title: epidermal stem cells aged animal T8, replicate 4

value: 102-116 week old


title: 656031

status: Public on Aug 10 2017

type: genomic

city: Ames

first: Maria

middle: Guadalupe

last: Salas Fernandez

state: IA

address: 1126E Agronomy Hall

department: Agronomy

country: USA

institute: Iowa State University

description: Sorghum breeding line

data_processing:
The Fluidigm SNP Genotyping Analysis software automatically analyzes the end-point image of a genotyping chip run and generates genotyping calls for each sample.
SNP calls for each allele

label: SNPtype-FAM, SNPtype-HEX

molecule: genomic DNA

organism: Sorghum bicolor

source_name: Sorghum Association Panel

label_protocol: SNPtype-FAM, SNPtype-HEX

growth_protocol: grow a single plant in a small pot for each sample

extract_protocol: Total DNA was extracted using CTAB DNA extraction protocol

treatment_protocol: No treatment

tag: tissue

value: young leaves


title: Hibernoma_9

type: RNA

city: Lund

first: Karolin

middle: H

last: Nord

address: BMC C13

department: Dept of Clinical Genetics

country: Sweden

institute: Lund University

description: Global gene expression data

hyb_protocol: Biotinylated cDNA was hybridized to GeneChip Gene 1_0 st arrays. Arrays were washed and stained on an Affymetrix Fluidics Station 450.

scan_protocol: Scanning was carried out with the GeneChip Scanner 3000 (Affymetrix).

data_processing: Image analysis was perfomed using the GeneChip Operating Software (GCOS, Affymetrix) or command console (Affymetrix). Background correction, normalization and probe summarization was done with the robust multichip average (RMA) algorithm implemented in the Expression Console software (Affymetrix).

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: soft tissue

label_protocol: cDNA was labelled with TdT using the WT Terminal Labeling kit (Affymetrix).

extract_protocol: RNA was extracted using the TRIzol reagent (Invitrogen) and purified with Qiagen´s RNeasy kit according to the manufacturers´ instructions.

value: Hibernoma

tag: tissue source

value: tumor biopsy


title: Hibernoma_8

description: Global gene expression data


title: 656030

description: Sorghum breeding line


title: 656029

description: Sorghum breeding line


title: Hibernoma_13

description: Global gene expression data


title: 656028

description: Sorghum breeding line


title: Hibernoma_10

description: Global gene expression data


title: epidermal stem cells aged animal T8, replicate 2

city: Barcelona

first: Aikaterini

last: Symeonidi

state: Barcelona

address: Baldiri i Reixac, 10

department: Oncology

country: Spain

institute: Institut for Research in Biomedicine (IRB-Barcelona)

hyb_protocol: Hybridisation mixture was prepared according to the Gene Atlas protocol (Affymetrix). Each sample target was hybridised to a Mouse Genome 430 PM array. After hybridisation for 16 hours at 45°C, washing and staining was performed in the GeneAtlas Fluidics Station (Affymetrix).

scan_protocol: The arrays were scanned in a GeneAtlas Imaging Station (Affymetrix). All processing was performed according to manufacturer’s recommendations.

data_processing: Overall array intensity was normalised between arrays and the probe intensity of all probes in a probe set summarised to a single value using RMA (Robust Multichip Average)

organism: Mus musculus

source_name: epidermal stem cells

label_protocol: cDNA library preparation and amplification were performed from 25ng total RNA using WTA2 (Sigma-Aldrich) with 17cycles of amplification. 8µg cDNA were subsequently fragmented by DNAseI and biotinylated by terminal transferase obtained from GeneChip Mapping 10Kv2 Assay Kit (Affymetrix).

extract_protocol: RNA was extracted using TRizol (Sigma-Aldrich).

value: epidermis

tag: Sex

value: female

tag: genotype/variation

value: wild type

tag: strain

tag: timepoint

tag: age


title: 656026

description: Sorghum breeding line


title: Hibernoma_5

description: Global gene expression data


title: Hibernoma_4

description: Global gene expression data


title: 656025

description: Sorghum breeding line


title: 656024

description: Sorghum breeding line


title: Hibernoma_6

description: Global gene expression data


title: Hibernoma_3

description: Global gene expression data


title: epidermal stem cells aged animal T4, replicate 4


title: epidermal stem cells aged animal T8, replicate 1


title: Hibernoma_7

description: Global gene expression data


title: epidermal stem cells aged animal T8, replicate 3


title: 656023

description: Sorghum breeding line


title: 656022

description: Sorghum breeding line


title: epidermal stem cells aged animal T4, replicate 3


title: Hibernoma_2

description: Global gene expression data


title: epidermal stem cells aged animal T4, replicate 2


title: 656019

description: Sorghum breeding line


title: 656018

description: Sorghum breeding line


title: epidermal stem cells aged animal T20, replicate 3


title: Hibernoma_1

description: Global gene expression data


title: epidermal stem cells aged animal T20, replicate 4


title: 656017

description: Sorghum breeding line


title: epidermal stem cells aged animal T4, replicate 1


title: 656016

description: Sorghum breeding line


title: epidermal stem cells aged animal T20, replicate 1


title: epidermal stem cells aged animal T16, replicate 4


title: epidermal stem cells aged animal T20, replicate 2


title: epidermal stem cells aged animal T16, replicate 1


title: 656015

description: Sorghum breeding line


title: epidermal stem cells aged animal T16, replicate 2


title: 656014

description: Sorghum breeding line


title: 656011

description: Sorghum breeding line


title: 656012

description: Sorghum breeding line


title: 656008

description: Sorghum breeding line


title: 656013

description: Sorghum breeding line


title: 656009

description: Sorghum breeding line


title: 656007

description: Sorghum breeding line


title: epidermal stem cells aged animal T12, replicate 3


title: 656006

description: Sorghum breeding line


title: 656005

description: Sorghum breeding line


title: 656004

description: Sorghum breeding line


title: 656003

description: Sorghum breeding line


title: 656002

description: Sorghum breeding line


title: epidermal stem cells aged animal T16, replicate 3


title: epidermal stem cells aged animal T0, replicate 4


title: epidermal stem cells aged animal T12, replicate 1


title: epidermal stem cells aged animal T0, replicate 1


title: epidermal stem cells aged animal T0, replicate 2


title: 656000

description: Sorghum breeding line


title: 655999

description: Sorghum breeding line


title: epidermal stem cells aged animal T0, replicate 3


title: epidermal stem cells high fat diet T8, replicate 2

treatment_protocol: mice were fed ad libitum either with high fat or with the respective control diet. The experiment lasted for 7 weeks.

tag: genotype/variaion

tag: time point

tag: diet

value: high fat

value: 15 week old


title: epidermal stem cells aged animal T12, replicate 4


title: epidermal stem cells high fat diet T4, replicate 4


title: 655998

description: Sorghum breeding line


title: epidermal stem cells high fat diet T8, replicate 1


title: epidermal stem cells high fat diet T4, replicate 3


title: 655997

description: Sorghum breeding line


title: 656001

description: Sorghum breeding line


title: 655995

description: Sorghum breeding line


title: epidermal stem cells aged animal T12, replicate 2


title: epidermal stem cells high fat diet T4, replicate 1


title: 655994

description: Sorghum breeding line


title: epidermal stem cells high fat diet T4, replicate 2


title: epidermal stem cells high fat diet T20, replicate 4


title: epidermal stem cells high fat diet T16, replicate 4


title: epidermal stem cells high fat diet T20, replicate 1


title: epidermal stem cells high fat diet T20, replicate 3


title: 655992

description: Sorghum breeding line


title: 655990

description: Sorghum breeding line


title: 656027

description: Sorghum breeding line


title: 655991

description: Sorghum breeding line


title: 655988

description: Sorghum breeding line


title: epidermal stem cells high fat diet T20, replicate 2


title: epidermal stem cells high fat diet T16, replicate 2


title: epidermal stem cells high fat diet T16, replicate 3


title: epidermal stem cells high fat diet T12, replicate 4


title: 655987

description: Sorghum breeding line


title: epidermal stem cells high fat diet T16, replicate 1


title: epidermal stem cells high fat diet T12, replicate 3


title: 655986

description: Sorghum breeding line


title: 655985

description: Sorghum breeding line


title: 655984

description: Sorghum breeding line


title: 655993

description: Sorghum breeding line


title: 655981

description: Sorghum breeding line


title: 655982

description: Sorghum breeding line


title: 655989

description: Sorghum breeding line


title: epidermal stem cells high fat diet T0, replicate 2


title: epidermal stem cells high fat diet T12, replicate 2


title: epidermal stem cells high fat diet T0, replicate 1


title: epidermal stem cells control diet T8, replicate 2

value: control


title: epidermal stem cells control diet T8, replicate 1


title: 655979

description: Sorghum breeding line


title: epidermal stem cells high fat diet T12, replicate 1


title: epidermal stem cells high fat diet T0, replicate 3


title: epidermal stem cells control diet T4, replicate 1


title: 655978

description: Sorghum breeding line


title: 655976

description: Sorghum breeding line


title: epidermal stem cells control diet T4, replicate 2


title: 655975

description: Sorghum breeding line


title: 655980

description: Sorghum breeding line


title: 655974

description: Sorghum breeding line


title: epidermal stem cells control diet T20, replicate 4


title: epidermal stem cells control diet T20, replicate 2


title: epidermal stem cells control diet T4, replicate 3


title: 655972

description: Sorghum breeding line


title: epidermal stem cells control diet T20, replicate 3


title: epidermal stem cells control diet T20, replicate 1


title: 655971

description: Sorghum breeding line


title: 655970

description: Sorghum breeding line


title: 653617

description: Sorghum breeding line


title: 653616

description: Sorghum breeding line


title: epidermal stem cells control diet T16, replicate 4


title: 651496

description: Sorghum breeding line


title: 651492

description: Sorghum breeding line


title: epidermal stem cells control diet T16, replicate 1


title: 642992

description: Sorghum breeding line


title: 655973

description: Sorghum breeding line


title: epidermal stem cells control diet T12, replicate 2


title: epidermal stem cells control diet T16, replicate 2


title: epidermal stem cells control diet T12, replicate 3


title: epidermal stem cells control diet T12, replicate 1


title: epidermal stem cells control diet T16, replicate 3


title: epidermal stem cells control diet T0, replicate 4


title: 641874

description: Sorghum breeding line


title: 641836

description: Sorghum breeding line


title: 641824

description: Sorghum breeding line


title: 629059

description: Sorghum breeding line


title: 629034

description: Sorghum breeding line


title: 626088

description: Sorghum breeding line


title: 609456

description: Sorghum breeding line


title: 601816

description: Sorghum breeding line


title: satellite cells high fat diet T8, biological replicate 2

source_name: muscle stem cells

value: skeletal muscle


title: satellite cells high fat diet T8, biological replicate 3


title: 598070

description: Sorghum breeding line


title: satellite cells high fat diet T4, biological replicate 3


title: satellite cells high fat diet T4, biological replicate 4


title: epidermal stem cells control diet T0, replicate 3


title: 598069

description: Sorghum breeding line


title: satellite cells high fat diet T8, biological replicate 1


title: epidermal stem cells control diet T0, replicate 1


title: 597980

description: Sorghum breeding line


title: satellite cells high fat diet T8, biological replicate 4


title: 613536

description: Sorghum breeding line


title: 597976

description: Sorghum breeding line


title: satellite cells high fat diet T20, biological replicate 3


title: satellite cells high fat diet T20, biological replicate 2


title: satellite cells high fat diet T16, biological replicate 3


title: satellite cells high fat diet T4, biological replicate 2


title: satellite cells high fat diet T16, biological replicate 2


title: satellite cells high fat diet T20, biological replicate 4


title: satellite cells high fat diet T20, biological replicate 1


title: satellite cells high fat diet T4, biological replicate 1


title: 597973

description: Sorghum breeding line


title: 597982

description: Sorghum breeding line


title: 597971

description: Sorghum breeding line


title: epidermal stem cells control diet T0, replicate 2


title: satellite cells high fat diet T16, biological replicate 1


title: satellite cells high fat diet T12, biological replicate 4


title: satellite cells high fat diet T12, biological replicate 3


title: 597965

description: Sorghum breeding line


title: satellite cells high fat diet T12, biological replicate 2


title: 597972

description: Sorghum breeding line


title: 655977

description: Sorghum breeding line


title: satellite cells high fat diet T0, biological replicate 3


title: satellite cells high fat diet T12, biological replicate 1


title: 597961

description: Sorghum breeding line


title: 597960

description: Sorghum breeding line


title: 597958

description: Sorghum breeding line


title: 597957

description: Sorghum breeding line


title: satellite cells high fat diet T0, biological replicate 4


title: satellite cells high fat diet T0, biological replicate 2


title: 597952

description: Sorghum breeding line


title: satellite cells high fat diet T0, biological replicate 1


title: satellite cells control diet T8, biological replicate 4


title: 597964

description: Sorghum breeding line


title: 597951

description: Sorghum breeding line


title: 597950

description: Sorghum breeding line


title: 655996

description: Sorghum breeding line


title: 597949

description: Sorghum breeding line


title: 597946

description: Sorghum breeding line


title: satellite cells control diet T8, biological replicate 1


title: 597945

description: Sorghum breeding line


title: 595745

description: Sorghum breeding line


title: satellite cells control diet T4, biological replicate 4


title: 595744

description: Sorghum breeding line


title: satellite cells control diet T4, biological replicate 3


title: satellite cells control diet T8, biological replicate 3


title: satellite cells control diet T8, biological replicate 2


title: satellite cells control diet T4, biological replicate 1


title: satellite cells control diet T20, biological replicate 3


title: satellite cells control diet T20, biological replicate 4


title: 595741

description: Sorghum breeding line


title: 595739

description: Sorghum breeding line


title: satellite cells control diet T20, biological replicate 2


title: 595740

description: Sorghum breeding line


title: 595720

description: Sorghum breeding line


title: 595718

description: Sorghum breeding line


title: satellite cells control diet T4, biological replicate 2


title: 595714

description: Sorghum breeding line


title: 595743

description: Sorghum breeding line


title: 595702

description: Sorghum breeding line


title: 595699

description: Sorghum breeding line


title: satellite cells control diet T16, biological replicate 4


title: 585295

description: Sorghum breeding line


title: 576435

description: Sorghum breeding line


title: 576437

description: Sorghum breeding line


title: satellite cells control diet T20, biological replicate 1


title: satellite cells control diet T16, biological replicate 2


title: satellite cells control diet T16, biological replicate 1


title: satellite cells control diet T12, biological replicate 3


title: satellite cells control diet T16, biological replicate 3


title: satellite cells control diet T12, biological replicate 1


title: satellite cells control diet T12, biological replicate 4


title: 576426

description: Sorghum breeding line


title: 576428

description: Sorghum breeding line


title: satellite cells control diet T12, biological replicate 2


title: satellite cells control diet T0, biological replicate 4


title: 576425

description: Sorghum breeding line


title: 576422

description: Sorghum breeding line


title: 576418

description: Sorghum breeding line


title: 576399

description: Sorghum breeding line


title: 576394

description: Sorghum breeding line


title: 576393

description: Sorghum breeding line


title: 576390

description: Sorghum breeding line


title: 576387

description: Sorghum breeding line


title: satellite cells control diet T0, biological replicate 3


title: 576386

description: Sorghum breeding line


title: 576385

description: Sorghum breeding line


title: satellite cells control diet T0, biological replicate 1


title: 576381

description: Sorghum breeding line


title: satellite cells control diet T0, biological replicate 2


title: 576391

description: Sorghum breeding line


title: 576376

description: Sorghum breeding line


title: 576373

description: Sorghum breeding line


title: 597968

description: Sorghum breeding line


title: 576375

description: Sorghum breeding line


title: 597966

description: Sorghum breeding line


title: 576380

description: Sorghum breeding line


title: Genomc DNA from 293T-TET3-RUNX1

city: Yokohama

first: Takahiro

last: Suzuki

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: Center for Integrative Medical Sciences

country: Japan

institute: RIKEN

description: TET3 and RUNX1 transduced

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

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

data_processing: Signal intensities were measured by GenomeStudio software v2010.3. Color balance adjustment, quantile normalization and M-value calculation were done by lumi, a bioconductor package.

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

growth_protocol: 293T cells were provided from RIKEN Bioresource Center (BRC) and were cultured in Dulbecco's modified Eagle's medium (DMEM) (Wako), supplemented with 10% FBS and penicillin/streptomycin (100 U/ml, 100 µg/ml) (Life Technologies) on Poly-D-lysine courted dish (Becton Dickinson).

extract_protocol: genomic DNA was extracted and purified using NucleoSpin Tissue (Macherey-Nagel) according to standard instructions

treatment_protocol: 293T cells were transduced genes of interest by using lentivirus vector system. Transduced cells were purified by antibiotics

tag: cell li ne

tag: gender

value: Female

value: Kidney

tag: developmental stage

value: Embryo

tag: transduced with

value: TET3 and RUNX1


title: 576366

description: Sorghum breeding line


title: 597967

description: Sorghum breeding line


title: BC

description: Genomic DNA from CD+ B cells

source_name: blood

value: Male

tag: cell type

value: CD+ B cells (BC)

value: Adult


title: Genomic DNA from 293T-TET3

description: TET3 transduced


title: 576352

description: Sorghum breeding line

value: young leaves


title: 576359

description: Sorghum breeding line


title: HPC

description: Genomic DNA from hematopoietic progenitor cells

source_name: Bone marrow

value: CD34+ hematopoietic progenotor cells (HPC)


title: 576350

description: Sorghum breeding line


title: iPSC

description: Genomic DNA from iPS cells

source_name: Skin

value: iPS cells (IPSC)


title: 576349

description: Sorghum breeding line


title: MON

description: Genomic DNA from CD14+ monocytes

value: CD14+ monocytes (MON)


title: TC

description: Genomic DNA from CD+ T cells

value: CD+ T cells (TC)


title: 576348

description: Sorghum breeding line


title: 576347

description: Sorghum breeding line


title: 576340

description: Sorghum breeding line


title: 576345

description: Sorghum breeding line


title: Jurkat

description: Genomic DNA from Jurkat

value: Jurkat


title: 576339

description: Sorghum breeding line


title: NN004531

city: Campinas

first: Mariana

last: Maschietto

state: São Paulo

address: Rua Márcia Mendes, 619

department: Research Center

country: Brazil

institute: Boldrini Children's Hospital

description: women

hyb_protocol: As per Illumina protocol

scan_protocol: iScan SQ scanner (Illumina) using  GenomeStudio software (v.2011.1)

data_processing:
Unreliable measurements were identified using Greedycut (p>0.05) that removed 1,478 probes. Probes located in SNPs (n=4,776) as well those located in specific contexts (n=5,926, non-CpG sites and additional SNPs) were also excluded. Samples were retained only if >99% of sites assayed had detection p>0.05. The background was corrected using noob method, which is based on a normal-exponential convolution using out-of-band probes. Signal intensities values from probes type I and II were normalized using SWAN method that adjusts the intensities based on a quantile approach.
Normalized data (SWAN and noob) were transformed into M-values for statistical analyses

source_name: bisulfite converted DNA from NN004531

label_protocol: As per Illumina protocol

extract_protocol: QIAamp DNA BloodMidi Kit as per protocol

treatment_protocol: DNA treated with sodium bisulfite

value: peripheral blood

value: female

tag: group

tag: inhibition (average values)

tag: facilitation values (average)


title: 576333

description: Sorghum breeding line

tag: tissue


title: NN004570

description: women

source_name: bisulfite converted DNA from NN004570

value: control


title: 576332

description: Sorghum breeding line


title: 576130

description: Sorghum breeding line


title: NN004492

description: women

source_name: bisulfite converted DNA from NN004492

value: case


title: NN004497

description: women

source_name: bisulfite converted DNA from NN004497


title: NN004488

description: women

source_name: bisulfite converted DNA from NN004488


title: NN005371

description: women

source_name: bisulfite converted DNA from NN005371


title: NN004496

description: women

source_name: bisulfite converted DNA from NN004496


title: 574455

description: Sorghum breeding line


title: 566819

description: Sorghum breeding line


title: NN004524

description: women

source_name: bisulfite converted DNA from NN004524


title: NN004528

description: women

source_name: bisulfite converted DNA from NN004528


title: NN004522

description: women

source_name: bisulfite converted DNA from NN004522


title: NN004462

description: women

source_name: bisulfite converted DNA from NN004462


title: 565121

description: Sorghum breeding line

source_name: Sorghum Association Panel


title: NN004468

description: women

source_name: bisulfite converted DNA from NN004468


title: NN004480

description: women

source_name: bisulfite converted DNA from NN004480


title: 576364

description: Sorghum breeding line


title: NN005853

description: women

source_name: bisulfite converted DNA from NN005853


title: NN004476

description: women

source_name: bisulfite converted DNA from NN004476


title: 561073

description: Sorghum breeding line


title: 564164

description: Sorghum breeding line


title: 564163

description: Sorghum breeding line


title: NN004445

description: women

source_name: bisulfite converted DNA from NN004445


title: NN004450

description: women

source_name: bisulfite converted DNA from NN004450


title: NN004523

description: women

source_name: bisulfite converted DNA from NN004523


title: NN004444

description: women

source_name: bisulfite converted DNA from NN004444


title: NN004569

description: women

source_name: bisulfite converted DNA from NN004569


title: 561071

description: Sorghum breeding line


title: NN004452

description: women

source_name: bisulfite converted DNA from NN004452


title: NN004461

description: women

source_name: bisulfite converted DNA from NN004461


title: NN004466

description: women

source_name: bisulfite converted DNA from NN004466


title: 564165

description: Sorghum breeding line


title: 561072

description: Sorghum breeding line


title: 552856

description: Sorghum breeding line


title: 542718

description: Sorghum breeding line


title: 542406

description: Sorghum breeding line


title: 540816

description: Sorghum breeding line


title: NN004432

description: women

source_name: bisulfite converted DNA from NN004432


title: 534167

description: Sorghum breeding line


title: NN004443

description: women

source_name: bisulfite converted DNA from NN004443


title: 548797

description: Sorghum breeding line


title: 534163

description: Sorghum breeding line


title: NN004441

description: women

source_name: bisulfite converted DNA from NN004441


title: 534155

description: Sorghum breeding line


title: NN004427

description: women

source_name: bisulfite converted DNA from NN004427


title: 534157

description: Sorghum breeding line

source_name: Sorghum Association Panel


title: 534148

description: Sorghum breeding line


title: NN004428

description: women

source_name: bisulfite converted DNA from NN004428


title: 534145

description: Sorghum breeding line


title: 561472

description: Sorghum breeding line


title: NN004429

description: women

source_name: bisulfite converted DNA from NN004429


title: 552861

description: Sorghum breeding line


title: NN004420

description: women

source_name: bisulfite converted DNA from NN004420


title: 534138

description: Sorghum breeding line


title: NN004419

description: women

source_name: bisulfite converted DNA from NN004419


title: 534132

description: Sorghum breeding line


title: 534135

description: Sorghum breeding line


title: 534128

description: Sorghum breeding line


title: 534139

description: Sorghum breeding line


title: NN004409

description: women

source_name: bisulfite converted DNA from NN004409


title: 534127

description: Sorghum breeding line


title: 534124

description: Sorghum breeding line


title: NN004417

description: women

source_name: bisulfite converted DNA from NN004417


title: 534123

description: Sorghum breeding line


title: 534117

description: Sorghum breeding line


title: NN004404

description: women

source_name: bisulfite converted DNA from NN004404


title: 534116

description: Sorghum breeding line


title: NN004376

description: women

source_name: bisulfite converted DNA from NN004376


title: 534144

description: Sorghum breeding line


title: NN004403

description: women

source_name: bisulfite converted DNA from NN004403


title: NN004396

description: women

source_name: bisulfite converted DNA from NN004396


title: 534115

description: Sorghum breeding line


title: NN004410

description: women

source_name: bisulfite converted DNA from NN004410


title: NN004373

description: women

source_name: bisulfite converted DNA from NN004373


title: NN004374

description: women

source_name: bisulfite converted DNA from NN004374


title: 534112

description: Sorghum breeding line


title: NN004392

description: women

source_name: bisulfite converted DNA from NN004392


title: 534114

description: Sorghum breeding line


title: 534108

description: Sorghum breeding line


title: NN004425

description: women

source_name: bisulfite converted DNA from NN004425


title: 534105

description: Sorghum breeding line


title: 534101

description: Sorghum breeding line


title: NN004401

description: women

source_name: bisulfite converted DNA from NN004401


title: Th17 cells repeat

city: cleveland

first: Yong

last: Lu

address: 9500 euclid avenue, NB40

institute: Cleveland Clinic

description: Th17 cells repeat

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

source_name: spleen

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

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: spleen

tag: background strain

tag: treatment

value: Th17 cells


title: Th1 cells

description: Th1 cells

value: Th1 cells


title: 534096

description: Sorghum breeding line

source_name: Sorghum Association Panel


title: 534097

description: Sorghum breeding line


title: NN004368

description: women

source_name: bisulfite converted DNA from NN004368


title: 534099

description: Sorghum breeding line


title: 534088

description: Sorghum breeding line


title: 534075

description: Sorghum breeding line


title: 534092

description: Sorghum breeding line


title: Th9 cells repeat

description: Th9 cells repeat

value: Th9 cells


title: 534104

description: Sorghum breeding line


title: NN004367

description: women

source_name: bisulfite converted DNA from NN004367


title: Th9 cells

description: Th9 cells


title: Genomc DNA from 293T-TET2-RUNX1

description: TET2 and RUNX1 transduced

tag: cell line

value: Female

value: Kidney

value: Embryo

value: TET2 and RUNX1


title: 534137

description: Sorghum breeding line

value: young leaves


title: Genomic DNA from 293T-mock

description: mock lentivirus vector transduced

value: mock lentivirus vector


title: 534054

description: Sorghum breeding line


title: Th1 cells repeat

description: Th1 cells repeat


title: 534063

description: Sorghum breeding line


title: 534079

description: Sorghum breeding line


title: 534021

description: Sorghum breeding line


title: 533998

description: Sorghum breeding line


title: 533997

description: Sorghum breeding line


title: Genomc DNA from 293T-RUNX1

description: RUNX1 transduced


title: 534009

description: Sorghum breeding line


title: 533996

description: Sorghum breeding line


title: 533989

description: Sorghum breeding line


title: 533987

description: Sorghum breeding line


title: NN004411

description: women

source_name: bisulfite converted DNA from NN004411


title: 533985

description: Sorghum breeding line


title: NN004370

description: women

source_name: bisulfite converted DNA from NN004370


title: 533976

description: Sorghum breeding line


title: 533972

description: Sorghum breeding line


title: 533980

description: Sorghum breeding line


title: 533961

description: Sorghum breeding line


title: 533979

description: Sorghum breeding line


title: 533962

description: Sorghum breeding line


title: 533955

description: Sorghum breeding line


title: 533967

description: Sorghum breeding line


title: 533970

description: Sorghum breeding line


title: 533964

description: Sorghum breeding line


title: 533957

description: Sorghum breeding line


title: 533965

description: Sorghum breeding line


title: 533956

description: Sorghum breeding line


title: 533938

description: Sorghum breeding line


title: 533986

description: Sorghum breeding line


title: 533940

description: Sorghum breeding line


title: 533937

description: Sorghum breeding line


title: 533948

description: Sorghum breeding line


title: 533936

description: Sorghum breeding line


title: 533939

description: Sorghum breeding line


title: 533927

description: Sorghum breeding line


title: 533991

description: Sorghum breeding line


title: 533924

description: Sorghum breeding line


title: 533919

description: Sorghum breeding line


title: 533921

description: Sorghum breeding line


title: Genomic DNA from 293T-TET2

description: TET2 transduced


title: 533913

description: Sorghum breeding line


title: 533901

description: Sorghum breeding line


title: 533878

description: Sorghum breeding line


title: 533877

description: Sorghum breeding line


title: 533910

description: Sorghum breeding line


title: 533902

description: Sorghum breeding line


title: 533911

description: Sorghum breeding line


title: 533882

description: Sorghum breeding line


title: 533876

description: Sorghum breeding line


title: 533871

description: Sorghum breeding line


title: 533912

description: Sorghum breeding line


title: 533842

description: Sorghum breeding line


title: 533841

description: Sorghum breeding line


title: 533822

description: Sorghum breeding line


title: 533852

description: Sorghum breeding line


title: 533845

description: Sorghum breeding line


title: 533838

description: Sorghum breeding line


title: 533869

description: Sorghum breeding line


title: 533856

description: Sorghum breeding line


title: 533833

description: Sorghum breeding line


title: 533843

description: Sorghum breeding line


title: 533839

description: Sorghum breeding line


title: 533855

description: Sorghum breeding line


title: 533863

description: Sorghum breeding line


title: 533821

description: Sorghum breeding line


title: 533810

description: Sorghum breeding line


title: 533807

description: Sorghum breeding line


title: 533800

description: Sorghum breeding line


title: 533866

description: Sorghum breeding line


title: 533788

description: Sorghum breeding line


title: 533792

description: Sorghum breeding line


title: 533799

description: Sorghum breeding line


title: 533794

description: Sorghum breeding line


title: 533785

description: Sorghum breeding line


title: 533776

description: Sorghum breeding line


title: 533766

description: Sorghum breeding line


title: 533824

description: Sorghum breeding line


title: 533761

description: Sorghum breeding line


title: 533758

description: Sorghum breeding line


title: 533760

description: Sorghum breeding line


title: 533759

description: Sorghum breeding line


title: 533752

description: Sorghum breeding line


title: 329440

description: Sorghum breeding line


title: 533755

description: Sorghum breeding line


title: 329435

description: Sorghum breeding line


title: 533757

description: Sorghum breeding line


title: 533754

description: Sorghum breeding line


title: 276837

description: Sorghum breeding line


title: 152651

description: Sorghum breeding line


title: 533750

description: Sorghum breeding line


title: 533769

description: Sorghum breeding line


title: 24969

description: Sorghum breeding line


title: 17548

description: Sorghum breeding line


title: 35038

description: Sorghum breeding line


title: 48770

description: Sorghum breeding line


title: 34911

description: Sorghum breeding line


title: 533762

description: Sorghum breeding line


title: Th17 cells

description: Th17 cells


title: p53R270H/ER REP4 2hr 4OHT a

status: Public on Aug 09 2017

city: Belfast

first: Emma

last: Kerr

address: 97 Lisburn Rd

department: PGJCCR

country: United Kingdom

institute: Queen's University Belfast

description: Lung tumour cell line, p53R270H/ER, biological replicate, VEH/4OHT treatment, probe intensity

data_processing: Illumina MouseWG6v2 BeadChip arrays were scanned using standard Illumina protocols and data analysed using R (R Development Core Team, 2010) and Bioconductor (Gentleman et al, 2004). Spatial artefacts were removed using BASH (Cairns et al, 2008) and HULK algorithms from the bead array package (Dunning et al, 2007). Data were log2 transformed and quantile normalised.

label_protocol: Not provided

growth_protocol: Tumours were collected in Hank’s Balanced Salt Solution, mashed and digested with 4 mg/ml collagenase/dispase (Roche; 37 oC for 2.5 hours). Cells were treated with HBSS containing 10 % FCS and DNase I, filtered (70 um) and plated in DMEM/F-12 media (Life Technologies) supplemented with 10% FCS and 2mM L-Glutamine. After 1.5 hrs the media was re-plated and tumour cell (media: slower adherence) and tumour associated fibroblast (fast adherence) enriched cultures maintained separately.

extract_protocol: RNA was extracted using QIAGEN RNeasy mini kit according to manufacturers instruction. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: 1,000,000 cells were plated 3:2 Matrigel:Media were plated/well (24-well plate) and cultured for 48hrs before treatment with vehicle or 4-OHT (100nM) for timepoints as indicated. 3D cultures were then washed with PBS, before dissociation with Corning Cell Recovery Solution for 45min at 4oC and cell pellets collected.

tag: strain

tag: tissue type

value: Lung tumour

tag: p53 genotype

tag: weeks post cre


title: p53R270H/ER REP4 8hr 4OHT a

source_name: Lung tumour cell line, p53R270H/ER, biological replicate, VEH/4OHT treatment


title: 534037

description: Sorghum breeding line


title: p53R270H/ER REP4 VEH b


title: 534070

description: Sorghum breeding line


title: p53R270H/ER REP4 8hr 4OHT b


title: p53R270H/ER REP4 2hr 4OHT b


title: p53R270H/ER REP3 8hr 4OHT b


title: p53R270H/ER REP3 2hr 4OHT b


title: p53R270H/ER REP3 2hr 4OHT a


title: p53R270H/ER REP4 VEH a


title: p53R270H/ER REP1 2hr 4OHT a


title: p53R172H/ER REP4 8hr 4OHT a

description: Lung tumour cell line, p53R172H/ER, biological replicate, VEH/4OHT treatment, probe intensity


title: p53R270H/ER REP2 8hr 4OHT b


title: p53R270H/ER REP3 VEH a


title: p53R270H/ER REP2 8hr 4OHT a


title: p53R270H/ER REP2 2hr 4OHT a


title: p53R270H/ER REP1 8hr 4OHT a


title: p53R270H/ER REP1 VEH a


title: p53R270H/ER REP1 8hr 4OHT b


title: p53R172H/ER REP4 2hr 4OHT b

source_name: Lung tumour cell line, p53R172H/ER, biological replicate, VEH/4OHT treatment


title: p53R270H/ER REP3 VEH b


title: p53R270H/ER REP2 2hr 4OHT b


title: p53R172H/ER REP4 VEH a


title: p53R172H/ER REP3 8hr 4OHT b


title: p53R172H/ER REP4 8hr 4OHT b


title: p53R270H/ER REP1 2hr 4OHT b


title: p53R270H/ER REP3 8hr 4OHT a


title: p53R270H/ER REP2 VEH b


title: p53R270H/ER REP2 VEH a


title: p53R172H/ER REP4 2hr 4OHT a


title: p53R172H/ER REP4 VEH b


title: p53R172H/ER REP3 8hr 4OHT a


title: p53R172H/ER REP3 2hr 4OHT b


title: p53R270H/ER REP1 VEH b


title: p53R172H/ER REP3 2hr 4OHT a


title: p53R172H/ER REP3 VEH a


title: p53R172H/ER REP2 8hr 4OHT b


title: p53R172H/ER REP3 VEH b


title: p53R172H/ER REP2 2hr 4OHT b


title: p53R172H/ER REP2 8hr 4OHT a


title: p53R172H/ER REP1 8hr 4OHT a


title: p53R172H/ER REP1 VEH b


title: p53R172H/ER REP1 2hr 4OHT b


title: p53R172H/ER REP1 2hr 4OHT a


title: p53R172H/ER REP2 VEH b


title: p53R172H/ER REP2 VEH a


title: p53R172H/ER REP1 8hr 4OHT b


title: p53Fx/ER REP4 2hr 4OHT b

description: Lung tumour cell line, p53Fx/ER, biological replicate, VEH/4OHT treatment, probe intensity


title: p53Fx/ER REP4 8hr 4OHT b

source_name: Lung tumour cell line, p53Fx/ER, biological replicate, VEH/4OHT treatment


title: p53Fx/ER REP3 VEH b


title: p53Fx/ER REP3 2hr 4OHT b


title: p53Fx/ER REP4 8hr 4OHT a


title: p53Fx/ER REP4 VEH b


title: p53Fx/ER REP3 VEH a


title: p53Fx/ER REP4 2hr 4OHT a


title: p53R172H/ER REP1 VEH a


title: p53Fx/ER REP2 8hr 4OHT b


title: p53Fx/ER REP3 8hr 4OHT a


title: p53Fx/ER REP3 8hr 4OHT b


title: p53R172H/ER REP2 2hr 4OHT a


title: p53Fx/ER REP4 VEH a


title: p53Fx/ER REP2 8hr 4OHT a


title: p53Fx/ER REP3 2hr 4OHT a


title: p53Fx/ER REP1 8hr 4OHT b


title: p53Fx/ER REP2 2hr 4OHT b


title: p53Fx/ER REP2 VEH a


title: p53Fx/ER REP2 VEH b


title: p53Fx/ER REP2 2hr 4OHT a


title: p53Fx/ER REP1 8hr 4OHT a


title: p53Fx/ER REP1 2hr 4OHT b


title: p53Fx/ER REP1 VEH b


title: SCC13 shFSTL1 Replicate 3

city: Singapore

first: Prabha

last: Sampath

state: Singapore

address: 8A Biomedical Grove

department: Institute of Medical Biology

country: Singapore

institute: Institute of Medical Biology

description:
Replicate 3
SAMPLE 6

data_processing: The data was back ground substracted and normalized using  Illumina Inc. GenomeStudio version 1.9.0

label: Biotin

source_name: SCC13 cutaneous squamous cell carcinoma cell line

label_protocol: Biotinylated cRNA were prepared with the Target Amp-Nano kit for Illumina arrays

extract_protocol: Total RNA was extracted using Exiqon miRcury total RNA extraction kit

treatment_protocol: SCC13 cells were transduced with lentivirus encoding a scrambled shRNA or shRNA specific to FSTL1. Five days post transduction, cells were treated with 1ug/ml of puromycin for 3 days to get rid of untranduced cells.

tag: shRNA


title: SCC13 shFSTL1 Replicate 2

description:
Replicate 2
SAMPLE 5


title: SCC13 shFSTL1 Replicate 1

description:
Replicate 1
SAMPLE 4


title: p53Fx/ER REP1 VEH a


title: p53Fx/ER REP1 2hr 4OHT a


title: Sample_261

status: Public on Aug 08 2017

first: Min Han

last: Tan

state: Sinagpore

address: 31 Biopolis Way,

institute: Institute of Bioengineering and Nanotechnology

description: CEL files were pre-processed and normalized using the RMA algorithm through the Affy package of R/Bioconductor.

hyb_protocol: In vitro transcription was done using Enzo Bioarray Transcript Labeling kit (Enzo, Farmingdale, NY). The biotinylated cRNA was subsequently fragmented, and 10 μg were hybridized to each array at 45°C over 16 hours

scan_protocol: The HGU133 Plus 2.0 GeneChips contain 54,675 probe sets, representing ∼47,000 transcripts and variants. Scanning was done in a GeneChip 3000 scanner.

data_processing: Quality assessment was done in GeneChip Operating System 1.1.1 (Affymetrix) using global scaling to a target signal of 500. Quality assessment was done using denaturing gel electrophoresis. The CEL file data were analyzed with BioConductor to generate probeset level data.

source_name: clinical renal cell carcinoma  samples

label_protocol: Synthesis of single-stranded and double-stranded cDNA was done with the use of T7-oligo(dT) primer (Affymetrix). In vitro transcription was done using Enzo Bioarray Transcript Labeling kit (Enzo, Farmingdale, NY).

extract_protocol: Total RNA (5-20 μg) was used to prepare antisense biotinylated RNA. A subset of cases was added to external poly(A) RNA-positive controls (Affymetrix, Santa Clara, CA).

value: renal cell carcinoma

value: M

tag: Stage

tag: grade


title: Sample_264

tag: gender

value: F


title: SCC13 scr shRNA Replicate 3

description:
Replicate 3
SAMPLE 3

value: Control shRNA


title: Sample_265


title: Sample_263


title: SCC13 scr shRNA Replicate 2

description:
Replicate 2
SAMPLE 2


title: Sample_260


title: SCC13 scr shRNA Replicate 1

description:
Replicate 1
SAMPLE 1


title: Sample_256


title: Sample_259


title: Sample_249


title: Sample_248


title: Sample_246


title: Sample_251


title: Sample_250


title: Sample_244


title: Sample_255


title: Sample_245


title: Sample_253


title: Sample_252


title: Sample_258


title: Sample_257


title: Sample_247


title: Sample_242


title: Sample_243


title: Sample_241


title: Sample_232


title: Sample_238


title: Sample_231


title: Sample_235


title: Sample_237


title: Sample_233


title: Sample_239


title: Sample_234


title: Sample_229


title: Sample_230


title: Sample_236


title: Sample_227


title: Sample_226


title: Sample_225


title: Sample_224


title: Sample_222


title: Sample_223


title: Sample_218


title: Sample_220


title: Sample_240


title: Sample_214


title: Sample_217


title: Sample_216


title: Sample_221


title: Sample_228


title: Sample_219


title: Sample_210


title: Sample_212


title: Sample_213


title: Sample_209


title: Sample_215


title: Sample_207


title: Sample_203


title: Sample_204


title: Sample_205


title: Sample_200


title: Sample_208


title: Sample_262


title: Sample_197


title: Sample_202


title: Sample_206


title: Sample_198


title: Sample_201


title: Sample_193


title: Sample_192


title: Sample_199


title: Sample_195


title: Sample_211


title: Sample_194


title: Sample_254


title: Sample_189


title: Sample_191


title: Sample_183


title: Sample_184


title: Sample_187


title: Sample_188


title: Sample_196


title: Sample_182


title: Sample_190


title: Sample_186


title: Sample_185


title: Sample_181


title: Sample_179


title: Sample_180


title: Sample_174


title: Sample_178


title: Sample_162


title: Sample_168


title: Sample_164


title: Sample_169


title: Sample_160


title: Sample_176


title: Sample_175


title: Sample_173


title: Sample_159


title: Sample_177


title: Sample_161


title: Sample_156


title: Sample_150


title: Sample_149


title: Sample_158


title: Sample_154


title: Sample_166


title: Sample_171


title: Sample_163


title: Sample_152


title: Sample_153


title: Sample_155


title: Sample_151


title: Sample_157


title: Sample_165


title: Sample_145


title: Sample_147


title: Sample_142


title: Sample_146


title: Sample_136


title: Sample_148


title: Sample_141


title: Sample_134


title: Sample_132


title: Sample_143


title: Sample_144


title: Sample_133


title: Sample_137


title: Sample_139


title: Sample_135


title: Sample_128


title: Sample_130


title: Sample_138


title: Sample_131


title: Sample_140


title: Sample_125


title: Sample_127


title: Sample_126


title: Sample_124


title: Sample_122


title: Sample_123


title: Sample_121


title: Sample_172


title: Sample_129


title: Sample_111


title: Sample_115


title: Sample_116


title: Sample_114


title: Sample_109


title: Sample_120


title: Sample_117


title: Sample_112


title: Sample_104


title: Sample_118


title: Sample_103


title: Sample_106


title: Sample_110


title: Sample_113


title: Sample_100


title: Sample_102


title: Sample_97


title: Sample_119


title: Sample_105


title: Sample_96


title: Sample_101


title: Sample_99


title: Sample_98


title: Sample_170


title: Sample_108


title: Sample_94


title: Sample_92

value: X


title: Sample_91


title: Sample_89


title: Sample_107


title: Sample_93


title: Sample_88


title: Sample_87


title: Sample_90


title: Sample_95


title: Sample_86


title: Sample_84


title: Sample_83


title: Sample_82


title: Sample_81


title: Sample_85


title: Sample_78


title: Sample_76


title: Sample_79


title: Sample_75


title: Sample_80


title: Sample_77


title: M5634= Gapmer control

city: Hannover

first: Julia

last: Beermann

address: Carl-Neuberg-Straße 1

department: IMTTS

country: Germany

institute: Hannover Medical School (MHH)

description: M5634 gProcessedSignal_QuantileNormalized_Surrogate20Used#

hyb_protocol: cRNA fragmentation, hybridization and washing steps were carried-out as recommended in the ‘One-Color Microarray-Based Gene Expression Analysis Protocol V5.7’ (Agilent), except that 700 ng of each labelled cRNA population were used for hybridization.

scan_protocol: Slides were scanned on the Agilent Micro Array Scanner G2565CA (pixel resolution 3 µm, bit depth 20).

data_processing: Data extraction and processing of raw fluorescence intensity values were performed with the ‘Feature Extraction Software V10.7.3.1’ using the extraction protocol file ‘GE1_107_Sep09.xml’ (gProcessedSignal_QuantileNormalized_Surrogate20Used)

source_name: 3T3_Gapmer control

label_protocol: Synthesis of cRNA was performed with the ‘Quick Amp Labeling kit, no color’ (#5190-0447, Agilent Technologies), except that contained NTP-mix (to be used in the T7 reaction) was exchanged by a mix composed of 15 mM of each ATP, CTP, GTP, 11.25 mM of UTP, and 3.75 mM of aaUTP (final concentration of each nucleotide was 1.875 mM). The labeling of aaUTP-cRNA was performed by use of the Amino Allyl MessageAmp™ II Kit (#AM1753; Life Technologies) and Alexa Fluor 555 Reactive Dye (#A32756; LifeTechnologies).

growth_protocol: 3T3 cells were grown in DMEM + 10% FBS + 1% PS

extract_protocol: miRNeasy Kit Qiagen

treatment_protocol: Treatment of cells with 50nM Gapmer Ntep/Gapmer control for 48h.

tag: treated with

value: 50nM GapmeR control for 48hrs


title: M5631= Gapmer Ntep

description: M5631 gProcessedSignal_QuantileNormalized_Surrogate20Used#

source_name: 3T3_Gapmer Ntep

value: 50nM Gapmer against Ntep for 48hrs


title: M5630= Gapmer control

description: M5630 gProcessedSignal_QuantileNormalized_Surrogate20Used#


title: Sample_74

tag: cell type


title: Sample_167


title: M5629= Gapmer Ntep

description: M5629 gProcessedSignal_QuantileNormalized_Surrogate20Used#


title: M5633= Gapmer Ntep

description: M5633 gProcessedSignal_QuantileNormalized_Surrogate20Used#


title: Sample_73


title: Ebf1-/- progenitors transduced with PAX5 (Mig-PAX5) retrovirus rep2 (second set)

city: Hyderabad

first: Jagan

last: Pongubala

state: Telangana

address: Gachibowli

department: Department of Animal Biology

country: India

institute: University of Hyderabad

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C. GeneChips were washed and stained I nthe Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using Affymetrix Genechip Scanner 3000.

data_processing: Data were analyzed as previously described (GSE9878)

label_protocol: Biotin-labeled cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Pre-pro-B cells (Ebf1-/- progenitors) were maintained on stromal layer (OP9 cells) in the presence of Opti-MEM (Gibco) containing 4% (v/v) fetal calf serum, β-mercaptoethanol (50 µM), penicillin (10 U/ml) and streptomycin (10 µg/ml) and supplemented with SCF (10 ng/ml), Flt3L (10 ng/ml) and IL-7 (5 ng/ml).

extract_protocol: Pre-pro-B cells were transduced by spin-infection with retrovirus encoding GFP or Ebf1-GFP or Pax5-GFP as previously described (Pongubala et al., 2008). After two days, GFP+ transductants were FACS-sorted, total RNA was isolated with TRIzol reagent (Invitrogen) and further purified on RNeasy columns (Qiagen). RNA quality control analysis was performed as previously described (Pongubala et al., 2008).

value: Pre-pro-B cells (Ebf1-/- progenitors)

tag: transduced by

value: PAX5 (Mig-PAX5) retrovirus


title: Ebf1-/- progenitors transduced with PAX5 (Mig-PAX5) retrovirus rep1 (second set)


title: Sample_70


title: Sample_71


title: Sample_67


title: Sample_65


title: Ebf1-/- progenitors transduced with control (MigR1) retrovirus rep2 (second set)

value: control (MigR1) retrovirus


title: Ebf1-/- progenitors transduced with PAX5 (Mig-PAX5) retrovirus rep3 (second set)


title: Sample_69


title: Ebf1-/- progenitors transduced with control (MigR1) retrovirus rep3 (second set)


title: Ebf1-/- progenitors transduced with EBF (Mig-EBF1) retrovirus rep2 (first set)

source_name: Ebf1-/- progenitors transduced with EBF (Mig-EBF) retrovirus

value: EBF (Mig-EBF) retrovirus


title: Ebf1-/- progenitors transduced with control (MigR1) retrovirus rep1 (second set)


title: Ebf1-/- progenitors transduced with control (MigR1) retrovirus rep3 (first set)


title: Sample_66


title: Ebf1-/- progenitors transduced with control (MigR1) retrovirus rep1 (first set)


title: Sample_68


title: Sample_72


title: Ebf1-/- progenitors transduced with EBF (Mig-EBF1) retrovirus rep1 (first set)


title: Sample_63


title: Sample_62


title: Sample_60


title: Sample_61


title: Sample_59


title: Sample_64


title: Sample_57


title: Sample_56


title: Sample_51


title: Sample_55


title: Sample_54


title: Sample_52


title: Sample_49


title: Sample_53


title: Sample_43


title: Sample_50


title: Sample_44


title: Sample_42


title: Sample_45


title: Sample_41


title: Sample_40


title: Sample_46


title: Sample_38


title: Sample_58


title: Sample_39


title: Sample_47


title: Sample_48


title: TIMP1_KD_rep5

city: Oxford

first: Ruud

last: van Stiphout

address: Old Road Campus Research Building

institute: University of Oxford

description: Knockdown 5

data_processing: The data were normalised using quantile normalisation with R-package LIMMA (normalizeQuantiles)

source_name: PANC-1 cell line

label_protocol: Labeled cRNA was prepared using an Illumina TotalPrep RNA Amplification Kit

growth_protocol: Cells were cultured in Standard DMEM supplemented with 10% FCS and 1µg/ml Puromycin.

extract_protocol: Total RNA was isolated using the Qiagen RNeasy mini kit


title: TIMP1_KD_rep6

description: Knockdown 6


title: TIMP1_KD_rep2

description: Knockdown 2


title: TIMP1_KD_rep3

description: Knockdown 3


title: TIMP1_KD_rep4

description: Knockdown 4


title: Ebf1-/- progenitors transduced with control (MigR1) retrovirus rep2 (first set)


title: WildType_rep4

description: Control 4


title: WildType_rep6

description: Control 6


title: Sample_31


title: Sample_35


title: Ebf1-/- progenitors transduced with EBF (Mig-EBF1) retrovirus rep3 (first set)


title: Sample_33


title: WildType_rep3

description: Control 3


title: WildType_rep5

description: Control 5


title: TIMP1_KD_rep1

description: Knockdown 1


title: Sample_36


title: Sample_30


title: Sample_34


title: Sample_37


title: WildType_rep1

description: Control 1


title: WildType_rep2

description: Control 2


title: Sample_27


title: Sample_28


title: Sample_32


title: Sample_25


title: Sample_26


title: Sample_24


title: Sample_23


title: Sample_19


title: Sample_22


title: Sample_18


title: M5632= Gapmer control

description: M5632 gProcessedSignal_QuantileNormalized_Surrogate20Used#


title: Sample_21


title: Sample_15


title: Sample_16


title: Sample_29


title: Sample_17


title: Sample_14


title: Sample_13


title: Sample_10


title: Sample_12


title: Sample_11


title: Sample_9


title: Sample_5


title: Sample_20


title: Sample_7


title: Sample_3


title: Sample_6


title: Sample_8


title: KRAS mutant NSCLC cell line [SW1573]

city: Boston

first: Anurag

last: Singh

state: MA

address: 72 E. Concord St.

department: Pharmacology and Experimental Therapeutics

institute: Boston University School of Medicine

description: KRAS independent, mesenchymal

data_processing:
Raw Ct data were normalized to endogenous U6 and RNU44 RNA (average of duplicates) to generate dCt values. Average dCt values were calculated for each miRNA in KM or KE cells. Fold differences were computed by subtracting average KE dCT values from average KM dCT values and raising to the power 2.
Fold change worksheet shows expression ratio of miRNAs in KE/KM cells.

label: FAM

source_name: ATCC cell line repository

label_protocol: cDNA was synthesized from 2µg total RNA using High Capacity cDNA Archive kit. The cDNA was diluted 1:50 and Taqman assays were performed using FAM-labelled probes.

growth_protocol: Cells were grown to confluency in 60mm tissue culture dishes (BD-Falcon Inc.).

extract_protocol: Total cellular RNA was extracted using the miRNeasy Kit (Qiagen Inc.). Cell lysis was peformed with Qiazol reagent.

treatment_protocol: Cells were washed in PBS and trypsinized in 0.5% Trypsin-EDTA. Cell pellets were collected for RNA extraction.

tag: kras dependency

value: Independent

tag: differentiation

value: Mesenchymal


title: KRAS mutant NSCLC cell line [H2009]

description: KRAS dependent, epithelial

value: Dependent

value: Epithelial


title: KRAS mutant NSCLC cell line [H460]

description: KRAS independent, mesenchymal


title: Sample_4


title: KRAS mutant NSCLC cell line [A549]

description: KRAS independent, mesenchymal


title: KRAS mutant NSCLC cell line [H441]

description: KRAS dependent, epithelial


title: KRAS mutant NSCLC cell line [H358]

description: KRAS dependent, epithelial


title: OsbHLH068OE_001

status: Public on Aug 07 2017

city: Taipei

first: Vicki

last: Hsieh-Feng

address: No. 1, Sec. 4, Roosevelt Rd.

country: Taiwan

institute: NTU

hyb_protocol: 1.65 μg of Cy3-labled cRNA was fragmented at 60°C for 30 minutes. Correspondingly fragmented labeled cRNA is then pooled and hybridized to Agilent Arabidopsis 4×44K V4 Microarray (Agilent Technologies, USA) at 65°C for 17 h.

scan_protocol: After washing the microarrays are scanned with an Agilent microarray scanner (Agilent Technologies, USA) at 535 nm for Cy3.

data_processing:
The array image was analyzed by the Feature Extraction software version 10.7.1.1 using the default setting.
Microarray raw data were analyzed with the Bioconductor Limma package (Ritchie et al. 2015). The raw data were background corrected using ‘normexp’ method and were then normalized using ‘quantile’ method.

organism: Arabidopsis thaliana

source_name: OsbHLH068OE, 17-day-old, replicate1

label_protocol: 200 ng of total RNA was amplified by a Low Input Quick-Amp Labeling kit (Agilent Technologies, USA) and labeled with Cy3 (CyDye, Agilent Technologies, USA) during the in vitro transcription process.

extract_protocol: Total RNA was extracted from plant tissue using an RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. To avoid genomic DNA contamination, total RNA was treated with Turbo DNA-freeTM DNase (Ambion) following the manufacturer’s instructions.

tag: tissue

value: aerial tissue

tag: genotype/variation

tag: age


title: Sample_1


title: OsbHLH068OE_002

source_name: OsbHLH068OE, 17-day-old, replicate2


title: Col-0_001

source_name: Col-0, 17-day-old, replicate1


title: genomic DNA from activated memory CD4+ T cell (2)

city: Gosselies

first: Martin

last: Bizet

address: Rue Adrienne Bolland, 8

country: Belgium

institute: Université Libre de Bruxelles

description: Activated memory CD4+ T cell

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylation450 Beadchip using standard Infinium HD Methylation Assay protocol.

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

data_processing: .idat files were loaded using methylumi R-package. High-detection p-value, SNP-containing, Cross-reactive and heterochromosomic probes were filtered out (set to 'null') and data were peak-based normalised using in-house R-scripts.

source_name: Activated memory CD4+ T cell (2)

label_protocol: Standard Infinium HD Methylation Assay protocol.

growth_protocol: Cells were maintained in RPMI 1640 media supplemented with 10% fetal bovine serum, 2mM glutamine and antibiotics (50µg/ml streptomycin and 50U/ml penicillin) at 37°C and 5% CO2.

extract_protocol: Genomic DNA was extracted and purified from CD4+ T cells using Qiagen 'DNeasy Blood and Tissue' Kit according to standard instructions. The recommended RNase treatment was performed.

tag: cell source

value: Sorted from PBMC

value: Memory CD4+

tag: activation state

tag: activation protocol

value: cells were stimulated by coated anti-CD3 (10µg/ml) and soluble anti-CD28 antibodies (1µg/ml)


title: OsbHLH068OE_003

source_name: OsbHLH068OE, 17-day-old, replicate3


title: genomic DNA from resting memory CD4+ T cell (3)

description: Resting memory CD4+ T cell

source_name: Resting memory CD4+ T cell (3)

value: Resting

value: cells were not stimulated


title: Sample_2

value: renal cell carcinoma

value: M


title: genomic DNA from activated naive CD4+ T cell (1)

description: Activated naive CD4+ T cell

source_name: Activated naive CD4+ T cell (1)

value: naive CD4+


title: Col-0_003

source_name: Col-0, 17-day-old, replicate3


title: Patient R164 biopsy 8

first: David

last: Lindgren

address: Building 404 A3, Scheelevägen 2, Medicon Village

department: Dept of Laboratory Medicine

hyb_protocol: According to the manufacturers specifications

data_processing:
Data management and normalization was carried out using BioArray Software Environment (BASE). Raw intensity values representing mean bead pool intensity values for each probe were background corrected, negative intensities were capped to zero, followed by addition of an intensity constant of 10 to all probe intensities. Data was normalized using a quantile normalization algorithm as implemented in BASE. Probes were re-annotated using the IlluminaHumanv4.db package and only probes flagged as perfect quality grade and annotated with a valid NCBI Gene ID were kept for further analyses.
The sample data table contains the final reporter intensity values (unlogged) that was used for downstream data analyses. Data is normalized and filtered as specified in the data processing section. The  non_normalized_bkgrnd_subtracted.txt contains background corrected intensity values prior normalization and filtering.

source_name: Patient R164 biopsy

label_protocol: Biotinylated cRNA were prepared with the Ambion Message Amp RNA Amplification kit according to the manufacturers specifications

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen), followed by purification using the Allprep micro kit (QIAGEN Inc.).

treatment_protocol: Samples from different parts of the kidneys were procured using core-sampling from approximately 10 mm thick sections obtained from nephrectomized patients in surgery for renal neoplasms. Sampling was performed in the part of the kidney that was farthest from the tumor. Sections were thereafter embedded and hematoxylin-eosin stained allowing for approximation of the respective site in kidney from which the sample was obtained.

tag: patient id

tag: patient type

value: Normal kidney tissue

tag: sampling depth

value: cortex


title: Col-0_002

source_name: Col-0, 17-day-old, replicate2


title: Patient R164 biopsy 7

scan_protocol: According to the manufacturers specifications


title: Patient R164 biopsy 4

value: cortex/medulla


title: Patient R164 biopsy 9

value: medulla


title: Patient R164 biopsy 22


title: Patient R164 biopsy 3


title: genomic DNA from resting naive CD4+ T cell (1)

description: Resting naive CD4+ T cell

source_name: Resting naive CD4+ T cell (1)


title: Patient R164 biopsy 6


title: Patient R164 biopsy 24


title: Patient R164 biopsy 5


title: genomic DNA from resting memory CD4+ T cell (2)

description: Resting memory CD4+ T cell

source_name: Resting memory CD4+ T cell (2)


title: genomic DNA from resting naive CD4+ T cell (2)

description: Resting naive CD4+ T cell

source_name: Resting naive CD4+ T cell (2)


title: genomic DNA from activated memory CD4+ T cell (3)

description: Activated memory CD4+ T cell

source_name: Activated memory CD4+ T cell (3)


title: genomic DNA from resting naive CD4+ T cell (3)

description: Resting naive CD4+ T cell

source_name: Resting naive CD4+ T cell (3)


title: Patient R164 biopsy 18


title: Patient R164 biopsy 21


title: Patient R164 biopsy 20


title: genomic DNA from activated memory CD4+ T cell (1)

description: Activated memory CD4+ T cell

source_name: Activated memory CD4+ T cell (1)


title: genomic DNA from activated naive CD4+ T cell (2)

description: Activated naive CD4+ T cell

source_name: Activated naive CD4+ T cell (2)


title: Patient R164 biopsy 19


title: Patient R164 biopsy 23


title: Patient R164 biopsy 15


title: genomic DNA from resting memory CD4+ T cell (1)

description: Resting memory CD4+ T cell

source_name: Resting memory CD4+ T cell (1)


title: Patient R164 biopsy 16


title: Patient R164 biopsy 2


title: genomic DNA from activated naive CD4+ T cell (3)

description: Activated naive CD4+ T cell

source_name: Activated naive CD4+ T cell (3)


title: Patient R164 biopsy 14


title: Patient R164 biopsy 17


title: Patient R164 biopsy 12


title: Patient R164 biopsy 13


title: Patient R134 biopsy 3

source_name: Patient R134 biopsy


title: Patient R134 biopsy 7


title: Patient R164 biopsy 11


title: Patient R134 biopsy 8


title: Patient R134 biopsy 4


title: Patient R134 biopsy 6


title: Patient R164 biopsy 10


title: Patient R164 biopsy 1


title: Patient R134 biopsy 5


title: Patient R127 biopsy 3

source_name: Patient R127 biopsy


title: Patient R134 biopsy 1


title: Patient R127 biopsy 1


title: Patient R116 biopsy 8

source_name: Patient R116 biopsy


title: Patient R134 biopsy 2


title: Patient R116 biopsy 7


title: Patient R127 biopsy 2


title: Patient R116 biopsy 6


title: Patient R127 biopsy 4


title: Patient R116 biopsy 9


title: Patient R116 biopsy 5


title: Patient R116 biopsy 3


title: Patient R116 biopsy 12


title: Patient R116 biopsy 2


title: Patient R116 biopsy 4


title: Patient R099 biopsy 3

source_name: Patient R099 biopsy


title: Patient R116 biopsy 11


title: Patient R099 biopsy 2


title: Patient R099 biopsy 1


title: Patient R099 biopsy 8


title: Patient R099 biopsy 4


title: Patient R116 biopsy 1


title: Patient R116 biopsy 10


title: pad21_MV biological rep3

first: Atsushi

last: Fukushima

address: 1-7-22 Suehiro, Tsurumi

department: Center for Sustainable Resource Science

description: pad2-1 samples were harvested at 18 day-old after germination under MV treatment.

hyb_protocol: standard Affymetrix protocol

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Bioconductor 'simpleaffy' package using RMA as normalization method.

label_protocol: standard Affymetrix protocol

growth_protocol: Arabidopsis ecotype Columbia (Col-0) was used for all experiments. Mutant plants used in this study were described previously (Fukushima et al. 2014). The mutant cad2-1 (Cobbett et al., 1998) was used as an allelic mutant of pad2-1 in this study Parisy et al., 2007). Plants were grown in Murashige and Skoog (MS) agar medium except for the oxidative and phosphorous deficiency condition. Sterilized seeds were stratified at 5°C for 2 days, and were sown on MS medium containing 1% sucrose.

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

treatment_protocol: Oxidative and low phosphorous conditions were produced adding 0.05 M Methyl viologen and reducing phosphate concentration to 1/5 of MS medium. Seedlings of Arabidopsis Col-0 and the mutants were cultivated in growth chambers at 22°C in the 16-h light and 8-h dark condition for 18 days (Light strength, approx. 80 PPF).

value: aerial parts

tag: genotype

tag: genetic background

tag: treatment

value: MV


title: pad21_MV biological rep2

source_name: pad2-1 samples were harvested at 18 day-old after germination under MV treatment.


title: pad21_P-lim biological rep2

description: pad2-1 samples were harvested at 18 day-old after germination under normal P-lim condition.

value: P-lim


title: Col0_MV biological rep3

description: Col-0 samples were harvested at 18 day-old after germination under normal MS condition.

value: wt


title: Col0_MV biological rep1

source_name: Col-0 samples were harvested at 18 day-old after germination under normal MS condition.


title: pad21_MV biological rep1


title: pad21_control biological rep2

description: pad2-1 samples were harvested at 18 day-old after germination under normal MS condition.

value: control


title: Col0_P-lim biological rep3


title: pad21_P-lim biological rep3

source_name: pad2-1 samples were harvested at 18 day-old after germination under normal P-lim condition.


title: Col0_P-lim biological rep1


title: pad21_control biological rep1

source_name: pad2-1 samples were harvested at 18 day-old after germination under normal MS condition.


title: pad21_control biological rep3


title: Col0_P-lim biological rep2


title: Col0_MV biological rep2


title: Col0_control biological rep1


title: Col0_control biological rep2


title: pad21_P-lim biological rep1


title: Col0_control biological rep3


title: blastomere pair 10 (after 2-cell stage bisection)

status: Public on Aug 06 2017

city: Muenster

first: Michele

last: Boiani

address: Roentgenstrasse 20

institute: Max Planck Institute Muenster

description: Single blastomere was lysed in Zymo buffer (Quick RNA micro prep) and total RNA was extracted in water

hyb_protocol: The GeneChip Hybridization, Wash and Stain Kit was used, for 16 h (+/- 1h) at 45°C with 60 rpm. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: The GeneChips were scanned using the Affymetrix 3000 7G scanner.

data_processing: The robust multiarray averaging method was applied for background correction, normalization, and probe summarization using the Affymetrix Expression Console.

source_name: 2-cell stage embryo

label_protocol: Biotinylated cDNA was prepared using GeneChip WT Pico kit, reverse-transcribing 20 micrograms cRNA and, of these, subjecting 5.5 micrograms to labeling

growth_protocol: 1-cell zygotes from B6C3F1 x CD1 mating (stimulated cycle) were collected from the oviducts and cultured in pools in KSOM(aa) medium

extract_protocol: Individual blastomeres were lysed in in Zymo buffer (Quick RNA micro prep) and total RNA was extracted in water according to the manufacturer's instructions.

treatment_protocol: At the 2-cell stage embryos were split mechanically, and each blastomere was promptly collected for lysis in Zymo buffer.

value: 2-cell stage embryo

value: B6C3F1 x CD1

value: Theiler stage 2; 1 dpc

tag: cell number

value: single cell


title: sister blastomere pair 10 (after 2-cell stage bisection)


title: blastomere pair 9 (after 2-cell stage bisection)


title: sister blastomere pair 9 (after 2-cell stage bisection)


title: sister blastomere pair 8 (after 2-cell stage bisection)


title: sister blastomere pair 6 (after 2-cell stage bisection)


title: blastomere pair 4 (after 2-cell stage bisection)


title: sister blastomere pair 7 (after 2-cell stage bisection)


title: blastomere pair 7 (after 2-cell stage bisection)


title: sister blastomere pair 3 (after 2-cell stage bisection)


title: sister blastomere pair 4 (after 2-cell stage bisection)


title: sister blastomere pair 5 (after 2-cell stage bisection)


title: blastomere pair 3 (after 2-cell stage bisection)


title: blastomere pair 2 (after 2-cell stage bisection)


title: sister blastomere pair 2 (after 2-cell stage bisection)


title: blastomere pair 6 (after 2-cell stage bisection)


title: blastomere pair 1 (after 2-cell stage bisection)


title: blastomere pair 5 (after 2-cell stage bisection)


title: control blastocyst 7 (no bisection)

description:
Single embryo was lysed in Zymo buffer (Quick RNA micro prep) and total RNA was extracted in water
Sample name: ctrl7

source_name: blastocyst stage embryo

label_protocol: Biotinylated cDNA was prepared using GeneChip WT Termina Labeling kit, reverse-transcribing 20 micrograms cRNA and, of these, subjecting 5.5 micrograms to labeling

extract_protocol: Individual blastocysts were lysed in in Zymo buffer (Quick RNA micro prep) and total RNA was extracted in water according to the manufacturer's instructions.

treatment_protocol: At the 2-cell stage embryos were split mechanically, and each blastomere was cultured individually in the well of a 96-well plate until the blastocyst stage, under 5% CO2 and atmospheric O2

value: Theiler stage 5; 4 dpc

value: normal

value: blastocyst stage embryo


title: blastomere pair 8 (after 2-cell stage bisection)


title: control blastocyst 6 (no bisection)

description:
Single embryo was lysed in Zymo buffer (Quick RNA micro prep) and total RNA was extracted in water
Sample name: ctrl6


title: control blastocyst 10 (no bisection)

description:
Single embryo was lysed in Zymo buffer (Quick RNA micro prep) and total RNA was extracted in water
Sample name: ctrl10


title: control blastocyst 8 (no bisection)

description:
Single embryo was lysed in Zymo buffer (Quick RNA micro prep) and total RNA was extracted in water
Sample name: ctrl8


title: control blastocyst 9 (no bisection)

description:
Single embryo was lysed in Zymo buffer (Quick RNA micro prep) and total RNA was extracted in water
Sample name: ctrl9


title: Myoepithelial_3A3L_day10_rep2

city: London

first: Emily

last: Saunderson

address: Charterhouse Square

institute: Barts Cancer Institute

description: raw data column header: 3A3L_2

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

data_processing: ChAMP and minfi packages in R (v.3.3.2 or v.3.4 respectively)

source_name: Myoepithelial

extract_protocol: genomic DNA was extracted and purified from myoepithelial cells using Thermo Fisher Scientific PureLink Kit according to standard instructions

tag: gender

value: Female

tag: transfection

value: dCas9 3a3l

tag: donor


title: Myoepithelial_3A3L_day10_rep1

description: raw data column header: 3A3L_1


title: control blastocyst 5 (no bisection)

description:
Single embryo was lysed in Zymo buffer (Quick RNA micro prep) and total RNA was extracted in water
Sample name: ctrl5


title: Myoepithelial_Donor2_day38_rep1

description: raw data column header: Donor2_p7


title: twin blastocyst pair 7 (after 2-cell bisection)

description:
Single embryo was lysed in Zymo buffer (Quick RNA micro prep) and total RNA was extracted in water
Sample name: twin7

value: half


title: sister blastomere pair 1 (after 2-cell stage bisection)


title: control blastocyst 3 (no bisection)

description:
Single embryo was lysed in Zymo buffer (Quick RNA micro prep) and total RNA was extracted in water
Sample name: ctrl3


title: Myoepithelial_3A3Ldelta_day10_rep3

description: raw data column header: delta_4

value: dCas9 3a3l delta


title: control blastocyst 2 (no bisection)

description:
Single embryo was lysed in Zymo buffer (Quick RNA micro prep) and total RNA was extracted in water
Sample name: ctrl2


title: twin blastocyst pair 6 (after 2-cell bisection)

description:
Single embryo was lysed in Zymo buffer (Quick RNA micro prep) and total RNA was extracted in water
Sample name: twin6


title: twin blastocyst pair 10 (after 2-cell bisection)

description:
Single embryo was lysed in Zymo buffer (Quick RNA micro prep) and total RNA was extracted in water
Sample name: twin10


title: twin blastocyst pair 3 (after 2-cell bisection)

description:
Single embryo was lysed in Zymo buffer (Quick RNA micro prep) and total RNA was extracted in water
Sample name: twin3


title: cotwin blastocyst pair 9 (after 2-cell bisection)

description:
Single embryo was lysed in Zymo buffer (Quick RNA micro prep) and total RNA was extracted in water
Sample name: cotwin9


title: cotwin blastocyst pair 3 (after 2-cell bisection)

description:
Single embryo was lysed in Zymo buffer (Quick RNA micro prep) and total RNA was extracted in water
Sample name: cotwin3


title: Myoepithelial_Donor2_earlypassage_rep1

description: raw data column header: Donor2_un

value: untransfected


title: Myoepithelial_Donor1_earlypassage_rep1

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC BeadChip using standard Illumina protocol

data_processing: ChAMP and Minfi in R (v.3.3.2 or v.3.4 respectively)

source_name: Myoepithelial cells

extract_protocol: Genomic DNA was extracted using PureLink® Genomic DNA extraction kit from Thermo Fisher Scientific following instructions


title: twin blastocyst pair 9 (after 2-cell bisection)

description:
Single embryo was lysed in Zymo buffer (Quick RNA micro prep) and total RNA was extracted in water
Sample name: twin9


title: cotwin blastocyst pair 7 (after 2-cell bisection)

description:
Single embryo was lysed in Zymo buffer (Quick RNA micro prep) and total RNA was extracted in water
Sample name: cotwin7


title: twin blastocyst pair 2 (after 2-cell bisection)

description:
Single embryo was lysed in Zymo buffer (Quick RNA micro prep) and total RNA was extracted in water
Sample name: twin2


title: cotwin blastocyst pair 2 (after 2-cell bisection)

description:
Single embryo was lysed in Zymo buffer (Quick RNA micro prep) and total RNA was extracted in water
Sample name: cotwin2


title: Myoepithelial_3A3Ldelta_day10_rep2

description: raw data column header: delta_2_3


title: Myoepithelial_3A3L_day10_rep3

description: raw data column header: 3A3L_3


title: Myoepithelial_3A3Ldelta_day10_rep1

description: raw data column header: delta_1


title: twin blastocyst pair 8 (after 2-cell bisection)

description:
Single embryo was lysed in Zymo buffer (Quick RNA micro prep) and total RNA was extracted in water
Sample name: twin8


title: cotwin blastocyst pair 1 (after 2-cell bisection)

description:
Single embryo was lysed in Zymo buffer (Quick RNA micro prep) and total RNA was extracted in water
Sample name: cotwin1


title: control blastocyst 1 (no bisection)

description:
Single embryo was lysed in Zymo buffer (Quick RNA micro prep) and total RNA was extracted in water
Sample name: ctrl1


title: Myoepithelial_Donor1_3A3L_day38_rep1


title: twin blastocyst pair 1 (after 2-cell bisection)

description:
Single embryo was lysed in Zymo buffer (Quick RNA micro prep) and total RNA was extracted in water
Sample name: twin1


title: Naïve CD8+ T cells

status: Public on Aug 05 2017

city: Columbus

first: Steve

last: Oghumu

address: 1841 Neil Ave

institute: Ohio State University

description: CXCR3-GFP Reporter C57BL/6 spleen and lymph node

hyb_protocol: Samples were hybridized using Herring sperm DNA, Acetylated BSA (50mg/mL), Affymetrix Eukaryotic Hybridization Controls (Affymetrix) and Oligo B2, 3nM (Affymetrix) •Heat 65oC for 5 minutes, 99oC for 5 minutes, 45oC for 5 minutes centrifuge top speed for 5 minutes  •Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0002

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G using AGCC

data_processing: Background correction and quantile normalization was performed to adjust technical bias, and expression levels were summarized over probeset using RMA method. A filtering method based on percentage of arrays above noise cutoff was applied to filter out low expression genes. Affymetrix software Expression Console and statistical package R was used for the analysis.

source_name: Naïve CD8+ T cells from spleen and lymph nodes

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: Naïve CXCR3-GFP Reporter mice were maintained in Pathogen free conditions at animal facility at The Ohio State University

extract_protocol: Total RNA was isolated from sorted CXCR3+ and CXCR3- innate CD8+ T cell as well as naïve CD8+ T cell populations from about 3 to 5 CIBER mice using an RNeasy kit (Qiagen Valencia, CA USA). RNA quantity, quality and integrity were confirmed by Nanodrop and Agilent Bioanalyzer before inclusion in the array.

treatment_protocol: Sigle cell suspensions from spleen and lymph nodes were stained with CD44, CD62L and CD8 antibodies then required T cell populations were sorted in a FACS Aria cell sorter

tag: strain

value: spleen and lymph node

tag: cell type

value: Naïve CD8


title: Rax_GFP-_rep2

city: Chicago

first: NOZOMU

last: TAKATA

state: Illinois

address: 303 East Superior Street, 10-220

department: Center for Vascular and Developmental Biology

institute: Northwestern University Feinberg School of Medicine

description: Rax::GFP- cells from differentiated mouse ES cells with SFEBq at day 4.5, duplicate2

hyb_protocol: RNA was subsequently fragmented and hybridized to the GeneChip according to manufacturer’s instructions. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: The microarray image data were processed with the GeneChip Scanner 3000 (Affymetrix).

data_processing: The raw data were summarized with the RMA algorithm (R 2.13.0, Bioconductor 2.8).

source_name: day4.5, differentiated mouse ES cells with SFEBq

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

extract_protocol: Total RNA was extracted using QIAcubu’s RNA micro extraction mode (Qiagen), and  cDNA was synthesized using SuperScript II Reverse Transcriptase  (invitrogen).


title: cotwin blastocyst pair 8 (after 2-cell bisection)

description:
Single embryo was lysed in Zymo buffer (Quick RNA micro prep) and total RNA was extracted in water
Sample name: cotwin8

tag: tissue


title: CXCR3+ innate CD8+ T cells

source_name: CXCR3+ innate CD8+ T cells from spleen and lymph nodes

value: CXCR3+ innate CD8


title: CXCR3- innate CD8+ T cells

source_name: CXCR3- innate CD8+ T cells from spleen and lymph nodes

value: CXCR3- innate CD8


title: Rax_GFP+_rep2

description: Rax::GFP+ cells from differentiated mouse ES cells with SFEBq at day 4.5, duplicate2


title: Olfactory Neuroblastoma (patient 3)

city: los angeles

first: anatole

last: ghazalpour

state: CA

address: 675 charles young dr south

institute: UCLA

description: SAMPLE 4

data_processing: The data were normalised using quantile normalization using the R limma package function normalizeBetweenArrays() functions with method argument set to 'quantile'

source_name: Olfactory Neuroblastoma (patient 3)

label_protocol: Standard Illumina labeling protocol

extract_protocol: RNA was extracted with QIAGEN RNeasy kit in accordance with the prescribed protocol provided with the kit.

value: olfactory neuroblastoma


title: Control from healthy nerve tissue (pooled from three healthy nerve tissues)

description: SAMPLE 1

value: nerve tissue


title: cotwin blastocyst pair 10 (after 2-cell bisection)

description:
Single embryo was lysed in Zymo buffer (Quick RNA micro prep) and total RNA was extracted in water
Sample name: cotwin10

value: B6C3F1 x CD1

tag: age


title: Rax_GFP-_rep1

description: Rax::GFP- cells from differentiated mouse ES cells with SFEBq at day 4.5, duplicate1


title: Olfactory Neuroblastoma (patient 2)

description: SAMPLE 3

source_name: Olfactory Neuroblastoma (patient 2)


title: Olfactory Neuroblastoma (patient 1)

description: SAMPLE 2

source_name: Olfactory Neuroblastoma (patient 1)


title: Rax_GFP+_rep1

description: Rax::GFP+ cells from differentiated mouse ES cells with SFEBq at day 4.5, duplicate1


title: mutant strain C27 24h rep3

city: Seoul

first: Soojin

last: Shim

address: Kwan-ak ro

country: South Korea

institute: Seoul National University

description: replicate 3

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

source_name: THP-1_B. abortus mutant

label_protocol: Total RNA was amplified and purified using a TargetAmp-Nano Labeling Kit for Illumina Expression BeadChip (Eicentre, Madison, WI, USA) to synthesize biotinylated cRNA according to the manufacturer’s instructions.

growth_protocol: THP-1 human leukemic monocyte cells line from Korea Cell Line Bank (KCLB, Seoul, Korea) were grown at 37°C in humidified air with 5% CO2 in RPMI 1640 supplemented with 10% fetal bovine serum (FBS; Gibco, OK, USA) and antibiotic–antimycotic solution (Sigma, MO, USA). THP-1 cells were differentiated into macrophages by stimulation with phorbol-12-myristate-13-acetate (PMA; Sigma, USA) (50 ng/ml) for 72 hr, washed with FBS-free RPMI 1640 medium and incubated with 5% FBS-RPMI 1640 medium without antibiotics for 24 hr before the experiments.

extract_protocol: Total RNA was then extracted from the infected cells using an RNeasy mini kit (Qiagen, Germany) as described by the manufacturer after washing three times with DPBS (Gibco, USA). The purity and integrity of RNA was determined by denaturing gel electrophoresis, the OD260/OD280 ratio, and analysis with an Agilent 2100 Bioanalyzer (Agilent Technologies, CA, USA).

tag: cell line

value: human leukemic monocyte cell line

tag: infected with

value: B. abortus mutant strain C27


title: wild type strain

description: replicate 3

source_name: THP-1_B. abortus wild type

value: B. abortus wild type


title: mutant strain C1 24h rep3

description: replicate 3

value: B. abortus mutant strain C1


title: mutant strain C10 24h rep3

description: replicate 3

value: B. abortus mutant strain C10


title: mutant strain C32 24h rep3

description: replicate 3

value: B. abortus mutant strain C32


title: Rictor -/- T cells (Cd4cre+ / Rictor fl/fl), replicate 3

status: Public on Aug 04 2017

city: Memphis

first: Geoffrey

last: Neale

state: TN

address: 262 Danny Thomas Place

department: Hartwell Center

institute: St Jude Childrens Research Hospital

hyb_protocol: Five micrograms (5 ug) of biotinylated cDNA was hybridized for 16h at 45C on a Mouse Gene 2.0 ST GeneChip array.

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

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

source_name: Peyer's patch CD4+CD25-CD44+CD62L-  cells

label_protocol: One to five nanograms (1-5 ng) of total RNA were converted into biotinylated cDNA using the NuGEN WTA Pico v2 protocol and the NuGEN Encore Biotin module

growth_protocol: Cells were freshly sorted from tissues of mice by FACS

extract_protocol: Qiagen RNeasy Micro Kit

tag: background strain

value: follicular helper T cell

tag: genotype/variation

value: Rictor-/-


title: Raptor -/- T cells (Cd4cre+ / Raptor fl/fl), replicate 3

value: Raptor-/-


title: Rictor -/- T cells (Cd4cre+ / Rictor fl/fl), replicate 2


title: Raptor -/- T cells (Cd4cre+ / Raptor fl/fl), replicate 2


title: cotwin blastocyst pair 6 (after 2-cell bisection)

description:
Single embryo was lysed in Zymo buffer (Quick RNA micro prep) and total RNA was extracted in water
Sample name: cotwin6

value: Theiler stage 5; 4 dpc

value: half

value: blastocyst stage embryo


title: Raptor -/- T cells (Cd4cre+ / Raptor fl/fl), replicate 1


title: Rictor -/- T cells (Cd4cre+ / Rictor fl/fl), replicate 4


title: Rictor -/- T cells (Cd4cre+ / Rictor fl/fl), replicate 1


title: WT T cells (Cd4cre- / Rictor fl/fl), replicate 5

value: wildtype


title: WT T cells (Cd4cre- / Raptor fl/fl), replicate 1


title: WT T cells (Cd4cre- / Rictor fl/fl), replicate 3


title: WT T cells (Cd4cre- / Raptor fl/fl), replicate 2


title: WT T cells (Cd4cre- / Rictor fl/fl), replicate 4


title: Olfactory Neuroblastoma (patient 4)

description: SAMPLE 5

source_name: Olfactory Neuroblastoma (patient 4)


title: CD3_48h_02_replicate 2

city: Cleveland

first: Ahmad

middle: Faisal

last: Karim

state: OH

address: 2109 Adelbert road; BRB 1010B

institute: Case Western Reserve University

description: Gene expression data from each experimental condition

hyb_protocol: Following fragmentation, 5.5 ug of cDNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: The data were analyzed with Affymetrix Expression consol software using default analysis settings and RMA scaling as normalization method to express intensity in log2 scale.

source_name: Naïve CD4+ T cells+CD3_48h

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: FACS sorted naïve CD4+ T cells were cultured in complete media, i.e. D10F, consisting of  DMEM (BioWhittaker, Walkersville, MD) supplemented with fetal calf serum (10% v/v, Gemini-Bioproducts, West Sacramento, CA; 100-106), penicillin (100 IU/ml), streptomycin (100 µg/ml), HEPES (100mM), nonessential amino acids (100mM), L-glutamine (2 mM), and 2-mercaptoethanol (0.05 mM) at 37˚C in 5% CO2.

extract_protocol: Total RNA were extracted using RNeasy Plus Mini Kit (Qiagen), according to the manufacturer’s protocol.

treatment_protocol: CD4+ T cells were cultured in the presence of plate-bound anti-mouse CD3 mAb alone and with anti mouse CD28mAb in presence of P3CSK4 or media alone for 24 and 48 hrs.

tag: cells

value: Spleenic CD4+ T cells


title: All_48h_01_replicate 1

source_name: Naïve CD4+ T cells+All stim_48h


title: CD3_P3C_48h_01_replicate 1

source_name: Naïve CD4+ T cells+CD3+P3C_48h


title: CD3_CD28_24h_01_replicate 1

source_name: Naïve CD4+ T cells+CD3+CD28_24h


title: All_48h_02_replicate 2


title: CD3_CD28_24h_02_replicate 2


title: CD3_24h_01_replicate 1

source_name: Naïve CD4+ T cells+CD3_24h


title: CD3_CD28_48h_02_replicate 2

source_name: Naïve CD4+ T cells+CD3+CD28_48h


title: All_24h_01_replicate 1

source_name: Naïve CD4+ T cells+All stim_24h


title: CD3_P3C_48h_02_replicate 2


title: Unstim02_replicate 2

source_name: Naïve CD4+ T cells


title: All_24h_02_replicate 2


title: CD3_24h_02_replicate 2


title: Unstim01_replicate 1


title: Plasma_pat62_melanoma_before_treatment_targeted_therapy

status: Public on Aug 03 2017

city: Stockholm

first: Fernanda

last: Costa Svedman

address: Solnavägen 1

institute: Karolinska Institute

description:
Other (exosomal microRNA)
This study has 28 patients. Samples before treatment are identified as the patient number only (ie 8) and the samples during trreatment are labeled with an additional T for treatment (ie 008T).

hyb_protocol: Not aplicable

scan_protocol: Not aplicable

data_processing: Raw Cq values and melting points detected by the Lightcycler software were exported. Reactions with several melting points or with melting points that were not within the assay specification were flagged and removed from the data set. An evaluation of the negative control was performed by removing the reactions giving Cq values that were within 5 Cq values of the negative control reaction. For assays that did not yield any signal on the negative control, the upper limit of detection was set to Cq = 37. Hemolysis assessment was performed by the detection of miR-451, a miRNA highly expressed in red blood cells and miR-23a which is unaffected by hemolysis. The data was considered as affected by hemolysis if delta Cq between these 2 miRNAs was more than 8. Normalization was performed based on the average of the assays detected in all samples as this is shown to be the best normalization for qPCR studies involving numerous assays (Mestdagh, P. et.al. 2009). For the present study, this included 24 assays. The stability of the average of 24 microRNAs is higher than any single microRNA in the data set as measured by the NormFinder software (Andersen, C. et al). The formula used to calculate the normalized Cq values are: Normalized Cq = average Cq (n=52) – assay Cq (sample) A higher value thus indicates that the microRNA is more abundant in the particular sample.

label: SYBR green

source_name: Plasma from patients with BRAF mutated metastatic melanoma before treatment with MAPKi

label_protocol: MiRNA expression profiling was performed using miRCURY LNA Universal RT miRNA PCR Human panel I (Exiqon, Denmark) covering 372 human miRNAs.  All miRNAs were polyadenylated and reverse transcribed in cDNA in a single reaction step. RNA isolation cDNA synthesis efficiency was examined by the detection of spike-in UniSp2, UniSp4 and UniSp6 to ensure that the quality of the input RNA was sufficiently high for effective amplification. cDNA and Exilent SYBR Green master mix (Exiqon, Denmark) were transferred to qPCR panels preloaded with primers. Amplification was performed in a Lightcycler 480 (Roche). We normalized miRNA expression to a set of miRNAs found to be most stable across conditions defined by the normfinder algorithm

growth_protocol: Plasma samples were store in -80 degrees Celsius until the extraction

extract_protocol: MiRCURY Exosome Isolation Kit-Serum and Plasma (Exiqon, Denmark) was used for isolation of plasmatic EVs. Briefly, 600 μl of plasma was treated with thrombin for 5 minutes at room temperature to remove clotting factors. The supernatant was mixed with 200 μl of precipitation buffer and incubated at 4°C for overnight and centrifuged (10,000 g for 30 min at room temperature). The pellet was vortexed for 5-15 minutes in 270 μl resuspension buffer until completely re-suspended. The EV miRNA was extracted using miRCURY RNA isolation kit-biofluids (Exiqon, Denmark) according to the manufacturer´s instruction. RNA spike-in template mixture (Exiqon, Denmark) was added as a quality control of the downstream PCR analysis.

treatment_protocol: Plasma samples were centrifugated and stored in -80 Celsius degree.

tag: Sex

value: male

tag: age years old

tag: metastatic stage

tag: response

value: Not evaluable

tag: progression free survival

value: 18 days


title: CD3_48h_01_replicate 1


title: Plasma_pat56_melanoma_during_treatment_targeted_therapy

source_name: Plasma from patients with BRAF mutated metastatic melanoma during treatment with MAPKi

value: female

value: Responder

value: 242 days


title: Plasma_pat54_melanoma_before_treatment_targeted_therapy

value: Non-responder

value: 91 days


title: Plasma_pat56_melanoma_before_treatment_targeted_therapy


title: Plasma_pat55_melanoma_before_treatment_targeted_therapy

value: 266 days


title: Plasma_pat55_melanoma_during_treatment_targeted_therapy


title: Norgestimate_2

city: Tokyo

first: Yutaka

last: Yoshii

address: 3-25-8 Nishi-Shimbashi, Minato-ku

department: Department of Bacteriology

institute: The Jikei University School of Medicine

hyb_protocol: Following fragmentation, 3 ug of cDNA were hybridized for 16 hr at 45C according to GeneChip expression Technical Manual.

scan_protocol: Scanning of cDNA on the array were performed according to the manufacturer’s instructions.

data_processing:
affymetrix-algorithm-name = ExpressionStat
affymetrix-algorithm-version = 5.0
Spotfire DecisionSite 9.1.1 was used to analyze the data.

organism: Staphylococcus aureus

source_name: whole cells

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA.

growth_protocol: S. aureus MR23 was grown in brain heart infusion broth supplemented with 1% glucose, 5% DMSO, with or without norgestimate at 37C for 12 h.

extract_protocol: Cells were harvested by centrifugation at 5,000 ×g at 25 ºC for 10 min and immediately incubated with an appropriate volume of RNA protect for 5 min. Cell were collected by centrifugation at 5,000 × g at 25 ºC for 10 min and stored at –80 ºC. Total RNA was extracted using an RNeasy Maxi Kit according to the manufacturer’s instructions, except that cells were treated with 0.2 mg/mL lysostaphin at 37 ºC for 30 min before extraction.

tag: agent

value: norgestimate


title: Plasma_pat53_melanoma_before_treatment_targeted_therapy

value: 169 days


title: Control_2

value: control


title: Control_1


title: Norgestimate_1


title: CD3_P3C_24_02_replicate 2

source_name: Naïve CD4+ T cells+CD3+P3C_24h


title: CD3_P3C_24_01_replicate 1


title: CD3_CD28_48h_01_replicate 1


title: Plasma_pat54_melanoma_during_treatment_targeted_therapy


title: Plasma_pat52_melanoma_during_treatment_targeted_therapy

value: 159 days


title: Plasma_pat49_melanoma_before_treatment_targeted_therapy

value: 199 days


title: Plasma_pat49_melanoma_during_treatment_targeted_therapy


title: Plasma_pat41_melanoma_during_treatment_targeted_therapy

value: 231 days


title: Plasma_pat43_melanoma_before_treatment_targeted_therapy

value: 335 days


title: Plasma_pat40_melanoma_during_treatment_targeted_therapy

value: 70 days


title: Plasma_pat48_melanoma_before_treatment_targeted_therapy

value: 387 days


title: Plasma_pat41_melanoma_before_treatment_targeted_therapy

value: male


title: Plasma_pat39_melanoma_before_treatment_targeted_therapy

value: 83 days


title: Plasma_pat43_melanoma_during_treatment_targeted_therapy


title: Plasma_pat39_melanoma_during_treatment_targeted_therapy


title: Plasma_pat22_melanoma_during_treatment_targeted_therapy

value: 98 days


title: Plasma_pat38_melanoma_before_treatment_targeted_therapy

value: female

value: Responder

value: 506 days


title: Plasma_pat12_melanoma_before_treatment_targeted_therapy

value: 282 days


title: Plasma_pat22_melanoma_before_treatment_targeted_therapy

value: Non-responder


title: Plasma_pat20_melanoma_during_treatment_targeted_therapy

value: 328 days


title: Plasma_pat23_melanoma_before_treatment_targeted_therapy

value: 224 days


title: Plasma_pat38_melanoma_during_treatment_targeted_therapy


title: Plasma_pat17_melanoma_before_treatment_targeted_therapy

value: 627 days


title: Plasma_pat48_melanoma_during_treatment_targeted_therapy


title: Plasma_pat8_melanoma_during_treatment_targeted_therapy

value: 148 days


title: Plasma_pat16_melanoma_targeted therapy

value: 80 days


title: Plasma_pat19_melanoma_during_treatment_targeted_therapy

value: 35 days


title: Plasma_pat19_melanoma_before_treatment_targeted_therapy


title: Plasma_pat40_melanoma_before_treatment_targeted_therapy


title: Plasma_pat13_melanoma_during_treatment_targeted_therapy

value: 118 days


title: Plasma_pat26_melanoma_before_treatment_targeted_therapy

value: 124 days


title: Plasma_pat12_melanoma_during_treatment_targeted_therapy


title: Plasma_pat23_melanoma_during_treatment_targeted_therapy


title: Plasma_pat25_melanoma_before_treatment_targeted_therapy

value: 245 days


title: Plasma_pat14_melanoma_before_treatment_targeted_therapy

value: male

value: Not evaluable


title: Plasma_pat4_melanoma_before_treatment_targeted_therapy

value: 186 days


title: Plasma_pat5_melanoma_during_treatment_targeted_therapy

value: female

value: 199 days


title: Plasma_pat4_melanoma_during_treatment_targeted_therapy

value: Responder


title: Plasma_pat25_melanoma_during_treatment_targeted_therapy


title: Plasma_pat5_melanoma_before_treatment_targeted_therapy


title: Plasma_pat26_melanoma_during_treatment_targeted_therapy


title: Plasma_pat17_melanoma_during_treatment_targeted_therapy


title: Plasma_pat16_melanoma_during_treatment_targeted_therapy


title: Plasma_pat13_melanoma_before_treatment_targeted_therapy


title: Plasma_pat14_melanoma_during_treatment_targeted_therapy


title: S25.2

type: protein

city: Worcester

first: Dr Yvonne

last: Edwards

address: 373 Plantation Street

department: Program in Molecular Medicine

institute: University of Massachusetts Medical School

description: 14 days follow up sample 32

hyb_protocol: As described elsewhere http://www.tandfonline.com/doi/abs/10.1586/erm.10.89

scan_protocol: Proteomic assessments were performed as described elsewhere [Gold L et al. N Biotechnol. 2012 Jun 15;29(5):543-9.].

data_processing: Normalization and interrun calibration were performed as described elsewhere http://www.tandfonline.com/doi/abs/10.1586/erm.10.89

molecule: protein

source_name: serum

extract_protocol: Non-fasting venous blood was drawn into SST tubes, spun, and frozen at -80°C. Samples were thawed, aliquoted into 0.5 ml screw top tubes in 96 well plates (Thermo Scientific), and shipped to an outside laboratory on dry ice where assays were performed using SOMAscan reagents according to the manufacturer’s protocol [ http://www.tandfonline.com/doi/abs/10.1586/erm.10.89; Hathout Y et al 2015. Proc Natl Acad Sci U S A. 2015;112:7153-8]

treatment_protocol: non fasting serum collected in SST tubes

tag: gender

value: F

tag: group

value: Follow Up SCM

tag: day

tag: peak troponin i (ng/ml)


title: S24.2

description: 14 days follow up sample 31

label_protocol: As described elsewhere http://www.tandfonline.com/doi/abs/10.1586/erm.10.89


title: S23.2

description: 14 days follow up sample 30


title: S5.2

description: 14 days follow up sample 22