title: KO_Ventral_rep3

city: Shanghai

first: yanhua

last: du

address: 227 South Chongqing Road, Huangpu District

department: Shanghai Institute of Immunology

institute: Shanghai Jiaotong University School of Medicine

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using histat2 with parameters -p 4 --no-unal --dta-cufflinks -k 1
Samtools with -bh -q 50 were used to filter mapping reads
Cuffdiff2 was used for generated the expression level.The expression level of each gene was normalized to Reads Per Kilobase of exon per Megabase of library size (RPKM)
For differential expression analysis, sequencing counts at the gene level were obtained using HTSeq v0.9.1. R package DESeq2 was then used to identify DEGs between different conditions. To assess the significance of differential gene expression, the P-value threshold was set at 0.05 and the fold change was set at 2.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

molecule: polyA RNA

source_name: hESC_derived NPCs

growth_protocol: hESCs were broken into small clumps and suspended in hESCM for 4 days to form EBs. The EBs were then switched to neural induction medium to direct cells toward a neuroectoderm (NE) fate for 2 days. At day 6, cell aggregates were plated on laminin-coated culture surface and neural tube-like rosettes could be seen at days 14-17.The neural progenitors were maintained in suspension culture as neurospheres in neural induction medium at day 18 through 25. All samples were collected at day25.

extract_protocol:
Total RNA was isolated using a TRIzol kit (Invitrogen) and used to prepare a library.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For ventralization, SHH and the smoothened activator purmorphamine were added into the neural induction medium during day10 to day17. To re-introduce ASCL1 expression in ASCL1-RE cell line, Dox was added during day22 to day25.

value: hESC_derived NPCs

value: ASCL1 KO

tag: cell fate

value: Ventral


title: CONTROL AUNC18

status: Public on Dec 21 2022

type: genomic

city: Dammam

first: Noor

middle: B

last: Almandil

address: C1 West Campus

department: Department of Clinical Pharmacy

country: Saudi Arabia

institute: Imam Abdulrahman Bin Faisal University

description:
CONTROL
Genomic DNA was genotyped using The Human Exome Bead Chip Kit v1.0 and v1.1 (Illumina).

hyb_protocol: According to the hybridazation protocol in manufacture's Reference Guide of The Human Exome Bead Chip Kit v1.0 and v1.1 Illumina

scan_protocol: According to the scan protocol in manufacture's Reference Guide

data_processing:
GenomeStudio 2,0 software
Genotype: AA,AB,BB,or NC (no call)

label: C-Bio and A-DNP

molecule: genomic DNA

organism: Homo sapiens

source_name: Buccal cells

label_protocol: standard Illumina protocol using C-Bio and A-DNP

growth_protocol: Not applicable

extract_protocol: Genomic DNA was extracted from  buccal cell using Gentra Puregene Cell Kit

treatment_protocol: Samples are buccal cell

tag: gender

value: Female


title: CONTROL AUNC17


title: KO_Ventral_rep1

type: SRA

country: China

library_source: transcriptomic

tag: cell type

tag: genotype

tag: cell line


title: CONTROL AUNC16


title: WT_Ventral_rep2

value: wild type


title: WT_Ventral_rep3


title: AUTISM AUN16

description:
AUTISM
Genomic DNA was genotyped using The Human Exome Bead Chip Kit v1.0 and v1.1 (Illumina).


title: WT_Ventral_rep1


title: AUTISM AUN20


title: CONTROL AUNC15


title: CONTROL AUNC14


title: AUTISM AUN12


title: AUTISM AUN43


title: CONTROL AUNC13


title: RE_Dorsal_rep3

value: ASCL1 Rescue

value: Dorsal


title: RE_Dorsal_rep1


title: RE_Dorsal_rep2


title: KO_Dorsal_rep3


title: CONTROL AUNC21


title: KO_Dorsal_rep2


title: CONTROL AUN3M1


title: KO_Ventral_rep2


title: WT_Dorsal_rep2


title: WT_Dorsal_rep3


title: KO_Dorsal_rep1


title: WT_Dorsal_rep1


title: participant_47L

city: Berlin

first: Anna-Lena

last: Lang

address: Charitéplatz 1

department: Institute of Neuropathology

country: Germany

institute: Charité – Universitätsmedizin Berlin

description: Illumina EPIC 850k methylation data from FFPE brain tissue

hyb_protocol: Hybridization to the Illumina 850k BeadChip was carried out as per manufacturers protocol.

scan_protocol: Scanning was carried out as per manufacturers protocol using the Illumina iScan System.

data_processing:
Bulk data processing description:
Data was normalized using noob implemented by minfi and BMIQ implemented by ChAMP. We kept the first processed sample and removed all replicates from the datasets after normalization. Processed average beta values from bulk data for each of the eight brain regions is available.
Cell type specific data processing description:
To estimate cell type heterogeneity in our bulk data, we used an existing cell type-specific DNA methylation reference matrix for brain tissue from EpiSCORE. Bulk data was processed for each brain region separately. First, CpGs were mapped to Entrez IDs using the constAvBetaTSS function from the EpiSCORE package. Cell type proportions were estimated using the wRPC function, using weights in the regression, setting the threshold on the weights to select the most informative genes to 0.4 and the maximum number of iterations in the robust linear regression to 300. The brain reference matrix for EpiSCORE can be used to estimate cell type proportions for neurons, astrocytes, endothelial cells, microglia, oligodendrocytes, and oligodendrocyte precursor cells (OPCs). Because we detected relatively small proportions for oligodendrocytes and OPCs and the cell types are highly related, we combined those proportions into one value for oligodendrocytes/OPCs (olig/OPC). The resulting estimated cell type proportions for the five cell types served as input for cell type deconvolution. Cell type deconvolution was performed using the Tensor Composition Analysis (TCA) package in R. Given the estimated cell type proportions, TCA uses a tensor generalization of matrix factorization to estimate CTS methylation profiles for each of the five cell types we considered. The resulting deconvolved data consists of a CTS methylation value for each CpG and sample. We deconvolved the five cell types within each of the eight brain regions separately. Given that some cell types had very low abundancy in some brain regions, 37 datasets with cell type specific processed average beta values is available.
Bulk CSV data:
Normalized average beta values (Data was normalized using noob implemented by minfi and BMIQ implemented by ChAMP) from bulk data including detection p-values.
Cell type specific CSV data:
Normalized average beta values (see definition above) were followed by cell type deconvolution using EpiSCORE and TCA. Cell type specific data is available for all brain regions. File name abbreviations follow cell descriptions documented in legend of the metadata file.
Additional data processing in the paper, data not available on GEO:
Within each CTS methylation profile, we further collapsed probe-level methylation to three genomic region types (promoters, genes, and CpG islands) using the RnBeads annotations, by calculating the average methylation value across all CpGs within the respective genomic region. These datasets were not uploaded to GEO, but can be easily reproduced using the code available on GitHub https://github.com/anna-lena-lang/90plus_brain_methylation.

label: Cy5 and Cy3

label_protocol: Depending on DNA concentration, 250ng to 1000ng of high-quality DNA were bisulfite converted using the Zymo EZ DNA Methylation Kit (Zymo Research, Orange, CA, USA). After bisulfite conversion, the entire yield (8 µl) was restored with the Infinium HD FFPE DNA Restore Kit. Samples were further processed as per the manufacturer’s standard protocol for FFPE samples on the Illumina Infinium Human MethylationEPIC BeadChip  (Illumina, USA).

extract_protocol: Cores were extracted from FFPE blocks with a biopsy punch needle 1 to 1.5mm in diameter and 2-3mm in length, assuring accurate dissection of very fine regions from FFPE. DNA was extracted from FFPE cores using the Zymo Research Quick DNA FFPE Miniprep kit following the manufacturer's instructions with one minor modification. During overnight digestion with proteinase K at 55°C, intermittent vortexing every 20 minutes at 2000rpm for 1 minute was used to facilitate more complete digestion of tissue chunks.

treatment_protocol: All brain tissue used for this study was formaline fixed, paraffine embedded (FFPE).

value: LC

value: locus coeruleus

tag: batch

tag: Sex

value: female

tag: age

tag: education

tag: flanitot

tag: niaaaascore

tag: niaaabscore

tag: niaaacscore

tag: adseverityscore


title: participant_47N

value: CBM

value: cerebellar cortex


title: NCBP mutant_2

city: Hefei

first: Chen

last: Hongyi

address: 130 Changjiang West Road

institute: Anhui Agricultural University

data_processing:
Illumina Hiseq X ten  used for sequencing.
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v4-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform and paired-end reads were generated.
The adaptor sequences and low-quality sequence reads were removed from the data sets. Raw sequences were transformed into clean reads after data processing. These clean reads were then mapped to the reference genome sequence. Only reads with a perfect match or one mismatch were further analyzed and annotated based on the reference genome. Hisat2 tools soft were used to map with reference genome.
Gene function was annotated based on the following databases:Nr (NCBI non-redundant protein sequences)；Nt (NCBI non-redundant nucleotide sequences)；Pfam (Protein family)；KOG/COG (Clusters of Orthologous Groups of proteins)；Swiss-Prot (A manually annotated and reviewed protein sequence database)；KO (KEGG Ortholog database)；GO (Gene Ontology).
Genome_build: GCA_000001735.1

molecule: total RNA

organism: Arabidopsis thaliana

source_name: whole plant

growth_protocol: 22°C in the greenhouse under a long-day photoperiod (16 hours light, 8 hours dark, LED light intensity: 153 μmol m–2 s–1) with normal plant maintenance.

extract_protocol:
Total RNA of the seedlings was extracted with RNAprep Pure Plant Kit（TIANGEN) method ,and then construction of sequencing libraries
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Grind the seedlings to powder with liquid nitrogen

value: 2-week-old seedlings


title: participant_47J2

value: EC

value: entorhinal cortex


title: participant_47DEN

value: DG

value: dentate gyrus


title: participant_47F

value: CG

value: cingulate gyrus


title: WT_3


title: participant_47CA1


title: NCBP mutant_1


title: WT_1


title: participant_46N


title: AUTISM AUN9


title: participant_46L


title: CONTROL AUNC11


title: participant_46F


title: RNA infected no shield_rep_2

city: Chicago

first: Mary

last: Hummel

state: IL

address: 303 E. Chicago Ave

country: USA

institute: Northwestern University

data_processing:
Adapters were trimmed from reads using cutadapt version 1.13
Trimmed reads were aligned using STAR version 020201
Gene counting was performed using htseq-count version 0.6.1p1
Differential expression was performed using DESeq2
bigWig files were created using deepTools
Genome_build: hg19
Genome_build: HHV5 TB40r-ddFKBP strain (HCMV genome fa and gtf files for alignment of bigwig files are available at https://github.com/Mary-Hummel/HCMV-reference-genomes.git)
Supplementary_files_format_and_content: bigWig files

organism:
Homo sapiens
Human betaherpesvirus 5

source_name: MRC-5 cells

growth_protocol: HCMV MRC5 infected with TB40R-mGFP-IE-FKBP mutant were kept in DMEM medium (Gibco) supplemented with 10% fetal bovine serum (Corning), 1,000 Units/ml Penicillin-Streptomycin (Gibco), and 1uM Shiled1 or vehicle control (Ethanol) at 37°C in a humidified incubator at 5% CO2.

extract_protocol:
For RNA extraction, cells were lysed in Trizol and total RNA was prepared using Direct-zol RNA miniprep kit (Zymo Research) following the manufacturer’s instructions that include an on-column DNase digestion step.
RNA quality was assessed on a Bioanalyzer, and libraries were prepared using IlluminaOligo dT selection kits according the to manufacturer’s instructions.  Libraries were sequenced on an Illumina NovaSEQ6000 (100bp paired-end reads).
RNA-seq of polyadenylated RNA

treatment_protocol: For each infection, 5x10^6 MRC5 were seeded in 15 cm dishes the day before the infection. The following day, medium was replaced with 10ml of DMEM supplemented with 10% FBS without antibiotics. Confluent MRC5 were infected with HCMV TB40R-mGFP-IE-FKBP mutant at MOI of 3 in presence of 1µM Shield1 (+Shield) or Ethanol (-Shield). After 1-hour incubation at 37°C, 10 ml of media without antibiotics  with Shield 1 or Ethanol were added to the plate and the cells incubated at 37°C for 23 hours. We conducted media changes at 24, 48, 72, and 96 hpi using DMEM -10% FBS- PS with either 1µM Shield1 or Ethanol. Cells were collected at 5dpi.

value: MRC-5 cells

tag: infection

value: HHV5 TB40r-ddFKBP strain

tag: treatment

value: treated with vehicle control


title: participant_46DEN


title: participant_46CA1


title: RNA infected no shield_rep_1


title: participant_46B

value: MFG

value: middle frontal gyrus


title: RNA infected + shield_rep_1

value: treated with shield-1


title: NCBP mutant_3


title: RNA infected + shield_rep_2


title: PolII_Infected-shield_ChIP_Rep1

description: ChIPseq

library_source: genomic

data_processing:
Adapters were trimmed from reads using cutadapt version 1.13
Trimmed reads were aligned to the reference genome using Bowtie2 version 2.2.6
bigWig files were created using deepTools
Genome_build: hg19
Genome_build: HHV5 TB40r-ddFKBP strain (HCMV genome fa and gtf files for alignment of bigwig files are available at https://github.com/Mary-Hummel/HCMV-reference-genomes.git)
Supplementary_files_format_and_content: bigWig files

extract_protocol:
After fixation, cells were lysed and sonication with a Bioruptor Plus sonication device (Diagenode). Sonication was conducted for 25 cycles, with 30 sec on/off at high intensity. ChIP was performed by incubating the sonicated sample with either Rpb1 NTD (D8L4Y) Rabbit mAb #14958 or Acetyl-Histone H3 (Lys27) (D5E4) XP Rabbit mAb #8173 (Cell Signaling Technologies) and the protein A/G agarose beads. Beads were washed and eluted in 200μl of elution buffer (50 mM Tris-HCl at pH 8.0, 10 mM EDTA, 1.0% SDS). The eluates were de-cross-linked and the DNA purified using the Qiagen PCR purification kit.
Libraries were prepared with the Illumina Chip-SEQ Kit multiplexed with IDT unique dual index barcodes. Library quality control was assessed using Bioanalyzer High Sensitivity DNA Analysis kit (Agilent) and sequenced on an Illumina NovaSEQ6000 (100bp paired-end reads).

value: infected no shield 4 dpi

tag: chip antibody

value: Rpb1 NTD (D8L4Y) Rabbit mAb #14958 (Cell Signaling Technologies)


title: PolII_Infected-shield_Input_Rep2

description: input


title: WT_2


title: participant_45L

value: LC

value: locus coeruleus

value: male


title: participant_47B

value: female


title: H3K27Ac_Infected-shield_ChIP_Rep2

description: ChIPseq

value: Acetyl-Histone H3 (Lys27) (D5E4) XP Rabbit mAb #8173 (Cell Signaling Technologies)


title: participant_45DEN_redoBatch9fail

value: DG


title: participant_45K

value: SN

value: substantia nigra


title: H3K27Ac_Infected-shield_ChIP_Rep1

description: ChIPseq


title: H3K27Ac_Infected-shield_Input_Rep2

description: input


title: H3K27Ac_Infected-shield_Input_Rep1

description: input


title: participant_45CA1


title: participant_46K


title: participant_45B


title: participant_44N

value: CBM

value: cerebellar cortex


title: PolII_Infected+shield_ChIP_Rep2

description: ChIPseq

value: MRC-5 cells

value: HHV5 TB40r-ddFKBP strain

value: infected +shield, 4 dpi


title: participant_44L


title: PolII_Infected+shield_ChIP_Rep1

description: ChIPseq


title: PolII_Infected-shield_ChIP_Rep2

description: ChIPseq


title: participant_44K


title: participant_45N


title: PolII_Infected+shield_Input_Rep1

description: input


title: participant_44F

value: CG

value: cingulate gyrus


title: participant_44J2

value: EC

value: entorhinal cortex


title: H3K27Ac_Infected+shield_ChIP_Rep2

description: ChIPseq


title: PolII_Infected-shield_Input_Rep1

description: input

value: infected no shield 4 dpi


title: H3K27Ac_Infected+shield_ChIP_Rep1

description: ChIPseq


title: participant_44DEN

value: dentate gyrus


title: H3K27Ac_Infected+shield_Input_Rep2

description: input


title: H3K27Ac_Infected+shield_Input_Rep1

description: input


title: participant_44B

value: MFG

value: middle frontal gyrus

value: male


title: participant_43TER

value: female


title: participant_43SN

value: SN


title: Lung, OVA challenged, replicate 1, scRNAseq, DJ-1 KO_OVA

city: Tianjin

first: Kuan

last: Li

state: Tianjin

address: Jingu road 890

institute: Tianjin Key Laboratory of Pulmonary Regenerative Medicine

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The Cell Ranger software pipeline provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

organism: Mus

source_name: whole lung

extract_protocol:
Single cells were suspended in calcium- and magnesium-free PBS containing 0.04% weight/volume BSA. Then Cells were added to each channel. After generation of GEMs, reverse transcription reactions were engaged barcoded full-length cDNA followed by the disruption of emulsions using the recovery agent and cDNA clean up with DynaBeads Myone Silane Beads (Thermo Fisher Scientific). Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed,  and index adaptor ligated and library amplification.
RNA libraries  were prepared with Chromium Single cell 3’ Reagent v3 Kits according to the manufacturer’s protocol.

tag: tissue

value: whole lung

value: 6-12 weeks old

value: DJ-1 KO

value: OVA challenged


title: participant_43MFG


title: participant_43LOC

value: LC

value: locus coeruleus


title: participant_43DEN

value: DG


title: participant_43CG

value: CG

value: cingulate gyrus


title: PolII_Infected+shield_Input_Rep2

description: input

value: MRC-5 cells

value: HHV5 TB40r-ddFKBP strain

value: infected +shield, 4 dpi


title: Berlin Strain, whole body, control, 72h [67_t6-5C_2]

city: Amsterdam

first: Ruben

last: Bakker

state: North-Holland

address: Boelelaan 1105

department: A-Life

country: Netherlands

institute: Vrije Universiteit Amsterdam

description: Sample 33

data_processing:
Raw reads were imported into R using tximport
Raw reads were compiled into a dataframe by DESeq2
Assembly: Ensembl Metazoa v40 (Folsomia candida Berlin Strain)
Supplementary files format and content: DESeq2 generated dataframe with raw read counts, tab delimited file

organism: Folsomia candida

source_name: whole body

extract_protocol:
RNA was isolated using TRIzol (Invitrogen). 1 ug of total RNA was used for generating the sequencing libraries, TruSeq Stranded mRNA Sample Preparation kit (Ilumina).
Raw data was trimmed by Trimgalore, a wrapper for cut-adapt v0.6.7, and sequences were aligned to the transcriptome with Salmon v1.4.0. Raw reads were normalized using DESeq2 v1.28.1

treatment_protocol:
A natural soil, LUFA2.2, was spiked with 0.25 mg / kg dry soil of imidacloprid or only mixed with water.The soils were distributed over glas jars and pools of 70 animals were added.
Samples were kept at a 16:8 ligth regime at 20 °C and a relative air humidity of 75 %.

tag: strain

value: Berlin Strain

value: whole body

value: WT

value: control

tag: time

value: 72 hours


title: Berlin Strain, whole body, imidaloprid, 72h [72_t6-4I_2]

description: Sample 36

tag: cell type

tag: genotype

value: imidacloprid


title: Berlin Strain, whole body, imidaloprid, 72h [69_t6-1I_2]

description: Sample 34


title: Lung, OVA challenged, replicate 1, scRNAseq, WT_PBS

description: 10x Genomics

value: whole lung

value: female

value: 6-12 weeks old

value: Wild type

value: PBS challenged


title: participant_43CBL

value: CBM

value: cerebellar cortex

tag: batch


title: Berlin Strain, whole body, control, 72h [66_t6-4C_2]

description: Sample 32


title: participant_43CA1

tag: Sex


title: participant_42TER

value: EC

value: entorhinal cortex

tag: age


title: participant_44CA1

value: male

tag: education


title: Berlin Strain, whole body, imidaloprid, 72h [71_t6-4I_2]

description: Sample 35


title: Berlin Strain, whole body, control, 72h [65_t6-3C_2]

description: Sample 31


title: Berlin Strain, whole body, imidaloprid, 60h [61_t5-5I_2]

description: Sample 30

value: 60 hours


title: participant_42SN

value: SN

value: substantia nigra

tag: flanitot


title: Berlin Strain, whole body, imidaloprid, 60h [59_t5-3I_2]

description: Sample 29

value: Berlin Strain

value: whole body

value: WT


title: participant_42LOC

value: LC

value: locus coeruleus

tag: niaaaascore


title: participant_42DEN

value: DG

value: dentate gyrus

value: female

tag: niaaabscore


title: Lung, OVA challenged, replicate 1, scRNAseq, WT_OVA

description: 10x Genomics

value: whole lung

value: 6-12 weeks old

value: Wild type

value: OVA challenged


title: participant_42MFG

value: MFG

value: middle frontal gyrus

tag: niaaacscore


title: Berlin Strain, whole body, control, 60h [57_t5-6C_2]

description: Sample 27

value: control

value: 60 hours


title: Berlin Strain, whole body, control, 60h [56_t5-5C_2]

description: Sample 26


title: Berlin Strain, whole body, imidaloprid, 60h [34_t5-1I_2]

description: Sample 28

value: imidacloprid


title: participant_42CBL

value: CBM

value: cerebellar cortex

tag: adseverityscore


title: Berlin Strain, whole body, control, 60h [53_t5-2C_2]

description: Sample 25

value: Berlin Strain

value: whole body

value: WT


title: participant_42CG

value: CG

value: cingulate gyrus


title: participant_42CA1

value: female


title: Berlin Strain, whole body, imidaloprid, 48h [51_t4-6I_2]

description: Sample 24

value: 48 hours


title: Berlin Strain, whole body, imidaloprid, 48h [50_t4-5I_2]

description: Sample 23


title: participant_41TER

value: EC

value: entorhinal cortex

value: male


title: Berlin Strain, whole body, imidaloprid, 48h [48_t4-3I_2]

description: Sample 22


title: participant_41SN

value: SN

value: substantia nigra


title: participant_41DEN

value: DG

value: dentate gyrus


title: participant_41L

value: LC

value: locus coeruleus


title: Berlin Strain, whole body, control, 48h [43_t4-4C_2]

description: Sample 20

value: control


title: Berlin Strain, whole body, control, 48h [41_t4-2C_2]

description: Sample 19

value: Berlin Strain


title: participant_41CG


title: participant_41MFG

value: MFG

value: middle frontal gyrus


title: participant_41CA1


title: participant_41CBL

value: CBM

value: cerebellar cortex


title: Berlin Strain, whole body, imidacloprid, 36h [35_t3-2I_2]

description: Sample 17

value: whole body

value: WT

value: imidacloprid

value: 36 hours


title: Berlin Strain, whole body, imidacloprid, 36h [39_t3-6I_2]

description: Sample 18


title: Berlin Strain, whole body, imidacloprid, 36h [33_t3-1I2_2]

description: Sample 16


title: Berlin Strain, whole body, control, 36h [30_t3-4C_2]

description: Sample 14


title: participant_40Lx

value: female


title: Berlin Strain, whole body, control, 36h [29_t3-3C_2]

description: Sample 13


title: Berlin Strain, whole body, imidacloprid, 24h [25_t2-6I_2]

description: Sample 12

value: 24 hours


title: Berlin Strain, whole body, imidacloprid, 24h [20_t2-2I_2]

description: Sample 10


title: participant_40CA1


title: participant_40DEN


title: participant_40N


title: Berlin Strain, whole body, imidacloprid, 24h [21_t2-3I_2]

description: Sample 11


title: Berlin Strain, whole body, control, 24h [4_t2-4C_2]

description: Sample 8


title: participant_40B


title: Berlin Strain, whole body, control, 24h [5_t2-3C_2]

description: Sample 7


title: participant_39SN

value: SN

value: substantia nigra

value: male


title: Berlin Strain, whole body, control, 48h [45_t4-6C_2]

description: Sample 21

value: 48 hours


title: participant_39MFG


title: Berlin Strain, whole body, imidaloprid, 12h [2_t1-6I_2]

description: Sample 6

value: 12 hours


title: Berlin Strain, whole body, control, 36h [31_t3-5C_2]

description: Sample 15

value: control


title: participant_39LOC

value: LC

value: locus coeruleus


title: Berlin Strain, whole body, imidaloprid, 12h [t1-5I_2]

description: Sample 5

value: Berlin Strain


title: participant_39CG

value: CG

value: cingulate gyrus


title: Berlin Strain, whole body, imidaloprid, 12h [8_t1-2I_2]

description: Sample 4

value: whole body


title: Berlin Strain, whole body, control, 12h [3_t1-3C_2]

description: Sample 2

value: WT


title: participant_40J2

value: EC

value: entorhinal cortex


title: participant_39CBL

value: CBM

value: cerebellar cortex


title: participant_40F

value: female


title: Berlin Strain, whole body, control, 12h [2_t1-2C]

description: Sample 1


title: participant_39CA1


title: Berlin Strain, whole body, control, 24h [8_t2-6C_2]

description: Sample 9

value: 24 hours


title: participant_38K

value: SN

value: substantia nigra


title: participant_38N


title: participant_38J2


title: participant_40K


title: participant_38F


title: participant_39DEN

value: DG

value: dentate gyrus

value: male


title: participant_38DEN


title: participant_38B

value: MFG

value: middle frontal gyrus


title: Empty well 10

type: other

city: Lincoln

first: Paul

last: Maclean

address: Cnr Springs Road and Gerald Street

country: New Zealand

institute: AgResearch NZ LTD

description:
Empty well 10
20200819_cJD immuno Run-4 555_01_08.RCC
Empty well 10

hyb_protocol: Hybrdization reactions were performed in final voulme of 15µl according to the manufacturer's instructions (MAN-10040-06). All hybridization reactions were incubated at 67°C for a minimum of 18 h

scan_protocol: Hybridized probes were purified and counted on the nCounter Prep Station and Digital Analyzer (NanoString) following the manufacturer’s instructions. For each assay, a high-density scan (600 fields of view) was performed

data_processing: The data were normalized for lane-to-lane variation with a dilution series of six spike-in positive controls using vsn normalization

label: Fluorescently labeled target sequences

molecule: other

organism: other sequences

source_name: Leukocytes

label_protocol: 1.1 µg of purified RNA in 7µl was added to tubes containing 8 µl of PlexSet master mix (Probe A & B as well as Reporter probes with flouresenct tags and Capture  probes) according to the manufacturer's instructions (MAN-10040-06).

extract_protocol: Total RNA was isolated from the samples using RNeasy kit according to the manufacturer’s instructions (Qiagen, Hilden, Germany).

treatment_protocol: Briefly, 3 mL of blood was transferred into a 50 mL falcon tube and 13.5 mL of chilled water was added (4.5 mL/ml of blood) to lyse the red blood cells. The tubes were quickly mix for 15 sec and 1.5 mL of 10X DPBS (500 µL/mL of blood) (Thermo Fisher Scientific, New Zealand) was added to equilibrate the sample. Subsequently, the cells were centrifuged at 250 μg for 10 min at 4°C, washed with PBS (10 mM, pH-7.3) and the cells were re-suspended in 0.5 mL of RPMI-1640 containing 10% fetal bovine serum (Thermo Fisher Scientific, New Zealand). Cell number and viability was measured by trypan blue exclusion method using TC20 cell counter (BioRad). A total of 2x106 cells were added to each well in a U-bottom 96-well tissue culture plate (Nunc(TM)) and stimulated with either media alone (un-stimulated), PPDA (24 μg/mL) or RA (10 µg/mL) at 37°C for 24 h. After incubation, plates were centrifuged in a swing out rotor at 350 μg for 10 min at room temperature. The supernatant was removed and 150 µL of a commercial lysis buffer for RNA preparation was added (RLT buffer, Qiagen, Hilden, Germany) to the samples and the plates were stored at –80°C until RNA isolation.

tag: nanostring plexset set in rcc files

value: Empty well 10

tag: antigen

tag: vaccine

value: Leukocytes


title: Berlin Strain, whole body, control, 12h [6_t1-6C_2]

description: Sample 3

value: Berlin Strain

value: whole body

tag: treatment

value: control

value: 12 hours


title: Empty well 14

description:
Empty well 14
20200819_cJD immuno Run-4 555_01_12.RCC
Empty well 14

value: Empty well 14


title: participant_37TER

value: EC

value: entorhinal cortex


title: Empty well 9

description:
Empty well 9
20200819_cJD immuno Run-4 555_01_07.RCC
Empty well 9

value: Empty well 9


title: Empty well 13

description:
Empty well 13
20200819_cJD immuno Run-4 555_01_11.RCC
Empty well 13

value: Empty well 13


title: Empty well 11

description:
Empty well 11
20200819_cJD immuno Run-4 555_01_09.RCC
Empty well 11

value: Empty well 11


title: Empty well 12

description:
Empty well 12
20200819_cJD immuno Run-4 555_01_10.RCC
Empty well 12

value: Empty well 12


title: participant_37MFG

value: female


title: Empty well 8

description:
Empty well 8
20200819_cJD immuno Run-4 555_01_06.RCC
Empty well 8

value: Empty well 8


title: participant_37DEN

value: DG

value: dentate gyrus


title: participant_37CBL

value: CBM

value: cerebellar cortex


title: participant_37CA1


title: participant_36N_cut

value: male


title: Empty well 4

description:
Empty well 4
20200819_cJD immuno Run-4 555_01_02.RCC
Empty well 4

value: Empty well 4

value: Leukocytes


title: Empty well 5

description:
Empty well 5
20200819_cJD immuno Run-4 555_01_03.RCC
Empty well 5

value: Empty well 5


title: participant_36K

value: SN

value: substantia nigra


title: participant_36L

value: LC

value: locus coeruleus


title: Empty well 3

description:
Empty well 3
20200819_cJD immuno Run-4 555_01_01.RCC
Empty well 3

value: Empty well 3


title: Empty well 6

description:
Empty well 6
20200819_cJD immuno Run-4 555_01_04.RCC
Empty well 6

value: Empty well 6


title: participant_36J3


title: participant_37LOC


title: 22N,W0_rep2

type: RNA

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Recombinant MAP fusion protein, sample taken 0 weeks after vaccination, stimulated with PBS antigen
20200819_cJD immuno Run-4 555_01_09.RCC

organism: Bos taurus

value: Week 0

value: PBS

value: Recombinant MAP fusion protein


title: participant_36J2_new

value: EC

value: entorhinal cortex


title: Empty well 1

description:
Empty well 1
20200819_cJD immuno Run-4 555_01_11.RCC
Empty well 1

value: Empty well 1


title: Empty well 7

description:
Empty well 7
20200819_cJD immuno Run-4 555_01_05.RCC
Empty well 7

value: Empty well 7


title: Empty well 2

description:
Empty well 2
20200819_cJD immuno Run-4 555_01_12.RCC
Empty well 2

value: Empty well 2


title: participant_36B_whole

value: MFG

value: middle frontal gyrus

value: male


title: 32RA,W9

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Protein particle displaying MAP fusion protein, sample taken 12 weeks after vaccination, stimulated with Recombinant antigen antigen
20200819_cJD immuno Run-4 555_01_08.RCC

value: Week 12

value: Recombinant antigen

value: Leukocytes


title: participant_36F

description: Illumina EPIC 850k methylation data from FFPE brain tissue

value: CG

value: cingulate gyrus


title: participant_35N

value: CBM

value: cerebellar cortex

value: female


title: participant_35K

value: SN

value: substantia nigra


title: participant_35L

value: LC

value: locus coeruleus


title: 27N,W0_rep2

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Protein particle displaying MAP fusion protein, sample taken 0 weeks after vaccination, stimulated with PBS antigen
20200819_cJD immuno Run-4 555_01_10.RCC

value: Week 0

value: PBS


title: 32A,W9

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Protein particle displaying MAP fusion protein, sample taken 12 weeks after vaccination, stimulated with PPBDA antigen
20200819_cJD immuno Run-4 555_01_07.RCC

value: PPBDA


title: 31N,W9

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Protein particle displaying MAP fusion protein, sample taken 12 weeks after vaccination, stimulated with PBS antigen
20200819_cJD immuno Run-4 555_01_03.RCC


title: participant_35J2

value: EC

value: entorhinal cortex


title: 31A,W9

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Protein particle displaying MAP fusion protein, sample taken 12 weeks after vaccination, stimulated with PPBDA antigen
20200819_cJD immuno Run-4 555_01_04.RCC

value: Week 12


title: 32N,W9

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Protein particle displaying MAP fusion protein, sample taken 12 weeks after vaccination, stimulated with PBS antigen
20200819_cJD immuno Run-4 555_01_06.RCC


title: 30RA,W9

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Protein particle displaying MAP fusion protein, sample taken 12 weeks after vaccination, stimulated with Recombinant antigen antigen
20200819_cJD immuno Run-4 555_01_02.RCC

value: Recombinant antigen


title: 30A,W9

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Protein particle displaying MAP fusion protein, sample taken 12 weeks after vaccination, stimulated with PPBDA antigen
20200819_cJD immuno Run-4 555_01_01.RCC

value: Leukocytes


title: participant_35F

value: CG


title: 30N,W9

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Protein particle displaying MAP fusion protein, sample taken 12 weeks after vaccination, stimulated with PBS antigen
20200819_cJD immuno Run-4 555_01_12.RCC


title: participant_35DEN_redoBatch9fail

value: DG

value: dentate gyrus


title: participant_36J1

value: male


title: participant_35B

value: MFG

value: middle frontal gyrus

value: female


title: participant_35CA1


title: 29N,W9

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Protein particle displaying MAP fusion protein, sample taken 12 weeks after vaccination, stimulated with PBS antigen
20200819_cJD immuno Run-4 555_01_09.RCC


title: 31RA,W9

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Protein particle displaying MAP fusion protein, sample taken 12 weeks after vaccination, stimulated with Recombinant antigen antigen
20200819_cJD immuno Run-4 555_01_05.RCC


title: 29RA,W9

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Protein particle displaying MAP fusion protein, sample taken 12 weeks after vaccination, stimulated with Recombinant antigen antigen
20200819_cJD immuno Run-4 555_01_11.RCC


title: 28RA,W9

value: Protein particle displaying MAP fusion protein


title: participant_34L

value: LC

value: locus coeruleus


title: participant_34J2


title: participant_34DEN


title: participant_34F

value: cingulate gyrus


title: 28A,W9

value: PPBDA


title: participant_34K

value: SN

value: substantia nigra


title: 27RA,W9

value: Week 12


title: 28N,W9

value: PBS


title: participant_34CA1_redoBatch9fail


title: 27N,W9

value: Leukocytes


title: 26RA,W9

value: Recombinant antigen


title: 29A,W9

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Protein particle displaying MAP fusion protein, sample taken 12 weeks after vaccination, stimulated with PPBDA antigen
20200819_cJD immuno Run-4 555_01_10.RCC


title: participant_34B


title: participant_34N

value: CBM

value: cerebellar cortex


title: participant_33N


title: 26N,W9


title: 26A,W9


title: participant_33L


title: participant_33K


title: 25RA,W9


title: 25A,W9


title: participant_33J2

value: EC

value: entorhinal cortex


title: participant_33F

value: CG


title: 24RA,W9

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Recombinant MAP fusion protein, sample taken 12 weeks after vaccination, stimulated with Recombinant antigen antigen
20200819_cJD immuno Run-4 555_01_08.RCC

value: Recombinant MAP fusion protein


title: 25N,W9

value: Protein particle displaying MAP fusion protein


title: participant_33DEN

value: DG

value: dentate gyrus

value: female


title: participant_33CA1_redoBatch9fail


title: 24A,W9

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Recombinant MAP fusion protein, sample taken 12 weeks after vaccination, stimulated with PPBDA antigen
20200819_cJD immuno Run-4 555_01_07.RCC

value: PPBDA


title: participant_32N


title: participant_33B

value: MFG

value: middle frontal gyrus


title: 24N,W9

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Recombinant MAP fusion protein, sample taken 12 weeks after vaccination, stimulated with PBS antigen
20200819_cJD immuno Run-4 555_01_06.RCC

value: Week 12


title: 23RA,W9

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Recombinant MAP fusion protein, sample taken 12 weeks after vaccination, stimulated with Recombinant antigen antigen
20200819_cJD immuno Run-4 555_01_05.RCC


title: 23A,W9

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Recombinant MAP fusion protein, sample taken 12 weeks after vaccination, stimulated with PPBDA antigen
20200819_cJD immuno Run-4 555_01_04.RCC


title: participant_32L

description: Illumina EPIC 850k methylation data from FFPE brain tissue

value: LC

value: locus coeruleus


title: participant_32K

value: SN

value: substantia nigra


title: 23N,W9

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Recombinant MAP fusion protein, sample taken 12 weeks after vaccination, stimulated with PBS antigen
20200819_cJD immuno Run-4 555_01_03.RCC

value: PBS

value: Leukocytes


title: participant_32F

value: cingulate gyrus


title: participant_32J2

value: EC

value: entorhinal cortex


title: participant_32DEN_redoBatch9fail


title: 22RA,W9

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Recombinant MAP fusion protein, sample taken 12 weeks after vaccination, stimulated with Recombinant antigen antigen
20200819_cJD immuno Run-4 555_01_02.RCC

value: Recombinant antigen

value: Recombinant MAP fusion protein


title: participant_32B


title: participant_32CA1


title: participant_31N

value: CBM

value: cerebellar cortex

value: male


title: 21RA,W9

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Recombinant MAP fusion protein, sample taken 12 weeks after vaccination, stimulated with Recombinant antigen antigen
20200819_cJD immuno Run-4 555_01_11.RCC


title: 21A,W9

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Recombinant MAP fusion protein, sample taken 12 weeks after vaccination, stimulated with PPBDA antigen
20200819_cJD immuno Run-4 555_01_10.RCC

value: PPBDA


title: 22N,W9

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Recombinant MAP fusion protein, sample taken 12 weeks after vaccination, stimulated with PBS antigen
20200819_cJD immuno Run-4 555_01_12.RCC


title: participant_31K


title: 22A,W9

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Recombinant MAP fusion protein, sample taken 12 weeks after vaccination, stimulated with PPBDA antigen
20200819_cJD immuno Run-4 555_01_01.RCC


title: 20A,W9


title: participant_31J2


title: 21N,W9

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Recombinant MAP fusion protein, sample taken 12 weeks after vaccination, stimulated with PBS antigen
20200819_cJD immuno Run-4 555_01_09.RCC


title: 20N,W9


title: 20RA,W9


title: participant_31F

value: CG


title: participant_31DEN

value: DG

value: dentate gyrus


title: participant_31CA1


title: participant_31B

value: MFG

value: middle frontal gyrus


title: participant_30L

value: LC

value: locus coeruleus

value: female


title: participant_30K

value: SN

value: substantia nigra


title: 19N,W9

value: Week 12

value: PBS

value: Leukocytes


title: 19RA,W9

value: Recombinant antigen

value: Recombinant MAP fusion protein


title: participant_30N

value: CBM

value: cerebellar cortex


title: 19A,W9

value: PPBDA


title: participant_30J2

value: EC

value: entorhinal cortex


title: participant_30F

value: CG

value: cingulate gyrus


title: 18A,W9


title: 18N,W9


title: participant_30DEN

value: DG

value: dentate gyrus


title: 17RA,W9


title: 27A,W9

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Protein particle displaying MAP fusion protein, sample taken 12 weeks after vaccination, stimulated with PPBDA antigen
20200819_cJD immuno Run-4 555_01_04.RCC


title: participant_30CA1

value: female


title: 8RA,W9

description:
Leukocytes from heparinized blood samples, from animal vaccinated with PBS, sample taken 12 weeks after vaccination, stimulated with PPBDA antigen
20200819_cJD immuno Run-4 555_01_08.RCC


title: participant_30B

value: MFG

value: middle frontal gyrus


title: 17N,W9

value: Week 12


title: 8N,W9

description:
Leukocytes from heparinized blood samples, from animal vaccinated with PBS, sample taken 12 weeks after vaccination, stimulated with PBS antigen
20200819_cJD immuno Run-4 555_01_06.RCC

value: PBS


title: participant_29N_whole

value: male


title: 8A,W9

description:
Leukocytes from heparinized blood samples, from animal vaccinated with PBS, sample taken 12 weeks after vaccination, stimulated with PPBDA antigen
20200819_cJD immuno Run-4 555_01_07.RCC

value: Leukocytes


title: 7RA,W9

description:
Leukocytes from heparinized blood samples, from animal vaccinated with PBS, sample taken 12 weeks after vaccination, stimulated with Recombinant antigen antigen
20200819_cJD immuno Run-4 555_01_05.RCC

value: Recombinant antigen


title: participant_29K

value: SN

value: substantia nigra


title: participant_29L

value: LC

value: locus coeruleus


title: participant_29Jx3


title: 7N,W9

description:
Leukocytes from heparinized blood samples, from animal vaccinated with PBS, sample taken 12 weeks after vaccination, stimulated with PBS antigen
20200819_cJD immuno Run-4 555_01_03.RCC


title: 6RA,W9

description:
Leukocytes from heparinized blood samples, from animal vaccinated with PBS, sample taken 12 weeks after vaccination, stimulated with Recombinant antigen antigen
20200819_cJD immuno Run-4 555_01_02.RCC


title: participant_29Jx2_new

value: EC

value: entorhinal cortex


title: participant_29Jx1


title: 6A,W9

description:
Leukocytes from heparinized blood samples, from animal vaccinated with PBS, sample taken 12 weeks after vaccination, stimulated with PPBDA antigen
20200819_cJD immuno Run-4 555_01_01.RCC

value: PPBDA


title: 18RA,W9

value: Recombinant MAP fusion protein


title: participant_29F

value: CG

value: cingulate gyrus


title: 17A,W9


title: 6N,W9

description:
Leukocytes from heparinized blood samples, from animal vaccinated with PBS, sample taken 12 weeks after vaccination, stimulated with PBS antigen
20200819_cJD immuno Run-4 555_01_12.RCC


title: 5RA,W9

description:
Leukocytes from heparinized blood samples, from animal vaccinated with PBS, sample taken 12 weeks after vaccination, stimulated with Recombinant antigen antigen
20200819_cJD immuno Run-4 555_01_11.RCC


title: participant_29B_cut

description: Illumina EPIC 850k methylation data from FFPE brain tissue

value: MFG


title: participant_28F_reex_failed

value: female


title: participant_28J2


title: participant_27N

value: CBM

value: cerebellar cortex


title: 5A,W9

description:
Leukocytes from heparinized blood samples, from animal vaccinated with PBS, sample taken 12 weeks after vaccination, stimulated with PPBDA antigen
20200819_cJD immuno Run-4 555_01_10.RCC

value: Week 12

value: PBS


title: 5N,W9

description:
Leukocytes from heparinized blood samples, from animal vaccinated with PBS, sample taken 12 weeks after vaccination, stimulated with PBS antigen
20200819_cJD immuno Run-4 555_01_09.RCC

value: Leukocytes


title: participant_27L


title: 4A,W9


title: 4RA,W9

description:
Leukocytes from heparinized blood samples, from animal vaccinated with PBS, sample taken 12 weeks after vaccination, stimulated with Recombinant antigen antigen
20200819_cJD immuno Run-4 555_01_08.RCC

value: Recombinant antigen


title: participant_27K

value: SN

value: substantia nigra


title: 7A,W9

description:
Leukocytes from heparinized blood samples, from animal vaccinated with PBS, sample taken 12 weeks after vaccination, stimulated with PPBDA antigen
20200819_cJD immuno Run-4 555_01_04.RCC


title: 3RA,W9


title: participant_27J2


title: participant_27F


title: 3A,W9


title: 4N,W9


title: participant_27DEN

value: DG

value: dentate gyrus


title: 3N,W9


title: participant_27B

value: middle frontal gyrus


title: 2RA,W9


title: 2A,W9

value: PPBDA


title: 2N,W9


title: participant_26N


title: participant_26K


title: 1A,W9


title: 1N,W9


title: 32RA,W6

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Protein particle displaying MAP fusion protein, sample taken 9 weeks after vaccination, stimulated with Recombinant antigen antigen
20200819_cJD immuno Run-4 555_01_08.RCC

value: Week 9


title: participant_26F

value: CG


title: 32A,W6

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Protein particle displaying MAP fusion protein, sample taken 9 weeks after vaccination, stimulated with PPBDA antigen
20200819_cJD immuno Run-4 555_01_07.RCC


title: participant_26CA1_redoBatch9fail


title: participant_26B


title: 31RA,W6

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Protein particle displaying MAP fusion protein, sample taken 9 weeks after vaccination, stimulated with Recombinant antigen antigen
20200819_cJD immuno Run-4 555_01_05.RCC


title: 31A,W6

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Protein particle displaying MAP fusion protein, sample taken 9 weeks after vaccination, stimulated with PPBDA antigen
20200819_cJD immuno Run-4 555_01_04.RCC


title: participant_26DEN


title: participant_25N


title: participant_25K


title: participant_25J2

value: EC

value: entorhinal cortex


title: participant_27CA1

value: female


title: participant_25L

value: LC

value: locus coeruleus


title: 30RA,W6

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Protein particle displaying MAP fusion protein, sample taken 9 weeks after vaccination, stimulated with Recombinant antigen antigen
20200819_cJD immuno Run-4 555_01_02.RCC


title: 31N,W6

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Protein particle displaying MAP fusion protein, sample taken 9 weeks after vaccination, stimulated with PBS antigen
20200819_cJD immuno Run-4 555_01_03.RCC


title: 30A,W6

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Protein particle displaying MAP fusion protein, sample taken 9 weeks after vaccination, stimulated with PPBDA antigen
20200819_cJD immuno Run-4 555_01_01.RCC


title: participant_26L


title: participant_25DEN


title: 30N,W6

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Protein particle displaying MAP fusion protein, sample taken 9 weeks after vaccination, stimulated with PBS antigen
20200729_cJD immune Run-3 555_01_12.RCC


title: participant_25CA1


title: 29RA,W6

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Protein particle displaying MAP fusion protein, sample taken 9 weeks after vaccination, stimulated with Recombinant antigen antigen
20200729_cJD immune Run-3 555_01_11.RCC


title: 1RA,W9

value: Week 12


title: participant_26J2


title: 29A,W6

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Protein particle displaying MAP fusion protein, sample taken 9 weeks after vaccination, stimulated with PPBDA antigen
20200729_cJD immune Run-3 555_01_10.RCC


title: participant_25B

value: MFG


title: 32N,W6

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Protein particle displaying MAP fusion protein, sample taken 9 weeks after vaccination, stimulated with PBS antigen
20200819_cJD immuno Run-4 555_01_06.RCC

value: PBS

value: Leukocytes


title: participant_24N

value: CBM

value: cerebellar cortex


title: participant_24L


title: 28A,W6

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Protein particle displaying MAP fusion protein, sample taken 9 weeks after vaccination, stimulated with PPBDA antigen
20200729_cJD immune Run-3 555_01_07.RCC


title: 28N,W6

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Protein particle displaying MAP fusion protein, sample taken 9 weeks after vaccination, stimulated with PBS antigen
20200729_cJD immune Run-3 555_01_06.RCC


title: 27RA,W6

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Protein particle displaying MAP fusion protein, sample taken 9 weeks after vaccination, stimulated with Recombinant antigen antigen
20200729_cJD immune Run-3 555_01_05.RCC

value: Recombinant antigen


title: participant_25F

description: Illumina EPIC 850k methylation data from FFPE brain tissue

value: cingulate gyrus


title: participant_24F


title: 27N,W6

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Protein particle displaying MAP fusion protein, sample taken 9 weeks after vaccination, stimulated with PBS antigen
20200729_cJD immune Run-3 555_01_03.RCC


title: 29N,W6

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Protein particle displaying MAP fusion protein, sample taken 9 weeks after vaccination, stimulated with PBS antigen
20200729_cJD immune Run-3 555_01_09.RCC


title: participant_23L


title: 26A,W6

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Protein particle displaying MAP fusion protein, sample taken 9 weeks after vaccination, stimulated with PPBDA antigen
20200729_cJD immune Run-3 555_01_01.RCC


title: 26RA,W6

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Protein particle displaying MAP fusion protein, sample taken 9 weeks after vaccination, stimulated with Recombinant antigen antigen
20200729_cJD immune Run-3 555_01_02.RCC


title: participant_23N


title: participant_23J2


title: participant_23DEN

value: DG

value: dentate gyrus


title: participant_23K

value: SN

value: substantia nigra


title: G_pBL_6

city: Griffin

first: Brendan

middle: G.

last: Hunt

state: GA

address: 125 Redding Building, Griffin Campus, 1109 Experiment Street

department: Entomology

institute: University of Georgia

data_processing:
Sequence reads were trimmed using TrimGalore
Trimmed reads were aligned to the “SINVBB1” genome assembly (Yan et al. 2020) using STAR (Dobin et al. 2013) with the 2-pass alignment procedure. Gene counts exported from STAR were used for differential expression analyses with edgeR (Robinson et al. 2009).
Assembly: SINVBB1
Supplementary files format and content: tab-delimited text files include geneIDs and raw counts generated by STAR for each sample. Brain samples utilize the second counts column in the file while gaster libraries utilize the fourth column

organism: Solenopsis invicta

source_name: Gaster of a polygyne SB/Sb worker cross-fostered into a polygyne colony as a pupae

growth_protocol: S. invicta fire ant colonies were collected in Florida, United States and reared for one month under standard laboratory conditions (Jouvenaz et al. 1977) before any experimental manipulations. Prior to and during experiments, ants were fed a diet of crickets, mealworms and a mixture of sugar, fruits, and vegetables. To study the indirect effects of the social environment arising during development up until the pupal stage and during the 14 first days as adults (i.e., after eclosion from the pupae), we transferred 25-40 dark worker pupae (i.e., 0-48h prior to emergence) between recipient colonies that were formed from 10 stock monogyne and 9 stock polygyne colonies: SB/SB worker pupae from monogyne donor colonies were transferred to both monogyne and polygyne recipient colonies and SB/SB and SB/Sb worker pupae from donor polygyne colonies to polygyne recipient colonies. A given stock colony was never used more than once as a donor or recipient colony for a given treatment and pupae were never transferred between donor and recipient colonies originating from the same stock colony. All recipient colonies contained 250 workers which were marked by cutting the middle leg at the level of the mid-femur, allowing the easy identification of cross-fostered workers. Monogyne recipient colonies contained one monogyne reproductive SB/SB queen while polygyne recipient colonies contained two egg-laying dealate SB/Sb queens (mating status unknown). Sixteen days after the cross-fostering, we sampled all 0.6-0.9 mg minor workers with six intact legs for the RNA-seq analyses (these individuals were all 14-16 day-old).

extract_protocol:
Dissected samples were stored in liquid nitrogen. Total nucleic acids from brains were extracted using an Agencourt FormaPure kit (Beckman Coulter Life Sciences, Indianapolis, Indiana) with volumes scaled down by a factor 4. The first two washing steps (wash buffer and 70% ethanol) were carried out twice. Half of the extracted nucleic acids were eluted with 20 µl of RNase free water and concentrated to 5 µl. The sample was digested by adding 20 µl of DNase I mix (60 µl contains 1.5 µl 1M Tris-HCl [pH 7.5], 3.75 µl 0.1M MgCl2, 1.5 µl 2.5 M KCl, 1.5 µl 0.1M DTT, 3.75 µl RNasin Plus [40u/µl; Promega, Madison Wisconsin], 5 units of DNase I [RNase-free; cat no. 04 716 728 001; Roche, Basel, Switzerland] and 47.5 µl RNase-free water) and incubating at 37°C for 15 min. Then 25 µl of T.E. buffer (pH 7.5) and SDS (0.2% final concentration) were added and RNA was extracted with chloropane. 8 µl of linear acrylamide (5 mg/ml; Ambion; Austin, Texas) was added as carrier to the aqueous phase and nucleic acids were precipitated by adding sodium acetate to 0.3 M and 2.5 volumes of ethanol followed by a wash in 70% ethanol. The pellet was air-dried for 5 min. and re-suspended in 9 µl of RNase-free water.
Sequencing libraries for brains were prepared using SMARTer Ultra Low Input RNA for Sequencing-V3 kit (Takara Bio, Kusatsu, Japan) with a modified protocol provided by manufacturer for brains. After the fragmentation step (volume 75 µl), 8 µl of acrylamide carrier was added and double-strand cDNA was precipitated with ethanol followed by a wash in 70% ethanol. The pellet was air-dried for 5 min., re-suspended in 10 µl 10 mM Tris-HCL (pH 8.5) and processed further with the sequencing kit. Sequencing libraries for gasters were prepared using the KAPA stranded RNA-seq kit (Kapa Biosystems, Wilmington, Massachusetts) following manufacturer’s instructions.

value: Gaster

value: SB/Sb

tag: individual id

value: adult polygyne worker cross-fostered into a polygyne colony upon pupation


title: participant_24TER

value: EC

value: entorhinal cortex

value: female


title: 28RA,W6

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Protein particle displaying MAP fusion protein, sample taken 9 weeks after vaccination, stimulated with Recombinant antigen antigen
20200729_cJD immune Run-3 555_01_08.RCC

tag: time

value: Week 9


title: G_pBL_7

tag: cell type


title: participant_23CA1_redoBatch9fail

tag: genotype


title: G_pBL_8


title: G_pBL_5


title: 25A,W6

value: PPBDA

value: Protein particle displaying MAP fusion protein


title: 25RA,W6

value: Leukocytes


title: 26N,W6

value: PBS


title: participant_24K

tag: batch


title: participant_23B

value: MFG

value: middle frontal gyrus

tag: Sex


title: participant_22N

value: CBM

value: cerebellar cortex

value: male

tag: age


title: participant_24CA1

tag: education


title: participant_22J2

tag: flanitot


title: 25N,W6


title: 27A,W6

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Protein particle displaying MAP fusion protein, sample taken 9 weeks after vaccination, stimulated with PPBDA antigen
20200729_cJD immune Run-3 555_01_04.RCC


title: G_pBL_3


title: participant_24B

tag: niaaaascore


title: 24RA,W6

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Recombinant MAP fusion protein, sample taken 9 weeks after vaccination, stimulated with Recombinant antigen antigen
20200729_cJD immune Run-3 555_01_08.RCC

value: Recombinant antigen

value: Recombinant MAP fusion protein


title: participant_22B

tag: niaaabscore


title: participant_21N

tag: niaaacscore


title: participant_21L

value: LC

value: locus coeruleus

tag: adseverityscore


title: participant_21DEN

value: DG

value: dentate gyrus


title: participant_21CA1

value: female


title: G_pBL_1

value: Gaster

value: SB/Sb

value: adult polygyne worker cross-fostered into a polygyne colony upon pupation


title: 24A,W6

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Recombinant MAP fusion protein, sample taken 9 weeks after vaccination, stimulated with PPBDA antigen
20200729_cJD immune Run-3 555_01_07.RCC

tag: nanostring plexset set in rcc files

value: Week 9

value: PPBDA

value: Leukocytes


title: participant_21J2

value: EC

value: entorhinal cortex


title: participant_20N

value: CBM

value: cerebellar cortex


title: participant_21K

value: SN

value: substantia nigra


title: G_pBB_8

source_name: Gaster of a polygyne SB/SB worker cross-fostered into a polygyne colony as a pupae

value: SB/SB


title: 23RA,W6

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Recombinant MAP fusion protein, sample taken 9 weeks after vaccination, stimulated with Recombinant antigen antigen
20200729_cJD immune Run-3 555_01_05.RCC

tag: antigen

value: Recombinant antigen

value: Recombinant MAP fusion protein


title: 24N,W6

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Recombinant MAP fusion protein, sample taken 9 weeks after vaccination, stimulated with PBS antigen
20200729_cJD immune Run-3 555_01_06.RCC

value: PBS

tag: vaccine


title: G_pBB_6

tag: treatment


title: participant_20K

value: female


title: participant_20CA1_redoBatch9fail


title: participant_19K


title: participant_20F

value: CG

value: cingulate gyrus


title: G_pBB_3

value: Gaster

tag: individual id

value: adult polygyne worker cross-fostered into a polygyne colony upon pupation


title: G_pBB_5


title: participant_19L

value: LC

value: locus coeruleus


title: G_pBB_7


title: participant_19N


title: participant_19J2

value: EC


title: participant_20J2

value: entorhinal cortex


title: G_pBB_1


title: G_mpBB_17

source_name: Gaster of a monogyne SB/SB worker cross-fostered into a polygyne colony as a pupae

value: adult monogyne worker cross-fostered into a polygyne colony upon pupation


title: 22A,W6

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Recombinant MAP fusion protein, sample taken 9 weeks after vaccination, stimulated with PPBDA antigen
20200729_cJD immune Run-3 555_01_01.RCC

tag: time

value: Week 9

value: PPBDA

value: Leukocytes


title: 22RA,W6

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Recombinant MAP fusion protein, sample taken 9 weeks after vaccination, stimulated with Recombinant antigen antigen
20200729_cJD immune Run-3 555_01_02.RCC

tag: cell type


title: 23A,W6

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Recombinant MAP fusion protein, sample taken 9 weeks after vaccination, stimulated with PPBDA antigen
20200729_cJD immune Run-3 555_01_04.RCC


title: 23N,W6

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Recombinant MAP fusion protein, sample taken 9 weeks after vaccination, stimulated with PBS antigen
20200729_cJD immune Run-3 555_01_03.RCC


title: participant_19F

tag: genotype


title: G_mpBB_15

value: SB/SB


title: participant_19DEN

value: DG

value: dentate gyrus

tag: batch


title: 22N,W6

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Recombinant MAP fusion protein, sample taken 9 weeks after vaccination, stimulated with PBS antigen
20200729_cJD immune Run-3 555_01_12.RCC

value: PBS

value: Recombinant MAP fusion protein


title: G_mpBB_14


title: participant_18F

value: CG

tag: Sex

value: female


title: participant_18B

value: MFG

value: middle frontal gyrus

tag: age


title: participant_19B

tag: education


title: G_mpBB_13

value: Gaster


title: participant_17K

value: SN

value: substantia nigra

tag: flanitot


title: participant_17CA1x

tag: niaaaascore


title: participant_19CA1

tag: niaaabscore


title: participant_18J2

value: EC

value: entorhinal cortex

tag: niaaacscore


title: 21A,W6

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Recombinant MAP fusion protein, sample taken 9 weeks after vaccination, stimulated with PPBDA antigen
20200729_cJD immune Run-3 555_01_10.RCC

value: Week 9


title: 21N,W6

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Recombinant MAP fusion protein, sample taken 9 weeks after vaccination, stimulated with PBS antigen
20200729_cJD immune Run-3 555_01_09.RCC


title: G_mpBB_10

value: adult monogyne worker cross-fostered into a polygyne colony upon pupation


title: G_mBB_8

source_name: Gaster of monogyne SB/SB worker cross-fostered into a monogyne colony as a pupae

value: adult monogyne worker cross-fostered into a monogyne colony upon pupation


title: participant_17N

description: Illumina EPIC 850k methylation data from FFPE brain tissue

value: CBM

value: cerebellar cortex

tag: adseverityscore


title: 21RA,W6

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Recombinant MAP fusion protein, sample taken 9 weeks after vaccination, stimulated with Recombinant antigen antigen
20200729_cJD immune Run-3 555_01_11.RCC

tag: nanostring plexset set in rcc files

value: Recombinant antigen

value: Leukocytes


title: 20RA,W6

tag: antigen

value: Recombinant MAP fusion protein


title: participant_17B


title: G_mpBB_11

value: SB/SB


title: participant_16N

value: female


title: 20N,W6

value: PBS

tag: vaccine


title: participant_16L

value: LC

value: locus coeruleus


title: 19RA,W6


title: G_mBB_6

value: Gaster

tag: treatment


title: participant_17L


title: participant_16K

value: SN

value: substantia nigra


title: participant_17F

value: CG

value: cingulate gyrus


title: participant_16F


title: participant_16DEN

value: DG

value: dentate gyrus


title: participant_16J2

value: EC

value: entorhinal cortex


title: G_mBB_5

tag: individual id

value: adult monogyne worker cross-fostered into a monogyne colony upon pupation


title: participant_16CA1


title: participant_15K_reexBatch9fail


title: G_mBB_1


title: participant_15L


title: 19N,W6

tag: time

value: Week 9

value: Leukocytes


title: 19A,W6

value: PPBDA

value: Recombinant MAP fusion protein

tag: cell type


title: participant_16B

value: MFG

value: middle frontal gyrus

value: female

tag: genotype


title: participant_14TER

tag: batch


title: G_mBB_7

value: Gaster

value: SB/SB


title: 20A,W6


title: G_mBB_3


title: participant_14SN

value: SN

value: substantia nigra

tag: Sex


title: 17RA,W6

value: Recombinant antigen


title: 18N,W6

value: PBS


title: B_pBL_7_merge

source_name: Brain of a polygyne SB/Sb worker cross-fostered into a polygyne colony as a pupae

value: Brain

value: SB/Sb

value: adult polygyne worker cross-fostered into a polygyne colony upon pupation


title: participant_15F

value: CG

value: cingulate gyrus

tag: age


title: B_pBL_6_merge


title: B_pBL_5


title: participant_14MFG

tag: education


title: participant_14LOC

value: LC

value: locus coeruleus

tag: flanitot


title: participant_14DEN

value: DG

value: dentate gyrus

tag: niaaaascore


title: 17A,W6

value: Week 9

value: PPBDA

value: Recombinant MAP fusion protein

value: Leukocytes


title: B_pBL_4


title: participant_15N

value: CBM

value: cerebellar cortex

value: female

tag: niaaabscore


title: 18RA,W6

value: Recombinant antigen


title: 18A,W6


title: participant_14CG

tag: niaaacscore


title: B_pBL_3

value: Brain


title: participant_14CBL

tag: adseverityscore


title: participant_14CA1


title: B_pBL_2

value: SB/Sb


title: participant_13N


title: participant_13K

value: SN

value: substantia nigra


title: participant_13L


title: B_pBL_1

value: adult polygyne worker cross-fostered into a polygyne colony upon pupation


title: B_pBB_7_merge

source_name: Brain of a polygyne SB/SB worker cross-fostered into a polygyne colony as a pupae

value: SB/SB


title: participant_13DEN


title: participant_13J2

value: EC

value: entorhinal cortex


title: participant_13CA1_new


title: 16A,W6

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Silirum®, sample taken 9 weeks after vaccination, stimulated with PPBDA antigen
20200729_cJD immune Run-3 555_01_07.RCC

tag: nanostring plexset set in rcc files

value: Silirum®


title: 16RA,W6

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Silirum®, sample taken 9 weeks after vaccination, stimulated with Recombinant antigen antigen
20200729_cJD immune Run-3 555_01_08.RCC

value: Week 9

tag: antigen


title: 16N,W6

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Silirum®, sample taken 9 weeks after vaccination, stimulated with PBS antigen
20200729_cJD immune Run-3 555_01_06.RCC

value: PBS

tag: vaccine


title: 15RA,W6

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Silirum®, sample taken 9 weeks after vaccination, stimulated with Recombinant antigen antigen
20200729_cJD immune Run-3 555_01_05.RCC


title: participant_13B

value: MFG

value: middle frontal gyrus


title: B_pBB_6_merge

tag: treatment


title: participant_12N

value: CBM

value: male


title: participant_12L

value: LC

value: locus coeruleus


title: participant_12K


title: 15A,W6

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Silirum®, sample taken 9 weeks after vaccination, stimulated with PPBDA antigen
20200729_cJD immune Run-3 555_01_04.RCC

value: PPBDA

value: Leukocytes


title: B_pBB_4

value: Brain

tag: individual id


title: B_pBB_5_merge


title: 15N,W6

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Silirum®, sample taken 9 weeks after vaccination, stimulated with PBS antigen
20200729_cJD immune Run-3 555_01_03.RCC

tag: time


title: participant_12J2


title: B_pBB_3

tag: cell type


title: 14RA,W6

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Silirum®, sample taken 9 weeks after vaccination, stimulated with Recombinant antigen antigen
20200729_cJD immune Run-3 555_01_02.RCC

value: Recombinant antigen


title: participant_12DEN

value: DG

value: dentate gyrus

tag: genotype


title: participant_12F

value: CG

value: cingulate gyrus

tag: batch


title: 17N,W6

value: Recombinant MAP fusion protein


title: participant_13F

tag: Sex

value: female


title: 14A,W6

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Silirum®, sample taken 9 weeks after vaccination, stimulated with PPBDA antigen
20200729_cJD immune Run-3 555_01_01.RCC

value: Week 9

value: Silirum®


title: participant_12B

value: MFG

value: middle frontal gyrus

tag: age


title: participant_11N

value: CBM

value: cerebellar cortex

tag: education


title: B_pBB_1

value: SB/SB

value: adult polygyne worker cross-fostered into a polygyne colony upon pupation


title: participant_11L

value: LC

value: locus coeruleus

tag: flanitot


title: B_mpBB_16

source_name: Brain of a monogyne SB/SB worker cross-fostered into a polygyne colony as a pupae

value: Brain

value: adult monogyne worker cross-fostered into a polygyne colony upon pupation


title: 14N,W6

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Silirum®, sample taken 9 weeks after vaccination, stimulated with PBS antigen
20200729_cJD immune Run-3 555_01_12.RCC

value: PBS

value: Leukocytes


title: participant_11K

value: SN

value: substantia nigra

tag: niaaaascore


title: participant_11J2

value: EC

value: entorhinal cortex

value: female

tag: niaaabscore


title: B_mpBB_15


title: participant_11F

value: CG

value: cingulate gyrus

tag: niaaacscore


title: participant_11DEN_redoBatch9fail

value: DG

value: dentate gyrus

tag: adseverityscore


title: participant_11CA1


title: participant_11B

value: MFG

value: middle frontal gyrus


title: 13N,W6

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Silirum®, sample taken 9 weeks after vaccination, stimulated with PBS antigen
20200729_cJD immune Run-3 555_01_09.RCC

tag: nanostring plexset set in rcc files

value: Week 9

value: Silirum®


title: B_mpBB_14_merge

value: Brain

value: SB/SB


title: 13A,W6

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Silirum®, sample taken 9 weeks after vaccination, stimulated with PPBDA antigen
20200729_cJD immune Run-3 555_01_10.RCC

tag: antigen

value: PPBDA


title: B_mpBB_13_merge

value: adult monogyne worker cross-fostered into a polygyne colony upon pupation


title: 12RA,W6

value: Recombinant antigen

tag: vaccine

value: Leukocytes


title: participant_12CA1

value: male


title: participant_10L

value: LC

value: locus coeruleus


title: participant_10N

value: CBM

value: cerebellar cortex


title: participant_10J2

value: EC

value: entorhinal cortex


title: B_mpBB_12

tag: treatment


title: B_pBB_2

tag: individual id

value: adult polygyne worker cross-fostered into a polygyne colony upon pupation


title: participant_10F

value: CG

value: cingulate gyrus


title: 12A,W6

tag: time

value: Week 9

value: Silirum®


title: participant_10DEN

value: DG

value: dentate gyrus


title: B_mpBB_11_merge

tag: cell type

value: Brain

value: SB/SB

value: adult monogyne worker cross-fostered into a polygyne colony upon pupation


title: participant_10B

value: MFG

value: middle frontal gyrus

value: male

tag: genotype


title: 13RA,W6

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Silirum®, sample taken 9 weeks after vaccination, stimulated with Recombinant antigen antigen
20200729_cJD immune Run-3 555_01_11.RCC

value: Recombinant antigen

value: Leukocytes


title: 12N,W6

value: PBS


title: participant_9N

value: CBM

value: cerebellar cortex

tag: batch

value: female


title: participant_9L

value: LC

value: locus coeruleus

tag: Sex


title: 11RA,W6

value: Week 9

value: Silirum®


title: B_mpBB_10


title: B_mBB_7

source_name: Brain of a monogyne SB/SB worker cross-fostered into a monogyne colony as a pupae

value: adult monogyne worker cross-fostered into a monogyne colony upon pupation


title: participant_9K

value: SN

value: substantia nigra

tag: age


title: participant_9J2

value: EC

value: entorhinal cortex

tag: education


title: 11N,W6


title: 11A,W6

value: PPBDA


title: B_mBB_6_merge

value: Brain

value: SB/SB


title: B_mBB_5_merge


title: participant_9F

value: CG

value: cingulate gyrus

tag: flanitot


title: 10RA,W6

value: Recombinant antigen

value: Leukocytes


title: P7C3, ApoeKO MifKO, 24 weeks HFD, mouse 159

city: Munich

first: Jürgen

last: Bernhagen

address: Feodor-Lynen-Straße 17

department: Division of Vascular Biology

institute: Institute for Stroke and Dementia Research (ISD), LMU University Hospital, Ludwig-Maximilians-University (LMU) Munich

data_processing:
Trimming: Cutadapt v1.18, Trim Galore v0.6.4_dev, trim_galore -j 2 --paired -q 20 --nextera --stringency 1
Quality-control: FastQC v0.11.5
Alignment: STAR v2.5.2b
Assembly: GRCm39
Supplementary files format and content: couts.txt: tab-separated value gene expression matrix of raw counts
Supplementary files format and content: vst.txt: tab-separated value gene expression matrix of variance stabilised expression values
Supplementary files format and content: colData.txt: tab-separated metadata for each sample

organism: Mus musculus

source_name: braciocephalic artery tissue section

extract_protocol:
5 μm OCT-embedded frozen sections from the BCA were gently thawed (room temperature, 5 min). Sections were immersed in 50 μL of freshly prepared RNA isolation buffer (20% proteinase K (Qiagen, Hilden, Germany) and 1:2400000 ERCC RNA spike-in mix in buffer PKD (Thermo Fisher Scientific) for approximately 30 seconds to permit lysis and homogenization of the whole BCA tissue. A 200-uL tip was used to scratch the BCA tissue lysate from the glass slide under a microscope. The BCA lysates from 3-4 BCA sections were pooled and collected in a 1.5 mL reaction tube and frozen at -80°C. The RNA in the BCA lysates was purified and washed with oligo dT25 magnetic beads (Thermo Fisher Scientific), followed by removing the beads via incubating the samples at 80°C and placing the samples on a magnet.
For library construction, 1 ng RNA was taken from each sample for reverse transcription and cDNA amplification following a Smart-seq2 protocol, followed by library construction as described before (34, 35). Briefly, samples were first thawed and then incubated for 3 min at 72°C and immediately placed on ice followed by the steps of reverse transcription (RT) and pre-amplification. The cDNA was then cleaned using AMPure bead (Beckman-Coulter) clean-up at a 0.7:1 beads:PCR product ratio. Libraries were assessed using Bio-analyzer (Agilent, catalog no. 2100), and the High Sensitivity DNA analysis kit, and also fluorometrically using Qubit’s DNA HS assay kits and a Qubit 4.0 Fluorometer (Invitrogen, Life Technologies) to measure the cDNA concentrations. After normalization to 160 pg/uL, 1.25 μL of cDNA samples were used for library construction using in-house Tn5 transposase. Libraries were barcoded and pooled, then cleaned up with three rounds of of AMPure bead (Beckman-Coulter) at a 0.8:1 ratio beads:library. Libraries were sequenced 2 x 100 reads bp paired-end on a DNB-seq platform to an average depth of 3 × 106 reads per sample. Sequencing was performed by BGI Tech Solutions (Hongkong) Co., Limited (Hongkong, China).

treatment_protocol: Female animals received a regular chow diet (SNIFF Spezialdiäten GmbH, Soest, Germany) until 6 weeks of age and then were subjected to a high-cholesterol (‘Western type’) diet (HFD) containing 0.2% cholesterol and 21.2% total fat (TD88137, SNIFF Spezialdiäten GmbH, Soest, Germany) for an additional 24, or 42 weeks.

tag: tissue

value: braciocephalic artery tissue section

value: mixed

value: Apoe-/-Mif-/-

value: 24W HFD


title: P7C4, ApoeKO MifKO, 24 weeks HFD, mouse 181


title: participant_9DEN

value: DG

value: dentate gyrus

value: female

tag: niaaaascore

tag: niaaabscore


title: P7C2, ApoeKO MifKO, 24 weeks HFD, mouse 151


title: P7C1, ApoeKO MifKO, 24 weeks HFD, mouse 137


title: participant_9CA1_redoBatch9fail

tag: niaaacscore

tag: adseverityscore


title: 10A,W6

tag: nanostring plexset set in rcc files

value: Week 9

tag: antigen

value: Silirum®


title: P7B12, ApoeKO, 24 weeks HFD, mouse 337

value: Apoe-/-

tag: treatment


title: B_mBB_4

tag: individual id

value: adult monogyne worker cross-fostered into a monogyne colony upon pupation


title: participant_9B

value: MFG

value: middle frontal gyrus


title: B_mBB_3

value: Brain

value: SB/SB


title: 10N,W6

tag: time

value: PBS

tag: vaccine


title: B_mBB_2

tag: cell type

tag: genotype


title: participant_8N

value: CBM

value: cerebellar cortex

tag: batch

tag: Sex


title: B_mBB_1


title: P7B11, ApoeKO, 24 weeks HFD, mouse 331

value: braciocephalic artery tissue section

value: mixed


title: 9A,W6

value: PPBDA

value: Leukocytes


title: 9RA,W6

value: Recombinant antigen


title: P7B10, ApoeKO, 24 weeks HFD, mouse 307

value: 24W HFD


title: fetal pancreas 20PCW_section 2

city: London

first: Oladapo

middle: Edward

last: Olaniru

address: Hodgkin building, Guy's campus

department: Department of Diabetes

country: United Kingdom

institute: King's College London

description: Spatial gene expression of cells from 20PCW pancreas, section 2.

data_processing:
Spaceranger software (version 3.1.0, 10x Genomics) was used to align and obtain raw counts from each of the spots on the Visium spatial transcriptomics slides against the GRCh38 human genome reference data
Raw gene expression matrix, together with spatial location of spots and tissue H&E images, were used to create a Seurat object with a Load10X_spatial function, and normalisation was carried out by SCTransform
Genome_build: hg38
Supplementary_files_format_and_content: cell-type annotation files: csv files containing cell-type predictions of spatial transcriptomics data inferred from scRNA-seq
Supplementary_files_format_and_content: Spaceranger outputs - raw feature barcode matrix in mtx format, feature list and spot barcodes in tab delimited format, tissue H&E images in jpeg format, spot position to image pixel coordinates

source_name: human fetal pancreas

extract_protocol:
Spatial transcriptomics was carried out using the 10x Genomics Visium platform. 10μm tissue sections from OCT-embedded fresh frozen human pancreases at 12, 15, 18 and 20 PCW were mounted onto Visium Spatial slides and the sections were permeabilised for 30min to release mRNAs, which bind to the spatially barcoded-oligos present in the underlying spots and reverse transcribed, according to the manufacturer’s protocol.
Libraries were prepared from cDNAs according to the 10x Visium protocol and cDNAs were sequenced on the Illumina NextSeq 2000 platform

value: human fetal pancreas

tag: developmental stage

value: 20 PCW


title: 9N,W6

value: Week 9

value: Silirum®


title: participant_8L

value: LC

value: locus coeruleus

value: female

tag: age

tag: education

tag: flanitot


title: P7B9, ApoeKO, 24 weeks HFD, mouse 303

tag: tissue

value: Apoe-/-


title: fetal pancreas 20PCW_section 1

description: Spatial gene expression of cells from 20PCW pancreas, section 1.


title: 8RA,W6

description:
Leukocytes from heparinized blood samples, from animal vaccinated with PBS, sample taken 9 weeks after vaccination, stimulated with Recombinant antigen antigen
20200729_cJD immune Run-3 555_01_08.RCC

value: PBS


title: participant_8K

description: Illumina EPIC 850k methylation data from FFPE brain tissue

value: SN

value: substantia nigra

tag: niaaaascore

tag: niaaabscore

tag: niaaacscore


title: participant_8J2

value: EC

value: entorhinal cortex

tag: adseverityscore


title: 8A,W6

description:
Leukocytes from heparinized blood samples, from animal vaccinated with PBS, sample taken 9 weeks after vaccination, stimulated with PPBDA antigen
20200729_cJD immune Run-3 555_01_07.RCC

tag: nanostring plexset set in rcc files

tag: antigen

value: PPBDA


title: P7B8, ApoeKO MifKO, 42 weeks HFD, mouse 91

value: braciocephalic artery tissue section

value: mixed

value: Apoe-/-Mif-/-

tag: treatment

value: 42W HFD


title: P7B7, ApoeKO MifKO, 42 weeks HFD, mouse 80


title: participant_8F

value: CG

value: cingulate gyrus


title: P7B6, ApoeKO MifKO, 42 weeks HFD, mouse 81


title: participant_8DEN_redo_failed

value: DG

value: dentate gyrus


title: 8N,W6

description:
Leukocytes from heparinized blood samples, from animal vaccinated with PBS, sample taken 9 weeks after vaccination, stimulated with PBS antigen
20200729_cJD immune Run-3 555_01_06.RCC

tag: time

value: Week 9

tag: vaccine

value: Leukocytes


title: fetal pancreas 15PCW_section 1

description: Spatial gene expression of cells from 15PCW pancreas, section 1.

value: human fetal pancreas

value: 15 PCW


title: P7B5, ApoeKO MifKO, 42 weeks HFD, mouse 78

tag: cell type

tag: genotype


title: fetal pancreas 18PCW_section 2

description: Spatial gene expression of cells from 18PCW pancreas, section 2.

value: 18 PCW


title: participant_8CA1_redoBatch9fail

tag: batch

tag: Sex

value: female


title: 7RA,W6

description:
Leukocytes from heparinized blood samples, from animal vaccinated with PBS, sample taken 9 weeks after vaccination, stimulated with Recombinant antigen antigen
20200729_cJD immune Run-3 555_01_05.RCC

value: Recombinant antigen

value: PBS


title: fetal pancreas 15PCW_section 2

description: Spatial gene expression of cells from 15PCW pancreas, section 2.

tag: developmental stage


title: P7B3, ApoeKO, 42 weeks HFD, mouse 214

value: Apoe-/-


title: P7B4, ApoeKO, 42 weeks HFD, mouse 220

value: braciocephalic artery tissue section


title: fetal pancreas 12PCW_section 2

description: Spatial gene expression of cells from 12PCW pancreas, section 2.

value: 12 PCW


title: participant_8B

value: MFG

value: middle frontal gyrus

tag: age

tag: education


title: fetal pancreas 12PCW_section 1

description: Spatial gene expression of cells from 12PCW pancreas, section 1.

tag: tissue


title: P7B2, ApoeKO, 42 weeks HFD, mouse 213

value: mixed

value: 42W HFD


title: participant_7N

value: CBM

value: cerebellar cortex

tag: flanitot

tag: niaaaascore


title: 6RA,W6

description:
Leukocytes from heparinized blood samples, from animal vaccinated with PBS, sample taken 9 weeks after vaccination, stimulated with Recombinant antigen antigen
20200729_cJD immune Run-3 555_01_02.RCC

value: Week 9


title: 7A,W6

description:
Leukocytes from heparinized blood samples, from animal vaccinated with PBS, sample taken 9 weeks after vaccination, stimulated with PPBDA antigen
20200729_cJD immune Run-3 555_01_04.RCC

value: PPBDA

value: Leukocytes


title: 7N,W6

description:
Leukocytes from heparinized blood samples, from animal vaccinated with PBS, sample taken 9 weeks after vaccination, stimulated with PBS antigen
20200729_cJD immune Run-3 555_01_03.RCC


title: fetal pancreas pool_3_131419_PCW_HTO library

description: Totalseq B HTO library of of single cells from 3 fetal pancreases at 13, 14 and 19 PCW

data_processing:
Generation of FASTQ files and alignment of raw sequencing reads were carried out using CellRanger (version 6.0.0, 10x Genomics).
Raw sequence data from HTO libraries were processed using CITE-Seq-Count, version 1.4.5
Genome_build: hg38
Supplementary_files_format_and_content: csv files contain de-hashing result of the pooled samples into their indvidual gestation age
Supplementary_files_format_and_content: final_matrix.csv.gz is a five-column filtered gene-count-matrix file from Cellranger output contatining 10x Genomics cellular barcode, feature ID, feature name, feature type and UMI count

extract_protocol:
Human fetal pancreases were dissociated into single cells by collagenase and trypsin/EDTA treatment. Each batch contains 3 samples from different gestational stages which were stained with oligonucleotide-conjugated antibodies from BioLegend and pooled
Single cell mRNA and antibody (HTO) libraries were prepared according to the manufacturer’s protocol and paired-end sequencing was carried out on an Illumina NextSeq 2000, except for batch 15, 18 and 20 PCW batch which was sequenced on a HiSeq 2500.

value: pancreas


title: participant_7K

value: SN

value: substantia nigra

tag: niaaabscore

tag: niaaacscore


title: fetal pancreas 18PCW_section 1

description: Spatial gene expression of cells from 18PCW pancreas, section 1.

value: human fetal pancreas

value: 18 PCW


title: participant_7J2

value: EC

value: entorhinal cortex

value: female

tag: adseverityscore


title: P7B1, ApoeKO, 42 weeks HFD, mouse 204

value: braciocephalic artery tissue section

value: Apoe-/-


title: fetal pancreas pool_2_121419_PCW_HTO library

description: Totalseq B HTO library of of single cells from 3 fetal pancreases at  12, 14 and 19 PCW


title: Quadriceps_Myriocin_6

city: Lausanne

first: Maroun

last: Bou Sleiman

state: Vaud

address: Rue Cantonale

department: IBI

country: Switzerland

institute: EPFL

data_processing:
RNA quality was assessed using Agilent 2100 BioAnalyzer (Agilent, Santa Clara, CA). Samples with RIN ≥ 8, 28S/18S ≥ 1.0, and c ≥ 20 ng/μL were included in analyses. Using these criteria, 9 (4 DMSO and 5 myriocin) samples passed and 2 samples failed to pass quality control criteria.
Sequencing libraries were prepared by BGI genomics using the DNBseqTM technology. Paired-end sequencing with 100 cycles was performed using the BGISEQ-500 instrument. After removal of adaptor sequences and low quality reads, we obtain at least 56 million reads per sample. SOAPnuke was used to obtain clean reads (parameters -l 15, -q 0.2, -n 0.05). Reads were mapped using STAR aligner version 2.5.2b using the mouse GRCm38 genome assembly and the release 91 GTF annotation from Ensembl. Htseq-count version 0.6.0 was used to count the number of reads mapping to genes (mode= union, type=exon, idattr=gene_id).
Assembly: GRCm38
Supplementary files format and content: counts

source_name: Skeletal muscle

extract_protocol:
RNA was isolated using Direct-zol RNA kit (Zymo, Irvine, CA).
Sequencing libraries were prepared by BGI genomics using the DNBseqTM technology.

value: Skeletal muscle

tag: muscle type

value: Quadriceps

value: Myriocin


title: fetal pancreas pool_1_121313_PCW_HTO library

description: Totalseq B HTO library of of single cells from 3 fetal pancreases at 12, 13 and 13 PCW


title: 6N,W6

description:
Leukocytes from heparinized blood samples, from animal vaccinated with PBS, sample taken 9 weeks after vaccination, stimulated with PBS antigen
20200729_cJD immune Run-3 555_01_12.RCC

tag: nanostring plexset set in rcc files

tag: antigen

value: PBS


title: participant_7DEN

description: Illumina EPIC 850k methylation data from FFPE brain tissue

value: DG

value: dentate gyrus


title: participant_7F

value: CG

value: cingulate gyrus


title: 5A,W6

description:
Leukocytes from heparinized blood samples, from animal vaccinated with PBS, sample taken 9 weeks after vaccination, stimulated with PPBDA antigen
20200729_cJD immune Run-3 555_01_10.RCC

tag: time

value: Week 9

value: PPBDA

tag: vaccine

value: Leukocytes


title: 5RA,W6

description:
Leukocytes from heparinized blood samples, from animal vaccinated with PBS, sample taken 9 weeks after vaccination, stimulated with Recombinant antigen antigen
20200729_cJD immune Run-3 555_01_11.RCC

value: Recombinant antigen

tag: cell type


title: fetal pancreas pool_3_131419_PCW_Gene expression

description: Gene expression of single cells from 3 fetal pancreases at 13, 14 and 19 PCW. Cells were tagged with oligonucleotide-conjugated antibodies, pooled, sequenced in a single 10x reaction and demultiplexed afterwards.

value: pancreas


title: Quadriceps_Myriocin_4

tag: genotype

tag: treatment


title: fetal pancreas pool_2_121419_PCW_Gene expression

description: Gene expression of single cells from 3 fetal pancreases at 12, 14 and 19 PCW. Cells were tagged with oligonucleotide-conjugated antibodies, pooled, sequenced in a single 10x reaction and demultiplexed afterwards.

data_processing:
Generation of FASTQ files and alignment of raw sequencing reads were carried out using CellRanger (version 6.0.0, 10x Genomics).
Raw sequence data from HTO libraries were processed using CITE-Seq-Count, version 1.4.5
Genome_build: hg38
Supplementary_files_format_and_content: csv files contain de-hashing result of the pooled samples into their individual gestation age
Supplementary_files_format_and_content: final_matrix.csv.gz is a five-column filtered gene-count-matrix file from Cellranger output containing 10x Genomics cellular barcode, feature ID, feature name, feature type and UMI count

tag: developmental stage


title: 5N,W6

description:
Leukocytes from heparinized blood samples, from animal vaccinated with PBS, sample taken 9 weeks after vaccination, stimulated with PBS antigen
20200729_cJD immune Run-3 555_01_09.RCC


title: participant_7CA1

tag: batch

tag: Sex

tag: age


title: Quadriceps_Myriocin_3

tag: tissue


title: participant_6L

value: LC

value: locus coeruleus

tag: education

tag: flanitot

tag: niaaaascore


title: fetal pancreas pool_1_121313_PCW_Gene expression

description: Gene expression of single cells from 3 fetal pancreases at 12, 13 and 13 PCW. Cells were tagged with oligonucleotide-conjugated antibodies, pooled, sequenced in a single 10x reaction and demultiplexed afterwards.


title: Quadriceps_Myriocin_2


title: 6A,W6

description:
Leukocytes from heparinized blood samples, from animal vaccinated with PBS, sample taken 9 weeks after vaccination, stimulated with PPBDA antigen
20200729_cJD immune Run-3 555_01_01.RCC


title: 4RA,W6

description:
Leukocytes from heparinized blood samples, from animal vaccinated with PBS, sample taken 9 weeks after vaccination, stimulated with Recombinant antigen antigen
20200729_cJD immune Run-3 555_01_08.RCC


title: participant_6B_redoBatch9fail

value: MFG

value: middle frontal gyrus

value: female

tag: niaaabscore

tag: niaaacscore

tag: adseverityscore


title: 4A,W6

description:
Leukocytes from heparinized blood samples, from animal vaccinated with PBS, sample taken 9 weeks after vaccination, stimulated with PPBDA antigen
20200729_cJD immune Run-3 555_01_07.RCC

tag: nanostring plexset set in rcc files

tag: antigen


title: Quadriceps_Myriocin_1

value: Skeletal muscle

tag: muscle type

value: Quadriceps


title: Quadriceps_DMSO_5

value: DMSO


title: Quadriceps_DMSO_4


title: participant_5K

value: SN

value: substantia nigra

value: male


title: participant_5L


title: 4N,W6

description:
Leukocytes from heparinized blood samples, from animal vaccinated with PBS, sample taken 9 weeks after vaccination, stimulated with PBS antigen
20200729_cJD immune Run-3 555_01_06.RCC

tag: time

value: PBS

tag: vaccine

tag: cell type


title: 3RA,W6

description:
Leukocytes from heparinized blood samples, from animal vaccinated with PBS, sample taken 9 weeks after vaccination, stimulated with Recombinant antigen antigen
20200729_cJD immune Run-3 555_01_05.RCC

value: Week 9


title: Quadriceps_Myriocin_5

tag: genotype

tag: treatment

value: Myriocin


title: Quadriceps_DMSO_3


title: participant_5B_redoBatch9fail

tag: batch

tag: Sex


title: participant_5CBLx

value: CBM

value: cerebellar cortex

tag: age


title: 3A,W6

description:
Leukocytes from heparinized blood samples, from animal vaccinated with PBS, sample taken 9 weeks after vaccination, stimulated with PPBDA antigen
20200729_cJD immune Run-3 555_01_04.RCC

value: PPBDA

value: Leukocytes


title: 3N,W6

description:
Leukocytes from heparinized blood samples, from animal vaccinated with PBS, sample taken 9 weeks after vaccination, stimulated with PBS antigen
20200729_cJD immune Run-3 555_01_03.RCC


title: Quadriceps_DMSO_1

tag: tissue


title: participant_4N

tag: education

tag: flanitot


title: 2RA,W6

description:
Leukocytes from heparinized blood samples, from animal vaccinated with PBS, sample taken 9 weeks after vaccination, stimulated with Recombinant antigen antigen
20200729_cJD immune Run-3 555_01_02.RCC

value: Recombinant antigen


title: Quadriceps_DMSO_2


title: participant_4L

value: LC

value: locus coeruleus

tag: niaaaascore

tag: niaaabscore


title: 2N,W6


title: shREN_4bulkRNAseq

city: Chengdu, Cihna

first: Xaingyu

last: Pan

state: Sichuan

address: No.17 Renming road section3

department: State Key Laboratory of Biotherapy, West China Hospital, Sihcuan University.

institute: Sichuan University

data_processing:
Illumina sequencing workflow
Sequenced reads were mapped to GRCm38 whole genome using STAR v2.6.0 .
Transcripts Per Kilobase Million of library size (TPM) were calculated .
Genome_build: GRCm38
Supplementary_files_format_and_content: xlsx  file includes TPM values for each Sample

source_name: pre B cells

extract_protocol: PreB cells from WT mice were harvested and transduced with shRNAs targeting either shAlox15b or shAlox12b, fluorescence activated cell sorting of transduced cells were conducted 48h post-infection and RNA was harvested using Trizol reagent.

tag: strain

value: pre B cells

value: shREN


title: shREN_3bulkRNAseq


title: 1RA,W6

tag: nanostring plexset set in rcc files


title: participant_5F

value: CG

value: cingulate gyrus

tag: niaaacscore

tag: adseverityscore


title: Pt2a Hi-C rep 2

city: San Francisco

first: Katherine

middle: S

last: Pollard

state: CA

address: 1650 Owens St

department: Institute of Data Science and Biotechnology

institute: Gladstone Institutes

data_processing:
Adapters were trimmed from raw FASTQ files using TrimGalore [v0.6.5] with options --illumina --paired.
The data were then processed from adapter-trimmed FASTQ files to Hi-C contacts as cooler files using Distiller [v0.3.3] (65). This processing includes read mapping with BWA-MEM (66), filtering (MAPQ >= 30), contact pair processing with pairtools (67) and normalization via matrix balancing (68). Samples were processed both per replicate, per individual and per species. For easier comparison of samples in some analyses, we mapped the data from each species to the reference genome of the other species (human to pantro6 and chimp to hg38).
Genome_build: hg38, panTro6
Supplementary_files_format_and_content: Cooler (Hi-C contact matrices)

organism: Pan troglodytes

growth_protocol: Two human (WTC11 and HS1) and two chimpanzee (C3649 and Pt2a) induced pluripotent cell lines (iPSCs) were cultured in Matrigel-coated plates with mTeSR media (WTC11 and C3649 were cultured in StemFlex) in an undifferentiated state. Cells were propagated at a 1:3 ratio by treatment with 200 U/mL collagenase IV (or PBS-EDTA) and mechanical dissection.   WTC11 and C3649 iPSCs were differentiated to neural progenitor cells (NPCs) as previously described (64). Briefly, 2-2.5×10⁵ cells per cm² were seeded on Matrigel-coated wells in StemFlex containing 2 μM Thiazovivin. The following day (Day 0), medium was replaced with E6 containing 500 nM LDN193189 (Selleckchem), 10 μM SB431542 (Selleckchem), and 5 μM XAV-939 (Selleckchem). Starting on Day 3, medium was replaced with E6 containing 500 nM LDN193189 and 10 μM SB431542 every 48 hrs. Starting on Day 12, medium was replaced with Neurobasal containing 2 mM GlutaMAX, 60 μg per ml L-Ascorbic acid 2-phosphate, N2, and B27 without Vitamin A every 48 hours. Around Day 16, cells were washed with PBS, dissociated with Accutase, pelleted and resuspended in Neurobasal containing 2 mM GlutaMAX, 60 μg per ml L-Ascorbic acid 2-phosphate, N2, and B27 without Vitamin A, 10 ng per ml fibroblast growth factor 2, and 10 ng per ml epidermal growth factor, and seeded on poly-L-ornithine-, fibronectin-, and laminin-coated wells. Cells were collected for HiC at passage 5-7.  To differentiate HS1 and Pt2a iPSCs into NPCs, cells were split with EDTA at 1:5 ratios in culture dishes coated with matrigel and culture in N2B27 medium (comprised of DMEM/F12 medium (Invitrogen) supplemented with 1% MEM-nonessential amino acids (Invitrogen), 1 mM L-glutamine, 1% penicillin-streptomycin, 50 ng/mL bFGF (FGF-2) (Millipore), 1x N2 supplement, and 1 x B27 supplement without Vitamin A (Invitrogen)) supplemented with 100 ng/ml mouse recombinant Noggin (R&D systems). Cells at passages 1-3 were split by collagenase into small clumps, and continuously cultured in N2B27 medium with Noggin. After passage 3, cells were plated at the density of 5×10⁵ cells/cm² after disassociation by TrypLE express (Invitrogen) into single-cell suspension, and cultured in N2B27 medium supplemented with 20 ng/mL bFGF and EGF. Cells were maintained and collected at passage 18-20. Our use of two differentiation protocols reflects rapid progress in stem cell research during the course of this study.

treatment_protocol: Hi-C was performed using the Arima Hi-C kit (Arima Genomics) according to the manufacturer’s instructions. 10 million cells were used. The sequencing library was prepared using Accel-NGS 2S Plus DNA Library Kit (Swift Biosciences) according to the manufacturer's protocol. Two independent biological replicates were prepared for each cell line. In total eight libraries were pooled and sequenced with paired-end 150-bp reads using two lanes of a NovaSeq6000 S2 (Illumina) at the Chan Zuckerberg Biohub.

tag: cell line

value: iPS-derived neural progenitor cells


title: participant_4J2

value: EC

value: entorhinal cortex

value: female


title: participant_4F


title: shREN_2bulkRNAseq


title: shREN_1bulkRNAseq


title: 1A,W6

tag: time

value: Week 9

tag: antigen

tag: vaccine

value: PBS


title: 1N,W6

tag: cell type


title: C3649 Hi-C rep 1

extract_protocol: The sequencing library was prepared using Accel-NGS 2S Plus DNA Library Kit (Swift Biosciences) according to the manufacturer's protocol. Two independent biological replicates were prepared for each cell line. In total eight libraries were pooled and sequenced with paired-end 150-bp reads using two lanes of a NovaSeq6000 S2 (Illumina) at the Chan Zuckerberg Biohub.


title: 2A,W6


title: shAlox15b.2865_2bulkRNAseq

tag: genotype


title: shAlox15b.2865_4bulkRNAseq


title: C3649 Hi-C rep 2


title: participant_4DEN_redoBatch9fail

value: DG

value: dentate gyrus

tag: batch

tag: Sex


title: participant_4CA1

tag: age


title: shAlox15b.2865_1bulkRNAseq


title: participant_4B

value: MFG

value: middle frontal gyrus

tag: education


title: 32N,W0

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Protein particle displaying MAP fusion protein, sample taken 0 weeks after vaccination, stimulated with PBS antigen
20200729_cJD immune Run-3 555_01_06.RCC

value: Week 0

value: Leukocytes


title: participant_3N

value: CBM

value: cerebellar cortex

value: male

tag: flanitot