title: Kidney Saline vs ACTH 121204 (4)

city: Sydney

first: Ruby

middle: CY

last: Lin

state: NSW

address: 176 Hawkesbury Road, Westmead

country: Australia

institute: The Westmead Institute for Medical Research

description:
Channel 1 (Cy3): Saline treated (Control)
Channel 2 (Cy5): ACTH treated

hyb_protocol: Post-printing treatment of the combined Compugen/MWG 10K rat arrays were baked at 80 °C for 80 min. Pre-hybridisation treatment included 0.1% SDS at 95 °C for 1 min, 5% ethanol for 1 min at room temperature (RT) and ddH2O for 1 min at RT, and dried by centrifugation at 100 x g. cDNA was synthesised using Invitrogen First Strand Synthesis Kit as per manufacturer’s instruction with modifications: 0.5 mM of d(ACG)TP, 0.34 mM amino allyl-dUTP and 0.16 mM dTTP.  cDNA was labeled with Cy3TM or Cy5TM dyes (GE Healthcare Life Sciences).  A total of 100 ul of Cy3- and Cy5-lablled cDNA in DIG Easy Hybridisation Buffer (Roche) plus 1 mg/ml of yeast tRNA (Sigma) and Herring sperm DNA (Sigma) each were incubated at 65 °C for 5 min, centrifuged for 5 min at 13,000 x g, and applied under a 25mm X 60mm Lifterslip (Erie Scientific) from the top right corner. Slides were sealed in a humidified chamber and incubated in a 37 °C oven overnight (13-18 h). After hybridization, slides were washed as follows: (i) 10-15 min of 1 X SSC, 0.1 % SDS at 50 °C; (ii) repeat; (iii) 15-20 min of 1 X SSC, 0.1 % SDS at 50 °C; (iv) rinse 3 times in 1 X SSC at 50°C, 1 min each and (v) 2 min in 0.2 X SSC at RT. Slides are dried by centrifugation at 100 x g for 5 min immediately after washing and then scanned using an Axon 4000B scanner (Molecular Devices).

scan_protocol: The labelled array was scanned using the GenePix® 4000B Microarray Scanner (Axon Instruments) at a resolution of 10 um, and a PMT (photomultiplier tube) gain of 700 for both red (Cy5-labelled) and green (Cy3-labelled) channels in all slides. Automatic and manual flagging were used to localize absent or very weak spots which were excluded from analysis. Corrected intensities were calculated for both the red and green channels by subtracting the median measure of background pixel intensities from the median measure of spot pixel intensity. IRcorr (Corrected red intensity) = IRspot – IRbackground IGcorr (Corrected green intensity) = IGspot – IGbackground

data_processing:
Array analysis was performed in R v2.2.1 using the Bioconductor v1.7 packages marray and limma.  The Python language was used for additional manipulations and scripting. Prior to analysis arrays were split into 5k MWG and 5k Compugen components using split10k.py; these were subsequently analysed for differential expression separately. GPR data files were imported into R using the marray package function read.GenePix. GenePix (GenePix Pro v6) flags were converted to weights to be used in subsequent analyses: unflagged spots and spots flagged as good were assigned a weight of 1, all other spots were assigned a weight of 0.
Control spots were identified, and were also assigned weights of 0. Background correction was not performed, and thus background information was zeroed prior to normalisation.
	Print-tip LOWESS normalisation was applied using the marray package maNormMain function.  Zero-weight and control spots were assigned NA values to ensure removal from subsequent differential expression analyses. The normalised arrays, with bad spots set to NA, were converted to MALists for use in limma. These arrays were subjected to between array normalisation by the scale method prior to model fitting.
	Correlation between duplicate spots within each array was estimated using the duplicateCorrelation function.  The consensus correlation value was supplied to the limma lmFit function in order to account for duplicate spots in the model.

source_name: Kidney tissue from rats treated with saline

label_protocol:
To label the probes, the samples were each resuspended in 9 μl 0.1 M NaHCO3, pH 9.0. 2 μl of Cy3 (green) monoreactive dye (Amersham) was added to the samples. The samples were incubated for 45 min at room
temperature in the dark. The Cy-dye labeled probes were then cleaned up using the same protocol mentioned above (Qiagen PCR purification kit) to remove any unincorporated dyes.

growth_protocol: Male Sprague Dawley (SD) rats were housed in plastic cages at the John Curtin School of Medical Research, Canberra. The facility is temperature controlled (21-23 degree celcius) and maintains a 12 h light/dark cycle. Rats were given standard rat chow and tap water ad libitum. They were acclimatized for two weeks to their surroundings, water and food, handling and blood pressure (BP) measuring equipment prior to experimental procedure.

extract_protocol:
Whole kidney tissues were collected for RNA extraction. These tissues from each rat were homogenized separately using mortar and pestle in liquid nitrogen. Total RNA was extracted using TRIzol® reagent. Cells suspended in TRIzol® reagent were disrupted by repeated pipetting and then transferred into microfuge tubes. This protocol was modified
from manufacturer’s instructions and is described here. The lysate was further homogenized using syringe and needle for 30 s and incubated at room temperature (~21ºC) for 5 min, and 200 ul of chloroform was added. The tubes were shaken vigorously for 15 s to mix the
phases and incubated for 3 min at room temperature. The phases were separated by centrifugation at 12,000 x g for 15 min at 4ºC. The upper aqueous phase was transferred into a fresh microfuge tube and 500 µl of ice cold isopropanol added to precipitate the RNA. The contents were mixed by gentle inversion and then incubated for 10 min at room
temperature. The RNA was recovered by centrifugation at 12,000 x g for 10 min at 4ºC. A gelatinous pellet was left on the side of the tube after removal of the supernatant. The RNA pellet was washed with 1 ml of 75% ethanol and the tube was vortexed briefly to resuspend
the pellet. The RNA was recovered by centrifugation at 7,500 x g for 5 min at 4ºC. This washing step was repeated twice. After removal of the supernatant, the RNA pellet was airdried briefly and then resuspended in 20 µl Nuclease-free H2O (Ambion Inc., Austin, TX, USA) and stored in -80ºC for further processing.

treatment_protocol: Rats were treated with saline (1.0 ml/kg per day) for 12 days to serve as controls. Systolic blood pressure (SBP) was measured on alternate days.

tag: Organism

value: Rattus norvegicus

tag: Strain

value: Sprague Dawley (SD)

tag: Gender

value: Male

tag: Age

value: 4 weeks

tag: Body weight

value: app. 200g

tag: Treatment

value: Saline

tag: Source organ

value: Kidney

source_name: Kidney tissue from rats treated with adrenocorticotrophin (ACTH)

treatment_protocol: Rats were treated with ACTH (Tetracosacrin, Synthacen Depot, generously provided by Novartis Pharmaceuticals Australia; 0.2 mg/kg per day) for 12 days. Systolic blood pressure (SBP) was measured on alternate days.


title: Kidney Saline vs ACTH 091204.2

status: Public on Dec 31 2018

type: RNA

molecule: total RNA

organism: Rattus norvegicus


title: Kidney Saline vs ACTH 011204.2


title: Kidney Saline vs ACTH 011204.1

value: Adrenocorticotrophin


title: CSMN-C P1 sample2

city: Cambridge

first: Vibhu

last: Sahni

address: 7 Divinity Avenue

country: USA

institute: Harvard University

description: Gene expression data from purified corticospinal motor neurons in rostro-lateral  sensorimotor cortex at postnatal day 1

hyb_protocol: RNA samples were hybridized to Affymetrix GeneChip Mouse Genome 430 2.0 Array chips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix Scanner 3000 7G

data_processing: Data fies were uploaded with Rosetta Resolver software. Robust Multiarray Average (RMA) was used for normalization

label: biotin

organism: Mus musculus

source_name: FACS purified corticospinal motor neurons in rostro-lateral sensorimotor cortex from wild type mice at P1

label_protocol: RNA was amplified in two rounds of amplification using the MessageAmpII aRNA Amplification kit and THE MessageAmp-II-biotin enhanced kits (Ambion) for the first and second rounds of amplification, respectively.

extract_protocol: RNA was extracted using Absolutely RNA Micro Prep Kits (Stratagene) according to the manufacturer's instructions.

treatment_protocol: CSMN in C57BL/6 mice were retrogradely labeled with green fluorescent microspheres (Lumafluor Corp., FL) injected into either the cerebral peduncles of P0 mice or the cervical spinal cord of P3, and P5 mice. The rostrol-lateral and caudomedial cortex was microdissected from these labeled brains at P1, P4, and P7. The cortices were collected and dissociated; CSMN from these micro-dissected cortices were purified by FACS as described in (Catapano et al., 2001, and Arlotta et al., 2005)

tag: gentotype

tag: Stage

value: postnatal day 1

tag: cell type

value: corticospinal motor neuron


title: EPC_HDAC7_NC_rep1

city: Wuhan

first: Ye

last: Wei

state: Hubei

address: Tongji Medical College, Huazhong University of Science and Technology

country: China

institute: Cancer Center, Union Hospital

description: Gene expression data from HDAC7 NC EPCs.

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

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

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

organism: Homo sapiens

source_name: EPCs infected with lentivirus carrying nonspecific random shRNA

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Isolated mononuclear cells were collected and plated on human plasma fibronectin-coated culture dishe for 3 days, nonadherent cells were discarded and fresh endothelial basal medium 2 supplemented with EGM-2 MV Single-Quots was added. Typical EPC colonies appeared after 2-3 weeks, and these cells were collected and incubated at 37C in a humidified 5% CO2 atmosphere.

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

treatment_protocol: EPCs and infected by lentivirus (NC/KD) at MOI 20 according to the manufacture’s instructions.

tag: tissue

value: umbilical cord blood

tag: infection


title: EPC_HDAC7_KD_rep1

description: Gene expression data from HDAC7 KD EPCs.

source_name: EPCs infected with lentivirus carrying HDAC7 shRNA

value: lentivirus carrying HDAC7 shRNA


title: HH2_late_rep3

city: Kyoto

first: Cantas

last: Alev

address: Medical Faculty Bldg. B, Yoshida-Konoe-cho, Sakyo-ku

department: Institute for the Advanced Study of Human Biology (ASHBi)

country: Japan

institute: Kyoto University

description:
Epiblast-3_9h-3
Gene expression data from primitive streak region in chicken HH2 late (9hour), biological replicate 2.

hyb_protocol: RNA was subsequently fragmented and hybridized to the GeneChip according to manufacturer’s instructions. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: The microarray image data were processed with the GeneChip Scanner 3000 (Affymetrix).

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and expression values are quantified with the RMA method (Bioconductor 3.6).

organism: Gallus gallus

source_name: Fertilized egg, Chicken HH2 Late (9hour)

label_protocol: cDNA samples were subjected to the two-cycle target labeling procedure for biotin labeling by in vitro transcription (Affymetrix).

growth_protocol: Fertilized hens’ eggs were incubated at 38.5°C for 0.5h, 5h, 9h or 14h in a humid incubator.

extract_protocol: Two independent sets of total RNA from pooled AP samples of the different time points were isolated using Qiagen RNeasy kit. RNA concentrations were measured and equalized, and RNA quality was checked on gel. 100ng of total RNA were used for each array.

treatment_protocol: The area pelucida (AP) region of 0.5h, 5h, 9h and 14h incubated embryos, containing both the epiblast and hypoblast was cut out in Pannett-Compton solution. Isolated area pellucida tissues were collected and used for RNA isolation.

value: Area pelucida (AP) region

tag: developmental stage

value: HH2 Late (9 hour)


title: HH3_late_rep1

description:
Epiblast-2 14h-1
Gene expression data from primitive streak region in chicken HH3 late (14hour), biological replicate 1.

source_name: Fertilized egg, Chicken HH3 Late (14hour)

value: HH3 Late (14 hour)


title: 28686-1-ME

type: SRA

city: Houston

first: Priyanka

last: Kachroo

address: 6670 Bertner Avenue

institute: Houston Methodist Research Institute

library_source: transcriptomic

data_processing:
Multiplexed single-end (SE) libraries were sequenced on an Illumina NextSeq 500 instrument, basecalling and demultiplexing was done on the instrument, and the RNA-Seq data was output as fastq files
RNA-seq reads from all strains were mapped to reference strain MGAS6180 (GenBank accession number CP000056), using Edge-pro v1.3.1 (Estimated Degree of Gene Expression for Prokaryotes).
Low-expressed genes and genes encoding ribosomal RNAs and tRNAs were filtered out prior to running differential expression analyses
Differential expression analysis was perfomed using DESeq2 v1.6.3 running in R version 3.3.2. Raw reads were used as the input and normalized expression generated using DESeq2's default normalization method Relative log expression (RLE) approach was used to generate fold change values for each gene. Multiple testing correction was performed using Bonferroni method.
Genome_build: reference strain MGAS6180 (GenBank accession number CP000056)
Supplementary_files_format_and_content: normalized counts

organism: Streptococcus pyogenes

source_name: 28686_ME_cell pellet

growth_protocol: Cells were grown in Todd-Hewitt broth supplemented with yeast extract (THY media) at 37 C in atmosphere supplemented with 5% CO2

extract_protocol:
Pelleted cells were mechanically disrupted using silica beads, RNA was isolated using RNeasy kit, contaminating DNA was degraded using Turbo DNA-free (Ambion), and rRNA was depleted using Ribo-Zero (Illumina)
Resultant RNA was reverse transcribed to cDNA and sequencing libraries were generated using ScriptSeq RNA-seq preparation kit (Illumina)

treatment_protocol: At the desired growth stage, mid-exponential (OD 600nm=0.5) or early-stationary (OD 600nm=1.65), the culture was treated with RNAprotect Bacteria Reagent and cells were harvested by centrifugation

tag: subclade

value: Subclade2A (SC2A)

tag: site of isolation

value: invasive infection isolate

tag: strain

tag: growth phase

value: Mid-exponential (ME, OD600nm=0.5)


title: Kidney Saline vs ACTH 121204 (3)

tag: Organism

value: Rattus norvegicus

value: Sprague Dawley (SD)


title: 20160916_101342_003: T2D

city: Jaipur

first: Dr. Sandeep

middle: Kumar

last: Mathur

state: Rajasthan

address: Tonk Road

department: Department of Endocrinology

country: India

institute: SMS Medical College and Hospital

hyb_protocol: Incubate 173.3 μL Hybridization Master Mix with 26.7 μL (10 μg) Fragmented and Labeled cRNA at 990 C for 5 minutes and then at 450 C for 5 Minutes in a thermal cycler using the“Hybridization Cocktail” program then rotate at 60 rpm for 16 hr at 45ºC

scan_protocol: GeneChip Scanner 3000 Dx V.2 was used for scanning arrays as per protocol supplied by Affymetrix inc.

data_processing: Bioconductor package affy, method rma

source_name: Visceral

label_protocol: 3’ IVT Biotin Labelling of aRNA

extract_protocol: RNA is isolated using Qiagen RNeasy® Mini Kit

tag: gender

value: F

tag: diagnosis

value: Type-2 Diabetes

value: Visceral


title: 20160916_101344_009: T2D


title: 20160916_101343_007: T2D


title: HH3_late_rep2

description:
Epiblast-2 14h-2
Gene expression data from primitive streak region in chicken HH3 late (14hour), biological replicate 2.


title: 20160714_103119_007: T2D


title: HH2_late_rep1

description:
Epiblast-2 9h-1
Gene expression data from primitive streak region in chicken HH2 late (9hour), biological replicate 1.


title: 20160714_103118_005: T2D


title: 28669-2-ME

source_name: 28669_ME_cell pellet


title: 28669-3-ME


title: 28669-1-ME


title: Kidney Saline vs ACTH 091204.1

tag: Strain

tag: Gender

value: Male

tag: Age

value: 4 weeks

value: app. 200g

value: Saline

value: Kidney


title: 28647-3-ME

source_name: 28647_ME_cell pellet


title: 28647-2-ME


title: 28647-1-ME


title: 28597-3-ME

source_name: 28597_ME_cell pellet


title: 28597-2-ME


title: HH1_late_rep2

description:
Epiblast-2 5h-2
Gene expression data from primitive streak region in chicken HH1 late (5hour), biological replicate 2.

source_name: Fertilized egg, Chicken HH1 Late (5hour)

value: HH1 Late (5 hour)


title: HH1_early_rep2

description:
Epiblast-2 0.5h-2
Gene expression data from (potential) primitive streak region in chicken HH1 early (0.5hour), biological replicate 2.

source_name: Fertilized egg, Chicken HH1 Early (0.5hour)

value: Area pelucida (AP) region

value: HH1 Early (0.5 hour)


title: 20150930_104728_001: T2D


title: 28597-1-ME


title: 20160714_103113_001: T2D


title: Heart Saline vs ACTH 050305 slide 17

description:
Channel 1 (Cy3): Heart tissue - Saline treated (Control)
Channel 2 (Cy5): Heart tissue - ACTH treated

hyb_protocol: Post-printing treatment of the combined Compugen/MWG 10K rat arrays were baked at 80 °C for 80 min. Pre-hybridisation treatment included 0.1% SDS at 95 °C for 1 min, 5% ethanol for 1 min at room temperature (RT) and ddH2O for 1 min at RT, and dried by centrifugation at 100 x g. cDNA was synthesised using Invitrogen First Strand Synthesis Kit as per manufacturer’s instruction with modifications: 0.5 mM of d(ACG)TP, 0.34 mM amino allyl-dUTP and 0.16 mM dTTP.  cDNA was labeled with Cy3TM or Cy5TM dyes (GE Healthcare Life Sciences).  A total of 100 l of Cy3- and Cy5-lablled cDNA in DIG Easy Hybridisation Buffer (Roche) plus 1 mg/ml of yeast tRNA (Sigma) and Herring sperm DNA (Sigma) each were incubated at 65 °C for 5 min, centrifuged for 5 min at 13,000 x g, and applied under a 25mm X 60mm Lifterslip (Erie Scientific) from the top right corner. Slides were sealed in a humidified chamber and incubated in a 37 °C oven overnight (13-18 h). After hybridization, slides were washed as follows: (i) 10-15 min of 1 X SSC, 0.1 % SDS at 50 °C; (ii) repeat; (iii) 15-20 min of 1 X SSC, 0.1 % SDS at 50 °C; (iv) rinse 3 times in 1 X SSC at 50°C, 1 min each and (v) 2 min in 0.2 X SSC at RT. Slides are dried by centrifugation at 100 x g for 5 min immediately after washing and then scanned using an Axon 4000B scanner (Molecular Devices).

data_processing:
Array analysis was performed in R v2.2.1 using the Bioconductor v1.7 packages marray and limma.  The Python language was used for additional manipulations and scripting. Prior to analysis arrays were split into 5k MWG and 5k Compugen components using split10k.py; these were subsequently analysed for differential expression separately. GPR data files were imported into R using the marray package function read.GenePix. GenePix (GenePix Pro v6) flags were converted to weights to be used in subsequent analyses: unflagged spots and spots flagged as good were assigned a weight of 1, all other spots were assigned a weight of 0. Control spots were identified, and were also assigned weights of 0. Background correction was not performed, and thus
background information was zeroed prior to normalisation.
	Print-tip LOWESS normalisation was applied using the marray package maNormMain function.  Zero-weight and control spots were assigned NA values to ensure removal from subsequent differential expression analyses. The normalised arrays, with bad spots set to NA, were converted to MALists for use in limma. These arrays were subjected to between array normalisation by the scale method prior to model fitting.
	Correlation between duplicate spots within each array was estimated using the duplicateCorrelation function.  The consensus correlation value was supplied to the limma lmFit function in order to account for duplicate spots in the model.

source_name: Heart tissue from rats treated with saline

extract_protocol:
Whole heart tissues were collected for RNA extraction. These tissues from each rat were homogenized separately using mortar and pestle in liquid nitrogen. Total RNA was extracted using TRIzol® reagent. Cells suspended in TRIzol® reagent were disrupted by repeated pipetting and then transferred into microfuge tubes. This protocol was modified
from manufacturer’s instructions and is described here. The lysate was further homogenized using syringe and needle for 30 s and incubated at room temperature (~21ºC) for 5 min, and 200 ul of chloroform was added. The tubes were shaken vigorously µ for 15 s to mix the
phases and incubated for 3 min at room temperature. The phases were separated by centrifugation at 12,000 x g for 15 min at 4ºC. The upper aqueous phase was transferred into a fresh microfuge tube and 500 µl of ice cold isopropanol added to precipitate the RNA. The contents were mixed by gentle inversion and then incubated for 10 min at room
temperature. The RNA was recovered by centrifugation at 12,000 x g for 10 min at 4ºC. A gelatinous pellet was left on the side of the tube after removal of the supernatant. The RNA pellet was washed with 1 ml of 75% ethanol and the tube was vortexed briefly to resuspend
the pellet. The RNA was recovered by centrifugation at 7,500 x g for 5 min at 4ºC. This washing step was repeated twice. After removal of the supernatant, the RNA pellet was airdried briefly and then resuspended in 20 µl Nuclease-free H2O (Ambion Inc., Austin, TX, USA) and stored in -80ºC for further processing.

tag: Body weight

tag: Treatment

tag: Source organ

value: Heart

source_name: Heart tissue from rats treated with adrenocorticotrophin (ACTH)

label_protocol:
To label the probes, the samples were each resuspended in 9 μl 0.1 M NaHCO3, pH 9.0. 2 μl of Cy5 (red) monoreactive dye (Amersham) was added to the sample. The samples were incubated for 45 min at room
temperature in the dark. The Cy-dye labeled probes were then cleaned up using the same protocol mentioned above (Qiagen PCR purification kit) to remove any unincorporated dyes.

value: Adrenocorticotrophin


title: HH1_early_rep1

description:
Epiblast-2 0.5h-1
Gene expression data from (potential) primitive streak region in chicken HH1 early (0.5hour), biological replicate 1.


title: Heart Saline vs ACTH 220105


title: HH1_late_rep1

description:
Epiblast-2 5h-1
Gene expression data from primitive streak region in chicken HH1 late (5hour), biological replicate 1.


title: Heart Saline vs ACTH 030305 slide 19


title: 20150910_102147_009: T2D

value: M


title: 28533-3-ME

source_name: 28533_ME_cell pellet

value: Subclade2A (SC2A)

value: invasive infection isolate

value: Mid-exponential (ME, OD600nm=0.5)


title: Kidney_Low Salt Diet_HighSLC

city: San Antonio

first: Laura

middle: L

last: Cox

state: Texas

department: Genetics

institute: Texas Biomedical Research Institute

hyb_protocol: Illumina SOP for beadchips

scan_protocol: Illumina SOP for beadchips

data_processing: Beadstudio average normalization

organism: Papio hamadryas

source_name: Kidney biopsy from high SLC phenotype on low salt diet

label_protocol: Illumina TotalPrep

extract_protocol: Trizol with Qiagen RNeasy cleanup

tag: phenotype

value: High SLC


title: Kidney_High Salt Diet_NormSLC

source_name: Kidney biopsy from normal SLC phenotype on high salt diet

value: Normal SLC


title: 20150910_102146_007: T2D

value: Type-2 Diabetes

tag: tissue

value: Visceral


title: 20150910_102146_005: T2D


title: 20150930_104732_003: T2D


title: 20150910_102145_003: T2D

value: F


title: Heart Saline vs ACTH 030305 slide 16

value: Rattus norvegicus

value: Sprague Dawley (SD)

value: Male

value: 4 weeks

value: app. 200g


title: Kidney_High Salt Diet_HighSLC

source_name: Kidney biopsy from high SLC phenotype on high salt diet


title: 20160714_103117_003: T2D


title: 20150623_103237_009: T2D


title: Kidney_Low Salt Diet_NormSLC

source_name: Kidney biopsy from normal SLC phenotype on low salt diet


title: 28533-2-ME


title: 28533-1-ME


title: EPC_HDAC7_NC_rep2

source_name: EPCs infected with lentivirus carrying nonspecific random shRNA

value: umbilical cord blood

tag: infection


title: Silex_nucleus_Rep3

city: Beaucouzé

first: Jean-Marc

last: Celton

address: 42 rue Georges Morel

country: France

institute: INRA-IRHS

hyb_protocol: The hybridization performed in a 65°C oven overnight. Afterwards, the slide were washed in agilent wash buffer 1 and wash buffer2, dried, and scanned.

scan_protocol: Slides were scanned at 532/635nm at 2 μm resolution and high sensitivity with a Roche-NimbleGen MS200. NimbleScan Software v2.4 was used to extract pair-data files from the scanned images.

data_processing: All statistical analyses on the gene expression data were performed using the R language, version 2.5.1 (R Development Core Team, 2011) and the package LIMMA (Smyth G.K., 2005) from the Bioconductor project. For the processing step, data were normalized by the lowess method in LIMMA.

organism: Arabidopsis thaliana

source_name: Silex leaf nucleus extract

label_protocol: 400ng of total RNAs were amplified using the Ambion messageAmp II (Ambion, Austin TX) following manufacturer's instructions. 5µg of each aRNAs were retrotranscribed with 400U of Superscript II reverse-transcriptase (Invitrogen Corp., Carlsbad, CA) and labelled with 1,5mmol of Cyanine-3 (Cy3) or Cyanine-5 (Cy5) (Interchim, France), then purified with NucleoSpin Gel and PCR Clean-up column kits (Macherey-Nagel, GmbH & Co. KG, Germany). Purified labeled cDNA were quantified using NanoDrop ND-1000 (Nanodrop Technologies, DE, USA). Labelled samples were combined as 30 pmol for each dye and co-hybridized to the Medtr_v1 12x135K arrays.

growth_protocol: 24°C with 16 hours of light

extract_protocol: Nuclear-cytoplasmic fractioning performed as described in Wang et al. 2011, RNA purification was performed using TRI Reagent (Sigma)

value: leaf

tag: genetic background/cultivar

tag: genotype

value: Wild-type

tag: age

value: 3 weeks


title: Silex_nucleus_Rep2


title: 28392-3-ME

source_name: 28392_ME_cell pellet

tag: subclade

value: Subclade2A (SC2A)

tag: site of isolation

tag: strain


title: Silex_cytoplasm_Rep3

source_name: Silex leaf cytoplasm extract

value: whole flower


title: 20150623_103235_007: T2D

source_name: Visceral

tag: gender


title: osteoclast, LysM-St18flox

city: Tsukuba

first: Yutaro

last: Kumagai

state: Ibaraki

address: Central 5-41, Higashi 1-1-1

department: BRD

institute: AIST

hyb_protocol: Following fragmentation, 1.65 ug of cRNA were hybridized to the Agilent expression microarray according to the protocols provided by the manufacturer.

scan_protocol: Arrays were scanned using the Agilent Technologies G4900DA SG12494263.

data_processing:
Spot intensities were measured by using Agilent Feature Extraction 11.0.1.1.
After filtering out probes having one or more A flag, the intensities were log2 transformed and quantile normalized by using a R library preprocessCore.

source_name: osteoclast, LysM-St18flox

label_protocol: Labeled cRNA were prepared from 100 ng total RNA using the Agilent’s Quick Amp Labeling Kit according to the manufacturer's instruction.

growth_protocol: RPMI1640 medium with 10 % FBS

extract_protocol: Total RNA was extracted by using TRIzol reagent (Invitrogen).

treatment_protocol: MDMs were derived by culturing bone marrow cells with 25 ng/ml of M-CSF for 4 days. OCs were prepared by culturing MDMs with 25 ng/ml of M-CSF and 50 ng/ml of RANKL for 3 days.

tag: cell type

value: osteoclast


title: 20160916_101343_005: Normal

tag: diagnosis

value: Normal


title: 28386-3-ME

source_name: 28386_ME_cell pellet

value: invasive infection isolate

tag: growth phase

value: Mid-exponential (ME, OD600nm=0.5)


title: 28392-1-ME


title: 28392-2-ME


title: Silex_cytoplasm_Rep2


title: 28386-2-ME


title: 28386-1-ME


title: Silex_nucleus_Rep1


title: M-CSF-derived macrophage, wild-type

source_name: M-CSF-derived macrophage, wild-type

value: M-CSF-derived macrophage

value: wild-type


title: 28271-3-ME

source_name: 28271_ME_cell pellet


title: Silex_cytoplasm_Rep1


title: 20160706_102223_007: Normal

value: F

value: Visceral


title: HVT_1336_post

city: Stevenage

first: Glyn

last: Bradley

address: Medicines Research Centre

department: Computational Biology

country: United Kingdom

institute: GSK

description: Gene expression data whole blood

hyb_protocol: Labelled cDNA was hybridized onto Mouse Genome 430 2.0  GeneChip oligonucleotide arrays (Affymetrix).

scan_protocol: Standard protocols

data_processing: Data were analysed in R/Bioconductor, normalised by RMA

label: Biotin

source_name: Whole Blood from HV

label_protocol: FL-Ovation cDNA Biotin Module V2 kit (NuGen).

extract_protocol: WT-Ovation Pico RNA Amplification System (NuGen).

treatment_protocol: intranasal

tag: challenge

value: LPS

tag: disease

value: HVT

value: post


title: osteoclast, wild-type

source_name: osteoclast, wild-type


title: 20160706_102227_009: Normal


title: 28271-2-ME


title: 20160706_102222_005: Normal


title: M-CSF-derived macrophage, LysM-St18flox

source_name: M-CSF-derived macrophage, LysM-St18flox


title: LysM-St18flox PEC, 0h after LPS stimulation

source_name: peritoneal macrophage from a LysM-St18flox mouse stimulated with LPS for 0h

treatment_protocol: Peritoneal macrophage were prepared by collecting peritoneal lavage fluid from mice injected with 4 % thioglycollate for 3 days. The cells were stimulated with LPS for 0 or 3 hours.

value: peritoneal macrophage

tag: genotpye

tag: lps stimulation


title: 28271-1-ME


title: LysM-St18flox PEC, 3h after LPS stimulation

source_name: peritoneal macrophage from a LysM-St18flox mouse stimulated with LPS for 3h


title: HVT_1336_pre

description: Gene expression data whole blood

value: pre


title: 20160706_102222_003: Normal


title: 20160706_102218_001: Normal


title: HVT_1335_post

description: Gene expression data whole blood

value: saline


title: 20150930_104734_007: Normal

value: M


title: Wild-type PEC, 3h after LPS stimulation

source_name: peritoneal macrophage from a wild-type mouse stimulated with LPS for 3h

value: wildtype


title: Wild-type PEC, 0h after LPS stimulation

source_name: peritoneal macrophage from a wild-type mouse stimulated with LPS for 0h


title: 20150930_104735_009: Normal


title: HVT_1335_pre

description: Gene expression data whole blood


title: 20150930_104733_005: Normal


title: 28191-3-ME

source_name: 28191_ME_cell pellet

value: Subclade2A (SC2A)


title: 28191-2-ME


title: 28191-1-ME


title: 20150923_095452_009: Normal


title: HVT_1330_pre

description: Gene expression data whole blood


title: 20150923_095452_007: Normal


title: HVT_1330_post

description: Gene expression data whole blood


title: 28078-2-ME

source_name: 28078_ME_cell pellet


title: 28078-3-ME


title: HVT_1332_post

description: Gene expression data whole blood


title: HVT_1332_pre

description: Gene expression data whole blood


title: HVT_1329_post

description: Gene expression data whole blood


title: 20150923_095451_005: Normal


title: 20150923_095450_003: Normal


title: HVT_1328_post

description: Gene expression data whole blood


title: 27961-2-ME

source_name: 27961_ME_cell pellet


title: 27961-3-ME


title: 27961-1-ME


title: 28078-1-ME


title: 20160916_101345_010: T2D

source_name: Sudcutaneous

value: Type-2 Diabetes

value: Sudcutaneous


title: 20150923_095446_001: Normal

value: Normal


title: HVT_1328_pre

description: Gene expression data whole blood


title: 29573-2_ME

source_name: 29573_ME_cell pellet

value: Subclade1B (SC1B)

value: invasive infection isolate

value: Mid-exponential (ME, OD600nm=0.5)


title: 29573-1_ME


title: HVT_1329_pre

description: Gene expression data whole blood


title: 20150910_102141_001: Normal

source_name: Visceral

value: F


title: 29573-3_ME


title: 20160916_101344_008: T2D


title: HVT_1327_post

description: Gene expression data whole blood


title: HVT_1324_pre

description: Gene expression data whole blood


title: 20160916_101342_004: T2D


title: HVT_1324_post

description: Gene expression data whole blood


title: HVT_1313_pre

description: Gene expression data whole blood


title: HVT_1313_post

description: Gene expression data whole blood


title: HVT_1214_post

description: Gene expression data whole blood


title: 20160714_103118_006: T2D


title: HVT_1327_pre

description: Gene expression data whole blood


title: 29553-3-ME

source_name: 29553_ME_cell pellet


title: 29553-2-ME


title: 20150930_104732_004: T2D


title: 29502-3-ME

source_name: 29502_ME_cell pellet


title: 29502-2-ME


title: 29502-1-ME


title: 20160714_103119_008: T2D


title: 29553-1-ME


title: 20160714_103117_004: T2D


title: 29409-3-ME

source_name: 29409_ME_cell pellet


title: 29409-2-ME


title: HVT_1214_pre

description: Gene expression data whole blood


title: 29409-1-ME


title: 20150930_104731_002: T2D


title: 20150910_102147_008: T2D


title: HVT_1213_post

description: Gene expression data whole blood


title: 20160714_103117_002: T2D


title: 20150623_103237_010: T2D


title: HVT_1205_pre

description: Gene expression data whole blood


title: 29379-3-ME

source_name: 29379_ME_cell pellet


title: HVT_1213_pre

description: Gene expression data whole blood

source_name: Whole Blood from HV


title: HVT_1211_post

description: Gene expression data whole blood


title: 20150910_102147_010: T2D


title: HVT_1205_post

description: Gene expression data whole blood


title: HVT_1211_pre

description: Gene expression data whole blood


title: HVT_1110_post

description: Gene expression data whole blood


title: 20150623_103236_008: T2D


title: 20150910_102146_006: T2D


title: 20160706_103045_001: Normal


title: 20150910_102145_004: T2D


title: 20160916_101343_006: Normal


title: 29379-2-ME


title: 29379-1-ME


title: 29326-2-ME

source_name: 29326_ME_cell pellet


title: 29326-3-ME


title: SC-50 (B_3)

city: Yangzhou

first: Hou

last: Zhaofeng

state: Jiangsu

address: No. 12, Wenhui East Road

institute: Yangzhou University

data_processing:
Illumina Casava1.8 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for poly-N, with 5’ adapter contaminants, without 3’ adapter or the insert tag, containing ploy A or T or G or C and low quality reads sequence, and reads with lengths shorter than 18 nt or longer than 35 nt were filtered, then mapped to Sscrofa 10.2 whole genome using bowtie-v0.12.9 with parameters -v 0 -k 1 for alignment analysis of short sequences.
Tags originating from protein-coding genes, repeat sequences, rRNA, tRNA, snRNA and snoRNA were removed by mapping to RepeatMasker open-4.0.3, Rfam database (http://rfam.xfam.org/) or those types of data from pig.
Known miRNA were identified from the mapped sRNA tags in miRBase 20.0 (http://www.mirbase.org/), and the available software miREvo_v1.1, mirdeep2_0_0_5 and ViennaRNA-2.1.1 were integrated to predict novel miRNA
MiRNA which might have base edit could be detected by aligning all the sRNA tags to mature miRNA, allowing one mismatch
Known miRNA used miFam.dat (http://www.mirbase.org/ftp.shtml) to look for families; novel miRNA precursor was submitted to Rfam (http://rfam.sanger.ac.uk/search/) to look for Rfam families.
MiRNA expression levels were estimated by TPM (transcript per million) through the following criteria (Zhou et al., 2010): Normalization formula: Normalized expression = mapped readcount/Total reads*1000000
Genome_build: Sscrofa 10.2
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample.

organism: Sus scrofa

source_name: spleen

extract_protocol:
Spleens were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
Three individuals’ RNA samples, of the same group at each time point were equally mixed to generate an RNA pool. A total amount of 3 μg total RNA per pool was used as input material for the small RNA library. Sequencing libraries were generated using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (NEB, USA.).

tag: group

value: control

value: post inoculation day 50

value: spleen

value: Landrace


title: 20160706_102227_010: Normal

tag: tissue


title: 20160706_102223_006: Normal


title: 20160706_102222_004: Normal


title: 20160706_102221_002: Normal


title: HVT_1103_pre

description: Gene expression data whole blood

value: LPS

value: HVT


title: HVT_1011_pre

description: Gene expression data whole blood

value: pre


title: HVT_1108_post

description: Gene expression data whole blood

value: post


title: HVT_1110_pre

description: Gene expression data whole blood


title: 20150930_104734_008: Normal

value: M


title: 29284-3-ME

source_name: 29284_ME_cell pellet


title: HVT_1108_pre

description: Gene expression data whole blood


title: 29198-3-ME

source_name: 29198_ME_cell pellet


title: 20150930_104733_006: Normal


title: HVT_1011_post

description: Gene expression data whole blood


title: 20150923_095453_010: Normal


title: HVT_1103_post

description: Gene expression data whole blood


title: 20150930_104735_010: Normal


title: 29284-2-ME


title: SI-50 (A_3)

value: infected


title: SC-25 (B_2)

value: post inoculation day 25


title: SI-25 (A_2)


title: 29326-1-ME


title: SC-10 (B_1)

value: post inoculation day 10


title: 29284-1-ME


title: HVT_1010_post

description: Gene expression data whole blood


title: SI-10 (A_1)


title: HVT_1010_pre

description: Gene expression data whole blood


title: 29184-2-ME

source_name: 29184_ME_cell pellet


title: 29184-3-ME


title: 29198-1-ME


title: HVT_1009_post

description: Gene expression data whole blood


title: 29198-2-ME


title: 29184-1-ME


title: HVT_1009_pre

description: Gene expression data whole blood


title: HVT_1006_pre

description: Gene expression data whole blood


title: 20150923_095451_006: Normal

value: Normal

value: Sudcutaneous


title: 20150923_095452_008: Normal


title: 29159-3-ME

source_name: 29159_ME_cell pellet

value: Subclade1B (SC1B)

value: invasive infection isolate


title: 20150910_102144_002: Normal

value: F


title: HVT_1006_post

description: Gene expression data whole blood


title: 29159-2-ME

value: Mid-exponential (ME, OD600nm=0.5)


title: 20150923_095450_004: Normal


title: HVT_1005_post

description: Gene expression data whole blood


title: 20150923_095450_002: Normal


title: HVT_1005_pre

description: Gene expression data whole blood


title: 29159-1-ME


title: 29093-3-ME

source_name: 29093_ME_cell pellet


title: HVT_1004_post

description: Gene expression data whole blood


title: male_mouse_liver_NatKO_rcd_biorep4

city: Toronto

first: Stephenie

last: Prokopec

state: Ontario

address: 661 University Avenue, Suite 510

country: Canada

institute: Ontario Institute for Cancer Research

hyb_protocol: Manufacturer's recommended protocols as followed by the TCAG Facility at the Hospital for Sick Kid's in Toronto, Canada

data_processing: Raw array data (CEL files) were loaded into the R statistical environment (v3.4.3) using the affy package (v1.48.0) of the BioConductor library. Data was investigated for distributional homogeneity, then pre-processed using the RMA algorithm. No samples were identified as outliers. An updated Probe to Entrez Gene ID map, mogene20stmmentrezgcdf (v22.0.0), was used for annotation.

source_name: male, Nat1/2 knockout liver, rcd diet for 12 weeks

growth_protocol: Mice (12 weeks old) were housed individually in stainless steel cages in a room maintained at 22.5±1°C with lights scheduled from 7 am to 7 pm. Animals had access to water and food ad libitum unless otherwise specified.

extract_protocol: RNA was isolated from liver tissue (~10 mg) with 1 ml TRI Reagent followed by RNA clean-up and on-column DNase digestion (Purelink RNA extraction kit).  RNA was quantified using a Nanodrop with ratios greater than 1.8, and initial integrity was inspected by running on an agarose gel.   An Agilent Bioanalyzer was used to assess RIN.

treatment_protocol: KO mice and their wild-type (WT) littermate controls were fed a regular-chow (RCD; 13.5 kcal% fat, 25.2 kcal% protein, 61.3 kcal% carbohydrates; 3,236 kcal/kg; R03-10; SAFE, France) diet for 12 weeks then a high-fat/high-sucrose (HFHS; 45 kcal% fat, 20 kcal% protein, 35 kcal% carbohydrates; 4,730 kcal/kg; D12451, OpenSource Diets) diet for 12 weeks.

tag: batch

tag: Sex

value: male

value: Nat1/2 knockout

tag: diet

value: regular chow diet


title: 20160916_101338_001: T2D

source_name: Limb

value: Type-2 Diabetes

value: Limb


title: male_mouse_liver_NatKO_rcd_biorep3

scan_protocol: Manufacturer's recommended protocols as followed by the TCAG Facility at the Hospital for Sick Kid's in Toronto, Canada

tag: genotype


title: 29093-2-ME

tag: subclade


title: male_mouse_liver_NatKO_rcd_biorep1

label_protocol: Manufacturer's recommended protocols as followed by the TCAG Facility at the Hospital for Sick Kid's in Toronto, Canada


title: male_mouse_liver_NatKO_rcd_biorep2


title: 20160819_094519_002: T2D


title: 20160819_094516_001: T2D


title: HVT_1004_pre

description: Gene expression data whole blood

value: LPS

value: HVT

value: pre


title: male_mouse_liver_wildtype_rcd_biorep4

source_name: male, Nat1/2 wildtype liver, rcd diet for 12 weeks

value: wildtype


title: 20160916_101342_002: T2D

value: M


title: COPD_2039

description: Gene expression data whole blood

source_name: Whole Blood from COPD subject

value: COPD


title: 29064-3-ME

source_name: 29064_ME_cell pellet

tag: site of isolation


title: COPD_2046

description: Gene expression data whole blood


title: male_mouse_liver_wildtype_rcd_biorep3

tag: strain


title: COPD_2037

description: Gene expression data whole blood


title: 20160422_102233_010: T2D

tag: gender


title: 29064-2-ME


title: 20150903_103936_010: T2D


title: male_mouse_liver_wildtype_rcd_biorep1


title: COPD_2036

description: Gene expression data whole blood


title: male_mouse_liver_NatKO_hfhs_biorep3_techrep2

source_name: male, Nat1/2 knockout liver, hfhs diet for 12 weeks

value: high fat/high sucrose


title: COPD_2031

description: Gene expression data whole blood


title: 20150903_103935_008: T2D


title: male_mouse_liver_wildtype_rcd_biorep2


title: 29064-1-ME


title: 20150903_103936_009: T2D


title: COPD_2028

description: Gene expression data whole blood


title: 29093-1-ME


title: 28932-3-ME

source_name: 28932_ME_cell pellet


title: COPD_2035

description: Gene expression data whole blood


title: 28932-2-ME


title: 20150903_103935_007: T2D


title: 28932-1-ME


title: 20150903_103934_005: T2D


title: 20150903_103935_006: T2D


title: 28869-3-ME

source_name: 28869_ME_cell pellet


title: COPD_2026

description: Gene expression data whole blood


title: 28869-2-ME


title: COPD_2025

description: Gene expression data whole blood


title: male_mouse_liver_NatKO_hfhs_biorep1


title: male_mouse_liver_NatKO_hfhs_biorep2


title: 28869-1-ME


title: male_mouse_liver_wildtype_hfhs_biorep1_techrep2

source_name: male, Nat1/2 wildtype liver, hfhs diet for 12 weeks


title: male_mouse_liver_NatKO_hfhs_biorep3_techrep1


title: male_mouse_liver_wildtype_hfhs_biorep2


title: 20150903_103933_002: T2D


title: male_mouse_liver_wildtype_hfhs_biorep3


title: male_mouse_liver_wildtype_hfhs_biorep1_techrep1


title: 20150903_103933_003: T2D


title: COPD_2016

description: Gene expression data whole blood


title: COPD_2018

description: Gene expression data whole blood


title: female_mouse_liver_NatKO_hfhs_biorep2

source_name: female, Nat1/2 knockout liver, hfhs diet for 12 weeks

value: female


title: COPD_2024

description: Gene expression data whole blood


title: female_mouse_liver_NatKO_hfhs_biorep1


title: 20150903_103934_004: T2D


title: 28746-2-ME

source_name: 28746_ME_cell pellet

value: Subclade1B (SC1B)


title: female_mouse_liver_NatKO_hfhs_biorep3


title: COPD_2017

description: Gene expression data whole blood


title: COPD_2015

description: Gene expression data whole blood


title: 20150623_103235_006: T2D


title: 28746-1-ME

value: invasive infection isolate


title: 28650-3-ME

source_name: 28650_ME_cell pellet


title: 28746-3-ME


title: 20150623_103234_005: T2D

value: F


title: female_mouse_liver_wildtype_hfhs_biorep3

source_name: female, Nat1/2 wildtype liver, hfhs diet for 12 weeks


title: female_mouse_liver_wildtype_hfhs_biorep2


title: COPD_2012

description: Gene expression data whole blood


title: 20150903_103929_001: T2D


title: 28582-3-ME

source_name: 28582_ME_cell pellet

value: Mid-exponential (ME, OD600nm=0.5)


title: 28650-1-ME


title: 20150623_103233_003: T2D


title: COPD_2013

description: Gene expression data whole blood


title: 20150623_103234_004: T2D


title: 20141224_122411_003: T2D


title: COPD_2014

description: Gene expression data whole blood


title: 28582-2-ME


title: OMTX703 hu 60mg-571

type: protein

first: Joseph

middle: A.

last: Ludwig

department: Sarcoma Medical Oncology

institute: UT-MD-Anderson Cancer Center

description:
RPPA
SAMPLE 38

scan_protocol: Slides were scanned on a flatbed scanner to produce 16-bit tiff images. Spots from tiff images were identified and their densities were quantified by MicroVigene. Relative protein levels for each sample were determined by interpolation of each dilution curve from the standard curve (supercurve) of the slide (antibody). Supercurve is constructed from a script in R written by the informatics department. These values are given as Normalized values.

data_processing:
Expression data was normalized for possible unequal protein loading, taking into account the signal intensity for each sample for all antibodies tested. Log2 values were media-centered by protein to account for variability in signal intensity by time and were calculated using the formula log2 signal – log2 median. Principal component analysis was used to check for a batch effect and feature-by-feature two-sample t-tests were used to assess differences between treatment and control groups. We also used feature-by-feature one-way analysis of variance (ANOVA) followed by the Tukey test to perform pair comparisons for all groups. Beta-uniform mixture models were used to fit the resulting p value distributions to adjust for multiple comparisons. The cutoff p values and number of significant proteins were computed for several different false discovery rates (FDRs).
Biostatistical analyses comparing two groups were performed using an unpaired t-test with Gaussian distribution followed by the Welch correction. To distinguish between treatment groups, we used one-way ANOVA with the Geisser-Greenhouse correction. Differences with p values <0.05 were considered significant. Within clustered image maps (CIM), unsupervised double hierarchical clustering used the Pearson correlation distance and Ward’s linkage method as the clustering algorithm to link entities (proteins or genes) and samples.

label: 246 Primary Antibodies

molecule: protein

source_name: ES8 xenografts treated with OMTX703

label_protocol: Using a 2470 Arrayer (Aushon BioSystems, tumor or normal tissue lysates were serially diluted 2-fold for 5 dilutions (From undiluted to 1:16 dilutio) and arrayed on nitrocellulose-coated FAST slides in an 11X11 format. Samples were probed with antibodies using the Dako CSA tyramide-amplification approach and visualized by DAB colorimetric reaction.

growth_protocol: Proteomic analysis using a reverse-phase protein lysate array (RPPA) was used to elucidate biomarkers that distinguish ES8 xenografts that are treated with OMTX003 (n=8, a nacked mAb anti endoglin at 10 mg/kg), OMTX703 (an endoglin-targeting antibody-drug conjugate with cytolisin at 10, 30 and 60 mg/kg (n=8 each)) or control vehicle (n=7)

extract_protocol: Protein extraction from tumor was performed by homogenizing an approximate 10 mg of frozen tissue in 500 ul of the lysis buffer containing protease and phosphatase inhibitors using an electric tissue homogenizer (Pro Scientific). Total lysed proteins were quantified using BCA protein assay kit and stored for further analyses for RPPA.

treatment_protocol: ES8 xenografts treated with OMTX003 (n=8, a nacked mAb anti endoglin at 10 mg/kg), OMTX703 (an endoglin-targeting antibody-drug conjugate with cytolisin at 10, 30 and 60 mg/kg (n=8 each)) or control vehicle (n=7)

value: ES8 Ewing sarcoma xenograft

tag: treated with

value: OMTX703  60mg/kg


title: OMTX703 hu 60mg-542

description:
RPPA
SAMPLE 36

hyb_protocol: Samples were probed with antibodies using the Dako CSA tyramide-amplification approach and visualized by DAB colorimetric reaction.


title: 20141219_100317_003: T2D

tag: diagnosis


title: 28650-2-ME

tag: growth phase


title: COPD_2005

description: Gene expression data whole blood

tag: challenge


title: OMTX703 hu 60mg-568

description:
RPPA
SAMPLE 37


title: OMTX703 hu 60mg-576

description:
RPPA
SAMPLE 39


title: 20141219_100318_004: T2D


title: female_mouse_liver_wildtype_hfhs_biorep1


title: COPD_2003

description: Gene expression data whole blood

tag: disease


title: 28582-1-ME


title: OMTX703 hu 60mg-538

description:
RPPA
SAMPLE 35


title: 20141219_100317_002: T2D


title: 28278-3-ME

source_name: 28278_ME_cell pellet


title: 28278-2-ME


title: 20141217_103248_001: T2D


title: high activity_female_87 yrs

city: Irvine

first: Nicole

middle: Claudia

last: Berchtold

state: CA

address: 1226 Gillespie Neuroscience Facility

department: Institute for Memory Impairments and Neurological Disorders

institute: UC Irvine

description: Gene expression data from aged human post-mortem hippocampus

hyb_protocol: 10 ug of fragmented target cRNA was hybridized at 45°C with rotation for 16 hours (Affymetrix GeneChip® Hybridization Oven 640) to probe sets present on an Affymetrix HgU133 plus2.0 array. The GeneChip® arrays were washed and then stained (SAPE, streptavidin-phycoerythrin) on an Affymetrix Fluidics Station 450,

scan_protocol: GeneChip® Scanner 3000

data_processing: GeneSpring (version 14) software: quantile normalization followed by baseline transformation to the median of all samples.    For CyberT analysis: raw untransformed data were normalized using log transformation.   MAS5.0 used for Flag detection

source_name: post-mortem hippocampus

label_protocol: Eluted total RNAs were quantified with a portion of the recovered total RNA adjusted to a final concentration of 1.25 ug/ul. All starting total RNA samples were quality assessed prior to beginning target preparation/processing steps by running out a small amount of each sample (typically 25-250 ng/well) onto a RNA Lab-On-A-Chip (Caliper Technologies Corp., Mountain View, CA) that was evaluated on an Agilent Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA). Single-stranded, then double-stranded cDNA was synthesized from the poly(A)+ mRNA  present in the isolated total RNA (typically 10 ug total RNA starting material each sample reaction) using the SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen Corp., Carlsbad, CA ) and poly (T)-nucleotide primers that contained a sequence recognized by T7 RNA polymerase.  A portion of the resulting ds cDNA was used as a template to generate biotin-tagged cRNA from an in vitro transcription reaction (IVT), using the BioArray High-Yield RNA Transcript Labeling Kit (T7) (Enzo Diagnostics, Inc., Farmingdale, NY). 15ug of the resulting biotin-tagged cRNA was fragmented to an average strand length of 100 bases (range 35-200 bases) following prescribed protocols (Affymetrix GeneChip® Expression Analysis Technical Manual).

extract_protocol: Trizol extraction, RNA treated with DNAse and purified using Rneasy spin columns (Qiagen)

treatment_protocol: frozen hippocampus was obtained from post-mortem brain

value: hippocampus

tag: sex (self-reported)

tag: age

tag: physical activity tier

value: high activity

tag: physical activity

value: Actical average counts/day:2.91

tag: education

tag: depression

tag: cognitive frequency

tag: social frequency


title: high activity_male_95 yrs

tag: tissue

value: male

value: Actical average counts/day:2.9


title: COPD_2002

description: Gene expression data whole blood


title: OMTX703 hu 60mg-529

description:
RPPA
SAMPLE 33


title: 20141217_103251_002: T2D

value: Type-2 Diabetes

value: Limb


title: 28278-1-ME

tag: subclade

tag: site of isolation


title: 27784-2-ME

source_name: 27784_ME_cell pellet

tag: strain


title: 27784-3-ME


title: OMTX703 hu 30mg-578

description:
RPPA
SAMPLE 31

tag: treated with

value: OMTX703  30mg/kg


title: OMTX703 hu 60mg-501

description:
RPPA
SAMPLE 32


title: high activity_female_76 yrs

value: Actical average counts/day:2.7


title: 27784-1-ME


title: 11115-3-ME

source_name: 11115_ME_cell pellet


title: OMTX703 hu 60mg-532

description:
RPPA
SAMPLE 34


title: 11115-2-ME


title: 20141101_110100_001: T2D

source_name: Limb

tag: gender

value: M

tag: diagnosis


title: 20160422_102233_009: Normal

value: Normal


title: high activity_male_85 yrs

value: Actical average counts/day:3.26


title: high activity_female_79 yrs

value: female

value: Actical average counts/day:2.99


title: high activity_male_93 yrs

value: Actical average counts/day:4.7


title: OMTX703 hu 30mg-530

description:
RPPA
SAMPLE 28

value: ES8 Ewing sarcoma xenograft


title: OMTX703 hu 30mg-523

description:
RPPA
SAMPLE 27


title: 20141101_110103_002: T2D

value: F


title: OMTX703 hu 30mg-575

description:
RPPA
SAMPLE 30


title: 20141205_101308_001: T2D


title: 11115-1-ME

value: Subclade1B (SC1B)

value: invasive infection isolate

tag: growth phase

value: Mid-exponential (ME, OD600nm=0.5)


title: high activity_female_92 yrs

value: hippocampus

value: high activity

value: Actical average counts/day:5.6


title: high activity_female_89 yrs

value: Actical average counts/day:4.19


title: OMTX703 hu 30mg-516

description:
RPPA
SAMPLE 26

value: OMTX703  30mg/kg


title: OMTX703 hu 30mg-569

description:
RPPA
SAMPLE 29


title: high activity_female_81 yrs

value: Actical average counts/day:2.82


title: 20140703_142347_003: T2D

value: M

value: Type-2 Diabetes

value: Limb


title: 20160422_102232_007: Normal

value: Normal


title: 11108-3-ME

source_name: 11108_ME_cell pellet


title: OMTX703 hu 30mg-514

description:
RPPA
SAMPLE 25


title: 20140709_185210_002: T2D


title: high activity_male_86 yrs

value: male

value: Actical average counts/day:3.53


title: 11108-2-ME


title: 20160422_102232_008: Normal


title: 11107-3-ME

source_name: 11107_ME_cell pellet


title: high activity_female_80 yrs

value: female

value: Actical average counts/day:2.6


title: 20160422_102232_006: Normal


title: 11108-1-ME

value: Subclade1B (SC1B)


title: OMTX703 hu 10mg-548

description:
RPPA
SAMPLE 22

value: ES8 Ewing sarcoma xenograft

value: OMTX703  10mg/kg


title: high activity_male_92 yrs

value: hippocampus

value: Actical average counts/day:2.32


title: 20160422_102231_004: Normal


title: 20160422_102231_005: Normal


title: moderate activity_female_89 yrs -2

value: moderate activity

value: Actical average counts/day:2.06


title: moderate activity_female_99 yrs

value: Actical average counts/day:1.44


title: OMTX703 hu 30mg-507

description:
RPPA
SAMPLE 24

value: OMTX703  30mg/kg


title: 11107-1-ME

value: invasive infection isolate

value: Mid-exponential (ME, OD600nm=0.5)


title: OMTX703 hu 10mg-528

description:
RPPA
SAMPLE 21


title: OMTX703 hu 10mg-520

description:
RPPA
SAMPLE 20


title: 11052-3-ME

source_name: 11052_ME_cell pellet


title: 11052-2-ME


title: 11052-1-ME


title: OMTX703 hu 10mg-505

description:
RPPA
SAMPLE 17


title: OMTX703 hu 10mg-513

description:
RPPA
SAMPLE 18


title: moderate activity_female_91 yrs

value: Actical average counts/day:1.8


title: 20160422_102230_003: Normal

value: M

value: Normal

value: Limb


title: 20160422_102226_001: Normal


title: moderate activity_female_88 yrs -2

value: female

value: Actical average counts/day:1.87


title: moderate activity_female_89 yrs

value: Actical average counts/day:1.99


title: 28426-3-ME

source_name: 28426_ME_cell pellet

value: Subclade1A (SC1A)


title: moderate activity_male_81 yrs

value: male

value: Actical average counts/day:1.4


title: 20150623_103229_001: Normal

value: F


title: moderate activity_female_88 yrs

value: hippocampus

value: moderate activity

value: Actical average counts/day:1.72


title: 20150623_103233_002: Normal


title: OMTX703 hu 10mg-519

description:
RPPA
SAMPLE 19

value: ES8 Ewing sarcoma xenograft

value: OMTX703  10mg/kg


title: 20150103_101422_004: Normal


title: OMTX003hu 10mg-559

description:
RPPA
SAMPLE 15

source_name: ES8 xenografts treated with OMTX003

value: OMTX003 10mg/kg


title: 28426-2-ME

value: invasive infection isolate

value: Mid-exponential (ME, OD600nm=0.5)


title: moderate activity_female_85 yrs

value: Actical average counts/day:2


title: OMTX703 hu 10mg-502

description:
RPPA
SAMPLE 16


title: moderate activity_male_89 yrs

value: Actical average counts/day:2.06


title: 20160422_102230_002: Normal

value: M

value: Normal

value: Limb


title: 20150103_101422_003: Normal


title: 28426-1-ME

value: Subclade1A (SC1A)


title: 20141224_122410_002: Normal


title: 28360-3-ME

source_name: 28360_ME_cell pellet


title: moderate activity_female_86 yrs

value: female

value: Actical average counts/day:1.48


title: 20150103_101421_002: Normal

value: F


title: 20150103_101418_001: Normal


title: moderate activity_male_78 yrs

value: hippocampus

value: male

value: Actical average counts/day:1.75


title: low activity_female_92 yrs

value: low activity

value: Actical average counts/day:0.57


title: OMTX003hu 10mg-544

description:
RPPA
SAMPLE 14

value: ES8 Ewing sarcoma xenograft

value: OMTX003 10mg/kg


title: 28360-2-ME

value: invasive infection isolate

value: Mid-exponential (ME, OD600nm=0.5)


title: 28360-1-ME


title: OMTX003hu 10mg-527

description:
RPPA
SAMPLE 12


title: OMTX003hu 10mg536

description:
RPPA
SAMPLE 13


title: 28330-3-ME

source_name: 28330_ME_cell pellet


title: OMTX003hu 10mg-525

description:
RPPA
SAMPLE 10


title: 28330-2-ME


title: OMTX003hu 10mg-526

description:
RPPA
SAMPLE 11


title: low activity_male_92 yrs

value: Actical average counts/day:0.65


title: 28323-3-ME

source_name: 28323_ME_cell pellet


title: 28330-1-ME


title: OMTX003hu 10mg-518

description:
RPPA
SAMPLE 9


title: 20141220_095344_003: Normal


title: Control-580

description:
RPPA
SAMPLE 7

source_name: ES8 xenografts control

value: vehicle (control)


title: low activity_female_85 yrs

value: Actical average counts/day:0.94


title: OMTX003hu 10mg-508

description:
RPPA
SAMPLE 8


title: low activity_male_101 yrs

value: Actical average counts/day:0.89


title: 20141224_122409_001: Normal

value: Normal

value: Limb


title: 20141220_095340_001: Normal


title: 20141220_095343_002: Normal


title: 28323-2-ME

value: Subclade1A (SC1A)


title: 20141219_100313_001: Normal

value: F


title: Control-557

description:
RPPA
SAMPLE 6


title: 28323-1-ME


title: low activity_female_80 yrs

value: hippocampus

value: female

value: Actical average counts/day:0.37


title: low activity_female_96 yrs

value: low activity

value: Actical average counts/day:1.06


title: 20140731_113349_003: Normal


title: 20140731_113345_001: Normal


title: Control-556

description:
RPPA
SAMPLE 5

value: ES8 Ewing sarcoma xenograft


title: low activity_female_76 yrs

value: Actical average counts/day:0.71


title: low activity_female_84 yrs

value: Actical average counts/day:1.05


title: 28309-3-ME

source_name: 28309_ME_cell pellet

value: invasive infection isolate

value: Mid-exponential (ME, OD600nm=0.5)


title: 20141205_101311_002: Normal


title: 28309-2-ME


title: 20140731_113348_002: Normal

value: M


title: Control-550A

description:
RPPA
SAMPLE 3

value: vehicle (control)


title: 20140709_185207_001: Normal


title: 28309-1-ME


title: Control-551

description:
RPPA
SAMPLE 4


title: low activity_female_86 yrs

value: Actical average counts/day:0.13


title: Control-547

description:
RPPA
SAMPLE 2


title: Control-546

description:
RPPA
SAMPLE 1


title: 10826-2-ME

source_name: 10826_ME_cell pellet


title: 10826-1-ME


title: 10812-3-ME

source_name: 10812_ME_cell pellet


title: 10826-3-ME


title: OMTX703 hu 10mg-550B

description:
RPPA
SAMPLE 23

source_name: ES8 xenografts treated with OMTX703

value: OMTX703  10mg/kg


title: 10812-2-ME


title: low activity_female_95 yrs

source_name: post-mortem hippocampus

value: Actical average counts/day:0.74


title: low activity_female_89 yrs

value: Actical average counts/day:1.02


title: Patient_17_cancer_rep1_HG-U133_Plus_2

city: Athens

first: Aristotelis

last: Chatziioannou

state: Not in US

address: 48 Vassileos Constantinou Avenue

department: Institute of Biology, Medicinal Chemistry and Biotechnology

country: Greece

institute: National Hellenic Research Foundation

description:
PET-FDG protocol: PET-FDG data were acquired according to Cancer Imaging (2012) 12, 283289 DOI: 10.1102/1470-7330.2012.0033
PET kinetic parameters description:
k1 = transport rate constant related with glucose transporters into the cells (influx)
k2 = transport rate constant related with glucose transporters outof  the cells (efflux)
k3 = rate constant associated with the phosphorylation process of FDG
k4 = rate constant associated with the dephosphorylation process of FDG
FD = fractal dimension of the time-activity curves of FDG, which illustrates the overall heterogeneity of the tracer  (FDG) distribution
SUV = represents the overall tracer uptake within a specific time range (55-60 min post injection)
VB = fractional blood volume-illustrates the fraction of blood within the evaluated volume of interest (tumor or reference tissue)
INF = (k1*k3)/(k2+k3)

hyb_protocol: Affymetrix HG-U133 Plus 2.0 GeneChip arrays hybridization was performed using Affymetrix standard protocols (Affymetrix, Santa Clara, CA).

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Rstudio console using the affy R package and RMA as the normalization method.

source_name: Patient 17 primary colorectal adenocarcinoma

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

extract_protocol: Total RNA was extracted by Rneasy kit (Qiagen , Inc)

value: primary colorectal adenocarcinoma

tag: anatomic location

value: right colic flexure

tag: presence of synchronous distant metastasis

value: No

tag: suv pet variable values

tag: vb pet variable values

tag: k1 pet variable values

tag: k2 pet variable values

tag: k3 pet variable values

tag: k4 pet variable values

tag: fd pet variable values

tag: inf pet variable values


title: 20140703_142346_002: Normal

value: Normal

tag: tissue

value: Limb


title: 10812-1-ME

tag: subclade

value: Subclade1A (SC1A)

tag: site of isolation


title: 20140703_142346_001: Normal


title: Patient_17_normal_rep1_HG-U133_Plus_2

source_name: Patient 17 normal adjacent sample

value: normal adjacent


title: Patient_16_cancer_rep1_HG-U133_Plus_2

source_name: Patient 16 primary colorectal adenocarcinoma

value: ascending colon


title: 20140522_155148_002: Normal

source_name: Limb


title: Patient_15_normal_rep1_HG-U133_Plus_2

source_name: Patient 15 normal adjacent sample


title: KT.RNASeq Rep 3

city: Nottingham

first: Richard

middle: D

last: Emes

state: Nottinghamshire

department: School of Veterinary Medicine and Sciences.

institute: University of Nottingham

data_processing:
Genome_build:AgamP4.4
Genome index was built using hisat2-build (version 2.1.0)
Reads trimmed using scythe and Tru-seq adapters (version 0.981)
Alignment of reads using hisat2 (version 2.1.0)
Assemble GTF using stringtie (version 1.2.3)
Generate normalized transcript abundances using stringtie (version 1.2.3)
Genome_build: www.vectorbase.org
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Anopheles gambiae

source_name: Testes

growth_protocol: All the mosquito stocks were obtained from the Malaria Research and Reference Reagent Resource Center (MR4) in Atlanta (https://www.beiresources.org/Catalog/BEIVectors/MRA-762.aspx).

extract_protocol: Preparation of Illumina libraries  The total RNA libraries were prepared in accordance with the Illumina TruSeq RNA sample preparation  v2 guide (Part # 15026495, rev.D, September 2012) for Illumina Paired-End Indexed Sequencing.  Step 1: RNA purification and fragmentation  According to the Illumina mRNA libraries preparation protocol, poly-A mRNA in the tRNA samples  were first purified using Illumina poly-T oligo-attached magnetic beads and two rounds of purification.  During the second elution of the poly-A-RNA, the mRNA was also fragmented and primed with random  hexamers for cDNA synthesis.  Step2: Generation of double-stranded cDNA  Cleaved mRNAs were reverse transcribed into first strand cDNA using reverse transcriptase and  random primers. The RNA template was then removed and a replacement strand synthesized to  generate double-stranded cDNA.  Step 3: Preparation of ds cDNA samples for Indexed paired-end sequencing  Following the standard protocol, after the first and second strand cDNA synthesis, ends were repaired,  dA base added, and Illumina indexing adapters were ligated. Finally, cDNA fragments that have  adapter molecules on both ends underwent 15 cylcles of PCR to amplify the amount of prepared  material.

value: Testes


title: 20140523_121040_001: Normal


title: NCI-H716_ customer-designed_180K_CGH

type: genomic

city: Harbin

first: Xueyuan

last: Jia

address: 157 Baojian Road, Nangang District

institute: Harbin Medical University

hyb_protocol: After sample denaturation and pre-annealing with 5µl of Human Cot-1 DNA (Invitrogen, Carlsbad, CA), hybridization was performed at 65°C with shaking for 24 hours.

scan_protocol: Scanned on an Agilent scanner. Images were quantified using Agilent Feature Extraction Software (version 9.1).

data_processing: The data was processed on Cytogenomics 2.9.1.3 using the Default Analysis Method (The z-score algorithm at threshold 4) - CGH v2 proposed by Agilent.

molecule: genomic DNA

source_name: Human colorectal cancer cell line NCI-H716

label_protocol: Tumor and control DNA were labeled by random priming with Cy5- and Cy3-dUTP dyes, respectively using the Agilent Genomic DNA Enzymatic Labeling Kit.

growth_protocol: The cells were cultured in RPMI1640 medium (Gibco, Carlsbad, CA, US) supplemented with 10% fetal bovine serum (Gibco, Carlsbad, CA, US) in a humidified atmosphere of 5% CO2 at 37°C. Cells were authenticated by short tandem repeat profiling analysis (Beijing Microread Genetics, Beijing, China).

extract_protocol: Genomic DNA from cultured cells were isolated with an AllPrep DNA/RNA mini kit (Qiagen, Hilden, Germany) following the manufacturer's protocol.

value: colorectal adenocarcinoma

tag: cell line

tag: cell type

value: cancer cell line

value: male

source_name: Commercial Male DNA reference from Agilent

value: peripheral blood


title: Patient_15_cancer_rep1_HG-U133_Plus_2

source_name: Patient 15 primary colorectal adenocarcinoma


title: Patient_16_normal_rep1_HG-U133_Plus_2

source_name: Patient 16 normal adjacent sample


title: Patient_14_cancer_rep1_HG-U133_Plus_2

source_name: Patient 14 primary colorectal adenocarcinoma

value: rectosigmoid


title: 10786-3-ME

source_name: 10786_ME_cell pellet

value: invasive infection isolate

tag: strain

value: Mid-exponential (ME, OD600nm=0.5)


title: KT.RNASeq Rep 2

address: School of Veterinary Medicine and Science


title: 11107-2-ME

source_name: 11107_ME_cell pellet

value: Subclade1B (SC1B)

tag: growth phase


title: 10786-2-ME


title: KT.RNASeq Rep 1


title: 10786-1-ME


title: KM.RNASeq Rep 3

source_name: Male Acessory Glands (MAGs)

value: Male Acessory Glands (MAGs)


title: KM.RNASeq Rep 2


title: 8347-3-ME

source_name: 8347_ME_cell pellet


title: DT.RNASeq Rep 3

data_processing:
Genome_build:AaraD1.4
Genome index was built using hisat2-build (version 2.1.0)
Reads trimmed using scythe and Tru-seq adapters (version 0.981)
Alignment of reads using hisat2 (version 2.1.0)
Assemble GTF using stringtie (version 1.2.3)
Generate normalized transcript abundances using stringtie (version 1.2.3)
Genome_build: www.vectorbase.org
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Anopheles arabiensis


title: NB4-shCDK2 #1 at Day5

city: Hangzhou

first: Meidan

last: Ying

address: No.866 Yuhangtang Road

department: College of Pharmaceutical Sciences

institute: Zhejiang University

hyb_protocol: Hybridization was done in a Hybridization Oven 645. The experiment was performed by the 'Gene Company Limited' in Shanghai, China.

scan_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip primeView Human Gene expression Array. GeneChips were washed in Fluidics Station 450 and were scanned using Genechip Scanner 3000 7G.

data_processing: Data were analyzed with a commercial software Partek GS 6.5. The analysis was performed in the 'Gene Company Limited' located in Shanghai, China.

source_name: NB4 cells transduced with shCDK2 #1 for 5 days

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).Labeling was performed by the 'Gene Company Limited' in Shanghai, China.

growth_protocol: NB4 cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum (Gibco BRL) and 1% penicillin/streptomycin. Cells were maintained at 37°C in a humidified atmosphere containing 5% CO2

treatment_protocol: NB4 cells were transduced with lentivirus at a multiplicity of infection (MOI) of 10 for 2 or 5 days.

value: NB4 myeloid cell line

tag: transduction

value: shCDK2 #1

tag: time

value: 5 days


title: KM.RNASeq Rep 1


title: Patient_14_normal_rep1_HG-U133_Plus_2

source_name: Patient 14 normal adjacent sample

tag: anatomic location

tag: presence of synchronous distant metastasis

tag: suv pet variable values


title: NB4-shCDK2 #3 at Day5

source_name: NB4 cells transduced with shCDK2 #3 for 5 days

value: shCDK2 #3


title: 8347-1-ME

value: Subclade1A (SC1A)


title: 7941-3-ME

source_name: 7941_ME_cell pellet


title: DT.RNASeq Rep 2


title: NB4-scramble at Day5

source_name: NB4 cells transduced with the scrambled control for 5 days

value: scrambled control


title: NB4-shCDK2 #10 at Day5

source_name: NB4 cells transduced with shCDK2 #10 for 5 days

value: shCDK2 #10


title: 7941-2-ME


title: NB4-shCDK2 #10 at Day2

source_name: NB4 cells transduced with shCDK2 #10 for 2 days

value: 2 days


title: 7941-1-ME


title: Patient_13_normal_rep1_HG-U133_Plus_2

source_name: Patient 13 normal adjacent sample

value: normal adjacent

value: coecum

tag: vb pet variable values

tag: k1 pet variable values

tag: k2 pet variable values


title: DT.RNASeq Rep 1

source_name: Testes

value: Testes


title: Patient_11_normal_rep1_HG-U133_Plus_2

source_name: Patient 11 normal adjacent sample

value: descending colon

tag: k3 pet variable values

tag: k4 pet variable values

tag: fd pet variable values


title: NB4-shCDK2 #3 at Day2

source_name: NB4 cells transduced with shCDK2 #3 for 2 days


title: Patient_10_cancer_rep1_HG-U133_Plus_2

source_name: Patient 10 primary colorectal adenocarcinoma

tag: tissue

value: primary colorectal adenocarcinoma

value: ascending colon

value: No

tag: inf pet variable values


title: Patient_11_cancer_rep1_HG-U133_Plus_2

source_name: Patient 11 primary colorectal adenocarcinoma


title: NB4-scramble at Day2

source_name: NB4 cells transduced with the scrambled control for 2 days

tag: cell line


title: Patient_10_norma_rep1_HG-U133_Plus_2

source_name: Patient 10 normal adjacent sample


title: 7914-3-ME

source_name: 7914_ME_cell pellet

tag: subclade

tag: site of isolation

value: invasive infection isolate

value: Mid-exponential (ME, OD600nm=0.5)


title: NB4-shCDK2 #1 at Day2

source_name: NB4 cells transduced with shCDK2 #1 for 2 days

value: NB4 myeloid cell line


title: Patient_12_cancer_rep1_HG-U133_Plus_2

source_name: Patient 12 primary colorectal adenocarcinoma

value: sigmoid


title: Patient_13_cancer_rep1_HG-U133_Plus_2

source_name: Patient 13 primary colorectal adenocarcinoma


title: Patient_12_normal_rep1_HG-U133_Plus_2

source_name: Patient 12 normal adjacent sample


title: Patient_9_cancerl_rep1_HG-U133_Plus_2

source_name: Patient 9 primary colorectal adenocarcinoma


title: 7914-2-ME

tag: strain

tag: growth phase


title: 7914-1-ME


title: DM.RNASeq Rep 2

source_name: Male Acessory Glands (MAGs)

value: Male Acessory Glands (MAGs)


title: DM.RNASeq Rep 1


title: DM.RNASeq Rep 3


title: 7888-3-ME

source_name: 7888_ME_cell pellet


title: 7888-2-ME


title: MGAS28575

data_processing:
Multiplexed SE libraries were sequenced on an Illumina NextSeq 500 instrument. Reads from each pool were demultiplexed into separate fastq files corresponding to individual samples based on the inline barcodes using FASTX-toolkit.
RNAtag-seq reads from all strains were mapped to reference strain MGAS6180 (GenBank accession number CP000056), using Edge-pro v1.3.1 (Estimated Degree of Gene Expression for Prokaryotes).
Low-expressed genes and genes encoding ribosomal RNAs and tRNAs were filtered out prior to running differential expression analyses
Differential expression analysis was perfomed using DESeq2 v1.6.3 and NOISeq-sim (NOISeq package) running in R version 3.4.0. Differentially expressed genes were identified in each of the 441 strains compared to a common reference strain (MGAS28737).
Genome_build: reference strain MGAS6180 (GenBank accession number CP000056)
Supplementary_files_format_and_content: normalized counts

source_name: cell pellet

extract_protocol:
Pelleted cells were mechanically disrupted using silica beads, RNA was isolated using RNeasy kit, contaminating DNA was degraded using Turbo DNA-free (Ambion), and rRNA was depleted using Ribo-Zero (Illumina)
Resultant RNAs were tagged and pooled, reverse transcribed to cDNA, tagged a second time, pooled into superpools and sequenced

treatment_protocol: At the desired growth stage, early-stationary (OD 600nm 1.65), the culture was treated with RNAprotect Bacteria Reagent and cells were harvested by centrifugation

value: Subclade2B (SC2B)

value: Early-stationay (ES, OD600nm=1.65)


title: 7888-1-ME

data_processing:
Multiplexed single-end (SE) libraries were sequenced on an Illumina NextSeq 500 instrument, basecalling and demultiplexing was done on the instrument, and the RNA-Seq data was output as fastq files
RNA-seq reads from all strains were mapped to reference strain MGAS6180 (GenBank accession number CP000056), using Edge-pro v1.3.1 (Estimated Degree of Gene Expression for Prokaryotes).
Low-expressed genes and genes encoding ribosomal RNAs and tRNAs were filtered out prior to running differential expression analyses
Differential expression analysis was perfomed using DESeq2 v1.6.3 running in R version 3.3.2. Raw reads were used as the input and normalized expression generated using DESeq2's default normalization method Relative log expression (RLE) approach was used to generate fold change values for each gene. Multiple testing correction was performed using Bonferroni method.
Genome_build: reference strain MGAS6180 (GenBank accession number CP000056)
Supplementary_files_format_and_content: normalized counts

value: Subclade1A (SC1A)


title: MGAS11151


title: MGAS11147


title: Patient_9_normal_rep1_HG-U133_Plus_2

source_name: Patient 9 normal adjacent sample


title: Mother_P189

city: Maastricht

first: Masoud

last: Zamani Esteki

state: Limburg

address: P. Debyelaan 25

department: Clinical Genetics

country: Netherlands

institute: Maastricht University Medical Center

description:
Sample 464
DNA extracted from peripheral venous blood of the mother.

hyb_protocol: According to the manual of Infinium II Assay (Illumina, USA).

scan_protocol: The scanning of the bead-chips was performed on an iScan, using the iScan Control software (Illumina, USA)

data_processing: The genotypes, B allele frequencies and LogR values were processed by the Genotyping module of GenomeStudio software. We subsequently fed these data into siCHILD algorithm, which is equipted with haplarithmisis (Zamani Esteki et al. 2015, AJHG). Image data was analyzed using Genomestudio with genotyping module (Illumina).

label: Cy5, Cy3

source_name: Peripheral blood

label_protocol: The samples were not labelled before the hybridization. The staining is based on post-hybridization Cy5/Cy3 labelling by extension, according to the manual of Infinium II Assay (Illumina, USA).

extract_protocol: A total of 9 mL of peripheral venous blood from parents and 4 mL of umbilical cord blood were collected into ethylenediaminetetraacetic acid-containing tubes (BD Vacutainer, Becton, Dickinson and Co) for DNA extraction. DNA was isolated from blood and the placental tissue using PureLink® Genomic DNA Kit (Invitrogen, Life Technologies™) according to manufacturer’s protocol. DNA samples were eluted with 200 µL of PureLink® Genomic Elution Buffer (10 mM Tris-HCl, pH 9.0, 0.1 mM EDTA) and stored at -20 °C until analysis. NanoDrop 2000 (Thermo Fisher Scientific Inc.) was used to assess DNA concentration and purity.

treatment_protocol: Full-thickness placental blocks of around 1 cm were taken from the placenta and stored at -80 °C for subsequent DNA extraction. The maturity and health of the term placenta were confirmed by histological examination.

tag: dna sample

value: Multi cell

tag: quartet

tag: conception

value: IVF

tag: birthweight at delivery

value: AGA


title: Father_P189

description:
Sample 463
DNA extracted from peripheral venous blood of the father.


title: Patient_7_normal_rep1_HG-U133_Plus_2

source_name: Patient 7 normal adjacent sample

value: normal adjacent

tag: anatomic location

value: rectum

tag: presence of synchronous distant metastasis

tag: suv pet variable values

tag: vb pet variable values


title: DP31 FGF(-)

city: Gifu City

first: Ken-ichi

last: Tezuka

state: Gifu

address: 1-1 Yanagido

department: Gifu University Graduate School of Medicine

description: Gene expression in cells after FGF2 treatment

hyb_protocol: Following labeling and clean up, the amplified RNA and dye incorporation were quantified using a ND-1000 Spectrophotometer (Nano Drop Technologies, Wilmington, DE) and hybridized to Agilent whole human genome 4 × 44 K oligo-DNA microarray (Agilent Technologies). After hybridization, the arrays were washed consecutively by using Gene Expression Wash Pack (Agilent Technologies).

scan_protocol: Fluorescence images of the hybridized arrays were generated using the Agilent DNA Microarray Scanner, and the intensities were extracted with Agilent Feature Extraction software ver.10.7.3.1. Each sample was analyzed once.

data_processing: Agilent gProcessed signal intensities are uploaded.

source_name: DP31 FGF(-)

label_protocol: After RNA was qualified by the Agilent 2100 Bioanalyzer, 250 ng of total RNA was converted to cDNA, amplified, and labeled with Cy3-labeled CTP using the Low Input Quick Amp Labeling kit (Agilent Technologies, Santa Clara, CA) according to the protocol supplied by the manufacturer.

growth_protocol: Dental pulp cells were cultured in α-MEM medium (Sigma-Aldrich).

extract_protocol: RNA extraction (RNeasy Plus Mini Kit; Qiagen, Valencia, CA, USA)

treatment_protocol: FGF2 was added to the medium each day (10 ng/μl)

value: dental pulp cells

tag: gender

value: female

tag: age


title: Patient_5_cancer_rep1_HG-U133_Plus_2

source_name: Patient 5 primary colorectal adenocarcinoma

tag: tissue

value: primary colorectal adenocarcinoma

tag: k1 pet variable values

tag: k2 pet variable values

tag: k3 pet variable values

tag: k4 pet variable values

tag: fd pet variable values


title: DP165 FGF(+)

institute: Gifu University Graduate School of Medicine

description: Gene expression in cells


title: MGAS10792

tag: subclade

tag: site of isolation

tag: growth phase


title: DP1 FGF(-)

source_name: DP1 FGF(-)

value: male


title: MGAS8396

value: invasive infection isolate


title: Patient_8_cancer_rep1_HG-U133_Plus_2

source_name: Patient 8 primary colorectal adenocarcinoma

value: coecum

value: Yes

tag: inf pet variable values


title: Patient_8_normal_rep1_HG-U133_Plus_2

source_name: Patient 8 normal adjacent sample


title: Patient_6_normal_rep1_HG-U133_Plus_2

source_name: Patient 6 normal adjacent sample


title: Patient_5_normal_rep1_HG-U133_Plus_2

source_name: Patient 5 normal adjacent sample

value: sigmoid


title: Patient_7_cancer_rep1_HG-U133_Plus_2

source_name: Patient 7 primary colorectal adenocarcinoma

value: No


title: UmbilicalCord_P189

description:
Sample 462
DNA extracted from umbilical cord blood of the newborn.

source_name: Cord blood

tag: dna sample

tag: quartet

tag: conception

tag: birthweight at delivery


title: Patient_6_cancer_rep1_HG-U133_Plus_2

source_name: Patient 6 primary colorectal adenocarcinoma

tag: anatomic location

tag: presence of synchronous distant metastasis

tag: suv pet variable values

tag: vb pet variable values


title: DP31 FGF(+)

description: Gene expression in cells

source_name: DP31 FGF(+)

tag: tissue

tag: gender

tag: age


title: Placenta_P189

description:
Sample 461
DNA extracted from placenta tissue.

source_name: Placenta tissue


title: MGAS29431

value: Subclade2A (SC2A)


title: DP1 FGF(+)

description: Gene expression in cells

source_name: DP1 FGF(+)


title: DP165 FGF(-)


title: MGAS28948

source_name: cell pellet

value: Early-stationay (ES, OD600nm=1.65)


title: Patient_4_normal_rep1_HG-U133_Plus_2

source_name: Patient 4 normal adjacent sample

tag: k1 pet variable values

tag: k2 pet variable values

tag: k3 pet variable values

tag: k4 pet variable values


title: Mother_P187

description:
Sample 460
DNA extracted from peripheral venous blood of the mother.

source_name: Peripheral blood


title: Father_P187

description:
Sample 459
DNA extracted from peripheral venous blood of the father.


title: MGAS28928

tag: subclade

tag: site of isolation

tag: growth phase


title: MGAS28942


title: STER_rep_3

city: TOULOUSE

first: Olivier

last: PUEL

address: 180 chemin de Tournefeuille

department: TOXALIM UMR 1331

institute: INRAE

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 10x Agilent fragmentation buffer and 25x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human Gene Expression 8x60K v2 Microarray (Design 039494)  enclosed in Agilent SureHyb-enabled hybridization chambers for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed sequentially in Wash buffer 1 (Agilent Technologies, 1 min), Wash buffer 2 (Agilent Technologies, 37°C, 1 min).

scan_protocol: Slides were scanned immediately after washing on a Agilent G2505C Microarray Scanner with Agilent Scan Control A.8.5.1 software

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent) using default parameters (protocol GE1_1010_Sep10 and Grid: 039494_D_F_20120628). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot): myfunw<-function(x) {okType<-x$ControlType==0; okFoundGreen<-x$gIsFound==1; okPos=x$gIsPosAndSignif==1; okWellAbove<- x$gIsWellAboveBG==1; as.numeric(okType & okFoundGreen & okPos & okWellAbove);}. After data quality control, we decided to exclude 3 individuals from the initial 24 individuals experiment, leading to 21 individuals microarray data. We then selected the spots with a minimal weight of 1 for 17 out of 21 microarrays or with a minimal weight of 2 per group from at least one experimental group. At this step, 37765 spots out of 62976 were selected. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore R library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 31205 rows each corresponding to a unique ProbeName (provided as data Matrix).

source_name: Caco-2, sterigmatocystine, 24h

label_protocol: For each sample, Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng of total RNA using the One-Color Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by Agencourt RNAClean XP (Agencourt Bioscience Corporation, Beverly, Massachusetts). Dye incorporation and cRNA yield were checked with the Biospec nano spectrophotometer (Shimadzu).

growth_protocol: Briefly, 1.5×105 Caco-2 cells were seeded into 6-well flat-bottomed plates and incubated at 37°C for 24 h.

extract_protocol: Total RNA from Caco-2 cells was extracted using EXTRACT-ALL® reagent (Eurobio, Les Ulis, France) following the manufacturer’s manual.

treatment_protocol: After 24 h, the medium was replaced by a fresh one without serum containing 1 µM of aflatoxin B1, 1µM versicolorin A, 1µM sterigmatoxin,3 µM of patulin, 3 µM of E-ascladiol or DMSO for the control condition.

tag: cell type

tag: treatment

value: STERIGMATOCYSTIN


title: UmbilicalCord_P187

description:
Sample 458
DNA extracted from umbilical cord blood of the newborn.

tag: dna sample

value: Multi cell

tag: quartet

tag: conception

tag: birthweight at delivery


title: VERS_rep_4

source_name: Caco-2, versicolorine, 24h

value: VERSICOLORIN A


title: Placenta_P187

description:
Sample 457
DNA extracted from placenta tissue.

value: IVF

value: AGA


title: STER_rep_2


title: Mother_P186

description:
Sample 456
DNA extracted from peripheral venous blood of the mother.


title: MGAS28906

first: Priyanka

last: Kachroo

institute: Houston Methodist Research Institute


title: MGAS28925


title: VERS_rep_3


title: Patient_4_cancer_rep1_HG-U133_Plus_2

source_name: Patient 4 primary colorectal adenocarcinoma

tag: anatomic location

tag: presence of synchronous distant metastasis

tag: suv pet variable values

tag: vb pet variable values

tag: fd pet variable values

tag: inf pet variable values


title: Patient_3_cancer_rep1_HG-U133_Plus_2

source_name: Patient 3 primary colorectal adenocarcinoma

tag: tissue

value: rectum

tag: k1 pet variable values

tag: k2 pet variable values

tag: k3 pet variable values


title: STER_rep_4


title: Father_P186

description:
Sample 455
DNA extracted from peripheral venous blood of the father.


title: VERS_rep_2


title: Patient_3_normal_rep1_HG-U133_Plus_2

source_name: Patient 3 normal adjacent sample

value: normal adjacent

tag: k4 pet variable values


title: AFB1_rep_4

source_name: Caco-2, AFB1, 24h

tag: cell type


title: MGAS28898

tag: subclade

tag: site of isolation

tag: growth phase


title: VERS_rep_1

tag: treatment


title: MGAS28897


title: AFB1_rep_3


title: ASCL_rep_4

source_name: Caco-2, ascladiol, 24h

value: ASCLADIOL


title: Patient_2_cancer_rep1_HG-U133_Plus_2

source_name: Patient 2 primary colorectal adenocarcinoma

value: primary colorectal adenocarcinoma

value: descending colon


title: Patient_2_normal_rep1_HG-U133_Plus_2

source_name: Patient 2 normal adjacent sample


title: Patient_1_normal_rep1_HG-U133_Plus_2

source_name: Patient 1 normal adjacent sample


title: AFB1_rep_1


title: MGAS28886

value: invasive infection isolate


title: Patient_1_cancer_rep1_HG-U133_Plus_2

source_name: Patient 1 primary colorectal adenocarcinoma

value: coecum


title: Mother_P185

description:
Sample 452
DNA extracted from peripheral venous blood of the mother.

tag: dna sample

tag: quartet

tag: conception

tag: birthweight at delivery


title: MGAS28872


title: UmbilicalCord_P186

description:
Sample 454
DNA extracted from umbilical cord blood of the newborn.

source_name: Cord blood


title: Father_P185

description:
Sample 451
DNA extracted from peripheral venous blood of the father.


title: UmbilicalCord_P185

description:
Sample 450
DNA extracted from umbilical cord blood of the newborn.


title: MGAS28864


title: Placenta_P186

description:
Sample 453
DNA extracted from placenta tissue.

source_name: Placenta tissue


title: Placenta_P185

description:
Sample 449
DNA extracted from placenta tissue.


title: MGAS28851


title: MGAS28883


title: MGAS28842


title: PAT_rep_1

source_name: Caco-2, patuline, 24h

value: PATULIN


title: ASCL_rep_1


title: TB651, Non-PDAC Sample 2017

city: Milwaukee

first: Martin

last: Hessner

state: WI

address: 8701 Watertown Plank Road

department: Pediatrics

institute: Medical College of Wisconsin

description:
TB651_NonPDAC17
Gene expression data from Non-PDAC

hyb_protocol: The GeneChip human genome U133 plus 2.0 array was selected for these studies for its overall comprehensive coverage.

scan_protocol: After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001 and scanned with a 7G Affymetrix GeneChip Scanner

data_processing: Image data were normalized and analyzed Partek Genomic Suite (Partek GS) to determine signal log intensity/ratios.  The statistical significance of differential gene expression and false discovery rates (FDR) were derived through RandProd package in Bioconductor.

source_name: Non-PDAC

label_protocol: cRNA was synthesized, labeled, fragmented, and hybridized to an array in accordance to the Affymetrix GeneChip expression analysis technical manual.

growth_protocol: PBMCs were co-cultured with 40% patient serum in RPMI 1640 medium supplemented with 100 U/ml penicillin and 100 ug/ml streptomycin at 37 degrees in 5% CO2. Cultures were prepared in a Costar 24 well plate (Corning) using 500,000 cells in 500 ul of media per well. After 9 hours of culture, total RNA was extracted.

extract_protocol: Total RNA was extracted and amplified using an Affymetrix Express cDNA synthesis kit (Affymetrix, Santa Clara, CA).

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

value: peripheral blood mononuclear cells (PBMC) obtained from a normal donor

tag: incubted with

value: serum from patients without PDAC progression

tag: run date


title: TB554, Non-PDAC Sample 2017

description:
TB554_NonPDAC17
Gene expression data from Non-PDAC


title: ASCL_rep_2


title: TB762, PDAC Sample 2017

description:
TB762_PDAC17
Gene expression data from PDAC

source_name: PDAC

value: serum from patients with PDAC metastasis


title: Father_P184

description:
Sample 447
DNA extracted from peripheral venous blood of the father.

source_name: Peripheral blood


title: MGAS28831

city: Houston

source_name: cell pellet

value: Subclade2A (SC2A)

value: Early-stationay (ES, OD600nm=1.65)


title: TB831, Non-PDAC Sample 2016

description:
TB831_NonPDAC16
Gene expression data from Non-PDAC


title: PAT_rep_3


title: PAT_rep_2


title: ASCL_rep_3


title: TB701, Non-PDAC Sample 2017

description:
TB701_NonPDAC17
Gene expression data from Non-PDAC


title: TB945, PDAC Sample 2017

description:
TB945_PDAC17
Gene expression data from PDAC


title: CTRL_rep_3

source_name: Caco-2, control, 24h

value: DMSO


title: TB847, Non-PDAC Sample 2016

description:
TB847_NonPDAC16
Gene expression data from Non-PDAC


title: MGAS28826


title: CTRL_rep_4


title: TB892, PDAC Sample 2016

description:
TB892_PDAC16
Gene expression data from PDAC


title: UmbilicalCord_P184

description:
Sample 446
DNA extracted from umbilical cord blood of the newborn.

value: Multi cell


title: Mother_P184

description:
Sample 448
DNA extracted from peripheral venous blood of the mother.

value: IVF


title: Placenta_P184

description:
Sample 445
DNA extracted from placenta tissue.

value: AGA


title: 8347-2-ME

source_name: 8347_ME_cell pellet

extract_protocol:
Pelleted cells were mechanically disrupted using silica beads, RNA was isolated using RNeasy kit, contaminating DNA was degraded using Turbo DNA-free (Ambion), and rRNA was depleted using Ribo-Zero (Illumina)
Resultant RNA was reverse transcribed to cDNA and sequencing libraries were generated using ScriptSeq RNA-seq preparation kit (Illumina)

value: Subclade1A (SC1A)

tag: strain

value: Mid-exponential (ME, OD600nm=0.5)


title: Mother_P183

description:
Sample 444
DNA extracted from peripheral venous blood of the mother.


title: MGAS28801


title: Father_P183

description:
Sample 443
DNA extracted from peripheral venous blood of the father.


title: MGAS28788


title: MGAS28809


title: UmbilicalCord_P183

description:
Sample 442
DNA extracted from umbilical cord blood of the newborn.


title: Placenta_P183

description:
Sample 441
DNA extracted from placenta tissue.


title: MGAS28787


title: MGAS28785


title: Mother_P179

description:
Sample 440
DNA extracted from peripheral venous blood of the mother.


title: Father_P179

description:
Sample 439
DNA extracted from peripheral venous blood of the father.


title: MGAS28784


title: TB839, Non-PDAC Sample 2016

description:
TB839_NonPDAC16
Gene expression data from Non-PDAC


title: TB1175, PDAC Sample 2016

description:
TB1175_PDAC16
Gene expression data from PDAC


title: MGAS28805


title: CTRL_rep_1


title: TB1003, PDAC Sample 2016

description:
TB1003_PDAC16
Gene expression data from PDAC


title: BAL_IPF_Leuven_64

city: Hannover

first: Antje

last: Prasse

address: Carl-Neubergstrasse 1

department: Pneumology

country: Germany

institute: Medical School Hannover

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 µl containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ml of 2x GEx Agilent hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays, 4x44K (Freiburg and Siena) or  8 x 60K (Leuven) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA High Resolution Microarray Scanner (G2505C US45102918) using one color scan setting for 8 x 60K array slides (Freiburg and Siena) and  8 x 60K array slides (Leuven). Scan Area 61x21.6 mm, Scan resolution 5 μm, Tiff 20 bit, Dye channel is set to Green.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Gene expression data was normalized to the geometric mean of all the IPF samples and controls using quantile normalization. Non-expressed and invariant transcripts were removed.  For statiscal analysis we used the average gene expression values of the replicated probes. After merging the datasets of the 3 cohorts we obtained a final dataset of 20330 transcript measurements across the 176 IPF samples and 20 healthy donor samples.

source_name: BAL cells

label_protocol: Labeling reactions were performed for each sample using Agilent Low Input Quick Amp Labeling, One-Color (Agilent Technologies, Santa Clara, CA). Briefly, with a starting concentration of 100 nanograms of total RNA, an initial cDNA strand was synthesized using a oligo(dT)24 primer containing a T7 RNA polymerase, this cDNA was then used as a template to generate Cy3 labeled cRNA by a reverse transcriptase enzyme. After the cRNA was obtained a purification step was performed using RNeasy Mini Kit (74104, Qiagen, Valencia, CA) followed by measurement of the yield and specific activity of each sample

extract_protocol:
[Isolation protocol] BAL cells were obtained by bronchoscopy, immediately isolated and 1 ml of TRIzol (15596018, life technologies, Darmstadt, Germany) was added to the cell pellet, which was then immediately snap frozen in -80 celsius.
Total RNA of TRIzol samples was extracted and purified using the RNeasy Mini Kit (217004, Qiagen, Valencia, CA), under fully automated sample preparation by the assistance of the QIAcube device (9001292, Qiagen, Valencia CA) following the manufacturer’s protocol. After extraction, total RNA yield and quality were evaluated using NanoDrop at 260 nm and the 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA)

value: bronchoalveolar lavage (BAL) cells

tag: diagnosis

value: IPF

tag: cohort

value: LEUVEN

tag: age

tag: sex (0=female, 1=male)

tag: time to death (days)

tag: survival status, 0 = censored, 1 = death

tag: gap


title: UmbilicalCord_P179

description:
Sample 438
DNA extracted from umbilical cord blood of the newborn.


title: MGAS28781

address: 6670 Bertner Avenue

tag: subclade

tag: site of isolation

value: invasive infection isolate


title: CTRL_rep_2

tag: cell type

tag: treatment


title: Placenta_P179

description:
Sample 437
DNA extracted from placenta tissue.

tag: dna sample

tag: quartet


title: BAL_IPF_Leuven_60


title: BAL_IPF_Leuven_61