title: Thymus KO DMBA DN rep2

status: Public on Sep 30 2017

type: RNA

city: Salamanca

first: L. Francisco

last: Lorenzo-Martín

state: Castilla y León

address: Campus Miguel de Unamuno

country: Spain

institute: University of Salamanca (USAL) – Centro de Investigación del Cáncer (CIC)

description: Gene expression data from thymus

hyb_protocol: Mouse Gene 1.0 ST arrays (Affymetrix) under standard conditions

scan_protocol: Standard Affymetrix protocol

data_processing: Upon microarray hybridization, the raw data was normalized with RMA using R (v.3.0.3).

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Thymus from DMBA-treated Vav1-/- mouse

label_protocol: Total RNA was quantified using 6000 Nano Chips (Agilent Technologies, Santa Clara, CA) and used (2.3 mg/sample) to generated labeled cRNA probes according to the manufacturer's instructions (Affymetrix).

growth_protocol: This experiment has been done with animals.

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

treatment_protocol: DMBA was administered weekly via intragastric intubation to female mice of indicated genotypes for a total of six weeks.

tag: strain

tag: genotype

tag: tissue

value: Whole thymus

tag: treatment

value: DMBA-treated


title: Thymus KO CTL rep3

description: Gene expression data from thymus

source_name: Thymus from control Vav1-/- mouse

value: control


title: Thymus KO DMBA ISP rep3

description: Gene expression data from thymus


title: Thymus KO DMBA ISP rep1

description: Gene expression data from thymus


title: Thymus KO DMBA DN rep3

description: Gene expression data from thymus


title: Thymus KO DMBA ISP rep2

description: Gene expression data from thymus


title: Thymus WT DMBA ISP rep2

description: Gene expression data from thymus

value: WT


title: Thymus WT DMBA ISP rep1

description: Gene expression data from thymus


title: Thymus WT CTL rep1

description: Gene expression data from thymus

source_name: Thymus from control WT mouse


title: Thymus KO CTL rep2

description: Gene expression data from thymus


title: Thymus WT CTL rep2

description: Gene expression data from thymus


title: Thymus WT DMBA ISP rep3

description: Gene expression data from thymus


title: MBFM (CTL)_frozen tissue

city: Marseille

first: Christophe

last: Chevillard

state: BDR

address: 27 bd Jean Moulin faculté de médecine

country: France

institute: INSERM

description: Total RNA extract from frozen tissue

hyb_protocol: The hybridization was performed for 17 hours at 10 rpm and 65°C in a Hybridization Oven (Robbins Scientific). Slide Wash was done according to the manufacturer's recommendation.

scan_protocol: Cy3 intensities were detected by one-color scanning using Agilent DNA microarray scanner at 3 micron resolution. Raw data from scanned image files were extracted using Feature Extraction software (10.7.3.1). Spike-in used in the experiment gave reliable data and all arrays passed the quality control.

data_processing: The microarrays were therefore analyzed using both GeneSpring software (11.5.1). Threshold raw signals to 1.0. Normalization algorithm: Percentile shift. Percentile target: 75. Baseline option: baseline to median of all samples. Group comaraison: Moderated T-Test.

organism: Homo sapiens

source_name: control_left ventricular free wall heart tissue

label_protocol: Microarrays were done using the Low Input Quick Amp Labeling One-Color Kit (Agilent Technologies) and the One-color RNA Spike-in Kit (Agilent Technologies) following the manufacturer's standard protocol (Agilent One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling). 100 ng of total RNA input was used. After cDNA synthesis, amplification, labeling and purification, the reaction efficacy was checked using the NanoDrop.

extract_protocol: Tissue (20-30mg of tissue) homogenization was carried out with the Precellys-24 device (Bertin Technologies, Ozyme), with ceramic beads (1.4mm in diameter, CK14), in 400 µl of lysis buffer RLT plus (Qiagen) supplemented with 4µl β-mercapto-ethanol. RNA was recovered with the RNeasy plus following the manufacturer's instructions (Qiagen). RNA integrity was assessed with a 2100 Bioanalyzer (Agilent). Total RNA (1µg), with a RIN > 7, was reverse-transcribed with the high Capacity cDNA Reverse Transcription Kit (Applied Biosystems).

tag: subject status

value: healthy hearts of organ donors

value: left ventricular free wall heart tissue


title: Thymus WT CTL rep3

description: Gene expression data from thymus


title: Thymus KO CTL rep1

description: Gene expression data from thymus


title: ZFS (CTL)_frozen tissue

description: Total RNA extract from frozen tissue


title: FJR (CTL)_frozen tissue

description: Total RNA extract from frozen tissue


title: Thymus KO DMBA DN rep1

description: Gene expression data from thymus


title: ESS (CTL)_frozen tissue

description: Total RNA extract from frozen tissue


title: ZMC (CCC)_frozen tissue

description: Total RNA extract from frozen tissue

source_name: CCC_left ventricular free wall heart tissue

value: end-stage heart failure patients at the moment of heart transplantation


title: 3557 (CTL) _frozen tissue

description: Total RNA extract from frozen tissue


title: LO (CTL)_frozen tissue

description: Total RNA extract from frozen tissue


title: SCS (CCC)_frozen tissue

description: Total RNA extract from frozen tissue


title: EMBT (CTL)_frozen tissue

description: Total RNA extract from frozen tissue


title: MCRS (CCC)_frozen tissue

description: Total RNA extract from frozen tissue


title: GO_10_µg-ml_6h_A09

city: Stockholm

first: Pekka

middle: Juhani

last: Kohonen

address: Nobelsväg 13, Box 210

department: IMM Institute of Environmental Medicine

country: Sweden

institute: Karolinska Institutet

description: hMDM cells were seeded in 24-well plates at a density of 106 cells/well in a final volume of 1 ml.

hyb_protocol: Affymetrix arrays were hybridized to GeneChip Human Genome U219 array plate with specific protocols for using the GeneTitan Hybridization, Wash and Stain Kit for 39 IVT Array Plates (P/N 901530). GeneTitan Instrument was used to hybridize, wash, stain and scan the arrays.

scan_protocol: Specific protocols for using the GeneTitan Hybridization, Wash and Stain Kit for 39 IVT Array Plates (P/N 901530) were also employed in the scanning phase.

data_processing: Affymetrix GeneChip Command Console 3.1 was used to control the process and to summarize probe cell intensity data. Hybridization quality was checked with Affymetrix GeneChip Command Console and Expression ConsoleTM 1.1s.

label_protocol: For Affymetrix analysis 250 ng of total RNA was processed with GeneChip 39 IVT Express Kit (Part no. 901229). Both before and after the amplifications the RNA/cRNA concentrations where checked with Nanodrop ND-1000, and integrity and amplification profile controlled with BioRad’s Experion Automated Electrophoresis System (Bio-Rad).

extract_protocol: Cells were collected to RNAlater buffer (Ambion) and total RNA isolated with RNAqueous Small Scale Phenol-Free Total RNA Isolation Kit (Ambion) according to manufacturer’s protocol.

treatment_protocol: The cells were treated with the indicated concentrations of ENM for the indicated times. Materials (GO - graphene oxide), HCS (hollow carbon spheres) and SWCNT (single-walled arbon nanotubes)

tag: cell type

value: primary human monocyte-derived macrophages (hMDMs)


title: Day6Ablation_whole larvae_Rep2

city: Glendale

first: Jennifer

last: Hackney Price

state: Arizona

address: 4701 Thunderbird Rd  M/C 2352, New College

department: Mathematical and Natural Sciences

country: USA

institute: Arizona State University

description: Ablated genotype: (rnGAL4,UASegr,tubGAL80[ts]/+). Control genotype (TM6,Tb[1],tubGAL80)

hyb_protocol: Slides were prehybridized, hybridized, and washed according to the recommendations of Microarray Inc.

scan_protocol: Scanned on an Axon GenePix 4100A Microarray scanner. Local background intensities were subtracted from feature signal intensities. Images were quantified using GenePix Pro (versio 7.0) software.

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Ablated signal/processed Control signal. A student's t-test was used to to identify differentially expressed genes. Images were processed using ArrayStar software (Version 5).

organism: Drosophila melanogaster

source_name: Third instar larvae, wing disc ablation, 24hrs

label_protocol: 10 µg of total RNA were primed with 1 µl of Anchored Oligo(dT)20Primer (2.5μg/μl) at 80°C for 10 min, then reversed transcribed at 42°C for 2 h in the presence of 800 U SuperScript III RTase (Invitrogen), and 2 µl of 10mM dNTP mix (contains dATP, dTTP, dCTP, dGTP, with one aminoallyl-modified nucleotide, and one aminohexyl-modified nucleotide at optimal concentrations). Each cDNA sample was labeled with either Cy3 or Cy5 dye.

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

treatment_protocol: The cell-death gene, eiger, was expressed in the pouch of wing imaginal discs using the UAS-GAL4 system. Eiger expression was regulated by a temperature-sensitive GAL80 variant, which permits GAL4 expression at 18, but inhibits GAL4 function at 30 degrees.

tag: gender

value: Female

tag: developmental stage

value: 3rd Instar Larvae

tag: genotype/variation

value: Ablated (rnGAL4,UASegr,tubGAL80[ts]/+)

source_name: Third instar larvae, no wing disc ablation

value: Control (TM6,Tb[1],tubGAL80)


title: HBO (CCC)_frozen tissue

description: Total RNA extract from frozen tissue


title: APA (CCC)_frozen tissue

description: Total RNA extract from frozen tissue


title: EBS (CCC)_frozen tissue

description: Total RNA extract from frozen tissue


title: SWCNTs_10_µg-ml_24h_B05

growth_protocol: hMDM cells were seeded in 24-well plates at a density of 106 cells/well in a final volume of 1 ml.


title: Control_6h_A04


title: PMG (CCC)_frozen tissue

description: Total RNA extract from frozen tissue


title: AAF (CCC)_frozen tissue

description: Total RNA extract from frozen tissue


title: Day6Ablation_whole larvae_Rep1


title: HCS_10_µg-ml_6h_A12


title: Control_24h_B03


title: Control_0h_A02


title: GO_30_µg-ml_24h_B09


title: Control_24h_B02


title: GO_10_µg-ml_24h_B07


title: SWCNTs_30_µg-ml_24h_B06


title: Ctrl vs Stg cortex_6

city: Paris

first: Luce

last: Dauphinot

address: 47 boulevard de l'hôpital

department: ICM

institute: INSERM U1127-CNRS UMR7225-UPMC

description: Dye swap of replicate 2

hyb_protocol: Labeled cDNAs were purified on Qiaquick PCR purification kit (Qiagen) and hybridized to the RNG-MRC_MM25k_EVRY microarrays  according to the RNG procedures

scan_protocol: Microarrays data were acquired on a GenePix 4000B Microarray Scanner ( Molecular Devices) with a resolution of 5 µm at wavelengths 532 and 635 nm

data_processing: Raw data were obtained with Genepix 4.1 software (Molecular Devices) . Processed data consisted of the Median Feature Intensity /Median Background Intensity (F/B ratio) ratio normalized by Lowess Fit

source_name: Ctrl Litter 2

label_protocol:
For the cortex, 5µg of total RNA were reverse-transcribed in the presence of 7.5µM random hexamers (GE Healthcare), 75µM aa-dUTP (Sigma-Aldrich) and 100U Rtases Reverse-iT Blend (ABgene) overnight at 37°C. Aminoallyl cDNAs were then labelled with Cy5 or Cy3 mono-Reactive Dye (GE Healthcare) according to the manufacturer’s instructions
For the VB, 500ng of total RNA was mixed with 1µM 3’ SMART CDS primer IIA (5’AAGCAGTG-GTATCAACGCAGAGTACT30VN-3’) and 1µM template switching primer (5’AAGCAGTGGTATCAACGCAGAGTACGCGGG-3’) and incubated at 70°C for 2 minutes. The following reagents were then added, 1X 1st strand synthesis buffer, 5mM DTT, 1mM dNTPs and 140U Rtases Reverse-iT Blend (ABgene), and the reaction incubated overnigth at 37°C. After the reverse-transcription was achieved, the cDNAs were amplified in the presence of 1X Advantage® 2 polymerase (BD Clontech) and 1.25µM 5’PCR primer (AAGCAGTGGTATCAACGCAGAGT) by TS-PCR: 95°C for 2 minutes then 14 cycles 95°C for 15s, 65°C for 30s and 68°C for 6 minutes. After purification using the Qiaquick PCR prurification kit (Qiagen), amplified cDNAs were labelled with 20µM dUTP-Cy5 or dUTP-Cy3 (GE Healthcare) and 100mM random hexamers (GE Healthcare) in the presence of 50U Klenow fragment (Ozyme) overnight at 37°C

extract_protocol: Total RNAs was extracted independently from each tissue sample and treated with DNAse1 using Nucleospin RNA II kit (Macherey-Nagel) according to the manufacturer’s instructions.

treatment_protocol: P5-P6 mice were anesthetized on ice and decapitated, their brains were rapidly cut to 250 ìm thick slices using a vibratome (VT 1000S; Leica). The somatosensory cortex and VB were dissected out under a dissecting microscope from relevant sections and frozen on dry-ice

value: Cortex

source_name: Stg Litter 2

value: Stagerrer mutant


title: HCS_30_µg-ml_24h_B12


title: MAP (CCC)_frozen tissue

description: Total RNA extract from frozen tissue


title: GO_30_µg-ml_6h_A10


title: Ctrl vs Stg cortex_8

description: Dye swap of replicate 4

source_name: Ctrl Litter 4

source_name: Stg Litter 4


title: HCS_10_µg-ml_24h_B10


title: Ctrl vs Stg cortex_5

description: Dye swap of replicate 1

source_name: Ctrl Litter 1

source_name: Stg Litter 1


title: SWCNTs_10_µg-ml_6h_A05


title: Ctrl vs Stg cortex_7

description: Dye swap of replicate 3

source_name: Ctrl Litter 3

source_name: Stg Litter 3


title: Ctrl vs Stg cortex_1

description: Biological replicate 1 of 4


title: SWCNTs_10_µg-ml_24h_B04


title: Ctrl vs Stg VB_8

description: Dye swap of replicate 4

value: VB


title: Ctrl vs Stg VB_7

description: Dye swap of replicate 3


title: Ctrl vs Stg cortex_3

description: Biological replicate 3 of 4


title: Ctrl vs Stg VB_6

description: Dye swap of replicate 2


title: HCS_10_µg-ml_6h_A11


title: Ctrl vs Stg VB_4

description: Biological replicate 4 of 4


title: Ctrl vs Stg cortex_4

description: Biological replicate 4 of 4


title: Control_0h_A01


title: Ctrl vs Stg VB_2

description: Biological replicate 2 of 4


title: Ctrl vs Stg VB_1

description: Biological replicate 1 of 4


title: NSR (CCC)_frozen tissue

description: Total RNA extract from frozen tissue


title: Ctrl vs Stg VB_3

description: Biological replicate 3 of 4


title: Ctrl vs Stg VB_5

description: Dye swap of replicate 1


title: Ctrl vs Stg cortex_2

description: Biological replicate 2 of 4


title: TALL45

city: padova

first: silvia

last: bresolin

state: padova

address: via giustiniani 3

department: department of women's and children's health

country: Italy

institute: università di padova

description: Gene expression data from a T-ALL pediatric patient at diagnosis

hyb_protocol: Following fragmentation, 11 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Scan GCS3000.

data_processing: The data were normalized using R software [www.r-ptoject.org] with BioConductor package [www.bioconductor.org] using RMA. For T-ALL samples removal batch effect were applied using ComBat in the sva package

source_name: T-ALL pediatric patient_bone marrow

label_protocol: For Batch1: Biotinylated cRNA were prepared according to the standard 3'IVT Affymetrix protocol from 100ng of Total RNA. For Batch2: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2ug of Total RNA(Expression Analysis Technical Manual, 2001, Affymetrix)

growth_protocol: No growth protocol

extract_protocol: For T-ALL patients RNA was exctracted from mononuclear cells using Trizol. For xenograft experiments, RNA was exctracted from engrafted T-cells in the spleen of mice using Trizol.

treatment_protocol: No treatment protocol

value: pediatric T-cell Acute Lymphoblastic Leukemia (T-ALL) patient

value: Bone Marrow

tag: mrd +78

value: Negative

tag: batch

value: Batch 2


title: XENO6

description: Gene expression data from T-ALL patients xenografted in NOD/SCID mouse

source_name: T-ALL xenografts in NOD/SCID mouse

value: Spleen

tag: tissue subtype

value: engrafted T-cells in the spleen of mice

value: PGR


title: XENO9

value: PPR


title: XENO25


title: TALL47

value: Positive


title: TALL42


title: TALL46


title: TALL34

value: Batch 1


title: TALL48


title: XENO15


title: TALL40


title: TALL43


title: XENO43


title: XENO5


title: TALL44


title: TALL36


title: TALL35


title: TALL38


title: TALL41


title: TALL30


title: TALL37


title: TALL32


title: TALL39


title: TALL31


title: TALL33


title: TALL28


title: TALL29


title: TALL26


title: TALL22


title: TALL24


title: TALL23


title: TALL25


title: TALL13


title: TALL17


title: TALL12


title: TALL27


title: TALL10


title: TALL19


title: TALL20


title: TALL14


title: Drd4 RGCs, rep2

city: Los Angeles

first: Yi-Rong

last: Peng

state: CA

address: 100 Stein Plaza Driveway, B-133

department: Department of Ophthalmology

institute: University of California, Los Angeles

hyb_protocol: 20ug of aRNA were fragmented and hybridized according to standard Affymetrix protocols for 16 h at 45 degrees C. Arrays were washed and stained in Affymetrix Fluidics Station 450.

scan_protocol: Affymetrix GeneChip Scanner 3000 7G

data_processing: Data were analyzed in dChip

source_name: retinal cells

label_protocol: MessageAmp II-biotin system (Ambion). Two rounds of amplification were used.

growth_protocol: Postnatal day 6 mice.

extract_protocol: PicoPure RNA Isolation Kit (MDS).

treatment_protocol: Papain-dissociated retinal cell suspension.

tag: developmental age

value: postnatal day 6

value: retina

value: GFP+ Thy1+ retinal cells

tag: neuron subtype

value: Drd4 retinal ganglion cells (RGCs)


title: Hb9 RGCs, rep1

value: Hb9 retinal ganglion cells (RGCs)


title: TALL21


title: Hb9 RGCs, rep2


title: TALL5


title: Thy1 RGCs, rep1

value: Thy1+ retinal cells

value: Retinal ganglion cells (RGCs)


title: Thy1 RGCs, rep2


title: TALL15

value: pediatric T-cell Acute Lymphoblastic Leukemia (T-ALL) patient


title: TALL18

value: Bone Marrow


title: TALL9


title: Drd4 RGCs, rep1


title: knu-1 crc-1_rep3

city: Singapore

first: Yifeng

last: XU

address: 1 Research Link

country: Singapore

institute: Temasek Life Sciences Laboratory

hyb_protocol: Hybridization was performed  following NimbleGen standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed  following NimbleGen standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Arabidopsis thaliana

source_name: crc-1 knu-1

label_protocol: Labeling was performed following NimbleGen standard operating protocol. See www.nimblegen.com.

growth_protocol: The seeds of the indicated genotype were planted on soil, and grown at 22°C under continuous light conditions. The inflorescence with flower buds earlier than stage 10 was sampled from knu-1 and crc-1 knu-1.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen).

treatment_protocol: No treatment applied

value: crc-1 knu-1

tag: phenotype

value: around ten rounds of iterations of carpels and stamens  break through the original gynoecium and grow outside the crc-1 knu-1 flower

value: inflorescence


title: knu-1_rep2

value: the knu-1 flower develops bulged carpels with additional whorls of stamens and carpels inside


title: TALL8


title: TALL7


title: TALL11

value: Negative


title: TALL4


title: knu-1 crc-1_rep2


title: knu-1_rep3


title: TALL1


title: TALL3


title: knu-1 crc-1_rep1


title: TALL2


title: TALL6


title: knu-1_rep1


title: BX_non-AR_pt_4

status: Public on Sep 29 2017

city: Vancouver

first: Bruce

middle: Maxwell

last: McManus

state: BC

address: 1081 Burrard Street

department: UBC James Hogg Research Centre

country: Canada

institute: PROOF Centre of Excellence

hyb_protocol: Following fragmentation, the cRNA was hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 array. Equilibrate probe array to room temperature immediately before use.  Then, heat the hybridization cocktail to 99°C for 5 minutes in heatblock.  Next, wet the array by filling it through one of the septa with appropriate volume of 1X MES Hybridization Buffer using a micropipettor and appropriate tips. Last, incubate the probe array for 10 minutes at 45°C in the hybridization oven with rotation.

scan_protocol: The Probe Array is scanned using the Affymetrix System.  The scanner is controlled by the GeneChip software.  The probe array is scanned after the wash protocols are complete

data_processing: RMA

source_name: non-AR

label_protocol: Biotin-labeled cRNA were prepared according to the standard Affymetrix protocol from 15 ug total RNA.

extract_protocol: Isolation begins with a centrifugation step to pellet nucleic acids in the PAXgene Blood RNA Tube. The pellet is washed, resuspended, and incubated in optimized buffers containing Proteinase K to digest proteins. A second centrifugation step is carried out to remove residual cell debris, and the supernatant is transferred to a fresh microcentrifuge tube. Ethanol is added to adjust binding conditions, and the lysate is applied to a PAXgene RNA spin column. During a brief centrifugation, RNA is selectively bound to the silica-gel membrane of the spin column as contaminants pass through. Remaining contaminants are removed in three wash steps, and pure RNA is then eluted in Buffer BR5. Generally, DNase digestion is not required for RNA purified with the PAXgene Blood RNA Kit, since PAXgene silica-gel–membrane technology efficiently removes most of the DNA without DNase treatment. However, further DNA removal is recommended for RNA applications that are sensitive to DNA contamination. In these cases, residual DNA can be removed either by using the RNase-Free DNase Set for on-column DNase digestion, or by treating the eluted RNA with DNase.

tag: sample id

tag: tissue type

value: transplant donor heart tissue biopsy (BX)

tag: age (years)

tag: Sex

value: M

tag: race

value: Caucasian

tag: original disease


title: BX_non-AR_pt_7

value: F


title: BX_non-AR_pt_9


title: BX_non-AR_pt_10


title: BX_AR_pt_5

source_name: AR


title: BX_non-AR_pt_5


title: BX_non-AR_pt_3


title: BX_non-AR_pt_6


title: BX_non-AR_pt_2

value: Unknown


title: BX_AR_pt_3


title: BX_non-AR_pt_8


title: BX_AR_pt_4

value: Other/multiracial


title: BX_AR_pt_7


title: WB_non-AR_pt_11

value: pre-transplant recipient whole blood (WB)

value: Asian Oriental

value: cardiogenic shock


title: WB_non-AR_pt_9

value: Ischemic heart disease


title: BX_non-AR_pt_1


title: BX_AR_pt_1


title: BX_AR_pt_6


title: WB_non-AR_pt_6


title: BX_non-AR_pt_11


title: WB_AR_pt_1

value: Non-ischemic cardiomyopathy


title: WB_non-AR_pt_2


title: WB_non-AR_pt_7

value: Asian Filipino


title: WB_non-AR_pt_10


title: BX_AR_pt_2


title: WB_non-AR_pt_4

value: Congenital heart disease


title: WB_non-AR_pt_1


title: WB_AR_pt_4


title: WB_non-AR_pt_3


title: WB_AR_pt_5


title: WB_AR_pt_7


title: Mir-21_KO,CD4+CD25High

city: Charlottesville

first: Yong

last: Huang

state: VA

address: 1340 Jefferson Park Ave

department: Medicine

institute: University of Viginia

hyb_protocol: Illumina MouseRef-8 v2.0 expression beadchip

data_processing: raw data were processed using the R/Bioconductor package limma for background correction and quantile normalization

source_name: (1) CD4+CD25High

treatment_protocol: One set of these T cells were stimulated with anti-CD3 and anti-CD28 antibodies for 30 min prior to RNA isolation.

value: T cell

tag: cell subtype

tag: genotype


title: Mir-21_KO,CD4+CD25High, stimulated

scan_protocol: Illumina MouseRef-8 v2.0 expression beadchip

tag: cell type


title: WB_non-AR_pt_8


title: wild type,CD4+CD45High

source_name: (2) CD4+CD45High

label_protocol: Illumina MouseRef-8 v2.0 expression beadchip

value: wild type


title: WB_non-AR_pt_5


title: WB_AR_pt_6


title: Ilea_M_balbc_rep4

city: Bethesda

first: Aleksandra

last: Nita-Lazar

state: MD

address: 9000 Rockville Pike BLDG 4 RM 109 MSC 0421

department: Laboratory of Immune System Biology, NIAID

institute: National Institutes of Health

description:
Array18
Microarray Barcode: 251713810417_1_3

hyb_protocol: Each sample pair (green and red; 38 samples total) was co-hybridized to a microarray using the MAUI Hybridization System (BioMicro Systems Inc., Salt Lake City, UT).

scan_protocol: The dual-color microarrays were scanned using a Microarray Scanner System, and the resulting images were processed using Feature Extraction (both Agilent Technologies) to produce the raw data (one TXT file per microarray).

data_processing: The reporter spot foreground and background intensity values (median pixel intensity) were imported into MS Excel. Each background intensity value was set to be a maximum of four times the median value (calculated across each microarray and color-channel; this affected 251 of the 1,427,204 background intensity values). For each ileum sample and spot, if the net intensity (foreground - background) was <10, it was replaced with a random number between 10 and 20 (this range was roughly consistent with the range of the background values as the median background intensity value was 35.5; this affected 31,139 of the 1,427,204 net intensity values). The data were imported into BRB-ArrayTools (http://brb.nci.nih.gov/BRB-ArrayTools/) (Simon et al. 2007 Cancer Inform 3:11-17). For each microarray/color-channel/probe, the arithmetic mean of the net intensity values was calculated across the replicate spots. The values were Log2-transformed. Intra-array LOWESS normalizations (span = 0.4) were performed.

label: Cy5 (red)

source_name: Mouse OME17, germ-free, terminal ileum, male, BALB/c

label_protocol: Fluorescently labeled cDNA (green and red) was prepared using 20 ug of total RNA, 2 ul of 1 mM Cy3-dUTP or Cy5-dUTP (respectively; GE Healthcare, Chicago, IL), 1 ug of Oligo(dT)12-18 Primer, 0.5 mM dATP, 0.5 mM dCTP, 0.5 mM dGTP, 0.15 mM dTTP, 10 mM dithiothreitol, 1.5 ul of 200 U/ul SuperScript II reverse transcriptase, and 0.5 ul of 20 U/ul RNase Inhibitor (all from Thermo Fisher Scientific Inc. unless noted otherwise). The resulting cDNA was purified using Vivaspin 500 columns (10,000 MWCO, Sartorius AG, Gottingen, Germany).

growth_protocol: This study was approved by the NIH Animal Care and Use Committee. Re-derived germ-free (GF) and conventional mice (female and male; BALB/c and C57BL/10A; 6 - 8 months old) were prepared by Taconic Biosciences, Inc. (Hudson, NY). The conventional mice were housed under normal conditions and maintained using standard procedures. Six GF mice were prepared for each experimental class (two sexes, two strains, 24 GF mice total) with the goal of having five mice per experimental class (two germ statuses, two sexes, two strains, 40 mice total). Samples (e.g., feces) from the GF mice were analyzed to ensure the complete absence of any microbial contamination, and mice were discarded if any sample tested positive. This resulted in only four GF female C57BL/10A ilea being available. The ilea were harvested, placed into and gently flushed with ice-cold phosphate-buffered saline to wash away microbes, segmented, and immediately frozen on dry ice. One set of the segments was used for the transcriptomics experiments.

extract_protocol: Total RNA was isolated from the ilea using Total RNeasy Mini kits (Qiagen, Hilden, Germany).

tag: strain/background

value: BALB/c

value: Male

tag: tissue

value: terminal ileum

value: Germ-free

label: Cy3 (green)

source_name: Mouse OME07, conventional, terminal ileum, male, BALB/c

value: Conventional


title: wild type,CD4+CD45High, stimulated


title: Mir-21_KO,CD4+CD45High, stimulated


title: Ilea_M_balbc_rep1

description:
Array15
Microarray Barcode: 251713810415_1_2

source_name: Mouse OME20, germ-free, terminal ileum, male, BALB/c

source_name: Mouse OME10, conventional, terminal ileum, male, BALB/c


title: wild type,CD4+CD25High


title: WB_AR_pt_2

value: M

value: Caucasian


title: wild type,CD4+CD25High, stimulated


title: Ilea_M_balbc_rep5

description:
Array19
Microarray Barcode: 251713810417_1_4

source_name: Mouse OME16, germ-free, terminal ileum, male, BALB/c

source_name: Mouse OME06, conventional, terminal ileum, male, BALB/c


title: Ilea_M_B10A_rep5

description:
Array14
Microarray Barcode: 251713810442_1_4

source_name: Mouse OME40, germ-free, terminal ileum, male, C57BL/10A

source_name: Mouse OME30, conventional, terminal ileum, male, C57BL/10A


title: Ilea_M_B10A_rep4

description:
Array13
Microarray Barcode: 251713810442_1_3

source_name: Mouse OME39, germ-free, terminal ileum, male, C57BL/10A

source_name: Mouse OME29, conventional, terminal ileum, male, C57BL/10A


title: WB_AR_pt_3


title: Ilea_M_balbc_rep3

description:
Array17
Microarray Barcode: 251713810417_1_2

source_name: Mouse OME18, germ-free, terminal ileum, male, BALB/c

source_name: Mouse OME09, conventional, terminal ileum, male, BALB/c


title: Mir-21_KO,CD4+CD45High


title: Ilea_M_B10A_rep1

description:
Array10
Microarray Barcode: 251713810411_1_4

source_name: Mouse OME36, germ-free, terminal ileum, male, C57BL/10A

source_name: Mouse OME26, conventional, terminal ileum, male, C57BL/10A


title: Ilea_M_B10A_rep2

description:
Array11
Microarray Barcode: 251713810442_1_1

source_name: Mouse OME37, germ-free, terminal ileum, male, C57BL/10A

source_name: Mouse OME27, conventional, terminal ileum, male, C57BL/10A


title: Ilea_M_balbc_rep2

description:
Array16
Microarray Barcode: 251713810417_1_1

source_name: Mouse OME19, germ-free, terminal ileum, male, BALB/c

source_name: Mouse OME08, conventional, terminal ileum, male, BALB/c


title: Sample 6 - hMYC-ER - Z14

city: Padova

first: Chiara

last: Borga

address: Corso Stati Uniti,4

institute: University of Padua

description: Gene expression data from FACS purified GFP+ T-lymphoblasts of hMYC-ER specimen at the final stage of disease

hyb_protocol: Following fragmentation, 12,5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Zebrafish Genome Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450DX.

data_processing: The data were normalized using R software [www.r-ptoject.org] with BioConductor package [www.bioconductor.org]

organism: Danio rerio

source_name: FACS purified GFP+ T-lymphoblasts

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Expression Analysis Technical Manual, 2008, Affymetrix).

extract_protocol: Total RNA extraction using Trizol protocol

treatment_protocol: FACS purified GFP+ T-lymphoblasts from the bodies of hMYC-ER and hlk zebrafish models at the final stage of disease

tag: model

value: hMYC-ER sample

value: Sorted GFP+ T-lymphoblasts


title: Sample 7 - hlk - Z20

description: Gene expression data from FACS purified GFP+ T-lymphoblasts of hlk specimen at the final stage of disease

value: hlk sample


title: Sample 9 - hlk - Z28


title: Sample 8 - hlk - Z27


title: Sample 5 - hMYC-ER - Z13


title: Ilea_F_balbc_rep5

description:
Array09
Microarray Barcode: 251713810418_1_4

source_name: Mouse OME12, germ-free, terminal ileum, female, BALB/c

value: Female

source_name: Mouse OME01, conventional, terminal ileum, female, BALB/c


title: Ilea_F_balbc_rep3

description:
Array07
Microarray Barcode: 251713810418_1_2

source_name: Mouse OME13, germ-free, terminal ileum, female, BALB/c

source_name: Mouse OME04, conventional, terminal ileum, female, BALB/c


title: Sample 2 - hMYC-ER - Z10


title: Sample 4 - hMYC-ER - Z12


title: Ilea_M_B10A_rep3

description:
Array12
Microarray Barcode: 251713810442_1_2

source_name: Mouse OME38, germ-free, terminal ileum, male, C57BL/10A

source_name: Mouse OME28, conventional, terminal ileum, male, C57BL/10A


title: Ilea_F_balbc_rep4

description:
Array08
Microarray Barcode: 251713810418_1_3

source_name: Mouse OME14, germ-free, terminal ileum, female, BALB/c

source_name: Mouse OME05, conventional, terminal ileum, female, BALB/c


title: Ilea_F_balbc_rep1

description:
Array05
Microarray Barcode: 251713810415_1_1

source_name: Mouse OME11, germ-free, terminal ileum, female, BALB/c

source_name: Mouse OME02, conventional, terminal ileum, female, BALB/c


title: Sample 3 - hMYC-ER - Z11


title: Ilea_F_B10A_rep3

description:
Array03
Microarray Barcode: 251713810439_1_3

source_name: Mouse OME32, germ-free, terminal ileum, female, C57BL/10A

source_name: Mouse OME22, conventional, terminal ileum, female, C57BL/10A


title: Ilea_F_balbc_rep2

description:
Array06
Microarray Barcode: 251713810418_1_1

source_name: Mouse OME15, germ-free, terminal ileum, female, BALB/c

source_name: Mouse OME03, conventional, terminal ileum, female, BALB/c


title: Ilea_F_B10A_rep1

description:
Array01
Microarray Barcode: 251713810439_1_1

source_name: Mouse OME35, germ-free, terminal ileum, female, C57BL/10A

source_name: Mouse OME25, conventional, terminal ileum, female, C57BL/10A


title: Ilea_F_B10A_rep2

description:
Array02
Microarray Barcode: 251713810439_1_2

source_name: Mouse OME31, germ-free, terminal ileum, female, C57BL/10A

source_name: Mouse OME21, conventional, terminal ileum, female, C57BL/10A


title: Sample 1 - hMYC-ER - Z9

source_name: FACS purified GFP+ T-lymphoblasts


title: Ilea_F_B10A_rep4

description:
Array04
Microarray Barcode: 251713810439_1_4

source_name: Mouse OME34, germ-free, terminal ileum, female, C57BL/10A

source_name: Mouse OME23, conventional, terminal ileum, female, C57BL/10A


title: Clone E IL10+

city: Boston

first: Dan

last: Hu

address: 60 Fenwood Road

institute: Brigham and Women's Hospital

hyb_protocol: Hybridization of RNA (100 ng per samples) with Reporter Probes (DNA probes provided by the manufacturer) was performed following the manufacturer's instruction. Briefly, 5 μl of RNA (100 ng) sample was mixed with 20 μl of hybridization buffer and Reproter Probes mix. Pre-heated thermocycler to 65°C. Added 5μL of Capture ProbeSet to each tube immediately before placing at 65°C. Incubated hybridization assays at 65°C for over night.

scan_protocol: Hybrided cartridges were washed with the nCounter Prep Station and scanned with the nCounter Digital Analyzer DA61 for high resolution data collection (600 images per samples)

data_processing: nCounter gene expression data was normalized for code count using the geometric mean, for background using the mean, and for sample content using the geometric mean of housekeeping genes (B2M, GAPDH and beta actin) with the R 3.4.0 and NanoString Norm package.

label: Nanostring

source_name: E IL10+

extract_protocol: IL-10– and IL-10+ TH17 clones from an individual donor were pooled. They were stimulated with plate-bound anti-CD3 (clone TR66, 5μg/ml) and anti-CD28 (clone CD28.2, 1μg/ml) (αCD3/CD28) for 4 h. Pooled TH17 clone cells were subjected to RNA isolation. Total RNA was extracted with the E.Z.N.A. Total RNA kit I (Omega Bio-tek, product number R6834)).

treatment_protocol: PBMC were isolated from healthy donors (n=5) by Ficoll-Paque PLUS (GE Healthcare) separation. CD4+ T cells were isolated from PBMC by positive selection using CD4 magnetic microbeads (Miltenyi Biotec). CCR6+CCR4+CXCR3–CD45RA–CD25–CD8–CD14–CD19–CD56– (enriched in TH17 cells) memory CD4 T cells were sorted with a FACSAria (BD Biosciences) and seeded at 0.6 cells per well in a 384 well plate. CD4 T cell clones were established in the presence of irradiated (45Gy) allogeneic PBMC (25,000 cells per well) and phytohaemagglutinin (PHA-L) (1μg/ml) in medium supplemented with IL-2 (500U/ml). IL-10– and IL-10+ TH17 clones were selected for further analysis.

tag: patient id

value: E

value: blood

value: PBMC

value: IL10+ Cells


title: Clone D IL10+

source_name: D IL10+

value: D


title: Clone B IL10+

source_name: B IL10+

value: B


title: Patient_C_DN

hyb_protocol: Hybridization of mRNA in cell lysate with Reporter Probes (DNA probes provided by the manufacturer) was performed following the manufacturer's instruction. Briefly, 4 μl of cell lysate was mixed with 20 μl of hybridization buffer and Reproter Probes mix. One μl of RNAse-free water was added to bring the assay volume to 25 μl. Pre-heated thermocycler to 65°C. Added 5μL of Capture ProbeSet to each tube immediately before placing at 65°C. Incubated hybridization assays at 65°C for over night.

data_processing: nCounter gene expression data was normalized for code count using the geometric mean, for background using the mean, and for sample content using the geometric mean of housekeeping genes (B2M, RPL3 and beta actin) with the R 3.4.0 and NanoString Norm package.

source_name: C DN

extract_protocol: Cell lysates (500-1,000 cells/μl RLT-Plus) of sorted TH1/17, TH17, TH1 and DN cells were prepared with the RLT-Plus buffer of the RNeasy Plus Mini Kit (Qiagen, catalog number 74134)

treatment_protocol: PBMC were isolated with Ficoll-Pague PLUS (GE Healthcare) gradient centrifugation from the peripheral blood of healthy donors. Total CD4+ T cells were purified with the EasySep human CD4+ T cell enrichment kit (StemCell Technologies). CD4+ T cells seeded in a 96-well plate (1x106 cells/well) were stimulated with PMA (30 ng/ml) and ionomycin (1 μg/ml) for 3-4 h (3 h for fresh blood samples and 4 h for frozen PBMC samples). Viable TH1/17, TH17, TH1 and DN cells were sorted with a FACSAria (BD Biosciences) after being stained with IFN-γ and IL-17 cytokine secretion detection kits (Miltenyi Biotec) and fluorescence-conjugated anti-CD3 and anti-CD4 antibodies following the manufacturer’s suggested protocol.

value: C

value: DN Cells


title: Patient_C_TH17

source_name: C TH17

value: TH17 Cells


title: Clone C IL10+

source_name: C IL10+


title: Patient_C_TH1/17

value: TH1/17 Cells


title: Patient_E_TH1/17


title: Patient_E_TH17

source_name: E TH17


title: Patient_D_TH17

source_name: D TH17


title: Patient_D_TH1/17


title: Patient_C_TH1

source_name: C TH1

value: TH1 Cells


title: Patient_E_TH1

source_name: E TH1


title: Patient_E_DN

source_name: E DN


title: Patient_D_DN

source_name: D DN


title: Patient_D_TH1

source_name: D TH1


title: Patient_B_TH1

source_name: B TH1


title: Patient_B_TH1/17


title: Patient_B_TH17

source_name: B TH17


title: Patient_A_TH1/17

value: A


title: Clone D IL10-

source_name: D IL10-

value: IL10- Cells


title: Clone A IL10+

source_name: A IL10+


title: Clone E IL10-

source_name: E IL10-


title: Patient_B_DN

source_name: B DN


title: Clone C IL10-

source_name: C IL10-


title: Patient_A_TH17

source_name: A TH17


title: Clone B IL10-

source_name: B IL10-


title: Patient_A_TH1

source_name: A TH1


title: Clone A IL10-

source_name: A IL10-


title: Patient_A_DN

source_name: A DN


title: SubjectID 34, low MC-SFA, after

status: Public on Sep 28 2017

city: Wageningen

first: Juri

middle: C

last: Matualatupauw

address: PO Box 17

department: Human Nutrition

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Human Gene 1.1 ST arrays were performed on a GeneTitan Instrument (Affymetrix, Santa Clara, CA) according to the manufacturer's recommendations.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.34.2).

source_name: subcutaneous adipose tissue, low MC-SFA, after

label_protocol: One hundred nanogram of RNA was used for whole transcript cDNA synthesis with the Ambion WT expression kit [catalog number 4411974] (Applied Biosystems/Life Technologies, Nieuwekerk a/d IJssel, The Netherlands).

growth_protocol: Participants needed to be ≥18 y of age, have an abdominal circumference of ≥80 cm for women or ≥94 cm for men, and be weight stabile for at least 3 months prior to inclusion. Furthermore, they could not be diabetic, pregnant, lactating, or suffer from severe cardiovascular, renal, endocrine, or psychiatric disease. All participants gave written informed consent to participate in the study and the study protocol was approved by the Central Denmark Region Committees on Health Research Ethics. The study was registered at clinicaltrials.gov as NCT01472666.

extract_protocol: Total RNA was isolated using RNeasy micro kit from Qiagen. RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 7.0).

treatment_protocol: This study is a secondary analysis of a randomized, parallel-controlled, double-blinded, 12-wk diet intervention study that was designed to examine the effects of milk fat, with a high or low MC-SFA content, and of milk protein, whey or casein, on post-prandial lipemia. Design and methods of the original study were described in detail previously (Bohl et al. 2015, doi: 10.3945/ajcn.114.097923). Briefly, 52 participants were randomized in a 2 × 2 factorial design to one of 4 diets: high MC-SFA + casein, low MC-SFA + casein, high MC-SFA + whey, and low MC-SFA + whey. In this paper, we examine the effects of MC-SFAs on whole genome gene expression in subcutaneous adipose tissue in a subpopulation of 12 subjects, 6 in the high MC-SFA + casein group and 6 in the low MC-SFA + casein groups.

tag: gender

value: male

tag: individual

value: low MC-SFA + casein

value: subcutaneous adipose tissue

tag: metabolic syndrome

value: y

tag: age

tag: weight

tag: height

tag: waisttohipratio


title: SubjectID 64, high MC-SFA, before

source_name: subcutaneous adipose tissue, high MC-SFA, before

value: high MC-SFA + casein

value: n


title: SubjectID 88, high MC-SFA, after

source_name: subcutaneous adipose tissue, high MC-SFA, after

value: female


title: SubjectID 65, high MC-SFA, after


title: SubjectID 34, low MC-SFA, before

source_name: subcutaneous adipose tissue, low MC-SFA, before


title: SubjectID 88, high MC-SFA, before


title: SubjectID 87, high MC-SFA, before


title: SubjectID 22, low MC-SFA, after


title: SubjectID 64, high MC-SFA, after


title: SubjectID 8, low MC-SFA, after


title: SubjectID 89, low MC-SFA, after


title: SubjectID 63, low MC-SFA, after


title: SubjectID 93, low MC-SFA, after


title: SubjectID 96, high MC-SFA, before


title: SubjectID 65, high MC-SFA, before


title: SubjectID 87, high MC-SFA, after


title: SubjectID 8, low MC-SFA, before


title: SubjectID 36, high MC-SFA, after


title: SubjectID 96, high MC-SFA, after


title: SubjectID 22, low MC-SFA, before


title: SubjectID 89, low MC-SFA, before


title: SubjectID 36, high MC-SFA, before


title: SubjectID 63, low MC-SFA, before


title: SubjectID 93, low MC-SFA, before


title: ChRO1 depleted C2C12 by shRNA against ChRO1 introduction, 3 days-differentiated myotubes

city: Suwon

first: Jinyoung

last: Park

address: Seobu-ro 2066, Jangan-gu

country: South Korea

institute: Sungkyunkwan University

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

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

data_processing: Array data export processing and analysis was performed using Illumina GenomeStudio v2011.1 (Gene Expression Module v1.9.0)

label: Biotin

source_name: ChRO1 shRNA introduced C2C12

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

growth_protocol: Control C2C12 and ChRO1 depleted C2C12 growth was performed in DMEM containing 10% FBS(Fetal Bovine Serum) with 1% P/S(Penicillin/Streptomycin), and differentiation into myotubes of these cells were performed in DMEM containing 2% HS(Horse serum) with 1% P/S.

extract_protocol: RNA was extracted with Nucleospin RNA kit(Machery-Nagel) in accordance with the prescribed protocol provided with the kit. Quality control was performed with Nanodrop 2000c.

tag: cell line

tag: genotype/variation

value: ChRO1 depleted

value: 3 days-differentiated myotubes


title: ChRO1 depleted C2C12 by shRNA against ChRO1 introduction, undifferentiated myoblasts

value: undifferentiated myoblasts


title: Control C2C12, undifferentiated myoblasts

source_name: Control C2C12

value: wild type


title: Control C2C12, 3 days-differentiated myotubes


title: 22Rv1 0.3 µM A-485 6 h rep 1

status: Public on Sep 27 2017

city: North Chicago

first: Xin

last: Lu

state: IL

address: 1 North Waukegan Rd

department: Oncology Discovery

institute: Abbvie

description: Sample 15

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Human Genome U133 Plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Genechip Scanner 3000

data_processing: Background subtraction, normalization and gene expression index calculation were performed using Rosetta Resolver software

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200 ng total RNA (using Affymetrix 3IVT Plus amplification kit).

growth_protocol: RPMI media + 10% Charcoal Stripped Fetal Bovine Serum

extract_protocol: Qiazol extraction of total RNA followed by Qiagen Rneasy purification was performed according to the manufacturer's instructions.

treatment_protocol: Cells were treated with either A-485 or enzalutamide for 30 minutes and then further treated with either DHT or ethanol for 6 h.


title: LnCap-FGC DHT + 3 µM A-485 6 h rep 1

description: Sample 7

source_name: LnCap-FGC DHT + 3 uM A-485 6 h

value: LNCaP-FGC


title: 22Rv1 Control 6 h rep 2

description: Sample 14

source_name: 22Rv1 Control 6 h


title: LnCap-FGC DHT 6 h rep 2

description: Sample 4

source_name: LnCap-FGC DHT 6 h


title: LnCap-FGC DHT 6 h rep 1

description: Sample 3


title: LnCap-FGC DHT + 3 µM A-485 6 h rep 2

description: Sample 8


title: LnCap-FGC Control 6 h rep 2

description: Sample 2

source_name: LnCap-FGC Control 6 h


title: 22Rv1 0.3 µM A-485 6 h rep 2

description: Sample 16


title: LnCap-FGC DHT +0.3 µM A-485 6 h rep 1

description: Sample 5

source_name: LnCap-FGC DHT + 0.3 uM A-485 6 h


title: LnCap-FGC DHT +0.3 µM Enzalutamide 6 h rep 1

description: Sample 9

source_name: LnCap-FGC DHT + 0.3 uM Enzalutamide 6 h


title: LnCap-FGC DHT + 3 µM Enzalutamide 6 h rep 1

description: Sample 11

source_name: LnCap-FGC DHT + 3 uM Enzalutamide 6 h


title: LnCap-FGC DHT +0.3 µM Enzalutamide 6 h rep 2

description: Sample 10


title: LnCap-FGC DHT +0.3 µM A-485 6 h rep 2

description: Sample 6


title: 22Rv1 3 µM A-485 6 h rep 2

description: Sample 18


title: 22Rv1 3 µM A-485 6 h rep 1

description: Sample 17


title: LnCap-FGC DHT + 3 µM Enzalutamide 6 h rep 2

description: Sample 12


title: LnCap-FGC Control 6 h rep 1

description: Sample 1


title: 22Rv1 Control 6 h rep 1

description: Sample 13


title: Pancreas from a pancreas-specific Jarid2 knockout (KO) E15.5 mouse embryo 3

status: Public on Sep 26 2017

city: Barcelona

first: Joan Marc

last: Servitja

state: Catalonia

address: Rosselló, 153

institute: IDIBAPS

description: Gene expression data from old islets at 11mM glucose

hyb_protocol: Following fragmentation, cRNA was hybridized to Genechip Mouse 430 2.0 Affymetrix arrays, washed and stained according to the standard Affymetrix protocol.

scan_protocol: GeneChips were scanned according to the standard Affymetrix protocol (Affymetrix Genechip Command Console program 3.0.0.1214, scanner GCS 3000-7G)

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol through two cycles of cDNA synthesis (50 ng starting total RNA).

growth_protocol: Pancreases from pancreas-specific Jarid2 knockout and control embryos were harvested at embryonic day 15.5.

extract_protocol: RNA was extracted with the Rneasy mini kit from Qiagen

tag: strain

value: Embryonic pancreas

value: Jarid2 knock-out


title: Pancreas from a wild-type E15.5 mouse embryo 3

description: Gene expression data from old islets at 5mM glucose

value: wild-type


title: Pancreas from a pancreas-specific Jarid2 knockout (KO) E15.5 mouse embryo 2


title: Pancreas from a pancreas-specific Jarid2 knockout (KO) E15.5 mouse embryo 1


title: Pancreas from a wild-type E15.5 mouse embryo 2

description: Gene expression data from old islets at 3mM glucose


title: Pancreas from a wild-type E15.5 mouse embryo 1


title: Pancreatic islets from untreated hIAPP Tg mice isolated at week 20 rep1

hyb_protocol: Following fragmentation, cRNA was hybridized to Affymetrix GeneChip® Mouse HT_MG-430_PM arrays, washed and stained according to the standard Affymetrix protocol.

data_processing: Expression data were normalized with Robust Multi-array Average (RMA)  from the affy package (www.bioconductor.org)

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

growth_protocol: Islets from wild type and hIAPP Tg mice left untreated or treated with PBA were isolated at week 20.

extract_protocol: RNA was extracted with the Rneasy Mini kit from Qiagen

treatment_protocol: 8 weeks old wild type and hIAPP Tg mice were left untreated or treated with PBA (1g/kg/day) during 12 weeks. Islets were isolated at week 20.

tag: strain background

value: hIAPP transgenic

value: 20 weeks

tag: treated with

value: none (untreated)

value: Islets of Langerhans


title: brain STR_saline yoked shock resistant_rep3

city: Baltimore

first: Jean Lud

last: Cadet

address: 251 Bayview Blvd, Suite 200

department: Molecular Neuropsychiatry Research Branch

institute: NIDA, IRP

description: whole transcript gene expression profiling on rats that self administer methamphetamine and use footshocks as adverse consequences

hyb_protocol: Following fragmentation, 5.5 ug of ss DNA were hybridized for 16 hr at 45C on GeneChip Rat Transcriptome 1.0 arrays. Arrays were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000.

data_processing: The data were analyzed with Expression Console Software using Affymetrix default analysis settings.

organism: Rattus norvegicus

source_name: striatum tissue

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (GeneChip WT Plus Reagent Kit Manual, Affymetrix).

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

value: Sprague Dawley


title: Pancraetic islets from PBA-treated hIAPP Tg mice isolated at week 20 rep1

value: PBA (1g/kg/day) dissolved in water for 12 wks


title: Pancreatic islets from untreated wild type mice isolated at week 20 rep1


title: Pancreatic islets from untreated hIAPP Tg mice isolated at week 20 rep2


title: Pancreatic islets from PBA-treated wild type mice isolated at week 20 rep1


title: Tumor_Vector_rep1

type: genomic

city: Guangzhou

first: Lu

address: No.12,Airport Road,Baiyun District

country: China

institute: Guangzhou University of Chinese Medicine

description: Chemo-resistant cells

hyb_protocol: Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylation450 BeadChip using standard Illumina protocol.

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

data_processing: Data was normalized and analyzed using partek software and R packages. Specifically centered logit transformation was used for data normalization.

label: Cy3, Cy5

molecule: genomic DNA

source_name: Colorectal cancer cells with vector 1

label_protocol: Standard Illumina labelling protocol.

growth_protocol: Stable FIBP knockdown cell lines were produced by lentivirus infection with shRNA, while reverse of  GSK3β were achieved by plasmid transfection. shRNA lentivirus encoding FIBP was synthesized by Genepharma (Shanghai, China). Target cells were infected with PCDH-shFIBP or PCDH-NC lentivirus in the presence of 5μg/ml polybrene. The stable cell lines were established after 1 week of selection with puromycin (1 mg/ml), and the FIBP protein levels were subsequently analyzed by western blotting.

extract_protocol: Genomic DNA was bisulfite-treated and purified using the EpiTect Bisulfite Plus Kit (QIAGEN K.K., Tokyo, Japan).

tag: genotype

value: control


title: brain STR_saline yoked shock sensitive_rep2


title: Pancreatic islets from untreated wild type mice isolated at week 20 rep2


title: brain STR_shock sensitive_rep4


title: Pancraetic islets from PBA-treated hIAPP Tg mice isolated at week 20 rep2


title: brain STR_saline yoked shock sensitive_rep1


title: brain STR_saline yoked shock resistant_rep2


title: brain STR_shock sensitive_rep5


title: brain STR_shock sensitive_rep3


title: Pancreatic islets from PBA-treated wild type mice isolated at week 20 rep2


title: brain STR_shock sensitive_rep2


title: Tumor_Vector_rep2

description: Chemo-resistant cells

source_name: Colorectal cancer cells with vector 2


title: brain STR_saline yoked shock sensitive_rep3


title: brain STR_saline yoked shock resistant_rep1


title: Tumor_FIBP_knockdown_rep1

description: Chemo-resistant cells

source_name: Colorectal cancer cells with FIBP knockdown 1

value: FIBP knockdown


title: brain STR_shock resistant_rep5


title: brain STR_shock sensitive_rep6


title: brain STR_shock resistant_rep6


title: Tumor_FIBP_knockdown_rep2

description: Chemo-resistant cells

source_name: Colorectal cancer cells with FIBP knockdown 2


title: Tumor_FIBP/GSK3b_knockdown_rep2

description: Chemo-resistant cells

source_name: Colorectal cancer cells with FIBP/GSK3b knockdown 2

value: FIBP/GSK3b knockdown


title: brain STR_shock resistant_rep3


title: Tumor_FIBP/GSK3b_knockdown_rep1

description: Chemo-resistant cells

source_name: Colorectal cancer cells with FIBP/GSK3b knockdown 1


title: brain STR_shock resistant_rep2


title: brain STR_shock resistant_rep4


title: brain STR_shock resistant_rep1


title: brain STR_shock sensitive_rep1


title: brain STR_control_rep6


title: brain STR_control_rep5


title: brain STR_control_rep4


title: brain STR_control_rep2


title: brain NAc_saline yoked shock sensitive_rep2

source_name: Nucleus Accumbens tissue


title: brain STR_control_rep1


title: brain STR_control_rep3


title: brain NAc_saline yoked shock resistant_rep3


title: brain NAc_saline yoked shock sensitive_rep1


title: brain NAc_saline yoked shock resistant_rep2


title: brain NAc_saline yoked shock resistant_rep1


title: brain NAc_shock sensitive_(2)_rep2


title: brain NAc_shock sensitive_(2)_rep6


title: brain NAc_shock sensitive_(2)_rep4


title: brain NAc_shock sensitive_(2)_rep3


title: brain NAc_shock resistant_(2)_rep3


title: brain NAc_shock sensitive_(2)_rep5


title: brain NAc_shock resistant_(2)_rep5


title: brain NAc_shock sensitive_(2)_rep1


title: brain NAc_control_(2)_rep6


title: brain NAc_shock resistant_(2)_rep6


title: brain NAc_shock resistant_(2)_rep2


title: brain NAc_shock resistant_(2)_rep4


title: brain NAc_control_(2)_rep5


title: brain NAc_control_(2)_rep4


title: brain NAc_control_(2)_rep3


title: SM296 D3 + 24h estrogen treated Replicate 2

status: Public on Sep 25 2017

city: Munich

first: Bettina

last: Kempkes

address: Marchioninistr. 25

department: AGV

country: Germany

institute: HMGU

description: Gene expression data from SM296 cells treated with estrogen for 24 h

hyb_protocol: GeneChip® WT Terminal Labeling and Hybridization Kit (Affymetrix)

scan_protocol: GeneChip Scanner 3000 7G

data_processing: Affymetrix CEL files have been processed in Bioconductor/R using robust multiarray average (RMA) for normalization and summarization and limma for differential expression and significance. Quality has been checked using the array QualityMetrics package.

source_name: SM296 B cell line

label_protocol: Ambion® WT Expression Kit (Applied Biosystems)

growth_protocol: The cell lines have been described in: Maier S, Santak M, Mantik A, Grabusic K, Kremmer E, Hammerschmidt W, et al. A somatic knockout of CBF1 in a human B-cell line reveals that induction of CD21 and CCR7 by EBNA-2 is strictly CBF1 dependent and that downregulation of immunoglobulin M is partially CBF1 independent. Journal of virology. 2005 Jul;79(14):8784-92. PubMed PMID: 15994772.

extract_protocol: Quiagen RNeasy Mini Kit

treatment_protocol: All cells  were cultivated in estrogen supplemented medium for 24 h or were left untreated. Total cellular RNA was isolated and submitted to gene expression analysis.

tag: er/ebna2 expressed

value: yes

tag: estrogen treatment

value: ko


title: SM296 D3 Replicate 2

description: Gene expression data from SM296 cells untreated control samples

value: no


title: brain NAc_control_(2)_rep2


title: brain NAc_shock resistant_(2)_rep1


title: SM224.9 + 24h estrogen treated Replicate 3

description: Gene expression data from SM224.9 cells treated with estrogen for 24 h

source_name: SM224.9 B cell line


title: SM296 D3 + 24h estrogen treated Replicate 1


title: SM296 D3 + 24h estrogen treated Replicate 3


title: SM224.9 + 24h estrogen treated Replicate 2


title: SM296 D3 Replicate 3


title: SM224.9 Replicate 2

description: Gene expression data from SM224.9 cells untreated control samples


title: brain NAc_control_(2)_rep1


title: SM224.9 + 24h estrogen treated Replicate 1

value: wt


title: SM296 D3 Replicate 1


title: SM224.9 Replicate 1


title: SM224.9 Replicate 3


title: SM295 D6 Replicate 3

description: Gene expression data from SM295 cells untreated control samples

source_name: SM295 B cell line


title: SM295 D6 Replicate 1


title: SM295 D6 Replicate 2


title: G1805_DKO_B_IL7R

type: SRA

city: Memphis

first: Geoffrey

last: Neale

state: TN

address: 262 Danny Thomas Place

department: Hartwell Center

institute: St Jude Childrens Research Hospital

description: B_IL7R PLC Gamma1/2 DKO replicate 3

library_source: transcriptomic

data_processing:
RNA-seq alignment was done by RNA-Seq Alignment software v1.0, Illumina, Inc. Sequences were un-trimmed and aligned to Mus musculus UCSC mm10 RefSeq by STAR aligner v2.5.0a.
Genome_build: mm10
Supplementary_files_format_and_content: Gene counts as output from STAR aligner

source_name: bone marrow cells

extract_protocol:
Total RNA was extracted by using TRIzol LS reagent. mRNA was purified by using NEBNext poly(A) mRNA magnetic Isolation module.
Library was prepared by using NEBNext Ultra RNA Library Prep Kit for Illumina.

tag: cell population

value: B cell progenitor

tag: facs sorting surface marker


title: G1803_G2KO_B_IL7R

description: B_IL7R PLC Gamma2 KO replicate 3


title: G1801_WT_B_IL7R

description: B_IL7R WT replicate 3


title: SM295 D6 + 24h estrogen treated Replicate 3

description: Gene expression data from SM295 cells treated with estrogen for 24 h


title: SM295 D6 + 24h estrogen treated Replicate 1


title: DLD-1/FTD (miRNA)

city: tokushima

first: kenta

last: tsunekuni

state: tokushima

address: Ebisuno Hiraishi, Kawauchi-cho

department: Translational Research Laboratory

country: Japan

institute: taiho parmaceutical

description: miRNA profiling

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: colorectal cancer cell lines

label_protocol: Extracted total RNA was labeled with Cy5 using the 3D-Gene miRNA labeling kit (Toray, Kamakura, Japan)

growth_protocol: Cell lines were  grown in Dulbecco’s modified Eagle’s medium (DMEM; Sigma-Aldrich, MO, USA) supplemented with 10% fetal bovine serum (FBS; Thermo Fisher Scientific, MA, USA), 100 U mL−1 penicillin, and 100 U mL−1 streptomycin (Life Technologies, CA, USA) at 37°C in a humidified atmosphere with 5% CO2.

extract_protocol: RNA samples were extracted from cells using miRNesy mini kit (Quiagen).

treatment_protocol: About 80% confluent cells were cllected to extract total RNA.

tag: phenotype

value: FTD resistant


title: DG75 + 24h estrogen treated Replicate 3

description: Gene expression data from DG75 cells treated with estrogen for 24 h

source_name: DG75 B cell line


title: RKO (miRNA)

description: miRNA profiling

value: RKO

value: parent


title: DLD-1 (miRNA)

description: miRNA profiling


title: RKO/FTD (miRNA)

description: miRNA profiling


title: HCT-116 (miRNA)

description: miRNA profiling


title: HCT-116/FTD (miRNA)

description: miRNA profiling


title: SM295 D6 + 24h estrogen treated Replicate 2


title: DG75 + 24h estrogen treated Replicate 2


title: DG75 Replicate 2

description: Gene expression data from DG75 cells untreated control samples


title: G1804_G1KO_B_IL7R

description: B_IL7R PLC Gamma1 KO replicate 3


title: DG75 Replicate 1


title: G1789_G2KO_B_IL7R

description: B_IL7R PLC Gamma2 KO replicate 2


title: G1806_DKO_B_IL7R

description: B_IL7R PLC Gamma1/2 DKO replicate 2


title: DG75 Replicate 3


title: G1790_DKO_B_IL7R

description: B_IL7R PLC Gamma1/2 DKO replicate 1


title: G1808_G1KO_B_IL7R

description: B_IL7R PLC Gamma1 KO replicate 2


title: G1807_WT_B_IL7R

description: B_IL7R WT replicate 2


title: G1809_G2KO_B_IL7R

description: B_IL7R PLC Gamma2 KO replicate 1


title: Tum008

first: David

last: Finkelstein

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

description: Neuroblastoma tumor model

hyb_protocol: Followed standard protocol for  Affymetrix Mouse 2.0 ST arrays.

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

data_processing: The data were analyzed with Partek Genomics Suite version 6.5 using the RMA method

label: Biotin (Affyexpress)

source_name: primary tumor

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

growth_protocol: N-Myc transduced cells are a mixture of both p53+/- and p53-/- NCCs and are designated as N-Myc; p53mixed.  At 48 hours post infection, N-Myc; p53mixed NCCs were harvested and ~10,000 cells were injected subcutaneously into nude mice or into C57Bl/6 mice After ~ 50 days primary tumors were removed from the mice

extract_protocol: Total RNAs were extracted with Trizol reagent (Invitrogen) according to a supplied RNA isolation protocol.

tag: tissue

value: N-Myc NCC-derived neuroblastoma


title: Tum007

description: Neuroblastoma tumor model


title: Tum004

description: Neuroblastoma tumor model


title: Tum006

description: Neuroblastoma tumor model


title: Tum002

description: Neuroblastoma tumor model


title: Tum005

description: Neuroblastoma tumor model


title: G1810_WT_B_IL7R

description: B_IL7R WT replicate 1


title: G1789_G2KO_CLP

description: CLP PLC Gamma2 KO replicate 2

value: CLP


title: G1801_WT_CLP

description: CLP WT replicate 3


title: G1804_G1KO_CLP

description: CLP PLC Gamma1 KO replicate 3


title: G1806_DKO_CLP

description: CLP PLC Gamma1/2 DKO replicate 2


title: G1805_DKO_CLP

description: CLP PLC Gamma1/2 DKO replicate 3


title: G1790_DKO_CLP

description: CLP PLC Gamma1/2 DKO replicate 1


title: G1803_G2KO_CLP

description: CLP PLC Gamma2 KO replicate 3


title: G1807_WT_CLP

description: CLP WT replicate 2


title: G1811_G1KO_B_IL7R

description: B_IL7R PLC Gamma1 KO replicate 1


title: Tum001

description: Neuroblastoma tumor model


title: Lin-CD34+CD38- NormalDonor#4

city: Modena

first: Rossella

last: Manfredini

address: Via Gottardi 100

department: Life Sciences

institute: Centre for Regenerative Medicine

description:
miEP of Lineage-Negative CD34-positive CD38-negative cells Normal Donor #4
Sample name: Normal Donor 4 34+38-

data_processing:
RT-qPCR data were analysed using the Exiqon GenEx software for the inter-plate calibration, the definition of a Ct=40 as detection cutoff, the labeling of not-amplified wells as missing data and the setting of a cutoff for miRNAs with a low call-rate (i.e. assays with a detection rate <33,3%, i.e. assays not detected in 12 out of 18 samples, were excluded from analysis). For RT-qPCR data normalization, the comparative cycle threshold (CT) method was used by setting miR-23a-3p, miR-24-3p and miR-324-3p as reference miRNAs, as the best normalizers identified among the candidates by the NormFinder algorithm. The RQ value was expressed as 2−ΔΔCT.
Statistical analyses on ΔCT values between CML Lin-CD34-CD38- and Normal donor Lin-CD34-CD38- (set as calibrator) and between CML Lin-CD34+CD38- and Normal donor Lin-CD34+CD38- (set as calibrator) were performed by a two-tail unpaired t-Student test using the GenEx software. Fold Change (FC) worksheet reports the relative quantity (RQ) = 2^-ΔΔCt. To make the RQ value symmetric for up- and down-regulated genes, FC was used in the Tables for ease of interpretation (for RQ > 1, FC = RQ; for RQ < 1 FC = −1/RQ).

label: SYBR Green

label_protocol: miEP was performed by using the miRCURY LNATM Universal RT microRNA PCR system, Ready-to-use Human miRNome Panels I and II (Exiqon, Copenhagen, Denmark).

growth_protocol: Cells were lysated right after isolation, no growth in culture

extract_protocol: Total cellular RNA was harvested from 1×10^5 cells from each sample using the miRNeasy Micro RNA isolation kit (QIAGEN), according to the manufacturer’s instructions. RNA samples concentration and purity (assessed as 260/280 nm and 260/230 nm ratios) were evaluated by NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies; Wilmington, DE), while RNA integrity was assessed by using the Agilent 2100 Bioanalyzer (Agilent Technologies; Waldbrunn, Germany).

treatment_protocol: Leukemic cells were obtained from 5 chronic phase Ph+ CML patients at diagnosis. Normal samples were leukapheresis products from 4 healthy donors receiving recombinant human granulocyte colony-stimulating factor (G-CSF; Lenograstim; Sanofi-Aventis).

tag: disease state

value: Normal Donor

tag: subject id

value: normal donor 4

value: peripheral blood

tag: cell markers


title: Lin-CD34-CD38- NormalDonor#4

description:
miEP of Lineage-Negative CD34-negative CD38-negative cells CML Normal Donor #4
Sample name: Normal Donor 4 34-38-

source_name: leukapheresis products from 4 healthy donors receiving recombinant human granulocyte colony-stimulating factor (G-CSF; Lenograstim; Sanofi-Aventis).


title: brain NAc_saline yoked shock sensitive_rep3

value: Sprague Dawley

tag: weight


title: Lin-CD34+CD38- NormalDonor#3

description:
miEP of Lineage-Negative CD34-positive CD38-negative cells Normal Donor #3
Sample name: Normal Donor 3 34+38-

value: normal donor 3


title: G1808_G1KO_CLP

description: CLP PLC Gamma1 KO replicate 2


title: Lin-CD34-CD38- NormalDonor#1

description:
miEP of Lineage-Negative CD34-negative CD38-negative cells CML Normal Donor #1
Sample name: Normal Donor 1 34-38-

value: normal donor 1


title: G1809_G2KO_CLP

description: CLP PLC Gamma2 KO replicate 1


title: G1810_WT_CLP

description: CLP WT replicate 1


title: Lin-CD34-CD38- NormalDonor#2

description:
miEP of Lineage-Negative CD34-negative CD38-negative cells CML Normal Donor #2
Sample name: Normal Donor 2 34-38-

value: normal donor 2


title: G1811_G1KO_CLP

description: CLP PLC Gamma1 KO replicate 1


title: Lin-CD34-CD38- NormalDonor#3

description:
miEP of Lineage-Negative CD34-negative CD38-negative cells CML Normal Donor #3
Sample name: Normal Donor 3 34-38-


title: Lin-CD34+CD38- NormalDonor#2

description:
miEP of Lineage-Negative CD34-positive CD38-negative cells Normal Donor #2
Sample name: Normal Donor 2 34+38-


title: Lin-CD34-CD38- CML#1

description:
miEP of Lineage-Negative CD34-negative CD38-negative cells CML patient #1
Sample name: CML 1 34-38-

source_name: Chronic Myeloid Leukemia, Peripheral Blood

value: Chronic Myeloid Leukemia (CML)

value: patient 1


title: Lin-CD34-CD38- CML#4

description:
miEP of Lineage-Negative CD34-negative CD38-negative cells CML patient #4
Sample name: CML 4 34-38-

value: patient 4


title: BORIS_1

city: Bhopal

first: Sanjeev

last: Shukla

state: Madhya Prades

address: Bhopal Bypass Road, Bhauri Bhopal 462 066 Madhya Pradesh, INDIA

department: Biological Sciences

country: India

institute: Indian Institute of Science Education and Research Bhopal

description: MCF7 cells transfected with BORIS shRNA

hyb_protocol: Samples were hybridized with Human Transcriptome 2.0 Arrays (Affymetrix) and scanned.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing:
Raw data were processed with the Exon Array Computational Tool (ExACT) (Affymetrix) for background correction and normalization. Data analysis and statistical evaluations were performed with customized R codes (version 2.3.1, http://www.r-project.org/). We defined a probeset as present when it had a P value <0.001 and an Intensity value >200. These criteria were suggested by the results of preliminary experiments. The SECT includes all probesets present in at least 16 of the 18 arrays. In addition, we refined the SECT to remove GC-rich (i.e., >=80%) probesets. The concordance between the SECT and the normal salivary core transcriptome (NSCT) was evaluated assuming hypergeometric distributions.
RMA

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT plus reagent Kit (Affymetrix).

growth_protocol: MCF7 cells were grown under standard cell culture conditions

extract_protocol: RNA was isolated from MCF7 with the RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions.

treatment_protocol: MCF7 cells were transfected with shControl and shBORIS and selected with puromycin for 7 days

tag: source

value: Luminal


title: Lin-CD34-CD38- CML#2

description:
miEP of Lineage-Negative CD34-negative CD38-negative cells CML patient #2
Sample name: CML 2 34-38-

value: patient 2


title: Lin-CD34+CD38- CML#1

description:
miEP of Lineage-Negative CD34-positive CD38-negative cells CML patient #1
Sample name: CML 1 34+38-


title: DG75 + 24h estrogen treated Replicate 1

value: no

value: yes

value: wt


title: Lin-CD34+CD38- NormalDonor#1

description:
miEP of Lineage-Negative CD34-positive CD38-negative cells Normal Donor #1
Sample name: Normal Donor 1 34+38-


title: Lin-CD34+CD38- CML#5

description:
miEP of Lineage-Negative CD34-positive CD38-negative cells CML patient #5
Sample name: CML 5 34+38-

value: patient 5


title: BORIS_2

description: MCF7 cells transfected with BORIS shRNA


title: Lin-CD34-CD38- CML#5

description:
miEP of Lineage-Negative CD34-negative CD38-negative cells CML patient #5
Sample name: CML 5 34-38-


title: Lin-CD34-CD38- CML#3

description:
miEP of Lineage-Negative CD34-negative CD38-negative cells CML patient #3
Sample name: CML 3 34-38-

value: patient 3


title: Lin-CD34+CD38- CML#4

description:
miEP of Lineage-Negative CD34-positive CD38-negative cells CML patient #4
Sample name: CML 4 34+38-


title: Lin-CD34+CD38- CML#3

description:
miEP of Lineage-Negative CD34-positive CD38-negative cells CML patient #3
Sample name: CML 3 34+38-


title: Lin-CD34+CD38- CML#2

description:
miEP of Lineage-Negative CD34-positive CD38-negative cells CML patient #2
Sample name: CML 2 34+38-


title: Tum003

description: Neuroblastoma tumor model

value: N-Myc NCC-derived neuroblastoma


title: DLD-1/FTD (mRNA)

description: mRNA profiling

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

tag: cell line

value: FTD resistant


title: HCT-116 (mRNA)

description: mRNA profiling

value: parent


title: mutS::kan cells replicate 1

city: Warsaw

first: Monika

middle: Julita

last: Adamczyk-Poplawska

address: Miecznikowa 1

country: Poland

institute: University of Warsaw

description: total RNA from not pooled samples

hyb_protocol: Equal amounts of Cy5- and Cy3-labeled cRNAs were hybridized onto the microarray for 17 h at 65°C and hybridized microarrays were washed according to the Agilent protocol. Gene Expression Hybridization Kit and Gene Expression Wash Buffer Kit were used respectively to hybridize and wash the hybridized microarray.

scan_protocol: Microarray slides were scanned using the Agilent G2565CA Microarray Scanner System.

data_processing:
GeneSpring version 12.5 (Agilent Technologies) was used for data analysis. Normalized data from all samples were filtered on genes flagged as present or marginal with the resulting gene list used for further gene expression analysis and clustering (Student’s t-test against zero, asymptotic P value computation and Benjamini Hochberg FDR multiple testing correction).
Arbitrary fold change (FC) cut-offs of >1.5 or >2 tested/reference

organism: Neisseria gonorrhoeae

source_name: mutS::kan cells replicate 1

label_protocol: The Low Input Quick Amp Labeling WT (LIQA WT) Kit (Agilent Technologies) was used to amplify and label whole transcripts. Additionally, the RNA Spike In Kit for Two color v4.0 (Agilent Technologies) was used according to manufacturer`s instructions. (i) cDNA synthesis using total RNA (50 ng) as template; (ii) cRNA synthesis and labeling using cDNA as template, T7 RNA polymerase, NTPs and fluorescent dye. Simultaneously two mixtures were prepared, one reaction with Cy3 as fluorescent dye, the second one with Cy5; (iii) purification of labeled cRNA and measurement of the efficiency of incorporation of the Cy5 or Cy3 dye. The Cy3 dye was used to label the cRNA wt strain, and the Cy5 dye to label the cRNA N. gonorrhoeae mutant strain.

growth_protocol: Cells were grown overnight on GCB agar plate with hemoglobin and Kellog supplement at 37C and 5 % CO2

extract_protocol: Cells were then harvested from one plate and total RNA was isolated using the High Pure RNA Isolation Kit (Roche), according to the manufacturer’s recommendations.

value: interrupted mutS gene

source_name: N. gonorrhoae wild type

value: wild type


title: DLD-1 (mRNA)

description: mRNA profiling


title: CONTROL_2

description: MCF7 cells transfected with control shRNA


title: mutS::kan cells replicate 4

description: total RNA from not pooled samples

source_name: mutS::kan cells replicate 4


title: RKO/FTD (mRNA)

description: mRNA profiling

value: RKO


title: vsrB::kan cells replicate 4

description: total RNA from not pooled samples

source_name: N. gonorrhoeae wild type

source_name: vsrB::kan cells replicate 4

value: interrupted ngoAXIV gene


title: CONTROL_1


title: HCT-116/FTD (mRNA)

description: mRNA profiling


title: mutS::kan cells replicate 2

description: total RNA from not pooled samples

source_name: mutS::kan cells replicate 2


title: mutS::kan cells replicate 3

description: total RNA from not pooled samples

source_name: mutS::kan cells replicate 3


title: vsrB::kan cells replicate 3

description: total RNA from not pooled samples

source_name: vsrB::kan cells replicate 3


title: RKO (mRNA)

description: mRNA profiling


title: vsrB::kan cells replicate 1

description: total RNA from not pooled samples

source_name: vsrB::kan cells replicate 1


title: mutL::kan cells replicate 2

description: total RNA from not pooled samples

source_name: mutL::kan cells replicate 2

value: interrupted mutL gene


title: mutL::kan cells replicate 1

description: total RNA from not pooled samples

source_name: mutL::kan cells replicate 1


title: IAP- (sorted d16, d50)_2

city: Bergisch Gladbach

first: Jutta

last: Kollet

address: Friedrich-Ebert-Str. 68

department: Bioinformatics

institute: Miltenyibiotec GmbH

description: hESC-derived mesDA progenitor cells (day16 IAP-, day50)

hyb_protocol: Cy3 labeled cRNAs were hybridized overnight (17 hours, 65°C) to Agilent Whole Human Genome Oligo Microarrays 8x60K v2 (Design ID 039494) using Agilent’s recommended hybridization chamber and oven.Finally, microarrays were washed once with wash buffer 1 for 1 min at RT followed by a second wash with wash buffer 2 for 1 min at 37°C.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (G2505C, Agilent Technologies, Palo Alto, USA).

data_processing: The Agilent Feature Extraction Software (FES 10.7.3.1 ) was used to read out and process the microarray image files. Backgorund corrected intensities of the FES derived output files were normalized between arrays using quanitle normalization method, followed by log2 transformation using R/bioconductor and apckages therein.

label_protocol: 100 ng of each RNA was used as template to produce Cy3- labeled cRNA. The RNA samples were amplified and labeled using the Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer’s protocol.

growth_protocol: The differentiation protocol was adapted from Kirkeby et al. 2012. For differentiation, the cells were harvested with TrypLE. The cells from feeder co-cultivation underwent a feeder removal step (Feeder Removal MicroBeads, Miltenyi Biotec). Single cells were seeded in low attachment plates (2x10^6 per 6well) to form EBs in DMEM/F12:MACS Neuro (1:1), 2 mM L-glutamine, N2 supplement (1:100; Gibco), NB-21 w/o vitamin A (1:50). ROCK-Inhibitor (Thiazovivin 2 µM, Miltenyi Biotec) was added for the first two days. On d4, the cells were plated on polyornithine (PO; 15 µg/ml; Sigma), Fibronectin (FN; 5 µg/ml; Biopur AG) and laminin (LN; 5 µg/ml; Sigma) coated plastic ware. From d0 to d9 the following neuralization and patterning factors were present SB431542 (10 µM, Stemgent), LDN193189 (100 nM, Stemgent), CHIR99021 (0.8 µM, Stemgent), hSHH-C24-II (200 ng/ml, Miltenyi Biotec). From d2-d9 Purmorphamine (0.5 µM, Stemgent) was added to the medium.  On d11 of differentiation, the cells were dissociated into single cells with accumax (eBioscience) and  replated on dry PO/LN/FN coated plates in droplets of 10,000 cells/µl in MACS Neuro, 2 mM L-glutamine, NB-21 w/o vitamin A (1:50) BDNF (20 ng/ml; Miltenyi Biotec), GDNF (10 ng/ml; Miltenyi Biotec) and ascorbic acid (200 µM, Sigma) until d16. For the replating on d11, medium was supplemented with Rock-Inhhibitor (Thiazovivin 2 µM, Stemgent). From d16 onwards, db-cAMP (0.5 µM; Sigma) and DAPT (2.5 µM, Miltenyi Biotec) was added to the medium for terminal differentiation until d50.

extract_protocol: RNA was extracted using the RNeasy® Mini Kit (Qiagen) following manufacturer's instructions

tag: cell type

value: hESC-derived cells

tag: treatment

value: cells were harvested after an enzymatic dissociation

tag: duration

value: cells were differentiated for 16 days, harvested and replated for terminal differentiation after IAP separation until day 50


title: IAP+ (sorted d16, d50)_1

description: hESC-derived mesDA progenitor cells (day16 IAP+, day50)


title: mutL::kan cells replicate 3

description: total RNA from not pooled samples

source_name: mutL::kan cells replicate 3


title: IAP- (sorted d16, d50)_3

source_name: hESC-derived mesDA progenitor cells (day16 IAP-, day50)


title: vsrA::kan cells replicate 4

description: total RNA from not pooled samples

source_name: vsrA::kan cells replicate 4

value: interrupted ngoAXIII gene


title: IAP- (sorted d16, d50)_1


title: IAP+ (sorted d16, d50)_3

source_name: hESC-derived mesDA progenitor cells (day16 IAP+, day50)


title: IAP+ (sorted d16, d50)_2


title: unsorted ( d16 unsorted; d50)_3

description: hESC-derived mesDA progenitor cells (day16 unsorted, day50)


title: unsorted ( d16 unsorted; d50)_2

source_name: hESC-derived mesDA progenitor cells (day16 unsorted, day50)


title: mutL::kan cells replicate 4

description: total RNA from not pooled samples

source_name: mutL::kan cells replicate 4


title: unsorted ( d16 unsorted; d50)_1


title: vsrB::kan cells replicate 2

description: total RNA from not pooled samples

source_name: vsrB::kan cells replicate 2


title: vsrA::kan cells replicate 1

description: total RNA from not pooled samples

source_name: vsrA::kan cells replicate 1


title: vsrA::kan cells replicate 2

description: total RNA from not pooled samples

source_name: vsrA::kan cells replicate 2


title: vsrA::kan cells replicate 3

description: total RNA from not pooled samples

source_name: N. gonorrhoeae wild type

source_name: vsrA::kan cells replicate 3


title: CON-2

city: Changsha

first: Hongyan

last: Wei

state: Hunan

address: No. 61 Jiefang West Road, Changsha, Hunan, China

department: Pharmacy

institute: Hunan Provincial People’s Hospital

description: Gene expression data from GK rats' liver

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

source_name: GK rats' liver

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).

tag: Sex

value: male

tag: strain

value: Goto-Kakizaki

value: liver

tag: symptom

value: undepression


title: CON-3


title: IAP+ d16_3  (hIPSC)

description: hiPSC-derived mesDA progenitor cells (day16, IAP+)

value: hiPSC-derived cells

value: cells were differentiated for 16 days


title: IAP- d16_1  (hIPSC)

description: hiPSC-derived mesDA progenitor cells (day16, IAP-)


title: CUMS_3

value: Major Depression


title: CUMS_5

value: Mild Depression


title: IAP- d16_3  (hIPSC)

source_name: hiPSC-derived mesDA progenitor cells (day16, IAP-)


title: unsorted d16_3  (hIPSC)

description: hiPSC-derived mesDA progenitor cells (day16, unsorted)


title: CUMS_2


title: IAP- d16_2  (hIPSC)


title: IAP+ d16_2  (hIPSC)

source_name: hiPSC-derived mesDA progenitor cells (day16, IAP+)


title: unsorted d16_1 (hIPSC)

source_name: hiPSC-derived mesDA progenitor cells (day16, unsorted)


title: IAP+ d16_1  (hIPSC)


title: IAP- d16_1 (hESC)

description: hESC-derived mesDA progenitor cells (day16, IAP-)


title: unsorted d16_2 (hIPSC)


title: CUMS_4


title: IAP+ d16_3 (hESC)

description: hESC-derived mesDA progenitor cells (day16, IAP+)


title: unsorted d16_1 (hESC)

description: hESC-derived mesDA progenitor cells (day16, unsorted)


title: unsorted d16_2 (hESC)

source_name: hESC-derived mesDA progenitor cells (day16, unsorted)


title: IAP+ d16_1 (hESC)

source_name: hESC-derived mesDA progenitor cells (day16, IAP+)


title: unsorted d16_3 (hESC)


title: IAP- d16_3 (hESC)

source_name: hESC-derived mesDA progenitor cells (day16, IAP-)


title: IAP+ d16_2 (hESC)


title: IAP- d16_2 (hESC)


title: CON_1


title: CUMS_1


title: Patient 3 primary tumour

status: Public on Sep 24 2017

city: Parkville

first: Oliver

last: Sieber

state: VIC

address: 1G Royal Parade

country: Australia

institute: Walter and Eliza Hall Insitute of Medical Reseach

description: Primary tumour sample.

hyb_protocol: Standard Affymetrix procedures.

scan_protocol: Standard Affymetrix procedures.

data_processing: RMA-sketch on the core probeset, which approximates a full quantile normalization in APT.

source_name: primary colorectal adenocarcinoma

label_protocol: Approximately 8 ug of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Surgically isolated colorectal cancers/metastases were immediately frozen in liquid nitrogen. Total RNA was extracted from cancer tissue using Trizol reagent (Invitrogen).

value: Colorectal cancer

tag: primary site

value: Right colon

value: Primary colorectal adenocarcinoma

tag: cms subtype

tag: patient sex

value: Male

tag: patient identifier


title: Patient 3 metastasis (1)

description: Liver metastasis sample.

source_name: colorectal metastasis (liver)

tag: tissue

value: Colorectal metastasis (liver)


title: Patient 4 metastasis

description: Liver metastasis sample.

tag: disease state

value: Left colon


title: Patient 2 metastasis

description: Liver metastasis sample.

value: Rectum


title: Patient 2 primary tumour

description: Primary tumour sample.


title: Patient 4 primary tumour

description: Primary tumour sample.


title: Patient 1 metastasis

description: Liver metastasis sample.

value: Female


title: Patient 5 primary tumour

description: Primary tumour sample.


title: Patient 5 metastasis

description: Liver metastasis sample.


title: Patient 1 primary tumour

description: Primary tumour sample.


title: CUMS_6


title: MaternalGrandfather_Cross9617

city: Maastricht

first: Masoud

last: Zamani Esteki

state: Limburg

address: P. Debyelaan 25

department: Clinical Genetics

institute: Maastricht University Medical Center

description:
DNA extracted from a large amount of cells derived from the bull's semen using DNeasy Blood and Tissue kit (Qiagen). Used for subsequent computational workflow and embryo analysis in pedigree 9617
data structures: The data is provided as five family pedigrees (Cross4757, Cross4006, Cross4770, Cross9617 and Cross8301).

hyb_protocol: According to the manual of Infinium II Assay (Illumina, USA).

scan_protocol: The scanning of the bead-chips was performed on an iScan, using the iScan Control software (Illumina, USA)

data_processing: The genotypes, B allele frequencies and LogR values were processed by the Genotyping module of GenomeStudio software. The discrete genotypes were determined using a threshold of 0,75. We subsequently fed these data into siCHILD algorithm, which is equipted with haplarithmisis (Zamani Esteki et al. 2015, AJHG).

organism: Bos taurus

source_name: Semen

label_protocol: The samples were not labelled before the hybridization. The staining is based on post-hybridization Cy5/Cy3 labelling by extension, according to the manual of Infinium II Assay (Illumina, USA).

growth_protocol: The zygotes of IVM-IVF and OPU-IVF embryos were transferred to synthetic oviductal fluid (SOF) supplemented with essential and non-essential amino acids (SOFaa), 0.4% BSA and ITS (5 µg/ml insulin, 5 µg/ml transferrin and 5 ng/ml selenium). In vitro culture (IVC) occurred in 4-well dishes in 20 µL drops (1 per donor cow) covered with mineral oil. Embryos were incubated at 38.5°C in 5% CO2, 5% O2 and 90% N2. In vivo derived embryos were obtained by flushing of the oviduct

extract_protocol: The isolated blastomeres were placed immediately on dry ice and stored in -20oC for 30 minutes prior to whole genome amplification (WGA). WGA was performed on the day of blastomere isolation. DNA from single blastomeres was whole-genome amplified using commercial MDA kit (REPLI-g Single Cell Kit, Qiagen). MDA amplification of single blastomeres with the single-cell Repli-g kit was performed according to the manufacturer’s instructions for the fast 3-hour protocol. WGA products were purified using SPRI-beads (AMPure) at 0.8x of total reaction volume.

treatment_protocol: The embryos were treated with pronase to dissolve the zona pellucida (0.1% protease from S. griseus, P88110, Sigma-Aldrich in TCM-199 for IVM-IVF and OPU-IVF embryos and 1% for in vivo derived embryos) and were subsequently washed in TCM-199 with 10% FBS followed by Ca+2/Mg+2 free PBS with 0.05% BSA to stimulate blastomere dissociation. Subsequently, the zona-free embryos were washed in Ca+2/ Mg+2 free PBS with 0.1% PVP (wash medium) and were transferred onto a petri dish for blastomere dissociation. Blastomere pick-up and tubing was performed with the use of a mouth-pipetting system using a 75μm capillary.

value: Semen

tag: dna sample

value: Multi cell

tag: wga


title: MaternalGrandmother_Cross9617

description:
DNA extracted from a large amount of cells derived from the cow's blood using DNeasy Blood and Tissue kit (Qiagen).  Used for subsequent computational workflow and embryo analysis in pedigree 9617
data structures: The data is provided as five family pedigrees (Cross4757, Cross4006, Cross4770, Cross9617 and Cross8301).

source_name: Blood

value: Blood


title: E06_Bl002_Cross9617

description:
DNA extracted from single blastomere derived from cleavage stage in vivo derived embryo of pedigree 9617 and subsequently whole genome amplified by Repli-G Single cell kit according to manufacturer's 3h protocol
data structures: The data is provided as five family pedigrees (Cross4757, Cross4006, Cross4770, Cross9617 and Cross8301).

source_name: Blastomere

value: Blastomere

value: Single Cell

value: MDA (Repli-G Single Cell kit)


title: E06_Bl003_Cross9617


title: E07_Bl001_Cross9617


title: Mother_Cross9617

description:
DNA extracted from a large amount of cells derived from the cow's blood using DNeasy Blood and Tissue kit (Qiagen). Used for embryo production in pedigree 9617
data structures: The data is provided as five family pedigrees (Cross4757, Cross4006, Cross4770, Cross9617 and Cross8301).


title: E04_Bl005_Cross9617


title: E09_Bl003_Cross9617

description:
DNA extracted from single blastomere derived from cleavage stage IVM-IVF embryo of pedigree 9617 and subsequently whole genome amplified by Repli-G Single cell kit according to manufacturer's 3h protocol
data structures: The data is provided as five family pedigrees (Cross4757, Cross4006, Cross4770, Cross9617 and Cross8301).


title: E04_Bl003_Cross9617


title: E05_Bl002_Cross9617


title: E04_Bl004_Cross9617


title: E07_Bl002_Cross9617


title: E04_Bl001_Cross9617


title: E06_Bl001_Cross9617


title: E09_Bl002_Cross9617


title: E03_Bl007_Cross9617


title: E07_Bl003_Cross9617


title: E05_Bl003_Cross9617


title: E04_Bl006_Cross9617


title: E03_Bl006_Cross9617


title: E03_Bl005_Cross9617


title: E04_Bl002_Cross9617


title: E08_Bl002_Cross9617


title: E04_Bl007_Cross9617


title: E06_Bl004_Cross9617


title: E03_Bl004_Cross9617


title: E09_Bl001_Cross9617


title: E08_Bl001_Cross9617


title: E05_Bl001_Cross9617


title: E05_Bl004_Cross9617


title: E02_Bl003_Cross9617


title: E01_Bl001_Cross9617

description:
DNA extracted from single blastomere derived from cleavage stage OPU-IVF embryo of pedigree 9617 and subsequently whole genome amplified by Repli-G Single cell kit according to manufacturer's 3h protocol
data structures: The data is provided as five family pedigrees (Cross4757, Cross4006, Cross4770, Cross9617 and Cross8301).


title: E03_Bl001_Cross9617


title: E03_Bl002_Cross9617


title: E03_Bl003_Cross9617


title: MaternalGrandfather_Cross8301

description:
DNA extracted from a large amount of cells derived from the bull's semen using DNeasy Blood and Tissue kit (Qiagen). Used for subsequent computational workflow and embryo analysis in pedigree 8301
data structures: The data is provided as five family pedigrees (Cross4757, Cross4006, Cross4770, Cross9617 and Cross8301).


title: E01_Bl002_Cross9617


title: E13_Bl004_Cross8301

description:
DNA extracted from single blastomere derived from cleavage stage IVM-IVF embryo of pedigree 8301 and subsequently whole genome amplified by Repli-G Single cell kit according to manufacturer's 3h protocol
data structures: The data is provided as five family pedigrees (Cross4757, Cross4006, Cross4770, Cross9617 and Cross8301).


title: E12_Bl006_Cross8301


title: E02_Bl001_Cross9617


title: E13_Bl003_Cross8301


title: Mother_Cross8301

description:
DNA extracted from a large amount of cells derived from the cow's blood using DNeasy Blood and Tissue kit (Qiagen). Used for embryo production in pedigree 8301
data structures: The data is provided as five family pedigrees (Cross4757, Cross4006, Cross4770, Cross9617 and Cross8301).


title: E01_Bl003_Cross9617


title: E12_Bl003_Cross8301


title: E02_Bl002_Cross9617


title: E12_Bl005_Cross8301


title: MaternalGrandmother_Cross8301

description:
DNA extracted from a large amount of cells derived from the cow's blood using DNeasy Blood and Tissue kit (Qiagen).  Used for subsequent computational workflow and embryo analysis in pedigree 8301
data structures: The data is provided as five family pedigrees (Cross4757, Cross4006, Cross4770, Cross9617 and Cross8301).


title: E12_Bl001_Cross8301


title: E02_Bl004_Cross9617


title: E12_Bl004_Cross8301


title: E12_Bl002_Cross8301


title: E13_Bl002_Cross8301


title: E13_Bl001_Cross8301


title: E10_Bl002_Cross8301


title: E09_Bl002_Cross8301

description:
DNA extracted from single blastomere derived from cleavage stage in vivo derived embryo of pedigree 8301 and subsequently whole genome amplified by Repli-G Single cell kit according to manufacturer's 3h protocol
data structures: The data is provided as five family pedigrees (Cross4757, Cross4006, Cross4770, Cross9617 and Cross8301).


title: E10_Bl001_Cross8301


title: E11_Bl001_Cross8301


title: E08_Bl002_Cross8301


title: E10_Bl003_Cross8301


title: E09_Bl004_Cross8301


title: E07_Bl007_Cross8301


title: E06_Bl005_Cross8301


title: E07_Bl005_Cross8301


title: E08_Bl001_Cross8301


title: E07_Bl006_Cross8301


title: E06_Bl003_Cross8301


title: E07_Bl001_Cross8301


title: E07_Bl004_Cross8301


title: E05_Bl006_Cross8301


title: E06_Bl006_Cross8301


title: E06_Bl002_Cross8301


title: E09_Bl003_Cross8301


title: E07_Bl002_Cross8301


title: E06_Bl007_Cross8301


title: E06_Bl001_Cross8301


title: E06_Bl004_Cross8301


title: E07_Bl003_Cross8301


title: E05_Bl004_Cross8301


title: E05_Bl005_Cross8301


title: E13_Bl005_Cross8301


title: E05_Bl002_Cross8301


title: E07_Bl008_Cross8301


title: E11_Bl002_Cross8301


title: E09_Bl001_Cross8301


title: E04_Bl007_Cross8301

description:
DNA extracted from single blastomere derived from cleavage stage OPU-IVF embryo of pedigree 8301 and subsequently whole genome amplified by Repli-G Single cell kit according to manufacturer's 3h protocol
data structures: The data is provided as five family pedigrees (Cross4757, Cross4006, Cross4770, Cross9617 and Cross8301).


title: E04_Bl005_Cross8301


title: E04_Bl008_Cross8301


title: E04_Bl003_Cross8301


title: E02_Bl008_Cross8301


title: E04_Bl001_Cross8301


title: E03_Bl004_Cross8301


title: E03_Bl001_Cross8301


title: E02_Bl003_Cross8301


title: E05_Bl007_Cross8301


title: E03_Bl002_Cross8301


title: E05_Bl001_Cross8301


title: E05_Bl003_Cross8301


title: E02_Bl007_Cross8301


title: E02_Bl005_Cross8301


title: E02_Bl006_Cross8301


title: E02_Bl001_Cross8301


title: E04_Bl002_Cross8301


title: E01_Bl005_Cross8301


title: E01_Bl008_Cross8301


title: E01_Bl004_Cross8301


title: E02_Bl002_Cross8301


title: E01_Bl007_Cross8301


title: E11_Bl006_Cross4770

description:
DNA extracted from single blastomere derived from cleavage stage IVM-IVF embryo of pedigree 4770 and subsequently whole genome amplified by Repli-G Single cell kit according to manufacturer's 3h protocol
data structures: The data is provided as five family pedigrees (Cross4757, Cross4006, Cross4770, Cross9617 and Cross8301).


title: Mother_Cross4770

description:
DNA extracted from a large amount of cells derived from the cow's blood using DNeasy Blood and Tissue kit (Qiagen). Used for embryo production in pedigree 4770
data structures: The data is provided as five family pedigrees (Cross4757, Cross4006, Cross4770, Cross9617 and Cross8301).


title: E02_Bl004_Cross8301


title: E11_Bl005_Cross4770


title: E10_Bl010_Cross4770


title: E11_Bl004_Cross4770


title: E10_Bl004_Cross4770


title: E11_Bl001_Cross4770


title: E10_Bl005_Cross4770


title: E10_Bl003_Cross4770


title: E03_Bl003_Cross8301


title: E11_Bl002_Cross4770


title: E10_Bl006_Cross4770


title: E04_Bl006_Cross8301


title: E11_Bl003_Cross4770


title: E10_Bl008_Cross4770


title: E04_Bl004_Cross8301


title: E01_Bl001_Cross8301


title: E10_Bl007_Cross4770


title: E10_Bl001_Cross4770


title: E10_Bl009_Cross4770


title: E01_Bl003_Cross8301


title: E09_Bl008_Cross4770


title: E10_Bl002_Cross4770


title: E01_Bl006_Cross8301


title: E09_Bl007_Cross4770


title: E09_Bl004_Cross4770


title: E09_Bl006_Cross4770


title: E09_Bl001_Cross4770


title: E09_Bl002_Cross4770


title: E08_Bl004_Cross4770


title: E01_Bl002_Cross8301


title: E06_Bl001_Cross4770

description:
DNA extracted from single blastomere derived from cleavage stage in vivo derived embryo of pedigree 4770 and subsequently whole genome amplified by Repli-G Single cell kit according to manufacturer's 3h protocol.
data structures: The data is provided as five family pedigrees (Cross4757, Cross4006, Cross4770, Cross9617 and Cross8301).


title: E09_Bl003_Cross4770


title: E09_Bl005_Cross4770


title: E08_Bl003_Cross4770