title: pancreatic beta suckling_11

city: Jerusalem

first: Miri

last: Stolovich-Rain

address: Ein Karem

department: Department of Developmental Biology and Cancer Research

country: Israel

institute: The Hebrew University-Hadassah Medical School

hyb_protocol: The amplified cDNA samples were hybridized to Mouse Gene 1.0 ST GeneChip array (Affymetrix). The material from each individual mouse was hybridized to one chip.

scan_protocol: the arrays were scanned in the Affymetrix GeneArray® 3000 scanner to generate fluorescent images, as described in the Affymetrix GeneChip® protocol

data_processing: The data were modeled using the RMA (Robust Multichip Average) approach, followed by mean one step Probe Set summarization giving each gene a single expression value, all done using the software package Partek Genomics Suite 6.6.

source_name: beta cell, suckling

label_protocol: Labeled using the Ovation Pico System V2 amplification kit from Nugene according to manufactures instructions.

growth_protocol: P25 insulin-Cre; Rosa26-LSL-YFP mice were either suckling or prematurely weaned at p18.

extract_protocol: RNA was prepared using Qiagen RNeasy micro kit.

treatment_protocol: 2000-6000 YFP+ cells were sorted from each mouse (one biological repetition).

tag: strain background

value: ICR

tag: genotype/variation

value: insulin-Cre; Rosa26-LSL-YFP mice

tag: mice group

value: suckling

value: pancreatic beta cell


title: XX Ctnnb1/Sox9 DKO_Rep2

status: Public on May 26 2015

type: RNA

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

country: USA

institute: NIEHS

description: Gene expression from E14.5 XX Ctnnb1/Sox9 DKO gonads

hyb_protocol: 4.6 μg of amplified biotin-aRNAs were fragmented and hybridized to each array for 18 hours at 45°C in a rotating hybridization. Array slides were stained with streptavidin/phycoerythrin utilizing a double-antibody staining procedure and then washed for antibody amplification according to the GeneChip Hybridization, Wash and Stain Kit and user manual following protocol FS450-0004.

scan_protocol: Arrays were scanned in an Affymetrix Scanner 3000.

data_processing: Data was obtained using the GeneChip® Command Console Software (AGCC; Version 1.1) using the MAS5 algorithm to generate .CHP files.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: E14.5 XX Ctnnb1/Sox9 DKO gonads

label_protocol: Forty (40) nanograms of total RNA (due to varying concentrations among samples) was amplified as directed in the WT-Ovation Pico RNA Amplification System protocol, and labeling with biotin following the Encore Biotin Module.

extract_protocol: A single pair of gonads (14.5 dpc) was separated from the mesonephros and was used as one biological replicate (3 to 4 biological replicates were included for each genotype). Total RNA was isolated using Picopure extraction kit (Arcturus). RNA quality and concentration were determined using N Agilent 2100 BioAnalyzer (Agilent Technologies, Santa Clara, California)

treatment_protocol: All embryos used in this study resulted from the crossing between Ctnnb1f/f; Sox9f/f females with Sf1-cre+/Tg ; Ctnnb1+/f; Sox9+/f males. The genotype of the gonads used in this study is as follows: Sf1-cre+/Tg ; Ctnnb1+/f; Sox9+/f as control, Sf1-cre+/Tg; Ctnnb1f/f; Sox9+/f as Ctnnb1 KO, Sf1-cre+/Tg; Ctnnb1+/f; Sox9f/f as Sox9 KO, and Sf1-cre+/Tg ; Ctnnb1f/f; Sox9f/f as Ctnnb1/Sox9 DKO

tag: genotype

value: Sf1-cre+/Tg ; Ctnnb1f/f; Sox9f/f

tag: tissue

value: gonads

tag: developmental stage

value: fetus

tag: embryonic stage

tag: chromosome composition

value: XX


title: pancreatic beta suckling_9

tag: cell type


title: pancreatic beta suckling_12


title: XX Sox9KO_Rep4

description: Gene expression from E14.5 XX Sox9KO gonads

source_name: E14.5 XX Sox9KO gonads

value: Sf1-cre+/Tg; Ctnnb1+/f; Sox9f/f


title: pancreatic beta suckling_2


title: XX Ctnnb1/Sox9 DKO_Rep3


title: XX Ctnnb1/Sox9 DKO_Rep1


title: genomic DNA from whole blood of male 20M05

type: genomic

city: Seoul

first: Hwan Young

last: Lee

address: 103 Daehak-ro, Jongno-gu

department: Forensic Medicine

country: South Korea

institute: Seoul National University College of Medicine

hyb_protocol: bisulfite converted DNA was amplified, fagmented 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; the non_normalized.txt contains unmethylated and methylated signal intensities

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: male_young_whole blood

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted using QIAamp DNA Investigator Kit and Mini Kit

tag: age (years)

tag: gender

value: Male

tag: ethnicity

value: Korean-Asian

value: whole blood


title: XX Sox9KO_Rep3


title: genomic DNA from whole blood of male 50M01

source_name: male_old_whole blood


title: genomic DNA from whole blood of male 30M04

source_name: male_30s_whole blood


title: 2xNEG cells, derived from the EpCAM positive population whithin the xenograft

city: Oslo

first: Nirma

last: Skrbo

address: Ullernchauseen 70

department: Dep of Genetics

country: Norway

institute: Oslo University Hospital

description: genomic DNA extracted from sorted xenograft cells,was genotyped using Infinium HumanOmniexpressExome Genotyping BeadChips (Illumina)

hyb_protocol: Standard Illumina Infinium HD protocol

scan_protocol: Standard Illumina Infinium HD protocol

data_processing: Intensity data were extracted in Genome studio (v2011.1)

label: c-bio; a-DNP

source_name: patient derived xenograft

label_protocol: Standard Illumina Infinium HD protocol

extract_protocol: Total DNAfrom FACS sorted cell subpopulations was isolated using Qiagen DNA extraction kit according to manufacturers protocol.

treatment_protocol: Single cell suspension from an luminal-like breast cancer was prepared by enzymatic disaggregation of tumours. The cells were re-suspended in cold staining buffer (PBS containing 0.5 % FCS and 3 % human immune globulin (Gammaguard) (N.V Baxter S.A, Belgium) and stained with fluorescently-labelled antibodies, diluted according to the manufacturers’s recommendation. Following 30 min incubation at 4 oC, the stained cells were washed ones with PBS, then re-suspended in DMEM/F12 with 0.,5% human serum albumin, 2% Hepes, Penicillin and Streptomycin and further sorted by FACS DIVA flow cytometer (Becton Dickinson), equipped with a 488nm Argon laser (Coherent) and 633nm HeNe laser (Spectra Physics).The single cell suspensions were stained with 1 µg/ml propidium iodide (PI) (Sigma) prior to sorting to exclude the dead cells from the analysis.

tag: xenograft model

tag: sub-population


title: 2xPOS cells, derived from the EpCAM positive population whithin the xenograft


title: pancreatic beta weaned_12

source_name: beta cell, weaned

value: prematurely weaned at P18


title: SSEA-4 positive cells, derived from the EpCAM positive population whithin the xenograft


title: XX Ctnnb1KO_Rep4

description: Gene expression from E14.5 XX Ctnnb1KO gonads

source_name: E14.5 XX Ctnnb1KO gonads

value: Sf1-cre+/Tg; Ctnnb1f/f; Sox9+/f


title: pancreatic beta weaned_5


title: XX Sox9KO_Rep1


title: XX Sox9KO_Rep2


title: genomic DNA from menstrual blood of female 20F09

source_name: female_old_vaginal swab

value: Female

value: menstrual blood


title: genomic DNA from menstrual blood of female 20F06


title: CD24 positive cells, derived from the EpCAM positive population whithin the xenograft


title: genomic DNA from menstrual blood of female 20F02


title: pancreatic beta weaned_4


title: XX Ctnnb1KO_Rep3


title: IMR90 siRB1 OIS, biological replicate 2

city: Tsu

first: Shin-ichiro

last: Takebayashi

state: Mie

address: 2-174, Edobashi

department: Graduate School of Medicine

country: Japan

institute: Mie University

description: OHT-treated

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on Human Genome U133 Plus 2.0 Array.

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

data_processing: The data were normalized using MAS5 (TGT=500) in Expression Console.

source_name: Oncogene-induced senescent IMR90 cells

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 250 nanog total RNA

extract_protocol: Total cellular RNA was isolated from cells with RNeasy kit (Qiagen), according to the manufacture’s instructions.

tag: cell line

value: IMR90 expressing a 4-OHT inducible ER:Ras

tag: treatment

value: OHT-treatment

tag: sirna transfection


title: XX Ctnnb1KO_Rep2


title: genomic DNA from vaginal swab of female 20F02

source_name: female_young_vaginal swab

value: vaginal swab


title: genomic DNA from whole blood of male 20M01


title: genomic DNA from semen of male 50M05

value: semen


title: genomic DNA from vaginal swab of female 20F06


title: genomic DNA from whole blood of male 50M04


title: genomic DNA from vaginal swab of female 20F07


title: genomic DNA from semen of male 50M06


title: IMR90 siRB1 OIS, biological replicate 1

description: OHT-treated


title: Apc+/-Atg7-/- rep3

city: 91400 Orsay

first: Florent

last: Dumont

state: Ile de France

address: 17 avenue des sciences

country: France

institute: Université Paris-Saclay

hyb_protocol: Following fragmentation, 10 ug of cDNA were hybridized for 16 hr at 45C on GeneChip Mouse Gene from Affymetrix GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: the data were RMA normalized  and  analysed with Partek Genomic Suite

label: Biotin

source_name: Normal tissue

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Following the GeneChip whole transcript (WT) Sense Target labelling assay kit Affymetrix)

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

treatment_protocol: Normal duodenum of both genotype were dissected

tag: genetic background

value: Duodenum


title: Apc+/-Atg7-/- rep2


title: Apc+/- rep3

description: Apc+/-

value: Apc+/-


title: IMR90 siControl OIS, biological replicate 2

description: OHT-treated

value: control siRNA


title: IMR90 growing, biological replicate 1

description: no OHT treatment

source_name: Growing IMR90 cells

value: no OHT


title: IMR90 growing, biological replicate 2

description: no OHT treatment


title: genomic DNA from semen of male 50M04


title: XX Ctr_Rep4

description: Gene expression from E14.5 XX gonads

source_name: E14.5 XX gonads

value: Sf1-cre+/Tg ; Ctnnb1+/f; Sox9+/f

value: gonads

value: fetus

value: XX


title: Apc+/-Atg7-/- rep1


title: genomic DNA from semen of male 20M06

value: Male

value: Korean-Asian


title: XX Ctnnb1KO_Rep1

value: Sf1-cre+/Tg; Ctnnb1f/f; Sox9+/f


title: IMR90 siConrol OIS, biological replicate 1

description: OHT-treated


title: Microglia_germfree_4d_after_LCMV_ic_10

status: Public on May 25 2015

city: Freiburg

first: Ori

last: Staszewski

address: Breisacher Str. 64

department: Institute of Neuropathology

country: Germany

institute: University Medical Center Freiburg

description: Microglia from germ free (GF) mice treated with LCMV i.c.

hyb_protocol: Biotinylated cRNA was hybridized on GeneChip® Mouse Gene 2.1 ST Arrays , that were stained, washed and scanned following standard procedures.

data_processing: Background correction and normalization was performed using the RMA-Sketch implementation in Affymetrix Expression Console

source_name: Microglia, LCMV i.c., GF

label_protocol: Total RNA was amplified using the Ovation PicoSL WTA System V2 and further processed using the Encore Biotin Module according to the instructions supplied by the manufacturer (NuGen).

growth_protocol: Mice were housed under SPF or germ-free condiotions. Animals were 6-10 weeks old.

extract_protocol: Adult microglia were harvested using density gradient separation. CD11b+CD45lo microglial cell populations were FACS-sorted and collected directly in cell lysis buffer and subsequently RNA was isolated with the Arcturus Pico Pure RNA Isolation Kit (Life Technologies) according to the manufacturer's protocol.

treatment_protocol: Lymphocytic Choriomeningitis Virus (LCMV) strain WE was propagated and titrated as plaque forming units (PFU) on L929 cells as described before 12. PFU were multiplied by the factor 10 to be converted into infectious units (IU). Mice were infected by intracerebral inoculation of 103 IU into the right hemisphere

value: LCMV

tag: condition

value: germ free (GF)

value: microglia


title: genomic DNA from semen of male 20M03


title: XX Ctr_Rep2

description: Gene expression from E14.5 XX gonads


title: Microglia_germfree_4d_after_LCMV_ic_09

scan_protocol: Biotinylated cRNA was hybridized on GeneChip® Mouse Gene 2.1 ST Arrays , that were stained, washed and scanned following standard procedures.


title: Apc+/- rep1

description: Apc+/-


title: Microglia_germfree_4d_after_LCMV_ic_06


title: genomic DNA from semen of male 20M02


title: XX Ctr_Rep1

description: Gene expression from E14.5 XX gonads


title: Microglia_germfree_4d_after_LCMV_ic_07


title: Microglia_germfree_4d_after_LCMV_ic_03


title: Microglia_germfree_4d_after_LCMV_ic_05


title: Microglia_germfree_4d_after_LCMV_ic_01


title: Microglia_germfree_4d_after_LCMV_ic_04


title: genomic DNA from saliva of male 50M05

description:
fragmented genomic DNA
50M05SA

value: saliva


title: Microglia_germfree_4d_after_LCMV_ic_08


title: Microglia_germfree_4d_after_LCMV_ic_02


title: genomic DNA from saliva of male 20M05

description:
fragmented genomic DNA
20M05SA


title: genomic DNA from saliva of male 20M03

description:
fragmented genomic DNA
20M03SA


title: Microglia_specificpathogenfree_4d_after_LCMV_ic_09

description: Microglia from specifc pathogen free (SPF) mice treated with LCMV i.c.

source_name: Microglia, LCMV i.c., SPF

value: specifc pathogen free (SPF)


title: Microglia_specificpathogenfree_4d_after_LCMV_ic_10


title: Microglia_specificpathogenfree_4d_after_LCMV_ic_05


title: GIST-T1 cells with control molecule_1

city: Sapporo

first: Hiromu

last: Suzuki

state: Hokkaido

address: S1, W17, Chuo-ku

department: Department of Molecular Biology

institute: Sapporo Medical University

description:
gene expression in GIST-T1 cells transfected with control miRNA (replicate 1)
negative_control_1

hyb_protocol: Hybridization was performed using a Gene Expression Hybridization kit (Agilent Technologies) according to manufacturer's instruction.

scan_protocol: Array was scanned with an Agilent G2565BA Microarray Scanner.

data_processing: Agilent Feature Extraction Software (v 10.7) was used for background subtraction.

label_protocol: Total RNA (100 ng) was labeled using a Low Input Quick Amp Labeling Kit One-Color (Agilent Technologies) according to manufacturer's instruction.

growth_protocol: GIST-T1 cells were cultured in Dulbecco's Modified Eagle's Medium supplemented with 10% heat-inactivated fetal bovine serum.  The cultures were incubated at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: Total RNA was extracted using a TRIZOL reagent (Invitrogen).

treatment_protocol: GIST-T1 cells (3.0E+6 cells) were transfected with 100 pmol of a miR-34a mirVana miRNA mimics (Ambion) or a mirVana miRNA mimic Negative Control #1 (Ambion) using a Cell Line Nucleofector kit L (Lonza) and a Nucleofector device (Lonza) according to the manufacturer’s instructions.  Forty-eight hours after transfection, total RNA extraction was carried out.

tag: transfection

value: control miRNA


title: Microglia_specificpathogenfree_4d_after_LCMV_ic_08


title: GIST-T1 cells with miR-335 mimic molecule_2

description:
gene expression in GIST-T1 cells transfected with miR-335 mimic molecule (replicate 2)
miR-34a_mimic_2

treatment_protocol: GIST-T1 cells (3.0E+6 cells) were transfected with 100 pmol of a miR-335 mirVana miRNA mimics (Ambion) or a mirVana miRNA mimic Negative Control #1 (Ambion) using a Cell Line Nucleofector kit L (Lonza) and a Nucleofector device (Lonza) according to the manufacturer’s instructions.  Forty-eight hours after transfection, total RNA extraction was carried out.

value: miR-335 mimic


title: GIST-T1 cells with control molecule_3


title: XX Ctr_Rep3

description: Gene expression from E14.5 XX gonads

tag: genotype


title: genomic DNA from saliva of male 20M06

description:
fragmented genomic DNA
20M06SA

tag: tissue


title: genomic DNA from saliva of male 50M01

description:
fragmented genomic DNA
50M01SA


title: Microglia_specificpathogenfree_4d_after_LCMV_ic_07


title: GIST-T1 cells with miR-34a mimic molecule_2

description:
gene expression in GIST-T1 cells transfected with miR-34a mimic molecule (replicate 2)
miR-34a_mimic_2

value: miR-34a mimic


title: Microglia_specificpathogenfree_4d_after_LCMV_ic_03


title: genomic DNA from saliva of male 50M07

description:
fragmented genomic DNA
50M07SA


title: GIST-T1 cells with control molecule_4

description:
gene expression in GIST-T1 cells transfected with control miRNA (replicate 2)
negative_control_2


title: GIST-T1 cells with miR-335 mimic molecule_1

description:
gene expression in GIST-T1 cells transfected with miR-335 mimic molecule (replicate 1)
miR-34a_mimic_1


title: Microglia_germfree_6hr_after_PBS_ic_3

description: Microglia from germ free (GF) mice treated with PBS i.c.

source_name: Microglia, PBS i.c., GF

growth_protocol: Mice were housed under SPF or germ-free conditions. Animals were 6-8 weeks old.

treatment_protocol: 5 µg LPS were diluted in 10 µl PBS and applied intracranially under isofluoran anesthesia. Animals returned to their cages once they had recovered their righting reflex. 6 hours later, animals were analyzed. Control animals were injected with 10 µl sterile PBS i.c.

value: PBS i.c.

tag: age

value: 6-8 weeks old

tag: strain


title: Microglia_germfree_6hr_after_LPS_ic_3

description: Microglia from germ free (GF) mice treated with LPS i.c.

source_name: Microglia, LPS i.c., GF

value: LPS i.c.


title: Microglia_specificpathogenfree_4d_after_LCMV_ic_02


title: Microglia_specificpathogenfree_4d_after_LCMV_ic_01


title: Microglia_germfree_6hr_after_LPS_ic_1


title: Microglia_germfree_6hr_after_LPS_ic_2


title: GIST-T1 cells with miR-34a mimic molecule_1

description:
gene expression in GIST-T1 cells transfected with miR-34a mimic molecule (replicate 1)
miR-34a_mimic_1


title: GEK19

type: SRA

city: Porto Alegre

first: Rogerio

last: Margis

state: RS

address: Av. Bento Goncalves 9500

department: Centro de Biotecnologia

country: Brazil

institute: Universidade Federal do Rio Grande do Sul

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
low quality reads with 'n' were removed using PrinSeq script (Schmieder and Edwards, 2011)
Unique raw reads counted obtained with perl and python scripts
Supplementary_files_format_and_content: tab-delimited text files with abundance of unique sequences

organism: Glycine max

source_name: mature seed

growth_protocol: Glycine max (cultivar Conquista) seeds were grown in a greenhouse with 26 +/-2 °C, in the dark for two days. After, the seeds were cultivated for 3, 5 and 7 days, in a greenhouse with same temperature regime with 12h photoperiod regime. The mature seed used for RNA exctraction was stored in dark and 12 °C. After collecting each time point, the seeds were immediately frozen in liquid nitrogen and stored at -80°C until RNA extraction.

extract_protocol: Total RNA was isolated from the seed material using NucleoSpin (MN) according to the manufactures’ protocol, and the RNA quantity and quality were evaluated by NanoDrop (Thermo Scientific) and electrophoresis on a 1% agarose gel, respectively. Total RNA (> 10 μg) was sent to Fasteris Life Sciences SA (Plan-les-Ouates, Switzerland) for processing. Two sRNA libraries were constructed, one from mature seeds and one from an equivalent mixture of RNA from three germinating seeds stages.They were sequenced by Illumina GAII. Briefly, the construction of the small RNA libraries consisted of the following successive steps: acrylamide gel purification of the RNA bands corresponding to the size range 20-30 nt, ligation of the 3p and 5p adapters to the RNA in two separate subsequent steps, each followed by acrylamide gel purification, cDNA synthesis followed by acrylamide gel purification, and a final step of PCR amplification to generate a cDNA colony template library for Illumina sequencing.

tag: sample

value: single

tag: days after germination

value: seeds

tag: rna subtype

value: small RNA


title: Microglia_germfree_6hr_after_PBS_ic_1

tag: cell type


title: Microglia_specificpathogenfree_6hr_after_LPS_ic_2

description: Microglia from specifc pathogen free (SPF) mice treated with LPS i.c.

source_name: Microglia, LPS i.c., SPF


title: Microglia_specificpathogenfree_4d_after_LCMV_ic_04


title: Microglia_germfree_6hr_after_PBS_ic_2


title: Microglia_specificpathogenfree_6hr_after_LPS_ic_1


title: Microglia_specificpathogenfree_6hr_after_PBS_ic_3

description: Microglia from specifc pathogen free (SPF) mice treated with PBS i.c.

source_name: Microglia, PBS i.c., SPF


title: GIST-T1 cells with control molecule_2


title: mTEC-AireKO

city: Rehovot

first: Jakub

last: Abramson

address: Herzl 234

department: Immunology

institute: Weizmann Institute

description: Gene expression data from sorted MHC-II mTEC isolated from Sirt1cKO mice

hyb_protocol: 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Mo1ST. GeneChips were washed and stained in the Affymetrix Fluidics Station

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

data_processing: Raw data were processed with the RMA algorithm for probe-level normalization and analyzed using GenePattern software

source_name: mTECs (EpCAM+, CD45-, Ly51low, MHC-II high)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA

growth_protocol: Mice were maintained under specific-pathogen-free conditions at the Weizmann Institute’s animal facility and sacrifised at 6weeks of age by CO2.

treatment_protocol: Thymi were surgically removed from mice and placed into cold 1× PBS supplemented with 2% Fetal Bovine Serum (FBS, Invitrogen). Thymi were trimmed of fat and connective tissues, chopped into small pieces and then disintegrated by sequential enzymatic digestion using Collagenase D (Roche #1088858) and Collagenase-Dispase cocktail (Roche #269638). Thymic stroma, containing the TEC fraction, was enriched using a Percoll gradient (Sigma #P1644) and was subjected to staining with the appropriate antibodies. All types of cells were then stained in 100µl MACS buffer, with the specific fluorophore-labeled antibodies for 20-60 minutes on ice. Cells were then washed, re-suspended in MACS buffer, filtered through a 50mm mesh and sorted on BD FACS Aria III cell sorter into Trizol reagent

value: Aire–/–


title: mTEC-cSirt1KO

description: Gene expression data from sorted MHC-II mTEC isolated from AireKO mice

value: Sirt1fl/fl Foxn1-Cre (Sirt1cKO)


title: Microglia_specificpathogenfree_6hr_after_LPS_ic_3


title: Microglia_specificpathogenfree_6hr_after_PBS_ic_1


title: Microglia_specificpathogenfree_6hr_after_PBS_ic_2


title: IPS_Control_3

city: Wako

first: Eiji

last: Matsunaga

address: Hirosawa 2-1

institute: RIKEN Brain Science Institute

description:
IPS_C3
Gene expression data from the surrounding area of Intraparietal sulcus (IPS) of left hemisphere of control monkey

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45 ˚C on GeneChip Rhesus Macaque Genome Array. GeneChips were washed and stained in the GeneChip Fluidics Station 450.

data_processing: CHP data was generated by GeneChip Operating Software (Affymetrix) with MAS5 and probe intensity was normalized by 75th percentile shift (GeneSpring GX).

organism: Macaca fuscata

label_protocol: Biotinylated cRNA were prepared by GeneChip 3’IVT Expression Kit (Affimetrix).

extract_protocol: Extraction of total RNA was performed by RNeasy Lipid Tissue Mini Kit (Qiagen) and the quality was checked by 2100 Bioanalyzer (Agilent technologies).

value: Control

value: Surrounding area of Intraparietal sulcus of left hemisphere

tag: gender

value: Male

value: 3 years 9 month old


title: IPS_Tool-use training_1

description:
IPS_E1
Gene expression data from the surrounding area of Intraparietal sulcus (IPS) of left hemisphere of tool-use trained monkey

value: Tool-use training

value: 5 years 7 months old


title: IPS_Tool-use training_2

description:
IPS_E2
Gene expression data from the surrounding area of Intraparietal sulcus (IPS) of left hemisphere of tool-use trained monkey

value: 6 years


title: IPS_Tool-use training_3

description:
IPS_E3
Gene expression data from the surrounding area of Intraparietal sulcus (IPS) of left hemisphere of tool-use trained monkey

value: 5 years 1 month old


title: Apc+/- rep2

description: Apc+/-

value: Duodenum

value: Apc+/-


title: IPS_Control_1

description:
IPS_C1
Gene expression data from the surrounding area of Intraparietal sulcus (IPS) of left hemisphere of control monkey

value: 5 years 4 months old


title: IPS_Control_2

description:
IPS_C2
Gene expression data from the surrounding area of Intraparietal sulcus (IPS) of left hemisphere of control monkey

value: 5 years 10 months old


title: GEK15

source_name: germinating seed

value: pool


title: SII_Tool-use training_2

description:
Rhesus_E2
Gene expression data from the surronding area of lateral sulcus including the secondary somatosensory cortex (SII) of tool-use trained monkey

value: Surrounding area of lateral sulcus including the secondary somatosensory cortex (SII) of left hemisphere

value: Female

value: 3 years 10 months old


title: mTEC-WT

description: Gene expression data from sorted MHC-II mTEC isolated from WT mice

value: Sirt1fl/fl (WT)


title: SII_Tool-use training_3

description:
Rhesus_E3
Gene expression data from the surronding area of lateral sulcus including the secondary somatosensory cortex (SII) of tool-use trained monkey


title: SII_Control_3

description:
Rhesus_C3
Gene expression data from the surronding area of lateral sulcus including the secondary somatosensory cortex (SII) of control monkey

value: Control


title: SII_Tool-use training_1

description:
Rhesus_E1
Gene expression data from the surronding area of lateral sulcus including the secondary somatosensory cortex (SII) of tool-use trained monkey


title: SII_Control_1

description:
Rhesus_C1
Gene expression data from the surronding area of lateral sulcus including the secondary somatosensory cortex (SII) of control monkey

value: 4 years 6 months old


title: P. aeruginosa PAO1, 1 mM ZnO added

city: Gyeongsan-Si

first: Jintae

state: Gyeongsangbuk-Do

address: 214-1 Daedong

department: Chemical engineering

institute: Yeungnam University

description:
SAMPLE 2
Gene expression data of Pseudomonas aeruginosa PAO1 incubated for 5 hrs with 1 mM ZnO nanoparticle at 37oC with 250 rpm shaking

hyb_protocol: Following affymetrix protocol.  Prepared hybridization cocktail for Single Probe Array (49 Format) with total 200 ul volume including 1X hybrization buffer, 50 pM B2 Control Oligo, 0.1 mg/mL Herring Sperm DNA, 0.5 mg/mL BSA, and at least 1 ug fragmented and labelled cDNA.  After loading of hybridization cocktail in Affymetrix E. coli Antisense Genome Array, the hybridization was performed at 45ºC, with 60 rpm for 16 hours.    After hybridization, the probe array was washed and stained using Affymetrix Genechip Fluidics Station 450 and the software GenomeChipOperating Software (GCOS).

scan_protocol: Following affymetrix protocol. After washing and staining, the probe array was scanned using Affymetrix Genechip scanner GCS3000 7G system and the software GenomeChipOperating Software (GCOS).

data_processing: MAS 5.0 Expression Analysis Default Setting

organism: Pseudomonas aeruginosa PAO1

source_name: P. aeruginosa PAO1, 1 mM ZnO added

label_protocol: Following affymetrix protocol. cDNA was synthesized first using Promega M-MLV Reverse transcriptase (cat# M1705). After removing RNA, DNA fragmentation was performed to obtain and 50-200 base cDNA fragments. The fragmented cDNA was labelled with Biotin-ddUTP using Enzo BioArray Terminal Labeling Kit (Affymetrix, P/N 900181).

extract_protocol: DNA microarray analysis with one biological replicate was performed with an Affymetrix system. P. aeruginosa was inoculated in 25 ml of LB medium in 250 ml shaker flasks with overnight cultures (1 : 100 dilution). Cells were cultured for 5 h with shaking at 250 rpm with and without ZnO nanoparticles (1 mM). Before sample collection, RNase inhibitor (RNAlater, Ambion, TX, USA) was added, and the cells were immediately chilled with dry ice and 95% ethanol (to prevent RNA degradation) for 30 s before centrifugation at 16,000 g for 2 min. The cell pellets were immediately frozen with dry ice and stored at –80°C. Total RNA was isolated using a Qiagen RNeasy mini Kit (Valencia, CA, USA) with Qiagen RNase-free DNase I (Cat# 79254).

treatment_protocol: Sample 2 was incuabted with 1 mM ZnO nanoparticle at 37oC for 5 hrs with 250 rpm shaking

tag: agent

value: ZnO nanoparticle


title: P. aeruginosa PAO1, control

description:
SAMPLE 1
Gene expression data of Pseudomonas aeruginosa PAO1 incubated for 5 hrs at 37oC with 250 rpm shaking

source_name: P. aeruginosa PAO1, control

growth_protocol: P. aeruginosa was inoculated in 25 ml of LB medium in 250 ml shaker flasks with overnight cultures (1 : 100 dilution). Cells were cultured for 5 h with shaking at 250 rpm with and without ZnO nanoparticles (1 mM).

value: control


title: Microglia_specificpathogenfree_4d_after_LCMV_ic_06

description: Microglia from specifc pathogen free (SPF) mice treated with LCMV i.c.

value: LCMV

value: specifc pathogen free (SPF)

value: microglia


title: human_cortical_spheroids_day52 [9665647054_J]

city: Los Angeles

first: Daniel

middle: H.

last: Geschwind

state: California

address: 2309 Gonda Bldg, 695 Charles E. Young Dr. South

department: Neurology

institute: UCLA

hyb_protocol: Illumina protocol

scan_protocol: Illumina protocol

data_processing: Log2 normalization and quantile normalization

source_name: human cortical spheroids derived from pluripotent stem cells

label_protocol: Illumina protocol

growth_protocol: Neurobasal + B27 media

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

tag: line

value: F

tag: differentiation stage

tag: rin


title: PBMC-control-08

city: Tampa

first: Steven

last: Eschrich

state: FL

address: 12902 Magnolia Drive

department: Biostatistics & Bioinformatics

institute: Moffitt Cancer Center

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: The array data was processed and normalized using RMA (Affymetrix APT 1.12.0)

source_name: PBMC, healthy control subject

label_protocol: The poly(A) RNA was converted to cDNA, then amplified and labeled with biotin following the procedure initially described by Van Gelder et al

extract_protocol: Peripheral blood mononuclear cells (PBMC) were isolated from blood. RNA extraction was performed using the RNAeasy Mini Kit (Qiagen)

tag: individual

value: healthy control subject

value: PBMC


title: VEPH1 expressing SKOV3 cells treated with TGF-ß rep1

city: Toronto

first: carl

last: virtanen

state: Ontario

address: 101 College St

department: Princess Margaret Genomics Centre

country: Canada

institute: University Health Network

description: replicate number 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with GeneSpring v.12.1

source_name: SKOV3 Ovarian cancer cell line

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

extract_protocol: Standard Trizol extractions, assessed the RNA using the Agilent Bioanalyzer (all RINS were 10)

tag: treatment

value: TGF-ß 3 hr treatment


title: human_cortical_spheroids_day76 [9665647054_G]


title: VEPH1 expressing SKOV3 cells treated with TGF-ß rep2

description: replicate number 2


title: human_cortical_spheroids_day52 [9665647054_K]

value: M


title: human_cortical_spheroids_day76 [9665647054_F]


title: PBMC-control-05


title: PBMC-control-07


title: Mock vector expressing SKOV3 cells rep2

description: replicate number 2

value: no treatment

value: Mock


title: PBMC-control-09


title: PBMC-control-06


title: Mock vector expressing SKOV3 cells treated with TGF-ß rep1

description: replicate number 1


title: human_cortical_spheroids_day76 [9665647054_A]


title: Mock vector expressing SKOV3 cells treated with TGF-ß rep3

description: replicate number 3


title: PBMC-control-10


title: SII_Control_2

description:
Rhesus_C2
Gene expression data from the surronding area of lateral sulcus including the secondary somatosensory cortex (SII) of control monkey

value: Surrounding area of lateral sulcus including the secondary somatosensory cortex (SII) of left hemisphere

value: Male

value: 5 years 4 months old


title: VEPH1 expressing SKOV3 cells treated with TGF-ß rep3

description: replicate number 3


title: VEPH1 expressing SKOV3 cells rep 1

description: replicate number 1


title: human_cortical_spheroids_day52 [9665647054_E]


title: Mock vector expressing SKOV3 cells rep1

description: replicate number 1


title: PBMC-control-02


title: Mock vector expressing SKOV3 cells rep3

description: replicate number 3


title: PBMC-control-01


title: PBMC-control-03


title: VEPH1 expressing SKOV3 cells rep 2

description: replicate number 2


title: PBMC-control-04


title: SU46A 3/8

city: Edinburgh

first: Fiach

last: O'Mahony

address: Crewe Road South

department: Pathology

country: United Kingdom

institute: University of Edinburgh

description:
array no.: 8
array position: 11

data_processing: The data were normalised using the lumi package in R using variance and robust spline.

source_name: Patient Number SU46 Nephrectomy Biological Repeat 2

label_protocol: Biotinylated cRNA were prepared with the Nugen Ovation FFPE WTA System and Encore BiotinIL Module kits

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

tag: diagnosis

value: clear cell renal cell carcinoma

tag: sunitinib treatment

value: Yes

value: kidney


title: Mock vector expressing SKOV3 cells treated with TGF-ß rep2

description: replicate number 2

tag: transfection


title: PBMC-non-tolerant-05

source_name: PBMC, non-tolerant HCT patient

value: non-tolerant HCT patient


title: PBMC-non-tolerant-03


title: PBMC-non-tolerant-01


title: SU41A 1

description:
array no.: 8
array position: 7

source_name: Patient Number SU41 Nephrectomy Biological Repeat 1

tag: tissue


title: VEPH1 expressing SKOV3 cells rep 3

description: replicate number 3


title: PBMC-non-tolerant-06


title: PBMC-non-tolerant-07


title: PBMC-non-tolerant-02


title: SU46A 2/8

description:
array no.: 8
array position: 10

source_name: Patient Number SU46 Nephrectomy Biological Repeat 1


title: SU41A 2

description:
array no.: 8
array position: 8

source_name: Patient Number SU41 Nephrectomy Biological Repeat 2


title: SU39A 2

description:
array no.: 8
array position: 4

source_name: Patient Number SU39 Nephrectomy Biological Repeat 2


title: SU32 A2

description:
array no.: 7
array position: 8

source_name: Patient Number SU32 Nephrectomy Biological Repeat 2


title: PBMC-non-tolerant-11


title: PBMC-non-tolerant-08


title: UHRR CTRL 16

description:
array no.: 8
array position: 1

source_name: Universal Human Reference RNA Control Array 16

value: Universal Human Reference RNA


title: PBMC-non-tolerant-09


title: SU36A 4

description:
array no.: 7
array position: 12

source_name: Patient Number SU36 Nephrectomy Biological Repeat 1


title: SU39A 3

description:
array no.: 8
array position: 5

source_name: Patient Number SU39 Nephrectomy Biological Repeat 3


title: SU39A 1

description:
array no.: 8
array position: 3

source_name: Patient Number SU39 Nephrectomy Biological Repeat 1


title: SU46A 4/8

description:
array no.: 8
array position: 12

source_name: Patient Number SU46 Nephrectomy Biological Repeat 3


title: PBMC-non-tolerant-10


title: PBMC-non-tolerant-04


title: SU32 A1

description:
array no.: 7
array position: 7

source_name: Patient Number SU32 Nephrectomy Biological Repeat 1


title: PBMC-non-tolerant-16


title: PBMC-non-tolerant-12


title: SU26 B1

description:
array no.: 7
array position: 2

source_name: Patient Number SU26 Nephrectomy Biological Repeat 2


title: PBMC-non-tolerant-15


title: SU26 B2

description:
array no.: 7
array position: 3

source_name: Patient Number SU26 Nephrectomy Biological Repeat 3


title: SU26 C2

description:
array no.: 7
array position: 5

source_name: Patient Number SU26 Nephrectomy Biological Repeat 5


title: UHRR CTRL 15

description:
array no.: 7
array position: 1

source_name: Universal Human Reference RNA Control Array 15


title: PBMC-tolerant-05

source_name: PBMC, tolerant HCT patient

value: tolerant HCT patient


title: PBMC-non-tolerant-13

source_name: PBMC, non-tolerant HCT patient


title: SU26 B3

description:
array no.: 7
array position: 4

source_name: Patient Number SU26 Nephrectomy Biological Repeat 4


title: PBMC-tolerant-01


title: PBMC-tolerant-10


title: SU23A 3

description:
array no.: 6
array position: 2

source_name: Patient Number SU23 Nephrectomy Biological Repeat 2


title: SU25 A7

description:
array no.: 6
array position: 11

source_name: Patient Number SU25 Nephrectomy Biological Repeat 4


title: SU25 A2

description:
array no.: 6
array position: 8

source_name: Patient Number SU25 Nephrectomy Biological Repeat 1


title: SU23A 4

description:
array no.: 6
array position: 3

source_name: Patient Number SU23 Nephrectomy Biological Repeat 3


title: PBMC-tolerant-09


title: SU23A 6

description:
array no.: 6
array position: 5

source_name: Patient Number SU23 Nephrectomy Biological Repeat 4


title: PBMC-tolerant-03


title: PBMC-non-tolerant-14


title: PBMC-tolerant-06


title: PBMC-tolerant-04


title: SU25 A5

description:
array no.: 6
array position: 9

source_name: Patient Number SU25 Nephrectomy Biological Repeat 2


title: PBMC-tolerant-07


title: SU25 A6

description:
array no.: 6
array position: 10

source_name: Patient Number SU25 Nephrectomy Biological Repeat 3


title: PBMC-tolerant-08


title: PBMC-non-tolerant-17


title: SU23A 2

description:
array no.: 6
array position: 4

source_name: Patient Number SU23 Nephrectomy Biological Repeat 1


title: PBMC-tolerant-11


title: SU26 A2

description:
array no.: 6
array position: 12

source_name: Patient Number SU26 Nephrectomy Biological Repeat 1


title: UHRR CTRL 14

description:
array no.: 6
array position: 1

source_name: Universal Human Reference RNA Control Array 14


title: SU22A 4

description:
array no.: 5
array position: 10

source_name: Patient Number SU22 Nephrectomy Biological Repeat 3


title: SU22A 9

description:
array no.: 5
array position: 12

source_name: Patient Number SU22 Nephrectomy Biological Repeat 7


title: PBMC-tolerant-14


title: PBMC-tolerant-13


title: PBMC-tolerant-16


title: SU19A 6

description:
array no.: 5
array position: 2

source_name: Patient Number SU19 Nephrectomy Biological Repeat 4


title: SU22A 6

description:
array no.: 5
array position: 6

source_name: Patient Number SU22 Nephrectomy Biological Repeat 4


title: PBMC-tolerant-12

source_name: PBMC, tolerant HCT patient


title: SU22A 21

description:
array no.: 5
array position: 8

source_name: Patient Number SU22 Nephrectomy Biological Repeat 1


title: Patient Number SU49 Nephrectomy Biological Repeat 2

description: array number 561569

hyb_protocol: Hybridisation was conducted using theNimbleGen Arrays User’s Guide CGH Arrays following the manufacurers instructions (http://www.nimblegen.com/downloads/support/05434483001_NG_CGHLOH_UGuide_v9p1.pdf).

scan_protocol: Arrays were scanned on a MS200 Microarray scanner per manufacturer's protocol(http://www.nimblegen.com/downloads/support/05434483001_NG_CGHLOH_UGuide_v9p1.pdf).

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.5 ChIP data extraction.

label_protocol: DNA was labeled using theNimbleGen Arrays User’s Guide CGH Arrays following the manufacurers instructions (http://www.nimblegen.com/downloads/support/05434483001_NG_CGHLOH_UGuide_v9p1.pdf)

extract_protocol: DNA was extracted using Qiagen DNeasy Blood and Tissue kit according to the manufacturers recommendations

tag: Sex

tag: sample source

value: Nephrectomy

tag: treatment with tki

value: Treated

tag: disease state

tag: tissue type

value: Fresh Frozen

source_name: Input DNA from a pool of 5 LCL-derived DNAs

growth_protocol: Cells grow at  37°C using RPMI 1640 ( + glutamine) supplemented with 10% FCS,1% Oxaloacetate 1 mM + Pyruvate 0.45 mM, 1% Glutamine, Insulin 100 I.U/ml (final concentration of  0.2 I.U/ml),1% Pen and Strep.

value: Pool of LCL cell line DNA absent of chromosomal aberrations

value: No

tag: sample type


title: SU22A 7

description:
array no.: 5
array position: 7

source_name: Patient Number SU22 Nephrectomy Biological Repeat 5


title: SU19A 1

description:
array no.: 4
array position: 10

source_name: Patient Number SU19 Nephrectomy Biological Repeat 1


title: SU19A 3

description:
array no.: 4
array position: 11

source_name: Patient Number SU19 Nephrectomy Biological Repeat 2


title: Patient Number SU48 Nephrectomy Biological Repeat 3

description: array number 534338

value: M

value: Input DNA from a pool of 5 LCL-derived DNAs


title: SU19A 4

description:
array no.: 4
array position: 12

source_name: Patient Number SU19 Nephrectomy Biological Repeat 3


title: SU17A 5

description:
array no.: 4
array position: 7

source_name: Patient Number SU17 Nephrectomy Biological Repeat 3


title: Patient Number SU46 Nephrectomy Biological Repeat 3

description: array number 534338

value: F


title: SU17A 6

description:
array no.: 4
array position: 8

source_name: Patient Number SU17 Nephrectomy Biological Repeat 4


title: Patient Number SU54 Nephrectomy Biological Repeat 1

description: array number 534336


title: SU17A 7

description:
array no.: 4
array position: 9

source_name: Patient Number SU17 Nephrectomy Biological Repeat 5


title: Patient Number SU48 Nephrectomy Biological Repeat 1

description: array number 534336


title: UHRR CTRL 13

description:
array no.: 5
array position: 1

source_name: Universal Human Reference RNA Control Array 13


title: Patient Number SU54 Nephrectomy Biological Repeat 2

description: array number 534092


title: Patient Number SU49 Nephrectomy Biological Repeat 1

description: array number 561569


title: Patient Number SU48 Nephrectomy Biological Repeat 2

description: array number 534092


title: SU22A 8

description:
array no.: 5
array position: 11

source_name: Patient Number SU22 Nephrectomy Biological Repeat 6


title: Patient Number SU46 Nephrectomy Biological Repeat 2

description: array number 534336


title: SU17A 4

description:
array no.: 4
array position: 5

source_name: Patient Number SU17 Nephrectomy Biological Repeat 2


title: Patient Number SU46 Nephrectomy Biological Repeat 1

description: array number 534102


title: SU17A 3

description:
array no.: 4
array position: 6

source_name: Patient Number SU17 Nephrectomy Biological Repeat 1


title: Patient Number SU41 Nephrectomy Biological Repeat 2

description: array number 561530


title: Patient Number SU41 Nephrectomy Biological Repeat 3

description: array number 561569


title: Patient Number SU41 Nephrectomy Biological Repeat 1

description: array number 561530


title: SU11A 12

description:
array no.: 3
array position: 4

source_name: Patient Number SU11 Nephrectomy Biological Repeat 2


title: Patient Number SU39 Nephrectomy Biological Repeat 1

description: array number 534102


title: SU11A 6

description:
array no.: 3
array position: 5

source_name: Patient Number SU11 Nephrectomy Biological Repeat 5


title: SU16A 4

description:
array no.: 4
array position: 3

source_name: Patient Number SU16 Nephrectomy Biological Repeat 2


title: SU11A 9

description:
array no.: 3
array position: 6

source_name: Patient Number SU11 Nephrectomy Biological Repeat 8


title: SU11A 1

description:
array no.: 3
array position: 7

source_name: Patient Number SU11 Nephrectomy Biological Repeat 1


title: SU11A 7

description:
array no.: 3
array position: 8

source_name: Patient Number SU11 Nephrectomy Biological Repeat 6


title: Patient Number SU39 Nephrectomy Biological Repeat 3

description: array number 534338

source_name: Input DNA from a pool of 5 LCL-derived DNAs


title: SU16A 3

description:
array no.: 4
array position: 2

source_name: Patient Number SU16 Nephrectomy Biological Repeat 1


title: SU11A 4

description:
array no.: 3
array position: 3

source_name: Patient Number SU11 Nephrectomy Biological Repeat 3


title: SU13B 2

description:
array no.: 3
array position: 12

source_name: Patient Number SU13 Nephrectomy Biological Repeat 2


title: SU11A 8

description:
array no.: 3
array position: 9

source_name: Patient Number SU11 Nephrectomy Biological Repeat 7


title: Patient Number SU36 Nephrectomy Biological Repeat 3

description: array number 534338


title: Patient Number SU36 Nephrectomy Biological Repeat 1

description: array number 534092


title: UHRR CTRL 12

description:
array no.: 4
array position: 1

source_name: Universal Human Reference RNA Control Array 12


title: Patient Number SU39 Nephrectomy Biological Repeat 2

description: array number 534336


title: SU11A 5

description:
array no.: 3
array position: 2

source_name: Patient Number SU11 Nephrectomy Biological Repeat 4


title: Patient Number SU32 Nephrectomy Biological Repeat 2

description: array number 534102


title: Patient Number SU36 Nephrectomy Biological Repeat 2

description: array number 534102


title: UHRR CTRL 11

description:
array no.: 3
array position: 1

source_name: Universal Human Reference RNA Control Array 11


title: Patient Number SU32 Nephrectomy Biological Repeat 3

description: array number 534338


title: Patient Number SU32 Nephrectomy Biological Repeat 1

description: array number 534092


title: Patient Number SU26 Nephrectomy Biological Repeat 2

description: array number 561530


title: SU04A 5

description:
array no.: 2
array position: 4

source_name: Patient Number SU04 Nephrectomy Biological Repeat 3


title: SU22A 3

description:
array no.: 5
array position: 9

source_name: Patient Number SU22 Nephrectomy Biological Repeat 2


title: SU09A 2

description:
array no.: 2
array position: 8

source_name: Patient Number SU09 Nephrectomy Biological Repeat 1


title: PBMC-tolerant-15

source_name: PBMC, tolerant HCT patient

tag: cell type

value: PBMC


title: SU04A 1

description:
array no.: 1
array position: 11

source_name: Patient Number SU04 Nephrectomy Biological Repeat 1


title: SU09A 3

description:
array no.: 2
array position: 9

source_name: Patient Number SU09 Nephrectomy Biological Repeat 2


title: SU04A 3

description:
array no.: 2
array position: 3

source_name: Patient Number SU04 Nephrectomy Biological Repeat 2


title: SU04A 8

description:
array no.: 2
array position: 2

source_name: Patient Number SU04 Nephrectomy Biological Repeat 4


title: Patient Number SU25 Nephrectomy Biological Repeat 1

description: array number 534102


title: Patient Number SU26 Nephrectomy Biological Repeat 1

description: array number 561530


title: SU05 H 4/4

description:
array no.: 2
array position: 7

source_name: Patient Number SU05 Nephrectomy Biological Repeat 2


title: Patient Number SU25 Nephrectomy Biological Repeat 2

description: array number 534336

source_name: Input DNA from a pool of 5 LCL-derived DNAs


title: SU01F 1/3

description:
array no.: 1
array position: 8

source_name: Patient Number SU01 Nephrectomy Biological Repeat 3


title: SU01H 1/2

description:
array no.: 1
array position: 10

source_name: Patient Number SU01 Nephrectomy Biological Repeat 8


title: Patient Number SU23 Nephrectomy Biological Repeat 3

description: array number 534092


title: SU09A 5

description:
array no.: 2
array position: 10

source_name: Patient Number SU09 Nephrectomy Biological Repeat 3


title: SU01G 2/3

description:
array no.: 1
array position: 9

source_name: Patient Number SU01 Nephrectomy Biological Repeat 6


title: Patient Number SU23 Nephrectomy Biological Repeat 1

description: array number 534102


title: Patient Number SU22 Nephrectomy Biological Repeat 2

description: array number 561530


title: Patient Number SU26 Nephrectomy Biological Repeat 3

description: array number 561569


title: UHRR CTRL 10

description:
array no.: 2
array position: 1

source_name: Universal Human Reference RNA Control Array 10


title: Patient Number SU22 Nephrectomy Biological Repeat 3

description: array number 561569


title: SU05 G 2/5

description:
array no.: 2
array position: 6

source_name: Patient Number SU05 Nephrectomy Biological Repeat 1


title: Patient Number SU23 Nephrectomy Biological Repeat 2

description: array number 534336


title: Patient Number SU25 Nephrectomy Biological Repeat 3

description: array number 534092


title: Patient Number SU19 Nephrectomy Biological Repeat 1

description: array number 561530


title: Patient Number SU19 Nephrectomy Biological Repeat 2

description: array number 561530


title: Patient Number SU19 Nephrectomy Biological Repeat 3

description: array number 561569


title: Patient Number SU16 Nephrectomy Biological Repeat 3

description: array number 534338


title: UHRR CTRL 9

description:
array no.: 1
array position: 1

source_name: Universal Human Reference RNA Control Array 09


title: SU01F 2/3

description:
array no.: 1
array position: 6

source_name: Patient Number SU01 Nephrectomy Biological Repeat 4


title: SU01E 4/4

description:
array no.: 1
array position: 7

source_name: Patient Number SU01 Nephrectomy Biological Repeat 2


title: SU01G 3/3

description:
array no.: 1
array position: 5

source_name: Patient Number SU01 Nephrectomy Biological Repeat 7


title: SU01G 1/3

description:
array no.: 1
array position: 4

source_name: Patient Number SU01 Nephrectomy Biological Repeat 5


title: Patient Number SU16 Nephrectomy Biological Repeat 2

description: array number 534336


title: SU01E 1/4

description:
array no.: 1
array position: 3

source_name: Patient Number SU01 Nephrectomy Biological Repeat 1


title: RN000184 C

description:
array no.: 15
array position: 9

source_name: Patient Number RN000184 Nephrectomy Biological Repeat 3


title: Patient Number SU22 Nephrectomy Biological Repeat 1

description: array number 561530


title: RN000173 D

description:
array no.: 15
array position: 6

source_name: Patient Number RN000173 Nephrectomy Biological Repeat 3


title: Patient Number SU13 Nephrectomy Biological Repeat 3

description: array number 534338


title: Patient Number SU09 Nephrectomy Biological Repeat 3

description: array number 534338


title: Patient Number SU13 Nephrectomy Biological Repeat 2

description: array number 534336


title: RN000184 B

description:
array no.: 15
array position: 8

source_name: Patient Number RN000184 Nephrectomy Biological Repeat 2


title: RN000184 A

description:
array no.: 15
array position: 7

source_name: Patient Number RN000184 Nephrectomy Biological Repeat 1


title: UHRR CTRL 8

description:
array no.: 16
array position: 1

source_name: Universal Human Reference RNA Control Array 08


title: RN000173 B

description:
array no.: 15
array position: 5

source_name: Patient Number RN000173 Nephrectomy Biological Repeat 2


title: RN000173 A

description:
array no.: 15
array position: 4

source_name: Patient Number RN000173 Nephrectomy Biological Repeat 1


title: Patient Number SU11 Nephrectomy Biological Repeat 3

description: array number 561530

source_name: Input DNA from a pool of 5 LCL-derived DNAs


title: Patient Number SU13 Nephrectomy Biological Repeat 1

description: array number 534102


title: UHRR CTRL 7

description:
array no.: 15
array position: 1

source_name: Universal Human Reference RNA Control Array 07


title: RN000160 C

description:
array no.: 14
array position: 12

source_name: Patient Number RN000160 Nephrectomy Biological Repeat 2


title: Patient Number SU11 Nephrectomy Biological Repeat 2

description: array number 561569


title: Patient Number SU16 Nephrectomy Biological Repeat 1

description: array number 534102


title: Patient Number SU11 Nephrectomy Biological Repeat 1

description: array number 561530


title: Patient Number SU06 Nephrectomy Biological Repeat 1

description: array number 534102


title: Patient Number SU09 Nephrectomy Biological Repeat 1

description: array number 534102


title: Patient Number SU09 Nephrectomy Biological Repeat 2

description: array number 534336


title: RN000160 B

description:
array no.: 14
array position: 11

source_name: Patient Number RN000160 Nephrectomy Biological Repeat 1


title: RN000147 A

description:
array no.: 14
array position: 9

source_name: Patient Number RN000147 Nephrectomy Biological Repeat 1


title: Patient Number SU06 Nephrectomy Biological Repeat 2

description: array number 534336


title: Patient Number SU06 Nephrectomy Biological Repeat 3

description: array number 534338


title: Patient Number SU05 Nephrectomy Biological Repeat 2

description: array number 534336


title: RN000086 A

description:
array no.: 14
array position: 5

source_name: Patient Number RN000086 Nephrectomy Biological Repeat 1


title: UHRR CTRL 6

description:
array no.: 14
array position: 1

source_name: Universal Human Reference RNA Control Array 06


title: RN000065 D

description:
array no.: 14
array position: 2

source_name: Patient Number RN000065 Nephrectomy Biological Repeat 3


title: Patient Number SU05 Nephrectomy Biological Repeat 3

description: array number 534092


title: RN000060 B

description:
array no.: 13
array position: 10

source_name: Patient Number RN000060 Nephrectomy Biological Repeat 1


title: Patient Number SU04 Nephrectomy Biological Repeat 1

description: array number 534102


title: RN000035 B

description:
array no.: 13
array position: 9

source_name: Patient Number RN000035 Nephrectomy Biological Repeat 2


title: Patient Number SU01 Nephrectomy Biological Repeat 2

description: array number 561569


title: Patient Number SU05 Nephrectomy Biological Repeat 1

description: array number 534102


title: Patient Number SU01 Nephrectomy Biological Repeat 3

description: array number 561530


title: RN000035 A

description:
array no.: 13
array position: 8

source_name: Patient Number RN000035 Nephrectomy Biological Repeat 1


title: RN000028 B

description:
array no.: 13
array position: 7

source_name: Patient Number RN000028 Nephrectomy Biological Repeat 2


title: RN000065 B

description:
array no.: 13
array position: 11

source_name: Patient Number RN000065 Nephrectomy Biological Repeat 1


title: Patient Number RN000193 Nephrectomy Biological Repeat 3

description: array number 561830

value: Untreated

value: FFPE


title: RN000065 C

description:
array no.: 13
array position: 12

source_name: Patient Number RN000065 Nephrectomy Biological Repeat 2

value: clear cell renal cell carcinoma


title: Patient Number SU01 Nephrectomy Biological Repeat 1

description: array number 561530


title: RN000095 B

description:
array no.: 14
array position: 8

source_name: Patient Number RN000091 Nephrectomy Biological Repeat 1


title: RN000028 A

description:
array no.: 13
array position: 6

source_name: Patient Number RN000028 Nephrectomy Biological Repeat 1


title: RN000027 B

description:
array no.: 13
array position: 5

source_name: Patient Number RN000027 Nephrectomy Biological Repeat 2


title: Patient Number RN000193 Nephrectomy Biological Repeat 2

description: array number 561864

source_name: Input DNA from a pool of 5 LCL-derived DNAs


title: RN000027 A

description:
array no.: 13
array position: 4

source_name: Patient Number RN000027 Nephrectomy Biological Repeat 1


title: RN000026A

description:
array no.: 13
array position: 2

source_name: Patient Number RN000026 Nephrectomy Biological Repeat 2


title: Patient Number RN000184 Nephrectomy Biological Repeat 2

description: array number 561830


title: RN000026 B

description:
array no.: 13
array position: 3

source_name: Patient Number RN000026 Nephrectomy Biological Repeat 1


title: Patient Number RN000184 Nephrectomy Biological Repeat 1

description: array number 561830


title: Patient Number RN000184 Nephrectomy Biological Repeat 4

description: array number 561569


title: Patient Number RN000193 Nephrectomy Biological Repeat 1

description: array number 561864


title: Patient Number SU04 Nephrectomy Biological Repeat 3

description: array number 534092


title: Patient Number RN000173 Nephrectomy Biological Repeat 3

description: array number 561495


title: Patient Number SU04 Nephrectomy Biological Repeat 2

description: array number 534336


title: Patient Number RN000184 Nephrectomy Biological Repeat 3

description: array number 561569


title: Patient Number RN000173 Nephrectomy Biological Repeat 2

description: array number 561864


title: Patient Number RN000173 Nephrectomy Biological Repeat 1

description: array number 561864


title: UHRR CTRL 5

description:
array no.: 13
array position: 1

source_name: Universal Human Reference RNA Control Array 05


title: RN000010 B

description:
array no.: 12
array position: 12

source_name: Patient Number RN000010 Nephrectomy Biological Repeat 2


title: BB100486 A

description:
array no.: 12
array position: 4

source_name: Patient Number BB100486 Nephrectomy Biological Repeat 1


title: RN000010 A

description:
array no.: 12
array position: 11

source_name: Patient Number RN000010 Nephrectomy Biological Repeat 1


title: RN000006 A

description:
array no.: 12
array position: 9

source_name: Patient Number RN000006 Nephrectomy Biological Repeat 1


title: RN000003 C

description:
array no.: 12
array position: 8

source_name: Patient Number RN000003 Nephrectomy Biological Repeat 2


title: BB100486 B

description:
array no.: 12
array position: 5

source_name: Patient Number BB100486 Nephrectomy Biological Repeat 2


title: Patient Number RN000160 Nephrectomy Biological Repeat 3

description: array number 561495


title: Patient Number RN000147 Nephrectomy Biological Repeat 1

description: array number 561523


title: RN000006 B

description:
array no.: 12
array position: 10

source_name: Patient Number RN000006 Nephrectomy Biological Repeat 2


title: UHRR CTRL 4

description:
array no.: 12
array position: 1

source_name: Universal Human Reference RNA Control Array 04


title: Patient Number RN000160 Nephrectomy Biological Repeat 2

description: array number 561864


title: Patient Number RN000147 Nephrectomy Biological Repeat 4

description: array number 561830


title: BB100333 B

description:
array no.: 10
array position: 12

source_name: Patient Number BB100333 Nephrectomy Biological Repeat 2


title: Patient Number RN000147 Nephrectomy Biological Repeat 2

description: array number 561524


title: RN000003 B

description:
array no.: 12
array position: 7

source_name: Patient Number RN000003 Nephrectomy Biological Repeat 1


title: 12 BB100333 A

description:
array no.: 10
array position: 11

source_name: Patient Number BB100333 Nephrectomy Biological Repeat 1


title: Patient Number RN000147 Nephrectomy Biological Repeat 3

description: array number 561830


title: BB100333 E

description:
array no.: 12
array position: 3

source_name: Patient Number BB100333 Nephrectomy Biological Repeat 3


title: 11 BB100322 E

description:
array no.: 10
array position: 10

source_name: Patient Number BB100322 Nephrectomy Biological Repeat 1


title: Patient Number RN000095 Nephrectomy Biological Repeat 3

description: array number 561830

source_name: Input DNA from a pool of 5 LCL-derived DNAs


title: Patient Number RN000086 Nephrectomy Biological Repeat 1

description: array number 561523


title: Patient Number RN000065 Nephrectomy Biological Repeat 3

description: array number 561830


title: Patient Number RN000086 Nephrectomy Biological Repeat 2

description: array number 561523


title: Patient Number RN000095 Nephrectomy Biological Repeat 2

description: array number 561523


title: Patient Number RN000160 Nephrectomy Biological Repeat 1

description: array number 561864


title: Patient Number RN000095 Nephrectomy Biological Repeat 1

description: array number 561523


title: Patient Number RN000086 Nephrectomy Biological Repeat 3

description: array number 561830


title: 9 BB100322 B

description:
array no.: 10
array position: 8

source_name: Patient Number BB100322 Nephrectomy Biological Repeat 3


title: Patient Number RN000065 Nephrectomy Biological Repeat 2

description: array number 561523


title: BB100186 B

description:
array no.: 10
array position: 5

source_name: Patient Number BB100186 Nephrectomy Biological Repeat 1


title: 8 BB100322 A

description:
array no.: 10
array position: 7

source_name: Patient Number BB100322 Nephrectomy Biological Repeat 2


title: Patient Number RN000065 Nephrectomy Biological Repeat 1

description: array number 561523


title: Patient Number RN000060 Nephrectomy Biological Repeat 3

description: array number 561830


title: Patient Number RN000060 Nephrectomy Biological Repeat 2

description: array number 561523


title: BB90363 F

description:
array no.: 10
array position: 2

source_name: Patient Number BB090363 Nephrectomy Biological Repeat 3


title: BB90363 B

description:
array no.: 10
array position: 12

source_name: Patient Number BB090363 Nephrectomy Biological Repeat 2


title: UHRR CTRL 3

description:
array no.: 10
array position: 1

source_name: Universal Human Reference RNA Control Array 03


title: Patient Number RN000028 Nephrectomy Biological Repeat 2

description: array number 472992


title: Patient Number RN000028 Nephrectomy Biological Repeat 4

description: array number 472939


title: Patient Number RN000028 Nephrectomy Biological Repeat 3

description: array number 472939


title: Patient Number RN000028 Nephrectomy Biological Repeat 5

description: array number 472992


title: BB100186A

description:
array no.: 10
array position: 4

source_name: Patient Number BB100186 Nephrectomy Biological Repeat 2


title: BB90363 A

description:
array no.: 10
array position: 11

source_name: Patient Number BB090363 Nephrectomy Biological Repeat 1


title: Patient Number RN000035 Nephrectomy Biological Repeat 2

description: array number 561523


title: Patient Number RN000035 Nephrectomy Biological Repeat 3

description: array number 561524


title: Patient Number RN000028 Nephrectomy Biological Repeat 1

description: array number 472939


title: BB90175 A

description:
array no.: 10
array position: 8

source_name: Patient Number BB090175 Nephrectomy Biological Repeat 1


title: Patient Number RN000035 Nephrectomy Biological Repeat 1

description: array number 561523


title: Patient Number RN000060 Nephrectomy Biological Repeat 1

description: array number 561523


title: BB90175 E

description:
array no.: 10
array position: 10

source_name: Patient Number BB090175 Nephrectomy Biological Repeat 3


title: BB90175 B

description:
array no.: 10
array position: 9

source_name: Patient Number BB090175 Nephrectomy Biological Repeat 2


title: Patient Number RN000010 Nephrectomy Biological Repeat 1

description: array number 472939


title: Patient Number RN000027 Nephrectomy Biological Repeat 3

description: array number 472939


title: Patient Number RN000027 Nephrectomy Biological Repeat 1

description: array number 472939


title: Patient Number RN000010 Nephrectomy Biological Repeat 2

description: array number 472939


title: Patient Number RN000006 Nephrectomy Biological Repeat 3

description: array number 472939


title: Patient Number RN000010 Nephrectomy Biological Repeat 3

description: array number 472939


title: BB70193 F

description:
array no.: 10
array position: 6

source_name: Patient Number BB070193 Nephrectomy Biological Repeat 2


title: Patient Number RN000006 Nephrectomy Biological Repeat 2

description: array number 472939


title: Patient Number RN000027 Nephrectomy Biological Repeat 2

description: array number 472939


title: Patient Number RN000010 Nephrectomy Biological Repeat 4

description: array number 472992


title: BB70193 B

description:
array no.: 10
array position: 5

source_name: Patient Number BB070193 Nephrectomy Biological Repeat 1


title: Patient Number RN000003 Nephrectomy Biological Repeat 2

description: array number 561495


title: Patient Number RN000006 Nephrectomy Biological Repeat 1

description: array number 472939


title: Patient Number RN000003 Nephrectomy Biological Repeat 1

description: array number 561495


title: UHRR CTRL 2

description:
array no.: 10
array position: 1

source_name: Universal Human Reference RNA Control Array 02


title: Patient Number BB100186 Nephrectomy Biological Repeat 1

description: array number 561864


title: SU48A 3/4

description:
array no.: 9
array position: 7

source_name: Patient Number SU48 Nephrectomy Biological Repeat 3

value: Yes


title: Patient Number BB090363 Nephrectomy Biological Repeat 1

description: array number 561495


title: Patient Number BB100333 Nephrectomy Biological Repeat 3

description: array number 561864


title: SU46C 5/8

description:
array no.: 9
array position: 2

source_name: Patient Number SU46 Nephrectomy Biological Repeat 4

value: kidney


title: Patient Number BB100486 Nephrectomy Biological Repeat 1

description: array number 561864

source_name: Input DNA from a pool of 5 LCL-derived DNAs


title: SU49A 2

description:
array no.: 9
array position: 11

source_name: Patient Number SU49 Nephrectomy Biological Repeat 1


title: SU48A 4/4

description:
array no.: 9
array position: 8

source_name: Patient Number SU48 Nephrectomy Biological Repeat 4


title: SU48A 2/4

description:
array no.: 9
array position: 6

source_name: Patient Number SU48 Nephrectomy Biological Repeat 2


title: SU48A 1/4

description:
array no.: 9
array position: 5

source_name: Patient Number SU48 Nephrectomy Biological Repeat 1


title: SU49A4 1/2

description:
array no.: 9
array position: 10

source_name: Patient Number SU49 Nephrectomy Biological Repeat 2


title: Patient Number BB100333 Nephrectomy Biological Repeat 1

description: array number 561864


title: Patient Number BB090175 Nephrectomy Biological Repeat 4

description: array number 561830


title: Patient Number BB100486 Nephrectomy Biological Repeat 3

description: array number 561495


title: Patient Number BB100186 Nephrectomy Biological Repeat 3

description: array number 561495


title: Mouse germ_cell, 8 month, Gfra1 negative, biological rep2

status: Public on May 24 2015

city: Shatin

first: Alfred

middle: Chun Shui

last: LUK

address: LKS Integrated Biomedical Sciences Building, Area 39, The Chinese University of Hong Kong, Shatin

department: School of Biomedical Sciences

country: Hong Kong

institute: The Chinese University of Hong Kong

description: Mouse 430 v2.0

hyb_protocol: Purified biotin-labelled cDNA was hybrided to the microarray gene for 16 hours at 45C with 60-r.p.m rotation on GeneChip Mouse Genome 430 ver2.0 Array. GeneChips were washed and stained in the Afymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner 3000 7G and the images were obtained by the Affymetrix GeneChip Operating Software (GCOS).

data_processing: Expression data were analyzed with Partek Genomic Suite 6.6.

source_name: Mouse germ cell, MACS with Gfra1 antibody

label_protocol: 30 ng total RNA from each sample was used in cDNA synthesis. cDNA was then amplified and labeled using the Ovation Biotin RNA Amplification and Labeling System, version 1.0 (NuGEN Technologies).

growth_protocol: C57BL/c mice were on a 12 h light-dark cycle in a pathogen-free animal facility.

extract_protocol: Total RNA from both Gfra1-positive and -negative cells was extracted with Rneasy Mini Kit (Qiagen) and treated with RNase-free DNase I (Qiagen) to remove genomic DNA.

treatment_protocol: Testes from mice at different ages were harvested, decapsulated. Isolated seminiferous tubules were enzymatic digested and mechanically dissociated to single cells, and undergo differential plating for 2 hours to eliminate Sertoli cells. The suspending cells were then treated by magnetic-assisted cell sorting (MACS) for Gfra1 marker.

tag: strain

tag: gender

value: male

tag: age

value: 8 months

tag: gfra1 status

value: negative


title: Patient Number BB090175 Nephrectomy Biological Repeat 2

description: array number 561524

value: Nephrectomy


title: Patient Number BB100486 Nephrectomy Biological Repeat 2

description: array number 561864


title: Patient Number BB090175 Nephrectomy Biological Repeat 3

description: array number 561495


title: UHRR CTRL 1

description:
array no.: 9
array position: 1

source_name: Universal Human Reference RNA Control Array 01

value: Universal Human Reference RNA


title: Patient Number BB100333 Nephrectomy Biological Repeat 2

description: array number 561495

value: Fresh Frozen


title: Patient Number BB070193 Nephrectomy Biological Repeat 1

description: array number 561524

value: Pool of LCL cell line DNA absent of chromosomal aberrations


title: Mouse germ_cell, 8 month, Gfra1 negative, biological rep1

description: Mouse 430 v2.0


title: Mouse germ_cell, 8 month, Gfra1 positive, biological rep1

description: Mouse 430 v2.0

value: positive


title: Patient Number BB070193 Nephrectomy Biological Repeat 2

description: array number 561524

value: M

value: No


title: Patient Number BB090363 Nephrectomy Biological Repeat 2

description: array number 561830

value: Input DNA from a pool of 5 LCL-derived DNAs


title: Patient Number BB070193 Nephrectomy Biological Repeat 3

description: array number 561495


title: Mouse germ_cell, 60 day, Gfra1 positive, biological rep2

description: Mouse 430 v2.0

value: 60 days


title: Mouse germ_cell, 21 day, Gfra1 negative, biological rep2

description: Mouse 430 v2.0

value: 21 days


title: Mouse_germ_cell, 6 day, Gfra1 positive, biological rep 2

description: Mouse 430 v2.0

value: 6 days


title: Mouse_germ_cell, 6 day, Gfra1 negative, biological rep1

description: Mouse 430 v2.0


title: Mouse_germ_cell, 21 day, Gfra1 negative, biological rep1

description: Mouse 430 v2.0


title: Mouse_germ_cell, 21 day, Gfra1 positive, biological rep1

description: Mouse 430 v2.0


title: Mouse germ_cell, 60 day, Gfra1 negative, biological rep2

description: Mouse 430 v2.0


title: Mouse_germ_cell, 21 day, Gfra1 positive, biological rep2

description: Mouse 430 v2.0


title: Mouse germ_cell, 60 day, Gfra1 positive, biological rep1

description: Mouse 430 v2.0


title: Mouse_germ_cell, 6 day, Gfra1 positive, biological rep 1

description: Mouse 430 v2.0


title: Mouse germ_cell, 60 day, Gfra1 negative, biological rep1

description: Mouse 430 v2.0


title: JFL3-5

status: Public on May 23 2015

city: Changsha

first: Jing

last: Cong

address: Yuelushan

country: China

institute: Central South University

description: GeoChip data for soil sample collected at about N18°, replicate 5

hyb_protocol: Then DNA was dried in a SpeedVac (ThermoSavant, Milford, MA, USA) at 45°C for 45 minutes.The dried DNA was rehydrated with 13 μL of DNase/RNase-free distilled water, mixed completely, and then centrifuged to collect all liquid at the bottom of the tube. A total of 42 μL of buffer, including 1×HI-RPM hybridization buffer,1×aCGH blocking agent, 0.05 μg/μL Cot-1 DNA, 10 pM universal standard, and 10% formamide (final concentrations), was added to each sample. After mixing completely, the solution was spun down and incubated at 95°C for 3 min, then incubated at 37°C for 30 min. The prepared samples were hybridized with GeoChip 5.0 arrays (60 K) at 67°C for 24 h with a rotation at 20 rpm in a hybridization oven.

scan_protocol: After purification, GeoChip microarrays were scanned by a NimbleGen MS200 scanner (Roche, Madison, WI, USA) at 633 nm using a laser power and photomultiplier tube (PMT) gain of 100% and 75%, respectively.

data_processing: The scanned images of hybridized GeoChips were converted and extracted using Agilent Feature Extraction 11.5 software (Agilent Technologies, Inc., CA, USA). Signal intensities were quantified and processed using the data analysis pipeline as previously described (He et al 2010). Then processed GeoChip data were analyzed using the following steps: (i) remove the poor quality spots, which were flagged as 1 or 3 by ImaGene or with a signal to noise ratio (SNR) of less than 2.0; (ii) normalize the signal intensity of each spot by dividing the signal intensity by the total intensity of the microarray followed by multiplying by a constant; (iii) transform the data to the natural logarithmic form; and (iv)  remove genes detected in at least two out of ten samples from the same site.

organism: Bacteria

source_name: Soil microbes along the latitudinal gradient

label_protocol: As previously described (Qingyun Yan et al 2013), DNA samples were labeled with the fluorescent dye Cy3 using a random priming method and purified using the QIA quick purification kit (Qiagen, Valencia, CA, USA) and then dried in a SpeedVac (Thermo Savant, NY, USA).

extract_protocol: Soil genomic DNA was extracted using a FastDNA spin kit for soil (MP Biomedical, Carlsbad, CA, USA) following the manufacturer’s instructions. To purify it, DNA extract was mixed with 2.5 volume of 100% ice cold ethanol and 0.1 volume of 3 M NaOAc (pH 5.2) prior to overnight incubation at -20°C. DNA was precipitated by centrifugation for 30 minutes at 13,000 x g. Then supernatant was decanted and washed with 1 ml of 70% ethanol. DNA was air-dried and dissolved in 50 µl of nuclease-free water. DNA quality and quantity were measured using NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies Inc., Wilmington, DE, USA) and with PicoGreen (Ahn et al 1996) using a FLUOstar Optima (BMG Labtech, Jena, Germany), respectively.

treatment_protocol: From August to November 2012, soil samples were collected from all of the plots. Ten soil cores at a depth of 0-10 cm were randomly taken from each plot and mixed thoroughly to generate a soil sample representing the plot. Soil samples were kept on ice when transporting to laboratory, and sieved with 2 mm mesh to remove roots and stones. Soil samples were preserved at -80°C before DNA extraction.

tag: different latitudes


title: JFL3-1

description: GeoChip data for soil sample collected at about N18°, replicate 1


title: JFL3-9

description: GeoChip data for soil sample collected at about N18°, replicate 9


title: JFL2-10

description: GeoChip data for soil sample collected at about N18°, replicate 10


title: JFL3-3

description: GeoChip data for soil sample collected at about N18°, replicate 3


title: JFL3-10


title: JFL2-9


title: JFL3-8

description: GeoChip data for soil sample collected at about N18°, replicate 8


title: Mouse_germ_cell, 6 day, Gfra1 negative, biological rep2

description: Mouse 430 v2.0


title: Patient Number BB100186 Nephrectomy Biological Repeat 2

description: array number 561569

value: Untreated

value: clear cell renal cell carcinoma


title: JFL3-7

description: GeoChip data for soil sample collected at about N18°, replicate 7


title: JFL3-4

description: GeoChip data for soil sample collected at about N18°, replicate 4


title: JFL2-3


title: JFL2-1


title: JFL1-6

description: GeoChip data for soil sample collected at about N18°, replicate 6


title: JFL3-6


title: JFL1-9


title: JFL2-6


title: JFL2-4


title: JFL2-2

description: GeoChip data for soil sample collected at about N18°, replicate 2


title: JFL2-5


title: JFL3-2


title: JFL2-8


title: JFL1-7


title: JFL2-7


title: JFL1-1


title: JFL1-8


title: DMS8

description: GeoChip data for soil sample collected at about N23°, replicate 8


title: DMS6

description: GeoChip data for soil sample collected at about N23°, replicate 6


title: DMS9

description: GeoChip data for soil sample collected at about N23°, replicate 9


title: JFL1-4


title: DMS10

description: GeoChip data for soil sample collected at about N23°, replicate 10


title: JFL1-5


title: DMS5

description: GeoChip data for soil sample collected at about N23°, replicate 5


title: DMS7

description: GeoChip data for soil sample collected at about N23°, replicate 7


title: JFL1-10


title: DMS3

description: GeoChip data for soil sample collected at about N23°, replicate 3


title: JFL1-2


title: JFL1-3


title: DMS4

description: GeoChip data for soil sample collected at about N23°, replicate 4


title: DYS8

description: GeoChip data for soil sample collected at about N24°, replicate 8


title: DYS9

description: GeoChip data for soil sample collected at about N24°, replicate 9


title: DMS1

description: GeoChip data for soil sample collected at about N23°, replicate 1


title: DYS6

description: GeoChip data for soil sample collected at about N24°, replicate 6


title: DMS2

description: GeoChip data for soil sample collected at about N23°, replicate 2


title: HP10

description: GeoChip data for soil sample collected at about N25°, replicate 10


title: HP9

description: GeoChip data for soil sample collected at about N25°, replicate 9


title: DYS3

description: GeoChip data for soil sample collected at about N24°, replicate 3


title: Patient Number BB090175 Nephrectomy Biological Repeat 1

description: array number 561524


title: HP1

description: GeoChip data for soil sample collected at about N25°, replicate 1


title: HP4

description: GeoChip data for soil sample collected at about N25°, replicate 4


title: HP8

description: GeoChip data for soil sample collected at about N25°, replicate 8


title: HP6

description: GeoChip data for soil sample collected at about N25°, replicate 6


title: HP5

description: GeoChip data for soil sample collected at about N25°, replicate 5


title: MES10


title: MES9


title: DYS2

description: GeoChip data for soil sample collected at about N24°, replicate 2


title: Mouse germ_cell, 8 month, Gfra1 positive, biological rep2

description: Mouse 430 v2.0


title: HP3

description: GeoChip data for soil sample collected at about N25°, replicate 3


title: MES6


title: DYS10

description: GeoChip data for soil sample collected at about N24°, replicate 10


title: DYS4

description: GeoChip data for soil sample collected at about N24°, replicate 4


title: HP7

description: GeoChip data for soil sample collected at about N25°, replicate 7


title: MES2

description: GeoChip data for soil sample collected at about N25°, replicate 2


title: DYS7

description: GeoChip data for soil sample collected at about N24°, replicate 7


title: MES7


title: HP2


title: HS8

description: GeoChip data for soil sample collected at about N26°, replicate 8


title: DYS5

description: GeoChip data for soil sample collected at about N24°, replicate 5


title: MES5


title: HS10

description: GeoChip data for soil sample collected at about N26°, replicate 10


title: HS7

description: GeoChip data for soil sample collected at about N26°, replicate 7


title: HS6

description: GeoChip data for soil sample collected at about N26°, replicate 6


title: HS4

description: GeoChip data for soil sample collected at about N26°, replicate 4


title: HS2

description: GeoChip data for soil sample collected at about N26°, replicate 2


title: HS3

description: GeoChip data for soil sample collected at about N26°, replicate 3


title: HS9

description: GeoChip data for soil sample collected at about N26°, replicate 9


title: HS5

description: GeoChip data for soil sample collected at about N26°, replicate 5


title: MES8

description: GeoChip data for soil sample collected at about N25°, replicate 8


title: FJS8

description: GeoChip data for soil sample collected at about N27°, replicate 8


title: FJS2

description: GeoChip data for soil sample collected at about N27°, replicate 2


title: FJS6

description: GeoChip data for soil sample collected at about N27°, replicate 6


title: FJS9

description: GeoChip data for soil sample collected at about N27°, replicate 9


title: MES4

description: GeoChip data for soil sample collected at about N25°, replicate 4


title: FJS10

description: GeoChip data for soil sample collected at about N27°, replicate 10


title: FJS7

description: GeoChip data for soil sample collected at about N27°, replicate 7


title: FJS3

description: GeoChip data for soil sample collected at about N27°, replicate 3


title: MES1

description: GeoChip data for soil sample collected at about N25°, replicate 1


title: FJS4

description: GeoChip data for soil sample collected at about N27°, replicate 4


title: FJS5

description: GeoChip data for soil sample collected at about N27°, replicate 5


title: GWJ10

description: GeoChip data for soil sample collected at about N28°, replicate 10


title: GWJ4

description: GeoChip data for soil sample collected at about N28°, replicate 4


title: GWJ9

description: GeoChip data for soil sample collected at about N28°, replicate 9


title: GWJ8

description: GeoChip data for soil sample collected at about N28°, replicate 8


title: FJS1

description: GeoChip data for soil sample collected at about N27°, replicate 1


title: GWJ3

description: GeoChip data for soil sample collected at about N28°, replicate 3


title: GWJ6

description: GeoChip data for soil sample collected at about N28°, replicate 6


title: HS1

description: GeoChip data for soil sample collected at about N26°, replicate 1


title: BYS9


title: BYS10


title: GWJ7

description: GeoChip data for soil sample collected at about N28°, replicate 7


title: GWJ1

description: GeoChip data for soil sample collected at about N28°, replicate 1


title: BYS8


title: GWJ5

description: GeoChip data for soil sample collected at about N28°, replicate 5


title: MYH10


title: BYS2

description: GeoChip data for soil sample collected at about N28°, replicate 2


title: BYS7


title: BYS3


title: BYS1


title: BYS4


title: MYH5


title: MYH6


title: MYH4


title: MYH7


title: BDGS9

description: GeoChip data for soil sample collected at about N29°, replicate 9


title: MYH3


title: MYH1


title: BDGS4

description: GeoChip data for soil sample collected at about N29°, replicate 4


title: GWJ2


title: BDGS5

description: GeoChip data for soil sample collected at about N29°, replicate 5


title: BDGS7

description: GeoChip data for soil sample collected at about N29°, replicate 7


title: BDGS3

description: GeoChip data for soil sample collected at about N29°, replicate 3


title: BDGS8

description: GeoChip data for soil sample collected at about N29°, replicate 8


title: BDGS6

description: GeoChip data for soil sample collected at about N29°, replicate 6


title: BDGS2

description: GeoChip data for soil sample collected at about N29°, replicate 2


title: MYH2


title: BDGS10

description: GeoChip data for soil sample collected at about N29°, replicate 10


title: MYH9

description: GeoChip data for soil sample collected at about N28°, replicate 9


title: BYS5


title: HPS8

description: GeoChip data for soil sample collected at about N30°, replicate 8


title: HPS10

description: GeoChip data for soil sample collected at about N30°, replicate 10


title: HPS3

description: GeoChip data for soil sample collected at about N30°, replicate 3


title: HPS4

description: GeoChip data for soil sample collected at about N30°, replicate 4


title: HPS1

description: GeoChip data for soil sample collected at about N30°, replicate 1


title: HPS5

description: GeoChip data for soil sample collected at about N30°, replicate 5


title: HPS2

description: GeoChip data for soil sample collected at about N30°, replicate 2


title: HPS6

description: GeoChip data for soil sample collected at about N30°, replicate 6


title: HPS9

description: GeoChip data for soil sample collected at about N30°, replicate 9


title: MLZ10


title: MLZ9


title: MLZ5


title: HPS7

description: GeoChip data for soil sample collected at about N30°, replicate 7


title: MLZ7


title: MLZ2


title: MLZ6


title: BYS6

description: GeoChip data for soil sample collected at about N28°, replicate 6


title: HH8


title: MYH8

description: GeoChip data for soil sample collected at about N28°, replicate 8


title: MLZ4


title: DYS1

description: GeoChip data for soil sample collected at about N24°, replicate 1


title: HH10


title: MLZ3


title: HH6


title: HH4


title: MLZ1


title: HH7


title: MLZ8


title: HH3


title: BDGS1

description: GeoChip data for soil sample collected at about N29°, replicate 1


title: HH2


title: HH1


title: SNJ9

description: GeoChip data for soil sample collected at about N31°, replicate 9


title: HH9


title: SNJ8

description: GeoChip data for soil sample collected at about N31°, replicate 8


title: SNJ7

description: GeoChip data for soil sample collected at about N31°, replicate 7


title: SNJ3

description: GeoChip data for soil sample collected at about N31°, replicate 3


title: MES3

description: GeoChip data for soil sample collected at about N25°, replicate 3


title: DHY10

description: GeoChip data for soil sample collected at about N31°, replicate 10


title: SNJ6

description: GeoChip data for soil sample collected at about N31°, replicate 6


title: HH5


title: SNJ4

description: GeoChip data for soil sample collected at about N31°, replicate 4


title: SNJ10


title: SNJ2

description: GeoChip data for soil sample collected at about N31°, replicate 2


title: DHY9


title: DHY8


title: DHY7


title: DHY4


title: DHY6


title: SWD9

description: GeoChip data for soil sample collected at about N32°, replicate 9


title: SNJ1

description: GeoChip data for soil sample collected at about N31°, replicate 1


title: SWD4

description: GeoChip data for soil sample collected at about N32°, replicate 4


title: SWD3

description: GeoChip data for soil sample collected at about N32°, replicate 3


title: SWD8

description: GeoChip data for soil sample collected at about N32°, replicate 8


title: SWD5

description: GeoChip data for soil sample collected at about N32°, replicate 5


title: SWD7

description: GeoChip data for soil sample collected at about N32°, replicate 7


title: SWD1

description: GeoChip data for soil sample collected at about N32°, replicate 1


title: SWD10

description: GeoChip data for soil sample collected at about N32°, replicate 10


title: DHY3


title: DHY2


title: DHY5

description: GeoChip data for soil sample collected at about N31°, replicate 5


title: DHY1


title: SWD6

description: GeoChip data for soil sample collected at about N32°, replicate 6


title: BTM10

description: GeoChip data for soil sample collected at about N33°, replicate 10


title: BTM7

description: GeoChip data for soil sample collected at about N33°, replicate 7


title: BTM8

description: GeoChip data for soil sample collected at about N33°, replicate 8


title: BTM3

description: GeoChip data for soil sample collected at about N33°, replicate 3


title: BTM9

description: GeoChip data for soil sample collected at about N33°, replicate 9


title: BTM4

description: GeoChip data for soil sample collected at about N33°, replicate 4


title: BTM5

description: GeoChip data for soil sample collected at about N33°, replicate 5


title: SNJ5


title: BTM6

description: GeoChip data for soil sample collected at about N33°, replicate 6


title: SWD2

description: GeoChip data for soil sample collected at about N32°, replicate 2


title: NZ10


title: BTM2

description: GeoChip data for soil sample collected at about N33°, replicate 2


title: NZ8


title: BTM1

description: GeoChip data for soil sample collected at about N33°, replicate 1


title: NZ6


title: NZ9


title: NZ5


title: LYW9


title: NZ4


title: NZ1


title: NZ2


title: LYW8


title: LYW5


title: LYW10


title: NZ7


title: LYW4


title: NZ3


title: LYW2


title: XQL10

description: GeoChip data for soil sample collected at about N34°, replicate 10


title: LYW1


title: Tiep53_ZEB2tg_tg_6_thymus

city: Ghent

first: Kaat

last: Durinck

address: Corneel Heymanslaan 10

department: Biomolecular Medicine

country: Belgium

institute: Center for Medical Genetics

description: Gene expression p53 null ZEB2 transgenic homozygous

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x GEx Hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to the array for 17 hours at 65°C in a rotating  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).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner with SureScan High-Resolution Technology using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3µm, Dye channel is set to Green).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-105_Dec08 and Grid: 028005_D_F_20120201) to obtain background subtracted and spatially detrended Processed Signal intensities. Normalization was performed using the quantile normalization method in R.

source_name: Tie2, p53 null ZEB2 transgenic homozygous

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the One-Color Low Input Quick Amp Labling kit (Agilent) according to the manufacturer's instructions, followed by miRNeasy column purification (Qiagen).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was harvested with the miRNeasy mini kit (Qiagen) with Dnase treatment on-column.

value: mixed background, mainly CD1 outbred and C57BL/6

value: thymus


title: Tiep53_ZEB2tg_tg_32_thymus


title: LYW7


title: LYW3


title: XQL8

description: GeoChip data for soil sample collected at about N34°, replicate 8


title: XQL7

description: GeoChip data for soil sample collected at about N34°, replicate 7


title: Tiep53_ZEB2tg_wt_41_thymus

description: Gene expression p53 null ZEB2 transgenic heterozygous

source_name: Tie2, p53 null ZEB2 transgenic heterozygous


title: XQL9

description: GeoChip data for soil sample collected at about N34°, replicate 9


title: LYW6


title: XQL4

description: GeoChip data for soil sample collected at about N34°, replicate 4


title: XQL6

description: GeoChip data for soil sample collected at about N34°, replicate 6


title: XQL5

description: GeoChip data for soil sample collected at about N34°, replicate 5


title: XQL2

description: GeoChip data for soil sample collected at about N34°, replicate 2


title: XQL3

description: GeoChip data for soil sample collected at about N34°, replicate 3


title: Tiep53_10_thymus

description: Gene expression p53 null control tumor

source_name: Tie2,p53 null control


title: Tiep53_1919_thymus

description: Gene expression p53 null control tumor


title: XQL1

description: GeoChip data for soil sample collected at about N34°, replicate 1


title: Old naive CD4

city: Groningen

first: Anke

last: van den Berg

address: Hanzeplein 1

department: Department of Pathology and Medical Biology

country: Netherlands

institute: University Medical Center Groningen

description: microRNA expression

hyb_protocol: Microarray hybridization  was performed  according to manufacturer’s protocol (Agilent Technologies, Santa Clara, California, USA)

scan_protocol: Microarray data analysis was performed using Agilent data extraction software on the Agilent microarray scanner (G2565BA)

data_processing: For data analysis, array spot intensities were log2 transformed, background corrected with normalization using a 90th percentile shift using GeneSpring software (v.11.5.1)

label_protocol: Microarray labeling  was performed  according to manufacturer’s protocol (Agilent Technologies, Santa Clara, California, USA)

extract_protocol: Total RNA was extracted using the miRNeasy Mini Kit (Qiagen, Venlo, The Netherlands) following the manufacturer’s instructions

value: Whole blood

value: T cells

tag: cell markers


title: Young memory CD8

description: microRNA expression


title: MH10

description: GeoChip data for soil sample collected at about N35°, replicate 10


title: Old naive CD8

description: microRNA expression


title: MH9

description: GeoChip data for soil sample collected at about N35°, replicate 9


title: Young memory CD4

description: microRNA expression


title: Old memory CD4

description: microRNA expression


title: Old memory CD8

description: microRNA expression


title: MH8

description: GeoChip data for soil sample collected at about N35°, replicate 8


title: Young naive CD8

description: microRNA expression


title: MH7

description: GeoChip data for soil sample collected at about N35°, replicate 7


title: Young naive CD4

description: microRNA expression


title: MH3

description: GeoChip data for soil sample collected at about N35°, replicate 3


title: MH6

description: GeoChip data for soil sample collected at about N35°, replicate 6


title: MH4

description: GeoChip data for soil sample collected at about N35°, replicate 4


title: MH2

description: GeoChip data for soil sample collected at about N35°, replicate 2


title: LS9


title: LS10


title: LS6


title: MH5

description: GeoChip data for soil sample collected at about N35°, replicate 5


title: MH1

description: GeoChip data for soil sample collected at about N35°, replicate 1


title: LS2


title: LS7


title: LS1


title: LS3


title: LS5


title: LS4


title: LS8


title: HLS9


title: HLS5


title: HLS4


title: HLS2


title: HLS1


title: HLS7


title: HLS6


title: WLS5

description: GeoChip data for soil sample collected at about N36°, replicate 5


title: WLS6

description: GeoChip data for soil sample collected at about N36°, replicate 6


title: WLS7

description: GeoChip data for soil sample collected at about N36°, replicate 7


title: WLS8

description: GeoChip data for soil sample collected at about N36°, replicate 8


title: WLS3

description: GeoChip data for soil sample collected at about N36°, replicate 3


title: WLS2

description: GeoChip data for soil sample collected at about N36°, replicate 2


title: PQG9

description: GeoChip data for soil sample collected at about N37°, replicate 9


title: WLS1

description: GeoChip data for soil sample collected at about N36°, replicate 1


title: HLS3


title: WLS10

description: GeoChip data for soil sample collected at about N36°, replicate 10


title: PQG2

description: GeoChip data for soil sample collected at about N37°, replicate 2


title: WLS4

description: GeoChip data for soil sample collected at about N36°, replicate 4


title: PQG6

description: GeoChip data for soil sample collected at about N37°, replicate 6


title: PQG4

description: GeoChip data for soil sample collected at about N37°, replicate 4


title: WLS9

description: GeoChip data for soil sample collected at about N36°, replicate 9


title: PQG8

description: GeoChip data for soil sample collected at about N37°, replicate 8


title: PQG1

description: GeoChip data for soil sample collected at about N37°, replicate 1


title: LYS10

description: GeoChip data for soil sample collected at about N38°, replicate 10


title: PQG3

description: GeoChip data for soil sample collected at about N37°, replicate 3


title: LYS9

description: GeoChip data for soil sample collected at about N38°, replicate 9


title: LYS6

description: GeoChip data for soil sample collected at about N38°, replicate 6


title: LYS8

description: GeoChip data for soil sample collected at about N38°, replicate 8


title: HLS8

description: GeoChip data for soil sample collected at about N35°, replicate 8


title: PQG5

description: GeoChip data for soil sample collected at about N37°, replicate 5


title: LYS7

description: GeoChip data for soil sample collected at about N38°, replicate 7


title: PQG10

description: GeoChip data for soil sample collected at about N37°, replicate 10


title: LYS2

description: GeoChip data for soil sample collected at about N38°, replicate 2


title: LYS4

description: GeoChip data for soil sample collected at about N38°, replicate 4


title: DQS10

description: GeoChip data for soil sample collected at about N40°, replicate 10


title: LYS3

description: GeoChip data for soil sample collected at about N38°, replicate 3


title: LYS1

description: GeoChip data for soil sample collected at about N38°, replicate 1


title: DQS9

description: GeoChip data for soil sample collected at about N40°, replicate 9


title: LYS5

description: GeoChip data for soil sample collected at about N38°, replicate 5


title: PQG7

description: GeoChip data for soil sample collected at about N37°, replicate 7


title: DQS7

description: GeoChip data for soil sample collected at about N40°, replicate 7