title: atbmi1ab_weak_7DAG_1

city: Sevilla

first: Myriam

last: Calonje

address: Americo Vespucio 49

country: Spain

institute: Institute for Plant Biochemistry and Photosynthesis (CSIC -  University of Sevilla)

data_processing:
Quality control  was performed using the software packges FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Read mapping to the reference genome was performed using Hisat2 (https://ccb.jhu.edu/software/hisat2/index.shtml)
Transcript assembly was performed using StringTie (http://ccb.jhu.edu/software/stringtie/)
Gene expression level measured in FPKM (fragments per kilobase of exon and million of mapped reads) was perfomed using R bioconductor package Ballgown (https://bioconductor.org/packages/release/bioc/html/ballgown.html)
Subsequent data analysis and visualization was performed using the R bioconductor package Ballgown and Limma (https://bioconductor.org/packages/release/bioc/html/ballgown.html; https://bioconductor.org/packages/release/bioc/html/limma.html)
Genome_build: tair10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

organism: Arabidopsis thaliana

source_name: Seedlings

extract_protocol:
RNA extraction was performed using Qiagen-RNAesy mini-kit, following the manufacturer’s instruction.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: ecotype

value: atbmi1ab_weak double mutant


title: hta9hta11_FLAG-HTA9_RR_7DAG_2

status: Public on May 24 2019

type: SRA

library_source: transcriptomic

molecule: total RNA

tag: genotype

tag: age


title: atbmi1ab_weak_7DAG_2


title: hta9hta11_FLAG-HTA9_RR_7DAG_1


title: hta9hta11_FLAG-HTA9_N_7DAG_1


title: hta9hta11_FLAG-HTA9_N_7DAG_2


title: hta9hta11_7DAG_2

value: hta9hta11 doble mutant


title: Whole Red Blood Cells Sample 39705 BCD

status: Public on May 25 2019

type: genomic

city: Newark

first: Behnam

last: Abasht

state: DE

address: 531 South College Avenue

department: Animal and Food Sciences

country: USA

institute: University of Delaware

hyb_protocol: Performed by Neogen following manufactures specification (Affymetrix), the hyb-ready DNA mixture was transferred to a GeneTital Multi-Channel instrument for automated processing of the hybridization step.

scan_protocol: Arrays were processed and imaged using a Affymetrix Gene Titan Multi-Channel (MC) Instrument by Neogen following manufacturers instructions

data_processing: Raw cell files were analyzed using Axiom Analysis Suite Software (version 3.0.1) with Gallus gallus 5.0 (Axiom_GW_GT_Chicken.na35.annot.db) using the software's Best Practices for Agricultural animals and a VCF file exported for all SNPs.

label: biotin

molecule: genomic DNA

organism: Gallus gallus

source_name: whole red blood cells

label_protocol: Performed by Neogen following manufacturers specification (Affymetrix) using a Biomek FX robot, the DNA was amplified, fragmented and purified to create a hybridization ready (hyb-ready) mixture.

growth_protocol: Animal experiments for crossbred (BCD) and purebred chickens (B and C) are described in studies by Zhou et al. (Zhou, N., Lee, W.R. and Abasht, B., 2015. Messenger RNA sequencing and pathway analysis provide novel insights into the biological basis of chickens’ feed efficiency. BMC genomics, 16(1), p.195.) and Mutryn et al. (Mutryn, M.F., Brannick, E.M., Fu, W., Lee, W.R. and Abasht, B., 2015. Characterization of a novel chicken muscle disorder through differential gene expression and pathway analysis using RNA-sequencing. BMC genomics, 16(1), p.399.), respectively.

extract_protocol: DNA was extracted from whole blood using DNeasy Blood & Tissue Kit (Qiagen)

tag: line

value: Cross BCD

tag: gender

value: male

tag: developmental stage

value: 46 days post-hatch


title: hta9hta11_7DAG_1


title: WT_7DAG_2

value: Wild Type


title: WT_7DAG_1


title: CD3_B71_100k_rep_1_Ampliseq

city: Gaithersburg

first: Jingya

last: Wang

state: Maryland

address: 1 Medimmune Way

department: Early respiratory and immunology

institute: Astrazeneca

description: 100,000 human naïve T cells treated with anti-CD3+B71 Fc, and RNA sequencing performed using Ampliseq protocol, replicate 1

data_processing:
For SMART_Nxt and SMART_CC samples, fastq files were quality checked using FastQC and further aligned to human genome (hg19) using Hisat2 (2.0.2-beta). Gene count tables were generated using HTSeq
For Ampliseq samples, alignment and gene expression count were performed using Ion Torrent ampliSeqRNA Plugin v0.5.4.0 (Thermo Fisher)
Genome_build: hg19
Supplementary_files_format_and_content: raw count table in txt files

organism: Homo sapiens

source_name: T cells

growth_protocol: Naïve CD4 T cells were isolated from the PBMC of donors with Easy Sep negative selection kit

extract_protocol:
Total RNA from the cells was extracted using Qiagen’s RNeasy Micro Kit
The SMART-Seq v4 Ultra-low Input RNA Kit for Sequencing (Takara #634888) was used to generate high-quality full-length cDNA. For SMART_CC, The cDNA was sheared using the Covaris M220 focused-ultra sonicator (SonoLab version 7.1) with run settings for desired target size between 200-500bp. Library preparation was then performed following manufacturer’s instructions for Low Input Library Prep Kit v2 (Clontech # 634899). For SMART_Nxt, The cDNA was normalized to the modified recommended input amount. The samples were then tagmented according to Nextera XT DNA Library Prep Protocol (Illumina # FC-131-1024). For Ampliseq, 3.5ul of RNA was used for input into the Ion Ampliseq Transcriptome Human Gene Expression Kit (Thermo Fisher # A26325), and libraries were prepared following manufacturer's instructions

treatment_protocol: The cells were then plated in 24-well plates that were previously coated with anti-CD3  alone or anti-CD3 and B7.1-Fc .  The plates were coated at 37C for 2 hours, and washed with PBS extensively prior to the addition of cells

tag: cell type

value: T cells

tag: treatment

value: anti-CD3+B71 Fc

tag: protocol

value: Ampliseq

tag: cell input

tag: replicate


title: CD3_B71_1k_rep_2_SMART_CC

description: 1,000 human naïve T cells treated with anti-CD3+B71 Fc, and RNA sequencing performed using SMART_CC protocol, replicate 2


title: CD3_B71_1k_rep_1_SMART_CC

description: 1,000 human naïve T cells treated with anti-CD3+B71 Fc, and RNA sequencing performed using SMART_CC protocol, replicate 1


title: CD3_B71_100_rep_1_SMART_CC

description: 100 human naïve T cells treated with anti-CD3+B71 Fc, and RNA sequencing performed using SMART_CC protocol, replicate 1


title: Huh-7 macroH2A1 knock-down (KD) 3 [ko3]

city: S. Giovanni Rotondo (FG)

first: Tommaso

last: Mazza

address: Viale Cappuccini, 1

department: Bioinformatics

country: Italy

institute: IRCCS Casa Sollievo della Sofferenza

data_processing:
Reads trimmed using Trimmomatic
Reads aligned with STAR (ver. 2.6.1a)
Reads counted with htseq-count
Normalization and comparisons performed using edgeR
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include CPM values for each sample

source_name: Huh-7 macroH2A1 knock-down (KD)

growth_protocol: Huh-7 cell line was purchased from ATCC and cultured in DMEM (1X) supplemented with 10% fetal bovine serum (FBS), with 1% penicillin/streptomycin.

extract_protocol:
Total RNA was extracted from control and macroH2A1 KD Huh-7 cells using TRIzol Reagent (ThermoFisher Scientific, Waltham, USA).
Indexed libraries were prepared from 250 ng purified RNA using the NEBNext Ultra II Directional RNA Library preparation kit with polyA selection module (New England Biolabs, Ipswich, USA). Libraries and input RNA samples were quality checked using Fragment Analyzer (Advanced Analytical, Ankeny, US). The libraries were pooled so that each index-tagged sample was present in equimolar amounts. The pooled samples then underwent cluster generation and sequencing using an Illumina NextSeq 500 (Illumina, San Diego, US) in a 2 x 75 paired-end format.

treatment_protocol: After plating, Huh-7 an cells were transduced with retroviral macroH2A-specific shRNA cassettes as described (Kong R et al., Nucleic Acid Res, 2014; PMID: 24071584), and selected with 2 μg/ml puromycin.

tag: cell line

value: immortalized hepatocellular carcinoma cell line

tag: cell line tissue source

value: Liver

tag: cell line source

value: 57-years-old Japanese male

tag: genotype/variation

value: macroH2A1 knockdown

tag: rin


title: Huh-7 conditioned media KD 1 [cm1]

source_name: Huh-7 conditioned media KD

value: conditioned medium from KD cells


title: Huh-7 CTL 2 [ctl2]

source_name: Huh-7 CTL

value: control


title: Huh-7 CTL 3 [ctl3]


title: Huh-7 CTL 1 [ctl1]


title: CD3_B71_100k_rep_2_SMART_CC

description: 100,000 human naïve T cells treated with anti-CD3+B71 Fc, and RNA sequencing performed using SMART_CC protocol, replicate 2


title: Huh-7 macroH2A1 knock-down (KD) 2 [ko2]


title: Huh-7 conditioned media KD 2 [cm2]


title: CD3_100_rep1_SMART_CC

description: 100 human naïve T cells treated with anti-CD3, and RNA sequencing performed using SMART_CC protocol, replicate 1


title: CD3_100_rep2_SMART_CC

description: 100 human naïve T cells treated with anti-CD3, and RNA sequencing performed using SMART_CC protocol, replicate 2


title: Huh-7 conditioned media KD 3 [cm3]


title: CD3_1k_rep1_SMART_CC

description: 1,000 human naïve T cells treated with anti-CD3, and RNA sequencing performed using SMART_CC protocol, replicate 1


title: CD3_5k_rep2_SMART_CC

description: 5,000 human naïve T cells treated with anti-CD3, and RNA sequencing performed using SMART_CC protocol, replicate 2


title: CD3_1k_rep2_SMART_CC

description: 1,000 human naïve T cells treated with anti-CD3, and RNA sequencing performed using SMART_CC protocol, replicate 2


title: CD3_5k_rep1_SMART_CC

description: 5,000 human naïve T cells treated with anti-CD3, and RNA sequencing performed using SMART_CC protocol, replicate 1


title: CD3_100k_rep2_SMART_CC

description: 100,000 human naïve T cells treated with anti-CD3, and RNA sequencing performed using SMART_CC protocol, replicate 2


title: CD3_100k_rep1_SMART_CC

description: 100,000 human naïve T cells treated with anti-CD3, and RNA sequencing performed using SMART_CC protocol, replicate 1


title: su008_pre_Tumor_RNA

city: Stanford

first: Howard

middle: Y

last: Chang

state: CA

address: CCSR 2130, 269 Campus Drive

department: Center for Personal Dynamic Regulomes

institute: Stanford University

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

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.

molecule: polyA RNA

source_name: Basal cell carinoma tumor

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

tag: donor

value: pre


title: CD3_B71_100k_rep_1_SMART_CC

description: 100,000 human naïve T cells treated with anti-CD3+B71 Fc, and RNA sequencing performed using SMART_CC protocol, replicate 1


title: Huh-7 macroH2A1 knock-down (KD) 1 [ko1]


title: su008_pre_Tcell_RNA


title: su008_pre_CD45_RNA


title: CD3_B71_100_rep_2_SMART_CC

description: 100 human naïve T cells treated with anti-CD3+B71 Fc, and RNA sequencing performed using SMART_CC protocol, replicate 2


title: CD3_B71_5k_rep_2_SMART_CC

description: 5,000 human naïve T cells treated with anti-CD3+B71 Fc, and RNA sequencing performed using SMART_CC protocol, replicate 2


title: Sox9 Sublow atac Rep C

city: Chapel Hill

first: Jesse

last: Raab

address: 120 Mason Farm Rd

department: Genetics

institute: University of North Carolina Chapel Hill

description:
Sublow_consensus.bed
SISox9SL.merged.sorted.depthnorm.bw

library_source: genomic

data_processing:
trim: trim_galore /0.4.3 --nextera --paired
align: bowtie2/2.3.4 -X 2000
remove duplicates: picard/2.10.3 MarkDuplicates REMOVE_DUPLICATES=true
signal tracks: deeptools/2.5.2 bamCoverage --binSize 1 --normalizeUsing RPKM --ignoreForNormalization chrM chrX chrY --extendReads --centerReads --minFragmentLength 40 --maxFragmentLength 130
calll peaks: macs2/2.1.2 callpeak --keep-dup all -f BAMPE -g mm --call-summits -q 0.001
Genome_build: mm9
Supplementary_files_format_and_content: Processed data files contain the consensus peak calls (bed format) and the merged signal from 3 replicates (bigWig format)

organism: Mus musculus

source_name: Intestinal epithelial cells

extract_protocol:
12,000 cells per Sox9EGFP population were collected directly into 250uL 1X sort media, pelleted by centrifugation at 2,000g for 5min, and subjected to Omni-ATAC as previously described in (Corces et al., 2017).
Paired end omni-atac protocol

tag: strain

value: Intestinal epithelial cells

tag: cell population

value: Sox9 Sublow


title: CD3_B71_5k_rep_1_SMART_CC

description: 5,000 human naïve T cells treated with anti-CD3+B71 Fc, and RNA sequencing performed using SMART_CC protocol, replicate 1


title: Sox9 Negative atac Rep B

description:
Neg_consensus.bed
SISox9N.merged.sorted.depthnorm.bw

value: Sox9 Negative


title: Sox9 Low atac Rep C

description:
Low_consensus.bed
SISox9L.merged.sorted.depthnorm.bw

value: Sox9 Low


title: Sox9 High atac Rep A

description:
High_consensus.bed
SISox9H.merged.sorted.depthnorm.bw

value: Sox9 High


title: Sox9 Low atac Rep A


title: Sox9 High atac Rep B


title: Sox9 High atac Rep C


title: Sox9 Sublow atac Rep A


title: Sox9 Negative atac Rep A


title: Sox9 High 5hmc Rep B

description: Sox9_High_5hmc.merged.sorted.rmdup.depthnorm.bw

data_processing:
Library strategy: 5hmc-seal-seq
trim: trim_galore/0.4.3
align: bowtie2/2.3.4 --sensitive
remove duplicates: picard/2.10.3 MarkDuplicates REMOVE_DUPLICATES=true
create bigwig: deeptools/2.5.2 bamCoverage --binSize 10 -extendReads 150 --normalizeUsingRPKM --numberOfProcessors
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files of signal over genome.

extract_protocol:
12,000 cells per Sox9EGFP population were collected via FACS (above) and subjected to hmC-Seal as previously described (Han et al., 2016).
Single end libraries

tag: sample type


title: Sox9 Sublow 5hmc Rep B

description: Sox9_SubLow_5hmc.merged.sorted.rmdup.depthnorm.bw


title: Sox9 High 5hmc Rep C


title: Sox9 Low 5hmc Rep C

description: Sox9_Low_5hmc.merged.sorted.rmdup.depthnorm.bw


title: Sox9 Low 5hmc Rep B


title: Sox9 Sublow Input Rep A

description: Sox9_SubLow_Input.merged.sorted.rmdup.depthnorm.bw

value: input


title: Sox9 Sublow 5hmc Rep C


title: Sox9 Negative Input Rep A

description: Sox9_Neg_Input.merged.sorted.rmdup.depthnorm.bw


title: Sox9 Negative 5hmc Rep B

description: Sox9_Neg_5hmc.merged.sorted.rmdup.depthnorm.bw


title: Sox9 Negative atac Rep C


title: Sox9 Low Input Rep A

description: Sox9_Low_Input.merged.sorted.rmdup.depthnorm.bw


title: Sox9 Negative 5hmc Rep A


title: Sox9 Sublow 5hmc Rep A


title: Sox9 High Input Rep A

description: Sox9_High_Input.merged.sorted.rmdup.depthnorm.bw


title: Sox9 Low 5hmc Rep A


title: Sox9 High 5hmc Rep A


title: Sox9 Low atac Rep B


title: Sox9 Low rna Rep C

data_processing:
quantification: salmon/0.8.2 -l -A
Genome build: Gencode vM1
Supplementary_files_format_and_content: normalized_counts.csv

extract_protocol:
12000 cells  from Sox9-GFP populations was Ribo depleted and libraries were generated using Clontech Total RNA Pico, SMARTER v2 Kit
single-end RNAseq


title: Sox9 Sublow atac Rep B


title: Sox9 Sublow rna Rep C


title: Sox9 Negative rna Rep C


title: Sox9 Negative 5hmc Rep C


title: Sox9 Sublow rna Rep A


title: Sox9 High rna Rep C


title: Sox9 Negative rna Rep A


title: Sox9 High rna Rep B


title: Sox9 Negative rna Rep B


title: Sox9 Low rna Rep A


title: Sox9 Sublow rna Rep B


title: Sox9 Low rna Rep B


title: Sox9 High rna Rep A


title: ESC_NOMeSeq

city: Granada

first: Jordi

last: Martorell-Marugan

address: Avenida de la Ilustración 114

department: Bioinformatics Unit

institute: GENyO

description: Jarid2 fl/fl were derived from fl/fl blastocysts obtained from chimeric mice produced  with Jarid2 floxed 129/Sv ESCs and C57BL/C6 mice

data_processing:
bcl2fastq v2.18.0.12 used for basecalling
Cutadapt 1.9.1 with parameters -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -q 30 -m 100 used for trimming sequences
Bwa-meth 0.10 used for alignment
Picard 2.2.2 used for marking duplicates
BisSNP 0.82.2 used for extracting methylation counts
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated with rphast 1.6.9 R package, using a fixed step. For WCG file, scores represent the ratio between methylated and unmethylated reads. For 1 minus GCH file, scores represent 1 – ratio.

source_name: Jarid2 fl/fl ESC

growth_protocol: Mouse embryonic stem cells were cultured in 5% CO2 at 37 ºC on 0.1% gelatin-coated dishes DMEM KO (Gibco) media supplemented with 10% FCS, leukaemia-inhibiting factor (LIF), penicillin/streptomycin (Gibco), L-glutamine (Gibco) and 2-mercaptoethanol (Gibco) as described previously (Landeira et al. 2015).

extract_protocol: NOMe-seq libraries were prepared from 1 µg of DNA using the SureSelectXT Methyl-seq library prep kit (Agilent technologies) as described in manufactures’ instructions. Bisulfite conversion was performed using EZ DNA Methylation Gold kit (Zymo Research).

treatment_protocol: M.CviPI treatment was performed as described previously (Taberlay et al. 2014). Briefly, isolated nuclei were resuspended in 1x reaction buffer containing 200 U of M.CviPI (NEB) and incubated for 15 min at 37ºC.

value: Mouse embryonic stem cells

value: Mixed background:129/Sv / C57BL/C6


title: Braak_NFT_stage_V-VI_subject-15_FC (exon-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_15_FC
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.

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

tag: tissue

value: brain

tag: tissue region

value: Frontal cortex (FC)

tag: Sex

value: F

tag: braak nft stage

value: V-VI


title: Braak_NFT_stage_V-VI_subject-19_TC (exon-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)


title: Braak_NFT_stage_V-VI_subject-19_EC (exon-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)

value: Entorhinal cortex (EC)


title: Braak_NFT_stage_V-VI_subject-19_FC (exon-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-17_FC (exon-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: M


title: Braak_NFT_stage_V-VI_subject-14_EC (exon-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-18_TC (exon-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-13_EC (exon-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: Braak_NFT_stage_V-VI_subject-16_EC (exon-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 (exon-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-14_FC (exon-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_TC (exon-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: Braak_NFT_stage_V-VI_subject-15_TC (exon-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-17_TC (exon-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-11_EC (exon-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: Braak_NFT_stage_V-VI_subject-16_FC (exon-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_EC (exon-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: Braak_NFT_stage_V-VI_subject-17_EC (exon-level)

description:
BN_V-VI_17_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-12_EC (exon-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: Braak_NFT_stage_V-VI_subject-12_TC (exon-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-10_FC (exon-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-11_TC (exon-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-13_TC (exon-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-16_TC (exon-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-10_TC (exon-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-18_FC (exon-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-10_EC (exon-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-11_FC (exon-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: Braak_NFT_stage_V-VI_subject-13_FC (exon-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: Braak_NFT_stage_V-VI_subject-09_FC (exon-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-08_EC (exon-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: Braak_NFT_stage_V-VI_subject-12_FC (exon-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: Braak_NFT_stage_V-VI_subject-07_FC (exon-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-08_FC (exon-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: Braak_NFT_stage_V-VI_subject-07_EC (exon-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-09_TC (exon-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: Braak_NFT_stage_V-VI_subject-09_EC (exon-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: Braak_NFT_stage_V-VI_subject-07_TC (exon-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-08_TC (exon-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-05_TC (exon-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-05_FC (exon-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-04_EC (exon-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-05_EC (exon-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: Braak_NFT_stage_V-VI_subject-06_TC (exon-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: Braak_NFT_stage_V-VI_subject-06_FC (exon-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-04_FC (exon-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_EC (exon-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_EC (exon-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: Braak_NFT_stage_V-VI_subject-03_FC (exon-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_III-IV_subject-19_TC (exon-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: Braak_NFT_stage_V-VI_subject-01_EC (exon-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_V-VI_subject-03_TC (exon-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: Braak_NFT_stage_V-VI_subject-01_TC (exon-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: Braak_NFT_stage_V-VI_subject-01_FC (exon-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-02_FC (exon-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: Braak_NFT_stage_III-IV_subject-16_TC (exon-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: Braak_NFT_stage_III-IV_subject-18_EC (exon-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: Braak_NFT_stage_III-IV_subject-17_FC (exon-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: Braak_NFT_stage_V-VI_subject-06_EC (exon-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_III-IV_subject-18_FC (exon-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-19_FC (exon-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: Braak_NFT_stage_III-IV_subject-17_EC (exon-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: Braak_NFT_stage_III-IV_subject-18_TC (exon-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_V-VI_subject-04_TC (exon-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_III-IV_subject-14_TC (exon-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-16_FC (exon-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: Braak_NFT_stage_III-IV_subject-14_FC (exon-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: Braak_NFT_stage_III-IV_subject-17_TC (exon-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: Braak_NFT_stage_III-IV_subject-14_EC (exon-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-13_EC (exon-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_TC (exon-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-15_FC (exon-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: Braak_NFT_stage_III-IV_subject-15_TC (exon-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-19_EC (exon-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_V-VI_subject-02_TC (exon-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: Braak_NFT_stage_III-IV_subject-16_EC (exon-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-15_EC (exon-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-13_FC (exon-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-11_FC (exon-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: Braak_NFT_stage_III-IV_subject-12_TC (exon-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-10_FC (exon-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 (exon-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-12_EC (exon-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-11_EC (exon-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: Braak_NFT_stage_III-IV_subject-11_TC (exon-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: Braak_NFT_stage_III-IV_subject-12_FC (exon-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: Braak_NFT_stage_III-IV_subject-09_EC (exon-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: Braak_NFT_stage_III-IV_subject-07_EC (exon-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: Braak_NFT_stage_III-IV_subject-10_EC (exon-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: Braak_NFT_stage_III-IV_subject-08_FC (exon-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: Braak_NFT_stage_III-IV_subject-04_EC (exon-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-09_TC (exon-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-09_FC (exon-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: Braak_NFT_stage_III-IV_subject-06_TC (exon-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-02_FC (exon-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: Braak_NFT_stage_III-IV_subject-04_TC (exon-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: Braak_NFT_stage_III-IV_subject-05_EC (exon-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-02_TC (exon-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_EC (exon-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-04_FC (exon-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-05_FC (exon-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: Braak_NFT_stage_III-IV_subject-05_TC (exon-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-08_EC (exon-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: Braak_NFT_stage_III-IV_subject-08_TC (exon-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: Braak_NFT_stage_III-IV_subject-07_FC (exon-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-07_TC (exon-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-06_EC (exon-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-03_TC (exon-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: Braak_NFT_stage_III-IV_subject-03_FC (exon-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_I-II_subject-20_TC (exon-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: Braak_NFT_stage_III-IV_subject-06_FC (exon-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-01_EC (exon-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: Braak_NFT_stage_III-IV_subject-02_EC (exon-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: Braak_NFT_stage_I-II_subject-20_FC (exon-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_III-IV_subject-01_TC (exon-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-01_FC (exon-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: Braak_NFT_stage_I-II_subject-20_EC (exon-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-19_FC (exon-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: Braak_NFT_stage_I-II_subject-18_EC (exon-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_TC (exon-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-19_EC (exon-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: Braak_NFT_stage_I-II_subject-18_FC (exon-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: Braak_NFT_stage_I-II_subject-17_TC (exon-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_TC (exon-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: Braak_NFT_stage_I-II_subject-17_FC (exon-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-12_FC (exon-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-14_TC (exon-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-17_EC (exon-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-16_FC (exon-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-16_TC (exon-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-12_EC (exon-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-13_EC (exon-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-11_FC (exon-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: Braak_NFT_stage_I-II_subject-11_EC (exon-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-16_EC (exon-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: Braak_NFT_stage_I-II_subject-12_TC (exon-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-10_FC (exon-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: Braak_NFT_stage_I-II_subject-15_TC (exon-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-10_EC (exon-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: Braak_NFT_stage_I-II_subject-15_FC (exon-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: Braak_NFT_stage_I-II_subject-15_EC (exon-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-10_TC (exon-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: Braak_NFT_stage_I-II_subject-11_TC (exon-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-14_EC (exon-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-14_FC (exon-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: Braak_NFT_stage_I-II_subject-13_FC (exon-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: Braak_NFT_stage_I-II_subject-09_FC (exon-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-13_TC (exon-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-09_TC (exon-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-08_TC (exon-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: Braak_NFT_stage_I-II_subject-08_FC (exon-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 (exon-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: Braak_NFT_stage_I-II_subject-09_EC (exon-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-07_TC (exon-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: Braak_NFT_stage_I-II_subject-07_EC (exon-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-07_FC (exon-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_TC (exon-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: Braak_NFT_stage_I-II_subject-06_FC (exon-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_EC (exon-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-03_TC (exon-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: Braak_NFT_stage_I-II_subject-05_EC (exon-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-03_EC (exon-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-01_EC (exon-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: Braak_NFT_stage_I-II_subject-03_FC (exon-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-04_FC (exon-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: Braak_NFT_stage_I-II_subject-02_FC (exon-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 (exon-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: Braak_NFT_stage_I-II_subject-04_TC (exon-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: Braak_NFT_stage_I-II_subject-05_FC (exon-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: Braak_NFT_stage_I-II_subject-02_EC (exon-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: Braak_NFT_stage_I-II_subject-01_TC (exon-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-04_EC (exon-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_0_subject-13_TC (exon-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-10_TC (exon-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_I-II_subject-02_TC (exon-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_0_subject-13_EC (exon-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 (exon-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: Braak_NFT_stage_0_subject-13_FC (exon-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-11_FC (exon-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-12_EC (exon-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: Braak_NFT_stage_0_subject-11_EC (exon-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-10_EC (exon-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: Braak_NFT_stage_0_subject-11_TC (exon-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: Braak_NFT_stage_0_subject-12_FC (exon-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-08_TC (exon-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-10_FC (exon-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: Braak_NFT_stage_I-II_subject-05_TC (exon-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: Braak_NFT_stage_0_subject-09_TC (exon-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-09_EC (exon-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: Braak_NFT_stage_0_subject-09_FC (exon-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_FC (exon-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: Braak_NFT_stage_0_subject-08_EC (exon-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: CD3_B71_100_rep_1_SMART_Nxt

description: 100 human naïve T cells treated with anti-CD3+B71 Fc, and RNA sequencing performed using SMART_Nxt protocol, replicate 1

tag: cell type

value: T cells

tag: treatment

value: anti-CD3+B71 Fc

tag: protocol


title: CD3_B71_1k_rep_2_SMART_Nxt

description: 1,000 human naïve T cells treated with anti-CD3+B71 Fc, and RNA sequencing performed using SMART_Nxt protocol, replicate 2

tag: cell input

tag: replicate


title: CD3_B71_1k_rep_1_SMART_Nxt

description: 1,000 human naïve T cells treated with anti-CD3+B71 Fc, and RNA sequencing performed using SMART_Nxt protocol, replicate 1


title: CD3_B71_5k_rep_2_SMART_Nxt

description: 5,000 human naïve T cells treated with anti-CD3+B71 Fc, and RNA sequencing performed using SMART_Nxt protocol, replicate 2


title: CD3_B71_100k_rep_2_SMART_Nxt

description: 100,000 human naïve T cells treated with anti-CD3+B71 Fc, and RNA sequencing performed using SMART_Nxt protocol, replicate 2


title: CD3_B71_100_rep_2_SMART_Nxt

description: 100 human naïve T cells treated with anti-CD3+B71 Fc, and RNA sequencing performed using SMART_Nxt protocol, replicate 2


title: Braak_NFT_stage_0_subject-07_TC (exon-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 (exon-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: Braak_NFT_stage_0_subject-05_FC (exon-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-06_EC (exon-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: CD3_100_rep2_SMART_Nxt

description: 100 human naïve T cells treated with anti-CD3, and RNA sequencing performed using SMART_Nxt protocol, replicate 2


title: CD3_B71_100k_rep_1_SMART_Nxt

description: 100,000 human naïve T cells treated with anti-CD3+B71 Fc, and RNA sequencing performed using SMART_Nxt protocol, replicate 1


title: CD3_100_rep1_SMART_Nxt

description: 100 human naïve T cells treated with anti-CD3, and RNA sequencing performed using SMART_Nxt protocol, replicate 1


title: CD3_1k_rep2_SMART_Nxt

description: 1,000 human naïve T cells treated with anti-CD3, and RNA sequencing performed using SMART_Nxt protocol, replicate 2


title: CD3_1k_rep1_SMART_Nxt

description: 1,000 human naïve T cells treated with anti-CD3, and RNA sequencing performed using SMART_Nxt protocol, replicate 1


title: CD3_5k_rep1_SMART_Nxt

description: 5,000 human naïve T cells treated with anti-CD3, and RNA sequencing performed using SMART_Nxt protocol, replicate 1


title: CD3_B71_5k_rep_1_SMART_Nxt

description: 5,000 human naïve T cells treated with anti-CD3+B71 Fc, and RNA sequencing performed using SMART_Nxt protocol, replicate 1


title: Braak_NFT_stage_0_subject-07_EC (exon-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: Braak_NFT_stage_0_subject-05_EC (exon-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-02_FC (exon-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-06_FC (exon-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: CD3_100k_rep1_SMART_Nxt

description: 100,000 human naïve T cells treated with anti-CD3, and RNA sequencing performed using SMART_Nxt protocol, replicate 1


title: CD3_100k_rep2_SMART_Nxt

description: 100,000 human naïve T cells treated with anti-CD3, and RNA sequencing performed using SMART_Nxt protocol, replicate 2


title: CD3_5k_rep2_SMART_Nxt

description: 5,000 human naïve T cells treated with anti-CD3, and RNA sequencing performed using SMART_Nxt protocol, replicate 2


title: Braak_NFT_stage_0_subject-05_TC (exon-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: CKO1_brain

city: Beijing

first: Jianwei

last: Jiao

state: Beijing

address: 1 Beichen West Road

department: State Key Laboratory of Reproductive Biology

country: China

institute: Institute of Zoology, Chinese Academy of Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw Data was processed with Perl scripts to ensure the quality of data used in further analysis. The adopted filtering criteria are as follows：1) Remove the adaptor-polluted reads. (Reads containing more than 5 adapter-polluted bases were regarded as adaptor-polluted reads and would be filtered out; 2) Remove the low-quality reads. Reads with the number of low quality bases (phred Quality value less than 19) accounting for more than 15% of total bases are regarded as low-quality reads; 3) Remove reads with number of N bases accounting for more than 5 %.
Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was mapped to the reference genome using TopHat v2.0.12.
The IGV (Integrative Genomics Viewer) was used to view the mapping result by the Heatmap, histogram, scatter plot or other stytle.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and RPKM (Reads Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include count, normalized data, fold-change values etc.

extract_protocol:
Total RNA was extracted by using Trizol reagent. Total 2ug RNA for the construction of sequencing libraries
mRNA were enriched by Oligo(dT) bread and then fragmented by fragmentation buffer. cDNA was synthesized by reverse transcription using 6bp random primers and purified by QIAQuick PCR kit. After adapter ligation, DNA was PCR amplified sequences and band isolated from an agarose gel.

tag: strain background

tag: developmental stage


title: WT1_brain

tag: genotype/variation

value: WT; Wt1fl/fl


title: Braak_NFT_stage_0_subject-04_TC (exon-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: Braak_NFT_stage_0_subject-03_EC (exon-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-02_TC (exon-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-03_FC (exon-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: Braak_NFT_stage_0_subject-03_TC (exon-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: 8667184130_R02C01

city: Hefei

first: Chao

last: Yang

address: #69 Meishan Road, Hefei230032, Anhui, 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

source_name: Psoriasis

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

value: Whole blood

tag: disease state

value: Chronic inflammatory skin disease


title: 8667184130_R01C02

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


title: 8667184130_R02C02


title: 8667184130_R01C01


title: Braak_NFT_stage_0_subject-04_EC (exon-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-01_EC (exon-level)

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


title: 9235752085_R06C02


title: 9235752085_R06C01


title: 9235752085_R05C01


title: Braak_NFT_stage_0_subject-04_FC (exon-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: Braak_NFT_stage_0_subject-06_TC (exon-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-01_FC (exon-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: 9235752085_R04C02


title: 9235752085_R05C02


title: S1_H001: 3 hr Control

city: Tainan

first: Bu-Miin

last: Huang

address: No. 1, University Rd.

department: Cell Biology and Anatomy

country: Taiwan

institute: National Cheng Kung University

description: Gene expression after 3 hrs Control (PBS) treatment

hyb_protocol: The Mouse miRNA OneArray® v4 in Phalanx hybridization buffer in the OneArray® Hybridization Chamber. After overnight hybridization at 37 °C, non-specifically bound targets were removed by three washing steps (Wash I, 37 °C, 5 min; Wash II, 37 °C, 5 min and 25 °C, 5 min; and Wash III, rinse 20 times).

scan_protocol: Slides were dried by centrifugation and scanned using an Axon 4000B scanner (Molecular Devices, Sunnyvale, CA).

data_processing: The signal intensities of Cy5 fluorescence in each spot were analyzed using GenePix 4.1 software (Molecular Devices, Sunnyvale, CA)

source_name: Mouse Leydig tumor cell

label_protocol: 10 mg of total RNA was reverse-transcribed using oligo-dT primers (Invitrogen) and SuperScript II reverse transcriptase (Invitrogen) in the presence of 100 mCi of [33P]dCTP (Amersham Bioscience, Piscataway, NJ) according to the instructions for the Gene

growth_protocol: MA-10 cells were maintain in Maymouth medium with 10%FBS and incubated in a humidified atmosphere containing 95% air and 5% CO2 at 37°C.

extract_protocol: Total RNA was extracted, by using TRIzol (TRI reagent), from vehicle- or 20 mg/mL cordycepin-treated MA-10 cells. RNA quantity and purity was assessed using NanoDrop ND-1000. Pass criteria for absorbance ratios are established at A260/A280 ≥ 1.8 and A260/A230 ≥ 1.5 indicating acceptable RNA purity. RNA integrity number (RIN)values are ascertained using Agilent RNA 6000.

treatment_protocol: MA-10 cells were treated with 100 uM cordycepin or PBS (vehicle control) for 3 hours, and with duplicates were analysis.

tag: cell line

value: Mouse Leydig tumor cell


title: S2_H004: 3 hr Cordycepin 100 μM

description: Gene expression after 3 hrs cordycepin 100 μM treatment


title: 9235752085_R03C02


title: 9235752085_R03C01


title: 9235752085_R04C01


title: S2_H003: 3 hr Cordycepin 100 μM


title: S1_H002: 3 hr Control


title: 9235752085_R02C02


title: 9235752085_R02C01


title: 9235752085_R01C01


title: 9235752085_R01C02


title: 8667192020_R06C02


title: Braak_NFT_stage_0_subject-02_EC (exon-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_TC (exon-level)

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


title: 8667192020_R05C02


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