title: WT vs cyc- logarithmic growth phase

description: 1:1 combined, labeled cDNA of the WT and KO strain cultured until logarithmic growth phase

tag: strain

value: logarithmic


title: MiR155ko_NonPhagocytic_03

status: Public on Sep 19 2017

type: RNA

city: Boston

first: Oleg

last: Butovsky

state: MA

address: 77 Avenue Louis Pasteur, Office 614

department: Center of Neurologic Diseases

country: USA

institute: Brigham and Women's Hospital, Harvard Medical School

hyb_protocol: Refer to the NanoString nCounter Assay System Manual.

data_processing: The raw data were normalized using 6 housekeeping genes.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: FACS sorted MG cells

extract_protocol: none provided by the submitter

tag: cells

value: microglia


title: MiR155ko_Phagocytic_02

scan_protocol: Refer to the NanoString nCounter Assay System Manual.


title: PSV-G+satRNA_rep1_vs_ref

status: Public on Sep 20 2017

city: Poznan

first: Agnieszka

last: Zmienko

address: Noskowskiego 12/14

country: Poland

institute: Institute of Bioorganic Chemistry PAS

hyb_protocol: All of the hybridization, washing and drying steps were performed in 2x105K Chambers in an HS 4800 Pro (Tecan) automatic hybridization station according to the manufacturer’s guidelines regarding Agilent microarrays treatment. A Gene Expression Hybridization Kit (Agilent) and Gene Expression Wash Buffer Kit solutions (Agilent) were used for the hybridization and washing steps, respectively.

scan_protocol: The intensity data were collected with 4200AL GenePix scanner and GenePix Pro 6.1 software at 5 µm resolution, at green and red channel.

data_processing: The scans were processed with GenePix Pro 6.1 software using morphological opening background method. Intensity data were analyzed with R/Bioconductor limma package. Background was subtracted. Loess within-array normalization and Aquantile between-array normalization was applied.

organism: Nicotiana benthamiana

source_name: ref

label_protocol: Labeled cRNA samples were prepared from 200 ng RNA each, using Quick Amp Labeling Kit (Agilent). The labeling efficiency was monitored with Nanodrop 2000 spectrophotometer.

growth_protocol: N. benthamiana plants were grown in separate cabins under 14h light/ 10h dark at 21°C day/16°C night.

extract_protocol: Samples from 3 biological replicates per treatment were obtained. Total RNA was extracted from upper parts of plants using spin-columns (RNeasy Plant Mini Kit, QIAGEN) and DNase-digested with TURBO DNA-free kit (Ambion) according to the manufacturers’ standard protocols. RNA quality was determined using Nanodrop 2000 and 2100 Bioanalyzer (Agilent). All of the samples used for the study were pure (A260/A280 ≥ 1.9; A260/A230 ≥ 2) and showed no visible signs of degradation.

treatment_protocol: Plants were inoculated with Peanut stunt virus strain G (PSV-G) or PSV-G and satellite RNA-P (PSV-G+satRNA) infectious copies in 0.5 M phosphate, pH 7.5, after carborund dusting. Mock-inoculated plants were treated as controls. Plants were harvested when first symptoms of infection occurred (20 dpi).

tag: tissue

value: upper part of plant

tag: treatment

value: peanut stunt virus strain G and satellite RNA-P


title: PSV-G_rep3_vs_ref

value: peanut stunt virus strain G


title: MiR155ko_NonPhagocytic_02

label_protocol: Refer to the NanoString nCounter Assay System Manual.


title: PSV-G+satRNA_rep2_vs_ref


title: MiR155ko_NonPhagocytic_01


title: WT_NonPhagocytic_01


title: PSV-G_rep2_vs_ref


title: MiR155ko_Phagocytic_01


title: PSV-G_rep1_vs_ref


title: APP-PS1controlTrem2ko_04


title: APP-PS1:Trem2ko_07


title: APP-PS1:Trem2ko_06


title: APP-PS1controlTrem2ko_02


title: APP-PS1:Trem2ko_05


title: APP-PS1:Trem2ko_04


title: APP-PS1:Trem2ko_03


title: APP-PS1controlTrem2ko_03


title: APP-PS1:Trem2ko_01


title: APP-PS1controlTrem2ko_01


title: Apoeko_recombinantApoeinjected_02


title: Apoeko_recombinantApoeinjected_01


title: APP-PS1:Trem2ko_02


title: Thymus sample 8, Grade 1-4

city: Washington DC

first: Manjistha

last: Sengupta

state: District of Columbia

address: 2300 Eye Street NW, Ross Hall,  Room #723

department: Neurology

institute: George Washington University

description: Gene expression data

hyb_protocol: The samples were hybridized to GeneChip human transcriptome array 2.0 (Affymetrix). Washed and stained by Gene Chip Fluid Station 450

scan_protocol: They were scanned by Affymetrix GeneChip Scanner (GC30007G).

data_processing: Array data was normalized, batch corrected and analyzed (1-way ANOVA) using Partek Genomics Suite program.

organism: Homo sapiens

source_name: myasthenia gravis thymus

label_protocol: Three hundred nanogram of total RNA was used for ss cDNA synthesis and labeling by GeneChip WT plus reagent kit (Affymetrix).

extract_protocol: Total RNA was extracted by Trizol reagent according to the manufacturers protocol.

value: Thymus

tag: grade

value: Grade 1-4

tag: morphology

value: Germinal Center


title: Thymus sample 10, Grade 0

description: Gene expression data

value: Grade 0

value: No Germinal Center


title: Thymus sample 4, Grade 1-4

description: Gene expression data


title: Apoeko_recombinantApoeinjected_03


title: Thymus sample 9, Grade 0

description: Gene expression data


title: Thymus sample 12, Grade 1-4

description: Gene expression data


title: Thymus sample 2, Grade 1-4

description: Gene expression data


title: Thymus sample 11, Grade 0

description: Gene expression data


title: Thymus sample 3, Grade 1-4

description: Gene expression data


title: Thymus sample 6, Grade 0

description: Gene expression data


title: KMS11plus2_5uM_2

first: Mehmet

middle: Kemal

last: Samur

address: 450 Brookline Ave

institute: Dana Farber Cancer Institute

hyb_protocol: The targets are then hybridized onto GeneChip® Human Transcriptome Array 2.0 . They are hybridized at 45C for 16-18 hours. The arrays were washed and stained on Fluidics Stations 450 using the Affymetrix Hybe/Wash/Stain.

scan_protocol: The arrays were scanned on GeneChip Scanner 3000 7G

data_processing:
Data was processed using Affymetrix Expression Suite software
RMA

source_name: MM KMS11 Cell Line

label_protocol: The Affymetrix GeneChip WT Plus Reagent Kit is used to convert 100ng of total RNA into biotinylated sense-strand DNA targets.

extract_protocol: total RNA was extracted from MM cell lines by using Rneasy kit from Qiagen

tag: cell type

value: Multiple myeloma cell line KMS11 with EPZ025666 treatment


title: Apoeko_PBSinjected_03


title: Thymus sample 1, Grade 1-4

description: Gene expression data


title: Thymus sample 7, Grade 0

description: Gene expression data


title: Thymus sample 14, Grade 1-4

description: Gene expression data


title: Apoeko_PBSinjected_02


title: Apoeko_PBSinjected_01


title: KMS11plus2_5uM_1


title: WT_EAE_score3_06


title: WT_EAE_score4_01


title: WT_EAE_score3_05


title: WT_EAE_score3_04


title: WT_EAE_score3_01


title: MHC_6W_KO1

city: New York

first: Marion

middle: Dejosez

last: Zwaka

state: NY

address: 1425 Madison Ave

department: Black Family Stem Cell Institute

institute: Icahn School of Medicine at Mount Sinai

description: Replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using cubic spline normalisation with GenePattern

label: Biotin

source_name: Mouse embryonic heart, 6 weeks, MHC::Cre-driven Ronin knockout

label_protocol: Standard Illumina labeling protocol

extract_protocol: RNeasy Mini kit (Qiagen) including Dnase I digest according to the manufacturer's protocol

tag: genotype

value: Nkx2.5::Cre, RoninloxP/loxP

tag: age

value: 6 weeks

value: Heart


title: WT_EAE_score3_02


title: KMS11minus_2

value: Multiple myeloma cell line KMS11


title: Thymus sample 13, Grade 0

description: Gene expression data


title: KMS11minus_1


title: Adipocytes from obese human adipose tissue [JL49_M_15]

city: Stockholm

first: Jurga

last: Laurencikiene

address: Hälsovägen 7

country: Sweden

institute: Karolinska Institutet

hyb_protocol: Affymetrix standard protocol for hybridization of cartridge arrays

scan_protocol: Arrays were scanned in Affymetrix GeneChip Scanner 3000 7G

data_processing: CEL files were analyzed in Affymetrix Expression Console using RMA

source_name: Subcutaneous white adipose tissue

label_protocol: Affymetrix WT Plus protocol was used for 100ng total RNA input

growth_protocol: Not applicable

extract_protocol: Adipose tissue samples were obtained from either liposuctions or  abdominoplasty. Adipose tissue were cut into small pieces and collagenase treated. Adipocytes and stromal vascular fractions were separated by centrifugation. SVF were further sorted using flow cytometry with CD45, CD34 and CD31 markers. CD45-/CD31- cells were called as Progenitors, CD45+/CD34 were called as Monocytes/Macrophages and CD45+/CD34 were called as Leukocytes. Total RNA was prepared using the XXX from YYY

treatment_protocol: Not applicable

value: Adipocyte

tag: facs markers

value: Collagenase float

tag: weight status

value: Obese

tag: patient number


title: Adipocytes from obese human adipose tissue [JL50_M_16]


title: MHC_6W_Ctrl2

description: Replicate 2

source_name: Mouse embryonic heart, 6 weeks, MHC::Cre Control

value: MHC::Cre; RoninloxP/+


title: Adipocytes from obese human adipose tissue [JL47_M_13]


title: Adipocytes from obese human adipose tissue [JL51_M_17]


title: MHC_P0_KO2

description: Replicate 2

source_name: Mouse embryonic heart, P0, MHC::Cre-driven Ronin knockout


title: Adipocytes from obese human adipose tissue [JL48_M_14]


title: MHC_P0_KO1

description: Replicate 1


title: WT_EAE_score2_06

value: microglia


title: Adipocytes from obese human adipose tissue [JL45_M_11]


title: MHC_6W_Ctrl1

description: Replicate 1


title: MHC_P0_Ctrl1

description: Replicate 1

source_name: Mouse embryonic heart, P0, MHC::Cre Control


title: Adipocytes from non-obese human adipose tissue [JL44_M_8]

value: Non-obese


title: MHC_E11.5_KO2

description: Replicate 2

source_name: Mouse embryonic heart, E11.5, MHC::Cre-driven Ronin knockout


title: WT_EAE_score2_05


title: MHC_P0_Ctrl2

description: Replicate 2


title: WT_EAE_score3_03


title: WT_EAE_score2_02


title: WT_EAE_score2_01


title: WT_EAE_score1_04


title: WT_EAE_score2_03


title: MHC_E11.5_Ctrl2

description: Replicate 2

source_name: Mouse embryonic heart, E11.5, MHC::Cre Control


title: Nkx2.5_E11.5_KO3

description: Replicate 3

source_name: Mouse embryonic heart, E11.5, Nkx2.5-driven Ronin knockout


title: MHC_E11.5_KO1

description: Replicate 1


title: MHC_E11.5_Ctrl1

description: Replicate 1


title: WT_EAE_score2_04


title: WT_EAE_score1_03


title: WT_Phagocytic_deadneurons_04


title: WT_NonPhagocytic_deadneurons_04


title: WT_EAE_score1_01


title: WT_EAE_score1_02


title: Nkx2.5_E11.5_KO1

description: Replicate 1


title: WT_NonPhagocytic_deadneurons_01


title: WT_Phagocytic_deadneurons_01


title: WT_naive_score0_04


title: Nkx2.5_E11.5_Ctrl3

description: Replicate 3

source_name: Mouse embryonic heart, E11.5, Nkx2.5::Cre Control

value: Nkx2.5::Cre, RoninloxP/+


title: WT_naive_score0_03


title: Nkx2.5_E11.5_Ctrl2

description: Replicate 2


title: WT_Phagocytic_deadneurons_03


title: Nkx2.5_E11.5_Ctrl1

description: Replicate 1


title: Nkx2.5_E9.5_KO2

description: Replicate 2 - Pool of 10

source_name: Mouse embryonic heart, E9.5, Nkx2.5-driven Ronin knockout


title: Nkx2.5_E11.5_KO2

description: Replicate 2


title: WT_NonPhagocytic_deadneurons_03


title: WT_naive_score0_02


title: Nkx2.5_E9.5_Ctrl1

description: Replicate 1 - Pool of 10

source_name: Mouse embryonic heart, E9.5, Nkx2.5::Cre Control


title: WT_NonPhagocytic_deadneurons_02


title: WT_Phagocytic_deadneurons_02


title: WT_naive_score0_01


title: WT_controlAPP-PS1_Clec7apositive_05

extract_protocol: none provided by the submiitter


title: APP-PS1_2months_02


title: APP-PS1_2months_03


title: WT_controlAPP-PS1_Clec7apositive_04


title: Adipocytes from obese human adipose tissue [JL46_M_12]


title: WT_controlAPP-PS1_Clec7aintermediate_05


title: Nkx2.5_E9.5_KO1

description: Replicate 1 - Pool of 10


title: APP-PS1_2months_01


title: APP-PS1_7months_03


title: WT_controlAPP-PS1_Clec7apositive_02


title: APP-PS1_7months_01


title: WT_controlAPP-PS1_Clec7aintermediate_04


title: WT_controlAPP-PS1_Clec7aintermediate_03


title: WT_controlAPP-PS1_Clec7apositive_03


title: MHC_6W_KO2

description: Replicate 2


title: WT_controlAPP-PS1_Clec7aintermediate_06


title: Starv H3

city: Nagoya

first: Mikako

last: Ito

address: 65 Tsurumai, Showa-ku

country: Japan

institute: Nagoya University Graduate School of Medicine

description: Gene expression data of liver sample from BL6J mouse drinking hydrogen water for 4 weeks, and after 17h fasting

hyb_protocol: Hydridization; 45ºC 60rpm, Wash and Stain; following Fluidics Protocol

scan_protocol: Affymetrics GeneChip Scanner 3000 7G

data_processing: Affymetrix Expression console

source_name: mouse liver drinking hydrogen water after fasting 17h

label_protocol: Ambion WT Expression Kit

growth_protocol: Mice housed at 24 degree C in a light-dark 12-12h photoperiod.

extract_protocol: QIAGEN RNeasy Mini

treatment_protocol: Drink hydrogen water for 4 weeks since age of 7 week, 17h fasting before sacrifice

value: liver


title: WT_controlAPP-PS1_Clec7aintermediate_01


title: Starv Cont2

description: Gene expression data of liver sample from BL6J mouse after 17h fasting

source_name: mouse liver after fasting 17h


title: APP-PS1_7months_02

source_name: FACS sorted MG cells


title: Starv H4


title: Starv H1


title: Starv Cont3


title: Starv Cont4


title: Starv Cont1


title: Nkx2.5_E9.5_Ctrl2

description: Replicate 2 - Pool of 10

source_name: Mouse embryonic heart, E9.5, Control


title: Starv H2


title: WT_controlAPP-PS1_Clec7aintermediate_02


title: SOD1:Trem2ko_12


title: SOD1:Trem2ko_13


title: WT_7months_01


title: WT_2months_01


title: WT_7months_03


title: SOD1:Trem2ko_11


title: APP-PS1_10months_02


title: WT_2months_02


title: SOD1:Trem2het_09


title: APP-PS1_10months_01


title: WT_controlAPP-PS1_Clec7apositive_01


title: SOD1:Trem2het_08


title: WT_10months_01


title: WT_7months_02


title: APP-PS1_17months_03


title: WT_2months_03


title: SOD1:Trem2het_07


title: APP-PS1_10months_03


title: SOD1:Trem2ko_09


title: APP-PS1_17months_02


title: APP-PS1_17months_01


title: SOD1:Trem2ko_06


title: SOD1:Trem2ko_07


title: SOD1:Trem2het_06


title: WT_10months_03


title: SOD1:Trem2ko_10


title: WT_17months_03


title: WT_10months_02


title: SOD1:Trem2het_05


title: SOD1:Trem2ko_05


title: WT_17months_02


title: Apoeko_NonPhagocytic_03


title: Apoeko_Phagocytic_03


title: WT_17months_01


title: SOD1:Trem2het_04


title: Apoeko_NonPhagocytic_02


title: SOD1:Trem2ko_03


title: SOD1:Trem2ko_08


title: SOD1:Trem2ko_01


title: Apoeko_NonPhagocytic_01


title: WTcontrolApoeko_Phagocytic_03


title: SOD1:Trem2het_03


title: SOD1:Trem2ko_04


title: Apoeko_Phagocytic_01


title: WTcontrolApoeko_NonPhagocytic_03


title: APP-PS1_Clec7anegative_06


title: WTcontrolApoeko_NonPhagocytic_02


title: WTcontrolApoeko_Phagocytic_02


title: WTcontrolApoeko_NonPhagocytic_01


title: APP-PS1_Clec7aintermediate_05


title: SOD1:Trem2het_02


title: SOD1:Trem2het_01


title: WTcontrolApoeko_Phagocytic_01


title: Apoeko_Phagocytic_02


title: APP-PS1_Clec7anegative_05


title: APP-PS1_Clec7anegative_04


title: SOD1:Trem2ko_02


title: APP-PS1_Clec7aintermediate_04


title: WT_2months_LPSinjected_01


title: APP-PS1_Clec7apositive_03


title: WT_2months_LPSinjected_03


title: WT_2months_LPSinjected_02


title: WT_2months_PBSinjected_03


title: WT_2months_PBSinjected_02


title: APP-PS1_Clec7apositive_02


title: WT_2months_PBSinjected_01


title: WT_controlAPP-PS1_Clec7anegative_06


title: SOD1_02_score1


title: WT_controlAPP-PS1_Clec7anegative_05


title: SOD1_04_score3


title: WTcontrolSOD1_01_score0


title: APP-PS1_Clec7anegative_01


title: SOD1_03_score3


title: APP-PS1_Clec7aintermediate_03


title: APP-PS1_Clec7anegative_03


title: SOD1_01_score2


title: SOD1_01_score1


title: APP-PS1_Clec7apositive_05


title: APP-PS1_Clec7apositive_06


title: APP-PS1_Clec7anegative_02


title: SOD1_02_score2


title: WT_controlAPP-PS1_Clec7anegative_02


title: APP-PS1_Clec7aintermediate_02


title: APP-PS1_Clec7aintermediate_01


title: SOD1_03_score2


title: APP-PS1_Clec7apositive_01


title: WT_controlAPP-PS1_Clec7anegative_04


title: WT_controlAPP-PS1_Clec7anegative_01


title: WTcontrolSOD1_02_score0


title: WT_controlAPP-PS1_Clec7anegative_03


title: ep8

status: Public on Sep 18 2017

first: Thomas

middle: W

last: Battaglia

address: 423 E 23rd Street

department: Medicine

institute: NYU School of Medicine

hyb_protocol: Hydridized according to the manufacturer's protocol. the hybridization mixture is allowed to bind to the magnetic beads by the Capture Probe. Wash steps are performed and excess Reporter Probes and non-target cellular transcripts are removed during wash steps. After washing, the Capture Probes and Target/Probe complexes are eluted off of the beads and are hybridized to magnetic beads complementary to the Reporter Probe. Wash steps are performed and excess Capture Probes are washed away. Finally, the purified Target/Probe complexes are eluted off and are immobilized in the cartridge for data collection. http://www.nanostring.com/media/pdf/MAN_nCounter_Gene_Expression_Assay.pdf

scan_protocol: Scanned according to the manufacturer's protocol. Data Collection is carried out in the nCounterÎ Digital Analyzer. At the highest standard data resolution, 555_1155 fields of view (FOV) are collected per flow cell using a microscope objective and a CCD camera yielding data of hundreds of thousands of target molecule counts. Digital images are processed on the nCounter Digital Analyzer and the barcode counts are tabulated in a comma separated value (CSV) format. (http://www.nanostring.com/media/pdf/MAN_nCounter_Gene_Expression_Assay.pdf)

data_processing: Probe set summarization was performed using the R/Bioconductor package NanoStringNorm and normalized using the package DESeq2.

label: Nanostring fluorescence oligonucleotide probe (3'-biotin)

source_name: Terminal Ileum

label_protocol: Labeled according to the manufacturer's protocol.  The probe pair consists of a Reporter Probe, which carries the signal on its 5' end, and a Capture Probe which carries a biotin on the 3' end. The color codes carry six positions and each position can be one of four colors, thus allowing for a large diversity of tags that can be mixed together in a single well for direct hybridization to target and yet still be individually resolved and identified during data collection. http://www.nanostring.com/media/pdf/MAN_nCounter_Gene_Expression_Assay.pdf

extract_protocol: TRIzol (Invitrogen) followed by RNeasy column cleanup (Qiagen) using the manufacturers protocols

tag: gender

value: Female

tag: time

value: Week 7

value: Ileum


title: WTcontrolSOD1_03_score0


title: SOD1_02_score3


title: SOD1_01_score3


title: SOD1_04_score2


title: ep47

description: Control

value: Control


title: ep4


title: ep6


title: ep39


title: ep46

description: Control


title: ep48

description: Control

value: Male


title: ep35


title: ep22


title: ep45

description: Control


title: ep1

description: Control


title: APP-PS1_Clec7apositive_04


title: ep24


title: ep21


title: ep38


title: ep44

description: Control


title: ep37


title: ep13


title: ep19


title: ep15


title: ep43

description: Control


title: ep40


title: ep14


title: ep26


title: OSCC_25_1

city: Taoyuan

first: Yi-Hsuan

last: Lai

address: No.259, Wenhua 1st Rd., Guishan Dist.

country: Taiwan

institute: Chang Gung University

scan_protocol: Real-time PCR was performed on an Applied Biosystems 7500 Fast PCR System using the standard SYBR green method

data_processing: The raw data were expressed as 40-Ct

source_name: oral tumor tissue

label_protocol: For miRNA RT reaction, 1 µg of total RNA was first converted into cDNA by Superscript III reverse transcriptase, in which miRNA-specific stem-looped RT primers were used.

extract_protocol: Total RNA was isolated from cells by the TRIzol reagent according to manufacturer’s instructions

value: M

value: buccal mucosa

tag: differentiation stage

value: mod

tag: tumor stage


title: OSCC_26_1

value: F

value: tongue


title: OSCC_29_1

value: well


title: OSCC_27_1


title: OSCC_30_1


title: OSCC_23_1

value: gum


title: ep27


title: OSCC_28_1


title: OSCC_14_1

value: poor


title: OSCC_15_1


title: OSCC_12_1

value: uvula


title: OSCC_19_1


title: OSCC_04_1


title: OSCC_07_1


title: OSCC_05_1


title: OSCC_09_1


title: OSCC_22_1


title: OSCC_24_1


title: OSCC_20_1


title: OSCC_08_1


title: OSCC_18_1


title: OSCC_21_1


title: OSCC_10_1


title: OSCC_11_1


title: OSCC_17_1


title: OSCC_06_1


title: normal_17_1

source_name: oral normal tissue


title: normal_16_1


title: normal_15_1


title: normal_14_1


title: OSCC_03_1

value: hard palate


title: normal_13_1


title: normal_10_1


title: normal_09_1


title: normal_11_1


title: normal_12_1


title: normal_18_1


title: OSCC_13_1


title: OSCC_16_1


title: normal_06_1


title: normal_19_1


title: normal_02_1


title: OSCC_01_1

value: mouth floor


title: normal_08_1


title: OSCC_02_1


title: X43

description: PATGF

value: Tylosin

tag: timepoint

tag: colonized

value: Germ-free


title: X37

description: ControlGF

value: Week 7


title: normal_03_1


title: normal_01_1


title: normal_07_1


title: X8

description: ControlSPF

value: Wild-type


title: normal_04_1


title: X39

description: ControlGF

value: Control


title: X41

description: PATGF

value: Male


title: X38

description: ControlGF


title: normal_05_1

value: M


title: X7

description: ControlSPF


title: X42

description: PATGF


title: X27

description: PATSPF


title: X21

description: PATSPF


title: X2

description: ControlSPF


title: X26

description: PATSPF


title: A549 Low attachment+LA717 7days 2

status: Public on Sep 17 2017

city: Shiraoka-shi

first: Natsuki

last: Abe

state: Saitama

address: Shiraoka 1470

institute: NISSAN CHEMICAL INDUSTORIES, LTD

description: Gene expression data from A549 cells cultured in 3D condition.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Gene 2.0ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 with Hybridization, Wash and Stain Kit.

scan_protocol: GeneChips were scanned using the Affymetrix GCS3000 scanner.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was set to 500.

source_name: A549 cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (3' IVT Express Kit User Manual, 2008, Affymetrix).

growth_protocol: A549 cells were cultured in DMEM supplemented with 10% FBS.

extract_protocol: Extraction of total RNA was performed with Quiagen RNeasy mini kit according to the manufacturer's instructions.

treatment_protocol: A549 cells were cultured for 7 days in attachment or low-attachment 96 well plates with 10 % FBS/DMEM supplemented with LA717 (0.03 w/v%) or Milli-Q water.

tag: condition

value: ow-attachment plate with LA717 containing medium


title: A549 Low attachment 7days 1

value: low-attachment plate with normal medium


title: altitude exposure at post21, biological rep 007

status: Public on Sep 16 2017

city: Aurora

first: Robert

middle: C

last: Roach

state: CO

address: Campus Box F-524, 12469 E. 17th Place

department: Department of Pulmonology

institute: University of Colorado

hyb_protocol: Hybridization to the Affymetrix Human Gene 1.0 ST Array was performed per manufacturer guidelines.

scan_protocol: GeneChip Scanner 3000 7G.

data_processing: Raw expression data was normalized with the RMA algorithm using the R/Bioconductor affy package. Probe annotation was retrieved from BioMart with the useMart() function of the biomaRt package.

source_name: post21, PBMC

label_protocol: cDNA synthesis and amplification were performed using the Sigma-Aldrich TransPlex Complete Whole Transcriptome Amplification (WTA) Kit.

extract_protocol: Peripheral blood samples were collected from an antecubital vein prior to exercise on the first, seventh, and sixteenth days of initial altitude exposure (ALT1, ALT7, and ALT16) and on the re-exposure days (POST7 and POST21), and placed into a BD Vacutainer Cell Preparation Tube containing sodium citrate and Ficoll Hypaque density fluid. PBMC (peripheral blood mononuclear cell) pellets were stored at -80C until analysis.

treatment_protocol: Exposure to altitude.

value: altitude re-exposure

tag: time point

value: day 21 post-descent

tag: subject

value: peripheral blood mononuclear cells (PMBCs)

tag: Sex

tag: height (inches)

tag: weight (kg)


title: A549 Attachment 7days 3

description: Gene expression data from A549 cells cultured in 2D condition. (Control)

tag: cell type

value: normal medium


title: A549 Low attachment+LA717 7days 3


title: A549 Low attachment+LA717 7days 1


title: altitude exposure at post7, biological rep 025

source_name: post7, PBMC

tag: treatment

value: day 7 post-descent

tag: age

value: F


title: A549 Low attachment 7days 2


title: A549 Low attachment 7days 3


title: altitude exposure at post21, biological rep 004


title: altitude exposure at post7, biological rep 023


title: altitude exposure at post21, biological rep 006


title: altitude exposure at post21, biological rep 001


title: A549 Attachment 7days 1


title: altitude exposure at post7, biological rep 021


title: A549 Attachment 7days 2


title: altitude exposure at post21, biological rep 005


title: altitude exposure at post7, biological rep 014


title: altitude exposure at post7, biological rep 022


title: altitude exposure at post7, biological rep 017


title: altitude exposure at alt16, biological rep 023

source_name: alt16, PBMC

value: initial altitude exposure

value: day 16


title: altitude exposure at post7, biological rep 013


title: altitude exposure at post21, biological rep 002


title: altitude exposure at post7, biological rep 015


title: altitude exposure at post7, biological rep 019


title: altitude exposure at post7, biological rep 018


title: altitude exposure at alt16, biological rep 025


title: altitude exposure at alt16, biological rep 022


title: altitude exposure at post7, biological rep 020


title: altitude exposure at post7, biological rep 012


title: altitude exposure at post7, biological rep 011


title: altitude exposure at alt16, biological rep 020


title: altitude exposure at alt16, biological rep 013


title: altitude exposure at alt16, biological rep 019


title: altitude exposure at alt16, biological rep 021


title: altitude exposure at alt16, biological rep 017


title: altitude exposure at alt16, biological rep 018


title: altitude exposure at alt16, biological rep 015


title: altitude exposure at alt16, biological rep 014


title: altitude exposure at alt16, biological rep 004


title: altitude exposure at alt16, biological rep 012


title: altitude exposure at alt16, biological rep 003


title: altitude exposure at alt16, biological rep 011


title: altitude exposure at alt16, biological rep 010


title: altitude exposure at alt16, biological rep 007


title: altitude exposure at alt7, biological rep 025

source_name: alt7, PBMC

value: day 7


title: altitude exposure at alt7, biological rep 021


title: altitude exposure at alt7, biological rep 022


title: altitude exposure at alt7, biological rep 023


title: altitude exposure at alt16, biological rep 006


title: altitude exposure at alt16, biological rep 005


title: altitude exposure at alt7, biological rep 018


title: altitude exposure at alt16, biological rep 002


title: altitude exposure at alt7, biological rep 013


title: altitude exposure at alt16, biological rep 001


title: altitude exposure at alt7, biological rep 014


title: altitude exposure at alt7, biological rep 017


title: altitude exposure at alt7, biological rep 015


title: altitude exposure at alt7, biological rep 019


title: altitude exposure at alt7, biological rep 012


title: altitude exposure at alt7, biological rep 005


title: altitude exposure at alt7, biological rep 002


title: altitude exposure at alt7, biological rep 010


title: altitude exposure at alt7, biological rep 001


title: altitude exposure at alt1pm, biological rep 025

source_name: alt1pm, PBMC

value: day 1, 1pm


title: altitude exposure at alt7, biological rep 011


title: altitude exposure at alt7, biological rep 007


title: altitude exposure at alt7, biological rep 006


title: altitude exposure at alt1pm, biological rep 018


title: altitude exposure at alt1pm, biological rep 017


title: altitude exposure at alt1pm, biological rep 022


title: altitude exposure at alt1pm, biological rep 014


title: altitude exposure at alt1pm, biological rep 023


title: altitude exposure at alt1pm, biological rep 021


title: altitude exposure at alt1pm, biological rep 011


title: altitude exposure at alt1pm, biological rep 010


title: altitude exposure at alt1noon, biological rep 023

source_name: alt1noon, PBMC

value: day 1, noon


title: altitude exposure at alt1pm, biological rep 013


title: altitude exposure at alt1pm, biological rep 015


title: altitude exposure at alt1pm, biological rep 007


title: altitude exposure at alt1pm, biological rep 012


title: altitude exposure at alt1noon, biological rep 025


title: altitude exposure at alt1noon, biological rep 020


title: altitude exposure at alt1noon, biological rep 019


title: altitude exposure at alt1noon, biological rep 022


title: altitude exposure at alt1noon, biological rep 021


title: altitude exposure at post7, biological rep 010


title: altitude exposure at alt1noon, biological rep 018


title: shLDHA_rep2

city: ANN ARBOR

first: Weiping

last: Zou

state: MI

address: 109 Zina Pitcher PL

department: Surgery

institute: University of Michigan

description: Gene expression in LDHA KD cells

hyb_protocol: Following labeling procedure, 2.76 ug of cDNA were hybridized at 48C on a Mouse Gene ST 2.1 Array, and washed and stained using the Affymetrix Gene Atlas system (software version 2.0.0.460)

scan_protocol: Arrays were scanned using the Affymetrix Gene Atlas system (software version 2.0.0.460)

data_processing: RMA was used to fit log2 expression values to the data using the oligo bioconductor package in R version 3.4.0

source_name: LDHA KD 4T1 cells cultured in vitro

label_protocol: Biotinylated cDNA were prepared according to the Affymetrix Plus WT kit protocol (GeneChip® WT Plus Reagent Kit Manual P/N 703174 Rev. 2) from 400 ng total RNA

growth_protocol: Sramble and LDHA knocked down 4T1 cells were cultured in RPMI 1640 complete medium for 24 hours

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

value: LDHA

tag: genotype/variation

value: shLDHA

tag: growth

value: In vitro culture


title: shLDHA_rep1

description: Gene expression in LDHA KD cells


title: Sramble_rep1

description: Gene expression in Scramble cells

source_name: Scramble 4T1 cells cultured in vitro

value: scramble shRNA


title: Sramble_rep2

description: Gene expression in Scramble cells


title: altitude exposure at alt1noon, biological rep 017


title: altitude exposure at alt1noon, biological rep 015


title: altitude exposure at alt1noon, biological rep 013

value: M


title: altitude exposure at alt1noon, biological rep 010


title: altitude exposure at alt1noon, biological rep 014


title: altitude exposure at alt1noon, biological rep 007


title: altitude exposure at alt1noon, biological rep 011


title: altitude exposure at alt1noon, biological rep 012


title: altitude exposure at alt1noon, biological rep 001


title: baseline condition at sea level, biological rep 025

source_name: sea level, PBMC

value: sea level

value: baseline


title: altitude exposure at alt1noon, biological rep 002


title: altitude exposure at alt1noon, biological rep 005


title: altitude exposure at alt1noon, biological rep 006


title: baseline condition at sea level, biological rep 023


title: baseline condition at sea level, biological rep 022


title: baseline condition at sea level, biological rep 021


title: baseline condition at sea level, biological rep 020


title: baseline condition at sea level, biological rep 019


title: baseline condition at sea level, biological rep 017


title: patient 241

type: genomic

city: Amsterdam

first: Fleur

last: Peters

address: Meibergdreef 9

country: Netherlands

institute: Amsterdam UMC (AMC)

hyb_protocol: Isolated genomic DNA (500 ng) was treated with sodium bisulphite using the EZ-96 DNA methylation kit (Zymo Research, Irvine, CA, USA). Hybridization was performed following manufacturer’s instructions. DNA methylation of CpGs was measured by the Illumina HumanMethylation450K BeadChip using the manufacturer’s protocol (Illumina, Inc., San Diego, CA, USA)

scan_protocol: Array was scanned using the iScan beadchip scanner according to Illumina protocol.

data_processing: All data pre-processing and statistical analysis were performed in R software version 3.2.5. Raw methylation data was normalized with lumi (Bioconductor R) to account for differences between the type I and type II intensities. The data quality was examined using the Methylaid package and all samples passed the five quality controls using the default Methylaid tresholds. Probes with a detection p-value below 0.01 were removed from the dataset. Also probed on sex chromosomes were removed since our patient group was a mixture of male and female.

label: Cy5 and Cy3

molecule: genomic DNA

source_name: T cells

label_protocol: Standard Infinium Methylation array protocol

extract_protocol: Genomic DNA was extracted using a Qiagen QIAamp Micro kit according to the manufacturers protocol.

treatment_protocol: Flow cytometry assisted cell sorting of the T cells from peripheral blood mononuclear cells.

tag: gender

value: Female

value: Pre-transplantation

tag: future cscc

value: No

tag: current cscc


title: patient 221

value: Male


title: patient 231


title: patient 240


title: baseline condition at sea level, biological rep 015

value: peripheral blood mononuclear cells (PMBCs)

value: F


title: patient 229


title: patient 233


title: patient 246


title: patient 237


title: patient 245


title: baseline condition at sea level, biological rep 018


title: patient 238


title: patient 234


title: baseline condition at sea level, biological rep 013


title: patient 218


title: patient 247


title: patient 222


title: patient 248


title: patient 219


title: patient 243


title: patient 216


title: patient 224


title: baseline condition at sea level, biological rep 011


title: patient 212


title: patient 213


title: patient 204


title: baseline condition at sea level, biological rep 014


title: patient 215


title: patient 210


title: baseline condition at sea level, biological rep 010


title: baseline condition at sea level, biological rep 005


title: baseline condition at sea level, biological rep 006


title: patient 214


title: baseline condition at sea level, biological rep 007


title: baseline condition at sea level, biological rep 003


title: baseline condition at sea level, biological rep 002


title: patient 202


title: baseline condition at sea level, biological rep 001


title: KO GDX male adrenal biological replicate 2

city: Clermont-Ferrand

first: Antoine

last: Martinez

address: Faculté de Médecine, CRBC, 28 place Henri Dunant

department: GReD

country: France

institute: CNRS, INSERM, Université Clermont Auvergne

hyb_protocol: following fragmentation, cDNA were hybridized for 17h at 45°C on GenChip MouseGene2.0 from Affymetrix. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GenChips were scanned using the GCS 3000 scanner (Affymetrix).

data_processing:
RMA normalization was performed with R and the BioConductor package.
All the probeset associated with a gene symbol were extracted using the annotation R package "mogene20sttranscriptcluser.db"
When multiple probesets were available for one gene, gene expression was calculated as the average of the values for the differents probesets.

source_name: Prkar1a conditional KO GDX male mouse adrenal

label_protocol: biotinylated cDNA were prepared according to the standard Affymetrix protocol from 500ng of total RNA (following the GeneChip® WT PLUS Reagent Kit Affymetrix).

extract_protocol: total RNA were extracted from whole adrenal glands using RNAII nucleotide extraction kit from Macherey-Nagel. RNA quality was assessed by Agilent Bioanalyzer chips.

tag: strain background

value: mixed sv129-C57Bl/6

value: male

value: adult 7 months

tag: castration

value: GDX during last 2 months

tag: tissue

value: Whole adrenal gland


title: baseline condition at sea level, biological rep 004


title: KO GDX male adrenal biological replicate 3


title: KO GDX male adrenal biological replicate 4


title: patient 147

tag: timepoint

value: Yes


title: baseline condition at sea level, biological rep 012

tag: time point


title: patient 145


title: KO GDX male adrenal biological replicate 1


title: patient 146


title: patient 203


title: WT GDX male adrenal biological replicate 4

source_name: WT GDX male mouse adrenal


title: N1

city: Guangzhou

first: Bowei

last: Han

address: No. 651, Dongfeng Road East

country: China

institute: SUN YAT-SEN UNIVERSITY CANCER CENTER

hyb_protocol: The Array was prehybridized for 30 min at 45℃ with 2X Hybridization Mix (Invitrogen) in 10 ml of AlkPhos DIRECT hybridization buffer (Amersham Bioscience) and then hybridized for 16 h at 45℃. Finally, the array was washed twice with wash buffer A (Invitrogen).

scan_protocol: The arrays were then exposed for 2 hours to an Imaging Plate and scanned at 25-mm resolution with a BAS5000 phosphoimager (Fuji Photo Film), images of the hybridized arrays were processed with L Process (Fuji Photo Film) and signal intensities quantified

data_processing: The raw data were re-scaled to account for the differences in individual hybridization intensities. We employed a rank-invariant scaling method to select genes (Tseng et al., 2001), which were then used for fitting of a non-linear normalization curve.

source_name: Normal tissue 1

label_protocol: Three mg of total RNA was reverse-transcribed using oligo-dT primers (Invitrogen) and SuperScript II reverse transcriptase (Invitrogen) in the presence of 100 mCi of [33P]dCTP (Amersham Bioscience, Piscataway, NJ) according to the instructions.

extract_protocol: Total RNA of tissue were extract using TRIzol

value: Normal tissue


title: N3

source_name: Normal tissue 3


title: N2

source_name: Normal tissue 2


title: P9_Normal

source_name: Adjacent tissue of patient 9

value: Adjacent tissue of Cholangiocarcinoma patient


title: patient 143


title: WT GDX male adrenal biological replicate 2


title: P8_Normal

source_name: Adjacent tissue of patient 8


title: P9_Tumor

source_name: Cancerous tissue of patient 9

value: Cancerous tissue of Cholangiocarcinoma patient


title: KO male adrenal biological replicate 4

source_name: Prkar1a conditional KO male mouse adrenal


title: WT GDX male adrenal biological replicate 1


title: WT GDX male adrenal biological replicate 3


title: P8_Tumor

source_name: Cancerous tissue of patient 8


title: patient 134


title: KO male adrenal biological replicate 3


title: KO male adrenal biological replicate 2


title: P7_Normal

source_name: Adjacent tissue of patient 7


title: patient 133


title: patient 148


title: KO male adrenal biological replicate 1


title: patient 138


title: patient 122


title: patient 137


title: WT male adrenal biological replicate 3

source_name: WT male mouse adrenal


title: patient 129


title: P7_Tumor

source_name: Cancerous tissue of patient 7


title: WT male adrenal biological replicate 2


title: P6_Tumor

source_name: Cancerous tissue of patient 6


title: WT male adrenal biological replicate 1


title: P5_Normal

source_name: Adjacent tissue of patient 5


title: KO female adrenal biological replicate 4

source_name: Prkar1a conditional KO female mouse adrenal

value: female


title: patient 124

source_name: T cells


title: patient 141


title: patient 118


title: patient 119


title: patient 121


title: patient 140


title: P5_Tumor

source_name: Cancerous tissue of patient 5


title: P6_Normal

source_name: Adjacent tissue of patient 6


title: KO female adrenal biological replicate 3


title: P4_Tumor

source_name: Cancerous tissue of patient 4


title: KO female adrenal biological replicate 1


title: patient 113


title: patient 116


title: WT female adrenal biological replicate 4

source_name: WT female mouse adrenal


title: patient 112


title: P3_Tumor

source_name: Cancerous tissue of patient 3


title: P3_Normal

source_name: Adjacent tissue of patient 3


title: P1_Normal

source_name: Adjacent tissue of patient 1


title: WT male adrenal biological replicate 4


title: KO female adrenal biological replicate 2


title: P1_Tumor

source_name: Cancerous tissue of patient 1


title: P2_Tumor

source_name: Cancerous tissue of patient 2


title: P2_Normal

source_name: Adjacent tissue of patient 2


title: P4_Normal

source_name: Adjacent tissue of patient 4


title: patient 110


title: WT female adrenal biological replicate 2


title: HepaRG_Control_Exp3_rep3

status: Public on Sep 15 2017

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 HepaRG cells treated with 0 uM of As2O3, Experiment 3

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-039494 SurePrint G3 Human GE v2 8x60K Microarray 039381 or Agilent-072363 SurePrint G3 Human GE v3 8x60K Microarray 039494 for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

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

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

source_name: HepaRG, Control, Exp3, replicate-3

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

growth_protocol: The human liver HepaRG cell line was obtained from Biopredic International (Overland Park, Kansas), and the cells were maintained according to the manufacturer’s recommendations. Briefly, the cells were seeded at a density of 1.3 × 104 cells/cm2 and maintained in William’s E medium supplemented with growth additives for HepaRG cells (Biopredic International) for 14 days. The cells were then differentiated by adding a differentiation supplement (Biopredic International) for an additional 14 days. The medium was changed every other day.

extract_protocol: Total RNA was extracted from HepaRG cells 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: Progenitor and differentiated HepaRG cells were treated with 1 µM  NaAsO2. Following the treatment, the cells were harvested by mild trypsinization, washed in phosphate-buffered saline, and immediately frozen at −80°C for subsequent analyses.

value: HepaRG cells

value: Differentiated cells

value: 0 uM of As2O3

tag: experiment


title: patient 102

value: Pre-transplantation

value: No


title: patient 104

value: Male


title: HepaRG_Control_Exp3_rep2

source_name: HepaRG, Control, Exp3, replicate-2

value: Female


title: HepaRG_As-1uM_Exp3_rep3

description: Gene expression in HepaRG cells treated with 1 uM of As2O3, Experiment 3

source_name: HepaRG, As-1uM, Exp3, replicate-3

value: 1 uM of As2O3


title: A549_Attachment 7days_2

description:
A2
Gene expression data from A549 cells cultured in 2D condition; Control

data_processing:
affymetrix-algorithm-name = rma-gene-full
affymetrix-algorithm-version = 1.0
affymetrix-array-type = HuGene-2_0-st
program-name = Expression Console
program-version = 1.3.1.187

source_name: A549_Attachment 7days

treatment_protocol: A549 cells were cultured for 7 days in attachment 96 well plates with 10 % FBS/DMEM supplemented with LA717 (0.03 w/v%) or Milli-Q water.

tag: cell line

tag: culture condition

value: normal attachment plates with normal medium (as control)


title: A549_Attachment+LA717 7days_1

description:
AL1
Gene expression data from A549 cells cultured in 2D condition with LA717

source_name: A549_Attachment+LA717 7days

value: low-attachment plates with LA717 containing medium


title: HepaRG_As-1uM_Exp3_rep1

source_name: HepaRG, As-1uM, Exp3, replicate-1


title: HepaRG_Control_Exp3_rep1

source_name: HepaRG, Control, Exp3, replicate-1


title: A549_Attachment+LA717 7days_2

description:
AL2
Gene expression data from A549 cells cultured in 2D condition with LA717


title: A549_Attachment 7days_3

description:
A3
Gene expression data from A549 cells cultured in 2D condition; Control


title: patient 115

source_name: T cells


title: inN2

city: PALO ALTO

first: Li

last: Ye

state: California

address: 1050 Arastradero Rd Bulding B

institute: Stanford University

description: translating mRNA from NAC projecting mPFC cells

hyb_protocol: Following fragmentation, cRNA were hybridized at 45C on Affymetrix mouse gene expression arrays

scan_protocol: The label, hyb and scan were performed by the Stanford PAN Core facility according to established methods.

data_processing:
The data were processed using Transcriptome Analysis Console.
affymetrix-algorithm-name = rma-gene-full
affymetrix-algorithm-version = 1.0

source_name: NAC-projecting-input

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

extract_protocol: Trizonl followed by MicroRNA kit from Qiagen

treatment_protocol: CAV2-Cre injected in NAC or VTA in mouse brain

value: NAC-projecting mPFC cells

tag: immunoprecipitation reagent

value: none (input)


title: VA2

description: translating mRNA fromVTA projecting mPFC cells

source_name: VTA-projecting

tag: cell type

value: VTA-projecting mPFC cells

value: GFP-trap


title: inVA2

source_name: VTA-projecting-input


title: A549_Attachment 7days_1

description:
A1
Gene expression data from A549 cells cultured in 2D condition; Control


title: N2

source_name: NAC-projecting


title: inN1


title: VA1


title: patient 114

value: Yes


title: inVA1


title: patient 131


title: N1


title: GMCSF + IL-4 mo-DC donor 6

city: Paris

first: Elodie

last: Segura

address: 156 rue de Vaugirard

department: INSERM U1151

institute: INSERM

hyb_protocol: Labelled DNA was hybrized on the Affymetrix Human Gene 1.1 ST processed on an Affymetrix GeneTitan device.

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

data_processing: Microarray data were carried out with R (version 3.1.0) using packages from the Bioconductor. Raw data CEL files were used and the quality control analysis was performed using ArrayQualityMetrics package. The raw data were preprocessed using the RMA (Robust Multi-array Average) method available in oligo package. Gene expression levels were analyzed on a base-2 logarithmic scale.

source_name: healthy donor monocytes

label_protocol: 100 ng of polysomal-bound RNA were employed to synthesize double-stranded cDNA using 2 successive reverse-transcription reactions according to the std affymetrix protocol

extract_protocol: Qiagen RNAEasy micro-kit

tag: individual

value: donor 6

tag: treatment

value: GMCSF + IL-4

value: mo-DC


title: A549_Attachment+LA717 7days_3

description:
AL3
Gene expression data from A549 cells cultured in 2D condition with LA717


title: MSCF + IL-4 + TNFa mo-Mac donor 5

value: donor 5

value: MSCF + IL-4 + TNFa

value: mo-Mac


title: MSCF + IL-4 + TNFa mo-DC donor 6


title: GMCSF + IL-4 mo-DC donor 5


title: IL-34 + IL-4 + TNFa mo-Mac donor 6

value: IL-34 + IL-4 + TNFa


title: MSCF + IL-4 + TNFa mo-Mac donor 6


title: patient 103

value: Male

tag: age

value: Pre-transplantation

value: No


title: GMCSF + IL-4 mo-DC donor 4

value: donor 4


title: MSCF + IL-4 + TNFa mo-DC donor 4


title: HepaRG_As-1uM_Exp3_rep2

source_name: HepaRG, As-1uM, Exp3, replicate-2

value: HepaRG cells

value: Female

value: Differentiated cells

value: 1 uM of As2O3


title: IL-34 + IL-4 + TNFa mo-DC donor 6


title: MSCF + IL-4 + TNFa mo-Mac donor 3

value: donor 3


title: IL-34 + IL-4 + TNFa mo-Mac donor 4


title: MSCF + IL-4 + TNFa mo-DC donor 5


title: MSCF + IL-4 + TNFa mo-DC donor 3


title: IL-34 + IL-4 + TNFa mo-Mac donor 3


title: G-CSF_2

city: Osaka

first: Kiyoshi

last: Higashi

address: 1-98, Kasugadenaka 3-chome, Konohana-ku

institute: Sumitomo Chemical Co. Ltd.

description: bone marrow-derived cells migrating to fibrotic liver tissue

hyb_protocol: Following fragmentation, 15 μg of cRNA were hybridized for 16 hr at 45ºC on Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Genechip Fluidics Station450.Fluidics Station 400.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: Liver tissue from mice exposed to carbon tetrachloride and G-CSF

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 40 ng total RNA (GeneChip 3' IVT Express Kit User Manual, Affymetrix).

extract_protocol: Total RNA were prepared using RNeasy Mini Kit purchased from Qiagen

treatment_protocol: Mice were injected with 1 ml/kg BW of carbon tetrachloride for a total of 30 times and either 100 μg/kg BW of recombinant human G-CSF or 0.1% mouse serum albumin in phosphate-buffered saline during the last 7 days before the ﬁnal CCl4 injection.

value: liver

value: bone marrow-derived cells

tag: strain


title: IL-34 + IL-4 + TNFa mo-Mac donor 5


title: GMCSF + IL-4 mo-DC donor 3

value: GMCSF + IL-4


title: IL-34 + IL-4 + TNFa mo-DC donor 4

value: mo-DC


title: PBS_2

source_name: Liver tissue from mice exposed to carbon tetrachloride and PBS


title: WT female adrenal biological replicate 1

source_name: WT female mouse adrenal

value: mixed sv129-C57Bl/6

tag: genotype/variation

tag: gender

value: female

value: adult 7 months

value: Whole adrenal gland


title: WT female adrenal biological replicate 3


title: IL-34 + IL-4 + TNFa mo-DC donor 5

value: donor 5

value: IL-34 + IL-4 + TNFa


title: G-CSF_1


title: GMCSF + IL-4 mo-DC donor 2

value: donor 2


title: IL-34 + IL-4 + TNFa mo-DC donor 3


title: MSCF + IL-4 + TNFa mo-Mac donor 2

value: MSCF + IL-4 + TNFa

value: mo-Mac


title: EGFP_2

description: regenerating liver tissue obtained after EGFP-expressing cell administration

hyb_protocol: Following fragmentation, 15 μg of cRNA were hybridized for 16 hr at 45ºC on Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Genechip Fluidics Station 400.Fluidics Station450.Fluidics Station 400.

source_name: regenerating liver tissue obtained after an intrasplenic injection of EGFP-expressing human bone marrow mesenchymal stem cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (IVT Labering Kit User Manual, Affymetrix).

treatment_protocol: Nude mice injected with 0.25 ml/kg BW of carbon tetrachloride for a total of 23 times received an intrasplenic injection of 1 x 10^6 human bone marrow mesenchymal stem cells expressing either EGFP or OGFRL1. On day 21, they underwent partial hepatectomy, and the regenerating liver tissues were obtained on day 8 after hepatectomy. albumin in phosphate-buffered saline during the last 7 days before the ﬁnal CCl4 injection.

value: BALB/c nu/nu


title: MSCF + IL-4 + TNFa mo-Mac donor 4

value: donor 4


title: OGFRL1_2

description: regenerating liver tissue obtained after OGFRL1-expressing cell administration

source_name: regenerating liver tissue obtained after an intrasplenic injection of OGFRL1-expressing human bone marrow mesenchymal stem cells


title: PBS_1


title: EGFP_1


title: OGFRL1_1


title: IL-34 + IL-4 + TNFa mo-DC donor 2


title: MSCF + IL-4 + TNFa mo-Mac donor 1

value: donor 1


title: MSCF + IL-4 + TNFa mo-DC donor 2


title: MSCF + IL-4 + TNFa mo-DC donor 1


title: IL-34 + IL-4 + TNFa mo-Mac donor 2


title: GMCSF + IL-4 mo-DC donor 1


title: IL-34 + IL-4 + TNFa mo-Mac donor 1


title: HepaRG_As-1uM_Exp2_rep3

description: Gene expression in HepaRG cells treated with 1 uM of As2O3, Experiment 2

source_name: HepaRG, As-1uM, Exp2, replicate-3

value: HepaRG cells

value: Female

value: Differentiated cells

value: 1 uM of As2O3


title: IL-34 + IL-4 + TNFa mo-DC donor 1

value: mo-DC


title: HepaRG_Control_Exp1-2_rep3

description: Gene expression in HepaRG cells treated with 0 uM of As2O3, Experiment 1 and 2

source_name: HepaRG, Control, Exp1-2, replicate-3

value: 0 uM of As2O3

value: 1 and 2


title: HepaRG_As-1uM_Exp1_rep2

description: Gene expression in HepaRG cells treated with 1 uM of As2O3, Experiment 1

source_name: HepaRG, As-1uM, Exp1, replicate-2


title: HepaRG_As-1uM_Exp1_rep1

source_name: HepaRG, As-1uM, Exp1, replicate-1


title: HepaRG_As-1uM_Exp2_rep2

source_name: HepaRG, As-1uM, Exp2, replicate-2


title: HepaRG_As-1uM_Exp2_rep1

source_name: HepaRG, As-1uM, Exp2, replicate-1


title: HepaRG_Control_Exp1-2_rep2

source_name: HepaRG, Control, Exp1-2, replicate-2


title: MLP.refed4

status: Public on Sep 14 2017

city: Tokyo

first: Noriko

last: Sato

address: 1-5-45, Yushima, Bunkyo-ku

department: Molecular Epidemiology & Epigenetic Epidemiology

institute: Medical Research Institute, Tokyo Medical and Dental University

hyb_protocol: Hybridization on SurePrint G3 Mouse GE 8 x 60 K microarrays (Agilent Technologies) was performed according to the manufacturer’s instructions.

scan_protocol: Arrays were scanned on an Agilent G2565CA scanner using one-color setting for 8 x 60 K slides at 3 um resolution using Green channel at 100%.

data_processing: Raw microarray data were extracted using Agilent Feature Extraction Software (ver. 11.0.1.1). Microarray data were 75 % tile-normalized and log2-transformed according to the manufacturer’s recommendation using R software (ver. 3.3.1).

source_name: liver, early gestational maternal low protein diet, after 24h refeeding following the 24h fasting

label_protocol: Three animal samples from each group were randomly selected. Each RNA sample (150 ng) was used to synthesize, amplify, and label cRNA using the Low Input QuickAmp Labeling kit (Agilent Technologies).

growth_protocol: Animals were kept under standard temperature- and humidity-controlled conditions on a 12:12 h light (08:00-20:00)-dark (20:00-08:00) cycle. Two-cell embryos of C57BL/6J mice obtained by in vitro fertilization were transferred into pseudo-pregnant ICR female mice (Sankyo Labo Service, Tokyo, Japan). The surrogate mothers (F0 dams) were randomized into two different diet groups: normal protein diet (Ctrl, 18 % casein, Oriental Yeast, Tokyo, Japan) throughout the entire gestation and lactation period or low protein diet (MLP, 9 % casein, Oriental Yeast) for the initial 10 days followed by normal protein diet for the rest of the gestation and lactation period. At delivery, litters were standardized to ~8 offspring. The offspring were weaned onto a standard laboratory chow diet on postnatal day 20.

extract_protocol: Eight to 10 animals from each group were weighted and sacrificed. Liver was weighted, dissected, quickly frozen in liquid nitrogen, and stored at -80 °C until used in the analyses. To negate time differences between the six groups, all samples were collected between 9:30 AM and 1:00 PM and every control and MLP sample were collected alternately. Total RNA was extracted from the left medial lobe of the liver using the RNeasy mini kit (Qiagen). RNA quality and quantity was evaluated using a NanoDrop spectrophotometer (Thermo Fisher Scientific, Wilmington, USA) and an Agilent Bioanalyzer (Agilent Technologies, CA, USA).

treatment_protocol: On postnatal day 60, F1 males were randomized into three different feeding groups: ad libitum feeding, 24-h fasting, and 24-h fasting followed by 24-h re-feeding.

value: male

value: 9 weeks

tag: early gestational maternal diet

value: low protein diet

value: refed for 24 hours following the fasting

value: liver


title: MLP.refed1


title: HepaRG_Control_Exp1-2_rep1

source_name: HepaRG, Control, Exp1-2, replicate-1


title: Ctrl.refed1

source_name: liver, early gestational control diet, after 24h refeeding following the 24 h fasting

value: control diet


title: Ctrl.fasted3

source_name: liver, early gestational control diet, after 24h fasting

value: fasted for 24 hours


title: MLP.fasted4

source_name: liver, early gestational maternal low protein diet, after 24h fasting


title: MLP.refed2


title: Ctrl.refed4


title: Ctrl.refed3


title: MLP.refed3


title: MLP.fasted1


title: MLP.fasted3


title: IKKalpha f/fCd19Cre_splenic newly formed B cells

city: Boston

first: Mumtaz

last: Yaseen

address: 800 Washington st

institute: Tufts University Medical Center

description:
Gene expression data obtained from Newly formed B cells
IKK alpha f/fCD19Cre Mean(F19_M19) biological replicates

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

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

source_name: newly formed B cells migrating into spleen

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: Newly formed B cells were flow sorted from whole splenocytes of 4-6 wk control mice and mice ikk alpha f/fCd19Cre.

treatment_protocol: flow cytomerty sorted newly formed B cells were subjected to RNA isolation.

value: spleen

value: pro B cells

tag: genotype

value: IKK alpha Deleted

value: 4-6 weeks


title: Ctrl.refed2


title: Ctrl.fasted1


title: Control_splenic newly formed B cells

description:
Gene expression data obtained from Newly formed B cells
IKK alpha f/+ CD19 CreMean (CNT_M19) biological replicates

value: IKK alpha wild type


title: MLP.fasted2


title: adipose tissues in response to amphiregulin overexpression.

city: Higashi-Hiroshima

first: Yanaka

last: Noriyuki

address: Kagamiyama 1-4-4

department: Graduate School of Biosphere Science

institute: Hiroshima University

hyb_protocol: Hybridization was performed according to manufacturer's instructions (Agilent).

scan_protocol: Scanned on an Agilent G2565BA scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software (version 9.5).

source_name: control

label_protocol: 1 µg of total RNA were primed with T7 promoter primer, then reversed transcribed in the presence of MMLV-RT. cRNAs were synthesized in the presence of each dATP, dTTP, dGTP, dCTP with Cy3-labeled or Cy5-labeled dCTP according to manufacturer's instructions (Agilent).

growth_protocol: Mouse 3T3-L1 preadipocytes were cultured in a maintenance medium (10% fetal bovine serum, 100 units/ml penicillin and 100 μg/ml streptomycin in Dulbecco’s modified medium) .

extract_protocol: Total RNAs of 3T3-L1 cells were extracted using QIAzol following manufacturer's instructions.

treatment_protocol: Stealth siRNA duplex oligoribonucleotides against mouse GDE5 were synthesized by Invitrogen. The sequences were as follows: mouse GDE5, sense 5′-CAGUGUGUUGUGGAAAGCAGUGAUU-3, antisense 5′-AAUCACUGCUUUCCACAACACACUG-3′ . 3T3-L1 cells were transfected with siRNAs in a final concentration of 20 nM using LipofectAMINE RNAimax (Invitrogen).

value: adipose tissues

tag: variation

value: control

source_name: amphiregulin overexpression

value: amphiregulin overexpression


title: Ctrl.fasted2

tag: tissue


title: P_gingivalis_wild-type-AN_rep4

city: Loma Linda

first: Yuetan

last: Dou

state: CA

address: 11021 Campus Street AH114

department: Microbiology and Molecular Genetics

institute: Loma Linda University

description:
PG0162PG1660 mutant microarray.xlsx
This sample is of wild-type Porphyromonas gingivalis under anaerobic conditions. It is the fourth of three wild-type biological replicates used in this experiment, each from separate cultures.

hyb_protocol: Slides were hybridized in hybridization buffer containing labelled probed for 16-20 hrs and then washed in 2×SSC/0.1%SDS, 0.1×SSC/0.1%SDS, 0.1×SSC and ddH2O to remove non-specific binding.

scan_protocol: The slides were scanned using ScannArray 4000 scanned (GSI Lumonics) and the images were acquired by using ScanArray software.

data_processing: The data were subquently analyzed using c5B Quantarray software (Version 2.0) and normalized. The raw data (.pair file) was subjected to RMA then using GeneSpring software (Silicon Genetics) to analyze.  McKenzie et al., Microbiology, 158(Pt 10):2465-79.

organism: Porphyromonas gingivalis W83

source_name: Porphyromonas gingivalis W83 wild-type

label_protocol: Cyanine dyes Cy3 (Amersham Biosciences) was used to label the sample cDNA.

growth_protocol: Porphyromonas gingivalis cultures were grown to mid-log phase (O.D.600nm 0.8) anerobically (80% N2, 10% CO2, 10% H2) at 37°C in BHI media (Dou et al. FEMS Micro Lett. 312(1):24-32).

extract_protocol: RNA was extracted by using SV Total RNA Isolation system (Promega); cDNA was synthesized by using Transcriptor High Fidelity cDNA Synthesis kit (Roche). Dou et al., Journal of Bacteriology, 196(23):4057-70.

treatment_protocol: Porphyromonas gingivalis were grown to mid-log phase (O.D.600nm 0.8) anerobically (80% N2, 10% CO2, 10% H2) at 37°C in BHI media. One group was kept under anaerobic conditions, and another group was stressed by 0.25 mM of hydrogen peroxide for 15 min . McKenzie et al., Microbiology, 158(Pt 10):2465-79.

value: Wild-type


title: P_gingivalis_wild-type-AN_rep6

description:
PG0162PG1660 mutant microarray.xlsx
This sample is of wild-type Porphyromonas gingivalis under anaerobic conditions. It is the sixth of three wild-type biological replicates used in this experiment, each from separate cultures.


title: P_gingivalis_wild-type-AN_rep5

description:
PG0162PG1660 mutant microarray.xlsx
This sample is of wild-type Porphyromonas gingivalis under anaerobic conditions. It is the fifth of three wild-type biological replicates used in this experiment, each from separate cultures.


title: P_gingivalis_PG1660-H2O2_rep2

description:
PG1660 mutant H2O2 microarray.xlsx
This sample is of Porphyromonas gingivalis PG1660 deletion mutant under H2O2 stress conditions. It is the second of three mutant biological replicates used in this experiment, each from separate cultures.

source_name: Porphyromonas gingivalis PG1660 mutant

value: PG1660 deletion mutant


title: P_gingivalis_PG0162PG1660-AN_rep3

description:
PG0162PG1660 mutant microarray.xlsx
This sample is of Porphyromonas gingivalis PG0162-PG1660 deletion mutant under anaerobic conditions. It is the third of three mutant biological replicates used in this experiment, each from separate cultures.

source_name: Porphyromonas gingivalis PG0162- PG1660 mutant

value: PG10162 and PG1660 double deletion mutant


title: P_gingivalis_wild-type-H2O2_rep2

description:
PG1660 mutant H2O2 microarray.xlsx
This sample is of wild-type Porphyromonas gingivalis under H2O2 stress conditions. It is the second of three wild-type biological replicates used in this experiment, each from separate cultures.


title: P_gingivalis_PG0162PG1660-AN_rep1

description:
PG0162PG1660 mutant microarray.xlsx
This sample is of Porphyromonas gingivalis PG0162-PG1660 deletion mutant under anaerobic conditions. It is the first of three mutant biological replicates used in this experiment, each from separate cultures.


title: P_gingivalis_PG0162PG1660-AN_rep2

description:
PG0162PG1660 mutant microarray.xlsx
This sample is of Porphyromonas gingivalis PG0162-PG1660 deletion mutant under anaerobic conditions. It is the second of three mutant biological replicates used in this experiment, each from separate cultures.


title: P_gingivalis_PG1660-AN_rep3

description:
PG1660 mutant microarray.xlsx
This sample is of Porphyromonas gingivalis PG1660 deletion mutant under anaerobic conditions. It is the third of three mutant biological replicates used in this experiment, each from separate cultures.


title: MLP.ad_lib1

source_name: liver, early gestational maternal low protein diet, ad libitum

value: male

value: 9 weeks

value: ad libitum fed


title: MLP.ad_lib2

value: low protein diet

value: liver


title: Ctrl.ad_lib2

source_name: liver, early gestational control diet, ad libitum

value: control diet


title: MLP.ad_lib4


title: Ctrl.ad_lib3


title: MLP.ad_lib3


title: P_gingivalis_PG1660-H2O2_rep3

description:
PG1660 mutant H2O2 microarray.xlsx
This sample is of Porphyromonas gingivalis PG1660 deletion mutant under H2O2 stress conditions. It is the third of three mutant biological replicates used in this experiment, each from separate cultures.


title: P_gingivalis_PG1660-AN_rep1

description:
PG1660 mutant microarray.xlsx
This sample is of Porphyromonas gingivalis PG1660 deletion mutant under anaerobic conditions. It is the first of three mutant biological replicates used in this experiment, each from separate cultures.


title: P_gingivalis_PG1660-H2O2_rep1

description:
PG1660 mutant H2O2 microarray.xlsx
This sample is of Porphyromonas gingivalis PG1660 deletion mutant under H2O2 stress conditions. It is the first of three mutant biological replicates used in this experiment, each from separate cultures.


title: Ctrl.ad_lib1


title: P_gingivalis_wild-type-H2O2_rep1

description:
PG1660 mutant H2O2 microarray.xlsx
This sample is of wild-type Porphyromonas gingivalis under H2O2 stress conditions. It is the first of three wild-type biological replicates used in this experiment, each from separate cultures.


title: P_gingivalis_wild-type-H2O2_rep3

description:
PG1660 mutant H2O2 microarray.xlsx
This sample is of wild-type Porphyromonas gingivalis under H2O2 stress conditions. It is the third of three wild-type biological replicates used in this experiment, each from separate cultures.


title: P_gingivalis_PG1660-AN_rep2

description:
PG1660 mutant microarray.xlsx
This sample is of Porphyromonas gingivalis PG1660 deletion mutant under anaerobic conditions. It is the second of three mutant biological replicates used in this experiment, each from separate cultures.


title: P_gingivalis_wild-type-AN_rep2

description:
PG1660 mutant microarray.xlsx
This sample is of wild-type Porphyromonas gingivalis under anaerobic conditions. It is the second of three wild-type biological replicates used in this experiment, each from separate cultures.


title: P_gingivalis_wild-type-AN_rep1

description:
PG1660 mutant microarray.xlsx
This sample is of wild-type Porphyromonas gingivalis under anaerobic conditions. It is the first of three wild-type biological replicates used in this experiment, each from separate cultures.


title: P_gingivalis_wild-type-AN_rep3

description:
PG1660 mutant microarray.xlsx
This sample is of wild-type Porphyromonas gingivalis under anaerobic conditions. It is the third of three wild-type biological replicates used in this experiment, each from separate cultures.


title: Thymus sample 6, Grade 0

city: Washington DC

first: Manjistha

last: Sengupta

address: 2300 Eye Street NW, Ross Hall,  Room #723

institute: George Washington University

description: miRNA expression data

hyb_protocol: Labeled samples with eukaryotic hybridization control were hybridized to GeneChip® miRNA 4.0 Array (Affymetrix) chips in a Gene Chip hybridization Oven 640 (Affymetrix) for 18hrs.

scan_protocol: These were then scanned by an Affymetrix GeneChip Scanner (GC30007G).

data_processing: CHP file was generated by Expression Console (Affymetrix).  Array data was normalized, batch corrected and analyzed (1-way ANOVA) using Partek Genomics Suite program.

source_name: myasthenia gravis thymus

label_protocol: 250ng of total RNA was labeled by FlashTag™ Biotin HSR RNA Labeling Kit (Affymetrix, Inc., Santa Clara, CA).

extract_protocol: Total RNA was extracted from thymus blocks using mirVana™ miRNA isolation kit (Ambion) according to the manufacturer’s protocol. The RNA samples were treated with RNase Free DNase (QIAGEN, Valencia, CA) and were purified using RNeasy mini kit (QIAGEN) according to the manufacturer’s protocol.

tag: disease state

value: myasthenia gravis

value: Thymus

tag: grade

value: Grade 0

tag: morphology

value: No Germinal Center


title: Thymus sample 8, Grade 1-4

description: miRNA expression data

value: Grade 1-4

value: Germinal Center


title: Thymus sample 11, Grade 0

description: miRNA expression data


title: Thymus sample 16, Grade 0

description: miRNA expression data


title: Thymus sample 10, Grade 1-4

description: miRNA expression data


title: Thymus sample 19, Grade 0

description: miRNA expression data


title: Thymus sample 13, Grade 1-4

description: miRNA expression data


title: Thymus sample 15, Grade 0

description: miRNA expression data


title: Thymus sample 17, Grade 0

description: miRNA expression data


title: Thymus sample 18, Grade 1-4

description: miRNA expression data


title: Thymus sample 20, Grade 1-4

description: miRNA expression data


title: Thymus sample 7, Grade 0

description: miRNA expression data


title: Genomic DNA from MS hippocampus 6

city: Cleveland

first: Ranjan

last: Dutta

state: OH

address: 9500 Euclid Avenue, NC-30

department: Neuroscience

institute: Lerner Research Institute

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

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

data_processing: BeadStudio software v3.2

source_name: Myelinated MS Hippocampus

label_protocol: Standard Illumina protocol

extract_protocol: Genomic DNA was extracted and purified from tissue samples using Qiagen DNeasy Kit according to standard instructions

value: Hippocampus

tag: diagnosis

value: multiple sclerosis (MS)

tag: myelination status

value: Myelinated


title: 3NF/pCI, biological repD3

city: Warsaw

first: Róża

last: Sawicka

address: Pawinskiego

department: Department of Protein Biosynthesis

institute: Institute of Biochemistry and Biophysics PAS

description:
Spleen 3NF/pCI D3
Gene expression data from spleen of the mouse prime/boost immunized with 3NF/pCI plasmid.

hyb_protocol: Samples were hybridized for 20h in 48 deg. Cent.

scan_protocol: The chips were scanned using the Affymetrix GeneAtlas Scanner.

data_processing: The microarray gene expression data was analyzed using Partek Genomic Suite 6.6 beta software (Partek Inc., Louis, MO). Raw data (.cel files) were imported and processed, using Robust Multiarray Averaging (RMA) background correction, quantile normalization, Log2 transformation and median polish summarization.

source_name: Spleen, 3NF/pCI

label_protocol: Biotinylated cDNAs were prepared according to the standard Affymetrix protocol from 100ng total RNA.

extract_protocol: Three or two independent biological replicates of total RNA were isolated from each strain using an RNeasy mini-kit with on-column DNase digestion (Qiagen) according to the manufacturer’s instructions followed by DNase digestion using TURBO DNase kit (Ambion) to eliminate DNA contamination.

tag: strain/background

value: BALB/c

value: Female

value: Spleen


title: Thymus sample 5, Grade 0

description: miRNA expression data


title: Thymus sample 3, Grade 1-4

description: miRNA expression data


title: Thymus sample 2, Grade 0

description: miRNA expression data


title: pCI, biological repE2

description:
Spleen pCI E2
Gene expression data from spleen of the control mouse prime/boosted with the empty vector (pCI plasmid).

source_name: Spleen, pCI

value: pCI


title: Thymus sample 1, Grade 1-4

description: miRNA expression data


title: pCI, biological repE1

description:
Spleen pCI E1
Gene expression data from spleen of the control mouse prime/boosted with the empty vector (pCI plasmid).


title: 3NF/pCI, biological repD2

description:
Spleen 3NF/pCI D2
Gene expression data from spleen of the mouse prime/boost immunized with 3NF/pCI plasmid.


title: Genomic DNA from MS hippocampus 7


title: Genomic DNA from MS hippocampus 1


title: Genomic DNA from MS hippocampus 5


title: Genomic DNA from MS hippocampus 12

source_name: Demyelinated MS hippocampus

value: Demyelinated


title: Genomic DNA from MS hippocampus 4


title: Genomic DNA from MS hippocampus 3


title: Genomic DNA from MS hippocampus 15


title: 3NF/pCI, biological repD1

description:
Spleen 3NF/pCI D1
Gene expression data from spleen of the mouse prime/boost immunized with 3NF/pCI plasmid.


title: HAneo/pCI, biological repC1

description:
SpleenHAneo/pCI C1
Gene expression data from spleen of the mouse prime/boost immunized with HAneo/pCI plasmid.

source_name: Spleen, HAneo/pCI

value: HAneo/pCI


title: GK/pCI, biological repB2

description:
SpleenGK/pCI B2
Gene expression data from spleen of the mouse prime/boost immunized with GK/pCI plasmid.

source_name: Spleen, GK/pCI

value: GK/pCI


title: Genomic DNA from MS hippocampus 10


title: HAneo/pCI, biological repC3

description:
SpleenHAneo/pCI C3
Gene expression data from spleen of the mouse prime/boost immunized with HAneo/pCI plasmid.


title: GK/pCI, biological repB1

description:
SpleenGK/pCI B1
Gene expression data from spleen of the mouse prime/boost immunized with GK/pCI plasmid.


title: Genomic DNA from MS hippocampus 9


title: K3/pCI, biological repA3

description:
SpleenK3/pCI A3
Gene expression data from spleen of the mouse prime/boost immunized with K3/pCI plasmid.

source_name: Spleen, K3/pCI


title: Genomic DNA from MS hippocampus 11


title: Genomic DNA from MS hippocampus 8


title: Genomic DNA from MS hippocampus 2


title: Genomic DNA from MS hippocampus 13


title: Genomic DNA from MS hippocampus 14


title: K3/pCI, biological repA2

description:
SpleenK3/pCI A2
Gene expression data from spleen of the mouse prime/boost immunized with K3/pCI plasmid.


title: HAneo/pCI, biological repC2

description:
SpleenHAneo/pCI C2
Gene expression data from spleen of the mouse prime/boost immunized with HAneo/pCI plasmid.


title: K3/pCI, biological repA1

description:
SpleenK3/pCI A1
Gene expression data from spleen of the mouse prime/boost immunized with K3/pCI plasmid.


title: HOTAIR3

city: Natori, Miyagi

first: Keiichi

last: Tamai

address: 1-47, Nodayama, Shiote, Medeshima

institute: Miyagi Cancer Center

description: SAMPLE 7

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°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 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (GE1_107_Sep09) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label_protocol: 100 ng of total RNA was labeled using Low Input Quick Amp Labeling Kit

extract_protocol: RNA from ACHN cells was purified using RNeasy Mini Kits (Qiagen, Canada)

tag: cell line

value: ACHN

tag: cell type

value: renal cell adenocarcinoma cell line

value: HOTAIR overexpression


title: EV2

description: SAMPLE 2

value: control


title: HOTAIR1

description: SAMPLE 5


title: HOTAIR2

description: SAMPLE 6


title: HUVEC_thrombin

city: Budapest

first: Zsuzsanna

last: Németh

address: Kútvölgyi út 4.

country: Hungary

institute: Semmelweis University

description: Thrombin treated human umbilical vein endothelial cells, prepared from fresh umbilical cords during normal deliveries of healthy neonates.

hyb_protocol: Equal amounts of Cy3‑labeled (untreated) and Cy5-labeled (treated) cRNA (25 ng) from samples were simultaneously co-hybridized onto the arrayed oligonucleotids on the same G3 Human Gene Expression 8×60K v2 Microarray (G4858A) (Agilent Technologies) slide at 65°C for 17 h using an Agilent Gene Expression Hybridization Kit in Agilent’s SureHyb Hybridization Chambers (G2545A). The hybridized microarrays were then washed according to manufacturer’s instructions.

scan_protocol: Scanned on an Agilent G2505C Microarray scanner at 2µm resolution and 20-bit color-depth.

data_processing:
Agilent GeneSpring 14.5‑GX software,was used for background subtraction and LOWESS normalization.
The aim of the study is to investigate the expression of genes with known functions. Thus, the spots which have only LOC or XLOC identifiers or do not have any gene names were excluded.

source_name: human umbilical vein endothelial cells, control

label_protocol: Samples were processed according to Agilent Two-color Microarray Based Gene Expression Analysis Low Input Quick Amp Labeling Kit protocol, and using Agilent Spike-In Kit, following the instructions provided by the manufacturer. The experimental protocol is available at: http://www.agilent.com/cs/library/usermanuals/Public/G4140-90050_GeneExpression_TwoColor_6.9.pdf

growth_protocol: HUVECs were grown in gelatin-precoated flasks (Corning® Costar®) in MCDB131 medium (Life Technologies) completed with 5% heat‑inactivated, fetal calf serum (FCS), 2 ng/ml human recombinant epidermal growth factor (R&D Systems), 1 ng/ml human recombinant basic fibroblast growth factor (Sigma), 0.3% Insulin Transferrin Selenium (Life Technologies), 1% Chemically Defined Lipid Concentrate (Life Technologies), 1% Glutamax (Life Technologies), 1% Penicillin‑Streptomycin antibiotics (Sigma), 5 µg/ml Ascorbic acid (Sigma), 250 nM Hydrocortisone (Sigma), 10 mM Hepes (Sigma), and 7.5 U/ml Heparin (hereinafter: Comp‑MCDB). Each experiment was performed on primary HUVEC cultures from different individuals before the 4th passage.

extract_protocol: HUVECs were lysed and stored in TRI® reagent. Total RNA purification was performed with NucleospinO RNA XS (Macherey-Nagel), and analyzed by Agilent Bioanalyzer. The RIN of all RNA samples were above 9.

treatment_protocol: Cells were treated for 1, 2 or 6 h with 0.6 µM rMASP-1, or had been pre-incubated for 30 min with 2 µM p38-MAPK inhibitor (SB203580) or 5 µM NFκB inhibitor (Bay-11 7082) pathway inhibitors and then treated with 2 µM rMASP-1 for 2h. Cells were treated with thrombin (300nM), TNFα (10 ng/mL), LPS (100 ng/mL) or histamine (50 µM) for 2h.

value: human umbilical vein endothelial cells

tag: treatment

value: untreated control

source_name: human umbilical vein endothelial cells, thrombin

value: 300 nM thrombin

tag: treatment time


title: HUVEC_MASP1+NFKB_inhibitor

description: NFKB inhibitor and MASP-1 treated human umbilical vein endothelial cells, prepared from fresh umbilical cords during normal deliveries of healthy neonates.

source_name: human umbilical vein endothelial cells, MASP1-NFKB

value: 5 µM Bay-11 7082 + 2 µM rMASP-1

value: 30 min + 2h


title: EV4

description: SAMPLE 4


title: HUVEC_TNFalpha_replicate1

description: Biological replicate 1 of 2. TNFalpha treated human umbilical vein endothelial cells, prepared from fresh umbilical cords during normal deliveries of healthy neonates.

source_name: human umbilical vein endothelial cells, TNF

value: 10 ng/ml TNF alpha


title: HUVEC_TNFalpha_replicate2


title: EV1

description: SAMPLE 1


title: HUVEC_MASP-1+p38-MAPK_inhibitor

description: P38-MAPK inhibitor and MASP-1 treated human umbilical vein endothelial cells, prepared from fresh umbilical cords during normal deliveries of healthy neonates.

source_name: human umbilical vein endothelial cells, MASP1-P38MAPK

value: 2 µM SB203580 + 2 µM rMASP-1


title: HUVEC_LPS

description: LPS treated human umbilical vein endothelial cells, prepared from fresh umbilical cords during normal deliveries of healthy neonates.

source_name: human umbilical vein endothelial cells, LPS

value: 100 ng/ml LPS


title: HUVEC_histamine

description: Histamine treated human umbilical vein endothelial cells, prepared from fresh umbilical cords during normal deliveries of healthy neonates.

source_name: human umbilical vein endothelial cells, histamine

value: 50 µM histamine


title: 42-2

status: Public on Sep 13 2017

city: Homburg

first: Nicole

last: Ludwig

address: Kirrberger Strasse

department: Human Genetics

country: Germany

institute: Saarland University

description: miRNA abundance in serum

hyb_protocol: The expression profile of 2549 human miRNAs was determined using SurePrint G3 8x60k miRNA microarrays (Agilent) according to the manufacturers recommendations

scan_protocol: Array´s were scanned with the Agilent Scanner with default settings.

data_processing: Raw expression values were extracted using the Feature Extraction Software of Agilent. Raw signal intensities were quantil-normalized and log2 transformed.

label: Cyanine 3-pcp

source_name: serum

extract_protocol: Total RNA including miRNAs was isolated using the miRNeasy Serum/Plasma Kit (Qiagen, Hilden, Germany) according to manufacturer’s instructions. In detail, 100µl serum was mixed with 100µl RNase-free water and 1ml Qiazol lysis solution and incubated for 5 min at room temperature. After addition of 200 µl chloroform, the samples were vigorously shaken for 15s and phase and centrifuged at 12.000 rpm and 4°C for 15 min. Aqueous phase was transferred into an empty tube and mixed with 3µl glycogen solution (20mg/ml) to facilitate RNA precipitation. Subsequently, the samples were transferred into the Qiacube instrument and RNA was isolated according to the manufacturers protocol automatically. RNA concentration and integrity were assessed was measured using NanoDrop2000 (Thermo Fisher Scientific, Waltham, MA, USA) and RNA quality was measured in a bioanalyzer run using the PicoRNA SmallRNA Chip (Agilent Technologies, Santa Clara, CA, USA).

tag: proband id

tag: time point


title: 58-2

description: miRNA abundance in serum

label_protocol: The expression profile of 2549 human miRNAs was determined using SurePrint G3 8x60k miRNA microarrays (Agilent) according to the manufacturers recommendations


title: 48-2

description: miRNA abundance in serum


title: 44-3

description: miRNA abundance in serum


title: 48-3

description: miRNA abundance in serum


title: 44-1

description: miRNA abundance in serum


title: HUVEC_MASP1_2h_replicate4

description: Biological replicate 1 of 4. MASP-1 treated human umbilical vein endothelial cells, prepared from fresh umbilical cords during normal deliveries of healthy neonates.

source_name: human umbilical vein endothelial cells, MASP1

value: 0.6 µM rMASP-1


title: HUVEC_MASP1_2h_replicate3


title: 52-1

description: miRNA abundance in serum


title: HUVEC_MASP1_2h_replicate2


title: HUVEC_MASP1_1h

description: MASP-1 treated human umbilical vein endothelial cells, prepared from fresh umbilical cords during normal deliveries of healthy neonates.

source_name: human umbilical vein endothelial cells, MASP1-1h


title: HUVEC_MASP1_6h

source_name: human umbilical vein endothelial cells, MASP1-6h


title: HUVEC_MASP1_2h_replicate1


title: 46-3

description: miRNA abundance in serum


title: 56-3

description: miRNA abundance in serum


title: 56-2

description: miRNA abundance in serum


title: 54-2

description: miRNA abundance in serum


title: 6-1

description: miRNA abundance in serum


title: 10-3

description: miRNA abundance in serum


title: 6-3

description: miRNA abundance in serum


title: 14-3

description: miRNA abundance in serum


title: 58-3

description: miRNA abundance in serum


title: 8-1

description: miRNA abundance in serum


title: 16-1

description: miRNA abundance in serum


title: 10-1

description: miRNA abundance in serum


title: 14-2

description: miRNA abundance in serum


title: 4-1

description: miRNA abundance in serum


title: 8-3

description: miRNA abundance in serum


title: 4-3

description: miRNA abundance in serum


title: 2-1

description: miRNA abundance in serum


title: 4-2

description: miRNA abundance in serum


title: 2-2

description: miRNA abundance in serum


title: 8-2

description: miRNA abundance in serum


title: 6-2

description: miRNA abundance in serum


title: 18-3

description: miRNA abundance in serum


title: 16-3

description: miRNA abundance in serum


title: 18-1

description: miRNA abundance in serum


title: 12-3

description: miRNA abundance in serum


title: 20-3

description: miRNA abundance in serum


title: 20-2

description: miRNA abundance in serum


title: 10-2

description: miRNA abundance in serum


title: 2-3

description: miRNA abundance in serum


title: 12-2

description: miRNA abundance in serum


title: 48-1

description: miRNA abundance in serum


title: 18-2

description: miRNA abundance in serum


title: 50-3

description: miRNA abundance in serum


title: 44-2

description: miRNA abundance in serum


title: 50-2

description: miRNA abundance in serum


title: 50-1

description: miRNA abundance in serum


title: 42-3

description: miRNA abundance in serum


title: 46-2

description: miRNA abundance in serum


title: 42-1

description: miRNA abundance in serum


title: 32-3

description: miRNA abundance in serum


title: 52-2

description: miRNA abundance in serum


title: 30-3

description: miRNA abundance in serum


title: 40-3

description: miRNA abundance in serum


title: 38-3

description: miRNA abundance in serum


title: 22-2

description: miRNA abundance in serum


title: 46-1

description: miRNA abundance in serum


title: 36-2

description: miRNA abundance in serum


title: 14-1

description: miRNA abundance in serum


title: 36-3

description: miRNA abundance in serum


title: 38-2

description: miRNA abundance in serum


title: 34-3

description: miRNA abundance in serum


title: 38-1

description: miRNA abundance in serum


title: 40-2

description: miRNA abundance in serum


title: 22-1

description: miRNA abundance in serum


title: 22-3

description: miRNA abundance in serum


title: 30-1

description: miRNA abundance in serum


title: 32-1

description: miRNA abundance in serum


title: 16-2

description: miRNA abundance in serum


title: 34-2

description: miRNA abundance in serum


title: 24-2

description: miRNA abundance in serum


title: 30-2

description: miRNA abundance in serum


title: 32-2

description: miRNA abundance in serum


title: 34-1

description: miRNA abundance in serum


title: 28-3

description: miRNA abundance in serum


title: 40-1

description: miRNA abundance in serum


title: 36-1

description: miRNA abundance in serum


title: 24-1

description: miRNA abundance in serum


title: 24-3

description: miRNA abundance in serum


title: EV3

description: SAMPLE 3

tag: genotype/variation


title: 28-2

description: miRNA abundance in serum


title: 26-1

description: miRNA abundance in serum


title: 60-1

description: miRNA abundance in serum


title: 28-1

description: miRNA abundance in serum


title: 26-2

description: miRNA abundance in serum


title: 60-3

description: miRNA abundance in serum


title: 58-1

description: miRNA abundance in serum


title: 54-1

description: miRNA abundance in serum


title: 56-1

description: miRNA abundance in serum


title: 54-3

description: miRNA abundance in serum


title: 60-2

description: miRNA abundance in serum


title: 26-3

description: miRNA abundance in serum


title: 52-3

description: miRNA abundance in serum


title: Unstimulated Neutrophils donor 6

city: Berlin

first: Brian

last: Caffrey

address: Ihnestrasse 63-73

institute: Max Planck Institute for molecular Genetics

hyb_protocol: mRNA was reverse transcribed and amplified using an oligo-dT-T7 promoter primer, T7 RNA Polymerase and Cyanine 3-CTP. After precipitation, purification, and quantification, 0.75 μg labeled cRNA was fragmented and hybridized to custom-commercial in situ oligonucleotide whole genome human 8 × 60k multipack microarrays (Agilent-048908) according to the supplier’s protocol (Agilent Technologies).

scan_protocol: Scanning of microarrays was carried out with 3 μm resolution using a G2565CA high-resolution laser microarray scanner (Agilent Technologies

data_processing: Microarray image data were analyzed with the Image Analysis/Feature Extraction software G2567AA v. A.11.5.1.1 (Agilent Technologies) using default settings and the GE1_1105_Oct12 extraction protocol.

source_name: Human primary Neutrophils donor 6

label_protocol: RNA labeling was done with the one-color Low Input Quick Amp Labeling Kit (Agilent Technologies).

extract_protocol: Trizol

value: blood

value: human primary neutrophils

tag: donor


title: Unstimulated Neutrophils donor 7

source_name: Human primary Neutrophils donor 7


title: mRNA_BreastCancer_rep27

city: Koto

first: Nobuyuki

last: Fukui

state: Tokyo

institute: Japanese Foundation For Cancer Research

hyb_protocol: After fragmentation, cRNA was hybridized with Affymetrix Hybridization,Wash, and Stain Kit on Affymetrix Human Genome GeneChip U133 Plus 2.0 array following manufactuer's instruction.

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

data_processing: Data was processed with RMA using Affymetrix Expression Console software.

source_name: mRNA from fresh frozen breast cancer tissue

label_protocol: Biotinylated cRNA was prepared with Affymetrix GeneChip 3'IVT Plus kit  according to the manufactuer's instruction.

extract_protocol: Total RNA was extracted using QIAGEN RNeasy mini kit following manufacturer's instruction.

tag: age

tag: gender

value: female


title: mRNA_BreastCancer_rep24


title: Unstimulated Neutrophils donor 5

source_name: Human primary Neutrophils donor 5

tag: tissue


title: Unstimulated Neutrophils donor 1

source_name: Human primary Neutrophils donor 1


title: mRNA_BreastCancer_rep25


title: Unstimulated Neutrophils donor 8

source_name: Human primary Neutrophils donor 8


title: mRNA_BreastCancer_rep28


title: Unstimulated Neutrophils donor 3

source_name: Human primary Neutrophils donor 3


title: Unstimulated Neutrophils donor 2

source_name: Human primary Neutrophils donor 2


title: Unstimulated Neutrophils donor 4

source_name: Human primary Neutrophils donor 4


title: mRNA_BreastCancer_rep26


title: mRNA_BreastCancer_rep29


title: mRNA_BreastCancer_rep22


title: mRNA_BreastCancer_rep23


title: mRNA_BreastCancer_rep19


title: Myocytes_H/R_rep3

city: WenZhou

first: Bozhi

state: ZheJiang

address: 2 Fuxue Road

department: Department of Cardiology

institute: the First Affiliated Hospital of WenZhou Medical University

description: Gene expression after H/R in H9c2 myocyte

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 3 out of 6 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering.

organism: Rattus norvegicus

source_name: Myocytes, H/R, replicate 3

label_protocol: Each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

growth_protocol: H9c2 myocytes were maintained in DMEM containing 4,500 mg/L glucose and supplemented with 10% (v/v) FBS, 10 mM HEPES (Sigma), and 1% pen/strep solution at 37 °C in a humidified 5% CO2 incubator.

extract_protocol: mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis

treatment_protocol: H9c2 myocytes cultured in FBS and glucose-deprived in DMEM, were first cultured under hypoxic condition (1% O2, 5% CO2, and 94% N2) for 1 h and then under normoxic condition for 3 h. Total RNAs were extracted from the ischemia cortex of each mouse using TRIzol reagent.

value: H9c2 myocytes


title: mRNA_BreastCancer_rep16


title: Myocytes_H/R_rep2

source_name: Myocytes, H/R, replicate 2


title: Myocytes_H/R_rep1

source_name: Myocytes, H/R, replicate 1


title: Myocytes_control_rep3

description: Gene expression  in control H9c2 myocytes

source_name: Myocytes, control, replicate 3


title: mRNA_BreastCancer_rep18


title: mRNA_BreastCancer_rep17


title: mRNA_BreastCancer_rep14


title: Myocytes_control_rep2

source_name: Myocytes, control, replicate 2


title: mRNA_BreastCancer_rep20


title: mRNA_BreastCancer_rep21


title: mRNA_BreastCancer_rep15


title: mRNA_BreastCancer_rep13


title: mRNA_BreastCancer_rep12


title: mRNA_BreastCancer_rep10


title: mRNA_BreastCancer_rep11


title: mRNA_BreastCancer_rep9


title: mRNA_BreastCancer_rep7


title: mRNA_BreastCancer_rep4


title: mRNA_BreastCancer_rep8


title: mRNA_BreastCancer_rep5


title: mRNA_BreastCancer_rep6


title: mRNA_BreastCancer_rep3


title: mRNA_BreastCancer_rep2


title: Myocytes_control_rep1

source_name: Myocytes, control, replicate 1


title: mRNA_BreastCancer_rep1


title: 401304_A

city: Lübeck

first: Hauke

last: Busch

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: Lübeck Institute of Experimental Dermatology

institute: University of Lübeck

hyb_protocol: Hybridisation was performed according to the standard Illumina Infinium HD Methylation protocol for Infinium® HumanMethylation450 BeadChip assays

scan_protocol: Arrays were imaged using iScan Reader with default Illumina scanner settings

data_processing: Microarray data was pre-processed using the Illumina Genome Studio software before analysis using the R minfi package.

source_name: Patient 401304; Tissue tumor

label_protocol: Labelling was performed according to the standard Illumina Infinium HD Methylation protocol for Infinium® HumanMethylation450 BeadChip assays

extract_protocol: Tumour tissue and adjacent mucosa were collected from patients undergoing surgery. All tissues samples were reviewed by a pathologist to ensure their quality and high content of malignant cells. Genomic DNA was extracted from the tissues using the Qiagen QIAamp AllPrep DNA/RNA mini kit, according to the manufacturer's  protocol.

tag: patientid

value: F

value: tumor

tag: disease state

value: Colorectal cancer


title: 401320_A

source_name: Patient 401320; Tissue tumor

value: M


title: 401248_A

source_name: Patient 401248; Tissue tumor


title: 400712_C

source_name: Patient 400712; Tissue mucosa

value: mucosa


title: 401368_A2

source_name: Patient 401368; Tissue tumor


title: 401256_C

source_name: Patient 401256; Tissue mucosa


title: 401248_C

source_name: Patient 401248; Tissue mucosa


title: 400480_A

source_name: Patient 400480; Tissue tumor


title: 401256_A

source_name: Patient 401256; Tissue tumor


title: 401176_A

source_name: Patient 401176; Tissue tumor


title: 401320_C

source_name: Patient 401320; Tissue mucosa


title: 401304_C

source_name: Patient 401304; Tissue mucosa


title: 401176_C

source_name: Patient 401176; Tissue mucosa


title: 400488_A

source_name: Patient 400488; Tissue tumor