title: Sham 2

city: Austin

first: Qi

last: Tan

address: 801 16th Ave NE

department: The Hormel Institute

institute: Univesity of Minnesota

data_processing:
Mayo Clinic’s MAPR-Seq# software was used to process the raw paired end reads from the RNA sequencing experiments
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Kalari et al. 2014
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with RPKM for every gene and every sample

source_name: lung

extract_protocol:
RNA quality was determined using the Fragment Analyzer from AATI (AATI, Ankeny, IA). RNA samples that have RQN values ≥6 were approved for library prep and sequencing. RNA libraries were prepared using 200 ng of good quality total RNA according to the manufacturer’s instructions for the TruSeq RNA Sample Prep Kit v2 (Illumina, San Diego, CA), employing poly-A mRNA enrichment using oligo dT magnetic beads. The final adapter-modified cDNA fragments were enriched by 12 cycles of PCR using Illumina TruSeq PCR primers. The concentration and size distribution of the completed libraries were determined using a Fragment Analyzer (AATI, Ankeny, IA) and Qubit fluorometry (Invitrogen, Carlsbad, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Col1a1-GFP mice

tag: treament

value: Sham


title: D30 Bleo 4

status: Public on Nov 13 2020

type: SRA

state: MN

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: strain

tag: age

value: 8 weeks

value: Bleomycin

tag: time point


title: D14 Bleo 3


title: D30 Bleo 2


title: D30 Bleo 5


title: D30 Bleo 1


title: Sham 1


title: D14 Bleo 1


title: D30 Bleo 3


title: DIV10B (BS-seq)

city: brookline

first: Harrison

middle: Wren

last: Gabel

state: Massachusetts

address: 220 longwood avenue

department: Neurbiology

institute: Harvard Medical School

description:
Mixed Male and Female cells
geo_bs_lowcov2.tsv

library_source: genomic

data_processing:
Data were adapter-trimmed, mapped to mm9, then deduplicated and called for methylation using BS-seeker2. Methylation levels across regions was assessed using bedtools map -o sum, summing the number of reads mapping to Cs (supporting mC), and the amount of coverage in the region, then dividing those two numbers(Quinlan and Hall, 2010). Hydroxymethylation was calculated as the percent methylation found in the BS-seq minus the percent methylation found in the matching oxBS-seq. Due to count noise, this occasionally resulted in apparent negative hydroxymethylation. During bisulfite sequencing not all DNA can be efficiently bisulfite converted. Though our methods should maximize the amount of converted unmethylated C, there is still a small percentage of unmethylated cytosines that are called as methylated due to non-conversion (0.2-0.3%). Due to this non-conversion, very lowly methylated regions (e.g. mCA at CpG islands) may not show the same percent reduction in mCA as highly methylated regions. Data were visualized using the UCSC genome browser (http://genome.ucsc.edu) (Kent et al., 2002).
Genome_build: mm9
Supplementary_files_format_and_content: mdt_table_GEO2.tsv: Tab-separated table (with header) of genes, and acetyl peaks, of mCA and mCG values of these regions in DNMT3A heterozygous KO and WT cortex.
geo_bs_lowcov2.tsv is a tab-separated table (with header) of the average genome-wide methylation values for each dinucleotide context (columns) for each sample (rows).

molecule: genomic DNA

source_name: Cultured cortical neurons from E14.5

growth_protocol: For cortical cultures, samples were chosen for whole genome bisulfite sequencing if mutant and WT samples expressed equal amounts of Dnmt3a mRNA as measured by qRT-PCR. For tissue samples, tissue was taken from mice maintained under standard housing conditions.

extract_protocol:
For tissue samples, tissue was dissected from littermate mice in ice-cold PBS, flash-frozen in liquid nitrogen, and stored at -80°C. DNA was isolated from tissue and cultured cells using the DNEasy Kit.
DNA was bisulfite converted and prepared for sequencing using the Tecan Ovation Ultralow Methyl-Seq Kit and the Epitect Bisulfite Kit was used for bisulfite conversion. We used alternate bisulfite conversion cycling conditions ([95°C, 5 min; 60°C, 20 min] x 4 cycles, 20°C hold) to ensure lowest possible bisulfite non-conversion rate.
Libraries were either sequenced at a depth of 0.01-0.03x genomic coverage using an Illumina MiSeq 2x150 through the Spike-In Cooperative at Washington University in St. Louis, or sequenced at 6.4-7.8x coverage per biological rep with a Illumina HiSeq3000 at the Genome Technology Access Center at Washington University in St. Louis

tag: genotype

value: wild type

tag: Sex

value: Pooled male and female

tag: cell type

value: Cultured cortical neurons from E14.5

value: DIV 10


title: DIV10A (BS-seq)


title: D14 Bleo 2


title: Gabel_pYL7_14C_S18 (BS-seq)


title: Con-3-722

status: Public on Nov 14 2020

city: ChengDu

first: Jinen

last: Song

address: Renmin road

country: China

institute: Sichuan university

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using kallisto (Bray et al., 2016)
Transcripts Per Million (TPM) were calculated using sleuth (Pimentel et al., 2017)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample ...

source_name: melanoma

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

tag: tissue

value: melanoma

tag: treatment

value: untreated

tag: cell line

tag: gender

value: female


title: Gabel_pYL7_14A_S17 (BS-seq)


title: Gabel_pYL5_NV_C_12_S20 (BS-seq)

value: No virus control


title: Gabel_pYL14_13_7B_S16 (BS-seq)


title: p9pYL14-27-9B_TGGTGAATCT_S20 (BS-seq)


title: Gabel_p7pYL9-14_3A_S42 (BS-seq)


title: Gabel_p7pYL11-41B_AGTGAGATCT_S21 (BS-seq)


title: Gabel_p7pYL8-16A_L001 (BS-seq)


title: Gabel_p9pYL11_48_8A_S43 (BS-seq)


title: Gabel_p7pYL11-41B_S57 (BS-seq)


title: Gabel_p5pYL9-14-3B (BS-seq)


title: Gabel_p5pYL9-14-3C_S55 (BS-seq)


title: Gabel_p7pYL10-23-2_S56 (BS-seq)


title: p7pYL10-23-2B_GCACTAATCT_S22 (BS-seq)


title: Gabel_p7pYL11-41A_S13 (BS-seq)


title: Gabel_p5pYL8-20B_S54 (BS-seq)


title: Gabel_p3pYL7-9-2B (BS-seq)


title: Gabel_p3pYL6-25-9BB (BS-seq)


title: Gabel_p3pYL7-9-2A_S12 (BS-seq)


title: Gabel_p3pYL8-16C_L001 (BS-seq)


title: Gabel_p1pYL5-7_2C_L001 (BS-seq)

value: WT


title: Gabel_p3pYL6-25_9A_S41 (BS-seq)


title: Gabel_p1-Cre-A (BS-seq)

value: DNMT3a knockout


title: Gabel_p15pYL15-20-9_S58 (BS-seq)


title: Gabel_p3pYL8-20B_L001 (BS-seq)


title: Gabel_p1-NV-A (BS-seq)


title: Gabel_p1pYL5-7-2A_S11 (BS-seq)


title: Gabel_p15pYL5-7-2A (BS-seq)


title: Gabel_p3pYL7-9-2C_S53 (BS-seq)


title: Gabel_p1pYL5-7-7B_S51 (BS-seq)


title: Gabel_p3pYL8-16A_L001 (BS-seq)


title: Gabel_p1pYL5-5_7B_S40 (BS-seq)


title: Gabel_p13pYL15-20-9A_S14 (BS-seq)


title: Gabel_p15-CreA_S15 (BS-seq)


title: Gabel_p13-NVd_S38 (BS-seq)


title: Gabel_p11-CreA_S39 (BS-seq)


title: Gabel_p13pYL14_37_9A_S44 (BS-seq)


title: p13pYL15-29-9B_AACCAGATCT_S19 (BS-seq)


title: Gabel_pYL9-14_5A_S02277_S6 (BS-seq)


title: Gabel_pYL6-2_4B_S02275_S4 (BS-seq)


title: Gabel_NV_A_12_S21 (BS-seq)


title: Gabel_NV_A_S14 (BS-seq)


title: Gabel_Cre_A_S19 (BS-seq)


title: Gabel_pYL5-5_7B_S02274_S3 (BS-seq)


title: Gabel_p15-NoVirusA_S16 (BS-seq)


title: Gabel_p3pYL6-25-9C_S52 (BS-seq)


title: Gabel_pYL5-5_7A_S02273_S2 (BS-seq)


title: Gabel_pYL5-5_7A_S15 (BS-seq)


title: Gabel_pYL10-32_2A_S18 (BS-seq)


title: Gabel_p5-pYL8-20C_S318 (BS-seq)


title: p3pYL8-16B_AAGCCTATCTCGT_S128 (BS-seq)


title: Gabel_p5pYL7-11_1C_S19 (BS-seq)


title: Gabel_p9pYL11-48_8B_S22 (BS-seq)


title: Gabel_p3pYL6-25_9C_S18 (BS-seq)


title: p1pYL5-7_2C_SIC_index_1578_TCGCGAGGGATCT_S131 (BS-seq)


title: p3-NV_SIC_index_1576_CTCAGGGCCATCT_S135 (BS-seq)


title: p1pYL5-7_2A_GTGCTTATCTCGT_S127 (BS-seq)


title: Gabel_p7pYL9-14_3B_S21 (BS-seq)


title: p1-NV_GCACTAATCTCGT_S125 (BS-seq)


title: Gabel_p1-Cre-B_S315 (BS-seq)


title: p1-Cre-A_ACCTCAATCTCGT_S126 (BS-seq)


title: Gabel_p17pYL8-20A_S20 (BS-seq)


title: p1-Cre-B_SIC_index_1577_TGCATGTAGATCT_S130 (BS-seq)


title: Gabel_p15-pYL15-29-9_S322 (BS-seq)


title: Gabel_NV-A_S02272_S1 (BS-seq)


title: Gabel_p13pYL14-37_9B_S25 (BS-seq)


title: Gabel_Nva_S16 (BS-seq)


title: Gabel_p13-pYL15-29-9A_S321 (BS-seq)


title: Gabel_pYL10-10_5C_S02278_S7 (BS-seq)


title: Gabel_CreA_S17 (BS-seq)


title: Gabel_p9pYL11-48_8C_S23 (BS-seq)


title: Gabel_Cre-A_S02279_S8 (BS-seq)


title: Gabel_p5-pYL8-16C_S317 (BS-seq)


title: p3pYL8-20A_SIC_index_1579_CTTCCCATGATCT_S132 (BS-seq)


title: Gabel_33_p7pYL9-14_3C_S127 (BS-seq)


title: Gabel_33_p3pYL6-25_9B_S125 (BS-seq)


title: Gabel_33_p9pYL10-32_2B_S128 (BS-seq)


title: Gabel_33_p17pYL8-20B_S131 (BS-seq)


title: Gabel21_pYL9-14_5C_GTGCTTATCT_S49_L001 (BS-seq)


title: Gabel_33_p5pYL7-11_1B_S126 (BS-seq)


title: Gabel_33_p1pYL5-5_7C_S124 (BS-seq)


title: Gabel_33_p11CreB_S130 (BS-seq)


title: Gabel21_pYL10-10_5A_AAGCCTATCT_S50_L001 (BS-seq)


title: Gabel21_pYL9-7_3C_ACCTCAATCT_S48_L001 (BS-seq)


title: Gabel21_pYL11-3_4A_AGTGAGATCT_S46_L001 (BS-seq)


title: Gabel_p15-pYL5-7-2C_S316 (BS-seq)


title: Gabel21_NV-C_AACCAGATCT_S44_L001 (BS-seq)


title: Gabel21_Cre-B_GTCGTAATCT_S51_L001 (BS-seq)


title: 701-1_cor (BS-seq)

source_name: Cortex

value: Male

value: Cortex


title: 622-2_cor (BS-seq)


title: 703-2_cor (BS-seq)

value: 4 weeks


title: 602-2_str (BS-seq)

source_name: Striatum

value: Striatum


title: 602-2_cor1 (BS-seq)


title: 602-2_cb (BS-seq)

source_name: Cerebellum

value: Cerebellum


title: 602-2_cor3 (BS-seq)

value: 8 weeks


title: 306-4_cor2 (BS-seq)

value: Female


title: 602-2_cor2 (BS-seq)

value: wild type


title: 047-1_cor2 (BS-seq)

value: Heterozygous KO


title: Gabel21_pYL5-5_7C_TGGTGAATCT_S45_L001 (BS-seq)

value: Pooled male and female

value: Cultured cortical neurons from E14.5


title: J029-3_cor (BS-seq)


title: 047-2_cor2 (BS-seq)


title: Gabel21_pYL6-4_8B_GCACTAATCT_S47_L001 (BS-seq)


title: 439F_cor (BS-seq)

value: 0 weeks


title: 602-2_hip (BS-seq)

source_name: Hippocampus

value: Hippocampus


title: 306-1_liv (BS-seq)

source_name: Liver

value: Liver


title: 602-2_liv (BS-seq)


title: 306-4_cor1 (BS-seq)


title: 306-1_cor3 (BS-seq)


title: 047-2_liv (BS-seq)


title: 439B_cor (BS-seq)


title: 046-2_liv (BS-seq)


title: 306-1_str (BS-seq)


title: 306-1_cor2 (BS-seq)


title: 695_cor (BS-seq)


title: 306-1_hip (BS-seq)


title: 047-1_liv (BS-seq)


title: 046-2_cor3 (BS-seq)


title: 046-1_cor3 (BS-seq)


title: 306-1_cb (BS-seq)


title: WT1_cor (BS-seq)

value: 2 weeks


title: 046-2_cor2 (BS-seq)


title: 183-7_cor (BS-seq)


title: 269-2_cor (BS-seq)


title: 046-1_cor2 (BS-seq)


title: 146-3_cor (BS-seq)


title: 306-1_cor1 (BS-seq)


title: 269-1_cor (BS-seq)


title: 046-1_liv (BS-seq)


title: 049-3_cor (BS-seq)

value: 20 weeks


title: 049-1_cor (BS-seq)


title: 146-4_cor (BS-seq)


title: 001-3_cor (BS-seq)

value: 1 weeks


title: 694_cor (BS-seq)

value: Male


title: 047-1_str (BS-seq)


title: 001-1_cor (BS-seq)

value: Cortex


title: 047-1_hip (BS-seq)


title: 047-2_hip (BS-seq)


title: 047-2_str (BS-seq)


title: 047-1_cb (BS-seq)


title: 006-5_cb (BS-seq)


title: 184-2_cor (BS-seq)


title: 006-2_cb (BS-seq)


title: 006-3_cor (BS-seq)

value: 4 weeks


title: 006-4_cor (BS-seq)


title: 001-4_cor (BS-seq)


title: 001-2_cor (BS-seq)


title: 046-2_str (BS-seq)

value: Striatum


title: 046-2_hip (BS-seq)


title: 046-1_str (BS-seq)


title: 047-2_cb (BS-seq)

value: Cerebellum


title: 046-1_hip (BS-seq)

value: 8 weeks


title: 046-1_cb (BS-seq)


title: 046-1_cor1 (BS-seq)


title: 046-2_cor1 (BS-seq)


title: 146-7_cor (BS-seq)


title: 047-1_cor1 (BS-seq)

value: Female


title: 002-4_cor (BS-seq)

value: wild type


title: 002-1_cor (BS-seq)

value: Heterozygous KO


title: 146-6_cor (BS-seq)


title: 047-2_cor1 (BS-seq)


title: 008-4_cor (BS-seq)


title: 146-8_cor (BS-seq)


title: 184-1_cor (BS-seq)


title: 071-1_cor (BS-seq)


title: 183-3_cor (BS-seq)


title: 183-4_cor (BS-seq)


title: 071-3_cor (BS-seq)


title: 007-2_cor (BS-seq)


title: 008-3_cor (BS-seq)


title: 007-3_cor (BS-seq)


title: 006-2_cor (BS-seq)


title: 046-2_cb (BS-seq)


title: 723_cor (BS-seq)


title: 724_cor (BS-seq)


title: 1009_cor (BS-seq)

value: 3 weeks


title: 728_cor (BS-seq)


title: 146-9_cor (BS-seq)


title: 726_cor (BS-seq)


title: 721_cor (BS-seq)


title: 720_cor (BS-seq)


title: 046-2_hKO (BS-seq)


title: 046-1_WT (BS-seq)


title: 728 (ChIP-seq)

data_processing:
Sequenced reads were mapped to the mm9 genome using bowtie2 alignment, and reads were deduplicated to consolidate PCR duplicate reads. Deduplicated reads were used to quantify read density normalized by the number of reads per sample and by read length in basepairs. edgeR was then used to determine differential ChIP-signal across genotypes.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-separated table (with header) of H3K27ac peaks defined by Clemens et.al, 2019, identifiers, and results of differential activity analysis

growth_protocol: Brain tissue was taken from DNMT3A heterozygous KO and wild-type mice maintained under standard housing conditions.

extract_protocol:
Cerebral cortex was dissected on ice in PBS from DNMT3AKO/+ and WT littermates at 8-weeks old (n=5 pairs, 3 male, 2 female). The tissue was flash-frozen in liquid nitrogen and stored at -80°C
ChIP libraries for H3K27ac were generated using Ovation Ultralow Library System V2 (NuGEN).
Libraries were pooled to a final concentration of 8-10nM and sequenced using Illumina HiSeq 3000 with the Genome Technology Access Center at Washington University in St. Louis, typically yielding 15-40 million single-end reads per sample.

value: Heterozygous Knockout

tag: chip antibody

value: H3K27ac (Abcam ab4729)


title: 726 (ChIP-seq)


title: 695_WT (BS-seq)


title: 119-2 (ChIP-seq)


title: 694_hKO (BS-seq)


title: 651-5 (ChIP-seq)


title: 006-5_cor (BS-seq)


title: 651-4 (ChIP-seq)


title: 141-3 (ChIP-seq)


title: 119-1 (ChIP-seq)


title: 141-1 (ChIP-seq)


title: 266-1_cor (BS-seq)


title: 650-1 (ChIP-seq)


title: 650-2 (ChIP-seq)


title: 16_THP1-DB818-Treated-4

type: RNA

city: lille

first: frédéric

last: leprêtre

address: Boulevard du Pr Leclercq

department: CHU of Lille, CBP

country: France

institute: Lille University

description: SAMPLE 16

hyb_protocol: Agilent-039494 SurePrint G3 Human GE v2 8x60K Microarray 039381  were scanned on an Agilent G2505B scanner.

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version V.10.7.3.1).

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

organism: Homo sapiens

source_name: THP-1 DB818-treated 24h

label_protocol: manufacturer's instructions

growth_protocol: RPMI-1640, 10% FCS, 0.05 mM 2-mercaptoethanol, 1% Pen/Strep, 37°C, 5% CO2

extract_protocol: Total RNA extracted using manufacturer's instructions

treatment_protocol: Human AML THP-1 cell line was (1) infected for 48h with shRNA expressing lentivirus for HOXA9 expression knowkdown (shHOXA9-1F3) or not (shCTR), or was treated or not for 24h with DB818 or DB1055

value: AML cell line

tag: treated with


title: 20_THP1-DB1055-Treated-4

description: SAMPLE 20

source_name: THP-1 DB1055-treated 24h


title: 19_THP1-DB1055-Treated-3

description: SAMPLE 19


title: 06_THP1-shHOXA9-1F3-2

description: SAMPLE 6

source_name: THP-1 + shHOXA9-1F3 48h

tag: infected with

value: shRNA expressing lentivirus for HOXA9 expression knowkdown (shHOXA9-1F3)


title: 11_THP1-Untreated-3

description: SAMPLE 11

source_name: THP-1 Untreated 24h

value: none (untreated)


title: 07_THP1-shHOXA9-1F3-3

description: SAMPLE 7


title: 09_THP1-Untreated-1

description: SAMPLE 9


title: 18_THP1-DB1055-Treated-2

description: SAMPLE 18


title: 08_THP1-shHOXA9-1F3-4

description: SAMPLE 8


title: 12_THP1-Untreated-4

description: SAMPLE 12


title: 17_THP1-DB818-Treated-1

description: SAMPLE 13


title: 14_THP1-DB818-Treated-2

description: SAMPLE 14


title: 17_THP1-DB1055-Treated-1

description: SAMPLE 17


title: 15_THP1-DB818-Treated-3

description: SAMPLE 15


title: 01_THP1-shCTR-1

description: SAMPLE 1

source_name: THP-1 + shCTR 48h

value: shRNA expressing lentivirus for control


title: 10_THP1-Untreated-2

description: SAMPLE 10


title: 05_THP1-shHOXA9-1F3-1

description: SAMPLE 5


title: 02_THP1-shCTR-2

description: SAMPLE 2


title: 04_THP1-shCTR-4

description: SAMPLE 4


title: 03_THP1-shCTR-3

description: SAMPLE 3


title: Whole blood, nfvPPA, 3999230062_L [ftd]

city: Los Angeles

first: Daniel

last: Nachun

state: CA

address: 695 Charles E Young Dr S

institute: UCLA

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing:
Data was imported from BeadStudio/GenomeStudio output (raw_data.txt) using lumi.  Illumina Ids were converted to nuIDs and expression values were normalized using variance-stabilizing transform.  Interarray normalization was done using robust spline normalization (normalized_data.txt).  Probes were dropped if their detection score p-value was greater than 0.01 or if they were not annotated with a gene symbol.  Outlier samples were identified by estimating connectivity Z-scores and dropping any sample with a Z-score less than -2.    Batches with only a single sample were also dropped.  Batch correction was performed using ComBat.  Duplicate probes for the same gene symbol were dropped from the batch corrected data by choosing the probe with the highest mean expression across all samples, and nuIDs were converted to gene symbols.  Expression values were also adjusted for age because of correlation between age and diagnosis (final_normalized_data.txt).
Sample data from normalized_data.txt represented in the Data table below.

label: biotin

source_name: Whole blood

label_protocol: Standard Illumina labeling protocol

extract_protocol: Peripheral blood collected in Paxgene tubes and extracted with Qiacube.  RNA quantity estimated with Nanodrop and RIN estimated with BioAnalyzer

tag: diagnosis

value: nfvPPA

tag: batch


title: Whole blood, PSP, 3999230075_C [ftd]

description: replicate 1

value: PSP


title: Whole blood, nfvPPA, 3999230064_J [ftd]

description: replicate 1

value: Male


title: Whole blood, bvFTD, 3999230064_G [ftd]

description: replicate 1

value: bvFTD


title: Whole blood, Control, 3999230064_A [ftd]

description: replicate 1

value: Control


title: Whole blood, svPPA, 3999230071_I [ftd]

description: replicate 1

value: svPPA


title: Whole blood, nfvPPA, 3999230071_H [ftd]

description: replicate 1


title: Whole blood, Control, 3999230060_H [ftd]

description: replicate 1


title: Whole blood, Control, 3999230071_B [ftd]

description: replicate 1


title: Whole blood, bvFTD, 3999230071_K [ftd]

description: replicate 1


title: Whole blood, Control, 3999230060_F [ftd]

description: replicate 1


title: Whole blood, Control, 9463775101_K [ftd]

description: replicate 1


title: Whole blood, nfvPPA, 3999230062_A [ftd]

description: replicate 1


title: Whole blood, PSP, 3999230064_L [ftd]

description: replicate 1


title: Whole blood, Control, 9463775101_I [ftd]

description: replicate 1


title: Whole blood, svPPA, 3999230062_G [ftd]

description: replicate 1


title: Whole blood, Control, 3999230060_G [ftd]

description: replicate 1


title: Whole blood, Control, 3999230060_E [ftd]

description: replicate 1


title: Whole blood, Control, 9463775101_D [ftd]

description: replicate 1


title: Whole blood, bvFTD, 9463775099_I [ftd]

description: replicate 1


title: Whole blood, Control, 9463775101_B [ftd]

description: replicate 1


title: Whole blood, bvFTD, 9463775101_E [ftd]

description: replicate 1


title: Whole blood, Control, 9463775099_L [ftd]

description: replicate 1


title: Whole blood, PSP, 9463775101_C [ftd]

description: replicate 1


title: Whole blood, Control, 3999230060_D [ftd]

description: replicate 1


title: Whole blood, PSP, 9463775101_H [ftd]

description: replicate 1


title: Whole blood, bvFTD, 3999230062_F [ftd]

description: replicate 1


title: Whole blood, Control, 9463775101_F [ftd]

description: replicate 1


title: Whole blood, CBS, 9463775099_H [ftd]

description: replicate 1

value: CBS


title: Whole blood, Control, 9461595121_I [ftd]

description: replicate 1

value: Female


title: Whole blood, bvFTD, 9461595121_D [ftd]

description: replicate 1


title: Whole blood, Control, 9461595121_H [ftd]

description: replicate 1


title: Whole blood, nfvPPA, 9443362106_G [ftd]

description: replicate 1


title: Whole blood, PSP, 9443362106_F [ftd]

description: replicate 1


title: Whole blood, PSP, 9443362106_E [ftd]

description: replicate 1


title: Whole blood, bvFTD, 9443362011_G [ftd]

description: replicate 1


title: Whole blood, Control, 9443362009_I [ftd]

description: replicate 1


title: Whole blood, nfvPPA, 9443362106_I [ftd]

description: replicate 1


title: Whole blood, Control, 9443362009_E [ftd]

description: replicate 1


title: Whole blood, svPPA, 9443362106_K [ftd]

description: replicate 1


title: Whole blood, CBS, 7166142013_B [ftd]

description: replicate 1


title: Whole blood, Control, 9443362009_B [ftd]

description: replicate 1


title: Whole blood, svPPA, 6898325083_C [ftd]

description: replicate 1


title: Whole blood, Control, 6898325083_E [ftd]

description: replicate 1


title: Whole blood, Control, 6898325082_D [ftd]

description: replicate 1


title: Whole blood, Control, 6898325082_E [ftd]

description: replicate 1


title: Whole blood, Control, 6898325082_B [ftd]

description: replicate 1


title: Whole blood, svPPA, 9463775099_G [ftd]

description: replicate 1


title: Whole blood, Control, 9443362106_L [ftd]

description: replicate 1


title: Whole blood, Control, 6898325082_A [ftd]

description: replicate 1


title: Whole blood, CBS, 6898325083_A [ftd]

description: replicate 1


title: Whole blood, svPPA, 6898325082_C [ftd]

description: replicate 1


title: Whole blood, Control, 7166142013_F [ftd]

description: replicate 1


title: Whole blood, Control, 7166142013_E [ftd]

description: replicate 1


title: Whole blood, CBS, 9443362009_H [ftd]

description: replicate 1


title: Whole blood, PSP, 3999230060_I [ftd]

description: replicate 1


title: Whole blood, Control, 6898325080_F [ftd]

description: replicate 1


title: Whole blood, Control, 6898325079_A [ftd]

description: replicate 1


title: Whole blood, nfvPPA, 6898325079_B [ftd]

description: replicate 1


title: Whole blood, svPPA, 6898325079_F [ftd]

description: replicate 1


title: Whole blood, bvFTD, 6898325080_D [ftd]

description: replicate 1


title: Whole blood, Control, 6898325063_E [ftd]

description: replicate 1


title: Whole blood, Control, 6898325063_B [ftd]

description: replicate 1


title: Whole blood, Control, 6898325057_D [ftd]

description: replicate 1


title: Whole blood, bvFTD, 6898325063_F [ftd]

description: replicate 1


title: Whole blood, Control, 8845526029_G [ftd]

description: replicate 1


title: Whole blood, Control, 6898325079_D [ftd]

description: replicate 1


title: Whole blood, Control, 8845526029_D [ftd]

description: replicate 1


title: Whole blood, Control, 6898325060_E [ftd]

description: replicate 1


title: Whole blood, Control, 6898325079_C [ftd]

description: replicate 1


title: Whole blood, Control, 6898325060_F [ftd]

description: replicate 1


title: Whole blood, Control, 8845526029_K [ftd]

description: replicate 1


title: Whole blood, CBS, 8845526039_K [ftd]

description: replicate 1


title: Whole blood, Control, 8845526029_C [ftd]

description: replicate 1


title: Whole blood, nfvPPA, 8845526039_C [ftd]

description: replicate 1


title: Whole blood, Control, 8845526029_J [ftd]

description: replicate 1


title: Whole blood, Control, 6898325057_E [ftd]

description: replicate 1


title: Whole blood, Control, 6898325057_B [ftd]

description: replicate 1


title: Whole blood, Control, 8845526017_I [ftd]

description: replicate 1


title: Whole blood, svPPA, 8845526013_K [ftd]

description: replicate 1


title: Whole blood, bvFTD, 8845526017_K [ftd]

description: replicate 1


title: Whole blood, Control, 6898325063_A [ftd]

description: replicate 1


title: Whole blood, Control, 8845526017_G [ftd]

description: replicate 1


title: Whole blood, nfvPPA, 8845526013_H [ftd]

description: replicate 1


title: Whole blood, svPPA, 8845526039_I [ftd]

description: replicate 1


title: Whole blood, nfvPPA, 8845526017_F [ftd]

description: replicate 1


title: Whole blood, nfvPPA, 9444048022_D [ftd]

description: replicate 1


title: Whole blood, CBS, 8845526013_J [ftd]

description: replicate 1


title: Whole blood, PSP, 9461595121_J [ftd]

description: replicate 1


title: Whole blood, Control, 8845526013_C [ftd]

description: replicate 1


title: Whole blood, CBS, 8845526013_D [ftd]

description: replicate 1


title: Whole blood, bvFTD, 8845526007_B [ftd]

description: replicate 1


title: Whole blood, nfvPPA, 8845526007_K [ftd]

description: replicate 1


title: Whole blood, PSP, 8845526007_J [ftd]

description: replicate 1


title: Whole blood, bvFTD, 8845526007_C [ftd]

description: replicate 1


title: Whole blood, Control, 6303281019_H [ftd]

description: replicate 1


title: Whole blood, Control, 6303248057_F [ftd]

description: replicate 1


title: Whole blood, bvFTD, 8845526007_E [ftd]

description: replicate 1


title: Whole blood, bvFTD, 8845526007_F [ftd]

description: replicate 1


title: Whole blood, nfvPPA, 8381645089_F [ftd]

description: replicate 1


title: Whole blood, CBS, 6303281019_L [ftd]

description: replicate 1


title: Whole blood, svPPA, 8381645085_C [ftd]

description: replicate 1


title: Whole blood, Control, 8381645089_H [ftd]

description: replicate 1


title: Whole blood, nfvPPA, 8381645086_K [ftd]

description: replicate 1


title: Whole blood, bvFTD, 8381645083_H [ftd]

description: replicate 1


title: Whole blood, svPPA, 8381645083_G [ftd]

description: replicate 1


title: Whole blood, nfvPPA, 8381645089_J [ftd]

description: replicate 1


title: Whole blood, Control, 8381645086_I [ftd]

description: replicate 1


title: Whole blood, bvFTD, 8381645085_B [ftd]

description: replicate 1


title: Whole blood, bvFTD, 8381645083_F [ftd]

description: replicate 1


title: Whole blood, Control, 8381645086_F [ftd]

description: replicate 1


title: Whole blood, Control, 8381645083_D [ftd]

description: replicate 1


title: Whole blood, Control, 8381645085_G [ftd]

description: replicate 1


title: Whole blood, Control, 8381645080_K [ftd]

description: replicate 1


title: Whole blood, Control, 8381645089_D [ftd]

description: replicate 1


title: Whole blood, Control, 8381645085_A [ftd]

description: replicate 1


title: Whole blood, Control, 8381645089_C [ftd]

description: replicate 1


title: Whole blood, PSP, 8845526007_D [ftd]

description: replicate 1


title: Whole blood, Control, 8381645086_H [ftd]

description: replicate 1


title: Whole blood, Control, 8381645085_E [ftd]

description: replicate 1


title: Whole blood, bvFTD, 8381645080_J [ftd]

description: replicate 1


title: Whole blood, bvFTD, 7656791045_F [ftd]

description: replicate 1


title: Whole blood, svPPA, 7656791045_H [ftd]

description: replicate 1


title: Whole blood, bvFTD, 7656791042_D [ftd]

description: replicate 1


title: Whole blood, svPPA, 7656791042_L [ftd]

description: replicate 1


title: Whole blood, PSP, 7656791045_D [ftd]

description: replicate 1


title: Whole blood, svPPA, 7656791042_K [ftd]

description: replicate 1


title: Whole blood, nfvPPA, 7656791042_A [ftd]

description: replicate 1


title: Whole blood, Control, 6303248029_D [ftd]

description: replicate 1


title: Whole blood, Control, 7656791031_H [ftd]

description: replicate 1


title: Whole blood, bvFTD, 7649540078_I [ftd]

description: replicate 1


title: Whole blood, Control, 7649540078_H [ftd]

description: replicate 1


title: Whole blood, bvFTD, 6303230098_F [ftd]

description: replicate 1


title: Whole blood, bvFTD, 7649540078_D [ftd]

description: replicate 1


title: Whole blood, bvFTD, 6303248071_G [ftd]

description: replicate 1


title: Whole blood, Control, 6303230097_C [ftd]

description: replicate 1


title: Whole blood, Control, 6303248029_J [ftd]

description: replicate 1


title: Whole blood, Control, 7656791031_J [ftd]

description: replicate 1


title: Whole blood, CBS, 6303248071_F [ftd]

description: replicate 1


title: Whole blood, Control, 7656791031_C [ftd]

description: replicate 1


title: Whole blood, Control, 6303248067_H [ftd]

description: replicate 1


title: Whole blood, CBS, 7656791031_I [ftd]

description: replicate 1


title: Whole blood, bvFTD, 7656791045_J [ftd]

description: replicate 1


title: Whole blood, PSP, 7656791031_K [ftd]

description: replicate 1


title: Whole blood, nfvPPA, 7656791042_J [ftd]

description: replicate 1


title: Whole blood, Control, 6303230098_H [ftd]

description: replicate 1


title: Whole blood, svPPA, 7656791031_G [ftd]

description: replicate 1


title: Whole blood, Control, 6303230097_D [ftd]

description: replicate 1


title: Whole blood, Control, 6303230098_G [ftd]

description: replicate 1


title: Whole blood, Control, 6260962092_H [ftd]

description: replicate 1


title: Whole blood, Control, 6260962092_G [ftd]

description: replicate 1


title: Whole blood, Control, 6116750081_D [ftd]

description: replicate 1


title: Whole blood, Control, 6116750081_J [ftd]

description: replicate 1


title: Whole blood, svPPA, 6116750081_L [ftd]

description: replicate 1


title: Whole blood, Control, 6116750081_I [ftd]

description: replicate 1


title: Whole blood, bvFTD, 8381645080_C [ftd]

description: replicate 1


title: Whole blood, svPPA, 6116768129_F [ftd]

description: replicate 1


title: Whole blood, Control, 6260962092_E [ftd]

description: replicate 1


title: Whole blood, Control, 6260962092_C [ftd]

description: replicate 1


title: Whole blood, CBS, 6260962092_F [ftd]

description: replicate 1


title: Whole blood, PSP, 6116768119_B [ftd]

description: replicate 1


title: Whole blood, PSP, 6116768127_D [ftd]

description: replicate 1


title: Whole blood, bvFTD, 6116750027_F [ftd]

description: replicate 1


title: Whole blood, PSP, 6116733121_H [ftd]

description: replicate 1


title: Whole blood, Control, 6116768119_L [ftd]

description: replicate 1


title: Whole blood, CBS, 6116733118_G [ftd]

description: replicate 1


title: Whole blood, nfvPPA, 6116733138_D [ftd]

description: replicate 1


title: Whole blood, Control, 6116733001_F [ftd]

description: replicate 1


title: Whole blood, Control, 6116733070_G [ftd]

description: replicate 1


title: Whole blood, Control, 6116750051_H [ftd]

description: replicate 1


title: Whole blood, Control, 6116733121_B [ftd]

description: replicate 1


title: Whole blood, Control, 6116733118_L [ftd]

description: replicate 1


title: Whole blood, PSP, 6116750027_A [ftd]

description: replicate 1


title: Whole blood, Control, 6116768119_D [ftd]

description: replicate 1


title: Whole blood, Control, 6016741008_J [ftd]

description: replicate 1


title: Whole blood, Control, 6016741008_B [ftd]

description: replicate 1


title: Whole blood, nfvPPA, 6016741009_F [ftd]

description: replicate 1


title: Whole blood, bvFTD, 6116750027_K [ftd]

description: replicate 1


title: Whole blood, Control, 6016741008_K [ftd]

description: replicate 1


title: Whole blood, nfvPPA, 6016741009_E [ftd]

description: replicate 1


title: Whole blood, Control, 6016741008_A [ftd]

description: replicate 1


title: Whole blood, Control, 6016741006_L [ftd]

description: replicate 1


title: Whole blood, svPPA, 6016741003_J [ftd]

description: replicate 1


title: Whole blood, CBS, 6016741004_H [ftd]

description: replicate 1


title: Whole blood, bvFTD, 6016741003_C [ftd]

description: replicate 1


title: Whole blood, Control, 6016741006_J [ftd]

description: replicate 1


title: Whole blood, Control, 6016741004_F [ftd]

description: replicate 1


title: Whole blood, PSP, 5975106007_B [ftd]

description: replicate 1


title: Whole blood, Control, 6016741003_D [ftd]

description: replicate 1


title: Whole blood, Control, 6016741003_K [ftd]

description: replicate 1


title: Whole blood, svPPA, 6016741002_K [ftd]

description: replicate 1


title: Whole blood, bvFTD, 6016741003_B [ftd]

description: replicate 1


title: Whole blood, Control, 5975106007_I [ftd]

description: replicate 1


title: Whole blood, Control, 5975106040_B [ftd]

description: replicate 1


title: Whole blood, bvFTD, 6016741002_J [ftd]

description: replicate 1


title: Whole blood, Control, 5975106007_C [ftd]

description: replicate 1


title: Whole blood, CBS, 5937337074_C [ftd]

description: replicate 1


title: Whole blood, Control, 5975106019_F [ftd]

description: replicate 1


title: Whole blood, PSP, 5937337095_C [ftd]

description: replicate 1


title: Whole blood, Control, 5937337095_B [ftd]

description: replicate 1


title: Whole blood, Control, 5937345070_H [ftd]

description: replicate 1


title: Whole blood, bvFTD, 5859990059_L [ftd]

description: replicate 1


title: Whole blood, Control, 5937345070_G [ftd]

description: replicate 1


title: Whole blood, Control, 5937345007_G [ftd]

description: replicate 1


title: Whole blood, Control, 5975106007_J [ftd]

description: replicate 1


title: Whole blood, Control, 5937337074_L [ftd]

description: replicate 1


title: Whole blood, Control, 5975106038_E [ftd]

description: replicate 1


title: Whole blood, Control, 6016741002_C [ftd]

description: replicate 1


title: Whole blood, svPPA, 5937337074_K [ftd]

description: replicate 1


title: Whole blood, Control, 5937345070_F [ftd]

description: replicate 1


title: Whole blood, Control, 5937345007_F [ftd]

description: replicate 1


title: Whole blood, Control, 5786049087_H [ftd]

description: replicate 1


title: Whole blood, Control, 5786049087_E [ftd]

description: replicate 1


title: Whole blood, PSP, 5859990059_K [ftd]

description: replicate 1


title: Whole blood, bvFTD, 5872641070_K [ftd]

description: replicate 1


title: Whole blood, Control, 5859990059_I [ftd]

description: replicate 1


title: Whole blood, Control, 5872641070_C [ftd]

description: replicate 1


title: Whole blood, Control, 5872641070_B [ftd]

description: replicate 1


title: Whole blood, nfvPPA, 5786049087_F [ftd]

description: replicate 1


title: Whole blood, svPPA, 5872641070_F [ftd]

description: replicate 1


title: Whole blood, Control, 5872641059_H [ftd]

description: replicate 1


title: Whole blood, PSP, 5872641054_A [ftd]

description: replicate 1


title: Whole blood, PSP, 5872641059_E [ftd]

description: replicate 1


title: Whole blood, Control, 5872641054_K [ftd]

description: replicate 1


title: Whole blood, Control, 5859990059_J [ftd]

description: replicate 1


title: Whole blood, Control, 5872641054_C [ftd]

description: replicate 1


title: Whole blood, Control, 5872641070_A [ftd]

description: replicate 1


title: Whole blood, Control, 5872641070_H [ftd]

description: replicate 1


title: Whole blood, Control, 5872641059_L [ftd]

description: replicate 1


title: Whole blood, Control, 5872641053_I [ftd]

description: replicate 1


title: Whole blood, CBS, 5872641054_J [ftd]

description: replicate 1


title: Whole blood, Control, 5872641054_H [ftd]

description: replicate 1


title: Whole blood, nfvPPA, 5872641054_B [ftd]

description: replicate 1


title: Whole blood, PSP, 5872641059_A [ftd]

description: replicate 1


title: Whole blood, Control, 5872641054_I [ftd]

description: replicate 1


title: Whole blood, Control, 5872641054_D [ftd]

description: replicate 1


title: Whole blood, bvFTD, 5872641053_J [ftd]

description: replicate 1


title: Whole blood, svPPA, 5872641053_D [ftd]

description: replicate 1


title: Whole blood, Control, 5872641053_H [ftd]

description: replicate 1


title: Whole blood, PSP, 5872641054_G [ftd]

description: replicate 1


title: Whole blood, PSP, 5872641053_F [ftd]

description: replicate 1


title: Whole blood, bvFTD, 5872641032_H [ftd]

description: replicate 1


title: Whole blood, svPPA, 5872641032_G [ftd]

description: replicate 1


title: Whole blood, bvFTD, 5872641032_I [ftd]

description: replicate 1


title: Whole blood, bvFTD, 5872641018_K [ftd]

description: replicate 1


title: Whole blood, Control, 5872641031_L [ftd]

description: replicate 1


title: Whole blood, Control, 5872641012_J [ftd]

description: replicate 1


title: Whole blood, nfvPPA, 5872641053_E [ftd]

description: replicate 1


title: Whole blood, Control, 5872641016_B [ftd]

description: replicate 1


title: Whole blood, Control, 5872641032_E [ftd]

description: replicate 1


title: Whole blood, Control, 5872641032_B [ftd]

description: replicate 1


title: Whole blood, CBS, 5872641031_I [ftd]

description: replicate 1


title: Whole blood, Control, 5872641032_D [ftd]

description: replicate 1


title: Whole blood, Control, 5872641016_G [ftd]

description: replicate 1


title: Whole blood, Control, 5872641016_J [ftd]

description: replicate 1


title: Whole blood, Control, 5872641053_B [ftd]

description: replicate 1


title: Whole blood, bvFTD, 5872641018_J [ftd]

description: replicate 1


title: Whole blood, Control, 5872641018_A [ftd]

description: replicate 1


title: Whole blood, Control, 5872641032_C [ftd]

description: replicate 1


title: Whole blood, svPPA, 5872641053_L [ftd]

description: replicate 1


title: Whole blood, Control, 5872641018_D [ftd]

description: replicate 1


title: Whole blood, PSP, 5872641053_K [ftd]

description: replicate 1


title: Whole blood, nfvPPA, 5872641016_I [ftd]

description: replicate 1


title: Whole blood, Control, 5872641016_K [ftd]

description: replicate 1


title: Whole blood, Control, 5872641018_F [ftd]

description: replicate 1


title: Whole blood, PSP, 5872641012_K [ftd]

description: replicate 1


title: Whole blood, Control, 5872641012_H [ftd]

description: replicate 1


title: Whole blood, Control, 5872641012_D [ftd]

description: replicate 1


title: Whole blood, Control, 5872641011_L [ftd]

description: replicate 1


title: Whole blood, svPPA, 5872641012_G [ftd]

description: replicate 1


title: Whole blood, svPPA, 5872641012_E [ftd]

description: replicate 1


title: Whole blood, bvFTD, 5872641012_A [ftd]

description: replicate 1


title: Whole blood, Control, 5872641012_F [ftd]

description: replicate 1


title: Whole blood, bvFTD, 5872641012_C [ftd]

description: replicate 1


title: Whole blood, Control, 5872641011_I [ftd]

description: replicate 1


title: Whole blood, svPPA, 5872641011_C [ftd]

description: replicate 1


title: Whole blood, Control, 5872641011_G [ftd]

description: replicate 1


title: Whole blood, MCI, 9682760081_H [ad_mci]

description: replicate 2

data_processing:
Data was imported from BeadStudio/GenomeStudio output (raw_data.txt) using lumi.  Illumina Ids were converted to nuIDs and expression values were normalized using variance-stabilizing transform.  Interarray normalization was done using robust spline normalization (normalized_data.txt).  Probes were dropped if their detection score p-value was greater than 0.01 or if they were not annotated with a gene symbol.  Outlier samples were identified by estimating connectivity Z-scores and dropping any sample with a Z-score less than -2.    Batches with only a single sample were also dropped.  Batch correction was performed using ComBat.  Duplicate probes for the same gene symbol were dropped from the batch corrected data by choosing the probe with the highest mean expression across all samples, and nuIDs were converted to gene symbols (final_normalized_data.txt).
Sample data from normalized_data.txt represented in the Data table below.

value: MCI


title: Whole blood, Control, 5872617031_E [ftd]

description: replicate 1


title: Whole blood, Control, 5872641011_B [ftd]

description: replicate 1


title: Whole blood, Control, 5872641011_F [ftd]

description: replicate 1


title: Whole blood, Control, 200661380042_J [ad_mci]

description: replicate 2


title: Whole blood, Control, 200316700083_H [ad_mci]

description: replicate 1


title: Whole blood, Control, 5872641011_K [ftd]

description: replicate 1


title: Whole blood, Control, 5872641011_D [ftd]

description: replicate 1


title: Whole blood, Control, 200316700083_A [ad_mci]

description: replicate 1


title: Whole blood, AD, 200661380042_K [ad_mci]

description: replicate 2

value: AD


title: Whole blood, bvFTD, 5872617031_F [ftd]

description: replicate 1


title: Whole blood, Control, 5786049087_D [ftd]

description: replicate 1


title: Whole blood, MCI, 200661920039_E [ad_mci]

description: replicate 1


title: Whole blood, MCI, 200795790038_J [ad_mci]

description: replicate 1


title: Whole blood, Control, 5872617031_C [ftd]

description: replicate 1


title: Whole blood, Control, 5872617031_A  [ftd]

description: replicate 1


title: Whole blood, MCI, 200661920003_C [ad_mci]

description: replicate 2


title: Whole blood, Control, 200661920002_H [ad_mci]

description: replicate 1


title: Whole blood, AD, 200795790038_K [ad_mci]

description: replicate 1


title: Whole blood, MCI, 200795790040_L [ad_mci]

description: replicate 1


title: Whole blood, AD, 200661920067_L [ad_mci]

description: replicate 1


title: Whole blood, AD, 200665010002_K [ad_mci]

description: replicate 1


title: Whole blood, Control, 200661920039_C [ad_mci]

description: replicate 1


title: Whole blood, MCI, 200665010044_H [ad_mci]

description: replicate 1


title: Whole blood, AD, 200795790040_F [ad_mci]

description: replicate 1


title: Whole blood, Control, 200665010052_F [ad_mci]

description: replicate 1


title: Whole blood, AD, 200665010062_B [ad_mci]

description: replicate 1


title: Whole blood, MCI, 200665010044_L [ad_mci]

description: replicate 1


title: Whole blood, AD, 200661920067_D [ad_mci]

description: replicate 1


title: Whole blood, Control, 200665010044_A [ad_mci]

description: replicate 1


title: Whole blood, Control, 200665010023_I [ad_mci]

description: replicate 1


title: Whole blood, AD, 200661920067_G [ad_mci]

description: replicate 1


title: Whole blood, Control, 200795790042_E [ad_mci]

description: replicate 1


title: Whole blood, MCI, 200795790038_H [ad_mci]

description: replicate 1


title: Whole blood, Control, 200665010052_A [ad_mci]

description: replicate 1


title: Whole blood, MCI, 200661920001_C [ad_mci]

description: replicate 1


title: Whole blood, Control, 200795790038_G [ad_mci]

description: replicate 1


title: Whole blood, AD, 200667730024_K [ad_mci]

description: replicate 1


title: Whole blood, AD, 200795790038_A [ad_mci]

description: replicate 1


title: Whole blood, MCI, 200665010052_J [ad_mci]

description: replicate 1


title: Whole blood, Control, 200795790042_D [ad_mci]

description: replicate 1


title: Whole blood, AD, 200667730024_I [ad_mci]

description: replicate 1


title: Whole blood, Control, 200665010044_C [ad_mci]

description: replicate 1


title: Whole blood, AD, 200665010062_D [ad_mci]

description: replicate 1


title: Whole blood, AD, 200667730024_G [ad_mci]

description: replicate 1


title: Whole blood, Control, 200795790038_I [ad_mci]

description: replicate 1


title: Whole blood, Control, 200665010062_K [ad_mci]

description: replicate 1


title: Whole blood, Control, 200667730024_L [ad_mci]

description: replicate 1


title: Whole blood, Control, 200667730024_C [ad_mci]

description: replicate 1


title: Whole blood, Control, 200667730024_D [ad_mci]

description: replicate 1


title: Whole blood, Control, 200667730024_B [ad_mci]

description: replicate 1


title: Whole blood, Control, 200667730024_H [ad_mci]

description: replicate 1


title: Whole blood, AD, 200667730024_F [ad_mci]

description: replicate 1


title: Whole blood, AD, 200665010062_H [ad_mci]

description: replicate 1


title: Whole blood, MCI, 200795790042_J [ad_mci]

description: replicate 1


title: Whole blood, MCI, 200665010062_G [ad_mci]

description: replicate 1


title: Whole blood, AD, 200665010039_I [ad_mci]

description: replicate 1


title: Whole blood, AD, 200665010039_D [ad_mci]

description: replicate 1


title: Whole blood, AD, 200665010044_I [ad_mci]

description: replicate 1


title: Whole blood, Control, 200665010039_C [ad_mci]

description: replicate 1


title: Whole blood, AD, 200665010039_K [ad_mci]

description: replicate 1


title: Whole blood, Control, 200665010029_K [ad_mci]

description: replicate 1


title: Whole blood, Control, 200665010029_G [ad_mci]

description: replicate 1


title: Whole blood, MCI, 200665010002_F [ad_mci]

description: replicate 1


title: Whole blood, Control, 200665010029_A [ad_mci]

description: replicate 1


title: Whole blood, Control, 200665010029_I [ad_mci]

description: replicate 1


title: Whole blood, MCI, 200665010029_L [ad_mci]

description: replicate 1


title: Whole blood, MCI, 200665010029_B [ad_mci]

description: replicate 1


title: Whole blood, Control, 200665010002_D [ad_mci]

description: replicate 1


title: Whole blood, AD, 200661920067_J [ad_mci]

description: replicate 1


title: Whole blood, AD, 200665010023_C [ad_mci]

description: replicate 1


title: Whole blood, Control, 200665010029_E [ad_mci]

description: replicate 1


title: Whole blood, Control, 200665010002_L [ad_mci]

description: replicate 1


title: Whole blood, Control, 200665010029_J [ad_mci]

description: replicate 1


title: Whole blood, Control, 200661920067_I [ad_mci]

description: replicate 1


title: infected_B

city: Würzburg

first: Falk

last: Ponath

address: Josef-Schneider-Straße 2

country: Germany

institute: Helmholtz Institute for RNA-based Infection Research (HIRI)

description: infected samples

data_processing:
Demultiplexing
FastQ quality trimming using FastX and a cut-off value of 20
Fastq to fasta conversion using FastX (v0.11.7)
Size filtering: discarding reads shorter than 20 nt (via READemption v0.4.3)
Read mapping via READemption (v0.4.3)
Counting of reads per gene via READemption (v0.4.3)
Genome_build: Pseudomonas aeruginosa (AE004091.2); Pseudomonas virus phiKZ (AF399011.1)
Supplementary_files_format_and_content: CSV (comma separated) of gene count per gene per sample

organism:
Phikzvirus phiKZ
Pseudomonas aeruginosa PAO1

source_name: infected samples

growth_protocol: P. aeruginosa was grown in lysogeny broth (LB) at 37°C and 220rpm. Bacteriophage phiKZ was expanded by liquid culture and purified by subsequent filitration.

extract_protocol:
Flash frozen samples were used for RNA using the Hot phenol protocol (described e.g. in PMID: 31796567)
Total RNA extracted from ɸKZ-infected and uninfected P. aeruginosa PAO1 cells was divided in two pools, named TEX- and TEX+. Samples were examined by capillary electrophoresis and fragmented using ultrasound (4 pulses of 30 sec at 4 °C), followed by T4 Polynucleotide Kinase (NEB) treatment. TEX+ samples were subjected to Terminator-5´-phosphate-dependent exonuclease to enrich primary transcripts whereas TEX- samples remained untreated. For cDNA synthesis RNA samples were poly(A)-tailed and remaining 5´PPP structures were removed. After ligation of an RNA adapter to the 5´P end, first-strand cDNA synthesis was performed using an oligo(dT)-adapter primer and M-MLV reverse transcriptase. PCR amplification of cDNAs was conducted using a high-fidelity DNA polymerase and cDNAs were purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics). Quality control was carried out by capillary electrophoresis. All described procedures were performed by Vertis Biotechnology (Germany).
TruSeq Stranded Library Preparation Kit (Illumina)

treatment_protocol: P. aeruginosa was grown to early exponetial phase before being infected with phiKZ (MOI of 15) for 10min. Uninfected bacteria were used as control.

tag: infection status

value: infected with phiKZ


title: ifnected_B+TEX

description: infected samples (TEX treated)

source_name: infected samples (TEX treated)


title: Whole blood, AD, 200665010039_J [ad_mci]

description: replicate 1


title: infected_A+TEX

description: infected samples (TEX treated)


title: infected_A

description: infected samples


title: Whole blood, MCI, 200665010023_G [ad_mci]

description: replicate 1


title: Whole blood, MCI, 200795790042_I [ad_mci]

description: replicate 1


title: control_B+TEX

description: uninfected control (TEX treated)

organism: Pseudomonas aeruginosa PAO1

source_name: uninfected control (TEX treated)

value: uninfected


title: Whole blood, Control, 200661920067_A [ad_mci]

description: replicate 1


title: control_A+TEX

description: uninfected control (TEX treated)


title: control_B

description: uninfected control

source_name: uninfected control


title: control_A

description: uninfected control


title: Whole blood, Control, 200661920039_J [ad_mci]

description: replicate 1


title: Whole blood, Control, 200661920037_F [ad_mci]

description: replicate 1


title: Whole blood, Control, 200661920037_J [ad_mci]

description: replicate 1


title: Whole blood, Control, 200661920039_I [ad_mci]

description: replicate 1


title: Whole blood, Control, 200661920037_D [ad_mci]

description: replicate 1


title: Whole blood, Control, 200661920067_H [ad_mci]

description: replicate 1


title: Whole blood, Control, 200661920039_B [ad_mci]

description: replicate 1


title: Whole blood, Control, 200661920037_G [ad_mci]

description: replicate 1


title: Whole blood, Control, 200661920015_H [ad_mci]

description: replicate 1


title: Whole blood, Control, 200661920015_G [ad_mci]

description: replicate 1


title: Whole blood, MCI, 200661920031_D [ad_mci]

description: replicate 1


title: Whole blood, MCI, 200661920037_I [ad_mci]

description: replicate 1


title: Whole blood, Control, 200661920031_L [ad_mci]

description: replicate 1


title: Whole blood, MCI, 200661920037_C [ad_mci]

description: replicate 1


title: Whole blood, MCI, 200661920015_F [ad_mci]

description: replicate 1


title: Whole blood, Control, 200363680055_A [ad_mci]

description: replicate 1


title: PF1-rep3

city: Shenzhen

first: Hui

last: Wang

state: Guangdong

address: Taoyuanjiedao

institute: Shenzhen University

data_processing:
The sepuencing data was filtered with SOAPnuke(v1.5.2)by removing reads containing sequencing adapter.
Removing reads whose low-quality base ratio(base quality less than or equal to 5) is more than 20%,Removing reads whose unknown base ('N'base) ratio is more than 5%，afterwards clean reads were obtained and stored in FASTQ format,
The clean reads were mapped to the reference genome using HISAT2(v2.0.4).
Bowtie(v2.2.5) was applied to align the clean reads to the reference coding gene set,then expression level of gene was calculated by RSEM(v1.2.12).
The heatmap was drawn by pheatmap(v 1.0.8)according to the gene expression in different samples.
Genome_build: UCSC Genome Brower assembly ID:rn6     NCBI Genome ID:73
Supplementary_files_format_and_content: ab-delimited text files include RSEM values of each sample

organism: Rattus norvegicus

source_name: Rat basophilic leukemia 2H3 cells

growth_protocol: RBL-2H3 cells were cultured in complete Dulbecco’s modifed eagle medium with 4.0  mM  l-glutamine with sodium pyruvate penicillin (100 U/ml), 100 μg/ml streptomycin, non-essential amino acids, and 10% fetal bovine serum in a humidifed incubator at 37 °C, 5% CO2

extract_protocol:
RNA was harvested using Trizol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: RBL-2H3 cells  were sensitized with 50ng/ml anti-DNP IgE for 12h, washed with Tyrode's buffer, and stimulated with 100ng/ml DNP-HSA  for 4h.

value: Peripheral blood

value: Blood corpuscle

value: RBL-2H3 cells  were sensitized with 50ng/ml anti-DNP IgE for 12h,  pretreated with PF for 1h and stimulated with 100ng/ml DNP-HSA  for 6h.


title: PF1-rep2

value: RBL-2H3 cells  were sensitized with 50ng/ml anti-DNP IgE for 12h,  pretreated with PF for 1h and stimulated with 100ng/ml DNP-HSA  for 5h.


title: Whole blood, MCI, 200661920031_G [ad_mci]

description: replicate 1


title: Whole blood, AD, 200661920031_B [ad_mci]

description: replicate 1


title: Whole blood, AD, 200661920014_F [ad_mci]

description: replicate 1


title: Whole blood, Control, 200661920015_E [ad_mci]

description: replicate 1


title: Whole blood, Control, 200661920031_E [ad_mci]

description: replicate 1


title: Whole blood, MCI, 200661920031_J [ad_mci]

description: replicate 1


title: Whole blood, MCI, 200661920039_D [ad_mci]

description: replicate 1


title: Whole blood, MCI, 200665010023_E [ad_mci]

description: replicate 1


title: Whole blood, Control, 200661920015_D [ad_mci]

description: replicate 1


title: PF1-rep1

value: RBL-2H3 cells  were sensitized with 50ng/ml anti-DNP IgE for 12h,  pretreated with PF for 1h and stimulated with 100ng/ml DNP-HSA  for 4h.


title: IgE/DNP-rep3

value: RBL-2H3 cells  were sensitized with 50ng/ml anti-DNP IgE for 12h,  and stimulated with 100ng/ml DNP-HSA  for 4h.


title: IgE/DNP-rep2


title: Ctrl-rep3

value: untreated


title: Ctrl-rep2


title: Whole blood, MCI, 200665010039_G [ad_mci]

description: replicate 1

value: Male


title: Ctrl-rep1


title: P64 Lung 1

city: Nashville

first: Jennifer

last: Sucre

state: TN

address: 2215 B Garland Ave, 1125 Light Hall

department: Division of Neonatology, Department of Pediatrics

institute: Vanderbilt University Medical Center

data_processing:
Reads with read quality less than 30 were filtered out and CellRanger Count v3.1 (10X Genomics) was used to align reads onto mm10 reference genome.
Ambient background RNA were cleaned from the scRNA-seq data with “SoupX” (version 1.2.2). We utilized the following genes to estimate the non-expressing cells, calculate the contamination fraction, and adjust the gene expression counts: Dcn, Bgn, Aspn, Ecm2, Fos, Hbb-bs, Hbb-bt, Hba-a1, Hba-a2, Lyz1, Lyz2, Mgp, Postn, Scgb1a1.
Data integration and clustering was performed using a standard Scanpy workflow (Scanpy v1.46). Individual SoupX “cleaned” libraries were concatenated and analyzed jointly. After quality filtering (removal of cells with <500 or >5000 genes, or >10% mitochondrial gene expression), data were normalized, log-transformed, highly-variable genes were identified, and percent mitochondrial gene expression and read depth were regressed.
Genome_build: mm10
Supplementary_files_format_and_content: Compressed comma separated values (csv.gz files) of normalized counts per cell after SoupX normalization.

source_name: Lung

extract_protocol:
At the indicated timepoints, lung lobes were harvested, minced, and incubated for 30 minutes at 37°C in dissociation media (RPMI-1640 with 0.7 mg/ml collagenase XI and 30 mg/ml type IV bovine pancreatic DNase). After incubation, lobes were passed through a wide bore pipet tip and filtered through a 40 μm filter. Single cell lung suspension was then counted, aliquoted, and blocked with CD-32 Fc block (BD cat #553142) for 20 minutes on ice. After 2% FBS staining buffer wash, cells were incubated with the conjugated primary antibodies anti-CD45 (BD cat # 559864) and anti-Ter119 (BD cat# 116211). In the same manner, fluorescence minus one controls were blocked and stained with the appropriate antibody controls. Cells from individual mice were then incubated with identifiable hashtags, resuspended in staining buffer, and treated with PI viability dye. CD45 negative, Ter119 negative, viable cells were collected by fluorescence associated cell sorting using a 70 μm nozzle on a 4-laser FACSAria III Cell Sorter. Both single and fluorescence-minus-one controls were used for compensation.
ScRNA-seq libraries were generated using the 10X Chromium platform 5’ library preparation kits (10X Genomics) following the manufacturer's recommendations and targeting 10,000 - 20,000 cells per sample.

value: lung

value: enriched for cells that were CD45 negative, Ter119 negative, and viable

value: post natal day 64

value: wild type


title: P64 Lung 2


title: P14 Lung 1

value: post natal day 14


title: P14 Lung 2


title: P7 Lung 1

value: post natal day 7


title: P7 Lung 2


title: P0 Lung 2

value: post natal day 0


title: IgE/DNP-rep1


title: Whole blood, Control, 200661920039_K [ad_mci]

description: replicate 1

value: Control

value: Female


title: P0 Lung 1


title: Whole blood, AD, 200661920014_C [ad_mci]

description: replicate 1

value: AD


title: Whole blood, Control, 200316700083_G [ad_mci]

description: replicate 1


title: Whole blood, AD, 200661920011_L [ad_mci]

description: replicate 1


title: E18 Lung 1

value: embryonic day 18


title: Whole blood, Control, 200795790042_C [ad_mci]

description: replicate 1


title: Whole blood, MCI, 200661920011_F [ad_mci]

description: replicate 1

value: MCI


title: Whole blood, AD, 200661920011_E [ad_mci]

description: replicate 1


title: Whole blood, AD, 200661920011_C [ad_mci]

description: replicate 1


title: Whole blood, Control, 200363680054_I [ad_mci]

description: replicate 1


title: Whole blood, Control, 200661920003_L [ad_mci]

description: replicate 1


title: Whole blood, MCI, 200661920011_J [ad_mci]

description: replicate 1


title: Whole blood, Control, 200661920011_G [ad_mci]

description: replicate 1


title: bKO3_In

city: Harbin

first: Zheng

last: Chen

state: Heilongjiang

address: 92 Xidazhijie  Harbin Institute of Technology

institute: Harbin Institute of Technology

data_processing:
Raw data (raw reads) of fastq format were firstly processed using fastp (version 0.19.11).
Index of the reference genome was built using BWA v0.7.12 and clean  reads were aligned to the reference genome using BWA mem v 0.7.12.
exomePeak R package (version 2.16.0) was used for the m6A peak identification
The m6A-enriched motifs of each group were identified by HOMER (version 4.9.1).
GO enrichment analysis was implemented by the GOseq R package.
Genome_build: GRCm38.p6

source_name: Pancreatic islets

extract_protocol:
Total RNAs were extracted using TriPure Isolation Reagent (Roche, Mannheim, Germany) from pancreatic islets of Mettl3flox/flox and β-Mettl3-KO mice.  A total of 2-3 μg RNAs were pooled from nine Mettl3flox/flox mice and twelve β-Mettl3-KO mice, respectively. Three independent biological replicates of each group were used for MeRIP-seq.
Fragmented RNA (~100 nt) was incubated for 2 hr at 4oC with anti-m6A polyclonal antibody (Merk Millipore) in the immunoprecipitation experiment. Then, immunoprecipitated RNAs or Input was used for library construction with Ovation SoLo RNA-Seq System Core Kit (NuGEN). The library preparations were sequenced on an Illumina Novaseq platform with a paired-end read length of 150 bp according to the standard protocols.

treatment_protocol: Mettl3flox/flox and β-Mettl3-KO mice were fed with normal chow diet for 8 weeks old

value: beta-Mettl3-KO (Mettl3 flox/flox RIP-Cre)


title: bKO2_In


title: bKO1_In


title: Whole blood, Control, 200316700083_F [ad_mci]

description: replicate 1


title: Whole blood, AD, 200363680055_B [ad_mci]

description: replicate 1


title: Whole blood, Control, 200363680055_D [ad_mci]

description: replicate 1


title: bKO2_IP

value: m6A antibody (Merk Millipore)


title: bKO3_IP


title: Whole blood, AD, 200661920003_I [ad_mci]

description: replicate 1


title: Whole blood, AD, 200400280015_L [ad_mci]

description: replicate 1


title: Whole blood, AD, 200661920014_D [ad_mci]

description: replicate 1


title: FF1_In

value: Mettl3 flox/flox


title: Whole blood, AD, 200363680059_F [ad_mci]

description: replicate 1


title: FF3_In


title: FF2_In


title: FF2_IP


title: FF1_IP


title: BKO 3

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house  perl scripts. In this step, clean data (clean reads) were obtained by removing reads  containing adapter, reads containing ploy-N and low quality reads from raw data. At  the same time, Q20, Q30 and GC content the clean data were calculated. All the  downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from  genome website directly. Index of the reference genome was built using Hisat2 v2.0.5  and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database  of splice junctions based on the gene model annotation file and thus a better mapping  result than other non-splice mapping tools
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each  gene. And then FPKM of each gene was calculated based on the length of the gene  and reads count mapped to this gene. FPKM, expected number of Fragments Per  Kilobase of transcript sequence per Millions base pairs sequenced, considers the  effect of sequencing depth and gene length for the reads count at the same time, and is  currently the most commonly used method for estimating gene expression levels.
Differential expression analysis of two  conditions/groups (two biological replicates per condition) was performed using the  DESeq2 R package (1.16.1). DESeq2 provide statistical routines for determining  differential expression in digital gene expression data using a model based on the  negative binomial distribution. The resulting P-values were adjusted using the  Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes  with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially  expressed
Genome_build: GRCm38.p6

extract_protocol:
Total RNAs were extracted using TriPure Isolation Reagent (Roche, Mannheim, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols


title: BKO 1


title: BKO 2


title: FF 3


title: FF 2


title: Whole blood, Control, 200400280016_L [ad_mci]

description: replicate 1


title: Whole blood, Control, 200363680054_J [ad_mci]

description: replicate 1


title: Whole blood, MCI, 200661920003_J [ad_mci]

description: replicate 1


title: Whole blood, Control, 200661920014_H [ad_mci]

description: replicate 1


title: Whole blood, MCI, 200400280017_J [ad_mci]

description: replicate 1


title: Whole blood, AD, 200363680014_D [ad_mci]

description: replicate 1


title: FF 1


title: Whole blood, Control, 200316700083_C [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_A7_AD006

city: La Jolla

first: Joseph

middle: R

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 INTACT reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10 INTACT
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

source_name: C57BL/6J P56 Mouse Brain

growth_protocol: All experimental procedures using live animals were approved by the Salk Institute Animal Care and Use Committee. The knock-in mouse line, R26R-CAG-loxp-stop-loxp-Sun1-sfGFP-Myc (INTACT) was used for most experiments4 and they were maintained on a C57BL/6J background. 42-49 day old adult male and female INTACT mice were used for the retrograde labeling experiment.

extract_protocol:
Approximately two weeks after the AAVretro injection, brains were extracted from the 56-63 day old INTACT mice, immediately submerged in ice-cold slicing buffer (2.5mM KCl, 0.5mM CaCl2, 7mM MgCl2, 1.25mM NaH2PO4, 110mM sucrose, 10mM glucose and 25mM NaHCO3) that was bubbled with carbogen, and sliced into 0.6 mm coronal sections starting from the frontal pole. From each AAVretro-injected brain, the slices were kept in the ice-cold dissection buffer from which selected brain regions (Supplementary Table 1) were manually dissected under a fluorescent dissecting microscope (Olympus SZX16), following the Allen Mouse Common Coordinate Framework (CCF), Reference Atlas, Version 3 (2015) (Extended Data Fig. 1). The dissected brain tissues were transferred to prelabeled microcentrifuge tubes, immediately frozen in dry ice, and subsequently stored at -80oC.   For each dissected brain region, samples from 2 males and 2 females were pooled separately as biological replicates for nuclei preparation. The 2-mL glass tissue dounce homogenizer and pestles (Sigma-Aldrich D8938-1SET) were pre-chilled on ice. Nuclei were prepared using a modified protocol as reported by Lacar et al., 201622. In summary, the frozen brain tissues were transferred to the dounce homogenizer with 1 mL ice-cold NIM buffer (0.25M sucrose, 25mM KCl, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT (Sigma 646563), 10μl of protease inhibitor (Sigma P8340)), with 0.1% Triton X-100 and 5μM Hoechst 33342 (Invitrogen H3570), and gently homogenized on ice with the pestle 10-15 times. The homogenate was transferred to pre-chilled microcentrifuge tubes and centrifuged at 1000 rcf for 8 min at 4oC to pellet the nuclei. The pellet was resuspended in 1 mL ice-cold NIM buffer, and again centrifuged at 1000 rcf for 8 min at 4oC. The pellet was then resuspended in 450 μL of ice-cold NSB buffer (0.25M sucrose, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT, 9ul of Protease inhibitor), and filtered through 40μM cell strainer. The filtered nuclei suspension was incubated on ice for at least 30 minutes with 50μl of nuclease-free BSA for at least 10 minutes, then incubated with GFP antibody, Alexa Fluor 488 (Invitrogen, A-21311) and anti-NeuN antibody (EMD Millipore MAB377) conjugated with Alexa Fluor 647 (Invitrogen A20173). GFP+/NeuN+ single nuclei were isolated using fluorescence-activated nuclei sorting (FANS) on a BD Influx sorter with 100μm nozzle, and sorted into 384-well plates preloaded with 2μl of digestion buffer for snmC-seq215 (20 mL digestion buffer consists of 10 mL M-digestion buffer (2×, Zymo D5021-9), 1 ml Proteinase K (20 mg, Zymo D3001-2-20), 9 mL water, and 10 µL unmethylated lambda DNA (100 pg/µL, Promega, D1521)). The collected plates were incubated at 50oC for 20 minutes then stored at -20 oC.
The bisulfite conversion and library preparation were performed following the detailed snmC-seq2 protocol as previously described (Luo, C. et al., Nat. Commun. 2018, 9(1):3824.). The snmC-Seq2 libraries were sequenced on Illumina Novaseq 6000 using the S4 flow cell 2 x 150 bp mode.

treatment_protocol: To label neurons projecting to regions of interest, injections of rAAV2-retro-Cre (produced by Salk Vector Core or Vigene, 2x10^12 to 1x10^13 viral genomes/ml, produced with capsid from Addgene plasmid #81070 packaging pAAV-EF1a-Cre from Addgene plasmid #55636) were made into both hemispheres of the INTACT mice. Animals were anesthetized with either ketamine/xylazine or isoflurane, placed in a stereotaxic frame, and 0.1 to 0.5 microliters of AAV was injected by pressure into stereotaxic coordinates corresponding to the desired projection target.

value: brain

tag: source

value: MOp

tag: target

value: SSp

value: male


title: FF3_IP

tag: strain


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_A7_AD004

tag: age


title: Whole blood, Control, 200363680018_J [ad_mci]

description: replicate 1

value: Male


title: Whole blood, Control, 200661920011_K [ad_mci]

description: replicate 1


title: Whole blood, Control, 200363680018_I [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_A7_AD002


title: bKO1_IP

tag: genotype


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_A7_AD001


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_A6_AD012

value: SC

value: female


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_A6_AD010


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_A6_AD004


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_A6_AD007


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_A6_AD006


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_A6_AD001


title: Whole blood, AD, 200661920003_A [ad_mci]

description: replicate 1

tag: Sex


title: Whole blood, Control, 200373830057_B [ad_mci]

description: replicate 1


title: Whole blood, Control, 200661920003_G [ad_mci]

description: replicate 1


title: Whole blood, Control, 200661920002_J [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_A5_AD010


title: Whole blood, Control, 200400280016_J [ad_mci]

description: replicate 1


title: Whole blood, MCI, 200363680054_K [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_A5_AD012


title: Whole blood, Control, 200363680054_H [ad_mci]

description: replicate 1


title: Whole blood, Control, 200373830016_D [ad_mci]

description: replicate 1


title: Whole blood, Control, 200373830011_D [ad_mci]

description: replicate 1


title: Whole blood, AD, 200316700083_D [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_A5_AD008


title: Whole blood, MCI, 200373830050_J [ad_mci]

description: replicate 1


title: Whole blood, AD, 200373830050_E [ad_mci]

description: replicate 1


title: Whole blood, Control, 200795790042_H [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_A5_AD007


title: Whole blood, AD, 200373830050_L [ad_mci]

description: replicate 1


title: Whole blood, Control, 200363680054_E [ad_mci]

description: replicate 1


title: Whole blood, AD, 200373830048_I [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_A5_AD004


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_A5_AD006


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_A5_AD002


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_A5_AD001


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_A4_AD010


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_A4_AD012


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_A4_AD008


title: Whole blood, Control, 200363680018_H [ad_mci]

description: replicate 1


title: Whole blood, Control, 200373830042_F [ad_mci]

description: replicate 1


title: Whole blood, MCI, 200373830048_L [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_A4_AD004


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_A4_AD001


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_A4_AD007


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_A4_AD006


title: Whole blood, AD, 200373830036_E [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_A4_AD002


title: Whole blood, Control, 200373830036_C [ad_mci]

description: replicate 1


title: Whole blood, AD, 200373830041_A [ad_mci]

description: replicate 1


title: Whole blood, AD, 200373830036_A [ad_mci]

description: replicate 1


title: Whole blood, AD, 200373830021_H [ad_mci]

description: replicate 1


title: Whole blood, Control, 200373830021_E [ad_mci]

description: replicate 1


title: Whole blood, Control, 200373830016_A [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_A3_AD010


title: Whole blood, Control, 200373830021_B [ad_mci]

description: replicate 1


title: Whole blood, Control, 200373830016_I [ad_mci]

description: replicate 1


title: Whole blood, AD, 200363680054_C [ad_mci]

description: replicate 1


title: Whole blood, AD, 200363680059_I [ad_mci]

description: replicate 1


title: Whole blood, AD, 200363680054_A [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_A3_AD007


title: Whole blood, Control, 200316700083_B [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_A3_AD012


title: Whole blood, AD, 200363680054_B [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_A3_AD006


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_A3_AD002


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_A3_AD004


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_A3_AD001


title: Whole blood, Control, 3999230060_E [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_A3_AD008


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_A2_AD012


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_A2_AD007


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_A2_AD008


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_A2_AD010


title: Whole blood, Control, 3999230060_H [ad_mci]

description: replicate 1


title: Whole blood, Control, 3999230060_G [ad_mci]

description: replicate 1


title: Whole blood, MCI, 200373830016_F [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_A2_AD006


title: Whole blood, AD, 200363680055_F [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_A2_AD004


title: Whole blood, AD, 200363680055_G [ad_mci]

description: replicate 1


title: Whole blood, Control, 3999230060_D [ad_mci]

description: replicate 1


title: Whole blood, MCI, 200400280017_K [ad_mci]

description: replicate 1


title: Whole blood, AD, 3999230060_J [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_A2_AD002


title: Whole blood, AD, 200400280017_I [ad_mci]

description: replicate 1


title: Whole blood, Control, 3999230064_A [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_A1_AD010


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_A2_AD001


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_A1_AD008


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_A1_AD007


title: Whole blood, MCI, 3999230060_B [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_A1_AD006


title: Whole blood, AD, 200400280017_B [ad_mci]

description: replicate 1


title: Whole blood, Control, 3999230060_F [ad_mci]

description: replicate 1


title: Whole blood, AD, 3999230071_D [ad_mci]

description: replicate 1


title: Whole blood, MCI, 3999230064_C [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_A1_AD004


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_A1_AD001


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_A1_AD002


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_A12_AD007


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_A12_AD010


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_A12_AD008


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_A12_AD006


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_A12_AD012


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_A10_AD010


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_A10_AD012


title: Whole blood, AD, 3999230062_J [ad_mci]

description: replicate 1


title: Whole blood, AD, 200400280016_B [ad_mci]

description: replicate 1


title: Whole blood, MCI, 3999230075_A [ad_mci]

description: replicate 1


title: Whole blood, Control, 200316700083_E [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_A12_AD004


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_A10_AD008


title: Whole blood, Control, 3999230071_B [ad_mci]

description: replicate 1


title: Whole blood, AD, 3999230060_L [ad_mci]

description: replicate 1


title: Whole blood, AD, 3999230075_E [ad_mci]

description: replicate 1


title: Whole blood, MCI, 200373830057_K [ad_mci]

description: replicate 1


title: Whole blood, AD, 200373830057_C [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_A12_AD001


title: Whole blood, AD, 3999230062_K [ad_mci]

description: replicate 1


title: Whole blood, AD, 3999230064_B [ad_mci]

description: replicate 1


title: Whole blood, MCI, 3999230062_B [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_A10_AD006


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_A10_AD007


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_A10_AD004


title: Whole blood, Control, 200363680059_D [ad_mci]

description: replicate 1


title: Whole blood, AD, 200373830042_J [ad_mci]

description: replicate 1


title: Whole blood, MCI, 200373830048_D [ad_mci]

description: replicate 1


title: Whole blood, AD, 3999230064_D [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_H9_AD012

value: STR


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_H9_AD008


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_H9_AD007


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_H9_AD010


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_H9_AD002


title: Whole blood, Control, 200373830011_B [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_H8_AD012


title: Whole blood, AD, 200373830041_D [ad_mci]

description: replicate 1


title: Whole blood, AD, 200373830057_E [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_H9_AD001


title: Whole blood, MCI, 200373830042_E [ad_mci]

description: replicate 1


title: Whole blood, MCI, 9703627107_D [ad_mci]

description: replicate 1


title: Whole blood, AD, 3999230071_G [ad_mci]

description: replicate 1


title: Whole blood, Control, 200373830011_C [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_H8_AD008


title: Whole blood, AD, 200373830042_L [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_H8_AD007


title: Whole blood, MCI, 3999230064_E [ad_mci]

description: replicate 1


title: Whole blood, MCI, 3999230075_L [ad_mci]

description: replicate 1


title: Whole blood, AD, 3999230071_A [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_H9_AD004


title: Whole blood, AD, 200373830021_D [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_H8_AD010


title: Whole blood, AD, 200373830041_H [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_H8_AD004


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_H8_AD006


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_A10_AD001


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_H7_AD010


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_H7_AD012


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_H7_AD007


title: Whole blood, Control, 9682760081_C [ad_mci]

description: replicate 1


title: Whole blood, MCI, 3999230071_E [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_H7_AD002


title: Whole blood, Control, 9682760081_D [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_H7_AD004


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_H7_AD006


title: Whole blood, Control, 9682760081_E [ad_mci]

description: replicate 1


title: Whole blood, MCI, 200373830016_L [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_H8_AD002


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_H7_AD001


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_H6_AD012


title: Whole blood, AD, 200373830016_C [ad_mci]

description: replicate 1


title: Whole blood, MCI, 3999230075_F [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_H7_AD008


title: Whole blood, AD, 9682760080_C [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_H6_AD008


title: Whole blood, AD, 200373830048_E [ad_mci]

description: replicate 1


title: Whole blood, AD, 9682760076_A [ad_mci]

description: replicate 1


title: Whole blood, AD, 9682760080_B [ad_mci]

description: replicate 1


title: Whole blood, MCI, 9682760076_H [ad_mci]

description: replicate 1


title: Whole blood, MCI, 9682760076_L [ad_mci]

description: replicate 1


title: Whole blood, AD, 9682760080_I [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_H6_AD007


title: Whole blood, MCI, 9682760074_K [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_H6_AD006


title: Whole blood, AD, 9682760079_L [ad_mci]

description: replicate 1


title: Whole blood, MCI, 9682760074_L [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_H6_AD004


title: Whole blood, AD, 9682760074_I [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_H5_AD012


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_H5_AD010


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_H5_AD006


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_H5_AD007


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_H5_AD008


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_H5_AD002


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_H4_AD012


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_H4_AD010


title: Whole blood, AD, 9682760073_G [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_H4_AD008


title: Whole blood, AD, 9682760074_F [ad_mci]

description: replicate 1


title: Whole blood, AD, 9682760074_D [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_H4_AD006


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_H4_AD007


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_H4_AD004


title: Whole blood, MCI, 9682760074_C [ad_mci]

description: replicate 1


title: Whole blood, Control, 9682760073_K [ad_mci]

description: replicate 1


title: Whole blood, AD, 3999230071_L [ad_mci]

description: replicate 1


title: Whole blood, MCI, 9682760072_L [ad_mci]

description: replicate 1


title: Whole blood, AD, 9682760073_E [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_H3_AD012


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_H3_AD010


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_H3_AD008


title: Whole blood, AD, 9682760073_D [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_H3_AD007


title: Whole blood, MCI, 9682760072_J [ad_mci]

description: replicate 1


title: Whole blood, MCI, 9682760072_H [ad_mci]

description: replicate 1


title: Whole blood, AD, 9682760072_G [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_H3_AD006


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_H4_AD001


title: Whole blood, MCI, 9682760074_B [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_H3_AD004


title: Whole blood, MCI, 9682760072_C [ad_mci]

description: replicate 1


title: Whole blood, Control, 9682760072_K [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_H3_AD001


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_H2_AD012


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_H2_AD010


title: Whole blood, Control, 9682760071_F [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_H2_AD008


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_H2_AD006


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_H2_AD004


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_H2_AD001


title: Whole blood, AD, 9682760062_K [ad_mci]

description: replicate 1


title: Whole blood, AD, 9682760071_A [ad_mci]

description: replicate 1


title: Whole blood, MCI, 9682760071_K [ad_mci]

description: replicate 1


title: Whole blood, AD, 9665647062_E [ad_mci]

description: replicate 1


title: Whole blood, MCI, 9665647062_G [ad_mci]

description: replicate 1


title: Whole blood, AD, 200363680017_J [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_H1_AD012


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_H1_AD010


title: Whole blood, AD, 9665647061_L [ad_mci]

description: replicate 1


title: Whole blood, AD, 9665647061_I [ad_mci]

description: replicate 1


title: Whole blood, MCI, 9682760071_J [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_H9_AD006


title: Whole blood, AD, 9665647061_H [ad_mci]

description: replicate 1


title: Whole blood, AD, 9631032050_B [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_H2_AD007


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_H1_AD007


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_H1_AD008


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_H1_AD006


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_H1_AD004


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_H1_AD001


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_H12_AD008


title: Whole blood, AD, 9631032049_J [ad_mci]

description: replicate 1


title: Whole blood, AD, 9631032050_A [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_H12_AD010


title: Whole blood, AD, 9631032049_I [ad_mci]

description: replicate 1


title: Whole blood, MCI, 9631032050_C [ad_mci]

description: replicate 1


title: Whole blood, Control, 9631032049_F [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_H12_AD004


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_H12_AD006


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_H12_AD002


title: Whole blood, Control, 9631032047_F [ad_mci]

description: replicate 1


title: Whole blood, AD, 9631032049_A [ad_mci]

description: replicate 1


title: Whole blood, Control, 9631032049_B [ad_mci]

description: replicate 1


title: Whole blood, MCI, 9631032047_I [ad_mci]

description: replicate 1


title: Whole blood, MCI, 9631032047_J [ad_mci]

description: replicate 1


title: Whole blood, Control, 9631032047_L [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_H11_AD012


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_H12_AD001


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_H11_AD008


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_H12_AD012


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_H11_AD006


title: Whole blood, MCI, 9631032047_H [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_H11_AD004


title: Whole blood, Control, 9631032047_G [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_H11_AD002


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_H11_AD007


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_H10_AD012


title: Whole blood, MCI, 9631032043_F [ad_mci]

description: replicate 1


title: Whole blood, MCI, 9631032043_L [ad_mci]

description: replicate 1


title: Whole blood, Control, 9631032043_G [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_H10_AD010


title: Whole blood, Control, 9631032043_H [ad_mci]

description: replicate 1


title: Whole blood, Control, 9631032043_I [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_H10_AD007


title: Whole blood, AD, 9631032043_E [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_H10_AD008


title: Whole blood, MCI, 9631032043_C [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_H10_AD006


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_G9_AD012


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_G9_AD008


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_G9_AD010


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_H10_AD002


title: Whole blood, AD, 9631032043_D [ad_mci]

description: replicate 1


title: Whole blood, Control, 9682760073_L [ad_mci]

description: replicate 1


title: Whole blood, Control, 9631032047_B [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_G9_AD006


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_G9_AD002


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_G9_AD007


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_G9_AD001


title: Whole blood, AD, 9631032042_K [ad_mci]

description: replicate 1


title: Whole blood, Control, 9631032042_H [ad_mci]

description: replicate 1


title: Whole blood, AD, 9631032042_D [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_G8_AD008


title: Whole blood, AD, 9631032042_F [ad_mci]

description: replicate 1


title: Whole blood, Control, 9631032039_G [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_G8_AD010


title: Whole blood, Control, 9631032042_C [ad_mci]

description: replicate 1


title: Whole blood, MCI, 9631032039_L [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_G8_AD007


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_G8_AD006


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_G8_AD004


title: Whole blood, AD, 9631032039_B [ad_mci]

description: replicate 1


title: Whole blood, MCI, 9631032039_A [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_G8_AD002


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_G8_AD012


title: Whole blood, AD, 9631032039_K [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_G8_AD001


title: Whole blood, AD, 9682760081_I [ad_mci]

description: replicate 1


title: Whole blood, Control, 9631032033_G [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_G7_AD010


title: Whole blood, Control, 9631032033_I [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_G7_AD008


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_G7_AD007


title: Whole blood, Control, 9631032033_B [ad_mci]

description: replicate 1


title: Whole blood, AD, 9631032033_C [ad_mci]

description: replicate 1


title: Whole blood, AD, 9461595121_L [ad_mci]

description: replicate 1


title: Whole blood, MCI, 200667730024_A [ad_mci]

description: replicate 1


title: Whole blood, Control, 9631032033_E [ad_mci]

description: replicate 1


title: Whole blood, Control, 9631032042_E [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_G7_AD006


title: Whole blood, MCI, 9631032033_F [ad_mci]

description: replicate 1


title: Whole blood, AD, 9461595121_F [ad_mci]

description: replicate 1


title: Whole blood, Control, 9461595121_H [ad_mci]

description: replicate 1


title: Whole blood, Control, 9461595121_I [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_G7_AD012


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_G7_AD002


title: Whole blood, MCI, 9631032033_A [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_G6_AD010


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_G7_AD004


title: Whole blood, Control, 200363680055_K [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_G6_AD012


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_G6_AD007


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_G6_AD008


title: Whole blood, Control, 9463775101_D [ad_mci]

description: replicate 1


title: Whole blood, AD, 9461595121_E [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_G6_AD006


title: Whole blood, Control, 9463775101_I [ad_mci]

description: replicate 1


title: Whole blood, Control, 9463775101_K [ad_mci]

description: replicate 1


title: Whole blood, AD, 9463775101_A [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_G6_AD004


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_G5_AD008


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_G5_AD012


title: Whole blood, AD, 9463775016_G [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_G6_AD001


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_G5_AD007


title: Whole blood, AD, 9463775016_F [ad_mci]

description: replicate 1


title: Whole blood, AD, 9463775016_K [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_G5_AD006


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_G5_AD004


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_G4_AD012


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_G4_AD010


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_G5_AD010


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_G4_AD008


title: Whole blood, AD, 9463775016_B [ad_mci]

description: replicate 1


title: Whole blood, AD, 9463775016_D [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_G4_AD007


title: Whole blood, AD, 9463775099_F [ad_mci]

description: replicate 1


title: Whole blood, Control, 9463775099_L [ad_mci]

description: replicate 1


title: Whole blood, AD, 9463775099_E [ad_mci]

description: replicate 1


title: Whole blood, AD, 9463775099_B [ad_mci]

description: replicate 1


title: Whole blood, AD, 9463775099_J [ad_mci]

description: replicate 1


title: Whole blood, AD, 9444048022_B [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_G4_AD006


title: Whole blood, Control, 9443362106_L [ad_mci]

description: replicate 1


title: Whole blood, AD, 9444048022_A [ad_mci]

description: replicate 1


title: Whole blood, AD, 9443362106_J [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_G5_AD001


title: Whole blood, AD, 9443362106_B [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_G4_AD001


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_G4_AD004


title: Whole blood, AD, 9443362106_C [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_G3_AD010


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_G3_AD012


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_G3_AD008


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_G3_AD006


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_G2_AD010


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_G2_AD012


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_G3_AD007


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_G2_AD008


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_G2_AD007


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_G2_AD006


title: Whole blood, MCI, 8845526029_B [ad_mci]

description: replicate 1


title: Whole blood, Control, 9443362009_I [ad_mci]

description: replicate 1


title: Whole blood, Control, 8845526013_C [ad_mci]

description: replicate 1


title: Whole blood, AD, 9443362106_H [ad_mci]

description: replicate 1


title: Whole blood, AD, 8845526013_I [ad_mci]

description: replicate 1


title: Whole blood, MCI, 8845526017_A [ad_mci]

description: replicate 1


title: Whole blood, AD, 9443362009_G [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_G2_AD004


title: Whole blood, Control, 8845526029_K [ad_mci]

description: replicate 1


title: Whole blood, MCI, 8845526029_L [ad_mci]

description: replicate 1


title: Whole blood, Control, 8845526029_G [ad_mci]

description: replicate 1


title: Whole blood, AD, 9443362009_K [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_G1_AD012


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_G3_AD004


title: Whole blood, AD, 9443362009_C [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_G2_AD001


title: Whole blood, Control, 9443362009_B [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_G1_AD008


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_G1_AD007


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_G1_AD004


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_G1_AD006


title: Whole blood, AD, 9443362011_I [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_G1_AD010


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_G1_AD001


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_G12_AD010


title: Whole blood, AD, 8845526017_J [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_G12_AD007


title: Whole blood, AD, 8845526039_D [ad_mci]

description: replicate 1


title: Whole blood, AD, 8845526039_G [ad_mci]

description: replicate 1


title: Whole blood, MCI, 8845526029_A [ad_mci]

description: replicate 1


title: Whole blood, AD, 9631032028_E [ad_mci]

description: replicate 1


title: Whole blood, AD, 8845526017_D [ad_mci]

description: replicate 1


title: Whole blood, AD, 8845526017_H [ad_mci]

description: replicate 1


title: Whole blood, MCI, 9443362011_J [ad_mci]

description: replicate 1


title: Whole blood, MCI, 8845526013_F [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_G12_AD006


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_G12_AD008


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_G12_AD002


title: Whole blood, AD, 8845526017_E [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_G12_AD001


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_G11_AD008


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_G11_AD010


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_G11_AD012


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_G11_AD007


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_G11_AD006