title: whole blood-MDD-basal-MDD09

description:
Basal gene expression in MDD patient.
MDD09_basal

value: male


title: whole blood-MDD-basal-MDD08

status: Public on Oct 05 2011

type: RNA

city: Amsterdam

first: sabine

last: Spijker

address: De Boelelaan 1085

department: Center for Neurogenomics and Cognitive Research

country: Netherlands

institute: Neuroscience Campus Amsterdam

description:
Basal gene expression in MDD patient.
MDD08_basal

hyb_protocol: From each subject, labeled cRNA (1.5 µg Cy3-labeled basal blood sample; 1.25 µg Cy-5 labeled LPS-stimulated blood sample) was hybridized for 15-17 h at 65 °C onto the 44K Human Agilent whole genome arrays according to the manufacturer’s protocol. After washing, the arrays were quick-dried using acetonitrile.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using two color scan setting for 1x44k array slides. Scan resolution 10 µm. PMT set to 100%.

data_processing: Signal intensities were extracted using Agilent Feature Extraction (v8.0). Data were analyzed with Limma (Bioconductor) using median signals and median background. Control spots were normalized, but were set not to influence normalization. Non-uniform signals were removed prior to further analysis. After background subtraction (Edwards, offset 30), within normalization (Loess) and between array normalization (Aquantile) data were exported to SPSS. Further data selection for inclusion consisted of the following criteria (in this order): 1) Signal intensities for any gene should be 1.3x background (> 6.8 (log2)), and have non-saturated levels (<15.7 (log2)); 2) In addition, for any gene the signal should be present in >80% of the control as well as in >80% of the MDD samples to avoid type-1 errors due to a limited number of participants in each group. Genes present in <80 % of MDD or control samples were given an absent-call. From the total of 41,675 spots, filtering resulted in 22,789 spots for the basal sample and 22,935 spots in the LPS-stimulated sample, with an overlap of 21,107 spots (>92%).

molecule: total RNA

organism: Homo sapiens

source_name: peripheral blood, basal

label_protocol: Labeling of RNA (1 µg) was according to the Agilent protocol (Agilent technologies, Palo Alto, USA). Using spectrophotometry, cRNA concentration and labeling efficiency were determined (Nanodrop ND-1000 UV-Vis Spectrophotometer, Nanodrop Technologies). For all subjects, the same set-up has been used with the basal sample labeled with Cy3 (green) and the LPS-stimulated sample labeled with Cy5 (red), except for one subject (MDD31). This excludes the possibility that differences between subjects are due to a color bias for which two-color arrays are known.

growth_protocol: NA.

extract_protocol: RNA was prepared using PAX (PreAnalytiX; Qiagen) gene blood collection tubes following the manufacturer's recommendations (after thawing of the PAX tubes for 2 h at room temperature). The protocol includes lysis of blood cells, digestion of proteins (prot K treatment), and an on-column DNaseI digestion. The purity of RNA was first determined by spectrophotometry (NanoDrop ND–1000 UV-Vis Spectrophotometer, Nanodrop Technologies). Because of contaminants due to the isolation procedure, visible in the spectrophotogram at 200-230 nm, RNA samples were precipitated using ethanol, and NaAc with addition of 0.1 µg linear acryl-amide. Subsequently, RNA quality was determined by spectrophotometry and by using the RNA 6000 NanoChip kit on an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). Only RNA passing quality control criteria (RIN values > 8) was used for further analysis.

treatment_protocol:
Serial venous whole blood samples were obtained between 8:00 a.m. and 10:00 a.m., after overnight fasting, in one 7 ml heparin-coated tube (Greiner). Between 10-60 minutes after blood draw, 2.5 ml of blood was transferred into a PAXgene tube (Qiagen) and used as the basal (non-LPS stimulated) sample. This tube was kept at room temperature for a minimum of 2 h, and subsequently stored at –20 °C. The remaining blood (4.5 ml) was stimulated by addition of LPS (10 ng/ml blood; E. coli, Sigma). LPS-stimulated samples were laid flat and incubated at a slow rotation for 5-6 h at 37° C before a 2.5 ml sample of this LPS-stimulated blood was transferred into a PAXgene tube (Qiagen), and treated as described for the basal sample.

Patients were arbitrarily selected from all patients to serve as primary cohort (nMDD = 21 (#MDD01-MDD21); nControls = 21 (#Con01-Con21)), or replication cohort (nMDD = 12 (#MDD22-35); nControls = 13 (#Con22-37)) using microarrays.

tag: tissue

value: whole blood

tag: gender

tag: age

tag: smoking status

value: quit smoking

tag: disease

value: major depressive disorder (MDD)

tag: sample type

value: patient

tag: treatment


title: Ma70-3

city: Albany

first: Debbie

last: Laudencia-Chingcuanco

state: CA

address: 800 Buchanan Street

department: Western Regional Research Center

country: USA

institute: USDA-ARS

description: SAMPLE 72

hyb_protocol: Microarray slides were hybridized to Biotin-labelled RNA using Affymetrix standard protocol

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 from Affymetrix

data_processing: The data were analyzed with GeneSpring GX using RMA as normalization method.

label: Biotin

organism: Triticum aestivum

source_name: Crown

label_protocol: The RNA was labelled with biotin according to standard Affymetrix protocol

extract_protocol: RNA was isolated using TRIZOL following the protocol recommended by the manufacturer

treatment_protocol: Wheat seedlings at 3-leaf stage were cold treated at 6 degree centigrade for 0, 2, 14, 28, 35, 42, 56 and 70 days.

tag: genotype/variation

value: spring Manitou

tag: developmental stage

value: seedling (3-leaf stage)

tag: biorep

tag: stress

value: low temperature

tag: time (duration of cold-treatment)

value: 70 days


title: No02-1

description: SAMPLE 76

value: winter Norstar

value: 2 days


title: Ma70-2

description: SAMPLE 71


title: Bone marrow transduced with CALM(400-648)+AF10 (677-758), biological replicate-1

city: Ulm

first: Karlheinz

last: Holzmann

address: Helmholtzstreet 8/1

department: Medical Faculty

country: Germany

institute: Ulm University

description: Gene expression data from bone marrow cells 96 hours post-transdution with CALM(400-648)+AF10 (677-758)

hyb_protocol: accoring to the recommended protocol followed by washing at a Fluidics Station 450 using fluidics script FS450_0003

scan_protocol: according to Affymetrix protocols using a GeneChip 3000 Scanner

data_processing: Data were processed using the miRNAQC tool from Affymetrix following the recommended workflow from Genisphere (Background Detection -> RMA Global Background Correction -> Quantile Normalization -> Median polish Summarization); Statistical analysis was done using BRB Array-Tools Software by Richard Simon

label: biotin

organism: Mus musculus

source_name: Adult mouse bone marrow

label_protocol: Samples were labeled using the FlashTag™ Biotin HSR Kit from Genisphere starting with 1µg of totel RNA according to the protocol of the manufaturer

growth_protocol: Adult C57/BL6/C3H mice were injected with 30µg/µl working solution of 5-Fluorouracil (100µl per 20gr of weight) to enrich for stem and progenitor cells. Four days post injection, total bone marrow

extract_protocol: Total RNA was extracted from FACS sorted GFP+ cells using the Qiagen miRNeasy Mini Kit For purification of microRNA and total RNA from tissues and cells per manufacturer's instructions

treatment_protocol: After 48 hours of pre-stimulation, the BM cells were transduced with different viruses, containing the relevent constructs, by overlaying them on virus-producing irradiated (40 Gy) GFP+E86 producers in the presence of cytokines and protamine sulfate (5ug/ml). The transduction was stopped by removing the BM cells from the GFP+E86 cells and plating them in BM medium with cytokines for another 48 hours to allow for GFP expression. Retrovirally transduced cells were FACS sorted based on expression of GFP.

tag: strain

tag: cell type

value: bone marrow cells

tag: transducer


title: No00-3

description: SAMPLE 75

value: control

value: 0 days


title: whole blood-MDD-basal-MDD05

description:
Basal gene expression in MDD patient.
MDD05_basal

value: female


title: whole blood-MDD-basal-MDD06

description:
Basal gene expression in MDD patient.
MDD06_basal

value: non-smoking


title: whole blood-MDD-basal-MDD03

description:
Basal gene expression in MDD patient.
MDD03_basal


title: Ma56-3

description: SAMPLE 69

value: 56 days


title: whole blood-MDD-basal-MDD02

description:
Basal gene expression in MDD patient.
MDD02_basal

value: smoking


title: Bone marrow transduced with CALM-AF10 ΔOM-LZ, biological replicate-2

description: Gene expression data from bone marrow cells 96 hours post-transdution with CALM-AF10 ΔOM-LZ

value: CALM-AF10 ΔOM-LZ


title: Ma56-2

description: SAMPLE 68


title: Ma56-1

description: SAMPLE 67


title: Ma42-2

description: SAMPLE 65

value: 42 days


title: whole blood-MDD-basal-MDD01

description:
Basal gene expression in MDD patient.
MDD01_basal

value: whole blood

value: male

value: major depressive disorder (MDD)


title: Ma42-1

description: SAMPLE 64

value: spring Manitou

value: seedling (3-leaf stage)


title: Bone marrow transduced with CALM-AF10 ΔOM-LZ, biological replicate-1


title: Bone marrow transduced with CALM-AF10, biological replicate-3

description: Gene expression data from bone marrow cells 96 hours post-transdution with CALM-AF10


title: Bone marrow transduced with CALM-AF10, biological replicate-2


title: Ma42-3

description: SAMPLE 66

value: low temperature


title: Ma35-3

description: SAMPLE 63

value: 35 days


title: Ma35-2

description: SAMPLE 62


title: whole blood-control-basal-CON37

description:
Basal gene expression in healthy control.
CON37_basal

value: healthy


title: Bone marrow transduced with MIG, biological replicate-2

description: Gene expression data from bone marrow cells 96 hours post-transdution with MIG

value: bone marrow cells

value: MIG


title: Ma21-3

description: SAMPLE 60

value: 21 days


title: whole blood-control-basal-CON36

description:
Basal gene expression in healthy control.
CON36_basal

value: quit smoking

value: control


title: Bone marrow transduced with MIG, biological replicate-3


title: Bone marrow transduced with CALM-AF10, biological replicate-1


title: Ma14-3

description: SAMPLE 57

value: 14 days


title: Ma35-1

description: SAMPLE 61


title: whole blood-control-basal-CON32

description:
Basal gene expression in healthy control.
CON32_basal


title: Ma21-1

description: SAMPLE 58


title: Ma02-3

description: SAMPLE 54

value: 2 days


title: Ma14-1

description: SAMPLE 55


title: Ma21-2

description: SAMPLE 59


title: Ma14-2

description: SAMPLE 56


title: Bone marrow transduced with MIG, biological replicate-1


title: whole blood-control-basal-CON31

description:
Basal gene expression in healthy control.
CON31_basal

value: female

value: non-smoking


title: whole blood-control-basal-CON30

description:
Basal gene expression in healthy control.
CON30_basal

value: whole blood


title: Ma02-2

description: SAMPLE 53


title: Ma00-2

description: SAMPLE 50

value: 0 days


title: Macrophage_PBS_rep2

city: Herston

first: Melissa

middle: Louise

last: Burke

state: QLD

address: 300 Herston Road

department: Division of Infectious Diseases and Immunology

country: Australia

institute: Queensland Institute of Medical Research

description:
4531950149_A_PBSR2
Gene expression in peritoneal macrophages stimulated with PBS

hyb_protocol: cRNA was hybridised to Illumina mouse-6 v2 expression beadchips according to the manufacturers instructions

scan_protocol: Microarrays were scanned using a Beadstation 500 at Green factor level 2

data_processing:
Data was analysed using GenomeStudio version 1.1.1 and Genespring GX 11
Values reported were derived using Illumina GenomeStudio version 1.1.1 and GenesSpring GX 11. Non-normalised data represent relative signal intensity; normalised data are shown as log base two of data normalised to the 75th percentile.

source_name: Peritoneal macrophages stimulated three times by intraperitoneal injection with PBS

label_protocol: cRNA was synthesised from total RNA with an Illumina Total Prep RNA Amplification Kit (Ambion Inc., USA) according to the manufacturers instructions

extract_protocol: Total RNA was extracted from the macrophages by phase separation with Trizol (Invitrogen, USA) and column chromatography using an Rneasy Mini kit (Qiagen Inc, USA), RNA quantity was measured using a Nanodrop (Nanodrop Technologies, USA) and quality was assessed using an Agilent Bioanalyzer Nanochip (Agilent Technologies, USA)

treatment_protocol: Six- to eight-week-old female BALB/c mice  were exposed three times on alternate days by intraperitoneal (IP) injection with 5μg of Schistosoma japonicum-derived soluble egg antigen (n=6) or sterile PBS as a control (n=6). Peritoneal exudate cells (PECs) were collected one day after final challenge by peritoneal lavage with 5mL sterile PBS. PECs were pelleted, counted using a haemocytometer, and resuspended to a concentration of 5 x 105 cells/mL in RPMI. Macrophages were purified from PECs by adherence to 6-well plastic tissue culture plates for 3 hrs at 37oC as described (Donnelly, Stack et al. 2008). Non-adherent cells were removed by washing three times with ice-cold PBS. Adherent macrophages were removed with a cell scraper, washed and resuspended in RPMI, counted, pooled, pelleted and resuspended in Trizol (Invitrogen, USA) for total RNA extraction. The experiment was performed twice creating two biological replicates (R1 and R2).

value: BALB/c

value: PBS


title: Ma00-3

description: SAMPLE 51

value: spring Manitou

value: seedling (3-leaf stage)


title: whole blood-control-basal-CON28

description:
Basal gene expression in healthy control.
CON28_basal

value: smoking


title: whole blood-control-basal-CON29

description:
Basal gene expression in healthy control.
CON29_basal

value: male

value: healthy


title: 8S70-2

description: SAMPLE 47

value: spring Norstar

value: low temperature

value: 70 days


title: Macrophage_SEA_rep2

description:
4531950149_E_SEAR2
Gene expression in peritoneal macrophages stimulated with SEA

source_name: Peritoneal macrophages stimulated three times by intraperitoneal injection with SEA

value: SEA


title: Ma00-1

description: SAMPLE 49

value: control


title: 8S70-3

description: SAMPLE 48


title: Ma02-1

description: SAMPLE 52

value: 2 days


title: Macrophage_PBS_rep1

description:
4466975090_A_PBSR1
Gene expression in peritoneal macrophages stimulated with PBS

value: female


title: 8S56-3

description: SAMPLE 45

value: 56 days


title: whole blood-control-basal-CON26

description:
Basal gene expression in healthy control.
CON26_basal

value: whole blood

value: non-smoking


title: Macrophage_SEA_rep1

description:
4466975090_E_SEAR1
Gene expression in peritoneal macrophages stimulated with SEA

value: BALB/c


title: 8S70-1

description: SAMPLE 46


title: whole blood-control-basal-CON24

description:
Basal gene expression in healthy control.
CON24_basal


title: 8S56-1

description: SAMPLE 43


title: 8S42-3

description: SAMPLE 42

value: 42 days


title: whole blood-control-basal-CON25

description:
Basal gene expression in healthy control.
CON25_basal


title: d8 PSGL1hi Ly6Clo 3

city: New Haven

first: Hailong

last: Meng

state: CT

address: 300 George Str

institute: Yale University

description: CD4 T Cell

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with lumi in R

source_name: Splenocytes

label_protocol: Double stranded cDNA and biotin-labeled cRNA was synthesized and purified from 500 ng of total RNA.  Purification of the cRNA and integrity of the cRNA was be assessed by running aliquots on the Bioanalyzer prior to hybridization.   Hybridization buffer from the BeadChip kit (Illumina) was mixed with 1500 ng of biotin-labeled cRNA, heated to 65°C for 5 minutes, and then loaded onto the BeadChip.  The BeadChips were sealed in a hybridization chamber and placed in an oven at 58°C with a rocker for 16-20 hours.  After the hybridization, the BeadChips were washed and stained in a series of washes and stains as outlined in the Illumina protocol.  The BeadChips were scanned on the Illumina Iscan.

extract_protocol: RNA was isolated with RNeasy mini elute kit (QIAGEN, Valencia, CA)

value: Smarta

value: d8 PSGL1hi Ly6Clo CD4 T Cell


title: 8S56-2

description: SAMPLE 44

value: seedling (3-leaf stage)


title: d8 PSGL1hi Ly6Clo 1

description: CD4 T Cell


title: d8 PSGL1hi Ly6Clo 2

description: CD4 T Cell


title: 8S42-1

description: SAMPLE 40


title: 8S42-2

description: SAMPLE 41


title: 8S35-3

description: SAMPLE 39

value: 35 days


title: whole blood-control-basal-CON27

description:
Basal gene expression in healthy control.
CON27_basal

value: smoking

value: healthy


title: 8S35-2

description: SAMPLE 38

value: spring Norstar

value: low temperature


title: 8S21-3

description: SAMPLE 36

value: 21 days


title: d8 PSGL1hi Ly6Chi 2

description: CD4 T Cell

value: d8 PSGL1hi Ly6Chi CD4 T Cell


title: whole blood-control-basal-CON21

description:
Basal gene expression in healthy control.
CON21_basal

value: male

value: control


title: 8S21-1

description: SAMPLE 34


title: 8S14-1

description: SAMPLE 31

value: 14 days


title: whole blood-control-basal-CON19

description:
Basal gene expression in healthy control.
CON19_basal

value: whole blood

value: quit smoking


title: 8S14-2

description: SAMPLE 32


title: 8S21-2

description: SAMPLE 35


title: 8S02-2

description: SAMPLE 29

value: 2 days


title: d8 PSGL1lo Ly6Clo 2

description: CD4 T Cell

value: d8 PSGL1lo Ly6Clo CD4 T Cell


title: whole blood-control-basal-CON17

description:
Basal gene expression in healthy control.
CON17_basal

value: female


title: 8S02-1

description: SAMPLE 28


title: 8S14-3

description: SAMPLE 33


title: 8S02-3

description: SAMPLE 30


title: whole blood-control-basal-CON18

description:
Basal gene expression in healthy control.
CON18_basal


title: day 60 memory PSGL1hi 3

description: CD4 T Cell

value: Smarta

value: day 60 memory PSGL1hi CD4 T Cell


title: d8 PSGL1hi Ly6Chi 3

description: CD4 T Cell


title: d8 PSGL1hi Ly6Chi 1

description: CD4 T Cell


title: whole blood-control-basal-CON23

description:
Basal gene expression in healthy control.
CON23_basal


title: 8S35-1

description: SAMPLE 37

value: seedling (3-leaf stage)

value: 35 days


title: whole blood-control-basal-CON22

description:
Basal gene expression in healthy control.
CON22_basal

value: non-smoking

value: healthy


title: 8S00-2

description: SAMPLE 26

value: spring Norstar

value: 0 days


title: 8S00-3

description: SAMPLE 27


title: whole blood-control-basal-CON16

description:
Basal gene expression in healthy control.
CON16_basal


title: 12W70-3

description: SAMPLE 24

value: winter Manitou

value: low temperature

value: 70 days


title: d8 PSGL1lo Ly6Clo 1

description: CD4 T Cell


title: whole blood-control-basal-CON20

description:
Basal gene expression in healthy control.
CON20_basal

value: control


title: 8S00-1

description: SAMPLE 25


title: day 60 memory PSGL1hi 2

description: CD4 T Cell


title: Naive 3

description: CD4 T Cell

value: Naive CD4 T Cell


title: 12W70-1

description: SAMPLE 22


title: whole blood-control-basal-CON13

description:
Basal gene expression in healthy control.
CON13_basal

value: whole blood

value: smoking


title: whole blood-control-basal-CON15

description:
Basal gene expression in healthy control.
CON15_basal

value: male


title: whole blood-control-basal-CON12

description:
Basal gene expression in healthy control.
CON12_basal

value: female


title: 12W56-3

description: SAMPLE 21

value: 56 days


title: 12W56-1

description: SAMPLE 19


title: Naive 2

description: CD4 T Cell

value: Smarta


title: day 60 memory PSGL1hi 1

description: CD4 T Cell

value: day 60 memory PSGL1hi CD4 T Cell


title: 12W42-2

description: SAMPLE 17

value: seedling (3-leaf stage)

value: 42 days


title: 12W56-2

description: SAMPLE 20


title: Naive 1

description: CD4 T Cell


title: 12W70-2

description: SAMPLE 23


title: 12W35-3

description: SAMPLE 15

value: 35 days


title: whole blood-control-basal-CON14

description:
Basal gene expression in healthy control.
CON14_basal

value: non-smoking

value: healthy


title: whole blood-control-basal-CON11

description:
Basal gene expression in healthy control.
CON11_basal


title: 12W42-3

description: SAMPLE 18

value: winter Manitou


title: Bone marrow transduced with CALM(400-648)+AF10 (677-758), biological replicate-3

description: Gene expression data from bone marrow cells 96 hours post-transdution with CALM(400-648)+AF10 (677-758)

hyb_protocol: according to Affymetrix Whole Transcript (WT) Sense Target Labeling Assay

data_processing: Affymetrix® Expression Console™ Software for normalization, BRB Array Tools for statistical analysis

value: bone marrow


title: 12W42-1

description: SAMPLE 16

value: low temperature


title: 12W35-2

description: SAMPLE 14


title: 12W35-1

description: SAMPLE 13


title: Bone marrow transduced with CALM(400-648)+AF10 (677-758), biological replicate-2

label_protocol: Whole Transcript (WT) Sense Target Labeling Assay


title: 12W21-2

description: SAMPLE 11

value: 21 days


title: whole blood-control-basal-CON09

description:
Basal gene expression in healthy control.
CON09_basal

value: control


title: whole blood-control-basal-CON10

description:
Basal gene expression in healthy control.
CON10_basal

value: whole blood


title: 12W21-3

description: SAMPLE 12


title: 12W21-1

description: SAMPLE 10


title: whole blood-control-basal-CON08

description:
Basal gene expression in healthy control.
CON08_basal

value: quit smoking


title: Bone marrow transduced with CALM-AF10 ΔOM-LZ, biological replicate-3

description: Gene expression data from bone marrow cells 96 hours post-transdution with CALM-AF10 ΔOM-LZ

value: CALM-AF10 ΔOM-LZ


title: 12W14-1

description: SAMPLE 7

value: 14 days


title: 12W14-3

description: SAMPLE 9


title: 12W14-2

description: SAMPLE 8


title: whole blood-control-basal-CON07

description:
Basal gene expression in healthy control.
CON07_basal

value: female


title: 12W00-2

description: SAMPLE 2

value: 0 days


title: 12W00-3

description: SAMPLE 3


description: Gene expression data from bone marrow cells 96 hours post-transdution with CALM-AF10


title: whole blood-control-basal-CON05

description:
Basal gene expression in healthy control.
CON05_basal

value: smoking


title: whole blood-control-basal-CON04

description:
Basal gene expression in healthy control.
CON04_basal


title: whole blood-control-basal-CON02

description:
Basal gene expression in healthy control.
CON02_basal


title: 12W02-2

description: SAMPLE 5

value: seedling (3-leaf stage)

value: 2 days


title: 12W02-3

description: SAMPLE 6


title: 12W02-1

description: SAMPLE 4


title: whole blood-control-basal-CON03

description:
Basal gene expression in healthy control.
CON03_basal


title: whole blood-control-basal-CON06

description:
Basal gene expression in healthy control.
CON06_basal


title: 12W00-1

description: SAMPLE 1


description: Gene expression data from bone marrow cells 96 hours post-transdution with MIG

value: MIG


title: whole blood-control-basal-CON01

description:
Basal gene expression in healthy control.
CON01_basal

value: male


title: arrested 1-cell embryo

status: Public on Oct 04 2011

city: New York

first: Dieter

middle: M

last: Egli

state: NY

address: 1150 St. Nicholas Avenue, room 607B, New York NY 10032

institute: Columbia University

description:
1 of 1 sample.
Sample 23

hyb_protocol: Hybridization according to Illumina protocols on an Illumina Sentrix Human Expression BeadChip RefSeq 8 v3.0. Arrays were hybridized, washed, blocked and stained with streptavidin-Cy3. The protocol is WGGEX Direct Hybridization Assay Guide (11322355 A).

scan_protocol: According to Illumina protocols with the BeadArray Reader.

data_processing: Analysis done using Illumina GenomeStudio program. Data were normalized to average signal. Background was subtracted. Samples with the same title were grouped, and groups were compared to each other to identify genes that were reliably up or downregulated. This was done to reduce noise originating from the amplification steps.

source_name: arrested 1-cell embryo (entered first mitosis, inhibition of first cytokinesis, arrested at the 2nd interphase)

label_protocol: A biotin label was introduced according to the protocols of the Illumina Total Prep RNA Amplification Kit.

growth_protocol: Human embryos were cultured in Global medium.

extract_protocol: PicoPure RNA isolation (Arcturus).

treatment_protocol: Embryos were allowed to develop after the manipulations. Somatic cells were harvested after growth to confluence. These same cells were used as donor cells for nuclear transfer.

value: embryonic

value: 1-cell embryo

tag: chip #

tag: array

value: H


title: vaccinated fish followed by challenge RNA sample_challenge_rep3

city: AUBURN

first: julia

last: pridgeon

state: AL

address: 990 WIRE ROAD

department: AAHRU

institute: USDA, ARS

description: This sample is of challenge vaccinated fish. It is the second of the two vaccinated fish replicates used in this experiment. Each sample is pooled from 5 fish.

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Ictalurus punctatus

source_name: challenged vaccinated channel catfish anterior kidney

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

extract_protocol: Total RNA was extracted using the RNeasy Plus Mini kit (Qiagen Inc., Valencia, CA, USA).

tag: genotype

value: wild type

tag: phenotype

value: normal

tag: tissue type

value: kidney


title: vaccinated fish followed by challenge RNA sample_challenge_rep1

description: This sample is of challenged vaccinated fish. It is the first of the two vaccinated fish replicates used in this experiment. Each sample is pooled from 5 fish.


value: bone marrow


title: vaccinated fish followed by challenge RNA sample_challenge_rep2


title: IVF control embryos d3, rep2

description:
2 of 2 samples.
Sample 21

source_name: IVF cleavage stage embryos harvested late on day 3 post fertilization

tag: tissue

value: IVF embryo

tag: days post-fertilization

value: E


title: somatic donor cell 1-011, rep2

description:
2 of 2 samples.
Sample 16

source_name: somatic donor cell ID 1-011

value: adult

value: skin


title: IVF control embryos d3, rep1

description:
1 of 2 samples.
Sample 20

value: D


title: amanitin-treated embryos, d3,  rep1

description:
1 of 2 samples.
Sample 17

source_name: amanitin-treated IVF embryos harvested late on day 3 post fertilization

value: amanitin

value: A


title: IVF control embryos d4, rep3

description:
3 of 3 samples.
Sample 12

source_name: IVF cleavage stage embryos harvested early on day 4 post fertilization


title: amanitin-treated embryos, d5, rep5

description:
5 of 5 samples.
Sample 9

source_name: amanitin-treated IVF embryos harvested day 5 post fertilization


title: amanitin-treated embryos, d5, rep4

description:
4 of 5 samples.
Sample 8

value: G


title: zygote nuclear transfer embryo, rep2

description:
2 of 2 samples.
Sample 19

source_name: zygote NT embryo harvested early on day 4 post fertilization

value: zygote

value: C


title: somatic donor cell 1-011, rep1

description:
1 of 2 samples.
Sample 15


title: IVF control embryos d4, rep2

description:
2 of 3 samples.
Sample 11

value: embryonic


title: zygote

description:
1 of 1 sample.
Sample 13

source_name: zygote harvested d1 post fertilization


title: amanitin-treated embryos, d5, rep1

description:
1 of 5 samples.
Sample 4


title: amanitin-treated embryos, d5, rep3

description:
3 of 5 samples.
Sample 7

value: F


title: abnormally cleaved embryo

description:
1 of 1 sample.
Sample 22

source_name: abnormally cleaved embryo harvested early on day 4 post fertilization

value: abnormally cleaved embryo


title: amanitin-treated embryos, d3,  rep2

description:
2 of 2 samples.
Sample 18

value: B


title: somatic donor cell 1-000, rep2

description:
2 of 2 samples.
Sample 3

source_name: fibroblast ID 1-000

value: skin fibroblast

value: H


title: IVF control embryos d4, rep1

description:
1 of 3 samples.
Sample 10


title: zygote nuclear transfer embryo, rep1

description:
1 of 2 samples.
Sample 14


title: human blastocyst, rep2

description:
2 of 2 samples.
Sample 6

source_name: human blastocysts day 5

value: blastocyst


title: human blastocyst, rep1

description:
1 of 2 samples.
Sample 1


title: amanitin-treated embryos, d5, rep2

description:
2 of 5 samples.
Sample 5

value: IVF embryo


title: somatic donor cell 1-000, rep1

description:
1 of 2 samples.
Sample 2


title: KMCHNSPZEB2

city: Bethesda

first: Daekwan

last: Seo

state: MD

address: 37 Convent Dr. Rm 4140

department: NCI

institute: NIH

description:
SAMPLE 33
replicate 2

data_processing: Data was processed by using Gene Expression Module v 1.1.1 in Genome Studio V2009.1 from illumina, Inc. The background noise was substrated and quantile normalization was applied.

source_name: KMCH

label_protocol: Biotinylated cRNA were prepared with the Ambion Totalprep RNA Amplification kit for Illumina arrays

growth_protocol: DMEM (+10% fetal bovine serum)

extract_protocol: Total RNA was extracted with Quiagen Rneasy Kit. Quality control and measurement were performed using NanoDrop and Agilent Bioanalyser.

treatment_protocol: 100uM Zebularine for 72h

tag: cell line

value: KMCH

value: non-side population


title: KMCHNSP2

description:
SAMPLE 27
replicate 2


title: KMCHSP3

description:
SAMPLE 31
replicate 3

value: side population


title: WRL68SPZEB1

description:
SAMPLE 23
replicate 1


title: KMCHSPZEB2

description:
SAMPLE 37
replicate 2


title: KMCHSPZEB3

description:
SAMPLE 38
replicate 3


title: KMCHNSPZEB4

description:
SAMPLE 35
replicate 4


title: WRL68NSPZEB3

description:
SAMPLE 22
replicate 3


title: KMCHSPZEB1

description:
SAMPLE 36
replicate 1


title: KMCHNSPZEB1

description:
SAMPLE 32
replicate 1


title: KMCHSP1

description:
SAMPLE 29
replicate 1


title: KMCHNSP3

description:
SAMPLE 28
replicate 3


title: WRL68SPZEB3

description:
SAMPLE 25
replicate 3


title: KMCHNSPZEB3

description:
SAMPLE 34
replicate 3


title: WRL68SPZEB2

description:
SAMPLE 24
replicate 2


title: KMCHNSP1

description:
SAMPLE 26
replicate 1


title: WRL68NSPZEB1

description:
SAMPLE 20
replicate 1


title: KMCHSP2

description:
SAMPLE 30
replicate 2


title: WRL68SP3

description:
SAMPLE 19
replicate 3


title: WRL68SP2

description:
SAMPLE 18
replicate 2


title: WRL68NSPZEB2

description:
SAMPLE 21
replicate 2


title: WRL68SP1

description:
SAMPLE 17
replicate 1


title: D1-6 lung microRNA

city: Ottawa

first: Andrew

last: Williams

state: ON

address: 50 Columbine

country: Canada

institute: Health Canada

description: microRNA

hyb_protocol: Freshly isolated individual lung total RNA samples (100 ng, n=5/group) from control and treated groups (150 and 300 mg/kg, 4 hour group) were dephosphorylated by incubation with calf intestinal phosphatase at 37ºC for 30 min, denatured using 100 % DMSO at 100ºC for 5 min, then labelled with pCp-Cy3 using T4 ligase by incubation at 16ºC for 1 hour (Agilent miRNA Complete Labelling and Hybridisation Kit, Agilent Tech, Mississauga, ON, Canada). Labelled RNA samples were hybridised to an individual array on 8 x 15K format Agilent mouse miRNA array slides, with each array containing probes for 567 mouse miRNAs and 10 mouse gamma herpes virus miRNAs. Hybridisations were performed in SureHyb chambers (Agilent) for 20 hours at 55ºC and washed according to the manufacturer’s instructions. Arrays were scanned at a resolution of 5 m using an Agilent G2505B scanner and data were acquired using Agilent Feature Extraction software version 9.5.3.1.

scan_protocol: Arrays were scanned at a resolution of 5 um using an Agilent G2505B scanner and data were acquired using Agilent Feature Extraction software version 9.5.3.1.

data_processing:
Non-background subtracted raw data were quantile normalized [56]. Present calls were determined as signals that were greater than 3 trimmed SDs above the trimmed mean of the (-)3xSLv1 probes on the array. Technical replicates for individual miRNAs were averaged using the median signal intensity. Boxplots and cluster analyses were used to identify potential outliers (poor quality chips). This quality control check resulted in the elimination of one array from the analysis. Identification of differentially expressed miRNAs was carried out on the probe level as well as the miRNA level. The MAANOVA model included the sample identity as a random effect and the gene specific variance estimate (F1 Test) was used to test for differences between the controls and treated samples. In this analysis, parametric p-values were obtained and were then FDR corrected.
Cy3 is the median of the technical replicates of the normalized signal intensity.  Flag = 1 indicates if the median signal intensity was absent.

source_name: Lung tissue

extract_protocol: The mirVana miRNA Isolation Kit (Ambion, Streetsville, ON, Canada) was used to isolate RNA from random left lung sections, according to the manufacturer’s protocol and as described in [29]. RNA quality and quantity was determined as described above.

treatment_protocol: Age matched adult male B6C3F1 mice (27-30 d, Charles Rivers Laboratories, St Constant, Quebec, Canada) were housed individually under a 12:12 h light: dark cycle with food and water available ad libitum. Mice were randomly assigned (6 per group) to a control or treatment group. Mice were treated with a daily dose of BaP in corn oil with 5, 50, 150 or 300 mg/kg (oral gavage, 10 ml/kg) for three consecutive days. Control mice received corn oil only. Mice were anaesthetized under isofluorane and sacrificed by exsanguination 4 or 24 hours after the last treatment. Right and left lung lobes were removed and immediately snap frozen and stored at -80ºC until use. Blood serum was collected as described below. All animal procedures were in accordance with the guidelines of the Canadian Council for Animal Care and approved by the Health Canada Animal Care Committee.

value: adult

tag: gender

value: male

value: lung

tag: treatment group

value: 300 mg/kg dose 4 hours


title: D2-5 lung microRNA

description: microRNA

label_protocol: Freshly isolated individual lung total RNA samples (100 ng, n=5/group) from control and treated groups (150 and 300 mg/kg, 4 hour group) were dephosphorylated by incubation with calf intestinal phosphatase at 37ºC for 30 min, denatured using 100 % DMSO at 100ºC for 5 min, then labelled with pCp-Cy3 using T4 ligase by incubation at 16ºC for 1 hour (Agilent miRNA Complete Labelling and Hybridisation Kit, Agilent Tech, Mississauga, ON, Canada). Labelled RNA samples were hybridised to an individual array on 8 x 15K format Agilent mouse miRNA array slides, with each array containing probes for 567 mouse miRNAs and 10 mouse gamma herpes virus miRNAs. Hybridisations were performed in SureHyb chambers (Agilent) for 20 hours at 55ºC and washed according to the manufacturer’s instructions. Arrays were scanned at a resolution of 5 m using an Agilent G2505B scanner and data were acquired using Agilent Feature Extraction software version 9.5.3.1.

tag: developmental stage

value: 150 mg/kg dose 4 hours


title: D2-7 lung microRNA

description: microRNA


title: D2-2 lung microRNA

description: microRNA


title: D2-6 lung microRNA

description: microRNA


title: D0-6 lung microRNA

description: microRNA

value: Control


title: D1-5 lung microRNA

description: microRNA


title: D1-3 lung microRNA

description: microRNA


title: D2-1 lung microRNA

description: microRNA


title: Huh7SPZEB2

description:
SAMPLE 12
replicate 2


title: WRL68NSP1

description:
SAMPLE 14
replicate 1


title: Huh7NSPZEB2

description:
SAMPLE 8
replicate 2


title: D1-2 lung microRNA

description: microRNA


title: WRL68NSP3

description:
SAMPLE 16
replicate 3


title: WRL68NSP2

description:
SAMPLE 15
replicate 2


title: Huh7NSPZEB4

description:
SAMPLE 10
replicate 4


title: Huh7SPZEB3

description:
SAMPLE 13
replicate 3


title: Huh7NSPZEB3

description:
SAMPLE 9
replicate 3


title: Huh7SPZEB1

description:
SAMPLE 11
replicate 1


title: Huh7SP2

description:
SAMPLE 5
replicate 2


title: D1-1 lung microRNA

description: microRNA


title: Huh7NSPZEB1

description:
SAMPLE 7
replicate 1


title: Huh7NSP1

description:
SAMPLE 1
replicate 1


title: Huh7NSP3

description:
SAMPLE 3
replicate 3


title: Huh7SP3

description:
SAMPLE 6
replicate 3


title: Huh7SP1

description:
SAMPLE 4
replicate 1


title: Huh7NSP2

description:
SAMPLE 2
replicate 2


title: D0-3 lung microRNA

description: microRNA


title: TS1-iPS-C5P20

city: guangzhou

first: wang

last: xianming

country: China

institute: Guangzhou Institutes of Biomedicine and Health,Chinese Academy of Sciences

description:
Ts-iPS-C5_LW-1001
Gene expression data from TS1-iPS-C5P20

hyb_protocol: Following fragmentation and labeling, 10 ug of cDNA were hybridized for 16 hr at 45C on GeneChip Human Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Robust Multichip Average (RMA) using Partek software.

source_name: induced pluripotent stem cell

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Whole Transcript (WT) Sense Target   Labeling Assay Manual, 2007, Affymetrix).

growth_protocol: human iPSCs were cultured on Matrigel using mTeSR1 medium. Media were changed everyday.

extract_protocol: Cells were trypsinized and feeder cells were eliminated. Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: No special treatment during the culture.


title: CMC-iPS-C1P20

description:
CMC-ips-C1_LW_0908
Gene expression data from CMC-iPS-C1P20


title: CMC-iPS-C28P20

description:
CMC-ips-C28_LW_0908
Gene expression data from CMC-iPS-C28P20


title: Peri-iPS-C2P20

description:
Peri-ips-C2_LW_0908
Gene expression data from Peri-iPS-C2P20


title: D0-1 lung microRNA

description: microRNA


title: Peri-iPS-C1P20

description:
Peri-ips-C1_LW_0908
Gene expression data from Peri-iPS-C1P20


title: TS1-iPS-C3P24

description:
Ts-iPS-C3_LW-1001
Gene expression data from TS1-iPS-C3P24


title: blastomere NT embryo (4852796008 B)

description:
4852796008 B

blastomere NT embryo 14h post transfer

hyb_protocol: Hybridization according to Illumina protocols on  Illumina Sentrix Mouse Expression BeadChip RefSeq 8 v1.1 (GPL6103) or Mouse Expression BeadChip® RefSeq 8 v2.0 (GPL6885) as indicated. Arrays are hybridized, washed, blocked and stained with streptavidin-Cy3. The protocol is WGGEX Direct Hybridization Assay Guide (11322355 A).

scan_protocol: According to Illumina protocols with Illumina iScan.  Protocols can be found on the illumina web page.

data_processing: Data were normalized to average signal, background was subtracted using Illumina GenomeStudio. There are two series presented in a SuperSeries. One series was generated with GPL6103, the other with GPL6885. Normalized data are presented only for probes present in both GPL6103 AND GPL6885. Hybridization duplicates were not used for data analysis, but only for quality control.

source_name: NT embryo

label_protocol: Biotin label introduced according to protocols of the Illumina Total Prep RNA Amplification Kit

growth_protocol: mouse embryos were cultured in KSOM

extract_protocol: PicoPure RNA isolation kit (Arcturus)

treatment_protocol: The genome of the mouse zygote or the mouse blastomere was exchanged at mitosis. The extent of reprogramming was determined during the following cell cycle.

value: NT embryo


title: blastomere NT embryo (4852796008 A)

description:
4852796008 A

blastomere NT embryo 14h post transfer


title: ES interphase NT embryos #44 (4125661075 G)

description: NT embryo generated with interphase zygotes and ES cells at interphase as nuclear donors, 1d post transfer


title: 4-cell stage control (4852796007 H)

description:
4852796007 H

4-cell stage control 14h post release from mitotic block

source_name: blastomere

value: blastomere


title: TS1 amniocytes

description:
Tuner-Amniocyte_LW-1001
Gene expression data from TS1 amniocytes

source_name: placenta

value: TS1 amniocytes


title: Fib-1

description:
CNS-fibroblast_LW-1001
Gene expression data from Fib-1

source_name: fibroblast


title: parthenotes control (4852796007 B)

description:
4852796007 B

parthenogenetic embryos 2d post activation


title: TS1-iPS-C1P22

description:
Ts-iPS-C1_LW-1001
Gene expression data from TS1-iPS-C1P22


title: 4-cell stage control (4852796007 C)

description:
4852796008 C

4-cell stage control 14h post release from mitotic block


title: prometaphase NT embryo #28 (4068264030 F)

description: NT embryo generated at prometaphase of mitosis with interphase tail tip cells as nuclear donors, biological duplicate

source_name: zygote

value: zygote


title: 2-cell stage control embryo #22 (4068264030 A)

description: 2-cell stage control embryo, approx. 22-24h post first mitosis

source_name: 2-cell stage

value: 2-cell stage


title: Fib-3

description:
OTCD-fibroblast_LW-0912
Gene expression data from Fib-3


title: 2-cell stage control embryo #23 (4068264030 B)

description: 2-cell stage control embryo biological duplicate


title: MII oocytes (4852796007 D)

description:
4852796007 D

MII oocytes

source_name: oocyte

value: oocyte


title: genome less embryo (4852796008 F)

description:
4852796008 F
no number
embryos developing for 1d without a genome


title: MII oocytes (4852796007 E)

description:
4852796007 E

MII oocytes


title: blastomere NT embryo (4852796008 H)

description:
4852796008 H

blastomere NT embryo 14h post transfer


title: genome less embryo #49 (4125661075 H)

description: embryos developing for 1d without a genome


title: prometaphase NT embryo #27 (4068264030 D)

description: NT embryo generated at prometaphase of mitosis with interphase tail tip cells as nuclear donors, 22-24h post transfer


title: oocyte NT embryo (4852796007 F)

description:
4852796007 F

NT embryos generated with MII oocytes and tail tip fibroblasts at interphase as nuclear donors. 2d post transfer


title: M phase zygotes #26 (4125661008 D)

description: M phase zygotes biological duplicate


title: ES interphase NT embryos (4852796008 G)

description:
4852796008 G
no number
NT embryo generated with interphase zygotes and ES cells at interphase, biological duplicate


title: M phase zygotes (4068264030 H)

description:
sample 17 duplicate
hybridization duplicate


title: oocyte NT embryo (4852796007 C)

description:
4852796007 C

NT embryos generated with MII oocytes and tail tip fibroblasts at interphase as nuclear donors. Biological duplicate. 2d post transfer


title: 2-cell stage control embryo (4991825016 D)

description:
4991825016 D
sample 13 duplicate
hybridization duplicate on v2 platform


title: M phase zygotes  #24 (4068264030 C)

description: M phase zygotes biological duplicate


title: M phase zygotes #25 (4068264018 H)

description: M phase zygotes


title: 2-cell stage control embryo (4991825016 C)

description:
4991825016 C
sample 12 duplicate
hybridization duplicate on v2 platform


title: cleavage inhibition control (4991825016 B)

description:
4991825016 B
sample 14 duplicate
hybridization duplicate on v2 platform


title: cleavage inhibition control #38 (4125661075 B)

description: 1-cell embryo at 2-cell timing (cleavage inhibition) biological duplicate


title: cleavage inhibition control #20 (4068264018 F)

description: 1-cell embryo at 2-cell timing (cleavage inhibition), , approx. 22-24h post first mitosis


title: cleavage inhibition control (4068264030 G)

description:
sample 11 duplicate
hybridization duplicate


title: anaphase NT embryo (4068264030 E)

description:
sample 8 duplicate
hybridization duplicate


title: US-897_TC1-3

city: Fort Pierce

first: Ute

last: Albrecht

state: FL

address: 2001 South Rock Road

institute: USDA, ARS, US Horticultural Research Laboratory

description: leaves, healthy, 32 wai, biological rep 3

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45 °C on the GeneChip Citrus Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using GeneChip® 7G Scanner (Affymetrix, Inc).

data_processing: The data were analyzed with Partek Genomic Suite version 6.5 (Partek Inc., MO, USA).  Robust Multiarray Analysis (RMA) normalization of probe intensity values was performed using default settings.

organism: Citrus reticulata x Citrus trifoliata

source_name: US-897 leaves, non-infected, 32 weeks after graft (mock)-inoculation

label_protocol: Biotinylated cRNA were prepared according to Affymetrix GeneChip® 3’ IVT Express protocol from 250 ug total RNA (Affymetrix P/N 702646 Rev. 1).

growth_protocol: Plants were grown in the greenhouse and kept under natural light conditions at a temperature of 21 to 28 °C. Plants were irrigated as needed and fertilized every 3 weeks using a water-soluble fertlizer mix, 20N-10P-20K (Peters Professional, The Scotts Company, Marysville, OH).

extract_protocol: Leaves were excised and immediately frozen in liquid nitrogen. One gram of leaf tissue was ground in liquid nitrogen with a mortar and pestle and resuspended in 10 mL guanidinium isothiocyanate buffer (Chomczynski & Sacci, Anal. Biochem. 162 (1987) 156-159).  Total RNA was extracted according to Albrecht & Bowman (Plant Sci. 175 (2008) 291-306).  RNA was further purified using the RNeasy® MinElute Cleanup kit (Qiagen, Valencia, CA, USA) according to the manufacturer’s instructions.  Total RNA was DNase-treated using the TURBO DNA-free-KitTM (Ambion, Austin, TX, USA) according to the manufacturer’s instructions.

treatment_protocol: Plants were graft-inoculated with non-infected (control) or Ca. L. asiaticus-infected bark-/bud- and leaf pieces from greenhouse-grown 'Valencia' plants and pruned immediately at 24 weeks after inoculation.

tag: type of plants

value: greenhouse-grown seedling

tag: age of plants

value: 23 months

value: mature leaves


title: anaphase NT embryo #15 (4068264018 B)

description: NT embryo generated at anaphase of mitosis with interphase tail tip cells as nuclear donors, 22-24h post transfer


title: US-897_TI1-3

description: leaves, infected, 32 wai, biological rep 3

source_name: US-897 leaves, infected with Ca. L. asiaticus, 32 weeks after graft-inoculation


title: anaphase NT embryo #19 (4068264018 E)

description: NT embryo generated at anaphase of mitosis with interphase tail tip cells as nuclear donors, biological duplicate


title: P. graminicola-infected rice roots, 4 dpi, rep2

city: Gent

first: David

last: De Vleesschauwer

address: Coupure Links 653

department: Crop Protection

country: Belgium

institute: Ghent University

description: P. graminicola-inoculated Nipponbare, 4 dpi, biological replicate 2 of 3

hyb_protocol: Hybridization_Kit: in situ hybridization plus. Hybridization_Manufacturer: Agilent Technologies. Hybridization_Manual: Agilent Technologies

scan_protocol: Scanner: Agilent DNA microarray Scanner. Manufacturer: Agilent Technologies. Software: Scanner Control software. Manual: Agilent Technologies.

data_processing: Software: Feature Extraction ver 9.5. Manufacturer: Agilent Technologies. Manual: Agilent Technologies.

organism: Oryza sativa Japonica Group

source_name: Pathogen inoculation, 4 dpi

label_protocol: Kit: Low RNA Input Linear Amplification kit Manufacturer: Agilent Technologies. Manual: Low RNA Input Linear Amplification kit standard protocol  Kit: Low RNA Input Linear Amplification kit  Manufacturer: Agilent Technologies  Manual: Low RNA Input Linear Amplification kit standard protocol

growth_protocol: Rice seeds were surface sterilized by agitation in 2 % sodium hypochlorite for 20 min, rinsed three times with sterile demineralized water, plated in square Petri dishes (12 cm x 12 cm) on standard strength Gamborg’s B5/1% plant agar medium and subsequently grown in a growth chamber at 28 °C (day)/26 °C (night) under 12-h photoperiod.

extract_protocol: Total RNA was extracted from frozen root tissue (100 mg; roots pooled from 20-24 individual plants). Kit: Spectrum Plant Total RNA  (Sigma-Aldrich).

treatment_protocol: Three days after imbibition, i.e when primary roots were approximately 1 cm in length, germinated seedlings were inoculated by carefully placing a 0.6-cm-diameter agar plug taken from the margin of 7-day-old PDA cultures in between each two plants. Control samples were mock-inoculated with 0.6-cm-diameter PDA plugs.

tag: pythium strain

tag: rice cultivar

value: Nipponbare

value: Roots

tag: plant age

tag: agent

value: Pathogen

tag: dpi

source_name: Mock inoculation, 4 dpi

value: roots

value: mock


title: US-897_TI1-2

description: leaves, infected, 32 wai, biological rep 2


title: WT vs. pooled reference replicate 2

city: san francisco

first: Chris

last: Cain

address: 600 16th street

institute: UC San Francisco

hyb_protocol: Fluorescently labeled cDNAs from mutants were directly hybridized against those from wild type grown under the same conditions cDNA was labeled with Cy3 and Cy5 (Amersham), and 0.5 μg of each channel was hybridized to custom array following a protocol described by Hernday et al. (Methods Enzymol. 2010;470:737-58) The custom array, described here, uses multiple instances of Agilent v2 probes from GPL9825 plus additional tiling probes upstream of selected orfs taken from GPL4130.

scan_protocol: Arrays were scanned using a Genepix 4000A Axon scanner, and spots were filtered using GenePix Pro software.

data_processing: Data were normalized using Goulphar (LOWESS normalization)

organism: Saccharomyces cerevisiae

source_name: wildtype Sigma 2000 strain

label_protocol: 10 μg of each RNA was treated with DNase I (Turbo DNA-free kit, Ambion) and reverse transcribed using aminoallyl-dUTP and Superscript II (Invitrogen) according to manufacturers’ instructions. cDNA was labeled with Cy3 and Cy5 (Amersham).

growth_protocol: Yeast strains were grown in YPD media to an OD of mid-log phase, then harvested for total RNA preps

extract_protocol: Total RNA was prepared using a hot phenol method (Miller and Johnson, 2002).

tag: genotype/variation

value: wildtype parent MY1384

tag: strain

value: Sigma 2000

source_name: Pooled reference of mid-log growth of total RNA samples from at least 4 strains, WT, delta Mit1, delta Yhr177w, and double deletion, in sigma 2000 background

tag: reference


title: P. graminicola-infected rice roots, 4 dpi, rep1

description: P. graminicola-inoculated Nipponbare, 4 dpi, biological replicate 1 of 3


title: P. graminicola-infected rice roots, 2 dpi, rep2

description: P. graminicola-inoculated Nipponbare, 2 dpi, biological replicate 2 of 3

source_name: Pathogen inoculation, 2 dpi

source_name: Mock inoculation, 2 dpi


title: P. graminicola-infected rice roots, 4 dpi, rep3

description: P. graminicola-inoculated Nipponbare, 4 dpi, biological replicate 3 of 3


title: P. graminicola-infected rice roots, 1 dpi, rep2

description: P. graminicola-inoculated Nipponbare, 1 dpi, biological replicate 2 of 3

source_name: Pathogen inoculation, 1dpi

source_name: Mock inoculation, 1 dpi


title: P. graminicola-infected rice roots, 2 dpi, rep3

description: P. graminicola-inoculated Nipponbare, 2 dpi, biological replicate 3 of 3


title: Delta Mit1 Delta yhr177w vs. pooled reference replicate 2

source_name: Sigma 2000 strain with a deletion of Mit1 and Yhr177w

value: Mit1::hphMX Yhr177w:kanMX deletion

value: Pooled reference of mid-log growth of total RNA samples from at least 4 strains, WT, delta Mit1, delta Yhr177w, and double deletion, in sigma 2000 background


title: P. graminicola-infected rice roots, 1 dpi, rep3

description: P. graminicola-inoculated Nipponbare, 1 dpi, biological replicate 3 of 3


title: interphase zygote #31 (4125661008 F)

description: interphase mouse zygotes biological duplicate

tag: cell type


title: WT vs. pooled reference


title: Delta Mit1 vs. pooled reference replicate 2

source_name: Sigma 2000 strain with a deletion of Mit1

value: Mit1::KanMX deletion


title: P. graminicola-infected rice roots, 1 dpi, rep1

description: P. graminicola-inoculated Nipponbare, 1 dpi, biological replicate 1 of 3

tag: tissue


title: P. graminicola-infected rice roots, 2 dpi, rep1

description: P. graminicola-inoculated Nipponbare, 2 dpi, biological replicate 1 of 3


title: US-897_TC1-1

description: leaves, healthy, 32 wai, biological rep 1

tag: genotype


title: US-897_TI1-1

description: leaves, infected, 32 wai, biological rep 1


title: Delta yhr177w vs. pooled reference replicate 2

source_name: Sigma 2000 strain with a deletion of Yhr177w

value: Yhr177w:natmx deletion


title: US-897_TC1-2

description: leaves, healthy, 32 wai, biological rep 2


title: interphase zygote (4020498031 E)

description: interphase mouse zygotes (approx. 25h post hCG)

value: zygote


title: tail tip fibroblast, nuclear donor cells #8 (4125661008 A)

description: tail tip fibroblast isolated from agouti 129xB6 F1 mice biological duplicate

source_name: tail tip fibroblast

value: tail tip fibroblast


title: interphase zygote #30 (4125661008 E)

source_name: zygote


title: Delta Mit1 vs. pooled reference


title: Cleopatra_MC1-3

description: leaves, healthy, 32 wai, biological rep 3

organism: Citrus reticulata

source_name: Cleopatra leaves, non-infected, 32 weeks after graft (mock)-inoculation

value: Cleopatra


title: Delta Mit1 Delta yhr177w vs. pooled reference


title: Cleopatra_MI1-1

source_name: Cleopatra leaves, infected with Ca. L. asiaticus, 32 weeks after graft-inoculation

value: greenhouse-grown seedling


title: M9TMP_Ad_10min

city: Princeton

first: Dipen

last: Sangurdekar

state: NJ

address: 132 Carl Icahn laboratory, Princeton University

department: Lewis-Sigler Institute for Integrative Genomics

institute: Princeton University

description: E. coli MG1655 10 min after TMP+adenine treatment in M9 media

hyb_protocol: Relative mRNA levels were determined by parallel two color hybridization at single-gene resolution to whole-genome E. coli K-12 MG1655 spotted DNA microarrays

scan_protocol: Images were scanned using Axon GenePix scanner.

data_processing: Raw fluorescence intensity data were normalized in R (http://cran.r-project.org/) using the Limma (Bioconductor) package

organism: Escherichia coli

label_protocol: Fluorescence DNA probes were synthesized from 10~15 μg of total RNA with random hexamers and Cy-5 dUTP or Cy-3 dUTP dyes.

growth_protocol: Overnight cultures were resuspended in fresh medium and TMP was added when the optical density (O.D. 600 nm) of the culture reached 0.3-0.4.

extract_protocol: Total RNA samples were purified using the Qiagen RNeasy kit (Chatsworth, CA) according to the manufacturer’s protocol.

treatment_protocol: Time-point samples were taken every 15-30 minutes from 15 minutes to 2 hours post treatment.

source_name: E. coli MG1655 mid-log phase in M9 media


title: M9TMP_Ad_30min

description: E. coli MG1655 30 min after TMP+adenine treatment in M9 media


title: Delta yhr177w vs. pooled reference


title: M9TMP_AA_120min

description: E. coli MG1655 120 min after TMP+glycine+methionine treatment in M9 media


title: Cleopatra_MI1-3

description: leaves, infected, 32 wai, biological rep 3

value: 23 months


title: M9TMP_Ad_120min

description: E. coli MG1655 120 min after TMP+adenine treatment in M9 media


title: M9TMP_AA_60min

description: E. coli MG1655 60 min after TMP+glycine+methionine treatment in M9 media


title: D1-3 liver mRNA

description: Adult male mice, B6C3F1, necropsied 4 hours after the last exposure

hyb_protocol: Global mRNA profiling was conducted on 5 control samples alongside 5 mice exposed to 150 mg/kg and 5 mice exposed to 300 mg/kg BaP from the 4 hour time point for liver. Individual total RNA (250 ng) samples and universal reference total RNA (Stratagene) were used to synthesize double-stranded cDNA and cyanine labelled cRNA according to the manufacturer’s instructions (Agilent Linear Amplification Kits, Agilent Technologies). Experimental samples were labelled with Cyanine 5-CTP, and reference RNA with Cyanine 3-CTP (Perkin-Elmer Life Sciences, Woodbridge, ON, Canada). Cyanine-labelled cRNA targets were in vitro transcribed using T7 RNA polymerase and purified by RNeasy Mini Kit (Qiagen). Labelled cRNA was hybridized to Agilent mouse 4 x 44 oligonucleotide microarrays (Agilent Technologies) at 60ºC overnight. Arrays were washed and scanned on an Agilent G2505B scanner at 5 m resolution. Data were acquired using Agilent Feature Extraction software version 9.5.3.1.

scan_protocol: scanned on an Agilent G2505B scanner at 5 um resolution. Data were acquired using Agilent Feature Extraction software version 9.5.3.1.

data_processing:
A reference design [50, 51] was used to analyse gene expression microarray data. The design was blocked on the slide, since the Agilent arrays contain 4 arrays per slide. The background fluorescence was measured using the (-)3xSLv1 probes; probes with median signal intensities less than the trimmed mean (trim = 5%) plus three trimmed standard deviations of the (-)3xSLv1 probe were flagged as absent (within the background signal). Data were normalized using LOWESS in R [52]. Ratio intensity plots and heat maps for the raw and normalized data were constructed to identify outliers. One sample was removed from the analysis based on clustering. Genes that were differentially expressed as a result of treatment were determined using the MAANOVA library in R [53]. The main effect in the model was treatment. This model was applied to the log2 of the absolute intensities. The Fs statistic [54] was used to test for treatment effects. The p-values for all statistical tests were estimated by the permutation method using residual shuffling, followed by adjustment for multiple comparisons using the false discovery rate (FDR) approach [55]. The fold change calculations were based on the least-square means. Significant genes identified as having an adjusted p-value < 0.05 for any individual contrast.
RawCy5 and RawCy3 are the median signal intensities for the Cy5 and Cy3 channels on each microarray. NormCy5 and NormCy3 are the loess normalized signal intensities for the Cy5 and Cy3 channels within each array; this is a within-array normalization performed separately for each array. Flag indicates whether the median signal intensity falls in the background, i.e below threshold calculated from the negative controls (mean plus three standard deviations of the negative controls.) Ratio is calculated as log2(NormCy5/NormCy3)

source_name: Liver tissue

label_protocol: Global mRNA profiling was conducted on 5 control samples alongside 5 mice exposed to 150 mg/kg and 5 mice exposed to 300 mg/kg BaP from the 4 hour time point for liver . Individual total RNA (250 ng) samples and universal reference total RNA (Stratagene) were used to synthesize double-stranded cDNA and cyanine labelled cRNA according to the manufacturer’s instructions (Agilent Linear Amplification Kits, Agilent Technologies). Experimental samples were labelled with Cyanine 5-CTP, and reference RNA with Cyanine 3-CTP (Perkin-Elmer Life Sciences, Woodbridge, ON, Canada). Cyanine-labelled cRNA targets were in vitro transcribed using T7 RNA polymerase and purified by RNeasy Mini Kit (Qiagen). Labelled cRNA was hybridized to Agilent mouse 4 x 44 oligonucleotide microarrays (Agilent Technologies) at 60ºC overnight. Arrays were washed and scanned on an Agilent G2505B scanner at 5 m resolution. Data were acquired using Agilent Feature Extraction software version 9.5.3.1.

extract_protocol: Total RNA was isolated from random sections of the a section of liver tissue using TRIzol reagent (Invitrogen) and purified using RNeasy Mini Kit (Qiagen). All RNA samples showing A260/280 ratios between 2.0 and 2.1 were further analysed for RNA integrity using an Agilent 2100 Bioanalyzer (Agilent Technologies, Mississauga, ON, Canada). Only high quality RNA (28S/18S > 1.8) was used for analysis. Was quantified using UV spectrophotometer and quality was confirmed using the Agilent 2100 Bioanalyzer and RNA 6000 NanoLab Chip Kit (Agilent Technologies Canada Inc., Mississauga, ON, Canada).

treatment_protocol: Age matched adult male B6C3F1 mice (27-30 d, Charles Rivers Laboratories, St Constant, Quebec, Canada) were housed individually under a 12:12 h light: dark cycle with food and water available ad libitum. Mice were randomly assigned (6 per group) to a control or treatment group. Mice were treated with a daily dose of BaP in corn oil with 5, 50, 150 or 300 mg/kg (oral gavage, 10 ml/kg) for three consecutive days. Control mice received corn oil only. Mice were anaesthetized under isofluorane and sacrificed by exsanguination 4 or 24 hours after the last treatment. Liver lobes were removed and immediately snap frozen and stored at -80ºC until use. Blood serum was collected as described below. All animal procedures were in accordance with the guidelines of the Canadian Council for Animal Care and approved by the Health Canada Animal Care Committee.

value: adult

value: male

value: liver

value: 300 mg/kg dose 4 hours

source_name: universal mouse reference total RNA (Stratagene)

extract_protocol: Unknown: Material was purchased as total RNA (universal mouse reference total RNA (Stratagene, CA, USA))

tag: sample


title: tail tip fibroblast, nuclear donor cells #1 (4020498031 A)

description: tail tip fibroblast isolated from agouti 129xB6 F1 mice


title: D0-5 liver mRNA

tag: gender

value: Control

value: universal mouse reference total RNA (Stratagene)


title: M9TMP_Ad_60min

description: E. coli MG1655 60 min after TMP+adenine treatment in M9 media


title: M9TMP_AA_30min

description: E. coli MG1655 30 min after TMP+glycine+methionine treatment in M9 media


title: Cleopatra_MI1-2

description: leaves, infected, 32 wai, biological rep 2

value: mature leaves


title: Cleopatra_MC1-1

description: leaves, healthy, 32 wai, biological rep 1


title: tail tip fibroblast, nuclear donor cells #2 (4020498031 C)


title: B. pertussis strain 1496/57

type: genomic

city: Turku

first: Teemu

last: Kallonen

address: Kiinamyllynkatu 13

department: Derpartment of Infectious Disease Surveillance and Control

country: Finland

institute: National Institute for Health and Welfare

description: CGH

hyb_protocol: The labeled DNA was purified with the purification kit of the same manufacturer and then combined. The volume of labeled DNA was reduced below 15.7 µl in vacuum centrifuge, and 2.5 µl of yeast tRNA (10mg/ml, Invitrogen Life Technologies, Carlsbad, USA), 4.3 µl of 20 x SSC (1 x SSC was 8.8g/l NaCl and 4.4 g/ trisodiumcitrate) and 0.8 µl of 10% SDS were added. After denaturation at 100°C for 3 min, 1.7 µl of 10 x digoxigenin was added. The final volume for hybridization was adjusted with water to 25 µl. Before hybridization, slides were fixed by UV-cross linking with 90 mJ cm-2, washed for 1 min in 0.1% of SDS and 2 min in water to remove residual salt, and incubated at 50ºC for 30 min in BSA solution containing 1% of BSA fraction V, 2 x SSC and 0.1% of SDS to block nonspecific binding. The slides were further washed in 2 x SSC for 3 min and then in 0.2 x SSC for 3 min. Hybridization was conducted under 22 x 25mm LifterSlip ™ coverslip (Erie Scientific Company, Portsmouth, USA) in hybridization chamber at 65°C for 16 h. To control humidity inside the hybridization chamber, a strip of thin paper, humidified with approximately 100 µl of 3.4 x SSC, was placed under the slide. After hybridization slides were washed at 65°C for 10 min with 1 x SSC and 0.1% of SDS. The following washes were conducted at room temperature for 10 min with 0.5 x SSC and 0.01% SDS, and for 3 min and 1 min with 0.1 x SSC. Slides were dried in slide centrifuge.

scan_protocol: scanned with ScanArray ®5000 (PerkinElmer, Waltham, USA).

data_processing: Microarray data analysis was performed with R/Bioconductor. Print-tip-loess normalization was performed with default parameters and the gains/losses were filtered with Limma package.

molecule: genomic DNA

organism: Bordetella pertussis

source_name: Tohama I

label_protocol: The 4 µg of digested DNA was labelled with the dye (Amershham Biosciences UK Limited, Buckinghamshire, England) according to the protocol of BioPrime®Array CGH Genomic Labeling System (Invitrogen Life Technologies, Carlsbad, USA). The labeled DNA was purified with the purification kit of the same manufacturer.

growth_protocol: Bacteria stored in -70°C were recultured on Charcoal agar (Oxoid Ltd, Basingstoke, England) with 10% defibrinated sheep blood. The plates were incubated at 35-36°C for 3 days. Bacteria were harvested and suspended in distilled water. Prior to DNA isolation, the concentration of bacterial suspension was adjusted to 2 x 109 cells/ml.

extract_protocol: B. pertussis DNA was isolated with GenElute™ Bacterial Genomic DNA Kit (Sigma-Aldrich Inc., St. Louis, USA) and then digested with Sma I (10 U/µg DNA, New England Biolabs, Ipswich, USA) according to the protocol of BioPrime®Array CGH Genomic Labeling System (Invitrogen Life Technologies, Carlsbad, USA).

value: Tohama I

tag: year of isolation

tag: place of isolation

value: Serbia


title: B. pertussis strain 2154/58

description: CGH


title: Cleopatra_MC1-2

tag: type of plants


title: M9TMP_AA_10min

description: E. coli MG1655 10 min after TMP+glycine+methionine treatment in M9 media


title: B. pertussis strain 1828/57

description: CGH


title: M9_TMP5_THY_Ad_AA_120min

description: E. coli MG1655 120 min after TMP+thymine+adenine+glycine+methionine treatment in M9 media


title: D1-2 liver mRNA

tag: developmental stage

tag: treatment group


title: D0-2 liver mRNA


title: M9_TMP5_THY_Ad_AA_60min

description: E. coli MG1655 60 min after TMP+thymine+adenine+glycine+methionine treatment in M9 media


title: D1-6 liver mRNA


title: M9_TMP5_THY_Ad_AA_30min

description: E. coli MG1655 30 min after TMP+thymine+adenine+glycine+methionine treatment in M9 media


title: B. pertussis strain 162/54

description: CGH


title: B. pertussis strain 124/54

description: CGH


title: M9_TMP5_THY_Ad_AA_10min

description: E. coli MG1655 10 min after TMP+thymine+adenine+glycine+methionine treatment in M9 media


title: M9TMP5_AdAA_120min

description: E. coli MG1655 120 min after TMP+adenine+glycine+methionine treatment in M9 media


title: B. pertussis strain 8/84

description: CGH

value: vaccine strain


title: D0-6 liver mRNA


title: B. pertussis strain 22/53

description: CGH


title: D0-3 liver mRNA


title: M9TMP5_AdAA_90min

description: E. coli MG1655 90 min after TMP+adenine+glycine+methionine treatment in M9 media


title: B. pertussis strain 23/81

description: CGH


title: M9TMP5_AdAA_60min

description: E. coli MG1655 60 min after TMP+adenine+glycine+methionine treatment in M9 media


title: D1-1 liver mRNA


title: B. pertussis strain 9/68

description: CGH

value: Poland


title: B. pertussis strain 2047/57

description: CGH


title: M9TMP5_AdAA_10min

description: E. coli MG1655 10 min after TMP+adenine+glycine+methionine treatment in M9 media


title: D0-1 liver mRNA


title: D1-5 liver mRNA


title: M9TMP5_AdAA_30min

description: E. coli MG1655 30 min after TMP+adenine+glycine+methionine treatment in M9 media


title: B. pertussis strain 1772/57

description: CGH


title: D0-8 lung mRNA

hyb_protocol: Global mRNA profiling was conducted on 5 control samples alongside 5 mice exposed to 150 mg/kg and 5 mice exposed to 300 mg/kg BaP from the 4 hour time point for both liver and lung. Individual total RNA (250 ng) samples and universal reference total RNA (Stratagene) were used to synthesize double-stranded cDNA and cyanine labelled cRNA according to the manufacturer’s instructions (Agilent Linear Amplification Kits, Agilent Technologies). Experimental samples were labelled with Cyanine 5-CTP, and reference RNA with Cyanine 3-CTP (Perkin-Elmer Life Sciences, Woodbridge, ON, Canada). Cyanine-labelled cRNA targets were in vitro transcribed using T7 RNA polymerase and purified by RNeasy Mini Kit (Qiagen). Labelled cRNA was hybridized to Agilent mouse 4 x 44 oligonucleotide microarrays (Agilent Technologies) at 60ºC overnight. Arrays were washed and scanned on an Agilent G2505B scanner at 5 m resolution. Data were acquired using Agilent Feature Extraction software version 9.5.3.1.

source_name: Lung tissue

extract_protocol: Total RNA was isolated from random sections of the left lung using TRIzol reagent (Invitrogen) and purified using RNeasy Mini Kit (Qiagen). All RNA samples showing A260/280 ratios between 2.0 and 2.1 were further analysed for RNA integrity using an Agilent 2100 Bioanalyzer (Agilent Technologies, Mississauga, ON, Canada). Only high quality RNA (28S/18S > 1.8) was used for analysis. Was quantified using UV spectrophotometer and quality was confirmed using the Agilent 2100 Bioanalyzer and RNA 6000 NanoLab Chip Kit (Agilent Technologies Canada Inc., Mississauga, ON, Canada).

value: lung


title: D1-8 lung mRNA

scan_protocol: Global mRNA profiling was conducted on 5 control samples alongside 5 mice exposed to 150 mg/kg and 5 mice exposed to 300 mg/kg BaP from the 4 hour time point for both liver and lung. Individual total RNA (250 ng) samples and universal reference total RNA (Stratagene) were used to synthesize double-stranded cDNA and cyanine labelled cRNA according to the manufacturer’s instructions (Agilent Linear Amplification Kits, Agilent Technologies). Experimental samples were labelled with Cyanine 5-CTP, and reference RNA with Cyanine 3-CTP (Perkin-Elmer Life Sciences, Woodbridge, ON, Canada). Cyanine-labelled cRNA targets were in vitro transcribed using T7 RNA polymerase and purified by RNeasy Mini Kit (Qiagen). Labelled cRNA was hybridized to Agilent mouse 4 x 44 oligonucleotide microarrays (Agilent Technologies) at 60ºC overnight. Arrays were washed and scanned on an Agilent G2505B scanner at 5 m resolution. Data were acquired using Agilent Feature Extraction software version 9.5.3.1.


title: SH-iPS15-10, FGF, S2

city: Frederick

first: Jack

last: Chen

address: SAIC-Frederick Miller Dr

hyb_protocol: cRNA samples were hybridized onto Human HT-12 v3 and v4 Expression BeadChip (Illumina) according to manufacture’s protocols.

scan_protocol: Arrays were then scanned using the BeadXpress Reader (Illumina) according to manufacturer's protocols.

data_processing: Raw expression files were exported directly from BeadStudio and loaded into R/Bioconductor according to manufacturer's protocols. Sample data were normalized and then the mean value was calculated for each transcript from samples in the same group. Pearson correlation analysis of global gene expression (47232 transcripts) was performed on these arrays.

source_name: SH-iPS15-10, FGF, S2

label_protocol: All RNA samples were amplified and labelled using Illumina® TotalPrep™-96 RNA Amplification Kit according to manufacturer's protocol.

growth_protocol: All human induced pluripotent stem cell lines were grown on STO feeders in DMEM/F12 with Glutamax (Invitrogen), 20% Knockout Serum Replacement (Invitrogen), 10(6) U/ml human LIF (Chemicon), 1X NEAA (Invitrogen), 0.1 mM β-mercaptoethanol (β-ME, Sigma) and the inhibitors, CHIR99021 (5 μM) and PD0325901 (1 μM). All human dermal fibroblast lines were grown in Media 106 supplemented with low serum growth supplement (Invitrogen).

extract_protocol: All RNA samples were extracted using the RNeasy Mini Kit (Qiagen) according to manufacturer's protocols.

treatment_protocol: All human induced pluripotent stem cell lines were disociated with Accutase (Chemicon). All human dermal fibroblast cell lines were dissociated with 0.025% trypsin (Invitrogen)

tag: cell line

value: SH-iPS15-10, FGF

value: Human Dermal Fibroblast Cells

tag: parental line

tag: treatment

value: FGF


title: B. pertussis strain 7/68

description: CGH


title: M9TMP5_120min

description: E. coli MG1655 120 min after TMP treatment in M9 media


title: SH-iPS15-10, 2i, S2

value: Human Induced Pluripotent Stem Cells

value: 2i + LIF


title: D2-7 lung mRNA

label_protocol: Global mRNA profiling was conducted on 5 control samples alongside 5 mice exposed to 150 mg/kg and 5 mice exposed to 300 mg/kg BaP from the 4 hour time point for both liver and lung. Individual total RNA (250 ng) samples and universal reference total RNA (Stratagene) were used to synthesize double-stranded cDNA and cyanine labelled cRNA according to the manufacturer’s instructions (Agilent Linear Amplification Kits, Agilent Technologies). Experimental samples were labelled with Cyanine 5-CTP, and reference RNA with Cyanine 3-CTP (Perkin-Elmer Life Sciences, Woodbridge, ON, Canada). Cyanine-labelled cRNA targets were in vitro transcribed using T7 RNA polymerase and purified by RNeasy Mini Kit (Qiagen). Labelled cRNA was hybridized to Agilent mouse 4 x 44 oligonucleotide microarrays (Agilent Technologies) at 60ºC overnight. Arrays were washed and scanned on an Agilent G2505B scanner at 5 m resolution. Data were acquired using Agilent Feature Extraction software version 9.5.3.1.

value: adult

value: 150 mg/kg dose 4 hours


title: SH-iPS15-10, FGF, S1

source_name: SH-iPS15-10, FGF, S1


title: SH-iPS15-10, FGF, S3

source_name: SH-iPS15-10, FGF, S3


title: B. pertussis strain A/63

description: CGH


title: D2-6 lung mRNA

value: male


title: D1-7 lung mRNA

value: 300 mg/kg dose 4 hours


title: M9TMP5_60min

description: E. coli MG1655 60 min after TMP treatment in M9 media


title: M9TMP5_90min

description: E. coli MG1655 90 min after TMP treatment in M9 media


title: D1-6 lung mRNA


title: M9TMP5_10min

description: E. coli MG1655 10 min after TMP treatment in M9 media


title: B. pertussis strain 1326/62

description: CGH


title: SH-iPS15-10, 2i, S3


title: M9TMP5_30min

description: E. coli MG1655 30 min after TMP treatment in M9 media


title: SH-iPS15-10, 2i, S1


title: B. pertussis strain 7/60

description: CGH


title: B. pertussis strain 12/60

description: CGH


title: LBTMP50_120min

description: E. coli MG1655 120 min after TMP treatment in LB media

source_name: E. coli MG1655 mid-log phase in LB media


title: LBTMP50_60min

description: E. coli MG1655 60 min after TMP treatment in LB media


title: SH-iPS15-5, 2i, S3


title: D0-7 lung mRNA

value: Control


title: H1 hESC, S3

source_name: H1 hESC, S3

value: H1 hESC


title: SH-iPS15-5, 2i, S1


title: D2-3 lung mRNA

value: universal mouse reference total RNA (Stratagene)


title: B. pertussis strain 6/62

description: CGH

value: Tohama I


title: D2-4 lung mRNA


title: LBTMP50_30min

description: E. coli MG1655 30 min after TMP treatment in LB media


title: SH-iPS15-5, 2i, S2


title: B. pertussis strain 21/60

description: CGH


title: D0-4 lung mRNA


title: D2-2 lung mRNA


title: B. pertussis strain 3/60

description: CGH


title: LBTMP50_10min

description: E. coli MG1655 10 min after TMP treatment in LB media


title: H1 hESC, S2

source_name: H1 hESC, S2


title: H1 hESC, S1

source_name: H1 hESC, S1


title: D1-3 lung mRNA


title: B. pertussis strain 629/65

description: CGH


title: D1-2 lung mRNA


title: B. pertussis strain 606/77

description: CGH


title: B. pertussis strain 186/65

description: CGH


title: HDFa (439656)


title: HDFn (617769)


title: B. pertussis strain CN5476

description: CGH

value: the UK


title: D1-1 lung mRNA


title: D2-1 lung mRNA


title: B. pertussis strain CN0128

description: CGH


title: B. pertussis strain CN0142

description: CGH


title: B. pertussis strain CN0909

description: CGH


title: Yhr177 delete Rep2

hyb_protocol: At least 2 independent hybridization experiments were performed on biological replicates of the untagged control and Mit1-GFP and Yhr177w and Yhr177w deletion control. One experiment was performed on Wor1 overexpressing cells in a mit1/Yhr177w deletion, with vector control.  Protocol is available in Hernday et al. (Methods Enzymol. 2010;470:737-58).

scan_protocol: Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol.

data_processing: Normalized enrichment values were determined for every probe on the microarray by LOWESS normalization using Agilent Chip Analytics Version 1.2 software (Tuch et al., 2008), followed by visualization and additional analysis using MochiView v.1.39 (http://johnsonlab.ucsf.edu/).

source_name: Yhr ChIP IP DNA

label_protocol: IP genomic DNA samples were labeled with Cy5 and input genomic DNA samples were labeled with Cy3. Protocol is available in Hernday et al. (Methods Enzymol. 2010;470:737-58).

growth_protocol: Cells were grown overnight to an OD of low/mid log phase (.3- 1) in YPD or appropriate selectable media.

extract_protocol: Genomic DNA extracted using protocol in Methods Enzymol. 2010;470:737-58.

treatment_protocol: Cells were fixed, lysed, immunoprecipitated with antibody and genomic DNAs were sheared by sonication.

source_name: Yhr ChIP Input DNA


title: HDFa (709590)


title: B. pertussis strain CN0137

description: CGH


title: Wor1-ChIP

source_name: Wor1 ChIP IP DNA

value: pTEF-Wor1 CEN

source_name: Wor1 ChiP Input DNA


title: D0-3 lung mRNA


title: D2-5 lung mRNA


title: D0-2 lung mRNA


title: D0-1 lung mRNA


title: Yhr177w Rep2


title: Wor1 Vector Control

value: pTEF-CEN Vector


title: Yhr177 delete Rep1


title: D1-5 lung mRNA

value: lung


title: D0-6 lung mRNA


title: Yhr177w Rep1


title: B. pertussis strain CN3099

description: CGH

value: vaccine strain


title: B. pertussis strain CN2992

description: CGH


title: SS582

status: Public on Oct 03 2011

city: Baltimore

first: NIKHIL

last: KUMAR

address: 801 W. Baltimore Street

department: Institute for Genome Sciences

institute: University of Maryland, Baltimore

hyb_protocol: Slides were prehybridized in a 50 ml solution of 5X SSC, 0.1% SDS and 1% BSA for at least one hour at 42C, washed 10X in water and once in isopropanol, then dried by brief centrifugation. Labeled probes were re-suspended in hybridization buffer (50% formamide, 5X SSC, 0.1% SDS, 1 uL 0.1M DTT, 0.6 ug/uL salmon sperm DNA) and hybridized to the microarray slides in a 42C water bath for 16-20 h. Slides were washed twice in a low stringency buffer (2X SSC, 0.1% SDS) at 55C for 5 min, twice in a medium stringency buffer (0.1X SSC, 0.1% SDS) at room temperature for 5 min, twice in a high stringency buffer (0.1X SSC) at room temperature for 5 min, and finally in water for 2 min, and then dried by brief centrifugation.

scan_protocol: Scanned on GenePix 4000B.

data_processing: Iterative log-mean normalization and filtering using in-house scripts.

organism: Streptococcus sp. 'group A'

source_name: Group A Streptococcus strain SS582

label_protocol: 4 ug aliquots of genomic DNAs were aminoallyl-labeled with random hexamers (Invitrogen), Klenow buffer (New England Biolabs), DNA Polymerase I Klenow Fragment (New England Biolabs), 5-(3-aminoallyl)-dUTP (Sigma) and 100mM dNTP set PCR grade (Invitrogen). The mixture was incubated overnight at 37C. Amine-modified DNA was purified using QIAquick PCR purification kit (Qiagen), followed by chemical labeling with Cy3- or Cy5-NHS-ester fluorescent dyes (GE Healthcare).

extract_protocol: Genomic DNA was isolated using the Invitrogen Easy DNA Kit, following manufacturer's instructions.

tag: sample type

value: query

source_name: Cy3, Cy5Group A Streptococcus strain Alab49

tag: type

value: reference


title: MGAS10270

label: Cy3, Cy5

source_name: Group A Streptococcus strain MGAS10270

tag: strain


title: Mit1-Untagged Rep2

source_name: GFP ChIP IP DNA

tag: genotype/variation

value: MY1384 wt

source_name: GFP ChiP Input DNA


title: Mit1-GFP Rep 2


title: Mit1-Untagged Rep1


title: D0-5 lung mRNA

source_name: Lung tissue

source_name: universal mouse reference total RNA (Stratagene)


title: HiPS20-3

tag: cell type

value: Human Induced Pluripotent Stem Cells


title: HiPS28-23


title: HiPS24-2


title: Wild vs cg0196 Deletion Mutant_rep1

city: Seoul

first: Jeong Eun

last: Hyeon

address: Anamdong

country: South Korea

institute: Korea University

description:
harvested after culture in minimal medium containing glucose as a carbon source
Wild vs. Δcg0196

hyb_protocol: The Cy3 or Cy5-labeled cDNA probes were purified with QIAquick PCR Purification Kit (Qiagen, Valencia, CA). Dried Cy3 or Cy5-labeled cDNA probes were resuspended in hybridization buffer containing 30% formamide, 5X SSC, 0.1% SDS, 0.1mg/ml salmon sperm DNA. The Cy3 or Cy5-labeled cDNA probes were mixed together and hybridized to a microarray slide (Shigella flexneri 2a str. 2457T plus Shigella flexneri 2a str. 301 virulence plasmid pCP301 Oligonucleotide 3x15K microarray) (Mycroarray.com, Ann Arbor, MI). After overnight at 42C, the slide was washed twice with washing solution 1 containing 2X SSC, 0.1% SDS for 5 min at 42C, and once with washing solution 2 containing 0.1X SSC, 0.1% SDS for 10 min at room temperature, and finally four times with 0.1X SSC for 1 min at room temperature. The slide was dried by centrifugation at 650 rpm for 5min.

scan_protocol: Hybridization image on the slide was scanned by Axon 4000B (Axon Instrument, Union City, CA).

data_processing: Hybridization image was analyzed by GenePix Pro 3.0 software (Axon Instrument, Union City, CA) to obtain gene expression ratios (reference vs test sample). Microarray data analysis was carried out by Genowiz 4.0TM (Ocimum Biosolutions, India). Global lowess was used for data analysis with normalization.

organism: Corynebacterium glutamicum

source_name: cg0196 Deletion Mutant

label_protocol: cDNA probes for cDNA microarray analysis were prepared by the reverse-transcription of total RNA (25ug) in the presence of aminoallyl-dUTP and 6ug of random primers (Invitrogen, Carlsbad, CA) for 3 hrs. The cDNA probes were cleaned up using Microcon YM-30 column (Millipore, Bedford, MA) and then followed by coupling of Cy3 dye (for reference) or Cy5 dye (for test sample) (Amersham Pharmacia, Uppsala, Sweden).

growth_protocol: For growth on glucose as sole carbon source, the cells were precultured in nutrient medium. After the cells were washed in minimal medium, they were suspended in minimal medium containing glucose.

extract_protocol: The integrity of bacterial total RNA was checked by capillary electrophoresis with an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) and further purified with an RNeasy Mini Kit ( Qiagen, Valencia, CA).

value: cg0196 deletion

source_name: Wild-type

tag: genotype/varation

value: wild type


title: HiPS28-27


title: HiPS28-25


title: SS1098

source_name: Group A Streptococcus strain SS1098


title: HiPS20-9


title: HiPS24-1


title: SS636

source_name: Group A Streptococcus strain SS636


title: 3RP70

source_name: Group A Streptococcus strain 3RP70


title: Mit1-GFP Rep 1


title: SS1536

source_name: Group A Streptococcus strain SS1536


title: HiPS24-11


title: HiPS20-1


title: Whole embryo, E16.5

city: Bradford

first: Andrei

last: Mardaryev

address: Richmond Road

country: United Kingdom

institute: University of Bradford

description: gene expression of KO mouse

hyb_protocol: Performed using Gene Expression Hybridization Kit (Agilent)

scan_protocol: Scanned on an Agilent G2505C US83800207 scanner. Images were quantified using Agilent Feature Extraction Software (version 10.1.1.1)

data_processing: Dye biases between two signals, Red (WT) and Green (Lhx2KO), were corrected using Lowess normalization, subtracted background and converted to Log2 ratio of processed Red signal/processed Green signal.

source_name: Lhx2KO embryo (E16.5)

label_protocol: Sample labeling was done using Agilent’s Low RNA Fluorescent Linear Amplification Kit (Agilent) following manufacture’s instructions. Amplified cRNAs were quantified using the Agilent 2100 bioanalyzer and RNA 6000 Nano kit.

extract_protocol: RNA was extracted from cryopreserved mouse embryos using TRI Reagent (Ambion) and treated with Turbo-DNAse (Ambion) following manufacture's protocol. Total RNA was subjected for linear amplification using RiboAmp Plus Amplification Kit (Molecular Devices)

tag: tissue

value: whole embryo

value: Lhx2 knockout (+/-)

source_name: Wild-type Embryo (E16.5)

value: FVB


title: 6735-99

source_name: Group A Streptococcus strain 6735-99


title: D488

source_name: Group A Streptococcus strain D488


title: SS1408

source_name: Group A Streptococcus strain SS1408


title: MGAS275

source_name: Group A Streptococcus strain MGAS275

source_name: Cy3, Cy5Group A Streptococcus strain Alab49


title: A457

source_name: Group A Streptococcus strain A457


title: Alab53

source_name: Group A Streptococcus strain Alab53


title: SS795

source_name: Group A Streptococcus strain SS795


title: D316

source_name: Group A Streptococcus strain D316


title: CT95-121

source_name: Group A Streptococcus strain CT95-121


title: 29665

source_name: Group A Streptococcus strain 29665


title: MGAS2017

source_name: Group A Streptococcus strain MGAS2017


title: AA472

source_name: Group A Streptococcus strain AA472


title: 1RS79

source_name: Group A Streptococcus strain 1RS79


title: MGAS10750

source_name: Group A Streptococcus strain MGAS10750


title: 4770-01

source_name: Group A Streptococcus strain 4770-01


title: SS1447

source_name: Group A Streptococcus strain SS1447


title: 25RS84

source_name: Group A Streptococcus strain 25RS84


title: MGAS2096

source_name: Group A Streptococcus strain MGAS2096


title: MGAS5005

source_name: Group A Streptococcus strain MGAS5005


title: SF370

source_name: Group A Streptococcus strain SF370


title: SS951

source_name: Group A Streptococcus strain SS951

source_name: Cy3, Cy5Group A Streptococcus strain Alab49


title: 29454

source_name: Group A Streptococcus strain 29454


title: MGAS6180

source_name: Group A Streptococcus strain MGAS6180


title: CT95-122

source_name: Group A Streptococcus strain CT95-122


title: D502

source_name: Group A Streptococcus strain D502


title: SS1681

source_name: Group A Streptococcus strain SS1681


title: SS1371

source_name: Group A Streptococcus strain SS1371


title: D976

source_name: Group A Streptococcus strain D976


title: ACTH81

source_name: Group A Streptococcus strain ACTH81


title: Manfredo

source_name: Group A Streptococcus strain Manfredo

value: Manfredo


title: SS53

source_name: Group A Streptococcus strain SS53


title: 1165-99

source_name: Group A Streptococcus strain 1165-99


title: 86-809

source_name: Group A Streptococcus strain 86-809


title: NZ131

source_name: Group A Streptococcus strain NZ131


title: MGAS8232

source_name: Group A Streptococcus strain MGAS8232


title: D432

source_name: Group A Streptococcus strain D432


title: SS1434

source_name: Group A Streptococcus strain SS1434


title: A946

source_name: Group A Streptococcus strain A946

source_name: Cy3, Cy5Group A Streptococcus strain Alab49


title: 1RP278

source_name: Group A Streptococcus strain 1RP278


title: MGAS10394

source_name: Group A Streptococcus strain MGAS10394


title: SS1373

source_name: Group A Streptococcus strain SS1373


title: 4756-01

source_name: Group A Streptococcus strain 4756-01


title: MGAS315

source_name: Group A Streptococcus strain MGAS315


title: MGAS9429

source_name: Group A Streptococcus strain MGAS9429


title: D306

source_name: Group A Streptococcus strain D306


title: SS1363

source_name: Group A Streptococcus strain SS1363


title: 10RS57

source_name: Group A Streptococcus strain 10RS57


title: 29740

source_name: Group A Streptococcus strain 29740


title: 1GL217

source_name: Group A Streptococcus strain 1GL217


title: SS1541

source_name: Group A Streptococcus strain SS1541


title: AA348

source_name: Group A Streptococcus strain AA348


title: 1RP18RN

source_name: Group A Streptococcus strain 1RP18RN


title: D691

source_name: Group A Streptococcus strain D691


title: SS1550

source_name: Group A Streptococcus strain SS1550


title: 4500S

source_name: Group A Streptococcus strain 4500S

source_name: Cy3, Cy5Group A Streptococcus strain Alab49


title: SS1416

source_name: Group A Streptococcus strain SS1416


title: SS1402

source_name: Group A Streptococcus strain SS1402


title: SS1497

source_name: Group A Streptococcus strain SS1497


title: 3360-01

source_name: Group A Streptococcus strain 3360-01


title: SS1469

source_name: Group A Streptococcus strain SS1469


title: 89-456

source_name: Group A Streptococcus strain 89-456


title: 29689

source_name: Group A Streptococcus strain 29689


title: AA476

source_name: Group A Streptococcus strain AA476


title: MGAS261

source_name: Group A Streptococcus strain MGAS261


title: SS1676

source_name: Group A Streptococcus strain SS1676


title: SS1551

source_name: Group A Streptococcus strain SS1551


title: RNA_Pol2_Ser5phospho_mES_rep1, array1

city: Cambridge

first: Peter

last: Rahl

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute

description:
V6.5 murine ES cells were cultured as described in Boyer et al., Nature 2006 (PMID: 16625203).
LM-PCR immunoprecipitated DNA was labeled with Cy5.
LM-PCR input DNA was labeled with Cy3 using the Invitrogen Bioprime random primer labeling kit.

hyb_protocol: Agilent Mammalian ChIP-on-chip protocol (version 9.1, Nov 2006). In brief, mouse Cot1 DNA, Agilent blocking buffer (1X final conc.), and Agilent hybridization buffer (1X final conc.) were added to Cy5- and Cy3-labeled DNA. Mixture was incubated at 95C for 3 minutes, followed by 37C for 30 minutes. Sample was centrifuged for 1 min and sample was hybridized to the Agilent mouse promoter array set (2x244k feature set).

scan_protocol: Agilent DNA microarray scanner BA. PMT settings were set manually to normalize bulk signal in the Cy3 and Cy5 channel.

data_processing: Data was processed as described in Lee TI et al. Cell 2006 (PMID: 16630818) to calculate enrichment ratios and determine bound regions.

source_name: V6.5, RNA Pol2 phosphorylated Serine5 IP

extract_protocol: Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using RNA Polymerase II phosphoCTD (Serine 5) antibody. Purified immunoprecipitated DNA were amplified using two rounds of ligated mediated PCR, as described in Lee et al., Nature Protocols 2006 (PMID: 17406303).

value: embryonic stem cells

tag: antibody

value: anti-RNA Polymerase II phosphoCTD (Serine 5)

source_name: V6.5, input

extract_protocol: Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were extracted as described in Lee et al., Nature Protocols 2006 (PMID: 17406303).


title: AA401

source_name: Group A Streptococcus strain AA401


title: RNA_Pol2_Ser5phospho_mES_rep1, array2

label_protocol: Agilent Mammalian ChIP-on-chip protocol (version 9.1, Nov 2006).


title: cotyledon_Tendral_WMVinfected_7dpi_rep3

city: Espinardo

first: Daniel

last: Gonzalez-Ibeas

state: Murcia

address: Campus de Espinardo s/n

department: Biologia Estres y Patologia Vegetal

country: Spain

institute: CEBAS-CSIC

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: Data were normalised using the normalisation algorithm RMA with the package oligo version 1.8.2 (Carvalho et al. 2007, Biostatistics 8 (2): 485-499) written in R (R Development Core Team, http://www.R-project.org).

organism: Cucumis melo

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Germination of melon seeds was carried out in Petri dishes for 48 h at 25 ºC. After germination, seeds were sown in 0.5 L pots and kept in growth chambers (MLR-351H from Sanyo) with 16 h light/25 ºC and 8 h dark/18 ºC for about three weeks.

extract_protocol: Cotyledon samples were independently frozen in liquid N2 and stored at -80 ºC. RNA extracts were prepared from these samples using Tri-Reagent (Sigma Chemical Co., St. Louis, MO, USA) following the manufacturer´s instructions. To eliminate traces of genomic DNA, total RNA was incubated with DNAse I (New England Biolabs, London, UK) 10 min at 37 ºC. Then, reaction volume was adjusted to 100 µl and the aqueous phase extracted with phenol:chloroform:isoamilalcohol (125:24:1). Total RNA was precipitated with 10 % (v/v) NaCl 3M and 2.5 v of absolute ethanol by centrifugation (12.000 g, 20 min, 4º C).

treatment_protocol: The viral isolate used in this study was WMV-M116, kindly provided by Dr. Moriones (Estación Experimental “La Mayora”-CSIC, Málaga, Spain). Mechanical inoculations were carried out using standard procedures. Dehydrated viral inoculum was first revived by mechanical inoculation of squash fully-expanded cotyledons. Systemically infected squash leaves were harvested after 15 days post-inoculation (dpi) and used as inoculum source for melons. Squash leaves were ground in a sterile mortar in the presence of inoculation buffer (0.2 M phosphate buffer pH 8.0, 0.1 % v/v β-mercaptoethanol, 0.03 g/mL active charcoal) and, then, carborundum (0.037 mm diameter) dusted 7 days old melon cotyledons were rubbed with this infectious mixture. Control non-infected melon cotyledons were rubbed using only inoculation buffer (mock-inoculated controls).

value: cotyledon

tag: genotype

value: Tendral

tag: physiological condition

value: WMV infected

tag: days post-inoculation


title: cotyledon_Tendral_WMVinfected_7dpi_rep2


title: SS1096

source_name: Group A Streptococcus strain SS1096


title: AA188

source_name: Group A Streptococcus strain AA188


title: cotyledon_Tendral_mock_1dpi_rep1

value: mock inoculated


title: SS1468

source_name: Group A Streptococcus strain SS1468

source_name: Cy3, Cy5Group A Streptococcus strain Alab49


title: cotyledon_Tendral_WMVinfected_7dpi_rep1


title: cotyledon_Tendral_WMVinfected_3dpi_rep3


title: cotyledon_Tendral_WMVinfected_3dpi_rep1


title: SS1378

source_name: Group A Streptococcus strain SS1378


title: cotyledon_Tendral_WMVinfected_1dpi_rep3


title: cotyledon_Tendral_WMVinfected_1dpi_rep2


title: 2RSC3

source_name: Group A Streptococcus strain 2RSC3


title: cotyledon_Tendral_WMVinfected_1dpi_rep1


title: SS1376

source_name: Group A Streptococcus strain SS1376


title: cotyledon_Tendral_WMVinfected_3dpi_rep2


title: D998

source_name: Group A Streptococcus strain D998


title: 10RS101

source_name: Group A Streptococcus strain 10RS101


title: AA249

source_name: Group A Streptococcus strain AA249


title: D821

source_name: Group A Streptococcus strain D821


title: C142

source_name: Group A Streptococcus strain C142


title: cotyledon_TGR-1551_mock_7dpi_rep3


title: 19RS14

source_name: Group A Streptococcus strain 19RS14


title: SS1485

source_name: Group A Streptococcus strain SS1485


title: cotyledon_TGR-1551_mock_3dpi_rep3


title: cotyledon_TGR-1551_mock_7dpi_rep1


title: cotyledon_TGR-1551_mock_7dpi_rep2


title: AA216

source_name: Group A Streptococcus strain AA216