title: TrialNet T1D-patient 9

city: Stanford

first: Linda

last: Yip

state: CA

address: 269 Campus Drive West, CCSR Building Rm. 2240

department: Medicine

institute: Stanford University

description: Gene expression in peripheral whole blood of an established Type 1 diabetes patient

hyb_protocol: Hybridization was performed using the Agilent Gene Expression Hybridization Kit and the Agilent Microarray Hybridization Chamber as instructed by the manufacturer. Samples were hybridized for 17 h at 65ºC, and slides were washed with Gene Expression Wash Buffer (Agilent) according to maufacturer's instructions.

scan_protocol: Microarray chips were scanned using the DNA microarray scanner (Agilent Technologies) with the following parameters: 1 color scan; scan resolution 5 um, single pass, green dye channel. Data was extracted using Feature Extraction software (version 12.0.2.2).

data_processing: The scanned images were analyzed with Feature Extraction Software version 12.0.2.2 (Agilent).

source_name: whole blood

label_protocol: Cy3-labeled cRNA was prepared from 300 ng RNA using the Low input QuickAmp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted using the Kingfisher Purification system (Thermo Scientific).

treatment_protocol: Whole blood RNA was obtained from TrialNet (study TN08).  Peripheral blood was collected in Tempus Tubes.

tag: diagnosis

value: Type 1 diabetes

value: whole blood

tag: age

tag: Sex

value: F

tag: disease duration (years)

tag: serum autoantibodies

value: ICA512, mIAA, ICA


title: TrialNet T1D-patient 10

status: Public on Nov 15 2016

type: RNA

country: USA

molecule: total RNA

organism: Homo sapiens

tag: tissue

value: M

value: GAD65, ICA512, mIAA


title: TrialNet T1D-patient 7


title: TrialNet T1D-patient 8

value: GAD65, mIAA


title: HMEC_unstimulated_4h_apical

city: Vienna

first: Markus

last: Jeitler

address: Lazarettgasse 14

country: Austria

institute: Medical University Vienna

hyb_protocol: The hybridization cocktail  were hybridized to HU133A arrays (Affymetrix, Santa Clara, CA) at 45°C for 16 hours in a rotisserie oven at 60 rpm.  The arrays were washed using non-stringent buffer  at 25°C, followed by stringent buffer at 50°C.

scan_protocol: The arrays were scanned using the GeneArray scanner (Affymetrix).

data_processing: Hybridization intensity was obtained and detection p value and signal were calculated using MAS 5.0 software

label: Biotin

source_name: dermal microvascular endothelial cells, unstimulated apically

label_protocol: 5 µg of total RNA was used to generate double-stranded cDNA by reverse transcription using a cDNA synthesis kit (Superscript Choice System; Life Technologies, Inc., Rockville, MD). Labeled cRNA was prepared from the double-stranded cDNA by in vitro transcription using T7 RNA polymerase in the presence of biotin-11-CTP and biotin-16-UTP (Enzo, Farmington, NY). Fifteen µg of cRNA was fragmented and used to prepare the hybridization cocktail.

growth_protocol: Human microvascular endothelial cells (HMECs) were seeded at 3x10˄5 cells  in complete EGM2-MV growth medium on PET transwells of 1 µm pore size to form a confluent layer within 24 h and were then cultured for another 24 h in EGM2-MV medium including 5% FCS but no additional growth factor supplements. HT-29 colon carcinoma cells were seeded in the same growth medium at 4x10˄6 per 30 mm well and conditioned supernatant was collected from 24 to 48 h after cell seeding.

extract_protocol: HMECs were harvested from transwells, total RNA was extracted (Qiagen).

treatment_protocol: HMEC cultures in transwells were left untreated or were stimulated by tumor-conditioned medium from the basal or apical side for 4 hours prior to isolation of total RNA.

tag: cell type

value: dermal microvascular endothelial cells


title: TrialNet T1D-patient 4


title: TrialNet T1D-patient 5


title: HMEC_stimulated_4h_apical_HT29supernatant

description: stimulation with conditioned medium from HT29 colon carcinoma cells

source_name: dermal microvascular endothelial cells, stimulated apically for 4 h with HT-29 colon carcinoma supernatant


title: TrialNet T1D-patient 1

value: GAD65, ICA512, mIAA, ICA


title: TrialNet T1D-patient 3


title: Tempus system - individual 8

description: Gene expression in whole blood collected in a Tempus tubes and processed using the Tempus Spin RNA isolation kit

extract_protocol: Total RNA was extracted from samples collected in PAXgene and Tempus tubes using the PAXgene Blood RNA Kit and the Tempus Spin RNA Isolation Kit, respectively, according to manufacturer's instructions.

treatment_protocol: Two blood samples were collected from each healthy subect, one sample in a PAXgene tube (2.5 ml blood) and one sample in a Tempus tube (3 ml blood).

value: healthy


title: TrialNet T1D-patient 2


title: Tempus system - individual 9


title: Tempus system - individual 6


title: Tempus system - individual 7


title: Rat_Hep_D1_YAC(-)_1

city: Philadelphia

first: Takeshi

last: Katsuda

state: PA

address: 421 Curie Blvd, BRB II/III Rm531

department: Perelman School of Medicine

institute: University of Pennsylvania

description: Gene expression of hepatocytes cultured for 1 day without YAC

hyb_protocol: For each hybridization, 0.60 ug of Cy3 labeled cRNA were fragmented, and hybridized at 65 °C for 17 hours to an Agilent SurePrint G3 Rat GE 8x60K Microarray (Design ID: 028279).

scan_protocol: After washing, microarrays were scanned using an Agilent DNA microarray scanner.

data_processing: Intensity values of each scanned feature were quantified using Agilent feature extraction software version 10.7.3.1, which performs background subtractions. We only used features which were flagged as no errors (Detected flags) and excluded features which were not positive, not significant, not uniform, not above background, saturated and population outliers (Compromised and Not Detected flags). Normalization was performed using Agilent GeneSpring version 12.6.1. (per chip: normalization to 75 percentile shift; per gene: normalization to median of all samples). There are total of 30,367 probes on Agilent SurePrint G3 Rat GE 8x60K Microarray (Design ID: 028279) without control probes.

organism: Rattus norvegicus

source_name: Hepatocytes cultured, 1 day, YAC(-)

label_protocol: Total RNA was amplified and labeled with Cyanine 3 (Cy3) using Agilent Low Input Quick Amp Labeling Kit, one-color (Agilent Technologies, Palo Alto, CA) following the manufacturer's instructions. Briefly, 100 ng of total RNA was reversed transcribed to double-strand cDNA using a poly dT-T7 promoter primer. Primer, template RNA and quality-control transcripts of known concentration and quality were first denatured at 65 °C for 10 min and incubated for 2 hours at 40 °C with 5X first strand Buffer, 0.1 M DTT, 10 mM dNTP mix, and AffinityScript RNase Block Mix. The AffinityScript enzyme was inactivated at 70 °C for 15 min. cDNA products were then used as templates for in vitro transcription to generate fluorescent cRNA. cDNA products were mixed with a transcription master mix in the presence of T7 RNA polymerase and Cy3 labeled-CTP and incubated at 40 °C for 2 hours. Labeled cRNAs were purified using QIAGEN’s RNeasy mini spin columns and eluted in 30 ul of nuclease-free water. After amplification and labeling, cRNA quantity and cyanine incorporation were determined using a Nanodrop ND-1000 spectrophotometer and an Agilent Bioanalyzer.

extract_protocol: RNA was extracted using miRNeasy kit (Qiagen) following the manufacturer's instruction.

treatment_protocol: Primary rat hepatocytes were cultured for 14 days in the presence or absence of YAC. For hepatic induction, CLiPs were cultured in the presence or absence of oncostatin M and dexamethasone.

tag: strain

value: Wistar

tag: gender

value: Female

tag: yac stimulation

value: no

tag: time point

value: 1 day


title: PAXgene system - individual 8

description: Gene expression in whole blood collected in a PAXgene tubes and processed using the PAXgene Blood RNA Kit


title: PAXgene system - individual 9


title: PAXgene system - individual 7


title: Tempus system - individual 4


title: PAXgene system - individual 3


title: Tempus system - individual 3


title: PAXgene system - individual 6


title: Tempus system - individual 5


title: Rat_Hep_D14_YAC(+)_1

description: Gene expression of hepatocytes cultured for 14 days with YAC

source_name: Hepatocytes cultured, 14 day, YAC(+)

value: yes

value: 14 days


title: Tempus system - individual 1


title: PAXgene system - individual 4


title: PAXgene system - individual 5


title: Rat_Hep_D2_YAC(+)_1

description: Gene expression of hepatocytes cultured for 2 days with YAC

source_name: Hepatocytes cultured, 2 day, YAC(+)

value: 2 days


title: at-seed-wt-2d_after_pollination-replicate1

city: Uppsala

first: Juan

middle: C

last: Santos-González

state: Uppsala

address: Almas Allé 5

department: Department of Plant Biology and Forest Genetics

country: Sweden

institute: SLU

description: Gene expression of wild-type seeds at 2 days after pollination

hyb_protocol: The fragmented 15 μg of labelled cRNA was denatured for 5 min at 99 °C and hybridized to the arrays for 16 h as recommended by Affymetrix. Washing and detection of labelled cRNA with streptavidin phycoerythrin were performed according to the manufacturer’s instructions with the EukGE-WS2v3 protocol involving two streptavidin-phycoerythrin labelling steps.

scan_protocol: The arrays were scanned with a confocal scanner (Affymetrix).

data_processing:
Signal values were derived from Affymetrix*.cel files using RMA (Rehrauer et al. 2010). All data processing was done using the statistics package R (version 2.6.2) that is freely available at http://www.r‐project.org/. Quality control was done using the affyQCReport package in R.Differentially expressed genes were identified using the limma package in R (Smyth 2004). Multiple‐testing correction was done using the q‐value method (Storey and Tibshirani 2003).
Probesets were called significantly differentially expressed when q<0.05.

label: biotin

organism: Arabidopsis thaliana

source_name: seeds of wild type at 2 days after pollination, replicate 1

label_protocol: Total RNA was used to prepare cDNA with the SuperscriptDouble-Stranded cDNA Synthesis Kit (Invitrogen) according to the manufacturer’s instructions with oligodT-T7 oligonucleotides. The cDNA was subjected to in vitro transcription in the presence of 2 mM each biotin-11-CTP and biotin-16-UTP (ENZO Life Sciences, Farmingdale, NY) with the MegaScript High Yield Transcription Kit (Ambion, Austin, TX). After purification of the cRNA on RNeasy columns (Quiagen, Hilden, Germany), 15 μg cRNA was fragmented in a volume of 40 μl as recommended by Affymetrix.

growth_protocol: Seeds were sterilized in 5% commercial bleach and 0.01% Tween-20 for 10 min and washed three times in sterile ddH2O. Sterile seeds were plated on ½ MS-medium (0.43% MS-salts, 0.8% Bacto Agar, 0.19% MES hydrate and 1% Sucrose; when necessary, the medium was supplemented with the appropriate antibiotics) and stratified at 4 ºC in the dark for 48 h. Plates were then transferred to a growth chamber (16 h light / 8 h dark; 110 μmol.s-1.m-2; 21ºC; 70% humidity). After 10 days seedlings were transferred to soil and grown in a growth chamber (16 h light / 8 h dark; 110 μmol.s-1.m-2; 21ºC; 70% humidity).

extract_protocol: Ovules and seeds were collected in RNAlater (Sigma) and ground frozen in a Silamat S5 for 3 times 7 seconds. Three biological replicates were generated per sample. RNA was extracted using the QIAGEN RNeasy KIT followed by on-column DNase treatment.

treatment_protocol: WT (Ler) and double mutant vrn2/- emf2/+ plants were emasculated at 1-2 days prior to anthesis. Two days after emasculation half of the WT plants were hand-pollinated. Unfertilized ovules and young seeds were dissected from the siliques at 4 DAE and 2 DAP, respectively.

value: seeds

tag: genotype

value: wild type


title: at-seed-wt-2d_after_pollination-replicate3

source_name: seeds of wild type at 2 days after pollination, replicate 3


title: at-ovule-wt-4d_after_emasculation-replicate1

description: Gene expression data of ovules from wild-type plants at 4 days after emasculation

source_name: ovules of wild type at 4 days after emasculation, replicate 1

value: ovules


title: at-ovule-vrn2_emf2-4d_after_emasculation-replicate3

description: Gene expression data of ovules from vrn2/- emf2/+ plants at 4 days after emasculation

source_name: ovules of vrn2 emf2 at 4 ays after emasculation, replicate 3

value: vrn2/- emf2/+


title: at-ovule-wt-4d_after_emasculation-replicate3

source_name: ovules of wild type at 4 days after emasculation, replicate 3


title: at-ovule-vrn2_emf2-4d_after_emasculation-replicate2

source_name: ovules of vrn2 emf2 at 4 ays after emasculation, replicate 2


title: at-seed-wt-2d_after_pollination-replicate2

source_name: seeds of wild type at 2 days after pollination, replicate 2


title: at-ovule-vrn2_emf2-4d_after_emasculation-replicate1

source_name: ovules of vrn2 emf2 at 4 ays after emasculation, replicate 1


title: Tempus system - individual 2

value: whole blood

value: M


title: PAXgene system - individual 2


title: TrialNet T1D-patient 6

value: Type 1 diabetes

value: F

value: GAD65, mIAA


title: PAXgene system - individual 1

value: healthy


title: Gen2.2 shTCF4#1 - 24 hours - mAdbID:126365

city: Bethesda

first: Louis

middle: M.

last: Staudt

state: MD

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

department: Lymphoid Malignancies Branch

institute: National Cancer Institute

description: mAdb experiment ID: 126365

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

scan_protocol: Scan_MicronsPerPixelX: 5 Scan_MicronsPerPixelY: 5 Scan_ScannerName: Agilent Technologies Scanner G2505C US45102888

data_processing:
Agilent Data Processing Protocol (shRNA)
Calculation Method: Images were auto gridded, analyzed and data extracted using Agilent Feature Extraction Software. Spot values were normalized using the default linear-lowess normalization. For shRNA gene expression profiling, array elements were filtered for those meeting confidence thresholds for spot size, architecture, and level above local background. These criteria are a feature of the Agilent gene- expression software package. For each cell line, a gene universe was defined by selecting arrays elements with an average Cy3 or Cy5 value > 50. Array features were defined as down-regulated or up-regulated if the Log2 Fold Change was <-0.5 or >+0.5 for at least 2 time points, respectively. When multiple spots were present for the same gene, a representative spot was selected based on the smallest Log2 FC.
FeatureExtractor_Version: 10.1.1.1
Protocol_Name: GE2-v5_10_Apr08 (Read Only)

source_name: Gen2.2 shTCF4 with DOX - 24 hours

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

extract_protocol:
TRIzol Extraction Protocol
Other: Total RNA was extracted with TRIzol (Invitrogen) and subsequently cleaned-up with RNeasy mini columns (Qiagen).

treatment_protocol:
Treatment type: shRNA transduction
Treatment time: 24 hours
In-vitro treatment: Cells were infected with TCF4 shRNAs. Following puromycin selection, shRNA expression was induced by doxycycline (50 ug/ml) for 24 hours.

tag: treatment

value: shTCF4 with DOX

tag: time

value: 24 hours

tag: cell line

value: BPDCN (blastic plasmacytoid dendritic cell neoplasm) cells

tag: disease state

source_name: Gen2.2 shControl with DOX - 24 hours

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

treatment_protocol:
Treatment type: shRNA transduction
Treatment time: 24 hours
In-vitro treatment: Cells were infected with Contrl shRNAs. Following puromycin selection, shRNA expression was induced by doxycycline (50 ug/ml) for 24 hours.

value: shControl with DOX


title: Cal-1 shTCF4#1 - 24 hours - mAdbID:118980

description: mAdb experiment ID: 118980

source_name: Cal-1 shTCF4 with DOX - 24 hours

value: BPDCN (blastic plasmacytoid dendritic cell neoplasm)

source_name: Cal-1 shControl with DOX - 24 hours


title: HepG2/C3A_Resveratrol_72hrs

city: Rennes

first: Cedric

last: Coulouarn

address: CLCC Eugène Marquis, Rue de la Bataille Flandres Dunkerque, Bat D, 1er étage

country: France

institute: INSERM

hyb_protocol: 600 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 25 µ of 2x Agilent hybridization buffer (HI-RPM) was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE 8x60K for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray C Scanner (G2565) using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent Technologies) using default parameters (protocol GE1_107_Sep09_ssSurrogates and Grid: 028004_D_F_20101102). Gene expression data were further analyzed by using the GeneSpring software (Agilent Technologies). Features flagged in Feature Extraction as 'Feature not positive and significant' and 'Feature not above background' were excluded. Normalization was based on the 75th percentile shift.

source_name: Resveratrol-treated  HepG2/C3A cell line

label_protocol: Total RNA was amplified and labeled with Cy3 fluorescent dye using Agilent one color low-input QuickAmp labeling kit following according to the manufacturer's instructions. Starting from 150ng total RNA, amplification yield was 7.0±1.3μg cRNA and specific activity was 18.2±2.3pmol Cy3 per μg of cRNA.

growth_protocol: SNU-387 (ATCC® CRL-2237™, grade IV/V) and HepG2/C3A (ATCC® CRL-10741™) were grown in a RPMI-1640 medium supplemented with 100U/ml penicillin, 100μg/ml streptomycin and 10% fetal bovine serum. Cultures were performed at 37°C in a 5% CO2 atmosphere.

extract_protocol: Total RNA was extracted and purified using the RNAeasy kit (Qiagen, Valencia, CA, USA) following the manufacturer’s recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: Cells were treated for 72h with DMSO, vorinostat (3.7µM), sorafenib (0.65µM), and resveratrol (166µM).

value: Treated

value: hepatocellular carcinoma


title: SNU387_DMSO_72hrs

source_name: DMSO-treated  SNU387 cell line

value: Control


title: Gen2.2 shTCF4#2 - 24 hours - mAdbID:126367

description: mAdb experiment ID: 126367


title: HepG2/C3A_Vorinostat_72hrs

source_name: Vorinostat-treated  HepG2/C3A cell line


title: Chd4 KD rep 2

city: Pittsburgh

first: Sarah

middle: J

last: Hainer

address: 4249 Fifth Ave

department: Department of Biological Sciecnes

institute: University of Pittsburgh

description: Agilent 4X44K mouse whole-genome microarrays

hyb_protocol: 50 picomoles of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 125 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. Upon completion of the fragmentation reaction, 125 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent 4X44K Whole Mouse Genome Microarrays for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed for 1 minute at room temperature with GE Wash Buffer 1 (Agilent), 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned on the Agilent scanner (G2565CA) immediately after washing.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters (protocol GE1-107 and Grid: 026655_D_F_20120201) to obtain background subtracted and spatially detrended Processed Signal intensities. We used the quantile normalization in R (bioconductor) to obtain the value in the Sample data tables.

organism: Mus musculus

source_name: Chd4 KD rep 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from total RNA using Low Input Quick Amp Labeling Kit protocol (Agilent).

growth_protocol: E14 mouse embryonic stem cells (ESCs) were cultured on gelatin-coated dishes without feeder cells in high-glucose DMEM medium (Sigma) containing 10% serum (Corning) and LIF at 37°C with 5% CO2.

extract_protocol: TRIzol, followed by Zymo columns

treatment_protocol: One 10cm dish was transiently transfected with esiRNAs and lipofectamine 2000 and cultured 48 hours post transfection.

value: E14 murine embryonic stem cells


title: Cal-1 shTCF4#2 - 24 hours - mAdbID:118982

description: mAdb experiment ID: 118982


title: SNU423_LY294002_72hrs

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent Technologies) using default parameters (protocol GE1_107_Sep09_ssSurrogates and Grid: 039494_D_F_20120411). Gene expression data were further analyzed by using the GeneSpring software (Agilent Technologies). Features flagged in Feature Extraction as 'Feature not positive and significant' and 'Feature not above background' were excluded. Normalization was based on the 75th percentile shift.

source_name: LY294002-treated  SNU423 cell line

growth_protocol: SNU-423 cells (ATCC® CRL-2238™, grade III/IV) were grown in a RPMI-1640 medium supplemented with 100U/ml penicillin, 100μg/ml streptomycin and 10% fetal bovine serum. Cultures were performed at 37°C in a 5% CO2 atmosphere.

treatment_protocol: Cells were treated for 72h with DMSO, trichostatin A (0.6µM), alpha-estradiol (1µM), vorinostat (3.7µM), sorafenib (0.65µM), rapamycin (2µM), LY294002 (45µM) and resveratrol (166µM). These doses resulted in 50% viability after 72 hours.

value: SNU-423 hepatocellular carcinoma cell line

tag: agent


title: Gen2.2 shTCF4#1 - 12 hours - mAdbID:126364

description: mAdb experiment ID: 126364

source_name: Gen2.2 shTCF4 with DOX - 12 hours

treatment_protocol:
Treatment type: shRNA transduction
Treatment time: 12 hours
In-vitro treatment: Cells were infected with TCF4 shRNAs. Following puromycin selection, shRNA expression was induced by doxycycline (50 ug/ml) for 12 hours.

value: 12 hours

source_name: Gen2.2 shControl with DOX - 12 hours

treatment_protocol:
Treatment type: shRNA transduction
Treatment time: 12 hours
In-vitro treatment: Cells were infected with Contrl shRNAs. Following puromycin selection, shRNA expression was induced by doxycycline (50 ug/ml) for 12 hours.


title: Gen2.2 shTCF4#2 - 12 hours - mAdbID:126366

description: mAdb experiment ID: 126366


title: SNU423_A-Estradiol_72hrs

source_name: alpha-estradiol-treated  SNU423 cell line

value: A-Estradiol


title: HepG2/C3A_Sorafenib_72hrs

source_name: Sorafenib-treated  HepG2/C3A cell line


title: HepG2/C3A_DMSO_72hrs

source_name: DMSO-treated  HepG2/C3A cell line


title: Chd4 KD rep 1

source_name: Chd4 KD rep 1


title: at-ovule-wt-4d_after_emasculation-replicate2

source_name: ovules of wild type at 4 days after emasculation, replicate 2

value: ovules

value: wild type


title: Cal-1 shTCF4#2 - 48 hours - mAdbID:118983

description: mAdb experiment ID: 118983

source_name: Cal-1 shTCF4 with DOX - 48 hours

treatment_protocol:
Treatment type: shRNA transduction
Treatment time: 48 hours
In-vitro treatment: Cells were infected with TCF4 shRNAs. Following puromycin selection, shRNA expression was induced by doxycycline (50 ug/ml) for 48 hours.

value: 48 hours

source_name: Cal-1 shControl with DOX - 48 hours

treatment_protocol:
Treatment type: shRNA transduction
Treatment time: 48 hours
In-vitro treatment: Cells were infected with Contrl shRNAs. Following puromycin selection, shRNA expression was induced by doxycycline (50 ug/ml) for 48 hours.


title: SNU423_Resveratrol_72hrs

source_name: Resveratrol-treated  SNU423 cell line

value: Resveratrol


title: Cal-1 shTCF4#1 - 48 hours - mAdbID:118981

description: mAdb experiment ID: 118981


title: SNU387_Vorinostat_72hrs

source_name: Vorinostat-treated  SNU387 cell line


title: Mbd2 KD rep 2

source_name: Mbd2 KD rep 2


title: Mbd3 KD rep 2

source_name: Mbd3 KD rep 2


title: Mbd2 KD rep 1

source_name: Mbd2 KD rep 1


title: SNU423_Rapamycin_72hrs

source_name: Rapamycin-treated  SNU423 cell line

value: Rapamycin


title: Mbd3 KD rep 1

source_name: Mbd3 KD rep 1


title: Tet1 KD rep 2

source_name: Tet1 KD rep 2


title: N_LEF1_KD_1

city: Derio

first: Jose

middle: Luis

last: Lavin

state: Bizkaia

address: Parque Tecnológico de Bizkaia Building 502, Floor 0

country: Spain

institute: CIC bioGUNE

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with lumi in R. After background correction with GenomeStudio and log2 transformation, probes with a detection p-value greater than 0.01 for all samples were discarded, using the detectionCall function in the lumi R package. That is, probes with detection p-value smaller than 0.01 were chosen for the normalization.

source_name: CD8 Naive LEF1 KD 1

label_protocol: TargetAmp™ Nano-g™ Biotin-aRNA Labeling Kit for the Illumina® System (Epicentre)

growth_protocol: Naive CD8+ T cells were isolated from PBMCs by magnetic bead separation using a Naive CD8+ T cell isolation Kit (Myltenyi Biotec)

extract_protocol: RNA was extracted from naive CD8+ T cells using RNAqueous-Micro kit (Ambion)

value: Blood

value: CD8 Naive LEF1 KD


title: Tet1 KD rep 1

source_name: Tet1 KD rep 1


title: N_Ctrl_2

source_name: CD8 Naive Control 2

value: CD8 Naive Control cells


title: N_LEF1_KD_2

source_name: CD8 Naive LEF1 KD 2


title: N_Ctrl_1

source_name: CD8 Naive Control 1


title: SNU423_Sorafenib_72hrs

source_name: Sorafenib-treated  SNU423 cell line

value: Sorafenib


title: SNU423_DMSO_72hrs

source_name: DMSO-treated  SNU423 cell line


title: SNU423_Vorinostat_72hrs

source_name: Vorinostat-treated  SNU423 cell line

value: Vorinostat


title: TEMRA2

source_name: CD8 TEMRA 2

growth_protocol: CD8+ T cell subsets were isolated from peripheral blood by fluorescence-activated cell sorting (FACS)

extract_protocol: RNA was extracted from CD8+ T cell subsets using RNAqueous-Micro kit (Ambion)

tag: subset

value: CD8 TEMRA cells


title: SNU423_TSA_72hrs

source_name: TSA-treated  SNU423 cell line

value: TSA


title: EGFP KD rep 2

source_name: EGFP KD rep 2


title: Dnmt1 KD rep 2

source_name: Dnmt1 KD rep 2


title: EGFP KD rep 1

source_name: EGFP KD rep 1


title: EM2

source_name: CD8 EM 2

value: CD8 EM cells


title: EM1

source_name: CD8 EM 1


title: N2

source_name: CD8 Naive 2

value: CD8 Naive cells


title: TEMRA1

source_name: CD8 TEMRA 1


title: CD8_EM_1

type: genomic

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

label: Cy3, Cy5

molecule: genomic DNA

label_protocol: EZ DNA Methylation™ Kit (Zymo Research) Followed by Infinium HD Assay Methylation Protocol (Illumina Inc.)

extract_protocol: DNA was extracted from the livers using ATP™ Genomic DNA MiniKit (ATP Biotech)


title: CD8_TEMRA_1


title: CD8_EM_2


title: CD8_NAIVE_1

source_name: CD8 Naive 1


title: CD8_TEMRA_2


title: CD8_NAIVE_2


title: MOLM-13, DMSO treat, biol rep 3

status: Public on Nov 14 2016

city: Basel

first: Swann

last: Gaulis

address: Postfach

department: Oncology Research

country: Switzerland

institute: Novartis Institutes for Biomedical Research

hyb_protocol: Following fragmentation and labeling, 3.4 µg of cRNA were hybridized to the arrays following the manufaturer's instructions. Arrays were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: Arrays were scanned using the GeneChip Scanner 3000

data_processing: The data was summarized and normalized with the RMA method as implemented in the affy Bioconductor package installed under R-3.0.2. Normalizations were undertaken in 3 different batches: RS4;11 and SEM and REH cell line data, MOLM-13 cell line data and MLL-AF9 transformed mouse leukemic cell data. 4 samples were excluded from the normalizations for QC reasons (SEM-DMSO-1,SEM-MI22-2,SEM-COMBO-2,RS411-DMSO-1)

source_name: Immortalized cell line

label_protocol: 50 ng of total RNA were amplified with the Nugen Ovation RNA Amplification System followed by a Ovation WB treatment. Biotinilated cRNA were then prepared using the FL cDNA Biotin Module V2 kit.

growth_protocol: MOLM-13, Reh and RS4;11 were grown in RPMI 1640 (AMIMED), 10 % FCS (Fetal Calf Serum), 2mM L-Glutamine, 1mM Sodium Pyruvate, 10 mM HEPES. SEM cell line was cultured in IMDM (Iscove's – AMIMED), 10% FCS, 4 mM L-glutamine. MLL-AF9 tranformed mouse leukemic cells were maintained in RPMI-1640 (AMIMED), 10% FCS, 1% penicillin/streptomycin, 10 ng/ml of human interleukin-6 (IL-6), 6 ng/ml of murine interleukin-3 (IL-3) and 100 ng/ml of murine stem cell factor.

extract_protocol: Extraction of total RNA was performed according to the manufacturer's instructions (Qiagen: RNeasy).

treatment_protocol: MOLM-13 or mouse MLL-AF9 cells were treated for 4 days with either DMSO, 3 µM EPZ004777, 3 µM MI2-2 or a combination of both compounds. RS4;11, REH and SEM cells were treated for 6 days with either DMSO, 3 µM EPZ004777, 10 µM MI2-2 or a combination of both compounds


title: MOLM-13, DMSO treat, biol rep 2


title: pcDNA3.1-IRX1::GFP

city: Essen

first: Ludger

last: Klein-Hitpass

address: Virchowstr. 173

department: Universitaetsklinikum

country: Germany

institute: Institut fuer Zellbiologie

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip HG-U133Plus_2. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using the Affymetrix Hybridization, Wash and Stain Kit..

scan_protocol: Arrays were scanned in a GeneChip 3000 scanner with G7 update.

data_processing: The data were analyzed with MAS5 using Affymetrix default analysis settings and global scaling to a target intensity of 1000 as normalization method.

source_name: HEK293T + pcDNA3.1-IRX1::GFP

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix ExpressKit protocol starting from 200 ng total RNA.

growth_protocol: HEK293T cells were grown in DMEM supplemeted with 10 % (v/v) FCS , 2 mM L-Glutamine and 1 % (v/v) Pen Strep at 37°C and 5 % CO2

extract_protocol: Total RNA was extracted by using the RNeasy Mini Kit (Qiagen). Total-RNA concentration and purity of total-RNA samples was measured with the NanoDrop 1000 spectrophotometer (NanoDrop Technologies/Thermo Scientific).

treatment_protocol: Cells were transfected with polyethylenimine and harvest 48 hous after the transient expression of the pcDNA3.1-IRX1::GFP / pcDNA3.1-GFP vectors. GFP positive cells were sorted by FACS.


title: pcDNA3.1-GFP

source_name: HEK293T + pcDNA3.1-GFP


title: MOLM-13, DMSO treat, biol rep 1


title: N1


title: MOLM-13, EPZ004777 treat, bio rep 3


title: MOLM-13, EPZ004777 treat, biol rep 2


title: MOLM-13, Combo treat, biol rep 3


title: MOLM-13, MI-2-2 treat, biol rep 3


title: MOLM-13, EPZ004777 treat, biol rep 1


title: MOLM-13, Combo treat, biol rep 2


title: MOLM-13, Combo treat, biol rep 1


title: REH, MI-2-2 treat, biol rep 3

value: REH


title: REH, DMSO treat, biol rep 3


title: MOLM-13, MI-2-2 treat, biol rep 2


title: REH, DMSO treat, biol rep 1


title: REH, MI-2-2 treat, biol rep 2


title: REH, EPZ004777 treat, bio rep 3


title: REH, DMSO treat, biol rep 2


title: Dnmt1 KD rep 1

source_name: Dnmt1 KD rep 1

value: E14 murine embryonic stem cells


title: REH, MI-2-2 treat, biol rep 1


title: BM_1_KO_Transplant

city: Cincinnati

first: Marie-Dominique

last: Filippi

state: OH

address: 3333 Burnet Av

department: Experimental Hematology and Cancer Biology

institute: Cincinnati Children's Research Foundation

description: Gene expression of fresly isolated HSC

hyb_protocol: The Cy-3-labeled cDNA were hybridized overnight (17 hours, 65C) to an Agilent Whole Mouse Genome Oligo Microarrays 4x44KV2 using Agilent's recommended hybridization chamber and oven. Finally, the microarrays were washed once with the Agilent Gene Expression Wash Buffer 1 for 1 min at room temperature followed by a second wash with preheated Agilent Gene Expression Wash Buffer (37C) for 1 min. The last washing step was performed with acetonitrile.

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

data_processing: The Agilent Feature Extraction Software (FES) was used to read out and process the microarray images. The software determines feature intensities (including background substraction), rejects outliers and calculates statistical confidences.

source_name: KO bone marrow HSC replicate 1

label_protocol: 250 ng of each of the cDNA were used as template for Cy3 labeling which was performed according to <iltenyi Biotec's undisclosed protocol

extract_protocol: Bones were flushed and HSCs were pre-enriched using anti-Lineage microBeads and autoMACS Pro Separator (Miltenyi, San Diego, CA), and then Lin-negative c-Kit-positive Sca-positive CD150-positive CD48-negative cell were isolated by flow cytometry. Cells were lyzed using RNA-lysis buffer from Miltenyi and send to Miltenyi for RNA preparation, cDNA amplification and microarray analysis.

value: bone marrow hematopoietic stem cells

tag: genotype/variation


title: ARP-1  expressing CD85J (LILRB1)

city: Barcelona

first: Ester

last: Lozano

state: Barcelona

address: Rosselló, 153

department: Hemato-Oncology

institute: IDIBAPS

description: Gene expression data from ARP-1 lentivirally transduced to express human CD85J (LILRB1)

hyb_protocol: RNA samples were processed to Affymetrix GeneChip HT HG-U219 arrays.

scan_protocol: Scanning was processed in the GeneTitan instrument.

data_processing: Determination of the signal value for each probe set of the array were obtained with GeneChip® Command Console® Software (AGCC) (Affymetrix).  Raw data were normalized using the Robust Multichip Analysis (RMA) algorithm implemented in the Expression Console Software v1.1 (Affymetrix).

source_name: ARP-1  multiple myeloma cell line, expressing CD85J (LILRB1)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 150ng total RNA.

growth_protocol: MM cell lines RPMI-8226, U266 and ARP-1 were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum, 2mM glutamine, 100 U/mL penicillin and 100 µg/mL streptomycin and maintained at 37°C and 5% CO2.

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

treatment_protocol: MM cell lines (U266, RPMI-8226, ARP-1) were lentivirally transduced to express CD85j-GFP or GFP-control in the presence of 8 µg/mL polybrene. Lentiviral particles were generated using HEK293T cells and the Lenti-vpak packaging kit (packaging plasmids and MegaTran1.0 transfection reagent)  with Lenti ORF clone of human LILRB1, transcript variant 1, pLenti-C-mGFP vector purchased from OriGene Technologies, Inc. (Rockville, MD, USA). After 3 days, cells were FACS-sorted.

value: Multiple myeloma cell line

tag: transduced vector

value: ARP-1  expressing CD85J (LILRB1)


title: BM_2_KO_Transplant

description: Gene expression of fresly isolated HSC

source_name: KO bone marrow HSC replicate 2


title: BM_3_KO_Transplant

description: Gene expression of fresly isolated HSC

source_name: KO bone marrow HSC replicate 3


title: BM_2_WT_Transplant

description: Gene expression of fresly isolated HSC

source_name: WT bone marrow HSC replicate 2

value: WT


title: BM_3_WT_Transplant

description: Gene expression of fresly isolated HSC

source_name: WT bone marrow HSC replicate 3


title: MLL-AF9 transformed mouse leukemic cells, DMSO treat, biol rep 3

source_name: Primary cell culture


title: MOLM-13, MI-2-2 treat, biol rep 1


title: U266 expressing GFP

description: Gene expression data from U266 lentivirally transduced to express GFP

source_name: U266 multiple myeloma cell line, control expressing GFP

value: U266 expressing GFP


title: ARP-1 expressing GFP

description: Gene expression data from ARP-1 lentivirally transduced to express GFP

source_name: ARP-1 multiple myeloma cell line, control expressing GFP

value: ARP-1 expressing GFP


title: REH, EPZ004777 treat, biol rep 2


title: REH, EPZ004777 treat, biol rep 1


title: RPMI-8226 expressing CD85J (LILRB1)

description: Gene expression data from RPMI-8226 lentivirally transduced to express human CD85J (LILRB1)

source_name: RPMI-8226  multiple myeloma cell line, expressing CD85J (LILRB1)

value: RPMI-8226 expressing CD85J (LILRB1)


title: BM_1_WT_Transplant

description: Gene expression of fresly isolated HSC

source_name: WT bone marrow HSC replicate 1


title: MLL-AF9 transformed mouse leukemic cells, DMSO treat, biol rep 1


title: U266 expressing CD85J (LILRB1)

description: Gene expression data from U266 lentivirally transduced to express human CD85J (LILRB1)

source_name: U266 multiple myeloma cell line,  expressing CD85J (LILRB1)

value: U266 expressing CD85J (LILRB1)


title: REH, Combo treat, biol rep 3


title: MLL-AF9 transformed mouse leukemic cells, DMSO treat, biol rep 2


title: RPMI-8226 expressing GFP

description: Gene expression data from RPMI-8226 lentivirally transduced to express GFP

source_name: RPMI-8226  multiple myeloma cell line, control expressing GFP

value: RPMI-8226 expressing GFP


title: REH, Combo treat, biol rep 2

source_name: Immortalized cell line


title: REH, Combo treat, biol rep 1


title: SEM, DMSO treat, biol rep 3

value: SEM


title: SEM, EPZ004777 treat, bio rep 3


title: MLL-AF9 transformed mouse leukemic cells, EPZ004777 treat, biol rep 1


title: MLL-AF9 transformed mouse leukemic cells, EPZ004777 treat, bio rep 3


title: SEM, DMSO treat, biol rep 2


title: SEM, MI-2-2 treat, biol rep 3


title: MLL-AF9 transformed mouse leukemic cells, MI-2-2 treat, biol rep 1


title: MLL-AF9 transformed mouse leukemic cells, MI-2-2 treat, biol rep 2


title: MLL-AF9 transformed mouse leukemic cells, Combo treat, biol rep 3


title: SEM, MI-2-2 treat, biol rep 1


title: SEM, Combo treat, biol rep 3


title: MLL-AF9 transformed mouse leukemic cells, Combo treat, biol rep 2


title: MLL-AF9 transformed mouse leukemic cells, MI-2-2 treat, biol rep 3


title: MLL-AF9 transformed mouse leukemic cells, EPZ004777 treat, biol rep 2


title: SEM, EPZ004777 treat, biol rep 1


title: SEM, EPZ004777 treat, biol rep 2


title: RS4;11, DMSO treat, biol rep 3


title: RS4;11, MI-2-2 treat, biol rep 1


title: Dye Swap 1

city: Ithaca

first: Cresten

last: Mansfeldt

state: NY

address: 220 Hollister Hall

institute: Cornell University

description: Dye Swap 1

hyb_protocol: For each experiment, Cy5 labeled cDNA from the mixed community mRNA pool was hybridized against an aliquot of common control of Cy3 labeled cDNA from 3-day starved culture. The hybridization, washing, and scanning of the microarray samples was performed by the Cornell University Microarray Core Facility (http://cores.lifesciences.cornell.edu/brcinfo/) and followed the methods outlined by the manufacturer (Agilent Technologies). The general procedure mixed 25 μl (~400 ng) of the labeled cDNA sample with 25 μl 2x Gene Expression (GEx) Hybridization Buffer HI-RPM (5), hybridized the sample to the microarray slide at 65° C for 17 hours, and washed with GEx Wash Buffer 1 and 2 at room and elevated (37°C) temperatures.

scan_protocol: Scanned with an Agilent Technologies Scanner G2505C with a 5 μm resolution.

data_processing: Microarray image analysis was conducted using Agilent Feature Extraction 10.5 Image Analysis Software. The Feature Extraction Software was also utilized to perform a within array modified LOESS normalization between the Cy5 and Cy3 signals, to calculate a ratio between the Cy5 and Cy3 channels, and to calculate a modified Student t-test p-value between the Cy5 and Cy3 signal distributions.

organism: Dehalococcoides mccartyi

source_name: Mixed microbial community KB-1™

label_protocol: The Superscript I © DNAse RNA cleanup, amino-allyl cDNA formation, cDNA cleanup, and cDNA labeling with Cy3 or Cy5 followed the method outlined (Waller 2010). The quality and quantity of the RNA was determined using the RNA 6000 Nano assay on an Agilent 2100 bioanalyzer (Agilent Technologies). The quantity of resulting cDNA was determined by using the Quant-IT™ OliGreen® ssDNA Assay Kit (Invitrogen). A common control RNA pool sampled from the main Donna II reactor after 3 days of starvation was labeled with Cy3.

growth_protocol: KB-1™ culture from SiREM Laboratories Guelph, Laboratories was used in these studies. This mixed microbial, reductively-dechlorinating community contains populations of Dehalococcoides mccartyi, Geobacter, Spirochetes, methanogens, and fermeneters as previously described (Hug et al. 2012)

extract_protocol: 50 mL of liquid culture samples were centrifuged-at 14190×g. The centrifuged sample was split into 8 individual RNA extractions with each sample following the RNeasy© Mini Kit (Qiagen) extraction previously outlined (Rahm and Richardson 2008). The 8 distinct RNA extractions were recombined on the spin filter before the first RW1 buffer wash.

treatment_protocol: In brief, 160 mL glass serum bottles were filled with 100 mL of KB-1TM. Varying combination of Pressure Lok syringe volumes (10 mL, 5 mL, 2.5 mL, 500 μL, and 100 μL; VICI Precision Sampling) and concentrations of electron acceptor and donor in media were loaded on a Cole Palmer 74900 Syringe Pump to deliver an expected continuous rate for the continous experiments.  The batch fed experiments had TCE, acetate, and hydrogen added as the electron acceptor, carbon source, and electron donor, respectively.

tag: batch or continuous

value: batch

tag: electron acceptor

value: Control (none)

tag: electron donor

tag: purged and respiked at 24 hrs

value: no

tag: stress exposure

value: No

tag: time of sample (hrs)

tag: sample type

value: batch fed control

tag: sample condition

value: 3 day starved KB-1


title: Dye Swap 2

description: Dye Swap 2


title: RS4;11, MI-2-2 treat, biol rep 3


title: RS4;11, EPZ004777 treat, biol rep 2


title: RS4;11, DMSO treat, biol rep 2


title: Time Series T0

description: Time zero control


title: RS4;11, EPZ004777 treat, bio rep 3


title: SEM, Combo treat, biol rep 1


title: RS4;11, MI-2-2 treat, biol rep 2


title: MLL-AF9 transformed mouse leukemic cells, Combo treat, biol rep 1


title: RS4;11, Combo treat, biol rep 3


title: Time Series D1

description: Biologocial replicate 1 of 2

value: 220 µM trichloroethane (TCE)

value: hydrogen (in excess)


title: RS4;11, EPZ004777 treat, biol rep 1


title: Time Series E2

description: Biologocial replicate 2 of 2


title: Time Series D2

description: Biologocial replicate 2 of 2


title: Time Series E1

description: Biologocial replicate 1 of 2


title: Time Series C2

description: Biologocial replicate 2 of 2


title: Time Series B1

description: Biologocial replicate 1 of 2


title: Time Series C1

description: Biologocial replicate 1 of 2


title: RS4;11, Combo treat, biol rep 2


title: Time Series B2

description: Biologocial replicate 2 of 2


title: Time Series F1

description: Biologocial replicate 1 of 2


title: Time Series A2

description: Biologocial replicate 2 of 2


title: TCA C1

description: Biologocial replicate 1 of 2

value: yes

value: oxygen


title: Time Series F2

description: Biologocial replicate 2 of 2


title: Time Series A1

description: Biologocial replicate 1 of 2


title: TCA B2

description: Biologocial replicate 2 of 2


title: RS4;11, Combo treat, biol rep 1


title: TCA C2

description: Biologocial replicate 2 of 2


title: TCA Time Zero

description: Time zero control


title: TCA A2 Control

description: Biologocial replicate 2 of 2


title: Oxygen C2

description: Biologocial replicate 2 of 2

value: trichloroethane


title: TCA B1

description: Biologocial replicate 1 of 2


title: Oxygen A2 Control

description: Biologocial replicate 2 of 2


title: 3 Rates C1

description: Biologocial replicate 1 of 2

value: continuous

value: 4.2 µM/hr trichloroethane (TCE)


title: Oxygen Time Zero

description: Time zero control


title: Oxygen B2

description: Biologocial replicate 2 of 2


title: 3 Rates B1

description: Biologocial replicate 1 of 2

value: 10.5 µM/hr trichloroethane (TCE)


title: 3 Rates Time Zero

description: Time zero control


title: Oxygen A1 Control

description: Biologocial replicate 1 of 2


title: Oxygen B1

description: Biologocial replicate 1 of 2


title: 3 Rates B2

description: Biologocial replicate 2 of 2


title: 3 Rates A2

description: Biologocial replicate 2 of 2

value: 29.3 µM/hr trichloroethane (TCE)


title: TCA A1 Control

description: Biologocial replicate 1 of 2


title: 3 Rates A1

description: Biologocial replicate 1 of 2


title: Oxygen C1

description: Biologocial replicate 1 of 2


title: Yeast_wildtype_1

city: Roma

first: Ivan

last: Arisi

address: viale Regina Elena 295

department: Bioinformatics Facility

country: Italy

institute: European Brain Research Institute

hyb_protocol: One-color mixes of labelled cRNA pairs were hybridized to Agilent 8X15K whole yeast genome oligonucleotide microarrays (Grid ID 016322) , at 65°C for 17 hours using Agilent’s Gene Expression Hybridization Kit. The hybridized microarrays were disassembled at room temperature in Agilent Gene Expression Wash Buffer 1. After the disassembly, the microarrays were washed in Gene Expression Buffer 1 for one minute at room temperature, followed by washing with Gene Expression Wash Buffer 2 for one minute at 37°C. The microarrays were then treated with acetonitrile for one minute at room temperature.

scan_protocol: Post-hybridization image acquisition was accomplished using the Agilent Scanner G2564C. Data extraction from the 20 bits TIFF images was accomplished by Agilent Feature Extraction ver 10.7 software using the standard Agilent one-color gene expression extraction protocol (GE1_107_Sep09).

data_processing: The “gProcessedSignal” data column of the Feature Extraction *.txt output file was used, containing the median signals corrected by spatial and multiplicative detrend. Data quality filtering was performed using Microsoft Excel, discarding features with the Feature Extraction flag gIsWellAboveBG=0 in any sample, wich is a statistical method approximately equivalent to discarding features with a Signal/Noise ratio smaller than 2.0-3.0, where Signal = (median of the spot - median spot background level) and Noise is the Standard Deviation of the median spot background. Data were normalized to the 75th percentile in Log2 scale. Then differential gene lists were obtained from filtered data using Microsoft Excel. Differentially expressed genes were identified by a combination of 1-tail T test and foldchange ratio.

organism: Saccharomyces cerevisiae

source_name: Yeast cells

label_protocol: 200ng of Poly A+RNA were labelled, using Cyanine 3-CTP (Agilent) in separate labelling reactions, with the Agilent Low Imput Linear Amplification Kit and purified with Qiagen’s RNeasy mini spin columns.

growth_protocol: Yeast glycerol stocks are restreaked on fresh plates (YPD for L40 wild type and SD-Leu for 112A and 58F) and incubated at 30°C for 3d. A single CFU is disperdsed in 10mL liquid culture with appropriate medium and shaked at 240 rpm at 30°C overnight. Next day 1mL of culture is used to inoculate a larger culture of 50mL (using L40 or SD-Leu accordingly) and shaked at 240 rpm O/N at 30°C. Next day cultures are diluted in 50mL to OD600=0.2 in YPD and incubated O/N at 30°C with shaking 240 rpm. Next day yeast is centrifuged (5 min 3,000 xg) and total RNA is extracted.

extract_protocol: Yeast cell were collected for RNA extraction and microarray analysis. Total RNA was extracted  using Trizol (Invitrogen) and DNAse treated by Qiagen columns. Quality and integrity of each sample was checked using the Agilent BioAnalyzer 2100 (Agilent RNA 6000 nano kit): samples with a RNA Integrity Number (RIN) index lower than 8.0 were discarded. All the experimental steps involving the labelling, hybridization and washing of the samples were done following the one-color Agilent protocol.

treatment_protocol: Yeast samples are stably transfected with different intrabodies (58F= anti-acetyl-K9-H3; 112A= anti-acetyl-Integrase, control) or no intrabody (L40 wild type)

tag: tissue

value: Yeast cells

tag: strain

value: wildtype


title: 3 Rates C2

description: Biologocial replicate 2 of 2


title: Yeast_wildtype_3

tag: treatment


title: Yeast_wildtype_2


title: Yeast_express_ScFv_58F_4

value: Stable expression of ScFv-58F anti-acetylated H3 Histone intrabody


title: Yeast_express_ScFv_58F_3


title: Yeast_express_ScFv_112A_3

value: Stable expression of ScFv-112A anti-HIV1 acetylated Integrase intrabody


title: Yeast_wildtype_4


title: Yeast_express_ScFv_112A_4


title: Yeast_express_ScFv_112A_1


title: Yeast_express_ScFv_58F_1


title: fetalMG_3

city: Oxford

first: Sally

middle: A

last: Cowley

address: South Parks Road

department: Sir William Dunn School of Pathology

country: United Kingdom

institute: University of Oxford

description: single replicate

data_processing: Microarray data were pre-processed with the Bioconductor beadarray package (Dunning et al., 2007) using the neqc method to normalise expression levels within and between samples. Annotations were sourced from the Bioconductor illuminaHumanv4.db package: probes with an assigned quality of No match or lacking associated Entrez IDs (reannotated) were excluded from down-stream analysis. Following inspection of the data only the top two-thirds of probes (by maximum expression level) were retained for further analysis being considered to represent expressed genes.

label_protocol: Biotinylated cRNA were prepared as standard  for Illumina arrays, by Wellcome Trust Centre for Human Genomics, Oxford

extract_protocol: RNA was extracted using QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit and with on-column Dnase treatment. Quality control was performed with Agilent Bioanalyser and was RIN 10 for each sample.

treatment_protocol: Untreated cell samples, for details of culture conditions see manuscript.

tag: gender

value: undetermined

tag: culture conditions

value: DMEM + 5% FBS


title: fetalMG_2

description: single replicate


title: fetalMG_1

description: single replicate


title: Yeast_express_ScFv_112A_2


title: iMGL_3

description: single replicate

source_name: SFC856-03-04 iPSC-derived microglia-like cells

value: female

value: DMEM/F12 + N2 +100 ng/ml IL-34 + 10 ng/ml GM-CSF


title: co-iMG_1

description: single replicate

source_name: SFC180-01-01 iPSC-derived microglia extracted from co-culture with SBAD3-01 iPSC-derived cortical neurons

value: DMEM/F12 + N2 +100 ng/ml IL-34 + 10 ng/ml GM-CSF and co-culture with SBAD3-01 iPSC-cortical neurons


title: iMGL_2

description: single replicate

source_name: SFC840-03-03 iPSC-derived microglia-like cells


title: iMac_3

description: single replicate

source_name: SFC856-03-04 iPSC-derived macrophages

value: XVIVO15 + 100ng/ml M-CSF


title: iMGL_1

description: single replicate

source_name: SFC180-01-01 iPSC-derived microglia-like cells


title: iMono_3

description: single replicate

source_name: SFC856-03-04 iPSC-derived monocytes

value: XVIVO15 +25ng/ml IL3 + 100ng/ml M-CSF


title: iMac_1

description: single replicate

source_name: SFC180-01-01 iPSC-derived macrophages


title: iMono_1

description: single replicate

source_name: SFC180-01-01 iPSC-derived monocytes


title: co-iMG_2

description: single replicate

source_name: SFC840-03-03 iPSC-derived microglia extracted from co-culture with SBAD3-01 iPSC-derived cortical neurons


title: iMono_2

description: single replicate

source_name: SFC840-03-03 iPSC-derived monocytes


title: bloodMono_1

description: single replicate

value: male

value: extracted from PBMCs with CD14 MACS beads


title: bloodMono_3

description: single replicate


title: iMac_2

description: single replicate

source_name: SFC840-03-03 iPSC-derived macrophages


title: co-iMG_3

description: single replicate

source_name: SFC856-03-04 iPSC-derived microglia extracted from co-culture with SBAD3-01 iPSC-derived cortical neurons


title: bloodMono_2

description: single replicate


title: #33-SU042T-5

first: Andrew

last: Gentles

address: 1201 Welch Road

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to Infinium Methylation 450 arrays using standard Illumina protocol

scan_protocol: Arrays were scanned using recommened Illumina settings

data_processing: Beta values were calculated with Minfi v 1.12.0 (Aryee et al 2014)

label: Cy3 and Cy5

source_name: Undiff T-cell iPS_SU042

label_protocol: Standard Ilumina protocol

extract_protocol: Genomic DNA was isolated from the indicated populations using standard protocols (Qiagen Inc)

tag: sample  group

value: Undiff T-cell iPS

tag: subject


title: #28-WT3 iPSC

source_name: Undiff iPS line_WT3 cell line

value: Undiff iPS line

value: WT3 cell line


title: #36-SU223T-6

source_name: Undiff T-cell iPS_SU223


title: #34-SU223T-4


title: #26-H7 ES

source_name: Undiff ES line_H7 cell line

value: Undiff ES line

value: H7 cell line


title: Yeast_express_ScFv_58F_2

source_name: Yeast cells

value: Yeast cells

tag: genotype/variation


title: #16-SU042-4 Ms952

source_name: Engrafted diff iPS from AML_SU042

value: Engrafted diff iPS from AML


title: #14-SU042-2 Ms954


title: #30-TKDA3-4 iPSC

source_name: Undiff iPS line_TKDA3 cell line

value: TKDA3 cell line


title: #10-SU042-2

source_name: Undiff iPS from AML_SU042

value: Undiff iPS from AML


title: #21-SU223-A7 Ms006

source_name: Engrafted diff iPS from AML_SU223


title: #25-SU223-B3 Ms2


title: #24-SU223-B3 Ms008


title: #35-SU223T-5


title: #27-H1 ES

source_name: Undiff ES line_H1 cell line

value: H1 cell line


title: #13-SU042-2 Ms950


title: #15-SU042-4 Ms5


title: #19-SU223-A7

source_name: Undiff iPS from AML_SU223


title: #12-SU042-2 Ms3


title: #20-SU223-B3


title: #18-SU042-4 Ms4


title: #29-JMC1 iPSC

source_name: Undiff iPS line_JMC1 cell line

value: JMC1 cell line


title: #32-SU042T-4


title: #23-SU223-A7 Ms5


title: #11-SU042-4


title: #8-SU223 AML Ms4

source_name: Engrafted primary AML_SU223

value: Engrafted primary AML


title: #31-SU042T-2


title: #22-SU223-A7 Ms1


title: #17-SU042-4 Ms3


title: #9-SU223 AML Ms3


title: Bach2_KO_IL-2_(+)

city: Toon-shi

first: Makoto

last: Kuwahara

state: Ehime

address: Shitsukawa

department: Department of Immunology

country: Japan

institute: Graduate School of Medicine, Ehime University

hyb_protocol: Hybridization and washing were done according to Agilent One-Color Gene Expression protocol

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (G2565CA) using one color scan setting

data_processing: Raw signal intensities were extracted with Agilent Feature Extraction Software v10.7 using default parameters (protocol GE1-107_Sep09). The dataset was normalized using the 75 percentile median shift method.

source_name: Bach2 KO Th cells re-stimulated with immobilized anti-TCR-β mAb

label_protocol: 500 ng of total RNA was amplified and labeled using the One-Color Agilent Quick Amp Labeling kit

growth_protocol: Bach2 WT and Bach2 KO (Bach2flox/flox × CD4-Cre TG) naïve CD4 T (CD44lowCD62LhighCD25negative) cells were prepared using a CD4+CD62L+ T cell isolation kit II (Miltenyi Biotec).  Naïve CD4 T cells were stimulated with immobilized anti-TCR-β mAb (3 μg ml-1, H57-597; BioLegend) and an anti-CD28 mAb (1 μg ml-1, 37.5; BioLegend) for two days under the conditions indicated.  Next, the cells were transferred to a new plate and cultured for an additional three days in the presence of cytokines.  Th cells were re-stimulated with immobilized anti-TCR-β mAb for four hours in the absence of exogenous IL-2.  The cytokine conditions were as follows: IL-2 conditions (Th), IL-2 (2.5 ng ml-1)

extract_protocol: Total RNA was isolated with TRIZOL regent (invitrogen)

tag: strain background

value: Bach2 KO

value: female

value: spleen

tag: cell type

value: Primary naïve CD4 T cells


title: P009088-19032014-TB-01 [Whole blood]

status: Public on Nov 13 2016

city: Edinburgh

first: Nichols

last: Ventham

address: Western General Hospital

department: CGEM

institute: Univerisity of Edinburgh

description: sample

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

scan_protocol: HiScan H166

data_processing:
Data were processed using the lumi, methylumi and minfi packages in R (R Foundation for Statistical Computing, Vienna). Probes were filtered out if the detection p value of 0.01 or if >5% of probes failed. Probes containing single nucleotide polymorphisms (SNPs) with a minor allele frequency of 0.01 in the European population in the 1000 Genomes Project were also removed. Samples with >5% of probes failing and those failing a sex check (based on X chromosome methylation level) were also removed.The processed data matrix (ProcessedMethWb.txt) represents beta values following background adjustment and correction for dye colour bias. For the final analysis in the published paper additional whole blood DNA samples were added from GSE87640.
Whole blood DNA methylation samples were processed separately using the lumi, methylumi and minfi packages in R (R Foundation for Statistical Computing, Vienna). Probes were filtered out if the detection p value of 0.01 or if >5% of probes failed. Probes containing single nucleotide polymorphisms (SNPs) with a minor allele frequency of 0.01 in the European population in the 1000 Genomes Project were also removed. Samples with >5% of probes failing and those failing a sex check (based on X chromosome methylation level) were also removed. Probes were background adjusted, corrected from dye colour bias, and quantile normalised.  Whole blood samples from two datasets were combined at this stage. Subsequently, intra-array and probe design variation was corrected for using beta-mixture quantile dilatation (BMIQ) and inter-array batch effects were corrected for using ComBat. The data matrix can be found on the SuperSeries GSE87650 record.

label: Cy5 and Cy3

source_name: Whole blood

label_protocol: DNA was bisulphite converted using the EZ-96 DNA Methylation kit (Zymo Research, Irving CA). Standard Illumina Protocol

extract_protocol: DNA was extracted using the QIAGEN Allprep kit according to instructions

value: Whole blood

tag: Sex

value: F

tag: smoking status

value: Ex

value: UC

tag: age


title: 0006HC [Whole blood]

description: sample

value: M

value: Current

value: HL


title: 0196HC [Whole blood]

description: sample

value: Never


title: P007853-30052012-TB-S001 [Whole blood]

description: sample


title: P008819-25022013-TB-01 [Whole blood]

description: sample

value: CD


title: P008776-18012013-TB-01 [Whole blood]

description: sample


title: P009050-10012014-TB-01R3 [Whole blood]

description: replicate


title: P009094-24032014-TB-01 [Whole blood]

description: sample

value: HS


title: AhRCA_Epidermis_Neonate_replicate2

city: Sendai

first: Eri

middle: H

last: Kobayashi

state: Miyagi

address: 2-1 Seiryo-machi, Aobaku

department: Medical Biochemistry

institute: Tohoku University Graduate School of Medicine

description: Gene expression in AhRCA epidermis at postnatal day 0, replicate2

hyb_protocol: Cy3-labeled cRNA were mixed and fragmented using the Agilent In Situ Hybridization Kit protocol. Hybridizations were performed for 16 hours according to the Agilent 60-mer oligo microarray processing protocol prior to washing.

scan_protocol: Slides were scanned with an Agilent DNA Microarray Scanner.

data_processing: The data were normalized by percentile shift, using GeneSpring GX software (Silicon Genetics).

source_name: AhRCA, Epidermis, Neonate, replicate2

label_protocol: RNA samples were labeled with Cy3 using the Quick Amp Labeling kit (Agilent) according to the manufacturer's protocol.

extract_protocol: Total RNA was extracted from epidermis using RNeasy Micro kit (Qiagen).

value: AhRCA

value: epidermis

value: mix

value: postnatal day 0


title: P008894-05062013-TB-01 [Whole blood]

description: sample


title: 2094CD [Whole blood]

description: sample


title: #7-SU223 AML Ms5

city: Stanford

institute: Stanford University

value: Engrafted primary AML


title: 0169HC [Whole blood]

description: sample


title: P008785-28012013-TB-01 [Whole blood]

description: sample


title: #5-SU042 AML Ms2

source_name: Engrafted primary AML_SU042


title: P009122-21052014-TB-01 [Whole blood]

description: sample


title: Bach2_KO_IL-2_(-)

source_name: Bach2 KO Th cells

value: Bach2 KO

value: female

value: spleen


title: Bach2_WT_IL-2_(-)

source_name: Bach2 WT Th cells

value: Bach2 WT

value: Primary naïve CD4 T cells


title: AhRCA_Epidermis_Neonate_replicate1

description: Gene expression in AhRCA epidermis at postnatal day 0, replicate1

source_name: AhRCA, Epidermis, Neonate, replicate1


title: WT_Epidermis_Neonate_replicate2

description: Gene expression in wild-type epidermis at postnatal day 0, replicate2

source_name: WT, Epidermis, Neonate, replicate2

value: wild type


title: WT_Epidermis_Neonate_replicate1

description: Gene expression in wild-type epidermis at postnatal day 0, replicate1

source_name: WT, Epidermis, Neonate, replicate1


title: AhRCA_Epidermis_Neonate_replicate3

description: Gene expression in AhRCA epidermis at postnatal day 0, replicate3

source_name: AhRCA, Epidermis, Neonate, replicate3


title: Bach2_WT_IL-2_(+)

source_name: Bach2 WT Th cells re-stimulated with immobilized anti-TCR-β mAb


title: WT_Epidermis_Neonate_replicate3

description: Gene expression in wild-type epidermis at postnatal day 0, replicate3

source_name: WT, Epidermis, Neonate, replicate3


title: P008803-12022013-TB-01 [Whole blood]

description: sample

value: Whole blood

value: M


title: P008459-03102011-TB-S001 [Whole blood]

description: sample

value: F


title: 0693UC [Whole blood]

description: sample

value: Never

value: UC


title: 0270HC [Whole blood]

description: sample

value: Current

value: HL


title: P008904-19062013-TB-01 [Whole blood]

description: sample

value: CD


title: 0202HC [Whole blood]

description: sample

value: Ex


title: P009080-05032014-TB-01 [Whole blood]

description: sample


title: P008988-10102013-TB-01 [Whole blood]

description: sample


title: #3-SU042 AML Ms3


title: P008615-20022012-TB-S001 [Whole blood]

description: sample

value: HS


title: 803 [Whole blood]

description: sample


title: #6-SU042 AML Ms4

value: Engrafted primary AML


title: P009026-04122013-TB-01 [Whole blood]

description: sample


title: P008864-17042013-TB-01 [Whole blood]

description: sample


title: P008740-21112012-TB-S01 [Whole blood]

description: sample


title: #2-SU223 AML

source_name: Primary AML_SU223

value: Primary AML


title: 0165HC [Whole blood]

description: sample


title: P008857-08042013-TB-01 [Whole blood]

description: sample


title: P009075-26022014-TB-01 [Whole blood]

description: sample


title: 0217HC [Whole blood]

description: sample


title: 2205UC [Whole blood]

description: sample


title: P009103-02042014-TB-01 [Whole blood]

description: sample


title: 2066UC [Whole blood]

description: sample


title: P008464-08112011-TB-S001 [Whole blood]

description: sample


title: P008507-11012012-TB-S001 [Whole blood]

description: sample


title: P008652-05072012-TB-S001 [Whole blood]

description: sample

value: Don't know


title: #1-SU042 AML

source_name: Primary AML_SU042


title: P008795-04022013-TB-01 [Whole blood]

description: sample


title: P009166-14082014-TB-01 [Whole blood]

description: sample


title: 0144HC [Whole blood]

description: sample


title: P009002-01112013-TB-01 [Whole blood]

description: sample


title: 572 [Whole blood]

description: sample


title: P009104-07042014-TB-01 [Whole blood]

description: sample


title: P008616-21022012-TB-S001 [Whole blood]

description: sample


title: 0201HC [Whole blood]

description: sample


title: 0238HC [Whole blood]

description: sample


title: 0108HC [Whole blood]

description: sample


title: P008951-02092013-TB-01 [Whole blood]

description: sample


title: P009161-06082014-TB-01 [Whole blood]

description: sample


title: #4-SU042 AML Ms1


title: P008786-28012013-TB-01 [Whole blood]

description: sample


title: 0057HC [Whole blood]

description: sample


title: 588 [Whole blood]

description: sample


title: P009120-16052014-TB-01 [Whole blood]

description: sample


title: P008513-17012012-TB-S001 [Whole blood]

description: sample


title: P008772-16012013-TB-01 [Whole blood]

description: sample


title: P008638-09052012-TB-S001 [Whole blood]

description: sample


title: P008738-16112012-TB-S01 [Whole blood]

description: sample


title: P009024-04122013-TB-01 [Whole blood]

description: sample


title: P009117-07052014-TB-01 [Whole blood]

description: sample


title: P008910-03072013-TB-01 [Whole blood]

description: sample


title: P009048-08012014-TB-01 [Whole blood]

description: sample


title: P008982-08102013-TB-01 [Whole blood]

description: sample


title: 2157UC [Whole blood]

description: sample


title: 0130HC [Whole blood]

description: sample


title: P008668-02082012-TB-S001 [Whole blood]

description: sample


title: P008790-30012013-TB-01 [Whole blood]

description: sample


title: 0074HC [Whole blood]

description: sample


title: P008496-19122011-TB-S001 [Whole blood]

description: sample


title: 0524UC [Whole blood]

description: sample


title: 2095CD [Whole blood]

description: sample


title: P009022-02122013-TB-01 [Whole blood]

description: sample


title: 618 [Whole blood]

description: sample


title: P008811-19022013-TB-01 [Whole blood]

description: sample


title: P008625-05032012-TB-S001 [Whole blood]

description: sample


title: 974 [Whole blood]

description: sample


title: P009108-23042014-TB-01 [Whole blood]

description: sample


title: P009084-17032014-TB-01 [Whole blood]

description: sample


title: 0013HC [Whole blood]

description: sample


title: P008470-23112011-TB-S001 [Whole blood]

description: sample


title: P008424-19072011-TB-S001 [Whole blood]

description: sample


title: 2153UC [Whole blood]

description: sample


title: 0115HC [Whole blood]

description: sample


title: P007843-30052012-TB-S001 [Whole blood]

description: sample


title: 0193HC [Whole blood]

description: sample


title: P008481-05122011-TB-S001 [Whole blood]

description: sample


title: P008794-04022013-TB-01 [Whole blood]

description: sample


title: P009133-07062014-TB-01 [Whole blood]

description: sample


title: P008674-12092012-TB-S01 [Whole blood]

description: sample


title: P009118-14052014-TB-01 [Whole blood]

description: sample


title: P009041-18122013-TB-01 [Whole blood]

description: sample


title: P009162-06082014-TB-01 [Whole blood]

description: sample


title: P008817-20022013-TB-01 [Whole blood]

description: sample


title: 0157HC [Whole blood]

description: sample


title: P008928-08082013-TB-01 [Whole blood]

description: sample


title: P008965-17092013-TB-01 [Whole blood]

description: sample


title: P008663-26062012-TB-S001 [Whole blood]

description: sample


title: 0034HC [Whole blood]

description: sample


title: P009059-22012014-TB-01 [Whole blood]

description: sample


title: 0481UC [Whole blood]

description: sample


title: 0309HC [Whole blood]

description: sample


title: 0611CD [Whole blood]

description: sample


title: P009050-10012014-TB-01R2 [Whole blood]

description: replicate


title: P008980-07102013-TB-01 [Whole blood]

description: sample


title: P009010-11112013-TB-01 [Whole blood]

description: sample


title: 0308HC [Whole blood]

description: sample


title: P009070-12022014-TB-01 [Whole blood]

description: sample


title: 0036HC [Whole blood]

description: sample


title: P008808-18022013-TB-01 [Whole blood]

description: sample


title: P007968-10052012-TB-S001 [Whole blood]

description: sample


title: P009007-07112013-TB-02 [Whole blood]

description: sample


title: P009111-28042014-TB-01 [Whole blood]

description: sample


title: 0830UC [Whole blood]

description: sample


title: P009124-26052014-TB-01 [Whole blood]

description: sample


title: P008627-06032012-TB-S001 [Whole blood]

description: sample


title: P009134-07062014-TB-01 [Whole blood]

description: sample


title: P009100-26032014-TB-01 [Whole blood]

description: sample


title: P008997-21102013-TB-01 [Whole blood]

description: sample


title: 0792CD [Whole blood]

description: sample


title: P008986-09102013-TB-01 [Whole blood]

description: sample


title: P009157-25072014-TB-01 [Whole blood]

description: sample


title: 0605CD [Whole blood]

description: sample


title: P008503-09012012-TB-S001 [Whole blood]

description: sample


title: 851 [Whole blood]

description: sample


title: P008836-13032013-TB-01 [Whole blood]

description: sample


title: P009121-19052014-TB-01 [Whole blood]

description: sample


title: P009139-20062014-TB-01 [Whole blood]

description: sample


title: 0762CD [Whole blood]

description: sample


title: 0149HC [Whole blood]

description: sample


title: 0134HC [Whole blood]

description: sample


title: P008932-19082013-TB-01 [Whole blood]

description: sample


title: 0315HC [Whole blood]

description: sample


title: 0194HC [Whole blood]

description: sample


title: 0113HC [Whole blood]

description: sample


title: 0786UC [Whole blood]

description: sample


title: 0314HC [Whole blood]

description: sample


title: P008467-21112011-TB-S001 [Whole blood]

description: sample


title: P008962-11092013-TB-01 [Whole blood]

description: sample


title: 0607CD [Whole blood]

description: sample


title: P009164-13082014-TB-01 [Whole blood]

description: sample


title: P008890-29052013-TB-01 [Whole blood]

description: sample


title: P008510-16012012-TB-S001 [Whole blood]

description: sample


title: 0281HC [Whole blood]

description: sample


title: 0173HC [Whole blood]

description: sample


title: P008621-28022012-TB-S001 [Whole blood]

description: sample


title: P009066-05022014-TB-01 [Whole blood]

description: sample


title: P008878-15052013-TB-01 [Whole blood]

description: sample


title: P009140-23062014-TB-01 [Whole blood]

description: sample


title: 0143HC [Whole blood]

description: sample


title: P009085-17032014-TB-01 [Whole blood]

description: sample


title: 0150HC [Whole blood]

description: sample


title: P008511-16012012-TB-S001 [Whole blood]

description: sample


title: P008820-25022013-TB-01 [Whole blood]

description: sample


title: 2142CD [Whole blood]

description: sample


title: P009178-03092014-TB-01 [Whole blood]

description: sample


title: P008843-19032013-TB-01 [Whole blood]

description: sample


title: P009071-12022014-TB-01 [Whole blood]

description: sample


title: P009095-24032014-TB-01 [Whole blood]

description: sample


title: P009001-30102013-TB-01 [Whole blood]

description: sample


title: 0867UC [Whole blood]

description: sample


title: P008637-02052012-TB-S001 [Whole blood]

description: sample


title: 0068H [Whole blood]

description: sample


title: P009180-05092014-TB-01 [Whole blood]

description: sample


title: P008508-11012012-TB-S001 [Whole blood]

description: sample


title: 0625UC [Whole blood]

description: sample


title: P008646-26062012-TB-S001 [Whole blood]

description: sample


title: 0170HC [Whole blood]

description: sample


title: 0076HC [Whole blood]

description: sample


title: P009072-12022014-TB-01 [Whole blood]

description: sample


title: 0688CD [Whole blood]

description: sample


title: P009116-30042014-TB-01 [Whole blood]

description: sample


title: P008800-06022013-TB-01 [Whole blood]

description: sample


title: 0271HC [Whole blood]

description: sample


title: P008792-30012013-TB-01 [Whole blood]

description: sample


title: P009171-22082014-TB-01 [Whole blood]

description: sample


title: P008624-05032012-TB-S001 [Whole blood]

description: sample


title: P009106-16042014-TB-01 [Whole blood]

description: sample


title: P008514-18012012-TB-S001 [Whole blood]

description: sample


title: P008780-23012013-TB-01 [Whole blood]

description: sample


title: P008842-19032013-TB-01 [Whole blood]

description: sample


title: P008465-16112011-TB-S001 [Whole blood]

description: sample


title: P008848-25032013-TB-01 [Whole blood]

description: sample


title: P008802-06022013-TB-01 [Whole blood]

description: sample


title: 2115UC [Whole blood]

description: sample


title: 958 [Whole blood]

description: sample


title: P008673-12092012-TB-S01 [Whole blood]

description: sample


title: P008892-05062013-TB-01 [Whole blood]

description: sample


title: 0046HC [Whole blood]

description: sample


title: P008950-29082013-TB-01 [Whole blood]

description: sample


title: 0910UC [Whole blood]

description: sample


title: 0827UC [Whole blood]

description: sample


title: 592 [Whole blood]

description: sample


title: P009129-07062014-TB-01 [Whole blood]

description: sample


title: 0740UC [Whole blood]

description: sample


title: P009023-04122013-TB-01 [Whole blood]

description: sample


title: P008989-14102013-TB-01 [Whole blood]

description: sample


title: P008500-04012012-TB-S001 [Whole blood]

description: sample


title: 0225HC [Whole blood]

description: sample


title: 0148HC [Whole blood]

description: sample


title: P009141-23062014-TB-01 [Whole blood]

description: sample


title: 0017HC [Whole blood]

description: sample


title: 606 [Whole blood]

description: sample


title: 0084HC [Whole blood]

description: sample


title: 0307HC [Whole blood]

description: sample


title: P008827-04032013-TB-01 [Whole blood]

description: sample


title: P008469-21112011-TB-S001 [Whole blood]

description: sample


title: P009050-10012014-TB-01R1 [Whole blood]

description: replicate


title: P008807-13022013-TB-01 [Whole blood]

description: sample


title: P008466-21112011-TB-S001 [Whole blood]

description: sample


title: P008996-18102013-TB-01 [Whole blood]

description: sample


title: 0770CD [Whole blood]

description: sample


title: P008933-19082013-TB-01 [Whole blood]

description: sample


title: P008722-25102012-TB-S01 [Whole blood]

description: sample


title: P008488-12122011-TB-S001 [Whole blood]

description: sample


title: 0799UC [Whole blood]

description: sample


title: 0310HC [Whole blood]

description: sample


title: 0158HC [Whole blood]

description: sample


title: P009158-25072014-TB-02 [Whole blood]

description: sample


title: 0474CD [Whole blood]

description: sample


title: P008814-20022013-TB-01 [Whole blood]

description: sample


title: 491 [Whole blood]

description: sample


title: P009006-16122013-TB-01 [Whole blood]

description: sample


title: P009115-30042014-TB-01 [Whole blood]

description: sample


title: 0167HC [Whole blood]

description: sample


title: 0577UC [Whole blood]

description: sample


title: 0841UC [Whole blood]

description: sample


title: 0725CD [Whole blood]

description: sample


title: P008484-06122011-TB-S001 [Whole blood]

description: sample


title: P008844-19032013-TB-01 [Whole blood]

description: sample


title: P008837-14032013-TB-01 [Whole blood]

description: sample


title: 0141HC [Whole blood]

description: sample


title: P009020-02122013-TB-01 [Whole blood]

description: sample


title: P008454-30092011-TB-S001 [Whole blood]

description: sample


title: 2062UC [Whole blood]

description: sample


title: P009036-16122013-TB-01 [Whole blood]

description: sample


title: P009110-24042014-TB-01 [Whole blood]

description: sample


title: P009091-20032014-TB-01 [Whole blood]

description: sample


title: P008804-12022013-TB-01 [Whole blood]

description: sample


title: 0120H [Whole blood]

description: sample


title: P009145-27062014-TB-01 [Whole blood]

description: sample


title: 0229HC [Whole blood]

description: sample


title: P008977-02102013-TB-01 [Whole blood]

description: sample


title: 0140HC [Whole blood]

description: sample


title: P008832-11032013-TB-01 [Whole blood]

description: sample


title: P007860-30052012-TB-S001 [Whole blood]

description: sample


title: P009112-28042014-TB-01 [Whole blood]

description: sample


title: P008640-10052012-TB-S001 [Whole blood]

description: sample


title: 2090CD [Whole blood]

description: sample


title: P008861-11042013-TB-01 [Whole blood]

description: sample


title: 0190HC [Whole blood]

description: sample


title: 0912UC [Whole blood]

description: sample


title: P008613-20022012-TB-S001 [Whole blood]

description: sample


title: P008920-24072013-TB-01 [Whole blood]

description: sample


title: P009000-30102013-TB-01 [Whole blood]

description: sample


title: P008901-19062013-TB-01 [Whole blood]

description: sample


title: P008778-23012013-TB-01 [Whole blood]

description: sample


title: 0097HC [Whole blood]

description: sample


title: P008678-16102012-TB-S01 [Whole blood]

description: sample


title: P008838-18032013-TB-01 [Whole blood]

description: sample


title: 0703UC [Whole blood]

description: sample


title: 0160HC [Whole blood]

description: sample


title: P008671-08082012-TB-S01 [Whole blood]

description: sample


title: 0078HC [Whole blood]

description: sample


title: P008609-18022012-TB-S001 [Whole blood]

description: sample


title: P008839-18032013-TB-01 [Whole blood]

description: sample


title: 552 [Whole blood]

description: sample


title: P008952-02092013-TB-01 [Whole blood]

description: sample


title: 0316HC [Whole blood]

description: sample


title: 583 [Whole blood]

description: sample


title: P008967-18092013-TB-01 [Whole blood]

description: sample


title: P009144-25062014-TB-01 [Whole blood]

description: sample


title: 0814UC [Whole blood]

description: sample


title: 0052HC [Whole blood]

description: sample


title: P009175-27082014-TB-01 [Whole blood]

description: sample


title: 811 [Whole blood]

description: sample


title: 0071HC [Whole blood]

description: sample


title: 0266H [Whole blood]

description: sample


title: P009188-24092014-TB-01 [Whole blood]

description: sample


title: P008485-06122011-TB-S001 [Whole blood]

description: sample


title: 0943UC [Whole blood]

description: sample


title: P009097-25032014-TB-01 [Whole blood]

description: sample


title: P009183-10092014-TB-01 [Whole blood]

description: sample


title: 0312HC [Whole blood]

description: sample


title: 0941UC [Whole blood]

description: sample


title: 0880UC [Whole blood]

description: sample


title: 0146HC [Whole blood]

description: sample


title: 0216HC [Whole blood]

description: sample


title: 0269H [Whole blood]

description: sample


title: P008425-19072011-TB-S001 [Whole blood]

description: sample


title: P009181-08092014-TB-01 [Whole blood]

description: sample


title: 0243HC [Whole blood]

description: sample


title: P008939-22082013-TB-01 [Whole blood]

description: sample


title: 0642CD [Whole blood]

description: sample


title: 444 [Whole blood]

description: sample


title: P009170-20082014-TB-01 [Whole blood]

description: sample


title: 0010HC [Whole blood]

description: sample


title: P008499-04012012-TB-S001 [Whole blood]

description: sample


title: P008636-02052012-TB-S001 [Whole blood]

description: sample


title: 0757UC [Whole blood]

description: sample


title: 2217UC [Whole blood]

description: sample


title: 2130CD [Whole blood]

description: sample


title: P008458-03102011-TB-S001 [Whole blood]

description: sample


title: 0529CD [Whole blood]

description: sample


title: 0177HC [Whole blood]

description: sample


title: P008775-18012013-TB-01 [Whole blood]

description: sample


title: 0195H [Whole blood]

description: sample


title: P009017-20112013-TB-01 [Whole blood]

description: sample


title: P008810-19022013-TB-01 [Whole blood]

description: sample


title: P009113-28042014-TB-01 [Whole blood]

description: sample


title: P008736-07112012-TB-S01 [Whole blood]

description: sample


title: P009153-09072014-TB-01 [Whole blood]

description: sample


title: P008423-13072011-TB-S001 [Whole blood]

description: sample


title: P008617-28022012-TB-S001 [Whole blood]

description: sample


title: 2214UC [Whole blood]

description: sample


title: P008987-10102013-TB-01 [Whole blood]

description: sample


title: P008826-04032013-TB-01 [Whole blood]

description: sample


title: 0220HC [Whole blood]

description: sample


title: P007101-09102012-TB-S01 [Whole blood]

description: sample


title: P008995-17102013-TB-01 [Whole blood]

description: sample


title: P009147-02072014-TB-01 [Whole blood]

description: sample


title: 0126HC [Whole blood]

description: sample


title: P009128-04062014-TB-01 [Whole blood]

description: sample


title: P008770-14012013-TB-01 [Whole blood]

description: sample


title: P008783-24012013-TB-01 [Whole blood]

description: sample


title: 2127CD [Whole blood]

description: sample


title: P008051-30052012-TB-S001 [Whole blood]

description: sample


title: P008919-22072013-TB-01 [Whole blood]

description: sample


title: P008863-17042013-TB-01 [Whole blood]

description: sample


title: 0125HC [Whole blood]

description: sample


title: 2156UC [Whole blood]

description: sample


title: P008813-20022013-TB-01 [Whole blood]

description: sample


title: 0168H [Whole blood]

description: sample


title: P008830-24042013-TB-01 [Whole blood]

description: sample


title: P008777-23012013-TB-01 [Whole blood]

description: sample


title: P008959-09092013-TB-01 [Whole blood]

description: sample


title: P009146-30062014-TB-01 [Whole blood]

description: sample


title: 0001HC [Whole blood]

description: sample


title: 0261HC [Whole blood]

description: sample


title: 0037HC [Whole blood]

description: sample


title: P008791-30012013-TB-01 [Whole blood]

description: sample


title: P009004-06112013-TB-02 [Whole blood]

description: sample


title: 0009HC [Whole blood]

description: sample


title: 441 [Whole blood]

description: sample


title: P008752-03122012-TB-S01 [Whole blood]

description: sample


title: 0153HC [Whole blood]

description: sample


title: 0601CD [Whole blood]

description: sample


title: P009189-24092014-TB-01 [Whole blood]

description: sample


title: P008935-19082013-TB-01 [Whole blood]

description: sample


title: P009138-17062014-TB-01 [Whole blood]

description: sample


title: 0633UC [Whole blood]

description: sample


title: 358 [Whole blood]

description: sample


title: P008516-20012012-TB-S001 [Whole blood]

description: sample


title: P009143-25062014-TB-01 [Whole blood]

description: sample


title: 983 [Whole blood]

description: sample


title: P008648-28062012-TB-S001 [Whole blood]

description: sample


title: P008979-07102013-TB-01 [Whole blood]

description: sample


title: 0028HC [Whole blood]

description: sample


title: P009123-23052014-TB-01 [Whole blood]

description: sample


title: P008434-22082011-TB-S001 [Whole blood]

description: sample


title: 576 [Whole blood]

description: sample


title: P008622-27022012-TB-S001 [Whole blood]

description: sample


title: 667 [Whole blood]

description: sample


title: 0069HC [Whole blood]

description: sample


title: 683 [Whole blood]

description: sample


title: P008797-06022013-TB-01 [Whole blood]

description: sample


title: P008941-26082013-TB-01 [Whole blood]

description: sample


title: 2096UC [Whole blood]

description: sample


title: P009102-02042014-TB-01 [Whole blood]

description: sample


title: Sample15

city: Ljubljana

first: Marija

last: Volk

address: slajmerjeva 003

department: Clinical institute of medical genetics

country: Slovenia

institute: UMC ljubljana

description:
For comparative microarray hybridization, a pooled RNA microarray design was employed, where RNA pool from all samples in the study was labelled with Cy3 and each sample was labelled separately with Cy5, after which both labelled population were co-hybridized on the array.
US11113888_251485061219_S01_GE2_107_Sep09_1_3.txt

hyb_protocol: Hybridization of labeled samples was performed according to manufacturer's instructions (Agilent Low Input Quick Amp Labeling protocol).

scan_protocol: Microarray slides were scanned using GenePix 4100A and Agilent G2565CA Microarray Scanner.

data_processing: Post-processing steps included intra-array loess and inter-array quantile normalization to correct for potential bias resulting from differential stability of cyanine dyes (Limma version 2.12 in Bioconductor 2.12 environment).

label_protocol: Labeling of RNA samples was performed according to manufacturer's instructions (Agilent Low Input Quick Amp Labeling protocol).

growth_protocol: Amniotic fluid samples were collected between 16th and 18th week of gestation for routine cytogenetic analysis. Primary cell cultures of amniotic fluid were performed according to standard protocols using tissue culture flasks (TPP, Switzerland). Cell cultures were grown in Amnio Max C100 Basal Medium and Amnio Max C100 Supplement (Invitrogen, CA, USA) at 37°C in 5% CO2 environment.

extract_protocol: Isolation of RNA from cultured amniocytes was performed using Fujifilm QuickGene-810 automated isolation system (Fujifilm Life Sciences, Tokyo, Japan), using columns in the Fujifilm RNA Cultured Cell kit to capture purified RNA samples. The purity and yield of isolated RNA samples was determined using NanoDrop 2000c spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA).

value: male

tag: aneuploidy condition

value: 16th-18th week of gestation

value: Amniotic fluid cells

tag: arrayslide

source_name: RNA pool from all samples in the study

value: Pooled common reference RNA sample


title: Sample17

description:
For comparative microarray hybridization, a pooled RNA microarray design was employed, where RNA pool from all samples in the study was labelled with Cy3 and each sample was labelled separately with Cy5, after which both labelled population were co-hybridized on the array.
US11113888_251485061220_S01_GE2_107_Sep09_1_1.txt

value: female

value: Euploid

tag: sample type


title: Sample18

description:
For comparative microarray hybridization, a pooled RNA microarray design was employed, where RNA pool from all samples in the study was labelled with Cy3 and each sample was labelled separately with Cy5, after which both labelled population were co-hybridized on the array.
US11113888_251485061220_S01_GE2_107_Sep09_1_2.txt


title: 0586CD [Whole blood]

description: sample

value: Whole blood

value: F


title: Sample16

description:
For comparative microarray hybridization, a pooled RNA microarray design was employed, where RNA pool from all samples in the study was labelled with Cy3 and each sample was labelled separately with Cy5, after which both labelled population were co-hybridized on the array.
US11113888_251485061219_S01_GE2_107_Sep09_1_4.txt


title: 0131HC [Whole blood]

description: sample

value: M


title: Sample9

description:
For comparative microarray hybridization, a pooled RNA microarray design was employed, where RNA pool from all samples in the study was labelled with Cy3 and each sample was labelled separately with Cy5, after which both labelled population were co-hybridized on the array.
US11113888_251485061218_S01_GE2_107_Sep09_1_1.txt


title: Sample6

description:
For comparative microarray hybridization, a pooled RNA microarray design was employed, where RNA pool from all samples in the study was labelled with Cy3 and each sample was labelled separately with Cy5, after which both labelled population were co-hybridized on the array.
US11113888_251485061217_S01_GE2_107_Sep09_1_2.txt


title: P008798-06022013-TB-01 [Whole blood]

description: sample

value: Never


title: Sample14

description:
For comparative microarray hybridization, a pooled RNA microarray design was employed, where RNA pool from all samples in the study was labelled with Cy3 and each sample was labelled separately with Cy5, after which both labelled population were co-hybridized on the array.
US11113888_251485061219_S01_GE2_107_Sep09_1_2.txt


title: Sample11

description:
For comparative microarray hybridization, a pooled RNA microarray design was employed, where RNA pool from all samples in the study was labelled with Cy3 and each sample was labelled separately with Cy5, after which both labelled population were co-hybridized on the array.
US11113888_251485061218_S01_GE2_107_Sep09_1_3.txt


title: P009008-07112013-TB-01 [Whole blood]

description: sample

value: Current

value: UC


title: Sample8

description:
For comparative microarray hybridization, a pooled RNA microarray design was employed, where RNA pool from all samples in the study was labelled with Cy3 and each sample was labelled separately with Cy5, after which both labelled population were co-hybridized on the array.
US11113888_251485061217_S01_GE2_107_Sep09_1_4.txt


title: 0026H [Whole blood]

description: sample

value: HL


title: Sample2

description:
For comparative microarray hybridization, a pooled RNA microarray design was employed, where RNA pool from all samples in the study was labelled with Cy3 and each sample was labelled separately with Cy5, after which both labelled population were co-hybridized on the array.
US11113888_251485061216_S01_GE2_107_Sep09_1_2.txt


title: Sample7

description:
For comparative microarray hybridization, a pooled RNA microarray design was employed, where RNA pool from all samples in the study was labelled with Cy3 and each sample was labelled separately with Cy5, after which both labelled population were co-hybridized on the array.
US11113888_251485061217_S01_GE2_107_Sep09_1_3.txt


title: Sample12

description:
For comparative microarray hybridization, a pooled RNA microarray design was employed, where RNA pool from all samples in the study was labelled with Cy3 and each sample was labelled separately with Cy5, after which both labelled population were co-hybridized on the array.
US11113888_251485061218_S01_GE2_107_Sep09_1_4.txt


title: Sample4

description:
For comparative microarray hybridization, a pooled RNA microarray design was employed, where RNA pool from all samples in the study was labelled with Cy3 and each sample was labelled separately with Cy5, after which both labelled population were co-hybridized on the array.
US11113888_251485061216_S01_GE2_107_Sep09_1_4.txt


title: P009050-10012014-TB-01 [Whole blood]

description: sample


title: Sample1

description:
For comparative microarray hybridization, a pooled RNA microarray design was employed, where RNA pool from all samples in the study was labelled with Cy3 and each sample was labelled separately with Cy5, after which both labelled population were co-hybridized on the array.
US11113888_251485061216_S01_GE2_107_Sep09_1_1.txt


title: Sample13

description:
For comparative microarray hybridization, a pooled RNA microarray design was employed, where RNA pool from all samples in the study was labelled with Cy3 and each sample was labelled separately with Cy5, after which both labelled population were co-hybridized on the array.
US11113888_251485061219_S01_GE2_107_Sep09_1_1.txt


title: Sample3

description:
For comparative microarray hybridization, a pooled RNA microarray design was employed, where RNA pool from all samples in the study was labelled with Cy3 and each sample was labelled separately with Cy5, after which both labelled population were co-hybridized on the array.
US11113888_251485061216_S01_GE2_107_Sep09_1_3.txt


title: Sample5

description:
For comparative microarray hybridization, a pooled RNA microarray design was employed, where RNA pool from all samples in the study was labelled with Cy3 and each sample was labelled separately with Cy5, after which both labelled population were co-hybridized on the array.
US11113888_251485061217_S01_GE2_107_Sep09_1_1.txt


title: Sample10

description:
For comparative microarray hybridization, a pooled RNA microarray design was employed, where RNA pool from all samples in the study was labelled with Cy3 and each sample was labelled separately with Cy5, after which both labelled population were co-hybridized on the array.
US11113888_251485061218_S01_GE2_107_Sep09_1_2.txt


title: P009090-19032014-TB-01 [Whole blood]

description: sample

value: Ex


title: 0050H [Whole blood]

description: sample


title: P008960-09092013-TB-01 [Whole blood]

description: sample

value: HS


title: P008743-22112012-TB-S01 [Whole blood]

description: sample


title: P008608-17022012-TB-S001 [Whole blood]

description: sample


title: 0835UC [Whole blood]

description: sample


title: P008937-21082013-TB-01 [Whole blood]

description: sample

value: CD


title: 0255HC [Whole blood]

description: sample


title: P008846-20032013-TB-01 [Whole blood]

description: sample


title: 2099CD [Whole blood]

description: sample


title: P008856-08042013-TB-01 [Whole blood]

description: sample


title: Sample19

description:
For comparative microarray hybridization, a pooled RNA microarray design was employed, where RNA pool from all samples in the study was labelled with Cy3 and each sample was labelled separately with Cy5, after which both labelled population were co-hybridized on the array.
US11113888_251485061220_S01_GE2_107_Sep09_1_3.txt


title: P009032.11122013.TTC8.01

description:
Sample 243
P009032.11122013.TTC8.01

hyb_protocol: Standard Illumina hybridization protocol,18 hour

scan_protocol: Standard Illumina scanning protocol,iScan NO660

data_processing: Data read into R using lumi, background adjusted, variance stabilzed and quantile normalized.

label_protocol: For the whole blood PAXgene samples (WB), sample concentration and cleanup was performed using the MinElute RNA cleanup kit (Qiagen), globin mRNA transcripts were depleted using GlobinClear (Ambion, Life Technologies USA). All RNA was subsequently amplified and biotylated using the Illumina® TotalPrep™ RNA Amplification Kit (Ambion, Life Technology).

extract_protocol: Separated cell RNA was extracted using the Allprep DNA/RNA miRNA universal kit (Qiagen). Whole blood RNA was extracted from PAXgene tubes using the PAXgene blood miRNA kit (PreAnalytix®, Switzerland). The RNA was quantified and assessed for quality using the Agilent BioAnalyzer with only samples with a RNA-integrity number of >7 being used for downstream analyses.

tag: disease state (diagnosisfull)

value: UC (Ulcerative colitis)

tag: disease state (simplediagnosis)

tag: scandate

tag: samplenumber

tag: sentrixbarcode

tag: samplesection

value: C


title: X9111.PAX.GC

description:
Sample 252
X9111.PAX.GC

source_name: WB

value: IB (IBS)

value: HC

value: WB

value: L


title: P009005.06112013.TTC14.01

description:
Sample 242
P009005.06112013.TTC14.01

value: CD (Crohn's disease)

value: B


title: X8928.PAX.GC

description:
Sample 248
X8928.PAX.GC

value: H


title: P008983.08102013.TTC14.01

description:
Sample 246
P008983.08102013.TTC14.01

value: M

value: HL (Healthy control (Lab volunteer))

value: F


title: X9004.PAX.GC

description:
Sample 251
X9004.PAX.GC

value: HF (Healthy control with FHx)

value: Never

value: K


title: P009034.16122013.TTC8.01

description:
Sample 245
P009034.16122013.TTC8.01

value: Ex

value: UC

value: E


title: X8996.PAX.GC

description:
Sample 249
X8996.PAX.GC

value: I


title: P009011.13112013.TTCgP.01

description:
Sample 241
P009011.13112013.TTCgP.01

value: IB (IBS)

value: Current

value: A


title: P009030.09122013.TTC4.01

description:
Sample 244
P009030.09122013.TTC4.01

value: HC

value: D


title: P008975-02102013-TDM-01

description: sample

data_processing:
Data were processed using the lumi, methylumi and minfi packages in R (R Foundation for Statistical Computing, Vienna). Probes were filtered out if the detection p value of 0.01 or if >5% of probes failed. Probes containing single nucleotide polymorphisms (SNPs) with a minor allele frequency of 0.01 in the European population in the 1000 Genomes Project were also removed. Samples with >5% of probes failing and those failing a sex check (based on X chromosome methylation level) were also removed. In methylumi, probes were background adjusted, corrected from dye colour bias, and quantile normalised. Intra-array and probe design variation was corrected for using beta-mixture quantile dilatation (BMIQ). Inter-array batch effects were corrected for using ComBat.
Whole blood DNA methylation samples were processed separately using the lumi, methylumi and minfi packages in R (R Foundation for Statistical Computing, Vienna). Probes were filtered out if the detection p value of 0.01 or if >5% of probes failed. Probes containing single nucleotide polymorphisms (SNPs) with a minor allele frequency of 0.01 in the European population in the 1000 Genomes Project were also removed. Samples with >5% of probes failing and those failing a sex check (based on X chromosome methylation level) were also removed. Probes were background adjusted, corrected from dye colour bias, and quantile normalised.  Whole blood samples from two datasets were combined at this stage. Subsequently, intra-array and probe design variation was corrected for using beta-mixture quantile dilatation (BMIQ) and inter-array batch effects were corrected for using ComBat. The data matrix can be found on the SuperSeries GSE87650 record.

source_name: monocytes

value: monocytes

tag: age at sample


title: P009034.16122013.TTC14.01

description:
Sample 239
P009034.16122013.TTC14.01

value: UC (Ulcerative colitis)


title: P008970.24102013.TTC8.01

description:
Sample 240
P008970.24102013.TTC8.01

value: CD (Crohn's disease)

value: CD

value: L


title: P007821.10102013.TTC8.01

description:
Sample 238
P007821.10102013.TTC8.01

value: F

value: HL (Healthy control (Lab volunteer))

value: J