title: iHepatocytes_7days_AFB2_0-2uM_replicate 3

description:
18_AFB2_0-2uM
Gene expression in iPSC-derived human treated with 0.2 μM AFB2 for 7 days


title: iHepatocytes_7days_AFB2_0-2uM_replicate 1

status: Public on Mar 05 2019

type: RNA

city: Jefferson

first: Volodymyr

last: Tryndyak

address: 3900 NCTR Rd

department: Division of Biochemical Toxicology

country: USA

institute: US-FDA National Center for Toxicological Research

description:
16_AFB2_0-2uM
Gene expression in iPSC-derived human treated with 0.2 μM AFB2 for 7 days

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-072363 SurePrint G3 Human GE v3 8x60K Microarray (G4858A-072363) 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 dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. The raw data were normalized using ArrayTrack software (USFDA National Center for Toxicological Research, Jefferson, AR).

molecule: total RNA

organism: Homo sapiens

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the 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 the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: iPSC-derived human hepatocytes (iCell® Hepatocytes 2.0) were obtained from FUJIFILM Cellular Dynamics (Madison, WI).  iPSC-derived human hepatocytes were plated using Plating Medium (FUJIFILM Cellular Dynamics) on the collagen I-coated cell culture plates following the manufacturer’s recommendations. On the 4th day after initial plating, Plating Medium was replaced with Maintenance Medium.  The Maintenance Medium was changed every 2 days.

extract_protocol: Total RNA was extracted from iPSC-derived human hepatocytes using RNeasy Mini kits (Qiagen, Valencia, CA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-2000C spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: iPSC-derived human hepatocytes (on the 4th day after seeding) were treated with 0.2 µM AFB1 or AFB2, 1 µM B[a]P or B[e]P, or 20 µM methapyrilene for 7 consecutive days.

tag: cell type

value: iPSC-derived human hepatocytes

tag: treatment


title: iHepatocytes_7days_control_replicate 5

description:
14_Control
Gene expression in control iPSC-derived human hepatocytes after 7 days of incubation

value: control


title: 090_OPTC_D00_6028: IIV-Day-0

type: SRA

city: Pittsburgh

first: Uma

last: Chandran

state: PA

address: 5150 Center Ave

department: BioMedical Informatics

institute: University of Pittsburgh

library_source: transcriptomic

data_processing:
Targeted RNA-Seq analysis completed in Illumina BaseSpace using TruSeq Targeted RNA version 1.0.1.
In summary, alignment using Smith-Waterman algorithm. Alignments that include more than 3 indels are filtered from alignment results.
Read 1 is evaluated against the reverse complement of the downstream locus-specific oligos (ULSO). Read 2 is evaluated against locus-specific oligos. If the start of a read matches a probe sequence with no more than 1 mismatch, the full length of the read is aligned against the amplicon target for that sequence. Alignments that include more than 3 indels are filtered from alignment results.
Differential expression analysis comprises three steps: depth of sequencing normalization, variance estimation, and p-value calculation.
Paired comparisons for RNA seq differential expression were completed using DESeq2 with non-default options for sharingMode =”fit-only” and fitType=”local”
Genome_build: Targeted RNA-Seq build Hg19
Supplementary_files_format_and_content: Targeted RNA-Seq inexcel format includes, Raw Mean counts, Normalized Mean Counts, Fold Change, Log2 Fold Change, p-value, and q-value.

source_name: Blood

extract_protocol:
Total RNA was isolated from PAXgene tubes using the PAXgene Blood RNA Kit following the manufacturer’s protocol. RNA Quality and quantity were assessed by Agilent Tapestation 2200 and Invitrogen Qubit 2.0 fluorometer.
50ng of Total RNA was used to perform a multiplexed gene expression profiling panel of 81 select targets using the TruSeq Targeted RNA Expression guide rev. C following the manufacturer’s protocol. In summary, the chemistry begins with reverse transcribing cDNA from purified total RNA. Two custom-designed oligonucleotide probes with adapter sequences hybridize up and downstream of the region of interest. An Extension-ligation reaction, following by amplification creates a new template strand. Templates are then PCR amplified to add indices, creating sequence-ready libraries. Final cDNA libraries quality and quantity were assessed following the previously discussed methods.

treatment_protocol: Whole human blood collected in Paxgene Tubes

tag: tissue

value: Blood

value: IIV

tag: day


title: cerebellum_bs_53

type: genomic

city: Exeter

first: Katie

last: Lunnon

address: RILD Level 4, Barrack Road

department: Medical Research

country: United Kingdom

institute: University of Exeter Medical School

description: whole blood taken from sample 5742

hyb_protocol: Samples were processed according to the Illumina Infinium HumanMethylation450K BeadChip (Illumina) protocol with the exception that 7ul of treated material was input into the whole genome amplicifaction reaction instead of 4ul.

scan_protocol: Samples were assessed using the Illumina Infinium HumanMethylation450K BeadChip (Illumina) using a Illumina iScan System (Illumina).

data_processing: Data was imported using the final report files generated by Genome Studio (Illumina) software. Data was then  pre-processed in the R package wateRmelon using the pfilter and dasen functions. Pfilter function removed 15 samples and 38737 probes where 5% of sites had a detection p-value > 0.05

label: Cy5 and Cy3

molecule: genomic DNA

source_name: cerebellum

label_protocol: 1μg DNA from each sample was treated with sodium BS and OxBS in parallel using the true-methyl CEGX 96 kit (CEGX, Cambridge, UK) according to the manufacturer’s standard protocol

extract_protocol: Genomic DNA was extracted from frozen 100mg postmortem brain samples using a standard cell lysis, proteinase K digestion, phenol/chloroform, ethanol precipitation method.

tag: post-mortem diagnosis

value: Alzheimer's disease

tag: gender

value: M

tag: age at death

tag: braak stage

value: VI

tag: post-mortem interval(min)


title: cerebellum_oxbs_56

description: whole blood taken from sample 5741

value: Control


title: cerebellum_bs_52

description: whole blood taken from sample 5702


title: cerebellum_oxbs_50

description: whole blood taken from sample 5701

value: F

value: III


title: cerebellum_bs_50

description: whole blood taken from sample 5942


title: 09_OPTC_D07_5030: IIV-Day-7


title: cerebellum_bs_56

description: whole blood taken from sample 5732


title: cerebellum_oxbs_49

description: whole blood taken from sample 5941


title: 088_OPTC_D00_6021: LAIV-Day-0

value: LAIV


title: cerebellum_bs_47

description: whole blood taken from sample 5892


title: cerebellum_oxbs_52

description: whole blood taken from sample 5731


title: 087_OPTC_D07_6024: IIV-Day-7


title: 089_OPTC_D07_6031: IIV-Day-7


title: cerebellum_bs_49

description: whole blood taken from sample 5922


title: TS222

city: Vancouver

first: Michael

middle: S.

last: Kobor

state: BC

address: 950 West 28th Avenue

department: Medical Genetics

country: Canada

institute: Centre for Molecular Medicine and Therapeutics / University of British Columbia

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to Illumina Infinium HumanMethylation450k Beadchip using standard Illumina protocol

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

data_processing: GenomeStudio software V2011.1 with GenomeStudio Methylation Analysis Module Version 1.9.1000 (background-subtraction, colour-correction)

source_name: Human cord blood

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was isolated using the DNeasy Blood & Tissue kit (Qiagen) as per manufacturer’s instructions. DNA was then purified and concentrated using the DNA Clean & Concentrator kit (Zymo Research).

tag: subject status

value: healthy child born via caesarian section

value: Human cord blood

tag: monocytes

tag: granulocytes

tag: nrbcs

tag: nk cells

tag: b cells

tag: cd4t cells

tag: cd8t cells


title: iHepatocytes_7days_MP_20uM_replicate 3

description:
12_MP_20uM
Gene expression in iPSC-derived human treated with 20 μM MP for 7 days

tag: cell type


title: iHepatocytes_7days_control_replicate 4

description:
13_Control
Gene expression in control iPSC-derived human hepatocytes after 7 days of incubation

tag: treatment


title: iHepatocytes_7days_MP_20uM_replicate 1

description:
10_MP_20uM
Gene expression in iPSC-derived human treated with 20 μM MP for 7 days


title: cerebellum_bs_48

description: whole blood taken from sample 5692

value: V


title: 086_OPTC_D07_6027: IIV-Day-7

tag: tissue


title: cerebellum_oxbs_46

description: whole blood taken from sample 5691


title: cerebellum_oxbs_47

description: whole blood taken from sample 5921


title: cerebellum_oxbs_48

description: whole blood taken from sample 5891


title: 085_OPTC_D07_6030: IIV-Day-7

tag: day


title: cerebellum_bs_46

description: whole blood taken from sample 5632

tag: post-mortem diagnosis


title: cerebellum_bs_45

description: whole blood taken from sample 5612

tag: gender


title: 084_OPTC_D07_6021: LAIV-Day-7


title: iHepatocytes_7days_MP_20uM_replicate 2

description:
11_MP_20uM
Gene expression in iPSC-derived human treated with 20 μM MP for 7 days


title: cerebellum_oxbs_44

description: whole blood taken from sample 5611

tag: age at death

value: II


title: cerebellum_oxbs_43

description: whole blood taken from sample 5881

tag: braak stage


title: cerebellum_bs_43

description: whole blood taken from sample 5802

tag: post-mortem interval(min)


title: cerebellum_oxbs_42

description: whole blood taken from sample 5801


title: 082_OPTC_D00_6027: IIV-Day-0


title: 081_OPTC_D00_6030: IIV-Day-0


title: cerebellum_bs_42

description: whole blood taken from sample 5722


title: iHepatocytes_7days_BaP_1uM_replicate 3

description:
9_BaP_1uM
Gene expression in iPSC-derived human treated with 1 μM BaP for 7 days


title: iHepatocytes_7days_BaP_1uM_replicate 2

description:
8_BaP_1uM
Gene expression in iPSC-derived human treated with 1 μM BaP for 7 days


title: cerebellum_oxbs_55

description: whole blood taken from sample 5721


title: iHepatocytes_7days_AFB1_0-2uM_replicate 3

description:
6_AFB1_0-2uM
Gene expression in iPSC-derived human treated with 0.2 μM AFB1 for 7 days


title: iHepatocytes_7days_BaP_1uM_replicate 1

description:
7_BaP_1uM
Gene expression in iPSC-derived human treated with 1 μM BaP for 7 days


title: cerebellum_oxbs_45

description: whole blood taken from sample 5631


title: iHepatocytes_7days_AFB1_0-2uM_replicate 2

description:
5_AFB1_0-2uM
Gene expression in iPSC-derived human treated with 0.2 μM AFB1 for 7 days


title: cerebellum_oxbs_41

description: whole blood taken from sample 5591


title: cerebellum_bs_55

description: whole blood taken from sample 5592


title: 08_OPTC_D07_5009: LAIV-Day-7


title: cerebellum_bs_44

description: whole blood taken from sample 5882


title: cerebellum_oxbs_40

description: whole blood taken from sample 5571


title: PSMα (5μg/mL)

city: La Jolla

middle: Rey

last: Williams

state: CA

address: 9452 Medical Center Drive LL1W 420C

department: Dermatology

institute: UC San Diego

description: RNA-Seq Protocol

data_processing:
Illumina Hiseq 4000 reads were trimmed and filtered using Partek Flow. High quality reads were aligned using TopHat v2.1.0 for alignment into BAM files.
BAM files were imported into the RNA-seq pipeline of Partek Genomic Suite, version 6.6 (Copyright 2009, Partek Inc., St. Louis, MO, USA), and RPKM counts were calculated (RefSeq Transcripts 85 2018-05-02). Exclusions include a mininum reads of 10 in one out of 4 samples. RPKM values were log2-transformed with an offset value of 0.000001.
Genome_build: hg19

source_name: Neonatal foreskin

growth_protocol: Primary human keratinocytes (neonatal; NHEKs) were incubated at 37°C in 5% CO2 in Epilife medium supplemented with CaCl2 (60μM), Epilife Defined Growth Supplement (EDGS), penicillin (100 units/mL), streptomycin (100μg/mL), and Amphotericin B (250ng/mL). Cells were grown to passage 3 for experiment.

extract_protocol:
RNA was extracted using a Purelink RNA isolation kit as indicated by the manufacture's instructions.
Library was constructed by the UCSD Genome Core facility using the TruSeq mRNA library prep kit (Illumina) and a HiSeq4000 sequencing run.

treatment_protocol: NHEKs grown to 70-80% confluency in a 24 well tissue culture treated plate prior to differentiation for 48h in high calcium solution (2mM CaCl2). Differentiated NHEKS were than treated an additional 24h with either a DMSO (-) control or a synthetic Staphylococcus aureus phenol-soluble modulin alpha 3 (PSMα3) peptide dissolved in pure DMSO and added to cells at a final concentration of 5μg/mL (n=1).

value: Normal Human Epidermal Keratinocyte (NHEK)

tag: cell modifications prior to treatment

value: 48h 2mM CaCl2 Differentiation

tag: passage


title: cerebellum_bs_41

description: whole blood taken from sample 5572


title: 079_OPTC_D07_6023: IIV-Day-7


title: DMSO (-) Ctl

description: RNA-Seq Protocol


title: 083_OPTC_D00_6024: IIV-Day-0


title: cerebellum_oxbs_39

description: whole blood taken from sample 5551


title: cerebellum_bs_40

description: whole blood taken from sample 5552


title: Hypoxia_120hour_lane7_24

city: San Francisco

first: Arthur

middle: Jeremy

last: Willsey

address: 675 Nelson Rising Lane

department: Institute for Neurodegenerative Diseases

institute: UCSF

description:
raw_read_counts.txt
normalized_read_counts.txt
lane7_24

data_processing:
Aligned to GRCh37 using STAR 2.5.2b with parameters --quantMode GeneCounts and --sjdbGTFfile [Ensembl GRCh37 gff]
Generated gene expression counts using HTSeq with parameter --mode=intersection-strict
Trimmed raw transcript lists to transcripts with at least one read in more than 50% of the samples. The CQN R package (version 1.24.0) normalized filtered transcripts for gene length, GC content, and sample library size. We obtained gene length directly from the gene annotation file (.GTF) of the human GRCh37 genome reference and Bedtools (version 2.25.0) computed per gene GC content. After normalization, we further removed genes whose expression value did not change across all samples or with average normalized expression value less than one.
Genome_build: GRCh37
Supplementary_files_format_and_content: raw counts, normalized counts

source_name: brain

growth_protocol: Human cortical spheroids were derived from induced pluripotent stem cells and cultured for ~75 days, as per Pasca et al. (2015). Reference https://www.ncbi.nlm.nih.gov/pubmed/26005811

extract_protocol:
mRNA was isolated using the miRNeasy micro Kit and RNase-Free DNase set (Qiagen)
Library preparation was conducted by Macrogen (https://www.macrogenusa.com) using the TruSeq Stranded Total RNA LT Sample Prep Kit. Samples were then sequenced on the Illumina HiSeq 4000 System using paired-end, 101 base pair-long reads to a minimum of 40 million reads per sample.

treatment_protocol: Experimental cells were exposed to < 1% Oxygen for 48 hours, then reoxygenated to atmospheric levels (~21% Oxygen). Control cells were continuously exposed to atmospheric oxygen.

tag: stress

value: Hypoxia

tag: time

value: 120 hours (48 hours of <1% O2, 72 hours of re-oxygenation at 21% O2)

tag: rin


title: cerebellum_bs_39

description: whole blood taken from sample 5662


title: 078_OPTC_D00_6026: IIV-Day-0

value: Blood


title: Hypoxia_120hour_lane8_24

description:
raw_read_counts.txt
normalized_read_counts.txt
lane8_24


title: cerebellum_oxbs_38

description: whole blood taken from sample 5661


title: 080_OPTC_D07_6020: LAIV-Day-7


title: cerebellum_bs_38

description: whole blood taken from sample 5652


title: 077_OPTC_D07_6029: LAIV-Day-7


title: cerebellum_bs_36

description: whole blood taken from sample 5562


title: cerebellum_oxbs_36

description: whole blood taken from sample 5651


title: cerebellum_oxbs_37

description: whole blood taken from sample 5561


title: 076_OPTC_D00_6020: LAIV-Day-0


title: cerebellum_bs_37

description: whole blood taken from sample 5512


title: Hypoxia_48hour_lane7_23

description:
raw_read_counts.txt
normalized_read_counts.txt
lane7_23

value: 48 hours


title: 074_OPTC_D07_6026: IIV-Day-7

value: IIV


title: iHepatocytes_7days_control_replicate 1

description:
1_Control
Gene expression in control iPSC-derived human hepatocytes after 7 days of incubation

value: iPSC-derived human hepatocytes

value: control


title: cerebellum_oxbs_34

description: whole blood taken from sample 5491

value: Control

value: M

value: I


title: iHepatocytes_7days_control_replicate 2

description:
2_Control
Gene expression in control iPSC-derived human hepatocytes after 7 days of incubation


title: 07_OPTC_D07_5001: LAIV-Day-7

value: LAIV


title: cerebellum_oxbs_35

description: whole blood taken from sample 5511

value: Alzheimer's disease

value: VI


title: cerebellum_oxbs_33

description: whole blood taken from sample 5481

value: F


title: Hypoxia_24hour_lane7_22

description:
raw_read_counts.txt
normalized_read_counts.txt
lane7_22

value: 24 hours


title: Hypoxia_48hour_lane8_23

description:
raw_read_counts.txt
normalized_read_counts.txt
lane8_23


title: Control_120hour_lane7_21

description:
raw_read_counts.txt
normalized_read_counts.txt
lane7_21

value: 120 hours


title: iHepatocytes_7days_AFB1_0-2uM_replicate 1

description:
4_AFB1_0-2uM
Gene expression in iPSC-derived human treated with 0.2 μM AFB1 for 7 days


title: Hypoxia_24hour_lane8_22

description:
raw_read_counts.txt
normalized_read_counts.txt
lane8_22


title: cerebellum_bs_33

description: whole blood taken from sample 5152


title: cerebellum_bs_34

description: whole blood taken from sample 5482


title: cerebellum_oxbs_32

description: whole blood taken from sample 5151


title: 05_OPTC_D00_5035: IIV-Day-0


title: cerebellum_oxbs_31

description: whole blood taken from sample 5121

value: V


title: cerebellum_bs_32

description: whole blood taken from sample 5122


title: Control_48hour_lane8_20

description:
raw_read_counts.txt
normalized_read_counts.txt
lane8_20


title: 075_OPTC_D00_6023: IIV-Day-0


title: cerebellum_oxbs_30

description: whole blood taken from sample 5071


title: 04_OPTC_D00_5034: IIV-Day-0


title: Control_48hour_lane7_20

description:
raw_read_counts.txt
normalized_read_counts.txt
lane7_20


title: cerebellum_bs_35

description: whole blood taken from sample 5492


title: 03_OPTC_D00_5030: IIV-Day-0


title: cerebellum_oxbs_29

description: whole blood taken from sample 5161


title: cerebellum_bs_30

description: whole blood taken from sample 5162


title: cerebellum_oxbs_28

description: whole blood taken from sample 5141


title: 02_OPTC_D00_5009: LAIV-Day-0


title: Control_24hour_lane7_19

description:
raw_read_counts.txt
normalized_read_counts.txt
lane7_19


title: cerebellum_bs_29

description: whole blood taken from sample 5142


title: cerebellum_bs_28

description: whole blood taken from sample 5132


title: Hypoxia_120hour_lane7_18

description:
raw_read_counts.txt
normalized_read_counts.txt
lane7_18

value: Hypoxia


title: 01_OPTC_D00_5001: LAIV-Day-0


title: Control_24hour_lane8_19

description:
raw_read_counts.txt
normalized_read_counts.txt
lane8_19


title: Hypoxia_120hour_lane8_18

description:
raw_read_counts.txt
normalized_read_counts.txt
lane8_18

value: 120 hours (48 hours of <1% O2, 72 hours of re-oxygenation at 21% O2)


title: cerebellum_oxbs_25

description: whole blood taken from sample 5061


title: cerebellum_bs_25

description: whole blood taken from sample 5022


title: cerebellum_bs_26

description: whole blood taken from sample 5062


title: Control_120hour_lane8_21

description:
raw_read_counts.txt
normalized_read_counts.txt
lane8_21


title: cerebellum_oxbs_21

description: whole blood taken from sample 5021

value: II


title: Hypoxia_48hour_lane7_17

description:
raw_read_counts.txt
normalized_read_counts.txt
lane7_17

value: 48 hours


title: cerebellum_bs_21

description: whole blood taken from sample 5002


title: Hypoxia_48hour_lane8_17

description:
raw_read_counts.txt
normalized_read_counts.txt
lane8_17


title: cerebellum_bs_31

description: whole blood taken from sample 5072


title: cerebellum_oxbs_27

description: whole blood taken from sample 5001


title: cerebellum_oxbs_24

description: whole blood taken from sample 5111


title: Hypoxia_24hour_lane8_16

description:
raw_read_counts.txt
normalized_read_counts.txt
lane8_16


title: cerebellum_bs_24

description: whole blood taken from sample 5092


title: cerebellum_oxbs_22

description: whole blood taken from sample 5091


title: cerebellum_bs_27

description: whole blood taken from sample 5112


title: Hypoxia_24hour_lane7_16

description:
raw_read_counts.txt
normalized_read_counts.txt
lane7_16


title: cerebellum_bs_22

description: whole blood taken from sample 5082


title: cerebellum_oxbs_20

description: whole blood taken from sample 5081


title: cerebellum_oxbs_26

description: whole blood taken from sample 5131


title: cerebellum_bs_20

description: whole blood taken from sample 4992


title: Control_120hour_lane8_15

description:
raw_read_counts.txt
normalized_read_counts.txt
lane8_15


title: Control_48hour_lane6_14

description:
raw_read_counts.txt
normalized_read_counts.txt
lane6_14


title: cerebellum_bs_14

description: whole blood taken from sample 4892


title: cerebellum_bs_19

description: whole blood taken from sample 4982


title: 06_OPTC_D00_5039: LAIV-Day-0

value: Blood


title: cerebellum_oxbs_23

description: whole blood taken from sample 4891

value: III


title: cerebellum_bs_23

description: whole blood taken from sample 5042


title: cerebellum_oxbs_18

description: whole blood taken from sample 5041


title: Control_48hour_lane8_14

description:
raw_read_counts.txt
normalized_read_counts.txt
lane8_14


title: Control_24hour_lane6_13

description:
raw_read_counts.txt
normalized_read_counts.txt
lane6_13


title: cerebellum_oxbs_13

description: whole blood taken from sample 4881


title: cerebellum_bs_13

description: whole blood taken from sample 4972


title: cerebellum_oxbs_19

description: whole blood taken from sample 4991


title: cerebellum_bs_18

description: whole blood taken from sample 4882


title: Control_24hour_lane8_13

description:
raw_read_counts.txt
normalized_read_counts.txt
lane8_13


title: Hypoxia_120hour_lane6_12

description:
raw_read_counts.txt
normalized_read_counts.txt
lane6_12


title: cerebellum_bs_12

description: whole blood taken from sample 4762


title: cerebellum_bs_11

description: whole blood taken from sample 4742


title: cerebellum_oxbs_10

description: whole blood taken from sample 4741


title: Hypoxia_120hour_lane8_12

description:
raw_read_counts.txt
normalized_read_counts.txt
lane8_12


title: Control_120hour_lane6_15

description:
raw_read_counts.txt
normalized_read_counts.txt
lane6_15


title: cerebellum_oxbs_17

description: whole blood taken from sample 4711


title: cerebellum_oxbs_14

description: whole blood taken from sample 4981


title: Hypoxia_48hour_lane8_11

description:
raw_read_counts.txt
normalized_read_counts.txt
lane8_11


title: Hypoxia_24hour_lane6_10

description:
raw_read_counts.txt
normalized_read_counts.txt
lane6_10


title: cerebellum_oxbs_11

description: whole blood taken from sample 4761


title: cerebellum_oxbs_16

description: whole blood taken from sample 4851

value: IV


title: Hypoxia_24hour_lane8_10

description:
raw_read_counts.txt
normalized_read_counts.txt
lane8_10


title: Control_120hour_lane8_9

description:
raw_read_counts.txt
normalized_read_counts.txt
lane8_9

value: Control


title: cerebellum_oxbs_9

description: whole blood taken from sample 4831


title: cerebellum_oxbs_8

description: whole blood taken from sample 4821


title: cerebellum_bs_9

description: whole blood taken from sample 4822


title: Hypoxia_48hour_lane6_11

description:
raw_read_counts.txt
normalized_read_counts.txt
lane6_11


title: cerebellum_bs_17

description: whole blood taken from sample 4852

value: M


title: cerebellum_oxbs_12

description: whole blood taken from sample 4971


title: cerebellum_bs_8

description: whole blood taken from sample 4702


title: cerebellum_oxbs_7

description: whole blood taken from sample 4701


title: Control_120hour_lane6_9

description:
raw_read_counts.txt
normalized_read_counts.txt
lane6_9


title: cerebellum_bs_7

description: whole blood taken from sample 4662


title: cerebellum_oxbs_6

description: whole blood taken from sample 4661


title: cerebellum_bs_15

description: whole blood taken from sample 4802


title: cerebellum_bs_6

description: whole blood taken from sample 4612


title: cerebellum_bs_10

description: whole blood taken from sample 4712


title: EC095_Rt_ETOH_24H

city: University

first: Zhiqiang

last: Pan

state: MS

address: 1558 University Ave

institute: USDA-ARS-NPURU

data_processing:
Raw RNA-Seq reads of the cDNA libraries were trimmed and filtered to remove adaptor sequences, low-quality reads containing poly-N using the CLC Genomics Workbench 7.0 (CLC bio, Denmark).
Trimmed reads of each sample in the experiment were mapped to the Arabidopsis thaliana reference genome (Col-0 TAIR 10) and counted using the RNA-Seq mapping algorithm in the CLC Genomics Workbench
Expression values (fragments per kilobase per million) for all known genes were calculated for each sample.
Gene counts were tested for differential expression using the R package DESeq2 (version 1.14.1).
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample.

organism: Arabidopsis thaliana

source_name: Roots_0.1% EtOH ctrl for 24 h

growth_protocol: Sterile square Petri dishes (100x15 mm) were prepared with 0.44% macro-and micronutrients and 1% sucrose in 0.8% agar. Twenty-four seeds were sown per plate, which were sealed with tape and placed in a growth chamber at 22 ºC and 16/8 h light/ dark photoperiod under light intensity of 120 µmol/m2sec.

extract_protocol:
Total RNAs were isolated from flash frozen Arabidopsis tissues using an RNeasy plant mini kit (Qiagen) according to the manufacturer’s instructions.
Library construction, quantification and qualification were performed by Global Biologics (Columbia, MO) using 1 μg of total RNA and the IlluminaTruSeq RNA Library Preparation Kits.

treatment_protocol: Plants were grown on agar plates for 14 days in a growth chamber and then treated at 7 h after the beginning of the photoperiod by adding 8 mL per plate of the IC50 concentration (21 µM) of t-chalcone. After treatment, plants were incubated for 0, 1, 3, 6, 12 and 24 h.

tag: age

value: seedlings (14 days-old)

value: Treated with 0.1% EtOH ctrl for 24 h

value: Roots


title: cerebellum_oxbs_5

description: whole blood taken from sample 4801

value: Alzheimer's disease

value: VI


title: EC096_Rt_ETOH_24H


title: cerebellum_bs_5

description: whole blood taken from sample 4792


title: Control_24hour_lane8_7

description:
raw_read_counts.txt
normalized_read_counts.txt
lane8_7

value: 24 hours


title: Control_24hour_lane6_7

description:
raw_read_counts.txt
normalized_read_counts.txt
lane6_7


title: cerebellum_bs_16

description: whole blood taken from sample 4832


title: Hypoxia_120hour_lane6_6

description:
raw_read_counts.txt
normalized_read_counts.txt
lane6_6


title: Hypoxia_120hour_lane8_6

description:
raw_read_counts.txt
normalized_read_counts.txt
lane8_6


title: EC090_Sht_CHAL_24H

source_name: Shoots_t-chalcone for 24 h

value: Treated with t-chalcone for 24 h

value: Shoots


title: cerebellum_oxbs_3

description: whole blood taken from sample 4771

value: F

value: V


title: EC089_Sht_CHAL_24H


title: cerebellum_oxbs_2

description: whole blood taken from sample 4601


title: cerebellum_bs_2

description: whole blood taken from sample 4572


title: Control_48hour_lane8_8

description:
raw_read_counts.txt
normalized_read_counts.txt
lane8_8


title: EC087_Sht_ETOH_24H

source_name: Shoots_0.1% EtOH ctrl for 24 h


title: cerebellum_oxbs_15

description: whole blood taken from sample 4611

value: II


title: cerebellum_oxbs_1

description: whole blood taken from sample 4571


title: cerebellum_bs_1

description: whole blood taken from sample 4562


title: cerebellum_bs_3

description: whole blood taken from sample 4602


title: EC085_Sht_ETOH_24H


title: iHepatocytes_7days_control_replicate 3

description:
3_Control
Gene expression in control iPSC-derived human hepatocytes after 7 days of incubation

value: iPSC-derived human hepatocytes

value: control


title: Control_48hour_lane6_8

description:
raw_read_counts.txt
normalized_read_counts.txt
lane6_8

value: 48 hours


title: entorhinal cortex_oxbs_96

description: whole blood taken from sample 4752

source_name: entorhinal cortex


title: EC081_Rt_CHAL_12H

source_name: Roots_t-chalcone for 12 h

value: Treated with t-chalcone for 12 h


title: Hypoxia_48hour_lane8_5

description:
raw_read_counts.txt
normalized_read_counts.txt
lane8_5

value: Hypoxia


title: entorhinal cortex_bs_96

description: whole blood taken from sample 4751

value: M


title: EC094_Rt_ETOH_24H

value: seedlings (14 days-old)


title: Hypoxia_24hour_lane6_4

description:
raw_read_counts.txt
normalized_read_counts.txt
lane6_4


title: cerebellum_oxbs_4

description: whole blood taken from sample 4791


title: entorhinal cortex_oxbs_95

description: whole blood taken from sample 4722

value: IV


title: EC080_Rt_CHAL_12H

value: Roots


title: Hypoxia_48hour_lane6_5

description:
raw_read_counts.txt
normalized_read_counts.txt
lane6_5


title: cerebellum_bs_4

description: whole blood taken from sample 4772

value: Alzheimer's disease


title: entorhinal cortex_bs_95

description: whole blood taken from sample 4721


title: entorhinal cortex_oxbs_94

description: whole blood taken from sample 4552

value: Control

value: I


title: Hypoxia_24hour_lane8_4

description:
raw_read_counts.txt
normalized_read_counts.txt
lane8_4

value: 24 hours


title: EC078_Rt_ETOH_12H

source_name: Roots_0.1% EtOH ctrl for 12 h

value: Treated with 0.1% EtOH ctrl for 12 h


title: entorhinal cortex_oxbs_93

description: whole blood taken from sample 4632

value: F


title: entorhinal cortex_bs_94

description: whole blood taken from sample 4551


title: entorhinal cortex_bs_93

description: whole blood taken from sample 4631

value: V


title: EC072_Sht_CHAL_12H

source_name: Shoots_t-chalcone for 12 h

value: Shoots


title: Control_120hour_lane6_3

description:
raw_read_counts.txt
normalized_read_counts.txt
lane6_3

value: 120 hours


title: entorhinal cortex_bs_92

description: whole blood taken from sample 4621


title: entorhinal cortex_oxbs_92

description: whole blood taken from sample 4622


title: EC077_Rt_ETOH_12H


title: entorhinal cortex_oxbs_91

description: whole blood taken from sample 4482

value: VI


title: Control_48hour_lane8_2

description:
raw_read_counts.txt
normalized_read_counts.txt
lane8_2

value: 48 hours


title: EC071_Sht_CHAL_12H

value: Treated with t-chalcone for 12 h


title: entorhinal cortex_bs_91

description: whole blood taken from sample 4481


title: Control_48hour_lane6_2

description:
raw_read_counts.txt
normalized_read_counts.txt
lane6_2


title: entorhinal cortex_oxbs_90

description: whole blood taken from sample 4422

value: II


title: entorhinal cortex_bs_90

description: whole blood taken from sample 4421


title: EC069_Sht_ETOH_12H

source_name: Shoots_0.1% EtOH ctrl for 12 h


title: EC070_Sht_CHAL_12H


title: Control_24hour_lane8_1

description:
raw_read_counts.txt
normalized_read_counts.txt
lane8_1


title: entorhinal cortex_oxbs_89

description: whole blood taken from sample 4302

value: M


title: entorhinal cortex_bs_89

description: whole blood taken from sample 4301


title: entorhinal cortex_oxbs_88

description: whole blood taken from sample 4532


title: EC099_Rt_CHAL_24H

source_name: Roots_t-chalcone for 24 h

value: seedlings (14 days-old)

value: Treated with t-chalcone for 24 h


title: entorhinal cortex_bs_88

description: whole blood taken from sample 4531

value: IV


title: EC067_Sht_ETOH_12H


title: EC068_Sht_ETOH_12H


title: EC098_Rt_CHAL_24H

value: Roots


title: entorhinal cortex_oxbs_87

description: whole blood taken from sample 4502

value: Alzheimer's disease


title: EC063_Rt_CHAL_6H

source_name: Roots_t-chalcone for 6 h

value: Treated with t-chalcone for 6 h


title: entorhinal cortex_oxbs_85

description: whole blood taken from sample 4472


title: Control_120hour_lane8_3

description:
raw_read_counts.txt
normalized_read_counts.txt
lane8_3

value: Control


title: entorhinal cortex_bs_83

description: whole blood taken from sample 4291


title: EC088_Sht_CHAL_24H


title: entorhinal cortex_oxbs_86

description: whole blood taken from sample 4282


title: entorhinal cortex_oxbs_83

description: whole blood taken from sample 4292


title: EC062_Rt_CHAL_6H


title: entorhinal cortex_bs_87

description: whole blood taken from sample 4501


title: EC097_Rt_CHAL_24H


title: Control_24hour_lane6_1

description:
raw_read_counts.txt
normalized_read_counts.txt
lane6_1

value: 24 hours


title: entorhinal cortex_bs_82

description: whole blood taken from sample 4271


title: EC060_Rt_ETOH_6H

source_name: Roots_0.1% EtOH ctrl for 6 h

value: Treated with 0.1% EtOH ctrl for 6 h


title: EC061_Rt_CHAL_6H


title: EC079_Rt_CHAL_12H


title: EC059_Rt_ETOH_6H


title: EC076_Rt_ETOH_12H

value: Treated with 0.1% EtOH ctrl for 12 h


title: entorhinal cortex_oxbs_80

description: whole blood taken from sample 4462


title: entorhinal cortex_oxbs_79

description: whole blood taken from sample 4452


title: entorhinal cortex_bs_80

description: whole blood taken from sample 4461


title: entorhinal cortex_bs_85

description: whole blood taken from sample 4471

value: F

value: V


title: entorhinal cortex_oxbs_78

description: whole blood taken from sample 4442


title: entorhinal cortex_bs_79

description: whole blood taken from sample 4451


title: EC054_Sht_CHAL_6H

source_name: Shoots_t-chalcone for 6 h

value: Shoots


title: EC058_Rt_ETOH_6H


title: entorhinal cortex_bs_78

description: whole blood taken from sample 4441


title: EC053_Sht_CHAL_6H


title: entorhinal cortex_bs_86

description: whole blood taken from sample 4281


title: entorhinal cortex_oxbs_82

description: whole blood taken from sample 4272


title: entorhinal cortex_oxbs_84

description: whole blood taken from sample 4232


title: entorhinal cortex_bs_75

description: whole blood taken from sample 4251

value: VI


title: EC086_Sht_ETOH_24H

value: Treated with 0.1% EtOH ctrl for 24 h


title: entorhinal cortex_bs_84

description: whole blood taken from sample 4231


title: EC052_Sht_CHAL_6H


title: entorhinal cortex_oxbs_75

description: whole blood taken from sample 4252


title: entorhinal cortex_bs_76

description: whole blood taken from sample 4211


title: entorhinal cortex_oxbs_74

description: whole blood taken from sample 4402


title: entorhinal cortex_oxbs_76

description: whole blood taken from sample 4212


title: EC051_Sht_ETOH_6H

source_name: Shoots_0.1% EtOH ctrl for 6 h


title: entorhinal cortex_bs_74

description: whole blood taken from sample 4401


title: entorhinal cortex_oxbs_73

description: whole blood taken from sample 4382


title: EC050_Sht_ETOH_6H


title: EC049_Sht_ETOH_6H


title: EC045_Rt_CHAL_3H

source_name: Roots_t-chalcone for 3 h

value: Treated with t-chalcone for 3 h


title: entorhinal cortex_oxbs_67

description: whole blood taken from sample 4362


title: Control150

type: protein

city: Tempe

first: Xiaofang

last: Bian

address: 1001 S. McAllister Ave.

institute: Arizona State University

description:
No additional extraction step was performed on the serum sample
Serum sample are not labeled
The serum was applied on the protein array, secondary anti-human IgG antibody used for detection.

hyb_protocol: 1. Protein Arrays were blocked with 5% milk PBST (0.2% Tween) for 1 hour at RT; 2. 2mL 1:300 diluted serum was applied to each slide in a slide hybridization chamber with constant agitation  for 16 hrs at 4oC; 3. Slides were incubated with 2mL 1:500 dilution of HRP-linked anti-human secondary antibodies(Jackson Immunoresearch) in Milk PBST; 4.Slides were developed by 500uL Tyramide Signal Amplification (Perkin Elmer) in amplification buffer (Perkin Elmer).

scan_protocol: Sldies were scanned in ScanArray ProScanArray HT scanner(Perkin Elmer) at 35 PMT gain, 80% laser power and 20 μm resolution.

data_processing: 1. Remove within-block and pin effects, removed spots were replaced as a missing value(shown null in Matrix table); 2. The background signal estimated by the 25th percentile of the negative control;3. Normaliza the array data by median; 4. Average the normalized value for duplicate spots.

label: HRP-Tyramide

molecule: protein

source_name: Peripheral blood

label_protocol: No label was performed on the serum sample.

extract_protocol: Peripheral blood samples were drawn from the antecubital vein and serum was prepared according to a standardized protocol before freezing serum aliquots at -80oC

tag: sample type

value: Serum

tag: disease state


title: entorhinal cortex_bs_73

description: whole blood taken from sample 4381

value: M


title: Control147


title: Control149


title: Control146


title: Control148


title: entorhinal cortex_bs_67

description: whole blood taken from sample 4361


title: Control151


title: entorhinal cortex_oxbs_71

description: whole blood taken from sample 4192


title: entorhinal cortex_bs_71

description: whole blood taken from sample 4191


title: Control145


title: EC044_Rt_CHAL_3H

value: seedlings (14 days-old)


title: EC043_Rt_CHAL_3H


title: entorhinal cortex_bs_81

description: whole blood taken from sample 4131

value: III


title: entorhinal cortex_oxbs_70

description: whole blood taken from sample 4352


title: entorhinal cortex_oxbs_72

description: whole blood taken from sample 4092


title: EC041_Rt_ETOH_3H

source_name: Roots_0.1% EtOH ctrl for 3 h

value: Treated with 0.1% EtOH ctrl for 3 h

value: Roots


title: EC042_Rt_ETOH_3H


title: Control143


title: Control142


title: entorhinal cortex_bs_72

description: whole blood taken from sample 4091

value: Alzheimer's disease


title: Control141

value: Control


title: Control144


title: entorhinal cortex_oxbs_69

description: whole blood taken from sample 4342


title: entorhinal cortex_bs_70

description: whole blood taken from sample 4351


title: EC040_Rt_ETOH_3H


title: entorhinal cortex_oxbs_61

description: whole blood taken from sample 4332


title: EC036_Sht_CHAL_3H

source_name: Shoots_t-chalcone for 3 h


title: entorhinal cortex_bs_61

description: whole blood taken from sample 4331


title: entorhinal cortex_bs_69

description: whole blood taken from sample 4341


title: EC035_Sht_CHAL_3H


title: entorhinal cortex_oxbs_81

description: whole blood taken from sample 4132


title: entorhinal cortex_oxbs_65

description: whole blood taken from sample 4072

value: II


title: Control139


title: entorhinal cortex_oxbs_77

description: whole blood taken from sample 4052


title: Control140


title: Control137


title: EC034_Sht_CHAL_3H


title: Control136


title: entorhinal cortex_bs_65

description: whole blood taken from sample 4071


title: entorhinal cortex_bs_77

description: whole blood taken from sample 4051


title: entorhinal cortex_oxbs_68

description: whole blood taken from sample 4032


title: Control_3

city: Milano

first: Luca

last: Massimino

state: MI

address: Via Olgettina, 58

department: Gastroenterology

country: Italy

institute: Ospedale San Raffaele

data_processing:
Fastq files were adapter-trimmed and wuality-filtered with Trimmomatic.
High quality fastq files were aligned to the human genome by using Bowtie2
Gene read counts were calculated with featureCounts.
Differential gene expression was performed with DESeq2.
Genome_build: mm10

molecule: polyA RNA

organism: Mus musculus

source_name: Primary neuronal culture

growth_protocol: Cells were cultured in Neurobasal culture medium plus B27 supplement

extract_protocol:
RNA was isolated with Trizol according to manufacturer's instructions
Libraries were constructed with the QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina, in accordance with manufacturer's instructions

treatment_protocol: dCas9 and sgRNAs were transfected with lentiviral vectors

value: Cortical neurons

tag: expression

value: control


title: entorhinal cortex_bs_68

description: whole blood taken from sample 4031


title: EC032_Sht_ETOH_3H

source_name: Shoots_0.1% EtOH ctrl for 3 h

tag: treatment


title: EC033_Sht_ETOH_3H

tag: tissue


title: Control_2


title: Control_1


title: Control134


title: Control135


title: EC027_Rt_CHAL_1H

source_name: Roots_t-chalcone for 1 h

value: Treated with t-chalcone for 1 h


title: Scn1a_3

value: Scn1a sgRNA


title: Control133


title: EC031_Sht_ETOH_3H

value: Shoots


title: EC026_Rt_CHAL_1H


title: Control132


title: entorhinal cortex_bs_66

description: whole blood taken from sample 4311

source_name: entorhinal cortex


title: entorhinal cortex_oxbs_66

description: whole blood taken from sample 4312


title: Scn1a_2


title: entorhinal cortex_oxbs_63

description: whole blood taken from sample 4262

value: IV


title: Control131


title: entorhinal cortex_bs_63

description: whole blood taken from sample 4261


title: entorhinal cortex_oxbs_58

description: whole blood taken from sample 4242

value: F

value: V


title: EC024_Rt_ETOH_1H

source_name: Roots_0.1% EtOH ctrl for 1 h

value: Treated with 0.1% EtOH ctrl for 1 h


title: Scn1a_1


title: entorhinal cortex_bs_54

description: whole blood taken from sample 4011


title: EC018_Sht_CHAL_1H

source_name: Shoots_t-chalcone for 1 h


title: Control130

value: Serum


title: EC023_Rt_ETOH_1H

value: seedlings (14 days-old)


title: Control128


title: Control126


title: Control129


title: entorhinal cortex_bs_60

description: whole blood taken from sample 3991

value: M


title: EC016_Sht_CHAL_1H


title: EC015_Sht_ETOH_1H

source_name: Shoots_0.1% EtOH ctrl for 1 h


title: entorhinal cortex_oxbs_54

description: whole blood taken from sample 4012


title: entorhinal cortex_oxbs_59

description: whole blood taken from sample 3972


title: Control127


title: EC017_Sht_CHAL_1H


title: Control122


title: EC022_Rt_ETOH_1H


title: Hela1R

city: guangzhou

first: zou

middle: wen

last: chong

state: guangdong

address: Sha Tai ROAD

department: Department of Cell Biology

country: China

institute: Southern Medical University

data_processing:
Illumina Casava1.8 software used for basecalling.
For all generated raw reads, adaptor sequences, low-quality reads, contaminant reads, and reads that were shorter than 18 nt or larger than 30 nt were eliminated and trimmed with the Fastx-Toolkit software.
The resulting set of trimmed reads were then mapped against the Homo sapiens  of Ensembl (Release 80, http://www.ensembl.org/) using the program SOAP . Subsequently, by the same approach, the perfectly matched reads were screened against miRBase (Release 21, http://www.mirbase.org/)  and human non-coding RNA sequence of Ensembl (Release 80, http://www.ensembl.org/) to obtain the annotation of known mature miRNAs and other small non-coding RNAs (allowing two mismatches)
To correct for the difference in tag counts between samples, the tag counts were scaled to the copy number of transcripts per million (TPM) based on the total number of tags aligned to known human mature miRNAs in miRBase 21.
Genome_build: Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file includes TPM values and Counts for each Sample

source_name: HeLa cells

extract_protocol: Hela cells were treated with 100 nM rapamycin or vehicle control for 24 hr. Exosomes isolated from culture media at the end of rapamycin-treatment were subjected to microRNA sequence analysis.

tag: cell line

value: HeLa

tag: cell type

value: cervical cancer cells

tag: agent

value: rapamycin


title: EC025_Rt_CHAL_1H

value: Roots


title: Control123

value: Control


title: Control125


title: Hela


title: entorhinal cortex_oxbs_57

description: whole blood taken from sample 4202

tag: post-mortem diagnosis

value: Alzheimer's disease

tag: gender

tag: age at death

value: VI


title: EC014_Sht_ETOH_1H


title: entorhinal cortex_bs_58

description: whole blood taken from sample 4241

tag: braak stage

tag: post-mortem interval(min)


title: entorhinal cortex_bs_57

description: whole blood taken from sample 4201


title: EC011_Rt_CTRL_w_ETOH_0H

source_name: Roots_0.1% EtOH ctrl at 0 h

value: Treated with 0.1% EtOH ctrl at 0 h


title: Control121


title: EC013_Sht_ETOH_1H


title: EC012_Rt_CTRL_w_ETOH_0H


title: entorhinal cortex_oxbs_60

description: whole blood taken from sample 3992

value: II


title: EC010_Rt_CTRL_w_ETOH_0H


title: entorhinal cortex_bs_64

description: whole blood taken from sample 4181


title: Control120


title: Control124


title: EC008_Rt_CTRL_wo_ETOH_0H

source_name: Roots_untreated_ 0 h

value: Treated without EtOH ctrl at 0 h


title: entorhinal cortex_oxbs_62

description: whole blood taken from sample 4172


title: Control119


title: entorhinal cortex_oxbs_51

description: whole blood taken from sample 3962


title: EC007_Rt_CTRL_wo_ETOH_0H


title: Control116


title: entorhinal cortex_oxbs_53

description: whole blood taken from sample 3952


title: entorhinal cortex_bs_59

description: whole blood taken from sample 3971

value: IV


title: Control115


title: entorhinal cortex_oxbs_64

description: whole blood taken from sample 4182

value: F


title: EC005_Sht_CTRL_w_ETOH_0H

source_name: Shoots_0.1% EtOH ctrl at 0 h

value: Shoots


title: Control117


title: entorhinal cortex_bs_53

description: whole blood taken from sample 3951


title: entorhinal cortex_oxbs_56

description: whole blood taken from sample 3922


title: entorhinal cortex_bs_62

description: whole blood taken from sample 4171

value: V


title: Control118

value: Serum


title: EC006_Sht_CTRL_w_ETOH_0H

value: seedlings (14 days-old)


title: Control112


title: Control114


title: entorhinal cortex_oxbs_52

description: whole blood taken from sample 4162

value: M


title: EC004_Sht_CTRL_w_ETOH_0H


title: EC002_Sht_CTRL_wo_ETOH_0H

source_name: Shoots_untreated_ 0 h


title: EC001_Sht_CTRL_wo_ETOH_0H


title: Control111


title: entorhinal cortex_bs_51

description: whole blood taken from sample 3961


title: Control113


title: entorhinal cortex_bs_52

description: whole blood taken from sample 4161


title: Control109


title: entorhinal cortex_bs_50

description: whole blood taken from sample 4151

value: III


title: entorhinal cortex_oxbs_50

description: whole blood taken from sample 4152


title: EC003_Sht_CTRL_wo_ETOH_0H


title: SJG6+NICD 3

city: London

first: Vasiliki

last: Salameti

address: Great Maze pond, Guy's Hospital, 28th Floor

department: CSCRM

institute: King's College London

description: Biological Replicate

hyb_protocol: The labelled DNA target and fragmented cDNA were hybridized on Human Gene 1.0 ST Arrays (Affymetrix).

scan_protocol: The microarrays were scanned on a GeneChip scanner 3000 (Affymetrix).

data_processing:
affymetrix-algorithm-name = rma-gene-full
affymetrix-algorithm-version = 1.0
affymetrix-array-type = HuGene-2_0-st
program-name = Expression Console
program-version = 1.2.1.20
Data were mined in R environment
Normalized values (logFC, p.value) NICD/CONTROL

label: biotin

source_name: Oral Tumor derived Cell line

label_protocol: cDNA was fragmented and labelled with the Affymetrix GeneChip Labeling Kit

growth_protocol: SJG6 was cultured on a feeder layer of J2 3T3 cells in complete FAD medium.

extract_protocol: RNA was extracted using RNAeasy kit, QIAGEN. RNA quantification was performed on Nanodrop-1000 spectrophotometer (Thermo Scientific: 1000).

value: OSCC line SJG6

value: a lentiviral system was used to restore active domain of NOTCH1 (NICD)


title: Control108


title: Control105


title: Control106


title: Control107


title: Control104


title: si-Dppa2-4_rep2

city: Beijing

first: Yangming

last: Wang

address: 5 Yiheyuan Road

department: Institute of Molecular Medicine

institute: Peking University

description:
replicate2
si-Dppa2-4_FPKM.txt

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using STAR v2.6.0
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Cufflinks v2.2.1
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample in txt file

source_name: Embryonic stem cell

growth_protocol: Mouse ESCs were cultured on 0.1% gelatin-coated plates in serum medium and leukemia inhibitory factor (1,000 unit /ml).

extract_protocol:
For RNA-seq, cells were treated with TRIzol and followed with phase seperation, RNA precipitation and RNA wash. Finally, RNA were dissolved in DEPC water.
For RNA-seq, total RNA was subjected to two rounds of purification using poly-T oligo-attached magnetic beads before the synthesis of double-stranded (ds) cDNA. The ds cDNA was ligated to adaptors and sequenced with illumina Hiseq2000 platform.

tag: genotype/variation

value: Dppa2/4 knock down

value: Mouse embryonic stem cell

tag: strain

tag: developmental stage

value: 3.5 days


title: si-Dppa2-4_rep1

description:
replicate1
si-Dppa2-4_FPKM.txt


title: si-Dppa4_rep1

description:
replicate1
si-Dppa2-4_FPKM.txt

value: Dppa4 knock down


title: entorhinal cortex_bs_49

description: whole blood taken from sample 4141

value: Control


title: EC009_Rt_CTRL_wo_ETOH_0H

tag: age

value: Roots


title: entorhinal cortex_bs_56

description: whole blood taken from sample 3921


title: Control103

source_name: Peripheral blood

tag: sample type


title: entorhinal cortex_oxbs_49

description: whole blood taken from sample 4142


title: entorhinal cortex_bs_47

description: whole blood taken from sample 3911

value: Alzheimer's disease

value: VI


title: Uninfected control

city: Bandar Sunway

first: Lian Yih

last: Pong

state: Selangor

address: Jalan Lagoon Selatan

department: Jeffrey Cheah School of Medicine and Health Sciences

country: Malaysia

institute: University Monash Malaysia

data_processing:
The post sequencing data processing was carried out using the UEA sRNA Workbench.
The adaptor sequences were trimmed and removed from the raw reads according to the 3’ adapter sequence (AGATCGGAAGAGCACACGTCT) obtained from the NEBNext® Small RNA Library Prep Set for Illumina® (NEB) instruction manual using the first eight nucleotides.
The adapter-removed reads were then filtered to the length between 16 bp and 35 bp followed by filtering against low complexity sequences which contain less than three distinct nucleotides.
The reads matching to known transfer and ribosomal RNA sequences were excluded using the database from RFAM, v10.
The clean reads were converted into FASTA format and then were mapped to the Mus musculus miRNA dataset from miRBase (version 20) using miRProf tool from UEA sRNA Workbench.
Genome_build: Mus musculus miRNA dataset from miRBase (version 20)
Supplementary_files_format_and_content: Microsoft Excel files containing sequences and expression value of miRNAs.

source_name: liver

extract_protocol:
The livers of three six-week old male BALB/c mice were harvested after 3 days of post infection with DENV-1. The small RNA of each sample was isolated from a pool of three mouse livers by using mirVana miRNA Isolation kit (Ambion).
A total of 100 ng of enriched sRNA from each sample was used to construct a respective library by using the NEBNext® Small RNA Library Prep Set for Illumina® (NEB).

tag: infection

value: Uninfected control

value: BALB/c

value: liver

value: six-week old


title: si-Dppa2_rep1

description:
replicate1
si-Dppa2-4_FPKM.txt

value: Dppa2 knock down


title: si-Dppa4_rep2

description:
replicate2
si-Dppa2-4_FPKM.txt


title: SJG6+NICD 1

description: Biological Replicate


title: Control110

value: Serum

tag: disease state


title: SJG6-CONTROL 2

description: Biological Replicate

tag: treatment

value: untreated


title: SJG6-CONTROL 3

description: Biological Replicate

value: OSCC line SJG6


title: si-NC_for_Dppa2-4_rep1

description:
replicate1
si-Dppa2-4_FPKM.txt

value: control


title: entorhinal cortex_oxbs_47

description: whole blood taken from sample 3912

value: F


title: Sample_SM1

city: Boston

first: Adam

middle: C

last: Gower

state: MA

address: 72 East Concord Street, E632

department: Department of Medicine

institute: Boston University School of Medicine

description:
Gene expression from laser-capture-microdissected cells with mild dysplasia from animal treated with acetone vehicle.
Sample_SM1

data_processing:
Demultiplexing and creation of FASTQ files was performed using the Illumina BaseSpace platform.
Trimmomatic was used to trim adapter sequences as well as to trim reads of poor quality using the following parameters:  ILLUMINACLIP:TruSeq3-SE.fa:2:30:10, LEADING:20, TRAILING:20, SLIDINGWINDOW:4:20, and MINLEN:20.  Greater than 99% of all reads in all samples were retained.
Samples were subsequently aligned using mm9 and 2-pass STAR alignment.  Gene and transcript level counts were calculated using RSEM using Ensembl annotation (build 65).
Quality metrics were calculated by STAR and RSeQC. edgeR was used to compute normalized data (library sizes normalized using TMM, trimmed mean of M-values, and log2 counts per million computed) and genes were excluded that either had an interquartile range equal to zero or a sum across samples equal or less than 1. A total of 15 samples were then removed that met 1 or more of the following filters:  1) less than 10% uniquely aligned reads per sample 2) values greater than 2 standard deviations from the mean for the mean Pearson correlation with all other samples calculated across all filtered genes 3) the number of genes detected per sample (defined as genes with cpm > 1) more than 1 standard deviation below the mean 4) 1st principal component values more than 1 standard deviation from the mean 5) 2nd principal component values more than 1 standard deviation from the mean 6) transcript integrity number (TIN, computed by RSeQC) values more than 1 standard deviation below the mean. After sample filtering, gene filtering was recomputed as described above on the final set of high-quality samples.
Genome_build: mm9
Supplementary_files_format_and_content: counts

source_name: laser-capture-microdissected cells

extract_protocol:
RNA from 40 fresh frozen samples of whole lung sections and LCM tissue from SWR/J and A/J mice treated with NTCU was extracted using the miRNAeasy kit (QIAGEN) according to manufacturer's protocol.
Sequencing libraries were prepared from total RNA samples using Illumina® TruSeq® RNA Sample Preparation Kit v2.

value: AJ

tag: total umol ntcu

tag: dysplasia grade

value: normal

tag: total reads

tag: uniquely aligned reads

tag: median tin

tag: passed qc

value: TRUE


title: si-NC_for_Dppa2-4_rep2

description:
replicate2
si-Dppa2-4_FPKM.txt

tag: cell type

value: Mouse embryonic stem cell

value: 3.5 days


title: Sample_8c

description:
Gene expression from laser-capture-microdissected cells with normal histology from animal treated with 15 umol NTCU.
Sample_8c

value: SWJ

value: mild dysplasia

value: FALSE


title: SJG6-CONTROL 1

description: Biological Replicate

tag: cell line


title: entorhinal cortex_bs_46

description: whole blood taken from sample 3871

tag: post-mortem diagnosis

value: Control

tag: gender

tag: age at death

tag: braak stage

tag: post-mortem interval(min)


title: Patient57

tag: sample type


title: Sample_84

description:
Gene expression from whole lung section from animal treated with 20 umol NTCU where the worst histological grade was carcinoma in situ.
Sample_84

source_name: whole lung section

tag: strain

value: carcinoma in situ


title: Control102

tag: disease state


title: Patient56


title: Patient55


title: entorhinal cortex_oxbs_48

description: whole blood taken from sample 3902

value: Alzheimer's disease

value: M

value: V


title: SJG6+NICD 2

description: Biological Replicate

tag: treatment

value: a lentiviral system was used to restore active domain of NOTCH1 (NICD)


title: Control101

value: Serum


title: entorhinal cortex_bs_48

description: whole blood taken from sample 3901


title: Patient58


title: DENV-1-infected

tag: infection

value: BALB/c

tag: tissue

value: liver

tag: age

value: six-week old


title: si-Dppa2_rep2

description:
replicate2
si-Dppa2-4_FPKM.txt

tag: genotype/variation

value: Dppa2 knock down

tag: developmental stage


title: Sample_82

description:
Gene expression from whole lung section from animal treated with 14 umol NTCU where the worst histological grade was moderate to severe dysplasia.
Sample_82

value: AJ

tag: total umol ntcu

tag: dysplasia grade

value: moderate to severe dysplasia

tag: total reads

tag: uniquely aligned reads

tag: median tin

tag: passed qc

value: TRUE


title: entorhinal cortex_oxbs_46

description: whole blood taken from sample 3872

tag: post-mortem diagnosis

tag: gender

value: F

tag: age at death

tag: braak stage


title: OE-Dppa2_rep2

description:
replicate2
OE-Dppa2_FPKM.txt

value: Dppa2 overexpression

tag: cell type

value: Mouse embryonic stem cell

tag: strain

value: 3.5 days


title: entorhinal cortex_bs_44

description: whole blood taken from sample 4081

value: Control

value: II

tag: post-mortem interval(min)


title: entorhinal cortex_oxbs_44

description: whole blood taken from sample 4082

value: M


title: entorhinal cortex_oxbs_43

description: whole blood taken from sample 3862

value: Alzheimer's disease

value: VI


title: si-Pias4_rep1

description:
replicate1
si-Pias4_FPKM.txt

value: Pias4 knock down


title: entorhinal cortex_bs_45

description: whole blood taken from sample 4111

value: V


title: OE-Empty_rep2

description:
replicate2
OE-Dppa2_FPKM.txt

value: control


title: OE-Dppa2_rep1

description:
replicate1
OE-Dppa2_FPKM.txt


title: OE-Empty_rep1

description:
replicate1
OE-Dppa2_FPKM.txt


title: Sample_83

description:
Gene expression from whole lung section from animal treated with 20 umol NTCU where the worst histological grade was SCC tumor.
Sample_83

value: SCC tumor

value: FALSE


title: Sample_81

description:
Gene expression from whole lung section from animal treated with acetone vehicle where the worst histological grade was normal.
Sample_81

value: AJ

value: normal


title: Sample_80

description:
Gene expression from whole lung section from animal treated with 50 umol NTCU where the worst histological grade was severe dysplasia.
Sample_80

value: SWJ

value: severe dysplasia


title: entorhinal cortex_oxbs_45

description: whole blood taken from sample 4112

value: F


title: Sample_8

description:
Gene expression from laser-capture-microdissected cells with normal histology from animal treated with 15 umol NTCU.
Sample_8

value: mild dysplasia


title: Sample_7c

description:
Gene expression from laser-capture-microdissected cells with normal histology from animal treated with 15 umol NTCU.
Sample_7c

value: TRUE


title: Patient51b

tag: sample type

value: Serum

tag: disease state


title: Patient50a


title: Patient50b


title: Patient52a


title: entorhinal cortex_oxbs_42

description: whole blood taken from sample 3852


title: Sample_78

description:
Gene expression from whole lung section from animal treated with 25 umol NTCU where the worst histological grade was moderate to severe dysplasia.
Sample_78

value: moderate to severe dysplasia


title: entorhinal cortex_bs_43

description: whole blood taken from sample 3861


title: Young 5

city: Palo Alto

first: Liana

middle: Nicole

last: Bonanno

state: California

address: 3801 Miranda Ave, Bldg 100 Rm D3-111

department: Neurology

institute: Stanford University

data_processing:
The quality of fastq files was assessed using FASTQC (v 0.11.2)
Trimmed reads were mapped to mouse mm9 reference genome using STAR (v 2.4.2a).
CuffDiff (v2.2.1) was used to perform differential analysis for RNAseq based on gene and transcript abundance  in terms of FPKM
R (v 3.2.2) and CummerRbund(v2.12.1) were used for visualization of various output files
Genome_build: mm9
Supplementary_files_format_and_content: Excel sheel of normalized read counts

source_name: young_brain endothelial cells

growth_protocol: Mice aged 3 (young) and 19 (Old) months

extract_protocol:
Hippocampi and cortex (pooled n=2 per sample) were dissected using Miltenyi neural dissociation kit. Brain endothelial cells were isolated via FACS. Total RNA was isolated with Rneasy Plus Micro kit with quality analyzed by Agilent 2100 Bioanalyzer.
cDNA was generated using SMART-seq v4 Ultra Low Input RNA kit from Clontech. Libraries were made via Illumina Nextera XT kit.

tag: age

value: 3 (young) months

tag: genotype/variation

value: Wild Type

tag: tissue

value: Brain>Cortex + Hippocampus

value: Brain endothelial cells


title: si-NC_rep1

description:
replicate1
si-Pias4_FPKM.txt

value: Mouse embryonic stem cell

tag: developmental stage

value: 3.5 days


title: Young 9


title: Sample_79

description:
Gene expression from whole lung section from animal treated with 50 umol NTCU where the worst histological grade was severe dysplasia.
Sample_79

tag: total umol ntcu

tag: dysplasia grade

tag: total reads


title: entorhinal cortex_bs_42

description: whole blood taken from sample 3851

value: Alzheimer's disease

value: M

value: VI


title: entorhinal cortex_oxbs_55

description: whole blood taken from sample 3812

value: Control

value: III


title: Patient49b


title: Young 4


title: Patient51a


title: entorhinal cortex_bs_55

description: whole blood taken from sample 3811


title: Patient48b


title: entorhinal cortex_oxbs_41

description: whole blood taken from sample 4022

value: V


title: Patient49a


title: Young 3


title: Sample_75

description:
Gene expression from whole lung section from animal treated with 30 umol NTCU where the worst histological grade was moderate to severe dysplasia.
Sample_75

value: SWJ

tag: uniquely aligned reads

tag: median tin

tag: passed qc


title: Patient47b


title: Sample_76

description:
Gene expression from whole lung section from animal treated with 30 umol NTCU where the worst histological grade was moderate to severe dysplasia.
Sample_76


title: entorhinal cortex_bs_41

description: whole blood taken from sample 4021

tag: post-mortem diagnosis

tag: gender

value: F

tag: age at death


title: Patient47a


title: Young 1

tag: strain

tag: cell type


title: Old 9

source_name: old_brain endothelial cells

value: 19 (Old) months


title: Sample_74

description:
Gene expression from whole lung section from animal treated with 15 umol NTCU where the worst histological grade was mild dysplasia.
Sample_74

value: mild dysplasia

value: TRUE


title: entorhinal cortex_bs_40

description: whole blood taken from sample 3931

source_name: entorhinal cortex

tag: braak stage

tag: post-mortem interval(min)


title: Sample_73

description:
Gene expression from whole lung section from animal treated with 15 umol NTCU where the worst histological grade was mild dysplasia.
Sample_73


title: Sample_77

description:
Gene expression from whole lung section from animal treated with 25 umol NTCU where the worst histological grade was moderate to severe dysplasia.
Sample_77

value: moderate to severe dysplasia

value: FALSE


title: Patient46b

description:
No additional extraction step was performed on the serum sample
Serum sample are not labeled
The serum was applied on the protein array, secondary anti-human IgG antibody used for detection.

tag: sample type

value: Serum

tag: disease state


title: Sample_72

description:
Gene expression from whole lung section from animal treated with acetone vehicle where the worst histological grade was normal.
Sample_72

value: normal


title: Patient46a


title: entorhinal cortex_oxbs_39

description: whole blood taken from sample 3882

value: II


title: Patient45b


title: Sample_71

description:
Gene expression from whole lung section from animal treated with acetone vehicle where the worst histological grade was normal.
Sample_71


title: Old 4

tag: age

tag: genotype/variation

value: Wild Type

tag: tissue

value: Brain>Cortex + Hippocampus

value: Brain endothelial cells


title: Young 2

value: 3 (young) months


title: Sample_70

description:
Gene expression from whole lung section from animal treated with acetone vehicle where the worst histological grade was normal.
Sample_70

tag: total umol ntcu

tag: dysplasia grade


title: entorhinal cortex_oxbs_38

description: whole blood taken from sample 3782

value: Alzheimer's disease

value: M

value: VI


title: Patient44b


title: Sample_7

description:
Gene expression from laser-capture-microdissected cells with mild dysplasia from animal treated with 15 umol NTCU.
Sample_7

value: SWJ

tag: total reads

tag: uniquely aligned reads


title: entorhinal cortex_oxbs_40

description: whole blood taken from sample 3932


title: entorhinal cortex_bs_38

description: whole blood taken from sample 3781


title: Patient44a


title: Old 1


title: Sample_50

description:
Gene expression from laser-capture-microdissected cells with carcinoma in situ from animal treated with 20 umol NTCU.
Sample_50

value: AJ

value: carcinoma in situ

tag: median tin

tag: passed qc


title: Sample_5

description:
Gene expression from laser-capture-microdissected cells with mild dysplasia from animal treated with 15 umol NTCU.
Sample_5

value: mild dysplasia


title: Sample_49

description:
Gene expression from laser-capture-microdissected cells from SCC tumor from animal treated with 20 umol NTCU.
Sample_49

value: SCC tumor

value: TRUE


title: entorhinal cortex_bs_36

description: whole blood taken from sample 3771

tag: post-mortem diagnosis

tag: gender

value: F

value: V


title: Patient43b

value: Serum


title: Old 7

tag: strain

value: 19 (Old) months


title: Patient43a


title: entorhinal cortex_oxbs_37

description: whole blood taken from sample 3752

value: Control

tag: age at death


title: Patient45a


title: entorhinal cortex_bs_39

description: whole blood taken from sample 3881

tag: braak stage

value: II


title: entorhinal cortex_bs_37

description: whole blood taken from sample 3751

tag: post-mortem interval(min)


title: Sample_48

description:
Gene expression from laser-capture-microdissected cells with moderate to severe dysplasia from animal treated with 14 umol NTCU.
Sample_48

value: moderate to severe dysplasia


title: Patient42b

tag: sample type


title: Old 3

value: Wild Type

value: Brain>Cortex + Hippocampus

tag: cell type

value: Brain endothelial cells


title: Patient42a

tag: disease state


title: Patient41b


title: Sample_47

description:
Gene expression from laser-capture-microdissected cells with moderate to severe dysplasia from animal treated with 14 umol NTCU.
Sample_47


title: Patient41a


title: Old 2

tag: age

tag: genotype/variation


title: entorhinal cortex_bs_35

description: whole blood taken from sample 3841

value: Alzheimer's disease

value: M

value: VI


title: Sample_46

description:
Gene expression from laser-capture-microdissected cells with normal histology from animal treated with acetone vehicle.
Sample_46

value: AJ

tag: total umol ntcu

value: normal


title: entorhinal cortex_oxbs_34

description: whole blood taken from sample 3822

value: I


title: Sample_45

description:
Gene expression from laser-capture-microdissected cells with moderate to severe dysplasia from animal treated with 25 umol NTCU.
Sample_45

value: SWJ

tag: dysplasia grade

value: TRUE


title: Patient40b


title: entorhinal cortex_bs_34

description: whole blood taken from sample 3821


title: entorhinal cortex_oxbs_36

description: whole blood taken from sample 3772

value: F

value: V


title: entorhinal cortex_oxbs_33

description: whole blood taken from sample 3802


title: Patient40a

value: Serum


title: entorhinal cortex_bs_33

description: whole blood taken from sample 3801


title: Patient39b


title: Sample_42

description:
Gene expression from laser-capture-microdissected cells with severe dysplasia from animal treated with 50 umol NTCU.
Sample_42

value: severe dysplasia

tag: total reads


title: Sample_43

description:
Gene expression from laser-capture-microdissected cells with severe dysplasia from animal treated with 50 umol NTCU.
Sample_43

tag: uniquely aligned reads

value: FALSE


title: Sample_41

description:
Gene expression from laser-capture-microdissected cells with moderate to severe dysplasia from animal treated with 30 umol NTCU.
Sample_41

value: moderate to severe dysplasia

tag: median tin


title: Patient39a


title: Patient38b


title: entorhinal cortex_bs_32

description: whole blood taken from sample 3721


title: entorhinal cortex_oxbs_35

description: whole blood taken from sample 3842


title: entorhinal cortex_oxbs_32

description: whole blood taken from sample 3722


title: entorhinal cortex_oxbs_31

description: whole blood taken from sample 3652


title: Patient38a


title: Sample_40

description:
Gene expression from laser-capture-microdissected cells with moderate to severe dysplasia from animal treated with 30 umol NTCU.
Sample_40

tag: passed qc


title: Sample_25

description:
Gene expression from laser-capture-microdissected cells with severe dysplasia from animal treated with 50 umol NTCU.
Sample_25


title: Patient37a

description:
No additional extraction step was performed on the serum sample
Serum sample are not labeled
The serum was applied on the protein array, secondary anti-human IgG antibody used for detection.


title: entorhinal cortex_oxbs_30

description: whole blood taken from sample 3632

tag: post-mortem diagnosis

value: Control


title: entorhinal cortex_bs_31

description: whole blood taken from sample 3651

tag: gender


title: Sample_44

description:
Gene expression from laser-capture-microdissected cells with moderate to severe dysplasia from animal treated with 25 umol NTCU.
Sample_44

tag: strain


title: Sample_2B

description:
Gene expression from laser-capture-microdissected cells with normal histology from animal treated with acetone vehicle.
Sample_2B


title: entorhinal cortex_bs_30

description: whole blood taken from sample 3631

tag: age at death


title: Patient34b


title: Sample_2

description:
Gene expression from laser-capture-microdissected cells with normal histology from animal treated with acetone vehicle.
Sample_2


title: Sample_20

description:
Gene expression from laser-capture-microdissected cells with moderate to severe dysplasia from animal treated with 25 umol NTCU.
Sample_20


title: sEV_Mphi_rep1

city: Erlangen

first: Martin

last: Eberhardt

address: Hartmannstr. 14

country: Germany

institute: University Hospital Erlangen

hyb_protocol: The hybridization procedure was performed according to the “miRNA Complete Labeling and Hyb Kit” protocol using the miRNA Complete Labeling and Hyb Kit (Agilent Technologies). Briefly, Cy3-labeled RNA in hybridization buffer was hybridized overnight (20 hours, 55 °C) to Agilent Human microRNA Microarrays 8x60K v16 (Design ID 046064) using Agilent’s recommended hybridization chamber and oven. Following hybridization, the microarrays were washed once with the Agilent Gene Expression Wash Buffer 1 for 5 min at room temperature followed by a second wash with preheated Agilent Gene Expression Wash Buffer 2 (37 °C) for 5 min

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

data_processing: The Agilent Feature Extraction Software (FES 10.7.3.1 ) was used to read out and process the microarray image files. Afterwards, signal intensities were normalized by input plasma volume with a volume of 15 ml as reference. For differential expression analysis in R, the 54-sample microarray dataset (14 healthy, 14 tumor, 15 high-risk, 11 low-risk) was quantile-normalized and log2-transformed. The human miRNAs on the array were then extracted, and those that failed to yield at least one intensity value above background were discarded (658 of 1205, 54 %). Limma was used on the remaining 547 miRNAs to fetch out pairwise differentially expressed ones between groups.

source_name: sEV from monocyte-derived macrophages

label_protocol: Sample labeling was performed as detailed in the “miRNA Microarray System with miRNA Complete Labeling and Hyb Kit” protocol (version 2.4, part number G4170-90011; Agilent Technologies).

growth_protocol:
Cell lines: Liver cell lines Huh7 and Sk-Hep-1 were grown in DMEM supplemented with 10 % Fetal calf serum and 1% penicillin-streptomycin. Sk-Hep1 cells were additionally maintained in 40 mM b-mercaptoethanol. LX-2 cells were cultured in DMEM high glucose supplemented with 2 % FCS, 1 % penicillin-streptomycin. All cells were grown at 37 °C under 5 % CO2.
Generation of immature/mature dendritic cells (DC): Leukoreduction system chambers (LRSCs) from healthy donors were acquired after plateletpheresis. The resulting platelet free cell sample was diluted 1:2 in PBS and the PBMC containing buffy coat was isolated after density gradient centrifugation on Lymphoprep (Axix Shield 1114544). Monocytes were isolated from PBMCs using BD IMag Anti-Human CD14 Magnetic Particles (BD Biosciences 557769). 6.0 x 106 monocytes were seeded in a 6-well plate in RPMI supplemented with 1 % human serum. Monocyte-derived DC were generated adding 800 IU/ml of recombinant GM-CSF and 250 IU/ml of recombinant IL-4. To generate mature DC, immature DC cultures were supplemented for 24 h with LPS (100 ng/ml) or a maturation cocktail (MC) (200 IU/ml IL-1ß, 1,000 IU/ml IL-6, 10 ng/ml TNF and 1 µg/ml Prostin E2.
Generation of Macrophages: Leukoreduction system chambers (LRSCs) from healthy donors were acquired after plateletpheresis. The resulting platelet free cell sample was diluted 1:2 in PBS and the PBMC containing buffy coat was isolated after density gradient centrifugation on Lymphoprep (Axix Shield 1114544). Monocytes were separated from the non-adherent fraction (NAF) by plastic adherence on cell culture flasks and cultured in RPMI supplemented with 1 % human serum and 1 % of penicillin/streptomycin. On days 1, 3, 5, 7 and 9 medium was supplemented with 800 IU/ml of GM-CSF. On day 11, medium was removed, cells were washed and 20 ml of RPMI supplemented with 1 % of EV-depleted human serum was added.

extract_protocol:
For EV isolation from cell cultures, cells were washed and 24 h later the supernatant was harvested (10 ml). Cell culture supernatants were collected after 48 h and centrifuged for 20 min at 2,000 g, 30 min at 10,000 g and ultra-centrifuged for 1 h at 100,000 g. Pellets were resuspended in 35 ml PBS and centrifuged at 100,000 g for 1 h. Pellets were resuspended in 100 µl PBS and considered as EV preparations.
Plasma samples were obtained from patients attending outpatients departments at the Universitätsklinikum Erlangen after signing an informed consent. The study was approved by the local ethics committee. Patients were assigned to the respective study groups based on their clinical stage. R0 operated patients were subdivided into high risk (HR) (stage II-IV) and low risk (LR) patients (stage I). T patients harbored tumor metastases (clinical stage III and IV), or primary tumors (clinical stage I – II) before surgery. Blood was drawn and 30 ml blood plasma was diluted with 30 ml PBS and centrifuged for 30 min at 2,000 g, 45 min at 12,000 g and ultra-centrifuged for 2 h at 110,000 g. Pellets were resuspended in 30 ml PBS and centrifuged at 110,000 g for 1 h. Pellets were again resuspended in 100 µl PBS and considered as EV preparations. For gradient purification, pEV were diluted in 2 ml of 2.5 M sucrose, 20 mM Hepes/NaOH, pH 7.4 and a linear sucrose gradient (2 - 0,25 M sucrose, 20 mM Hepes/NaOH pH 7.4) was layered on top of the EV suspension. The samples were then centrifuged at 210,000 g for 15 h. Gradient fractions were collected and ultra-centrifuged for 1 h at 110,000 g. Pellets were solubilized in SDS sample buffer or resuspended in 100 µl PBS. RNA was isolated with the use of Trizol (Sigma-Aldrich) followed by miRNeasy Kit (Qiagen)

tag: tissue

value: culture supernatant extracellular vesicles


title: Patient36b


title: entorhinal cortex_oxbs_29

description: whole blood taken from sample 3792

tag: braak stage

tag: post-mortem interval(min)


title: Patient32b

tag: sample type


title: Sample_13B

description:
Gene expression from laser-capture-microdissected cells with moderate to severe dysplasia from animal treated with 30 umol NTCU.
Sample_13B


title: sEV_mDC_rep1

source_name: sEV from mature monocyte-dervied dendritic cells


title: Sample_19

description:
Gene expression from laser-capture-microdissected cells with moderate to severe dysplasia from animal treated with 25 umol NTCU.
Sample_19


title: entorhinal cortex_bs_29

description: whole blood taken from sample 3791


title: Sample_3

description:
Gene expression from laser-capture-microdissected cells with normal histology from animal treated with acetone vehicle.
Sample_3


title: entorhinal cortex_bs_28

description: whole blood taken from sample 3761


title: sEV_SK-Hep1_rep1

source_name: sEV from liver cell line SK-Hep1


title: entorhinal cortex_oxbs_28

description: whole blood taken from sample 3762


title: Sample_1

description:
Gene expression from laser-capture-microdissected cells with normal histology from animal treated with acetone vehicle.
Sample_1


title: entorhinal cortex_bs_26

description: whole blood taken from sample 3701


title: Patient37b

tag: disease state


title: Control32


title: Patient31b


title: entorhinal cortex_oxbs_26

description: whole blood taken from sample 3702


title: Control31


title: Patient30b


title: entorhinal cortex_oxbs_25

description: whole blood taken from sample 3612


title: entorhinal cortex_bs_25

description: whole blood taken from sample 3611


title: pEV_MS_rep3

source_name: pEV from Multiple-Sclerosis patient, individual 60

tag: melanoma clinical stage

tag: melanoma at sampling date

value: blood extracellular vesicles


title: sEV_Huh7_rep1

source_name: sEV from liver cell line Huh7


title: sEV_Lx-2_rep1

source_name: sEV from liver cell line Lx-2


title: entorhinal cortex_oxbs_21

description: whole blood taken from sample 3592

value: II


title: Patient29b


title: Control30


title: sEV_immDC_rep1

source_name: sEV from immature monocyte-dervied dendritic cells


title: pEV_MS_rep1

source_name: pEV from Multiple-Sclerosis patient, individual 58


title: pEV_MS_rep2

source_name: pEV from Multiple-Sclerosis patient, individual 59


title: Patient28b


title: Control29


title: pEV_Kaposi_rep1

source_name: pEV from HIV-associated Kaposi subject, individual 57


title: entorhinal cortex_bs_21

description: whole blood taken from sample 3591


title: Patient27b

source_name: Peripheral blood


title: entorhinal cortex_oxbs_27

description: whole blood taken from sample 3552

value: M


title: pEV_preR0_rep2

source_name: pEV from melanoma bearer, individual 56

tag: primary-melanoma thickness (mm)

value: IA

value: primary

value: m

tag: age

tag: plasma input (ml)


title: entorhinal cortex_bs_27

description: whole blood taken from sample 3551


title: entorhinal cortex_oxbs_24

description: whole blood taken from sample 3692

value: Alzheimer's disease

value: VI


title: pEV_postR0_rep2

source_name: pEV from melanoma survivor, individual 56, two weeks after resection


title: Control27a


title: pEV_preR0_rep1

source_name: pEV from melanoma bearer, individual 55


title: Patient26b


title: entorhinal cortex_bs_24

description: whole blood taken from sample 3691


title: pEV_postR0_rep1

source_name: pEV from melanoma survivor, individual 55, two weeks after resection


title: entorhinal cortex_oxbs_22

description: whole blood taken from sample 3662


title: Patient25b


title: Control26a


title: pEV_low-risk_rep11

source_name: pEV from melanoma survivor with low relapse risk, individual 54


title: entorhinal cortex_bs_22

description: whole blood taken from sample 3661

source_name: entorhinal cortex


title: Control28a


title: Patient24b


title: pEV_low-risk_rep10

source_name: pEV from melanoma survivor with low relapse risk, individual 53


title: entorhinal cortex_oxbs_20

description: whole blood taken from sample 3642


title: entorhinal cortex_bs_20

description: whole blood taken from sample 3641


title: Patient23b


title: Control24a


title: pEV_low-risk_rep9

source_name: pEV from melanoma survivor with low relapse risk, individual 52

value: f


title: entorhinal cortex_oxbs_19

description: whole blood taken from sample 3542

value: F

value: I


title: pEV_low-risk_rep8

source_name: pEV from melanoma survivor with low relapse risk, individual 51


title: pEV_low-risk_rep7

source_name: pEV from melanoma survivor with low relapse risk, individual 50


title: entorhinal cortex_bs_14

description: whole blood taken from sample 3531


title: Control23a

value: Serum


title: entorhinal cortex_bs_19

description: whole blood taken from sample 3541


title: entorhinal cortex_oxbs_14

description: whole blood taken from sample 3532


title: entorhinal cortex_oxbs_23

description: whole blood taken from sample 3522

value: III


title: Patient22b


title: entorhinal cortex_bs_23

description: whole blood taken from sample 3521


title: pEV_low-risk_rep6

source_name: pEV from melanoma survivor with low relapse risk, individual 49


title: Control21a


title: entorhinal cortex_oxbs_13

description: whole blood taken from sample 3602


title: Control22a


title: pEV_low-risk_rep4

source_name: pEV from melanoma survivor with low relapse risk, individual 47

value: IB


title: pEV_low-risk_rep2

source_name: pEV from melanoma survivor with low relapse risk, individual 45


title: Patient21b


title: Control25a


title: pEV_low-risk_rep5

source_name: pEV from melanoma survivor with low relapse risk, individual 48


title: entorhinal cortex_oxbs_18

description: whole blood taken from sample 3622

value: V


title: Patient20b


title: Control19a

value: Control


title: pEV_low-risk_rep1

source_name: pEV from melanoma survivor with low relapse risk, individual 44


title: entorhinal cortex_bs_13

description: whole blood taken from sample 3601


title: pEV_high-risk_rep15

source_name: pEV from melanoma survivor with high relapse risk, individual 43

value: unknown primary

value: IIIC


title: Control20a

source_name: Peripheral blood


title: entorhinal cortex_bs_18

description: whole blood taken from sample 3621


title: Patient19b


title: entorhinal cortex_oxbs_11

description: whole blood taken from sample 3502


title: pEV_high-risk_rep12

source_name: pEV from melanoma survivor with high relapse risk, individual 40

value: IIIB

value: blood extracellular vesicles


title: pEV_high-risk_rep11

source_name: pEV from melanoma survivor with high relapse risk, individual 39

value: IIA


title: pEV_high-risk_rep13

source_name: pEV from melanoma survivor with high relapse risk, individual 41

value: IIC


title: entorhinal cortex_oxbs_12

description: whole blood taken from sample 3452


title: entorhinal cortex_bs_11

description: whole blood taken from sample 3501


title: Patient18b


title: pEV_high-risk_rep14

source_name: pEV from melanoma survivor with high relapse risk, individual 42

value: IV

value: m


title: entorhinal cortex_oxbs_10

description: whole blood taken from sample 3472

value: Alzheimer's disease

value: VI


title: pEV_high-risk_rep10

source_name: pEV from melanoma survivor with high relapse risk, individual 38

value: IIIA


title: Patient16b


title: entorhinal cortex_bs_12

description: whole blood taken from sample 3451

source_name: entorhinal cortex

value: F


title: Patient15b

value: Serum


title: Control17a


title: Control15a


title: Patient17b


title: pEV_high-risk_rep8

source_name: pEV from melanoma survivor with high relapse risk, individual 36

value: f


title: entorhinal cortex_bs_10

description: whole blood taken from sample 3471


title: Control18a


title: pEV_high-risk_rep9

source_name: pEV from melanoma survivor with high relapse risk, individual 37

value: IIB


title: pEV_high-risk_rep5

source_name: pEV from melanoma survivor with high relapse risk, individual 33


title: entorhinal cortex_oxbs_16

description: whole blood taken from sample 3412

value: M


title: entorhinal cortex_oxbs_17

description: whole blood taken from sample 3462


title: pEV_high-risk_rep7

source_name: pEV from melanoma survivor with high relapse risk, individual 35


title: pEV_high-risk_rep4

source_name: pEV from melanoma survivor with high relapse risk, individual 32


title: pEV_high-risk_rep6

source_name: pEV from melanoma survivor with high relapse risk, individual 34


title: Control14a

value: Control


title: entorhinal cortex_bs_16

description: whole blood taken from sample 3411


title: pEV_high-risk_rep3

source_name: pEV from melanoma survivor with high relapse risk, individual 31


title: Patient14b


title: pEV_high-risk_rep2

source_name: pEV from melanoma survivor with high relapse risk, individual 30


title: entorhinal cortex_bs_17

description: whole blood taken from sample 3461


title: Patient13b


title: Control13a


title: pEV_high-risk_rep1

source_name: pEV from melanoma survivor with high relapse risk, individual 29


title: entorhinal cortex_oxbs_8

description: whole blood taken from sample 3312

value: II


title: pEV_tumor_rep14

source_name: pEV from melanoma bearer, individual 28

value: primary


title: entorhinal cortex_bs_8

description: whole blood taken from sample 3311


title: Patient11b

source_name: Peripheral blood


title: Control12a


title: Patient12b


title: entorhinal cortex_oxbs_7

description: whole blood taken from sample 3442


title: pEV_tumor_rep13

source_name: pEV from melanoma bearer, individual 27

value: metastases


title: entorhinal cortex_bs_7

description: whole blood taken from sample 3441


title: entorhinal cortex_oxbs_6

description: whole blood taken from sample 3432


title: Patient10b


title: entorhinal cortex_bs_9

description: whole blood taken from sample 3341


title: pEV_tumor_rep12

source_name: pEV from melanoma bearer, individual 26

value: blood extracellular vesicles


title: Control11a


title: pEV_tumor_rep10

source_name: pEV from melanoma bearer, individual 24


title: pEV_tumor_rep11

source_name: pEV from melanoma bearer, individual 25


title: entorhinal cortex_oxbs_9

description: whole blood taken from sample 3342


title: entorhinal cortex_bs_6

description: whole blood taken from sample 3431


title: Control10a


title: Patient9b


title: pEV_tumor_rep9

source_name: pEV from melanoma bearer, individual 23

value: not measured


title: Control9a


title: entorhinal cortex_oxbs_15

description: whole blood taken from sample 3212

source_name: entorhinal cortex


title: entorhinal cortex_oxbs_5

description: whole blood taken from sample 3162


title: entorhinal cortex_bs_5

description: whole blood taken from sample 3161


title: pEV_tumor_rep8

source_name: pEV from melanoma bearer, individual 22


title: Patient7b


title: Control8a


title: pEV_tumor_rep7

source_name: pEV from melanoma bearer, individual 21


title: Patient7a


title: entorhinal cortex_oxbs_4

description: whole blood taken from sample 2792


title: pEV_tumor_rep5

source_name: pEV from melanoma bearer, individual 19


title: Patient6a


title: entorhinal cortex_oxbs_3

description: whole blood taken from sample 3392

value: V


title: Patient6b


title: Patient5b


title: entorhinal cortex_bs_3

description: whole blood taken from sample 3391


title: entorhinal cortex_bs_4

description: whole blood taken from sample 2791


title: pEV_tumor_rep3

source_name: pEV from melanoma bearer, individual 17

value: III


title: entorhinal cortex_oxbs_2

description: whole blood taken from sample 2692


title: Patient8b


title: Patient5a


title: pEV_tumor_rep4

source_name: pEV from melanoma bearer, individual 18

value: IIIB

value: m


title: entorhinal cortex_bs_2

description: whole blood taken from sample 2691

value: Alzheimer's disease

value: VI


title: pEV_tumor_rep2

source_name: pEV from melanoma bearer, individual 16

value: IV


title: Patient4b

value: Serum


title: Patient4a


title: entorhinal cortex_oxbs_1

description: whole blood taken from sample 2622

value: F


title: pEV_tumor_rep1

source_name: pEV from melanoma bearer, individual 15

value: f


title: Patient3b


title: pEV_healthy_rep14

source_name: pEV from healthy control, individual 14


title: entorhinal cortex_bs_15

description: whole blood taken from sample 3211

value: M


title: entorhinal cortex_bs_1

description: whole blood taken from sample 2621

value: Control


title: Patient2b


title: pEV_healthy_rep13

source_name: pEV from healthy control, individual 13


title: pEV_healthy_rep11

source_name: pEV from healthy control, individual 11


title: pEV_healthy_rep10

source_name: pEV from healthy control, individual 10


title: pEV_healthy_rep9

source_name: pEV from healthy control, individual 9


title: pEV_tumor_rep6

source_name: pEV from melanoma bearer, individual 20

value: IIC


title: Patient1b

source_name: Peripheral blood


title: Patient2a


title: Patient1a


title: pEV_healthy_rep8

source_name: pEV from healthy control, individual 8


title: pEV_healthy_rep12

source_name: pEV from healthy control, individual 12


title: pEV_healthy_rep7

source_name: pEV from healthy control, individual 7


title: pEV_healthy_rep6

source_name: pEV from healthy control, individual 6


title: pEV_healthy_rep3

source_name: pEV from healthy control, individual 3


title: pEV_healthy_rep5

source_name: pEV from healthy control, individual 5


title: pEV_healthy_rep1

source_name: pEV from healthy control, individual 1


title: pEV_healthy_rep2

source_name: pEV from healthy control, individual 2


title: adult (rep3)

city: Warsaw

first: Iga

last: Wasilewska

address: 4 Ks. Trojdena Street

country: Poland

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using Bio-Rad CFX Maestro 1.0 software
For the normalization it uses the geometrical average of four housekeeping genes: Actin beta 1 (actb1), glyceraldehyde-3-phosphate dehydrogenase (gapdh), tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein zeta polypeptide (yhwaz), and ribosomal protein S18 (rps18). Stability of the reference genes was checked using Reference Gene Selection Tool and all of them were evaluated as at least acceptable.
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
Fold Change worksheet reports adult/larvae ratios.

label: SYBR Green

organism: Danio rerio

source_name: brain,1-year-old adult zebrafish

label_protocol: RNA templates (1000 ng) were used to synthesize first-strand cDNA using iScript reverse transcription supermix (Bio-Rad, catalog no. 1708840). Real-time polymerase chain reaction (RT-PCR) was performed in duplicate using SsoAdvanced Universal SYBR Green Supermix (Bio-Rad, catalog no. 1725274) and 96-well custom plates that contained primers for target and reference genes (Bio-Rad). RT-PCR were performed (CFX RT-PCR Detection System, Bio-RAD) with 40 cycles at 95 oC for 5 seconds and 60 oC for 30 seconds.

growth_protocol: Wildtype (AB line) zebrafish were used in the study. All of the animals were maintained according to previously described methods in the Zebrafish Core Facility (ZCF) that is a licensed breeding and research facility (PL14656251 – registry of the District Veterinary Inspectorate in Warsaw; 064 and 051 – registry of the Ministry of Science and Higher Education) at the International Institute of Molecular and Cell Biology in Warsaw. All experiments with larvae and adult fish were performed in accordance to the European Communities Council Directive (63/2010/EEC). Adult zebrafish and larvae were kept in E3 medium (2.48 mM NaCl, 0.09 mM KCl, 0.164 mM CaCl2·2H2O, and 0.428 mM MgCl2·6H2O) at 28.5°C.

extract_protocol: Adult, 1-year-old zebrafish were anesthetized with MS-222, and brains were dissected. Material from six fish was mixed for one RNA sample and homogenized in Qiazol (Qiagen, catalog no. 79306). Total RNA was extracted using TRIzol/chloroform method, digested with DNase I, and purified with the RNA Clean and Concentrator Kit (ZYMO Research, catalog no. R1013) according to the manufacturer’s instructions. RNA from zebrafish larvae was prepared using the same protocol, with the exception that 50 heads were dissected from larvae with needles at 5 days postfertilization (dpf) and pooled as one sample. The RNA quality was verified by measuring absorbance at 260, 280, and 230 nm. Only samples with A260/280 nm and A230/280 nm > 1.8 were used for the analysis.

value: AB


title: adult (rep2)

institute: International Institute of Molecular and Cell Biology


title: Patient3a


title: adult (rep1)


title: pEV_low-risk_rep3

source_name: pEV from melanoma survivor with low relapse risk, individual 46

value: IA


title: larvae (rep3)

source_name: head, 5 dpf zebrafish


title: larvae (rep1)


title: larvae (rep2)


title: pEV_healthy_rep4

source_name: pEV from healthy control, individual 4

value: blood extracellular vesicles


title: Hwt4_No_2_b2

status: Public on Mar 04 2019

city: Lausanne

first: Frederic

last: Raymond

address: Campus EPFL - Quartier de l'Innovation

department: Functional Genomics

country: Switzerland

institute: Nestle Institute of Health Sciences

hyb_protocol: Affymetrix hybridization procedure.

scan_protocol: Affymetrix GeneChip scanner 3000 7G.

data_processing: Data were background subtracted, log2 transformed, and quantile normalized using RMA in Partek GS software.

label: Biotin

source_name: Hepatocytes, WT, Vehicle

label_protocol: Labeled-cRNA was performed following TotalPrep RNA Amplification Kit. cRNA fragmentation was done following Affymetrix procedure, prior to hybridization.

growth_protocol:
C57BL/6 mice were obtained from Jackson Laboratories.
Mouse embryonic fibroblasts (MEFs) control or AMPK α1-/-/α2-/- were cultured in DMEM-Glutamax supplemented with 10% fetal calf serum (FCS) and 1% penicillin streptomycin. Cells were treated with vehicle (DMSO), AICAR 2 mM or 991 10 μM for 4 h and subsequently harvested.
Primary hepatocytes were isolated by collagenase perfusion and prepared as previously described (Fullerton et al., 2009). More in details, cells were plated on collagen-coated plates in M199-Glutamax containing 10% FCS, 1% penicillin streptomycin, 1 M HEPES, 10 nM insulin, 200 nM T3, 100 nM dexamethasone, and allowed to adhere for 4 h. Then cells were washed with PBS and provided with media comprising M199-Glutamax, 1% penicillin streptomycin and 100 nM dexamethasone. Hepatocytes were incubated overnight at 37 °C, and the experiments were performed the following morning. Briefly, hepatocytes were exposed to vehicle (DMSO), AICAR 300 μM or 991 3 μM for 4 h and then harvested.

extract_protocol: Total RNA was extracted using the RNAdvance Tissue Kit (A32645; Agencourt) and quantified by RiboGreen (R11490; ThermoFisher). RNA integrity was determined by Fragment Analyzer.

tag: strain/background

tag: cell type

value: Hepatocytes

tag: genotype/variation

value: WT

tag: treatment

value: Vehicle

tag: technical replicate

tag: biological replicate


title: Hwt4_AICAR_300uM_5_b2

source_name: Hepatocytes, WT, AICAR

value: AICAR


title: Hwt4_AICAR_300uM_4_b2


title: Hwt4_No_5_b2


title: Hwt4_No_3_b2


title: Hwt4_991_3uM_3_b2

source_name: Hepatocytes, WT, 991


title: Hwt4_AICAR_300uM_1_b2


title: Hwt4_No_1_b2


title: Hwt4_991_3uM_1_b2


title: Hwt4_No_4_b2


title: Hwt4_AICAR_300uM_3_b2


title: Hwt4_991_3uM_4_b2


title: Hko4_No_4_b2

source_name: Hepatocytes, dKO, Vehicle

value: AMPK alpha1-/- alpha2-/-


title: Hko4_No_5_b2


title: Hko4_AICAR_300uM_3_b2

source_name: Hepatocytes, dKO, AICAR


title: Hko4_AICAR_300uM_4_b2


title: Hko4_AICAR_300uM_2_b2


title: Hko4_No_1_b2


title: Hko4_991_3uM_2_b2

source_name: Hepatocytes, dKO, 991


title: Hko4_AICAR_300uM_1_b2


title: Hko4_991_3uM_5_b2


title: Hko4_AICAR_300uM_5_b2


title: Hko4_991_3uM_4_b2


title: Hwt4_991_3uM_2_b2


title: Hwt4_991_3uM_5_b2


title: Hwt4_AICAR_300uM_2_b2


title: Hko4_No_3_b2


title: Hko4_991_3uM_3_b2


title: Hko4_991_3uM_1_b2


title: Hwt4_AICAR_300uM_4_b1


title: Hwt4_AICAR_300uM_5_b1


title: Hwt4_No_4_b1


title: Hwt4_991_3uM_4_b1


title: Hwt4_AICAR_300uM_2_b1


title: Hwt4_No_1_b1


title: Hwt4_No_3_b1


title: Hko4_No_2_b2


title: Hwt4_991_3uM_3_b1


title: Hwt4_No_5_b1


title: Hwt4_AICAR_300uM_1_b1


title: Hwt4_AICAR_300uM_3_b1


title: Hwt4_No_2_b1


title: Hko4_No_5_b1


title: Hko4_No_1_b1


title: Hko4_No_3_b1


title: Hwt4_991_3uM_2_b1


title: Hwt4_991_3uM_5_b1


title: Hko4_991_3uM_4_b1


title: Hko4_AICAR_300uM_3_b1


title: Hko4_AICAR_300uM_2_b1


title: Hko4_991_3uM_5_b1


title: Hko4_991_3uM_2_b1


title: Hwt4_991_3uM_1_b1


title: Hko4_991_3uM_1_b1


title: Hko4_AICAR_300uM_1_b1


title: Hko4_991_3uM_3_b1


title: Hko4_AICAR_300uM_5_b1


title: E24 MEF wt P25 4H_0004 No Treat

source_name: MEF, WT, Vehicle

value: MEF

value: Not Applicable