title: WT_NPC_RAD21

city: Santander

first: Alvaro

last: Rada-Iglesias

state: Cantabria

address: Albert Einstein 22, PCTCAN

country: Spain

institute: Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), CSIC/University of Cantabria

data_processing:
Basic read quality check was performed using FastQC (Babraham Bioinformatics) and MultiQC. The removal of read adapters and low-quality filtering was done with trimmomatic.
Reads were mapped to the mm10 reference genome with Bowtie2. After reads mapping, only those with a mapping quality above 10 were kept. In addition, duplicated reads were discarded with SAMtools.
Bigwig files were generated with deepTools using bamCoverage (reads per genomic content normalization).
Assembly: mm10
Supplementary files format and content: Bigwig files for each sample.

source_name: WT mESC

growth_protocol: E14Tg2a (E14) mouse ESCs were cultured on gelatin-coated plates using Knock-out DMEM (Life Technologies, 10829018) supplemented with 15% FBS (Life Technologies, 10082147), leukemia inhibitory factor (LIF), antifungal and antibiotics (Sigma-Aldrich, A5955), β-mercaptoethanol (ThermoFisher Scientific, 21985023), Glutamax (ThermoFisher Scientific, 35050038) and MEM NEAA (ThermoFisher Scientific, 11140035). Cells were cultured at 37°C with 5% C02. For the NPC differentiation 80, ESCs were plated at 20,000 cells/cm2 on geltrex-coated plates (ThermoFisher, A1413302) and grown in N2B27 medium_ Advanced Dulbecco’s Modified Eagle Medium F12 (Life Technologies, 21041025) and Neurobasal medium (Life Technologies, 12348017) (1_1), supplemented with 1× N2 (R&D Systems, AR009), 1× B27 (Life Technologies, 12587010), 2 mM L-glutamine (Life Technologies, 25030024) and 0.1 mM 2-mercaptoethanol (Life Technologies, 31350010)). During the six days of differentiation, the N2B27 medium was additionally supplemented with the following components_ bFGF (ThermoFisher Scientific, PHG0368) 10 ng/ml from day 0 to day 2, Xav939 (Sigma-Aldrich, X3004-5MG) 5µM from day 2 to day 6, BSA (ThermoFisher Scientific, 15260037) 1mg/ml at day 0 and 40 µg/mL the remaining days.

extract_protocol:
~4 × 107 cells were used for RAD21 (abcam, ab154769) and ~1 × 107 cells for H3K27ac (Active Motif, 39133). Cells were crosslinked with 1% formaldehyde for 10 min at room temperature (RT) and quenched with 0.125 M glycine for 10 min. Cells were consecutively incubated with three different lysis buffers (Buffer 1_ 50 mM HEPES, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% TX-100; Buffer 2_ 10 mM Tris, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA; Buffer 3_ 10 mM Tris, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-deoxycholate, 0.5% N-lauroylsarcosine) in order to isolate chromatin. Next, chromatin was sonicated for 8 minutes in Buffer 3 (20 s on, 30 s off, 25% amplitude) using an EpiShear probe sonicator (Active Motif).  The sonicated chromatin was mixed with 3 μg of H3K27ac antibody or 10 μg of Rad21 antibody and incubated overnight at 4°C. Next, 50-100 μl of Dynabeads (Thermo Fisher, 10-002-D) were aliquoted into a microtube for each ChIP reaction. The dynabeads were washed with 1 ml of cold blocking solution (0,5% BSA and 1x PBS). The antibody bound chromatin was added to the washed beads and incubated for four hours at 4ºC. Magnetic beads were washed five times with RIPA buffer (50 mM Hepes, 500 mM LiCl, 1 mM EDTA, 1% NP-40 and 0,7% Na-Deoxycholate). The chromatin was eluted and incubated at 65 °C overnight to reverse the crosslinking. Next, samples were treated with 0,2 mg/ml Rnase A and 0,2 mg/ml proteinase K. DNA  purification was performed using Zymoclean Gel DNA Recovery kit (Zymo Research, D4008).
DNA libraries were prepared using theTruSeq ChIP-seq sample preparation kit. 10 ng of ChIP DNA was used as starting material.

treatment_protocol: Transgenic mESC lines with different genomic re-arrangements were generated using CRISPR/Cas9 technology. The design of the CRISPR/Cas9 guide sequences (gRNA) was performed using the CRISPR Benchling software tool (https_//www.benchling.com/crispr/) (Data S3). In order to increase the cutting efficiency of the gRNA, a guanine nucleotide was added at the first position of the sequence and a restriction site for the BbsI enzyme (R0539L, NEB) was added to the beginning of the gRNA for cloning purposes. For each sgRNA, two oligonucleotides were synthesized (Sigma) annealed and cloned into a CRISPR-Cas9 expression vector (pX330-hCas9-long-chimeric-grna-g2p; gift from Leo Kurian’s laboratory). The hybridized oligos were cloned into the pX330-hCas9-long-chimeric-grna-g2p using 50 ng of BbsI-digested vectors and 1 ul ligase (Thermo Fisher, EL0013) in a total volume of 20 μl. The ligation reaction was incubated for 1 h at room temperature. For each cell line,  ESC were transfected with the corresponding pair of gRNAs-Cas9 expressing vectors using Lipofectamine following manufactured recommendations (Thermo Scientific, L3000001). After 24 hours, transfected cells were selected by treating them with for 48 hours. Single-cell isolation of surviving cells was performed by serial dilution and seeding in 96-well plates. Next, clones with the desired genetic rearrangements (i.e. deletions or inversions) were identified by PCR using the primers listed in Data S3. DNA extraction was performed using Lysis Buffer_ 25 mM KCl (SigmaAldrich, 27810.295), 5mM TRIS (Sigma-Aldrich, 0497-5KG) pH8.3, 1.25mM MgCl2 (VWR BDH7899-1), 0.225% IGEPAL (Sigma-Aldrich, I8896-50ML) and 0.225% Tween20 (VWR). Proteinase K (ThermoFisher Scientific, EO0492) was added to a final concentration of 0.4 µg/ul before use.

value: WT mESC

value: NPC

value: WT

value: mESC differentiation into NPC; RAD21 antibody (Abcam; ab154769)


title: Six3KO_NPC_H3K27ac

status: Public on Dec 29 2023

type: SRA

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

source_name: Six3KO mESC

tag: cell line

value: Six3KO mESC

tag: cell type

tag: genotype

value: Six3KO 27 Kb deletion

tag: treatment

value: mESC differentiation into NPC; H3K27ac antibody (39133, Active Motif)


title: Δ6XCTCF_NPC_H3K27ac

source_name: delta6XCTCF mESC

value: delta6XCTCF mESC

value: delta6XCTCF 36 Kb deletion


title: Δ6XCTCF_NPC_RAD21


title: Δ6XCTCF_Six3KO_NPC_RAD21

source_name: delta6XCTCF_Six3KO mESC

value: delta6XCTCF_Six3KO mESC

value: delta6XCTCF 36 Kb deletion and Six3KO 27 Kb deletion


title: Six3KO_NPC_RAD21


title: Δ6XCTCF_Six3KO_NPC_H3K27ac


title: WT_NPC_H3K27ac


title: BALBc_1

city: Bethesda

first: Mingming

last: Zhao

address: 9000 Rockville Pike

country: USA

institute: national institutes of health

library_source: transcriptomic

data_processing:
TheReal Time Analysis software (RTA 3.4.4) was used for processing raw data files, the Illumina bcl2fastq v2.20 was used to demultiplex and convert binary base calls and qualities to fastq format.
Reads were trimmed for adapters and low-quality bases using Cutadapt(1.18)
Alignment with the reference genome (mm10) and the annotated transcripts using STAR(2.6.0c)
Gene expression quantification analysis was performed for all samples using STAR/RSEM ( v1.3.2) tools
EBSeq (1.24.0)and DESeq2(1.24.0) were used to find differential RNA expression
Assembly: mm10
Supplementary files format and content: raw counts text files were produced by RSEM( v1.3.2)

molecule: total RNA

source_name: Peritoneal Macrophage

growth_protocol: Macrophage cells were isolated from the peritoneal cells by using EasySep™ Mouse F4/80 Positive Selection Kit (100-0659, Stemcell Technologies)

extract_protocol:
Total RNA was isolated using the RNeasy Plus Mini Kit (74134, QIAGEN)
mRNA-Seq samples were pooled and sequenced on NextSeq 2000 P2 using Illumina Illumina® Stranded mRNA Prep and paired-end sequencing.

treatment_protocol: Mice were treated with IL4,H. polygyrus or LPS in vivo or in vitro

value: Macrophage

tag: strain

value: BALB/c

value: untreated


title: BALBc_input

data_processing:
TheReal Time Analysis software (RTA 3.4.4) was used for processing raw data files, the Illumina bcl2fastq v2.20 was used to demultiplex and convert binary base calls and qualities to fastq format.
Samples were trimmed for adapters using Cutadapt (1.18) before the alignment.
The trimmed reads were aligned with mm10 reference using Bowtie2(2.2.6) alignment.
Peaks were called by MACS2 (2.2.6) with –broad option on.
HOMER (v4.11) findPeaks -style super was used to find super enhancer in ChIP-seq
findMotifs-Genome.pl and findMotifs.pl from HOMER (v4.11) were used to identify transcription factor binding motifs within peaks or promoter regions (−400 to +100 bp from TSSs)
Assembly: mm10
Supplementary files format and content: bigwig files were generated using bamCoverage from deepTools (3.5.0)

source_name: Pritoneal Macrophage

extract_protocol:
Cells were washed twice with PBS and then were fixed at room temperature with 1% formaldehyde in PBS for 10 min for H3K27ac ChIP. Reactions were quenched by adding glycine to a final concentration of 0.125 M, and cells were washed twice with cold PBS. Cells were resuspended in cell lysis buffer (1% SDS, 10mM EDTA, 50mM Tris-HCl pH8.1), incubated in ice for 1 hour. The crosslinked chromatin was fragmented by sonication (Covaris, M220) to sheer size 200-2000bp. The final sonication product was diluted 5 times by dilution buffer(0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7mM Tris-Hcl pH 8.0, 167mM NaCl). ChIP was performed with 3 μg anti-H3K27ac (39133, Active Motif) antibody-bound Protein A beads (10001D, Invitrogen) and incubated at 4°C overnight. Beads were collected by centrifugation, washed, and incubated at 65°C for 4h in elution buffer (50 mM Tris-HCl, pH 7.5; 10 mM EDTA; 1% SDS) to reverse cross-linking. ChIP DNA was purified by ChIP DNA Clean & Concentrator (Zymo Research:D5205).
For sequencing, ChIP-seq samples were pooled and sequenced on NextSeq2000 using TruSeq ChIP Library Prep Kit (IP-202-1012) and single-end sequencing.

treatment_protocol: Two replicates were IL4 treated for 4 days in vivo

tag: chip antibody

value: treated with A fusion protein of mouse IL-4 with the Fc portion of IgG1


title: BL6_input


title: 1-4 MV

city: Houston

first: exRNA

last: BRL

state: TX

address: One Baylor Plaza

department: Molecular & Human Genetics - Milosavljevic

institute: Baylor College of Medicine

description:
Plasma/Serum Circulating and Exosomal RNA Purification Kit(Norgen Biotek)
EXR-LLAUR1AFSRR1BS61-BS

data_processing:
All FASTQ files were processed uniformly through the extra-cellular RNA processing toolkit (exceRpt). Information about exceRpt is available at https://github.gersteinlab.org/exceRpt/.
Assembly: hg19
Supplementary files format and content: Each processed data file is a core results archive generated by exceRpt. The core results archive contains read counts for alignments to the different transcriptome libraries used by exceRpt (miRNA / piRNA / tRNA / GENCODE annotations / circRNA), taxonomy trees for exogenous rRNA and genomic reads aligned by exceRpt, and a variety of other files generated by exceRpt.

organism: Homo sapiens

source_name: Saliva

extract_protocol:
RNA Isolation method was . RNA Isolation kit was Plasma/Serum Circulating and Exosomal RNA Purification Kit(Norgen Biotek).
Library construction kit was NEBNext small RNA library prep (NEB). Samples were multiplexed. Type of Starting Material was total RNA.

tag: condition

value: Healthy Subject

tag: anatomical location

value: Oral cavity structure

tag: rna source

value: total cell-free biofluid RNA


title: Δ3XCTCF_ΔPromGbx2_ESC_RAD21

source_name: delta3XCTCF_deltaPromGbx2 mESC

value: delta3XCTCF_deltaPromGbx2 mESC

value: mESC

value: delta3XCTCF 10 Kb deletion and deltaPromGbx2 1 Kb deletion

value: RAD21 antibody (Abcam; ab154769)


title: 2-3 MV

description:
Plasma/Serum Circulating and Exosomal RNA Purification Kit(Norgen Biotek)
EXR-LLAUR1AFSRR1BS63-BS


title: HGC27-control-rep1

type: RNA

city: Beijing

first: Zhengsen

last: Jin

address: Chaoyang District North Third Ring Road East No.11

country: China

institute: Beijing University of Chinese Medicine

hyb_protocol: Labeled cRNA samples were hybridized onto Agilent Human ceRNA Microarray 2019 (4*180k, Design ID: 086188) chips according to the manufacturer's protocol. Briefly, hybridization was performed at 65°C for 17 hours in Agilent's SureHyb chambers.

scan_protocol: After hybridization, the microarray slides were washed with Agilent wash buffers and scanned on an Agilent Microarray Scanner (model number G2505C) using the one color scan setting for 4x180k array slides (Scan Resolution = 3 μm, 20 bit). The scanned images were analyzed with Feature Extraction Software (version 10.7.1.1, Agilent Technologies) using default parameters.

data_processing: Raw data was extracted with Feature Extraction Software and normalized using the quantile normalization method. Probes detected (Detected flag) in at least one sample per group were retained. Differentially expressed genes were identified based on fold change ≥ 2 and p-value ≤ 0.05 calculated by t-test.

source_name: cells, no treatment

label_protocol: Total RNA was reverse transcribed to double strand cDNA then synthesized into cRNA labeled with Cyanine-3-CTP using the Quick Amp Labeling Kit, One-Color (Agilent Technologies) following the manufacturer's protocol.

growth_protocol: Human gastric cancer cell line HGC-27 was obtained from the Cell Bank of the Chinese Academy of Sciences (Shanghai, China). The HGC-27 cells were maintained in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS) and 1% penicil-lin/streptomycin at 37°C in a humidified incubator with 5% CO2.

extract_protocol: Total RNA was extracted from the HGC-27 cells using TRIzol reagent according to the manufacturer's protocol. RNA concentration and purity were measured using a NanoDrop ND-2000 spectrophotometer. RNA integrity was assessed with an Agilent 2100 Bioanalyzer. Only RNA samples with sufficient concentration, purity, and integrity (RIN ≥ 7) were used for downstream microarray analysis.

treatment_protocol: OMT


title: BALBc_IL4_H3K27ac_2

value: anti-H3K27ac (39133, Active Motif)


title: ΔPromGbx2_ESC_RAD21

source_name: deltaPromGbx2 mESC

value: deltaPromGbx2 mESC

value: deltaPromGbx2 1 Kb deletion


title: Δ3XCTCF_ESC_H3K27ac

source_name: delta3XCTCF mESC

value: delta3XCTCF mESC

value: delta3XCTCF 10 Kb deletion

value: H3K27ac antibody (39133, Active Motif)


title: ΔPromGbx2_ESC_H3K27ac


title: HGC27-control-rep2


title: HGC27-control-rep3


title: HGC27-OMT-rep1

source_name: HGC-27 cells, treated with 2.64 mg/mL OMT, 48 h

value: OMT


title: HGC27-OMT-rep3


title: HGC27-OMT-rep2


title: Δ3XCTCF_ΔPromGbx2_ESC_H3K27ac


title: BALBc_IL4_H3K27ac_1

value: Macrophage

value: BALB/c


title: BL6_IL4_H3K27ac_2

value: treated with A fusion protein of mouse IL-4 with the Fc portion of IgG1


title: 2_6

description:
Plasma/Serum Circulating and Exosomal RNA Purification Kit(Norgen Biotek)
EXR-LLAUR1AFSRR1BS92-BS

value: Healthy Subject


title: 2_10

description:
Plasma/Serum Circulating and Exosomal RNA Purification Kit(Norgen Biotek)
EXR-LLAUR1AFSRR1BS96-BS

value: Oral cavity structure


title: 2_8

description:
Plasma/Serum Circulating and Exosomal RNA Purification Kit(Norgen Biotek)
EXR-LLAUR1AFSRR1BS94-BS

value: total cell-free biofluid RNA


title: BL6_IL4_H3K27ac_1


title: WT_ESC_H3K27ac

value: WT mESC

value: WT


title: WT_ESC_RAD21

value: mESC


title: Δ6XCTCF_Six3KO_NPC_Six2_rep1

data_processing:
Capture C reads were subject to quality control and trimming of low quality regions and/or adapters using fastqc (https_//www.bioinformatics.babraham.ac.uk/projects/fastqc/), MultiQC and trimmomatic .
Reads were processed with capC-MAP, considering the restriction enzyme NlaIII (cutting site CATG), the mm10 reference genome and normalize = TRUE. The coordinates (mm10) of the viewpoints (i.e. «targets» according to capC-MAP terminology) were_ Gbx2 SE _ chr1 89869929 89870764 ; Six3 SE _ chr17 85484699 85485038; Asb18 TSS_ chr1 90013014 90013383; Six2 TSS_ chr17 85688402 85689017
After running capC-MAP, the normalized pileup bedgraph files for intra-chromosomal contacts for each viewpoint were collected. According to capC-MAP documentation, the number of piled-up interactions per restriction fragment are normalized to reads per million, so that the sum ofthe number of reads associated to each viewpoint genome-wide is equal to one million. Subsequently, for the restriction sites without any detected interactions, a signal equal to 0 wasassigned. In addition, only data from the regions chr1 89228752 90664659 (Gbx2-Asb18 locus) and chr17 84890284 86289254 (Six3-Six2 locus) was considered. Next, the bedgraph files of both replicates were averaged and the resulting bedgraph was converted to a bigwig with the usage of thebedGraphToBigWig UCSC tool.
Assembly: mm10
Supplementary files format and content: Bigwig; for each sample the bigwig files show the average Capture-C signals obtained for two independent biological replicates (rep1 and rep2)

source_name: delta-6XCTCF_Six3KO mESC

extract_protocol:
Capture-C experiments were performed as previously described. 5 _ 106 cells were crosslinked with 2% formaldehyde for 10 minutes and quenched with 0.125 M glycine for 10 minutes. Cells were washed with PBS and resuspended in lysis buffer (10 mM Tris pH 8, 10 mM NaCl, 0.2% NP-40 and 1_ protease inhibitors) during 20 minutes on ice. Following centrifugation, the pellet was resuspended in 215 µL 1_CutSmart buffer and transferred to a microcentrifuge tube. The resuspended pellet was mixed with 60 ul 10_ CutSmart buffer, 393,5 µl water and 9,5 µl 20% (vol/vol) SDS (0.28% final concentration) (Invitrogen, cat. no. AM9820) followed by 1 h incubation at 37¡C while shaking on a thermomixer at 500 rpm (intermittent shaking_ 30s on / 30s off).  Then, 20% vol/vol Triton X 100 was added at a final concentration of 1.67% vol/vol followed by another incubation at 37¡C for 1h while shaking. Chromatin was digested by adding 25 µL NlaIII (250 U, R0125L) and incubating at 37 ¡C for several hours, followed by addition of another 25 µL of NlaIII and incubation at 37 ¡C overnight. The digested chromatin was ligated with 8 µl (240U) of T4 DNA ligase (Life Tech, cat. no. EL0013) for 18 hours at 16¡C. Samples were treated with Proteinase K (3U; Thermo Fisher, cat. no. EO0491) and RNase A (7,5 mU; Roche_ 1119915), and DNA was purified using the Qiagen kit (28506). After checking the quality of the digestion and subsequent ligation, chromatin was sonicated for 30 cycles (30 s on, 30 s off, 25% amplitude) using an EpiShear probe sonicator (Active Motif) and DNA samples were purified using AMPure XP SPRI beads (Beckman Coulter, cat. no. A63881).
Libraries were prepared using the NEBNext Ultra II kit (New England Biolabs, cat. no. E7645S/L). Index primers set 1 and 2 from the NEBNext Multiplex Oligos for Illumina kit (New England Biolabs, E7335S/L E7500S/L) were incorporated using Herculase II Fusion Polymerase Kit (Agilent, cat. no. 600677). The resulting libraries were pooled (six libraries/pool) and a double Hybridization capture using ssDNA probes was performed following a modified version of the Roche HyperCapture streptavidin pull-down protocol (Roche, cat. no. 09075763001) described in 81. Libraries were sequenced using Novaseq6000_150PE_2,25Gb/lib (15 Mreads/lib). For each of the investigated cell lines, Capture-C experiments were performed as two independent biological replicates.

value: delta-6XCTCF_Six3KO mESC

value: NPC

value: delta-6XCTCF 36 Kb deletion and Six3KO 27 Kb deletion

value: Double hybridization capture using ssDNA probes within the Six2 promoter (viewpoint coordinates_ chr17_85688401-85689019)


title: Δ6XCTCF_Six3KO_NPC_Six3SE_rep2

value: Double hybridization capture using ssDNA probes within the Six3 SE (viewpoint coordinates_ chr17_85484698-85485040)


title: Δ3XCTCF_ESC_RAD21

value: delta3XCTCF mESC

value: delta3XCTCF 10 Kb deletion

value: RAD21 antibody (Abcam; ab154769)


title: 1_10

description:
Plasma/Serum Circulating and Exosomal RNA Purification Kit(Norgen Biotek)
EXR-LLAUR1AFSRR1BS100-BS


title: Six3KO_NPC_Six2_rep2

value: Six3KO mESC

value: Six3KO 27 Kb deletion


title: Δ6XCTCF_Six3KO_NPC_Six3SE_rep1


title: BALBc_IL4_2

data_processing:
TheReal Time Analysis software (RTA 3.9.25) was used for processing raw data files, the Illumina bcl2fastq v2.17 was used to demultiplex and convert binary base calls and qualities to fastq format.
Samples were trimmed for adapters using Cutadapt (1.18) before the alignment.
The trimmed reads were aligned with mm10 reference using Bowtie2(2.2.6) alignment.
The peaks were called using Genrich (0.6.1) (genrich -t sample_sortedByRead.bam -o sample.narroPeak -j -y -r -v -d 150 -m 5 -e chrM,chrY -E blacklist_regions.bed-f sample.bdg -b sample.bed)
Assembly: mm10
Supplementary files format and content: bigwig files were generated using Genrich (0.6.1)

source_name: peritoneal cells

extract_protocol:
100,000 macrophage cells were subjected to lysis using 100 µl of Lysis buffer (containing 10 mM Tris-Cl at pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40, and 0.1% Tween-20). Following a centrifugation at 500g for 10 minutes at 4°C, the resulting nuclei were reconstituted with 50 µl of a transposition mixture (FC-121-1030, Illumina; comprising 1X Tagment DNA buffer, Tn5 Transposase, and nuclease-free H2O), and this mixture was then incubated for 30 minutes at 37°C in a thermomixer. The transposed DNA was subsequently purified using MinElute columns (28004, QIAGEN) and then amplified using Nextera sequencing primers and the NEB high-fidelity 2X PCR master mix for 11 cycles (M0541, New England Biolabs). PCR-amplified DNA was purified using MinElute columns
ATAC-seq samples were pooled and sequenced on NextSeq 2000 P2 using PI lab prepared library and paired-end sequencing.

treatment_protocol: Two replicates were IL-4 treated for 4 days in BL/6 and BALB/c mice

value: macrophages

value: BALB/c

value: treated with A fusion protein of mouse IL-4 with the Fc portion of IgG1


title: Six3KO_NPC_Six2_rep1


title: 1-10 MV

description:
Plasma/Serum Circulating and Exosomal RNA Purification Kit(Norgen Biotek)
EXR-LLAUR1AFSRR1BS48-BS

value: Healthy Subject

value: Oral cavity structure

value: total cell-free biofluid RNA


title: Δ6XCTCF_Six3KO_NPC_Six2_rep2


title: Six3KO_NPC_Six3SE_rep2


title: 1_1

description:
Plasma/Serum Circulating and Exosomal RNA Purification Kit(Norgen Biotek)
EXR-LLAUR1AFSRR1BS73-BS


title: BALBc_Ctrl_2

value: untreated


title: BALBc_IL4_1


title: 1-1 MV

description:
Plasma/Serum Circulating and Exosomal RNA Purification Kit(Norgen Biotek)
EXR-LLAUR1AFSRR1BS47-BS


title: Six3KO_NPC_Six3SE_rep1


title: Δ6XCTCF_NPC_Six2_rep1

source_name: delta-6XCTCF mESC

value: delta-6XCTCF mESC

value: delta-6XCTCF 36 Kb deletion


title: Δ6XCTCF_NPC_Six2_rep2

value: NPC


title: BALBc_Ctrl_1


title: 1-2 MV

description:
Plasma/Serum Circulating and Exosomal RNA Purification Kit(Norgen Biotek)
EXR-LLAUR1AFSRR1BS49-BS


title: 2-1 MV

description:
Plasma/Serum Circulating and Exosomal RNA Purification Kit(Norgen Biotek)
EXR-LLAUR1AFSRR1BS50-BS


title: BL6_IL4_1


title: Δ6XCTCF_NPC_Six3SE_rep2


title: WT_NPC_Six2_rep2

value: WT mESC

value: WT

value: Double hybridization capture using ssDNA probes within the Six2 promoter (viewpoint coordinates_ chr17_85688401-85689019)


title: Δ6XCTCF_NPC_Six3SE_rep1

value: Double hybridization capture using ssDNA probes within the Six3 SE (viewpoint coordinates_ chr17_85484698-85485040)


title: WT_NPC_Six3SE_rep2


title: 2-5 EXO

description:
Plasma/Serum Circulating and Exosomal RNA Purification Kit(Norgen Biotek)
EXR-LLAUR1AFSRR1BS58-BS


title: BL6_Ctrl_2


title: Δ3XCTCF_71Kb_INV_ESC_Asb18_rep2

source_name: delta-3XCTCF_71Kb INV mESC

value: delta-3XCTCF_71Kb INV mESC

value: mESC

value: delta-3XCTCF 10 Kb deletion and 71 Kb inversion

value: Double hybridization capture using ssDNA probes within the Asb18 promoter (viewpoint coordinates_ chr1_90013013-90013385)


title: 1-9 MV

description:
Plasma/Serum Circulating and Exosomal RNA Purification Kit(Norgen Biotek)
EXR-LLAUR1AFSRR1BS79-BS


title: WT_NPC_Six3SE_rep1


title: Δ3XCTCF_71Kb_INV_ESC_Asb18_rep1


title: Δ3XCTCF_71Kb_INV_ESC_Gbx2SE_rep2

value: Double hybridization capture using ssDNA probes within the Gbx2 SE (viewpoint coordinates_ chr1_89869928-89870766)


title: 2_5

description:
Plasma/Serum Circulating and Exosomal RNA Purification Kit(Norgen Biotek)
EXR-LLAUR1AFSRR1BS83-BS


title: Δ3XCTCF_71Kb_INV_ESC_Gbx2SE_rep1


title: 71Kb_INV_ESC_Asb18_rep2

source_name: 71Kb INV mESC

value: 71Kb INV mESC

value: 71 Kb inversion


title: Lib185

city: Boston

first: Elliot

last: Akama-Garren

state: MA

address: 200 Longwood Ave

institute: Harvard Medical School

data_processing:
Open reading frames (ORFs) were determined from raw FASTA files using orfipy (version 0.0.4)1 with a minimum length of 60 nt.  MCR peptide sequences were extracted from ORFs as peptide sequences flanked by PRTE and SGGS amino acids using str_match from tidyverse (version 2.0.0).
Supplementary files format and content: comma seperated value file contains raw peptide counts for each Sample
Library strategy: amplicon seq

source_name: MCR-Lib

extract_protocol:
DNA was isolated from MCR cells using the DNeasy Blood & Tissue Kit (Qiagen) with RNaseA (Qiagen) pre-treatment.
NGS libraries were prepared by a two-step PCR protocol. First, MCR peptide sequences were PCR amplified from 5 mg of genomic DNA using PCR1_MCR_F 5’- TCTTGTGGAAAGGACGAAACACCGGCTGCTGTGGTGGTGCTGATGG-3’ and PCR1_MCR_R 5’-TCTACTATTCTTTCCCCTGCACTGTCCGTTGGTGAAGTAGCACTC-3’ with NEBNext Ultra II Q5 Master Mix (NEB) in a 50 mL reaction for 15-35 cycles. Cycle counts necessary to reach but not exceed the linear range were determined by quantitative real time PCR (qRT-PCR) with SYBR Green Supermix (Bio-Rad). PCR products were pooled when multiple reactions were performed for the same sample, concentrated using DNA Clean & Concentrator (Zymo), and size selected by gel electrophoresis and extraction (Qiagen). Purified products were diluted and 1 ng of each sample was PCR amplified using unique barcoded sequencing adapters PCR2_Fx 5’- AATGATACGGCGACCACCGAGATCTACAC[barcode]ACACTCTTTCCCTACACGACGCTCTTCCGATCT[stagger]TCTTGTGGAAAGGACGAAACACCG-3’ and PCR_Rx 5’- CAAGCAGAAGACGGCATACGAGAT[barcode]GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT[stagger]TCTACTATTCTTTCCCCTGCACTGT-3’ with Q5 Hot Start High-Fidelity 2X Master Mix (NEB) for 16 cycles. Libraries were purified using AMPure XP Beads (Beckman Coulter), quantified by qRT-PCR using i5_F 5’- AATGATACGGCGACCACCGAGATCTACAC-3’ and i7_R 5’- CAAGCAGAAGACGGCATACGAGAT-3’, and pooled to equimolar ratios.

treatment_protocol: MCR-Lib cells were co-cultured with a five-fold excess orphan TCR-expressing A2 cells in 96 well U-bottom plates at 1 x 105 total cells per well.  After 12 hr, Ametrine-GFP+NFAT-Blue+ cells were sorted as described above and expanded.  After six rounds of iterative co-culture and sorting, DNA was isolated from sorted reporter cells.

value: MCR-Lib

value: Hybridoma


title: 2-10 EXO

description:
Plasma/Serum Circulating and Exosomal RNA Purification Kit(Norgen Biotek)
EXR-LLAUR1AFSRR1BS45-BS

value: Healthy Subject

value: Oral cavity structure

value: total cell-free biofluid RNA


title: 2-6 EXO

description:
Plasma/Serum Circulating and Exosomal RNA Purification Kit(Norgen Biotek)
EXR-LLAUR1AFSRR1BS59-BS


title: WT_NPC_Six2_rep1

source_name: WT mESC

value: NPC


title: 71Kb_INV_ESC_Asb18_rep1


title: 71Kb_INV_ESC_Gbx2SE_rep1


title: Lib182


title: 71Kb_INV_ESC_Gbx2SE_rep2


title: Lib184

value: ref


title: Δ3XCTCF_ΔPromGbx2_ESC_Asb18_rep2

source_name: delta-3XCTCF_delta-PromGbx2 mESC

value: delta-3XCTCF_delta-PromGbx2 mESC

value: delta-3XCTCF 10 Kb deletion and delta-PromGbx2 1 Kb deletion


title: Lib181


title: Lib180


title: 2-9 EXO

description:
Plasma/Serum Circulating and Exosomal RNA Purification Kit(Norgen Biotek)
EXR-LLAUR1AFSRR1BS89-BS


title: 2-9 MV

description:
Plasma/Serum Circulating and Exosomal RNA Purification Kit(Norgen Biotek)
EXR-LLAUR1AFSRR1BS91-BS


title: Δ3XCTCF_ΔPromGbx2_ESC_Asb18_rep1


title: Δ3XCTCF_ΔPromGbx2_ESC_Gbx2SE_rep1


title: ΔPromGbx2_ESC_Asb18_rep2

source_name: delta-PromGbx2 mESC

value: delta-PromGbx2 mESC

value: delta-PromGbx2 1 Kb deletion


title: Δ3XCTCF_ΔPromGbx2_ESC_Gbx2SE_rep2

value: mESC


title: 2_7

description:
Plasma/Serum Circulating and Exosomal RNA Purification Kit(Norgen Biotek)
EXR-LLAUR1AFSRR1BS93-BS


title: ΔPromGbx2_ESC_Asb18_rep1


title: Lib172


title: Lib170


title: 1-5 EXO

description:
Plasma/Serum Circulating and Exosomal RNA Purification Kit(Norgen Biotek)
EXR-LLAUR1AFSRR1BS55-BS


title: 1-3 MV

description:
Plasma/Serum Circulating and Exosomal RNA Purification Kit(Norgen Biotek)
EXR-LLAUR1AFSRR1BS60-BS


title: Δ3XCTCF_ESC_Asb18_rep1

source_name: delta-3XCTCF mESC

value: delta-3XCTCF mESC

value: delta-3XCTCF 10 Kb deletion


title: Δ3XCTCF_ESC_Gbx2SE_rep1

value: Double hybridization capture using ssDNA probes within the Gbx2 SE (viewpoint coordinates_ chr1_89869928-89870766)


title: Δ3XCTCF_ESC_Gbx2SE_rep2


title: 1-7 EXO

description:
Plasma/Serum Circulating and Exosomal RNA Purification Kit(Norgen Biotek)
EXR-LLAUR1AFSRR1BS68-BS


title: WT_ESC_Asb18_rep2

value: WT mESC

value: WT

value: Double hybridization capture using ssDNA probes within the Asb18 promoter (viewpoint coordinates_ chr1_90013013-90013385)


title: Lib173

value: MCR-Lib

value: Hybridoma


title: Lib169


title: BALBc_LPS_1

source_name: Peritoneal Macrophage

value: Macrophage

value: BALB/c

value: treated with LPS


title: WT_ESC_Asb18_rep1


title: 2-4 EXO

description:
Plasma/Serum Circulating and Exosomal RNA Purification Kit(Norgen Biotek)
EXR-LLAUR1AFSRR1BS57-BS

source_name: Saliva

value: Healthy Subject

value: Oral cavity structure

value: total cell-free biofluid RNA


title: WT_ESC_Gbx2SE_rep2


title: Lib159

value: G


title: WT_ESC_Gbx2SE_rep1


title: ΔPromGbx2_ESC_Gbx2SE_rep1

value: delta-PromGbx2 mESC

value: delta-PromGbx2 1 Kb deletion


title: 1-4 EXO

description:
Plasma/Serum Circulating and Exosomal RNA Purification Kit(Norgen Biotek)
EXR-LLAUR1AFSRR1BS54-BS


title: Lib168

value: ref


title: 1-5 MV

description:
Plasma/Serum Circulating and Exosomal RNA Purification Kit(Norgen Biotek)
EXR-LLAUR1AFSRR1BS62-BS


title: Δ3XCTCF_ESC_Asb18_rep2

value: delta-3XCTCF mESC

value: mESC

value: delta-3XCTCF 10 Kb deletion


title: 1-6 MV

description:
Plasma/Serum Circulating and Exosomal RNA Purification Kit(Norgen Biotek)
EXR-LLAUR1AFSRR1BS69-BS


title: ΔPromGbx2_ESC_Gbx2SE_rep2

value: Double hybridization capture using ssDNA probes within the Gbx2 SE (viewpoint coordinates_ chr1_89869928-89870766)


title: Lib158


title: 1_9

description:
Plasma/Serum Circulating and Exosomal RNA Purification Kit(Norgen Biotek)
EXR-LLAUR1AFSRR1BS99-BS


title: mESC, KI, LIF, Rep2, RNA-Seq

city: Montreal

first: Mehdi

last: Amiri

state: Quebec

address: 1160 Pine Avenue West

department: Biochemistry

country: Canada

institute: McGill University

data_processing:
Sequenced libraries were trimmed using Cutadapt 3.4 by removing the constant adapter (AGATCGGAAGAGCAC) from reads without allowing any mismatches. Any reads shorter than six nt and without the adapter were discarded.
Trimmed reads were demultiplexed using the sample barcode anchored to the 5’ end of reads without allowing any mismatch in the barcodes and deposited here.
The multiplexed reads were then processed for alignments to the mouse transcriptome using the following criteria: First, low-quality reads and reads shorter than 25 were discarded, then reads were sequentially aligned to cytoplasmic and mitochondrion rRNA and tRNA using Bowtie 1.3.0, allowing three mismatches in the reads (parameters: -v 3 --norc -p 12).
The remaining reads were aligned to mouse Gencode version M25 comprehensive transcriptome with Bowtie 1.3.0 allowing two mismatches with the following parameters:(--norc -a -p 12 -m 100 -n 2 --seedlen 25). SAM files were converted to BAM files, sorted, indexed, and then PCR duplicates were removed using UMI-Tools 1.0.1.
The final BAM file was converted to an SQLite file compatible with Trips-Viz (https://trips.ucc.ie/), a platform for the Ribo-Seq data analysis and read count table function was used to extract the read counts for each sample.
Assembly: Gencode version M25 comprehensive transcriptome
Supplementary files format and content: comma separated file includes the rawr ead_count for each sample

source_name: mouse embryonic stem cells

growth_protocol: mESCs were maintained in a serum-free ESC media (EmbryoMax DMEM (Millipore, SLM-220-B) supplemented with 10% KnockOut™ Serum Replacement (Invitrogen, Cat#10828-028), 1X MEM non-essential Amino Acid Solution (Invitrogen, Cat#11140-050), 1 mM Sodium Pyruvate (Invitrogen, Cat#11360-070),  2 mM GlutaMax (Invitrogen, Cat#35050-061), 100 U/mL Penicillin, 100 mg/mL Streptomycin (Invitrogen, Cat#15140-122), 0.11 mM b-mercaptoethanol (Invitrogen, Cat#21985-023), 1 mM PD0325901 (BioVision, Cat#1643-2) and 3 mM CHIR99021 (Stemgent, Cat#04-0004), and 1000 U/mL ESGRO Leukemia Inhibitory Factor (LIF) (EMD Millipore, Cat# ESG1107) at 37°C with 5% CO2.

extract_protocol:
Cells were washed twice with ice-cooled PBS containing 100 μg/mL CHX, and lysed. Lysates were incubated on ice for 10 min, followed by centrifugation at 16000 x g for 10 min at 4°C. A portion of supernatants was saved for RNA-Seq and total RNA was extracted using Trizol from the  this portion.
For RNA-Seq library prep, the same procedure was performed as for Ribo-Seq library preparation except for the following changes. rRNA depletion was performed on total RNA using NEBNext® rRNA Depletion Kit (Human/Mouse/Rat) strictly according to the manufacturer’s instruction. rRNA-depleted RNAs were fragmented using NEBNext® Magnesium RNA Fragmentation Module for 6 min at 94°C. Fragmented RNAs were processed as for Ribo-Seq libraries.

treatment_protocol: mESCs were maintained in serum-free ESC media supplemented with either LIF/2i or LIF for 6 days.

value: mouse embryonic stem cells

value: eIF2{alpha}A/A (KI)

value: LIF


title: Lib157

value: MCR-Lib

value: Hybridoma


title: mESC, KI, LIF, Rep1, RNA-Seq


title: mESC, KI, LIF2i, Rep1, RNA-Seq


title: mESC, KI, LIF2i, Rep2, RNA-Seq


title: mESC, KI, LIF2i, Rep3, RNA-Seq


title: 1-3_W

description: Plasma/Serum Circulating and Exosomal RNA Purification Kit(Norgen Biotek)


title: 1-7 MV

description:
Plasma/Serum Circulating and Exosomal RNA Purification Kit(Norgen Biotek)
EXR-LLAUR1AFSRR1BS70-BS


title: mESC, WT, LIF, Rep1, RNA-Seq

value: eIF2{alpha}+/+ (WT)


title: Lib147

value: F


title: mESC, WT, LIF, Rep2, RNA-Seq


title: Lib156


title: Lib145


title: mESC, KI, LIF, Rep3, RNA-Seq


title: 2-1_W

value: Healthy Subject

value: Oral cavity structure


title: mESC, WT, LIF2i, Rep1, RNA-Seq


title: mESC, WT, LIF, Rep3, RNA-Seq


title: Lib146


title: 2-8_C

value: total cell-free biofluid RNA


title: 1-2_W


title: mESC, WT, LIF2i, Rep2, RNA-Seq


title: mESC, WT, LIF2i, Rep3, RNA-Seq


title: Lib144


title: mESC, KI, LIF, Rep1, Ribo-Seq (RNaseI)

data_processing:
Sequenced libraries were trimmed using Cutadapt 3.4 by removing the constant adapter (AGATCGGAAGAGCAC) from reads without allowing any mismatches. Any reads shorter than six nt and without the adapter were discarded.
Trimmed reads were demultiplexed using the sample barcode anchored to the 5’ end of reads without allowing any mismatch in the barcodes and deposited here.
The multiplexed reads were then processed for alignments to the mouse transcriptome using the following criteria: First, low-quality reads and reads shorter than 25 were discarded, then reads were sequentially aligned to cytoplasmic and mitochondrion rRNA and tRNA using Bowtie 1.3.0, allowing three mismatches in the reads (parameters: -v 3 --norc -p 12).
The remaining reads were aligned to mouse Gencode version M25 comprehensive transcriptome with Bowtie 1.3.0 allowing two mismatches with the following parameters:(--norc -a -p 12 -m 100 -n 2 --seedlen 25). SAM files were converted to BAM files, sorted, indexed, and then PCR duplicates were removed using UMI-Tools 1.0.1.
The final BAM file was converted to an SQLite file compatible with Trips-Viz (https://trips.ucc.ie/), a platform for the Ribo-Seq data analysis and read count table function was used to extract the read counts for each sample.
Assembly: Gencode version M25 comprehensive transcriptome
Supplementary files format and content: comma separated file includes the raw read_count for each sample
Library strategy: Ribo-Seq

extract_protocol:
Cells were washed twice with ice-cooled PBS containing 100 μg/mL CHX, and lysed. Lysates were incubated on ice for 10 min, followed by centrifugation at 16000 x g for 10 min at 4°C. A portion of supernatants was saved for RNA-Seq. Ribo-Seq samples were digested with MNase or RNAse I (Epicenter) and digested polysomes were loaded on a 10-50% sucrose density gradient and centrifuged at 36,000 rpm for 3 hours at 4°C. Fractions corresponding to monosome peak fractions were collected, pooled, and RNAs were extracted using Trizol.
For Ribo-Seq library prep, we followed McGlincy and Ingolia 2017 ribosome profiling technique with some modification. RNA was electrochemically separated on a 15% TBU-Urea gel, and fragments of 25-40 nt were selected. After gel extraction, rRNA depletion, and dephosphorylation, ligation was performed with pre-adenylated linkers containing Unique Molecular Identifiers (UMIs) and barcodes. The ligated samples underwent gel purification, reverse transcription, and circularization using CircLigase I. Another rRNA depletion step was done before qPCR optimization. The final PCR product, confirmed for size and quantity, was sequenced on an Illumina NovaSeq 6000 System.

tag: rnasei treatment

value: yes


title: mESC, KI, LIF, Rep1, Ribo-Seq

value: no


title: 1-8_W


title: mESC, KI, LIF, Rep2, Ribo-Seq (RNaseI)


title: Lib136


title: Lib135


title: mESC, KI, LIF, Rep3, Ribo-Seq


title: 2-7_C


title: mESC, KI, LIF2i, Rep1, Ribo-Seq


title: mESC, KI, LIF2i, Rep1, Ribo-Seq (RNaseI)


title: 1-3_C


title: mESC, KI, LIF2i, Rep2, Ribo-Seq


title: Lib134


title: 1-5_C


title: 2-1_C


title: Lib133


title: mESC, KI, LIF, Rep2, Ribo-Seq


title: mESC, KI, LIF2i, Rep2, Ribo-Seq (RNaseI)


title: 2-4_W


title: mESC, KI, LIF2i, Rep3, Ribo-Seq


title: mESC, WT, LIF, Rep1, Ribo-Seq


title: mESC, WT, LIF, Rep1, Ribo-Seq (RNaseI)


title: 2-2_W


title: Lib124


title: 1-7_W


title: mESC, WT, LIF, Rep2, Ribo-Seq (RNaseI)


title: mESC, WT, LIF, Rep3, Ribo-Seq


title: Lib123


title: Lib125

value: D


title: 2-2_C


title: mESC, WT, LIF, Rep2, Ribo-Seq


title: mESC, WT, LIF2i, Rep1, Ribo-Seq


title: mESC, WT, LIF2i, Rep2, Ribo-Seq


title: Lib122

value: ref


title: mESC, WT, LIF2i, Rep1, Ribo-Seq (RNaseI)


title: Lib114

value: C


title: 2-6_C


title: mESC, WT, LIF2i, Rep2, Ribo-Seq (RNaseI)


title: 2-9_W


title: Lib113


title: mESC, WT, LIF2i, Rep3, Ribo-Seq


title: 1-4_C


title: BALB6_macrophage

description: 10x Genomics

library_source: genomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger ATAC 2.0.0 software using the default parameters.  (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Integration of scATAC-seq samples,clustering of cells, and visualization of chromatin accessibility and pseudobulk coverage tracks was performed with Seurat (version 3.0) and its extension Signac (version 0.15;https://github.com/timoast/signac).
Assembly: mm10
Supplementary files format and content: fragments.and peaks files

source_name: Peritoneal cells

extract_protocol:
Peritoneal cells were isolated from both BL/6 and BALB/c mice after IL-4 treatment.Nuclei isolation for snRNA-seq and snATAC-seq was optimized and performed following the demonstrated protocol CG000365 from 10x Genomics.
The libraries were prepared following the 10x Genomics user guide CG000338 for Single Cell Multiome ATAC + Gene Expression Reagent Bundle (PN-1000285,10xGenomics). Only the ATAC Library Construction is performed by Sample Index Plate N, Set A (3000427, 10xGenomics).

value: Peritoneal cells

value: BALB/c

tag: age

value: 6-8 weeks old


title: Lib112


title: 2-4_C


title: 1-7_C


title: 1-1_W


title: BALBc_IL4

data_processing:
TheReal Time Analysis software (RTA 3.4.4) was used for processing raw data files, the Illumina bcl2fastq v2.20 was used to demultiplex and convert binary base calls and qualities to fastq format.
All Hi-C data were processed with Juicer (v.1.6 ), pipelines with default settings.
MEME-FIMO (5.4.1) was uesd to  scan for the locations of strain-specific active transcription factors (TFs) within promoter-distal regions (enhancers)
Juicebox (2.3.0)was used to visualize the Hi-C heatmap.
Assembly: mm10
Supplementary files format and content: Loops hic files are generated by Juicer (v.1.6 )

source_name: Pritoneal Macrophage

extract_protocol:
Chromatin interaction (Hi-C) libraries preparations were performed by Arima Genomics (https://arimagenomics.com/) using the Arima-HiC kit
HiC-seq samples were pooled and sequenced on NovaSeq and paired-end sequencing

treatment_protocol: IL4 treated for 4 days for both BL/6 and BALB/c strains

value: Macrophage

value: treated with A fusion protein of mouse IL-4 with the Fc portion of IgG1


title: BL6_macrophage

description: 10x Genomics


title: Lib111

value: MCR-Lib


title: Lib102

value: Hybridoma


title: Lib103


title: 2-9_C


title: Lib101


title: E0771 cells_SHPC 28 LG3

city: chapel hill

first: michael

middle: francis

last: coleman

state: North Carolina

address: 235 dauer drive

institute: UNC

hyb_protocol: Labeled cDNA was hybridized to the plate using GeneTitan Hybridization Wash and Stain Kit for WT Arrays (Affymetrix)

scan_protocol: arrays were scanned using GeneTitan

data_processing: Quality control and differential gene expression was conducted using TAC4 software (Affymetrix)

label: biotin

source_name: cell culture

label_protocol: The GeneChip® WT PLUS Reagent Kit (Affymetrix, Santa Clara, CA) was used to prepare the samples

growth_protocol: E0771 cells transduced with PC targeting  or scramble controls cultured in DMEM with 5.6mM glucose, 4mM glutamine, and 10%FBS

extract_protocol: RNA was isolated with EZNA HP Total RNA kit (omega bio-tek)

treatment_protocol: cells were not treated

tag: group


title: E0771 cells_SHPC 28 LG2


title: E0771 cells_SHPC 28 LG1


title: E4 knock-in replicate 5

city: New York

first: Alon

last: Millet

state: NY

address: 1230 York Ave

institute: The Rockefeller University

data_processing:
Fastqs were aligned and counted using Salmon.
Assembly: mm10
Supplementary files format and content: Salmon-generated quantification file.

source_name: Hippocampal and cortical regions of brain

extract_protocol:
Briefly, mice were anesthetized with a ketamine/xylazine cocktail and perfused with 25 ml of Ca2+/Mg2+-free DPBS (Sigma). Cortex and hippocampus were removed and placed in FACS buffer (PBS containing 5% FBS and 10 mM HEPES), minced with scissors, and incubated with 80 U/mL of collagenase D (Roche, 11088858001) at 37°C for 30 min. Collagenase was inactivated by adding 10 mM EDTA for an additional 5-min incubation at 37°C. Digested material was passed through a 70μm cell strainer, centrifuged at 1500rpm for 10min, pellet was then resuspended in 7mL of  38% Percoll followed by a centrifugation at 2000rpm for 30 min. Nonspecific binding to FC receptors was blocked by incubation with a CD16- and CD32-specific antibody (BD-Pharmingen 553141) for 15 min. Lastly, cells were washed and stained with an anti-CD45 antibody (Invitrogen 56-0451-82) and 0.05 µg/mL DAPI and, then washed and resuspended in FACS buffer. Cells were sorted on an LSR-II flow cytometer (Becton Dickinson) for singlet DAPI- CD45+ cells.
Cells were sorted directly into lysis buffer and RNA was extracted by RNeasy Micro Kit (QIAGEN). RNA was used as input for SMARTseq low input prep.

tag: tissue

value: Cd45+ cells

value: 5XFADhet APOE-knockin, E4


title: E0771 cells_SCRAM LG3

value: scram


title: E0771 cells_SHPC 25 LG2


title: 1-1_C

value: Healthy Subject

value: Oral cavity structure


title: E0771 cells_SCRAM LG2


title: 1-10_W

value: total cell-free biofluid RNA


title: E0771 cells_SHPC 25 LG3


title: BL6_IL4


title: E4 knock-in replicate 3

value: Hippocampal and cortical regions of brain


title: Lib104

value: B


title: 2-10_C


title: E4 knock-in replicate 4


title: RNA-Seq GM12878 UV rep3

city: Jerusalem

first: Sheera

last: Adar

state: Israel

address: Botnar Building Room 001, Faculty of Medicine, Hebrew University, Ein Kerem

department: Department of Microbiology and Molecular Genetics

country: Israel

institute: Hebrew University of Jerusalem

data_processing:
Salmon index was constructed for and GENECODE v36 human reference transcriptome
Quantification of transcript expression was performed using Salmon GC bias aware quantification
Summarizing transcript-level quantifications to gene -level obtained by tximeta mapping to GENECODE v36 reference data
DESeq2 was applied using R version 4.0.0
Assembly: hg38
Supplementary files format and content: Plain-text, tab-separated file with a single header line (which names all of the columns). Contains the number of reads mapping to each transcript that was quantified.

source_name: B-cells lymphoblastoid

extract_protocol:
Total RNA was extracted using GENEzol™ TriRNA Pure with DNaseI Kit (Geneaid, GZXD).
RNA-seq library preparation was performed using the KAPA biosystems stranded mRNA-seq kit (KR0960, KAPA biosystems, Wilmington, Massachesetts, USA) starting with 1 μg total RNA according to manufacturer’s protocol.

value: B-cells lymphoblastoid

value: 20 J/m2 UVC

tag: treatment duration


title: E4 knock-in replicate 2


title: 2-6_W


title: E0771 cells_SHPC 25 LG1


title: RNA-Seq GM12878 UV rep1


title: RNA-Seq GM12878 UV rep2


title: 1-2_C


title: E4 knock-in replicate 1


title: E3 knock-in replicate 5

value: 5XFADhet APOE-knockin, E3


title: E0771 cells_SCRAM LG1


title: 1-8_C


title: RNA-Seq GM12878 control rep3

value: untreated


title: RNA-Seq GM12878 control rep2


title: E0771 tumor excised from C57BL6J mouse_LFD SHPC 28 4

source_name: E0771 tumor

growth_protocol: 500,000 E0771 cells transduced with PC targeting  or scramble controls were injected into the 4th mammary fat pad of C57BL6J mice.

extract_protocol: RNA was isolated by bead beating in TRIzol reagent, followed by isolation with EZNA HP Total RNA kit (omega bio-tek)

treatment_protocol: Mice were not treated


title: E3 knock-in replicate 4


title: 1-4_W


title: E0771 tumor excised from C57BL6J mouse_LFD SHPC 28 3


title: E0771 tumor excised from C57BL6J mouse_LFD SHPC 28 2


title: E3 knock-in replicate 3


title: RNA-Seq GM12878 control rep1


title: 2-8_W


title: RNA-Seq GM12878 Cisplatin rep3

value: 200μM of cisplatin


title: 1-10_C


title: E3 knock-in replicate 1


title: 1-5_W


title: RNA-Seq GM12878 Cisplatin rep2


title: E2 knock-in replicate 5

value: 5XFADhet APOE-knockin, E2


title: E0771 tumor excised from C57BL6J mouse_LFD SHPC 25 1


title: RNA-Seq GM12878 BPDE rep3

value: 5μM of BPDE


title: RNA-Seq GM12878 Cisplatin rep1


title: E0771 tumor excised from C57BL6J mouse_LFD SHPC 25 2


title: E0771 tumor excised from C57BL6J mouse_LFD SHPC 25 3


title: RNA-Seq GM12878 BPDE rep2


title: E3 knock-in replicate 2


title: E2 knock-in replicate 4


title: RNA-Seq GM12878 BPDE rep1


title: E0771 tumor excised from C57BL6J mouse_LFD SHPC 28 1


title: E0771 tumor excised from C57BL6J mouse_LFD SCR 4


title: lung progenitor organoids 2

city: Yangling

first: Xinchun

last: Yang

state: shannxi

address: No. 3, Taicheng Road

institute: Northwest A&F University

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Sus scrofa

source_name: lung progenitor organoids 2

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina NovaseqTM 6000 following the vendor's recommended protocol.

value: lung progenitor organoids 2


title: lung progenitor organoids 1

source_name: lung progenitor organoids 1

value: lung progenitor organoids 1


title: 2-7_W


title: anterior foregut endoderm 2

source_name: anterior foregut endoderm 2

value: anterior foregut endoderm 2


title: 2-10_W


title: E2 knock-in replicate 3

value: Cd45+ cells


title: E2/E3/E4 5XFAD mice, 60 weeks, aducanumab or IgG, HTO for demuxing

library_source: other

data_processing:
Counts matrices were produced using Cell Ranger version 6.1.1. For downstream processing steps, refer to code available at https://github.com/alonmillet/apoe-ad-age-atlas.
Assembly: mm10
Supplementary files format and content: Feature barcode matrix output from Cell Ranger.

molecule: protein

extract_protocol:
Briefly, mice were anesthetized with a ketamine/xylazine cocktail and perfused with 25 ml of Ca2+/Mg2+-free DPBS (Sigma). Cortex and hippocampus were removed and placed in FACS buffer (PBS containing 5% FBS and 10 mM HEPES), minced with scissors, and incubated with 80 U/mL of collagenase D (Roche, 11088858001) at 37°C for 30 min. Collagenase was inactivated by adding 10 mM EDTA for an additional 5-min incubation at 37°C. Digested material was passed through a 70μm cell strainer, centrifuged at 1500rpm for 10min, pellet was then resuspended in 7mL of  38% Percoll followed by a centrifugation at 2000rpm for 30 min. Nonspecific binding to FC receptors was blocked by incubation with a CD16- and CD32-specific antibody (BD-Pharmingen 553141) for 15 min. Lastly, cells were washed and stained with an anti-CD45 antibody (Invitrogen 56-0451-82) and 0.05 µg/mL DAPI and, then washed and resuspended in FACS buffer. Cells were sorted on an LSR-II flow cytometer (Becton Dickinson) for singlet DAPI- CD45+ cells.
Libraries were prepared according to manufacturer's instructions (5'v2, multiome; 10X Genomics).

value: 5XFADhet APOE-knockin


title: E0771 tumor excised from C57BL6J mouse_LFD SCR 1

value: scram


title: M-Wnt tumor excised from C57BL6J mouse_shPC5

source_name: M-Wnt tumor

growth_protocol: 50,000 M-Wnt cells transduced with PC targeting doxycycline inducible shRNA were injected into the 4th mammary fat pad of C57BL6J mice.

treatment_protocol: Mice were provided 150µg/ml doxycycline in drinking water or standard drinking water ad lib

value: shPC


title: E2 knock-in replicate 2


title: anterior foregut endoderm 1

source_name: anterior foregut endoderm 1

value: anterior foregut endoderm 1


title: definitive endoderm 2

source_name: definitive endoderm 2

value: definitive endoderm 2


title: RNA-Seq A549 UV rep1

source_name: Non-small cell lung cancer

value: Non-small cell lung cancer


title: E2/E3/E4 5XFAD mice, 60 weeks, aducanumab or IgG, scRNAseq

library_source: transcriptomic single cell

value: Hippocampal and cortical regions of brain


title: E2/E3/E4 5XFAD mice, 60 weeks, high and low abeta uptake, HTO for demuxing


title: M-Wnt tumor excised from C57BL6J mouse_Ctrl5

value: Ctrl


title: RNA-Seq A549 control rep3


title: RNA-Seq A549 UV rep3

value: 20 J/m2 UVC


title: E0771 tumor excised from C57BL6J mouse_LFD SCR 3


title: definitive endoderm 1

source_name: definitive endoderm 1

value: definitive endoderm 1


title: M-Wnt tumor excised from C57BL6J mouse_shPC4


title: porcine pluripotent stem cells 2

source_name: porcine pluripotent stem cells 2

value: porcine pluripotent stem cells 2


title: M-Wnt tumor excised from C57BL6J mouse_shPC3


title: RNA-Seq A549 control rep1

value: untreated


title: RNA-Seq A549 control rep2


title: E0771 tumor excised from C57BL6J mouse_LFD SCR 2


title: RNA-Seq A549 UV rep2


title: M-Wnt tumor excised from C57BL6J mouse_Ctrl4


title: porcine pluripotent stem cells 1

source_name: porcine pluripotent stem cells 1

value: porcine pluripotent stem cells 1


title: E3 5XFAD mice, 96weeks, scRNAseq

description: 10X Genomics 3'v2

data_processing:
Counts matrices were produced using Cell Ranger version 6.1.1. For downstream processing steps, refer to code available at https://github.com/alonmillet/apoe-ad-age-atlas.
Assembly: mm10
Supplementary files format and content: HDF5 file containing tab-separated values and matrix files.
Supplementary files format and content: Tab-separated file containing ATAC fragment information and accompanying index file.

extract_protocol:
Briefly, mice were anesthetized with a ketamine/xylazine cocktail and perfused with 25 ml of Ca2+/Mg2+-free DPBS (Sigma). Cortex and hippocampus were removed and placed in FACS buffer (PBS containing 5% FBS and 10 mM HEPES), minced with scissors, and incubated with 80 U/mL of collagenase D (Roche, 11088858001) at 37°C for 30 min. Collagenase was inactivated by adding 10 mM EDTA for an additional 5-min incubation at 37°C. Digested material was passed through a 70μm cell strainer, centrifuged at 1500rpm for 10min, pellet was then resuspended in 7mL of  38% Percoll followed by a centrifugation at 2000rpm for 30 min. Nonspecific binding to FC receptors was blocked by incubation with a CD16- and CD32-specific antibody (BD-Pharmingen 553141) for 15 min. Lastly, cells were washed and stained with an anti-CD45 antibody (Invitrogen 56-0451-82) and 0.05 µg/mL DAPI and, then washed and resuspended in FACS buffer. Cells were sorted on an LSR-II flow cytometer (Becton Dickinson) for singlet DAPI- CD45+ cells.
Libraries were prepared according to manufacturer's instructions (3'v2, 5'v2, multiome; 10X Genomics). For 10-week and 20-week samples, hashed demultiplexing was performed using Cell Ranger multi, with read R2 and pattern 5PNNNNNNNNNN(BC)NNNNNNNNN. Samples from APOE2-bearing mice were barcoded with GGTCGAGAGCATTCA; samples from APOE3-bearing mice were barcoded with CTTGCCGCATGTCAT; samples from APOE4-bearing mice were barcoded with AAAGCATTCTTCACG.


title: RNA-Seq A549 Cisplatin rep3

value: 200μM of cisplatin


title: E4 5XFAD mice, 96weeks, scRNAseq

description: 10X Genomics 3'v2


title: E4 5XFAD mice, 60weeks, scATACseq

description: 10X Genomics Multiome


title: RNA-Seq A549 Cisplatin rep2


title: RNA-Seq A549 Cisplatin rep1


title: P90_CUTNTAG_heaEC_P30Tam_Sox9_OE_r2

city: Mannheim

first: Joerg

last: Heineke

state: Baden Wuttemberg

address: Ludolf-Krehl-Str. 7-11

department: – Department of Cardiovascular Research (HKF)

country: Germany

institute: Medizinische Fakultät Mannheim

data_processing:
Raw fastq files were trimmed with Ngmerge (defaut settings).
Trimmed reads were mapped with Bowtie2 (bowtie2 -p 16 --local --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700)
sam files were converted to bam files using samtools view (default settings)
Bam files were merged with bamtools merge (v. 2.5.1) (default settings)
bamCoverage was used to create the bw files (-p max -bs 20 --smoothLength 40 --normalizeUsing RPKM )
Assembly: mm10 from UCSC genome
Supplementary files format and content: BigWig files

source_name: Cardiac ECs

growth_protocol: Adult mice in mixed cohorts based on sex animals were bred (approximately 5-7 weeks of age) were injected i.p. with Tamoxifen at a dosage of 25 mg/kg×d for 5 consecutive days. With regard to the animal study where endothelial SOX9 ablation was done in pre-existing disease, the Tamoxifen injection was administered on 5 consecutive days following the 10th day after surgery. Cre-/- littermates served as controls and received Tamoxifen in equivalent frequency and dosage.

extract_protocol:
Cardiac EC were isolated based on MACS-magnetic MicroBeads technology from Miltenyi Biotec and FACS sorted for CD146 for a 80-90% purity.
Isolated cardiac EC were used for cut and Tag standard protocols. Briefly, cells were incubated with SOX9 primary antibody (Millipore, AB5535), followed by a secondary antibody conjugated to the protein A-Tn5 fusion protein. The transposed DNA was purified and amplified by PCR, and the resulting library was sequenced at 100bp paired end.

treatment_protocol: animals were injected with Tamoxifen for 5 consecutive days and rested for 1 M before EC isolation

value: Cardiac ECs

value: 3 M

value: 1 Month post Tamoxifen

tag: antibody

value: Millipore, AB5535


title: M-Wnt tumor excised from C57BL6J mouse_Ctrl3


title: E2/E3/E4 5XFAD mice, 60 weeks, high and low abeta uptake, scRNAseq

value: Cd45+ cells

value: 5XFADhet APOE-knockin


title: E4 5XFAD mice, 60weeks, scRNAseq

description: 10X Genomics Multiome


title: P90_CUTNTAG_heaEC_P30Tam_Sox9_OE_r1


title: E2/E3/E4 5XFAD mice, 20weeks, HTO for demuxing

description: 10X Genomics 5'v2

molecule: other


title: M-Wnt tumor excised from C57BL6J mouse_shPC2

value: shPC


title: RNA-Seq A549 BPDE rep3

value: 5μM of BPDE


title: P90_CUTNTAG_heaEC_P30Tam_WT_r3

value: Ctr


title: E2/E3/E4 5XFAD mice, 20weeks, scRNAseq

description: 10X Genomics 5'v2

value: Hippocampal and cortical regions of brain


title: P90_CUTNTAG_heaEC_P30Tam_Sox9_OE_r3


title: M-Wnt tumor excised from C57BL6J mouse_Ctrl1

value: Ctrl


title: P90_CUTNTAG_heaEC_P30Tam_WT_r2


title: RNA-Seq A549 BPDE rep2

value: Non-small cell lung cancer


title: RNA-Seq A549 BPDE rep1


title: output library replication 2

city: Xi'an

first: Xiao-Feng

last: Chen

state: Shaanxi

address: No.28 Xianning West Road

department: School of Life Sciences and Technology

institute: Xi'an Jiaotong University

description: output sequencing library

data_processing:
Each replicated sample paired reads were separated firstly according to 8-bp barcode sequences with no more than two mismatches/deletions of nucleotides permitted
Trimmed low quality reads (Q-score<30) were filtered using fastp 0.20.1 with -q 30 -u 50
The 120-bp SNP element sequences were extracted and merged reads were aligned to our selected SNP sequences using Bowtie 2.4.1 with default parameters
All 100% matched reads were extracted and each SNP reference/alternative allele was counted according to unique UMI (removing PCR duplicates)
Assembly: h19
Supplementary files format and content: A text file with raw reads counts (UMI) for all detected SNP variants in input and output samples (Any SNP allele with no expressions in any one sample or with pooled input/output expression counts less than 10 were excluded)
Library strategy: DNA sequencing

source_name: output library

extract_protocol:
Total RNA was extracted using Monarch Total RNA Miniprep Kit (New England Biolabs), and treated with TURBO DNA-free Kit (Thermo Fisher) following the manufacturer’s protocol. We then isolated the poly(A) RNA using NEB Next Poly(A) mRNA Magnetic Isolation Module (New England Biolabs) and precipitated each replicate using Monarch RNA Cleanup Kit (New England Biolabs).
The plasmid library before transfection were used for constructing input sequencing library. Firstly, one-step PCR was performed with 100ng plasmid library using RT-UMI primer (unique random molecular identifiers, 5'-ACACGACGCTCTTCCGATCTNNNNNNNNNNNNNTCGAAGCGGCCGGCCGAATTCG-3').Then the first round of amplification was performed with Vector-F(5'-GCTAGGCTAGCAAAGGAGAAGAAC-3') and Read1-R (5'-ACACGACGCTCTTCCGATCT-3') for each replicate. The second round of PCR was performed using barcode primers for each biological replicate and further purified with Agencourt AMPure XP beads. For the output sequencing library, total RNA was extracted after plasmid library transfection. The poly(A) mRNA was reverse transcripted using RT-UMI primer and treated with RNase A. Next, the cDNA was amplified using junction primer (5'-TCGTGAGGCACTGGGCAG*G*T*G*T*C-3', * = phosphorothioate bond) and Read1-R. The second round of PCR was applied with barcode primers for each replicate and purified with Agencourt AMPure XP beads. Finally, input and output sequencing libraries were generated using NEB Next Ultra DNA Library Prep Kit for Illumina (New England Biolabs) following manufacturer’s recommendations and index codes were added for each sample.

treatment_protocol: 12 μg plasmid library was transfected into 3.6×106 U2OS cells using ViaFect transfection reagent (Promega, Cat#E4981, USA) for three biological replicates.

value: 12 ug plasmid library was transfected into 3.6×106 U2OS cells using ViaFect transfection reagent (Promega, Cat#E4981, USA)


title: output library replication 1

description: output sequencing library


title: P90_CUTNTAG_heaEC_P30Tam_WT_r1


title: input library replication 3

description: input sequencing library

source_name: input library


title: E2/E3/E4 5XFAD mice, 10weeks, scRNAseq

description: 10X Genomics 5'v2


title: M-Wnt tumor excised from C57BL6J mouse_Ctrl2


title: P90_ATAC_heaEC_P30Tam_Sox9_OE_r3

data_processing:
Raw fastq files were trimmed with Ngmerge (defaut settings).
Trimmed reads were mapped with Bowtie2 (bowtie2 -p 16 --local --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700)
sam files were converted to bam files using samtools view (default settings)
PCR duplicated were removed using MarkDuplicates.jar from picard-tools (v1.119)
Peaks fro ATAC-seq were called with macs (v1.14) (-p 1e-5 -g mm --nomodel --shiftsize 100)
The peaks were annotated using annotatePeaks.pl function from Homer (v3.12).
Bam files were merged with bamtools merge (v. 2.5.1) (default settings)
bamCoverage was used to create the bw files (-p max -bs 20 --smoothLength 40 --normalizeUsing RPKM )
Assembly: mm10 from UCSC genome
Supplementary files format and content: BigWig files

extract_protocol:
cardiac EC were isolated based on MACS-magnetic MicroBeads technology from Miltenyi Biotec and FACS sorted for CD146 for a 80-90% purity.
Isolated cardiac EC were used for ATACseq was performed using standard protocols with minor modifications. Briefly, nuclei were isolated from the cells of interest and subjected to transposition with sequencing adapters. The transposed DNA was purified and amplified by PCR, and the resulting library was sequenced at 100bp paired end.


title: output library replication 3

description: output sequencing library


title: s72_3

city: Madrid

first: Jose

middle: Luis

last: Cabrera

state: Madrid

address: Melchor Fernández Almagro, 3

institute: CNIC

data_processing:
Fastq files containing reads for each library were extracted and demultiplexed using bcltofastQ (Illumina).
Adaptors from RNAseq were removed from reads using the trimgalore v-0.6.6 and cutadapt v-1.18 software.
Trimmed reads were mapped and quantified on the transcriptome GRCm38 gene-build 91 using RSEM v-1.3.1 (calling STAR aligner).
Expected expression counts were then processed with an analysis pipeline that used Bioconductor package Limma for normalization (using TMM method, included in edgeR Bioconductor package).
Assembly: GRCm38 gene-build 91
Supplementary files format and content: TMM-normalized counts (CPM) for genes with expression level of at least 1 count per million (CPM).

source_name: MAFs

extract_protocol:
Total RNA from mose adult fibroblasts (MAFs) was extracted using Rneasy Kit (Qiagen) by standard protocols
RNA libraries were produced using TrueSeq RNASeq kit from Illumina and sequenced in the HiSeq2500 Illumina Sequencer.

value: MAFs

value: DPI 72 hours


title: s72_2


title: M-Wnt tumor excised from C57BL6J mouse_shPC1


title: P90_ATAC_heaEC_P30Tam_Sox9_OE_r1


title: input library replication 2

description: input sequencing library


title: Tumor_infiltrated_Treg_KO

city: Nanjing

first: Yuchao

last: Jing

state: Jiangsu

address: 101 Longmian Ave Jiangning District

department: Immunology

institute: Nanjing Medical University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: tumor tissue

extract_protocol:
Tumor tissue was resected and digested with enzyme. Lymphocytes were purified using percoll. Treg cells were purified by magnetic-activated cell sorting (MACS) positive selection. Tumor infiltrated treg of the WT and jmjd1c tregcKO mice were isolated by Fluorescence-activated cell sorting (FACS) according to the presence or absence of fluorence signal and analyzed using scRNAseq and then constructed library.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: tumor tissue

value: 8-12 weeks old

value: Treg cells


title: Tumor_infiltrated_Treg_WT

description: 10x Genomics


title: s24_2

value: DPI 24 hours


title: advanced melanoma patient 2, 5uM Ibrutinib

city: Columbus

first: William

last: Carson III

state: OH

address: 420 W 12th ave

institute: The Ohio State University

description: 10x Genomics

data_processing:
All data analyses were performed using R version 4.0.2. Cells with less than 500 unique genes expressed in each sample were discarded to eliminate low quality and dying cells. Similarly, gene features that were detected in less than 5 cells were discarded. Gene expression was log-normalized and variable features were extracted for each sample individually using the standard workflow implemented in the R package Seurat version 4. Then, all samples were integrated as described by Stuart and Butler et al. To facilitate visualization, the high dimensional gene expression features were subjected to dimension reduction using the Uniform Manifold Approximation and Projection (UMAP) algorithm. The cells were then clustered using the Louvain algorithm and clusters were annotated with cell types using SingleR. The Wilcoxon Rank Sum test was used for differential expression (DE) analyses. All DE p values were adjusted for multiple comparisons using the Bonferroni correction.
Assembly: hg38
Supplementary files format and content: CSV format, gene-cell raw count matrix and metadata for each cell

source_name: advanced melanoma

extract_protocol:
Approximately 30 mL of peripheral venous blood was collected from each patient. Peripheral blood mononuclear cells (PBMC) were isolated from peripheral venous blood via density gradient centrifugation with Ficoll, as previously described. Samples were layered carefully on top of the Ficoll density gradient medium and centrifuged for 25 minutes at 1500 rotations per minute with the brake off. Enriched cell populations were removed from the density gradient medium (plasma interface) and residual red blood cells were lysed. PBMC were stained with MDSC markers via fluorescent antibodies: PE anti-CD11b, APC anti-CD33, PeCy7 anti-HLA-DR (Biolegend), and isolated via fluorescence-activated cell sorting (FACS) based on (CD11b+/ CD33+/HLA-Drlo/-) expression. The purity of samples averaged 70%. Freshly purified MDSC from melanoma patients were treated with 5 µM Ibrutinib or DMSO for 4 h and RNA was processed using the Chromium 10X genomic platform.
Single cells were isolated using the 10X Chromium Next GEM 5’ gene expression kit, targeting recovery of ~4000 cells per sample. Gene expression libraries were constructed and sequenced according to the manufacturer’s instructions (Illumina NovaSeq, Nationwide Children’s Hospital Institute for Genomic Medicine/Genomic Services Laboratory). Sequence data were processed using Cell Ranger v3.1.0. Cell recovery was 3374 (+/- 1154) cells per sample.

value: advanced melanoma

value: peripheral blood mononuclear cells (PBMC)

value: 5uM Ibrutinib


title: s72_1


title: input library replication 1

description: input sequencing library


title: P90_ATAC_heaEC_P30Tam_WT_r3

value: Cardiac ECs

value: 3 M


title: s24_3


title: advanced melanoma patient 2, DMSO

description: 10x Genomics

value: DMSO


title: Inhibitor-3

city: Guangzhou

first: Wenbin

last: Zhong

address: No.601, West Huangpu Avenue

institute: Jinan University

data_processing:
bcl2fastq v2.20
Use the FANse3 ultra-high-precision sequence alignment algorithm to compare the reads which obtained by sequencing each sample with the reference sequence (reference library: Mouse RefSeq-RNA mm10 2017-03-25).
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files

source_name: bone marrow

extract_protocol:
RNA was extracted following the Trizol reagent (Invitrogen) manual. RNA was precipitated in 1:1 isopropanol (v/v) and 1 μL glycogen at -20°C overnight.
mRNA library was constructed using VAHTS mRNA-seq V3 Library Prep Kit (Cellagen Technology, San Diego, CA) following the manufacturer’s instructions.

value: bone marrow

value: Hematopoietic stem cells

value: 6 months

value: miR-31-5p inhibitor


title: s24_1


title: Inhibitor-1


title: P90_ATAC_heaEC_P30Tam_WT_r2

value: Ctr


title: P90_ATAC_heaEC_P30Tam_WT_r1


title: C_3

value: MAFs

value: Control


title: advanced melanoma patient 1, DMSO

description: 10x Genomics


title: P90_ATAC_heaEC_P30Tam_Sox9_OE_r2

value: 1 Month post Tamoxifen


title: Control-2

value: control


title: thymic_iNKT_WT_n2

city: Kisarazu

first: Toshio

last: Kanno

state: Chiba

address: 2-6-7 Kazusa-kamatari

country: Japan

institute: KAZUSA DNA Research Institute

data_processing:
Cell Ranger v7.0.0 was used to align the sequencing reads to the mm10 mouse transcriptome and quantify the expression of transcripts in each cell. This pipeline produced a gene expression matrix for each sample, which records the number of UMIs for each gene associated with each cell barcode.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: thymus

extract_protocol:
For sample preparation of scRNA-seq, thymocytes were prepared from young adult mice (6–8 weeks old) and CD3+CD1d tetramer+ iNKT cells were collected with cell sorter.
Libraries were prepared using Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1, 4 rxns (10× Genomics #PN-1000128) according to the manufacturer’s protocol.

value: thymus

value: primary

value: iNKT cell

value: Wiled type


title: breast cancer patient

description: 10x Genomics

source_name: breast cancer

value: breast cancer

value: peripheral blood mononuclear cells (PBMC)

value: No treatment


title: C_2


title: thymic_iNKT_WT_n1


title: Control-1


title: Oligo 25% F

status: Public on Dec 28 2023

city: Chicago

first: Xiaolong

last: Cui

state: IL

address: 680 N Lake Shore Drive

department: Department of Preventive Medicine

institute: Northwestern University

data_processing:
Sequencing reads were trimmed by Trim_galore to remove low-quality nucleotides.
Clean reads were aligned to E.coli reference genome by Bowtie2.
Mutation calling was performed by VarScan.
Assembly: ecoli_mutated
Supplementary files format and content: reads count on mutational A sites.
Library strategy: DRM-Seq

organism: synthetic construct

source_name: synthetic construct

extract_protocol:
Genomic DNA from Escherichia coli strain K-12 was purchased from ATCC (10798D-5). All the DNA samples were harshly treated with RNase A (NEB, T3018L) again prior to libraries construction to get rid of any RNA contaminants.
For E.coli DNA, 400 ng~1 μg RNA-free DNA was diluted by TE buffer (Invitrogen, AM9849) with 0.1 M NaOH and sonicated using Bioruptor Pico sonication device to 100~300 nt length. The fragmented DNA was mixed with 15% (mass percentage) spike-in probes (Supplementary Table 1) and then spited into three in the proportion of 3:4:1, each for mutation group, demethylation control and high-fidelity control. The three groups of DNAs was denatured and subjected to splint ligation following a previous protocol (Supplementary Table 1) [10.1093/nar/gkw1110]. The ligation products of mutation group and demethylation control underwent primer extension at 60℃ for 3 hours in the 50 μL reaction containing 6 μM biosample-primer-extension primer (Supplementary Table 1), 1200 units of Bst 2.0 DNA polymerase (NEB, M0537M), 1× EpiMark Hot Start Taq Reaction Buffer (NEB, M0490S), 8mM dATP (NEB, N0446S), 2mM dCTP (NEB, N0446S), 2mM dGTP (NEB, N0446S), 0.02 mM 2-thio-dTTP (Trilink, N-2035), 6 mM magnesium sulfate (NEB) and 8% PEG4000 (Rigaku, # 25322-68-3). The resulting libraries were purified by gel electrophoresis and recovery, and finally sequenced at 60~100M depth with single-ended 100 bp mode.
The 100-mer biotin-tagged NN-6mA-NN model DNA oligo and primer-extension primer was synthesized by IDT (Integrated DNA Technologies). At first, the primer-extension primer was denatured at 70 for 2 min and immediately chilled on ice. In a total volume of 50 L, 50 ng model DNA and 2.5 L 2 M oligo-primer-extension primer were mixed with different DNA polymerases, such as OneTaq DNA Polymerase, Vent DNA Polymerase, phi29 DNA Polymerase, Pwo SuperYield DNA Polymerase, EpiMark Hot Start Taq DNA Polymerase, Bst DNA Polymerase-full length, Bst 2.0 DNA Polymerase, Bst 2.0 WarmStart DNA Polymerase, Bst 3.0 DNA Polymerase, Recombinant HIV reverse transcriptase), and the supplied buffers, with the supplement of different concentration of magnesium sulfate, manganese chloride, polyethylene glycol (PEG8000, PEG4000, PEG1000, PEG600, PEG600, PEG200), dATP/dCTP/dGTP and modified dTTP/UTP (dUTP, UTP, 2-Thio-dTTP, 4-Thio-dTTP, 5-Aminoallyl -dUTP, Fluorescein-12-dUTP). Primer extension tests were further carried out under different temperatures. The newly synthesized strands by extension were subsequentially released from the biotinylated template strands immobilized on Streptavidin C1 beads (Thermo Fisher, 65001) by incubation in 150 mM NaOH. The released strands were neutralized, cleaned up by Oligo Clean & Concentrator Kit (Zymo Research, D4061), and incubated with Streptavidin C1 beads again for the complete removal of template strands. The supernatant was cleaned up with Oligo Clean & Concentrator Kit and amplified for 10 cycles by NEBNext Ultra II Q5 Master Mix (NEB, M0544S) and NEBNext Multiplex Oligos for Illumina (NEB, E7335S).
The resulting libraries were purified by gel electrophoresis and recovery (NEB, T1020S). All libraries were sequenced at 2M reads depth in single-ended 100 bp mode at NovaSeq 6000 sequencer (Illumina). The primer extension condition was finalized as: 1500 units of Bst 2.0 DNA polymerase (NEB, M0537M), 1× EpiMark Hot Start Taq Reaction Buffer (NEB, M0490S), 8mM dATP (NEB, N0446S), 2mM dCTP (NEB, N0446S), 2mM dGTP (NEB, N0446S), 0.02 mM 2-Thio-dTTP (Trilink, N-2035), 6 mM magnesium sulfate (NEB) and 8% PEG4000 (Rigaku, # 25322-68-3). All reactions were incubated at 60 for 1 h.

value: synthetic construct

value: Mutation + demethylation group


title: Oligo 25% H

value: Control group


title: Oligo 20% H


title: Oligo 15% H


title: Oligo 20% B

value: Mutation group


title: Oligo 10% H


title: Oligo 15% B


title: Oligo 20% F


title: Control-3

value: bone marrow

value: Hematopoietic stem cells

value: 6 months


title: Oligo 10% F


title: Oligo 10% B


title: Oligo 25% B


title: Oligo 5% F


title: Oligo 5% B


title: Oligo 15% F


title: 7015-H08-ACTGAGCG-TCGCATAA_S231

city: Lausanne

first: Yun-Tsan

last: Chang

address: Avenue de Beaumont 29

department: Dermatology

country: Switzerland

institute: CHUV

description:
fluidigm C1
Healthy_T_cells.csv

data_processing:
The quality control was done using fastQC (v. 0.11.7) and the adaptors and low quality bases having phred quality score less than 20 were trimmed from the ends of the reads using Trim Galore (v. 0.4.4). The T-cell receptors (TCR) were identified using TraCeR and gene expressions were quantified with Kallisto (v. 0.45.0) for cells with an identified T cell receptor as part of the TraCeR workflow. TraCeR was also used to group the cells with identified TCR into groups of clones of different sizes, which all were required to have at least one TCR monomer in common with the other cells in the same clone. The remaining cells with TCR, sharing no identical TCR monomer with each other, were considered as heterogeneous cells. The gene expression data was normalised using Scater (v. 1.10.1) using CPM (counts per million).
Assembly: GRCh37
Supplementary files format and content: Matrix table with counts for every transcript and every cell

molecule: polyA RNA

source_name: Healthy

extract_protocol:
Capture and processing of single skin and blood T cells was performed using the Fluidigm C1 Autoprep system. Cells were loaded at a concentration of 2,000 cells/µL onto C1 integrated fluidic circuit chips for 5–10-µm cells. All C1 capture sites were microscopically inspected to identify the sites that contained only a single cell. Empty sites and those with multiple cells were excluded from further analysis. External RNA Controls Consortium spike-in RNAs served as a control. The SMARTer® Ultra® Low RNA Kit (Clontech) was used for reverse transcription and cDNA pre-amplification. The single-cell cDNA products from each cell were then used to prepare Illumina sequencing libraries and sequenced as paired-end 150-base reads on the Illumina HiSeq 4000 platform. Quality control was performed using FastQC v. 0.11.7 (Babraham Bioinformatics), and the adaptors and low-quality bases with a Phred quality score <20 were trimmed from the ends of the reads using Trim Galore v. 0.4.4 (Babraham Bioinformatics)
Cells were captured and performed using the Fluidigm C1 Autoprep system. The SMARTer® Ultra® Low RNA Kit (Clontech) was used for reverse transcription and cDNA pre-amplification. The single-cell cDNA products from each cell were then used to prepare Illumina sequencing libraries and sequenced as paired-end 150-base reads on the Illumina HiSeq 4000 platform.

value: blood

tag: patient diagnosis

value: healthy

value: T cells


title: 7015-H07-TAGCGCTC-TCGCATAA_S225

description:
fluidigm C1
Healthy_T_cells.csv


title: 7015-H12-TCGACGTC-TCGCATAA_S250

description:
fluidigm C1
Healthy_T_cells.csv


title: Oligo 5% H


title: 7015-H04-CGGAGCCT-TCGCATAA_S209

description:
fluidigm C1
Healthy_T_cells.csv


title: C_1

value: MAFs

value: Control


title: 7015-H06-ATGCGCAG-TCGCATAA_S219

description:
fluidigm C1
Healthy_T_cells.csv


title: 7015-H02-GGAGCTAC-TCGCATAA_S198

description:
fluidigm C1
Healthy_T_cells.csv


title: E2 knock-in replicate 1

source_name: Hippocampal and cortical regions of brain

value: Cd45+ cells

value: 5XFADhet APOE-knockin, E2


title: advanced melanoma patient 1, 5uM Ibrutinib

description: 10x Genomics

value: advanced melanoma

value: 5uM Ibrutinib


title: 7015-E04-CGGAGCCT-CTTAATAG_S206

description:
fluidigm C1
Healthy_T_cells.csv


title: 7015-G08-ACTGAGCG-TAAGGCTC_S230

description:
fluidigm C1
Healthy_T_cells.csv


title: 7015-E11-TGCAGCTA-CTTAATAG_S243

description:
fluidigm C1
Healthy_T_cells.csv


title: 7015-E09-CCTAAGAC-CTTAATAG_S235

description:
fluidigm C1
Healthy_T_cells.csv


title: 7015-E07-TAGCGCTC-CTTAATAG_S224

description:
fluidigm C1
Healthy_T_cells.csv


title: 7015-E12-TCGACGTC-CTTAATAG_S248

description:
fluidigm C1
Healthy_T_cells.csv


title: 7015-F04-CGGAGCCT-ATAGCCTT_S207

description:
fluidigm C1
Healthy_T_cells.csv


title: 7015-G04-CGGAGCCT-TAAGGCTC_S208

description:
fluidigm C1
Healthy_T_cells.csv


title: 7015-E10-CGATCAGT-CTTAATAG_S238

description:
fluidigm C1
Healthy_T_cells.csv


title: 7015-G02-GGAGCTAC-TAAGGCTC_S197

description:
fluidigm C1
Healthy_T_cells.csv


title: 7015-F11-TGCAGCTA-ATAGCCTT_S244

description:
fluidigm C1
Healthy_T_cells.csv


title: 7015-G03-GCGTAGTA-TAAGGCTC_S203

description:
fluidigm C1
Healthy_T_cells.csv


title: 7015-E02-GGAGCTAC-CTTAATAG_S195

description:
fluidigm C1
Healthy_T_cells.csv


title: 7015-E05-TACGCTGC-CTTAATAG_S213

description:
fluidigm C1
Healthy_T_cells.csv


title: 7015-D12-TCGACGTC-TCTTACGC_S247

description:
fluidigm C1
Healthy_T_cells.csv


title: 7015-D11-TGCAGCTA-TCTTACGC_S242

description:
fluidigm C1
Healthy_T_cells.csv


title: E2/E3/E4 5XFAD mice, 10weeks, HTO for demuxing

description: 10X Genomics 5'v2

value: Hippocampal and cortical regions of brain

value: 5XFADhet APOE-knockin


title: 7015-F02-GGAGCTAC-ATAGCCTT_S196

description:
fluidigm C1
Healthy_T_cells.csv


title: head & neck squamous cell carcinoma patient

description: 10x Genomics

source_name: head & neck squamous cell carcinoma

value: head & neck squamous cell carcinoma

value: peripheral blood mononuclear cells (PBMC)

value: No treatment


title: 7015-C09-CCTAAGAC-ACTCTAGG_S233

description:
fluidigm C1
Healthy_T_cells.csv


title: 7015-C11-TGCAGCTA-ACTCTAGG_S241

description:
fluidigm C1
Healthy_T_cells.csv


title: 7015-D03-GCGTAGTA-TCTTACGC_S201

description:
fluidigm C1
Healthy_T_cells.csv


title: 7015-C07-TAGCGCTC-ACTCTAGG_S222

description:
fluidigm C1
Healthy_T_cells.csv


title: 7015-D07-TAGCGCTC-TCTTACGC_S223

description:
fluidigm C1
Healthy_T_cells.csv


title: 7015-D06-ATGCGCAG-TCTTACGC_S217

description:
fluidigm C1
Healthy_T_cells.csv


title: 7015-D09-CCTAAGAC-TCTTACGC_S234

description:
fluidigm C1
Healthy_T_cells.csv


title: 7015-C08-ACTGAGCG-ACTCTAGG_S226

description:
fluidigm C1
Healthy_T_cells.csv


title: 7015-C12-TCGACGTC-ACTCTAGG_S246

description:
fluidigm C1
Healthy_T_cells.csv


title: 7015-D10-CGATCAGT-TCTTACGC_S237

description:
fluidigm C1
Healthy_T_cells.csv


title: 7015-F03-GCGTAGTA-ATAGCCTT_S202

description:
fluidigm C1
Healthy_T_cells.csv


title: 7015-G01-ACTCGCTA-TAAGGCTC_S192

description:
fluidigm C1
Healthy_T_cells.csv


title: 7015-C10-CGATCAGT-ACTCTAGG_S236

description:
fluidigm C1
Healthy_T_cells.csv


title: 7015-F01-ACTCGCTA-ATAGCCTT_S191

description:
fluidigm C1
Healthy_T_cells.csv


title: 7015-C06-ATGCGCAG-ACTCTAGG_S216

description:
fluidigm C1
Healthy_T_cells.csv


title: 7015-G12-TCGACGTC-TAAGGCTC_S249

description:
fluidigm C1
Healthy_T_cells.csv


title: 7015-E06-ATGCGCAG-CTTAATAG_S218

description:
fluidigm C1
Healthy_T_cells.csv


title: 7015-D08-ACTGAGCG-TCTTACGC_S227

description:
fluidigm C1
Healthy_T_cells.csv


title: 7015-F10-CGATCAGT-ATAGCCTT_S239

description:
fluidigm C1
Healthy_T_cells.csv


title: 7015-E08-ACTGAGCG-CTTAATAG_S228

description:
fluidigm C1
Healthy_T_cells.csv


title: 7015-C05-TACGCTGC-ACTCTAGG_S211

description:
fluidigm C1
Healthy_T_cells.csv


title: 7015-D02-GGAGCTAC-TCTTACGC_S194

description:
fluidigm C1
Healthy_T_cells.csv


title: 7015-F08-ACTGAGCG-ATAGCCTT_S229

description:
fluidigm C1
Healthy_T_cells.csv


title: Inhibitor-2

value: bone marrow

value: miR-31-5p inhibitor


title: 7015-B06-ATGCGCAG-AGCTAGAA_S215

description:
fluidigm C1
Healthy_T_cells.csv


title: 7015-C04-CGGAGCCT-ACTCTAGG_S205

description:
fluidigm C1
Healthy_T_cells.csv


title: 7015-B07-TAGCGCTC-AGCTAGAA_S221

description:
fluidigm C1
Healthy_T_cells.csv


title: 7015-C01-ACTCGCTA-ACTCTAGG_S190

description:
fluidigm C1
Healthy_T_cells.csv


title: 7015-C02-GGAGCTAC-ACTCTAGG_S193

description:
fluidigm C1
Healthy_T_cells.csv


title: 7010-H06-TAGGCATG-CGGAGAGA_S34

description:
fluidigm C1
Healthy_T_cells.csv


title: 7010-G11-GCTCATGA-ATTAGACG_S65

description:
fluidigm C1
Healthy_T_cells.csv


title: 7010-F06-TAGGCATG-AGGCTTAG_S33

description:
fluidigm C1
Healthy_T_cells.csv


title: 7010-H02-CGTACTAG-CGGAGAGA_S13

description:
fluidigm C1
Healthy_T_cells.csv


title: 7010-F10-GTAGAGGA-AGGCTTAG_S57

description:
fluidigm C1
Healthy_T_cells.csv


title: 7010-G04-TCCTGAGC-ATTAGACG_S24

description:
fluidigm C1
Healthy_T_cells.csv


title: 7010-H10-GTAGAGGA-CGGAGAGA_S59

description:
fluidigm C1
Healthy_T_cells.csv


title: 7010-H11-GCTCATGA-CGGAGAGA_S66

description:
fluidigm C1
Healthy_T_cells.csv


title: 7010-F07-CTCTCTAC-AGGCTTAG_S38

description:
fluidigm C1
Healthy_T_cells.csv


title: 7010-H09-AAGAGGCA-CGGAGAGA_S52

description:
fluidigm C1
Healthy_T_cells.csv


title: 7015-A07-TAGCGCTC-CTAGTCGA_S220

description:
fluidigm C1
Healthy_T_cells.csv


title: 7010-G07-CTCTCTAC-ATTAGACG_S39

description:
fluidigm C1
Healthy_T_cells.csv


title: 7010-F02-CGTACTAG-AGGCTTAG_S12

description:
fluidigm C1
Healthy_T_cells.csv


title: 7010-G01-TAAGGCGA-ATTAGACG_S5

description:
fluidigm C1
Healthy_T_cells.csv


title: 7015-A12-TCGACGTC-CTAGTCGA_S245

description:
fluidigm C1
Healthy_T_cells.csv


title: 7010-G12-ATCTCAGG-ATTAGACG_S72

description:
fluidigm C1
Healthy_T_cells.csv


title: 7015-A01-ACTCGCTA-CTAGTCGA_S188

description:
fluidigm C1
Healthy_T_cells.csv


title: 7010-G08-CGAGGCTG-ATTAGACG_S46

description:
fluidigm C1
Healthy_T_cells.csv


title: 7015-A06-ATGCGCAG-CTAGTCGA_S214

description:
fluidigm C1
Healthy_T_cells.csv


title: 7010-H05-GGACTCCT-CGGAGAGA_S28

description:
fluidigm C1
Healthy_T_cells.csv


title: 7015-B01-ACTCGCTA-AGCTAGAA_S189

description:
fluidigm C1
Healthy_T_cells.csv


title: 7010-H07-CTCTCTAC-CGGAGAGA_S40

description:
fluidigm C1
Healthy_T_cells.csv


title: 7015-A11-TGCAGCTA-CTAGTCGA_S240

description:
fluidigm C1
Healthy_T_cells.csv


title: 7015-B05-TACGCTGC-AGCTAGAA_S210

description:
fluidigm C1
Healthy_T_cells.csv


title: 7010-H01-TAAGGCGA-CGGAGAGA_S6

description:
fluidigm C1
Healthy_T_cells.csv


title: 7010-F11-GCTCATGA-AGGCTTAG_S64

description:
fluidigm C1
Healthy_T_cells.csv


title: 7015-B04-CGGAGCCT-AGCTAGAA_S204

description:
fluidigm C1
Healthy_T_cells.csv


title: 7010-F01-TAAGGCGA-AGGCTTAG_S4

description:
fluidigm C1
Healthy_T_cells.csv


title: 7010-H03-AGGCAGAA-CGGAGAGA_S18

description:
fluidigm C1
Healthy_T_cells.csv


title: 7010-F04-TCCTGAGC-AGGCTTAG_S23

description:
fluidigm C1
Healthy_T_cells.csv


title: 7010-E12-ATCTCAGG-TACTCCTT_S70

description:
fluidigm C1
Healthy_T_cells.csv


title: 7010-E06-TAGGCATG-TACTCCTT_S32

description:
fluidigm C1
Healthy_T_cells.csv


title: 7010-E04-TCCTGAGC-TACTCCTT_S22

description:
fluidigm C1
Healthy_T_cells.csv


title: 7010-E03-AGGCAGAA-TACTCCTT_S16

description:
fluidigm C1
Healthy_T_cells.csv


title: 7010-E01-TAAGGCGA-TACTCCTT_S3

description:
fluidigm C1
Healthy_T_cells.csv


title: 7010-D04-TCCTGAGC-TATGCAGT_S21

description:
fluidigm C1
Healthy_T_cells.csv


title: 7010-D02-CGTACTAG-TATGCAGT_S10

description:
fluidigm C1
Healthy_T_cells.csv


title: 7010-E07-CTCTCTAC-TACTCCTT_S37

description:
fluidigm C1
Healthy_T_cells.csv


title: 7010-E08-CGAGGCTG-TACTCCTT_S45

description:
fluidigm C1
Healthy_T_cells.csv


title: 7010-E02-CGTACTAG-TACTCCTT_S11

description:
fluidigm C1
Healthy_T_cells.csv


title: 7010-C12-ATCTCAGG-CTCCTTAC_S68

description:
fluidigm C1
Healthy_T_cells.csv


title: 7010-D11-GCTCATGA-TATGCAGT_S62

description:
fluidigm C1
Healthy_T_cells.csv


title: 7010-E10-GTAGAGGA-TACTCCTT_S56

description:
fluidigm C1
Healthy_T_cells.csv


title: 7010-C11-GCTCATGA-CTCCTTAC_S61

description:
fluidigm C1
Healthy_T_cells.csv


title: 7010-D12-ATCTCAGG-TATGCAGT_S69

description:
fluidigm C1
Healthy_T_cells.csv


title: 7010-D10-GTAGAGGA-TATGCAGT_S55

description:
fluidigm C1
Healthy_T_cells.csv


title: 7010-D09-AAGAGGCA-TATGCAGT_S49

description:
fluidigm C1
Healthy_T_cells.csv


title: 7010-C04-TCCTGAGC-CTCCTTAC_S20

description:
fluidigm C1
Healthy_T_cells.csv


title: 7010-D08-CGAGGCTG-TATGCAGT_S44

description:
fluidigm C1
Healthy_T_cells.csv


title: 7010-C10-GTAGAGGA-CTCCTTAC_S54

description:
fluidigm C1
Healthy_T_cells.csv


title: 7010-B09-AAGAGGCA-AGAGGATA_S47

description:
fluidigm C1
Healthy_T_cells.csv


title: 7010-C02-CGTACTAG-CTCCTTAC_S9

description:
fluidigm C1
Healthy_T_cells.csv


title: 7010-C09-AAGAGGCA-CTCCTTAC_S48

description:
fluidigm C1
Healthy_T_cells.csv


title: 7010-D01-TAAGGCGA-TATGCAGT_S2

description:
fluidigm C1
Healthy_T_cells.csv


title: 7010-B06-TAGGCATG-AGAGGATA_S30

description:
fluidigm C1
Healthy_T_cells.csv


title: 7010-C08-CGAGGCTG-CTCCTTAC_S43

description:
fluidigm C1
Healthy_T_cells.csv


title: 7010-C06-TAGGCATG-CTCCTTAC_S31

description:
fluidigm C1
Healthy_T_cells.csv


title: 7010-E05-GGACTCCT-TACTCCTT_S26

description:
fluidigm C1
Healthy_T_cells.csv


title: 7010-A11-GCTCATGA-ATAGAGAG_S60

description:
fluidigm C1
Healthy_T_cells.csv


title: 7010-A10-GTAGAGGA-ATAGAGAG_S53

description:
fluidigm C1
Healthy_T_cells.csv


title: 7010-B02-CGTACTAG-AGAGGATA_S8

description:
fluidigm C1
Healthy_T_cells.csv


title: 7010-B12-ATCTCAGG-AGAGGATA_S67

description:
fluidigm C1
Healthy_T_cells.csv


title: 7010-A06-TAGGCATG-ATAGAGAG_S29

description:
fluidigm C1
Healthy_T_cells.csv


title: 7010-C03-AGGCAGAA-CTCCTTAC_S14

description:
fluidigm C1
Healthy_T_cells.csv


title: 7010-D03-AGGCAGAA-TATGCAGT_S15

description:
fluidigm C1
Healthy_T_cells.csv


title: 7010-A01-TAAGGCGA-ATAGAGAG_S1

description:
fluidigm C1
Healthy_T_cells.csv


title: 7010-A04-TCCTGAGC-ATAGAGAG_S19

description:
fluidigm C1
Healthy_T_cells.csv


title: 20180320.A-Plate_11_N715_S516

description:
fluidigm C1
MF046_S.csv

value: skin

value: cutaneous T-cell lymphoma


title: 7010-B08-CGAGGCTG-AGAGGATA_S42

description:
fluidigm C1
Healthy_T_cells.csv

value: blood

value: healthy


title: 7010-D07-CTCTCTAC-TATGCAGT_S36

description:
fluidigm C1
Healthy_T_cells.csv

value: T cells


title: 7010-A05-GGACTCCT-ATAGAGAG_S25

description:
fluidigm C1
Healthy_T_cells.csv


title: 7010-A08-CGAGGCTG-ATAGAGAG_S41

description:
fluidigm C1
Healthy_T_cells.csv


title: 20180320.A-Plate_11_N715_S515

description:
fluidigm C1
MF046_S.csv


title: 7010-B07-CTCTCTAC-AGAGGATA_S35

description:
fluidigm C1
Healthy_T_cells.csv


title: 20180320.A-Plate_11_N714_S517

description:
fluidigm C1
MF046_S.csv


title: 20180320.A-Plate_11_N711_S520

description:
fluidigm C1
MF046_S.csv


title: 20180320.A-Plate_11_N712_S516

description:
fluidigm C1
MF046_S.csv


title: 20180320.A-Plate_11_N712_S513

description:
fluidigm C1
MF046_S.csv


title: 20180320.A-Plate_11_N714_S516

description:
fluidigm C1
MF046_S.csv


title: 20180320.A-Plate_11_N712_S517

description:
fluidigm C1
MF046_S.csv


title: 20180320.A-Plate_11_N712_S515

description:
fluidigm C1
MF046_S.csv


title: 20180320.A-Plate_11_N711_S522

description:
fluidigm C1
MF046_S.csv


title: 20180320.A-Plate_11_N711_S515

description:
fluidigm C1
MF046_S.csv


title: 20180320.A-Plate_11_N712_S520

description:
fluidigm C1
MF046_S.csv


title: 20180320.A-Plate_11_N711_S517

description:
fluidigm C1
MF046_S.csv


title: 20180320.A-Plate_11_N710_S520

description:
fluidigm C1
MF046_S.csv


title: 20180320.A-Plate_11_N710_S517

description:
fluidigm C1
MF046_S.csv


title: 20180320.A-Plate_11_N711_S518

description:
fluidigm C1
MF046_S.csv


title: 20180320.A-Plate_11_N707_S522

description:
fluidigm C1
MF046_S.csv


title: 20180320.A-Plate_11_N710_S516

description:
fluidigm C1
MF046_S.csv


title: 20180320.A-Plate_11_N706_S517

description:
fluidigm C1
MF046_S.csv


title: 20180320.A-Plate_11_N706_S518

description:
fluidigm C1
MF046_S.csv


title: 20180320.A-Plate_11_N706_S520

description:
fluidigm C1
MF046_S.csv


title: 20180320.A-Plate_11_N706_S513

description:
fluidigm C1
MF046_S.csv


title: 20180320.A-Plate_11_N705_S520

description:
fluidigm C1
MF046_S.csv


title: 20180320.A-Plate_11_N705_S518

description:
fluidigm C1
MF046_S.csv


title: 20180320.A-Plate_11_N705_S521

description:
fluidigm C1
MF046_S.csv


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fluidigm C1
MF046_S.csv


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fluidigm C1
MF046_S.csv


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fluidigm C1
MF046_S.csv


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fluidigm C1
MF046_S.csv


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fluidigm C1
MF046_S.csv


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fluidigm C1
MF046_S.csv


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fluidigm C1
MF046_S.csv


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fluidigm C1
MF046_S.csv


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description:
fluidigm C1
MF046_S.csv


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fluidigm C1
MF046_S.csv


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description:
fluidigm C1
MF046_S.csv


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description:
fluidigm C1
MF046_S.csv


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description:
fluidigm C1
MF046_S.csv


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fluidigm C1
MF042_S.csv


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fluidigm C1
MF046_S.csv


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fluidigm C1
MF042_S.csv


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fluidigm C1
MF042_S.csv


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fluidigm C1
MF042_S.csv


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fluidigm C1
MF042_S.csv


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fluidigm C1
MF042_S.csv


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fluidigm C1
MF042_S.csv


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fluidigm C1
MF042_S.csv


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fluidigm C1
MF042_S.csv


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fluidigm C1
MF042_S.csv


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fluidigm C1
MF042_S.csv


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fluidigm C1
MF042_S.csv


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fluidigm C1
MF042_S.csv


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fluidigm C1
MF042_S.csv


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fluidigm C1
MF042_S.csv


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fluidigm C1
MF042_S.csv


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fluidigm C1
MF042_S.csv


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fluidigm C1
MF042_S.csv


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fluidigm C1
MF042_S.csv


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fluidigm C1
MF042_S.csv


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fluidigm C1
MF042_S.csv


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fluidigm C1
MF042_S.csv


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fluidigm C1
MF042_S.csv


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fluidigm C1
MF042_S.csv


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fluidigm C1
MF042_S.csv


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fluidigm C1
MF042_S.csv


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fluidigm C1
MF042_S.csv


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fluidigm C1
MF042_S.csv


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fluidigm C1
MF042_S.csv


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fluidigm C1
MF042_S.csv


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fluidigm C1
MF042_S.csv


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fluidigm C1
MF042_S.csv


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description:
fluidigm C1
MF042_S.csv