title: 3012

description:
MZ twin
SAMPLE 70


title: 2106

status: Public on Dec 15 2014

type: genomic

city: Denmark

first: Qihua

last: Tan

address: J. B. Winsløws Vej 9B

country: Denmark

institute: University of Southern Denmark

description:
MZ twin
SAMPLE 69

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

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

data_processing: minfi; Data were normalized by SWAN. Average Beta values for each sample are included in the "Processed.csv" file available on the series record.

label: Cy3, Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: genomic DNA extracted and purified

label_protocol: Standard Illumina Protocol

extract_protocol: The blood was centrifuged at 1000 g for 10 min, and buffy-coat was frozen in aliquots at −80 °C. DNA was isolated from the buffy-coats using the salt precipitation method applying either a manual protocol or a semi-automated protocol based on the Autopure System (Qiagen, Hilden, Germany). Bisulphite treatment of 500 ng template genomic DNA was carried out with the EZ-96 DNA methylation kit (Zymo Research, Orange County, USA) following the manufacturer’s protocol.

tag: tissue

value: whole blood

tag: age

tag: birth-weight

tag: pair id


title: 1057

description:
MZ twin
SAMPLE 68


title: 2041_A

description:
MZ twin
SAMPLE 67


title: 3016

description:
MZ twin
SAMPLE 66


title: INF IgG

city: Pune

first: Debashis

last: Mitra

state: Maharashtra

address: Ganeshkhind

country: India

institute: National Centre for Cell Science

description: INF IgG_IP_IgG (Cy5) vs.WCE 4 (Cy3)

hyb_protocol: 5 μg of each Cy-labeled samples were hybridized onto the human promoter 244K ChIP-on-chip Array. Hybridization was performed in the hybridization oven at 65°C for 40 hours, followed by washes with ChIP-on-chip Wash buffer 1 and 2 (Agilent, USA).

scan_protocol: The washed slides were scanned at 5 μm scan resolution using Agilent DNA microarray scanner as per Agilent Protocol.

data_processing: Data extraction done using Agilent Feature extraction software and normalized Using Agilent DNA Analytics software.

source_name: Input DNA from HIV-1 NL4-3 infected CEM-GFP cells

label_protocol: The DNA samples were blunted at 12°C for 20 minutes using T4 DNA polymerase as per the Mammalian Chip on Chip Protocol of Agilent Technologies.The blunted DNA was cleaned, precipitated and resuspended in water. Each sample was labeled using Agilent Genomic DNA Labeling Kit PLUS (5188-5309) with Cy3 or Cy5 dUTP. DNA yield and incorporation of label (specific activity) was measured using NanoDrop spectrophotometer.

growth_protocol: Infected CEM-GFP cells were maintained in RPMI with 10% fetal calf serum

extract_protocol: HIV-1 NL4.3-infected Day7 CEM-GFP cells (10E7) were cross-linked using 1% formaldehyde for 10 min at room temperature followed by quenching with 125 mM glycine for 5 min. The fixed cells were then sequentially washed twice with ice-cold PBS, once with wash buffer 1 {0.25% Triton X-100, 10 mM EDTA, 0.5 mM EGTA, 10 mM HEPES pH 7.5, 1 mM PMSF, 10 mM sodium butyrate and 2X protease inhibitor cocktail (Roche)} and then using wash buffer 2 (0.2 M NaCl, 1 mM EDTA, 0.5 mM EGTA, 10 mM HEPES pH 7.5, 1 mM PMSF, 10 mM sodium butyrate and 2X protease inhibitor cocktail). The washed pellet was then lysed in 500 μl of lysis buffer (150 mM NaCl, 25 mM Tris-HCl pH 7.5, 5 mM EDTA pH 8.0, 1% Triton X- 100, 0.1% SDS, 0.5% sodium deoxycholate, 1 mM PMSF, 10 mM sodium butyrate, 2X protease inhibitor cocktail), followed by sonication to shear the chromatin using Bioruptor (Diagenode, Europe). The lysates were centrifuged at 13,000 rpm for 10 min at 4°C to remove cell debris. Chromatin was estimated using NanoDrop 1000 Spectrophotometer (Thermo Fisher Scientific, USA). 100 μg of chromatin was taken and diluted in dilution buffer {0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl (pH 8.1), 167 mM NaCl) which was then pre-cleared by incubation with Protein A/G beads (Pierce, USA), salmon sperm DNA (Sigma, USA) and BSA (New England Biolabs, USA) followed by centrifugation. 10% of the precleared lysate was used as input. Rest 90% of the supernatant was used for immunoprecipitation with purified anti-Tat antibody or isotype-matched irrelevant antibody (GST antibody) as negative control. The chromatin antibody complex was immobilized on Protein A/G beads for 2 hours at 4°C followed by three washes each with RIPA wash buffer (0.1% SDS, 1% sodium deoxycholate, 150 mM NaCl, 10 mM sodium phosphate, pH 7.2, 2 mM EDTA, 1% IGEPAL) and TE (10 mM Tris HCl; pH 8.0, 1 mM EDTA). Immune complexes were then eluted in 100 μl of 2% SDS, 0.1 M NaHCO3 and 10 mM DTT. DNA was extracted after reverse crosslinking, proteinase K treatment and phenol chloroform extraction.

treatment_protocol: CEM-GFP cells were infected with HIV-1 NL4-3 at an MOI of 0.1 and harvested at day 7 post infection

tag: cell line

value: CEM-GFP

tag: cell type

value: T cell line

tag: hiv-1 infection stage

value: Day 7 post infection

tag: antibody

source_name: IgG ChIP DNA from HIV-1 NL4-3 Infected CEM-GFP cells

value: Rabbit anti- GST (Z-5) IgG

tag: catalog number

tag: manufacturer

value: Santa Cruz Biotechnology

tag: lot/ batch no.


title: 3017

description:
MZ twin
SAMPLE 72


title: INF Tat1

description: INF Tat1_IP2 (Cy5) vs.WCE (Cy3)

source_name: Tat ChIP DNA from HIV-1 NL4-3 infected CEM-GFP cells

value: IgG purified from HIV-1_BH10 Tat antiserum raised in rabbit

value: AIDS Research and Reference Reagent program (NIH)


title: 3036

description:
MZ twin
SAMPLE 65


title: hippocampus_freshfrozen_51

type: RNA

city: Bonn

first: Albert

last: Becker

address: Sigmund-Freud Str. 25

department: Neuropathology

country: Germany

institute: University of Bonn Medical Center

description: human brain tissue from pharmacoresistant TLE patients

hyb_protocol: Illumina Direct Hybridization Assay Kit according standard protocol

scan_protocol: Standard Illumina scanning protocol uisng Illumina BeadArray Reader

data_processing: Gene expression data were normalized using Illumina BeadStudio software suite by means of quantile normalization with background subtraction

label: biotin

molecule: total RNA

source_name: hippocampal formation

label_protocol: Biotinylated cRNA were prepared with Illumina TotalPrep-96 RNA Amplification Kit (Life Technologies Corporation, Darmstadt).

extract_protocol: Total RNA was isolated from hippocampal tissue samples using ALLPrep DNA/RNA Mini Kit (Qiagen, Hilden) according manufacturer's protocoll. Tissue lysate was passed trough an AllPrep Rneasy spin collum to selectively isolate RNA.

value: hippocampal formation

tag: phenotype

value: epilepsy


title: hippocampus_freshfrozen_55


title: hippocampus_freshfrozen_48


title: hippocampus_freshfrozen_50


title: hippocampus_freshfrozen_53


title: hippocampus_freshfrozen_56


title: hippocampus_freshfrozen_52


title: hippocampus_freshfrozen_54


title: hippocampus_freshfrozen_47


title: hippocampus_freshfrozen_49


title: hippocampus_freshfrozen_45


title: hippocampus_freshfrozen_44


title: 1011

description:
MZ twin
SAMPLE 64


title: hippocampus_freshfrozen_42


title: hippocampus_freshfrozen_43


title: hippocampus_freshfrozen_46


title: 2129

description:
MZ twin
SAMPLE 63


title: 1058

description:
MZ twin
SAMPLE 62


title: 2042_A

description:
MZ twin
SAMPLE 61


title: 1027

description:
MZ twin
SAMPLE 60


title: 3027

description:
MZ twin
SAMPLE 59


title: 2085_A

description:
MZ twin
SAMPLE 58


title: NPC_WBS1-C2 (GDB-339_C3)

city: Milano

first: Giuseppe

last: Testa

address: Via Adamello, 16

country: Italy

institute: European Institute of Oncology & University of Milano, Italy

description: Neural progenitors expressing FOXG1, OTX2 and ZO1, typically arranged in neural rosettes with TBR2+ intermediate progenitors surrounding apical Pax6+ progenitors.

hyb_protocol: Hybridization was performed using the GeneAtlas™ Hybridization, Wash and Stain Kit. It contains a mix for target dilution, DMSO at a final concentration of 10% and pre-mixed biotin-labeled control oligo B2 and bioB, bioC, bioD and Cre controls (Affymetrix cat# 900299) at a final concentration of 50 pM, 1.5 pM, 5 pM, 25 pM and 100 pM respectively. Targets were diluted in hybridization buffer at a concentration of 0.05 μg/ul, denatured at 99 °C for 5 minutes, incubated at 45 °C for 5 minutes and centrifugated at 5,000 rpm for 1 minute. The Array Strip is then moved to an hybridization tray, which contains the hybridization cocktails . A single Gene 2.1 PEG Array Strip is hybridized with four  different biotin-labeled target. Hybridizations were performed for 20 hours at 48°C in the GeneAtlas™ Hybridization Station. The Array Strips were washed and stained in the GeneAtlas™ Personal Fluidics Station. At the end of this procedure the array strips were placed into the imaging tray, which contains the Array Holding buffer.

scan_protocol: The array strips were imaged using the GeneAtlas™ Imaging Station. Affymetrix GeneAtlas™ Command Console software was used to acquire the Array Strip images and generate .DAT and .CEL files, which were used for subsequent analysis.

data_processing: Analysis was performed with the Affy R package, using Marc Carlson's Hugene 2.1st RefSeq annotation file version 18, RMA for background normalization, quantile normalization between samples, and using only PM-probes.

source_name: Neural Progenitor Cells (NPC), iPSC-derived

label_protocol: The quality of total RNA was first assessed using an Agilent Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA). Biotin-labeled cDNA targets were synthesized starting from 150 ng of total RNA. Double stranded cDNA synthesis and related cRNA was performed with Ambion® WT Expression Kit (Ambion, Austin, TX). With the same kit was synthesized the sense strand cDNA before to be fragmented and labeled with Affymetrix GeneChip® WT Teminal Labeling Kit (Affymetrix, Santa Clara, CA). All steps of the labeling protocol were performed as suggested by Affymetrix. Each eukaryotic GeneChip® probe array contains probe sets for several B. subtilis genes that are absent in the samples analyzed (lys, phe, thr, and dap). This Poly-A RNA Control Kit contains in vitro synthesized, polyadenylated transcripts for these B. subtilis genes that are pre-mixed at staggered concentrations to allow GeneChip® probe array users to assess the overall success of the assay. Poly-A RNA Controls final concentration in each target are lys 1:100,000, phe 1:50,000, thr 1:25,000 and dap 1:6,667.

growth_protocol: Differentiation and culture of NCSC was performed as described in Menendez et al., Nat Protoc 8, 203-12 (2013). For NPC, differentiation by dual Smad inhibition was performed as described in Shi et al., Nat Protoc 7, 1836-46 (2012).

extract_protocol: RNA was extracted using the RNeasy Mini Plus Kit (Qiagen) with DNase treatment.

tag: gender

value: male

tag: genotype

value: WBS

tag: donor


title: 1050

description:
MZ twin
SAMPLE 56


title: 1019

description:
MZ twin
SAMPLE 57


title: hippocampus_freshfrozen_41


title: hippocampus_freshfrozen_37


title: hippocampus_freshfrozen_35


title: NPC_WBS1-C1 (GDB-339_C2)

value: Neural Progenitor Cells (NPC), iPSC-derived


title: 1047

description:
MZ twin
SAMPLE 55


title: hippocampus_freshfrozen_40


title: hippocampus_freshfrozen_39


title: MCF7_CTRL_3DCol_72h

city: Liège

first: Erik

last: Maquoi

address: Tour de Pathologie, B23 Sart-Tilman

country: Belgium

institute: University of Liège

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data was preprocessed by Bioconductor lumi package. It was VST transformed and quantile normalized (log2 values are shown)

label_protocol: Biotinylated cRNA were prepared with the Ambion Illumina TotalPre-96 RNA Amplification Kit for Illumina arrays

growth_protocol: Cells were passaged in DMEM medium (Invitrogen) supplemented with heat-inactivated fetal bovine serum (Invitrogen), 2mM L-glutamine (Invitrogen) and penicillin-streptomycin (Invitrogen). Cells were routinely cultured in 37°C with 5% CO2. For the monolayer cultures, cells were seeded in 12-well plates, 20000 cells/well, in 1 ml of medium supplemented with 5.5% serum. For the 3D environment, cells were suspended in neutralized native rat tail type I collagen gels, 200000 cells/800 µl gel in 12-well plates and incubated 30 min at 37°C to allow polymerization of the collagen fibers. After polymerization, 1 ml of medium supplemented with 10% serum was added to each well, resulting in a final serum concentration of 5.5%. The culture medium was refreshed after 48 hours and cells were allowed to grow for 24, 48 and 72 hours. Four independent replicates were prepared for each treatment-time combination.

extract_protocol: RNA was extracted with TRIzol reagent (Invitrogen), followed by clean-up with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: MCF-7 cells were stably transfected with either an empty pcDNA3.1/Zeo expression vector (Invitrogen) or human MMP-14 cDNA subcloned in pcDNA3.1/Zeo.

value: MCF-7 human breast adenocarcinoma cell line

tag: transfection

value: pcDNA3.1/Zeo (control)

tag: culture condition

value: 3D type I collagen gel

tag: time (culture duration)

value: 72 hours


title: NPC_WBS2-C2 (GDB-316_M)

value: female


title: NPC_WBS3-C3 (GDB-361_E)


title: NPC_CTL3-C1 (Bu1Cre)

value: Control


title: hippocampus_freshfrozen_36

tag: tissue


title: NPC_CTL2-C1 (Miff_1)

value: Miff


title: NPC_WBS4-C1 (GDB-306_O)


title: NPC_CTL1R-C2 (GDB-339-1_R)


title: hippocampus_freshfrozen_38


title: 2023

description:
MZ twin
SAMPLE 53

value: whole blood

tag: age

tag: birth-weight


title: hippocampus_freshfrozen_33


title: 1026

description:
MZ twin
SAMPLE 54

tag: pair id


title: hippocampus_freshfrozen_32


title: 2086_A

description:
MZ twin
SAMPLE 52


title: 1048

description:
MZ twin
SAMPLE 49


title: hippocampus_freshfrozen_34


title: NPC_AtWBS1-C2 (GDB-192_B)

value: AtWBS

tag: cell type


title: 1024

description:
MZ twin
SAMPLE 50


title: NPC_AtWBS1-C3 (GDB-192_D)


title: NPC_7dupASD2-C1 (GDB-242_K)


title: NPC_7dupASD2-C2 (GDB-242_J)


title: hippocampus_freshfrozen_28


title: 2055

description:
MZ twin
SAMPLE 48


title: NCSC_WBS1-C1 (GDB-339_C2)

description: Neural crest stem cells with homogeneous (>90% cells in FACS gate) expression of HNK1 and NGFR.

source_name: Neural Crest Stem Cells (NCSC), iPSC-derived


title: hippocampus_freshfrozen_29


title: 3055

description:
MZ twin
SAMPLE 47


title: hippocampus_freshfrozen_30


title: NCSC_WBS4-C1 (GDB-306_O)

value: Neural Crest Stem Cells (NCSC), iPSC-derived


title: NPC_7dupASD1-C2 (GDB-CF_G)

value: GDB-CF


title: 1018

description:
MZ twin
SAMPLE 51


title: NPC_7dupASD1-C1 (GDB-CF_C)


title: hippocampus_freshfrozen_31


title: 2113

description:
MZ twin
SAMPLE 46


title: hippocampus_freshfrozen_26


title: hippocampus_freshfrozen_27


title: NCSC_WBS2-C2 (GDB-316_M)


title: hippocampus_freshfrozen_25


title: 1052

description:
MZ twin
SAMPLE 44


title: NCSC_CTL2-C2 (Miff_3)


title: 3061

description:
MZ twin
SAMPLE 45


title: 2029

description:
MZ twin
SAMPLE 43


title: NCSC_CTL3-C1 (Bu1Cr3-1)


title: 2062

description:
MZ twin
SAMPLE 41


title: hippocampus_freshfrozen_24


title: hippocampus_freshfrozen_23


title: 2054

description:
MZ twin
SAMPLE 42


title: NCSC_CTL1R-C3 (GDB-339-1_S), rep1


title: 2114

description:
MZ twin
SAMPLE 40


title: NPC_CTL2-C2 (Miff_3)


title: NCSC_CTL1R-C3 (GDB-339-1_S), rep2


title: NCSC_AtWBS1-C2 (GDB-192_B)


title: hippocampus_freshfrozen_21


title: hippocampus_freshfrozen_22


title: 3060

description:
MZ twin
SAMPLE 39


title: hippocampus_freshfrozen_20


title: 1051

description:
MZ twin
SAMPLE 38


title: hippocampus_freshfrozen_16


title: 1021

description:
MZ twin
SAMPLE 37


title: NCSC_7dupASD1-C2 (GDB-CF_G)


title: hippocampus_freshfrozen_18


title: hippocampus_freshfrozen_17


title: NCSC_7dupASD2-C1 (GDB-242_K)


title: NCSC_7dupASD2-C2 (GDB-242_J)


title: 1023

description:
MZ twin
SAMPLE 35


title: 2012

description:
MZ twin
SAMPLE 34


title: 2035

description:
MZ twin
SAMPLE 33


title: hippocampus_freshfrozen_14


title: 2043

description:
MZ twin
SAMPLE 36


title: hippocampus_freshfrozen_15


title: 3022

description:
MZ twin
SAMPLE 32


title: 1013

description:
MZ twin
SAMPLE 31


title: hippocampus_freshfrozen_10


title: hippocampus_freshfrozen_11


title: hippocampus_freshfrozen_13


title: hippocampus_freshfrozen_8


title: 1025

description:
MZ twin
SAMPLE 29


title: hippocampus_freshfrozen_12


title: 2013

description:
MZ twin
SAMPLE 28


title: hippocampus_freshfrozen_19


title: 2028

description:
MZ twin
SAMPLE 30


title: 3042

description:
MZ twin
SAMPLE 27


title: hippocampus_freshfrozen_7


title: hippocampus_freshfrozen_9


title: 3010

description:
MZ twin
SAMPLE 25


title: hippocampus_freshfrozen_5


title: hippocampus_freshfrozen_4


title: 3028

description:
MZ twin
SAMPLE 24


title: hippocampus_freshfrozen_1


title: 3023

description:
MZ twin
SAMPLE 23


title: hippocampus_freshfrozen_2


title: hippocampus_freshfrozen_3


title: hippocampus_freshfrozen_6


title: HGFs HEMA 96h (D) vs HGFs control 96h (G) biological replicate

city: Chieti

first: Valentina

last: Gatta

state: Abruzzo

address: Via Colle Dell'Ara

department: Department of Psychological SciencesDepartment of Psychological Sciences

institute: University G.d'Annunzio

description: Experiment 6 biological replicate

hyb_protocol: 2 µg of respectively Cy3-Cy5 labeled aRNA, from each treated cell culture and control culture, were fragmented and then hybridized on a Phalanx Human OneArray™  using 1.5X OneArray hybridization Buffer at 42°C in oven for 14-16 hrs.

scan_protocol: After hybridization, Cy3-Cy5 fluorescent signals were captured by a Confocal Laser Scanner ScanArray Express (Perkin Elmer, Waltham, MA, USA) and analysed using the software ScanArray Express - MicroArray Analysis System version 3.0 (Perkin Elmer, Waltham, MA, USA). The values of the median signal intensity from each spot were subtracted from the local median background intensity. For each slide after local background subtraction, a LOWESS algorithm was used for row data normalization to evaluate signal to noise ratio and generate log ratios of sample vs. reference signal.

data_processing: A gene was considered to be significantly expressed when showing an absolute value of log-ratio higher or equal to 0.5, an index that translates to a fold-change > 0.7 or < 1.4 in transcript quantity, a present call in at least the 75% of experiments and a p-Value <0.05. Probes from the platform GPL13693 were manually matched to probes from the platform GPL6254. In the analysis were excluded probes spotted only in GPL13693. The resulting gene lists underwent a clustering analysis (Cluster 3.0 and TreeView, Stanford University Labs) to unravel Genes Differentially Expressed (DEGs). Identified DEGs were, then, analysed by Ingenuity Pathways Analysis (IPA) software (Ingenuity Systems, Redwood City, CA, USA) to disclose the biological functions and the functional networks they are involved in.

source_name: cultured HGFs treated with 3mM HEMA for 96h (D)

label_protocol: Extracted RNA was linearly amplified using the Amino Allyl MessageAmp™ II aRNA Amplification Kit (Ambion, Austin, TX, USA), following the 2 rounds amplification protocol. 10 to 20 µg of amplified aRNA were fluorescently labeled with Cy3 or Cy5 cyanins.

extract_protocol: After HEMA incubation, cells were trypsinized. Pellets (about 7∙106 cells/pellet) were washed with 1 ml of PBS and centrifuged at1,200 rpm for 5 min at 4°C three times.

value: HGFs obtained from fragments of healthy marginal gingival tissue from the retromolar area taken during surgical extraction of impacted third molars

source_name: cultured HGFs without HEMA harvested at 96 h (G)


title: 1004

description:
MZ twin
SAMPLE 22


title: HGFs HEMA 96h (H) vs HGFs control 96h (G)

description: Experiment 5

source_name: cultured HGFs treated with 3mM HEMA for 96h (H)


title: 3004

description:
MZ twin
SAMPLE 21


title: HGFs HEMA 96h (D) vs HGFs control 96h (C)

description: Experiment 4

source_name: cultured HGFs without HEMA harvested at 96 h (C)


title: 3001

description:
MZ twin
SAMPLE 20


title: HGFs HEMA 24h (F) vs HGFs control 24h (A) biological replicate

description: Experiment 3 biological replicate

source_name: cultured HGFs treated with 3mM HEMA for 24h (F)

source_name: cultured HGFs without HEMA harvested at 24 h (A)


title: HGFs HEMA 24h (F) vs HGFs control 24h (E)

description: Experiment 2

source_name: cultured HGFs without HEMA harvested at 24 h (E)


title: 2009

description:
MZ twin
SAMPLE 19


title: HGFs HEMA 24h (B) vs HGFs control 24h (A)

description: Experiment 1

source_name: cultured HGFs treated with 3mM HEMA for 24h (B)


title: 3021

description:
MZ twin
SAMPLE 26


title: MC5+0.5DC

city: New York

first: Mayte

last: Suarez-Farinas

state: NY

address: 1425 Madison Ave, L2-70C, Box 1077,

country: USA

institute: Mount SinaiSchool of Medicine

description: RU-NG

hyb_protocol: RNA was hybridized to HGU133 Plus 2.0 chips to measure relative gene expression.

scan_protocol: Hewlett-Packard GeneArray Scanner

data_processing: GCRMA (using gcrma package from R/Bioconductor). Batch effect was eliminated using Combat. For a proper estimation of the  adjustment parameters, genes with small standard deviation before the batch adjustment, were filter out.

label_protocol: GeneChip Affymetrix protocol

extract_protocol: Total RNA was extracted using RNeasy Mini Kit (Qiagen, Valencia, CA) according to the manufacturer’s protocol with on-column DNase digestion

tag: cell population

value: melanocytes after coculture with dendritic cells in a 2:1 melanocyte:dendritic cell ratio


title: 3024

description:
MZ twin
SAMPLE 17


title: MC5

description: RU-NG

value: melanocytes alone


title: iPSC_CTL2-C1 (MIFF_1) aCGH

description: Hybridized to CytoScan HD

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

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000 7G.

data_processing:
The array image was acquired using Affymetrix GeneChip® Command Console Software 4.1.2. Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using Chromosome Analysis Suite (ChAS) software. Inferred copy number states were derived from a Hidden Markov Model (HMM) based algorithm implemented in ChAS.
CHP files.

label: Biotin

source_name: fibroblast-derived iPSC

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from fibroblasts and feeder-free iPSC lines using the DNeasy Blood and Tissue Kit (Qiagen) according to manufacturer specifications. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and agarose gel electrophoresis.

value: male

tag: culture

value: iPSC colonies were grown on feeder-free conditions on plates coated with human-qualified Matrigel (BD Biosciences) diluted 1:40 in DMEM-F12 and in mTeSR-1 (StemCell Technologies) medium.

tag: reprogramming method

value: mRNA reprogramming

value: fibroblast-derived iPSC


title: 3029

description:
MZ twin
SAMPLE 18


title: 1001

description:
MZ twin
SAMPLE 16


title: iPSC_CTL2-C2 (MIFF_3) aCGH

description: Hybridized to CytoScan HD


title: iPSC_CTL1R-C1 (GDB-339-1_1B) aCGH

description: Hybridized to CytoScan HD


title: HF_7dupASD1 (GDB-CF_HF) aCGH

description: Hybridized to CytoScan HD

source_name: primary skin fibroblast

value: Fibroblasts were grown in HF medium (RPMI 1640, 1% L-Glutamine, 1% Pen-Strep, 15% FBS).

value: primary skin fibroblast


title: MC4+0.5DC

description: RU-NG


title: 3002

description:
MZ twin
SAMPLE 14

source_name: genomic DNA extracted and purified


title: MC4

description: RU-NG


title: iPSC_CTL3-C1 (Bu1Cr3-1) aCGH

description: Hybridized to CytoScan HD

value: Reprogramming using excisable OKSM Lentivirus, followed by CRE-mediated excision.


title: HF_CTL1R (GDB-339-1_HF) aCGH

description: Hybridized to CytoScan HD

value: female


title: iPSC_7dupASD1-C2 (GDB-CF_G) aCGH

description: Hybridized to CytoScan HD


title: iPSC_7dupASD1-C3 (GDB-CF_F) aCGH

description: Hybridized to CytoScan HD


title: iPSC_CTL1R-C3 (GDB-339-1_1S) aCGH

description: Hybridized to CytoScan HD

value: Control


title: 3003

description:
MZ twin
SAMPLE 15


title: 2010

description:
MZ twin
SAMPLE 13


title: iPSC_WBS3-C1 (GDB-361_F) aCGH

description: Hybridized to CytoScan HD

value: WBS


title: MC2

description: RU-NG


title: MC1

description: RU-NG


title: MC+0.5DC

description: RU-NG


title: 3007

description:
MZ twin
SAMPLE 10

value: whole blood


title: iPSC_WBS1-C3 (GDB-339_C7) aCGH

description: Hybridized to CytoScan HD


title: iPSC_WBS3-C3 (GDB-361_E) aCGH

description: Hybridized to CytoScan HD


title: iPSC_WBS3-C2 (GDB-361_O) aCGH

description: Hybridized to CytoScan HD


title: 2032_A

description:
MZ twin
SAMPLE 9


title: iPSC_7dupASD1-C1 (GDB-CF_C) aCGH

description: Hybridized to CytoScan HD


title: 2025

description:
MZ twin
SAMPLE 8


title: HF_WBS3 (GDB-361_HF) aCGH

description: Hybridized to CytoScan HD


title: 1007

description:
MZ twin
SAMPLE 6


title: 2008

description:
MZ twin
SAMPLE 7


title: DC

description: RU-NG

value: dendritic cells alone


title: 1020

description:
MZ twin
SAMPLE 11


title: 3008

description:
MZ twin
SAMPLE 4


title: HF_WBS1 (GDB-339_HF) aCGH

description: Hybridized to CytoScan HD


title: 2033_A

description:
MZ twin
SAMPLE 3


title: iPSC_CTL1R-C2 (GDB-339-1_1R) aCGH

description: Hybridized to CytoScan HD


title: 2040

description:
MZ twin
SAMPLE 5


title: 3013

description:
MZ twin
SAMPLE 2


title: iPSC_WBS1-C2 (GDB-339_C3) aCGH

description: Hybridized to CytoScan HD


title: 2026

description:
MZ twin
SAMPLE 1


title: iPSC_WBS2-C1 (GDB-316_L) aCGH

description: Hybridized to CytoScan HD


title: iPSC_WBS2-C3 (GDB-316_B) aCGH

description: Hybridized to CytoScan HD


title: HF_WBS2 (GDB-316_HF) aCGH

description: Hybridized to CytoScan HD


title: iPSC_WBS2-C2 (GDB-316_M) aCGH

description: Hybridized to CytoScan HD


title: iPSC_WBS4-C2 (GDB-306_M) aCGH

description: Hybridized to CytoScan HD


title: 24h-1-2

status: Public on Dec 14 2014

city: Mengla

first: MaoSheng

last: Chen

state: Yunnan

address: Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences

department: Molecular breeding of energy plants

country: China

description: Gene expression of flower bud after 24hr BA treatment

hyb_protocol: A total of 875 ng Cy3 cRNA was fragmented and hybridized with 4 × 44 k arrays. After hybridization, the arrays washed according to the manufacturer instructions

scan_protocol: Slides were scanned twice using an Agilent scanner at 100% and 10% photo multiplier tube.

data_processing: Raw data from arrays was normalized by log2 transformation and analyzed using GeneSpring GX software (Agilent).

organism: Jatropha curcas

source_name: flower bud, 24hr, replicate 2

label_protocol: A total of 2 ug RNA was reverse-transcribed to cDNA with a one-step method. The cDNA was transcribed into RNA by T7 RNA polymerase, modified by aa-UTP at 40 ℃, purified by Qiagen RNeasy mini kit and quantified by the Bioanalyzer. A total of 4 ug cRNA was labeled with Cy3 fluorescence dye at 25 ℃ and purified by Qiagen RNeasy mini kit.

growth_protocol: One year old Jatropha plants were grown in a field with the density of 2×2m at Xishuangbanna Tropical Botanical Garden of the Chinese Academy of Sciences (21° N, 101° E) located in Mengla County, Yunnan Province, china

extract_protocol: The total RNA was extracted from tissues using TRIzol (Invitrogen), concentration was determined by Nanodrop ND-1000 (Thermo Scientific), integrity was confirmed by Agilent 2100 Bioanalyzer (Agilent) and the total RNA was purified by QIAGEN RNasy kit.

treatment_protocol: The flower buds were collected at 0h, 3h, 12h, 24h and 48h time point after 1mM 6-benzylaminopurine treatment.

value: flower bud

tag: treatment

value: benzylaminopurine

tag: time


title: 1006

description:
MZ twin
SAMPLE 12


title: 12h-1-2

institute: Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences

description: Gene expression of flower bud after 12hr BA treatment

source_name: flower bud, 12hr, replicate 2


title: 48h-1-3

description: Gene expression of flower bud after 48hr BA treatment

source_name: flower bud, 48hr, replicate 3


title: 12h-1-1

source_name: flower bud, 12hr, replicate 1


title: 48h-1-2

source_name: flower bud, 48hr, replicate 2


title: 3h-1-3

description: Gene expression of flower bud after 3hr BA treatment

source_name: flower bud, 3hr, replicate 3


title: 3h-1-1

source_name: flower bud, 3hr, replicate 1


title: 24h-1-3

source_name: flower bud, 24hr, replicate 3


title: iPSC_WBS4-C1 (GDB-306_O) aCGH

description: Hybridized to CytoScan HD


title: 0h-1-2

description: Gene expression of flower bud after 0hr BA treatment

source_name: flower bud, 0hr, replicate 2


title: 3h-1-2

source_name: flower bud, 3hr, replicate 2


title: 12h-1-3

source_name: flower bud, 12hr, replicate 3


title: 24h-1-1

source_name: flower bud, 24hr, replicate 1


title: 48h-1-1

source_name: flower bud, 48hr, replicate 1


title: 0h-1-1

source_name: flower bud, 0hr, replicate 1


title: 0h-1-3

source_name: flower bud, 0hr, replicate 3


title: Liver_high fat diet_12week_DBA

city: shanghai

first: Mingzhe

last: Zhu

address: south chongqing Road

institute: hsc

description: gene expression data from DBA liver after fed high fat diet 12week

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45°C on GeneChip Mouse Genome 430 2.0 Array,then washed and stained in the Fluidics Station 450

scan_protocol: scanned on the Affymetrix Scanner 3000

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

organism: Mus musculus

source_name: DBAmice liver after fed high diet 12week

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from  total RNA

growth_protocol: C57 and DBA mice were fed high fat diet for 0,1, 4,12,21week respectively. Liver tiusses were removed at each time-poine for two mice strains.

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

treatment_protocol: Liver tissues were washed in 0.9% saline and then stored in liquid nitrogen until use

tag: strain


title: Liver_high fat diet_1week_DBA

description: gene expression data from DBA liver after fed high fat diet 1week

source_name: DBAmice liver after fed high diet 1week

tag: gender


title: Liver_high fat diet_21week_DBA

description: gene expression data from DBA liver after fed high fat diet 21week

source_name: DBAmice liver after fed high diet 21week


title: Liver_high fat diet_0week_DBA

description: gene expression data from DBA liver after fed high fat diet 0week

source_name: DBAmice liver after fed high diet 0week


title: Liver_high fat diet_21week_C57

description: gene expression data from C57 liver after fed high fat diet 21week

source_name: C57mice liver after fed high diet 21week


title: Liver_high fat diet_1week_C57

description: gene expression data from C57 liver after fed high fat diet 1week

source_name: C57mice liver after fed high diet 1week


title: iPSC_WBS4-C3 (GDB-306_E) aCGH

description: Hybridized to CytoScan HD

source_name: fibroblast-derived iPSC

tag: genotype


title: Liver_high fat diet_0week_C57

description: gene expression data from C57 liver after fed high fat diet 0week

source_name: C57mice liver after fed high diet 0week


title: iPSC_7dupASD2-C2 (GDB-242_J) aCGH

description: Hybridized to CytoScan HD

tag: donor


title: wild-type B. napus rep 2

status: Public on Dec 13 2014

city: Edmonton

first: Guanqun

state: Alberta

address: University of Alberta

department: Department of Agricultural, Food & Nutritional Science

country: Canada

institute: University of Alberta

description: 2-dap samples

hyb_protocol: Hybridization was produced with the Quick Amp Labeling Kit, one-color (Agilent Technologies) according the manufacturer’s instructions.

scan_protocol: Slides were scanned at 5 μm resolution with a GenePix 4000B scanner (Molecular Device, USA).

data_processing: Image processing was performed with Feature Extraction Software 10.5.1.1 (Agilent Technologies). Microarray data were analyzed using the open-source R statistical programming language (http://www.r-project.org/) and Bioconductor packages (Gentleman et al. 2004). The raw data were imported into the R statistical environment, and their overall high quality was determined using the arrayQualityMetrics package (Kauffmann et al. 2009). Data were normalized using Variance Stabilization Normalization. Differential gene expression analysis was subsequently performed using an empirical Bayes method implemented in Linear Models for Microarray Analysis (Smyth 2004). A gene was considered differentially expressed in the tt16 RNAi line compared with the wild-type if its B statistic (log odds of differential expression) was ≥ 2.0, corresponding to a ≥80% probability of differential expression. The functional annotations of differentially expressed genes (DEGs) in Brassica were updated by running BLAST analysis (E value ≤ 10-5) against TAIR 10, the latest Arabidopsis genome release at The Arabidopsis Information Resource (http://www.arabidopsis.org). The PA- and seed coat-associate genes reported in other plants were also used to assist gene identification. The gene ontology (GO) annotation of Arabidopsis genes was used for GO analysis of the DEGs.   References:  1. Gentleman, R.C., et al., Bioconductor: open software development for computational biology and bioinformatics. Genome Biology, 2004. 5(10): p. R80.  2. Kauffmann, A., R. Gentleman, and W. Huber, arrayQualityMetrics-a bioconductor package for quality assessment of microarray data. Bioinformatics, 2009. 25(3): p. 415-6.  3. Smyth, G.K., Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Statistical applications in genetics and molecular biology, 2004. 3: p. Article3.

organism: Brassica napus

source_name: wild-type B. napus DAP2 sample

label_protocol: Cy3-labeled cRNA was produced with the Quick Amp Labeling Kit, one-color (Agilent Technologies) according the manufacturer’s instructions.

growth_protocol: Brassica napus (DH12075) plants were grown in the greenhouse or growth chamber. The growth conditions were set as follows: 16 h day/8 h night cycle, 25/20ºC day/night temperature, 60% relative humidity, 250 μmol m-2 s-1 intense light.

extract_protocol: Total RNA was isolated using RNeasy plant mini kit (Qiagen, Toronto, Canada) according to the manufacturer’s instructions.

treatment_protocol: Samples were immediately freezed in liquid nitrogen after harvesting and stored in -80 deg C freezer before RNA extraction

tag: genotype/variation

value: wild type

value: silique with developing seeds


title: iPSC_7dupASD2-C3 (GDB-242_O) aCGH

description: Hybridized to CytoScan HD


title: Bntt16 RNAi B. napus rep 1

description: 2-dap samples

source_name: Bntt16 RNAi B. napus DAP2 sample

value: Bntt16 RNAi


title: HF_WBS4 (GDB-306_HF) aCGH

description: Hybridized to CytoScan HD

source_name: primary skin fibroblast

value: male


title: Bntt16 RNAi B. napus rep 3

description: 2-dap samples


title: Bntt16 RNAi B. napus rep 4

description: 2-dap samples


title: wild-type B. napus rep 1

description: 2-dap samples


title: wild-type B. napus rep 4

description: 2-dap samples


title: Non-melanoma skin cancer PS_022

city: Suwon

first: Hyun Goo

last: Woo

address: 164 Worldcup-ro Yeongtong-gu

country: South Korea

institute: Ajou University School of Medicine

hyb_protocol: Following fragmentation, 0.75 ug of cRNA were hybridized to the Illumina HumanHT-12  Expression Beadchip according to the protocols provided by the manufacturer

scan_protocol: Arrays were scanned using the Illumina Bead Array Reader  Confocal  Scanner

data_processing: Array data export processing and analysis was performed using Illumina GenomeStudio v2009.2

source_name: NORMAL

label_protocol: Biotinylated cRNA were prepared from 0.55 ug total RNA using the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin,TX).

extract_protocol: RNA was extracted with Trizol reagent(Invitrogen Life Technologies, Carlsbad, USA), purified using RNeasy columns (Qiagen, Valencia, USA) according to the manufacturers’ protocol. Quality control was performed with Agilent Bioanalyser.

value: Female

value: Normal skin


title: Non-melanoma skin cancer PS_066


title: wild-type B. napus rep 3

description: 2-dap samples


title: Non-melanoma skin cancer PS_046


title: HF_7dupASD2 (GDB-242_HF) aCGH

description: Hybridized to CytoScan HD


title: Non-melanoma skin cancer PS_040


title: Liver_high fat diet_4week_C57

description: gene expression data from C57 liver after fed high fat diet 4week

source_name: C57mice liver after fed high diet 4week


title: Non-melanoma skin cancer PS_052


title: Non-melanoma skin cancer PS_051

source_name: SCC

value: Male

value: SCC


title: Bntt16 RNAi B. napus rep 2

description: 2-dap samples


title: Non-melanoma skin cancer PS_061

source_name: BCC

value: BCC


title: Non-melanoma skin cancer PS_065


title: Liver_high fat diet_12week_C57

description: gene expression data from C57 liver after fed high fat diet 12week

source_name: C57mice liver after fed high diet 12week


title: Non-melanoma skin cancer PS_045


title: Non-melanoma skin cancer PS_063


title: Non-melanoma skin cancer PS_059


title: Non-melanoma skin cancer PS_047


title: Liver_high fat diet_4week_DBA

description: gene expression data from DBA liver after fed high fat diet 4week

source_name: DBAmice liver after fed high diet 4week


title: Old striatum, Drd1a cells, replicate 4

city: Cambridge

first: Myriam

last: Heiman

state: MA

address: 77 Massachusetts Avenue

institute: MIT

description:
Entire striatum used for purification
TRAP purified total RNA

hyb_protocol: Affymetrix S.O.P. for Exon chips

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using Genespring software, using RMA-16 normalization.
MoEx-1_0-st-v1.r2.pgf
MoEx-1_0-st-v1.r2.dt1.mm8.mps

source_name: Old striatum, Drd1a cells

label_protocol: Samples were fragmented and biotinylated using the Encore Biotin Module (NuGEN)

growth_protocol: Mice were grown to 6 weeks or 2 years of age

extract_protocol: Cortical or striatal tissue samples were processed for translating ribosome affinity purification as described in Nat Protoc. 2014;9(6):1282-91.

treatment_protocol: Not applicable

value: 2 years

tag: brain region

value: Striatum


title: Old striatum, Drd1a cells, replicate 3


title: Old cortex, Drd1a cells, replicate 4

description:
Entire cortex used for purification
TRAP purified total RNA

source_name: Old cortex, Drd1a cells

value: Cortex


title: Old cortex, Drd1a cells, replicate 3


title: Old striatum, Drd1a cells, replicate 2


title: iPSC_AtWBS1-C1 (GDB-192_P) aCGH

description: Hybridized to CytoScan HD

value: female

value: AtWBS

value: iPSC colonies were grown on feeder-free conditions on plates coated with human-qualified Matrigel (BD Biosciences) diluted 1:40 in DMEM-F12 and in mTeSR-1 (StemCell Technologies) medium.

value: mRNA reprogramming

value: fibroblast-derived iPSC


title: Old cortex, Drd1a cells, replicate 2


title: Old striatum, Drd1a cells, replicate 1


title: Non-melanoma skin cancer PS_057


title: Non-melanoma skin cancer PS_039


title: Non-melanoma skin cancer PS_037


title: iPSC_AtWBS1-C3 (GDB-192_D) aCGH

description: Hybridized to CytoScan HD


title: Non-melanoma skin cancer PS_029


title: Old cortex, Drd1a cells, replicate 1


title: Non-melanoma skin cancer PS_013


title: HF_AtWBS1 (GDB-192_HF) aCGH

description: Hybridized to CytoScan HD

value: Fibroblasts were grown in HF medium (RPMI 1640, 1% L-Glutamine, 1% Pen-Strep, 15% FBS).

value: primary skin fibroblast


title: Young striatum, Drd1a cells, replicate 3

source_name: Young striatum, Drd1a cells

value: 6 weeks


title: Young cortex, Drd1a cells, replicate 4

source_name: Young cortex, Drd1a cells


title: Non-melanoma skin cancer PS_006


title: Young striatum, Drd1a cells, replicate 2


title: Non-melanoma skin cancer PS_023


title: Non-melanoma skin cancer PS_019


title: Young cortex, Drd1a cells, replicate 1


title: Non-melanoma skin cancer PS_004


title: Non-melanoma skin cancer PS_021


title: Non-melanoma skin cancer PS_002


title: Old striatum, Drd2 cells, replicate 4

source_name: Old striatum, Drd2 cells


title: Old cortex, Drd2 cells, replicate 4

source_name: Old cortex, Drd2 cells


title: Young striatum, Drd1a cells, replicate 1


title: iPSC_7dupASD2-C1 (GDB-242_K) aCGH

description: Hybridized to CytoScan HD

source_name: fibroblast-derived iPSC


title: Old striatum, Drd2 cells, replicate 3


title: Young cortex, Drd1a cells, replicate 2


title: Non-melanoma skin cancer PS_001


title: Old cortex, Drd2 cells, replicate 3


title: Non-melanoma skin cancer PS_031


title: iPSC_AtWBS1-C2 (GDB-192_B) aCGH

description: Hybridized to CytoScan HD


title: Old striatum, Drd2 cells, replicate 1


title: Non-melanoma skin cancer PS_055


title: Young cortex, Drd1a cells, replicate 3


title: WT, 48h, rep4

city: Richmond

first: Mikhail

last: Dozmorov

state: VA

address: 830 E Main St

department: Biostatistics

institute: Virginia Commonwealth University

description:
Sample name: WT.48.4
rep4

hyb_protocol: This RNA was hybridized overnight at 58C to mouse WG-6_v2 Expression BeadChip™ microarrays (Illumina Corp., San Diego), washed under high stringency conditions, labeled with streptavidin-Cy3.

scan_protocol: Mouse WG-6_v2 Expression BeadChip™ microarrays scanned with an Illumina iSCAN scanner.

data_processing: Raw microarray data were processed using within the R statistical environment (http://www.R-project.org) and using BioConductor packages15. Quality control of the data included a comparison of boxplots of gene expression level among the conditions, and hierarchical clustering of condition-specific gene expression profiles to identify potential outliers. The log2 data were quantile normalized.

source_name: Mouse splenic B cells

label_protocol: After purification, RNA concentrations were determined with a scanning spectrophotometer (Nanodrop, Wilmington), and qualitatively assessed for degradation by capillary gel electrophoresis (Agilent 2100 Bionalalyzer, Agilent Technologies). Biotinylated, amplified RNA was produced from 150 ng total RNA per sample using a modification of the Eberwine protocol14 as described in the Illumina® TotalPrep RNA Amplification Kit (Ambion, Inc., Austin). Briefly, RNA was reverse-transcribed with oligo(dT) primers containing a T7 promoter and amplified by in vitro transcription to generate anti-sense RNA containing biotin-UTP ribonucleotides.

growth_protocol: Bank1-/- mice were kindly provided by Dr T. Kurosaki (Riken Research Centre for Allergy and Immunology, Kyoto, Japan) and were backcrossed 9 generations onto the C57BL/6 background). C57BL/6J mice were purchased from Jackson Laboratory, Bar Harbor, Maine, USA. Mice were maintained under specific pathogen free (SPF) barrier conditions

extract_protocol: Splenic B cells were purified by negative selection using magnetic bead separation. Briefly, spleen cells from Bank1+/+, and Bank1-/- littermates were labeled with a cocktail of biotin-conjugated antibodies for 15 minutes. Cells were incubated an additional 15 minutes with anti-biotin micro beads (B Cell isolation Kit, mouse; Miltenyi Biotech, Auburn, CA) at 4 degrees C. The labeled non-B cells were depleted by magnetic retention in a MACS column while unlabeled B cells were recovered. The purity of the resulting cell population was typically more than 95% B220+CD3- as assessed by flow cytometry analysis. Cell culture was performed with RPMI 1640 medium supplemented with 10% FBS, L-glutamine (2mM), 2-ME (50uM) and antibiotics for all experiments except for p38 analyses where cells were serum-starved.

treatment_protocol: The MNK1 specific inhibitor, CGP57380 [4-Amino-5-(4-fluoroanilino)-pyrazolo[3,4-d] pyrimidine] was obtained from Calbiochem®-Millipore (Billerica, MA) and MK2 inhibitor, PF-3644022 [(10R)-9,10,11,12-tetrahydro-10-methyl-3-(6-methyl-3-pyridinyl)-8H-[1,4]diazepino[5’,6’:4,5]thieno[3,2-f ]quinolin-8-one hydrate] was purchased from Sigma-Aldrich (USA). The purified splenic B cells (5×105 cells/ well) were seeded in complete RPMI1640 medium in a 48 well tissue culture plate. Then the cells were pretreated with and without drugs, CGP57380 and PF-3644022 for 30min and an hour respectively before CpG stimulation. Purified splenic B cells were cultured in 5 biological replicates for 0, 6, 24 and 48hs with CpG in both Bank1-/- and WT conditions. IL6 was measured using a capture ELISA. The control well contained CpG and cell-culture grade DMSO (Pierce, USA) only.

value: WT

value: CpG stimulation

value: splenic B cells


title: Old cortex, Drd2 cells, replicate 2


title: WT, 48h, rep5

description:
Sample name: WT.48.5
rep5


title: Young cortex, Drd2 cells, replicate 4

source_name: Young cortex, Drd2 cells


title: Young striatum, Drd2 cells, replicate 3

source_name: Young striatum, Drd2 cells


title: Old striatum, Drd2 cells, replicate 2


title: WT, 48h, rep3

description:
Sample name: WT.48.3
rep3


title: WT, 48h, rep1

description:
Sample name: WT.48.1
rep1


title: WT, 24h, rep5

description:
Sample name: WT.24.5
rep5


title: Young striatum, Drd2 cells, replicate 2


title: Young striatum, Drd2 cells, replicate 4


title: WT, 24h, rep4

description:
Sample name: WT.24.4
rep4


title: Young cortex, Drd2 cells, replicate 2


title: WT, 24h, rep1

description:
Sample name: WT.24.1
rep1


title: WT, 24h, rep3

description:
Sample name: WT.24.3
rep3


title: WT, 48h, rep2

description:
Sample name: WT.48.2
rep2


title: Old cortex, Drd2 cells, replicate 1


title: WT, 6h, rep5

description:
Sample name: WT.6.5
rep5


title: WT, 24h, rep2

description:
Sample name: WT.24.2
rep2


title: Young cortex, Drd2 cells, replicate3


title: WT, 6h, rep4

description:
Sample name: WT.6.4
rep4


title: Young cortex, Drd2 cells, replicate 1


title: Young striatum, Drd2 cells, replicate 1


title: WT, 6h, rep1

description:
Sample name: WT.6.1
rep1


title: WT, 6h, rep2

description:
Sample name: WT.6.2
rep2


title: Bank1-/-, 48h, rep5

description:
Sample name: KO.48.5
rep5


title: WT, 0h, rep2

description:
Sample name: WT.0.2
rep2

value: control


title: WT, 0h, rep3

description:
Sample name: WT.0.3
rep3


title: WT, 0h, rep4

description:
Sample name: WT.0.4
rep4


title: Bank1-/-, 24h, rep3

description:
Sample name: KO.24.3
rep3


title: WT, 0h, rep1

description:
Sample name: WT.0.1
rep1


title: Bank1-/-, 48h, rep4

description:
Sample name: KO.48.4
rep4


title: hcs15_07

city: Bethesda

first: Katherine

middle: MacLean

last: Peterson

state: MD

address: Building 6 Room 107B

institute: NEI, NIH

hyb_protocol: The ethanol precipitated and dried labeled cDNA was resuspended in hybridization buffer.  Each hybridization buffer contained two labeled samples, experiment and control labeled with either Alexa555 or Alexa647.  The probe was hybridized to the slide arrays using a Biomicro MAUI mixing hybridization incubator.

scan_protocol: Post-washing, the arrays were scanned using a ScanArray Express scanner from Perkin Elmer.  Each slide was scanned for both green and red channels.

data_processing: Data analysis was carried out using BlueFuse for Microarrays.  .tiff image scans were imported to BlueFuse, grids placed, and features scanned and filtered for quality.  Global Lowess normalization was applied.  Values for each slide were calculated as the ratio of days serum starvation divided by day0 value log2 transformed.  There are 4 technical replicates (2pairs of dye swaps) of each of 3 biological replicates for each day1, 3, 5, and 7.

source_name: HEK293T, Day0, serum supplemented

label_protocol: Samples were labeled by converting RNA to cDNA incorporating amino-allyl dUTP using SuperScriptII (Life Technologies).  The cDNA with incorporated amino-allyl was cross-linked to Allexa 555 or Alexa 647.

growth_protocol: HEK293T cells were grown to confluent in DMEM+10%fbs at 37C and 5% CO2.

extract_protocol: Media was removed from the cell culture, lysed, and RNA extracted using Trizol (Life Technologies).

treatment_protocol: The DMEM+10%fbs media was removed and replaced with DMEM for 3 days.

value: kidney

tag: media

value: DMEM + 10% fbs

tag: days serum starvation

source_name: HEK293T, Day3, serum starved

value: DMEM


title: Bank1-/-, 24h, rep5

description:
Sample name: KO.24.5
rep5


title: hcs15_60

hyb_protocol: The ethanol precipitated, and dried labeled cDNA was resuspended in hybridization buffer.  Each hybridization buffer contained two labeled samples, experiment and control labeled with either Alexa555 or Alexa647.  The probe was hybridized to the slide arrays using a Biomicro MAUI mixing hybridization incubator.

source_name: ARPE-19, Day7, serum starved

growth_protocol: ARPE-19 cells were grown to confluent in DMEM+10%fbs at 37C and 5% CO2.

treatment_protocol: The DMEM+10%fbs media was removed and replaced with DMEM for the indicated number of days.

tag: tissue

value: retinal pigment epithelium

source_name: ARPE-19, Day0, serum supplemented


title: Bank1-/-, 6h, rep5

description:
Sample name: KO.6.5
rep5


title: Bank1-/-, 24h, rep4

description:
Sample name: KO.24.4
rep4


title: WT, 0h, rep5

description:
Sample name: WT.0.5
rep5


title: Bank1-/-, 48h, rep1

description:
Sample name: KO.48.1
rep1


title: hcs15_62


title: Bank1-/-, 48h, rep2

description:
Sample name: KO.48.2
rep2


title: Bank1-/-, 24h, rep1

description:
Sample name: KO.24.1
rep1


title: Bank1-/-, 6h, rep3

description:
Sample name: KO.6.3
rep3


title: hcs15_03


title: Bank1-/-, 6h, rep4

description:
Sample name: KO.6.4
rep4


title: WT, 6h, rep3

description:
Sample name: WT.6.3
rep3


title: hcs15_02


title: hcs15_04


title: Bank1-/-, 48h, rep3

description:
Sample name: KO.48.3
rep3


title: Bank1-/-, 24h, rep2

description:
Sample name: KO.24.2
rep2


title: hcs15_59


title: hcs15_52


title: hcs15_55

source_name: ARPE-19, Day5, serum starved


title: Bank1-/-, 6h, rep2

description:
Sample name: KO.6.2
rep2


title: hcs15_50


title: hcs15_54

source_name: ARPE-19, Day3, serum starved


title: hcs15_58


title: hcs15_65


title: hcs15_64


title: Bank1-/-, 0h, rep5

description:
Sample name: KO.0.5
rep5


title: Bank1-/-, 6h, rep1

description:
Sample name: KO.6.1
rep1


title: hcs15_46


title: hcs15_63


title: Bank1-/-, 0h, rep3

description:
Sample name: KO.0.3
rep3


title: hcs15_56

source_name: ARPE-19, Day1, serum starved


title: hcs15_38


title: RS-146_08

city: München

first: Florian

last: Beigel

address: Marchioninistr. 15

department: Medizinische Klinik und Poliklinik II

institute: Klinikum Grosshadern

description: Gene expression of HCT116 cells stimulated with OSM for 6 hours

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-014850 Whole Human Genome Microarray 4x44K (G4112F) for 17 hours at 65°C in a rotating hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 014850_D_F_20100115 to obtain background subtracted and spatially detrended Processed Signal intensities. Features which were not positive and significant, not above background or were population outliers were flagged as “Compromised”. If features were flagged “Compromised” in all samples, than those were excluded.

source_name: intestinal epithelial cell

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Quick-Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer

growth_protocol: HCT116 cells were grown in Dulbecco's modified Eagle medium, high glucose, with 100 IU/mL penicillin, 100 µg/mL streptomycin, and 10% heat-inactivated fetal calf serum in a humidified 5% CO2 atmosphere at 37˚C.

extract_protocol: RNA was isolated 6 hours after stimulation and RNA concentration and purity was measured.

treatment_protocol: HCT116 cells were starved overnight with medium containing 1% FCS after reaching 70% confluency. On the next day, cells were stimulated in quadruplicates with 100 ng/mL OSM or left unstimulated.

tag: cell line

tag: agent

value: 100 ng/mL OSM


title: Bank1-/-, 0h, rep2

description:
Sample name: KO.0.2
rep2

tag: cell type


title: RS-146_05


title: RS-146_04

description: Gene expression of unstimulated HCT116 cells


title: Subject5_day10

city: Stockholm

first: Anna

last: Krook

address: von Eulers väg 4a

country: Sweden

institute: Karolinska Institutet

description: Sample 35

hyb_protocol: Hybridization to miRCURY™ LNA array version 11.0 arrays (Exiqon, Denmark) was performed according to the miRCURY™ LNA array manual using a Tecan HS4800 hybridization station (Tecan, Austria).

scan_protocol: Microarrays were stored in an ozone free environment (ozone level below 2.0 ppb) in order to prevent potential bleaching of the fluorescent dyes. Slides were scanned using the Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA).

data_processing:
Image analysis was carried out using the ImaGene 8.0 software (BioDiscovery, Inc., USA). Quantified signals were background corrected (Normexp with offset value 10) and normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm.
Data repressents normalized log2 ratio (Hy3/Hy5) representing test/reference. When calling of a particular miRNA failed on an array this is indicated by 'null'.  In the expression matrix,  all capture probes with both Hy3 and Hy5 signals lower than 1.5x of the median signal intensity of the given slide, or which are annotated null, are excluded as indicated by 'null'.

source_name: Muscle cells_differentiating_10 days

label_protocol: 300 ng of total RNA from samples and a reference pool was labeled with Hy3™ and Hy5™ fluorescent label, respectively, using the miRCURY™ LNA Array power labeling kit (Exiqon, Denmark) following the procedure described by the manufacturer.

growth_protocol: Human skeletal muscle cells (extracted from vastus lateralis muscle) was cultured in Dulbecco's Modified Eagle Medium (DMEM):Nutrient Mixture F-12 supplemented with 20% FBS, 1% fungizone and 1% Penicillin-Streptomycin. Cultures were subcultured with trypsin before reaching 70% confluence. Differentiation of myoblasts into myotubes were induced by switching to differentiation medium (DMEM (low glucose) supplemented with 2% FBS, 1% PeSt and 1% Fungizone) when cells were 80% confluent. Cultures were incubated at 37°C in 7.5% CO2 humidified chambers.

extract_protocol: Extraction of total RNA by TRIzol (Invitrogen). Modifications of manufacturer's protocol include addition of 0.75 ml isopropanol (compared to 0.5 ml) containing glycogen with 20 minutes incubation at -20°C to precipitate RNA.

tag: subject id

value: subject 5

value: vastus lateralis muscle

value: Human skeletal muscle cells

tag: time point

value: 10 days after induction of differentiation

source_name: Mixed pool of total RNA

tag: sample type

value: Total RNA from pooled samples from channel1 input.


title: Bank1-/-, 0h, rep4

description:
Sample name: KO.0.4
rep4

tag: treatment


title: hcs15_61


title: hcs15_48


title: RS-146_03


title: RS-146_07


title: RS-146_01


title: hcs15_51


title: Bank1-/-, 0h, rep1

description:
Sample name: KO.0.1
rep1

tag: time


title: hcs15_44


title: RS-146_06


title: hcs15_42


title: hcs15_41


title: hcs15_43


title: Subject2_day10

description: Sample 32

value: subject 2


title: Subject3_day10

description: Sample 33

value: subject 3


title: RS-146_02


title: hcs15_32


title: hcs15_45


title: hcs15_29


title: Subject4_day10

description: Sample 34

value: subject 4


title: Subject4_day8

description: Sample 28

source_name: Muscle cells_differentiating_8 days

value: 8 days after induction of differentiation


title: Subject1_day10

description: Sample 31

value: subject 1


title: Subject5_day8

description: Sample 29


title: Subject6_day8

description: Sample 30

value: subject 6


title: Subject3_day8

description: Sample 27


title: Subject2_day8

description: Sample 26


title: hcs15_34


title: Subject1_day8

description: Sample 25


title: Subject6_day6

description: Sample 24

source_name: Muscle cells_differentiating_6 days

value: 6 days after induction of differentiation


title: hcs15_28


title: hcs15_39


title: hcs15_33


title: hcs15_36


title: Subject5_day6

description: Sample 23


title: hcs15_30


title: Subject4_day6

description: Sample 22


title: Subject3_day10

description: Sample 9

hyb_protocol: Hybridized to Affymetrix Human Gene 1.0 ST Array according to manufacturer's protocols in a GeneChip Hybridization Oven 640 (Affymetrix). Arrays were washed and stained with a GeneChip Gluidics station 450 (Affymetrix).

scan_protocol: Arrays were scanned with a GeneChip Scanner 3000 7G (Affymetrix).

data_processing: Pre-processing of data was performed using Robust Multi-array Average (RMA) with sketch quantile normalization with the Expression Console™ software (Affymetrix).

source_name: Skeletal muscle cells_differentiating_10 days

label_protocol: Sense strand cDNA was synthesized from total RNA with Ambion® WT Expression Kit (Life Techniologies) and biotin labeled with the Affymetrix® GeneChip WT Terminal Labeling Kit (Affymetrix).


title: Subject2_day10

description: Sample 8


title: Subject1_day10

description: Sample 7


title: Subject3_day4

description: Sample 6

source_name: Skeletal muscle cells_differentiating_4 days

value: 4 days after induction of differentiation


title: hcs15_27

value: DMEM + 10% fbs


title: Subject3_day6

description: Sample 21


title: Subject1_day4

description: Sample 4


title: Subject2_day4

description: Sample 5


title: Subject1_day0

description: Sample 1

source_name: Skeletal muscle cells_proliferating (myoblasts)

value: before induction of differentiation (proliferating myoblasts)


title: hcs15_14

value: retinal pigment epithelium

value: DMEM


title: Subject3_day0

description: Sample 3


title: Subject2_day0

description: Sample 2


title: hcs15_11


title: hcs15_35


title: Subject2_day6

description: Sample 20


title: Subject6_day4

description: Sample 18

source_name: Muscle cells_differentiating_4 days


title: Subject5_day4

description: Sample 17

value: subject 5


title: Subject1_day6

description: Sample 19

value: vastus lateralis muscle


title: Subject3_day4

description: Sample 15

value: Human skeletal muscle cells


title: hcs15_23


title: hcs15_19


title: hcs15_12


title: Cas9_D7_Rep3

city: Faridabad

first: Nisheeth

last: Agarwal

state: Haryana

address: 3rd Milestone, Faridabad-Gurugram Expressway

department: Infection and Immunity

institute: Translational Health Science and Technology Institute

description: Technical replicate 3 of 3.

hyb_protocol: Labeled cDNAs and hybridization buffer (10X SSC, 50% Formamide and 0.2% SDS containing 10µg Salmon sperm DNA and 8µg yeast tRNA ) were added, and samples were applied to microarrays enclosed in hybridization chambers. After hybridization, slides were washed sequentially with buffers containing decreasing concentrations of SSC and SDS.

scan_protocol: Scanned on a GenePix 4000A microarray scanner (Axon Instruments).

data_processing:
Images were quantified using GenePix Pro 7.2.22 software (Axon Instruments).
Normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal.

label: alexa fluor 647

organism: Mycobacterium tuberculosis H37Rv

source_name: Total RNA from ATc-treated cells

label_protocol: 6 µg of total RNA were primed with 0.5 µg of random hexamer primer at 70°C for 10 min, then reversed transcribed at 46°C for 3 h in the presence of alexa fluor 647- or 555-aha-dCTP by using SuperScript Direct cDNA labeling system (Invitrogen) according to manufacturer's instructions.

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

treatment_protocol: cells grown in 7H9-OADS medium containing 100ng/ml ATc for 7 days at 37°C

tag: strain

value: transformed with ptetInt-dcas9

label: alexa fluor 555

source_name: Total RNA from ATc-untreated cells

treatment_protocol: cells grown in 7H9-OADS medium for 7 days at 37°C


title: hcs15_20


title: Subject2_day4

description: Sample 14

value: Total RNA from pooled samples from channel1 input.


title: Subject1_day4

description: Sample 13


title: hcs15_09


title: Subject6_day2

description: Sample 12

source_name: Muscle cells_differentiating_2 days

value: 2 days after induction of differentiation


title: hcs15_15


title: hcs15_25


title: Subject4_day4

description: Sample 16


title: Cas9_D4_Rep2

description: Technical replicate 2 of 3.

treatment_protocol: cells grown in 7H9-OADS medium containing 100ng/ml ATc for 4 days at 37°C

treatment_protocol: cells grown in 7H9-OADS medium for 4 days at 37°C


title: Subject4_day2

description: Sample 10


title: Subject5_day2

description: Sample 11


title: Cas9_D7_Rep1

description: Technical replicate 1 of 3.


title: Cas9_D4_Rep3

description: Technical replicate 3 of 3.


title: Cas9_D7_Rep2

description: Technical replicate 2 of 3.


title: Cas9_D4_Rep1

description: Technical replicate 1 of 3.


title: Subject2_day2

description: Sample 8

value: subject 2


title: Subject3_day2

description: Sample 9

value: subject 3


title: hcs15_17


title: hcs15_13


title: hcs15_26


title: hcs15_21


title: Dressler_004.EGFP/EGFP

city: Ann Arbor

first: Greg

last: Dressler

state: MI

address: 109 Zina Pitcher Drive

department: Pathology

institute: University of Michigan

hyb_protocol: Following Labeling, 4 ug of cDNA were hybridized for 16 hr at 45C on a Mouse 430 2.0 cartridge array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Data were analyzed using the limma and affy Bioconductor packages implemented in the R-statistical environment. RMA was used to normalize the data and fit log2 transformed expression values.

source_name: EGFP+ cells

label_protocol: Biotinylated cDNA were prepared according to the Nugen WT-Pico Ovation kit protocol from 10 ng total RNA (WT-Pico Ovation RNA Amplification System Manual, 2007, NuGEN). Subsequently cDNA is made double stranded fragmented and end-labeled following manufacturers standard protocol (NuGEN exon module, encore end-labeling module).

growth_protocol: Embryos were dissected and single cell suspensions were made from the intermediate mesoderm region.  EGFP positive cells were isolated by FACS

extract_protocol: RNA was isolated from EGFP positive cells using the RNA easy mini kit from Qiagen

value: Pax2 null

tag: developmental stage

value: E11.5 embryos

value: intermediate mesoderm EGFP positive cells


title: Dressler_005 EGFP/+

value: Pax2 heterozygote


title: Subject1_day2

description: Sample 7

value: subject 1


title: Dressler_006 EGFP/+


title: Dressler_003_EGFP/EGFP


title: Subject6_day0

description: Sample 6

source_name: Muscle cells_proliferating (myoblasts)

value: subject 6


title: Subject5_day0

description: Sample 5

value: before induction of differentiation (proliferating myoblasts)


title: hcs15_24

source_name: ARPE-19, Day0, serum supplemented

value: retinal pigment epithelium

value: DMEM + 10% fbs


title: Subject4_day0

description: Sample 4

value: subject 4


title: Dressler_002_EGFP/EGFP


title: hcs15_18

value: DMEM


title: 2XR rep2

city: Bangalore

first: Nagasuma

last: Chandra

state: Karnataka

address: New Biological Science Building, IISc

department: Department of Biochemistry

institute: Indian Institute of Science

hyb_protocol: 700ng of the cy3 labeled cRNA samples (600ng of oligodT labeled + 100ng of Random hexamer labeled samples)  were fragmented at 60 º C and hybridized on to a Genotypic designed Custom M. smegmatis_GXP_8X15K (AMADID No: 020791) arrays. Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Agilent Technologies, Part Number 5188-5325)

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

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

organism: Mycolicibacterium smegmatis

source_name: in vitro batch culture of isoniazid resistant strain

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). 500ng each of the Control and test samples were reverse transcribed at 40°C using oligodT primer with a T7 polymerase promoter and Random hexamer primer with a T7 polymerase promoter in two individual reactions and converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNesay columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

extract_protocol: RNA concentration and purity was determined at an optical density ratio of 260/280 using the Nanodrop® ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE) and the integrity of total RNA was verified on an Agilent 2100 Bioanalyzer using the RNA 6000 Nano LabChip (Agilent Technologies)

tag: genotype

value: INH resistant


title: Subject3_day0

description: Sample 3

value: vastus lateralis muscle

value: Human skeletal muscle cells


title: Subject1_day0

description: Sample 1

value: Total RNA from pooled samples from channel1 input.


title: 2XR rep1


title: Subject2_day0

description: Sample 2

value: subject 2


title: hcs15_10

source_name: ARPE-19, Day1, serum starved


title: 4XR rep1

value: INHR1 (4XR1)


title: Sub-MIC INH

source_name: in vitro batch culture of wild-type strain subjected to sub-MIC concentration of INH

value: Wild-type


title: Wild-type rep3

source_name: in vitro batch culture of wild-type strain


title: Wild-type rep2


title: 4XR rep2

source_name: in vitro batch culture of isoniazidresistant strain

value: INHR2 (4XR2)


title: MS514_LPS_160305_P8_260405

status: Public on Dec 12 2014

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

hyb_protocol: hybridization to Affymetrix (Santa Clara, CA) Human Genome 133 Plus 2.0 Gene Chip arrays

scan_protocol: Fluorescent signals  were detected by the Hewlett-Packard G2500A Gene Array Scanner (Affymetrix).

data_processing: Data were imported into Partek Genomics Suite V6.6 (PGS) (Partek) using RMA (Robust Multi-array Average, an algorithm used for background correction, log2-transformation and quantile normalization of Affymetrix expression data) prior to batch-correction.

source_name: human blood monocyte stimulated with LPS for 4h

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Affymetrix Gene Chip Expression 3´Amplification: one-cycle cDNA synthesis and IVT labeling; Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Extraction of total RNA was performed with chaotropic ions and silica membran according to the manufacturer's instructions (Macherey-Nagel RNA isolation user manual).

value: human blood monocyte

value: LPS


title: Wild-type rep1


title: MS514_LPS_020305_P5_260405


title: Dressler_001.EGFP/+

value: Pax2 heterozygote

value: E11.5 embryos

value: intermediate mesoderm EGFP positive cells


title: subject 14064 UVB area at t23

city: BETHESDA

first: Vincent

middle: J.

last: Hearing

address: BG 37 RM 2132B 37 CONVENT DR

institute: National Cancer Institute

hyb_protocol: The hybridization procedure was performed according to the Agilent 60-mer oligo microarray processing  protocol using the Agilent Gene Expression Hybridization Kit (Agilent Technologies).

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: whole human skin from subject 14064 UVB area at t23

label_protocol: To produce Cy3-labeled cRNA, the RNA samples were amplified and labeled using the Agilent Low RNA  InputLinear Amp Kit (Agilent Technologies) following the manufac-turer’s protocol.

extract_protocol: RNA was prepared from each biopsy using standard RNA extraction protocols (Trizol, Sigma, St Louis, MO), and were quality-checked using an Agilent 2100 Bioanalyzer platform (Agilent Technologies,Waldbronn, Germany).

treatment_protocol: 4mm human skin punch biopsies were taken from subjects

tag: area

value: UVB

value: whole human skin

tag: gender

value: Male

tag: hybridization date


title: subject 16531 UVB area at t23

source_name: whole human skin from subject 16531 UVB area at t23


title: MS514_LPS_160205_P2_260405


title: subject 4371 UVB area at t23

source_name: whole human skin from subject 4371 UVB area at t23


title: subject 19181 UVB area at t23

source_name: whole human skin from subject 19181 UVB area at t23

value: Female


title: MS514_KO_020305_P4_260405

source_name: human blood monocyte

value: control


title: MS514_KO_160205_P1_260405


title: subject 16531 UVA area at t23

source_name: whole human skin from subject 16531 UVA area at t23

value: UVA


title: MS514_KO_160305_P7_260405


title: subject 6382 UVA area at t23

source_name: whole human skin from subject 6382 UVA area at t23


title: subject 19107 SSR area at t23

source_name: whole human skin from subject 19107 SSR area at t23

value: SSR


title: subject 14064 UVA area at t23

source_name: whole human skin from subject 14064 UVA area at t23


title: subject 19181 UVA area at t23

source_name: whole human skin from subject 19181 UVA area at t23


title: subject 8194 UVB area at t23

source_name: whole human skin from subject 8194 UVB area at t23


title: subject 19107 UVB area at t23

source_name: whole human skin from subject 19107 UVB area at t23


title: subject 19107 UVA area at t23

source_name: whole human skin from subject 19107 UVA area at t23


title: subject 6382 UVB area at t23

source_name: whole human skin from subject 6382 UVB area at t23


title: subject 19181 SSR area at t23

source_name: whole human skin from subject 19181 SSR area at t23


title: subject 14064 SSR area at t23

source_name: whole human skin from subject 14064 SSR area at t23


title: subject 8194 UVA area at t23

source_name: whole human skin from subject 8194 UVA area at t23


title: subject 4371 UVA area at t23

source_name: whole human skin from subject 4371 UVA area at t23


title: subject 6382 SSR area at t23

source_name: whole human skin from subject 6382 SSR area at t23


title: subject 8194 SSR area at t23

source_name: whole human skin from subject 8194 SSR area at t23


title: subject 16531 SSR area at t23

source_name: whole human skin from subject 16531 SSR area at t23


title: subject 19181 control area at t23

source_name: whole human skin from subject 19181 control area at t23


title: Control red eye of SDR

city: Aomori

first: Naoki

last: Nanashima

state: Aomori

address: 58-1 Mase, Hamadate

department: Department of Nutrition

country: Japan

institute: Aomori University of Health and Welfare

description: Gene expression control

hyb_protocol: 0.6 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Rattus norvegicus

source_name: SDR Eye

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1ug Total RNA using the Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification.

growth_protocol: Free access to water and food.

extract_protocol: Total RNA was extracted by using the RNeasy mini kit (Qiagen, Tokyo, Japan).

value: Whole eye

tag: genetic background

value: SDR

tag: phenotype


title: subject 16531 control area at t23

source_name: whole human skin from subject 16531 control area at t23

tag: tissue


title: subject 14064 control area at t23

source_name: whole human skin from subject 14064 control area at t23


title: subject 19107 control area at t23

source_name: whole human skin from subject 19107 control area at t23


title: subject 8194 control area at t23

source_name: whole human skin from subject 8194 control area at t23


title: subject 6382 control area at t23

source_name: whole human skin from subject 6382 control area at t23


title: subject 19107 challenge area at t23

source_name: whole human skin from subject 19107 challenged area at t23

value: challenged


title: subject 8194 challenge area at t23

source_name: whole human skin from subject 8194 challenged area at t23


title: subject 19181 challenge area at t23

source_name: whole human skin from subject 19181 challenged area at t23


title: subject 4371 control area at t23

source_name: whole human skin from subject 4371 control area at t23


title: subject 16531 challenge area at t23

source_name: whole human skin from subject 16531 challenged area at t23


title: subject 14064 challenge area at t23

source_name: whole human skin from subject 14064 challenged area at t23


title: subject 19107 UVB area at t18

source_name: whole human skin from subject 19107 UVB area at t18


title: subject 6382 challenge area at t23

source_name: whole human skin from subject 6382 challenged area at t23


title: subject 4371 challenge area at t23

source_name: whole human skin from subject 4371 challenged area at t23


title: subject 16531 UVB area at t18

source_name: whole human skin from subject 16531 UVB area at t18


title: subject 8194 UVB area at t18

source_name: whole human skin from subject 8194 UVB area at t18


title: subject 19181 UVB area at t18

source_name: whole human skin from subject 19181 UVB area at t18


title: subject 6382 UVB area at t18

source_name: whole human skin from subject 6382 UVB area at t18


title: White eye (with opacity) of HiSER

description: Gene expression in the HiSER eye

source_name: HiSER Eye

value: Hirosaki Small Eye Rat (HiSER)


title: subject 8194 UVA area at t18

source_name: whole human skin from subject 8194 UVA area at t18


title: subject 14064 UVB area at t18

source_name: whole human skin from subject 14064 UVB area at t18


title: subject 19107 SSR area at t18

source_name: whole human skin from subject 19107 SSR area at t18


title: subject 19107 UVA area at t18

source_name: whole human skin from subject 19107 UVA area at t18


title: subject 16531 UVA area at t18

source_name: whole human skin from subject 16531 UVA area at t18


title: subject 19181 SSR area at t18

source_name: whole human skin from subject 19181 SSR area at t18


title: OPMD-day11-Cy3-17

city: Paris

first: Capucine

last: TROLLET

address: GH Pitie Salpetriere Bat Babinski 47 bd de l'hopital

country: France

institute: Myology Research Center UMRS974 INSERM

description:
OPMD day 11 replicate 5
OPMD17

hyb_protocol: The INDAC oligo set (15K, produced by Illumina) was printed in duplicate on poly-L-lysine coated slides by the Leiden Genome Technology Center (LGTC). For all samples, 1.5 μg of labeled cRNA was hybridized to the oligonucleotide arrays against a common reference and dye-swap experiments were performed (in total: 6 hybridizations per condition, per time-point). The common reference is made of a pool of triplicate Mhc-Gal4/+ samples at day 2.

scan_protocol: Slides were scanned with an Agilent scanner (Model 2565BA) and spot intensities were quantified with the GenePix Pro 5.0 program (Axon).

data_processing: For data analysis, raw intensity files were imported into Rosetta Resolver® v7.0 (RosettaBio, Seattle, USA) and normalized with the Axon/Genepix error model. A two-way ANOVA was performed to identify genes that were differentially expressed between any of the two genotypes per time point. In data table, empty values correspond to excluded values due to poor quality of the signal.

organism: Drosophila melanogaster

source_name: Thorax_UAS-PABPN1-17ala/+; Mhc-Gal4/+

label_protocol: Per sample, 1 μg of total RNA was amplified with the Message Amp kit (Ambion) and the cRNA labeled through incorporation of aa-UTP and coupling with Amersham monoreactive Cy3 or Cy5 dyes.

extract_protocol: RNA was extracted using Trizol (Invitrogen) as recommended by the manufacturer, followed by a RNA cleanup using the RNeasy mini kit (Quiagen). Quality and quantity of the RNA were checked using the Bioanalyzer Lab-on-a- Chip.

value: UAS-PABPN1-17ala/+; Mhc-Gal4/+

tag: age (days)

value: thorax

source_name: common reference sample_pool of triplicate Mhc-Gal4/+ samples at day 2


title: subject 6382 UVA area at t18

source_name: whole human skin from subject 6382 UVA area at t18


title: subject 4371 UVB area at t18

source_name: whole human skin from subject 4371 UVB area at t18


title: subject 4371 UVA area at t18

source_name: whole human skin from subject 4371 UVA area at t18


title: subject 14064 UVA area at t18

source_name: whole human skin from subject 14064 UVA area at t18


title: OPMD-day11-Cy3-16

description:
OPMD day 11 replicate 4
OPMD16


title: OPMD-day11-Cy3-18

description:
OPMD day 11 replicate 6
OPMD18


title: OPMD-day11-Cy5-14

description:
OPMD day 11 replicate 2
OPMD14


title: subject 16531 SSR area at t18

source_name: whole human skin from subject 16531 SSR area at t18


title: OPMD-day11-Cy5-13

description:
OPMD day 11 replicate 1
OPMD13


title: OPMD-day6-Cy3-12

description:
OPMD day 6 replicate 6
OPMD12


title: subject 6382 SSR area at t18

source_name: whole human skin from subject 6382 SSR area at t18


title: subject 8194 SSR area at t18

source_name: whole human skin from subject 8194 SSR area at t18


title: subject 4371 SSR area at t23

source_name: whole human skin from subject 4371 SSR area at t23


title: subject 14064 SSR area at t18

source_name: whole human skin from subject 14064 SSR area at t18


title: subject 4371 SSR area at t18

source_name: whole human skin from subject 4371 SSR area at t18


title: OPMD-day6-Cy3-10

description:
OPMD day 6 replicate 4
OPMD10


title: subject 19107 control area at t18

source_name: whole human skin from subject 19107 control area at t18


title: OPMD-day6-Cy5-7

description:
OPMD day 6 replicate 1
OPMD7


title: subject 16531 control area at t18

source_name: whole human skin from subject 16531 control area at t18


title: OPMD-day2-Cy3-6

description:
OPMD day 2 replicate 6
OPMD6


title: OPMD-day6-Cy5-9

description:
OPMD day 6 replicate 3
OPMD9


title: OPMD-day6-Cy3-11

description:
OPMD day 6 replicate 5
OPMD11


title: subject 8194 control area at t18

source_name: whole human skin from subject 8194 control area at t18


title: OPMD-day2-Cy3-5

description:
OPMD day 2 replicate 5
OPMD5


title: OPMD-day2-Cy5-2

description:
OPMD day 2 replicate 2
OPMD2


title: OPMD-day6-Cy5-8

description:
OPMD day 6 replicate 2
OPMD8


title: OPMD-day11-Cy5-15

description:
OPMD day 11 replicate 3
OPMD15


title: subject 19181 control area at t18

source_name: whole human skin from subject 19181 control area at t18


title: OPMD-day2-Cy5-3

description:
OPMD day 2 replicate 3
OPMD3


title: WT-day11-Cy3-16

description:
Control day 11 replicate 4
WT16


title: OPMD-day2-Cy3-4

description:
OPMD day 2 replicate 4
OPMD4


title: subject 6382 control area at t18

source_name: whole human skin from subject 6382 control area at t18


title: WT-day11-Cy5-14

description:
Control day 11 replicate 2
WT14


title: WT-day11-Cy3-18

description:
Control day 11 replicate 6
WT18


title: subject 19181 challenge area at t18

source_name: whole human skin from subject 19181 challenged area at t18


title: WT-day11-Cy3-17

description:
Control day 11 replicate 5
WT17

source_name: common reference sample_pool of triplicate Mhc-Gal4/+ samples at day 2


title: subject 19107 challenge area at t18

source_name: whole human skin from subject 19107 challenged area at t18


title: subject 14064 challenge area at t18

source_name: whole human skin from subject 14064 challenged area at t18


title: WT-day11-Cy5-15

description:
Control day 11 replicate 3
WT15


title: subject 4371 control area at t18

source_name: whole human skin from subject 4371 control area at t18


title: subject 8194 challenge area at t18

source_name: whole human skin from subject 8194 challenged area at t18


title: WT-day6-Cy3-12

description:
Control day 6 replicate 6
WT12


title: subject 16531 UVB area at t15

source_name: whole human skin from subject 16531 UVB area at t15


title: subject 19181 UVB area at t15

source_name: whole human skin from subject 19181 UVB area at t15


title: WT-day11-Cy5-13

description:
Control day 11 replicate 1
WT13


title: OPMD-day2-Cy5-1

description:
OPMD day 2 replicate 1
OPMD1


title: subject 14064 control area at t18

source_name: whole human skin from subject 14064 control area at t18


title: subject 16531 challenge area at t18

source_name: whole human skin from subject 16531 challenged area at t18


title: subject 6382 challenge area at t18

source_name: whole human skin from subject 6382 challenged area at t18


title: WT-day6-Cy3-11

description:
Control day 6 replicate 5
WT11


title: subject 19107 UVB area at t15

source_name: whole human skin from subject 19107 UVB area at t15


title: subject 4371 challenge area at t18

source_name: whole human skin from subject 4371 challenged area at t18


title: subject 14064 UVB area at t15

source_name: whole human skin from subject 14064 UVB area at t15


title: WT-day2-Cy3-5

description:
Control day 2 replicate 5
WT5


title: WT-day6-Cy5-7

description:
Control day 6 replicate 1
WT7


title: WT-day6-Cy3-10

description:
Control day 6 replicate 4
WT10


title: WT-day2-Cy3-4

description:
Control day 2 replicate 4
WT4


title: WT-day6-Cy5-8

description:
Control day 6 replicate 2
WT8


title: subject 4371 UVB area at t15

source_name: whole human skin from subject 4371 UVB area at t15


title: WT-day2-Cy5-1

description:
Control day 2 replicate 1
WT1


title: subject 19181 UVA area at t15

source_name: whole human skin from subject 19181 UVA area at t15


title: subject 8194 UVB area at t15

source_name: whole human skin from subject 8194 UVB area at t15


title: subject 14064 UVA area at t15

source_name: whole human skin from subject 14064 UVA area at t15


title: subject 19107 UVA area at t15

source_name: whole human skin from subject 19107 UVA area at t15


title: WT-day6-Cy5-9

description:
Control day 6 replicate 3
WT9

source_name: common reference sample_pool of triplicate Mhc-Gal4/+ samples at day 2


title: WT-day2-Cy5-2

description:
Control day 2 replicate 2
WT2


title: WT-day2-Cy5-3

description:
Control day 2 replicate 3
WT3


title: subject 6382 UVB area at t15

source_name: whole human skin from subject 6382 UVB area at t15


title: WT-day2-Cy3-6

description:
Control day 2 replicate 6
WT6


title: subject 8194 UVA area at t15

source_name: whole human skin from subject 8194 UVA area at t15


title: subject 19107 SSR area at t15

source_name: whole human skin from subject 19107 SSR area at t15


title: subject 6382 UVA area at t15

source_name: whole human skin from subject 6382 UVA area at t15


title: subject 4371 UVA area at t15

source_name: whole human skin from subject 4371 UVA area at t15


title: subject 14064 SSR area at t15

source_name: whole human skin from subject 14064 SSR area at t15


title: subject 16531 SSR area at t15

source_name: whole human skin from subject 16531 SSR area at t15


title: subject 16531 UVA area at t15

source_name: whole human skin from subject 16531 UVA area at t15


title: 355219_q3

city: San Antonio

first: Deepak

last: Kaushal

state: TX

address: 8715 W Military Dr

department: HPI

institute: Texas Biomedical Research Institute

hyb_protocol: Hybridization to arrays was performed as described earlier (Mehra and Kaushal, PMCID: PMC2698404)

scan_protocol: Slides were scanned as described earlier (Mehra and Kaushal, PMCID: PMC2698404)

data_processing: Data analysis was performed as described earlier (Mehra and Kaushal, PMCID: PMC2698404)

organism: Mycobacterium tuberculosis CDC1551

source_name: Mycobacterium tuberculosis CDC1551 D-Rv2745c knockout mutant

label_protocol: cDNA labeling was performed as described earlier (Mehra and Kaushal, PMCID: PMC2698404)

growth_protocol: Mtb strains were cultured as described earlier (Mehra and Kaushal, PMCID: PMC2698404)

extract_protocol: RNA was extracted as described earlier (Mehra and Kaushal, PMCID: PMC2698404)

treatment_protocol: Bacterial cultures were treated with either hypoxia or reaeration

tag: genotype/variation

value: D-Rv2745c knockout mutant

value: hypoxia

value: t = 48 hr

value: reaeration


title: 355219_q1


title: A00459_q3

value: t = 24 hr


title: A00459_q2


title: 355219_q2


title: A00459_q1


title: A00303_q2

value: t = 12 hr


title: A00303_q3


title: 355227_q3

value: t = 4 hr


title: A01068_q3

value: t = 6 hr


title: A00303_q1


title: A00071_q1


title: subject 6382 SSR area at t15

source_name: whole human skin from subject 6382 SSR area at t15

value: whole human skin

value: Female


title: subject 8194 SSR area at t15

source_name: whole human skin from subject 8194 SSR area at t15

value: SSR

value: Male


title: 353034_q2


title: subject 14064 control area at t15

source_name: whole human skin from subject 14064 control area at t15

value: control


title: subject 4371 SSR area at t15

source_name: whole human skin from subject 4371 SSR area at t15


title: subject 6382 control area at t15

source_name: whole human skin from subject 6382 control area at t15


title: subject 19107 control area at t15

source_name: whole human skin from subject 19107 control area at t15


title: subject 16531 control area at t15

source_name: whole human skin from subject 16531 control area at t15


title: subject 8194 control area at t15

source_name: whole human skin from subject 8194 control area at t15


title: subject 19181 SSR area at t15

source_name: whole human skin from subject 19181 SSR area at t15


title: A01068_q2

value: t = 1 hr


title: A01068_q1


title: 353034_q1


title: A00071_q2


title: subject 19181 control area at t15

source_name: whole human skin from subject 19181 control area at t15


title: A00073_q1


title: subject 19107 challenge area at t15

source_name: whole human skin from subject 19107 challenged area at t15

value: challenged


title: A01067_1

value: t= 7 day


title: A01067_3


title: subject 19181 challenge area at t15

source_name: whole human skin from subject 19181 challenged area at t15


title: subject 4371 control area at t15

source_name: whole human skin from subject 4371 control area at t15


title: A01067_2


title: subject 16531 challenge area at t15

source_name: whole human skin from subject 16531 challenged area at t15


title: A00472_q1

value: t= 5 day


title: subject 6382 challenge area at t15

source_name: whole human skin from subject 6382 challenged area at t15


title: subject 14064 challenge area at t15

source_name: whole human skin from subject 14064 challenged area at t15


title: A01066_q3

source_name: Mycobacterium tuberculosis CDC1551 D-Rv2745c knockout mutant

value: D-Rv2745c knockout mutant


title: subject 8194 challenge area at t15

source_name: whole human skin from subject 8194 challenged area at t15


title: A01066_q2

value: hypoxia


title: A00471_q3

value: t= 1 day


title: 355220_q3

source_name: Mycobacterium tuberculosis CDC1551

value: Wild-type

value: t = 48 hr

value: reaeration


title: A00471_q2


title: A01066_q1


title: subject 19181 UVB area at t14

source_name: whole human skin from subject 19181 UVB area at t14

value: UVB


title: subject 16531 UVB area at t14

source_name: whole human skin from subject 16531 UVB area at t14


title: 355227_q1


title: subject 14064 UVB area at t14

source_name: whole human skin from subject 14064 UVB area at t14


title: A00127_q3

value: t = 24 hr


title: A00127_q2


title: 355220_q1


title: subject 6382 UVB area at t14

source_name: whole human skin from subject 6382 UVB area at t14

value: whole human skin


title: A01057_q3

value: t = 12 hr


title: A00127_q1


title: A01057_q1


title: subject 8194 UVB area at t14

source_name: whole human skin from subject 8194 UVB area at t14


title: subject 19107 UVB area at t14

source_name: whole human skin from subject 19107 UVB area at t14

value: Female


title: A01057_q2


title: subject 4371 challenge area at t15

source_name: whole human skin from subject 4371 challenged area at t15

value: Male


title: subject 4371 UVB area at t14

source_name: whole human skin from subject 4371 UVB area at t14


title: A00478_q1

value: t = 6 hr


title: A00478_q2


title: A00476_q3

value: t = 4 hr


title: subject 19107 UVA area at t14

source_name: whole human skin from subject 19107 UVA area at t14

value: UVA


title: subject 16531 UVA area at t14

source_name: whole human skin from subject 16531 UVA area at t14


title: A00478_q3


title: subject 6382 UVA area at t14

source_name: whole human skin from subject 6382 UVA area at t14


title: subject 19181 UVA area at t14

source_name: whole human skin from subject 19181 UVA area at t14


title: subject 14064 UVA area at t14

source_name: whole human skin from subject 14064 UVA area at t14


title: subject 8194 UVA area at t14

source_name: whole human skin from subject 8194 UVA area at t14


title: subject 19181 SSR area at t14

source_name: whole human skin from subject 19181 SSR area at t14

value: SSR


title: subject 4371 UVA area at t14

source_name: whole human skin from subject 4371 UVA area at t14


title: A00476_q2

source_name: Mycobacterium tuberculosis CDC1551


title: subject 6382 SSR area at t14

source_name: whole human skin from subject 6382 SSR area at t14


title: A00475_q1

value: t = 1 hr


title: subject 8194 SSR area at t14

source_name: whole human skin from subject 8194 SSR area at t14


title: A00475_q2


title: A00476_q1


title: A00475_q3


title: A00126_q2

value: t= 7 day


title: subject 19107 SSR area at t14

source_name: whole human skin from subject 19107 SSR area at t14


title: A01056_q2

value: hypoxia

value: t= 5 day


title: A00126_q3

value: Wild-type


title: A00479_q3

value: t= 1 day


title: A00126_q1


title: subject 19181 control area at t14

source_name: whole human skin from subject 19181 control area at t14

value: control


title: subject 14064 control area at t14

source_name: whole human skin from subject 14064 control area at t14


title: A01056_q1


title: subject 14064 SSR area at t14

source_name: whole human skin from subject 14064 SSR area at t14


title: subject 4371 SSR area at t14

source_name: whole human skin from subject 4371 SSR area at t14


title: subject 16531 control area at t14

source_name: whole human skin from subject 16531 control area at t14


title: subject 4371 control area at t14

source_name: whole human skin from subject 4371 control area at t14


title: subject 6382 control area at t14

source_name: whole human skin from subject 6382 control area at t14


title: A00479_q1


title: subject 8194 control area at t14

source_name: whole human skin from subject 8194 control area at t14


title: A01056_q3


title: subject 19107 control area at t14

source_name: whole human skin from subject 19107 control area at t14


title: A00479_q2


title: H3K9me2_wt_2

city: Chestnut Hill

first: Hugh

middle: P

last: Cam

address: Higgins Hall Room 355, 140 Commonwealth Avenue

department: Biology

institute: Boston College

description: ChIP-chip profiling of H3K9me2 in wildtype cells replicate 2

hyb_protocol: 500 ng of AlexaFluor 555 labeled Input DNA was mixed with 500 ng of AlexaFluro 647 labeled ChIP DNA plus 50 ul Agilent 10X control targets and 250 ul of 2X Agilent Hybridization buffer. Combined samples were hybridized to Agilent 4x44k array slides in an Agilent SureHyb chamber at 65° C, 20 RPM for 24 hours. Slides were washed once with 6X SSPE. (Invitrogen)/0.005% N-Lauroylsarcosine (Sigma L7414), once with 0.06X SSPE/0.005%  N-Lauroylsarcosine, and once with Agilent Stabilization and Drying solution according to Agilent protocols.

scan_protocol: Slides were scanned using an Agilent G2565CA Scanner.

data_processing: Scanned slides were processed using Agilent Feature Extraction Software (v.10.5.1.1), extraction protocol GE2_105_Jul10. Red and green channel spot and background intensities from Feature Extraction files were processed using the R/Bioconductor Ringo package (v1.3.0) using the read.maimages function (source=agilent). ChIP vs. input ratios (log2) were determined with the preprocess function using the loess normalization method.

label: Alexa Fluor 647

organism: Schizosaccharomyces pombe

source_name: Schizosaccharomyces pombe cells, H3K9me2 wt ChIP

label_protocol: ChIP and Input DNA were amplified by random priming PCR incorporating amino-allyl dUTP, then covalently coupled with Cy5 mono NHS ester in 100 mM sodium bicarbonate for 1 hr at room temperature. Labeled DNA was recovered using Qiagen QIAquick PCR columns.

growth_protocol: Logarithmically growing cultures were grown 18 hours to mid-exponential phase (A595 ~ 0.5) in standard rich media (YEA) shaking at 250 RPM at 30° C.

extract_protocol: Chromatin was extracted from cross-linked cells following bead beater lysis and sonication.  Following immunoprecipitation of ChIP samples, ChIP and input DNA samples were incubated overnight at 65 deg C in TE buffer to reverse cross-links and digested with Rnase A and proteinase K. DNA was recovered by phenol/chloroform extraction and ethanol precipitation

treatment_protocol: 50 mL cultures were cross-linked with paraformadehyde at 18 deg C for 30 minutes, followed by dimethyl adipimidate crosslinking at room temperature for 45 min.

value: wildtype

label: Alexa Fluor 555

source_name: Schizosaccharomyces pombe cells, input


title: subject 16531 SSR area at t14

source_name: whole human skin from subject 16531 SSR area at t14


title: H3K9me2_set1D_clr3D_2

description: ChIP-chip profiling of H3K9me2 in set1 clr3 deletion mutant cells replicate 2

source_name: Schizosaccharomyces pombe cells, H3K9me2 set1 clr3 deletion ChIP

value: set1 clr3 deletion mutant


title: H3K4me3_atf1D_2

description: ChIP-chip profiling of H3K4me3 in atf1 deletion mutant cells replicate 2

source_name: Schizosaccharomyces pombe cells, H3K4me3 atf1 deletion ChIP

value: atf1 deletion mutant