title: F.candida_pentachlorophenol_Day7_2

city: Beijing

first: Min

last: Qiao

address: Shuangqing Road 18

country: China

institute: Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences

description: Pool of approximately thirty animals of F.candida, age 23 days old, exposed for 7 days in a jar containing pentachlorophenol spiked artificial soil

hyb_protocol: Gene Expression Hybridization Kit (Agilent Technologies) was used for hybridization,which was done at 65°C for 17 hours rotating at 10 rpm in an incubator. After hybridization the arrays were washed using Gene Expression Wash Buffer Kit (Agilent Technologies).

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

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Folsomia candida

source_name: F.candida, pentachlorophenol, 7 day

label_protocol: 875 ng input of total RNA was used for ampliﬁcation and labeling with the Agilent Low-Input Fluorescent Linear Ampliﬁcation Kit (Agilent Technologies), according to the manufacturer’s guidelines. Labeled and amplified cRNA was purified using RNeasy Mini kit (Qiagen)

growth_protocol: Organisms were cultured in a mixture of plaster of Paris and charcoal (9:1) and kept under controlled conditions with a photoperiod 12:12 h (light:dark), a temperature of 20oC±2oC and a humidity of 70±5%

extract_protocol: RNA was extracted from each replicate (pool of 30 animals) using the Trizol extraction method (Invitrogen)

treatment_protocol: 30 animals (23 days old) were exposed per jar containing 30g of pentachlorophenol polluted soil with three replicates per treatment

tag: treatment

value: pentachlorophenol

tag: time

value: 7 day


title: F.candida_pentachlorophenol_Day2_3

status: Public on Oct 30 2016

type: RNA

description: Pool of approximately thirty animals of F.candida, age 23 days old, exposed for 2 days in a jar containing pentachlorophenol spiked artificial soil

molecule: total RNA

source_name: F.candida, pentachlorophenol, 2 day

value: 2 day


title: F.candida_pentachlorophenol_Day1_3

description: Pool of approximately thirty animals of F.candida, age 23 days old, exposed for 1 days in a jar containing pentachlorophenol spiked artificial soil

source_name: F.candida, pentachlorophenol, 1 day

value: 1 day


title: F.candida_pentachlorophenol_Day7_3


title: F.candida_pentachlorophenol_Day2_1


title: F.candida_control_3

description: Pool of approximately thirty animals of F.candida, age 23 days old, exposed for 7 days in a jar containing 30g of control/untreated artificial soil

source_name: F.candida, untreated, 7 day

value: untreated


title: F.candida_pentachlorophenol_Day1_1


title: F.candida_pentachlorophenol_Day1_2


title: F.candida_pentachlorophenol_Day2_2


title: F.candida_control_2

description: Pool of approximately thirty animals of F.candida, age 23 days old, exposed for 2 days in a jar containing 30g of control/untreated artificial soil

source_name: F.candida, untreated, 2 day


title: F.candida_control_1

description: Pool of approximately thirty animals of F.candida, age 23 days old, exposed for 1 days in a jar containing 30g of control/untreated artificial soil

source_name: F.candida, untreated, 1 day


title: miRNAs from ICC.V78 patient

city: Seoul

first: Jaehoon

last: Lee

address: 38, Baumoe-ro

country: South Korea

institute: LG Electronics

description: serum miRNAs from ICC patient

hyb_protocol: labelled RNA was heated to 99°C for 5 minutes and then to 45°C for 5 minutes. RNA-array hybridization was performed with agitation at 60 rotations per minute for 16 hours at 48°C on an Affymetrix® 450 Fluidics Station

scan_protocol: The chips were washed and stained using a Genechip Fluidics Station 450 (Affymetrix). The chips were then scanned using an Affymetrix GCS 3000 scanner

data_processing: cel files were analysed and rma-normalized by using the Expression Console software

label: biotin

organism: Homo sapiens

source_name: serum miRNA (intrahepatic cholangiocarcinoma): validation

label_protocol: RNA samples (130 ng) were labelled using the FlashTag™ Biotin RNA Labeling Kit (Genisphere, Hatfield, PA)

extract_protocol: Total RNA containing miRNA was extracted from the serum samples using the Serum miRNA purification kit (Genolution, Seoul, Korea) according to the manufacturer’s instructions, and the RNA was resuspended with 12 μL of RNase-free water and stored at -80°C until microarray or qRT-PCR

treatment_protocol: Serum samples were collected in 10-mL BD serum tubes and centrifuged at 4°C for 20 minutes at 3000 rpm.

tag: gender

value: M

tag: age


title: miRNAs from ICC.V77 patient

description: serum miRNAs from ICC patient


title: miRNAs from ICC.V79 patient

description: serum miRNAs from ICC patient


title: miRNAs from ICC.V80 patient

description: serum miRNAs from ICC patient


title: miRNAs from ICC.V81 patient

description: serum miRNAs from ICC patient


title: miRNAs from ICC.V75 patient

description: serum miRNAs from ICC patient


title: miRNAs from ICC.V74 patient

description: serum miRNAs from ICC patient

value: F


title: F.candida_pentachlorophenol_Day7_1


title: miRNAs from ICC.V76 patient

description: serum miRNAs from ICC patient


title: miRNAs from ICC.V71 patient

description: serum miRNAs from ICC patient


title: miRNAs from ICC.V72 patient

description: serum miRNAs from ICC patient


title: miRNAs from ICC.V70 patient

description: serum miRNAs from ICC patient


title: miRNAs from ICC.V67 patient

description: serum miRNAs from ICC patient


title: Arabidopsis Col-Fe root biological rep2

city: Taichung

first: I-Chun

last: Pan

address: Kuo-Kuang

department: Horticulture

country: Taiwan

institute: Chung Hsing University

description: R Col-Fe-2

hyb_protocol: 11 ug labeled samples were hybridized to GeneChip at 45℃ for 16.5 hours.

scan_protocol: the GeneChip were scanned with Affymetrix GeneChip Scanner 7G.

data_processing:
The data were analyzed with GeneSpring  5.0 (version 11.5, Agilent, Santa Clara, USA) using RMA method.
Data was Filter by expression, the lower and upper cut-off values are 20.0 and 19195.738 respectively.Entities where at least 100 percent of samples in any 1 out of 8 conditions have values within cut-off.

organism: Arabidopsis thaliana

source_name: 10 days plants treated with iron deficiency mediem for 3 days

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

growth_protocol: Arabidopsis plants grown in a growth chamber with 21C under continuous illumination

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

treatment_protocol: Ten days old plants were treated with iron-suficient(40 uM FeEDTA) or iron-deficiency (100 µM 3-(2-pyridyl)-5,6-diphenyl-1,2,4-triazine sulfonate) mediem for 3 days.

tag: ecotype

value: Col

tag: genotype/variation

value: wild type

tag: tissue

value: Roots

value: 13 days

tag: treated with

value: iron deficiency medium for 3 days


title: miRNAs from ICC.V73 patient

description: serum miRNAs from ICC patient


title: miRNAs from ICC.V69 patient

description: serum miRNAs from ICC patient


title: miRNAs from ICC.V64 patient

description: serum miRNAs from ICC patient


title: miRNAs from ICC.V61 patient

description: serum miRNAs from ICC patient


title: miRNAs from ICC.V62 patient

description: serum miRNAs from ICC patient


title: miRNAs from ICC.V68 patient

description: serum miRNAs from ICC patient


title: miRNAs from ICC.V59 patient

description: serum miRNAs from ICC patient


title: miRNAs from ICC.V65 patient

description: serum miRNAs from ICC patient


title: miRNAs from ICC.V60 patient

description: serum miRNAs from ICC patient


title: miRNAs from ICC.V66 patient

description: serum miRNAs from ICC patient


title: miRNAs from ICC.V57 patient

description: serum miRNAs from ICC patient


title: miRNAs from ICC.V58 patient

description: serum miRNAs from ICC patient


title: miRNAs from ICC.V55 patient

description: serum miRNAs from ICC patient


title: miRNAs from ICC.V54 patient

description: serum miRNAs from ICC patient


title: miRNAs from ICC.V56 patient

description: serum miRNAs from ICC patient


title: miRNAs from ICC.V47 patient

description: serum miRNAs from ICC patient


title: miRNAs from ICC.V49 patient

description: serum miRNAs from ICC patient


title: miRNAs from ICC.V52 patient

description: serum miRNAs from ICC patient


title: miRNAs from ICC.V51 patient

description: serum miRNAs from ICC patient


title: miRNAs from ICC.V48 patient

description: serum miRNAs from ICC patient


title: miRNAs from ICC.V50 patient

description: serum miRNAs from ICC patient


title: miRNAs from ICC.V42 patient

description: serum miRNAs from ICC patient


title: miRNAs from ICC.V43 patient

description: serum miRNAs from ICC patient


title: miRNAs from ICC.V46 patient

description: serum miRNAs from ICC patient


title: miRNAs from ICC.V41 patient

description: serum miRNAs from ICC patient


title: miRNAs from ICC.V44 patient

description: serum miRNAs from ICC patient


title: miRNAs from ICC.V45 patient

description: serum miRNAs from ICC patient


title: miRNAs from ICC.V63 patient

description: serum miRNAs from ICC patient


title: miRNAs from ICC.V40 patient

description: serum miRNAs from ICC patient


title: miRNAs from ICC.V53 patient

description: serum miRNAs from ICC patient


title: miRNAs from ICC.V39 patient

description: serum miRNAs from ICC patient


title: miRNAs from ICC.V35 patient

description: serum miRNAs from ICC patient


title: miRNAs from ICC.V37 patient

description: serum miRNAs from ICC patient


title: miRNAs from ICC.V33 patient

description: serum miRNAs from ICC patient


title: miRNAs from ICC.V30 patient

description: serum miRNAs from ICC patient


title: miRNAs from ICC.V31 patient

description: serum miRNAs from ICC patient


title: miRNAs from ICC.V36 patient

description: serum miRNAs from ICC patient


title: miRNAs from ICC.V38 patient

description: serum miRNAs from ICC patient


title: miRNAs from ICC.V34 patient

description: serum miRNAs from ICC patient


title: miRNAs from ICC.V27 patient

description: serum miRNAs from ICC patient


title: miRNAs from ICC.V29 patient

description: serum miRNAs from ICC patient


title: miRNAs from ICC.V25 patient

description: serum miRNAs from ICC patient


title: miRNAs from ICC.V26 patient

description: serum miRNAs from ICC patient


title: miRNAs from ICC.V28 patient

description: serum miRNAs from ICC patient


title: miRNAs from ICC.V21 patient

description: serum miRNAs from ICC patient


title: miRNAs from ICC.V22 patient

description: serum miRNAs from ICC patient


title: miRNAs from ICC.V18 patient

description: serum miRNAs from ICC patient


title: miRNAs from ICC.V16 patient

description: serum miRNAs from ICC patient


title: miRNAs from ICC.V32 patient

description: serum miRNAs from ICC patient


title: miRNAs from ICC.V14 patient

description: serum miRNAs from ICC patient


title: miRNAs from ICC.V19 patient

description: serum miRNAs from ICC patient


title: miRNAs from ICC.V23 patient

description: serum miRNAs from ICC patient


title: miRNAs from ICC.V20 patient

description: serum miRNAs from ICC patient


title: miRNAs from ICC.V17 patient

description: serum miRNAs from ICC patient


title: miRNAs from ICC.V12 patient

description: serum miRNAs from ICC patient


title: miRNAs from ICC.V13 patient

description: serum miRNAs from ICC patient


title: miRNAs from ICC.V11 patient

description: serum miRNAs from ICC patient


title: miRNAs from ICC.V10 patient

description: serum miRNAs from ICC patient


title: miRNAs from ICC.V15 patient

description: serum miRNAs from ICC patient


title: miRNAs from ICC.V8 patient

description: serum miRNAs from ICC patient


title: miRNAs from ICC.V6 patient

description: serum miRNAs from ICC patient


title: miRNAs from ICC.V7 patient

description: serum miRNAs from ICC patient


title: miRNAs from ICC.V9 patient

description: serum miRNAs from ICC patient


title: miRNAs from ICC.V4 patient

description: serum miRNAs from ICC patient


title: miRNAs from ICC.V2 patient

description: serum miRNAs from ICC patient


title: miRNAs from ICC.V3 patient

description: serum miRNAs from ICC patient


title: miRNAs from ICC.V24 patient

description: serum miRNAs from ICC patient


title: miRNAs from ICC.V1 patient

description: serum miRNAs from ICC patient


title: miRNA from N19

description: serum miRNAs from healthy control

source_name: serum miRNA (healthy control)


title: miRNA from N17

description: serum miRNAs from healthy control


title: miRNA from N16

description: serum miRNAs from healthy control


title: miRNA from N18

description: serum miRNAs from healthy control


title: miRNA from N12

description: serum miRNAs from healthy control


title: miRNA from N10

description: serum miRNAs from healthy control


title: miRNA from N11

description: serum miRNAs from healthy control


title: miRNA from N13

description: serum miRNAs from healthy control


title: miRNA from N15

description: serum miRNAs from healthy control


title: miRNA from N6

description: serum miRNAs from healthy control


title: miRNA from N7

description: serum miRNAs from healthy control


title: miRNA from N8

description: serum miRNAs from healthy control


title: miRNA from N5

description: serum miRNAs from healthy control


title: miRNA from N4

description: serum miRNAs from healthy control


title: miRNA from N3

description: serum miRNAs from healthy control


title: miRNA from N2

description: serum miRNAs from healthy control


title: miRNAs from Ch10

description: serum miRNAs from cholelithiasis

source_name: serum miRNA (cholelithiasis)


title: miRNA from N1

description: serum miRNAs from healthy control


title: miRNAs from Ch8

description: serum miRNAs from cholelithiasis


title: miRNAs from Ch7

description: serum miRNAs from cholelithiasis


title: miRNAs from Ch5

description: serum miRNAs from cholelithiasis


title: miRNA from N9

description: serum miRNAs from healthy control


title: miRNAs from Ch6

description: serum miRNAs from cholelithiasis


title: miRNAs from Ch4

description: serum miRNAs from cholelithiasis


title: miRNAs from Ch3

description: serum miRNAs from cholelithiasis


title: miRNAs from Ch2

description: serum miRNAs from cholelithiasis


title: miRNAs from GIST1 patient

description: serum miRNAs from GIST patient

source_name: serum miRNA (GIST)


title: miRNAs from GIST2 patient

description: serum miRNAs from GIST patient


title: miRNAs from CC5 patient

description: serum miRNAs from CC patient

source_name: serum miRNA (colorectal cancer)


title: miRNAs from Ch1

description: serum miRNAs from cholelithiasis


title: miRNAs from CC1 patient

description: serum miRNAs from CC patient


title: miRNAs from Ch9

description: serum miRNAs from cholelithiasis


title: miRNAs from CC4 patient

description: serum miRNAs from CC patient


title: miRNAs from SC1 patient

description: serum miRNAs from SC patient

source_name: serum miRNA (stomach cancer)


title: miRNAs from SC6 patient

description: serum miRNAs from SC patient


title: miRNAs from SC5 patient

description: serum miRNAs from SC patient


title: miRNAs from SC2 patient

description: serum miRNAs from SC patient


title: miRNAs from CC3 patient

description: serum miRNAs from CC patient


title: miRNAs from ICC20 patient

description: serum miRNAs from ICC patient

source_name: serum miRNA (intrahepatic cholangiocarcinoma)


title: miRNAs from SC3 patient

description: serum miRNAs from SC patient


title: miRNAs from SC4 patient

description: serum miRNAs from SC patient


title: miRNAs from CC2 patient

description: serum miRNAs from CC patient


title: miRNAs from ICC16 patient

description: serum miRNAs from ICC patient


title: miRNAs from ICC15 patient

description: serum miRNAs from ICC patient


title: miRNAs from ICC14 patient

description: serum miRNAs from ICC patient


title: miRNAs from ICC13 patient

description: serum miRNAs from ICC patient


title: miRNAs from ICC18 patient

description: serum miRNAs from ICC patient


title: miRNAs from ICC19 patient

description: serum miRNAs from ICC patient


title: miRNAs from SC7 patient

description: serum miRNAs from SC patient


title: miRNAs from ICC11 patient

description: serum miRNAs from ICC patient


title: miRNAs from ICC10 patient

description: serum miRNAs from ICC patient


title: miRNAs from ICC12 patient

description: serum miRNAs from ICC patient


title: miRNAs from ICC9 patient

description: serum miRNAs from ICC patient


title: miRNAs from ICC8 patient

description: serum miRNAs from ICC patient


title: miRNAs from ICC7 patient

description: serum miRNAs from ICC patient


title: miRNAs from ICC6 patient

description: serum miRNAs from ICC patient


title: miRNAs from PC83 patient

description: serum miRNAs from PC patient

source_name: serum miRNA (pancreatic cancer)


title: miRNAs from PC84 patient

description: serum miRNAs from PC patient


title: miRNAs from ICC4 patient

description: serum miRNAs from ICC patient


title: miRNAs from ICC2 patient

description: serum miRNAs from ICC patient


title: miRNAs from ICC3 patient

description: serum miRNAs from ICC patient


title: miRNAs from PC77 patient

description: serum miRNAs from PC patient


title: miRNAs from ICC17 patient

description: serum miRNAs from ICC patient


title: miRNAs from ICC1 patient

description: serum miRNAs from ICC patient


title: miRNAs from PC88 patient

description: serum miRNAs from PC patient


title: miRNAs from PC76 patient

description: serum miRNAs from PC patient


title: miRNAs from PC87 patient

description: serum miRNAs from PC patient


title: miRNAs from PC82 patient

description: serum miRNAs from PC patient


title: miRNAs from PC86 patient

description: serum miRNAs from PC patient


title: miRNAs from PC78 patient

description: serum miRNAs from PC patient


title: miRNAs from PC75 patient

description: serum miRNAs from PC patient


title: miRNAs from PC80 patient

description: serum miRNAs from PC patient


title: miRNAs from PC81 patient

description: serum miRNAs from PC patient


title: miRNAs from PC79 patient

description: serum miRNAs from PC patient


title: miRNAs from PC74 patient

description: serum miRNAs from PC patient


title: miRNAs from ICC5 patient

description: serum miRNAs from ICC patient


title: miRNAs from PC73 patient

description: serum miRNAs from PC patient


title: miRNAs from PC85 patient

description: serum miRNAs from PC patient


title: miRNAs from PC71 patient

description: serum miRNAs from PC patient


title: miRNAs from PC72 patient

description: serum miRNAs from PC patient


title: miRNAs from PC69 patient

description: serum miRNAs from PC patient


title: miRNAs from PC70 patient

description: serum miRNAs from PC patient


title: miRNAs from PC63 patient

description: serum miRNAs from PC patient


title: miRNAs from PC64 patient

description: serum miRNAs from PC patient


title: miRNAs from PC66 patient

description: serum miRNAs from PC patient


title: miRNAs from PC65 patient

description: serum miRNAs from PC patient


title: miRNAs from PC60 patient

description: serum miRNAs from PC patient


title: miRNAs from PC62 patient

description: serum miRNAs from PC patient


title: miRNAs from PC61 patient

description: serum miRNAs from PC patient


title: miRNAs from PC55 patient

description: serum miRNAs from PC patient


title: miRNAs from PC53 patient

description: serum miRNAs from PC patient


title: miRNAs from PC54 patient

description: serum miRNAs from PC patient


title: miRNAs from PC52 patient

description: serum miRNAs from PC patient


title: miRNAs from PC56 patient

description: serum miRNAs from PC patient


title: miRNAs from PC59 patient

description: serum miRNAs from PC patient


title: miRNAs from PC68 patient

description: serum miRNAs from PC patient


title: miRNAs from PC51 patient

description: serum miRNAs from PC patient


title: miRNAs from PC47 patient

description: serum miRNAs from PC patient


title: miRNAs from PC57 patient

description: serum miRNAs from PC patient


title: miRNAs from PC49 patient

description: serum miRNAs from PC patient


title: miRNAs from PC50 patient

description: serum miRNAs from PC patient


title: miRNAs from PC48 patient

description: serum miRNAs from PC patient


title: miRNAs from PC46 patient

description: serum miRNAs from PC patient


title: miRNAs from PC43 patient

description: serum miRNAs from PC patient


title: miRNAs from PC44 patient

description: serum miRNAs from PC patient


title: miRNAs from PC42 patient

description: serum miRNAs from PC patient


title: miRNAs from PC67 patient

description: serum miRNAs from PC patient


title: miRNAs from PC45 patient

description: serum miRNAs from PC patient


title: miRNAs from PC58 patient

description: serum miRNAs from PC patient


title: miRNAs from PC41 patient

description: serum miRNAs from PC patient


title: miRNAs from PC38 patient

description: serum miRNAs from PC patient


title: miRNAs from PC39 patient

description: serum miRNAs from PC patient


title: miRNAs from PC37 patient

description: serum miRNAs from PC patient


title: miRNAs from PC40 patient

description: serum miRNAs from PC patient


title: miRNAs from PC35 patient

description: serum miRNAs from PC patient


title: miRNAs from PC36 patient

description: serum miRNAs from PC patient


title: Control

city: Genova

first: Ulrich

last: Pfeffer

address: L. Benzi 10

country: Italy

institute: IRCCS AOU San Martino - IST

description: SAMPLE 2

hyb_protocol: Affymetrix standard

scan_protocol: Affymetrix standard

data_processing: Pre-processing using RMA in R/BioConductor, quintile normalization, medianpolish summarization

organism: Mus musculus

source_name: Doxorubicin-treated

label_protocol: Affymetrix standard

growth_protocol: Cardiomyocytes were isolated and cultured for 48 up to 72hrs in complete medium (DMEM, 10% fetal bovine serum, 5% horse serum)

extract_protocol: RNAeasy kit (Qiagen, Hilden, Germany) follwoing the procedure indicated by the provider

treatment_protocol: Incubation in 0.5% FBS supplemented medium for 1 hour. Pretreated with (treated) or without (control) human amniotic fluid stem cell secretome for three hours followed by incubation with 1µM Doxorubicin for 21 hrs.

tag: strain

tag: developmental stage

value: 2 days postnatal

tag: cell type

value: neonatal cardiomyocytes

tag: pretreated with

value: none (control)

value: 1µM Doxorubicin for 21 hrs


title: miRNAs from PC32 patient

description: serum miRNAs from PC patient


title: miRNAs from PC30 patient

description: serum miRNAs from PC patient


title: miRNAs from PC29 patient

description: serum miRNAs from PC patient


title: miRNAs from PC34 patient

description: serum miRNAs from PC patient


title: miRNAs from PC24 patient

description: serum miRNAs from PC patient


title: miRNAs from PC25 patient

description: serum miRNAs from PC patient


title: miRNAs from PC31 patient

description: serum miRNAs from PC patient


title: miRNAs from PC27 patient

description: serum miRNAs from PC patient


title: miRNAs from PC26 patient

description: serum miRNAs from PC patient


title: miRNAs from PC22 patient

description: serum miRNAs from PC patient


title: miRNAs from PC28 patient

description: serum miRNAs from PC patient


title: miRNAs from ICC.V5 patient

description: serum miRNAs from ICC patient


title: miRNA from N14

description: serum miRNAs from healthy control


title: WT HO-3

city: Chicago

first: Zarema

middle: H

last: Arbieva

state: IL

address: 835 S. Wolcott A301

department: RRC

country: USA

institute: UIC

hyb_protocol: Samples were labeled using the Affymetrix GeneChip® WT PLUS Kit as per manufacturer's protocols.

scan_protocol: The GeneChip® Hybridization, Wash, and Stain Kit was used as per manufacturer’s protocols. The GeneChip® Fluidics Station 450 was used for washing and staining using fluidics script FS450_0002.

data_processing: Signal acquisition done using on the GeneChip® Scanner 3000 7G with AGCC version 4.0.0.1567.

source_name: Superior lobe of right lung

label_protocol: Affymetrix WT Plus labeling protocol

growth_protocol: Litter size of each newborn mice group limited to 6 per nursing mom. Feeding moms alternated between room air and hyperoxia to reduce the effect of toxicity in the mom as per approved protocol

extract_protocol: Lung tissue collected and placed in RNA later at collection. RNA extracted using miniQuiagen's RNeasy® kit

treatment_protocol: One day old Wild type (WT) control and Sphingosine Kinase-1 knock out  (SphK-1 KO)pups exposed to room air (RA) or hyperoxia (HO). Analyzed lung tissue after 7 days of hyperoxia of 75%

value: hyperoxia


title: miRNAs from PC33 patient

description: serum miRNAs from PC patient


title: Treated

description: SAMPLE 1

source_name: human amniotic fluid stem cell secretome + Doxorubicin treated

treatment_protocol: Incubation in 0.5% FBS supplemented medium for 1 hour. Pretreated with (treated) or without (control) human amniotic fluid stem cell secretome for three hours followed by incubation with 1µM Doxorubicin for 6 hrs.

value: 1µM Doxorubicin for 6 hrs


title: miRNAs from PC21 patient

description: serum miRNAs from PC patient


title: miRNAs from PC19 patient

description: serum miRNAs from PC patient


title: miRNAs from PC20 patient

description: serum miRNAs from PC patient


title: SphK-1 KO HO- 2

value: Sphingosine Kinase-1 knock out


title: SphK-1 KO HO- 1


title: WT HO-2


title: SphK-1 KO HO- 3


title: miRNAs from PC23 patient

description: serum miRNAs from PC patient


title: WT HO-1


title: miRNAs from PC18 patient

description: serum miRNAs from PC patient


title: WT RA-3

value: room air


title: WT RA-2


title: miRNAs from PC17 patient

description: serum miRNAs from PC patient


title: miRNAs from PC14 patient

description: serum miRNAs from PC patient


title: miRNAs from PC16 patient

description: serum miRNAs from PC patient


title: SphK-1 KO RA- 1


title: miRNAs from PC12 patient

description: serum miRNAs from PC patient


title: miRNAs from PC13 patient

description: serum miRNAs from PC patient


title: miRNAs from PC15 patient

description: serum miRNAs from PC patient


title: miRNAs from PC11 patient

description: serum miRNAs from PC patient


title: miRNAs from PC9 patient

description: serum miRNAs from PC patient


title: miRNAs from PC10 patient

description: serum miRNAs from PC patient


title: WT RA-1


title: miRNAs from PC8 patient

description: serum miRNAs from PC patient


title: miRNAs from PC7 patient

description: serum miRNAs from PC patient


title: miRNAs from PC6 patient

description: serum miRNAs from PC patient


title: miRNAs from PC5 patient

description: serum miRNAs from PC patient


title: miRNAs from PC4 patient

description: serum miRNAs from PC patient


title: miRNAs from PC3 patient

description: serum miRNAs from PC patient


title: SphK-1 KO RA- 3


title: miRNAs from PC2 patient

description: serum miRNAs from PC patient


title: miRNAs from PC1 patient

description: serum miRNAs from PC patient


title: SphK-1 KO RA- 2


title: Cplex6

type: genomic

city: Houston

first: Shen

last: Gu

state: TX

address: 1 Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

hyb_protocol: Hybridization controls were gender matched (HapMap individual NA10851 as male control and HapMap individual NA15510 as female control).

scan_protocol: Scanned array images were processed using Agilent Feature Extraction software (version 10).

data_processing: Extracted files were analyzed using Agilent Genomic Workbench (version 7.0.4.0).

molecule: genomic DNA

source_name: Cplex6 Genomic DNA

label_protocol: Patient DNA was labeled with Cy5 and control DNA was labeled with Cy3.

extract_protocol: Genomic DNA from whole blood was extracted from each individual.

value: Peripheral blood

value: female

source_name: NA15510 Genomic DNA


title: 172_FollowUp

status: Public on Oct 29 2016

city: New York City

first: Joel

last: Dudley

state: NY

address: 770, Lexington Ave, 15th Floor

department: Genetics and Genomics Sciences

institute: Mount Sinai Health System

description:
172
FollowUp

hyb_protocol: Standard Illumina protocol

scan_protocol: Standard Illumina protocol

data_processing: GSGX Version 1.9.0 is used to compile the raw data from the array instrument. The following Bioconductor packages are used for data processing including quality control, normalization, differential expression estimation, WGCNA.limma 3.28.17; lumi 2.24.0; genefilter 1.54.2; lumiHumanAll.db 1.22.0; data.table 1.9.6; sva 3.20.0;   gplots 3.0.1; pairheatmap 1.0.1

source_name: PBMC

label_protocol: Standard Illumina protocol

extract_protocol: Peripheral blood mononuclear cells were isolated by density gradient centrifugation using Ficoll-paque premium (GE Healthcare, Marlborough, MA).  In brief, buffy coat was isolated from 20 ml of blood and mixed with 20 times the volume of DPBS and layered over 10 ml of Ficoll-paque and centrifuged. The PBMC layer was removed, washed and centrifuged twice with DPBS.  The cells were counted using a hemocytometer and processed for RNA isolation using PureLink RNA mini kit with TRIzol reagent from Ambion (Life technologies, Carlsbad, CA) per the manufacturer’s instructions. The kit includes PureLink DNase treatment to remove DNA from the sample allowing subsequent purification of RNA. The RNA concentration and quality was assessed on an Agilent BioAnalyzer 2100 RNA Nano 6000 Series II according to manufacturer’s instructions and stored at −80°C.

tag: sibship (sampleid)

value: 40 mg rosuvastatin every day for 8-12 weeks

value: FollowUp

value: PBMC


title: 85_BaseLine

description:
85
BaseLine

value: control

value: BaseLine


title: BAB1381_chrX

source_name: BAB1381 Genomic DNA


title: Cplex9

source_name: Cplex9 Genomic DNA

value: male

source_name: NA10851 Genomic DNA


title: 148_BaseLine

description:
148
BaseLine


title: 93_BaseLine

description:
93
BaseLine


title: Cplex5

source_name: Cplex5 Genomic DNA


title: 95_BaseLine

description:
95
BaseLine


title: 122_FollowUp

description:
122
FollowUp


title: Cplex12

source_name: Cplex12 Genomic DNA


title: 79_FollowUp

description:
79
FollowUp


title: 71_BaseLine

description:
71
BaseLine


title: Cplex11

source_name: Cplex11 Genomic DNA


title: 164_FollowUp

description:
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title: 99_FollowUp

description:
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title: BAB1381_chr19


title: 80_BaseLine

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title: 106_FollowUp

description:
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title: 83_BaseLine

description:
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title: Cplex4

source_name: Cplex4 Genomic DNA


title: 96_FollowUp

description:
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description:
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description:
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description:
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title: 55_FollowUp

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title: 32_BaseLine

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title: SPC-A1 study group, with NJ001 treatment  for 48h, biological rep3

city: Nanjing

first: Yan

last: Cao

state: Jiangsu

address: NO.140 Hanzhong Road

department: Laboratory medicine

institute: Nanjing medical university

description: miRNA expression data from SPC-A1 cells  with NJ001 treatment for 48h

hyb_protocol: Complex probes were hybridized to each GeneChip miRNA 2.0 array according to the manufacturer's recommendations (Affymetrix).

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: Data files were analyzed with Affymetrix miRNAQCtool using RMA background correction and quantile normalization (Default settings). Since the miRNA 2.0 array covers 131 organisms, we sorted out Human only.

source_name: SPC-A1 cells treated with monoclonal antibody NJ001 for 48h

label_protocol: A total of 1000ng of total RNA was labelled using the Genisphere HSR labelling Kit.

growth_protocol: The human lung adenocarcinoma cell line (SPC-A1) maintained in RPMI-1640 supplemented with 10% (v/v) fetal bovine serum in a 37°C, 5% CO2 incubator

treatment_protocol: SPC-A1 cells were seeded in a 6-well plate at 2 ×106cells per well. After overnight incubation, SPC-A1 cells were cultured with or without 400 μg/mL NJ001.

tag: cell line

value: lung adenocarcinoma


title: 25_BaseLine

description:
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title: SPC-A1 control group, without NJ001 treatment  for 48h, biological rep3

description: miRNA expression data from SPC-A1 cells untreated for 48h

source_name: SPC-A1 cells treated without monoclonal antibody NJ001 for 48h


title: 41_FollowUp

description:
41
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title: SPC-A1 study group, with NJ001 treatment  for 48h, biological rep2


title: SPC-A1 study group, with NJ001 treatment  for 48h, biological rep1


title: 22_BaseLine

description:
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title: 39_FollowUp

description:
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title: 28_FollowUp

description:
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title: 35_FollowUp

description:
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title: 19_BaseLine

description:
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title: 15_BaseLine

description:
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title: SPC-A1 control group, without NJ001 treatment  for 48h, biological rep2


title: 13_BaseLine

description:
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title: SPC-A1 study group, with NJ001 treatment  for24h, biological rep3

description: miRNA expression data from SPC-A1 cells  with NJ001 treatment for 24h

source_name: SPC-A1 cells treated with monoclonal antibody NJ001 for 24h


title: 17_FollowUp

description:
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title: SPC-A1 study group, with NJ001 treatment  for 24h, biological rep1


title: SPC-A1 control group, without NJ001 treatment  for 24h, biological rep2

description: miRNA expression data from SPC-A1 cells untreated for 24h

source_name: SPC-A1 cells treated without monoclonal antibody NJ001 for 24h


title: SPC-A1 control group, without NJ001 treatment  for 48h, biological rep1


title: SPC-A1 control group, without NJ001 treatment  for 24h, biological rep3


title: SPC-A1 study group, with NJ001 treatment  for 24h, biological rep2


title: 27_FollowUp

description:
27
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title: SPC-A1 study group, with NJ001 treatment for 12h, biological rep3

description: miRNA expression data from SPC-A1 cells  with NJ001 treatment for 12h

source_name: SPC-A1 cells treated with monoclonal antibody NJ001 for 12h


title: 157_FollowUp

description:
157
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title: SPC-A1 control group, without NJ001 treatment for 24h, biological rep1


title: SPC-A1 study group, with NJ001 treatment for 12h, biological rep2


title: 16_FollowUp

description:
16
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title: SPC-A1 control group, without NJ001 treatment for 12h, biological rep3

description: miRNA expression data from SPC-A1 cells untreated for 12h

source_name: SPC-A1 cells treated without monoclonal antibody NJ001 for 12h


title: SPC-A1 control group, without NJ001 treatment for 12h, biological rep1


title: SPC-A1 study group, with NJ001 treatment for 12h, biological rep1


title: SPC-A1 control group, without NJ001 treatment for 12h, biological rep2


title: 8_BaseLine

description:
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description:
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title: 4_BaseLine

description:
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title: 14_FollowUp

description:
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title: 24_FollowUp

description:
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title: 2_BaseLine

description:
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title: colon_tumor_epithelial125

city: Leiden

first: Martijn

last: Cordes

state: Zuid-Holland

address: Albinusdreef 2

department: Immunology

country: Netherlands

institute: Leiden University Medical Centre

hyb_protocol: GE 4x44k hybridization protocol according manufacturer (Agilent)

scan_protocol: Agilent scanner G2505C US22502676 GE2_107_Sep09

data_processing: Agilent Feature Extraction Software (v10.7.3.1) was used for background subtraction and LOWESS normalization.

source_name: primary cells

label_protocol: LowInputQuickAmp labelings kit according manufacturer protocol (Agilent)

extract_protocol: TRIzol according manufacturer protocol (Invitrogen)

treatment_protocol: A single cell suspension was obtained from primary tissues using enzymatical and mechanical disruption. Red blood cells were removed by lysis and specific cell types were isolated using specific markers (endothelial cells; CD31+CD45-) that enabled sorting by FACS. Bulk samples were collected upfront isolation. RNA was isolated using the conventional TriZol method and RNA quality was determined using a Bioanalyzer (inclusion criteria microarrays RIN >6).

tag: diagnosis

value: tumour

value: epithelial


title: colon_tumor_bulk121.9

value: bulk


title: colon_tumor_bulk121.10


title: colon_tumor_bulk121.12


title: kidney_tumor_epithelial8I


title: colon_tumor_epithelial121


title: colon_tumor_bulk125


title: colon_tumor_bulk123


title: colon_tumor_epithelial136


title: colon_tumor_epithelial124.1


title: colon_tumor_bulk121.11


title: colon_normal_bulk154

value: normal


title: liver_tumor_bulk150


title: colon_tumor_EC109.1

value: EC


title: colon_tumor_EC123


title: colon_tumor_epithelial154


title: liver_tumor_bulk149


title: colon_tumor_epithelial124


title: colon_tumor_bulk121.6


title: colon_tumor_bulk132


title: colon_normal_EC89.1


title: colon_tumor_bulk124


title: colon_tumor_bulk121.8


title: colon_tumor_bulk121.7


title: kidney_tumor_bulk6


title: colon_tumor_EC121


title: colon_tumor_bulk126


title: colon_tumor_EC154


title: kidney_tumor_TAM CD163 sort14

description: TAM sorted

value: TAM


title: colon_normal_bulk125


title: colon_normal_bulk94


title: colon_normal_epithelial158


title: colon_tumor_bulk148


title: SPC-A1 study group, with NJ001 treatment  for 72h, biological rep3

description: miRNA expression data from SPC-A1 cells  with NJ001 treatment for 72h

hyb_protocol: Complex probes were hybridized to each GeneChip miRNA 1.0 array according to the manufacturer's recommendations (Affymetrix).

data_processing: Data files were analyzed with Affymetrix miRNAQCtool using RMA background correction and quantile normalization (Default settings). Since the miRNA 1.0 array covers 71 organisms, we sorted out Human only.

source_name: SPC-A1 cells treated with monoclonal antibody NJ001 for 72h


title: colon_normal_bulk157


title: colon_tumor_bulk121.4


title: colon_tumor_bulk121.5


title: colon_adenoma_epithelial104


title: colon_tumor_EC94


title: colon_tumor_bulk139


title: colon_tumor_EC99.1


title: colon_tumor_bulk121.3


title: colon_normal_EC158


title: SPC-A1 study group, with NJ001 treatment  for 72h, biological rep2


title: liver_tumor_TAM149

description: TAM plastic adherance


title: SPC-A1 control group, without NJ001 treatment  for 72h, biological rep3

description: miRNA expression data from SPC-A1 cells untreated for 72h

source_name: SPC-A1 cells treated without monoclonal antibody NJ001 for 72h


title: SPC-A1 control group, without NJ001 treatment  for 72h, biological rep2


title: colon_normal_epithelial159


title: SPC-A1 control group, without NJ001 treatment  for 72h, biological rep1


title: colon_tumor_epithelial139


title: colon_normal_bulk159


title: Lung_R_HCC827-2

city: Philadelphia

first: Ravi

last: Amaravadi

state: PA

address: BRB II/III 8th floor 465 Curie Blvd

department: Medicine

institute: University of Pennsylvania

hyb_protocol: hybridization to Affymetrix Human Gene 1.0ST

scan_protocol: not provided

data_processing: RMA was used to normalize and summarize the probe intensities using Partek Genomics Suite (Partek, Inc. St. Louis, MO) resulting in log2-transformed normalize expression intensities. Statistical analyses included a 2-way ANOVA with an interaction term, and 6 pairwise contrasts. For all resulting p-values, a false discovery rate corrected value was calculated using the step up method of Benjamini-Hochberg

label_protocol: not provided

growth_protocol: RPMI + 10% Serum

extract_protocol: Total RNA extraction with QIAGEN RNeasy

treatment_protocol: No treatment

value: EGFR mutant lung adenocarcinoma

tag: phenotype

value: HCQ-R


title: colon_tumor_bulk121.2


title: Lung_R_HCC827-3


title: SPC-A1 study group, with NJ001 treatment  for 72h, biological rep1


title: colon_tumor_bulk103


title: Lung_S_PC9-3

value: HCQ-S


title: Lung_S_PC9-2


title: Lung_R_HCC827-1


title: Colon_R_HCT115-3

value: colon cancer


title: Colon_R_HCT115-1


title: Colon_S_HT-29-1


title: Lung_S_PC9-1


title: Colon_S_HT-29-3


title: Colon_S_HT-29-2


title: colon_tumor_bulk99.1


title: colon_tumor_bulk94.1


title: colon_normal_EC160


title: colon_tumor_bulk121


title: colon_tumor_bulk99


title: Colon_R_HCT115-2


title: colon_tumor_EC109


title: colon_normal_EC81.1


title: colon_tumor_EC118


title: colon_normal_EC70


title: colon_normal_EC68


title: colon_normal_EC81


title: colon_tumor_EC68


title: colon_tumor_EC80


title: colon_tumor_bulk121.1


title: colon_tumor_EC71


title: colon_normal_EC89


title: colon_tumor_bulk100


title: colon_tumor_EC99


title: colon_normal_EC82.1


title: colon_normal_EC82


title: colon_tumor_EC80.1


title: colon_tumor_bulk94


title: liver_metastasis_EC72


title: HPC_+DOX_12hr_rep2

city: Manchester

first: Andrew

middle: Joshua

last: Lilly

address: Wilmslow Road

department: Stem Cell Haematopoiesis

country: United Kingdom

institute: CRUK Manchester Institute

description: RNA expression value

hyb_protocol: Labeled RNA was hybridised to GeneChip Mouse Exon 1.0 ST Arrays (Affymetrix), following the manufacturer’s instructions

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

data_processing: Expression signals were generated with robust multichip average normalisation, followed by detection above background scoring, using the Affymetrix Power Tools software package (Affymetrix).

label_protocol: 1µg or RNA was used to produce biotinylated sense-strand DNA with the Whole Transcript Sense Target Labelling Assay (Affymetrix)

growth_protocol: ES cell–derived hematopoietic precursor cells (HPCs) were routinely generated by isolating FLK1+ cells from d3 embryonic body differentiations followed by culture in conditions promoting the emergence of HPCs. FLK1+ cells where maintained on gelatin coated plates in liquid blast medium (IMDM supplemented with 10% FCS, P/S, 2mM L-Glutamine, 20μg/ml transferrin, 0.45mM MTG, 25μg/ml AA, 15% D4T conditioned medium, 5ng/ml VEGF and 10ng/ml IL6). After 3 days of liquid blast culture HPCs where isolated by sorting for a CD41+/CD34-  phenotype.

extract_protocol: RNA was isolated from the cells using an RNeasy kit (Qiagen) according to the manufacturer's instructions

treatment_protocol: HPCs were cultured for 12 and 24 hours with and without doxycycine to induce SOX7 expression

value: CD41+/CD34- hpc

tag: derivative


title: eEF1A-3

city: Canterbury

first: Daniel

last: Tarrant

address: Stacey Building

institute: University of Kent

description: Gene expression data from log phase cells

hyb_protocol: Hybridisation was carried out by Source Biosciences as per their protocol

scan_protocol: Scanning was carried out by Source Biosciences as per their protocol

data_processing: Data processing was carried out in R using the affylmGUI package in Bioconductor. Normalisation of the data was achieved by applying an RMA algorithm.

organism: Saccharomyces cerevisiae

source_name: S.Cerevisiae with 2u leu2 Tef1 plasmid

label_protocol: Labelling was carried out by Source Biosciences as per their protocol

growth_protocol: Cells were grown overnight in SC -leu at 30C. They were then reinnoculated to an OD 0.1 and grown at 30C to OD 0.7

extract_protocol: RNA extraction was performed as outlines in the RNeasy mini kit handbook

treatment_protocol: Cells were lysed using mechanical disruption as outlined in the RNeasy mini kit handbook

tag: size

value: Enlarged


title: HPC_-DOX_24hr_rep2

description: RNA expression value


title: HPC_+DOX_24hr_rep2

description: RNA expression value


title: WT 4

source_name: S.Cerevisiae with 2u leu2 control plasmid

value: Normal


title: WT 3


title: HPC_-DOX_12hr_rep2

description: RNA expression value


title: WT 1


title: HPC_-DOX_24hr_rep1

description: RNA expression value


title: HPC_+DOX_12hr_rep1

description: RNA expression value


title: WT 2


title: HPC_+DOX_24hr_rep1

description: RNA expression value


title: eEF1A-2


title: p53-TG strain x OTA Treated Diet Sample 6

status: Public on Oct 28 2016

city: Ottawa

first: Ivan

last: Curran

state: Ontario

address: 251 Sir Frederick Banting Driveway

department: Health Protection Food Branch

country: Canada

institute: Health Canada

description: Equal volumes of RNA from all 24 biological samples were combined to make a common Reference Pool: Control, Treated, p53-WT, p53-TG

hyb_protocol: Purified cRNA labeled with Cy3-labeled for common reference cRNA or Cy5-labeled for test sample cRNA were combined and applied to the Agilent Mouse V2 (G4121B) oligonucleotide microarrays in Agilent hybridization chambers.  Following 16hr hybridization at 60ºC, slides were washed sequentially using SSPE wash solution 1 & 2 followed by Agilent Stabilization and Drying Solution.  Slides were scanned immediately using a ScanArray Express scanner (Perkin-Elmer Life Sciences).

scan_protocol: Arrays were scanned using a ScanArray Express scanner (Perkin-Elmer).  Images were quantified using ImaGene5.5 (BioDiscovery)

data_processing: Log2 of the ratio (sample-Cy5/reference-Cy3), using median signal intensities, were normalized using global LOWESS normalization in R-software (maanova library).

source_name: Kidney

label_protocol: cDNA was synthesized from 3ug of total RNA using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies), and labeled by fluorescent cRNA synthesis via in vitro transcription with cyanine-3-CTP (common reference) or cyanine-5-CTP (biological sample RNA).

growth_protocol: Forty male p53-WT (+/+) mice and forty male p53-TG(+/-) mice, 5-7 weeks old were purchased from Taconic Farms Inc. (Germantown, NY, USA).    Mice received clean modified AIN-93M diet and water ad libitum for one week prior to the study while acclimating to the animal facility and isolator units.  During acclimation, p53-WT and p53-TG mice were divided randomly into 4 groups of 10 mice/dose/strain.  During the study mice received water and control or test diet ad libitum.  At the beginning of the study, p53-WT and p53-TG mice received feed containing 0, 1, 15 or 40 mg OTA/kg diet.  By the end of Week 2, body weights in p53-WT mice had fallen by 20 and 28% in the 15 and 40 mg/kg dose groups, respectively; in p53-TG mice, body weights had fallen by 27 and 31% in the 15 and 40 mg/kg dose groups, respectively.   At the end of Week 2, test diets were removed from the p53-WT and p53-TG medium and high dose groups and replaced with clean, OTA-free diet for 24 hours.  After 24 hours reformulated diets were given to all test groups to ensure that OTA levels in diet would permit survival until the end of the 26-week period.  For the remainder of the study mice received 0, 0.5, 2 or 10 mg OTA/kg diet.

extract_protocol: Total RNA was extracted from frozen mouse kidney using RNeasy Lipid Mini Kits (Qiagen).  N=6 biological samples per group (p53-WT Cont; p53-WT Treated; p53-TG Cont; p53-TG Treated).  A common RNA reference was created by pooling equal volumes of RNA from each kidney sample.  RNA quality was accessed using a Bioanalyzer (Agilent Technologies).

treatment_protocol: At the end of the 26 week exposure, mice were sacrificed and the left kidney from each mouse was quickly weighed, transferred to a vial, and frozen in liquid N2.  Frozen kidneys were transferred to a -80˚C freezer for storage immediately post-necropsy.

value: kidney

tag: Sex

value: Male

tag: genotype

tag: treatment

value: 2.0 ppm OTA Diet

source_name: Common source pooled RNA Reference


title: p53-TG strain x OTA Treated Diet Sample 5


title: p53-TG strain x Control Diet Sample 3

value: Control Diet


title: p53-TG strain x Control Diet Sample 4


title: p53-TG strain x OTA Treated Diet Sample 1


title: p53-TG strain x Control Diet Sample 5


title: p53-TG strain x Control Diet Sample 6


title: p53-WT strain x OTA Treated Diet Sample 5


title: p53-TG strain x OTA Treated Diet Sample 4


title: HPC_-DOX_12hr_rep1

description: RNA expression value


title: p53-TG strain x OTA Treated Diet Sample 3


title: p53-WT strain x OTA Treated Diet Sample 6


title: p53-TG strain x Control Diet Sample 1


title: p53-WT strain x OTA Treated Diet Sample 4


title: p53-TG strain x OTA Treated Diet Sample 2


title: p53-WT strain x OTA Treated Diet Sample 2


title: p53-WT strain x OTA Treated Diet Sample 3


title: p53-TG strain x Control Diet Sample 2


title: p53-WT strain x Control Diet Sample 5


title: p53-WT strain x Control Diet Sample 3


title: p53-WT  strain x Control Diet Sample 1


title: p53-WT strain x Control Diet Sample 6


title: p53-WT strain x Control Diet Sample 2


title: p53-WT strain x OTA Treated Diet Sample 1


title: Descending aorta from wild type p0 pup, biological rep 1

city: St. Louis

first: Jessica

last: Wagenseil

state: Missouri

address: One Brookings Dr.

department: Mechanical Engineering and Materials Science

institute: Washington Univeristy

description: LOX WT DscAo Sample1

hyb_protocol: 5ug of cDNA were fragmented and hybridized into the GeneChip Hybridization Oven 640 for 18 hr at 45C onto Mouse Gene 2.0 ST Array.  Affymetrix Gene 2.0 microarrays were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned with an Affymetrix GeneChip 7G 3000 scanner

data_processing:
The gene array data was analyzed with the Affymetrix GeneChip Command Console and raw .CEL files generated were analyzed using Expression Console software with Affymetrix default RMA Gene analysis settings
affymetrix-algorithm-name = rma-gene-full
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.4.1.46

source_name: Descending aorta from wild type p0 pup

label_protocol: Targets were labeled using Nugen Encore Biotin kit according to the standard NuGenOvationPico WTA System Amplification from 50ng of total RNA

extract_protocol: Total RNA was extracted according to manufacturer protocol (Qiagen)

treatment_protocol: p0 mouse pups were scarificed, tissues were isolated and snap frozen. Mouse were genotyped and like-genotypes from the same anatomical location were pooled in groups of eight.

tag: strain background

value: albino C57BL/6J

value: wild type (control)

tag: age

value: descending aorta

tag: tissue info.

value: section of aorta from vena cava to the diaphragm


title: Descending aorta from knockout p0 pup, biological rep 1

description: LOX KO DscAo Sample1

source_name: Descending aorta from knockout p0 pup

tag: genotype/variation

value: Lysyl oxidase (LOX) knockout

tag: tissue


title: 26-miRNA

first: Satish

last: Rattan

address: 1025 Walnut St., Room 320 College

institute: Thomas Jefferson University

description: miRNA fractions

hyb_protocol: Affymetrix gene chips, miRNA 4.0 array (Affymetrix, Santa Clara, CA), were hybridized with biotin-labeled target in 130 ul of hybridization cocktail. Target denaturation was performed at 99°C for 5 min. and then 45°C for 5 min, followed by hybridization for 18 h.

scan_protocol: Chips were scanned on an Affymetrix Gene Chip Scanner 3000, using Command Console Software.

data_processing: Background correction and normalization were done using RMA with GeneSpring V12.0 software (Agilent, Palo Alto, CA, USA). 1.5-fold differentially expressed gene list was generated. The differentially expressed gene list was loaded into Ingenuity Pathway Analysis (IPA) 8.0 software (http://www.ingenuity.com) to perform biological network and functional analyses.

organism: Rattus norvegicus

source_name: National Institutes of Aging

label_protocol: For miRNA expression: 500 ng RNA was labeled with FlashTag Biotin HSR RNA labeling procedure.

growth_protocol: The smooth muscle cells (SMCs) from the internal anal sphincter (IAS) smooth muscle were isolated following the protocol by Rattan and Singh, AJP, 2012

extract_protocol: mRNAs and miRNA fractions were isolated from purified SMCs from above age groups were isolated using mRNA and miRVana miRNA Isolation kits following the manufacturer’s (Qiagen) protocol.

treatment_protocol: since these smooth muscle cells are known to be inherently different, and may be uniquely affected during aging, these cells were isolated from different age groups (6, 16, and 26 month old) during the basal state only

tag: sample type

value: Male, Fischer 344 rats of 26 months of age

tag: gender

value: male

tag: strain

value: Fischer 344

value: smooth muscle cell


title: Ascending aorta from knockout p0 pup, biological rep 2

description: LOX KO AscAo Sample2

source_name: Ascending aorta from knockout p0 pup

value: ascending aorta

value: section of aorta from the aortic valve to the ductus arteriousus


title: Ascending aorta from knockout p0 pup, biological rep 1

description: LOX KO AscAo Sample1


title: Descending aorta from wild type p0 pup, biological rep 2

description: LOX WT DscAo Sample2


title: Descending aorta from knockout p0 pup, biological rep 2

description: LOX KO DscAo Sample2


title: Ascending aorta from wild type p0 pup, biological rep 2

description: LOX WT AscAo Sample2

source_name: Ascending aorta from wild type p0 pup


title: Bronchospheres, biological rep2

city: Hamilton

first: Jon

last: Draper

state: On

address: 1200 Main Street West

department: Pathology and Molecular Medicine

institute: McMaster University

description: Airway epithelial spheroids or bronchospheres generated from HBEC/NHBE cells.

hyb_protocol: Hybridization: 16 hr at 45 deg C; Washing: FS450_0002.

scan_protocol: Affymetrix GeneChip Scanner 3000.

data_processing: The data was processed in R environment using the oligo and limma packages (limma_3.26.9, oligo_1.34.2). The data was normalized by the RMA method.

source_name: HBEC bronchospheres

label_protocol: Biotin Allonamide Triphosphate.

growth_protocol: For hESC-derived samples, cells were differentiated as described in the associated manuscript. Human bronchial epithelial cell (HBEC)-derived bronchospheres were developed and cultured as described in other studies (PMID: 21760947; PMID: 25558064).

treatment_protocol: Harvested cells/tissues were washed with cold PBS, then processed for RNA extraction using Trizol LS Reagent (ThermoFisher).

value: Lung

tag: cell type

value: Bronchospheres


title: Ascending aorta from wild type p0 pup, biological rep 1

description: LOX WT AscAo Sample1


title: Bronchospheres, biological rep1


title: ECAD- cells, biological rep3

description: Gene expression data of ECAD- non-epithelial cells FACS-isolated from H9 wt hESC-derived endoderm tissues.

source_name: H9 wt ECAD- cells

tag: cell line

value: WT

value: hESC-derived endoderm tissues

value: ECAD- non-epithelial cells


title: ECAD- cells, biological rep1

description: Gene expression data of ECAD- non-epithelial cells FACS-isolated from H1 wt hESC-derived endoderm tissues.

source_name: H1 wt ECAD- cells


title: hEnS, biological rep2

description: Enterosphere-like tissues differentiated from H1 wt hESCs.

source_name: H1 wt hEnS

value: hESC-derived intestinal tissue

value: Enterosphere-like tissues


title: ECAD- cells, biological rep2


title: hEnS, biological rep1


title: ECAD+ cells, biological rep3

description: Gene expression data of ECAD+ epithelial cells FACS-isolated from H9 wt hESC-derived endoderm tissues.

source_name: H9 wt ECAD+ cells

value: ECAD+ epithelial cells


title: ECAD+ cells, biological rep1

description: Gene expression data of ECAD+ epithelial cells FACS-isolated from H1 wt hESC-derived endoderm tissues.

source_name: H1 wt ECAD+ cells


title: ECAD+ cells, biological rep2


title: 6108 T0

city: Los Angeles

first: Maura

last: Rossetti

address: 1000 Veteran Avenue

institute: UCLA

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: All pre-processing steps were performed with R v3 and the packages minfi, limma, illuminaHumanv4.db, impute and dplyr. Data were analyzed according to the recommended pipeline of the minfi package. Data were background-subtracted and normalized in GenomeStudio (Illumina), then further processed with subset-quantile within array normalization (SWAN). We excluded probes targeting sex chromosomes or CH sites, and we imposed a detection p-value threshold of 0.01. If a CpG site showed unacceptable detection p-values in more than 10% of samples, that CpG site was discarded entirely. Otherwise, missing values were imputed using the k-nearest neighbor averaging algorithm. We also excluded probes containing a SNP at the CpG interrogation point or at the single nucleotide extension (Illumina SNP table v1.2 based on dbSNP build 137). Finally, only probes with annotated genes were retained. The methylation levels β, which range from 0 (totally unmethylated) to 1 (completely methylated), were logit-transformed to M-values to mitigate the heteroscedasticity of β-values.

label: Cy3 and Cy5

source_name: circulating CD4+ T cells

label_protocol: Standard Illumina labeling protocol (Illumina reagents)

growth_protocol: forzen viable human PBMCs

extract_protocol: AllPrep DNA/RNA/miRNA Universal Isolation Kit (Qiagen)

treatment_protocol: FACS sorting

value: Male

tag: age (ys)

tag: clinical activity

value: ID


title: 5021 Tend

value: NO ID


title: 5021 T0


title: 15122 Tend

value: Female


title: 06-miRNA

description: miRNA fractions

value: Male, Fischer 344 rats of 6 months of age

value: male

value: 6 m


title: 18-miRNA

description: miRNA fractions

value: Male, Fischer 344 rats of 18 months of age

value: Fischer 344

value: smooth muscle cell


title: 6129 T0

value: flare


title: 8130 Tend


title: 6070 Tend


title: 1017 T0


title: 1041 T0


title: 8053 T0


title: 8053 Tend


title: 15122 T0


title: 2022 Tend


title: 1087 T0


title: 3062 Tend


title: 1041 Tend


title: 1125 Tend


title: 6108 Tend


title: p53-WT strain x Control Diet Sample 4

value: kidney

value: Control Diet


title: 1011 Tend


title: 5137 Tend


title: 1125 T0


title: 1017 Tend


title: 1032 Tend


title: 1075 T0


title: 8079 Tend


title: 1094 T0


title: 4014 Tend


title: 7063 T0


title: 2057 Tend


title: 1125 T0

data_processing: All pre-processing steps were performed with R v3 and the packages minfi, limma, illuminaHumanv4.db, impute and dplyr. Data were analyzed according to the recommended pipeline of the limma package. Data were background-corrected and quantile-normalized, using negative control probes for background correction, and both negative and positive controls for normalization. Probes annotated as bad quality or no match were excluded from analysis. Finally, only probes targeting expressed transcripts (detection p < 0.05) in at least 10% of samples were retained.

label_protocol: Biotin-labeled cRNA from Ambion (Life Technologies) ILLUMINA TOTALPRE-96 RNA AMP. KIT


title: 1094 T0


title: 2020 Tend


title: 1125 Tend


title: 2057 Tend


title: 2042 T0


title: 6128 T0


title: 1075 T0


title: 1068 T0


title: 6128 T0


title: 2114 Tend


title: 5015 T0


title: 11100 T0


title: 1087 T0


title: 8079 Tend


title: 1068 T0


title: 16111 Tend


title: 1029 Tend


title: 4014 Tend


title: 2042 T0


title: 8045 T0


title: 16111 T0


title: 1037 T0


title: 5127 T0


title: 5127 Tend


title: 7063 T0


title: 1029 T0


title: 3062 T0


title: 5115 Tend


title: 11060 T0


title: 8120 Tend


title: 1075 Tend


title: 6128 Tend


title: 1126 Tend


title: 6105 T0


title: 1039 Tend


title: 2057 T0


title: 2050 T0


title: 2043 T0


title: 1094 Tend


title: 1126 T0


title: 2050 Tend


title: 8079 T0


title: 1101 Tend


title: 8046 Tend


title: 1011 T0


title: 4090 Tend


title: 1032 T0


title: 1101 T0


title: 1039 T0


title: 1044 T0


title: 4073 T0


title: 4073 Tend


title: 4090 T0


title: 8045 Tend


title: 1087 Tend


title: 1044 Tend


title: 6048 Tend


title: 5121 Tend


title: 6129 Tend


title: 1004 Tend


title: 5110 T0


title: 6105 Tend


title: 10107 T0


title: 1124 Tend


title: 6048 T0


title: 10107 Tend


title: 11060 Tend


title: 1004 T0


title: 8046 T0


title: 1124 T0


title: 8120 T0


title: 6097 T0


title: 1034 T0


title: 6097 Tend


title: 1078 Tend


title: 1034 Tend


title: 5121 T0


title: 5089 T0


title: 1023 Tend


title: 2114 T0


title: 4093 T0


title: 5110 Tend


title: 5115 T0


title: 6051 Tend


title: 6070 T0


title: 4093 Tend


title: 1078 T0


title: 1068 Tend


title: 1036 Tend


title: 4014 T0


title: 8130 T0


title: 5015 T0


title: 6051 T0


title: 1023 T0


title: 1028 Tend


title: 11100 T0


title: 1037 Tend


title: 1029 Tend


title: 1029 T0


title: 5115 Tend


title: 2114 Tend


title: 16111 Tend


title: 8120 Tend


title: 1037 T0


title: 8054 Tend


title: 8054 T0


title: 1018 Tend


title: 1018 T0


title: 3066 Tend


title: 7063 Tend


title: 5089 Tend


title: 1028 T0


title: 6070 T0


title: 2043 Tend


title: 8045 T0


title: GSS Cortex pool (iii)

city: Easter Bush

first: Jean

middle: C

last: Manson

state: Midlothian

address: The Roslin Institute Building

department: The Neurobiology Division

institute: The Roslin Institute, The University of Edinburgh

description: Mice exhibiting a proline to leucine alteration at codon 101 (101LL) of the murine prion protein gene have had i.c. inoculation of Gerstmann Straussler Scheinker (GSS) to examine the gene expression changes within individual brain regions and between brain regions of GSS/101LL mice.

hyb_protocol: Arrays were hybridized, washed and stained using the Affymetrix HybWash Stain Kit according to manufacturer's instructions.

scan_protocol: Arrays were scanned using GeneTitan and all default scanning settings were used.

data_processing: The data were analyzed using Affymetrix Expression Console default analysis settings and global scaling as normalization method.

label: Sape stain

source_name: Cortex dissected from GSS/101LL mice at terminal endpoint of disease

label_protocol: Ambion WT Expression Kit with GeneChip WT Terminal Labelling and Controls Kit was used according to manufacturer's instructions.

treatment_protocol: At terminal end point of GSS/101LL disease (and in aged matched NBH/101LL controls), brain were extracted and immediately flash frozen. At a later date, brains were then thawed, dissected into four brain regions (brain stem, cerebellum, thalamus and cortex) under sterile aseptic conditions in autoclaved artificial cerebral spinal fluid.

tag: inoculum

value: Gerstmann Strausller Scheinker (GSS) human prion disease homogenate

value: brain

tag: tissue compartment

value: Cortex

tag: mouse genotype


title: 1078 T0

tag: Sex


title: 1032 T0


title: GSS Cortex pool (i)


title: 1087 Tend


title: 4090 Tend


title: 1011 T0


title: 8120 T0


title: 1023 Tend


title: 4090 T0


title: 1023 T0


title: 1036 T0


title: GSS Thalamus pool (i)

source_name: Thalamus dissected from GSS/101LL mice at terminal endpoint of disease

value: Thalamus


title: 6097 Tend


title: 6097 T0


title: GSS Thalamus pool (iii)

value: Male


title: GSS Cerebellum pool (ii)

source_name: Cerebellum dissected from GSS/101LL mice at terminal endpoint of disease

value: Cerebellum


title: 4093 T0

value: NO ID


title: GSS Thalamus pool (ii)


title: 5110 T0

value: Female

value: ID


title: 1078 Tend


title: GSS Cerebellum pool (i)


title: GSS Cerebellum pool (iii)


title: 10107 Tend


title: 8045 Tend


title: 4073 T0


title: GSS Brain Stem pool (iii)

source_name: Brain stem dissected from GSS/101LL mice at terminal endpoint of disease

value: Brain stem


title: 5110 Tend


title: 5015 Tend


title: 4093 Tend


title: 3066 T0


title: 5031 Tend


title: 1036 Tend


title: 4073 Tend


title: 11100 Tend


title: GSS Brain Stem pool (i)


title: 1036 T0


title: NBH Cortex pool (iii)

description: Mice exhibiting a proline to leucine alteration at codon 101 (101LL) of the murine prion protein gene have had i.c. inoculation of normal brain homogenate (NBH) as controls. Upon terminal end point of experimental samples, NBH/101LL samples were also taken for analysis

source_name: Cortex dissected from NBH/101LL aged matched control mice

value: normal brain homogenate (NBH)


title: 10107 T0


title: 8054 Tend


title: 8054 T0


title: 6051 T0


title: 6051 Tend


title: 7063 Tend


title: NBH Cortex pool (ii)


title: 6109 Tend


title: NBH Thalamus pool (iii)

source_name: Thalamus dissected from NBH/101LL aged matched control mice


title: NBH Cortex pool (i)


title: NBH Thalamus pool (ii)


title: 3066 Tend


title: 3066 T0


title: 2022 T0


title: 1028 T0


title: 1028 Tend


title: NBH Cerebellum pool (iii)

source_name: Cerebellum dissected from NBH/101LL aged matched control mice


title: NBH Thalamus pool (i)


title: 5137 T0


title: GSS Brain Stem pool (ii)


title: 5031 T0


title: 1018 Tend


title: 13106 Tend


title: 2042 Tend


title: NBH Cerebellum pool (i)


title: NBH Cerebellum pool (ii)


title: 1018 T0


title: 6109 T0


title: 2043 Tend


title: NBH Brain Stem pool (ii)

source_name: Brain stem dissected from NBH/101LL aged matched control mice


title: 2020 T0


title: 6108 Tend


title: NBH Brain Stem pool (i)


title: 13106 T0


title: 15122 Tend


title: 2114 T0


title: 6108 T0


title: 15122 T0


title: 11060 Tend


title: 1017 Tend


title: 5115 T0


title: 1017 T0


title: 5021 Tend


title: 4014 T0


title: 3062 Tend


title: 1034 T0


title: 5089 Tend


title: 5021 T0


title: 1011 Tend


title: 8053 T0


title: 1032 Tend


title: 5089 T0


title: 1044 T0


title: 6048 Tend


title: 6048 T0


title: 8130 T0


title: 5121 Tend


title: 1044 Tend


title: 1037 Tend


title: 1068 Tend


title: 6129 Tend


title: 18-mRNA

description: mRNA fractions

hyb_protocol: Affymetrix gene chips, Rat gene 1.0 ST array (Affymetrix, Santa Clara, CA), were hybridized with fragmented and biotin-labeled target (2.5 ug) in 110 ul of hybridization cocktail. Target denaturation was performed at 99°C for 2 min. and then 45°C for 5 min, followed by hybridization for 18 h.

data_processing: Background correction and normalization were done using Iterative Plier 16 with GeneSpring V12.0 software (Agilent, Palo Alto, CA, USA). 2-fold (p-value<0.05) differentially expressed gene list was generated. The differentially expressed gene list was loaded into Ingenuity Pathway Analysis (IPA) 8.0 software (http://www.ingenuity.com) to perform biological network and functional analyses.

source_name: National Institutes of Aging

label_protocol: For mRNA expression: 2.5 ug ST-cDNAs were fragmented and chemically labeled with biotin to generate biotinylated ST-cDNA using FL-Ovation cDNA biotin module V2 (NuGen Technologies, Inc.).

value: Male, Fischer 344 rats of 18 months of age

value: male


title: 06-mRNA

description: mRNA fractions

value: Male, Fischer 344 rats of 6 months of age

value: Fischer 344

value: 6 m

value: smooth muscle cell


title: HeLa_S200A_IP_rep3

type: SRA

city: Boston

first: Areum

last: Han

state: MA

address: Karp Family Building, 7th Floor. 300 Longwood Ave.

institute: Boston Children's Hospital

library_source: transcriptomic

data_processing:
From the raw reads, we removed adaptor sequences using a Cutadapt tool, allowing some mismatches (The specific parameters we used were -n 2 -e 0.1 -O 15 --quality-base=33).
Then, the cleaned reads were aligned to the human genome/transcriptome (hg19 and corresponding UCSC gene model) using a TopHat2 software with the following parameters (--library-type=fr-firststrand --min-intron-length=10 --no-coverage-search --microexon-search --min-isoform-fraction=0).
To estimate expression levels for each gene, we counted aligned reads per gene and using a htseq-count tool.
And calculated CPM (Counts Per Million) values were converted to RPKM (Reads Per Kilobase per Million mapped reads) values corresponding to gene lengths.
Genome_build: hg19
Supplementary_files_format_and_content: excel, RPKM values of genes after corresponding immunoprecipitation

molecule: polyA RNA

growth_protocol: HeLa cells were maintained in DMEM/10% FBS.

extract_protocol:
Cells were harvested in cold PBS and immediately lysed in M2 lysis buffer (50 mM Tris-HCl pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100) containing 100 U/ml RNasin (Promega) and 2X protease and phosphatase inhibitors (Pierce). FLAG-tagged LIN28 variants were purified using the anti-FLAG M2 affinity gel following the manufacturer’s specifications (Sigma). Parental HeLa cells (no FLAG) were used as controls for antibody specificity. RNA was isolated from the beads using Trizol (Invitrogen) and RNeasy columns (Qiagen). Purified RNA was subjected to polyA selection using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB).
Libraries were prepared with the NEBNext Ultra RNA Library Prep Kit (NEB).

value: HeLa

value: Cervical carcinoma cells

tag: transgene

value: FLAG-LIN28 (S200A)

tag: rip antibody

value: FLAG M2 (Sigma #A2220)


title: 26-mRNA

description: mRNA fractions

value: Male, Fischer 344 rats of 26 months of age

tag: age


title: NBH Brain Stem pool (iii)

value: brain

value: Male


title: 5121 T0


title: 1004 T0


title: 1004 Tend


title: HeLa_S200A_IP_rep1


title: 16111 T0

value: Female


title: HeLa_WT_IP_rep2

value: FLAG-LIN28 (WT)


title: HeLa_WT_IP_rep3


title: 3062 T0

value: flare


title: 5127 T0

value: ID


title: 1094 Tend


title: 2050 T0


title: HeLa_WT_IP_rep1


title: HeLa_S200A_IP_rep2


title: 1034 Tend


title: 1124 T0


title: 1124 Tend


title: 1041 Tend


title: 8053 Tend

value: NO ID


title: HeLa_Ctrl_IP_rep3


title: 1041 T0


title: 1075 Tend


title: HeLa_Ctrl_IP_rep2


title: 6128 Tend


title: 2050 Tend


title: 5127 Tend


title: HeLa_Ctrl_IP_rep1


title: HeLa_S200A_Input_rep3


title: 6129 T0


title: 6070 Tend


title: 2057 T0


title: HeLa_S200A_Input_rep2


title: HeLa_S200A_Input_rep1


title: 8079 T0


title: HeLa_WT_Input_rep2


title: 8130 Tend


title: HeLa_WT_Input_rep3


title: 2043 T0


title: 2022 Tend


title: 5137 Tend


title: 5015 Tend


title: HeLa_Ctrl_Input_rep3


title: Station 93.40 Control R3

city: Livermore

first: Rhona

last: Stuart

state: CA

address: 7000 East Ave.

institute: Lawrence Livermore National Laboratory

hyb_protocol: After purification on the columns provided in the kit, outputs were between 0.6 and 1.1 mg of ss-cDNA with a dye incorporation of 20 – 25 nucleotide bases per dye unit. 300ng of Alexa 555-labeled ss-cDNA was heat denatured for three minutes at 98°C and cooled to room temperature over a period of five minutes before adding 2X Hi-RPM Hybridization Buffer from the Agilent GE Hyb Kit (Agilent Technologies, Santa Clara, CA) and applying the hybridization mixture to an Agilent custom, 8x15k gene expression microarray. The arrays were hybridized for 17 hours at 65°C and 10rpm in an Agilent hybridization oven. They were disassembled and washed in Agilent Gene Expression Wash Buffers (Agilent Technologies, Santa Clara, CA).

scan_protocol: Microarray slides were scanned on an Agilent C scanner at 5 mm resolution using 20 bit imaging.

data_processing: Data was extracted using Agilent Feature Extraction 10.10.1.1. Microarray results were analyzed using Agilent GeneSpring GX software to normalize signal intensity across arrays and generate both gene-level and probe level signals. Log2 transformed signal ratios were then calculated on each replicate Cu and no-Cu control and Statistical Analyses of Microarrays algorithms used with a 5% (or 15%) false discovery rate (FDR).

label: Alexa Fluor 555

organism: Bacteria

source_name: Field assemblage, Control, 2 h

label_protocol: RNA integrity was determined using a Bioanalyzer RNA 6000 Nano chip run on prokaryotic total RNA nano setting on an Agilent Bioanalyzer 2100. For culture-derived RNA single-stranded cDNA was generated from 10 μg of total RNA using the Invitrogen SuperScript Plus Indirect cDNA Labeling Kit Core Module (Life Technologies, Carlsbad, CA). For environmental-derived RNA single-stranded cDNA was generated from 1 μg of total RNA using Agilent Low input Quick Amp labeling kit (Agilent Technologies, Santa Clara, CA) and using the Invitrogen SuperScript Plus Indirect cDNA Labeling Kit Core Module (Life Technologies, Carlsbad, CA). Single-stranded cDNA was labeled using the Alexa Fluor 555 dye provided in the labeling kit.

growth_protocol: unknown growth rates, field samples

extract_protocol:
RNA treatment: amplification with Agilent Low input Quick Amp labeling kit
Cells or filters were suspended in Trizol (Life Technologies, Carlsbad CA), incubated at 65ºC for 30 min, centrifuged at 15,000 x g, and supernatant removed. Supernatant was then precipitated with 70% cold EtOH and resuspended in sterile water and purified using a Zymo PCR inhibitor removal kit.

treatment_protocol: Control

value: mixed marine microbial community


title: 5137 T0


title: 11100 Tend


title: Station 93.40 Control R1


title: Station 93.40 Cu R3

source_name: Field assemblage, Cu stress, 2 h

treatment_protocol: CuSO4 8nM


title: Station 93.40 Control R2


title: HeLa_Ctrl_Input_rep2


title: HeLa_WT_Input_rep1


title: 2020 T0


title: Station 93.40 Cu R2


title: Station 93.40 Cu R1


title: 2042 Tend


title: HeLa_Ctrl_Input_rep1


title: 9902_Control_R3

organism: Synechococcus sp. CC9902

source_name: CC9902, Control 2 h

growth_protocol: exponential, defined artificial seawater media

extract_protocol:
RNA treatment: none
Cells or filters were suspended in Trizol (Life Technologies, Carlsbad CA), incubated at 65ºC for 30 min, centrifuged at 15,000 x g, and supernatant removed. Supernatant was then precipitated with 70% cold EtOH and resuspended in sterile water and purified using a Zymo PCR inhibitor removal kit.


title: 2022 T0


title: 5031 Tend


title: 9902_Cu_R3

source_name: CC9902, Cu stress 2 h

treatment_protocol: CuEDTA 10 µM


title: 5031 T0


title: 9902_Control_R2


title: 2020 Tend


title: 6109 T0


title: 9902_Cu_R2


title: 6109 Tend


title: Mouse 99

city: Paris

first: Franck

last: Letourneur

address: 22 rue mechain

country: France

institute: INSERM

hyb_protocol: cDNA is then hybridized to GeneChip® MouseGene1.0 (Affymetrix) at 45°C for 17 hours

scan_protocol: After overnight hybridization, chips are washed on the fluidic station FS450 following specific protocols (Affymetrix) and scanned using the GCS3000 7G

data_processing: Data were normalized using RMA and statistical analysis was realized on Partek Genomics Suite

source_name: mouse liver 2 days after sh scramble injection

label_protocol: 200 ng of total RNA is reverse transcribed  following the Applause® WT-Amp Plus ST Systems (Nugen). Briefly, the resulting double strand cDNA is used for amplification based on SPIA technology. After purification according to Nugen protocol, 2,5 ug of Sens Target DNA are fragmented and biotin labelled using Encore Biotin Module kit (Nugen)

treatment_protocol: in vivo adenovirus injection

value: liver

value: 10 weeks


title: 13106 Tend


title: 9902_Cu_R1


title: 13106 T0


title: Mouse 100


title: Mouse 98


title: Mouse 102

source_name: mouse liver 2 days after shGrb14 injection


title: Arabidopsis_Control_9h_rep1

status: Public on Oct 27 2016

city: Trondheim

first: Per

last: Winge

address: Høgskoleringen 5e

department: Department of Biology

country: Norway

institute: Norwegian University of Science and Technology

hyb_protocol: 1650 ng cRNA from each sample was fragmented and hybridized on 4x44K Arabidipsis thaliana whole-genome 60-mer oligonucleotide microarrays (Agilent Technologies) in an Agilent G2545A Hybridization rotary oven (10 rpm, 65°C, 17.5 h). Hybridization was performed with the Gene Expression Hybridization Kit (Agilent p/n 5188-5242). The slides were washed with buffer 1 & 2 from Gene Expression Wash Buffer kit (Agilent p/n 5188-5327)

scan_protocol: The microarray sides were scanned twice at 5 µm resolution on a laser scanner (G2505 B from Agilent Technologies), using the “dynamic range expander” option in the scanner software. The resulting images were processed using Agilent Feature Extraction software v9.5.

data_processing: The median signal intensities (gMedianSignal) were normalized using the quantile method, and no background subtraction was performed. Spots identified as feature outliers were excluded from analysis, and weak or non-detected spots were given reduced weight (0.5). Genes with statistically significant differential expression were identified using the Limma package (version 3.2.3) and R (version 2.10.1).

source_name: Rosette leaves, 10 days, Control, 9h

label_protocol: Total RNA (83 - 200 ng) was reverse transcribed, amplified and labelled with Cy3-CTP using the Low Input Quick Amp Labelling Kit, One-Color (Agilent p/n 5190-2305)

growth_protocol: Seeds of the A. thaliana accession Col-0 were surface sterilised and sown on Petri dishes (9 cm diameter) containing solid in vitro cultivation medium consisting of ½ x Murashige and Skoog basal salt mixture (Sigma-Aldrich, Saint Louis, USA), 2% sucrose, 0.6% phytoagar (w/v), pH 5.7. Seeds were stratified for 2 days at 4°C before being transferred to a controlled growth chamber under a 16 hour photoperiod (light intensity: 75 µmol.m-2.sec-1) at 21-23°C.

extract_protocol: Shoots from 10 days old in vitro grown plantlets were harvested separately from two individual petri dishes and immediately flash-frozen in liquid N2. The harvested tissue was stored at -80°C until further processing. Precooled (-80°C) 5 mm stainless steel beads (QIAGEN) were added to the tubes with frozen plant tissue, and the samples were mechanically disrupted and homogenized using the TissueLyser system (QIAGEN). Disruption was carried out for 2 x 2 min at 25 Hz. The samples were placed in a precooled (-80°C) adapter set for the first shaking step. Before the second shaking step, the samples were transferred to a room temperate adapter set and 0.5 ml lysis buffer (SpectrumTM Plant Total RNA kit, Sigma-Aldrich) was added to each tube. Total RNA was isolated from the homogenized lysate using the SpectrumTM Plant Total RNA kit (Sigma-Aldrich). On-column digestion of DNA with DNase I (QIAGEN) was included for all RNA preparations. The concentration of the RNA was determined by measuring the absorbance at 260 nm with the NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies), and the purity of the RNA was estimated by the OD260/OD280 nm absorption ratio (all ratios were > 2.0). The integrity of the RNA was verified by denaturing agarose gel electrophoresis and ethidium bromide staining following the protocol described in the RNeasy Mini handbook (QIAGEN).

treatment_protocol: Allyl-isothiocyanate (Sigma-Aldrich, Saint Louis, USA; Cat Nb 377430) was freshly diluted in commercial rape seed oil to a concentration of 0.05M and 200 µl of this solution was applied to a piece of filter paper that was placed into a 14-cm diameter Petri dish. Exposure to allyl-isothiocyanate was obtained by putting a 9-cm dish (lid removed) containing ten-day old A. thaliana plants into this 14-cm diameter dish for 30 minutes, 1 hour or 9 hours. The plants were hence exposed to vapors of allyl-isothiocyanate in a closed atmosphere. The control consisted of filter paper onto which 200 µl of rape seed oil was applied.

tag: ecotype


title: 9902_Control_R1


title: Mouse 101

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


title: Arabidopsis_ITC-0.05M_9h_rep2

source_name: Rosette leaves, 10 days, 0.05M ITC, 9h


title: Mouse 103


title: Arabidopsis_Control_1h_rep1

source_name: Rosette leaves, 10 days, Control, 1h


title: Arabidopsis_Control_9h_rep2


title: Arabidopsis_ITC-0.05M_9h_rep1


title: Arabidopsis_ITC-0.05M_30min_rep2

source_name: Rosette leaves, 10 days, 0.05M ITC, 30 min


title: Arabidopsis_ITC-0.05M_1h_rep2

source_name: Rosette leaves, 10 days, 0.05M ITC, 1h


title: Arabidopsis_Control_1h_rep2


title: Arabidopsis_Control_30min_rep2

source_name: Rosette leaves, 10 days, Control, 30 min


title: Arabidopsis_ITC-0.05M_1h_rep1


title: Arabidopsis_ITC-0.05M_30min_rep1


title: M28_Pre2

city: Dallas

first: Jason

middle: A

last: Skinner

address: 3434 Live Oak

institute: Baylor Institute for Immunology Research

description:
M28_Pre2
9248833101_F.AVG_Signal

hyb_protocol: Standard Illumina HT-12 V4 hybridization protocol

scan_protocol: Standard Illumina iScan protocol

data_processing: Following background subtraction, the raw signal intensities extracted with Illumina Genome Studio v2010.1 Gene Expression 1.6.0 software were scaled to the mean intensity of the datase to yield the Matrix normalized data available here.  Data was further filtered on probes for which pval detection  was below 0.01 in at least one sample were kept for analysis. The ComBat method (Johnson et al, Biostatistics, 2007) was used on those normalized data to correct for batch effects (namely a small Hybridization chamber effect and the Training/test set effect), that was identified through Principal Variance Component Analysis (PVCA)

label: Biotin

organism: Macaca fascicularis

source_name: total RNA (globin reduced)

label_protocol: Biotinylated cRNA were prepared using Illumina Totalprep-96 Amplification Kits with 250ng input

extract_protocol: RNA was extracted from Applied Biosystems Tempus Blood RNA Tubes using the Ambion MagMax-96 total RNA Isolation kits, Globin message reduction was conducted using Ambion GlobinClear Human 96 Kits

value: Whole Blood

tag: ChIP

tag: hyb chamber

tag: dataset

value: Test

tag: synchroset

value: No

tag: pittid

tag: monkeyid

tag: time point

tag: infection time

tag: clinical status

value: Latent

tag: FDG avidity

tag: FDG group

value: Low

tag: hemoglobin

tag: hematocrit

tag: wbc

tag: platelet

tag: per neutrophils

tag: per lymphocytes

tag: per monocytes

tag: per eosinophils

tag: per basophils

tag: abs neutrophils

tag: abs lymphocytes

tag: abs monocytes

tag: abs eosinophils

tag: per monos by lymphos

tag: abs monos by lymphos

tag: per lymphosstained

tag: per cd3stained

tag: per cd8

tag: per cd16pos cd3neg

tag: per cd20


title: M26_10

description:
M26_10
9248833101_I.AVG_Signal

tag: tissue

tag: ChIP

tag: hyb chamber

tag: dataset

tag: synchroset

tag: pittid

tag: monkeyid

tag: time point

tag: infection time

tag: clinical status

tag: FDG avidity

tag: FDG group

value: High

tag: hemoglobin

tag: hematocrit

tag: wbc

tag: platelet


title: Arabidopsis_Control_30min_rep1

tag: ecotype


title: M21_150

description:
M21_150
9248833101_H.AVG_Signal

tag: tissue

tag: per neutrophils

tag: per lymphocytes

tag: per monocytes

tag: per eosinophils

tag: per basophils

tag: abs neutrophils

tag: abs lymphocytes

tag: abs monocytes

tag: abs eosinophils

tag: per monos by lymphos

tag: abs monos by lymphos

tag: per lymphosstained

tag: per cd3stained

tag: per cd8

tag: per cd16pos cd3neg

tag: per cd20


title: M20_Pre2

description:
M20_Pre2
9248833101_G.AVG_Signal

tag: tissue

tag: ChIP

tag: hyb chamber

tag: dataset

tag: synchroset

tag: pittid

tag: monkeyid

tag: time point

tag: infection time

tag: clinical status

tag: FDG avidity

tag: FDG group

tag: hemoglobin

tag: hematocrit

tag: wbc

tag: platelet


title: M21_20

description:
M21_20
9248833101_E.AVG_Signal

tag: per neutrophils

tag: per lymphocytes

tag: per monocytes

tag: per eosinophils

tag: per basophils

tag: abs neutrophils

tag: abs lymphocytes

tag: abs monocytes

tag: abs eosinophils

tag: per monos by lymphos

tag: abs monos by lymphos


title: M27_42

description:
M27_42
9248833101_D.AVG_Signal

tag: tissue

tag: ChIP

tag: hyb chamber

tag: dataset

tag: synchroset

tag: pittid

tag: monkeyid

tag: time point

tag: infection time

tag: clinical status

tag: FDG avidity

tag: per lymphosstained

tag: per cd3stained

tag: per cd8

tag: per cd16pos cd3neg

tag: per cd20


title: M29_7

description:
M29_7
9248833101_C.AVG_Signal

tag: FDG group

tag: hemoglobin

tag: hematocrit

tag: wbc

tag: platelet

tag: per neutrophils

tag: per lymphocytes

tag: per monocytes

tag: per eosinophils

tag: per basophils

tag: abs neutrophils

tag: abs lymphocytes

tag: abs monocytes

tag: abs eosinophils

tag: per monos by lymphos

tag: abs monos by lymphos


title: M30_90

description:
M30_90
9248833101_A.AVG_Signal

tag: tissue

tag: ChIP

tag: hyb chamber

tag: dataset

tag: synchroset

tag: pittid

tag: monkeyid

tag: time point

tag: infection time

tag: clinical status

value: Active

tag: FDG avidity


title: M34_180

description:
M34_180
9248833101_B.AVG_Signal

value: Yes

tag: FDG group

tag: hemoglobin

tag: hematocrit

tag: wbc

tag: platelet

tag: per neutrophils

tag: per lymphocytes

tag: per monocytes

tag: per eosinophils

tag: abs neutrophils

tag: per lymphosstained

tag: per cd3stained

tag: per cd8

tag: per cd16pos cd3neg

tag: per cd20


title: M22_56

description:
M22_56
9248833095_J.AVG_Signal

tag: tissue

tag: ChIP

tag: hyb chamber

tag: dataset

tag: synchroset

tag: pittid

tag: monkeyid

tag: time point

tag: infection time

tag: clinical status

tag: per basophils

tag: abs lymphocytes

tag: abs monocytes

tag: abs eosinophils

tag: per monos by lymphos

tag: abs monos by lymphos


title: M26_Pre1

description:
M26_Pre1
9248833095_F.AVG_Signal

tag: FDG avidity

tag: FDG group

tag: hemoglobin

tag: hematocrit

tag: wbc

tag: platelet

tag: per neutrophils

tag: per lymphocytes

tag: per monocytes

tag: per eosinophils

tag: abs neutrophils

tag: per lymphosstained

tag: per cd3stained

tag: per cd8

tag: per cd16pos cd3neg

tag: per cd20


title: M20_30

description:
M20_30
9248833095_C.AVG_Signal

tag: tissue

tag: ChIP

tag: hyb chamber

tag: dataset

tag: synchroset

tag: pittid

tag: monkeyid

tag: time point

tag: infection time

tag: clinical status

tag: per basophils

tag: abs lymphocytes

tag: abs monocytes

tag: abs eosinophils

tag: per monos by lymphos

tag: abs monos by lymphos


title: M35_30

description:
M35_30
9248833095_B.AVG_Signal

tag: FDG avidity

tag: FDG group

tag: hemoglobin

tag: hematocrit

tag: wbc

tag: platelet

tag: per neutrophils

tag: per lymphocytes

tag: per monocytes

tag: per eosinophils

tag: abs neutrophils

tag: per lymphosstained

tag: per cd3stained

tag: per cd8

tag: per cd16pos cd3neg

tag: per cd20


title: M36_30

description:
M36_30
9248833095_D.AVG_Signal

tag: tissue

tag: ChIP

tag: hyb chamber

tag: dataset

tag: synchroset

tag: pittid

tag: monkeyid

tag: time point

tag: infection time

tag: clinical status

tag: abs lymphocytes

tag: abs monocytes

tag: abs eosinophils

tag: per monos by lymphos

tag: abs monos by lymphos


title: M33_20

description:
M33_20
9248833093_L.AVG_Signal

tag: FDG avidity

tag: FDG group

tag: hemoglobin

tag: hematocrit

tag: wbc

tag: platelet

tag: per neutrophils

tag: per lymphocytes

tag: per monocytes

tag: per eosinophils

tag: abs neutrophils

tag: per lymphosstained

tag: per cd3stained

tag: per cd8

tag: per cd16pos cd3neg


title: M28_30

description:
M28_30
9248833095_A.AVG_Signal

tag: tissue

tag: ChIP

tag: hyb chamber

tag: dataset

tag: synchroset

tag: pittid

tag: monkeyid

tag: time point

tag: infection time

tag: clinical status

tag: per basophils

tag: abs lymphocytes

tag: abs monocytes

tag: abs eosinophils

tag: per monos by lymphos

tag: per cd20


title: M24_20

description:
M24_20
9248833093_K.AVG_Signal

tag: FDG avidity

tag: FDG group

tag: hemoglobin

tag: hematocrit

tag: wbc

tag: platelet

tag: per neutrophils

tag: per lymphocytes

tag: per monocytes

tag: per eosinophils

tag: abs neutrophils

tag: abs monos by lymphos

tag: per lymphosstained

tag: per cd3stained

tag: per cd8

tag: per cd16pos cd3neg


title: M32_150

description:
M32_150
9248833093_I.AVG_Signal

tag: tissue

tag: ChIP

tag: hyb chamber

tag: dataset

tag: synchroset

tag: pittid

tag: monkeyid

tag: time point

tag: infection time

tag: clinical status

tag: abs lymphocytes

tag: abs monocytes

tag: abs eosinophils

tag: per monos by lymphos

tag: per cd20


title: M22_7

description:
M22_7
9248833093_J.AVG_Signal

tag: FDG avidity

tag: FDG group

tag: hemoglobin

tag: hematocrit

tag: wbc

tag: platelet

tag: per neutrophils

tag: per lymphocytes

tag: per monocytes

tag: per eosinophils

tag: per basophils

tag: abs neutrophils

tag: abs monos by lymphos

tag: per lymphosstained

tag: per cd3stained

tag: per cd8


title: M22_120

description:
M22_120
9248833093_H.AVG_Signal

tag: tissue

tag: ChIP

tag: hyb chamber

tag: dataset

tag: synchroset

tag: pittid

tag: monkeyid

tag: time point

tag: infection time

tag: clinical status

tag: abs lymphocytes

tag: abs monocytes

tag: abs eosinophils

tag: per monos by lymphos

tag: per cd16pos cd3neg

tag: per cd20


title: M20_20

description:
M20_20
9248833092_G.AVG_Signal

tag: FDG avidity

tag: FDG group

tag: hemoglobin

tag: hematocrit

tag: wbc

tag: platelet

tag: per neutrophils

tag: per lymphocytes

tag: per monocytes

tag: per eosinophils

tag: per basophils

tag: abs neutrophils

tag: abs monos by lymphos

tag: per lymphosstained

tag: per cd3stained

tag: per cd8


title: M33_30

description:
M33_30
9248833092_C.AVG_Signal

tag: tissue

tag: ChIP

tag: hyb chamber

tag: dataset

tag: synchroset

tag: pittid

tag: monkeyid

tag: time point

tag: infection time

tag: clinical status

tag: abs lymphocytes

tag: abs monocytes

tag: abs eosinophils

tag: per monos by lymphos

tag: per cd16pos cd3neg

tag: per cd20


title: M21_7

description:
M21_7
9248833095_E.AVG_Signal

tag: FDG avidity

tag: FDG group

tag: hemoglobin

tag: hematocrit

tag: wbc

tag: platelet

tag: per neutrophils

tag: per lymphocytes

tag: per monocytes

tag: per eosinophils

tag: per basophils

tag: abs neutrophils

tag: abs monos by lymphos

tag: per lymphosstained

tag: per cd3stained

tag: per cd8


title: M27_150

description:
M27_150
9248833092_J.AVG_Signal

tag: tissue

tag: ChIP

tag: hyb chamber

tag: dataset

tag: synchroset

tag: pittid

tag: monkeyid

tag: time point

tag: infection time

tag: clinical status

tag: abs lymphocytes

tag: abs monocytes

tag: abs eosinophils

tag: per monos by lymphos

tag: per cd16pos cd3neg

tag: per cd20


title: M37_7

description:
M37_7
9248833093_E.AVG_Signal

tag: FDG avidity

tag: FDG group

tag: hemoglobin

tag: hematocrit

tag: wbc

tag: platelet

tag: per neutrophils

tag: per lymphocytes

tag: per monocytes

tag: per eosinophils

tag: abs neutrophils

tag: abs monos by lymphos

tag: per lymphosstained

tag: per cd3stained

tag: per cd8


title: M38_Pre2

description:
M38_Pre2
9248833092_F.AVG_Signal

tag: tissue

tag: ChIP

tag: hyb chamber

tag: dataset

tag: synchroset

tag: pittid

tag: monkeyid

tag: time point

tag: infection time

tag: clinical status

tag: abs lymphocytes

tag: abs monocytes

tag: abs eosinophils

tag: per monos by lymphos

tag: per cd16pos cd3neg


title: M26_20

description:
M26_20
9248833092_D.AVG_Signal

tag: FDG avidity

tag: FDG group

tag: hemoglobin

tag: hematocrit

tag: wbc

tag: platelet

tag: per neutrophils

tag: per lymphocytes

tag: per monocytes

tag: per eosinophils

tag: per basophils

tag: abs neutrophils

tag: abs monos by lymphos

tag: per lymphosstained

tag: per cd3stained

tag: per cd20


title: M26_30

description:
M26_30
9248833093_G.AVG_Signal

tag: tissue

tag: ChIP

tag: hyb chamber

tag: dataset

tag: synchroset

tag: pittid

tag: monkeyid

tag: time point

tag: infection time

tag: clinical status

tag: abs lymphocytes

tag: abs monocytes

tag: abs eosinophils

tag: per monos by lymphos

tag: per cd8

tag: per cd16pos cd3neg


title: M38_30

description:
M38_30
9248833092_K.AVG_Signal

tag: FDG avidity

tag: FDG group

tag: hemoglobin

tag: hematocrit

tag: wbc

tag: platelet

tag: per neutrophils

tag: per lymphocytes

tag: per monocytes

tag: per eosinophils

tag: abs neutrophils

tag: abs monos by lymphos

tag: per lymphosstained

tag: per cd3stained

tag: per cd20


title: M33_Pre2

description:
M33_Pre2
9248833091_K.AVG_Signal

tag: tissue

tag: ChIP

tag: hyb chamber

tag: dataset

tag: synchroset

tag: pittid

tag: monkeyid

tag: time point

tag: infection time

tag: clinical status

tag: abs lymphocytes

tag: abs monocytes

tag: abs eosinophils

tag: per monos by lymphos

tag: per cd8


title: M34_90

description:
M34_90
9248833092_B.AVG_Signal

tag: FDG avidity

tag: FDG group

tag: hemoglobin

tag: hematocrit

tag: wbc

tag: platelet

tag: per neutrophils

tag: per lymphocytes

tag: per monocytes

tag: per eosinophils

tag: abs neutrophils

tag: abs monos by lymphos


title: M24_150

description:
M24_150
9248833092_I.AVG_Signal

tag: tissue

tag: ChIP

tag: hyb chamber

tag: dataset

tag: synchroset

tag: pittid

tag: monkeyid

tag: time point

tag: infection time

tag: clinical status

tag: per basophils

tag: abs lymphocytes

tag: per lymphosstained

tag: per cd3stained

tag: per cd16pos cd3neg

tag: per cd20


title: M38_7

description:
M38_7
9248833091_J.AVG_Signal

tag: FDG avidity

tag: FDG group

tag: hemoglobin

tag: hematocrit

tag: wbc

tag: platelet

tag: per neutrophils

tag: per lymphocytes

tag: per monocytes

tag: per eosinophils

tag: abs neutrophils

tag: abs monocytes

tag: abs eosinophils

tag: per monos by lymphos

tag: abs monos by lymphos

tag: per cd8