title: C57BL/6 osteoblasts from tumor bearing mice_replicate 1

description: biological replicate 1


title: NOD SCID endothelial cells from tumor free mice_replicate 3

status: Public on Feb 23 2017

type: RNA

city: Basel

first: Tim

last: Roloff

address: Maulbeerstrasse 66

department: Functional Genomics

country: Switzerland

institute: FMI

description: biological replicate 3

hyb_protocol: 5.5ug amplified sense-target cDNA was fragmented and labeled using the the GeneChip WT Terminal Labelling Kit (Affymetrix) and 2.75ug hybridized to GeneChip Mouse Gene 1.0 ST Arrays for 16h at 45C.

scan_protocol: Scanning was performed with Affymetrix GCC Scan Control v. 3.0.0.1214 on a GeneChip Scanner 3000 with autoloader

data_processing: Arrays were normalized and probeset-level expression values were calculated with R/Bioconductor's (v3.1.1) 'affy' package using the rma() function

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: endothelial cells from long bones of tumor free mice

label_protocol: Total RNA was converted into cDNA and SPIA amplified with the Ovation Pico WTA System (NuGen Technologies Inc). Sense target cDNA was generated with the WT-Ovation Exon Module (NuGen Technologies Inc) from 3ug SPIA cDNA.

growth_protocol: MDA-MB231 scp1833 cells (2x10^5 cells) were injected in NOD-SCID mice by the intracardiac route and growth of tumor cells in the long bones was monitored for c.a. 2 weeks by in-vivo bioluminescence.

extract_protocol: Total RNA was extracted with the Pico Pure RNA Isolation Kit (Arcturus cat. KIT0204)

treatment_protocol: Long bones were excised from tumor bearing (tum) and tumor free (ctr) mice and different population were isolated via FACS sorting with the following markers: Osteoblasts (OB) GFP-TR119-CD45-SCA1-CD31-CD51+, and endothelial cells (EC) GFP-TR119-CD45-SCA1+CD31+.

tag: gender

value: female

tag: strain

value: NOD SCID

tag: tissue

value: long bones


title: 6week_Female_Cyp51WT_1

city: Ljubljana

first: Peter

last: Juvan

address: Zaloska 4

department: Institute of Biochemistry

country: Slovenia

description: Gene expression data from a 6-week female wild type mouse LKO586

hyb_protocol: 250 ng of total RNA was used for hybridization of Affymetrix Gene Chip Mouse 2.0 ST Arrays according to the manufacturer’s instructions (Genechip® Whole Transcript (wt) Sense Ttarget Labeling Assay Manual – P/N 701880 Rev 4). Labeled samples were injected into Affymetrix arrays and hybridized at 45°C and 60 rpm for 16 h in an Affymetrix Hybridization Oven. Arrays were stained and washed in the Affymetrix GeneChip Fluidic Station 450.

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

data_processing:
GeneChip data was processed and analyzed using R/Bioconductor packages. Data were summarized (w.r.t. core meta-probeset annotations and AFFX control probes, probes grouped to the level of transcripts) and quantile-normalized (background computed from antigenomic probes) using RMA algorithm from XPS package.
MoGene-2_0-st.pgf
MoGene-2_0-st.mps

source_name: 6-week old female hepatocyte specific wild type mouse

label_protocol: Total RNA was used to synthesize double-stranded cDNA with random hexamer primers tagged with a T7 promoter sequence. The double-stranded cDNA was subsequently used as a template and amplified by T7 RNA polymerase producing cRNA. In the second cycle of cDNA synthesis, random hexamers were used to prime reverse transcription of the cRNA and dUTP was incorporated to produce single-stranded DNA. This single-stranded DNA samples were then treated with a combination of uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1) that specifically recognized the unnatural dUTP residues and broke the DNA strand. DNA was labeled by terminal eoxynucleotidyl transferase (TdT) with the Affymetrix proprietary DNA Labeling Reagent that is covalently linked to biotin.

growth_protocol: Hepatocyte specific Cyp51 KO mice and their control littermates (WT) were bred at the Medical Experimental Centre, Faculty of Medicine, University of Ljubljana, Slovenia and maintained in a temperature and humidity controlled environment under 12h light/dark cycle (lights were on from 7.00 am to 7.00 pm). Animals had ad libitum access to food (standard laboratory chow -1324, Altromin, Lage, Germany) and acidified tap water (pH = 3).

extract_protocol: Mice of aged 3, 6 or 19 weeks were euthanized between 7:30 and 13:30 via cervical dislocation. Runt mice were euthanized at humane time points to minimize their suffering. Liver was removed, weighed, snap-frozen in liquid nitrogen and stored at -80° C. Livers were pulverized and the RNA was isolated using QuickGene Tissue Kit S II and QuickGene-810 (Fujifilm, Singapore) according to the manufacturer’s instructions. RNA quantity and quality were assessed with NanoDrop-1000 and Agilent 2100 Bioanalyzer instruments. All samples were of sufficient purity (OD260/280 and OD230/280 > 1.8) and integrity (RIN > 8) for microarray hybridization.

treatment_protocol: not applicable

value: liver

tag: age

tag: genotype

value: LWT

tag: Sex

value: F

tag: phenotype

value: wild type

tag: animal


title: 6week_Male_Cyp51KO_2

institute: Faculty of Medicine, University of Ljubljana

description: Gene expression data from a 6-week male hepatocyte specific Cyp51 knockout mouse LKO684

source_name: 6-week old male hepatocyte specific Cyp51knockout mouse

value: Cyp51 LKO

value: M

value: knockout


title: NOD SCID endothelial cells from tumor free mice_replicate 1

description: biological replicate 1


title: 6week_Male_Cyp51KO_1

description: Gene expression data from a 6-week male hepatocyte specific Cyp51 knockout mouse LKO628


title: 6week_Female_Cyp51KO_1

description: Gene expression data from a 6-week female hepatocyte specific Cyp51 knockout mouse LKO682

source_name: 6-week old female hepatocyte specific Cyp51knockout mouse


title: NOD SCID endothelial cells from tumor free mice_replicate 2

description: biological replicate 2


title: PBMCs BOR vs unifected control-rep4

city: Pulawy

first: Magdalena

last: Materniak-Kornas

address: Partyzantow 57

department: Biochemistry

country: Poland

institute: National Veterinary Research Institute

description: Technical replicate 4 of 4

hyb_protocol: according to the Agilent manufacturer's protocol

scan_protocol: Scanned on an Agilent G2505C US10353831 scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).

data_processing: Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction and LOWESS normalization.

organism: Sus scrofa

source_name: PBMCs of mock-infected pigs

extract_protocol: RNeasy Mini Kit following manufacturer's instructions (Qiagen, USA)

tag: infection strain

value: control - mock-nfected

tag: time

value: 7 days post mock-infection

source_name: PBMCs of infected pigs

value: PRRSV BOR

value: 7 days post infection


title: PBMCs BOR vs unifected control-rep2

description: Technical replicate 2 of 4

label_protocol: according to the Agilent manufacturer's protocol


title: PBMCs BOR vs unifected control-rep3

description: Technical replicate 3 of 4


title: NOD SCID endothelial cells from tumor bearing mice_replicate 3

description: biological replicate 3

source_name: endothelial cells from long bones of tumor bearing mice


title: 3week_Female_Cyp51WT_1

description: Gene expression data from a 3-week female wild type mouse M23

source_name: 3-week old female hepatocyte specific wild type mouse


title: NOD SCID endothelial cells from tumor bearing mice_replicate 2

description: biological replicate 2


title: Unt-0B

city: Bethesda

first: Timothy

middle: G

last: Myers

state: MD

address: 50 South Drive, Room 5509

department: Research Technologies Branch

country: USA

institute: National Institute of Allergy and Infectious Diseases

description: RAW264.7 cell line

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol with Illumina HiScan-SQ

data_processing: Signal data was extracted from the image files with the Gene Expression module (v. 1.9.0) of the GenomeStudio software (v. 2011.1) from Illumina, Inc. Signal intensities were converted to log 2 scale. Probes that didn't show detection p-value < 0.1 in at least 2 arrays were removed from the dataset.  After filtering probes, quantile normalization was applied across all arrays.

source_name: RAW264.7 cell line

label_protocol: Illumina TotalPrep RNA Amplification Kit (Ambion)

growth_protocol: RAW264.7 cells were maintained in DMEM, 10%FBS, 20mM Hepes, and 2mM glutamine by standard procedures.

extract_protocol: RNA was purified by Qiagen RNAeasy kit

treatment_protocol: RAW264.7 cells were treated with either 0 or 10 ng/ml LPS for 4 hr. LPS was from Alexis Biochemicals, Salmonella minnesota R595 TLRgrade, ALX-581-008-L002.

tag: cell line

value: Zero

tag: experimental replicate

value: B

tag: cell type

value: Macrophage


title: Unt-0A

description: RAW264.7 cell line

value: A


title: PBMCs BOR vs unifected control-rep1

description: Technical replicate 1 of 4


title: LPS-4B

description: RAW264.7 cell line


title: 3week_Male_Cyp51WT_2

description: Gene expression data from a 3-week male wild type mouse M28

source_name: 3-week old male hepatocyte specific wild type mouse


title: PBMCs ILI vs unifected control-rep 2

description: Technical replicate 2 of 4

value: PRRSV ILI


title: PBMCs ILI vs unifected control-rep 3

description: Technical replicate 3 of 4


title: 3week_Female_Cyp51WT_2

description: Gene expression data from a 3-week female wild type mouse M41


title: NOD SCID osteoblasts from tumor free mice_replicate 2

description: biological replicate 2

source_name: mouse osteoblasts from long bones of tumor free mice

value: female

value: NOD SCID

value: long bones


title: NOD SCID endothelial cells from tumor bearing mice_replicate 1

description: biological replicate 1


title: PBMCs ILI vs unifected control-rep 1

description: Technical replicate 1 of 4


title: PBMCs ILI vs unifected control-rep 4

description: Technical replicate 4 of 4


title: blm121 (Blbp-MYC_LL13-04)

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Partek Genomics Suite version 6.5 using the RMA method.

label: Biotin (Affyexpress)

source_name: Electroporation-based Group3 medulloblastoma model, sample identical to GSM1608331, used to cross platform correct

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix one-Cycle protocol).  Some samples were amplified and labeled using the Affyexpress method. Three samples were amplified by both method to serve as basis for batch correction. Biotinylated cRNA were prepared according to the standard Affymetrix one-Cycle protocol).  Some samples were amplified and labeled using the Affyexpress method. Three samples were amplified by both method to serve as basis for batch correction

growth_protocol: Spontaneous CPC  and Grp3 medullblastoma were generated by electroporating plasmids containing Myc and dominant negative Trp53 flanked by loxP sites into the fourth ventricle of E13.5 mouse embryos of Blbp-Cre [dka081, 087, 089, 090, 091 and blm121], Gad2-IRES-Cre [blm128-130 and blm134] or Ptf1a-Cre [blm135-137] mice.  FACS-sorted GFP-positive [dka040, 042, 044] GNPs were obtained from P6 [Cdkn2c-/-, Trp53-/-, Atoh1-GFP] mouse pups.

extract_protocol: Total RNAs were extracted with Trizol reagent (Invitrogen) according to a supplied RNA isolation protocol.

treatment_protocol: Tumor cells were dissociated and purified by percoll-gradient before RNA extraction.

tag: genotype/variation

value: Gad2-IRES-Cre electroporated with Myc and dominant negative p53


title: NOD SCID osteoblasts from tumor free mice_replicate 1

description: biological replicate 1


title: 3week_Female_Cyp51KO_2

description: Gene expression data from a 3-week female hepatocyte specific Cyp51 knockout mouse M30

source_name: 3-week old female hepatocyte specific Cyp51knockout mouse

value: liver

value: F


title: blm122 (CPC)

source_name: Electroporation-based Choriod Plexus Carcinoma model


title: NOD SCID osteoblasts from tumor bearing mice_replicate 3

description: biological replicate 3

source_name: mouse osteoblasts from long bones of tumor bearing mice


title: 3week_Female_Cyp51KO_1

description: Gene expression data from a 3-week female hepatocyte specific Cyp51 knockout mouse M29

value: Cyp51 LKO


title: 3week_Male_Cyp51WT_1

description: Gene expression data from a 3-week male wild type mouse M20

value: LWT

value: M

value: wild type


title: LPS-4A

description: RAW264.7 cell line


title: NOD SCID osteoblasts from tumor bearing mice_replicate 2

description: biological replicate 2


title: PBMCS DAN vs unifected control-rep 3

description: Technical replicate 3 of 4

value: control - mock-nfected

value: 7 days post mock-infection

value: PRRSV DAN


title: blm120 (CPC)


title: blm119 (CPC)


title: PBMCS DAN vs unifected control-rep 4

description: Technical replicate 4 of 4

value: 7 days post infection


title: 3week_Male_Cyp51KO_2

description: Gene expression data from a 3-week male hepatocyte specific Cyp51 knockout mouse M34

source_name: 3-week old male hepatocyte specific Cyp51knockout mouse

value: knockout


title: PBMCS DAN vs unifected control-rep 2

description: Technical replicate 2 of 4


title: 3week_Male_Cyp51KO_1

description: Gene expression data from a 3-week male hepatocyte specific Cyp51 knockout mouse M18


title: spleen_PBS injected_control_2h_mouse 1

status: Public on Feb 22 2017

city: Braga

first: Ângela

last: França

address: Campus de Gualtar

department: Biological Engineering

country: Portugal

institute: University of Minho

description: Gene expression data of mouse spleen cells 2 hours after injection of PBS - Control

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

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

data_processing: The 10 arrays were analyzed using Chipster 2.9 using custom cdf file in mogene21stmmentrezg.db as available from Brainarray database version 17. Following RMA normalization and biomaRt annotation, differential expression was determined by empirical Bayes two-group test with Benjamini-Hochberg multiple testing correction and a P value cut-off of 0.05.

source_name: spleen cells, 2 hours post PBS injection - control

label_protocol: RNA was processed for use on Affymetrix (Santa Clara, CA, USA) Mouse Gene 2.1 ST Array Strip by using the Ambion WT Expression Kit (Life Technologies, CA, USA) and Affymetrix GeneChip WT Terminal Labeling Kit, according to the manufacturer’s protocols. Briefly, 100 ng of total RNA containing spiked in Poly-A RNA controls (GeneChip Expression GeneChip Eukaryotic Poly-A RNA Control Kit; Affymetrix) was used in a reverse transcription reaction (Ambion WT Expression Kit) to generate first-strand cDNA. After second-strand synthesis, double-stranded cDNA was used in an in vitro transcription (IVT) reaction to generate cRNA (Ambion WT Expression Kit). 15 ug of this cRNA was used for a second cycle of first-strand cDNA synthesis (Ambion WT Expression Kit). 5.5 ug of single stranded cDNA was fragmented and end-labeled (GeneChip WT Terminal Labeling Kit; Affymetrix). Size distribution of the fragmented and end-labeled cDNA, respectively, was assessed using an Agilent 2100 Bioanalyzer with a RNA 6000 Nano Assay.

growth_protocol: For this study S. epidermidis strain 9142 was used. In brief, one single colony was inoculated into 2 mL of Tryptic Soy Broth (TSB) (Liofilchem, Roseto degli Abruzzi, Italy) and incubated overnight at 37 oC and 120 rpm. The overnight grown cells were then diluted in TSB in order to obtain a suspension with an optical density (OD), at 640 nm, of 0.250 ± 0.05. Biofilms were formed by inoculating 15 µL of this suspension into 1 mL of TSB supplemented with 0.4% glucose (TSBG) and incubated in a 24-well plate (Orange Scientific,Braine-l’Alleud, Belgium) at 37 oC and 120 rpm. After 24 hours of growth, spent medium was removed and biofilms were washed twice with PBS to remove non-attached cells. One mL of fresh TSBG was then added in order to allow for additional 24 hours of growth under the same temperature and agitation conditions. Planktonic cultures were prepared by adding 150 µL of a bacterial suspension with OD640nm= 0.25 ± 0.05 into 10 mL TSBG and then incubated for 24 hours at 37 oC and 120 rpm. Biofilm-released cells, the cells in the biofilms’ supernatant, were collected by careful aspiration; biofilms were then washed twice with PBS and suspended in 1 mL of PBS by scraping the cells from the plastic surface with a syringe embolus. Afterwards, planktonic, biofilm and biofilm-released cells were sonicated once for 10 seconds at 18 Watts using a Branson model W 185 D ultrasonic cell disrupter (Heat Systems-Ultrasonics, New York, US) in order to dissociate cell clusters and create a homogenous suspension.

extract_protocol: Spleen cells were thawed and total RNA was immediately extracted using RNeasy mini kit (QIAGEN) and following the manufacturer’s instructions. DNase treatment was performed on-column using RNase-free DNase set (QIAGEN). Total RNA integrity was determined by Bioanalyzer 2100 and only samples with RIN higher than 7 were considered and prepared for microarrays analysis.

treatment_protocol: The concentration of S. epidermidis planktonic, biofilm and biofilm-released cells was adjusted, by flow cytometry, to 1 × 108 live cells/mL and 0.2 mL of this suspension was then intravenously injected via lateral tail vein of 8-12 weeks old BALB/c females. Two hours post infection, mice were anesthetized, euthanized and spleens were aseptically removed and immediately homogenized in PBS. Spleen cell suspensions were passed through a column to remove the rest of the organ and then treated with Ammonium-Chloride-Potassium (ACK), washed and counted by flow cytometry.  5 × 106 spleen cells of each condition were harvested by centrifugation, suspended in RLT buffer (QIAGEN) and frozen at -80 oC until RNA extraction procedure.

value: BALB/c

value: Female

value: 8-12 weeks

value: Spleen

tag: infection

value: post PBS injection - control


title: NOD SCID osteoblasts from tumor bearing mice_replicate 1

description: biological replicate 1

value: female

value: NOD SCID

value: long bones


title: spleen_infected with biofilm-released cells_2h_mouse 2

description: Gene expression data of mouse spleen cells 2 hours post infection with cells released from S. epidermidis biofilms

source_name: spleen cells, 2 hours post infection with cells released from S. epidermidis biofilms


title: spleen_infected with biofilm-released cells_2h_mouse 1

value: post infection with cells released from S. epidermidis biofilms


title: spleen_infected with biofilm-released cells_2h_mouse 3


title: blm085 (CPC)

value: Blbp-Cre electroporated with Myc and dominant negative p53


title: PBMCS DAN vs unifected control-rep 1

description: Technical replicate 1 of 4


title: spleen_infected with planktonic cells_2h_mouse 1

description: Gene expression data of mouse spleen cells 2 hours post infection with S. epidermidis planktonic cells

source_name: spleen cells, 2 hours post infection with S. epidermids planktonic cells


title: spleen_infected with biofilm cells_2h_mouse 2

description: Gene expression data of mouse spleen cells 2 hours post infection with S. epidermidis biofilm cells

source_name: spleen cells, 2 hours post infection with S. epidermids biofilm cells


title: spleen_infected with biofilm cells_2h_mouse 3

value: post infection with S. epidermids biofilm cells


title: spleen_PBS injected_control_2h_mouse 2


title: spleen_infected with biofilm cells_2h_mouse 1


title: unfractionated human gastric tunica muscularis_replicate 4

city: Rochester

first: Tamas

last: Ordog

state: MN

address: 200 1st St SW

institute: Mayo Clinic

hyb_protocol: The SPIA cDNA was then bead-purified, fragmented, and hybridized onto Affymetrix GeneChip Human Genome U133 Plus 2.0 array (Affymetrix, Santa Clara, CA).  Subsequent to hybridization, the arrays were washed and stained with streptavidin-phycoerythrin.

scan_protocol: The arrays were scanned in an Affymetrix GeneChip® Scanner 3000 (Santa Clara, CA). All control parameters were confirmed to be within normal ranges before normalization and data reduction was initiated.

data_processing: Analysis was performed using Bioconductor, a publicly available group of software packages. Affy was used to preprocess individual probe intensities from CEL files into RMA-normalized values.

label: biotin/streptavidin-phycoerythrin

organism: Homo sapiens

label_protocol: The Ovation Pico WTA system (NuGEN, San Carlos, CA) was used to prepare cDNA by single primer isothermal amplification (SPIA®).

extract_protocol: Total RNA was prepared from cells using the Total RNA Purification Kit (Norgen, Ontario, Canada).  RNA quality was assessed by Agilent Bioanalyzer (Santa Clara, CA).

tag: tissue source

value: De-identified human gastric tissues


title: FACS-sorted human NOT-ICC

description: NOTICC

source_name: FACS-sorted human NOT-ICC

value: FACS-sorted human NOT-ICC


title: FACS-sorted human ICC_replicate_5

source_name: FACS-sorted human ICC

value: FACS-sorted human intersitial cells of Cajal (ICC)


title: FACS-sorted human ICC_replicate_4


title: unfractionated human gastric tunica muscularis_replicate 2


title: FACS-sorted human ICC_replicate_3


title: FACS-sorted human ICC_replicate_6


title: FACS-sorted human hematopoietic cells_replicate_2

source_name: FACS-sorted human hematopoietic cells

value: FACS-sorted human hematopoietic cells


title: spleen_infected with planktonic cells_2h_mouse 2

value: post infection with S. epidermids planktonic cells


title: FACS-sorted human hematopoietic cells_replicate_1


title: unfractionated human gastric tunica muscularis_replicate 3


title: FACS-sorted human ICC_replicate_2


title: FACS-sorted human hematopoietic cells_replicate_3


title: unfractionated human gastric tunica muscularis_replicate 1


title: FACS-sorted human ICC_replicate_1


title: Spleen_WT.untreated_rep1

city: Copenhagen

last: Garred

address: Ole Maaløesvej 26

department: Department of Clinical Immunology, Section 7631

country: Denmark

institute: Rigshospitalet, University of Copenhagen

hyb_protocol: Hybridization with GeneChip Mouse Genome 2.0 ST arrays (Affymetrix) according to the manufacturer standard protocol available at www.affymetrix.com. The arrays were washed and stained with phycoerytrin conjugated streptavidin using the Affymetrix Fluidics Station 450

scan_protocol: The arrays were scanned in the Affymetrix GeneArray 3000 7G scanner to generate fluorescent images .Cell intensity files (.CEL files) were generated in the GeneChip Command Console Software (AGCC; Affymetrix).

data_processing: Bioinformatics analysis was performed using Qlucore Omics Explorer 3.2. Raw intensity .CEL files were preprocessed by quantile normalization, and gene summaries were extracted via robust multi-array average (RMA ).  Hierarchical cluster analysis was performed and visualized using the Qlucore Omics Explorer™ software. All hierarchical clusters are build using average linkage and heat map was generated based on mean m = 0, variance 1 normalization

label: phycoerytrin

source_name: WT spleen, untreated

label_protocol: RNA was reverse transcribed and used for cRNA synthesis and labelling with GeneChip Mouse Genome 2.0 ST arrays (Affymetrix) according to the manufacturer standard protocol available at www.affymetrix.com

growth_protocol: Female mice were used at 10 weeks of age

extract_protocol: RNA was extracted using the Maxwell 16 tissue LEV Total RNA Purification Kit (Promega) following the manufacturer’s recommendations.

value: WT

tag: treatment

value: untreated

value: 10 weeks


title: NOD SCID osteoblasts from tumor free mice_replicate 3

description: biological replicate 3

tag: gender


title: Slpeen_KO.LPS_rep2

source_name: Ficolin KO spleen, LPS treated (10mg/kg i.p.), 6hours

value: Ficolin KO

value: LPS

tag: strain


title: CD8+T cell activated WT rep1

city: Ann Arbor

first: Shannon

last: Carty

state: MI

address: 109 Zina Pitcher Place

institute: University of Michigan

hyb_protocol: Affymetrix GeneChip Hybridization Wash and Stain Kit (PN:  900720) protocol was used for all hybridization, wash and staining steps.  Fragmented and labeled cDNA (130ul at 25ng/uL) were hybridized for 17hrs at 45C to Affymetrix GeneChip Mouse Gene 2.0ST Arrays (PN:  902118).

scan_protocol: Chips were washed and stained on an Affymetrix Genechip Wash Station 450 using the FS450_0002 protocol and scanned on the Affymetrix GeneChip Scanner 3000.  Cel files were generated for analysis using Affymetrix GeneChip Command Console v3.2.

source_name: CD8+ T cell, activated in vitro, 3d

label_protocol: Sense-strand single-stranded cDNA was prepared from 200ng of total RNA using the Ambion WT Expression Kit (PN:  4411974).  Both cRNA and cDNA were assessed using UV absorbance.  5.5ug of single-stranded cDNA was fragmented and labeled using the Affymetrix GeneChip WT Terminal Labeling kit (PN: 900671).

growth_protocol: WT or TET2-deficient naive CD8+ T cells were cultured on plate-bound anti-CD3 (1ug/ml) and anti-CD28 (5ug/ml) with soluble hIL-2 (100U/ml) in complete IMDM for 3 days.

extract_protocol: Total RNA extracted using RNeasy MIni kit (Qiagen) according to manufacturer's instructions. Total RNA was assessed by UV absorbance and all had 260/280 ratios above 1.7.  Additionally, samples were run on the Agilent RNA 6000 Nano chip and all had RINs above 8.6.


title: Spleen_KO.untreated_rep3

source_name: Ficolin KO spleen, untreated

tag: tissue

value: Spleen


title: CD8+T cell activated WT rep3

data_processing: Affymetrix GeneChip Command Console v3.2.


title: Spleen_WT.untreated_rep3

value: female

tag: age


title: Spleen_KO.LPS_rep1

tag: genotype


title: CD8+T cell activated TET2cKO rep3


title: Spleen_KO.untreated_rep1


title: CD8+T cell activated TET2cKO rep1


title: Spleen_WT.LPS_rep2

source_name: WT spleen, LPS treated (10mg/kg i.p.), 6hours


title: CD8+T cell activated TET2cKO rep2


title: CD8+T cell activated WT rep2


title: Spleen_WT.LPS_rep1

source_name: WT spleen, LPS treated (10mg/kg, i.p.), 6hours


title: Spleen_KO.LPS_rep3


title: lung, high stretch, hypercapnia, biological replicate 10

city: Toronto

first: Gail

last: Otulakowski

state: ON

address: 555 University Ave

department: Physiology & Experimental Medicine

country: Canada

institute: Hospital for Sick Children Research Institute

description: gene expression data from mouse lung following 3 hours of injurious ventilation using hypercapnia

hyb_protocol: GeneChips were hybridized with labeled cRNA and washed according to the protocol described in the WT sense target labeling assay manual from Affymetrix (version 4; FS450_0007).

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: Data were RMA normalized using Affymetrix Expression Console and further analyzed using Partek Genomics Suite

source_name: lung, high stretch mechanical ventilation, 3 hours, FiCO2 = 0.12

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5.5 ug total RNA using the Affy WT Kit

growth_protocol: Adult male C57BL/6J mice maintained on normal diet, weighing 20-25 g

extract_protocol: RNA was extracted with Trizol according to the manufacturer's instructions, followed by Rneasy clean-up

treatment_protocol: mice were anesthetized, tracheostomized, and ventilated using a computer controlled small animal ventilator.  After completion of experiment, mice were killed by exsanguination under anesthesia, bronchoalbeolar lavage was performed, and lungs removed and snap frozen.  Lungs were stored at -80C until RNA was extracted.

value: lung

tag: Sex

value: male

tag: ventilation protocol

value: 3 hours, tidal volume (VT) approx 35-40 mL/kg, peak Inspiratory Pressure of 27 cmH2O, PEEP 0 cm H2O, frequency 30-35/min

tag: inspired gas

value: FIO2 = 0.75, FiCO2 = 0.12, balance N2


title: lung, high stretch, hypercapnia, biological replicate 7


title: Spleen_WT.untreated_rep2


title: Spleen_WT.LPS_rep3


title: lung, high stretch, hypercapnia, biological replicate 8


title: Spleen_KO.untreated_rep2


title: lung, high stretch, hypercapnia, biological replicate 5


title: lung, high stretch, hypercapnia, biological replicate 6


title: lung, high stretch, hypercapnia, biological replicate 4


title: lung, high stretch, hypercapnia, biological replicate 9


title: blood Control rep11

city: New York

first: Sally

last: Amundson

state: NY

department: Center for Radiological Research

institute: Columbia University

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 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x GEx hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) 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).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan setting with eXtended dynamic range, Scan area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to XDR Hi 100% and XDR Lo 10%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters to obtain background subtracted and spatially detrended green Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers or Features not Positive and significant were excluded.  Data were filtered to exclude features not positive and significant in ≥25% of the samples, or those without at least a 1.5-fold change in expression values across the samples.

source_name: blood Control

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the One-Color Low Input Quick Amp Labeling Kit  (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: After irradiation, blood samples were diluted 1:1 with RPMI 1640 medium (Mediatech, Herndon, VA) supplemented with 10% heat-inactivated fetal bovine serum (HyClone, Logan, UT), as previously described (Grace et al., Int J Radiat Biol 2002; 78:1011-21; PMID 12456288), and were incubated for 24 h  at 37º C in a humidified incubator with 5% CO2

extract_protocol: The RNA was prepared using the PerfectPure RNA blood kit (PerfectPure, Gaithersburg, MD) following the manufacturer’s recommendations. This protocol differentially lyses red and white blood cells in whole blood to preferentially deplete   globin mRNA. Remaining globin mRNA was further reduced using GLOBINclear (Ambion Inc., Austin, TX) specifically to remove both a- and b-globin. The RNA was quantified using a NanoDrop-1000 spectrophotometer, and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Peripheral blood from healthy volunteers was drawn into 0.105 mol/l sodium citrate Vacutainer tubes (Becton Dickinson and Company, Franklin Lakes, NJ). The blood was divided into 3-ml aliquots and exposed to either X-rays or IND-spectrum neutrons (PMID 26414507).

tag: donor

value: Donor 12

value: peripheral blood


title: lung, high stretch, hypercapnia, biological replicate 1


title: lung, high stretch, hypercapnia, biological replicate 2


title: lung, high stretch, hypercapnia, biological replicate 3


title: lung, high stretch, normocapnia, biological replicate 10

description: gene expression data from mouse lung following 3 hours of injurious ventilation using normocapnia

source_name: lung, high stretch mechanical ventilation, 3 hours, FiCO2 = 0

value: FIO2 = 0.75, FiCO2 = 0, balance N2


title: blood 1 Gy Neutron rep12

source_name: blood 1 Gy Neutron


title: blood 0.3 Gy X-ray rep6

source_name: blood 0.3 Gy X-ray


title: lung, high stretch, normocapnia, biological replicate 8


title: blood 0.1 Gy X-ray rep6

source_name: blood 0.1 Gy X-ray


title: lung, high stretch, normocapnia, biological replicate 5


title: lung, high stretch, normocapnia, biological replicate 4


title: blood 0.5 Gy X-ray rep12

source_name: blood 0.5 Gy X-ray


title: blood 0.3 Gy Neutron rep6

source_name: blood 0.3 Gy Neutron


title: blood Control rep10

value: Donor 11


title: blood 0.1 Gy Neutron rep6

source_name: blood 0.1 Gy Neutron


title: lung, high stretch, normocapnia, biological replicate 2


title: blood 0.5 Gy Neutron rep11

source_name: blood 0.5 Gy Neutron


title: lung, high stretch, normocapnia, biological replicate 7


title: lung, high stretch, normocapnia, biological replicate 9


title: lung, high stretch, normocapnia, biological replicate 3


title: lung, low stretch, hypercapnia, biological replicate 5

description: gene expression data from mouse lung following 3 hours of protective ventilation using hypercapnia

source_name: lung, low stretch mechanical ventilation, 3 hours, FiCO2 = 0.12

value: 3 hours, tidal volume (VT) 10 ml/kg, PEEP 2.0 cm H2O, frequency 135/min

value: FiCO2 = 0.12, balance room air


title: blood 1Gy X-ray rep11

source_name: blood 1Gy X-ray


title: lung, low stretch, hypercapnia, biological replicate 4


title: lung, high stretch, normocapnia, biological replicate 6


title: lung, low stretch, hypercapnia, biological replicate 3


title: blood 1Gy X-ray rep10


title: lung, high stretch, normocapnia, biological replicate 1


title: blood 1 Gy Neutron rep11


title: blood 0.5 Gy X-ray rep11


title: blood 0.3 Gy X-ray rep5


title: lung, low stretch, normocapnia, biological replicate 4

description: gene expression data from mouse lung following 3 hours of protective ventilation using normocapnia

source_name: lung, low stretch mechanical ventilation, 3 hours, FiCO2 = 0

value: room air


title: lung, low stretch, normocapnia, biological replicate 5


title: lung, non-ventilated, biological replicate 5

description: gene expression data from control (ie spontaneously breathing room air) mouse lung

source_name: lung, non-ventilated

value: spontaneous breathing


title: lung, low stretch, normocapnia, biological replicate 3


title: lung, low stretch, normocapnia, biological replicate 1


title: lung, low stretch, hypercapnia, biological replicate 1


title: blood 0.5 Gy Neutron rep10


title: lung, low stretch, normocapnia, biological replicate 2


title: lung, non-ventilated, biological replicate 1


title: blood 0.3 Gy Neutron rep5


title: lung, non-ventilated, biological replicate 4


title: lung, low stretch, hypercapnia, biological replicate 2


title: blood 1Gy X-ray rep9

value: Donor 10


title: blood 1 Gy Neutron rep10


title: lung, non-ventilated, biological replicate 2


title: blood Control rep9


title: blood 0.1 Gy X-ray rep5


title: blood 0.1 Gy Neutron rep5


title: blood 0.5 Gy Neutron rep9


title: lung, non-ventilated, biological replicate 3


title: blood 0.5 Gy X-ray rep10


title: blood 0.3 Gy X-ray rep4


title: blood Control rep8

value: Donor 9


title: blood 0.1 Gy Neutron rep4


title: blood 1Gy X-ray rep8


title: 776_TAKI5

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

hyb_protocol: For each sample, 1.65ug of Cy3 labeled cRNAs were fragmented and hybridized for 17 hours in a rotating hybridization oven.

scan_protocol: Slides were washed and then scanned with an Agilent Scanner.

data_processing: Data was obtained using the Agilent Feature Extraction software (v9.5), using the 1-color defaults for all parameters.

source_name: TAKI liver fed with a western-style high fat diet for 5 months

label_protocol: Starting with 500ng of total RNA, Cy3 labeled cRNA was produced according to manufacturer’s protocol.

growth_protocol: Male mice were fed with a western-style high fat diet for 5 months

extract_protocol: Qiagen RNA easy mini kit with on-column DNAseI treatment

treatment_protocol: No special treatment

tag: strain background

value: SIRT1 TA KI allele

tag: fed with

value: liver


title: 776_TAKI2

value: western-style high fat diet for 5 months


title: 776_TEKI3

source_name: TEKI liver fed with a western-style high fat diet for 5 months

value: SIRT1 TE KI allele


title: blood 0.1 Gy X-ray rep4


title: blood 1 Gy Neutron rep9


title: 776_TAKI3

value: male


title: 776_TEKI1


title: blood 0.5 Gy X-ray rep9


title: 776_WT2

source_name: WT liver fed with a western-style high fat diet for 5 months

value: WT SIRT1


title: blood 0.3 Gy Neutron rep4


title: 776_TEKI2


title: blood 0.5 Gy Neutron rep8


title: 776_TAKI4


title: 776_WT5


title: 776_WT4


title: 776_TAKI1


title: 776_WT3


title: blood 0.3 Gy X-ray rep3


title: 776_WT1


title: blood 0.3 Gy Neutron rep3


title: blood 0.1 Gy X-ray rep3


title: blood Control rep7

value: Donor 8


title: Normal bladder 2

city: Wuhan

first: Yu

last: Xiao

address: Donghu Road 169

department: Department of Urology

country: China

institute: Zhongnan Hospital of Wuhan University

description: Normal bladder from donors undergoing transplant by accidental death

hyb_protocol: Following labeling, 5.5 ug of cDNA were hybridized for 16 hr at 45℃ on GeneChip Human Transcriptome Array 2.0 in Hybridization Oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scaned by using Affymetrix® GeneChip Command Console (AGCC) which installed in GeneChip® Scanner 3000 7G.

data_processing: The data were analyzed with Robust Multichip Analysis (RMA) algorithm using Affymetrix default analysis settings and global scaling as normalization method.

source_name: normal bladder

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA by using Ambion® WT Expression Kit. WT Expression Kit

extract_protocol: Total RNA was isolated from tissues at indicated time point with RNeasy Mini Kit (Qiagen)

treatment_protocol: The tissues were obtained from the operation room and were snap-frozen immediately, stored at liquid nitrogen.

value: bladder

tag: disease state

value: healthy


title: Bladder cancer 5

description: Bladder cancer patient in Stage II after surgery

source_name: bladder cancer

value: bladder cancer


title: Normal bladder 4


title: Bladder cancer 4


title: Normal bladder 5


title: blood 0.5 Gy Neutron rep7

value: peripheral blood


title: blood 0.3 Gy Neutron rep2


title: blood 0.3 Gy X-ray rep2


title: blood 1 Gy Neutron rep8


title: blood 0.1 Gy X-ray rep2


title: blood 1 Gy Neutron rep7

value: Donor 7


title: blood 0.1 Gy Neutron rep2


title: blood 0.5 Gy X-ray rep8


title: blood 0.5 Gy X-ray rep7


title: blood 0.1 Gy X-ray rep1


title: blood 0.3 Gy X-ray rep1


title: blood 1Gy X-ray rep7


title: blood 0.1Gy Neutron rep1

source_name: blood 0.1Gy Neutron


title: blood 4Gy X-ray rep6

source_name: blood 4Gy X-ray

value: Donor 6


title: blood 2Gy X-ray rep5

source_name: blood 2Gy X-ray

value: Donor 5


title: blood 0.3 Gy Neutron rep1


title: blood 4Gy X-ray rep5


title: blood 0.5Gy Neutron rep6

source_name: blood 0.5Gy Neutron


title: blood 0.25Gy Neutron rep6

source_name: blood 0.25Gy Neutron


title: blood Control rep5

source_name: blood Control


title: Bladder cancer 3


title: blood Control rep6


title: blood 1Gy X-ray rep5


title: blood 1Gy X-ray rep6


title: blood 1Gy Neutron rep5

source_name: blood 1Gy Neutron


title: blood 0.5Gy Neutron rep5


title: blood 1Gy Neutron rep6


title: cd8_dr3_after_rep3

city: Nizhny Novgorod

first: Dmitry

last: Knyazev

address: Malaya Yamskaya, 71

country: Russia

institute: I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology

description:
the original feature data file;
18.10.2016_81572.ecd.txt
Aft-18DR3_3

hyb_protocol: Fragmented labeled RNA (2 ug) was hybridized at 40oC for 18-20 hours in Hyb-solution (6xSSPE, 20mM EDTA, 0,05% Tween-20, salmon sperm DNA 10 mg/ml, 0,04% SDS,  formamide 25%vol). Arrays were sequentially washed  by 3хSSPE, 0,05% Tween-20 → 0,5хSSPE, 0,05% ТTween20 → 2xPBS 0,1% Tween-20. Subsequent blocking, labeling, label wash, substrate solution treatment were fulfilled using ElectraSense Detection Kit (CustomArray Inc., WA, USA)

scan_protocol: Amperometric signal measurements were performed using ElectraSense Reader device and ElectraSense application software (CustomArray Inc., WA, USA)

data_processing: Feature data from .ecd files was exported to csv files using ElectraSense Analysis 3.4.2. From each array 4 samples were extracted and pm signals used. All calculations were performed in Mathworks Matlab. Background correction was made using rmabackadj() function. Samples of same type were organized in matrix 1042xN, where 1042 – number of zonds and N – number of repeating mesuers of sample. Two matrix of samples to compare were normalized using quantilenorm() function from Matlab. To calculate fold-change and its significance, mattest() was used. rmasummary() was used to calculate overall gene expression, using all zonds aimed to isoforms of gene. P=0.05 was selected as threshold value.

source_name: DR3-activated naïve CTLs after convalescence

label_protocol: 1. Total RNA (1,5-2 ug) was converted to T7promoter-containing cDNA by Mint cDNA synthesis kit (Evrogen, Russia, http://evrogen.ru/technologies/Mint-cDNA-synthesis.shtml), kit' 3'-oligo-T-primer was replaced by T7promoter-containing-oligo-T-primer (DNA-synthesis, Russia); 2. cDNA was complemented to ds-cDNA by 15-cycles PCR amplification; 3. ds-cDNA (2 ug) was transcribed by T7 RNA-polimerase (Thermo Scientific, EU). Biotin-labeled RNA was obtained using biotinylated UTP (DNA-synthesis, Russia) by substitution of a half of its unlabeled counterpart in reaction mix.

growth_protocol: Naïve T-cells were isolated by negative magnetic separation using EasySep kits (Stemcell Technologies, UK). Cells were subjected to either immediate NA extraction or cultivation as follows: cells in concentration 10^6 cells/ml were kept in RPMI-1647 medium with 10% fetal bovine serum and 2 mM L-glutamine at 37oC in a humidified atmosphere with 5% CO2 for 24 hours.

extract_protocol: Total RNA was isolated by magnetic beads-containg kit (Magnosorb kit, Russia) followed by phenol-chloroform purification

treatment_protocol: Cells were treated with murine monoclonal antibodies against human CD95 (IgМ isotype, clone CH-11, Beckman Coulter, USA) or against human DR3 (clone JD3, IgG1 kappa isotype, eBioscience, USA) in a final concentration 200 ng/ml for 24 hours

value: female

tag: Stage

value: after convalescence

tag: cultivation

tag: activator

value: anti-DR3 MAb

tag: cell type


title: blood 0.25Gy Neutron rep5


title: cd8_control_after_rep3

description:
the original feature data file;
18.10.2016_81572.ecd.txt
Aft-18K_3

source_name: naïve CTLs  after convalescence control cultivation

value: no


title: cd8_fas_after_rep1

description:
the original feature data file;
28.07.2016_81579.ecd.txt
Aft-18Fas_1

source_name: Fas-activated naïve CTLs after convalescence

value: anti-CD95 MAb


title: cd8_dr3_after_rep1

description:
the original feature data file;
28.07.2016_81579.ecd.txt
Aft-18DR3_1


title: cd8_fas_after_rep3

description:
the original feature data file;
18.10.2016_81572.ecd.txt
Aft-18Fas_3


title: cd8_fas_after_rep2

description:
the original feature data file;
28.07.2016_81579.ecd.txt
Aft-18Fas_2


title: blood 2Gy X-ray rep4

value: Donor 4


title: ivermectin, replicate 2

city: Geneva

first: Ariel

last: Ruiz i Altaba

address: 1 rue Michel Servet

department: GEDEV

institute: University of Geneva Medical School

description: IV2 - norm.exp. - linear

hyb_protocol: Following fragmentation,  cRNA were hybridized for 16 hr (at 60 rpm) to PrimeView U219 human array (Affymetrix) in the Genomic Platform at the 131 Faculty of Medicine, University of Geneva.

scan_protocol: Arrays were scanned on the 3000 7G Affymetrix scanner. Fluorescence signals were analyzed with Affymetrix GCOS software

data_processing: Data processing with Partek Genomics Suite software which include RMA algorithm (used for the background correction, the normalization and the summarization).

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 0.3 ug total RNA

growth_protocol: Cells were cultured in DMEM-F12, 10% FBS

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

treatment_protocol: Cells were treated in DMEM-F12, 2.5% FBS with 5uM drug or DMSO for 16h

tag: cell line

tag: tissue source

value: colon

value: colorectal adenocarcinoma cell line

tag: treated with

value: 5uM ivermectin for 16h


title: blood 0.5Gy Neutron rep4

tag: tissue


title: blood 1Gy Neutron rep4


title: blood 1Gy X-ray rep4

source_name: blood 1Gy X-ray


title: blood Control rep4


title: blood 4Gy X-ray rep4


title: cd8_control_after_rep2

description:
the original feature data file;
28.07.2016_81568.ecd.txt
Aft-18K_2

tag: gender

tag: age


title: cd8_dr3_after_rep2

description:
the original feature data file;
28.07.2016_81579.ecd.txt
Aft-18DR3_2


title: blood 0.25Gy Neutron rep4


title: ivermectin, replicate 1

description: IV1- norm.exp. - linear


title: CAP2, replicate 2

description: CAP2_2 - norm.exp. - linear

value: 5uM CAP2  for 16h


title: CAP2, replicate 3

description: CAP2_3 - norm.exp. - linear


title: control for CAP2 and ivermectin, replicate 3

description: CT3 - norm.exp. - linear

value: DMSO for 16h


title: control for CAP2 and ivermectin, replicate 2

description: CT2 - norm.exp. - linear


title: selamectin, replicate 3

description: SV3 - norm. exp. (linear scale)

treatment_protocol: Cells were treated in DMEM-F12, 2.5% FBS with 5uM selamectin or DMSO for 16h

value: 5uM Selamectin for 16h


title: cd8_control_after_rep1

description:
the original feature data file;
28.07.2016_81568.ecd.txt
Aft-18K_1


title: blood 2Gy X-ray rep6


title: cd4_dr3_after_rep3

description:
the original feature data file;
18.10.2016_81568.ecd.txt
Aft-14DR3_3

source_name: DR3-activated naïve T helpers after convalescence


title: CAP2, replicate 1

description: CAP2_1 - norm.exp. - linear


title: cd4_dr3_after_rep1

description:
the original feature data file;
26.07.2016_81580.ecd.txt
Aft-14DR3_1


title: blood Control rep3

value: Donor 3


title: cd4_fas_after_rep2

description:
the original feature data file;
26.07.2016_81580.ecd.txt
Aft-14Fas_2

source_name: Fas-activated naïve T helpers after convalescence


title: selamectin, replicate 2

description: SV2 - norm. exp. (linear scale)


title: blood 4Gy X-ray rep3

value: peripheral blood


title: control for CAP2 and ivermectin, replicate 1

description: CT1 - norm.exp. - linear


title: blood 0.5Gy Neutron rep3


title: blood 1Gy Neutron rep3


title: blood 0.25Gy Neutron rep3


title: cd4_control_after_rep3

description:
the original feature data file;
18.10.2016_81515.ecd.txt
Aft-14K_3

source_name: naïve T helpers after convalescence control cultivation


title: cd4_fas_after_rep1

description:
the original feature data file;
26.07.2016_81580.ecd.txt
Aft-14Fas_1


title: control for selamectin, replicate 3

description: CT3 - norm. exp. (linear scale)


title: cd4_fas_after_rep3

description:
the original feature data file;
18.10.2016_81568.ecd.txt
Aft-14Fas_3


title: blood 4Gy X-ray rep2

value: Donor 2


title: cd4_dr3_after_rep2

description:
the original feature data file;
26.07.2016_81580.ecd.txt
Aft-14DR3_2


title: blood Control rep2


title: blood 2Gy X-ray rep3


title: selamectin, replicate 1

description: SV1 - norm. exp. (linear scale)


title: control for selamectin, replicate 2

description: CT2  - norm. exp. (linear scale)


title: cd8_fresh_after_rep3

description:
the original feature data file;
13.10.2016_81580.ecd.txt
Aft-08_3

source_name: freshly isolated naïve CTLs after convalescence


title: cd4_control_after_rep1

description:
the original feature data file;
26.07.2016_81572.ecd.txt
Aft-14K_1


title: blood 1Gy X-ray rep3


title: cd4_control_after_rep2

description:
the original feature data file;
26.07.2016_81572.ecd.txt
Aft-14K_2


title: 0GyP7/ reference male mouse3

type: genomic

city: Rokkasho-mura,Kamikita-gun,

first: Keiji

last: OGURA

state: Aomori

address: Takahoko, Hacchasawa,

department: Department of Radiobiology

country: Japan

institute: Institute for Environmental Science

hyb_protocol: Oligonucleotide Array-Based CGH for Genomic DNA Analysis, protocol version 4.0.8

scan_protocol: Scanned on an Agilent G2565BA scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.1.1).

data_processing: Agilent Genomic Workbench Software (v 7.0.) was used.

molecule: genomic DNA

extract_protocol: PI-50a (Kurabo Industries LTD.) tissue DNA extraction protocol.

tag: strain

value: tail

source_name: reference male mouse3


title: control for selamectin, replicate 1

description: CT1 - norm. exp. (linear scale)


title: blood 2Gy X-ray rep2


title: blood 1Gy X-ray rep2


title: cd8_fresh_after_rep2

description:
the original feature data file;
13.10.2016_81572.ecd.txt
Aft-08_2


title: 0GyP6/ reference male mouse3

label_protocol: Oligonucleotide Array-Based CGH for Genomic DNA Analysis, protocol version 4.0.8


title: reference male mouse3/ 0GyP7


title: reference male mouse3/ 0GyP6


title: 0GyP5/ reference male mouse3


title: reference male mouse3/ 0GyP5


title: 0GyP4/ reference male mouse3


title: cd8_fresh_after_rep1

description:
the original feature data file;
13.10.2016_81571.ecd.txt
Aft-08_1


title: cd4_fresh_after_rep3

description:
the original feature data file;
13.10.2016_81580.ecd.txt
Aft-04_3

source_name: freshly isolated naïve T helpers after convalescence


title: cd8_dr3_before_rep3

description:
the original feature data file;
18.10.2016_81572.ecd.txt
Bef-18DR3_3

source_name: DR3-activated naïve CTLs acute mononucleosis

value: acute mononucleosis


title: cd4_fresh_after_rep1

description:
the original feature data file;
13.10.2016_81580.ecd.txt
Aft-04_1

value: female


title: cd4_fresh_after_rep2

description:
the original feature data file;
13.10.2016_81580.ecd.txt
Aft-04_2

value: after convalescence


title: cd8_dr3_before_rep1

description:
the original feature data file;
28.07.2016_81568.ecd.txt
Bef-18DR3_1

value: anti-DR3 MAb


title: cd8_dr3_before_rep2

description:
the original feature data file;
28.07.2016_81568.ecd.txt
Bef-18DR3_2


title: blood Control rep1

value: Donor 1


title: blood 1Gy Neutron rep2


title: blood 0.25Gy Neutron rep2


title: blood 4Gy X-ray rep1

source_name: blood 4Gy X-ray


title: blood 2Gy X-ray rep1

source_name: blood 2Gy X-ray


title: blood 1Gy Neutron rep1


title: cd8_fas_before_rep3

description:
the original feature data file;
18.10.2016_81568.ecd.txt
Bef-18Fas_3

source_name: Fas-activated naïve CTLs  acute mononucleosis

value: anti-CD95 MAb


title: blood 0.5Gy Neutron rep2

source_name: blood 0.5Gy Neutron


title: cd8_fas_before_rep2

description:
the original feature data file;
28.07.2016_81515.ecd.txt
Bef-18Fas_2


title: blood 1Gy X-ray rep1


title: cd8_fas_before_rep1

description:
the original feature data file;
28.07.2016_81515.ecd.txt
Bef-18Fas_1


title: reference male mouse3/ 0GyP3


title: blood 0.25Gy Neutron rep1

source_name: blood 0.25Gy Neutron


title: NK brain d3 003

city: Tianjin

first: Fu-Dong

last: Shi

address: 154 Anshan Rd.

institute: Tianjin Medical University General Hospital

data_processing: Data was proccessed using nSolver, normalized to Positive controls, Housekeeping genes and negative controls

source_name: brain NK cell

label_protocol: nCounter Mouse Inflammation Kit

extract_protocol: Total RNA was extracted using mirVanaTM miRNA isolation kit (Ambion) according to the manufacturer’s protocol

treatment_protocol: RNA of FACS-sorted brain-infiltrating NK cells was obtained from pooled brain tissues of MCAO mice. RNA of FACS-sorted NK cells in spleens was obtained from single mouse spleens of MCAO mice.

value: brain

value: natural killer (NK) cells


title: NK brain d3 002

hyb_protocol: according to the manufacturer’s protocol


title: reference male mouse3/ 0GyP4


title: blood 0.5Gy Neutron rep1


title: NK brain d3 001

scan_protocol: according to the manufacturer’s protocol


title: S26

city: Guangzhou

first: Jun

last: Ma

address: 651 Dongfeng Road East

institute: Sun Yat-sen University Cancer Center

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

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C). Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images.

data_processing: Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). Differentially expressed LncRNAs and mRNAs between the high and low metastatic potential cell lines (5-8F vs. 6-10B and S18 vs. S26) were identified through Fold Change and Normalized Intensities filtering.

label_protocol: Sample labeling was performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, each mRNA sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing random priming. The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: Total RNA was extracted from the 4 cell lines using TRIzol reagent (Invitrogen, Grand Island, NY, USA) according to the manufacturer’s instructions. mRNA was purified from the total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). RNA quantity and quality were measured by NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

value: nasopharyngeal carcinoma cell line S26

tag: phenotype

value: low metastatic potential


title: 0GyP1/ reference male mouse3


title: 0GyP2/ reference male mouse3


title: 0GyPF/ reference male mouse3


title: S18

value: nasopharyngeal carcinoma cell line S18

value: high metastatic potential


title: cd8_control_before_rep2

description:
the original feature data file;
28.07.2016_81515.ecd.txt
Bef-18K_2

source_name: naïve CTLs acute mononucleosis control cultivation

value: no


title: NK brain d1 003


title: 0GyPM/ reference male mouse3


title: reference male mouse3/ 0GyP1


title: reference male mouse3/ 0GyPF


title: 0GyP3/ reference male mouse3


title: reference male mouse3/ 0GyP2


title: 6-10B

value: nasopharyngeal carcinoma cell line 6-10B


title: 5-8F

value: nasopharyngeal carcinoma cell line 5-8F


title: 0GyO8/ reference male mouse3


title: NK brain d1 002


title: cd8_control_before_rep1

description:
the original feature data file;
28.07.2016_81515.ecd.txt
Bef-18K_1


title: NK brain d1 001


title: cd8_control_before_rep3

description:
the original feature data file;
18.10.2016_81568.ecd.txt
Bef-18K_3


title: cd4_dr3_before_rep2

description:
the original feature data file;
26.07.2016_81572.ecd.txt
Bef-14DR3_2

source_name: DR3-activated naïve T helpers acute mononucleosis


title: cd4_dr3_before_rep3

description:
the original feature data file;
18.10.2016_81515.ecd.txt
Bef-14DR3_3


title: cd4_dr3_before_rep1

description:
the original feature data file;
26.07.2016_81572.ecd.txt
Bef-14DR3_1


title: NK brain control 003


title: NK brain control 002


title: NK brain control 001


title: reference male mouse3/ 0GyPM


title: NK spleen d3 003

source_name: spleen NK cell

value: spleen


title: cd4_fas_before_rep3

description:
the original feature data file;
18.10.2016_81515.ecd.txt
Bef-14Fas_3

source_name: Fas-activated naïve T helpers acute mononucleosis


title: cd4_fas_before_rep2

description:
the original feature data file;
26.07.2016_81571.ecd.txt
Bef-14Fas_2


title: NK spleen d3 002


title: reference male mouse3/ 0GyO8

value: tail


title: cd4_fas_before_rep1

description:
the original feature data file;
26.07.2016_81571.ecd.txt
Bef-14Fas_1

value: acute mononucleosis


title: reference male mouse3/ 0GyO7


title: NK spleen d3 001


title: cd4_control_before_rep3

description:
the original feature data file;
18.10.2016_81515.ecd.txt
Bef-14K_3

source_name: naïve T helpers acute mononucleosis control cultivation

value: female


title: 0GyO6/ reference male mouse3


title: cd4_control_before_rep2

description:
the original feature data file;
26.07.2016_81571.ecd.txt
Bef-14K_2


title: NK spleen d1 003


title: NK spleen d1 002


title: cd4_control_before_rep1

description:
the original feature data file;
26.07.2016_81571.ecd.txt
Bef-14K_1


title: NK spleen control 003


title: cd8_fresh_before_rep3

description:
the original feature data file;
13.10.2016_81572.ecd.txt
Bef-08_3

source_name: freshly isolated naïve CTLs acute mononucleosis


title: 0GyO7/ reference male mouse3


title: cd8_fresh_before_rep1

description:
the original feature data file;
13.10.2016_81572.ecd.txt
Bef-08_1


title: NK spleen control 001


title: cd8_fresh_before_rep2

description:
the original feature data file;
13.10.2016_81572.ecd.txt
Bef-08_2


title: NK spleen d1 001


title: cd4_fresh_before_rep3

description:
the original feature data file;
13.10.2016_81571.ecd.txt
Bef-04_3

source_name: freshly isolated naïve T helpers acute mononucleosis


title: cd4_fresh_before_rep1

description:
the original feature data file;
13.10.2016_81571.ecd.txt
Bef-04_1


title: cd4_fresh_before_rep2

description:
the original feature data file;
13.10.2016_81571.ecd.txt
Bef-04_2


title: reference male mouse3/ 0GyO6


title: 0GyO5/ reference male mouse3


title: NK spleen control 002


title: reference male mouse3/ 0GyO3


title: reference male mouse3/ 0GyO5


title: 0GyO2/ reference male mouse3


title: 0GyO4/ reference male mouse3


title: 0GyO1/ reference male mouse3


title: reference male mouse3/ 0GyO4


title: 0GyO3/ reference male mouse3


title: reference male mouse3/ 0GyO2


title: reference male mouse3/ 0GyO1


title: 0GyOM/ reference male mouse3


title: reference male mouse3/ 0GyOF


title: 0GyOF/ reference male mouse3


title: RBD 7850

status: Public on Feb 21 2017

city: Waterloo

first: Patricija

last: Marjan

state: Ontario

address: 200 University Avenue  West

department: Department of Biology

institute: Univesity of Waterloo

hyb_protocol: Agilent Technologies One-Color Microarray-Based Gene Expression Analysis Protocol was used. 600 ng of Cy3-labeled cRNA was used.

scan_protocol: Microarrays were kept in the dark until scanned at 5 μm, laser G, with the Agilent G2505 C Microarray Scanner.

data_processing: Agilent Feature Extraction Software (v. 10.1.1.1) was used to extract raw signal intensities from microarray images.

organism: Etheostoma caeruleum

source_name: Liver; Wildlife collection

label_protocol: Agilent one color protocol for Cy3 following manufacturer's protocol

extract_protocol: QIAzol protocol for total RNA following manufacturer's protocol

tag: developmental stage

value: adult

value: liver

tag: collection site

tag: collection year


title: RBD 7852


title: RBD 7847


title: RBD 7842


title: RBD 7845


title: RBD 7804

value: DSW


title: RBD 7843


title: RBD 7775


title: RBD 7803


title: RBD 7731


title: RBD 7708


title: RBD 7781


title: RBD 7784


title: RBD 7851


title: RBD 7711


title: RBD 7712


title: RBD 5436


title: RBD 7779


title: RBD 7713


title: RBD 7716


title: RBD 7773


title: reference male mouse3/ 0GyOM

source_name: reference male mouse3


title: RBD 5450


title: RBD 5429


title: RBD 5860 A


title: RBD 5446 A


title: RBD 5861


title: RBD 5449


title: RBD 5862


title: RBD 5577


title: RBD 5371


title: RBD 5379


title: RBD 5370


title: RBD 5864


title: RBD 5372


title: RBD 1457


title: RBD 5368


title: RBD 5585


title: RBD 5380


title: RBD 1348


title: RBD 1455


title: RBD 1484


title: RBD 1462


title: RBD 1344


title: RBD 5860


title: RBD 1320


title: RBD 1489


title: RBD 5446


title: RBD 1490


title: RBD 1494


title: RBD 1491


title: RBD 5375


title: RBD 1587


title: RBD 1585


title: RBD 1492


title: RBD 1467


title: RBD 1590


title: RBD 151


title: RBD 1582


title: RBD 49


title: RBD 43


title: RBD 1588


title: RBD 26


title: RBD 150


title: RBD 1568


title: RBD 141


title: RBD 37


title: RBD 45


title: RBD 146


title: RBD 25


title: RBD 51


title: RBD 130


title: RBD 1567


title: RBD 16


title: RBD 152


title: RBD 8


title: RBD 19


title: RBD 6


title: RBD 5655


title: RBD 5641


title: RBD 46


title: RBD 1454


title: RBD 5625


title: RBD 5608


title: RBD 5613


title: RBD 5654


title: RBD 5616


title: RBD 5622


title: RBD 5627


title: RBD 5653


title: RBD 5598


title: RBD 5658


title: RBD 5656


title: RBD 5446


title: RBD 5471


title: RBD 5446 B


title: RBD 5474


title: RBD 5429


title: RBD 5448


title: RBD 5480


title: RBD 5460


title: RBD 5464


title: RBD 5449


title: RBD 5450


title: RBD 5479


title: RBD 5505

value: INT


title: RBD 5530


title: RBD 5528


title: RBD 5436


title: RBD 5517


title: RBD 5861


title: RBD 5529


title: RBD 5525


title: RBD 5860 B


title: RBD 5559


title: RBD 5862


title: RBD 5562


title: RBD 5516


title: RBD 5860


title: RBD 5550


title: RBD 5577


title: RBD 5585


title: RBD 5372


title: RBD 5370


title: RBD 5864


title: RBD 5375


title: RBD 5380


title: RBD 5371


title: RBD 5568


title: RBD 5567


title: RBD 5379


title: RBD 5569


title: RBD 5565


title: RBD 5571


title: RBD 5406


title: RBD 5389


title: RBD 5404


title: RBD 5387


title: RBD 5407


title: RBD 5401


title: ATAC seq for MSC infected with empty vector

type: SRA

city: Boston

first: Sowmya

last: Iyer

state: MA

department: Pathology

institute: Massachusetts General Hospital

library_source: genomic

data_processing:
Paired end reads were aligned to hg19 using BWA. Read start sites were adjusted to represent the center of the transposon binding event (+4 bp in the plus strand and -5 bp in the minus strand). Signal densities were calculated over a sliding 150 bp window at 20 bp steps and normalized to 10M reads in each experiment.
Genome_build: hg19

source_name: MSC

extract_protocol:
5x10^4 cells for each condition were first incubated in hypotonic buffer then resuspended in lysis buffer, centrifugated and resuspended in Transposase reaction mix for additional 30 min at 37C, following manufacturer recommendations (Nextera DNA sample Prep Kit, Illumina).
DNA was purified and adaptor sequences were added to the fragmented DNA by PCR to construct Illumina sequencing libraries. Purified PCR products were sequenced using the Illumina Nextseq device.

value: primary medulloblastoma

tag: source type

value: primary tissue


title: ATAC seq for MSC infected with OTX2


title: MSC_NEUROD1_INPUT_2

description: MSC

data_processing:
ChIP-seq reads were aligned to the reference genome (hg19) using BWA
Genome_build: hg19
Supplementary_files_format_and_content: We extended aligned reads to 200 bp to approximate fragment sizes and derived 25-bp resolution density maps by counting the number of fragments overlapping each position with IGVtools. All density maps were normalized to 10M reads.

source_name: INPUT ChIP-seq in primary medulloblastoma MSC infected with NEUROD1

extract_protocol:
Chromatin from formaldehyde-fixed cells (3-5 x 10^6 cells per epitope) was fragmented to a size range of 200 - 700 bases with a Branson 250 Sonifier. Solubilized chromatin was immunoprecipitated with the indicated antibodies and Protein G-Dynabeads (Life Technologies). Immunoprecipitated DNA was extracted with AMP Pure beads(Beckman Coulter) after crosslink reversal, RNAse A and Proteinase K treatment.
ChIP DNA samples were used to generate Illumina sequencing libraries following standard protocols.

tag: chip antibody

value: INPUT


title: MSC_NEUROD1_OTX2_2

description: MSC

source_name: OTX2 ChIP-seq in primary medulloblastoma MSC infected with NEUROD1


title: MSC_NEUROD1_H3K27ac_2

description: MSC

source_name: H3K27ac ChIP-seq in primary medulloblastoma MSC infected with NEUROD1


title: RNA seq of primary medulloblastoma T2

library_source: transcriptomic

data_processing:
RNA-seq reads were mapped using STAR. Counts were generated using HT-seq and normalized to sequencing depth. We used Cufflinks to calculate FPKMs
Genome_build: hg19
Supplementary_files_format_and_content: text file with raw counts or fpkm.

extract_protocol:
Total RNA was isolated using NucleoSpin RNA (Clontech).  1 μg of total RNA was treated with Ribogold zero to remove ribosomal RNA. Remaining RNA was used to construct Illumina sequencing libraries with random primers according to manufacturer instructions using the Truseq Stranded RNA LT Kit.
RNA samples were used to generate Illumina sequencing libraries following standard protocols.


title: RNA seq of primary medulloblastoma T1


title: RNA seq of primary medulloblastoma T5


title: MSC_NEUROD1_NEUROD1_2

description: MSC

source_name: NEUROD1 ChIP-seq in primary medulloblastoma MSC infected with NEUROD1


title: MSC_NEUROD1_H3K4m1_2

description: MSC

source_name: H3K4m1 ChIP-seq in primary medulloblastoma MSC infected with NEUROD1


title: RNA seq of primary medulloblastoma T3


title: MSC_OTX2_NEUROD1_2

description: MSC

source_name: NEUROD1 ChIP-seq in primary medulloblastoma MSC infected with OTX2


title: MSC_OTX2_OTX2_2

description: MSC

source_name: OTX2 ChIP-seq in primary medulloblastoma MSC infected with OTX2


title: RBD 5400


title: MSC_OTX2_INPUT_2

description: MSC

source_name: INPUT ChIP-seq in primary medulloblastoma MSC infected with OTX2


title: RNA seq of primary medulloblastoma T4


title: MSC_empty_NEUROD1_2

description: MSC

source_name: NEUROD1 ChIP-seq in primary medulloblastoma MSC infected with empty vector


title: MSC_empty_OTX2_2

description: MSC

source_name: OTX2 ChIP-seq in primary medulloblastoma MSC infected with empty vector


title: MSC_empty_H3K27ac_2

description: MSC

source_name: H3K27ac ChIP-seq in primary medulloblastoma MSC infected with empty vector


title: MSC_OTX2_H3K4m1_2

description: MSC

source_name: H3K4m1 ChIP-seq in primary medulloblastoma MSC infected with OTX2


title: MSC_OTX2_H3K27ac_2

description: MSC

source_name: H3K27ac ChIP-seq in primary medulloblastoma MSC infected with OTX2


title: MSC_empty_INPUT_2

description: MSC

source_name: INPUT ChIP-seq in primary medulloblastoma MSC infected with empty vector


title: MSC_OTX2_INPUT_1

description: MSC


title: MSC_empty_H3K4m1_2

description: MSC

source_name: H3K4m1 ChIP-seq in primary medulloblastoma MSC infected with empty vector


title: MSC_OTX2_OTX2_1

description: MSC


title: MSC_OTX2_H3K4m1_1

description: MSC


title: MSC_OTX2_H3K27ac_1

description: MSC


title: MSC_empty_INPUT_1

description: MSC


title: MSC_empty_OTX2_1

description: MSC


title: MSC_empty_H3K4m1_1

description: MSC


title: Uninfected HaCaT

first: Alice

last: Prince

state: New York

description: Raw read files not included in submission because they were deleted by core facility.

data_processing:
RTA (Illumina) was used for for base calling and bcl2fastq (version 1.8.4) for converting BCL to fastq format, coupled with adaptor trimming. The reads were mapped to a reference genome (Human:NCBI/build37.2)
The reads were mapped to a reference genome (Human: NCBI/build37.2; Mouse: UCSC/mm9) using Tophat (Trapnell et al., 2009) with 4 mismatches (--readmismatches = 4) and 10 maximum multiple hits (--max-multihits = 10).
To tackle the mapping issue of reads that are from exon-exon junctions, Tophat infers novel exon-exon junctions ab initio, and combine them with junctions from known mRNA sequences (refgenes) as the reference annotation. The relative abundance (aka expression level) of genes and splice isoforms were estimated usingcufflinks (Trapnell et al., 2010) with default settings.
Differentially expressed genes were tested under various conditions using DEseq (Anders S et al 2010 Genome Biology).
It is an R package based on a negative binomial distribution that models the number reads from RNA-seq experiments and test for differential expression.
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: HaCaT

growth_protocol: The human HaCaT keratinocyte cell line was grown in DMEM with 10% FBS and 1% penicillin/streptomycin. Primary human keratinocytes (HEKn) cells were obtained from Gibco and grown in Dermalife (Lifeline Cell Technologies) with 1% FBS and 1% penicillin/streptomycin.

extract_protocol:
Cells were removed from plates, flash frozen on dry ice, and RNA was harvested using TRK lysis buffer  Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HaCaTs and primary keratinocytes were infected with WT USA300 S. aureus (MOI 100:1) for 1 hour before cell lysates were prepared.

value: HaCaT

value: skin

tag: agent

value: none (uninfected)


title: agr HaCaT

value: Methicillin-resistant Staphylococcus aureus strain USA300 (agr mutant)


title: WT HEKn

source_name: HEKn

value: HEKn

value: Methicillin-resistant Staphylococcus aureus strain USA300 (wild type)


title: agr HEKn


title: WT HaCaT


title: Uninfected HEKn


title: T5_H3K4m3

source_name: H3K4m3 ChIP-seq in primary medulloblastoma T5


title: T5_H3K27m3

source_name: H3K27m3 ChIP-seq in primary medulloblastoma T5


title: T5_H3K27ac

source_name: H3K27ac ChIP-seq in primary medulloblastoma T5


title: T5_H3K4m1

source_name: H3K4m1 ChIP-seq in primary medulloblastoma T5


title: T4_INPUT

source_name: INPUT ChIP-seq in primary medulloblastoma T4


title: T4_H3K4m3

source_name: H3K4m3 ChIP-seq in primary medulloblastoma T4


title: T4_H3K27m3

source_name: H3K27m3 ChIP-seq in primary medulloblastoma T4


title: T5_INPUT

source_name: INPUT ChIP-seq in primary medulloblastoma T5


title: T4_H3K4m1

source_name: H3K4m1 ChIP-seq in primary medulloblastoma T4


title: MSC_empty_H3K27ac_1

description: MSC


title: T4_H3K27ac

source_name: H3K27ac ChIP-seq in primary medulloblastoma T4


title: T3_H3K4m1

source_name: H3K4m1 ChIP-seq in primary medulloblastoma T3


title: T2_INPUT

source_name: INPUT ChIP-seq in primary medulloblastoma T2


title: T2_H3K27m3

source_name: H3K27m3 ChIP-seq in primary medulloblastoma T2


title: T3_H3K4m3

source_name: H3K4m3 ChIP-seq in primary medulloblastoma T3


title: DHT + Enzalutamide [PEH0005436]

city: North Chicago

first: Xin

last: Lu

state: IL

address: 1 North Waukegan Rd

department: Oncology Discovery

institute: Abbvie

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Human Genome U133 Plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Genechip Scanner 3000

data_processing: Background subtraction, normalization and gene expression index calculation were performed using Rosetta Resolver software

source_name: steroid starved LNCaP-FGC cells pretreated with 3 mM Enzalutamide for 45 minutes, followed by 5 nM DHT 24 hrs

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200 ng total RNA (using Affymetrix 3' IVT Plus amplification kit).

growth_protocol: Cells were cultured in phenol-red free RPMI supplemented with 7.5% charcoal stripped FBS for 3 days. for an additional 24 hrs.

extract_protocol: Qiazol extraction of total RNA followed by Qiagen Rneasy purification was performed according to the manufacturer's instructions.

treatment_protocol: Inhibitor or DMSO vehicle pretreatment for 45 minutes, followed by direct addition of 5 nM DHT or EtOH vehicle control for 24 hrs. The media was removed by aspiration, cells were washed 2x with PBS and cells were lysed by the direct addition of trizol.

value: LNCaP-FGC prostate adenocarcinoma cancer cell line


title: DHT  [PEH0005434]

source_name: steroid starved LNCaP-FGC cells pretreated with vehicle for 45 minutes, followed by 5 nM DHT 24 hrs


title: DHT + ABBV-075 (20 nM) [PEH0005440]

source_name: steroid starved LNCaP-FGC cells pretreated with 0.02 mM ABBV-075 for 45 minutes, followed by 5 nM DHT 24 hrs


title: DHT  [PEH0005433]


title: DHT + ABBV-075 (60 nM) [PEH0005438]

source_name: steroid starved LNCaP-FGC cells pretreated with 0.06 mM ABBV-075 for 45 minutes, followed by 5 nM DHT 24 hrs


title: DHT + ABBV-075 (6 nM) [PEH0005442]

source_name: steroid starved LNCaP-FGC cells pretreated with 0.006 mM ABBV-075 for 45 minutes, followed by 5 nM DHT 24 hrs


title: T2_H3K4m1

source_name: H3K4m1 ChIP-seq in primary medulloblastoma T2


title: T1_H3K27m3

source_name: H3K27m3 ChIP-seq in primary medulloblastoma T1


title: T3_H3K27ac

source_name: H3K27ac ChIP-seq in primary medulloblastoma T3


title: T1_H3K4m3

source_name: H3K4m3 ChIP-seq in primary medulloblastoma T1


title: unstimulated (EtOH vehicle control) [PEH0005437]

source_name: steroid starved LNCaP-FGC cells pretreated with vehicle for 45 minutes, followed by EtOH (DHT vehicle control) 24 hrs


title: unstimulated (EtOH vehicle control) [PEH0005435]


title: T2_H3K27ac

source_name: H3K27ac ChIP-seq in primary medulloblastoma T2


title: T3_INPUT

source_name: INPUT ChIP-seq in primary medulloblastoma T3


title: T3_H3K27m3

source_name: H3K27m3 ChIP-seq in primary medulloblastoma T3


title: T1_INPUT

source_name: INPUT ChIP-seq in primary medulloblastoma T1


title: RBD 5484

source_name: Liver; Wildlife collection


title: 0GyU4/ reference male mouse4

value: tail

source_name: reference male mouse4


title: reference male mouse4/ 0GyU5


title: 0GyU5/ reference male mouse4


title: RBD 5657


title: T1_H3K4m1

source_name: H3K4m1 ChIP-seq in primary medulloblastoma T1


title: pseudarthrosis tissue from Individual 4

city: Salt Lake City

first: Rebecca

last: Margraf

state: UT

address: 500 Chipeta Way

institute: ARUP

hyb_protocol: As per manufacturer (Affymetrix, cytoscan HD)

data_processing: Affymetrix CHAS software (Chromosome Analysis suite) - NetAffxGenomicAnnotations Browser annotation database file version 32.3

source_name: pseudarthrosis tissue from Individual 4

extract_protocol: DNA was extracted from peripheral blood Qiagen Puregene DNA Extraction kit. DNA was extracted from frozen tissue taken from the pseudarthosis site (after mechanical sheraring) with the PerkinElmer Chemagic Tissue 10 kit.

value: pseudarthrosis tissue


title: peripheral blood from Individual 4

scan_protocol: As per manufacturer (Affymetrix, cytoscan HD)

source_name: peripheral blood from Individual 4

value: peripheral blood


title: pseudarthrosis tissue from Individual 2

source_name: pseudarthrosis tissue from Individual 2

label_protocol: As per manufacturer (Affymetrix, cytoscan HD)


title: 0GyU1/ reference male mouse4


title: 0GyU2/ reference male mouse4


title: pseudarthrosis tissue from Individual 1

source_name: pseudarthrosis tissue from Individual 1


title: 0GyUF/ reference male mouse4


title: reference male mouse4/ 0GyUF


title: 0GyUM/ reference male mouse4


title: T2_H3K4m3

source_name: H3K4m3 ChIP-seq in primary medulloblastoma T2


title: reference male mouse4/ 0GyU2


title: reference male mouse4/ 0GyUM


title: reference male mouse12/ 0GyL6

source_name: reference male mouse12


title: reference male mouse12/ 0GyL5


title: 0GyL6/ reference male mouse12


title: 0GyL5/ reference male mouse12


title: reference male mouse4/ 0GyU1


title: Infiltrating Ductal Carcinima of breast

city: Houston

first: Liuqing

last: Yang

state: Texas

address: 1515 Holcombe Blvd.

department: Molecular and Cellular Oncology

institute: The University of Texas MD Anderson Cancer Center

description: Lipid-bound lncRNAs in breast cancer tissue of patient 1

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

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.0 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 2 out of 4 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs were identified through Fold Change filtering between two samples. Hierarchical Clustering was performed using the Agilent GeneSpring GX software (version 12.0). GO analysis and Pathway analysis were performed in the standard enrichment computation method.

source_name: Breast tissue, fresh frozen_cancer

label_protocol: Sample labeling was performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method. The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: Total lipid fractions were first isolated from from human breast cancers and their matched adjacent normal tissues using Barocycler NEP3229 (Pressure Biosciences Inc.). The lipid-asscociated RNAs were further extracted using TRIzol® Plus RNA Purification Kit (Life Technologies, Grand Island NY) following the manufacturer's recommendations. RNA quantity and quality were measured by NanoDrop ND-2000 and RNA integrity was assessed by Bioanalyzer.

value: Breast

value: Female


title: P-CC8-A-g093-pop-DNA

city: Seattle

first: Maitreya

middle: J.

last: Dunham

state: WA

address: Foege Building, S403B, Box 355065

department: Genome Sciences

institute: University of Washington

hyb_protocol: reference URL : http://dunham.gs.washington.edu/MDhomemadeDNA.pdf

scan_protocol: Pixel Size : 5 Scan Date : 2007-11-21 Scan Time : 11:20:11 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 5.1.0.10
Datafile type : GenePix Results 3
Image Origin : 0, 0

organism: Saccharomyces cerevisiae

extract_protocol:
Extracted molecule : Genomic DNA
Extraction method : Hoffman-Winston prep http://dunham.gs.washington.edu/UWyeastDNAprep.pdf

value: ancestral S. cerevisiae strain

value: evolved S. cerevisiae strain


title: P-BB-2N-B-g211-pop-DNA

scan_protocol: Pixel Size : 5 Scan Date : 2007-11-21 Scan Time : 10:43:44 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

organism: Saccharomyces uvarum

source_name: BB

label_protocol: reference URL : http://dunham.gs.washington.edu/MDhomemadeDNA.pdf

value: ancestral S. uvarum strain

value: evolved S. uvarum strain


title: 0GyU3/ reference male mouse4


title: Normal adjacent breast tissue

description: Lipid-bound lncRNAs in normal adjacent breast tissue of patient 1

source_name: Breast tissue, fresh frozen_normal_adjacent


title: 0GyL4/ reference male mouse12


title: reference male mouse12/ 0GyL4


title: NS_d0_2

first: Jianlong

last: Wang

department: Department of Medicine

institute: Columbia University Irving Medical Center

description: Nanog + Sin3a Day 0, rep2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Raw data were processed and normalized using quantile normalisation by GenomeStudio (Illumina, GSGX Version 1.9.0) Gene Expression software

label: Biotin

source_name: pre-iPSCs in somatic cell reprogramming

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: Female neural stem cell (NSC)-derived pre-iPSCs containing an Oct4-GFP-IRES-puro reporter were generated and used for reprogramming. Briefly, pre-iPSCs maintained in standard mESC (“serum + LIF”) culture medium [DMEM high glucose (Gibco), 15% heat inactivated FBS (Corning), Pen/Strep (Gibco), Nucleoside mix (Sigma), L-glutamine (Gibco), MEM Non-essential amino acids (Gibco), β-mercaptoethanol (0.1 mM), and recombinant LIF (20 ng/mL)] on gelatinized cell culture dishes.

extract_protocol: Total RNA was isolated using the RNeasy kit (#74136, Qiagen) according to manufacturer’s instructions.

treatment_protocol: Pre-iPSCs were stably transfected with combinations of PiggyBac-CAG (PB) transposon vectors along with PB transposase (PBase) in a 1:2 PB:PBase ratio. Transfections for pre-iPSCs were performed in suspension using 1 μL of Lipofectamine 2000 transfection reagent (Invitrogen) per μg of transfected DNA. 24 hours after transfection, stable line selection began with 200-250 μg/mL hygromycin (“Hygro”) and/or 10-20 μg/mL blasticidin S (“Blast”) for 5-7 days, with passaging of cells at least once during drug selection. For pre-iPSC reprogramming, 1.0 x 104 or 2.0 x 104 pre-iPSCs were seeded after selection onto gelatin-coated 12-well plates and grown in serum + LIF for 2 days before medium switch to serum-free, N2B27 medium [DMEM/F12 (Gibco) and Neurobasal (Gibco) media were used in a 1:1 ratio, N2 supplement (Gibco), B27 supplement (Gibco), L-glutamine (Gibco), Pen/Strep (Gibco), and β-mercaptoethanol (0.1 mM)] supplemented with recombinant LIF (20 ng/mL), MEK inhibitor (PD325901; 1 μM final), and GSK3β inhibitor (CHIR99021; 3 μM final) (“2i + LIF” medium).

tag: ectopic gene

tag: reprogramming time


title: EE_d0_1

description: EV + EV Day 0, rep1

value: Empty Vector


title: NE_d0_2

description: Nanog + EV Day 0, rep2

value: Nanog


title: 0GyL3/ reference male mouse12


title: SE_d0_1

description: Sin3a + EV Day 0, rep1


title: SE_d0_2

description: Sin3a + EV Day 0, rep2


title: 0GyL2/ reference male mouse12


title: NS_d0_1

description: Nanog + Sin3a Day 0, rep1


title: NE_d0_1

description: Nanog + EV Day 0, rep1


title: EE_d0_2

description: EV + EV Day 0, rep2


title: reference male mouse12/ 0GyL1


title: reference male mouse12/ 0GyL2


title: 0GyL1/ reference male mouse12


title: MRC5VA shASCC3 long UV rep3

city: London

first: Laura

last: Williamson

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

hyb_protocol: Whole-Gene Expression Direct Hybridization Assay #11286340.

scan_protocol: Illumina iScanner using Standard Illumina scanning protocol 2011.

data_processing: The data were preprocessed using Illumina® GenomeStudio V2011. They were then VST transformed and quantile normalised using the Lumi package from Bioconductor.

source_name: shASCC3 long cells, UV treated, 20 hr

label_protocol: Illumina TotalPrep-96 RNA amplification kit Ambion #4393543 to generate biotin-labelled cRNA probes.

growth_protocol: DMEM + 10% FBS + pen/strep, 37 C, 5% CO2.

extract_protocol: RNeasy Kit (Qiagen).

treatment_protocol: UVC irradiation, 20 hours recovery.

tag: shRNA

value: ASCC3 long isoform

tag: treatment

value: UVC irradiated

tag: time

value: 20 hours

tag: cell line derivation

value: normal lung fibroblasts


title: 0GyLF/ reference male mouse12

tag: tissue


title: D-BC3-A-g125-pop-DNA

scan_protocol: Pixel Size : 5 Scan Date : 2005-07-05 Scan Time : 11:24:20 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

organism: Saccharomyces cerevisiae x Saccharomyces uvarum

value: ancestral hybrid strain

value: evolved hybrid strain


title: MRC5VA shASCC3 long UN rep3

source_name: shASCC3 long cells, untreated

tag: cell line

value: Untreated

value: 0 hours


title: MRC5VA shASCC3 long UV rep2


title: MRC5VA shASCC3 long UN rep1


title: MRC5VA shASCC3 long UV rep1


title: MRC5VA shSCR UV rep3

source_name: shNon-targeting cells, UV treated, 20 hr

value: non-targeting control


title: D-BC4-B-g124-pop-DNA

scan_protocol: Pixel Size : 5 Scan Date : 2005-07-05 Scan Time : 12:14:04 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: MRC5VA KO short UV rep3

source_name: ASCC3 short KO cells, UV treated, 20 hr

tag: genotype/variation

value: ASCC3 short isoform knockout


title: reference male mouse12/ 0GyLM

tag: strain

value: tail


title: MRC5VA KO short UV rep2


title: MRC5VA shASCC3 long UN rep2


title: D-BC4-A-g100-pop-DNA

scan_protocol: Scan Power : 100 PMT Volts : 490 Pixel Size : 5 Laser on time : 4646 Laser Power : 2.51 Scan Date : 2005-07-16 Scan Temperature : 26.38 Scan Time : 22:03:23 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4200A 01 [111967] Scanning software : AxImageIO Scanning software version : 2.0.3.1 Focus Position : 0

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 5.1.0.10
Datafile type : GenePix Results 3
Image Origin : 1080, 3880


title: D-BB-2N-B-g486-pop-DNA

scan_protocol: Scan Power : 100 PMT Volts : 490 Pixel Size : 5 Laser on time : 4580 Laser Power : 2.47 Scan Date : 2005-07-16 Scan Temperature : 26.13 Scan Time : 20:56:26 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4200A 01 [111967] Scanning software : AxImageIO Scanning software version : 2.0.3.1 Focus Position : 0


title: reference male mouse12/ 0GyLF


title: MRC5VA shSCR UN rep3

source_name: shNon-targeting cells, untreated


title: MRC5VA shSCR UV rep1


title: 0GyLM/ reference male mouse12


title: MRC5VA shSCR UV rep2


title: MRC5VA shSCR UN rep1


title: MRC5VA KO short UN rep3

source_name: ASCC3 short KO cells, untreated


title: MRC5VA shSCR UN rep2


title: MRC5VA KO short UV rep1


title: T1_H3K27ac

source_name: H3K27ac ChIP-seq in primary medulloblastoma T1

value: primary medulloblastoma

value: primary tissue


title: MRC5VA KO short UN rep2


title: D-BB-2N-A-g468-pop-DNA

scan_protocol: Scan Power : 100 PMT Volts : 490 Pixel Size : 5 Laser on time : 4595 Laser Power : 2.49 Scan Date : 2005-07-16 Scan Temperature : 26.13 Scan Time : 21:12:09 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4200A 01 [111967] Scanning software : AxImageIO Scanning software version : 2.0.3.1 Focus Position : 0

value: ancestral S. uvarum strain


title: reference male mouse11/ 0GyS2

source_name: reference male mouse11


title: reference male mouse4/ 0GyU3

source_name: reference male mouse4


title: MRC5VA WT UV rep3

source_name: Parental cells, UV treated, 20 hr

value: WT


title: reference male mouse11/ 0GySF


title: 0GySM/ reference male mouse11


title: reference male mouse11/ 0GyS5


title: reference male mouse4/ 0GyU4


title: 0GySF/ reference male mouse11


title: 0GyS2/ reference male mouse11


title: 0GyS1/ reference male mouse11


title: MRC5VA WT UV rep2


title: MRC5VA KO short UN rep1


title: MRC5VA WT UN rep2

source_name: Parental cells, untreated


title: reference male mouse11/ 0GySM


title: reference male mouse11/ 0GyS1


title: MRC5VA WT UN rep1


title: 0GyS3/ reference male mouse11


title: reference male mouse11/ 0GyS6


title: MRC5VA WT UN rep3


title: 0GyS4/ reference male mouse11


title: reference male mouse11/ 0GyT5


title: 0GyS5/ reference male mouse11


title: reference male mouse11/ 0GyS3


title: reference male mouse11/ 0GyS4


title: MRC5VA WT UV rep1


title: 0GyS6/ reference male mouse11


title: 0GyT5/ reference male mouse11


title: OT-I Fasbp4/5 dKO skin infiltrating cells 10 days post infection

first: Youdong

last: Pan

address: 77 Avenue Louis Pasteur

department: Dermatology

institute: Harvard Medical School

description:
Gene expression data
113_2215M

hyb_protocol: Following fragmentation, 4.1 ug of cDNA were hybridized for 16 hr at 45 C on GeneChip Mouse 2.0 ST Array in an Affymetrix GeneChip Hybridization Oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G running Affymetrix Gene Command Console ver 3.2.

data_processing: The data were analyzed with using Affymetrix Expression Console ver 1.3.0.187 using Analysis algorithm RMA.

source_name: OT-I Fabp4/5 dKO skin infiltrating T cells were sorted from infected skin sites of mice 10 days post infected with VACV-Ova

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 33.5 ng total RNA using amplification kit Nugen Ovation Pico WTA, Lot # 1408175A, followed by labeling 5 ug cDNA using kit Encore Biotin Module, Lot # 1409115-A.

growth_protocol: OT-I naïve WT or Fabp4/5 dKO T cells were sorted from naïve OT-I Thy1.1+ Rag1-/- mice and adoptively transferred into cognate recipient mice one day before infection

extract_protocol: RNA was extracted with an RNeasy Micro kit (74004; Qiagen). RNA quality and quantity was assessed with a Bioanalyzer 2100 (Agilent).

treatment_protocol: Mice was infected with 2 × 10^6 p.f.u. of VACV-Ova by skin scarification

tag: infection

value: VACV-Ova

value: 10 days post VACV-Ova infection

tag: cell type

value: spleen


title: OT-I Fasbp4/5 dKO skin infiltrating cells 30 days post infection

description:
Gene expression data
114_2215N

source_name: OT-I Fabp4/5 dKO skin infiltrating T cells were sorted from infected skin sites of mice 30 days post infected with VACV-Ova

value: 30 days post VACV-Ova infection


title: reference male mouse12/ 0GyL3

scan_protocol: Scanned on an Agilent G2565BA scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.1.1).

source_name: reference male mouse12


title: 0GyT4/ reference male mouse11


title: S-CC9-B-g178-pop-DNA

scan_protocol: Pixel Size : 5 Scan Date : 2006-12-20 Scan Time : 15:05:15 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

value: ancestral S. cerevisiae strain

value: evolved S. cerevisiae strain


title: P-BC4-B-g100-pop-DNA

scan_protocol: Pixel Size : 5 Scan Date : 2007-01-26 Scan Time : 10:44:41 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

value: ancestral hybrid strain


title: P-BC4-A-g105-pop-DNA

scan_protocol: Pixel Size : 5 Scan Date : 2007-01-26 Scan Time : 10:23:14 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

value: evolved hybrid strain


title: OT-I skin infiltrating cells 90 days post infection

description:
Gene expression data
112_2215L

source_name: OT-I skin infiltrating T cells were sorted from infected skin sites of mice 90 days post infected with VACV-Ova

value: 90 days post VACV-Ova infection

value: OT-I skin infiltrating T cells


title: OT-I skin infiltrating cells 45 days post infection

description:
Gene expression data
111_2215J

source_name: OT-I skin infiltrating T cells were sorted from infected skin sites of mice 45 days post infected with VACV-Ova

value: 45 days post VACV-Ova infection


title: P-BC3-B-g167-pop-DNA

scan_protocol: Pixel Size : 5 Scan Date : 2006-12-29 Scan Time : 13:48:28 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1


title: reference male mouse11/ 0GyT3


title: P-BC3-C-g103-pop-DNA

scan_protocol: Pixel Size : 5 Scan Date : 2007-01-26 Scan Time : 09:53:17 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1


title: 0GyT3/ reference male mouse11


title: S-CC8-B-g170-pop-DNA

description: probably population (originally not labeled)

scan_protocol: Pixel Size : 5 Scan Date : 2006-12-29 Scan Time : 14:50:38 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1


title: OT-I skin infiltrating cells 5 days post infection

description:
Gene expression data
104_2215D

source_name: OT-I skin infiltrating T cells were sorted from infected skin sites of mice 5 days post infected with VACV-Ova

value: 5 days post VACV-Ova infection


title: reference male mouse11/ 0GyT1

value: tail


title: OT-I skin infiltrating cells 60 days post infection

description:
Gene expression data
113_2215K

source_name: OT-I skin infiltrating T cells were sorted from infected skin sites of mice 60 days post infected with VACV-Ova

value: 60 days post VACV-Ova infection


title: OT-I skin infiltrating cells 20 days post infection

description:
Gene expression data
107_2215G

source_name: OT-I skin infiltrating T cells were sorted from infected skin sites of mice 20 days post infected with VACV-Ova

value: 20 days post VACV-Ova infection


title: P-BC3-A-g099-pop-DNA

scan_protocol: Pixel Size : 5 Scan Date : 2006-12-29 Scan Time : 14:07:26 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1


title: 0GyT1/ reference male mouse11


title: P-CC8-B-g140-pop-DNA

scan_protocol: Pixel Size : 5 Scan Date : 2006-12-29 Scan Time : 14:18:53 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1


title: OT-I skin infiltrating cells 15 days post infection

description:
Gene expression data
106_2215F

source_name: OT-I skin infiltrating T cells were sorted from infected skin sites of mice 15 days post infected with VACV-Ova

value: 15 days post VACV-Ova infection


title: P-CC9-B-g137-pop-DNA

scan_protocol: Pixel Size : 5 Scan Date : 2007-01-26 Scan Time : 10:33:58 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1


title: OT-I skin infiltrating cells 10 days post infection

description:
Gene expression data
105_2215E

source_name: OT-I skin infiltrating T cells were sorted from infected skin sites of mice 10 days post infected with VACV-Ova


title: reference male mouse11/ 0GyT4


title: OT-I Effector memory T cells

description:
Gene expression data
103_2215C

source_name: OT-I effector memory T cells were sorted from spleen of mice 30 days post infected with VACV-Ova

value: OT-I effector memory T cells


title: 0GyTF/ reference male mouse11


title: P-BB-2N-A-g229-pop-DNA

scan_protocol: Pixel Size : 5 Scan Date : 2006-12-20 Scan Time : 15:24:15 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: BB

value: ancestral S. uvarum strain

value: evolved S. uvarum strain


title: reference male mouse11/ 0GyT2


title: 0GyT2/ reference male mouse11


title: OT-I skin infiltrating cells 25 days post infection

description:
Gene expression data
108_2215H

source_name: OT-I skin infiltrating T cells were sorted from infected skin sites of mice 25 days post infected with VACV-Ova

value: VACV-Ova

value: 25 days post VACV-Ova infection

value: spleen


title: OT-I skin infiltrating cells 30 days post infection

description:
Gene expression data
110_2215I

source_name: OT-I skin infiltrating T cells were sorted from infected skin sites of mice 30 days post infected with VACV-Ova

value: 30 days post VACV-Ova infection


title: D-CC9-A-g157-pop-DNA

scan_protocol: Pixel Size : 5 Scan Date : 2006-12-20 Scan Time : 14:44:06 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

value: ancestral S. cerevisiae strain

value: evolved S. cerevisiae strain


title: reference male mouse11/ 0GyTM

source_name: reference male mouse11


title: P-CC9-A-g090-pop-DNA

scan_protocol: Pixel Size : 5 Scan Date : 2006-12-20 Scan Time : 15:14:44 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1


title: reference male mouse11/ 0GyTF


title: OT-I Naïve T cells

description:
Gene expression data
101_2215A

source_name: OT-I T cells were sorted from spleen of naïve OT-I mice

value: OT-I naïve T cells