title: MC-02-5-EB-R-1

description: Test


title: MC-02-2-EB-R-1

status: Public on Jun 20 2017

type: RNA

city: Sheffield

first: Paul

last: Gokhale

address: Western Bank

department: Biomedical Science

country: United Kingdom

institute: University of Sheffield

description: Test

data_processing: Low-quality data was removed and raw Ct values were capped (Ct_max=35), scaled to the level of control genes (GAPDH, ACTB), quantile-normalized and finally inverted by subtracting each value from the maximum Ct_max.

label: EvaGreen

molecule: total RNA

organism: Homo sapiens

source_name: MEL1/INS GFP

label_protocol: High-Capacity cDNA Archive Kit (ThermoFisher Scientific) following manufacturers protocols with 10 cycles of amplification

extract_protocol: PicoPure RNA Isolation Kit (Arcturus Bioscience), QCed with 2100 Bioanalyzer (Agilent Technologies)

tag: cell line

value: MEL1/INS GFP

tag: cell type

value: ES

tag: cell line code

tag: starting culture conditions

value: DMEM/F-12 + 20% KOSR, 10ng/ml FGF2, MEF feeders

tag: teratoma, injected cell number(106)

tag: teratoma, volume of injection (ul)

tag: teratoma injection site

tag: teratoma injection position

tag: teratoma, mouse strain

tag: teratoma, mouse age (weeks)

tag: teratoma, mouse sex

tag: replicate

tag: time point (days)

value: EMBYOID BODY

tag: differentiation condition

value: NEUTRAL

tag: differentiation condition (details)

value: APEL


title: MC-02-22-EB-R-2

description: Test

value: MESODERM

value: APEL, 20ng/ml Activin A, 20ng/ml BMP4


title: MC-02-1-T-R-1

description: Test

value: subcutaneous

value: Back of the neck   or  Caudal flank near the hip.

value: NOD/SCID IL2R

value: Female

value: TERATOMA


title: MC-02-24-EB-R-2

description: Test

value: ECTODERM

value: APEL, 10uM Dorsomorphin, 10uM SB431542, 100ng/ml bFGF


title: MC-02-23-EB-R-2

description: Test


title: MC-02-1-EB-R-1

description: Test

value: START


title: MC-02-19-EB-R-2

description: Test


title: MC-02-21-EB-R-2

description: Test

value: ENDODERM

value: APEL, 100ng/ml Activin A, 1ng/ml BMP4


title: MC-02-26-EB-R-2

description: Test

value: MEL1/INS GFP

value: ES


title: MC-02-25-EB-R-2

description: Test

value: DMEM/F-12 + 20% KOSR, 10ng/ml FGF2, MEF feeders

value: EMBYOID BODY


title: MC-02-20-EB-R-2

description: Test


title: MC-02-29-EB-R-3

description: Test


title: MC-02-28-EB-R-3

description: Test

value: NEUTRAL

value: APEL


title: MC-02-18-EB-R-2

description: Test

value: MESODERM

value: APEL, 20ng/ml Activin A, 20ng/ml BMP4


title: MC-02-16-EB-R-2

description: Test


title: MC-02-12-EB-R-1

description: Test


title: MC-02-14-EB-R-2

description: Test


title: MC-02-15-EB-R-2

description: Test


title: MC-02-13-EB-R-1

description: Test


title: MC-01-4-EB-R-1

description: Test

value: HES3/MIXL1 GFP

value: Z


title: MC-01-9-EB-R-1

description: Test


title: MC-01-8-EB-R-1

description: Test


title: MC-01-7-EB-R-1

description: Test


title: MC-01-6-EB-R-1

description: Test


title: MC-01-5-EB-R-1

description: Test


title: MC-02-10-EB-R-1

description: Test


title: MC-01-3-EB-R-1

description: Test


title: MC-01-3-T-R-3

description: Test

source_name: HES3/MIXL1 GFP

value: subcutaneous

value: Back of the neck   or  Caudal flank near the hip.

value: NOD/SCID IL2R

value: Female


title: MC-02-17-EB-R-2

description: Test


title: MC-01-37-EB-R-3

description: Test

value: ECTODERM

value: APEL, 10uM Dorsomorphin, 10uM SB431542, 100ng/ml bFGF


title: MC-01-39-EB-R-3

description: Test


title: MC-01-38-EB-R-3

description: Test

value: ENDODERM

value: APEL, 100ng/ml Activin A, 1ng/ml BMP4


title: MC-01-29-EB-R-3

description: Test

value: ES


title: MC-01-2-T-R-2

description: Test

value: DMEM/F-12 + 20% KOSR, 10ng/ml FGF2, MEF feeders

value: TERATOMA


title: MC-01-36-EB-R-3

description: Test

value: EMBYOID BODY

value: NEUTRAL


title: MC-01-35-EB-R-3

description: Test

value: MESODERM


title: MC-01-31-EB-R-3

description: Test

value: APEL, 20ng/ml Activin A, 20ng/ml BMP4


title: MC-01-34-EB-R-3

description: Test

value: HES3/MIXL1 GFP


title: MC-01-32-EB-R-3

description: Test

value: Z

value: APEL


title: MC-01-2-EB-R-1

description: Test


title: MC-02-11-EB-R-1

description: Test

value: MEL1/INS GFP


title: MC-01-26-EB-R-2

description: Test


title: MC-01-25-EB-R-2

description: Test


title: MC-01-23-EB-R-2

description: Test


title: MC-01-24-EB-R-2

description: Test


title: MC-01-21-EB-R-2

description: Test


title: MC-01-20-EB-R-2

description: Test


title: MC-01-1-EB-R-1

description: Test

value: START


title: MC-01-1-T-R-1

description: Test

value: subcutaneous

value: Back of the neck   or  Caudal flank near the hip.

value: NOD/SCID IL2R

value: Female


title: MC-01-22-EB-R-2

description: Test


title: MC-01-15-EB-R-2

description: Test


title: MC-01-19-EB-R-2

description: Test


title: MC-01-16-EB-R-2

description: Test

value: ECTODERM

value: APEL, 10uM Dorsomorphin, 10uM SB431542, 100ng/ml bFGF


title: MC-01-14-EB-R-2

description: Test

value: ES

value: DMEM/F-12 + 20% KOSR, 10ng/ml FGF2, MEF feeders


title: MC-01-33-EB-R-3

description: Test

value: EMBYOID BODY


title: MC-01-27-EB-R-3

description: Test


title: MC-01-12-EB-R-1

description: Test

value: ENDODERM

value: APEL, 100ng/ml Activin A, 1ng/ml BMP4


title: MC-01-13-EB-R-1

description: Test

value: MESODERM

value: APEL, 20ng/ml Activin A, 20ng/ml BMP4


title: MC-01-11-EB-R-1

description: Test

value: HES3/MIXL1 GFP

value: Z


title: MC-01-10-EB-R-1

description: Test

value: NEUTRAL

value: APEL


title: G-Z-079-EB-R-3

description: Test

value: DMEM/F12 + 20% KOSR, 5ng/mL bFGF, MEF feeders


title: G-Z-14-T-R-1

description: Test

value: ESC

value: center of upper back

value: SCID-Beige

value: TERATOMA


title: MC-01-17-EB-R-2

description: Test


title: G-Z-195-T-R-3

description: Test

value: Female


title: G-Z-043-EB-R-3

description: Test

value: ES


title: G-Z-045-EB-R-3

description: Test


title: G-Z-047-EB-R-3

description: Test


title: G-Z-076-EB-R-3

description: Test


title: G-Z-077-EB-R-3

description: Test

value: ECTODERM

value: APEL, 10uM Dorsomorphin, 10uM SB431542, 100ng/ml bFGF


title: G-Z-049-EB-R-3

description: Test

value: EMBYOID BODY

value: ENDODERM


title: G-Z-050-EB-R-3

description: Test


title: G-Z-044-EB-R-3

description: Test


title: G-Z-035-EB-R-3

description: Test

value: START


title: G-Z-031-EB-R-2

description: Test


title: G-Z-027-EB-R-2

description: Test


title: G-Z-030-EB-R-2

description: Test


title: G-Z-029-EB-R-2

description: Test

value: MESODERM

value: APEL, 20ng/ml Activin A, 20ng/ml BMP4


title: G-Z-024-EB-R-2

description: Test

value: Z


title: G-Z-023-EB-R-2

description: Test


title: G-Z-032-EB-R-2

description: Test

value: APEL, 100ng/ml Activin A, 1ng/ml BMP4


title: G-Z-033-EB-R-2

description: Test


title: G-Z-022-EB-R-2

description: Test


title: G-Z-017-EB-R-1

description: Test


title: G-Z-019-EB-R-1

description: Test

value: NEUTRAL

value: APEL


title: G-Z-013-EB-R-1

description: Test

value: DMEM/F12 + 20% KOSR, 5ng/mL bFGF, MEF feeders


title: G-Z-021-EB-R-2

description: Test


title: G-Z-018-EB-R-1

description: Test


title: G-Z-004-EB-R-1

description: Test


title: G-Z-003-EB-R-1

description: Test


title: G-Z-028-EB-R-2

description: Test


title: G-Z-009-EB-R-1

description: Test


title: G-Z-034-EB-R-2

description: Test


title: G-Z-011-EB-R-1

description: Test


title: G-Z-002-EB-R-1

description: Test


title: G-Z-012-EB-R-1

description: Test


title: G-Z-001-EB-R-1

description: Test


title: G-03-136-EB-R-2

description: Test

value: IPS


title: G-03-137-EB-R-2

description: Test


title: G-03-156-EB-R-3

description: Test


title: G-03-131-T-R-3

description: Test

value: center of upper back

value: SCID-Beige


title: G-03-121-EB-R-1

description: Test


title: G-03-129-T-R-2

description: Test

value: Female

value: TERATOMA


title: G-03-119-EB-R-1

description: Test


title: G-03-120-EB-R-1

description: Test


title: G-03-134-EB-R-2

description: Test


title: G-03-127-T-R-1

description: Test


title: G-03-109-EB-R-1

description: Test

value: ECTODERM


title: G-03-123-EB-R-1

description: Test


title: G-03-143-EB-R-3

description: Test


title: G-03-108-EB-R-1

description: Test


title: G-02-190-EB-R-3

description: Test

value: ES


title: G-02-193-EB-R-3

description: Test

value: EMBYOID BODY


title: G-02-191-EB-R-3

description: Test

value: APEL, 10uM Dorsomorphin, 10uM SB431542, 100ng/ml bFGF


title: G-02-192-EB-R-3

description: Test

value: ENDODERM


title: G-03-093-EB-R-1

description: Test

value: START


title: G-02-189-EB-R-3

description: Test

value: MESODERM

value: APEL, 20ng/ml Activin A, 20ng/ml BMP4


title: G-02-194-EB-R-3

description: Test


title: G-02-182-EB-R-3

description: Test


title: G-02-188-EB-R-3

description: Test

value: APEL, 100ng/ml Activin A, 1ng/ml BMP4


title: G-02-185-EB-R-3

description: Test


title: G-02-186-EB-R-3

description: Test

value: NEUTRAL


title: G-02-187-EB-R-3

description: Test


title: G-02-184-EB-R-3

description: Test


title: G-02-175-EB-R-2

description: Test

value: APEL


title: G-02-183-EB-R-3

description: Test

value: DMEM/F12 + 20% KOSR, 5ng/mL bFGF, MEF feeders


title: G-02-167-EB-R-2

description: Test


title: G-02-165-EB-R-2

description: Test


title: G-02-174-EB-R-2

description: Test


title: G-02-162-T-R-2

description: Test


title: G-02-155-EB-R-2

description: Test


title: G-02-154-EB-R-2

description: Test


title: G-02-160-T-R-1

description: Test


title: G-02-152-EB-R-2

description: Test


title: G-02-102-EB-R-1

description: Test


title: G-02-145-EB-R-2

description: Test


title: chip4_0Cu_Cy5_75Cu_Cy3 Replicate 2

city: Cologne

first: Fernando

last: Andres

address: Carl von Linne 10

department: Plant Developmental Biology

country: Germany

institute: Max Planck Institute for Plant Breeding Research

hyb_protocol: From http://ag.arizona.edu/microarray/Microarraymethod1.doc Microarrays were re-hydrated by exposing them to water vapor for 10 seconds (four times). Next microarrays were cross-linked by ultraviolet (UV) irradiation of 180 mJ in a Stratalinker 1800 UV (Stratagene). Subsequently, microarrays were washed with 1% SDS (w/v) (Sodium Dodecyl Sulfate) for 5 min and 10 times with H2O milliQ (Millipore), washed with 100% ethanol 5 times and then dried by centrifugation at 200 g. After this pre-treatment, microarrays were hybridized overnight at 55 °C with hybridization solution [48 pmol of each labeled sample; deionized formamide 50% (v/v);] 3X SSC (Saline-Sodium Citrate); Denhardt´s solution [5 X and SDS 0.1% (w/v)]. The hybridization solution was denaturalized for 5 min at 65 °C and applied between the microarray and a coverslip LifterSlipTM (Erie Scientific).

scan_protocol: The hybridized microarray slides were washed and scanned using a Gene Pix Autoloader (Axon/Molecular Devices, 4200A01, Sunnyvale, CA). Spot finding and data extraction was done using GenePix Pro 6 software (Axon/Molecular Devices, Sunnyvale, CA).

data_processing: Quality control, normalization and determination of the differentially expressed genes were conducted in R using the Limma package (Smyth 2005), as previously described in (Andrés et al. 2009). To determine the false-positive ratio (FDR), the P values were adjusted by a test multiple test according to the method of Benjamini and Hochberg´s (Benjamini and Hochberg 1995). The genes that showed a differential expression with fold-change (FC) minimum of 2 for both conditions, represented as log2(FC) ≥ |1|of > 2-fold (-1 > log-fold change [½MS + 75 µM/ ½MS] > 1) with a P value of 0.05 (FDR = 0.5%) were selected.

organism: Oryza sativa

source_name: Seedlings

label_protocol: The obtained amplified RNA (aRNA) was labeled by using the CyDye Post-Labeling Reactive Dye Pack, which generates fluorescent Cy3- and Cy5-labeled probes by a post-labeling (amino allyl) method (GE Healthcare). Each biological replicate was labeled with Cy3 and Cy5 to produce four pairs of replicate dye-swaps, which were used for microarray hybridization

growth_protocol: The plants were cultured in plates during 8 days under diferent concentration of CuSO4 in the medium.

extract_protocol: Total RNAs were isolated with the RNeasy plant mini kit (QIAgen, Hilden, Germany; Ref. 74904), following the manufacturer’s instructions. The aRNA amplification and labeling were performed with the AminoAllyl MessageAmpTM II aRNA Amplification kit (Ambion) according to the manufacturer’s instructions. One microgram of total RNA of each sample was used for the amplification. The final concentration of obtained aRNA was determined with NanoDrop ND1000 Spectrophotometer.

treatment_protocol: Rice (Oryza sativa subsp japonica), cv. Nipponbare, seeds were surface-sterilized and stratified for 2 d at 4° C, and then germinated on ½MS plates with 1% Sucrose (Murashige and Skoog 1962). Two different Cu concentration conditions were compared, slight Cu deficiency (0 µM CuSO4) and Cu excess (75 µM CuSO4).

tag: treatment

value: 0µM CuSO4

tag: variety

value: Nippombare

tag: age

value: 8 days

value: 75µM CuSO4


title: G-02-101-EB-R-1

description: Test

tag: cell line

tag: cell type


title: chip7_0Cu_Cy3_75Cu_Cy5 Replicate 3


title: chip10_0Cu_Cy5_75Cu_Cy3 Replicate 4


title: G-02-100-EB-R-1

description: Test

tag: cell line code

tag: starting culture conditions


title: chip5_0Cu_Cy5_75Cu_Cy3 Replicate 1


title: chip2_0Cu_Cy3_75Cu_Cy5 Replicate 2


title: chip9_0Cu_Cy3_75Cu_Cy5 Replicate 4


title: chip6_0Cu_Cy3_75Cu_Cy5 Replicate 1


title: G-02-086-EB-R-1

description: Test

tag: teratoma, injected cell number(106)

tag: teratoma, volume of injection (ul)


title: G-02-085-EB-R-1

description: Test

tag: teratoma injection site

tag: teratoma injection position


title: chip3_0Cu_Cy5_75Cu_Cy3 Replicate 3


title: G-02-084-EB-R-1

description: Test

tag: teratoma, mouse strain

tag: teratoma, mouse age (weeks)


title: glp-4_DMSO_C

city: Houston

first: Natalia

middle: V

last: Kirienko

state: TX

address: 6100 Main St. MS140

department: BioSciences

country: USA

institute: Rice University

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: Data were analyzed with GC-RMA in the R programming language, using the Bioconductor package gcrma. Analysis was performed using default settings.

label: biotin

organism: Caenorhabditis elegans

source_name: glp-4,OP50+DMSO, 8h, S Basal liquid

label_protocol: Affymetrix standard protocol

growth_protocol: glp-4(bn2ts) worms were synchronized by hypochlorite treatment. Arrested L1s were plated on 10 cm NGM plates seeded with E. coli OP50 and grown at 15°C overnight then shifted to 25°C for 44h until they reached sterile young adult stage.

extract_protocol: RNA was extracted using TRI Reagent (Molecular Research Center) according to manufacturer's instructions and purified using an RNeasy column (Qiagen).

treatment_protocol: Animals were grown until young adult stage. Afterward, worms were incubated for 8 hours at 25°C on 10 cm plates with solid agar or in 6-well plates with liquid media with appropriate bacterial strain and/or chemical.

tag: media

value: S Basal

value: E. coli OP50 + 1% DMSO

tag: tissue

value: Whole organism


title: glp-4_PA14_SK_B

source_name: glp-4,PA14, 8h, SK agar

value: P. aeruginosa PA14


title: glp-4_PA14_SK_C


title: glp-4_Phe_C

source_name: glp-4,OP50+Phe, 8h,  S Basal liquid

value: E. coli OP50 + 1mM 1,10-phenanthroline (1% DMSO total)


title: glp-4_Phe_A


title: glp-4_Phe_B


title: glp-4_OP50_LK_B

source_name: glp-4,OP50, 8h, LK liquid

value: E. coli OP50


title: glp-4_PA14_LK_C

source_name: glp-4,PA14, 8h, LK liquid


title: glp-4_PA14_LK_A


title: glp-4_DMSO_B


title: G-02-073-EB-R-1

description: Test

value: ES

tag: teratoma, mouse sex

tag: replicate

tag: time point (days)

value: EMBYOID BODY

tag: differentiation condition


title: glp-4_DMSO_A

tag: treatment


title: glp-4_OP50_LK_C


title: glp-4_PA14_LK_B


title: G-02-071-EB-R-1

description: Test

tag: cell line

value: ECTODERM

tag: differentiation condition (details)

value: APEL, 10uM Dorsomorphin, 10uM SB431542, 100ng/ml bFGF


title: glp-4_PA14_SK_A


title: G-02-060-EB-R-1

description: Test

tag: cell type

tag: cell line code

value: START


title: glp-4_OP50_SK_C

source_name: glp-4,OP50, 8h, SK agar


title: glp-4_OP50_LK_A


title: glp-4_OP50_NGM_B

source_name: glp-4,OP50, 8h, NGM agar

value: NGM


title: glp-4_OP50_SK_B


title: glp-4_OP50_NGM_C


title: glp-4_OP50_SK_A


title: glp-4_OP50_NGM_A


title: G-01-201-T-R-2

description: Test

value: IPS

tag: starting culture conditions

value: DMEM/F12 + 20% KOSR, 5ng/mL bFGF, MEF feeders

tag: teratoma, injected cell number(106)

value: center of upper back

value: SCID-Beige

value: Female

value: TERATOMA


title: G-01-202-T-R-3

description: Test

tag: teratoma, volume of injection (ul)

tag: teratoma injection site


title: G-01-200-T-R-1

description: Test

tag: teratoma injection position

tag: teratoma, mouse strain


title: G-02-072-EB-R-1

description: Test

tag: teratoma, mouse age (weeks)

value: MESODERM

value: APEL, 20ng/ml Activin A, 20ng/ml BMP4


title: G-01-117-EB-R-3

description: Test

value: NEUTRAL

value: APEL


title: G-02-070-EB-R-1

description: Test

value: ENDODERM

value: APEL, 100ng/ml Activin A, 1ng/ml BMP4


title: G-01-115-EB-R-3

description: Test

value: EMBYOID BODY


title: G-01-116-EB-R-3

description: Test


title: G-01-107-EB-R-3

description: Test

value: ECTODERM


title: G-01-114-EB-R-3

description: Test

value: APEL, 10uM Dorsomorphin, 10uM SB431542, 100ng/ml bFGF


title: G-01-106-EB-R-3

description: Test


title: G-01-105-EB-R-3

description: Test


title: G-01-104-EB-R-3

description: Test


title: 21LH+8

type: genomic

city: Tartu

first: Triin

last: Laisk-Podar

address: Puusepa 8

department: Obstetrics and Gynecology

country: Estonia

institute: University of Tartu

description:
Reanalysis of GSM1906645
SAMPLE 32

hyb_protocol: According to Illumina protocol

scan_protocol: According to Illumina protocol

data_processing:
Data quality control and preprocessing were performed using the Bioconductor package RnBeads ver. 1.1.8.The data was normalized using methylumi-implemented Illumina scaling normalization method.
Matrix signal intensities (non-normalized) contains unmethylated  and methylated  signal intensities

label: Cy3, Cy5

molecule: genomic DNA

source_name: Endometrium

label_protocol: According to Illumina protocol

extract_protocol: Genomic DNA was isolated using AllPrep DNA/RNA/miRNA Universal Kit (Qiagen) according to the manufacturer’s instructions

tag: time point

tag: menstrual phase

value: Mid secretory

tag: age

tag: type

value: Receptive endometrium


title: G-01-098-EB-R-2

description: Test

value: IPS

tag: teratoma, mouse sex

tag: replicate

tag: time point (days)

tag: differentiation condition


title: G-01-097-EB-R-2

description: Test

tag: cell line

tag: cell type

value: DMEM/F12 + 20% KOSR, 5ng/mL bFGF, MEF feeders

tag: differentiation condition (details)


title: BALF Cells_15mg silica_44 week post-exposure_rep3

city: Morgantown

first: Rajendran

last: Sellamuthu

state: WV

address: 1095 Willowdale Rd

department: HELD

description: Sample name: T44_BALF_S(15)_3

hyb_protocol: Employing materials and protocols provided by Illumina, Inc (San Diego, CA,), each labeled cRNA sample was hybridized to RatRef-12 v1.0 expression beadchip (Illumina, Inc,) for 20 hrs at 580C. Following hybridization, microarrays were washed to remove unbound and non-specifically hybridized target molecules and stained with Cy3-streptavidin conjugate (Illumina, Inc,). This was followed by a non-stringent washing to remove unbound conjugate. The hybridization of microarrays were performed at National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV

scan_protocol: The arrays were scanned with the Illumina BeadStation 500 platform, following the protocol provided by the manufacturer (Illumina, Inc). Scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.

data_processing: Array data were extracted using Illumina's BeadStudio software (Framework version 3.0.19.0). Normalization and statistical analysis of the expression data were carried out in R/Bioconducter using the ‘lumi’ and ‘limma’ packages. The ‘lumi’ Bioconductor package covered the data input, quality control, force positive background correction, variance stabilization, normalization and gene annotation (http://bioconductor.org/packagees/2.2/ bioc/vignettes/lumi/inst/doc/lumi.pdf). Robust spline normalization was used to generate the values in the data table. After normalization, Lumi code deletes genes undetected (detection p-value, >0.01) and resulting in a subset of genes detected (detection p-value, <0.01) on the array. A linear model analysis using ‘limma’ package in R was conducted to identify differentially expressed genes. p values were calculated and log fold changes were converted to standard fold changes.  Resulting raw p-values were corrected for false discovery rate using the Benjamini-Hochberg method.

label: Biotin

organism: Rattus norvegicus

source_name: 15mg/m3 silica, 44 week post-exposure rat 195 BALF Cells

label_protocol:
Biotin-labeled cRNA was generated from 375 ng RNA samples each by employing the Illumina TotalPrep RNA Amplification Kit (Ambion, Inc, Austin, TX).
The labeling of microarrays were performed at National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV

growth_protocol: Rats were housed in the animal facility at the National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV. The animals were kept under controlled lighting (12-hour light-dark cycle), temperature (72 ± 50 F), and humidity (50 ± 20%) with free access to food and water.

extract_protocol: Total RNA was isolated from the BALF cells samples using RNeasy  Mini Kit (Qiagen, Inc, Valencia, CA) with on-column DNA digestion following the manufacturer's instructions.

treatment_protocol: Rats were exposed to air (control) or crystalline silica by inhalation (15 mg/m3, 6 hours/day, 5 days). Rats were sacrificed at 44 weeks following the last silica exposure.

tag: strain

value: Fisher (CDF) 344

tag: gender

value: Male

value: Approximately 3 month old

value: BALF cells

tag: stress

value: silica


title: BALF Cells_0mg silica_44 week post-exposure_rep5

institute: National Institute for Occupational Safety and Health

description: Sample name: T44_BALF_S(0)_5

source_name: 0mg/m3 silica, 44 week post-exposure rat 206 BALF Cells

value: control


title: BALF Cells_15mg silica_44 week post-exposure_rep6

description: Sample name: T44_BALF_S(15)_6

source_name: 15mg/m3 silica, 44 week post-exposure rat 198 BALF Cells


title: BALF Cells_0mg silica_44 week post-exposure_rep3

description: Sample name: T44_BALF_S(0)_3

source_name: 0mg/m3 silica, 44 week post-exposure rat 203 BALF Cells


title: BALF Cells_0mg silica_44 week post-exposure_rep1

description: Sample name: T44_BALF_S(0)_1

source_name: 0mg/m3 silica, 44 week post-exposure rat 201 BALF Cells


title: 48LH+2

description: SAMPLE 33

value: Early secretory

value: Pre-receptive endometrium


title: G-01-096-EB-R-2

description: Test

tag: cell line code

tag: starting culture conditions

tag: teratoma, injected cell number(106)

tag: teratoma, volume of injection (ul)

tag: teratoma injection site

tag: teratoma injection position

value: ENDODERM


title: G-01-095-EB-R-2

description: Test

tag: teratoma, mouse strain

tag: teratoma, mouse age (weeks)


title: BALF Cells_0mg silica_44 week post-exposure_rep6

description: Sample name: T44_BALF_S(0)_6

source_name: 0mg/m3 silica, 44 week post-exposure rat 208 BALF Cells

tag: age


title: G-01-091-EB-R-3

description: Test

tag: teratoma, mouse sex

tag: replicate

tag: time point (days)


title: 15LH+8

description:
Reanalysis of GSM1906643
SAMPLE 31

tag: time point

tag: menstrual phase

tag: type


title: G-01-090-EB-R-3

description: Test

tag: cell line

tag: cell type

tag: differentiation condition

tag: differentiation condition (details)

value: APEL, 100ng/ml Activin A, 1ng/ml BMP4


title: 01LH+8

description:
Reanalysis of GSM1906632
SAMPLE 23


title: 12009LH+2

description: SAMPLE 34


title: BALF Cells_0mg silica_44 week post-exposure_rep4

description: Sample name: T44_BALF_S(0)_4

source_name: 0mg/m3 silica, 44 week post-exposure rat 205 BALF Cells

tag: strain

tag: gender

tag: stress


title: 05LH+8

description:
Reanalysis of GSM1906635
SAMPLE 20


title: 40LH+2

description: SAMPLE 29


title: 25LH+2

description: SAMPLE 28


title: BALF Cells_15mg silica_44 week post-exposure_rep5

description: Sample name: T44_BALF_S(15)_5

source_name: 15mg/m3 silica, 44 week post-exposure rat 197 BALF Cells


title: BALF Cells_15mg silica_44 week post-exposure_rep2

description: Sample name: T44_BALF_S(15)_2

source_name: 15mg/m3 silica, 44 week post-exposure rat 194 BALF Cells


title: 15LH+2

description: SAMPLE 21


title: BALF Cells_15mg silica_44 week post-exposure_rep1

description: Sample name: T44_BALF_S(15)_1

source_name: 15mg/m3 silica, 44 week post-exposure rat 193 BALF Cells


title: 17LH+8

description:
Reanalysis of GSM1906644
SAMPLE 30


title: 12LH+8

description:
Reanalysis of GSM1906640
SAMPLE 24


title: G-01-089-EB-R-3

description: Test

tag: cell line code

tag: starting culture conditions

tag: teratoma, injected cell number(106)

tag: teratoma, volume of injection (ul)

tag: teratoma injection site

tag: teratoma injection position

value: EMBYOID BODY

value: MESODERM

value: APEL, 20ng/ml Activin A, 20ng/ml BMP4


title: 17LH+2

description: SAMPLE 25

tag: age


title: 12LH+2

description: SAMPLE 15

tag: time point


title: 21LH+2

description: SAMPLE 22

tag: menstrual phase


title: 13LH+8

description:
Reanalysis of GSM1906641
SAMPLE 19

value: Mid secretory

tag: type


title: 14LH+8

description:
Reanalysis of GSM1906642
SAMPLE 26

value: Receptive endometrium


title: 13LH+2

description: SAMPLE 18


title: 14LH+2

description: SAMPLE 17


title: G-01-083-EB-R-2

description: Test

tag: cell line

value: IPS

tag: teratoma, mouse strain

tag: teratoma, mouse age (weeks)

tag: teratoma, mouse sex

tag: replicate

tag: time point (days)

value: NEUTRAL

value: APEL


title: BALF Cells_0mg silica_44 week post-exposure_rep2

description: Sample name: T44_BALF_S(0)_2

source_name: 0mg/m3 silica, 44 week post-exposure rat 202 BALF Cells

tag: strain

value: Fisher (CDF) 344

tag: gender

value: Male

tag: cell type

tag: stress


title: 03LH+8

description:
Reanalysis of GSM1906633
SAMPLE 27


title: G-01-082-EB-R-2

description: Test

tag: cell line code

tag: starting culture conditions

value: DMEM/F12 + 20% KOSR, 5ng/mL bFGF, MEF feeders

tag: teratoma, injected cell number(106)

tag: teratoma, volume of injection (ul)

tag: differentiation condition

tag: differentiation condition (details)


title: 06LH+2

description: SAMPLE 14

tag: time point

tag: menstrual phase

tag: age

tag: type


title: G-01-080-EB-R-2

description: Test

tag: cell line

tag: teratoma injection site

tag: teratoma injection position

tag: teratoma, mouse strain

tag: teratoma, mouse age (weeks)

tag: teratoma, mouse sex


title: G-01-074-EB-R-3

description: Test

tag: cell type

tag: replicate

tag: time point (days)

value: START


title: G-01-081-EB-R-2

description: Test

tag: cell line code

tag: starting culture conditions

tag: teratoma, injected cell number(106)

value: ECTODERM

value: APEL, 10uM Dorsomorphin, 10uM SB431542, 100ng/ml bFGF


title: 06LH+8

description:
Reanalysis of GSM1906636
SAMPLE 16


title: BALF Cells_15mg silica_44 week post-exposure_rep4

description: Sample name: T44_BALF_S(15)_4

source_name: 15mg/m3 silica, 44 week post-exposure rat 196 BALF Cells

tag: strain

tag: gender

value: Approximately 3 month old

value: BALF cells

tag: stress

value: silica


title: G-01-069-EB-R-1

description: Test

tag: teratoma, volume of injection (ul)

value: EMBYOID BODY

tag: differentiation condition

tag: differentiation condition (details)


title: G-01-068-EB-R-1

description: Test

tag: cell line

tag: teratoma injection site

value: MESODERM


title: Blood_0mg silica_44 week post-exposure_rep6

description: Sample name: T44_B_S(0)_6

source_name: 0mg/m3 silica, 44 week post-exposure rat 208 Blood

extract_protocol: Total RNA was isolated from the blood samples using Mouse RibopureTM Blood isolation kit (Ambion Inc, Austin, TX) following the protocol provided by the kit manufacturer. The total RNA isolated was digested with RNase-free DNase and further purified using RNeasy Mini kit (Qiagen Inc, Valencia, CA) following the recommendations of the supplier. The globin mRNA present in abundance in the blood RNA samples was depleted using the GlobinclearTM – Mouse/Rat globin mRNA removal kit (Ambion Inc, Austin, TX).

tag: age

tag: tissue

value: Blood

value: control


title: Blood_15mg silica_44 week post-exposure_rep4

description: Sample name: T44_B_S(15)_4

source_name: 15mg/m3 silica, 44 week post-exposure rat 196 Blood


title: G-01-067-EB-R-1

description: Test

tag: teratoma injection position

tag: teratoma, mouse strain

tag: teratoma, mouse age (weeks)

tag: teratoma, mouse sex


title: Blood_0mg silica_44 week post-exposure_rep1

description: Sample name: T44_B_S(0)_1

source_name: 0mg/m3 silica, 44 week post-exposure rat 201 Blood


title: 04LH+8

description:
Reanalysis of GSM1906634
SAMPLE 11

tag: time point

tag: menstrual phase

value: Mid secretory

tag: type

value: Receptive endometrium


title: 12011LH+8

description:
Reanalysis of GSM1906638
SAMPLE 13


title: Blood_15mg silica_44 week post-exposure_rep6

description: Sample name: T44_B_S(15)_8

source_name: 15mg/m3 silica, 44 week post-exposure rat 198 Blood

tag: strain


title: G-01-065-EB-R-2

description: Test

tag: cell type

value: IPS

tag: cell line code

tag: starting culture conditions

tag: teratoma, injected cell number(106)

tag: replicate

tag: time point (days)

value: NEUTRAL


title: Blood_0mg silica_44 week post-exposure_rep3

description: Sample name: T44_B_S(0)_3

source_name: 0mg/m3 silica, 44 week post-exposure rat 203 Blood

value: Fisher (CDF) 344

tag: gender

tag: stress


title: Blood_0mg silica_44 week post-exposure_rep2

description: Sample name: T44_B_S(0)_2

source_name: 0mg/m3 silica, 44 week post-exposure rat 202 Blood

value: Male

tag: age

tag: tissue


title: G-01-063-EB-R-2

description: Test

tag: cell line

value: DMEM/F12 + 20% KOSR, 5ng/mL bFGF, MEF feeders

tag: teratoma, volume of injection (ul)

tag: teratoma injection site

tag: teratoma injection position

tag: teratoma, mouse strain

tag: differentiation condition

tag: differentiation condition (details)


title: 12013LH+8

description:
Reanalysis of GSM1906639
SAMPLE 12

source_name: Endometrium

tag: time point

tag: menstrual phase

tag: type


title: 05LH+2

description: SAMPLE 10

value: Early secretory

value: Pre-receptive endometrium


title: Blood_0mg silica_44 week post-exposure_rep4

description: Sample name: T44_B_S(0)_4

source_name: 0mg/m3 silica, 44 week post-exposure rat 205 Blood

tag: strain


title: G-01-062-EB-R-2

description: Test

tag: cell type

tag: cell line code

tag: starting culture conditions

tag: teratoma, injected cell number(106)

tag: teratoma, mouse age (weeks)

tag: teratoma, mouse sex

tag: replicate

value: ENDODERM

value: APEL, 100ng/ml Activin A, 1ng/ml BMP4


title: G-01-064-EB-R-2

description: Test

tag: cell line

tag: teratoma, volume of injection (ul)

tag: time point (days)

value: APEL, 20ng/ml Activin A, 20ng/ml BMP4


title: Blood_15mg silica_44 week post-exposure_rep3

description: Sample name: T44_B_S(15)_3

source_name: 15mg/m3 silica, 44 week post-exposure rat 195 Blood

tag: gender

tag: age

value: Approximately 3 month old

tag: tissue

tag: stress

value: silica


title: Blood_15mg silica_44 week post-exposure_rep1

description: Sample name: T44_B_S(15)_1

source_name: 15mg/m3 silica, 44 week post-exposure rat 193 Blood


title: G-01-056-EB-R-2

description: Test

tag: teratoma injection site

tag: teratoma injection position

tag: teratoma, mouse strain

value: EMBYOID BODY

tag: differentiation condition

value: START

tag: differentiation condition (details)


title: 25LH+8

description:
Reanalysis of GSM1906646
SAMPLE 8

tag: time point

tag: menstrual phase

tag: type


title: G-01-054-EB-R-1

description: Test

tag: cell type

tag: cell line code

tag: starting culture conditions

tag: teratoma, injected cell number(106)

tag: teratoma, mouse age (weeks)

tag: teratoma, mouse sex

value: ECTODERM

value: APEL, 10uM Dorsomorphin, 10uM SB431542, 100ng/ml bFGF


title: 12011LH+2

description: SAMPLE 5

tag: age


title: G-01-051-EB-R-1

description: Test

tag: cell line

tag: teratoma, volume of injection (ul)

tag: replicate

tag: time point (days)

value: APEL


title: Blood_15mg silica_44 week post-exposure_rep2

description: Sample name: T44_B_S(15)_2

source_name: 15mg/m3 silica, 44 week post-exposure rat 194 Blood

tag: strain

tag: gender

tag: tissue

value: Blood

tag: stress


title: Lung_15mg silica_44 week post-exposure_rep5

description: Sample name: T44_L_S(15)_5

source_name: 15mg/m3 silica, 44 week post-exposure rat 197 Lung

extract_protocol: Total RNA was isolated from the lung samples using RNeasy Fibrous Tissue Mini Kit (Qiagen, Inc, Valencia, CA) with on-column DNA digestion following the manufacturer's instructions.

value: Lung

tag: time

value: 44 week post-exposure


title: Blood_15mg silica_44 week post-exposure_rep5

description: Sample name: T44_B_S(15)_5

source_name: 15mg/m3 silica, 44 week post-exposure rat 197 Blood

value: Fisher (CDF) 344

value: Male


title: G-01-052-EB-R-1

description: Test

value: IPS

value: DMEM/F12 + 20% KOSR, 5ng/mL bFGF, MEF feeders

tag: teratoma injection site

tag: teratoma injection position

tag: teratoma, mouse strain

tag: differentiation condition

tag: differentiation condition (details)


title: Lung_15mg silica_44 week post-exposure_rep2

description: Sample name: T44_L_S(15)_2

source_name: 15mg/m3 silica, 44 week post-exposure rat 194 Lung


title: 12013LH+2

description: SAMPLE 2

tag: time point

tag: menstrual phase

value: Early secretory

tag: type

value: Pre-receptive endometrium


title: G-01-042-EB-R-1

description: Test

tag: cell line

tag: cell type

tag: cell line code

tag: starting culture conditions

tag: teratoma, injected cell number(106)

tag: teratoma, mouse age (weeks)

tag: teratoma, mouse sex


title: 04LH+2

description: SAMPLE 1

tag: age


title: 03LH+2

description: SAMPLE 9


title: G-01-041-EB-R-1

description: Test

tag: teratoma, volume of injection (ul)

tag: replicate

tag: time point (days)

value: ENDODERM

value: APEL, 100ng/ml Activin A, 1ng/ml BMP4


title: 40LH+8

description:
Reanalysis of GSM1906647
SAMPLE 4

value: Mid secretory

value: Receptive endometrium


title: G-01-040-EB-R-1

description: Test

tag: teratoma injection site

tag: teratoma injection position

tag: teratoma, mouse strain

value: EMBYOID BODY

value: MESODERM

value: APEL, 20ng/ml Activin A, 20ng/ml BMP4


title: Lung_0mg silica_44 week post-exposure_rep3

description: Sample name: T44_L_S(0)_3

source_name: 0mg/m3 silica, 44 week post-exposure rat 203 Lung

tag: strain

tag: gender

value: Approximately 3 month old

tag: tissue

tag: stress

value: control

tag: time


title: 12009LH+9

description:
Reanalysis of GSM1906637
SAMPLE 3

tag: time point

tag: menstrual phase

tag: type


title: Lung_15mg silica_44 week post-exposure_rep1

description: Sample name: T44_L_S(15)_1

source_name: 15mg/m3 silica, 44 week post-exposure rat 193 Lung

value: Lung

value: silica


title: G-01-036-EB-R-1

description: Test

tag: cell line

tag: cell type

tag: cell line code

tag: starting culture conditions

tag: teratoma, injected cell number(106)

tag: teratoma, mouse age (weeks)

tag: differentiation condition

value: START

tag: differentiation condition (details)


title: B-Z-9-EB-R-1

description: Test

value: ES

value: Z

tag: teratoma, volume of injection (ul)

tag: teratoma injection site

tag: teratoma injection position

tag: teratoma, mouse strain

tag: teratoma, mouse sex

tag: replicate

tag: time point (days)


title: G-01-053-EB-R-1

description: Test

value: IPS

value: DMEM/F12 + 20% KOSR, 5ng/mL bFGF, MEF feeders


title: K104766

city: Hanover

first: Kevin

middle: Crowley

last: Johnson

state: NH

address: 72 College Street

department: Epidemiology

institute: Geisel School of Medicine at Dartmouth College

description: normal breast biopsy from healthy subjects

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

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

data_processing: minfi, Aryee et al Bioinformatics 2014; BMIQ normalization, Teschendorff et al Bioinformatics 2013

label: Cy5 and Cy3

source_name: healthy breast biopsy

label_protocol: Standard Illumina Protocol

extract_protocol: Frozen normal breast tissue DNA was extracted with the QIAmp DNeasy tissue kit (Qiagen) according to the manufacturer’s instructions.

tag: tissue

value: breast biopsy

tag: Sex

value: female

tag: subject age

tag: body mass index

tag: pregnancy (ever)

value: Yes

tag: family history (first-degree relative with breast or ovarian cancer)

tag: gail risk model score (for women over 36 years old)


title: Blood_0mg silica_44 week post-exposure_rep5

description: Sample name: T44_B_S(0)_5

source_name: 0mg/m3 silica, 44 week post-exposure rat 206 Blood

tag: strain

value: Fisher (CDF) 344

tag: gender

value: Male

tag: age

value: Blood

tag: stress


title: K104402


title: Lung_0mg silica_44 week post-exposure_rep4

description: Sample name: T44_L_S(0)_4

source_name: 0mg/m3 silica, 44 week post-exposure rat 205 Lung

tag: time

value: 44 week post-exposure


title: Lung_0mg silica_44 week post-exposure_rep2

description: Sample name: T44_L_S(0)_2

source_name: 0mg/m3 silica, 44 week post-exposure rat 202 Lung


title: Lung_15mg silica_44 week post-exposure_rep3

description: Sample name: T44_L_S(15)_3

source_name: 15mg/m3 silica, 44 week post-exposure rat 195 Lung


title: K105115


title: Lung_0mg silica_44 week post-exposure_rep1

description: Sample name: T44_L_S(0)_1

source_name: 0mg/m3 silica, 44 week post-exposure rat 201 Lung


title: B-Z-6-EB-R-2

description: Test

tag: cell line

tag: cell type

tag: cell line code

tag: starting culture conditions

tag: teratoma, injected cell number(106)

tag: teratoma, volume of injection (ul)

tag: teratoma injection site

tag: teratoma injection position

tag: teratoma, mouse age (weeks)

value: EMBYOID BODY

tag: differentiation condition

tag: differentiation condition (details)


title: 01LH+2

description: SAMPLE 6

tag: time point

tag: menstrual phase

value: Early secretory

tag: type

value: Pre-receptive endometrium


title: B-Z-7-EB-R-1

description: Test

tag: teratoma, mouse strain

tag: teratoma, mouse sex

tag: replicate

tag: time point (days)

value: NEUTRAL

value: APEL


title: K104495

tag: tissue

tag: Sex

tag: subject age

tag: body mass index

tag: pregnancy (ever)

value: No

tag: family history (first-degree relative with breast or ovarian cancer)

tag: gail risk model score (for women over 36 years old)


title: 48LH+8

description:
Reanalysis of GSM1906648
SAMPLE 7

value: Mid secretory

tag: age

value: Receptive endometrium


title: K104489


title: B-Z-4-EB-R-1

description: Test

tag: cell line

tag: cell type

value: ES

tag: cell line code

value: Z

tag: starting culture conditions

tag: teratoma, injected cell number(106)

tag: teratoma, volume of injection (ul)

tag: teratoma injection site

tag: teratoma injection position

tag: teratoma, mouse age (weeks)

tag: differentiation condition

value: MESODERM

value: APEL, 20ng/ml Activin A, 20ng/ml BMP4


title: Lung_15mg silica_44 week post-exposure_rep4

description: Sample name: T44_L_S(15)_4

source_name: 15mg/m3 silica, 44 week post-exposure rat 196 Lung

tag: strain

tag: gender

value: Approximately 3 month old

tag: tissue

value: Lung

tag: stress

value: silica

tag: time


title: K104398

value: breast biopsy

tag: Sex

value: female

tag: subject age

tag: body mass index

tag: pregnancy (ever)

value: Yes

tag: family history (first-degree relative with breast or ovarian cancer)

tag: gail risk model score (for women over 36 years old)


title: K104397


title: K104368


title: Lung_0mg silica_44 week post-exposure_rep6

description: Sample name: T44_L_S(0)_6

source_name: 0mg/m3 silica, 44 week post-exposure rat 208 Lung

value: Fisher (CDF) 344

value: Male

tag: age

value: control

value: 44 week post-exposure


title: K104370

value: No


title: K104388


title: K104377


title: B-Z-3-EB-R-1

description: Test

tag: cell line

tag: cell type

tag: cell line code

tag: starting culture conditions

value: DMEM/F12 + 20% KOSR, 5ng/mL bFGF, MEF feeders

tag: teratoma, injected cell number(106)

tag: teratoma, volume of injection (ul)

tag: teratoma, mouse strain

tag: teratoma, mouse sex

tag: replicate

tag: time point (days)

value: EMBYOID BODY

value: ENDODERM

tag: differentiation condition (details)

value: APEL, 100ng/ml Activin A, 1ng/ml BMP4


title: B-Z-36-EB-R-3

description: Test

value: ES

value: Z

tag: teratoma injection site

tag: teratoma injection position

tag: teratoma, mouse age (weeks)

tag: differentiation condition

value: NEUTRAL

value: APEL


title: B-Z-39-EB-R-3

description: Test

value: ECTODERM

value: APEL, 10uM Dorsomorphin, 10uM SB431542, 100ng/ml bFGF


title: B-Z-35-EB-R-3

description: Test


title: K104365

tag: tissue

value: breast biopsy

tag: Sex

value: female

tag: subject age

tag: body mass index

tag: pregnancy (ever)

tag: family history (first-degree relative with breast or ovarian cancer)

tag: gail risk model score (for women over 36 years old)


title: B-Z-38-EB-R-3

description: Test

tag: cell line

tag: cell type

tag: cell line code

tag: starting culture conditions

tag: teratoma, injected cell number(106)

tag: teratoma, volume of injection (ul)

value: MESODERM

value: APEL, 20ng/ml Activin A, 20ng/ml BMP4


title: AE9a leukemia blast, AES knockout replicate 2

city: Heidelberg

first: Christian

last: Rohde

address: Im Neuenheimer Feld 410

institute: Heidelberg University

description: Cell type: FACS sorted GFP+ (AML1-ETO9a expressing cells from spleen)

hyb_protocol: Standard Affymetrix recommended protocols were followed for all hybridization, wash, stain and scanning steps.

data_processing:
The data were imported to BRB-ArrayTools and log2 transformed. The data was normalized to reference array which was the “median” array automatically selected by BRB-ArrayTools.
mogene10sttranscriptcluster.db(Version:8.0.1)

organism: Mus musculus

source_name: FACS sorted GFP+ cells from spleen

label_protocol: Biotin

growth_protocol: AML1-ETO9a transcuded AES wildtype or floxed E14.5 fetal licer cells were transplanted into recipient mice.

extract_protocol: RNeasy Mini Kit (Invitrogen)

treatment_protocol: AML1-ETO9a transcuded AES wildtype or floxed fetal licer cells were transplanted into recipient mice. 4 weeks after transplantation, recipients were treated with tamoxifen to indeuce AES deletion. Cells were isolated after animal death (caused by leukemia for AES wildtye) or the end of the experiment (for AES knockout).

tag: genotype/variation

value: AES knockout

tag: strain


title: B-Z-34-EB-R-3

description: Test

tag: teratoma injection site

tag: teratoma injection position

tag: teratoma, mouse strain

tag: teratoma, mouse age (weeks)

tag: teratoma, mouse sex

tag: replicate

tag: time point (days)

tag: differentiation condition (details)


title: K104359

tag: tissue

tag: Sex

tag: subject age

tag: body mass index

tag: pregnancy (ever)

tag: family history (first-degree relative with breast or ovarian cancer)

value: Yes

tag: gail risk model score (for women over 36 years old)


title: K104352


title: B-Z-33-EB-R-3

description: Test

tag: cell line

tag: cell type

tag: cell line code

tag: starting culture conditions

tag: teratoma, injected cell number(106)

tag: teratoma, volume of injection (ul)

tag: differentiation condition


title: AE9a leukemia blast, AES knockout replicate 1

scan_protocol: Standard Affymetrix recommended protocols were followed for all hybridization, wash, stain and scanning steps.

tag: genotype/variation

tag: strain


title: B-Z-32-EB-R-3

description: Test

tag: teratoma injection site

tag: teratoma injection position

tag: teratoma, mouse strain

tag: teratoma, mouse age (weeks)

tag: teratoma, mouse sex

tag: replicate

tag: time point (days)

tag: differentiation condition (details)


title: AE9a leukemia blast, AES wildtype replicate 3

value: AES wildtype


title: AE9a leukemia blast, AES wildtype replicate 2


title: AE9a leukemia blast, AES knockout replicate 3


title: B-Z-31-EB-R-2

description: Test

tag: cell line

value: DMEM/F12 + 20% KOSR, 5ng/mL bFGF, MEF feeders


title: AE9a leukemia blast, AES wildtype replicate 1


title: B-Z-2-EB-R-1

description: Test

tag: cell type

value: EMBYOID BODY


title: B-Z-29-EB-R-2

description: Test

tag: cell line code

value: ENDODERM


title: B-Z-26-EB-R-3

description: Test

tag: starting culture conditions


title: B-Z-27-EB-R-3

description: Test

tag: teratoma, injected cell number(106)


title: B-Z-30-EB-R-2

description: Test

tag: teratoma, volume of injection (ul)


title: B-Z-28-EB-R-2

description: Test

tag: differentiation condition


title: Lung_0mg silica_44 week post-exposure_rep5

description: Sample name: T44_L_S(0)_5

source_name: 0mg/m3 silica, 44 week post-exposure rat 206 Lung

value: Fisher (CDF) 344

tag: gender

value: Male

tag: age

value: Approximately 3 month old

tag: tissue

value: Lung

tag: stress

value: control

tag: time

value: 44 week post-exposure


title: B-Z-24-EB-R-3

description: Test

value: ES

value: Z

tag: teratoma injection site

tag: teratoma injection position

tag: teratoma, mouse strain

tag: teratoma, mouse age (weeks)

value: NEUTRAL

value: APEL


title: B-Z-25-EB-R-3

description: Test

tag: teratoma, mouse sex

tag: replicate

tag: time point (days)

tag: differentiation condition (details)

value: APEL, 100ng/ml Activin A, 1ng/ml BMP4


title: K104364

value: breast biopsy

tag: Sex

value: female

tag: subject age

tag: body mass index

tag: pregnancy (ever)

value: No

tag: family history (first-degree relative with breast or ovarian cancer)

tag: gail risk model score (for women over 36 years old)


title: NMuMG-FLAG-MAFK clone 4

city: Tsukuba

first: Yukari

last: Okita

address: 1-1-1 Tnnodai

country: Japan

institute: University of Tsukuba

description: Gene expression data from mouse mammary gland epithelium, NMuMG cells

hyb_protocol: Labeled single-strand DNA was hybridized for 17 hr at 45ºC on GeneChip Mouse Gene 1.0 ST Array (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Raw data CEL files were normalised using the Robust Multi-Array (RMA-16) algorithm in GeneSpring version 11.0 (Agilent Technologies)

source_name: NMuMG, FLAG-MAFK clone 4

label_protocol: Biotinylated probe DNA was prepared from 100 ng total RNA according to the protocol of Ambion WT Expression Kit (Applied Biosystems) for Affymetrix GeneChip.

growth_protocol: Cells were cultured in D-MEM supplemented with 10% FCS, 1% penicillin and streptomycin, and 1 µg/ml puromycin at 37ºC.

extract_protocol: Total RNA was extracted by ISOGEN following the manufacturer's instructions.

tag: cell line

value: NMuMG

tag: clone

tag: transgene

value: pCAGIP-FLAG-MafK


title: K104348

tag: tissue

value: Yes


title: B-Z-23-EB-R-2

description: Test

tag: cell type

tag: cell line code

tag: starting culture conditions

value: DMEM/F12 + 20% KOSR, 5ng/mL bFGF, MEF feeders

tag: teratoma, injected cell number(106)

tag: teratoma, volume of injection (ul)

tag: teratoma injection site

tag: teratoma injection position

value: EMBYOID BODY

tag: differentiation condition

value: ECTODERM

value: APEL, 10uM Dorsomorphin, 10uM SB431542, 100ng/ml bFGF


title: K104298

tag: Sex

tag: subject age


title: B-Z-22-EB-R-2

description: Test

tag: teratoma, mouse strain

tag: teratoma, mouse age (weeks)

tag: teratoma, mouse sex

tag: replicate

tag: time point (days)

value: MESODERM

tag: differentiation condition (details)

value: APEL, 20ng/ml Activin A, 20ng/ml BMP4


title: K104313

tag: tissue

tag: body mass index

tag: pregnancy (ever)

tag: family history (first-degree relative with breast or ovarian cancer)

tag: gail risk model score (for women over 36 years old)


title: Lung_15mg silica_44 week post-exposure_rep6

description: Sample name: T44_L_S(15)_6

source_name: 15mg/m3 silica, 44 week post-exposure rat 198 Lung

tag: strain

value: Fisher (CDF) 344

tag: gender

value: Male

tag: age

value: Approximately 3 month old

value: Lung

tag: stress

value: silica

tag: time

value: 44 week post-exposure


title: K104307

value: breast biopsy

tag: Sex

value: female

tag: subject age


title: NMuMG-FLAG-MAFK clone 10

source_name: NMuMG, FLAG-MAFK clone 10

tag: cell line

value: NMuMG

tag: clone

tag: transgene


title: NMuMG-mock

source_name: NMuMG, mock

value: pCAGIP


title: B-Z-21-EB-R-2

description: Test

tag: cell type

value: ES

tag: cell line code

value: Z

tag: starting culture conditions

tag: teratoma, injected cell number(106)

tag: teratoma, volume of injection (ul)

tag: teratoma injection site

tag: teratoma injection position

tag: teratoma, mouse strain

tag: teratoma, mouse age (weeks)

tag: teratoma, mouse sex

tag: replicate

tag: time point (days)

tag: differentiation condition

value: ENDODERM

value: APEL, 100ng/ml Activin A, 1ng/ml BMP4


title: B-Z-20-EB-R-2

description: Test

value: DMEM/F12 + 20% KOSR, 5ng/mL bFGF, MEF feeders

value: EMBYOID BODY

value: NEUTRAL

tag: differentiation condition (details)

value: APEL


title: K104332

tag: tissue

tag: Sex

tag: subject age

tag: body mass index

tag: pregnancy (ever)

value: Yes

tag: family history (first-degree relative with breast or ovarian cancer)

value: No

tag: gail risk model score (for women over 36 years old)


title: K104296


title: B-Z-1-EB-R-1

description: Test

tag: cell line

tag: cell type

tag: cell line code

tag: starting culture conditions

tag: teratoma, injected cell number(106)

tag: teratoma, volume of injection (ul)

value: START


title: B-Z-19-EB-R-3

description: Test

tag: teratoma injection site

tag: teratoma injection position

tag: teratoma, mouse strain

tag: teratoma, mouse age (weeks)

tag: teratoma, mouse sex

tag: replicate


title: B-Z-18-EB-R-1

description: Test

tag: time point (days)

tag: differentiation condition

value: ECTODERM

tag: differentiation condition (details)

value: APEL, 10uM Dorsomorphin, 10uM SB431542, 100ng/ml bFGF


title: K104281

tag: tissue

value: breast biopsy

tag: Sex

tag: subject age

tag: body mass index

tag: pregnancy (ever)

tag: family history (first-degree relative with breast or ovarian cancer)


title: B-Z-16-EB-R-1

description: Test

tag: cell line

tag: cell type

tag: cell line code

tag: starting culture conditions

tag: teratoma, injected cell number(106)


title: K104304

value: female

tag: gail risk model score (for women over 36 years old)


title: B-Z-15-EB-R-1

description: Test

tag: teratoma, volume of injection (ul)

tag: teratoma injection site

tag: teratoma injection position

tag: teratoma, mouse strain

tag: teratoma, mouse age (weeks)

tag: teratoma, mouse sex


title: B-Z-14-EB-R-2

description: Test

tag: replicate

tag: time point (days)

tag: differentiation condition

tag: differentiation condition (details)


title: B-Z-13-EB-R-2

description: Test

value: MESODERM

value: APEL, 20ng/ml Activin A, 20ng/ml BMP4


title: K104286

tag: tissue

tag: Sex

tag: subject age

tag: body mass index

tag: pregnancy (ever)

tag: family history (first-degree relative with breast or ovarian cancer)


title: K104295

tag: gail risk model score (for women over 36 years old)


title: B-Z-123-T-R-3

description: Test

tag: cell line

tag: cell type

value: ES

tag: cell line code

tag: starting culture conditions

tag: teratoma, injected cell number(106)

tag: teratoma, volume of injection (ul)

value: subcutaneous

value: FOX CHASE SCID C.B-17/lcr-scid/scidJcl

value: Male

value: TERATOMA


title: B-Z-10-EB-R-1

description: Test

value: Z

value: DMEM/F12 + 20% KOSR, 5ng/mL bFGF, MEF feeders

tag: teratoma injection site

tag: teratoma injection position

tag: teratoma, mouse strain

tag: teratoma, mouse age (weeks)

tag: teratoma, mouse sex

tag: replicate

value: EMBYOID BODY


title: B-Z-12-EB-R-2

description: Test

tag: time point (days)

tag: differentiation condition

value: ENDODERM

tag: differentiation condition (details)

value: APEL, 100ng/ml Activin A, 1ng/ml BMP4


title: K104268

tag: tissue

tag: Sex

tag: subject age

tag: body mass index

tag: pregnancy (ever)

value: No

tag: family history (first-degree relative with breast or ovarian cancer)


title: K104280

value: Yes

tag: gail risk model score (for women over 36 years old)


title: K104273


title: K104283


title: B-03-7-EB-R-1

description: Test

tag: cell line

tag: cell type

value: iPS

tag: cell line code

tag: starting culture conditions

value: DMEM/F12 + 20% KOSR, 5ng/mL bFGF, SNL feeders.

tag: teratoma, injected cell number(106)

tag: teratoma, volume of injection (ul)

value: NEUTRAL

value: APEL


title: K104276

value: breast biopsy

value: female


title: K104252


title: B-03-8-EB-R-1

description: Test

tag: teratoma injection site

tag: teratoma injection position

tag: teratoma, mouse strain

tag: teratoma, mouse age (weeks)

tag: teratoma, mouse sex

tag: replicate


title: B-03-9-EB-R-1

description: Test

tag: time point (days)

tag: differentiation condition

value: MESODERM

tag: differentiation condition (details)

value: APEL, 20ng/ml Activin A, 20ng/ml BMP4


title: K104270

tag: tissue

tag: Sex

tag: subject age

tag: body mass index

tag: pregnancy (ever)

tag: family history (first-degree relative with breast or ovarian cancer)


title: K104260

tag: gail risk model score (for women over 36 years old)


title: K104221


title: K104249


title: K104261


title: K104263


title: B-03-5-EB-R-1

description: Test

tag: cell line

tag: cell type

tag: cell line code

tag: starting culture conditions

tag: teratoma, injected cell number(106)

tag: teratoma, volume of injection (ul)


title: B-03-6-EB-R-1

description: Test

tag: teratoma injection site

tag: teratoma injection position

tag: teratoma, mouse strain

tag: teratoma, mouse age (weeks)

tag: teratoma, mouse sex

tag: replicate

value: ECTODERM

value: APEL, 10uM Dorsomorphin, 10uM SB431542, 100ng/ml bFGF


title: B-03-42-EB-R-3

description: Test

tag: time point (days)

tag: differentiation condition

tag: differentiation condition (details)


title: B-03-40-EB-R-3

description: Test


title: K104285

tag: tissue

tag: Sex

tag: subject age

tag: body mass index

tag: pregnancy (ever)

tag: family history (first-degree relative with breast or ovarian cancer)


title: K104193

tag: gail risk model score (for women over 36 years old)


title: K104214


title: B-03-3-EB-R-1

description: Test

tag: cell line

tag: cell type

tag: cell line code

tag: starting culture conditions

tag: teratoma, injected cell number(106)

tag: teratoma, volume of injection (ul)


title: B-03-35-EB-R-3

description: Test

tag: teratoma injection site

tag: teratoma injection position

tag: teratoma, mouse strain

tag: teratoma, mouse age (weeks)

tag: teratoma, mouse sex

tag: replicate


title: K104178

tag: tissue

tag: Sex

tag: subject age


title: B-03-34-EB-R-3

description: Test

tag: time point (days)

tag: differentiation condition

tag: differentiation condition (details)


title: B-03-33-EB-R-3

description: Test

tag: cell line

tag: cell type


title: B-03-32-EB-R-3

description: Test

tag: cell line code

tag: starting culture conditions


title: K104182

tag: body mass index

tag: pregnancy (ever)

tag: family history (first-degree relative with breast or ovarian cancer)

tag: gail risk model score (for women over 36 years old)


title: B-03-30-EB-R-3

description: Test

tag: teratoma, injected cell number(106)

tag: teratoma, volume of injection (ul)

tag: teratoma injection site

tag: teratoma injection position

tag: teratoma, mouse strain

tag: teratoma, mouse age (weeks)

value: START


title: K104205

tag: tissue

tag: Sex

tag: subject age


title: K104210


title: B-03-2-EB-R-1

description: Test

tag: cell line

tag: teratoma, mouse sex

tag: replicate

tag: time point (days)

tag: differentiation condition

tag: differentiation condition (details)


title: K104158

tag: body mass index

tag: pregnancy (ever)

tag: family history (first-degree relative with breast or ovarian cancer)


title: K104159

tag: gail risk model score (for women over 36 years old)


title: K104167


title: B-03-28-EB-R-2

description: Test

tag: cell type

tag: cell line code

tag: starting culture conditions

tag: teratoma, injected cell number(106)

tag: teratoma, volume of injection (ul)

tag: teratoma injection site


title: B-03-27-EB-R-2

description: Test

tag: teratoma injection position

tag: teratoma, mouse strain

tag: teratoma, mouse age (weeks)


title: K104196

tag: tissue

tag: Sex

tag: subject age


title: B-03-39-EB-R-3

description: Test

tag: cell line

tag: teratoma, mouse sex

tag: replicate

tag: time point (days)

tag: differentiation condition

tag: differentiation condition (details)


title: B-03-26-EB-R-2

description: Test

tag: cell type

tag: cell line code


title: B-03-4-EB-R-1

description: Test

tag: starting culture conditions

tag: teratoma, injected cell number(106)


title: B-03-25-EB-R-2

description: Test

tag: teratoma, volume of injection (ul)

tag: teratoma injection site


title: K104162

tag: body mass index

tag: pregnancy (ever)

tag: family history (first-degree relative with breast or ovarian cancer)

tag: gail risk model score (for women over 36 years old)


title: K103104

tag: tissue

tag: Sex

tag: subject age


title: K104157


title: B-03-24-EB-R-2

description: Test

tag: cell line

tag: teratoma injection position

tag: teratoma, mouse strain

tag: teratoma, mouse age (weeks)

tag: teratoma, mouse sex

tag: replicate


title: K104174


title: K102686


title: B-03-22-EB-R-2

description: Test

tag: cell type

tag: cell line code

tag: starting culture conditions

tag: time point (days)

tag: differentiation condition

tag: differentiation condition (details)


title: KhES-1_r1_L1

description:
Replicate 1
KhES.1_r1_HS.1

hyb_protocol: standard protocol according to vendor guidlines (www.illumina.com)

data_processing: data was extracted with GenomeStudio 2010 with no background correction, VST transformation and RSN normalization (both as provided by the lumi R/Bioconductor package) towards a target array hybridized with WA09 hESC

source_name: embryonic stem cells

growth_protocol: DMEM/F12 + 20% KOSR, 5ng/mL bFGF, MEF feeders

extract_protocol: mRNA extraction kit (Quiagen)

treatment_protocol: steady state proliferating cultures, no additional treatment,

tag: laboratory

value: Lab 1

value: ES

value: Female


title: B-03-21-EB-R-2

description: Test

tag: teratoma, injected cell number(106)

tag: teratoma, volume of injection (ul)

tag: teratoma injection site

value: EMBYOID BODY


title: K102685

tag: tissue

tag: Sex

tag: subject age

tag: body mass index

tag: pregnancy (ever)

value: No

tag: family history (first-degree relative with breast or ovarian cancer)

tag: gail risk model score (for women over 36 years old)


title: K103103


title: B-03-20-EB-R-2

description: Test

tag: cell line

tag: cell type

tag: teratoma injection position

tag: teratoma, mouse strain

tag: teratoma, mouse age (weeks)

tag: teratoma, mouse sex

tag: replicate


title: KhES-1_r2_L1

description:
Replicate 2
KhES.1_r2_HS.1

scan_protocol: standard protocol according to vendor guidlines (www.illumina.com)

tag: laboratory


title: K102669

value: Yes


title: K104173


title: H9(WA09)_r2_L2

description:
Replicate 2
WA09_r2_AE

label_protocol: standard protocol according to vendor guidlines (www.illumina.com)

value: Lab 2

tag: alt cell line name


title: K104204


title: NIBSC_5_r2_L4

description:
Replicate 2
I9_r2_OO

growth_protocol: mTeSR1, Matrigel

value: Lab 4

value: NIBSC 5

value: iPS


title: HES3_MIXL1_GFP/w_r2_L2

description:
Replicate 2
hES3_Mixl_GFP_r2_AE

value: HES3/MIXL1 GFP/w


title: B-03-18-EB-R-2

description: Test

tag: cell line code

tag: starting culture conditions

value: DMEM/F12 + 20% KOSR, 5ng/mL bFGF, SNL feeders.

tag: teratoma, injected cell number(106)

tag: teratoma, volume of injection (ul)

tag: teratoma injection site

tag: time point (days)

tag: differentiation condition

value: ENDODERM

tag: differentiation condition (details)

value: APEL, 100ng/ml Activin A, 1ng/ml BMP4


title: B-03-17-EB-R-2

description: Test

tag: cell line

value: NEUTRAL

value: APEL


title: NIBSC_5_r1_L4

description:
Replicate 1
I9_r1_OO

tag: cell type

tag: Sex


title: H9(WA09)_r1_L2

description:
Replicate 1
WA09_r1_AE


title: K104153

tag: tissue

value: breast biopsy

value: female

tag: subject age

tag: body mass index

tag: pregnancy (ever)

tag: family history (first-degree relative with breast or ovarian cancer)

tag: gail risk model score (for women over 36 years old)


title: B-03-16-EB-R-2

description: Test

tag: cell line code

tag: teratoma injection position

tag: teratoma, mouse strain

tag: teratoma, mouse age (weeks)

tag: teratoma, mouse sex

tag: replicate

value: START


title: K102629


title: B-03-14-EB-R-1

description: Test

tag: starting culture conditions

tag: teratoma, injected cell number(106)

tag: teratoma, volume of injection (ul)

tag: teratoma injection site

tag: time point (days)

tag: differentiation condition

value: ECTODERM

value: APEL, 10uM Dorsomorphin, 10uM SB431542, 100ng/ml bFGF


title: B-03-19-EB-R-2

description: Test

tag: cell line

tag: cell type

value: EMBYOID BODY

value: MESODERM

tag: differentiation condition (details)

value: APEL, 20ng/ml Activin A, 20ng/ml BMP4


title: B-03-12-EB-R-1

description: Test


title: DF19-9-11T.H_r2_L3

description:
Replicate 2
DF19.9.11T_4_r2_JB

source_name: induced pluripotent stem cells

growth_protocol: DMEM/F-12 + 20% KOSR, 10ng/ml FGF2, MEF feeders

tag: laboratory

value: Lab 3

tag: Sex

value: Male


title: HES3_MIXL1_GFP/w_r1_L2

description:
Replicate 1
hES3_Mixl_GFP_r1_AE

value: Lab 2

value: ES

value: Female


title: K102625

tag: tissue

tag: subject age

tag: body mass index

tag: pregnancy (ever)

value: Yes

tag: family history (first-degree relative with breast or ovarian cancer)

value: No

tag: gail risk model score (for women over 36 years old)


title: K102609


title: DF19-9-11T.H_r1_L3

description:
Replicate 1
DF19.9.11T_4_r1_JB

value: iPS


title: K102675


title: K102591


title: B-03-11-EB-R-1

description: Test

tag: cell line code

tag: starting culture conditions

value: DMEM/F12 + 20% KOSR, 5ng/mL bFGF, SNL feeders.

tag: teratoma injection position

tag: teratoma, mouse strain

tag: teratoma, mouse age (weeks)

tag: teratoma, mouse sex

tag: replicate

value: NEUTRAL

value: APEL


title: Oxford2_r1_L4

description:
Replicate 1
Oxford2_r1_OO

value: Lab 4

tag: cell line

tag: alt cell line name

tag: cell type


title: K102639

value: breast biopsy

tag: Sex

value: female


title: MEL1_INS_GFP/w_r1_L2 MG4

description:
Replicate 2
MEL1_INS_GFP_MG4_r1_AE.1

tag: laboratory

value: MEL1/INS GFP/w


title: K102623

tag: tissue

tag: subject age


title: K102574

tag: body mass index

tag: pregnancy (ever)


title: MEL1_INS_GFP/w_r1_L2 MG3

description:
Replicate 1
MEL1_INS_GFP_MG3_r1_AE


title: B-03-117-T-R-3

description: Test

tag: teratoma, injected cell number(106)

tag: teratoma, volume of injection (ul)

tag: teratoma injection site

value: subcutaneous

value: FOX CHASE SCID C.B-17/lcr-scid/scidJcl

tag: time point (days)

value: TERATOMA

tag: differentiation condition

tag: differentiation condition (details)


title: B-03-115-T-R-2

description: Test

tag: cell line code

tag: starting culture conditions

value: mTeSR1, Matrigel

tag: teratoma injection position

tag: teratoma, mouse strain

tag: teratoma, mouse age (weeks)

tag: teratoma, mouse sex

value: Male


title: K102602

tag: Sex

tag: family history (first-degree relative with breast or ovarian cancer)

tag: gail risk model score (for women over 36 years old)


title: K102590

tag: tissue

tag: subject age

tag: body mass index


title: K102664

tag: pregnancy (ever)


title: K102573


title: B-03-113-T-R-1

description: Test

tag: cell line

tag: cell type

tag: teratoma, injected cell number(106)

tag: teratoma, volume of injection (ul)

tag: teratoma injection site

tag: replicate


title: H14(WA14)_r2_L3

description:
Replicate 2
WA14_r2_JB

tag: laboratory

value: Lab 3

tag: alt cell line name

value: ES


title: K102690

value: Yes


title: B-02-9-EB-R-1

description: Test

tag: cell line code

tag: starting culture conditions

tag: teratoma injection position

tag: teratoma, mouse strain

tag: teratoma, mouse age (weeks)

tag: time point (days)

value: EMBYOID BODY

tag: differentiation condition

value: MESODERM

tag: differentiation condition (details)

value: APEL, 20ng/ml Activin A, 20ng/ml BMP4


title: K102575

tag: tissue

tag: Sex

tag: subject age

tag: body mass index

tag: pregnancy (ever)

value: No

tag: family history (first-degree relative with breast or ovarian cancer)

tag: gail risk model score (for women over 36 years old)


title: B-02-8-EB-R-1

description: Test

tag: cell line

tag: cell type

value: iPS

value: DMEM/F12 + 20% KOSR, 5ng/mL bFGF, SNL feeders.

tag: teratoma, injected cell number(106)

tag: teratoma, volume of injection (ul)

tag: teratoma injection site

tag: teratoma, mouse sex

tag: replicate

value: ENDODERM

value: APEL, 100ng/ml Activin A, 1ng/ml BMP4


title: H14(WA14)_r1_L3

description:
Replicate 1
WA14_r1_JB

tag: laboratory

tag: alt cell line name


title: B-02-6-EB-R-1

description: Test

tag: cell line code

tag: starting culture conditions

tag: teratoma injection position

tag: teratoma, mouse strain

tag: teratoma, mouse age (weeks)

tag: time point (days)

tag: differentiation condition

value: ECTODERM

tag: differentiation condition (details)

value: APEL, 10uM Dorsomorphin, 10uM SB431542, 100ng/ml bFGF


title: 201B7_r2_L1

description:
Replicate 2
iPS201B7_r2_HS

growth_protocol: DMEM/F12 + 20% KOSR, 5ng/mL bFGF, SNL feeders.

value: Lab 1

tag: cell line

tag: Sex

value: Female


title: H9(WA09)_r2_L3

description:
Replicate 2
WA09_r2_TEL.1

tag: cell type


title: 201B7_r1_L1

description:
Replicate 1
iPS201B7_r1_HS


title: B-02-5-EB-R-1

description: Test

tag: teratoma, injected cell number(106)

tag: teratoma, volume of injection (ul)


title: B-02-55-EB-R-4

description: Test

tag: teratoma injection site

tag: teratoma, mouse sex


title: B-03-13-EB-R-1

description: Test

tag: replicate


title: K102536

tag: tissue

value: breast biopsy

value: female

tag: subject age

tag: body mass index

tag: pregnancy (ever)

tag: family history (first-degree relative with breast or ovarian cancer)

tag: gail risk model score (for women over 36 years old)


title: B-02-54-EB-R-4

description: Test

tag: cell line code

tag: starting culture conditions

tag: teratoma injection position

tag: teratoma, mouse strain

tag: teratoma, mouse age (weeks)

tag: time point (days)


title: K102546

tag: Sex


title: H9(WA09)_r1_L3

description:
Replicate 1
WA09_r1_TEL.1

tag: laboratory

value: Lab 3

tag: cell line

tag: alt cell line name

tag: cell type


title: H9(WA09)_r1_L4

description:
Replicate 1
WA09_r1_OO

value: Lab 4

value: ES


title: H9(WA09)_r2_L4

description:
Replicate 2
WA09_r2_OO


title: K102535

tag: tissue

value: Yes


title: Oxford2_r2_L4

description:
Replicate 2
Oxford2_r2_OO


title: B-02-52-EB-R-4

description: Test

tag: teratoma, injected cell number(106)

tag: teratoma, volume of injection (ul)

tag: teratoma injection site

tag: teratoma, mouse sex

tag: replicate

value: EMBYOID BODY

tag: differentiation condition

value: NEUTRAL

tag: differentiation condition (details)

value: APEL


title: Tig108-4f3_r2_L1

description:
Replicate 2
Tig108_4f3_r2_HS

value: iPS


title: K102530

tag: subject age

tag: body mass index

tag: pregnancy (ever)

value: No

tag: family history (first-degree relative with breast or ovarian cancer)

tag: gail risk model score (for women over 36 years old)


title: Tig108-4f3_r1_L1

description:
Replicate 1
Tig108_4f3_r1_HS

tag: laboratory

tag: Sex


title: B-02-50-EB-R-4

description: Test

tag: cell line

tag: cell line code

tag: starting culture conditions

value: DMEM/F12 + 20% KOSR, 5ng/mL bFGF, SNL feeders.

tag: teratoma injection position

tag: teratoma, mouse strain

tag: teratoma, mouse age (weeks)

tag: time point (days)

value: MESODERM

value: APEL, 20ng/ml Activin A, 20ng/ml BMP4


title: B-02-4-EB-R-1

description: Test

tag: cell type

tag: teratoma, injected cell number(106)

tag: teratoma, volume of injection (ul)

tag: teratoma injection site

tag: teratoma, mouse sex

tag: replicate

value: ENDODERM

value: APEL, 100ng/ml Activin A, 1ng/ml BMP4


title: B-02-48-EB-R-4

description: Test

tag: differentiation condition

tag: differentiation condition (details)


title: B-02-51-EB-R-4

description: Test

value: ECTODERM

value: APEL, 10uM Dorsomorphin, 10uM SB431542, 100ng/ml bFGF


title: K102529

tag: tissue

value: breast biopsy

value: female

tag: subject age

tag: body mass index

tag: pregnancy (ever)

tag: family history (first-degree relative with breast or ovarian cancer)

tag: gail risk model score (for women over 36 years old)


title: K102531

tag: Sex


title: B-02-47-EB-R-4

description: Test

tag: cell line

tag: cell line code

tag: starting culture conditions

tag: teratoma injection position

tag: teratoma, mouse strain

tag: teratoma, mouse age (weeks)


title: iPSC_RM3.5C_r2_L2

description:
Replicate 2
RM31

tag: laboratory

value: Lab 2

value: iPSC RM3.5

tag: cell type

value: Male


title: Shef3_r1_L4

description:
Replicate 1
Shef3_r1_OO

value: Lab 4

tag: alt cell line name

value: ES

value: Female


title: Shef3_r2_L4

description:
Replicate 2
Shef3_r2_OO


title: K102522

value: Yes


title: K102559

value: No


title: K102524


title: iPS(IMR90)-4_r2_L3

description:
Replicate 2
IMR90C4_r2_TEL.1

value: Lab 3

value: iPS


title: B-02-46-EB-R-4

description: Test

value: DMEM/F12 + 20% KOSR, 5ng/mL bFGF, SNL feeders.

tag: teratoma, injected cell number(106)

tag: teratoma, volume of injection (ul)

tag: teratoma injection site

tag: teratoma, mouse sex

tag: replicate

tag: time point (days)

value: EMBYOID BODY

tag: differentiation condition

value: MESODERM

tag: differentiation condition (details)

value: APEL, 20ng/ml Activin A, 20ng/ml BMP4


title: iPSC_RM3.5C_r1_L2

description:
Replicate 1
RM3

tag: cell line

tag: Sex


title: K102503

tag: tissue

tag: subject age

tag: body mass index

tag: pregnancy (ever)

tag: family history (first-degree relative with breast or ovarian cancer)

tag: gail risk model score (for women over 36 years old)


title: K102511


title: iPS(IMR90)-4_r1_L3

description:
Replicate 1
IMR90C4_r1_TEL.1

tag: laboratory

tag: cell type


title: B-02-45-EB-R-4

description: Test

tag: cell line code

tag: starting culture conditions

tag: teratoma, injected cell number(106)

tag: teratoma, volume of injection (ul)

tag: teratoma injection position

tag: teratoma, mouse strain

tag: teratoma, mouse age (weeks)

value: ENDODERM

value: APEL, 100ng/ml Activin A, 1ng/ml BMP4


title: K102499

value: breast biopsy

value: female


title: B-02-42-EB-R-3

description: Test

tag: cell line

tag: teratoma injection site

tag: teratoma, mouse sex

tag: replicate

tag: time point (days)

tag: differentiation condition

value: ECTODERM

tag: differentiation condition (details)

value: APEL, 10uM Dorsomorphin, 10uM SB431542, 100ng/ml bFGF


title: B-02-44-EB-R-4

description: Test

value: NEUTRAL

value: APEL


title: B-02-40-EB-R-3

description: Test


title: B-02-3-EB-R-1

description: Test


title: B-02-39-EB-R-3

description: Test


title: K102500

tag: tissue

tag: Sex

tag: subject age

tag: body mass index

tag: pregnancy (ever)

tag: family history (first-degree relative with breast or ovarian cancer)

tag: gail risk model score (for women over 36 years old)


title: H9(WA09)_r2_L1

description:
Replicate 2
WA09_r2_HS

tag: laboratory

value: Lab 1

tag: alt cell line name

tag: cell type

value: ES

value: Female


title: B-02-41-EB-R-3

description: Test

tag: cell line

tag: cell line code

tag: starting culture conditions

tag: teratoma, injected cell number(106)

tag: teratoma, volume of injection (ul)

tag: teratoma injection position

tag: teratoma, mouse strain

tag: teratoma, mouse age (weeks)


title: K102490

tag: tissue

tag: Sex

value: Yes

value: No


title: B-02-38-EB-R-3

description: Test

value: iPS

value: DMEM/F12 + 20% KOSR, 5ng/mL bFGF, SNL feeders.

tag: teratoma injection site

tag: teratoma, mouse sex

tag: replicate

tag: time point (days)

tag: differentiation condition

tag: differentiation condition (details)


title: K102547

tag: subject age

tag: body mass index

tag: pregnancy (ever)

tag: family history (first-degree relative with breast or ovarian cancer)

tag: gail risk model score (for women over 36 years old)


title: K102517


title: K102572


title: B-02-53-EB-R-4

description: Test

tag: cell line

tag: cell type

tag: cell line code

tag: starting culture conditions

tag: teratoma, injected cell number(106)

tag: teratoma, volume of injection (ul)

value: EMBYOID BODY


title: B-02-43-EB-R-4

description: Test

tag: teratoma injection site

tag: teratoma injection position

tag: teratoma, mouse strain

tag: teratoma, mouse age (weeks)

value: START


title: B-02-37-EB-R-3

description: Test

tag: teratoma, mouse sex

tag: replicate

tag: time point (days)

tag: differentiation condition

value: MESODERM

value: APEL, 20ng/ml Activin A, 20ng/ml BMP4


title: H9(WA09)_r1_L1

description:
Replicate 1
WA09_r1_HS

tag: laboratory

tag: alt cell line name

tag: Sex


title: K102491

tag: tissue

value: breast biopsy

tag: subject age

tag: body mass index

tag: pregnancy (ever)

tag: family history (first-degree relative with breast or ovarian cancer)

tag: gail risk model score (for women over 36 years old)


title: B-02-36-EB-R-3

description: Test

tag: cell line

tag: cell type

tag: cell line code

tag: starting culture conditions

tag: teratoma, injected cell number(106)

tag: teratoma, volume of injection (ul)

tag: teratoma injection site

value: ENDODERM

tag: differentiation condition (details)

value: APEL, 100ng/ml Activin A, 1ng/ml BMP4


title: Human iPS cell-derived cardiomyocytes overexpressing EGFP-KCNJ2

city: Aomori

first: Yuji

last: Nakai

state: Aomori

address: 2-1-1, Yanagawa

department: Institute of Regional Innovation

institute: Hirosaki University

description: Gene expression data from human iPS-derived cardiomyocytes overexpressed EGFP-KCNJ2

hyb_protocol: Following fragmentation, 12.5 µg cRNA were hybridized for 16 hr at 45°C on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

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

data_processing: The CEL files were quantified with Microarray Suite version 5.0 (MAS 5.0) using the statistical language R (R-3.0.1) and Bioconductor 2.12.

source_name: EGFP-KCNJ2-overexpressed iCell-CMs

label_protocol: Biotinylated aRNA were prepared according to the standard Affymetrix protocol from 150 ng total RNA.

growth_protocol: As a commercially available differentiated cardiac cell line derived from hiPS cells, iCell-CMs (Cellular Dynamics International; CDI, Madison, WI, USA) were purchased from iPS Academia Japan Inc. (Kyoto, Japan), and were thawed and cultured according to the manual provided from the company (CDI) before adenoviral infections. After pre-culture for 4 days, cells are replated to the culture substrate (collagen-coated 24-well plate). Initial plating cell numbers were 2.5 X 10^5 / well. The cells were then cultured for 4 days after replating, and were collected for total RNA preparation.

extract_protocol: Total RNA was extracted with an RNeasy micro kit (Qiagen K.K., Tokyo, Japan).

treatment_protocol: Ad-EGFP or Ad-KCNJ2-EGFP at 100 MOI (final) were applied to the cells for 24 h to achieve adenoviral infection.

value: differentiated cardiac cell line derived from hiPS cells (iCell-CMs)

tag: medium

value: iCell Cardiomyocytes Maintenance Medium

tag: culture substrate

value: BIOCOAT collagen-I-cellware 24-well plate (Becton Dickinson Labware, Bedford, MA)


title: Human iPS cell-derived cardiomyocytes overexpressing EGFP

description: Gene expression data from human iPS-derived cardiomyocytes overexpressed EGFP

source_name: EGFP-overexpressed iCell-CMs


title: B-02-34-EB-R-3

description: Test

tag: teratoma injection position

tag: teratoma, mouse strain

tag: teratoma, mouse age (weeks)

tag: teratoma, mouse sex

tag: replicate

tag: time point (days)

tag: differentiation condition

value: ECTODERM

value: APEL, 10uM Dorsomorphin, 10uM SB431542, 100ng/ml bFGF


title: B-02-32-EB-R-3

description: Test

tag: cell line


title: K102457

source_name: healthy breast biopsy

tag: tissue

tag: Sex

value: female

tag: subject age

tag: body mass index

tag: pregnancy (ever)

tag: family history (first-degree relative with breast or ovarian cancer)

tag: gail risk model score (for women over 36 years old)


title: K102460

value: Yes


title: B-02-31-EB-R-3

description: Test

tag: cell type

tag: cell line code

tag: starting culture conditions

tag: teratoma, injected cell number(106)

tag: teratoma, volume of injection (ul)

tag: teratoma injection site

value: NEUTRAL

tag: differentiation condition (details)

value: APEL


title: K102469

value: No


title: Patient T2

city: Bergen

first: Helge

last: Ræder

address: Jonas Lies vei

country: Norway

institute: Haukeland University Hospital

hyb_protocol: Protocol of microarray core at the Joslin Diabetes Center, Boston, US (hybridized RNA to Human Genome U133A Plus 2.0 microarray chips (Affymetrix)

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

source_name: PDAC pancreas

growth_protocol: N/A, we used human pancreatic tissue

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions (RNeasy protocol (Invitrogen))

treatment_protocol: N/A, we used human pancreatic tissue

tag: diagnosis

value: ductal adenocarcinoma

value: pancreas


title: Patient N2

scan_protocol: Protocol of microarray core at the Joslin Diabetes Center, Boston, US

source_name: Normal pancreas

value: healthy


title: B-02-30-EB-R-3

description: Test

value: iPS

value: DMEM/F12 + 20% KOSR, 5ng/mL bFGF, SNL feeders.

tag: teratoma injection position

tag: teratoma, mouse strain

tag: teratoma, mouse age (weeks)

tag: teratoma, mouse sex

tag: replicate

tag: time point (days)

value: EMBYOID BODY

tag: differentiation condition

value: START


title: Patient P2

source_name: PDAC pancreas CEL mut carrier surrounding tissue

label_protocol: Protocol of microarray core at the Joslin Diabetes Center, Boston, US

tag: tissue


title: K102475

value: breast biopsy

tag: Sex

tag: subject age

tag: body mass index

tag: pregnancy (ever)

tag: family history (first-degree relative with breast or ovarian cancer)

tag: gail risk model score (for women over 36 years old)


title: B-02-14-EB-R-1

description: Test

tag: cell line

tag: cell type

tag: cell line code

tag: starting culture conditions

tag: teratoma, injected cell number(106)

tag: teratoma, volume of injection (ul)

tag: teratoma injection site


title: B-02-2-EB-R-1

description: Test

tag: teratoma injection position

tag: teratoma, mouse strain

tag: teratoma, mouse age (weeks)

tag: teratoma, mouse sex

tag: replicate

tag: differentiation condition (details)


title: B-02-16-EB-R-2

description: Test

tag: time point (days)

tag: differentiation condition


title: B-02-11-EB-R-1

description: Test


title: B-02-12-EB-R-1

description: Test

value: ENDODERM

value: APEL, 100ng/ml Activin A, 1ng/ml BMP4


title: Patient P1

source_name: PDAC pancreas CEL mut carrier tumor tissue

tag: diagnosis

tag: tissue


title: K102440

tag: Sex

tag: subject age

tag: body mass index

tag: pregnancy (ever)

tag: family history (first-degree relative with breast or ovarian cancer)

tag: gail risk model score (for women over 36 years old)


title: B-02-109-T-R-2

description: Test

tag: cell line

tag: cell type

tag: cell line code

tag: starting culture conditions

value: DMEM/F12 + 20% KOSR, 5ng/mL bFGF, MEF feeders

tag: teratoma, injected cell number(106)

tag: teratoma, volume of injection (ul)

tag: teratoma injection site

value: subcutaneous

value: FOX CHASE SCID C.B-17/lcr-scid/scidJcl

value: Male

value: TERATOMA


title: B-02-10-EB-R-1

description: Test

tag: teratoma injection position

tag: teratoma, mouse strain

tag: teratoma, mouse age (weeks)

tag: teratoma, mouse sex

tag: replicate

tag: time point (days)

value: ECTODERM

tag: differentiation condition (details)

value: APEL, 10uM Dorsomorphin, 10uM SB431542, 100ng/ml bFGF


title: K102434

tag: tissue

tag: Sex

value: female

tag: subject age

tag: body mass index

tag: pregnancy (ever)

value: Yes


title: Patient C2

tag: diagnosis

value: healthy

value: pancreas


title: Patient C1


title: B-02-107-T-R-1

description: Test

tag: cell line

tag: cell type

value: iPS

tag: cell line code

tag: starting culture conditions

value: DMEM/F-12 + 20% KOSR, 10ng/ml FGF2, MEF feeders

tag: differentiation condition


title: B-01-9-EB-R-1

description: Test

value: ES

tag: teratoma, injected cell number(106)

tag: teratoma, volume of injection (ul)

tag: teratoma injection site

tag: teratoma injection position

tag: teratoma, mouse strain

value: EMBYOID BODY

value: MESODERM

value: APEL, 20ng/ml Activin A, 20ng/ml BMP4


title: B-02-111-T-R-3

description: Test

value: DMEM/F12 + 20% KOSR, 5ng/mL bFGF, MEF feeders

tag: teratoma, mouse age (weeks)

tag: teratoma, mouse sex

tag: replicate

tag: time point (days)


title: K102424

tag: tissue

value: breast biopsy

tag: Sex

tag: subject age

tag: body mass index

tag: family history (first-degree relative with breast or ovarian cancer)

tag: gail risk model score (for women over 36 years old)


title: B-01-8-EB-R-1

description: Test

tag: cell line

tag: cell type

tag: cell line code

tag: starting culture conditions

value: ENDODERM

tag: differentiation condition (details)

value: APEL, 100ng/ml Activin A, 1ng/ml BMP4


title: B-01-5-EB-R-1

description: Test

tag: teratoma, injected cell number(106)

tag: teratoma, volume of injection (ul)

tag: teratoma injection site

tag: teratoma injection position

tag: differentiation condition


title: B-01-7-EB-R-1

description: Test

tag: teratoma, mouse strain

tag: teratoma, mouse age (weeks)

tag: teratoma, mouse sex

tag: replicate

tag: time point (days)

value: NEUTRAL

value: APEL


title: B-01-42-EB-R-3

description: Test

value: ECTODERM

value: APEL, 10uM Dorsomorphin, 10uM SB431542, 100ng/ml bFGF


title: K102448

tag: tissue

tag: Sex

value: female

tag: subject age

tag: body mass index

tag: pregnancy (ever)

value: Yes

tag: family history (first-degree relative with breast or ovarian cancer)


title: B-01-6-EB-R-1

description: Test

tag: cell line

tag: cell type

tag: cell line code

tag: starting culture conditions

tag: differentiation condition (details)


title: Patient N1

tag: diagnosis

value: healthy

value: pancreas


title: B-02-35-EB-R-3

description: Test

value: iPS

value: DMEM/F12 + 20% KOSR, 5ng/mL bFGF, SNL feeders.

tag: teratoma, injected cell number(106)

tag: teratoma, volume of injection (ul)

tag: teratoma injection site

tag: teratoma injection position

tag: teratoma, mouse strain

tag: differentiation condition


title: K102449

tag: tissue

tag: Sex

value: No

tag: gail risk model score (for women over 36 years old)


title: B-01-40-EB-R-3

description: Test

value: ES

tag: teratoma, mouse age (weeks)

tag: teratoma, mouse sex

tag: replicate

tag: time point (days)

value: EMBYOID BODY


title: B-01-41-EB-R-3

description: Test

tag: cell line

tag: cell type

tag: cell line code

value: DMEM/F12 + 20% KOSR, 5ng/mL bFGF, MEF feeders

value: MESODERM

value: APEL, 20ng/ml Activin A, 20ng/ml BMP4


title: B-01-4-EB-R-1

description: Test

tag: starting culture conditions

value: ENDODERM

tag: differentiation condition (details)

value: APEL, 100ng/ml Activin A, 1ng/ml BMP4


title: B-01-38-EB-R-3

description: Test

tag: teratoma, injected cell number(106)

tag: teratoma, volume of injection (ul)


title: B-01-35-EB-R-3

description: Test

tag: teratoma injection site

tag: teratoma injection position

value: NEUTRAL

value: APEL


title: B-01-39-EB-R-3

description: Test

tag: teratoma, mouse strain

tag: differentiation condition


title: B-01-36-EB-R-3

description: Test


title: B-01-34-EB-R-3

description: Test

value: ECTODERM

value: APEL, 10uM Dorsomorphin, 10uM SB431542, 100ng/ml bFGF


title: B-01-30-EB-R-3

description: Test

value: START


title: B-01-23-EB-R-2

description: Test


title: B-01-27-EB-R-2

description: Test


title: B-01-2-EB-R-1

description: Test


title: B-01-22-EB-R-2

description: Test


title: B-01-21-EB-R-2

description: Test


title: B-01-19-EB-R-2

description: Test


title: B-01-17-EB-R-2

description: Test


title: B-01-26-EB-R-2

description: Test


title: B-01-24-EB-R-2

description: Test


title: B-01-18-EB-R-2

description: Test


title: B-01-12-EB-R-1

description: Test


title: B-01-31-EB-R-3

description: Test


title: B-01-10-EB-R-1

description: Test


title: B-01-14-EB-R-1

description: Test


title: B-01-105-T-R-3

description: Test

value: DMEM/F-12 + 20% KOSR, 10ng/ml FGF2, MEF feeders

value: subcutaneous

value: FOX CHASE SCID C.B-17/lcr-scid/scidJcl

value: Male

value: TERATOMA


title: B-01-101-T-R-1

description: Test

value: ES


title: B-01-11-EB-R-1

description: Test

value: EMBYOID BODY


title: B-01-28-EB-R-2

description: Test

value: DMEM/F12 + 20% KOSR, 5ng/mL bFGF, MEF feeders


title: Patient T1

tag: diagnosis

value: ductal adenocarcinoma

tag: tissue

value: pancreas


title: B-01-13-EB-R-1

description: Test

tag: teratoma, mouse age (weeks)

value: MESODERM

value: APEL, 20ng/ml Activin A, 20ng/ml BMP4


title: MtbΔwhiB4 untreated 1

city: New York

first: SAURABH

last: MISHRA

state: New York

address: 1300 York Ave, Box 62, New York

department: Microbiology and Immunology

institute: Weill Cornell Medicine

description:
MtbΔwhiB4 Control 1
Gene expression of MtbΔwhiB4 early log phase cultures in 7H9-ADS medium.

hyb_protocol: The Gene Expression Hybridization Kit (Agilent Technologies, 5188-5279) and associated protocols were used (G4140-90040). The purified cRNA (600ng) was fragmented with fragmentation blocking mix by incubating samples at 60°C for 30 minutes. Microarrays were prepared in Agilent Technologies Hybridization Chamber according to manufacturer's instructions (G2534-90001). Once loaded into the hybridization chamber, samples were placed in the hybridization oven (Agilent Technologies, G2505-80085) and incubated for 17 hours at 65°C while rotating at setting 10. Following hybridization, samples were washed according to procedure described by Agilent Technologies.

scan_protocol: Microarray slides were scanned at the resolution of 5µm using Agilent Microarray scanner (G2565CA) with scan control software as per manufacturer's instructions (G2505-90020). Settings included Agilent HD_GX_1colour (61X21.6mm), TIFF 20 bit, and Photomultiplier tube (PMT) gain 100%. Scanned image displays were analyzed by quantifying the pixel density of each hybridization spot using the Agilent Feature Extraction software (v10.5). Local background signals were subtracted from the data automatically by this software and raw data was obtained.

data_processing: Normalization was done to 50th percentile of each sample and data transformation was done to median of all samples using GeneSpring Gx V 12.0 from Agilent Technologies.

organism: Mycobacterium tuberculosis H37Rv

source_name: MtbΔwhiB4, untreated

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50 ng RNA using the One-Color Low RNA Input Quick Amplification Labelling kit (Agilent Technologies, G4140-90040) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Mtb H37Rv and MtbΔwhiB4 were grown till early log phase of ~0.4.

extract_protocol: Gene expression from Treated cultures were fixed using Guanidine thiocyanate, pelleted and total RNA was isolated using FastRNA PRO blue kit (according to manufacturer's instructions). RNA was purified using Qiagen RNeasy plus kit according to manufacturer's instructions. DNase treatment was done using Ambion TURBO DNA-free kit according to manufacturer's instructions. RNA quality was measured using Agilent Bioanalyzer.

treatment_protocol: Early log phase culture cells were taken. Mtb H37Rv and MtbΔwhiB4 were treated with 100 µg/ml of Amoxicillin and 8 µg/ml of Clavulanate in 7H9-ADS medium for 6 hrs.

tag: strain/background

tag: genotype/variation

tag: growth phase

value: early log

tag: treatment


title: Wt Mtb treated 10XAG 4

description:
Wt Mtb AG 4
Gene expression of Mtb early log phase cultures 6h after treatment with 100 µg/ml of Amoxicillin and 8 µg/ml of Clavulanate in 7H9-ADS medium.

source_name: Wt Mtb H37Rv, AG treated, 6h

value: wild type

value: Amoxicillin and Clavulanate


title: MtbΔwhiB4 treated 10XAG 2

description:
MtbΔwhiB4 AG 2
Gene expression of MtbΔwhiB4 early log phase cultures 6h after treatment with 100 µg/ml of Amoxicillin and 8 µg/ml of Clavulanate in 7H9-ADS medium.

source_name: MtbΔwhiB4, AG treated, 6h


title: Wt Mtb treated 10XAG 5

description:
Wt Mtb AG 5
Gene expression of Mtb early log phase cultures 6h after treatment with 100 µg/ml of Amoxicillin and 8 µg/ml of Clavulanate in 7H9-ADS medium.


title: MtbΔwhiB4 treated 10XAG 1

description:
MtbΔwhiB4 AG 1
Gene expression of MtbΔwhiB4 early log phase cultures 6h after treatment with 100 µg/ml of Amoxicillin and 8 µg/ml of Clavulanate in 7H9-ADS medium.


title: MtbΔwhiB4 untreated 2

description:
MtbΔwhiB4 Control 2
Gene expression of MtbΔwhiB4 early log phase cultures in 7H9-ADS medium.


title: MtbΔwhiB4 untreated 3

description:
MtbΔwhiB4 Control 3
Gene expression of MtbΔwhiB4 early log phase cultures in 7H9-ADS medium.


title: Wt Mtb untreated 1

description:
Wt Mtb Control 1
Gene expression of Mtb early log phase cultures in 7H9-ADS medium.

source_name: Wt Mtb H37Rv, untreated


title: Control 2

status: Public on Jun 19 2017

type: SRA

city: Bergamo

first: Marina

last: Morigi

address: Parco Scientifico Tecnologico Kilometro Rosso, via Stezzano, 87

department: Molecular Medicine

country: Italy

institute: IRCCS – Istituto di Ricerche Farmacologiche Mario Negri, Bergamo, Italy

library_source: transcriptomic

data_processing:
reads mapped to hg19_AmpliSeq_Transcriptome_ERCC.fasta from Thermo Fisher
read count obtained by ampliSeqRNA plugin on Torrent Server
Genome_build: hg19_ampliseq_transcriptome_ercc_v1.fasta
Supplementary_files_format_and_content: raw read count per amplicon per sample

source_name: renal proximal tubular epithelial cells

extract_protocol: none provided by the submitter

value: Control


title: Cisplatin 2

value: Cisplatin


title: Cispl+UCMSCs 2

value: Cispl+UCMSCs


title: Control 3


title: Cisplatin 1


title: Cispl+UCMSCs 1


title: Control 1


title: Cisplatin 3


title: Wt Mtb treated 10XAG 3

description:
Wt Mtb AG 3
Gene expression of Mtb early log phase cultures 6h after treatment with 100 µg/ml of Amoxicillin and 8 µg/ml of Clavulanate in 7H9-ADS medium.


title: Wt Mtb untreated 2

description:
Wt Mtb Control 2
Gene expression of Mtb early log phase cultures in 7H9-ADS medium.


title: MtbΔwhiB4 treated 10XAG 3

description:
MtbΔwhiB4 AG 3
Gene expression of MtbΔwhiB4 early log phase cultures 6h after treatment with 100 µg/ml of Amoxicillin and 8 µg/ml of Clavulanate in 7H9-ADS medium.


title: Wt Mtb treated 10XAG 2

description:
Wt Mtb AG 2
Gene expression of Mtb early log phase cultures 6h after treatment with 100 µg/ml of Amoxicillin and 8 µg/ml of Clavulanate in 7H9-ADS medium.


title: Cispl+UCMSCs 3


title: Wt Mtb treated 10XAG 1

description:
Wt Mtb AG 1
Gene expression of Mtb early log phase cultures 6h after treatment with 100 µg/ml of Amoxicillin and 8 µg/ml of Clavulanate in 7H9-ADS medium.


title: kidney_p1_tfcp2l1ko, biological rep2

first: Max

last: Werth

state: NY

address: 1150 St. Nicholas Ave.

department: Medicine

institute: Columbia University

hyb_protocol: performed at Columbia Core Facilities

scan_protocol: performed at Columbia Core Facilities

data_processing: Affymetrix Console

source_name: kidney, control!Sample_characteristics_ch1 = tissue: kidney

label_protocol: Affymetrix 3' IVT PLUS KIT according to manufacturer's instructions

extract_protocol: total RNA was purified by Qiagen RNAeasy Mini Kit according to the manufacturer's instructions.

value: Tfcp2l1 knockout

tag: developmental stage

value: postnatal day 1 (P1)


title: kidney_p1_wt, biological rep1

source_name: kidney, control

value: kidney


title: kidney_p1_wt, biological rep2


title: kidney_p1_tfcp2l1ko, biological rep1


title: CRC0004NL

city: Candiolo

first: Enzo

last: Medico

state: TO

address: Strada Prov. 142, km 3,95

department: Oncology

institute: Candiolo Cancer Institute, University of Torino

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data were normalized by Bioconductor (3.0) lumi pipeline with loess normalization

label: biotin-SA Cy3

source_name: Normal Liver

label_protocol: Synthesis of cDNA and biotinylated cRNA were performed using the Illumina Total-Prep RNA Amplification Kit (Ambion, Austin, TX, USA, cat. no. IL1791), according to the manufacturer’s protocol, for which hybridization was carried out on Illumina HumanHT-12 V3 arrays

growth_protocol: Tumor were collected upon surgical resection and stored in liquid nitrogen

extract_protocol: RNA was extracted using the Trizol Plus purification Kit (Invitrogen, Frederick, MD, USA, cat. no.12183555), according to the manufacturer’s protocol. Quantification and quality analysis of RNA was performed on a Bioanalyzer 2100 (Agilent, Santa Clara, CA, USA).

treatment_protocol: Cryostatic section of the frozen specimens were cut for RNA extraction

tag: tissue type

value: Normal Liver

tag: tissue id

tag: kras (1=mut;0=wt,na=not determined)

tag: cris class

tag: cris distance to template

tag: cris bh.fdr


title: CRC0016NL


title: kidney_p1_tfcp2l1ko, biological rep3


title: CRC0034NL


title: Normal Liver Sample


title: CRC0034PR

source_name: CRC Primary Tumor

value: CRC Primary Tumor


title: CRC0026PR


title: CRC0028NL


title: CRC0004PR


title: CRC0150_rep1

source_name: Liver Metastasis

value: frozen liver metastasis sample

value: CRISB


title: kidney_p1_wt, biological rep3


title: CRC0151

value: CRISE


title: CRC0171

value: CRISA


title: CRC0073_rep2


title: CRC0155

value: CRISC


title: CRC0166


title: CRC0161


title: CRC0156


title: CRC0169

value: CRISD


title: CRC0085_rep2


title: CRC0178


title: CRC0162


title: CRC0164


title: CRC0153


title: CRC0177


title: CRC0154


title: CRC0163


title: CRC0147_rep1


title: CRC0019_rep3


title: CRC0179


title: CRC0158


title: CRC0149


title: CRC0170


title: CRC0173


title: CRC0146_rep2


title: CRC0144_rep2


title: CRC0021_rep3


title: CRC0174


title: CRC0165


title: CRC0116


title: CRC0143


title: CRC0145_rep1


title: CRC0117


title: CRC0168


title: CRC0160


title: CRC0115


title: CRC0114


title: CRC0111


title: CRC0113


title: CRC0109


title: CRC0108


title: CRC0112


title: CRC0106


title: CRC0107


title: CRC0110