title: RNA-seq of Nep3-positive cells, replicate 5

description:
Library name: Nep3_pos_RNAseq_rep5
Nematostella vectensis tentacle nematocytes (Nep3-positive) isolated by FACS; bulk RNA-seq, replicate 1.

data_processing:
RNA-seq: Raw reads were trimmed with Trimmomatic and aligned to the Nematostella vectensis genome (Nv2 assembly) using STAR (v2.7.10a). Gene-level counts were obtained with featureCounts (v2.0.1).
Assembly: Nematostella vectensis genome assembly Nv2 (Zimmermann  et al., 2023).
Supplementary files format and content: RNAseq_counts_matrix.txt: tab-delimited matrix of raw gene counts (rows = genes, columns = samples).

extract_protocol:
Tentacle tissue was dissected and enzymatically dissociated into single cells. Ncol3::mOrange and Nep3::mOrange reporter lines were used for FACS isolation of positive and negative cnidocyte populations. Total RNA was extracted using TRIzol (for RNA-seq).
RNA-seq libraries were prepared using NEBNext Ultra II Directional RNA Library Prep Kit with Sample Purification Beads (New England Biolabs) according to the manufacturer’s protocol, selecting for poly(A)+ RNA.

value: Nep3-positive cnidocytes

value: Nep3::mOrange reporter line


title: KO3-HS

status: Public on Oct 05 2025

type: SRA

city: Durham

first: Kenneth

last: Scaglione

address: 3 Genome Court

country: USA

institute: Duke

library_source: transcriptomic

data_processing:
1) Remove reads containing adapters
2) Remove reads containing N>10% (N represents base that could not be determineed)
3) Remove low quality reads: The Qscore (Quality score) of over 50% bases of the read is <=5.
Data was processed to remove low confidence nucleotide base-calls and then mapped to the reference genome using HISAT2. Differential gene expression analysis was performed and genes with a fold change greater than 2 and a padj value of 0.05 were called hits.
Supplementary files format and content: FPKM

molecule: total RNA

organism: Mus musculus

source_name: MEF

extract_protocol:
RNA was extracted using the Qiagen RNAse Easy kit.
RNA libraries were constructed by Novogene using polyA capture snd reverse transcriptin of cDNA.

treatment_protocol: heat shock treatment = 1 hour at 43 degrees Celsius

tag: cell line

value: MEF

tag: genotype

value: CHIP-KO

tag: treatment

value: heat shock


title: F123 ChIPseq Input

city: Zurich

first: Raffaella

last: Santoro

address: Winterthurerstrasse 190

department: Dep. of Molecular Mechanisms  of Disease

country: Switzerland

institute: University of Zurich

library_source: genomic

data_processing:
N-masked genome was created using the mm10 reference genome and the Variant Call Format (VCF) file from the mouse genome project containing the SNP information for all strains. The SNPsplit package (Krueger & Andrews, 2016) was used to read the VCF file and extract the SNP information for the S129/SvJae and CAST strains and N-mask for the mm10 genome. ChIPseq reads were aligned to the N-masked mm10 reference genome with Bowtie2 (version 2.5.0; (Langmead & Salzberg, 2012)) using default parameters. PCR duplicates were removed using samtools. SNPsplit was then used to tag the SNPs for S129/SvJae and CAST alleles in the bam file and sort the haplotype-specific bam files for both the alleles. Bigwig files were created from the bam files using bamCoverage from deeptools (Ramirez et al., 2014) using default parameters. Integrative Genome Viewer (IGV, version 2.15.4) (Robinson et al., 2011) was used to visualize and extract representative ChIPseq tracks.
Assembly: mm10
Supplementary files format and content: BED

molecule: genomic DNA

source_name: F123 hyrbid ESC

growth_protocol: F123-ESCs (mouse male, hybrid cell line, F1 S129/Jae and Cast mouse cross) (Gribnau et al, 2003) were cultured on a layer of mitotically inactivated feeder murine embryonic fibroblasts under standard conditions (DMEM, supplemented with 15 % KSR, 1x Glutamax, 10 mM non-essential amino acids, 50 µM beta-mercaptoethanol, 1,000 U/ml LIF). Media was changed every 24h. Before harvesting, mESCs were passaged onto feeder-free ESGRO-gelatin (EMD Millipore SF008) coated plates for at least 2 passages to remove feeder cells. Cells were harvested after approximately 48 h at 70 – 80 % confluency.

extract_protocol:
ChIP was performed as previously described (Lerra et al, 2024). Briefly, 1% formaldehyde was added to cultured cells to cross-link proteins to DNA. Isolated nuclei were then lysed with lysis buffer (50 mM Tris-HCl, pH 8.1, 10 mM EDTA, pH 8, 1% SDS, 1X protease inhibitor complete EDTA-free cocktail, Roche). Nuclei were sonicated using a Bioruptor ultrasonic cell disruptor (Diagenode) to shear genomic DNA to an average fragment size of 200 bp. 20 μg of chromatin was diluted to a total volume of 500 μl with ChIP buffer (16.7 mM Tris-HCl, pH 8.1, 167 mM NaCl, 1.2 mM EDTA, 0.01% SDS, 1.1% Triton X-100) and incubated overnight with the ChIP-grade antibodies against H3K9me2, H3K9me3, H3K27me3, H3K4me1, H3K4me3 and H3K27ac. After washing, bound chromatin was eluted with the elution buffer (1% SDS, 100 mM NaHCO3). Upon proteinase K digestion (50 °C for 3 h) and reversion of cross- linking (65 °C, overnight), DNA was purified with phenol/chloroform, and ethanol precipitated.
The quality and quantity of the isolated DNA were determined with a Qubit® 4 Fluorometer (Life Technologies, California, USA) and the 4200 TapeStation system. Briefly, ChIP samples (10 ng) were end-repaired and polyadenylated before the ligation of Illumina compatible adapters. The adapters contain the index for multiplexing. The quality and quantity of the enriched libraries were validated using Qubit® 4 Fluorometer and the 4200 TapeStation system. The libraries were pooled to 10 nM in Tris-Cl 10 mM, pH8.5 with 0.1% Tween 20. Sequencing was performed on the NovaSeq 6000 for 100bp single end reads (Illumina, Inc, California, USA).

value: F123 hyrbid ESC


title: ChIP-seq of 3XFlag-SyCRP1 under high CO₂ condition

city: Hyderabad

first: Suraj

last: Chauhan

state: Telangana

address: Prof. C.R. Rao Road, Central University P.O., Gachibowli

department: Biotechnology and Bioinformatics

country: India

institute: University of Hyderabad

description: Library name: SyCRP1_HC_ChIP

data_processing:
Sequence reads were subjected to adaptor and quality trimming using fastp v0.23.4; a Phred quality score cutoff of 20 was applied for trimming.
Trimmed reads were aligned to the Synechocystis reference genome using BWA-MEM v0.7.17-r1188 with default parameters.
Alignments with a mapping quality score below 10 were filtered out using SAMtools.
Duplicate reads were removed using GATK v4.4.0.0. Peak calling was performed using MACS2 v2.2.9.1 with default parameters, using input DNA as the control.
Alignments were converted to BigWig format using deepTools v3.5.4, with read counts normalized to 1× genome coverage (RPGC).
Assembly: ASM972v1 (GCF_000009725.1)
Supplementary files format and content: bigWig, narrowPeak (except for INPUT sample)

organism: Geminocystis herdmanii PCC 6308

source_name: Synechocystis whole cells

growth_protocol: Cells were grown in BG11 media (buffered with HEPES, pH 7.8), at 34°C, under continuous illumination of 70 μmol photons m-2 s-1 and bubbled with filter sterilized air.

extract_protocol:
Cells were fixed by formaldehyde at a final concentration of 1%, the fixation was quenched with 125 mM Glycine. Cells were disrupted using glass-beads by vigorous mixing at maximum speed on a vortex mixer. The genomic DNA was fragmented by sonication using Sonics Vibracell, VC505 ultrasonicator. 3XFlag-SyCRP1 was immunoprecipitated with Anti-FLAG M2 affinity gel and eluted with 3xFLAG peptide. Protein and RNA was removed by Proteinase K and RNaseA; the DNA fragments were extracted by PCIA and precipitated by ethanol.
The input and immune-precipitated DNA was quantified by Qubit 4 flurometer from invitrogen. The NEBNext® Ultra™ II DNA Library Prep Kit for Illumina®  from NEB was used to prepare libraries. The cleaned libraries were quantitated on Qubit 4 flurometer and appropriate dilutions loaded on a High sensitivity D1000 screen tape on Agilent 4200 tapestation to determine the average size and range of the fragments.

treatment_protocol: High CO2 (HC) treatment. 5% (v/v) CO2 in sterile air was bubbled to the culture for 1h before collection

tag: cell type

value: Synechocystis whole cells

value: 3XFlag-SyCRP1 expressing in mutant sycrp1 background

tag: chip antibody

value: Anti-FLAG (Sigma-Aldrich, Cat. No. A2220)


title: NCH601-GPD1-sh3-4d

city: Heidelberg

first: Chunxuan

last: Shao

address: Im Neuenheimer Feld 581

country: Germany

institute: Deutsches Krebsforschungszentrum

data_processing:
Raw reads from RNA-seq experiments of NCH601 BTSC cell cultures under different treatment conditions were aligned to hg19 (ensemble version 75) by STAR (2.5.3a) with default parameters. The quality of alignments were examined by QoRTs  and read counts were quantified by “featureCounts” in the R package Rsubread4. DESeq2 was employed to identify the diffeentially regulated genes with the option “cooksCutoff = FALSE”. Samples collected in day 3 and 4 are grouped as “long_term”, and different GPD1 shRNAs were treated as batches.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include raw counts values for each Sample

organism: Homo sapiens

growth_protocol: NCH601 patient-derived glioblastoma stem cells were established at the Heidelberg University Hospital. NCH BTSC cells were cultured in DMEM/Ham F-12 medium (1-26F09-I, Bioconcept) supplemented with 20 % BIT supplement (Pelo Biotech), 1 % PenStrep (Thermo Fisher), GlutaMAX Supplement (0.5 mM, 35050061, ThermoFisher), Epidermal growth factor (20 ng/ml, E4127-5X.1MG, Sigma) and Fibroblast growth factor 2 (20 ng/ml, F0291-25UG, Sigma).

extract_protocol:
Total RNA was isolated using the RNeasy Micro kit (Cat.74004, Qiagen) according to the manufacturer's instruction. 1000 ng of total RNA was reverse transcribed with QuantiTect Rev transcription Kit (205311, Qiagen).
Total RNA  were sent in house facility for Illumina Hiseq sequencing according to related protocols

treatment_protocol: Lentiviruses contained one non-targeting control shRNA (SHC002) and four shRNAs targeting different regions in GPD1 (sh3, TRCN0000026517; sh5, TRCN0000026521; sh7, TRCN0000157054 and sh9 TRCN0000026507) were used to knock down GPD1 in human BTSCs. Medium replacement was conducted 24 h post infection. Cells were harvest at day1, 2, 3 and 4 post lenti-virus post-transduction. RNA was extracted with RNeasy Micro kit (Qiagen, Germany) and DNAse treatment was performed before RNAseq library preparation

value: cancer stem cells

value: GPD1 knock down

tag: time

value: 4 day


title: NCH601-GPD1-sh9-1d

value: 1 day


title: KO3


title: KO2-HS


title: NCH601-GPD1-sh3-2d

value: 2 day


title: NCH601-GPD1-sh3-1d


title: F123 ChIPseq H3K4me3


title: RNA-seq of Nep3-positive cells, replicate 3

city: Jerusalem

first: Itamar

last: Kozlovski

address: Alexander Silberman Institute of Life Sciences

department: Ecology, Evolution and Behavior

country: Israel

institute: The Hebrew University of Jerusalem

description:
Library name: Nep3_pos_RNAseq_rep3
Nematostella vectensis tentacle nematocytes (Nep3-positive) isolated by FACS; bulk RNA-seq, replicate 1.

molecule: polyA RNA

organism: Nematostella vectensis

source_name: tentacle

growth_protocol: N. vectensis polyps were maintained at 18 °C in 16 ‰ sea salt water (Red Sea, Israel), used as the growth medium. Polyps were fed with Artemia salina nauplii three times a week.

treatment_protocol: No experimental treatment was applied. Animals were collected untreated for cell isolation.

tag: tissue

value: tentacle

value: untreated

tag: batch


title: RNA-seq of Nep3-positive cells, replicate 1

description:
Library name: Nep3_pos_RNAseq_rep1
Nematostella vectensis tentacle nematocytes (Nep3-positive) isolated by FACS; bulk RNA-seq, replicate 1.


title: RNA-seq of Nep3-negative cells, replicate 5

description:
Library name: Nep3_neg_RNAseq_rep5
Nematostella vectensis tentacle cells (Nep3-negative) isolated by FACS; bulk RNA-seq, replicate 5.

value: Nep3-negative cells


title: KO1-HS


title: MIFE_13

data_processing:
Raw rnaseq datra from mice with GBM tumours treated with MIFE, DEXA and DMSO were aligned to mm10 (ensembl version 86) respectively by STAR (2.5.3a) with default parameters. The quality of alignments were examined by QoRTs and read counts were quantified by “featureCounts” in the R package Rsubread. DESeq2 was employed to identify the differentially regulated genes with the option “cooksCutoff = FALSE”.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw counts values for each Sample

source_name: tumour cells

growth_protocol: Mice were housed according to international standard conditions and all animal experiments were complied with local and international guidelines for the use of experimental animals with the ShanghaiTech University ethical approval number #20201208001. Tumor induction was used the RCAS-nTVA system as described previously1. The tumor growth was monitored by Bioluminescence Imaging (BLI) using the IVIS Lumina II In Vivo Imaging System (Perkin Elmer, US). Mice were given an injection of D-luciferin (BioVision, 7903-1g) intraperitoneally at a concentration of 150 mg/kg of body weight.

extract_protocol:
Mouse brain tumor tissues was sheared and homonized by RLT buffer from the RNA extraction kit (Cat.#74134, Qiagen). RNA samples were pretreated with DNase and 1 ug purified RNA was subjected to cDNA synthesis.
Library preparation following the standard protocol from TruSeq® RNA LT Sample Prep Kit v2 (Illumina, US). Sequencing was carried out on the HiSeq 2500 platform (Illumina) with output 8-10 giga bit sequencing data per sample.

treatment_protocol: When most of mice developed detectable tumors, mice were treated with DMSO (60313ES60, Yeasen, China), dexamethasone (DEXA, D4902-100MG, Sigma) and mifepristone (MIFE, M8046-500MG, Sigma) for 5 times every other day. In the following day, all the mice were treated with DMSO or temozolomide (TMZ, T2577-100MG, Sigma). TMZ and DEXA was dissolved in DMSO (stock: 25 mg/ml and 10 mg/ml, respectively) and freshly diluted in 0.9 % saline and injected intraperitoneally with 100 mg/kg/day for TMZ and 10 mg /kg/day for Dexamethasone. MIFE was dissolved in DMSO (80 mg/mL) and freshly diluted in sunflower seed oil (192-15262, Woko) and injected intraperitoneally with 20 mg/kg/day for 5 times every other day.

value: tumour cells

value: WT

tag: treament

value: mifepristone


title: RNA-seq of Nep3-positive cells, replicate 2

description:
Library name: Nep3_pos_RNAseq_rep2
Nematostella vectensis tentacle nematocytes (Nep3-positive) isolated by FACS; bulk RNA-seq, replicate 1.

value: Nep3-positive cnidocytes

value: Nep3::mOrange reporter line


title: MIFE_12


title: MIFE_10


title: RNA-seq of Nep3-negative cells, replicate 4

description:
Library name: Nep3_neg_RNAseq_rep4
Nematostella vectensis tentacle cells (Nep3-negative) isolated by FACS; bulk RNA-seq, replicate 4.


title: RNA-seq of Nep3-negative cells, replicate 3

description:
Library name: Nep3_neg_RNAseq_rep3
Nematostella vectensis tentacle cells (Nep3-negative) isolated by FACS; bulk RNA-seq, replicate 3.


title: MEF2-HS

value: MEF

value: heat shock


title: MIFE_11


title: NCH601-GPD1-sh3-3d

value: 3 day


title: RNA-seq of Nep3-negative cells, replicate 2

description:
Library name: Nep3_neg_RNAseq_rep2
Nematostella vectensis tentacle cells (Nep3-negative) isolated by FACS; bulk RNA-seq, replicate 2.


title: RNA-seq of Nep3-positive cells, replicate 4

description:
Library name: Nep3_pos_RNAseq_rep4
Nematostella vectensis tentacle nematocytes (Nep3-positive) isolated by FACS; bulk RNA-seq, replicate 1.


title: E14 RNAseq rep3 ActD

data_processing:
The quality of the reads was checked by FastQC, a quality control tool for high throughput sequence data (Andrews, 2010). The quality of the reads was increased by applying: a) SortMeRNA (Kopylova, 2012) (version 2.1) tool to filter ribosomal RNA; b) Trimmomatic (Bolger et al, 2014) (version 0.40) software package to trim the sorted (a) reads. For each gene, exon coverage was calculated using a custom pipeline and then normalized in reads per kilobase per million (RPKM) (Mortazavi et al, 2008), the method of quantifying gene expression from RNA sequencing data by normalizing for total read length and the number of sequencing reads.
Assembly: mm10
Supplementary files format and content: xlsx

growth_protocol: 129 mouse embryonic stem cells (E14 line) were cultured in serum medium containing Dulbecco’s modified Eagle’s medium + Glutamax (Life Technologies), 15% FCS (Life Technologies; Cat no. 10270106 FBS South American), 1× MEM NEAA (Life Technologies), 100 μM β-mercaptoethanol, recombinant leukemia inhibitory factor, LIF (Polygene, 1000 U/ml), 1× penicillin/streptomycin (Life Technologies).

extract_protocol:
Total RNA was purified with Zymo RNA extraction kit (Zymo Research). 1 million cells were used for RNA purification.All samples were spiked-in with ERCC control RNAs (Thermo Fisher Scientific) following manufacturer’s recommendations. The quality of the isolated RNA was determined with a Qubit® 4 fluorometer (Life  Technologies, California, USA) and 4200 TapeStation system (Agilent, Santa Clara, California, USA). Only those samples with a 260 nm/280 nm ratio between 1.8–2.1 and a 28S/18S ratio within 1.5-2 were further processed.
The TruSeq Stranded mRNA (Illumina, Inc, California, USA) was used in the succeeding steps. Briefly, total RNA samples (100–1000 ng) were polyA enriched and then reverse- transcribed into double-stranded cDNA. The cDNA samples were fragmented, end-repaired and adenylated before ligation of TruSeq adapters containing unique dual indices (UDI) for multiplexing. Fragments containing TruSeq adapters on both ends were selectively enriched with PCR. The quality and quantity of the enriched libraries were validated using Qubit® 4 fluorometer. The product is a smear with an average fragment size of approximately 260 bp. Libraries were normalized to 10 nM in Tris-Cl 10 mM, pH8.5 with 0.1% Tween 20. The NovaSeq X (Illumina, Inc, California, USA) was used for cluster generation and sequencing according to standard protocol. Sequencing was paired end at 2 × 150 bp.

treatment_protocol: ESCs were treated with Actinomycin D (10ng/ml) or left untreated for 24h before downstream processing.

value: ActD treated


title: DEXA_8

value: dexamethasone


title: MEF1-HS


title: KO2

value: CHIP-KO


title: MIFE_9


title: RNA-seq of Nep3-negative cells, replicate 1

description:
Library name: Nep3_neg_RNAseq_rep1
Nematostella vectensis tentacle cells (Nep3-negative) isolated by FACS; bulk RNA-seq, replicate 1.


title: MEF2


title: DEXA_6


title: MEF3-HS


title: MEF3


title: DEXA_5


title: E14 RNAseq rep1 ActD


title: Lateral sulcus, replicate 3

city: Shanghai

first: Youning

last: Lin

address: Rm 4027 Research Building II, Dong'an Rd. Xuhui District.

country: China

institute: Fudan University

data_processing:
Sequence reads were trimmed from 3' end until the final base had a quality score > 20, using Trimmomatic v0.33, discarding reads left with < 50 bp
Sequence reads were aligned to the Ensemble domestic ferret genome using HISAT2. Only uniquely mapping reads with at most two mismatches were retained
Sequence reads were  assembled using Cuffquant and Cuffnorm components of Cufflinks v2.2.1
Reads overlapping annotated genes were counted using HTSeq v0.6.0
Assembly: MusPutFur1.0
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Mustela putorius furo

source_name: brain

extract_protocol:
RNA was harvested using Rneasy Plus Micro kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TIANSeq Fast RNA Library Prep Kit (Illumina)  following manufacturer's protocols.

value: brain

tag: brain region

value: Lateral sulcus

value: wild type


title: DEXA_7


title: KO1


title: RNA-seq of Ncol3-positive cells, replicate 4

description:
Library name: Ncol3_pos_RNAseq_rep4
Nematostella vectensis tentacle cnidocytes (Ncol3-positive) isolated by FACS; bulk RNA-seq, replicate 4.

value: tentacle

value: Ncol3-positive cnidocytes

value: Ncol3::mOrange reporter line


title: E14 RNAseq rep2 ActD


title: MEF1


title: RNA-seq of Ncol3-negative cells, replicate 4

description:
Library name: Ncol3_neg_RNAseq_rep4
Nematostella vectensis tentacle cells (Ncol3-negative) isolated by FACS; bulk RNA-seq, replicate 4.

value: Ncol3-negative cells

value: untreated


title: DEXA_4

value: tumour cells

value: WT


title: E14 RNAseq rep1 untreated

value: Untreated


title: RNA-seq of Ncol3-positive cells, replicate 3

description:
Library name: Ncol3_pos_RNAseq_rep3
Nematostella vectensis tentacle cnidocytes (Ncol3-positive) isolated by FACS; bulk RNA-seq, replicate 3.


title: E14 RNAseq rep3 untreated


title: F123 RNAseq rep3

data_processing:
The quality of the reads was checked by FastQC, a quality control tool for high throughput sequence data (Andrews, 2010). The quality of the reads was increased by applying: a) SortMeRNA (Kopylova, 2012) (version 2.1) tool to filter ribosomal RNA; b) Trimmomatic (Bolger et al, 2014) (version 0.40) software package to trim the sorted (a) reads. N-masked genome was created using the mm10 reference genome and the VCF file from the mouse genome project containing the SNP information for all strains. The SNPsplit package (Krueger & Andrews, 2016) was used to read in the VCF file and extract the SNP information for the S129/SvJae and CAST strains and N-mask the mm10 genome. The sorted (a), trimmed (b) reads were mapped against the Nmasked mouse genome (mm10) using the default parameters of the STAR (Spliced Transcripts Alignment to a Reference, version 2.6, (Dobin et al, 2013)). SNPsplit was then used to tag the SNPs for S129/SvJae and CAST alleles in the bam file and sort the haplotype-specific bam files for both the alleles. For each gene, exon coverage was calculated using a custom pipeline and then normalized in reads per kilobase per million (RPKM) (Mortazavi et al, 2008), the method of quantifying gene expression from RNA sequencing data by normalizing for total read length and the number of sequencing reads.
Assembly: mm10
Supplementary files format and content: Bigwig

growth_protocol: F123-ESCs (mouse male, hybrid cell line, F1 S129/Jae and Cast mouse cross) (Gribnau et al, 2003) were cultured on a layer of mitotically inactivated feeder murine embryonic fibroblasts under standard conditions (DMEM, supplemented with 15 % KSR, 1x Glutamax, 10 mM non-essential amino acids, 50 µM beta-mercaptoethanol, 1,000 U/ml LIF). Media was changed every 24h. Before harvesting, mESCs were passaged onto feeder-free ESGRO-gelatin (EMD Millipore SF008). coated plates for at least 2 passages to remove feeder cells. Cells were harvested after approximately 48 h at 70 – 80 % confluency.

extract_protocol:
Total RNA was purified with TRIzol reagent (Life Technologies). The quality of the isolated RNA was determined with a Qubit® 4 fluorometer (Life  Technologies, California, USA) and 4200 TapeStation system (Agilent, Santa Clara, California, USA). Only those samples with a 260 nm/280 nm ratio between 1.8–2.1 and a 28S/18S ratio within 1.5-2 were further processed.
The TruSeq Stranded mRNA (Illumina, Inc, California, USA) was used in the succeeding steps. Briefly, total RNA samples (100–1000 ng) were polyA enriched and then reverse- transcribed into double-stranded cDNA. The cDNA samples were fragmented, end-repaired and adenylated before ligation of TruSeq adapters containing unique dual indices (UDI) for multiplexing. Fragments containing TruSeq adapters on both ends were selectively enriched with PCR. The quality and quantity of the enriched libraries were validated using Qubit® 4 fluorometer. The product is a smear with an average fragment size of approximately 260 bp. Libraries were normalized to 10 nM in Tris-Cl 10 mM, pH8.5 with 0.1% Tween 20. The NovaSeq X (Illumina, Inc, California, USA) was used for cluster generation and sequencing according to standard protocol. Sequencing was paired end at 2 × 150 bp.

value: F123 hyrbid ESC


title: RNA-seq of Ncol3-negative cells, replicate 2

description:
Library name: Ncol3_neg_RNAseq_rep2
Nematostella vectensis tentacle cells (Ncol3-negative) isolated by FACS; bulk RNA-seq, replicate 2.


title: DMSO_2

value: DMSO


title: F123 RNAseq rep4


title: RNA-seq of Ncol3-positive cells, replicate 1

description:
Library name: Ncol3_pos_RNAseq_rep1
Nematostella vectensis tentacle cnidocytes (Ncol3-positive) isolated by FACS; bulk RNA-seq, replicate 1.


title: Lateral sulcus, replicate 1


title: F123 RNAseq rep2


title: E14 RNAseq rep2 untreated


title: DMSO_3


title: RNA-seq of Ncol3-negative cells, replicate 3

description:
Library name: Ncol3_neg_RNAseq_rep3
Nematostella vectensis tentacle cells (Ncol3-negative) isolated by FACS; bulk RNA-seq, replicate 3.


title: Lateral gyurs, replicate 3

value: Lateral gyrus


title: Lateral sulcus, replicate 2


title: Lateral gyrus, replicate 1


title: RNA-seq of Ncol3-positive cells, replicate 2

description:
Library name: Ncol3_pos_RNAseq_rep2
Nematostella vectensis tentacle cnidocytes (Ncol3-positive) isolated by FACS; bulk RNA-seq, replicate 2.


title: Lateral gyurs, replicate 2


title: DMSO_1


title: NM8013 ΔscaRNA R3

status: Public on Oct 04 2025

city: Würzburg

first: Tom

last: Gräfenhan

address: Josef-Schneider-Str. 2, Bau D15

department: Core Unit SysMed

institute: University of Wuerzburg

data_processing:
Base calling with Illumina NextSeq RTA v2.4.11
FASTQ conversion with bcl2fastq v2.20.0.422
FASTQ quality and adapter trimming using Cutadapt (Martin, 2011) version 2.5 (cutadapt parameters: --nextseq-trim=20 -m 1 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC)
Alignment of reads longer than 11 nt to reference genome using segemehl version 0.2.0 with minimum accuracy 95% (parameters for reademption align: -l 12 -a 95) (READemption 0.4.5, Förstner et al., 2014)
Coverage calculation via reademption coverage based on all aligned reads (full-length); Normalization: coverage-tnoar_min_normalized (counts divided by total number of aligned reads and multiplied by the minimum over all libraries) (READemption 0.4.5, Förstner et al., 2014)
Assembly: Neisseria meningitidis 8013 (Assembly acc.: GCF_000026965.1, Sequence ID: NC_017501.1 )
Supplementary files format and content: wiggle files containing positional read coverage values

organism: Neisseria meningitidis

source_name: Neisseria meninigitidis cells

growth_protocol: Neisseria meninigitidis strains 8013 wild-type, cas9, tracrRNA and scaRNA deletion grown on solid media overnight were harvested and starter cultures were inoculated to a final optical density (OD600nm)  of 1.0 in 5 ml EMEM liquid medium supplemented with with 10% fetal calf serum (FCS), 1% nonessential amino acids (NEAA) and 1% Sodium pyruvate (NaPyr)  (EMEM+++) in 50ml Falcon-tubes. After one hour the starter cultures were used to inoculate EMEM+++ medium to a final OD600nm of 0.15. Bacteria were grown in 50 ml Falcon-tubes at 37 °C at 220 rpm without added CO2 until an OD600nm of 0.5 was reached.

extract_protocol:
Total RNA extraction with the hot phenol method.
RNA quality was checked using a 2100 Bioanalyzer with the RNA 6000 Nano kit (Agilent Technologies). cDNA libraries suitable for sequencing were prepared from 1000 ng of total RNA. RNAs were treated for rRNA depletion with beta version of Pan-Prok RiboPOOLs, except one sample (WT), were fragmented using Mg2+ ions 2 min 45 sec (NEBNext Magnesium RNA fragmentation module) and were treated with T4 PNK for phosphorylation/dephosphorylation and RppH for decapping followed by NEBNext® Multiplex Small RNA Library Prep. (New England Biolabs). The number of the PCR cycles was determined to 14 by qPCR and the elongation time was set to 15 sec. Libraries were quantified by QubitTM dsDNA HS Assay Kit 3.0 Fluorometer (ThermoFisher) and quality was checked using 2100 Bioanalyzer with High Sensitivity DNA kit (Agilent Technologies) before pooling.

treatment_protocol: When the cultures reached an OD600nm of 0.5, bacteria were snapfrozen in liquid nitrogen prior to total RNA extraction with the hot phenol method. Wild-type and deletion samples were treated equally.

tag: strain

value: scaRNA-


title: NM8013 ΔscaRNA R2


title: RNA-seq of Ncol3-negative cells, replicate 1

description:
Library name: Ncol3_neg_RNAseq_rep1
Nematostella vectensis tentacle cells (Ncol3-negative) isolated by FACS; bulk RNA-seq, replicate 1.


title: NM8013 Δcas9 R3


title: NM8013 Δcas9 R2


title: NM8013 wt R2


title: NM8013 wt R1


title: NM8013 ΔtracrRNA R1

value: tracrRNA-


title: NM8013 ΔtracrRNA R3


title: NM8013 ΔtracrRNA R2


title: NM8013 ΔscaRNA R1


title: NM8013 Δcas9 R1


title: anti-LeY CAR T cells - Control 2

city: Melbourne

first: Tony

last: Tiganis

state: Victoria

address: 23 Innovation Walk, Monash University, Clayton

country: Australia

institute: Monash University

description:
Library name: Ctl-2_S44
column Ctl-2_S44 in rawcounts.txt

data_processing:
Raw sequence reads were trimmed to remove illumina adaptor sequences from the reads using Trim Galore! Version 0.6.7. (https://https://github.com/FelixKrueger/ TrimGalore.com/fenderglass/Flye). Trimmed reads were aligned to human reference genome (HG38) using STAR 2.7.8a alignment tool (https://github.com/alexdobin/STAR/releases) and mapped reads were counted using featureCounts at the gene level (https://rnnh.github.io/bioinfo-notebook/docs/featureCounts.html).
Assembly: HG38
Supplementary files format and content: raw counts matrix (STAR feature counts) as .txt file

source_name: PBMC

extract_protocol:
Total RNA was isolated with RNeasy mini kits (Qiagen) after CAR T cells were stimulated with plate-coated anti-idiotype antibody (1 ?g/ml) to crosslink the LeY CAR for 6h
RNA-seq libraries were prepared from RNA using the Quant-seq 3 mRNA-seq Library Prep Kit for Illumina (Lexogen) as per the manufacturer’s instructions. NextSeq (Illumina, Inc., San Diego, CA) sequencing was performed to generate single-end, 75-bp RNA-seq short reads and subsequently CASAVA 1.8.2 was used for base calling. The quality of output was assessed using RNA-SeQC v1.1.7

value: PBMC

value: CAR T cell

value: Control

value: stimulation with anti-idiotype antibody for CAR crosslinking


title: NM8013 wt R3

value: wild type


title: anti-LeY CAR T cells - PTPN2 KO 1

description:
Library name: 2k1_S45
column 2k1_S45 in rawcounts.txt

value: PTPN2 deleted


title: F123 RNAseq rep1


title: anti-LeY CAR T cells - PTPN2 KO 2

description:
Library name: 2k2_S46
column 2k2_S46 in rawcounts.txt


title: RD-132

city: London

first: Guillermo

last: Carbajosa

address: Guy’s Hospital, St Thomas Street

department: Medical and Molecular Genetics

country: United Kingdom

institute: King's College London

data_processing:
Illumina NextSeq 500 platform 76bp reads
RNA-seq reads were aligned to the human GRCh38 rel 13 reference transcriptome using Kallisto version 0.42.4
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include TPM values and counts for each Sample

source_name: hippocampus

extract_protocol:
Frozen tissue containing hippocampus and cortex were selected because these areas are affected in AD at early and late stages, respectively (Mastrangelo and Bowers, 2008; Matarin et al., 2015). Where available, ~100 mg of frozen tissue from post mortem entorhinal cortex containing the hippocampus and pre-association cortex (BA9) from each donor were homogenized in matrix-lysing D tubes containing Qiazol reagent and RNA isolated using the miRNeasy Mini Kit (Qiagen). Both total RNA and small RNA fractions were extracted separately according to the manufacturer’s instructions.
100ng of total RNA from each sample was used to prepare total RNA libraries using the KAPA Stranded RNA-Seq Kit with RiboErase (KAPA Biosystems, Massachusetts, USA). Fragmentation prior to first strand cDNA synthesis was carried out using incubation conditions recommended by the manufacturer. For degraded samples (those with a RIN<7) 65°C for 1 minute was used, while 94°C for 6 minutes was used for the remaining samples. 14 cycles of PCR were performed for final library amplification. Resulting libraries were quantified using the Qubit 2.0 spectrophotometer (Life Technologies, California, USA) and average fragment size assessed using the Agilent 2200 Tapestation (Agilent Technologies, Waldbronn, Germany). Equimolar amounts of each library with compatible indexes were pooled together for sequencing, resulting in 5 pools with 22 samples, and one pool of 23. 75bp paired-end reads were generated for each library pool using the Illumina NextSeq®500 (Illumina Inc., Cambridge, UK) in conjunction with the NextSeq®500/550 High-Output 150cycle kit. Each pool was sequenced a total of 6 times in order to achieve 100 million reads per sample

tag: rin score

tag: Sex

value: FEMALE

tag: age

tag: diagnosis

value: AD

tag: trem2 variant

value: hippocampus


title: RD-127


title: RD-125

source_name: Entorhinal cortex

value: MALE

value: Entorhinal cortex


title: RD-133

source_name: superior frontal gyrus

value: superior frontal gyrus


title: RD-124


title: RD-130

source_name: medial frontal gyrus

value: medial frontal gyrus


title: RD-121

value: AD modified Braak stage V-VI with extensive pathology (estimated by tau pathology) in the CA1 and CA4 regions of the hippocampus


title: RD-129


title: RD-131


title: RD-126


title: RD-123


title: RD-122


title: RD-120


title: RD-118


title: RD-117

value: MCI


title: CLL_to_DLBCL_Lymphoma_Paraffin_section

city: New Haven

first: Rong

last: Fan

state: CT

address: 55 Prospect Street

department: Biomedical Engineering

institute: Yale University

description:
Library name: Human_lymphoma_2
FFPE spatial transcriptomic sequencing

data_processing:
Read 2 from the FASTQ file was processed to extract unique molecular identifiers (UMIs) and spatial Barcodes A and B. Read 1, containing cDNA sequences, was aligned to the mouse GRCm39 or human GRCh38 reference genome using STAR V2.7.8a. Spatial barcode sequences were demultiplexed with ST_Pipeline V1.8.1, using the predefined coordinates of the microfluidic channels, and ENSEMBL IDs were converted to gene names. This generated a gene-by-spot expression matrix for downstream analysis. Entries in the matrix that corresponded to spot positions without tissue were excluded.
The spatial transcriptomic data from Human_lymphoma_2 (CLL_to_DLBCL_Lymphoma_Paraffin_section) was preprocessed following the ASTRO Pipeline(Zhang, D. et al. ASTRO: Automated Spatial Whole-Transcriptome RNA-Expression Workflow (Cold Spring Harbor Laboratory, 2025), also utilized in Bai, Z. et al. Cell (2024).
Assembly: GRCm39 (mouse) and GRCh38 (human)
Supplementary files format and content: Black and white contrasted image of the region of interest for generating the position file. File format (.png)
Supplementary files format and content: Image of the region of interest (ROI). File format (.png)
Supplementary files format and content: Position of spatial pixels aligned to ROI image. File format (.txt)
Supplementary files format and content: Gene expression matrix. File format (.tsv)
Supplementary files format and content: Aligned coordinates and cell types from spatial transcriptomic spots and multiplexed immunofluorescence. File type (.csv)
Supplementary files format and content: Anndata object of annotated and deconvoluted spatial transcriptomic spots (.h5ad)
Library strategy: Spatial Transcriptomics

source_name: Lymph node (lymphoma)

extract_protocol:
Fresh frozen (FF) samples were OCT embedded. Both FF and FFPE samples were sectioned at a thickness of 7-10 μm and mounted on the center of poly-l-lysine-covered glass slides (63478-AS, Electron Microscopy Sciences). E11 mouse whole embryo paraffin sagittal sections were made of freshly harvested tissues, fixed in 10% neutral buffered formalin, and processed for paraffin embedding. Paraffin blocks were also sectioned at a thickness of 7-10 μm and mounted on the center of poly-l-lysine-covered glass slides. De-identified archived formalin-fixed paraffin-embedded (FFPE) human reactive lymph node and lymphoma tissue blocks were obtained from Yale Pathology Tissue Services (YPTS). The tissue retrieval and distribution for research was conducted with the approval of the Yale University Institutional Review Board (Approved IRB #1401013259) and oversight by the Tissue Resource Oversight Committee. Written informed consent for participation in any cases where identification was collected alongside the specimen, was obtained from patients or their guardians, in accordance with the principles of the Declaration of Helsinki. Each sample was handled in strict compliance with HIPAA regulations, University Research Policies, Pathology Department diagnostic requirements, and Hospital by-laws. For human samples, after review of all slides by board-certified pathologist and selection of the optimal block, paraffin blocks were sectioned at a thickness of 7-10 μm and mounted on the center of Poly-L-Lysine coated 1 x 3" glass slides. The sectioning was carried out by YPTS. Paraffin sections were stored at −80°C until use.
The SEQuoia RiboDepletion Kit was used to remove rRNA and mitochondrial rRNA from the amplified cDNA, following the manufacturer’s instructions. 20 ng of cDNA was used as the input amount, and three rounds of depletion were performed. We did observe that two rounds of depletion could suffice. Next, following the PCR steps described in the previous step, 10 PCR cycles was sufficient to directly ligate sequencing primers, using a 100 μl system consisting of 50 μl 2X KAPA HiFi HotStart ReadyMix, ~42 μl solution from the rRNA removal step, 4 μl 10 μM Modified N501 Primer, and 4 μl 10 μM P7 Primer. The library product was purified using SPRIselect beads at a 0.8X ratio, according to the manufacturer's standard protocol.

value: Lymph node (lymphoma)


title: RD-113


title: RD-116


title: RD-115

value: AD Braak VI


title: B.KPC-Hdac5KO rep4

city: Wuhan

first: Haixin

last: Yu

state: Hubei Province

address: 1277, Jiefang Avenue

institute: Wuhan union hospital

description: Library name: Sample 9

data_processing:
Basecalls performed using bcl2fastq v2.19.0
Sequencing read quality was inspected using fastp v0.24.0. Adapter removal and read trimming were performed. Sequencing reads were trimmed from the end (base quality less than Q20) and filtered by length (less than 25).
Paired-end reads were aligned to the mm39  (Subread v2.0.8) . FeatureCounts (Subread v2.0.8) was used to count the reads numbers mapped to each gene. And then FPKM/TPM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Supplementary_files_format_and_content: text file include gene names, sample name, read-counts values for each Sample
/
Assembly: mm39
Supplementary files format and content: txt file includes read counts for each sample.

source_name: mouse pancreatic cancer

extract_protocol:
RNA was harvested using Trizol reagent(Life Technologies). Illumina NEB Ultra directional RNA library Prep Kit was used with 1 ug of total RNA for the construction sequencing libraries.
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: mouse pancreatic cancer


title: B.KPC-Hdac5KO rep5

description: Library name: Sample 10


title: RD-111


title: RD-114


title: anti-LeY CAR T cells - Control 1

description:
Library name: Ctl-1_S43
column Ctl-1_S43 in rawcounts.txt

value: PBMC

value: CAR T cell


title: B.KPC-Hdac5KO rep2

description: Library name: Sample 7


title: A.KPC-WT rep4

description: Library name: Sample 4

value: WT


title: RD-128

value: Control


title: B.KPC-Hdac5KO rep1

description: Library name: Sample 6


title: RD-112


title: A.KPC-WT rep3

description: Library name: Sample 3


title: A.KPC-WT rep2

description: Library name: Sample 2


title: NHSK-1 Cells, no IFN treatment, experiment 2, replicate 8

city: Iowa City

first: Jonah

last: Elliff

state: Iowa

address: 51 Newton Rd

institute: University of iowa

description:
Library name: Baseline untreated exp2 8
Column name in "raw_counts_All_samples" - K8

data_processing:
RStudio (v. R 4.1.1) accessed through the University of Iowa Interactive Data Analysis Service utilizing the high-performance computing cluster as needed
Adapter sequences from raw FASTQ files were trimmed utilizing Trim Galore! (v. 0.0.6; Babraham Bioinformatics - Trim Galore!) as well as analyzed with the included FastQC program.
Utilizing Salmon [58] (v.1.5.2), we created a decoy-aware transcriptome utilizing the whole human genome as a decoy (Selective Alignment (combine-lab.github.io)) using Homo Sapiens genome and annotated files from Gencode (GRCh38.p13; Gencode.v.38.annotatio.gtf).
Gene counts were obtained utilizing aligned reads utilizing the Salmon quant feature. All samples resulted in ≥80% of reads mapped to our generated index and were utilized in downstream differential gene expression (DEG) analysis
Assembly: GRCh38
Supplementary files format and content: tab delimited text file includes raw counts for each sample

source_name: Human Skin

growth_protocol: Keratinocytes were maintained at 37°C, 5% CO2 in keratinocyte serum-free media (K-SFM, Gibco, Waltham, MA) supplemented with 25 µg/mL bovine pituitary extract, 0.16 ng/mL epidermal growth factor, and 1% penicillin/streptomycin. Keratinocytes were utilized at 70-80% confluence.

extract_protocol:
RNA was extracted from cells utilizing the RNeasy® Mini Kit from Qiagen as described by the manufacturer.
High quality RNA samples were verified by Bioanalyzer (Agilent) used as input to generate mRNA-seq libraries for the Illumina platform performed at the Iowa Institute of Human Genetics (IIHG), Genomic Division

treatment_protocol: Human IFN-α, human IFN-β, human IFN-γ, or human IFN-λ was used in these studies. Semi-confluent (70-80%) cultures of NHSK-1 cells were treated with the  type of IFN noted or K-SFM alone (control) for 6 or 24 hours in quadruplicate, washed gently with sterile PBS, and media was replaced. RNA was then isolated for transcriptomic studies.

value: Human Skin

value: Normal human skin keratinocyte

value: no treatment


title: RD-119


title: RD-108


title: A.KPC-WT rep5

description: Library name: Sample 5


title: RD-107

value: AD


title: A.KPC-WT rep1

description: Library name: Sample 1


title: B.KPC-Hdac5KO rep3

description: Library name: Sample 8


title: RD-110

value: FEMALE


title: NHSK-1 Cells, no IFN treatment, experiment 2, replicate 6

description:
Library name: Baseline untreated exp2 6
Column name in "raw_counts_All_samples" - K6


title: NHSK-1 Cells, no IFN treatment, experiment 2, replicate 7

description:
Library name: Baseline untreated exp2 7
Column name in "raw_counts_All_samples" - K7


title: RD-106

value: MALE

value: Entorhinal cortex


title: RD-104


title: RD-105


title: NHSK-1 Cells, no IFN treatment, experiment 2, replicate 3

description:
Library name: Baseline untreated exp2 3
Column name in "raw_counts_All_samples" - K3


title: RD-100

value: AD Braak V, HP-Tau IV; AD modified Braak stage IV


title: NHSK-1 Cells, no IFN treatment, experiment 2, replicate 4

description:
Library name: Baseline untreated exp2 4
Column name in "raw_counts_All_samples" - K4


title: RD-99


title: NHSK-1 Cells, no IFN treatment, experiment 2, replicate 1

description:
Library name: Baseline untreated exp2 1
Column name in "raw_counts_All_samples" - K1


title: RD-103


title: RD-101


title: NHSK-1 Cells, no IFN treatment, experiment 1, replicate 7

description:
Library name: Baseline untreated exp1 7
Column name in "raw_counts_All_samples" - N7


title: NHSK-1 Cells, no IFN treatment, experiment 2, replicate 5

description:
Library name: Baseline untreated exp2 5
Column name in "raw_counts_All_samples" - K5


title: RD-102


title: RD-97


title: RD-96


title: RD-109


title: NHSK-1 Cells, no IFN treatment, experiment 1, replicate 8

description:
Library name: Baseline untreated exp1 8
Column name in "raw_counts_All_samples" - N8


title: NHSK-1 Cells, no IFN treatment, experiment 1, replicate 6

description:
Library name: Baseline untreated exp1 6
Column name in "raw_counts_All_samples" - N6


title: NHSK-1 Cells, no IFN treatment, experiment 2, replicate 2

description:
Library name: Baseline untreated exp2 2
Column name in "raw_counts_All_samples" - K2


title: RD-98


title: NHSK-1 Cells, no IFN treatment, experiment 1, replicate 5

description:
Library name: Baseline untreated exp1 5
Column name in "raw_counts_All_samples" - N5


title: RD-94


title: NHSK-1 Cells, no IFN treatment, experiment 1, replicate 2

description:
Library name: Baseline untreated exp1 2
Column name in "raw_counts_All_samples" - N2


title: RD-90


title: NHSK-1 Cells, 24 hour IFN lambda treatment replicate 4

description:
Library name: Interferon lambda 24h treatment 4
Column name in "raw_counts_All_samples" - M8

value: 24 hour IFN lambda


title: RD-89


title: RD-93


title: RD-92


title: NHSK-1 Cells, no IFN treatment, experiment 1, replicate 3

description:
Library name: Baseline untreated exp1 3
Column name in "raw_counts_All_samples" - N3


title: RD-91

value: AD modified Braak stage V-VI with extensive pathology (estimated by tau pathology) in the CA1 and CA4 regions of the hippocampus


title: RD-85


title: RD-95


title: NHSK-1 Cells, 24 hour IFN lambda treatment replicate 3

description:
Library name: Interferon lambda 24h treatment 3
Column name in "raw_counts_All_samples" - M7


title: C57_Embryo_Sagittal_Paraffin_Sections_E11

description:
Library name: Mouse_embryo_FFPE_1
FFPE spatial transcriptomic sequencing

source_name: Mouse embryo

value: Mouse embryo


title: RD-82


title: FF_Mouse_Embryo_RNaseH_V2

description:
Library name: Mouse_embryo_sample_4
Fresh frozen spatial transcriptomic sequencing


title: NHSK-1 Cells, 6 hour IFN lambda treatment replicate 1

description:
Library name: Interferon lambda 6h treatment 1
Column name in "raw_counts_All_samples" - M1

value: 6 hour IFN lambda


title: NHSK-1 Cells, 24 hour IFN lambda treatment replicate 1

description:
Library name: Interferon lambda 24h treatment 1
Column name in "raw_counts_All_samples" - M5


title: NHSK-1 Cells, 24 hour IFN lambda treatment replicate 2

description:
Library name: Interferon lambda 24h treatment 2
Column name in "raw_counts_All_samples" - M6


title: NHSK-1 Cells, 24 hour IFN gamma treatment replicate 3

description:
Library name: Interferon gamma 24h treatment 3
Column name in "raw_counts_All_samples" - G7

value: 24 hour IFN gamma


title: RD-77


title: RD-87


title: RD-86


title: NHSK-1 Cells, 6 hour IFN lambda treatment replicate 4

description:
Library name: Interferon lambda 6h treatment 4
Column name in "raw_counts_All_samples" - M4


title: RD-76

value: AD + PS1 mutation


title: C57_Embryo_Sagittal_Paraffin_Sections_E11_Control

description:
Library name: Mouse_embryo_FFPE_2
FFPE spatial transcriptomic sequencing


title: FF_Mouse_Embryo_Control_V1

description:
Library name: Mouse_embryo_sample_1
Fresh frozen spatial transcriptomic sequencing


title: RD-75


title: RD-74


title: NHSK-1 Cells, 6 hour IFN lambda treatment replicate 3

description:
Library name: Interferon lambda 6h treatment 3
Column name in "raw_counts_All_samples" - M3


title: RD-84


title: RD-73


title: RD-83


title: NHSK-1 Cells, 6 hour IFN lambda treatment replicate 2

description:
Library name: Interferon lambda 6h treatment 2
Column name in "raw_counts_All_samples" - M2


title: NHSK-1 Cells, no IFN treatment, experiment 1, replicate 4

description:
Library name: Baseline untreated exp1 4
Column name in "raw_counts_All_samples" - N4


title: RD-81


title: RD-80


title: NHSK-1 Cells, 24 hour IFN beta treatment replicate 4

description:
Library name: Interferon beta 24h treatment 4
Column name in "raw_counts_All_samples" - B8

value: 24 hour IFN beta


title: PBS rep1

first: Wei

last: Yan

address: College of Life Science, Wuhan University, Luojiashan Road, Wuchang District, Wuhan City, Hubei Province, China

department: College of life science

institute: Wuhan university

description: Library name: Sample 16

data_processing:
The raw paired end reads were trimmed and quality controlled by SeqPrep  and Sickle with default parameters.
Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software.
The mapped reads of each sample were assembled by StringTie in a reference-based approach.
The expression level of each transcript was calculated according to the transcripts per million reads (TPM) method.RSEM was used to quantify gene abundances.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: Lung

extract_protocol:
RNA-seq transcriptome library was prepared following TruSeq RNA sample preparation Kit from Illumina (San Diego, CA) using 1 μg of total RNA.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Mice that received an equal volume (50 μL) of PBS via tail vein injection were used as the solvent control group of EV injection group.

value: Lung


title: 4T1/DDAH1KO

description:
Library name: Sample 2
10× Genomics

library_source: transcriptomic single cell

data_processing:
Data quality statistics were performed on the raw Fastq data using Cell Ranger software, and STAR was used to align the read2 sequences to the reference genome of the Ensembl database (https://asia.ensembl.org/index.html). Distinguish the barcode sequence of the cell and the UMI markers of different mRNA molecules in each cell, and use the average value of the 50% barcode with the least UMI content as the empty cell, and check whether the transcriptional profile of each remaining barcode is similar to the empty cell. Quantification of high-throughput single-cell transcriptome results.
Assembly: GRCm38 (mm10)
Supplementary files format and content: Tab-separated values files and matric files

source_name: lung

growth_protocol: 4T1 and 4T1/DDAH1 KO cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
Fresh lung tissue harvested from the mice were dissociated into single-cell suspensions using Mouse Lung Dissociation Kit (Miltenyi Biotec, USA).
The cellular suspensions that cell survival rate was above 80% were resuspended to prepare a suitable cell concentration of 700~1200 cells/μl for Chromium Controller instrument (10x Genomics) to generate single-cell Gel-Bead-in-Emulsions (GEMs), followed by reverse-transcribed and indexed for library construction according to the manufacturer’s instructions. The final library pool was sequenced on the Illumina Nova6000 instrument using 150-base-pair paired-end reads.

value: lung


title: FF_Mouse_Embryo_Control_V2

description:
Library name: Mouse_embryo_sample_3
Fresh frozen spatial transcriptomic sequencing


title: RD-79

value: Control


title: RD-66


title: RD-78


title: NHSK-1 Cells, 24 hour IFN gamma treatment replicate 2

description:
Library name: Interferon gamma 24h treatment 2
Column name in "raw_counts_All_samples" - G6

value: Human Skin

value: Normal human skin keratinocyte

value: WT


title: NHSK-1 Cells, 24 hour IFN gamma treatment replicate 1

description:
Library name: Interferon gamma 24h treatment 1
Column name in "raw_counts_All_samples" - G5


title: PBS rep3

description: Library name: Sample 18


title: NHSK-1 Cells, 6 hour IFN gamma treatment replicate 2

description:
Library name: Interferon gamma 6h treatment 2
Column name in "raw_counts_All_samples" - G2

value: 6 hour IFN gamma


title: RD-88

value: FEMALE


title: RD-72

value: MALE

value: AD


title: 231/DDAH1 KO rep1

description: Library name: Sample 13

growth_protocol: 10A or 10A/DDAH1 cells were maintained in DMEM/F12 with 5% HS, 20ng/ml EGF, 0.5μg/ml Hydrocortisone, 10μg/mL Insulin, 100ng/ml Toxin, 1% P/S; MDA-MB-231/DDAH1 KO cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37°C.

treatment_protocol: For EVs tail vein injection mouse model, EVs were injected into the tail vein semiweekly for 5 weeks (~10 μg EVs per injection per mouse). For tumor-bearing model, orthotopic injection 2 × 105 231/DDAH1 KO cells into the fourth pair of mammary fat pad.

value: 231/DDAH1 KO


title: NHSK-1 Cells, 6 hour IFN beta treatment replicate 4

description:
Library name: Interferon beta 6h treatment 4
Column name in "raw_counts_All_samples" - B4

value: 6 hour IFN beta


title: RD-60


title: RD-61


title: NHSK-1 Cells, 6 hour IFN beta treatment replicate 3

description:
Library name: Interferon beta 6h treatment 3
Column name in "raw_counts_All_samples" - B3


title: RD-62

value: Entorhinal cortex


title: NHSK-1 Cells, 6 hour IFN gamma treatment replicate 1

description:
Library name: Interferon gamma 6h treatment 1
Column name in "raw_counts_All_samples" - G1


title: PBS rep2

description: Library name: Sample 17


title: FF_Mouse_Embryo_RNaseH_V1

description:
Library name: Mouse_embryo_sample_2
Fresh frozen spatial transcriptomic sequencing

value: Mouse embryo


title: RD-71


title: RD-70


title: RD-69


title: RD-68


title: NHSK-1 Cells, 24 hour IFN beta treatment replicate 3

description:
Library name: Interferon beta 24h treatment 3
Column name in "raw_counts_All_samples" - B7


title: RD-67

value: AD - PS1 to match the TREM2+ case


title: NHSK-1 Cells, 24 hour IFN beta treatment replicate 2

description:
Library name: Interferon beta 24h treatment 2
Column name in "raw_counts_All_samples" - B6


title: 4T1/Ctrl

description:
Library name: Sample 1
10× Genomics


title: NHSK-1 Cells, 24 hour IFN alpha treatment replicate 4

description:
Library name: Interferon alpha 24h treatment 4
Column name in "raw_counts_All_samples" - A8

value: 24 hour IFN alpha


title: RD-51


title: NHSK-1 Cells, 24 hour IFN alpha treatment replicate 3

description:
Library name: Interferon alpha 24h treatment 3
Column name in "raw_counts_All_samples" - A7


title: 231/DDAH1 KO rep3

description: Library name: Sample 15


title: RD-64


title: RD-63


title: NHSK-1 Cells, 24 hour IFN beta treatment replicate 1

description:
Library name: Interferon beta 24h treatment 1
Column name in "raw_counts_All_samples" - B5

value: 24 hour IFN beta


title: RD-49


title: 231/DDAH1 KO rep2

description: Library name: Sample 14

value: Lung


title: RD-65


title: NHSK-1 Cells, 24 hour IFN alpha treatment replicate 1

description:
Library name: Interferon alpha 24h treatment 1
Column name in "raw_counts_All_samples" - A5


title: RD-46


title: RD-58


title: RD-59


title: tumor-free rep3

description: Library name: Sample 12

value: tumor-free


title: RD-57


title: RD-56


title: tumor-free rep2

description: Library name: Sample 11


title: RD-54


title: 231 EV rep2

description: Library name: Sample 5


title: RD-43

value: AD modified Braak stage V-VI with extensive pathology (estimated by tau pathology) in the CA1 and CA4 regions of the hippocampus


title: RD-53

value: Control


title: tumor-free rep1

description: Library name: Sample 10


title: RD-50


title: NHSK-1 Cells, 6 hour IFN alpha treatment replicate 3

description:
Library name: Interferon alpha 6h treatment 3
Column name in "raw_counts_All_samples" - A3

value: Human Skin

value: Normal human skin keratinocyte

value: 6 hour IFN alpha


title: 10A/DDAH1 EV rep2

description: Library name: Sample 8

value: 10A/DDAH1 EV


title: RD-40

value: FEMALE


title: 10A/DDAH1 EV rep3

description: Library name: Sample 9


title: RD-42

value: MALE


title: RD-55


title: NHSK-1 Cells, 6 hour IFN beta treatment replicate 2

description:
Library name: Interferon beta 6h treatment 2
Column name in "raw_counts_All_samples" - B2

value: WT


title: 10A EV rep3

description: Library name: Sample 3

value: 10A EV


title: RD-39

value: AD


title: NHSK-1 Cells, 6 hour IFN alpha treatment replicate 2

description:
Library name: Interferon alpha 6h treatment 2
Column name in "raw_counts_All_samples" - A2


title: NHSK-1 Cells, 24 hour IFN alpha treatment replicate 2

description:
Library name: Interferon alpha 24h treatment 2
Column name in "raw_counts_All_samples" - A6


title: RD-48

value: Entorhinal cortex


title: 10A EV rep2

description: Library name: Sample 2


title: 10A EV rep1

description: Library name: Sample 1


title: 10A/DDAH1 EV rep1

description: Library name: Sample 7


title: RD-47


title: RD-52

value: AD - PS1 to match the TREM2+ case


title: RD-35


title: Lymph_node_2_Paraffin_section_50_um

description:
Library name: Human_lymph_node_2
FFPE spatial transcriptomic sequencing

source_name: Lymph node

value: Lymph node


title: 231 EV rep3

description: Library name: Sample 6


title: RD-45


title: Lymph_node_2_Paraffin_section_25_um

description:
Library name: Human_lymph_node_1
FFPE spatial transcriptomic sequencing


title: RD-44


title: RD-41


title: NHSK-1 Cells, 6 hour IFN alpha treatment replicate 4

description:
Library name: Interferon alpha 6h treatment 4
Column name in "raw_counts_All_samples" - A4


title: RD-30


title: 231 EV rep1

description: Library name: Sample 4


title: RD-38

value: MCI


title: RD-36


title: MZL_Paraffin_section

description:
Library name: Human_lymphoma_1
FFPE spatial transcriptomic sequencing

value: Lymph node (lymphoma)


title: Toxicodendron succedaneum,  Explant,48h, replicate 3

city: Kunming

first: cai

last: wang

address: qingyun street

institute: Southwest forestry university

data_processing:
Toxicodendron succedaneum
Based on sequencing-by-synthesis (Sequencing By Synthesis, SBS) technology, cDNA libraries were sequenced on Illumina high-throughput platform.
Assembly: CNP 0003406
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Toxicodendron succedaneum

source_name: stem segments

extract_protocol:
The different rooting abilities of stem segments of Toxicodendron succedaneum after being cultured in a rooting medium for 6, 12, 24, and 48 hours  .
The mRNA was collected from the stem segments of Toxicodendron succedaneum after being cultured for 0, 6, 12, 24, and 48 hours, respectively.

value: stem segments

value: growth stage

value: tissue culture

value: Explant are cultured in a rooting medium for 48 hours


title: RD-25

value: Control


title: RD-33


title: LT_HSC_DCAF8_WT2

first: Pengfei

last: Xu

address: Ruijin Rd. II

institute: Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

data_processing:
Low-quality reads and adapter sequences were removed using Trimmomatic (version 0.39).
The paired-end reads were mapped to the reference genome of mouse (mm39) using HISAT2 (version 2.2.1).
PCR duplicates were removed with Picard (version 2.26.1), and the reads were counted with HTSeq (version 1.99.2).
Read count normalization and differential gene expression analysis were performed with R package DESeq2 (version 1.38.3).
Assembly: mm39
Supplementary files format and content: csv file includes raw counts for each sample

source_name: bone marrow

extract_protocol:
LT-HSCs (Lin-Sca-1+c-Kit+CD150+CD48-) were sorted by FACS, resuspended and counted with microscopy. 50 LT-HSCs were obtained and subjected to mRNA amplification with Single Cell Full Length mRNA Amplification Kit (Vazyme N712). The amplified cDNA was purified with VAHTS DNA Clean Beads (Vazyme N411), and the concentration was determined using Equalbit dsDNA HS Assay Kit (Vazyme EQ111) by a Qubit Flex Fluorometer (Thermo Fisher Scientific) and fragment size distributions were confirmed by a 2100 Bioanalyzer (Agilent).
For library preparation, 1 ng amplified cDNA was tagmented with TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme TD503) and 12 cycles of PCR were performed. The resulting libraries were purified and the concentrations and fragment size distributions were determined as described before. The libraries were sequenced on a NovaSeq6000 (Illumina).

value: bone marrow

value: LT-HSC

value: wild-type


title: LT_HSC_DCAF8_KO3

value: Dcaf8 KO


title: RD-34

value: FEMALE


title: Toxicodendron succedaneum,  Explant,48h, replicate 2


title: RD-32

value: MALE


title: LT_HSC_DCAF8_KO2


title: RD-31

value: AD


title: Toxicodendron succedaneum,  Explant,48h, replicate 1


title: scATAC-seq of clear cell renal cell carcinoma with sarcomatoid differentiation

city: Nanning

first: Zhenyuan

state: Guangxi

address: Shuangyong road 22

department: Center for Genomic and Personalized Medicine

institute: Guangxi Medical University

description:
Library name: RCC122_scATAC
scATAC-seq for RCC122

library_source: genomic single cell

data_processing:
Preliminary sequencing results (bcl files) were converted to FASTQ files with Cell Ranger V3.0 and CellRanger ATAC V1.2.0
The CellRanger (10X Genomics) secondary analysis pipeline was used to generate a digital gene expression matrix
Normalization and additional analysis by Seurat and Signac R package
Assembly: GRCh38 for human data
Supplementary files format and content: The .rds.tar files for scRNA-seq and scATAC-seq.

source_name: Total clear cell renal cell carcinoma with sarcomatoid differentiation Homogenate

extract_protocol:
We used 10x Genomics Chromium Single Cell 3′ Reagents Kit v3 user guide to perform single cell suspension which were prepared before. Briefly, the single-cell samples were passed through a 40μm cells strainer and counted using a hemocytometer with trypan blue. Subsequently, the appropriate volume for each sample was calculated to recover 10,000 cells. With the 10x protocol, we added the single cells, the Gel Beads and the oils onto the 10x Genomics single-cell-A chip and run this machine. After droplet generation, samples were transferred onto a PCR tube and reverse transcription was performed using T100 Thermal Cycler (BIO-RAD). After the reverse transcription, cDNA was recovered using Recovery Agent provided by 10x genomics followed by a Silane DynaBead clean-up as outlined in the user guide. Purified cDNA was amplified for 10 cycles before being cleaned up by using SPRIselect beads. The samples were detected by Qubit2.0 Fluorometer (invitrogen) to determine cDNA concentration.Suitable nuclei concentrations were adjusted from the above experiment. As mentioned in the previous study (avoiding potential cell duplets), the number of target nucleus captured in each sample was 6,000. We adopted 10x Genomics ‘Chromium Single Cell ATAC Reagent Kits User Guide’ for library preparation (https://support.10xgenomics.com/single-cell-atac/library-prep/doc/technical-note-chromium-next-gem-single-cell-atac-v11-reagent-workflow-and-software-updates). Briefly, the ATAC Buffer (10x Genomics, 200122) and ATAC Enzyme (10x Genomics, 200123) were added to the 5 µL nuclei, which was incubated for 60 min at 37 °C. We prepared ‘Master Mix’, including 56.5 µL of Barcoding Reagent B (10x Genomics, 2000194), 1.5 µL of Reducing Agent B (10x Genomics, 2000087) and 2 µL of Barcoding Enzyme (10x Genomics, 2000125). After mixing the nuclei with the Master Mix, we added it to the Chromium Chip E (10x Genomics, 2000121). At the same time, we added Partitioning Oil (10x Genomics, 220088) and Chromium Single Cell ATAC Gel Beads (10x Genomics, 2000132) to the Chromium Chip E. The Chromium Chip E was placed into a Chromium Single Cell Controller instrument (10x Genomics) before attaching a 10x Gasket (10x Genomics, 3000072). Then, the Chromium Single Cell Controller Instrument could be run. The gel bead in emulsions (GEMs) were generated after the above steps. Subsequently, GEMs were incubated and cleaned by using Dynabeads (10x Genomics, 2000048) and SPRIselect (Beckman Coulter, B23318). scATAC-seq library construction eliminates the process of reverse transcription compared with scRNA-seq. PCR was performed after ‘Sample Index PCR Mix’ and Single Index Kit N Set A (10x Genomics, 1000212) were added into the samples. The details of PCR parameters could be referred to Chromium Single Cell ATAC Reagent Kits User Guide. DNA libraries were sequenced by NovaSeq 6000 (Illumina, San Diego, CA). Consistent with previous studies, we followed the 2 × 50 paired-end sequencing scheme: 50 bp read 1N, 8 bp i7 index, 16 bp i5 index and 50 bp read 2N.
10X Genomics Single Cell 3' v3 Reagent Kit and Chromium Single Cell ATAC Reagent Kits V1


title: RD-22


title: LT_HSC_DCAF8_KO1


title: NHSK-1 Cells, 6 hour IFN alpha treatment replicate 1

description:
Library name: Interferon alpha 6h treatment 1
Column name in "raw_counts_All_samples" - A1

value: Human Skin

value: Normal human skin keratinocyte

value: WT

value: 6 hour IFN alpha


title: RD-29

value: Entorhinal cortex


title: RD-21


title: RD-20


title: scRNA-seq of clear cell renal cell carcinoma with sarcomatoid differentiation

description:
Library name: RCC122_scRNA
scRNA-seq for RCC122

value: Total clear cell renal cell carcinoma with sarcomatoid differentiation Homogenate


title: Toxicodendron succedaneum,  Explant,24h, replicate 2

value: stem segments

value: growth stage

value: Explant are cultured in a rooting medium for 24 hours


title: Toxicodendron succedaneum,  Explant,24h, replicate 1

value: tissue culture


title: RD-18


title: RD-17


title: Chronic-Adult-Control

city: Milwaukee

first: Murray

last: Blackmore

state: WI

address: 561 N 16th St

department: Biomedical Sciences

institute: Marquette University

description:
Library name: Chronic-Control-1
10x Genomics

data_processing:
NovaSeq X Plus used for base-calling
CellRanger pipeline (10X Genomics) used for base-cell demultiplexing, alignment, read filtering, and UMI counting.
Low quality cells removed based on total UMI count
Software: CellRanger (7.0.1)
Assembly: mm10
Supplementary files format and content: .txt file of gene-barcode matrix for each sample, with genes along rows and cell-barcodes along columns.

molecule: nuclear RNA

source_name: Brain

extract_protocol:
For extraction of nuclei, frozen tissue was promptly transferred from -80 °C storage to a chilled 2mL dounce (KIMBLE, Ref. DWK885300-0000) with chilled Nuclei EZ Lysis Buffer (Sigma-Aldrich N 3408). The sample was dounced 25 times with pestle A and 20 times with pestle B. The dounced sample was then transferred to a chilled 15mL conical tube and an additional 2mL of Nuclei EZ Lysis Buffer was added and gently mixed by inversion. The sample was incubated on ice for 5 minutes and centrifuged at 500G at 4 °C. The supernatant was removed, and the pellet was resuspended in 4mL of Nuclei EZ Lysis Buffer. The sample was incubated on ice and centrifuged at 500G at 4 °C for 5 minutes. Following the centrifugation, the supernatant was removed, and the pellet resuspended in 750 µl of Nuclei Suspension Buffer (NSB) (2% Bovine Serum Albumin (BSA, Sigma-Aldrich Ref. A9418), 40U/ µl RNase Inhibitor (Invitrogen Ref. AM2684), 1X PBS). For embryonic samples, which lacked AAV-derived nuclear mGl fluorescence propidium, iodide (Sigma, P4864, 1:500 dilution) was added to NSB to facilitate sorting.
5000 and 7000 nuclei were sorted directly into the Reverse Transcription Master Mix and single-nuclei libraries were prepared using Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (PN-1000269).

treatment_protocol: Embryonic neurons were left untreated, while adult corticospinal tract neurons received either Sox11 or control treatment and were subjected to either no injury or a contusion injury.

value: Brain


title: RD-37

value: AD Braak VI


title: RD-28


title: RD-27

value: Control


title: RD-15


title: Toxicodendron succedaneum,  Explant,12h, replicate 3

value: Explant are cultured in a rooting medium for 12 hours


title: LT_HSC_DCAF8_WT3

value: bone marrow

value: LT-HSC

value: wild-type


title: LT_HSC_DCAF8_WT1


title: RD-24

value: MALE


title: RD-23

value: AD


title: RD-12

value: FEMALE


title: Uninjured-Adult-Sox11-Timecourse

description:
Library name: Sox11-TC-CST-1
10x Genomics


title: RD-11


title: RD-9


title: RD-8


title: Toxicodendron succedaneum,  Explant,24h, replicate 3


title: MPC5_SPARC_overexpression5

city: Beijing

first: Dongxuan

last: Chi

state: China

address: No.5 Le Yuan Road, Daxing District

institute: Peking University First Hospital

description: Library name: Spa-oe-5

data_processing:
To avoid reads with artificial bias (i.e., low-quality paired reads, which primarily result from base-calling duplicates and adaptor contamination), we removed the following types of reads: (i) reads with 3nt unidentified nucleotides (N); (ii) reads aligned to the adaptor; (iii) reads with ≥20% bases having phred quality ≤5. Then, map the clean reads to the silva database to remove the rRNA by bowtie2 software. All the downstream analyses were based on the clean data without rRNA.
Paired-end clean reads were aligned to the reference genome using HISAT2 software. Featurecount was used to count the reads numbers of each gene.
Assembly: Mus musculus5
Supplementary files format and content: Identification of differentially expressed genes EdgeR was used for differential expression analysis. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with |log2 (Fold Change) | > 1 & q value < 0.05 were assigned as differentially expressed. GO and KEGG Pathway Enrichment GO and KEGG enrichment analysis of differentially expressed gene sets were implemented by the topG and KOBAS package, respectively. PPI Network Construction STRING (https://cn.string-db.org/) database was used to construct a protein-protein interaction (PPI) network based on the differentially expressed gene sets and the names of all the interacting proteins and the protein-coding genes were extracted from the network. After obtaining the PPI relationship, a network diagram was constructed with Cytoscape software. Transcription Factors Prediction The differentially expressed gene sets were used as candidate genes, and transcription factors (TFs) were predicted with iTAK for plants and with TFDB database by hmmsearch for animals and human. Splicing Event Quantification Alternative splicing events were detected and quantified using the rMATS software. The rmats2sashimiplot  software was used to plot the alternative splicing events. Variation Detection SAMtools and Picard-tools   were used to sort and mark duplicated reads of alignment results of each sample. SNPs and Indels were identified with SAMtools software and annotated by ANNOVAR  software.

growth_protocol: DMEM supplemented with 10%FBS and antibiotics in humidified atomosphere with 5%CO2 at 37

extract_protocol:
Total RNA from treated MPC5 cells was extracted using TRIzol reagent.  Total RNA was qualified and quantified as follows: (1) RNA purity and concentration were then examined using NanoDrop 2000; (2) RNA integrity and quantity were measured using the Agilent 2100/4200 system.
RNA library for RNA-seq was prepared as fllows: mRNA was purified from total RNA using polyT and then fragmented into 300~350 bp fragments, the first strand cDNA was reverse-transcribed using fragmented RNA and dNTPs (dATP, dTTP, dCTP and dGTP) and second strand cDNA synthesis was subsequently performed.
Remaining overhangs of double-strand cDNA were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, sequencing adaptors were ligated to the cDNA and the library fragments were purified. The template was enriched by PCR, and the PCR product was purified to obtain the final library.

treatment_protocol: Vec is the mouse podocyte cell line (MPC5) transfected with the empty vector plasmid. Spa is the mouse podocyte cell line (MPC5) transfected with the Sparc overexpression plasmid.

value: Mouse podocyte cell

value: Sparc overexpression

value: transfected Sparc overexpression plasmid


title: MPC5_SPARC_overexpression4

description: Library name: Spa-oe-4


title: RD-26

value: AD + PS1 mutation


title: Chronic-Adult-Sox11

description:
Library name: Chronic-1M-Sox11-2WK
10x Genomics


title: MPC5_SPARC_overexpression3

description: Library name: Spa-oe-3


title: RD-19

value: Entorhinal cortex


title: Toxicodendron succedaneum, Sterile seedings,48h, replicate 3

value: stem segments

value: growth stage

value: Sterile seedings are cultured in a rooting medium for 48 hours


title: RD-16


title: NHSK-1 Cells, 6 hour IFN beta treatment replicate 1

description:
Library name: Interferon beta 6h treatment 1
Column name in "raw_counts_All_samples" - B1

value: Human Skin

value: Normal human skin keratinocyte

value: WT

value: 6 hour IFN beta


title: RD-14

value: Control


title: Uninjured-Adult-Control

description:
Library name: CST-Control-1
10x Genomics

value: Brain


title: Embryonic-2

description:
Library name: E18-ADULT-2
10x Genomics


title: Toxicodendron succedaneum, Sterile seedings,48h, replicate 2

value: tissue culture


title: Toxicodendron succedaneum,  Explant,12h, replicate 2

value: Explant are cultured in a rooting medium for 12 hours


title: RD-13

value: FEMALE

value: AD


title: shHDAC5-1

description: Library name: Sample 5

data_processing:
Sequencing read quality was inspected using the fastqc v0.11.9. Adapter removal and read trimming were performed using fastp v0.23.3. Sequencing reads were trimmed from the end (base quality less than Q20) and filtered by length (less than 20).
Alignment performed using bwa-mem2 2.2.1
deepTools v3.5.0 was used to generate bigWig files.
macs3 v3.0.3 was used to call peaks.
Assembly: hg38
Supplementary files format and content: BW (BigWig) files contain the genome data for each sample.

source_name: human pancreatic cancer cells

growth_protocol: DMEM,15% fetal bovine serum,2mM glutamine,1x penicillin/streptomycin..Cells were cultured at 37℃ at 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutesAfter auenching and cell livsis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris).
ChIP-Seq libraries were prepared using the KAPA HTP Library Preparaion Kit comoemented wih NEXTflex DNA Barcodes from Bioo Scientific. 10ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in lenath using Agencourt AlMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

value: human pancreatic cancer cells


title: Embryonic-1

description:
Library name: E18-1
10x Genomics


title: Toxicodendron succedaneum,  Explant,12h, replicate 1


title: RD-3

value: MALE


title: RD-10


title: MPC5_SPARC_overexpression6

description: Library name: Spa-oe-6

value: Mouse podocyte cell

value: Sparc overexpression

value: transfected Sparc overexpression plasmid


title: MPC5_control6

description: Library name: Vec-6

value: transfected vector plasmid as control


title: Toxicodendron succedaneum,  Explant,6h, replicate 3

value: stem segments

value: growth stage

value: Explant are cultured in a rooting medium for 6 hours


title: RD-7

value: Entorhinal cortex


title: Input-shHDAC5

description: Library name: Sample 2


title: Toxicodendron succedaneum,  Explant,6h, replicate 2


title: MPC5_control5

description: Library name: Vec-5

value: WT


title: RD-5


title: RD-6


title: Toxicodendron succedaneum, Sterile seedings,24h, replicate 2

value: Sterile seedings are cultured in a rooting medium for 24 hours


title: Toxicodendron succedaneum,  Explant,6h, replicate 1


title: RD-4


title: MPC5_control4

description: Library name: Vec-4


title: D.shHDAC5+MRTX1133 rep2

description: Library name: Sample 11

data_processing:
Sequencing read quality was inspected using fastp v0.24.0. Adapter removal and read trimming were performed. Sequencing reads were trimmed from the end (base quality less than Q20) and filtered by length (less than 25).
Paired-end reads were aligned to the hg38 (Subread v2.0.8) . FeatureCounts (Subread v2.0.8) was used to count the reads numbers mapped to each gene. And then FPKM/TPM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Supplementary_files_format_and_content: text file include gene names, sample name, read-counts values for each Sample
/
Assembly: hg38
Supplementary files format and content: txt file includes read counts for each sample.

source_name: pancreatic ductal adenocarcinoma cell line


title: Toxicodendron succedaneum, Sterile seedings,12h, replicate 3

value: Sterile seedings are cultured in a rooting medium for 12 hours


title: MPC5_SPARC_overexpression2

description: Library name: Spa-oe-2


title: MPC5_control2

description: Library name: Vec-2


title: RD-1


title: shHDAC5-2

description: Library name: Sample 6


title: MPC5_SPARC_overexpression1

description: Library name: Spa-oe-1


title: Toxicodendron succedaneum, Sterile seedings,12h, replicate 2

value: tissue culture


title: Toxicodendron succedaneum, Sterile seedings,48h, replicate 1

value: Sterile seedings are cultured in a rooting medium for 48 hours


title: NC-2.

description: Library name: Sample 4


title: Liver, CR, Day 25 - 03

city: St Louis

first: Hector

middle: H

last: Palacios

state: MO

address: 00201 West Building

institute: Washington University School of Medicine

data_processing:
The raw sequencing files were processed with CASAVA 1.8.2 (Illumina) to generate fastq files.
We obtained read quality reports by using the FastQC tool (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
The fastq files were then uploaded onto the Galaxy project portal (https://usegalaxy.org/)
The reads were then mapped to the mouse reference genome (mm10) using the Burrows-Wheeler Aligner (BWA) module.
Differential gene expression of RNA-seq was determined using DESeq2 .
Assembly: mm10
Supplementary files format and content: tab-delimited text file containing FPKM values

source_name: Liver

growth_protocol: mouse condition: All mice were maintained were maintained under temperature- and light-controlled conditions (12h:12h light-dark cycle, lights on at 0700h and off at 1900h).

extract_protocol:
Total RNA was isolated from mouse livers using RNeasy Micro Kit from Qiagen (Hilden, Germany). RNA Quantity was determined using a Qubit (TM) fluorometric assay and quality was determined using Eukaryote Total RNA Pico (Agilent Bioanalyzer 2100)
The library preparation and sequencing were done on a single lane (Illumina HiSeq4000) at 100bp pair-end (PE) reads and performed at the Vincent J. Coates Genomics Sequencing Laboratory at University of California (UC), Berkeley.

treatment_protocol: 6-week-old male C57Bl/6J mice (Jackson laboratory, Bar Harbor, ME) were used. All mice were housed individually. Mice were randomly assigned to one of the following two groups: ad libitum-fed (AL) or CR (30% less than what AL group consumed).

value: Liver

tag: time of_intervention

value: 25 days

value: male

value: Caloric Restriction


title: RD-2

source_name: Entorhinal cortex

value: MALE

value: AD


title: NC-1.

description: Library name: Sample 3

value: human pancreatic cancer cells

tag: cell line


title: Toxicodendron succedaneum, Sterile seedings,24h, replicate 3


title: C.shHDAC5+Vehicle rep1

description: Library name: Sample 7

value: pancreatic ductal adenocarcinoma cell line

tag: genotype


title: Input-NC

description: Library name: Sample 1


title: Toxicodendron succedaneum, Sterile seedings,24h, replicate 1

value: stem segments

tag: treatment


title: N2, EV, D3A, rep2

city: HsinChu

first: Yen-Hung

state: East district

address: No. 101, Section 2, Kuang-Fu Road

department: Institute of Biotechnology

country: Taiwan

institute: National Tsing Hua University, Taiwan

description: Library name: N2, EV, D3A, rep2

data_processing:
Quality Control and Trimming:Raw Fastq reads were assessed for quality using FastQC (v0.11.9). Low-quality bases and adapter sequences were trimmed using Trimgalore (v0.6.7). The original sequencing output (R1, R2, and I1 files) are not available. The processed paired and unpaired reads generated by Trimgalore (e.g., ..._1_paired.fq.gz, ..._2_paired.fq.gz, ..._1_unpaired.fq.gz, and ..._2_unpaired.fq.gz) were submitted as the raw data. The overall post-trimming quality was summarized by MultiQC (v1.12).
Alignment to Genome:The high-quality reads were aligned to the C. elegans reference genome (Version WBcel235) using the STAR aligner (v2.7.9a).
Quantification:Gene-level raw read counts were generated from the alignment files using FeatureCounts (v2.0.1). FPKM and TPM values were also calculated for comparison.
Normalization and DEA:Differential expression analysis was performed using the DESeq2 package. Raw counts were normalized using the internal median of ratios method to account for library size and composition differences. Filtering Criteria: Differentially Expressed Genes (DEGs) were defined as those satisfying the criteria of adjusted P-value (FDR) < 0.05 and ∣Fold Change$\mid$ > 2 (log2(Fold Change) > 1.0 or < -1.0).
Assembly: The high-quality reads were aligned to the C. elegans reference genome build/assembly: WBcel235 (WormBase Release WS235) using the STAR aligner (v2.7.9a).
Supplementary files format and content: The processed data is provided as a single Tab−delimited plain text file (.txt) containing the expression matrix for all 8 core biological replicate samples. The file contains 25 columns: WBGene IDs (identifier), Raw Read Counts (integers, generated by FeatureCounts and used for DESeq2), FPKM, and TPM normalized values.

organism: Caenorhabditis elegans

source_name: whole worm

growth_protocol: The N2 wild-type strain and the pitp−1 mutant strain (pe1297) were cultured on Nematode Growth Medium (NGM) agar plates at 20∘C, maintained with E.coli OP50 bacteria.

extract_protocol:
For all experiments, worms were synchronized by bleaching gravid adults to collect eggs, and the resulting synchronized L1 larvae were used to initiate the experiment. All worms were collected at the Day 3 of Adulthood (D3A) stage. Worms were washed multiple times with M9 buffer to remove food, checked under a microscope for purity, and the final pellets were snap-frozen in liquid nitrogen and stored at −80 ∘C prior to RNA extraction. RNA was extracted using RNeasy Kit (Qiagen, #74004).
[1] RNA Quality Control:Total RNA was quantified, and its purity was assessed based on OD 260/280 (1.8−2.2) and OD 260/230 (≥1.8) ratios. Only samples with a RIN ≥7.0 were processed for sequencing. 0.1–5 μg of total RNA was used as input. [2] Library Preparation:RNA sequencing libraries were prepared by the Taiwan Genomics Industry Alliance (TGIA) using a standard protocol for Illumina sequencing. The mRNA fraction was enriched via poly-A selection, followed by fragmentation, cDNA synthesis, and adapter ligation. [3] Sequencing:The resulting libraries were pooled and sequenced on an Illumina NovaSeq 6000 System to generate 150 bp, paired−end reads.

treatment_protocol: For pitp−1 mutant samples: Synchronized L1 larvae of the pitp−1 mutant strain were transferred to NGM plates seeded with E. coli OP50 and cultured at 20 ∘C. For pitp−1(RNAi) samples: Synchronized L1 larvae of N2 worms were transferred to NGM plates containing 1 mM IPTG, seeded with E.coli HT115(DE3) expressing dsRNA targeting pitp-1 (or the Empty Vector (EV) RNAi control). RNAi feeding began at the L4(D0A) stage and continued throughout development.

value: whole worm


title: Toxicodendron succedaneum, Sterile seedings,6h, replicate 1

value: growth stage

tag: cell type

value: Sterile seedings are cultured in a rooting medium for 6 hours


title: Liver, CR, Day 30 - 01

value: 30 days


title: C.shHDAC5+Vehicle rep3

description: Library name: Sample 9


title: Liver, CR, Day 30 - 02


title: D.shHDAC5+MRTX1133 rep1

description: Library name: Sample 10


title: MPC5_control1

description: Library name: Vec-1

value: Mouse podocyte cell

value: WT

value: transfected vector plasmid as control


title: pitp-1(pe1297), D3A, rep2

description: Library name: pitp-1(pe1297), D3A, rep2


title: Toxicodendron succedaneum, Sterile seedings,12h, replicate 1

value: tissue culture

value: Sterile seedings are cultured in a rooting medium for 12 hours


title: D.shHDAC5+MRTX1133 rep3

description: Library name: Sample 12


title: C.shHDAC5+Vehicle rep2

description: Library name: Sample 8


description: Library name: N2, pitp-1(RNAi), adult-onset, D3A, rep2


title: Liver, CR, Day 30 - 03

value: Liver


title: Liver, CR, Day 25 - 02

value: 25 days

value: male


title: PTPN2KO 2 human anti-LeY CAR T cells from OVCAR-3 tumour-bearing mouse spleen

description:
Library name: KO2
All barcodes with 'KO2' in column 'Assignment' of assignment_confidence_table.csv

data_processing:
Raw sequence reads were trimmed to remove illumina adaptor sequences from the reads using Trim Galore! Version 0.6.7. (https://https://github.com/FelixKrueger/ TrimGalore.com/fenderglass/Flye). Trimmed reads were aligned to human reference genome (HG38) using STAR 2.7.8a alignment tool (https://github.com/alexdobin/STAR/releases) and mapped reads were counted using featureCounts at the gene level (https://rnnh.github.io/bioinfo-notebook/docs/featureCounts.html).
Gene expression counts were obtained by aligning against the human genome GRCh38 using “multi” function from CellRanger software (v7.0.1). Cell Multiplexing oligos (CMO) were utilized to categorize the experimental cell groups (PTPN2 sgRNA or Control sgRNA) and doublets were removed for cells contains multiple CMO tags. Feature references were used to identify T cell population (CD8 and CD4) and generated the Antibody- Derived Tag (ADT) matrix (CD8, CD4 and CD45RA).
Assembly: GRCh38
Supplementary files format and content: gzipped barcodes and feature files (tab separated) and counts matrix. Assignment confidence table (comma separated) with barcode-sample mapping information.

source_name: PBMC

extract_protocol:
Female NSG mice were injected subcutaneously with 5 x 10^6 OVCAR-3 cells resuspended in 100 ?l D-PBS into the flank. At day 14 post tumor cell injection, NSG mice were pre-conditioned with total-body irradiation (1 Gy) prior to the adoptive transfer of 20 × 106 PTPN2 deleted or PTPN2 expressing human LeY CAR T cells. At day 14 post adoptive transfer, the spleens from 6 NSG recipients per genotype were pooled, tissues homogenised, and cells stained with APC-conjugated antihuman CD3 sort-purified (500,000 per genotype) for CD3+ human a-LeY+ CAR T and nontransduced T cells). Dead cells were excluded with the LIVE/DEAD™ Fixable Near-IR Dead Cell Stain Kit (Thermo Fisher Scientific).
For assessing cell surface protein expression combined with 3’ digital gene expression of the same cell, 18,000 pooled CD3+ T cells were loaded onto the Agilent 2100 Bioanalyzer Instrument (CA, Santa Clara) resulting in a recovery of 10,000 cells. GEMs were generated by coating CD3+ T cells with 10x Single Cell 3’ v3.1 Gel Beads (containing ~3.5x10^6 barcodes, reverse transcription (RT) enzyme mix, template switch oligos, poly(dT) primer, sequencing primer and two capture primers; Chromium Next GEM Single Cell 3’ GEM Kit v3.1 16 rxns; PN-1000123) in partitioning oil in situ on the Chromium NextGEM Chip G. To generate full-length cDNA from poly-adenylated mRNA and barcoded DNA from the cell surface protein feature barcode by RT-PCR, GEMs were transferred to reaction tubes and incubated in a thermal cycler (Agilent SureCycler 8800; CA, Santa Clara). To purify the cell barcoded products from the post GEM-RT reaction mixture post reaction, Silane magnetic beads were used (Dynabeads MyOne SILANE PN-12000048). The size of the amplified cDNA was optimised by enzymatic fragmentation and size selection by incubation in a thermal cycler (Agilent SureCycler 8800; CA, Santa Clara) using the 10x Library Construction Kit 4 rxns (PN-1000196) containing the fragmentation enzyme, DNA ligase and adaptor oligos. Generated libraries were pooled at equimolar ratios and sequenced on a DNBSEQ-G400 (MGI Tech Co., Ltd) instrument, in a paired-end run configuration using the following read lengths: Read1 100 bp; Read2 100 bp; Index1 10bp; Index2 10 bp with a sequencing depth of at least 20,000 read pairs for 3’ gene expression library sequencing and 5,000 read pairs for cell surface protein expression library sequencing.

value: PBMC

value: CAR T cell

value: PTPN2 deleted

value: adoptive transfer to OVCAR-3 tumour-bearing mice


title: Toxicodendron succedaneum, Sterile seedings,6h, replicate 3

value: stem segments


title: MPC5_control3

description: Library name: Vec-3


title: Liver, Control, Day 25 - 01

value: Ad Lib


title: Toxicodendron succedaneum, Sterile seedings,6h, replicate  2

value: growth stage


title: B.shNC+MRTX1133 rep3

description: Library name: Sample 6

value: pancreatic ductal adenocarcinoma cell line


title: Liver, Control, Day 30 - 03

value: 30 days


title: B.shNC+MRTX1133 rep2

description: Library name: Sample 5


title: GBM11Periphery

status: Public on Oct 03 2025

city: Houston

first: Ailiang

last: Zeng

state: TX

address: 12515 stoney creek dr

department: Cancer Biology

institute: MD Anderson Cancer Center

description: Library name: GBM11Periphery

data_processing:
FastQ preparation: mkfastq (cellranger): https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/mkfastq
Count Matrix Generation: count (cellranger): https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/count
Data Normalization: scTransform (Satija): https://satijalab.org/seurat/v3.1/sctransform_vignette.html
https://satijalab.org/seurat/articles/integration_large_datasets.html
Assembly: mm10-3.0.0 (mouse), GRCh38-3.0.0 (human)
Supplementary files format and content: tsv.gz/barcodes
Supplementary files format and content: tsv.gz/genes
Supplementary files format and content: mtx.gz/counts

source_name: glioblastoma

extract_protocol:
Tumor samples were mechanically minced before enzymatic digestion, cells were then spun down at 800g with the brake off in a 0.9M sucrose solution to remove myelin. Cell pellets were then frozen. Upon bringing samples back up CD45+ FACs selection was performed before entering the 10x protocol
https://assets.ctfassets.net/an68im79xiti/4tjk4KvXzTWgTs8f3tvUjq/2259891d68c53693e753e1b45e42de2d/CG000183_ChromiumSingleCell3__v3_UG_Rev_C.pdf

value: glioblastoma

tag: spatial sampling

value: Periphery

value: immune cells


title: GBM10Core

description: Library name: GBM10Core

value: Core


title: N2, EV, D3A, rep1

description: Library name: N2, EV, D3A, rep1

value: whole worm


title: Liver, Control, Day 30 - 02

value: Liver


title: B.shNC+MRTX1133 rep1

description: Library name: Sample 4

value: WT


title: GBM10Border

description: Library name: GBM10Border

value: Border


title: GBM6Border

description: Library name: GBM6Border


title: N2, D3A, rep1

description: Library name: N2, D3A, rep1


title: Liver, Control, Day 30 - 01

value: male


description: Library name: N2, pitp-1(RNAi), adult-onset, D3A, rep1


title: PTPN2KO 1 human anti-LeY CAR T cells from OVCAR-3 tumour-bearing mouse spleen

description:
Library name: KO1
All barcodes with 'KO1' in column 'Assignment' of assignment_confidence_table.csv

value: PBMC

value: CAR T cell


title: GBM6Periphery

description: Library name: GBM6Periphery


title: A.shNC+Vehicle rep3

description: Library name: Sample 3


title: Sample11, asymptomatic

city: zhengzhou

first: Shen

last: Li

address: No. 1 East Jianshe Road

department: The Department of Neurology

institute: The Department of Neurology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China

description:
Library name: Sample11
SeekOne® MM

data_processing:
The scRNA-seq data were analyzed using R version 4.02 as follows: (1) Seurat R package was used to convert scRNA-seq data as a Seurat object and the “FindVariableFeatures” function was used to select the highly variable genes after quality control; (2) principal component analysis was performed based on the selected variable genes to analyze the scRNA-seq data; (3) Merge R package was used to integrate single-cell data, and the “Merge” function was applied in the Seurat object to integrated scRNA-seq data from 12 atherosclerotic plaques; (4) after integration, uniform manifold approximation and projection (UMAP) were applied to analyze the scRNA-seq data; (5) Cell types (e.g., endothelial cells, smooth muscle cells, macrophages) were annotated using CellMarker and PanglaoDB dataset, as well as previous studies. Gene expression was visualized using a violin plot, feature plot, dot plot, and heatmap, generated with the Seurat function. Markers for a specific cluster against all remaining cells were identified using the “FindAllMarkers” function (only.pos=TRUE, min.pct=0.25).
Assembly: HG38
Assembly: GRCm38
Supplementary files format and content: processed data files format and content
Supplementary files format and content: Tab-separated values files and matrix files

source_name: carotid atherosclerosis plaque

extract_protocol:
After harvested, CAS plaques and mouse carotid arteries were washed in ice-cold RPMI1640 and dissociated using SeekOne® Multi-tissue dissociation kit 2 from Miltenyi Biotec as instructions. DNase treatment was optional according to the viscosity of the homogenate. Cell count and viability was estimated using fluorescence Cell Analyzer (Countstar® Rigel S2) with AO/PI reagent after removal erythrocytes (Miltenyi 130-094-183) and then debris and dead cells removal was decided to be performed or not (Miltenyi 130-109-398/130-090-101). Finally fresh cells were washed twice in the RPMI1640 and then resuspended at 1×106 cells per ml in 1×PBS and 0.04% bovine serum albuminat.
scRNA-seq libraries were prepared using the SeekOne® MM Single Cell 3’ library preparation kit. Briefly, appropriate number of cells were loaded into the flow channel of the SeekOne® MM chip that has 170,000 microwells; the cells were allowed to settle in microwells by gravity. After removing the unsettled cells, sufficient cell-barcoded magnetic beads (CBBs) were pipetted into the flow channel and allowed to settle in the microwells under a magnetic field. Next, excess CBBs were rinsed out, and the cells in the MM chip were lysed to release RNA, which was captured by the CBB in the same microwell. Subsequently, all CBBs were collected, and reverse transcription was performed at 37 ℃ for 30 min to label the complementary DNA (cDNA) with cell barcode on the beads. Exonuclease I treatment was performed to remove unused primers from the CBBs. Subsequently, thebarcoded cDNA on the CBBs was hybridized with a random primer containing reads 2 SeqPrimer sequence on the 5’ end to generate second strand DNA with the cell barcode on the 3’ end. The resulting second-strand DNA was denatured from the CBBs, purified, and amplified using PCR. The amplified cDNA product was cleaned to remove unwanted fragments and added to a full-length sequencing adapter and sample index using indexed PCR. The indexed sequencing libraries were cleaned with solid phase reversible immobilization beads, quantified using quantitative PCR (KAPA Biosystems KK4824), and sequenced on an Illumina NovaSeq 6000 with a PE150 read length or a DNBSEQ-T7 platform with a PE100 read length

treatment_protocol: 12 CAS plaques obtained following carotid endarterectomy (CEA) and carotid arteries from mice

value: carotid atherosclerosis plaque

value: tissue


title: control 2 human anti-LeY CAR T cells from OVCAR-3 tumour-bearing mouse spleen

description:
Library name: WT2
All barcodes with 'WT2' in column 'Assignment' of assignment_confidence_table.csv

value: Control

value: adoptive transfer to OVCAR-3 tumour-bearing mice


title: Liver, CR, Day 25 - 01

value: 25 days

value: Caloric Restriction


title: pitp-1(pe1297), D3A, rep1

description: Library name: pitp-1(pe1297), D3A, rep1


title: Liver, Control, Day 25 - 03

value: Ad Lib


title: A.shNC+Vehicle rep2

description: Library name: Sample 2

value: pancreatic ductal adenocarcinoma cell line


title: N2, D3A, rep2

description: Library name: N2, D3A, rep2


title: Liver, Control, Day 25 - 02


title: Sample7, asymptomatic

description:
Library name: Sample7
SeekOne® MM


title: control 1 human anti-LeY CAR T cells from OVCAR-3 tumour-bearing mouse spleen

description:
Library name: WT1
All barcodes with 'WT1' in column 'Assignment' of assignment_confidence_table.csv


title: Sample5, symptomatic

description:
Library name: Sample5
SeekOne® MM


title: Sample4, symptomatic

description:
Library name: Sample4
SeekOne® MM


title: GBM11Core

description: Library name: GBM11Core

value: glioblastoma

value: immune cells