title: AstrocyteRiboTag_male_2h_ischemia_6h_reperfusion_ipsi_rep3

city: Baltimore

first: Prajwal

last: Ciryam

state: MD

address: 670 W. Baltimore St.

institute: University of Maryland School of Medicine

description: Library name: Astrocyte Specific Ribotag RNA mouse ischemia/reperfusion ipsilateral 3

data_processing:
Raw R1 and R2 fastq files were trimmed to remove adapter sequences and low-quality reads using the Trimmomatic software v0.33 under the following parameters: simple clip threshold (7), seed mismatches (2), palindrome threshold (40), minimum sequence length (3), and trailing quality (20). Trimmed sequences were followed by quality control evaluation using FastQC v0.12.0. Trimmed sequences were aligned using STAR v2.7.5a [65] to the Mus musculus mm39 primary assembly. These were quantified at the gene level using the STAR geneCounts function to obtain reverse/forward strand-specific counts. Analysis of unmapped, multi-mapped, and ambiguously mapped reads was performed using blastn [66] with default settings.
Assembly: mm39
Supplementary files format and content: Gene counts from STAR geneCounts showing reverse/forward strand-specific counts

extract_protocol:
MCA territories were dissected, then homogenized by hemisphere in a 7 mL glass Dounce homogenizer (12–15 strokes) in 1× HBSS containing Ca2+/Mg2+ (Gibco, Waltham, MA, USA) and supplemented with HEPES. Homogenates were centrifuged at 2000× g for 10 min at 4 °C. Pellets were resuspended in 18% dextran (from Leuconostoc spp., Mr~70,000, MilliporeSigma, Burlington, MA, USA), then centrifuged at 10,000× g for 15 min at 4 °C. Myelin-cleared pellets were resuspended in 1% bovine serum albumin, then filtered through a 20 μm nylon mesh. Microvessels caught in the mesh were retrieved and centrifuged at 2000× g for 10 min. For RiboTag immunoprecipitation, solutions were supplemented with 100 µg/mL cycloheximide and 200 U/mL RNAsin. For RiboTag IP, all steps were performed in 4 °C and RNase-free (RNaseZAP, ThermoFisher, Waltham, MA, USA) conditions. Microvessels were lysed in freshly prepared lysis buffer (150 mM KCl, 20 mM HEPES [pH 7.4]), 5 mM MgCl2, 1 mM DTT, 1% NP-40, 100 µg/mL cycloheximide, and 30 mM DHPC [1,2-dicaproyl-sn-glycero-3-phosphocholine, 07:0]) supplemented with 200 U/mL RNAsin (ProMega, Madison, WI, USA) and cOmplete protease inhibitor (MilliporeSigma). Following homogenization using a handheld pestle motor mixer, lysates were centrifuged at 18,000× g at 4 °C for 10 min. IP was performed by incubating the soluble fraction with magnetic bead-conjugated anti-GFP antibody (#67090, Cell Signaling Technology, Danvers, MA, USA) or magnetic bead-conjugated control IgG (#5873, Cell Signaling Technology) overnight (~16 h) with end-over-end rotation. Following magnetic separation from the supernatant (DynaMag-2, ThermoFisher), beads were washed three times in a high-salt (300 mM KCl) lysis buffer supplemented with 200 U/mL RNAsin. Unpurified RNA was collected from the magnetic beads using the TriZOL reagent (Invitrogen, Waltham, MA, USA) according to the manufacturer’s instructions.
Total mRNA (in ultrapure water) following RiboTag IP was quantified using the Bioanalyzer 2100 (Agilent, Santa Clara, CA, USA). Strand-specific RNA sequencing was performed by Maryland Genomics in NovaSeq S4 flow cells (NovaSeq6000, Illumina, San Diego, CA, USA) with 100 bp paired-end reads, with 67 ± 18 million (mean ± SD) reads per sample.

value: brain

tag: tissue type

value: ipsilateral tissue

tag: Sex

value: male

value: Astrocyte-specific RiboTag mice (FVB-Tg(Aldh1l1-EGFP/Rpl10a)JD133Htz/J, #030248, Jackson Laboratory, Bar Harbor, ME, USA)

value: Middle Cerebral Artery Occlusion:Ischemia 2h, Reperfusion 6h


title: AstrocyteRiboTag_male_2h_ischemia_6h_reperfusion_ipsi_rep2

status: Public on Jan 27 2025

type: SRA

country: USA

description: Library name: Astrocyte Specific Ribotag RNA mouse ischemia/reperfusion ipsilateral 2

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

source_name: brain

tag: tissue

tag: genotype

tag: treatment


title: PBMCs, Severe patient 4 (2nd week of infection) BCR

city: Seoul

first: Hang-Rae

last: Kim

address: 103 Daehak-ro, Jongno-gu

department: Anatomy and Cell Biology

country: South Korea

institute: Seoul National University College of Medicine

description:
S4_2_B
BCR_seq_data.xlsx

data_processing:
Library strategy: BCR-seq
Basecalls performed using bcl2fastq v2.20.0.422
scRNA reads were filtering and align to GRCh38 genome using CellRanger 4.0
Gene count was performed using CellRanger and loaded into single cell objects in Seurat package (v4.0)
Filtering out qualified cells based on the plot displaying the average gene expression versus -log10 p-value or versus mitochondrial gene counts.
Filtering out cell types by annotations based on DEGs, CITE-seq and BCR/TCR-seq.
Inegration was perforemd using Seurat package with the RPCA method.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text, xlsx or csv files include cell infromation or normalized gene counts

molecule: polyA RNA

organism: Homo sapiens

source_name: Peripheral blood mononuclear cells (PBMCs)

extract_protocol:
PBMCs were purified from heparinized peripheral whole blood using a Ficoll-Histopaque gradient.
The user guide of Chromium Next GEM Single Cell V(D)J Reagent Kits v1.1 (10× Genomics, Pleasanton, CA, USA) was used to prepare the cDNA libraries for single-cell RNA sequencing (scRNA-seq) assay. To check the viability of the sorted cells, a Countess™ II FL Automated Cell Counter (Thermo Fisher Scientific) was used with trypan blue. About 10,000 cells for each sample were determined as target cells, and the master mix and single-cell suspensions were dispensed into a Chromium Next GEM G Chip (10× Genomics). For each sample, 5 L of supernatant cDNA was prepared, amplification master mix, SI-PCR primer, and index kit were added, and sample index PCR was performed in a thermal cycler. The clean-up process was performed using 1.2× SPRIselect reagent, and elution was performed with buffer EB.
Single cell RNAseq, TCR/BCR sequencing, CITEseq

tag: cell type

tag: individual

value: Severe patient 4

tag: infection

tag: severity

value: Severe

tag: time

value: 2nd week of infection


title: mRNA, vrn2prt6_R3

city: Birmingham

first: Rory

last: Osborne

address: Edgbaston

country: United Kingdom

institute: University of Birmingham

data_processing:
Reads were trimmed and aligned to TAIR10 using bowtie. Differential gene expression analysis was performed using DEseq13
Supplementary files format and content: Processed data files contain read counts (mRNA sequencing) and called peaks (ChIP)

organism: Arabidopsis thaliana

source_name: Whole seedling

extract_protocol:
RNA was isolated using Qiagen Rneasy extraction kit according to manufacturing instructions.
Illumina TruSeq mRNA kit

value: Whole seedling


title: mRNA, pif4_F_R2

data_processing:
Reads were trimmed and aligned to TAIR10 using bowtie. Differential gene expression analysis was performed using DEseq2
Supplementary files format and content: Processed data files contain read counts (mRNA sequencing)

extract_protocol: RNA was isolated using Qiagen Rneasy extraction kit according to manufacturing instructions.

tag: cell line

value: Whole rosette


title: HsGC_WQS_1

city: Stockholm

first: Anastasios

middle: Erik

last: Damdimopoulos

state: Huddinge

address: Hälsovägen 7c

department: Department of Biosciences and Nutrition

country: Sweden

institute: Karolinska Institute

data_processing:
The fastq files were demultiplexed using umi_tools (v1.0.0). The umi_tools whitelist function was used to whitelist the indexes. Then the umi_tools extract function was used to extract and mark the fastq sequence names with the UMI and indexes which were then used to demultiplex the data
STAR 2.7.9a was used to map the fastq files aginast human (hg38/GRCh38) and mouse (mm10/GRCm38) refernce genomes obtained from Ensembl
The aligned bam files were deduplicated with the umi_tools dedup function based on their UMI sequence
The deduplicated mapped reads were counted using featureCounts v1.5.1 with ensembl gene annotations, Homo_sapiens.GRCh38.101.gtf and Mus_musculus.GRCm38.86.gtf
Supplementary files format and content: Tab separated text files with raw gene counts

source_name: ovary

extract_protocol:
RNA was harvested using RNeasy micro and mini plus kit (Qiagen). 10 ng of total RNA was used for the construction of sequencing libraries.
Libraries was prepared using QIAseq UPX 3’Transcriptome kit (Qiagen) according to manufacturer's protocol

value: ovary

value: Human primary granulosa cells, patient 1

value: WT

value: WQS-mixture 1x


title: AstrocyteRiboTag_male_2h_ischemia_6h_reperfusion_ipsi_rep1

description: Library name: Astrocyte Specific Ribotag RNA mouse ischemia/reperfusion ipsilateral 1


title: mRNA, vrn2prt6_R2

data_processing:
Reads were trimmed and aligned to TAIR10 using bowtie. Differential gene expression analysis was performed using DEseq12
Supplementary files format and content: Processed data files contain read counts (mRNA sequencing) and called peaks (ChIP)


title: HsGC_DMSO_3

value: Human primary granulosa cells, patient 3

value: DMSO


title: mRNA, vrn2pif4_F_R2


title: HsGC_DMSO_2

value: Human primary granulosa cells, patient 2


title: AstrocyteRiboTag_male_2h_ischemia_6h_reperfusion_contra_rep3

description: Library name: Astrocyte Specific Ribotag RNA mouse ischemia/reperfusion contralateral 3

value: brain

value: contralateral tissue


title: mRNA, vrn2pif4_F_R1


title: mRNA, vrn2prt6_R1

data_processing:
Reads were trimmed and aligned to TAIR10 using bowtie. Differential gene expression analysis was performed using DEseq11
Supplementary files format and content: Processed data files contain read counts (mRNA sequencing) and called peaks (ChIP)


title: AstrocyteRiboTag_male_2h_ischemia_6h_reperfusion_contra_rep2

description: Library name: Astrocyte Specific Ribotag RNA mouse ischemia/reperfusion contralateral 2

value: male


title: PBMCs, Severe patient 4 (2nd week of infection) 5' Expression

description:
S4_2_Exp
pbmc_meta.data.txt
pbmc_normalized_count_integrated.txt
T_cell_normalized_count_integrated.txt
T_cell_meta.data.txt
B_cell_normalized_count_integrated.txt
B_cell_meta.data.txt
Monocyte_normalized_count_integrated.txt
Monocyte_meta.data.txt
NK_cell_normalized_count_integrated.txt
NK_cell_meta.data.txt

data_processing:
Library strategy: CITEseq
Basecalls performed using bcl2fastq v2.20.0.422
scRNA reads were filtering and align to GRCh38 genome using CellRanger 4.0
Gene count was performed using CellRanger and loaded into single cell objects in Seurat package (v4.0)
Filtering out qualified cells based on the plot displaying the average gene expression versus -log10 p-value or versus mitochondrial gene counts.
Filtering out cell types by annotations based on DEGs, CITE-seq and BCR/TCR-seq.
Inegration was perforemd using Seurat package with the RPCA method.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text, xlsx or csv files include cell infromation or normalized gene counts

value: Peripheral blood mononuclear cells (PBMCs)


title: AstrocyteRiboTag_male_2h_ischemia_6h_reperfusion_contra_rep1

description: Library name: Astrocyte Specific Ribotag RNA mouse ischemia/reperfusion contralateral 1

value: Astrocyte-specific RiboTag mice (FVB-Tg(Aldh1l1-EGFP/Rpl10a)JD133Htz/J, #030248, Jackson Laboratory, Bar Harbor, ME, USA)

value: Middle Cerebral Artery Occlusion:Ischemia 2h, Reperfusion 6h


title: mRNA, prt6_R3

data_processing:
Reads were trimmed and aligned to TAIR10 using bowtie. Differential gene expression analysis was performed using DEseq10
Supplementary files format and content: Processed data files contain read counts (mRNA sequencing) and called peaks (ChIP)


title: PBMCs, Severe patient 4 (1st week of infection) Feature Barcode

description:
S4_1_FB
Feature_barcode_CITE-seq.csv

library_source: genomic

molecule: protein

value: Severe patient 4

value: Severe

value: 1st week of infection


title: COV434_MHHP100_3

value: Granulosa cancer cell line COV434

value: MEHHP 100x


title: PBMCs, Severe patient 4 (1st week of infection) BCR

description:
S4_1_B
BCR_seq_data.xlsx


title: HsGC_WQS_2

value: ovary


title: mRNA, prt6_R2

data_processing:
Reads were trimmed and aligned to TAIR10 using bowtie. Differential gene expression analysis was performed using DEseq9
Supplementary files format and content: Processed data files contain read counts (mRNA sequencing) and called peaks (ChIP)

value: Whole seedling


title: BMDMs,PAC-CM1-KD,rep3

city: Shanghai

first: Ruiyan

last: Wang

address: 650 New Songjiang Road

department: Department of Gastroenterology

country: China

institute: Shanghai General Hospital

description: Library name: PAC-CM-KD3

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina NovaSeq 6000 platform and 150 bp paired-end reads were generated using NovaSeq control software (v1.6.0), RTA (v3.4.4), and bcl2fastq2 (v2.20).
The raw data was handled by Skewer v0.2.2 (https://sourceforge.net/projects/skewer/files/?source=navbar) and data quality was checked by FastQC v0.11.2 (http:// www.bioinformatics.babraham.ac.uk/projects/fastqc/).
The read length was 2×150 bp. Clean reads were aligned to reference genome from ensmble using STAR (https://github.com/alexdobin/STAR), with one mismatch allowed.
StringTie (v1.3.1c) was used to generate gene expression data and differential gene expression was analysed by DESeq2 (v1.16.1) (https://bioconductor.org/packages/release/bioc/html/DESeq2.html) .
Then DEGs were chosen for function and signaling pathway enrichment analysis using TopGO (https://www.bioconductor.org/packages/release/bioc/html/topGO.html) and KEGG database (https://www.genome.jp/kegg/pathway.html). The significantly enriched pathways were determined when P < 0.05 .
Assembly: GRCm38
Supplementary files format and content: table of gene counts with gene symbol in format of tab-separated txt

source_name: BMDMs

growth_protocol: BMDMs were cultured in high-glucose DMEM containing 10% fetal bovine serum,1% Penicillin-Streptomycin and 20 ng/mL recombinant mouse M-CSF.

extract_protocol:
Total RNA of BMDMs was extracted using Trizol reagent.1.0 ug of  total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared using the VVAHTS® Universal V8 RNA-seq Library Prep Kit for Illumina (NR605-0, Vazyme), followed sequencing using the Illumina NovaSeq 6000 platform with the 150 paired-end sequencing strategy.Enrichment of mRNA, library construction, sequencing and data analysis were performed by Shanghai Xu Ran Biotechnology Co., Ltd (http://www.xurangene.com）.

treatment_protocol: PAC-CM was added to BMDMs on day 5, with or without 400μM KD treatment

value: BMDMs

value: stimulated by injured pancreatic acinar cell conditioned media (PAC-CM) treated with kinsenoside


title: COV434_MHHP100_2

value: WT


title: BMDMs,PAC-CM1-KD,rep2

description: Library name: PAC-CM-KD2


title: PBMCs, Severe patient 4 (1st week of infection) TCR

description:
S4_1_T
TCR_seq_data.xlsx

data_processing:
Library strategy: TCR-seq
Basecalls performed using bcl2fastq v2.20.0.422
scRNA reads were filtering and align to GRCh38 genome using CellRanger 4.0
Gene count was performed using CellRanger and loaded into single cell objects in Seurat package (v4.0)
Filtering out qualified cells based on the plot displaying the average gene expression versus -log10 p-value or versus mitochondrial gene counts.
Filtering out cell types by annotations based on DEGs, CITE-seq and BCR/TCR-seq.
Inegration was perforemd using Seurat package with the RPCA method.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text, xlsx or csv files include cell infromation or normalized gene counts


title: PBMCs, Severe patient 4 (1st week of infection) 5' Expression

description:
S4_1_Exp
pbmc_meta.data.txt
pbmc_normalized_count_integrated.txt
T_cell_normalized_count_integrated.txt
T_cell_meta.data.txt
B_cell_normalized_count_integrated.txt
B_cell_meta.data.txt
Monocyte_normalized_count_integrated.txt
Monocyte_meta.data.txt
NK_cell_normalized_count_integrated.txt
NK_cell_meta.data.txt


title: BMDMs,PAC-CM1-KD,rep1

description: Library name: PAC-CM-KD1


title: mRNA, vrn2_R3

data_processing:
Reads were trimmed and aligned to TAIR10 using bowtie. Differential gene expression analysis was performed using DEseq7
Supplementary files format and content: Processed data files contain read counts (mRNA sequencing) and called peaks (ChIP)


title: COV434_MHHP100_1


title: PBMCs, Severe patient 4 (2nd week of infection) TCR

description:
S4_2_T
TCR_seq_data.xlsx

value: 2nd week of infection


title: PBMCs, Severe patient 3 (4th week of infection) Feature Barcode

description:
S3_4_FB
Feature_barcode_CITE-seq.csv

value: Severe patient 3

value: 4th week of infection


title: PBMCs, Severe patient 3 (4th week of infection) BCR

description:
S3_4_B
BCR_seq_data.xlsx


title: BMDMs,PAC-CM1,rep3

description: Library name: PAC-CM3

value: stimulated by injured pancreatic acinar cell conditioned media (PAC-CM) treated without kinsenoside


title: mRNA, vrn2_R2

data_processing:
Reads were trimmed and aligned to TAIR10 using bowtie. Differential gene expression analysis was performed using DEseq6
Supplementary files format and content: Processed data files contain read counts (mRNA sequencing) and called peaks (ChIP)


title: HsGC_DMSO_1

value: Human primary granulosa cells, patient 1

value: DMSO


title: mRNA, Col0_R3

data_processing:
Reads were trimmed and aligned to TAIR10 using bowtie. Differential gene expression analysis was performed using DEseq4
Supplementary files format and content: Processed data files contain read counts (mRNA sequencing) and called peaks (ChIP)


title: COV434_MHHP_3

value: MEHHP 1x


title: COV434_MHHP_2


title: BMDMs,PAC-CM1,rep1

description: Library name: PAC-CM1


title: COV434_MHHP_1


title: COV434_EQUI100_3

value: Equimolar mixture 100x


title: PBMCs, Severe patient 3 (4th week of infection) TCR

description:
S3_4_T
TCR_seq_data.xlsx

value: Peripheral blood mononuclear cells (PBMCs)

value: Severe


title: mRNA, vrn2_R1

data_processing:
Reads were trimmed and aligned to TAIR10 using bowtie. Differential gene expression analysis was performed using DEseq5
Supplementary files format and content: Processed data files contain read counts (mRNA sequencing) and called peaks (ChIP)


title: BMDMs,PAC-CM1,rep2

description: Library name: PAC-CM2


title: NIH3T3-U6-10-R2

city: guangzhou

first: chengguo

last: yao

address: No. 74 zhongshan 2rd road

department: school of medicine

institute: sysu

description:
Library name: sample 30
10 uM U6 AMO treated,repeat 2

data_processing:
Bioinformatics analysis were subsequently carried out using our published pipeline QuantifyPoly(A) (https://pubmed.ncbi.nlm.nih.gov/34255024/)
Assembly: GRCm39 - mm39
Supplementary files format and content: bw files

growth_protocol: NIH3T3 cells were grown in commercial medium (CM-0171， Procell)

extract_protocol:
total RNAs were harvested at 12 hour time points upon U1/U6/U4/U2 AMOs transfection using TRIZOL reagents.
mRNA 3'-seq library was constructed using lexogen kit (REV. 016.24).

treatment_protocol: U1/U2/U4/U6 AMOs were transfected into cells by electroporation

value: cancer stem cell

value: 10 uM U6 AMO treated

tag: batch


title: COV434_EQUI100_2

value: ovary

value: Granulosa cancer cell line COV434


title: PBMCs, Severe patient 3 (2nd week of infection) Feature Barcode

description:
S3_2_FB
Feature_barcode_CITE-seq.csv


title: mRNA, Col0_R1

data_processing:
Reads were trimmed and aligned to TAIR10 using bowtie. Differential gene expression analysis was performed using DEseq2
Supplementary files format and content: Processed data files contain read counts (mRNA sequencing) and called peaks (ChIP)

value: Whole seedling


title: PBMCs, Severe patient 3 (4th week of infection) 5' Expression

description:
S3_4_Exp
pbmc_meta.data.txt
pbmc_normalized_count_integrated.txt
T_cell_normalized_count_integrated.txt
T_cell_meta.data.txt
B_cell_normalized_count_integrated.txt
B_cell_meta.data.txt
Monocyte_normalized_count_integrated.txt
Monocyte_meta.data.txt
NK_cell_normalized_count_integrated.txt
NK_cell_meta.data.txt


title: mRNA, prt6_R1

data_processing:
Reads were trimmed and aligned to TAIR10 using bowtie. Differential gene expression analysis was performed using DEseq8
Supplementary files format and content: Processed data files contain read counts (mRNA sequencing) and called peaks (ChIP)


title: NIH3T3-U6-10-R1

description:
Library name: sample 29
10 uM U6 AMO treated,repeat 1


title: COV434_EQUI100_1


title: COV434_EQUI_3

value: Equimolar mixture 1x


title: PBMCs, Severe patient 3 (2nd week of infection) BCR

description:
S3_2_B
BCR_seq_data.xlsx

data_processing:
Library strategy: BCR-seq
Basecalls performed using bcl2fastq v2.20.0.422
scRNA reads were filtering and align to GRCh38 genome using CellRanger 4.0
Gene count was performed using CellRanger and loaded into single cell objects in Seurat package (v4.0)
Filtering out qualified cells based on the plot displaying the average gene expression versus -log10 p-value or versus mitochondrial gene counts.
Filtering out cell types by annotations based on DEGs, CITE-seq and BCR/TCR-seq.
Inegration was perforemd using Seurat package with the RPCA method.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text, xlsx or csv files include cell infromation or normalized gene counts


title: PBMCs, Severe patient 3 (2nd week of infection) TCR

description:
S3_2_T
TCR_seq_data.xlsx


title: ypdF_3

city: Xuzhou

first: Dianshuang

last: Zhou

state: Jiangsu

address: 209 Tongshan Road

institute: Xuzhou Medical University

description: Library name: Sample 33

data_processing:
The raw sequencing reads underwent a series of filtering steps to eliminate rRNA sequences, low-quality reads, and adapter contamination. Reads containing a high proportion of unknown bases were also discarded. The cleaned reads were then aligned to the reference genome (NCBI: GCF_000002985.6_WBcel235) using HISAT and assembled using StringTie software. Additionally, Bowtie 2 software was employed to align against the reference sequence for comparative analysis.
Assembly: GCF_000002985.6_WBcel235
Supplementary files format and content: Raw counts and TPM for each sample

organism: Caenorhabditis elegans

source_name: Whole body

extract_protocol:
Total RNA was extracted from the synchronized adult C. elegans using Trizol  according to the manufacturing instructions. RNA was qualified and quantified using NanoDrop bioanalyzer and Agilent 5300.
In this study, 33 samples were sequenced by DNBSEQ platform.

value: Whole body

value: fed with ypdF mutant bacteria


title: NIH3T3-U6-05-R1

description:
Library name: sample 27
0.5 uM U6 AMO treated,repeat 1

value: 0.5 uM U6 AMO treated


title: ypdF_2

description: Library name: Sample 32


title: COV434_EQUI_2

data_processing:
The fastq files were demultiplexed using umi_tools (v1.0.0). The umi_tools whitelist function was used to whitelist the indexes. Then the umi_tools extract function was used to extract and mark the fastq sequence names with the UMI and indexes which were then used to demultiplex the data
STAR 2.7.9a was used to map the fastq files aginast human (hg38/GRCh38) and mouse (mm10/GRCm38) refernce genomes obtained from Ensembl
The aligned bam files were deduplicated with the umi_tools dedup function based on their UMI sequence
The deduplicated mapped reads were counted using featureCounts v1.5.1 with ensembl gene annotations, Homo_sapiens.GRCh38.101.gtf and Mus_musculus.GRCm38.86.gtf
Supplementary files format and content: Tab separated text files with raw gene counts

value: WT


title: mRNA, Col0_R2

data_processing:
Reads were trimmed and aligned to TAIR10 using bowtie. Differential gene expression analysis was performed using DEseq3
Supplementary files format and content: Processed data files contain read counts (mRNA sequencing) and called peaks (ChIP)


title: PBMCs, Severe patient 3 (2nd week of infection) 5' Expression

description:
S3_2_Exp
pbmc_meta.data.txt
pbmc_normalized_count_integrated.txt
T_cell_normalized_count_integrated.txt
T_cell_meta.data.txt
B_cell_normalized_count_integrated.txt
B_cell_meta.data.txt
Monocyte_normalized_count_integrated.txt
Monocyte_meta.data.txt
NK_cell_normalized_count_integrated.txt
NK_cell_meta.data.txt

value: Severe patient 3

value: 2nd week of infection


title: ypdF_1

description: Library name: Sample 31


title: NIH3T3-U6-005-R2

description:
Library name: sample 26
0.05 uM U6 AMO treated,repeat 2

value: 0.05 uM U6 AMO treated


title: COV434_EQUI_1


title: yjgU_3

description: Library name: Sample 30

value: fed with yigU mutant bacteria


title: COV434_EPIDEM100_3

value: Epidemiological mixture 100x


title: PBMCs, Severe patient 3 (1st week of infection) Feature Barcode

description:
S3_1_FB
Feature_barcode_CITE-seq.csv

value: Peripheral blood mononuclear cells (PBMCs)

value: 1st week of infection


title: NIH3T3-U6-005-R1

description:
Library name: sample 25
0.05 uM U6 AMO treated,repeat 1

value: cancer stem cell


title: NIH3T3-U4-10-R2

description:
Library name: sample 24
10 uM U4 AMO treated,repeat 2

value: 10 uM U4 AMO treated


title: PBMCs, Severe patient 3 (1st week of infection) BCR

description:
S3_1_B
BCR_seq_data.xlsx

value: Severe


title: yjgU_1

description: Library name: Sample 28


title: PBMCs, Severe patient 3 (1st week of infection) TCR

description:
S3_1_T
TCR_seq_data.xlsx


title: PBMCs, Severe patient 3 (1st week of infection) 5' Expression

description:
S3_1_Exp
pbmc_meta.data.txt
pbmc_normalized_count_integrated.txt
T_cell_normalized_count_integrated.txt
T_cell_meta.data.txt
B_cell_normalized_count_integrated.txt
B_cell_meta.data.txt
Monocyte_normalized_count_integrated.txt
Monocyte_meta.data.txt
NK_cell_normalized_count_integrated.txt
NK_cell_meta.data.txt


title: COV434_EPIDEM100_1

value: ovary

value: Granulosa cancer cell line COV434


title: COV434_EPIDEM100_2


title: NIH3T3-U4-05-R2

description:
Library name: sample 22
0.5 uM U4 AMO treated,repeat 2

value: 0.5 uM U4 AMO treated


title: NIH3T3-U4-10-R1

description:
Library name: sample 23
10 uM U4 AMO treated,repeat 1


title: yghZ_3

description: Library name: Sample 27

value: Whole body

value: fed with yghZ mutant bacteria


title: yjgU_2

description: Library name: Sample 29


title: NIH3T3-U6-05-R2

description:
Library name: sample 28
0.5 uM U6 AMO treated,repeat 2

value: 0.5 uM U6 AMO treated


title: PBMCs, Severe patient 2 (4th week of infection) Feature Barcode

description:
S2_4_FB
Feature_barcode_CITE-seq.csv

value: Severe patient 2

value: 4th week of infection


title: COV434_EPIDEM_3

value: WT

value: Epidemiological mixture 1x


title: NIH3T3-U4-05-R1

description:
Library name: sample 21
0.5 uM U4 AMO treated,repeat 1


title: yghZ_2

description: Library name: Sample 26


title: PBMCs, Severe patient 2 (4th week of infection) BCR

description:
S2_4_B
BCR_seq_data.xlsx


title: yghZ_1

description: Library name: Sample 25


title: COV434_EPIDEM_2


title: NIH3T3-U4-005-R2

description:
Library name: sample 20
0.05 uM U4 AMO treated,repeat 2

value: 0.05 uM U4 AMO treated


title: PBMCs, Severe patient 2 (4th week of infection) TCR

description:
S2_4_T
TCR_seq_data.xlsx


title: NIH3T3-U4-005-R1

description:
Library name: sample 19
0.05 uM U4 AMO treated,repeat 1


title: PBMCs, Severe patient 2 (4th week of infection) 5' Expression

description:
S2_4_Exp
pbmc_meta.data.txt
pbmc_normalized_count_integrated.txt
T_cell_normalized_count_integrated.txt
T_cell_meta.data.txt
B_cell_normalized_count_integrated.txt
B_cell_meta.data.txt
Monocyte_normalized_count_integrated.txt
Monocyte_meta.data.txt
NK_cell_normalized_count_integrated.txt
NK_cell_meta.data.txt


title: ycgJ_2

description: Library name: Sample 23

value: fed with ycgJ mutant bacteria


title: NIH3T3-U2-10-R2

description:
Library name: sample 18
10 uM U2 AMO treated,repeat 2

value: 10 uM U2 AMO treated


title: COV434_WQS100_2

value: WQS-mixture 100x


title: PBMCs, Severe patient 2 (2nd week of infection) Feature Barcode

description:
S2_2_FB
Feature_barcode_CITE-seq.csv

value: Peripheral blood mononuclear cells (PBMCs)

value: 2nd week of infection


title: ycgJ_1

description: Library name: Sample 22


title: COV434_WQS100_1


title: COV434_WQS_3

value: WQS-mixture 1x


title: ycdC_3

description: Library name: Sample 21

value: fed with ycdC mutant bacteria


title: PBMCs, Severe patient 2 (2nd week of infection) TCR

description:
S2_2_T
TCR_seq_data.xlsx

value: Severe


title: NIH3T3-U2-05-R2

description:
Library name: sample 16
0.5 uM U2 AMO treated,repeat 2

value: cancer stem cell

value: 0.5 uM U2 AMO treated


title: NIH3T3-U2-05-R1

description:
Library name: sample 15
0.5 uM U2 AMO treated,repeat 1


title: ycdC_2

description: Library name: Sample 20

value: Whole body


title: PBMCs, Severe patient 2 (2nd week of infection) 5' Expression

description:
S2_2_Exp
pbmc_meta.data.txt
pbmc_normalized_count_integrated.txt
T_cell_normalized_count_integrated.txt
T_cell_meta.data.txt
B_cell_normalized_count_integrated.txt
B_cell_meta.data.txt
Monocyte_normalized_count_integrated.txt
Monocyte_meta.data.txt
NK_cell_normalized_count_integrated.txt
NK_cell_meta.data.txt


title: ycgJ_3

description: Library name: Sample 24


title: COV434_WQS_2

value: ovary

value: Granulosa cancer cell line COV434


title: COV434_WQS_1


title: ycdC_1

description: Library name: Sample 19


title: NIH3T3-U2-005-R2

description:
Library name: sample 14
0.05 uM U2 AMO treated,repeat 2

value: 0.05 uM U2 AMO treated


title: PBMCs, Severe patient 2 (1st week of infection) Feature Barcode

description:
S2_1_FB
Feature_barcode_CITE-seq.csv

value: Severe patient 2

value: 1st week of infection


title: COV434_EPIDEM_1

value: WT

value: Epidemiological mixture 1x


title: yccU_3

description: Library name: Sample 18

value: fed with yccU mutant bacteria


title: NIH3T3-U2-005-R1

description:
Library name: sample 13
0.05 uM U2 AMO treated,repeat 1


title: PBMCs, Severe patient 2 (1st week of infection) BCR

description:
S2_1_B
BCR_seq_data.xlsx


title: NIH3T3-U2-10-R1

description:
Library name: sample 17
10 uM U2 AMO treated,repeat 1

value: 10 uM U2 AMO treated


title: COV434_DMSO_3

value: DMSO


title: COV434_WQS100_3

value: WQS-mixture 100x


title: yccU_2

description: Library name: Sample 17


title: PBMCs, Severe patient 2 (2nd week of infection) BCR

description:
S2_2_B
BCR_seq_data.xlsx

value: Peripheral blood mononuclear cells (PBMCs)

value: 2nd week of infection


title: NIH3T3-U1-10-R2

description:
Library name: sample 12
10 uM U1 AMO treated,repeat 2

value: 10 uM U1 AMO treated


title: COV434_DMSO_2


title: yccU_1

description: Library name: Sample 16


title: COV434_DMSO_1


title: NIH3T3-U1-10-R1

description:
Library name: sample 11
10 uM U1 AMO treated,repeat 1

value: cancer stem cell


title: NIH3T3-U1-05-R2

description:
Library name: sample 10
0.5 uM U1 AMO treated,repeat 2

value: 0.5 uM U1 AMO treated


title: PBMCs, Severe patient 2 (1st week of infection) TCR

description:
S2_1_T
TCR_seq_data.xlsx

value: Severe


title: PAO1_PL-DMEM_3

city: Braunschweig

first: Matthias

last: Preusse

address: Inhoffenstr. 7

department: Molecular Bacteriology

country: Germany

institute: Helmholtz Center for Infection Research

data_processing:
bacterial cells: cutadapt
host cells: STAR aligner
all sample: bowtie2
featureCounts
Assembly: NC_002516.2, GRCh38.p13
Supplementary files format and content: reads per gene

organism: Pseudomonas aeruginosa

source_name: PAO1 - planctonic DMEM culture 3

growth_protocol:
bacterial cells: Planktonic cultures in DMEM & Calu-3 ALI cultures
host cells: Air-liquid interface (ALI)

extract_protocol:
all samples: RNeasy Mini Kit & Qiashredder columns
all samples: NEBNext Ultra II Directional RNA library prep kit

treatment_protocol:
bacterial cells: Planktonic cultures in DMEM & Calu-3 ALI cultures + tobramycin treated
host cells: Controls & infected with PAO1 + tobramycin treated

value: bacteria

value: wild type


title: PBMCs, Severe patient 2 (1st week of infection) 5' Expression

description:
S2_1_Exp
pbmc_meta.data.txt
pbmc_normalized_count_integrated.txt
T_cell_normalized_count_integrated.txt
T_cell_meta.data.txt
B_cell_normalized_count_integrated.txt
B_cell_meta.data.txt
Monocyte_normalized_count_integrated.txt
Monocyte_meta.data.txt
NK_cell_normalized_count_integrated.txt
NK_cell_meta.data.txt

data_processing:
Library strategy: CITEseq
Basecalls performed using bcl2fastq v2.20.0.422
scRNA reads were filtering and align to GRCh38 genome using CellRanger 4.0
Gene count was performed using CellRanger and loaded into single cell objects in Seurat package (v4.0)
Filtering out qualified cells based on the plot displaying the average gene expression versus -log10 p-value or versus mitochondrial gene counts.
Filtering out cell types by annotations based on DEGs, CITE-seq and BCR/TCR-seq.
Inegration was perforemd using Seurat package with the RPCA method.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text, xlsx or csv files include cell infromation or normalized gene counts


title: PAO1_PL-DMEM_2

source_name: PAO1 - planctonic DMEM culture 2


title: PBMCs, Severe patient 1 (4th week of infection) Feature Barcode

description:
S1_4_FB
Feature_barcode_CITE-seq.csv

value: Severe patient 1

value: 4th week of infection


title: torY_2

description: Library name: Sample 14

value: Whole body

value: fed with torY mutant bacteria


title: torY_1

description: Library name: Sample 13


title: NIH3T3-U1-05-R1

description:
Library name: sample 9
0.5 uM U1 AMO treated,repeat 1


title: PBMCs, Severe patient 1 (4th week of infection) TCR

description:
S1_4_T
TCR_seq_data.xlsx


title: PBMCs, Severe patient 1 (4th week of infection) BCR

description:
S1_4_B
BCR_seq_data.xlsx


title: SOX9_cKO3

city: Kumaoto

first: Hiroki

last: Hirao

state: Kumamoto

address: 1-1-1, Honjo, Chuo-ku,

country: Japan

institute: Kumamoto university

description: Library name: 6.fastq

data_processing:
RNA-seq data were aligned to the mouse genome (UCSC mm10) using STAR ver. 2.6.0a after trimming to remove adapter sequences and removal of low-quality ends using Trim Galore! v0.5.0 (cutadapt v1.16). Gene expression levels are reported as transcripts per million, as determined using RSEM v1.3.1.
Assembly: UCSC mm10
Supplementary files format and content: TPM for each sample

source_name: Liver

extract_protocol:
For RNA-seq analysis of liver samples (CT n=3, KO n=3), total RNA was prepared using Trizol extraction (Thermo Fisher, Waltham, MA, USA), and the quality of the total RNA was confirmed using a BioAnalyzer 2100 (RNA integrity number > 9).
DNA libraries were prepared according to the Illumina TruSeq protocol using a TruSeq Stranded mRNA LT sample prep kit (Illumina, San Diego, CA, USA) and sequenced using an Illumina NextSeq 500 (Illumina) with a NextSeq 500/550 High Output v2 kit (Illumina) to obtain single-end, 75-nt reads.

value: Liver

value: Alb-Cre+/+;Sox9 flox/flox


title: PAO1_PL-DMEM_1

source_name: PAO1 - planctonic DMEM culture 1


title: purH_3

description: Library name: Sample 12

value: fed with purH mutant bacteria


title: NIH3T3-U1-005-R2

description:
Library name: sample 8
0.05 uM U1 AMO treated,repeat 2

value: 0.05 uM U1 AMO treated


title: SOX9_cKO2

description: Library name: 5.fastq


title: purH_1

description: Library name: Sample 10


title: NIH3T3-NC-10-R1

description:
Library name: sample 5
10 uM negative control AMO treated,repeat 1

value: negative control

value: 10 uM negative control AMO treated


title: NIH3T3-NC-10-R2

description:
Library name: sample 6
10 uM negative control AMO treated,repeat 2


title: PBMCs, Severe patient 1 (2nd week of infection) BCR

description:
S1_2_B
BCR_seq_data.xlsx

value: Peripheral blood mononuclear cells (PBMCs)

value: 2nd week of infection


title: NIH3T3-U1-005-R1

description:
Library name: sample 7
0.05 uM U1 AMO treated,repeat 1

value: cancer stem cell


title: PBMCs, Severe patient 1 (4th week of infection) 5' Expression

description:
S1_4_Exp
pbmc_meta.data.txt
pbmc_normalized_count_integrated.txt
T_cell_normalized_count_integrated.txt
T_cell_meta.data.txt
B_cell_normalized_count_integrated.txt
B_cell_meta.data.txt
Monocyte_normalized_count_integrated.txt
Monocyte_meta.data.txt
NK_cell_normalized_count_integrated.txt
NK_cell_meta.data.txt


title: NIH3T3-NC-05-R2

description:
Library name: sample 4
0.5 uM negative control AMO treated,repeat 2

value: 0.5 uM negative control AMO treated


title: purH_2

description: Library name: Sample 11


title: torY_3

description: Library name: Sample 15


title: iaaA_3

description: Library name: Sample 9

value: fed with iaaA mutant bacteria


title: PBMCs, Severe patient 1 (2nd week of infection) TCR

description:
S1_2_T
TCR_seq_data.xlsx

value: Severe


title: iaaA_2

description: Library name: Sample 8


title: NIH3T3-NC-05-R1

description:
Library name: sample 3
0.5 uM negative control AMO treated,repeat 1


title: CT2

description: Library name: 2.fastq

value: WT


title: PBMCs, Severe patient 1 (2nd week of infection) 5' Expression

description:
S1_2_Exp
pbmc_meta.data.txt
pbmc_normalized_count_integrated.txt
T_cell_normalized_count_integrated.txt
T_cell_meta.data.txt
B_cell_normalized_count_integrated.txt
B_cell_meta.data.txt
Monocyte_normalized_count_integrated.txt
Monocyte_meta.data.txt
NK_cell_normalized_count_integrated.txt
NK_cell_meta.data.txt

value: Severe patient 1


title: iaaA_1

description: Library name: Sample 7


title: PBMCs, Severe patient 1 (1st week of infection) BCR

description:
S1_1_B
BCR_seq_data.xlsx

value: 1st week of infection


title: NP-OVA_DEC_OVAboost_24h, GC B cell, 10x VDJ (BCR)

city: New York

first: Gabriela

middle: S

last: Silva Santos

state: NY

address: 1230 York Avenue

institute: The Rockefeller University

description:
Library name: Tube_exprReferee4_1_BCR
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript

data_processing:
Single-cell RNA-Seq and Hashtag-oligos (HTOs) UMI quantification were performed with CellRanger multi v7.1.0 (10x Genomics), using the Cellranger GEX reference mm10, and analyzed in R with Seurat v.4.3.0. Cells were demultiplexed with MULTISeqDemux, and those classified as doublets or with mitochondrial content > 10% and feature count < 200 or > 2.500 were excluded. Sample batches were then merged, scaled, and normalized with SCTransform. Single-cell BCR libraries were mapped to the Cellranger VDJ GRCm38 reference using CellRanger multi v7.1.0.
Assembly: mm10
Supplementary files format and content: CellRanger output files:  GEX_HTO_barcodes.tsv.gz, GEX_HTO_features.tsv.gz, GEX_HTO_matrix.mtx.gz
Supplementary files format and content: CellRanger output files: airr_rearrangement.tsv
Library strategy: BCR-Seq

source_name: Lymph node

extract_protocol:
For single cell RNA sequencing, single cell suspensions were prepared from draining lymph nodes of immunized mice and treated mice. Single cell suspensions were indexed with TotalSeqC (BioLegend) cell surface antibodies. Gross or fractionated GC cells were purified by flow cytometry, pooled and loaded onto a Chromium Controller (10x Genomics).
Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 5′ v2 Reagent Kit (10x Genomics) according to manufacturer’s protocol. Libraries were loaded onto an Illumina NextSeq with the mid-Output Kit (150 paired end) for V-D-J analysis or onto an NOVAseq for pooled V-D-J and single  cell gene expression. Hashtag indexing was used to demultiplex the sequencing data and generate gene-barcode matrices, respectively.

value: Lymph node

value: GC B cells

value: B18hi DEC +/+

value: NP-OVA immunized, DEC-OVA boosted, doxycyline treated -24hr.


title: PBMCs, Severe patient 1 (1st week of infection) Feature Barcode

description:
S1_1_FB
Feature_barcode_CITE-seq.csv


title: NIH3T3-NC-005-R1

description:
Library name: sample 1
0.05 uM negative control AMO treated,repeat 1

value: 0.05 uM negative control AMO treated


title: MC38 SIS ECM MatriSphere Day 7_Sample 6

city: Bethesda

first: Thomas

middle: Joshua

last: Meyer

state: Maryland

address: 41 Center Drive, Building 41, Room B620

department: National Cancer Institute

institute: National Institutes of Health

data_processing:
Reads were trimmed for adapters and low-quality bases using Cutadapt v1.18.
Reads were aligned to reference genomes (mm10 for mouse, hg38 for human) using STAR v2.7.0f in 2-pass mode.
Gene expression was quantified using RSEM 1.3.1 with the GENCODE_30 (mouse) and GENCODE_M21 (human) gene annotations.
Low count genes were filtered prior to CPM and quantile normalization using Limma voom followed by different expression of genes analysis. Three samples did not pass QC, were excluded from downstream analysis, and are therefore excluded from this accession.
Preranked GSEA was performed using fGSEA and the HALLMARK collection was searched for both mouse and human datasets, with mouse genes being first converted to human orthologs for lookup using human databases.
Assembly: Human samples used hg38 & GENCODE_30. Mouse samples used mm10 & GENCODE_M21.
Supplementary files format and content: The CSV (.csv) files provided for all Raw Counts, DEG, & GSEA results (mouse & human).

growth_protocol: CRC Cells were grown in Roswell Park Memorial Institute (RPMI) media supplemented with L-glutamine (Thermo Fisher 11875119), 10% fetal bovine serum (Thermo Fisher 16000044), and 1% penicillin streptomycin (Thermo Fisher 15140122). Cells were maintained at 37°C with 5% CO2 humidified air.

extract_protocol:
After 7 days of culture, CRC spheroids were transferred to 5 mL tubes in batches of 10, the excess media was removed by pipetting, 1 mL of TRIzol (Invitrogen) was added to each sample, and the samples were stored at -80°C until further processing. Samples were thawed on ice and the RNA was extracted using the RNeasy Micro Kit (QIAGEN) in accordance with the manufacturer’s instructions.
All mRNA-seq samples were pooled within species and sequenced on NovaSeq 6000 SP using Illumina® Stranded mRNA Prep and paired-end sequencing.

treatment_protocol: Cells were seeded onto ULA U-bottom plates with or without SIS ECM and allowed to grow up to 7 days

value: colorectal carcinoma

value: ECM


title: PBMCs, Severe patient 1 (1st week of infection) TCR

description:
S1_1_T
TCR_seq_data.xlsx

data_processing:
Library strategy: TCR-seq
Basecalls performed using bcl2fastq v2.20.0.422
scRNA reads were filtering and align to GRCh38 genome using CellRanger 4.0
Gene count was performed using CellRanger and loaded into single cell objects in Seurat package (v4.0)
Filtering out qualified cells based on the plot displaying the average gene expression versus -log10 p-value or versus mitochondrial gene counts.
Filtering out cell types by annotations based on DEGs, CITE-seq and BCR/TCR-seq.
Inegration was perforemd using Seurat package with the RPCA method.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text, xlsx or csv files include cell infromation or normalized gene counts


title: crl_3

description: Library name: Sample 6

value: Whole body

value: fed with crl mutant bacteria


title: SOX9_cKO1

description: Library name: 4.fastq

value: Liver

value: Alb-Cre+/+;Sox9 flox/flox


title: RBD_bait_positive_mCherry_low_mRNA_DZ_mCherryhigh, GC B cell, 10x VDJ (BCR)

description:
Library name: Rebutal_4-5_Tube_C_BCR
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript

value: mRNA vaccinated or RBD vaccinated, doxycycline treated -36hr.


title: NIH3T3-NC-005-R2

description:
Library name: sample 2
0.05 uM negative control AMO treated,repeat 2

value: cancer stem cell

value: negative control


title: CT1

description: Library name: 1.fastq

value: WT


title: RBD_bait_positive_mCherry_high_mRNA_DZ_mCherrylow,GC B cell, 10x VDJ (BCR)

description:
Library name: Rebutal_4-5_Tube_D_BCR
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: PBMCs, Severe patient 1 (1st week of infection) 5' Expression

description:
S1_1_Exp
pbmc_meta.data.txt
pbmc_normalized_count_integrated.txt
T_cell_normalized_count_integrated.txt
T_cell_meta.data.txt
B_cell_normalized_count_integrated.txt
B_cell_meta.data.txt
Monocyte_normalized_count_integrated.txt
Monocyte_meta.data.txt
NK_cell_normalized_count_integrated.txt
NK_cell_meta.data.txt

value: Peripheral blood mononuclear cells (PBMCs)

value: Severe patient 1

value: Severe


title: crl_2

description: Library name: Sample 5


title: crl_1

description: Library name: Sample 4


title: Two pooled e14.5 pituitary glands from C57BL6 strain - scRNA-Seq

city: Ann Arbor

first: Lev

last: Prasov

state: MI

address: 1241 Catherine Street, 5704 Med Sci II

department: Department of Human Genetics

institute: University of Michigan

library_source: transcriptomic single cell

data_processing:
Sequencing outputs were demultiplexed using 10x Genomics Cell Ranger 7.1.0 software and FASTQ files were aligned to the Genome Reference Consortium Mouse Build 38, mm10 genome (Church et al., 2009; Mouse Genome Sequencing et al., 2002; Zheng et al., 2017, https://genomes.ucsc.edu).
Seurat/4.1.1 (Butler et al., 2018; Stuart et al., 2019) scRNAseq software was utilized to normalize data using the NormalizeData and FindVariableFeatures commands with nfeatures set to 2000. Poor quality cells were removed using cutoffs of nFeature_RNA < 200 and % mitochondrial RNA >15%. Doublet cells were considered those with nCounts > 2000 and removed from the study.
Core Seurat functions were used to read in cellranger output files, integrate samples, generate uniform manifold approximation and projection (UMAP) plots, calculate clusters, perform differential gene expression analyses, and generate plots of expression data.
Assembly: Genome Reference Consortium Mouse Build 38, mm10 genome
Supplementary files format and content: zipped versions of the matrix tables, with list of barcodes (column names for matrix) and features (i.e. genes, row names for matrix)

source_name: pituitary gland

extract_protocol:
Nxn -/- e14.5 samples were dissociated into single cells in 50 μl of a solution containing 1mg/ml Papain (Roche, cat#10108014001), 5mM L-Cysteine, 1mM EDTA, and 0.6mM 2-mercaptoethanol. Dissociation was performed at 37°C for 5 minutes, with titration every 2 minutes.
Single-cell RNA libraries were prepared by the University of Michigan’s Advanced Genomics Core under a standardized pipeline on the 10x Genomics Chromium platform and controller, following manufacturer’s instructions for Single Cell 3’ v3 reagents, and sequenced on the NovaSeq6000 platform with an S4 chip.  From our previous description in Cheung et al., 2018 Endocrinology: Following generation of single-cell gel bead-in-emulsions (GEMs), reverse transcription was performed and the resulting post-GEM reverse transcription product was cleaned up using DynaBeads MyOne silane beads (Thermo Fisher Scientific, Waltham, MA). The cDNA was amplified, SPRIselect (Beckman Coulter, Brea, CA) cleaned and quantified, and then enzymatically fragmented and size selected using SPRIselect beads to optimize the cDNA amplicon size prior to library construction. An additional round of double-sided SPRI bead cleanup was performed after end repair and A-tailing. Another single-sided cleanup was done after adapter ligation. Indexes were added during PCR amplification and a final double-sided SPRI cleanup was performed. Libraries were quantified by KAPA quantitative PCR for Illumina adapters (Roche, Pleasanton, CA) and size was determined by Agilent TapeStation D1000 tapes. Read 1 primer sequences were added to the molecules during GEM incubation. P5, P7, and sample index and read 2 primer sequences were added during library construction via end repair, A-tailing, adaptor ligation, and PCR. Libraries were generated with unique sample indices for each sample.

value: pituitary gland

value: total pitutary cells

tag: age

value: wild type


title: PBMCs, Severe patient 1 (2nd week of infection) Feature Barcode

description:
S1_2_FB
Feature_barcode_CITE-seq.csv

value: 2nd week of infection


title: MC38 SIS ECM MatriSphere Day 7_Sample 4

value: colorectal carcinoma


title: RBD_bait_negative_mCherry_high_mRNA_LZ_mCherrylow, GC B cell, 10x VDJ (BCR)

description:
Library name: Rebutal_4-5_Tube_B_BCR
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript

value: Lymph node

value: GC B cells


title: BW25113_2

description: Library name: Sample 2

value: Whole body

value: fed with BW25113 bacteria


title: BW25113_3

description: Library name: Sample 3


title: PBMCs, Mild patient 2 (4th week of infection) Feature Barcode

description:
M2_4_FB
Feature_barcode_CITE-seq.csv

value: Mild patient 2

value: Mild

value: 4th week of infection


title: PBMCs, Mild patient 2 (4th week of infection) BCR

description:
M2_4_B
BCR_seq_data.xlsx


title: MC38 SIS ECM MatriSphere Day 7_Sample 3

value: ECM


title: CT3

description: Library name: 3.fastq

value: Liver

value: WT


title: BW25113_1

description: Library name: Sample 1


title: MC38 SIS ECM MatriSphere Day 7_Sample 5


title: RBD_bait_negative_mCherry_low_mRNA_LZ_mCherryhigh, GC B cell, 10x VDJ (BCR)

description:
Library name: Rebutal_4-5_Tube_A_BCR
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript

value: mRNA vaccinated or RBD vaccinated, doxycycline treated -36hr.


title: MC38 Cells alone Spheroid Day 7_Sample 5

value: CA


title: MC38 SIS ECM MatriSphere Day 7_Sample 1


title: RBD_negative_gross, GC B cell, 10x VDJ (BCR)

description:
Library name: 6_CTRL_VDJ
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript

value: wildtype, C57BL/6J

value: RBD vaccinated


title: Ccr2-CreERT2, H2-Ab1-flox/flox replicate 2

city: Minneapolis

first: Samuel

last: Becker

state: MN

address: 2101 6th St SE

institute: University of Minnesota

description:
Library name: CreposMS4
10X Genomics

data_processing:
Demultiplexing and aggregation were performed using the 10X Genomics CellRanger program. This yielded a barcoded feature matrix "filtered_feature_bc_matrix 2.h5".
Assembly: Mouse GRCm39
Supplementary files format and content: filtered_feature_bc_matrix_2.h5 (Matrix file from Cellranger; aggregate of all 4 samples)
Supplementary files format and content: aggregation.csv (Cellranger output file)

source_name: lungs

growth_protocol: Mycobacterium tuberculosis H37Rv was grown in 7H11c complete broth to an OD600 of 0.3. Inoculum for infection was prepared in PBS with 0.05% Tween-80.

extract_protocol:
At 3 weeks post-infection, lungs were harvested and single cell suspensions were generated by mechanical homogenization at 4ºC without tissue digestion. Cells for encapsulation were enriched by cell sorting to exclude cells expressing the following markers: CD90, B220, CD19, NK1.1, Ly-6G, Siglec-F. IMDM complete media (Gibco IMDM supplemented with 10% fetal bovine serum, 200 µM beta-mercaptoethanol, and Gibco supplements Glutamax, pyruvate, non-essential amino acids) was used to prepare sorted cells. Approximately 30,000 cells were sorted for each sample. The cells were washed twice in PBS by centrifugation prior to encpasulation.
Library construction was performed according to the manufacturer's instructions (10X Genomics Chromium Next GEM Single Cell 3' Gene Expression Kit v.3.1 (dual index)). Cells in samples 1 through 4 were encapsulated in separate lanes of the same 10X chip. Encapsulation and library preparation was performed on each sample side-by side rather than pooling samples. Briefly, gel bead-in-emulsion (GEMs) were generated on the 10X Chromium X controller. Barcoded cDNA was generated using reverse transcription and barcoded adaptor oligonucleotides. The cDNA was amplified by PCR, then enzymatically fragmented to optimize cDNA amplicon size for sequencing. P5, P7, i7 and i5 sample indexes and TruSeq read 2 sequences were added via end repair, A-tailing, adaptor ligation and PCR.

treatment_protocol: Mice were infected via aerosol exposure at an infectious dose of ~100 colony-forming units per mouse. Mice were fed tamoxifen chow (500mg/kg chow, Envigo/Inotiv) starting the day of infection and continuously until the endpoint.

value: myeloid cell enriched

value: lungs

value: 6-8 weeks

value: female

tag: host genotype

value: C57BL/6 background; Ccr2-CreERT2, H2-Ab1-flox/flox

tag: bacterial strain

value: Mycobacterium tuberculosis strain H37Rv


title: PBMCs, Mild patient 2 (2nd week of infection) BCR

description:
M2_2_B
BCR_seq_data.xlsx

value: Peripheral blood mononuclear cells (PBMCs)

value: 2nd week of infection


title: PBMCs, Mild patient 2 (4th week of infection) 5' Expression

description:
M2_4_Exp
pbmc_meta.data.txt
pbmc_normalized_count_integrated.txt
T_cell_normalized_count_integrated.txt
T_cell_meta.data.txt
B_cell_normalized_count_integrated.txt
B_cell_meta.data.txt
Monocyte_normalized_count_integrated.txt
Monocyte_meta.data.txt
NK_cell_normalized_count_integrated.txt
NK_cell_meta.data.txt

value: Mild patient 2

value: Mild


title: Ccr2-CreERT2, H2-Ab1-flox/flox replicate 1

description:
Library name: CreposFS3
10X Genomics


title: M4, scRNAseq3

city: boston

first: Jiyuan

last: Liu

state: Massachusetts

address: 55 fruit st.

institute: Mass Gen Hospital

description:
Library name: Sample 9
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: comma-separated values files

source_name: Kidney

extract_protocol:
Single cells isolated from kidneys of control and transgenic mice were used for Single-cell RNA sequencing. In brief, kidney tissues from control or transgenic mice were cut into small pieces (~1mm2) on ice, washed with cold PBS, and digested at 37°C with a shaking speed of 150 rpm for 40 min in an air bath shaker. The digestion medium containing 450 units/ml collagenase1,  150 units/ml collagenase 2, 450 units/ml collagenase 3, 450 units/ml collagenase 4, 0.8 units/ml Elastase, 300 units/ml Hyaluronidase, 250 units/ml DNase I, and 1 units/ml Dispase. The digested cells were mixed with cold RPMI 1640 with 2% FBS, filtered through a prewetted 70-μm & 40 µm strainer and  centrifuged at 1500 rpm at 4°C for 5 minutes. The cell pellets were then treated for ACK lysis for 10 min, washed with ice-cold PBS+0.04%BSA, and resuspended in cold PBS+0.04%BSA. The prepared cells were then be resuspended for evaluating cell viability, adjusting cell number, and preparing cell library.
Single-cell library was prepared using the 10x Genomics Chromium Single Cell 5′ Library & Gel Bead Kit v2 (PN-1000014). Cell suspensions were loaded onto a Chromium Single-Cell Chip with the reverse transcription master mix and single cell 5′ gel beads, aiming for 10,000 cells per channel. Reverse transcription was performed using a C1000 Touch Thermal Cycler (Bio-Rad Laboratories). Quality control and quantification were performed using the Agilent 2100 Bioanalyzer with a DNA high-sensitivity chip. For input into the gene-expression library construction, 50 ng cDNA and 14 cycles were used. Libraries were sequenced using an Illumina HiSeq 2500 NexGen Sequencer

value: Kidney cells

value: Kidney

tag: strain

value: Adult

value: treated with doxycycline (Dox) for 4months


title: PBMCs, Mild patient 2 (2nd week of infection) Feature Barcode

description:
M2_2_FB
Feature_barcode_CITE-seq.csv


title: PBMCs, Mild patient 2 (2nd week of infection) 5' Expression

description:
M2_2_Exp
pbmc_meta.data.txt
pbmc_normalized_count_integrated.txt
T_cell_normalized_count_integrated.txt
T_cell_meta.data.txt
B_cell_normalized_count_integrated.txt
B_cell_meta.data.txt
Monocyte_normalized_count_integrated.txt
Monocyte_meta.data.txt
NK_cell_normalized_count_integrated.txt
NK_cell_meta.data.txt


title: Cre negative, H2-Ab1-flox/flox replicate 2

description:
Library name: CrenegMS2
10X Genomics

value: C57BL/6 background; Cre negative, H2-Ab1-flox/flox


title: mCherry_low, GC B cell, 10x VDJ (BCR)

description:
Library name: Princeton_GC_B_mCherry_Lo_rep2_VDJ
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript

value: Lymph node

value: GC B cells

value: NP-OVA immunized, doxycycline treated -36hr.


title: MC38 Cells alone Spheroid Day 7_Sample 4

value: colorectal carcinoma

value: CA


title: M4, scRNAseq2

description:
Library name: Sample 8
10x Genomics


title: RBD_positive_gross, GC B cell/contaminant CD8 T cell, 10x VDJ (BCR)

description:
Library name: 7_CTRL_VDJ
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript

value: GC B cells + contaminant CD8 T cells

value: wildtype, C57BL/6J

value: RBD vaccinated


title: PBMCs, Mild patient 2 (1st week of infection) Feature Barcode

description:
M2_1_FB
Feature_barcode_CITE-seq.csv

value: Peripheral blood mononuclear cells (PBMCs)

value: 1st week of infection


title: PBMCs, Mild patient 2 (4th week of infection) TCR

description:
M2_4_T
TCR_seq_data.xlsx

value: Mild patient 2

value: 4th week of infection


title: CT26 SIS ECM MatriSphere Day 7_Sample 6

value: ECM


title: Cre negative, H2-Ab1-flox/flox replicate 1

description:
Library name: CrenegFS1
10X Genomics

value: myeloid cell enriched

value: lungs

value: 6-8 weeks

value: female

value: Mycobacterium tuberculosis strain H37Rv


title: mCherry_high, GC B cell, 10x VDJ (BCR)

description:
Library name: Princeton_GC_B_mCherry_HI_rep2_VDJ
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript

value: Lymph node

value: GC B cells


title: MC38 Cells alone Spheroid Day 7_Sample 3

value: colorectal carcinoma


title: MC38 Cells alone Spheroid Day 7_Sample 1

value: CA


title: D7, scRNAseq3

description:
Library name: Sample 7
10x Genomics

value: Kidney cells

value: Kidney

value: Adult

value: treated with doxycycline (Dox) for 7days


title: D7, scRNAseq2

description:
Library name: Sample 6
10x Genomics


title: RNATCRseq_Rechallenge_ 8dpi_GP33pos_Lane1_RNA

city: Stanford

first: Colin

middle: J

last: Raposo

state: CA

address: 240 Pasteur Drive, BMI 4600

department: Pathology

institute: Stanford University

description: Library name: Rechallenge_GP33pos_Lane1_RNA

data_processing:
scRNA-seq data was processed using CellRanger Count (v3.1.0; 10X genomics) aligned to the mm10 genome.
scTCR-seq data was processed with CellRanger VDJ (v6.0.0; 10X genomics) and the `cellranger-vdj-GRCm38-alts-ensembl-3.1.0` reference.
LMO multiseq data were processed with `deMULTIplex2`
Assembly: Mouse mm10
Supplementary files format and content: scRNA: filtered_feature_bc_matrix.h5
Supplementary files format and content: scTCR: filtered_contig.annotations.csv and clonotypes.csv
Supplementary files format and content: LMO multiseq: BarcodeMatrix.csv and DemultiplexedIdentities.csv

source_name: Spleen

growth_protocol: Splenocytes were harvested 151 days post-infection from mice infected with LCMV-Cl13 or LCMV-Arm, and CD8+ T cells were enriched using magnetic separation. Approximately half of the enriched cells were sorted for TCR sequencing, while the remaining cells were divided into five recipient mice per group. One day later, the recipient mice were challenged with LCMV-Arm, and splenocytes were collected 8 days post-infection.

extract_protocol:
At 8 days post-rechallenge, cells were enriched for CD8+ T cells using magnetic separation and stained with sample-specific LMO, viability dye, GP33 tetramer,and surface antibodies. Live CD8+ Tetramer+/- donor T cells were sorted based on congenic allele expression using a BD FACSAria into RPMI supplemented with 10–50% FBS. Recipient GP33+ T cells were also sorted as controls. After sorting, samples were pooled and loaded into the Chromium Controller (10x Genomics).
scRNA and TCR libraries were prepared according to manufacturer's instructions (10X Genomics 5’ v2). MULTI-seq library preparation workflow performed following cDNA amplification, as described previously (McGinnis, Patterson, et al., Nature Methods, 2019).

value: Spleen


title: RNATCRseq_Rechallenge_ 8dpi_GP33pos_Lane1_TCR

description: Library name: Rechallenge_GP33pos_Lane1_TCR


title: RNATCRseq_Rechallenge_ 8dpi_GP33pos_Lane1_LMO

description: Library name: Rechallenge_GP33pos_Lane1_LMO

library_source: other

molecule: other


title: PBMCs, Mild patient 2 (1st week of infection) BCR

description:
M2_1_B
BCR_seq_data.xlsx

value: Peripheral blood mononuclear cells (PBMCs)

value: Mild patient 2

value: Mild

value: 1st week of infection


title: RNATCRseq_Rechallenge_ 8dpi_GP33neg_Lane6_TCR

description: Library name: Rechallenge_GP33neg_Lane6_TCR


title: PBMCs, Mild patient 2 (2nd week of infection) TCR

description:
M2_2_T
TCR_seq_data.xlsx

value: 2nd week of infection


title: PBMCs, Mild patient 2 (1st week of infection) TCR

description:
M2_1_T
TCR_seq_data.xlsx


title: CTR, scRNAseq2

description:
Library name: Sample 4
10x Genomics

value: treated with doxycycline (Dox) for 0days


title: CT26 SIS ECM MatriSphere Day 7_Sample 4

value: ECM


title: PBMCs, Mild patient 1 (4th week of infection) BCR

description:
M1_4_B
BCR_seq_data.xlsx

value: Mild patient 1

value: 4th week of infection


title: PBMCs, Mild patient 2 (1st week of infection) 5' Expression

description:
M2_1_Exp
pbmc_meta.data.txt
pbmc_normalized_count_integrated.txt
T_cell_normalized_count_integrated.txt
T_cell_meta.data.txt
B_cell_normalized_count_integrated.txt
B_cell_meta.data.txt
Monocyte_normalized_count_integrated.txt
Monocyte_meta.data.txt
NK_cell_normalized_count_integrated.txt
NK_cell_meta.data.txt


title: RNATCRseq_Rechallenge_ 8dpi_GP33neg_Lane6_LMO

description: Library name: Rechallenge_GP33neg_Lane6_LMO


title: RNATCRseq_Rechallenge_ 8dpi_GP33neg_Lane5_RNA

description: Library name: Rechallenge_GP33neg_Lane5_RNA


title: PBMCs, Mild patient 1 (4th week of infection) Feature Barcode

description:
M1_4_FB
Feature_barcode_CITE-seq.csv


title: CT26 SIS ECM MatriSphere Day 7_Sample 1


title: PBMCs, Mild patient 1 (4th week of infection) TCR

description:
M1_4_T
TCR_seq_data.xlsx


title: RNATCRseq_Rechallenge_ 8dpi_GP33neg_Lane6_RNA

description: Library name: Rechallenge_GP33neg_Lane6_RNA


title: CT26 SIS ECM MatriSphere Day 7_Sample 3


title: RNATCRseq_Rechallenge_ 8dpi_GP33neg_Lane5_TCR

description: Library name: Rechallenge_GP33neg_Lane5_TCR


title: P30SV, replicate 1, scRNAseq

first: Robert

last: Morell

address: 35A Convent Drive, Room 1F-103

institute: National Institute on Deafness and Other Communication Disorders

description: 10X Genomics

data_processing:
Libraries were sequenced on a Nextseq 500 instrument (Illumina, San Diego, CA, United States) reads were subsequently processed using 10x Genomics CellRanger analytical pipeline using default settings and 10x Genomics downloadable mm10 genome.
Quality control was conducted using the following parameters: nFeature_RNA >900 & nFeature_RNA <5000 & percent.mt <15. Doublet detection was conducted with scDblFinder using the default parameters without clustering information. The raw gene expression matrix was normalized using the scTransform function in Seurat, and the P1 and P30 datasets were integrated after batch correction using the reciprocal principal component analysis (RPCA) method.
Assembly: GRCm38
Supplementary files format and content: Tab-separated tables and matrix files

source_name: stria vascularis

extract_protocol:
Inner ears from a total of four P1 mice and four P30 mice were collected. The SV was micro-dissected from the spiral ligament and lysed in either 0.5 mg/ml trypsin at 37°C for 7 min for P1 tissue, or 400-600 units/mL accutase at 37°C for 25 min for P30 tissue. Media was gently replaced with 5% FBS in DMEM to stop lysis, and the tissue was triturated and then filtered using a 20 µm filter (pluriSelect Life Science, El Cajon, CA, United States), and the cells were kept on ice for 35 min. The cell pellet was then suspended in 50 µL of the filtered media and cell counts were performed using a Luna automated cell counter (Logos Biosystems, Annandale, VA, United States). A cell density of 1 x 106 cells/ml was used to load onto the 10X genomics chip.
Library preparation was performed according to the instructions in the 10x Genomics Chromium Single Cell 3’ Chip Kit V2.

value: stria vascularis

value: CBA/J

tag: developmental stage

value: adult (P30)


title: CTR, scRNAseq3

description:
Library name: Sample 5
10x Genomics

value: Kidney cells


title: MC38 Cells alone Spheroid Day 7_Sample 2

value: colorectal carcinoma

value: CA


title: CT26 SIS ECM MatriSphere Day 7_Sample 2


title: CT26 SIS ECM MatriSphere Day 7_Sample 5


title: D7, scRNAseq

description: 10x Genomics

value: Kidney

value: Adult

value: treated with doxycycline (Dox) for 7days


title: RNATCRseq_Rechallenge_ 8dpi_GP33neg_Lane5_LMO

description: Library name: Rechallenge_GP33neg_Lane5_LMO

value: Spleen


title: CT26 Cells alone Spheroid Day 7_Sample 4


title: RNATCRseq_Rechallenge_ 8dpi_GP33neg_Lane4_RNA

description: Library name: Rechallenge_GP33neg_Lane4_RNA


title: P1SV, replicate 2, scRNAseq

description: 10X Genomics

value: neonatal (post-natal day 1, P1)


title: CT26 Cells alone Spheroid Day 7_Sample 6


title: PBMCs, Mild patient 1 (4th week of infection) 5' Expression

description:
M1_4_Exp
pbmc_meta.data.txt
pbmc_normalized_count_integrated.txt
T_cell_normalized_count_integrated.txt
T_cell_meta.data.txt
B_cell_normalized_count_integrated.txt
B_cell_meta.data.txt
Monocyte_normalized_count_integrated.txt
Monocyte_meta.data.txt
NK_cell_normalized_count_integrated.txt
NK_cell_meta.data.txt

value: Peripheral blood mononuclear cells (PBMCs)

value: Mild


title: RNATCRseq_Rechallenge_ 8dpi_GP33neg_Lane4_TCR

description: Library name: Rechallenge_GP33neg_Lane4_TCR


title: CT26 Cells alone Spheroid Day 7_Sample 5


title: CTR, scRNAseq

description: 10x Genomics

value: treated with doxycycline (Dox) for 0days


title: MmGC_MHHP100_4

value: ovary

value: Mouse primary granulosa cells

value: WT

value: MEHHP 100x


title: PBMCs, Mild patient 1 (2nd week of infection) Feature Barcode

description:
M1_2_FB
Feature_barcode_CITE-seq.csv

value: Mild patient 1

value: 2nd week of infection


title: PBMCs, Mild patient 1 (2nd week of infection) BCR

description:
M1_2_B
BCR_seq_data.xlsx


title: P1SV, replicate 1, scRNAseq

description: 10X Genomics

value: stria vascularis

value: CBA/J


title: RNATCRseq_Rechallenge_ 8dpi_GP33neg_Lane4_LMO

description: Library name: Rechallenge_GP33neg_Lane4_LMO


title: RNATCRseq_Rechallenge_ 8dpi_GP33neg_Lane3_TCR

description: Library name: Rechallenge_GP33neg_Lane3_TCR


title: PBMCs, Mild patient 1 (2nd week of infection) TCR

description:
M1_2_T
TCR_seq_data.xlsx


title: M4, scRNAseq

description: 10x Genomics

value: Kidney cells

value: treated with doxycycline (Dox) for 4months


title: RNATCRseq_Rechallenge_ 8dpi_GP33neg_Lane3_LMO

description: Library name: Rechallenge_GP33neg_Lane3_LMO


title: RNATCRseq_Rechallenge_ 8dpi_GP33neg_Lane3_RNA

description: Library name: Rechallenge_GP33neg_Lane3_RNA


title: CT26 Cells alone Spheroid Day 7_Sample 2

value: colorectal carcinoma

value: CA


title: PBMCs, Mild patient 1 (2nd week of infection) 5' Expression

description:
M1_2_Exp
pbmc_meta.data.txt
pbmc_normalized_count_integrated.txt
T_cell_normalized_count_integrated.txt
T_cell_meta.data.txt
B_cell_normalized_count_integrated.txt
B_cell_meta.data.txt
Monocyte_normalized_count_integrated.txt
Monocyte_meta.data.txt
NK_cell_normalized_count_integrated.txt
NK_cell_meta.data.txt


title: MmGC_MHHP100_2


title: RNATCRseq_Rechallenge_ 8dpi_GP33neg_Lane2_TCR

description: Library name: Rechallenge_GP33neg_Lane2_TCR

value: Spleen


title: CT26 Cells alone Spheroid Day 7_Sample 1


title: CD45-EPCAM+, young recipient, untreated

city: Vienna

first: Stephan

last: Gruener

address: Borschkegasse 8a

department: Center for Cancer Research

country: Austria

institute: Medical University of Vienna

description: 10x Genomics

data_processing:
Reads were processed with CellRanger v6.1.2 using mm10 as reference genome (refdata-gex-mm10-2020-A).
Assembly: mm10
Supplementary files format and content: Space Ranger HDF5 Feature-Barcode Matrix Format (filtered_feature_bc_matrix.h5 & raw_feature_bc_matrix.h5) generated by CellRanger

growth_protocol: 4T1 cells were purchased from ATCC, expanded, and stored according to the producer's instructions. Cells were tested and authenticated by the StemElite ID System (Promega). Cells were tested every 6 months for Mycoplasma by means of the ATCC Universal Mycoplasma Detection Kit 30-1012, cultured for no more than 2 weeks, and used for no longer than 15 passages. Cells were stably infected with vector expressing luciferase. Mice were maintained in animal facilties under standard conditions.

extract_protocol:
Tumors were surgically removed after 28 days from tumor injection to generate a single cell suspension. Briefly, after mechanical dissociation, tumors were placed in culture medium (1:1 of DMEM with high glucose and Ham's F-12 Nutrient Mixture; EuroClone) supplemented by 2 mg/mL collagenase (Merck) and 0.1 mg/mL Dnase I (Qiagen), and digested for 1 to 2 hours at 37°C.
A single cell suspension was obtained by sequential dissociation of the fragments by gentle pipetting, to further disintegrate cell clumps, followed by filtration through a 100-μmol/L nylon mesh. After cell suspension preparation, cells were incubated with PE-conjugated murine CD45 antibody (BD Biosciences, clone 30-F11), murine PeCy7 Epcam (BD Bioscience) for 20 minutes at 4°C. Cells were then washed twice with PBS+0.2% BSA and prepared for cell sorting. Before sorting, cells were co-stained with 0.1 μg/mL 4′,6-diamidino-2-phenylindole (DAPI, Merck). Cells were sorted using different gating strategies using FACS Fusion sorter (BD Bioscience): EPCAM-CD45+DAPI− for immune cells, EPCAM+CD45-DAPI- for tumor cells and EPCAM-CD45-DAPI− for stromal cells. Cells were then counted, and 10,000 cells/conditions underwent scRNA-seq library preparation following 10X Genomic V3.1 protocol.

treatment_protocol: Young and adult tumor-bearing mice (n = 10, per study arm) were treated with either vehicle or triple therapy. Triple therapy comprises Cyclophosphamide (C140) at 140 mg/kg, Vinorelbine (V) was used at 9 mg/kg as we have previously shown (PMIDs: 33268528, 37048617). Chemotherapeutic drugs were dissolved in PBS and administrated, once a week, every 6 days, for 3 weeks by intraperitoneal injection. Mouse monoclonal PD-1-targeting antibody was purchased by Bioxcell (clone RMP1-14) and was administered intraperitoneally 0.2 mg/mouse every 2 days for a total of five doses.

tag: mouse strain

value: Balb/c

tag: # injected_cells

tag: 10x chemistry_version

value: Vehicle


title: PBMCs, Mild patient 1 (1st week of infection) Feature Barcode

description:
M1_1_FB
Feature_barcode_CITE-seq.csv

extract_protocol:
PBMCs were purified from heparinized peripheral whole blood using a Ficoll-Histopaque gradient.
The user guide of Chromium Next GEM Single Cell V(D)J Reagent Kits v1.1 (10× Genomics, Pleasanton, CA, USA) was used to prepare the cDNA libraries for single-cell RNA sequencing (scRNA-seq) assay. To check the viability of the sorted cells, a Countess™ II FL Automated Cell Counter (Thermo Fisher Scientific) was used with trypan blue. About 10,000 cells for each sample were determined as target cells, and the master mix and single-cell suspensions were dispensed into a Chromium Next GEM G Chip (10× Genomics). For each sample, 5 L of supernatant cDNA was prepared, amplification master mix, SI-PCR primer, and index kit were added, and sample index PCR was performed in a thermal cycler. The clean-up process was performed using 1.2× SPRIselect reagent, and elution was performed with buffer EB.
Single cell RNAseq, TCR/BCR sequencing, CITEseq

value: Peripheral blood mononuclear cells (PBMCs)

value: Mild

value: 1st week of infection


title: PBMCs, Mild patient 1 (1st week of infection) BCR

description:
M1_1_B
BCR_seq_data.xlsx


title: CD45+EPCAM-, adult recipient, TT treated

description: 10x Genomics

value: Cyclophosphamide (C140) + Vinorelbine + alphaPD-1


title: PBMCs, Mild patient 1 (1st week of infection) TCR

description:
M1_1_T
TCR_seq_data.xlsx


title: MmGC_MHHP_4

tag: tissue

value: ovary

value: Mouse primary granulosa cells

tag: genotype

value: WT

value: MEHHP 1x


title: RNATCRseq_Rechallenge_ 8dpi_GP33neg_Lane2_RNA

description: Library name: Rechallenge_GP33neg_Lane2_RNA


title: MmGC_MHHP100_3

tag: treatment

value: MEHHP 100x


title: CT26 Cells alone Spheroid Day 7_Sample 3

tag: cell type


title: CD45+EPCAM-, adult recipient, untreated

description: 10x Genomics


title: CD45-EPCAM+, adult recipient, untreated

description: 10x Genomics


title: MmGC_MHHP_3


title: RNATCRseq_Rechallenge_ 8dpi_GP33neg_Lane2_LMO

description: Library name: Rechallenge_GP33neg_Lane2_LMO


title: MmGC_MHHP_2


title: MmGC_MHHP_1


title: CD45-EPCAM-, adult recipient, untreated

description: 10x Genomics


title: MmGC_MHHP100_1


title: PBMCs, Asymptomatic patient 2 Feature Barcode

description:
C2_FB
Feature_barcode_CITE-seq.csv

tag: individual

value: Asymptomatic patient 2

tag: infection

value: Asymptomatic


title: RNATCRseq_Rechallenge_ 8dpi_GP33neg_Lane1_TCR

description: Library name: Rechallenge_GP33neg_Lane1_TCR


title: CD45-EPCAM-, adult recipient, TT treated

description: 10x Genomics


title: MmGC_EQUI100_4

value: Equimolar mixture 100x


title: PBMCs, Asymptomatic patient 2 BCR

description:
C2_B
BCR_seq_data.xlsx

tag: severity


title: RNATCRseq_Rechallenge_ 8dpi_GP33neg_Lane1_RNA

description: Library name: Rechallenge_GP33neg_Lane1_RNA


title: CD45-EPCAM-, young recipient, untreated

description: 10x Genomics

tag: cell line


title: MmGC_EQUI100_3


title: PBMCs, Asymptomatic patient 2 5' Expression

description:
C2_Exp
pbmc_meta.data.txt
pbmc_normalized_count_integrated.txt
T_cell_normalized_count_integrated.txt
T_cell_meta.data.txt
B_cell_normalized_count_integrated.txt
B_cell_meta.data.txt
Monocyte_normalized_count_integrated.txt
Monocyte_meta.data.txt
NK_cell_normalized_count_integrated.txt
NK_cell_meta.data.txt


title: RNATCRseq_aPDL1_GP33pos_Lane3_TCR

description: Library name: aPDL1_Lane3_TCR

growth_protocol: Mice were infected with LCMV-CL13 and dosed with 200ug aPDL1 (B7-H1) or PBS by IP injected every 2-3 days from 22-34 dpi.

extract_protocol:
At 102 days post-infection, splenocytes were enriched for CD8+ T cells using magnetic separation and stained with sample-specific LMO, viability dye, GP33 tetramer, and surface antibodies. Live CD8+ Tetramer+ T cells were sorted into RPMI supplemented with 10% FBS. After sorting, samples were pooled and loaded into the Chromium Controller (10x Genomics).
scRNA and TCR libraries were prepared according to manufacturer's instructions (10X Genomics 5’ v2). MULTI-seq library preparation workflow performed following cDNA amplification, as described previously (McGinnis, Patterson, et al., Nature Methods, 2019).


title: CD45-EPCAM-, young recipient, TT treated

description: 10x Genomics


title: PBMCs, Asymptomatic patient 1 Feature Barcode

description:
C1_FB
Feature_barcode_CITE-seq.csv

value: Asymptomatic patient 1


title: RNATCRseq_aPDL1_GP33pos_Lane3_RNA

description: Library name: aPDL1_Lane3_RNA


title: PBMCs, Mild patient 1 (1st week of infection) 5' Expression

description:
M1_1_Exp
pbmc_meta.data.txt
pbmc_normalized_count_integrated.txt
T_cell_normalized_count_integrated.txt
T_cell_meta.data.txt
B_cell_normalized_count_integrated.txt
B_cell_meta.data.txt
Monocyte_normalized_count_integrated.txt
Monocyte_meta.data.txt
NK_cell_normalized_count_integrated.txt
NK_cell_meta.data.txt

value: Mild patient 1

tag: time


title: MASLD4

city: Chongqing

first: Zhiwei

last: Chen

address: The Second Affiliated Hospital of Chongqing Medical University, 74  Linjiang Road, Yuzhong District, Chongqing

description:
Library name: samples35
Column name in raw_counts_Mouse.txt: nafld_64

data_processing:
Raw data(raw reads) of fastq format were firstly processed through in-house perl scripts
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene
Assembly: hg38,GRCm39
Supplementary files format and content: Human_FPKMs.csv
Supplementary files format and content: Mouse_FPKMs.csv
Supplementary files format and content: raw_counts_Human.txt
Supplementary files format and content: raw_counts_Mouse.txt

source_name: liver

extract_protocol:
RNA was harvested using  RNA Nano 6000 Assay Kit of the Bioanalyz 2100 system (Agilent Technologies,CA,USA). 1.3 ug of total RNA was used for the construction of sequencing libraries
RNA libraries for RNA-seg were prepared using SMARTER mRNA-Seq Library Prep Kifollowing manufacturer's protocols

value: liver

value: high fat diet

tag: batch


title: MmGC_EQUI100_1

extract_protocol:
RNA was harvested using RNeasy micro and mini plus kit (Qiagen). 10 ng of total RNA was used for the construction of sequencing libraries.
Libraries was prepared using QIAseq UPX 3’Transcriptome kit (Qiagen) according to manufacturer's protocol


title: RNATCRseq_aPDL1_GP33pos_Lane3_LMO

description: Library name: aPDL1_Lane3_LMO

value: Spleen


title: MASLD3

institute: The Second Affiliated Hospital of Chongqing Medical University

description:
Library name: samples34
Column name in raw_counts_Mouse.txt: nafld_63


title: PBMCs, Asymptomatic patient 1 BCR

first: Hang-Rae

last: Kim

address: 103 Daehak-ro, Jongno-gu

institute: Seoul National University College of Medicine

description:
C1_B
BCR_seq_data.xlsx

data_processing:
Library strategy: BCR-seq
Basecalls performed using bcl2fastq v2.20.0.422
scRNA reads were filtering and align to GRCh38 genome using CellRanger 4.0
Gene count was performed using CellRanger and loaded into single cell objects in Seurat package (v4.0)
Filtering out qualified cells based on the plot displaying the average gene expression versus -log10 p-value or versus mitochondrial gene counts.
Filtering out cell types by annotations based on DEGs, CITE-seq and BCR/TCR-seq.
Inegration was perforemd using Seurat package with the RPCA method.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text, xlsx or csv files include cell infromation or normalized gene counts

value: Peripheral blood mononuclear cells (PBMCs)


title: PBMCs, Asymptomatic patient 1 TCR

description:
C1_T
TCR_seq_data.xlsx


title: MmGC_EQUI_3

value: Equimolar mixture 1x


title: MASLD2

description:
Library name: samples33
Column name in raw_counts_Mouse.txt: nafld_62


title: MmGC_EQUI_2


title: PBMCs, Asymptomatic patient 2 TCR

description:
C2_T
TCR_seq_data.xlsx


title: PBMCs, Healthy donor 2 Feature Barcode

description:
H2_FB
Feature_barcode_CITE-seq.csv

value: Healthy donor 2

value: control


title: MASLD1

description:
Library name: samples32
Column name in raw_counts_Mouse.txt: nafld_61


title: RNATCRseq_aPDL1_GP33pos_Lane2_RNA

description: Library name: aPDL1_Lane2_RNA


title: RNATCRseq_Rechallenge_ 8dpi_GP33neg_Lane1_LMO

description: Library name: Rechallenge_GP33neg_Lane1_LMO


title: RNATCRseq_aPDL1_GP33pos_Lane2_LMO

description: Library name: aPDL1_Lane2_LMO


title: RNATCRseq_aPDL1_GP33pos_Lane2_TCR

description: Library name: aPDL1_Lane2_TCR


title: PBMCs, Healthy donor 2 BCR

description:
H2_B
BCR_seq_data.xlsx


title: MmGC_EQUI_4

value: ovary


title: Control4

description:
Library name: samples31
Column name in raw_counts_Mouse.txt: c57_58

value: chow diet


title: MmGC_EQUI_1

value: Mouse primary granulosa cells

value: WT


title: Control3

description:
Library name: samples30
Column name in raw_counts_Mouse.txt: c57_57


title: MmGC_EQUI100_2


title: MmGC_EPIDEM100_4

value: Epidemiological mixture 100x


title: PBMCs, Healthy donor 2 TCR

description:
H2_T
TCR_seq_data.xlsx


title: Control2

description:
Library name: samples29
Column name in raw_counts_Mouse.txt: c57_50


title: MmGC_EPIDEM100_3


title: PBMCs, Healthy donor 2 5' Expression

description:
H2_Exp
pbmc_meta.data.txt
pbmc_normalized_count_integrated.txt
T_cell_normalized_count_integrated.txt
T_cell_meta.data.txt
B_cell_normalized_count_integrated.txt
B_cell_meta.data.txt
Monocyte_normalized_count_integrated.txt
Monocyte_meta.data.txt
NK_cell_normalized_count_integrated.txt
NK_cell_meta.data.txt


title: RNATCRseq_aPDL1_GP33pos_Lane1_TCR

description: Library name: aPDL1_Lane1_TCR


title: MmGC_EPIDEM100_2


title: PBMCs, Asymptomatic patient 1 5' Expression

description:
C1_Exp
pbmc_meta.data.txt
pbmc_normalized_count_integrated.txt
T_cell_normalized_count_integrated.txt
T_cell_meta.data.txt
B_cell_normalized_count_integrated.txt
B_cell_meta.data.txt
Monocyte_normalized_count_integrated.txt
Monocyte_meta.data.txt
NK_cell_normalized_count_integrated.txt
NK_cell_meta.data.txt


title: PBMCs, Healthy donor 1 Feature Barcode

description:
H1_FB
Feature_barcode_CITE-seq.csv

value: Healthy donor 1


title: Control1

description:
Library name: samples28
Column name in raw_counts_Mouse.txt: c57_49


title: scRNATCRseq_GP33_Lane3_TCR

description: Library name: GP33_Lane3_TCR

growth_protocol: Mice were infected with LMCV-Arm or LCMV-Cl13 and sacraficed at various dpi from the spleen.

extract_protocol:
CD8+ T cells were enriched using magnetic separation and stained with sample-specific LMO, viability dye, GP33 tetramer,and surface antibodies. Live CD8+ GP33+ T cells were sorted using a BD FACSAria into RPMI supplemented with 10–50% FBS. Sorted cells were pooled and loaded into the Chromium Controller (10x Genomics). Naïve T cells were also sorted as controls. In batch 2, samples were further divided based on CD62L expression,; batch 1, total GP33+ cells were sequenced. Each batch was processed independently, with separate library preparation and sequencing.
scRNA and TCR libraries were prepared according to manufacturer's instructions (10X Genomics 5’ v2). MULTI-seq library preparation workflow performed following cDNA amplification, as described previously (McGinnis, Patterson, et al., Nature Methods, 2019).


title: MmGC_EPIDEM100_1


title: HBV-MASLD4

description:
Library name: samples27
Column name in raw_counts_Mouse.txt: hbv_nafld29

value: rAAV8-1.6 HBV injection + high fat diet


title: PBMCs, Healthy donor 1 BCR

description:
H1_B
BCR_seq_data.xlsx


title: scRNATCRseq_GP33_Lane3_RNA

description: Library name: GP33_Lane3_RNA


title: HBV-MASLD3

description:
Library name: samples26
Column name in raw_counts_Mouse.txt: hbv_nafld26

value: rAAV8-1.5 HBV injection + high fat diet


title: MmGC_EPIDEM_4

value: Epidemiological mixture 1x


title: PBMCs, Healthy donor 1 TCR

description:
H1_T
TCR_seq_data.xlsx


title: scRNATCRseq_GP33_Lane3_LMO

description: Library name: GP33_Lane3_LMO


title: HBV-MASLD2

description:
Library name: samples25
Column name in raw_counts_Mouse.txt: hbv_nafld23

value: rAAV8-1.4 HBV injection + high fat diet


title: Control Cardiomyocytes

city: Carpi

first: Emiliano

last: Bolesani

state: Modena

address: Via Giuliano Benassi, 7

department: Process Development & Cell Therapy

country: Italy

institute: Evotec SE

description: Biphasic WNT pathway derived human Cardiomyocytes

data_processing:
Compute resource: Raw data processing was conducted on a High Performance Computing cluster (HPC-seq). This cluster provides significant compute power (600 cores in 13 nodes, a total of 5 TB RAM, 300TB storage, Ubuntu Linux, SLURM job scheduler) to allow large workloads to be efficiently processed in a timely fashion, and furthermore provides the backbone for resource-intensive graphical applications such as the locally implemented MHH Galaxy instance. A three tiered storage system has been implemented, with jobs transiently stored on a fast 24TB SSD shelf, with important results saved into mid-term redundant NetApp shelves.
Raw data processing: BCL files were converted to FASTQ files using bcl2fastq Conversion Software (Illumina) using the respective sample sheet with utilized 10X barcodes. The proprietary 10x Genomics CellRanger pipeline (v3.0.2) was used with default parameters except for the setting of expected cells (--expect-cells 5000 ).
Genome_build: CellRanger was used to align read data to the reference genome provided by 10X Genomics (Human reference dataset 3.0.0; GrCh38) using the aligner STAR, counting aligned reads per gene, and calculating clustering and summary statistics.
Supplementary_files_format_and_content: The Loupe Cell Browser from 10x Genomics was used to view and revise annotated clusters, based on the implemented tSNE algorithm.

source_name: human Pluripotent Stem Cells (hPSCs)

extract_protocol: Library generation: Library preparation for single cell mRNA-Seq analysis was performed according to the Chromium NextGEM Single Cell 3ʹ Reagent Kits v3.1 User Guide (Manual Part Number CG000204 Rev B; 10x Genomics). According to the protocol a given excess of cells was loaded to the 10x controller in order to reach a target number of 10000  cells per sample. Fragment length distribution of generated libraries was monitored using ‘Bioanalyzer High Sensitivity DNA Assay’ (5067-4626; Agilent Technologies). Quantification of libraries was performed by use of the ‘Qubit® dsDNA HS Assay Kit’ (Q32854; ThermoFisher Scientific). Sequencing run: Libraries were pooled, denatured with NaOH, and were finally diluted accordingly in order to be sequenced on an Illumina NovaSeq6000 sequencer using an S4 flowcell. Samples were sequenced according to the following settings: 150bp as sequence read 1; 150bp as sequence read 2; 8bp as index read 1; no index read 2. An average number of 135 million reads passing filter per sample were finally retrieved, yielding in roughly 29.000 reads per cell.

value: hPSC-derived cardiac progenies

tag: cell line / strain

value: hESC3 NKX2-5 wt/GFP


title: scRNATCRseq_GP33_Lane2_RNA

description: Library name: GP33_Lane2_RNA

value: Spleen


title: HBV5

description:
Library name: samples23
Column name in raw_counts_Mouse.txt: hbv79

value: liver

value: rAAV8-1.3 HBV injection + chow diet


title: PBMCs, Healthy donor 1 5' Expression

city: Seoul

description:
H1_Exp
pbmc_meta.data.txt
pbmc_normalized_count_integrated.txt
T_cell_normalized_count_integrated.txt
T_cell_meta.data.txt
B_cell_normalized_count_integrated.txt
B_cell_meta.data.txt
Monocyte_normalized_count_integrated.txt
Monocyte_meta.data.txt
NK_cell_normalized_count_integrated.txt
NK_cell_meta.data.txt

source_name: Peripheral blood mononuclear cells (PBMCs)


title: MmGC_EPIDEM_3

first: Anastasios

last: Damdimopoulos

address: Hälsovägen 7c

institute: Karolinska Institute

data_processing:
The fastq files were demultiplexed using umi_tools (v1.0.0). The umi_tools whitelist function was used to whitelist the indexes. Then the umi_tools extract function was used to extract and mark the fastq sequence names with the UMI and indexes which were then used to demultiplex the data
STAR 2.7.9a was used to map the fastq files aginast human (hg38/GRCh38) and mouse (mm10/GRCm38) refernce genomes obtained from Ensembl
The aligned bam files were deduplicated with the umi_tools dedup function based on their UMI sequence
The deduplicated mapped reads were counted using featureCounts v1.5.1 with ensembl gene annotations, Homo_sapiens.GRCh38.101.gtf and Mus_musculus.GRCm38.86.gtf
Supplementary files format and content: Tab separated text files with raw gene counts


title: MmGC_EPIDEM_1


title: RNATCRseq_aPDL1_GP33pos_Lane1_RNA

description: Library name: aPDL1_Lane1_RNA


title: scRNATCRseq_GP33_Lane2_TCR

description: Library name: GP33_Lane2_TCR


title: HBV-MASLD1

description:
Library name: samples24
Column name in raw_counts_Mouse.txt: hbv_nafld16

value: rAAV8-1.3 HBV injection + high fat diet


title: RNATCRseq_aPDL1_GP33pos_Lane1_LMO

description: Library name: aPDL1_Lane1_LMO


title: SCPs (IQ-1/CHIR) 2

description: Stabilized human Cardiac Progenies


title: scRNATCRseq_GP33_Lane2_LMO

description: Library name: GP33_Lane2_LMO


title: HBV3

description:
Library name: samples21
Column name in raw_counts_Mouse.txt: hbv11


title: MmGC_WQS100_3

value: WQS-mixture 100x


title: HBV4

description:
Library name: samples22
Column name in raw_counts_Mouse.txt: hbv12


title: scRNATCRseq_GP33_Lane1_TCR

description: Library name: GP33_Lane1_TCR


title: shoot, EXPA1 line (8-4), Dex 7 days, replicate 4

city: Brno

first: Core Facility

last: Bioinformatics

address: Kamenice 5

country: Czech Republic

institute: CEITEC - Masaryk University

description:
Library name: S_Mut_dex7d_rep4
S_Mut_dex7d_rep4

data_processing:
Sequence reads were trimmed for low-quality sequence using Trimmomatic (parameter LEADING: 3 TRAILING: 3 SLIDINGWINDOW: 4:5)
Trimmed sequence reads were mapped to Arabidopsis thaliana genome (TAIR10) using STAR
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: TAIR10
Supplementary files format and content: TAB-delimited file with the read counts from featureCount.
Supplementary files format and content: TAB-delimited file with the read counts from RSEM.

source_name: shoot

growth_protocol: Arabidopsis thaliana seedlings (ecotype Col-0) of wild-type (WT) and EXPA1 overexpressing line 8-4 (Samalova et al., 2024) were germinated and grown in growth chambers under long-day conditions 16 h light/8 h dark at 21°C/19°C for 7 days.

extract_protocol:
RNA was harvested using Rneasy plant mini kit (Qiagen). 10 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NextSeq2000 P3 50bp Directional RNA Library Prep Kit for Illumina and polyA selection. Sequencing was made at GeneCore (EMBL Heidelberg, Germany).

treatment_protocol: Seedlings were grown on MS media with or without dexamethasone (Dex) for 7 days or induced with Dex for 3 hours, with four biological replicas for each treatment.

value: shoot

value: EXPA1 line (8-4)

value: Dex 7 days


title: scRNATCRseq_GP33_Lane1_RNA

description: Library name: GP33_Lane1_RNA


title: MmGC_WQS100_4

city: Stockholm

source_name: ovary

value: ovary

value: Mouse primary granulosa cells

value: WT


title: MmGC_EPIDEM_2


title: MmGC_WQS100_2


title: shoot, EXPA1 line (8-4), Dex 7 days, replicate 3

description:
Library name: S_Mut_dex7d_rep3
S_Mut_dex7d_rep3


title: HBV1

description:
Library name: samples19
Column name in raw_counts_Mouse.txt: hbv4


title: scRNATCRseq_GP33_Lane1_LMO

description: Library name: GP33_Lane1_LMO


title: shoot, EXPA1 line (8-4), Dex 7 days, replicate 2

description:
Library name: S_Mut_dex7d_rep2
S_Mut_dex7d_rep2


title: HBV2

description:
Library name: samples20
Column name in raw_counts_Mouse.txt: hbv10


title: scRNATCRseq_CD62LposGP33_Lane1_TCR

description: Library name: CD62LposGP33_Lane1_TCR


title: MmGC_WQS_4

value: WQS-mixture 1x


title: B3 (miRNA) S. aureus + Erastin

city: 绵阳

first: Anlong

last: Li

state: 四川

address: 四川省绵阳市涪城区教育中路1号

institute: 四川中医药高等专科学校

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp with default parameters. Thencleanreads were separately aligned to reference genome with orientation mode using HISAT2 software. The mappedreads of each sample were assembled by StringTie in a reference-based approach.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes TPM values for each Sample

source_name: Mus Blood

extract_protocol:
RNA extraction was performed using the standardized reagent kit RNAiso Plus (Takara, Japan).
The library was constructed utilizing the Illumina® Stranded mRNA Prep, Ligation Kit (Illumina, USA)

value: Mus Blood

value: tumour cell

value: 6 h


title: SCPs (IQ-1/CHIR) 1

description: Stabilized human Cardiac Progenies

value: hPSC-derived cardiac progenies


title: shoot, EXPA1 line (8-4), Dex 3 hours, replicate 4

description:
Library name: S_Mut_dex3h_rep4
S_Mut_dex3h_rep4

value: Dex 3 hours


title: scRNATCRseq_CD62LposGP33_Lane1_RNA

description: Library name: CD62LposGP33_Lane1_RNA

value: Spleen


title: MmGC_WQS_3


title: B2 (miRNA) S. aureus + Erastin

address: 四川省绵阳市涪城区教育中路1号


title: scRNATCRseq_CD62LposGP33_Lane1_LMO

description: Library name: CD62LposGP33_Lane1_LMO


title: B1 (miRNA) S. aureus + Erastin

address: 四川省绵阳市涪城区教育中路1号


title: shoot, EXPA1 line (8-4), Dex 3 hours, replicate 3

description:
Library name: S_Mut_dex3h_rep3
S_Mut_dex3h_rep3


title: scRNATCRseq_CD62LnegGP33_Lane3_TCR

description: Library name: CD62LnegGP33_Lane3_TCR


title: A3 (miRNA) S. aureus

address: 四川省绵阳市涪城区教育中路1号


title: MmGC_WQS_1


title: shoot, EXPA1 line (8-4), Dex 3 hours, replicate 2

description:
Library name: S_Mut_dex3h_rep2
S_Mut_dex3h_rep2


title: scRNATCRseq_CD62LnegGP33_Lane3_LMO

description: Library name: CD62LnegGP33_Lane3_LMO


title: shoot, EXPA1 line (8-4), Dex 3 hours, replicate 1

description:
Library name: S_Mut_dex3h_rep1
S_Mut_dex3h_rep1


title: MmGC_WQS100_1


title: shoot, EXPA1 line (8-4), control, replicate 4

description:
Library name: S_Mut_ctl_rep4
S_Mut_ctl_rep4

value: control


title: A1 (miRNA) S. aureus

address: 四川省绵阳市涪城区教育中路1号


title: MmGC_DMSO_3

value: DMSO


title: B3 (mRNA) S. aureus + Erastin

address: 四川省绵阳市涪城区教育中路1号

description: longRNA gene.TPM.matrix.annot


title: MmGC_DMSO_2


title: shoot, EXPA1 line (8-4), control, replicate 3

description:
Library name: S_Mut_ctl_rep3
S_Mut_ctl_rep3


title: A2 (miRNA) S. aureus

address: 四川省绵阳市涪城区教育中路1号


title: shoot, EXPA1 line (8-4), Dex 7 days, replicate 1

description:
Library name: S_Mut_dex7d_rep1
S_Mut_dex7d_rep1


title: MmGC_DMSO_4


title: scRNATCRseq_CD62LnegGP33_Lane2_RNA

description: Library name: CD62LnegGP33_Lane2_RNA


title: MmGC_DMSO_1


title: B2 (mRNA) S. aureus + Erastin

address: 四川省绵阳市涪城区教育中路1号

description: longRNA gene.TPM.matrix.annot


title: MmGC_WQS_2


title: scRNATCRseq_CD62LnegGP33_Lane2_TCR

description: Library name: CD62LnegGP33_Lane2_TCR


title: scRNATCRseq_CD62LnegGP33_Lane2_LMO

description: Library name: CD62LnegGP33_Lane2_LMO


title: B1 (mRNA) S. aureus + Erastin

address: 四川省绵阳市涪城区教育中路1号

description: longRNA gene.TPM.matrix.annot


title: RNAseq_ovary_shwhite_rep2

city: Beijing

first: Ming

last: Wang

state: Beijing

address: #15 Datun Road, Chaoyang, Beijing 100101, China

department: Key Laboratory of RNA Biology

institute: Institute of Biophysics, Chinese Academy of Sciences

data_processing:
Paired-end reads were processed with cutadapt v4.11 to remove adapters and low quality bases. Furthermore, 9 bp from both ends of reads were further trimmed.
Trimmed reads were aligned to dm6 with hisat2 v2.2.1 with default parameters
Read counts were calculated using featureCounts
Assembly: dm6
Supplementary files format and content: tab-delimited text file contains raw read counts for each sample

organism: Drosophila melanogaster

growth_protocol: All fly strains were maintained at 25 °C and used for analysis at the age of 3–5 days.

extract_protocol:
Total RNA was isolated from dissected ovaries with TRIzol (Thermo Fisher Scientific, 15596018) and treated with the RQ1 RNase-Free DNase (Promega, #M6101).
RNA library was generated using an NSR method as described (Armour, C. D., 2009).

treatment_protocol: Short hairpin RNA (shRNA) lines targeting dPcf11 (THU0857) and Eggless (THU0892) were obtained from the Tsinghua Fly Center. Short hairpin RNA lines targeting white (BL2448), Nanos-GAL4 (BL25751), and dPcf11 deficiency strain (BL24933) were obtained from the Bloomington Stock Collection. A second shRNA line against the dPcf11 mRNA (GCAATACGAAGAAATCGAAGA) was cloned to the V22 vector integrated at the landing site attP2. The RNAi strains used in the screen were either purchased from Tsinghua Fly Center and Bloomington (shRNA), or VDRC (dsRNA); certain lines were made in-house and integrated at the landing site attP2, with details listed in table S1.

value: 3-5 days

value: control knockdown


title: shoot, EXPA1 line (8-4), control, replicate 2

description:
Library name: S_Mut_ctl_rep2
S_Mut_ctl_rep2

value: shoot


title: shoot, EXPA1 line (8-4), control, replicate 1

description:
Library name: S_Mut_ctl_rep1
S_Mut_ctl_rep1

value: EXPA1 line (8-4)


title: scRNATCRseq_CD62LnegGP33_Lane1_TCR

description: Library name: CD62LnegGP33_Lane1_TCR


title: RNAseq_ovary_shwhite_rep1


title: A3 (mRNA) S. aureus

address: 四川省绵阳市涪城区教育中路1号

description: longRNA gene.TPM.matrix.annot


title: shoot, wild type, Dex 7 days, replicate 4

description:
Library name: S_WT_dex7d_rep4
S_WT_dex7d_rep4

value: Dex 7 days


title: scRNATCRseq_CD62LnegGP33_Lane3_RNA

description: Library name: CD62LnegGP33_Lane3_RNA


title: RNAseq_ovary_shpcf11E_rep2

value: ovary

value: pcf11E knockdown


title: A2 (mRNA) S. aureus

address: 四川省绵阳市涪城区教育中路1号

description: longRNA gene.TPM.matrix.annot

value: WT


title: scRNATCRseq_CD62LnegGP33_Lane1_LMO

description: Library name: CD62LnegGP33_Lane1_LMO


title: shoot, wild type, Dex 7 days, replicate 3

description:
Library name: S_WT_dex7d_rep3
S_WT_dex7d_rep3


title: RNAseq_ovary_shpcf11E_rep1


title: A1 (mRNA) S. aureus

address: 四川省绵阳市涪城区教育中路1号

description: longRNA gene.TPM.matrix.annot


title: RNAseq_L2_rescue_WT_rep2

source_name: 2nd instar larva

value: 2nd instar larva

value: wildtype

value: rescued by wildtype