title: mel167-shG3-3 RNA-seq

city: Boston

first: Ben

middle: S.

last: Wittner

state: MA

address: 149 13th Street

department: Center for Cancer Research

institute: Massachusetts General Hospital

data_processing:
RNA-seq reads were aligned to the GRCh38 build of the human genome reference using STAR 2.6.1d (PMID: 23104886).
Duplicated reads were identified and flagged using Picard Tools v2.18.24 MarkDuplicates.
Gene-level TPM values were calculated using RNA-SeQC v2.2.2 (PMID: 22539670).
The GENCODE v26 annotation was used for the STAR alignment and all other quantifications. All methods were run as part of the pipeline developed for the GTEx Consortium(PMID: 29022597).
Gene-level quantifications were obtained by collapsing the GENCODE annotation to a single transcript per gene, using the procedure described in GTEx Consortium(PMID: 29022597)
Genome_build: GRCh38
Supplementary_files_format_and_content: Transcripts Per Million (TPM). Rows correspond to genes, columns correspond to samples.

molecule: polyA RNA

source_name: TF KD shRNA

growth_protocol: For ex vivo culture of melanoma CTCs, microfluidically processed samples were incubated in hypoxic, anchorage independent conditions as described in Yu et al (PMID: 25013076) with modifications. CTC cultures were grown in ultralow attachment plates (Corning) containing tumor sphere medium consisting of RPMI-1640 medium (with phenol red) supplemented with EGF (20ng/ml), basic FGF (20ng/ml), B27 (10ml), 1x Antibiotic-antimycotic (Life Technologies), 5μg/ml Heparin (Stemcell Technologies) and 100nM Rock inhibitor Y-27632 (EMD Millipore). Cells were cultured in a humid 37oC incubator with 5% CO2 and 4% O2. Medium was replenished 2-3 times per week, until CTCs initiated in vitro proliferation (4-8 weeks) with the following components included in CTC culture media: Mel-182 and Pem-22 blood samples were processed through the CTC-iChip using a recently developed blood stabilization method (PMID: 29170510) followed by 3-D fibrin matrigel culture initially and switched to anchorage independent condition after initial proliferation.

extract_protocol:
Cells of about 10^5-10^6 in total are disrupted in 350 microliter RLT buffer with the addition of  beta-mecaptoenthanol and then homogenized as described in the kit (RNeasy mini kit, Qiagen Cat # 74104). 70% Ethanol is added to the lysate with the volume ratio 1:1 which is then followed by column purification steps. The residual amount of DNA remaining is removed using on-column DNase treatment and RNA is eluted in 30 µl of nuclease-free water.
SmartSeqHT: According to the manufacturer’s protocol, amplified cDNA was generated by using the SMARTer HT RNA kit (Clontech/Takara) followed by Nextera® XT DNA Library Preparation kit (Illumina) for sample barcoding and fragmentation. Briefly, 10 ng of RNA was subjected to first‐strand synthesis of RNA molecules was performed using the poly‐dT‐based 3’‐SMART CDS primer II A (Clontech) followed by extension and template switching by the reverse transcriptase. The second strand synthesis and amplification polymerase chain reaction (PCR) was run for 18 cycles, and the amplified cDNA was purified with a 1× Agencourt AMPure XP bead cleanup (Beckman Coulter,). The Nextera XT DNA Library Preparation kit (Illumina) was used for sample barcoding and fragmentation according to the manufacturer's protocol. One nanogram of amplified cDNA was used for the enzymatic tagmentation, followed by 12 cycles of amplification and unique dual‐index barcoding of individual libraries. PCR product was purified with a 1.8× Agencourt AMPure XP bead cleanup (Beckman Coulter).

treatment_protocol: shRNAs in lentiviral backbone against TF and scramble shRNA control vector were purchased from TRC shRNA library in Broad Institute. shRNA Lentivirus were produced and packaged in 293T cells as described previously (PMID: 16564017). Virus transduction was carried out in CTCs incubated in sealed 6-well plates by centrifugation followed by puromycin (2 μg/ml) selection for 6-8 days. shRNA sequence targeting TF: shG3: 5-ACTACAATAAGAGCGATAATT-3.

tag: donor


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_B8_AD012

status: Public on Nov 13 2020

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

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: Whole blood, Control, 200373830042_F [ftd]

type: RNA

city: Los Angeles

first: Daniel

last: Nachun

address: 695 Charles E Young Dr S

institute: UCLA

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

label: biotin

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: mel167-shG3-2 RNA-seq

library_source: transcriptomic

tag: cell line


title: +Serine/Glycine Replicate 1_From Donor 1

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

tag: treatment

value: plus serine/glycine


title: Whole blood, CBS, 200373830042_H [ftd]

description: replicate 1

value: CBS

value: Female


title: K562_H3K4me2_RT_p-w_(20201012_SH_Hs_K4me2E_RT_1004)

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 K4me2 20 min 22deg in K562cells 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: H3K4me2 Epicypher cat# 13-0027

tag: cell type

value: K562 human immortalised myelogenous leukemia cell line


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_B8_AD010

value: male


title: mel167-shTRC-3 RNA-seq

source_name: TF Ctrl shRNA


title: K562_K4me3_dil20_(20200804_SH_Hs_LK5n_K4me3_0615)

description: CUTAC Dilution for K4me3 60 min 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 normalize_counts.bedgraph.gz).

value: H3K4me3 Active Motif cat# 39159 lot# 22118006


title: K562_K9me3_(20200804_SH_Hs_K9m3_0801)

description: CUT&Tag for K9me3 in K562 cells at home

value: H3K9me3 Abcam ab8898 lot GR3302452-1


title: K562_K9me3_rem10_(20200804_SH_Hs_K9m3_10_0801)

description: CUTAC Removal for K9me3 20 min in K562 cells at home


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_B8_AD007


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

description: replicate 1

value: bvFTD


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_B8_AD008


title: K562_NPAT_(20200804_SH_Hs_NPAT_0801)

description: CUT&Tag for NPAT in K562 cells at home

value: Thermo cat# PA566839


title: K562_NPAT_rem10_(20200804_SH_Hs_NPAT_10_0801)

description: CUTAC Removal for NPAT 20 min in K562 cells at home


title: mel167-shG3-1 RNA-seq


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_B8_AD006

value: SC


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

description: replicate 1


title: mel167-shTRC-1 RNA-seq


title: mel167-shTRC-2 RNA-seq


title: K562_K4me3_6k_lab_(20200728_SH_Hs_K4m3_6500_0311)

description: CUT&Tag for K4me3 in 6,000 K562 cells in lab

source_name: CUT&TAG

extract_protocol:
CnTathome_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


title: Whole blood, CBS, 200373830041_J [ftd]

description: replicate 1


title: K562_K4me3_6k_home_(20200728_SH_Hs_K4m3_6500_0321)

description: CUT&Tag for K4me3 in 6,000 K562 cells at home


title: WBC6_donor1 scRNA-seq

source_name: white blood cell

growth_protocol: Following microfluidic enrichment from primary blood specimens (PMID: 23552373, PMID: 24577360) we picked 76 individual CTCs freshly isolated from 22 melanoma patients and validated them to be melanoma cells by their expression of melanoma lineage markers (PMID: 29453278). We also picked 20 single CTCs that had been incubated in culture medium for 4-8 weeks, a condition in which only viable CTCs persist, but before they initiate in vitro proliferation. We also picked six individual leukocytes from a healthy donor.

extract_protocol:
Freshly isolated individual CTCs were selected using a micromanipulator and introduced into a 0.5ml tube with 7ul of 1x lysis buffer (Takara, Cat#634891) containing recombinant RNase inhibitor (0.4U/ul; Takara, Cat#2313A), snap frozen and maintained at -80oC until processing. Single cell lysates were transferred into 96-well plates (Eppendorf, 951020401), and RNA extraction and clean up were carried out using Agencourt RNAClean XP SPRI beads (Beckman Coulter, A63987). Prior to library construction using the Nextera XT library Prep kit (Illumina, FC-131-1096), two steps of quality control were done to evaluate the concentration of each single cell, using Qubit dsDNA high sensitivity assay kit (Life Technologies, Q32854), according to the manufacturer’s instructions.
Single cell CTC libraries were prepared using a modified Smart-Seq2 protocol (PMID: 30388456). Combined libraries were sequenced on a NextSeq 500 sequencer (Illumina) using the 75 cycles kit, with paired-end 38-base-reads and dual barcoding.


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_B8_AD004

value: brain


title: K562_K4me3_60_lab_(20200804_SH_Hs_K4m3_65_0311)

description: CUT&Tag for K4me3 in 60 K562 cells in lab


title: Whole blood, bvFTD, 200373830041_I [ftd]

description: replicate 1


title: WBC5_donor1 scRNA-seq


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_B8_AD001

value: MOp


title: Whole blood, svPPA, 200373830041_F [ftd]

description: replicate 1

value: svPPA


title: Whole blood, PSP, 200373830041_E [ftd]

description: replicate 1

value: PSP


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

description: replicate 1

value: Control


title: Whole blood, nfvPPA, 200373830021_K [ftd]

description: replicate 1

value: nfvPPA


title: Whole blood, PSP, 200373830036_G [ftd]

description: replicate 1

value: Male


title: Whole blood, nfvPPA, 200373830021_F [ftd]

description: replicate 1


title: WBC4_donor1 scRNA-seq


title: K562_K4me3_60k_lab_(20200804_SH_Hs_K4m3_65k_0311)

description: CUT&Tag for K4me3 in 60,000 K562 cells in lab


title: K562_K4me3_60_home_(20200804_SH_Hs_K4m3_65_0321)

description: CUT&Tag for K4me3 in 60 K562 cells at home


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_B7_AD010

value: STR


title: K562_K4me3_60k_home_(20200804_SH_Hs_K4m3_65k_0321)

description: CUT&Tag for K4me3 in 60,000 K562 cells at home


title: K562_K4me3_600_home_(20200804_SH_Hs_K4m3_650_0321)

description: CUT&Tag for K4me3 in 600 K562 cells at home


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_B7_AD012

value: female


title: WBC2_donor1 scRNA-seq


title: WBC1_donor1 scRNA-seq


title: PEM97_2 scRNA-seq

source_name: Primary CTC


title: K562_K4me3_600_lab_(20200731_SH_Hs_K4m3_650_0311)

description: CUT&Tag for K4me3 in 600 K562 cells in lab


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_B7_AD008


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_B7_AD006


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_B7_AD007


title: PEM95_6 scRNA-seq


title: WBC3_donor1 scRNA-seq


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_B7_AD004


title: K562_K4me3_2_(20200804_SH_Hs_K4m3_K5A_0802)

description: CUTAC Removal for K4me3 20 min in K562 cells at home


title: PEM95_3 scRNA-seq


title: K562_K4me3_3_(20200804_SH_Hs_K5n_K4m3_0615)

description: CUT&Tag for K4me3 in K562 cells at home


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_B7_AD001


title: K562_K4me3_2k_lab_(20200728_SH_Hs_K4m3_2000_0311)

description: CUT&Tag for K4me3 in 2,000 K562 cells in lab


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

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_B6_AD012


title: PEM95_17 scRNA-seq


title: K562_K4me3_20k_lab_(20200804_SH_Hs_K4me3_20k_0311)

description: CUT&Tag for K4me3 in 20,000 K562 cells in lab


title: PEM95_15 scRNA-seq


title: K562_K4me3_2k_home_(20200728_SH_Hs_K4m3_2000_0321)

description: CUT&Tag for K4me3 in 2,000 K562 cells at home


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

description: replicate 1

value: Female


title: Whole blood, bvFTD, 200373830021_C [ftd]

description: replicate 1


title: PEM95_12 scRNA-seq


title: PEM95_13 scRNA-seq


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

description: replicate 1


title: K562_K4me3_20k_home_(20200728_SH_Hs_K4m3_20k_0321)

description: CUT&Tag for K4me3 in 20,000 K562 cells at home

value: K562 human immortalised myelogenous leukemia cell line


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_B6_AD008


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

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_B6_AD006


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_B6_AD010

value: male


title: K562_K4me3_200_lab_(20200728_SH_Hs_K4m3_200_0311)

description: CUT&Tag for K4me3 in 200 K562 cells in lab

value: H3K4me3 Active Motif cat# 39159 lot# 22118006


title: Whole blood, Control, 200373830011_F [ftd]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_B6_AD004


title: PEM93_4 scRNA-seq


title: K562_K4me3_200_home_(20200728_SH_Hs_K4m3_200_0321)

description: CUT&Tag for K4me3 in 200 K562 cells at home


title: Whole blood, Control, 200373830011_E [ftd]

description: replicate 1


title: Whole blood, Control, 200373830011_H [ftd]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_B6_AD001


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_B5_AD012


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

description: replicate 1


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

description: replicate 1


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

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_B5_AD010


title: PEM95_1 scRNA-seq


title: K562_K4me2M_dil20_(20200313_SH_Hs_20_2K4me2M_0627)

description: CUTAC Dilution for K4me2 20 min in K562 cells at home

value: H3K4me2 Millipore cat# 07-030 lot 3229364


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_B5_AD007


title: PEM93_1 scRNA-seq


title: PEM93_2 scRNA-seq


title: Whole blood, Control, 200363680059_K [ftd]

description: replicate 1


title: PEM62_2 scRNA-seq


title: PEM62_5 scRNA-seq


title: K562_K4me2_p-w_60_(20200728_SH_Hs_K4m2E_60_0809)

description: CUTAC Post-wash for K4me2 60 min in K562 cells at home

value: H3K4me2 Epicypher cat# 13-0027


title: K562_K4me3_1_(20200804_SH_Hs_K4m3_K5_0802)

description: CUT&Tag for K4me3 in K562 cells at home


title: K562_K4me2M_CnT_RT_(20200617_SH_Hs_HRT_K4me2M_0627)

description: CUT&Tag for K4me2 in K562 22deg in K562 cells at home


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_B5_AD006


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

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_B5_AD008


title: PEM93_3 scRNA-seq


title: K562_K4me2M_dil120RT_(20200812_SH_Hs_RT2h_2K4me2M_0627)

description: CUTAC Dilution for K4me2 pAG-Tn5 120 min 22deg in K562 cells at home


title: K562_K4me2M_dil5_(20200402_SH_Hs_5_2K4me2M_0627)

description: CUTAC Dilution for K4me2 pAG-Tn5 5 min in K562 cells at home


title: Whole blood, Control, 200363680059_A [ftd]

description: replicate 1


title: K562_K4me2_dil60RT_(20200812_SH_Hs_RT60_2K4me2M_0627)

description: CUTAC Dilution for K4me2 pAG-Tn5 60 min 22deg in K562 cells at home


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_B5_AD001


title: PEM61_9 scRNA-seq


title: Whole blood, Control, 200363680055_E [ftd]

description: replicate 1


title: PEM62_12_1 scRNA-seq


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_B5_AD004


title: Whole blood, Control, 200363680059_E [ftd]

description: replicate 1


title: K562_K4me2_dil60L_(20200402_SH_Hs_60L_K4me2_0620)

description: CUTAC Dilution for K4me2 pAG-Tn5 1:60 60 min in K562 cells at home


title: PEM61_8 scRNA-seq


title: K562_K4me2_dil60_2_(20200402_SH_Hs_60_K4me2_0622)

description: CUTAC Dilution for K4me2 pAG-Tn5 1:20 60 min in K562 cells at home


title: PEM61_7 scRNA-seq


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_B4_AD012


title: K562_K4me2_dil60_1_(20200402_SH_Hs_60_K4me2_0620)


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_B4_AD008


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_B4_AD010


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

description: replicate 1


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

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_B4_AD007


title: K562_K4me2_dil5_(20200402_SH_Hs_5_K4me2E_0627)


title: PEM61_4 scRNA-seq


title: PEM61_2 scRNA-seq


title: PEM58_4 scRNA-seq


title: K562_K4me2_dil5_2_(20200402_SH_Hs_5m_K4m2E_0629)


title: K562_K4me2_dil5RT_(20200812_SH_Hs_RT5_K4me2E_0627)

description: CUTAC Dilution for K4me2 pAG-Tn5 5 min 22deg in K562 cells at home


title: PEM52_3 scRNA-seq


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

description: replicate 1


title: K562_K4me2_dil30_(20200402_SH_Hs_30_K4me2_0620)

description: CUTAC Dilution for K4me2 pAG-Tn5 1:20 30 min in K562 cells at home


title: PEM31_5 scRNA-seq


title: K562_K4me2_dil30L_(20200402_SH_Hs_30L_K4me2_0620)

description: CUTAC Dilution for K4me2 pAG-Tn5 1:60 30 min in K562 cells at home


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

description: replicate 1


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

description: replicate 1


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

description: replicate 1


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

description: replicate 1


title: Whole blood, CBS, 200316700083_L [ftd]

description: replicate 1

value: CBS


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

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_B4_AD001

value: SC


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

description: replicate 1


title: Mel233_8 scRNA-seq


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_B4_AD006

value: brain


title: K562_K4me2_dil20_(20200804_SH_Hs_LK5n_K4m2E_0615)

description: CUTAC Dilution for K4me2 60 min in K562 cells at home


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_B4_AD004

value: MOp


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_B3_AD010


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

description: replicate 1


title: K562_K4me2_dil20RT_(20200804_SH_Hs_RT20_K4me2E_0627)

description: CUTAC Dilution for K4me2 pAG-Tn5 20 min 22deg in K562 cells at home


title: Mel233_7 scRNA-seq


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_B3_AD008


title: Mel233_1 scRNA-seq


title: K562_K4me2_dil120RT_(20200812_SH_Hs_RT2h_K4me2E_0627)


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_B3_AD007


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_B3_AD012


title: K562_K4me2_dil10_(20200313_SH_Hs_10_K4me2_0620)

description: CUTAC Dilution for K4me2 pAG-Tn5 1:20 10 min in K562 cells at home


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_B3_AD004


title: Mel232_9 scRNA-seq


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

description: replicate 1


title: K562_K4me2_dil10L_(20200313_SH_Hs_10L_K4me2_0620)

description: CUTAC Dilution for K4me2 pAG-Tn5 1:60 10 min in K562 cells at home


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

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_B3_AD002


title: K562_K4me2_CnT_RT_(20200617_SH_Hs_HRT_K4me2E_0627)


title: Mel233_3 scRNA-seq


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_B3_AD001


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

description: replicate 1


title: K562_K4me2_CnT_8_(20200804_SH_Hs_K5n_K4m2E_0615)

description: CUT&Tag for K4me2 in K562 cells at home


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

description: replicate 1


title: Mel232_15 scRNA-seq


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

description: replicate 1


title: Mel232_14 scRNA-seq


title: K562_K4me2_CnT_7_(20200804_SH_Hs_K5n_K4m2E_0613)

description: CUT&Tag for K4me2 in K562 cells at home


title: Mel232_13 scRNA-seq


title: K562_K4me2_CnT_6_(20200728_SH_Hs_K4m2E_K5A_0802)

description: CUTAC Removal for K4me2 20 min in K562 cells at home


title: Mel232_12 scRNA-seq


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_B2_AD008


title: Mel232_11 scRNA-seq


title: K562_K4me2_CnT_5_(20200728_SH_Hs_K4m2E_K5_0802)

description: CUT&Tag for K4me2 in K562 cells at home


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_B2_AD006


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_B2_AD010


title: K562_K4me2_CnT_4_(20200624_SH_Hs_K4m2_0727)

description: CUT&Tag for K4me2 in K562 cells at home


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_B2_AD004


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_B2_AD012


title: Whole blood, nfvPPA, 9682760080_L [ftd]

description: replicate 1


title: Mel232_1 scRNA-seq


title: Mel219_9 scRNA-seq


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

description: replicate 1


title: K562_K4me2_CnT_3_(20200624_SH_Hs_K4m2_0726)

description: CUT&Tag for K4me2 in K562 cells at home


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_B2_AD002


title: Mel219_8 scRNA-seq


title: K562_K4me2_CnT_2_(20200617_SH_Hs_HL_K4me2_0620)

description: CUT&Tag for K4me2 in K562 1:60 in K562 cells at home


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

description: replicate 1


title: K562_K4me2_CnT_1_(20200617_SH_Hs_H_K4me2_0620)

description: CUT&Tag for K4me2 1:20 in K562 cells at home


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_B1_AD012


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_B2_AD001


title: Mel219_4 scRNA-seq


title: K562_K4me2_a-b_60_(20200728_SH_Hs_K4m2Es2_60_0809)

description: CUTAC 1% Add-back for K4me2 60 min in K562 cells at home


title: Mel219_10 scRNA-seq


title: Whole blood, bvFTD, 9682760080_J [ftd]

description: replicate 1

value: bvFTD


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_B1_AD010


title: Whole blood, bvFTD, 9682760080_H [ftd]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_B1_AD008


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_B1_AD007


title: Mel209_5 scRNA-seq


title: Mel208_7 scRNA-seq


title: Whole blood, nfvPPA, 9682760080_E [ftd]

description: replicate 1


title: Mel208_5 scRNA-seq


title: K562_K4me1_dil20_(20200804_SH_Hs_LK5n_K4me1_0615)

description: CUTAC Dilution for K4me1 60 min in K562 cells at home


title: Whole blood, PSP, 9682760080_D [ftd]

description: replicate 1

value: PSP


title: K562_K4m2M_rem20_2_(20200728_SH_Hs_K4m2M_15kA_0803)


title: Whole blood, svPPA, 9682760079_A [ftd]

description: replicate 1

value: svPPA


title: Whole blood, Control, 9682760079_D [ftd]

description: replicate 1

value: Control


title: K562_K4me1_(20200804_SH_Hs_K5n_K4me1_0615)

description: CUT&Tag for K4me1 in K562 cells at home


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_B1_AD006


title: Mel208_4 scRNA-seq


title: Whole blood, nfvPPA, 9682760079_C [ftd]

description: replicate 1

value: nfvPPA


title: Whole blood, PSP, 9682760076_F [ftd]

description: replicate 1

value: Male


title: K562_K4m2M_rem20_1_(20200728_SH_Hs_K4m2M_15k_0803)

description: CUT&Tag for K4me2 in K562 cells at home


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

description: replicate 1


title: Whole blood, svPPA, 9682760076_E [ftd]

description: replicate 1


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

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_B1_AD004


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_B1_AD002

value: female


title: Mel208_1 scRNA-seq


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_B12_AD012

value: STR


title: K562_K27me3_60_lab_(20200313_SH_Hs_27m3_65_0311)

description: CUT&Tag for K27me3 in 60 K562 cells in lab

value: H3K27me3 Cell Signaling Technology cat# 9733

value: K562 human immortalised myelogenous leukemia cell line


title: Mel207_2 scRNA-seq


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_B1_AD001

value: male


title: K562_K27me3_6k_lab_(20200313_SH_Hs_27m3_6500_0311)

description: CUT&Tag for K27me3 in 6,000 K562 cells in lab


title: K562_K27me3_60k_lab_(20200402_SH_Hs_27m3_65k_0311)

description: CUT&Tag for K27me3 in 60,000 K562 cells in lab


title: Mel203_9 scRNA-seq


title: Whole blood, Control, 9682760076_B [ftd]

description: replicate 1


title: Mel203_7 scRNA-seq


title: Whole blood, CBS, 9682760075_K [ftd]

description: replicate 1


title: K562_K27me3_60k_home_(20200402_SH_Hs_27m3_65k_0321)

description: CUT&Tag for K27me3 in 60,000 K562 cells at home


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_B12_AD010


title: Whole blood, Control, 9682760075_J [ftd]

description: replicate 1

value: Female


title: Mel203_8 scRNA-seq


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_B12_AD008


title: Mel203_3 scRNA-seq


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_B12_AD007


title: K562_K27me3_6k_home_(20200313_SH_Hs_27m3_6500_0321)

description: CUT&Tag for K27me3 in 6,000 K562 cells at home


title: K562_K27me3_60_home_(20200324_SH_Hs_27m3_65_0321)

description: CUT&Tag for K27me3 in 60 K562 cells at home


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_B12_AD006


title: K562_K27me3_600_home_(20200313_SH_Hs_27m3_650_0321)

description: CUT&Tag for K27me3 in 600 K562 cells at home


title: Mel203_2 scRNA-seq


title: K562_K27me3_600_lab_(20200313_SH_Hs_27m3_650_0311)

description: CUT&Tag for K27me3 in 600 K562 cells in lab


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_B12_AD004


title: Mel201_4_1 scRNA-seq


title: Whole blood, svPPA, 9682760075_H [ftd]

description: replicate 1


title: Mel201_2 scRNA-seq


title: Whole blood, bvFTD, 9682760075_D [ftd]

description: replicate 1


title: K562_K27me3_2k_lab_(20200313_SH_Hs_27m3_2000_0311)

description: CUT&Tag for K27me3 in 2,000 K562 cells in lab


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_B12_AD002


title: Whole blood, Control, 9682760075_I [ftd]

description: replicate 1


title: Whole blood, nfvPPA, 9682760075_F [ftd]

description: replicate 1


title: Mel201 scRNA-seq


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_B12_AD001


title: Whole blood, CBS, 9682760074_G [ftd]

description: replicate 1


title: Whole blood, svPPA, 9682760074_J [ftd]

description: replicate 1


title: K562_K27me3_2k_home_(20200313_SH_Hs_27m3_2000_0321)

description: CUT&Tag for K27me3 in 2,000 K562 cells at home


title: K562_K27me3_20k_home_(20200313_SH_Hs_27m3_20k_0321)

description: CUT&Tag for K27me3 in 20,000 K562 cells at home


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_B11_AD012


title: Mel197_7 scRNA-seq


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_B11_AD010


title: Mel197_6 scRNA-seq


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

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_B11_AD008


title: Mel197_4 scRNA-seq


title: K562_K27me3_200_lab_(20200313_SH_Hs_27m3_200_0311)

description: CUT&Tag for K27me3 in 200 K562 cells in lab


title: Mel197_11 scRNA-seq


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

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_B11_AD007


title: Whole blood, bvFTD, 9682760073_J [ftd]

description: replicate 1


title: K562_H3K4me2_rem60_1_(20200701_SH_Hs_K4m2_37con60a_0726)

description: CUTAC Removal for K4me2 5 min in K562 cells at home

value: H3K4me2 Epicypher cat# 13-0027


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_B11_AD006


title: Mel196_4 scRNA-seq


title: Whole blood, PSP, 9682760073_B [ftd]

description: replicate 1


title: K562_K27me3_20k_lab_(20200313_SH_Hs_27m3_20k_0311)

description: CUT&Tag for K27me3 in 20,000 K562 cells in lab


title: K562_H3K4me2_rem5_2_(20200701_SH_Hs_K4m2_37con5b_0726)


title: Whole blood, svPPA, 9682760073_C [ftd]

description: replicate 1


title: K562_K27me3_200_home_(20200313_SH_Hs_27m3_200_0321)

description: CUT&Tag for K27me3 in 200 K562 cells at home


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_B11_AD004


title: K562_H3K4me2_rem5_1_(20200701_SH_Hs_K4m2_37con5a_0726)


title: Mel196_3 scRNA-seq


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_B11_AD002


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_B11_AD001


title: K562_H3K4me2_rem20_1_(20200624_SH_Hs_K4m2_37con20a_0726)

description: CUTAC Removal for K4me2 20 min in K562 cells at home


title: Mel195_8 scRNA-seq


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_B10_AD012


title: Mel195_9 scRNA-seq


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

description: replicate 1


title: Whole blood, CBS, 9682760072_B [ftd]

description: replicate 1

value: CBS


title: Mel195_7 scRNA-seq


title: K562_H3K4me2_hex5_(20200701_SH_Hs_K4m2_37hex5b_0726)


title: Whole blood, PSP, 9682760073_I [ftd]

description: replicate 1


title: K562_H3K4me2_hex20_1_(20200701_SH_Hs_K4m2_37hex20a_0726)

description: CUTAC Removal for K4me2 20 min hex in K562 cells at home


title: Mel195_6 scRNA-seq


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_B10_AD010


title: Mel195_4 scRNA-seq


title: Whole blood, PSP, 9682760062_J [ftd]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_B10_AD008


title: K562_H3K4me2_he60_(20200701_SH_Hs_K4m2_37hex60a_0726)


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_B10_AD007


title: Whole blood, bvFTD, 9682760062_I [ftd]

description: replicate 1


title: K562_H3K4me2_hd60_55deg_(20200728_SH_Hs_K4m2_55hd60a_0726)

description: CUTAC Removal for K4me2 60 min hex + dmf 55deg in K562 cells at home


title: Mel195_3 scRNA-seq


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

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_B10_AD002

value: SC


title: Whole blood, PSP, 9682760062_F [ftd]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_A9_AD012

value: brain


title: Mel195_12 scRNA-seq


title: Mel195_1 scRNA-seq


title: K562_H3K4me2_hd20_55deg_(20200728_SH_Hs_K4m2_55hd20a_0726)

description: CUTAC Removal for K4me2 20 min hex dmf in K562 cells at home


title: K562_H3K4me2_dmf60_(20200701_SH_Hs_K4m2_37dmf60_0726)

description: CUTAC Removal for K4me2 60 min dmf in K562 cells at home


title: Mel195_2 scRNA-seq


title: K562_H3K4me2_hex20_2_(20200701_SH_Hs_K4m2_37hex20b_0726)

description: CUTAC Removal for K4me2 5 min hex in K562 cells at home


title: Whole blood, bvFTD, 9682760062_E [ftd]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_A9_AD008

value: MOp


title: Mel194_7 scRNA-seq


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_A9_AD010


title: K562_H3K4me2_dmf5_(20200701_SH_Hs_K4m2_37dmf5a_0726)

description: CUTAC Removal for K4me2 5 min dmf in K562 cells at home


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_A9_AD007


title: Whole blood, bvFTD, 9682760062_D [ftd]

description: replicate 1

value: bvFTD


title: Mel194_5 scRNA-seq


title: Whole blood, PSP, 9682760062_A [ftd]

description: replicate 1

value: PSP


title: Whole blood, nfvPPA, 9665647062_L [ftd]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_A9_AD006


title: Whole blood, CBS, 9682760062_H [ftd]

description: replicate 1


title: K562_H3K4me2_dmf20_(20200701_SH_Hs_K4m2_37dmf20_0726)

description: CUTAC Removal for K4me2 20 min dmf in K562 cells at home


title: Whole blood, Control, 9665647062_J [ftd]

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_A9_AD004


title: Whole blood, nfvPPA, 9665647062_D [ftd]

description: replicate 1


title: K562_H3K4me1_(20200624_SH_Hs_K4m1_0801)

description: CUT&Tag for K4me1 in K562 cells at home

value: Epicypher 13-0040


title: Whole blood, PSP, 9665647062_I [ftd]

description: replicate 1


title: Mel192_1_2 scRNA-seq


title: Mel194_2 scRNA-seq


title: Mel188_6 scRNA-seq


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_A8_AD008


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_A8_AD010


title: K562_H3K36me3_(20200624_SH_Hs_K36m3_0801)

description: CUT&Tag for K36me3 in K562 cells at home

value: H3K36me36 Epicypher cat# 13-0031


title: K562_H3K36me3_rem10_(20200624_SH_Hs_K36m3_10_0801)

description: CUTAC Removal for K36me3 20 min in K562 cells at home


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_A8_AD007


title: Mel188_2 scRNA-seq


title: K562_H3K4me1_rem10_(20200624_SH_Hs_K4m1_10_0801)

description: CUTAC Removal for K4me1 20 min in K562 cells at home


title: Mel188_11 scRNA-seq


title: K562_H3K4me2_hd5_55deg_(20200728_SH_Hs_K4m2_55hd5a_0726)

description: CUTAC Removal for K4me2 5 min hex dmf in K562 cells at home


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_A8_AD006


title: Whole blood, PSP, 9665647062_C [ftd]

description: replicate 1


title: Whole blood, PSP, 9665647061_E [ftd]

description: replicate 1


title: Whole blood, nfvPPA, 9665647061_D [ftd]

description: replicate 1

value: nfvPPA


title: Whole blood, CBS, 9665647061_F [ftd]

description: replicate 1


title: PEM22_5 scRNA-seq

source_name: CTC Culture


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_A8_AD012


title: Whole blood, PSP, 9665647061_G [ftd]

description: replicate 1

value: Male


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_A8_AD004


title: PEM22_4 scRNA-seq


title: Mel192_1_1 scRNA-seq


title: Mel232_5 scRNA-seq


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_A8_AD001


title: K562_H3K27me3_(20200624_SH_Hs_K27m3_0801)

description: CUT&Tag for K27me3 in K562 cells at home

value: H3K27me3 Cell Signalling Technoloties cat#9733


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_A7_AD012

value: STR

value: female


title: PEM22_2 scRNA-seq


title: PEM22_3 scRNA-seq


title: K562_H2AZ_rem10_(20200617_SH_Hs_H2AZ_10_0801)

description: CUTAC Removal for H2AZ 10 min in K562 cells at home

value: H2AZ Active Motif cat. #39113

value: K562 human immortalised myelogenous leukemia cell line


title: Whole blood, CBS, 9665647061_A [ftd]

description: replicate 1


title: K562_H2AZ_(20200402_SH_Hs_H2AZ_0801)

description: CUT&Tag for H2AZ in K562 cells at home


title: PEM22_1 scRNA-seq


title: Whole blood, bvFTD, 9703627107_C [ftd]

description: replicate 1


title: K562_H3K27ac_(20200617_SH_Hs_K27ac_0801)

description: CUT&Tag for K27ac in K562 cells at home

value: H3K27ac Millipore MABE647 lot RM172


title: H1_K4me2_p-w_60_(20200402_SH_Hs_H1_K4m2E_60_0810)

description: CUTAC Post-wash for K4me2 60 min in H1 ES cells at home

value: H3K4me2 Epicypher cat# 13-0027

value: H1 human embryonic stem cell line


title: Mel182_L2_9_2 scRNA-seq


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_A7_AD007

value: male


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_A7_AD008

value: brain


title: K562_H3K27me3_rem10_(20200624_SH_Hs_K27m3_10_0801)

description: CUTAC Removal for K27me3 20 min in K562 cells at home


title: K562_H3K27ac_rem10_(20200617_SH_Hs_K27ac_10_0801)

description: CUTAC Removal for K27ac 20 min in K562 cells at home


title: Mel182_L2_9_1 scRNA-seq


title: Mel182_L2_8 scRNA-seq


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_A7_AD010

value: MOp


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_A7_AD006

value: SC


title: Mel182_L2_7 scRNA-seq


title: nasal respiratory epithelium, patient 5

city: Geneva

first: Ivan

last: Rodriguez

address: 30 quai Ernest Anrsermet

department: Genetics and Evolution

country: Switzerland

institute: University of Geneva

description:
patient5_re
11554_fz20yIVbXESs
bulk tissue RNA-seq of a ~3 mm diameter intraoperative biopsie of the nasal respiratory epithelium

data_processing:
RNA-seq reads were mapped onto the GRCh38 human genome assembly with STAR version 2.7.0a using the Ensembl v99 gene annotation file (GTF). Mutlimapped reads were filtered out with the option --outFilterMultimapNmax set to 1.
Reversely stranded gene expression quantification was carried using featureCounts version 1.6.3 and a modified version of the aforementioned GTF file. The records corresponding to AC097625.2, a newly annotated long non-coding RNA that spans and shares most exons of ACE2, were removed from the GTF file as they hampered ACE2 quantification (due to ambiguous read counting)
Differential gene expression analysis between olfactory epithelial (OE) biopsies and respiratory epithelial (RE) biopsies was performed using the DESeq2 Bioconductor package version 1.22.2 in R version 3.5.0. After fitting a negative binomial generalized linear model (GLM), the Wald test (two-tailed) was used to test for significance of gene expression differences as a function of biopsies at a log2 fold change threshold of 0. To control the false discovery rate, the Wald test p-values were adjusted for multiple comparisons using the Benjamini–Hochberg procedure
Genome_build: GRCm38
Supplementary_files_format_and_content: *featureCounts.txt files are featureCounts output files
Supplementary_files_format_and_content: The quantifications.rds file contains an R serialized data.frame with the RNA-seq quantification data, comprising counts and TPM for each gene in each sample, in long format
Supplementary_files_format_and_content: The DE.csv file contains the result of the differential expression analysis in comma-separated values

source_name: respiratory epithelium, nasal cavity

extract_protocol:
Biopsies were snap frozen in liquid nitrogen immediately upon collection. For RNA extraction, tissues were placed in RLT Buffer (Qiagen) with beta-mercaptoethanol and lysed with stainless steel balls (5mm diameter, Schieritz and Huenstein AG) using a homogenizer (Big Prep, MB Biomedicals). Total RNA was isolated using RNeasy Mini Kit (Qiagen) following the manufacturer protocol. The quality and quantity of total RNA were evaluated with a Bioanalyzer (Agilent).
Stranded cDNA libraries with suitable adapters for multiplexing were generated with Truseq RNA and DNA sample preparation kits (Illumina) following ribodepletion of the total RNA (200ng of total RNA per sample). Samples were multiplexed for sequencing in a HiSeq 2500 Sequencing system, generating 100bp single-end reads.

tag: patient id

value: patient 5

value: respiratory epithelium, nasal cavity


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_A7_AD004


title: Whole blood, nfvPPA, 9631032047_K [ftd]

description: replicate 1

value: Female


title: nasal respiratory epithelium, patient 7

description:
patient7_re
11572_xPZjjObaf5vq
bulk tissue RNA-seq of a ~3 mm diameter intraoperative biopsie of the nasal respiratory epithelium

value: patient 7


title: Whole blood, bvFTD, 9703627107_B [ftd]

description: replicate 1

value: bvFTD

value: Male


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

description: replicate 1

value: Control


title: olfactory epithelium, patient 7

description:
patient7_moe
11573_4wBmqN38vDpL
bulk tissue RNA-seq of a ~3 mm diameter intraoperative biopsie of the olfactory epithelium

source_name: olfactory epithelium, nasal cavity

value: olfactory epithelium


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

description: replicate 1


title: Mel182_L2_3 scRNA-seq


title: olfactory epithelium, patient 4

description:
patient4_moe
11541_7ihPY4IiZOzL
bulk tissue RNA-seq of a ~3 mm diameter intraoperative biopsie of the olfactory epithelium

value: patient 4


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

description: replicate 1


title: Mel182_L2_1 scRNA-seq


title: Mel182_L2_6_2 scRNA-seq


title: Mel182_L1_8 scRNA-seq


title: Mel182_L1_7 scRNA-seq


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_A6_AD008

value: STR

value: female


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_A6_AD007


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

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_A6_AD006


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

description: replicate 1


title: olfactory epithelium, patient 3

description:
patient3_moe
11537_LdiyNWUC33IA
bulk tissue RNA-seq of a ~3 mm diameter intraoperative biopsie of the olfactory epithelium

value: patient 3


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_A6_AD012


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_A6_AD010


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

description: replicate 1


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

description: replicate 1


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

description: replicate 1


title: Whole blood, PSP, 9631032047_E [ftd]

description: replicate 1

value: PSP


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

description: replicate 1


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

description: replicate 1


title: Mel182_L1_6 scRNA-seq


title: 12: Donor7_3

city: Cambridge

first: John

middle: Robert

last: Ferdinand

address: Department of Medicine

country: United Kingdom

institute: University of Cambridge

data_processing:
Files were demutiplexed using Casava
Reads were checked for quality with FastQC and trimmed using TrimGalore!
Trimed reads were alligned to the mm10 genome with Hisat2 and counted usign Feature Counts from Rseubread
Genome_build: mm10

source_name: Meninges

extract_protocol:
Meninges were extracted and placed into RNAlater and stored at -80 until processing. RNA was extracted with Rneasy plus micro kit (Qiagen).
Libraries were produced with TruSeq Stranded Total RNA Kit (Illumina) as per manufactuers instructions

treatment_protocol: Mice were culled and the Meninges isolated

tag: microbiome status

value: Donor 7

value: Meninges


title: Mel182_L1_5 scRNA-seq


title: Mel182_L1_3 scRNA-seq


title: 11: Donor7_2


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_A6_AD004

value: brain

value: MOp

value: male


title: 9: Donor3_3

value: Donor 3


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_A5_AD012


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_A6_AD001

value: SC


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_A5_AD010


title: Mel167_2 scRNA-seq


title: Mel167_1 scRNA-seq


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_A5_AD008


title: 8: Donor3_2


title: CTC_5E7_2 RNA-seq

source_name: isogenic melanoma CTC lines

tag: vemurafenib sensitivity

value: resistant


title: 10: Donor7_1


title: 7: Donor3_1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_A5_AD006


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_A5_AD004


title: 6: GF_3

value: Germ Free


title: CTC_5E7_1 RNA-seq

tag: donor


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

description: replicate 1

value: Female


title: Whole blood, CBS, 9631032042_B [ftd]

description: replicate 1

value: CBS


title: Whole blood, PSP, 9631032042_G [ftd]

description: replicate 1

value: Male


title: Whole blood, PSP, 9631032039_H [ftd]

description: replicate 1


title: Whole blood, CBS, 9631032039_J [ftd]

description: replicate 1


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

description: replicate 1

value: Control


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_A5_AD001

tag: strain


title: 4: GF_1


title: Whole blood, CBS, 9631032039_F [ftd]

description: replicate 1


title: CTC_5E5_2 RNA-seq

value: sensitive


title: 3: SPF_3

value: Specific Pathogen Free


title: CTC_5B10_2 RNA-seq


title: 5: GF_2


title: CTC_5E5_1 RNA-seq


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_A4_AD010

tag: age

value: STR


title: CTC_5B10_1 RNA-seq


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_A4_AD012

tag: tissue

value: female


title: 2: SPF_2


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_A4_AD006

tag: source


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_A4_AD008

tag: target


title: Whole blood, bvFTD, 9631032039_E [ftd]

description: replicate 1

value: bvFTD


title: 1: SPF_1

value: Meninges


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_A4_AD004

value: brain

tag: gender


title: CTC_4G7_2 RNA-seq


title: Whole blood, Control, 9631032039_C [ftd]

description: replicate 1

tag: diagnosis


title: CTC_4G7_1 RNA-seq


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_A4_AD002

value: MOp


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_A4_AD001

value: male


title: CTC_4E7_2 RNA-seq


title: SUV420H2_WT_mESC

city: Detroit

first: Benjamin

middle: L

last: Kidder

state: MI

address: 4100 John R St

department: Oncology

institute: Wayne State University

description: Chromatin IP against H4K20me3

data_processing:
Sequence reads were obtained and mapped to the mouse (mm9) genomes with Bowtie2.
The RBPM measure (reads per base per million reads) was used to generate graph files.
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph

source_name: ESC

growth_protocol: ES cells were cultured on gelatin-coated dishes in ES cell media containing 1.5 µM CHIR9901 (GSK3 inhibitor) for several passages to remove feeder cells. ES cells were passed by washing with PBS, and dissociating with trypsin.

extract_protocol:
Cells were crosslinked with formaldehyde and subsequently sonicated. Sonicated cell extracts were used for ChIP assays.
ChIP-enriched DNA was end-repaired using the End-It DNA End-Repair kit (Epicentre), followed by addition of a single A nucleotide, and ligation of PE adapters (Illumina) or custom indexed adapters. PCR was performed using Phusion High Fidelity PCR master mix

value: ESC

tag: genotype/variation

value: wild type

value: Anti-GFP antibody (Abcam; ab290)


title: ChIP_Input_SUV420H2_KO_mESC

description: Direct sequencing following sonication of x-linked chromatin


title: Whole blood, bvFTD, 9631032033_J [ftd]

description: replicate 1

tag: Sex

tag: batch


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_A3_AD012


title: ChIP_Input_SUV420H1_H2_DKO_mESC


title: CTC_4G7_3 RNA-seq

tag: cell line


title: CTC_3E7_3 RNA-seq

value: resistant


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_A3_AD010


title: CTC_4E7_1 RNA-seq


title: ChIP_Input_mESC

tag: antibody


title: Mel182_L2_6_1 scRNA-seq


title: CTC_3E7_2 RNA-seq


title: ChIP_Input_WT_mESC

tag: cell type


title: Whole blood, Control, 9631032033_L [ftd]

description: replicate 1

value: Female


title: Whole blood, svPPA, 9631032033_K [ftd]

description: replicate 1

value: svPPA


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

description: replicate 1


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

description: replicate 1


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

description: replicate 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_A3_AD007


title: CTC_3E7_1 RNA-seq


title: H4K20me3_SUV420H1_H2_DKO_mESC

description: Chromatin IP against H4K20me3

value: Anti-H4K20me3 antibody (Abcam; 9053)


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

description: replicate 1

value: Control

value: Male


title: CTC_3D2_3 RNA-seq


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_A3_AD008


title: CTC_3D2_2 RNA-seq


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_A3_AD006

value: SC


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_A3_AD001


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_A3_AD004


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_A3_AD002


title: H4K20me3_WT_mESC

description: Chromatin IP against H4K20me3


title: CTC_3D2_1 RNA-seq


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

description: replicate 1


title: Whole blood, CBS, 9631032033_H [ftd]

description: replicate 1

value: CBS


title: Whole blood, nfvPPA, 9631032028_K [ftd]

description: replicate 1

value: nfvPPA


title: CTC_3C8_2 RNA-seq


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

description: replicate 1


title: Whole blood, Control, 9631032028_G [ftd]

description: replicate 1


title: CTC_3C8_1 RNA-seq


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_A2_AD012

value: STR

value: female


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_A2_AD010

value: brain


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_A2_AD008

value: MOp


title: IV LUHMES GFP - MPP+  [mRNA]

city: Homburg

first: Lena

last: Krammes

address: Kirrbergerstraße

department: Institute for Human Genetics

country: Germany

institute: Saarland University

description: Gene expression without MPP+ treatment of LUHMES cells

hyb_protocol: The expression profile of more than 58000 probes was determined using SurePrint G3 Human Gene Expression 8x60Kv3 Microarray (Cat. No. G4851C, Agilent Technologies, Santa Clara, CA, USA) according to the manufacturer's recommendations.

scan_protocol: Arrays were scanned with the Agilent Scanner with default settings.

data_processing: Analysis of the received fluorescence signals was done by using Agilent AGW Feature Extraction software (version 10.7.1.1, Agilent Technologies, Santa Clara, CA, USA). Normalization of background corrected values was performed using GeneSpring by biological significance analysis (version 14.9, Agilent Technologies, Santa Clara, CA, USA).

label: Cyanine 3

source_name: LUHMES cell line

label_protocol: The expression profile of more than 58000 probes was determined using Agilent Low Input, one-color, Quick Amp Labeling Kit (Agilent, Cat. No 5190-2305) according to the manufacturer's recommendations.

growth_protocol: LUHMES cells were cultured in flasks pre-coated with 50 µg/mL Poly-L-ornithin and 1 µg/mL Fibronectin. Cells were cultured in advanced DMEM/F12 (Life Technologies GmbH, Darmstadt, Germany) supplemented with 1% N2-Supplement, 2 mM L-glutamine and 40 ng/mL basic fibroblast growth factor.

extract_protocol: Total RNA including miRNAs was isolated using the Qiagen miRNeasy Kit according to manufacturers recommendations.

treatment_protocol: For differentiation of LUHMES cells towards dopaminergic neurons, cells were cultured in advanced DMEM/F12 (Life Technologies GmbH, Darmstadt, Germany) supplemented with 1% N2-Supplement, 2 mM L‑glutamine, 1 mM dibutyryl cAMP, 2 ng/mL GDNF and 1 μg/mL tetracycline. After 48 hours, cells were trypsinized and seeded with 7.5 x 104 cell/cm² in pre-coated flasks. Every 48 hours after re-seeding, fresh differentiation medium was added to the cells for six days. To induce a PD-like phenotype, LUHMES cells were treated with 10 µM 1-methyl-4-phenylpyridinium (MPP+; Sigma Aldrich, Munich, Germany) 6 days after initiation of differentiation for 48 hours. Control cells were supplemented with H2O.

tag: pd phenotype

value: n


title: CTC_3C1_2 RNA-seq


title: CTC_3C1_1 RNA-seq


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_A2_AD007

value: male


title: CTC_3A9_3 RNA-seq


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_A2_AD006


title: Whole blood, Control, 9631032028_F [ftd]

description: replicate 1


title: IV LUHMES GFP + MPP+  [mRNA]

description: Gene expression after MPP+ treatment of LUHMES cells

value: y


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_A2_AD004


title: CTC_3A9_2 RNA-seq


title: CTC_2F9_1 RNA-seq

value: sensitive


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_A2_AD002


title: CTC_2F9_3 RNA-seq


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_A2_AD001


title: H4K20me3_SUV420H2_KO_mESC

description: Chromatin IP against H4K20me3

value: ESC


title: ChIPSeq_PSEN1_A246E_iPSCNeuron_H3K27Me3

first: Shankar

last: Subramaniam

address: 9500 Gilman Drive

department: Department of Bioengineering

institute: University of California, San Diego

data_processing:
ChIP-Seq data preprocessing was performed using the BBDuk package (v37.95) in the BBTools suite, removing sequencing adaptors and selecting for all -end reads above a quality score threshold (Phred Q>10).
Trimmed ChIP-Seq reads were aligned to the GRCh38 human genome (GCA_000001405.15 with no alternative analysis) using BBMap v37.95 in the BBtools suite with the options maxindel=20 ambig=random.
Sorting and indexing of bam files was performed using Samtools v1.3, and annotation of PCR duplicates using the Picard v2.3.0 markDuplicates function with the option VALIDATION_STRINGENCY=LENIENT.
Differential ChIP-Seq peaks between the NDC and PSEN1M146L or NDC and PSEN1A246E conditions were identified with the sicer_df function in the sicer2 package with the filter threshold |FC| > 1.5 and FDR p-value < 0.05. REST TF ChIP-Seq peak calling and differential histone methylation was performed using Homer v4.10; tags were generated from preprocessed bam files using the function makeTagDirectory, peaks called at a FDR of 0.05 using the function findPeaks with the options -style factor -gsize 2.7e9 -fdr 0.05 -region -size 250. The Homer function annotatePeaks was used to annotate REST bound genes to the GRCh38 genome.
Genome_build: GCA_000001405.15
Supplementary_files_format_and_content: sicer2 peaks relative to 1% genomic DNA input

source_name: hiPSC-derived neurons from human EOFAD patient, psen1 A246E mutation

growth_protocol: Non-Demented Control (NDC), and PSEN1M146L fibroblasts were derived from skin biopsies in accordance with UC San Diego IRB approval, whereas PSEN1A246E fibroblasts were obtained commercially (Coriell Cat. AG06840). The generation and characterization of the hiPSC lines were carried out as previously reported from fibroblasts by retroviral transduction using the reprogramming factors OCT4, SOX2, KLF4, and c-MYC. PA6 cells were plated in a 10 cm dish and seeded with 100,000 cells iPSC next day. To enhance neural induction, cultures were treated with 500ng/ml Noggin (R&D Systems) and 10μM SB431542 (Tocris) for the first 6 days of differentiation. On day 12, neural stem cells (NSCs) were sorted using cell surface signature CD24+/CD184+/CD44-/CD271-. NSCs were expanded in NSC growth medium (DMEM:F12+GlutamaxTM (Thermo Fisher Cat. 10565018), 1x B-27 (Thermo Fisher Cat. 17504044), 1x N-2 (Thermo Fisher Cat. 17502001), 1x Penicillin-Streptomycin (Thermo Fisher Cat. 15070063), and 20ng/mL human bFGF-2 (BioPioneer Cat. HRP-0011)). At 80% confluence, the medium was changed to neuron differentiation medium (DMEM:F12+GlutamaxTM, 1x B-27, 1x N-2, 1x Penicillin-Streptomycin) for 3 weeks of differentiation. After differentiation, the cultures were dissociated with Accutase (Sigma Cat. A6964). Cells were resuspended in 200μL of iMag buffer (1x neural differentiation medium, 0.5µM EDTA, 0.5% Bovine Serum Albumin) followed by incubation with PE Mouse Anti-Human CD184 and CD44 antibodies (BD Biosciences Cat. 561733 and 561858, respectively) for 15min on ice in the dark. The mixture was washed with iMag buffer and subsequently incubated with anti-PE conjugated magnetic beads (BD Biosciences) for 30min at room temperature. Magnetic bead separation was carried out for 8min according to the manufacturer’s protocol (BD Biosciences). The supernatant containing purified CD184-/CD44- neurons was then removed and spun down for sequencing.

extract_protocol:
NDC and PSEN1M146L, and PSEN1A246E (biological replicates, n = 1) hiPSC-derived neurons were processed using the Active Motif ChIP-IT High Sensitivity kit according to the manufacturer’s recommendations (Active Motif, Cat. 53040). Briefly, cells were washed with cold 1x PBS and collected in a 1.5 mL tube in PBS, followed by formaldehyde fixation for 10 min at room temperature. After addition of stop solution, cells were incubated at room temperature for 5 min and subsequently washed with 1x PBS Wash Buffer and resuspended in Chromatin Prep Buffer. Following incubation on ice for 10 min, cells were lysed by performing 30 plunges in a chilled dounce homogenizer. Samples were then resuspended in Active Motif ChIP Buffer and chromatin sonication performed using a probe tip sonicator on ice for a total of 10 min per sample (30x 20 sec intervals). Optimal sonicated chromatin fragment lengths were confirmed by agarose gel and used for IP reactions. 500 ng of purified, sonicated chromatin was incubated with 5 µL of H3K4Me3 (Active Motif, Cat. 39159) or H3K27Me3 (Active Motif, Cat. 39155) Rabbit polyclonal antibody overnight at 4C. After de-crosslinking, ChIP DNA was purified using the Qiagen MinElute PCR Purification Kit (Qiagen, Cat. 28004).
Libraries for H3K4Me3, H3K27Me3, and 1% Input were generated for NDC and psen1M146L conditions at the UC San Diego IGM sequencing core using Illumina TruSeq LT adaptors (Illumina Cat. FC-121-2001). Sequencing performed on Illumina HiSeq4000 generating Single-Read, 75bp reads with an average of 20 million reads per sample.

value: hiPSC-derived neuron

tag: chip antibody

value: H3K27Me3 (Active Motif, Cat. 39155)


title: Whole blood, nfvPPA, 9631032028_C [ftd]

description: replicate 1

value: Female


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_A1_AD012


title: ChIPSeq_PSEN1_A246E_iPSCNeuron_H3K4Me3

value: H3K4Me3 (Active Motif, Cat. 39159)


title: III LUHMES GFP + MPP+  [mRNA]


title: CTC_2F11_3 RNA-seq

tag: vemurafenib sensitivity

value: resistant


title: Whole blood, CBS, 3999230075_I [ftd]

description: replicate 1


title: II LUHMES GFP + MPP+  [mRNA]


title: CTC_2F11_2 RNA-seq

tag: donor


title: Whole blood, svPPA, 9631032028_B [ftd]

description: replicate 1

value: svPPA

value: Male


title: ChIPSeq_PSEN1_M146L_iPSCNeuron_REST

source_name: hiPSC-derived neurons from human EOFAD patient, psen1 M146L mutation

value: REST (Millipore, Cat. 17-641)


title: 8donor_PBMC_AD_MULTI

city: San Francisco

first: Christopher

middle: S

last: McGinnis

address: 600 16th Street

department: Pharmaceutical Chemistry

institute: University of California, San Francisco

description: MULTI-seq DNA barcode

data_processing:
FASTQ files were generated directly from Illumina BCL files using Illumina bcl2fastq version 2.19
Gene-barcode matrices were determined using 10X Genomics Cellranger version 2.2 with default parameters (cellranger count).
Read-depth normalization was performed (when appropriate) using 10X Genomics CellRanger version 3.1 with default parameters (cellranger aggr).
Low-quality cell barcodes were excluded as described in the paper.
MULTI-seq and SCMK barcode alignment and sample classification results were performed using the deMULTIplex R package (https://github.com/chris-mcginnis-ucsf/MULTI-seq)
Genome_build: hg19
Supplementary_files_format_and_content: Expression Libraries: gene-cell matrices are provided in the format produced by CellRanger. The matrix itself is in matrix market exchange format, with the column (cell barcodes) and row (gene identities) labels given in TSV format as described in the cellranger documentation. MULTI-seq Libraries: MULTI-seq barcode-cell matrices are provided in CSV format. SCMK Libraries: SMCK barcode-cell matrices are provided in CSV format.

source_name: PBMC

extract_protocol:
Single cells were lysed in droplets using the 10X Chromium instrument. Reverse transcription was performed in droplet and library construction was performed according to the 10X Chromium Single Cell 3' Reagent Kit User Guide Rev C.
Library preparation was performed according to the 10X Chromium Single Cell 3' Reagent Kit User Guide Rev C and using custom MULTI-seq and/or SCMK library preparation protocols.

tag: multiplexing reagent

value: LMO


title: Whole blood, bvFTD, 3999230075_G [ftd]

description: replicate 1

source_name: Whole blood

value: bvFTD


title: 8donor_PBMC_AH_MULTI

description: MULTI-seq DNA barcode


title: III LUHMES GFP - MPP+  [mRNA]


title: WTrep2

city: Ithaca

first: Jeffrey

last: Pleiss

state: NY

address: 453 Biotech

institute: Cornell University

data_processing:
Fastq reads aligned to PomBase S. pombe genome (Assembly and annotations ASM294v2.26) using STAR (v2.5) with the following parameters: {--alignIntronMin 10 --alignIntronMax 1000} in multi-sample two-pass mode for most sensitive detection of splice junctions
Uniquely mapping splice junction read counts for each sample extracted from SJ.out.tab files generated by STAR
Intron-exon junction reads (indicative of intron retention) that overlap annotated intron-exon boundaries (minimum overhang of 3bp) were counted for each sample using bedtools (v2.26) in a strand specific manner
Splicing-relevant count table (processed data file) created by merging spliced junction count for all annotated and unannotated junctions, with the unspliced read counts that overlap intron-exon boundaries. Unannotated splice junctions may have NA as intron-exon junction count
Splice junctions in this processed data table are classified by whether their splice acceptor and/or splice donor is annotated or unannotated in the PomBase genome annotations
Genome_build: ASM294v2.26
Supplementary_files_format_and_content: Tab delmited file with position of junction as well as unspliced and spliced counts for each sample

organism: Schizosaccharomyces pombe

source_name: Culture

growth_protocol: Single colonies were inoculated into liquid YPD media and grown overnight at 25℃ with shaking at 200rpm. Overnight cultures were then inoculated into fresh liquid YPD, seeding cultures at OD600 =0.05 and grown to mid-log phase (OD600 =.8)

extract_protocol:
Temperature shifted cells were collected via vacuum filtration, flash frozen in liquid nitrogen, and pellets were stored at -80˚C. RNA was extracted using Phenol:Chloroform extraction as presented in Xu et al. Nature Methods 2019
Libraries were prepared according to manufacturer's protocols with NEBNext® Ultra™ II Directional RNA Library Prep Kit and NEBNext Poly(A) mRNA Magnetic Isolation kit,using 1ug total RNA input

treatment_protocol: Cells were shifted to 37˚C with shaking at 200 rpm for 15 minutes.

tag: strain

tag: genotype

value: WT


title: Whole blood, svPPA, 9631032039_D [ftd]

description: replicate 1


title: CTC_2F11_1 RNA-seq


title: ChIPSeq_PSEN1_A246E_iPSCNeuron_INPUT 2

value: 1% Input


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_A1_AD010

source_name: C57BL/6J P56 Mouse Brain

tag: age

tag: tissue

value: brain

tag: source

value: MOp

value: STR


title: WTrep1


title: Whole blood, bvFTD, 9631032028_A [ftd]

description: replicate 1

tag: diagnosis


title: ChIPSeq_PSEN1_A246E_iPSCNeuron_INPUT 1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_A1_AD008

tag: target

tag: gender

value: female


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_A7_AD001

value: SC

value: male


title: II LUHMES GFP - MPP+  [mRNA]

value: n


title: CTC_1F3_2 RNA-seq

value: sensitive


title: 106C01


title: Whole blood, svPPA, 3999230075_H [ftd]

description: replicate 1

tag: Sex

tag: batch


title: RNASeq_PSEN1_A431E_iPSCNeuron_rep3

description: Batch 2, DMSO

data_processing:
RNA-Seq data preprocessing was performed using the TrimGalore! Package, removing sequencing adaptors and selecting for all paired-end reads above a quality score threshold (Phred Q>20).
Trimmed RNA-Seq reads were mapped to the GRCh38.99 human transcriptome using kallisto v0.46.1 with the options -bias, --rf-stranded, and -b 100.
Transcript level summation to the gene level using the R package tximport v1.8.0. Counts were normalized for batch effects and modeled with the voomwithqualityweights function in the R package limma.
Differential expression analysis was performed for all four PSEN1 mutant iPSC-derived neurons relative to NDC using the TREAT method in the R package limma with a null-hypothesis t-test fold-change (FC) threshold of 1.5 and selection of DEGs with a FDR-adjusted p-value of < 0.05.
Genome_build: GRCh38.99
Supplementary_files_format_and_content: Normalized count matrix for all RNA-Seq samples

source_name: hiPSC-derived neurons from human EOFAD patient, psen1 A431E mutation

growth_protocol: Non-Demented Control (NDC), PSEN1M146L, and PSEN1H163R, and PSEN1A431E fibroblasts were derived from skin biopsies in accordance with UC San Diego IRB approval, whereas PSEN1A246E fibroblasts were obtained commercially (Coriell Cat. AG06840). The generation and characterization of the hiPSC lines were carried out as previously reported from fibroblasts by retroviral transduction using the reprogramming factors OCT4, SOX2, KLF4, and c-MYC. PA6 cells were plated in a 10 cm dish and seeded with 100,000 cells iPSC next day. To enhance neural induction, cultures were treated with 500ng/ml Noggin (R&D Systems) and 10μM SB431542 (Tocris) for the first 6 days of differentiation. On day 12, neural stem cells (NSCs) were sorted using cell surface signature CD24+/CD184+/CD44-/CD271-. NSCs were expanded in NSC growth medium (DMEM:F12+GlutamaxTM (Thermo Fisher Cat. 10565018), 1x B-27 (Thermo Fisher Cat. 17504044), 1x N-2 (Thermo Fisher Cat. 17502001), 1x Penicillin-Streptomycin (Thermo Fisher Cat. 15070063), and 20ng/mL human bFGF-2 (BioPioneer Cat. HRP-0011)). At 80% confluence, the medium was changed to neuron differentiation medium (DMEM:F12+GlutamaxTM, 1x B-27, 1x N-2, 1x Penicillin-Streptomycin) for 3 weeks of differentiation. After differentiation, the cultures were dissociated with Accutase (Sigma Cat. A6964). Cells were resuspended in 200μL of iMag buffer (1x neural differentiation medium, 0.5µM EDTA, 0.5% Bovine Serum Albumin) followed by incubation with PE Mouse Anti-Human CD184 and CD44 antibodies (BD Biosciences Cat. 561733 and 561858, respectively) for 15min on ice in the dark. The mixture was washed with iMag buffer and subsequently incubated with anti-PE conjugated magnetic beads (BD Biosciences) for 30min at room temperature. Magnetic bead separation was carried out for 8min according to the manufacturer’s protocol (BD Biosciences). The supernatant containing purified CD184-/CD44- neurons was then removed and spun down for sequencing.

extract_protocol:
Total RNA from magnetically purified human NDC (replicates, n = 8), PSEN1M146L (replicates, n = 4), PSEN1H163R (replicates, n = 3) , PSEN1A246E (replicates, n = 3), and PSEN1A431E (replicates, n = 4) hiPSC-derived neurons was prepared using RNeasy Plus Micro Kit (Qiagen Cat. 74034) according to the manufacturer’s protocol. On-column DNAse digestion was subsequently performed on total RNA extracts according to the manufacturer’s recommendations to remove any genomic contamination (Qiagen Cat. 79254).
Libraries were prepared for RNA-Seq using the TruSeq Stranded Total RNA Library prep kit (Illumina, Cat. RS-122-2303) by the Ribo-Zero ribosomal RNA reduction method (Illumina, Cat. MRZG12324). Samples were sequenced at the UC San Diego Institute for Genomics Medicine (IGM) sequencing core on an Illumina HiSeq4000 generating Paired-End, 100bp reads with an average of 25 million reads per sample (Illumina, Cat. FC-410-1001).

value: hiPSC-derived neuron


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_A1_AD007


title: CTC_1F3_1 RNA-seq

tag: cell line


title: I LUHMES GFP + MPP+  [mRNA]

value: y


title: I LUHMES GFP - MPP+ [mRNA]


title: 106A18


title: s167In ChIP-seq

data_processing:
ChIP-seq reads were aligned to the GRCh38 build of the human genome reference using the Bowtie2 (PMID: 22388286)
Only uniquely mapped reads with mapping quality higher than 30 were retained and duplicated reads were removed.
Reads overlapping with ENCODE blacklist regions were also removed. (https://www.encodeproject.org/files/ENCFF419RSJ/@@download/ENCFF419RSJ.bed.gz)
Peaks from each MEL-167 replicate were called using the MACS2(PMID: 18798982) with a liberal P value threshold of 1 x 10^(-3) for the Irreproducible Discovery Rate (IDR) framework (Li Q, Brown JB, Huang H, Bickel PJ. Measuring reproducibility of high-throughput experiments. The Annals of Applied Statistics 2011;5(3):1752-79 doi DOI: 10.1214/11-AOAS466) and (PMID: 22955991).
Genome_build: GRCh38
Supplementary_files_format_and_content: Both processed data files are narrowPeak format files (https://genome.ucsc.edu/FAQ/FAQformat.html#format12)

source_name: MEL167 SREBP2 ChIPseq

extract_protocol:
Cultured CTCs were washed with ice-cold phosphate buffered saline (PBS) and homogenized while on ice using lysis buffer (0.32M sucrose, 5 mM CaCl2, 3 mM MgAc, 0.1 mM EDTA, 10 mM Tris-HCL (pH 8.0), 1 mM DTT and 0.1% Triton X-100). The lysate was crosslinked using 1% formaldehyde for 10 min at room temperature and then quenched with glycine. ChIP was performed using Magna ChIP(TM) Hisens Chromatin Immunoprecipitation Kit (Millipore Cat#17-104-60) following the manufacturer’s instructions. Briefly, the precipitated nuclei were resuspended in SCW buffer containing protease inhibitor cocktail, followed by sonication using a Covaris S2, yielding an average fragment size of 250bp. The chromatin was then immunoprecipitated using Protein A Dynabeads (In vitrogen) with 5mg of ChIP-grade antibody overnight at 4oC. The beads were repeatedly washed with high- and low-salt buffers, and the DNA fragments were then de-crosslinked using proteinase K at 65oC for 4 hrs, followed by ethanol precipitation.
ChIP-seq library was constructed using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (Catlog# E7645L).


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_A1_AD006


title: RNASeq_PSEN1_A431E_iPSCNeuron_rep2

description: Batch 2, DMSO

tag: cell type


title: 105M13


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_A1_AD004


title: RNASeq_PSEN1_A431E_iPSCNeuron_rep1

description: Batch 2, DMSO


title: s167FLAGrep1 ChIP-seq


title: RNASeq_PSEN1_H163R_iPSCNeuron_rep3

description: Batch 2, DMSO

source_name: hiPSC-derived neurons from human EOFAD patient, psen1 H163R mutation


title: Mel-167-primary-2 RNA-seq

source_name: melanoma primary tumor


title: RNASeq_PSEN1_H163R_iPSCNeuron_rep2

description: Batch 2, DMSO


title: 104O20


title: s167FLAGrep2 ChIP-seq


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_A1_AD001


title: 102B12


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_A12_AD012


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_A1_AD002


title: RNASeq_PSEN1_H163R_iPSCNeuron_rep1

description: Batch 2, DMSO


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_A12_AD010


title: RNASeq_NDC_iPSCNeuron_rep8

description: Batch 3, DMSO

source_name: hiPSC-derived neurons from human Non-Demented Control patient


title: nasal respiratory epithelium, patient 3

description:
patient3_re
11532_P3PlQh01jaVm
bulk tissue RNA-seq of a ~3 mm diameter intraoperative biopsie of the nasal respiratory epithelium

source_name: respiratory epithelium, nasal cavity

tag: patient id

value: patient 3

value: respiratory epithelium, nasal cavity


title: Cfast Kd replicate-3

city: Hang Zhou

first: Feng

last: Zhang

state: Zhejiang

address: Kaixuan road number 258

country: China

institute: Zhejiang University

description: Cfast Kd vs Ctrl_deg_all.txt

data_processing:
Illumina Casava1.7 software used for basecalling.
Quality control: Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads mapping to the reference genome: Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using STAR and paired-end clean reads were aligned to the reference genome using STAR (v2.5.1b). STAR used the method of Maximal Mappable Prefix(MMP) which can generate a precise mapping  result for junction reads.
Differential expression analysis: Differential expression analysis of two  conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.10.1). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed.
GO and KEGG enrichment analysis of differentially expressed genes: Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the clusterProfiler R package, in which gene length bias wascorrected. GO terms with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes.  KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-through put experimental technologies (http://www.genome.jp/kegg/). We used clusterProfiler R package to test the statistical enrichment of differential expression genes in KEGG pathways.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample …

source_name: cardiac fibroblast

growth_protocol: Neonatal mouse cardiac fibroblasts were isolated by enzymatic disassociation according to the manual of neonatal heart dissociation Kit and cultured in DMEM Medium containing 10% fetal bovine serum (FBS) and Penicillin-Streptomycin (100 U/mL).

extract_protocol:
Total RNA was isolated from fresh ventricular tissue using Trizol. mRNA was then purified from total RNA using poly-T oligo-attached magnetic beads.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations, and index codes were added to attribute sequences to each sample.

treatment_protocol: For infection, cells plated at density of 1×105 /cm2, were infected with indicated lentiviruses expressing of shRNA targeting Cfast or scramble shRNA as control for 24 hours at infection of 50 MOI, and then refreshed with fresh medium. After 72 hours harvested by Trizol.

tag: lentivirus

value: shRNA targeting Cfast

value: Heart

value: cardiac fibroblast


title: PEM-22-met-RA RNA-seq

source_name: melanoma metastatic tumor

extract_protocol:
Cells of about 10^5-10^6 in total are disrupted in 350 microliter RLT buffer with the addition of  beta-mecaptoenthanol and then homogenized as described in the kit (RNeasy mini kit, Qiagen Cat # 74104). 70% Ethanol is added to the lysate with the volume ratio 1:1 which is then followed by column purification steps. The residual amount of DNA remaining is removed using on-column DNase treatment and RNA is eluted in 30 µl of nuclease-free water.
SmartSeqHT: According to the manufacturer’s protocol, amplified cDNA was generated by using the SMARTer HT RNA kit (Clontech/Takara) followed by Nextera® XT DNA Library Preparation kit (Illumina) for sample barcoding and fragmentation. Briefly, 10 ng of RNA was subjected to first‐strand synthesis of RNA molecules was performed using the poly‐dT‐based 3’‐SMART CDS primer II A (Clontech) followed by extension and template switching by the reverse transcriptase. The second strand synthesis and amplification polymerase chain reaction (PCR) was run for 18 cycles, and the amplified cDNA was purified with a 1× Agencourt AMPure XP bead cleanup (Beckman Coulter,). The Nextera XT DNA Library Preparation kit (Illumina) was used for sample barcoding and fragmentation according to the manufacturer's protocol. One nanogram of amplified cDNA was used for the enzymatic tagmentation, followed by 12 cycles of amplification and unique dual‐index barcoding of individual libraries. PCR product was purified with a 1.8× Agencourt AMPure XP bead cleanup (Beckman Coulter).


title: Mel-167-primary-1 RNA-seq


title: Cfast Kd replicate-2

description: Cfast Kd vs Ctrl_deg_all.txt


title: RNASeq_NDC_iPSCNeuron_rep7

description: Batch 2, DMSO


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_A12_AD008

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.


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

description: replicate 1

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

value: PSP

value: Male


title: PEM-22-met-LRL RNA-seq


title: 103A10


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_A12_AD007

value: brain


title: Ctrl replicate-3

description: Cfast Kd vs Ctrl_deg_all.txt

value: scramble shRNA


title: PEM-22-met-LL RNA-seq


title: PEM-22-met-Liver-LL RNA-seq


title: Ctrl replicate-2

description: Cfast Kd vs Ctrl_deg_all.txt


title: RNASeq_NDC_iPSCNeuron_rep5

description: Batch 2, DMSO


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_A12_AD004

value: MOp


title: PEM-22-met-LD RNA-seq


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_A12_AD006

value: female


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_A12_AD002

value: SC


title: Ctrl replicate-1

description: Cfast Kd vs Ctrl_deg_all.txt


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_A12_AD001

value: male


title: PEM-22-met-B RNA-seq


title: ATACSeq_PSEN1_A431E_iPSCNeuron_rep2

data_processing:
ATAC-Seq data preprocessing was performed using the TrimGalore! Package, removing sequencing adaptors and selecting for all paired-end reads above a quality score threshold (Phred Q>20).
Trimmed reads were aligned to the GRCh38 human genome (GCA_000001405.15 with no alternative analysis) using BBMap v37.95 in the BBtools suite with the options maxindel=20 ambig=random.
Sorting and indexing of bam files was performed using Samtools v1.3, and annotation of PCR duplicates using the Picard v2.3.0 markDuplicates function with the option VALIDATION_STRINGENCY=LENIENT. All duplicates and Mitochondrial, Chromosome X, Chromosome Y, and EBV reads were removed using Samtools v1.3 command view with the options -b -h -f 3 -F 4 -F 8 -F 256 -F 1024 -F 2048.
To determine regions of open chromatin, HMMRATAC v1.2.4 was used to call peaks on the ATAC-Seq data and determine regions of open chromatin with the options –m 50,200,400,600 --score all.
Genome_build: GCA_000001405.15
Supplementary_files_format_and_content: Bed files of HMMRATAC summits

extract_protocol:
ATAC-Seq transposition experiments were performed as previously reported on 50,000 NDC (n = 5), PSEN1M146L (n = 2), PSEN1H163R (n = 3), PSEN1A246E (n = 2), and PSEN1A431E (n = 3) hiPSC-derived neurons using the Illumina Nextera DNA Sample Preperation kit (Illumina, Cat. 15028523) and Qiagen MinElute PCR Purification kit (Qiagen, Cat. 28004).
ATAC-Seq libraries were generated from transposed DNA using the Kapa Biosystems Real-Time Library Amplification kit (Kapa Biosystems, Cat. 07959028001) according to the manufacturer’s recommendations, monitoring amplification by qPCR and stopping the reaction when all samples reached a fluorescence amplification intensity between standards 1 and 3. ATAC-Seq libraries were further purified using the Qiagen MinElute PCR Purification kit and sequenced at the UC San Diego IGM sequencing core on an Illumina HiSeq4000 platform generating Paired-End, 50bp reads with an average of 25 million reads per sample.


title: ATACSeq_PSEN1_H163R_iPSCNeuron_rep3


title: Cfast Kd replicate-1

description: Cfast Kd vs Ctrl_deg_all.txt


title: ATACSeq_PSEN1_A431E_iPSCNeuron_rep1


title: ATACSeq_PSEN1_A431E_iPSCNeuron_rep3


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_A11_AD012

value: STR


title: RNASeq_NDC_iPSCNeuron_rep6

description: Batch 2, DMSO


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_A11_AD008


title: PEM-78_2 RNA-seq

data_processing:
RNA-seq reads were aligned to the GRCh38 build of the human genome reference using STAR 2.6.1d (PMID: 23104886).
Duplicated reads were identified and flagged using Picard Tools v2.18.24 MarkDuplicates.
Gene-level TPM values were calculated using RNA-SeQC v2.2.2 (PMID: 22539670).
The GENCODE v26 annotation was used for the STAR alignment and all other quantifications. All methods were run as part of the pipeline developed for the GTEx Consortium(PMID: 29022597).
Gene-level quantifications were obtained by collapsing the GENCODE annotation to a single transcript per gene, using the procedure described in GTEx Consortium(PMID: 29022597)
Genome_build: GRCh38
Supplementary_files_format_and_content: Transcripts Per Million (TPM). Rows correspond to genes, columns correspond to samples.

source_name: melanoma CTC line


title: PEM-78_1 RNA-seq


title: ATACSeq_PSEN1_H163R_iPSCNeuron_rep1


title: PEM-22_3 RNA-seq


title: Patient P P2

city: Manchester

first: Jorge

last: Barriuso

state: Please Select

address: Wilmslow Road

department: Division of Cancer Sciences

institute: University of Manchester

hyb_protocol: Hybridation protocol as manufacturer using the Nanostring protocol for codeset plus / panel plus.

scan_protocol: Analysed in the Nanostring Digital Analyser at 555 field of view (FOV) count. Quality checks ran using Nanostring nSolverTM Software analysis was performed with no flags for any of the samples.

data_processing: Normalization was performed using the nCounter® Advanced Analysis Software 2.0. The setting was to allow the software to automatically select the best performing probes. The Advanced Nalysis uses the NormqPCR R packageto select co-expressed housekeeping genes prior to normalization and automatically find good normalization probes the threshold to omit low count data was set at 10.

label: Nanostring bar coding

source_name: peritoneal metastases

extract_protocol: Four 5μm FFPE sections mounted on unstained slides were marked up by a pathologist prior to macro-dissection and then deparaffinised using Qiagen deparaffination solution. Following RNA extraction using the RNeasy FFPE Kit from Qiagen RNA abundance was measured using a Qubit fluorometer.  The extracted RNA was then stored at minus 80°C. Total RNA average input into the hybridisation step was 103 ng.NA average input into the hybridisation step was 103 ng.

tag: subject id

value: Patient P

tag: status at the end of study

value: Dead

tag: histology

value: non mucinous

value: Female

tag: Stage

value: IV

tag: overall survival in months

tag: tissue type

value: peritoneal metastases


title: Patient Q Q2

label_protocol: Qiagen RNA abundance was measured using a Qubit fluorometer.  The extracted RNA was then stored at minus 80°C. Total RNA average input into the hybridisation step was 103 ng.NA average input into the hybridisation step was 103 ng.

value: Patient Q

value: Alive

value: mucinous

tag: age


title: PEM-22_2 RNA-seq

tag: donor


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_A11_AD006

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

tag: strain

tag: tissue

tag: source


title: Patient P P1

source_name: primary colon cancer

tag: Sex

value: primary colon cancer


title: Patient N N2

value: Patient N


title: ATACSeq_PSEN1_A246E_iPSCNeuron_rep1

source_name: hiPSC-derived neurons from human EOFAD patient, psen1 A246E mutation

value: hiPSC-derived neuron


title: PEM-78_3 RNA-seq


title: Patient Q Q1

value: Male


title: Patient N N1


title: PEM-22_1 RNA-seq


title: ATACSeq_PSEN1_H163R_iPSCNeuron_rep2


title: ATACSeq_NDC_iPSCNeuron_rep5


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_A11_AD002

value: brain

value: MOp

tag: target

tag: gender

value: female


title: ATACSeq_NDC_iPSCNeuron_rep4

tag: cell type


title: Mel-182-2_1 RNA-seq

tag: cell line


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_A10_AD012

value: STR


title: Mel-182-1_2 RNA-seq


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_A11_AD001

value: SC

value: male


title: ATACSeq_NDC_iPSCNeuron_rep3


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_A11_AD007


title: Patient K K2

value: Patient K

value: Dead