title: Subject 03

description: Library name: L3

value: Female

value: Lewy body diffuse/neocortical

value: Braak stage 2


title: Subject 05

status: Public on Apr 29 2026

type: SRA

city: South San Francisco

first: Mitchell

last: Rezzonico

state: CA

address: 1 DNA Way

country: USA

institute: Genentech

description: Library name: L5

library_source: transcriptomic single cell

data_processing:
Raw sequence files were demultiplexed into FASTQ format using the Cell Ranger mkfastq command (v6, 10x Genomics). Reads were aligned to the human GRCh38 reference genome, including intronic regions, and gene counts were quantified as UMI (Unique Molecular Identifier) counts using Cell Ranger count (v6, 10x Genomics).
Ambient RNA contamination was removed by processing all samples with CellBender (v0.2), using the raw_feature_bc_matrix.h5 output file from Cell Ranger as input, with default parameters.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values file and h5 files

molecule: polyA RNA

organism: Homo sapiens

source_name: Brain: Amygdala

extract_protocol:
Post-mortem frozen samples of brains were obtained from the Harvard Brain Tissue Resource Center (HBTRC)/NIH NeuroBioBank and the Massachusetts Alzheimer’s Disease Research Center (ADRC) neuropathology core and stored at -80ºC. Frozen samples of the amygdala gray matter were dissected and dissociated to prepare nuclei suspensions as previously described (Limone, Mordes et al. 2024). Aliquots (10 µl) of each preparation were stained with diluted Hoechst 33342 dye and examined on a Countess III FL with brightfield and fluorescence to verify the presence of nuclei.
Nuclei were processed on a 10x chromium controller, and libraries were prepared using the 10X genomics single cell 3’ V3.1 kit. Reactions were sequenced on a NovaSeq (Illumina) at the UCSF IHG.

tag: tissue

tag: Sex

tag: age

tag: disease state

value: Control

tag: cohort

value: Cohort 01

tag: pathology

tag: braak and_braak_nft_stage

value: Braak stage 1


title: Germination_Transverse_6HAI_A

city: Bundoora

first: Marta

last: Peirats Llobet

state: Victoria

address: 5 Ring road

country: Australia

institute: La Trobe University

description: Library name: GTR_6HAI_A

library_source: transcriptomic

data_processing:
Raw sequencing data was processed using 10x Genomics Space Ranger pipeline to generate FASTQ files.
Sequences were aligned to IBSC v2.51 genome to get gene expression counts using Space Ranger's default settings.
Assembly: Barley genome, ((International Barley Sequencing Consortium (IBSC) v2.51 served as a reference genome for aligning the sequencing reads.
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: spatial_enrichment.cvs: spatial autocorrelation coefficient table in csv format
Supplementary files format and content: filtered_feature_bc_matrix.h5: gene expression matrix in h5 format
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: high-res image of the tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of the tissue
Supplementary files format and content: tissue_positions.csv: list of spatial barcodes and coordinates specifying spots
Library strategy: Spatial Transcriptomics

molecule: total RNA

organism: Hordeum vulgare

source_name: grain

extract_protocol:
Fresh frozen tissue embedded in OCT and sectioned to 8 µm thick in the cryostat.
Spatial sequencing libraries were synthesized as described in 10x User guide (PN-1000190, CG000239_VisiumSpatialGeneExpression_UserGuide_RevD). Visium libraries were sequenced on an Illumina NextSeq 550 platform according to the 10x Genomics Visium manufacturer’s instructions (NextSeq 500/550 High Output kit v2.5 (150 cycles) 20024907, CG00023_VisiumSpatialGeneExpression_UserGuide_RevD), targeting 100 million reads using dual indexing kit TT set A (PN-1000215, 10x Genomics).

treatment_protocol: No treatments

value: grain

tag: genotype

value: La Trobe

tag: treatment

value: no


title: WT,CD44hi, rep1

city: Beijing

first: Weixuan

last: Wang

address: No. 38 Xueyuan Road, Haidian District

country: China

institute: Peking University

description:
Library name: WT-hi-1
10X Genomics

data_processing:
Illumina Casava2.19 software used for basecalling.Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v2.0.5
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm39
Supplementary files format and content: FPKM

organism: Mus musculus

source_name: CD44hi Tvm

extract_protocol:
Total RNA was extracted with Trizol reagent (Invitrogen) and reverse transcribed into cDNA with GoScriptTM Reverse Transcription System (Promega). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using standard Illumina protocols.

treatment_protocol: Primary CD8⁺ T cells isolated from lymph nodes of WT and Cd4-Cre Rpa1fl/fl mice were resuspended in T cell medium (RPMI-1640 supplemented with 10% FBS, 1 × Pen-Strep, 1 mM sodium pyruvate and 0.05 mM 2-mercaptoethanol). Cells were seeded into 48-well plates pre-coated with anti-CD3 antibody (1 μg/mL) at a density of 2 × 10^6 cells/mL and stimulated with anti-CD28 antibody (1 μg/mL), IFN-α (50 ng/mL) and IL-4 (20 ng/mL). Cells were harvested 18 hours after activation and sorted into CD44super-high and CD44lo CD8⁺ T cell subsets.

tag: cell type

value: CD44hi Tvm

value: WT


title: Subject 07

description: Library name: L7

value: Male

value: Braak stage 0


title: Germination_Transverse_3HAI_A

description: Library name: GTR_3HAI_A


title: Germination_Transverse_1HAI_D

description: Library name: GTR_1HAI_D


title: Subject 01-1

description: Library name: L1


title: Germination_Transverse_3HAI_D

description: Library name: GTR_3HAI_D


title: Subject 02

description: Library name: L2

value: PD


title: Germination_Transverse_3HAI_C

description: Library name: GTR_3HAI_C


title: Germination_Transverse_3HAI_B

description: Library name: GTR_3HAI_B


title: pbmc, PAC1 knockout

description:
Library name: KO
10X Genomics

data_processing:
The Cell ranger software pipeline (version 6.0.1) provided by 10xGenomics was used to demultiplex cellular barcodes,map reads to the transcriptome, control quality and generate quantitative matrix.
The R package Seurat (version 4.3.0) was used for generation of Seurat object.
The count matrix was normalized with NormalizeData function.
tSNE and UMAP were performed by R package Seurat (version 4.3.0).
Assembly: mm39
Supplementary files format and content: Tab-separated values files and matrix files

source_name: pbmc

extract_protocol:
Single cells were mixed with Gel Beads, Partitioning Oil and glycerol, using for preparation of GEMs with ChromiumTM Next GEM Chip G Single Cell Kit. The GEMs were subjected to RT-PCR, and the products were purified with Dynabeads, followed by cDNA amplification.
RNA libraries were prepared with ChromiumTM Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1 according to the manufacturer's protocol.

treatment_protocol: Six-week-old male WT or Dusp2-/- mice were infected with VSV at a dose of 2 × 10^7 plaque-forming units (p.f.u.) for 18 hours. CD8+ T cells from peripheral blood were isolated using a magnetic positive selection kit.

value: pbmc

value: KO


title: Germination_Transverse_1HAI_B

description: Library name: GTR_1HAI_B


title: WT,CD44hi, rep2

description:
Library name: WT-hi-2
10X Genomics


title: Germination_Transverse_0HAI_D

description: Library name: GTR_0HAI_D


title: Germination_Transverse_1HAI_C

description: Library name: GTR_1HAI_C


title: pbmc, WT

description:
Library name: WT
10X Genomics


title: Germination_Transverse_0HAI_C

description: Library name: GTR_0HAI_C


title: WT,CD44lo, rep1

description:
Library name: WT-low-1
10X Genomics

source_name: CD44lo Tvm

value: CD44lo Tvm


title: pool-13,well-4,GEX

city: San Francisco

first: Ravi

last: Patel

address: 513 Parnassus Ave

department: CoLabs

institute: University of California San Francisco

description:
Library name: XVIR1-POOL-SCG51_GEX
Pool of XVIR1-HS12-SNEGB3,XVIR1-HS15-NCTLB6,XVIR1-HS21-NCTLB9,XVIR1-HS3-SNEGB5,XVIR1-HS37-NCTLB5,XVIR1-HS40-NCTLB1,XVIR1-HS41-SNEGB6,XVIR1-HS42-SNEGB3,XVIR1-HS43-SNEGB3,XVIR1-HS6-SNEGB6,XVIR1-HS7-SNEGB4,XVIR1-HS9-SNEGB2

data_processing:
Sequencer-obtained bcl files were demultiplexed using mkfastq program from Cell Ranger v6.0.2   (10x Genomics). Feature-barcode matrices were obtained for each library by aligning the raw fastqs of gene expression to GRCh38 reference genome (Ensembl v98) and the raw fastqs of surface protein expression to a TotalSeq-A antibody reference panel using the Cell Ranger count. Raw feature-barcode matrices were imported and analyzed using Seurat (v4.0.3).
Each library was demultiplexed to map individual cells to their sample of origin using freemuxlet (vAug2021), SNP profiles were mapped to the genotypes of patients from bulk RNA-seq using bcftools gtcheck (v1.10.2), and inter-sample doublets and empty droplets were removed.
DoubletFinder (v2.0.3)22 was used to filter barcodes containing heterotypic intra-sample doublets.
Barcodes containing less than 100 genes and genes that are detected in fewer than 3 cells were removed. We further filtered out the barcodes based on library-specific cutoffs for the number of genes per cell (nFeature_RNA <300-400 and >4,000), the number of unique molecular indexes (UMIs) per cell (nCount_RNA <700-2,000 and >20,000; nCount_ADT >20,000), mitochondrial content (>20%), and ribosomal content (<2-13% and >60%) to remove poor quality cells. The RNA and ADT count data for the resulting high-quality cell-barcodes are provided here.
Assembly: GRCh38
Supplementary files format and content: *.h5 files contain raw count data in 10X H5 format
Supplementary files format and content: CITEseq_cell_metadata.rds is an R object file containing metadata for single-cells, including patient, sample, library, and pool ids, study group, timepoint, cell annotations, and additional sample-specific metadata
Library strategy: CITE-seq

source_name: PBMC

extract_protocol:
PBMCs were isolated from whole blood using Ficoll-Paque PLUS density gradient and were stored in freezing medium (9:1 FBS/DMSO) in liquid nitrogen (<-135C). Thawed PBMC suspensions from 16 individual patients were pooled together with equivalent numbers of live cells.  10^6 pooled cells were Fc blocked  for 10 min at room temperature followed by staining with a custom TotalSeqTM-A antibody panel for 45 minutes at 4°C. Cells were washed 3 times with Cell Staining Buffer resuspended in DPBS (w/o Ca2+, Mg2+)  with 0.04% BSA at 2,000 cells/uL and loaded onto a 10X Genomics Chromium Controller.
Stained cells were loaded onto a Chromium Next GEM Chip G at 65,000 cells per well, 4 wells per pool (except for one pool  with only 2 wells per pool (XVIR1-POOL-SC[G/C]2 and XVIR1-POOL-SC[G/C]3)) and processed for single-cell encapsulation and cDNA library generation using the Chromium Single Cell 3′ v3.1 Reagent Kits (User guide CG000206 Rev D; 10X Genomics) and Single Index Kit T Set A according to the manufacturer’s instructions. Gene Expression (GEX) and surface protein-targeting Antibody Derived Tag (ADT) libraries were pooled at 2.5:1 and the libraries were sequenced on Illumina NovaSeq 6000 (S4-200, ~2.5B reads per library) at the Center for Advanced Technology at UCSF at a depth of 25,000 reads per cell for GEX and 10,000 reads per cell for ADT using the recommended cycle numbers: Read 1 28 cycles, i7 index 8 cycles, Read 2 91 cycles.

value: PBMC


title: Germination_Transverse_1HAI_A

description: Library name: GTR_1HAI_A


title: KO, CD8+T, CD3/CD28+IFN-α+IL-4

description: Library name: KO-a

library_source: genomic

data_processing:
Illumina Casava2.19 software used for basecalling.Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v2.0.5
Assembly: mm39
Supplementary files format and content: bigWig

molecule: genomic DNA

extract_protocol:
Genomic DNA was extracted under gentle conditions to preserve R-loops. Briefly, cells were lysed in lysis buffer containing SDS and proteinase K and incubated at 37°C overnight. Genomic DNA was then purified by phenol-chloroform extraction followed by ethanol precipitation. The DNA pellet was resuspended in TE buffer. Purified DNA was digested with a cocktail of restriction enzymes (EcoRI, BamHI, HindIII, BsrGI, and XbaI) to generate fragments of approximately 100-500 bp. DNA concentration was determined using a NanoDrop spectrophotometer, and samples were used for subsequent DRIP assays.
DNA libraries for DNA-seq were prepared using standard Illumina protocols.

treatment_protocol: Primary CD8⁺ T cells isolated from lymph nodes of WT and Cd4-Cre Rpa1fl/fl mice were resuspended in T cell medium (RPMI-1640 supplemented with 10% FBS, 1 × Pen-Strep, 1 mM sodium pyruvate and 0.05 mM 2-mercaptoethanol). Cells were seeded into 48-well plates at a density of 2 × 10^6 cells/mL and stimulated with anti-CD3/28 antibodies (1 μg/mL+1 μg/mL), anti-CD3/28 antibodies (1 μg/mL+1 μg/mL)+IFN-α (50 ng/mL)+IL-4 (20 ng/mL) or left untreated. Cells were harvested 18 hours after activation

value: Cd4-Cre Rpa3fl/fl


title: KO, CD8+T, CD3/CD28

description: Library name: KO-328

value: Cd4-Cre Rpa2fl/fl


title: pool-13,well-3,ADT

description:
Library name: XVIR1-POOL-SCC50_ADT
Pool of XVIR1-HS12-SNEGB3,XVIR1-HS15-NCTLB6,XVIR1-HS21-NCTLB9,XVIR1-HS3-SNEGB5,XVIR1-HS37-NCTLB5,XVIR1-HS40-NCTLB1,XVIR1-HS41-SNEGB6,XVIR1-HS42-SNEGB3,XVIR1-HS43-SNEGB3,XVIR1-HS6-SNEGB6,XVIR1-HS7-SNEGB4,XVIR1-HS9-SNEGB2

library_source: other

molecule: protein


title: Development_20DAP_section_D

description: Library name: DEV_20DAP_D

source_name: caryopsis

value: caryopsis


title: Development_20DAP_section_C

description: Library name: DEV_20DAP_C


title: Germination_Transverse_0HAI_B

description: Library name: GTR_0HAI_B


title: Germination_Transverse_0HAI_A

description: Library name: GTR_0HAI_A


title: pool-13,well-2,ADT

description:
Library name: XVIR1-POOL-SCC49_ADT
Pool of XVIR1-HS12-SNEGB3,XVIR1-HS15-NCTLB6,XVIR1-HS21-NCTLB9,XVIR1-HS3-SNEGB5,XVIR1-HS37-NCTLB5,XVIR1-HS40-NCTLB1,XVIR1-HS41-SNEGB6,XVIR1-HS42-SNEGB3,XVIR1-HS43-SNEGB3,XVIR1-HS6-SNEGB6,XVIR1-HS7-SNEGB4,XVIR1-HS9-SNEGB2


title: pool-13,well-3,GEX

description:
Library name: XVIR1-POOL-SCG50_GEX
Pool of XVIR1-HS12-SNEGB3,XVIR1-HS15-NCTLB6,XVIR1-HS21-NCTLB9,XVIR1-HS3-SNEGB5,XVIR1-HS37-NCTLB5,XVIR1-HS40-NCTLB1,XVIR1-HS41-SNEGB6,XVIR1-HS42-SNEGB3,XVIR1-HS43-SNEGB3,XVIR1-HS6-SNEGB6,XVIR1-HS7-SNEGB4,XVIR1-HS9-SNEGB2


title: Development_12DAP_section_D

description: Library name: DEV_12DAP_D


title: pool-13,well-1,ADT

description:
Library name: XVIR1-POOL-SCC48_ADT
Pool of XVIR1-HS12-SNEGB3,XVIR1-HS15-NCTLB6,XVIR1-HS21-NCTLB9,XVIR1-HS3-SNEGB5,XVIR1-HS37-NCTLB5,XVIR1-HS40-NCTLB1,XVIR1-HS41-SNEGB6,XVIR1-HS42-SNEGB3,XVIR1-HS43-SNEGB3,XVIR1-HS6-SNEGB6,XVIR1-HS7-SNEGB4,XVIR1-HS9-SNEGB2


title: pool-13,well-2,GEX

description:
Library name: XVIR1-POOL-SCG49_GEX
Pool of XVIR1-HS12-SNEGB3,XVIR1-HS15-NCTLB6,XVIR1-HS21-NCTLB9,XVIR1-HS3-SNEGB5,XVIR1-HS37-NCTLB5,XVIR1-HS40-NCTLB1,XVIR1-HS41-SNEGB6,XVIR1-HS42-SNEGB3,XVIR1-HS43-SNEGB3,XVIR1-HS6-SNEGB6,XVIR1-HS7-SNEGB4,XVIR1-HS9-SNEGB2


title: Development_20DAP_section_A

description: Library name: DEV_20DAP_A


title: WT, CD8+T, CD3/CD28+IFN-α+IL-4

description: Library name: WT-a


title: WT, CD8+T, CD3/CD28

description: Library name: WT-328


title: Development_12DAP_section_B

description: Library name: DEV_12DAP_B


title: Development_12DAP_section_C

description: Library name: DEV_12DAP_C


title: WT, CD8+T, UT

description: Library name: WT-UT

value: UT


title: Development_20DAP_section_B

description: Library name: DEV_20DAP_B


title: Development_12DAP_section_A

description: Library name: DEV_12DAP_A


title: B16F10_Tada2bsg2_rep3

city: Grand Rapids

first: Xiaobing

last: Shi

address: 333 Bostwick Ave. NE

institute: Van Andel Institute

description: Library name: Sample 9

data_processing:
Base calling was done by Illumina RTA3 and output of NCS was demultiplexed and converted to FastQ format with Illumina Bcl2fastq
Fastq files were mapped to mm10 human genome by HISAT2
Gene reads count tables were generated by HTSeq
Assembly: mm10
Supplementary files format and content: text files includes raw reads count

growth_protocol: The B16F10 cell line was cultured in DMEM supplemented with 10% FBS.

extract_protocol:
Total RNA was extracted using the QIAGEN RNeasy Plus Mini Kit according to the manufacturer’s instructions.
KAPA Stranded mRNA-Seq Kit

tag: cell line

value: mouse melanoma cells

value: Tada2b knockout


title: pool-13,well-1,GEX

description:
Library name: XVIR1-POOL-SCG48_GEX
Pool of XVIR1-HS12-SNEGB3,XVIR1-HS15-NCTLB6,XVIR1-HS21-NCTLB9,XVIR1-HS3-SNEGB5,XVIR1-HS37-NCTLB5,XVIR1-HS40-NCTLB1,XVIR1-HS41-SNEGB6,XVIR1-HS42-SNEGB3,XVIR1-HS43-SNEGB3,XVIR1-HS6-SNEGB6,XVIR1-HS7-SNEGB4,XVIR1-HS9-SNEGB2


title: KO, CD8+T, UT

description: Library name: KO-UT

value: Cd4-Cre Rpa1fl/fl


title: Development_6DAP_section_C

description: Library name: DEV_6DAP_C

value: La Trobe

value: no


title: Development_6DAP_section_D

description: Library name: DEV_6DAP_D


title: pool-12,well-4,ADT

description:
Library name: XVIR1-POOL-SCC47_ADT
Pool of XVIR1-HS12-SNEGB7,XVIR1-HS15-NCTLB5,XVIR1-HS17-SNEGB7,XVIR1-HS20-NCTLB3,XVIR1-HS3-SNEGB4,XVIR1-HS36-NCTLB5,XVIR1-HS37-NCTLB4,XVIR1-HS41-SNEGB2,XVIR1-HS42-SNEGB2,XVIR1-HS43-SNEGB2,XVIR1-HS44-NCTLB7,XVIR1-HS5-SNEGB2,XVIR1-HS6-SNEGB5


title: Development_6DAP_section_B

description: Library name: DEV_6DAP_B


title: pool-13,well-4,ADT

description:
Library name: XVIR1-POOL-SCC51_ADT
Pool of XVIR1-HS12-SNEGB3,XVIR1-HS15-NCTLB6,XVIR1-HS21-NCTLB9,XVIR1-HS3-SNEGB5,XVIR1-HS37-NCTLB5,XVIR1-HS40-NCTLB1,XVIR1-HS41-SNEGB6,XVIR1-HS42-SNEGB3,XVIR1-HS43-SNEGB3,XVIR1-HS6-SNEGB6,XVIR1-HS7-SNEGB4,XVIR1-HS9-SNEGB2


title: Development_6DAP_section_A

description: Library name: DEV_6DAP_A


title: B16F10_Tada2bsg2_rep2

description: Library name: Sample 8


title: pool-12,well-4,GEX

description:
Library name: XVIR1-POOL-SCG47_GEX
Pool of XVIR1-HS12-SNEGB7,XVIR1-HS15-NCTLB5,XVIR1-HS17-SNEGB7,XVIR1-HS20-NCTLB3,XVIR1-HS3-SNEGB4,XVIR1-HS36-NCTLB5,XVIR1-HS37-NCTLB4,XVIR1-HS41-SNEGB2,XVIR1-HS42-SNEGB2,XVIR1-HS43-SNEGB2,XVIR1-HS44-NCTLB7,XVIR1-HS5-SNEGB2,XVIR1-HS6-SNEGB5


title: Development_3DAP_section_D

description: Library name: GE3DAP-D1


title: Development_3DAP_section_B

description: Library name: GE3DAP-B1


title: pool-12,well-3,ADT

description:
Library name: XVIR1-POOL-SCC46_ADT
Pool of XVIR1-HS12-SNEGB7,XVIR1-HS15-NCTLB5,XVIR1-HS17-SNEGB7,XVIR1-HS20-NCTLB3,XVIR1-HS3-SNEGB4,XVIR1-HS36-NCTLB5,XVIR1-HS37-NCTLB4,XVIR1-HS41-SNEGB2,XVIR1-HS42-SNEGB2,XVIR1-HS43-SNEGB2,XVIR1-HS44-NCTLB7,XVIR1-HS5-SNEGB2,XVIR1-HS6-SNEGB5


title: run_0394a_A549, H460, SW1573

city: Boston

first: Teng

last: Teng

state: MA

address: 201 Brookline Ave Suite 901

institute: Tango Therapeutics

description:
Library name: SAMPLE 10
CRSIPR-UMI validation Library infected A549, H460 or SW1573 cells engrafted into NOG mice

data_processing:
In-house customized pipeline for mapping and counting for sgRNAs
Assembly: GrCh38
Supplementary files format and content: Tab-delimited text files include guide count and clone count values for each sample
Supplementary files format and content: gene_symbol: gene name
Supplementary files format and content: gene_sgrna_id: gRNA identifier of each gene (1-4 or 1-6)
Supplementary files format and content: umi_barcode: unique molecular identifier barcode sequence
Supplementary files format and content: sample_counts: number of counts for a specific guide and barcode
Library strategy: CRISPR Screen

growth_protocol: A549, H460 or SW1573 cells were grown in DMEM + 10% FBS

extract_protocol:
Tumor were homogenized using gentleMACS dissociator (Miltenyi Biotec) following manufacturer protocol and gDNA extracted using Maxwell RSC 48 (Promega) with Maxwell® CSC Genomic DNA Kit
sgRNA sequences were PCR amplified with primers forward: F: 5′- AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTNNNNNNNNNNNNNNNNNNNCTTGTGGAAAGGACGAAACACCG-3′, reverse: R: 5′-CAAGCAGAAGACGGCATACGAGATGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT-3′ and purified with Kapa Pure Beads (Roche, KK8802)

treatment_protocol: A549, H460 or SW1573 cells were infected with the indicated CRISPR library and selected with puromycin (2ug/mL) and expanded in vitro before engrafted into NOG mice. For CRISPR-StAR library, Tamoxifen (Sigma Aldrich, T5648) was delivered in corn oil (Sigma Aldrich, C8267. Concentration 100 mg/mL) at a dose of 75 mg/kg by intraperitoneal injection (IP), once a day for 2 consecutive days to initate recombination

value: Lung cancer cell line


title: B16F10_Tada2bsg2_rep1

description: Library name: Sample 7


title: Development_3DAP_section_C

description: Library name: GE3DAP-C1


title: B16F10_Tada2bsg1_rep3

description: Library name: Sample 6


title: run_0338_A549

description:
Library name: SAMPLE 5
Druggable Genome Library infected A549 cells cultured in vitro for the in vitro arm


title: B16F10_Tada2bsg1_rep2

description: Library name: Sample 5


title: run_0393a_A549, H460, SW1573

description:
Library name: SAMPLE 9
CRISPR-StAR validation Library infected A549, H460 or SW1573 cells engrafted into NOG mice


title: pool-12,well-3,GEX

description:
Library name: XVIR1-POOL-SCG46_GEX
Pool of XVIR1-HS12-SNEGB7,XVIR1-HS15-NCTLB5,XVIR1-HS17-SNEGB7,XVIR1-HS20-NCTLB3,XVIR1-HS3-SNEGB4,XVIR1-HS36-NCTLB5,XVIR1-HS37-NCTLB4,XVIR1-HS41-SNEGB2,XVIR1-HS42-SNEGB2,XVIR1-HS43-SNEGB2,XVIR1-HS44-NCTLB7,XVIR1-HS5-SNEGB2,XVIR1-HS6-SNEGB5


title: pool-12,well-2,GEX

description:
Library name: XVIR1-POOL-SCG45_GEX
Pool of XVIR1-HS12-SNEGB7,XVIR1-HS15-NCTLB5,XVIR1-HS17-SNEGB7,XVIR1-HS20-NCTLB3,XVIR1-HS3-SNEGB4,XVIR1-HS36-NCTLB5,XVIR1-HS37-NCTLB4,XVIR1-HS41-SNEGB2,XVIR1-HS42-SNEGB2,XVIR1-HS43-SNEGB2,XVIR1-HS44-NCTLB7,XVIR1-HS5-SNEGB2,XVIR1-HS6-SNEGB5


title: B16F10_Tada2bsg1_rep1

description: Library name: Sample 4


title: B16F10_GFPsg_rep3

description: Library name: Sample 3

value: WT


title: run_0333_A549

description:
Library name: SAMPLE 1
Druggable Genome Library infected A549 cells engrafted into 120 NOG mice for the in vivo arm (mouse#1-30)


title: pool-12,well-2,ADT

description:
Library name: XVIR1-POOL-SCC45_ADT
Pool of XVIR1-HS12-SNEGB7,XVIR1-HS15-NCTLB5,XVIR1-HS17-SNEGB7,XVIR1-HS20-NCTLB3,XVIR1-HS3-SNEGB4,XVIR1-HS36-NCTLB5,XVIR1-HS37-NCTLB4,XVIR1-HS41-SNEGB2,XVIR1-HS42-SNEGB2,XVIR1-HS43-SNEGB2,XVIR1-HS44-NCTLB7,XVIR1-HS5-SNEGB2,XVIR1-HS6-SNEGB5


title: pool-12,well-1,ADT

description:
Library name: XVIR1-POOL-SCC44_ADT
Pool of XVIR1-HS12-SNEGB7,XVIR1-HS15-NCTLB5,XVIR1-HS17-SNEGB7,XVIR1-HS20-NCTLB3,XVIR1-HS3-SNEGB4,XVIR1-HS36-NCTLB5,XVIR1-HS37-NCTLB4,XVIR1-HS41-SNEGB2,XVIR1-HS42-SNEGB2,XVIR1-HS43-SNEGB2,XVIR1-HS44-NCTLB7,XVIR1-HS5-SNEGB2,XVIR1-HS6-SNEGB5


title: Primary human CD4 T cell, 7 ORF screen, 90 min stimulation, channel 2, ORF library

city: Cambridge

first: Adam

middle: J

last: Rubin

state: Massachusetts

address: 415 Main St.

institute: Broad Institute

description: Library name: Primary_Experiment_1_CITE_channel_2_ORF

data_processing:
Raw Illumina outupt files were processed into fastq files using the Cumulus V2.1.1 Cell Ranger workflow on the Terra platform. The Cumulus workflow operated on the fastq files to generate processed data files for single-cell RNA, ADT, and HTO libraries. In the associated raw data fastq files, R1 corresponds to the 10x cell barcode and UMI, and R2 corresponds to the transcript, ADT-identifying, or HTO-identifying read.
For ORF barcode libraries, a custom Python script (shared in the linked manuscript, called process_CITE_ORF_barcode.py) was used to process fastq files into a matrix of cell barcodes versus ORF barcodes, with counts of each ORF barcode observed in each cell. In the associated raw data fastq files, R1 corresponds to the 10x cell barcode and UMI, and R2 corresponds to the ORF barcode read. As described in feature_reference.csv, the ORF barcode is found in positions 19-28 of the R2 read.
Seurat v4.3.0 was used to merge single-cell RNA, ADT, HTO, and ORF library processed data from multiple channels and perform final analyses.
Assembly: GRCh38
Supplementary files format and content: Cell Ranger output files: *filtered_feature_bc_matrix.h5, *adt.csv, and *hto.csv files can be loaded directly into Seurat..

molecule: other

source_name: Primary CD4 T cell

growth_protocol: Jurkat T cells were grown in RPMI supplemented 10% FBS and 1% penicillin/streptomycin. Primary human CD4 T cells were grown in the same media with the addition of 50 U/ml IL-2.

extract_protocol:
Cells were subjected to the 10x Genomics Next GEM single-cell 3' RNA-seq v3.1 protocol with modifications for Feature Barcoding to amplify ADT and HTO libraries.
Gene expression, ADT, and HTO libraries were generated following the protocol from 10x Genomics. ORF barcode libraries were generated using cDNA material from the 10x Genomics gene expression library generation protocol as input,with a detailed description in Rubin et al. bioRxiv 2024.

treatment_protocol: Cells were stimulated by the addition of anti-CD3 and anti-IgG antibodies for 30 or 90 minutes. For the screen experiment using Jurkat T cells, one sample of cells was stimulated for each time point. The cells from each time point were stained with hashtag antibodies (to record the time point in the HTO library) and surface protein detection (ADT library) antibodies, and then all cells were combined into a single pool that was loaded onto multiple channels in the 10x Genomics controller. For experiments using primary human CD4 T cells, cells were stimulated in biological replicate samples. Then each replicate sample was stained with hashtag antibodies, and all replciates were combined into a single pool that was loaded onto multiple channels in the 10x Genomics controller.

value: Primary CD4 T cell

value: TCR stimulation


title: run_0337_A549

description:
Library name: SAMPLE 4
Druggable Genome Library infected A549 cells engrafted into 120 NOG mice for the in vivo arm (mouse#93-120)


title: run_0336_A549

description:
Library name: SAMPLE 3
Druggable Genome Library infected A549 cells engrafted into 120 NOG mice for the in vivo arm (mouse#62-92)


title: run_0335_A549

description:
Library name: SAMPLE 2
Druggable Genome Library infected A549 cells engrafted into 120 NOG mice for the in vivo arm (mouse#31-61)


title: Primary human CD4 T cell, 7 ORF screen, 90 min stimulation, channel 2, HTO library

description: Library name: Primary_Experiment_1_CITE_channel_2_HTO

data_processing:
Raw Illumina outupt files were processed into fastq files using the Cumulus V2.1.1 Cell Ranger workflow on the Terra platform. The Cumulus workflow operated on the fastq files to generate processed data files for single-cell RNA, ADT, and HTO libraries. In the associated raw data fastq files, R1 corresponds to the 10x cell barcode and UMI, and R2 corresponds to the transcript, ADT-identifying, or HTO-identifying read.
For ORF barcode libraries, a custom Python script (shared in the linked manuscript, called process_CITE_ORF_barcode.py) was used to process fastq files into a matrix of cell barcodes versus ORF barcodes, with counts of each ORF barcode observed in each cell. In the associated raw data fastq files, R1 corresponds to the 10x cell barcode and UMI, and R2 corresponds to the ORF barcode read. As described in feature_reference.csv, the ORF barcode is found in positions 19-28 of the R2 read.
Seurat v4.3.0 was used to merge single-cell RNA, ADT, HTO, and ORF library processed data from multiple channels and perform final analyses.
Assembly: GRCh38
Supplementary files format and content: Cell Ranger output files: *filtered_feature_bc_matrix.h5, *adt.csv, and *hto.csv files can be loaded directly into Seurat..
Library strategy: CITE-seq


title: Development_3DAP_section_A

description: Library name: GE3DAP-A1


title: B16F10_GFPsg_rep2

description: Library name: Sample 2


title: run_0351_A549

description:
Library name: SAMPLE 6
Druggable Genome Library infected A549 cells engrafted into 49 NOG mice for the in vivo arm repeat


title: pool-12,well-1,GEX

description:
Library name: XVIR1-POOL-SCG44_GEX
Pool of XVIR1-HS12-SNEGB7,XVIR1-HS15-NCTLB5,XVIR1-HS17-SNEGB7,XVIR1-HS20-NCTLB3,XVIR1-HS3-SNEGB4,XVIR1-HS36-NCTLB5,XVIR1-HS37-NCTLB4,XVIR1-HS41-SNEGB2,XVIR1-HS42-SNEGB2,XVIR1-HS43-SNEGB2,XVIR1-HS44-NCTLB7,XVIR1-HS5-SNEGB2,XVIR1-HS6-SNEGB5


title: Primary human CD4 T cell, 7 ORF screen, 90 min stimulation, channel 1, RNA library

description: Library name: Primary_Experiment_1_CITE_channel_1_RNA


title: B16F10_p300KO_rep3

description: Library name: Sample 12

value: Ep300 knockout


title: Primary human CD4 T cell, 7 ORF screen, 90 min stimulation, channel 1, ORF library

description: Library name: Primary_Experiment_1_CITE_channel_1_ORF


title: Jurkat T cell, 132 ORF screen, 90 min stimulation, channel 2, ORF library

description: Library name: Jurkat_Screen_CITE_90min_channel_2_ORF

source_name: Jurkat T cell

value: Jurkat T cell


title: Primary human CD4 T cell, 7 ORF screen, 90 min stimulation, channel 1, HTO library

description: Library name: Primary_Experiment_1_CITE_channel_1_HTO


title: pool-11,well-4,ADT

description:
Library name: XVIR1-POOL-SCC43_ADT
Pool of XVIR1-HS11-SNEGB7,XVIR1-HS12-SNEGB1,XVIR1-HS14-NCTLB1,XVIR1-HS15-NCTLB4,XVIR1-HS21-NCTLB8,XVIR1-HS3-SNEGB3,XVIR1-HS41-SNEGB1,XVIR1-HS42-SNEGB1,XVIR1-HS44-NCTLB2,XVIR1-HS6-SNEGB4,XVIR1-HS8-SNEGB1,XVIR1-HS9-SNEGB7


title: Primary human CD4 T cell, 7 ORF screen, 90 min stimulation, channel 2, RNA library

description: Library name: Primary_Experiment_1_CITE_channel_2_RNA


title: Jurkat T cell, 132 ORF screen, 90 min stimulation, channel 1, ORF library

description: Library name: Jurkat_Screen_CITE_90min_channel_1_ORF


title: B16F10_GFPsg_rep1

description: Library name: Sample 1


title: pool-11,well-4,GEX

description:
Library name: XVIR1-POOL-SCG43_GEX
Pool of XVIR1-HS11-SNEGB7,XVIR1-HS12-SNEGB1,XVIR1-HS14-NCTLB1,XVIR1-HS15-NCTLB4,XVIR1-HS21-NCTLB8,XVIR1-HS3-SNEGB3,XVIR1-HS41-SNEGB1,XVIR1-HS42-SNEGB1,XVIR1-HS44-NCTLB2,XVIR1-HS6-SNEGB4,XVIR1-HS8-SNEGB1,XVIR1-HS9-SNEGB7


title: B16F10_p300KO_rep2

description: Library name: Sample 11


title: pool-11,well-3,ADT

description:
Library name: XVIR1-POOL-SCC42_ADT
Pool of XVIR1-HS11-SNEGB7,XVIR1-HS12-SNEGB1,XVIR1-HS14-NCTLB1,XVIR1-HS15-NCTLB4,XVIR1-HS21-NCTLB8,XVIR1-HS3-SNEGB3,XVIR1-HS41-SNEGB1,XVIR1-HS42-SNEGB1,XVIR1-HS44-NCTLB2,XVIR1-HS6-SNEGB4,XVIR1-HS8-SNEGB1,XVIR1-HS9-SNEGB7


title: Jurkat T cell, 132 ORF screen, 30 min stimulation, channel 2, ORF library

description: Library name: Jurkat_Screen_CITE_30min_channel_2_ORF


title: pool-11,well-3,GEX

description:
Library name: XVIR1-POOL-SCG42_GEX
Pool of XVIR1-HS11-SNEGB7,XVIR1-HS12-SNEGB1,XVIR1-HS14-NCTLB1,XVIR1-HS15-NCTLB4,XVIR1-HS21-NCTLB8,XVIR1-HS3-SNEGB3,XVIR1-HS41-SNEGB1,XVIR1-HS42-SNEGB1,XVIR1-HS44-NCTLB2,XVIR1-HS6-SNEGB4,XVIR1-HS8-SNEGB1,XVIR1-HS9-SNEGB7


title: B16F10_p300KO_rep1

description: Library name: Sample 10


title: B16F10_dKO_rep3

description: Library name: Sample 9

value: Ep300 Crebbp knockout


title: pool-11,well-2,ADT

description:
Library name: XVIR1-POOL-SCC41_ADT
Pool of XVIR1-HS11-SNEGB7,XVIR1-HS12-SNEGB1,XVIR1-HS14-NCTLB1,XVIR1-HS15-NCTLB4,XVIR1-HS21-NCTLB8,XVIR1-HS3-SNEGB3,XVIR1-HS41-SNEGB1,XVIR1-HS42-SNEGB1,XVIR1-HS44-NCTLB2,XVIR1-HS6-SNEGB4,XVIR1-HS8-SNEGB1,XVIR1-HS9-SNEGB7

value: PBMC


title: Jurkat T cell, 132 ORF screen, 30 min stimulation, channel 1, ORF library

description: Library name: Jurkat_Screen_CITE_30min_channel_1_ORF


title: Jurkat T cell, 132 ORF screen, 30 min stimulation, channel 2, HTO library

description: Library name: Jurkat_Screen_CITE_30min_channel_2_HTO


title: pool-11,well-2,GEX

description:
Library name: XVIR1-POOL-SCG41_GEX
Pool of XVIR1-HS11-SNEGB7,XVIR1-HS12-SNEGB1,XVIR1-HS14-NCTLB1,XVIR1-HS15-NCTLB4,XVIR1-HS21-NCTLB8,XVIR1-HS3-SNEGB3,XVIR1-HS41-SNEGB1,XVIR1-HS42-SNEGB1,XVIR1-HS44-NCTLB2,XVIR1-HS6-SNEGB4,XVIR1-HS8-SNEGB1,XVIR1-HS9-SNEGB7


title: Jurkat T cell, 132 ORF screen, 90 min stimulation, channel 2, HTO library

description: Library name: Jurkat_Screen_CITE_90min_channel_2_HTO


title: Jurkat T cell, 132 ORF screen, 90 min stimulation, channel 1, HTO library

description: Library name: Jurkat_Screen_CITE_90min_channel_1_HTO


title: Jurkat T cell, 132 ORF screen, 90 min stimulation, channel 2, ADT library

description: Library name: Jurkat_Screen_CITE_90min_channel_2_ADT


title: Jurkat T cell, 132 ORF screen, 30 min stimulation, channel 1, HTO library

description: Library name: Jurkat_Screen_CITE_30min_channel_1_HTO


title: pool-11,well-1,ADT

description:
Library name: XVIR1-POOL-SCC40_ADT
Pool of XVIR1-HS11-SNEGB7,XVIR1-HS12-SNEGB1,XVIR1-HS14-NCTLB1,XVIR1-HS15-NCTLB4,XVIR1-HS21-NCTLB8,XVIR1-HS3-SNEGB3,XVIR1-HS41-SNEGB1,XVIR1-HS42-SNEGB1,XVIR1-HS44-NCTLB2,XVIR1-HS6-SNEGB4,XVIR1-HS8-SNEGB1,XVIR1-HS9-SNEGB7


title: Jurkat T cell, 132 ORF screen, 90 min stimulation, channel 1, ADT library

description: Library name: Jurkat_Screen_CITE_90min_channel_1_ADT


title: B16F10_dKO_rep2

description: Library name: Sample 8


title: Jurkat T cell, 132 ORF screen, 30 min stimulation, channel 2, ADT library

description: Library name: Jurkat_Screen_CITE_30min_channel_2_ADT


title: B16F10_dKO_rep1

description: Library name: Sample 7


title: B16F10_CbpKO_rep3

description: Library name: Sample 6

value: Crebbp knockout


title: pool-11,well-1,GEX

description:
Library name: XVIR1-POOL-SCG40_GEX
Pool of XVIR1-HS11-SNEGB7,XVIR1-HS12-SNEGB1,XVIR1-HS14-NCTLB1,XVIR1-HS15-NCTLB4,XVIR1-HS21-NCTLB8,XVIR1-HS3-SNEGB3,XVIR1-HS41-SNEGB1,XVIR1-HS42-SNEGB1,XVIR1-HS44-NCTLB2,XVIR1-HS6-SNEGB4,XVIR1-HS8-SNEGB1,XVIR1-HS9-SNEGB7


title: B16F10_CbpKO_rep2

description: Library name: Sample 5


title: Jurkat T cell, 132 ORF screen, 30 min stimulation, channel 2, RNA library

description: Library name: Jurkat_Screen_CITE_30min_channel_2_RNA


title: Jurkat T cell, 132 ORF screen, 90 min stimulation, channel 1, RNA library

description: Library name: Jurkat_Screen_CITE_90min_channel_1_RNA


title: Jurkat T cell, 132 ORF screen, 30 min stimulation, channel 1, RNA library

description: Library name: Jurkat_Screen_CITE_30min_channel_1_RNA


title: Jurkat T cell, 132 ORF screen, 30 min stimulation, channel 1, ADT library

description: Library name: Jurkat_Screen_CITE_30min_channel_1_ADT


title: pool-10,well-4,ADT

description:
Library name: XVIR1-POOL-SCC39_ADT
Pool of XVIR1-HS12-SNEGB5,XVIR1-HS14-NCTLB8,XVIR1-HS15-NCTLB3,XVIR1-HS20-NCTLB5,XVIR1-HS21-NCTLB7,XVIR1-HS22-NCTLB6,XVIR1-HS3-SNEGB1,XVIR1-HS37-NCTLB2,XVIR1-HS43-SNEGB5,XVIR1-HS6-SNEGB3,XVIR1-HS8-SNEGB4,XVIR1-HS9-SNEGB6


title: Jurkat T cell, 132 ORF screen, 90 min stimulation, channel 2, RNA library

description: Library name: Jurkat_Screen_CITE_90min_channel_2_RNA


title: Primary human CD4 T cell, 25 ORF screen, 90 min stimulation, replicate 3, ATAC library

description: Library name: Primary_Experiment_2_ATAC_replicate_3_ATAC

library_source: genomic single cell

data_processing:
Raw Illumina outupt files were processed into fastq files filtered using the Cumulus V2.1.1 Cell Ranger workflow on the Terra platform. The Cumulus workflow operated on the fastq files to generate processed data files for single-cell ATAC libraries (filtered aligned fragments, single cell calls, peak calls). In the associated raw data fastq files, R1 corresponds to the forward genomic DNA read, R2 corresponds to the 10x cell barcode, and R3 corresponds to the reverse genomic DNA read.
For ORF barcode libraries, a custom Python script (shared in the linked manuscript, called process_ATAC_ORF_barcode.py) was used to process fastq files into a matrix of cell barcodes versus ORF barcodes, with counts of each ORF barcode observed in each cell. In the associated raw data fastq files, R2 corresponds to the 10x cell barcode, and R3 corresponds to the ORF barcode read. As described in feature_reference.csv, the ORF barcode is found in positions 19-28 of the R3 read.
Signac v1.9.0 was used to merge single-cell ATAC library processed data from multiple channels and perform final analyses.
Assembly: GRCh38
Supplementary files format and content: Cell Ranger output files: *fragments.tsv.gz, *fragments.tsv.gz.tbi, *peaks.bed, and *singlecell.csv files can be loaded directly into Signac.

extract_protocol:
Cells were subjected to the 10x Genomics single-cell ATAC-seq protocol with modifications for the Spear-ATAC (Pierce et al., Nature Communications 2021) amplification of genetic barcodes.
ATAC chromatin accessibility libraries were generated following the protocol from 10x Genomics. ORF barcode libraries were generated using the final ATAC libraries as input, as described in the Spear-ATAC protocol, with modifications described in detail in Rubin et al. 2024 bioRxiv.

treatment_protocol: Cells were stimulated by the addition of anti-CD3 and anti-IgG antibodies for specified times. For the screen experiment using Jurkat T cells, one sample of cells were stimulated for each time point and these cells were split to be loaded onto separate channels in 10x Genomics controller. For experiments using primary human CD4 T cells, cells were stimulated in biological replicate samples, and each replicate was loaded separately into a channel in the 10x Genomics controller.


title: pool-10,well-4,GEX

description:
Library name: XVIR1-POOL-SCG39_GEX
Pool of XVIR1-HS12-SNEGB5,XVIR1-HS14-NCTLB8,XVIR1-HS15-NCTLB3,XVIR1-HS20-NCTLB5,XVIR1-HS21-NCTLB7,XVIR1-HS22-NCTLB6,XVIR1-HS3-SNEGB1,XVIR1-HS37-NCTLB2,XVIR1-HS43-SNEGB5,XVIR1-HS6-SNEGB3,XVIR1-HS8-SNEGB4,XVIR1-HS9-SNEGB6


title: pool-10,well-3,ADT

description:
Library name: XVIR1-POOL-SCC38_ADT
Pool of XVIR1-HS12-SNEGB5,XVIR1-HS14-NCTLB8,XVIR1-HS15-NCTLB3,XVIR1-HS20-NCTLB5,XVIR1-HS21-NCTLB7,XVIR1-HS22-NCTLB6,XVIR1-HS3-SNEGB1,XVIR1-HS37-NCTLB2,XVIR1-HS43-SNEGB5,XVIR1-HS6-SNEGB3,XVIR1-HS8-SNEGB4,XVIR1-HS9-SNEGB6


title: Primary human CD4 T cell, 25 ORF screen, 90 min stimulation, replicate 2, ATAC library

description: Library name: Primary_Experiment_2_ATAC_replicate_2_ATAC


title: B16F10_CbpKO_rep1

description: Library name: Sample 4


title: B16F10_ctl_rep2

description: Library name: Sample 2


title: B16F10_ctl_rep1

description: Library name: Sample 1


title: Primary human CD4 T cell, 25 ORF screen, 90 min stimulation, replicate 1, ATAC library

description: Library name: Primary_Experiment_2_ATAC_replicate_1_ATAC


title: Jurkat T cell, 132 ORF screen, 90 min stimulation, channel 2, ATAC library

description: Library name: Jurkat_Screen_ATAC_90min_channel_2_ATAC


title: pool-10,well-3,GEX

description:
Library name: XVIR1-POOL-SCG38_GEX
Pool of XVIR1-HS12-SNEGB5,XVIR1-HS14-NCTLB8,XVIR1-HS15-NCTLB3,XVIR1-HS20-NCTLB5,XVIR1-HS21-NCTLB7,XVIR1-HS22-NCTLB6,XVIR1-HS3-SNEGB1,XVIR1-HS37-NCTLB2,XVIR1-HS43-SNEGB5,XVIR1-HS6-SNEGB3,XVIR1-HS8-SNEGB4,XVIR1-HS9-SNEGB6


title: pool-10,well-2,ADT

description:
Library name: XVIR1-POOL-SCC37_ADT
Pool of XVIR1-HS12-SNEGB5,XVIR1-HS14-NCTLB8,XVIR1-HS15-NCTLB3,XVIR1-HS20-NCTLB5,XVIR1-HS21-NCTLB7,XVIR1-HS22-NCTLB6,XVIR1-HS3-SNEGB1,XVIR1-HS37-NCTLB2,XVIR1-HS43-SNEGB5,XVIR1-HS6-SNEGB3,XVIR1-HS8-SNEGB4,XVIR1-HS9-SNEGB6


title: pool-10,well-2,GEX

description:
Library name: XVIR1-POOL-SCG37_GEX
Pool of XVIR1-HS12-SNEGB5,XVIR1-HS14-NCTLB8,XVIR1-HS15-NCTLB3,XVIR1-HS20-NCTLB5,XVIR1-HS21-NCTLB7,XVIR1-HS22-NCTLB6,XVIR1-HS3-SNEGB1,XVIR1-HS37-NCTLB2,XVIR1-HS43-SNEGB5,XVIR1-HS6-SNEGB3,XVIR1-HS8-SNEGB4,XVIR1-HS9-SNEGB6


title: B16F10_ctl_rep3

description: Library name: Sample 3


title: Jurkat T cell, 132 ORF screen, 90 min stimulation, channel 1, ATAC library

description: Library name: Jurkat_Screen_ATAC_90min_channel_1_ATAC


title: Jurkat T cell, 132 ORF screen, 30 min stimulation, channel 1, ATAC library

description: Library name: Jurkat_Screen_ATAC_30min_channel_1_ATAC


title: Liver tumor, TREM2_neg_TAM, rep3

city: Hong Kong

first: Alfred Sze-Lok

last: Cheng

address: Lo Kwee-Seong Integrated Biomedical Sciences Building, Area 39, CUHK

department: School of Biomedical Sciences

country: Hong Kong

institute: The Chinese University of Hong Kong

description: Library name: TREM2_neg_TAM_3

data_processing:
Reads were aligned to the mouse reference genome (mm10) using STAR (v2.7.10a). The read counts were calculated using subread-featureCounts (v2.0.3) and then obtain the values of transcripts per million (TPM).
Assembly: mm10
Supplementary files format and content: csv files include TPM values for each Sample

source_name: liver tumor

extract_protocol:
Total RNA was extracted from TAMs using TRIzol (Invitrogen) according to manual instruction. RNA integrity and concentration were assessed on the Agilent 4200 TapeStation System. Complementary DNA (cDNA) synthesis, library preparation, and sequencing were conducted using Illumina NovaSeq 6000 with paired-end 150 bp sequencing by Novogene.
Librariy construction for RNA-seq were prepared by Novogene Co., Ltd following standard protocols.

value: liver tumor


title: Jurkat T cell, 132 ORF screen, 30 min stimulation, channel 2, ATAC library

description: Library name: Jurkat_Screen_ATAC_30min_channel_2_ATAC


title: Primary human CD4 T cell, 7 ORF screen, 90 min stimulation, replicate 2, ATAC library

description: Library name: Primary_Experiment_1_ATAC_replicate_2_ATAC


title: Primary human CD4 T cell, 7 ORF screen, 90 min stimulation, replicate 1, ATAC library

description: Library name: Primary_Experiment_1_ATAC_replicate_1_ATAC


title: E1

city: Wuhan City

first: Chengming

last: Qu

state: Hubei

address: No.299 Bayi Road, Wuchang District

institute: Wuhan University

description: Library name: Sample4

data_processing:
Paired-end reads were harvested from sequencer, and were quality controlled by Q30.
After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v4.6), the high quality clean reads were aligned to the reference genome with STAR software (v2.7.11b)
Raw read counts were extracted from the second column of the STAR output file 'ReadsPerGene.out.tab', which contained the unstranded RNA-seq read counts.
Assembly: Mus_musculus.GRCm39
Supplementary files format and content: raw counts for each Sample

source_name: TGF-beta-activated 10T1/2 cells

extract_protocol:
Total RNA was extracted with Trizol (Invitrogen, Carlsbad, CA, USA), and subjected to ribosomal RNA (rRNA) removal using GenSeq® rRNA Removal Kit (GenSeq, Inc., Shanghai, China).
The rRNA-depleted samples were used for library construction with GenSeq® Directional RNA Library Prep Kit (GenSeq, Inc., Shanghai, China) by following manufacturer’s recommendations.

value: TGF-beta-activated 10T1/2 cells

value: Ce6@D4-EV–mediated targeted photodynamic therapy


title: pool-10,well-1,ADT

description:
Library name: XVIR1-POOL-SCC36_ADT
Pool of XVIR1-HS12-SNEGB5,XVIR1-HS14-NCTLB8,XVIR1-HS15-NCTLB3,XVIR1-HS20-NCTLB5,XVIR1-HS21-NCTLB7,XVIR1-HS22-NCTLB6,XVIR1-HS3-SNEGB1,XVIR1-HS37-NCTLB2,XVIR1-HS43-SNEGB5,XVIR1-HS6-SNEGB3,XVIR1-HS8-SNEGB4,XVIR1-HS9-SNEGB6


title: E2

description: Library name: Sample5


title: Liver tumor, TREM2_neg_TAM, rep2

description: Library name: TREM2_neg_TAM_2


title: E3

description: Library name: Sample6


title: pool-9,well-4,GEX

description:
Library name: XVIR1-POOL-SCG35_GEX
Pool of XVIR1-HS11-SNEGB1,XVIR1-HS12-SNEGB4,XVIR1-HS14-NCTLB5,XVIR1-HS19-NCTLB4,XVIR1-HS21-NCTLB6,XVIR1-HS22-NCTLB5,XVIR1-HS4-SNEGB6,XVIR1-HS40-NCTLB6,XVIR1-HS41-SNEGB3,XVIR1-HS42-SNEGB6,XVIR1-HS44-NCTLB6,XVIR1-HS9-SNEGB4


title: Liver tumor, TREM2_neg_TAM, rep1

description: Library name: TREM2_neg_TAM_1


title: Liver tumor, TREM2_pos_TAM, rep3

description: Library name: TREM2_pos_TAM_3


title: pool-10,well-1,GEX

description:
Library name: XVIR1-POOL-SCG36_GEX
Pool of XVIR1-HS12-SNEGB5,XVIR1-HS14-NCTLB8,XVIR1-HS15-NCTLB3,XVIR1-HS20-NCTLB5,XVIR1-HS21-NCTLB7,XVIR1-HS22-NCTLB6,XVIR1-HS3-SNEGB1,XVIR1-HS37-NCTLB2,XVIR1-HS43-SNEGB5,XVIR1-HS6-SNEGB3,XVIR1-HS8-SNEGB4,XVIR1-HS9-SNEGB6


title: B2

description: Library name: Sample2

value: PBS


title: pool-9,well-3,ADT

description:
Library name: XVIR1-POOL-SCC34_ADT
Pool of XVIR1-HS11-SNEGB1,XVIR1-HS12-SNEGB4,XVIR1-HS14-NCTLB5,XVIR1-HS19-NCTLB4,XVIR1-HS21-NCTLB6,XVIR1-HS22-NCTLB5,XVIR1-HS4-SNEGB6,XVIR1-HS40-NCTLB6,XVIR1-HS41-SNEGB3,XVIR1-HS42-SNEGB6,XVIR1-HS44-NCTLB6,XVIR1-HS9-SNEGB4


title: Ce6@D4-EV–mediated targeted photodynamic therapy_rep1

description:
Library name: Sample5
sample_6

source_name: Tumor tissue sorted from KPC subcutaneous tumor


title: B1

description: Library name: Sample1


title: pool-9,well-4,ADT

description:
Library name: XVIR1-POOL-SCC35_ADT
Pool of XVIR1-HS11-SNEGB1,XVIR1-HS12-SNEGB4,XVIR1-HS14-NCTLB5,XVIR1-HS19-NCTLB4,XVIR1-HS21-NCTLB6,XVIR1-HS22-NCTLB5,XVIR1-HS4-SNEGB6,XVIR1-HS40-NCTLB6,XVIR1-HS41-SNEGB3,XVIR1-HS42-SNEGB6,XVIR1-HS44-NCTLB6,XVIR1-HS9-SNEGB4


title: Ce6@D4-EV–mediated targeted photodynamic therapy_rep4

description:
Library name: Sample8
sample_10

value: Tumor tissue sorted from KPC subcutaneous tumor


title: Liver tumor, TREM2_pos_TAM, rep2

description: Library name: TREM2_pos_TAM_2


title: pool-9,well-2,ADT

description:
Library name: XVIR1-POOL-SCC33_ADT
Pool of XVIR1-HS11-SNEGB1,XVIR1-HS12-SNEGB4,XVIR1-HS14-NCTLB5,XVIR1-HS19-NCTLB4,XVIR1-HS21-NCTLB6,XVIR1-HS22-NCTLB5,XVIR1-HS4-SNEGB6,XVIR1-HS40-NCTLB6,XVIR1-HS41-SNEGB3,XVIR1-HS42-SNEGB6,XVIR1-HS44-NCTLB6,XVIR1-HS9-SNEGB4


title: BMDM, with AC treatment, rep1

description: Library name: BMDM_AC_1

source_name: BMDM

extract_protocol:
Total RNA was extracted from BMDMs using TRIzol (Invitrogen) according to manual instruction. RNA integrity and concentration were assessed on the Agilent 4200 TapeStation System. Complementary DNA (cDNA) synthesis, library preparation, and sequencing were conducted using Illumina NovaSeq 6000 with paired-end 150 bp sequencing by Novogene.
Librariy construction for RNA-seq were prepared by Novogene Co., Ltd following standard protocols.

value: BMDM


title: Ce6@D4-EV–mediated targeted photodynamic therapy_rep3

description:
Library name: Sample7
sample_9


title: Rice plants with CS8-gfp inoculation rep3

city: Zhoukou

first: Xuejin

last: Liu

state: Henan

address: No. 26 East Renmin Road

department: Department of Gastroenterology

institute: Zhoukou Central Hospital Affiliated to Henan Medical University

description: Library name: CS8-3

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: https://data.jgi.doe.gov/refine-download/phytozome?genome_id=323&_gl=1*sg2gsk*_ga*NTMyNDc0MDkwLjE3MDQ2OTY2ODc.*_ga_YBLMHYR3C2*MTc0NTI5MzQ2OC45My4wLjE3NDUyOTM0NjguMC4wLjA.
Supplementary files format and content: xlsx file includes FPKM values for each Sample

organism: Oryza sativa

source_name: whole rice seedlings

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

value: whole rice seedlings

value: Rice plants with CS8-gfp inoculation


title: pool-9,well-3,GEX

description:
Library name: XVIR1-POOL-SCG34_GEX
Pool of XVIR1-HS11-SNEGB1,XVIR1-HS12-SNEGB4,XVIR1-HS14-NCTLB5,XVIR1-HS19-NCTLB4,XVIR1-HS21-NCTLB6,XVIR1-HS22-NCTLB5,XVIR1-HS4-SNEGB6,XVIR1-HS40-NCTLB6,XVIR1-HS41-SNEGB3,XVIR1-HS42-SNEGB6,XVIR1-HS44-NCTLB6,XVIR1-HS9-SNEGB4


title: BMDM, with AC treatment, rep3

description: Library name: BMDM_AC_3


title: Liver tumor, TREM2_pos_TAM, rep1

description: Library name: TREM2_pos_TAM_1


title: PBS_rep2

description:
Library name: Sample2
sample_C2


title: BMDM, with AC treatment, rep2

description: Library name: BMDM_AC_2


title: Ce6@D4-EV–mediated targeted photodynamic therapy_rep2

description:
Library name: Sample6
sample_7


title: PBS_rep3

description:
Library name: Sample3
sample_C3


title: PBS_rep1

description:
Library name: Sample1
sample_C1


title: PBS_rep4

description:
Library name: Sample4
sample_C5


title: BMDM, without AC treatment, rep3

description: Library name: BMDM_3


title: pool-9,well-2,GEX

description:
Library name: XVIR1-POOL-SCG33_GEX
Pool of XVIR1-HS11-SNEGB1,XVIR1-HS12-SNEGB4,XVIR1-HS14-NCTLB5,XVIR1-HS19-NCTLB4,XVIR1-HS21-NCTLB6,XVIR1-HS22-NCTLB5,XVIR1-HS4-SNEGB6,XVIR1-HS40-NCTLB6,XVIR1-HS41-SNEGB3,XVIR1-HS42-SNEGB6,XVIR1-HS44-NCTLB6,XVIR1-HS9-SNEGB4


title: Tonsil, Replicate 3, scRNAseq

city: Saint Louis

first: Alina

last: Ulezko Antonova

state: MO

address: 660 S. Euclid Ave

department: Path/Immuno

institute: WUSM

description: Library name: TONSIL3

data_processing:
scRNAseq downstream analyses were performed using the Seurat software package version 4.0 for R (http://satijalab.org/seurat/). For barcoded samples, Seurat’s 4 HTODemux() function was used as described previously (https://satijalab.org/seurat/articles/hashing_vignette). After removing unwanted cells and genes from the dataset, raw UMIs in each cell were both scaled and normalized via the SCTransform function. To improve downstream dimensionality reduction and clustering, we regressed out unwanted source of variation arising from the percentage of mitochondrial genes. Then, highly variable genes were identified and selected for PCA reduction of high-dimensional data. Cells in this reduced space were harmonized to adjust for batch effects coming from multiple donors using the Harmony tool implemented in Seurat. These low dimensional corrected Harmony embeddings were used for downstream analyses. Graph-based clustering analysis was performed on the reduced data with Seurat. The resolution in the FindClusters function from Seurat was set at values between 0.3 and 0.7, and the clustering results were shown in a computed UMAP plot (dims = 1:20). Different cell types were grouped based on top markers.
Assembly: GRCh38
Supplementary files format and content: CellRanger count output (features.tsv/matrix.mtx/barcodes.tsv), zipped

source_name: Tonsil

extract_protocol:
Fresh, magnetically enriched cells were washed in MACS buffer and counted to analyze cell viability. Next, cells were resuspended in a cell staining buffer and stained with antibodies for the identification of pDC. All samples were stained with the same antibodies. Specifically, samples were stained with anti-CD3 (PerCP-Cy5.5, Biolegend), anti-CD19 (PerCP-Cy5.5, Biolegend), and anti-CD14 (PerCP-Cy5.5, Biolegend) to exclude T cells, B cells and monocytes, respectively, anti-CD1c (BV510, Biolegend) to exclude mature DC2, and anti-ILT3 (PE-Cy7, Biolegend), anti-CD123 (PE, Biolegend) and anti-BDCA2 (FITC, Millteny) to select pDC. We performed purity checks and achieved a very high purity (>98%). The cells were sorted using flow cytometry on BD FACS Aria II
For library preparation, the 10X Genomics Next GEM Single Cell 3’ Reagents Kit was used. This process utilized the Chromium Next GEM Single Cell 3′ Kit v3.1 (16 rxns), Chromium Next GEM Chip G Single Cell Kit (48 rxns), and Dual Index Kit TT Set A (96 rxns). In brief, up to 23,000 cells were partitioned into nanoliter Gel-bead-in-Emulsions (GEMs) droplets, each containing retro-transcriptase reaction mix. Single-cell cDNA received a unique 12-nucleotide barcode and unique molecular identifier (UMI). Subsequently, GEM cDNA underwent 11 cycles of amplification before purification using SPRIselect beads. The generation of gene-expression (GEX)  followed the recommendations provided in the 10x Genomics Chromium Single Cell 3′ Reagent Kits User Guide (v3.1 Chemistry Dual Index), with modifications to PCR cycles based on the calculated cDNA concentration. The concentration of each library was determined using qPCR with the KAPA library Quantification Kit following the manufacturer’s protocol (KAPA Biosystems/Roche). The sequencing of normalized cDNA libraries was performed on a NovaSeq6000 S4 Flow Cell using the XP workflow and a 28×10×10×150 sequencing recipe as per the manufacturer's protocol (Illumina). A median sequencing depth of 50,000 and 5,000 reads per cell was targeted for the GEX and HTO library, respectively.

value: Tonsil

tag: batch


title: Blood, Replicate 2, scRNAseq

description: Library name: PBMC3

source_name: Blood

value: Blood


title: pool-9,well-1,ADT

description:
Library name: XVIR1-POOL-SCC32_ADT
Pool of XVIR1-HS11-SNEGB1,XVIR1-HS12-SNEGB4,XVIR1-HS14-NCTLB5,XVIR1-HS19-NCTLB4,XVIR1-HS21-NCTLB6,XVIR1-HS22-NCTLB5,XVIR1-HS4-SNEGB6,XVIR1-HS40-NCTLB6,XVIR1-HS41-SNEGB3,XVIR1-HS42-SNEGB6,XVIR1-HS44-NCTLB6,XVIR1-HS9-SNEGB4


title: Rice plants with CS8-gfp inoculation rep1

description: Library name: CS8-1


title: pool-9,well-1,GEX

description:
Library name: XVIR1-POOL-SCG32_GEX
Pool of XVIR1-HS11-SNEGB1,XVIR1-HS12-SNEGB4,XVIR1-HS14-NCTLB5,XVIR1-HS19-NCTLB4,XVIR1-HS21-NCTLB6,XVIR1-HS22-NCTLB5,XVIR1-HS4-SNEGB6,XVIR1-HS40-NCTLB6,XVIR1-HS41-SNEGB3,XVIR1-HS42-SNEGB6,XVIR1-HS44-NCTLB6,XVIR1-HS9-SNEGB4


title: BMDM, without AC treatment, rep2

description: Library name: BMDM_2


title: BMDM, without AC treatment, rep1

description: Library name: BMDM_1


title: Tonsil, Replicate 1, scRNAseq

description: Library name: TONSIL1


title: Rice plants without CS8-gfp inoculation rep3

description: Library name: UCS8-3

value: Rice plants without CS8-gfp inoculation


title: pool-8,well-4,ADT

description:
Library name: XVIR1-POOL-SCC31_ADT
Pool of XVIR1-HS14-NCTLB4,XVIR1-HS17-SNEGB5,XVIR1-HS21-NCTLB5,XVIR1-HS22-NCTLB4,XVIR1-HS36-NCTLB1,XVIR1-HS37-NCTLB1,XVIR1-HS40-NCTLB4,XVIR1-HS41-SNEGB1,XVIR1-HS43-SNEGB1,XVIR1-HS44-NCTLB8,XVIR1-HS6-SNEGB7,XVIR1-HS7-SNEGB3,XVIR1-HS8-SNEGB2


title: Rice plants without CS8-gfp inoculation rep2

description: Library name: UCS8-2


title: Rice plants with CS8-gfp inoculation rep2

description: Library name: CS8-2


title: Stim9_24hr_Rep2

description: Library name: Stim9_24hr_Rep2

data_processing:
Raw fastq reads were processed using the ENCODE bulk ATAC-seq pipeline (https://github.com/ENCODE-DCC/atac-seq-pipeline). The chromVAR package in R was used to compute transcription factor activities, which are reported as deviation z-scores in the processed data file.
Assembly: GRCh38
Supplementary files format and content: The processed data file Stim_ATAC_deviations_z.txt is a matrix where rows represent JASPAR motifs and columns represent samples. The values correspond to deviation z-scores computed using the chromVAR package.

source_name: Jurkat T cells

growth_protocol: Jurkat T cells were grown in RPMI supplemented 10% FBS and 1% penicillin/streptomycin

extract_protocol:
5e4 cells were pelleted and resuspended in 50ul of ATAC RSB with 0.1% NP40, 0.1% Tween-20, and 0.01%. After three minutes, 1ml of ATAC RSB with 0.1% Tween-20 was added, tubes were inverted, and nuclei were centrifuged at 500 rcf for 10 min. Supernatant was carefully removed and nuclei were resuspended in 50ul transposition mix (25ul TD buffer, 2.5ul transposase, 16.5ul PBS, 0.5ul 0.1% digitonin, 0.5ul 10% Tween-20, and 5ul water). Transposition was performed for 30 minutes at 37 C with shaking in a thermomixer at 1000 RPM. Reactions were purified with a Zymo DNA Clean & Concentrator 5 kit.
Libraries were generated largely following the Omni-ATAC protocol (Corces et al., 2017, Nature Methods). Purified ATAC fragments were amplified for eight cycles and purified using SPRIselect beads (1.2x). Libraries were quantified by Qubit and Bioanalyzer before sequencing on an Illumina NextSeq 500 targeting 2e6 read-pairs per library.

treatment_protocol: Cells were stimulated by the addition of anti-CD3 and anti-IgG antibodies for specified times

value: Jurkat T cells

value: TCR stimulation


title: pool-8,well-4,GEX

description:
Library name: XVIR1-POOL-SCG31_GEX
Pool of XVIR1-HS14-NCTLB4,XVIR1-HS17-SNEGB5,XVIR1-HS21-NCTLB5,XVIR1-HS22-NCTLB4,XVIR1-HS36-NCTLB1,XVIR1-HS37-NCTLB1,XVIR1-HS40-NCTLB4,XVIR1-HS41-SNEGB1,XVIR1-HS43-SNEGB1,XVIR1-HS44-NCTLB8,XVIR1-HS6-SNEGB7,XVIR1-HS7-SNEGB3,XVIR1-HS8-SNEGB2


title: Rice plants without CS8-gfp inoculation rep1

description: Library name: UCS8-1


title: pool-8,well-3,ADT

description:
Library name: XVIR1-POOL-SCC30_ADT
Pool of XVIR1-HS14-NCTLB4,XVIR1-HS17-SNEGB5,XVIR1-HS21-NCTLB5,XVIR1-HS22-NCTLB4,XVIR1-HS36-NCTLB1,XVIR1-HS37-NCTLB1,XVIR1-HS40-NCTLB4,XVIR1-HS41-SNEGB1,XVIR1-HS43-SNEGB1,XVIR1-HS44-NCTLB8,XVIR1-HS6-SNEGB7,XVIR1-HS7-SNEGB3,XVIR1-HS8-SNEGB2


title: DMD-3

city: Leiden

first: Clara

last: Martinez Mir

address: Einthovenweg 20

department: Anatomy and Embryology

country: Netherlands

institute: Leiden University Medical Center

description: Library name: DMD-3

data_processing:
Sequencing libraries were mapped using STAR (v.2.7.7a) with default parameters to the mouse GRCm38 genome (Ensembl 102). Only reads mapping to gene bodies (exons or introns) were used for downstream analysis. Sections were filtered based on their total transcript counts. Genes linked to mapping errors (Kcnq1ot1, Mir5109, Lars2 and Malat1), spike-ins, ribosomal genes, low detected genes and genes with saturated UMI counts were excluded from downstream analysis. For each muscle, data was normalized to 300,000 counts per section.
Assembly: Ensemble version 102 of the mouse genome (GRCm38)
Supplementary files format and content: Tabular-separated file indicating number of transcripts per section obtained as previously described (Grün, Dominic, Lennart Kester, and Alexander Van Oudenaarden. "Validation of noise models for single-cell transcriptomics." Nature methods 11.6 (2014): 637). We refer to transcripts as unique molecules based on UMI correction.

source_name: tibialis anterior muscle

extract_protocol:
After cryosecioning, total RNA is extracted from individual sections using TRIZOL.
Total RNA from individual sections is sorted into 96-well plates containing mineral oil, and uniquely barcoded section specific primers (read 2 contain the unique molecular identifier in the first 8 bases, followed by the 8-nucleotide long section barcode) for mRNA detection.

value: tibialis anterior muscle


title: DMD-2

description: Library name: DMD-2


title: Stim9_24hr_Rep1

description: Library name: Stim9_24hr_Rep1


title: adult neural complex, cryosection D

city: Minato-ku

first: Xin

last: Zeng

state: Tokyo

address: 8F General Research Bldg.,4-6-1 Shirokanedai

department: The Institute of Medical Science

country: Japan

institute: The University of Tokyo

description: Library name: D_Crobusta220127nc4

data_processing:
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline to generate FASTQ files
Sequences were aligned to KH2013 genome
Assembly: KH2013
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors.json.json: scale factor in jason format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial Transcriptomics

organism: Ciona robusta

source_name: adult neural complex

extract_protocol:
Fresh frozen tissues were OCT embedded, and 10µm frozen sections were cut with cryostat
Spatial transcriptome sequencing libraries were prepared with 10x Genomics Visium Spatial Gene Expression Slides & Reagent kit according to manufacturer's construction

value: adult neural complex

value: wild type


title: pool-8,well-3,GEX

description:
Library name: XVIR1-POOL-SCG30_GEX
Pool of XVIR1-HS14-NCTLB4,XVIR1-HS17-SNEGB5,XVIR1-HS21-NCTLB5,XVIR1-HS22-NCTLB4,XVIR1-HS36-NCTLB1,XVIR1-HS37-NCTLB1,XVIR1-HS40-NCTLB4,XVIR1-HS41-SNEGB1,XVIR1-HS43-SNEGB1,XVIR1-HS44-NCTLB8,XVIR1-HS6-SNEGB7,XVIR1-HS7-SNEGB3,XVIR1-HS8-SNEGB2

value: PBMC


title: Tonsil, Replicate 2, scRNAseq

description: Library name: TONSIL2


title: DMD-1

description: Library name: DMD-1


title: Stim8_16hr_Rep1

description: Library name: Stim8_16hr_Rep1


title: Ctr-2

description: Library name: Ctr-2


title: adult neural complex, cryosection C

description: Library name: C_Crobusta220127nc3


title: adult neural complex, cryosection B

description: Library name: B_Crobusta220127nc2


title: pool-8,well-2,ADT

description:
Library name: XVIR1-POOL-SCC29_ADT
Pool of XVIR1-HS14-NCTLB4,XVIR1-HS17-SNEGB5,XVIR1-HS21-NCTLB5,XVIR1-HS22-NCTLB4,XVIR1-HS36-NCTLB1,XVIR1-HS37-NCTLB1,XVIR1-HS40-NCTLB4,XVIR1-HS41-SNEGB1,XVIR1-HS43-SNEGB1,XVIR1-HS44-NCTLB8,XVIR1-HS6-SNEGB7,XVIR1-HS7-SNEGB3,XVIR1-HS8-SNEGB2


title: adult neural complex, cryosection A

description: Library name: A_Crobusta220127nc1


title: Stim8_16hr_Rep2

description: Library name: Stim8_16hr_Rep2


title: Stim7_8hr_Rep1

description: Library name: Stim7_8hr_Rep1


title: Stim7_8hr_Rep2

description: Library name: Stim7_8hr_Rep2


title: Ctr-1

description: Library name: Ctr-1


title: pool-8,well-1,ADT

description:
Library name: XVIR1-POOL-SCC28_ADT
Pool of XVIR1-HS14-NCTLB4,XVIR1-HS17-SNEGB5,XVIR1-HS21-NCTLB5,XVIR1-HS22-NCTLB4,XVIR1-HS36-NCTLB1,XVIR1-HS37-NCTLB1,XVIR1-HS40-NCTLB4,XVIR1-HS41-SNEGB1,XVIR1-HS43-SNEGB1,XVIR1-HS44-NCTLB8,XVIR1-HS6-SNEGB7,XVIR1-HS7-SNEGB3,XVIR1-HS8-SNEGB2


title: pool-8,well-2,GEX

description:
Library name: XVIR1-POOL-SCG29_GEX
Pool of XVIR1-HS14-NCTLB4,XVIR1-HS17-SNEGB5,XVIR1-HS21-NCTLB5,XVIR1-HS22-NCTLB4,XVIR1-HS36-NCTLB1,XVIR1-HS37-NCTLB1,XVIR1-HS40-NCTLB4,XVIR1-HS41-SNEGB1,XVIR1-HS43-SNEGB1,XVIR1-HS44-NCTLB8,XVIR1-HS6-SNEGB7,XVIR1-HS7-SNEGB3,XVIR1-HS8-SNEGB2


title: B3

description: Library name: Sample3


title: Strain Y168, pSer2-RNAPII, biol rep 3, ChIP

city: Munich

first: Ioannis

last: Tsirkas

address: Feodor-Lynen-Strasse 21

department: Institute of Epigenetics and Stem Cells

country: Germany

institute: Helmholtz Zentrum München, GmbH

description: Library name: Y168_IP_BioRep3

data_processing:
sequencing reads were aligned to the Saccharomyces cerevisiae genome (sacCer3) using STARaligner (version 2.7.6a), including the annotations for the integrated mAIRN reporter sequence
Assembly: sacCer3
Supplementary files format and content: subsampled BigWig files to equal sequencing depth per condition

organism: Saccharomyces cerevisiae

source_name: yeast cell

growth_protocol: Cells were inoculated in 5 ml Yeast Peptone media +2% Raffinose (RAF) (YPR) in 50 ml falcon tubes and were grown overnight (O/N) at 30oC at 230 rpm. The next day, the starters were diluted in 50 ml YPR in 100 or 250 ml glass flasks and were grown O/N until mid-exponential (0D600 = 0.5). When yeast cultures have reached the desired OD600, Pgal-14xPP7-mAIRN was induced with 2% Galactose (GAL) (5 ml 20% GAL) and were grown for an additional 2 hr.

extract_protocol:
Cells were fixed with 1% Formaldehyde (FA) for 15 min at 30oC at 230 rpm and were quenched with 128 mM Glycine. Upon lysis, chromatin was sheared in a Covaris Sonicator. pSer2-RNAPII-Immunoprecipitated chromatin was treated with Rnase A and Proteinase K, and DNA was isolated and precipitated with Phenol-Chloroform extraction and Ethanol 100%.
ChIP-seq were prepared using NEBNext® Ultra™ II DNA Library Prep with Sample Purification Beads according to manufacturer’s protocol. To account for the smaller amounts of immunoprecipitated materials in ChIP, adaptor was diluted 10-fold before adaptor ligation. Libraries were amplified with 3 and 7 cycles of PCR for input and ChIP samples respectively. Fragment size and quantification of amplified libraries were analyzed on fragment analyzer (Agilent) and size selected with QIAseq® Beads if needed before library pooling and sequencing. Libraries were sequenced for 150 cycles in paired-end mode on the Illumina NovaSeq X+ 1.5B platform

treatment_protocol: In strains with Pgal-RNase H1 overexpression (RNH1 OE) (Y167 and Y168), RNH1 was endogenously induced with 2%GAL for 2 hr, simultaneously with Pgal-14xPP7-mAIRN induction

value: yeast cell

tag: strain

value: Pgal-14xPP7-mAIRN HO Pgal-RNH1-3xHA (Y168)

value: Pgal-14xPP7-mAIRN and Pgal-RNH1-3xHA transcription induction with Galactose 2% for 2hr

tag: chip antibody

value: pSer2-RNAPII (Abcam, #ab5095)


title: Stim6_4hr_Rep2

description: Library name: Stim6_4hr_Rep2


title: pool-8,well-1,GEX

description:
Library name: XVIR1-POOL-SCG28_GEX
Pool of XVIR1-HS14-NCTLB4,XVIR1-HS17-SNEGB5,XVIR1-HS21-NCTLB5,XVIR1-HS22-NCTLB4,XVIR1-HS36-NCTLB1,XVIR1-HS37-NCTLB1,XVIR1-HS40-NCTLB4,XVIR1-HS41-SNEGB1,XVIR1-HS43-SNEGB1,XVIR1-HS44-NCTLB8,XVIR1-HS6-SNEGB7,XVIR1-HS7-SNEGB3,XVIR1-HS8-SNEGB2


title: Strain Y167, pSer2-RNAPII, biol rep 3, ChIP

description: Library name: Y167_IP_BioRep3

value: Pgal-14xPP7-mAIRN CoD Pgal-RNH1-3xHA (Y167)


title: WT-2

description: Library name: WT-2


title: Stim6_4hr_Rep1

description: Library name: Stim6_4hr_Rep1


title: WT-1

description: Library name: WT-1


title: pool-7,well-3,ADT

description:
Library name: XVIR1-POOL-SCC26_ADT
Pool of XVIR1-HS11-SNEGB5,XVIR1-HS12-SNEGB2,XVIR1-HS16-NCTLB6,XVIR1-HS20-NCTLB7,XVIR1-HS21-NCTLB4,XVIR1-HS22-NCTLB3,XVIR1-HS36-NCTLB3,XVIR1-HS4-SNEGB5,XVIR1-HS41-SNEGB6,XVIR1-HS44-NCTLB1,XVIR1-HS6-SNEGB1,XVIR1-HS7-SNEGB2,XVIR1-HS8-SNEGB5


title: ChIPseq_H3K27me3_Microglia_WT_Male_Adult_Basal_rep2_BC143_R1

city: Québec

first: David

last: Gosselin

state: Quebec

address: CRCHUL - 2705 Boulevard Laurier, Bloc T - 2-34

department: Molecular Medicine

country: Canada

institute: Université Laval

description:
Library name: Sample_3
ChIP-seq
H3K27me3_Basal_regions.txt
H3K27me3_Basal_regions.bed

data_processing:
Alignment: FASTQ files from sequencing experiments were mapped to the mouse mm10 reference genome. Bowtie2 (2.3.4.1) with default parameters was used to map ChIP-seq. HOMER was used to convert aligned reads into “tag directories” for further analyses.
Sequencing data analysis preprocessing Only R1 sequencing files were used for alignment and analyses. For PE 150 sequencing files, 50 bp were first trimmed off the 3’ end of R1 reads using fastp (fastp-0.20.0; command -t 50). Then, R1 reads FASTQ sequencing files were mapped to the mouse GRCm38 - mm10 reference genome using STAR (2.7.0f) with default parameters. HOMER was used to convert aligned reads into “tag directories” for further analyses.
ChIP-seq – H3K27me3 analysis Regions positive for H3K27me3 in adult male homeostatic microglia were first identified with HOMER’s getDiffPeakReplicate.pl program, using two independent biological replicates and their associated input HOMER’s (command: -genome mm10 -DESeq2 -size 1250 -L 0 -F 2 -region). To that file, the Bhlhe40 gene body coordinates were appended (chr6 108660629 108666925). Then, to quantify and compare H3K27me3 abundance in homeostatic vs CPZ inflammatory microglia subsets, H3K27me27+ regions identified above were annotated with sequencing reads from H3K27me3 ChIP-seq tag directories from 3 independent replicates generated from homeostatic, CPZ CD229-CD11c-, CPZ CD229+CD11c- and CPZ CD229+CD11c+ microglia (n = 3), using HOMER’s annotatePeak.pl program with mm10 -noadj parameters. Then, regions with differential H3K27me3 abundance were identified using HOMER’s getDiffExpression.pl program, which leveraged R/DESeq2 to assess differential enrichment (-AvsA -simpleNorm), using threshold of FDR 0.05. The 3 homeostatic files used for differential abundance were distinct from the 2 homeostatic files used to identify H3K27me3+ regions.
ChIP-seq data visualization: The UCSC genome browser was used to visualize ChIP-seq sequencing data. Bedgraph.gz files were generated using HOMER's makeUCSCfile.pl. For H3K27me3 UCSC data visualization, original tag directories were downsampled, randomly, to 20 million tags using HOMER?s getRandomReads.pl; tags.tsv file were then converted to tag directories and used for makeUCSCfile.pl. Lastly, for visualization of H3K27me3+ regions, region.bed files were generated using called regions.txt files using HOMER?s pos2bed.pl. H3K4me3 files used for UCSC data visualization were previously generated. UCSC genome browser visualization of H3K4me3 ChIP-seq data from adult male mouse microglia was performed using the makeUCSCfile.pl command, using ChIP-seq sequencing files from Belhocine et al. 2022 (GEO accession GSM5066662 and GSM5066664).
Assembly: mm10
Supplementary files format and content:
H3K27me3_Basal_regions.txt: Tab-delimited text files of H3K27me3+ regions identified in basal, homeostatic adult male microglia
H3K27me3_Basal_regions.bed: bed file of H3K27me3+ regions identified in basal, homeostatic adult male microglia
H3K27me3_Basal_regions_BasalvsCuprizone_DE_RawData.txt: Tab-delimited text files of raw read counts at H3K27me3+ regions, first identified in basal/homeostatic adult male microglia, for homeostatic and inflammatory microglia subsets
H3K27me3_Basal_regions_BasalvsCuprizone_DE_simpleNorm.txt: Tab-delimited text files of normalized read counts at H3K27me3+ regions, first identified in basal/homeostatic adult male microglia, for homeostatic and inflammatory microglia subsets (10 million reads/sample). Results from differential enrichment analyses are also annotated.

extract_protocol:
Mice were euthanized with an overdose of ketamine-xylazine solution (90 ml/kg & 10 ml/kg) injected intraperitoneally and subsequently perfused transcardially with ice-cold 0.9% NaCl saline solution (Sigma-Aldrich, S5886-1K6). Brains were extracted and placed in ice-cold base buffer (BB) solution (HBSS 1X (Life Technologies, 14175-095), 1% BSA (Sigma-Aldrich, A9647), 1mM EDTA (Thermo Fisher Scientific, 15575020), 1 mM sodium butyrate (Sigma-Aldrich, B5887), 1 mM Flavoperidol (Sigma-Aldrich, F3055))35. For flow cytometry, brains were cut into smaller pieces in BB solution before adding Accutase solution (Sigma-Aldrich, A6964) to enzymatically dissociate the brain. After 1 hour of incubation, brains were further homogenized on ice using a cut P1000 tip, then an uncut tip and finally a P200 tip. For FACS, brains from 2-6 mice were from same conditions were pooled and homogenized in BB solution by gentle mechanical dissociation on ice using a 7 ml polytetrafluoroethylene pestle (Duran Wheaton Kimble, 357542) and filtered through a 100 µm cell strainer (ThermoFisher 22-363-549).  Following brain homogenization, homogenates were resuspended in 37% Percoll (Thermo Fisher Scientific (Cytivia) 17089101; 8 ml/brain, in 15 ml tubes (1 tube/brain), which were then centrifuged at 600 x g for 20 min at 20°C, with medium acceleration and no deceleration. Pellets were then recovered and washed once in with BB solution, centrifuged at 300 RCF at 4°C for 7 min, resuspended in 4 ml HBSS 1X and then centrifuged at 300 RCF at 4°C for 7 min to remove proteins. Cells were resuspended in 100 µl HBSS1x and incubated on ice in the dark for 10 min with 1:100 anti-CD16/CD32 receptor unconjugated antibody (BioLegend 101302, clone 93). Then, cells were incubated on ice in the dark for 10 min with 1:1000 Live/Dead yellow stain (Thermo Fisher Scientific L34959) and conjugated antibodies directed against cell surface proteins: 1:167 anti-Ace-Alexa 750 (R&D Systems FAB15131S, clone 230214), 1:100 anti-CD11b-Brilliant Violet 421 (BioLegend 101251, clone M1/70), 1:100 anti-CD44-APC/Cy7 (BioLegend 103027, clone IM7), 1:200 anti-CD45-BB700 (BD Biosciences 566439, clone 30-F11), 1:100 anti-CD229-Alexa 647 (BD Biosciences 566689, clone Ly9.7.144), 1:133 anti-CD11c-PE (BioLegend 117308, clone N418) and 1:100 anti-Clec7a-PE/Cy7 (Thermo Fisher Scientific 25-5859-80, clone bg1fpj). After incubation, cells were washed in HBSS1x and centrifuged at 300 RCF at 4°C for 7 min. Then, cell pellets were either 1) resuspended in BB and filtered through a 35 µm cell strainer and sorted for RNA-seq and ATAC samples, or 2) underwent cross-linking for ChIP-seq samples. For cross-linking, cell pellets were resuspended in HBSS 1x and fixed with 1% PFA at RT in the dark for 10 min, after which 1/20th volume of 2.625 M glycine (Thermo Fisher Scientific BP381-500) was added for quenching for 10 min. Cells were washed in BB, centrifuged at 1000 RCF at 4°C for 10 min and filtered through a 35 µm cell strainer using BB and then sorted. Flow cytometry data was acquired with a BD FACSymphonyA1 instrument. Data was analyzed with FlowJo (v10.10.0). Microglia were sorted with BD FACSAria Fusion instrument (100 µm nozzle).
Chromatin immunoprecipitation Following sorting, aliquots of 400,000 to 600,000 microglia were centrifuge (1000 RCF at 4°C for 10 min), and cell pellet were snap-frozen in liquid nitrogen and stored at -80°C. When ready, chromatin immunoprecipitation for histone modification H3K27me3 was performed as follows, using microglia 400,000 to 600,000 per replicates. First microglia were briefly thawed on ice and lysed by incubation in 1 ml of lysis buffer (0.5% IGEPAL CA-630, 10 mM HEPES pH 7.9, 85 mM KCl, 1 mM EDTA pH 8.0, in molecular grade water) for 10 min on ice. Lysates were centrifuged at 800 RCF for 5 min at 4°C, and pellets were resuspended in 200 µl of sonication/ immunoprecipitation buffer (10 mM Tris-HCl pH 7.5, 100 mM NaCl, 0.5 mM EGTA, 0.1% Deoxcycholate, 0.5% Sarkosyl, in molecular grade water). Sonication was performed with a Bioruptor Standard Sonicator (Diagenode) and consisted of two rounds of 10 cycle of 30 sec “sonication-on”, 90 sec “sonication-off”.  Twenty-two microliters of 10% Triton-X were then added to samples (1% final concentration) on ice, and lysates were cleared by centrifugation for 5 min at 18,000 RCF at 4°C. Two microliters of supernatant were then set aside for input library sequencing controls. Each sample supernatants were then immunoprecipitated with 5.0 µg H3K27me3 antibody (Active Motif 39155) pre-bound to 17 µl Protein A Dynabeads (Thermo Fisher Scientific 10001D), on a rotator for three hours at 4°C.  Immunoprecipitates were washed three times each on ice with ice-cold wash buffer I (150 mM NaCl, 1% Triton X-100, 0.1% SDS, 2 mM EDTA pH 8.0 in molecular grade water), wash buffer III (10 mM Tris-HCl, 250 mM LiCl, 1% IGEPAL CA-630, 0.7% Deoxycholate, 1mM EDTA in water) and TET (10 mM Tris-HCl pH 7.5, 1 mM EDTA pH 8.0, 0.1% Tween-20, in molecular grade water) and eluted with 1% SDS/TE at RT in a final volume of 100 µl.  Reverse-crosslinking was then performed on immunoprecipitates and saved input aliquots. First, 6.38 µl of 5 M NaCl (final concentration 300 mM; Thermo Fisher Scientific AM9759) was added to each sample immersed in 100 µl SDS/TE. Crosslinking was then reversed by overnight incubation at 65-68°C in a hot air oven. Potentially contaminating RNA was then digested for one hour at 37°C with 0.33 mg/ml RNase A, proteins were digested for one hour at 55°C with 0.5 mg/ml proteinase K (NEB P8107S), and DNA was extracted using Sera-Mag SpeedBeads (Thermo Fisher Scientific 6515205050250).  DNA was then purified by addition of 1.5 µl Sera-Mag SpeedBeads Carboxyl Magnetic Beads (Cytivia 45152105050250), resuspended in 150 µl 20% PEG 8000/2.5 M NaCl (PEG 8000 from Sigma-Aldrich P2139; NaCl 5M from Thermo Fisher Scientific AM9759), incubated at RT for 15 min and placed on a magnet for two rounds of bead washing with 80% EtOH. Beads were then air dried for 6-10 min and DNA was eluted from the beads by adding 40 µl of water. Supernatant was then collected on a magnet and placed on ice or stored at -20°C until DNA blunting, poly(A)-tailing, and adapter ligation (see below).  ChIP-seq final library preparation Sequencing libraries were prepared from recovered DNA (ChIP) by blunting, A-tailing, and adapter ligation using barcoded adapters (NEXTflex Unique Dual Index Barcodes (Set B)(Bioo Scientific NOVA-514151), as described in Gosselin et al. 2014. Libraries were PCR-amplified for 14 cycles and size selected for fragments (200-400 bp for ChIP-seq) by gel extraction (10% TBE gels, Thermo Fisher Scientific Technologies EC62752BOX).  ChIP-seq libraries were single- or paired-end sequenced for 100 or 150 cycles on an Illumina NovaSeq X Plus or NovaSeq 6000 (Illumina, San Diego, CA) according to manufacturer’s instruction.  Illumina sequencing Sequencing for ChIP-seq samples was performed on NovaSeq X Plus at the IGM Genomics Center, University of California, San Diego, La Jolla, CA, USA, or NovaSeq 6000 at The Centre for Applied Genomics (TCAG) at The Hospital for Sick Children, Toronto, ON, Canada.

value: WT

tag: developmental stage

value: Adult

value: None; Regular diet

tag: read length


title: pool-7,well-3,GEX

description:
Library name: XVIR1-POOL-SCG26_GEX
Pool of XVIR1-HS11-SNEGB5,XVIR1-HS12-SNEGB2,XVIR1-HS16-NCTLB6,XVIR1-HS20-NCTLB7,XVIR1-HS21-NCTLB4,XVIR1-HS22-NCTLB3,XVIR1-HS36-NCTLB3,XVIR1-HS4-SNEGB5,XVIR1-HS41-SNEGB6,XVIR1-HS44-NCTLB1,XVIR1-HS6-SNEGB1,XVIR1-HS7-SNEGB2,XVIR1-HS8-SNEGB5


title: ChIPseq_InputH3K27me3_Microglia_WT_Male_Adult_Basal_rep2_BC150_R1

description:
Library name: Sample_4
Input DNA for associated H3K27me3 sample replicate


title: ChIPseq_InputH3K27me3_Microglia_WT_Male_Adult_Basal_rep1_BC141_R1

description:
Library name: Sample_2
Input DNA for associated H3K27me3 sample replicate


title: Strain Y153, pSer2-RNAPII, biol rep 3, ChIP

description: Library name: Y153_IP_BioRep3

value: Pgal-14xPP7-mAIRN HO (Y153)

value: Pgal-14xPP7-mAIRN transcription induction with Galactose 2% for 2hr


title: Stim5_3hr_Rep2

description: Library name: Stim5_3hr_Rep2


title: Strain Y167, pSer2-RNAPII, biol rep 2, ChIP

description: Library name: Y167_IP_BioRep2


title: Stim5_3hr_Rep1

description: Library name: Stim5_3hr_Rep1


title: Strain Y152, pSer2-RNAPII, biol rep 3, ChIP

description: Library name: Y152_IP_BioRep3

value: Pgal-14xPP7-mAIRN CoD (Y152)


title: pool-7,well-2,ADT

description:
Library name: XVIR1-POOL-SCC25_ADT
Pool of XVIR1-HS11-SNEGB5,XVIR1-HS12-SNEGB2,XVIR1-HS16-NCTLB6,XVIR1-HS20-NCTLB7,XVIR1-HS21-NCTLB4,XVIR1-HS22-NCTLB3,XVIR1-HS36-NCTLB3,XVIR1-HS4-SNEGB5,XVIR1-HS41-SNEGB6,XVIR1-HS44-NCTLB1,XVIR1-HS6-SNEGB1,XVIR1-HS7-SNEGB2,XVIR1-HS8-SNEGB5


title: Angpt2 deletion-3, Adenine 3 weeks

city: Taipei

first: An Jie

last: Luo

department: Graduate Institute of Physiology

country: Taiwan

institute: National Taiwan University College of Medicine

description: Library name: N11273_08

data_processing:
The high-quality reads were then aligned to the mouse reference genome
GRCm38 using STAR aligner(v2.7.8a)with the--quant Mode parameter,
generating gene-level counts based on the GENCODE vM25 gene annotation.
Cross-sample normalization was performed using the trimmed mean of M-values (TMM) method, and TPM values were calculated for downstream analysis.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: kidney

extract_protocol:
Total RNA was extractedfrom mouse kidneys using TRIzol (15596018,
Thermo Fisher Scientific), with one kidney from each mouse forming
one sample.
RNA libraries of RNA-seq were prepared from Illumina Stranded
mRNA Prep

value: kidney

value: Angpt2 deletion

value: adenine diet 3 weeks


title: pool-7,well-2,GEX

description:
Library name: XVIR1-POOL-SCG25_GEX
Pool of XVIR1-HS11-SNEGB5,XVIR1-HS12-SNEGB2,XVIR1-HS16-NCTLB6,XVIR1-HS20-NCTLB7,XVIR1-HS21-NCTLB4,XVIR1-HS22-NCTLB3,XVIR1-HS36-NCTLB3,XVIR1-HS4-SNEGB5,XVIR1-HS41-SNEGB6,XVIR1-HS44-NCTLB1,XVIR1-HS6-SNEGB1,XVIR1-HS7-SNEGB2,XVIR1-HS8-SNEGB5

data_processing:
Sequencer-obtained bcl files were demultiplexed using mkfastq program from Cell Ranger v6.0.2   (10x Genomics). Feature-barcode matrices were obtained for each library by aligning the raw fastqs of gene expression to GRCh38 reference genome (Ensembl v98) and the raw fastqs of surface protein expression to a TotalSeq-A antibody reference panel using the Cell Ranger count. Raw feature-barcode matrices were imported and analyzed using Seurat (v4.0.3).
Each library was demultiplexed to map individual cells to their sample of origin using freemuxlet (vAug2021), SNP profiles were mapped to the genotypes of patients from bulk RNA-seq using bcftools gtcheck (v1.10.2), and inter-sample doublets and empty droplets were removed.
DoubletFinder (v2.0.3)22 was used to filter barcodes containing heterotypic intra-sample doublets.
Barcodes containing less than 100 genes and genes that are detected in fewer than 3 cells were removed. We further filtered out the barcodes based on library-specific cutoffs for the number of genes per cell (nFeature_RNA <300-400 and >4,000), the number of unique molecular indexes (UMIs) per cell (nCount_RNA <700-2,000 and >20,000; nCount_ADT >20,000), mitochondrial content (>20%), and ribosomal content (<2-13% and >60%) to remove poor quality cells. The RNA and ADT count data for the resulting high-quality cell-barcodes are provided here.
Assembly: GRCh38
Supplementary files format and content: *.h5 files contain raw count data in 10X H5 format
Supplementary files format and content: CITEseq_cell_metadata.rds is an R object file containing metadata for single-cells, including patient, sample, library, and pool ids, study group, timepoint, cell annotations, and additional sample-specific metadata
Library strategy: CITE-seq

extract_protocol:
PBMCs were isolated from whole blood using Ficoll-Paque PLUS density gradient and were stored in freezing medium (9:1 FBS/DMSO) in liquid nitrogen (<-135C). Thawed PBMC suspensions from 16 individual patients were pooled together with equivalent numbers of live cells.  10^6 pooled cells were Fc blocked  for 10 min at room temperature followed by staining with a custom TotalSeqTM-A antibody panel for 45 minutes at 4°C. Cells were washed 3 times with Cell Staining Buffer resuspended in DPBS (w/o Ca2+, Mg2+)  with 0.04% BSA at 2,000 cells/uL and loaded onto a 10X Genomics Chromium Controller.
Stained cells were loaded onto a Chromium Next GEM Chip G at 65,000 cells per well, 4 wells per pool (except for one pool  with only 2 wells per pool (XVIR1-POOL-SC[G/C]2 and XVIR1-POOL-SC[G/C]3)) and processed for single-cell encapsulation and cDNA library generation using the Chromium Single Cell 3′ v3.1 Reagent Kits (User guide CG000206 Rev D; 10X Genomics) and Single Index Kit T Set A according to the manufacturer’s instructions. Gene Expression (GEX) and surface protein-targeting Antibody Derived Tag (ADT) libraries were pooled at 2.5:1 and the libraries were sequenced on Illumina NovaSeq 6000 (S4-200, ~2.5B reads per library) at the Center for Advanced Technology at UCSF at a depth of 25,000 reads per cell for GEX and 10,000 reads per cell for ADT using the recommended cycle numbers: Read 1 28 cycles, i7 index 8 cycles, Read 2 91 cycles.


title: ChIPseq_H3K27me3_Microglia_WT_Male_Adult_Basal_rep1_BC129_R1

description:
Library name: Sample_1
ChIP-seq
H3K27me3_Basal_regions.txt
H3K27me3_Basal_regions.bed


title: Stim4_2hr_Rep1

description: Library name: Stim4_2hr_Rep1

value: Jurkat T cells

value: TCR stimulation


title: Stim4_2hr_Rep2

description: Library name: Stim4_2hr_Rep2


title: Angpt2 deletion-2, Adenine 3 weeks

description: Library name: N11273_07


title: Strain Y153, pSer2-RNAPII, biol rep 2, ChIP

description: Library name: Y153_IP_BioRep2


title: Strain Y152, pSer2-RNAPII, biol rep 2, ChIP

description: Library name: Y152_IP_BioRep2


title: Strain Y168, pSer2-RNAPII, biol rep 1, ChIP

description: Library name: Y168_IP_BioRep1


title: Stim3_90min_Rep1

description: Library name: Stim3_90min_Rep1


title: Angpt2 deletion-1, Adenine 3 weeks

description: Library name: N11273_06


title: pool-7,well-1,ADT

description:
Library name: XVIR1-POOL-SCC24_ADT
Pool of XVIR1-HS11-SNEGB5,XVIR1-HS12-SNEGB2,XVIR1-HS16-NCTLB6,XVIR1-HS20-NCTLB7,XVIR1-HS21-NCTLB4,XVIR1-HS22-NCTLB3,XVIR1-HS36-NCTLB3,XVIR1-HS4-SNEGB5,XVIR1-HS41-SNEGB6,XVIR1-HS44-NCTLB1,XVIR1-HS6-SNEGB1,XVIR1-HS7-SNEGB2,XVIR1-HS8-SNEGB5

value: PBMC


title: pool-6,well-4,ADT

description:
Library name: XVIR1-POOL-SCC23_ADT
Pool of XVIR1-HS12-SNEGB6,XVIR1-HS15-NCTLB10,XVIR1-HS16-NCTLB5,XVIR1-HS17-SNEGB4,XVIR1-HS21-NCTLB3,XVIR1-HS36-NCTLB2,XVIR1-HS4-SNEGB4,XVIR1-HS40-NCTLB3,XVIR1-HS42-SNEGB5,XVIR1-HS7-SNEGB5,XVIR1-HS9-SNEGB10


title: pool-6,well-4,GEX

description:
Library name: XVIR1-POOL-SCG23_GEX
Pool of XVIR1-HS12-SNEGB6,XVIR1-HS15-NCTLB10,XVIR1-HS16-NCTLB5,XVIR1-HS17-SNEGB4,XVIR1-HS21-NCTLB3,XVIR1-HS36-NCTLB2,XVIR1-HS4-SNEGB4,XVIR1-HS40-NCTLB3,XVIR1-HS42-SNEGB5,XVIR1-HS7-SNEGB5,XVIR1-HS9-SNEGB10


title: Stim3_90min_Rep2

description: Library name: Stim3_90min_Rep2


title: Strain Y168, pSer2-RNAPII, biol rep 1, INPUT

description: Library name: Y168_IN_BioRep1

value: yeast cell


title: Stim2_1hr_Rep2

description: Library name: Stim2_1hr_Rep2


title: Strain Y167, pSer2-RNAPII, biol rep 1, INPUT

description: Library name: Y167_IN_BioRep1


title: Control-1, Adenine 3 weeks

description: Library name: N11273_01

value: wild type


title: pool-7,well-1,GEX

description:
Library name: XVIR1-POOL-SCG24_GEX
Pool of XVIR1-HS11-SNEGB5,XVIR1-HS12-SNEGB2,XVIR1-HS16-NCTLB6,XVIR1-HS20-NCTLB7,XVIR1-HS21-NCTLB4,XVIR1-HS22-NCTLB3,XVIR1-HS36-NCTLB3,XVIR1-HS4-SNEGB5,XVIR1-HS41-SNEGB6,XVIR1-HS44-NCTLB1,XVIR1-HS6-SNEGB1,XVIR1-HS7-SNEGB2,XVIR1-HS8-SNEGB5


title: pool-6,well-3,GEX

description:
Library name: XVIR1-POOL-SCG22_GEX
Pool of XVIR1-HS12-SNEGB6,XVIR1-HS15-NCTLB10,XVIR1-HS16-NCTLB5,XVIR1-HS17-SNEGB4,XVIR1-HS21-NCTLB3,XVIR1-HS36-NCTLB2,XVIR1-HS4-SNEGB4,XVIR1-HS40-NCTLB3,XVIR1-HS42-SNEGB5,XVIR1-HS7-SNEGB5,XVIR1-HS9-SNEGB10


title: pool-6,well-3,ADT

description:
Library name: XVIR1-POOL-SCC22_ADT
Pool of XVIR1-HS12-SNEGB6,XVIR1-HS15-NCTLB10,XVIR1-HS16-NCTLB5,XVIR1-HS17-SNEGB4,XVIR1-HS21-NCTLB3,XVIR1-HS36-NCTLB2,XVIR1-HS4-SNEGB4,XVIR1-HS40-NCTLB3,XVIR1-HS42-SNEGB5,XVIR1-HS7-SNEGB5,XVIR1-HS9-SNEGB10


title: Stim2_1hr_Rep1

description: Library name: Stim2_1hr_Rep1


title: Stim1_30min_Rep2

description: Library name: Stim1_30min_Rep2


title: Mettl3OE_EtOH-fed-3

city: Hefei

first: Jinghao

last: Yao

state: Anhui

address: NO. 218 Jixi Road

department: Oncology

institute: First Affiliated Hospital of Anhui Medical University

description:
Library name: Sample 9
Column name in M3_E-vs-Ctrl_E.txt: FPKM_M3_E3
M3_E-vs-Ctrl_E.txt

data_processing:
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: mm10
Supplementary files format and content: FPKM values for each Sample

source_name: Liver

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol.
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

value: Liver

value: Mettl3 overexpression

value: Ethanol-fed


title: Stim1_30min_Rep1

description: Library name: Stim1_30min_Rep1


title: Control-2, Adenine 3 weeks

description: Library name: N11273_03


title: Strain Y167, pSer2-RNAPII, biol rep 1, ChIP

description: Library name: Y167_IP_BioRep1

value: Pgal-14xPP7-mAIRN CoD Pgal-RNH1-3xHA (Y167)

value: Pgal-14xPP7-mAIRN and Pgal-RNH1-3xHA transcription induction with Galactose 2% for 2hr

value: pSer2-RNAPII (Abcam, #ab5095)


title: Control-3, Adenine 3 weeks

description: Library name: N11273_04


title: Ctl_24hr_Rep2

description: Library name: Ctl_24hr_Rep2


title: pool-6,well-2,ADT

description:
Library name: XVIR1-POOL-SCC21_ADT
Pool of XVIR1-HS12-SNEGB6,XVIR1-HS15-NCTLB10,XVIR1-HS16-NCTLB5,XVIR1-HS17-SNEGB4,XVIR1-HS21-NCTLB3,XVIR1-HS36-NCTLB2,XVIR1-HS4-SNEGB4,XVIR1-HS40-NCTLB3,XVIR1-HS42-SNEGB5,XVIR1-HS7-SNEGB5,XVIR1-HS9-SNEGB10

source_name: PBMC


title: pool-6,well-2,GEX

description:
Library name: XVIR1-POOL-SCG21_GEX
Pool of XVIR1-HS12-SNEGB6,XVIR1-HS15-NCTLB10,XVIR1-HS16-NCTLB5,XVIR1-HS17-SNEGB4,XVIR1-HS21-NCTLB3,XVIR1-HS36-NCTLB2,XVIR1-HS4-SNEGB4,XVIR1-HS40-NCTLB3,XVIR1-HS42-SNEGB5,XVIR1-HS7-SNEGB5,XVIR1-HS9-SNEGB10


title: Strain Y152, pSer2-RNAPII, biol rep 1, ChIP

description: Library name: Y152_IP_BioRep1


title: Mettl3OE_EtOH-fed-1

description:
Library name: Sample 7
Column name in M3_E-vs-Ctrl_E.txt: FPKM_M3_E1
M3_E-vs-Ctrl_E.txt


title: Strain Y153, pSer2-RNAPII, biol rep 1, ChIP

description: Library name: Y153_IP_BioRep1

value: Pgal-14xPP7-mAIRN HO (Y153)


title: Strain Y153, pSer2-RNAPII, biol rep 1, INPUT

description: Library name: Y153_IN_BioRep1

value: Pgal-14xPP7-mAIRN transcription induction with Galactose 2% for 2hr


title: Ctl_24hr_Rep1

description: Library name: Ctl_24hr_Rep1


title: Mettl3OE_EtOH-fed-2

description:
Library name: Sample 8
Column name in M3_E-vs-Ctrl_E.txt: FPKM_M3_E2
M3_E-vs-Ctrl_E.txt


title: WT_EtOH-fed-3

description:
Library name: Sample 6
Column name in Ctrl_E-vs-Ctrl_PF.txt: FPKM_Ctrl_E3
Ctrl_E-vs-Ctrl_PF.txt
M3_E-vs-Ctrl_E.txt

value: WT


title: pool-6,well-1,GEX

description:
Library name: XVIR1-POOL-SCG20_GEX
Pool of XVIR1-HS12-SNEGB6,XVIR1-HS15-NCTLB10,XVIR1-HS16-NCTLB5,XVIR1-HS17-SNEGB4,XVIR1-HS21-NCTLB3,XVIR1-HS36-NCTLB2,XVIR1-HS4-SNEGB4,XVIR1-HS40-NCTLB3,XVIR1-HS42-SNEGB5,XVIR1-HS7-SNEGB5,XVIR1-HS9-SNEGB10


title: Strain Y152, pSer2-RNAPII, biol rep 1, INPUT

description: Library name: Y152_IN_BioRep1

value: Pgal-14xPP7-mAIRN CoD (Y152)


title: Ctl_8hr_Rep2

description: Library name: Ctl_8hr_Rep2


title: Ctl_8hr_Rep1

description: Library name: Ctl_8hr_Rep1


title: PNR-7-02_TDP1_Biotin

city: Philadelphia

first: Paul

middle: M

last: Lieberman

state: Pennsylvania

address: 3601 Spruce Street

institute: The Wistar Institute

description: Library name: Sample 6

data_processing:
DNA sequening reads were aligned to human gamma herpesvirus 8 BCBL-1 genome (GCA_027939675.1) using Bowtie 2 program (version 2.2.2)
Assembly: human gamma herpesvirus 8 BCBL-1 genome (GCA_027939675.1)
Supplementary files format and content: Bedgraph

organism:
Homo sapiens
Human gammaherpesvirus 8

extract_protocol:
Genomic DNA from 5 × 107 cells treated with DMSO or PNR07-02 was purified and treated with 5 μg of pancreatic RNase (Roche) followed by with or without 1 μg of TDP1 in 80 mM KCl, 50 mM Tris–HCl pH 8.0, 2 mM EDTA,2 mM DTT for 1 h at 37 °C, adjusted to 0.5% SDS and incubated for 1 h at 55 °C with proteinase K (200 μg/mL). DNA was extracted twice with phenol and precipitated with ethanol in the presence of 2 M ammonium acetate.
The Epicentre DNA END-Repair kit (Epicentre Biotechnologies, Madison, WI, USA) was used to generate blunt-ended DNA. SSB and DSB DNA libraries were prepared using NEBNext utra II DNA library prep kit for Illumina (NEB). The purified DNA was used directly for cluster generation and sequencing analysis using the Illumina Genome Analyzer (Illumina, San Diego, USA) following manufacturer protocols.

value: B lymphocyte (PEL-derived)

value: KSHV+


title: pool-5,well-4,ADT

description:
Library name: XVIR1-POOL-SCC19_ADT
Pool of XVIR1-HS11-SNEGB4,XVIR1-HS14-NCTLB3,XVIR1-HS16-NCTLB4,XVIR1-HS17-SNEGB2,XVIR1-HS20-NCTLB2,XVIR1-HS21-NCTLB2,XVIR1-HS22-NCTLB1,XVIR1-HS37-NCTLB7,XVIR1-HS41-SNEGB5,XVIR1-HS42-SNEGB4,XVIR1-HS44-NCTLB5,XVIR1-HS5-SNEGB9,XVIR1-HS7-SNEGB1


title: PNR-7-02_noTDP1_Biotin

description: Library name: Sample 4


title: WT_EtOH-fed-2

description:
Library name: Sample 5
Column name in Ctrl_E-vs-Ctrl_PF.txt: FPKM_Ctrl_E2
Ctrl_E-vs-Ctrl_PF.txt
M3_E-vs-Ctrl_E.txt


title: PNR-7-02_TDP1_noBiotin

description: Library name: Sample 2


title: WT_Pair-fed-3

description:
Library name: Sample 3
Column name in Ctrl_E-vs-Ctrl_PF.txt: FPKM_Ctrl_PF3
Ctrl_E-vs-Ctrl_PF.txt

value: Pair-fed


title: pool-6,well-1,ADT

description:
Library name: XVIR1-POOL-SCC20_ADT
Pool of XVIR1-HS12-SNEGB6,XVIR1-HS15-NCTLB10,XVIR1-HS16-NCTLB5,XVIR1-HS17-SNEGB4,XVIR1-HS21-NCTLB3,XVIR1-HS36-NCTLB2,XVIR1-HS4-SNEGB4,XVIR1-HS40-NCTLB3,XVIR1-HS42-SNEGB5,XVIR1-HS7-SNEGB5,XVIR1-HS9-SNEGB10


title: pool-5,well-4,GEX

description:
Library name: XVIR1-POOL-SCG19_GEX
Pool of XVIR1-HS11-SNEGB4,XVIR1-HS14-NCTLB3,XVIR1-HS16-NCTLB4,XVIR1-HS17-SNEGB2,XVIR1-HS20-NCTLB2,XVIR1-HS21-NCTLB2,XVIR1-HS22-NCTLB1,XVIR1-HS37-NCTLB7,XVIR1-HS41-SNEGB5,XVIR1-HS42-SNEGB4,XVIR1-HS44-NCTLB5,XVIR1-HS5-SNEGB9,XVIR1-HS7-SNEGB1


title: CHIKV non-infected, long RNA, rep2

city: Helsingør

first: Niels-Ulrik

last: Frigaard

address: Strandpromenaden 5

department: Department of Biology

country: Denmark

institute: University of Copenhagen

description:
Library name: CONTROL-IP-2_S5
CHIKV-long-RNA_diffexpr.csv
CHIKV-long-RNA_diffpeaks.csv

data_processing:
Read quality was controlled using fastx toolkits cutadapt: remove adapters, discard reads of Phred score lower than 10 (or 20) and shorten reads to a fixed length of 130 nts or 60 nts for long and short RNA-seq, respectively.
Read mapping to virus genomes and GRCh38 with Bowtie v1.2.2 (paramters -n 1 -l 8 -a --best --strata --phred33-qual) for small RNA-seq and STAR v2.5.2a (parameters --outSAMstrandField intronMotif --outSJfilterCountUniqueMin 3 2 2 2).
Filter ribosomal RNAs (RepeatMasker v4.0.5 and repeat library db20140131).
Gene quantification (Gencode human v45 or v27) with Subread featureCounts or HTSeq, and differential gene expression analysis with DESeq2 or edgeR.
Peak calling of bin size 100 nts and step size 50 nts using Piranha v1.2.1 (parameters -s -p 0.5), and differential peak analysis using DiffBind and DESeq2 or edgeR.
Assembly: GRCh38, HCV J6/JFH1 cl2, YFV 17D, pCHIKV
Supplementary files format and content: csv files including differential expressed genes called with DESeq2 or edgeR for each of the four experiments
Supplementary files format and content: csv files including differential expressed peaks called with DiffBind for each of the four experiments

molecule: cytoplasmic RNA

growth_protocol: Huh-7.5 hepatoma cells were maintained in Dulbecco’s Modified  Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and keptT at 37°C and 5% CO2.

extract_protocol:
Briefly, in the modified RAP-RNA protocol, RNA molecules in close proximity were cross-linked using UV365 in the presence of the psoralen molecule, 4′-aminomethyltrioxsalen (AMT). Cells were then fractionated into nuclear and cytoplasmic constituents, and cytoplasmic viral RNA was enriched using pull-down with specific DNA probes. The enriched RNA was then DNAse treated to remove the DNA probes, and reverse cross-linked using UV254.
To allow efficient identification of both short and long RNA interactors, two parallel strand-specific RNA-library methods were applied, based on poly-adenylation and template switching (CATS small-RNAseq-kit (Diagenode)), or random hexamer priming (NEBnext Ultra II), respectively.

treatment_protocol: Cells were infected with the HCV genotype 2a recombinant, J6/JFH1-c2 (72 hpi, MOI=1), YFV strain 17D (24 hpi, MOI=1), or CHIKV strain LR (24 hpi, MOI=1).

value: Hepatoma cells

value: Non-infected