title: Donor 25 Stimulation HKEC

value: HKEC


title: Donor 25 Stimulation IL-1B

status: Public on Aug 04 2016

type: RNA

city: Paris

first: Vincent

last: Rouilly

state: Paris

address: 25 rue Dr Roux

country: France

institute: Institut Pasteur

hyb_protocol: NanoString nCounter, a hybridization-based multiplex assay.

scan_protocol: Data were collected and analyzed using the nCounter Digital Analyze according to the manufacturer’s instructions (NanoStrings Technologies, Seattle, WA).

data_processing: To normalize we used the same method as in the positive control normalization, except that geometric means were calculated over four housekeeping genes (RPL19, TBP, POLR2A, HPRT1). These genes were selected using geNorm method.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Whole Blood

label_protocol: Biotin & color-coded tag, 100ng (5μl) of total RNA from each sample was analyzed using the Human Immunology kit v2 according to the manufacturers instructions.

growth_protocol: Incubation inside a Truculture stimulation tube (from Myriad RBM), 37C, 22h.

extract_protocol: A specific chloroform-free one step protocol was adapted for automation to guarantee a reproducible and high-throughput RNA extraction protocol.

treatment_protocol: At the end of the incubation period, upon removal of the liquid supernatant cell pellets were resuspended in 2ml Trizol LS (Sigma) and vortexed for 2min, rested for 10 min at RT before storage at -80°C.

tag: individual

value: Donor 25

tag: donor id

tag: stimulus id

tag: age

tag: gender

value: M

tag: tissue

value: whole blood


title: Donor 25 Stimulation IFN-B

value: IFN-B


title: Donor 25 Stimulation FSL

value: FSL


title: Donor 25 Stimulation Null


title: Donor 25 Stimulation IAV

value: IAV


title: Donor 25 Stimulation FLA

value: FLA


title: Donor 25 Stimulation pIC

value: pIC


title: 16462 wild type M

status: Public on Aug 05 2016

city: Ann Arbor

first: Sally

middle: Ann

last: Camper

state: MI

address: 1241 Catherine St

department: Human Genetics

country: USA

institute: University of Michigan

hyb_protocol: 1500 ng cRNA was direct hybridized for 18 hours at 58 C by standard Illumina protocol.

scan_protocol: Signal intensity recorded with an Illumina iScan by standard protocol.

data_processing: Image data was analyzed and quantile normalized with Illumina Genome Studio (v2011.1, Data Analysis Software package with Gene Expression Module v1.9.0)

organism: Mus musculus

source_name: Mouse pituitary gland

label_protocol: Biotin-labelled cRNA was generated using 500 ng RNA with the Illumina TotalPrep RNA Amplification kit.

extract_protocol: RNA was extracted from homogenized tissue using the RNAqueous 4PCR kit and treated with DNAse I. RNA was quantified with Nanodrop and quality was assessed with 2100 BioAnalyzer. RNA Integrity Number was 9.50 ± 0.13 (SD), 28S/18S was 1.60 ± 0.12 (SD).

tag: strain

value: Mixed C57Bl6j 129S2SvPas

value: 8 week

value: pituitary

value: male

tag: genotype

value: wild


title: Donor 25 Stimulation HKCA

value: HKCA


title: Donor 25 Stimulation SeV

value: SeV


title: Donor 24 Stimulation HKSA

value: Donor 24

value: HKSA


title: Donor 25 Stimulation SEB

value: Donor 25

value: SEB


title: Donor 24 Stimulation IFN-B

value: M

value: whole blood


title: Donor 24 Stimulation IAV


title: Donor 25 Stimulation IFN-G

value: IFN-G


title: Donor 24 Stimulation TNFa

value: TNFa


title: Donor 24 Stimulation Null


title: Donor 24 Stimulation BCG

value: BCG


title: Donor 24 Stimulation SeV


title: Donor 24 Stimulation IFN-G


title: Donor 24 Stimulation HKEC

value: HKEC


title: Donor 24 Stimulation FLA

value: FLA


title: Donor 24 Stimulation pIC

value: pIC


title: Donor 24 Stimulation HKCA


title: Donor 23 Stimulation TNFa

value: Donor 23


title: Donor 24 Stimulation LPS

value: LPS


title: Donor 23 Stimulation HKSA


title: Donor 24 Stimulation FSL

value: FSL


title: Donor 24 Stimulation HKLR

value: HKLR


title: Donor 24 Stimulation HKHP

value: HKHP


title: Donor 24 Stimulation ODN

value: Donor 24

value: ODN


title: Donor 24 Stimulation r848


title: Donor 23 Stimulation HKLR


title: Donor 23 Stimulation IAV

value: IAV


title: Donor 24 Stimulation IL-1B


title: Donor 23 Stimulation FLA


title: Donor 24 Stimulation SEB

value: SEB


title: Donor 23 Stimulation SEB

value: M


title: Donor 23 Stimulation pIC

value: whole blood


title: Donor 23 Stimulation LPS


title: Donor 24 Stimulation GARD

value: GARD


title: Donor 23 Stimulation IL-1B


title: Donor 23 Stimulation SeV

value: SeV


title: Donor 23 Stimulation r848


title: Donor 23 Stimulation ODN


title: Donor 23 Stimulation HKCA

value: HKCA


title: Donor 23 Stimulation GARD


title: Donor 23 Stimulation IFN-G

value: IFN-G


title: Donor 23 Stimulation HKHP


title: Donor 23 Stimulation BCG

value: BCG


title: Donor 23 Stimulation HKEC

value: HKEC


title: Donor 23 Stimulation FSL

value: Donor 23


title: Donor 22 Stimulation HKCA

value: Donor 22


title: Donor 22 Stimulation IL-1B


title: Donor 22 Stimulation GARD


title: Donor 22 Stimulation Null


title: Donor 23 Stimulation Null


title: Donor 22 Stimulation IFN-B

value: IFN-B


title: Donor 22 Stimulation pIC

value: pIC


title: Donor 22 Stimulation IAV


title: Donor 22 Stimulation LPS

value: LPS


title: Donor 22 Stimulation BCG


title: Donor 22 Stimulation HKLR

value: HKLR


title: Donor 22 Stimulation r848


title: Donor 22 Stimulation TNFa

value: TNFa


title: Donor 23 Stimulation IFN-B


title: Donor 22 Stimulation SEB


title: Donor 22 Stimulation SeV


title: Donor 22 Stimulation HKSA

value: HKSA


title: Donor 22 Stimulation FLA

value: FLA


title: Donor 22 Stimulation HKHP

value: HKHP

value: M


title: Donor 21 Stimulation IL-1B

value: Donor 21

value: whole blood


title: Donor 22 Stimulation ODN

value: ODN


title: Donor 22 Stimulation FSL

value: FSL


title: Donor 21 Stimulation SEB

value: SEB


title: Donor 21 Stimulation HKEC

value: HKEC


title: Donor 21 Stimulation r848


title: Donor 21 Stimulation HKHP


title: Donor 21 Stimulation HKSA


title: Donor 21 Stimulation SeV

value: SeV


title: Donor 21 Stimulation Null


title: Donor 21 Stimulation FLA


title: Donor 21 Stimulation pIC


title: Donor 21 Stimulation TNFa


title: Donor 21 Stimulation HKLR


title: Donor 21 Stimulation LPS


title: Donor 21 Stimulation BCG

value: BCG


title: Donor 21 Stimulation FSL


title: Donor 22 Stimulation IFN-G

value: Donor 22

value: IFN-G


title: Donor 22 Stimulation HKEC


title: Donor 21 Stimulation ODN


title: Donor 21 Stimulation HKCA

value: HKCA


title: Donor 21 Stimulation IFN-G


title: Donor 21 Stimulation IAV

value: IAV


title: Donor 20 Stimulation GARD

value: Donor 20

value: GARD


title: Donor 20 Stimulation IL-1B


title: Donor 20 Stimulation SeV


title: Donor 21 Stimulation GARD


title: Donor 20 Stimulation HKHP


title: Donor 20 Stimulation HKSA

value: HKSA


title: Donor 20 Stimulation Null


title: Donor 20 Stimulation SEB


title: Donor 20 Stimulation HKEC


title: Donor 20 Stimulation LPS

value: LPS


title: Donor 20 Stimulation ODN

value: M


title: Donor 20 Stimulation BCG


title: Donor 20 Stimulation HKLR

value: HKLR


title: Donor 20 Stimulation r848

value: whole blood


title: Donor 20 Stimulation IFN-B

value: IFN-B


title: Donor 21 Stimulation IFN-B

value: Donor 21


title: Donor 20 Stimulation IAV


title: Donor 20 Stimulation HKCA


title: Donor 19 Stimulation SEB

value: Donor 19

value: SEB


title: Donor 19 Stimulation FSL

value: FSL


title: Donor 20 Stimulation TNFa

value: TNFa


title: Donor 19 Stimulation LPS


title: Donor 19 Stimulation HKCA


title: Donor 20 Stimulation pIC

value: pIC


title: Donor 19 Stimulation TNFa


title: Donor 19 Stimulation IAV


title: Donor 19 Stimulation ODN

value: ODN


title: Donor 19 Stimulation IL-1B


title: Donor 19 Stimulation r848


title: Donor 20 Stimulation IFN-G

value: IFN-G


title: Donor 19 Stimulation FLA

value: FLA


title: Donor 20 Stimulation FLA

value: Donor 20


title: Donor 20 Stimulation FSL


title: Donor 19 Stimulation GARD

value: GARD


title: Donor 19 Stimulation HKEC

value: HKEC


title: Donor 19 Stimulation HKLR


title: Donor 19 Stimulation pIC


title: Donor 19 Stimulation Null


title: Donor 19 Stimulation IFN-G


title: Donor 19 Stimulation HKHP

value: HKHP


title: Donor 19 Stimulation BCG

value: BCG

value: M


title: Donor 19 Stimulation IFN-B

value: whole blood


title: Donor 19 Stimulation SeV

value: SeV


title: Donor 18 Stimulation pIC

value: Donor 18


title: Donor 18 Stimulation IFN-B

value: IFN-B


title: Donor 18 Stimulation IAV

value: IAV


title: Donor 18 Stimulation SeV


title: Donor 18 Stimulation IFN-G


title: Donor 19 Stimulation HKSA

value: Donor 19

value: HKSA


title: Donor 18 Stimulation FLA


title: Donor 18 Stimulation r848


title: Donor 18 Stimulation BCG


title: Donor 18 Stimulation FSL

value: FSL


title: Donor 18 Stimulation LPS

value: LPS


title: Donor 18 Stimulation ODN

value: ODN


title: Donor 18 Stimulation SEB

value: SEB


title: Donor 18 Stimulation Null


title: Donor 18 Stimulation IL-1B


title: Donor 18 Stimulation HKEC


title: Donor 17 Stimulation HKHP

value: Donor 17


title: Donor 18 Stimulation HKCA

value: HKCA


title: Donor 18 Stimulation GARD

value: GARD


title: Donor 18 Stimulation TNFa

value: TNFa


title: Donor 18 Stimulation HKHP

value: HKHP


title: Donor 17 Stimulation HKLR

value: HKLR

value: M


title: Donor 18 Stimulation HKLR

value: whole blood


title: Donor 17 Stimulation TNFa


title: Donor 17 Stimulation HKSA


title: Donor 17 Stimulation HKEC

value: HKEC


title: Donor 17 Stimulation IFN-G

value: IFN-G


title: Donor 17 Stimulation SEB


title: Donor 17 Stimulation IFN-B

value: IFN-B


title: Donor 17 Stimulation FSL


title: Donor 17 Stimulation IL-1B


title: Donor 17 Stimulation Null


title: Donor 17 Stimulation LPS


title: Donor 17 Stimulation HKCA


title: Donor 18 Stimulation HKSA

value: Donor 18


title: Donor 17 Stimulation FLA

value: FLA


title: Donor 17 Stimulation ODN


title: Donor 17 Stimulation r848


title: Donor 17 Stimulation GARD


title: Donor 17 Stimulation pIC

value: pIC


title: Donor 17 Stimulation BCG

value: BCG


title: Donor 17 Stimulation SeV

value: SeV


title: Donor 17 Stimulation IAV

value: IAV


title: Donor 16 Stimulation IFN-G

value: Donor 16


title: Donor 16 Stimulation FLA


title: Donor 16 Stimulation TNFa


title: Donor 16 Stimulation GARD


title: Donor 16 Stimulation HKHP


title: Donor 16 Stimulation Null


title: Donor 16 Stimulation HKLR


title: Donor 16 Stimulation BCG


title: Donor 16 Stimulation IL-1B


title: Donor 16 Stimulation ODN

value: ODN


title: Donor 16 Stimulation IFN-B


title: Donor 16 Stimulation HKEC


title: Donor 16 Stimulation SeV


title: Donor 16 Stimulation SEB

value: SEB


title: Donor 16 Stimulation pIC


title: Donor 16 Stimulation IAV


title: Donor 15 Stimulation IFN-G

value: Donor 15


title: Donor 15 Stimulation r848


title: Donor 15 Stimulation HKLR


title: Donor 15 Stimulation HKHP

value: HKHP


title: Donor 15 Stimulation ODN


title: Donor 15 Stimulation HKSA

value: HKSA


title: Donor 15 Stimulation IAV

value: M


title: Donor 15 Stimulation LPS

value: LPS

value: whole blood


title: Donor 16 Stimulation LPS


title: Donor 16 Stimulation HKCA

value: HKCA


title: Donor 15 Stimulation FSL

value: FSL


title: Donor 15 Stimulation HKEC

value: HKEC


title: Donor 15 Stimulation GARD

value: GARD


title: Donor 16 Stimulation r848


title: Donor 15 Stimulation pIC

value: pIC


title: Donor 15 Stimulation HKCA


title: Donor 15 Stimulation IFN-B

value: IFN-B


title: Donor 16 Stimulation FSL


title: Donor 16 Stimulation HKSA


title: Donor 15 Stimulation IL-1B


title: Donor 15 Stimulation SeV

value: SeV


title: Donor 15 Stimulation SEB


title: Donor 15 Stimulation BCG

value: BCG


title: Donor 15 Stimulation Null


title: Donor 15 Stimulation TNFa

value: TNFa


title: Donor 14 Stimulation HKLR

value: Donor 14

value: HKLR


title: Donor 14 Stimulation pIC


title: Donor 14 Stimulation Null


title: Donor 14 Stimulation IFN-B


title: Donor 14 Stimulation FSL


title: Donor 14 Stimulation IAV

value: IAV


title: Donor 14 Stimulation HKHP

value: HKHP


title: Donor 14 Stimulation ODN

value: ODN


title: Donor 14 Stimulation SeV

value: M


title: Donor 15 Stimulation FLA

value: Donor 15

value: FLA


title: Donor 14 Stimulation HKCA

value: HKCA

value: whole blood


title: Donor 14 Stimulation GARD


title: Donor 14 Stimulation HKSA

value: HKSA


title: Donor 14 Stimulation BCG


title: Donor 14 Stimulation FLA


title: Donor 14 Stimulation TNFa


title: Donor 13 Stimulation IL-1B

value: Donor 13

value: F


title: Donor 13 Stimulation SEB

value: SEB


title: Donor 14 Stimulation LPS

value: LPS


title: Donor 14 Stimulation IFN-G

value: IFN-G


title: Donor 13 Stimulation Null


title: Donor 14 Stimulation HKEC

value: HKEC


title: Donor 14 Stimulation IL-1B

value: Donor 14


title: Donor 13 Stimulation FLA


title: Donor 13 Stimulation TNFa

value: TNFa


title: Donor 13 Stimulation pIC

value: pIC


title: Donor 13 Stimulation LPS


title: Donor 13 Stimulation GARD

value: GARD


title: Donor 13 Stimulation IFN-B

value: IFN-B


title: Donor 13 Stimulation HKCA


title: Donor 13 Stimulation IFN-G


title: Donor 13 Stimulation BCG

value: BCG


title: Donor 14 Stimulation SEB

value: M


title: Donor 13 Stimulation HKHP

value: HKHP


title: Donor 14 Stimulation r848


title: Donor 13 Stimulation HKSA


title: Donor 13 Stimulation HKEC


title: Donor 13 Stimulation FSL

value: FSL


title: Donor 13 Stimulation ODN

value: ODN

value: whole blood


title: Donor 13 Stimulation HKLR

value: Donor 13

value: HKLR


title: Donor 13 Stimulation SeV

value: SeV

value: F


title: Donor 12 Stimulation LPS

value: Donor 12

value: LPS


title: Donor 12 Stimulation r848


title: Donor 12 Stimulation TNFa


title: Donor 12 Stimulation FSL


title: Donor 13 Stimulation IAV

value: IAV


title: Donor 12 Stimulation SEB

value: SEB


title: Donor 12 Stimulation SeV


title: Donor 12 Stimulation GARD


title: Donor 12 Stimulation ODN


title: Donor 12 Stimulation IFN-G

value: IFN-G


title: Donor 12 Stimulation IL-1B


title: Donor 12 Stimulation IFN-B


title: Donor 12 Stimulation FLA

value: FLA


title: Donor 12 Stimulation HKHP


title: Donor 12 Stimulation pIC

value: pIC


title: Donor 12 Stimulation HKEC

value: HKEC


title: Donor 12 Stimulation HKCA

value: HKCA


title: Donor 13 Stimulation r848


title: Donor 12 Stimulation BCG

value: BCG


title: Donor 12 Stimulation IAV


title: Donor 12 Stimulation HKLR


title: Donor 12 Stimulation HKSA

value: HKSA


title: Donor 11 Stimulation FLA

value: Donor 11


title: Donor 11 Stimulation FSL

value: FSL

value: whole blood


title: Donor 11 Stimulation SeV


title: Donor 12 Stimulation Null


title: Donor 11 Stimulation IAV


title: Donor 11 Stimulation TNFa

value: TNFa


title: Donor 11 Stimulation pIC


title: Donor 11 Stimulation HKSA


title: Donor 11 Stimulation HKLR

value: HKLR


title: Donor 11 Stimulation GARD

value: GARD

value: F


title: Donor 11 Stimulation Null


title: Donor 11 Stimulation SEB


title: Donor 11 Stimulation HKEC


title: Donor 11 Stimulation IFN-G


title: Donor 11 Stimulation BCG


title: Donor 11 Stimulation ODN

value: ODN


title: Donor 10 Stimulation IL-1B

value: Donor 10


title: Donor 11 Stimulation HKHP

value: HKHP


title: Donor 10 Stimulation BCG


title: Donor 11 Stimulation IFN-B

value: IFN-B


title: Donor 10 Stimulation IFN-B


title: Donor 11 Stimulation IL-1B


title: Donor 10 Stimulation pIC


title: Donor 10 Stimulation LPS

value: LPS


title: Donor 10 Stimulation IFN-G

value: IFN-G


title: Donor 11 Stimulation LPS


title: Donor 10 Stimulation IAV

value: IAV


title: Donor 11 Stimulation HKCA

value: HKCA


title: Donor 11 Stimulation r848


title: Donor 10 Stimulation TNFa


title: Donor 10 Stimulation ODN


title: Donor 10 Stimulation FLA

value: FLA


title: Donor 10 Stimulation SeV

value: SeV


title: Donor 10 Stimulation GARD


title: Donor 10 Stimulation HKEC

value: HKEC


title: Donor 10 Stimulation Null


title: Donor 09 Stimulation SeV

value: Donor 09


title: Donor 09 Stimulation HKLR

value: whole blood


title: Donor 09 Stimulation HKEC


title: Donor 09 Stimulation SEB

value: SEB


title: Donor 09 Stimulation TNFa

value: TNFa


title: Donor 08 Stimulation SEB

value: Donor 08


title: Donor 09 Stimulation pIC

value: pIC

value: F


title: Donor 09 Stimulation Null


title: Donor 08 Stimulation TNFa


title: Donor 09 Stimulation HKCA


title: Donor 09 Stimulation GARD

value: GARD


title: Donor 09 Stimulation ODN

value: ODN


title: Donor 09 Stimulation BCG

value: BCG


title: Donor 09 Stimulation LPS

value: LPS


title: Donor 09 Stimulation IL-1B


title: Donor 09 Stimulation HKHP

value: HKHP


title: Donor 09 Stimulation IAV

value: IAV


title: Donor 10 Stimulation HKCA

value: Donor 10

value: HKCA


title: Donor 10 Stimulation SEB


title: Donor 09 Stimulation FLA

value: FLA


title: Donor 09 Stimulation r848


title: Donor 09 Stimulation IFN-G

value: IFN-G


title: Donor 10 Stimulation r848


title: Donor 09 Stimulation IFN-B

value: Donor 09

value: IFN-B


title: Donor 10 Stimulation HKLR

value: HKLR

value: whole blood


title: Donor 10 Stimulation FSL

value: FSL


title: Donor 10 Stimulation HKSA

value: HKSA


title: Donor 09 Stimulation FSL

value: F


title: Donor 09 Stimulation HKSA


title: Donor 10 Stimulation HKHP


title: Donor 08 Stimulation pIC

value: Donor 08

value: pIC


title: Donor 08 Stimulation ODN

value: ODN


title: Donor 08 Stimulation HKCA


title: Donor 07 Stimulation HKSA

value: Donor 07


title: Donor 07 Stimulation HKHP

value: HKHP


title: Donor 07 Stimulation FSL


title: Donor 08 Stimulation HKHP


title: Donor 08 Stimulation SeV

value: SeV


title: Donor 08 Stimulation IL-1B


title: Donor 08 Stimulation IAV

value: IAV


title: Donor 08 Stimulation HKSA


title: Donor 08 Stimulation IFN-G


title: Donor 08 Stimulation HKLR


title: Donor 08 Stimulation FSL


title: Donor 08 Stimulation LPS

value: LPS


title: Donor 08 Stimulation HKEC

value: HKEC


title: Donor 08 Stimulation Null


title: Donor 08 Stimulation GARD

value: GARD


title: Donor 08 Stimulation r848


title: Donor 07 Stimulation LPS


title: Donor 07 Stimulation HKLR


title: Donor 07 Stimulation BCG

value: BCG


title: Donor 07 Stimulation FLA

value: FLA


title: Donor 08 Stimulation BCG


title: Donor 08 Stimulation FLA


title: Donor 07 Stimulation ODN


title: Donor 08 Stimulation IFN-B

value: IFN-B


title: Donor 07 Stimulation IFN-G

value: IFN-G

value: whole blood


title: Donor 07 Stimulation r848


title: Donor 07 Stimulation pIC


title: Donor 07 Stimulation IAV


title: Donor 07 Stimulation SEB

value: SEB


title: Donor 07 Stimulation HKCA

value: HKCA

value: F


title: Donor 06 Stimulation SeV

value: Donor 06


title: Donor 06 Stimulation pIC

value: pIC


title: Donor 06 Stimulation BCG


title: Donor 06 Stimulation HKLR

value: HKLR


title: Donor 06 Stimulation LPS


title: Donor 06 Stimulation HKCA


title: Donor 07 Stimulation SeV

value: Donor 07


title: Donor 06 Stimulation IL-1B


title: Donor 06 Stimulation r848


title: Donor 07 Stimulation HKEC


title: Donor 06 Stimulation TNFa

value: TNFa


title: Donor 06 Stimulation FSL

value: FSL


title: Donor 06 Stimulation IFN-B


title: Donor 07 Stimulation IFN-B


title: Donor 06 Stimulation HKHP

value: HKHP


title: Donor 07 Stimulation GARD


title: Donor 06 Stimulation Null


title: Donor 06 Stimulation FLA


title: Donor 06 Stimulation HKSA

value: HKSA


title: Donor 06 Stimulation IFN-G


title: Donor 06 Stimulation HKEC

value: HKEC


title: Donor 06 Stimulation SEB


title: Donor 07 Stimulation Null


title: Donor 06 Stimulation GARD

value: GARD


title: Donor 06 Stimulation ODN

value: ODN


title: Donor 07 Stimulation IL-1B


title: Donor 05 Stimulation HKCA

value: Donor 05


title: Donor 06 Stimulation IAV

value: IAV


title: Donor 05 Stimulation ODN

value: whole blood


title: Donor 05 Stimulation IAV


title: Donor 05 Stimulation IFN-G

value: IFN-G


title: Donor 05 Stimulation LPS

value: LPS


title: Donor 05 Stimulation SEB

value: SEB

value: F


title: Donor 05 Stimulation GARD


title: Donor 05 Stimulation HKHP


title: Donor 05 Stimulation SeV

value: SeV


title: Donor 04 Stimulation SeV

value: Donor 04


title: Donor 05 Stimulation BCG

value: BCG


title: Donor 05 Stimulation TNFa

value: TNFa


title: Donor 05 Stimulation IL-1B


title: Donor 05 Stimulation FSL

value: FSL


title: Donor 05 Stimulation FLA

value: FLA


title: Donor 05 Stimulation IFN-B

value: IFN-B


title: Donor 05 Stimulation Null


title: Donor 07 Stimulation TNFa

value: Donor 07


title: Donor 05 Stimulation r848


title: Donor 05 Stimulation pIC

value: pIC


title: Donor 04 Stimulation r848


title: Donor 04 Stimulation BCG


title: Donor 04 Stimulation SEB


title: Donor 04 Stimulation IFN-B


title: Donor 04 Stimulation FLA


title: Donor 04 Stimulation FSL


title: Donor 05 Stimulation HKEC

value: HKEC


title: Donor 05 Stimulation HKLR

value: Donor 05

value: HKLR


title: Donor 04 Stimulation Null

value: whole blood


title: Donor 05 Stimulation HKSA

value: HKSA


title: Donor 04 Stimulation GARD

value: GARD


title: Donor 04 Stimulation HKLR


title: Donor 04 Stimulation TNFa


title: Donor 04 Stimulation HKSA


title: Donor 04 Stimulation HKHP

value: HKHP


title: Donor 04 Stimulation ODN

value: ODN

value: F


title: Donor 04 Stimulation pIC

value: Donor 04


title: Donor 04 Stimulation IFN-G

value: IFN-G


title: Donor 04 Stimulation IL-1B


title: Donor 04 Stimulation HKCA

value: HKCA


title: Donor 04 Stimulation IAV

value: IAV


title: Donor 04 Stimulation HKEC


title: Donor 03 Stimulation SEB

value: Donor 03

value: SEB


title: Donor 03 Stimulation FSL

value: FSL


title: Donor 03 Stimulation HKLR


title: Donor 03 Stimulation Null


title: Donor 04 Stimulation LPS

value: LPS


title: Donor 03 Stimulation SeV

value: SeV


title: Donor 03 Stimulation ODN


title: CiRA00009_iPSC derived vascular smooth muscle cells_rep1

city: Kyoto

first: Akira

last: Watanabe

state: Kyoto

address: Rm504, Miyako Bldg, 233, Isa-cho, kamigyo-ku

country: Japan

institute: CyberomiX Inc

description: CiRA00009 SMC

hyb_protocol: Labeling, hybridization and scanning were performed as per Affymetrix GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Manual version 4.

data_processing: Data from RNA expression array experiments in the form of .cel files was normalized, background corrected and summarized using the RMA algorithm implemented in the Affymetrix Expression Console(TM) version 1.0 software.

source_name: ADPKD-specific iPSC derived vascular smooth muscle cells

growth_protocol: The differentiation of the iPSCs into vascular cells was carried out as described previously (Sone et al., 2007; Tatsumi et al., 2011). Briefly, undifferentiated human iPSCs were harvested and transferred to a collagen I-coated dish after adjusting the colonies to an appropriate size. On the second day of incubation, the culture medium was replaced with Primate ES medium without basic fibroblast growth factor (bFGF), supplemented with N2 supplement (Invitrogen)/B27 supplement (Invitrogen) and 6-bromoindirubin-3'-oxime (BIO, 5 μM, SIGMA). Thereafter, the cells were incubated for another 3 days, at which time the culture medium was replaced with StemPro-34 SFM (Invitrogen) supplemented with recombinant human vascular endothelial growth factor (VEGF, 50 ng/ml, PeproTech). After another 3–5 days of incubation, FLK1 (+) VE-cadherin (+) and FLK1 (+) VE-cadherin (-) cells were sorted individually using a FACSAria flow cytometer (BD). Sorted FLK1 (+) VE-cadherin (+) cells were confirmed to remain VE-cadherin positive during the subsequent cell culture and analyses. On the other hand, the sorted FLK1 (+) VE-cadherin (-) cells were differentiated into vascular smooth muscle cells after an additional 18-22 days of differentiation on collagen I-coated dishes supplemented with recombinant human platelet-derived growth factor-BB (PDGF-BB, 20 ng/ml, PeproTech).

extract_protocol: RNA was prepared using the miRNeasy Purification kit (Qiagen) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies).

tag: subject/sample source id

tag: subject status

value: autosomal dominant polycystic kidney disease (ADPKD) patient

value: Female

tag: cell type


title: CiRA00008_iPSC derived vascular smooth muscle cells_rep1

description: CiRA00008 SMC

scan_protocol: Labeling, hybridization and scanning were performed as per Affymetrix GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Manual version 4.

value: Male


title: CiRA00004_iPSC derived vascular smooth muscle cells_rep1

description: CiRA00004 SMC

label_protocol: Labeling, hybridization and scanning were performed as per Affymetrix GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Manual version 4.


title: CiRA00006_iPSC derived vascular smooth muscle cells_rep1

description: CiRA00006 SMC


title: Donor 03 Stimulation IAV

value: whole blood


title: Donor 03 Stimulation HKHP


title: CiRA00010_iPSC derived endothelial cells_rep1

description: CiRA00010 EC

source_name: ADPKD-specific iPSC derived endothelial cells

value: iPSC derived endothelial cells


title: CiRA00007_iPSC derived vascular smooth muscle cells_rep1

description: CiRA00007 SMC


title: Donor 03 Stimulation IFN-B

value: IFN-B


title: CiRA00010_iPSC derived vascular smooth muscle cells_rep1

description: CiRA00010 SMC


title: Donor 03 Stimulation pIC

value: pIC


title: Donor 03 Stimulation LPS

value: F


title: CiRA00009_iPSC derived endothelial cells_rep1

description: CiRA00009 EC


title: CiRA00008_iPSC derived endothelial cells_rep1

description: CiRA00008 EC


title: Donor 03 Stimulation IL-1B


title: Donor 03 Stimulation FLA

value: FLA


title: CiRA00005_iPSC derived vascular smooth muscle cells_rep1

description: CiRA00005 SMC


title: Donor 03 Stimulation BCG

value: BCG


title: Donor 03 Stimulation HKEC

value: HKEC


title: Donor 03 Stimulation IFN-G

value: IFN-G


title: Donor 03 Stimulation HKCA

value: Donor 03

value: HKCA


title: Donor 03 Stimulation HKSA

value: HKSA


title: Donor 02 Stimulation BCG

value: Donor 02


title: Donor 03 Stimulation TNFa

value: TNFa


title: Donor 02 Stimulation HKHP

value: HKHP


title: Donor 03 Stimulation r848


title: Donor 02 Stimulation SEB

value: SEB


title: Donor 02 Stimulation HKSA


title: Donor 02 Stimulation FSL

value: FSL


title: CiRA00007_iPSC derived endothelial cells_rep1

description: CiRA00007 EC

value: autosomal dominant polycystic kidney disease (ADPKD) patient

value: Male


title: Donor 02 Stimulation Null

value: whole blood


title: Donor 02 Stimulation ODN

value: ODN


title: CiRA00006_iPSC derived endothelial cells_rep1

description: CiRA00006 EC

value: iPSC derived endothelial cells


title: Donor 02 Stimulation IL-1B

value: F


title: Donor 02 Stimulation TNFa


title: Donor 02 Stimulation LPS

value: LPS


title: Donor 02 Stimulation IAV

value: IAV


title: Donor 02 Stimulation GARD

value: GARD


title: Donor 02 Stimulation pIC

value: pIC


title: CiRA00005_iPSC derived endothelial cells_rep1

description: CiRA00005 EC

value: Female


title: CiRA00004_iPSC derived endothelial cells_rep1

description: CiRA00004 EC


title: Donor 02 Stimulation HKLR

value: HKLR


title: Donor 01 Stimulation SeV

value: Donor 01

value: SeV


title: Donor 02 Stimulation FLA

value: Donor 02

value: FLA


title: Donor 02 Stimulation r848


title: Donor 02 Stimulation HKEC

value: HKEC


title: Donor 02 Stimulation HKCA

value: HKCA


title: Donor 02 Stimulation SeV


title: Donor 02 Stimulation IFN-B

value: IFN-B


title: Donor 02 Stimulation IFN-G

value: IFN-G

value: whole blood


title: Donor 01 Stimulation HKLR


title: Donor 01 Stimulation SEB

value: SEB


title: Donor 01 Stimulation GARD

value: F


title: Donor 01 Stimulation FLA


title: Donor 01 Stimulation HKHP

value: HKHP


title: Donor 01 Stimulation HKEC


title: Donor 01 Stimulation FSL

value: FSL


title: Donor 01 Stimulation HKCA


title: Donor 01 Stimulation IFN-G


title: Donor 03 Stimulation GARD

value: Donor 03

value: GARD


title: Donor 01 Stimulation BCG

value: BCG


title: Donor 01 Stimulation IFN-B


title: Donor 01 Stimulation IAV

value: IAV


title: Donor 01 Stimulation LPS

value: Donor 01

value: LPS


title: Donor 01 Stimulation TNFa

value: TNFa


title: Donor 01 Stimulation Null


title: Donor 01 Stimulation HKSA

value: HKSA


title: Donor 01 Stimulation r848


title: Donor 01 Stimulation IL-1B


title: Donor 01 Stimulation ODN

value: ODN


title: Donor 01 Stimulation pIC

value: pIC


description:
CiRA00007 SMC
Gene expression of ADPKD-specific iPSC derived vascular smooth muscle cells

hyb_protocol: Manufature's protocol

scan_protocol: Slides were scanned on the G2565CA Microarray Scanner System (Agilent).

data_processing: Logbase 2-transformed signal data were normalized to the 75 percentile with baseline transformation to median of all samples by Agilent GeneSpring GX.

label_protocol: Manufature's protocol

value: autosomal dominant polycystic kidney disease (ADPKD) patient

value: Male


description:
CiRA00006 SMC
Gene expression of ADPKD-specific iPSC derived vascular smooth muscle cells


description:
CiRA00007 EC
Gene expression of ADPKD-specific iPSC derived endothelial cells

value: iPSC derived endothelial cells


description:
CiRA00004 SMC
Gene expression of ADPKD-specific iPSC derived vascular smooth muscle cells

value: Female


description:
CiRA00008 EC
Gene expression of ADPKD-specific iPSC derived endothelial cells


description:
CiRA00009 SMC
Gene expression of ADPKD-specific iPSC derived vascular smooth muscle cells


title: cell_24h_pEGFP-N1-miR3131-WT vetor_rep1

city: Suzhou

first: wang

last: chaoqun

state: Jiangsu

address: Room 806-1, Engineering Building, North Campus ,Soochow University, No. 178, Ganjiang East Road, Gusu District

department: Department of Forensic Medicine

country: China

institute: Medical College of Soochow University

description: After pEGFP-N1-miR3131-WT being transfected in sk-Hep-1 cells for 24h, human genome-wide gene expression profile chip was adopted to screen the differentially expressed genes.

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturer instructions. On completion of the fragmentation reaction, 25ul of 2xGEx Hybridization Buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Feature Extraction software (version10.7.1.1, Agilent Technologies) was used to analyze array images to get raw data. Genespring (version 12.5, Agilent Technologies) were employed to finish the basic analysis with the raw data. To begin with, the raw data was normalized with the quantile algorithm. The probes that at least 100% of the values in any 1 out of all conditions have flags in Detected were chosen for further data analysis. Differentially expressed genes were then identified through fold change. The threshold set for up- and down-regulated genes was a fold change>= 2.0. Afterwards, GO analysis and KEGG analysis were applied to determine the roles of these differentially expressed mRNAs.

source_name: Sk-Hep-1 cell line, transfected pEGFP-N1-miR3131-WT vetor 24h, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color LowInput Quick-Amp Labeling Kit (Cat # 5190-2305, Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (Cat #74106, QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: Sk-Hep-1 cell line was cultured in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin at 37°C in a humidified chamber supplemented with 5% CO2. Upon resuscitation, the cell lines were characterized by Genetic Testing Biotechnology Corporation (Suzhou, China) using short tandem repeat (STR) markers.

extract_protocol: Total RNA was extracted from cell line according to the manufacturer's protocol (Cat #74106, Qiagen). Total RNA was quantified by the NanoDrop ND-2000 (Thermo Scientific) and the RNA integrity was assessed using Agilent Bioanalyzer 2100 (Agilent Technologies).

treatment_protocol: The fragment of 366bp including the insert allele of rs57408770 in pre-miR-3131 was directly synthesized by Genewiz Company (Suzhou, China) and cloned into BamHI and EcoRI sites of pEGFP-N1 (Cat#6085-1, Promega) yielding the wild-type vector (pEGFP-N1-miR3131-WT). The mutant-type vector (pEGFP-N1-miR3131-MT) including the delete allele of rs57408770 was generated using QuikChange Lightening Site-Directed Mutagenesis Kit (Cat # 210518, Stratagene). The resulting constructs were verified by direct sequencing. For overexpression experiments, cells were cultured in 6-well plates at a density of 200 000 cells per well the day before transfection. 2.5μg plasmids of empty vector pEGFP-N1, pEGFP-N1-miR3131-WT or pEGFP-N1-miR3131-MT were transfected into the growing cells (about 80%-90% confluent) using Lipofectamine2000 (Invitrogen). After 24 hours of the transfection, the cells were collected for subsequent experiments.

tag: cell line

value: Sk-Hep-1, Hepatocellular carcinoma cell line

tag: transfection vector


description:
CiRA00010 SMC
Gene expression of ADPKD-specific iPSC derived vascular smooth muscle cells


title: 585A1_iPSC derived vascular smooth muscle cells_rep1

description:
585A1 SMC
Gene expression of healthy-control iPSC derived vascular smooth muscle cells

value: healthy control


description:
CiRA00005 EC
Gene expression of ADPKD-specific iPSC derived endothelial cells


title: sst5TMD4_3

city: Madrid

first: Gema

last: Moreno-Bueno

state: Madrid

address: Arturo Duperier

department: Biochemistry

country: Spain

institute: IIB

hyb_protocol: In Situ Hybridization Kit Plus (Agilent technologies) protocols

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version 10.0).

data_processing: Agilent Feature Extraction Software (v 10.0) was used for background subtraction and LOWESS normalization.

source_name: Total RNA_sst5TMD4-pCDNA3.1_1 cells

label_protocol: Four independent passages from stably-transfected sst5TMD4-pCDNA3.1 and empty-pCDNA3.1 vector, used as control (mock), MFC7 cells were used. Total RNA (1mg)from cell lines was isolated using Trizol reagent (Life Technologies) as indicated by the manufacturer. Purity of isolated RNA was evaluated spectrophotometrically by the A260/A280 absorbance ratio. RNA was labeled and array hybridized using the Low RNA Linear Amplification Kit and the In Situ Hybridization Kit Plus (Agilent technologies), respectively, following manufacturer’s protocol.

growth_protocol: MCF-7 cells were maintained in Dulbecco’s Modified Eagle Medium (Sigma, San Louis, MO) supplemented with 10% fetal bovine serum, 1% antibiotic-antimycotic and 2mM L-glutamine, in a constant atmosphere with 37ºC and 5% CO2.

extract_protocol: Total RNA was extracted from paraffin-embedded breast cancer samples, frozen xenografted tumors and MCF-7 cell lines using Trizol (Life Technologies, Barcelona, Spain) following the manufacturer’s protocol and subsequently treated with DNase (Promega, Barcelona, Spain). Total RNA concentration and purity was assessed using Nanodrop 2000 spectrophotometer (Thermo Scientific, Wilmington, NC, USA), and subsequently retro-transcribed using random hexamer primers and cDNA First Strand Synthesis kit (MRI Fermentas, Hanover, MD, USA)

value: Epithelial

source_name: Pool from MCF7 cells transfected with empty vector


title: Cathepsin B-/- BMDM, rep 2

city: Memphis

first: Geoffrey

last: Neale

state: TN

address: 262 Danny Thomas Place

department: Hartwell Center

institute: St Jude Childrens Research Hospital

description:
SMM004
Cathepsin B-/- mouse backcrossed to the C57BL/6 background.

hyb_protocol: Five micrograms of cDNA was hybridized for 16h at 45C on an Affymetrix  Mouse Gene 2.0 ST GeneChip array.

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

data_processing: Probe signals were quantile normalized and summarized by the RMA algorithm using Partek Genomics Suite software v6.6.

source_name: Cathepsin B-/- BMDM

label_protocol: Sense target cDNA was prepared from 100ng of total RNA using the Ambion® WT Expression Kit (Life Technologies P/N 4411973). cDNA was fragmented and biotin-labeled using the Affymetrix® GeneChip® WT Terminal Labeling Kit (Affymetrix P/N 900671).

growth_protocol: Primary BMDMs were grown for 5-6 days in DMEM (Gibco) supplemented with 1% non-essential amino acids (Gibco), 10% FBS (Atlanta Biologicals), 30% medium conditioned by L929 mouse fibroblasts, and 1% penicillin and streptomycin (Sigma).

extract_protocol: Total RNA was extracted using the Trizol protocol according to the manufacturer's recommended methods.

tag: strain/background

tag: genotype/variation

value: cathepsin B-/-

value: bone marrow-derived macrophages


title: TIG975E4_iPSC derived vascular smooth muscle cells_rep1

description:
TIG975E4 SMC
Gene expression of healthy-control iPSC derived vascular smooth muscle cells


title: TIG975E2_iPSC derived vascular smooth muscle cells_rep1

description:
TIG975E2 SMC
Gene expression of healthy-control iPSC derived vascular smooth muscle cells


title: sst5TMD4_1


title: Cathepsin B-/- BMDM, rep 1

description:
SMM002
Cathepsin B-/- mouse backcrossed to the C57BL/6 background.


description:
CiRA00010 EC
Gene expression of ADPKD-specific iPSC derived endothelial cells


title: sst5TMD4_2


description:
CiRA00006 EC
Gene expression of ADPKD-specific iPSC derived endothelial cells


description:
CiRA00005 SMC
Gene expression of ADPKD-specific iPSC derived vascular smooth muscle cells


description:
CiRA00008 SMC
Gene expression of ADPKD-specific iPSC derived vascular smooth muscle cells


title: cell_24h_pEGFP-N1-miR3131-MT vetor_rep1

description: After pEGFP-N1-miR3131-MT being transfected in sk-Hep-1 cells for 24h, human genome-wide gene expression profile chip was adopted to screen the differentially expressed genes.

source_name: Sk-Hep-1 cell line, transfected pEGFP-N1-miR3131-MT vetor 24h, replicate 1


title: sst5TMD4_4


title: Wild-type BMDM, rep 2

description:
SMM003
C57BL/6 wild-type mouse.

source_name: Wild-type BMDM

value: wild-type


description:
CiRA00009 EC
Gene expression of ADPKD-specific iPSC derived endothelial cells


title: TIG120 3F7_iPSC derived vascular smooth muscle cells_rep1

description:
TIG120 3F7 SMC
Gene expression of healthy-control iPSC derived vascular smooth muscle cells


title: 585B1_iPSC derived vascular smooth muscle cells_rep1

description:
585B1SMC
Gene expression of healthy-control iPSC derived vascular smooth muscle cells


title: cell_24h_pEGFP-N1 vetor_rep1

description: After pEGFP-N1 transfected in sk-Hep-1 cells for 24h, human genome-wide gene expression profile chip was adopted to screen the differentially expressed genes.

source_name: Sk-Hep-1 cell line, transfected pEGFP-N1 vetor 24h, replicate 1


description:
CiRA00004 EC
Gene expression of ADPKD-specific iPSC derived endothelial cells


title: TIG121 4F4_iPSC derived vascular smooth muscle cells_rep1

description:
TIG121 4F4 SMC
Gene expression of healthy-control iPSC derived vascular smooth muscle cells


title: TIG114 4F1_iPSC derived vascular smooth muscle cells_rep1

description:
TIG114 4F1SMC
Gene expression of healthy-control iPSC derived vascular smooth muscle cells


title: 585B1_iPSC derived endothelial cells_rep1

description:
585B1 EC
Gene expression of healthy-control iPSC derived endothelial cells


title: TIG975E4_iPSC derived endothelial cells_rep1

description:
TIG975E4 EC
Gene expression of healthy-control iPSC derived endothelial cells


title: TIG118 4F1_iPSC derived vascular smooth muscle cells_rep1

description:
TIG118 4F1 SMC
Gene expression of healthy-control iPSC derived vascular smooth muscle cells


title: TIG107 4F1_iPSC derived vascular smooth muscle cells_rep1

description:
TIG107 4F1 SMC
Gene expression of healthy-control iPSC derived vascular smooth muscle cells


title: TIG121 4F4_iPSC derived endothelial cells_rep1

description:
TIG121 4F4 EC
Gene expression of healthy-control iPSC derived endothelial cells


title: 585A1_iPSC derived endothelial cells_rep1

description:
585A1 EC
Gene expression of healthy-control iPSC derived endothelial cells


title: WKY_CAF_biological rep 2

city: London

first: Jacques

last: Behmoaras

address: Du Cane Road

country: United Kingdom

institute: Imperial College London

description: Gene expression data from rat PBMCs under STD or CAF diet

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

scan_protocol: GeneChips were scanned using Genechip scanner 3000-7G

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

organism: Rattus norvegicus

source_name: WKY rats fed with cafeteria diet

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Male LEW and WKY rats were housed in a 22C temperature-controlled room

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions (invitrogen). Total RNA was purified using Rneasy microkits (Qiagen)

treatment_protocol: After an adaptation period, rats from each strain were randomly distributed into two experimental groups (n=5) and fed with either standard or cafteria diet for 7 weeks, after which blood was collected from abdominal aorta  and circulating monocytes were isolated using density gradient centrifugation using Histopaque-1083

value: male

value: WKY/NCrl

tag: diet

value: cafeteria diet

value: PBMC


title: LEW_CAF_biological rep 1

source_name: LEW rats fed with cafeteria diet

value: LEW/Crl


title: WKY_CAF_biological rep 4


title: TIG118 4F1_iPSC derived endothelial cells_rep1

description:
TIG118 4F1 EC
Gene expression of healthy-control iPSC derived endothelial cells


title: WKY_CAF_biological rep 1


title: Wild-type BMDM, rep 1

description:
SMM001
C57BL/6 wild-type mouse.


title: WKY_CAF_biological rep 5


title: LEW_CAF_biological rep 3


title: LEW_CAF_biological rep 4


title: LEW_CAF_biological rep 2


title: WKY_CAF_biological rep 3


title: TIG114 4F1_iPSC derived endothelial cells_rep1

description:
TIG114 4F1 EC
Gene expression of healthy-control iPSC derived endothelial cells


title: TIG119 4F1_iPSC derived endothelial cells_rep1

description:
TIG119 4F1 EC
Gene expression of healthy-control iPSC derived endothelial cells


title: anti-PD-1_Response_rep4

city: Baltimore

first: Alan

middle: E.

last: Berger

state: MD

address: 5501 Hopkins Bayview Circle Room 3B.74C

department: School of Medicine

institute: Johns Hopkins University

description:
PD-L1 positve renal cell carcinoma
RCC-8

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Signal intensity quantification was performed using an Illumina BeadStation 500GX Genetic Analysis Systems scanner, using the standard Illumina scanning protocol.

data_processing:
For each sample, a single intensity (expression) value for each Illumina probe on the array was obtained using Illumina GenomeStudio software with standard settings and no background correction.  For the data matrices, the ID_REF is the Illumina Probe_ID, and the Detection Pval is as provided by the Illumina software.  Detection Pvalues < 0.01 were taken to  indicate Present  (i.e., the corresponding expression level was considered to be above background).  Normalization of the expression values in each sample was done by scaling: for each sample all its expression values were multiplied by the constant which made the median of the expression values for that sample equal to 256. The scaled values were then log base 2 transformed.
Note the sample names are as designated in the paper associated with this dataset. RCC-9 was not subjected to microarray analysis and is therefore not included in this GEO submission.

source_name: RCC Metastasis (uterus and colon)

label_protocol: Total RNA was biotin labeled with the WG-DASL pre 1 MCS4 w/UDG Kit according to the manufacturers suggested protocol.

extract_protocol: Sample acquisition and RNA isolation from FFPE renal cell carcinoma specimens were performed as described in the reference above.

tag: response to anti-pd-1 (nivolumab) immunotherapy (response or no-response)

value: response

tag: response to anti-pd-1 (nivolumab) immunotherapy (complete response (cr) or partial response (pr) or stable disease (sd) or no response (nr))

value: CR

value: female

tag: primary tumor or metastasis

value: Metastasis

tag: interval between specimen collection and anti-pd1 therapy (months)


title: WKY_STD_biological rep 4

source_name: WKY rats fed with standard diet

value: standard diet

tag: age


title: WKY_STD_biological rep 3

tag: gender


title: anti-PD-1_Response_rep2

description:
PD-L1 positve renal cell carcinoma
RCC-3

source_name: RCC Primary tumor

value: PR

value: Primary


title: WKY_STD_biological rep 5


title: anti-PD-1_Response_rep1

description:
PD-L1 positve renal cell carcinoma
RCC-1

source_name: RCC Metastasis (IVC thrombus)


title: WKY_STD_biological rep 2


title: anti-PD-1_Response_rep3

description:
PD-L1 positve renal cell carcinoma
RCC-7

source_name: RCC Metastasis (humerus)


title: WKY_STD_biological rep 1


title: LEW_CAF_biological rep 5


title: Nucleus pulposus_degenerated_3_circRNA

city: Xi'an

first: Hai-Qiang

last: Wang

email: hqwang@sntcm.edu.cn, drwanghq@163.com

address: Xixian Avenue, Xixian District

department: Insititute of Integrative Medicine

institute: Shaanxi University of Chinese Medicine

description: Same RNA as GSM1354771, GSM1551031

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide.  The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned using the Agilent Scanner G2505C.

data_processing:
Scanned images were imported into Agilent Feature Extraction software for raw data extraction. Quantile normalization of raw data and subsequent data processing were performed using the R software package. After quantile normalization of the raw data, low intensity filtering was performed, and the circRNAs that at least 5 out of 10 samples have flags in “P” or “M” (“All Targets Value”) were retained for further analyses.
When comparing two groups of profile differences (such as disease versus control), the “fold change” (i.e. the ratio of the group averages) between the groups for each circRNA is computed. The statistical significance of the difference may be conveniently estimated by t-test. circRNAs having fold changes >2 and p-values < 0.05 are selected as the significantly differentially expressed.

source_name: Nucleus pulposus tissue,degenerated

label_protocol: CcircRNA were treated with Rnase R (Epicentre, Inc.) to remove linear RNAs. Then, each sample was amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and miRNeasy mini kit (QIAGEN) according to manufacturer’s instructions, which efficiently recovered all RNA species, including circRNAs. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis

treatment_protocol: All the specimens were collected from intervertebral discs of cadaveric donors or patients within 3 hours after anatomy or surgery respectively, following rinsed with phosphate-buffered saline, the nucleus pulposus tissue was carefully collected under stereoscopic microscope.

tag: tissue

value: Nucleus pulposus

tag: condition

value: Degenerated

tag: idd related diseases

value: Intervertebral disc herniation

value: Male

value: 42 years

tag: degeneration grading

value: Grading IV

tag: disc level


title: Nucleus pulposus_degenerated_4_circRNA

description: Same RNA as GSM1354772, GSM1551032

value: 45 years

value: Grading V


title: TIG120 4F1_iPSC derived vascular smooth muscle cells_rep1

description:
TIG120 4F1SMC
Gene expression of healthy-control iPSC derived vascular smooth muscle cells

tag: subject/sample source id

tag: subject status

value: healthy control

value: Female

tag: cell type


title: Nucleus pulposus_degenerated_5_circRNA

description: Same RNA as GSM1354773, GSM1551033

value: 27 years


title: Nucleus pulposus_degenerated_2_circRNA

description: Same RNA as GSM1354770, GSM1551030

value: 38 years


title: Nucleus pulposus_degenerated_1_circRNA

description: Same RNA as GSM1354769, GSM1551029

value: 32 years


title: anti-PD-1_No_Response_rep7

description:
PD-L1 positve renal cell carcinoma
RCC-12

value: NR

value: female


title: LEW_STD_biological rep 3

source_name: LEW rats fed with standard diet

value: male

tag: strain

value: LEW/Crl

value: standard diet

value: PBMC


title: anti-PD-1_No_Response_rep5

description:
PD-L1 positve renal cell carcinoma
RCC-10

source_name: RCC Metastasis (lymph node)

value: Metastasis


title: Nucleus pulposus_control_5_circRNA

description: Same RNA as GSM1354768, GSM1551028

source_name: Nucleus pulposus tissue,normal

value: Nucleus pulposus

value: Control

value: No

value: Male

value: 52 years

value: Grading I


title: Nucleus pulposus_control_3_circRNA

description: Same RNA as GSM1354766, GSM1551026

value: 41 years


title: LEW_STD_biological rep 4


title: LEW_STD_biological rep 5


title: anti-PD-1_No_Response_rep4

description:
PD-L1 positve renal cell carcinoma
RCC-6

value: Primary


title: anti-PD-1_No_Response_rep2

description:
PD-L1 positve renal cell carcinoma
RCC-4

source_name: RCC Metastasis (lung)


title: Nucleus pulposus_control_4_circRNA

description: Same RNA as GSM1354767, GSM1551027

value: Female

value: 43 years


title: LEW_STD_biological rep 2


title: anti-PD-1_No_Response_rep6

description:
PD-L1 positve renal cell carcinoma
RCC-11

value: NR


title: Nucleus pulposus_control_2_circRNA

description: Same RNA as GSM1354765, GSM1551025

value: 35 years


title: Nucleus pulposus_control_1_circRNA

description: Same RNA as GSM1354764, GSM1551024

value: 33 years


title: LEW_STD_biological rep 1

value: male

value: LEW/Crl


title: anti-PD-1_No_Response_rep3

description:
PD-L1 positve renal cell carcinoma
RCC-5

value: SD

value: female


title: Doxorubicin1 vs Control1, 7 week post treatment, reverse labelling

city: Didcot

first: Emma

middle: Louise

last: Marczylo

state: Oxfordshire

address: Harwell Campus, Chilton

department: Toxicology

institute: Public Health England

description: Biological replicate 1 of 3, reverse labelling, 7 week

hyb_protocol: Control and doxorubicin samples were randomly paired and pooled and treated according to the labelling kit's manufacturer's instructions. Prior to hybridisation pooled samples were fragmented using fragmentation reagent (Ambion) according to the manufacturer's instructions; mixed with years tRNA and 2X enhanced hybridisation buffer (Genisphere); denatured for 5 min at 100oC and incubated for 30 min at 42oC. Hybridisation was then performed overnight at 42oC using a Genetix hybridisation chamber. Arrays were washed on a rocking platform set at 50 oscillations per min for 5 min each at RT, firstly in 1X SSC containing 0.03% (w/v) SDS, secondly in 0.2X SSC and finally in 0.05X SSC, and dried by centrifugation.

scan_protocol: Slides scanned on a 4200 Axon scanner and data acquired using GenePix Pro v.6.0.

data_processing: Result files were normalised using the LOESS within array followed by the quantile between array commands in the Bioconductor limma library package of R version 2.15.2. Normalised log2[Cy5/Cy3] for forward labelling arrays and log2[Cy3/Cy5] for reverse labelling arrays were compiled into a single matrix file. All array control and empty values were removed and excluded from normalisation in R.

source_name: Testis RNA, Doxorubicin1, 7 week post treatment

label_protocol: 200 ng of total RNA was labelled with the Two-Colour Low Input Quick Amp Labelling Kit (Agilent Technologies) according to the manufacturer's instructions.

growth_protocol: Male C57BL/6J mice, 8-10 weeks old. 12 hour light/dark cycle. Food and water provided ad libitum, 24 hours a day.

extract_protocol: 1 whole testis was lysed in 1ml of Tri reagent (Sigma). RNA was extracted according to the manufacturer's instructions.

treatment_protocol: Mice were randomly assigned to groups. Dosing was performed via intraperitoneal injection. Treated mice received 3 x 3mg/kg of doxorubicin (in 0.85% (v/v) saline) per week (9mg/kg in total), controls received vehicle only; in a dose volume of 10ml/kg. 1, 4 or 7 wk after the final administration mice were sacrificed under isoflurane anaesthesia and exsanguinated. Testes were taken for analysis.

value: Testis

source_name: Testis RNA, Vehicle only1, 7 week post treatment


title: Doxorubicin3 vs Control3, 7 week post treatment, reverse labelling

description: Biological replicate 3 of 3, reverse labelling, 7 week

source_name: Testis RNA, Doxorubicin3, 7 week post treatment

source_name: Testis RNA, Vehicle only3, 7 week post treatment


title: Control1 vs Doxorubicin1, 7 week post treatment, forward labelling

description: Biological replicate 1 of 3, forward labelling, 7 week


title: Doxorubicin2 vs Control2, 7 week post treatment, reverse labelling

description: Biological replicate 2 of 3, reverse labelling, 7 week

source_name: Testis RNA, Doxorubicin2, 7 week post treatment

source_name: Testis RNA, Vehicle only2, 7 week post treatment


title: anti-PD-1_No_Response_rep1

description:
PD-L1 positve renal cell carcinoma
RCC-2


title: Control2 vs Doxorubicin2, 7 week post treatment, forward labelling

description: Biological replicate 2 of 3, forward labelling, 7 week


title: Doxorubicin3 vs Control3, 4 week post treatment, reverse labelling

description: Biological replicate 3 of 3, reverse labelling, 4 week

source_name: Testis RNA, Doxorubicin3, 4 week post treatment

source_name: Testis RNA, Vehicle only3, 4 week post treatment


title: Control3 vs Doxorubicin3, 7 week post treatment, forward labelling

description: Biological replicate 3 of 3, forward labelling, 7 week


title: Doxorubicin2 vs Control2, 4 week post treatment, reverse labelling

description: Biological replicate 2 of 3, reverse labelling, 4 week

source_name: Testis RNA, Doxorubicin2, 4 week post treatment

source_name: Testis RNA, Vehicle only2, 4 week post treatment


title: Control3 vs Doxorubicin3, 4 week post treatment, forward labelling

description: Biological replicate 3 of 3, forward labelling, 4 week


title: Control3 vs Doxorubicin3, 1 week post treatment, forward labelling

description: Biological replicate 3 of 3, forward labelling, 1 week

source_name: Testis RNA, Vehicle only3, 1 week post treatment

source_name: Testis RNA, Doxorubicin3, 1 week post treatment


title: Control2 vs Doxorubicin2, 4 week post treatment, forward labelling

description: Biological replicate 2 of 3, forward labelling, 4 week


title: Doxorubicin1 vs Control1, 4 week post treatment, reverse labelling

description: Biological replicate 1 of 3, reverse labelling, 4 week

source_name: Testis RNA, Doxorubicin1, 4 week post treatment

source_name: Testis RNA, Vehicle only1, 4 week post treatment


title: Control2 vs Doxorubicin2, 1 week post treatment, forward labelling

description: Biological replicate 2 of 3, forward labelling, 1 week

source_name: Testis RNA, Vehicle only2, 1 week post treatment

source_name: Testis RNA, Doxorubicin2, 1 week post treatment


title: Control1 vs Doxorubicin1, 4 week post treatment, forward labelling

description: Biological replicate 1 of 3, forward labelling, 4 week


title: Brain_hypoxia-rep3

city: Adelaide

first: Esmaeil

last: Ebrahimie

address: School of Biological Sciences, North Tce

country: Australia

institute: The University of Adelaide

description: Low oxygene treatment

hyb_protocol: Hybridisation to the array, Zebrafish Gene 1.0 ST Array, carried out  at 45 °C for 16 hours.

scan_protocol: The signal intensity of the chip was scanned using a GeneChipR Scanner 3000TG.

data_processing: Intensity files were analysed using Expression Console software (www. Affymetrix.com). CEL files were imported and intensities adjusted by RMA background correction and quantile normalization

organism: Danio rerio

source_name: Zebrafish, brain, hypoxia

label_protocol: Microarray analysis of gene expression was performed using the Zebrafish Gene 1.0 ST Array (Affymetrix Inc. Santa Clara, CA). Briefly, 300ng of total RNA derived from a single adult brain was converted to amplified sense strand cDNA using the Ambion WT Expression Kit (Life Technologies, Carlsbad, CA).  The resulting sense cDNA was fragmented and Biotin end-labelled using the Affymetrix Genechip WT Terminal Labeling Kit prior to hybridisation to the array at 45 °C for 16 hours.

growth_protocol: Adult zebrafish (Tübingen strain, sex not specified) at approximately 1 year of age were analysed.

extract_protocol: Total RNA was extracted from samples mentioned above using the QIAGEN RNeasy mini kit (QIAGEN, GmbH, Hilden, Germany) and stored at −80°C before further analysis. RNA concentration was determined with a NanoVue™ UV–vis spectrophotometer (GE Healthcare Life Sciences, Fairfield, USA). RNA integrity and quality were then estimated using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA) and the RNA integrity number (RIN) index was calculated for each sample. Only RNAs with a RIN number >7.0 were processed further.

treatment_protocol: For experiments conducted under low oxygen conditions, nitrogen gas was bubbled through water to deplete oxygen before exposure of individual fish to the medium. Oxygen concentrations were measured using a dissolved oxygen meter (DO 6+, EUTECH instruments, Singapore). The dissolved oxygen level for hypoxia treatment was measured to be 1.20 ± 0.6 mg/l, whereas normal ambient oxygen levels were 6.6 ± 0.45 mg/l. Zebrafish were exposed to the hypoxic medium for 3 hours. Briefly, after each hypoxia trial, the animals were euthanized by hypothermic shock and then decapitated to remove the brain.

value: Adult zebrafish, 1 year age


title: Control1 vs Doxorubicin1, 1 week post treatment, forward labelling

description: Biological replicate 1 of 3, forward labelling, 1 week

source_name: Testis RNA, Vehicle only1, 1 week post treatment

source_name: Testis RNA, Doxorubicin1, 1 week post treatment


title: Doxorubicin3 vs Control3, 1 week post treatment, reverse labelling

description: Biological replicate 3 of 3, reverse labelling, 1 week


title: InfectedVsUninfected-exp2

first: Francisco

last: García-del Portillo

address: Darwin 3

institute: Centro Nacional de Biotecnología (CNB-CSIC)

hyb_protocol: 825 ng of Cy3 and Cy5 probes were mixed and hybridized for 17 hours at 65ºC in GEx Hybridization Buffer HI-RPM in a hybridization oven. Arrays were washed according to the manufacturer’s instructions and dried by centrifugation.

scan_protocol: Images were scanned at 5um resolution in Agilent DNA Microarray Scanner (G2565BA, Agilent Technologies) and spots quantified with Feature Extraction software (Agilent Technologies).

data_processing: Raw intensities were background-substracted by NORMEXP method with a offset of 50. Signals (in log2 scale) were LOWESS-nomalized (intra-array normalization) followed by adjustment of their quantiles (inter-array normalization).

source_name: Infected subpopulation

label_protocol: 1 ug of total RNA was amplified with aRNA MessageAmp II kit (Ambion) and 5 ug of aminoallyl-labeled aRNA were resuspended in 0.1 M Na2CO3 (pH 9.0) and labeled either with Cy3 or Hype5 Mono NHS Ester (CyTMDye Post-labeling Reactive Dye Pack, GE Heathcare). Samples were purified following the manufacturer's instructions for Megaclear TM (Ambion)

growth_protocol: BJ5-ta human foreskin fibroblasts (ATCC CRL-1004) were cultured in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% (vol/vol) fetal bovine serum (FBS)

extract_protocol: total RNA was purified with Trizol, following manufacturer’s recommendations

treatment_protocol: Fibroblast cultures were infected with a Salmonella enterica serovar Typmimurium (His+ derivative of the mouse-virulent stran SL1344) at a bearing pAD1-GFP expressing plasmid at a multiplicity of infection (MOI) of 10:1). Confluency of the fibroblast culture was maintained at 60-90% at the time of infection. Fibroblast cell cultures were subjected to FACS protocol for separation of infected from uninfected cells.

tag: infected with

value: GFP-expressing S. enterica serovar Typmimurium

source_name: Uninfected subpopulation

value: none (uninfected control)


title: Brain_normoxia_rep2

description: Normal condition

source_name: Zebrafish, brain, normoxia


title: Brain_normoxia_rep1

description: Normal condition


title: Brain_hypoxia-rep1

description: Low oxygene treatment


title: Brain_hypoxia-rep2

description: Low oxygene treatment


title: Doxorubicin2 vs Control2, 1 week post treatment, reverse labelling

description: Biological replicate 2 of 3, reverse labelling, 1 week

value: Male


title: InfectedVsUninfected-exp3

value: BJ5-ta human foreskin fibroblasts (ATCC CRL-1004)


title: siRNA_Control_REP3

status: Public on Aug 03 2016

city: Pamplona

first: Maite

last: Huarte

state: Navarra

address: c/ Avd Pio XII, 55

institute: Centro de Investigación Médica Aplicada

hyb_protocol: Labeled sense cDNA was hybridized to the Affymetrix Human Transcriptome Array 2.0 according to the manufacturer protocols and using GeneChip® Hybridization, Wash and Stain Kit.

scan_protocol: Genechips were scanned with the Affymetrix GeneChip® Scanner 3000.

data_processing: Both background correction and normalization were done using RMA algorithm using Affymetrix Power Tools.

source_name: A549 cells_siRNA_control

label_protocol: The sense cDNA was prepared from 300 ng of total RNA using the Ambion® WT Expression Kit. The sense strand cDNA was then fragmented and biotinylated with the Affymetrix GeneChip® WT Terminal Labeling Kit (PN900671).

growth_protocol: A549 cells were cultured in RPMI 1640 medium supplemented with 10% fetal calf serum. Cells were maintained at 37°C in the presence of 5% CO2.

extract_protocol: Total RNA was isolated using TRIzol. As a last step of the extraction procedure, the RNA was purified with the RNeasy Mini-kit (Qiagen).

treatment_protocol: For RNAi, cells were transfected twice, 24 h apart, using 40 nM siRNA (final concentration) and Lipofectamine 2000 (Invitrogen).

tag: cell line


title: Doxorubicin1 vs Control1, 1 week post treatment, reverse labelling

description: Biological replicate 1 of 3, reverse labelling, 1 week


title: siRNA_CONCR_REP1

source_name: A549 cells_siRNA_CONCR


title: Brain_normoxia_rep3

description: Normal condition


title: siRNA_Control_REP1


title: siRNA_Control_REP2


title: siRNA_CONCR_REP3


title: InfectedVsUninfected-exp1


title: siRNA_CONCR_REP2


title: skeletal muscle, INTV_t0, p40_rep13

city: Maastricht

first: Ellen

last: Blaak

address: PO Box 616

department: Dept. of Human Biology

country: Netherlands

institute: Maastricht University Medical Center+

description: Gene expression data from human skeletal muscle

hyb_protocol: In a 2nd cycle cDNA was synthezised from 15 ug cRNA and purified. Following fragmentation, 5.5 ug of ss-cDNA were hybridized for 16 h at 60rpm and 45°C on GeneChip HTA 2.0 (Human Transcripotom Array 2.0). GeneChips were washed and stained in the Affymetrix Fluidics Station 450/250.

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

data_processing: For analysis the MADMAX - DB (basically it is an Oracle database linked to an R-server): http://www.ncbi.nlm.nih.gov/pubmed/21778530 was used. More specific, the limma R-package was applied for the data analysis. Shortly, the data was normalized by RMA with median polish, the limma paired t-test was used to compare t3 vs t0 for both PLA and INTV group, subsequently the log ratios obtained in the first comparisons were used for the unpaired contrast (INT_t3 – INT_t0) – (PLA_t3 – PLA_t0).

source_name: vastus lateralis muscle_INTV_before intervention

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (GeneChip® WT PLUS Reagent Kit Manual Target Preparation for GeneChip® Whole Transcript (WT) Expression Arrays, 2013, Affymetrix).

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

treatment_protocol: Male and female subjects received 12 weeks supplementation with Epigallocatechin-gallate (E, 282 mg/d) and Resveratrol (R; 80 mg/d) or placebo. Skeletal muscle biopsies were collected before and after intervention after an overnight fasting. The portion for microarray experiment was directly frozen in isopentane and stored at -80 °C until further analyses.

tag: treatment

tag: time point

value: before intervention

value: vastus lateralis muscle

tag: bmi


title: skeletal muscle, INTV_t3, p40_rep13

source_name: vastus lateralis muscle_INTV_after intervention

value: Epigallocatechin-gallate (E, 282 mg/d) and Resveratrol (R; 80 mg/d)

value: after intervention


title: skeletal muscle, PLA_t0, p6_rep14

source_name: vastus lateralis muscle_PLA_before intervention

value: placebo


title: skeletal muscle, INTV_t3, p38_rep3


title: skeletal muscle, INTV_t0, p9_rep12


title: skeletal muscle, PLA_t3, p8_rep13

source_name: vastus lateralis muscle_PLA_after intervention


title: skeletal muscle, INTV_t0, p18_rep8


title: skeletal muscle, PLA_t3, p6_rep14


title: skeletal muscle, PLA_t0, p10_rep4


title: skeletal muscle, INTV_t0, p36_rep10


title: skeletal muscle, PLA_t0, p19_rep11


title: skeletal muscle, INTV_t3, p4_rep9


title: skeletal muscle, PLA_t3, p19_rep11


title: skeletal muscle, INTV_t3, p16_rep11


title: skeletal muscle, PLA_t0, p37_rep10


title: skeletal muscle, PLA_t3, p17_rep9


title: skeletal muscle, PLA_t3, p20_rep12


title: skeletal muscle, PLA_t0, p8_rep13


title: skeletal muscle, INTV_t0, p11_rep7


title: skeletal muscle, INTV_t3, p9_rep12


title: skeletal muscle, PLA_t3, p37_rep10


title: skeletal muscle, PLA_t0, p20_rep12


title: skeletal muscle, INTV_t3, p24_rep4


title: skeletal muscle, INTV_t0, p41_rep5


title: skeletal muscle, PLA_t3, p3_rep8


title: skeletal muscle, INTV_t3, p29_rep2


title: skeletal muscle, INTV_t3, p36_rep10


title: skeletal muscle, PLA_t3, p33_rep3


title: skeletal muscle, INTV_t0, p16_rep11


title: skeletal muscle, PLA_t3, p14_rep7


title: skeletal muscle, PLA_t3, p15_rep5


title: skeletal muscle, INTV_t0, p4_rep9


title: skeletal muscle, PLA_t0, p39_rep6


title: skeletal muscle, PLA_t0, p17_rep9


title: skeletal muscle, INTV_t0, p35_rep6


title: skeletal muscle, INTV_t3, p35_rep6


title: skeletal muscle, PLA_t0, p42_rep1


title: skeletal muscle, PLA_t3, p10_rep4


title: skeletal muscle, PLA_t0, p15_rep5


title: skeletal muscle, INTV_t0, p5_rep1


title: skeletal muscle, INTV_t3, p18_rep8


title: skeletal muscle, PLA_t0, p2_rep2


title: skeletal muscle, INTV_t3, p41_rep5


title: skeletal muscle, INTV_t0, p38_rep3


title: skeletal muscle, INTV_t3, p11_rep7


title: skeletal muscle, PLA_t0, p33_rep3


title: skeletal muscle, PLA_t0, p3_rep8


title: MM sample 10

city: Durham

first: Wenbin

last: Wei

address: Stockton Road

department: Biosciences

institute: Durham University

description:
M149
Gene expression of bone marrow mesenchymal stem cells grown out from bone marrow aspirates for 3 passages

hyb_protocol: The cDNA was hybridized to Affymetrix HuEx-1_0-st-v2 using Affymetrix standard protocol.

scan_protocol: Affymetrix standard protocol

data_processing:
Gene level analysis was performed using the Affymetrix® Expression Console™ software with the default settings of the Extended: RMA-Sketch workflow.
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.extended.mps

label: Biotin

source_name: MM_primary BMMSCs

label_protocol: Fragmentation and labeling was performed using the Affymetrix GeneChip WT terminal Labeling Kit.

growth_protocol: RPMI + 10% FBS, cultured until passage 3, then RNA extracted

extract_protocol: RNeasy mini kit (Qiagen)

tag: disease state

value: Multiple myeloma (MM)

tag: Sex

value: M

tag: creatinine

tag: paraprotein type and level

value: SFLC l4140

value: primary bone marrow mesenchymal stem cell (BMMSC)


title: skeletal muscle, PLA_t3, p2_rep2

tag: gender

value: male

tag: tissue

tag: age


title: skeletal muscle, PLA_t0, p14_rep7


title: skeletal muscle, INTV_t0, p29_rep2

value: female


title: skeletal muscle, INTV_t0, p24_rep4


title: MM sample 7

description:
M071
Gene expression of bone marrow mesenchymal stem cells grown out from bone marrow aspirates for 3 passages

value: F

value: IgG/l 19g/L


title: MM sample 6

description:
M059
Gene expression of bone marrow mesenchymal stem cells grown out from bone marrow aspirates for 3 passages

value: IgG/l  83g/L


title: skeletal muscle, PLA_ t3, p42_rep1


title: skeletal muscle, INTV_t3, p5_rep1


title: skeletal muscle, PLA_t3, p39_rep6


title: MM sample 9

description:
M137
Gene expression of bone marrow mesenchymal stem cells grown out from bone marrow aspirates for 3 passages

value: IgG/k 39g/L


title: MM sample 8

description:
M083
Gene expression of bone marrow mesenchymal stem cells grown out from bone marrow aspirates for 3 passages

value: IgA/k 15g/L


title: MGUS sample 6

description:
B053
Gene expression of bone marrow mesenchymal stem cells grown out from bone marrow aspirates for 3 passages

source_name: MGUS_primary BMMSCs

value: Monoclonal gammopathy of undetermined significance (MGUS)

value: IgG/K, 2g/L


title: MM sample 4

description:
M043
Gene expression of bone marrow mesenchymal stem cells grown out from bone marrow aspirates for 3 passages

value: IgA/k  7g/L


title: MM sample 3

description:
M023
Gene expression of bone marrow mesenchymal stem cells grown out from bone marrow aspirates for 3 passages

value: IgG/k 32g/L


title: MM sample 2

description:
M019
Gene expression of bone marrow mesenchymal stem cells grown out from bone marrow aspirates for 3 passages

value: IgG/l 30g/L


title: MGUS sample 9

description:
B095
Gene expression of bone marrow mesenchymal stem cells grown out from bone marrow aspirates for 3 passages

value: IgG/K, 14g/L


title: MGUS sample 4

description:
B037
Gene expression of bone marrow mesenchymal stem cells grown out from bone marrow aspirates for 3 passages

value: IgG/L, 2g/L


title: Control sample 8

description:
C595
Gene expression of bone marrow mesenchymal stem cells grown out from bone marrow aspirates for 3 passages

source_name: Control_primary BMMSCs

value: Control

value: M


title: Control sample 3

description:
C527
Gene expression of bone marrow mesenchymal stem cells grown out from bone marrow aspirates for 3 passages

value: primary bone marrow mesenchymal stem cell (BMMSC)


title: MGUS sample 8

description:
B073
Gene expression of bone marrow mesenchymal stem cells grown out from bone marrow aspirates for 3 passages

value: IgG/L, 11g/L


title: MGUS sample 3

description:
B031
Gene expression of bone marrow mesenchymal stem cells grown out from bone marrow aspirates for 3 passages

value: IgA/L, N.D.


title: MM sample 5

description:
M047
Gene expression of bone marrow mesenchymal stem cells grown out from bone marrow aspirates for 3 passages

value: Multiple myeloma (MM)

value: IgG/k 25g/L


title: MGUS sample 1

description:
B001
Gene expression of bone marrow mesenchymal stem cells grown out from bone marrow aspirates for 3 passages

value: F

value: IgG/L, 4g/L


title: MGUS sample 2

description:
B029
Gene expression of bone marrow mesenchymal stem cells grown out from bone marrow aspirates for 3 passages


title: MGUS sample 7

description:
B055
Gene expression of bone marrow mesenchymal stem cells grown out from bone marrow aspirates for 3 passages

value: IgG/K, 6g/L


title: Control sample 2

description:
C513
Gene expression of bone marrow mesenchymal stem cells grown out from bone marrow aspirates for 3 passages


title: Control sample 4

description:
C533
Gene expression of bone marrow mesenchymal stem cells grown out from bone marrow aspirates for 3 passages


title: MGUS sample 5

description:
B051
Gene expression of bone marrow mesenchymal stem cells grown out from bone marrow aspirates for 3 passages

value: Monoclonal gammopathy of undetermined significance (MGUS)

value: IgG/K, 5g/L


title: MGUS sample 10

description:
B101
Gene expression of bone marrow mesenchymal stem cells grown out from bone marrow aspirates for 3 passages

value: IgG/L, 12g/L


title: MM sample 1

description:
M005
Gene expression of bone marrow mesenchymal stem cells grown out from bone marrow aspirates for 3 passages

value: IgA/k 42g/L


title: Control sample 5

description:
C540
Gene expression of bone marrow mesenchymal stem cells grown out from bone marrow aspirates for 3 passages


title: Control sample 7

description:
C568
Gene expression of bone marrow mesenchymal stem cells grown out from bone marrow aspirates for 3 passages


title: Control sample 1

description:
C507
Gene expression of bone marrow mesenchymal stem cells grown out from bone marrow aspirates for 3 passages


title: Control sample 10

description:
C612
Gene expression of bone marrow mesenchymal stem cells grown out from bone marrow aspirates for 3 passages


title: Control sample 9

description:
C598
Gene expression of bone marrow mesenchymal stem cells grown out from bone marrow aspirates for 3 passages


title: Sample 72 Fetal Brain (Temporal) - Normal

type: genomic

city: Würzburg

first: Marcus

last: Dittrich

address: Biozentrum, Am Hubland

department: Biozentrum

country: Germany

institute: University of Würzburg

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina HumanMethylation450 BeadChip using standard Illumina protocol

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

data_processing: R (version 3.2.0) and Bioconductor (version 3.1)

label: Cy5 and Cy3

molecule: genomic DNA

source_name: Fetal Brain (Temporal) - Normal

label_protocol: Standard Illumina Protocol

extract_protocol: Standard Illumina Protocol

value: temporal fetal brain

value: normal

value: female


title: Sample 68 Fetal Brain (Temporal) - Trisomy

source_name: Fetal Brain (Temporal) - Trisomy

value: trisomy


title: Sample 71 Adult Brain (Frontal) - Normal

source_name: Adult Brain (Frontal) - Normal

value: frontal adult brain


title: Sample 67 Fetal Brain (Frontal) - Normal

source_name: Fetal Brain (Frontal) - Normal

value: frontal fetal brain

value: male


title: Sample 61 Fetal Brain (Frontal) - Trisomy

source_name: Fetal Brain (Frontal) - Trisomy


title: Sample 70 Fetal Brain (Temporal) - Normal


title: Control sample 6

description:
C542
Gene expression of bone marrow mesenchymal stem cells grown out from bone marrow aspirates for 3 passages

value: Control

value: primary bone marrow mesenchymal stem cell (BMMSC)


title: Sample 54 Adult Brain (Frontal) - Trisomy

source_name: Adult Brain (Frontal) - Trisomy


title: Sample 69 Fetal Brain (Frontal) - Normal


title: Sample 48 Fetal Brain (Temporal) - Normal


title: Sample 59 Fetal Brain (Temporal) - Trisomy


title: Sample 58 Fetal Brain (Frontal) - Normal


title: Sample 63 Fetal Brain (Frontal) - Normal


title: Sample 51 Fetal Brain (Frontal) - Normal


title: Sample 62 Fetal Brain (Frontal) - Normal


title: Sample 57 Fetal Brain (Frontal) - Normal


title: Sample 52 Fetal Brain (Frontal) - Trisomy


title: Sample 60 Fetal Brain (Temporal) - Normal


title: Sample 53 Fetal Brain (Frontal) - Trisomy


title: Sample 65 Fetal Brain (Frontal) - Normal


title: Sample 47 Fetal Brain (Temporal) - Trisomy


title: Sample 66 Fetal Brain (Temporal) - Trisomy


title: Sample 64 Adult Brain (Frontal) - Normal


title: Sample 49 Fetal Brain (Frontal) - Trisomy


title: Sample 55 Fetal Brain (Frontal) - Normal


title: Sample 46 Adult Brain (Frontal) - Normal


title: Sample 45 Adult Brain (Frontal) - Normal


title: Sample 56 Adult Brain (Frontal) - Normal


title: Sample 50 Fetal Brain (Frontal) - Normal


title: Sample 44 Fetal Brain (Frontal) - Trisomy


city: Lisbon

first: Rita

middle: Maria

last: Batista

address: Av Padre Cruz

department: Food safety and nutrition

country: Portugal

institute: Instituto Nacional de Saude Dr. Ricardo Jorge

description: Gene expression data from Generation F8, Negative segregant seedlings salinity stressed in F6 generation, biological rep1

hyb_protocol: End-labeled, fragmented cDNA (3.5 µg) was used in a 150-µL hybridization cocktail containing hybridization controls (GeneAtlas Hybridization, Wash, and Stain Kit for WT Array Strips, Affymetrix), of which 120 µL were hybridized on array strips for 20 h at 48°C.

scan_protocol: Standard post hybridization wash and double-stain protocols (GeneAtlas Hybridization, Wash, and Stain Kit for WT Array Strips, Affymetrix) were used on an Affymetrix GeneAtlas system, followed by scanning of the array strips.

data_processing: Gene level normalization (RMA-sketch) and signal summarization was performed on Affymetrix Expression Console Software. Chipster software was used for gene filter by standard deviation (Bayes t-test, p value<0.05) and for Benjamini and Hochberg’s false discovery rate test (0.05 threshold) of filtered data.

organism: Oryza sativa

source_name: Generation F8, Nipponbare Negative segregant seedlings salinity stressed in F6 generation

label_protocol: RNA was processed for use on Affymetrix GeneChip RUSGene 1.1ST ArrayStrips, according to the manufacturer’s GeneChip WT PLUS Reagent Kit. Briefly, 100 ng of total RNA containing spiked in Poly-A RNA controls  was used in a reverse transcription reaction to generate first-strand cDNA. After second-strand synthesis, double-stranded cDNA was used in an in vitro transcription (IVT) reaction to generate cRNA . 15 ug of this cRNA was used for a second cycle of first-strand cDNA synthesis. Single stranded cDNA (5.5 µg) was fragmented and end-labeled using GeneChip WT Terminal Labeling Kit (Affymetrix) and following the manufacturer’s instruction.

growth_protocol: Rice seeds were treated at 50ºC in 0.1% Carbendazim (fungicide) for 30 min, and surface disinfected using standard procedures. Seeds were germinated in darkness, for two days at 28ºC. Seedlings were grown for 13 days in Yoshida medium at 28ºC/24ºC (light/night), 12h photoperiod; 70% relative humidity. Salinity stress (12 dS/m final concentration) was imposed on half of the seedlings (C, Ta and NSb) in F6 generation. Fifteen days-old seedlings were collected after 12 days of salinity stress imposition. From F6 generation onwards, we worked with six rice lines (C, Csalt, Ta, Tasalt, NSb, NSbsalt).

extract_protocol: RNA from three pools of 10 whole-seedlings was isolated using RNeasy Plant Mini Kit (Qiagen) following the manufacturer’s instructions.

treatment_protocol: Fifteen days-old seedlings were frozen in liquid nitrogen and kept at -80ºC until RNA extractions.

value: pool of 10 whole-seedlings

tag: genotype

value: Oryza sativa L. ssp. japonica cv. Nipponbare

value: Fifteen days-old


description: Gene expression data from Generation F8, Transgenic seedlings salinity stressed in F6 generation, biological rep3

source_name: Generation F8, Nipponbare Transgenic seedlings salinity stressed in F6 generation


description: Gene expression data from Generation F8, Negative segregant seedlings , biological rep3

source_name: Generation F8, Nipponbare Negative segregant seedlings


description: Gene expression data from Generation F8, Negative segregant seedlings salinity stressed in F6 generation, biological rep3


description: Gene expression data from Generation F8, Negative segregant seedlings , biological rep2


description: Gene expression data from Generation F8, Negative segregant seedlings , biological rep1


description: Gene expression data from Generation F8, Transgenic seedlings salinity stressed in F6 generation, biological rep2


description: Gene expression data from Generation F8, Transgenic seedlings salinity stressed in F6 generation, biological rep1


title: Sample 42 Fetal Brain (Frontal) - Normal


description: Gene expression data from Generation F8, Transgenic seedlings , biological rep2

source_name: Generation F8, Nipponbare Transgenic seedlings


description: Gene expression data from Generation F8, Transgenic seedlings , biological rep1


description: Gene expression data from Generation F8, Transgenic seedlings , biological rep3


title: Sample 36 Fetal Brain (Temporal) - Normal


title: Sample 41 Fetal Brain (Frontal) - Normal


title: Sample 38 Fetal Brain (Frontal) - Trisomy


title: Sample 43 Fetal Brain (Frontal) - Normal


title: Sample 32 Adult Brain (Frontal) - Trisomy


description: Gene expression data from Generation F8, Negative segregant seedlings salinity stressed in F6 generation, biological rep2


title: T-LPC_p49_rep3

city: Perth

first: Adam

last: Passman

state: WA

address: 35 Stirling Highway

institute: University of Western Australia

description: Gene expression data from EPCAM+ selected LPCs

hyb_protocol: Using the Hybridisation Module of the GeneChip Hybridisation, Wash and Stain Kit (Affymetrix) as per manufacturer's instructions

scan_protocol: GeneChips were scanned with the GeneChip Scanner 3000 (Affymetrix), in conjuction with the reagents from the GeneChip Hybridisation, Wash and Stain Kit (Affymetrix)

data_processing: Avadis Version 4.3 was used for GCRMA probe summarisation. MAS 5.0 was used to obtain present and absent calls. Partek Genomics Suite was for quantile normalisation and log transformation.

source_name: LPC line, derived from DDC-injured mouse liver

label_protocol: The GeneChip IVT Labelling Kit (Affymetrix) was used according to the manufacturer's instructions, starting with 1 ug total RNA

growth_protocol: LPCs were cultured in William's E Medium containing supplements. See DOI: 10.1242/dmm.022020 for further details

extract_protocol: Combination of TriZOL and RNeasy spin column

treatment_protocol: No treatment

value: WT C57BL/6

value: liver progenitor cell (LPC)

tag: injury model

value: 8-12 wko mice placed on 1-6 DDC diet

tag: selection

value: EPCAM+


title: Sample 40 Fetal Brain (Frontal) - Normal


title: Jurkat cells overexpressing EV

city: Groningen

first: Joost

last: Kluiver

state: Groningen

address: Hanzeplein 1

department: Pathology and Medical Biology

institute: University Medical Center Groningen

description:
This Sample represents 2 dye-swaps.
US45102948_252800415105_S01_GE2_107_Sep09_2_1.txt: EV IP-Cy3, EV Total-Cy5
US45102948_252800415105_S01_GE2_107_Sep09_2_2.txt: EV IP-Cy5, EV Total-Cy3

hyb_protocol: Hybridization was performed using two-color Low Input Quick Amp Labeling Kit, according to the manufacturer's protocol (Agilent, Santa Clara, USA). Equal amounts of cRNA Cy-3 and Cy-5 labelled samples were combined and hybridized at 65°C for 17hrs on the 60k SurePrint G3 Human Whole Genome Oligo Microarray (Agilent).

scan_protocol: Microarray data analysis was performed using Agilent data extraction software on the Agilent SureScan Dx Microarray Scanner.

data_processing: For data analysis, array spot intensities were log2 transformed, GeneSpring software (v.10.5) was applied to convert images into Linear and Lowess normalized data.

label: Cy3, Cy5

source_name: human acute leukemic T-cell line, EV, Ago2 RIP

label_protocol: Labeling was performed using two-color Low Input Quick Amp Labeling Kit, according to the manufacturer's protocol (Agilent, Santa Clara, USA). Briefly, 40-100ng of RNA from total cell lysate and Ago2-IP samples was used for cDNA synthesis, followed by cRNA amplification and Cy-3 and Cy-5 labeling.

growth_protocol: The Jurkat human acute leukemic T-cell line was cultured in RPMI 1640 supplemented with 10% fetal bovine serum (FBS), 200 mM L-glutamine, 100 mM Na-pyruvate, 10 mg/ml gentamycin (Lonza, Breda, The Netherlands), 0.05M β-mercapto-ethanol (Merck, Darmstadt, Germany) at 37°C in 5% CO2 (complete media).

extract_protocol: Total cellular RNA was extracted using the miRNeasy Mini Kit (Qiagen, Venlo, The Netherlands) following the manufacturer’s instructions. Cleared lysates of 40 million cells were incubated with protein G Sepharose beads (GE Healthcare) coated with anti-Ago2 antibody (Clone 2E12-1C9; Abnova, catalog number: H00027161-M01, lot number: D3152-S2, Taiwan) at 4C overnight. IP with Anti-IgG antibody was used as a negative control (Millipore BV, Amsterdam, The Netherlands). After washing the beads, RNA was harvested for microarray. RNA from total (sample taken before start of the IP procedure), flow through (sample taken of the supernatant after collection of the IP fraction) and IP fractions were isolated with miRNeasy Mini kit (Qiagen, Venlo, The Netherlands) according to manufacturer's protocol. RNA from total and Ago2-IP fractions of Jurkat-miR-21 and Jurkat-EV cells was used for microarray analysis.

value: Jurkat

tag: cell type

value: acute leukemic T-cell line

tag: expression

value: empty vector

tag: rip antibody

label: Cy5, Cy3

source_name: human acute leukemic T-cell line, EV, total


title: Sample 30 Fetal Brain (Frontal) - Normal

value: normal

value: female


title: T-LPC_p49_rep2

tag: strain


title: Sample 33 Fetal Brain (Temporal) - Trisomy

value: temporal fetal brain

value: trisomy


title: Sample 39 Fetal Brain (Frontal) - Trisomy

value: frontal fetal brain

value: male


title: Sample 35 Fetal Brain (Temporal) - Normal


title: Sample 28 Fetal Brain (Frontal) - Trisomy


title: T-LPC_p49_rep1


title: Sample 37 Fetal Brain (Frontal) - Normal


title: Sample 31 Fetal Brain (Frontal) - Trisomy


title: Sample 29 Fetal Brain (Frontal) - Normal


title: Sample 25 Fetal Brain (Frontal) - Normal


title: Sample 27 Fetal Brain (Frontal) - Trisomy


title: Jurkat cells overexpressing miR-21

description:
This Sample represents 2 dye-swaps.
US45102948_252800414109_S01_GE2_107_Sep09_1_3.txt: miR-21 IP-Cy3, miR-21 Total-Cy5
US45102948_252800414109_S01_GE2_107_Sep09_1_4.txt: miR-21 IP-Cy5, miR-21 Total-Cy3

source_name: human acute leukemic T-cell line, miR-21, Ago2 RIP

tag: cell line

source_name: human acute leukemic T-cell line, miR-21, total


title: Sample 21 Fetal Brain (Temporal) - Normal


title: BMOL_p25_rep3

description: Gene expression data from WT LPCs

source_name: LPC line, derived from CDE-injured mouse liver

value: 4 wko mice placed on 2-3 wk CDE diet


title: Sample 26 Fetal Brain (Frontal) - Normal


title: BMOL_p19_rep4

description: Gene expression data from WT LPCs


description: Gene expression data from Generation F8, Control seedlings , biological rep1

source_name: Generation F8, Nipponbare Control seedlings

value: pool of 10 whole-seedlings


description: Gene expression data from Generation F8, Control seedlings , biological rep3

value: Oryza sativa L. ssp. japonica cv. Nipponbare


description: Gene expression data from Generation F8, Control seedlings salinity stressed in F6 generation, biological rep1

source_name: Generation F8, Nipponbare Control seedlings salinity stressed in F6 generation

value: Fifteen days-old


title: Sample 24 Fetal Brain (Temporal) - Trisomy

source_name: Fetal Brain (Temporal) - Trisomy


title: Sample 34 Adult Brain (Frontal) - Normal

source_name: Adult Brain (Frontal) - Normal

value: frontal adult brain


title: Sample 22 Fetal Brain (Temporal) - Trisomy


title: Sample 23 Adult Brain (Frontal) - Normal


title: BMOL_p25_rep1

description: Gene expression data from WT LPCs

value: WT C57BL/6

value: liver progenitor cell (LPC)


title: Sample 20 Fetal Brain (Frontal) - Normal

source_name: Fetal Brain (Frontal) - Normal


title: BMOL_p25_rep2

description: Gene expression data from WT LPCs


title: PIL5_p40_rep3

description: Gene expression data from Trp53 -/- LPCs

value: 3-4 wko mice placed on 3 wk CDE diet


description: Gene expression data from Generation F8, Control seedlings salinity stressed in F6 generation, biological rep2


title: PIL5_p40_rep2


description: Gene expression data from Generation F6, salinity stressed Negative segregant seedlings, biological rep3

source_name: Generation F6, Nipponbare salinity stressed Negative segregant seedlings


description: Gene expression data from Generation F6, salinity stressed Negative segregant seedlings, biological rep2


description: Gene expression data from Generation F6, salinity stressed Negative segregant seedlings, biological rep1


title: PIL5_p40_rep1


title: Sample 19 Fetal Brain (Frontal) - Trisomy

source_name: Fetal Brain (Frontal) - Trisomy


title: PIL4_p15_rep4


description: Gene expression data from Generation F6, Negative segregant seedlings , biological rep3

source_name: Generation F6, Nipponbare Negative segregant seedlings


description: Gene expression data from Generation F8, Control seedlings , biological rep2


description: Gene expression data from Generation F8, Control seedlings salinity stressed in F6 generation, biological rep3


description: Gene expression data from Generation F6, Negative segregant seedlings , biological rep1


title: Sample 18 Fetal Brain (Frontal) - Trisomy


title: PIL4_p23_rep2


title: PIL4_p23_rep1


title: PIL4_p23_rep3


description: Gene expression data from Generation F6, Negative segregant seedlings , biological rep2


description: Gene expression data from Generation F6, salinity stressed Transgenic seedlings , biological rep3

source_name: Generation F6, Nipponbare salinity stressed Transgenic seedlings


title: Sample 16 Fetal Brain (Frontal) - Normal


description: Gene expression data from Generation F6, salinity stressed Transgenic seedlings , biological rep2


title: Sample 15 Fetal Brain (Frontal) - Normal


title: PIL3_p32_rep3


title: PIL3_p32_rep2


title: PIL3_p32_rep1


description: Gene expression data from Generation F6, salinity stressed Transgenic seedlings , biological rep1


description: Gene expression data from Generation F6, Transgenic seedlings , biological rep3

source_name: Generation F6, Nipponbare Transgenic seedlings


description: Gene expression data from Generation F6, Transgenic seedlings , biological rep2


description: Gene expression data from Generation F6, Transgenic seedlings , biological rep1


title: PIL2_p17_rep4


title: PIL2_p25_rep3


title: PIL2_p25_rep2


title: Sample 11 Adult Brain (Frontal) - Trisomy

source_name: Adult Brain (Frontal) - Trisomy


title: Sample 12 Adult Brain (Frontal) - Normal


title: Sample 14 Adult Brain (Frontal) - Normal


title: PIL1_p40_rep2


description: Gene expression data from Generation F6, salinity stressed Control seedlings , biological rep1

source_name: Generation F6, Nipponbare salinity stressed Control seedlings


description: Gene expression data from Generation F6, Control seedlings , biological rep3

source_name: Generation F6, Nipponbare Control seedlings


title: Sample 9 Fetal Brain (Temporal) - Trisomy


title: Sample 17 Fetal Brain (Frontal) - Normal


title: Sample 13 Adult Brain (Frontal) - Trisomy


description: Gene expression data from Generation F6, Control seedlings , biological rep2


title: Sample 10 Fetal Brain (Temporal) - Normal

source_name: Fetal Brain (Temporal) - Normal


description: Gene expression data from Generation F4, Negative segregant seedlings , biological rep3

source_name: Generation F4, Nipponbare Negative segregant seedlings


title: Sample 6 Fetal Brain (Frontal) - Normal


description: Gene expression data from Generation F6, salinity stressed Control seedlings , biological rep2


description: Gene expression data from Generation F6, Control seedlings , biological rep1


title: Sample 8 Fetal Brain (Frontal) - Trisomy


title: Sample 4 Fetal Brain (Frontal) - Trisomy


title: PIL2_p25_rep1

description: Gene expression data from Trp53 -/- LPCs


title: Sample 7 Fetal Brain (Frontal) - Normal


title: PIL1_p40_rep3


title: ileum stressed rep4

city: Tsukuba

first: Chise

last: Suzuki

state: Ibaraki

address: 2 Ikenodai

department: Animal Products Res. Division

institute: NARO Institute of Livestock and Grassland Science

description: Gene expression data from ileum of mouse suffered from subchronic and mild social defeat stress

hyb_protocol: Fragmented cRNA was hybridised to mouse 430 2.0 arrays (Affymetrix) during 16 h at 45°C.

scan_protocol: After hybridization, the gene chips were washed and stained using a GeneChip Fluidics Station 450 (Affymetrix) and then scanned (GeneChip Scanner; Affymetrix) with the GeneChip Operation Software Ver. 1.4 (Affymetrix).

data_processing: The microarray data were analyzed using R. Affymetrix CEL files were quantified by the RMA summarization.

source_name: teminal ileum of stressed mouse

label_protocol: cRNA was prepared using the Affymetrix GeneChip 3’IVT Epess kit, using 100 ng total RNA as starting material.

growth_protocol: Male C57BL/6JJmsSlc (B6) mice (7 weeks of age; 21-23 g) for intruders and male Slc:ICR (ICR) mice (retired, older than 5 months of age) for residents (purchased from SLC Japan, Shizuoka, Japan) were used. First, these mice were housed individually in single cages (cage size 143 mm × 293 mm × 148 mm; Charles River Laboratories Japan, Kanagawa, Japan) with wood-shaving bedding and were habituated to their environments for a week. AIN-93G diet (Oriental Yeast, Tokyo, Japan) was fed to B6 mice, and standard laboratory diet (MF diet; Oriental Yeast) was fed to ICR mice. Food and water were available ad libitum. Animals were maintained at constant temperature (23 ± 1°C) and humidity (61 ± 1%) under a 12 h light-dark cycle (light on 8:00 am).

extract_protocol: After 3 hr fasting, the lower small intestines were taken and immediately kept in RNAlater (Qiagen). RNA was prepared by RNeasy kit (Qiagen).

treatment_protocol: The sCSDS paradigm was performed in the afternoon (14:00 pm-16:00 pm). The duration of physical contacts was set at 5 min after the first attack bite at Day 1, and then was reduced 0.5 min per day from Day 2 to Day 10. Thus, 0.5 min of physical contact was carried out at Day 10.

tag: treatment

value: stressed

value: teminal ileum


title: PIL1_p40_rep1

source_name: LPC line, derived from CDE-injured mouse liver


title: Generation F4, Transgenic seedlings , biological rep2

description: Gene expression data from Generation F4Transgenic seedlings , biological rep2

source_name: Generation F4, Nipponbare Transgenic seedlings


description: Gene expression data from Generation F4, Control seedlings , biological rep3

source_name: Generation F4, Nipponbare Control seedlings


title: ileum stressed rep3


title: ileum stressed rep5


title: ileum stressed rep1


description: Gene expression data from Generation F4, Negative segregant seedlings , biological rep1


description: Gene expression data from Generation F6, salinity stressed Control seedlings , biological rep3


description: Gene expression data from Generation F4, Negative segregant seedlings , biological rep2


title: ileum stressed rep2


title: Generation F4, Transgenic seedlings , biological rep1

description: Gene expression data from Generation F4Transgenic seedlings , biological rep1


title: ileum control rep5

description: Gene expression data from ileum of unstressed control mouse

source_name: teminal ileum of unstressed mouse

value: control


title: ileum control rep3


description: Gene expression data from Generation F4, Control seedlings , biological rep1


title: Sample 1 Fetal Brain (Frontal) - Normal

value: normal


title: ileum control rep4


title: Generation F4, Transgenic seedlings , biological rep3

description: Gene expression data from Generation F4Transgenic seedlings , biological rep3


title: wt_ctrl_rep3

status: Public on Aug 02 2016

city: Huddinge

first: Rune

last: Toftgård

address: Hälsovägen 7

department: Biosciences and Nutrition

country: Sweden

institute: Karolinska Institutet

description: expression data of controls

hyb_protocol: affymetrix standard protocols were used for hybridization

scan_protocol: affymetrix standard protocols were used for scanning

data_processing: Affymetrix Eexpression Console was used for analysis with following settings: med-polish (rma-bg,quant-norm, sketch=-1, bioc=true, lowprecision=false, usepm=true, target=0, doavg=false)

source_name: colon of control mouse

label_protocol: affymetrix standard protocols were used for labeling

extract_protocol: Qiagen Rneasy mini extraction kits were used according to the manufacturer's instructions.

treatment_protocol: Tamoxifen was diluted at 20mg/ml in corn oil, sonicated at 37°C for 30 min and injected at 5 mg/25 g mouse i.p. One week later, mice were sacrificed, the colon extracted and a 1 cm piece starting 1.5 cm from the anus immediately frozen in liquid nitrogen.

value: colon

value: female