title: microglia-CV-KO-mouse 2

city: Saint Louis

first: Marco

last: Colonna

state: Missouri

address: 660 S Euclid Ave

institute: Washington University in St. Louis

description: Gene expression of sorted microglia from 8.5 month old 5XFAD mice

hyb_protocol: Samples are prepared using a Nugen Ovation Pico SL kit.

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

data_processing: Data were analyzed using GenePattern (Broad Institute)

label: Biotin

source_name: sorted microglia from 8.5 month old mice, CV-KO

label_protocol: Biotinylated cRNA were prepared using a Nugen Encore Biotin kit from 2 ng total RNA.

growth_protocol: 8.5 month old 5XFAD mice

extract_protocol: Cells were sorted directly into RLT buffer (Qiagen). A Rneasy micro kit (Qiagen) was used for subsquent RNA extraction.

treatment_protocol: Brains were harvested from PBS perfused animal. Single cell suspension was made using a neuronal tissue dissociation kit (Miltenyi). Microglia were then purified using FACS.

tag: disease model

value: 5XFAD mouse model of AD

tag: genotype

value: CV

tag: Sex

value: Male

value: CD45+ CD11b+ microglia

tag: age

value: 8.5 months old


title: MM001_Mouse_4_MERS_10e5_Day_4_1-27-2017

status: Public on Dec 29 2017

type: RNA

city: Richland

first: Natalie

last: Heller

address: 902 Battelle Blvd.

country: USA

institute: PNNL

hyb_protocol: Hybridization was performed according to Agilent One-Color Microarray-Based Gene Expression Analysis Protocol (Agilent Technology). 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. 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60 °C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100μl of hybridization solution was dispensed into the gasket slide and assembled to the gene 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: Scanned images were analyzed using Agilent Feature Extraction Software (v11.0.1.1). The limma package for R (available on Bioconductor) was used to perform background correction, quantile normalization (normalizeBetweenArrays), and summarization (avereps) to derive a single normalized intensity value per probe. Outlier samples were detected using PCA and by visual inspection of heatmaps, and all data was re-processed after removing outlier samples. All data processing for each of the biological replicates was performed independently of the other.

molecule: total RNA

organism: Mus musculus

source_name: Mouse lung cells, MERS-CoV-inoculated, 10e5 dose, 4 day, bioreplicate 4

label_protocol: Total RNA was labeled according to Agilent’s Quick Amp Labeling protocol as part of the Agilent One-Color Microarray-Based Gene Expression Analysis Protocol (Agilent Technology). Total RNA from each sample was linearly amplified and labeled with Cy3-UTP.

extract_protocol:
MERSCOV004.0P
plaque assay protocol: MERSCOV005.0P

treatment_protocol: MERSCOV004.0P: Cells were infected with a multiplicity of infection of 3 PFU.

tag: tissue

value: Mouse lung cells

tag: time

tag: virus


title: MM001_Mouse_2_MERS_10e5_Day_4_1-27-2017

source_name: Mouse lung cells, MERS-CoV-inoculated, 10e5 dose, 4 day, bioreplicate 2


title: MM001_Mouse_1_MERS_10e5_Day_4_1-27-2017

source_name: Mouse lung cells, MERS-CoV-inoculated, 10e5 dose, 4 day, bioreplicate 1


title: MM001_Mouse_3_MERS_10e5_Day_2_1-25-2017

source_name: Mouse lung cells, MERS-CoV-inoculated, 10e5 dose, 2 day, bioreplicate 3


title: microglia-CV-KO-mouse 1

value: Female

tag: cell type


title: microglia-R47H-KO-mouse 3

source_name: sorted microglia from 8.5 month old mice, R47H-KO


title: microglia-CV-KO-mouse 3


title: MM001_Mouse_2_MERS_10e5_Day_2_1-25-2017

source_name: Mouse lung cells, MERS-CoV-inoculated, 10e5 dose, 2 day, bioreplicate 2


title: microglia-R47H-KO-mouse 1


title: MM001_Mouse_1_MERS_10e5_Day_2_1-25-2017

source_name: Mouse lung cells, MERS-CoV-inoculated, 10e5 dose, 2 day, bioreplicate 1


title: microglia-R47H-KO-mouse 2


title: microglia-KO-mouse 3

source_name: sorted microglia from 8.5 month old mice, KO

value: KO


title: MM001_Mouse_4_MERS_10e5_Day_2_1-25-2017

source_name: Mouse lung cells, MERS-CoV-inoculated, 10e5 dose, 2 day, bioreplicate 4


title: MM001_Mouse_3_MERS_10e4_Day_7_1-30-2017

source_name: Mouse lung cells, MERS-CoV-inoculated, 10e4 dose, 7 day, bioreplicate 3


title: ELBW30

city: Birmingham

first: Charitharth

last: Lal

state: AL

address: 619 South 19th Street

institute: University of Alabama at Birmingham

description: as per nanostring protocol

hyb_protocol: Detailed methodology can be found in company website at www.nanostring.com

data_processing: Software used for analysis in nSolver Analysis Software version 2.5 by Nanostring Technologies.

label: DEPC

organism: Homo sapiens

source_name: Tracheal Aspirate

tag: cohort

value: Validation

value: AT BIRTH


title: ELBW27

description: as per nanostring protocol

scan_protocol: Detailed methodology can be found in company website at www.nanostring.com


title: ELBW29

description: as per nanostring protocol

label_protocol: Detailed methodology can be found in company website at www.nanostring.com


title: MM001_Mouse_4_MERS_10e4_Day_7_1-30-2017

source_name: Mouse lung cells, MERS-CoV-inoculated, 10e4 dose, 7 day, bioreplicate 4


title: microglia-KO-mouse 1


title: ELBW26

description: as per nanostring protocol

extract_protocol: Detailed methodology can be found in company website at www.nanostring.com


title: MM001_Mouse_2_MERS_10e4_Day_7_1-30-2017

source_name: Mouse lung cells, MERS-CoV-inoculated, 10e4 dose, 7 day, bioreplicate 2


title: ELBW28

description: as per nanostring protocol


title: MM001_Mouse_1_MERS_10e4_Day_7_1-30-2017

source_name: Mouse lung cells, MERS-CoV-inoculated, 10e4 dose, 7 day, bioreplicate 1


title: meningioma sample: Jed88_MN

city: Jeddah

first: Hans-Juergen

last: Schulten

department: Center of Excellence in Genomic Medicine Research

country: Saudi Arabia

institute: King Abdulaziz University

hyb_protocol: Following fragmentation, 6 ug of cDNA were hybridized for 17 hr at 45C on GeneChip HuGene-1.0-st arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: Data were generated using the Affymetrix Expression Console Software using Affymetrix default analysis settings.

label: biotin

source_name: brain tumor tissue

label_protocol: Biotinylated cRNAs were prepared according to the standard Affymetrix protocol from 250 ng total RNA

extract_protocol: Total RNA from biospecimens was extracted using the Quagen RNeasy mini kit according to the manufacturer's instructions and integrity of RNA was checked by using the Agilent Bioanalyzer.

value: brain tumor

tag: histology

value: secretory

tag: grade

value: grade I

tag: gender

value: M


title: meningioma sample: Jed103_MN

value: fibroblastic

value: F


title: meningioma sample: Jed101_MN

value: malignant

value: grade 3


title: meningioma sample: Jed85_MN

value: meningiothelial


title: MM001_Mouse_4_MERS_10e4_Day_4_2017

source_name: Mouse lung cells, MERS-CoV-inoculated, 10e4 dose, 4 day, bioreplicate 4


title: meningioma sample: Jed61_MN


title: meningioma sample: Jed75_MN


title: ELBW25

description: as per nanostring protocol


title: meningioma sample: Jed64_MN


title: meningioma sample: Jed92_MN

value: meningothelial


title: MM001_Mouse_3_MERS_10e4_Day_4_2017

source_name: Mouse lung cells, MERS-CoV-inoculated, 10e4 dose, 4 day, bioreplicate 3


title: ELBW23

description: as per nanostring protocol


title: meningioma sample: Jed58_MN

value: atypical

value: grade 2


title: microglia-KO-mouse 2

value: 5XFAD mouse model of AD

value: Male

value: CD45+ CD11b+ microglia

value: 8.5 months old


title: meningioma sample: Jed91_MN


title: MM001_Mouse_2_MERS_10e4_Day_4_1-27-2017

source_name: Mouse lung cells, MERS-CoV-inoculated, 10e4 dose, 4 day, bioreplicate 2

value: Mouse lung cells


title: meningioma sample: Jed40_MN

value: brain tumor

value: transitional


title: ELBW22

description: as per nanostring protocol

value: Validation

value: AT BIRTH


title: ELBW24

description: as per nanostring protocol


title: meningioma sample: Jed53_MN

value: transitional, with brain invasion


title: ELBW19

description: as per nanostring protocol


title: BCBM sample: Jed89_MT

source_name: breast cancer brain metastasis tissue

value: breast cancer brain metastasis

value: IDC

value: brain metastasis, grade 3

value: F

tag: age (years)

tag: her2 ihc status

value: HER2 1+


title: MM001_Mouse_3_MERS_10e4_Day_2_1-25-2017

source_name: Mouse lung cells, MERS-CoV-inoculated, 10e4 dose, 2 day, bioreplicate 3


title: ELBW20

description: as per nanostring protocol


title: ELBW18

description: as per nanostring protocol

value: Discovery


title: meningioma sample: Jed57_MN

value: grade I


title: MM001_Mouse_1_MERS_10e4_Day_4_1-27-2017

source_name: Mouse lung cells, MERS-CoV-inoculated, 10e4 dose, 4 day, bioreplicate 1


title: meningioma sample: Jed26_MN

value: meningiothelial

value: M


title: meningioma sample: Jed13_MN


title: meningioma sample: Jed04_MN


title: BC sample: TM-2607-10R

source_name: breast tumor tissue

value: grade 2/3


title: MM001_Mouse_1_MERS_10e4_Day_2_1-25-2017

source_name: Mouse lung cells, MERS-CoV-inoculated, 10e4 dose, 2 day, bioreplicate 1


title: BC sample: TM-2047-10R

value: grade 3

value: HER2 0


title: BC sample: TM-312-09R

value: mixed

value: grade 1

value: HER2 3+


title: ELBW21

description: as per nanostring protocol

value: Validation

value: AT BIRTH


title: ELBW17

description: as per nanostring protocol


title: BC sample: TM-1182-09R

value: grade NA


title: BCBM sample: Jed82_MT

value: breast cancer brain metastasis

value: IDC


title: BCBM sample: Jed81_MT

value: brain metastasis, grade 3

value: F


title: BC sample: TM-2195-10R

value: HER2 1+


title: BC sample: TM-260-10R


title: MM001_Mouse_4_MERS_10e4_Day_2_1-25-2017

source_name: Mouse lung cells, MERS-CoV-inoculated, 10e4 dose, 2 day, bioreplicate 4

value: Mouse lung cells


title: BC sample: TM-2080-10R


title: MM001_Mouse_2_MERS_10e4_Day_2_1-25-2017

source_name: Mouse lung cells, MERS-CoV-inoculated, 10e4 dose, 2 day, bioreplicate 2


title: ELBW16

description: as per nanostring protocol

value: Discovery


title: BC sample: TM-249-08R


title: ELBW15

description: as per nanostring protocol


title: ELBW11

description: as per nanostring protocol


title: ELBW13

description: as per nanostring protocol


title: ELBW9

description: as per nanostring protocol


title: ELBW12

description: as per nanostring protocol


title: ELBW7

description: as per nanostring protocol


title: BC sample: TM-316-10R


title: ELBW8

description: as per nanostring protocol


title: BC sample: TM-159-09R

value: grade 2


title: ELBW10

description: as per nanostring protocol


title: ELBW5

description: as per nanostring protocol


title: ELBW4

description: as per nanostring protocol


title: ELBW6

description: as per nanostring protocol


title: BC sample: TM-012-10R


title: ELBW3

description: as per nanostring protocol


title: BC sample: TM-125-08R


title: BC sample: TM-236-08R

value: ILC


title: BC sample: TM-151-09R


title: ELBW2

description: as per nanostring protocol


title: ELBW1

description: as per nanostring protocol


title: BC sample: TM-019-10R

value: grade 3


title: BC sample: TM-014-09R

value: HER2 2+


title: ELBW14

description: as per nanostring protocol


title: Thailand3

status: Public on Dec 28 2017

type: genomic

city: Baltimore

first: Shannon

last: Takala-Harrison

state: MD

address: 685 W Baltimore St

department: Division of Malaria Research

institute: Institute for Global Health, University of Maryland School of Medicine

hyb_protocol: Described by previous publication (PMCID:PMC4153902)

scan_protocol: Arrays were scanned on a NimbleGen MS 200 scanner using autogain setting per manufacture's protocol (www.nimblegen.com)

data_processing: Data were processed by both a previously published method (PMCID:PMC3218861) and by a custom algorithm (PMCID:PMC4153902)

molecule: genomic DNA

organism: Plasmodium falciparum

source_name: clinical isolate

extract_protocol: All samples were extracted using a Qiagen blood extraction mini prep (qiagen.com)

tag: province

value: Kanchanaburi

tag: country

value: Thailand


title: Thailand7

label_protocol: Described by previous publication (PMCID:PMC4153902)


title: Thailand8


title: Thailand1


title: Cambodia174

value: Preah Sihanouk

value: Cambodia


title: Thailand5


title: Cambodia175

value: Oddar Meanchey


title: Thailand4


title: Thailand2


title: Cambodia172

value: Kampot


title: Cambodia173


title: Thailand6


title: Cambodia159

value: Preah Vihear


title: Cambodia154


title: Cambodia160


title: Cambodia168


title: Cambodia166


title: Cambodia158


title: Cambodia167


title: Cambodia165


title: Cambodia162


title: Cambodia157


title: Cambodia170


title: Cambodia171


title: Cambodia155


title: Cambodia164


title: Cambodia161


title: Cambodia156


title: Cambodia163


title: Cambodia169

value: Koh Kong


title: Cambodia147


title: Cambodia150


title: Cambodia144


title: Cambodia142


title: Cambodia153


title: Cambodia149


title: Cambodia141


title: Cambodia136


title: Cambodia138


title: Cambodia148


title: Cambodia145


title: Cambodia135

value: Pailin


title: Cambodia137


title: Cambodia146


title: Cambodia151


title: Cambodia152


title: Cambodia143


title: Cambodia140


title: Cambodia139


title: Cambodia131


title: Cambodia134


title: Cambodia129


title: Cambodia123


title: Cambodia127


title: Cambodia128


title: Cambodia132


title: Cambodia130


title: Cambodia126


title: Cambodia124


title: Cambodia122


title: Cambodia117

value: Kampong Speu


title: Cambodia133


title: Cambodia121


title: Cambodia120


title: Cambodia115


title: Cambodia113


title: Cambodia107


title: Cambodia106


title: Cambodia112


title: Cambodia110


title: Cambodia125


title: Cambodia119


title: Cambodia109


title: Cambodia118


title: Cambodia105


title: Cambodia111


title: Cambodia108


title: Cambodia116


title: Cambodia114


title: Cambodia104


title: Cambodia102


title: Cambodia101


title: Cambodia100


title: Cambodia103


title: Cambodia95


title: Cambodia98


title: Cambodia93


title: Cambodia96


title: Cambodia97


title: Cambodia99


title: Cambodia88


title: Cambodia89


title: Cambodia91


title: Cambodia90


title: Cambodia94


title: Cambodia80


title: Cambodia76


title: Cambodia74

value: Battambang


title: Cambodia84


title: Cambodia87


title: Cambodia85


title: Cambodia81


title: Cambodia86


title: Cambodia77


title: Cambodia70


title: Cambodia71


title: Cambodia78


title: Cambodia75


title: Cambodia82


title: Cambodia65


title: Cambodia72


title: Cambodia66


title: Cambodia83


title: Cambodia79


title: Cambodia61


title: Cambodia68


title: Cambodia92


title: Cambodia73


title: pUC19-5

type: SRA

city: aarhus

first: Yonglun

last: Luo

address: Wilhelm Meyers Allé 4

country: Denmark

institute: Aarhus University

library_source: genomic

data_processing:
Illumina Casava1.8 software used for basecalling.
Bisulfite-Seq clean reads were aligned to the human reference genome (hg19) by BSMAP(v2.74) with the parameter “-u -v 5 -z 33 -p 6 -n 0 -w 20 -s 16 -r 0 -f 10 -L 140”.
Only the CpG sites with read depths >=4 were taken into consideration for DNA methylation level calculation.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: The cout.gz file for each cytosine context (CG, CHG, or CHH where H=A,T,C) with following tab-separated information: Chromosome, coordinate, strand, cytosine type, cytosine context, methylated cytosines reads and unmethylated cytosines reads.
Supplementary_files_format_and_content: The bedGraph format files for each cytosine context with following tab-separated information: Chromosome, start coordinate, stop coordinate, and methylation level (%) (#methylated cytosines reads/#total cytosines reads).

source_name: Human embryonic kidney cells

growth_protocol: Human embryonic kidney HEK293T cells were cultured in Dulbecco's modified Eagle's medium (DMEM, Life Technologies), 10% fetal bovine serum (Sigma), 1% penicillin-streptomycin (Sigma), 1X GlutaMAX (Life Technologies).

extract_protocol:
Genomic DNA was extracted using the DNeasy Blood & Tissue Kit (Qiagen, 69506) according to the manufacturer’s instructions, and subject to WGBS SOP analysis in BGI tech.
For Bisulfite-Seq, genomic DNA was fragmented by sonication to a mean size of 250bp using a Bioruptor (Diagenode, Belgium). Bisulphite conversion was conducted with the EZ DNA Methylation-Gold kit (ZYMO). The libraries were sequenced on Illumina HiSeq X Ten. The 48502 bp lambda DNA was used as an extra reference for calculating the bisulphite conversion rate. Nearly complete (>99%) bisulfite conversion was documented in all libraries.

treatment_protocol: Unless stated elsewhere, cells were transfected with gRNAs (total 500 ng) and a CRISPRme expression vector (500 ng) in six-well plates using X-tremeGENE 9 DNA transfection reagent (Roche). For single gRNA or pUC19 control transfections, the amount of plasmid added was equivalent to the total amount of plasmid added for multiple gRNA transfections.

tag: cell line

value: Human embryonic kidney cell line


title: pUC19-4


title: Cambodia59


title: pUC19-6


title: Cambodia56


title: Cambodia64


title: Cambodia63


title: Cambodia54


title: Cambodia57


title: dCas9-BFP-DNMT3A (500 ng) + uPA gRNA (500 ng) -3


title: dCas9-BFP-DNMT3A (500 ng) + uPA gRNA (500 ng) -2


title: Cambodia58


title: Cambodia69


title: Cambodia55


title: dCas9-BFP-DNMT3A (500 ng) + uPA gRNA (500 ng) -1


title: Cambodia60


title: Cambodia67


title: Cambodia53


title: Cambodia62


title: BMPi-2

city: Shanghai

first: Xiang-Chun

last: Ju

address: Yueyang Road 320

country: China

institute: Institute of Neuroscience

description: 3' RNA

library_source: transcriptomic

data_processing:
Cellranger mkfastq
Cellranger count
Cellranger aggr
Cellranger R Kit
Genome_build: GRCh38
Supplementary_files_format_and_content: Hierarchical data format (HDF5)

source_name: Brain organoid

extract_protocol:
Organoids were minced into small pieces and then digested in 0.25% trypsin, 10 g/ml Dnase, 100 nM TTX, 10 μM DNQX, 50 μM DL-AP5 in HBSS at 37 °C for 20 min and stopped digestion with 100 μg/ml trypsin inhibitor. Single cell suspension was genetrated by pipetting for ~ 25 cycles and filtered through a 45 μm cell strainer. Cells were washed with PBS before counting and sorting.
Library construction follows the manufactural standard protocol

tag: developmental stage

value: day 32

tag: stem cell line

tag: protocol

value: BMPi


title: BMPi-1

description: 3' RNA


title: BMPa-1

description: 3' RNA

value: BMPa


title: BMPa-2

description: 3' RNA


title: FFJ ATAC deltaCre 90m B2

city: Boston

first: Michael

last: Greenberg

address: 200 Longwood Ave

institute: Harvard Medical School

data_processing:
Sequenced reads were demultiplexed, trimmed for adaptor sequences, and mapped to mm10 whole genome using Bowtie (1.1.1) with parameters -p 4 -S -n 2 -e 70 -m 1 -k 1 -l 49 --best mm10 --chunkmbs 200
Sam files were converted to bam files using samtools (1.1) view with parameters -h -b -F 3844 -q 10
Peaks were called via the IDR pipeline (https://sites.google.com/site/anshulkundaje/projects/idr). Optimal sets of peaks were called on pseudoreplicates of pooled data by both MACS (2.1.0) and SPP (phantompeakqualtools), and the two sets of peaks were intersected to obtain a consensus peakset for further analyses.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files of histograms normalized to 10M reads for mapped, in silico extended reads

source_name: Primary fibroblasts

growth_protocol: Mouse embryonic fibroblasts (MEFs) were grown in DMEM with 10% FBS.

extract_protocol:
Growth media was removed and MEFs were lysed in hypotonic lysis buffer to isolate nuclei. Approximately 40,000 nuclei were used as input to the Nextera DNA Sample Preparation Kit (FC-121-1030).
ATAC libraries were prepared using the standard library preparation protocol outlined in the Nextera DNA Sample Preparation Kit (FC-121-1030).

treatment_protocol: MEFs were serum starved for 26-30 hours in 0.5% serum MEF media and stimulated for the indicated times at a final concentration of 15% serum.

tag: strain

tag: age

tag: genotype

value: Fos fl/fl; Fosb fl/fl; Junb fl/fl deltaCre

tag: treatment

value: 90m stimulation with 15% serum media

tag: passage

tag: chip antibody

value: Primary fibroblasts

tag: serum stimulation


title: FFJ ATAC deltaCre 90m B1


title: FFJ ATAC Cre 90m B1

value: Fos fl/fl; Fosb fl/fl; Junb fl/fl Cre


title: FFJ ATAC deltaCre 0hr B1

value: starved with 0.5% serum media


title: FFJ ATAC Cre 0hr B1


title: Cambodia48

value: Cambodia


title: Cambodia52

value: Oddar Meanchey


title: Cambodia45


title: Cambodia46


title: ANM Smarca4 90m B3

extract_protocol:
Growth media was removed and MEFs were crosslinked in EGS for 30 minutes at room temperature, followed by 1% formaldehyde for 10 minutes at room temperature before quenching with glycine at a final concentration of 0.125M. Sonicated chromatin from isolated nuclei were used as input to ChIP.
2-40 ng of each ChIP sample was used to prepare ChIP-Seq libraries with the NuGEN Ovation Ultralow Library System v2 kit.

value: wild-type

value: 90m stimulation with 15% serum media + anisomycin

value: Abcam ab4081 lot GR152856-1


title: Cambodia43


title: FFJ ATAC deltaCre 0hr B2


title: ANM Smarca4 90m B1


title: ANM Smarca4 90m B2


title: FFJ ATAC Cre 90m B2


title: FFJ ATAC Cre 0hr B2


title: ANM Smarca4 0hr B3

value: starved with 0.5% serum media + anisomycin


title: Cambodia51


title: Cambodia49


title: Cambodia44


title: Cambodia40


title: Cambodia42


title: Cambodia47


title: Cambodia50


title: Cambodia39


title: ANM Smarca4 0hr B2


title: Cambodia41


title: ANM Smarca4 0hr B1


title: Cambodia38


title: Smarca4 90m B1


title: Smarca4 90m B3


title: Smarca4 90m B2


title: Smarca4 0hr B2


title: Smarca4 0hr B3


title: Smarca4 0hr B1


title: H3K4me1 90m B2

extract_protocol:
Growth media was removed and MEFs were crosslinked in 1% formaldehyde for 10 minutes at room temperature before quenching with glycine at a final concentration of 0.125M. Sonicated chromatin from isolated nuclei were used as input to ChIP.
2-40 ng of each ChIP sample was used to prepare ChIP-Seq libraries with the NuGEN Ovation Ultralow Library System v2 kit.

value: Abcam ab8895


title: H3K4me1 0hr B2


title: H3K4me1 90m B1

value: Abcam ab176877


title: Cambodia36


title: Total H3 0hr B2

value: Abcam ab1791


title: Total H3 0hr B1

value: Abcam ab176842


title: Total H3 90m B1


title: Cambodia34


title: Cambodia33


title: Cambodia30

value: Battambang


title: SPREB H3K4me2 cycling B3

value: C57BL/6J x SPRET/EiJ F1 hybrid

value: Abcam ab7766 lot GR160184-1


title: Cambodia28


title: Total H3 90m B2

value: 90m stimulation with 15% serum media


title: Cambodia26


title: Cambodia37


title: SPREB H3K4me2 cycling B2

value: Primary fibroblasts


title: Cambodia21


title: Cambodia31


title: Cambodia32


title: Cambodia24


title: Cambodia25


title: SPRET H3K4me1 90m B2

value: SPRET/EiJ


title: Cambodia17


title: Cambodia29


title: Cambodia22


title: SPREB H3K4me2 cycling B1


title: Cambodia19


title: SPRET H3K4me1 0hr B2

value: starved with 0.5% serum media


title: Cambodia27

value: Cambodia


title: Cambodia35

value: Oddar Meanchey


title: SPRET H3K4me1 0hr B1

value: wild-type


title: Cambodia20


title: Cambodia18


title: Cambodia13


title: SPRET JunD 90m B2

value: Santa Cruz sc-74 lot I1014


title: Cambodia15


title: Cambodia16


title: Cambodia14


title: SPRET JunD 0hr B1


title: Cambodia23


title: SPRET H3K4me1 90m B1


title: SPRET JunD 90m B1


title: Cambodia10


title: SPRET JunD 0hr B2


title: Cambodia11


title: SEP23-8

status: Public on Dec 27 2017

city: Durham

first: Thomas

middle: M

last: Price

state: NC

address: 5704 Fayetteville Rd

institute: Duke University

hyb_protocol: Targets were hybridized to the Mouse430_plus_2 (Affymetrix, Santa Clara, CA).  Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse430_plus_2  Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: Partek Genomics Suite 6.6 (Partek Inc., St. Louis, MO) was used to perform data analysis. Robust multi-chip analysis (RMA) normalization was done on the entire data set. Multi-way ANOVA and fold change were performed to select target genes that were differentially expressed between AUG and SEP. Top differentially expressed genes were selected with p value cutoff of0.05 based on ANOVA test and fold change cutoff of 2.

source_name: PR-M non-expressing

label_protocol: 500 ng of total RNA was amplified according to the MessageAmp Premier protocol (Ambion).  Affymetrix GeneChip analysis was performed according to the manufacturer’s instructions,

extract_protocol: Trizol RNA isolation for heart tissue

treatment_protocol: 19 - 21 days of 2.5 mg progesterone in oil subcutaneously

tag: tissue

value: heart


title: AUG24-1

source_name: PR-M expressing


title: SEP18-3


title: AUG24-7


title: AUG24-8


title: SEP23-9


title: Cambodia4


title: Cambodia8


title: H3K4me1 0hr B1


title: Cambodia6


title: Cambodia3


title: Cambodia1


title: Cambodia7


title: Cambodia9


title: Cambodia2


title: Cambodia5


title: Hippocampus_6w_Pool2

city: Kyoto-shi

first: Takashi

last: Kuramoto

state: Kyoto

address: yoshida-konoe-cho,sakyo-ku

department: Graduate School of medicine

country: Japan

institute: Kyoto University

description: Biomaterial Provider: Institute of Laboratory Animals, Graduate School of Medicine, Kyoto University

hyb_protocol: We followed protocol of manual that is Low Input Quick Amp Labeling Kit, Two-Color.

scan_protocol: We followed manufacturer's protocol, and used Agilent Technologies Scanner G2505C.

data_processing: Data acquisition and normalization (LOWESS) were used Agilent Feature Extraction Software (v 10.7.3.1).

organism: Rattus norvegicus

source_name: NER, GTCS (Generalized Tonic-Clonic Seizure)-positive strain, hippocampus, under interictal conditions with no observable seizures for at least 2 h before sampling, pooled from 3 rats, 6 weeks of age

growth_protocol: All rats had ad libitum access to food pellets and tap water and were maintained on a 14 h light/10 h dark cycle with lights on at 7:00 am. Animal experiments were approved by the Animal Research Committees of Kyoto University and conducted according to the Regulations on Animal Experimentation of Kyoto.

extract_protocol: Rats were deeply anesthetized with pentobarbital (80 mg/kg, i.p.), and brains were removed and chilled in ice-cold saline. The amygdala, cortex and hippocampus were then dissected immediately and stored in RNAlater (Qiagen, Tokyo, Japan). Total RNA was isolated using ISOGEN II (Nippon Gene Co., Ltd, Tokyo, Japan).

treatment_protocol: NER rat strain: an inbred strain developed by selective inbreeding of rats showing generalized tonic-clonic seizure (GTCS) from an outbred stock Crj:Wistar in Japan.  NF-Chr1e/5d rat strain: a newly developed double congenic strain with NER background, and the chromosomal segments Chr1e (30Mb) and Chr5d (15Mb) are replaced with F344 strain.

value: NER

tag: gender

value: male

value: 6 weeks

value: hippocampus

tag: epileptic stage

source_name: NF-Chr1e/5d GTCS-resistant congenic strain, hippocampus, pooled from 3 rats, 6 weeks of age

value: normal


title: Right cortex_6w_Pool2

source_name: NER, GTCS (Generalized Tonic-Clonic Seizure)-positive strain, right cortex, under interictal conditions with no observable seizures for at least 2 h before sampling, pooled from 3 rats, 6 weeks of age

label_protocol: We followed protocol of manual that is Low Input Quick Amp Labeling Kit, Two-Color.

value: right cortex

source_name: NF-Chr1e/5d, GTCS-resistant congenic strain, right cortex, pooled from 3 rats, 6 weeks of age


title: Right cortex_18w_Pool2

source_name: NER, GTCS (Generalized Tonic-Clonic Seizure)-positive strain, right cortex, under interictal conditions with no observable seizures for at least 2 h before sampling, pooled from 3 rats, 18 weeks of age

value: 18 weeks

source_name: NF-Chr1e/5d, GTCS-resistant congenic strain, right cortex, pooled from 3 rats, 18 weeks of age


title: Left cortex_6w_Pool1

source_name: NER, GTCS (Generalized Tonic-Clonic Seizure)-positive strain, left cortex, under interictal conditions with no observable seizures for at least 2 h before sampling, pooled from 3 rats, 6 weeks of age

value: left cortex

source_name: NF-Chr1e/5d, GTCS-resistant congenic strain, left cortex, pooled from 3 rats, 6 weeks of age


title: Amygdala_6w_Pool2

source_name: NER, GTCS (Generalized Tonic-Clonic Seizure)-positive strain, amygdala, under interictal conditions with no observable seizures for at least 2 h before sampling, pooled from 3 rats, 6 weeks of age

value: amygdala

source_name: NF-Chr1e/5d, GTCS-resistant congenic strain, amygdala, pooled from 3 rats, 6 weeks of age


title: Hippocampus_6w_Pool1

value: under interictal conditions with no observable seizures for at least 2 h before sampling

source_name: NF-Chr1e/5d, GTCS-resistant congenic strain, hippocampus, pooled from 3 rats, 6 weeks of age


title: Left cortex_6w_Pool2


title: Right cortex_6w_Pool1


title: Left cortex_18w_Pool2

source_name: NER, GTCS (Generalized Tonic-Clonic Seizure)-positive strain, left cortex, under interictal conditions with no observable seizures for at least 2 h before sampling, pooled from 3 rats, 18 weeks of age

source_name: NF-Chr1e/5d, GTCS-resistant congenic strain, left cortex, pooled from 3 rats, 18 weeks of age


title: Amygdala_6w_Pool1


title: Amygdala_18w_Pool2

source_name: NER, GTCS (Generalized Tonic-Clonic Seizure)-positive strain, amygdala, under interictal conditions with no observable seizures for at least 2 h before sampling, pooled from 3 rats, 18 weeks of age

source_name: NF-Chr1e/5d, GTCS-resistant congenic strain, amygdala, pooled from 3 rats, 18 weeks of age


title: Hippocampus_18w_Pool2

source_name: NER, GTCS (Generalized Tonic-Clonic Seizure)-positive strain, hippocampus, under interictal conditions with no observable seizures for at least 2 h before sampling, pooled from 3 rats, 18 weeks of age

source_name: NF-Chr1e/5d, GTCS-resistant congenic strain, hippocampus, pooled from 3 rats, 18 weeks of age


title: Hippocampus_18w_Pool1


title: Left cortex_18w_Pool1


title: M31m

city: Otsu

first: Hiroyuki

last: Sugihara

state: Shiga

address: Seta, Tsukinowa-cho

department: Pathology

institute: Shiga University of Medical Science

description:
TU-A11-TU011_TU011R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014

hyb_protocol: Labelled samples were hybridized on SurePrint G3 Human CGH Microarray 8x60K  (Agilent, GPL10152) according to the manufacturer's instructions.

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505C Microarray Scanner at 3 micron resolution.

data_processing:
Signal intensity extraction, and normalization were performed using the Agilent Feature Extraction software 11.5.1.1
Linear normalization method with default parameters (protocol CGH_1105_Oct12 and Grid: 021924_D_F_20090227) was used in signal intensity extraction procedure

source_name: intramucosal part of invasive gastric cancer

label_protocol: 250ng DNA was labelled using the SureTag DNA Labeling Kit coupling method (Agilent – 5190-3400)

extract_protocol:
Qubid 10ng
The samples were obtained from 5-micrometer-thick tissue sections using a laser microdissection system (LMD6000, Leica Microsystems, Wetzlar, Germany). Each  samples were dissected from at least > 6mm2 area, in which neoplastic cells accounted for 90% of total cell count. These cells were then digested in 200 mg/ml proteinase K solution for 70±2 hours at 37ºC. GenomeDNA was extracted with phenol-chloroform-isoamylalcohol extraction method and further treated using the Maxtract high density extraction column(QIAGEN).Eluted DNA was assessed for purity using the Nanodrop-1000 and double stranded DNA was quantified using the Qubit® fluorometer (Invitrogen) as per manufacturer's instructions. GenomeDNA was amplified using the GenomePlex Complete Whole Genome Amplification (WGA) Kit(SIGMA). For each WGA 100 ng (Nanodrop) or 10 ng (Qubit) of starting material was used. The amplified DNA product was purified using the GeneElute PCR Clean-Up Kit(SIGMA).

tag: excision year

tag: analysis year

value: F

tag: pathologic stage

tag: ffpe tissue from

value: ESD

source_name: corresponding non-neoplastic sample

value: corresponding non-neoplastic sample


title: Right cortex_18w_Pool1


title: M35m

description:
TU-A15-TU015_TU015R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014

value: M

value: intramucosal part of invasive gastric cancer


title: S4m

description:
302m_vs_302R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014

data_processing:
Signal intensity extraction, and normalization were performed using the Agilent Feature Extraction software 10.7.3.1
Linear normalization method with default parameters (protocol CGH_105_Jan09 and Grid: 021924_D_F_20090930) was used in signal intensity extraction procedure

label_protocol: 250ng DNA was labelled using the Genomic DNA ULS Labeling Kit coupling method (Agilent – 5190-0419)

extract_protocol:
Nanodrop 100ng
The samples were obtained from 5-micrometer-thick tissue sections using a laser microdissection system (LMD6000, Leica Microsystems, Wetzlar, Germany). Each  samples were dissected from at least > 6mm2 area, in which neoplastic cells accounted for 90% of total cell count. These cells were then digested in 200 mg/ml proteinase K solution for 70±2 hours at 37ºC. GenomeDNA was extracted with phenol-chloroform-isoamylalcohol extraction method and further treated using the Maxtract high density extraction column(QIAGEN).Eluted DNA was assessed for purity using the Nanodrop-1000 and double stranded DNA was quantified using the Qubit® fluorometer (Invitrogen) as per manufacturer's instructions. GenomeDNA was amplified using the GenomePlex Complete Whole Genome Amplification (WGA) Kit(SIGMA). For each WGA 100 ng (Nanodrop) or 10 ng (Qubit) of starting material was used. The amplified DNA product was purified using the GeneElute PCR Clean-Up Kit(SIGMA).

value: operative resection


title: M28m

description:
TU-A7-TU007_TU007R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014


title: M27m

description:
TU-A6-TU006_TU006R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014


title: M30m

description:
TU-A10-TU010_TU010R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014


title: A9i

description:
305i_vs_305R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014

source_name: invasive part of invasive gastric cancer


title: M34m

description:
TU-A14-TU014_TU014R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014


title: M33m

description:
TU-A13-TU013_TU013R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014


title: M36m

description:
TU-A19-TU019_TU019R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014


title: A8i

description:
304i_vs_304R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014

value: invasive part of invasive gastric cancer


title: Amygdala_18w_Pool1

value: NER


title: A7i

description:
303i_vs_303R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014


title: A7m

description:
303m_vs_303R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014


title: A9ln

description:
A38-1001_1001R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014

data_processing:
Signal intensity extraction, and normalization were performed using the Agilent Feature Extraction software 10.7.3.1
Linear normalization method with default parameters (protocol CGH_107_Sep09 and Grid: 021924_D_F_20111015) was used in signal intensity extraction procedure

source_name: lymph node metastasis from gastric cancer


title: A9m

description:
305m_vs_305R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014


title: M29m

description:
TU-A9-TU009_TU009R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014


title: A8ln

description:
A14-1008_1008R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014

value: lymph node metastasis from gastric cancer


title: S4i

description:
302i_vs_302R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014


title: A6i

description:
203i_vs_203R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014


title: S4ln

description:
A11-1004_1005R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014


title: M32m

description:
TU-A12-TU012_TU012R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014


title: A7ln

description:
A13-1007_1007R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014


title: A6ln

description:
A01-1006_1006R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014


title: Cambodia12

source_name: clinical isolate

tag: province

value: Battambang

tag: country

value: Cambodia


title: M8mr

description:
19_A6-1906_1906R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014


title: M9mr

description:
19_A7-1907_1907R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014


title: M4mr

description:
19_A2-1902_1902R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014


title: M6mr

description:
19_A4-1904_1904R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014


title: A8m

description:
304m_vs_304R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014


title: M7mr

description:
19_A5-1905_1905R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014


title: A35i

description:
21-A12-2112_2112R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014


title: M5mr

description:
19_A3-1903_1903R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014


title: M3mr

description:
19_A1-1901_1901R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014


title: S2mr

description:
19_A10-1910_1910R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014


title: A32i

description:
21-A9-2109_2108R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014


title: A33i

description:
21-A10-2110_2110R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014


title: A30m2

description:
21-A5-2105_2103R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014


title: A34i

description:
21-A11-2111_2111R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014


title: A30m

description:
21-A3-2103_2103R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014


title: A31m

description:
21-A6-2106_2106R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014


title: A2mr

description:
19_A11-1911_1911R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014


title: A30i

description:
21-A4-2104_2103R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014


title: A32m

description:
21-A8-2108_2108R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014


title: A31i

description:
21-A7-2107_2106R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014


title: A29m

description:
21-A2-2101_2101R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014


title: INT_ALL_MOCK_26_MVE_B_6hr

data_processing: Scanned images were analyzed using Agilent Feature Extraction Software (v11.0.1.1). The limma package for R (available on Bioconductor) was used to perform background correction, quantile normalization (normalizeBetweenArrays), and summarization (avereps) to derive a single normalized intensity value per probe. Outlier samples were detected using PCA and by visual inspection of heatmaps, and all data was re-processed after removing outlier samples. All data processing for each of the biological replicates was performed independently of the other.  No outliers were identified in this study.

source_name: Primary human lung microvascular endothelial cells, Mock-inoculated 26, 6hr, bioreplicate 2

extract_protocol:
MERSCOV002.0P
plaque assay protocol: MERSCOV005.0P

treatment_protocol: MERSCOV002.0P: Cells were infected with a multiplicity of infection of 5 PFU.

value: lung

tag: cell type

value: microvascular endothelial cells

tag: time

value: Mock


title: INT_ALL_MOCK_63_MVE_A_6hr

source_name: Primary human lung microvascular endothelial cells, Mock-inoculated 63, 6hr, bioreplicate 1


title: INT_ALL_MOCK_26_MVE_B_3hr

source_name: Primary human lung microvascular endothelial cells, Mock-inoculated 26, 3hr, bioreplicate 2


title: INT_ALL_MOCK_63_MVE_A_3hr

source_name: Primary human lung microvascular endothelial cells, Mock-inoculated 63, 3hr, bioreplicate 1


title: INT_ALL_MOCK_63_MVE_B_3hr

source_name: Primary human lung microvascular endothelial cells, Mock-inoculated 63, 3hr, bioreplicate 2


title: INT_ALL_MOCK_63_MVE_A_24hr

source_name: Primary human lung microvascular endothelial cells, Mock-inoculated 63, 24hr, bioreplicate 1


title: INT_ALL_MOCK_26_MVE_A_24hr

source_name: Primary human lung microvascular endothelial cells, Mock-inoculated 26, 24hr, bioreplicate 1


title: INT_ALL_MOCK_63_MVE_B_24hr

source_name: Primary human lung microvascular endothelial cells, Mock-inoculated 63, 24hr, bioreplicate 2


title: INT_ALL_MOCK_26_MVE_B_24hr

source_name: Primary human lung microvascular endothelial cells, Mock-inoculated 26, 24hr, bioreplicate 2


title: INT_ALL_MOCK_26_MVE_A_6hr

source_name: Primary human lung microvascular endothelial cells, Mock-inoculated 26, 6hr, bioreplicate 1


title: A29i

description:
21-A1-2102_2101R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014

tag: age


title: A28m2

description:
19-A25-1926_1922R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014


title: INT_ALL_MOCK_63_MVE_B_6hr

source_name: Primary human lung microvascular endothelial cells, Mock-inoculated 63, 6hr, bioreplicate 2


title: A28sm2

description:
19-A26-1927_1922R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014


title: INT_ALL_MOCK_26_MVE_A_3hr

source_name: Primary human lung microvascular endothelial cells, Mock-inoculated 26, 3hr, bioreplicate 1


title: INT_GAMMA_63_MVE_B_24hr

source_name: Primary human lung microvascular endothelial cells, IFNγ-inoculated 63, 24hr, bioreplicate 2

value: IFNgamma


title: A28i

description:
19-A22-1923_1922R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014

source_name: corresponding non-neoplastic sample


title: INT_GAMMA_26_MVE_B_24hr

source_name: Primary human lung microvascular endothelial cells, IFNγ-inoculated 26, 24hr, bioreplicate 2


title: A28m

description:
19-A21-1922_1922R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014

source_name: intramucosal part of invasive gastric cancer


title: INT_GAMMA_26_MVE_B_6hr

source_name: Primary human lung microvascular endothelial cells, IFNγ-inoculated 26, 6hr, bioreplicate 2


title: INT_GAMMA_26_MVE_A_6hr

source_name: Primary human lung microvascular endothelial cells, IFNγ-inoculated 26, 6hr, bioreplicate 1


title: A23i

description:
A14-1827_1826R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014

source_name: invasive part of invasive gastric cancer


title: A22ln

description:
A12-1818_1816R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014

source_name: lymph node metastasis from gastric cancer


title: A28ln

description:
19-A23-1924_1922R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014


title: INT_GAMMA_63_MVE_A_24hr

source_name: Primary human lung microvascular endothelial cells, IFNγ-inoculated 63, 24hr, bioreplicate 1


title: INT_GAMMA_63_MVE_B_3hr

source_name: Primary human lung microvascular endothelial cells, IFNγ-inoculated 63, 3hr, bioreplicate 2


title: INT_GAMMA_63_MVE_A_6hr

source_name: Primary human lung microvascular endothelial cells, IFNγ-inoculated 63, 6hr, bioreplicate 1


title: A26ln

description:
18_A25-1806_1801R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014


title: A26i

description:
18_A21-1802_1801R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014


title: INT_GAMMA_26_MVE_A_3hr

source_name: Primary human lung microvascular endothelial cells, IFNγ-inoculated 26, 3hr, bioreplicate 1


title: A22i

description:
A11-1817_1816R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014


title: INT_GAMMA_63_MVE_B_6hr

source_name: Primary human lung microvascular endothelial cells, IFNγ-inoculated 63, 6hr, bioreplicate 2


title: INT_ALPHABETA_26_MVE_A_24hr

source_name: Primary human lung microvascular endothelial cells, IFNαβ-inoculated 26, 24hr, bioreplicate 1

value: IFNalphaBeta


title: A20ln

description:
A3-1809_1807R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014


title: A23m

description:
A13-1826_1826R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014


title: INT_GAMMA_26_MVE_B_3hr

source_name: Primary human lung microvascular endothelial cells, IFNγ-inoculated 26, 3hr, bioreplicate 2


title: INT_ALPHABETA_63_MVE_A_24hr

source_name: Primary human lung microvascular endothelial cells, IFNαβ-inoculated 63, 24hr, bioreplicate 1


title: INT_ALPHABETA_26_MVE_B_24hr

source_name: Primary human lung microvascular endothelial cells, IFNαβ-inoculated 26, 24hr, bioreplicate 2


title: A20m

description:
A1-1807_1807R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014


title: A21m

description:
A7-1813_1813R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014


title: A22m

description:
A10-1816_1816R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014


title: A21ln

description:
A9-1815_1813R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014


title: A20i

description:
A2-1808_1807R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014


title: A21i

description:
A8-1814_1813R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014


title: INT_ALPHABETA_63_MVE_B_24hr

source_name: Primary human lung microvascular endothelial cells, IFNαβ-inoculated 63, 24hr, bioreplicate 2


title: INT_GAMMA_63_MVE_A_3hr

source_name: Primary human lung microvascular endothelial cells, IFNγ-inoculated 63, 3hr, bioreplicate 1


title: INT_ALPHABETA_63_MVE_A_6hr

source_name: Primary human lung microvascular endothelial cells, IFNαβ-inoculated 63, 6hr, bioreplicate 1


title: INT_ALPHABETA_63_MVE_B_6hr

source_name: Primary human lung microvascular endothelial cells, IFNαβ-inoculated 63, 6hr, bioreplicate 2


title: INT_ALPHABETA_63_MVE_B_3hr

source_name: Primary human lung microvascular endothelial cells, IFNαβ-inoculated 63, 3hr, bioreplicate 2


title: INT_ALPHABETA_63_MVE_A_3hr

source_name: Primary human lung microvascular endothelial cells, IFNαβ-inoculated 63, 3hr, bioreplicate 1


title: M18m

description:
A44-1711_1711R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014

source_name: intramucosal part of invasive gastric cancer

source_name: corresponding non-neoplastic sample


title: INT_ALPHABETA_26_MVE_A_6hr

source_name: Primary human lung microvascular endothelial cells, IFNαβ-inoculated 26, 6hr, bioreplicate 1


title: A19i

description:
A36-1111_1110R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014

source_name: invasive part of invasive gastric cancer


title: INT_ALPHABETA_26_MVE_B_3hr

source_name: Primary human lung microvascular endothelial cells, IFNαβ-inoculated 26, 3hr, bioreplicate 2


title: M23m

description:
A49-1716_1716R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014


title: INT_ALPHABETA_26_MVE_B_6hr

source_name: Primary human lung microvascular endothelial cells, IFNαβ-inoculated 26, 6hr, bioreplicate 2


title: MMVE001_B_FB_MOCK_A_24hr_35

source_name: Primary human fibroblasts, Mock-inoculated 63, 24hr, bioreplicate 1

extract_protocol: All samples were harveted in 1mL trizol.    The time matched mock will have the viral infection medium added instead of the actual inoculum.

treatment_protocol: Time Points = 3, 6, and 24 hrs post treatment.  Time matched mocks done in duplicate from same cell stock as rest of samples.

value: fibroblasts

value: MOCK


title: A19m

description:
A35-1110_1110R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014


title: A18m

description:
A53-1720_1720R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014


title: A19ln

description:
A37-1112_1110R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014

source_name: lymph node metastasis from gastric cancer


title: MMVE001_B_FB_MOCK_B_24hr_36

source_name: Primary human fibroblasts, Mock-inoculated 63, 24hr, bioreplicate 2


title: M22m

description:
A48-1715_1715R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014


title: M17m

description:
A43-1710_1710R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014


title: MMVE001_B_FB_MOCK_A_24hr_33

source_name: Primary human fibroblasts, Mock-inoculated 26, 24hr, bioreplicate 1


title: MMVE001_B_FB_MOCK_B_6hr_32

source_name: Primary human fibroblasts, Mock-inoculated 63, 6hr, bioreplicate 2


title: INT_ALPHABETA_26_MVE_A_3hr

source_name: Primary human lung microvascular endothelial cells, IFNαβ-inoculated 26, 3hr, bioreplicate 1


title: A18i

description:
A54-1721_1720R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014


title: MMVE001_B_FB_MOCK_B_6hr_30

source_name: Primary human fibroblasts, Mock-inoculated 26, 6hr, bioreplicate 2


title: A17i2

description:
A30-1630_1627R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014


title: MMVE001_B_FB_MOCK_B_24hr_34

source_name: Primary human fibroblasts, Mock-inoculated 26, 24hr, bioreplicate 2


title: MMVE001_B_FB_MOCK_A_6hr_29

source_name: Primary human fibroblasts, Mock-inoculated 26, 6hr, bioreplicate 1


title: A17m2

description:
A29-1629_1627R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014


title: A17ln

description:
A31-1631_1627R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014


title: M15m

description:
A41-1708_1705R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014

value: F


title: A17i1

description:
A28-1628_1627R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014

value: corresponding non-neoplastic sample


title: MMVE001_B_FB_MOCK_A_3hr_27

source_name: Primary human fibroblasts, Mock-inoculated 63, 3hr, bioreplicate 1


title: MMVE001_B_FB_MOCK_A_6hr_31

source_name: Primary human fibroblasts, Mock-inoculated 63, 6hr, bioreplicate 1


title: MMVE001_B_FB_MOCK_B_3hr_28

source_name: Primary human fibroblasts, Mock-inoculated 63, 3hr, bioreplicate 2


title: S5m2

description:
A32-1632_1632R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014

source_name: intramucosal part of invasive gastric cancer

value: M

source_name: corresponding non-neoplastic sample


title: A16i

description:
A25-1625_1624R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014

source_name: invasive part of invasive gastric cancer


title: A17m1

description:
A27-1627_1627R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014

value: intramucosal part of invasive gastric cancer


title: A16ln

description:
A26-1626_1624R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014

value: operative resection


title: MMVE001_B_FB_MOCK_B_3hr_26

source_name: Primary human fibroblasts, Mock-inoculated 26, 3hr, bioreplicate 2


title: MMVE001_B_FB_GAMMA_A_24hr_23

source_name: Primary human fibroblasts, IFNγ-inoculated 63, 24hr, bioreplicate 1


title: MMVE001_B_FB_GAMMA_B_24hr_22

source_name: Primary human fibroblasts, IFNγ-inoculated 26, 24hr, bioreplicate 2


title: MMVE001_B_FB_GAMMA_B_6hr_20

source_name: Primary human fibroblasts, IFNγ-inoculated 63, 6hr, bioreplicate 2


title: A15m

description:
A21-1621_1621R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014


title: S8i

description:
A14-1614_1613R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014

value: invasive part of invasive gastric cancer


title: M24m

description:
A50-1717_1717R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014


title: MMVE001_B_FB_GAMMA_B_3hr_16

source_name: Primary human fibroblasts, IFNγ-inoculated 63, 3hr, bioreplicate 2


title: MMVE001_B_FB_MOCK_A_3hr_25

source_name: Primary human fibroblasts, Mock-inoculated 26, 3hr, bioreplicate 1


title: MMVE001_B_FB_GAMMA_B_24hr_24

source_name: Primary human fibroblasts, IFNγ-inoculated 63, 24hr, bioreplicate 2


title: MMVE001_B_FB_GAMMA_A_6hr_19

source_name: Primary human fibroblasts, IFNγ-inoculated 63, 6hr, bioreplicate 1


title: A16m

description:
A24-1624_1624R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014


title: S7i

description:
A19-1015_1015R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014


title: MMVE001_B_FB_GAMMA_A_24hr_21

source_name: Primary human fibroblasts, IFNγ-inoculated 26, 24hr, bioreplicate 1


title: A15i

description:
A22-1622_1621R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014


title: MMVE001_B_FB_GAMMA_A_3hr_15

source_name: Primary human fibroblasts, IFNγ-inoculated 63, 3hr, bioreplicate 1


title: A13m2

description:
A21-1102_1102R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014


title: S8m

description:
A13-1613_1613R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014


title: A14ln

description:
A17-1013_1008R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014

source_name: lymph node metastasis from gastric cancer


title: MMVE001_B_FB_GAMMA_A_6hr_17

source_name: Primary human fibroblasts, IFNγ-inoculated 26, 6hr, bioreplicate 1


title: MMVE001_B_FB_GAMMA_B_3hr_14

source_name: Primary human fibroblasts, IFNγ-inoculated 26, 3hr, bioreplicate 2


title: A14i

description:
A16-1012_1007R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014


title: MMVE001_B_FB_GAMMA_A_3hr_13

source_name: Primary human fibroblasts, IFNγ-inoculated 26, 3hr, bioreplicate 1


title: MMVE001_B_FB_ALPHABETA_A_24hr_11

source_name: Primary human fibroblasts, IFNαβ-inoculated 63, 24hr, bioreplicate 1


title: S8i2

description:
A15-1615_1613R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014

source_name: corresponding non-neoplastic sample


title: MMVE001_B_FB_ALPHABETA_B_24hr_12

source_name: Primary human fibroblasts, IFNαβ-inoculated 63, 24hr, bioreplicate 2


title: MMVE001_B_FB_GAMMA_B_6hr_18

source_name: Primary human fibroblasts, IFNγ-inoculated 26, 6hr, bioreplicate 2


title: S5i

description:
A01-812INV_811R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014

source_name: invasive part of invasive gastric cancer


title: A14m

description:
A15-1011_1007R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014

source_name: intramucosal part of invasive gastric cancer


title: A13m

description:
A05-1105_1105R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014


title: S7m

description:
A18-1014_1014R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014


title: MMVE001_B_FB_ALPHABETA_A_24hr_9

source_name: Primary human fibroblasts, IFNαβ-inoculated 26, 24hr, bioreplicate 1


title: xRNA 6h rep 3

city: Minneapolis

last: Gale

state: Minnesota

address: 689 23rd Ave SE

department: Microbiology and Immunology

institute: University of Minnesota

data_processing:
Constructed libraries were sequenced on an NextSeq 500 Illumina platform, producing 2x100nt stranded paired end reads (52 Gb). Image analysis, base calling, and error estimation were performed using Illumina Analysis Pipeline (version 2.8).
Quality control of the primary sequencing data was performed using FastQC (version 0.11.3) and included adapter trimming using cutadapt (version 1.8.3).
Reads were aligned using STAR (version 2.4.2)
Gene counts were then loaded in the R statistical programming language (version 3.2.0) and genes were filtered by a row sum 75 or greater across all samples. Exploratory analysis and statistics were also run using R and bioconductor. The gene count matrix was normalized using voom through the limma bioconductor package (3.26.9) and batch corrected using the sva package (3.2). Statistical analysis (including differential expression) were performed using the limma package.
Genome_build: human genome (build NCBI_build 37.2
Supplementary_files_format_and_content: raw count matrix

source_name: Plasmacytoid dendritic cells

growth_protocol: CAL-1 cells were cultured in RPMI 1640 supplemented with 10% FBS, L-glutamine, sodium pyruvate, HEPES, and β-mercaptoethanol.

extract_protocol:
mRNA was isolated using the QIAGEN miRNeasy Kit.
Illumina Truseq
Library quality was evaluated using the Qubit® 3.0 Fluorometer and the Agilent 2100 Bioanalyzer instrument. Constructed libraries were sequenced on an NextSeq 500 Illumina platform, producing 2x75nt stranded paired end reads (52 Gb). Image analysis, base calling, and error estimation were performed using Illumina Analysis Pipeline (version 2.8).

treatment_protocol: CAL-1 cells treated with 1ug/ml R848 for 2 hours. CAL-1 cells were transfected using the Amaxa 96-well shuttle nucleofector system with 1 ug RNA

tag: time point

value: xRNA

tag: replicate


title: xRNA 6h rep 2

tag: treatment


title: A12i

description:
A02-806C_806R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014


title: A13i

description:
A06-1106_1106R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014


title: MMVE001_B_FB_ALPHABETA_A_3hr_3

source_name: Primary human fibroblasts, IFNαβ-inoculated 63, 3hr, bioreplicate 1


title: MMVE001_B_FB_ALPHABETA_B_3hr_4

source_name: Primary human fibroblasts, IFNαβ-inoculated 63, 3hr, bioreplicate 2


title: S5m

description:
A07-811C_811R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014


title: MMVE001_B_FB_ALPHABETA_B_3hr_2

source_name: Primary human fibroblasts, IFNαβ-inoculated 26, 3hr, bioreplicate 2


title: MMVE001_B_FB_ALPHABETA_B_6hr_6

source_name: Primary human fibroblasts, IFNαβ-inoculated 26, 6hr, bioreplicate 2


title: S7ln

description:
A03-1016_1016R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014

value: lymph node metastasis from gastric cancer


title: S5ln

description:
A02-1010_1404R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014


title: A11m

description:
A05-809C_809R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014


title: A13ln

description:
A04-1104_1104R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014


title: MMVE001_B_FB_ALPHABETA_B_24hr_10

source_name: Primary human fibroblasts, IFNαβ-inoculated 26, 24hr, bioreplicate 2


title: MMVE001_B_FB_ALPHABETA_B_6hr_8

source_name: Primary human fibroblasts, IFNαβ-inoculated 63, 6hr, bioreplicate 2


title: MMVE001_B_FB_ALPHABETA_A_6hr_5

source_name: Primary human fibroblasts, IFNαβ-inoculated 26, 6hr, bioreplicate 1


title: 113 osteoarthritis

first: Bo

last: Zhang

state: MO

address: 660 S. Euclid Avenue

department: Developmental Biology

institute: Washington University School of Medicine

description: Gene expression in OA meniscus

hyb_protocol: For hybridization, amplified RNA samples were suspended in Agilent 2X Gene Expression buffer, Agilent 10X blocking agent, and Kreablock. The hybridization solution was applied to human SurePrint G3 Human 8X60K microarrays (Catalog # G4851C, Agilent Technologies) and incubated with streptavidin-cyanine 5 at 65oC for 20h. Washing procedures were performed according to Agilent Gene Expression protocol.

scan_protocol: Slides were  scanned on an Agilent C-class Microarray scanner to detect Cy5 fluorescence as per manufacturer’s specification.

data_processing: Gridding and analysis of images were performed using Feature Extraction software v. 11.5.1.1 (Agilent Technologies). Raw data (probe intensity) were preprocessed by using R package ‘oligo’, and were quantile normalized across all samples. The lowly expressed probeset was further removed by using cutoff at 0.95 quantile probe intensity. R package ‘limma’ was used to build one linear regression model for identifying differentially expressed genes (DEGs) between TKA and APM meniscus, while considering covariance of patients’ age, body mass index and gender at same time.

source_name: Knee meniscus

label_protocol: 20 ng of RNA transcripts were amplified with the use of Sigma-WTA2 kit (Sigma-Aldrich) and then complementary DNA (cDNA) was labelled with Kreatech ULS RNA labeling kit (Kreatech Diagnostics). Briefly, 3 g of cDNA was mixed with Kreatech 10X labeling buffer and Kreatech cyanine 5/DY-ULS. The reaction mixture was incubated at 85oC for 15 min in the dark and then quenched on ice for 3 min. Labelled cDNA was purified with Qiagen purification columns according to the supplier’s protocol (Qiagen).

extract_protocol: RNA was isolated using a combination of TRIzol:Chloroform (5:1 ratio) method and Minispin columns (Qiagen).  The pulverized tissues were first dissolved in 1 ml of TRIzol reagent (Invitrogen) followed by addition of 0.2 ml of Chloroform. Sample were then vortexed and transferred to phase lock gel tubes. Tubes were centrifuged for 15 min at 4°C. The clear aqueous layer was transferred by decanting of pipetting and 1 volume of 70% RNase-free ethanol was added to precipitate RNA. Finally, RNA was collected using RNeasy spin columns (Qiagen). The quality of the RNA was assessed by Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: A small segment of the injured meniscus was resected from 12 patients during arthroscopic partial meniscectomy and a location-matched segment was obtained from 12 patients during total knee arthroplasty. Tissues were homogenized prior to RNA isolation.

tag: age (years)

tag: Sex

value: Female

tag: bmi (kg/m2)


title: A11i

description:
A06-810C_810R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014

tag: gender

tag: tissue


title: A12ln

description:
A03-807C_807R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014

source_name: lymph node metastasis from gastric cancer

tag: excision year


title: MMVE001_B_FB_ALPHABETA_A_3hr_1

source_name: Primary human fibroblasts, IFNαβ-inoculated 26, 3hr, bioreplicate 1


title: MMVE001_B_FB_ALPHABETA_A_6hr_7

source_name: Primary human fibroblasts, IFNαβ-inoculated 63, 6hr, bioreplicate 1


title: 114 osteoarthritis

description: Gene expression in OA meniscus


title: xRNA 6h rep 1


title: 112 osteoarthritis

description: Gene expression in OA meniscus


title: xRNA 16h rep 3


title: xRNA 16h rep 1


title: vehicle 6h rep 1

value: vehicle


title: R848 6h rep 1


title: vehicle 6h rep 2


title: vehicle 16h rep 2


title: R848 6h rep 3


title: R848 6h rep 2


title: A15ln

description:
A23-1623_1621R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014

tag: analysis year

source_name: corresponding non-neoplastic sample


title: vehicle 16h rep 3


title: R848 16h rep 3


title: 109 osteoarthritis

description: Gene expression in OA meniscus


title: 012 arthroscopic partial meniscectomy

description: Gene expression in torn meniscus

value: Male


title: 105 osteoarthritis

description: Gene expression in OA meniscus


title: vehicle 16h rep 1


title: vehicle 6h rep 3


title: 103 osteoarthritis

description: Gene expression in OA meniscus


title: 111 osteoarthritis

description: Gene expression in OA meniscus


title: 013 arthroscopic partial meniscectomy

description: Gene expression in torn meniscus


title: 010 arthroscopic partial meniscectomy

description: Gene expression in torn meniscus


title: R848 16h rep 1


title: xRNA 16h rep 2


title: 104 osteoarthritis

description: Gene expression in OA meniscus


title: 102 osteoarthritis

description: Gene expression in OA meniscus


title: S8ln

description:
A16-1616_1613R
gastric archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of gastric carcinomas from 55 patients from 2009 to 2014

tag: pathologic stage


title: 009 arthroscopic partial meniscectomy

description: Gene expression in torn meniscus


title: 107 osteoarthritis

description: Gene expression in OA meniscus


title: 108 osteoarthritis

description: Gene expression in OA meniscus


title: pU/UC 6h rep 2

value: pU/UC


title: 008 arthroscopic partial meniscectomy

description: Gene expression in torn meniscus


title: pU/UC 6h rep 3


title: 011 arthroscopic partial meniscectomy

description: Gene expression in torn meniscus


title: pU/UC 6h rep 1


title: noRNA 6h rep 3

data_processing:
Constructed libraries were sequenced on an NextSeq 500 Illumina platform, producing 2x100nt stranded paired end reads (52 Gb). Image analysis, base calling, and error estimation were performed using Illumina Analysis Pipeline (version 2.8).
Quality control of the primary sequencing data was performed using FastQC (version 0.11.3) and included adapter trimming using cutadapt (version 1.8.3).
Gene counts were then loaded in the R statistical programming language (version 3.2.0) and genes were filtered by a row sum 75 or greater across all samples. Exploratory analysis and statistics were also run using R and bioconductor. The gene count matrix was normalized using voom through the limma bioconductor package (3.26.9) and batch corrected using the sva package (3.2). Statistical analysis (including differential expression) were performed using the limma package.
Reads were aligned using STAR (version 2.4.2)
Genome_build: human genome (build NCBI_build 37.2
Supplementary_files_format_and_content: raw count matrix

value: noRNA


title: noRNA 6h rep 2


title: pU/UC 16h rep 3


title: pU/UC 16h rep 1


title: 007 arthroscopic partial meniscectomy

description: Gene expression in torn meniscus


title: 005 arthroscopic partial meniscectomy

description: Gene expression in torn meniscus


title: noRNA 16h rep 3


title: Vehicle_EAE

city: Taipei

first: I-Tsu

last: Chyuan

address: No.1 Jen Ai Rord Section 1

country: Taiwan

institute: National Taiwan University

data_processing:
Basecalls performed using bcl2fastq 2.1.7
Quality/Adaptor adapter sequence were trimmed by Trimmomatics 0.3.2 for clean reads.
Clean reads were aligned to GRCm38 with Tophat 2.1.1
Expresiion profiling and differential expressed analysis by cuffdiff 2.2.1
Genome_build: GRCm38
Supplementary_files_format_and_content: Expresiion profiling data in FPKM

source_name: splenic CD4+ T cell

extract_protocol:
Splenic CD4+ T cells were isolated, flash frozen on dry ice, and RNA was harvested using Trizol reagent. RNA purified was quantified at OD260nm by using a ND-1000 spectrophotometer (Nanodrop Technology, USA) and qualitated by using a Bioanalyzer 2100 (Agilent Technology, USA) with RNA 6000 labchip kit (Agilent Technologies, USA).
Libraries were prepared according to Agilent's SureSelect Strand Specific RNA Library Preparation Kit (Cat no.G9691A ).

tag: strain

value: splenic CD4+ T cell

tag: agent


title: pU/UC 16h rep 2


title: Ctrl


title: 106 osteoarthritis

description: Gene expression in OA meniscus


title: noRNA 16h rep 2


title: ChIP-seq for SATB1

first: Yang

last: Li

address: Dongchuan Rd. 800

institute: Shanghai Jiao Tong University

description: ChIP-seq data

data_processing:
Basecall was performed using CAVASA version 1.8
ChIP-seq reads were aligned to human genome hg19 using bowtie 1.1.2.
samtools was used to selecte the unique mapping data and remove the duplications.
peaks were called using macs2 2.1.1 with default setting.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig file generated using deeptools and the bed files were generated using macs2 2.1.1.

source_name: HepG2 Cell line (ATCC® HB-8065™)

growth_protocol: Cells were cultured in DMEM  median following ATCC cell culture   guide.

extract_protocol:
The chromatin was decross-linked at 65 oC over night in TE buffer with 1% SDS, 500 mM NaCl, 20 ug of Proteinase K. DNA was extracted and purified with Qiagen MinElute kit.
After reverse crosslinking, ChIP and input DNA fragments were used for library construction  with NEBNext Ultra Ligation Module (E7445, NEB)

treatment_protocol: Cells were crossed linked with 1% formaldehyde for 10 min at room temperature.

tag: cell line

tag: antibody


title: noRNA 6h rep 1


title: ChIP-seq for NFIC

description: ChIP-seq data

value: NFIC


title: Trail_EAE

tag: cell type

value: TRAIL


title: 002 arthroscopic partial meniscectomy

description: Gene expression in torn meniscus


title: 001 arthroscopic partial meniscectomy

description: Gene expression in torn meniscus


title: noRNA 16h rep 1


title: 003 arthroscopic partial meniscectomy

description: Gene expression in torn meniscus


title: 004 arthroscopic partial meniscectomy

description: Gene expression in torn meniscus


title: R848 16h rep 2


title: ChIP-seq for SMRC1

description: ChIP-seq data


title: Input

description: Input data


title: CT06_104

status: Public on Dec 25 2017

city: Hoesholm

first: Anker

last: Hansen

address: Venlighedsvej 1

institute: Medical Prognosis Institute A/S

description:
FFPE
pre-treatment

hyb_protocol: Affymetrix standardized protocol for U133p2 array

data_processing: R, affypackage, justRMA

label: Biotin-PE

source_name: non-small cell lung cancer

label_protocol: Affymetrix SensationPlus™ FFPE Amplification and 3’ IVT Labeling

extract_protocol: RecoverAll total RNA extraction

value: non-small cell lung cancer


title: CT06_101

description:
FFPE
pre-treatment

scan_protocol: Affymetrix standardized protocol for U133p2 array


title: CT06_098

description:
FFPE
pre-treatment


title: CT06_076

description:
FFPE
pre-treatment


title: CT06_102

description:
FFPE
pre-treatment


title: CT06_084

description:
FFPE
pre-treatment


title: CT06_083

description:
FFPE
pre-treatment


title: CT06_092

description:
FFPE
pre-treatment


title: CT06_090

description:
FFPE
pre-treatment


title: CT06_100

description:
FFPE
pre-treatment


title: CT06_089

description:
FFPE
pre-treatment


title: CT06_087

description:
FFPE
pre-treatment


title: CT06_085

description:
FFPE
pre-treatment


title: CT06_081

description:
FFPE
pre-treatment


title: CT06_073

description:
FFPE
pre-treatment


title: CT06_080

description:
FFPE
pre-treatment


title: CT06_096

description:
FFPE
pre-treatment


title: CT06_094

description:
FFPE
pre-treatment


title: CT06_093

description:
FFPE
pre-treatment


title: CT06_095

description:
FFPE
pre-treatment


title: CT06_091

description:
FFPE
pre-treatment


title: CT06_099

description:
FFPE
pre-treatment


title: CT06_086

description:
FFPE
pre-treatment


title: CT06_075

description:
FFPE
pre-treatment


title: CT06_097

description:
FFPE
pre-treatment


title: CT06_077

description:
FFPE
pre-treatment


title: CT06_074

description:
FFPE
pre-treatment


title: CT06_079

description:
FFPE
pre-treatment


title: CT06_072

description:
FFPE
pre-treatment


title: CT06_071

description:
FFPE
pre-treatment


title: CT06_068

description:
FFPE
pre-treatment


title: CT06_067

description:
FFPE
pre-treatment


title: CT06_065

description:
FFPE
pre-treatment


title: Mckrae_infected_day7_splenocyte_rep1

city: Kunming

first: Xiaolong

address: 935 jiaoling Road

institute: Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College

description:
Mckrae-day7-1
Gene expression of Mckrae infected mice splenocytes at day 7 post-infection.

hyb_protocol: Each slide was hybridized with 600 ng Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent Technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent Technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit (Cat.# 5188-5327, Agilent Technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent Technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit. Data were extracted with Feature Extraction software 10.7 (Agilent Technologies, Santa Clara, CA, US).

data_processing:
The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
Raw data were normalized by Quantile algorithm, limma packages in R.

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat.# 5190-2305, Agilent Technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

extract_protocol: Total RNA was extracted and purified using miRNeasy Mini Kit (Cat#217004, QIAGEN, GmBH, Germany) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, US).

treatment_protocol: The HSV-1 mutant strain M3 or wild type strain Mckrae infected BALB/c mice and uninfected control mice were sacrificed at indicated time points post-infection (day 7/ day 30/ day 60). The splenocyte of the mice were homogenated into single cells.

tag: strain/background

value: BALB/c

value: female

tag: age

value: 4 weeks

value: splenocytes

tag: infection

value: HSV-1 wild type strain Mckrae

value: day 7


title: CT06_070

description:
FFPE
pre-treatment


title: M3_infected_day60_splenocyte_rep2

description:
M3-day60-2
Gene expression of M3 infected mice splenocytes at day 60 post-infection.

value: HSV-1 mutant strain M3

tag: time point

value: day 60


title: M3_infected_day60_splenocyte_rep1

description:
M3-day60-1
Gene expression of M3 infected mice splenocytes at day 60 post-infection.


title: CT06_066

description:
FFPE
pre-treatment


title: CT06_061

description:
FFPE
pre-treatment


title: CT06_056

description:
FFPE
pre-treatment


title: CT06_055

description:
FFPE
pre-treatment


title: CT06_063

description:
FFPE
pre-treatment


title: M3_infected_day7_splenocyte_rep3

description:
M3-day7-3
Gene expression of M3 infected mice splenocytes at day 7 post-infection.


title: CT06_057

description:
FFPE
pre-treatment


title: M3_infected_day30_splenocyte_rep1

description:
M3-day30-1
Gene expression of M3 infected mice splenocytes at day 30 post-infection.

value: day 30


title: CT06_064

description:
FFPE
pre-treatment


title: CT06_051

description:
FFPE
pre-treatment


title: CT06_060

description:
FFPE
pre-treatment


title: Mckrae_infected_day7_splenocyte_rep3

description:
Mckrae-day7-3
Gene expression of Mckrae infected mice splenocytes at day 7 post-infection.


title: CT06_052

description:
FFPE
pre-treatment


title: CT06_054

description:
FFPE
pre-treatment


title: CT06_058

description:
FFPE
pre-treatment


title: CT06_069

description:
FFPE
pre-treatment


title: M3_infected_day30_splenocyte_rep2

description:
M3-day30-2
Gene expression of M3 infected mice splenocytes at day 30 post-infection.


title: Mckrae_infected_day7_splenocyte_rep2

description:
Mckrae-day7-2
Gene expression of Mckrae infected mice splenocytes at day 7 post-infection.


title: M3_infected_day30_splenocyte_rep3

description:
M3-day30-3
Gene expression of M3 infected mice splenocytes at day 30 post-infection.


title: uninfected-mice_splenocyte_rep2

description:
control-2
Gene expression of uninfected mice splenocytes.


title: M3_infected_day7_splenocyte_rep2

description:
M3-day7-2
Gene expression of M3 infected mice splenocytes at day 7 post-infection.


title: CT06_047

description:
FFPE
pre-treatment


title: CT06_050

description:
FFPE
pre-treatment


title: CT06_049

description:
FFPE
pre-treatment


title: uninfected-mice_splenocyte_rep1

description:
control-1
Gene expression of uninfected mice splenocytes.


title: CT06_048

description:
FFPE
pre-treatment


title: CT06_046

description:
FFPE
pre-treatment


title: CT06_040

description:
FFPE
pre-treatment


title: CT06_045

description:
FFPE
pre-treatment


title: CT06_044

description:
FFPE
pre-treatment


title: CT06_039

description:
FFPE
pre-treatment


title: CT06_078

description:
FFPE
pre-treatment


title: CT06_043

description:
FFPE
pre-treatment


title: uninfected-mice_splenocyte_rep3

description:
control-3
Gene expression of uninfected mice splenocytes.


title: CT06_042

description:
FFPE
pre-treatment


title: CT06_037

description:
FFPE
pre-treatment