title: s.c.adiposetissue_subject355


title: s.c.adiposetissue_subject354

status: Public on Jan 22 2013

type: RNA

city: Little Rock

first: Intawat

last: Nookaew

address: 4301 W Markham St

department: Department of Biomedical Informatics

country: USA

institute: University of Arkansas for Medical Sciences

description: Gene expression data from white adipose tissue.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Human U133 Plus 2.0 arrays. Arrays were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: After hybridization, the arrays were scanned using an Affymetrix confocal laser scanner (GeneArray scanner GCS3000) and visualized using GeneChip Operating Software (GCOS, Affymetrix).

data_processing: The raw expression signals were preprocessed following the method of Probe Logarithmic Intensity Error (PLIER) based on perfect match only (pm-only) calculation (Affymetrix). The robust quantile method was applied to get normalized expression values.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: subcutaneous adipose tissue

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA was prepared using the RNeasy Lipid Tissue Kit (Qiagen).

treatment_protocol: Tissues were snap frozen in liquid nitrogen.

tag: tissue

value: subcutaneous adipose tissue

tag: Sex

value: male


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value: female


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title: s.c.adiposetissue_subject161


title: s.c.adiposetissue_subject148


title: s.c.adiposetissue_subject144


title: s.c.adiposetissue_subject145


title: s.c.adiposetissue_subject142


title: s.c.adiposetissue_subject140


title: s.c.adiposetissue_subject146


title: s.c.adiposetissue_subject139


title: s.c.adiposetissue_subject138


title: s.c.adiposetissue_subject143


title: CBC, 9727d

city: Moscow

first: Pavel

last: Mazin

address: Skolkovo Innovation Center, Building 3

department: Biomed

country: Russia

institute: Skolkovo Institute of Science and Technology

description: cerebellum, pooled

hyb_protocol: Affymetrix Human Exon 1.0 ST arrays

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: All microarray probes were aligned to the human reference genome (hg19) using the Bowtie software. Only probes uniquely matching the genomes were included in the analysis. Probe intensities were exacted using the R package “affy”. Probe intensities were background corrected and quantile normalized. Probes with intensity < 100 were excluded from analyses. To calculate the expression level of gene segments, we collected the probes located in each segment. If more than half of the probe length was located within a segment, then the probe was assigned to this segment. In cases where a probe could be mapped to multiple segments, we gave priority to exonic segments. The expression levels of segments were summarized by the median polish function in the R package “affy”.

source_name: Dissected Human post-mortem cerebellum

label_protocol: Biotinylated cRNA were prepared from 2 microg. total RNA following standard Affymetrix protocols.

growth_protocol: Human samples were obtained from the NICHD Brain and Tissue Bank for Developmental Disorders at the University of Maryland, USA, the Netherlands Brain Bank, Amsterdam, Netherlands and the Chinese Brain Bank Center, Wuhan, China. All subjects were defined as normal by forensic pathologists at the corresponding brain bank. All subjects suffered sudden death with no prolonged agonal state.

extract_protocol: Total RNA was extracted from 100 mg of the same 12 pooled samples using Trizol reagent (Invitrogen) and purified with the QIAGEN® RNeasy MiniElute kit.

treatment_protocol: not applicable

tag: brain region

value: cerebellum

tag: age

value: 9727 days


title: CBC, 27338d

description: cerebellum, pooled


title: s.c.adiposetissue_subject141


title: s.c.adiposetissue_subject136


title: s.c.adiposetissue_subject137


title: s.c.adiposetissue_subject133


title: CBC, 6648d

description: cerebellum, pooled

value: 6648 days


title: s.c.adiposetissue_subject134


title: s.c.adiposetissue_subject132


title: s.c.adiposetissue_subject130


title: s.c.adiposetissue_subject131


title: s.c.adiposetissue_subject129


title: s.c.adiposetissue_subject135


title: PFC, 9727d

description: cerebellar cortex, pooled

source_name: Dissected Human post-mortem cerebellar cortex

value: cortex


title: PFC, 34237d

description: cerebellar cortex, pooled


title: CBC, 216d

description: cerebellum, pooled

value: 216 days


title: s.c.adiposetissue_subject171


title: PFC, 216d

description: cerebellar cortex, pooled


title: s.c.adiposetissue_subject127


title: PFC, 6648d

description: cerebellar cortex, pooled


title: CBC, 15d

description: cerebellum, pooled

value: 15 days


title: s.c.adiposetissue_subject126


title: s.c.adiposetissue_subject121


title: s.c.adiposetissue_subject125


title: s.c.adiposetissue_subject124


title: s.c.adiposetissue_subject123


title: PFC, 15d

description: cerebellar cortex, pooled


title: CBC, 34237d

description: cerebellum, pooled


title: s.c.adiposetissue_subject122


title: s.c.adiposetissue_subject120


title: s.c.adiposetissue_subject128


title: s.c.adiposetissue_subject119


title: s.c.adiposetissue_w47

description: gene expression data from subcutaneous adipose tissue

hyb_protocol: Following fragmentation,cRNA were hybridized for 16 hr at 45C on Human U133A arrays. Arrays were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: After hybridisation (according to the Minimum Information About a Microarray Experiment guideline, the arrays were scanned using an Affymetrix confocal laser scanner (Affymetrix, GeneArray scanner GCS3000) and visualised using GeneChip Operating Software (GCOS, Affymetrix).

data_processing: The raw expression signals were preprocessed following the method of Probe Logarithmic Intensity Error (PLIER) based on perfect match only (pm-only) calculation (Affymetrix).The robust quantile method was applied to get normalized expression values

label: Biotin

source_name: After diet

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

extract_protocol: RNA was isolated as described by Chomczynski and Sacchi (1987, Anal Biochem) and further purified with RNeasy clean-up columns (QIAGEN, Hilden, Germany).

treatment_protocol: Tissues were snap frozen in liquid nitrogen

tag: patient

value: female 6

tag: diet

value: After diet


title: s.c.adiposetissue_subject114


title: s.c.adiposetissue_subject118


title: s.c.adiposetissue_w45

value: male 18


title: s.c.adiposetissue_subject112


title: s.c.adiposetissue_subject113


title: s.c.adiposetissue_w42

source_name: Before diet

value: male 17

value: Before diet


title: s.c.adiposetissue_subject111


title: s.c.adiposetissue_subject115


title: s.c.adiposetissue_w43


title: s.c.adiposetissue_w46


title: s.c.adiposetissue_w44


title: s.c.adiposetissue_subject110


title: s.c.adiposetissue_subject117


title: s.c.adiposetissue_subject116


title: s.c.adiposetissue_w41

value: male 16


title: s.c.adiposetissue_w40


title: s.c.adiposetissue_subject109


title: PFC, 27338d

description: cerebellar cortex, pooled


title: s.c.adiposetissue_w39

value: male 15


title: s.c.adiposetissue_subject108


title: s.c.adiposetissue_subject107


title: s.c.adiposetissue_w34

value: male 13


title: s.c.adiposetissue_subject103

value: subcutaneous adipose tissue


title: s.c.adiposetissue_subject104

value: male


title: s.c.adiposetissue_subject106


title: s.c.adiposetissue_w33

value: male 12


title: s.c.adiposetissue_w36

value: male 14


title: s.c.adiposetissue_w37


title: s.c.adiposetissue_subject101

value: female


title: s.c.adiposetissue_subject105


title: s.c.adiposetissue_w38


title: s.c.adiposetissue_subject97


title: s.c.adiposetissue_subject102


title: s.c.adiposetissue_w27

value: male 9


title: s.c.adiposetissue_subject100


title: s.c.adiposetissue_w30

value: male 11


title: s.c.adiposetissue_w31


title: s.c.adiposetissue_w32


title: s.c.adiposetissue_w26


title: s.c.adiposetissue_subject99


title: s.c.adiposetissue_w25

value: male 8


title: s.c.adiposetissue_subject96


title: s.c.adiposetissue_subject98


title: s.c.adiposetissue_w24


title: s.c.adiposetissue_subject95


title: s.c.adiposetissue_w28

value: male 10


title: s.c.adiposetissue_subject94


title: s.c.adiposetissue_w29


title: s.c.adiposetissue_w22

value: male 7


title: s.c.adiposetissue_w23

value: After diet


title: s.c.adiposetissue_subject92


title: s.c.adiposetissue_subject93


title: s.c.adiposetissue_subject91


title: s.c.adiposetissue_subject90


title: s.c.adiposetissue_subject89


title: s.c.adiposetissue_w21

value: male 6


title: s.c.adiposetissue_w18

value: male 5


title: s.c.adiposetissue_subject85


title: s.c.adiposetissue_w16

value: female 5


title: s.c.adiposetissue_w14

value: Before diet


title: s.c.adiposetissue_subject87


title: s.c.adiposetissue_w20


title: s.c.adiposetissue_w17

value: male 4


title: s.c.adiposetissue_w11

value: male 2


title: s.c.adiposetissue_subject88

value: subcutaneous adipose tissue


title: s.c.adiposetissue_w13

value: male 3

value: male


title: s.c.adiposetissue_w12


title: s.c.adiposetissue_w19


title: s.c.adiposetissue_subject86


title: s.c.adiposetissue_subject83


title: s.c.adiposetissue_w10


title: s.c.adiposetissue_subject80


title: s.c.adiposetissue_subject76


title: s.c.adiposetissue_w7

value: female 4


title: s.c.adiposetissue_subject84

value: female


title: s.c.adiposetissue_subject79


title: s.c.adiposetissue_subject82


title: s.c.adiposetissue_subject77


title: s.c.adiposetissue_subject78


title: s.c.adiposetissue_subject81


title: s.c.adiposetissue_w9

value: male 1


title: s.c.adiposetissue_w8


title: s.c.adiposetissue_w15


title: s.c.adiposetissue_w6


title: s.c.adiposetissue_w4

value: female 3


title: s.c.adiposetissue_w5


title: s.c.adiposetissue_w3

value: female 2


title: s.c.adiposetissue_subject75


title: s.c.adiposetissue_subject74


title: s.c.adiposetissue_subject71


title: s.c.adiposetissue_subject72


title: s.c.adiposetissue_subject70


title: s.c.adiposetissue_subject73


title: s.c.adiposetissue_w0

value: female 1


title: s.c.adiposetissue_w1


title: s.c.adiposetissue_subject68


title: s.c.adiposetissue_subject66


title: s.c.adiposetissue_subject69


title: s.c.adiposetissue_subject65


title: s.c.adiposetissue_subject59


title: s.c.adiposetissue_subject63


title: s.c.adiposetissue_subject67


title: s.c.adiposetissue_subject62


title: s.c.adiposetissue_subject61


title: s.c.adiposetissue_subject64


title: Adult sample 2

city: Groningen

first: Floris

last: Foijer

address: Antonius Deusinglaan 1

department: European Institute for the Biology of Ageing

country: Netherlands

institute: University Medical Center Groningen

hyb_protocol: RNA was hybridyzed using Illumina standard protocols

scan_protocol: Slides were scanned using Illumina standard protocols

data_processing: Data were quantile normalized following scanning and analyzed using Bioconductor lumi and limma packages.

organism: Mus musculus

source_name: Adult

label_protocol: Biotinylated cRNA was hybridized to llumina Sentrix Bead Chips and next labeled with streptavidin-conjugated Cy3 (Amersham) according to manufacturer’s protocol.

growth_protocol: Mice were sacrificed at indicated time points

extract_protocol: Tissue was homogenized using bead-homogenization in Qiagen RNA-easy buffer 1. RNA was then purified using RNA-easy columns using manufacturer's protocols

treatment_protocol: Epidermis was separated from dermis by peeling following overnight trypsin at 4 degrees

value: Epidermis

tag: genotype

value: Mad2f/f; K14Cre+

tag: type

value: Experiment

tag: strain

value: B6-129Sv mixed

tag: add. info

value: Nude


title: s.c.adiposetissue_w35

value: male 13

value: After diet


title: s.c.adiposetissue_w2

value: Before diet


title: Postnatal day 20 sample 2

source_name: Postnatal day 20


title: colon Dox -

city: Tokyo

first: Yasuhiro

last: Yamada

address: 7-3-1 Hongo, Bunkyo-ku

department: Department of Molecular Pathology

country: Japan

institute: University of Tokyo

hyb_protocol: Twenty microgram of labeled cRNA was fragmented, and hybridized to GeneChips.

scan_protocol: The arrays were stained and scanned by GeneChip® Scanner 3000 according to the protocol from Affymetrix.

data_processing: The data were processed using GeneChip Operating Software. GCRMA normalization performed in GeneSpring.

source_name: Mouse colonic epithelium without β-catenin induction

label_protocol: Biotin-labeled cRNA was prepared using a MessageAmp™ II-Biotin Enhanced kit (Ambion).

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

tag: gender

value: Male

tag: tissue type

value: colon

tag: genotype/variation

value: doxycycline-inducible β-catenin

tag: cell type

value: Wnt-non-activated colonic crypt cells


title: Adult sample 3

value: Mad2f/f; p53f/+; K14Cre+


title: s.c.adiposetissue_subject60

value: subcutaneous adipose tissue

value: female


title: s.c.adiposetissue_subject58


title: s.c.adiposetissue_subject56


title: Adult sample 1


title: Postnatal day 20 sample 4

value: Cre-Neg

value: Control

value: No phenotype


title: s.c.adiposetissue_subject57


title: s.c.adiposetissue_subject55

value: male


title: s.c.adiposetissue_subject54


title: Postnatal day 20 sample 3

value: Epidermis


title: Postnatal day 20 sample 1

value: Mad2f/f; K14Cre+

value: Experiment

value: B6-129Sv mixed


title: Postnatal day 20 sample 5


title: colon Dox +

source_name: Mouse colonic epithelium with β-catenin induction

value: Wnt-activated colonic crypt cells


title: s.c.adiposetissue_subject52


title: s.c.adiposetissue_subject53


title: Postnatal day 13 sample 3

source_name: Postnatal day 13


title: Postnatal day 13 sample 4


title: Postnatal day 13 sample 1

value: Nude


title: H2B GFP colon High

source_name: Non-proliferating cells in normal mouse colon

value: Male

value: non-proliferating colonic crypt cells


title: s.c.adiposetissue_subject50


title: Postnatal day 6 sample 4

source_name: Postnatal day 6


title: s.c.adiposetissue_subject51


title: L9_AIL_rep8

city: The University of Sydney

first: Jerry

last: Wei

state: NSW

address: B19  RMC Gunn

department: Facuulty of Veterinary Science

country: Australia

institute: University of Sydney

description:
peak-lactation
AQ3_L9

hyb_protocol: Hybridization was conducted as per Affymetrix instructions (processed in the Australian Genome Research Facility Ltd.)

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 7G System as per Affymetrix instructions (processed in the Australian Genome Research Facility Ltd.)

data_processing: Row data (.CEL files) were normalized using Robust Multichip Average (RMA) method incor and futher integration of microarray data using the RMA++ package implemented in the R program.

source_name: AIL mouse at Day 9 of lactation

label_protocol: Biotinylated cRNA was processed following the standard Affymetrix protocol from 5 ug total RNA (processed in the Australian Genome Research Facility Ltd.).

growth_protocol: Mammary gland samples were collected from the CBA/CaH and QSi5 mice at pregnancy day 12 (P12), and CBA/CaH, Advanced Intercross Line (AIL) and QSi5 mice at lactation day 9 (L9)

extract_protocol: Total RNA was extrected using the Qiagene Rneasy Mini kit instruction as per manufacturer's instruction

treatment_protocol: Mammary glands were immediately frozen in liquid nitrogen upon collection

value: Advance Intercross Line

value: mammary gland

tag: Stage

value: lactation day 9


title: H2B GFP colon Low

source_name: Proliferating cells in normal mouse colon

value: colon

value: proliferating colonic crypt cells


title: Postnatal day 6 sample 2


title: s.c.adiposetissue_subject47

value: subcutaneous adipose tissue


title: Postnatal day 6 sample 3

value: Cre-Neg

value: Control


title: s.c.adiposetissue_subject49

value: female


title: L9_AIL_rep9

description:
peak-lactation
AQ4_L9


title: Postnatal day 3 sample 4

source_name: Postnatal day 3

value: Epidermis

value: No phenotype


title: Postnatal day 3 sample 6


title: Postnatal day 3 sample 7


title: Postnatal day 6 sample 1

value: Mad2f/f; K14Cre+

value: Experiment


title: Postnatal day 3 sample 3

value: B6-129Sv mixed


title: L9_AIL_rep7

description:
peak-lactation
AQ2_L9


title: s.c.adiposetissue_subject48


title: Postnatal day 3 sample 5


title: L9_AIL_rep10

description:
peak-lactation
AQ5_L9


title: L9_AIL_rep6

description:
peak-lactation
AQ1_L9


title: Postnatal day 3 sample 2


title: Postnatal day 3 sample 1


title: Postnatal day 13 sample 2

value: Nude


title: s.c.adiposetissue_subject46

value: male


title: L9_AIL_rep5

description:
peak-lactation
AC5_L9


title: s.c.adiposetissue_subject45


title: HEK293 Flp-In TRIM71 rep3

city: Basel

first: Tim

last: Roloff

address: Maulbeerstrasse 66

department: Functional Genomics

country: Switzerland

institute: FMI

hyb_protocol: Affymetrix Gene Chip Arrays were hybridized following the GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual (Affymetrix) with a hybridization time of 16h. The Affymetrix Fluidiscs protocol FS450_0007 was used for washing.

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

data_processing: Arrays were normalized and probeset-level log2 expression values were calculated using the rma function from the R/Bioconductor (v2.14) package affy.

source_name: FHA-TRIM71 HEK293

label_protocol: 100ng of extracted total RNA was amplified using the Ambion WT Expression kit (Ambion) and the resulting sense-strand cDNA was fragmented and labeled using the Affymetrix GeneChip WT Terminal Labeling kit (Affymetrix).

growth_protocol: HEK293 cells were grown in DMEM supplemented with 2 mM glutamine and 10% FCS. 50 ug/ml hygromycin B was added to the culture medium for the maintance of FHA-TRIM71 expressing cell lines.

extract_protocol: RNA was extracted using Trizol and further cleaned up using RNeasy Columns.

tag: cell line

value: FHA-TRIM71 overexpression


title: HEK293 Flp-In TRIM71 rep2


title: mES cells TR71 KD rep2

source_name: TR71 KD mES

growth_protocol: For Trim71 KD, mES cells were treated with a combination of three diffrent siRNAs specific to Trim71 or a non-targeting negative control siRNA and Dharmafect1 according to manufacturers instructions. Cells were harvested 72h post transfection.

value: embryonic stem cells

value: Trim71 KD


title: HEK293 Flp-In TRIM71 rep1


title: L9_AIL_rep4

description:
peak-lactation
AC4_L9

value: Advance Intercross Line

value: mammary gland

value: lactation day 9


title: s.c.adiposetissue_subject42

source_name: subcutaneous adipose tissue

value: subcutaneous adipose tissue


title: s.c.adiposetissue_subject44


title: mES cells rep3

source_name: wild-type mES

value: wild-type


title: L9_AIL_rep1

description:
peak-lactation
AC1_L9


title: mES cells TR71 KD rep3


title: mES cells rep2


title: L9_AIL_rep2

description:
peak-lactation
AC2_L9


title: L9_QSi5_rep3

description:
peak-lactation
q5_L9

source_name: QSi5 mouse at Day 9 of lactation


title: s.c.adiposetissue_subject43


title: L9_QSi5_rep1

description:
peak-lactation
q3_L9


title: L9_AIL_rep3

description:
peak-lactation
AC3_L9


title: mES cells TR71 KD rep1


title: parental HEK293 Flp-In rep3

source_name: wild-type HEK293 Flp-In


title: L9_QSi5_rep2

description:
peak-lactation
q4_L9


title: parental HEK293 Flp-In rep2


title: parental HEK293 Flp-In rep1


title: s.c.adiposetissue_subject39


title: s.c.adiposetissue_subject41


title: L9_CBA_rep3

description:
peak-lactation
c5_L9

source_name: CBA/CaH mouse at Day 9 of lactation

value: CBA/CaH


title: mES cells rep1


title: s.c.adiposetissue_subject40

value: female


title: s.c.adiposetissue_subject38


title: s.c.adiposetissue_subject37


title: s.c.adiposetissue_subject36


title: L9_CBA_rep2

description:
peak-lactation
c4_L9


title: P12_QSi5_rep5

description:
mid-pregnancy
q5_p12

source_name: QSi5 mouse at Day 12 of pregnancy

value: pregnancy day 12


title: P12_QSi5_rep3

description:
mid-pregnancy
q16_p12


title: L9_CBA_rep1

description:
peak-lactation
c1_L9


title: P12_QSi5_rep4

description:
mid-pregnancy
q2_p12


title: s.c.adiposetissue_subject34


title: P12_CBA_rep 2

description:
mid-pregnancy
c31345_p12

source_name: CBA/CaH mouse at Day 12 of pregnancy


title: s.c.adiposetissue_subject28


title: s.c.adiposetissue_subject29


title: s.c.adiposetissue_subject33


title: s.c.adiposetissue_subject31


title: s.c.adiposetissue_subject27


title: s.c.adiposetissue_subject26


title: P12_CBA_rep 3

description:
mid-pregnancy
c32675_p12


title: s.c.adiposetissue_subject30


title: s.c.adiposetissue_subject35


title: s.c.adiposetissue_subject32


title: P12_QSi5_rep1

description:
mid-pregnancy
q1_p12


title: P12_QSi5_rep2

description:
mid-pregnancy
q1285_p12


title: P12_CBA_rep 5

description:
mid-pregnancy
ct2-2675_p12


title: Adult sample 4

source_name: Adult

value: Epidermis

value: Mad2f/+; K14-Cre+

value: Control

value: No phenotype


title: s.c.adiposetissue_subject25


title: s.c.adiposetissue_subject24


title: s.c.adiposetissue_subject22


title: s.c.adiposetissue_subject23


title: P12_CBA_rep 4

description:
mid-pregnancy
cba-2_p12


title: s.c.adiposetissue_subject19


title: s.c.adiposetissue_subject16


title: s.c.adiposetissue_subject21


title: s.c.adiposetissue_subject12


title: s.c.adiposetissue_subject18


title: s.c.adiposetissue_subject17


title: s.c.adiposetissue_subject20


title: P12_CBA_rep 1

description:
mid-pregnancy
c185_p12


title: s.c.adiposetissue_subject14


title: s.c.adiposetissue_subject13


title: s.c.adiposetissue_subject11


title: s.c.adiposetissue_subject15


title: s.c.adiposetissue_subject9


title: s.c.adiposetissue_subject8


title: 57N vs 57T

type: genomic

city: Leiden

first: Eddy

last: van Roon

address: Albinusdreef 2

department: Pathology

institute: LUMC

hyb_protocol: Hybridization was performed according to the standard Agilent protocol for 244 CpG island microarray hybridization

scan_protocol: Detection was done on a G2565BA scanner (Agilent Technologies) and feature extraction using Feature Extraction Software version 9.5.3.1 (Agilent Technologies)

data_processing: The raw text files were normalized by within-array loess normalization followed by between-array aquantile normalization using limma v3.2.1

molecule: genomic DNA

label_protocol: genomic DNA (500 ng) was digested with MseI, ligated to linkers, and sequentially digested with two methylation-sensitive restriction enzymes (HpaII and BstUI). Digested linker-ligated DNA was used as template for polymerase chain reaction (PCR) amplification (20 cycles) and coupled to fluorescent dyes. Cy5- or Cy3-labeled amplicons.

extract_protocol: genomic DNA was isolated by phenol/chloroform extraction and ethanol precipitation from 10-20 sections of 30 mm and yielded 10-50 mg

value: Colon

value: Normal

value: Tumor (Carcinoma)


title: 117T vs 117N (2)

value: Tumor (Adenoma)


title: 97N vs 97T


title: s.c.adiposetissue_subject10


title: 57T vs 57N


title: s.c.adiposetissue_subject7

value: male


title: 117N vs 117T


title: 577N vs 577T


title: 127N vs 127T


title: s.c.adiposetissue_subject6


title: 577T vs 577N (2)


title: s.c.adiposetissue_subject5


title: 63T vs 63N


title: 49N vs 49T


title: s.c.adiposetissue_subject1


title: 503N vs 503T


title: s.c.adiposetissue_subject2


title: 118N vs 118T


title: 601N vs 601T


title: s.c.adiposetissue_subject4


title: s.c.adiposetissue_subject3


title: 179N vs 179T


title: 119N vs 119T


title: 187N vs 187T


title: 499N vs 499T


title: PTadiposetissue_subjectI

city: Gothenburg

first: Per-Arne

last: Svensson

department: Department of molecular and clinical medicine

country: Sweden

institute: institute of medicine

description: gene expression data from adipose tissue

hyb_protocol: Following fragmentation,15 ug of cRNA were hybridized for 16 hr at 45C on Human U133 Plus 2.0 arrays. Arrays were washed and stained in the Affymetrix Fluidics Station 450.

data_processing: RMA normalization using the GCOS software (affymetrix)

source_name: adipose tissue

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

extract_protocol: Total RNA was prepared using the phenol-chloroform extraction method of Chomczynski and Sacchi  the phenol-chloroform extraction method of Chomczynski  and Sacchi

value: perithyroid adipose

value: Female


title: 131N vs 131T


title: 56N vs 56T


title: PTadiposetissue_subjectH


title: PTadiposetissue_subjectD


title: PTadiposetissue_subjectC

value: Male


title: PTadiposetissue_subjectE


title: 132N vs 132T


title: PTadiposetissue_subjectB


title: PTadiposetissue_subjectF


title: 132T vs 132N


title: 63N vs 63T


title: 180N vs 180T


title: PTadiposetissue_subjectG


title: s.c.adiposetissue_subjectI

value: subcutaneous adipose


title: 577T vs 577N (1)


title: 49T vs 49N


title: s.c.adiposetissue_subjectH


title: PTadiposetissue_subjectA


title: 505N vs 505T


title: 505T vs 505N


title: s.c.adiposetissue_subjectF


title: s.c.adiposetissue_subjectD


title: s.c.adiposetissue_subjectC


title: s.c.adiposetissue_subjectE


title: 97T vs 97N


title: s.c.adiposetissue_subjectA


title: 117T vs 117N (1)


title: s.c.adiposetissue_subjectG


title: 503T vs 503N


title: 601T vs 601N


title: bone marrow_029, baseline

city: salt lake city

first: fenghuang

last: zhan

state: UT

institute: university of utah

description: Gene expression data from  bone marrow sample of multiple myeloma patient at baseline.

hyb_protocol: standard Affymetrix protocol

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000.

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

source_name: Patient bone marrow sample at baseline

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500 ng total RNA (Expression Analysis Technical Manual, 2008, Affymetrix).

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

tag: individual

value: Primary multiple myeloma patient

tag: tumor stage

value: baseline

value: myeloma tumor cell


title: s.c.adiposetissue_subjectB

tag: tissue

tag: Sex


title: bone marrow_029, pre-1st transplant

description: Gene expression data from  bone marrow sample of multiple myeloma patient after chemotherapy (pre-1st transplant).

source_name: Patient bone marrow sample after chemotherapy (pre-1st transplant)

value: pre-1st transplant


title: 187T vs 187N


title: 119T vs 119N


title: 499T vs 499N


title: 118T vs 118N


title: bone marrow_028, pre-1st transplant


title: 179T vs 179N


title: 56T vs 56N


title: 127T vs 127N


title: bone marrow_028, baseline


title: bone marrow_020, pre-1st transplant


title: MeHg_2mg5_treated_54706602

city: Bergen

first: Fekadu

last: Yadetie

address: Thormøhlensgt. 53A/B

department: Biology

country: Norway

institute: University of Bergen

description:
About 1.5-year-old male and female juvenile Atlantic Cod (260–530 g body weight) injected (i.p.) with 2 mg MeHg/kg BW, and sample collected after 14 days.
The fourth of 5 biological replicates treated with 2 mg MeHg/kg BW.

hyb_protocol: Hybridization was performed by Roche NimbleGen following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by Roche NimbleGen following their standard operating protocol. See www.nimblegen.com.

data_processing: Expression values were generated using quantile normalization (Bolstad et al., 2003, Bioinformatics, 19:185) and the Robust Multichip Average (RMA) algorithm (Irizarry et al., 2003, Nucleic Acids Res. 31: e15 and Irizarry et al., 2003, Biostatistics 4:249), as performed by NimbleGen. See www.nimblegen.com.

organism: Gadus morhua

source_name: liver from juvenile cod, treated with 2 mg MeHg/kg BW

label_protocol: Labeling was performed by Roche NimbleGen (Madison, WI) following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Fish were maintained in 500 l tanks with continuously flowing seawater at 10 °C, 34% salinity and a 12h light/dark cycle and were fed daily with commercial pellets (EWOS, Bergen, Norway).

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit according to the manufacturer's protocol (Qiagen, Inc., Hilden, Germany).

treatment_protocol: After acclimation for 6 days, the fish were injected (i.p.) with vehicle, 0.5 or 2 mg/kg BW methylmercury chloride. The doses were given in two aliquots with a 1-week interval. 14 days after the first injection, the fish were sacrificed and tissues were sampled.

value: male and female

tag: age

value: 1.5 years

tag: developmental stage

value: juvenile

tag: body weight

value: liver

tag: treatment

value: 2 mg methylmercury (MeHg)/kg body weight


title: 131T vs 131N

value: Colon

value: Normal


title: bone marrow_020, pre-2st transplant

description: Gene expression data from  bone marrow sample of multiple myeloma patient after chemotherapy (pre-2st transplant).

source_name: Patient bone marrow sample after chemotherapy (pre-2st transplant)

value: pre-2st transplant


title: MeHg_0.5mg8_treated_57660302

description:
About 1.5-year-old male and female juvenile Atlantic Cod (260–530 g body weight) injected (i.p.) with 0.5 mg MeHg/kg BW, and sample collected after 14 days.
The fifth of 5 biological replicates treated with 0.5 mg MeHg/kg BW.

source_name: liver from juvenile cod, treated with 0.5 mg MeHg/kg BW

value: 0.5 mg methylmercury (MeHg)/kg body weight


title: bone marrow_026, pre-1st transplant


title: MeHg_2mg4_treated_54706302

description:
About 1.5-year-old male and female juvenile Atlantic Cod (260–530 g body weight) injected (i.p.) with 2 mg MeHg/kg BW, and sample collected after 14 days.
The third of 5 biological replicates treated with 2 mg MeHg/kg BW.


title: MeHg_2mg6_treated_54560102

description:
About 1.5-year-old male and female juvenile Atlantic Cod (260–530 g body weight) injected (i.p.) with 2 mg MeHg/kg BW, and sample collected after 14 days.
The fifth of 5 biological replicates treated with 2 mg MeHg/kg BW.


title: bone marrow_026, baseline


title: MeHg_2mg3_treated_54559802

description:
About 1.5-year-old male and female juvenile Atlantic Cod (260–530 g body weight) injected (i.p.) with 2 mg MeHg/kg BW, and sample collected after 14 days.
The second of 5 biological replicates treated with 2 mg MeHg/kg BW.


title: bone marrow_020, baseline


title: bone marrow_017, pre-2st transplant


title: MeHg_0.5mg6_treated_54560802

description:
About 1.5-year-old male and female juvenile Atlantic Cod (260–530 g body weight) injected (i.p.) with 0.5 mg MeHg/kg BW, and sample collected after 14 days.
The third of 5 biological replicates treated with 0.5 mg MeHg/kg BW.


title: MeHg_K6control_54560002

description:
About 1.5-year-old male and female juvenile Atlantic Cod (260–530 g body weight) injected (i.p.) with vehicle (20% acetone and 80% soybean), and sample collected after 14 days.
The fifth of 5 biological replicate controls.

source_name: liver from juvenile cod, control

value: vehicle control


title: bone marrow_016, pre-consolidation

description: Gene expression data from  bone marrow sample of multiple myeloma patient after chemotherapy (pre-consolidation).

source_name: Patient bone marrow sample after chemotherapy (pre-consolidation)

value: pre-consolidation


title: MeHg_0.5mg5_treated_57661202

description:
About 1.5-year-old male and female juvenile Atlantic Cod (260–530 g body weight) injected (i.p.) with 0.5 mg MeHg/kg BW, and sample collected after 14 days.
The second of 5 biological replicates treated with 0.5 mg MeHg/kg BW.


title: 180T vs 180N

value: Tumor (Adenoma)


title: bone marrow_015, pre-2st transplant


title: bone marrow_015, pre-consolidation


title: MeHg_0.5mg7_treated_57660502

description:
About 1.5-year-old male and female juvenile Atlantic Cod (260–530 g body weight) injected (i.p.) with 0.5 mg MeHg/kg BW, and sample collected after 14 days.
The fourth of 5 biological replicates treated with 0.5 mg MeHg/kg BW.


title: bone marrow_016, pre-2st transplant


title: bone marrow_015, pre-1st transplant


title: bone marrow_017, pre-1st transplant


title: bone marrow_014, baseline


title: bone marrow_016, baseline


title: bone marrow_017, baseline


title: bone marrow_014, pre-1st transplant


title: bone marrow_016, pre-1st transplant


title: bone marrow_012, pre-consolidation


title: bone marrow_013, pre-2st transplant


title: bone marrow_012, pre-2st transplant


title: MeHg_K4control_54560302

description:
About 1.5-year-old male and female juvenile Atlantic Cod (260–530 g body weight) injected (i.p.) with vehicle (20% acetone and 80% soybean), and sample collected after 14 days.
The third of 5 biological replicate controls.


title: bone marrow_013, pre-1st transplant


title: bone marrow_015, baseline


title: MeHg_K5control_54706002

description:
About 1.5-year-old male and female juvenile Atlantic Cod (260–530 g body weight) injected (i.p.) with vehicle (20% acetone and 80% soybean), and sample collected after 14 days.
The fourth of 5 biological replicate controls.


title: bone marrow_013, pre-consolidation


title: MeHg_K1control_54560402

description:
About 1.5-year-old male and female juvenile Atlantic Cod (260–530 g body weight) injected (i.p.) with vehicle (20% acetone and 80% soybean), and sample collected after 14 days.
The first of 5 biological replicate controls.


title: MeHg_0.5mg3_treated_54637202

description:
About 1.5-year-old male and female juvenile Atlantic Cod (260–530 g body weight) injected (i.p.) with 0.5 mg MeHg/kg BW, and sample collected after 14 days.
The first of 5 biological replicates treated with 0.5 mg MeHg/kg BW.


title: MeHg_2mg2_treated_54637502

description:
About 1.5-year-old male and female juvenile Atlantic Cod (260–530 g body weight) injected (i.p.) with 2 mg MeHg/kg BW, and sample collected after 14 days.
The first of 5 biological replicates treated with 2 mg MeHg/kg BW.


title: MeHg_K2control_57660602

description:
About 1.5-year-old male and female juvenile Atlantic Cod (260–530 g body weight) injected (i.p.) with vehicle (20% acetone and 80% soybean), and sample collected after 14 days.
The second of 5 biological replicate controls.


title: bone marrow_012, pre-1st transplant

description: Gene expression data from  bone marrow sample of multiple myeloma patient after chemotherapy (pre-1st transplant).


title: bone marrow_013, baseline

description: Gene expression data from  bone marrow sample of multiple myeloma patient at baseline.


title: peripheral blood T-cells Patient9 [miRNA]

description: gene expression data from T-cell

hyb_protocol: Samples were hybridized for 16 hr at 45C on miRNA 2.0 arrays. Arrays were washed and stained in the Affymetrix Fluidics Station 450.

data_processing: The raw expression signals were preprocessed following the method of Robust Multi-array Analysis (RMA)  with quantile normailization.

source_name: peripheral blood T-cell

label_protocol: 1000 ng RNA from T-cells were biotin labeled using the FlashTag Biotin HSR kit (Genisphere, Hatfield, PA) according to the manufacturer's instructions

extract_protocol: Total RNA was prepared using Chomczynski's method (Anal Biochem 162, 156-9 (1987))

treatment_protocol: Cells were snap frozen in -80 C

tag: group

value: ITP patient


title: peripheral blood T-cells Patient8 [miRNA]

description: gene expression data from T-cell


title: bone marrow_010, pre-2st transplant

description: Gene expression data from  bone marrow sample of multiple myeloma patient after chemotherapy (pre-2st transplant).

value: Primary multiple myeloma patient


title: bone marrow_009, pre-maintenance

description: Gene expression data from  bone marrow sample of multiple myeloma patient after chemotherapy (pre-maintenace).

source_name: Patient bone marrow sample after chemotherapy (pre-maintenance)

value: pre-maintenance


title: bone marrow_009, pre-2st transplant

value: myeloma tumor cell


title: bone marrow_012, baseline

value: baseline


title: bone marrow_007, post-2st transplant

description: Gene expression data from  bone marrow sample of multiple myeloma patient after chemotherapy (post-2st transplant).

source_name: Patient bone marrow sample after chemotherapy (post-2st transplant)

value: post-2st transplant


title: peripheral blood T-cells Patient4 [miRNA]

description: gene expression data from T-cell


title: bone marrow_010, pre-1st transplant

value: pre-1st transplant


title: bone marrow_008, baseline


title: bone marrow_009, pre-1st transplant


title: bone marrow_010, baseline


title: bone marrow_007, pre-1st transplant


title: peripheral blood T-cells Patient6 [miRNA]

description: gene expression data from T-cell


title: bone marrow_010, post-2st transplant


title: peripheral blood T-cells Patient5 [miRNA]

description: gene expression data from T-cell


title: bone marrow_007, baseline


title: bone marrow_006, pre-2st transplant


title: bone marrow_006, pre-consolidation


title: peripheral blood T-cells Patient1 [miRNA]

description: gene expression data from T-cell


title: peripheral blood T-cells Patient7 [miRNA]

description: gene expression data from T-cell


title: bone marrow_008, pre-1st transplant


title: bone marrow_009, baseline


title: bone marrow_007, pre-2st transplant


title: bone marrow_006, pre-1st transplant


title: bone marrow_006, baseline


title: peripheral blood T-cells Control11 [miRNA]

description: gene expression data from T-cell

value: Control


title: peripheral blood T-cells Patient3 [miRNA]

description: gene expression data from T-cell


title: peripheral blood T-cells Patient2 [miRNA]

description: gene expression data from T-cell


title: Map_naive_24h_rep2

city: Madison

first: CHIA-WEI

last: WU

state: WI

address: 1656 Linden Dr

department: Pathobiological Sciences

institute: University of Wisconsin-Madison

description:
Intracellular condition, 24 h in naïve macrophage. Second of two biological replicates used in this condition, each from separate culture
SAMPLE 8

hyb_protocol: Three micrograms of the labeled cDNA sample was mixed with NimbleGen hybridization buffer and hybridization component A, covered with a lifted coverslip and hybridized on a NimbleGen microarray chip at 42°C for 16 to 20 hrs.  The hybridized chips were washed with NimbleGen wash solutions I, II and III according to Nimblegen's parotocol.

scan_protocol: Scanning was done with an Axon GenePix 4000B scanner (Molecular Devices) at 5 micron resolution. PMT was adjusted following the suggestions in Nimblegen's protocol.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan 2.2.33 (NimbleGen, Inc.). Intensities on each chip were centered to 1,000 for MeV v4.4.

source_name: Intracellular M. ap isolated from infected naïve J774A.1, 24 h post-infection

label_protocol: Labeling was performed following the standard protocol of NimbleGen Systems Inc., Madison, WI USA.

growth_protocol: Mycobacterium avium subsp. paratuberculosis K-10 was grown to OD600=0.5 at 37 degrees and 115 rpm in 7H9 medium (Difco) supplemented with 0.5% glycerol, 0.05% Tween 80, 2 µg/ml mycobactin J (Allied Monitor) and 10% ADC (2% glucose, 5% BSA fraction V, and 0.85% NaCl).

extract_protocol: Infected J774A.1 cells were washed with 15 ml ice-cold PBS at least five times or until no visible bacterial particles was observed under an inverted microscope.  The washed cells on each dish were then lysed with 10 ml cell lysis buffer (4 M guanidine thiocyanate, 0.5% sodium N-lauryl sarcosine, 25 mM sodium citrate, 0.5% Tween 80 and 0.1 M β-mercaptoethanol) and collected with a rubber cell scrapper.  To reduce viscosity and help dissolve cell debris, cell lysats from all dishes were pooled and passed through a 23-gauge needle five times.  The lysate was then split into four 14-ml polypropylene centrifuge tubes (Falcon 352059) and centrifuged at 3,200 × g, 4°C for 25 min.  Each pellet was washed in 1 ml of TRIzol regent (Invitrogen) twice and then resuspended in 2 ml of TRIzol and split into two 2-ml screw-capped tubes each with 3.0 g of 0.1 mm Zirconia/Silica beads (BioSpect Products) and disrupted in a Mini-BeadBeater-8 (BioSpect Products) at top speed for three pulses of 60 sec with 30 sec intervals on ice.  Following a 5-min incubation at room temperature, the supernatant was transferred to RNase-free tubes and centrifuged at 12,000 × g for 15 min.  RNA was then isolated according to manufacturer’s instruction.  To remove genomic DNA contamination, RNA samples were treated with 10 U of Turbo DNase (Ambion) at 37°C for 30 min.  An IS900 241-bp PCR reaction was performed to confirm that no genomic DNA was detectable in the RNA samples.  DNase treatments were repeated if needed.  Quality of the extracted RNA was examined with a NanoDrop 1000.  The ratios of A260/A280 and A260/ A230 must be higher than 1.8 and 1.5, respectively, before proceeding to cDNA synthesis for transcriptome studies.

treatment_protocol: Immediately before infection, M. avium subsp. paratuberculosis culture was pelleted, resuspended in warm RPMI-1640 and passed through a 23-gauge needle five times or until bacterial clumps were dispersed.  An approximate 109 CFU bacterial suspension was mixed with 12 ml of RPMI-1640/10% FBS and added to each decanted 15-cm cell culture dish (MOI=50) where J774A.1 cells were grown with or without interferon-gamma treatment.  The cells were incubated at 37°C with 5% CO2 for 2 h or 24 h before intracellular bacteria isolation. For the 24 h time point experiments, extracellular bacteria were washed away at 2 h post-infection with 15 ml of warm PBS at least five times or until no visible bacterial particles were observed under an inverted microscope.

value: Wild-type

tag: host cell

value: Naïve macrophage


title: bone marrow_005, baseline


title: peripheral blood T-cells Control7 [miRNA]

description: gene expression data from T-cell


title: Map_activated_2h_rep1

description:
Intracellular condition, 2 h in pre-activated macrophage. First of two biological replicates used in this condition, each from separate culture
SAMPLE 5

organism: Mycobacterium avium subsp. paratuberculosis K-10

source_name: Intracellular M. ap isolated from infected pre-acivated J774A.1, 2 h post-infection

value: Pre-activated macrophage


title: Map_naive_24h_rep1

description:
Intracellular condition, 24 h in naïve macrophage. First of two biological replicates used in this condition, each from separate culture
SAMPLE 7


title: Map_activated_2h_rep2

description:
Intracellular condition, 2 h in pre-activated macrophage. Second of two biological replicates used in this condition, each from separate culture
SAMPLE 6


title: Map_naive_2h_rep2

description:
Intracellular condition, 2 h in naïve macrophage. Second of two biological replicates used in this condition, each from separate culture
SAMPLE 4

source_name: Intracellular M. ap isolated from infected naïve J774A.1, 2 h post-infection


title: peripheral blood T-cells Control6 [miRNA]

description: gene expression data from T-cell


title: peripheral blood T-cells Control8 [miRNA]

description: gene expression data from T-cell


title: peripheral blood T-cells Control10 [miRNA]

description: gene expression data from T-cell


title: Map_activated_24h_rep1

description:
Intracellular condition, 24 h in pre-activated macrophage. First of two biological replicates used in this condition, each from separate culture
SAMPLE 9

source_name: Intracellular M. ap isolated from infected pre-acivated J774A.1, 24 h post-infection


title: Map_activated_24h_rep2

description:
Intracellular condition, 24 h in pre-activated macrophage. Second of two biological replicates used in this condition, each from separate culture
SAMPLE 10


title: peripheral blood T-cells Control4 [miRNA]

description: gene expression data from T-cell


title: Map_naive_2h_rep1

description:
Intracellular condition, 2 h in naïve macrophage. First of two biological replicates used in this condition, each from separate culture
SAMPLE 3


title: bone marrow_005, pre-1st transplant


title: bone marrow_004, pre-1st transplant


title: Map_RPMI_2h_rep1

description:
As the control condition. First of two biological replicates used in this condition, each from separate cultures.
SAMPLE 1

source_name: M. ap incubated in RPMI-1640/10% FBS for 2h

value: Cell culture medium


title: Map_RPMI_2h_rep2

description:
As the control condition. Second of two biological replicates used in this condition, each from separate cultures.
SAMPLE 2


title: bone marrow_004, pre-consolidation

description: Gene expression data from  bone marrow sample of multiple myeloma patient after chemotherapy (pre-consolidation).


title: peripheral blood T-cells Control3 [miRNA]

description: gene expression data from T-cell


title: bone marrow_004, pre-2st transplant

value: pre-2st transplant


title: peripheral blood T-cells Control2 [miRNA]

description: gene expression data from T-cell


title: bone marrow_005, pre-2st transplant


title: bone marrow_004, baseline


title: peripheral blood T-cells Control1 [miRNA]

description: gene expression data from T-cell


title: bone marrow_003, pre-1st transplant


title: bone marrow_001, pre-1st transplant


title: bone marrow_001, baseline


title: NORMAL, PediatricTemporal1, ID00514

status: Public on Jan 21 2013

city: Aurora

first: Diane

middle: K

last: Birks

state: CO

department: Neurosurgery

institute: University of Colorado, Denver - Anschutz Medical Campus

description: normal brain control, temporal, pediatric

hyb_protocol: Standard Affymetrix procedure

scan_protocol: Standard Affymetrix procedure

data_processing: Data were background corrected and normalized using gcRMA (as implemented in Bioconductor).

label_protocol: For most samples, five micrograms of total RNA was reverse-transcribed using a T7-(dT) 24 oligomer and Superscript II Reverse Transcriptase (Invitrogen Corp., Carlsbad, CA). Subsequently, biotin-labeled cRNA was generated from the double-stranded cDNA template by in vitro transcription using T7 RNA polymerase and a BioArray High Yield RNA Transcript Labeling Kit (Enzo Diagnostics, Farmingdale, NY). Biotinylated cRNA (20 micrograms) was fragmented to an average size of 35 to 200 bases with fragmentation buffer. For a few samples, limited amount of starting RNA precluded use of this protocol. Instead, RNA was prepared using the Ambion Message Amp Premier RNA Amplification Kit (Applied Biosystems) according to manufacturer's directions, using a starting amount of 400 nanograms of RNA.

growth_protocol: All samples were collected at time of surgery

extract_protocol: RNA was extracted from each sample using an RNeasy or DNA/RNA AllPrep kit (Qiagen) according to the manufacturer’s directions

value: normal brain


title: NORMAL, PediatricParietal2, ID00605

description: normal brain control, parietal, pediatric


title: bone marrow_003, baseline

description: Gene expression data from  bone marrow sample of multiple myeloma patient at baseline.


title: MED_ID00898

description: brain tumor, medulloblastoma

source_name: brain tumor, medulloblastoma

value: medulloblastoma


title: NORMAL, PediatricOccipital2, ID00605

description: normal brain control, occipital, pediatric


title: MED_ID00529

description: brain tumor, medulloblastoma


title: NORMAL, PediatricOccipital1, ID00514

source_name: normal brain control, occipital, pediatric


title: NORMAL, PediatricTemporal2, ID00605

source_name: normal brain control, temporal, pediatric


title: MED_ID00851

description: brain tumor, medulloblastoma


title: MED, ID00801

description: brain tumor, medulloblastoma


title: NORMAL, PediatricCerebellum1, ID00605

description: normal brain control, cerebellum, pediatric


title: MED_ID00719

description: brain tumor, medulloblastoma


title: MED_ID00791

description: brain tumor, medulloblastoma


title: NORMAL, PediatricParietal1, ID00514

source_name: normal brain control, parietal, pediatric


title: MED, ID00565

hyb_protocol: Standard Affymetrix procedure.

scan_protocol: Standard Affymetrix procedure.

label_protocol: For most samples, five micrograms of total RNA was reverse-transcribed using a T7-(dT) 24 oligomer and Superscript II Reverse Transcriptase (Invitrogen Corp., Carlsbad, CA). Subsequently, biotin-labeled cRNA was generated from the double-stranded cDNA template by in vitro transcription using T7 RNA polymerase and a BioArray High Yield RNA Transcript Labeling Kit (Enzo Diagnostics, Farmingdale, NY). Biotinylated cRNA (20 micrograms) was fragmented to an average size of 35 to 200 bases with fragmentation buffer.  For a few samples, limited amount of starting RNA precluded use of this protocol. Instead, RNA was prepared using the Ambion Message Amp Premier RNA Amplification Kit (Applied Biosystems) according to manufacturer's directions, using a starting amount of 400 nanograms of RNA.

growth_protocol: All samples were collected at time of surgery.

extract_protocol: RNA was extracted from each sample using an RNeasy or DNA/RNA AllPrep kit (Qiagen) according to the manufacturer’s directions.


title: MED, ID00797


title: NORMAL, PediatricCerebellum1

source_name: normal brain control, cerebellum, pediatric

value: normal cerebellum

value: pediatric


title: MED_ID00877

description: brain tumor, medulloblastoma


title: NORMAL, PediatricFrontal1

source_name: normal brain control, frontal, pediatric

value: normal frontal


title: MED, ID00288


title: MED, ID00254


title: MED, ID00277


title: MED, ID00258


title: MED, ID00330


title: MED, ID00437


title: MED, ID00186


title: MED, ID00262


title: GBM, ID00637

source_name: brain tumor, glioblastoma

value: glioblastoma


title: GBM, ID00434


title: MED, ID00613

source_name: brain tumor, medulloblastoma, large-cell

value: medulloblastoma, large-cell


title: GBM, ID00271


title: GBM, ID00309


title: GBM, ID00089


title: GBM, ID00668


title: GBM, ID00391


title: GBM, ID00281


title: GBM, ID00057


title: GBM, ID00098


title: iPS-DMC72-PCMDM01 (Passage 30)

status: Public on Jan 20 2013

city: Osaka

first: Yonehiro

last: Kanemura

address: 2-1-14 Hoenzaka, Chuo-ku

department: Division of Regenerative Medicine Institute for Clinical Research

institute: National Hospital Organization Osaka National Hospital

description: Gene expression data from induced pluripotent stem cells (iPS-DMC72-PCMDM01) cultured on PCM-DM at later passage

hyb_protocol: After aRNA purification, 15 μg of aRNA was fragmented and hybridized with a pre-equilibrated GeneChip array (Human Genome U133 Plus 2.0 gene expression array, Affymetrix) at 45°C for 16 hours.

scan_protocol: The arrays were scanned using an Affimetrix GeneChip Scanner 3000.

data_processing: The images obtained were processed to data using the Expression ConsoleTM (Affymetrix).

source_name: cultured in StemPro on PCM-DM

label_protocol: Total RNA (100 ng) was used to synthesize aRNA using the 3’ IVT Express Kit, according to the manufacturer’s instructions (Affymetrix).

growth_protocol: Cultured in StemPro on PCM-DM

extract_protocol: RNeasy

treatment_protocol: Harvested cells at  early and later passages.

tag: cells

value: human induced pluripotent stem cells

tag: medium

value: StemPro

tag: culture substrate

value: PCM-DM

tag: passage

value: late


title: iPS-DMC72-PCMDM02 (Passage 30)

description: Gene expression data from induced pluripotent stem cells (iPS-DMC72-PCMDM02) cultured on PCM-DM at later passage


title: iPS-DMC72-PCMDM02 (Passage 8)

description: Gene expression data from induced pluripotent stem cells (iPS-DMC72-PCMDM02) cultured on PCM-DM at early passage

value: early


title: flight sample, biological rep 9

city: Milan

first: Silvia

last: Bradamante

address: Via Golgi 19

country: Italy

institute: CNR-ISTM, Institute of Molecular Science and Technology

description: Gene expression data from spaceflight sample 9

hyb_protocol: Hybridization was performed using the GeneChip® Hybridization, Wash and Stain Kit. GeneChip® cartridges were washed and stained with GeneChip® Hybridization, Wash and Stain Kit in the Affymetrix Fluidics Station 450 following the FS450_0007 standard protocol

scan_protocol: GeneChip arrays were scanned using an Affymetrix GeneChip® Scanner 3000 7G using default parameters

data_processing: Gene chip data were imported in Partek Genomic Suite 6.5 software and pre-processed with Robust Multichip Analysis. An ANOVA statistical test, analysis of variance model (as implemented in Partek) was used to describe the experimental model, remove batch effects, and compute fold changes and statistics

source_name: HUVEC cultured in space

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 150 ug total RNA

growth_protocol: SPHINX was launched with Progress 40P and, as soon as docking was complete (four days after launch, T0), the experiment was started inside a KUBIC incubator on the ISS.  Timeline: T0: installation in KUBIK; T0 + 7 hrs: first medium exchange; T0 + 91 hrs: second medium exchange; T0 + 167 hrs: third medium exchange with PBS.  The experiment was stopped by means of two subsequent RNAlater fixations separated by an interval of six minutes. After the experiment had been completed, the samples were kept at 6°C inside the KUBIK incubator before being returned to Earth on Soyuz 23S.   Twelve control experiments were carried out in parallel using the same hardware and experimental protocol.

extract_protocol: HUVEC, preserved in RNAlater solution, were subjected to total RNA extraction following the double extraction protocol: RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction (Trizol Invitrogen) followed by a Qiagen RNeasy clean-up procedure.

treatment_protocol: Samples were preserved in RNAlater and mantained at 6°C before analyses

value: Cells derived from the endothelium of veins from the umbilical cord


title: flight sample, biological rep 3

description: Gene expression data from spaceflight sample 3


title: ground control, biological rep 5

description: Gene expression data from control 5

source_name: HUVEC cultured at 1g


title: iPS-DMC72-PCMDM01 (Passage 8)

description: Gene expression data from induced pluripotent stem cells (iPS-DMC72-PCMDM01) cultured on PCM-DM at early passage


title: ground control, biological rep 1

description: Gene expression data from control 1


title: IM006_PB1-F2Del_10^3pfu_7d_5

status: Public on Jan 19 2013

city: Seattle

first: Michael

last: Katze

state: WA

address: Rosen Building 960 Republican St.

department: Microbiology

institute: University of Washington

hyb_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for hybridization and array washing. Two hundred fifty ng of each RNA sample was hybridized to one Agilent 4X44K mouse genome (Design ID 014868) array.

scan_protocol: Dry slides were scanned on an Agilent DNA microarray scanner (Model G2505B) using the XDR setting.

data_processing: Raw images were analyzed using the Agilent Feature Extraction software (version 9.5.3.1) and the GE1-v5_95_Feb07 extraction protocol. All arrays were required to pass Agilent QC flags. Extracted raw data were background corrected using the norm-exp method and quantile normalized using Agi4x44PreProcess and RMA Bioconductor packages.

source_name: lung, PB1-F2del infected, 7d

label_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for the Cy3-cDNA probe preparation.

extract_protocol:
Specific lobes of the lung from each animal were harvested and briefly rinsed in cold (4ºC) PBS. Following the RNAlater (Ambion) protocol, tissue was cut into small chunks (<0.5cm in any single dimension) and placed immediately into 10-20 volumes (w/v) (e.g., 100mg/ml) RNAlater. After a 4ºC incubation for overnight, samples were stored at -80ºC until further processing. Lung tissue was removed from RNAlater, washed in a small volume of Trizol, homogenized in 10-20 volumes (w/v) TRIzol and stored at -80°C until RNA isolation.
All TRIzol lysates were processed simultaneously: they were phase-separated, and RNA was isolated from the aqueous phase (diluted 2 fold with RLT buffer) using Qiagen RNeasy Mini columns and the manufacturer's recommended protocol (Qiagen, Inc., Valencia, CA). RNA quality was assessed on an Agilent 2100 Bioanalyzer using the nanochip format, and only intact RNA was used for microarray analyses.

treatment_protocol: Twenty-week-old C57BL/6 mice were infected by intranasal instillation of 10^3 PFU of PB1-F2del: A/Vietnam/1203-CIP048_RG3/2004 (H5N1) in 50 µl of PBS or mock-infected with PBS alone. At days 1, 2, 4 and 7 days post-infection, lungs were harvested.

tag: strain

value: lung

tag: infection code

tag: dosage

tag: time point

tag: biological replicate


title: IM006_PB1-F2Del_10^3pfu_4d_3

source_name: lung, PB1-F2del infected, 4d

tag: tissue


title: IM006_PB1-F2Del_10^3pfu_2d_5

source_name: lung, PB1-F2del infected, 2d


title: flight sample, biological rep 8

description: Gene expression data from spaceflight sample 8


title: ground control, biological rep 9

description: Gene expression data from control 9


title: IM006_PB1-F2Del_10^3pfu_2d_1


title: GBM, ID00000


title: IM006_PB1-F2Del_10^3pfu_2d_2


title: IM006_mock_2d_1

source_name: lung, mock infected, 2d

value: mock


title: IM006_mock_7d_2

source_name: lung, mock infected, 7d


title: IM006_mock_7d_3


title: IM006_mock_1d_3

source_name: lung, mock infected, 1d


title: IM006_mock_2d_3


title: IM006_PB1-F2Del_10^3pfu_7d_1


title: IM006_PB1-F2Del_10^3pfu_1d_2

source_name: lung, PB1-F2del infected, 1d


title: IM006_PB1-F2Del_10^3pfu_7d_2


title: IM006_mock_1d_1


title: IM006_PB1-F2Del_10^3pfu_4d_4


title: IM006_mock_4d_3

source_name: lung, mock infected, 4d


title: IM006_PB1-F2Del_10^3pfu_1d_5


title: IM006_mock_4d_2


title: IM006_PB1-F2Del_10^3pfu_4d_1


title: IM006_PB1-F2Del_10^3pfu_2d_4


title: IM006_mock_1d_2


title: IM006_PB1-F2Del_10^3pfu_1d_1


title: IM006_PB1-F2Del_10^3pfu_1d_3


title: IM006_mock_7d_1


title: IM006_PB1-F2Del_10^3pfu_1d_4


title: BMSC 7 days neural differentiation

city: Lodz

first: Mariola

last: Matysiak

address: Kopcinskiego 22

department: Neurology

country: Poland

institute: Medical University of Lodz

hyb_protocol: Using Tecan hybridization stations the hybridization and washing steps are fully automated for exellent reproducibility (Exiqon)

scan_protocol: Arrays are scanned with highly sensitive equipment in ozone free environment to reduce day-to-day variation to a minimum.Image analysis then performed to quantify the signals on the array (Exiqon).

data_processing: Normalization methods: LOWESS. The data obtained is normalizaed using methods applicable to the performed experiment (Exiqon). Depending on the experimental setup and the size of the project customized data analysis is provided (including heat map/unsupervised hierarchical clustering, PCA-plots etc based on TTest or ANOVA)(Exiqon).

source_name: bone marrow stem cell

label_protocol: Our miRCURY LNA Array Power labeling kit allows highly efficient and uniform labeling of microRNAs with minimal sequence bias (Exiqon)

extract_protocol: miRVana kit (Ambion)

tag: cell type

value: bone marrow stem cells 7 days neural differentiation

value: SJL mice

source_name: common reference pool

value: pooled differentiated and non-differentiated bone marrow stem cells


title: BMSC not differentiated

value: bone marrow stem cells not differentiated


title: IM006_mock_2d_2


title: IM006_PB1-F2Del_10^3pfu_4d_5


title: R481

city: Detroit

first: Hui

last: JIA

state: MI

address: 275 E. Hancock

institute: wsu

hyb_protocol: Amount of 1.5ug of Alexa 555 labeled aminoallyl-aRNA was used to hybridize on the Agilent custom 60-mer oligo array (1X244K lncRNA microarrays) for 17 hours at 65°C at 10rpm in the hybridization oven following Agilent's protocol.

scan_protocol: Scanned using Agilent Technologies Scanner G2505A US1470236.

data_processing: We defined a probe to be detectable (present) if at least one on-chip replicate (out of the 5 on-chip replicates) was detectable by the Agilent Feature Extraction well above background (gIsWellAboveBg = 1) criterion in at least half (15) of the 31 samples with age <18years. The green channel intensity (gProcessedSignal) was log2 transformed and averaged over the 5 on-chip replicates. Data from the 31 samples (age<18years) were then quantile normalized together using normalize.quantiles from the preprocessCore package (R version 2.15.1).

label: Alexa 555

source_name: temporal neocortex, 13.67 yrs

label_protocol: To produce aminoallyl-aRNA, 50 ng of total RNA for each sample, Agilent Spike-in Controls for one color, and the TargetAMP 1-Round Aminoallyl-aRNA Amplification Kit 101 (Epicentre, Madison, WI) were used. The Alexa Fluor 555 (Molecular Probes, Eugene, OR) and 2.5ug of each aminoallyl-aRNA sample were used for the labeling step.

extract_protocol: Either the MagMax-96 kit (Applied Biosystems/Ambion) or a commercial version of the TRIzol protocol.

treatment_protocol: Tissue samples were homogenized in TRI Reagent (Applied Biosytems/Ambion, Austin, TX).

value: temporal neocortex

tag: gender

value: female

tag: age

tag: race

value: not available


title: R455

source_name: temporal neocortex, 47.83 yrs

value: male

value: White


title: IM006_PB1-F2Del_10^3pfu_7d_3


title: IM006_mock_4d_1


title: IM006_PB1-F2Del_10^3pfu_2d_3


title: R493

source_name: temporal neocortex, 7.33 yrs


title: R460

source_name: temporal neocortex, 17.67 yrs


title: R490

source_name: temporal neocortex, 0.92 yrs


title: R473

source_name: temporal neocortex, 36.92 yrs


title: R487

source_name: posterior neocortex, 7.42 yrs

value: posterior neocortex


title: R475

source_name: temporal neocortex, 3.33 yrs


title: R454

source_name: temporal neocortex, 3.42 yrs


title: R492

source_name: temporal neocortex, 24.33 yrs


title: R477

source_name: temporal neocortex, 15.92 yrs


title: R462

source_name: temporal neocortex, 43.5 yrs


title: R491

source_name: parietal neocortex, 2.58 yrs

value: parietal neocortex


title: R476

source_name: temporal neocortex, 3.5 yrs

value: 3.5 yrs

value: Hispanic


title: BMSC 4 days neural differentiation

value: bone marrow stem cells 4 days neural differentiation


title: female ischemic

city: Jinan

first: Fan

last: Jiang

state: Shandong

address: 107 Wen Hua Xi Road

country: China

institute: Shandong University

description: miRNA level in plasma

hyb_protocol: Each slide was hybridized with 100ng Cy3-labeled RNA using miRNA Complete Labeling and Hyb Kit(Cat#5190-0456, Agilent technologies, Santa Clara, CA, US)in hybridization Oven(Cat#G2545A, Agilent technologies, Santa Clara, CA, US)at 55℃，20rpm for 20 hours according to the manufacturer’s instructions, hybridization section. After hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US).

scan_protocol: Slides were scanned by Agilent Microarray Scanner(Cat#G2565BA，Agilent technologies, Santa Clara, CA, US)and Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US)with default settings.

data_processing: Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0(Agilent technologies, Santa Clara, CA, US).

source_name: female ischemic stroke patient plasma

label_protocol: miRNA was labeled by miRNA Complete Labeling and Hyb Kitn(Cat#5190-0456, Agilent technologies, Santa Clara, CA, US) following the manufacturer’s instruction's labeling section.

extract_protocol: Total RNA was extracted and purified using mirVana™ miRNA Isolation Kit (Cat#AM1560, Ambion, Austin, TX, US) following the manufacturer’s instructions and checked by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US)

tag: disease state

value: ischemic stroke

tag: pooled sample


title: male ischemic

description: miRNA level in plasma

source_name: male ischemic stroke patient plasma


title: R452

source_name: temporal neocortex, 8 yrs

value: 8 yrs


title: Beas-2B parental cells [DEG.ABC]

city: Tuxedo

first: Lisa

last: Passantino

state: New York

address: 57 Old Forge Road

department: School of Medicine

institute: New York University

description: treatment protocol 1

hyb_protocol: Samples were hybridized with Affymetrix Human Gene 1.0 ST Arrays and scanned at the NYU Cancer Institute Genomics Facility.

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

data_processing: Data were processed using R. Data were imported and normalized using SCAN.UPC with a custum library provided by BrainArray [HuGene10stv1_Hs_ENTREZG_15.1.0]. Data presented contain EntrezIDs - expression set was filtered to remove negative expression values. EntrezID mapped to gene symbol using R package org.Hs.eg. Data were analyzed for significance using LIMMA with FDR correction.

source_name: Beas-2B unexposed parental

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Immortalized human bronchial epithelial cells (Beas-2B; #CRL-9609, ATCC, Manassas, VA) were cultured in 1X Dulbecco’s Modified Eagle Medium (DMEM; ordered in-house from NYU) supplemented with 10% fetal bovine serum (FBS; Atlanta Biologicals, Lawrenceville, GA) and 100ug/mL Pen Strep (GIBCO, Grand Island, NY) (“complete culture media”). The cells were maintained in 25 cm2 polystyrene tissue culture flasks in an incubator at 37oC with 5% CO2 and 100% humidity. The media was changed every 2 days, and the cells were passaged every 4 days using 0.05% trypsin-EDTA (GIBCO).

extract_protocol: Total RNA was isolated using Trizol (Invitrogen). The isolated T.RNA was subjected to a colum purification using Rneasy Plus Micro Kit (Qiagen)

treatment_protocol: Treatment protocol 1: Beas-2B cells were seeded at 3X105 into 25 cm2 polystyrene tissue culture flasks. The flasks then received media containing 10 µM NaVO3 and the cells were cultured for 4 weeks. Control cells received distilled water in place of NaVO3. Control parental cells did not recieve distilled water. Every 3-4 days, the cells were trypsinized, counted, and re-seeded into fresh 25 cm2 flasks at a density of 3X105 live cells/flask, and given fresh media with 10 µM NaVO3. A subset of cells were only treated for 24 hours (acute exposure). Soft Agar Assay: Warm (37oC, 2 mL/well) base agar solution (0.5% [w/v] agar [#214530, BD Biosciences, San Diego, CA] in 1X DMEM complete culture media) was poured into each well of 6-well untreated polystyrene plates. The base layer was allowed to solidify at 4oC for 2 hours. Then 2 mL of a warm (37oC) top agar solution consisting of 5,000 cells in 0.35% agar + 1X DMEM complete tissue culture media was added over the base layer. Duplicate wells were used for each treatment and control cells. The 6-well plates were then incubated at 37oC in the tissue culture incubator for 3 weeks; 0.5 mL of fresh media was added once per week without disturbing the cells. After 3 weeks, the colonies were either stained overnight with INT/BCIP solution (#11-681-460-001, Roche, New York, NY) in 0.1 M Tris/0.05 M MgCl2/0.1 M NaCl to visualize (and subsequently permit a count of) all colonies, or colonies were instead extracted from the agar. Each extracted colony was trypsinized in a 96-well plate in order to break up the colony, and then transferred into a 24-well plate to begin expansion of the individual transformed and control clones. Control parental cells were not grown in soft agar.  Treatment protocol 2: Beas-2B cells were seeded at 3X105 into 25 cm2 polystyrene tissue culture flasks. The flasks then received media containing 10 µM NaVO3 and the cells were cultured for 4 weeks. Control cells received distilled water in place of NaVO3. Every 3-4 days, the cells were trypsinized, counted, and re-seeded into fresh 25 cm2 flasks at a density of 3X105 live cells/flask, and given fresh media with the appropriate concentration of NaVO3. A subset of these cells were cultured in media with 10 µM NaVO3 for 1 extra week, totalling 5 weeks of exposure, and the second set was cultured in the presence of NaVO3 for 4 weeks and then recovered in the absence of NaVO3 for 1 week.

tag: cell line

tag: treatment

value: unexposed to vanadate


title: Vanadate recovered cells_rep2 [DEG.ABC]

description: treatment protocol 2

source_name: Vanadate recovered cells

value: exposed to vanadate


title: Vanadate recovered cells_rep1 [DEG.ABC]

description: treatment protocol 2


title: male control

description: miRNA level in plasma

source_name: male control plasma

value: healthy


title: Vanadate exposed cells_rep1 [DEG.ABC]

description: treatment protocol 2

source_name: Vanadate exposed cells


title: Vanadate exposed cells_rep2 [DEG.ABC]

description: treatment protocol 2


title: R449

source_name: temporal neocortex, 8.17 yrs


title: R458

source_name: temporal neocortex, 10.5 yrs


title: R446

source_name: temporal neocortex, 8.08 yrs


title: Control unexposed cells_rep2 [DEG.ABC]

description: treatment protocol 2

source_name: Control unexposed cells


title: female control

description: miRNA level in plasma

source_name: female control plasma


title: R451

source_name: temporal neocortex, 42.5 yrs


title: R445

source_name: frontal neocortex, 6.25 yrs

value: frontal neocortex


title: Pi_adult_mi_RNA_pool_c

city: Dummerstorf

first: Klaus

last: Wimmers

address: Wilhelm-Stahl-Allee 2

country: Germany

institute: Leibniz Institute for Farm Animal Biology (FBN)

description: Gene expression data from skeletal muscle of adult pig breed (Pi).

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 42C on Affymetrix GeneChip miRNA arrays. GeneChips were washed and processed to detect biotin-containing transcripts by Streptavidin-PE (Phycoerythrin) conjugate.

scan_protocol: Scanning using the GeneChip scanner 3000 were performed according to Affymetrix protocols

data_processing: Data were analysed with Affymetrix GCOS 1.1.1 software using global scaling to a target signal of 500.

organism: Sus scrofa

source_name: Musculus longissimus dorsi tissue from adult pig taken at slaughter

label_protocol: Biotinylated cRNA were prepared from miRNA according to FlashTag™ Biotin RNA Labeling Kit for Affymetrix GeneChip miRNA arrays (Genisphere, Hatfield, PA, USA) according to the manufacturer’s recommendations Affymetrix® GeneChip® miRNA Array protocols (Affymetrix, Santa Clara, CA, USA)

extract_protocol: Total RNA was isolated using Qiagen miReasy Mini kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol for small-RNA. Then small RNA was cleaned up using the Rneasy MinElute Clean up kit  (Qiagen, Hilden, Germany).

tag: breed

value: Pietrain

tag: developmental stage

value: adult

tag: tissue type

value: skeletal muscle


title: female-ICH

description: miRNA level in plasma

source_name: female-ICH patient plasma

value: female

value: intracerebral hemorrhage


title: male-ICH

description: miRNA level in plasma

source_name: male-ICH patient plasma

value: male


title: Transformed vanadate exposed clone_rep5 [DEG.ABC]

description: treatment protocol 1

source_name: Transformed vanadate exposed clone


title: R439

source_name: frontal neocortex, 11 yrs

value: 11 yrs

value: Black


title: R447

source_name: temporal neocortex, 2.58 yrs

value: temporal neocortex

value: White


title: Control unexposed cells_rep1 [DEG.ABC]

description: treatment protocol 2


title: Pi_adult_mi_RNA_pool_a


title: Pi_adult_mi_RNA_pool_b


title: Transformed vanadate exposed clone_rep4 [DEG.ABC]

description: treatment protocol 1


title: Pi_91_mi_RNA_pool_c

description: Gene expression data from skeletal muscle of peripubertal pigs breed (Pi).

source_name: Musculus longissimus dorsi tissue from embryo taken at slaughter, pregnancy day 91

value: 91 dpc


title: Pi_91_mi_RNA_pool_b


title: R438

source_name: temporal neocortex, 11.08 yrs


title: R442

source_name: temporal neocortex, 8.58 yrs


title: Transformed vanadate exposed clone_rep3 [DEG.ABC]

description: treatment protocol 1


title: Pi_63_mi_RNA_pool_c

source_name: Musculus longissimus dorsi tissue from embryo taken at slaughter, pregnancy day 63

value: 63 dpc


title: Transformed vanadate exposed clone_rep1 [DEG.ABC]

description: treatment protocol 1


title: IM006_PB1-F2Del_10^3pfu_4d_2

source_name: lung, PB1-F2del infected, 4d

tag: strain

value: lung


title: R437

source_name: temporal neocortex, 10.33 yrs


title: R436

source_name: temporal neocortex, 10.17 yrs


title: Transformed vanadate exposed clone_rep2 [DEG.ABC]

description: treatment protocol 1


title: Pi_63_mi_RNA_pool_b


title: Pi_91_mi_RNA_pool_a


title: Control unexposed clone_rep2 [DEG.ABC]

description: treatment protocol 1

source_name: Control unexposed clone

value: unexposed to vanadate


title: R431

source_name: temporal neocortex, 15.58 yrs


title: Pi_63_mi_RNA_pool_a


title: R432

source_name: temporal neocortex, 3 yrs

value: 3 yrs


title: DL_adult_mi_RNA_pool_c

description: Gene expression data from skeletal muscle of adult pig breed (DL).

value: German landrace


title: R435

source_name: inferior occipital, 7.17 yrs

value: inferior occipital


title: Control unexposed clone_rep3 [DEG.ABC]

description: treatment protocol 1


title: R433

source_name: temporal neocortex, 10.92 yrs


title: R426

source_name: frontal neocortex, 0.92 yrs

value: frontal neocortex

value: Asian


title: DL_adult_mi_RNA_pool_b

source_name: Musculus longissimus dorsi tissue from adult pig taken at slaughter

value: adult

value: skeletal muscle


title: DL_adult_mi_RNA_pool_a


title: R430

source_name: temporal neocortex, 6 yrs

value: female

value: 6 yrs


title: IV B vs. IV b

city: Seoul

first: Sang Hyuk

last: Park

address: Dongdaemungu, Hoegidong 1

country: South Korea

institute: Kyung Hee University

description: cultured human periodontal ligament cells (control) VS cryopreserved and cultured periodontal ligament cells (cryopreserved group) replicate 3

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing: Agilent Feature Extraction Software (v 9.3.2.1) was used for background subtraction and LOWESS normalization.

source_name: cryopreserved human periodontal ligament cells

label_protocol: 10 µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label

growth_protocol: Immediately after the teeth were extracted, periodontal ligament tissues were gently separated from the lower 2/3 of the root surface of the premolars with a No. 11 scalpel blade, maintaining aseptic conditions. Then tissues from each tooth were cut into small pieces for cell culture in medium made by mixing Dulbecco's modified Eagle's medium (Gibco BRL, Life Technologies, Grand Island, NY, USA), 10% fetal bovine serum (Gibco BRL, Life Technologies, Grand Island, NY, USA) and antibiotics, consisting of penicillin-G (100U/ml), streptomycin (100 ㎍/ml), Fungizone (0.25 g/ml) (Gemini Bio-Products, Inc., Woodland, CA, USA), in a humidified atmosphere of 5% CO2 at 37℃.   Periodontal ligament cells out-grown from the tissues were subcultured and grown to confluence. Then subcultures were successively passed at 1:2 ratio until three passages. PDL cells that had been cultured through three passages were used in the experiments.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions.

treatment_protocol: The premolars were placed in cryopreservation vials containing 10% dimethyl sulfoxide (Me2SO: Sigma Chemical, St. Louis. MO, USA) within 5 minutes and stored in a liquid nitrogen at -196℃ for 1 week. Then thawed in a water bath rapidly at 37℃ for 3 minutes. For the experiment, when the preservation medium became liquid, the teeth were taken out of the cryopreservation vials, and washed with PBS. Then periodontal ligament tissues were separated and PDL cells out-grown from the tissues had been cultured through three passages.

value: primary cell

value: 3 passages


title: lll B vs. lll a

description: cultured human periodontal ligament cells (control) VS cryopreserved and cultured periodontal ligament cells (cryopreserved group) replicate 2

value: cryopreserved human periodontal ligament cells


title: Control unexposed clone_rep1 [DEG.ABC]

description: treatment protocol 1


title: R425

source_name: temporal neocortex, 6.17 yrs

value: temporal neocortex

value: male

value: White


title: miR Clip CD3-28-T cells biological rep 2

city: Ann Arbor

first: yaping

last: sun

state: Michigan

address: 1500 E Medical Center Dr.

department: internal medicine

institute: university of michigan

description:
AGO-Clip Enriched miRNA from CD3-CD28 antibody activated T cells
Hy3 is used as a slide marker

hyb_protocol: The denatured labeled samples were hybridized to microRNA Array slides at 56 ºC for 16 h using an Agilent Hybridization SureHyb chamber and gasket slide followed by stringency wash protocol.

scan_protocol: Stained slides were scanned using GenePix 4000 microarray scanner. Because the design for quality control has to be monitored with green (Hy3-F532) channel for demonstrating existing internal markers on Exiqon 6th generation miRCURY LNA microRNA Arrays, the scanning parameters were set as dual channels (Hy5-F635 for labeled samples with PMTGain 600 and Hy3-532 for internal markers with PMTGain 100 or 600).

data_processing: The images were captured and analyzed by GAL-file (Exiqon Inc, Woburn, MA) which covers 1032 miRNA IDs annotated by version 16.0 of miRBase (http://microrna.sanger.ac.uk). The median of the spot median signals after substraction of relative background signals was used as the expression value. The expression levels were calculated with signals above the background level.

source_name: T cells cultivated with anti-CD3e and anti-CD28 mAB9

label_protocol: miRNA microarray experiments were conducted with single label Hy5 on Exiqon 6th generation miRCURY LNA microRNA Array.

growth_protocol: Mixed T cell culture was performed with 2x106/ml T cells in the presence of syngeneic C57BL/6, or allogeneic BALB/c Dendritic cells (at the ratio of 20:1) or cultivated with 0.1 ug/ml anti-CD3e and anti-CD28 mAB (BD Biosciences) for 24 h. All cells were collected, incubated with CD11c microbead for 30 min and T cells were isolated by magnetically negative selection (MACS).

extract_protocol: The total RNA, including miRNA and other small RNA molecules was purified from CLIP agarose beads using miRNeasy Mini Kit according to the manufacturer's instructions and the RNA was verified by an Agilent 2100 Bioanalyzer profile.

treatment_protocol: Purified T cells were exposed to 400 m J/cm2 UVA light first, and additional 200 ml/ cm2  from a UVAR light set. Cells were collected and lysed on ice for 20 min with lysis buffer. The supernatants were subjected to preclearance. Protein A agarose beads were added with bridge Ab at room temperature for 60 min, then added with AGO antibody at 4°C for 5 h, finally added with crosslinked and pre-cleared lysate to prepared beads. Beads/lysates mix was rotated for 4 h at 4°C. Then, the beads were washed with lysis buffer, high salt lysis buffer and a final wash with lysis buffer containing 0.05% NP-40 and followed by DNase treatment.

value: T lymphocytes

tag: clip antibody

value: AGO


title: DL_91mi_RNA_pool_c

description: Gene expression data from skeletal muscle of peripubertal pigs breed (DL).

source_name: Musculus longissimus dorsi tissue from embryo taken at slaughter, pregnancy day 91

value: 91 dpc


title: R422

source_name: frontal neocortex, 14.25 yrs


title: miR Clip CD3-28-T cells biological rep 1

value: T cells cultivated with anti-CD3e and anti-CD28 mAB9


title: DL_91mi_RNA_pool_b

value: German landrace


title: R420

source_name: temporal neocortex, 8.75 yrs


title: R421

source_name: occipital neocortex, 11.58 yrs

value: occipital neocortex


title: Affy ClipCD3-28-T cells biological rep 2

description: AGO-Clip Enriched transcripts from CD3-CD28 antibody activated T cells

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on GeneChip Affymetrix mouse genome 430 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Stained arrays were scanned on an Agilent Gene Array Scanner (Affymetrix) with a 560-nm filter.

data_processing: Data were published and analyzed using R statistical environment (http://cran.r-project.org/) provided by Bioconductor (http://www.bioconductor.org/). The expression values were calculated for each gene using a robust multi-array average (RMA) (Irizarry RA, 2003). This is a modeling strategy that converts the PM probe values into an expression value (log2 transformed) for each gene.

label_protocol: Samples were processed using WT-Ovation™ Pico System  ( Affymetrix) which requires only 500 pg of total RNA and a single round of amplification for samples with even stricter concentration restraints. This system incorporates oligo dT and random primers for amplification at the 3’ end and throughout the whole transcriptome.Biotinylated cRNA were prepared according to the Affymetrix protocol.

growth_protocol: Mixed T cell culture was performed with 2x106/ml T cells in the presence of syngeneic C57BL/6, or allogeneic BALB/c Dendritic cells (at the ratio of 20:1) or cultivated with 0.1 ug/ml anti-CD3e and anti-CD28 mAB9 (BD Biosciences) for 24 h. All cells were collected, incubated with CD11c microbead for 30 min and T cells were isolated by magnetically negative selection ( MACS, Pan T cell isolation Kit II).

extract_protocol: Trizol LS extraction of total RNA was performed according to the manufacturer's instructions and the total RNA was verified by an Agilent 2100 Bioanalyzer profile.


title: Affy ClipCD3-28-T cells biological rep 1


title: miR Clip Allo-T cells biological rep 2

description:
AGO-Clip Enriched miRNA from Allo-T cells
Hy3 is used as a slide marker

source_name: T cells co-cultured with allongeneic dendritic cells


title: DL_91mi_RNA_pool_a


title: lll C vs. ll b

description: cultured human periodontal ligament cells (control) VS cryopreserved and cultured periodontal ligament cells (cryopreserved group) replicate 1


title: Affy ClipAllo-T cells biological rep 3

description: AGO-Clip Enriched transcripts from Allo-T cells

value: T cells co-cultured with allongeneic dendritic cells


title: Transformed vanadate exposed clone_rep1 [DEG.C]

description: soft agar assay

data_processing:
Gene expression changes for transformed clones and parental cells versus control clones were analyzed using GeneSpring GX software (Agilent Technologies, Santa Clara, CA). Significant genes were determined by a moderated T-test with p-values < 0.05. The p-values were subjected to FDR correction for multiple hypothesis testing. Control clones were used as the controls for all samples to be compared to.
probe group file: HuGene-1_0-st-v1_na31_hg19_2010-09-03.pgf
meta-probeset file: HuGene-1_0-st-v1_na31_hg19_2010-09-03.mps

source_name: Vanadate exposed clone

treatment_protocol: Beas-2B cells were seeded at 3X105 into 25 cm2 polystyrene tissue culture flasks. The flasks then received media containing 10 µM NaVO3 and the cells were cultured for 4 weeks. Control cells received distilled water in place of NaVO3. Every 3-4 days, the cells were trypsinized, counted, and re-seeded into fresh 25 cm2 flasks at a density of 3X105 live cells/flask, and given fresh media with 10 µM NaVO3. A subset of cells were only treated for 24 hours (acute exposure). Soft Agar Assay: Warm (37oC, 2 mL/well) base agar solution (0.5% [w/v] agar [#214530, BD Biosciences, San Diego, CA] in 1X DMEM complete culture media) was poured into each well of 6-well untreated polystyrene plates. The base layer was allowed to solidify at 4oC for 2 hours. Then 2 mL of a warm (37oC) top agar solution consisting of 5,000 cells in 0.35% agar + 1X DMEM complete tissue culture media was added over the base layer. Duplicate wells were used for each treatment and control cells. The 6-well plates were then incubated at 37oC in the tissue culture incubator for 3 weeks; 0.5 mL of fresh media was added once per week without disturbing the cells. After 3 weeks, the colonies were either stained overnight with INT/BCIP solution (#11-681-460-001, Roche, New York, NY) in 0.1 M Tris/0.05 M MgCl2/0.1 M NaCl to visualize (and subsequently permit a count of) all colonies, or colonies were instead extracted from the agar. Each extracted colony was trypsinized in a 96-well plate in order to break up the colony, and then transferred into a 24-well plate to begin expansion of the individual transformed and control clones.

value: exposed to vanadate


title: Affy ClipCD3-28-T cells biological rep 3


title: miR Clip Allo-T cells biological rep 1


title: Transformed vanadate exposed clone_rep4 [DEG.C]

description: soft agar assay


title: DL_63_mi_RNA_pool_c

source_name: Musculus longissimus dorsi tissue from embryo taken at slaughter, pregnancy day 63

value: 63 dpc

value: skeletal muscle


title: Transformed vanadate exposed clone_rep3 [DEG.C]

description: soft agar assay


title: DL_63_mi_RNA_pool_b


title: miR Clip Syn-T cells biological rep 1

description:
AGO-Clip Enriched miRNA from Syn-T cells
Hy3 is used as a slide marker

source_name: T cells co-cultured with syngeneic dendritic cells


title: DL_63_mi_RNA_pool_a


title: Vanadate acute exposure [DEG.C]

description: culture dish only

source_name: Vanadate acute exposure


title: Affy ClipAllo-T cells biological rep 2


title: Transformed vanadate exposed clone_rep2 [DEG.C]

description: soft agar assay


title: Transformed vanadate exposed clone_rep5 [DEG.C]

description: soft agar assay


title: Affy ClipAllo-T cells biological rep 1


title: Affy ClipSyn-T cells biological rep 3

description: AGO-Clip Enriched transcripts from Syn-T cells

value: T cells co-cultured with syngeneic dendritic cells


title: Control unexposed clone_rep1 [DEG.C]

description: soft agar assay

source_name: Control unexposed clone

value: unexposed


title: Control unexposed clone_rep3 [DEG.C]

description: soft agar assay


title: Control unexposed clone_rep2 [DEG.C]

description: soft agar assay


title: Sample_20

status: Public on Jan 18 2013

city: Cambridge

first: Suraj

last: Menon

address: Li Ka Shing Center, Robinson Way

country: United Kingdom

institute: Cambridge Research Institute, Cancer Research UK

description:
Sample name: 5627224057_K
MCF7 cells treated with 6 hrs of 100nM E2 after 48hrs of siGREB1 transfection
Bead-level data: 5627224057_K.txt

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing:
The bead-level data were preprocessed using BASH (Cairns et al. (2008) Bioinformatics 24(24):2921-2), a function from the beadarray package (Dunning et al (2007) Bioinformatics 23(16):2183-4) in Bioconductor, and also log base 2 transformed and quantile normalised using the beadarray package.
NOTE: At our institute we use the Bioconductor beadarray software to carry out spatial artefact removal(e.g. with tools such as BASH and HULK), and this can only be carried out on the bead-level data as is provided in the text files. This cannot be carried out on the bead-summarised data such as is provided in the non-normalised data matrices or the output of BeadStudio. As such we would prefer for Illumina microarray users to provide these text files on GEO so that artefact correction can be carried out.
Related to the bead-level .txt files are the two Metrics.txt files (linked as supplementary files on the Series record) which are generated by the scanner and contain metrics such as signal and noise levels which are useful for array QC.

source_name: MCF-7 human cell lines

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

growth_protocol: Cells were grown in charcoal dextran treated DMEM for three days prior to siRNA treatment

extract_protocol: Cells were extracted using Qiagen RNAeasy extraction kit

treatment_protocol: Cells were treated with 100nm siNT or siGREB1 by lipofectamine based transfection for 6 hours. 100nM of drug ICI182 was added the next day for 24hrs. Cells were then treated with 100nM of Estrogen or vehicle for 6 or 24 hrs

value: MCF-7 cells (human breast adenocarcinoma cell line)

tag: sample group

tag: sitype

value: siGreb

tag: treatment time (hours)


title: Sample_18

description:
Sample name: 5627224057_I
MCF7 cells treated with 24 hrs of 100nM E2 after 48hrs of siGREB1 transfection
Bead-level data: 5627224057_I.txt


title: Sample_10

description:
Sample name: 5627224057_L
MCF7 cells  48hrs of siNT transfection
Bead-level data: 5627224057_L.txt

value: siNT

value: vehicle

value: control


title: Sample_12

description:
Sample name: 5627224057_F
MCF7 cells treated with 24 hrs of 100nM E2 after 48hrs of siNT transfection
Bead-level data: 5627224057_F.txt


title: Sample_21

description:
Sample name: 5627224039_L
MCF7 cells treated with 24 hrs of 100nM E2 after 48hrs of siGREB1 transfection
Bead-level data: 5627224039_L.txt


title: Sample_19

description:
Sample name: 5627224057_G
MCF7 cells  48hrs of siGREB1 transfection
Bead-level data: 5627224057_G.txt


title: Sample_05

description:
Sample name: 5627224057_H
MCF7 cells treated with 6 hrs of 100nM E2 after 48hrs of siNT transfection
Bead-level data: 5627224057_H.txt


title: Sample_22

description:
Sample name: 5627224057_A
MCF7 cells  48hrs of siGREB1 transfection
Bead-level data: 5627224057_A.txt