title: BCG-328_smallRNAseq

description: Library name: BCG-328_smallRNAseq

tag: tissue

tag: age

tag: race

tag: ethnicity

value: Hispanic or Latino

tag: er

value: ER-positive

tag: gender

tag: treatment

tag: clinical stage

value: IA

tag: adi (state_decile)

tag: nseas composite_score

tag: nseas safety_score

tag: nseas social_cohesion_score

tag: nseas aesthetic_quality_score

tag: eeds discrimination_score

tag: batch


title: I16H2_spleen_GEX

status: Public on Aug 15 2025

type: SRA

city: Boston

first: Liang

last: Yang

state: MA

address: 77 Avenue Louis Pasteur

department: Pathology

country: USA

institute: Harvard Medical School

description: Library name: I16H2_spleen_GEX

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcode process and gene/ ADT/ hash counts were generated using Cellranger software v7.0.0.
TCRab contig annotations were generating using the cellranger vdj function from Cellranger software v7.0.0. The contigs generated were then mapped to with IMGT, and TRA and TRB chains put back together to create a summary table.
GEX and FBC libraries were processed using Seurat, where RNA, ADT QC was performed, a long with HTO demultiplexing to assign each cell a sample
Assembly: mm10
Supplementary files format and content: Cellranger output files: cells.tsv, matrix_rna.mtx, genes.tsv, matrix_protein.mtx, proteins.tsv,  - Processed data from GEX, ADT and HTO.
Supplementary files format and content: Cellranger output files: summary_table.csv - Mapped TCR contigs with TCR gene annotations for VDJ library of IGT36

molecule: total RNA

organism: Mus musculus

source_name: spleen

extract_protocol:
Lymphocytes were prepared by either digestion with liberase (submandibular gland) or mechanical dissociation (spleen) , followed by staining with fluorescent antibodies, hashing with Totalseq-C antibodies against MHCI and CD45,  and flow sorting CD3+ T cells into DMEM+ 2%FCS. Cells were stained using a custom Totalseq-C antibody panel then sorted again into DMEM + 2% FCS
Libraries were prepared according to the 10x Genomics 5'v2 protocol for GEX, VDJ, and FBC

value: spleen

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

value: TRUE

tag: exp name

value: Submandibular salivary gland T cells in WT and PD1KO

tag: lab

value: Brossay

tag: organism name

tag: strain

tag: genetics

value: wt

tag: Sex

value: female

tag: age weeks

tag: pool of_mice

tag: prep description

value: liberase, DNAse I

tag: organ

tag: organ uberon_id

tag: target cells

value: splenocytes

tag: gating strategy

tag: mouse comments

value: pool of 9 females DOB 5/10/22

tag: cell type

value: T cells


title: Pilot DC-TAP-seq for 97 genes in K562 infected with 97 guides in sgOpti-CS vector at MOI14. mRNA

city: Stanford

first: Jesse

last: Engreitz

state: CA

address: 450 Serra Mall

department: Genetics

institute: Stanford University

description:
Library name: K562_sgOpti-CS_DC-TAP_MOI14_pilot_mRNA
10x Genomics
k562_14-MOI_filtered_feature_bc_matrix.tar.gz

data_processing:
We aligned reads to transcripts and identified cells using the 10x Genomics cloud analysis web browser version with Cell Ranger Count v7.0.0 or v7.0.1 or v7.1.0 or v7.2.0, using the GRCh38-2020-A transcriptome. For DC-TAP-seq and TAP-seq analysis, we input our transcriptome FASTQ files as Targeted Next GEM 3’ Gene Expression libraries with a custom reference file containing bait sequences for the targeted genes. We generated this reference file by subsetting the bait sequences found in 10x Genomics’ human_pulldown_probes.csv file (built on GRCh38-2020-A). For guide RNA (gRNA) analysis, we processed guide FASTQ files as CRISPR Guide Capture libraries using a feature_reference.csv file containing the guide sequences.
Assembly: human hg38
Supplementary files format and content: filtered feature bc matrix file (.tar.gz format) that is output directly from cellranger. Contains matrix, barcodes and features files. The all_guide_info.txt file contains guide UMI information for the pilot TAP-seq sample.

molecule: polyA RNA

organism: Homo sapiens

growth_protocol: We grew K562 cells harboring dCas9-KRAB  in RPMI-1640 (Thermo Fisher Scientific, Waltham, MA) with 10% heat-inactivated FBS (HIFBS (Thermo Fisher Scientific), 2 mM L-glutamine, and 100 units/ml streptomycin and 100 mg/ml penicillin. We maintained K562 cells at a density between 100K and 1M per mL. We seeded human iPS cells (WTC11) harboring dCas9-KRAB (Metzl-Raz et al., Stem Cell Res., 2022) in 6-well plates coated with 1:100 LDEV-Free Reduced Growth Factor Basement Membrane Matrix (Thermo Fisher Scientific). The culture medium used was StemFlex Medium supplemented with 10% StemFlex supplement (SF complete media, Thermo Fisher Scientific), 2 µl of Normacin per ml of media (1:500 final, Invivogen), and 0.4 µl of 10 mM Rock Inhibitor (Y-27632 Dihydrochloride, STEMCELL Technologies). After 24 hours of seeding, we continued to maintain the cells with SF complete media without Rock Inhibitor and passaged them with 1 ml of accutase (STEMCELL Technologies) as necessary, aiming to maintain at 80-90% confluence to prevent stacked cell growth.

extract_protocol:
Cells were collected using centrifugation, washed with PBS+BSA and subjected to droplet formation for DC-TAP-seq or TAP-seq or scRNA-seq using the 10x Genomics v3.1 kit.
DC-TAP-seq libraries were constructed according to the protocol detailed in Ray et al 2025 (dx.doi.org/10.17504/protocols.io.3byl4z7drvo5/v1). TAP-seq libraries were prepared according to Schraivogel et al., Nat Methods, 2020 and scRNA-seq libraries with guide capture were generated according to the 10x Genomics protocol.

tag: cell line


title: Pilot DC-TAP-seq for 203 genes in WTC11 infected with 98 guides in sgOpti-CS vector at MOI1. mRNA

description:
Library name: WTC11_sgOpti-CS_DC-TAP_MOI1_pilot_mRNA
10x Genomics
wtc11_1_MOI_filtered_feature_bc_matrix.tar.gz


title: BSSR0567_smallRNAseq

city: Miami

first: Aristeidis

middle: G

last: Telonis

state: FL

address: 1550 NW 10th Ave

institute: University of Miami

description: Library name: BSSR0567_smallRNAseq

library_source: transcriptomic

data_processing:
Adapters were trimmed from the acquired fastq files with cutadapt (v. 1.18) with parameter -m 15 -e 0.12 filtering out reads without adapters
Reads were processed with isomiRmap (v. 1.0.0) and MINTmap (v.1 .0)
Assembly: GRCh37
Supplementary files format and content: Table with counts per small RNA molecule

source_name: Breast tumor

extract_protocol:
RNA was extracted with Thermo MagMAX mirVana Total RNA Isolation kit (A27828) on a Thermo Kingfisher Apex
NEBNext® Small RNA Library Prep Set following manufacturer’s instructions for synthesis without size selection (New England Biolabs, E7330L)

tag: tissue

value: Breast tumor

tag: age

tag: race

value: White

tag: ethnicity

tag: er

tag: gender

value: Female

tag: treatment

value: No

tag: clinical stage

value: IIA

tag: adi (state_decile)

tag: nseas composite_score

tag: nseas safety_score

tag: nseas social_cohesion_score

tag: nseas aesthetic_quality_score

tag: eeds discrimination_score

tag: batch


title: Pilot DC-TAP-seq for 97 genes in K562 infected with 97 guides in sgOpti-CS vector at MOI9. mRNA

description:
Library name: K562_sgOpti-CS_DC-TAP_MOI9_pilot_mRNA
10x Genomics
k562_9-MOI_filtered_feature_bc_matrix.tar.gz


title: Pilot DC-TAP-seq for 97 genes in K562 infected with 97 guides in sgOpti-CS vector at MOI3. gRNA

description:
Library name: K562_sgOpti-CS_DC-TAP_MOI3_pilot_gRNA
10x Genomics
k562_3-MOI_filtered_feature_bc_matrix.tar.gz

library_source: other

molecule: other


title: BSSR0558_smallRNAseq

description: Library name: BSSR0558_smallRNAseq

value: Hispanic or Latino

value: ER-positive


title: Pilot DC-TAP-seq for 97 genes in K562 infected with 97 guides in sgOpti-CS vector at MOI3. mRNA

description:
Library name: K562_sgOpti-CS_DC-TAP_MOI3_pilot_mRNA
10x Genomics
k562_3-MOI_filtered_feature_bc_matrix.tar.gz


title: I16H10_salivarygland_PD1KO_TCR

description: Library name: I16H10_salivarygland_PD1KO_TCR

data_processing:
The demultiplexing, barcode process and gene/ ADT/ hash counts were generated using Cellranger software v7.0.0.
TCRab contig annotations were generating using the cellranger vdj function from Cellranger software v7.0.0. The contigs generated were then mapped to with IMGT, and TRA and TRB chains put back together to create a summary table.
GEX and FBC libraries were processed using Seurat, where RNA, ADT QC was performed, a long with HTO demultiplexing to assign each cell a sample
Assembly: mm10
Supplementary files format and content: Cellranger output files: cells.tsv, matrix_rna.mtx, genes.tsv, matrix_protein.mtx, proteins.tsv,  - Processed data from GEX, ADT and HTO.
Supplementary files format and content: Cellranger output files: summary_table.csv - Mapped TCR contigs with TCR gene annotations for VDJ library of IGT36
Library strategy: TCR-seq

source_name: submandibular gland

value: submandibular gland

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

tag: exp name

tag: lab

tag: organism name

tag: strain

tag: genetics

value: PD1 KO (CRISPR in B6NJ backcrossed with B6J)

tag: Sex

value: male

tag: age weeks

tag: pool of_mice

value: FALSE

tag: prep description

tag: organ

tag: organ uberon_id

tag: target cells

value: all T

tag: gating strategy

value: CD45+ CD3e+

tag: mouse comments

tag: cell type


title: Pilot DC-TAP-seq for 97 genes in K562 infected with 97 guides in sgOpti-CS vector at MOI1 (replicate 2). mRNA

description:
Library name: K562_sgOpti-CS_DC-TAP_MOI1_pilot_rep2_mRNA
10x Genomics
k562_1-MOI_filtered_feature_bc_matrix.tar.gz

tag: cell line


title: Pilot DC-TAP-seq for 97 genes in K562 infected with 97 guides in sgOpti-CS vector at MOI6. mRNA

description:
Library name: K562_sgOpti-CS_DC-TAP_MOI6_pilot_mRNA
10x Genomics
k562_6-MOI_filtered_feature_bc_matrix.tar.gz


title: I16H2_spleen_FBC

description: Library name: I16H2_spleen_FBC

data_processing:
The demultiplexing, barcode process and gene/ ADT/ hash counts were generated using Cellranger software v7.0.0.
TCRab contig annotations were generating using the cellranger vdj function from Cellranger software v7.0.0. The contigs generated were then mapped to with IMGT, and TRA and TRB chains put back together to create a summary table.
GEX and FBC libraries were processed using Seurat, where RNA, ADT QC was performed, a long with HTO demultiplexing to assign each cell a sample
Assembly: mm10
Supplementary files format and content: Cellranger output files: cells.tsv, matrix_rna.mtx, genes.tsv, matrix_protein.mtx, proteins.tsv,  - Processed data from GEX, ADT and HTO.
Supplementary files format and content: Cellranger output files: summary_table.csv - Mapped TCR contigs with TCR gene annotations for VDJ library of IGT36
Library strategy: CITE-seq

tag: tissue

value: spleen

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

value: TRUE

value: Submandibular salivary gland T cells in WT and PD1KO

value: Brossay

value: wt

value: female

value: liberase, DNAse I


title: Pilot DC-TAP-seq for 97 genes in K562 infected with 97 guides in sgOpti-CS vector at MOI 20. mRNA

description:
Library name: K562_sgOpti-CS_DC-TAP_pilot_moi20_mRNA
10x Genomics
H-SG-TAP_filtered_feature_bc_matrix.tar.gz


title: Pilot DC-TAP-seq for 97 genes in K562 infected with 97 guides in sgOpti-CS vector at MOI1 (replicate 1). mRNA

description:
Library name: K562_sgOpti-CS_DC-TAP_MOI1_pilot_rep1_mRNA
10x Genomics
L-SG-TAP_filtered_feature_bc_matrix.tar.gz


title: BSSR0727_smallRNAseq

description: Library name: BSSR0727_smallRNAseq

value: Breast tumor

tag: age

tag: race

value: White

tag: ethnicity

tag: er

tag: gender

value: Female

tag: treatment

value: No

tag: clinical stage

value: IA

tag: adi (state_decile)

tag: nseas composite_score

tag: nseas safety_score

tag: nseas social_cohesion_score

tag: nseas aesthetic_quality_score

tag: eeds discrimination_score

tag: batch


title: BSSR0551_smallRNAseq

description: Library name: BSSR0551_smallRNAseq

tag: tissue

value: Hispanic or Latino

value: ER-positive

value: IIA


title: I16H10_salivarygland_PD1KO_GEX

description: Library name: I16H10_salivarygland_PD1KO_GEX

value: submandibular gland

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: exp name

tag: lab

tag: organism name

tag: strain

tag: genetics

value: PD1 KO (CRISPR in B6NJ backcrossed with B6J)

tag: Sex

value: male

tag: age weeks

tag: pool of_mice

value: FALSE

tag: prep description

tag: organ

tag: organ uberon_id

tag: target cells

value: all T

tag: gating strategy

tag: mouse comments

tag: cell type

value: T cells


title: Pilot DC-TAP-seq for 97 genes in K562 infected with 99 guides in pBA904 vector. mRNA

description:
Library name: K562_pBA904_DC-TAP_pilot_mRNA
10x Genomics
H-DC-TAP_filtered_feature_bc_matrix.tar.gz

tag: cell line


title: P2-Pre_2, CD45+

city: Minneapolis

first: Justin

last: Hwang

state: MN

address: 420 Delaware Street SE

department: Department of Medicine

institute: University of Minnesota

description: Library name: P2-Pre_2_CD45+

data_processing:
The Illumina FASTQ sequence files were mapped to each sample and processed to raw counts using the GeoMx NGS pipeline with default settings.
The limit of quantification (LOQ) was set to be the geometric mean of the negative control probes multiplied by the squared standard deviation of the negative control probes. Low probe count AOIs, AOIs with less than 5% of genes above the LOQ, and genes with less than 5% of AOIs above the LOQ were removed.
The counts were then normalized using variance stabilizing normalization (VSN) for subsequent analyses.
Assembly: Human NGS Whole Transcriptome Atlas RNA
Supplementary files format and content: CD45_5_percent_target_segment_filtered.csv: CD45+ AOI counts after gene and AOI filtering (samples with low quality were filtered out)
Supplementary files format and content: PanCK_5_percent_target_segment_filtered.csv: PanCK+ AOI counts after gene and AOI filtering
Supplementary files format and content: CD45_5_vsn_matrix.csv: VSN normalized counts for CD45+ AOIs (samples with low quality were filtered out)
Supplementary files format and content: PanCK_5_vsn_matrix.csv: VSN normalized counts for PanCK+ AOIs

source_name: FFPE tumor

extract_protocol:
Blocks of formalin-fixed paraffin-embedded (FFPE) tumors were prepared for spatial transcriptomic analysis. One 5 µm section from each tumor specimen was placed on a glass slide for Nanostring GeoMx analysis (Seattle, WA). The slide was incubated with Ki-67 antibodies and the Regions of interest (ROIs) were chosen. ROIs were selected after histopathological review of tissue quality. ROIs were further selected for based on the presence of significant quantities of epithelial and immune cells, which was a pre-requisite to acquire significant RNA material from each cell type for subsequent spatial transcriptomic analysis.
GeoMx Digital Spatial Profiling is a probe-based sequencing method to detect RNA spatially in tissue. We used the GeoMx Human Whole Transcriptome Atlas (18,816 genes) to sequence our tissue samples for the three patients.

tag: tissue

value: FFPE tumor

tag: pre vs_post_covid

value: Pre

tag: high covid


title: Pilot whole transcriptome scRNA-seq with guide capture in K562 infected with 16 guides in pBA904 vector. mRNA

description:
Library name: K562_pBA904_scRNA_pilot_mRNA
10x Genomics
P16-scRNAseq_filtered_feature_bc_matrix.tar.gz


title: Pilot TAP-seq for 97 genes in K562 infected with 10 guides in CROP-HyPR vector. mRNA + gRNA

description:
Library name: K562_CROP_TAP_pilot
10x Genomics
P10-TAP_filtered_feature_bc_matrix.tar.gz


title: P2-Post_5, CD45+

description: Library name: P2-Post_5_CD45+

value: Post

value: TRUE


title: BSSR0542_smallRNAseq

description: Library name: BSSR0542_smallRNAseq

value: Breast tumor

tag: age

tag: race

value: White

tag: ethnicity

tag: er

tag: gender

tag: treatment

tag: clinical stage

tag: adi (state_decile)

tag: nseas composite_score

tag: nseas safety_score

tag: nseas social_cohesion_score

tag: nseas aesthetic_quality_score

tag: eeds discrimination_score

tag: batch


title: I16H10_salivarygland_PD1KO_FBC

description: Library name: I16H10_salivarygland_PD1KO_FBC

tag: tissue

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

tag: exp name

value: Submandibular salivary gland T cells in WT and PD1KO

tag: lab

value: Brossay

tag: organism name

tag: strain

tag: genetics

tag: Sex

tag: age weeks

tag: pool of_mice

tag: prep description

value: liberase, DNAse I

tag: organ

tag: organ uberon_id

tag: target cells

tag: gating strategy

value: CD45+ CD3e+

tag: mouse comments

tag: cell type


title: I16H1_spleen_TCR

description: Library name: I16H1_spleen_TCR

tag: tissue

value: spleen

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

value: wt

value: female

value: mechanical dissociation alone

value: splenocytes

value: pool of 9 females DOB 5/10/22


title: BSSR0740_smallRNAseq

description: Library name: BSSR0740_smallRNAseq

tag: age

tag: race

tag: ethnicity

value: Hispanic or Latino

tag: er

value: ER-positive

tag: gender

value: Female

tag: treatment

value: No

tag: clinical stage

value: IIA

tag: adi (state_decile)

tag: nseas composite_score

tag: nseas safety_score

tag: nseas social_cohesion_score

tag: nseas aesthetic_quality_score

tag: eeds discrimination_score

tag: batch


title: hiPSC-CMs treated with vehicle biol rep 2

city: Maastricht

first: Brigitta

middle: Rita

last: Szabo

address: Minderbroedersberg 4-6

department: CARIM

country: Netherlands

institute: Maastricht University

description: Library name: 53_18_2

data_processing:
First, raw reads were quality and adapter trimmed with Trim Galore v.0.6.7.
The trimmed reads were mapped against the human genome (GRCh38.104) with STAR v.2.7.9a.
Unique Molecular Identifiers were used during the sequencing and were processed with UMI-tools v.1.1.2.
The RSEM software v.1.3.134 was used to generate the count tables.
Assembly: GRCh38.104
Supplementary files format and content: file includes raw counts for each sample

source_name: Ncyte vCardiomyocytes

growth_protocol: hiPSC-CMs were maintained in serum-free medium at 37°C and 5% CO2 with regular medium changes every 48 hours.

extract_protocol:
RNA was extracted using the RNA Nucleospin RNA kit (Bioke) per manufacturer’s instructions
After RNA extraction, the concentration and quality of the total extracted RNA were evaluated by using the 'Quant-it ribogreen RNA assay' (Life Technologies, Grand Island, NY, USA) and the RNA 6000 Nano chip (Agilent Technologies, Santa Clara, CA, USA), respectively. Subsequently, 10 ng of RNA was used to perform an Illumina sequencing library preparation using the QuantSeq 3' mRNA-Seq Library Prep FWD Kit (Lexogen, Vienna, Austria) per manufacturer’s instructions. During library preparation, 17 PCR cycles were used. Libraries were quantified by qPCR, according to Illumina's protocol 'Sequencing Library qPCR Quantification protocol guide', version February 2011. A High Sensitivity DNA chip (Agilent Technologies, Santa Clara, CA, US) was used to control the library's size distribution and quality. Sequencing was performed on a high throughput Illumina NextSeq 500 flow cell generating 75 bp single reads.

treatment_protocol: On day 7 post seeding, 3 replicates were exposed to one concentration of a single compound or to vehicle control (0.1% DMSO) for 24 hours. Compound solutions were administered at final concentration of 0.1% DMSO.

tag: cell line

value: Ncyte vCardiomyocytes

tag: cell type

value: hiPSC-CMs

tag: genotype

value: wild type

value: Vehicle


title: I16H1_spleen_GEX

description: Library name: I16H1_spleen_GEX

tag: tissue

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

value: TRUE

tag: exp name

value: Submandibular salivary gland T cells in WT and PD1KO

tag: lab

value: Brossay

tag: organism name

tag: strain

tag: genetics

tag: Sex

tag: age weeks

tag: pool of_mice

tag: prep description

tag: organ

tag: organ uberon_id

tag: target cells

tag: gating strategy

tag: mouse comments

value: T cells


title: hiPSC-CMs treated with empagliflozin biol rep 3

description: Library name: 51_17_3

tag: cell line

tag: cell type

tag: genotype

tag: treatment

value: Empagliflozin 1 µM


title: hiPSC-CMs treated with empagliflozin biol rep 2

description: Library name: 50_17_2


title: I16H1_spleen_FBC

description: Library name: I16H1_spleen_FBC

tag: tissue

value: spleen

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

tag: exp name

tag: lab

value: wt

value: female

value: mechanical dissociation alone


title: BSSR3054

description: Library name: BSSR3054_RNAseq

data_processing:
Adapters were trimmed from the acquired fastq files with cutadapt (v. 1.18) with parameter -m10
Reads were mapped on the GRCh37 human genome with STAR (v. 2.7.1a)
Gene expression profiles were extracted with RSEM (v. 1.2.28) using Ensembl v75 for gene annotations
Assembly: GRCh37
Supplementary files format and content: Table with counts and FPKM values per gene

extract_protocol:
RNA was extracted with Thermo MagMAX mirVana Total RNA Isolation kit (A27828) on a Thermo Kingfisher Apex
Illumina TruSeq Stranded Total RNA with Ribo-Zero Gold (RS-122-2303)

value: Breast tumor

tag: age

tag: race

value: White

tag: ethnicity

value: Hispanic or Latino

tag: er

value: ER-positive

tag: gender

tag: clinical stage

tag: adi (state_decile)

tag: nseas composite_score

tag: nseas safety_score

tag: nseas social_cohesion_score

tag: nseas aesthetic_quality_score

tag: eeds discrimination_score

tag: batch


title: hiPSC-CMs treated with empagliflozin biol rep 1

description: Library name: 49_17_1

tag: cell line

value: Ncyte vCardiomyocytes

tag: cell type

tag: genotype

tag: treatment


title: BCG-389

description: Library name: BCG-389_RNAseq

tag: tissue

tag: age

value: Female

value: No

value: IIB


title: hiPSC-CMs treated with ASA biol rep 2

description: Library name: 47_16_2

value: hiPSC-CMs

value: wild type

value: ASA 10 µM


title: hiPSC-CMs treated with erlotinib biol rep 1

description: Library name: 43_15_1

value: Erlotinib 0.3 µM


title: BSSR2060

description: Library name: BSSR2060_RNAseq

tag: race

tag: ethnicity

value: IA


title: I15H9_salivarygland_PD1KO_FBC

description: Library name: I15H9_salivarygland_PD1KO_FBC

value: submandibular gland

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

value: TRUE

tag: exp name

value: Submandibular salivary gland T cells in WT and PD1KO

tag: lab

value: Brossay

tag: organism name

tag: strain

tag: genetics

value: PD1 KO (CRISPR in B6NJ backcrossed with B6J)

tag: Sex

value: male

tag: age weeks

tag: pool of_mice

value: FALSE

tag: prep description

value: liberase, DNAse I

tag: organ

tag: organ uberon_id

tag: target cells

value: all T

tag: gating strategy

value: CD45+ CD3e+

tag: mouse comments

value: T cells


title: I15H9_salivarygland_PD1KO_TCR

description: Library name: I15H9_salivarygland_PD1KO_TCR

tag: tissue

tag: immgent igt_10xlane_id

tag: hashtag number

tag: cell type


title: BCG-385

description: Library name: BCG-385_RNAseq

value: Breast tumor

tag: age

tag: race

value: White

tag: ethnicity

value: Hispanic or Latino

tag: er

value: ER-positive

tag: gender

value: Female

tag: treatment

value: No

tag: clinical stage

tag: adi (state_decile)

tag: nseas composite_score

tag: nseas safety_score

tag: nseas social_cohesion_score

tag: nseas aesthetic_quality_score

tag: eeds discrimination_score

tag: batch


title: hiPSC-CMs treated with ASA biol rep 3

description: Library name: 48_16_3

tag: cell line

value: Ncyte vCardiomyocytes

value: hiPSC-CMs

tag: genotype

value: wild type

value: ASA 10 µM


title: hiPSC-CMs treated with vehicle biol rep 3

description: Library name: 54_18_3

tag: cell type

value: Vehicle


title: hiPSC-CMs treated with chlorpromazine biol rep 3

description: Library name: 42_14_3

value: Chlorpromazine 1 µM


title: hiPSC-CMs treated with vehicle biol rep 1

description: Library name: 52_18_1


title: BSSR0553_smallRNAseq

description: Library name: BSSR0553_smallRNAseq

tag: tissue

tag: age

value: IIB


title: I15H8_salivarygland_PD1KO_TCR

description: Library name: I15H8_salivarygland_PD1KO_TCR

value: submandibular gland

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

value: TRUE

tag: exp name

value: Submandibular salivary gland T cells in WT and PD1KO

tag: lab

value: Brossay

tag: organism name

tag: strain

tag: genetics

value: PD1 KO (CRISPR in B6NJ backcrossed with B6J)

tag: Sex

value: male

tag: age weeks

tag: pool of_mice

value: FALSE

tag: prep description

value: liberase, DNAse I

tag: organ

tag: organ uberon_id

tag: target cells

tag: gating strategy

tag: mouse comments


title: hiPSC-CMs treated with chlorpromazine biol rep 1

description: Library name: 40_14_1

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: BCG-344

description: Library name: BCG-344_RNAseq

tag: tissue

value: Breast tumor

tag: age

tag: race

value: White

tag: ethnicity

value: Hispanic or Latino

tag: er

value: ER-positive

tag: gender

value: Female

tag: clinical stage

tag: adi (state_decile)

tag: nseas composite_score

tag: nseas safety_score

tag: nseas social_cohesion_score

tag: nseas aesthetic_quality_score

tag: eeds discrimination_score

tag: batch


title: I15H8_salivarygland_PD1KO_GEX

description: Library name: I15H8_salivarygland_PD1KO_GEX

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

tag: exp name

tag: lab

tag: organism name

tag: strain

tag: genetics

tag: Sex

tag: age weeks

tag: pool of_mice

tag: prep description

tag: organ

tag: organ uberon_id

tag: target cells

value: all T

tag: gating strategy

value: CD45+ CD3e+

tag: mouse comments

tag: cell type

value: T cells


title: hiPSC-CMs treated with chlorpromazine biol rep 2

description: Library name: 41_14_2

tag: cell line

value: Ncyte vCardiomyocytes

value: hiPSC-CMs

tag: genotype

value: wild type

tag: treatment

value: Chlorpromazine 1 µM


title: BCG-343

description: Library name: BCG-343_RNAseq

tag: tissue

tag: age

tag: race

tag: ethnicity

tag: er

tag: gender

value: No

tag: clinical stage

value: IIA

tag: adi (state_decile)

tag: nseas composite_score

tag: nseas safety_score

tag: nseas social_cohesion_score

tag: nseas aesthetic_quality_score

tag: eeds discrimination_score

tag: batch


title: I15H8_salivarygland_PD1KO_FBC

description: Library name: I15H8_salivarygland_PD1KO_FBC

value: submandibular gland

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

value: TRUE

tag: exp name

value: Submandibular salivary gland T cells in WT and PD1KO

tag: lab

value: Brossay

tag: organism name

tag: strain

tag: genetics

value: PD1 KO (CRISPR in B6NJ backcrossed with B6J)

tag: Sex

value: male

tag: age weeks

tag: pool of_mice

tag: prep description

tag: organ

tag: organ uberon_id

tag: target cells

tag: gating strategy

tag: mouse comments

tag: cell type


title: BCG-335

description: Library name: BCG-335_RNAseq

tag: tissue

value: Breast tumor

tag: age

tag: race

value: White

tag: ethnicity

value: Hispanic or Latino

tag: er

value: ER-positive

tag: gender

tag: treatment

tag: clinical stage

tag: adi (state_decile)

tag: nseas composite_score

tag: nseas safety_score

tag: nseas social_cohesion_score

tag: nseas aesthetic_quality_score

tag: eeds discrimination_score

tag: batch


title: hiPSC-CMs treated with dofetilide biol rep 3

description: Library name: 36_12_3

tag: cell line

tag: genotype

value: Dofetilide 0.01 µM


title: BSSR1957

description: Library name: BSSR1957_RNAseq

tag: tissue

value: Female


title: hiPSC-CMs treated with digoxin biol rep 1

description: Library name: 37_13_1

value: Ncyte vCardiomyocytes

tag: cell type

value: hiPSC-CMs

value: Digoxin 0.01 µM


title: hiPSC-CMs treated with ASA biol rep 1

description: Library name: 46_16_1

value: wild type

value: ASA 10 µM


title: I15H7_salivarygland_PD1KO_TCR

description: Library name: I15H7_salivarygland_PD1KO_TCR

value: submandibular gland

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

tag: exp name

tag: lab

tag: organism name

tag: strain

tag: genetics

tag: Sex

value: female

tag: age weeks

tag: pool of_mice

value: FALSE

tag: prep description

value: liberase, DNAse I

tag: organ

tag: organ uberon_id

tag: target cells

value: all T

tag: gating strategy

value: CD45+ CD3e+

tag: mouse comments

value: T cells


title: I15H9_salivarygland_PD1KO_GEX

description: Library name: I15H9_salivarygland_PD1KO_GEX

tag: tissue

tag: immgent igt_10xlane_id

tag: hashtag number

value: TRUE

value: Submandibular salivary gland T cells in WT and PD1KO

value: Brossay

value: PD1 KO (CRISPR in B6NJ backcrossed with B6J)

value: male

tag: cell type


title: hiPSC-CMs treated with erlotinib biol rep 3

description: Library name: 45_15_3

tag: cell line

value: Ncyte vCardiomyocytes

tag: genotype

tag: treatment

value: Erlotinib 0.3 µM


title: hiPSC-CMs treated with erlotinib biol rep 2

description: Library name: 44_15_2

value: hiPSC-CMs


title: BCG-328

description: Library name: BCG-328_RNAseq

value: Breast tumor

tag: age

tag: race

value: White

tag: ethnicity

value: Hispanic or Latino

tag: er

value: ER-positive

tag: gender

value: Female

value: No

tag: clinical stage

value: IA

tag: adi (state_decile)

tag: nseas composite_score

tag: nseas safety_score

tag: nseas social_cohesion_score

tag: nseas aesthetic_quality_score

tag: eeds discrimination_score

tag: batch


title: hiPSC-CMs treated with dofetilide biol rep 2

description: Library name: 35_12_2

tag: cell type

value: wild type

value: Dofetilide 0.01 µM


title: hiPSC-CMs treated with dofetilide biol rep 1

description: Library name: 34_12_1

tag: cell line


title: hiPSC-CMs treated with amiodarone biol rep 2

description: Library name: 32_11_2

tag: genotype

value: Amiodarone 1 µM


title: I15H7_salivarygland_PD1KO_FBC

description: Library name: I15H7_salivarygland_PD1KO_FBC

tag: tissue

value: submandibular gland

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

value: TRUE

tag: exp name

value: Submandibular salivary gland T cells in WT and PD1KO

tag: lab

tag: organism name

tag: strain

tag: genetics

tag: Sex

value: female

tag: age weeks

tag: pool of_mice

value: FALSE

tag: prep description

value: liberase, DNAse I

tag: organ

tag: organ uberon_id

tag: target cells

value: all T

tag: gating strategy

value: CD45+ CD3e+

tag: mouse comments

value: T cells


title: hiPSC-CMs treated with amiodarone biol rep 3

description: Library name: 33_11_3

tag: cell line

value: Ncyte vCardiomyocytes

tag: cell type

value: hiPSC-CMs

tag: genotype

tag: treatment


title: BCG-314

description: Library name: BCG-314_RNAseq

tag: tissue

value: Breast tumor

tag: age

tag: race

value: White

tag: ethnicity

value: Hispanic or Latino

tag: er

value: ER-positive

tag: gender

value: Female

tag: clinical stage

value: IIA

tag: adi (state_decile)

tag: nseas composite_score

tag: nseas safety_score

tag: nseas social_cohesion_score

tag: nseas aesthetic_quality_score

tag: eeds discrimination_score

tag: batch


title: hiPSC-CMs treated with digoxin biol rep 3

description: Library name: 39_13_3

tag: cell line

tag: cell type

value: wild type

value: Digoxin 0.01 µM


title: hiPSC-CMs treated with bupivacaine biol rep 3

description: Library name: 30_10_3

tag: genotype

tag: treatment

value: Bupivacaine 1 µM


title: hiPSC-CMs treated with amiodarone biol rep 1

description: Library name: 31_11_1

value: Amiodarone 1 µM


title: hiPSC-CMs treated with bupivacaine biol rep 2

description: Library name: 29_10_2


title: hiPSC-CMs treated with bupivacaine biol rep 1

description: Library name: 28_10_1


title: I15H6_salivarygland_PD1KO_GEX

description: Library name: I15H6_salivarygland_PD1KO_GEX

tag: tissue

value: submandibular gland

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

value: TRUE

tag: exp name

value: Submandibular salivary gland T cells in WT and PD1KO

tag: lab

value: Brossay

tag: organism name

tag: strain

tag: genetics

value: PD1 KO (CRISPR in B6NJ backcrossed with B6J)

tag: Sex

value: female

tag: age weeks

tag: pool of_mice

value: FALSE

tag: prep description

tag: organ

tag: organ uberon_id

tag: target cells

tag: gating strategy

tag: mouse comments


title: BCG-270

description: Library name: BCG-270_RNAseq

tag: tissue

value: Breast tumor

tag: age

tag: race

tag: ethnicity

tag: er

tag: gender

tag: treatment

value: No

tag: clinical stage

tag: adi (state_decile)

tag: nseas composite_score

tag: nseas safety_score

tag: nseas social_cohesion_score

tag: nseas aesthetic_quality_score

tag: eeds discrimination_score

tag: batch


title: hiPSC-CMs treated with digoxin biol rep 2

description: Library name: 38_13_2

tag: cell line

value: Ncyte vCardiomyocytes

tag: cell type

value: hiPSC-CMs

tag: genotype


title: I15H6_salivarygland_PD1KO_TCR

description: Library name: I15H6_salivarygland_PD1KO_TCR

tag: tissue

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

tag: exp name

tag: lab

tag: organism name

tag: strain

tag: genetics

tag: Sex

tag: age weeks

tag: pool of_mice

tag: prep description

value: liberase, DNAse I

tag: organ

tag: organ uberon_id

tag: target cells

value: all T

tag: gating strategy

value: CD45+ CD3e+

tag: mouse comments

value: T cells


title: hiPSC-CMs treated with propofol biol rep 3

description: Library name: 27_9_3

tag: cell line

tag: cell type

tag: genotype

value: wild type

tag: treatment

value: Propofol 100 µM


title: BCG-253

description: Library name: BCG-253_RNAseq

tag: tissue

tag: age

tag: race

value: White

tag: ethnicity

value: Hispanic or Latino

tag: er

value: ER-positive

tag: gender

value: Female

tag: clinical stage

value: IA

tag: adi (state_decile)

tag: nseas composite_score

tag: nseas safety_score

tag: nseas social_cohesion_score

tag: nseas aesthetic_quality_score

tag: eeds discrimination_score

tag: batch


title: hiPSC-CMs treated with propofol biol rep 1

description: Library name: 25_9_1

tag: cell line

tag: cell type


title: I15H6_salivarygland_PD1KO_FBC

description: Library name: I15H6_salivarygland_PD1KO_FBC

value: submandibular gland

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

value: TRUE

tag: exp name

value: Submandibular salivary gland T cells in WT and PD1KO

tag: lab

value: Brossay

tag: organism name

tag: strain

tag: genetics

value: PD1 KO (CRISPR in B6NJ backcrossed with B6J)

tag: Sex

value: female

tag: age weeks

tag: pool of_mice

tag: prep description

tag: organ

tag: organ uberon_id

tag: target cells

tag: gating strategy

tag: mouse comments


title: hiPSC-CMs treated with omecamtiv_mecarbil biol rep 3

description: Library name: 24_8_3

tag: cell line

value: Ncyte vCardiomyocytes

tag: cell type

value: hiPSC-CMs

tag: genotype

tag: treatment

value: Omecamtiv_Mecarbil 1 µM


title: I15H5_salivarygland_PD1KO_TCR

description: Library name: I15H5_salivarygland_PD1KO_TCR

tag: tissue

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

tag: exp name

tag: lab

value: FALSE

value: liberase, DNAse I

value: all T

value: CD45+ CD3e+

value: T cells


title: hiPSC-CMs treated with omecamtiv_mecarbil biol rep 2

description: Library name: 23_8_2

value: wild type


title: hiPSC-CMs treated with omecamtiv_mecarbil biol rep 1

description: Library name: 22_8_1


title: Smad1/5 dKO mESCs, KDM1A ChIP-seq, rep2

city: Tokyo

first: Masato

last: Morikawa

address: 2-21-1 Kaga, Itabashi-ku

department: Advanced Comprehensive Research Organization

country: Japan

institute: Teikyo University

description: KDM1A ChIP-seq

library_source: genomic

data_processing:
The libraries were sequenced on the Ion Proton sequencer (Thermo Fisher Scientific). Both reference genomes and gene models were obtained from Illumina iGenome website (https://support.illumina.com/sequencing/sequencing_software/igenome.html).
All ChIP-seq data sets were trimmed down to 50 bp using FASTP (version 0.23.2) (Chen et al., 2018) and were aligned to the mouse reference genome GRCm38/mm10 with Bowtie 2 (version 2.2.5) (Langmead and Salzberg, 2012) with default parameters.
Peaks were called using MACS3 (Model based analysis of ChIP-seq) (version 3.0.0a6) (Zhang et al., 2008) with the following parameters: "-g mm --broad-cutoff 0.1 --broad" for H3K4me1/broad peaks, "-g mm --q 0.05" for H3K4me2/narrow peaks, and "-g mm --q 0.01" for DNA-binding transcription factors/narrow peaks such as SMAD1/5 and KDM1A. Peak calling for H3K9me2 was performed using Epic2 (version 0.0.52) (Stovner and Saetrom, 2019) with the following parameters: "-gn mm10 -fs 50 -bin 500 -g 8 -kd -fdr 0.05".
Common regions of the duplicate ChIP-seq data were generated using R package ChIPpeakAnno (version 3.36.1) (Zhu et al., 2010). Assignment of genes to regions was done using the ChIPpeakAnno, taking the closest gene within a maximum distance of 10 kb.
Bigwig files with 1-bp resolution were generated and scaled to 1× coverage (reads per genome coverage, 1×RPGC) using bamCoverage function of deeptools2 package (version 3.5.1) (Ramírez et al., 2016) with the following parameters: "--binSize 1 --normalizeUsing RPGC --extendReads 200 --ignoreDuplicates --effectiveGenomeSize 2308125349". Input tracks were thereafter subtracted by using deeptools2 bigWigCompare with the following parameters: "--binSize 1 --operation subtract".
Assembly: mm10
Supplementary files format and content: BED, narrowPeak or broadPeak format
Supplementary files format and content: BigWig format

molecule: genomic DNA

source_name: mouse ESCs (E14)

growth_protocol: Feeder-free E14 mouse ESCs were maintained in serum-containing conditions, and Smad1/5 double knockout mESCs (S1/5 dKO) was generated using CRISPR-Cas9 system (Morikawa et al., 2016). These cells were cultured at 37°C in 5% CO2 and were maintained on gelatin (Millipore, Merck, Darmstadt, Germany, or FUJIFILM Wako, Tokyo, Japan)-coated dishes in Dulbecco's modified Eagle's medium (DMEM) (Gibco, Thermo Fisher Scientific, Waltham, MA, USA), with 15% ES-qualified fetal bovine serum (FBS) (Millipore, Merck), 0.1 mM β-mercaptoethanol (FUJIFILM Wako), 2 mM L-glutamine, 1×MEM nonessential amino acids, 100 U/ml penicillin and 100 μg/ml streptomycin (all from Gibco), and 1000 U/ml LIF (Millipore).

extract_protocol:
Chromatin isolation, sonication and immunoprecipitation using antibody were performed essentially as described previously (Morikawa et al., 2019), and were conducted in accordance with the ENCODE guidelines. Briefly, approximately 1×10^7 cells were used for one immunoprecipitation. Cells were fixed in 1% formaldehyde for 10 min at RT with swirling. Cross-linking was stopped by adding glycine to a final concentration of 125 mM and washing twice in ice-cold PBS. The cross-linked mESCs were harvested by scraping, pelleted, and resuspended in 1 ml of lysis buffer containing 50 mM Tris-HCl, pH 8.0, 10 mM EDTA, 1% SDS, and cOmplete EDTA-free protease inhibitor cocktail (Roche, Merck). Chromatin was sonicated using the Bioruptor sonicator for 2−10 cycles of 30 sec ON and 30 sec OFF at 'high' power, in order to shear DNA to an average fragment size of 200-500 bp. Cell extract was diluted 10-fold in ChIP dilution buffer (20 mM Tris-HCl, pH 8.0, 2 mM EDTA, 1% Triton X-100, 150 mM NaCl, cOmplete EDTA-free). One hundred and fifty µl of Anti-mouse IgG Dynabeads (Invitrogen Life Technologies) for mouse antibody or 75 µl of Protein A Dynabeads (Invitrogen Life Technologies) for rabbit antibody was preincubated with 10 µg of antibody at 4°C overnight; chromatin was then added and was incubated at 4°C for at least another 6 h. The beads were then washed five times in RIPA buffer (50 mM HEPES-KOH, pH 7.0, 0.5 M LiCl, 1 mM EDTA, 0.7% deoxycholate, 1% NP-40) and once in TE buffer (10 mM Tris-HCl, pH 8.0, 1 mM EDTA). Immunoprecipitated samples were eluted and reverse crosslinked by incubation in elution buffer (50 mM Tris-HCl, pH 8.0, 10 mM EDTA, 1% SDS) at 65°C overnight. Genomic DNA was then extracted with a QIAquick PCR purification kit (Qiagen).
The libraries were constructed using IonXpress Plus Fragment Library Kit (Thermo Fisher Scientific).

treatment_protocol: FBS and LIF

value: mouse ESCs (E14)

value: mouse embryonic stem cells

value: Smad1/5 dKO

value: FBS and LIF

tag: chip antibody


title: I15H5_salivarygland_PD1KO_GEX

description: Library name: I15H5_salivarygland_PD1KO_GEX

value: submandibular gland

value: TRUE

value: Submandibular salivary gland T cells in WT and PD1KO

tag: organism name

tag: strain

tag: genetics

tag: Sex

tag: age weeks

tag: pool of_mice

tag: prep description

tag: organ


title: I15H7_salivarygland_PD1KO_GEX

description: Library name: I15H7_salivarygland_PD1KO_GEX

value: Brossay

value: PD1 KO (CRISPR in B6NJ backcrossed with B6J)

value: female

tag: organ uberon_id

tag: target cells

tag: gating strategy

tag: mouse comments

tag: cell type


title: wild-type mESCs, KDM1A ChIP-seq, rep2

description: KDM1A ChIP-seq

tag: cell line

tag: genotype

value: wild-type

tag: treatment


title: hiPSC-CMs treated with methotrexate biol rep 3

description: Library name: 21_7_3

value: Ncyte vCardiomyocytes

value: hiPSC-CMs

value: Methotrexate 1 µM


title: Smad1/5 dKO mESCs, KDM1A ChIP-seq, rep1

description: KDM1A ChIP-seq

tag: chip antibody


title: hiPSC-CMs treated with methotrexate biol rep 1

description: Library name: 19_7_1


title: I15H5_salivarygland_PD1KO_FBC

description: Library name: I15H5_salivarygland_PD1KO_FBC

tag: tissue

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

tag: exp name

tag: lab

tag: organism name

value: FALSE

value: liberase, DNAse I

value: all T

value: CD45+ CD3e+


title: hiPSC-CMs treated with 5-fluoro-uracil biol rep 3

description: Library name: 18_6_3

value: wild type

value: 5-Fluoro-uracil 10 µM


title: BCG-265

description: Library name: BCG-265_RNAseq

value: Breast tumor

tag: age

tag: race

value: White

tag: ethnicity

value: Hispanic or Latino

tag: er

value: ER-positive

tag: gender

value: Female

value: No

tag: clinical stage

value: IIB

tag: adi (state_decile)

tag: nseas composite_score

tag: nseas safety_score

tag: nseas social_cohesion_score

tag: nseas aesthetic_quality_score

tag: eeds discrimination_score

tag: batch


title: I15H4_salivarygland_GEX

description: Library name: I15H4_salivarygland_GEX

tag: tissue

value: submandibular gland

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

value: salivarygland

tag: cite seq

value: TRUE

value: Submandibular salivary gland T cells in WT and PD1KO

value: Brossay

tag: strain

tag: genetics

value: wt

tag: Sex

value: male

tag: age weeks

tag: pool of_mice

tag: prep description

tag: organ

tag: organ uberon_id

tag: target cells

tag: gating strategy

tag: mouse comments

value: pool of 9 males DOB 5/10/22

tag: cell type

value: T cells


title: hiPSC-CMs treated with 5-fluoro-uracil biol rep 1

description: Library name: 16_6_1

tag: cell line

value: Ncyte vCardiomyocytes

value: hiPSC-CMs

tag: genotype

value: wild type

tag: treatment

value: 5-Fluoro-uracil 10 µM


title: wild-type mESCs, KDM1A ChIP-seq, rep1

description: KDM1A ChIP-seq

value: mouse ESCs (E14)

value: mouse embryonic stem cells

value: wild-type

value: FBS and LIF

tag: chip antibody


title: hiPSC-CMs treated with 5-fluoro-uracil biol rep 2

description: Library name: 17_6_2


title: I15H4_salivarygland_TCR

description: Library name: I15H4_salivarygland_TCR

tag: tissue

value: submandibular gland

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

tag: exp name

tag: lab

tag: organism name

value: liberase, DNAse I

value: all T

value: CD45+ CD3e+


title: hiPSC-CMs treated with lapatinib biol rep 3

description: Library name: 15_5_3

value: Lapatinib 10 µM


title: hiPSC-CMs treated with lapatinib biol rep 1

description: Library name: 13_5_1


title: Smad1/5 dKO mESCs, H3K9me2 ChIP-seq, rep1

description: H3K9me2 ChIP-seq

value: Smad1/5 dKO


title: Smad1/5 dKO mESCs, H3K9me2 ChIP-seq, rep2

description: H3K9me2 ChIP-seq


title: hiPSC-CMs treated with lapatinib biol rep 2

description: Library name: 14_5_2


title: I15H4_salivarygland_FBC

description: Library name: I15H4_salivarygland_FBC

value: salivarygland

value: TRUE

value: Submandibular salivary gland T cells in WT and PD1KO

value: Brossay

tag: strain

tag: genetics

value: wt

tag: Sex

value: male

tag: age weeks

tag: pool of_mice

tag: prep description

tag: organ

tag: organ uberon_id


title: hiPSC-CMs treated with propofol biol rep 2

description: Library name: 26_9_2

tag: cell line

value: Ncyte vCardiomyocytes

tag: cell type

value: hiPSC-CMs

tag: genotype

value: wild type

tag: treatment

value: Propofol 100 µM


title: hiPSC-CMs treated with dasatinib biol rep 3

description: Library name: 12_4_3

value: Dasatinib 0.3 µM


title: hiPSC-CMs treated with dasatinib biol rep 1

description: Library name: 10_4_1


title: hiPSC-CMs treated with ponatinib biol rep 3

description: Library name: 9_3_3

value: Ponatinib 1 µM


title: wild-type mESCs, H3K9me2 ChIP-seq, rep1

description: H3K9me2 ChIP-seq

value: mouse ESCs (E14)

value: mouse embryonic stem cells

value: wild-type

value: FBS and LIF

tag: chip antibody


title: hiPSC-CMs treated with dasatinib biol rep 2

description: Library name: 11_4_2


title: hiPSC-CMs treated with methotrexate biol rep 2

description: Library name: 20_7_2

value: Methotrexate 1 µM


title: I15H3_salivarygland_TCR

description: Library name: I15H3_salivarygland_TCR

tag: tissue

value: submandibular gland

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

value: salivarygland

tag: cite seq

value: female

value: liberase, DNAse I

tag: target cells

value: all T

tag: gating strategy

value: CD45+ CD3e+

tag: mouse comments

value: pool of 9 females DOB 5/10/22

value: T cells


title: wild-type mESCs, H3K9me2 ChIP-seq, rep2

description: H3K9me2 ChIP-seq


title: hiPSC-CMs treated with ponatinib biol rep 1

description: Library name: 7_3_1

value: Ncyte vCardiomyocytes

value: hiPSC-CMs

value: wild type


title: I15H3_salivarygland_GEX

description: Library name: I15H3_salivarygland_GEX

value: TRUE

tag: exp name

value: Submandibular salivary gland T cells in WT and PD1KO

tag: lab

value: Brossay

tag: organism name

tag: strain

tag: genetics

value: wt

tag: Sex

tag: age weeks

tag: pool of_mice


title: Smad1/5 dKO mESCs, H3K4me2 ChIP-seq, rep2

description: H3K4me2 ChIP-seq

tag: cell line

value: mouse ESCs (E14)

tag: cell type

value: mouse embryonic stem cells

tag: genotype

value: Smad1/5 dKO

tag: treatment

value: FBS and LIF

tag: chip antibody


title: I15H2_spleen_TCR

description: Library name: I15H2_spleen_TCR

tag: tissue

value: spleen

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

value: female

tag: prep description

tag: organ

tag: organ uberon_id

value: splenocytes


title: hiPSC-CMs treated with cisplatin biol rep 2

description: Library name: 5_2_2

value: Cisplatin 10 µM


title: I15H3_salivarygland_FBC

description: Library name: I15H3_salivarygland_FBC

value: submandibular gland

value: salivarygland

tag: exp name

tag: lab

tag: organism name

tag: strain

tag: genetics

value: liberase, DNAse I

tag: target cells

value: all T

tag: gating strategy

value: CD45+ CD3e+

tag: mouse comments

value: pool of 9 females DOB 5/10/22


title: hiPSC-CMs treated with ponatinib biol rep 2

description: Library name: 8_3_2

tag: cell line

value: Ncyte vCardiomyocytes

tag: cell type

value: hiPSC-CMs

tag: genotype

value: wild type

tag: treatment

value: Ponatinib 1 µM


title: hiPSC-CMs treated with doxorubicin biol rep 2

description: Library name: 2_1_2

value: Doxorubicin 0.1 µM


title: wild-type mESCs, H3K4me2 ChIP-seq, rep1

description: H3K4me2 ChIP-seq

value: mouse ESCs (E14)

value: mouse embryonic stem cells

value: wild-type

tag: chip antibody


title: Smad1/5 dKO mESCs, H3K4me2 ChIP-seq, rep1

description: H3K4me2 ChIP-seq

value: Smad1/5 dKO

value: FBS and LIF


title: hiPSC-CMs treated with doxorubicin biol rep 1

description: Library name: 1_1_1


title: hiPSC-CMs treated with cisplatin biol rep 3

description: Library name: 6_2_3

value: Cisplatin 10 µM


title: I15H2_spleen_GEX

description: Library name: I15H2_spleen_GEX

tag: tissue

value: spleen

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

value: TRUE

value: Submandibular salivary gland T cells in WT and PD1KO

value: Brossay

value: wt

tag: Sex

value: female

tag: age weeks

tag: pool of_mice

value: splenocytes

value: T cells


title: wild-type mESCs, H3K4me2 ChIP-seq, rep2

description: H3K4me2 ChIP-seq


title: I15H10_salivarygland_PD1KO_TCR

description: Library name: I15H10_salivarygland_PD1KO_TCR

value: submandibular gland

tag: exp name

tag: lab

tag: organism name

tag: strain

tag: genetics

value: PD1 KO (CRISPR in B6NJ backcrossed with B6J)

value: male

value: FALSE

tag: prep description

value: liberase, DNAse I

tag: organ

tag: organ uberon_id

value: all T

value: CD45+ CD3e+


title: Smad1/5 dKO mESCs, H3K4me1 ChIP-seq, rep2

description: H3K4me1 ChIP-seq

tag: cell line

value: mouse ESCs (E14)

tag: cell type

value: mouse embryonic stem cells

tag: genotype

value: Smad1/5 dKO

tag: treatment

value: FBS and LIF

tag: chip antibody


title: Smad1/5 dKO mESCs, H3K4me1 ChIP-seq, rep1

description: H3K4me1 ChIP-seq


title: THP-1 coculture with SiGPNMB2 - Hs578T replication 3

city: Shinagawa-ku

first: Kunio

last: Kawanishi

state: Tokyo

address: 1-5-8 Hatanodai

institute: Showa Medical University

data_processing:
CLC Genomics Workbench 23.02 software
iDEP1.1
The KEGG (Kyoto Encyclopedia of Genes and Genomics) database
DAVID (Database for Annotation, Visualization, and Integrated Discovery)
Assembly: human
Supplementary files format and content: text file includes total counts, RPKM, TPM, CPM  for each Sample

growth_protocol: DMEM: F12 = 1:1; 20 ng/ml EGF, 20 ng/ml BFGF and 2 % of B27

extract_protocol:
Total RNA was extracted using Trizol (Life Technologies)
NEBNext Poly(A) mRNA Magnetic Isolation Module (E7490) and NEBNext Ultra II RNA Library Prep Kit for Illumina (E7770L) with 12 final PCR cycles

treatment_protocol: 20 nM siRNA against GPNMB or control siRNA using Lipofectamine (TM) RNAiMax Transfection Reagent (Invitrogen)

value: Monocyte - Macrophage

value: Knock down GPNMB on Hs578T

value: coculture


title: THP-1 coculture with SiGPNMB2 - Hs578T replication 2


title: THP-1 coculture with SiGPNMB2 - Hs578T replication 1


title: THP-1 coculture with SiGPNMB1 - Hs578T replication 3


title: wild-type mESCs, H3K4me1 ChIP-seq, rep2

description: H3K4me1 ChIP-seq

value: wild-type


title: I15H10_salivarygland_PD1KO_GEX

description: Library name: I15H10_salivarygland_PD1KO_GEX

tag: tissue

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

value: TRUE

value: Submandibular salivary gland T cells in WT and PD1KO

value: Brossay

tag: target cells

tag: gating strategy

tag: mouse comments


title: THP-1 coculture with SiGPNMB1 - Hs578T replication 1


title: I15H10_salivarygland_PD1KO_FBC

description: Library name: I15H10_salivarygland_PD1KO_FBC

value: submandibular gland

tag: exp name

tag: lab

tag: organism name

tag: strain

tag: genetics

value: PD1 KO (CRISPR in B6NJ backcrossed with B6J)

tag: Sex

tag: age weeks

tag: pool of_mice

value: T cells


title: THP-1 coculture with Hs578T replication 3

tag: cell line

tag: cell type

tag: genotype

value: WT

tag: treatment


title: THP-1 coculture with Hs578T replication 2


title: I15H1_spleen_TCR

description: Library name: I15H1_spleen_TCR

tag: tissue

value: spleen

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

value: wt

value: female

tag: prep description

value: mechanical dissociation alone

tag: organ

tag: organ uberon_id

value: splenocytes

value: pool of 9 females DOB 5/10/22


title: hiPSC-CMs treated with cisplatin biol rep 1

description: Library name: 4_2_1

value: Ncyte vCardiomyocytes

value: hiPSC-CMs

value: wild type

value: Cisplatin 10 µM


title: THP-1 without any treatment replication 3

value: Monocyte - Macrophage

value: only THP-1


title: I15H1_spleen_GEX

description: Library name: I15H1_spleen_GEX

tag: cite seq

value: TRUE

tag: exp name

value: Submandibular salivary gland T cells in WT and PD1KO

tag: lab

value: Brossay

tag: organism name

tag: target cells

tag: gating strategy

tag: mouse comments


title: Smad1/5 dKO mESCs, ChIP-seq input

description: ChIP-seq input

tag: cell line

value: mouse ESCs (E14)

tag: cell type

value: mouse embryonic stem cells

value: Smad1/5 dKO

value: FBS and LIF

tag: chip antibody


title: hiPSC-CMs treated with doxorubicin biol rep 3

description: Library name: 3_1_3

tag: genotype

tag: treatment

value: Doxorubicin 0.1 µM


title: THP-1 coculture with Hs578T replication 1

value: WT

value: coculture


title: I15H2_spleen_FBC

description: Library name: I15H2_spleen_FBC

tag: tissue

value: spleen

tag: immgent igt_10xlane_id

tag: hashtag number

tag: strain

tag: genetics

value: wt

tag: Sex

value: female

tag: age weeks

tag: pool of_mice

value: liberase, DNAse I

value: splenocytes

value: pool of 9 females DOB 5/10/22

value: T cells


title: wild-type mESCs, ChIP-seq input

description: ChIP-seq input

value: wild-type


title: THP-1 without any treatment replication 1

value: Monocyte - Macrophage

value: only THP-1


title: BCG-222

description: Library name: BCG-222_RNAseq

value: Breast tumor

tag: age

tag: race

value: White

tag: ethnicity

value: Hispanic or Latino

tag: er

value: ER-positive

tag: gender

value: Female

value: No

tag: clinical stage

value: IIA

tag: adi (state_decile)

tag: nseas composite_score

tag: nseas safety_score

tag: nseas social_cohesion_score

tag: nseas aesthetic_quality_score

tag: eeds discrimination_score

tag: batch


title: I15H1_spleen_FBC

description: Library name: I15H1_spleen_FBC

tag: tissue

value: spleen

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

value: TRUE

tag: exp name

value: Submandibular salivary gland T cells in WT and PD1KO

tag: lab

value: Brossay

tag: organism name

tag: strain

tag: genetics

tag: prep description

value: mechanical dissociation alone

tag: organ

tag: organ uberon_id

tag: target cells

tag: gating strategy

tag: mouse comments

tag: cell type


title: THP-1 without any treatment replication 2

tag: cell line

tag: genotype

value: WT

tag: treatment


title: gc_null_4

city: Cambridge

first: Dustin

middle: Eliot

last: Tillman

address: 7 Divinity Ave, Bauer Laboratory 103

department: Stem Cell and Regenerative Biology, Center for Brain Science

institute: Harvard University

data_processing:
Reads from two sequencing runs and two sequencing lanes were concatenated, adapter sequences were clipped, and unpaired reads were trimmed with Trimmomatic.
Reads were aligned to the GRCm39 mouse genome with STAR in 2-pass mode, and reads mapping to exons were quantified with featureCounts.
Variants were called on all samples with GATK HapotypeCaller
Assembly: Grcm39
Supplementary files format and content: Tab-delimited text files include read counts for each gene.
Supplementary files format and content: Tab-delimited text files include counts and base identities for each variant.

source_name: brain

growth_protocol: Mice were housed in groups of 2-4, except males that were single housed post-breeding for timed pregnancy, all on standard 12h light / 12h dark cycle.

extract_protocol:
The QIAGEN Allprep Mini kit was used for total RNA extraction of sorted GCs and somata.
RNA samples were converted to cDNA using the SMART-seq v4 Ultra Low Input RNA Kit, and cDNA libraries were generated with the Nextera XT DNA Library Preparation Kit.

treatment_protocol:
Following anesthetization of timed pregnant mice, the uterine horns were exposed, and the plasmids mixed with Fast Green dye were microinjected into one of the lateral ventricles. Five 34 volt pulses (50 ms on and 950 ms off per pulse) were delivered in appropriate orientation across the embryonic head using 5mm diameter platinum plate electrodes and a CUY21EDIT square wave electroporator. In the DNA mixture, the fluorophore-expressing plasmid concentration was around 4 µg/µl.
Contralateral cortical hemispheres containing axonal GCs were micro-dissected rapidly and homogenized in 0.32M sucrose supplemented with 4mM HEPES, Halt protease and phosphatase inhibitor cocktail, and RNasin ribonuclease inhibitors at 900 RPM in a glass-Teflon tissue grinder with 10-12 strokes. Following a low speed centrifuge at 1700 RPM for 15 min at 4 °C, “post-nuclear homogenate” (PNH; input) supernatant was collected, and layered onto 0.83 M and 2.5 M sucrose gradient (Top-to-bottom: Input, 0.83 M sucrose, 2.5 M sucrose). The discontinuous sucrose gradient was centrifuged at 242K g for 47 min at 4 °C in a vertical rotor. The bulk GC fraction (GCF) was extracted from the interface between 0.32 M and 0.83 M sucrose. Labeled superficial layer CPN axonal GCs were purified from bulk GCF via fluorescent small particle sorting (FSPS) utilizing customized BD SORP FACS AriaII instrument. Bulk GCF in sucrose solution were diluted with 4- to 6-fold in chilled PBS prior to loading into the sorter. GCs were sorted directly into the RLT lysis buffer for total RNA extraction. Paired ipsilateral cortical hemispheres were collected in chilled dissociation solution and micro-dissected in chilled HBSS using a fluorescent dissection microscope to remove meninges and ventricular zone, and enrich for labeled CPN. Cortical tissues were returned to dissociation solution and enzymatically dissociated for FACS. Fluorescently labeled somata were isolated by sorting on a FACS AriaII instrument equipped with and 85 µm nozzle operated at 45 p.s.i. Somata were sorted directly into the RLT lysis buffer for total RNA extraction.

tag: tissue

value: brain

tag: mouse strain

value: CPN

tag: developmental stage

tag: Sex

value: mixed

tag: compartment

value: growth cone

tag: number of_hemispheres

tag: number of_supplmented_cd1_hemispheres

tag: tissue mass_(g)

tag: number collected

tag: esitmated rna_concentration_(ng/ul)

tag: 28s to_18s_ratio

tag: rin


title: gc_null_2


title: gc_null_3


title: gc_null_1


title: BCG-174

description: Library name: BCG-174_RNAseq

value: Breast tumor

tag: age

tag: race

tag: ethnicity

tag: er

tag: gender

tag: clinical stage

value: IA

tag: adi (state_decile)

tag: nseas composite_score

tag: nseas safety_score

tag: nseas social_cohesion_score

tag: nseas aesthetic_quality_score

tag: eeds discrimination_score

tag: batch


title: gc_het_4

tag: tissue

tag: mouse strain

tag: cell type

tag: genotype

tag: developmental stage

tag: Sex

tag: compartment

tag: number of_hemispheres

tag: number of_supplmented_cd1_hemispheres

tag: tissue mass_(g)

tag: number collected


title: THP-1 coculture with SiGPNMB1 - Hs578T replication 2

tag: cell line

value: Monocyte - Macrophage

value: Knock down GPNMB on Hs578T

tag: treatment

value: coculture


title: BCG-187

description: Library name: BCG-187_RNAseq

tag: age

tag: race

value: White

tag: ethnicity

value: Hispanic or Latino

tag: er

value: ER-positive

tag: gender

value: Female

value: No

tag: clinical stage

tag: adi (state_decile)

tag: nseas composite_score

tag: nseas safety_score

tag: nseas social_cohesion_score


title: gc_het_2

tag: tissue

tag: mouse strain

tag: cell type

tag: genotype

tag: developmental stage

tag: Sex

tag: compartment

tag: esitmated rna_concentration_(ng/ul)

tag: 28s to_18s_ratio

tag: rin


title: BCG-110

description: Library name: BCG-110_RNAseq

tag: age

tag: race

tag: ethnicity

tag: er

tag: treatment

tag: nseas aesthetic_quality_score

tag: eeds discrimination_score

tag: batch


title: skin cells,WT,A

city: Shanghai

first: Junjie

last: Gao

address: 600 Yishan Road

country: China

institute: Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

description: Library name: wtA_1

data_processing:
The scRNA-seq libraries were checked for quality using the Agilent Bioanalyzer High Sensitivity chip. Sequencing results were converted to FASTQ files using Illumina bcl2fastq software (version 5.01). Raw data were demultiplexed, barcode and mapped to the goat reference genome using the Cell Ranger package (version 3.1.0). Feature-barcode raw digital gene expression matrix (UMI counts per gene per cell) was filtered and normalized by using the R package Seurat  (Version 3.1.1).Genes detected in fewer than one cell were filtered out, and cells were removed if they expressed fewer than 500 detected genes, UMI counts less than Inf, and the percent of mitochondrial-DNA derived gene-expression < 25%. The Doublet Finder package (version 2.0.3) was also used to remove doublets.
Assembly: GCF_001704415.1_ARS1
Supplementary files format and content: matrix files

source_name: skin

extract_protocol:
Mice were anesthetized, and the dorsal hair was shaved and removed using a depilatory cream. Dorsal skin tissues were excised, and subcutaneous fat was carefully scraped using a surgical scalpel. The harvested tissues were immediately transferred to a culture dish containing ice-cold 1× phosphate-buffered saline (PBS) devoid of RNase, calcium, and magnesium ions. Tissues were then cut into ~0.5 mm² fragments and washed repeatedly with 1× PBS to eliminate surface blood, oil, and other contaminants。The tissue fragments were incubated in a dissociation solution comprising 0.35% collagenase IV, 2 mg/mL papain, and 120 U/mL DNase I at 37°C for 20 minutes in a shaking water bath (100 rpm). Tissue digestion was terminated by adding 1× PBS supplemented with 10% fetal bovine serum (FBS), followed by gentle pipetting (5–10 times) to further dissociate cells while minimizing shear-induced damage. The resulting suspension was filtered sequentially through 70 μm and 30 μm cell strainers, then centrifuged at 300 × g for 5 minutes at 4°C. The cell pellet was resuspended in 100 μL of 1× PBS containing 0.04% bovine serum albumin (BSA). To remove red blood cells, 1 mL of 10× red blood cell lysis buffer (MACS, Cat# 130-094-183) was added, and the sample was incubated for 2–10 minutes at room temperature or on wet ice. After lysis, the suspension was centrifuged again at 300 × g for 5 minutes. The pellet was resuspended in 100 μL of 1× PBS (0.04% BSA), and dead cells were removed using Dead Cell Removal MicroBeads (MACS, Cat# 130-090-101) following the manufacturer’s instructions. The procedure was repeated twice, each with centrifugation at 300 × g for 3 minutes at 4°C. The final single-cell suspension was prepared by resuspending the cell pellet in 50 μL of 1× PBS (0.04% BSA). Cell viability was assessed using trypan blue staining, with samples required to exceed 85% viability. Cell counts were determined using a hemocytometer, and cell concentrations were adjusted to 700–1200 cells/μL.
Single-cell suspensions were processed using the 10x Genomics Chromium system to capture approximately 5,000 individual cells, following the manufacturer’s instructions as detailed in the Chromium Single Cell 3' Reagent Kits User Guide (v3). Subsequent cDNA amplification and library preparation were performed according to the standard protocol. The resulting libraries were sequenced on an Illumina NovaSeq 6000 platform (paired-end, 150 bp) by LC-Bio Technology Co., Ltd. (Hangzhou, China), achieving a minimum sequencing depth of 20,000 reads per cell.

tag: tissue

value: skin

value: skin cells


title: skin cells,WT,B

description: Library name: wtB_1

tag: cell type


title: wild-type mESCs, H3K4me1 ChIP-seq, rep1

description: H3K4me1 ChIP-seq

tag: cell line

value: mouse ESCs (E14)

value: mouse embryonic stem cells

tag: genotype

value: wild-type

value: FBS and LIF

tag: chip antibody


title: skin cells,DTA,M925

description: Library name: DTA_M925_1


title: skin cells,DTA,M927

description: Library name: DTA_M927_1


title: BCG-118

description: Library name: BCG-118_RNAseq

tag: gender

tag: clinical stage

value: IIB

tag: adi (state_decile)

tag: nseas composite_score

tag: nseas safety_score

tag: nseas social_cohesion_score


title: gc_het_3

value: brain

tag: mouse strain

value: CPN

tag: developmental stage

tag: Sex

value: mixed

tag: compartment

value: growth cone

tag: number of_hemispheres

tag: number of_supplmented_cd1_hemispheres

tag: tissue mass_(g)

tag: number collected

tag: esitmated rna_concentration_(ng/ul)

tag: 28s to_18s_ratio

tag: rin


title: gc_het_1

tag: tissue

tag: cell type

tag: genotype


title: gc_wt_3


title: BCG-057

description: Library name: BCG-057_RNAseq

value: Breast tumor

tag: age

tag: race

tag: ethnicity

tag: er

tag: gender

tag: treatment

tag: clinical stage

value: IIA

tag: adi (state_decile)

tag: nseas composite_score

tag: nseas aesthetic_quality_score

tag: eeds discrimination_score

tag: batch


title: LCK project (CSP)

city: Prague

first: Juraj

last: Michalik

address: Vídeňská 1083

country: Czech Republic

institute: Institute of Molecular Genetics of the Czech Academy of Sciences

description: Library name: LCK_CSP

data_processing:
Resulting cDNA libraries were sequenced on NovaSeq 6000 (Illumina, NovaSeq Control Software 1.8.1) with the NovaSeq 6000 S4 Reagent Kits 300 cycles. The reads were then demultiplexed using Illumina BCL convert.
The generated reads were mapped using 10X Cell Ranger v7.1.0 to the Mus musculus reference genome provided by Ensembl (GRCm39, version 109).
The results were subsequently processed using Seurat v4.3.0 in R v4.2.1. Mitochondrial genes, ribosomal genes, and genes matching the regular expression Tr[ab][vdj] (primarily TCR V(D)J genes) were removed. Cells expressing fewer than 200 genes were also excluded. Sample demultiplexing was performed using the HTOdemux function from the Seurat package. Hashtag doublets and cells lacking a sufficient number of hashtag reads were filtered out.
The preprocessed dataset was normalized and scaled using the default method in the Seurat package. The top 750 variable genes were selected for dimensionality reduction via principal component analysis (PCA), followed by uniform manifold approximation and projection (UMAP) using 12 principal components. Clustering was performed with the Louvain algorithm implemented in Seurat. In a second, more stringent quality-control step, clusters consisting of dead or low-quality cells were removed. The final dataset contained 5,241 cells. Cell cycle effects were regressed out by specifying the parameter vars.to.regress = c("S.Score", "G2M.Score") during the ScaleData step in the Seurat workflow.
To quantify the expression of gene signatures, we used the AddModuleScore function implemented in the Seurat package. We computed module scores for curated gene sets: Hallmark Interferon Gamma Response (MM3878) and Biocarta TCR Pathway (MM1504) from the Mouse MSigDB collection, and GSE9650 Naïve vs Eff CD8 Tcell DN, originally defined in human genes, which we converted to murine orthologs using the Ensembl BioMart database (release December 2021). The conversion was performed using the getLDS function from the biomaRt R package (v2.60.1) to map human HGNC symbols to mouse MGI symbols.
Assembly: GRCm39
Supplementary files format and content: RDS file of finalized scRNA data in Seurat object generated by R, with CSP (HTO) and VDJ (TCR) information in meta data, used directly for manuscript figure generation.
Supplementary files format and content: Standard CSV file formatted according to 10X instructions for CSP mapping with additional column "multiplexed_sample" used to specify samples.
Library strategy: CITE-seq

molecule: protein

source_name: Spleen

growth_protocol: CD8+ T cells were purified from the spleens and lymph nodes of OT-I mice (either WT, CA, or KO) by FACS sorting based on CD8α⁺ CD5⁺ expression. 10^4 to 10^5 cells in 200 μl PBS were adoptively transferred into Ly5.1 congenic host mice intravenously.

extract_protocol:
Splenocytes were collected on day 5 post LM-OVA-immunization. Samples were enriched for CD8+ cells by using Dynabeads™ Untouched™ Mouse CD8 Cells Kit (Cat#11417D, Invotrogen) according to manufacturer’s instructions. The cells were resuspended in HBSS and stained with with LIVE/DEAD near-IR dye, anti-CD8a BV421, anti-CD45.1 PE, and anti-CD45.2 APC antibodies together with TotalSeq-C Hashtag antibodies for multiplexing (BioLegend; MH1: #155861, MH2: #155863, MH3: #155865, MH5: #155869, MH6: #155871, MH7: #155873, MH8: #155875, MH9: #155877). Viable CD8a+, CD45.2+OT-I cells were FACS sorted. The viability and concentration of cells after sort were measured using the TC20 Automated Cell Counter (1450102, Bio-Rad). The viability of the cells pre-loading was 85%. Cells were loaded onto a 10X Chromium machine (10X Genomics) aiming at the yield of X cells per sample
The sequencing libraries were prepared using Chromium Next GEM Single Cell 5’ Reagent Kits v2 with Feature Barcode technology for CRISPR Screening and Cell Surface Protein (10X Genomics, #PN-1000263, #PN-1000286, #PN-1000541, #PN-1000190, #PN-1000215, #PN-1000250) according to the protocol provided by the manufacturer (#CG000511 Rev C).

treatment_protocol: The following day the mice were infected with 5,000 CFU/200 µl PBS of transgenic Listeria monocytogenes (LM) expressing OVA or its lower affinity variant (Q4R7) i.v., or 31.5 PFU/30 µl PBS of transgenic Influenza A-OVA (IAV, strain A/Puerto Rico/8/34, from Carolyn King, University of Basel) intranasally.

value: Spleen

value: CD8+ T cells

value: LCK WT, KO or CA

tag: library type

value: HTO

tag: hto

value: TotalSeq-C0301 anti-mouse Hashtag 1 Antibody (48K-57152 WT OT-I), TotalSeq-C0302 anti-mouse Hashtag 2 Antibody (48K-57153 CA OT-I), TotalSeq-C0303 anti-mouse Hashtag 3 Antibody (48K-57154 KO OT-I), TotalSeq-C0305 anti-mouse Hashtag 5 Antibody (48K-57156 KO OT-I), TotalSeq-C0306 anti-mouse Hashtag 6 Antibody (48K-57148 CA OT-I), TotalSeq-C0307 anti-mouse Hashtag 7 Antibody (48K-57149 WT OT-I), TotalSeq-C0308 anti-mouse Hashtag 8 Antibody (48K-57150 KO OT-I), TotalSeq-C0309 anti-mouse Hashtag 9 Antibody (48K-57151 CA OT-I)


title: soma_het_4

tag: tissue

tag: mouse strain

tag: developmental stage

tag: Sex

tag: compartment

value: soma

tag: number of_hemispheres

tag: number collected

tag: esitmated rna_concentration_(ng/ul)

tag: 28s to_18s_ratio

tag: rin


title: HTO_MG

city: Fukuoka

first: Minako

last: Ito

address: 3-1-1 Maidashi, Higashi-ku

institute: Kyushu University

description: Library name: HTO_MG

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: tsv files and mtx files

source_name: Brain

growth_protocol: 12 weeks old mice were bred under SPF conditions.

extract_protocol:
Brains were excised from mice transcardially perfused with PBS, and CD11b+ CD45+ Ly6G- CD206- microglia were collected by CytoFlex SRT(Beckman Coulter, Inc).
Single-cell suspensions were processed using a Chromium Controller (10x Genomics) to generate single-cell gel beads in GEMs. scRNA-seq libraries were prepared using the Chromium Next GEM Single Cell 3’ Gel Bead and Library Kit v3.1, following the manufacturer's instructions. Sequencing was performed using a NovaSeq 6000 at the Laboratory for Research Support of the Institute of Bioregulatory Medicine at Kyushu University.

treatment_protocol: Cx3cr1CreERT2(Litt) mice were treated with Tamoxifen for 4 weeks

value: Brain

tag: cell type

value: Microglia

tag: genotype

value: Cx3cr1CreERT2(Litt) Hetero

tag: treatment

value: Oil or TAM


title: GEX_MG

description: Library name: GEX_MG


title: LCK Project (GEX)

description: Library name: LCK_GEX

data_processing:
Resulting cDNA libraries were sequenced on NovaSeq 6000 (Illumina, NovaSeq Control Software 1.8.1) with the NovaSeq 6000 S4 Reagent Kits 300 cycles. The reads were then demultiplexed using Illumina BCL convert.
The generated reads were mapped using 10X Cell Ranger v7.1.0 to the Mus musculus reference genome provided by Ensembl (GRCm39, version 109).
The results were subsequently processed using Seurat v4.3.0 in R v4.2.1. Mitochondrial genes, ribosomal genes, and genes matching the regular expression Tr[ab][vdj] (primarily TCR V(D)J genes) were removed. Cells expressing fewer than 200 genes were also excluded. Sample demultiplexing was performed using the HTOdemux function from the Seurat package. Hashtag doublets and cells lacking a sufficient number of hashtag reads were filtered out.
The preprocessed dataset was normalized and scaled using the default method in the Seurat package. The top 750 variable genes were selected for dimensionality reduction via principal component analysis (PCA), followed by uniform manifold approximation and projection (UMAP) using 12 principal components. Clustering was performed with the Louvain algorithm implemented in Seurat. In a second, more stringent quality-control step, clusters consisting of dead or low-quality cells were removed. The final dataset contained 5,241 cells. Cell cycle effects were regressed out by specifying the parameter vars.to.regress = c("S.Score", "G2M.Score") during the ScaleData step in the Seurat workflow.
To quantify the expression of gene signatures, we used the AddModuleScore function implemented in the Seurat package. We computed module scores for curated gene sets: Hallmark Interferon Gamma Response (MM3878) and Biocarta TCR Pathway (MM1504) from the Mouse MSigDB collection, and GSE9650 Naïve vs Eff CD8 Tcell DN, originally defined in human genes, which we converted to murine orthologs using the Ensembl BioMart database (release December 2021). The conversion was performed using the getLDS function from the biomaRt R package (v2.60.1) to map human HGNC symbols to mouse MGI symbols.
Assembly: GRCm39
Supplementary files format and content: RDS file of finalized scRNA data in Seurat object generated by R, with CSP (HTO) and VDJ (TCR) information in meta data, used directly for manuscript figure generation.
Supplementary files format and content: Standard CSV file formatted according to 10X instructions for CSP mapping with additional column "multiplexed_sample" used to specify samples.

value: GEX


title: soma_null_4

value: brain


title: gc_wt_1

value: CPN

value: wild-type

tag: number of_supplmented_cd1_hemispheres

tag: tissue mass_(g)


title: soma_null_3

value: mixed


title: BCG-052

description: Library name: BCG-052_RNAseq

value: Breast tumor

tag: age

tag: race

value: White

tag: ethnicity

value: Hispanic or Latino

tag: er

value: ER-positive

tag: gender

value: Female

value: No

tag: clinical stage

value: IA

tag: adi (state_decile)

tag: nseas composite_score

tag: nseas safety_score

tag: nseas social_cohesion_score

tag: nseas aesthetic_quality_score

tag: eeds discrimination_score

tag: batch


title: soma_het_1

tag: tissue

tag: mouse strain

tag: cell type

tag: genotype

tag: developmental stage

tag: Sex

tag: compartment

value: soma

tag: number of_hemispheres

tag: number collected

tag: esitmated rna_concentration_(ng/ul)

tag: 28s to_18s_ratio

tag: rin


title: soma_null_1


title: soma_null_2


title: BCG-045

description: Library name: BCG-045_RNAseq

tag: age

tag: race

tag: ethnicity

tag: er

tag: gender

tag: treatment

tag: clinical stage

tag: adi (state_decile)

tag: nseas composite_score

tag: nseas safety_score


title: BSSR2083

description: Library name: BSSR2083_RNAseq

tag: tissue

value: IIA

tag: nseas social_cohesion_score

tag: nseas aesthetic_quality_score

tag: eeds discrimination_score

tag: batch


title: soma_het_2

tag: mouse strain

tag: cell type

tag: genotype

tag: developmental stage

tag: Sex

tag: compartment

tag: number of_hemispheres

tag: number collected

tag: esitmated rna_concentration_(ng/ul)

tag: 28s to_18s_ratio


title: soma_wt_3

tag: rin


title: BSSR3009

description: Library name: BSSR3009_RNAseq

tag: age

tag: race

tag: ethnicity

tag: er

tag: gender

tag: treatment

tag: clinical stage

tag: adi (state_decile)

tag: nseas composite_score

tag: nseas safety_score


title: TBCF5326

description: Library name: TBCF5326_RNAseq

tag: tissue

value: IIB

tag: nseas social_cohesion_score

tag: nseas aesthetic_quality_score

tag: eeds discrimination_score

tag: batch


title: soma_het_3

tag: mouse strain

tag: cell type

tag: genotype

tag: developmental stage

tag: Sex

tag: compartment

tag: number of_hemispheres

tag: number collected

tag: esitmated rna_concentration_(ng/ul)

tag: 28s to_18s_ratio


title: Spikevax (s.c.)

city: Helsinki

first: Bishwa

middle: Raj

last: Ghimire

address: Tukholmankatu 8

department: Institute for Molecular Medicine Finland

country: Finland

institute: University of Helsinki

description:
Library name: Spikevax (s.c.)
10x Genomics

data_processing:
Demultiplexing and barcoad processing was performed using the Cell Ranger software v6.1.1 (10x Genomics).
Assembly: mm10
Supplementary files format and content: Count data in sparse matrix format

source_name: Lymph node

extract_protocol:
Draining popliteal lymph nodes were mechanically cut into smaller pieces and enzymatically digested with Dispase (0.8 mg/ml), Collagenase P (0.2 mg/ml) and DNase I (0.1 mg/ml) in RPMI-1640 in +37 C for 20 min. Extracted cells were collected into FACS buffer (2% FCS and 0.25% NaN3 in PBS). Remaining tissue fragments were digested for a second (or third, if needed) 10 min digestion cycle with freshly added enzymes. Finally all supernatants were pooled, cells were counted and subjected for library preparation.
Library preparation was performed according to the manufacturer’s instructions (Chromium Next GEM Single Cell 3’ Dual Index v3.1, 10x Genomics). Briefly, cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was reverse transcribed to cDNA, containing an Illumina R1 primer sequence, Unique Molecular Identifier (UMI) and a cell barcode sequence. The pooled barcoded cDNA was cleaned up with Silane beads, amplified by PCR and the appropriated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Illumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and dual sample index sequences were added.

treatment_protocol: Mice were immunized (i.m. or s.c.) with COVID-19 vaccines or vehicle control (PBS)

value: Lymph node

value: CD45- Ter119- stromal cells

value: C57BL/6N, female

tag: treatment

value: s.c. Spikevax COVID-19 vaccine


title: gc_wt_2

value: brain

value: CPN

value: growth cone

tag: number of_supplmented_cd1_hemispheres

tag: tissue mass_(g)

tag: rin


title: BSSR1918

description: Library name: BSSR1918_RNAseq

tag: tissue

value: Breast tumor

tag: age

tag: race

tag: ethnicity

tag: er

tag: gender

tag: clinical stage

tag: adi (state_decile)

tag: nseas composite_score

tag: nseas safety_score

tag: nseas social_cohesion_score

tag: nseas aesthetic_quality_score


title: Nuvaxovid (i.m.)

description:
Library name: Nuvaxovid (i.m.)
10x Genomics

tag: cell type

tag: genotype

value: i.m. Nuvaxovid COVID-19 vaccine


title: RNA-Seq of Human: Wild type 34

city: Natal

first: Selma

middle: MB

last: Jeronimo

state: Rio Grande do Norte

address: 655 Av Passeio dos Girassois, Capim Macio

department: Tropical Medicine Institute (IMT-RN)

country: Brazil

institute: Federal University of Rio Grande do Norte (UFRN)

data_processing:
Illumina HiSeq 2000 (75 bp, paired-end), each sample with 8 experimental replicates
Aligmntent HISAT2 2.2.0 in default parameters
Files were compressed into BAM using Samtools 1.15
The counts assigned were accessed by FeatureCounts
Differential expression analysis: DESeq2 3.14 (Bioconductor)
Assembly: GRCh38
Supplementary files format and content: Gene counts matrix from FeatureCounts of all samples together

source_name: Whole blood

extract_protocol:
Whole blood was stored in Tempus Blood RNA Tube, and the RNA extraction was performed using a Tempus Spin RNA Isolation Kit.
RNA libraries were prepared according to Illumina HiSeq 2000 protocols.

tag: Sex

value: Male

tag: group

value: Wild type

tag: disease

value: Guillain-Barre syndrome


title: soma_wt_2

tag: tissue

tag: mouse strain

value: wild-type

tag: developmental stage

value: mixed

tag: compartment

tag: number of_hemispheres

tag: number collected

tag: esitmated rna_concentration_(ng/ul)

tag: 28s to_18s_ratio

tag: rin


title: soma_wt_1

value: soma


title: BSSR1944

description: Library name: BSSR1944_RNAseq

tag: age

tag: race

value: White

tag: ethnicity

value: Hispanic or Latino

tag: er

value: ER-positive

tag: gender

value: Female

tag: treatment

value: No

tag: clinical stage

tag: adi (state_decile)

tag: nseas composite_score

tag: nseas safety_score

tag: eeds discrimination_score

tag: batch


title: Comirnaty (i.m.)

description:
Library name: Comirnaty (i.m.)
10x Genomics

tag: tissue

value: Lymph node

tag: cell type

value: CD45- Ter119- stromal cells

tag: genotype

value: C57BL/6N, female

value: i.m. Comirnaty COVID-19 vaccine


title: Spikevax (i.m.)

description:
Library name: Spikevax (i.m.)
10x Genomics

value: i.m. Spikevax COVID-19 vaccine


title: BCG-400

description: Library name: BCG-400_RNAseq

value: Breast tumor

value: IIA

tag: nseas social_cohesion_score

tag: nseas aesthetic_quality_score


title: RNA-Seq of Human: Wild type 33

tag: Sex

tag: group

value: Wild type

tag: disease


title: RNA-Seq of Human: Wild type 11

value: Male

value: Guillain-Barre syndrome


title: Vehicle control

description:
Library name: Vehicle control
10x Genomics

value: i.m. PBS


title: RNA-Seq of Human: Wild type 20


title: RNA-Seq of Human: GBS Post-acute phase 39

value: Post-acute phase


title: RNA-Seq of Human: Wild type 10


title: BCG-379

description: Library name: BCG-379_RNAseq

tag: age

tag: race

value: White

tag: ethnicity

tag: er

value: IIIB


title: RNA-Seq of Human: Wild type 19


title: BCG-390

description: Library name: BCG-390_RNAseq

value: Hispanic or Latino

value: ER-positive

tag: gender

tag: treatment

tag: clinical stage

value: IA

tag: adi (state_decile)


title: RNA-Seq of Human: GBS Post-acute phase 38


title: Naive control

description:
Library name: Naive control
10x Genomics

value: Lymph node

value: no treatment


title: KP Tumor TNG260+aPD1 input

city: New York

first: Hideo

last: Watanabe

state: NY

address: One Gustave L. Levy Place

department: Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine

institute: Icahn School of Medicine at Mount Sinai

description: Library name: KP1_input

data_processing:
Both ChIP and input samples were adapter trimmed with trimmomatic and aligned by bowtie2 (-k 1) to the mm10 reference genome, filtered for ENCODE blacklist (ENCFF547MET) and repeat masker, histone K9 acetylated regions are called by MACS/2.1.0 (-f BAMPE) with merged replicate input samples as control.
Assembly: mm10
Supplementary files format and content: bed

source_name: Subcutaneous tumor

extract_protocol:
Approximately 20x106 cells or  50-100 mg of pulverized tumors were crosslinked with 1% formaldehyde in PBS for 10-12 minutes at room temperature, quenched with 5 mg/mL bovine serum albumin in PBS and then washed twice with cold PBS. Cell pellets were resuspended in 1mL lysis buffer [50 mM Tris-HCl, pH 8.1, 10 mM EDTA, 1% SDS, 1× protease inhibitor cocktail (Thermo Fisher Scientific)] and sonicated with a Covaris M220 sonicator for 25 minutes and 22 minutes for tumors and cell lines, respectively, to obtain chromatin fragment lengths of 100 to 1,000 bp. Fragments were evaluated by Bioanalyzer DNA High Sensitivity kit (Agilent). Fragmented chromatin was diluted in IP buffer (20 mM Tris-HCl pH 8.1, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100) and incubated overnight at 4°C with Protein G magnetic beads (Dynabeads: Life Technologies) that had been pre-incubated with anti-H3K9ac (Abcam, ab4441) antibody. Immunoprecipitants were washed six times with wash buffer (50 mM HEPES pH 7.6, 0.5 M LiCl, 1 mM EDTA, 0.7% Na deoxycholate, 1% NP-40) and twice with TE buffer. Immunoprecipitated and IP input was treated with RNase A and Proteinase K on the beads, recovered in 1% SDS and 0.1 M NaHCO3 over a period of 6 h at 65 °C, and purified with DNA clean and concentrator-25 (Zymo Research).
Up to 10 ng of DNA was used for the library construction using NEBNext Ultra II DNA Library Prep Kit (NEB, E7645). Sequencing was performed on NovaSeq (Illumina) for 150 nucleotides from paired ends according to the manufacturer's instructions.

value: Subcutaneous tumor

tag: cell line

value: Lung cancer

tag: chip antibodies

value: input


title: RNA-Seq of Human: GBS Post-acute phase 28


title: BCG-310

description: Library name: BCG-310_RNAseq

tag: tissue

value: Breast tumor

value: Female

value: No

tag: nseas composite_score

tag: nseas safety_score

tag: eeds discrimination_score

tag: batch


title: KP Tumor TNG260+aPD1 H3K9ac ChIP

description: Library name: KP1_ab4441

tag: cell type

tag: genotype

value: H3K9ac (Abcam, #ab4441)


title: RNA-Seq of Human: GBS Post-acute phase 30

tag: Sex

tag: group

tag: disease

value: Guillain-Barre syndrome


title: RNA-Seq of Human: GBS Post-acute phase 29

value: Male


title: RNA-Seq of Human: GBS Post-acute phase 27

value: Post-acute phase


title: RNA-Seq of Human: GBS Post-acute phase 16


title: RNA-Seq of Human: GBS Post-acute phase 09


title: BCG-228

description: Library name: BCG-228_RNAseq

tag: age

tag: race

value: White

tag: ethnicity

tag: er

tag: nseas social_cohesion_score

tag: nseas aesthetic_quality_score


title: BCG-254

description: Library name: BCG-254_RNAseq

tag: gender

tag: treatment

tag: clinical stage

value: IIB

tag: adi (state_decile)


title: Vaxzevria (i.m.)

description:
Library name: Vaxzevria (i.m.)
10x Genomics

tag: tissue

value: CD45- Ter119- stromal cells

value: C57BL/6N, female

value: i.m. Vaxzevria COVID-19 vaccine


title: RNA-Seq of Human: GBS Post-acute phase 08


title: KP Tumor Control H3K9ac ChIP

description: Library name: KP11_ab4441

tag: cell line

value: DMSO

tag: chip antibodies


title: RNA-Seq of Human: GBS Post-acute phase 07


title: BCG-209

description: Library name: BCG-209_RNAseq

value: Hispanic or Latino

value: ER-positive

tag: nseas composite_score

tag: nseas safety_score

tag: eeds discrimination_score

tag: batch


title: RNA-Seq of Human: GBS Acute phase 26

tag: Sex

tag: group

value: Acute phase

tag: disease


title: KL Tumor TNG260+aPD1 input

description: Library name: KL1_input

value: Subcutaneous tumor

tag: cell type

value: Lung cancer

tag: genotype

value: input


title: RNA-Seq of Human: GBS Acute phase 25

value: Female


title: BCG-164

description: Library name: BCG-164_RNAseq

value: Breast tumor

tag: age

tag: race

tag: ethnicity

tag: er

value: No

value: IIA

tag: nseas social_cohesion_score

tag: nseas aesthetic_quality_score


title: RNA-Seq of Human: GBS Acute phase 04

value: Guillain-Barre syndrome


title: RNA-Seq of Human: GBS Acute phase 13

value: Male


title: RNA-Seq of Human: GBS Acute phase 02


title: BCG-155

description: Library name: BCG-155_RNAseq

tag: tissue

value: White

tag: gender

tag: treatment

tag: clinical stage

value: IIB

tag: adi (state_decile)


title: RNA-Seq of Human: GBS Acute phase 01


title: KL Tumor Control input

description: Library name: KL11_input

tag: cell line

tag: chip antibodies


title: KL Tumor Control H3K9ac ChIP

description: Library name: KL11_ab4441

value: H3K9ac (Abcam, #ab4441)


title: ki6 CD8

city: La Jolla

first: Gerald

middle: Patrick

last: Morris

address: 9500 Gilman Drive

institute: University of California San Diego

description:
Library name: 14
PE300bp

data_processing:
MiXCR 4.1.1
command line-- analyze_takara-mouse-tcr-full-length_--rna_data.R1.fastq_data.R2.fastq_result
Assembly: MiXCR 4.1.1
Supplementary files format and content: MiXCR 4.1.1
Supplementary files format and content: TCRa and TCRb clonotypes- V(D)J use, CDR3 sequence, clonotype frequencies
Library strategy: TCR-Seq

extract_protocol:
RNEasy Mini
TAKARA SMARTer mouse TCRa/b

value: spleen

value: CD8 T cell

tag: batch


title: KP Tumor Control input

description: Library name: KP11_input

value: DMSO


title: BCG-047

description: Library name: BCG-047_RNAseq

value: Hispanic or Latino

value: ER-positive

tag: nseas composite_score

tag: nseas safety_score

tag: eeds discrimination_score


title: KP TNG260 Rep2 input

description: Library name: KPTNG2_input

value: KP

tag: cell type

tag: genotype


title: ki5 CD8

description:
Library name: 12
PE300bp


title: BCG-036

description: Library name: BCG-036_RNAseq

tag: age

tag: race

tag: ethnicity

value: IA


title: ki5 CD4

description:
Library name: 11
PE300bp

value: CD4 T cell


title: ki4b CD8

description:
Library name: 10
PE300bp


title: KP TNG260 Rep2 H3K9ac ChIP

description: Library name: KPTNG2_ab4441

value: Lung cancer


title: ki4b CD4

description:
Library name: 9
PE300bp


title: BCG-026

description: Library name: BCG-026_RNAseq

value: Breast tumor

tag: er

value: Female

tag: nseas social_cohesion_score

tag: nseas aesthetic_quality_score


title: KP TNG260 Rep1 input

description: Library name: KPTNG1_input

tag: tissue

tag: treatment

value: input


title: ki4a CD8

description:
Library name: 8
PE300bp


title: wt3 CD8

description:
Library name: 6
PE300bp

value: wt


title: BCG-023

description: Library name: BCG-023_RNAseq

tag: gender

value: No

tag: clinical stage

value: IIA

tag: adi (state_decile)


title: KP TNG260 Rep1 H3K9ac ChIP

description: Library name: KPTNG1_ab4441

tag: cell line

tag: chip antibodies


title: KL Tumor TNG260+aPD1 H3K9ac ChIP

description: Library name: KL1_ab4441

value: Subcutaneous tumor


title: BCG-006

description: Library name: BCG-006_RNAseq

value: White

tag: nseas composite_score

tag: nseas safety_score

tag: batch


title: BCG-148

description: Library name: BCG-148_RNAseq

tag: eeds discrimination_score


title: wt2 CD8

description:
Library name: 4
PE300bp

value: spleen

tag: cell type

tag: genotype


title: KP Control Rep2 input

description: Library name: KPCTL2_input


title: wt2 CD4

description:
Library name: 3
PE300bp


title: ki6 CD4

description:
Library name: 13
PE300bp


title: wt1 CD8

description:
Library name: 2
PE300bp

value: CD8 T cell


title: KP Control Rep2 H3K9ac ChIP

description: Library name: KPCTL2_ab4441

value: DMSO

value: H3K9ac (Abcam, #ab4441)


title: BSSR1390

description: Library name: BSSR1390_RNAseq

tag: age

tag: race

tag: ethnicity

value: Hispanic or Latino

value: ER-positive

value: IIB


title: BSSR1378

description: Library name: BSSR1378_RNAseq

tag: er

tag: nseas social_cohesion_score

tag: nseas aesthetic_quality_score


title: wt1 CD4

description:
Library name: 1
PE300bp

tag: tissue

value: CD4 T cell


title: ki4a CD4

description:
Library name: 7
PE300bp


title: B409_WGS_rep2

city: Wuhan

first: Junlin

last: Chen

address: No.1, Shizishan Street

institute: Huazhong Agricultural University

description: Library name: Sample109

data_processing:
RNA-seq Reads were aligned to brassica napus reference genome (Brassica napus.ZS11.v0.genome.fa) using hisat2.
ATAC-seq Reads were aligned to brassica napus reference genome (Brassica napus.ZS11.v0.genome.fa) using bowtie2.
Bisulfite sequencing Reads were aligned to brassica napus reference genome (Brassica napus.ZS11.v0.genome.fa) using BatMeth2.
Whole-Genome sequencing Reads were aligned to brassica napus reference genome (Brassica napus.ZS11.v0.genome.fa) using bwa.
FeatureCounts was used to count the number of paired mapping reads for each gene.
Assembly: Brassica_napus.ZS11.v0.genome.fa
Supplementary files format and content: bw files for each Sample
Library strategy: WGS

organism: Brassica napus

growth_protocol: growth in Hoagland nutrient solution

extract_protocol:
Toal RNA was extracted by using Eastep® Super Total RNA Extraction Kit (Promega) from cotyledon with three replications. For ATAC-seq, the extracted nuclei were incubated with Tn5 transposase and tagmentation buffer following the manufacturer’s instructions (Vazyme, TD501-01).
mRNAs with polyA tails were enriched by Oligo(dT) magnetic beads, and mRNAs were obtained by removing ribosomal RNAs from the total RNAs. For ATAC-seq, DNA was purified using the MinElute PCR Purification Kit (QIAGEN, 28004). Genomic DNA for was extracted using the DNeasy Plant Mini Kit (QIAGEN, 69104). Bisulfite-treated DNA libraries were prepared with the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England BioLabs, E7645) following the manufacturer’s instructions.

treatment_protocol: under 0 mM/L NaCl or 220 mM/L NaCl condition.

tag: treatment

value: growth in Hoagland nutrient solution with 0 mM/L NaCl condition.


title: HZ62_WGBS

description: Library name: Sample110

data_processing:
RNA-seq Reads were aligned to brassica napus reference genome (Brassica napus.ZS11.v0.genome.fa) using hisat2.
ATAC-seq Reads were aligned to brassica napus reference genome (Brassica napus.ZS11.v0.genome.fa) using bowtie2.
Bisulfite sequencing Reads were aligned to brassica napus reference genome (Brassica napus.ZS11.v0.genome.fa) using BatMeth2.
Whole-Genome sequencing Reads were aligned to brassica napus reference genome (Brassica napus.ZS11.v0.genome.fa) using bwa.
FeatureCounts was used to count the number of paired mapping reads for each gene.
Assembly: Brassica_napus.ZS11.v0.genome.fa
Supplementary files format and content: bw files for each Sample


title: B409_WGS_rep1

description: Library name: Sample108


title: KP Control Rep1 input

description: Library name: KPCTL1_input

value: KP

value: Lung cancer


title: 2063A_WGS_rep2

description: Library name: Sample107


title: BSSR1297

description: Library name: BSSR1297_RNAseq

value: Breast tumor

tag: gender

value: Female

tag: clinical stage

tag: adi (state_decile)


title: 2063A_WGS_rep1

description: Library name: Sample106


title: BSSR1186

description: Library name: BSSR1186_RNAseq

value: No

value: IA

tag: nseas composite_score


title: HZ62_48h_RNA_rep3

description: Library name: Sample105

value: growth in Hoagland nutrient solution with 220 mM/L NaCl condition for 48 h.


title: KL TNG260 Rep2 input

description: Library name: KLTNG2_input

tag: cell line

value: KL

tag: chip antibodies

value: input


title: HZ62_48h_RNA_rep2

description: Library name: Sample104


title: BSSR1153

description: Library name: BSSR1153_RNAseq

value: White

tag: nseas safety_score

tag: eeds discrimination_score

tag: batch


title: KL TNG260 Rep2 H3K9ac ChIP

description: Library name: KLTNG2_ab4441

tag: cell type

tag: genotype


title: wt3 CD4

description:
Library name: 5
PE300bp

value: spleen

value: wt


title: BSSR1131

description: Library name: BSSR1131_RNAseq

tag: age

tag: race

tag: ethnicity

value: Hispanic or Latino

value: IIA


title: KL TNG260 Rep1 input

description: Library name: KLTNG1_input


title: HZ62_24h_RNA_rep3

description: Library name: Sample102

value: growth in Hoagland nutrient solution with 220 mM/L NaCl condition for 24 h.


title: HZ62_24h_RNA_rep2

description: Library name: Sample101


title: BSSR1123

description: Library name: BSSR1123_RNAseq

tag: er

value: ER-positive

tag: nseas social_cohesion_score

tag: nseas aesthetic_quality_score


title: HZ62_12h_RNA_rep3

description: Library name: Sample99

tag: tissue

tag: treatment

value: growth in Hoagland nutrient solution with 220 mM/L NaCl condition for 12 h.


title: KL TNG260 Rep1 H3K9ac ChIP

description: Library name: KLTNG1_ab4441

value: H3K9ac (Abcam, #ab4441)


title: BSSR1118

description: Library name: BSSR1118_RNAseq

tag: gender

tag: clinical stage

tag: adi (state_decile)


title: HZ62_24h_RNA_rep1

description: Library name: Sample100


title: KL Control Rep2 input

description: Library name: KLCTL2_input

tag: cell line

value: Lung cancer

value: DMSO

tag: chip antibodies


title: KP Control Rep1 H3K9ac ChIP

description: Library name: KPCTL1_ab4441

value: KP


title: HZ62_12h_RNA_rep2

description: Library name: Sample98


title: BSSR1030

description: Library name: BSSR1030_RNAseq

value: Breast tumor

value: Female

value: No

value: IIB

tag: nseas composite_score

tag: nseas safety_score

tag: eeds discrimination_score


title: HZ62_6h_RNA_rep3

description: Library name: Sample96

tag: genotype

value: growth in Hoagland nutrient solution with 220 mM/L NaCl condition for 6 h.


title: KL Control Rep2 H3K9ac ChIP

description: Library name: KLCTL2_ab4441

value: KL

tag: cell type


title: HZ62_12h_RNA_rep1

description: Library name: Sample97


title: BSSR1017

description: Library name: BSSR1017_RNAseq

tag: age

tag: race

value: White

tag: batch


title: KL Control Rep1 input

description: Library name: KLCTL1_input

value: input


title: HZ62_3h_RNA_rep2

description: Library name: Sample92

value: growth in Hoagland nutrient solution with 220 mM/L NaCl condition for 3 h.


title: HZ62_3h_RNA_rep3

description: Library name: Sample93


title: BSSR0997

description: Library name: BSSR0997_RNAseq

tag: ethnicity

value: Hispanic or Latino

tag: er

value: IIA

tag: nseas social_cohesion_score


title: KL Control Rep1 H3K9ac ChIP

description: Library name: KLCTL1_ab4441

tag: tissue

tag: treatment


title: HZ62_48h_RNA_rep1

description: Library name: Sample103

value: growth in Hoagland nutrient solution with 220 mM/L NaCl condition for 48 h.


title: HZ62_6h_RNA_rep1

description: Library name: Sample94


title: HZ62_6h_RNA_rep2

description: Library name: Sample95