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

description: replicate 1


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

status: Public on Nov 13 2020

type: RNA

city: Los Angeles

first: Daniel

last: Nachun

state: CA

address: 695 Charles E Young Dr S

country: USA

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 (final_normalized_data.txt).
Sample data from normalized_data.txt represented in the Data table below.

label: biotin

molecule: total RNA

organism: Homo sapiens

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: Control

tag: Sex

value: Male

tag: batch


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

description: replicate 1

value: MCI

value: Female


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_G10_AD012

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

library_source: genomic

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

molecule: genomic DNA

organism: Mus musculus

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.

tag: strain

tag: age

tag: tissue

value: brain

tag: source

value: MOp

tag: target

value: STR

tag: gender

value: female


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_G10_AD010

value: male


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

description: replicate 1

value: AD


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

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_G10_AD007


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

description: replicate 1


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

description: replicate 1


title: Whole blood, MCI, 8845526007_A [ad_mci]

description: replicate 1


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

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_G10_AD006

value: SC


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_G11_AD004


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_G11_AD002


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_G10_AD001


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_G10_AD002


title: Whole blood, AD, 8845526029_H [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_G11_AD001


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_G10_AD008


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

description: replicate 1


title: Whole blood, AD, 5872641018_L [ad_mci]

description: replicate 1


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

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_G10_AD004


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

description: replicate 1


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

description: replicate 1


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

description: replicate 1


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

description: replicate 1


title: Whole blood, AD, 5872641032_L [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_F9_AD010


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

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_F9_AD007


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_F9_AD008


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_F9_AD006


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_F9_AD002


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

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_F9_AD004


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_F9_AD012


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_F8_AD012


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

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_F8_AD010


title: Whole blood, MCI, 5872641016_L [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_F8_AD008


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_F8_AD006


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_F8_AD002


title: Whole blood, MCI, 8381645085_H [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_F8_AD007


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

description: replicate 1


title: Whole blood, AD, 8845526007_H [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_F7_AD012


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_F8_AD001


title: Whole blood, MCI, 8845526007_I [ad_mci]

description: replicate 1


title: Whole blood, AD, 8381645080_G [ad_mci]

description: replicate 1


title: Whole blood, MCI, 8381645080_B [ad_mci]

description: replicate 1


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

description: replicate 1


title: Whole blood, MCI, 8381645083_I [ad_mci]

description: replicate 1


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

description: replicate 1


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

description: replicate 1


title: Whole blood, AD, 8381645080_A [ad_mci]

description: replicate 1


title: Whole blood, AD, 200363680018_L [ad_mci]

description: replicate 1


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

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_F7_AD004


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_F7_AD006


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_F7_AD008


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_F7_AD007


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_F7_AD002


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_F7_AD010


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_F7_AD001


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_F6_AD012


title: Whole blood, AD, 8381645086_D [ad_mci]

description: replicate 1


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

description: replicate 1


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

description: replicate 1


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

description: replicate 1


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

description: replicate 1


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

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_F6_AD007


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_F6_AD008


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

description: replicate 1


title: Whole blood, AD, 8845526007_L [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_F6_AD001


title: Whole blood, MCI, 8381645083_L [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_F5_AD012


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_F6_AD006


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_F6_AD004


title: Whole blood, AD, 8381645085_L [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_F5_AD010


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_F5_AD008


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_F4_AD012


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_F5_AD007


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

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_F4_AD010


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_F4_AD008


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_F5_AD001


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_F4_AD006


title: Whole blood, AD, 8381645085_D [ad_mci]

description: replicate 1


title: Whole blood, MCI, 8381645083_K [ad_mci]

description: replicate 1


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

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_F5_AD004


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

description: replicate 1


title: Whole blood, AD, 8381645086_E [ad_mci]

description: replicate 1


title: Whole blood, MCI, 8381645080_I [ad_mci]

description: replicate 1


title: Whole blood, MCI, 8381645083_C [ad_mci]

description: replicate 1


title: Whole blood, AD, 8381645086_G [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_F4_AD001


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_F4_AD004


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_F3_AD012


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

description: replicate 1


title: Whole blood, MCI, 8381645080_H [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_F3_AD010


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_F3_AD008


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_F3_AD007


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_F3_AD006


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_F3_AD004


title: Whole blood, AD, 8381645080_L [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_F3_AD001


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_F2_AD012


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_F2_AD010


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_F2_AD008


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_F2_AD006


title: Whole blood, AD, 8381645085_K [ad_mci]

description: replicate 1


title: Whole blood, MCI, 7649540078_K [ad_mci]

description: replicate 1


title: Whole blood, AD, 7656791042_F [ad_mci]

description: replicate 1


title: Whole blood, MCI, 7649540078_E [ad_mci]

description: replicate 1


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

description: replicate 1


title: Whole blood, AD, 7656791031_E [ad_mci]

description: replicate 1


title: Whole blood, AD, 7649540078_J [ad_mci]

description: replicate 1


title: Whole blood, AD, 7656791045_K [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_F2_AD004


title: Whole blood, MCI, 7656791045_E [ad_mci]

description: replicate 1


title: Whole blood, MCI, 7656791045_C [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_F2_AD001


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

description: replicate 1


title: Whole blood, MCI, 7656791031_D [ad_mci]

description: replicate 1


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

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_F3_AD002


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_F1_AD012


title: Whole blood, AD, 7656791042_H [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_F1_AD010


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_F1_AD008


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_F1_AD006


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

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_F9_AD001


title: Whole blood, AD, 7649540078_B [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_F12_AD012


title: Whole blood, MCI, 7656791045_B [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_F12_AD010


title: Whole blood, AD, 7656791042_B [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_F12_AD008


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_F12_AD007


title: Whole blood, MCI, 7656791031_B [ad_mci]

description: replicate 1


title: Whole blood, MCI, 7656791042_C [ad_mci]

description: replicate 1


title: Whole blood, AD, 6898325057_F [ad_mci]

description: replicate 1


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

description: replicate 1


title: Whole blood, AD, 7656791031_A [ad_mci]

description: replicate 1


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

description: replicate 1


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

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_F1_AD004


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_F12_AD006


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_F12_AD004


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_F1_AD001


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_F11_AD012


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_F12_AD002


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_F11_AD010


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

description: replicate 1


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

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_F11_AD008


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_F12_AD001


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_F11_AD007


title: Whole blood, MCI, 6898325083_F [ad_mci]

description: replicate 1


title: Whole blood, AD, 6898325083_D [ad_mci]

description: replicate 1


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

description: replicate 1


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

description: replicate 1


title: Whole blood, MCI, 7166142013_C [ad_mci]

description: replicate 1


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

description: replicate 1


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

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_F11_AD001


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_F11_AD006


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_F10_AD008


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_F10_AD010


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_F10_AD012


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_F11_AD004


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

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_F11_AD002


title: Whole blood, MCI, 6898325083_B [ad_mci]

description: replicate 1


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

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_F10_AD004


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

description: replicate 1


title: Whole blood, MCI, 7166142013_A [ad_mci]

description: replicate 1


title: Whole blood, MCI, 6898325060_B [ad_mci]

description: replicate 1


title: Whole blood, AD, 6898325057_A [ad_mci]

description: replicate 1


title: Whole blood, AD, 6898325060_A [ad_mci]

description: replicate 1


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

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_F10_AD007


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_F10_AD006


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_F10_AD001


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

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_F10_AD002


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_E9_AD012


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

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_E9_AD008


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

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_E9_AD010


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_E9_AD004


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_E9_AD006


title: Whole blood, MCI, 6898325080_A [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_E9_AD001


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

description: replicate 1


title: Whole blood, MCI, 6303248067_C [ad_mci]

description: replicate 1


title: Whole blood, AD, 6303248029_L [ad_mci]

description: replicate 1


title: Whole blood, MCI, 6303248029_K [ad_mci]

description: replicate 1


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

description: replicate 1


title: Whole blood, MCI, 6303248067_B [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_E8_AD007


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_E8_AD008


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_E8_AD010


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_E8_AD012


title: Whole blood, MCI, 6303230097_J [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_E9_AD002


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_E8_AD002


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_E8_AD001


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_E8_AD006


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_E8_AD004


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_E7_AD012


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_E7_AD010


title: Whole blood, AD, 6303230097_I [ad_mci]

description: replicate 1


title: Whole blood, MCI, 6303248029_C [ad_mci]

description: replicate 1


title: Whole blood, MCI, 6303230097_B [ad_mci]

description: replicate 1


title: Whole blood, AD, 6303230097_K [ad_mci]

description: replicate 1


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

description: replicate 1


title: Whole blood, AD, 6303281019_B [ad_mci]

description: replicate 1


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

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_E7_AD007


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_E9_AD007


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_E7_AD008


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_E7_AD004


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_E6_AD012


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_E7_AD002


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_E7_AD006


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_E6_AD008


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_E6_AD007


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

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_E6_AD010


title: Whole blood, AD, 6303248057_L [ad_mci]

description: replicate 1


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

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_E6_AD004


title: Whole blood, MCI, 6260971012_H [ad_mci]

description: replicate 1


title: Whole blood, MCI, 6303230097_A [ad_mci]

description: replicate 1


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

description: replicate 1


title: Whole blood, AD, 6116750081_K [ad_mci]

description: replicate 1


title: Whole blood, MCI, 6116750051_A [ad_mci]

description: replicate 1


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

description: replicate 1


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

description: replicate 1


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

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_E6_AD006


title: Whole blood, AD, 6116750051_J [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_E5_AD008


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_E5_AD012


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_E5_AD006


title: Whole blood, AD, 6116750051_L [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_E5_AD010


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_E6_AD001


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_E5_AD004


title: Whole blood, MCI, 6116750051_F [ad_mci]

description: replicate 1


title: Whole blood, MCI, 6116750081_B [ad_mci]

description: replicate 1


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

description: replicate 1


title: Whole blood, AD, 6116750051_D [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_E5_AD007


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_E5_AD001


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_E4_AD012


title: Whole blood, MCI, 6116750081_F [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_E4_AD008


title: Whole blood, MCI, 6116768127_J [ad_mci]

description: replicate 1


title: Whole blood, AD, 6260962092_A [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_E4_AD010


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

description: replicate 1


title: Whole blood, AD, 6116733001_H [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_E3_AD012


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_E4_AD001


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_E4_AD006


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_E4_AD004


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

description: replicate 1


title: Whole blood, AD, 6116733120_L [ad_mci]

description: replicate 1


title: Whole blood, MCI, 6260962092_B [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_E3_AD010


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_E3_AD007


title: Whole blood, MCI, 6116768129_D [ad_mci]

description: replicate 1


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

description: replicate 1


title: Whole blood, MCI, 6116733138_B [ad_mci]

description: replicate 1


title: Whole blood, AD, 6116733118_H [ad_mci]

description: replicate 1


title: Whole blood, AD, 6116733120_J [ad_mci]

description: replicate 1


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

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_E3_AD006


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_E3_AD004


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_E3_AD008


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_E2_AD007


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_E3_AD001


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_E2_AD006


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_E2_AD008


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_E2_AD010


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_E2_AD012


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

description: replicate 1


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

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_E2_AD001


title: Whole blood, AD, 6116733125_K [ad_mci]

description: replicate 1


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

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_E1_AD010


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

description: replicate 1


title: Whole blood, MCI, 6116768129_B [ad_mci]

description: replicate 1


title: Whole blood, AD, 6016741009_G [ad_mci]

description: replicate 1


title: Whole blood, MCI, 5975106038_F [ad_mci]

description: replicate 1


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

description: replicate 1


title: Whole blood, AD, 6116733120_I [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_E1_AD008


title: Whole blood, AD, 6016741008_C [ad_mci]

description: replicate 1


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

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_E1_AD012


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_E1_AD004


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_E1_AD007


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_E1_AD002


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_E1_AD006


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_E2_AD002


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_E2_AD004


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

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_E1_AD001


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_E12_AD012


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

description: replicate 1


title: Whole blood, AD, 6116733138_A [ad_mci]

description: replicate 1


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

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_E3_AD002


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

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_E11_AD010


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_E12_AD007


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_E12_AD008


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_E12_AD004


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_E12_AD001


title: Whole blood, AD, 6116733121_D [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_E12_AD002


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_E11_AD012


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_E12_AD006


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_E12_AD010


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_E11_AD008


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

description: replicate 1


title: Whole blood, AD, 5975106019_E [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_E11_AD006


title: Whole blood, AD, 6116733125_L [ad_mci]

description: replicate 1


title: Whole blood, AD, 5975106040_A [ad_mci]

description: replicate 1


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

description: replicate 1


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

description: replicate 1


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

description: replicate 1


title: Whole blood, MCI, 6016741002_I [ad_mci]

description: replicate 1


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

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_E11_AD007


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_E10_AD012


title: Whole blood, MCI, 5937337095_D [ad_mci]

description: replicate 1


title: Whole blood, AD, 6116733070_H [ad_mci]

description: replicate 1


title: Whole blood, AD, 5937337095_L [ad_mci]

description: replicate 1


title: Whole blood, AD, 5975106007_A [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_E11_AD004


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_E11_AD001


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_E11_AD002


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

description: replicate 1


title: Whole blood, Control, 9631032028_I [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_E10_AD010


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_E10_AD007


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_E10_AD004


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_E10_AD006


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_D9_AD008


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

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_D9_AD007


title: Whole blood, AD, 5937337074_D [ad_mci]

description: replicate 1


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

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_E10_AD008


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_D9_AD012


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_D9_AD006


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_D9_AD004


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

description: replicate 1


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

description: replicate 1


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

description: replicate 1


title: Whole blood, AD, 6016741006_C [ad_mci]

description: replicate 1


title: Whole blood, AD, 6016741004_G [ad_mci]

description: replicate 1


title: Whole blood, MCI, 5937337095_K [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_D8_AD012


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_D9_AD010


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_D9_AD001


title: Whole blood, MCI, 6016741006_B [ad_mci]

description: replicate 1


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

description: replicate 1


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

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_D8_AD007


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_D8_AD008


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

description: replicate 1


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

description: replicate 1


title: Whole blood, MCI, 5872641031_J [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_D8_AD010


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

description: replicate 1


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

description: replicate 1


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

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_D8_AD006


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_D8_AD002


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_D8_AD004


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_D8_AD001


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_D7_AD008


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_D7_AD010


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_D7_AD012


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_D7_AD006


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_D7_AD004


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_D7_AD007


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

description: replicate 1


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

description: replicate 1


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

description: replicate 1


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

description: replicate 1


title: Whole blood, AD, 5872641059_D [ad_mci]

description: replicate 1


title: Whole blood, AD, 5872641016_E [ad_mci]

description: replicate 1


title: Whole blood, AD, 5872641059_F [ad_mci]

description: replicate 1


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

description: replicate 1


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

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_D6_AD010


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_D6_AD012


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

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_D6_AD008


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

description: replicate 1


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

description: replicate 1


title: Whole blood, AD, 5872641059_C [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_D6_AD006


title: Whole blood, MCI, 5872641012_B [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_D6_AD007


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

description: replicate 1


title: Whole blood, AD, 5872641031_C [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_D6_AD004


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_D5_AD012


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_D7_AD002


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_D5_AD010


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_D5_AD007


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_D5_AD006


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_D5_AD008


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_D5_AD001


title: Whole blood, MCI, 5872641031_A [ad_mci]

description: replicate 1


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

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_D5_AD004


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

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_D4_AD012


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_D4_AD010


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_D4_AD007


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_D4_AD008


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

description: replicate 1


title: Whole blood, AD, 5872641059_I [ad_mci]

description: replicate 1


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

description: replicate 1


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

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_D4_AD004


title: Whole blood, AD, 5872641070_D [ad_mci]

description: replicate 1


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

description: replicate 1


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

description: replicate 1


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

description: replicate 1


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

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_D4_AD001


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_D3_AD010


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_D3_AD008


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_D3_AD012


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

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_D2_AD012


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_D3_AD001


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_D2_AD010


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_D2_AD008


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

description: replicate 1


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

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_D2_AD007


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_D3_AD006


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_D3_AD004


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

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_D2_AD006


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

description: replicate 1


title: Whole blood, AD, 5872641018_G [ad_mci]

description: replicate 1


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

description: replicate 1


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

description: replicate 1


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

description: replicate 1


title: Whole blood, MCI, 5872641054_F [ad_mci]

description: replicate 1


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

description: replicate 1


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

description: replicate 1


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

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_D2_AD004


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

description: replicate 1


title: Whole blood, MCI, 5786049087_G [ad_mci]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_D2_AD002


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

description: replicate 1


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

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_D2_AD001


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_D1_AD010


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_D1_AD008


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_D1_AD012


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_D1_AD006


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_D1_AD004


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_D1_AD002


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_D1_AD001


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

description: replicate 1

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.


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

description: replicate 1


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

description: replicate 1


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

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_D12_AD012


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

description: replicate 2


title: Whole blood, nfvPPA, 200661920001_E [ftd]

description: replicate 2

value: nfvPPA


title: Whole blood, PSP, 200795790042_K [ftd]

description: replicate 2

value: PSP


title: Whole blood, PSP, 9682760079_F [ftd]

description: replicate 2


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_D12_AD008


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_D12_AD007


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_D12_AD006


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_D12_AD004


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_D12_AD002


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

description: replicate 2

value: bvFTD


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

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_D11_AD012


title: Whole blood, MCI, 5872641031_H [ad_mci]

description: replicate 1


title: Whole blood, CBS, 200661380042_C [ftd]

description: replicate 2

value: CBS


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_D12_AD001


title: Whole blood, bvFTD, 200795790038_B [ftd]

description: replicate 1


title: Whole blood, bvFTD, 200795790038_C [ftd]

description: replicate 1


title: Whole blood, nfvPPA, 200795790038_E [ftd]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_D11_AD010


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_D11_AD008


title: Whole blood, PSP, 200795790035_L [ftd]

description: replicate 1


title: Whole blood, CBS, 200795790035_J [ftd]

description: replicate 1


title: Whole blood, bvFTD, 200795790035_H [ftd]

description: replicate 1


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

description: replicate 1


title: Whole blood, bvFTD, 200795790035_I [ftd]

description: replicate 1


title: Whole blood, PSP, 200795790035_D [ftd]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_D10_AD012


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_D10_AD010


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_D11_AD002


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_D11_AD006


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_D10_AD008


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

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_D11_AD007


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

description: replicate 1


title: Whole blood, svPPA, 200667730024_J [ftd]

description: replicate 1

value: svPPA


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_D10_AD007


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

description: replicate 1


title: Whole blood, bvFTD, 200665010062_J [ftd]

description: replicate 1


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

description: replicate 1


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

description: replicate 1


title: PAC2_Krt5_rep2

city: Shanghai

first: Xuelong

last: Wang

address: No. 100 Banxia Road

country: China

institute: Chinese Academy of Sciences

data_processing:
All ATAC-Seq data sets were trimmed and aligned to zebrafish genome build danRer10 genome using Bowtie2.
Duplicate reads were removed with SAMtools.
MACS2 was used to identify regions of ATAC-seq peaks.
The ATAC-seq peaks were used for known motif enrichment analysis, which were performed using HOMER (v4.9).
Genome_build: danRer10
Supplementary_files_format_and_content: BigWig (bw) files were generated using deepTools.

organism: Danio rerio

source_name: Zebrafish embryonic fibroblast cell line

growth_protocol: Zebrafish TAB lines (hybrid from AB and Tubingen lines) were maintained under an ambient temperature of 27uC with a timercontrolled light period 14 h light and 10 h dark. All experiments were performed in accordance with Animal Care and Use Committee guidelines of Shanghai Ocean University.

extract_protocol: Fresh cells were lysed in lysis buffer (10 mM Tris-HCl at pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630 [Sigma-Aldrich]) for 10 min on ice to prepare the nuclei. Immediately after lysis, nuclei were spun at 500 x g for 5 min to remove the supernatant. Nuclei were then incubated with the Tn5 transposome (Vazyme Biotech, China). Following the tagmentation at 37 °C for 30 min, the products were puriﬁed with QIAquick PCR Purification Kit (Qiagen, Germany), PCR was performed as described in a previous study [1]. After the amplification, libraries were purified with Agencourt Ampure XP beads (Beckman, USA) to remove contaminating primer dimmers and quantitated using Qubit 2.0 Fluorimeter (Invitrogen, USA). All libraries were sequenced on the Illumina HiSeq X Ten with 150 bp paired-end reads (Novogene Biotech, China)

tag: treatment

value: treated with Krt5 for 24h

tag: cell line

value: PAC2 cell line


title: PAC2_WT_rep2

value: untreated


title: PAC2_Krt5_Noggin_rep2

value: treated with Krt5 and Noggin for 24h


title: PAC2_Ktr5_rep1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_D10_AD006


title: PAC2_WT_rep1


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

description: replicate 1

value: Control

value: Male


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_D10_AD004

value: brain

value: MOp


title: Whole blood, CBS, 200665010052_L [ftd]

description: replicate 1

value: Female


title: exosome isolated from the serum of control 3

city: Changzhou

first: Yilin

last: Yang

state: Jiangsu

address: 185#, Juqian Road

department: Modern Medical Research Center

institute: Third Affiliated Hospital of Soochow University

hyb_protocol: DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized was preformed in a Agilent Hybridization Oven overnight at a rotation speed of 20 rpm at 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: Scanned on an Agilent G2565CA scanner.

data_processing: Feature Extraction v10.7 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and genespring software was used to analyze the raw data, which are normalized by quantile normalization.

label_protocol: cDNA labeled with a fluorescent dye (Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction. This procedure has been previously described, and the procedure has been improved by using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio) for producing higher yields of labeled cDNA.

extract_protocol: Exosomes were isolated from serum using the miRCURY Exosome Serum/Plasma Kit (Thermofisher, USA) according to the manufacturer’s instructions. Total RNA was extracted from exosomes and cells by using TRIzol reagent (Thermofisher, USA). The purity and concentration of RNA was analyzed by Nanodrop One (ThermoFisher, USA).

tag: disease state

value: control

value: serum


title: exosome isolated from the serum of control 2


title: exosome isolated from the serum of patient 3

value: postmenopausal osteoporosis


title: exosome isolated from the serum of patient 2


title: exosome isolated from the serum of patient 1


title: exosome isolated from the serum of control 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_D10_AD001

value: SC

value: male


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_D10_AD002

value: female


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_C9_AD012

value: STR


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_C9_AD010


title: Basal expression at P15 [P15d]

city: Rouen cedex

first: Celine

last: Derambure

address: 22 Bvd Gambetta

country: France

institute: INSERM U905

description: Biological replicate 3 of 4, Control in 15 day-old brain vs biological replicate 4

hyb_protocol: Hybridization was performed according to the Agilent instructions for Gene Expression Hybridization Kit (catalog number 5188-5242). Samples were applied to microarrays enclosed in Agilent SureHyb hybridization chambers (65°C, 17H). After hybridization, slides were washed and dried in acetonitril.

scan_protocol: Scanned on an Agilent G2565CA scanner. Images were quantified using Agilent Feature Extraction Software (v 10.5.1.1)

data_processing: Agilent Feature Extraction Software (v 10.5.1.1) was used for data extraction and LOWESS normalization.

source_name: Pool 4 Control_15 days post-natal_brain

label_protocol: Agilent Low input QuickAmp Labeling kit was used according to the manufacturer instructions (catalog number 5190-2306) with 100ng  of total starting RNA.

growth_protocol: Naval Medical Resarch Institute (NMRI)-mice housed in our laboratory. Day of birth was noted 1.

extract_protocol: Total RNA from brain hemisphere (deleted of olfactory bulb and sectionned anterior to colliculus) were extracted using Nucleospin RNA plus kit (Ref 740984-250; Macherey-Nagel) following manufacturer's instructions. RNA Integrity Number was obtained by BioAnalyzer 2100 (Agilent).

treatment_protocol: Animals at day 5 or day 10 were anesthetized using isoflurane. Right carotid was ligatured permanently. After 1 hour back to mother's cage, animals were hypoxied in a humidified-thermostated box using a flow of 8/92% O2/N2 for 40 minutes. Tissues were collected at 3h, 6h 12h or 24h after this t-zero time point. Controls from the same liters were collected at the same time. Control ontogenic basal levels were determined in 4 pools of 6 brains extracted at P2 and P15, each pool hybridized in dye-swaping.

value: Naval Medical Resarch Institute (NMRI)-mouse

tag: post natal days

value: 15 days post-natal

tag: condition

value: Pool 4 Control

tag: sublocalization/tissue

value: Forebrain

source_name: Pool 3 Control_15 days post-natal_brain

value: Pool 3 Control


title: Whole blood, nfvPPA, 200665010052_K [ftd]

description: replicate 1

value: nfvPPA


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_C9_AD008


title: Hypoxia-ischemia + 24h at day 10 [P10+24h-c]

description: Biological replicate 3 of 3. 10 day-old brain harvested 24h after treatment (control vs hyopxia-ischemia).

source_name: control_10 days post-natal_brain

value: 10 days post-natal

source_name: ischemic_10 days post-natal_brain

value: ischemic


title: Basal expression at P2 [P2a ]

description: Biological replicate 2 of 4, Control in 2 day-old brain vs biological replicate 1

source_name: Pool 1 Control_2 days post-natal_brain

value: 2 days post-natal

value: Pool 1 Control

source_name: Pool 2 Control_2 days post-natal_brain

value: Pool 2 Control


title: Basal expression at P15 [P15b]

description: Biological replicate 1 of 4, Control in 15 day-old brain vs biological replicate 2

source_name: Pool 2 Control_15 days post-natal_brain

source_name: Pool 1 Control_15 days post-natal_brain


title: Basal expression at P15 [P15a ]

description: Biological replicate 2 of 4, Control in 15 day-old brain vs biological replicate 1


title: Basal expression at P2 [P2c]

description: Biological replicate 4 of 4, Control in 2 day-old brain vs biological replicate 3

source_name: Pool 3 control_2 days post-natal_brain

value: Pool 3 control

source_name: Pool 4 control_2 days post-natal_brain

value: Pool 4 control


title: Basal expression at P15 [P15c]

description: Biological replicate 4 of 4, Control in 15 day-old brain vs biological replicate 3

source_name: Pool 3 control_15 days post-natal_brain

source_name: Pool 4 control_15 days post-natal_brain


title: Basal expression at P2 [P2d]

description: Biological replicate 3 of 4, Control in 2 day-old brain vs biological replicate 4

source_name: Pool 4 Control_2 days post-natal_brain

source_name: Pool 3 Control_2 days post-natal_brain


title: Basal expression at P2 [P2b]

description: Biological replicate 1 of 4, Control in 2 day-old brain vs biological replicate 2


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

description: replicate 1

source_name: Whole blood

value: Control

value: Female


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

description: replicate 1

value: Male


title: Whole blood, bvFTD, 200665010052_D [ftd]

description: replicate 1

value: bvFTD


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_C9_AD006

source_name: C57BL/6J P56 Mouse Brain

value: brain

value: MOp

value: SC

value: female


title: Whole blood, nfvPPA, 200665010044_G [ftd]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_D11_AD001

value: male


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_C9_AD001


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_D12_AD010

value: STR


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_C8_AD012


title: Hypoxia-ischemia + 12h at day 10 [P10+12h-a]

description: Biological replicate 1 of 3. 10 day-old brain harvested 12h after treatment (control vs hyopxia-ischemia).

value: Naval Medical Resarch Institute (NMRI)-mouse

value: 10 days post-natal

value: control

value: Forebrain


title: Hypoxia-ischemia + 24h at day 10 [P10+24h-b]

description: Biological replicate 2 of 3. 10 day-old brain harvested 24h after treatment (control vs hyopxia-ischemia).

value: ischemic


title: Hypoxia-ischemia + 12h at day 10 [P10+12h-c]

description: Biological replicate 3 of 3. 10 day-old brain harvested 12h after treatment (control vs hyopxia-ischemia).


title: Hypoxia-ischemia + 24h at day 10 [P10+24h-a]

description: Biological replicate 1 of 3. 10 day-old brain harvested 24h after treatment (control vs hyopxia-ischemia).


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_C8_AD010


title: Hypoxia-ischemia + 12h at day 10 [P10+12h-b]

description: Biological replicate 2 of 3. 10 day-old brain harvested 12h after treatment (control vs hyopxia-ischemia).


title: Hypoxia-ischemia + 6h at day 10 [P10+6h-c]

description: Biological replicate 3 of 3. 10 day-old brain harvested 6h after treatment (control vs hyopxia-ischemia).


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

description: replicate 1


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

description: replicate 1


title: Whole blood, svPPA, 200665010039_F [ftd]

description: replicate 1

value: svPPA


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_C8_AD007


title: Hypoxia-ischemia + 6h at day 10 [P10+6h-b]

description: Biological replicate 2 of 3. 10 day-old brain harvested 6h after treatment (control vs hyopxia-ischemia).


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_C8_AD006


title: Hypoxia-ischemia + 6h at day 10 [P10+6h-a]

description: Biological replicate 1 of 3. 10 day-old brain harvested 6h after treatment (control vs hyopxia-ischemia).


title: Hypoxia-ischemia + 3h at day 10 [P10+3h-b]

description: Biological replicate 2 of 3. 10 day-old brain harvested 3h after treatment (control vs hyopxia-ischemia).


title: Hypoxia-ischemia + 3h at day 10 [P10+3h-c]

description: Biological replicate 3 of 3. 10 day-old brain harvested 3h after treatment (control vs hyopxia-ischemia).


title: Hypoxia-ischemia + 3h at day 10 [P10+3h-a]

description: Biological replicate 1 of 3. 10 day-old brain harvested 3h after treatment (control vs hyopxia-ischemia).


title: Hypoxia-ischemia + 12h at day 5 [P5+12h-c]

description: Biological replicate 3 of 3. 5 day-old brain harvested 12h after treatment (control vs hyopxia-ischemia).

source_name: control_5 days post-natal_brain

value: 5 days post-natal

source_name: ischemic_5 days post-natal_brain


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

description: replicate 1

value: Control


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

description: replicate 1

value: Female


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

description: replicate 1

value: Male


title: Hypoxia-ischemia + 24h at day 5 [P5+24h-c]

description: Biological replicate 3 of 3. 5 day-old brain harvested 24h after treatment (control vs hyopxia-ischemia).


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_C8_AD008


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

description: replicate 1


title: Hypoxia-ischemia + 24h at day 5 [P5+24h-a]

description: Biological replicate 1 of 3. 5 day-old brain harvested 24h after treatment (control vs hyopxia-ischemia).


title: PAC2_Krt5_Noggin_rep1

source_name: Zebrafish embryonic fibroblast cell line

value: treated with Krt5 and Noggin for 24h

value: PAC2 cell line


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_C8_AD001

value: brain

value: MOp


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_C8_AD004

value: SC


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_C7_AD012

value: female


title: Hypoxia-ischemia + 24h at day 5 [P5+24h-b]

description: Biological replicate 2 of 3. 5 day-old brain harvested 24h after treatment (control vs hyopxia-ischemia).


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_C7_AD010

value: STR

value: male


title: Vgamma1.2_gdT_rep3

city: Vancouver

first: Kelly

middle: M

last: McNagny

state: BC

address: 2222 Health Sciences Mall

country: Canada

institute: University of British Columbia

data_processing:
Library strategy: DNA-seq
Demultiplexing software (BCL2FASTQ2) was used to generate fastq files
Sequenced reads were aligned to TCR genes of mm10 using MiXCR v3.0.13
Correction for sequencing error and determination of TCR clonotype functionality were done using vdjtools v1.2.1
Clonotype diversity calculation was done on tcR R package (immunarch)
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with TCR clonotype counts and their nucleotide/aa sequences

source_name: gdT cells

extract_protocol:
Single-cell suspensions from lung tissues were FACS sorted and the genomic DNA were extracted shortly after from the purified populations
Libraries were prepared for sequencing using standard Illumina protocols

value: Lung

tag: genotype

value: WT


title: Vgamma1.2_gdT_rep2


title: Hypoxia-ischemia + 12h at day 5 [P5+12h-b]

description: Biological replicate 2 of 3. 5 day-old brain harvested 12h after treatment (control vs hyopxia-ischemia).

value: Naval Medical Resarch Institute (NMRI)-mouse

value: control

value: Forebrain


title: Vgamma1.2_ILC2_rep3


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

description: replicate 1


title: Hypoxia-ischemia + 3h at day 5 [P5+3h-c]

description: Biological replicate 3 of 3. 5 day-old brain harvested 3h after treatment (control vs hyopxia-ischemia).

value: 5 days post-natal

value: ischemic


title: Hypoxia-ischemia + 12h at day 5 [P5+12h-a]

description: Biological replicate 1 of 3. 5 day-old brain harvested 12h after treatment (control vs hyopxia-ischemia).


title: Vgamma1.2_gdT_rep1


title: Hypoxia-ischemia + 6h at day 5 [P5+6h-b]

description: Biological replicate 2 of 3. 5 day-old brain harvested 6h after treatment (control vs hyopxia-ischemia).


title: Hypoxia-ischemia + 6h at day 5 [P5+6h-c]

description: Biological replicate 3 of 3. 5 day-old brain harvested 6h after treatment (control vs hyopxia-ischemia).


title: Vgamma1.2_ILC2_rep2


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_C7_AD006


title: Hypoxia-ischemia + 6h at day 5 [P5+6h-a]

description: Biological replicate 1 of 3. 5 day-old brain harvested 6h after treatment (control vs hyopxia-ischemia).


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_C7_AD008


title: Whole blood, bvFTD, 200665010029_F [ftd]

description: replicate 1

value: bvFTD


title: Hypoxia-ischemia + 3h at day 5 [P5+3h-a]

description: Biological replicate 1 of 3. 5 day-old brain harvested 3h after treatment (control vs hyopxia-ischemia).


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

description: replicate 1

value: Control

value: Female


title: Hypoxia-ischemia + 3h at day 5 [P5+3h-b]

description: Biological replicate 2 of 3. 5 day-old brain harvested 3h after treatment (control vs hyopxia-ischemia).


title: Whole blood, svPPA, 200665010062_I [ftd]

description: replicate 1

value: svPPA


title: Whole blood, bvFTD, 200665010029_C [ftd]

description: replicate 1

value: Male


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

description: replicate 1


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

description: replicate 1


title: Vgamma2_gdT_rep2


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

description: replicate 1


title: Vgamma2_gdT_rep1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_C7_AD001

value: brain

value: MOp


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_C7_AD004

value: SC


title: Vgamma1.2_ILC2_rep1


title: Vgamma2_ILC2_rep2


title: Vgamma2_ILC2_rep1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_C6_AD012

value: STR

value: female


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_C6_AD010

value: male


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_C6_AD008


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_C6_AD006


title: 141-2 (RNA-seq)

city: brookline

first: Harrison

middle: Wren

last: Gabel

state: Massachusetts

address: 220 longwood avenue

department: Neurbiology

institute: Harvard Medical School

data_processing:
Raw FASTQ files were trimmed with Trim Galore, using a quality filter of 20, then rRNA sequences were filtered out using Bowtie, using rRNA sequences from Mus Musculus obtained from the NCBI sequence database (see Key Resources Table). The unaligned reads from this step were then aligned to mm9 using STAR (Dobin et al., 2013), using the default parameters. Reads mapping to multiple regions in the genome were then filtered out, and uniquely mapping reads were converted to BED files. Intronic and exonic reads were then separated. To do this, splice-site reads were first filtered out of the BED read files, then reads that mapped entirely within exons were added to the splice-site reads to make the exonic read file. All remaining reads that overlapped introns were considered intronic reads. Finally, reads were assigned to genes using bedtools coverage -counts.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-separated table (with header) of genes, identifiers, and gene-associated exonic RNA coverage from each sample, and the results of differential expression analysis

source_name: Cortex

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

extract_protocol:
Brain tissue was dissected from DNMT3AKO/+ and WT littermate mice in ice-cold PBS, flash-frozen in liquid nitrogen, and stored at -80°C.
RNA libraries were generated from 250 ng of RNA with NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB) using a modified amplification protocol (37°C, 15 minutes; 98°C, 30 seconds; [98°C, 10 seconds; 65°C, 30 seconds; 72°C, 30 seconds]x13; 72°C, 5 minutes; 4°C hold).
RNA was sequenced sequenced using Illumina HiSeq3000 1x50bp with the Genome Technology Access Center at Washington University in St. Louis, typically yielding 15-30 million single-end reads per sample.

value: wild type

value: 8 weeks


title: 141-4 (RNA-seq)

value: Heterozygous KO


title: 119-1 (RNA-seq)


title: 141-3 (RNA-seq)


title: 119-2 (RNA-seq)


title: 047-1 (RNA-seq)


title: 141-1 (RNA-seq)


title: Whole blood, Control, 200665010002_B [ftd]

description: replicate 1


title: 048-2 (RNA-seq)


title: Vgamma2_ILC2_rep3

value: Lung

value: WT


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_C6_AD004


title: 046-2 (RNA-seq)


title: 047-2 (RNA-seq)


title: 046-1 (RNA-seq)


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_C6_AD001


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_C5_AD012


title: Whole blood, Control, 200665010002_A [ftd]

description: replicate 1


title: 048-3 (RNA-seq)


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_C5_AD010


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

description: replicate 1


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

description: replicate 1


title: Whole blood, bvFTD, 200665010062_C [ftd]

description: replicate 1


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

description: replicate 1


title: 139-3 (RNA-seq)


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

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_C5_AD008


title: 139-2 (RNA-seq)


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_C5_AD006


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

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_C5_AD007


title: DLBCL derived cell line U2932_3

city: Copenhagen

first: Nicolai

last: Krogh

address: Blegdamsvej 3B

department: Department of Cellular and Molecular Medicine

country: Denmark

institute: University of Copenhagen

description:
U2932_3
whole cell RNA

library_source: transcriptomic

data_processing:
Library strategy: RiboMeth-seq
Barcode separation using python script
Adaptor trimming using Cutadapt v. 2.0
Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1
Counting read ends and calculating RiboMeth-seq scores using python scripts
Genome_build: RDNA reference sequence from Krogh et al, NAR 2016
Supplementary_files_format_and_content: MS Excel file contains 5' and 3' read count and calculated RiboMeth-seq score at all positions in the rRNA sequence.

source_name: Cell line

extract_protocol:
Tissue and tumor samples were homogenized prior to RNA extraction, otherwise was whole cell RNA extracted using Trizol according to the manufacturer.
RiboMeth-seq: 5-10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20-40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2',3' cyclic phosphate and 5' phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U, Christensen-Dalsgaard M, Krogh N, Sabarinathan R, Gorodkin J, Nielsen H. Profiling of ribose methylations in RNA by high-throughput sequencing. Angewandte Chemie. 2015;54(2):451-5 for detailed description

tag: sample type

value: DLBCL derived cell line


title: DLBCL derived cell line U2932_2

description:
U2932_2
whole cell RNA


title: Adult Skeletal_muscle_3

description:
Skeletal_muscle_3
whole cell RNA

source_name: Tissue

value: Adult


title: Adult Skeletal_muscle_1

description:
Skeletal_muscle_1
whole cell RNA


title: DLBCL derived cell line RL_3

description:
RL_3
whole cell RNA


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_C5_AD004


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

description: replicate 1

tag: diagnosis

value: Control


title: DLBCL derived cell line U2932_1

description:
U2932_1
whole cell RNA


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

description: replicate 1

tag: Sex


title: Whole blood, Control, 200661920039_G [ftd]

description: replicate 1

tag: batch


title: DLBCL derived cell line RL_1

description:
RL_1
whole cell RNA


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_C4_AD012

tag: strain


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_C5_AD001

tag: age


title: Adult reactive_lymphnode_02-15017_3

description:
reactive_lymphnode_02-15017_3
whole cell RNA


title: Adult reactive_lymphnode_98-21123_1

description:
reactive_lymphnode_98-21123_1
whole cell RNA


title: Adult reactive_lymphnode_98-21123_3

description:
reactive_lymphnode_98-21123_3
whole cell RNA


title: Adult reactive_lymphnode_98-21123_2

description:
reactive_lymphnode_98-21123_2
whole cell RNA


title: Adult reactive_lymphnode_02-15017_2

description:
reactive_lymphnode_02-15017_2
whole cell RNA


title: Adult reactive_lymphnode_02-15017_1

description:
reactive_lymphnode_02-15017_1
whole cell RNA


title: DLBCL derived cell line RL_2

description:
RL_2
whole cell RNA


title: Adult reactive_lymphnode_01-30628_3

description:
reactive_lymphnode_01-30628_3
whole cell RNA


title: Adult reactive_lymphnode_01-30628_1

description:
reactive_lymphnode_01-30628_1
whole cell RNA


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_C4_AD010

tag: tissue


title: Adult reactive_lymphnode_01-30628_2

description:
reactive_lymphnode_01-30628_2
whole cell RNA


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_C4_AD008

tag: source


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

description: replicate 1

value: Female


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

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_C4_AD007

tag: target


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

description: replicate 1


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

description: replicate 1


title: DLBCL derived cell line OCI-Ly3_3

description:
OCI-Ly3_3
whole cell RNA


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

description: replicate 1


title: Whole blood, PSP, 200661920037_E [ftd]

description: replicate 1

value: PSP


title: Whole blood, Control, 200661920037_A [ftd]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_C4_AD006

tag: gender


title: DLBCL derived cell line OCI-Ly3_2

description:
OCI-Ly3_2
whole cell RNA


title: Whole blood, nfvPPA, 200661920037_B [ftd]

description: replicate 1

value: nfvPPA


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_C4_AD002

value: brain


title: Adult Liver_2

description:
Liver_2
whole cell RNA


title: Adult Liver_1

description:
Liver_1
whole cell RNA


title: Adult Liver_3

description:
Liver_3
whole cell RNA


title: DLBCL derived cell line HT_3

description:
HT_3
whole cell RNA


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_C3_AD012

value: MOp


title: DLBCL derived cell line HT_1

description:
HT_1
whole cell RNA


title: Tumor DLBCL_9016714_2

description:
DLBCL_9016714_2
whole cell RNA

value: Tumor


title: Tumor DLBCL_9016714_3

description:
DLBCL_9016714_3
whole cell RNA


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_C3_AD010

value: STR


title: DLBCL derived cell line OCI-Ly3_1

description:
OCI-Ly3_1
whole cell RNA


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_C4_AD001

value: SC


title: Whole blood, svPPA, 200661920031_H [ftd]

description: replicate 1

value: svPPA

value: Male


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

description: replicate 1


title: Tumor DLBCL_8019179_3

description:
DLBCL_8019179_3
whole cell RNA


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

description: replicate 1


title: Whole blood, PSP, 200661920015_K [ftd]

description: replicate 1


title: Tumor DLBCL_8019179_2

description:
DLBCL_8019179_2
whole cell RNA


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

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_C3_AD007

value: male


title: Tumor DLBCL_7019632_3

description:
DLBCL_7019632_3
whole cell RNA


title: Tumor DLBCL_8019179_1

description:
DLBCL_8019179_1
whole cell RNA


title: DLBCL derived cell line HT_2

description:
HT_2
whole cell RNA


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_C3_AD008

value: female


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_C3_AD006


title: Tumor DLBCL_7019632_1

description:
DLBCL_7019632_1
whole cell RNA


title: Tumor DLBCL_7019632_2

description:
DLBCL_7019632_2
whole cell RNA


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_C3_AD002


title: Tumor DLBCL_9016714_1

description:
DLBCL_9016714_1
whole cell RNA


title: Tumor DLBCL_6008010_3

description:
DLBCL_6008010_3
whole cell RNA


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

description: replicate 1


title: Tumor DLBCL_6008010_2

description:
DLBCL_6008010_2
whole cell RNA


title: Tumor DLBCL_5014505_3

description:
DLBCL_5014505_3
whole cell RNA


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_C3_AD001


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

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_C3_AD004


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

description: replicate 1


title: Tumor DLBCL_5012726_2

description:
DLBCL_5012726_2
whole cell RNA


title: Tumor DLBCL_5012726_3

description:
DLBCL_5012726_3
whole cell RNA


title: Tumor DLBCL_5014505_2

description:
DLBCL_5014505_2
whole cell RNA


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_C2_AD012


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_C2_AD010


title: Tumor DLBCL_5014505_1

description:
DLBCL_5014505_1
whole cell RNA


title: Tumor DLBCL_5012726_1

description:
DLBCL_5012726_1
whole cell RNA


title: Tumor DLBCL_3017349_2

description:
DLBCL_3017349_2
whole cell RNA


title: Tumor DLBCL_6008010_1

description:
DLBCL_6008010_1
whole cell RNA


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_C2_AD007


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_C2_AD008


title: Tumor DLBCL_2023999_2

description:
DLBCL_2023999_2
whole cell RNA


title: Tumor DLBCL_3017349_1

description:
DLBCL_3017349_1
whole cell RNA


title: Tumor DLBCL_2023999_3

description:
DLBCL_2023999_3
whole cell RNA


title: Tumor DLBCL_3017349_3

description:
DLBCL_3017349_3
whole cell RNA


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

description: replicate 1


title: Tumor DLBCL_2023999_1

description:
DLBCL_2023999_1
whole cell RNA


title: Tumor DLBCL_13-34950_3

description:
DLBCL_13-34950_3
whole cell RNA


title: Whole blood, nfvPPA, 200661920011_H [ftd]

description: replicate 1


title: Whole blood, svPPA, 200661920014_B [ftd]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_C2_AD004


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

description: replicate 1


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

description: replicate 1


title: Whole blood, bvFTD, 200661920003_D [ftd]

description: replicate 1

value: bvFTD


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_C2_AD002


title: Tumor DLBCL_13-34950_2

description:
DLBCL_13-34950_2
whole cell RNA


title: Tumor DLBCL_13-34950_1

description:
DLBCL_13-34950_1
whole cell RNA


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_C2_AD006


title: Tumor DLBCL_13-34824_3

description:
DLBCL_13-34824_3
whole cell RNA


title: Tumor DLBCL_13-34824_2

description:
DLBCL_13-34824_2
whole cell RNA


title: Tumor DLBCL_12-33637_2

description:
DLBCL_12-33637_2
whole cell RNA


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_C1_AD012


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_C1_AD010


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

description: replicate 1


title: Tumor DLBCL_12-33637_3

description:
DLBCL_12-33637_3
whole cell RNA


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_C2_AD001


title: Tumor DLBCL_12-33637_1

description:
DLBCL_12-33637_1
whole cell RNA


title: Whole blood, bvFTD, 200661920003_B [ftd]

description: replicate 1


title: Tumor DLBCL_13-34824_1

description:
DLBCL_13-34824_1
whole cell RNA


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

description: replicate 1


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

description: replicate 1


title: Tumor DLBCL_12-003909_3

description:
DLBCL_12-003909_3
whole cell RNA


title: Adult Skeletal_muscle_2

description:
Skeletal_muscle_2
whole cell RNA


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_C1_AD008


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_C1_AD007


title: Tumor DLBCL_12-003909_1

description:
DLBCL_12-003909_1
whole cell RNA


title: Whole blood, bvFTD, 200661920002_G [ftd]

description: replicate 1


title: Tumor DLBCL_11-14420_2

description:
DLBCL_11-14420_2
whole cell RNA


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_C1_AD006


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_C1_AD004


title: Tumor DLBCL_11-14420_3

description:
DLBCL_11-14420_3
whole cell RNA


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_C1_AD002


title: Tumor DLBCL_11-14420_1

description:
DLBCL_11-14420_1
whole cell RNA


title: siPPP1R2 transfected, rep1

city: New York

first: Won-Min

last: Song

state: New York

address: One Gustave L. Levy Place, Box 1123

institute: Icahn school of medicine at Mount Sinai

data_processing:
The reads were aligned using STAR 2-pass mapping to hg19 genome
Gene expressions for coding sequences were called by utilizing “featureCounts()” function from R package Rsubread by counting mapped reads to exonic regions, and summarizing to “gene_id” as the meta feature (GTF.featureType = "exon",GTF.attrType = "gene_id").
Multiple mapping reads were also counted as fractionated across the mapped regions (countMultiMappingReads = TRUE, fraction = TRUE).
The resulting count matrix was normalized by Transcripts Per Million (TPM), followed by quantile-normalization and log2-transformation.
Genome_build: hg19
Supplementary_files_format_and_content: tab-deliminated text file. Contains log2-transformed TPM values.

source_name: SkMel147 cells

growth_protocol: Cell line SKmel147 was obtained from Dr. Alan Houghton’s laboratory (MSKCC, New York). Cells were cultured in DMEM (Invitrogen) containing 10% (v/v) FBS and 1% (v/v) penicillin/streptomycin. Cell lines were maintained in a 5% CO2 incubator at 37C. Cell lines were routinely tested to exclude Mycoplasma contamination.

extract_protocol:
Total RNA was extracted using miRNeasy QIAGEN mini kit according to the manufacturer’s protocol. 500 ng of RNA were reverse transcribed using Taqman RT reagents (Applied Biosystems) with random hexamers following manufacturer’s recommendations. Transcripts were quantified by real-time qPCR using Power SYBR Green PCR MasterMix (Applied Biosystems) in StepOne System (ABI). Expression levels are calculated relative to housekeeping gene, GAPDH.
Total RNA was extracted 72 hr post transfection of siNTC, siZNF180, siZNF347 or siPPP1R2 in SKmel147 cell line in 3 replicates. RNA was extracted using miRNeasy QIAGEN mini kit. RNA was then processed with Ribo-Zero rRNA Removal Kit (Illumina) to remove rRNA, and further processed into sequencing libraries using Illumina TruSeq Stranded Total RNA Library Prep, following manufacturer’s protocol. All libraries were sequenced on Illumina HiSeq2500 ($150M, 50 bp paired-end).

treatment_protocol: Transfection conditions were optimized for SKmel147 melanoma cell lines using fluorescein labeled oligos (Block-IT, Invitrogen). Liposomal transfection complexes with siRNA pools for each of the candidate genes and with non-targeting control (siRNA ON-target plus SMARTpools, Dharmacon, 50 nM) were generated with Lipofectamine 2000 (Invitrogen), following manufacturer’s recommendations. Media was changed after 6 hr incubation with liposomal complexes. 48 hr after initiation of transfection, cells were used for RNA extraction, or for proliferation or invasion assays.

tag: treatment

value: siPPP1R2 transfected


title: siPPP1R2 transfected, rep3


title: siPPP1R2 transfected, rep2


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_C1_AD001


title: Tumor DLBCL_12-003909_2

description:
DLBCL_12-003909_2
whole cell RNA


title: Tumor DLBCL_09-32283_3

description:
DLBCL_09-32283_3
whole cell RNA


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

description: replicate 1


title: Tumor DLBCL_09-32283_2

description:
DLBCL_09-32283_2
whole cell RNA


title: siZNF180 transfected, rep3

value: siZNF180 transfected


title: normoxia

city: Toyama

first: Yoshiaki

last: Tabuchi

state: Toyama

address: 2630 Sugitani

department: Life Science Research Center

country: Japan

institute: University of Toyama

hyb_protocol: After fragmentation, the biotinylated cRNA was hybridized to arrays at 45°C for 16 h.

scan_protocol: The arrays were washed, stained with streptavidin-phycoerythrin and scanned with a probe array scanner (Affymetrix).

data_processing:
GeneChip Analysis Suite
affymetrix-algorithm-name = rma
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.3.1.187

label_protocol: 500 ng of total RNA was used to synthesize cRNA with a GeneChip 3’ IVT Express Kit (Affymetrix).

growth_protocol: Human cervical carcinoma cell line HeLa cells were cultured at 37°C in Dulbecco’s modified Eagle medium (DMEM) containing 10% FBS, 100 U/mL penicillin, and 100 μg/mL streptomycin.

extract_protocol: Total RNAs were prepared from cells using a total RNA isolation kit (Qiagen) along with on-column DNase I treatment. RNA quality was analyzed using a Bioanalyzer 2100 (Agilent Technologies). RNA samples with RIN (RNA integrity number) values >9.5 were considered acceptable..

treatment_protocol: Cells were incubated in a well-humidified 5% CO2 and 95% air for the normoxic culture, or in a RUSKINN INVIVO2 500 (Ruskinn Technology Limited) for hypoxic culture at < 0.1% O2.

tag: cell line

value: HeLa

tag: cell tye

value: Human cervical cervical epithelial adenocarcinoma cell line

value: 31 years

tag: tissue source

value: cervix

tag: life span

value: infinite

tag: morphology

value: epithelial-like


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_C12_AD012

value: brain

value: MOp


title: Whole blood, bvFTD, 200661920002_I [ftd]

description: replicate 1


title: Whole blood, CBS, 200661920001_H [ftd]

description: replicate 1

value: CBS

value: Female


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

description: replicate 1

value: Control


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

description: replicate 1

value: Male


title: Whole blood, PSP, 200661380042_B [ftd]

description: replicate 1

value: PSP


title: Whole blood, CBS, 200661920002_A [ftd]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_C12_AD010

value: STR

value: male


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

description: replicate 1


title: hypoxia


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

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_C12_AD008

value: female


title: siZNF180 transfected, rep1

value: siZNF180 transfected


title: siZNF347 transfected, rep3

value: siZNF347 transfected


title: Tumor DLBCL_0615594_3

description:
DLBCL_0615594_3
whole cell RNA

value: Tumor


title: Tumor DLBCL_09-32283_1

description:
DLBCL_09-32283_1
whole cell RNA


title: siZNF180 transfected, rep2


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_C12_AD007


title: Tumor DLBCL_0615594_2

description:
DLBCL_0615594_2
whole cell RNA


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_C12_AD006

value: SC


title: siZNF347 transfected, rep2


title: Tumor DLBCL_0615594_1

description:
DLBCL_0615594_1
whole cell RNA


title: siZNF347 transfected, rep1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_C12_AD002


title: Whole blood, nfvPPA, 200363680015_H [ftd]

description: replicate 1

value: nfvPPA


title: Tumor DLBCL_04-19157_3

description:
DLBCL_04-19157_3
whole cell RNA


title: non-transfected control, rep3

value: non-transfected control


title: Tumor DLBCL_04-19157_2

description:
DLBCL_04-19157_2
whole cell RNA


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_C11_AD012


title: Tumor DLBCL_04-19157_1

description:
DLBCL_04-19157_1
whole cell RNA


title: non-transfected control, rep2


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_C11_AD010


title: Whole blood, svPPA, 200363680018_G [ftd]

description: replicate 1

value: svPPA


title: Tumor DLBCL_02-9067_3

description:
DLBCL_02-9067_3
whole cell RNA


title: Tumor DLBCL_02-9067_2

description:
DLBCL_02-9067_2
whole cell RNA


title: non-transfected control, rep1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_C11_AD008

value: brain


title: Tumor DLBCL_02-9067_1

description:
DLBCL_02-9067_1
whole cell RNA


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_C11_AD006

value: MOp


title: Adult Brain_3

description:
Brain_3
whole cell RNA

value: Adult


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_C11_AD004


title: K562_H3K4me3_hex_p-w_(20201015_SH_Hs_K4me3_hex1005)

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description: CUTAC Post-wash for K4me3 20 min hex in K562 cells at home

data_processing:
Genome_build: UCSC hg19
1. We used Bowtie2 2.3.4.3 with options "--end-to-end --very-sensitive --no-mixed --no-discordant -q --phred33 -I 10 -X 700" to map the paired-end 25bp reads to hg19 of Homo sapiens genomic sequence obtained from UCSC. 2. We extracted properly paired reads from Homo sapiens alignments to generate a bed files <chr> <start> <stop> <length> <strand> (Supplementary file hg19_fragments.bed.gz).  3. We used bedtools genomecov to make normalized count bedgraph files, which are the fraction of counts at each base pair scaled by the size of the reference sequence (3095693983) so that if the scaled counts were uniformly distributed there would be 1 at each position (Supplementary file normalized_counts.bedgraph.gz).

source_name: CUT&TAG-direct

extract_protocol:
CUTnTag-direct_v2_Protocols.io.pdf
CUT&Tag uses tagmentation in which the barcoded adapters are integrated on both sides of the insert, so that the DNA that is released is already a barcoded library. PMID:31036827

tag: antibody

value: H3K4me3 Active Motif cat# 39159 lot# 22118006

tag: cell type

value: K562 human immortalised myelogenous leukemia cell line


title: K562_H3K4me3_con_p-w_(20201015_SH_Hs_K4me3_con_1005)

description: CUTAC Post-wash for K4me3 20 min in K562 cells at home


title: K562_H3K4me3_CnT_4_(20201015_SH_Hs_K4me3_1005)

description: CUT&Tag K4me3 in K562 cells at home


title: Adult Brain_2

description:
Brain_2
whole cell RNA

tag: sample type


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_C11_AD002


title: K562_H3K4me2_p-w_2_(20201012_SH_Hs_K4me2M_1004)

description: CUTAC Post-wash for K4me2 in K562 cells at home

value: H3K4me2 Epicypher cat# 13-0027


title: Adult Brain_1

description:
Brain_1
whole cell RNA


title: K562_H3K4me3_dmf_p-w_(20201015_SH_Hs_K4me3_dmf1005)

description: CUTAC Post-wash for K4me3 20 min dmf in K562 cells at home


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_C11_AD007


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_C11_AD001


title: K562_H3K4me2_p-w_1_(20201012_SH_Hs_K4me2E_1004)


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_C10_AD012


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_C10_AD010


title: K562_H3K4me2_hex_p-w_(20201012_SH_Hs_K4me2E_hex_1004)

description: CUTAC Post-wash for K4me2 20 min hex in K562 cells at home


title: K562_H3K4me2_hexRT_p-w_(20201012_SH_Hs_K4me2E_hexRT_1004)

description: CUTAC Post-wash for K4me2 20 min hex 22deg in K562 cells at home


title: K562_H3K4me2_dmf_p-w_(20201012_SH_Hs_K4me2E_dmf_1004)

description: CUTAC Post-wash for K4me2 20 min dmf in K562 cells at home


title: K562_H3K4me2_con_p-w_2_(20201012_SH_Hs_K4me2M_con_1004)

description: CUTAC Post-wash for K4me2 20 min in K562 cells at home


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_C10_AD008


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_C10_AD006


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_C10_AD007


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

description: replicate 1

tag: diagnosis

value: Control

tag: Sex

value: Male


title: Whole blood, nfvPPA, 200363680015_C [ftd]

description: replicate 1

value: Female

tag: batch


title: -Serine/Glycine Replicate 5_From Donor 5

city: Birmingham

first: Anna

middle: E

last: Thalacker-Merc er

state: Alabama

address: 1720 University Blvd

institute: University of Alabama at Birmingham

data_processing:
Cutadapt v1.8 was used to trim low quality reads and adaptor sequences (parameters: -m 50 -q 20 -a AGATCGGAAGAGCACACGTCTGAACTCCAG–match-read-wild cards)
Tophat v2.1 was used to map reads to the reference genome (parameters:-library-type=fr-firststrandon-no-novel-juncs-G<ref_genes.gtf>)
Differential gene expression analysis was performed using edgeR
Only genes with at least 2 counts per million in at least three of the samples were retained for analysis.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include CPM values for RNA-seq output

source_name: Human Muscle Progenitor Cells

growth_protocol: human muscle progenitor cells from 5 different donors were seeded on collagen (Type 1 rat tail) coated dishes.

extract_protocol:
RNA was isolated using an Omega E.Z.N.A.® Total RNA Kit I
The NEBNext Ultra II RNA Library Prep Kit (New England Biolabs) was used to generate TruSeq-barcoded RNA-Seq libraries. Libraries were quantified with the Qubit 2.0 (dsDNA HS kit; Thermo Fisher) and size distribution was measured with a Fragment Analyzer (Advanced Analytical) before pooling. A NextSeq500 (Illumina) was used for sequencing, and a minimum of 20 M single-end 75 bp reads per library were obtained.

treatment_protocol: +SG samples were harvested after 5 days of culture in a specially formulated DMEM with 1000 uM of serine and glycine and -SG samples were harvested after 5 days of culture in a specially formulated DMEM without serine and glycine

value: minus serine/glycine


title: K562_H3K4me2_con_p-w_1_(20201012_SH_Hs_K4me2E_con_1004)

description: CUTAC Post-wash for K4me2 20 min in K562cells at home


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_C10_AD004

tag: strain

tag: age

value: male


title: Whole blood, bvFTD, 200400280017_A [ftd]

description: replicate 1

value: bvFTD


title: Whole blood, bvFTD, 200363680015_G [ftd]

description: replicate 1


title: Whole blood, PSP, 200400280015_J [ftd]

description: replicate 1

value: PSP


title: Whole blood, bvFTD, 200400280016_G [ftd]

description: replicate 1


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

description: replicate 1


title: Whole blood, PSP, 200400280015_K [ftd]

description: replicate 1


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

description: replicate 1


title: Control IP-2 (no GFP Ab)

city: MONTPELLIER

first: Xavier

last: Pichon

state: herault

address: 1919 route de Mende

department: IGMM

institute: CNRS

hyb_protocol: Samples were hybridized with GeneChip Human Transcriptome Array 2.0 chips (Affymetrix) on an Affymetrix platform (Thermo Fisher).

scan_protocol: Array scanning was performed on a GeneChip Scanner 3000 7G according to the manufacturer's instruction (Affymetrix).

data_processing:
Affymetrix Expression Console software version 1.4.1.46 was used
ProcessedDatas_KIF1C.xls contains the processed signal intensity for IP-KIF1C over IP-Control for each affymetrix probesets.

source_name: Control IP-2 (no GFP Ab)

label_protocol: The resulting RNAs were amplified and converted into cDNAs by the WT PICO kit (Thermo Fisher).

growth_protocol: HeLa cells stably expressing the a KIF1C-GFP fusion from a Bacterial Artifical Chromosome (BAC) were grown to near confluence in 10 cm plates  in DMEM, 10% FCS, at 37°C, and two plates were used per Immunoprecipitation (IP),

extract_protocol: Beads were then incubated with Trizol to extract RNAs, and RNA purification was done as recommended by the manufacturer.

treatment_protocol: Cells were rinsed in ice-cold PBS, and all subsequent manipulations were performed at 4°C. Cells were scraped in HNTG buffer (20 mM HEPES-KOH pH 7.9, 150 mM NaCl, 1% Triton X-100, 10% glycerol, 1 mM MgCl2, 1 mM EGTA), containing an antiprotease cocktail (Roche). Cells were incubated for 20 minutes on a rotating wheel, and cellular debris were the removed by centrifugating the extracts 10 minutes at 20,000g. Beads coated with GFP-trap antibody (ChromoTek), or uncoated as control, were washed in HNTG (25 l of beads per IP). Beads were incubated 1h with a control extract to saturate non-specific binding and then incubated with the proper extract. After 4h of incubation on a rotating wheel, beads were washed four times in HNGT with anti-protease, and twice with PBS.

value: HeLa BAC KIF1C-GFP #3843


title: Whole blood, nfvPPA, 200400280016_A [ftd]

description: replicate 1

value: nfvPPA


title: -Serine/Glycine Replicate 4_From Donor 4


title: Whole blood, nfvPPA, 200373830057_F [ftd]

description: replicate 1


title: Whole blood, bvFTD, 200373830057_D [ftd]

description: replicate 1


title: Whole blood, bvFTD, 200373830048_K [ftd]

description: replicate 1


title: Whole blood, nfvPPA, 200373830050_I [ftd]

description: replicate 1


title: Whole blood, PSP, 200373830057_A [ftd]

description: replicate 1


title: Whole blood, bvFTD, 200373830050_B [ftd]

description: replicate 1


title: GFP-trap IP-1

source_name: GFP-trap IP-1

value: GFP-Trap


title: Whole blood, bvFTD, 200373830050_F [ftd]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_C10_AD002

tag: tissue

tag: source

value: SC

value: female


title: -Serine/Glycine Replicate 3_From Donor 3


title: H1_H3K4me2_p-w_(20201012_SH_Hs_H1K4me2E_1005)

description: CUT&Tag Post-wash for K4me2 60 min in H1 ES cells at home

value: H1 human embryonic stem cell line


title: -Serine/Glycine Replicate 2_From Donor 2


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_B9_AD012

value: brain

value: MOp

tag: target

value: STR

tag: gender


title: H1_H3K4me2_hdRT_p-w_(20201012_SH_Hs_H1K4me2E_hdRT_1005)

description: CUTAC Post-wash for K4me2 20 min hex dmf 22deg in H1 ES cells at home

value: H3K4me2 Epicypher cat# 13-0027


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_C10_AD001


title: H1_H3K4me2_hex_p-w_(20201012_SH_Hs_H1K4me2E_hex_1005)

description: CUTAC Post-wash for K4me2 20 min hex in H1 ES cells at home


title: H1_H3K4me2_dmf_p-w_(20201012_SH_Hs_H1K4me2E_dmf_1005)

description: CUTAC Post-wash for K4me2 20 min dmf in H1 ES cells at home


title: -Serine/Glycine Replicate 1_From Donor 1

tag: treatment


title: H1_H3K4me2_dmfRT_p-w_(20201012_SH_Hs_H1K4me2E_dmfRT_1005)

description: CUTAC Post-wash for K4me2 20 min dmf RT in H1 ES cells at home


title: Control IP-1 (no GFP Ab)

source_name: Control IP-1 (no GFP Ab)

tag: cell line


title: Whole blood, CBS, 200373830048_J [ftd]

description: replicate 1

value: CBS


title: Whole blood, svPPA, 200373830048_C [ftd]

description: replicate 1

value: svPPA


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_B9_AD007


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_B9_AD008


title: +Serine/Glycine Replicate 4_From Donor 4

value: plus serine/glycine


title: +Serine/Glycine Replicate 5_From Donor 5


title: Whole blood, PSP, 200373830048_A [ftd]

description: replicate 1

value: Female


title: GFP-trap IP-2

source_name: GFP-trap IP-2


title: +Serine/Glycine Replicate 3_From Donor 3


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_B9_AD006


title: Whole blood, bvFTD, 200373830042_K [ftd]

description: replicate 1


title: +Serine/Glycine Replicate 2_From Donor 2


title: H1_H3K4me2_con_p-w_(20201012_SH_Hs_H1K4me2E_con_1005)

description: CUTAC Post-wash for K4me2 20 min in H1 ES cells at home


title: H1_H3K4me2_RT_p-w_(20201012_SH_Hs_H1K4me2E_RT_1005)

description: CUTAC Post-wash for K4me2 20 min 22deg in H1 ES cells at home


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_B9_AD004

value: male


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_B9_AD010


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_B9_AD001