exposure


title: Tet-off vs Tat72_3

city: Belfast

first: Guillermo

last: López-Campos

state: Northern Ireland

address: 97 Lisburn road

department: Centre for Experimental Medicine

country: United Kingdom

institute: Queen's University of Belfast

description:
Jurkat cell line stably expressing Tat72
Analysis of the modifications in the miRNA expression profile induced by HIV-1 Tat72 in Jurkat cells.

hyb_protocol: Labeled samples were hybridized onto human dual color-based miRCURY LNA™ microRNA Array Kit 6th generation (Exiqon), which contained 2.383 capture probes with 4 capture probes for each miRNA. These probes were complementary to human miRNA sequences and related viral sequences obtained from the v.16.0 release of miRBase (www.mirbase.org) (Griffiths-Jones 2004), as well as human miRPlus™ sequences. Control capture probes were spike-in control probes to ensure optimal labeling and hybridization, negative control capture probes, and capture probes complementary to small nuclear RNAs.

scan_protocol: Slides were scanned at 5m resolution in an Axon 4000B scanner (Molecular Devices, Sunnyvale, CA) and spots quantified with GenePix 5.0 software.

data_processing:
Raw data imported from GenePix were normalized and subjected to statistical analysis of the differential expression using the Limma (Linear Models for Microarray Data) software package from Bioconductor (Smyth, 2005). Hy 3 controls where removed (as suggested by the manufacturer) and thendata were corrected for background  and normalized using a Loess normalization within the slides and a quantile normalization among the slides.
Analysis for differential gene expression was performed using the linear models and corrections for false discovery rate (FDR) and p-values were corrected by using the method of Benjamini and Hochberg (1995). Differentially expressed miRNAs were chosen according to fold change >1.5 or <1.5 and p values <0.05 in at least three probes.

source_name: Jurkat cell line, control

label_protocol: Jurkat-Tat101, Jurkat-Tat72, and control cell lines was subjected to specific labeling of miRNAs using miRCURY LNA™ microRNA Hy3/Hy5 Power labeling kit (Exiqon, Vedbaek, Denmark), according to manufacturer’s instructions.

growth_protocol: All Jurkat cell lines were cultured in RPMI 1640 medium ((Biowhittaker, Walkersville, MD) with 10% fetal calf serum (PAN Biotech GmbH, Aidenbach, Germany), 2mM L-glutamine, 100g/ml streptomycin and 100 U/ml penicillin (Lonza, Basel, Switzerland), at 37ºC and 5% CO2. Jurkat-TetOff pTRE2hyg were maintained in 300g/ml geneticin and both Jurkat-Tat72 and Jurkat-Tat101 cell lines were maintained in 300g/ml geneticin 300g/ml hygromycin B and (BD Biosciences Clontech).

extract_protocol: RNAs were extracted using Trizol reagent (Invitrogen) according to the manufacturer’s instructions and quantification and integrity of the RNAs were assessed in a Bionalyzer 2100 (Agilent Technologies).

treatment_protocol: Stable transfection with control vector, vector codifying for Tat72 and vector for Tat101. Vectors are maintained with antibiotics.

value: Jurkat

tag: genotype/variation

value: control

tag: cell line details

value: Human T-lymphocyte cell line that stably contains a control vector. These cell lines are maintained with antibiotics.

source_name: Jurkat Cell line, Transfected with Tat72

value: Human T-lymphocyte cell line that stably contains a vector encoding for HIV-1 protein Tat72 (first exon of Tat). These cell lines are maintained with antibiotics.


title: C2WT

description: control


title: C1WT

description: control


title: Tet-off vs Tat72_2


title: C1HZ

description: control


title: Tet-off vs Tat101_1

description:
Jurkat cell line stably expressing Tat101
Analysis of the modifications in the miRNA expression profile induced by HIV-1 Tat101 in Jurkat cells.

source_name: Jurkat Cell line, Transfected with Tat101

value: Human T-lymphocyte cell line that stably contains a vector encoding for HIV-1 protein Tat101 (complete two-exon Tat protein). These cell lines are maintained with antibiotics.


title: Tet-off vs Tat101_2


title: Tet-off vs Tat101_3


title: control-172

data_processing:
Raw signal intensities were extracted with feature extraction v11.5 software
Expression intensities were background corrected using the normal plus exponential convolutional method, followed by between-array quantile normalization in limma (version 3.26.9), resulting in log2-transformed intensity values.

tag: disease state

value: non-IBD control


title: Tet-off vs Tat72_1


title: day 5 differentiation siHIPK4 rep 2

city: heidelberg

first: Lionel

last: Larribere

address: im neuenheimer Feld

institute: DKFZ

description:
DKFZ
d5KD_2
replicate 2
9423641033_E

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

label: biotin

source_name: day 5 differentiation from hiPSCs, siHIPK4

extract_protocol: RNA was isolated with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Clean-up and DNase I treatment was included. Quality control was performed with Agilent Bioanalyser.

value: differentiated cells

tag: time


title: day 5 differentiation siControl rep 3

description:
DKFZ
d5_3
replicate 3
9423641033_K

source_name: day 5 differentiation from hiPSCs, siControl

value: siControl


title: day 10 differentiation siControl rep 3

description:
DKFZ
d10_3
replicate 3
9423641033_L

source_name: day 10 differentiation from hiPSCs, siControl


title: day 30 differentiation siControl rep 1

description:
DKFZ
d30_1
replicate 1
200641620027_K

source_name: day 30 differentiation from hiPSCs, siControl


title: day 10 differentiation siHIPK4 rep 1

description:
DKFZ
d10KD_2
replicate 1
9965581003_D

source_name: day 10 differentiation from hiPSCs, siHIPK4


title: day 10 differentiation siHIPK4 rep 3

description:
DKFZ
d10KD_3
replicate 3
9965581003_F


title: day 5 differentiation siHIPK4 rep 3

description:
DKFZ
d5KD_3
replicate 3
9423641033_I


title: day 5 differentiation siControl rep 1

description:
DKFZ
d5_1
replicate 1
9423641033_C


title: normal human keratinocytes rep 2

description:
isolated at DKFZ
NHK_2
replicate 2
9423641104_J

source_name: normal human keratinocytes from healthy donor

value: NHK


title: day 5 differentiation siHIPK4 rep 1

description:
DKFZ
d5KD_1
replicate 1
9423641033_A


title: day 30 differentiation siControl rep 2

description:
DKFZ
d30_2
replicate 2
200641620027_G


title: normal human keratinocytes rep 1

description:
isolated at DKFZ
NHK_1
replicate 1
8986302012_D


title: day 5 differentiation siControl rep 2

description:
DKFZ
d5_2
replicate 2
9423641033_G


title: day 30 differentiation siControl rep 3

description:
DKFZ
d30_3
replicate 3
8986302012_C


title: hiPSC rep 1

description:
reprogrammed at DKFZ
d0_1
replicate 1
8986302012_A

source_name: hiPSC from healthy donor

value: hiPSCs


title: normal human keratinocytes rep 3

description:
isolated at DKFZ
NHK_3
replicate 3
9423641104_K


title: day 10 differentiation siControl rep 1

description:
DKFZ
d10_1
replicate 1
9423641033_D


title: hiPSC rep 3

description:
reprogrammed at DKFZ
day0_3
replicate 3
9347704022_J


title: day 10 differentiation siControl rep 2

description:
DKFZ
d10_2
replicate 2
9423641033_H


title: GIST882 cell miR-494 transfected 72h rep3.

city: SEOUL

first: SeongJu

last: Yun

address: Sinchon-dong

country: South Korea

institute: Yonsei University

description: GIST 882 miR-494-3

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: Gastrointestinal Stromal tumor cells, miR-494 transfected, 72h.

growth_protocol: GIST430 cells were maintained in Iscove's Modified Dulbecco's Medium supplemented with 15% FCS and 1% penicillin/streptomycin, GIST882 cells were maintained in RPMI1640 medium supplemented with 15% FBS and 1% penicillin/streptomycin

extract_protocol: RNA was extracted with GE Health care illustra RNA spin kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: nontargeting microRNA or miR-494 treated

value: GIST cell line


title: hiPSC rep 2

description:
reprogrammed at DKFZ
day0_2
replicate 2
9347704022_I


title: 3hitNSCs_replicate1 (array)

type: genomic

city: New York

first: Aram

middle: S

last: Modrek

state: NY

address: 460 E 26th Street

department: Radiation Oncology

institute: New York University School of Medicine

description: 3 hit

hyb_protocol: According to manufacturer

scan_protocol: According to manufacturer

data_processing: BeadChip arrays were analyzed using the R package RnBeads verson 1.0.0 (Assenov et al., 2014). Probes overlapping single nucleotide polymorphisms (n=4713) were removed. The remaining probes were background-corrected using the “noob” method of the methylumi package, and the beta-values were normalized using the beta-mixture quantile method. Subsequent beta-values were used for principal component, exploratory hierarchical clustering, and differential methylation analyses.

label: Cy5 and Cy3

molecule: genomic DNA

source_name: hESC derived NSCs

growth_protocol: Human neural stem cells were grown in neural stem cell media: Neural Stem Cell Medium (NSCM) composed of DMEM/F12 (Invitrogen), N2 (Invitrogen), 20 ug/mL Insulin (Invitrogen), 1:1000 B27 (Invitrogen), 1.6 g/L glucose (Fisher) and 20 ng/mL EGF and FGF2 (R&D Systems).

extract_protocol: Genomic DNA was extracted from 5x10e5 cells in biological duplicates for vector, 1-hit, 2-hit and 3-hit NSCs using the DNeasy Blood and Tissue Kit (Qiagen). The Qubit 2.0 Fluorometer (Invitrogen Life Technologies) was used for DNA quantification with the Qubit dsDNA BR Assay Kit (Invitrogen Life Technologies).

treatment_protocol: All samples were grown and treated the same way.

tag: condition

value: R132H-IDH1 and P53 shRNA and ATRX shRNA

value: mutant-IDH1, P53 knockdown, ATRX knockdown


title: GIST882 cell Nontargeting microRNA transfected 72h rep3.

description: GIST 882 N.C-3

source_name: Gastrointestinal Stromal tumor cells, siRNA transfected, 72h.


title: 3hitNSCs_replicate2 (array)

description: 3 hit


title: GIST430 cell miR-494 transfected 72h rep2.

description: GIST 430 miR-494-2


title: 2hitNSCs_replicate2 (array)

description: 2 hit

value: R132H-IDH1 and P53 shRNA

value: mutant IDH1 and p53 knockdown


title: GIST882 cell miR-494 transfected 72h rep2.

description: GIST 882 miR-494-2


title: GIST430 cell miR-494 transfected 72h rep3.

description: GIST 430 miR-494-3


title: 1hitNSCs_replicate2 (array)

description: 1 hit


title: 1hitNSCs_replicate1 (array)

description: 1 hit


title: GIST882 cell Nontargeting microRNA transfected 72h rep1.

description: GIST 882 N.C-1


title: 2hitNSCs_replicate1 (array)

description: 2 hit


title: controlNSCs_replicate1 (array)

description: control


title: controlNSCs_replicate2 (array)

description: control


title: GIST882 cell Nontargeting microRNA transfected 72h rep2.

description: GIST 882 N.C-2


title: GIST430 cell Nontargeting microRNA transfected 72h rep3.

description: GIST 430 N.C-3


title: A2780_nc886.3

status: Public on Nov 08 2017

city: HOUSTON

first: Hyun-Sung

last: Lee

state: TX

address: One Baylor Plaza

department: Surgery

institute: BAYLOR COLLEGE OF MEDICINE

description: To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software.

hyb_protocol: Labeled, amplified material (750 ng per array) was hybridized to the Illumina HumanHT-12 V4.0 expression BeadChip according to the manufacturer's instructions (Illumina, Inc., San Diego, CA).

scan_protocol: Arrays were scanned with an Illumina BeadArray Reader confocal scanner (BeadStation 500GXDW; Illumina, Inc., San Diego, CA) according to the manufacturer's instructions.

data_processing: Array data processing were performed on Illumina BeadStudio software. We normalized gene expression data using Quantile normalization and log2 transformation. To export to a data matrix, Sample Gene Profile option of this software was used.

source_name: ovarian cancer cell line, nc886 overexpression

label_protocol: Biotin-labeled cRNA samples for hybridization were prepared according to Illumina's recommended sample labeling procedure: 500 ng of total RNA was used for cDNA synthesis, followed by an amplification/labeling step (in vitro transcription) to synthesize biotin-labeled cRNA using the Illumina TotalPrep RNA Amplification kit (Ambion Inc., Austin, TX). cRNA concentrations using spectrophotometer (NanoDrop, ND-1000).

extract_protocol: Total RNA was isolated from tissues with mirVana RNA Isolation labeling kit (Ambion, Inc.) according to the manufacturer protocol. RNA quality and integrity were confirmed by ExperionTM Automated Electrophoresis System (BIO-RAD).

value: ovarian cancer cell line

value: nc886 overexpression


title: SKOV3_TGF-β.1

source_name: ovarian cancer cell line, TGF-β overexpression

value: TGF-beta overexpression


title: SKOV3_nc886.3


title: SKOV3_nc886.2


title: SKOV3_vector.2

source_name: ovarian cancer cell line, Treatment-naïve

value: Treatment-naive


title: SKOV3_TGF-β.2


title: A2780_vector.3


title: SKOV3_nc886.1


title: SKOV3_vector.3


title: A2780_nc886.1


title: SKOV3_vector.1


title: A2780_nc886.2


title: GIST430 cell Nontargeting microRNA transfected 72h rep1.

description: GIST 430 N.C-1


title: GIST430 cell miR-494 transfected 72h rep1.

description: GIST 430 miR-494-1


title: A2780_vector.2


title: GIST430 cell Nontargeting microRNA transfected 72h rep2.

description: GIST 430 N.C-2


title: day 10 differentiation siHIPK4 rep 2

description:
DKFZ
d10KD_1
replicate 2
9965581003_B


title: OSE80PC_nc886-kd.2

source_name: immortalized ovarian epithelial cells, Knock-down of nc886

value: immortalized ovarian epithelial cells

value: Knock-down of nc886


title: SKOV3_TGF-β.3


title: OSE80PC_nc886-kd.1


title: A2780_vector.1


title: OSE80PC_control-kd.2

source_name: immortalized ovarian epithelial cells, Treatment-naïve


title: OSE80PC_control-kd.1


title: OSE80PC_nc886-kd.3


title: OSE80PC_control-kd.3


title: blood_CD4+Tcell_memory_rep2

city: Amsterdam

first: Perry

middle: D

last: Moerland

address: Meibergdreef 9

department: Epidemiology and Data Science

country: Netherlands

institute: Amsterdam UMC

scan_protocol: Arrays were scanned using the Illumina iScan array scanner

data_processing: Data were retrieved using Illumina's GenomeStudio v2011.1 software. Analyses were carried out with Bioconductor packages in the statistical software package R (version 3.0.0). Normexp-by-control background correction, quantile normalization, and log2 transformation (Shi et al, NAR, 2010) were performed on the Illumina sample and control probe profiles using the limma package (version 3.16.8), function neqc.

label_protocol: The Illumina TotalPrep-24 RNA Amplification Kit was used to generate biotin-labeled (biotin-16-UTP) amplified cRNA

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated from heparinized peripheral blood samples with standard density gradient techniques. For the lung material, after lobectomy the pathologist cut off a piece of peripheral normal looking lung tissue farthest away from the tumor. The lung mononuclear cells (LMC) were isolated from the tissue as previously described [Sathaliyawala, T. et al, Immunity 38, 187–197 (2013)]. In short, the tissue was sliced into 1 mm pieces using a McIlwain tissue chopper and incubated at 37°C in digestion medium (RPMI with 20 mM Hepes, 15% fetal calf serum (FCS), 50 U/ml DNAse type I (Sigma Aldrich)). The tissue pieces were dried with sterile gauze and incubated for 60 minutes with medium and collagenase type I or 4 (300 U/ml; Worthington) at 37°C while shaking. The digested tissue was passed through a flow-through chamber to achieve a cells suspension. To isolate mononuclear cells from the cell suspension standard density gradient techniques were used. The LMC and PBMC samples were cryopreserved in liquid nitrogen until further analysis.

extract_protocol: RNA was isolated from the sorted cell samples using the Nucleospin RNA XS and Nucleospin RNA II kit (Machery-Nagel) according to manufacturer’s instructions.

treatment_protocol: PBMC or LMC were labelled with combinations of the following antibodies: anti-CD4, anti-CD3, anti-CD8, anti-CD27, anti-CD45RA, anti-CD45RO, anti-CD69, anti-CD103. Near-IR fixable dye (Invitrogen) was used to exclude dead cells from the analysis. The samples were measured in PBS 0.5% FCS with a LSR Fortessa (BD) and the analysis was performed using FlowJo Version 10 software.

value: Pool

tag: subject status

value: healthy donor

value: blood

value: Peripheral blood mononuclear cells

value: NEG

value: POS


title: blood_CD4+Tcell_naive_rep2


title: blood_CD4+Tcell_effector_memory_rep2


title: lung_CD4+Tcell_CD103-CD27+_rep3

value: VK

value: non-small cell lung carcinoma patient

value: lung;  non-cancerous lobectomy tissue

value: Lung mononuclear cells


title: lung_CD4+Tcell_CD103-CD27-_rep1


title: lung_CD4+Tcell_CD103+CD27-_rep4


title: lung_CD4+Tcell_CD103-CD27-_rep3


title: lung_CD4+Tcell_CD103-CD27-_rep4


title: blood_CD4+Tcell_memory_rep1


title: blood_CD4+Tcell_naive_rep1


title: lung_CD4+Tcell_CD103+CD27-_rep3


title: GIST882 cell miR-494 transfected 72h rep1.

description: GIST 882 miR-494-1

value: GIST cell line


title: lung_CD4+Tcell_CD103-CD27-_rep2


title: lung_CD4+Tcell_CD103+CD27-_rep2


title: KO ileal mucosa pooled sample 2 replicate 2

city: Chicago

first: Christopher

middle: Robert

last: Manzella

state: IL

address: 820 S. Damen Ave.

department: Medicine

institute: University of Illinois at Chicago

description:
KO22
Gene expression under basal conditions.

hyb_protocol: OneArrayTM Hybridization process is a bubble-mixing-based protocol. Array is put together with OneArrayTM cover slide, spacer, and hyb-bag to make a sandwich-like assembly. Denatured, fragmented target mix with OneArray Hyb Buffer is then prepared to run on the arrays for overnight incubation at 2 rpm, 50°C oven. Post-Hybridization wash steps is performed with buffer I at 42°C for 5 min; buffer II at 42°C for 5 min; buffer II for another 5 min at 25°C and immersed with buffer III for 5 min at 25oC. Arrays are being span to dry. Wash Buffers, wash buffer I: 2xSSC + 0.2% SDS; wash buffer II: 2xSSC, wash buffer III 0.2xSSC.

scan_protocol: When arrays are hybridized and washed, we scan the arrays via Agilent Microarray Scanner (G2505C). Raw data extraction (gpr files) is generated from GenePix™ 4 with the images (tiff files).

data_processing: GPR files were loaded into Rosetta Resolver R System (Rosetta Biosoftware) to process data analysis.  1. Rosetta profile error model calculation: the error due to random factors and systematic biases are estimated by an error model.  2. Squeeze replicated probes: the repeated probes within one chip are averaged.  3. Normalize intensities: Median scaling performed on data set without flagged and control data.  4. Pearson's correlation coefficient: statistical analysis calculated on technical replicates to assess reproducibility.  5. Merge technical replicate data: Average intensity values calculated on technical replicates.  6. Pairwise ratio calculation: Probe filtering, normalization, pair-wise comparison and error-weighted modeling are performed

source_name: SERT KO ileal mucosa scrapings

label_protocol: In general, 1μg total RNA has been used to perform amplification process. The procedure consists of reverse transcription with an oligo(dT) primer bearing a T7 promoter, generating first-strand cDNA with T7 promoter. The cDNA then undergoes second-strand synthesis and cleanup to become a template for in vitro transcription (IVT) withT7 RNA polymerase. Amplified antisense RNA (aRNA) is then being produced to incorporate the modified nucleotides, 5-(3-aminoallyl)-UTP (aaUTP),during in vitro transcription. Yield of aaUTP-conjugated aRNA is then being purified and quantified via NanoDrop® ND-1000 Spectrophotometer and aRNA is ready to perform the following Dye coupling reaction. aaUTP contains a reactive primary amino group that can be chemically coupled toCy5Dye, in a simple, efficient reaction. aaUTP-conjugated aRNA is then coupled with Cy5 and being removed free dye by passing column-based purification steps, generating Cy5-coupled aRNA target for Phalanx Biotech whole genome microarray system. Quantification and labeling efficiency of labeled target is calculated on absorbance at 260nm and at the absorbance max for the dye on spectrophotometer.10ug labeled aRNA is ready to run on single whole genome expression microarray while the expected incorporation rate is >10 dye molecules per 1000nt.

growth_protocol: wild-type and SERT knockout mice obtained from Jackson Laboratories and maintained under normal housing conditions at the Jesse Brown Veterans Affairs Medical Center.

extract_protocol: Trizol RNA Extraction followed by Rneasy Column Purification

tag: strain

tag: gender

value: male

value: ileal mucosa

tag: age

value: 6-8 weeks

value: SERT KO


title: lung_CD4+Tcell_CD103+CD27-_rep1


title: lung_CD4+Tcell_CD103+CD27-_rep5


title: lung_CD4+Tcell_CD103-CD27+_rep2


title: lung_CD4+Tcell_CD103-CD27+_rep1


title: blood_CD4+Tcell_effector_memory_rep1


title: KO ileal mucosa pooled sample 1 replicate 1

description:
KO11
Gene expression under basal conditions.


title: KO ileal mucosa pooled sample 2 replicate 1

description:
KO21
Gene expression under basal conditions.


title: KO ileal mucosa pooled sample 3 replicate 2

description:
KO32
Gene expression under basal conditions.


title: KO ileal mucosa pooled sample 1 replicate 2

description:
KO12
Gene expression under basal conditions.


title: lung_CD4+Tcell_CD103-CD27-_rep5


title: KO ileal mucosa pooled sample 3 replicate 1

description:
KO31
Gene expression under basal conditions.


title: WT ileal mucosa pooled sample 3 replicate 1

description:
C31
Gene expression under basal conditions.

source_name: WT ileal mucosa scrapings

value: WT


title: WT ileal mucosa pooled sample 2 replicate 2

description:
C22
Gene expression under basal conditions.


title: CBS_12_M_2

status: Public on Nov 07 2017

city: Vienna

first: Monika

last: Schmoll

address: Djerassiplatz 1

department: Centre of Microbiology and Environmental Systems Science

country: Austria

institute: University of Vienna

description:
SAMPLE 4
one of two biological replicates

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

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

data_processing:
The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).
matrix_proteinIDs.txt (linked a supplementary file on the Series record) reports RMA signals for protein ID numbers which are similar in both Platform designs as they are based on homologues in the two T. reesei genomes on which the array is based.

organism: Trichoderma reesei

source_name: CBS999.97 MAT1-2 mated to a corresponding strain of opposite mating type

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

growth_protocol: Strains of this study were grown on 2% malt extract medium at 21 °C with 12:12 hours of light (1800 lux) and darkness, which facilitates mating, harvesting was done at subjective noon to avoid any influence of circadian rhythms, at this time, strains were at the contact stage; 2 biological replicates were included

extract_protocol: Total RNA was extracted as described in Tisch et al., 2011 (New insights into the mechanism of light modulated signaling by heterotrimeric G-proteins: ENVOY acts on gna1 and gna3 and adjusts cAMP levels in Trichoderma reesei (Hypocrea jecorina). Fungal Genet Biol, 48 (6): 631 – 40) with supplies provided by the RNeasy Plant Mini Kit (QIAGEN, Hilden, Germany). The quality of the RNA was controlled with the Experion Automated Electrophoresis System (Bio-Rad, Hercules, USA). Total RNA was treated with DNase (Fermentas, Vilnius, Lithuania) and purified using the RNeasy Mini Kit (QIAGEN). cDNA synthesis was done with the RevertAid H- First Strand cDNA Synthesis Kit (Fermentas) and Oligo-d(T) Primer.

treatment_protocol: Mycelium was harvested under red-safety light when cultivated in darkness and frozen in liquid nitrogen.

tag: mating type

tag: mated to


title: CBS_12_M_1

description:
SAMPLE 3
one of two biological replicates


title: CBS_11_M_1

description:
SAMPLE 1
one of two biological replicates

source_name: CBS999.97 MAT1-1 mated to a corresponding strain of opposite mating type


title: CBS_11_M_2

description:
SAMPLE 2
one of two biological replicates


title: WT ileal mucosa pooled sample 2 replicate 1

description:
C21
Gene expression under basal conditions.


title: WT ileal mucosa pooled sample 3 replicate 2

description:
C32
Gene expression under basal conditions.


title: WT ileal mucosa pooled sample 1 replicate 1

description:
C11
Gene expression under basal conditions.


title: Male2.15d.Kidney.2806sTS

type: SRA

city: Lausanne

first: Diego

last: Cortez

address: Rue de Lausanne

country: Switzerland

institute: Univerity of Lausanne - CIG

library_source: transcriptomic

data_processing:
Basecalls performed using CASAVA version 1.8.
RNA-seq reads were mapped to genomes using the GSNAP short read alignment program.
Gene expression estimates of protein-coding genes (FPKM) were performed using Cufflinks (v2.2.1).
Genome_build: version 77 of Ensembl
Supplementary_files_format_and_content: Text file to be opened in R. The file contains the final expression values for all species used in this study.

molecule: polyA RNA

organism: Anolis carolinensis

source_name: Kidney

extract_protocol:
QIAGEN RNeasy Kit
llumina TruSeq Stranded mRNA Library protocol

tag: Sex

value: Male

tag: Stage

value: Kidney


title: Male1.16d.Heart.2800sTS

source_name: Heart

value: Heart


title: Male1.15d.Heart.2791sTS


title: Male2.15d.Heart.2805sTS


title: Male2.10-11d.Embryo.2781sTS

source_name: Whole embryo

value: Whole embryo


title: Male1.10-11d.Embryo.2778sTS


title: Male1.10d.Embryo.2779sTS


title: Male1.16d.Gonads.2803sTS

source_name: Testis

value: Testis


title: Male2.15d.Brain.2804sTS

source_name: Brain

value: Brain


title: Male1.16d.Brain.2799sTS


title: Male1.15d.Liver.2793sTS

source_name: Liver

value: Liver


title: Male1.14d.Embryo.2764sTS


title: Male1.16d.Kidney.2801sTS


title: Male1.15d.Kidney.2792sTS


title: Male1.13d.Gonads.2810sTS


title: Male2.15d.Liver.2807sTS


title: Male1.8-9d.Embryo.2783sTS


title: Male1.9d.Embryo.2769sTS


title: Male1.16d.Liver.2802sTS


title: WT ileal mucosa pooled sample 1 replicate 2

description:
C12
Gene expression under basal conditions.


title: Male1.15d.Brain.2790sTS


title: Male2.8d.Embryo.2771sTS


title: Male3.8d.Embryo.2782sTS


title: Male1.8d.Embryo.2770sTS


title: Male2.15d.Gonads.2808sTS


title: Day 4 wild type mouse ES cells, replicate 2

city: Memphis

first: Geoffrey

last: Neale

state: TN

address: 262 Danny Thomas Place

department: Hartwell Center

institute: St Jude Childrens Research Hospital

description: Gene expression data from D4 retinal differentiated WT Rx-GFP aggregates

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

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

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

source_name: Day 4 retinal aggregate from embryonic stem cell line EB5, mouse strain 129/Ola in which GFP is knocked-in under Rx promoter

label_protocol: Sense target cDNA was prepared from 100ng of total RNA using the Ambion® WT Expression Kit (Life Technologies P/N 4411973). cDNA was fragmented and biotin-labeled using the Affymetrix® GeneChip® WT Terminal Labeling Kit (Affymetrix P/N 900671).

growth_protocol: ESC were cultured in 3% matrigel containing retinal differentiation medium as described by Eiraku and Sasai (Nat Protocols 7:69-79, 2012).

extract_protocol: Trizol extraction followed by column purification (Ambion) of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Corresponding aggregates from WT ESC were harvested at Day 4 and 7 of differentiation.

value: retinal ESC-derived aggregates

tag: differentiation day


title: Day 4 wild type mouse ES cells, replicate 1


title: Day 7 wild type mouse ES cells, replicate 1

description: Gene expression data from D7 retinal differentiated WT Rx-GFP aggregates

source_name: Day 7 retinal aggregate from embryonic stem cell line EB5, mouse strain 129/Ola in which GFP is knocked-in under Rx promoter


title: Day 7 wild type mouse ES cells, replicate 2


title: Male2.6-7d.Embryo.2785sTS


title: Male1.4-5d.Embryo.2775sTS


title: Female1.15d.Kidney.2796sTS

value: Female


title: Male2.5d.Embryo.2786sTS


title: Male1.5-6d.Embryo.2773sTS


title: QMF_12_M_C

description:
SAMPLE 8
one of two biological replicates

source_name: FF2b MAT1-2 mated to a corresponding strain of opposite mating type


title: Male1.6-7d.Embryo.2772sTS


title: Male2.5-6d.Embryo.2789sTS


title: Female1.15d.Heart.2795sTS


title: QMF_12_M_B

description:
SAMPLE 7
one of two biological replicates

source_name: FF2a MAT1-2 mated to a corresponding strain of opposite mating type


title: Male1.2-3d.Embryo.2763sTS


title: Female1.15d.Liver.2797sTS


title: Female1.15d.Brain.2794sTS


title: Male1.5d.Embryo.2774sTS


title: Female1.15d.Gonads.2798sTS

source_name: Ovary

value: Ovary


title: Female2.13d.Embryo.2766sTS


title: Female3.13d.Embryo.2776sTS


title: QMF_11_M_C

description:
SAMPLE 6
one of two biological replicates

source_name: FF1b MAT1-1 mated to a corresponding strain of opposite mating type


title: QM6a_12_M_1

description:
SAMPLE 9
one of two biological replicates

source_name: QM6a MAT1-2 mated to a corresponding strain of opposite mating type


title: QM6a_12_M_2

description:
SAMPLE 10
one of two biological replicates


title: QMF_11_M_B

description:
SAMPLE 5
one of two biological replicates

source_name: FF1a MAT1-1 mated to a corresponding strain of opposite mating type


title: Female1.9-10d.Embryo.2777sTS


title: Female1.13d.Embryo.2765sTS


title: Female1.11d.Embryo.2767sTS


title: Female2.11d.Embryo.2768sTS


title: Female1.9d.Embryo.2780sTS


title: Female1.6d.Embryo.2784sTS


title: Female2.5-6d.Embryo.2788sTS


title: Female1.5-6d.Embryo.2787sTS


title: 1 Month old thyroid of WT mouse fed LID_rep4

status: Public on Nov 06 2017

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: Gene expression from 1 month-old WT thyroid fed LID

hyb_protocol: For each sample, 3 ug of Cy3 labeled cDNA was hybridized for 17 hours in a rotating hybridization oven.

scan_protocol: Slides were washed and then scanned with an Agilent Scanner.

data_processing: Data was obtained using the Agilent Feature Extraction software (v12), using the 1-color defaults for all parameters.

source_name: 1 month old WT

label_protocol: Fifty nanograms (50 ng) of total RNA was amplified as directed in the NuGEN Ovation Pico WTA System and 5 ug of amplified cDNA was enzymatically labeled using the Agilent SureTag DNA Labeling Kit.

growth_protocol: Mice were weaned at 3 weeks and fed Normal diet (NIH31) or Low iodine diet (Harlan TD.95125).

extract_protocol: Ambion RNAqous mircro kit

treatment_protocol: Nothing was treated

value: 1 month old

value: thyroid


title: 1 Month old Glis3KO2 thyroid_rep2

description: Gene expression from 1 month-old Glis3KO2 thyroid

source_name: 1 month old Glis3KO2

tag: diet

value: normal


title: 1 Month old Glis3KO2 thyroid_rep3

tag: tissue


title: 1 Month old thyroid of Glis3KO2 mouse fed LID_rep2

description: Gene expression from 1 month-old Glis3KO2 thyroid fed LID


title: 1 Month old thyroid of Glis3KO2 mouse fed LID_rep3


title: 1 Month old WT thyroid_rep4

description: Gene expression from 1 month-old WT thyroid

value: wild type


title: 1 Month old WT thyroid_rep3


title: 1 Month old WT thyroid_rep5


title: 1 Month old thyroid of WT mouse fed LID_rep2


title: 1 Month old thyroid of Glis3KO2 mouse fed LID_rep4


title: 1 Month old thyroid of Glis3KO2 mouse fed LID_rep1


title: 1 Month old Glis3KO2 thyroid_rep4


title: STING-KO_mBMDM_Brucella abortus infected_17hrs

city: Miami

first: Anthony

last: Griswold

state: FL

address: 1501 NW 10th Ave, BRB 318

institute: University of Miami

description:
STI B. a 16
Gene expression data from STING knock-out mBMDM infected for 17 hours with Brucella abortus cells.

hyb_protocol: Fragmented and labeled products were hybridized to GeneChip Mouse Gene 2.0 ST Arrays (Affymetrix part# 902500). Washing and staining of arrays took place on the GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned with GeneChip Scanner 3000 7G system.

data_processing: Raw .CEL files were analyzed with Affymetrix Expression Console software v.1.3.1.187 using rma-sketch normalization with Affymetrix default analysis settings to generate .CHP files.

source_name: mBMDM, STING knock-out, B. abortus infection

label_protocol: 300ng of total RNA per sample was prepared using the GeneChip WT PLUS Reagent Kit (Affymetrix part#902280) and yielded cDNA product for fragmentation and labeling.

growth_protocol: DMEM supplemented with 10% FBS, 37 °C, 5% CO2.

extract_protocol: Total RNA extraction using QIAGEN RNeasy mini kit following kit instruction.

treatment_protocol: Macrophages were infected with a MOI 100:1 Brucella/cell or transfected with 1µg of bacterial DNA for 17 hrs.

tag: strain/background

value: STING knock-out

tag: cell type

value: Mouse bone marrow-derived macrophages (mBMDM)

tag: treatment

value: Brucella abortus infection

value: 17 hours


title: 1 Month old thyroid of WT mouse fed LID_rep1


title: STING-KO_mBMDM_medium mock treatment control_17hrs

description:
STI MEIO 13
Gene expression data from STING knock-out mBMDM medium mock treated for 17 hours.

source_name: mBMDM, STING knock-out, mock treated

tag: genotype/variation

value: medium mock treatment control


title: C57BL/6_mBMDM_Brucella abortus infected_17hrs

description:
B6 B. a 8
Gene expression data from wild type C57BL/6 mBMDM infected for 17 hours with Brucella abortus cells.

source_name: mBMDM, wild type, B. abortus infection

value: Wild type

tag: time


title: 1 Month old Glis3KO2 thyroid_rep1


title: 1 Month old WT thyroid_rep1


title: C57BL/6_mBMDM_Brucella abortus DNA transfected_17hrs

description:
B6 DNA 7
Gene expression data from wild type C57BL/6 mBMDM transfected for 17 hours with Brucella abortus DNA.

source_name: mBMDM, wild type, B. abortus DNA transfection

value: Brucella abortus DNA


title: 1 Month old Glis3KO2 thyroid_rep5


title: STING-KO_mBMDM_Brucella abortus DNA transfected_17hrs

description:
STI DNA 11
Gene expression data from STING knockout mBMDM transfected for 17 hours with Brucella abortus DNA.

source_name: mBMDM, STING knock-out, B. abortus DNA transfection


title: 1 Month old thyroid of WT mouse fed LID_rep3


title: 1 Month old WT thyroid_rep2


title: C57BL/6_mBMDM_medium mock treatment control_17hrs

description:
B6 MEIO 5
Gene expression data from wild type C57BL/6 mBMDM medium mock treated for 17 hours.

source_name: mBMDM, wild type, mock treated


title: Male1.13d.Brain.2809sTS

source_name: Brain

value: Male


title: genomic DNA from Primary-UtE1104_P11

city: Setagaya-ku

first: Akihiro

last: Umezawa

state: Tokyo

department: Center for Regenerative Medicine

institute: National Center for Child Health and Development

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450K Beadchip using standard Illumina protocol

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

data_processing:
GenomeStudio V2011.1
The non_normalized.txt contains unmethylated and methylated signal intensities

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from samples using Qiagen DNeasy Kit according to standard instructions

value: female

tag: cell line

value: Endometrium-derived cells


title: genomic DNA from Primary-AM936EP_P12

value: Amnion-derived cells

tag: iPScs generated by

value: episomal vectors


title: genomic DNA from Primary-Edom22_P5

value: Menstrual blood-derived cells


title: genomic DNA from Episomal-iPS-Edom-iPS-09_P30

source_name: Episomal-iPS-Edom-iPS

value: Edom33-derived iPS cells


title: genomic DNA from Episomal-iPS-Edom-iPS-08_P30

value: Edom32-derived iPS cells


title: Late globular (LG)_embryo, nuclei biological replicate 3 [nEMB_LG3]

city: Wageningen

first: Joakim

last: Palovaara

state: Gelderland

address: Stippeneng 4

department: Biochemistry

institute: Wageningen Univeristy

description:
Map2_nEMB_LG3
Gene expression data from nuclei isolated from LG stage Arabidopsis embryo

hyb_protocol: The Affymetrix Gene 1.1 ST 24-Array Plate was processed on the Affymetrix GeneTitan System and was performed according to the NuGEN Ovation PicoSL WTA System V2 user guide (Appendix C, page 28) using GeneTitan Hybridization, Wash, and Stain Kit for WT Array Plates (Affymetrix, P/N 901622) and GeneChip Hybridization Control Kit (Affymetrix, P/N 90457).

scan_protocol: Hybridization, washing, staining and scanning of the arrays were done on the Affymetrix GeneTitan System using the hyp-wash-scan protocol.

data_processing: The data were analyzed using the MadMax pipeline (https://madmax.bioinformatics.nl/) and a custom CDF file (aragene11st_At_TAIRG_19.0.0, http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/genomic_curated_CDF.asp), and normalized using RMA.

organism: Arabidopsis thaliana

source_name: Arabidopsis embryo_Late globular (LG)_embryo

label_protocol: RNA was amplified using the Ovation PicoSL WTA System V2 (NuGEN, P/N 3302-60) according to the manufacturer's instructions. For fragmentation and labelling, 3 ug of biotinylated cDNA was used in a half-volume reaction using the ENCORE Biotin Module kit (NuGEN, P/N 4200-60).

growth_protocol: Seedlings were grown on soil at a constant temperature of 22°C under long-day conditions (16 hours light/8 hours dark).

extract_protocol: RNA was extracted according to the TRIzol reagent protocol for small sample quantaties (ThermoFisher, P/N 15596026) with some modifications.

treatment_protocol: Embryos of the approriate stage where used for isolating nuclei using a two-compoenent labelling system called INTACT for immediate RNA extraction.

value: embryo

tag: developmental stage

value: Late globular (LG)

tag: molecule subtype

value: nuclear RNA


title: Late globular (LG)_embryo, nuclei biological replicate 4 [nEMB_LG4]

description:
Map2_nEMB_LG4
Gene expression data from nuclei isolated from LG stage Arabidopsis embryo


title: Late globular (LG)_embryo, nuclei biological replicate 2 [nEMB_LG2]

description:
Map2_nEMB_LG2
Gene expression data from nuclei isolated from LG stage Arabidopsis embryo


title: genomic DNA from Sendai-iPS-Edom-iPS-30_P30

source_name: Sendai-iPS-Edom-iPS

tag: gender

value: Edom27-derived iPS cells

value: Sendai virus


title: genomic DNA from Episomal-iPS-Edom-iPS-01_P30

value: Edom31-derived iPS cells


title: genomic DNA from Sendai-iPS-Edom-iPS-35_P30

value: Edom28-derived iPS cells


title: genomic DNA from Retro-iPS-UtE-iPS-07_P31

source_name: Retro-iPS-UtE-iPS

value: UtE1106-derived iPS cells

value: retrovirus


title: genomic DNA from Sendai-iPS-Edom-iPS-39_P30

value: Edom29-derived iPS cells


title: Late globular (LG)_QC, nuclei, biological replicate 3 [nQC_LG3]

description:
Map2_nQC_LG3
Gene expression data from QC nuclei isolated from LG stage Arabidopsis embryo

source_name: Arabidopsis embryo_Late globular (LG)_QC

value: QC


title: Late globular (LG)_QC, nuclei, biological replicate 2 [nQC_LG2]

description:
Map2_nQC_LG2
Gene expression data from QC nuclei isolated from LG stage Arabidopsis embryo


title: genomic DNA from Sendai-iPS-Edom-iPS-31_P30

value: female

value: Edom30-derived iPS cells


title: genomic DNA from Sendai-iPS-Edom-iPS-23_P30

value: Edom25-derived iPS cells


title: Late globular (LG)_embryo, nuclei biological replicate 1 [nEMB_LG1]

description:
Map2_nEMB_LG1
Gene expression data from nuclei isolated from LG stage Arabidopsis embryo


title: genomic DNA from Retro-iPS-UtE-iPS-11_P31

value: UtE1107-derived iPS cells


title: genomic DNA from Retro-iPS-Edom-iPS-01_P23

source_name: Retro-iPS-Edom-iPS

value: Edom22-derived iPS cells


title: genomic DNA from Retro-iPS-Edom-iPS-02_P31

value: Edom23-derived iPS cells


title: Late globular (LG)_suspensor, nuclei, biological replicate 3 [nSUS_LG3]

description:
Map2_nSUS_LG3
Gene expression data from suspensor nuclei isolated from LG stage Arabidopsis embryo

source_name: Arabidopsis embryo_Late globular (LG)_suspsensor

value: suspsensor


title: genomic DNA from Retro-iPS-AM-iPS-13_P05

source_name: Retro-iPS-AM-iPS

value: AM936EP-derived iPS cells


title: Late globular (LG)_suspensor, nuclei, biological replicate 1 [nSUS_LG1]

description:
Map2_nSUS_LG1
Gene expression data from suspensor nuclei isolated from LG stage Arabidopsis embryo

value: Late globular (LG)

value: nuclear RNA


title: genomic DNA from Retro-iPS-AM-iPS-20_P10


title: Late globular (LG)_ground tissue, nuclei, biological replicate 1 [nGSC_LG1]

description:
Map2_nGSC_LG1
Gene expression data from ground tissue nuclei isolated from LG stage Arabidopsis embryo

source_name: Arabidopsis embryo_Late globular (LG)_ground tissue

value: ground tissue


title: Late globular (LG)_ground tissue, nuclei, biological replicate 3 [nGSC_LG3]

description:
Map2_nGSC_LG3
Gene expression data from ground tissue nuclei isolated from LG stage Arabidopsis embryo


title: Late globular (LG)_vascular, nuclei, biological replicate 3 [nVSC_LG3]

description:
Map2_nVSC_LG3
Gene expression data from vascular nuclei isolated from LG stage Arabidopsis embryo

source_name: Arabidopsis embryo_Late globular (LG)_vascular

value: vascular


title: Late globular (LG)_ground tissue, nuclei, biological replicate 2 [nGSC_LG2]

description:
Map2_nGSC_LG2
Gene expression data from ground tissue nuclei isolated from LG stage Arabidopsis embryo


title: genomic DNA from Retro-iPS-AM-iPS-03_P21


title: Early globular (EG)_embryo, nuclei, biological replicate 4 [nEMB_EG4]

description:
Map2_nEMB_EG4
Gene expression data from nuclei isolated from EG stage Arabidopsis embryo

source_name: Arabidopsis embryo_Early globular (EG)_embryo

value: embryo

value: Early globular (EG)


title: Late globular (LG)_vascular, nuclei, biological replicate 1 [nVSC_LG1]

description:
Map2_nVSC_LG1
Gene expression data from vascular nuclei isolated from LG stage Arabidopsis embryo


title: Late globular (LG)_vascular, nuclei, biological replicate 2 [nVSC_LG2]

description:
Map2_nVSC_LG2
Gene expression data from vascular nuclei isolated from LG stage Arabidopsis embryo


title: genomic DNA from Retro-iPS-UtE-iPS-04_P30

value: UtE1104-derived iPS cells

value: retrovirus


title: genomic DNA from Retro-iPS-Edom-iPS-03_P29

value: Edom24-derived iPS cells


title: Late globular (LG)_QC, nuclei, biological replicate 1 [nQC_LG1]

description:
Map2_nQC_LG1
Gene expression data from QC nuclei isolated from LG stage Arabidopsis embryo

value: QC


title: Early globular (EG)_embryo, nuclei, biological replicate 3 [nEMB_EG3]

description:
Map2_nEMB_EG3
Gene expression data from nuclei isolated from EG stage Arabidopsis embryo


title: genomic DNA from Retro-iPS-AM-iPS-08_P29

value: female


title: genomic DNA from ES-SEES-02_P30

source_name: Blastocyst-derived ES cells

value: Blastocyst-derived ES cells


title: genomic DNA from ES-SEES-04_P11


title: genomic DNA from Sendai-iPS-Edom-iPS-05_P30

value: Edom26-derived iPS cells

value: Sendai virus


title: genomic DNA from ES-SEES-05_P45


title: Early globular (EG)_suspensor, nuclei, biological replicate 3 [nSUS_EG3]

description:
Map2_nSUS_EG3
Gene expression data from suspensor nuclei isolated from the whole EG stage Arabidopsis embryo

source_name: Arabidopsis embryo_Early globular (EG)_suspsensor


title: Late globular (LG)_suspensor, nuclei, biological replicate 2 [nSUS_LG2]

description:
Map2_nSUS_LG2
Gene expression data from suspensor nuclei isolated from LG stage Arabidopsis embryo


title: genomic DNA from ES-SEES-01_P30


title: genomic DNA from ES-SEES-07_P45


title: Early globular (EG)_suspensor, nuclei, biological replicate 1 [nSUS_EG1]

description:
Map2_nSUS_EG1
Gene expression data from suspensor nuclei isolated from the whole EG stage Arabidopsis embryo


title: Early globular (EG)_embryo, nuclei, biological replicate 2 [nEMB_EG2]

description:
Map2_nEMB_EG2
Gene expression data from nuclei isolated from EG stage Arabidopsis embryo


title: Early globular (EG)_ground tissue, nuclei, biological replicate 4 [nGSC_EG4]

description:
Map2_nGSC_EG4
Gene expression data from ground tissue nuclei isolated from EG stage Arabidopsis embryo

source_name: Arabidopsis embryo_Early globular (EG)_ground tissue


title: Early globular (EG)_suspensor, nuclei, biological replicate 2 [nSUS_EG2]

description:
Map2_nSUS_EG2
Gene expression data from suspensor nuclei isolated from the whole EG stage Arabidopsis embryo


title: genomic DNA from Retro-iPS-UtE-iPS-06_P30

value: UtE1105-derived iPS cells


title: genomic DNA from ES-HUES-09_P33


title: Early globular (EG)_vascular, nuclei biological replicate 4 [nVSC_EG4]

description:
Map2_nVSC_EG4
Gene expression data from vascular nuclei isolated from EG stage Arabidopsis embryo

source_name: Arabidopsis embryo_Early globular (EG)_vascular


title: Early globular (EG)_ground tissue, nuclei, biological replicate 1 [nGSC_EG1]

description:
Map2_nGSC_EG1
Gene expression data from ground tissue nuclei isolated from EG stage Arabidopsis embryo


title: Early globular (EG)_vascular, nuclei biological replicate 1 [nVSC_EG1]

description:
Map2_nVSC_EG1
Gene expression data from vascular nuclei isolated from EG stage Arabidopsis embryo


title: Early globular (EG)_ground tissue, nuclei, biological replicate 3 [nGSC_EG3]

description:
Map2_nGSC_EG3
Gene expression data from ground tissue nuclei isolated from EG stage Arabidopsis embryo


title: Early globular (EG)_vascular, nuclei biological replicate 2 [nVSC_EG2]

description:
Map2_nVSC_EG2
Gene expression data from vascular nuclei isolated from EG stage Arabidopsis embryo


title: genomic DNA from ES-HUES-06_P25


title: 16-cell_embryo, nuclei biological replicate 3 [nEMB_16C3]

description:
Map2_nEMB_16C3
Gene expression data from nuclei isolated from 16-cell stage Arabidopsis embryo

source_name: Arabidopsis embryo_16-cell_embryo


title: 16-cell_embryo, nuclei biological replicate 2 [nEMB_16C2]

description:
Map2_nEMB_16C2
Gene expression data from nuclei isolated from 16-cell stage Arabidopsis embryo


title: Early globular (EG)_vascular, nuclei biological replicate 3 [nVSC_EG3]

description:
Map2_nVSC_EG3
Gene expression data from vascular nuclei isolated from EG stage Arabidopsis embryo


title: embryo, cellular, biological replicate 3 [cEMB_16C3]

description:
cEMB_16C3
Gene expression data from whole 16-cell stage embryos

hyb_protocol: Hybridization of labelled cDNA was done overnight for 17 hours, at 60 rpm, at 45ºC in a Hybridization Oven 640 (Affymetrix). The protocol was conducted as described in the Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual, chapter 5 (P/N 701880, revision 5). Washing and staining of the arrays were done on an Affymetrix 450 fluidics station using the protocol FS450_0001, as described in the Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual.

scan_protocol: Arrays were scanned on an Affymetrix 3000 7G scanner, as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).

data_processing: The data were analyzed using the MadMax pipeline (https://madmax.bioinformatics.nl/) and a custom CDF file (aragene10st_At_TAIRG_19.0.0, http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/genomic_curated_CDF.asp), and normalized using RMA.

label_protocol: Biotinylated cDNA (4.25 ug) were prepared from RNA using the Ovation Pico WTA System V2 (NuGEN, P/N 3302-60) and the ENCORE Biotin Module (NuGEN, P/N 4200-60) according to the manufacturer's protocol.

growth_protocol: Seedlings  were grown on soil at a constant temperature of 22°C under long-day conditions (16 hours light/8 hours dark).

treatment_protocol: Embryos of the approriate stage where either 1) manually isolated using a inverted microscope together with an micromanipulator or 2) used for isolating nuclei using a two-compoenent labelling system called INTACT for immediate RNA extraction

value: total RNA


title: embryonic day 15_Riboflavin deficient_replicate4

status: Public on Nov 05 2017

city: Newark

first: Larry

middle: Albert

last: Cogburn

state: DE

address: 531 South College Ave.

department: Animal and Food Sciences

institute: University of Delaware

hyb_protocol: Each chicken oligo microarray was baked for 90 min at 90 degrees Celsius prior to use. The slide was pre-treated for 45 min at 42 degrees Celsius in pre-hybridization solution containing 5x SSC, 0.1 % SDS and 1 % BSA and followed by dipping for 5 min in 2x SSC and then 0.2x SSC. The slide was dried by centrifugation (5 min at 1,000 x g). An aliquot of five micrograms of purified labeled aRNA samples was fragmented in 1x fragmentation buffer (Ambion, Austin, TX) for 15 min at 70 degrees Celsius. The reaction was then terminated by adding stop solution and dried down in a SpeedVac (not over dried). Each fragmented aRNA sample was reconstituted prior to hybridization in 30 microliters of pre-warmed DIG Easy Hyb solution (Roche Diagnostics Corporation, Indianapolis, IN). All reference aRNA samples within the same hybridization day were pooled together, equally aliquoted (30 microliters) and co-hybridized with each target sample on a slide. The target and reference aRNA samples were mixed with 2.5 microliters of 10 mg/ml yeast tRNA and 2.5 microliters of 10 mg/ml salmon testes DNA (Sigma, Louis, MO). The reference/target mixture (65 microliters) was denatured for 2 min at 94 degrees Celsius, cooled at room temperature, carefully loaded onto the middle of a pre-treated slide held in a hybridization chamber (Corning #2551, Lowell, MA) and overlaid with a 22 x 65 mm LifterSlip (Erie Scientific, Portsmouth, NH). The sealed hybridization chamber was incubated overnight (14-16 hours) at 42 degrees Celsius in a water bath under a light-tight box. On the following day, the cover slip was flushed off in wash solution #1 and the slide was sequentially washed with pre-warmed wash solution #1 (1x SSC, 0.2% SDS, and 0.5% DTT) at 42 degrees Celsius for 10 min, then washed in solution #2 (0.1 x SSC, 0.2% SDS, and 0.5% DTT) for 5 min at room temperature, and finally washed in solution #3 (0.1 x SSC and 0.5% DTT) for 1 min at room temperature. The slide was subsequently rinsed in MilliQ water and dried by centrifugation. The slide was stored until scanning in individual 50 ml tubes covered in aluminum foil and flooded with pure nitrogen gas.

scan_protocol: For each slide, a high-resolution TIFF image file was generated using a GenePix 4000B microarray scanner and analyzed with GenePix Pro V4.1 software (Axon Laboratories, Palo Alto, CA). The TIFF image was acquired at 10 micron resolution by simultaneous scanning at two wavelengths [532 nm (green) and 635 nm (red)]. The PMT count ratio (635/532) was adjusted to 1 during preview at low resolution scanning.

data_processing: The TIFF image was further analyzed with GenePix Pro software which generated a GenePix report (gpr) file. Loess normalization was used in processing of microarray data (Smyth, G. K., and Speed, T. P. (2003) Normalization of cDNA microarray data. Methods 31, 265–273)

organism: Gallus gallus

source_name: liver

label_protocol: The dye labeling was performed according to the instructions for dye coupling and labeled aRNA cleanup with the Amino Allyl MessageAmp™ II aRNA Amplification Kit. Essentially, twenty micrograms of aRNA was dried down to a minimal volume (but not over-dried) in a SpeedVac concentrator, reconstituted in 9 microliters of coupling buffer and mixed with 11 microliters of prepared dye, 60 micrograms aliquot of Alexa 555 freshly dissolved in DMSO. The coupling reaction took place in the dark for one hour at room temperature. Dye incorporation and the concentration of purified labeled aRNA were determined with a NanoDrop and the incorporation efficiency was calculated with a web tool (www.ambion.com/tools/dye).

growth_protocol: Single-Comb White Leghorn chickens homozygous recessive for the riboflavin binding-protein deficient-allele (rd-/rd-) were maintained at the University of Delaware. The chickens were raised and cared for under protocols approved by the Institutional Animal Care and Use Committee (ICUC), University of Delaware. Fertile eggs, derived from riboflavin binding protein deficient (rd/rd) hens, were injected with riboflavin-5′-phosphate (FMN) [riboflavin-rescued (Rf+)] or sterile saline [riboflavin-deficient (Rf-)] at the onset of incubation (e0).

extract_protocol: Total RNA from frozen liver sample was isolated using a RNeasy Midi kit (Qiagen, Valencia, CA) following the manufacturer's protocol. The quantity of extracted total RNA was determined using a NanoDrop spectrophotometer (Wilmington, DE), and RNA quality was examined by microcapillary electrophoresis on a BioAnalyzer 2100 (Agilent, Wilmington, DE). The RNA amplification was performed with an Amino Allyl MessageAmp™ II aRNA Amplification Kit according to manufacturer’s instruction (Ambion, Austin, TX). A single round of RNA amplification was performed with 4 micrograms of total RNA. In vitro transcription (IVT) of amino allyl-modified aRNA was performed for 14 hr at 37 degrees Celsius. Integrity of aRNA was determined by a BioAnalyzer using the RNA 6000 Nano Assay kit and the concentration of aRNA with a NanoDrop ND-1000 spectrophotometer prior to the aRNA-dye coupling reaction.

treatment_protocol: Liver sample was excised from the chicken embryo, snap frozen in liquid nitrogen, and stored at -80 degrees Celsius until RNA isolation.

value: embryos

tag: day

tag: treatment group

value: riboflavin-deficiency

tag: sample type

value: reference RNA pool


title: embryo, cellular, biological replicate 2 [cEMB_16C2]

description:
cEMB_16C2
Gene expression data from whole 16-cell stage embryos


title: embryo, cellular, biological replicate 1 [cEMB_16C1]

description:
cEMB_16C1
Gene expression data from whole 16-cell stage embryos


title: embryo, nuclei, biological replicate 3 [nEMB_16C3]

description:
nEMB_16C3
Gene expression data from 16-cell stage embryos nuclei

value: nuclear RNA


title: embryo, nuclei, biological replicate 2 [nEMB_16C2]

description:
nEMB_16C2
Gene expression data from 16-cell stage embryos nuclei


title: 16-cell_embryo, nuclei biological replicate 1 [nEMB_16C1]

description:
Map2_nEMB_16C1
Gene expression data from nuclei isolated from 16-cell stage Arabidopsis embryo


title: embryo, nuclei, biological replicate 1 [nEMB_16C1]

description:
nEMB_16C1
Gene expression data from 16-cell stage embryos nuclei


title: 16-cell_inner lower tier, nuclei, biological replicate 1 [nILT_16C1]

description:
Map2_nILT_16C1
Gene expression data from inner lower tier cell nuclei isolated from 16-cell stage Arabidopsis embryo

source_name: Arabidopsis embryo_16-cell_inner lower tier cells

value: inner lower tier cells


title: embryonic day 15_Riboflavin rescued_replicate4

value: riboflavin-rescue


title: 16-cell_inner lower tier, nuclei, biological replicate 3 [nILT_16C3]

description:
Map2_nILT_16C3
Gene expression data from inner lower tier cell nuclei isolated from 16-cell stage Arabidopsis embryo


title: 16-cell_inner lower tier, nuclei, biological replicate 2 [nILT_16C2]

description:
Map2_nILT_16C2
Gene expression data from inner lower tier cell nuclei isolated from 16-cell stage Arabidopsis embryo


title: embryonic day 15_Riboflavin rescued_replicate2


title: embryonic day 15_Riboflavin deficient_replicate3


title: Early globular (EG)_ground tissue, nuclei, biological replicate 2 [nGSC_EG2]

description:
Map2_nGSC_EG2
Gene expression data from ground tissue nuclei isolated from EG stage Arabidopsis embryo

value: ground tissue

value: Early globular (EG)


title: embryonic day 13_Riboflavin rescued_replicate4


title: embryonic day 15_Riboflavin deficient_replicate2


title: embryonic day 15_Riboflavin rescued_replicate1


title: embryonic day 13_Riboflavin deficient_replicate3


title: embryonic day 15_Riboflavin rescued_replicate3


title: embryonic day 13_Riboflavin rescued_replicate2


title: embryonic day 13_Riboflavin rescued_replicate3


title: embryonic day 13_Riboflavin deficient_replicate2


title: embryonic day 13_Riboflavin deficient_replicate4


title: embryonic day 13_Riboflavin deficient_replicate1


title: Late globular (LG)_vascular, nuclei, biological replicate 4 [nVSC_LG4]

description:
Map2_nVSC_LG4
Gene expression data from vascular nuclei isolated from LG stage Arabidopsis embryo

value: vascular

value: Late globular (LG)


title: embryonic day 11_Riboflavin rescued_replicate4


title: embryonic day 15_Riboflavin deficient_replicate1


title: embryonic day 11_Riboflavin rescued_replicate3


title: embryonic day 11_Riboflavin deficient_replicate3


title: embryonic day 11_Riboflavin rescued_replicate2


title: embryonic day 11_Riboflavin rescued_replicate1


title: embryonic day 11_Riboflavin deficient_replicate1


title: embryonic day 11_Riboflavin deficient_replicate4


title: embryonic day 13_Riboflavin rescued_replicate1


title: embryonic day 9_Riboflavin rescued_replicate4


title: embryonic day 11_Riboflavin deficient_replicate2


title: embryonic day 9_Riboflavin rescued_replicate1


title: embryonic day 9_Riboflavin rescued_replicate2


title: embryonic day 9_Riboflavin rescued_replicate3


title: OELae1.6GLN_2

city: Freising

first: Ulrich

last: Guldener

state: Bavaria

address: Maximus-von-Imhof-Forum 3

department: Chair of genome-oriented bioinformatics

institute: Technische Universität München

hyb_protocol: Hybridization of microarrays was done at Arrows Biomedical (Münster, Germany) and Roche-Nimblegen (Iceland) following Nimblegens standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning of microarrays was done at Arrows Biomedical (Münster, Germany) and Roche-Nimblegen (Iceland) following Nimblegens standard operating protocol. See www.nimblegen.com.

data_processing: Preprocessing steps including background correction, normalization and summarization of probe intensities were performed in employing the oligo R package (Carvalho 2010) and its implementation of the RMA algorithm (Irizarry et al., 2003)

organism: Fusarium fujikuroi

source_name: F. fujikuroi OE:Lae1, 6 mM Gln

label_protocol: Labeling was done at Arrows Biomedical (Münster, Germany) and Roche-Nimblegen (Iceland) following Nimblegens standard operating protocol. See www.nimblegen.com.

growth_protocol: Strains were grown for three days in Darken medium and subsequently an aliquot of 500 µL was transferred to liquid ICI medium with either 6 mM or 60 mM glutamine and grown for additional three days on a rotary shaker (180 rpm) at 28 °C.

extract_protocol: Total RNA was extracted using the RNAgents total RNA isolation kit (Promega GmbH, Mannheim, Germany) and DNA was removed using DNAse I (Roche Diagnostics GmbH, Mannheim, Germany). RNA quality and concentration was measured with an Bioanalyzer (Agilent Technologies Deutschland, Böblingen, Germany).

treatment_protocol: Mycelium was harvested after 72h, directly frozen with liquid nitrogen and lyophilized prior to RNA extraction

value: 6 mM Gln


title: embryonic day 9_Riboflavin deficient_replicate2


title: OELae1.60GLN_1

source_name: F. fujikuroi OE:Lae1, 60 mM Gln

value: 60 mM Gln


title: embryonic day 9_Riboflavin deficient_replicate3


title: OELae1.6GLN_1


title: OELae1.60GLN_2


title: wt.60GLN_1

source_name: F. fujikuroi wildtype, 60 mM Gln


title: lae1.60GLN_2

source_name: F. fujikuroi Δlae1, 60 mM Gln


title: wt.6GLN_1

source_name: F. fujikuroi wildtype, 6 mM Gln


title: lae1.60GLN_1


title: embryonic day 9_Riboflavin deficient_replicate4


title: embryonic day 9_Riboflavin deficient_replicate1


title: lae1.6GLN_2

source_name: F. fujikuroi Δlae1, 6 mM Gln


title: wt.6GLN_2


title: lae1.6GLN_1


title: wt.60GLN_2


title: Early globular (EG)_embryo, nuclei, biological replicate 1 [nEMB_EG1]

description:
Map2_nEMB_EG1
Gene expression data from nuclei isolated from EG stage Arabidopsis embryo

value: embryo


title: Stable ccRCC line, UT56 of P1

status: Public on Nov 04 2017

city: Beijing

first: Hailiang

last: Feng

address: dong dan 3 tiao 5 hao

country: China

institute: Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences

description: Gene expression data of a stable clear cell renal cell carcinoma cell line, UT56 at Passage 1

hyb_protocol: One hundred nanograms of total RNA from each sample were used to generate amplified and biotinylated sense-strand cDNA from the entire expressed genome according to the GeneChip WT PLUS Reagent Kit User Manual (P/N 703174, Affymetrix Inc., Santa Clara, CA). GeneChip Human Transcriptome Array 2.0 were hybridized for 16 hours in a 45℃ incubator (Affymetrix GeneChipHybridization Oven 640), rotated at 60 rpm. After hybridization, the microarrays were stained using the Fluidics Station 450 followed by scanning with the Affymetrix Gene Chip Scanner 3000 7G according to manufacturer’s instructions.

scan_protocol: GeneChips were scanned using Affymetrix® GeneChip® Command Console® Software.

data_processing:
The raw data was normalized in the free software Expression Console 1.4 provided by Affymetrix using the quantile normalization of robust multiarray average (RMA) method (performed at the individual probe level). The transcript data, and exon data were analyzed using Affymetrix GeneChip Command Console Software (AGCC). S
Significance Analysis of Microarrays (SAM) was used to identify genes that are differentially expressed. SAM identifies genes with statistically significantchanges in expression by assimilating a set of gene-specific t-tests, and provides an estimate of the false discovery rate (FDR) from generated data by premutation process. Genes with scores higher than a threshold value or genes with FDR value lower than the threshold value were deemed significance. Furthermore, fold-change analysis which calculates the ratios of geometric means of expression intensities were performed. To select the differentially expressed genes, we used threshold values of ≥2 and ≤−2-fold change and a FDR significance level of <5%

source_name: Stable ccRCC line, UT56 of P1

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

growth_protocol: Cells were cultured in complete medium（DMEM/F12(1:1) supplemented with 10% FBS, 2 mM L-glutamine, 1% non-essential amino acid (NEAA) and 0.1% insulin-transferrin-selenium (ITS)) with a density of 2 × 104 cells/cm2

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

treatment_protocol: After the cells and fragments adhered to the flasks and grew to confluence, they were trypsinized and passaged by 1:2 or1:4 into new flasks with the cell generation number +1 or +2

value: male

value: clear cell renal cell carcinoma

tag: tumor stage

value: II

tag: passage number in vitro


title: Finite ccRCC line, UT41 of P2

description: Gene expression data of a finite clear cell renal cell carcinoma cell line, UT41 at Passage 2

source_name: Finite ccRCC line, UT41 of P2

value: female

value: III


title: Stable ccRCC line, UT16 of P2

description: Gene expression data of a stable clear cell renal cell carcinoma cell line, UT16 at Passage 2

source_name: Stable ccRCC line, UT16 of P2

value: I


title: Stable ccRCC line, UT48 of P2

description: Gene expression data of a stable clear cell renal cell carcinoma cell line, UT48 at Passage 2

source_name: Stable ccRCC line, UT48 of P2


title: Stable ccRCC line, UT14 of P18

description: Gene expression data of a stable clear cell renal cell carcinoma cell line, UT14 at Passage 18

source_name: Stable ccRCC line, UT14 of P18


title: Stable ccRCC line, UT33a of P3

description: Gene expression data of a stable clear cell renal cell carcinoma cell line, UT33a at Passage 3

source_name: Stable ccRCC line, UT33a of P3

value: I-II


title: Finite ccRCC line, UT54 of P3

description: Gene expression data of a finite clear cell renal cell carcinoma cell line, UT54 at Passage 3

source_name: Finite ccRCC line, UT54 of P3


title: Stable ccRCC line, UT14 of P38

description: Gene expression data of a stable clear cell renal cell carcinoma cell line, UT14 at Passage 38

source_name: Stable ccRCC line, UT14 of P38


title: Stable ccRCC line, UT14 of P2

description: Gene expression data of a stable clear cell renal cell carcinoma cell line, UT14 at Passage 2

source_name: Stable ccRCC line, UT14 of P2


title: Finite ccRCC line, UT37 of P2

description: Gene expression data of a finite clear cell renal cell carcinoma cell line, UT37 at Passage 2

source_name: Finite ccRCC line, UT37 of P2


title: Spleen, BALB/c, 8 week old

status: Public on Nov 03 2017

city: Gdansk

first: Pawel

last: Sachadyn

address: Narutowicza 11/12

department: Molecular Biotechnology and Microbiology

country: Poland

institute: Gdansk University of Technology

description: Genomic DNA methylation profile in the spleen of the BABL/c mouse

hyb_protocol: The combined test and input DNA samples were suspended in hybridization buffer (Roche, cat. no. 05583683001) cohybridized onto Mouse DNA Methylation 3x720K CpG Island Plus RefSeq Promoter Arrays for 20 hr at 42°C, following washing with Nimblegen Wash Kit (Roche cat. no. 05584507001).

scan_protocol: The image was acquisited with MS200 Scanner (Roche, NimbleGen) at 2 µm resolution by using high-sensitivity and autogain settings.

data_processing: The data from scanned images were extracted and processed with NimbleScan (2.6.0.0) (Roche, Nimblegen) using default parameters. Data processing included quantile normalization of each chanel separately, obtaining log2 ratios, P-scores and peak identification. Log2 ratios represent the ratios of the immunoprecipitated DNA signal to the input DNA signal. The mean log2 ratios were calculated using a Tukey biweight mean. P-scores were calculated from log2 ratios by performing sliding-window (750 bp) Kolmogorov-Smirnov (KS) test around each probe applied to determine -log10 p-value from the windowed KS test around that probe. The methylation peaks were obtained by merging consecutive probes with P scores over the assumed cut-off (default 2.0) with maximum 500 bp spacing and minimum of two probes per peak.

source_name: MeDIP enriched genomic DNA

label_protocol: DNA labeling and hybridization was performed according to NimbleGen’s protocol with our modifications. The immunoprecipitated CpG methylated DNA (test) and the untreated, sonicated DNA (input control) were labeled by using the random priming with the Nimblegen Dual-Color DNA Labeling kit (Roche-Nimblegen, cat. No. 06370250001) with fluorescent dyes Cy3 and Cy5, respectively.

extract_protocol: Hearts from 1-day, 7-day, 2-week old mice of C57BL6/J murine strain were purchased from  the Tri-City's Academic Animal Experiment Centre of the Medical University of Gdańsk. Hearts for 8-week-old mice of C57BL/6J murine strain were purchased form the Jackson Laboratories. Genomic DNA was isolated using DNeasy Blood&Tissue Kit (QIAGEN).

tag: strain

value: BALB/c

value: Spleen

source_name: input DNA


title: Bone Marrow, BALB/c, 8 week old

description: Genomic DNA methylation profile in the bone marrow of the BABL/c mouse

tag: tissue

value: Bone Marrow


title: Finite ccRCC line, UT13 of P3

description: Gene expression data of a finite clear cell renal cell carcinoma cell line, UT13 at Passage 3

source_name: Finite ccRCC line, UT13 of P3


title: Finite ccRCC line, UT27 of P3

description: Gene expression data of a finite clear cell renal cell carcinoma cell line, UT27 at Passage 3

source_name: Finite ccRCC line, UT27 of P3


title: Bone Marrow, C57BL/6J, 8 week old

description: Genomic DNA methylation profile in the bone marrow of the C57BL/6J mouse


title: Heart, BALB/c, 8 week old

description: Genomic DNA methylation profile in the heart of the BABL/c mouse

value: Hearts


title: Spleen, C57BL/6J, 8 week old

description: Genomic DNA methylation profile in the spleen of the C57BL/6J mouse


title: Spleen, MRL/MpJ, 8 week old

description: Genomic DNA methylation profile in the spleen of the MRL/MpJ mouse

value: MRL/MpJ


title: Liver, C57BL/6J, 8 week old

description: Genomic DNA methylation profile in the liver of the C57BL/6J mouse

value: Livers


title: Heart, C57BL/6J, 8 week old

description: Genomic DNA methylation profile in the heart of the C57BL/6J mouse


title: Liver, MRL/MpJ, 8 week old

description: Genomic DNA methylation profile in the liver of the MRL/MpJ mouse


title: Liver, BALB/c, 8 week old

description: Genomic DNA methylation profile in the liver of the BABL/c mouse


title: HDF 1388

city: Kyoto

first: Takuya

last: Yamamoto

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

department: CiRA

institute: Kyoto University

hyb_protocol: Fragmented and labelled cDNA was hybridized to GeneChip HG-U133_Plus_2 (Affymetrix).

scan_protocol: Arrays were scanned using the Affymetrix GeneChip Scanner 3000 TG.

data_processing: Arrays were normalized with Robust Multiarray Average (RMA) in GeneSpring 13.0.

source_name: Human dermal fibroblast 1388

label_protocol: GeneChip 3' IVT Express Kit (Affymetrix) was used according to Affymetrix protocol.

growth_protocol: HDF (1388) was cultured in DMEM supplemented with 10% FBS. iPSC (201B7) was cultured in Primate ES cellmedium (ReproCELL) supplemented with 4 ng/mL of human recombinant basic fibroblast growth factor (bFGF) on SNL feeders.

extract_protocol: RNA was isolated with RNeasy mini kits (QIAGEN).

treatment_protocol: SNL feeder cells were removed by CTK treatment.

value: dermal fibroblasts


title: Heart, MRL/MpJ, 8 week old

description: Genomic DNA methylation profile in the heart of the MRL/MpJ mouse


title: ful-1_FUL-GR_Mock_2

first: Marian

last: Bemer

address: Droevendaalsesteeg 1

department: Molecular Biology

institute: Wageningen University

hyb_protocol: According to Rehrauer et al. Plant Physiology (2010). DOI 10.1104/pp.109.150185

data_processing: RMA was used to normalize the data; Limma package was used to detect differential expression. RMA values are available on associated GSE entry.

source_name: dipped in Mock solution, harvested after 8 hrs

growth_protocol: Plants were grown on soil in a growth chamber at 22 0C and 16/8 h day/night

extract_protocol: RNA was extracted using Trizol and treated with DNase.

treatment_protocol: Inflorescences were dipped into 10 µM Dexamethasone (DEX) solution (10 µM DEX, 0.5 MS, 0.02% Silwet) or Mock solution (0.5 MS, 0.02% Silwet), and pistils/siliques were harvested after 8 hours.

tag: ecotype

value: Col/Ler F2

tag: genotype

value: Flower stage 12-16 (Smyth et al., 1990)

value: pistils/siliques


title: Ear, C57BL/6J, 8 week old

description: Genomic DNA methylation profile in the ear of the C57BL/6J mouse

value: Ears


title: Bone Marrow, MRL/MpJ, 8 week old

description: Genomic DNA methylation profile in the bone marrow of the MRL/MpJ mouse


title: iPS 201B7

source_name: Induced pluripotent stem cell 201B7

tag: cell type

value: induced pluripotent stem cells


title: ful-1_FUL-GR_DEX_2

scan_protocol: According to Rehrauer et al. Plant Physiology (2010). DOI 10.1104/pp.109.150185

source_name: dipped in 10 uM DEX, harvested after 8 hrs


title: ful_1_Mock_2

label_protocol: According to Rehrauer et al. Plant Physiology (2010). DOI 10.1104/pp.109.150185


title: ful-1_DEX_1


title: ful-1_DEX_2


title: ful-1_FUL-GR_DEX_1


title: ful_1_Mock_1


title: Stable ccRCC line, UT16 of P2_methylation

description: Methylation microarray data of a stable clear cell renal cell carcinoma cell line, UT16 at Passage 2

hyb_protocol: To minimize batch effects, cases and controls were randomly distributed to different arrays. The converted genomic DNA was eluted in 15 μl elution buffer. DNA methylation level was measured using the Illumina Infinium HD Methylation Assay (Illumina) according to the manufacturer's instructions. Briefly, 4 μl (50-100 ng/μL) of bisulfite-converted DNA was isothermally amplified overnight (20-24 h) and fragmented enzymatically. Precipitated DNA using isopropyl alcohol was resuspended in hybridization buffer and dispensed onto the Infinium HumanMethylation450 BeadChips (12 samples/chip). The hybridization procedure was performed at 48°C overnight (16-20 h) using an Illumina hybridization oven.

scan_protocol: After hybridization, free DNA was washed away and the BeadChips were processed through a single nucleotide extension followed by immunohistochemistry staining. Finally, we downloaded the manifest files of each array in advance and imaged the BeadChips using an Illumina iScan.

data_processing: The raw data were processed using the Methylation Module of GenomeStudio v1.9 software with default parameters, the criterion of screening CpG sites were |β-Difference|>0.2 and P values <0.05.

label: dinitrophenol and biotin

source_name: Stable ccRCC line, Passage 2 of UT16

label_protocol: According to the EZ DNA Methylation Kit (Zymo Research) manufacturer's recommendations, we used 1 μg of human genomic DNA for sodium bisulfite-treated assay.

extract_protocol: Total DNA was extracted using QIAamp DNA Mini Kit (QIAGEN) according to the manufactures’instructions. DNA purity was assessed by measuring the A260/A280 ratio using a NanoDrop (Thermo Scientific) and DNA quality checked by agarose gel electrophoresis for a strong band at high molecular weight

value: clear cell renal cell carcinoma


title: Stable ccRCC line, UT33a of P3_methylation

description: Methylation microarray data of a stable clear cell renal cell carcinoma cell line, UT33a at Passage 3

source_name: Stable ccRCC line, Passage 3 of UT33a

value: female


title: ful-1_FUL-GR_Mock_1


title: Finite ccRCC line, UT13 of P3_methylation

description: Methylation microarray data of a finite clear cell renal cell carcinoma cell line, UT13 at Passage 3

source_name: Finite ccRCC line, Passage 3 of UT13

value: male


title: Stable ccRCC line, UT14 of P2_methylation

description: Methylation microarray data of a stable clear cell renal cell carcinoma cell line, UT14 at Passage 2

source_name: Stable ccRCC line, Passage 2 of UT14

value: II


title: Stable ccRCC line, UT14 of P18_methylation

description: Methylation microarray data of a stable clear cell renal cell carcinoma cell line, UT14 at Passage 18

source_name: Stable ccRCC line, Passage 18 of UT14


title: Donor 3 CD56dim/CD94high

city: Columbus

first: Michael

last: Caligiuri

state: OH

address: 460 W 10th Ave

institute: The Ohio State University

description: Total RNA was annealed with multiplexed tags to 800 target miRNAs through a ligation reaction and purification step. Control RNA included in the nCounter Human miRNA Sample Preparation Kit was used to monitor the ligation efficiency and specificity through each step of the reaction. Controls included 6 positive controls, 6 negative controls, 3 ligation positive controls, 3 ligation negative controls, 5 mRNA reference controls, and 5 spike-in controls.

hyb_protocol: After hybridization, excess probes are washed away using a two step magnetic bead- based puri cation on the nCounter Prep Station. Magnetic beads derivatized with short nucleic acid sequences that are complementary to the Capture Probe and the Reporter Probes are used sequentially. First, the hybridization mixture containing target/probe complexes is allowed to bind to magnetic beads complementary to sequences on the Capture Probe. Wash steps are performed to remove excess Reporter Probes and non-target cellular transcripts. After washing, the Capture Probes and target/probe complexes are eluted o  the beads and are hybridized to magnetic beads complementary to sequences on the Reporter Probe. An additional wash is performed to remove excess Capture Probes. Finally, the puri ed target/probe complexes are eluted o  the beads and immobilized on the cartridge for data collection.  After hybridization, excess probes are washed away using a two step magnetic bead- based puri cation on the nCounter Prep Station. Magnetic beads derivatized with short nucleic acid sequences that are complementary to the Capture Probe and the Reporter Probes are used sequentially. First, the hybridization mixture containing target/probe complexes is allowed to bind to magnetic beads complementary to sequences on the Capture Probe. Wash steps are performed to remove excess Reporter Probes and non-target cellular transcripts. After washing, the Capture Probes and target/probe complexes are eluted o  the beads and are hybridized to magnetic beads complementary to sequences on the Reporter Probe. An additional wash is performed to remove excess Capture Probes. Finally, the puri ed target/probe complexes are eluted o  the beads and immobilized on the cartridge for data collection.

scan_protocol: Data Collection is carried out in the nCounter Digital Analyzer.

data_processing: Digital images are processed and the barcode counts are tabulated in a comma separated value (CSV) format. Quality control was performed by verifying that there was no discrepency between field of view counts attempted and successfully completed and verifying that the image was not saturated. Normalization was performed using the global sum method.

label: fluorescent reporter probe

source_name: peripheral blood

label_protocol: Total RNA was annealed with multiplexed tags to 800 target miRNAs through a ligation reaction and purification step. NanoString technology is based on the direct molecular barcoding and digital detection of target molecules through the use of a color-coded probe pair. The probe pair consists of a Reporter Probe, which carries the signal on its 5’ end, and a Capture Probe which carries a biotin on its 3’ end.

growth_protocol: Primary human natural killer cells were freshly isolated from normal donor peripheral blood obtained from the American Red Cross

extract_protocol: Natural killer cells were enriched by density gradient-based negative selection. Natural killer cells were sorted by lin-/CD3-/CD56+/CD94+-. Total RNA was isolated with the Norgen Total RNA Purification Plus kit.

treatment_protocol: The cells were note treated

tag: surface phenotype


title: Donor 4 CD56bright/CD94high


title: Donor 4 CD56dim/CD94low


title: Donor 3 CD56dim/CD94low


title: Stable ccRCC line, UT14 of P38_methylation

description: Methylation microarray data of a stable clear cell renal cell carcinoma cell line, UT14 at Passage 38

source_name: Stable ccRCC line, Passage 38 of UT14


title: Donor 3 CD56bright/CD94high


title: Finite ccRCC line, UT54 of P3_methylation

description: Methylation microarray data of a finite clear cell renal cell carcinoma cell line, UT54 at Passage 3

source_name: Finite ccRCC line, Passage 3 of UT54


title: Donor 2 CD56dim/CD94low


title: Ear, MRL/MpJ, 8 week old

description: Genomic DNA methylation profile in the ear of the MRL/MpJ mouse


title: Donor 2 CD56bright/CD94high


title: Donor 2 CD56dim/CD94high


title: Stable ccRCC line, UT56 of P1_methylation

description: Methylation microarray data of a stable clear cell renal cell carcinoma cell line, UT56 at Passage 1

source_name: Stable ccRCC line, Passage 1 of UT56


title: Finite ccRCC line, UT37 of P2_methylation

description: Methylation microarray data of a finite clear cell renal cell carcinoma cell line, UT37 at Passage 2

source_name: Finite ccRCC line, Passage 2 of UT37


title: Donor 1 CD56dim/CD94high


title: Donor 1 CD56dim/CD94low


title: Donor 1 CD56bright/CD94high


title: Donor 4 CD56dim/CD94high


title: Stable ccRCC line, UT48 of P2_methylation

description: Methylation microarray data of a stable clear cell renal cell carcinoma cell line, UT48 at Passage 2

source_name: Stable ccRCC line, Passage 2 of UT48

value: III


title: Ear, BALB/c, 8 week old

description: Genomic DNA methylation profile in the ear of the BABL/c mouse

source_name: MeDIP enriched genomic DNA

value: BALB/c

source_name: input DNA


title: Finite ccRCC line, UT41 of P2_methylation

description: Methylation microarray data of a finite clear cell renal cell carcinoma cell line, UT41 at Passage 2

source_name: Finite ccRCC line, Passage 2 of UT41


title: Finite ccRCC line, UT27 of P3_methylation

description: Methylation microarray data of a finite clear cell renal cell carcinoma cell line, UT27 at Passage 3

source_name: Finite ccRCC line, Passage 3 of UT27

value: I-II


title: 14_Breast_Normal_Same_Duct

status: Public on Nov 02 2017

city: Toronto

first: Susan

last: Done

state: Ontario

address: 200 Elizabeth St. Rm 11E-228

department: Laboratory Medicine and Pathobiology

country: Canada

institute: University of Toronto

description: Microdissected Normal Breast Epithelium

hyb_protocol: Hybridised using the Hi-RPM hybridization kit (per manufacturer's instructions). Dye Incorporation > 8 pmol/ug. Oven (speed/temperature/time): 20 rpm/60°C/17hr

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting for 4x44k array slides.

data_processing: Microarray data were pre-processed: background corrected (offset = 16) and quantile between-array normalized using the limma package in R. For differential gene expression, only probes that were at least 10% brighter than the 95th percentile of the negative control probes on nine arrays (for each condition) were kept.

source_name: Breast Normal Epithelium

label_protocol: Arrays labelled using the Agilent QuickAmp Kit; 100 ng of mRNA were reverse transcribed using Superscript II reverse transcriptase (Invitrogen Canada, Burlington, ON) while incorporating Cy3-dCTP (NEN, Boston, MA, USA). All protocols available from www.agilent.com.

extract_protocol: Snap frozen tissues were sectioned at 8 micron thickness using a microtome and lightly stained with hematoxylin.  Histological identification of tumour and normal ducts was confirmed by a pathologist.  Needle-microdissection was performed under a dissecting microscope for both tumour and ducts to ensure minimal stromal contamination of epithelial cells. RNA were extracted from microdissected tissue using the Qiagen Allprep RNA/DNA Micro Kit (Qiagen, Mississauga, ON, Canada).

treatment_protocol: Fifteen patients undergoing mastectomy for biopsy-proven carcinoma were recruited at the Princess Margaret Cancer Center, University Health Network (Toronto, ON, Canada) from 2005 to 2008.  Inclusion criteria were defined as breast tumours at least 2cm in largest diameter as measured by imaging, and located at least 3cm from the nipple. During surgery, prior to removal of the breast, a ductoscopy procedure was performed using a 0.7mm mammary ductoscope (MF2-707, MD Fibertech Co, Japan). The duct leading to the tumour was identified by visual inspection and identification of the tumour. Methylene blue dye was injected to identify the involved duct for tissue sampling.  Immediately after the mastectomy procedure, tissue sampling was performed. Two samples were taken along the duct between the tumour and the nipple (previously dye stained) (T1 and T2) and one from the opposite duct within the same breast (as a normal control) (T3). A sample from the tumour was also obtained (T4). All tissues obtained were bisected, with one half snap frozen and the other half formalin-fixed and paraffin-embedded. Normal skin tissue was also obtained for control DNA.

tag: location

value: breast


title: 10_Breast_Adjacent_to_tumor_Normal

description: Microdissected Normal Breast Epithelium

source_name: Breast Adjacent-to-tumor Epithelium


title: 14_Breast_Tumor

description: Microdissected Breast Tumor

source_name: Breast Tumor


title: 22_Breast_Normal_Contralateral_Duct

description: Microdissected Normal Breast Epithelium

source_name: Breast Normal Contraleteral Epithelium


title: 22_Breast_Tumor

description: Microdissected Breast Tumor


title: 14_Breast_Adjacent_to_tumor_Normal

description: Microdissected Normal Breast Epithelium


title: 22_Breast_Adjacent_to_tumor_Normal

description: Microdissected Normal Breast Epithelium


title: 14_Breast_Normal_Contralateral_Duct

description: Microdissected Normal Breast Epithelium


title: 10_Breast_Normal_Same_Duct

description: Microdissected Normal Breast Epithelium


title: 10_Breast_Tumor

description: Microdissected Breast Tumor


title: 22_Breast_Normal_Same_Duct

description: Microdissected Normal Breast Epithelium


title: 9_Breast_Tumor

description: Microdissected Breast Tumor


title: 10_Breast_Normal_Contralateral_Duct

description: Microdissected Normal Breast Epithelium


title: 9_Breast_Normal_Contralateral_Duct

description: Microdissected Normal Breast Epithelium


title: 8b_Breast_Adjacent_to_tumor_Normal

description: Microdissected Normal Breast Epithelium


title: 8b_Breast_Tumor

description: Microdissected Breast Tumor


title: 6_Breast_Tumor

description: Microdissected Breast Tumor


title: 9_Breast_Normal_Same_Duct

description: Microdissected Normal Breast Epithelium


title: 9_Breast_Adjacent_to_tumor_Normal

description: Microdissected Normal Breast Epithelium


title: 8a_Breast_Adjacent_to_tumor_Normal

description: Microdissected Normal Breast Epithelium


title: 8b_Breast_Normal_Same_Duct

description: Microdissected Normal Breast Epithelium


title: 8b_Breast_Normal_Contralateral_Duct

description: Microdissected Normal Breast Epithelium


title: 8a_Breast_Normal_Contralateral_Duct

description: Microdissected Normal Breast Epithelium


title: 6_Breast_Adjacent_to_tumor_Normal

description: Microdissected Normal Breast Epithelium


title: 4_Breast_Tumor

description: Microdissected Breast Tumor


title: 6_Breast_Normal_Same_Duct

description: Microdissected Normal Breast Epithelium


title: 6_Breast_Normal_Contralateral_Duct

description: Microdissected Normal Breast Epithelium


title: 8a_Breast_Tumor

description: Microdissected Breast Tumor


title: 8a_Breast_Normal_Same_Duct

description: Microdissected Normal Breast Epithelium


title: 4_Breast_Normal_Contralateral_Duct

description: Microdissected Normal Breast Epithelium


title: 4_Breast_Adjacent_to_tumor_Normal

description: Microdissected Normal Breast Epithelium


title: 2_Breast_Tumor

description: Microdissected Breast Tumor


title: 4_Breast_Normal_Same_Duct

description: Microdissected Normal Breast Epithelium


title: 2_Breast_Normal_Contralateral_Duct

description: Microdissected Normal Breast Epithelium


title: 2_Breast_Normal_Same_Duct

description: Microdissected Normal Breast Epithelium


title: 2_Breast_Adjacent_to_tumor_Normal

description: Microdissected Normal Breast Epithelium


title: HPC1 [9534190119_L]

city: London

first: Timothy

last: Powell

address: 16 De Crespigny Park

department: SGDP Centre

institute: King's College London

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data were backgroundcorrected, transformed (log2) and normalised (quantile) in Lumi (R package)

label_protocol: Standard Illumina TotalPrep kit amplification and labeling protocol

growth_protocol: The multipotent, human hippocampal progenitor cell line HPC0A07/03C (provided by ReNeuron, Surrey, UK) was used for all experiments. HPC03A/07 cells were grown in reduced modified media (RMM) consisting of Dulbecco’s Modified Eagle’s Media/ F12 (D6421, DMEM:F12, Invitrogen, UK) supplemented with 0.03% human albumin (Albunorm 20%, Octapharma, UK), 100 µg/ml human apo-transferrin (T1147, Sigma), 16.2 µg/ml human putrescine DiHCl (P5780, Sigma), 5 µg/ml human recombinant insulin (I9278, Sigma), 60ng/ml progesterone (P8783, Sigma), 2 mM L-glutamine (G7513, Sigma) and 40 ng/ml sodium selenite (S9133, Sigma). To maintain proliferation, 10 ng/ml human bFGF (EC100-18B, Peprotech), 20 ng/ml human EGF (AF100-15-500, Peprotech) and 100 nM 4-OHT (H7904, Sigma) were added. The cell culture media is free of any serum unless stated as a treatment in the experimental conditions. In addition, when serum is added, we also further supplement our media with 0.5mg/ml Penicillin Streptomycin (10,000 U/ml, 15140-122, Life Technologies).

extract_protocol: Trireagent (Sigma) following the standard protocol, with an additional ethanol precipitation step

treatment_protocol: Progenitor cells were plated on 6-well plates (Nunclon, Denmark) at a density of 30000 per well and cultured in the presence of EGF, bFGF and 4-OHT and treated with human serum during the initial proliferation phase for 48 hours and in the subsequent differentiation phase for 7 days or during the differentiation phase only.

tag: donor (sample)

value: MediaO

tag: group

tag: Sex

tag: time point (hours)

tag: batch (array/biological replicate)


title: HPC1 [9553572062_J]


title: HPC1 [9534190119_G]

value: old


title: HPC1 [9534190119_C]


title: HPC1 [9534190119_I]

value: young


title: HPC1 [9534190119_H]


title: HPC1 [9534190119_A]


title: HPC1 [9553572062_K]


title: HPC1 [9534190119_J]


title: HPC1 [9553572062_L]

value: MediaY


title: HPC1 [9553572062_G]


title: HPC1 [9553572062_H]


title: HPC1 [9534190119_K]


title: HPC1 [9534190119_E]


title: HPC1 [9553572062_D]


title: HPC1 [9553572062_I]