title: TET2KD_LSK

city: Miyazaki

first: Takuro

last: Kameda

address: 5200, Kihara, Kiyotake

department: Division of Gastroenterology and hematology, Department of Internal medicine

institute: University of Miyazaki

description: Gene expression in TET2KD LSK cells at 10-16 weeks post-transplantation

hyb_protocol: For each hybridization, 1.65 ug of Cy3 labeled cDNA were hybridized at 65  for 17 hours to an Agilent Mouse GE 8x60K Microarray (Design ID: 028005).

scan_protocol: After washing, microarrays were scanned using an Agilent DNA microarray scanner.

data_processing: Intensity values of each scanned feature were quantified using Agilent feature extraction software version 10.7.3.1, which performs background subtractions. We only used features which were flagged as no errors (present flags) and excluded features which were not positive, not significant, not uniform, not above background, saturated and population outliers (marginal and absent flags).

source_name: Bone marrow LSK cells, TET2 knock down

label_protocol: Two ug of purified, amplified cDNA were used as input into the Agilent Genomic DNA Enzymatic Labeling Kit according to the manufacturers instructions. The Cy3-labeled cDNA was quantitated and dye incorporation determined by Nanodrop.

extract_protocol: Total RNA was extracted by Trizol method, and was used as input into the Ovation Pico WTA System V2(NuGen,San Carlos, CA) according to the manufacturers instructions. The NuGEN Ovation amplification methodology uses an isothermal linear amplification using DNA/RNA chimeric primers.

treatment_protocol: Freshly isolated bone marrow cells were stained by appropriate antibodies, and then sorted on FACSAriaII (BD).

tag: transplantation

value: TET2KD E14.5 fetal liver cells

tag: background mouse strain


title: 5-1134-s3

status: Public on Oct 16 2014

type: RNA

city: Cleveland

first: John

last: Barnard

state: Ohio

address: 9500 Euclid Ave.

department: Quantitative Health Sciences

country: USA

institute: Cleveland Clinic Foundation

description: biological replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The raw data were log2 transformed and processed with background correction and quantile normalization using R statistical packages.  Linear models and empirical Bayes method in Lima (Smyth, Stat Appl Genet Mol Biol 2004; 3:Article3) were used to access the differential expression between the wild types and transgenics.

molecule: total RNA

organism: Mus musculus

source_name: 3 wk transgenic, severe line rep1

growth_protocol: Mice were housed in microinsular cages in a dedicated mouse room in the Lerner Research Institute's virarium.  Animals were fed a standard diet.

extract_protocol: Mice were euthanized by carbon dioxide inhalation, and hearts were excised postmortem.  Total RNA was extracted with Trizol Reagent (Invitrogen), DNase-treated using the DNA-free Kit (Ambion), and cleaned up using the RNeasy Kit (Qiagen) following manufacturers' protocols.  RNA concentrations and quality were confirmed on a Nanodrop ND-1000 spectrophotometer and Agilent Bio-analyzer.

tag: strain

value: FVB/N

tag: transgenic line

tag: genotype

value: transgenic

tag: gender

value: female

tag: age

value: 3 weeks

tag: tissue

value: Whole heart


title: E11.5 Sox9-1

city: Stanford

first: Seung

last: Kim

state: CA

address: 279 Campus Dr B303

department: Developmental Biology

institute: Stanford University

description: replicate 1

hyb_protocol: Affymetrix GeneChip Hybridization, Wash, and Stain Kit

scan_protocol: Affymetrix GeneChip Scanner 3000 7G

data_processing: RMA normalization using justRMA package in R 2.11.1

label: Biotin

label_protocol: NuGen Amplication and Biotin Labeling Kit V2

extract_protocol: PicoPure Kit

tag: strain background

tag: genotype/variation

value: wild type

tag: developmental stage

value: pancreas

tag: cell population


title: Double mutant_LSK

country: Japan

description: Gene expression in double mutant LSK cells at 10-16 weeks post-transplantation

source_name: Bone marrow LSK cells, double mutant

value: Double mutant

value: Double mutant E14.5 fetal liver cells


title: 4-3316-wm24

description: biological replicate 1

source_name: 24 wk wildtype, mild line rep1

value: wildtype

value: 24 weeks


title: BirA control replicate 1

city: Austin

first: Jonghwan

state: TX

address: 2506 Speedway NMS 4.246

department: Department of Molecular Cell and Developmental Biology, Institute for Cellular and Molecular Biology

institute: University of Texas at Austin

description: Gene expression data

hyb_protocol: A hybridization mixture of the fragmented DNA and probe array control was prepared, followed by hybridization to the probe array during a 16 hour incubation.

scan_protocol: GeneChips were scanned by Affymetrix Scanner 3000

data_processing: Expression data were normalized using a robust multiple array (RMA).

source_name: embryonic stem cells

label_protocol: cDNA synthesis was performed with qScript cDNA supermix (Qunata), followed by labelling with Cy3.

growth_protocol: Mouse J1 ES cells were maintained in DMEM (Dulbecco’s modified Eagle’s medium) supplemented with 20% fetal bovine serum (FBS), 2mM of L-glutamine, 100uM of non-essential amino acid, 1% of nucleoside mix (100X stock, Sigma), 100uM of β-mercaptoethanol, 1000U/ml of recombinant leukemia inhibitory factor (LIF, Chemicon) and 50U/ml of penicillin/streptomycin. ES cells were cultured in 0.1% gelatin coated dishes.

extract_protocol: Total RNA was isolated from cultured cells using RNeasy plus mini kit (Qiagen).

tag: treatment

value: BirA control

tag: cell line

value: J1 ES cells


title: AF0101_SR_T9

city: Guildford

first: Emma

last: Laing

address: Stag Hill

country: United Kingdom

institute: University of Surrey

description: Blood taken at 14:25 following 31.5 hours awake after following a Sleep Restriction protocol from a Per3 5\5 genotype subject (Subject AF0101)

hyb_protocol: Labelled cRNA (1.65 μg) was hybridized on a Whole Human Genome 4 x 44K custom oligonucleotide microarray (G2514F, AMADID 026817; Agilent Technologies). Standard manufacturer's instructions for one-colour gene expression hybridization and washing steps were followed. The microarrays were hybridized at 65°C for 17 h in an Agilent hybridization oven with rotisserie at 10 rpm. The microarrays were washed with Agilent Wash Buffer 1, pre-warmed Wash Buffer 2 (37°C) and acetonitrile according to the manufacturer’s instructions. The last washing step was performed with Agilent Stabilization and Drying Solution for 30 sec.

scan_protocol: The processed microarrays were scanned using an Agilent Microarray Scanner with a resolution of 5 μm, exploiting the extended dynamic range feature. The two images derived from each slide scanned at 10% and 100% PMT were imported into Agilent Feature Extraction software (Version 10.7.1.1) for image analysis.

data_processing: Individual samples were filtered based on AgilentQC metrics of reproducibility statistics, minimum detection level estimates and feature flags. Samples with a median coefficient of variation of less than 10% in spike ins or non-control replicated probes (NCRPs) were retained and quantile-normalised using the R Bioconductor package limma. NCRPs along with their corresponding flags were averaged. Probes with more than 5 flagged samples within a subject in more than half of the total number of subjects were excluded. In addition, for time-series analyses, series with 2 consecutive or more than 2 missing time points were excluded.

organism: Homo sapiens

label_protocol: cRNA was synthesized and fluorescently labelled with Cy3-CTP from 100 ng of total RNA using Agilent's Low Input Quick Amp Labeling Kit.

growth_protocol: Blood samples were collected via an indwelling venous cannula sited in the forearm for minimum discomfort and restriction of movement. Cannulae were kept patent by the use of sterile saline. Each sample tube was coded for subject and sample collection time (participant code/sample type/sequential number)

extract_protocol: Total RNA was isolated using a PAXgene Blood RNA Kit and a QiaCube robot (Qiagen, Hilden, Germany). The RNA was quantified and the A260/280 nm and A260/230 nm ratios were determined using a NanoDrop ND1000 spectrophotometer (Wilmington, DE). RNA quality was assessed using the Bioanalyzer 2100 (Agilent, Santa Clara, CA).

treatment_protocol: 2.5 ml of blood is drawn into the PAXGene tube at each sampling point. The tube is inverted 10 times to mix. The tube is then stored at room temperature for 4 hours in upright position. The tube is transferred to -50°C and placed lying down (never in upright position as this may cause the tube to crack) for storage at the university of Surrey Clinical Research Centre. The tube is transferred on ice to University of Surrey Faculty of Health and Medical Sciences for storage/processing

value: Blood

tag: sleepprotocol

value: Sleep Restriction

tag: hoursawake

tag: timesampletaken

tag: circadianphase


title: AF0033_SR_T8

description: Blood taken at 12:10 following 28.5 hours awake after following a Sleep Restriction protocol from a Per3 4\4 genotype subject (Subject AF0033)


title: WSB-mice_liver_CFDdiet-12wks_rep3

city: Jefferson

first: Volodymyr

last: Tryndyak

address: 3900 NCTR Rd

department: Division of Biochemical Toxicology

institute: US-FDA National Center for Toxicological Research

description: Gene expression in the livers of WSB/EiJ mice fed a CFD diet for 12 weeks

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 SurePrint G3 Mouse GE Oligo Microarrays (G4858A-028005) 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 5um, 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).

source_name: WSB-mice, liver, CFDdiet-12wks, replicate 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the Quick-Amp Labeling kit (Agilent Technologies) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted from liver tissue 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: Male A/J, C3H/HeJ and WSB/EiJ were housed in sterilized cages in a temperature-controlled room (24°C) with a 12-h light/dark cycle, and given ad libitum access to water and NIH-41 irradiated pelleted diet. At 8 weeks of age, mice from each strain were allocated randomly to control and experimental groups. Mice in the methyl-donor-deficient experimental groups were maintained on a diet low in methionine (0.17% w/w) and lacking choline and folic acid (diet no. 519541, choline- and folate-deficient, iron-supplemented, and l-amino acid-defined diet; Dyets, Bethlehem, PA, USA) for 12 weeks. Mice in the methyl-adequate control groups received the same diet supplemented with 0.4% methionine, 0.3% choline bitartrate, and 2 mg/kg folic acid. Experimental and control mice were euthanized by exsanguination following deep isoflurane anesthesia 12 weeks after diet initiation. The liver was snap-frozen immediately in liquid nitrogen and stored at −80 °C for subsequent analyses.

value: WSB/EiJ

value: liver

value: Male

value: 20 weeks


title: WSB-mice_liver_CFDdiet-12wks_rep4

source_name: WSB-mice, liver, CFDdiet-12wks, replicate 4


title: AF0122_SR_T4

description: Blood taken at 23:35 following 16.5 hours awake after following a Sleep Restriction protocol from a Per3 5\5 genotype subject (Subject AF0122)


title: Arid3a OE-Pool replicate 1

description: Gene expression data

value: Arid3a overexpression pool

tag: sample type

value: pool


title: AF0033_SE_T2

description: Blood taken at 20:00 following 10.5 hours awake after following a Sleep Exentsion protocol from a Per3 4\4 genotype subject (Subject AF0033)

value: Sleep Extension


title: AF0069_SE_T2

description: Blood taken at 20:35 following 10.5 hours awake after following a Sleep Exentsion protocol from a Per3 4\4 genotype subject (Subject AF0069)


title: RTE_bloto, biological rep3

city: Singapore

first: Brenda

middle: Yuyuan

last: Han

address: 61 Biopolis Drive, Proteos

country: Singapore

institute: Institute of Molecular and Cell Biology, A*STAR

description: Gene expression data from blt/blt CD4+ RTEs

hyb_protocol: Labeled libraries were hybridized to Affymetrix Mouse 1.0 ST arrays according to Affymetrix's GeneChip Expression Analysis Technical Manual 702232 Rev. 3. Arrays were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Arrays were scanned with the Affymetrix GeneChip® Scanner 3000 7G System.

data_processing: Affymetrix CEL files containing raw, probe-level signal intensities were analyzed in Bioconductor using the affy R package, with RMA normalization and probeset definitions from Brainarray custom CDF (mogene10st_Mm_ENTREZG_17.1.0).

label: biotin

source_name: CD4+ RTEs, blt/blt

label_protocol: cDNA was synthesized and amplified using the Ovation Pico WTA System V2 (NuGEN, San Carlos, CA). The resulting libraries were fragmented and labeled using the Encore Biotin Module (NuGEN).

growth_protocol: Hematopoietic chimeras were generated by reconstituting lethally irradiated CD45.1+ hosts with a mix of CD45.1+CD45.2+ Rag1-GFP WT and CD45.2+ Rag1-GFP blt/blt bone marrow. Cells were isolated from spleen and peripheral lymph nodes by mechanical disaggregation through a 40μm nylon sieve. WT and bloto RTEs (CD4+ CD62Lhi CD44lo GFPhi) were sorted on a FACSAria with ≥98% purity. Dead cells were excluded with DAPI.

extract_protocol: Total RNA was isolated using the RNeasy Micro Kit (Qiagen).

tag: cell type

value: CD4+ naïve T cells (recent thymic emigrants)

value: blt/blt

tag: background strain


title: JAK2V617F_LSK

description: Gene expression in JAK2V617F LSK cells at 10-16 weeks post-transplantation

source_name: Bone marrow LSK cells, JAK2V617F

tag: transplantation

value: JAK2V617F E14.5 fetal liver cells

tag: background mouse strain


title: KO-rep1

city: Dallas

first: Lora

middle: V

last: Hooper

address: 5323 Harry Hines Blvd.

department: Immunology

institute: The University of Texas Southwestern Medical Center at Dallas

data_processing: The data were processed with Illumina GenomeStudio and the Limmia package with R.

source_name: bone marrow common lymphoid progenitor (CLP) cells

label_protocol: Total RNA were amplified by two-round of amplification to generate Biotin-aRNA.

growth_protocol: Mice were maintained in specific pathogen free mouse facilities at The University of Texas Southwestern Medical Center.

extract_protocol: Total RNA was isolated with the PicoPure RNA Isolation Kit (Life Technologies).

treatment_protocol: Common lymphoid progenitor (CLP) cells were purified by FACS sorting, as Lin- CD45+ cKitlow CD127+ Sca1low Flt3+alpha4beta7 from the bone marrows of adult mice.

tag: genotype

value: common lymphoid progenitor (CLP) cell


title: KO-rep2


title: E15.5 Beta Cell -4

description: replicate 4

source_name: E15.5 Beta Cell

value: wild type

tag: tissue

value: pancreas

value: Beta Cell


title: WT_LSK

description: Gene expression in WT LSK cells at 10-16 weeks post-transplantation

source_name: Bone marrow LSK cells, wild type

value: Wild type

value: Wild type E14.5 fetal liver cells


title: Arid3a OE-Pool replicate 2

description: Gene expression data

value: J1 ES cells


title: WT-rep2

value: wild-type


title: WT-rep1


title: 2-3733-ws3

description: biological replicate 1

source_name: 3 wk wildtype, severe line rep1

tag: strain

value: FVB/N

tag: transgenic line

value: wildtype

tag: gender

value: female

tag: age

value: 3 weeks

value: Whole heart


title: AF0089_SR_T8

description: Blood taken at 13:00 following 28.5 hours awake after following a Sleep Restriction protocol from a Per3 4\4 genotype subject (Subject AF0089)

value: Blood

value: Sleep Restriction


title: AF0033_SE_T3

description: Blood taken at 23:04 following 13.5 hours awake after following a Sleep Exentsion protocol from a Per3 4\4 genotype subject (Subject AF0033)

value: Sleep Extension


title: KO-rep3


title: 3-2656-m24

description: biological replicate 1

source_name: 24 wk transgenic, mild line rep1

value: transgenic

value: 24 weeks


title: WT-rep3

value: common lymphoid progenitor (CLP) cell


title: 1-2798-s24

description: biological replicate 1

source_name: 24 wk transgenic, severe line rep1


title: AF0139_SE_T8

description: Blood taken at 11:45 following 28.5 hours awake after following a Sleep Exentsion protocol from a Per3 5\5 genotype subject (Subject AF0139)


title: SKBR3 cell tranfected with miR671-5p nucleotide, biological rep2

city: Washington

first: Sidney

middle: W

last: Fu

state: DC

address: 2300 Eye St. NW, Ross 402C

department: Medicine

institute: George Washington University

description:
Sample name: SKBR3 OV2
SKBR3 cell line, mammary gland, breast; derived from metastatic site: pleural effusion
Gene expression data from SKBR3 cell lines transfected with miR671-5p, bio rep 2

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Affymetrix Human Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with Agilent Genespring GX using default analysis and normalization method for Affymetrix Gene array. RMA normalization and baseline to the median.

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

growth_protocol: Cell lines are cultured in Dulbecco’s modified Eagle’s medium (DMEM) (Lonza) supplemented with 10% fetal bovine serum and 1% penicillin and streptomycin antibiotics.

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

treatment_protocol: For transient transfection, 240000 cells of each cell line were seeded in a 6-well plate,cultured in DMEM medium supplemented with 10% FBS in a 37°C humidified incubator with 5% CO2. After overnight incubation, cells reached 30%-50% confluence and were transiently transfected with miR-671-5p mimic or mock (Ambion) by Lipofectamine RNAiMAX (Life Technologies) using the Opti-MEM Reduced Serum Medium (Life Technologies). Cells were subjected for further analysis after 24 h transfection.

value: mammary gland, breast

tag: transfection

value: mature miR-671-5p sequence


title: RTE_WT, biological rep3

description: Gene expression data from WT CD4+ RTEs

source_name: CD4+ RTEs, wild-type

value: CD4+ naïve T cells (recent thymic emigrants)


title: RTE_bloto, biological rep1

value: blt/blt


title: SKBR3 cell tranfected with miR671-5p nucleotide, biological rep1

description:
Sample name: SKBR3 OV1
SKBR3 cell line, mammary gland, breast; derived from metastatic site: pleural effusion
Gene expression data from SKBR3 cell lines transfected with miR671-5p, bio rep 1

tag: cell line


title: AF0101_SE_T9

description: Blood taken at 15:25 following 31.5 hours awake after following a Sleep Exentsion protocol from a Per3 5\5 genotype subject (Subject AF0101)

tag: sleepprotocol


title: RTE_bloto, biological rep2


title: AF0033_SE_T4

description: Blood taken at 02:00 following 16.5 hours awake after following a Sleep Exentsion protocol from a Per3 4\4 genotype subject (Subject AF0033)

tag: hoursawake


title: AF0139_SR_T5

description: Blood taken at 01:45 following 19.5 hours awake after following a Sleep Restriction protocol from a Per3 5\5 genotype subject (Subject AF0139)

tag: timesampletaken


title: WSB-mice_liver_control_rep3

description: Gene expression in the livers of WSB/EiJ mice fed a control diet

source_name: WSB-mice, liver, control, replicate 3

value: WSB/EiJ

value: liver

value: Male

value: 20 weeks


title: WSB-mice_liver_CFDdiet-12wks_rep2

source_name: WSB-mice, liver, CFDdiet-12wks, replicate 2


title: WSB-mice_liver_control_rep4

source_name: WSB-mice, liver, control, replicate 4


title: WSB-mice_liver_CFDdiet-12wks_rep1

source_name: WSB-mice, liver, CFDdiet-12wks, replicate 1


title: SKBR3 cell tranfected with mock nucleotide, biological rep2

description:
Sample name: SKBR3 MO2
SKBR3 cell line, mammary gland, breast; derived from metastatic site: pleural effusion
Gene expression data from SKBR3 cell lines transfected with mock, bio rep 2

value: scramble nucleotides control


title: SKBR3 cell tranfected with mock nucleotide, biological rep1

description:
Sample name: SKBR3 MO1
SKBR3 cell line, mammary gland, breast; derived from metastatic site: pleural effusion
Gene expression data from SKBR3 cell lines transfected with mock, bio rep 1


title: MDA231 cell tranfected with miR671-5p nucleotide, biological rep2

description:
Sample name: MDA231 OV2
MDA231 cell line, mammary gland, breast; derived from metastatic site: pleural effusion
Gene expression data from mda231 cell lines transfected with miR671-5p, bio rep 2


title: RTE_WT, biological rep2

description: Gene expression data from WT CD4+ RTEs

value: wild-type


title: RTE_WT, biological rep1

description: Gene expression data from WT CD4+ RTEs


title: MDA231 cell tranfected with mock nucleotide, biological rep2

description:
Sample name: MDA231 MO2
MDA231 cell line, mammary gland, breast; derived from metastatic site: pleural effusion
Gene expression data from mda231 cell lines transfected with mock, bio rep 2


title: MCF7 cell tranfected with miR671-5p nucleotide, biological rep1

description:
Sample name: MCF7 OV1
MCF7 cell line, mammary gland, breast; derived from metastatic site: pleural effusion
Gene expression data from MCF7 cell lines transfected with miR671-5p, bio rep 1


title: bloto, biological rep3

description: Gene expression data from blt/blt mature CD4SP thymocytes

source_name: mature CD4SP thymocytes, blt/blt

growth_protocol: Hematopoietic chimeras were generated by reconstituting lethally irradiated CD45.1+ hosts with a mix of CD45.1+CD45.2+ Rag1-GFP WT and CD45.2+ Rag1-GFP blt/blt bone marrow. Cells were isolated from the thymus by mechanical disaggregation through a 40μm nylon sieve, and CD4SP thymocytes were enriched by MACS depletion with anti-CD8 microbeads (Miltenyi Biotech) prior to sorting. WT and bloto mature CD4SP thymocytes (GFPhi CD4+ CD8− CD62Lhi CD69lo) were sorted on a FACSAria with ≥98% purity. Dead cells were excluded with DAPI.

value: mature CD4SP thymocytes


title: C3H-mice_liver_CFDdiet-12wks_rep1

description: Gene expression in the livers of C3H/HeJ mice fed a CFD diet for 12 weeks

source_name: C3H-mice, liver, CFDdiet-12wks, replicate 1


title: bloto, biological rep2


title: C3H-mice_liver_CFDdiet-12wks_rep3

source_name: C3H-mice, liver, CFDdiet-12wks, replicate 3


title: WT, biological rep3

description: Gene expression data from WT mature CD4SP thymocytes

source_name: mature CD4SP thymocytes, wild-type


title: MDA231 cell tranfected with mock nucleotide, biological rep1

description:
Sample name: MDA231 MO1
MDA231 cell line, mammary gland, breast; derived from metastatic site: pleural effusion
Gene expression data from mda231 cell lines transfected with mock, bio rep 1


title: C3H-mice_liver_control_rep3

description: Gene expression in the livers of C3H/HeJ mice fed a control diet

source_name: C3H-mice, liver, control, replicate 3


title: WT, biological rep2


title: MCF7 cell tranfected with miR671-5p nucleotide, biological rep2

description:
Sample name: MCF7 OV2
MCF7 cell line, mammary gland, breast; derived from metastatic site: pleural effusion
Gene expression data from MCF7 cell lines transfected with miR671-5p, bio rep 2


title: C3H-mice_liver_CFDdiet-12wks_rep2

source_name: C3H-mice, liver, CFDdiet-12wks, replicate 2


title: C3H-mice_liver_CFDdiet-12wks_rep4

source_name: C3H-mice, liver, CFDdiet-12wks, replicate 4


title: MDA231 cell tranfected with miR671-5p nucleotide, biological rep1

description:
Sample name: MDA231 OV1
MDA231 cell line, mammary gland, breast; derived from metastatic site: pleural effusion
Gene expression data from mda231 cell lines transfected with miR671-5p, bio rep 1


title: G+ G- Day 6 - repeat 4 - mAdbID:55578

city: Fuchu

first: Tetsuya

last: Furuya

state: Tokyo

address: 3-5-8 Saiwai-cho

department: Veterinary Medicine

institute: Tokyo University of Agriculture and Technology

description: mAdb experiment ID: 55578

hyb_protocol: Hybridization Protocol Other: Following RNA degradation the Cy3- and Cy5-labeled cDNAs to be hybridized on the same slide were co-purified by filtering the samples through six successive washes in TE pH 8.0 (10K MWCO Vivaspin 500, Vivascience AG, Hanover, Germany). The P. falciparum oligonucleotide array set (Operon, Alameda, CA) was printed onto polylysine coated glass slides using an Omnigrid robotic arrayer (Genomic Solutions, Ann Arbor, MI) at the NIAID microarray facility. Hybridizations were performed on the MAUI hybridization system (BioMicro Systems, Salt Lake City, UT) using hybridization solution, 5x SSC, 0.2% SDS, 25% formamide with 10 ug salmon sperm DNA (Invitrogen, Carlsbad, CA). After an overnight incubation at 45C, the slides were washed twice with 0.05% SDS in 1x SSC followed by two washes of 0.1x SSC.

scan_protocol: Creator: GenePix Pro 4.0.0.54 Scanner: GenePix 4000B [82425] ScanPower: 100;; 100;; n/a;; n/a LaserPower: 3.37;; 3.19;; n/a;; n/a Temperature: 31.24 Scanning Protocol Other: Slides were scanned with a GenePix 4000B array scanner (Axon Instruments, Union City, CA).

data_processing:
Data Processing Protocol
Calculation Method: The microarray signals from each array spot were normalized so that the median Cy5/Cy3 ratio was set as 1.0. Collected data were analyzed with GenePix Pro 4.0 (Axon Instruments) and web-based microarray tools (mAdb) developed by the National Cancer Institute (http://nciarray.nci.nih.gov/).

organism: Plasmodium falciparum

source_name: G+ Clone Day 6

label_protocol:
Cy5 Labeling Protocol
Other: Fluorescently-labeled cDNA was produced from 30 ug of total RNA using 2 ug oligo dT12-20 primer, 3 ug random hexamer, Superscript II (Invitrogen, Carlsbad, CA) and 66.7 uM dUTP-Cy5 (Amersham Biosciences, Piscataway, NJ) according to the manufacture's directions.

extract_protocol:
TRIzol Extraction
Other: RNA was isolated using TRIzol reagent (Invitrogen, Carlsbad, CA) from parasite cultures that had been washed three times in 4C PBS before incubation at room temperature (RT) for 5 minutes in five times the cell pellet volume of 0.01% saponin/PBS, then washed three times in 4C PBS.

treatment_protocol:
Treatment time: 6 days
In-vitro treatment: P. falciparum parasites were maintained in culture and gametocytogenesis was induced. Clones obtained by limiting dilution of P. falciparum (strain 3D7) that had been transformed with pDT.Tg23.230-D1.356 (pD1.356) were screened for the ability to generate gametocytes and a gametocyte producing (G+) clone was isolated. Homologous integration of pD1.356 disrupted the Pfs230 gene at bp 1356 in the G+ clones. Parasites were synchronized during three asexual cycles by incubating the cells from a culture of early ring stage parasites for 5 minutes in five times the cell pellet volume of 5% sorbitol. The cells were then pelleted by centrifugation, resuspended in complete RPMI 1640 including 10% human serum and returned to the 37C incubator. The treatment was repeated 4 hours later and at the beginning of the next asexual cycle about 38-44 hours later until the culture was synchronized. The growth rate and synchronization of the cultures were monitored by Giemsa stain. In clone G+ the parasitemia plateaued for several days, then decreased as the number of morphologically distinct gametocytes began to increase. RNA was harvested from the cultures when the asexual parasitemia was 5.2-5.58% (day 6) prior to the appearance of morphologically distinct gametocytes.

source_name: G- Clone Day 6

label_protocol:
Cy3 Labeling Protocol
Other: Fluorescently-labeled cDNA was produced from 30 ug of total RNA using 2 ug oligo dT12-20 primer, 3 ug random hexamer, Superscript II (Invitrogen, Carlsbad, CA) and 66.7 uM dUTP-Cy3 (Amersham Biosciences, Piscataway, NJ) according to the manufacture's directions.

treatment_protocol:
Treatment time: 6 days
In-vitro treatment: P. falciparum parasites were maintained in culture and gametocytogenesis was induced. Clones obtained by limiting dilution of P. falciparum (strain 3D7) that had been transformed with pDT.Tg23.230-D1.356 (pD1.356) were screened for the ability to generate gametocytes and the non-producing (G-) clone was isolated. Homologous integration of pD1.356 disrupted the Pfs230 gene at bp 1356 in the G- clone. Parasites were synchronized during three asexual cycles by incubating the cells from a culture of early ring stage parasites for 5 minutes in five times the cell pellet volume of 5% sorbitol. The cells were then pelleted by centrifugation, resuspended in complete RPMI 1640 including 10% human serum and returned to the 37C incubator. The treatment was repeated 4 hours later and at the beginning of the next asexual cycle about 38-44 hours later until the culture was synchronized. The growth rate and synchronization of the cultures were monitored by Giemsa stain. Clone G- produces very few if any gametocytes. The initial asexual growth rate was the same in both clones, but after reaching a peak of about 20-30% the asexual parasitemia decreased in clone G-. RNA was harvested from the cultures when the asexual parasitemia was 5.2-5.58% (day 6) prior to the appearance of morphologically distinct gametocytes.


title: bloto, biological rep1


title: WSB-mice_liver_control_rep1

source_name: WSB-mice, liver, control, replicate 1


title: WT, biological rep1


title: C3H-mice_liver_control_rep4

source_name: C3H-mice, liver, control, replicate 4


title: MCF7 cell tranfected with mock nucleotide, biological rep2

description:
Sample name: MCF7 MO2
MCF7 cell line, mammary gland, breast; derived from metastatic site: pleural effusion
Gene expression data from MCF7 cell lines transfected with mock, bio rep 2


title: G+ G- Day 6 - repeat 3 - mAdbID:55577

description: mAdb experiment ID: 55577

scan_protocol: Creator: GenePix Pro 4.0.0.54 Scanner: GenePix 4000B [82425] ScanPower: 100;; 100;; n/a;; n/a LaserPower: 3.14;; 3.19;; n/a;; n/a Temperature: 31.12 Scanning Protocol Other: Slides were scanned with a GenePix 4000B array scanner (Axon Instruments, Union City, CA).


title: MCF7 cell tranfected with mock nucleotide, biological rep1

description:
Sample name: MCF7 MO1
MCF7 cell line, mammary gland, breast; derived from metastatic site: pleural effusion
Gene expression data from MCF7 cell lines transfected with mock, bio rep 1


title: G+ G- Day 6 - repeat 2 - mAdbID:55576

description: mAdb experiment ID: 55576

scan_protocol: Creator: GenePix Pro 4.0.0.54 Scanner: GenePix 4000B [82425] ScanPower: 100;; 100;; n/a;; n/a LaserPower: 3.23;; 3.19;; n/a;; n/a Temperature: 31.21 Scanning Protocol Other: Slides were scanned with a GenePix 4000B array scanner (Axon Instruments, Union City, CA).


title: G+ G- Day 6 - repeat 1 - mAdbID:55575

description: mAdb experiment ID: 55575

scan_protocol: Creator: GenePix Pro 4.0.0.54 Scanner: GenePix 4000B [82425] ScanPower: 100;; 100;; n/a;; n/a LaserPower: 3.35;; 3.19;; n/a;; n/a Temperature: 31.12 Scanning Protocol Other: Slides were scanned with a GenePix 4000B array scanner (Axon Instruments, Union City, CA).


title: C3H-mice_liver_control_rep1

source_name: C3H-mice, liver, control, replicate 1


title: AJ-mice_liver_CFDdiet-12wks_rep4

description: Gene expression in the livers of A/J mice fed a CFD diet for 12 weeks

source_name: AJ-mice, liver, CFDdiet-12wks, replicate 4

value: A/J


title: G+ G- Day 4 - repeat 4 - mAdbID:55574

description: mAdb experiment ID: 55574

scan_protocol: Creator: GenePix Pro 4.0.0.54 Scanner: GenePix 4000B [82425] ScanPower: 100;; 100;; n/a;; n/a LaserPower: 3.14;; 3.17;; n/a;; n/a Temperature: 31 Scanning Protocol Other: Slides were scanned with a GenePix 4000B array scanner (Axon Instruments, Union City, CA).

source_name: G+ Clone Day 4

treatment_protocol:
Treatment time: 4 days
In-vitro treatment: P. falciparum parasites were maintained in culture and gametocytogenesis was induced. Clones obtained by limiting dilution of P. falciparum (strain 3D7) that had been transformed with pDT.Tg23.230-D1.356 (pD1.356) were screened for the ability to generate gametocytes and a gametocyte producing (G+) clone was isolated. Homologous integration of pD1.356 disrupted the Pfs230 gene at bp 1356 in the G+ clones. Parasites were synchronized during three asexual cycles by incubating the cells from a culture of early ring stage parasites for 5 minutes in five times the cell pellet volume of 5% sorbitol. The cells were then pelleted by centrifugation, resuspended in complete RPMI 1640 including 10% human serum and returned to the 37C incubator. The treatment was repeated 4 hours later and at the beginning of the next asexual cycle about 38-44 hours later until the culture was synchronized. The growth rate and synchronization of the cultures were monitored by Giemsa stain. In clone G+ the parasitemia plateaued for several days, then decreased as the number of morphologically distinct gametocytes began to increase. RNA was harvested from the cultures when the asexual parasitemia was 0.9-1.48% (day 4).

source_name: G- Clone Day 4

treatment_protocol:
Treatment time: 4 days
In-vitro treatment: P. falciparum parasites were maintained in culture and gametocytogenesis was induced. Clones obtained by limiting dilution of P. falciparum (strain 3D7) that had been transformed with pDT.Tg23.230-D1.356 (pD1.356) were screened for the ability to generate gametocytes and the non-producing (G-) clone was isolated. Homologous integration of pD1.356 disrupted the Pfs230 gene at bp 1356 in the G- clone. Parasites were synchronized during three asexual cycles by incubating the cells from a culture of early ring stage parasites for 5 minutes in five times the cell pellet volume of 5% sorbitol. The cells were then pelleted by centrifugation, resuspended in complete RPMI 1640 including 10% human serum and returned to the 37C incubator. The treatment was repeated 4 hours later and at the beginning of the next asexual cycle about 38-44 hours later until the culture was synchronized. The growth rate and synchronization of the cultures were monitored by Giemsa stain. Clone G- produces very few if any gametocytes. The initial asexual growth rate was the same in both clones, but after reaching a peak of about 20-30% the asexual parasitemia decreased in clone G-. RNA was harvested from the cultures when the asexual parasitemia was 0.9-1.48% (day 4).


title: C3H-mice_liver_control_rep2

source_name: C3H-mice, liver, control, replicate 2


title: AJ-mice_liver_CFDdiet-12wks_rep3

source_name: AJ-mice, liver, CFDdiet-12wks, replicate 3


title: G+ G- Day 4 - repeat 1 - mAdbID:55571

description: mAdb experiment ID: 55571

scan_protocol: Creator: GenePix Pro 4.0.0.54 Scanner: GenePix 4000B [82425] ScanPower: 100;; 100;; n/a;; n/a LaserPower: 3.15;; 3.17;; n/a;; n/a Temperature: 30.6 Scanning Protocol Other: Slides were scanned with a GenePix 4000B array scanner (Axon Instruments, Union City, CA).


title: AJ-mice_liver_control_rep1

description: Gene expression in the livers of A/J mice fed a control diet

source_name: AJ-mice, liver, control, replicate 1


title: AJ-mice_liver_control_rep3

source_name: AJ-mice, liver, control, replicate 3


title: G+ G- Day 4 - repeat 3 - mAdbID:55573

description: mAdb experiment ID: 55573

scan_protocol: Creator: GenePix Pro 4.0.0.54 Scanner: GenePix 4000B [82425] ScanPower: 100;; 100;; n/a;; n/a LaserPower: 3.14;; 3.16;; n/a;; n/a Temperature: 30.78 Scanning Protocol Other: Slides were scanned with a GenePix 4000B array scanner (Axon Instruments, Union City, CA).


title: G+ G- Day 4 - repeat 2 - mAdbID:55572

description: mAdb experiment ID: 55572

scan_protocol: Creator: GenePix Pro 4.0.0.54 Scanner: GenePix 4000B [82425] ScanPower: 100;; 100;; n/a;; n/a LaserPower: 3.11;; 3.18;; n/a;; n/a Temperature: 30.78 Scanning Protocol Other: Slides were scanned with a GenePix 4000B array scanner (Axon Instruments, Union City, CA).


title: HF-AII6

type: genomic

city: Pittsburgh

first: Svetlana

middle: A

last: Yatsenko

state: PA

address: 300 Halket St

institute: University of Pittsburgh

description: homozygosity mapping

hyb_protocol: According to Agilent protocol

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Cytogenomics Software (2.5.8.1).

data_processing: Log ratios  of 59,645 SNP-containing probes were quantified and converted to genotype values using Cytogenomics Software (2.5.8.1). Loss of homozygosity (LOH) regions were detected according to the Agilent protocol.

molecule: genomic DNA

source_name: Unaffected Female AII5

label_protocol: According to Agilent protocol

growth_protocol: uncultured

extract_protocol: Genomic DNA extracted using Puregene Kit following manufacturer's instructions

value: Female

tag: tissue type

value: peripheral blood

source_name: Reference DNA


title: GDF-AII5

description: homozygosity mapping

source_name: Affected Female AII4


title: HF-AII3

description: homozygosity mapping

source_name: Unaffected Female AII3


title: AJ-mice_liver_CFDdiet-12wks_rep1

source_name: AJ-mice, liver, CFDdiet-12wks, replicate 1


title: MAF-AII8

description: homozygosity mapping

source_name: Female sibling AII7 with chromosome abnormality


title: AJ-mice_liver_CFDdiet-12wks_rep2

source_name: AJ-mice, liver, CFDdiet-12wks, replicate 2


title: GDF-AII7

description: homozygosity mapping

source_name: Affected Female AII6


title: AJ-mice_liver_control_rep4

source_name: AJ-mice, liver, control, replicate 4


title: HF-AII2

description: homozygosity mapping

source_name: Unaffected Female AII2


title: AJ-mice_liver_control_rep2

source_name: AJ-mice, liver, control, replicate 2


title: AGS_muscle_early_arousal_08-22

city: ShangHai

first: Haifang

last: Wang

address: NO 320, Yueyang Road

department: functional genomics group

country: China

institute: PICB

description: muscle tissue from active arctic ground squirrel

hyb_protocol: The hybridization was carried out for 18 hours at 42°C in 4 ml of MicroHyb buffer (Invitrogen). Filters were rinsed at room temperature with 2× SSC/1% SDS to remove residual probe and MicroHyb solution and then transferred to preheated wash solutions in a temperature-controlled shaking water bath. Filters were washed twice for 30 min in 1.5 l of 2× SSC/1% SDS at 50°C and then once for 30 min in 1.5 l of 0.5× SSC/1% SDS at 55°C.

scan_protocol: Filters were then exposed to phosphorimager screens for four days and scanned at 50-µm resolution in a Storm Phosphorimager.

data_processing: Image analysis was performed with the ImaGene program (Biodiscovery). Only nonempty spots with signal median density exceeding double background median in all individuals were included in the analysis. Background corrected signal was obtained by subtracting local background median density from signal median density. Background corrected signals were divided by their median on the array to obtain the normalized median densities representing the normalized expression values.

organism: Urocitellus parryii

source_name: muscle, early arousal

label_protocol: Samples of total RNA were linearly amplified with Illumina TotalPrep RNA Amplification Kit (Ambion), and 1.6 μg of the amplified RNA was labeled with 65 μCi of [33P]dCTP. All RNA samples were amplified, labeled and hybridized in the same batch.

extract_protocol: Total RNA was extracted from frozen tissues stored at -80 C by grinding in liquid nitrogen with mortar and pestle and using RNeasy Kit (Qiagen). Skeletal muscle tissue was treated by proteinase K and RNA was extracted by using RNeasy Fibrous Tissue Kit (Qiagen). All RNA samples were processed by DNase I (Qiagen) treatment. For cDNA library construction, mRNA was selected from total RNA with the oligo(dT) cellulose by the use of Poly(A) Purist Kit (Ambion).

tag: active state

value: early arousal

value: muscle


title: AGS_muscle_early_arousal_08-14


title: AGS_muscle_early_arousal_06-18


title: BA02_muscle_active_N04-113

description: muscle tissue from active black bear

organism: Ursus americanus

source_name: muscle, active

tag: activity state

value: active


title: AGS_muscle_early_arousal_08-27


title: BA02_muscle_active_N03-153

description: muscle tissue from active black bear


title: BA02_muscle_active_N04-104

description: muscle tissue from active black bear


title: AGS_muscle_late_torpor_08-32

description: muscle tissue from hibernating arctic ground squirrel

source_name: muscle, late torpor

value: late torpor


title: BA02_muscle_active_N03-152

description: muscle tissue from active black bear


title: BA02_muscle_hibernating_N06-030

description: muscle tissue from hibernating black bear

source_name: muscle, hibernating

value: hibernating


title: AGS_muscle_early_arousal_08-25


title: BA02_muscle_active_N05-132

description: muscle tissue from active black bear


title: BA02_muscle_hibernating_N07-027


title: BA02_muscle_active_N05-131

description: muscle tissue from active black bear


title: AGS_muscle_late_torpor_08-19


title: AGS_muscle_early_arousal_05-52


title: AGS_muscle_early_arousal_05-36


title: AGS_muscle_late_torpor_08-18


title: AGS_muscle_early_arousal_06-10


title: BA02_muscle_hibernating_N05-035


title: WSB-mice_liver_control_rep2

description: Gene expression in the livers of WSB/EiJ mice fed a control diet

source_name: WSB-mice, liver, control, replicate 2


title: AGS_muscle_late_torpor_08-133


title: AGS_muscle_late_torpor_07-50


title: BA02_muscle_hibernating_N05-034


title: AGS_muscle_late_torpor_07-08


title: AGS_muscle_late_torpor_07-47


title: AGS_muscle_early_arousal_05-48


title: AGS_muscle_late_torpor_05-46


title: AGS_muscle_late_torpor_06-109


title: AGS_muscle_late_torpor_06-111


title: BA02_muscle_hibernating_N04-047


title: BA02_muscle_hibernating_N03-056


title: Ise testis animal #3

city: Lexington

first: Phillip

middle: J

last: Bridges

state: KY

address: 206 WP Garrigus Building

department: Animal and Food Sciences

institute: University of Kentucky

description: Gene expression data from bull calf testis

hyb_protocol: Following fragmentation, 10 µg of labeled cRNA was hybridized to Affymetrix Bovine Genome Array for 16 hr at 45°C using the gene chips in the GeneChip Hybridization Oven 640, using 1 chip per RNA sample. GeneChips were washed and stained in the Affymetrix Fluidics Station 450. GeneChips were stained with R-Phycoerythrin Streotavidin, followed by an antibody solution and a second R-Physcoerythrin Streptavidin solution, with all lquid handling performed by a GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix 7G GeneChip Scanner (GCS) with AGCC software (Command Console).

data_processing: The raw data were collected with the GeneChip Operating Software (GCOS, version 1.2). The expression intensity values from the software (i.e., the .cel files) were imported into Partek Genomics Suite software (version 6.4; Partek Inc., St. Louis, MO, USA). The algorithm of Robust Multichip Averaging were further converted into expression values via the algorithms of Quantile normalization of different chips and then Median Polish summarization of multiple probes.

organism: Bos taurus

source_name: Ise testis

label_protocol: Biotinylated cRNA were prepared from 3 µg of total RNA according to Affymetrix protocol. Double-stranded cDNA was synthesized using SuperScriptII (Invitrogen, Carlsbad, CA, USA) and oligo(dT)24 primers. Bio-labeled cRNA was prepared by cDNA in vitro transcription biotinylated UTP.

growth_protocol: Twenty-four Angus cross cows were assigned randomly (n=8) to individual ad libitum intake of a common vitamin-mineral mix that contained 35 ppm of Se supplied as either inorganic (ISe, sodium selenite; Prince Se Concentrate, Prince Agri Products, Inc., Quincy, IL), organic (OSe, Sel-Plex; Alltech Inc., Nicholasville, KY), or a 50/50 mix of ISe/OSe (Mix) Se as described in the overall design section above.

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

treatment_protocol: The treatment protocol (i.e. dietary Se Supplementation) has been described in the overall design section above.

value: testis

tag: supplements

value: vitamin-mineral mix that contained 35 ppm of Se supplied as inorganic


title: Ose testis animal #3

source_name: Ose testis

value: vitamin-mineral mix that contained 35 ppm of Se supplied as organic


title: Ise testis animal #4


title: Ise testis animal #5


title: Mix testis animal #3

source_name: Mix testis

value: vitamin-mineral mix that contained 35 ppm of Se supplied as 50/50 ISe/OSe


title: Ose testis animal #2


title: Total Homogenate_Control_9_miRNA

first: Dana

last: Moat

state: Texas

address: 2500 Speedway, MBB 1.138

department: Waggoner center for alcohol and addiction research

description: Control mice were given a 24-hour access for 30 days to two bottle of water

hyb_protocol: Performed at University of Texas Southwestern Medical Center microarray facility

data_processing: We analyzed the array data using R programming language and the bioconductor packages (http://www.bioconductor.org). Preprocessing (RMA background correction and quantile normalization) of the microRNA data was performed with Bioconductor’s ‘Oligo’ package. Quality measures were taken before and after preprocessing using the Array Quality Metrics package (Kauffmann, Gentleman et al. 2009, Kauffmann and Huber 2010) to generate the principal component analysis. For all further analyses only the mouse mature microRNA data was used. The microarray expression data was then analyzed using the Bioconductor ‘Limma’ package (Smyth 2004). We used differential expression analysis between paired SN and TH samples (paired/dependent t-test) and between the alcohol and control samples in SN and TH (two independent t-tests). MicroRNA annotations, sequences, chromosomal locations and families were defined by miRbase version 17. We defined 10% as the threshold for determining if a certain chromosome was associated with a statistical measure and 5% as the threshold for determining if a microRNA family was associated.

source_name: Total Homogenates (the standard prep) from extended amygdala

label_protocol: Forty microRNA samples were labeled and hybridized to Affymetrix GeneChip microRNA 3.0 Arrays (Affymetrix, CA), at the University of Texas Southwestern Medical Center microarray facility in Dallas. This microarray platform uses miRBase version 17 and contains 19,724 probes for mature microRNAs from 153 organisms.

growth_protocol: Adult (two month old) C57BL/6J female mice were maintained at The University of Texas at Austin Animal Resources Center.

extract_protocol: After 30 days of the drinking paradigm, eight alcohol mice and 13 control mice were euthanized by cervical dislocation and then decapitated. Brains were removed and washed for one minute with 1ml of ice-cold Homogenizing Buffer (HB) containing 20mM Hepes, 1mM EDTA (pH 7.4), 40 U/ml RNAseOut (Invitrogen, CA), phosphatase inhibitor cocktail 3 (Sigma, MO) and protease inhibitors “Complete” (Roche, IN). Brains were then placed in a coronal Zivic mouse brain slicer with a 0.5mm resolution (Zivic Instruments, PA) and sliced in the following coordinates in order to isolate extended amygdala: coronal level 56-66 [Bregma (-0.18)-(-1.155)] and 66-80 [Bregma (-1.155)-(-2.55)]. The extended amygdala was dissected, placed in ice-cold HB (250ml) and homogenized for one minute using a VWR homogenizer and pestle (VWR, PA). To minimize homogenate loss, pestles were washed with 50ml HB after use and the wash was collected and added to the sample. Ten percent of the homogenate (30ml) was snap frozen in liquid nitrogen and stored at -80°C for subsequent RNA total homogenate (TH) analysis. Paired synaptoneurosomes (SN) were isolated from the rest of the homogenate (270ml), see Most, Ferguson et al. 2014 for detailed methodology. Briefly, homogenates were filtered through a 100um-pore filter and subsequently through a 5um-pore filter (Millipore, MA); filters were washed with HB before use for protection from RNAse. To maximize yield, the filters were washed with 50ml HB after use and the wash was collected and added to the homogenate. The homogenate was then centrifuged at 14,000g for 20 minutes at 4°C in order to pellet the cell fraction containing SN. The supernatant was removed and the pellet snap-frozen and stored at -80°C for SN RNA analysis. Microscopy was used to further characterize the SN preparation (see Most, Ferguson et al. 2014).  RNA was extracted from 21 paired SN and TH samples using the Direct-Zol RNA extraction kit (Zymo, Japan) with small IC extraction columns according to the manufacturer’s instructions. The RNA was quantified using a NanoDrop1000 (Thermo Fisher Scientific Inc., IL) and assayed for quality using an Agilent 2100 Tape Station (Agilent Technologies, CA) (Figure S1a). The criteria for RNA quantity and quality were as follows: total amount of RNA>500 ng, 280/260>1.7, and RIN>6.5. We measured RIN of five of the control samples using Agilent’s Bioanalyzer Nano kit. To ensure that samples with high RINs also included high quality and quantity of microRNAs, the same five control samples were subjected to a small RNA analysis using Agilent’s Bioanalyzer Small kit. MicroRNAs comprised > 10% of the small RNA population in the samples (Figure S1b). One TH control sample did not pass RNA quality criteria and was removed from the study as well as its corresponding SN, resulting in a total of 20 paired SN and TH samples.

treatment_protocol: Mice were given a one-week acclimation period in combined housing and another week to acclimate to the bottle positions in individual housing. Food and water were provided ad libitum and monitored daily, as were the temperature and light/dark cycles. Mice underwent a 30-day two-bottle choice paradigm with continuous (24-hour) access to one bottle of 20% ethanol and one bottle of water (Blednov, Mayfield et al. 2012). A control group of mice received two bottles of water. Bottle weights were recorded daily, mice were weighed every four days and the amount of alcohol consumed was calculated as g/kg. Ethanol bottle positions were alternated daily to control for position preferences. All procedures were approved by the Institutional Animal Care and Use Committee and adhere to NIH Guidelines for the ethical care and use of animals in research.

value: female

value: 2 months old

value: brain/extended amygdala


title: Total Homogenate_Control_7_miRNA

scan_protocol: Performed at University of Texas Southwestern Medical Center microarray facility


title: Total Homogenate_Control_12_miRNA


title: Mix testis animal #2


title: Ise testis animal #1


title: Mix testis animal #1


title: Total Homogenate_Control_11_miRNA


title: Total Homogenate_Control_6_miRNA


title: Total Homogenate_Control_8_miRNA


title: Total Homogenate_Control_10_miRNA


title: Mix testis animal #4


title: Total Homogenate_Control_13_miRNA


title: Total Homogenate_Control_5_miRNA


title: Total Homogenate_Control_1_miRNA


title: Total Homogenate_Control_2_miRNA


title: Total Homogenate_Control_3_miRNA


title: Ose testis animal #1


title: Total Homogenate_Alcohol_8_miRNA

description: Alcohol treated mice were given a 24-hour access for 30 days to a two-bottle choice, using a bottle containing water and a bottle containing 20% ethanol


title: Total Homogenate_Alcohol_6_miRNA


title: Ose testis animal #4


title: Total Homogenate_Alcohol_7_miRNA


title: Total Homogenate_Alcohol_5_miRNA


title: Total Homogenate_Alcohol_4_miRNA


title: patient 37 C20

city: Urumqi

first: Xiu-Juan

last: Wu

state: Xinjiang

address: 91 Tianchi Road

department: Department of Dermatology

institute: People’s Hospital of Xinjiang, Uygur Autonomous Region

description: After having passed RNA quantity measurement using the NanoDrop 1000, the samples were labeled using the miRCURY™ Hy3™/Hy5™ Power labeling kit and hybridized on the miRCURY™ LNA Array (v.18.0) which contains probes for 3100 mature miRNA.

hyb_protocol: After stopping the labeling procedure, the Hy3TM-labeled samples were hybridized on the miRCURYTM LNA Array (v.18.0) (Exiqon) according to array manual.

scan_protocol: Following hybridization, the slides were achieved, washed several times using Wash buffer kit (Exiqon), and finally dried by centrifugation for 5 min at 400 rpm. Then the slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).

data_processing:
Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities>=30 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. After normalization, significant differentially expressed miRNAs were identified through Volcano Plot filtering. Hierarchical clustering was performed using MEV software (v4.6, TIGR).
Only those with a greater than 2-fold increase or 2-fold decrease in expression in two paired samples were considered significantly changed.

source_name: Normal Skin Tissues

extract_protocol: Total RNA was harvested using TRIzol (Invitrogen) and miRNeasy mini kit (QIAGEN) according to manufacturer’s instructions.

tag: population

value: Uyghyr

value: woman

value: 19 years

value: normal skin


title: Total Homogenate_Alcohol_3_miRNA


title: patient 36 C19

label_protocol: After having passed RNA quantity measurement using the NanoDrop 1000, the samples were labeled using the miRCURY™ Hy3™/Hy5™ Power labeling kit and hybridized on the miRCURY™ LNA Array (v.18.0)

value: man

value: 7 years


title: patient 34 C17

value: 34 years


title: patient 33 C16

value: 6 years


title: Total Homogenate_Alcohol_2_miRNA


title: patient 32 C15


title: patient 31 C14

value: 44 years


title: Ise testis animal #2


title: patient 30 C13

value: 23 years


title: patient 29 C12

value: 45 years


title: patient 35 C18

value: 3 years


title: Total Homogenate_Alcohol_1_miRNA


title: patient 27 C10

value: Han


title: Synaptoneurosome_Control_11_miRNA

source_name: Synaptoneurosomes from extended amygdala


title: patient 26 C9


title: patient 25 C8

value: 27 years


title: patient 24 C7

value: 22 years


title: patient 28 C11

value: 50 years


title: Synaptoneurosome_Control_13_miRNA

value: female

value: 2 months old

value: brain/extended amygdala


title: Synaptoneurosome_Control_9_miRNA


title: Synaptoneurosome_Control_7_miRNA


title: Synaptoneurosome_Control_2_miRNA


title: Synaptoneurosome_Control_3_miRNA


title: patient 23 C6


title: Synaptoneurosome_Control_5_miRNA


title: Synaptoneurosome_Control_12_miRNA


title: Synaptoneurosome_Control_6_miRNA


title: Synaptoneurosome_Control_1_miRNA


title: Synaptoneurosome_Control_8_miRNA


title: Synaptoneurosome_Control_10_miRNA


title: Synaptoneurosome_Alcohol_8_miRNA


title: patient 22 C5

value: woman

value: 46 years


title: patient21 C4

value: 42 years

value: normal skin


title: patient 20 C3

value: man


title: patient 19 C2

value: 17 years


title: patient 18 C1

value: 56 years


title: Synaptoneurosome_Alcohol_7_miRNA


title: Synaptoneurosome_Alcohol_5_miRNA


title: mESC Mettl3 shRNA #2 replicate #2

first: Kun

last: Qu

address: 269 Campus Dr. CCSR 2150

department: Dermatology

description: replicate 2

hyb_protocol: The fragmented and labeled targets were hybridized to the arrays per standard Affymetrix protocol, which includes 16hr (overnight) hybridization at 45degC at 60rpm in an Affymetrix GeneChip Hybridization Oven 645. The arrays were then washed and stained in an Affymetrix GeneChip Fluidics Station 450.

scan_protocol: Affymetrix GeneChip Scanner 3000 7G

source_name: J-1 Mouse embryonic stem cell

label_protocol: Ambion WT Expression kit was used to generate ssDNA targets. Fragmentation and biotin-labeling were performed using Afymetrix WT Terminal Labeling and Hybridization kit.

growth_protocol: Lentiviral infected mouse embryonic stem cells were grown in full media.

extract_protocol: Trizol and qiagen RNeasy kits were used to isolate total RNA.

treatment_protocol: Lentiviral infection

tag: cell type

value: embryonic stem cells

tag: infection

value: Mettl3 shRNA #2


title: Synaptoneurosome_Alcohol_6_miRNA

tag: tissue


title: Synaptoneurosome_Alcohol_1_miRNA

tag: strain


title: U266_Hypoxia_24h-exosome

status: Public on Oct 15 2014

city: Shinjyuku

first: Tomohiro

last: Umezu

address: 6-1-1 Shinjyuku

department: Department of Molecular Pathology

institute: Tokyo Medical University

description:
SAMPLE 5
test

data_processing:
RNU6B and a spike control (ath-miR159) were used as an invariant control for the cell and exosome, respectively. QRT-PCR was carried out on an Applied Biosystems 7900HT thermal cycler using the manufacturer’s recommended program.
All the raw data from each array was retrieved from the 7900HT and was run on Data Assist Software ver.3.1 (Applied Biosystems).

label: TaqMan probe (FAM-MGB)

source_name: exosome derived from MM cell line _hypoxia (1% O2)

label_protocol: A fixed volume of 3 µl of RNA solution from 50 µl of the elute was used as input in each reverse transcription (RT) reaction. An RT reaction and pre-amplification step were set up according to manufacturers’ recommendations. miRNAs were reverse transcribed using the Megaplex Primer Pools (Human Pools A v2.1) from Applied Biosystems (Bedford, MA, USA). RT reaction products from the exosome sample were further amplified using the Megaplex PreAmp Primers (Primers A v2.1).

extract_protocol:
Exosome extract protocol: The 5 ml of culture media of U266 cells and U266HR cells were obtained and centrifuged at 3,000 × g for 15 min. The supernatant was filtered through a 0.22-µm PVDF filter (Millipore). The appropriate volume of Exoquick Exosome Precipitation Solution (System Biosciences, Mountain View, CA, USA) was added to the filtered culture medium and mixed well by inverting. After refrigeration for 12 h, the mixture was centrifuged at 1,500 × g for 30 min and all supernatant was removed by aspiration.
RNA extract protocol: The Cell or exosome pellets were dissolved with 700 µl of QIAzol lysis regent (Qiagen). After a 2-min incubation, 1 µl of 1 nM ath-miR-159 (Hokkaido System Science, Hokkaido, Japan) was added to each aliquot as a spike control for losses in preparation, followed by vortexing for 30 sec and incubation on ice for 10 min. Subsequent phenol extraction and cartridge filtration were carried out according to the manufacturer’s instructions.

treatment_protocol: U266 cells and U266HR cells were seeded at a density of 5 × 10^5 cells/ml, and cultured for 24 hours under hypoxic conditions (1% O2, 5% CO2, 94% N2) in a humidified gas-sorted hypoxic incubator (MCO-5M, Sanyo, Osaka, Japan) using the degassed culture mediums (AIM-V medium, Invitrogen).

tag: condition

value: hypoxia (1% O2)

tag: time


title: Oral 3D tissue non-irradiated (Control)

city: Pomona

first: Maria

middle: P

last: Lambros

address: 309 E Second Street

department: Pharmaceutical Sciences

institute: Western Univ of Health Sci

description:
Sample name: NTNI
CONTROL

hyb_protocol: Fragmented aRNA was hybridized at 42°c overnight using the HybBag mixing system with 1X OneArray® Hybridization Buffer (Phalanx Biotech), 0.01 mg/ml sheared salmon sperm DNA (Promega, Madison, WI, USA), at a concentration of 0.025 mg/ml labeled target. After hybridization, the arrays were washed according to the OneArray® protocol.

scan_protocol: Raw intensity signals for each microarray were captured using a Molecular Devicess™ Axon 4100A scanner, measured using GenePixPro™ Software, and stored in GPR format.

data_processing:
3 replicate samples were averaged.  The F532 channel data in each raw data file should be ignored. Only Cy5 dye was used for the experiment.  The data from all microarrays in each experimental set was then passed to Rosetta resolver (v.7.2.2.0.0) for analysis. Testing was performed by combining technical replicates and performing statistical analyses using Rosetta Resolver’s proprietary modeling techniques. Normalization algorithm -> Median scaling.
averaged normalized data, signals not significantly above background have been deleted

source_name: Human primary oral 3D tissue non irradiated (control)

label_protocol: High-quality RNA (RIN>9.5) was converted to double-stranded cDNA and amplified using in vitro transcription that included amino-allyl UTP. The product ws conjugated with Cy5 NHS ester.

growth_protocol: The primary 3-D cell culture of oral keratinocytes were grown on top of primary oral fibroblast and supplemented with MatTek serum free media.

extract_protocol: Six hours after the irradiation total RNA was extracted using Rneasy Plus kit, Qiagen

treatment_protocol: The tissues were irradiated with 12 and 2 Gy

value: oral keratinocytes

tag: growth

value: co-cultured with fibroblasts

tag: treatment

value: untreated

tag: dose

value: control


title: Synaptoneurosome_Alcohol_4_miRNA

tag: gender

value: female

tag: age


title: U266HR_Hypoxia_24h-exosome

description:
SAMPLE 6
test

source_name: exosome derived from hypoxia-resistant-MM cell line _hypoxia (1% O2)

tag: cell line


title: Oral 3D tissue irradiated 12 Gy

description: Sample name: NT12I

source_name: Human primary oral 3D tissue irradiated with 12 Gy

value: radiation

value: 12 Gy


title: U266_Hypoxia_24h-cell

description:
SAMPLE 2
test

source_name: Multiple Myeloma-derived cell line _hypoxia (1% O2)


title: U266_Normoxia_24h-exosome

description:
SAMPLE 4
control

source_name: exosome derived from MM cell line _normoxia (20% O2)

value: normoxia (20% O2)


title: Early bicellular pollen - stage 3 - replicate 2

city: Prague 6

first: David

last: Honys

state: CZ

address: Rozvojova 263

country: Czech Republic

institute: IEB ASCR

description: Gene expression profile of early bicellular pollen

hyb_protocol: 1650 ng of Cy3-labeled cRNA was hybridized to Agilent Tobacco Gene Expression Microarray 4x44K for 17 h at 65 °C in a rotating Agilent hybridization oven (Agilent).

scan_protocol: The slides were scanned on the Agilent High Resolution Microarray Scanner using default parameters for 4x44K microarray formats (Agilent). Background-subtracted and spatially-detrended Processed Signal intensities were obtained by Feature Extraction Software 11.0.1.1 (Agilent) used with default parameters (Protocol GE1_1100_Jul11 and Grid 21113_D_F_20130122).

data_processing: All transcriptomic data sets were normalized using publicly available dChip 1.3 software (http://www.hsph.harvard.edu/cli/complab/dchip/). The reliability and reproducibility of the analyses were ensured by the use of duplicates in each experiment, the normalization of all arrays to the median probe intensity level, and the use of normalized intensities of all arrays for the calculation of model-based gene expression values based on the Perfect Match-only model (Li C and Wong WH: Proc Natl Acad Sci U S A 98: 31-36, 2001). For each sample, only probes with the detection call of ‘present’ and an expression value detection level of ‘well above background’ (Boolean flag, two-sided t-test) in both replicates were considered to be expressed.

organism: Nicotiana tabacum

source_name: Early bicellular pollen - stage 3

label_protocol: Cyanine-3 (Cy3)-labeled cRNA was prepared from 66 ng of total RNA by Low Input Quick Amp Labeling Kit, One-Color (Agilent) according to the manufacturer's instruction. Cy3-labeled cRNA was purified by RNeasy Mini Kit (Qiagen). NanoDrop 2000c spectrophotometer (Thermo Fisher Scientific) was used to evaluate the cRNA yield and labeling efficiency. Cy3-labeled cRNA was then fragmented in a 30-minute incubation at 60 °C.

growth_protocol: Wild-type Nicotiana tabacum (cv. Samsun) seeds were sown in a greenhouse under 22-25°C and short-day conditions. Adult plants with fully developed roots were transplanted to an outdoor greenhouse to compost soil. There the plants were grown under the natural day-night photoperiod in spring and summer. Immature pollen grains at three stages of development were collected from August to September. The appropriate developmental stage was determined by the total length of flower buds including calyx as published previously by (Tupý J, Süss J, Hrabětová E and Říhová L: Biol Plant 25: 231-237, 1983). Flower bud lengths were as follows: uninuclear microspores (stage 1), 15-16 mm; early bicellular pollen (stage 3), 25-27 mm, late bicellular pollen (stage 5), 46-49 mm. After flower collection, the freshly isolated anthers were immediately processed by gentle mashing in a chilled mortar with 5% sucrose in sterile water. The mixture containing released pollen was filtered through an ordinary gauze to remove the anther debris. The pollen was then sedimented by centrifugation (2,000 g, 5 min, 4°C) and stored in -80°C.

extract_protocol: Total RNA was isolated from 100 mg of immature pollen using the Qiagen RNeasy Plant Kit according to the manufacturer’s instructions and treated with DNaseI (Promega). RNA was quantified using NanoDrop (Thermo Scientific). RNA concentration, purity and integrity (RIN) were assessed using an Agilent 2100 Bioanalyzer.

treatment_protocol: No treatment

value: Early bicellular pollen

tag: Stage


title: U266HR_Hypoxia_24h-cell

description:
SAMPLE 3
test

source_name: hypoxia-resistant-Multiple Myeloma-derived subl line _hypoxia (1% O2)


title: Oral 3D tissue irradiated 2 Gy

description: Sample name: NT2I

source_name: Human primary oral 3D tissue irradiated with 2 Gy

value: 2 Gy


title: RPMI8226_Hypoxia_24h-exosome

description:
SAMPLE 5
test

extract_protocol:
Exosome extract protocol: The 5 ml of culture media of RPMI8226 cells and RPMI8226HR cells were obtained and centrifuged at 3,000 × g for 15 min. The supernatant was filtered through a 0.22-µm PVDF filter (Millipore). The appropriate volume of Exoquick Exosome Precipitation Solution (System Biosciences, Mountain View, CA, USA) was added to the filtered culture medium and mixed well by inverting. After refrigeration for 12 h, the mixture was centrifuged at 1,500 × g for 30 min and all supernatant was removed by aspiration.
RNA extract protocol: The Cell or exosome pellets were dissolved with 700 µl of QIAzol lysis regent (Qiagen). After a 2-min incubation, 1 µl of 1 nM ath-miR-159 (Hokkaido System Science, Hokkaido, Japan) was added to each aliquot as a spike control for losses in preparation, followed by vortexing for 30 sec and incubation on ice for 10 min. Subsequent phenol extraction and cartridge filtration were carried out according to the manufacturer’s instructions.

treatment_protocol: RPMI8226 cells and RPMI8226HR cells were seeded at a density of 5 × 10^5 cells/ml, and cultured for 24 hours under hypoxic conditions (1% O2, 5% CO2, 94% N2) in a humidified gas-sorted hypoxic incubator (MCO-5M, Sanyo, Osaka, Japan) using the degassed culture mediums (AIM-V medium, Invitrogen).


title: Late bicellular pollen - stage 5 - replicate 1

description: Gene expression profile of late bicellular pollen

source_name: Late bicellular pollen - stage 5

value: Late bicellular pollen


title: mESC Mettl3 shRNA #1 replicate #1

description: replicate 1

value: Mettl3 shRNA #1


title: RPMI8226_Hypoxia_24h-cell

description:
SAMPLE 2
test


title: Synaptoneurosome_Alcohol_3_miRNA

value: 2 months old

value: brain/extended amygdala


title: Late bicellular pollen - stage 5 - replicate 2


title: U266_Normoxia_24h-cell

description:
SAMPLE 1
control

source_name: Multiple Myelima-derived cell line _normoxia (20% O2)


title: mESC luciferase shRNA, replicate #2

description: replicate 2

value: embryonic stem cells

value: control - luciferase shRNA


title: mESC luciferase shRNA, replicate #3

description: replicate 3


title: Microspores - stage 1 - replicate 1

description: Gene expression profile of microspores

source_name: Microspores - stage 1

value: Microspores


title: mESC Mettl3 shRNA #2 replicate #1

description: replicate 1

value: Mettl3 shRNA #2


title: mESC Mettl3 shRNA #1 replicate #2

description: replicate 2


title: Synaptoneurosome_Alcohol_2_miRNA


title: Early bicellular pollen - stage 3 - replicate 1


title: RPMI8226_Normoxia_24h-exosome

description:
SAMPLE 4
control


title: Microspores - stage 1 - replicate 2

description: Gene expression profile of microspores


title: mESC luciferase shRNA, replicate #1

description: replicate 1


title: RPMI8226HR_Hypoxia_24h-cell

description:
SAMPLE 3
test

value: hypoxia (1% O2)


title: KMS-11_Normoxia_24h-exosome

description:
SAMPLE 4
control

source_name: exosome derived from MM cell line_normoxia (20% O2)

extract_protocol:
Exosome extract protocol: The 5 ml of culture media of KMS-11 cells and KMS-11-HR cells were obtained and centrifuged at 3,000 × g for 15 min. The supernatant was filtered through a 0.22-µm PVDF filter (Millipore). The appropriate volume of Exoquick Exosome Precipitation Solution (System Biosciences, Mountain View, CA, USA) was added to the filtered culture medium and mixed well by inverting. After refrigeration for 12 h, the mixture was centrifuged at 1,500 × g for 30 min and all supernatant was removed by aspiration.
RNA extract protocol: The Cell or exosome pellets were dissolved with 700 µl of QIAzol lysis regent (Qiagen). After a 2-min incubation, 1 µl of 1 nM ath-miR-159 (Hokkaido System Science, Hokkaido, Japan) was added to each aliquot as a spike control for losses in preparation, followed by vortexing for 30 sec and incubation on ice for 10 min. Subsequent phenol extraction and cartridge filtration were carried out according to the manufacturer’s instructions.

treatment_protocol: KMS-11 cells and KMS-11-HR cells were seeded at a density of 5 × 10^5 cells/ml, and cultured for 24 hours under hypoxic conditions (1% O2, 5% CO2, 94% N2) in a humidified gas-sorted hypoxic incubator (MCO-5M, Sanyo, Osaka, Japan) using the degassed culture mediums (AIM-V medium, Invitrogen).


title: KMS-11_Hypoxia_24h-cell

description:
SAMPLE 2
test

source_name: Multiple Myeloma-derived cell line_hypoxia (1% O2)


title: RPMI8226_Normoxia_24h-cell

description:
SAMPLE 1
control


title: KMS-11-HR_Hypoxia_24h-cell

description:
SAMPLE 3
test

source_name: hypoxia-resistant-Multiple Myeloma-derived subl line_hypoxia (1% O2)


title: KMS-11-HR_Hypoxia_24h-exosome

description:
SAMPLE 6
test

source_name: exosome derived from hypoxia-resistant-MM cell line_hypoxia (1% O2)


title: KMS-11_Normoxia_24h-cell

description:
SAMPLE 1
control

source_name: Multiple Myelima-derived cell line_normoxia (20% O2)


title: RPMI8226HR_Hypoxia_24h-exosome

description:
SAMPLE 6
test


title: KMS-11_Hypoxia_24h-exosome

description:
SAMPLE 5
test

source_name: exosome derived from MM cell line_hypoxia (1% O2)


title: Fasted liver double knockout rep3

city: Philadelphia

first: John

last: Pehrson

address: 3800 Spruce Street

institute: University of Pennsylvania

hyb_protocol: Five and a half micrograms of labeled cDNA were added to Affymetrix hybridization cocktails, heated at 99ºC for 5 min and hybridized for 16 h at 45ºC to Mouse Gene 2.0 ST GeneChips (Affymetrix Inc., Santa Clara CA). The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain. A GeneChip 3000 7G scanner was used to collect fluorescence signal.

data_processing: Affymetrix Command Console and Expression Console were used to quantitate expression levels for targeted genes; default values provided by Affymetrix were applied to all analysis parameters. Border pixels were removed, and the average intensity of pixels within the 75th percentile was computed for each probe. The average of the lowest 2% of probe intensities occurring in each of the microarray sectors was set as background and subtracted from all features in that sector.

source_name: Liver, 2-month old male, fasted, macroH2A1/2 double knockout

label_protocol: Labeled cDNA was prepared from 250 ng of total RNA using the standard procedure of the Ambion WT Expression Kit (Life Technologies)

growth_protocol: Mice were maintained on a 12 hr day/night cycle with the lights coming on a 8 AM. They were given water and low fat rodent chow Ad libitum. They were killed mid-morning.

extract_protocol: Total liver RNA was extracted with Trizol (life technologies) following standard protocol

treatment_protocol: Mice were fasted overnight for ~ 16 hours and sacrificed between 9 and 10 AM.

value: Male

value: 129/S6 (taconic)

value: Liver

tag: animal age

tag: nutritional status

value: Overnight fast (~16 hours)

tag: genotype/variation

value: macroH2A1 macroH2A2 double knockout


title: serum_sALS patient_16

city: Ulm

first: Karlheinz

last: Holzmann

address: Helmholtzstreet 8/1

department: Medical Faculty

country: Germany

institute: Ulm University

hyb_protocol: according to the instructions in the FlashTagTM Biotin HSR RNA Labeling Kit

scan_protocol: according to Affymetrix protocols using a GeneChip 3000 Scanner

data_processing: Affymetrix Expression Console 1.3.1. for normalization (RMA+DBAG; human only); BRB Array tools for statistical analysis

source_name: serum

label_protocol: FlashTagTM Biotin HSR RNA Labeling Kit (Genisphere, LLC, Hatfield, PA, USA) according to the instructions of the manufacturer

extract_protocol: Total RNA from 8-10 ml of serum were extracted using the QIAzol lysis reagent (Qiagen) according to the manufacturer's instructions. The aqueous phase was collected and total RNA precipitated by addition of 1.4 volumes of isopropanol and overnight incubation at -20°C. Precipitated RNA was redissolved in water and purified a second time using the miRNeasy Mini Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Serum samples were processed within 1 h after blood drawing and stored at -80° C until further usage.

tag: samples of different individuals pooled?

value: no

value: male

tag: als mutation


title: 146

city: Beijing

first: Jinxue

last: Ruan

state: Beijing

address: No.2 Yuanmingyuan West Road

department: Institute of Animal Sciences

institute: Chinese Academy of Agricultural Sciences

description: Gene expression after 23 month high-fat high-sucrose diet induced

hyb_protocol: Each Slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings，Dye channel: Green ,Scan resolution=5μm, PMT 100%，10% ，16bit.

data_processing: The scanned images were analyzed with Feature Extraction software (Agilent technologies, Santa Clara, CA, US)with default settings.

organism: Sus scrofa

source_name: Muscle,23 month high-fat high-sucrose diet induced

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat#5190-2305, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

growth_protocol: Male and female Bama minipigs, aged 6 months at the start of the study, were divided into the following two groups for 23 months of treatment. Bama minipigon control (CD group, N=6) were fed standard pig chow. The experimental group (N=6) were fed high-fat high-sucrose diet (53% basal diet, 37% sucrose, 10% lard, HFHSD). Both groups of Bama swine were gonadally intact. All Swines were fed twice daily on a restricted schedule and dietary dose [3% of body weight monthly; facility certification No.: SYXK (Beijing) 2008-007] and housed in individual pens under controlled conditions (temperature, 18℃–22℃; relative air humidity, 30%–70%). Fasting overnight before dissection, swine were weighted.

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: Total RNA of Longissimus dorsi of the 9 pigs( 6 in HFHSD group and 3 in CD group ) were extracted using TRIzol reagent (Invitrogen) according to the manufacturer’s instructions.

value: muscle

tag: diet


title: serum_sALS patient_15


title: Fasted liver wild-type rep4

scan_protocol: A GeneChip 3000 7G scanner was used to collect fluorescence signal.

source_name: Liver, 2-month old male, fasted, wild-type

tag: tissue

value: Wild-type


title: Fasted liver wild-type rep5

tag: strain


title: Fasted liver double knockout rep4


title: 126

value: 23 month high-fat high-sucrose diet induced


title: serum_sALS patient_14


title: 161

description: Gene expression with control diet

source_name: Muscle, control diet

value: control


title: Fasted liver wild-type rep3


title: 159

description: Gene expression with control diet


title: 138


title: Fasted liver double knockout rep2


title: Fasted liver wild-type rep2


title: serum_sALS patient_13


title: 157

description: Gene expression with control diet


title: 144


title: serum_sALS patient_12


title: serum_sALS patient_18


title: Fasted liver wild-type rep1


title: 140


title: Fasted liver double knockout rep5


title: serum_sALS patient_10


title: serum_sALS patient_9

value: female


title: serum_sALS patient_8


title: serum_sALS patient_17


title: serum_sALS patient_5


title: serum_sALS patient_4


title: Fasted liver double knockout rep1


title: serum_sALS patient_1


title: serum_sALS patient_6


title: serum_sALS patient_2


title: serum_sALS patient_3


title: serum_sALS patient_7


title: serum_sALS patient_11


title: 120


title: serum_ALS mutation carrier pool 3

value: yes

value: both male

value: both C9ORF72 hexanucleotide expansion


title: serum_ALS mutation carrier_11

value: PFN T109M


title: serum_ALS mutation carrier pool 4

value: two male, one female

value: all PFN T109M


title: serum_ALS mutation carrier pool 2

value: all female

value: all C9ORF72 hexanucleotide expansion


title: serum_ALS mutation carrier_8

value: C9ORF72 hexanucleotide expansion


title: serum_ALS mutation carrier_5


title: serum_ALS mutation carrier_12

value: unknown


title: serum_ALS mutation carrier_3

value: no

value: SOD1 R115G


title: serum_ALS mutation carrier_4

value: male


title: serum_ALS mutation carrier_10


title: serum_ALS mutation carrier pool 1

value: female, male

value: SOD1 R115G and SOD1 E100K


title: serum_fALS patient_3

value: SOD1 D90A


title: serum_fALS patient pool 2

value: SOD1 R115G and SOD1 E133K


title: serum_fALS patient pool 1

value: yes

value: male, female

value: both SOD1 I104F


title: serum_ALS mutation carrier_2

value: female


title: serum_fALS patient_4


title: serum_fALS patient pool

value: both male

value: both C9ORF72 hexanucleotide expansion


title: serum_healthy control_16

description: control  for comparison with sALS and fALS


title: serum_healthy control_17

description: control  for comparison with carrier


title: serum_healthy control_9

description: control  for comparison with sALS, fALS and carrier


title: serum_healthy control_15


title: serum_healthy control_11

description: control  for comparison with sALS and carrier


title: serum_healthy control_12


title: serum_healthy control_14


title: serum_healthy control_13

description: control  for comparison with sALS


title: serum_healthy control_10

description: control  for comparison with sALS


title: serum_fALS patient_6

value: FUS R521H


title: serum_healthy control_8

description: control  for comparison with sALS


title: serum_healthy control_4


title: serum_healthy control_1


title: KC-low-Arsenic_Pool

city: Shanghai

first: Daiyin

last: Chao

address: 300 Fenglin Road

department: Shanghai Institute of Plant Physiology and Ecology

institute: Shanghai Institutes for Biological Sciences

description: The low arsenic pool from the F2s segregating from a Kr-0 x Col-0 cross used for eXtreme Array Mapping.

hyb_protocol: The labelled DNA from the two pools was hybridized to the Affymetrix SNP-tilling array Atsnptile 1 following standard Affymetrix protocols.

scan_protocol: Affymetrix standard

data_processing: The CEL files containing raw data of signal intensity for all probes were read and spatially corrected using previously described R scripts (Borevitz et al.,2003, Genome Research, 13:513-523) with the R program and the Bioconductor Affymetrix package. There are 4 probes for each SNP, antisense and sense probes for two alleles. The allele frequency difference between the two pools for each polymorphic SNP was then scored based on the signal intensity difference of the 4 probes. The whole process was carried out using R scripts described previously (Becker et al., 2011, PLoS One, 6:e15993), which is avaiable at http://ars.usda.gov/mwa/bsasnp.

organism: Arabidopsis thaliana

source_name: leaves

label_protocol: Invitrogen Bioprime labelling kit

extract_protocol: Qiagen DNeasy kit

value: ~6 weeks

value: leaves

tag: genotype

value: F2 plants from a cross between the high arsenic Arabidopsis thaliana accession Kr-0 and the low arsenic accession Col-0


title: KC-high-Arsenic_Pool

description: The high arsenic pool from the F2s segregating from a Kr-0 x Col-0 cross used for eXtreme Array Mapping.


title: serum_healthy control_2

value: no


title: serum_healthy control_5


title: serum_healthy control_7


title: serum_healthy control_6

description: control  for comparison with sALS


title: 42B

first: Ming

middle: zhe

last: Ma

state: Shanghai

address: 270 DongAn Road

department: Department of Gastric Surgery

institute: Fudan University Shanghai Cancer Center

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45c on gene chip. Genechips were washed and stained in the Affymetrix Fluicidics Station 450.

scan_protocol: Genechips were scanned by Affymetrix genechip Command Console (AGCC) which installed in GeneChip Scaner 3000 7G

data_processing:
The data were analyzed with Robust Multichip analysis (RMA) algothrim using Affymetrix default analysis settings and global scaling as normalization method.
Supplementary file: Differentially Expressed Genes.xlsx (where GroupA = gallbladder cancer and GroupB = adjacent normal tissue).

source_name: adjacent normal tissue

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

extract_protocol: Total RNA were prepared according to the standard Affymetrix protocol

tag: treatment(s)

value: No

tag: specimen id

value: adjacent normal tissue


title: 23B


title: 41A

source_name: gallbladder cancer

value: gallbladder cancer


title: 41B


title: 40A


title: keratinocytes with control shRNA replicate #2

city: La Jolla

first: George

last: Sen

address: 9500 GIlman Drive

department: Dermatology/CMM

institute: UCSD

hyb_protocol: Labeling and hybridization was perfomed at UCSD genechip core facility. Please refer to their website for specific details (http://www.vmrf.org/researchcenters/gene-chip/gene-chip.html)

scan_protocol: Affymetrix HG-U133 2.0 plus arrays were performed at the UCSD Genechip Microarray Core Facility.

data_processing:
program-name = Expression Console
program-version = 1.1.2800.28061
affymetrix-algorithm-name = plier-mm

source_name: Cells transduced with control shRNAs

growth_protocol: human keratinocytes grown in KCSFM (Life Technologies)

extract_protocol: Total RNA from cells was extracted using the RNeasy mini kit according to manufacturer's protocol.

treatment_protocol: Cells transduced with control or SNAI2 shRNAs. Cells transduced with LACZ or SNAI2 expression constructs.

tag: cell type

value: primary human keratinocytes


title: keratinocytes overexpressing SNAI2replicate #2

source_name: Cells transduced with SNAI2

label_protocol: Labeling and hybridization was perfomed at UCSD genechip core facility. Please refer to their website for specific details (http://www.vmrf.org/researchcenters/gene-chip/gene-chip.html)


title: keratinocytes overexpressing LacZ control replicate #1

source_name: Cells transduced with LacZ


title: 22B


title: keratinocytes with SNAI2 shRNA replicate #2

source_name: Cells transduced with SNAI2 shRNAs


title: serum_healthy control_3


title: keratinocytes with SNAI2 shRNA replicate #1


title: keratinocytes overexpressing SNAI2replicate #1


title: 22A


title: keratinocytes overexpressing LacZ control replicate #2


title: 42A


title: SIRT1tg rep6

city: Lausanne

first: Marie

last: Boutant

address: EPFL Innovation Park, Bâtiment G

country: Switzerland

institute: Nestle Institute of Health Sciences

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with Illumina Genome Studio software

source_name: Mouse brown adipose tissue

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

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

tag: genetic background

value: 3 months

value: Brown adipose tissue


title: 40B


title: 23A


title: SIRT1tg rep5


title: NasalMucosa_Healthy_Control_Sample41

city: Lørenskog

first: Christopher

middle: Stephen

last: Inchley

address: Sykehusveien

department: Department of Pediatric and Adolescent Medicine

country: Norway

institute: Akershus University Hospital

description: Nasal mucosal miRNA expression in healthy child without symptoms of respiratory infection

hyb_protocol: miRNA Spike-In Kit and miRNA Complete Labeling and Hyb Kit (Agilent), according to manufacturer's instructions

scan_protocol: Arrays were scanned on Agilent G2565BA Microarray Scanner. Data collection and quality assessment were performed using Agilent Feature Extraction Software v8.5

data_processing: The AgiMiRNA package for R was used to normalize data by Quantile normalization. miRNAs were removed if <50% of samples in all experimental groups expressed that miRNA or if < 25% of samples in all experimental groups had expression levels equal to or less than the mean + 1.5 standard deviations of negative control features.

source_name: Nasal mucosa

extract_protocol: Brushes were immediately immersed in RNA stabilization reagent RNAlater (Sigma-Aldrich, Saint Louis, Missouri, USA). Epithelial cells were detached from the brushes and stored at -80°C in RNAlater for miRNA analysis. Epithelial cells stored at -80℃ were pelleted before homogenization in QIAzolLysis Reagent (Qiagen, Hilden, Germany). The miRNeasy mini kit (Qiagen) was then used according to the manufacturer’s instructions with additional DNase treatment.

tag: disease state

value: Healthy Control

tag: age (months)

tag: gender

value: Male


title: 21_AGO2-rep2

city: Rome

first: Teresa

last: Colombo

address: p.le A. Moro 7

department: Institute of Molecular Biology and Pathology (IBPM)

country: Italy

institute: Consiglio Nazionale delle Ricerche (CNR)

description: AGO2 Immunopurified RNA

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® Human Genome U133 Plus 2.0

scan_protocol: GeneChips were scanned using the 7G Scanner

data_processing: Affymetrix .CEL files were separately processed for each replicate using the Robust Multi-array Average (RMA) algorithm with quantile normalization as implemented in the Bioconductor package 'simpleaffy'.

source_name: Jurkat cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (C_Total, 21_Total samples) or 100ng of Immunopurified RNA.

growth_protocol: Jurkat cells were grown in RPMI supplemented with 10% FBS, L-glutamine, pen/strep.

extract_protocol: RNA was extracted by proteinase K treatment followed by phenol-chloroform extraction

tag: cell line

value: Jurkat

tag: construct

value: MiR-21 overexpression

tag: fraction

value: AGO2 Immunopurified RNA


title: keratinocytes with control shRNA replicate #1


title: SIRT1tg rep4

tag: age


title: NasalMucosa_RSVpositive_SevereDisease_Sample40

description: Nasal mucosal miRNA expression on admission with Respiratory Syncytial Virus infection

label_protocol: miRNA Spike-In Kit and miRNA Complete Labeling and Hyb Kit (Agilent), according to manufacturer's instructions

value: Severe Respiratory Syncytial Virus Disease


title: 21_IgG-rep2

description: Control IgG immunopurified RNA

value: Control IgG immunopurified RNA


title: Ctrl_IgG-rep2

description: Control IgG immunopurified RNA

value: Control vector


title: NasalMucosa_RSVpositive_MildDisease_Sample39

value: Mild Respiratory Syncytial Virus Disease

value: Female


title: SIRT1tg rep3


title: NasalMucosa_RSVpositive_SevereDisease_Sample38


title: C_Total-rep2

description: Total RNA

value: Total RNA


title: 21_Total-rep2

description: Total RNA


title: 21_AGO2-rep1

description: AGO2 Immunopurified RNA


title: Ctrl_AGO2-rep1

description: AGO2 Immunopurified RNA


title: SIRT1tg rep2


title: WT rep5

value: wild type


title: 21_IgG-rep1

description: Control IgG immunopurified RNA


title: Ctrl_IgG-rep1

description: Control IgG immunopurified RNA


title: 21_Total-rep1

description: Total RNA


title: WT rep6


title: Ctrl_AGO2-rep2

description: AGO2 Immunopurified RNA


title: NasalMucosa_Healthy_Control_Sample37


title: SIRT1tg rep1


title: WT rep2


title: WT rep3


title: NasalMucosa_Healthy_Control_Sample35


title: NasalMucosa_RSVpositive_MildDisease_Sample36


title: WT rep4


title: NasalMucosa_RSVpositive_SevereDisease_Sample34


title: C_Total-rep1

description: Total RNA


title: NasalMucosa_Healthy_Control_Sample32


title: WT rep1


title: NasalMucosa_RSVpositive_SevereDisease_Sample31


title: NasalMucosa_RSVpositive_MildDisease_Sample30


title: Liver_Metastasis-HM_244_FP

city: Montpellier Cedex 5

first: Pierre

last: Martineau

address: 208 Rue des Apothicaires

department: IRCM

country: France

institute: Inserm

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133B  Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 with HWS kit.

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

data_processing: Signal intensity for each transcript and detection call (present, absent, or marginal) were determined using MAS 5.0 Software (Affymetrix). Interarray normalization was performed using a set of internal standard genes (normalization set ϩ internal controls) leading to the determination of a scaling factor.

source_name: Tissue samples taken from colorectal cancer patients

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix IVT protocol from 3µg total RNA (3'IVT ExpressTechnical Manual).

extract_protocol: Rneasy kit (Qiagen) for total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Samples were collected before chemotherapy

value: Liver Metastasis

tag: patient number

tag: Sex

tag: who performance status

tag: tumor location

value: Transverse colon

tag: differentiation

value: Moderate

tag: pn

tag: pt

tag: folfiri status

value: R


title: Liver_Metastasis-HM_223_GB

tag: tissue

value: Left colon

value: NR


title: NasalMucosa_RSVpositive_MildDisease_Sample27


title: NasalMucosa_Healthy_Control_Sample29

value: Healthy Control


title: NasalMucosa_RSVpositive_SevereDisease_Sample28


title: NasalMucosa_Healthy_Control_Sample33

value: Male


title: NasalMucosa_RSVpositive_SevereDisease_Sample26


title: Liver_Metastasis-HM_179_AB

value: Rectum


title: Liver_Metastasis-HM_196_TD

value: Well


title: NasalMucosa_RSVpositive_MildDisease_Sample25


title: Liver_Metastasis-HM_213_RG


title: Liver_Metastasis-HM_115_CB

value: Right colon


title: NasalMucosa_Healthy_Control_Sample23


title: NasalMucosa_RSVpositive_SevereDisease_Sample22

value: Severe Respiratory Syncytial Virus Disease


title: Liver_Metastasis-HM_109_JC


title: Liver_Metastasis-HM_149_JGI


title: Liver_Metastasis-HM_059_MT


title: NasalMucosa_Healthy_Control_Sample21


title: Liver_Metastasis-HM_073_PD


title: Liver_Metastasis-HM_089_NC


title: NasalMucosa_RSVpositive_MildDisease_Sample20


title: Liver_Metastasis-HM_094_AM

value: Rectum-sigmoid junction

value: Poor


title: GSC-DMSO 6hrs

city: Seoul

first: Young Dong

last: Yoo

state: Gyeonggi-do

address: 28 Yeon-gun dong Jongnogu

department: Biomedical Science

country: South Korea

institute: Seoul National University

description:
Sample name: GSC DMSO
Glioma stem cells(XO-10) cultured in suspension in serum-free media

hyb_protocol: 750 ng of labeled cRNA samples were hybridized to each human HT-12 expression v.4 bead array for 16-18 h at 58°C, according to the manufacturer's instructions (Illumina, Inc., San Diego, USA).   Detection of array signal was carried out using Amersham fluorolink streptavidin-Cy3 (GE Healthcare Bio-Sciences, Little Chalfont, UK) following the bead array manual.

scan_protocol: Arrays were scanned with an Illumina bead array Reader confocal scanner according to the manufacturer's instructions.

data_processing: Raw data were extracted using the software provided by the manufacturer(Illumina GenomeStudio v2009.2 (Gene Expression Module v1.5.4)). Array data were filtered by detection p-value < 0.05 (similar to signal to noise) in at least 50% samples (we applied a filtering criterion for data analysis; higher signal value was required to obtain a detection p-value < 0.05). Selected probe signal value was transformed by logarithm and normalized by quantile method. The comparative analysis between test group and control group was carried out using LPE test and fold-change. False discovery rate (FDR) was controlled by adjusting p value using Benjamini-Hochberg algorithm.

source_name: Glioma specimen

label_protocol: Total RNA was amplified and purified using the Ambion Illumina RNA amplification kit (Ambion, Austin, USA) to yield biotinylated cRNA according to the manufacturer’s instructions.

growth_protocol: GSCs were cultured in suspension condition in serum-free media. Differentiated cells were cultured in serum-containing media.

extract_protocol: Total RNA was extracted using Trizol (Invitrogen Life Technologies, Carlsbad, USA), purified using RNeasy columns (Qiagen, Valencia, USA) according to the manufacturers’ protocol.

treatment_protocol: GSCs cells were attached to the lamine-coated plate for 8 hes in serum-free media before MG132 treatment. Differentiated cells were cultured in serum-free media for 8 hrs before MG132 treatment. Both cells were treated with 0.1 μM MG132 or DMSO in serum-free media for 6 hrs.

value: brain

tag: cell type

value: GSC

tag: treatment

value: control


title: NasalMucosa_RSVpositive_MildDisease_Sample19

tag: disease state

value: Mild Respiratory Syncytial Virus Disease

tag: age (months)


title: NasalMucosa_RSVpositive_SevereDisease_Sample18

tag: gender


title: GSC-MG132 6hrs

description:
Sample name: GSC MG132
Glioma stem cells(XO-10) cultured in suspension in serum-free media


title: Differentiated cell-MG132 6hrs

description:
Sample name: Differentiated Cell MG132
Differentiated cells cultured in adhesive culture in serum-containing media

value: differentiated cell counterpart of GSC


title: Differentiated cell-DMSO 6hrs

description:
Sample name: Differentiated Cell DMSO
Differentiated cells cultured in adhesive culture in serum-containing media


title: Liver_Metastasis-HM_016_MV

value: Liver Metastasis

value: Female


title: NasalMucosa_RSVpositive_MildDisease_Sample17


title: Liver_Metastasis-HM_044_MB

value: Left colon

value: R


title: Liver_Metastasis-HM_005_JME

value: Moderate


title: Liver_Metastasis-HM_222_PEC

value: Male

value: NR


title: Liver_Metastasis-HM_050_NC1B

value: Rectum

value: Well