title: H9Hyb_PSC_2

city: Leiden

first: M.

middle: J.

last: Bouma

address: Einthovenweg 20

department: Anatomy & Embryology

institute: LUMC

description:
replicate 2
102178-016-034

hyb_protocol: Illumina protocol: Whole-Genome Gene Expression Direct Hybridization Assay. Performed at GenomeScan B.V. in Leiden, the Netherlands

scan_protocol: Standard Illumina scanning protocol. Performed at GenomeScan B.V. in Leiden, the Netherlands

data_processing: Data was normalized using the neqc function (Limma) in R. Batch effects were removed using ComBat (sva)

source_name: Undifferentiated H9 Hybrid cells

label_protocol: Illumina TotalPrep-96 RNA amplification Kit was used to generate Biotin labeled (Biotin-16-UTP) amplified cRNA starting from 200 ng of total RNA. Performed at GenomeScan B.V. in Leiden, the Netherlands

growth_protocol: Cells were cultured on VitronectinXF in TESR-E8 medium (Stem Cell Technologies). 8-10 weeks old male NSG mice (NOD.Cg-Prkdcscid IL2rgtm1Wjl/Szj, Charles River) were used for injections. 1x10^6 cells were injected subcutaneously in the flank region. Tumor growth was monitored weekly by palpation and mice were sacrificed when tumors reached a volume ≤ 2cm^3. Whole tumors were used for analysis.

extract_protocol: RNA was extracted with NucleoSpin RNA kit (Machery-Nagel) including DNase digestion according to manufacturers protocol. All pieces of the same xenograft were homogenized in RA1 buffer (Machery-Nagel) with 1% β-mercatoethanol. An aliquot of the homogenate was used for RNA isolation

treatment_protocol: LU07+Dox and H9+Dox: Cells were treated with 2µg/ml Doxycycline three days prior to harvesting or injection. Drinking water of the mice contained 2 mg/ml Doxycycline and 10mg/ml Sucrose one week prior to and after injections. Drinking water was changed every 2nd day until mice were sacrificed. H9, H9Hyb, LU07 and EC: Drinking water of the mice contained 10mg/ml Sucrose one week prior to and after injections. Drinking water was changed every 2nd day until mice were sacrificed.

tag: cell/tissue type

value: Undifferentiated cells


title: LU07_PSC_1

status: Public on Feb 24 2017

type: RNA

country: Netherlands

description:
replicate 1
102178-016-023

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: Undifferentiated LUMC007iCTR01 cells


title: EC_3

description:
replicate 3
102178-016-035

source_name: EC2102ep cells


title: EC_xenograft_3

description:
replicate 3
102178-016-018

source_name: EC2102ep xenograft

value: Xenograft


title: LU07+Dox_PSC_1

description:
replicate 1
102178-016-029

source_name: Undifferentiated LUMC007iCTR01 cells + Doxycyclin


title: reference male mouse3/ 20mGyLF

status: Public on Feb 25 2017

type: genomic

city: Rokkasho-mura,Kamikita-gun,

first: Keiji

last: OGURA

state: Aomori

address: Takahoko, Hacchasawa,

department: Department of Radiobiology

country: Japan

institute: Institute for Environmental Science

description: 20mGyLF Cy3

hyb_protocol: Oligonucleotide Array-Based CGH for Genomic DNA Analysis, protocol version 4.0.8

scan_protocol: Scanned on an Agilent G2565BA scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.1.1).

data_processing: Agilent Genomic Workbench Software (v 7.0.) was used.

molecule: genomic DNA

organism: Mus musculus

source_name: reference male mouse3

extract_protocol: PI-50a (Kurabo Industries LTD.) tissue DNA extraction protocol.

tag: strain

tag: tissue

value: tail


title: LU07_PSC_4

description:
replicate 4
102814-001-002


title: H9+Dox_PSC_2

description:
replicate 2
102178-016-027

source_name: Undifferentiated H9 cells + Doxycyclin


title: LU07_PSC_3

description:
replicate 3
102178-016-030


title: P2-A1

city: Prague 2

first: Vojtěch

last: Kulvait

address: U Nemocnice 5

department: Institute of Pathological Physiology

country: Czech Republic

institute: Charles University in Prague - 1st Faculty of Medicine

hyb_protocol: Standard Illumina protocol

scan_protocol: Standard Illumina protocol

data_processing: Image data was read by beadarray package (there are no detection p-values). Further data processing was performed using blima Bioconductor package. Averaged foreground values GrnF after background correction was used for Matrix non-normalized data.

label: biotin

source_name: Patient's primary lymphoma cells obtained from malignant ascites.

label_protocol: Standard Illumina protocol

extract_protocol: RNA extraction using Trizol, as per manufacturer's protocol

tag: cell type


title: LU07+Dox_PSC_4

description:
replicate 4
102814-001-003


title: LU07+Dox_PSC_3

description:
replicate 3
102814-001-001


title: H9_PCS_1

description:
replicate 1
102178-016-021

source_name: Undifferentiated H9 cells


title: H9+Dox_PSC_3

description:
replicate 3
102178-016-033


title: EC_1

description:
replicate 1
102178-016-020


title: LU07+Dox_xenograft_4

description:
replicate 4
102178-016-037

source_name: LUMC0007iCTR01 + Doxycycline xenograft


title: H9+Dox_PSC_1

description:
replicate 1
102178-016-022


title: H9_PSC_2

description:
replicate 2
102178-016-026


title: EC_2

description:
replicate 2
102178-016-025


title: LU07_PSC_2

description:
replicate 2
102178-016-028


title: H9Hyb_PSC_1

description:
replicate 1
102178-016-019


title: H9_PSC_3

description:
replicate 3
102178-016-032


title: H9Hyb_PSC_3

description:
replicate 3
102178-016-036


title: Lu07+Dox_PSC_2

description:
replicate 2
102178-016-031


title: EVI1 shRNA construct 2 1

city: Basel

first: Hui

last: Wang

address: Hebelstr. 20

country: Switzerland

institute: University Hospital Basel

hyb_protocol: Following cRNA clean-up and quantification 600 ng of each Cyanine-3-labeled cRNA sample was fragmented and prepared for one-color-based hybridization (Gene Expression Hybridization Kit, Agilent Technologies). Labeled cRNA samples were hybridized at 65°C for 17 hrs on separate Agilent SurePrint G3 Human Gene Expression 8x60K v2 Microarrays (AMADID 039494). Afterwards, microarrays were washed with increasing stringency using Gene Expression W ash Buffers (Agilent Technologies) followed by drying with acetonitrile (SIGMA).

scan_protocol: Fluorescent signal intensities were detected with Scan Control A.8.4.1 software (Agilent Technologies) on the Agilent DNA Microarray Scanner and extracted from the images using Feature Extraction 10.7.3.1 software (Agilent Technologies).

data_processing: The software tools Feature Extraction 10.7.3.1, GeneSpring GX 12.6 (both Agilent Technologies), Excel 2010 (Microsoft) and the IMGM internal tool marfin v1.9 were used for quality control, statistical data analysis, filtering of differentially expressed transcript, RNA annotation and visualization.

source_name: mammary gland/breast; derived from metastatic site: pleural effusion

label_protocol: 100 ng total RNA per sample were introduced into a reverse transcription with subsequent in vitro transcription (RT-IVT) reaction. Prior to RT-IVT, the total RNA samples were spiked with in vitro synthesized polyadenylated transcripts (One-Color RNA Spike-In Mix, Agilent Technologies) which serve as an internal labeling control for linearity, sensitivity and accuracy. The spiked total RNA was reverse transcribed into cDNA and then converted into Cyanine-3 labeled cRNA (Low Input Quick-Amp Labeling Kit One-Color, Agilent Technologies). All steps were carried out according to manufacturer’s instructions. cRNA concentration (ng/μl), RNA absorbance ratio (A260nm/A280nm) and Cyanine-3 dye concentration (pmol/μl) were recorded for all cRNA samples using NanoDrop ND-1000 UV- VIS spectrophotometer. Yield and specific activity of each reaction were determined. The RNA 6000 Nano LabChip Kit (Agilent Technologies) was used on the 2100 Bioanalyzer to analyze the quality of labeled non-fragmented cRNA.

growth_protocol: The MDA-MB-231 cell line was cultivated according to the data sheet

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (Qiagen) and RNA concentration and purity determined on the NanoDrop ND-1000 spectral photometer (peqlab). The 2100 Bioanalyzer (Agilent Technologies) and the RNA 6000 Nano as well as the 6000 Pico LabChip Kit (Agilent Technologies) were used to analyze RNA integrity.

treatment_protocol: Cells were lentivirally transduced as described in Konantz et al., Leukemia 2013

tag: cell line

value: breast carcinoma


title: EVI1 shRNA construct 2 2


title: EC_xenograft_2

description:
replicate 2
102178-016-017


title: EVI1 shRNA construct 2 3


title: H9Hyb_xenograft_3

description:
replicate 3
102178-016-015

source_name: H9 Hybrid xenograft


title: EVI1 shRNA construct 1 2


title: EVI1 shRNA construct 1 3


title: EC_xenograft_1

description:
replicate 1
102178-016-016


title: EVI1 shRNA construct 1 1


title: H9+Dox_xenograft_2

description:
replicate 2
102178-016-011

source_name: H9 + Doxycycline xenograft


title: H9_xenograft_1

description:
replicate 1
102178-016-007

source_name: H9 xenograft


title: H9Hyb_xenograft_1

description:
replicate 1
102178-016-013


title: H9+Dox_xenograft_3

description:
replicate 3
102178-016-012


title: control shRNA 2


title: H9Hyb_xenograft_2

description:
replicate 2
102178-016-014


title: H9+Dox_xenograft_1

description:
replicate 1
102178-016-010


title: H9_xenograft_2

description:
replicate 2
102178-016-008


title: H9_xenograft_3

description:
replicate 3
102178-016-009


title: control shRNA 1


title: control shRNA 3


title: LU07+Dox_xenograft_3

description:
replicate 3
102178-016-006


title: LU07+Dox_xenograft_1

description:
replicate 1
102178-016-004


title: Englerin A_20 h, rep. 1

city: Columbia

first: Diego

last: Altomare

state: SC

address: 715 Sumter Street, Room 617

department: Department of Drug Discovery and Biomedical Sciences

country: USA

institute: University of South Carolina

description: US10130359_253949437667_S01_GE1_107_Sep09_1_3.txt

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >= 15.6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human Gene Expression 8x60K v2 Microarrays (G4851B-039494) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then immersed in acetonitrile and dried immediately by slowly removing the slide.

scan_protocol: Slides were scanned immediately after washing on an Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3 um, Dye channel is set to Green at 20 bit).

data_processing: The scanned images were analyzed with Feature Extraction Software  10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid 039494_D_F_20140813) to obtain background subtracted and spatially detrended Processed Signal intensities.  Data was uploaded into Genespring version 11.5.1 where was thresholded to 1.0, log2 transformed, quantile normalized and base line transformed using the median of all samples. Data was filtered by flags in a way that at least 75% of the samples in any of the 2 experimental groups had DETECTED flags. Then, differentially expressed genes were determined using a moderated t-test statistics with p-value 0.01 and fold change 1.5 as cutoffs.

source_name: Englerin A, 20 h-treated A-498 cells

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng total RNA using the Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with a NanoDrop 2000c Spectrophotometer.

growth_protocol: A498 cells were purchased from ATTC and maintained in RPMI medium supplemented with 10% FBS, 2 mM L-glutamine, and 100 units/ml penicillin/streptomycin (complete RPMI). All experiments were conducted with cells of passage number less than 25.

extract_protocol: Cell extracts were prepared using 1 ml of TRI Reagent (Zymo Research, Irvine, CA) per dish. Total RNA was then purified from cell extracts using spin columns by Zymo Research according to the manufacturer’s directions.

treatment_protocol: A498 cells were plated in complete RPMI onto 100 mm dishes at 0.9 x 10E6 cells per dish. After cells were allowed to adhere overnight, cells were refed with complete RPMI containing 0.1% DMSO (vehicle) for 3 hours or 100 nM englerin A for 20 hours.

tag: tumor type

value: renal cell carcinoma

tag: gender

value: female

tag: treated with

value: ENGLERIN A for 20hrs


title: Control, rep. 4 [re-analysis 2]

description: US10130359_253949437668_S01_GE1_107_Sep09_1_4.txt

source_name: Control A-498 cells

value: CONTROL vehicle for 3hrs


title: Englerin A_20 h, rep. 4

description: US10130359_253949437668_S01_GE1_107_Sep09_2_2.txt


title: Englerin A_20 h, rep. 2

description: US10130359_253949437667_S01_GE1_107_Sep09_1_4.txt


title: Control, rep. 3 [re-analysis 2]

description: US10130359_253949437668_S01_GE1_107_Sep09_1_3.txt


title: Control, rep. 2 [re-analysis 2]

description: US10130359_253949437667_S01_GE1_107_Sep09_2_2.txt


title: Control, rep. 1 [re-analysis 2]

description: US10130359_253949437667_S01_GE1_107_Sep09_2_1.txt


title: LU07_xenograft_2

description:
replicate 2
102178-016-002

source_name: LUMC0007iCTR01 xenograft


title: LU07_xenograft_3

description:
replicate 3
102178-016-003


title: Englerin A_20 h, rep. 3

description: US10130359_253949437668_S01_GE1_107_Sep09_2_1.txt


title: Englerin A_8 h, rep. 4

description: US10130359_253949437668_S01_GE1_107_Sep09_2_4.txt

source_name: Englerin A, 8 h-treated A-498 cells

treatment_protocol: A498 cells were plated in complete RPMI onto 100 mm dishes at 0.9 x 10E6 cells per dish. After cells were allowed to adhere overnight, cells were refed with complete RPMI containing 0.1% DMSO (vehicle) for 3 hours or 100 nM englerin A for 8 hours.

value: ENGLERIN A for 8hrs


title: Control, rep. 3 [re-analysis]


title: hiPSC_D1 II

city: Heidelberg

first: Jochen

last: Utikal

address: Im Neuenheimer Feld 280

department: Clinical Cooperation Unit Dermato-Oncology

country: Germany

institute: German Cancer Research Center

description: replicate 1c

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: fibroblasts

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.


title: Control, rep. 1 [re-analysis]


title: LU07_xenograft_1

description:
replicate 1
102178-016-001


title: LU07+Dox_xenograft_2

description:
replicate 2
102178-016-005


title: Englerin A_8 h, rep. 2

description: US10130359_253949437667_S01_GE1_107_Sep09_1_2.txt


title: Englerin A_3 h, rep. 3

description: US10130359_253949437668_S01_GE1_107_Sep09_1_1.txt

source_name: Englerin A, 3 h-treated A-498 cells

treatment_protocol: A498 cells were plated in complete RPMI onto 100 mm dishes at 0.9 x 10E6 cells per dish. After cells were allowed to adhere overnight, cells were refed with complete RPMI containing 0.1% DMSO (vehicle) or 100 nM englerin A and incubated for 3 hours.

value: ENGLERIN A for 3hrs


title: Control, rep. 2 [re-analysis]


title: Control, rep. 4 [re-analysis]


title: iPCC I

description: replicate 1b

value: iPCC


title: hiPSC_VG2 II

description: replicate 2d


title: HT144 II

description: replicate 2a

source_name: melanoma metastasis

value: HT144 (ATCC)


title: Englerin A_8 h, rep. 3

description: US10130359_253949437668_S01_GE1_107_Sep09_2_3.txt


title: HT144 III

description: replicate 3a


title: iPCC II

description: replicate 2b


title: Englerin A_3 h, rep. 4

description: US10130359_253949437668_S01_GE1_107_Sep09_1_2.txt


title: hiPSC_VG2 I

description: replicate 1d


title: Englerin A_8 h, rep. 1

description: US10130359_253949437667_S01_GE1_107_Sep09_1_1.txt


title: PB_FA_011706

city: Barcelona

first: Luis Alberto

middle: Perez

last: Jurado

state: Barcelona

address: Doctor Aiguader, 88 (PRBB)

department: Department of Experimental and Health Sciences

country: Spain

institute: Universitat Pompeu Fabra

hyb_protocol: According to the manufacturer’s specifications

data_processing: LRR and BAF values were obtained by using Illumina GenomeStudio software

source_name: Peripheral Blood

extract_protocol: Extraction of genomic DNA from fresh frozen tissue was performed using standard phenol-chloroform extraction method or the Puregene DNA Isolation Kit (QiagenInc, US)

tag: disease state

value: Fanconi Anemia

value: Peripheral Blood

tag: age at sampling

tag: cancer diagnosis

value: Yes

tag: age at cancer diagnosis

tag: evolution

value: Alive

tag: age of exitus


title: Englerin A_3 h, rep. 2

description: US10130359_253949437667_S01_GE1_107_Sep09_2_4.txt


title: PB_FA_071306

scan_protocol: According to the manufacturer’s specifications

value: Not Available


title: HeyA8 PLTS 2

city: Houston

first: Monika

last: Haemmerle

address: 1881 East Rd

department: Gynecological Oncology

institute: UT MD Anderson Cancer Center

description:
replicate 2
SAMPLE 5

data_processing: Array data processing were performed on Illumina BeadStudio software. We normalized gene expression data using Quantile normalization and log2 transformatoin. To export to a data matrix, Sample Gene Profile option of this software was used. We used Sample Gene Profile option of Illumina BeadStudio software.

source_name: HeyA8 human ovarian cancer cells

label_protocol: Biotynilated cRNA was prepared using Illumina® TotalPrep™ RNA Amplification Kit

growth_protocol: Cells were cultured in 5% CO2 humidified chamber.

extract_protocol: RNA was extracted with mirVana RNA Isolation kit (Thermo Fisher Scientific) per the manufacturer’s instructions. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Cells were co-incubated with or without platelets for 24 hours.

tag: protocol

value: mouse platelets


title: PB_FA_071333

label_protocol: According to the manufacturer’s specifications

value: No


title: HeyA8 PLTS 3

description:
replicate 3
SAMPLE 6


title: PB_FA_051449


title: Control, rep. 2


title: Englerin A_3 h, rep. 1

description: US10130359_253949437667_S01_GE1_107_Sep09_2_3.txt


title: Control, rep. 4


title: PB_FA_041143


title: HT144 I

description: replicate 1a


title: HeyA8 PLTS 1

description:
replicate 1
SAMPLE 4


title: PB_FA_FA311


title: PB_FA_970094

value: Exitus


title: HeyA8 CTRL 2

description:
replicate 2
SAMPLE 2


title: HeyA8 CTRL 3

description:
replicate 3
SAMPLE 3


title: PB_FA_FA91


title: HeyA8 CTRL 1

description:
replicate 1
SAMPLE 1


title: Control, rep. 1


title: Rec z-VRPR-fmk 48h r1

city: Münster

first: Michael

last: Grau

state: Nordrhein-Westfalen

address: Albert-Schweitzer-Campus 1

department: Faculty of Medicine

institute: University of Münster

hyb_protocol: hybridization was performed with HumanHT-12 v4 Expression Bead Chip kit (Illumina) according to manufacturer's protocol

scan_protocol: scanning was performed according to manufacturer's protocol

data_processing: The preprocessing pipeline was implemented in Mathworks MATLAB(R) and works similar to preprocessing Affymetrix CEL files: Measured gene expressions were imported on raw bead level (cf. supplementary TXT files). All microarrays were preprocessed and normalized together. Their intensity distributions for all measured beads were equalized by quantile normalization. The background mode was fitted and removed and a spot filter was applied to exclude too dim beads (< mean background intensity). Intensities were log2-transformed and aggregated by measured sequence to form beadsets. Beadsets with more than 50% of their beads excluded by the spot filter were also excluded. Further analysis was performed on gene level using median aggregation and manufacturer’s annotations. For genes having multiple beadsets the one with the highest expression (in average over all arrays) was selected.

source_name: Rec z-VRPR-fmk 48h

label_protocol: RNA was transcribed and labeled by Illumina TotalPrep RNA Amplification kit according to manufacturer's protocol

growth_protocol: cell lines Mino and Rec were maintained in RPMI medium with 10% FBS at 37°C with 5% CO2

extract_protocol: total RNA was extracted using RNeasy kit (Qiagen) according to manufacturer's protocol

treatment_protocol: cell lines Mino and Rec were treated with either 50 µM z-VRPR-fmk or with DMSO

value: Rec

value: Mantle cell lymphoma (MCL) cell line

value: z-VRPR-fmk

tag: duration in hours

tag: replicate


title: Rec z-VRPR-fmk 36h r1

source_name: Rec z-VRPR-fmk 36h


title: Rec z-VRPR-fmk 42h r1

source_name: Rec z-VRPR-fmk 42h


title: Control, rep. 3

value: renal cell carcinoma

value: female


title: Rec z-VRPR-fmk 54h r1

source_name: Rec z-VRPR-fmk 54h


title: PB_FA_FA108


title: PB_FA_FA287


title: Rec z-VRPR-fmk 24h r1

source_name: Rec z-VRPR-fmk 24h


title: Rec DMSO 30h r1

source_name: Rec DMSO 30h

value: DMSO


title: PB_FA_FA163


title: Rec z-VRPR-fmk 30h r1

source_name: Rec z-VRPR-fmk 30h


title: Rec DMSO 48h r1

source_name: Rec DMSO 48h


title: PB_FA_110243


title: PB_FA_FA145


title: PB_FA_FA48


title: PB_FA_FA104


title: PB_FA_041271


title: Rec DMSO 54h r1

source_name: Rec DMSO 54h


title: PB_FA_061814


title: Rec DMSO 42h r1

source_name: Rec DMSO 42h


title: Rec DMSO 24h r1

source_name: Rec DMSO 24h


title: Mino z-VRPR-fmk 48h r2

source_name: Mino z-VRPR-fmk 48h

growth_protocol: cell line Mino was maintained in RPMI medium with 10% FBS at 37°C with 5% CO2

treatment_protocol: cell line Mino was treated with either 50 µM z-VRPR-fmk or with DMSO

value: Mino


title: Mino z-VRPR-fmk 42h r2

source_name: Mino z-VRPR-fmk 42h


title: Mino z-VRPR-fmk 36h r2

source_name: Mino z-VRPR-fmk 36h


title: Mino z-VRPR-fmk 54h r1

source_name: Mino z-VRPR-fmk 54h


title: Mino z-VRPR-fmk 30h r2

source_name: Mino z-VRPR-fmk 30h


title: Rec DMSO 36h r1

source_name: Rec DMSO 36h


title: Mino z-VRPR-fmk 54h r2


title: Mino z-VRPR-fmk 24h r1

source_name: Mino z-VRPR-fmk 24h


title: Mino z-VRPR-fmk 24h r2


title: Mino z-VRPR-fmk 48h r1


title: Mino z-VRPR-fmk 30h r1


title: Mino DMSO 54h r2

source_name: Mino DMSO 54h


title: Mino DMSO 48h r2

source_name: Mino DMSO 48h


title: Mino z-VRPR-fmk 42h r1


title: Mino z-VRPR-fmk 36h r1


title: Mino DMSO 24h r2

source_name: Mino DMSO 24h


title: Mino DMSO 36h r1

source_name: Mino DMSO 36h


title: Mino DMSO 36h r2


title: Mino DMSO 30h r2

source_name: Mino DMSO 30h


title: Mino DMSO 30h r1


title: Mino DMSO 24h r1


title: Mino DMSO 42h r1

source_name: Mino DMSO 42h


title: Mino DMSO 48h r1


title: hiPSC_D1 III

description: replicate 2c

source_name: fibroblasts


title: Mino DMSO 42h r2


title: Mino DMSO 54h r1


title: CB innate 8SP

city: Gent

first: Bart

last: Vandekerckhove

address: MRB2 1e verdieping, De Pintelaan 185

department: Department of Clinical chemistry, Microbiology and immunology

country: Belgium

institute: Ghent University

description: pooled RNA from 3 newborns

hyb_protocol: A mixture of fragmented biotinylated cDNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix GeneChip Human Gene 2.0 ST Arrays followed by staining and washing in a GeneChip® fluidics station 450 (Affymetrix) according to the manufacturer’s procedures.

scan_protocol: To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix).

data_processing: Affymetrix' CEL-files were processed with RMA as implemented in the R/Bioconductor package XPS. The reported values are on log2-scale.

source_name: 8SP PD1+CD3low isolated from cord blood

label_protocol: RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Using the Affymetrix GeneChip® WT PLUS Reagent Kit, per sample, an amount of 45-100 ng of total RNA spiked with bacterial poly-A RNA positive controls (Affymetrix) was converted to double stranded cDNA in a reverse transcription reaction. Next the sample was converted and amplified to antisense cRNA in an in vitro transcription reaction which was subsequently converted to single stranded sense cDNA. Finally, samples were fragmented and labeled with biotin in a terminal labeling reaction according to the Affymetrix WT Terminal Labeling Kit.

growth_protocol: no culture performed, RNA was extracted immediately upon ex vivo cell sorting

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

tag: markers

value: CD8a+ CD4- CD3low PD-1+


title: CB conv 8SP

description: pooled RNA from 3 newborns

source_name: 8SP PD1-CD3high isolated from cord blood

treatment_protocol: no culture performed, RNA was extracted immediately upon ex vivo cell sorting

value: CD8a+ CD4- CD3high PD-1-


title: Thy TCRgd+

description: pooled RNA from donors aged 0-8 years old

source_name: TCRgd+ isolated from thymus

value: CD3+ TCRgd+ CD27+ CD1a-


title: Bone Marrow Diagnosis 22570

city: Newcastle upon Tyne

first: Lisa

middle: J

last: Russell

address: Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Level 6, Herschel Building, Brewery Lane

country: United Kingdom

institute: Newcastle University

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

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

data_processing:
The .CEL files were imported into the software named Genotyping Console and the genotypes, copy number and copy number variation data were calculated for each sample.
affymetrix-algorithm-name = birdseed-v2
affymetrix-algorithm-version = 2.4

source_name: Diagnosis_Bone Marrow

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from mononuclear cell preparations of leukemic blasts obtained from the bone marrow at diagnosis or remission using the Qiagen DNeasy kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer or Qubit.

tag: all sample id

value: Bone Marrow

value: Acute lymphoblastic leukaemia (ALL)

tag: disease stage

value: Diagnosis


title: Bone Marrow Remission 21245

source_name: Remission_Bone Marrow

tag: tissue

tag: cell type

value: Remission


title: Thy conv 8SP

source_name: 8SP PD1-CD10- isolated from thymus

value: TCRgd- CD8a+ CD4- CD10- PD-1- CD27+ CD1a-


title: Bone Marrow Diagnosis 21470


title: Bone Marrow Diagnosis 24390


title: Bone Marrow Remission 21470


title: Bone Marrow Diagnosis 20033


title: Thy innate 8SP

source_name: 8SP PD1+CD10+ isolated from thymus

value: TCRgd- CD8a+ CD4- CD10+ PD-1+ CD27+ CD1a-


title: Bone Marrow Diagnosis 20984


title: Bone Marrow Diagnosis 21245


title: Yeast with 24 h growth in simulated asbestos mine drainage media, rep4

city: Northfield

first: Heather

middle: Elizabeth

last: Driscoll

state: VT

address: 158 Harmon Drive

department: Biology

institute: Norwich University

description:
Treatment #4
This sample is of Saccharomyces cerevisiae (ATCC® 18824) grown in simulated asbestos mine drainage media for 24 hours. It is the fourth of four treatment replicates used in this experiment, each from separate cultures.

hyb_protocol: A hybridization mixture with controls was added to all seven samples. 90 ml of this mixture was injected into a Affymetrix Yeast Genome 2.0 Array and placed in the Affymetrix Genechip Hybridization Oven 640 at 45° C and 60 RPM for 18 hours overnight. A staining mixture containing streptavidin-phycoerytherin dye (SAPE) and biotinylated anti-phycoerytherin antibody (BAP) was added to amplify signal intensities. Arrays were stained and washed in the Affymetrix Genechip Fluidics Station 450 using the Mini_euk2V3_450 fluidics script.

scan_protocol: All arrays were scanned with the Affymetrix Genechip Scanner 3000 and raw analysis performed with Affymetrix Expression ConsoleTM software. The raw data images produced from the scanner were processed into .CEL files, which contained measure intensities for each probe on the array.

data_processing: The .CEL files were imported into Partek Genomics SuiteTM (GS) version 6.6 (Partek Inc., St. Louis, MO, USA, www.partek.com). Background correction, quantile normalization, log2 transformation, and probe set summarization were performed using default settings for the Robust Multichip Average (RMA) procedure (see Bolstad et al. Bioinformatics 19(2):185; Irizarry et al. Biostatistics 4(2):249; Nucleic Acids Res. 31:e15). After removal of Schizosaccharomyces pombe probe sets, also present on the Yeast GeneChip 2.0 array, a one-way Analysis of Variance (ANOVA) was performed on the remaining RMA-normalized S. cerevisiae-only probesets to assess differential expression.

organism: Saccharomyces cerevisiae

source_name: yeast grown in YPD media made with asbestos mine tailings laden water

label_protocol: Approximately 4 µg of cDNA generated with the Ovation Pico WTA System V2 kit (NuGEN Technologies Inc., San Carlos, CA, USA) was fragmented and labeled with the NuGEN Encore Biotin Module. Efficiency of the biotin labeling reaction was verified using NeutrAvidin (10 mg/ml) with a gel-shift assay.

growth_protocol: A 48-hour culture of S. cerevisiae grown in the control YDP media (see treatment protocol) was used as inoculum for seven independent sample cultures, four experimental and three control. Growth was monitored by measuring the absorbance, A, at 600nm (A600) and samples were inoculated into fresh control YDP media or simulated asbestos mine drainage media (A600 0.05). The cultures were incubated aerobically (225 RPM) at 30°C for 24 hours, at which point cell pellets were harvested from each sample (centrifugation at 4000x g [6800 rpm] of 1.5 ml of culture media) for RNA isolation. The growth curve was generated using the same parameters except a 24-hour culture was used as the inoculum and absorbance (A600) was measured at time points from 0.5 - 54 hours after inoculation.

extract_protocol: Total RNA isolation for all samples was performed as described in Tighe et al. 2011 (http://dx.doi.org/10.3791/2585).

treatment_protocol: Simulated asbestos mine-tailings run-off was generated by mixing 250 g of the VAG mine asbestos mine tailings with an equal volume (250 ml) of deionized water followed by exposure to three freeze-thaw cycles (-80oC) over ten days. The thaw cycle was performed at room temperature with gentle rocking. Water was removed from settled tailings after centrifugation and filtered through a 0.22 µm polycarbonate filter. Modified YPD growth media was prepared with either simulated asbestos mine drainage or deionized water as follows; 12.5 g YPD powder (Fisher Scientific catalog #BP2469), 10 g glucose, 500 ml water and autoclaved.

tag: strain

value: Strain NRRL Y-12632 (ATCC 18824)

tag: genotype

value: cir+

tag: ncbi accession


title: Yeast with 24 h growth in control media, rep2

description:
Control #2
This sample is of Saccharomyces cerevisiae (ATCC® 18824) grown in control media for 24 hours. It is the second of four control replicates used in this experiment, each from separate cultures.

source_name: yeast grown in YPD media made with distilled water


title: Bone Marrow Diagnosis 21572


title: Yeast with 24 h growth In simulated asbestos mine drainage media, rep3

description:
Treatment #3
This sample is of Saccharomyces cerevisiae (ATCC® 18824) grown in simulated asbestos mine drainage media for 24 hours. It is the third of four treatment replicates used in this experiment, each from separate cultures.


title: Yeast with 24 h growth in control media, rep3

description:
Control #3
This sample is of Saccharomyces cerevisiae (ATCC® 18824) grown in control media for 24 hours. It is the third of four control replicates used in this experiment, each from separate cultures.


title: Bone Marrow 19599_Remission


title: Bone Marrow Diagnosis 19599


title: Yeast with 24 h growth in simulated asbestos mine drainage media, rep2

description:
Treatment #2
This sample is of Saccharomyces cerevisiae (ATCC® 18824) grown in simulated asbestos mine drainage media for 24 hours. It is the second of four treatment replicates used in this experiment, each from separate cultures.


title: Yeast with 24 h growth in control media, rep1

description:
Control #1
This sample is of Saccharomyces cerevisiae (ATCC® 18824) grown in control media for 24 hours. It is the first of four control replicates used in this experiment, each from separate cultures.


title: Bone Marrow Diagnosis 21991


title: Bone Marrow Remission 22452


title: Bone Marrow Remission 11543


title: Bone Marrow Remission 21918


title: Bone Marrow Diagnosis 7311


title: Bone Marrow Diagnosis 2326


title: Bone Marrow Diagnosis 22452


title: Bone Marrow Remission 21991


title: Bone Marrow Remission 22570


title: Liver_TgC6hp55_rep2

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum Muenchen

description:
Gene expression data from liver derived from TgC6hp55 animal
Tg_liver_1

scan_protocol: Standard Illumina scanning protocol using HiScan

data_processing: The data were normalized using cubic spline normalization with Illumina Genomestudio 2011.1; background subtraction was performed

source_name: Liver derived from TgC6hp55 animal 30302665

growth_protocol: Animals per housed under spf conditions

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up with QIAGEN RNeasy midi kits in accordance with the prescribed protocol provided with the kit. Quality control was performed with gel electrophoreses.

tag: age

value: 21 weeks

tag: gender

value: male

value: liver


title: Liver_TgC6hp55_rep3

source_name: Liver derived from TgC6hp55 animal 30302666


title: Liver_TgC6hp55_rep4

source_name: Liver derived from TgC6hp55 animal 30302664


title: Liver_TgC6hp55_rep1

source_name: Liver derived from TgC6hp55 animal 30302662


title: Liver_control_rep4

description:
Gene expression data from liver derived from control animal
WT_liver_4

source_name: Liver derived from control animal 30302668

value: WT


title: Liver_control_rep3

description:
Gene expression data from liver derived from control animal
WT_liver_3

source_name: Liver derived from control animal 30302661


title: Liver_control_rep2

description:
Gene expression data from liver derived from control animal
WT_liver_2

source_name: Liver derived from control animal 30302671


title: Bone Marrow Diagnosis 21819


title: Liver_control_rep1

description:
Gene expression data from liver derived from control animal
WT_liver_1

source_name: Liver derived from control animal 30302670


title: HDAC11_3

city: Philadelphia

first: Wayne

middle: W

last: Hancock

state: PA

address: 916B ARC, 3615 Civic Ctr Blvd

institute: CHOP/UPenn

hyb_protocol: 10 microgram of labeled aRNA was fragmented, and 6.5 microgram of the fragmented aRNA was hybridized to the Affymetrix Mouse 430A_2 chips.  Hybridization conditions were 16hrs at 45C.

scan_protocol: The chips were washed using Fluidics protocol midiEuk2v3_450 on an Affymetrix GeneChip Fluidics Station 450 and scanned on an Affymetrix Genechip Scanner.

data_processing: Microarray experiments were performed using whole-mouse-genome oligoarrays (Mouse430a, Affymetrix). Array data were analyzed using MAYDAY version 2.14

source_name: Regulatory T-cells CD4+CD25+

label_protocol: 100ng of totalRNA was labeled using Ambion's MessageAmp Premier RNA Amplification Kit (PN:4383452)

extract_protocol: Total RNA was isolated using Rneasy (Quiagen). RNA integrity and quantity was analyzed using a DU640 (Beckman-Coulter).


title: HDAC11_1


title: HDAC11_2


title: WT_2

value: Wild type C57BL6


title: WT_3


title: Bone Marrow Remission 20638


title: 20mGyE4/ reference male mouse2

label_protocol: Oligonucleotide Array-Based CGH for Genomic DNA Analysis, protocol version 4.0.8

value: tail

source_name: reference male mouse2


title: Bone Marrow Diagnosis 20753


title: Yeast with 24 h growth in simulated asbestos mine drainage media, rep1

description:
Treatment #1
This sample is of Saccharomyces cerevisiae (ATCC® 18824) grown in simulated asbestos mine drainage media for 24 hours. It is the first of four treatment replicates used in this experiment, each from separate cultures.


title: 0GyZ4/ reference male mouse6

source_name: reference male mouse6


title: WT_1


title: reference male mouse2/ 20mGyE4


title: Bone Marrow Remission 20753


title: 20mGyE3/ reference male mouse2


title: Bone Marrow Remission 21567


title: reference male mouse2/ 20mGyE5


title: reference male mouse6/ 0GyZ5


title: Bone Marrow Diagnosis 20638

source_name: Diagnosis_Bone Marrow


title: reference male mouse2/ 20mGyE3


title: reference male mouse2/ 20mGyE2


title: 0GyZ2/ reference male mouse6


title: 0GyZ5/ reference male mouse6


title: Bone Marrow Diagnosis 11403


title: Bone Marrow Diagnosis 11564


title: 20mGyE1/ reference male mouse2


title: Bone Marrow Diagnosis 11706


title: Bone Marrow Remission 11706

source_name: Remission_Bone Marrow


title: reference male mouse6/ 0GyZ2


title: Bone Marrow Diagnosis 11200


title: reference male mouse6/ 0GyZ1


title: reference male mouse2/ 20mGyE1


title: 20mGyE5/ reference male mouse2


title: 0GyZ1/ reference male mouse6


title: 20mGyE2/ reference male mouse2


title: Bone Marrow Remission 9534


title: 0GyZF/ reference male mouse6


title: 20mGyEF/ reference male mouse2


title: reference male mouse6/ 0GyZ4


title: Bone Marrow Diagnosis 10924


title: Bone Marrow Diagnosis 5674


title: Bone Marrow Remission 11538


title: Bone Marrow Diagnosis 9534


title: reference male mouse2/ 20mGyEM


title: reference male mouse6/ 0GyZ3


title: 20mGyC5/ reference male mouse2


title: Bone Marrow Diagnosis 11538


title: reference male mouse6/ 0GyZM


title: 20mGyC3/ reference male mouse2


title: reference male mouse2/ 20mGyC5


title: reference male mouse2/ 20mGyC4


title: 20mGyC4/ reference male mouse2


title: reference male mouse6/ 0GyX6


title: reference male mouse6/ 0GyX5


title: 20mGyEM/ reference male mouse2


title: 0GyX4/ reference male mouse6


title: Bone Marrow Diagnosis 11543


title: 0GyZ3/ reference male mouse6


title: PB_FA_FA531

description:
FA_Illumina_HumanOmniExpressExome-8-v1.2.txt
FA531

label: C-Bio and A-DNP

source_name: Peripheral Blood

tag: disease state

value: Fanconi Anemia

value: Peripheral Blood

tag: age at sampling

tag: cancer diagnosis

value: No

value: Alive


title: reference male mouse2/ 20mGyC2


title: 20mGyC2/ reference male mouse2


title: 0GyX3/ reference male mouse6


title: reference male mouse2/ 20mGyC3


title: reference male mouse6/ 0GyZF


title: reference male mouse2/ 20mGyEF


title: reference male mouse6/ 0GyX3


title: 0GyX2/ reference male mouse6


title: 0GyZM/ reference male mouse6


title: 20mGyC1/ reference male mouse2


title: reference male mouse2/ 20mGyC1


title: reference male mouse6/ 0GyX4


title: reference male mouse6/ 0GyX2


title: 20mGyCF/ reference male mouse2


title: reference male mouse2/ 20mGyCF


title: Bone Marrow Diagnosis 21918

value: Bone Marrow

value: Acute lymphoblastic leukaemia (ALL)


title: 0GyX1/ reference male mouse6


title: Bone Marrow Remission 21819

value: Remission


title: reference male mouse6/ 0GyX1


title: 0GyXF/ reference male mouse6


title: 20mGyCM/ reference male mouse2


title: 0GyXM/ reference male mouse6


title: H9+Dox_xenograft_2

description:
Gene expression data from xenograft of PSCs injected in NSG mouse
Fresal_018

hyb_protocol: Performed by MAD: Dutch Genomics Service & Support Provider

data_processing: Data was normalized using the rma function (Affy) in R

source_name: H9 + Doxycycline xenograft

label_protocol: Affymetrix 3' IVT-Express Labeling Kit (#901229). Performed at GenomeScan B.V. in Leiden, the Netherlands

growth_protocol: 8-10 weeks old male NSG mice (NOD.Cg-Prkdcscid IL2rgtm1Wjl/Szj, Charles River) were used for injections. 1x10^6 cells were injected subcutaneously in the flank region. Tumor growth was monitored weekly by palpation and mice were sacrificed when tumors reached a volume ≤ 2cm^3. Whole tumors were used for analysis.

treatment_protocol: LU07+Dox and H9+Dox: Cells were treated with 2µg/ml Doxycycline three days prior to injection. Drinking water of the mice contained 2 mg/ml Doxycycline and 10mg/ml Sucrose one week prior to and after injections. Drinking water was changed every 2nd day until mice were sacrificed. H9, H9Hyb, LU07 and EC: Drinking water of the mice contained 10mg/ml Sucrose one week prior to and after injections. Drinking water was changed every 2nd day until mice were sacrificed.

tag: host strain

tag: injected with

value: normal humaninduced  embryonic stem cell line (H9+Dox)

tag: material

value: Xenograft


title: 20mGyA5/ reference male mouse2


title: 20mGyA6/ reference male mouse2


title: reference male mouse2/ 20mGyCM


title: H9_xenograft_2

description:
Gene expression data from xenograft of PSCs injected in NSG mouse
Fresal_017

scan_protocol: Performed by MAD: Dutch Genomics Service & Support Provider

source_name: H9 xenograft

value: 8-10 weeks old male NSG mice (NOD.Cg-Prkdcscid IL2rgtm1Wjl/Szj, Charles River)

value: normal human embryonic stem cell line (H9)


title: reference male mouse2/ 20mGyA6


title: LU07_xenograft_2

description:
Gene expression data from xenograft of PSCs injected in NSG mouse
Fresal_016

source_name: LUMC0007iCTR01 xenograft

value: normal human induced pluripotent stem cell line (LU07)


title: EC_xenograft_1

description:
Gene expression data from xenograft of ECs injected in NSG mouse
FreSal_015

source_name: EC2102ep xenograft

value: human embryonal carcinoma cell line (EC)


title: reference male mouse6/ 0GyXF


title: 0GyW6/ reference male mouse6


title: H9Hyb_xenograft_2

description:
Gene expression data from xenograft of PSCs injected in NSG mouse
Fresal_019

source_name: H9 Hybrid xenograft

value: human embryonic stem cell line with a mesendodermal differentiation bias (H9Hyb)


title: 0GyX5/ reference male mouse6


title: reference male mouse2/ 20mGyA5


title: 0GyX6/ reference male mouse6


title: reference male mouse2/ 20mGyA4


title: reference male mouse6/ 0GyXM


title: reference male mouse6/ 0GyW6


title: 20mGyA3/ reference male mouse2


title: H9Hyb_xenograft_1

description:
Gene expression data from xenograft of PSCs injected in NSG mouse
FreSal_012


title: reference male mouse6/ 0GyW5


title: 20mGyA4/ reference male mouse2


title: 20mGyA2/ reference male mouse2


title: reference male mouse2/ 20mGyA3


title: reference male mouse6/ 0GyW4


title: 0GyW4/ reference male mouse6


title: 0GyW3/ reference male mouse6


title: 0GyW5/ reference male mouse6


title: reference male mouse2/ 20mGyA2


title: LU07+Dox_xenograft_3

description:
Gene expression data from xenograft of PSCs injected in NSG mouse
FreSal_006

source_name: LUMC0007iCTR01 + Doxycycline xenograft

value: human induced pluripotent stem cell line with reactivated transgenes (LU07+Dox)


title: H9_xenograft_1

description:
Gene expression data from xenograft of PSCs injected in NSG mouse
FreSal_007


title: H9+Dox_xenograft_1

description:
Gene expression data from xenograft of PSCs injected in NSG mouse
FreSal_010


title: LU07+Dox_xenograft_1

description:
Gene expression data from xenograft of PSCs injected in NSG mouse
FreSal_004


title: reference male mouse6/ 0GyW3


title: LU07+Dox_xenograft_2

description:
Gene expression data from xenograft of PSCs injected in NSG mouse
FreSal_005


title: 0GyW2/ reference male mouse6


title: 20mGyA1/ reference male mouse2


title: 0GyW1/ reference male mouse6


title: reference male mouse2/ 20mGyAF


title: LU07_xenograft_1

description:
Gene expression data from xenograft of PSCs injected in NSG mouse
FreSal_001


title: reference male mouse6/ 0GyW1


title: reference male mouse6/ 0GyWF


title: reference male mouse2/ 20mGyA1


title: 20mGyAF/ reference male mouse2


title: reference male mouse5/ 0GyR6

source_name: reference male mouse5


title: reference male mouse6/ 0GyW2


title: reference male mouse5/ 0GyV7


title: reference male mouse6/ 0GyWM


title: 0GyWM/ reference male mouse6


title: J82_siRNA_NC_72hr_rep1

city: shanghai

first: Shuxiong

last: Zeng

state: shanghai

address: 168 changhai road

country: China

institute: Changhai Hospital

description: Gene expression after 72hr control siRNA treatment

hyb_protocol: The Labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60°C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide.

scan_protocol: The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C)

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, genes that at least 3 out of 9 samples have flags in Detected (“All Targets Value”) were chosen for further data analysis. Differentially expressed genes with statistical significance between the two groups were identified through Volcano Plot filtering. Differentially expressed genes between the two samples were identified through Fold Change filtering. Hierarchical Clustering was performed using the R scripts. GO analysis and Pathway analysis were performed in the standard enrichment computation method.

source_name: J82, 72hr, siRNA-NC, replicate 1

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology). Briefly, total RNA from each sample was linearly amplified and labeled with Cy3-UTP

growth_protocol: Cells were cultured in Roswell Park Memorial Institute 1640 medium (Gibco®) supplemented with 10% fetal bovine serum and 100μg/ ml penicillin-streptomycin

extract_protocol: Total RNA was extracted using TRIzol reagent (Invitrogen) according to the manufacturer’s instructions

treatment_protocol: Cells were cultured to 70-80% confluence and transfected with siRNA using Lipofectamine RNAiMAX (Invitrogen), according to manufacturer’s instructions.

value: bladder cancer cell lines

tag: cell line


title: 0GyR6/ reference male mouse5

value: tail


title: 0GyR5/ reference male mouse5


title: reference male mouse2/ 20mGyAM


title: 20mGyAM/ reference male mouse2


title: 0GyV7/ reference male mouse5


title: reference male mouse5/ 0GyV6


title: 0GyWF/ reference male mouse6


title: Bone Marrow Diagnosis 21567

value: Diagnosis


title: J82_siRNA_NC_48hr_rep1

description: Gene expression after 48hr control siRNA treatment

source_name: J82, 48hr, siRNA-NC, replicate 1


title: reference male mouse5/ 0GyR4


title: 0GyV5/ reference male mouse5


title: reference male mouse5/ 0GyV5


title: 0GyR4/ reference male mouse5


title: J82_siRNA_NC_24hr_rep1

description: Gene expression after 24hr control siRNA treatment

source_name: J82, 24hr, siRNA-NC, replicate 1


title: J82_siRNA_ANLN_72hr_rep1

description: Gene expression after 72hr siRNA againt ANLN treatment

source_name: J82, 72hr, siRNA-ANLN, replicate 1


title: 0GyR3/ reference male mouse5


title: J82_siRNA_ANLN_48hr_rep1

description: Gene expression after 48hr siRNA againt ANLN treatment

source_name: J82, 48hr, siRNA-ANLN, replicate 1


title: reference male mouse5/ 0GyV4


title: 0GyV3/ reference male mouse5


title: J82_siRNA_ANLN_24hr_rep1

description: Gene expression after 24hr siRNA againt ANLN treatment

source_name: J82, 24hr, siRNA-ANLN, replicate 1


title: reference male mouse5/ 0GyV3


title: 0GyR2/ reference male mouse5


title: reference male mouse5/ 0GyR3


title: reference male mouse5/ 0GyV2


title: PB_FA_FA94

value: Fanconi Anemia

value: Peripheral Blood

tag: age at cancer diagnosis

tag: evolution

value: Exitus

tag: age of exitus


title: 0GyV1/ reference male mouse5

tag: tissue


title: 0GyV6/ reference male mouse5


title: 20mGyD5/ reference male mouse2

source_name: reference male mouse2


title: reference male mouse5/ 0GyR5


title: PB_FA_FA78

value: No


title: reference male mouse2/ 20mGyD5


title: 20mGyD4/ reference male mouse2


title: reference male mouse2/ 20mGyD4


title: reference male mouse2/ 20mGyD3


title: 20mGyD2/ reference male mouse2


title: reference male mouse5/ 0GyR2


title: 0GyR1/ reference male mouse5


title: reference male mouse5/ 0GyR1


title: 0GyRF/ reference male mouse5


title: PB_FA_FA681

value: Alive


title: PB_FA_FA664


title: PB_FA_FA663

value: Yes


title: reference male mouse5/ 0GyRF


title: 0GyRM/ reference male mouse5


title: reference male mouse5/ 0GyVF


title: PB_FA_FA652


title: reference male mouse5/ 0GyRM


title: 0GyVM/ reference male mouse5


title: reference male mouse5/ 0GyV1


title: 0GyVF/ reference male mouse5


title: 20mGyDF/ reference male mouse2


title: 0GyQ7/ reference male mouse3

source_name: reference male mouse3


title: reference male mouse5/ 0GyVM


title: 20mGyD1/ reference male mouse2


title: PB_FA_FA572


title: 0GyQ8/ reference male mouse3


title: 20mGyD3/ reference male mouse2


title: reference male mouse3/ 0GyQ8


title: reference male mouse3/ 0GyQ7


title: reference male mouse2/ 20mGyD1


title: reference male mouse2/ 20mGyD2


title: PB_FA_FA568


title: PB_FA_FA554


title: PB_FA_FA342


title: PB_FA_FA294


title: PB_FA_FA158


title: 20mGyF6/ reference male mouse2


title: reference male mouse2/ 20mGyDF


title: reference male mouse2/ 20mGyF6


title: 0GyV4/ reference male mouse5


title: reference male mouse3/ 0GyQ6


title: reference male mouse2/ 20mGyDM


title: 0GyQ5/ reference male mouse3


title: 20mGyF5/ reference male mouse2


title: 0GyQ6/ reference male mouse3


title: 20mGyDM/ reference male mouse2


title: reference male mouse2/ 20mGyF5


title: PB_FA_FA157


title: 20mGyF4/ reference male mouse2


title: 20mGyB5/ reference male mouse2


title: PB_FA_FA125


title: 0GyQ3/ reference male mouse3


title: 20mGyB3/ reference male mouse2


title: 0GyV2/ reference male mouse5


title: reference male mouse2/ 20mGyB5


title: reference male mouse2/ 20mGyB4


title: 20mGyB4/ reference male mouse2


title: 0GyQ4/ reference male mouse3


title: PB_FA_FA113

value: Missing


title: reference male mouse3/ 0GyQ3


title: reference male mouse2/ 20mGyF4


title: reference male mouse3/ 0GyQ5


title: reference male mouse2/ 20mGyB3


title: 20mGyF3/ reference male mouse2


title: reference male mouse3/ 0GyQ4


title: 20mGyF2/ reference male mouse2


title: Slide US45102948_256525610001_S01.2

city: STOCKHOLM

first: Sulman

last: Shafeeq

address: nobel vag 16

department: MTC

country: Sweden

institute: Karolinska Institutet

description: Sample 2

hyb_protocol: The protocol was performed as described in Kloosterman et al., 2006 and Shafeeq et al., 2011.

scan_protocol: Scanning was done using the Genepix 4200AL laser scanner.

data_processing: Dual-channel array images were analyzed with Genepix 6.  Spots were screened visually to identify those of low quality. Slide data were processed with MicroPreP software. Prior to analysis, automatically and manually flagged spots and spots with very low background subtracted signal intensity (5% of the weakest spots [sum of Cy3 and Cy5 net signals]) were filtered out of all data sets. Net signal intensities were calculated by grid-based background subtraction. A grid-based Lowess transformation was performed for slide normalization, negative and empty values were removed, and outliers were removed by the deviation test. Expression ratios  were calculated. Further analysis was performed with a Cyber-T Student T-test for paired data.

organism: Streptococcus pneumoniae D39

source_name: F550 Mean

label_protocol: Total RNA was incubated for 16 h at 42°C in the presence of 400 U Superscript III RNase H reverse transcriptase (Invitrogen), 0.2 mM aminoallyl dUTP (Amersham), 0.5 mM dATP, 0.5 mM dCTP, 0.5 mM dGTP, 0.3 mM dTTP, and 3.2 g random nonamers. The synthesized cDNA was then labeled by coupling either Cy3 or Cy5 to the dUTP aminoallyl reactive group (CyScribe postlabeling kit; Amersham Biosciences) and was purified using a GFX PCR, DNA, and gel band purification kit (Amersham Biosciences).

growth_protocol: Cells were grown in CDM medium with 0 mM and 10mM naicin and harvested at respective mid-exponential phase.

extract_protocol: RNA was isolated and purified using the High Pure RNA isolation kit (Roche diagnostics) as described (Kloosterman et al., 2006). Contaminating genomic DNA was removed by treatment with RNase-free DNase I (Roche diagnostics). RNA was isolated from three replicate cultures.

tag: treatment

value: 0 mM Naicin

source_name: F650 Mean

value: 10 mM Naicin


title: reference male mouse2/ 20mGyF3

tag: strain


title: Slide US45102948_256525610001_S01.1

description: Sample 1


title: reference male mouse2/ 20mGyF1


title: Slide US45102948_256525610006_S01.4

description: Sample 2

growth_protocol: Cells were grown in complete CDM medium and harvested at  OD600 of 0.3.

tag: genotype/variation

value: wild-type

value: NiaR mutant


title: Slide US45102948_256525610006_S01.3 (2)

description: Sample 1


title: 0GyQ1/ reference male mouse3


title: 20mGyB2/ reference male mouse2


title: reference male mouse3/ 0GyQ2


title: 20mGyF1/ reference male mouse2


title: reference male mouse2/ 20mGyB2


title: 20mGyBF/ reference male mouse2


title: 0GyQ2/ reference male mouse3


title: 20mGyFF/ reference male mouse2


title: reference male mouse2/ 20mGyB1


title: reference male mouse3/ 0GyQM


title: reference male mouse2/ 20mGyFF


title: reference male mouse2/ 20mGyF2


title: 20mGyB1/ reference male mouse2


title: reference male mouse3/ 0GyQF


title: 0GyQF/ reference male mouse3


title: 0GyQM/ reference male mouse3


title: 20mGyFM/ reference male mouse2


title: reference male mouse2/ 20mGyBF


title: reference male mouse3/ 0GyQ1


title: PB_FA_FA110

source_name: Peripheral Blood


title: rt-PA treatment 1

status: Public on Feb 23 2017

city: guangzhou

first: Zhen

last: Deng

state: Guangdong

address: Nanfang Hospital,  #1838 Guangzhou Da dao North

department: Neurology

institute: southern medical university

description:
with thrombolysis treatment
Each pool sample contained 5 plasma samples.

hyb_protocol: After stopping the labeling procedure, the Hy3TM-labeled samples were hybridized on the miRCURYTM LNA Array (v.18.0) (Exiqon) according to array manual. The total 25 μL mixture from Hy3TM-labeled samples with 25 μL hybridization buffer were first denatured for 2 min at 95°C, incubated on ice for 2 min and then hybridized to the microarray for 16–20 h at 56°C in a 12-Bay Hybridization Systems (Hybridization System - Nimblegen Systems, Inc., Madison, WI, USA), which provides an active mixing action and constant incubation temperature to improve hybridization uniformity and enhance signal. Following hybridization, the slides were achieved, washed several times using Wash buffer kit (Exiqon), and finally dried by centrifugation for 5 min at 400 rpm.

scan_protocol: The slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction.

data_processing: Replicated miRNAs were averaged and miRNAs that intensities>=30 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. After normalization, significant differentially expressed miRNAs were identified through Volcano Plot filtering.The threshold we used to screen Up or Down regulated miRNAs is Fold Change>=2.0 and P-value<=0.05. Hierarchical clustering was performed using MEV software (v4.6, TIGR).

source_name: plasma

label_protocol: After RNA isolation from the samples, the miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling. One microgram of each sample was 3'-end-labeled with Hy3TM fluorescent label, using T4 RNA ligase by the following procedure: RNA in 2.0 μL of water was combined with 1.0 μL of CIP buffer and CIP (Exiqon). The mixture was incubated for 30 min at 37°C, and was terminated by incubation for 5 min at 95°C. Then 3.0 μL of labeling buffer, 1.5 μL of fluorescent label (Hy3TM), 2.0 μL of DMSO, 2.0 μL of labeling enzyme were added into the mixture. The labeling reaction was incubated for 1 h at 16°C, and terminated by incubation for 15 min at 65°C

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and miRNeasy mini kit (QIAGEN) according to manufacturer’s instructions, which efficiently recovered all RNA species, including miRNAs. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis.

value: acute ischemic stroke patients

value: blood


title: reference male mouse2/ 20mGyFM

data_processing: Agilent Genomic Workbench Software (v 7.0.) was used.


title: rt-PA treatment 2


title: health control 1

description: Each pool sample contained 5 plasma samples.

value: healthy control


title: stroke patient 3

description:
without thrombolysis treatment
Each pool sample contained 5 plasma samples.


title: health control 2


title: reference male mouse2/ 20mGyBM


title: health control 3


title: stroke patient 1


title: JSTHP1LPS4hRep2

city: Bethesda

first: Timothy

middle: G

last: Myers

state: MD

address: 50 South Drive, Room 5509

department: Research Technologies Branch

institute: National Institute of Allergy and Infectious Diseases

description: THP-1 cells

scan_protocol: Standard Illumina scanning protocol with Illumina HiScan-SQ

data_processing: Signal data was extracted from the image files with the Gene Expression module (v. 1.9.0) of the GenomeStudio software (v. 2011.1) from Illumina, Inc. Signal intensities were converted to log 2 scale. Probes that didn't show detection p-value < 0.1 in at least 2 arrays were removed from the dataset.  After filtering probes, quantile normalization was applied across all arrays.

source_name: THP-1 cell line

label_protocol: Illumina TotalPrep RNA Amplification Kit (Ambion)

growth_protocol: THP1  cells were maintained in RPMI, 10%FBS, 10mM Hepes, and 2mM glutamine by standard procedures.

extract_protocol: RNA was purified by Qiagen RNAeasy kit

treatment_protocol: THP1 B5 cells were treated with either 0 or 10 ng/ml LPS for 4 hr. LPS was from Alexis Biochemicals, Salmonella minnesota R595 TLRgrade, ALX-581-008-L002.

tag: experimental replicate

value: batch 2

tag: cell type

value: Macrophage


title: JSTHP1LPS04Rep3

description: THP-1 cells

value: batch 3


title: stroke patient 2


title: JSTHP1LPS00Rep3

description: THP-1 cells

value: Zero


title: JSTHP1LPS4hRep1

description: THP-1 cells

value: batch 1


title: JSTHP1LPS0hRep1

description: THP-1 cells


title: SAMPLE_306_CD8 RNA

city: Tartu

first: Pärt

last: Peterson

address: Ravila 19

country: Estonia

institute: University of Tartu

data_processing: Preprocessing and quality control of the data was done using R and the Bioconductor packages lumi (Du et al. 2008) and arrayQualityMetrics (Kauffmann et al. 2009). Good quality samples were retained and a sample was excluded if 1) it was considered to be an outlier based on at least two criteria (array intensity distribution and/or between array comparison and/or individual array quality) in microarray quality metrics reports; 2) the detection rate (using detection P-value cut-off 0.05) was less than 10% for CD4+ and CD8+ samples or 20% for whole blood samples; 3) it was an outlier based on XIST gene and Y chromosome expression patterns; 4) it was possibly contaminated or mixed up sample (defined by MixupMapper (Westra et al. 2011)). Then, gene expression data was quantile normalized to the median distribution and log2-transformed. Then separately for both cell types, probe and sample means were centered to zero, correction for possible population structure in the gene expression data was done by removing four multi-dimensional scaling components (MDS components obtained from genotype data using PLINK) using linear regression. Therefore, principal component analysis (PCA) was conducted on sample correlation matrix to correct for environmental and experimental variation. Optimal number of PC to remove were determined based on the maximum number of cis-eQTLs (described in Westra et al. 2013). Only PCs that were not affected by genetic variants (did not show significance at the FDR threshold of 0.0) were used to correct the gene expression data to minimize the amount of genetic variation removed. Optimal number of PCs to remove was 30 in CD4+, 45 in CD8+ and 20 in whole blood datasets. Illumina HT12-v4 BeadChip probe sequences were mapped to the human genome build GRCh37 using TopHat (Trapnell et al. 2009). Transcript and genome information was retrieved from Ensembl for genome assembly GRCh37.p13. Expression probes that mapped uniquely to the reference with no mismatches were retained. All expression probes mapping to either the X or Y chromosomes were removed. A total of 38,839 expression probes remained for analyses.

source_name: CD8+ T cells

label_protocol: The RNA was labeled and amplified using the TargetAmp Nano Labeling Kit for Illumina Expression BeadChip (Epicentre Biotechnologies) with SuperScript III Reverse Transcriptase (Life Technologies) according to the manufacturer's protocol, followed by purification with the RNeasy MinElute Cleanup Kit (Qiagen). RNA quality was assessed after extraction and after labelling using an Agilent 2100 Bioanalyzer and Agilent RNA 6000 Nano Kit (all from Agilent Technologies). The labelled RNA samples were hybridized to HumanHT12-v4 Expression BeadChips (Illumina) according to the manufacturer’s instructions.

extract_protocol: Peripheral blood mononuclear cells (PBMC) were extracted using Ficoll-Paque (GE Healthcare) gradient centrifugation. CD4+ T cells and CD8+ T cells were extracted from the PBMCs by consecutive positive separation using microbeads (CD4+ #130-045-101; CD8+ #130-045-201) and AutoMACS technology (Miltenyi Biotec) according to the manufacturer's protocol. The purity of the extracted CD4+ T cells was 91–95% and for CD8+ T cells 88–91%. All cell populations were collected and stored as cell pellets in a −80 °C freezer. RNA was extracted from the purified T cells using the miRNeasy Mini Kit combined with a recommended RNase-free DNase I treatment (both from Qiagen) according to the manufacturer’s protocol. RNA from whole blood was purified using the MagMAX™ for Stabilized Blood Tubes RNA Isolation Kit. RNA was concentrated using the Heraeus vacuum centrifugation system without heating.

tag: age

tag: gender

value: Male

value: C

value: CD8+ T cells


title: SAMPLE_300_CD4 RNA

source_name: CD4+ T cells

value: I

value: CD4+ T cells


title: SAMPLE_304_CD8 RNA

value: Female

value: D


title: SAMPLE_305_CD4 RNA

value: F


title: SAMPLE_300 RNA

source_name: Peripheral blood

value: B

value: Peripheral blood


title: JSTHP1LPS0hRep2

description: THP-1 cells


title: SAMPLE_298_CD4 RNA


title: SAMPLE_306_CD4 RNA

value: A


title: SAMPLE_302_CD8 RNA


title: SAMPLE_301_CD8 RNA

value: H


title: SAMPLE_305_CD8 RNA


title: SAMPLE_304 RNA


title: SAMPLE_303_CD8 RNA

value: K


title: SAMPLE_300_CD8 RNA


title: SAMPLE_301_CD4 RNA


title: rt-PA treatment 3

tag: disease state

value: acute ischemic stroke patients

value: blood


title: SAMPLE_297_CD4 RNA


title: SAMPLE_303_CD4 RNA


title: SAMPLE_297_CD8 RNA


title: SAMPLE_296 RNA


title: SAMPLE_299_CD4 RNA

value: G


title: SAMPLE_302_CD4 RNA


title: SAMPLE_304_CD4 RNA


title: SAMPLE_294_CD4 RNA


title: SAMPLE_293_CD8 RNA


title: SAMPLE_295_CD4 RNA


title: SAMPLE_296_CD4 RNA


title: SAMPLE_294_CD8 RNA


title: SAMPLE_295_CD8 RNA


title: SAMPLE_296_CD8 RNA


title: SAMPLE_292_CD4 RNA


title: SAMPLE_290_CD4 RNA


title: SAMPLE_291_CD8 RNA


title: SAMPLE_291_CD4 RNA


title: SAMPLE_292_CD8 RNA


title: SAMPLE_293_CD4 RNA


title: SAMPLE_287_CD8 RNA


title: SAMPLE_289_CD4 RNA

value: E


title: SAMPLE_288_CD8 RNA

value: Male


title: SAMPLE_293 RNA


title: SAMPLE_290_CD8 RNA


title: SAMPLE_287_CD4 RNA


title: SAMPLE_286_CD8 RNA


title: SAMPLE_283_CD8 RNA


title: SAMPLE_285_CD4 RNA


title: SAMPLE_286_CD4 RNA


title: SAMPLE_282_CD8 RNA

value: L


title: SAMPLE_288_CD4 RNA


title: SAMPLE_289_CD8 RNA

value: CD8+ T cells


title: SAMPLE_284_CD4 RNA


title: SAMPLE_285_CD8 RNA


title: SAMPLE_283_CD4 RNA


title: SAMPLE_281_CD4 RNA


title: SAMPLE_280_CD4 RNA

value: I


title: SAMPLE_282_CD4 RNA

value: J

value: CD4+ T cells


title: SAMPLE_277_CD8 RNA

value: Female


title: SAMPLE_275_CD8 RNA


title: SAMPLE_279_CD4 RNA


title: SAMPLE_272_CD8 RNA


title: SAMPLE_278_CD4 RNA


title: SAMPLE_280_CD8 RNA


title: SAMPLE_276_CD8 RNA


title: SAMPLE_277_CD4 RNA

value: D


title: SAMPLE_279_CD8 RNA


title: SAMPLE_278_CD8 RNA

value: B


title: SAMPLE_275_CD4 RNA


title: SAMPLE_272_CD4 RNA


title: SAMPLE_274_CD4 RNA


title: SAMPLE_273_CD4 RNA


title: SAMPLE_273_CD8 RNA


title: SAMPLE_276_CD4 RNA


title: SAMPLE_270_CD8 RNA


title: SAMPLE_267_CD8 RNA


title: SAMPLE_270_CD4 RNA


title: SAMPLE_271_CD4 RNA


title: SAMPLE_269_CD4 RNA

value: F


title: SAMPLE_268_CD4 RNA


title: SAMPLE_269_CD8 RNA


title: SAMPLE_268_CD8 RNA


title: SAMPLE_267_CD4 RNA


title: SAMPLE_264_CD4 RNA


title: SAMPLE_265_CD4 RNA


title: SAMPLE_266_CD8 RNA


title: SAMPLE_263_CD8 RNA


title: SAMPLE_262_CD8 RNA

value: C


title: SAMPLE_262_CD4 RNA

value: A


title: SAMPLE_265_CD8 RNA


title: SAMPLE_264_CD8 RNA


title: SAMPLE_263_CD4 RNA


title: SAMPLE_260_CD8 RNA


title: SAMPLE_261_CD8 RNA


title: SAMPLE_260_CD4 RNA


title: SAMPLE_261_CD4 RNA


title: SAMPLE_259_CD4 RNA


title: SAMPLE_258_CD8 RNA


title: SAMPLE_256_CD4 RNA


title: SAMPLE_259_CD8 RNA


title: SAMPLE_252_CD4 RNA


title: SAMPLE_256_CD8 RNA


title: SAMPLE_254_CD8 RNA


title: SAMPLE_257_CD8 RNA

value: H


title: SAMPLE_258_CD4 RNA


title: SAMPLE_253_CD8 RNA


title: SAMPLE_254_CD4 RNA


title: SAMPLE_253_CD4 RNA


title: SAMPLE_251_CD8 RNA


title: SAMPLE_255_CD4 RNA


title: SAMPLE_257_CD4 RNA


title: 20mGyBM/ reference male mouse2

city: Rokkasho-mura,Kamikita-gun,

first: Keiji

last: OGURA

address: Takahoko, Hacchasawa,

institute: Institute for Environmental Science

scan_protocol: Scanned on an Agilent G2565BA scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.1.1).

extract_protocol: PI-50a (Kurabo Industries LTD.) tissue DNA extraction protocol.

value: tail


title: SAMPLE_251_CD4 RNA


title: SAMPLE_250_CD4 RNA


title: SAMPLE_250_CD8 RNA

value: K


title: SAMPLE_246_CD4 RNA


title: SAMPLE_247_CD4 RNA


title: SAMPLE_248_CD8 RNA


title: SAMPLE_248_CD4 RNA

value: G


title: SAMPLE_246_CD8 RNA


title: SAMPLE_245_CD4 RNA


title: SAMPLE_249_CD4 RNA

value: E


title: SAMPLE_242_CD8 RNA

value: Male


title: SAMPLE_243_CD8 RNA


title: SAMPLE_237_CD8 RNA


title: SAMPLE_243_CD4 RNA


title: SAMPLE_238_CD8 RNA


title: SAMPLE_244_CD8 RNA


title: SAMPLE_249_CD8 RNA


title: SAMPLE_245_CD8 RNA


title: SAMPLE_244_CD4 RNA


title: SAMPLE_240_CD4 RNA


title: SAMPLE_239_CD4 RNA


title: SAMPLE_237_CD4 RNA


title: SAMPLE_235_CD4 RNA


title: SAMPLE_242_CD4 RNA


title: SAMPLE_236_CD8 RNA


title: SAMPLE_241_CD8 RNA


title: SAMPLE_238_CD4 RNA


title: SAMPLE_236_CD4 RNA


title: SAMPLE_240_CD8 RNA


title: SAMPLE_239_CD8 RNA


title: SAMPLE_241_CD4 RNA


title: SAMPLE_271_CD8 RNA


title: SAMPLE_235_CD8 RNA


title: SAMPLE_233_CD8 RNA


title: SAMPLE_234_CD8 RNA


title: SAMPLE_231_CD8 RNA


title: SAMPLE_228_CD4 RNA


title: SAMPLE_234_CD4 RNA


title: SAMPLE_233_CD4 RNA


title: SAMPLE_230_CD8 RNA


title: SAMPLE_229_CD8 RNA

value: L


title: SAMPLE_228_CD8 RNA

value: CD8+ T cells


title: SAMPLE_227_CD4 RNA


title: SAMPLE_232_CD8 RNA


title: SAMPLE_232_CD4 RNA


title: SAMPLE_223_CD8 RNA


title: SAMPLE_226_CD8 RNA


title: SAMPLE_227_CD8 RNA


title: SAMPLE_230_CD4 RNA


title: SAMPLE_231_CD4 RNA


title: SAMPLE_225_CD4 RNA


title: SAMPLE_224_CD8 RNA


title: SAMPLE_229_CD4 RNA


title: SAMPLE_221_CD4 RNA


title: SAMPLE_222_CD4 RNA


title: SAMPLE_224_CD4 RNA


title: SAMPLE_222_CD8 RNA


title: SAMPLE_221_CD8 RNA


title: SAMPLE_225_CD8 RNA


title: SAMPLE_223_CD4 RNA


title: SAMPLE_226_CD4 RNA


title: SAMPLE_217_CD8 RNA


title: SAMPLE_220_CD8 RNA


title: SAMPLE_220_CD4 RNA


title: SAMPLE_219_CD4 RNA


title: SAMPLE_216_CD8 RNA


title: SAMPLE_218_CD4 RNA


title: SAMPLE_219_CD8 RNA


title: SAMPLE_217_CD4 RNA


title: SAMPLE_215_CD4 RNA


title: SAMPLE_208_CD4 RNA


title: SAMPLE_216_CD4 RNA


title: SAMPLE_214_CD4 RNA


title: SAMPLE_208_CD8 RNA


title: SAMPLE_211_CD4 RNA


title: SAMPLE_210_CD4 RNA


title: SAMPLE_212_CD4 RNA


title: SAMPLE_213_CD8 RNA


title: SAMPLE_215_CD8 RNA


title: SAMPLE_207_CD4 RNA


title: SAMPLE_209_CD8 RNA


title: SAMPLE_206_CD4 RNA


title: SAMPLE_211_CD8 RNA


title: SAMPLE_206_CD8 RNA


title: SAMPLE_207_CD8 RNA


title: SAMPLE_214_CD8 RNA

value: I


title: SAMPLE_210_CD8 RNA


title: SAMPLE_209_CD4 RNA


title: SAMPLE_213_CD4 RNA

value: J


title: SAMPLE_212_CD8 RNA


title: SAMPLE_218_CD8 RNA


title: SAMPLE_205_CD8 RNA


title: SAMPLE_204_CD8 RNA


title: SAMPLE_201_CD4 RNA

value: CD4+ T cells


title: SAMPLE_203_CD4 RNA

value: Female


title: SAMPLE_205_CD4 RNA


title: SAMPLE_199_CD8 RNA

value: D


title: SAMPLE_202_CD8 RNA


title: SAMPLE_192_CD4 RNA


title: SAMPLE_191_CD4 RNA


title: SAMPLE_196_CD4 RNA


title: SAMPLE_199_CD4 RNA

value: B


title: SAMPLE_198_CD4 RNA


title: SAMPLE_195_CD4 RNA


title: SAMPLE_197_CD4 RNA


title: SAMPLE_203_CD8 RNA


title: SAMPLE_195_CD8 RNA


title: SAMPLE_194_CD8 RNA


title: SAMPLE_201_CD8 RNA


title: SAMPLE_197_CD8 RNA


title: SAMPLE_193_CD8 RNA


title: SAMPLE_192_CD8 RNA


title: SAMPLE_193_CD4 RNA


title: SAMPLE_190_CD8 RNA


title: SAMPLE_198_CD8 RNA


title: SAMPLE_196_CD8 RNA


title: SAMPLE_200_CD8 RNA


title: SAMPLE_190_CD4 RNA


title: SAMPLE_202_CD4 RNA

value: F


title: SAMPLE_191_CD8 RNA


title: SAMPLE_189_CD8 RNA


title: SAMPLE_188_CD8 RNA

value: C


title: SAMPLE_187_CD8 RNA


title: SAMPLE_189_CD4 RNA


title: SAMPLE_185_CD8 RNA


title: SAMPLE_200_CD4 RNA


title: SAMPLE_186_CD8 RNA


title: SAMPLE_187_CD4 RNA


title: SAMPLE_184_CD8 RNA


title: SAMPLE_184_CD4 RNA


title: SAMPLE_186_CD4 RNA


title: SAMPLE_182_CD8 RNA


title: SAMPLE_182_CD4 RNA


title: SAMPLE_181_CD8 RNA


title: SAMPLE_183_CD8 RNA


title: SAMPLE_180_CD8 RNA


title: SAMPLE_178_CD4 RNA

value: A


title: SAMPLE_179_CD8 RNA


title: SAMPLE_185_CD4 RNA


title: SAMPLE_178_CD8 RNA


title: SAMPLE_177_CD8 RNA


title: SAMPLE_179_CD4 RNA


title: SAMPLE_183_CD4 RNA


title: SAMPLE_180_CD4 RNA


title: SAMPLE_181_CD4 RNA


title: SAMPLE_176_CD4 RNA


title: SAMPLE_175_CD4 RNA


title: SAMPLE_174_CD4 RNA


title: SAMPLE_176_CD8 RNA

value: H


title: SAMPLE_175_CD8 RNA


title: SAMPLE_171_CD4 RNA


title: SAMPLE_173_CD4 RNA


title: SAMPLE_177_CD4 RNA


title: SAMPLE_169_CD8 RNA


title: SAMPLE_172_CD4 RNA


title: SAMPLE_188_CD4 RNA


title: SAMPLE_171_CD8 RNA


title: SAMPLE_172_CD8 RNA


title: SAMPLE_170_CD4 RNA


title: SAMPLE_167_CD4 RNA


title: SAMPLE_166_CD4 RNA


title: SAMPLE_168_CD8 RNA


title: SAMPLE_163_CD8 RNA


title: SAMPLE_165_CD4 RNA


title: SAMPLE_174_CD8 RNA


title: SAMPLE_162_CD4 RNA


title: SAMPLE_163_CD4 RNA


title: SAMPLE_166_CD8 RNA


title: SAMPLE_168_CD4 RNA


title: SAMPLE_162_CD8 RNA


title: SAMPLE_164_CD8 RNA


title: SAMPLE_165_CD8 RNA


title: SAMPLE_164_CD4 RNA


title: SAMPLE_173_CD8 RNA


title: SAMPLE_169_CD4 RNA


title: SAMPLE_161_CD4 RNA


title: SAMPLE_161_CD8 RNA


title: SAMPLE_155_CD8 RNA


title: SAMPLE_158_CD8 RNA


title: SAMPLE_157_CD8 RNA


title: SAMPLE_160_CD4 RNA


title: SAMPLE_158_CD4 RNA


title: SAMPLE_154_CD4 RNA


title: SAMPLE_153_CD8 RNA


title: SAMPLE_151_CD8 RNA


title: SAMPLE_147_CD8 RNA


title: SAMPLE_155_CD4 RNA


title: SAMPLE_156_CD8 RNA


title: SAMPLE_148_CD8 RNA


title: SAMPLE_157_CD4 RNA


title: SAMPLE_150_CD8 RNA


title: SAMPLE_156_CD4 RNA


title: SAMPLE_160_CD8 RNA


title: SAMPLE_152_CD4 RNA


title: SAMPLE_148_CD4 RNA


title: SAMPLE_147_CD4 RNA


title: SAMPLE_153_CD4 RNA


title: SAMPLE_151_CD4 RNA


title: SAMPLE_149_CD8 RNA


title: SAMPLE_152_CD8 RNA


title: SAMPLE_159_CD8 RNA


title: SAMPLE_150_CD4 RNA


title: SAMPLE_149_CD4 RNA


title: SAMPLE_146_CD8 RNA


title: SAMPLE_146_CD4 RNA


title: SAMPLE_154_CD8 RNA


title: SAMPLE_144_CD8 RNA


title: SAMPLE_142_CD8 RNA


title: SAMPLE_145_CD4 RNA


title: SAMPLE_142_CD4 RNA


title: SAMPLE_141_CD4 RNA


title: SAMPLE_141_CD8 RNA


title: SAMPLE_140_CD4 RNA


title: SAMPLE_139_CD4 RNA


title: SAMPLE_143_CD8 RNA


title: SAMPLE_143_CD4 RNA


title: SAMPLE_140_CD8 RNA


title: SAMPLE_138_CD4 RNA


title: SAMPLE_134_CD8 RNA


title: SAMPLE_136_CD8 RNA


title: SAMPLE_139_CD8 RNA


title: SAMPLE_136_CD4 RNA


title: SAMPLE_138_CD8 RNA


title: SAMPLE_135_CD4 RNA


title: SAMPLE_135_CD8 RNA


title: SAMPLE_137_CD8 RNA


title: SAMPLE_137_CD4 RNA


title: SAMPLE_130_CD8 RNA


title: SAMPLE_134_CD4 RNA


title: SAMPLE_132_CD8 RNA


title: SAMPLE_144_CD4 RNA


title: SAMPLE_133_CD8 RNA


title: SAMPLE_130_CD4 RNA


title: SAMPLE_133_CD4 RNA


title: SAMPLE_132_CD4 RNA


title: SAMPLE_131_CD8 RNA


title: SAMPLE_131_CD4 RNA


title: SAMPLE_129_CD4 RNA


title: SAMPLE_127_CD8 RNA


title: SAMPLE_120_CD8 RNA


title: SAMPLE_125_CD4 RNA


title: SAMPLE_128_CD4 RNA


title: SAMPLE_123_CD4 RNA


title: SAMPLE_126_CD8 RNA


title: SAMPLE_122_CD4 RNA


title: SAMPLE_114_CD4 RNA


title: SAMPLE_129_CD8 RNA


title: SAMPLE_121_CD8 RNA


title: SAMPLE_116_CD8 RNA


title: SAMPLE_127_CD4 RNA


title: SAMPLE_121_CD4 RNA


title: SAMPLE_119_CD8 RNA


title: SAMPLE_119_CD4 RNA


title: SAMPLE_126_CD4 RNA


title: SAMPLE_122_CD8 RNA


title: SAMPLE_118_CD8 RNA


title: SAMPLE_117_CD4 RNA


title: SAMPLE_115_CD4 RNA


title: SAMPLE_116_CD4 RNA


title: SAMPLE_125_CD8 RNA


title: SAMPLE_124_CD4 RNA


title: SAMPLE_115_CD8 RNA


title: SAMPLE_124_CD8 RNA


title: SAMPLE_120_CD4 RNA


title: SAMPLE_114_CD8 RNA


title: SAMPLE_118_CD4 RNA


title: SAMPLE_117_CD8 RNA


title: SAMPLE_113_CD8 RNA


title: SAMPLE_113_CD4 RNA


title: SAMPLE_111_CD8 RNA


title: SAMPLE_112_CD8 RNA


title: SAMPLE_110 RNA

value: Peripheral blood


title: SAMPLE_110_CD4 RNA


title: SAMPLE_111_CD4 RNA


title: SAMPLE_109_CD8 RNA


title: SAMPLE_104_CD4 RNA


title: SAMPLE_102_CD8 RNA


title: SAMPLE_103_CD8 RNA


title: SAMPLE_112_CD4 RNA


title: SAMPLE_108 RNA


title: SAMPLE_106_CD4 RNA


title: SAMPLE_107_CD4 RNA


title: SAMPLE_101_CD8 RNA


title: SAMPLE_101_CD4 RNA

value: K


title: SAMPLE_101 RNA


title: SAMPLE_102_CD4 RNA


title: SAMPLE_105_CD4 RNA


title: SAMPLE_106_CD8 RNA


title: SAMPLE_109_CD4 RNA


title: SAMPLE_105_CD8 RNA


title: SAMPLE_100_CD8 RNA


title: SAMPLE_99_CD4 RNA


title: SAMPLE_103_CD4 RNA


title: SAMPLE_104_CD8 RNA


title: SAMPLE_99_CD8 RNA


title: SAMPLE_98_CD8 RNA


title: SAMPLE_107_CD8 RNA


title: SAMPLE_100 RNA

value: G


title: SAMPLE_100_CD4 RNA


title: SAMPLE_98 RNA


title: SAMPLE_91_CD8 RNA


title: SAMPLE_93_CD8 RNA


title: SAMPLE_95_CD4 RNA


title: SAMPLE_92_CD4 RNA


title: SAMPLE_97_CD4 RNA


title: SAMPLE_89_CD8 RNA


title: SAMPLE_88_CD8 RNA


title: SAMPLE_94_CD4 RNA


title: SAMPLE_98_CD4 RNA


title: SAMPLE_96 RNA


title: SAMPLE_95 RNA


title: SAMPLE_96_CD8 RNA


title: SAMPLE_90_CD8 RNA


title: SAMPLE_94 RNA


title: SAMPLE_97_CD8 RNA


title: SAMPLE_88_CD4 RNA


title: SAMPLE_90_CD4 RNA


title: SAMPLE_85 RNA

value: E


title: SAMPLE_92_CD8 RNA

value: Male


title: SAMPLE_94_CD8 RNA


title: SAMPLE_95_CD8 RNA


title: SAMPLE_86 RNA


title: SAMPLE_88 RNA


title: SAMPLE_86_CD4 RNA


title: SAMPLE_89_CD4 RNA


title: SAMPLE_85_CD8 RNA


title: SAMPLE_93_CD4 RNA


title: SAMPLE_87_CD4 RNA


title: SAMPLE_91_CD4 RNA


title: SAMPLE_89 RNA

value: L


title: N6

city: Guiyang

first: Nianchun

last: Peng

state: Guizhou

address: No. 9 Beijing road, Yunyan district, Guiyang, Guizhou, China

department: Endocrinology and Metabolism

institute: Affiliated Hospital of Guizhou Medical University

description: circular RNA

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Human circRNA Array (8x15K, Arraystar).

scan_protocol: After having washed the slides, the arrays were scanned by the Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the R software package. Differentially expressed circRNAs with statistical significance between two groups were identified through Volcano Plot filtering. Differentially expressed circRNAs between two samples were identified through Fold Change filtering. Hierarchical Clustering was performed to show the distinguishable circRNAs expression pattern among samples.

source_name: tumor adjacent tissues from matching contralateral lobe

label_protocol: The enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar).

extract_protocol: The sample preparation and microarray hybridization were performed based on the Arraystar’s standard protocols. Briefly, total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs.

value: thyroid

value: female

tag: sample type

value: adjacent tumor tissue


title: PTC4

description: circular RNA

source_name: papillary thyroid carcinoma PTC

value: male

value: PTC


title: N3

description: circular RNA


title: N5

description: circular RNA


title: N4

description: circular RNA


title: PTC3

description: circular RNA


title: PTC5

description: circular RNA


title: PTC2

description: circular RNA


title: SAMPLE_81_CD8 RNA

value: Female

value: CD8+ T cells


title: SAMPLE_82_CD4 RNA

value: J

value: CD4+ T cells


title: SAMPLE_80 RNA

value: F


title: N2

description: circular RNA


title: SAMPLE_77_CD8 RNA

value: B


title: SAMPLE_81 RNA

value: Peripheral blood


title: SAMPLE_82_CD8 RNA


title: SAMPLE_80_CD4 RNA


title: SAMPLE_83_CD8 RNA


title: SAMPLE_84_CD8 RNA


title: SAMPLE_85_CD4 RNA

value: A


title: SAMPLE_80_CD8 RNA

value: D


title: SAMPLE_78 RNA

value: K


title: SAMPLE_83_CD4 RNA


title: SAMPLE_77 RNA

value: Male


title: SAMPLE_79_CD4 RNA

value: G


title: SAMPLE_78_CD8 RNA

value: C


title: SAMPLE_78_CD4 RNA


title: SAMPLE_79_CD8 RNA

value: I


title: SAMPLE_84_CD4 RNA


title: PTC6

description: circular RNA

value: thyroid

value: female


title: PTC1

description: circular RNA

value: PTC


title: N1

description: circular RNA

value: adjacent tumor tissue


title: MG2

description: circular RNA

source_name: thyroid multinodular goiter

value: multinodular goiter


title: MG3

description: circular RNA

value: male


title: MG1

description: circular RNA


title: FA3

description: circular RNA

source_name: thyroid follicular adenoma

value: follicular adenoma


title: FA1

description: circular RNA


title: FA2

description: circular RNA


title: SAMPLE_76 RNA

value: E


title: SAMPLE_77_CD4 RNA

value: CD4+ T cells


title: SAMPLE_76_CD8 RNA

value: CD8+ T cells


title: SAMPLE_75 RNA

value: L

value: Peripheral blood


title: SAMPLE_75_CD4 RNA


title: SAMPLE_74_CD8 RNA


title: SAMPLE_74_CD4 RNA

value: A


title: SAMPLE_72 RNA

value: Male

value: F


title: SAMPLE_73_CD4 RNA

value: Female

value: H


title: SAMPLE_73_CD8 RNA

value: J


title: SAMPLE_74 RNA


title: SAMPLE_76_CD4 RNA


title: SAMPLE_73 RNA


title: SAMPLE_72_CD8 RNA

value: D


title: SAMPLE_71 RNA

value: I


title: SAMPLE_68_CD4 RNA


title: SAMPLE_75_CD8 RNA


title: SAMPLE_69_CD8 RNA

value: G


title: SAMPLE_71_CD4 RNA


title: SAMPLE_67 RNA

value: B


title: SAMPLE_67_CD8 RNA

value: K


title: SAMPLE_72_CD4 RNA


title: SAMPLE_69_CD4 RNA


title: SAMPLE_66 RNA


title: SAMPLE_69 RNA


title: SAMPLE_70_CD8 RNA


title: SAMPLE_66_CD8 RNA


title: SAMPLE_65 RNA


title: SAMPLE_65_CD4 RNA


title: SAMPLE_67_CD4 RNA


title: SAMPLE_71_CD8 RNA


title: SAMPLE_68 RNA


title: SAMPLE_64_CD8 RNA


title: SAMPLE_65_CD8 RNA

value: C


title: SAMPLE_68_CD8 RNA


title: SAMPLE_66_CD4 RNA


title: SAMPLE_64_CD4 RNA


title: SAMPLE_62 RNA


title: SAMPLE_62_CD8 RNA


title: SAMPLE_61_CD8 RNA


title: SAMPLE_62_CD4 RNA


title: SAMPLE_81_CD4 RNA


title: SAMPLE_60_CD4 RNA


title: SAMPLE_57_CD8 RNA


title: SAMPLE_58_CD8 RNA


title: SAMPLE_59_CD4 RNA


title: SAMPLE_61_CD4 RNA


title: SAMPLE_60_CD8 RNA


title: SAMPLE_56_CD4 RNA


title: SAMPLE_56 RNA

value: E


title: SAMPLE_59_CD8 RNA


title: SAMPLE_55_CD8 RNA


title: SAMPLE_57 RNA


title: SAMPLE_55 RNA


title: SAMPLE_54_CD4 RNA

value: CD4+ T cells


title: SAMPLE_57_CD4 RNA


title: SAMPLE_58_CD4 RNA


title: SAMPLE_53_CD8 RNA

value: CD8+ T cells


title: SAMPLE_51 RNA


title: SAMPLE_54 RNA


title: SAMPLE_54_CD8 RNA


title: SAMPLE_55_CD4 RNA


title: SAMPLE_51_CD4 RNA


title: SAMPLE_51_CD8 RNA


title: SAMPLE_52 RNA

value: L


title: SAMPLE_56_CD8 RNA


title: SAMPLE_52_CD8 RNA


title: SAMPLE_52_CD4 RNA


title: SAMPLE_53_CD4 RNA


title: SAMPLE_50 RNA

value: Peripheral blood


title: SAMPLE_50_CD8 RNA


title: SAMPLE_50_CD4 RNA


title: SAMPLE_49_CD4 RNA

value: A


title: SAMPLE_48_CD4 RNA

value: Male


title: SAMPLE_47_CD8 RNA


title: SAMPLE_47_CD4 RNA


title: SAMPLE_48_CD8 RNA


title: SAMPLE_45 RNA


title: SAMPLE_45_CD4 RNA


title: SAMPLE_42 RNA


title: SAMPLE_41_CD8 RNA

value: F


title: SAMPLE_40 RNA


title: SAMPLE_49_CD8 RNA


title: SAMPLE_44_CD8 RNA


title: SAMPLE_44_CD4 RNA


title: SAMPLE_43_CD4 RNA


title: SAMPLE_43_CD8 RNA


title: SAMPLE_44 RNA


title: SAMPLE_38_CD4 RNA

value: Female


title: SAMPLE_41 RNA

value: H


title: SAMPLE_42_CD8 RNA


title: SAMPLE_39 RNA


title: SAMPLE_43 RNA


title: SAMPLE_38 RNA


title: SAMPLE_38_CD8 RNA


title: SAMPLE_39_CD4 RNA


title: SAMPLE_39_CD8 RNA


title: SAMPLE_40_CD4 RNA


title: SAMPLE_41_CD4 RNA


title: SAMPLE_45_CD8 RNA

value: J


title: SAMPLE_42_CD4 RNA


title: SAMPLE_34 RNA


title: SAMPLE_32_CD8 RNA


title: SAMPLE_33_CD8 RNA


title: SAMPLE_32_CD4 RNA


title: SAMPLE_30_CD8 RNA


title: SAMPLE_33_CD4 RNA


title: SAMPLE_37_CD4 RNA

value: D


title: SAMPLE_34_CD4 RNA


title: SAMPLE_37 RNA


title: SAMPLE_36_CD8 RNA


title: SAMPLE_36 RNA


title: SAMPLE_37_CD8 RNA


title: SAMPLE_29_CD4 RNA


title: SAMPLE_35_CD8 RNA


title: SAMPLE_36_CD4 RNA


title: SAMPLE_31_CD4 RNA

value: I


title: SAMPLE_30 RNA


title: SAMPLE_35_CD4 RNA


title: SAMPLE_33 RNA


title: SAMPLE_31_CD8 RNA


title: SAMPLE_28_CD8 RNA


title: SAMPLE_28_CD4 RNA


title: SAMPLE_34_CD8 RNA


title: SAMPLE_29_CD8 RNA


title: SAMPLE_27_CD4 RNA


title: SAMPLE_32 RNA


title: SAMPLE_28 RNA


title: SAMPLE_29 RNA


title: SAMPLE_27_CD8 RNA


title: SAMPLE_30_CD4 RNA


title: SAMPLE_24_CD8 RNA


title: SAMPLE_26_CD8 RNA


title: SAMPLE_20_CD8 RNA


title: SAMPLE_26_CD4 RNA


title: SAMPLE_23 RNA


title: SAMPLE_22 RNA


title: SAMPLE_21_CD4 RNA


title: SAMPLE_24 RNA


title: SAMPLE_22_CD8 RNA


title: SAMPLE_20 RNA


title: SAMPLE_25_CD8 RNA


title: SAMPLE_17 RNA


title: SAMPLE_17_CD4 RNA


title: SAMPLE_23_CD8 RNA


title: SAMPLE_19 RNA


title: SAMPLE_15_CD4 RNA


title: SAMPLE_25_CD4 RNA


title: SAMPLE_18_CD4 RNA


title: SAMPLE_16_CD4 RNA


title: SAMPLE_22_CD4 RNA


title: SAMPLE_21 RNA


title: SAMPLE_21_CD8 RNA


title: SAMPLE_14_CD8 RNA


title: SAMPLE_16_CD8 RNA


title: SAMPLE_17_CD8 RNA


title: SAMPLE_18 RNA


title: SAMPLE_15_CD8 RNA


title: SAMPLE_19_CD8 RNA


title: SAMPLE_20_CD4 RNA


title: SAMPLE_14 RNA


title: SAMPLE_13 RNA


title: SAMPLE_14_CD4 RNA


title: SAMPLE_12_CD4 RNA


title: SAMPLE_13_CD8 RNA


title: SAMPLE_13_CD4 RNA


title: SAMPLE_12_CD8 RNA


title: SAMPLE_10 RNA


title: SAMPLE_9_CD4 RNA


title: SAMPLE_11 RNA


title: SAMPLE_8_CD8 RNA


title: SAMPLE_12 RNA


title: SAMPLE_9 RNA


title: SAMPLE_11_CD8 RNA


title: SAMPLE_7 RNA


title: HECD-1-exo-HUVEC

city: Hong Kong

first: Alice

middle: Sze Tsai

last: Wong

address: 4S-14 Kadoorie Biological Sciences Building, University of Hong Kong, Pokfulam Road

department: School of Biological Sciences

country: Hong Kong

institute: The University of Hong Kong

description: Gene expression data from HUVEC treated with HECD-1-exosomes

hyb_protocol: Biotinylated labelled targets were hybridized on Affymetrix Genechip Human Gene 2.0 ST Array according to manufacturer’s instruction using Affymetrix GeneChip® Hybridization, Wash, and Stain Kit.

scan_protocol: Each Array was washed and stained using the Affymetrix Fluidics Station 450 then scanned using the Affymetrix GeneChip Scanner 7G with Command Console® (AGCC) Software to generate a CEL file.

data_processing:
The Affymetrix Expression Console Software (version 1.4) was used to perform quality assessment.
affymetrix-algorithm-name = rma-gene-full
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.4.1.46

source_name: HUVEC treated with HECD-1-exo

label_protocol: The generation of fragmented and biotin labelled cDNA for hybridization was performed according to the manufacturer’s instruction using the Affymetrix GeneChip® WT PLUS Reagent Kit (WT PLUS Kit) with 500ng of total RNA per sample as starting material.

growth_protocol: HUVEC is cultured with standard protocol.

extract_protocol: Total RNA is extracted with TRIZOL, quality determined with Agilent2100 bioanalyzer RNA 6000 Nano total RNA kit

treatment_protocol: HUVEC were incubated with exosomes pre-treated with IgG or HECD-1

value: HUVEC

tag: treated with

value: HECD-1 treated exosomes


title: SAMPLE_11_CD4 RNA


title: SAMPLE_7_CD4 RNA


title: SAMPLE_5 RNA


title: SAMPLE_6_CD8 RNA


title: IgG-exo-HUVEC

description: Gene expression data from HUVEC treated with IgG-exosomes

source_name: HUVEC treated with IgG-exo

value: IgG-treated exosomes


title: SAMPLE_10_CD4 RNA

value: G


title: SAMPLE_8 RNA

value: K


title: SAMPLE_9_CD8 RNA

value: C


title: SAMPLE_7_CD8 RNA

value: CD8+ T cells


title: SAMPLE_6_CD4 RNA

value: CD4+ T cells


title: SAMPLE_6 RNA

value: Peripheral blood


title: 19week_Female_Cyp51WT_1

city: Ljubljana

first: Peter

last: Juvan

address: Zaloska 4

department: Institute of Biochemistry

country: Slovenia

description: Gene expression data from a 19-week female wild type mouse X005

hyb_protocol: 250 ng of total RNA was used for hybridization of Affymetrix Gene Chip Mouse 2.0 ST Arrays according to the manufacturer’s instructions (Genechip® Whole Transcript (wt) Sense Ttarget Labeling Assay Manual – P/N 701880 Rev 4). Labeled samples were injected into Affymetrix arrays and hybridized at 45°C and 60 rpm for 16 h in an Affymetrix Hybridization Oven. Arrays were stained and washed in the Affymetrix GeneChip Fluidic Station 450.

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

data_processing:
GeneChip data was processed and analyzed using R/Bioconductor packages. Data were summarized (w.r.t. core meta-probeset annotations and AFFX control probes, probes grouped to the level of transcripts) and quantile-normalized (background computed from antigenomic probes) using RMA algorithm from XPS package.
MoGene-2_0-st.pgf
MoGene-2_0-st.mps

source_name: 19-week old female hepatocyte specific wild type mouse

label_protocol: Total RNA was used to synthesize double-stranded cDNA with random hexamer primers tagged with a T7 promoter sequence. The double-stranded cDNA was subsequently used as a template and amplified by T7 RNA polymerase producing cRNA. In the second cycle of cDNA synthesis, random hexamers were used to prime reverse transcription of the cRNA and dUTP was incorporated to produce single-stranded DNA. This single-stranded DNA samples were then treated with a combination of uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1) that specifically recognized the unnatural dUTP residues and broke the DNA strand. DNA was labeled by terminal eoxynucleotidyl transferase (TdT) with the Affymetrix proprietary DNA Labeling Reagent that is covalently linked to biotin.

growth_protocol: Hepatocyte specific Cyp51 KO mice and their control littermates (WT) were bred at the Medical Experimental Centre, Faculty of Medicine, University of Ljubljana, Slovenia and maintained in a temperature and humidity controlled environment under 12h light/dark cycle (lights were on from 7.00 am to 7.00 pm). Animals had ad libitum access to food (standard laboratory chow -1324, Altromin, Lage, Germany) and acidified tap water (pH = 3).

extract_protocol: Mice of aged 3, 6 or 19 weeks were euthanized between 7:30 and 13:30 via cervical dislocation. Runt mice were euthanized at humane time points to minimize their suffering. Liver was removed, weighed, snap-frozen in liquid nitrogen and stored at -80° C. Livers were pulverized and the RNA was isolated using QuickGene Tissue Kit S II and QuickGene-810 (Fujifilm, Singapore) according to the manufacturer’s instructions. RNA quantity and quality were assessed with NanoDrop-1000 and Agilent 2100 Bioanalyzer instruments. All samples were of sufficient purity (OD260/280 and OD230/280 > 1.8) and integrity (RIN > 8) for microarray hybridization.

treatment_protocol: not applicable

value: liver

tag: genotype

value: LWT

tag: Sex

tag: phenotype

value: wild type

tag: animal


title: SAMPLE_8_CD4 RNA

scan_protocol: Standard Illumina scanning protocol

value: Male


title: 19week_Female_Cyp51WT_2

institute: Faculty of Medicine, University of Ljubljana

description: Gene expression data from a 19-week female wild type mouse X109

value: F


title: SAMPLE_5_CD4 RNA

value: Female

value: A


title: SAMPLE_5_CD8 RNA


title: SAMPLE_4 RNA

value: L


title: 19week_Male_Cyp51WT_2

description: Gene expression data from a19-week male wild type mouse X614

source_name: 19-week old male hepatocyte specific wild type mouse

value: M


title: SAMPLE_4_CD8 RNA

value: J


title: 19week_Male_Cyp51WT_1

description: Gene expression data from a 19-week male wild type mouse X510


title: SAMPLE_3_CD8 RNA


title: SAMPLE_1_CD4 RNA

value: H


title: SAMPLE_1 RNA


title: SAMPLE_2_CD8 RNA


title: 19week_Female_Cyp51KO_2

description: Gene expression data from a 19-week female hepatocyte specific Cyp51 knockout mouse X701

source_name: 19-week old female hepatocyte specific Cyp51knockout mouse

value: Cyp51 LKO

value: knockout


title: SAMPLE_3_CD4 RNA


title: SAMPLE_2_CD4 RNA


title: SAMPLE_2 RNA


title: Runt_Female_Cyp51KO_3

description: Gene expression data from a 5-7-week female hepatocyte specific Cyp51 knockout runt mouse LKO381

source_name: 5-7 week old female hepatocyte specific Cyp51 knockout runt mouse

value: runt


title: 19week_Male_Cyp51KO_1

description: Gene expression data from a 19-week male hepatocyte specific Cyp51 knockout mouse X008

source_name: 19-week old male hepatocyte specific Cyp51knockout mouse


title: Uninfected replicate 1

first: Bernett

last: Lee

address: 8A Biomedical Grove #03-06 Immunos

country: Singapore

institute: Singapore Immunology Network

description: Sample name: UN_1

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Arrays were scanned using BeadArray Scanner 500GX.

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

source_name: THP1, uninfected

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

growth_protocol: THP1 cells (treated and untreated) were grown in RPMI complete medium, in a 37C, 5% CO2 incubator over 24 h.

extract_protocol: RNA was extracted with mirVana lysis/binding buffer, followed by clean-up with mirVana™ miRNA Isolation Kit (Ambion) in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: THP1 cells were uninfected and untreated.

tag: cell line

tag: infection


title: 19week_Male_Cyp51KO_2

description: Gene expression data from a 19-week male hepatocyte specific Cyp51 knockout mouse X406

tag: tissue


title: 19week_Female_Cyp51KO_1

description: Gene expression data from a 19-week female hepatocyte specific Cyp51 knockout mouse X101


title: Infected + RES replicate 2

description: Sample name: IN_RES_2

source_name: THP1, infected + RES

treatment_protocol: Mtb-infected THP1 cells were treated with 100uM resveratrol over 24h.

value: Mycobacterium tuberculosis

tag: treatment

value: resveratrol


title: SAMPLE_3 RNA

value: E

value: Peripheral blood


title: Uninfected replicate 2

description: Sample name: UN_2


title: Uninfected replicate 3

description: Sample name: UN_3


title: Runt_Female_Cyp51KO_2

description: Gene expression data from a 5-7-week female hepatocyte specific Cyp51 knockout runt mouse LKO204

tag: strain

value: liver


title: Runt_Female_Cyp51KO_1

description: Gene expression data from a 5-7-week female hepatocyte specific Cyp51 knockout runt mouse LKO104


title: Infected replicate 2

description: Sample name: IN_2

source_name: THP1, infected

treatment_protocol: THP1 cells were infected with Mtb.


title: Infected + RES replicate 1

description: Sample name: IN_RES_1


title: Infected replicate 3

description: Sample name: IN_3


title: Infected + RES replicate 3

description: Sample name: IN_RES_3


title: Runt_Male_Cyp51KO_3

description: Gene expression data from a 5-7-week male hepatocyte specific Cyp51 knockout runt mouse LKO650

source_name: 5-7 week old male hepatocyte specific Cyp51 knockout runt mouse


title: Runt_Male_Cyp51KO_2

description: Gene expression data from a 5-7-week male hepatocyte specific Cyp51 knockout runt mouse LKO281


title: C57BL/6 endothelial cells from tumor bearing mice_replicate 3

city: Basel

first: Tim

last: Roloff

address: Maulbeerstrasse 66

department: Functional Genomics

institute: FMI

description: biological replicate 3

hyb_protocol: 5.5ug amplified sense-target cDNA was fragmented and labeled using the the GeneChip WT Terminal Labelling Kit (Affymetrix) and 2.75ug hybridized to GeneChip Mouse Gene 1.0 ST Arrays for 16h at 45C.

scan_protocol: Scanning was performed with Affymetrix GCC Scan Control v. 3.0.0.1214 on a GeneChip Scanner 3000 with autoloader

data_processing: Arrays were normalized and probeset-level expression values were calculated with R/Bioconductor's (v3.1.1) 'affy' package using the rma() function

source_name: endothelial cells from long bones of tumor bearing mice

label_protocol: Total RNA was converted into cDNA and SPIA amplified with the Ovation Pico WTA System (NuGen Technologies Inc). Sense target cDNA was generated with the WT-Ovation Exon Module (NuGen Technologies Inc) from 3ug SPIA cDNA.

growth_protocol: EO771 cells (5x10^5 cells) were injected in C57BL/6 mice by the intracardiac route and growth of tumor cells in the long bones was monitored for c.a. 2 weeks by in-vivo bioluminescence.

extract_protocol: Total RNA was extracted from 5000 cells with the Pico Pure RNA Isolation Kit (Arcturus cat. KIT0204)

treatment_protocol: Long bones were excised from tumor bearing (tum) and tumor free (ctr) mice and different population were isolated via FACS sorting with the following markers: osteoblasts (OB) GFP-TR119-CD45-SCA1-CD31-CD51+, and endothelial cells (EC) GFP-TR119-CD45-SCA1+CD31+.

value: female

value: long bones


title: Runt_Male_Cyp51KO_1

description: Gene expression data from a 5-7-week male hepatocyte specific Cyp51 knockout runt mouse LKO207


title: 6week_Female_Cyp51WT_2

description: Gene expression data from a 6-week female wild type mouse LKO588

source_name: 6-week old female hepatocyte specific wild type mouse

value: LWT

value: F

value: wild type


title: C57BL/6 endothelial cells from tumor free mice_replicate 2

description: biological replicate 2

source_name: endothelial cells from long bones of tumor free mice


title: Infected replicate 1

description: Sample name: IN_1


title: C57BL/6 endothelial cells from tumor free mice_replicate 3

description: biological replicate 3


title: C57BL/6 endothelial cells from tumor free mice_replicate 1

description: biological replicate 1


title: 6week_Male_Cyp51WT_2

description: Gene expression data from a 6-week male wild type mouse LKO651

source_name: 6-week old male hepatocyte specific wild type mouse


title: C57BL/6 osteoblasts from tumor free mice_replicate 3

description: biological replicate 3

source_name: mouse osteoblasts from long bones of tumor free mice


title: 6week_Male_Cyp51WT_1

description: Gene expression data from a 6-week male wild type mouse LKO632


title: 6week_Female_Cyp51KO_2

description: Gene expression data from a 6-week female hepatocyte specific Cyp51 knockout mouse LKO686

source_name: 6-week old female hepatocyte specific Cyp51knockout mouse


title: C57BL/6 endothelial cells from tumor bearing mice_replicate 2

description: biological replicate 2


title: C57BL/6 endothelial cells from tumor bearing mice_replicate 1

description: biological replicate 1


title: C57BL/6 osteoblasts from tumor free mice_replicate 2

description: biological replicate 2


title: C57BL/6 osteoblasts from tumor bearing mice_replicate 3

description: biological replicate 3

source_name: mouse osteoblasts from long bones of tumor bearing mice


title: C57BL/6 osteoblasts from tumor bearing mice_replicate 2

description: biological replicate 2


title: C57BL/6 osteoblasts from tumor free mice_replicate 1

description: biological replicate 1