title: 7802946015_R02C02


title: 7785496019_R05C01

status: Public on May 24 2019

type: genomic

city: Hefei

first: Chao

last: Yang

address: #69 Meishan Road, Hefei230032, Anhui, China

country: China

institute: First Affiliated Hospital of Anhui Medical University

hyb_protocol: The whole genome genotyping was conducted at Chinese National Human Genome  Center at Shanghai, China. Approximately 200ng of genomic DNA was used for  genotyping analysis. Briefly, each sample was whole-genome amplified, fragmented,  precipitated and resuspended in appropriate hybridization buffer.

scan_protocol: After  hybridization, the BeadChip oligonucleotides were extended by a single labeled base,  which was detected by fluorescence imaging with an Illumina Bead Array Reader.

data_processing:
Genomic DNA extracted from whole blood was genotyped using Illumina Human Exome Asian BeadChip  (Illumina).
Processed data file includes: Genotype: AA,AB,BB,or NC (no call), GC Score, Theta, R, B Allele Freq and Log R ratio

label: not provided

molecule: genomic DNA

organism: Homo sapiens

source_name: Public control

label_protocol: not provided

extract_protocol: Genomic DNA was extracted from peripheral blood lymphocytes by standard  procedures (Miller et al, 1988) using Flexi Gene DNA kits (QIAGEN, Germany)

tag: gender

value: Unknown

tag: tissue

value: Whole blood

tag: disease state

value: Chronic inflammatory skin disease


title: 7785496083_R06C02

description: Genomic DNA extracted from whole blood was genotyped using Illumina Human Exome Asian BeadChip  (Illumina).


title: 7785496083_R05C02


title: 7802946015_R01C01


title: 7802946015_R02C01


title: 7802946015_R01C02


title: 7785496083_R06C01


title: 7785496019_R01C01


title: 7785496083_R03C01


title: 7785496083_R04C01


title: 7802946015_R06C02


title: 7785496083_R02C02


title: 7785496083_R01C02


title: 7785496083_R02C01


title: 7785496083_R03C02


title: 7785496083_R01C01


title: 7785496083_R05C01


title: 7785496082_R06C02


title: 7785496082_R06C01


title: 7785496082_R05C01


title: 7785496082_R05C02


title: 7785496082_R04C02


title: 7785496082_R03C02


title: 7785496082_R03C01


title: 7785496082_R04C01


title: 7785496082_R02C01


title: 7785496082_R01C02


title: 7785496083_R04C02


title: 7785496082_R01C01


title: 7802962180_R05C01


title: 7802962180_R06C01


title: 7802962180_R05C02


title: 7802962180_R04C02


title: 7802962180_R06C02


title: 7802962180_R04C01


title: 7802962180_R03C02


title: 7802962180_R03C01


title: 7802962180_R01C02


title: 7802962180_R02C01


title: 7802962180_R01C01


title: 7785517064_R06C02


title: 7802962180_R02C02


title: 7785517064_R05C02


title: 7785517064_R04C02


title: 7785517064_R05C01


title: 7785496082_R02C02


title: 7785517064_R03C02


title: 7785517064_R04C01


title: 7785517064_R02C02


title: 7785445020_R01C01


title: 7785517064_R01C02


title: 7785517064_R03C01


title: 7785517064_R02C01


title: 7785517064_R01C01


title: 7802946146_R06C02


title: 7785445097_R02C01


title: 7802946146_R06C01


title: 7802946146_R04C02


title: 7802946146_R03C02


title: 7802946146_R05C02


title: 7802946146_R04C01


title: 7802946146_R03C01


title: 7802946146_R02C02


title: 7802946146_R02C01


title: 7802946146_R01C02


title: 7802946146_R05C01


title: 7762551075_R06C02


title: 7762551075_R06C01


title: 7802946146_R01C01


title: 7762551075_R05C02


title: 7762551075_R03C01


title: 7762551075_R05C01


title: 7762551075_R03C02


title: 7762551075_R02C01


title: 7762551075_R04C02


title: 7762551075_R04C01


title: 7762551075_R02C02


title: 7785496029_R06C01


title: 7785496029_R05C01


title: 7785496029_R04C02


title: 7785496029_R06C02


title: 7785496029_R04C01


title: 7762551075_R01C02


title: 7785496029_R05C02


title: 7762551075_R01C01


title: 7785496029_R03C01


title: 7785496029_R03C02


title: 7785445006_R06C02


title: 7785496029_R02C01


title: 7785496029_R02C02


title: 7785496029_R01C02


title: 7785445006_R04C01


title: 7785445006_R04C02


title: 7785517064_R06C01


title: 7785445006_R05C01


title: 7785445006_R06C01


title: 7785445006_R01C02


title: 7785445006_R02C01


title: 7785445006_R03C01


title: 7785445006_R02C02


title: 7802962156_R06C01


title: 7785445006_R01C01


title: 7802962156_R05C01


title: 7802962156_R04C02


title: 7802962156_R04C01


title: 7802962156_R03C02


title: 7802962156_R01C01


title: 7802962066_R05C02


title: 7785496029_R01C01


title: 7802962066_R05C01


title: 7802962066_R04C02


title: 7785445006_R05C02


title: 7802962066_R06C02


title: 7785445006_R03C02


title: 7802962066_R03C02


title: 7802962066_R02C02


title: 7785496060_R06C02


title: 7802962156_R05C02


title: 7802962066_R06C01


title: 7785496060_R06C01


title: 7785496060_R05C02


title: 7802962156_R06C02


title: 7802962066_R02C01


title: 7802962066_R01C02


title: 7802962066_R01C01


title: 7802962156_R02C02


title: 7802962156_R03C01


title: 7785496060_R05C01


title: 7802962066_R03C01


title: 7785496060_R04C02


title: 7802962156_R01C02


title: 7802962066_R04C01


title: 7785496060_R03C01


title: 7785461054_R06C02


title: 7785496060_R01C01


title: 7785496060_R04C01


title: 7802962156_R02C01


title: 7785461054_R06C01


title: 7785461054_R05C01


title: 7785496060_R02C01


title: 7785496060_R01C02


title: 7785461054_R05C02


title: 7785461054_R02C02


title: 7785461054_R04C02


title: 7785461054_R02C01


title: 7785496060_R02C02


title: 7785461054_R03C02


title: 7787539004_R06C02


title: 7787539004_R05C02


title: 7785461054_R03C01


title: 7787539004_R05C01


title: 7785461054_R01C02


title: 7785461054_R01C01


title: 7785461054_R04C01


title: 7787539004_R02C02


title: 7787539004_R03C02


title: 7787539004_R01C02


title: 7787539004_R01C01


title: 7787539004_R02C01


title: 7785461084_R06C01


title: 7787539004_R06C01


title: 7787539004_R04C02


title: 7785496060_R03C02


title: 7785461084_R05C01


title: Control_ASO_2

type: SRA

city: La Jolla

first: Max

last: Chang

state: CA

address: 9500 Gilman Drive

country: USA

institute: University of California, San Diego

library_source: transcriptomic

data_processing:
transcripts were quantified using kallisto 0.43.1 with parameters --bias --single --rf-stranded -l 200 -s 20
gene expression was merged from transcript-level quantification using txImport version 1.10.1
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text file containing TPM values per sample per gene

molecule: total RNA

organism: Mus musculus

source_name: Liver

extract_protocol:
Total RNA was isolated with Trizol from homogenized tissue and cells and purified using RNeasy columns and RNase free DNase digestion according to the manufacturer’s instructions (QIAGEN).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: antisense oligonucleotide target

value: control


title: ApoCIII_ASO_5

value: apoC-III


title: ApoCIII_ASO_4


title: 7787539004_R04C01


title: 7785461084_R04C02


title: Control_ASO_3


title: Control_ASO_1


title: 7785461084_R03C02


title: 7785461084_R05C02


title: ApoCIII_ASO_2


title: 7785461084_R04C01


title: ApoCIII_ASO_3


title: 7785461084_R03C01


title: ApoCIII_ASO_1


title: Microglia 10 days post LPC 3

city: Edinburgh

first: Veronique

last: Miron

address: 49 Little France Crescent

department: UK DRI

country: United Kingdom

institute: The University of Edinburgh

description:
100 paired end sequence reads
Sample 6

data_processing:
Alignment to mouse genome (GRCm38): STAR aligner v2.5.2a
Number of mapped read pairs/gene: GENCODE vM12
Normalization (TMM): R v3.3.2, edgeR v3.16.5
Transformation (VOOM): R v3.3.2, limma v3.30.8
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited text files with raw gene counts for each sample, and normalised data as log2 CPM

molecule: polyA RNA

source_name: Microglia

extract_protocol:
Mice were perfused with ice cold PBS with 10% sodium citrate. Lesions were isolated, manually dounced, and cells isolated by Percoll gradient. Microglia were FACS isolated, first excluding dead cells, then gating on Cd11b+ Ly6G- CD3- Cd45lo cells.
NuGEN Ovation RNAseq System v2 kit (NuGEN) by BGI (Hong Kong). End Repair Mix was added to the amplified cDNA and incubated at 20°C for 30 min. AxyPrep Mag PCR clean up kit (Axygen) was used to purify the end-repaired DNA, which was then combined with A-tailing Mix (Enzymatic) and incubated at 37°C for 30 min. Adaptors (Invitrogen) were ligated to the Adenylate 3’ ends DNA, and incubated at 16°C for 16 h. Insert size was used to select the adaptor-ligated DNA fragments. Several rounds of PCR amplification with PCR Primer cocktail (Invitrogen) and PCR Master Mix (New England Biolabs) were performed to enrich the adaptor-ligated DNA fragments to produce the final library, purified using AxyPrep Mag PCR clean up kit (Axygen). The final library average molecule length was determined using the Bioanalyser 2100 using the DNA 1000 kit (Agilent) and was quantified by real-time qPCR (TaqMan probe). cBot (Illumina) was used to amplify the libraries to generate the cluster on the Flow Cell (HiSeq 4000, Illumina).

treatment_protocol: LPC stereotaxic injection into the corpus callosum and sacrifice at 3 or 10 days post injection.

tag: strain

tag: Sex

value: male

tag: age

value: 10 weeks

tag: cell type

value: Microglia

tag: time point

value: 10 days

tag: agent

value: LPC stereotaxic


title: Microglia 10 days post LPC 2

description:
100 paired end sequence reads
Sample 5


title: Microglia 3 days post LPC 3

description:
100 paired end sequence reads
Sample 3

value: 3 days


title: Microglia 10 days post LPC 1

description:
100 paired end sequence reads
Sample 4


title: 7785461084_R02C01


title: su014_pre_Tcell_TCR

city: Stanford

first: Howard

middle: Y

address: CCSR 2130, 269 Campus Drive

department: Center for Personal Dynamic Regulomes

institute: Stanford University

description: TCR library (10X Genomics)

data_processing:
Processed with cellranger pipeline, version 2.1.0
Genome_build: GRCh38

source_name: Squamous cell carcinoma tumor

extract_protocol: 10X Genomics Single Cell 5' Library & Gel Bead Kit

tag: donor

tag: treatment

value: pre


title: 7787539004_R03C01


title: 7785461084_R01C02


title: 7802946010_R06C02


title: 7785461084_R06C02


title: 7802946010_R04C02


title: 7802946010_R06C01


title: 7802946010_R05C02


title: su013_pre_Tcell_TCR

description: TCR library (10X Genomics)


title: su014_post_Tcell_TCR

description: TCR library (10X Genomics)

value: post


title: Control_ASO_4


title: 7802946010_R05C01


title: su012_pre_Tcell_TCR

description: TCR library (10X Genomics)

source_name: Basal cell carcinoma tumor


title: 7802946010_R03C02


title: 7785461084_R02C02


title: su012_post_Tcell_TCR

description: TCR library (10X Genomics)


title: su011_pre_Tcell_rep1_TCR

description: TCR library (10X Genomics)


title: Microglia 3 days post LPC 1

description:
100 paired end sequence reads
Sample 1


title: su013_post_Tcell_TCR

description: TCR library (10X Genomics)


title: 7802946010_R02C02


title: 7802946010_R02C01


title: su011_post_Tcell_TCR

description: TCR library (10X Genomics)


title: 7802946010_R01C01


title: 7785461091_R06C01


title: 7802946010_R01C02


title: 7802946010_R04C01


title: su010_pre_BCC_Tcell_TCR

description: TCR library (10X Genomics)


title: su010_pre_SCC_Tcell_rep1_TCR

description: TCR library (10X Genomics)


title: 7785461084_R01C01


title: 7785461091_R06C02


title: su011_pre_Tcell_rep2_TCR

description: TCR library (10X Genomics)


title: su010_post_SCC_CD39_Tcell_TCR

description: TCR library (10X Genomics)


title: 7802946010_R03C01


title: su009_post_Tcell_TCR

description: TCR library (10X Genomics)


title: su014_pre_Tcell_RNA

description: 5' gene expression library (10X Genomics)


title: 7785461091_R05C02


title: su010_post_BCC_Tcell_TCR

description: TCR library (10X Genomics)


title: su010_post_SCC_Tcell_TCR

description: TCR library (10X Genomics)


title: 7785461091_R02C02


title: su014_post_Tcell_RNA


title: su009_pre_Tcell_TCR

description: TCR library (10X Genomics)


title: su013_post_Tcell_RNA


title: 7785461091_R04C01


title: 7785461091_R04C02


title: 7785461091_R03C02


title: 7785461091_R03C01


title: 7785461091_R01C02


title: 7785461091_R01C01


title: 7785461091_R02C01


title: su012_pre_Tcell_RNA


title: su012_post_Tcell_RNA


title: su010_pre_SCC_Tcell_rep2_RNA


title: 7785496097_R06C01


title: 7785496097_R05C01


title: su010_pre_SCC_Tcell_rep1_RNA


title: 7785496097_R06C02


title: su011_pre_Tcell_rep1_RNA


title: su011_post_Tcell_RNA


title: su010_post_SCC_Tcell_RNA


title: 7785496097_R05C02


title: 7785496097_R04C01


title: su010_post_SCC_CD39_Tcell_RNA


title: su010_post_BCC_Tcell_RNA


title: 7785496097_R03C01


title: su010_pre_SCC_Tcell_rep2_TCR

description: TCR library (10X Genomics)


title: 7785496097_R02C02


title: 7785496097_R03C02


title: 7785496097_R04C02


title: su009_pre_Tcell_RNA


title: su010_pre_BCC_Tcell_RNA


title: 7785496097_R01C01


title: 7785496097_R01C02


title: 7785461091_R05C01


title: su003_post1_Tcell_CD45_RNA


title: su009_post_Tcell_RNA


title: su013_pre_Tcell_RNA


title: su008_post_Tcell_RNA


title: 7785488012_R06C02


title: su003_post1_Tumor_RNA


title: su011_pre_Tcell_rep2_RNA


title: 7785488012_R06C01


title: su007_post_TCR

description: TCR library (10X Genomics)

data_processing:
Library strategy: TCR-seq
Processed with cellranger pipeline, version 2.1.0
R1 contains barcode at bp 1-16 and UMI at bp 17-26
R2 contains the biological sequence.
Genome_build: GRCh38
Supplementary_files_format_and_content: text file with raw counts for scRNA-seq; tcr_all.txt processed data consists of amino acid and nucleotide sequences for the TCR sequences assigned to each cell.

source_name: Basal cell carinoma tumor

value: All


title: 7785488012_R05C01


title: 7785488012_R05C02


title: su007_pre_TCR

description: TCR library (10X Genomics)


title: 7785488012_R04C02


title: su005_post_TCR

description: TCR library (10X Genomics)


title: su005_pre_TCR

description: TCR library (10X Genomics)


title: 7785488012_R02C02


title: su004_post_TCR

description: TCR library (10X Genomics)


title: 7785488012_R03C01


title: 7785496097_R02C01


title: su002_post_TCR

description: TCR library (10X Genomics)


title: su004_pre_TCR

description: TCR library (10X Genomics)


title: 7785488012_R01C01


title: 7785488076_R06C01


title: su001_pre2_TCR

description: TCR library (10X Genomics)


title: su001_post_TCR

description: TCR library (10X Genomics)


title: 7785488076_R06C02


title: su008_post_Tumor_CD45_RNA

data_processing:
Processed with cellranger pipeline, version 2.1.0
R1 contains barcode at bp 1-16 and UMI at bp 17-26
R2 contains the biological sequence.
Genome_build: GRCh38
Supplementary_files_format_and_content: text file with raw counts for scRNA-seq; tcr_all.txt processed data consists of amino acid and nucleotide sequences for the TCR sequences assigned to each cell.


title: 7785488076_R05C02


title: 7785488012_R04C01


title: su007_pre_Tumor_CD45_RNA


title: su007_pre_Tcell_RNA


title: su006_post_Tumor_RNA


title: 7785488076_R04C01


title: 7785488076_R04C02


title: 7785488012_R03C02


title: su006_post_Tcell_RNA


title: 7785488012_R02C01


title: 7785488076_R03C01


title: su003_pre_TCR

description: TCR library (10X Genomics)


title: 7785488076_R02C02


title: su006_post_CD45_RNA


title: 7785488012_R01C02


title: su002_pre_TCR

description: TCR library (10X Genomics)


title: su006_pre_Tumor_RNA


title: 7785488076_R02C01


title: 7785488076_R01C02


title: su006_pre_CD45_RNA


title: su005_post_Tumor_CD45_RNA


title: 7785488076_R05C01


title: su007_post_All_RNA


title: 7787547080_R06C02


title: su005_post_Tcell_RNA


title: su005_pre_Tumor_RNA


title: 7785488076_R01C01


title: su005_pre_CD45_RNA


title: su004_post_Tumor_CD45_RNA


title: 7787547080_R05C02


title: su005_pre_Tcell_RNA


title: 7787547080_R04C02


title: su008_post_TCR

description: TCR library (10X Genomics)


title: 7787547080_R05C01


title: 7787547080_R04C01


title: 7787547080_R03C02


title: 7787547080_R03C01


title: su004_pre_Tcell_RNA


title: su004_pre_Tumor_CD45_RNA


title: 7787547080_R02C02


title: 7787547080_R02C01


title: su006_pre_Tcell_RNA


title: 7785488076_R03C02


title: su003_post2_All_RNA


title: 7787547080_R01C02


title: su003_pre_All_RNA


title: su002_post_Tumor_CD45_RNA


title: 7787547080_R06C01


title: 7802954052_R06C02


title: 7787547080_R01C01


title: su002_pre_All_RNA


title: 7802954052_R06C01


title: su001_post_Tumor_CD45_RNA


title: su001_post_Tcell_RNA


title: 7802954052_R05C02


title: 7802954052_R05C01


title: su001_pre1_Tumor_CD45_RNA


title: su004_post_Tcell_RNA


title: su001_pre2_All_RNA


title: 7802954052_R04C02


title: su001_pre1_Tcell_RNA


title: 7802954052_R04C01


title: 7802954052_R03C02


title: 7802954052_R03C01


title: 7802954052_R02C02


title: 7802954052_R01C02


title: 7802954052_R02C01


title: 7802954052_R01C01


title: 7785488086_R06C02


title: su002_post_Tcell_RNA


title: 7785488086_R05C02


title: 7785488086_R06C01


title: 7785488086_R05C01


title: 7785488086_R03C01


title: 7785488086_R04C01


title: 7785488086_R03C02


title: 7785488086_R02C02


title: 7785488086_R01C02


title: 7785488086_R02C01


title: 7785488086_R01C01


title: Braak_NFT_stage_V-VI_subject-17_EC (gene-level)

type: RNA

city: Niigata

first: Akinori

last: Miyashita

address: 1-757 Asahimachi, Chuo-ku

department: Department of Molecular Genetics

country: Japan

institute: Brain Research Institute, Niigata University

description:
BN_V-VI_17_EC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)

hyb_protocol: Samples were hybridized with GeneChip Human Exon 1.0 ST Arrays (Affymetrix) and scanned in our laboratory.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: The initial raw data (DAT files) were processed into CEL files via the Affymetrix GeneChip Operating Software. The CEL files were imported into Partek Genomics Suite 6.4 (Partek, St Louis, MO, USA) and then normalized, and their backgrounds were corrected by means of a robust multi-array average method with adjustment for GC content. The expression levels of all probesets in the CEL files were log2-transformed. Core meta-probesets including 232,479 probesets (Affymetrix reference file name: HuEx-1_0-st-v2.r2.dtl.hg18.core.mps) were used. Among them, we excluded probesets that did not have an official gene symbol and did not exhibit a maximum signal intensity of 5.0 across all exon arrays (N = 213). Consequently, 190,447 probesets per CEL file were analyzed in further examinations.

label: biotin

source_name: Braak NFT stage V-VI

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Not applied

extract_protocol: Total RNA from brain tissues was extracted with a TRIzol Plus RNA Purification System (Life Technologies, Carlsbad, CA, USA). Genomic DNA was removed through on-column DNase I treatment during the RNA preparation. For determination of the RNA integrity number (1 [totally degraded] to 10 [intact]), a 2100 Bioanalyzer instrument was used with the RNA 6000 Pico Assay (Agilent, Santa Clara, CA, USA). We fluorometrically determined the concentration of total RNA with a Quant-iT RiboGreen RNA Assay Kit (Life Technologies).

treatment_protocol: Not applied

tag: subject id

value: brain

tag: tissue region

value: Entorhinal cortex (EC)

value: M

tag: braak nft stage

value: V-VI


title: 7802962094_R06C01

value: Unknown

value: Whole blood


title: Braak_NFT_stage_V-VI_subject-17_FC (gene-level)

description:
BN_V-VI_17_FC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)

value: Frontal cortex (FC)


title: 7802962094_R06C02

value: Chronic inflammatory skin disease


title: 7785488086_R04C02


title: Braak_NFT_stage_V-VI_subject-19_TC (gene-level)

description:
BN_V-VI_19_TC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)

value: Temporal cortex (TC)

value: F


title: Braak_NFT_stage_V-VI_subject-17_TC (gene-level)

description:
BN_V-VI_17_TC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_V-VI_subject-19_FC (gene-level)

description:
BN_V-VI_19_FC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_V-VI_subject-18_FC (gene-level)

description:
BN_V-VI_18_FC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_V-VI_subject-16_TC (gene-level)

description:
BN_V-VI_16_TC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_V-VI_subject-18_TC (gene-level)

description:
BN_V-VI_18_TC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_V-VI_subject-15_FC (gene-level)

description:
BN_V-VI_15_FC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_V-VI_subject-16_EC (gene-level)

description:
BN_V-VI_16_EC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_V-VI_subject-18_EC (gene-level)

description:
BN_V-VI_18_EC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_V-VI_subject-19_EC (gene-level)

description:
BN_V-VI_19_EC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_V-VI_subject-16_FC (gene-level)

description:
BN_V-VI_16_FC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_V-VI_subject-15_TC (gene-level)

description:
BN_V-VI_15_TC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_V-VI_subject-14_FC (gene-level)

description:
BN_V-VI_14_FC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_V-VI_subject-14_EC (gene-level)

description:
BN_V-VI_14_EC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_V-VI_subject-14_TC (gene-level)

description:
BN_V-VI_14_TC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: 7802962094_R05C02

description: Genomic DNA extracted from whole blood was genotyped using Illumina Human Exome Asian BeadChip  (Illumina).


title: Braak_NFT_stage_V-VI_subject-15_EC (gene-level)

description:
BN_V-VI_15_EC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: 7802962094_R05C01


title: 7802962094_R04C02


title: Braak_NFT_stage_V-VI_subject-13_FC (gene-level)

description:
BN_V-VI_13_FC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: 7802962094_R04C01


title: Braak_NFT_stage_V-VI_subject-13_TC (gene-level)

description:
BN_V-VI_13_TC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_V-VI_subject-12_TC (gene-level)

description:
BN_V-VI_12_TC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_V-VI_subject-13_EC (gene-level)

description:
BN_V-VI_13_EC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: 7802962094_R03C02


title: 7802962094_R02C02


title: 7802962094_R03C01


title: 7802962094_R02C01


title: Braak_NFT_stage_V-VI_subject-12_FC (gene-level)

description:
BN_V-VI_12_FC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: 7802962094_R01C01


title: 7785496041_R06C02


title: 7785496041_R05C02


title: 7785496041_R06C01


title: Braak_NFT_stage_V-VI_subject-12_EC (gene-level)

description:
BN_V-VI_12_EC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: 7785496041_R03C02


title: 7785496041_R04C02


title: Braak_NFT_stage_V-VI_subject-11_FC (gene-level)

description:
BN_V-VI_11_FC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: 7785496041_R04C01


title: Braak_NFT_stage_V-VI_subject-11_TC (gene-level)

description:
BN_V-VI_11_TC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_V-VI_subject-11_EC (gene-level)

description:
BN_V-VI_11_EC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: 7785496041_R02C02


title: 7802962094_R01C02


title: Braak_NFT_stage_V-VI_subject-10_TC (gene-level)

description:
BN_V-VI_10_TC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_V-VI_subject-08_TC (gene-level)

description:
BN_V-VI_08_TC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_V-VI_subject-09_EC (gene-level)

description:
BN_V-VI_09_EC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: 7785496041_R05C01


title: Braak_NFT_stage_V-VI_subject-10_EC (gene-level)

description:
BN_V-VI_10_EC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_V-VI_subject-10_FC (gene-level)

description:
BN_V-VI_10_FC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_V-VI_subject-09_FC (gene-level)

description:
BN_V-VI_09_FC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_V-VI_subject-09_TC (gene-level)

description:
BN_V-VI_09_TC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: 7785496041_R02C01

description: Genomic DNA extracted from whole blood was genotyped using Illumina Human Exome Asian BeadChip  (Illumina).


title: Braak_NFT_stage_V-VI_subject-08_FC (gene-level)

description:
BN_V-VI_08_FC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: 7785496041_R03C01


title: Braak_NFT_stage_V-VI_subject-08_EC (gene-level)

description:
BN_V-VI_08_EC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: 7802946043_R06C01


title: 7785496041_R01C02


title: 7785496041_R01C01


title: 7802946043_R04C02


title: 7802946043_R03C02


title: 7802946043_R02C02


title: 7802946043_R03C01


title: Braak_NFT_stage_V-VI_subject-06_TC (gene-level)

description:
BN_V-VI_06_TC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: 7802946043_R05C02


title: 7802946043_R06C02


title: 7802946043_R02C01


title: 7802946043_R05C01


title: 7802946043_R01C02


title: Braak_NFT_stage_V-VI_subject-07_TC (gene-level)

description:
BN_V-VI_07_TC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_V-VI_subject-06_FC (gene-level)

description:
BN_V-VI_06_FC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_V-VI_subject-07_FC (gene-level)

description:
BN_V-VI_07_FC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_V-VI_subject-06_EC (gene-level)

description:
BN_V-VI_06_EC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_V-VI_subject-04_FC (gene-level)

description:
BN_V-VI_04_FC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_V-VI_subject-03_FC (gene-level)

description:
BN_V-VI_03_FC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_V-VI_subject-04_EC (gene-level)

description:
BN_V-VI_04_EC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_V-VI_subject-07_EC (gene-level)

description:
BN_V-VI_07_EC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_V-VI_subject-05_EC (gene-level)

description:
BN_V-VI_05_EC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: 7802946043_R04C01


title: Braak_NFT_stage_V-VI_subject-04_TC (gene-level)

description:
BN_V-VI_04_TC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_V-VI_subject-05_TC (gene-level)

description:
BN_V-VI_05_TC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_V-VI_subject-03_EC (gene-level)

description:
BN_V-VI_03_EC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_V-VI_subject-02_TC (gene-level)

description:
BN_V-VI_02_TC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: 7802946043_R01C01

description: Genomic DNA extracted from whole blood was genotyped using Illumina Human Exome Asian BeadChip  (Illumina).


title: Braak_NFT_stage_V-VI_subject-03_TC (gene-level)

description:
BN_V-VI_03_TC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: 7785533096_R06C02


title: 7785533096_R03C02


title: 7785533096_R06C01


title: Braak_NFT_stage_V-VI_subject-05_FC (gene-level)

description:
BN_V-VI_05_FC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_V-VI_subject-02_FC (gene-level)

description:
BN_V-VI_02_FC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: 7785533096_R05C02


title: Braak_NFT_stage_III-IV_subject-19_TC (gene-level)

description:
BN_III-IV_19_TC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)

source_name: Braak NFT stage III-IV

value: III-IV


title: 7785533096_R02C02


title: Braak_NFT_stage_V-VI_subject-02_EC (gene-level)

description:
BN_V-VI_02_EC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: 7785533096_R05C01


title: Braak_NFT_stage_V-VI_subject-01_TC (gene-level)

description:
BN_V-VI_01_TC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: 7785533096_R01C01


title: 7785533096_R01C02


title: 7785533096_R04C02


title: Braak_NFT_stage_III-IV_subject-19_EC (gene-level)

description:
BN_III-IV_19_EC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_III-IV_subject-18_FC (gene-level)

description:
BN_III-IV_18_FC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_III-IV_subject-18_TC (gene-level)

description:
BN_III-IV_18_TC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_III-IV_subject-18_EC (gene-level)

description:
BN_III-IV_18_EC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: 7785533096_R04C01


title: Braak_NFT_stage_V-VI_subject-01_FC (gene-level)

description:
BN_V-VI_01_FC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_V-VI_subject-01_EC (gene-level)

description:
BN_V-VI_01_EC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_III-IV_subject-17_FC (gene-level)

description:
BN_III-IV_17_FC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: 7785533096_R02C01


title: Braak_NFT_stage_III-IV_subject-17_TC (gene-level)

description:
BN_III-IV_17_TC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: 7802962059_R05C02


title: 7802962059_R06C02


title: Braak_NFT_stage_III-IV_subject-19_FC (gene-level)

description:
BN_III-IV_19_FC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: 7802962059_R06C01


title: 7785533096_R03C01


title: 7802962059_R05C01


title: 7802962059_R04C02


title: Braak_NFT_stage_III-IV_subject-16_TC (gene-level)

description:
BN_III-IV_16_TC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: 7802962059_R04C01

description: Genomic DNA extracted from whole blood was genotyped using Illumina Human Exome Asian BeadChip  (Illumina).


title: 7802962059_R03C02


title: 7802962059_R03C01


title: Braak_NFT_stage_III-IV_subject-16_FC (gene-level)

description:
BN_III-IV_16_FC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: 7802962059_R02C02


title: 7802962059_R02C01


title: Braak_NFT_stage_III-IV_subject-15_EC (gene-level)

description:
BN_III-IV_15_EC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_III-IV_subject-17_EC (gene-level)

description:
BN_III-IV_17_EC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: 7802962059_R01C02


title: 7802962059_R01C01


title: Braak_NFT_stage_III-IV_subject-15_FC (gene-level)

description:
BN_III-IV_15_FC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: 7802962169_R05C02


title: 7802962169_R05C01


title: 7802962169_R06C01


title: 7802962169_R04C02


title: 7802962169_R04C01


title: 7802962169_R03C02


title: 7802962169_R03C01


title: Braak_NFT_stage_III-IV_subject-12_TC (gene-level)

description:
BN_III-IV_12_TC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_III-IV_subject-16_EC (gene-level)

description:
BN_III-IV_16_EC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_III-IV_subject-14_TC (gene-level)

description:
BN_III-IV_14_TC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_III-IV_subject-13_TC (gene-level)

description:
BN_III-IV_13_TC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_III-IV_subject-14_EC (gene-level)

description:
BN_III-IV_14_EC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_III-IV_subject-15_TC (gene-level)

description:
BN_III-IV_15_TC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_III-IV_subject-13_EC (gene-level)

description:
BN_III-IV_13_EC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_III-IV_subject-13_FC (gene-level)

description:
BN_III-IV_13_FC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_III-IV_subject-14_FC (gene-level)

description:
BN_III-IV_14_FC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: 7802962169_R02C02


title: Braak_NFT_stage_III-IV_subject-12_EC (gene-level)

description:
BN_III-IV_12_EC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_III-IV_subject-12_FC (gene-level)

description:
BN_III-IV_12_FC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: 7802962169_R01C01


title: Braak_NFT_stage_III-IV_subject-10_FC (gene-level)

description:
BN_III-IV_10_FC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_III-IV_subject-10_TC (gene-level)

description:
BN_III-IV_10_TC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_III-IV_subject-11_TC (gene-level)

description:
BN_III-IV_11_TC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: 7802962169_R06C02

description: Genomic DNA extracted from whole blood was genotyped using Illumina Human Exome Asian BeadChip  (Illumina).


title: 7802962169_R02C01


title: Braak_NFT_stage_III-IV_subject-09_TC (gene-level)

description:
BN_III-IV_09_TC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_III-IV_subject-11_EC (gene-level)

description:
BN_III-IV_11_EC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: 7785445039_R06C02


title: 7785445039_R06C01


title: Braak_NFT_stage_III-IV_subject-10_EC (gene-level)

description:
BN_III-IV_10_EC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: 7785445039_R04C02


title: 7785445039_R05C01


title: Braak_NFT_stage_III-IV_subject-09_EC (gene-level)

description:
BN_III-IV_09_EC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: 7785445039_R04C01


title: 7785445039_R02C02


title: 7785445039_R05C02


title: Braak_NFT_stage_III-IV_subject-11_FC (gene-level)

description:
BN_III-IV_11_FC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: 7785445039_R03C02


title: Braak_NFT_stage_III-IV_subject-09_FC (gene-level)

description:
BN_III-IV_09_FC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: 7802962169_R01C02


title: 7785445039_R01C02


title: 7785445039_R03C01


title: Braak_NFT_stage_III-IV_subject-08_FC (gene-level)

description:
BN_III-IV_08_FC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: 7785445039_R02C01


title: Braak_NFT_stage_III-IV_subject-07_TC (gene-level)

description:
BN_III-IV_07_TC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_III-IV_subject-07_FC (gene-level)

description:
BN_III-IV_07_FC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_III-IV_subject-08_TC (gene-level)

description:
BN_III-IV_08_TC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: 7785445039_R01C01


title: 7785496050_R05C01


title: 7785496050_R06C02


title: Braak_NFT_stage_III-IV_subject-07_EC (gene-level)

description:
BN_III-IV_07_EC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: 7785496050_R04C02


title: Braak_NFT_stage_III-IV_subject-08_EC (gene-level)

description:
BN_III-IV_08_EC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: 7785496050_R05C02


title: 7785496050_R03C02


title: 7785496050_R03C01


title: Braak_NFT_stage_III-IV_subject-06_EC (gene-level)

description:
BN_III-IV_06_EC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_III-IV_subject-05_FC (gene-level)

description:
BN_III-IV_05_FC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: 7785496050_R02C02


title: 7785496050_R04C01


title: Braak_NFT_stage_III-IV_subject-05_TC (gene-level)

description:
BN_III-IV_05_TC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_III-IV_subject-04_FC (gene-level)

description:
BN_III-IV_04_FC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_III-IV_subject-06_FC (gene-level)

description:
BN_III-IV_06_FC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_III-IV_subject-05_EC (gene-level)

description:
BN_III-IV_05_EC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_III-IV_subject-04_EC (gene-level)

description:
BN_III-IV_04_EC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_III-IV_subject-06_TC (gene-level)

description:
BN_III-IV_06_TC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_III-IV_subject-04_TC (gene-level)

description:
BN_III-IV_04_TC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: 7785461005_R06C02

description: Genomic DNA extracted from whole blood was genotyped using Illumina Human Exome Asian BeadChip  (Illumina).


title: Braak_NFT_stage_III-IV_subject-03_TC (gene-level)

description:
BN_III-IV_03_TC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: 7785496050_R01C01


title: 7785496050_R06C01


title: 7785496050_R02C01


title: Braak_NFT_stage_III-IV_subject-03_EC (gene-level)

description:
BN_III-IV_03_EC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_III-IV_subject-02_TC (gene-level)

description:
BN_III-IV_02_TC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_III-IV_subject-03_FC (gene-level)

description:
BN_III-IV_03_FC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_III-IV_subject-01_TC (gene-level)

description:
BN_III-IV_01_TC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_III-IV_subject-02_EC (gene-level)

description:
BN_III-IV_02_EC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: 7785496050_R01C02


title: Braak_NFT_stage_III-IV_subject-02_FC (gene-level)

description:
BN_III-IV_02_FC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: 7785461005_R05C01


title: 7785461005_R05C02


title: Braak_NFT_stage_III-IV_subject-01_FC (gene-level)

description:
BN_III-IV_01_FC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: 7785461005_R06C01


title: 7785461005_R04C02


title: 7785461005_R03C01


title: Braak_NFT_stage_III-IV_subject-01_EC (gene-level)

description:
BN_III-IV_01_EC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: 7785461005_R02C02


title: 7785461005_R04C01


title: Braak_NFT_stage_I-II_subject-20_TC (gene-level)

description:
BN_I-II_20_TC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)

source_name: Braak NFT stage I-II

value: I-II


title: 7785461005_R03C02


title: Braak_NFT_stage_I-II_subject-20_FC (gene-level)

description:
BN_I-II_20_FC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_I-II_subject-19_EC (gene-level)

description:
BN_I-II_19_EC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: 7785488007_R06C01


title: 7785488007_R05C02


title: 7785461005_R02C01


title: Braak_NFT_stage_I-II_subject-20_EC (gene-level)

description:
BN_I-II_20_EC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_I-II_subject-17_TC (gene-level)

description:
BN_I-II_17_TC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_I-II_subject-18_EC (gene-level)

description:
BN_I-II_18_EC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_I-II_subject-19_FC (gene-level)

description:
BN_I-II_19_FC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: 7785461005_R01C02

description: Genomic DNA extracted from whole blood was genotyped using Illumina Human Exome Asian BeadChip  (Illumina).


title: Braak_NFT_stage_I-II_subject-19_TC (gene-level)

description:
BN_I-II_19_TC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_I-II_subject-17_EC (gene-level)

description:
BN_I-II_17_EC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_I-II_subject-18_FC (gene-level)

description:
BN_I-II_18_FC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: 7785461005_R01C01


title: Braak_NFT_stage_I-II_subject-16_TC (gene-level)

description:
BN_I-II_16_TC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_I-II_subject-17_FC (gene-level)

description:
BN_I-II_17_FC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_I-II_subject-18_TC (gene-level)

description:
BN_I-II_18_TC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: 7785488007_R05C01


title: 7785488007_R04C01


title: 7785488007_R04C02


title: Braak_NFT_stage_I-II_subject-14_TC (gene-level)

description:
BN_I-II_14_TC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_I-II_subject-16_FC (gene-level)

description:
BN_I-II_16_FC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_I-II_subject-15_EC (gene-level)

description:
BN_I-II_15_EC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_I-II_subject-15_TC (gene-level)

description:
BN_I-II_15_TC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_I-II_subject-16_EC (gene-level)

description:
BN_I-II_16_EC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: 7785488007_R01C02


title: 7785488007_R01C01


title: 7785488007_R06C02


title: 7785488007_R02C02


title: Braak_NFT_stage_I-II_subject-15_FC (gene-level)

description:
BN_I-II_15_FC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: 7802962089_R06C01


title: 7802962089_R06C02


title: 7802962089_R05C02


title: Braak_NFT_stage_I-II_subject-14_FC (gene-level)

description:
BN_I-II_14_FC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: 7802962089_R05C01


title: 7802962089_R04C02


title: 7785488007_R03C02


title: 7785488007_R03C01


title: 7802962089_R04C01


title: 7785488007_R02C01


title: Braak_NFT_stage_I-II_subject-13_TC (gene-level)

description:
BN_I-II_13_TC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_I-II_subject-12_TC (gene-level)

description:
BN_I-II_12_TC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_I-II_subject-13_EC (gene-level)

description:
BN_I-II_13_EC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_I-II_subject-12_FC (gene-level)

description:
BN_I-II_12_FC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_I-II_subject-13_FC (gene-level)

description:
BN_I-II_13_FC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: 7802962089_R02C01

description: Genomic DNA extracted from whole blood was genotyped using Illumina Human Exome Asian BeadChip  (Illumina).


title: Braak_NFT_stage_I-II_subject-11_FC (gene-level)

description:
BN_I-II_11_FC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: 7802962089_R01C02


title: Braak_NFT_stage_I-II_subject-12_EC (gene-level)

description:
BN_I-II_12_EC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_I-II_subject-14_EC (gene-level)

description:
BN_I-II_14_EC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_I-II_subject-10_TC (gene-level)

description:
BN_I-II_10_TC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: 7802962089_R01C01


title: Braak_NFT_stage_I-II_subject-11_EC (gene-level)

description:
BN_I-II_11_EC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_I-II_subject-09_TC (gene-level)

description:
BN_I-II_09_TC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_I-II_subject-10_FC (gene-level)

description:
BN_I-II_10_FC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: 7802962176_R06C02


title: 7802962176_R06C01


title: Braak_NFT_stage_I-II_subject-10_EC (gene-level)

description:
BN_I-II_10_EC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: 7802962176_R05C02


title: 7802962176_R05C01


title: 7802962089_R03C02


title: 7802962089_R03C01


title: Braak_NFT_stage_I-II_subject-09_FC (gene-level)

description:
BN_I-II_09_FC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_I-II_subject-11_TC (gene-level)

description:
BN_I-II_11_TC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_I-II_subject-09_EC (gene-level)

description:
BN_I-II_09_EC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_I-II_subject-08_TC (gene-level)

description:
BN_I-II_08_TC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: 7802962176_R04C02


title: Braak_NFT_stage_I-II_subject-08_FC (gene-level)

description:
BN_I-II_08_FC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_I-II_subject-08_EC (gene-level)

description:
BN_I-II_08_EC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: 7802962089_R02C02


title: 7802962176_R03C02


title: Braak_NFT_stage_I-II_subject-07_TC (gene-level)

description:
BN_I-II_07_TC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: 7802962176_R02C01


title: 7762551106_R06C02


title: 7802962176_R03C01


title: 7802962176_R02C02


title: 7762551106_R06C01


title: 7802962176_R01C01


title: Braak_NFT_stage_I-II_subject-07_FC (gene-level)

description:
BN_I-II_07_FC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_I-II_subject-06_FC (gene-level)

description:
BN_I-II_06_FC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_I-II_subject-06_TC (gene-level)

description:
BN_I-II_06_TC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: 7762551106_R04C02

description: Genomic DNA extracted from whole blood was genotyped using Illumina Human Exome Asian BeadChip  (Illumina).


title: Braak_NFT_stage_I-II_subject-07_EC (gene-level)

description:
BN_I-II_07_EC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_I-II_subject-06_EC (gene-level)

description:
BN_I-II_06_EC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_I-II_subject-05_EC (gene-level)

description:
BN_I-II_05_EC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_I-II_subject-05_FC (gene-level)

description:
BN_I-II_05_FC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: 7762551106_R05C02


title: 7762551106_R03C02


title: Braak_NFT_stage_I-II_subject-05_TC (gene-level)

description:
BN_I-II_05_TC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: 7762551106_R04C01


title: Braak_NFT_stage_I-II_subject-04_EC (gene-level)

description:
BN_I-II_04_EC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_I-II_subject-04_TC (gene-level)

description:
BN_I-II_04_TC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: 7802962176_R04C01


title: Braak_NFT_stage_I-II_subject-04_FC (gene-level)

description:
BN_I-II_04_FC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: 7802962176_R01C02


title: 7762551106_R02C01


title: 7762551106_R05C01


title: 7762551106_R02C02


title: 7762551106_R01C02


title: 7762551106_R03C01


title: Braak_NFT_stage_I-II_subject-03_EC (gene-level)

description:
BN_I-II_03_EC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_I-II_subject-03_TC (gene-level)

description:
BN_I-II_03_TC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: 7762551106_R01C01


title: 7802946145_R06C01


title: 7802946145_R05C02


title: Braak_NFT_stage_I-II_subject-03_FC (gene-level)

description:
BN_I-II_03_FC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_I-II_subject-01_TC (gene-level)

description:
BN_I-II_01_TC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_I-II_subject-01_EC (gene-level)

description:
BN_I-II_01_EC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: 7802946145_R04C02


title: 7802946145_R04C01


title: Braak_NFT_stage_I-II_subject-02_TC (gene-level)

description:
BN_I-II_02_TC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_I-II_subject-02_FC (gene-level)

description:
BN_I-II_02_FC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_I-II_subject-01_FC (gene-level)

description:
BN_I-II_01_FC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: 7802946145_R03C01

description: Genomic DNA extracted from whole blood was genotyped using Illumina Human Exome Asian BeadChip  (Illumina).


title: Braak_NFT_stage_I-II_subject-02_EC (gene-level)

description:
BN_I-II_02_EC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: 7802946145_R03C02


title: 7802946145_R05C01


title: 7802946145_R02C01


title: Braak_NFT_stage_0_subject-13_TC (gene-level)

description:
BN_0_13_TC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)

source_name: Braak NFT stage 0


title: Braak_NFT_stage_0_subject-12_EC (gene-level)

description:
BN_0_12_EC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: 7802946145_R02C02


title: Braak_NFT_stage_0_subject-13_FC (gene-level)

description:
BN_0_13_FC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_0_subject-13_EC (gene-level)

description:
BN_0_13_EC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_0_subject-12_TC (gene-level)

description:
BN_0_12_TC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: 7802946145_R06C02


title: 7802946145_R01C02


title: Braak_NFT_stage_0_subject-11_TC (gene-level)

description:
BN_0_11_TC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: 7802946145_R01C01


title: 7785488049_R06C02


title: Braak_NFT_stage_0_subject-11_FC (gene-level)

description:
BN_0_11_FC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_0_subject-11_EC (gene-level)

description:
BN_0_11_EC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_0_subject-12_FC (gene-level)

description:
BN_0_12_FC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_0_subject-10_TC (gene-level)

description:
BN_0_10_TC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_0_subject-10_FC (gene-level)

description:
BN_0_10_FC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: 7785488049_R05C01


title: 7785488049_R06C01


title: 7785488049_R03C02


title: Braak_NFT_stage_0_subject-10_EC (gene-level)

description:
BN_0_10_EC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: 7785488049_R05C02


title: 7785488049_R02C02


title: 7785488049_R04C01


title: 7785488049_R04C02


title: Braak_NFT_stage_0_subject-09_EC (gene-level)

description:
BN_0_09_EC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: 7785488049_R01C02


title: 7785488049_R03C01


title: 7785488049_R02C01


title: 7785488049_R01C01


title: Braak_NFT_stage_0_subject-07_EC (gene-level)

description:
BN_0_07_EC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: 7802954167_R06C02


title: 7802954167_R06C01


title: Braak_NFT_stage_0_subject-09_FC (gene-level)

description:
BN_0_09_FC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_0_subject-08_TC (gene-level)

description:
BN_0_08_TC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_0_subject-07_TC (gene-level)

description:
BN_0_07_TC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_0_subject-07_FC (gene-level)

description:
BN_0_07_FC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: 7802954167_R05C02

description: Genomic DNA extracted from whole blood was genotyped using Illumina Human Exome Asian BeadChip  (Illumina).


title: Braak_NFT_stage_0_subject-08_FC (gene-level)

description:
BN_0_08_FC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: 7802954167_R05C01


title: 7802954167_R04C02


title: Braak_NFT_stage_0_subject-06_TC (gene-level)

description:
BN_0_06_TC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_0_subject-08_EC (gene-level)

description:
BN_0_08_EC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_0_subject-09_TC (gene-level)

description:
BN_0_09_TC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_0_subject-06_EC (gene-level)

description:
BN_0_06_EC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_0_subject-06_FC (gene-level)

description:
BN_0_06_FC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: 7802954167_R04C01


title: 7802954167_R03C01


title: 7802954167_R02C02


title: Braak_NFT_stage_0_subject-05_EC (gene-level)

description:
BN_0_05_EC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_0_subject-05_FC (gene-level)

description:
BN_0_05_FC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_0_subject-04_FC (gene-level)

description:
BN_0_04_FC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: 7802954167_R02C01


title: 7802954167_R01C02


title: Braak_NFT_stage_0_subject-03_EC (gene-level)

description:
BN_0_03_EC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_0_subject-05_TC (gene-level)

description:
BN_0_05_TC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_0_subject-03_TC (gene-level)

description:
BN_0_03_TC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: 7787539009_R06C01


title: Braak_NFT_stage_0_subject-04_EC (gene-level)

description:
BN_0_04_EC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_0_subject-03_FC (gene-level)

description:
BN_0_03_FC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: 7787539009_R05C02


title: 7802954167_R03C02


title: 7787539009_R05C01


title: 7787539009_R06C02


title: 7787539009_R04C01


title: 7787539009_R03C02


title: 7787539009_R03C01


title: 7787539009_R04C02


title: mm_M1 RNA-seq

city: Szeged

first: Dezső

middle: Peter

last: Virok

state: Please select

address: Dóm tér 10.

department: Department of Medical Microbiology and Immunobiology

country: Hungary

institute: University of Szeged

description: total RNA

data_processing:
standard Illumina basecalling, bcl2fastq Conversion Software v1.8.4
TopHat and Cufflinks was used to align and assemble mapped reads and generate transcriptome assembly
Downstream statistical and differential gene expression analysis was performed using StrandNGS 2.0 software
Genome_build: mm10
Supplementary_files_format_and_content: raw and normalized

source_name: Chlamydia muridarum infected lung tissue homogenate

extract_protocol:
Lungs were removed, homogenized with sterile sand, and total RNA was extracted according to the Tri-Reagent protocol (SIGMA).
cDNA library for RNA-Seq was generated from 1ug total RNA using TruSeq RNA Sample Preparation Kit (Illumina) according to the manufacturer’s protocol.

treatment_protocol: BALB/c mice were infected intranasally with 1000 IFU of C. muridarum in 20 ul SPG buffer. The mice were anaesthetized and sacrificed 7 days after infection.

value: Chlamydia muridarum

value: 7 days post infection

value: BALB/c


title: Braak_NFT_stage_0_subject-02_FC (gene-level)

description:
BN_0_02_FC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_0_subject-04_TC (gene-level)

description:
BN_0_04_TC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: mm_M2 RNA-seq

description: total RNA


title: mm_K3 RNA-seq

description: total RNA

source_name: uninfected lung tissue homogenate

value: uninfected


title: mm_M3 RNA-seq

description: total RNA


title: mm_K2 RNA-seq

description: total RNA


title: 7787539009_R02C02

description: Genomic DNA extracted from whole blood was genotyped using Illumina Human Exome Asian BeadChip  (Illumina).


title: 7802954167_R01C01


title: Braak_NFT_stage_0_subject-02_TC (gene-level)

description:
BN_0_02_TC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_0_subject-02_EC (gene-level)

description:
BN_0_02_EC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: Braak_NFT_stage_0_subject-01_FC (gene-level)

description:
BN_0_01_FC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)


title: DVI459

city: Milwaukee

first: Alison

middle: J.

last: Kriegel

state: WI

address: 8701 Watertown Plank Rd.

department: Physiology

institute: Medical College of Wisconsin

description:
11to15_vs_6to10_mat.xlsx
11to15_vs_6to10_mat.xlsx

data_processing:
Adapter sequences were first removed from the output reads by the tool cutadapt (http://code.google.com/p/cutadapt/); sequences with low quality (base quality < 13) at both ends of reads were further trimmed and trimmed reads with less than 25 bp were removed using the SolexaQA (http://solexaqa.sourceforge.net/).
The trimmed short sequencing reads were aligned to miRbase  to identify microRNAs using Bowtie, those that didn't map ewere mapped against Rfam and RepBase.
DESeq was implemented to identify differential expression.
The Benjamini-Hochberg method was used to control false discovery rate in differential expression analysis.
Data was sorted by DH adjusted p-value (p<0.05)
The Benjamini-Hochberg method was used to control false discovery rate in differential expression analysis.
Low reads miRNA were cut off at 450 reads or less
miRNA from species other than rat were ignored
Genome_build: Fold change cut-off in sorted data was 2
Supplementary_files_format_and_content: Fold change in each group comparison

organism: Rattus norvegicus

source_name: Kidney cotrical tissue

growth_protocol: Rats were purchased from Charles River Laboratories at 4 weeks of age and placed on Dyets chow at 6 weeks of age for 8 weeks, food and water was provided ad libitum

extract_protocol:
Kidney tissues were isolated and flash frozen in liquid nitrogen.  Total RNA was extracted using a Trizol-based method and quantified by Nanodrop. Small RNA deep sequencing and analysis was performed as previously described by the Human Molecular Genetic Center at the Medical College of Wisconsin (Kriegel et al, Physiol Genomics, 2013; PMID 24085797).
Small RNA libraries were constructed for pools of 2-3 rats, 2 pools per condition, using the TruSeq Small Sample Preparation RNA Kit.
Samples were multiplexed sequenced with an Illumina HiSeq 2000 using the TruSeq SBS kit v2-HS.

treatment_protocol: No other treatment apart from dietary regime was provided.

tag: rat strain

tag: diet

value: 4%NaCl, Dyets


title: 7787539009_R01C02

tag: gender


title: DVI458


title: Braak_NFT_stage_0_subject-01_TC (gene-level)

description:
BN_0_01_TC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)

tag: tissue

value: brain


title: DVI457


title: 7787539009_R02C01

tag: disease state


title: Braak_NFT_stage_0_subject-01_EC (gene-level)

description:
BN_0_01_EC
For each subject information, see Supplementary Table S8 of our paper (Miyashita A. et al., Transl Psychiatry. 2014)

value: Entorhinal cortex (EC)


title: 7802946022_R06C02


title: DVI456


title: DVI455

description:
1to5_vs_11to15_mat.xlsx
11to15_vs_6to10_mat.xlsx


title: 7802946022_R05C02


title: 7802946022_R06C01


title: DVI454

description:
1to5_vs_6to10_mat.xlsx
11to15_vs_6to10_mat.xlsx

value: 0.4%NaCl, Dyets


title: DVI453


title: 7802946022_R05C01


title: 7802946022_R03C01


title: 7802946022_R04C02


title: DVI452


title: 7802946022_R03C02


title: 7802946022_R04C01


title: DVI450


title: DVI451


title: 7802946022_R02C02


title: mm_K1 RNA-seq

description: total RNA


title: DVI445

description:
1to5_vs_6to10_mat.xlsx
1to5_vs_11to15_mat.xlsx

value: 0.01%NaCl, Dyets


title: DVI446


title: 7787539009_R01C01

value: Unknown


title: 7802946022_R02C01

value: Whole blood


title: 7802946022_R01C01


title: 7785445069_R05C02


title: 7802946022_R01C02


title: DVI444


title: 7785445069_R05C01


title: 7785445069_R06C01


title: DVI443


title: 7785445069_R04C02


title: 7785445069_R03C02


title: 7785445069_R04C01


title: 7785445069_R02C01


title: 7785445069_R06C02


title: 7785445069_R02C02


title: 7785445069_R01C01


title: 7787555047_R06C02


title: 7787555047_R06C01


title: 7785445069_R01C02


title: 7787555047_R04C02


title: 7787555047_R03C02


title: 7787555047_R03C01


title: 7787555047_R05C01


title: 7785445069_R03C01


title: 7787555047_R02C02


title: 7787555047_R02C01


title: 7787555047_R01C02


title: 7787555047_R01C01


title: 7802962040_R06C02


title: DVI442


title: 7802962040_R06C01


title: 7802962040_R05C01


title: 7802962040_R04C02


title: 7802962040_R04C01


title: su008_pre_TCR

description: TCR library (10X Genomics)

value: pre


title: su006_post_TCR

description: TCR library (10X Genomics)

value: post


title: 7802962040_R03C02

value: Chronic inflammatory skin disease


title: su001_pre1_TCR

description: TCR library (10X Genomics)


title: su006_pre_TCR

description: TCR library (10X Genomics)


title: su003_post_TCR

description: TCR library (10X Genomics)


title: 7787555047_R05C02


title: 7787555047_R04C01


title: 7802962040_R02C02


title: 7802962040_R01C02


title: Treg_3

description: Ensemble RNA-seq

data_processing:
Adapter trimming by cutadapt (version 1.17)
Aligned to the GRCh38 reference genome using STAR (version 2.6.1a)
Filter multi-mapping reads with samtools (version 1.7)
Count using featureCounts (version 1.6.2) using Ensembl GRCh38 GTF transcript annotations
Genome_build: GRCh38
Supplementary_files_format_and_content: text file with raw read counts

source_name: Primary T cell sorted from peripheral blood

growth_protocol: Sorted from PBMCs

extract_protocol:
SMART-Seq v4 Ultra Low Input RNA Kit (Clontech);
Nextera XT DNA Library Prep Kit (Illumina)

value: Treg CD4+ T cell

tag: disease status

value: healthy


title: 7802962040_R01C01


title: 7802962040_R05C02


title: Treg_1

description: Ensemble RNA-seq


title: 7802954053_R06C02


title: Th2_4

description: Ensemble RNA-seq

value: Th2 CD4+ T cell


title: 7802962040_R03C01


title: 7802954053_R06C01


title: 7802962040_R02C01


title: Treg_4

description: Ensemble RNA-seq


title: 7802954053_R05C01


title: Th2_3

description: Ensemble RNA-seq


title: Th2_2

description: Ensemble RNA-seq


title: 7802954053_R05C02


title: Th2_1

description: Ensemble RNA-seq


title: 7802954053_R04C02


title: young ovarian cancer cells for chemiotherapy induction in vitro, biological rep 02

city: Poznan

first: Anna

last: Witucka

state: Greater Poland

address: Dluga 1/2

department: Department and Clinic of Hypertensiology, Angiology and Internal Medicine

country: Poland

institute: Poznan University of Medical Sciences

description:
cells collected at early passage
Gene expression data from young ovarian cancer cells for chemiotherapy induction in vitro

hyb_protocol: Biotin-labeled fragments of cDNA (5.5 μg) were hybridized by the Affymetrix Human Gene 2.1 ST ArrayStrip (20 h, 48°C).

scan_protocol: Microarrays were washed and stained according to the technical protocol, using AffymetrixGeneAtlasFuidics Station. The array strips were scanned employing Imaging Station of GeneAtlas System.

data_processing: Obtained CEL files were subjected for background correction and normalization using RobustMultiarrayAveraging (RMA) algorithm implemented in affy package of BioConductor.

source_name: young ovarian cancer cells isolated from tissue from patient without chemiotherapy

label_protocol: The entire procedure for preparing RNA for hybridization was performed using the GeneChip WT PLUS Reagent Kit (Affymetrix, Santa Clara, CA, USA). One-hundred ng of RNA was subjected to a two-step cDNA synthesis reaction using random primers extended by the T7 RNA polymerase promoter sequence. Synthesis of cRNA was performed using in vitro transcription. cRNA was purified and re-transcribed into cDNA, which was biotin labeled and fragmented using the Affymetrix GeneChip WT Terminal Labeling and Hybridization kit (Affymetrix, Santa Clara, CA, USA).

growth_protocol: Primary and metastatic ovarian tumors were excised from patients undergoing cytoreductive surgery. The tissue samples were placed into sterile tubes and cut into smaller pieces. The samples were processed via enzymatic digestion by 0.05% trypsin and 0.02% EDTA (40min, 37oC). Finally, the ovarian cancer cells were cultured in RPMI-1640 medium supplemented with L-glutamine (2mM), sodium pyruvate (1mM), glucose (4500mg/L), and 20% FBS

extract_protocol: Total RNA were extracted by TRI Reagent (SIGMA-ALDRICH) according to the manufacturer's instructions.

treatment_protocol: Young cells were collected at early passage for total RNA isolation or submited the senescence induction by serial passaging or chemiotherapy (see SAMPLES section, characteristics:cells preparation procedures)

value: ovarian cancer


title: senescence ovarian cancer cells after chemiotherapy in vitro, biological rep 01

description:
cells collected after senescence induced by chemiotherapy with paclitaxel (25nM) and carboplatin (50μM) for 72h
Gene expression data from senescence ovarian cancer cells after chemiotherapy in vitro

source_name: young ovarian cancer cells isolated from tissue from patient without chemiotherapy and senescence by chemiotherapy in vitro


title: young ovarian cancer cells, biological rep 03

description:
cells collected at early passage
Gene expression data from young ovarian cancer cells


title: spontenous senescence ovarian cancer cells, biological rep 03

description:
cells collected after senescence induced by serial passaging at 4-7 day intervals at a low seeding-density. The cells were considered senescent when they displayed enlarged, hypertrophic morphology and failed to divide for 3 weeks
Gene expression data from spontenous senescence ovarian cancer cells

source_name: young ovarian cancer cells isolated from tissue from patient without chemiotherapy and senescence by serial passaging


title: spontenous senescence ovarian cancer cells, biological rep 01


title: spontenous senescence ovarian cancer cells, biological rep 02


title: senescence ovarian cancer cells after chemiotherapy in vivo, biological rep 02

description:
cells collected after senescence induced by serial passaging at 4-7 day intervals at a low seeding-density. The cells were considered senescent when they displayed enlarged, hypertrophic morphology and failed to divide for 3 weeks
Gene expression data from senescence ovarian cancer cells after chemiotherapy in vivo

source_name: young ovarian cancer cells isolated from tissue from patient after chemiotherapy and senescence by serial passaging


title: senescence ovarian cancer cells after chemiotherapy in vivo, biological rep 01


title: young ovarian cancer cells after chemiotherapy in vivo, biological rep 01

description:
cells collected at early passage
Gene expression data from young ovarian cancer cells after chemiotherapy in vivo

source_name: young ovarian cancer cells isolated from tissue from patient after chemiotherapy


title: Th17_4

description: Ensemble RNA-seq

value: Th17 CD4+ T cell


title: senescence ovarian cancer cells after chemiotherapy in vitro, biological rep 03

description:
cells collected after senescence induced by chemiotherapy with paclitaxel (25nM) and carboplatin (50μM) for 72h. Next, cells were cultured with cultured medium for 24h and passaged. The cultures
Gene expression data from senescence ovarian cancer cells after chemiotherapy in vitro


title: young ovarian cancer cells after chemiotherapy in vivo, biological rep 03


title: senescence ovarian cancer cells after chemiotherapy in vitro, biological rep 02


title: young ovarian cancer cells for chemiotherapy induction in vitro, biological rep 03


title: young ovarian cancer cells for chemiotherapy induction in vitro, biological rep 01


title: 7802954053_R04C01

description: Genomic DNA extracted from whole blood was genotyped using Illumina Human Exome Asian BeadChip  (Illumina).

source_name: Public control


title: senescence ovarian cancer cells after chemiotherapy in vivo, biological rep 03


title: control B cells in the presence of DFO (iron-deficient B cells) with anti-IgM stimulation

city: Shanghai

first: Yuhang

last: Jiang

address: 320 Yueyang Road

department: Institute of Health Sciences

institute: Shanghai Institutes for Biological Sciences, CAS

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the mm9 genome assembly using EasyAlign version 3.2 to obtain localization information, the condition is set to allow 1 mismatch, and the number of Reads and the comparison ratio on the alignment are counted.
Comparison of the full-genome coverage depth cumulative distribution of Reads, distribution in the Repeatas region, and distribution on functional elements of genes.
Whole genome Peaks scan refer to Model-based Analysis of ChIP-Seq (Genome Biology 2008, 9:R137), for the predicted Peaks, the Poisson distribution model is used to calculate the p-value of each potential region using the aligned Reads. When p-value < 1e-5, this area is considered to be a Peaks.
Genome_build: mm9
Supplementary_files_format_and_content: The wig file contains Peaks information for visual analysis in the UCSC Genome Browser.

source_name: primary B cells

growth_protocol: Normal culture medium for primary splenic B cells was 1640 medium with 10% (vol/vol) FBS, 0.05 mM β-mercaptoethanol, 1 mM sodium pyruvate, 100 U/ml penicillin and 100 µg/ml streptomycin.

extract_protocol:
After stimulation with anti-IgM (10 µg/ml) for 48 h, splenic B cells were cross-linked with 1% fresh formaldehyde for 10 min at room temperature, neutralized with glycine for 5 min and lysed in SDS lysis buffer. The cross-linked DNA was then sonicated and sheared into fragments 200-1000 base pairs in length with UCD-300 (Bioruptor).
Libraries were prepared for sequencing according to standard Illumina's instructions.

treatment_protocol: B cells at a density of 1 × 10^6 cells/ml were cultured in normal culture medium in the presence or absence of 20 μM DFO, and stimulated with F(ab’)2 goat anti-mouse IgM

value: spleen

value: primary B cells

tag: chip antibody

value: H3K9me2 (Active motif, 39239)

tag: strain


title: control B cells with anti-IgM stimulation


title: control B cells


title: Th17_3

description: Ensemble RNA-seq


title: young ovarian cancer cells, biological rep 01


title: young ovarian cancer cells, biological rep 02


title: young ovarian cancer cells after chemiotherapy in vivo, biological rep 02


title: Th17_2

description: Ensemble RNA-seq


title: Zeb1 (+/-)-Set 2

city: Barcelona

first: Antonio

last: Postigo

state: BARCELONA

address: Casanova 143. Cellex 1B

country: Spain

institute: IDIBAPS/ICREA

description:
COUNTS_genes_POST_01
AA9321

data_processing:
RNA-seq reads were mapped against Mus musculus reference genome with STAR (ENCODE parameters)
Genes were quantified with RSEM (default parameters)
Normalization and differential expression was performed with edgeR R package
GO/KEGG enrichment analysis was performed with DAVID
Genome_build: GRCm38
Supplementary_files_format_and_content: txt file containing RSEM expected counts

source_name: Zeb1 (+/-) Peritoneal Macrophages-Set 2

growth_protocol: Freshly isolated peritoneal macrophages

extract_protocol:
Total RNA was isolated using RNAzol (Sigma-Aldrich)
TruSeq®Stranded mRNA LT Sample Prep Kit

treatment_protocol: Basal (untreated) peritoneal macrophages

value: Peritoneal lavage macrophages sorted by flow cytometry using CD11b and F4/80 markers

tag: genotype

value: Zeb1 (+/-) heterozygous

tag: age

value: 6-8 weeks old mice


title: Zeb1 (+/-)-Set 1

description:
COUNTS_genes_POST_01
AA9320

source_name: Zeb1 (+/-) Peritoneal Macrophages-Set 1


title: 7802954053_R03C01


title: Wild-type-Set 2

description:
COUNTS_genes_POST_01
AA9318

source_name: Wild-type Peritoneal Macrophages-Set 2

value: Wild-type


title: Th17_1

description: Ensemble RNA-seq

tag: cell type


title: Wild-type-Set 3

description:
COUNTS_genes_POST_01
AA9319

source_name: Wild-type Peritoneal Macrophages-Set 3


title: Th1_4

description: Ensemble RNA-seq

value: Th1 CD4+ T cell


title: Wild-type-Set 1

description:
COUNTS_genes_POST_01
AA9317

source_name: Wild-type Peritoneal Macrophages-Set 1


title: 7802954053_R02C01

value: Unknown

value: Whole blood


title: 7802954053_R02C02


title: 7802954053_R01C02


title: Th1_2

description: Ensemble RNA-seq


title: 7802954053_R03C02


title: Zeb1 (+/-)-Set 3

description:
COUNTS_genes_POST_01
AA9322

source_name: Zeb1 (+/-) Peritoneal Macrophages-Set 3


title: Th1_1

description: Ensemble RNA-seq


title: Th1_3

description: Ensemble RNA-seq


title: 7785496089_R06C02


title: 7785496089_R06C01


title: Th1-17_3

description: Ensemble RNA-seq

value: Th1-17 CD4+ T cell


title: Mouse placenta RNAseq CB E17

city: Ithaca

first: Andrew

last: Clark

address: 227 Biotech Building

institute: Cornell University

description: Illumina mRNA-seq

data_processing:
Illumina short reads were mapped to the mouse reference genome (UCSC mm9) using TopHat program with a maximum of 3 mismatches. Only uniquely mapped reads were used for allele-specific expression quantification. On average, 84% of the reads were uniquely mapped to the mouse genome. AKR-PWD and B6-CAST SNP information is obtained from Sanger mouse SNP database.
Genome Build:
mouse153_CB_E17_SNP_counts.txt: UCSC mm9

source_name: mouse embryonic day 17.5 placental tissue

extract_protocol: mRNA-seq libraries were made for F1 female placenta total RNA from AKRxPWD E17.5, PWDxAKR E17.5, B6xCAST E17.5, CASTxB6 E17.5, B6xCAST E13.5 and CASTxB6 E13.5 (mother comes first) crosses, using Illumina TruSeq RNA Sample Prep Kit (Illumina Inc., CA) with 4 µg of total mRNA input . The six mRNA-seq libraries were pooled and sequenced for three 51bp lanes on Illumina HiSeq2000 machine (Illumina Inc., CA). Image analysis and base calling were performed by the Illumina instrument software (Illumina pipeline CASAVA v1.7).

tag: genetic background

value: CAST/EiJ mother x C57BL/6 father

tag: developmental stage

value: placenta

tag: Sex

value: Female


title: Mouse placenta RNAseq CB E13

description: Illumina mRNA-seq

data_processing:
Illumina short reads were mapped to the mouse reference genome (UCSC mm9) using TopHat program with a maximum of 3 mismatches. Only uniquely mapped reads were used for allele-specific expression quantification. On average, 84% of the reads were uniquely mapped to the mouse genome. AKR-PWD and B6-CAST SNP information is obtained from Sanger mouse SNP database.
Genome Build:
mouse198_CB_E13_SNP_counts.txt: UCSC mm9

source_name: mouse embryonic day 13.5 placental tissue


title: Mouse placenta RNAseq PA E17

description: Illumina mRNA-seq

data_processing:
Illumina short reads were mapped to the mouse reference genome (UCSC mm9) using TopHat program with a maximum of 3 mismatches. Only uniquely mapped reads were used for allele-specific expression quantification. On average, 84% of the reads were uniquely mapped to the mouse genome. AKR-PWD and B6-CAST SNP information is obtained from Sanger mouse SNP database.
Genome Build:
mouse66_PA_E17_SNP_counts.txt: UCSC mm9

value: PWD/PhJ mother x AKR/J father


title: Th1-17_4

description: Ensemble RNA-seq

tag: donor

value: healthy


title: Mouse placenta RNAseq BC E17

description: Illumina mRNA-seq

data_processing:
Illumina short reads were mapped to the mouse reference genome (UCSC mm9) using TopHat program with a maximum of 3 mismatches. Only uniquely mapped reads were used for allele-specific expression quantification. On average, 84% of the reads were uniquely mapped to the mouse genome. AKR-PWD and B6-CAST SNP information is obtained from Sanger mouse SNP database.
Genome Build:
mouse188_BC_E17_SNP_counts.txt: UCSC mm9

value: C57BL/6 mother x CAST/EiJ father


title: Mouse placenta RNAseq AP E17

description: Illumina mRNA-seq

data_processing:
Illumina short reads were mapped to the mouse reference genome (UCSC mm9) using TopHat program with a maximum of 3 mismatches. Only uniquely mapped reads were used for allele-specific expression quantification. On average, 84% of the reads were uniquely mapped to the mouse genome. AKR-PWD and B6-CAST SNP information is obtained from Sanger mouse SNP database.
Genome Build:
mouse139_AP_E17_SNP_counts.txt: UCSC mm9

value: AKR/J mother x PWD/PhJ father


title: Time series in DD conditions in the OE1 line [OE-1_25_C]

city: Paris

first: Angela

last: Falciatore

address: 15 rue de l'ecole de Medicine

department: UMR 7238, LCQB

country: France

institute: CNRS

description:
OE-1_25_C
Raw data: OE-1_C.xlsx
Replica 3/3. Time point 0 corresponds to the light onset.

hyb_protocol: For each hybridization, 100 ng of was used. Hybridization and washes were performed according to manufacturer’s protocols (http://www.nanostring.com) by the Plateforme nanostring, Institut Curie, Paris, France.

scan_protocol: Scanning was performed according to manufacturer’s protocols (http://www.nanostring.com) by the Plateforme nanostring, Institut Curie, Paris, France.

data_processing: Raw data were normalized using the internal spike-in control probes, then RNA counts were normalized using the geometric mean of three reference genes (rps, tbp and actin12) and presented as the log2 ratio between the gene and the normalizers expression.

organism: Phaeodactylum tricornutum

source_name: Cellular culture, preadapted to 16L:8D cycles

label_protocol: Un-labeled total RNA has been hybridized using biotin and fluorescence tag labeled gene-specific probes.

growth_protocol: The Wt CCMP632 strain of Phaeodactylum tricornutum Bohlin (Pt1 8.6) and the OE-1 line were routinely grown in f/2 medium (Guillard, 1975) at 18°C under white fluorescent lights (Philips TL-D De Luxe Pro 950) in 16L:8D cycles under 40 µmol m-2 s-1 of photons. Cultures were kept in exponential growth phase diluting them every three days with fresh medium and their axenicity assessed through contamination tests. Triplicate cultures of each treatment were grown in 1000 ml Erlenmeyers, shaked at 100 rpm to prevent settling of cells.

extract_protocol: 100 ml of culture (10^8 total cells) were filtered (grade 589/2, Whatman, 28414108), washed with PBS and flash frozen in liquid nitrogen. Total RNA was extracted by adding TriPure isolation Reagent (Roche, 11667165001) to the frozen filters and following the manufacturer’s instructions, with a further purification by ammonium acetate precipitation as described in Huysman et al., 2013. The recovered RNA was then quantified using a spectrophotometer and its integrity checked on 2% agar gel.

treatment_protocol: bHLH1a overexpressing line cell culture was pre-adapted to 16L:8D regime and put in DD condition. Sampling started at the beginning of the day (time point 1), sampling every 3 hours for 24 hours.

tag: strain/background

tag: genotype/variation

value: bHLH1a Overexpressing

value: Culture

tag: light-dark cycle

value: Continuous darkness

tag: time point


title: Time series in DD conditions in the OE1 line [OE-1_16_C]

description:
OE-1_16_C
Raw data: OE-1_C.xlsx
Replica 3/3. Time point 0 corresponds to the light onset.


title: Time series in DD conditions in the OE1 line [OE-1_19_C]

description:
OE-1_19_C
Raw data: OE-1_C.xlsx
Replica 3/3. Time point 0 corresponds to the light onset.


title: 7785496089_R05C02

data_processing:
Genomic DNA extracted from whole blood was genotyped using Illumina Human Exome Asian BeadChip  (Illumina).
Processed data file includes: Genotype: AA,AB,BB,or NC (no call), GC Score, Theta, R, B Allele Freq and Log R ratio

tag: gender

value: Chronic inflammatory skin disease


title: Th1-17_2

description: Ensemble RNA-seq

source_name: Primary T cell sorted from peripheral blood


title: Mouse placenta RNAseq BC E13

description: Illumina mRNA-seq

data_processing:
Illumina short reads were mapped to the mouse reference genome (UCSC mm9) using TopHat program with a maximum of 3 mismatches. Only uniquely mapped reads were used for allele-specific expression quantification. On average, 84% of the reads were uniquely mapped to the mouse genome. AKR-PWD and B6-CAST SNP information is obtained from Sanger mouse SNP database.
Genome Build:
mouse148_BC_E13_SNP_counts.txt: UCSC mm9

tag: tissue


title: 7785496089_R05C01

tag: disease state


title: 7802954053_R01C01


title: Time series in DD conditions in the OE1 line [OE-1_13_C]

description:
OE-1_13_C
Raw data: OE-1_C.xlsx
Replica 3/3. Time point 0 corresponds to the light onset.


title: Time series in DD conditions in the OE1 line [OE-1_7_C]

description:
OE-1_7_C
Raw data: OE-1_C.xlsx
Replica 3/3. Time point 0 corresponds to the light onset.


title: Time series in DD conditions in the OE1 line [OE-1_10_C]

description:
OE-1_10_C
Raw data: OE-1_C.xlsx
Replica 3/3. Time point 0 corresponds to the light onset.


title: 7785496089_R04C02


title: Th1-17_1

description: Ensemble RNA-seq

tag: disease status


title: Time series in DD conditions in the OE1 line [OE-1_4_C]

description:
OE-1_4_C
Raw data: OE-1_C.xlsx
Replica 3/3. Time point 0 corresponds to the light onset.


title: Tfh2_4

description: Ensemble RNA-seq

value: Tfh2 CD4+ T cell


title: 7785496089_R04C01


title: Time series in DD conditions in the OE1 line [OE-1_22_C]

description:
OE-1_22_C
Raw data: OE-1_C.xlsx
Replica 3/3. Time point 0 corresponds to the light onset.


title: Time series in DD conditions in the OE1 line [OE-1_25_B]

description:
OE-1_25_B
Raw data: OE-1_B.xlsx
Replica 2/3. Time point 0 corresponds to the light onset.


title: Time series in DD conditions in the OE1 line [OE-1_22_B]

description:
OE-1_22_B
Raw data: OE-1_B.xlsx
Replica 2/3. Time point 0 corresponds to the light onset.


title: Tfh2_3

description: Ensemble RNA-seq


title: Tfh2_2

description: Ensemble RNA-seq


title: 7785496089_R03C02


title: Time series in DD conditions in the OE1 line [OE-1_19_B]

description:
OE-1_19_B
Raw data: OE-1_B.xlsx
Replica 2/3. Time point 0 corresponds to the light onset.


title: Tfh2_1

description: Ensemble RNA-seq


title: 7785496089_R03C01


title: Time series in DD conditions in the OE1 line [OE-1_16_B]

description:
OE-1_16_B
Raw data: OE-1_B.xlsx
Replica 2/3. Time point 0 corresponds to the light onset.


title: Time series in DD conditions in the OE1 line [OE-1_13_B]

description:
OE-1_13_B
Raw data: OE-1_B.xlsx
Replica 2/3. Time point 0 corresponds to the light onset.


title: Time series in DD conditions in the OE1 line [OE-1_7_B]

description:
OE-1_7_B
Raw data: OE-1_B.xlsx
Replica 2/3. Time point 0 corresponds to the light onset.


title: Time series in DD conditions in the OE1 line [OE-1_10_B]

description:
OE-1_10_B
Raw data: OE-1_B.xlsx
Replica 2/3. Time point 0 corresponds to the light onset.


title: Time series in DD conditions in the OE1 line [OE-1_4_B]

description:
OE-1_4_B
Raw data: OE-1_B.xlsx
Replica 2/3. Time point 0 corresponds to the light onset.


title: Tfh17_4

description: Ensemble RNA-seq

value: Tfh17 CD4+ T cell


title: 7785496089_R02C01

description: Genomic DNA extracted from whole blood was genotyped using Illumina Human Exome Asian BeadChip  (Illumina).


title: Time series in DD conditions in the OE1 line [OE-1_1_B]

description:
OE-1_1_B
Raw data: OE-1_B.xlsx
Replica 2/3. Time point 0 corresponds to the light onset.


title: 7785496089_R01C02


title: Tfh17_3

description: Ensemble RNA-seq


title: Time series in DD conditions in the OE1 line [OE-1_25_A]

description:
OE-1_25_A
Raw data: OE-1_A.xlsx
Replica 1/3. Time point 0 corresponds to the light onset.


title: Tfh17_2

description: Ensemble RNA-seq


title: Time series in DD conditions in the OE1 line [OE-1_22_A]

description:
OE-1_22_A
Raw data: OE-1_A.xlsx
Replica 1/3. Time point 0 corresponds to the light onset.


title: Time series in DD conditions in the OE1 line [OE-1_19_A]

description:
OE-1_19_A
Raw data: OE-1_A.xlsx
Replica 1/3. Time point 0 corresponds to the light onset.


title: Time series in DD conditions in the OE1 line [OE-1_16_A]

description:
OE-1_16_A
Raw data: OE-1_A.xlsx
Replica 1/3. Time point 0 corresponds to the light onset.


title: Time series in DD conditions in the OE1 line [OE-1_10_A]

description:
OE-1_10_A
Raw data: OE-1_A.xlsx
Replica 1/3. Time point 0 corresponds to the light onset.


title: 7785488092_R06C02


title: Time series in DD conditions in the OE1 line [OE-1_7_A]

description:
OE-1_7_A
Raw data: OE-1_A.xlsx
Replica 1/3. Time point 0 corresponds to the light onset.


title: Time series in DD conditions in the OE1 line [OE-1_1_C]

description:
OE-1_1_C
Raw data: OE-1_C.xlsx
Replica 3/3. Time point 0 corresponds to the light onset.


title: 7785488092_R06C01


title: 7785496089_R02C02


title: Tfh1_4

description: Ensemble RNA-seq

value: Tfh1 CD4+ T cell


title: 7785488092_R05C02

value: Unknown