title: Infant at timeC, rep77

source_name: Infant at 24-33 days of life rep 77

value: blood

tag: days of life

value: 2 (male)

tag: gestational age (weeks)

tag: birth weight (grams)

tag: oxygen 28 days

value: 1 (oxygen therapy =>28 days)

tag: oxygen 36 weeks postmenstrual age (wpma)

value: 0 (finished oxygen therapy earlier than the age of 36 wPMA)

tag: bronchopulmonary dysplasia (bpd) group

value: 1 (mild BPD)

tag: retinopathy of prematurity (rop) group

value: 2 (ROP which need laser therapy)

tag: rop lasertherapy

value: 1 (laser therapy  due to prethreshold or threshold ROP)

tag: periventricular leukomalacia (pvl)

value: 0 (no PVL)


title: SM001 SARS 10^5pfu D7 3

status: Public on Nov 01 2011

type: RNA

city: Seattle

first: Michael

last: Katze

state: WA

address: Rosen Building 960 Republican St.

department: Microbiology

country: USA

institute: University of Washington

hyb_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for hybridization and array washing. Two hundred fifty ng of each RNA sample was hybridized to one Agilent 4X44K human HG (Design ID 014850) array.

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

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

molecule: total RNA

organism: Mus musculus

source_name: SM001 SARS 10^5pfu D7 3

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

growth_protocol: Twenty-week-old C57BL/6 mice were infected by intranasal instillation of 10^2,10^3, 10^4 or 10^5 PFU of SARS CoV MA15 in 50 µl of PBS or mock-infected with PBS alone.  At days 1, 2, 4 and 7 days post-infection, lungs were harvested.

extract_protocol: All TRIzol lysates were processed simultaneously: they were phase-separated, and RNA was isolated from the aqueous phase (diluted 2 fold with RLT buffer) using Qiagen RNeasy Mini columns and the manufacturer’s recommended protocol (Qiagen Inc., Valencia, CA). RNA quality was assessed on an Agilent 2100 Bioanalyzer using the nanochip format, and only intact RNA was used for microarray analyses.

treatment_protocol: Specific lobs of the lung from each animal were harvested and briefly rinse tissue in cold (4ºC) PBS. Following the RNAlater (Ambion) protocol, tissue was cut into small chunks (<0.5cm in any single dimension) and place immediately into a 10-20 volumes (w/v) (e.g. 100mg/ml) RNAlater. After a 4ºC incubation for overnight, samples were stored at -80ºC further processing. Lung tissue was removed from RNAlater, washed in a small volume of Trizol, homogenized in 10-20 volumes (w/v) TRIzol and stored at -80°C until RNA isolation.

tag: strain

tag: gender

value: Female

tag: time (post-infection)

value: 7 day

tag: age

value: 20 week old

tag: treatment

value: SARS CoV MA15 infected with 10^5 PFU

tag: tissue

value: lung


title: Infant at timeC, rep78

city: Oslo

first: Ståle

last: Nygård

address: Institute for Experimental Medical Research, Oslo University Hospital - Ulleval

country: Norway

institute: University of Oslo

hyb_protocol: GeneChip Hybridization Oven, 16-18 hours, 45oC, 60 rotations/min; washing and staining on Fluidics Station 450, protocol FS450_0007

scan_protocol: GeneChip Scanner 3000 7G controlled by GeneChip Operating Software

data_processing: Robust multiarray average (R/Bioconductor, using the library aroma.affymetrix)

label: biotin

organism: Homo sapiens

source_name: Infant at 24-33 days of life rep 78

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Samples were collected from children in the Neonatal Intensive Care Unit of the University Children's Hospital

extract_protocol: Ficoll isopaque gradient centrifugation and RiboPure Blood Kit (Ambion, Life Technologies, Carlsbad, USA) were used for total RNA extraction

treatment_protocol: Blood samples (0.3 ml) were drawn from all the study participants on the 5th, 14th and 28th day of life for the assessment of whole genome expression in peripheral blood leukocytes.

value: 1 (female)


title: Infant at timeC, rep74

source_name: Infant at 24-33 days of life rep 74

value: 0 (oxygen therapy <28 days)

value: 0 (no BPD)

value: 0 (no ROP)

value: 0 (no lasertherapy)


title: Infant at timeC, rep73

source_name: Infant at 24-33 days of life rep 73

value: blood


title: KH014

city: Chuo-ku

first: Takashi

last: Kohno

address: 5-1-1 Tsukiji

country: Japan

institute: National Cancer Center Research Institute

description: Gene expression data from primary lung ADC

hyb_protocol: Following fragmentation, cRNA was hybridized on the GeneChip Human U133 Plus 2.0 array according to the Affymetrix standard protcol.

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

data_processing: The data were normalized by the MAS5 algorhythm.

label: Biotin

source_name: frozen tissue of primary lung tumors

label_protocol: 100ng of total RNA was labeled using a Two-Cycle Target Labeling and Control Reagents.

extract_protocol: Trizol extraction according to the manufacturer's instructions.

value: primary lung tumor

tag: age (years)

value: female

tag: smoking status

value: Never-smoker

tag: bi

tag: pathological stage

value: IB

tag: pstage iorii

value: I

tag: gene alteration status

value: KRAS mutation +

tag: myc

value: Low

tag: relapse

value: relapsed

tag: days before relapse/censor

tag: months before relapse/censor

tag: death

value: dead

tag: days before death/censor

tag: exclude for prognosis analysis due to incomplete resection or adjuvant therapy


title: SM001 SARS 10^5pfu D7 1

source_name: SM001 SARS 10^5pfu D7 1

tag: strain

tag: gender

value: Female

tag: time (post-infection)

value: 7 day

value: 20 week old

value: SARS CoV MA15 infected with 10^5 PFU


title: KH020

tag: tissue

value: II


title: SM001 SARS 10^5pfu D7 2

source_name: SM001 SARS 10^5pfu D7 2

tag: age

tag: treatment

value: lung


title: Infant at timeC, rep81

source_name: Infant at 24-33 days of life rep 81

tag: days of life

value: 2 (male)

tag: gestational age (weeks)

tag: birth weight (grams)

tag: oxygen 28 days

value: 0 (oxygen therapy <28 days)

tag: oxygen 36 weeks postmenstrual age (wpma)

value: 0 (finished oxygen therapy earlier than the age of 36 wPMA)

tag: bronchopulmonary dysplasia (bpd) group

value: 0 (no BPD)

tag: retinopathy of prematurity (rop) group

value: 0 (no ROP)

tag: rop lasertherapy

value: 0 (no lasertherapy)

tag: periventricular leukomalacia (pvl)

value: 0 (no PVL)


title: Infant at timeC, rep69

source_name: Infant at 24-33 days of life rep 69

value: blood

value: 1 (female)

value: 1 (oxygen therapy =>28 days)

value: 1 (mild BPD)


title: Infant at timeC, rep71

source_name: Infant at 24-33 days of life rep 71


title: Infant at timeC, rep68

source_name: Infant at 24-33 days of life rep 68

value: 1 (on oxygen at the age of 36 wpma)

value: 2 (moderate BPD)

value: 2 (ROP which need laser therapy)

value: 1 (laser therapy  due to prethreshold or threshold ROP)

value: 1 (PVL)


title: Infant at timeC, rep70

source_name: Infant at 24-33 days of life rep 70


title: KH259

value: primary lung tumor

tag: age (years)

value: female

tag: smoking status

value: Ever-smoker

tag: bi

tag: pathological stage

value: IA

tag: pstage iorii

value: I

tag: gene alteration status

value: ALK-fusion +

tag: myc

value: Low

tag: cluster

tag: relapse

value: not relapsed

tag: days before relapse/censor

tag: months before relapse/censor

tag: death

value: alive

tag: days before death/censor


title: KH029

tag: tissue

tag: gender

value: male

value: II

value: KRAS mutation +

value: relapsed

value: dead

tag: exclude for prognosis analysis due to incomplete resection or adjuvant therapy


title: KH139

value: Never-smoker

value: IB


title: KH189


title: Infant at timeC, rep67

source_name: Infant at 24-33 days of life rep 67

value: blood

tag: days of life

value: 2 (male)

tag: gestational age (weeks)

tag: birth weight (grams)

tag: oxygen 28 days

value: 0 (oxygen therapy <28 days)

tag: oxygen 36 weeks postmenstrual age (wpma)

value: 0 (finished oxygen therapy earlier than the age of 36 wPMA)

tag: bronchopulmonary dysplasia (bpd) group

value: 0 (no BPD)

tag: retinopathy of prematurity (rop) group

value: 1 (ROP not requiring treatment)

tag: rop lasertherapy

value: 0 (no lasertherapy)

tag: periventricular leukomalacia (pvl)

value: 0 (no PVL)


title: Infant at timeC, rep64

source_name: Infant at 24-33 days of life rep 64

value: 1 (oxygen therapy =>28 days)

value: 1 (mild BPD)

value: 0 (no ROP)


title: SM001 SARS 10^5pfu D4 3

source_name: SM001 SARS 10^5pfu D4 3

tag: strain

value: Female

tag: time (post-infection)

value: 4 day

tag: age

value: 20 week old

tag: treatment

value: SARS CoV MA15 infected with 10^5 PFU

value: lung


title: SM001 SARS 10^5pfu D4 4

source_name: SM001 SARS 10^5pfu D4 4


title: Infant at timeC, rep60

source_name: Infant at 24-33 days of life rep 60


title: Infant at timeC, rep63

source_name: Infant at 24-33 days of life rep 63

value: 1 (female)


title: Infant at timeC, rep62

source_name: Infant at 24-33 days of life rep 62

value: blood


title: SM001 SARS 10^5pfu D4 2

source_name: SM001 SARS 10^5pfu D4 2


title: SM001 SARS 10^5pfu D4 5

source_name: SM001 SARS 10^5pfu D4 5


title: KH119

source_name: frozen tissue of primary lung tumors

value: primary lung tumor

tag: age (years)

value: male

tag: smoking status

value: Ever-smoker

tag: bi

tag: pathological stage

value: II

tag: pstage iorii

tag: gene alteration status

value: ALK-fusion +

tag: myc

value: Low

tag: cluster

tag: relapse

value: not relapsed

tag: days before relapse/censor

tag: months before relapse/censor

tag: death

value: dead

tag: days before death/censor


title: Infant at timeC, rep59

source_name: Infant at 24-33 days of life rep 59

tag: tissue

tag: days of life

tag: gender

tag: gestational age (weeks)

tag: birth weight (grams)

tag: oxygen 28 days

value: 0 (oxygen therapy <28 days)

tag: oxygen 36 weeks postmenstrual age (wpma)

value: 0 (finished oxygen therapy earlier than the age of 36 wPMA)

tag: bronchopulmonary dysplasia (bpd) group

value: 0 (no BPD)

tag: retinopathy of prematurity (rop) group

tag: rop lasertherapy

value: 0 (no lasertherapy)

tag: periventricular leukomalacia (pvl)

value: 0 (no PVL)


title: Infant at timeC, rep61

source_name: Infant at 24-33 days of life rep 61

value: 2 (male)

value: 0 (no ROP)


title: KH083

tag: age (years)

value: female

tag: smoking status

value: Never-smoker

tag: bi

tag: pathological stage

tag: pstage iorii

tag: gene alteration status

tag: myc

tag: cluster

value: alive

tag: exclude for prognosis analysis due to incomplete resection or adjuvant therapy

value: exclude


title: SM001 SARS 10^5pfu D2 5

source_name: SM001 SARS 10^5pfu D2 5

tag: strain

tag: gender

value: Female

tag: time (post-infection)

value: 2 day

tag: age

value: 20 week old

tag: treatment

value: SARS CoV MA15 infected with 10^5 PFU

tag: tissue

value: lung


title: KH012

value: primary lung tumor

value: II

value: ALK-fusion +

value: Low

tag: relapse

value: not relapsed

tag: days before relapse/censor

tag: months before relapse/censor

tag: death

tag: days before death/censor


title: SM001 SARS 10^5pfu D4 1

source_name: SM001 SARS 10^5pfu D4 1

value: 4 day


title: Infant at timeC, rep54

source_name: Infant at 24-33 days of life rep 54

value: blood

tag: days of life

value: 1 (female)

tag: gestational age (weeks)

tag: birth weight (grams)

tag: oxygen 28 days

value: 0 (oxygen therapy <28 days)

tag: oxygen 36 weeks postmenstrual age (wpma)

value: 0 (finished oxygen therapy earlier than the age of 36 wPMA)

tag: bronchopulmonary dysplasia (bpd) group

value: 0 (no BPD)

tag: retinopathy of prematurity (rop) group

tag: rop lasertherapy

value: 0 (no lasertherapy)

tag: periventricular leukomalacia (pvl)

value: 0 (no PVL)


title: Infant at timeC, rep58

source_name: Infant at 24-33 days of life rep 58

tag: gender

value: 0 (no ROP)


title: Infant at timeC, rep55

source_name: Infant at 24-33 days of life rep 55


title: Infant at timeC, rep52

source_name: Infant at 24-33 days of life rep 52

value: 2 (male)

value: 1 (oxygen therapy =>28 days)

value: 1 (mild BPD)


title: KH027

value: primary lung tumor

tag: age (years)

value: female

tag: smoking status

value: Never-smoker

tag: bi

tag: pathological stage

tag: pstage iorii

tag: gene alteration status

tag: myc

tag: cluster

value: alive

tag: exclude for prognosis analysis due to incomplete resection or adjuvant therapy


title: Infant at timeC, rep51

source_name: Infant at 24-33 days of life rep 51

tag: tissue

tag: days of life

tag: gestational age (weeks)

tag: birth weight (grams)

value: 1 (on oxygen at the age of 36 wpma)

value: 2 (moderate BPD)


title: Infant at timeC, rep57

source_name: Infant at 24-33 days of life rep 57

value: blood

tag: oxygen 28 days

tag: oxygen 36 weeks postmenstrual age (wpma)

tag: bronchopulmonary dysplasia (bpd) group

tag: retinopathy of prematurity (rop) group

value: 2 (ROP which need laser therapy)

value: 1 (laser therapy  due to prethreshold or threshold ROP)

value: 1 (PVL)


title: KH066

tag: age (years)

tag: gender

value: II

value: ALK-fusion +

value: nd

tag: relapse

value: not relapsed

tag: days before relapse/censor

tag: months before relapse/censor

tag: death

tag: days before death/censor

value: exclude


title: KH007

value: male

tag: smoking status

value: Ever-smoker

tag: bi

tag: pathological stage

tag: pstage iorii

tag: gene alteration status

tag: myc

value: Low

tag: cluster


title: Infant at timeC, rep49

source_name: Infant at 24-33 days of life rep 49

tag: tissue

tag: days of life

value: 2 (male)

tag: gestational age (weeks)

tag: birth weight (grams)

tag: oxygen 28 days

value: 1 (oxygen therapy =>28 days)

tag: oxygen 36 weeks postmenstrual age (wpma)

value: 0 (finished oxygen therapy earlier than the age of 36 wPMA)

value: 1 (mild BPD)

value: 0 (no ROP)

tag: rop lasertherapy

value: 0 (no lasertherapy)

tag: periventricular leukomalacia (pvl)

value: 0 (no PVL)


title: Infant at timeC, rep50

source_name: Infant at 24-33 days of life rep 50

value: blood

tag: gender

value: 1 (female)

tag: bronchopulmonary dysplasia (bpd) group

tag: retinopathy of prematurity (rop) group

value: 1 (ROP not requiring treatment)


title: SM001 SARS 10^5pfu D2 3

source_name: SM001 SARS 10^5pfu D2 3

tag: strain

value: Female

tag: time (post-infection)

value: 2 day

tag: age

value: 20 week old

tag: treatment

value: SARS CoV MA15 infected with 10^5 PFU

value: lung


title: Infant at timeC, rep53

source_name: Infant at 24-33 days of life rep 53

value: 0 (oxygen therapy <28 days)

value: 0 (no BPD)


title: KH024

value: primary lung tumor

tag: age (years)

value: female

tag: smoking status

value: Never-smoker

tag: bi

tag: pathological stage

value: II

tag: pstage iorii

tag: gene alteration status

value: ALK-fusion +

tag: myc

value: Low

tag: relapse

value: relapsed

tag: days before relapse/censor

tag: months before relapse/censor

tag: death

value: dead

tag: days before death/censor

tag: exclude for prognosis analysis due to incomplete resection or adjuvant therapy

value: exclude


title: Infant at timeC, rep47

source_name: Infant at 24-33 days of life rep 47

tag: tissue

value: blood

tag: days of life

tag: gender

value: 2 (male)

tag: gestational age (weeks)

tag: birth weight (grams)

tag: oxygen 28 days

tag: oxygen 36 weeks postmenstrual age (wpma)

value: 0 (finished oxygen therapy earlier than the age of 36 wPMA)

tag: bronchopulmonary dysplasia (bpd) group

tag: retinopathy of prematurity (rop) group

value: 0 (no ROP)

tag: rop lasertherapy

value: 0 (no lasertherapy)

tag: periventricular leukomalacia (pvl)

value: 0 (no PVL)


title: Infant at timeC, rep103

source_name: Infant at 24-33 days of life rep 103

value: 1 (female)

value: 1 (oxygen therapy =>28 days)

value: 1 (on oxygen at the age of 36 wpma)

value: 2 (moderate BPD)


title: SM001 SARS 10^5pfu D2 2

source_name: SM001 SARS 10^5pfu D2 2

tag: strain

value: Female

tag: time (post-infection)

value: 2 day

tag: age

value: 20 week old

tag: treatment

value: SARS CoV MA15 infected with 10^5 PFU

value: lung


title: SM001 SARS 10^5pfu D2 1

source_name: SM001 SARS 10^5pfu D2 1


title: KH244

source_name: frozen tissue of primary lung tumors

value: primary lung tumor

tag: age (years)

value: female

tag: smoking status

value: Never-smoker

tag: bi

tag: pathological stage

value: IA

tag: pstage iorii

value: I

tag: gene alteration status

value: ALK-fusion +

tag: myc

value: Low

tag: cluster

tag: relapse

value: not relapsed

tag: days before relapse/censor

tag: months before relapse/censor

tag: death

value: alive

tag: days before death/censor


title: KH081

tag: tissue

tag: gender

value: Ever-smoker

value: II

value: relapsed

tag: exclude for prognosis analysis due to incomplete resection or adjuvant therapy


title: Infant at timeC, rep44

source_name: Infant at 24-33 days of life rep 44

value: blood

tag: days of life

value: 1 (female)

tag: gestational age (weeks)

tag: birth weight (grams)

tag: oxygen 28 days

value: 1 (oxygen therapy =>28 days)

tag: oxygen 36 weeks postmenstrual age (wpma)

value: 0 (finished oxygen therapy earlier than the age of 36 wPMA)

tag: bronchopulmonary dysplasia (bpd) group

value: 1 (mild BPD)

tag: retinopathy of prematurity (rop) group

value: 2 (ROP which need laser therapy)

tag: rop lasertherapy

value: 1 (laser therapy  due to prethreshold or threshold ROP)

tag: periventricular leukomalacia (pvl)

value: 1 (PVL)


title: SM001 SARS 10^5pfu D1 5

source_name: SM001 SARS 10^5pfu D1 5

tag: strain

value: Female

tag: time (post-infection)

value: 1 day

tag: age

value: 20 week old

tag: treatment

value: SARS CoV MA15 infected with 10^5 PFU

value: lung


title: SM001 SARS 10^5pfu D1 4

source_name: SM001 SARS 10^5pfu D1 4


title: Infant at timeC, rep45

source_name: Infant at 24-33 days of life rep 45

value: 1 (ROP not requiring treatment)

value: 0 (no lasertherapy)

value: 0 (no PVL)


title: Infant at timeC, rep43

source_name: Infant at 24-33 days of life rep 43

value: 2 (male)

value: 1 (on oxygen at the age of 36 wpma)

value: 3 (severe BPD)

value: 0 (no ROP)


title: SM001 SARS 10^5pfu D1 3

source_name: SM001 SARS 10^5pfu D1 3


title: Infant at timeC, rep41

source_name: Infant at 24-33 days of life rep 41

value: blood

value: 1 (oxygen therapy =>28 days)

value: 0 (finished oxygen therapy earlier than the age of 36 wPMA)


title: Infant at timeC, rep42

source_name: Infant at 24-33 days of life rep 42

value: 1 (female)


title: Infant at timeC, rep66

source_name: Infant at 24-33 days of life rep 66

value: 1 (mild BPD)

value: 2 (ROP which need laser therapy)

value: 1 (laser therapy  due to prethreshold or threshold ROP)


title: Infant at timeC, rep48

source_name: Infant at 24-33 days of life rep 48

value: 0 (oxygen therapy <28 days)

value: 0 (no BPD)


title: SM001 SARS 10^5pfu D1 2

source_name: SM001 SARS 10^5pfu D1 2

value: Female

value: 1 day

value: 20 week old

value: SARS CoV MA15 infected with 10^5 PFU

value: lung


title: Infant at timeC, rep40

source_name: Infant at 24-33 days of life rep 40

value: 2 (male)

value: 1 (ROP not requiring treatment)

value: 0 (no lasertherapy)

value: 1 (PVL)


title: Infant at timeC, rep37

source_name: Infant at 24-33 days of life rep 37

value: blood

value: 0 (no ROP)

value: 0 (no PVL)


title: Infant at timeC, rep39

source_name: Infant at 24-33 days of life rep 39

value: 1 (oxygen therapy =>28 days)

value: 0 (finished oxygen therapy earlier than the age of 36 wPMA)

value: 1 (mild BPD)


title: Infant at timeC, rep38

source_name: Infant at 24-33 days of life rep 38


title: REH_shG1_rep1

city: Vienna

first: Maximilian

last: Kauer

address: Zimmermannplatz 10

department: Molecular Biology

country: Austria

institute: CCRI, St.Anna Children Cancer Research Institute

description: REH treated with specific E/R targeting shRNA, replica 1

hyb_protocol: Following RNA purification, 20µg of cRNA were fragmented at 95°C using the Affymetrix fragmentation buffer, mixed with 200µl hybridization buffer containing hybridization controls and hybridized to U133-A2 microarrays. The arrays were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol

scan_protocol: Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2).

data_processing: The data was analyzed in R statistical environment using Bioconductor packages. Normalization was done using the gcRMA algorithm

source_name: REH E/R positive leukemia cell line

label_protocol: Target labelling and hybridization. For Affymetrix GeneChip analysis, 2.0µg total RNA was processed to generate a biotinylated hybridization target using One Cycle cDNA Synthesis and One Cycle Target Labelling kits from Affymetrix (Affymetrix, Santa Clara, CA). All procedures were performed according to the manufacturer's protocols (Gene Expression Analysis, Technical Manual, Revison #4; Eukaryotic Target Preparation, Revison #3).

growth_protocol: Cells were cultured in RPMI 1640 medium with Glutamax (Invitrogen, Carlsbad, CA), supplemented with 10% heat-inactivated FCS, 100 IU/mL penicillin and 100 g/mL streptomycin (all PAA Laboratories, Pasching, Austria) and kept in humidified incubators at 37° C and 5% CO2

extract_protocol: RNA was extrated usingTrizol according to the manufacturer's instructions.

treatment_protocol: lentiviral transduction of E/R specific shRNA

tag: cell line

value: REH E/R positive leukemia


title: SM001 SARS 10^4pfu D7 5

source_name: SM001 SARS 10^4pfu D7 5

value: 7 day

value: SARS CoV MA15 infected with 10^4 PFU

tag: tissue


title: REH_control_rep3

description: REH treated with non targeting lacZ shRNA, replica 3

treatment_protocol: lentiviral transduction of non targeting lacZ shRNA /control

value: treated with non targeting lacZ shRNA


title: SM001 SARS 10^5pfu D1 1

source_name: SM001 SARS 10^5pfu D1 1

tag: gender

value: Female

value: 1 day

value: 20 week old


title: REH_shG1_rep2

description: REH treated with specific E/R targeting shRNA, replica 2


title: REH_shG1_rep3

description: REH treated with specific E/R targeting shRNA, replica 3


title: Infant at timeC, rep36

source_name: Infant at 24-33 days of life rep 36

value: 1 (female)

value: 0 (oxygen therapy <28 days)

value: 0 (no BPD)


title: REH_control_rep2

description: REH treated with non targeting lacZ shRNA, replica 2


title: Infant at timeC, rep31

source_name: Infant at 24-33 days of life rep 31

value: 0 (no lasertherapy)


title: Infant at timeC, rep34

source_name: Infant at 24-33 days of life rep 34

value: blood

value: 1 (ROP not requiring treatment)


title: Infant at timeC, rep35

source_name: Infant at 24-33 days of life rep 35

value: 0 (no ROP)

value: 0 (no PVL)


title: SM001 SARS 10^4pfu D7 4

source_name: SM001 SARS 10^4pfu D7 4

value: lung


title: SM001 SARS 10^4pfu D7 3

source_name: SM001 SARS 10^4pfu D7 3


title: Infant at timeC, rep30

source_name: Infant at 24-33 days of life rep 30

value: 2 (male)

value: 0 (finished oxygen therapy earlier than the age of 36 wPMA)


title: Infant at timeC, rep32

source_name: Infant at 24-33 days of life rep 32

value: 1 (oxygen therapy =>28 days)

value: 1 (on oxygen at the age of 36 wpma)

value: 3 (severe BPD)

value: 2 (ROP which need laser therapy)

value: 1 (laser therapy  due to prethreshold or threshold ROP)

value: 1 (PVL)


title: Infant at timeC, rep29

source_name: Infant at 24-33 days of life rep 29

value: 1 (mild BPD)


title: REH_control_rep1

description: REH treated with non targeting lacZ shRNA, replica 1

value: REH E/R positive leukemia

value: treated with non targeting lacZ shRNA


title: Infant at timeC, rep28

source_name: Infant at 24-33 days of life rep 28


title: Infant at timeC, rep26

source_name: Infant at 24-33 days of life rep 26


title: AT2_shG1_rep2

description: AT2 treated with specific E/R targeting shRNA, replica 2

source_name: AT2 E/R positive leukemia cell line

value: AT2 E/R positive leukemia


title: SM001 SARS 10^4pfu D7 1

source_name: SM001 SARS 10^4pfu D7 1

value: Female

value: 7 day

value: 20 week old

value: SARS CoV MA15 infected with 10^4 PFU


title: SM001 SARS 10^4pfu D7 2

source_name: SM001 SARS 10^4pfu D7 2

value: lung


title: Infant at timeC, rep24

source_name: Infant at 24-33 days of life rep 24

value: blood

value: 2 (male)

value: 0 (no PVL)


title: AT2_shG1_rep1

description: AT2 treated with specific E/R targeting shRNA, replica 1


title: SM001 SARS 10^4pfu D4 5

source_name: SM001 SARS 10^4pfu D4 5

value: 4 day


title: Infant at timeC, rep23

source_name: Infant at 24-33 days of life rep 23

value: 0 (oxygen therapy <28 days)

value: 0 (finished oxygen therapy earlier than the age of 36 wPMA)

value: 0 (no BPD)

value: 0 (no ROP)

value: 0 (no lasertherapy)


title: Infant at timeC, rep19

source_name: Infant at 24-33 days of life rep 19

value: 1 (oxygen therapy =>28 days)

value: 1 (mild BPD)

value: 2 (ROP which need laser therapy)

value: 1 (laser therapy  due to prethreshold or threshold ROP)


title: Infant at timeC, rep21

source_name: Infant at 24-33 days of life rep 21

value: 1 (female)


title: SM001 SARS 10^4pfu D4 4

source_name: SM001 SARS 10^4pfu D4 4

value: Female

value: 20 week old


title: Infant at timeC, rep15

source_name: Infant at 24-33 days of life rep 15

value: 1 (on oxygen at the age of 36 wpma)

value: 3 (severe BPD)


title: SM001 SARS 10^4pfu D4 3

source_name: SM001 SARS 10^4pfu D4 3

value: SARS CoV MA15 infected with 10^4 PFU

value: lung


title: AT2_control_rep1

description: AT2 treated with non targeting lacZ shRNA, replica 1

value: AT2 E/R positive leukemia

value: treated with non targeting lacZ shRNA


title: Infant at timeC, rep22

source_name: Infant at 24-33 days of life rep 22

value: blood

value: 0 (no PVL)


title: Infant at timeC, rep17

source_name: Infant at 24-33 days of life rep 17

value: 2 (male)

value: 1 (PVL)


title: SM001 SARS 10^4pfu D4 1

source_name: SM001 SARS 10^4pfu D4 1

value: 4 day


title: Infant at timeC, rep14

source_name: Infant at 24-33 days of life rep 14

value: 1 (oxygen therapy =>28 days)


title: SM001 SARS 10^4pfu D2 5

source_name: SM001 SARS 10^4pfu D2 5

value: 2 day


title: SM001 SARS 10^4pfu D4 2

source_name: SM001 SARS 10^4pfu D4 2


title: Infant at timeC, rep10

source_name: Infant at 24-33 days of life rep 10

value: 0 (oxygen therapy <28 days)

value: 0 (finished oxygen therapy earlier than the age of 36 wPMA)

value: 0 (no BPD)

value: 0 (no ROP)

value: 0 (no lasertherapy)


title: SM001 SARS 10^5pfu D2 4

source_name: SM001 SARS 10^5pfu D2 4

value: Female

value: 20 week old

value: SARS CoV MA15 infected with 10^5 PFU


title: Infant at timeC, rep13

source_name: Infant at 24-33 days of life rep 13


title: IP-control technical 1

city: Curitiba

first: PATRICIA

last: SHIGUNOV

state: Paraná

address: Rua Prof. Algacyr Munhoz Mader, 3775

country: Brazil

institute: Instituto Carlos Chagas - FIOCRUZ-PR

description: non-specifically enriched RNAs

hyb_protocol: RNA was processed for hybridization with GeneChip 3’ IVT Express (Affymetrix - Santa Clara, USA), in accordance with the manufacturer’s instructions. After purification and fragmentation, cRNA (1µg) was hybridized for 16 hr at 45C on GeneChip Affymetrix Human Genome U133 Plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix.

scan_protocol: Post-hybridization washes were preformed on an Affymetrix GeneChip® Fluidics Station 450. Arrays were scanned on an Affymetrix GeneChip® Scanner 3000.

data_processing: Data was imported into Partek software using GCRMA protocol (Partek Incorporated. St. Louis, MO). Differentially enriched RNAs were found comparing immunoprecipitated samples against control samples.

source_name: IP-control

label_protocol: cDNA was synthesized from immunoprecipitated RNA using reverse transcriptase followed by second-strand synthesis to generate double-stranded cDNA. An in vitro transcription reaction was used to generate biotinylated cRNA from 100 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: HeLa cells were cultivated in T75 culture flasks in RPMI (Gibco Invitrogen) supplemented with 10% FCS, penicillin (100 units/ml), and streptomycin (100 lg/ml). The culture medium was then replaced twice each week.

extract_protocol: RNA was extracted using the RNeasy kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Immunoprecipitation (IP) reactions were performed with 2 µg of anti-DZIP1 antibody (SC-84091 -lot# L2308, rabbit polyclonal, Santa Cruz Biotechnology, CA, USA) bound to protein A-agarose beads (Sigma, Deisenhofen, Germany). MSCs were lysed in polysome lysis buffer (Tris-HCl pH 7,4 15mM, MgCl2 15 mM, NaCl 0,3 M, 1% Triton X-100, 1 mM DTT, 100 U / ml RNase Out, PMSF 1mM and E64 10uM) for 1 hat 4°C. Beads were washed, then buffer and cell lysate were added, and the reaction mixtures were tumbled for 2 h at 4°C. After this incubation, the beads were thoroughly washed again with polysome lysis buffer and then their RNA extracted for microarray and RT-PCR experiments. Identical IPs were performed with beads precoated with rabbit IgG as a negative control.

value: HeLa

tag: ip antibody

value: rabbit IgG


title: IP-control technical 2

description: non-specifically enriched RNAs


title: Infant at timeC, rep11

source_name: Infant at 24-33 days of life rep 11

value: blood

tag: days of life

value: 1 (female)

value: 1 (mild BPD)

value: 1 (ROP not requiring treatment)


title: Infant at timeC, rep12

source_name: Infant at 24-33 days of life rep 12

value: 2 (male)

tag: gestational age (weeks)

value: 1 (PVL)


title: Infant at timeC, rep3

source_name: Infant at 24-33 days of life rep 3

tag: birth weight (grams)

value: 0 (no PVL)


title: IP-control technical 3

description: non-specifically enriched RNAs


title: IP-DZIP1 technical 3

description: mRNAs associated with human DZIP1 protein

source_name: IP-DZIP

value: rabbit anti-DZIP1 polyclonal

tag: antibody vendor

value: Santa Cruz Biotechnology

tag: antibody catalog number

tag: antibody lot number


title: Infant at timeC, rep7

source_name: Infant at 24-33 days of life rep 7

tag: oxygen 28 days

value: 1 (oxygen therapy =>28 days)

tag: oxygen 36 weeks postmenstrual age (wpma)

value: 0 (finished oxygen therapy earlier than the age of 36 wPMA)

tag: bronchopulmonary dysplasia (bpd) group

tag: retinopathy of prematurity (rop) group


title: Infant at timeC, rep4

source_name: Infant at 24-33 days of life rep 4

value: 0 (oxygen therapy <28 days)

value: 0 (no BPD)

value: 0 (no ROP)

tag: rop lasertherapy

value: 0 (no lasertherapy)

tag: periventricular leukomalacia (pvl)


title: IP-DZIP1 technical 2

value: HeLa


title: SM001 SARS 10^4pfu D2 3

source_name: SM001 SARS 10^4pfu D2 3

tag: strain

value: Female

tag: time (post-infection)

value: 2 day

tag: age

value: 20 week old

tag: treatment

value: SARS CoV MA15 infected with 10^4 PFU

value: lung


title: IP-DZIP1 technical 1

tag: cell line

tag: ip antibody


title: Infant at timeC, rep1

source_name: Infant at 24-33 days of life rep 1

tag: tissue

value: blood

tag: days of life

tag: gender

value: 1 (female)

tag: gestational age (weeks)


title: Infant at timeC, rep6

source_name: Infant at 24-33 days of life rep 6

value: 2 (male)

tag: birth weight (grams)

value: 1 (ROP not requiring treatment)

value: 1 (PVL)


title: Infant at timeB, rep131

source_name: Infant at 12-17 days of life rep 131

tag: oxygen 28 days

value: 0 (no PVL)


title: SM001 SARS 10^4pfu D2 2

source_name: SM001 SARS 10^4pfu D2 2


title: Experiment_Post_Surgical_10

city: Brisbane

first: Gareth

last: Price

state: Queensland

address: Carmody Road

country: Australia

institute: Queensland Facility for Advanced Bioinformatics

description: Collected within 24 hours post surgery, major open chest surgery

hyb_protocol: 10ug of fragmented biotinylated cRNA was hybridised for 16hrs at 45oC on a HGU133 Plus 2.0 GeneChip. After 16hrs GeneChips were washed on a FS_450 Fluidics Station using the EukGE-Ws2v5 script.

scan_protocol: Data was acquired on a 7G GeneChip Scanner 3000 and data extraction performed in GCOS v1.2.

data_processing: CHP files were generated using a combination of Affymetrix Power Tools, R and Perl scripts to filter background noise and normalise data based on a detection metric used to identify perfect match probes relative to other background probes. Differentially expressed genes were compared if the signal was >100 and the fold change was >2.0.

source_name: Whole blood

label_protocol: Biotinylated cRNA were prepared using the One-Cycle Target Labelling and Control Reagents Kit, according to manufacturers protocol from 10ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA was extracted using PAXgene Blood RNA kits (PreAnalytix, a Qiagen/BD Company, Feldbachstrasse, Switzerland), according to manufacturer's protocol.

value: whole blood

tag: health status


title: SM001 SARS 10^4pfu D2 4

source_name: SM001 SARS 10^4pfu D2 4


title: Infant at timeB, rep129

source_name: Infant at 12-17 days of life rep 129

value: 0 (oxygen therapy <28 days)

tag: oxygen 36 weeks postmenstrual age (wpma)

value: 0 (finished oxygen therapy earlier than the age of 36 wPMA)

tag: bronchopulmonary dysplasia (bpd) group


title: Experiment_Post_Surgical_11


title: SM001 SARS 10^4pfu D1 5

source_name: SM001 SARS 10^4pfu D1 5

value: 1 day


title: Infant at timeC, rep2

source_name: Infant at 24-33 days of life rep 2

value: 0 (no BPD)

tag: retinopathy of prematurity (rop) group

value: 0 (no ROP)

tag: rop lasertherapy

value: 0 (no lasertherapy)


title: Infant at timeB, rep124

source_name: Infant at 12-17 days of life rep 124

value: 1 (oxygen therapy =>28 days)

value: 1 (on oxygen at the age of 36 wpma)

value: 2 (moderate BPD)

tag: periventricular leukomalacia (pvl)


title: Infant at timeB, rep122

source_name: Infant at 12-17 days of life rep 122


title: Infant at timeB, rep121

source_name: Infant at 12-17 days of life rep 121

value: 2 (ROP which need laser therapy)

value: 1 (laser therapy  due to prethreshold or threshold ROP)


title: Infant at timeB, rep127

source_name: Infant at 12-17 days of life rep 127

value: blood

value: 1 (female)


title: Experiment_Post_Surgical_9


title: Infant at timeB, rep118

source_name: Infant at 12-17 days of life rep 118

value: 2 (male)

value: 1 (mild BPD)


title: Infant at timeB, rep119

source_name: Infant at 12-17 days of life rep 119

value: 0 (no PVL)


title: Experiment_Post_Surgical_8

value: whole blood


title: SM001 SARS 10^4pfu D2 1

source_name: SM001 SARS 10^4pfu D2 1

tag: strain

value: Female

tag: time (post-infection)

value: 2 day

value: 20 week old

value: SARS CoV MA15 infected with 10^4 PFU

value: lung


title: SM001 SARS 10^4pfu D1 3

source_name: SM001 SARS 10^4pfu D1 3

value: 1 day

tag: age

tag: treatment


title: SM001 SARS 10^4pfu D1 4

source_name: SM001 SARS 10^4pfu D1 4


title: Experiment_Post_Surgical_6


title: Infant at timeB, rep120

source_name: Infant at 12-17 days of life rep 120

value: 1 (oxygen therapy =>28 days)

value: 0 (finished oxygen therapy earlier than the age of 36 wPMA)


title: Experiment_Post_Surgical_7


title: Experiment_Post_Surgical_5


title: SM001 SARS 10^4pfu D1 2

source_name: SM001 SARS 10^4pfu D1 2


title: Infant at timeB, rep117

source_name: Infant at 12-17 days of life rep 117

value: 1 (on oxygen at the age of 36 wpma)

value: 3 (severe BPD)


title: Infant at timeB, rep128

source_name: Infant at 12-17 days of life rep 128

value: 2 (ROP which need laser therapy)

value: 1 (laser therapy  due to prethreshold or threshold ROP)

value: 1 (PVL)


title: Infant at timeB, rep116

source_name: Infant at 12-17 days of life rep 116

value: blood

value: 1 (female)

value: 2 (moderate BPD)


title: SM001 SARS 10^4pfu D1 1

source_name: SM001 SARS 10^4pfu D1 1


title: Infant at timeB, rep115

source_name: Infant at 12-17 days of life rep 115

value: 0 (oxygen therapy <28 days)

value: 0 (no BPD)

value: 0 (no ROP)

value: 0 (no lasertherapy)

value: 0 (no PVL)


title: Infant at timeB, rep111

source_name: Infant at 12-17 days of life rep 111

value: 2 (male)

value: 1 (ROP not requiring treatment)


title: Infant at timeB, rep109

source_name: Infant at 12-17 days of life rep 109

value: 1 (oxygen therapy =>28 days)

value: 1 (mild BPD)


title: SM001 SARS 10^3pfu D7 5

source_name: SM001 SARS 10^3pfu D7 5

value: Female

value: 7 day

value: 20 week old

value: SARS CoV MA15 infected with 10^3 PFU

value: lung


title: Infant at timeB, rep108

source_name: Infant at 12-17 days of life rep 108

value: blood

value: 0 (finished oxygen therapy earlier than the age of 36 wPMA)


title: SM001 SARS 10^3pfu D7 3

source_name: SM001 SARS 10^3pfu D7 3


title: Experiment_Post_Surgical_4

source_name: Whole blood

value: whole blood


title: Experiment_Post_Surgical_1


title: Infant at timeB, rep114

source_name: Infant at 12-17 days of life rep 114

value: 2 (ROP which need laser therapy)

value: 1 (laser therapy  due to prethreshold or threshold ROP)


title: Experiment_Post_Surgical_2


title: Infant at timeB, rep110

source_name: Infant at 12-17 days of life rep 110

value: 1 (female)

value: 1 (on oxygen at the age of 36 wpma)

value: 3 (severe BPD)


title: Experiment_Post_Surgical_3


title: Infant at timeB, rep101

source_name: Infant at 12-17 days of life rep 101

value: 2 (male)

value: 2 (moderate BPD)

value: 0 (no PVL)


title: Infant at timeB, rep103

source_name: Infant at 12-17 days of life rep 103

value: 1 (oxygen therapy =>28 days)

value: 0 (no ROP)

value: 0 (no lasertherapy)


title: Infant at timeB, rep106

source_name: Infant at 12-17 days of life rep 106

value: 1 (mild BPD)


title: SM001 SARS 10^3pfu D7 4

source_name: SM001 SARS 10^3pfu D7 4

value: Female

value: 7 day

value: 20 week old

value: SARS CoV MA15 infected with 10^3 PFU


title: Infant at timeB, rep104

source_name: Infant at 12-17 days of life rep 104

value: blood

value: 1 (ROP not requiring treatment)


title: SM001 SARS 10^3pfu D7 1

source_name: SM001 SARS 10^3pfu D7 1

value: lung


title: SM001 SARS 10^3pfu D4 5

source_name: SM001 SARS 10^3pfu D4 5

value: 4 day


title: Infant at timeB, rep100

source_name: Infant at 12-17 days of life rep 100

value: 1 (female)

value: 0 (finished oxygen therapy earlier than the age of 36 wPMA)


title: Infant at timeB, rep105

source_name: Infant at 12-17 days of life rep 105

value: 2 (male)

value: 1 (on oxygen at the age of 36 wpma)

value: 3 (severe BPD)

value: 1 (PVL)


title: Infant at timeB, rep107

source_name: Infant at 12-17 days of life rep 107

value: 0 (oxygen therapy <28 days)

value: 0 (no BPD)

value: 0 (no ROP)

value: 0 (no PVL)


title: SM001 SARS 10^3pfu D4 4

source_name: SM001 SARS 10^3pfu D4 4

value: Female


title: SM001 SARS 10^3pfu D7 2

source_name: SM001 SARS 10^3pfu D7 2

value: 7 day

value: 20 week old


title: Infant at timeB, rep99

source_name: Infant at 12-17 days of life rep 99

value: blood

value: 0 (no lasertherapy)


title: AT2_control_rep2

description: AT2 treated with non targeting lacZ shRNA, replica 2

source_name: AT2 E/R positive leukemia cell line

tag: cell line

value: AT2 E/R positive leukemia

value: treated with non targeting lacZ shRNA


title: Infant at timeB, rep98

source_name: Infant at 12-17 days of life rep 98

tag: tissue

value: 1 (oxygen therapy =>28 days)

value: 1 (mild BPD)

value: 2 (ROP which need laser therapy)

value: 1 (laser therapy  due to prethreshold or threshold ROP)


title: Infant at timeB, rep92

source_name: Infant at 12-17 days of life rep 92

tag: days of life

value: 1 (female)

value: 0 (finished oxygen therapy earlier than the age of 36 wPMA)


title: SM001 SARS 10^3pfu D4 3

source_name: SM001 SARS 10^3pfu D4 3

tag: gender

value: 4 day

value: SARS CoV MA15 infected with 10^3 PFU

value: lung


title: Infant at timeB, rep93

source_name: Infant at 12-17 days of life rep 93

tag: gestational age (weeks)

value: 1 (on oxygen at the age of 36 wpma)

value: 2 (moderate BPD)

value: 0 (no PVL)


title: SM001 SARS 10^3pfu D4 2

source_name: SM001 SARS 10^3pfu D4 2

value: Female

value: 20 week old


title: SM001 SARS 10^3pfu D4 1

source_name: SM001 SARS 10^3pfu D4 1


title: Infant at timeB, rep91

source_name: Infant at 12-17 days of life rep 91

value: blood

value: 2 (male)

tag: birth weight (grams)


title: Infant at timeB, rep89

source_name: Infant at 12-17 days of life rep 89

tag: oxygen 28 days

value: 0 (no ROP)

value: 0 (no lasertherapy)


title: Infant at timeB, rep96

source_name: Infant at 12-17 days of life rep 96

value: 1 (oxygen therapy =>28 days)

value: 1 (mild BPD)


title: Infant at timeB, rep84

source_name: Infant at 12-17 days of life rep 84


title: SM001 SARS 10^3pfu D2 5

source_name: SM001 SARS 10^3pfu D2 5

value: 2 day


title: Infant at timeB, rep85

source_name: Infant at 12-17 days of life rep 85

value: 0 (oxygen therapy <28 days)

value: 0 (no BPD)


title: Infant at timeB, rep88

source_name: Infant at 12-17 days of life rep 88

value: 1 (female)

value: 0 (finished oxygen therapy earlier than the age of 36 wPMA)


title: Infant at timeB, rep86

source_name: Infant at 12-17 days of life rep 86


title: Infant at timeB, rep82

source_name: Infant at 12-17 days of life rep 82

value: 2 (ROP which need laser therapy)

value: 1 (laser therapy  due to prethreshold or threshold ROP)

value: 1 (PVL)


title: SM001 SARS 10^3pfu D2 4

source_name: SM001 SARS 10^3pfu D2 4

value: SARS CoV MA15 infected with 10^3 PFU

value: lung


title: SM001 SARS 10^3pfu D2 3

source_name: SM001 SARS 10^3pfu D2 3

value: Female

value: 20 week old


title: Infant at timeB, rep80

source_name: Infant at 12-17 days of life rep 80

value: blood

value: 0 (no PVL)


title: Infant at timeB, rep78

source_name: Infant at 12-17 days of life rep 78


title: Infant at timeB, rep73

source_name: Infant at 12-17 days of life rep 73

value: 0 (no ROP)

value: 0 (no lasertherapy)


title: SM001 SARS 10^3pfu D2 2

source_name: SM001 SARS 10^3pfu D2 2


title: Infant at timeB, rep83

source_name: Infant at 12-17 days of life rep 83

value: 1 (oxygen therapy =>28 days)

value: 1 (on oxygen at the age of 36 wpma)

value: 3 (severe BPD)


title: Infant at timeB, rep71

source_name: Infant at 12-17 days of life rep 71

value: 0 (oxygen therapy <28 days)

value: 0 (no BPD)


title: Infant at timeB, rep74

source_name: Infant at 12-17 days of life rep 74

value: 2 (male)

value: 0 (finished oxygen therapy earlier than the age of 36 wPMA)


title: SM001 SARS 10^3pfu D1 5

source_name: SM001 SARS 10^3pfu D1 5

value: 1 day


title: Infant at timeB, rep72

source_name: Infant at 12-17 days of life rep 72

value: 1 (female)

value: 2 (ROP which need laser therapy)

value: 1 (laser therapy  due to prethreshold or threshold ROP)


title: SM001 SARS 10^3pfu D2 1

source_name: SM001 SARS 10^3pfu D2 1

value: Female

value: 2 day

value: SARS CoV MA15 infected with 10^3 PFU

value: lung


title: Infant at timeB, rep81

source_name: Infant at 12-17 days of life rep 81

value: blood

value: 0 (no ROP)

value: 0 (no PVL)


title: Infant at timeB, rep70

source_name: Infant at 12-17 days of life rep 70

value: 1 (oxygen therapy =>28 days)

value: 1 (mild BPD)

value: 0 (no lasertherapy)

value: 1 (PVL)


title: SM001 SARS 10^3pfu D1 4

source_name: SM001 SARS 10^3pfu D1 4

value: 20 week old


title: Infant at timeB, rep66

source_name: Infant at 12-17 days of life rep 66

value: 2 (male)

value: 0 (finished oxygen therapy earlier than the age of 36 wPMA)


title: SM001 SARS 10^3pfu D1 3

source_name: SM001 SARS 10^3pfu D1 3

value: 1 day


title: Infant at timeB, rep69

source_name: Infant at 12-17 days of life rep 69

value: 1 (female)


title: SM001 SARS 10^3pfu D1 2

source_name: SM001 SARS 10^3pfu D1 2


title: Infant at timeB, rep64

source_name: Infant at 12-17 days of life rep 64


title: Infant at timeB, rep63

source_name: Infant at 12-17 days of life rep 63


title: Infant at timeB, rep62

source_name: Infant at 12-17 days of life rep 62

value: 0 (oxygen therapy <28 days)

value: 0 (no BPD)


title: Infant at timeB, rep67

source_name: Infant at 12-17 days of life rep 67

value: 1 (ROP not requiring treatment)


title: Infant at timeB, rep61

source_name: Infant at 12-17 days of life rep 61


title: SM001 SARS 10^3pfu D1 1

source_name: SM001 SARS 10^3pfu D1 1

value: Female

value: SARS CoV MA15 infected with 10^3 PFU


title: Infant at timeB, rep60

source_name: Infant at 12-17 days of life rep 60

value: blood


title: SM001 SARS 10^2pfu D7 4

source_name: SM001 SARS 10^2pfu D7 4

value: 7 day

value: SARS CoV MA15 infected with 10^2 PFU

value: lung


title: SM001 SARS 10^2pfu D7 5

source_name: SM001 SARS 10^2pfu D7 5


title: Infant at timeB, rep59

source_name: Infant at 12-17 days of life rep 59

value: 0 (no ROP)

value: 0 (no PVL)


title: Infant at timeB, rep55

source_name: Infant at 12-17 days of life rep 55

value: 0 (no lasertherapy)


title: SM001 SARS 10^2pfu D7 3

source_name: SM001 SARS 10^2pfu D7 3

value: 20 week old


title: SM001 SARS 10^2pfu D7 2

source_name: SM001 SARS 10^2pfu D7 2


title: Infant at timeB, rep58

source_name: Infant at 12-17 days of life rep 58


title: Infant at timeB, rep54

source_name: Infant at 12-17 days of life rep 54


title: Infant at timeB, rep51

source_name: Infant at 12-17 days of life rep 51

value: 2 (male)

value: 1 (oxygen therapy =>28 days)

value: 1 (on oxygen at the age of 36 wpma)

value: 2 (moderate BPD)


title: Infant at timeB, rep52

source_name: Infant at 12-17 days of life rep 52

value: 0 (finished oxygen therapy earlier than the age of 36 wPMA)

value: 1 (mild BPD)


title: SM001 SARS 10^2pfu D4 5

source_name: SM001 SARS 10^2pfu D4 5

value: 4 day


title: Infant at timeB, rep56

source_name: Infant at 12-17 days of life rep 56

value: 1 (female)

value: 2 (ROP which need laser therapy)

value: 1 (laser therapy  due to prethreshold or threshold ROP)


title: Infant at timeB, rep53

source_name: Infant at 12-17 days of life rep 53

value: blood

value: 0 (oxygen therapy <28 days)

value: 0 (no BPD)


title: SM001 SARS 10^2pfu D7 1

source_name: SM001 SARS 10^2pfu D7 1

value: Female

value: 7 day

value: SARS CoV MA15 infected with 10^2 PFU

value: lung


title: SM001 SARS 10^2pfu D4 4

source_name: SM001 SARS 10^2pfu D4 4

value: 20 week old


title: Infant at timeB, rep57

source_name: Infant at 12-17 days of life rep 57

value: 1 (oxygen therapy =>28 days)

value: 1 (PVL)


title: Infant at timeB, rep50

source_name: Infant at 12-17 days of life rep 50

value: 1 (ROP not requiring treatment)

value: 0 (no lasertherapy)

value: 0 (no PVL)


title: Infant at timeB, rep48

source_name: Infant at 12-17 days of life rep 48

value: 0 (finished oxygen therapy earlier than the age of 36 wPMA)

value: 0 (no ROP)


title: Infant at timeB, rep49

source_name: Infant at 12-17 days of life rep 49

value: 2 (male)

value: 1 (mild BPD)


title: SM001 SARS 10^2pfu D4 3

source_name: SM001 SARS 10^2pfu D4 3

value: 4 day


title: Infant at timeB, rep44

source_name: Infant at 12-17 days of life rep 44

value: blood

value: 1 (female)

value: 2 (ROP which need laser therapy)

value: 1 (laser therapy  due to prethreshold or threshold ROP)


title: Infant at timeB, rep45

source_name: Infant at 12-17 days of life rep 45


title: Infant at timeB, rep41

source_name: Infant at 12-17 days of life rep 41


title: SM001 SARS 10^2pfu D2 5

source_name: SM001 SARS 10^2pfu D2 5

value: Female

value: 2 day

value: SARS CoV MA15 infected with 10^2 PFU


title: Infant at timeB, rep40

source_name: Infant at 12-17 days of life rep 40

value: 1 (oxygen therapy =>28 days)


title: SM001 SARS 10^2pfu D4 2

source_name: SM001 SARS 10^2pfu D4 2

value: 20 week old

value: lung


title: Infant at timeB, rep39

source_name: Infant at 12-17 days of life rep 39

value: 0 (no lasertherapy)

value: 1 (PVL)


title: Infant at timeB, rep47

source_name: Infant at 12-17 days of life rep 47

value: 0 (oxygen therapy <28 days)

value: 0 (finished oxygen therapy earlier than the age of 36 wPMA)

value: 0 (no BPD)

value: 0 (no PVL)


title: Infant at timeB, rep37

source_name: Infant at 12-17 days of life rep 37

value: 0 (no ROP)


title: SM001 SARS 10^2pfu D2 4

source_name: SM001 SARS 10^2pfu D2 4


title: SM001 SARS 10^2pfu D4 1

source_name: SM001 SARS 10^2pfu D4 1

value: 4 day


title: Infant at timeB, rep34

source_name: Infant at 12-17 days of life rep 34

value: blood

value: 1 (female)

value: 1 (mild BPD)

value: 1 (ROP not requiring treatment)


title: Infant at timeB, rep35

source_name: Infant at 12-17 days of life rep 35


title: Infant at timeB, rep38

source_name: Infant at 12-17 days of life rep 38

value: 2 (male)


title: SM001 SARS 10^2pfu D2 3

source_name: SM001 SARS 10^2pfu D2 3

value: Female

value: 2 day

value: SARS CoV MA15 infected with 10^2 PFU


title: Infant at timeB, rep32

source_name: Infant at 12-17 days of life rep 32

value: 1 (oxygen therapy =>28 days)

value: 1 (on oxygen at the age of 36 wpma)

value: 3 (severe BPD)

value: 2 (ROP which need laser therapy)

value: 1 (laser therapy  due to prethreshold or threshold ROP)


title: Infant at timeB, rep36

source_name: Infant at 12-17 days of life rep 36

value: 0 (oxygen therapy <28 days)

value: 0 (finished oxygen therapy earlier than the age of 36 wPMA)

value: 0 (no BPD)

value: 0 (no lasertherapy)


title: Infant at timeB, rep31

source_name: Infant at 12-17 days of life rep 31

value: blood

value: 0 (no ROP)

value: 0 (no PVL)


title: Infant at timeB, rep30

source_name: Infant at 12-17 days of life rep 30


title: SM001 SARS 10^2pfu D2 2

source_name: SM001 SARS 10^2pfu D2 2

value: 20 week old

value: lung


title: Infant at timeB, rep29

source_name: Infant at 12-17 days of life rep 29

value: 2 (male)

value: 1 (mild BPD)

value: 1 (PVL)


title: SM001 SARS 10^2pfu D2 1

source_name: SM001 SARS 10^2pfu D2 1

value: Female

value: 2 day

value: SARS CoV MA15 infected with 10^2 PFU


title: Patient 8807 glu

city: Hasselt

first: An

middle: M

last: Voets

address: Martelarenlaan 42

department: BIOMED

country: Belgium

institute: Hasselt University

description: Gene expression data from fibroblasts of cell line 8807 on galactose

hyb_protocol: A mixture of cDNA and added hybridization controls was hybridized on Affymetrix HG-U133 Plus 2.0 chips, followed by staining and washing steps in the Affymetrix GeneChip fluidics station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: MAS 5.0 normalized. The data were analyzed with R, a free software program for statistical computing and graphics. Normal linear regression models were used to asses significantly differentially expressed genes between patients and controls.

source_name: fibroblast CI deficient 8807

label_protocol: 150ng fibroblast RNA was reverse transcribed into cDNA and amplified in a two-round amplification according to the manufacturer's protocol (Affymetrix)

growth_protocol: Fibroblasts were cultured in Dulbecco’s modified Eagle medium (DMEM; Gibco) with high glucose (4.5 g/L) supplemented with 10% fetal bovine serum (FBS), 0.2 mM uridine (Acros), penicillin and streptomycin. To stimulate energy production by oxidative phosphorylation, fibroblasts were cultured for 48 hours without glucose in de presence of galactose. Galactose medium consisted of DMEM without glucose supplemented with 5.5mM  galactose (Sigma), 20% FBS, 0.2 mM uridine, penicillin and streptomycin.

extract_protocol: Total RNA was isolated using the TRIzol reagent and purified with the Rneasy clean-up kit (Qiagen)

value: female

value: 7 months

tag: culture condition

value: glucose

tag: cell type

value: fibroblast

tag: disease state

value: defective complex I


title: Infant at timeB, rep21

source_name: Infant at 12-17 days of life rep 21

value: 1 (female)

value: 1 (oxygen therapy =>28 days)

tag: oxygen 36 weeks postmenstrual age (wpma)

tag: bronchopulmonary dysplasia (bpd) group

tag: retinopathy of prematurity (rop) group


title: SM001 SARS 10^2pfu D1 4

source_name: SM001 SARS 10^2pfu D1 4

tag: strain

value: 1 day


title: SM001 SARS 10^2pfu D1 5

source_name: SM001 SARS 10^2pfu D1 5

tag: time (post-infection)


title: Infant at timeB, rep13

source_name: Infant at 12-17 days of life rep 13

value: blood

value: 0 (oxygen therapy <28 days)

value: 0 (finished oxygen therapy earlier than the age of 36 wPMA)

value: 0 (no BPD)

value: 0 (no ROP)

tag: rop lasertherapy

value: 0 (no lasertherapy)

tag: periventricular leukomalacia (pvl)

value: 0 (no PVL)


title: Patient 8328 glu

description: Gene expression data from fibroblasts of cell line 8328 on glucose

source_name: fibroblast CI deficient 8328

value: male

tag: age

value: 1 year


title: Infant at timeB, rep15

source_name: Infant at 12-17 days of life rep 15

tag: tissue

value: 1 (on oxygen at the age of 36 wpma)

value: 3 (severe BPD)

value: 2 (ROP which need laser therapy)

value: 1 (laser therapy  due to prethreshold or threshold ROP)


title: SM001 SARS 10^2pfu D1 3

source_name: SM001 SARS 10^2pfu D1 3

value: Female

value: 20 week old

tag: treatment

value: SARS CoV MA15 infected with 10^2 PFU

value: lung


title: Patient 8807 gal

tag: gender

value: female

value: 7 months

value: galactose

value: fibroblast

value: defective complex I


title: Infant at timeB, rep17

source_name: Infant at 12-17 days of life rep 17

value: blood

tag: days of life

value: 2 (male)

tag: gestational age (weeks)

value: 1 (oxygen therapy =>28 days)

value: 1 (PVL)


title: Infant at timeB, rep22

source_name: Infant at 12-17 days of life rep 22

value: 1 (female)

tag: birth weight (grams)

tag: oxygen 28 days

value: 1 (on oxygen at the age of 36 wpma)

value: 0 (no PVL)


title: Infant at timeB, rep19

source_name: Infant at 12-17 days of life rep 19

value: 0 (finished oxygen therapy earlier than the age of 36 wPMA)

value: 1 (mild BPD)

value: 2 (ROP which need laser therapy)

value: 1 (laser therapy  due to prethreshold or threshold ROP)


title: Infant at timeB, rep24

source_name: Infant at 12-17 days of life rep 24


title: Patient 8328 gal

description: Gene expression data from fibroblasts of cell line 8328 on galactose

value: male

value: 1 year

tag: culture condition

tag: cell type


title: Patient 7898 glu

description: Gene expression data from fibroblasts of cell line 7898 on glucose

source_name: fibroblast CI deficient 7898

value: <7 months

value: glucose

tag: disease state


title: Infant at timeB, rep14

source_name: Infant at 12-17 days of life rep 14

tag: oxygen 36 weeks postmenstrual age (wpma)

tag: bronchopulmonary dysplasia (bpd) group

value: 3 (severe BPD)


title: Infant at timeB, rep26

source_name: Infant at 12-17 days of life rep 26

tag: retinopathy of prematurity (rop) group


title: Infant at timeB, rep8

source_name: Infant at 12-17 days of life rep 8

value: 0 (oxygen therapy <28 days)

value: 0 (no BPD)

value: 0 (no ROP)

value: 0 (no lasertherapy)


title: Patient 7898 gal

description: Gene expression data from fibroblasts of cell line 7898 on galactose

value: galactose

value: fibroblast

value: defective complex I


title: Infant at timeB, rep12

source_name: Infant at 12-17 days of life rep 12

value: blood

value: 2 (male)

value: 1 (oxygen therapy =>28 days)

value: 1 (PVL)


title: SM001 SARS 10^2pfu D1 1

source_name: SM001 SARS 10^2pfu D1 1

tag: strain

value: Female

tag: time (post-infection)

value: 1 day

value: 20 week old

value: SARS CoV MA15 infected with 10^2 PFU

value: lung


title: SM001 SARS 10^2pfu D1 2

source_name: SM001 SARS 10^2pfu D1 2


title: Infant at timeB, rep6

source_name: Infant at 12-17 days of life rep 6

value: 0 (finished oxygen therapy earlier than the age of 36 wPMA)

value: 1 (ROP not requiring treatment)

tag: rop lasertherapy

tag: periventricular leukomalacia (pvl)


title: Infant at timeB, rep4

source_name: Infant at 12-17 days of life rep 4

tag: tissue

value: 0 (oxygen therapy <28 days)

value: 0 (no BPD)

value: 0 (no PVL)


title: SM001 Mock D7 3

source_name: SM001 Mock D7 3

value: 7 day

tag: age

tag: treatment

value: Time-matched mock


title: Patient 6613 glu

description: Gene expression data from fibroblasts of cell line 6613 on glucose

source_name: fibroblast CI deficient 6613

tag: gender

value: male

value: <1 month

value: glucose

value: fibroblast

value: defective complex I


title: Patient 6613 gal

description: Gene expression data from fibroblasts of cell line 6613 on galactose

value: galactose


title: Infant at timeB, rep7

source_name: Infant at 12-17 days of life rep 7

value: blood

tag: days of life

value: 1 (female)

tag: gestational age (weeks)

value: 1 (oxygen therapy =>28 days)

value: 1 (mild BPD)

value: 0 (no ROP)

value: 0 (no lasertherapy)

value: 1 (PVL)


title: Infant at timeB, rep3

source_name: Infant at 12-17 days of life rep 3

value: 2 (male)

tag: birth weight (grams)

tag: oxygen 28 days

value: 0 (oxygen therapy <28 days)

value: 0 (finished oxygen therapy earlier than the age of 36 wPMA)

value: 0 (no BPD)


title: SM001 Mock D7 2

source_name: SM001 Mock D7 2

value: Female

value: 7 day

value: 20 week old

value: Time-matched mock

value: lung


title: Infant at timeB, rep2

source_name: Infant at 12-17 days of life rep 2

value: 0 (no PVL)


title: Patient 5175 glu

description: Gene expression data from fibroblasts of cell line 5175 on glucose

source_name: fibroblast CI deficient 5175

value: male

value: 3 years

tag: culture condition

value: glucose

tag: cell type

value: fibroblast

value: defective complex I


title: SM001 Mock D7 1

source_name: SM001 Mock D7 1


title: Infant at timeB, rep1

source_name: Infant at 12-17 days of life rep 1

value: blood

value: 1 (female)

tag: oxygen 36 weeks postmenstrual age (wpma)

value: 0 (no ROP)

value: 0 (no lasertherapy)


title: SM001 Mock D4 2

source_name: SM001 Mock D4 2

value: 4 day


title: Control MW25 gal

description: Gene expression data from fibroblasts of cell line MW25 on galactose

source_name: fibroblast control MW25

value: 1 year 7 months

value: galactose

tag: disease state

value: control


title: Infant at timeA, rep131

source_name: Infant at 4-6 days of life rep 131

value: 0 (oxygen therapy <28 days)

value: 0 (finished oxygen therapy earlier than the age of 36 wPMA)

tag: bronchopulmonary dysplasia (bpd) group

value: 0 (no BPD)

tag: retinopathy of prematurity (rop) group


title: SM001 Mock D4 3

source_name: SM001 Mock D4 3

tag: strain

value: Female

tag: time (post-infection)

value: 20 week old

value: Time-matched mock

value: lung


title: Control 9481 glu

description: Gene expression data from fibroblasts of cell line 9481 on glucose

source_name: fibroblast control 9481

value: male

value: 3 years 3 months

value: glucose

value: fibroblast


title: Infant at timeA, rep124

source_name: Infant at 4-6 days of life rep 124

value: blood

value: 2 (male)

value: 1 (oxygen therapy =>28 days)

value: 1 (on oxygen at the age of 36 wpma)

value: 2 (moderate BPD)

value: 0 (no ROP)

tag: rop lasertherapy

tag: periventricular leukomalacia (pvl)

value: 0 (no PVL)


title: Control MW25 glu

description: Gene expression data from fibroblasts of cell line MW25 on glucose

tag: age

value: 1 year 7 months

value: control


title: Infant at timeA, rep128

source_name: Infant at 4-6 days of life rep 128

tag: tissue

value: 3 (severe BPD)

value: 2 (ROP which need laser therapy)

value: 1 (laser therapy  due to prethreshold or threshold ROP)

value: 1 (PVL)


title: Infant at timeA, rep127

source_name: Infant at 4-6 days of life rep 127

tag: gender

value: 1 (female)

value: 0 (oxygen therapy <28 days)

value: 0 (finished oxygen therapy earlier than the age of 36 wPMA)

value: 0 (no BPD)

value: 0 (no lasertherapy)


title: Infant at timeA, rep130

source_name: Infant at 4-6 days of life rep 130

value: blood

tag: days of life

value: 1 (mild BPD)


title: SM001 Mock D4 1

source_name: SM001 Mock D4 1

value: Female

value: 4 day

value: 20 week old

tag: treatment

value: Time-matched mock

value: lung


title: Infant at timeA, rep122

source_name: Infant at 4-6 days of life rep 122

value: 2 (male)

tag: gestational age (weeks)

tag: birth weight (grams)

value: 0 (no ROP)

value: 0 (no PVL)


title: Patient 5175 gal

description: Gene expression data from fibroblasts of cell line 5175 on galactose

value: male

value: 3 years

tag: culture condition

value: galactose

value: fibroblast

value: defective complex I


title: Infant at timeA, rep123

source_name: Infant at 4-6 days of life rep 123

value: 1 (female)

tag: oxygen 28 days

value: 0 (oxygen therapy <28 days)

value: 0 (finished oxygen therapy earlier than the age of 36 wPMA)

value: 0 (no BPD)


title: Infant at timeA, rep121

source_name: Infant at 4-6 days of life rep 121

value: blood

value: 1 (oxygen therapy =>28 days)

tag: oxygen 36 weeks postmenstrual age (wpma)

value: 1 (on oxygen at the age of 36 wpma)

value: 2 (moderate BPD)

value: 2 (ROP which need laser therapy)

value: 1 (laser therapy  due to prethreshold or threshold ROP)


title: SM001 Mock D2 3

source_name: SM001 Mock D2 3

value: Female

value: 2 day

value: 20 week old

value: Time-matched mock

value: lung


title: Control 6855 glu

description: Gene expression data from fibroblasts of cell line 6855 on glucose

source_name: fibroblast control 6855

value: male

value: 6 months

value: glucose

tag: cell type

value: fibroblast

tag: disease state

value: control


title: SM001 Mock D2 2

source_name: SM001 Mock D2 2


title: Infant at timeA, rep119

source_name: Infant at 4-6 days of life rep 119

value: 1 (female)

value: 0 (finished oxygen therapy earlier than the age of 36 wPMA)

tag: bronchopulmonary dysplasia (bpd) group

value: 1 (mild BPD)

tag: retinopathy of prematurity (rop) group

value: 0 (no ROP)

value: 0 (no lasertherapy)

value: 0 (no PVL)


title: Infant at timeA, rep117

source_name: Infant at 4-6 days of life rep 117

value: blood

value: 2 (male)

value: 1 (oxygen therapy =>28 days)

value: 1 (on oxygen at the age of 36 wpma)

value: 3 (severe BPD)

value: 2 (ROP which need laser therapy)

value: 1 (laser therapy  due to prethreshold or threshold ROP)


title: Infant at timeA, rep120

source_name: Infant at 4-6 days of life rep 120


title: Control 9481 gal

description: Gene expression data from fibroblasts of cell line 9481 on galactose

value: male

value: 3 years 3 months

value: galactose


title: Infant at timeA, rep116

source_name: Infant at 4-6 days of life rep 116

value: 2 (moderate BPD)


title: Control 6855 gal

description: Gene expression data from fibroblasts of cell line 6855 on galactose

value: 6 months

value: fibroblast

value: control


title: Infant at timeA, rep111

source_name: Infant at 4-6 days of life rep 111

value: 1 (ROP not requiring treatment)


title: SM001 Mock D1 2

source_name: SM001 Mock D1 2

tag: strain

value: Female

tag: time (post-infection)

value: 1 day

value: 20 week old

value: Time-matched mock

value: lung


title: SM001 Mock D1 1

source_name: SM001 Mock D1 1


title: Infant at timeA, rep113

source_name: Infant at 4-6 days of life rep 113

value: blood

value: 2 (male)

value: 1 (oxygen therapy =>28 days)

value: 1 (on oxygen at the age of 36 wpma)

tag: rop lasertherapy

value: 0 (no lasertherapy)

tag: periventricular leukomalacia (pvl)

value: 0 (no PVL)


title: Infant at timeA, rep115

source_name: Infant at 4-6 days of life rep 115

tag: tissue

value: 1 (female)

value: 0 (oxygen therapy <28 days)

value: 0 (finished oxygen therapy earlier than the age of 36 wPMA)

value: 0 (no BPD)

value: 0 (no ROP)


title: Infant at timeA, rep110

source_name: Infant at 4-6 days of life rep 110

tag: gender

value: 3 (severe BPD)

value: 2 (ROP which need laser therapy)

value: 1 (laser therapy  due to prethreshold or threshold ROP)


title: SM001 Mock D1 3

source_name: SM001 Mock D1 3

value: Female

value: 1 day

tag: age

value: 20 week old


title: Control 4752 glu

description: Gene expression data from fibroblasts of cell line 4752 on glucose

source_name: fibroblast control 4752

value: female

value: 1 year 11 months

value: glucose

value: fibroblast

value: control


title: Infant at timeA, rep114

source_name: Infant at 4-6 days of life rep 114

value: blood

tag: days of life

value: 2 (male)

value: 1 (oxygen therapy =>28 days)

value: 1 (mild BPD)

value: 0 (no PVL)


title: Control 4673 gal

description: Gene expression data from fibroblasts of cell line 4673 on galactose

source_name: fibroblast control 4673

value: male

value: 1 year 6 months

value: galactose


title: Infant at timeA, rep109

source_name: Infant at 4-6 days of life rep 109

tag: gestational age (weeks)

value: 0 (finished oxygen therapy earlier than the age of 36 wPMA)

value: 0 (no ROP)

value: 0 (no lasertherapy)


title: Infant at timeA, rep105

source_name: Infant at 4-6 days of life rep 105

tag: birth weight (grams)

value: 1 (on oxygen at the age of 36 wpma)

value: 3 (severe BPD)

value: 1 (ROP not requiring treatment)

value: 1 (PVL)


title: Control 4673 glu

description: Gene expression data from fibroblasts of cell line 4673 on glucose

tag: culture condition

value: glucose

value: fibroblast


title: Infant at timeA, rep107

source_name: Infant at 4-6 days of life rep 107

value: blood

tag: oxygen 28 days

value: 0 (oxygen therapy <28 days)

value: 0 (no BPD)


title: Control 4752 gal

description: Gene expression data from fibroblasts of cell line 4752 on galactose

value: female

value: 1 year 11 months

value: control


title: IM001 VN1203 10^4pfu D4 5

growth_protocol: Twenty-week-old C57BL/6 mice were infected by intranasal instillation of 10^2, 10^3 or 10^4 PFU of VN1203 in 50 µl of PBS or mock-infected with PBS alone.  At days 1, 2, 4 and 7 days post-infection, lungs were harvested.

value: Female

value: 4 day

value: 20 week old

tag: treatment

value: Influenza A/VN/1203/04 infected with 10^4 PFU

value: lung


title: Infant at timeA, rep106

source_name: Infant at 4-6 days of life rep 106

value: 1 (female)

value: 1 (oxygen therapy =>28 days)

tag: oxygen 36 weeks postmenstrual age (wpma)

value: 0 (finished oxygen therapy earlier than the age of 36 wPMA)

value: 1 (mild BPD)

value: 0 (no ROP)

value: 0 (no lasertherapy)

value: 0 (no PVL)


title: Infant at timeA, rep104

source_name: Infant at 4-6 days of life rep 104

value: blood

value: 2 (male)

value: 1 (on oxygen at the age of 36 wpma)

value: 2 (moderate BPD)

value: 1 (ROP not requiring treatment)


title: Infant at timeA, rep112

source_name: Infant at 4-6 days of life rep 112

value: 3 (severe BPD)

value: 2 (ROP which need laser therapy)

value: 1 (laser therapy  due to prethreshold or threshold ROP)


title: Infant at timeA, rep103

source_name: Infant at 4-6 days of life rep 103


title: IM001 VN1203 10^4pfu D4 3

value: Female

value: 4 day

value: 20 week old

value: Influenza A/VN/1203/04 infected with 10^4 PFU


title: Infant at timeA, rep91

source_name: Infant at 4-6 days of life rep 91

value: 1 (oxygen therapy =>28 days)

value: 0 (finished oxygen therapy earlier than the age of 36 wPMA)


title: IM001 VN1203 10^4pfu D4 4

value: lung


title: Infant at timeA, rep101

source_name: Infant at 4-6 days of life rep 101


title: IM001 VN1203 10^4pfu D2 3

value: 2 day


title: IM001 VN1203 10^4pfu D4 1


title: IM001 VN1203 10^4pfu D4 2


title: Infant at timeA, rep93

source_name: Infant at 4-6 days of life rep 93

value: 1 (female)

value: 0 (no PVL)


title: Infant at timeA, rep88

source_name: Infant at 4-6 days of life rep 88

value: blood

value: 0 (oxygen therapy <28 days)

value: 0 (no BPD)

value: 0 (no ROP)

value: 0 (no lasertherapy)


title: Infant at timeA, rep96

source_name: Infant at 4-6 days of life rep 96

value: 2 (male)

value: 1 (mild BPD)


title: IM001 VN1203 10^4pfu D2 4

value: Female


title: IM001 VN1203 10^4pfu D2 5


title: Infant at timeA, rep86

source_name: Infant at 4-6 days of life rep 86


title: Infant at timeA, rep95

source_name: Infant at 4-6 days of life rep 95

value: 1 (on oxygen at the age of 36 wpma)

value: 3 (severe BPD)

value: 2 (ROP which need laser therapy)

value: 1 (laser therapy  due to prethreshold or threshold ROP)


title: Infant at timeA, rep92

source_name: Infant at 4-6 days of life rep 92

value: 0 (finished oxygen therapy earlier than the age of 36 wPMA)


title: Infant at timeA, rep83

source_name: Infant at 4-6 days of life rep 83

value: 1 (oxygen therapy =>28 days)


title: Infant at timeA, rep80

source_name: Infant at 4-6 days of life rep 80


title: Infant at timeA, rep98

source_name: Infant at 4-6 days of life rep 98


title: Infant at timeA, rep94

source_name: Infant at 4-6 days of life rep 94


title: Infant at timeA, rep85

source_name: Infant at 4-6 days of life rep 85


title: IM001 VN1203 10^4pfu D2 2

value: 2 day

value: 20 week old

value: Influenza A/VN/1203/04 infected with 10^4 PFU

value: lung


title: IM001 VN1203 10^4pfu D2 1


title: Infant at timeA, rep78

source_name: Infant at 4-6 days of life rep 78

value: blood

value: 1 (female)

value: 0 (no PVL)


title: Infant at timeA, rep74

source_name: Infant at 4-6 days of life rep 74

value: 0 (oxygen therapy <28 days)

value: 0 (no BPD)

value: 0 (no ROP)

value: 0 (no lasertherapy)


title: IM001 VN1203 10^4pfu D1 5

value: Female

value: 1 day


title: Infant at timeA, rep84

source_name: Infant at 4-6 days of life rep 84

value: 2 (male)

value: 1 (on oxygen at the age of 36 wpma)

value: 2 (moderate BPD)


title: Infant at timeA, rep72

source_name: Infant at 4-6 days of life rep 72

value: 1 (oxygen therapy =>28 days)

value: 3 (severe BPD)

value: 2 (ROP which need laser therapy)

value: 1 (laser therapy  due to prethreshold or threshold ROP)


title: IM001 VN1203 10^4pfu D1 4

value: 20 week old

value: Influenza A/VN/1203/04 infected with 10^4 PFU

value: lung


title: IM001 VN1203 10^4pfu D1 3


title: Infant at timeA, rep68

source_name: Infant at 4-6 days of life rep 68

value: blood

value: 1 (PVL)


title: Infant at timeA, rep64

source_name: Infant at 4-6 days of life rep 64

value: 0 (finished oxygen therapy earlier than the age of 36 wPMA)

value: 1 (mild BPD)

value: 0 (no PVL)


title: Infant at timeA, rep63

source_name: Infant at 4-6 days of life rep 63

value: 1 (female)

value: 0 (no ROP)

value: 0 (no lasertherapy)


title: IM001 VN1203 10^3pfu D7 3

value: Female

value: 7 day

value: Influenza A/VN/1203/04 infected with 10^3 PFU


title: IM001 VN1203 10^3pfu D7 2


title: Infant at timeA, rep69

source_name: Infant at 4-6 days of life rep 69

value: 1 (oxygen therapy =>28 days)


title: Infant at timeA, rep60

source_name: Infant at 4-6 days of life rep 60

value: 2 (male)

value: 0 (oxygen therapy <28 days)

value: 0 (no BPD)


title: Infant at timeA, rep58

source_name: Infant at 4-6 days of life rep 58


title: IM001 VN1203 10^4pfu D1 1

value: 1 day

value: 20 week old

value: Influenza A/VN/1203/04 infected with 10^4 PFU


title: Infant at timeA, rep59

source_name: Infant at 4-6 days of life rep 59

value: blood


title: Infant at timeA, rep67

source_name: Infant at 4-6 days of life rep 67

value: 0 (finished oxygen therapy earlier than the age of 36 wPMA)

value: 1 (ROP not requiring treatment)


title: Infant at timeA, rep54

source_name: Infant at 4-6 days of life rep 54

value: 0 (no PVL)


title: Infant at timeA, rep77

source_name: Infant at 4-6 days of life rep 77

value: 1 (mild BPD)

value: 2 (ROP which need laser therapy)

value: 1 (laser therapy  due to prethreshold or threshold ROP)


title: Infant at timeA, rep55

source_name: Infant at 4-6 days of life rep 55

value: 1 (female)

value: 0 (no ROP)

value: 0 (no lasertherapy)


title: Infant at timeA, rep66

source_name: Infant at 4-6 days of life rep 66

value: 1 (oxygen therapy =>28 days)


title: IM001 VN1203 10^4pfu D1 2

value: Female

value: lung


title: Infant at timeA, rep51

source_name: Infant at 4-6 days of life rep 51

value: 2 (male)

value: 1 (on oxygen at the age of 36 wpma)

value: 2 (moderate BPD)


title: IM001 VN1203 10^3pfu D4 5

value: 4 day

value: 20 week old

value: Influenza A/VN/1203/04 infected with 10^3 PFU


title: Infant at timeA, rep53

source_name: Infant at 4-6 days of life rep 53

value: blood

value: 0 (oxygen therapy <28 days)

value: 0 (finished oxygen therapy earlier than the age of 36 wPMA)

value: 0 (no BPD)


title: SM001 Mock D2 1

source_name: SM001 Mock D2 1

value: 2 day

value: Time-matched mock


title: Infant at timeA, rep71

source_name: Infant at 4-6 days of life rep 71

value: 1 (female)

value: 0 (no ROP)

value: 0 (no PVL)


title: Infant at timeA, rep62

source_name: Infant at 4-6 days of life rep 62

value: 0 (no lasertherapy)


title: Infant at timeA, rep52

source_name: Infant at 4-6 days of life rep 52

value: 1 (oxygen therapy =>28 days)

value: 1 (mild BPD)


title: Infant at timeA, rep56

source_name: Infant at 4-6 days of life rep 56

value: 1 (on oxygen at the age of 36 wpma)

value: 2 (ROP which need laser therapy)

value: 1 (laser therapy  due to prethreshold or threshold ROP)


title: Infant at timeA, rep57

source_name: Infant at 4-6 days of life rep 57

value: 2 (moderate BPD)

value: 1 (PVL)


title: IM001 VN1203 10^3pfu D4 3

value: Female

value: 4 day

value: 20 week old

value: Influenza A/VN/1203/04 infected with 10^3 PFU

value: lung


title: IM001 VN1203 10^3pfu D7 1

value: 7 day


title: Infant at timeA, rep49

source_name: Infant at 4-6 days of life rep 49

value: blood

value: 2 (male)

value: 0 (finished oxygen therapy earlier than the age of 36 wPMA)


title: Infant at timeA, rep50

source_name: Infant at 4-6 days of life rep 50

value: 1 (female)

value: 1 (ROP not requiring treatment)

value: 0 (no lasertherapy)

value: 0 (no PVL)


title: IM001 VN1203 10^3pfu D4 2


title: Infant at timeA, rep47

source_name: Infant at 4-6 days of life rep 47

value: 0 (oxygen therapy <28 days)

value: 0 (no BPD)

value: 0 (no ROP)


title: IM001 VN1203 10^3pfu D4 4


title: Infant at timeA, rep48

source_name: Infant at 4-6 days of life rep 48


title: Infant at timeA, rep45

source_name: Infant at 4-6 days of life rep 45

value: 1 (oxygen therapy =>28 days)

value: 1 (mild BPD)


title: IM001 VN1203 10^3pfu D4 1

value: Female

value: 4 day


title: Infant at timeA, rep44

source_name: Infant at 4-6 days of life rep 44

value: 2 (ROP which need laser therapy)

value: 1 (laser therapy  due to prethreshold or threshold ROP)

value: 1 (PVL)


title: Infant at timeA, rep40

source_name: Infant at 4-6 days of life rep 40

value: blood


title: Infant at timeA, rep39

source_name: Infant at 4-6 days of life rep 39

value: 2 (male)


title: Infant at timeA, rep42

source_name: Infant at 4-6 days of life rep 42


title: Infant at timeA, rep38

source_name: Infant at 4-6 days of life rep 38

value: 0 (finished oxygen therapy earlier than the age of 36 wPMA)


title: Infant at timeA, rep37

source_name: Infant at 4-6 days of life rep 37

value: 1 (female)


title: Infant at timeA, rep41

source_name: Infant at 4-6 days of life rep 41


title: IM001 VN1203 10^3pfu D2 4

value: 2 day

value: 20 week old

value: Influenza A/VN/1203/04 infected with 10^3 PFU

value: lung


title: IM001 VN1203 10^3pfu D2 5


title: Infant at timeA, rep36

source_name: Infant at 4-6 days of life rep 36

value: 0 (oxygen therapy <28 days)

value: 0 (no BPD)

value: 0 (no lasertherapy)

value: 0 (no PVL)


title: Infant at timeA, rep34

source_name: Infant at 4-6 days of life rep 34

value: 1 (oxygen therapy =>28 days)

value: 1 (mild BPD)

value: 1 (ROP not requiring treatment)


title: Infant at timeA, rep35

source_name: Infant at 4-6 days of life rep 35

value: 0 (no ROP)


title: IM001 VN1203 10^3pfu D2 2

value: Female


title: IM001 VN1203 10^3pfu D2 1


title: IM001 VN1203 10^3pfu D2 3


title: Infant at timeA, rep28

source_name: Infant at 4-6 days of life rep 28

value: blood

value: 2 (ROP which need laser therapy)

value: 1 (laser therapy  due to prethreshold or threshold ROP)

value: 1 (PVL)


title: Infant at timeA, rep31

source_name: Infant at 4-6 days of life rep 31

value: 1 (female)

value: 0 (finished oxygen therapy earlier than the age of 36 wPMA)


title: Infant at timeA, rep29

source_name: Infant at 4-6 days of life rep 29

value: 2 (male)


title: IM001 VN1203 10^3pfu D1 4

value: 1 day

value: 20 week old

value: Influenza A/VN/1203/04 infected with 10^3 PFU

value: lung


title: Infant at timeA, rep32

source_name: Infant at 4-6 days of life rep 32

value: 1 (on oxygen at the age of 36 wpma)

value: 3 (severe BPD)


title: IM001 VN1203 10^3pfu D1 3


title: Infant at timeA, rep24

source_name: Infant at 4-6 days of life rep 24

value: 1 (oxygen therapy =>28 days)

value: 1 (mild BPD)

value: 0 (no PVL)


title: Infant at timeA, rep11

source_name: Infant at 4-6 days of life rep 11

value: 1 (ROP not requiring treatment)

value: 0 (no lasertherapy)


title: Infant at timeA, rep19

source_name: Infant at 4-6 days of life rep 19

value: blood

value: 2 (ROP which need laser therapy)


title: Infant at timeA, rep15

source_name: Infant at 4-6 days of life rep 15

value: 1 (laser therapy  due to prethreshold or threshold ROP)


title: Infant at timeA, rep17

source_name: Infant at 4-6 days of life rep 17

value: 1 (PVL)


title: Infant at timeA, rep22

source_name: Infant at 4-6 days of life rep 22

value: 1 (female)


title: IM001 VN1203 10^3pfu D1 1

value: Female


title: Infant at timeA, rep12

source_name: Infant at 4-6 days of life rep 12

value: 2 (male)

value: 0 (finished oxygen therapy earlier than the age of 36 wPMA)

value: 0 (no ROP)


title: IM001 VN1203 10^2pfu D7 4

value: 7 day

value: 20 week old

value: Influenza A/VN/1203/04 infected with 10^2 PFU

value: lung


title: Infant at timeA, rep4

source_name: Infant at 4-6 days of life rep 4

value: 0 (oxygen therapy <28 days)

value: 0 (no BPD)


title: IM001 VN1203 10^3pfu D1 2

value: 1 day

value: Influenza A/VN/1203/04 infected with 10^3 PFU


title: Infant at timeA, rep8

source_name: Infant at 4-6 days of life rep 8

value: blood

value: 0 (no lasertherapy)

value: 0 (no PVL)


title: Infant at timeA, rep13

source_name: Infant at 4-6 days of life rep 13


title: IM001 VN1203 10^2pfu D4 5

value: 4 day


title: Infant at timeA, rep7

source_name: Infant at 4-6 days of life rep 7

value: 1 (female)

value: 1 (oxygen therapy =>28 days)

value: 1 (mild BPD)

value: 1 (PVL)


title: Infant at timeA, rep14

source_name: Infant at 4-6 days of life rep 14

value: 2 (male)

value: 1 (on oxygen at the age of 36 wpma)

value: 3 (severe BPD)

value: 2 (ROP which need laser therapy)

value: 1 (laser therapy  due to prethreshold or threshold ROP)


title: Infant at timeA, rep30

source_name: Infant at 4-6 days of life rep 30

value: 0 (oxygen therapy <28 days)

value: 0 (finished oxygen therapy earlier than the age of 36 wPMA)

value: 0 (no ROP)


title: Infant at timeA, rep23

source_name: Infant at 4-6 days of life rep 23

value: 0 (no BPD)


title: IM001 VN1203 10^2pfu D7 2

value: Female

value: 7 day

value: 20 week old

value: Influenza A/VN/1203/04 infected with 10^2 PFU

value: lung


title: Infant at timeA, rep6

source_name: Infant at 4-6 days of life rep 6

value: blood

value: 1 (ROP not requiring treatment)

value: 0 (no lasertherapy)


title: Infant at timeA, rep3

source_name: Infant at 4-6 days of life rep 3

value: 2 (male)

value: 0 (no PVL)


title: Infant at timeA, rep26

source_name: Infant at 4-6 days of life rep 26

value: 1 (oxygen therapy =>28 days)

value: 1 (on oxygen at the age of 36 wpma)

value: 3 (severe BPD)


title: IM001 VN1203 10^2pfu D7 1


title: IM001 VN1203 10^2pfu D7 3


title: IM001 VN1203 10^2pfu D4 4

value: 4 day


title: Infant at timeA, rep1

source_name: Infant at 4-6 days of life rep 1

value: 1 (female)

value: 0 (oxygen therapy <28 days)

value: 0 (finished oxygen therapy earlier than the age of 36 wPMA)


title: Infant at timeA, rep2

source_name: Infant at 4-6 days of life rep 2

value: 0 (no BPD)

value: 0 (no ROP)


title: IM001 VN1203 10^2pfu D2 4

value: Female

value: 2 day

value: 20 week old


title: IM001 VN1203 10^2pfu D4 3

value: Influenza A/VN/1203/04 infected with 10^2 PFU

value: lung


title: IM001 VN1203 10^2pfu D4 2


title: IM001 VN1203 10^2pfu D2 5


title: Infant at timeA, rep21

source_name: Infant at 4-6 days of life rep 21

value: blood


title: IM001 VN1203 10^2pfu D2 3


title: 6-HdhQ150-1016

city: CARDIFF

first: Peter

last: Giles

address: Heath Park

country: United Kingdom

institute: Cardiff University

description: Expression data from 6 month, HdhQ150 mouse

hyb_protocol: According to standard Affymetrix protocol

data_processing: The data were analyzed with Affymetrix Expression Console using the RMA algorithm

source_name: 6 month, HdhQ150, F

label_protocol: WT labeling kit (www.affymetrix.com)

growth_protocol: Not applicable

extract_protocol: TRIzol-chloroform extraction

treatment_protocol: Not applicable

tag: genotype/variation

value: 6 month

value: F

value: 129/Ola x C57BL6/J

value: caudate nucleus


title: 6-WT-1004

description: Expression data from 6 month, WT mouse

scan_protocol: According to standard Affymetrix protocol

source_name: 6 month, WT, M

value: wild-type

value: M


title: 18-WT-431

description: Expression data from 18 month, WT mouse

source_name: 18 month, WT, F

value: 18 month


title: 6-HdhQ150-1003

source_name: 6 month, HdhQ150, M


title: 6-WT-1002

description: Expression data from 6 month, WT mouse


title: 6-WT-1020

description: Expression data from 6 month, WT mouse

source_name: 6 month, WT, F


title: 6-HdhQ150-1001


title: 6-WT-1011

description: Expression data from 6 month, WT mouse


title: 6-WT-1018

description: Expression data from 6 month, WT mouse


title: 6-HdhQ150-1023


title: 18-WT-401

description: Expression data from 18 month, WT mouse


title: IM001 VN1203 10^2pfu D4 1

value: 4 day


title: IM001 VN1203 10^3pfu D1 5

value: 1 day

value: Influenza A/VN/1203/04 infected with 10^3 PFU


title: 18-WT-414

description: Expression data from 18 month, WT mouse


title: 6-HdhQ150-1017


title: IM001 VN1203 10^2pfu D2 2


title: IM001 VN1203 10^2pfu D1 5


title: IM001 VN1203 10^2pfu D2 1


title: 18-WT-400

description: Expression data from 18 month, WT mouse


title: 18-HdhQ150-412

description: Expression data from 18 month, HdhQ150 mouse

source_name: 18 month, HdhQ150, F


title: 18-HdhQ150-383


title: 18-HdhQ150-415


title: 12-WT-527

description: Expression data from 12 month, WT mouse

source_name: 12 month, WT, F

value: 12 month


title: 18-HdhQ150-426


title: 12-WT-508

description: Expression data from 12 month, WT mouse


title: IM001 VN1203 10^2pfu D1 4

value: Female


title: IM001 VN1203 10^2pfu D1 3


title: 12-WT-488

description: Expression data from 12 month, WT mouse


title: 12-HdhQ150-464

description: Expression data from 12 month, HdhQ150 mouse

source_name: 12 month, HdhQ150, F


title: 12-WT-454

description: Expression data from 12 month, WT mouse

source_name: 12 month, WT, M


title: 12-WT-461

description: Expression data from 12 month, WT mouse


title: 12-HdhQ150-526


title: IM001 VN1203 10^2pfu D1 2


title: 12-HdhQ150-462


title: 12-HdhQ150-451

source_name: 12 month, HdhQ150, M


title: IM001 VN1203 10^2pfu D1 1


title: 12-HdhQ150-487


title: IM001 Mock D7 1

source_name: IM001 Mock D7 1

value: 7 day

value: Time-matched mock


title: WT-5

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

description: This sample consists in 6 wildtype gonads without mesonephros

hyb_protocol: Following fragmentation and labeling, 3ug of DNA were hybridized for 17 hr at 45C on Mogene 1.0ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: data were analysed via the AMEN suite of tools using the module dedicated to Affymetrix Gene Array pre-processing with RMA as normalization method.

source_name: gonads

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 300 ng total RNA.

extract_protocol: RNeasy kit (Qiagen) extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Individual gonads without mesonephros dissected from E13.5 embryos were snap frozen at -80°C

value: wildtype

value: C57BL6/J crossed with 129 on a mixed background


title: IM001 Mock D7 3

source_name: IM001 Mock D7 3

value: 20 week old

value: lung


title: 12-HdhQ150-453


title: IM001 Mock D7 2

source_name: IM001 Mock D7 2


title: KO-3

description: this sample consists in 12 gonads from sox9flox/flox; sf1: creTr/+ mice without mesonephros

value: Sox9flox/flox; Sf1:creTr/+


title: KO-6


title: IM001 Mock D4 2

source_name: IM001 Mock D4 2


title: KO-4


title: WT-2


title: IM001 Mock D4 1

source_name: IM001 Mock D4 1


title: IM001 Mock D4 3

source_name: IM001 Mock D4 3


title: IM001 Mock D2 3

source_name: IM001 Mock D2 3

value: 2 day


title: IM001 Mock D2 1

source_name: IM001 Mock D2 1


title: Heart sedentary 7 day rep1

city: Gold Coast

middle: John

last: Ashton

state: QLD

address: University Drive

department: Health Sciences & Medicine

institute: Bond University

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were variance stabilized and robust spline normalized using the ‘lumi’ package in R/BioConductor

source_name: heart, sedentary, 7 days

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep RNA Amplification Kit from Ambion

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

value: male

value: 8 weeks

value: whole heart

value: sedentary


title: Heart sedentary 7 day rep5

description: replicate 5


title: Heart sedentary 7 day rep4

description: replicate 4


title: Heart exercised 7 day rep4

description: replicate 4

source_name: heart, exercised, 7 days

value: exercised


title: IM001 Mock D2 2

source_name: IM001 Mock D2 2


title: Heart sedentary 7 day rep3

description: replicate 3


title: Heart sedentary 7 day rep6

description: replicate 6


title: IM001 Mock D1 3

source_name: IM001 Mock D1 3

value: 1 day


title: IM001 Mock D1 1

source_name: IM001 Mock D1 1


title: Heart exercised 7 day rep1

description: replicate 1


title: IM001 Mock D1 2

source_name: IM001 Mock D1 2


title: Heart exercised 7 day rep5

description: replicate 5


title: Heart exercised 7 day rep2

description: replicate 2


title: Heart exercised 7 day rep3

description: replicate 3


title: Heart sedentary 7 day rep2

description: replicate 2


title: WT-1


title: BT12

city: ALLSTON

first: Nicolaos

middle: Jay

last: Palaskas

state: MA

address: 15 North Beacon St #502

institute: UCLA

description: low

hyb_protocol: GeneChips were washed and stained in the Affymetrix Fluidics Station 450

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

data_processing: GCOS 1.3 was used to convert intensities using Expression Analysis settings :  Parameters -default  Baseline - default  Probemask - default  Normalization - all probe sets  Scaling - all probe sets

source_name: BREAST

growth_protocol: All cell line cultures were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) during FDG-uptake assays.

extract_protocol: QIAGEN Rneasy

treatment_protocol: In-vitro FDG uptake assays. 2 x 105 cells were seeded in triplicate on 6-well plates and incubated overnight in culture medium.  The next morning, the culture medium was removed from the 6-well plates and cells were incubated for 2 hours in fresh culture medium containing (18)F-FDG at a concentration of 0.5 μCi/ml.  The medium was aspirated, cells washed 3 times in PBS, trypsinized, and resuspended in culture medium.  Two thirds of the suspension was used for (18) F-FDG uptake determination by a gamma-counter (Wallac Wizard model 1480-11 with a 3” crystal). One third was reserved for viable cell number counts using the VI-Cell XR automated cell-viability analyzer (Beckmann Coulter).  Disintegrations per minute per cell were calculated for each well and the average of three wells was reported as the FDG uptake for each cell line.

tag: cell type

value: primary tumor

tag: fdg uptake

value: low


title: Heart exercised 7 day rep6

description: replicate 6

tag: strain


title: Mouse Dendritic & Antigen Presenting Cell in the context of Ccl17, 1

city: Aachen

first: Alma

last: Dr. Zernecke

address: Pauwelsstr. 30

country: Germany

institute: IMCAR

description: The JPG pictures of the scaned array membranes were evaluated with GEArray Expression Analysis Suite 2.0.

hyb_protocol: The array filters were hybridized with these biotin-labeled targets (5µg/array) at 60°C for 17 hours. Filters were first washed with 2 x SSC/1% SDS and then with 0.1 x SSC/1% SDS at 60°C for 15 minutes each. Chemilumilescent detection steps were performed by subsequent incubation of the filters with alkaline phosphatase– conjugated streptavidin and CDP-Star substrate.

scan_protocol: The images were captured using LAS 3000 (Fuji). One picture per 5 minutes was taken over a period of 60 minutes.With multi gauge 3.0 the pictures were converted into JPG.

data_processing: For quantification, intensity of signal was first measured using GEArray Expression Analysis Suite 2.0 (SuperArray) with a local background subtraction method. These subtracted intensities were then normalized via house-keeping genes and negative controls (e.g. Blanks) to obtain a relative intensity for each spot. A spot is considered "Present" if its stretched average is greater then its stretched local background, and the average density of the spot is greater than 1.5x of the mean value of the local backgrounds of the lower 75 percentile of all non-bleeding spots. All other spots are considered Absent.  A spot is considered "Bleeding" if the average density of the spot is greater than 75% of the maxim average value of all spots and its stretched average differs from its stretched local background value by less then 50%. These relative intensities were used to compare samples.

source_name: bone marrow-derived DCs, unstimulated

label_protocol:
Biotin-labeled cRNAs, known as labeled cRNA targets, were generated using TrueLabeling-AMP Linear RNA Amplification Kit following manufacturer’s protocol (SuperArray Bioscience Corporation). Briefly, total RNA (5 µg/array) was first converted to cDNA at 42°C for 50 minutes. These cDNAs were then in vitro transcribed
to cRNAs in the presence of biotin-16-UTP (Roche). Biotin-labeled cRNAs were purified using a RNeasy Mini Kit (Qiagen). The concentration of cRNAs was measured with a NanoDrop spectrometer.

extract_protocol: Total RNAs from indicated cells were isolated using QIAGEN RNeasy Mini Kit by following the manufacturer’s instructions.

tag: bone marrow generated dcs from a ccl17 homozygous mouse

value: sorted for GFP+ cells.


title: Mouse Dendritic & Antigen Presenting Cell in the context of Ccl17, 2

tag: bone marrow generated dcs from a heterozygous ccl17 mouse


title: BT09

description: low


title: BT08

description: high

value: high


title: BT07

description: low


title: BT10

description: low


title: Day 18 pregnant, biological replicate 4

city: Lindau

first: Stefan

middle: Michael

last: Bauersachs

state: Zurich

address: Eschikon 27 EHB 23.1

department: Department for Farm Animals

country: Switzerland

institute: University of Zurich

description: endometrial tissue sample collected at day 18 of pregnancy after artificial insemination

hyb_protocol: For the hybridization, wash and staining process the GeneChip® Hybridization, Wash, and Stain Kit (Affymetrix) was used. GeneChips were processed using the Fluidics Station 450 (Affymetrix). All steps were done according to the manufacturer’s protocol.

scan_protocol: The processed arrays were scanned with a GeneChip® Scanner 3000 with AutoLoader (Affymetrix).

data_processing: Affymetrix CEL files were processed with the robust multi-array average (RMA) method (Irizarry et al. Biostatistics 2003). Quality control was done using a variety of tools, such as pseudo images (BioC package AffyPLM), RNA degradation plots (BioC package Affy), different box plots, distance matrices and heatmaps. Probe sets were filtered based on expression calls before significance analysis.

organism: Bos taurus

source_name: intercaruncular endometrium, day 18 of pregnancy

label_protocol: Preparation of hybridization probes (biotinylated cRNA) for Affymetrix GeneChip® Bovine Genome Arrays (Affymetrix, Santa Clara, USA) was performed using 10 µg total RNA and the One-Cycle Target Labeling and Control Reagent package (Affymetrix).

growth_protocol: Bavarian Simmental heifers, synchronized by an intramuscular injection of a single dose of 500 µg Cloprostenol (PGF2α, Estrumate®, Intervet, Munich, Germany) at diestrus

extract_protocol: Total RNA was isolated using Trizol reagent (Invitrogen) according to the manufactorer's recommendations. The quantity and quality of total RNA were determined by spectrometry, agarose gel electrophoresis and Agilent 2100 Bioanalyzer, respectively.

treatment_protocol: Experiment I: In the IFNA treatment group, a rod-shaped human IFNA-releasing lipid extrudate was loaded in PBS into a 0.50-ml artificial insemination straw and non-surgically (via the cervix) transferred into the uterine horn ipsilateral to the functional CL on day 14 using an insemination pipette. The placebo group received only the rod-shaped lipid extrudate, whereas the control group received PBS only. Based on in vitro release experiments, IFNA concentration and lipid formulation was adjusted to release 8-9x107 IU of IFNA over a period of two days. On day 16 of the estrous cycle, uteri were non-surgically flushed with 10 ml of PBS using an embryo-flushing catheter (Minitüb, type Dissi, CH12, Tiefenbach, Germany). After flushing, six (±1) endometrial biopsy samples were collected per animal from the ipsilateral horn by the use of an uterine biopsy forceps (Richard Wolf, type 8151.07, 450 mm in length, 2.2 mm in diameter, Knittlingen, Germany), which was non-surgically inserted into the uterine horn through a self-shortened transcervical plastic cannula (Henry Schein, type bovivet, Hamburg, Germany) under rectal palpation control. Experiment II: Animals of the insemination group were inseminated on day 1 with cryo-conserved sperm (ejaculate + diluter 1:10) of the same bull and slaughtered at days 12, 15, or 18. Cyclic control animals received sperm-free supernatant of centrifuged sperm and were also slaughtered at days 12, 15, or 18. The sperm supernatant was refrigerated at -20°C and warmed up to room temperature before use. In animals slaughtered at day 12, the uteri were flushed with PBS before opening to determine the presence of a blastocyst. Immediately afterwards each uterine horn was prepared and opened longitudinally. The embryo was identified in the collection medium under a stereomicroscope and carefully transferred into RNAlater™. In animals slaughtered on days 15 and 18 after insemination, conceptuses were carefully removed after opening the uteri and stored in RNAlater™. Endometrial tissue samples were collected from the uterine horns ipsilateral to the functional CL; from the cranial uterine part for day 12 animals, from the middle part for day 15 animals, and from the caudal part for day 18 animals. Samples were carefully cut out from the lamina propria of the intercaruncular endometrium with a scalpel and immediately transferred into vials containing 4 ml RNAlater™.

value: female

tag: breed

value: Bavarian Simmental

tag: localization

value: ipsilateral, caudal

tag: treatment group

value: artificial insemination

tag: pregnant

value: yes


title: BT05

description: high


title: Day 18 pregnant, biological replicate 2

tag: gender


title: Day 18 non-pregnant control, biological replicate 3

description: endometrial tissue sample collected at day 18 of estrous cycle after sham insemination

source_name: intercaruncular endometrium, day 18 of cycle

value: sham insemination

value: no


title: Day 18 pregnant, biological replicate 3


title: BT11

description: high


title: Day 18 non-pregnant control, biological replicate 4


title: BT03

description: high


title: Day 18 non-pregnant control, biological replicate 2


title: BT02

description: high


title: Day 18 pregnant, biological replicate 1


title: BT04

description: low


title: BT01

description: low