title: scRNA and V(D)J  sequencing of an histological normal human ileal sample

city: Barcelona

first: Júlia

last: Perera-Bel

address: Doctor Aiguader, 88

department: MARData-BU

country: Spain

institute: Hospital del Mar Research Institute

description:
HC_2_GEX
HC_2_BCR
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggretation were made using the Cell Ranger software (v.7.1.0) (10x Genomics, CA, USA).
For VDJ analysis, sequences were pre-processed using the Cell Ranger software pipeline (v.7.1.0) (10x Genomics, CA, USA). Singularity shell from the Immcantation Framework (v.4.4.0) (http://immcantation.org) was used to analyze sequencing data with Change-O (v.1.3.0), SHazaM (v.1.1.2), scoper (v.1.2.1) and dowser (v.1.1.1) packages. Annotation was performed using the reference V(D)J germline sequences in the Singularity container.
Assembly: GRCh38-2020-A
Supplementary files format and content: Cell Ranger software output files (barcodes.tsv.gz, features.tsv.gz and matrix.mtx.gz).
Supplementary files format and content: Contig annotations and cell barcode information (all_contig_annotations.csv).

source_name: Distal ileum

extract_protocol:
Histologically normal ileal gut tissue samples were processed as previously described (Magri et al. Immunity 2017) and lamina propria mononnuclear cells isolated from the tissue were stained with 4’-6’-diamidine-2’-phenylindole (DAPI) and viable cells (DAPI-) were sorted with a FACSAria II (BD bioscience) before library preparation.
Around 16000 viable cells were loaded for sequencing analysis. Generation of gel beads in emulsion (GEMs), barcoding and GEM-reverse transcription were performed using the Chromium Single Cell 5′ and V(D)J Reagent Kits (10x Genomics, CA, USA) according to manufacturer’s instructions.

value: Distal ileum

value: alive lamina propria cells


title: sErbB4- 3

status: Public on Oct 17 2024

type: SRA

city: Bethesda

first: David

middle: A

last: Talmage

state: MD

address: 35 Convent Dr, Room 3B-101

department: NINDS

country: USA

institute: National Institutes of Health

library_source: transcriptomic

data_processing:
QC inspection using FastQC, MultiQC, and Fastx_Screen
Adaptor sequences clipped, low quality and/or nucleotide biased positions in sequences were trimmed using Trimmomatic and QC was repeated
Alignment to ref. genome using HISAT2 and QC of alignment using RSeqC
Transcript assembly using StringTie, QC using gffcompare
Gene and isoform level enumeration using IsoformSwitchAnalyzeR
within sample normalization (cpm), cross-sample normalization CyclicLowess, PCA for outlier detection
Sequence batch correction using Limma, filter and floor values to 2.25
ANOVA for differential gene expression
Assembly: mm10
Supplementary files format and content: Gene level enumeration text file

molecule: total RNA

organism: Mus musculus

source_name: Brain

growth_protocol: See Manuscript for details on culture conditions

extract_protocol:
Qiagen RNeasy micro kit
NEBNext Library Prep Kit

tag: tissue

value: Hippocampus

tag: cell type

value: Neuronal culture

tag: genotype

value: WT

tag: treatment

value: sErbB4 20nM


title: hMedIP_P0_WT_hMeDIP_rep2_input

city: Houston

first: Yejing

last: Ge

state: Texas

department: Cancer Biology

institute: The University of Texas, MD Anderson Cancer Center

description: hMeDIP

library_source: genomic

data_processing:
Raw sequencing150-bp paired-end reads were aligned to mus musculus genome mm10 using STAR.
Reads mapped to a single genomic location were kept for peak identification using the Model based Analysis of Chip-seq 1 (MACS1) or Model based Analysis of Chip-seq 2 (MACS2) pipeline.
Assembly: mm10
Supplementary files format and content: bed or broadPeak files include peak informations for each Sample (except for control sample)
Library strategy: hMeDIP

molecule: genomic DNA

source_name: skin

growth_protocol: C57BL/6J mice cultured in a specific pathogen-free barrier facility on a standard light-dark cycle.

extract_protocol:
Freshly FACS-sorted cells were fixed with 1% formaldehyde for 10 minutes. For IgG and H3K9me3 ChIP, after quenching and cell lysis, chromatin was sonicated using Bioruptor Sonicator; for Setdb1 ChIP, use CST SimpleChIP protocol following manufacture recommendation.
For ChIPseq, the DNA extract was incubated overnight at 4°C with primary antibody. 10 μl of Dynal Protein G magnetic beadswas added to each sample the following day, incubated at 4°C for 2-4 h, followed by washes for several times. Bound complexes were treated with 5ul Tn5 transposase at 37°C for 5min, eluted and crosslinking was reversed by 6-10h incubation at 65°C, cleaned up with MinElute PCR Purification Kit and PCR-amplified for 10-12 cycles. Libraries were purified by Beckman Coulter AMPureXP beads and submitted to Novogene for library quality control (QC). For hMeDIP, fragmented DNA was used for end-repair, A-tailing and ligation of adapters using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (New England Biolabs).  10% of the ligated material was saved as input reference and the remaining material was immunoprecipitated using Diagenode’s hMeDIP kit (Diagenode, Denville, NJ). Final libraries from input and 5hmC-immunoprecipitate were obtained by PCR amplification using barcoded primers, followed by clean-up using magnetic beads.

treatment_protocol: For hair follicle cell isolation from P30 mice, back skin at anagen stage was removed and submerged in 0.25% collagenase/HBSS (Gibco) containing DNase I for 1hr at 37°C. Release cells were scraped off, resuspended in cold PBS, and the remaining skin was then incubated with 0.25% trypsin-EDTA (Gibco) for 10 min at 37C, neutralized by cold PBS containing 2% calcium-chelated fetal bovine serum FBS(-), and filtered through a 40-μm cell strainer. Cells were spin down at 400g for 10 min at 4°C, and washed once with cold PBS containing 2% FBS(-). Freshly isolated cells were incubated with conjugated antibodies and sorted using a 70-μm nozzle on a BD FACSAria equipped with FACSDiva software (BD Biosciences), gating on DAPI-CD31-CD140A-CD45-ITGA6+ to isolate epithelial cells, and further separated into epidermal (Sca1+) and hair follicle (Sca1-) cells. For epithelia cells islolation from P0 mice, back skin was dissected and submerged dermis side down on 2.5 U/mL Dispase (Gibco) in PBS overnight at 4°C. The epidermis was then peeled off and incubated with 0.25% trypsin-EDTA (Gibco) for 10 min at 37°C, minced, neutralized by cold PBS containing 2% calcium-chelated fetal bovine serum FBS(-), and filtered through a 40-μm cell strainer. Cells were spun down at 300 g for 10 min at 4°C and washed once with cold PBS containing 2% FBS(-).

value: skin

tag: cell line

value: P0 skin epithelia

value: wild type


title: MCF7 tumor,Glucose, UCP1l 2

city: San Francisco

first: Hai

middle: Phi

last: Nguyen

state: CA

department: Bioengineering

institute: UCSF

data_processing:
RNA-seq analysis was performed using Partek Flow
Sequences were trimmed for adapter sequence
Trimmed sequences were aligned to hg38 using STAR method
DEG were annonated using DE2Seq
Assembly: hg38
Supplementary files format and content: tab-demilited files include raw count for each sample
Supplementary files format and content: tab-demilited files include KRPM count for each sample

organism: Homo sapiens

source_name: Xenograft from breast cancer cells

extract_protocol:
Total RNA was isolated using RNEasy Plus Kit
Libraries were constructed using TruSeq Stranded Total RNA Library Prep Kit (Illumina)

value: Xenograft from breast cancer cells

value: Breast cancer

value: ER+, PR+, HER2+

value: 15% Glucose water


title: sErbB4- 2


title: hMedIP_P0_WT_hMeDIP_rep2

description: hMeDIP


title: MCF7 tumor,Glucose, UCP1l 1


title: hMedIP_P0_WT_hMeDIP_rep1_input

description: hMeDIP


title: sErbB4- 1


title: MCF7 tumor,Glucose, control 3


title: miR155, D7 endometriosis lesion, rep1

city: Adelaide

first: James

last: Breen

state: SA

address: 108 North Terrace (Ground Floor)

department: John Curtin School of Medical Research

country: Australia

institute: Australian National University

data_processing:
Illumina RNA sequencing data was processed using an in-house RNA-seq workflow. Quality control was carried out using FastQC [98], followed by quality and adapter trimming using AdapterRemoval2 [99], aligned to the GENCODE mm10 (GRCm38.p4) mouse reference genome using HISAT2 [100] and quantified to mm10 annotation using featureCounts [101, 102].
Additional sample quality control and normalisation were performed using the R Statistical Software Suite, and differential expression analyses carried out using R packages limma [103, 104] and edgeR [105] on a total of 36 biological samples, comprising 12 samples each from C57Bl/6 mice, miR-155-/- mice and miR-223-/- mice (Refer to Figure S1 and S2).
Significance was inferred from adjusting raw p values (p) using the Benjamini Hochberg false discovery rate method [106] to yield a false discovery rate (FDR) with ≤ 0.05 being the chosen cut-off. Using the limma::treat function, significance was determined based on a null hypothesis of log2FC (log2Fold Change) ≥ ±1
The Ingenuity Pathway Analysis software (IPA 2023; QIAGEN Inc.) was used to identify enriched cellular and molecular functions amongst differentially expressed genes, identify upstream regulators of genes, and to further classify these genes into functionally related groups.
NOTE: One sample pair was lost due to a data atsorage failure (KS_Kav_35_R2)
Assembly: GRCm38.p4
Supplementary files format and content: tsv gene counts

source_name: endometriosis lesion

extract_protocol:
Total RNA was extracted from snap-frozen samples using Qiagen miRNeasy RNA extraction and purification kit, followed by Dnase treatment using TURBO DNA-free kit
Libraries for a total of 36 samples (4 biological samples from each timepoint per genotype) were made from approximately 1ug total RNA. The mRNA sequencing library was prepared using Illumina’s TruSeq RNA Sample Preparation Kit for PolyA+ selection.

value: endometriosis lesion

value: B6.Cg-Mir155 tm1Rsky /J


title: hMedIP_P0_WT_hMeDIP_rep1

description: hMeDIP


title: ChIP_P0_Dnmt1cKO_H3K9me3

description: ChIP-seq

data_processing:
Raw sequencing150-bp paired-end reads were aligned to mus musculus genome mm10 using STAR.
Reads mapped to a single genomic location were kept for peak identification using the Model based Analysis of Chip-seq 1 (MACS1) or Model based Analysis of Chip-seq 2 (MACS2) pipeline.
Assembly: mm10
Supplementary files format and content: bed or broadPeak files include peak informations for each Sample (except for control sample)


title: Vehicle 2

value: Vehicle


title: Vehicle 3


title: miR155, decidualized endometrium, rep3

source_name: decidualized endometrium

value: decidualized endometrium


title: MCF7 tumor,Glucose, control 2


title: ChIP_P0_WT_H3K9me3

description: ChIP-seq


title: Vehicle 1


title: MCF7 tumor, HFD, UCP1 3

value: High-fat diet


title: MCF7 tumor, HFD, UCP1 2


title: miR155, D7 endometriosis lesion, rep2


title: miR155, decidualized endometrium, rep1


title: miR155, D7 endometriosis lesion, rep3


title: gADSCs TAZ_3

city: Hohhot

first: Dongjun

last: Liu

state: Inner Mongolia

address: 235 Daxue west road  Saihan District

country: China

institute: Inner Mongolia University

data_processing:
The libraries were sequenced on an Illumina HiSeq 2000 platform and 150 bp paired-end reads were generated.. Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads. The clean reads were mapped to the reference genome using HISAT2 . FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count .
Assembly: The clean reads were mapped to the reference genome using HISAT2 . FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count .
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Capra hircus

source_name: Adipose mesenchymal stem cells

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Then the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

value: Adipose mesenchymal stem cells

value: overexpressing TAZ

value: adipogenic differentiation


title: MCF7 tumor, HFD, UCP1 1


title: MCF7 tumor,Glucose, control 1


title: MCF7 tumor, HFD, control 3


title: miR155, decidualized endometrium, rep4


title: gADSCs TAZ_1


title: C57BL/6, D14 endometriosis lesion, rep4


title: MCF7 tumor, HFD, control 2


title: C57BL/6, D14 endometriosis lesion, rep2


title: C57BL/6, D14 endometriosis lesion, rep3


title: gADSCs Control_1

value: WT


title: MCF7 tumor, HFD, control 1


title: gADSCs Control_2


title: miR155, decidualized endometrium, rep2


title: MCF7 tumor, chow, UCP1 3

value: Chow diet


title: C57BL/6, D14 endometriosis lesion, rep1


title: UJ_40Bleo

type: RNA

city: Düsseldorf

first: Wasco

last: Wruck

address: Moorenstr. 5

country: Germany

institute: Universitätsklinikum Düsseldorf

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using rank invariant normalisation with BeadStudio version 3 (Illumina)

label: biotin

source_name: brain organoids derived from induced pluripotent stem cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: For the generation of cerebral organoids, iPSCs were differentiated as described [Sloan et al. Nat. Protoc. 2018, 13, 2062–2085], but with further optimization. On day 0, iPSCs were dissociated using TrypLE Express (Gibco, Waltham, MA, USA) and plated into a 96-well ultra-low-attachment (10,000 cells/well, NucleonTM SpheraTM, Thermo Scientific) in mTEST supplemented with 10 µM ROCK inhibitor Y-27632 (Tocris Bioscience, Bristol, UK). Neural induction was initiated on day 1 by adding Neural induction medium (NiM) (DMEM/F12, 20% Knock-out serum replacement, 1%NEAA, 0.5% GlutaMAX and 0.1mM 2-Mercaptoethanol (all from Gibco) with 10 µM SB-431542 (Tocris Bioscience), 5 µM Dorsomorphine (Tocris Bioscience) and 10 µM ROCK inhibitor Y-27632. The medium was changed daily. After five days, the spheroids were transferred to Neural differentiation medium (NdM) (Neurobasal, 2% B27, 1% GlutaMAX, 1% P/S (all from Gibco)) supplemented with 20 ng/mL of EGF and FGF2 (both PrepoTech, Cranbury, NJ, USA) in non-adhesive 100 mm dishes. Organoids were further cultured under continuous agitation (60 rpm) in a shaking incubator (New Brunswick S41i, Eppendorf) with daily medium change until day 16, and from day 16 onwards medium was changed every other day. At day 25, medium was replaced to NdM supplemented with 20 ng/mL of BDNF with medium change every 2–3 days. From day 40 onwards, organoids were kept in NdM with medium change every 4 days.

extract_protocol: The RNA was extracted using TRIzol reagent (Thermo Fisher Scientific) and the manufactural protocol. The quality of the RNA was checked with a NanodropTM spectrophotometer (Thermo Scientific).

treatment_protocol: To induce DNA damage, cerebral organoids at day 37 were incubated with 30 µg/mL of Bleomycin (Millipore, Darmstadt, Germany) for 72 h before harvesting for RNA extraction and for protein lysate preparation.

value: brain organoids

tag: condition

value: ctrl

value: UJ ctrl 40d Bleomycin

tag: replicate

value: replicate 1


title: UJ_40

value: UJ ctrl 40d


title: gADSCs TAZ_2


title: MCF7 tumor, chow, UCP1 2

value: Xenograft from breast cancer cells

value: Breast cancer

value: ER+, PR+, HER2+


title: Reference

city: Beijing

first: Zhen

last: Xiong

address: 15 Datun Road, Beijing 100101, China

department: Institute of Biophysics

institute: Chinese Academy of Sciences

description: Reference

library_source: transcriptomic single cell

data_processing:
Data were processed to generate gene expression profiles using scnasRNA-seq pipeline (https://github.com/singleron-RD/CeleScope/blob/master/doc/assay/multi_dynaseq.md). Briefly, raw reads were processed with fastQC and fastp to remove low quality reads, such as those without poly T tails, cell barcode and UMI. Adapters and poly A tails were trimmed by Cutadapt before aligning paired reads to the mouse reference genome (GRCm38 with ensemble version 92 gene annotation) using STAR (version 2.5.3a). We then acquired gene counts and UMI counts by assigning uniquely mapped reads to genomic features with FeatureCounts (version 1.6.2). To quantify S4U labeled and unlabeled reads, we got T-to-C substitutions in each read. After excluding background T-to-C substitutions (presenting in control samples without metabolic labeling), we distinguished nascent RNA from old RNA based on whether reads contained T-to-C substitutions. Reads with the same cell barcode, UMI and gene were grouped together to count numbers of labeled and unlabeled UMIs for each gene per cell. Finally, we obtained two gene expression matrices (nascent RNA count and old RNA count matrix) for each sample. Total RNA count matrix is the sum of nascent RNA count matrx and old RNA count matrix.
Assembly: GRCm38
Supplementary files format and content: tsv file includes raw counts of new RNA for each Sample
Supplementary files format and content: tsv file includes raw counts of old RNA for each Sample

source_name: bone marrow

extract_protocol:
Single-cell suspension was loaded onto microwell chips for single cell partition, followed with bead loading and cell lysis. After 20 min incubation at room temperature (RT), mRNA in each well was captured on a magnetic bead coated with oligonucleotides, each containing a primer sequence, a cell barcode, a unique molecular identifier (UMI), and a poly-T tail.
We used DynaSCOPETM Single Cell Dynamic RNA Library Kit (Singleron Biotechnologies) to construct scnasRNA-seq libraries. After collecting all beads that captured mRNA, S4U integrated on nascent RNA was converted into cytidine analogs. mRNA was incubated with conversion reagent at 25°C for 60 min. Mutations were inserted at the indicated sites on reverse transcription. For reference control samples, mRNA was incubated in the same condition but without conversion reagent. The reverse transcription reaction was incubated at 42°C for 90 min. cDNA amplification was performed by PCR using 13 cycles. PCR amplification products were purified using AMPure XP beads. After cDNA fragmentation and adaptor ligation, products were purified and amplified by PCR. After size selection, libraries were sequenced.

treatment_protocol: 8 to10 week-old mice were deprived of food and water for 4 h. Then mice were gavaged with 20 mg streptomycin sulfate in 200 ml PBS. 24 h later, mice were again deprived of food and water for 4 h, and then were gavaged with 10^8 CFUs of Salmonella. Bone marrow and small intestinal cells were collected at the indicated time point. Nacent RNA was labeled with S4U (1% of body weight) through tail vein injection

value: bone marrow

value: salmonella


title: scnasRNA-seq of BM, 72h post salmonella infection

description: total RNA and nascent RNA


title: C57BL/6, D7 endometriosis lesion, rep3

value: endometriosis lesion


title: A4_40

value: A4 ctrl 40d


title: MCF7 tumor, chow, UCP1 1


title: gADSCs Control_3

value: Adipose mesenchymal stem cells


title: C57BL/6, D7 endometriosis lesion, rep2


title: NBS8_20

value: NBS8 20d


title: NBS1_40Bleo

value: NBS1 40d Bleomycin


title: scnasRNA-seq of BM, 48h post salmonella infection

description: total RNA and nascent RNA

value: WT


title: C57BL/6, D7 endometriosis lesion, rep1


title: MCF7 tumor, chow, control 3

value: Chow diet


title: C57BL/6, D7 endometriosis lesion, rep4


title: UJ_20

value: brain organoids

value: UJ ctrl 20d


title: NBS1_40

value: NBS1 40d


title: C57BL/6, decidualized endometrium, rep4

value: decidualized endometrium


title: scnasRNA-seq of BM, 12h post salmonella infection

description: total RNA and nascent RNA


title: MCF7 tumor, chow, control 2


title: scnasRNA-seq of BM, 24h post salmonella infection

description: total RNA and nascent RNA


title: NBS1_20

value: NBS1 20d

value: replicate 1


title: NBS1_40Bleo_2

value: replicate 2


title: C57BL/6, decidualized endometrium, rep2


title: NBS1_40_2


title: scnasRNA-seq of BM, 6h post salmonella infection

description: total RNA and nascent RNA


title: scnasRNA-seq of BM, 2h post salmonella infection

description: total RNA and nascent RNA


title: A4_20

value: ctrl

value: A4 ctrl 20d


title: C57BL/6, decidualized endometrium, rep3


title: OCI-AML3_Ctrl2

city: Portland

first: Peter

last: Ryabinin

state: OR

address: 3181 SW Sam Jackson Park Rd

institute: Oregon Health and Science University

data_processing:
all paired end reads were trimmed using Trimmomatic 0.39 and the "TruSeq3.fa" adapter file with the following parameters: "2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36"
samples were aligned to GRCh38.110 using kallisto 0.46.2 and the following parameters: --bias --rf-stranded --plaintext --bootstrap-samples=50
Assembly: GRCh38.110
Supplementary files format and content: RNA230511HZ_gene_level_raw_counts.csv contains gene level counts in CSV file format
Supplementary files format and content: RNA230511HZ_gene_level_length.csv contains gene level lengths in CSV file format
Supplementary files format and content: RNA230511HZ_gene_level_abundance.csv contains gene level abundances in CSV file format

molecule: polyA RNA

extract_protocol:
RNA was harvested using Qiagen Rneasy mini kit. 1ug RNAs were used for RNA library preparation.
The RNA library was prepared using the Illumina Stranded mRNA Preparation kit, following the manufacturer's protocol.
RNA-Seq: Libraries are prepared from bulk RNA using Stranded with poly(A)+ selection (default) following the manufacturer's protocol. 50 million read-pairs per bulk RNA-seq library were generated.

value: Plex Control


title: scnasRNA-seq of BM, 0h post salmonella infection

description: total RNA and nascent RNA

value: bone marrow

value: salmonella


title: OCI-AML3_Ctrl1


title: noKO, induction0, 5hpi, Rep1, RNA

city: Regensburg

first: Simon

last: Holzinger

address: Universitätsstraße 31

institute: University of Regensburg

data_processing:
Image analysis and base calling were done by the Real Time Analysis Software (RTA) v3.7.17. The resulting .cbcl files were converted into .fastq files with the bcl2fastq v2.20 software.
Reads were trimmed with trimmomatic v0.39 and "ILLUMINACLIP:<ADAPTERS>:2:30:10", "MAXINFO:30:0.2" and "MINLEN:35" options
Alignment was done with STAR v2.7.4a using "--outFilterType BySJout --outFilterMultimapNmax 20 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 5 --alignIntronMax 1000 --alignMatesGapMax 1000000 --outMultimapperOrder Random"
Rsubread/FeatureCounts v2.12.2 was used to calculate read counts in a strand specific way, counting multimapping reads as fractional counts.
Assembly: P. falciparum 3D7 genome v3.0, plasmoDB release 52

organism: Plasmodium falciparum

growth_protocol: P. falciparum clone 3D7 was cultured according to standard procedures in RPMI 1640 with Albumax®. For synchronization, schizonts were purified on a bed of 70% Percoll®, incubated with new red blood cells for 1-2 h, before leftover schizonts were removed with Percoll and subsequent sorbitol treatment.

extract_protocol:
Total RNA from infected red blood cells containing highly synchronized parasites was isolated at the indicated timepoint using Whole Blood Quick RNA kit (Zymo Research) according to the manufacturer’s protocol.
300 ng total RNA were used as input for Illumina Stranded mRNA Prep Ligation (Illumina).

treatment_protocol: For KO induction, synchronous parasites were treated with 100 nM rapamycin for 4 h (DMSO treatment as control), washed and returned to culture.    For drug treatment, parasites were cultured after synchronization in media supplemented with 1 µM drug until RNA isolation.

tag: strain

tag: ko induction_time

tag: harvesting time

value: 5 hpi

value: not induced


title: C57BL/6, decidualized endometrium, rep1


title: MCF7 tumor, chow, control 1

value: Xenograft from breast cancer cells

value: Breast cancer

value: ER+, PR+, HER2+


title: OCI-AML3_CEBPB_2

value: Plex CEBPB


title: AKSP multiome - s.c ATAC

city: New York

first: BiNGS

last: Core

address: 1470 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

description: 10x Genomics

data_processing:
Cellranger-arc (v2.0.0) was applied to raw fastq files to align the reads to mm10 genome, count barcodes, call peaks and count of both ATAC and GEX molecules to generate features-barcodes matrix.
Assembly: mm10
Supplementary files format and content: cell ranger filtered tab-separated values files and matrix files

source_name: Epithelial intestinal tumoroids

extract_protocol:
Matrigel domes containing the indicated organoid lines were collected and washed with cold cell recovery solution, then incubated in TryPLE  for 10 mins at 37C. Next, they were dissociated to single cells with gentle tritruation. Cells were stained and counted with Trypan blue to estimate the live/dead ratio.
Single Cell Multiome ATAC and Gene Expression libraries were prepared according to the 10X Chromium Next GEM Single Cell Multiome ATAC + Gene Expression user guide for standard Illumina paired-end sequencing

value: colorectal cancer

value: Epithelial intestinal tumoroids


title: OCI-AML3_CEBPB_1


title: AKSP multiome - s.c GEX

description: 10x Genomics


title: No.2

status: Public on Oct 16 2024

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

data_processing:
Sequencing was performed on DNBSEQ-G400RS (MGI Tech) in paired-end mode (read1: 50bp; read2: 100bp).
Raw sequencing data were converted to a matrix of expression, and spatial information using Space Ranger 2.0.0 (10X Genomics).
Assembly: refdata-gex-GRCh38-2020-A
Supplementary files format and content: filtered_feature_bc_matrix.h5 : HDF5 format file including read counts data for each gene and spot-position (spatial barcode) combination
Supplementary files format and content: spatial.zip : This file includes spatial information such as positions of spatial barcodes and images of the sample. It is the zipped "spatial" folder which is one of output folders of Space Ranger software (10X genomics).
Library strategy: spatial transcriptomics

source_name: Gastric adenocarcinoma

extract_protocol:
Human gastric tissue FFPE slice gene expression were detected by 10x Visium Spatial Gene Expression Slide & Reagents Kit.
RNA libraries were prepared for sequencing using 10x Visium spatial protocols and standard MGI protocols.

value: Gastric adenocarcinoma


title: P2x1-WT

city: Shanghai

first: Xiaoxiao

last: He

state: Shanghai

address: 280 South Chongqing Road, Shanghai 200025

department: Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education,Faculty of Basic Medicine

institute: Shanghai Jiao Tong University School of Medicine

description: gene expression

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a)10% base quality <15 b) 13% base quality <20.
Hisat2 2.0.4 mapping to reference genome
count counting
Assembly: mm10
Supplementary files format and content: TXT file contain counts for each sample

source_name: leukemia leukemia-initiating cells

extract_protocol:
Wild Type (P2X1-Scr) and P2x1 knockout (P2X1-KD)  AML leukemia leukemia-initiating cells  were lysed by TRIzol reagent for extraction of RNA. RNA was prepared using RNasey Mini Kit(Qiagen p/n 74104) according to  the manufacturer's recommendations. After clean-up, RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored by RNA electrophoresis.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Wild Type (P2X1-Scr) and P2x1 knockout (P2X1-KD)  AML leukemia leukemia-initiating cells were sorted from bone marrow based on Mac1+ C-kit+.

tag: age

value: 8 weeks

value: wild type


title: ART-DMSO-2

city: Toulouse

first: Lucie

last: Paloque

address: 205 route de Narbonne

country: France

institute: CNRS

data_processing:
RNA sequencing and data processing were performed by Magrogen Europe. Sequences were generated by NovaSeq 6000.
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic 0.38.
Trimmed sequence reads were mapped to the Plasmodium falciparum genome (reference genome, P. falciparum 3D7 GCA_000002765) using HISAT2 (v2.1.0).
Transcript assembly was performed using StringTie (v2.1.3b), and the abundance of gene/transcript was calculated in the read count and normalized value as FPKM.
For Differentially Expressed Gene (DEG) analysis, the read count value of known genes obtained through –e option of the StringTie were used as the original data. Statistical analysis was then performed for each comparison pair by using Fold Change, exactTest via edgeR. The significant results were selected on conditions of │fc│ ≥ 2 and exactTest raw p-value < 0.05. Comparisons were carried out pairwise (DHA vs DMSO for each strain).
Assembly: GCA_000002765
Supplementary files format and content: Excel file includes read counts, FPKM values, and TMM values for each Sample

extract_protocol:
RNA was harvested using miRneasy mini kit (Qiagen) and used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA library prep Kit (Illumina) following manufacturer's protocols.

tag: strain source

value: laboratory strain

tag: phenotype

value: artemisinin-resistant

value: DMSO

tag: time

value: 6 h


title: ART-DMSO-1


title: ART-DHA-2

value: DHA 700 nM


title: RNA samples from JAR cells with scrambled control mimic transfection 2

city: Zuoying

first: Sung-Chou

last: Li

state: Kaohsiung

address: No. 386, Dazhong 1st Rd.

department: Department of Medical Education and Research

country: Taiwan

institute: Kaohsiung Veterans General Hospital

description:
RMA expression value derived from Expression Console software; core-exon analysis
SC-2

hyb_protocol: Samples were hybridized with GeneChip Human Clariom S Arrays (Affymetrix) and scanned at the Kaohsiung Chang Gung Memorial Hospital Microarray Core Facility.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing:
Raw data were processed with the Exon Array Computational Tool (ExACT) (Affymetrix) for background correction and normalization. Data analysis was conducted with Partek.
affymetrix-algorithm-name = gc-correction,scale-intensities,rma-bg,quant-norm.sketch=0.usepm=true.bioc=true,pm-only,med-polish
affymetrix-algorithm-version = 1.0

source_name: JAR cell

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

extract_protocol: standard protocol

treatment_protocol: JAR (HTB-144, ATCC) cells were transfected with scrambled control or miR-34a mimics

value: JAR (HTB-144, ATCC)

value: scrambled control mimic transfection


title: ART-DHA-1


title: RNA samples from JAR cells with miR-34a mimic transfection 1

description:
RMA expression value derived from Expression Console software; core-exon analysis
miR-34a-1

value: miR-34a mimic transfection


title: RNA samples from JAR cells with scrambled control mimic transfection 3

description:
RMA expression value derived from Expression Console software; core-exon analysis
SC-3


title: RNA samples from JAR cells with scrambled control mimic transfection 1

description:
RMA expression value derived from Expression Console software; core-exon analysis
SC-1


title: RNA samples from JAR cells with miR-34a mimic transfection 2

description:
RMA expression value derived from Expression Console software; core-exon analysis
miR-34a-2


title: P2x1-KO

description: gene expression


title: ART-DMSO-3


title: ART-DHA-3


title: WB_LTBI_NON_216

city: London

first: Myrsini

last: Kaforou

address: Norfolk Place

country: United Kingdom

institute: Imperial College London

data_processing: The data were normalised using R, with background correction, variance stabilization and robust spline normalization.

source_name: Whole blood from patient with TB infection unstimulated

label_protocol: Biotinylated cRNA was prepared using Illumina TotalPrep RNA Amplification kits (Applied Biosystems)

extract_protocol: RNA was extracted with Trizol reagent and isolated with a modified QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: PBMCs were isolated according to the Histopaque 1077 (Sigma-Aldrich) cell isolation procedure, cultured in 0.2 ml growing medium, and were exposed for 24 hours in triplicate to a) recombinant Mtb antigens, ESAT-6 and CFP-10, b) Tuberculin PPD , or c) remained in the nutrient agent without stimulation. The supernatant was removed from each well and the remaining culture medium was triturated to resuspend the attached cells, transferred to a new vial, and centrifuged. The supernatant was discarded and Trizol reagent was added to the cell pellet. After washing the cell monolayer with PBS, Trizol reagent was added to the culture plate, incubated for 5 minutes at RT, before being added to the cell pellet.

tag: patient id

tag: Sex

value: M

tag: age (years)

tag: disease group

value: LTBI

tag: stimulant


title: WB_TB_PPD_96

source_name: Whole blood from patient with TB disease PPD stimulated

value: TB

value: PPD


title: WB_TB_CFP10-ESAT6_220

source_name: Whole blood from patient with TB disease ESAT6-FP10 stimulated

value: F


title: WB_pneumonia_CFP10-ESAT6_207

source_name: Whole blood from patient with pneumonia ESAT6-FP10 stimulated

value: pneumonia


title: WB_TB_CFP10-ESAT6_96


title: WB_pneumonia_NON_207

source_name: Whole blood from patient with pneumonia unstimulated


title: WB_pneumonia_NON_201


title: WB_TB_PPD_220


title: WB_LTBI_CFP10-ESAT6_216

source_name: Whole blood from patient with TB infection ESAT6-FP10 stimulated


title: WB_TB_CFP10-ESAT6_98


title: WB_pneumonia_PPD_201

source_name: Whole blood from patient with pneumonia PPD stimulated


title: WB_control_PPD_316

source_name: Whole blood from control patient PPD stimulated

value: control


title: WB_TB_NON_96

source_name: Whole blood from patient with TB disease unstimulated


title: WB_TB_NON_98


title: WB_TB_NON_219


title: WB_LTBI_PPD_216

source_name: Whole blood from patient with TB infection PPD stimulated


title: WB_TB_CFP10-ESAT6_219


title: WB_control_NON_312

source_name: Whole blood from control patient unstimulated


title: WB_TB_PPD_219


title: WB_LTBI_PPD_211


title: WB_pneumonia_CFP10-ESAT6_206


title: WB_pneumonia_PPD_207


title: WB_control_PPD_312


title: WB_pneumonia_PPD_206


title: WB_pneumonia_CFP10-ESAT6_201


title: WB_pneumonia_NON_206


title: WB_control_CFP10-ESAT6_312

source_name: Whole blood from control patient ESAT6-FP10 stimulated


title: WB_LTBI_NON_211


title: WB_LTBI_CFP10-ESAT6_211


title: WB_TB_PPD_98


title: WB_pneumonia_NON_203


title: WB_LTBI_PPD_209


title: WB_pneumonia_PPD_208


title: WB_control_CFP10-ESAT6_315


title: WB_LTBI_CFP10-ESAT6_209


title: WB_LTBI_CFP10-ESAT6_210


title: WB_pneumonia_PPD_203


title: WB_pneumonia_CFP10-ESAT6_208


title: WB_pneumonia_CFP10-ESAT6_203


title: WB_LTBI_NON_209


title: WB_control_PPD_315


title: WB_control_NON_315


title: WB_LTBI_PPD_210


title: WB_TB_NON_217


title: WB_pneumonia_NON_204


title: WB_pneumonia_CFP10-ESAT6_204


title: WB_TB_PPD_217


title: WB_LTBI_NON_210


title: WB_LTBI_PPD_215


title: WB_control_PPD_314


title: WB_LTBI_NON_303


title: WB_LTBI_CFP10-ESAT6_215


title: WB_TB_PPD_301


title: WB_control_CFP10-ESAT6_314


title: WB_pneumonia_PPD_204


title: WB_control_NON_314


title: WB_LTBI_NON_215


title: WB_TB_CFP10-ESAT6_217


title: WB_control_PPD_309


title: WB_LTBI_PPD_303


title: WB_TB_NON_301


title: WB_control_CFP10-ESAT6_309


title: WB_control_PPD_313


title: WB_control_CFP10-ESAT6_317


title: WB_control_NON_309


title: WB_TB_CFP10-ESAT6_95


title: WB_control_CFP10-ESAT6_313


title: WB_control_PPD_317


title: WB_control_CFP10-ESAT6_311


title: WB_control_PPD_311


title: WB_TB_NON_95


title: WB_LTBI_CFP10-ESAT6_303


title: WB_control_NON_317


title: WB_LTBI_NON_214


title: WB_control_NON_311


title: WB_LTBI_CFP10-ESAT6_221


title: WB_LTBI_NON_307


title: WB_LTBI_NON_221


title: WB_LTBI_PPD_307


title: WB_control_PPD_308


title: WB_LTBI_PPD_214


title: WB_TB_PPD_95


title: WB_LTBI_CFP10-ESAT6_307


title: WB_LTBI_CFP10-ESAT6_214


title: WB_control_CFP10-ESAT6_308


title: WB_control_NON_313


title: WB_pneumonia_CFP10-ESAT6_200


title: WB_control_NON_308


title: WB_pneumonia_NON_200


title: WB_pneumonia_NON_205


title: WB_pneumonia_PPD_202


title: WB_TB_NON_302


title: WB_pneumonia_NON_202


title: WB_LTBI_NON_212


title: WB_pneumonia_CFP10-ESAT6_202


title: WB_LTBI_PPD_212


title: WB_TB_PPD_302


title: WB_pneumonia_PPD_305


title: WB_LTBI_PPD_221


title: WB_pneumonia_CFP10-ESAT6_305


title: WB_TB_CFP10-ESAT6_302


title: WB_pneumonia_CFP10-ESAT6_205


title: WB_TB_NON_222


title: WB_TB_PPD_222


title: WB_pneumonia_PPD_213


title: WB_TB_CFP10-ESAT6_218


title: WB_pneumonia_CFP10-ESAT6_213


title: WB_LTBI_CFP10-ESAT6_212


title: WB_TB_PPD_218


title: WB_pneumonia_NON_213


title: WB_TB_CFP10-ESAT6_222


title: WB_pneumonia_NON_305


title: WB_control_PPD_310


title: WB_pneumonia_NON_304


title: WB_pneumonia_PPD_304


title: WB_pneumonia_CFP10-ESAT6_304


title: WB_control_NON_310


title: WB_control_CFP10-ESAT6_310


title: WB_LTBI_CFP10-ESAT6_84


title: WB_TB_PPD_20


title: WB_LTBI_NON_44


title: WB_LTBI_NON_22


title: WB_control_CFP10-ESAT6_103


title: WB_LTBI_PPD_51


title: WB_control_CFP10-ESAT6_8


title: WB_LTBI_PPD_84


title: WB_control_CFP10-ESAT6_7


title: WB_LTBI_PPD_86


title: WB_control_PPD_101


title: WB_pneumonia_PPD_76


title: WB_LTBI_NON_25


title: WB_control_CFP10-ESAT6_6


title: WB_pneumonia_CFP10-ESAT6_62


title: WB_LTBI_PPD_65


title: WB_control_PPD_7


title: WB_control_NON_103


title: WB_LTBI_PPD_21


title: WB_TB_CFP10-ESAT6_79


title: WB_control_PPD_107


title: WB_control_CFP10-ESAT6_101


title: WB_pneumonia_PPD_200


title: WB_LTBI_PPD_23


title: WB_LTBI_PPD_89


title: WB_pneumonia_NON_59


title: WB_pneumonia_PPD_59


title: WB_TB_NON_79


title: WB_LTBI_PPD_22


title: WB_control_NON_9


title: WB_TB_CFP10-ESAT6_11


title: WB_pneumonia_PPD_70


title: WB_TB_CFP10-ESAT6_20


title: WB_pneumonia_CFP10-ESAT6_70


title: WB_LTBI_CFP10-ESAT6_55


title: WB_TB_CFP10-ESAT6_36


title: WB_pneumonia_PPD_57


title: WB_pneumonia_NON_75


title: WB_LTBI_NON_65


title: WB_control_PPD_8


title: WB_TB_CFP10-ESAT6_10


title: WB_control_PPD_103


title: WB_pneumonia_NON_69


title: WB_TB_NON_14


title: WB_LTBI_PPD_43


title: WB_control_PPD_2


title: WB_LTBI_NON_12


title: WB_LTBI_CFP10-ESAT6_65


title: WB_pneumonia_NON_74


title: WB_pneumonia_PPD_205


title: WB_TB_CFP10-ESAT6_18


title: WB_pneumonia_CFP10-ESAT6_75


title: WB_TB_PPD_82


title: WB_LTBI_NON_66


title: WB_TB_NON_218


title: WB_control_PPD_104


title: WB_LTBI_CFP10-ESAT6_21


title: WB_LTBI_PPD_90


title: WB_pneumonia_NON_61


title: WB_control_CFP10-ESAT6_1


title: WB_LTBI_NON_26


title: WB_pneumonia_NON_72


title: WB_TB_PPD_33


title: WB_control_NON_8


title: WB_LTBI_NON_84


title: WB_TB_PPD_11


title: WB_control_NON_13


title: WB_LTBI_CFP10-ESAT6_66


title: WB_pneumonia_CFP10-ESAT6_69


title: WB_control_PPD_106


title: WB_LTBI_PPD_19


title: WB_TB_PPD_78


title: WB_TB_PPD_60


title: WB_pneumonia_NON_94


title: WB_LTBI_PPD_25


title: WB_TB_NON_88


title: WB_pneumonia_CFP10-ESAT6_59


title: WB_control_CFP10-ESAT6_104


title: WB_LTBI_CFP10-ESAT6_90


title: WB_pneumonia_CFP10-ESAT6_76


title: WB_TB_CFP10-ESAT6_82


title: WB_pneumonia_PPD_94


title: WB_pneumonia_PPD_69


title: WB_control_NON_4


title: WB_TB_CFP10-ESAT6_33


title: WB_TB_NON_20


title: WB_control_PPD_102


title: WB_LTBI_NON_43


title: WB_LTBI_CFP10-ESAT6_26


title: WB_TB_CFP10-ESAT6_60


title: WB_control_NON_1


title: WB_pneumonia_PPD_62


title: WB_TB_NON_60


title: WB_pneumonia_PPD_74


title: WB_LTBI_CFP10-ESAT6_25


title: WB_pneumonia_NON_70


title: WB_LTBI_CFP10-ESAT6_19


title: WB_LTBI_CFP10-ESAT6_86


title: WB_pneumonia_PPD_71


title: WB_pneumonia_NON_76


title: WB_pneumonia_NON_57


title: WB_TB_PPD_54


title: WB_control_NON_101


title: WB_control_NON_6


title: WB_TB_NON_36


title: WB_TB_CFP10-ESAT6_14


title: WB_LTBI_CFP10-ESAT6_23


title: WB_control_NON_104


title: WB_TB_PPD_14


title: WB_pneumonia_CFP10-ESAT6_74


title: WB_control_CFP10-ESAT6_102


title: WB_control_PPD_9


title: WB_LTBI_NON_90


title: WB_TB_PPD_10


title: WB_pneumonia_NON_71


title: WB_pneumonia_PPD_72


title: WB_TB_PPD_79


title: WB_control_PPD_12


title: WB_LTBI_CFP10-ESAT6_44


title: WB_TB_NON_82


title: WB_pneumonia_CFP10-ESAT6_94


title: WB_TB_PPD_36


title: WB_control_NON_2


title: WB_TB_PPD_13


title: WB_TB_NON_78


title: WB_pneumonia_CFP10-ESAT6_63


title: WB_control_CFP10-ESAT6_106


title: WB_control_CFP10-ESAT6_107


title: WB_pneumonia_NON_62


title: WB_control_NON_106


title: WB_LTBI_CFP10-ESAT6_51


title: WB_control_PPD_1


title: WB_TB_CFP10-ESAT6_78


title: WB_LTBI_PPD_26


title: WB_LTBI_PPD_66


title: WB_pneumonia_CFP10-ESAT6_72


title: WB_control_PPD_13


title: WB_LTBI_NON_21


title: WB_control_PPD_4


title: WB_LTBI_CFP10-ESAT6_22


title: WB_pneumonia_PPD_75


title: WB_TB_PPD_18


title: WB_LTBI_NON_89


title: WB_pneumonia_CFP10-ESAT6_61


title: WB_TB_NON_10


title: WB_LTBI_PPD_44


title: WB_control_NON_102


title: P53ERTAM, Combo, rep3

city: houston

first: Longyong

last: Xu

state: TX

address: SCRB4, 1901 East Road

department: ET

institute: University of Texas MD Anderson Cancer Center

data_processing:
Raw reads were quality-checked using FastQC, and adapter sequences were trimmed with fastp. High-quality reads were aligned to the reference genome GRCm38.p5 (GENCODE Release M15) using STAR aligner. Gene expression quantification was performed using featureCounts.
Assembly: GRCm38.p5 (GENCODE Release M15)
Supplementary files format and content: tsv for count

source_name: Breast

growth_protocol: 2153L GEM tumor transplated into the mammary fat pad of female Balbc mice

extract_protocol:
RNA from bulk tumors was extract using Direct-zol RNA Microprep Kit (ZYMO Research, Cat# R2060).
Libraries were made using Illumina Stranded Total RNA Prep with Ribo-Zero Kit (Illumina, 20040525) following Illumina’s recommended protocol

treatment_protocol: tumors were treated with vehicle or combo (ORIN1001, 150 mg/kg; docetaxel 20 mg/kg)

tag: tissue

value: Breast

value: 2153L GEM tumor

tag: cell type

value: TNBC

tag: genotype

value: Combo


title: WB_LTBI_NON_86


title: P53ERTAM, Combo, rep2

tag: cell line

tag: treatment


title: P53ERTAM, Vehicle, rep3

value: Vehicle


title: EV, Combo, rep3

value: empty vector


title: P53ERTAM, Vehicle, rep2


title: P53ERTAM, Combo, rep1


title: EV, Combo, rep2


title: P53ERTAM, Vehicle, rep1


title: EV, Vehicle, rep3


title: WB_TB_PPD_88


title: WB_control_NON_107


title: WB_control_PPD_6


title: EV, Combo, rep1


title: EV, Vehicle, rep2


title: WB_pneumonia_PPD_63


title: WB_LTBI_PPD_12


title: WB_pneumonia_CFP10-ESAT6_71


title: WB_control_NON_7


title: WB_pneumonia_NON_63


title: WB_LTBI_CFP10-ESAT6_89


title: WB_LTBI_NON_19


title: WB_pneumonia_PPD_61


title: EV, Vehicle, rep1


title: WB_TB_NON_18


title: WB_TB_CFP10-ESAT6_88


title: BT549 in AAVS 3

type: genomic

city: Clayton

first: Laura

last: Perlaza-Jimenez

state: Victoria

address: 15 Innovation Walk

institute: Monash University

description: BT549 in AAVS 3

hyb_protocol: All samples wer ebisulfite converted and hybridised to the EPIC beadchip using the manufacturer's standard protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Quantile normalisation was performed before beta value quantification

label: Cy3, Cy5

source_name: Cell line

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted using DNeasy Blood and Tissue Kit (Qiagen, catalogue no. 69504) according to manufacturer’s instructions.

tag: tag

value: Female


title: WB_TB_PPD_38


title: MCF7 in AAVS 3

description: MCF7 in AAVS 3


title: MCF7 3A mock 3

description: MCF7 3A mock 3


title: BT549 in mock 3

description: BT549 in mock 3


title: BT549 3A mock 3

description: BT549 3A mock 3


title: MCF7 3A AAVS 3

description: MCF7 3A AAVS 3


title: BT549 3A AAVS 1

description: BT549 3A AAVS 1


title: MCF7 in mock 1

description: MCF7 in mock 1


title: BT549 in AAVS 2

description: BT549 in AAVS 2


title: BT549 3A AAVS 2

description: BT549 3A AAVS 2


title: MCF7 3A AAVS 1

description: MCF7 3A AAVS 1


title: MCF7 in AAVS 2

description: MCF7 in AAVS 2


title: BT549 3A mock 1

description: BT549 3A mock 1


title: MCF7 in AAVS 1

description: MCF7 in AAVS 1


title: BT549 in mock 2

description: BT549 in mock 2


title: BT549 in AAVS 1

description: BT549 in AAVS 1


title: MCF7 3A AAVS 2

description: MCF7 3A AAVS 2


title: MCF7 in mock 2

description: MCF7 in mock 2


title: T47D_SAM-DNMT3A-inactive_Nosg

label: cy3, cy5

tag: source gender

value: expressing inctive DNMT3A


title: BT549 in mock 1

description: BT549 in mock 1


title: MCF7 3A mock 1

description: MCF7 3A mock 1


title: BT549 3A mock 2

description: BT549 3A mock 2


title: MCF7 3A mock 2

description: MCF7 3A mock 2


title: T47D_SAM-DNMT3A-inactive_cg23214464


title: T47D_SAM-DNMT3A-inactive_cg02613435


title: IBD_246852, colon

city: Chapel Hill

first: Terrence

last: Furey

state: NC

address: 120 Mason Farm Rd

institute: University of North Carolina at Chapel Hill

description: IBD tissue

data_processing:
STAR v2.7.9a using --WaspOutputMode
Read counts quantified using QTLtools v1.3.1
Read counts were normalized using edgeR TMM and rank inverse normal transformed using R v4.1.3
Assembly: hg38, GENCODE v39
Supplementary files format and content: tab-delimited text file includes normalized count data for each sample
Supplementary files format and content: tab-delimited text file includes eQTL covariates for each sample

source_name: colon

extract_protocol:
Tissue was digested with TRIzol and RNA was extracted using chloroform. RNA was isolated using Norgen Biotek Total RNA Isolation Plus Kit (cat#48400).
Libraries were constructed using the Kapa Total RNA Stranded with Ribo Erase.

value: colon

tag: disease

value: IBD

tag: gender

value: Male

tag: batch

value: N


title: T47D_SAM-DNMT3A-inactive_sgAAVS118c


title: NCC_CDS1_X1_C1, control, rep2

first: Ross

last: Okimoto

address: 513 Parnassus Ave

institute: University of California, San Francisco

description: Column name in processed data: X1_control_2

data_processing:
FASTQ files were aligned to GRCh38 using STAR (version 2.7.10b).
Gene counts were extracted during alignment using STAR parameter --quantMode GeneCounts
Differental expression analysis was performed in R (version 4.2.2) with edgeR (version 3.40.2).
Log2(cpm) data were obtained from TMM-normalized data using edgeR with the cpm function (log = T) which with this version of edgeR adds an average prior count of 2.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file, STAR gene counts for all samples, data taken from column 2 of STAR output due to the unstranded nature of the library prep kit used. File name = gene_counts.txt
Supplementary files format and content: Tab-delimited text file, log2(counts per million) measurements for all samples after edgeR processing. File name = log2cpm.txt.

source_name: cell line

growth_protocol: NCC_CDS1_X1_C1 and NCC_CDS2_C1, patient-derived cell lines were grown in RPMI 1640 medium with 10% FBS. All cell lines were maintained at 37°C in a humidified atmosphere with 5% CO2.

extract_protocol:
RNA was extracted using the RNeasy Mini kit (Qiagen) and analyzed for integrity with a TapeStation (Agilent)
PolyA-enriched, unstranded libraries were prepared using the NEBNext Ultra II RNA Library Prep for Illumina kit. Libraries were PE150 sequenced on a Novaseq 6000 (Illumina).

treatment_protocol: Cells were transfected with RNA interference (RNAi) to silence POLE or ON-TARGET plus Non-Targeting Pool control in NCC_CDS2_C1 and NCC-CDS1_X1_C1 patient-derived sarcoma cells

value: cell line

value: CIC::DUX4+ patient derived

value: non-targeting siRNA


title: NCC_CDS1_X1_C1, control, rep1

description: Column name in processed data: X1_control_1


title: IBD_702815, colon

description: IBD tissue


title: IBD_358704, colon

description: IBD tissue


title: IBD_788288, colon

description: IBD tissue


title: IBD_102697, colon

description: IBD tissue


title: IBD_831558, colon

description: IBD tissue


title: IBD_938617, colon

description: IBD tissue


title: IBD_555726, colon

description: IBD tissue


title: T47D_SAM-DNMT3A-inactive_cg02100397


title: IBD_368166, colon

description: IBD tissue


title: IBD_725949, colon

description: IBD tissue


title: NCC_CDS1_X1_C1, siPOLE, rep1

description: Column name in processed data: X1_siPOLE_1

value: POLE-targeting siRNA


title: IBD_596319, colon

description: IBD tissue


title: IBD_155116, colon

description: IBD tissue


title: IBD_232667, colon

description: IBD tissue


title: IBD_472341, colon

description: IBD tissue


title: BT549 3A AAVS 3

description: BT549 3A AAVS 3


title: BRE80-T5_SAM-DNMT3A-inactive_cg02100397


title: IBD_400071, colon

description: IBD tissue


title: IBD_644739, colon

description: IBD tissue


title: IBD_923402, colon

description: IBD tissue


title: BRE80-T5_SAM-DNMT3A-inactive_cg02613435


title: IBD_185264, colon

description: IBD tissue


title: BRE80-T5_SAM-DNMT3A-inactive_Nosg


title: IBD_867142, colon

description: IBD tissue


title: IBD_613384, colon

description: IBD tissue


title: IBD_965451, colon

description: IBD tissue


title: IBD_509388, colon

description: IBD tissue


title: NCC_CDS1_X1_C1, siPOLE, rep2

description: Column name in processed data: X1_siPOLE_2


title: IBD_449147, colon

description: IBD tissue


title: T47D_SAM-DNMT3A_cg02100397

value: expressing active DNMT3A


title: IBD_634096, colon

description: IBD tissue

value: R


title: IBD_875477, colon

description: IBD tissue


title: T47D_SAM-DNMT3A_sgAAVS118c


title: IBD_221429, colon

description: IBD tissue


title: IBD_579383, colon

description: IBD tissue


title: BRE80-T5_SAM-DNMT3A-inactive_sgAAVS118c


title: BRE80-T5_SAM-DNMT3A-inactive_cg26469782


title: T47D_SAM-DNMT3A_Nosg


title: IBD_318496, colon

description: IBD tissue


title: IBD_592581, colon

description: IBD tissue


title: T47D_SAM-DNMT3A_cg02613435


title: BRE80-T5_SAM-DNMT3A_Nosg


title: MCF7 in mock 3

description: MCF7 in mock 3


title: IBD_385702, colon

description: IBD tissue


title: IBD_421299, colon

description: IBD tissue


title: T47D_SAM-DNMT3A-inactive_cg26469782


title: IBD_375530, colon

description: IBD tissue


title: IBD_973356, colon

description: IBD tissue


title: IBD_219838, colon

description: IBD tissue


title: IBD_470192, colon

description: IBD tissue


title: IBD_284657, colon

description: IBD tissue


title: IBD_159880, colon

description: IBD tissue


title: BRE80-T5_SAM-DNMT3A_cg23214464


title: IBD_393866, colon

description: IBD tissue


title: IBD_419013, colon

description: IBD tissue


title: T47D_SAM-DNMT3A_cg23214464


title: IBD_940680, colon

description: IBD tissue


title: BRE80-T5_SAM-DNMT3A-inactive_cg23214464


title: IBD_187832, colon

description: IBD tissue


title: BRE80-T5_SAM-DNMT3A_cg26469782


title: IBD_547284, colon

description: IBD tissue


title: IBD_554161, colon

description: IBD tissue


title: IBD_978722, colon

description: IBD tissue


title: IBD_950110, colon

description: IBD tissue


title: IBD_319421, colon

description: IBD tissue


title: IBD_432797, colon

description: IBD tissue


title: IBD_842051, colon

description: IBD tissue


title: IBD_387660, colon

description: IBD tissue


title: IBD_594973, colon

description: IBD tissue


title: IBD_905198, colon

description: IBD tissue


title: IBD_949827, colon

description: IBD tissue


title: BRE80-T5_SAM-DNMT3A_cg02100397


title: IBD_460669, colon

description: IBD tissue


title: IBD_111729, colon

description: IBD tissue


title: IBD_979280, colon

description: IBD tissue


title: IBD_221271, colon

description: IBD tissue


title: BRE80-T5_SAM-DNMT3A_cg02613435


title: IBD_327229, colon

description: IBD tissue


title: IBD_346417, colon

description: IBD tissue


title: IBD_880917, colon

description: IBD tissue


title: IBD_148655, colon

description: IBD tissue


title: IBD_588420, colon

description: IBD tissue


title: IBD_896949, colon

description: IBD tissue


title: IBD_899758, colon

description: IBD tissue


title: BRE80-T5_SAM-DNMT3A_sgAAVS118c


title: IBD_685264, colon

description: IBD tissue


title: IBD_932803, colon

description: IBD tissue


title: IBD_171087, colon

description: IBD tissue


title: IBD_140112, colon

description: IBD tissue


title: IBD_913124, colon

description: IBD tissue


title: IBD_783304, colon

description: IBD tissue


title: IBD_664906, colon

description: IBD tissue


title: IBD_650338, colon

description: IBD tissue


title: IBD_679255, colon

description: IBD tissue


title: IBD_595632, colon

description: IBD tissue


title: IBD_118451, colon

description: IBD tissue


title: IBD_463156, colon

description: IBD tissue


title: IBD_307232, colon

description: IBD tissue


title: IBD_265155, colon

description: IBD tissue


title: IBD_827856, colon

description: IBD tissue


title: IBD_607036, colon

description: IBD tissue


title: IBD_548801, colon

description: IBD tissue


title: T47D_SAM-DNMT3A_cg26469782


title: IBD_303678, colon

description: IBD tissue


title: IBD_727218, colon

description: IBD tissue


title: IBD_698752, colon

description: IBD tissue


title: IBD_626267, colon

description: IBD tissue


title: IBD_325497, colon

description: IBD tissue


title: IBD_852582, colon

description: IBD tissue


title: Overexpression of ZNF207 in MDA-MB-453 cells rep3

city: Shenyang

first: Huanyu

last: Wu

state: Liaoning

address: No. 77 Puhe Road

department: Pathology Teaching and Research Office of Basic Medical College

institute: China Medical University

data_processing:
Data filtering The sequencing data was filtered with SOAPnuke  by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com).
RNA identification Bowtie2 was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included.
Gene Quantification Differential Expression Analysis Expression level of gene was calculated by RSEM (v1.3.1) . The heatmap was drawn by pheatmap (v1.0.8)  according to the gene expression difference in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5)  (or DEGseq or PoissonDis)with Q value ≤ 0.05 (or FDR ≤ 0.001).
Gene Annotation To take insight to the change of phenotype, GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expression gene was performed by Phyper based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05) .
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
1. Experimental Procedures 1.1 Sample Lysis 1.1.1 Transfer appropriate tissue sample into corresponding tissue grinding tube (tissue≤30 mg, cell≤1×107). 1.1.2 Add 600 μL Buffer RLT Plus. Homogenize the lysate for using a rotor–stator homogenizer, stay at room temperature for 5 min. 1.1.3 Centrifuge at 12,000×g for 3 min in room temperature, transfer the supernatant to AllPrep DNA spin column. 1.1.4 Centrifuge 12,000×g for 30 s in room temperature, transfer the solution from the collection tube for the RNA purification. 1.1.5 Transfer the DNA spin column to the new collection tube for DNA purification. 1.2 DNA Purification 1.2.1 Add 500μL Buffer AW1 to AllPrep DNA spin column, centrifuge at 10,000×g for 30 s and discard the filtrate. 1.2.2 Add 500μL Buffer AW2 to AllPrep DNA spin column, centrifuge at 10,000×g for 30 s and discard the filtrate. 1.2.3 Centrifuge at 16,000×g for 2 min, transfer the AllPrep DNA spin column to 1.5mL centrifuge tube. 1.2.4 Add 50μL Buffer EB to AllPrep DNA spin column, stay at room temperature for 1 min. 1.2.5 Centrifuge at 16,000×g for 2 min and collect the DNA. 1.3 RNA Purification 1.3.1 Add the equal volume of 70% ethanol to the collection tube, mix by pipetting. 1.3.2 Transfer 700 μL mixed solution, to a RNeasy spin column placed in a 2 mL collection tube. 2.3.3 Centrifuge at 10,000×g for 30 s and allow it to empty by gravity flow. 1.3.4 Add 700 μL Buffer RW1 to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate. 1.3.5 Add 500 μL Buffer RPE to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate. 1.3.6 Add 500 μL Buffer RPE to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate. 1.3.7 Centrifuge at 16,000×g for 2 min and transfer the RNeasy spin column to the 1.5 mL centrifuge tube. 1.3.8 Add 35 μL RNase-free water to RNeasy spin column. Stay at room temperature for 1min. 1.3.9 Centrifuge at 16,000×g for 2 min at room temperature to collect RNA.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase, which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I, RNase H and dUTP Solution. An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

value: Overexpression of ZNF207


title: IBD_978559, colon

description: IBD tissue


title: IBD_487339, colon

description: IBD tissue


title: IBD_409005, colon

description: IBD tissue


title: IBD_230729, colon

description: IBD tissue


title: Overexpression of ZNF207 in MDA-MB-453 cells rep1


title: Control rep3

value: Control


title: IBD_248736, colon

description: IBD tissue


title: IBD_832506, colon

description: IBD tissue


title: IBD_123257, colon

description: IBD tissue


title: Overexpression of ZNF207 in MDA-MB-453 cells rep2


title: IBD_779104, colon

description: IBD tissue


title: Control rep1


title: D100_1208-2_hMeO_8

city: STANFORD

first: Yuki

last: Miura

state: California

address: 318 Campus Drive, W200

department: Department of Psychiatry and Behavioral Sciences

institute: Stanford University

description: 10x Genomics

data_processing:
Quality control, UMI counting of Ensembl genes and aggregation of samples were performed by the ‘count’ and ‘aggr’ functions in Cell Ranger software (version, Cellranger-6.0.1).
Assembly: Human: GRCh38
Supplementary files format and content: Count matrices, barcodes, and features

source_name: hiPS cell-deerived regionalized organoids

extract_protocol:
Four to five organoids from each condition were pooled at indicated day, incubated in 30 U/mL papain enzyme solution (Worthington Biochemical, LS003126) and 0.4% DNase (12,500 U/mL, Worthington Biochemical, LS2007) at 37 °C for 45 minutes. After enzymatic dissociation, spheres were washed with a solution including protease inhibitor and gently triturated to achieve a single cell suspension. Cells were resuspended in 0.04% BSA/PBS (Millipore-Sigma, B6917-25MG) and filtered through a 70 μm Flowmi Cell Strainer (Bel-Art, H13680-0070), and number of cells were counted.
To target 7,000 cells after recovery, approximately 11,600 cells were loaded per lane on a Chromium Single Cell 3′chip (Chromium Next GEM Chip G Single Cell Kit, 10x Genomics, PN-1000127) and cDNA libraries were generated with the Chromium Next GEM Single Cell 3ʹ GEM, Library & Gel Bead Kit v3.1 (10x Genomics, PN-1000128), according to the manufacturer’s instructions. Each library was sequenced using the Illumina NovaSeq S4 2 × 150 bp by Admera Health.

value: mesencephalic

tag: differentiation age_(days)

value: Day 100


title: D100_1208-2_hStrO_5

description: 10x Genomics

value: hiPS cell-deerived regionalized organoids

value: striatal


title: D100_1205-4_hDiO_10

description: 10x Genomics

value: diencephalic organoids


title: D100_1205-4_hMeO_9

description: 10x Genomics


title: D100_1208-2_hDiO_11

description: 10x Genomics


title: D100_1205-4_hMeO_7

description: 10x Genomics


title: D100_1205-4_hStrO_4

description: 10x Genomics


title: D100_1205-4_hDiO_12

description: 10x Genomics


title: D100_1205-4_hCO_2

description: 10x Genomics

value: cortical


title: D100_1205-4_hStrO_6

description: 10x Genomics


title: D113_1208-2_hCO_1

description: 10x Genomics

value: Day 113


title: Microrod, Day 5

city: Auburn University

first: Elizabeth

last: Lipke

state: AL

address: 212 Ross Hall

institute: Auburn University

description: hiPSC-laden microrod underwent 3D cardiac differentiation and were collected on day 5 of differentiation.

data_processing:
Partek Genomics Suite
Read count extraction were performed from raw data using Partek Flow
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw gene expression counts in Samples

source_name: 3D in vitro Engineered Cardiac Tissue

growth_protocol: Un-Arc 16 Facs II  were cultured on Geltrex (Gibco)-coated T-25 flasks in Essential E8 medium. Briefly, hiPSCs were passaged every three days using Accutase (Innovative Cell Technologies). Following passaging, hiPSCs were maintained in E8 medium supplemented with ROCK inhibitor (5-10 μM, Y 27632, Stem Cell Technologies) for 24 hours. Scaffold-free self-aggregates (referred to as 'aggregates') were generated by culturing hiPSCs in either a shaker flask or a well plate. To initiate aggregate formation, hiPSCs were detached from a tissue culture flask using Accutase (Innovative Cell Technologies), and the resulting cell pellet was suspended in E8 medium supplemented with 10 µM RI. This cell suspension was then placed on an orbital shaker plate (Infors) at 70 rpm on day -3. Daily media changes were carried out using fresh E8 medium leading up to the commencement of cardiac differentiation. Cardiac differentiation for both microspheres (MS) and microrod (MR) and self-aggregates (Agg) was initiated on day 0 following a well-established protocol. In the shaker flask platform, 3 million hiPSCs were seeded, and the number of cells on day 0 was used for differentiation without adjusting the cell density, i.e. cells per volume of media. The well plate platform was similar in that the number of cells on day 0 was used for differentiation without any adjustments prior to initiation of differentiation with chemically defined medium containing three components (CDM3) [51] supplemented with CHIR99021 (Stem Cell Technologies). For the F/P platform, 3 million cells were seeded in the shaker flask and on day 0, the cells were collected, a sample was counted, and the remaining aggregate were distributed to provide 0.5 million hiPSCs mL-1 cell density on day 0 and provide a similar microenvironment as the microspheres. The number of cells on day 0 was counted by dissociating the microspheres, and for the cell density in each well of a 6-well plate was set at 0.5 million hiPSCs mL-1 CDM3 before starting the differentiation. E8 medium was replaced with CDM3 medium supplemented with 5 µM CHIR99021 for the Un-Arc 16 Facs II cell line, and the well plate was placed on the shaker plate (Infors) on day 0. Precisely 24 hours later (day 1), the medium was replaced with a CDM3 medium, which was supplemented with 5 µM IWP2 (Stem Cell Technologies). After 48 hours (day 3), the media was replaced with 4 mL of fresh CDM3. The medium was changed every other day until day 7 and replaced with RPMI/B27 containing insulin (Invitrogen) on day 10. For long-term culturing, the media was changed every three days with RPMI/B27 containing insulin.

extract_protocol:
High-quality RNA was isolated using QIAshredder columns and RNeasy kit (Qiagen)
An RNA integrity number (RIN) threshold of 8 was applied and RNA-seq libraries were constructed using Illumina TruSeq RNA sample Preparation kit v2
Total RNA sequencing (150 bp PE, 40 million reads per sample).

value: 3D in vitro Engineered Cardiac Tissue

value: Un-Arc 16 Facs II

value: hiPSC derived cardiomyocyte (hiPSC-CM)


title: Aggregate, Day 15

description: Scaffold-free hiPSC aggergate underwent 3D cardiac differentiation and were collected on day 15 of differentiation.


title: D128_1205-4_hCO_3

description: 10x Genomics

value: Day 128


title: Microrod, Day 15

description: hiPSC-laden microrod underwent 3D cardiac differentiation and were collected on day 15 of differentiation.


title: MOLM-13 cells Vector

city: Jinan

first: bo

middle: lan

last: li

address: Wenhua West Road

institute: Qilu Hospital of Shandong University

data_processing:
Basecalls were performed using bcl2fastq v2.19 for Novaseq output.
mRNA-seq reads were trimmed from 3' end until the final base had a quality score > 20, using seqtk v1.0-r82-dirty, discarding reads left with < 25 bp
Trimmed sequence reads were mapped to GRCh38 using Hisat2(version:2.0.4)
The number of Fragments of each gene after Hisat2 comparison was counted by Stringtie (version:1.3.0), and then normalized by the original mean of M Values (TMM) method. Finally, the FPKM value of each gene was calculated by Perl script.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include count values for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

growth_protocol: MOLM-13 cells were maintained in 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37°C

extract_protocol:
Total RNA was extracted by customer following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent 4200 Bioanalyzer (Agilent technologies, Santa Clara, CA, US).Qualified total RNA by Qubit 2.0(Thermo Fisher Scientific)
According to the instructions of the experiment, the purified Total RNA was separated into mRNA, fragmented, first-strand cDNA synthesis, second-strand cDNA synthesis, end repair, adding A to the 3 'end, ligating connector, enrichment and other steps to complete the construction of sequencing sample library.

value: Human Acute Myeloid Leukemia Cell

value: Vector (OE-Control)


title: Aggregate, Day 5

description: Scaffold-free hiPSC aggergate underwent 3D cardiac differentiation and were collected on day 5 of differentiation.


title: Control rep2


title: Microsphere, Day 5

description: hiPSC-laden microspheres underwent 3D cardiac differentiation and were collected on day 5 of differentiation.


title: COH-110-C1D1 (Basline)

city: Duarte

first: Shiuan

last: Chen

address: 1500 E Duarte Rd

department: Cancer Biology-BRI

institute: City of Hope National Medical Center

description:
mRNA_GEX
55898

data_processing:
Raw sequencing data were processed using the 10x Genomics Cell Ranger pipeline to generate FASTQ files
Sequences were aligned to GRCh38 genome to gene expression count using CellRanger's default settings
Gene expression level of GENCODE coding genes were quantified using CellRanger's default settings
Assembly: GRCh38
Supplementary files format and content: text files containing the raw gene expression count

source_name: peripheral whole blood

extract_protocol:
Leukocyte cells were isolated from whole blood sample by using red cell  lysis buffer (10x Genomics protocoal CG000392)
Next GEM 10X Genomics 3’ V3.1 was used for single cell gene expression sequencing library preperation

treatment_protocol: Paired whole blood samples of four patients from timepoint of baseline vs. 3 months treatment were collected and processed based single immune cell profiling protocol.

value: peripheral whole blood

value: leukocytes

value: 6 months of white button mushroom consumption in freeze-dried tablet form


title: COH-108-C2D1 (3-month)

description:
mRNA_GEX
57108


title: COH-108-C1D1 (Baseline)

description:
mRNA_GEX
55888


title: COH-096-C2D1 (3-month)

description:
mRNA_GEX
55595


title: COH-110-C2D1 (3-month)

description:
mRNA_GEX
57080


title: COH-094-C2D1 (3-month)

description:
mRNA_GEX
55374


title: COH-096-C1D1 (Baseline)

description:
mRNA_GEX
54303


title: COH-094-C1D1 (Baseline)

description:
mRNA_GEX
53980


title: T47D 796 G2

city: Memphis

first: Daniel

middle: Lee

last: Johnson

state: Tennessee

address: 71 S Manassas

department: Molecular Informatics Core

institute: UTHSC

data_processing:
Data was aligned using hg38 and STAR 2.0
Counts were extracted using cellRanger
Assembly: hg38
Supplementary files format and content: raw count table

source_name: T47D cell line xenograft

extract_protocol:
Single nuclei were isolated and  sequenced
10x genomics

value: T47D cell line xenograft

value: breast cancer

value: DHT


title: T47D 778 G4

value: Enobosarm


title: T47D 780 G4R

value: Enobosarm Resistant


title: WHIM23 713 G2


title: WHIM23 723 G4


title: T47D 788 G1

value: Vehicle


title: IBD_916688, colon

description: IBD tissue

value: colon

value: IBD

value: Male

value: N


title: WHIM23 703 G1


title: WHIM23_G4R_3

data_processing:
Data was aligned using hg38 and STAR 2.0
Counts were normalized using CPM
Assembly: hg38
Supplementary files format and content: Raw counts

source_name: WHIM23 patient-derived xenograft

extract_protocol:
RNA was extracted using Rneasy plus kit (Qiagen). 1.5ug of RNA was used for the construction of sequencing libraries.
Illumina stranded RNA

value: WHIM23 patient-derived xenograft

value: WHIM23 PDX


title: WHIM23_G4R_2


title: WHIM23_G4_3


title: WHIM23_G4R_1


title: Microsphere, Day 15

description: hiPSC-laden microspheres underwent 3D cardiac differentiation and were collected on day 15 of differentiation.

value: 3D in vitro Engineered Cardiac Tissue

value: Un-Arc 16 Facs II

value: hiPSC derived cardiomyocyte (hiPSC-CM)


title: WHIM23_G2_3


title: WHIM23_G4_4


title: WHIM23_G2_2


title: WHIM23_G2_4


title: WHIM23_G4_2


title: WHIM23_G4_1


title: WHIM23_G2_1


title: T47D_G4R_3


title: WHIM23_G1_3


title: WHIM23_G1_4


title: WHIM2323_G1_1


title: WHIM23_G1_2


title: T47D_G4_4


title: T47D_G4R_1


title: T47D_G4_3


title: T47D_G2_4


title: T47D_G4_2


title: T47D_G4_1


title: T47D_G1_4


title: T47D_G1_3


title: T47D_G2_2


title: T47D_G2_3


title: T47D_G1_1


title: HBRT-1127-AR-low

data_processing:
Data was aligned using hg38 and STAR 2.0
Counts were normalized using CPM
Assembly: hg38
Supplementary files format and content: raw counts

source_name: breast

extract_protocol:
RNA was extracted using Rneasy plus kit (Qiagen). 1.5ug of RNA was used for the construction of sequencing libraries.
Platform is  GeoMx TAP NGS WTA
Illumina TruSeq RNA

value: breast


title: T47D_G1_2


title: T47D_G2_1


title: HBRT-1076-AR-low


title: DOD-0006-AR-low


title: DOD-0006-AR-high


title: HBRT-1224-AR-low


title: T47D_G4R_2


title: HBRT-1408-AR-low


title: HBRT-1093-AR-high


title: HBRT-1408-AR-high


title: HBRT-1224-AR-high


title: TT45RO_HU24

city: Erlangen

first: Krystelle

last: Nganou-Makamdop

address: Schlossgarten 4

department: Virology institute

institute: Universitätsklinikum Erlangen

data_processing:
Raw reads were trimmed for low-quality reads and miscalled nucleotides using Trimmomatic v. 0.36.
Reads that passed the trimming step were aligned to the human genome (Ensembl GRCh38 release 88) using the STAR aligner (version 2.5.3a).
Aligned reads were counted using HTSeq (version 0.9.1).
Read count files were merged and genes with mean of < 1 read per sample were excluded.
The expression and differential expression values were generated using DESeq2 in R
Assembly: hg38
Supplementary files format and content: excel file includes raw counts for each sample

source_name: Blood

growth_protocol: PBMC were stimulated with measles or tetanus antigens, or either left untreated and incubated at 37C 5% CO2.

extract_protocol:
RNA was extracted from sorted cells lysed in RNAzol RT (Molecular Research Center), according to the manufacturer’s instructions. Briefly, 0.4 volume of sterile water was added to each lysate to allow aqueous and organic phase separation. Total RNA was then extracted from the aqueous phase by isopropanol precipitation. RNA pellets were washed with 70% ethanol and resuspended in sterile water. Extracted RNA was stored at −80°C until preparation of mRNA libraries.
Messenger RNA libraries were constructed as described previously using the NEBNext Ultra RNA library preparation kit (New England Biolabs). Polyadenylated transcripts were purified with oligo-dT magnetic beads, fragmented, reverse transcribed using random hexamers and incorporated into barcoded cDNA libraries. Libraries were validated by microelectrophoresis on a tapestation 4200 (Agilent), quantified with Kapa Library Quantification Kits (Roche), pooled and clustered on an Illumina S2 flow cell. Clustered flow cells were sequenced in 2x75 base paired-end runs.

treatment_protocol: 2 x 106 cells per well were seeded in R10 medium containing CD28/CD49d (BD; 1µg/ml each) with either SEB (0.25 ug/ml), TT protein (Tetanol, GSK—0.5 I.E), a MV 20-mer overlapping peptide pool corresponding to the measles virus hemagglutinin and fusion proteins (EMC, 2.5µg/ml) or left unstimulated. After 24 hours incubation at 37C in presence of 2nM monensin and CD154-PE (BD, clone TRAP), cells were stained for sort of T cell subsets.

value: Blood

tag: disease state

value: HIV seronegative

value: CD4 T cells

value: tetanus toxoid antigen


title: TT45RO_HU25


title: TT45RO_HU20


title: TT45RO_HU22


title: TT45RO_HU23


title: TT45RO_HU18


title: TT45RO_HU19


title: TT45RO_HU17


title: TT45RO_HU15


title: TT45RO_HU13


title: MOLM-13 cells OE -UNC5B

value: Human Acute Myeloid Leukemia Cell

value: Over-expression UNC5B


title: HBRT-1127-AR-high

value: breast cancer


title: HBRT-1093-AR-low


title: TT45RO_HU09


title: TT45RO_HU04


title: TT45RO_HU06


title: TT45RO_HU03


title: TT45RO_HIV20

value: HIV seropositive


title: TT45RO_HIV23


title: TT45RO_HIV19


title: TT45RO_HIV18


title: TT45RO_HIV11


title: TT45RO_HIV12


title: HBRT-1076-AR-high


title: TT45RO_HIV10


title: TT45RO_HIV100


title: TT45RO_HIV09


title: TT45RO_HIV07


title: TT45RO_HIV06


title: TT45RO_HU12


title: TT45RO_HIV02


title: TT45RO_HIV08


title: TT45RO_HIV01


title: TT154_HU25


title: TT45RO_HU10


title: TT45RO_HIV24


title: TT154_HU23


title: TT45RO_HU21


title: TT154_HU22


title: TT154_HU21


title: TT154_HU19


title: TT154_HU24


title: TT154_HU13


title: TT154_HU18


title: TT154_HU17


title: TT154_HU10


title: TT45RO_HIV05


title: TT45RO_HIV04


title: TT154_HU06


title: WHIM23 737 G4R

value: T47D cell line xenograft

value: Enobosarm Resistant


title: TT154_HU02


title: TT154_HU20


title: parthenote2 BiSulfite-seq

city: Columbus

first: Jinsoo

last: Ahn

address: 2029 Fyffe Rd

institute: Ohio State Univesity

data_processing:
The raw WGBS reads were trimmed and filtered, using the default parameters of Trim Galore (v0.12.1).
The resulting cleaned reads were mapped to the pig reference genome (Sscrofa11.1/susScr11) using the Bismark aligner (v0.22.3) with default parameters.
Deduplication was performed with deduplicate_bismark and methylation percentages for cytosines in CpGs were determined using bismark_methylation_extractor.
Assembly: susScr11
Supplementary files format and content: methylation ratios in bedGraph format

organism: Sus scrofa

source_name: whole embryo

growth_protocol: After electric stimulation of oocytes followed by 2 h of stabilization period, parthenogenetic embryos were placed into oviducts of each of the two surrogate gilts aged 12 months at onset of estrus to produce developed parthenogenetic embryos.

extract_protocol:
From the whole collected embryos of CN and PA, genomic DNA was isolated and fragmented.
For optimization of bisulfite conversion of genomic DNA, Accel-NGS Methyl-Seq DNA Library Kit (Swift Biosciences, Inc. Ann Arbor, MI, USA) was used according to the manufacturer`s instructions.

treatment_protocol: In a fusion chamber with 250 µm diameter wire electrodes, selected oocytes were placed and fusion was achieved by two DC pulses (1 sec interval) of 1.2 kV/cm for 30 µs using an LF101 Electro Cell Fusion Generator.

value: whole embryo

value: parthenogenesis


title: TT154_HIV24


title: parthenote1 BiSulfite-seq


title: control2 BiSulfite-seq

value: untreated


title: TT154_HIV23


title: TT154_HIV20


title: TT154_HIV18


title: GmCOT_GLYMA.08G227700-ChIP_br2

city: Davis

first: John

last: Harada

address: One Shields Avenue

department: Plant Biology

institute: University of California

description: COT-WRI1-JP97-P1-BR4_q0.01_peaks.narrowPeak

data_processing:
Basecalls performed using RTA3 version 3.4.4.
Sequenced reads passing Illumina quality filter were aligned to the Glycine max genome (Wm82.a2.v1) using Bowtie v0.12.7 with parameters -v 2 -5 0 -3 0 -m 1 --best --strata
Reads from technical replicates were combined and peaks were identified for each biological replicates using MACS3, using default parameters and a q value threshold of 0.01.
Assembly: Wm82.a2.v1
Supplementary files format and content: NarrowPeak files generated by MACS3.

organism: Glycine max

source_name: cotyledon stage embryos

growth_protocol: Soybean cv Williams 82 plants were grown in 2 gallon pots containing Ron’s mix (1 part coarse sand, 1 part compost, 1 part peat moss, 3 pounds/yard Dolomite) in UC Davis greenhouses at temperatures ranging 22-30°C and under 16 hour-days.

extract_protocol:
Chromatin isolation and immunoprecipitation were performed as described in Gendrel AV, Lippman Z, Martienssen R, Colot V. Nat Methods. 2005;2:213–218, except that the isolated nuclei were resuspended in shearing buffer (10mM Tris pH8, 1mM EDTA, 0.1% SDS, 1mM PMSF), sonicated to achieve chromatin fragments ranging from 100 to 500 bp, and Triton X-100 and NaCl were added to chromatin to final concentrations of 1% and 150mM, respectively. Nuclear extracts were either set aside for whole genome extracts (input control) or incubated overnight with 3 ug of an antibody raised against the peptide FSTQPGDHETESDVN corresponding to the amino acids 352-366 of GLYMA.08G227700.  Crosslinks were reversed and protein digested as described in Dahl and Collas, Nat Protoc. 2008;3(6):1032-45, extracted with phenol:chloroform and precipitated using standard procedures.
ChIP and Input libraries were generated using Nugen Ovation Ultralow System V2, following the manufaturer's instructions and enriched by PCR using 15 cycles.  Libraries were size-selected by electrophoresis and purified using Qiagen MinElute gel purification kit

treatment_protocol: Cotyledon stage embryos were dissected from 3.5 to 4.5 mm seeds.  Tissues were crosslinked under vaccuum for 10 minutes in Buffer A (0.4M sucrose, 10 mM Tris pH 8.0, 1mM EDTA pH 8.0) containing 1% formaldehyde, at room temperature, then quenched in 100 mM Glycine for 5 minutes.  Tissues were rinsed twice with deionized water and stored at -80C until use.

value: cotyledon stage embryos

value: Williams 82

value: ChIP


title: TT154_HIV12


title: TT154_HIV19


title: GmCOT_Input_br1

description: COT-WRI1-JP97-P1-BR3_q0.01_peaks.narrowPeak

value: Input


title: TT154_HU12

value: Blood


title: GmCOT_Input_br2


title: TT154_HU15

value: HIV seronegative


title: GmCOT_GLYMA.08G227700-ChIP_br1


title: Gm.27hai.biorep3.run3

city: Kannapolis

first: Tzung-Fu

last: Hsieh

address: Tzung-Fu Hsieh, 600 Laureate Way

department: Plant and Microbial Biology

institute: North Carolina State University

data_processing:
Illumina raw reads were first trimmed at 5' and 3' ends with the positions error rates > 0.5%, trimmed 10 bases average error rate > 0.1% and trimmed the adapter using trimmomatic (v0.38). The trimmed RNA reads were mapped to soybean reference genome (v1.1; https://phytozome-next.jgi.doe.gov) using Hisat2.ESeq2 was used to identify differentially expressed genes.
Assembly: soybean reference genome v1.1
Supplementary files format and content: tab-delimited text file of normalized count matrix

source_name: whole seed

growth_protocol: Long day condition (16 hours light, 8 hours dark) at 22 °C

extract_protocol:
Embryos were collected from early, mid and late desiccation, mature dry seeds, and 3hai (hour after imbibition), 16hai and 27hai. Total RNA was extracted using RNAeasy kit (Qiagen) plus in-column DNase digestion.
Illumina cDNA libraries were constructed with the Illumina Tru-Seq RNA Prep kit per manufacturer’s instruction.

value: whole seed

value: Gm seed at 27 hours after imbibition


title: TT154_HIV100

value: CD4 T cells

value: tetanus toxoid antigen


title: Gm.27hai.biorep2.run2


title: TT154_HIV11


title: TT154_HU04


title: TT154_HIV10


title: TT154_HU09


title: TT154_HU03


title: Gm.27hai.biorep1.run2


title: TT154_HIV09


title: Gm.16hai.biorep3.run2

value: Gm seed at 16 hours after imbibition


title: TT154_HIV08

value: HIV seropositive


title: control1 BiSulfite-seq


title: Gm.16hai.biorep1.run2


title: Gm.16hai.biorep2.run2


title: TT154_HIV06


title: Gm.3hai.biorep2.run2

value: Gm seed at 3 hours after imbibition


title: TT154_HIV05


title: Gm.3hai.biorep3.run2


title: Gm.3hai.biorep1.run2


title: Gm.ld.biorep2.run2

value: Gm seed at late desiccation stage


title: TT154_HIV02


title: TT154_HIV04


title: Gm.ld.biorep3.run2


title: MV45RO_HU25

value: measles antigen


title: MV45RO_HU23


title: Gm.ld.biorep1.run2


title: MV45RO_HU24


title: Gm.md.biorep2.run2

value: Gm seed at mid desiccation stage


title: Gm.ed.biorep2.run3

value: Gm seed at early desiccation stage


title: Gm.ed.biorep1.run2


title: Gm.dry.biorep3.run3

value: Gm seed at dry seed stage


title: Gm.md.biorep1.run2

value: Williams 82


title: Gm.ed.biorep3.run2


title: MV45RO_HU20


title: Gm.dry.biorep2.run3


title: MV45RO_HU18


title: TT154_HIV01


title: MV45RO_HU15


title: MV45RO_HU13


title: Mouse CD8+ T cells, PDP1 retroviral transduction 4

city: Lebanon

first: Edward

last: Usherwood

state: NH

address: Rubin Building, Level 7, 710-53

department: Microbiology and Immunology

institute: Geisel School of Medicine at Dartmouth College

library_source: other

data_processing:
Single-end reads were subjected to base quality trimming using Cutadapt (v4.0) with parameters “-m 1 --max-n 0.8 –trim-n”
Trimmed reads were mapped to reference GRCm38 using STAR (v 2.7.10a) with parameters “--outSAMattributes NH HI AS NM MD --outFilterMultimapNmax 10 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --twopassMode Basic --outFilterScoreMinOverLread 0.3 --outFilterMatchNminOverLread 0.3”
Gene-level read counts were generated featureCounts (Subread package, v2.0.1) using Ensembl gene build version 98 for GRCm38 and the strand argument set to “1”
Assembly: GRCm38
Supplementary files format and content: tsv file containing raw counts for each sample as well as basic gene annotation information
Supplementary files format and content: tsv file containing TPM normalized counts for each sample as well as basic gene annotation information

molecule: other

source_name: Mouse splenic CD8+ T cells

growth_protocol: Isolated CD8+ T cells were stimulated for 2 days with anti-CD3/CD28 antibodies with 25 U/ml recombinant human IL-2 in RPMI 1640 with L-Glutamine (10-040-CV; Corning) supplemented with 10% FBS , 10 mM HEPES , 1× non-essential amino acids, 1 mM sodium pyruvate, and 44 μM 2-Mercaptoethanol. Activated cells were cultured in the same media with rhIL-2.

extract_protocol:
RNA was extracted from 500,000 cells using the RNeasy Mini Kit (Qiagen), quantified by Qubit (Thermo Fisher), and integrity was measured on a Fragment Analyzer instrument (Agilent).
3’ RNA-seq libraries were prepared from 100ng total RNA using the Quantseq FWD v2 workflow (Lexogen) following the manufacturer’s instructions.
RNA-seq libraries were pooled for sequencing on a NextSeq2000 instrument targeting 10M, single-end 100bp reads per sample.

treatment_protocol: Cells were retrovirally transduced with pCI-CD19 empty vector, or vector encoding PDK1 or PDP1, in the presence of 25U/mL IL-2.

value: Mouse splenic CD8+ T cells

value: Primary CD8+ T cells

value: Mouse CD8+ T cells

value: PDP1 overexpression

value: Retroviral transduction, IL-2 culture


title: TT154_HIV07

value: Blood


title: MV45RO_HU12

value: HIV seronegative

value: CD4 T cells


title: MV45RO_HU17


title: MV45RO_HU21


title: MV45RO_HU22


title: Gm.dry.biorep1.run2

value: whole seed


title: Mouse CD8+ T cells, PDP1 retroviral transduction 1


title: Gm.md.biorep3.run2


title: MV45RO_HU06


title: Mouse CD8+ T cells, PDP1 retroviral transduction 3


title: Mouse CD8+ T cells, PDK1 retroviral transduction 4

value: PDK1 overexpression


title: MV45RO_HU09


title: MV45RO_HU19


title: MV45RO_HU04


title: Mouse CD8+ T cells, PDK1 retroviral transduction 3


title: MV45RO_HU03


title: Mouse CD8+ T cells, PDK1 retroviral transduction 2


title: Mouse CD8+ T cells, PDK1 retroviral transduction 1


title: Mouse CD8+ T cells, empty vector retroviral transduction 4

value: WT


title: MV45RO_HIV23

value: HIV seropositive


title: MV45RO_HU10

value: measles antigen


title: MV45RO_HIV24


title: MV45RO_HIV19


title: MV45RO_HU02


title: Mouse CD8+ T cells, empty vector retroviral transduction 3


title: Mouse CD8+ T cells, PDP1 retroviral transduction 2


title: MV45RO_HIV18


title: MV45RO_HIV20


title: Mouse CD8+ T cells, empty vector retroviral transduction 2


title: Mouse CD8+ T cells, empty vector retroviral transduction 1


title: Control_platelets, biol rep 2

city: New York

first: Erik

last: Sulman

state: NY

address: 522 1st Ave, Smilow Bldg, Rm 801C

institute: NYU Grossman School of Medicine

data_processing:
Raw FASTQ files were processed using Trimmomatic version 0.36 for trimming and clipping sequence adapters.
Reads were aligned to the hg38 and mm10 reference genomes respectively using STAR.
Read counts were summarized using featureCounts.
Assembly: hg38, mm10
Supplementary files format and content: Two tab-delimited files of raw read counts for each sample aligned to hg38 and mm10 genomes, respectively

source_name: peripheral blood

extract_protocol:
Five weeks after tumor implantation, approximately 1 ml of blood was collected from each mouse in a BD Vacutainer yellow-top tube containing acid citrate dextrose to prevent platelet activation. Platelet-rich plasma (PRP) was collected by centrifuging the tubes at 100 × g for 15 min. The centrifuge was set to accelerations of 5 and 2 to avoid platelet activation. PRP was separated carefully from the other components of the blood and centrifuged at 1000 × g for 10 min after the addition of 2 µL of 1 mM PGE2 to 2 ml of PRP. RNA was isolated from the resulting platelet pellets using the mirVana™ miRNA Isolation Kit (Invitrogen, USA, Cat #AM1560).
RNA libraries were prepared using the Rneasy Plus Mini Kit (Qiagen) following manufacturer's protocols.

treatment_protocol: GS 8-11 glioblastoma sphere cells (1 × 105 per mouse) were implanted into the brains of 6- to 8-week-old Foxn1nu mice, one week after guide screw placement, using a stereotactic apparatus under anesthesia.

value: peripheral blood


title: MV45RO_HIV11


title: MV45RO_HIV100


title: GL261_platelets

value: GL261 implanted


title: GS_8-11_platelets, biol rep 4

value: GS8-11 implanted


title: MV45RO_HIV10


title: MV45RO_HIV07


title: MV45RO_HIV08


title: MV45RO_HIV09


title: GS_8-11_platelets, biol rep 3


title: GS_8-11_platelets, biol rep 2


title: Control_platelets, biol rep 3


title: GS_8-11_platelets, biol rep 1


title: Control_platelets, biol rep 4


title: Control_platelets, biol rep 1


title: MV45RO_HIV04


title: MV45RO_HIV12


title: control DLN

city: Kyoto

first: kenji

last: Chamoto

state: Kyoto

address: Yoshida Konoe-cho, Sakyo-ku

department: Department of Immunology and Genomic Medicine

description: mouse age : 6 weeks

data_processing:
The Cell Ranger Single-Cell toolkit (version 3.0.0) provided by 10× genomics was applied to align reads and generate the gene-cell unique molecular identifier (UMI) matrix for each sample (https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest). The read data were mapped using the corresponding Mus musculus reference genome. Different samples were merged using the cellranger aggr function. The obtained raw_feature_bc_matrix was loaded, and Seurat R package (v 3.2.2) was further used for downstream analyses .
Assembly: mm10
Supplementary files format and content: matrix.mtx.gz contain gene-barcode counts
Supplementary files format and content: features.tsv.gz contain gene file, barcodes.tsv.gz contain cell barcode file

source_name: draining lymph node

growth_protocol: Mice were maintained under specific pathogen-free conditions at the Institute of Laboratory Animals, Graduate School of Medicine, Kyoto University. All animal experiments were performed according to the guidelines approved by the respective institutional review boards.

extract_protocol:
Tumor bearing mice were sacrificed, tumor and draining lymph node was isolated and placed in ice-cold phosphate-buffered saline (PBS). For draining lymph node, the tissue was minced and dissociated with 0.25% trypsin in a centrifuge tube for 30 min at 28 °C, then the sample was filtered using a 70 µm strainer to obtain a single-cell suspension. for CD8 tumor infiltrating T cell, the tumor was digested by collagenase IV for 40 min, single cell suspension of tumor cell was stain with anti-CD8 and anti-CD3 antibody, CD8 tumor infiltrating T cell was sorted by flow cytometry (Melody,BD). Using single-cell 5 ‘Library and Gel Bead Kit V3 (10× Genomics) and Chromium Single Cell B Chip Kit (10× Genomics, 1000074), the cell suspension (10000 living cells per microliter determined by Count Star) was loaded onto the Chromium single cell controller (10× Genomics) to generate single-cell gel beads in the emulsion according to the manufacturer’s protocol. In short, single cells were suspended in PBS containing 0.04% bovine serum albumin (BSA). Approximately 10000 cells were added to each channel, and the target cell recovered was estimated to be approximately 3000 cells. Captured cells were lysed, and the released RNAs were barcoded through reverse transcription in individual GEMs. Reverse transcription was performed on an S1000TM Touch Thermal Cycler (Bio Rad) at 53 °C for 45 min followed by 85 °C for 5 min, and incubated at 4 °C. The complementary DNA (cDNA) was generated and then amplified, and the quality was assessed using an Agilent 4200. According to the manufacturer’s instruction, scRNA-seq libraries were constructed using Single Cell 5’ Library and Gel Bead Kit V3. The libraries were finally sequenced using an Illumina Nextseq 2000 sequencer with a sequencing depth of at least 100,000 reads per cell with a pair-end 150 bp reading strategy.
RNA libraries were prepared with Chromium Single cell 5' Reagent v3 kits according to the manufacturer's protocol

treatment_protocol: MC38 cells (2 × 106) or Bpmel-parent cells were intradermally (i.d.) injected into the left flank of mice (day 0). Bpmel-SIY-OVAII (1 × 106) that could naturally be rejected were injected 7 days after tumor cell inoculation by I.d. injection into another flank. After another 2 weeks, mice were sacrificed, MC38 tumor and draing lymph node for MC38 tumor was obtained.

value: draining lymph node

value: not applicable

value: pan cell in draining lymph node

value: MC38 tumor


title: MV45RO_HIV06


title: MV45RO_HIV05


title: control CD8 TILs

institute: Graduate School of Medicine, Kyoto University

description: mouse age : 6 weeks

source_name: tumor tissue

value: tumor tissue

value: Tumor infiltrating CD8 T cell


title: MV45RO_HIV01

value: Blood


title: SIY-OVAII CD8 TILs

description: mouse age : 6 weeks

value: MC38 tumor + Bpmel-SIY-OVAII alive adjuvant


title: Primary melanocytes treated w/A375 PRAME +/-, rep2

city: Oklahoma City

first: Jeffrey

middle: Don

last: McBride

state: OK

address: 1000 NE 13th St

department: Dermatology

institute: University of Oklahoma

data_processing:
Raw reads were cleaned using FastP (DOI: 10.1093/bioinformatics/bty560) program with the following parameters: -q 20 -l 30 -n 5 -e 25 –cut_front –cut_tail -M 30 -W 1 –trim_poly_g –trim_poly_x
Filtered reads were mapped to reference human genome (GRCh38), version 44 (Ensembl 110) using the STAR software v2.7.11b using default parameters
Gene counts were optained using STAR's option: --quantMode GeneCounts , and counts were taen from the 4th column: tail -n +5 5CP_S7.ReadsPerGene.out.tab | cut -f1 >> geneids.txt
Assembly: human genome (GRCh38), version 44 (Ensembl 110)
Supplementary files format and content: tab delimited text file includes raw counts for each sample

source_name: HEM

growth_protocol:
Human melanoma cell lines A375 (ATCC) were grown in DMEM supplemented with 10% fetal bovine serum (FBS), 50 U/ml penicillin, 50 µg/ml streptomycin. Primary epidermal melanocytes (ATCC) were cultured in dermal cell basal medium supplemented with Adult Melanocyte Growth Kit.  Primary dermal fibroblasts (ATCC)  were cultured in fibroblast basal medium supplemented with fibroblast growth kit.   Primary dermal microvascular endothelial cells were cultured in vascular cell basal medium supplemented with endothelial cell growth kit.
Cell cultures were maintained in a humidified atmosphere of 5% CO2 and 37 °C.

extract_protocol:
Qiagen Rneasy Mini kit
NEBNext Poly(A) mRNA Magnetic Isolation Module & IDT xGen Broad Range RNA Library Kit

treatment_protocol: Human melanoma A375 cells were cultured until they reached 80% confluency. The cells were then washed several times with PBS and switched to serum-free DMEM media for 72 hours to minimize protein contamination from serum. The medium was collected and centrifuged at 3,000 x g for 15 minutes to remove cellular debris, followed by ultrafiltration using 100 kDa filters (Amico Ultra-15, Millipore) at 4,000 x g for 15 minutes. PM, PF and EN cells were incubated with the collected condition medium for 72h respectively. Different groups of cells were collected separately and  performed RNAseq.

value: HEM

value: Primary epidermal melanocytes (ATCC)

value: Extracellular vesicle treatmant from A375 PRAME +/-


title: MV45RO_HIV02

value: CD4 T cells


title: Primary melanocytes treated w/A375 PRAME +/-, rep3

value: WT


title: SIY-OVAII DLN

description: mouse age : 6 weeks


title: MV154_HU25

value: HIV seronegative

value: measles antigen


title: MV154_HU23


title: MV154_HU24


title: Primary melanocytes treated w/A375 PRAME +/-, rep1


title: MV154_HU22


title: Primary melanocytes treated w/A375 PRAME +/+, rep3

value: Extracellular vesicle treatmant from A375 PRAME +/+


title: MV154_HU21


title: Primary melanocytes treated w/A375 PRAME +/+, rep2


title: MV154_HU17


title: MV154_HU19


title: Primary fibroblast treated w/A375 PRAME +/-, rep2

source_name: HDF

value: HDF

value: Primary dermal fibroblasts (ATCC)


title: MV154_HU18


title: Primary fibroblast treated w/A375 PRAME +/-, rep3


title: Primary melanocytes treated w/A375 PRAME +/+, rep1


title: Primary fibroblast treated w/A375 PRAME +/+, rep3


title: MV154_HU15


title: Primary fibroblast treated w/A375 PRAME +/+, rep1


title: MV154_HU10


title: MV154_HU12


title: MV154_HU13


title: Primary fibroblast treated w/A375 PRAME +/+, rep2


title: Primary fibroblast treated w/A375 PRAME +/-, rep1


title: A375 PRAME +/- melanoma cells, rep1

value: Human melanoma cell lines A375 (ATCC)

value: WT - PRAME +/-

value: no treatment


title: Endothelial cells treated w/A375 PRAME +/-, rep2

source_name: HDMVEC

value: HDMVEC

value: Primary dermal microvascular endothelial cells


title: MV154_HU09

value: Blood


title: A375 PRAME +/- melanoma cells, rep2


title: MV154_HU04


title: MV154_HU03


title: Endothelial cells treated w/A375 PRAME +/-, rep1


title: Endothelial cells treated w/A375 PRAME +/+, rep3


title: MV154_HIV23

value: HIV seropositive


title: MV154_HIV24


title: MV154_HU02


title: Endothelial cells treated w/A375 PRAME +/+, rep2


title: MV154_HU20