title: Blood-NS-FLX_73

city: MARSEILLE CEDEX 09

first: Aurelie

last: Bergon

address: parc scientifique de Luminy, case 928

institute: TAGC INSERM U1090

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity > 6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse Gene Expression 8x60K Microarray v1 (G4852B) for 17 hours at 65°C in a rotating Agilent hybridization oven (2 campaigns).  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters (protocol GE1_105_Dec08 and Grid: 028004_D_F_20110722) to obtain background subtracted and spatially detrended Processed Signal intensities. All data were normalized by quantile normalization.

source_name: Whole Blood_Fluoxetin-treated mice

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100ng RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: 0.4-0.5 ml of whole blood (WB) was collected from the submandibular vein and mixed by inversion to 1.3 ml of RNAlater (Ambion before storage at -20°C. Total RNA from WB was isolated using the mouse ribopure total RNA isolation kit (Ambion) according to manufacturer's recommendation. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: UCMS consists in chronic exposure to various mild social and environmental stressors, each of which is not sufficient to induce significant long-lasting effects alone. The stressors used are varied, and they are applied in a different sequence each week in order to avoid habituation, and consist of: removal of bedding, wetting the bedding, several repeated changes of bedding, tilting of cages by 45° for a variable time, placing approximately 2 cm of water into the home-cage (after having removed the bedding), exposure to predator sounds for 15 minutes, social stress (animals are either placed in a cage belonging to another mouse or placed in another animal's cage and then returned to their  own cage to find that it had been occupied by another mouse, lights on during the dark phase, lights off during the light phase, a succession of light and dark periods for 30 minutes, switching of the light/dark cycle for a variable length of time. When receiving Flx, mice were exposed to about 15-20 mg/kg of the antidepressant diluted to 120 mg/L in drinking water.To evaluate stress treatment and recovery, physical state has been evaluated and a variety of behavioural tests were conducted to assess different symptoms that collectively characterize the depressive state. The condition of the coat has been evaluated by examining the coat on different parts of the body: head, neck, dorsal coat, ventral coat, tail, front and hind paws and genital area. For each area, a score of 0 has been applied if the coat is in good condition, and a score of 1 if it is in very bad condition (disordered, piloerection). The total score is the sum of each area.Bodyweight gain has been assessed at the end of the UCMS procedure.

tag: strain

value: BALB/c

value: male

value: 17 weeks

tag: ucms

value: Unstressed

tag: flx

value: Whole Blood

tag: mean coating score the last week before sacrifice

tag: body weight gain (%)

tag: hybridization campaign


title: CD_ileum_active_48

status: Public on Sep 14 2017

type: RNA

city: Leuven

first: Ingrid

last: Arijs

address: Herestraat 49

department: Clinical and Experimental Medicine

country: Belgium

institute: KULeuven

description: Biopsy from inflamed ileal mucosa of active CD patient

hyb_protocol: After fragmentation of DNA, labeled DNA was hybridized for 16h at 45°C on Affymetrix Human Gene 1.0 ST arrays.

scan_protocol: The arrays were washed and stained in a fluidics station using the GeneChip hybridization, Wash end Stain kit (Affymetrix) and scanned using the Affymetrix 3000 GeneScanner.

data_processing: Probe level analysis was performed on the Affymetrix raw data (.cel files) with the robust multichip average (RMA) method implemented in the Bioconductor package 'aroma.affymetrix' to obtain a log2 expression value for each gene probe set

label: biotin

molecule: total RNA

organism: Homo sapiens

label_protocol: Biotin-labeled single-stranded DNA was synthesized using the Affymetrix GeneChip WT terminal Labeling kit (Affymetrix), according to manufacturer's instructions.

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (Qiagen, Benelux B.V.), according to the manufacturer’s instructions.

tag: tissue

value: ileum

tag: disease

value: CD

tag: disease activity

value: active


title: Blood-NS-FLX_72

country: France

organism: Mus musculus

tag: gender

tag: age

value: Yes


title: Blood-NS-FLX_71


title: Hu641

city: La Jolla

first: Sunil

last: Kurian

state: CA

address: 10550 N Torrey Pines Road

department: Molecular and Experimental Medicine

country: USA

institute: The Scripps Research Institute

description: SAMPLE 32

hyb_protocol: Standard Affymetrix 49 Format Hybridization with 15mg of fragmented cRNA

scan_protocol: Affymetrix EukGE-WS2v4

data_processing: RMAExpress

label: SAPE

source_name: Human Islet Cells

label_protocol: Ambion MessageAmp Biotin II Enhanced

growth_protocol: Islets frozen in RNA Later

extract_protocol: RNA was extracted using Trizol and purified on RNeasy Columns

tag: diabetes reversal status

value: No

value: pancreas

tag: cell type

value: islet cells


title: CD_ileum_active_46

source_name: Biopsy from inflamed ileal mucosa of active CD patient


title: Hu681

description: SAMPLE 34


title: CD_ileum_active_35


title: Blood-NS-FLX_59


title: Hu640

description: SAMPLE 31


title: CD_ileum_active_44


title: Hu623

description: SAMPLE 33


title: Hu638

description: SAMPLE 29


title: Hu637

description: SAMPLE 28


title: CD_ileum_active_33


title: CD_ileum_active_30


title: Blood-NS-FLX_46


title: CD_ileum_active_31


title: Blood-NS-FLX_58


title: CD_ileum_active_32


title: Blood-NS-FLX_45


title: Blood-NS-FLX_47


title: Blood-S-FLX_27

source_name: Whole Blood_stressed and Fluoxetin-treated mice

value: Stressed


title: Hu632

description: SAMPLE 25


title: Hu639

description: SAMPLE 30


title: CD_ileum_active_25


title: Blood-S-FLX_22


title: Blood-S-FLX_38


title: CD_ileum_active_23


title: Hu627

description: SAMPLE 22


title: CD_ileum_active_29


title: CD_ileum_active_28


title: Hu635

description: SAMPLE 26


title: CD_ileum_active_27


title: Blood-S-FLX_17


title: CD_ileum_active_26


title: CD_ileum_active_24


title: Hu626

description: SAMPLE 21


title: Hu636

description: SAMPLE 27


title: Hu630

description: SAMPLE 23


title: Blood-S-FLX_8


title: Blood-S-FLX_10


title: Hu631

description: SAMPLE 24


title: Hu624

description: SAMPLE 19


title: Blood-S-T_35

source_name: Whole Blood_stressed mice


title: Blood-S-FLX_14


title: CD_ileum_active_22


title: Blood-S-FLX_7


title: CD_ileum_active_21


title: Blood-S-T_32


title: CD_ileum_active_20


title: Hu625

description: SAMPLE 20


title: Hu621

description: SAMPLE 18


title: CD_ileum_active_19


title: CD_ileum_active_18


title: Blood-S-T_25


title: Blood-S-T_19


title: Hu620

description: SAMPLE 17


title: Hu619

description: SAMPLE 16


title: CD_ileum_active_16


title: Blood-S-T_15


title: Hu665

description: SAMPLE 15


title: Blood-S-T_13


title: CD_ileum_active_15


title: Hu664

description: SAMPLE 14


title: Hu662

description: SAMPLE 12


title: Blood-S-T_1


title: CD_ileum_active_14


title: Blood-S-T_11


title: Hu661

description: SAMPLE 11


title: Hu663

description: SAMPLE 13


title: CD_ileum_active_13


title: Hu656

description: SAMPLE 9


title: CD_ileum_active_10


title: CD_ileum_active_11


title: Blood-NS-T_66

source_name: Whole Blood_control mice


title: Blood-NS-T_65


title: CD_ileum_active_12


title: CD_ileum_active_9


title: Hu657

description: SAMPLE 10


title: Hu655

description: SAMPLE 8


title: Hu652

description: SAMPLE 7


title: Blood-NS-T_53


title: Blood-NS-T_54


title: CD_ileum_active_17


title: Hu650

description: SAMPLE 5


title: Cing_Gyr-NS-FLX_73

source_name: Cingulate Gyrus_Fluoxetin-treated mice

extract_protocol: Brains have been rapidly removed from CO2-euthanized mice and anterior cingulate cortex and dentate gyri (ACC and DG) have been dissected and immediately immersed in RNAlater and kept overnight at 4°C before freezing and stored at -20°C. Total RNAs from DG and CG were isolated using the mirVana miRNA isolation kit (Ambion) according to manufacturer's recommendation. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: Cingulate Gyrus


title: Hu646

description: SAMPLE 3


title: Cing_Gyr-NS-FLX_72


title: Hu645

description: SAMPLE 2


title: Hu648

description: SAMPLE 4


title: Blood-NS-T_40


title: Hu651

description: SAMPLE 6


title: Blood-NS-T_39


title: Blood-NS-T_64


title: S2_b: Primary cells

city: Lund

first: Shamit

last: Soneji

address: Solvegatan 19

country: Sweden

institute: BMC

scan_protocol: Standard Illumina iScan N240 scanning protocol

data_processing: The data were normalised using quantile normalisation with BASE

source_name: Primary cells

label_protocol: Illumina®Totalprep-96RNA Amplification kit 4397949 RevD, (Modification of Amplification kit v 2.2)

growth_protocol: Primary sorted  lin-CD45-CD31-CD71-CD235a-CD271+ cultured as adherent cells and as mesenspheres as described in Ghazanfari et al. 2016 (DOI: 10.1089/scd.2016.0169)

extract_protocol: Rneasy plus Micro Kit (Qiagen), TargetAmpTM 2-Round Biotin-aRNA Amplification kit 3.0 (epicentre)

treatment_protocol: No treatment

value: bone marrow

value: mesenchymal stromal cells

tag: condition

value: primary

tag: passage


title: Blood-NS-T_52

value: BALB/c


title: S12: P3 adherent cultured cells

source_name: P3 adherent cultured cells

value: adherent cultured


title: S10: P3 adherent cultured cells


title: Cing_Gyr-NS-FLX_59

value: male

value: 17 weeks


title: Hu644

description: SAMPLE 1


title: S1_b: Primary cells


title: S19: P3 sphere cultured cells

source_name: P3 sphere cultured cells

value: sphere cultured


title: S8: P0 adherent cultured cells

source_name: P0 adherent cultured cells


title: S13: P0 sphere cultured cells

source_name: P0 sphere cultured cells


title: S20: P3 sphere cultured cells


title: S6: P0 adherent cultured cells


title: S14: P0 sphere cultured cells


title: Cing_Gyr-NS-FLX_71

value: Unstressed


title: Cing_Gyr-NS-FLX_58


title: Cing_Gyr-NS-FLX_46


title: Cing_Gyr-NS-FLX_45


title: Cing_Gyr-NS-FLX_47


title: Cing_Gyr-S-FLX_17

source_name: Cingulate Gyrus_stressed and Fluoxetin-treated mice


title: S15: P0 sphere cultured cells


title: S9: P3 adherent cultured cells


title: Cing_Gyr-S-FLX_27


title: Cing_Gyr-S-FLX_38


title: Cing_Gyr-S-FLX_22


title: S18: P3 sphere cultured cells


title: S17: P3 sphere cultured cells


title: S16: P0 sphere cultured cells


title: S7: P0 adherent cultured cells


title: Cing_Gyr-S-FLX_14


title: S11: P3 adherent cultured cells


title: Cing_Gyr-S-FLX_10


title: Cing_Gyr-S-FLX_8


title: S5: P0 adherent cultured cells


title: S3: Primary cells


title: Cing_Gyr-S-FLX_7


title: Cing_Gyr-S-T_35

source_name: Cingulate Gyrus_stressed mice


title: AML Relapse LAM25

city: Padova

first: Matteo

last: Zampini

state: PD

address: corso stati uniti 4

country: Italy

institute: Istituto di Ricerca Pediatrica (IRP)  Città della Speranza

description: miRNA expression data from pediatric t(8;21)AML patient harboring FLT3-ITD mutation (gene-level)

hyb_protocol: The GeneChip® Hybridization, Wash, and Stain Kit was used as per manufacturer’s protocols. The GeneChip® Fluidics Station 450 was used for washing and staining with fluidics script FS450_0002.

scan_protocol: Microarray chips were read on the GeneChip® Scanner 3000 7G with AGCC version 4.0.0.1567.

data_processing: The CEL files generated were analyzed through Affymetrix Expression Console Software (version 1.3) which normalizes array signals using a robust multiarray averaging (RMA) algorithm.

source_name: pediatric t(8;21)RUNX1-RUNX1T1 AML BM

label_protocol: Samples were labeled using the Affymetrix FlashTag™ Biotin HSR RNA Labeling Kit as per manufacturer's protocols.

extract_protocol: Total bone marrow RNA was extracted using TRIzol reagent (Invitrogen) according to manufacturer guidelines, quantified using UV spectroscopy (Nanodrop Technologies), and qualitatively assessed using an Agilent2100 Bioanalyzer (Agilent Technologies).

value: Bone Marrow

tag: aberration

tag: dataset

value: Relapse

tag: age class

tag: ckit mutation

value: WT

tag: Sex

value: M


title: AML Relapse LAM24


title: Cing_Gyr-S-T_25

tag: strain

tag: ucms

tag: flx

value: No

tag: mean coating score the last week before sacrifice


title: AML Relapse LAM17

tag: tissue

value: Mut


title: AML Relapse LAM20


title: AML Relapse LAM19

value: F


title: Cing_Gyr-S-T_13

value: Stressed

value: Cingulate Gyrus

tag: body weight gain (%)

tag: hybridization campaign


title: MDA-MB-231 transfected with mir-34c mimic, rep3

city: Oslo

first: Leonardo

middle: A.

last: Meza-Zepeda

address: Ullernchausseen 70

department: Department of Tumor Biology

country: Norway

institute: Oslo University Hospital

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: Raw and quantile data were exported from GenomeStudio (Illumina) and further processed in J-Express.

label: Biotin

source_name: ATCC® HTB-26™

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

growth_protocol: Cells were grown in RPMI-1640 (Sigma-Aldrich) supplemented with 10 % foetal calf serum (Sigma-Aldrich) and glutamax (Sigma-Aldrich), at 37°C with 5 % CO2. The cell line was routinely tested for mycoplasma, and always found negative. The cell line was also subject to short tandem repeat (STR)-DNA profiling of 15 loci and amelogenin (Genotyping core facility, Oslo University Hospital) and matched the STR-profile available from ATTC.

extract_protocol: RNA was isolated 48h after transfection using standard TRIzol procedure (Invitrogen).

treatment_protocol: 24h after seeding, cells were transiently transfected using 18 nM mimics (Ambion) and INTERFERin (PolyPLUS), according to the manufacturer’s protocol.

tag: cell line

value: Triple-negative breast cancer cell line

tag: sample origin

value: Pleural effusion

tag: gender

value: Female

tag: miRNA

value: miR-34c mimic


title: MDA-MB-231 transfected with Negative Controls oligonucleotide, rep3

tag: cell type

value: Negative Controls oligonucleotide


title: MDA-MB-231 transfected with Negative Controls oligonucleotide, rep1


title: AML Relapse LAM18

tag: aberration


title: Primary AML patient LAM9

tag: dataset

value: Validation-set


title: Cing_Gyr-S-T_19

value: BALB/c

value: male

tag: age

value: 17 weeks


title: MDA-MB-231 transfected with mir-34b mimic, rep3

value: miR-34b mimic


title: MDA-MB-231 transfected with Negative Controls oligonucleotide, rep2


title: Cing_Gyr-S-T_11


title: MDA-MB-231 transfected with miR-34c mimic, rep1


title: Cing_Gyr-S-T_1


title: MDA-MB-231 transfected with miR-34c mimic, rep2


title: MDA-MB-231 transfected with miR-34b mimic, rep2


title: Primary AML patient LAM8

value: Bone Marrow

tag: age class

tag: ckit mutation


title: Cing_Gyr-NS-T_66

source_name: Cingulate Gyrus_control mice

tag: strain

value: Unstressed


title: MDA-MB-231 transfected with miR-34b mimic, rep1


title: Primary AML patient LAM6

value: WT

tag: Sex


title: Primary AML patient LAM7

value: Training-set

value: Mut


title: Cing_Gyr-S-T_15

tag: ucms

value: Stressed

tag: flx

value: No


title: Cing_Gyr-S-T_32

tag: tissue

value: Cingulate Gyrus

tag: mean coating score the last week before sacrifice


title: MDA-MB-231 transfected with mir-34a mimic, rep3

value: Triple-negative breast cancer cell line

value: Pleural effusion

value: miR-34a mimic


title: Primary AML patient LAM5

value: F


title: MDA-MB-231 transfected with miR-34a mimic, rep2

value: Female


title: MDA-MB-231 transfected with miR-34a mimic, rep1


title: Cing_Gyr-NS-T_64

value: BALB/c

tag: body weight gain (%)

tag: hybridization campaign


title: Primary AML patient LAM48

value: Validation-set


title: Primary AML patient LAM43


title: Primary AML patient LAM42


title: Cing_Gyr-NS-T_65

value: male

value: 17 weeks


title: Cing_Gyr-NS-T_53


title: Primary AML patient LAM4

value: Bone Marrow

value: M


title: Primary AML patient LAM41

value: WT


title: Cing_Gyr-NS-T_54

value: Unstressed


title: Cing_Gyr-NS-T_52


title: Primary AML patient LAM35

value: Training-set


title: Primary AML patient LAM32


title: Primary AML patient LAM33


title: Dent_Gyr-NS-FLX_72

source_name: Dentate Gyrus_Fluoxetin-treated mice

value: Yes

value: Dentate Gyrus


title: Primary AML patient LAM34

value: Mut


title: Dent_Gyr-NS-FLX_71


title: Dent_Gyr-NS-FLX_73


title: Primary AML patient LAM31


title: Dent_Gyr-NS-FLX_59


title: Cing_Gyr-NS-T_40

value: No

value: Cingulate Gyrus


title: Primary AML patient LAM29


title: Cing_Gyr-NS-T_39


title: Primary AML patient LAM3


title: Dent_Gyr-NS-FLX_58


title: Dent_Gyr-NS-FLX_47


title: Dent_Gyr-S-FLX_27

source_name: Dentate Gyrus_stressed and Fluoxetin-treated mice

value: Stressed


title: Primary AML patient LAM28


title: Dent_Gyr-NS-FLX_45


title: Dent_Gyr-S-FLX_22


title: Dent_Gyr-NS-FLX_46


title: Dent_Gyr-S-FLX_10


title: Dent_Gyr-S-FLX_17


title: Dent_Gyr-S-FLX_14


title: Primary AML patient LAM22


title: Primary AML patient LAM27


title: Primary AML patient LAM45

value: F


title: Primary AML patient LAM21


title: Dent_Gyr-S-FLX_38


title: Dent_Gyr-S-FLX_8


title: Primary AML patient LAM16


title: Dent_Gyr-S-FLX_7


title: Dent_Gyr-S-T_35

source_name: Dentate Gyrus_stressed mice


title: Primary AML patient LAM14


title: Primary AML patient LAM15


title: Dent_Gyr-S-T_32


title: Primary AML patient LAM11


title: Primary AML patient LAM12


title: Dent_Gyr-S-T_15


title: Primary AML patient LAM2


title: Dent_Gyr-S-T_25


title: Dent_Gyr-S-T_13


title: Dent_Gyr-S-T_11


title: Primary AML patient LAM1


title: patient 20 CRS

city: Luoyang

first: zhang

last: ying

state: Henan

address: No. 82, South Qiming Road

country: China

institute: Medical Center of Hip, Luoyang Orthopedic-Traumatological Hospital (Orthopaedic Hospital  of Henan Province)

hyb_protocol: 1. Prepare the hybridization mix in a PCR tube according to the table below:  Components Amount(ul)  Labeled sample 12.5 μlHybridization buffer 90  Nuclease-free Buffer 77.5  Total 180    2. Incubate at 95℃ for 2 min. During the incubation the target preparation should be protected from light.  3. Leave on ice for at least 2 min. and up to 15min. Briefly spin the reaction after ice incubation.  4. Take cover slide out of the package.         5. Carefully laid the miRCURYTM Array on top of the assembly of cover slide and spacer, where the printed side of array should be facing toward the cover slide, to form a hybridization assembly. The printed side of array is on the side of the label.         6. Insert the hybridization assembly into a (3.1 x 9cm) heat-shrank hybridization (hyb.) bag. Sample loading side of the hybridization assembly should face the opening side of film bag. Lower the assembly to the end of the bag (Assembly viewed from the other side).         7. Clip the bag with a clipper ecurely?from the opening end. Immerse the assembly to the rim of the slide in 95℃ hot water swiftly (approximately 2~5 sec). Do not dip the assembly too far into the water to avoid water leaking into the assembly. The hyb. bag will shrink and tightly wrap around the assembly.     8. Remove the assembly from water and wipe off the water from the assembly. Trim off the excess film from the top of the assembly. Keep the assembly in a 50℃ oven for at least 10 minutes.         9. Load the180ul target hybridization mix into the assembly through the sample loading opening. Fill up the hybridization space with 1X Hybridization buffer till the liquid level reaches to approximately 5 mm (0.5cm) away from the top rim.     10. Cut the second Hyb. Bag to approximately one-half of its original length.         11. Keep the assembly vertical and slip on the shortened hyb. bag from step 11 all the way until the assembly reaches the end of the hyb. bag.         12. Use a pair of forceps to hold onto the top of the assembly. Immerse the entire assembly into 95℃ hot water with the assembly in upright position.             13. Place the hybridization assembly into a 56℃ oven and set it on a rotator. Remember to rotate the assembly at 2 rotations per minute (RPM) for overnight.     14. After hybridization, disassembled the hybridization assembly, and wash the slides at 56℃ for 2min. using Wash buffer A.  15. Wash briefly at room temperature in Wash buffer B.  16. Wash for 2min. at room temperature in Wash buffer B.  17. Wash for 2min. at room temperature in Wash buffer C.  18. Wash briefly in water.  19. Dry the slides by centrifugation for 5 min. at 200* g(1000rpm). Scan slides immediately after drying.

scan_protocol: Scanning is performed with the Axon GenePix 4000B microarray scanner. GenePix pro V6.0 is used to read the raw intensity of the image.

data_processing: a) The intensity of green signal is calculated after background subtraction and four Replicated spots of each probe on the same slide have been averaged.  b) We use Median Normalization Method to obtain “Normalized Data”, Normalized Data= (Foreground-Background)/median, the median is 50 percent quantile of microRNA intensity which is larger than 50 in all samples after background correction.  c) After normalization, the statistical significance of differentially expressed miRNA was analyzed by T-test.

source_name: plasma necrosis

label_protocol: miRCURYTM Array Power Labeling kit (Cat #208032-A, Exiqon)

extract_protocol: WHOLE BLOOD  Add 0.2 ml of whole blood or plasma to 0.75 ml of TRI Reagent BD supplemented with 20 ul of 5 N acetic acid per 0.2 ml of whole blood or plasma

tag: individual

value: patient 20

tag: disease state

value: necrosis

tag: sample type

value: serum


title: patient 18 SSJ

value: patient 18


title: patient 17 GFJ

value: patient 17


title: patient 16 QRQ

value: patient 16


title: Dent_Gyr-NS-T_53

source_name: Dentate Gyrus_control mice

value: BALB/c

tag: gender

value: male

value: 17 weeks


title: Dent_Gyr-NS-T_66

value: Unstressed


title: Dent_Gyr-NS-T_54


title: Dent_Gyr-NS-T_52


title: Primary AML patient LAM10

value: Bone Marrow

tag: aberration

value: Training-set

value: WT

value: M


title: Dent_Gyr-NS-T_40

value: No

value: Dentate Gyrus


title: patient 15 ZFN

value: patient 15


title: patient 14 WGM

value: patient 14


title: patient 13 HMY

value: patient 13

value: necrosis


title: patient 19 NBF

value: patient 19

value: serum


title: patient 11 JYH

value: patient 11


title: patient 8 FJX

source_name: plasma no-necrosis

value: patient 8

value: no-necrosis


title: patient 9 WDZ

value: patient 9


title: patient 10 DH

value: patient 10


title: patient 7 ZCF

value: patient 7


title: Dent_Gyr-S-T_1

value: BALB/c

value: male

value: 17 weeks

value: Stressed


title: Dent_Gyr-NS-T_64

value: Unstressed

value: No

value: Dentate Gyrus


title: patient 5 YHT

value: patient 5


title: patient 4 SJS

value: patient 4


title: patient 3 WJM

value: patient 3


title: patient 12 MZC

value: patient 12

value: necrosis

value: serum


title: Primary AML patient LAM13

value: Bone Marrow

tag: dataset

value: Validation-set

value: Mut

value: M


title: Dent_Gyr-NS-T_39

value: BALB/c

tag: age


title: patient 2 WF

value: patient 2

value: no-necrosis


title: patient 1 JDQ

value: patient 1


title: Primary AML patient LAM47

tag: age class

value: WT


title: patient 6 ZCL

value: patient 6


title: Dent_Gyr-NS-T_65

value: male

value: 17 weeks

value: Unstressed

value: No

value: Dentate Gyrus


title: Mouse_KO3

status: Public on Sep 13 2017

city: Edinburgh

first: Takuya

last: Azami

address: Crewe Road

department: Institute of Genetics and Cancer

country: United Kingdom

institute: The University of Edinburgh

description: Gene expression data

hyb_protocol: Affimetrix GeneChip Expression Analysis Technical manual Rev3

extract_protocol: Kurimoto et al., 2007

value: embryo

tag: genotype

value: Klf5 KO


title: Mouse_KO5

description: Gene expression data

scan_protocol: Affimetrix GeneChip Expression Analysis Technical manual Rev3


title: Control (HOXB7-knockdown S2-013 cells transfected with rescue-HOXB7 plasmid but not treated with MEK inhibitor)

city: Nankoku

first: Keisuke

last: Taniuchi

address: Kohasu

country: Japan

institute: Kochi Medical School

hyb_protocol: ss-cDNA was fragmentated and biotinylated, then hybridized to Human Gene 2.0 ST arrays (Affymetrix) overnight at 45°C and stained on a Genechip Fluidics Station 450 (Affymetrix), according to the respective manufacturer’s instructions.

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

data_processing: Expression values were generated using Expression Console software, version 1.3 (Affymetrix, Inc.) with default robust multichip analysis parameters.

source_name: pancreatic cancer cell line (S2-013)

label_protocol: RNA (100 ng) from each sample was processed using Affymetrix GeneChip WT PLUS Reagent Kit (Affymetrix, Inc., Santa Clara, CA, USA) according to the manufacturer’s instructions. Briefly, first-strand cDNA was synthesized using the primers containing a T7 promoter sequence in 10 μl reactions at 25°C for 30 min and 42°C for 60 min. Second strand cDNA synthesis was performed using DNA polymerase and RNase H at 16°C for 60 min and 65°C for 10 min. Double stranded cDNA containing T7 promoter was used as the template for in vitro transcription  at 40°C for 16 hours to synthesyze cRNA. Then, sense-strand cDNA is synthesized by the reverse transcription of cRNA using 2nd-  Cycle Primers at 25°C for 10 min, 42°C for 90 min and 70°C for 10 min. After that cRNA was hydrolyzed by RNase H, and single-strand cDNA was released. ss-cDNA was fragmentated and biotinylated.

extract_protocol: Total RNA was extracted from Cont and Sample1 using the RNeasy kit.

tag: cell type

value: primary pancreatic cancer


title: Primary AML patient LAM30

value: Bone Marrow

value: Training-set

tag: ckit mutation

tag: Sex

value: F


title: Mouse_WT5

description: Gene expression data

data_processing: Affimetrix GeneChip Expression Analysis Technical manual Rev3

value: Wild Type


title: Mouse_KO4

description: Gene expression data

label_protocol: Affimetrix GeneChip Expression Analysis Technical manual Rev3


title: Mouse_WT2

description: Gene expression data


title: Mouse_WT4

description: Gene expression data


title: HOXB7-knockdown S2-013 cells transfected with rescue-HOXB7 plasmid and treated with MEK inhibitor


title: Mouse_KO2

description: Gene expression data


title: Dent_Gyr-S-T_19

tag: strain

value: BALB/c

tag: ucms

value: Stressed

tag: flx


title: Mouse_WT1

description: Gene expression data

tag: tissue


title: IS33

city: Groningen

first: Ana

last: Solopova

address: Nijenborgh 7

department: MolGen

country: Netherlands

institute: RUG

description: L. lactis MG1363ΔcelBΔptcCΔ0963 llmg_1239::IS905 biological replicate 2, labeled with Cy3

hyb_protocol: Superamin glass slides (ArrayIt, Sunnyvale, CA) were spotted with duplicates of approximately 2500 ORF amplicons of L. lactis subsp. MG1363.  Hybridization was performed in Ambion Slidehyb #1 hybridisation buffer (Ambion Biosystems, Foster City, CA) for 16 h at 45°C in a microarray hybridization incubator ISO20 (Grant Boekel, Cambridgeshire, UK).  Slides were washed in 2x SSC (+0.5 % SDS), 1x SSC (+0.25% SDS) and 1x SSC (+0.1% SDS), prior to drying and scanning.

scan_protocol: Slides were scanned using a GenePix Autoloader 4200AL scanner (Molecular Devices Corporation, Sunnyvale, CA)

data_processing:
Data analysis was carried out using ArrayPro 4.5 (Media Cybernetics, Silver Spring, MD) for image analysis and processed using a lowess normalization assuming that at least 50% of the genes will show no change in expression.  Data was compiled from two anaerobic cultures each with a dye-swap replicate, providing two biological repeats within four technical repeats.
Raw signals were normalized using lowess normalizaton and scaled using Trimmed Median Mean (TMM)

organism: Lactococcus cremoris

label_protocol: cDNA  was synthesized using Superscript III Reverse Transcriptase (Invitrogen, Carlsbad, CA) and allyl-modified dUTPs to allow indirect Cy-3/Cy-5 labelling according to manufacturers instructions (Amersham Biosciences, Piscataway, NJ).

growth_protocol: Cultures were grown in closed vessles at 30°C in rich M17 medium containing 1% cellobiose as a carbon source.

extract_protocol: As described in Marredy et al., 2011.  Cells were harvested immediately upon reaching the required optical density, snap frozen in liquid nitrogen and stored at -80°C.  Cells were lysed by bead beating and chromosomal DNA was removed by Macaloid suspension (Bentone MA, Hightstown, NJ).  Proteins were removed from the cell lysate by chloroform/phenol extraction and total RNA was isolated from the water phase using the Pure RNA Isolation Kit (Roche Molecular Biochemicals, Mannheim, Germany).

treatment_protocol: Cultures were grown to mid-exponential (OD600 of around 0,3 or 0,6) phase.

tag: genotype/variation

value: IS905 integration in llmg_1239


title: Cel35

description: L. lactis MG1363ΔcelBΔptcCΔ0963 llmg_1239::IS905 OD=0,3 biological replicate 2, labeled with Cy5


title: GFP33

description: L. lactis MG1363ΔcelBΔptcCΔ0963 llmg_1239::gfp biological replicate 2, labeled with Cy3

value: GFP integration in llmg_1239


title: Cel33

description: L. lactis MG1363ΔcelBΔptcCΔ0963 llmg_1239::IS905 OD=0,3 biological replicate 2, labeled with Cy3


title: IS35

description: L. lactis MG1363ΔcelBΔptcCΔ0963 llmg_1239::IS905 biological replicate 2, labeled with Cy5


title: WT35

description: L. lactis MG1363 biological replicate 1, labeled with Cy5

value: WT


title: Mouse_WT3

description: Gene expression data


title: GFP35

description: L. lactis MG1363ΔcelBΔptcCΔ0963 llmg_1239::gfp biological replicate 2, labeled with Cy5


title: Cel25

description: L. lactis MG1363ΔcelBΔptcCΔ0963 llmg_1239::IS905 OD=0,3 biological replicate 1, labeled with Cy5


title: GFP25

description: L. lactis MG1363ΔcelBΔptcCΔ0963 llmg_1239::gfp biological replicate 1, labeled with Cy5


title: Mouse_KO1

description: Gene expression data


title: WT33

description: L. lactis MG1363 biological replicate 1, labeled with Cy3


title: GFP23

description: L. lactis MG1363ΔcelBΔptcCΔ0963 llmg_1239::gfp biological replicate 1, labeled with Cy3


title: WT25

description: L. lactis MG1363 biological replicate 2, labeled with Cy5

value: wild type


title: Cel23

description: L. lactis MG1363ΔcelBΔptcCΔ0963 llmg_1239::IS905 OD=0,3 biological replicate 1, labeled with Cy3


title: WT23

description: L. lactis MG1363 biological replicate 2, labeled with Cy3


title: U266-CRP

status: Public on Sep 12 2017

city: Houston

first: Jing

last: Yang

state: Texas

address: 7455 Fannin

institute: MD Anderson Cancer Center

hyb_protocol: As per Illumina instructions, with detection by Streptavidin-Cy3 conjugate.

scan_protocol: As per instructions for Illumina BeadArray Reader

data_processing: The non-normalized data were generated by GenomeStudio with background correction.

source_name: Human myeloma cell line

label_protocol: 200 ng total RNA was amplified and biotin-labeled through a Eberwine procedure using Illumina TotalPrep RNA Amplification kits (Ambion).

growth_protocol: All myeloma cells were cultured in RPMI-1640 medium supplemented with 10% FBS (Invitrogen, Carlsbad, CA).

extract_protocol: Total RNA was extracted using the TRIzol reagent according to the manufactory's guideline. Then the RNA was purified by the Qiagen RNeasy Mini Kit column.

treatment_protocol: Three different human myeloma cell lines (ARP-1, MM.1S and U266) were treated with or without 5 ug/ml CRP for 24 hours.

tag: cell line

tag: treatment

value: 5 ug/ml CRP for 24 hours


title: Case: 1293; ROI: P

city: Boston

first: Svitlana

last: Tyekucheva

state: MA

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetric protocol

data_processing: Preprocessing of the microarray data consisted of adjusting raw data at the probe level for technical variables, such as batches, overall median of the fluorescence intensities in each array and fraction of the probes with intensity higher than background levels. Adjusted values were normalized using RMA (robust multichip average) method using Bioconductor package 'oligo'

source_name: RP

label_protocol: Affymetrix SensationPlus FFPE

extract_protocol: LCM was perfomed using Arcturus platform (Life Technologies), followed by overnight incubation in lysis buffer / Proteinase K and subsequent RNA extraction by AllPrep (Qiagen) and quantification by RiboGreen assay (Life Technology).

tag: case

tag: batch

tag: roi

value: P

tag: gleason


title: ARP-1-CRP


title: MM.1S-CRP


title: Case: HP328; ROI: AM

value: AM


title: ARP-1

value: Control


title: U266


title: Case: 17148; ROI: sP

value: sP


title: control, not used for analysis 88

value: control


title: MM.1S


title: Case: HP328; ROI: sP


title: Case: HP328; ROI: P


title: Genomic DNA from 184AA2

type: genomic

city: daejeon

first: Jonglyul

last: Park

address: 52, Eoeun-dong, Yuseong-gu

department: Medical genomics

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

description: immortal with AIG

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation850K Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using iSCAN using standard recommended Illumina scanner setting

data_processing: GenomeStudio software v2010.3

label: Cy5 and Cy3

molecule: genomic DNA

label_protocol: Standard Illumina Protocol

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

tag: gender

value: Female


title: Case: 1293; ROI: sP


title: Case: HP328; ROI: B

value: B


title: Genomic DNA from 184D

description: pre-stasis


title: Genomic DNA from 184B5ME

description: immortal with AIG


title: Case: HP328; ROI: T

value: T


title: Case: HP328; ROI: sB

value: sB


title: Case: 4570; ROI: sP


title: Case: 3292; ROI: AM


title: Case: 4570; ROI: B


title: Genomic DNA from 184AA3

description: immortal with AIG


title: Case: 4133; ROI: sP


title: Case: 4570; ROI: sB


title: Case: 4570; ROI: AM


title: Case: 4133; ROI: P


title: Case: 4570; ROI: T


title: IS23

description: L. lactis MG1363ΔcelBΔptcCΔ0963 llmg_1239::IS905 biological replicate 1, labeled with Cy3


title: Case: 4133; ROI: B


title: Case: 11200; ROI: AM


title: Case: 4570; ROI: P


title: Case: 4133; ROI: sT

value: sT


title: IS25

description: L. lactis MG1363ΔcelBΔptcCΔ0963 llmg_1239::IS905 biological replicate 1, labeled with Cy5


title: Case: 4133; ROI: AM


title: Genomic DNA from 184A1

description: immortal


title: Case: 4133; ROI: T


title: Genomic DNA from 184B5

description: immortal


title: Genomic DNA from 184FMY2

description: immortal with AIG


title: Genomic DNA from 184BE1

description: immortal


title: Case: HP328; ROI: sT


title: Case: HP81; ROI: sT


title: Case: HP81; ROI: P


title: Genomic DNA from 184AA4

description: immortal


title: Case: HP81; ROI: B


title: Case: HP81; ROI: sB


title: Case: 11200; ROI: sP


title: Case: HP81; ROI: sP


title: Case: HP95; ROI: sT


title: Case: 4570; ROI: sT


title: Case: HP95; ROI: T


title: Case: HP95; ROI: B


title: Case: 2045; ROI: T


title: Case: HP95; ROI: P


title: Case: HP95; ROI: AM


title: Case: 2045; ROI: sP


title: Case: HP81; ROI: T


title: Case: HP81; ROI: AM


title: Case: HP95; ROI: sB


title: Case: 3292; ROI: sT


title: Case: 3292; ROI: T


title: Case: 2045; ROI: sT


title: Case: 2045; ROI: AM


title: Case: 2045; ROI: P


title: Case: 11200; ROI: P


title: Case: HP95; ROI: sP


title: Case: 2045; ROI: B


title: Case: 2045; ROI: sB


title: Case: 11IB; ROI: B

source_name: cystoprostatectomy

value: NT


title: Case: 11IB; ROI: sB


title: Case: 93IC; ROI: B


title: Case: 93IC; ROI: sB


title: Case: 17148; ROI: P


title: Case: 3292; ROI: sB


title: Case: 76IC; ROI: B


title: Case: 76IC; ROI: sB


title: Case: 80ID; ROI: sB


title: Case: 80ID; ROI: B


title: Case: 3292; ROI: B


title: Case: 7214; ROI: sB


title: Case: 7214; ROI: B


title: Case: 27IC; ROI: B


title: Case: 7214; ROI: AM


title: Case: 27IC; ROI: sB


title: Case: 7214; ROI: sP


title: Case: 7637; ROI: sT


title: Case: 11200; ROI: B


title: Case: 7637; ROI: sB


title: Case: 7637; ROI: T


title: Case: 7637; ROI: AM


title: Case: 7637; ROI: B


title: Case: 7214; ROI: T


title: Case: 11200; ROI: sB


title: Case: 7214; ROI: sT


title: Case: 7637; ROI: sP


title: Case: 3292; ROI: sP


title: Case: 7214; ROI: P


title: Case: 7637; ROI: P


title: Case: 4133; ROI: sB


title: Case: 931; ROI: sB


title: Case: 931; ROI: B


title: Case: 931; ROI: T


title: Case: 931; ROI: AM


title: Case: 11200; ROI: sT


title: Case: 1293; ROI: sT


title: BC2

city: Cádiz

first: Antonio

last: Campos-Caro

state: Cádiz

address: Avda. Ana de Viya, 21

department: Unidad Investigación

country: Spain

institute: Hospital Universitario Puerta del Mar

hyb_protocol: The Cy3- labeled cDNAs were hybridized overnight (17 hours, 65°C) to an Agilent Whole Human Genome Oligo Microarrays 4x44K V1 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 2 (37 °C) 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 Technologies).

data_processing: The Agilent Feature Extraction Software (FES) was used to read out and process the microarray image files. The software determines feature intensities (including background subtraction), rejects outliers and calculates statistical confidences. For determination of differential gene expression FES derived output data files were further analyzed using the Rosetta Resolver gene expression data analysis system (Rosetta Biosoftware).

source_name: Isolate B cells from Peripheral Blood, donor 2

label_protocol: 250 ng of each of the cDNAs were used as template for Cy3 labeling which was performed according to Miltenyi Biotec’s undisclosed protocol.

growth_protocol: Peripheral blood (PB) samples were obtained from healthy volunteers.  All studies were approved by the Institutional Review Board.

extract_protocol: Cell samples were lysed using SuperAmp™ Lysis Buffer and stored appropriately according to the instructions of the SuperAmp Preparation Kit (Miltenyi Biotec). mRNA was isolated via magnetic bead technology. SuperAmp RNA amplification was performed according to Miltenyi Biotec’s undisclosed procedure, based on a global PCR protocol using mRNA-derived cDNA. The integrity of the cDNA was checked via the Agilent 2100 Bioanalyzer platform (Agilent Technologies).

treatment_protocol: Mononuclear cells were obtained from freshly-drawn blood by density gradient centrifugation on Hystopaque-1077 (Sigma-Aldrich, St Louis, MO). B naïve cells were isolated by sorting in a FACSAria instrument (BD), based on the gating on CD19+; CD27-:IgD+ cells. Post-sort purity was > 99%.

value: Peripheral Blood


title: Case: 931; ROI: sT


title: Case: 931; ROI: sP


title: Case: 17148; ROI: sT


title: Case: 1293; ROI: T


title: Case: 1293; ROI: AM


title: Case: 931; ROI: P


title: NRE_TKO_rep4

first: Tobias

last: Otto

address: 450 Brookline Avenue

department: Cancer Biology

description: RMA normalization

hyb_protocol: cDNA was hybridized onto Mouse Gene ST 2.0 chips in Affymetrix Hybridization Oven 645 at 45 degrees for 16 hours, and washed on a Affymetrix Fluidics Station 450

scan_protocol: chips were scanned on a 7G Gene Chip Scanner

data_processing: CHP data were generated using Affymetrix Expression Console using RMA normalization

source_name: respiratory epithelium of the nose, embryo E16.5, miR-34/449 KO

label_protocol: cDNA was made and labeled using the Affymetrix Sensation Plus WT FFPE Amplification and Labeling Kit

growth_protocol: standard animal housing

extract_protocol: 8 µm paraffin sections were cut, region of interest was cut out using Laser Capture Microdissection, total RNA isolated using Qiagen AllPrep DNA/RNA FFPE Kit

treatment_protocol: embryos were prepared at E16.5, fixed in 10% formalin for 24 hours at 4°C, then transferred into 70% ethanol, processed and embedded into paraffin

value: respiratory epithelium of the nose

tag: developmental stage

value: embryo E16.5

value: male


title: Case: 1293; ROI: sB


title: NRE_TKO_rep1

description: RMA normalization

tag: genotype

value: female


title: Case: 3292; ROI: P


title: BC1

source_name: Isolate B cells from Peripheral Blood, donor 1


title: Case: 17148; ROI: T


title: BC3

source_name: Isolate B cells from Peripheral Blood, donor 3


title: NRE_WT_rep5

description: RMA normalization

source_name: respiratory epithelium of the nose, embryo E16.5, wild-type

value: wild-type


title: Case: 17148; ROI: sB


title: NRE_TKO_rep5

description: RMA normalization


title: NRE_TKO_rep3

description: RMA normalization


title: Case: 17148; ROI: B


title: NRE_WT_rep4

description: RMA normalization


title: Case: 4645; ROI: P

value: P


title: NRE_WT_rep2

description: RMA normalization


title: NRE_TKO_rep2

description: RMA normalization


title: Case: 1293; ROI: B


title: NRE_WT_rep3

description: RMA normalization


title: control, not used for analysis 86


title: Case: 17148; ROI: AM

value: AM


title: Case: 11200; ROI: T


title: Case: 6042; ROI: sP


title: NRE_WT_rep1

description: RMA normalization


title: Case: 6042; ROI: P


title: Case: 6042; ROI: B


title: Case: pooled cystprostatetomies; ROI: NT.AM 79


title: Case: 6042; ROI: T


title: Case: pooled cystprostatetomies; ROI: NT.AM 78


title: Case: EAA91; ROI: sP


title: Case: EAA91; ROI: sT


title: Case: C5AC3; ROI: sT


title: Case: C5AC3; ROI: sB


title: Case: EAA91; ROI: P


title: Case: EAA91; ROI: B


title: Case: EAA91; ROI: AM


title: Case: EAA91; ROI: T


title: Case: EAA91; ROI: sB


title: Case: 4645; ROI: AM


title: Case: 129; ROI: sB


title: Case: C5AC3; ROI: B


title: Case: C5AC3; ROI: P


title: Case: C5AC3; ROI: AM


title: Case: C5AC3; ROI: T


title: Case: C5AC3; ROI: sP


title: Case: F2BDA; ROI: P


title: Case: 129; ROI: sT


title: Case: F2BDA; ROI: T


title: Case: F2BDA; ROI: sT


title: Case: F2BDA; ROI: sB


title: Case: F2BDA; ROI: AM


title: Case: F2BDA; ROI: sP


title: Case: F2BDA; ROI: B


title: Case: EEB22; ROI: B


title: Case: EEB22; ROI: sT


title: Case: EEB22; ROI: P


title: Case: E35CC; ROI: sB


title: Case: E35CC; ROI: B


title: Case: EEB22; ROI: T


title: Case: E35CC; ROI: sT


title: Case: E35CC; ROI: sP


title: Case: E35CC; ROI: AM


title: Case: E35CC; ROI: P


title: Case: 6042; ROI: sT


title: Case: EEB22; ROI: sP


title: Case: EEB22; ROI: sB


title: Case: E35CC; ROI: T


title: Case: 4095; ROI: sP


title: Case: EEB22; ROI: AM


title: Case: 4095; ROI: sB


title: Case: 129; ROI: sP


title: oxidative bisulphite converted DNA from human placenta 5

city: L'Hospitalet de Llobregat, Barcelona

first: Jose Ramon

last: Hernandez

address: Av. Gran Via de l'Hospitalet 199-203

department: Cancer Epigenetics and Biology Program (PEBC)

institute: Institut d'Investigació Biomèdica de Bellvitge (IDIBELL)

description:
200090270067_R05C01_Grn.idat
200090270067_R05C01_Red.idat
normal placenta sample

hyb_protocol: bisulphite or oxidative bisulphite converted DNA were amplified, fragmented and hybridised to Illumina HumanMethylation450 Beadchip using standard Illumina protocol

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

data_processing: Minfi package for the R statistical software and in-house R scripts

source_name: placenta 5 oxBS conversion

label_protocol: standard Illumina protocol

extract_protocol: genomic DNA was extracted from placenta samples using standard phenol/chloroform extraction protocol

value: placenta

tag: individual

tag: conversion

value: oxBS


title: Case: 4095; ROI: P


title: oxidative bisulphite converted DNA from human placenta 3

description:
200090270117_R03C01_Grn.idat
200090270117_R03C01_Red.idat
normal placenta sample

source_name: placenta 3 oxBS conversion


title: bisulphite converted DNA from human placenta 5

description:
200090270115_R05C02_Grn.idat
200090270115_R05C02_Red.idat
normal placenta sample

source_name: placenta 5 BS conversion

value: BS


title: oxidative bisulphite converted DNA from human placenta 64

description:
200090270115_R03C02_Grn.idat
200090270115_R03C02_Red.idat
normal placenta sample

source_name: placenta 64 oxBS conversion


title: oxidative bisulphite converted DNA from human placenta 67

description:
200090270069_R06C02_Grn.idat
200090270069_R06C02_Red.idat
normal placenta sample

source_name: placenta 67 oxBS conversion


title: bisulphite converted DNA from human placenta 67

description:
200090270069_R06C01_Grn.idat
200090270069_R06C01_Red.idat
normal placenta sample

source_name: placenta 67 BS conversion


title: bisulphite converted DNA from human placenta 3

description:
200090270104_R04C01_Grn.idat
200090270104_R04C01_Red.idat
normal placenta sample

source_name: placenta 3 BS conversion


title: bisulphite converted DNA from human placenta 64

description:
200090270117_R06C02_Grn.idat
200090270117_R06C02_Red.idat
normal placenta sample

source_name: placenta 64 BS conversion


title: Case: 129; ROI: P


title: Case: 4095; ROI: T


title: Case: 12781; ROI: sB


title: Case: 3720; ROI: T


title: Case: 3720; ROI: AM


title: Case: 12781; ROI: sP

value: sP


title: Case: 3720; ROI: P


title: Case: 129; ROI: AM


title: Case: 5072; ROI: P


title: Case: 3720; ROI: B

value: B


title: Case: 12781; ROI: B


title: 12h_Tet-_CAGATC_L002

type: SRA

city: Heidelberg

first: Chunxuan

last: Shao

address: Im Neuenheimer Feld 280

country: Germany

institute: German Cancer Research Center

library_source: transcriptomic

data_processing:
RTA 1.17.21.3
Raw reads were aligned to hg19 genome by Tophat (v2.0.5)
counts of genes were generated by Htseq
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files with counts for each samples

extract_protocol:
RNA was extracted from 10e6 cells using RNeasy mini kit (Qiagen) with a separate step for DNAse I digestion (Qiagen). ERCC Spike-in control mix-1 (Life technologies) was added to each sample prior to processing (1 μl of a 1:10 dilution of mix-1). RNA from each sample was processed using the RiboGold kit (Epicentre) to remove rRNA.
rRNA-depleted RNA was used to prepare libraries with the Ultra directional RNA library prep kit for Illumina (New England Bioscience) according to manufacturer's instructions.

value: IMR5/75 neuroblastoma cells with tetracycline-inducible MYCN shRNA

tag: time point

tag: tet treatment

value: minus


title: Case: 12781; ROI: T

value: T


title: Case: 5072; ROI: sT

value: sT


title: Case: 12781; ROI: AM


title: Case: 4095; ROI: AM


title: Case: 6042; ROI: sB

value: sB


title: Case: 129; ROI: T


title: Case: 4095; ROI: sT


title: Case: 12781; ROI: P


title: Case: 5072; ROI: sP


title: Case: 3720; ROI: sB


title: Case: 3720; ROI: sT


title: Case: 3720; ROI: sP


title: Case: 5072; ROI: sB


title: Case: 5072; ROI: B


title: Case: 4095; ROI: B


title: Case: 5072; ROI: T


title: Case: 4645; ROI: sB


title: Case: 5072; ROI: AM


title: Case: 4645; ROI: sT


title: Case: 129; ROI: B


title: Case: 4645; ROI: T


title: Case: 12781; ROI: sT


title: Case: 4645; ROI: B


title: Case: 4645; ROI: sP


title: Inactive CD_0432S

status: Public on Sep 11 2017

city: Barcelona

first: Azucena

last: Salas

address: Rosselló, 149-153

department: Gastroenterology

institute: IDIBAPS

description: Gene expression data from blood; peripheral whole blood sample from CD patient collected at the time of endoscopic evaluation

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol using a Gene chip scanner 3000

data_processing: The data was analyzed with Bioconductor tools in R (version 3.1.0; http://www.r-project.org) using RMA as normalization method. Probes were summarized using the revised entrez-based probe annotation of Dai (package hug133plus2hsentrezgcdf, version 18.0.1). Then, data was adjusted for batch effects using the ComBat method. Next we employ a probe-filtering step, excluding those probes that showed a lower coefficient of variation, low intensity levels in all observations (<5)  or which were non-informative (not annotated).

source_name: Human peripheral whole blood from endoscopically inactive CD patient

label_protocol: The derived cDNA from whole blood was produced by Ovation® PicoSL WTA System V2 (NuGEN, USA)

extract_protocol: Total RNA was extracted using the PAXgene Blood RNA Kit (Qiagen, Spain) in a QIAcube instrument (Qiagene, Spain) following the manufacturer's instructions. Additional DNase Treatment & Removal (Ambion, Life Technologies, USA) was used to safely eliminate DNA contamination from RNA samples.

tag: subject status

value: Crohn's disease (CD) patient

value: Crohn

value: Inactive

value: colonic

value: anti-TNF + Immunosupressors

tag: cdeis

tag: partial cdeis

tag: ibd_evolution_time (years)

tag: age (years)

value: Male

value: peripheral whole blood


title: Inactive CD_0349S

value: ileocolonic

tag: treatment

tag: tissue


title: Active CD_0441S

source_name: Human peripheral whole blood from endoscopically active CD patient

value: Active

value: Female


title: Inactive CD_0410S

value: No treatment


title: Inactive CD_0018S

value: Immunosupressors


title: Inactive CD_0092S

value: anti-TNF


title: DC, donor 3 [expression]

city: Badalona, Barcelona

first: Esteban

last: Ballestar

state: N/A = Not Applicable

address: Ctra de Can Ruti, Camí de les Escoles s/n

institute: Josep Carreras Research Institute (IJC)

hyb_protocol: After fragmentation, 600 ng of labeled cRNA from each sample was hybridized in in situ hybridization oven (Agilent) for 17 h at 65ºC and washed during 1 min at rt in Gene Expression Wash Buffer 1 (Agilent) and 1 min at 37 ºC with Gene Expression Wahs buffer 2 (Agilent).

scan_protocol: Scanned on an Agilent G2539A scanner at 3um resolution and 100%PMT. The intensity data of each individual hybridization were extracted and the quality was assessed with the Feature Extraction software 10.7 (Agilent).

data_processing:
Expression data has been normalized using functions from the R package limma. In detail, the data was background corrected using the function normexp and then normalized between arrays using quantile normalization. Normalized array feature values were grouped by gene name and summarized by mean. The patient effect was subtracted from the genewise data by a linear model using patient as predictor.
Given are the luminescence values (Cy3) from the Agilent array; as raw data for all array features and as normalized and summarized genewise expression values as described above.

source_name: CD14 cells treated with GM-CSF/IL4 for 6 days

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100ng of total RNA using the Low Input Quick Amp Labeling kit (Agilent 5190-2305) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol:
Human monocytes were isolated using MACS CD14 microbeads (Milteny) from peripheral blood mononuclear cells using the manufacturer's protocol.
Total RNA was isolated by standard procedures.

tag: cell type

value: dendritic cells

tag: donor


title: Inactive CD_0289S

value: ileal


title: Inactive CD_0149S


title: Inactive CD_0311S


title: Active CD_0445S

value: no treatment


title: Inactive CD_0009S


title: Active CD_0076S

value: anti-TNF + Steroids


title: CD14_monocyte, donor 1 [expression]

source_name: peripheral blood isolated CD14+ cells (monocytes)

value: CD14+ monocytes


title: MDSC, donor 1 [expression]

source_name: CD14 cells treated with GM-CSF/IL4/PGE2 for 6 days

value: myeloid-derived suppressor cells


title: MDSC, donor 3 [expression]


title: DC, donor 2 [expression]


title: Active CD_0440S

value: Crohn's disease (CD) patient

value: Crohn

value: Immunosupresor


title: MDSC, donor 2 [expression]


title: CD14_monocyte, donor 2 [expression]


title: DC, donor 1 [expression]


title: CD14_monocyte, donor 3 [expression]


title: Active CD_0412S


title: Active CD_0431S

value: Male


title: Active CD_0423S

value: Immunosupresor + Steroids

value: peripheral whole blood


title: Active CD_0416S

value: Active


title: Active CD_0377S

value: Female


title: Active CD_0258S

value: colonic


title: Active CD_0181S

value: ileocolonic


title: Active CD_0312S


title: Active CD_0142S


title: Active CD_0258Sbis


title: Active CD_0137S


title: Active CD_0415S


title: Active CD_0421S


title: Active CD_0405S

value: anti-TNF


title: Active CD_0273S


title: Active CD_0225S


title: Active CD_0128S


title: Active CD_0093S


title: Active CD_0100S


title: Active CD_0089S

value: Steroids


title: Active CD_0130S


title: Active CD_0110S


title: Active CD_0090S


title: Active CD_0084S


title: Active CD_0069S


title: Active CD_0057S


title: Active CD_0037S


title: Active CD_0108S


title: Active CD_0115S


title: Active CD_0438S


title: Active CD_0051S


title: Active CD_0342S


title: Active CD_0143S

value: ileal

value: anti-TNF + Immunosupresor


title: Control_0213S

description: Gene expression data from blood; peripheral whole blood sample from non-IBD control collected at the time of endoscopic evaluation

source_name: Human peripheral whole blood from non-IBD control

value: non-IBD (inflammatory bowel disease) control

value: Control


title: Control_0420S


title: Control_0249S


title: Control_0215S


title: Control_0212Sbis


title: Active CD_0143Sbis


title: Control_0212S


title: Active CD_0157S


title: Control_0193S


title: Active CD_0036S


title: Control_0229S


title: Control_0201S


title: Control_0211Sbis


title: Active CD_0144S


title: Control_0223S


title: Control_0224S


title: Control_0222S


title: Control_0185S


title: Control_0154S


title: Control_0214S


title: Control_0156S


title: Control_0211S


title: Control_0200S


title: Control_0170S


title: Inactive UC_0159S

description: Gene expression data from blood; peripheral whole blood sample from UC patient collected at the time of endoscopic evaluation

source_name: Human peripheral whole blood from endoscopically inactive UC patient

value: Ulcerative colitis (UC) patient

value: Colitis

value: Inactive

value: Pancolitis


title: Inactive UC_0307S

value: Proctitis

value: Male


title: Inactive UC_0308S

value: peripheral whole blood


title: Control_0152S


title: Control_0153S


title: Active UC_0219S

source_name: Human peripheral whole blood from endoscopically active UC patient

value: Active


title: Active UC_0145S

value: Left-sided colitis


title: Active UC_0218S

value: Female


title: Inactive UC_0125S

value: No treatment


title: Active UC_0186S


title: Active UC_0419S


title: Active UC_0155S


title: Inactive UC_0135S

value: Immunosupressors


title: Active UC_0097S

value: anti-TNF


title: Active UC_0164S


title: Inactive UC_0053S


title: Active UC_0169S

value: no treatment


title: Active UC_0091S

value: Steroids


title: Inactive UC_0103S


title: Active UC_0114S


title: KMH2_LY294002_rep2

city: Durham

first: Wenbin

last: Wei

address: Stockton Road

department: Biosciences

institute: Durham University

description: Gene expression data of KMH2 cells treated with LY294002 for 16 hours

hyb_protocol: Fragmented cRNA was hybridized to HG-Focus array using Affymetrix standard protocol

scan_protocol: Affymetrix Standard protocol  Affymetrix Standard protocol

data_processing: Probe level quantile normalisation and robust multi-array analysis on the raw CEL files were performed using the affy package of the Bioconductor project.

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

growth_protocol: RPMI1640, 10% FCS, 1% pen/strep

extract_protocol: RNA extraction was performed with Qiagen RNeasy Mini Kit

treatment_protocol: KMH2 were cultivated in RPMI1640, 10% FCS, 1% pen/strep in presence of 30uM LY294002 or control DMSO.

tag: cell line

tag: perturbagen


title: Active UC_0083S

tag: gender


title: Active UC_0182S


title: Inactive UC_0043S


title: Active UC_0038S

value: Immunosupresor + Steroids


title: KMH2_DMSO_rep1

description: Gene expression data of KMH2 cells

source_name: KMH2, DMSO, 16 hours

value: DMSO


title: Active UC_0112S

value: Ulcerative colitis (UC) patient


title: KMH2_DMSO_rep3

description: Gene expression data of KMH2 cells


title: KMH2_LY294002_rep1


title: KMH2_DMSO_rep2

description: Gene expression data of KMH2 cells


title: Active UC_0087S

value: Colitis

value: Immunosupresor


title: Active UC_0078S


title: L428_scr_rep2

description: Gene expression data of L428 cells treated with negative control siRNA

hyb_protocol: Fragmented cRNA was hybridized to PrimeView array using Affymetrix standard protocol

source_name: L428, Negative_Control_siRNA

treatment_protocol: L428 were nucleofected with L solution following Lonza optimzalized protocol with either 3ug BATF3siRNA or control siRNA and cultivated for 48 hours.


title: L428_scr_rep3


title: L428_BATF3_siRNA_rep3

description: Gene expression data of L428 cells treated with BATF3 siRNA

source_name: L428, BATF3_siRNA


title: L428_scr_rep1


title: L428_BATF3_siRNA_rep1


title: L428_BATF3_siRNA_rep2


title: MDSC_donor 2 with L-161,982 5 µM (EP4 antagonist)

description:
CD14 cells treated with IL4/ GM-CSF/PGE2 and EP4 antagonist for 6 days
MDSCs_4_2

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450k Beadchip using standard Illumina protocol

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

data_processing: Regular BeadStudio processing

extract_protocol: Human monocytes were isolated using MACS CD14 microbeads (Milteny) from peripheral blood mononuclear cells using the manufacturer's protocol

value: EP4 antagonized myeloid-derived suppressor cells


title: MDSC_donor 2 with PF 04418948 5 µM (EP2 antagonist)

description:
CD14 cells treated with IL4/ GM-CSF/PGE2 and EP2 antagonist for 6 days
MDSCs_2_2

value: EP2 antagonized myeloid-derived suppressor cells


title: MDSC_donor 1with PF 04418948 5 µM (EP2 antagonist) and L-161,982 5 µM (EP4 antagonist)

description:
CD14 cells treated with IL4/ GM-CSF/PGE2 and EP2 + EP4 antagonist for 6 days
MDSCs_2_4_1

value: EP2 + EP4 antagonized myeloid-derived suppressor cells


title: MDSC_donor 3 with L-161,982 5 µM (EP4 antagonist)

description:
CD14 cells treated with IL4/ GM-CSF/PGE2 and EP4 antagonist for 6 days
MDSCs_4_3


title: MDSC_donor 3 with PF 04418948 5 µM (EP2 antagonist) and L-161,982 5 µM (EP4 antagonist)

description:
CD14 cells treated with IL4/ GM-CSF/PGE2 and EP2 + EP4 antagonist for 6 days
MDSCs_2_4_3


title: MDSC_donor 1 with L-161,982 5 µM (EP4 antagonist)

description:
CD14 cells treated with IL4/ GM-CSF/PGE2 and EP4 antagonist for 6 days
MDSCs_4_1


title: MDSC_donor 3

description:
CD14 cells treated with IL4/ GM-CSF/PGE2 for 6 days
MDSCs_3

value: myeloid-deriver suppressor cells


title: MDSC_donor 2 with PF 04418948 5 µM (EP2 antagonist) and L-161,982 5 µM (EP4 antagonist)

description:
CD14 cells treated with IL4/ GM-CSF/PGE2 and EP2 + EP4 antagonist for 6 days
MDSCs_2_4_2


title: MDSC_donor 1 with PF 04418948 5 µM (EP2 antagonist)

description:
CD14 cells treated with IL4/ GM-CSF/PGE2 and EP2 antagonist for 6 days
MDSCs_2_1


title: MDSC_donor 3 with PF 04418948 5 µM (EP2 antagonist)

description:
CD14 cells treated with IL4/ GM-CSF/PGE2 and EP2 antagonist for 6 days
MDSCs_2_3


title: 145a: OvCa_donor 16

description: CD11b+ cells isolated from ovarian cancer patient ascitic fluid

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation850k Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader (Illumina HiSeq2000) using standard recommended Illumina scanner setting

data_processing: preprocesQuantile function from minfi r package

source_name: Ascitic fluid from ovarian cancer patient

extract_protocol: Human CD11b+ cells were isolated using MACS anti-CD11b+ microbeads (Milteny) from peripheral blood mononuclear cells or ascitic fluids using the manufacturer's protocol.

treatment_protocol: no treatment

tag: diagnosis

value: ovarian cancer

value: Ascitic fluid


title: 155a: OvCa_donor 22


title: 117a: OvCa_donor 14


title: 157a: OvCa_donor 21


title: 112a: OvCa_donor 19


title: 179a: OvCa_donor 20


title: 190a: OvCa_donor 15


title: 167a: OvCa_donor 18


title: 203b: OvCa_donor 5

description: CD11b+ cells isolated from ovarian cancer patient blood

source_name: Peripheral blood from ovarian cancer patient

value: Peripheral blood


title: 086b: OvCa_donor 2


title: 133b: OvCa_donor 11


title: 196b: OvCa_donor 10


title: 204b: OvCa_donor 1


title: 173b: OvCa_donor 3


title: 158b: OvCa_donor 6


title: 208b: OvCa_donor 8


title: MDSC_donor 2

description:
CD14 cells treated with IL4/ GM-CSF/PGE2 for 6 days
MDSCs_2


title: RRMS patient366

status: Public on Sep 10 2017

city: Cambridge

first: Jadwiga

last: Bienkowska

address: 45 Fayette Str Apt 3

institute: BiogenIdec

hyb_protocol: standard Affymetrix protcol

scan_protocol: HTAPS scanner was used

data_processing: data was normalized using  gcrma using R package for each set separately

source_name: whole blood from Relapsing Remitting Multiple Sclerosis patient

label_protocol: NuGEN Ovation

growth_protocol: Whole Blood samples in collected fom PAXgene tubes

extract_protocol: The RNA was extracted with Trizol reagent (Life Technologies) and cleaned up with RNA easy (Qiagen) according to the manufacturer’s protocols.

treatment_protocol: This is baseline whole blood expresion data for RRMS patients

value: Relapsing Remitting Multiple Sclerosis (RRMS)

value: whole blood

tag: onsyrs

tag: edssbl

tag: trelmos

tag: msssbl

tag: expertmix

value: RRMSB


title: 164b: OvCa_donor 9


title: RRMS patient261

value: RRMSA


title: RRMS patient426


title: 202b: OvCa_donor 7


title: 191b: OvCa_donor 4


title: RRMS patient456


title: DC_donor 3

description:
CD14 cells treated with IL4/ GM-CSF for 6 days
DC_3

value: immature dendritic cells


title: RRMS patient276


title: RRMS patient48


title: CD14_monocyte_3_donor 3

description:
peripheral blood isolated CD14+ cells (monocytes)
MO_3

value: CD14+ cells


title: 181a: OvCa_donor 12


title: RRMS patient543


title: RRMS patient447


title: DC_donor 2

description:
CD14 cells treated with IL4/ GM-CSF for 6 days
DC_2


title: RRMS patient371


title: RRMS patient179


title: CD14_monocyte_2_donor 2

description:
peripheral blood isolated CD14+ cells (monocytes)
MO_2


title: DC_donor 1

description:
CD14 cells treated with IL4/ GM-CSF for 6 days
DC_1


title: MDSC_donor 1

description:
CD14 cells treated with IL4/ GM-CSF/PGE2 for 6 days
MDSCs_1


title: RRMS patient51


title: RRMS patient351


title: RRMS patient282


title: RRMS patient96


title: RRMS patient343


title: RRMS patient152


title: RRMS patient146


title: RRMS patient415


title: RRMS patient376


title: CD14_monocyte_1_donor 1

description:
peripheral blood isolated CD14+ cells (monocytes)
MO_1


title: HD8: HD_donor 8

description: CD11b+ cells isolated from HD blood

source_name: Peripheral blood from healthy donor

value: healthy


title: RRMS patient268


title: RRMS patient466


title: RRMS patient241


title: HD7: HD_donor 7

description: CD11b+ cells isolated from HD blood


title: RRMS patient406


title: RRMS patient517


title: RRMS patient252


title: RRMS patient348


title: RRMS patient257


title: RRMS patient45


title: HD9: HD_donor 9

description: CD11b+ cells isolated from HD blood


title: HD2: HD_donor 2

description: CD11b+ cells isolated from HD blood


title: RRMS patient122


title: HD3: HD_donor 3

description: CD11b+ cells isolated from HD blood


title: RRMS patient149


title: HD10: HD_donor 10

description: CD11b+ cells isolated from HD blood


title: RRMS patient37


title: RRMS patient368


title: RRMS patient95


title: RRMS patient411


title: HD4: HD_donor 4

description: CD11b+ cells isolated from HD blood


title: HD6: HD_donor 6

description: CD11b+ cells isolated from HD blood


title: RRMS patient114


title: RRMS patient407


title: RRMS patient420


title: RRMS patient196


title: RRMS patient153


title: RRMS patient481


title: RRMS patient93


title: RRMS patient131


title: RRMS patient433


title: RRMS patient129


title: RRMS patient449


title: RRMS patient242


title: RRMS patient181


title: RRMS patient457


title: RRMS patient291


title: RRMS patient100


title: RRMS patient31


title: RRMS patient286


title: RRMS patient73


title: RRMS patient307


title: RRMS patient464


title: RRMS patient172


title: RRMS patient90


title: RRMS patient250


title: HD1: HD_donor 1

description: CD11b+ cells isolated from HD blood


title: RRMS patient77


title: RRMS patient32


title: RRMS patient258


title: RRMS patient260


title: RRMS patient274


title: RRMS patient193


title: RRMS patient28


title: RRMS patient493


title: RRMS patient444


title: RRMS patient237


title: RRMS patient471


title: RRMS patient336


title: RRMS patient110


title: RRMS patient165


title: RRMS patient299


title: RRMS patient163


title: RRMS patient8


title: RRMS patient429


title: RRMS patient117


title: RRMS patient119


title: RRMS patient523


title: RRMS patient360


title: RRMS patient207


title: RRMS patient223


title: RRMS patient498


title: RRMS patient178


title: RRMS patient278


title: RRMS patient13


title: RRMS patient170


title: RRMS patient116


title: RRMS patient208


title: RRMS patient340


title: RRMS patient164


title: RRMS patient427


title: RRMS patient512


title: RRMS patient142


title: RRMS patient528


title: RRMS patient292


title: RRMS patient305


title: RRMS patient499


title: RRMS patient3


title: RRMS patient344


title: RRMS patient350


title: RRMS patient365


title: RRMS patient352


title: RRMS patient186


title: RRMS patient201


title: RRMS patient370


title: RRMS patient387


title: RRMS patient212


title: RRMS patient231


title: RRMS patient332


title: RRMS patient392


title: RRMS patient540


title: RRMS patient91


title: RRMS patient326


title: RRMS patient367


title: RRMS patient308


title: RRMS patient306


title: RRMS patient327


title: RRMS patient442


title: RRMS patient17


title: RRMS patient298


title: RRMS patient157


title: RRMS patient454


title: RRMS patient357


title: RRMS patient26


title: RRMS patient397


title: RRMS patient324


title: RRMS patient161


title: RRMS patient355


title: RRMS patient139


title: RRMS patient189


title: RRMS patient187


title: RRMS patient511


title: RRMS patient285


title: RRMS patient199


title: RRMS patient425


title: RRMS patient349


title: RRMS patient194


title: RRMS patient339


title: RRMS patient60


title: RRMS patient12


title: RRMS patient68


title: RRMS patient135


title: RRMS patient403


title: RRMS patient63


title: RRMS patient358


title: RRMS patient469


title: RRMS patient143


title: RRMS patient99


title: RRMS patient118


title: RRMS patient1


title: RRMS patient386


title: RRMS patient378


title: RRMS patient440


title: RRMS patient294


title: RRMS patient530


title: RRMS patient253


title: RRMS patient62


title: RRMS patient419


title: RRMS patient109


title: RRMS patient70


title: RRMS patient438


title: RRMS patient488


title: RRMS patient519


title: RRMS patient515


title: RRMS patient19


title: RRMS patient15


title: RRMS patient311


title: RRMS patient329


title: RRMS patient545


title: RRMS patient312


title: RRMS patient84


title: RRMS patient249


title: RRMS patient475


title: RRMS patient389


title: RRMS patient80


title: RRMS patient448


title: RRMS patient101


title: RRMS patient342


title: RRMS patient338


title: RRMS patient525


title: RRMS patient198


title: RRMS patient219


title: RRMS patient548


title: RRMS patient490


title: RRMS patient215


title: RRMS patient421


title: RRMS patient300


title: RRMS patient195


title: RRMS patient106


title: RRMS patient432


title: RRMS patient228


title: RRMS patient470


title: RRMS patient467


title: RRMS patient14


title: RRMS patient254


title: RRMS patient318


title: RRMS patient504


title: RRMS patient453


title: RRMS patient489


title: RRMS patient526


title: RRMS patient443


title: RRMS patient167


title: RRMS patient16


title: RRMS patient30


title: RRMS patient302


title: RRMS patient50


title: RRMS patient388


title: RRMS patient255


title: RRMS patient290


title: RRMS patient25


title: RRMS patient97


title: RRMS patient217


title: RRMS patient270


title: RRMS patient225


title: RRMS patient145


title: RRMS patient128


title: RRMS patient64


title: RRMS patient188


title: RRMS patient346


title: RRMS patient82


title: RRMS patient47


title: RRMS patient500


title: RRMS patient497


title: RRMS patient177


title: RRMS patient301


title: RRMS patient123


title: RRMS patient22


title: RRMS patient331


title: RRMS patient369


title: RRMS patient127


title: RRMS patient36


title: RRMS patient465


title: RRMS patient428


title: RRMS patient478


title: RRMS patient103


title: RRMS patient423


title: RRMS patient168


title: RRMS patient501


title: RRMS patient264


title: RRMS patient322


title: RRMS patient206


title: RRMS patient315


title: RRMS patient377


title: RRMS patient226


title: RRMS patient78


title: RRMS patient405


title: RRMS patient216


title: RRMS patient140


title: RRMS patient134


title: RRMS patient502


title: RRMS patient49


title: RRMS patient418


title: RRMS patient74


title: RRMS patient75


title: RRMS patient310


title: RRMS patient162


title: RRMS patient281


title: RRMS patient224


title: RRMS patient461


title: RRMS patient112


title: RRMS patient430


title: RRMS patient353


title: RRMS patient330


title: RRMS patient211


title: RRMS patient413


title: RRMS patient240


title: RRMS patient362


title: RRMS patient52


title: RRMS patient21


title: RRMS patient230


title: RRMS patient184


title: RRMS patient288


title: RRMS patient541


title: RRMS patient484


title: RRMS patient269


title: RRMS patient180


title: RRMS patient476


title: RRMS patient213


title: RRMS patient87


title: RRMS patient304


title: RRMS patient229


title: RRMS patient233


title: RRMS patient10


title: RRMS patient531


title: RRMS patient534


title: RRMS patient394


title: RRMS patient247


title: RRMS patient363


title: RRMS patient401


title: RRMS patient280


title: RRMS patient239


title: RRMS patient151


title: RRMS patient132


title: RRMS patient434


title: RRMS patient130


title: RRMS patient384


title: RRMS patient246


title: RRMS patient494


title: RRMS patient409


title: RRMS patient266


title: RRMS patient59


title: RRMS patient203


title: RRMS patient393


title: RRMS patient61


title: RRMS patient115


title: RRMS patient503


title: RRMS patient382


title: RRMS patient538


title: RRMS patient197


title: RRMS patient39


title: RRMS patient111


title: RRMS patient141


title: RRMS patient395


title: RRMS patient46


title: RRMS patient159


title: RRMS patient354


title: RRMS patient120


title: RRMS patient380


title: RRMS patient190


title: RRMS patient160


title: RRMS patient445


title: RRMS patient273


title: RRMS patient54


title: RRMS patient451


title: RRMS patient71


title: RRMS patient227


title: RRMS patient147


title: RRMS patient533


title: RRMS patient200


title: RRMS patient85


title: RRMS patient524


title: RRMS patient375


title: RRMS patient383


title: RRMS patient416


title: RRMS patient459


title: RRMS patient460


title: RRMS patient486


title: RRMS patient267


title: RRMS patient359


title: RRMS patient256


title: RRMS patient546


title: RRMS patient79


title: RRMS patient209


title: RRMS patient108


title: RRMS patient536


title: RRMS patient20


title: RRMS patient66


title: RRMS patient40


title: RRMS patient491


title: RRMS patient404


title: RRMS patient235


title: RRMS patient495


title: RRMS patient477


title: RRMS patient11


title: RRMS patient518


title: RRMS patient356


title: RRMS patient508


title: RRMS patient487


title: RRMS patient210


title: RRMS patient41


title: RRMS patient171


title: RRMS patient314


title: RRMS patient496


title: RRMS patient43


title: RRMS patient385


title: RRMS patient408


title: RRMS patient57


title: RRMS patient439


title: RRMS patient2


title: RRMS patient133


title: RRMS patient485


title: RRMS patient321


title: RRMS patient24


title: RRMS patient372


title: RRMS patient527


title: RRMS patient27


title: RRMS patient53


title: RRMS patient458


title: RRMS patient424


title: RRMS patient455


title: RRMS patient287


title: RRMS patient33


title: RRMS patient414


title: RRMS patient104


title: RRMS patient507


title: RRMS patient379


title: RRMS patient293


title: RRMS patient176


title: RRMS patient462


title: RRMS patient121


title: RRMS patient544


title: RRMS patient537


title: RRMS patient148


title: RRMS patient347


title: RRMS patient446


title: RRMS patient69


title: RRMS patient238


title: RRMS patient191


title: RRMS patient513


title: RRMS patient535


title: RRMS patient320


title: RRMS patient182


title: RRMS patient506


title: RRMS patient333


title: RRMS patient173


title: RRMS patient204


title: RRMS patient514


title: RRMS patient309


title: RRMS patient81


title: RRMS patient126


title: RRMS patient410


title: RRMS patient222


title: RRMS patient262


title: RRMS patient150


title: RRMS patient521


title: RRMS patient295


title: RRMS patient505


title: RRMS patient390


title: RRMS patient422


title: RRMS patient398


title: RRMS patient441


title: RRMS patient83


title: RRMS patient547


title: RRMS patient492


title: RRMS patient4


title: RRMS patient296


title: RRMS patient125


title: RRMS patient192


title: RRMS patient374


title: RRMS patient474


title: RRMS patient364


title: RRMS patient361


title: RRMS patient236


title: RRMS patient7


title: RRMS patient303


title: RRMS patient35


title: RRMS patient289


title: RRMS patient42


title: RRMS patient522


title: RRMS patient72


title: RRMS patient98


title: RRMS patient214


title: RRMS patient480


title: RRMS patient313


title: RRMS patient92


title: RRMS patient76


title: RRMS patient391


title: RRMS patient94


title: RRMS patient89


title: RRMS patient234


title: RRMS patient244


title: RRMS patient221


title: RRMS patient473


title: RRMS patient550


title: RRMS patient259


title: RRMS patient265


title: RRMS patient284


title: RRMS patient279


title: RRMS patient479


title: RRMS patient136


title: RRMS patient277


title: RRMS patient169


title: RRMS patient275


title: RRMS patient113


title: RRMS patient463


title: RRMS patient323


title: RRMS patient412


title: RRMS patient341


title: RRMS patient417


title: RRMS patient396


title: RRMS patient155


title: RRMS patient18


title: RRMS patient174


title: RRMS patient509


title: RRMS patient472


title: RRMS patient334


title: RRMS patient220


title: RRMS patient124


title: RRMS patient38


title: RRMS patient381


title: RRMS patient251


title: RRMS patient335


title: RRMS patient6


title: RRMS patient166


title: RRMS patient542


title: RRMS patient532


title: RRMS patient402


title: RRMS patient436


title: RRMS patient34


title: RRMS patient539


title: RRMS patient156


title: RRMS patient88


title: RRMS patient65


title: RRMS patient431


title: RRMS patient202


title: RRMS patient67


title: RRMS patient482


title: RRMS patient337


title: RRMS patient319


title: RRMS patient483


title: RRMS patient44


title: RRMS patient55


title: RRMS patient452


title: RRMS patient317


title: RRMS patient58


title: RRMS patient399


title: RRMS patient29


title: RRMS patient185


title: RRMS patient435


title: RRMS patient283


title: RRMS patient316


title: RRMS patient271


title: RRMS patient232


title: RRMS patient154


title: RRMS patient510


title: RRMS patient272


title: RRMS patient56


title: RRMS patient23


title: RRMS patient175


title: RRMS patient450


title: RRMS patient205


title: RRMS patient243


title: RRMS patient520


title: RRMS patient400


title: RRMS patient138


title: RRMS patient297


title: RRMS patient529


title: RRMS patient105


title: RRMS patient328


title: RRMS patient248


title: RRMS patient158


title: RRMS patient107


title: RRMS patient245


title: RRMS patient468


title: RRMS patient437


title: RRMS patient102


title: RRMS patient516


title: RRMS patient183


title: RRMS patient345


title: RRMS patient137


title: RRMS patient9


title: RRMS patient263


title: RRMS patient218


title: RRMS patient549


title: Genomic DNA from blood leukocytes [9445229038_R06C02]

status: Public on Sep 09 2017

city: Darlinghurst

first: Timothy

middle: John

last: Peters

state: NSW

address: 384 Victoria St

department: Immunology

country: Australia

institute: Garvan Institute of Medical Research

description:
9445229038_R06C02
Matched with 10005833035_R05C01

hyb_protocol: Bisulphite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450k BeadChip using standard Illumina protocol.

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

data_processing: Data was normalized using Bioconductor package 'wateRmelon',

source_name: Blood leukocytes

label_protocol: Standard Illumina Protocol.

extract_protocol: Genomic DNA was extracted from 3x3mm dried blood spot punches using GenSolve technology followed by purification using the QIAamp DNA micro kit and an additional ethanol precipitation step. DNA was extracted from the peripheral blood leukocyte samples, using the QIAquick DNA extraction kit.

value: Blood leukocytes

tag: age

value: 5 years

value: Male


title: Genomic DNA from blood leukocytes [9445229039_R05C02]

description:
9445229039_R05C02
Matched with 10005833043_R05C02

value: Female


title: Genomic DNA from blood leukocytes [9445229039_R06C02]

description:
9445229039_R06C02
Matched with 10005833035_R03C01


title: Genomic DNA from blood leukocytes [9445229039_R06C01]

description:
9445229039_R06C01
Matched with 10003886016_R05C01


title: RRMS patient86


title: RRMS patient5


title: RRMS patient373


title: Genomic DNA from blood leukocytes [9445229038_R05C02]

description:
9445229038_R05C02
Matched with 10005833095_R05C01


title: Genomic DNA from blood leukocytes [9221198134_R06C02]

description:
9221198134_R06C02
Matched with 10003886104_R05C01


title: Genomic DNA from blood leukocytes [9445229038_R06C01]

description:
9445229038_R06C01
Matched with 10005833035_R04C02


title: CELLS OVEREXPRESSING SYNDECAN-1 LACKING RMKKKdel NUCLEAR LOCALIZATION SIGNAL, biological replicate3

city: Huddinge

first: Tünde

last: Szatmári

state: Stockholm

address: F42 Karolinska Universitetssjukhuset

department: Laboratory Medicine

institute: Karolinska Institute

hyb_protocol: From non-degraded high-quality total RNA we prepared and hybridized biotinylated complementary RNA to Gene 1.1 ST Arrays, and then washed, stained and scanned.

scan_protocol: Standardized Affymetrix protocols (Affymetrix Inc., Santa Clara, CA) was used.

data_processing: Subsequent data analyses were performed using the Affymetrix Gene Chip Command Console. The processing methods were: Summarization: PLIER, Background Correction: PM-GCBG, Normalization: Global Median.

source_name: B6FS_syndecan-1 gene lacking the region encoding the RMKKK sequence

label_protocol: Total RNA were amplified and biotynilated according to the standard Affymetrix protocol

extract_protocol: Total RNA was isolated from sub-confluent cell cultures, using the High Pure RNA isolation Kit (Roche, Mannheim, Germany),

value: human malignant fibrosarcoma cell-line

tag: transfected with

value: pN1 plasmid carrying syndecan-1 gene lacking the region encoding the RMKKK sequence

tag: genotype/variation

value: overexpression of modulated syndecan-1


title: VECTOR CONTROL CELLS, biological replicate3

source_name: B6FS_empty plasmid

value: pN1 empty plasmid

value: empty vector control


title: RRMS patient325


title: RRMS patient144


title: CELLS OVEREXPRESSING SYNDECAN-1 LACKING RMKKKdel NUCLEAR LOCALIZATION SIGNAL, biological replicate2


title: Genomic DNA from blood leukocytes [9221198134_R05C02]

description:
9221198134_R05C02
Matched with 10003886039_R05C01


title: 4T1LN (rep1-2)

city: Taipei

first: Shih-Chia

last: Huang

address: 128 Academia Road, Section 2, Nankang

country: Taiwan

institute: Academia Sinica

description:
S7_H013, S7_H014
cDNA expression profiling.
This Sample represents 2 replicates.

hyb_protocol: Fluorescent targets were hybridized to the Mouse Whole Genome OneArray® with Phalanx hybridization buffer using Phalanx Hybridization System. After 16 hrs hybridization at 50 ℃, non-speciﬁc binding targets were washed away by three different washing steps (Wash I 42 ℃ 5 mins; Wash II 42 ℃, 5 mins, 25 ℃ 5 mins; Wash III rinse 20 times).

scan_protocol: The arrays were scanned by Agilent G2505C Scanner (PMT: 30% Power: 100% Scan resolution: 10uM) and quantify the fluorescence intensity.

data_processing:
The signal intensity of each spot was loaded into Rosetta Resolver System® (Rosetta Biosoftware) to process data analysis. The error model of Rosetta Resolver System® could remove both systematic and random errors from the data. We ﬁltered out spots that the ﬂag is less than 0. Spots that passed the criteria were normalized by 50% median scaling normalization method. Normalize intensities: Median scaling performed on data set without flagged and control data. Merge technical replicate data: Average intensity values calculated on technical replicates.
Calculate average ratios of the hybridization replicates and find significant values for each gene by pairwise comparison (Ranking and hypothesis testing).

source_name: week3 4T1LN

label_protocol: 1 µg of total RNA was reverse-transcribed and amplified using Amino Allyl aRNA Amplification Kit (Phalanx Biotech Group, Taiwan) and Cy5 dyes (Amersham Pharmacia, Piscataway, NJ, USA).

growth_protocol: The single cell suspension were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS), 2 mM L-glutamine, 1 mM non-essential, amino acids (NEAA), 1 mM sodium pyruvate, antibiotics/antimycotics, and 60 μM 6-thioguanine in a humidified 37°C incubator supplemented with 5% CO2.

extract_protocol: RNA extraction by Trizol. RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis with the result of A260/A280≧1.8, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧7).

treatment_protocol: No treatment.

tag: originating cell line

tag: originating cell type

value: Breast cancer cell line

value: tumor-draining lymph node


title: VECTOR CONTROL CELLS, biological replicate2


title: VECTOR CONTROL CELLS, biological replicate1


title: CELLS OVEREXPRESSING FULL LENGTH SYNDECAN-1, biological replicate 2

source_name: B6FS_ full-length syndecan-1

value: pN1 plasmid carrying full-length syndecan-1 gene

value: overexpression of full-length syndecan-1


title: 4T1PT (rep1-2)

description:
S1_H001, S1_H002
cDNA expression profiling.
This Sample represents 2 replicates.

source_name: week3 4T1PT

tag: tissue

value: primary tumor


title: CELLS OVEREXPRESSING FULL LENGTH SYNDECAN-1, biological replicate 1

tag: cell type


title: Genomic DNA from blood leukocytes [9221198134_R04C02]

description:
9221198134_R04C02
Matched with 200190110102_R05C02


title: CELLS OVEREXPRESSING FULL LENGTH SYNDECAN-1, biological replicate 3


title: Genomic DNA from blood leukocytes [9221198134_R03C02]


title: Genomic DNA from blood leukocytes [9221198134_R02C02]


title: Genomic DNA from blood leukocytes [9221198134_R04C01]

description:
9221198134_R04C01
Matched with 10005833106_R01C01


title: Genomic DNA from blood leukocytes [9221198134_R03C01]

description:
9221198134_R03C01
Matched with 9904796235_R06C02


title: Genomic DNA from blood leukocytes [9221198134_R05C01]

description:
9221198134_R05C01
Matched with 200190110116_R01C02


title: Genomic DNA from blood leukocytes [9221198134_R02C01]

description:
9221198134_R02C01
Matched with 10005833073_R03C02


title: Genomic DNA from blood leukocytes [9221198134_R01C01]

description:
9221198134_R01C01
Matched with 10003886039_R02C01


title: Genomic DNA from blood leukocytes [9221198133_R06C02]


title: Genomic DNA from blood leukocytes [9221198133_R05C02]

description:
9221198133_R05C02
Matched with 10005833007_R05C02


title: CELLS OVEREXPRESSING SYNDECAN-1 LACKING RMKKKdel NUCLEAR LOCALIZATION SIGNAL, biological replicate1


title: Genomic DNA from blood leukocytes [9221198133_R04C02]

description:
9221198133_R04C02
Matched with 200190110084_R03C01


title: Genomic DNA from blood leukocytes [9221198133_R03C02]

description:
9221198133_R03C02
Matched with 10003885149_R06C01


title: Genomic DNA from blood leukocytes [9221198133_R02C02]

description:
9221198133_R02C02
Matched with 9904796235_R05C02


title: Genomic DNA from blood leukocytes [9221198133_R05C01]

description:
9221198133_R05C01
Matched with 9904796235_R01C02


title: Genomic DNA from blood leukocytes [9221198133_R03C01]

description:
9221198133_R03C01
Matched with 10005833073_R04C01


title: Genomic DNA from blood leukocytes [9221198134_R01C02]

description:
9221198134_R01C02
Matched with 10005833062_R03C01


title: Genomic DNA from blood leukocytes [9221198133_R04C01]

description:
9221198133_R04C01
Matched with 9904796235_R06C01


title: Genomic DNA from blood leukocytes [9221198133_R01C02]

description:
9221198133_R01C02
Matched with 10003886039_R05C02


title: Genomic DNA from blood leukocytes [8769527085_R04C02]

description:
8769527085_R04C02
Matched with 10005833032_R01C01


title: Genomic DNA from blood leukocytes [9221198133_R02C01]

description:
9221198133_R02C01
Matched with 10005833034_R02C01


title: Genomic DNA from blood leukocytes [8769527085_R03C02]

description:
8769527085_R03C02
Matched with 9904796235_R05C01


title: Genomic DNA from blood leukocytes [9221198133_R06C01]

description:
9221198133_R06C01
Matched with 10005833085_R01C01


title: Genomic DNA from blood leukocytes [8769527085_R01C02]

description:
8769527085_R01C02
Matched with 10003886068_R06C01


title: Genomic DNA from blood leukocytes [9221198133_R01C01]

description:
9221198133_R01C01
Matched with 10005833080_R06C02


title: Genomic DNA from blood leukocytes [8769527085_R05C01]

description:
8769527085_R05C01
Matched with 10005833034_R03C01


title: Genomic DNA from blood leukocytes [8769527085_R06C02]

description:
8769527085_R06C02
Matched with 10003886027_R04C01


title: Genomic DNA from blood leukocytes [8769527085_R03C01]

description:
8769527085_R03C01
Matched with 9904796235_R02C02


title: Genomic DNA from blood leukocytes [8769527085_R06C01]


title: Genomic DNA from blood leukocytes [8769527085_R04C01]

description:
8769527085_R04C01
Matched with 10005833085_R02C02


title: Genomic DNA from blood leukocytes [9221198134_R06C01]

description:
9221198134_R06C01
Matched with 10003886027_R06C01


title: Genomic DNA from blood leukocytes [8769527085_R01C01]

description:
8769527085_R01C01
Matched with 10003886104_R04C01


title: Genomic DNA from blood leukocytes [8769527038_R06C02]

description:
8769527038_R06C02
Matched with 10003885149_R02C01


title: Genomic DNA from blood leukocytes [8769527038_R03C02]

description:
8769527038_R03C02
Matched with 10005833094_R03C01


title: Genomic DNA from blood leukocytes [8769527038_R05C02]

description:
8769527038_R05C02
Matched with 9904796235_R03C02


title: Genomic DNA from blood leukocytes [8769527038_R02C02]

description:
8769527038_R02C02
Matched with 10005833085_R06C01


title: Genomic DNA from blood leukocytes [8769527038_R01C02]

description:
8769527038_R01C02
Matched with 10003886027_R04C02


title: Genomic DNA from blood leukocytes [8769527038_R05C01]

description:
8769527038_R05C01
Matched with 200275560101_R03C02


title: Genomic DNA from blood leukocytes [8769527038_R06C01]

description:
8769527038_R06C01
Matched with 10005833032_R05C02


title: Genomic DNA from blood leukocytes [8769527038_R04C01]

description:
8769527038_R04C01
Matched with 10003886023_R02C01


title: Genomic DNA from blood leukocytes [8769527038_R03C01]

description:
8769527038_R03C01
Matched with 10003885149_R05C01


title: Genomic DNA from blood leukocytes [8769527038_R02C01]

description:
8769527038_R02C01
Matched with 200275560101_R03C01


title: Genomic DNA from blood leukocytes [8769527085_R05C02]


title: Genomic DNA from blood leukocytes [8769527038_R01C01]


title: Genomic DNA from blood leukocytes [8963266087_R06C02]

description:
8963266087_R06C02
Matched with 10005833095_R01C02


title: Genomic DNA from blood leukocytes [8963266087_R05C02]

description:
8963266087_R05C02
Matched with 10005833034_R06C01


title: Genomic DNA from blood leukocytes [8963266087_R04C02]

description:
8963266087_R04C02
Matched with 200190110101_R06C01


title: Genomic DNA from blood leukocytes [8769527085_R02C01]


title: Genomic DNA from blood leukocytes [8963266087_R06C01]

description:
8963266087_R06C01
Matched with 200190110084_R01C01


title: Genomic DNA from blood leukocytes [8963266087_R03C01]

description:
8963266087_R03C01
Matched with 9904796235_R04C02


title: Genomic DNA from blood leukocytes [8963266087_R01C02]

description:
8963266087_R01C02
Matched with 10003885149_R04C01


title: Genomic DNA from blood leukocytes [8963266087_R02C01]

description:
8963266087_R02C01
Matched with 10003886146_R05C01


title: Genomic DNA from blood leukocytes [8963266087_R02C02]

description:
8963266087_R02C02
Matched with 10003886039_R01C02


title: Genomic DNA from blood leukocytes [8769527038_R04C02]

description:
8769527038_R04C02
Matched with 10005833007_R03C01


title: Genomic DNA from blood leukocytes [8963266087_R01C01]

description:
8963266087_R01C01
Matched with 10003886028_R04C02


title: Genomic DNA from blood leukocytes [200190110074_R04C02]

description:
200190110074_R04C02
Matched with 10005833034_R01C02


title: Genomic DNA from blood leukocytes [200190110074_R03C02]

description:
200190110074_R03C02
Matched with 10005833035_R01C01


title: Genomic DNA from blood leukocytes [200190110074_R05C02]

description:
200190110074_R05C02
Matched with 10003886028_R06C02


title: Genomic DNA from blood leukocytes [200190110074_R06C01]

description:
200190110074_R06C01
Matched with 10005833065_R05C01


title: Genomic DNA from blood leukocytes [200190110074_R01C02]

description:
200190110074_R01C02
Matched with 10005833079_R06C02


title: Genomic DNA from blood leukocytes [200190110074_R02C02]

description:
200190110074_R02C02
Matched with 10005833080_R03C02


title: Genomic DNA from blood leukocytes [200190110074_R04C01]

description:
200190110074_R04C01
Matched with 10005771156_R01C02


title: Genomic DNA from blood leukocytes [200190110074_R02C01]

description:
200190110074_R02C01
Matched with 10005833080_R05C01


title: Genomic DNA from blood leukocytes [200190110074_R03C01]

description:
200190110074_R03C01
Matched with 10005833034_R04C02


title: Genomic DNA from blood leukocytes [200190110074_R01C01]

description:
200190110074_R01C01
Matched with 10003886068_R06C02


title: Genomic DNA from blood leukocytes [8963266087_R03C02]

description:
8963266087_R03C02
Matched with 10003885149_R06C02


title: Genomic DNA from blood leukocytes [8963266087_R05C01]

description:
8963266087_R05C01
Matched with 10005833043_R03C01


title: Genomic DNA from blood leukocytes [200190110073_R06C02]

description:
200190110073_R06C02
Matched with 10005833064_R02C02


title: Genomic DNA from blood leukocytes [200190110073_R04C02]

description:
200190110073_R04C02
Matched with 10003886016_R06C02


title: Genomic DNA from blood leukocytes [8963266087_R04C01]

description:
8963266087_R04C01
Matched with 10003886051_R01C02


title: Genomic DNA from blood leukocytes [200190110073_R05C02]

description:
200190110073_R05C02
Matched with 10005833079_R03C01


title: Genomic DNA from blood leukocytes [200190110073_R01C02]

description:
200190110073_R01C02
Matched with 10003886023_R04C02


title: Genomic DNA from blood leukocytes [200190110073_R03C02]

description:
200190110073_R03C02
Matched with 10003886068_R01C02


title: Genomic DNA from blood leukocytes [200190110073_R02C02]

description:
200190110073_R02C02
Matched with 10005833063_R02C01


title: Genomic DNA from blood leukocytes [200190110073_R06C01]

description:
200190110073_R06C01
Matched with 10003886105_R04C01


title: Genomic DNA from blood leukocytes [200190110074_R05C01]

description:
200190110074_R05C01
Matched with 10005833007_R02C02


title: Genomic DNA from blood leukocytes [200190110073_R04C01]

description:
200190110073_R04C01
Matched with 10005833065_R02C01


title: Genomic DNA from blood leukocytes [200190110073_R03C01]

description:
200190110073_R03C01
Matched with 10003886105_R02C02


title: Genomic DNA from blood leukocytes [200190110073_R01C01]

description:
200190110073_R01C01
Matched with 10005833065_R02C02


title: Genomic DNA from blood leukocytes [200190110069_R06C02]

description:
200190110069_R06C02
Matched with 10005833073_R02C01


title: Genomic DNA from blood leukocytes [200190110069_R01C02]

description:
200190110069_R01C02
Matched with 10003886051_R04C02


title: Genomic DNA from blood leukocytes [200190110069_R04C02]

description:
200190110069_R04C02
Matched with 10003886051_R05C01


title: Genomic DNA from blood leukocytes [200190110069_R05C01]

description:
200190110069_R05C01
Matched with 10003886023_R03C01


title: Genomic DNA from blood leukocytes [200190110069_R05C02]

description:
200190110069_R05C02
Matched with 10005833035_R04C01


title: Genomic DNA from blood leukocytes [200190110073_R02C01]

description:
200190110073_R02C01
Matched with 10005833032_R04C02


title: Genomic DNA from blood leukocytes [200190110069_R02C02]

description:
200190110069_R02C02
Matched with 10005833064_R02C01


title: Genomic DNA from blood leukocytes [200190110069_R04C01]

description:
200190110069_R04C01
Matched with 10005833007_R01C01


title: Genomic DNA from blood leukocytes [200190110069_R06C01]

description:
200190110069_R06C01
Matched with 10003886104_R03C01


title: Genomic DNA from blood leukocytes [200190110069_R03C01]

description:
200190110069_R03C01
Matched with 10005833095_R05C02


title: Genomic DNA from blood leukocytes [200190110069_R02C01]

description:
200190110069_R02C01
Matched with 10005833080_R01C02


title: Genomic DNA from blood leukocytes [200190110066_R06C02]

description:
200190110066_R06C02
Matched with 10005833079_R01C02


title: Genomic DNA from blood leukocytes [200190110069_R01C01]

description:
200190110069_R01C01
Matched with 10005833079_R05C02


title: Genomic DNA from blood leukocytes [200190110066_R05C02]

description:
200190110066_R05C02
Matched with 10005833062_R02C01


title: Genomic DNA from blood leukocytes [200190110066_R04C02]

description:
200190110066_R04C02
Matched with 10005771156_R05C01


title: Genomic DNA from blood leukocytes [200190110073_R05C01]

description:
200190110073_R05C01
Matched with 10005833106_R02C02


title: Genomic DNA from blood leukocytes [200190110066_R03C02]

description:
200190110066_R03C02
Matched with 10003886146_R02C02


title: Genomic DNA from blood leukocytes [200190110066_R01C02]

description:
200190110066_R01C02
Matched with 10003886028_R06C01


title: Genomic DNA from blood leukocytes [200190110066_R06C01]

description:
200190110066_R06C01
Matched with 10005833007_R01C02


title: Genomic DNA from blood leukocytes [200190110066_R02C02]


title: Genomic DNA from blood leukocytes [200190110066_R03C01]

description:
200190110066_R03C01
Matched with 10005833063_R04C02


title: Genomic DNA from blood leukocytes [200190110066_R04C01]

description:
200190110066_R04C01
Matched with 200190110084_R06C02


title: Genomic DNA from blood leukocytes [200190110066_R05C01]

description:
200190110066_R05C01
Matched with 10005833065_R03C02


title: Genomic DNA from blood leukocytes [200190110066_R01C01]

description:
200190110066_R01C01
Matched with 10005833080_R02C01


title: Genomic DNA from blood leukocytes [200190110065_R06C02]

description:
200190110065_R06C02
Matched with 10005833035_R02C02


title: Genomic DNA from blood leukocytes [200190110069_R03C02]

description:
200190110069_R03C02
Matched with 200190110102_R01C02


title: Genomic DNA from blood leukocytes [200190110066_R02C01]

description:
200190110066_R02C01
Matched with 10005833064_R01C01