description:
Library name: I40H6_LNmesenteric_LCMVarm_D60_allT_P14_SMARTA_mouse0142_FBC
Two separate 10x lanes of 10 individually hashed samples: Control_spleen, Bone.Marrow.LCMV.D7, IEL.LCMV.D7, LPL.LCMV.D7, Lung.Draining.LN, Lung.LCMV.D7, Mesenteric.LN.LCMV.D7, Prostate.LCMV.D7, Salivary.LCMV.d7, Spleen.LCMV.D7.M

value: siIEL, siLPL, prostate, SG, lung, bone marrow, spleen, mesenteric lymph nodes, mediastinal lymph nodes

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

value: TRUE

tag: exp name

value: Pan organ and time course analysis of T cells in acute LCMV (armstrong day 60)

value: Goldrath

value: P14 and SMARTA > wt

value: male

value: FALSE

tag: infection agent

value: LCMV armstrong

tag: infection dose

value: 2?ó10E5 PFU

tag: prep description

value: anti-CD45 IV injection before tissue harvest, mechanical dissociation alone

tag: organ

value: mesenteric lymph node

tag: organ uberon_id

tag: t specificity

value: P14, SMARTA

tag: target cells

value: all T including P14 and SMARTA

tag: batch


title: Single nuclei, Subacute Day 7 post injection of ECM-H,  biol rep 1

status: Public on Aug 19 2025

type: SRA

city: La Jolla

first: Karen

last: Christman

state: California

address: 2880 Torrey Pines Scenic Drive

department: Shu Chien-Gene Lay Department of Bioengineering

country: USA

institute: University of California San Diego

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the 10x Genomics Cell Ranger software v6.1.1 (normal v3.1 10X single cell kit), Cell Ranger software v7.1.0 (10X v3.1 HT kit), or Space Ranger v1.3.1
Further processing was done with Seurat v4.1(cell and gene filtering, hashtag identification, clustering, differential gene expression analysis).
Highly variable gene markers were identified using FindVariableFeatures from Seurat R package version 4.1
Assembly: Rnor-6.0-premrna
Supplementary files format and content: Tab-separated values files and matrix files

molecule: total RNA

organism: Rattus norvegicus

source_name: Cardiac

extract_protocol:
As mentioned before, harvested OCT-embedded cardiac tissue was cryosectioned onto the fiduciary regions on a 10X Visium slide at 10 µm thickness. Sections were then stained with hematoxylin and eosin, with images obtained on a Nikon Eclipse Ti2-E widefield microscope at 10X magnification. Visium was performed as per manufacturer’s kit instructions (Visium Spatial Gene Expression), with tissue permeabilization time of infarcted rat hearts optimized at 42 minutes. Both protocols utilized barcoding and library preparation, which was validated using an Agilent TapeStation prior to sequencing and quantified via Qubit HS DNA Kit. Paired-end sequencing was done on a NovaSeq6000 instrument. Low-level analysis was performed by mapping to a rat reference genome (Rnor6.0, including introns). The SpaceRanger 1.3 pipeline (10X Genomics) was used to remove redundant UMIs.
Nuclei from cardiac tissue was isolated as mentioned previously. In brief, flash frozen LV free wall samples were resuspended in nuclei lysis buffer (Millipore Sigma, Nuclei EZ prep, NUC101), 0.2 U/L RNase inhibitor (Enzymatic Y9240L) and finely chopped with scissors. Samples were homogenized with a 2 mL dounce grinder (KIMBLE) with the lysates filtered through a 100 µm, 50 µm, 20 µm strainers (CellTrics filters), respectively. The samples were centrifuged at 1000g for 5 min at 4C to pellet nuclei. The nuclear pellet was resuspended in a sucrose gradient buffer  and centrifuged at 1000g at 4ºC for 10 minutes. The pellet was then washed with a nuclei storage buffer containing 10 μg ml−1 4′,6-diamidino-2-phenylindole DAPI and centrifuged at 500 g and 4ºC for 5 minutes, with the pellet resuspending in 200 mL of 2% BSA in 1x PBS. Nuclei were then counted on a hemocytometer and volume adjusted to 1000 nuclei/µL for loading. snRNA-seq was performed with a microfluidic droplet-based technique provided by 10X Genomics kits (Chromium Next GEM Single Cell 3’ GEM V3.1 and Chromium Next GEM Single Cell 3’ HT v3.1). Quality control for cDNA and libraries were performed on Aligent TapeStation, and library concentrations were determined via Qubit HS DNA kit. Paired-end sequencing was run on a NovaSeq6000 instrument. Demultiplexing of sequenced samples were mapped to a rat reference genome (Rnor6.0, including introns). Redundant unique molecular identifiers (UMIs) were eliminated via the Cell Ranger 7.1.0 pipeline from 10X Genomics.
snRNA-seq was performed with a microfluidic droplet-based technique provided by 10X Genomics kits (Chromium Next GEM Single Cell 3’ GEM V3.1 and Chromium Next GEM Single Cell 3’ HT v3.1). Quality control for cDNA and libraries were performed on Aligent TapeStation, and library concentrations were determined via Qubit HS DNA kit. Paired-end sequencing was run on a NovaSeq6000 instrument. Demultiplexing of sequenced samples were mapped to a rat reference genome (Rnor6.0, including introns). Redundant unique molecular identifiers (UMIs) were eliminated via the Cell Ranger 6.1.0 pipeline and Cell Ranger 7.1.0 pipeline from 10X Genomics.

tag: tissue

value: Cardiac

tag: disease state

value: IR surgery

tag: treatment

value: intramyocardial injection of ECM hydrogel


city: Boston

first: Liang

last: Yang

state: MA

address: 77 Avenue Louis Pasteur

department: Pathology

institute: Harvard Medical School

description:
Library name: I40H6_LNmesenteric_LCMVarm_D60_allT_P14_SMARTA_mouse0142_GEX
Two separate 10x lanes of 10 individually hashed samples: Control_spleen, Bone.Marrow.LCMV.D7, IEL.LCMV.D7, LPL.LCMV.D7, Lung.Draining.LN, Lung.LCMV.D7, Mesenteric.LN.LCMV.D7, Prostate.LCMV.D7, Salivary.LCMV.d7, Spleen.LCMV.D7.M

data_processing:
The demultiplexing, barcode process and gene/ ADT/ hash counts were generated using Cellranger software v7.0.0.
TCRab contig annotations were generating using the cellranger vdj function from Cellranger software v7.0.0. The contigs generated were then mapped to with IMGT, and TRA and TRB chains put back together to create a summary table.
GEX and FBC libraries were processed using Seurat, where RNA, ADT QC was performed, a long with HTO demultiplexing to assign each cell a sample
Assembly: mm10
Supplementary files format and content: Cellranger output files: IGT36_cells.tsv, IGT36_matrix_rna.mtx, genes.tsv, IGT36_matrix_protein.mtx, proteins.tsv,  - Processed data from GEX, ADT and HTO libraries for IGT36.
Supplementary files format and content: Cellranger output files: IGT36_summary_table.csv - Mapped TCR contigs with TCR gene annotations for VDJ library of IGT36
Supplementary files format and content: Cellranger output files: IGT38_cells.tsv, IGT38_matrix_rna.mtx, genes.tsv, IGT38_matrix_protein.mtx, proteins.tsv,  - Processed data from GEX, ADT and HTO libraries for IGT38.
Supplementary files format and content: Cellranger output files: IGT38_summary_table.csv - Mapped TCR contigs with TCR gene annotations for VDJ library of IGT38
Supplementary files format and content: Cellranger output files: IGT40_cells.tsv, IGT40_matrix_rna.mtx, genes.tsv, IGT40_matrix_protein.mtx, proteins.tsv,  - Processed data from GEX, ADT and HTO libraries for IGT40.
Supplementary files format and content: Cellranger output files: IGT40_summary_table.csv - Mapped TCR contigs with TCR gene annotations for VDJ library of IGT40

organism: Mus musculus

source_name: siIEL, siLPL, prostate, SG, lung, bone marrow, spleen, mesenteric lymph nodes, mediastinal lymph nodes

extract_protocol:
Single-cell suspensions of spleens and lymph nodes were prepared by mechanical disruption, followed by ACK-lysing buffer. For tissue preparations, siIEL were prepared by excision of Peyer’s patches and removal of luminal contents. Then the entire tissue section was cut longitudinally, then cut laterally into 1 cm pieces, which were then incubated at 37°C for 30 minutes in Hanks’ balanced salt solution with 2.4 mg ml−1 of Hepes, 2.1 mg ml−1 of sodium bicarbonate, 8% bovine growth serum and 0.154 mg ml−1 of DTE (EMD Millipore). After collecting the siIEL sample, RPMI with 1.2 mg ml−1 of Hepes, 292 µg ml−1 of L-glutamine, 1 mM MgCl2, 1 mM CaCl2, 5% FBS and 100 U ml−1 of collagenase (Worthington) was added to the SI pieces at 37°C for 30 minutes for siLPL isolation. The SG and lung were cut into small pieces then incubated with shaking at 37°C for 30 minutes (SG) or 1 hour (lung) in the same RPMI-collagenase solution as listed previously for the siLPL. Prostate tissue was dissected from the bladder and seminal vesicles, cut into small pieces, the incubated shaking at 37°C for 30 minutes in the same RPMI-collagenase solution as listed previously. Bone marrow was isolated by harvesting the femurs and tibias and pushing out the bone marrow with a syringe. Lymphocytes from non-lymphoid tissues were further enriched using a 44%/67% Percoll density gradient. Cells were incubated with FC block and stained with Live/Dead, CD3, CD45.2 and CD45.1 on ice prior to sorting.
Libraries were prepared according to the 10x Genomics 5'v2 protocol for GEX, VDJ, and FBC

tag: lab

tag: organism name

tag: strain

tag: genetics

tag: Sex

tag: age weeks

tag: pool of_mice

tag: jax

tag: gating strategy

value: CD45+ CD3e+

tag: sample comments

value: 100x10E3 SMARTA (male, CD45.1.2) and 50x10E3 P14 (male, CD45.1), intravenous, 1 day before infection

tag: cell type

value: T cells


title: HME_MSL3_3

city: London

first: Paola

last: Scaffidi

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick Institute

description: Library name: HME_MSL3_3

library_source: transcriptomic

data_processing:
RNAseq reads were aligned to the hg38 genome using nf-core/rnaseq pipeline version 3.13.2  with star_rsem aligner
BigWig files and count tables were generated within the nf-core/rnaseq pipeline
Assembly: hg38
Supplementary files format and content: bigWig for genome browser visualization
Supplementary files format and content: tab-delimited text files includes raw counts for each sample

organism: Homo sapiens

growth_protocol: hTert-HME1 (ME16C, American Type Culture Collection (ATCC) CRL-4010) were grown in DMEM/F12 (Thermo Fisher, 11330057) with the addition of 2% Fetal Bovine Serum (FBS, Gibco 16000-044), 100 U/ml penicillin and 100 μg/mL streptomycin (Thermo Fisher 15140122), 20ng/ml EGF (Merck, E9644), 0.5μg/ml Hydrocortisone (Merck, H0888), 10ug/ml rh Insulin (Merck, I9278).

extract_protocol:
RNA was extracted using a RNeasy Plus Micro Kit (Qiagen, 74034)
For total experiment, ribosomal RNA removal was performed with FastSelect -rRNA HMR Kit (Qiagen, 334386) and libraries were prepared using NEBNext UltraII Directional RNA Library Prep Kit (NEB, E7760). For spike-in experiment, RNA concentration was checked with the nanodrop. 1ug of RNA was taken from the lowest concentrated sample and same volume was taken for all the other samples. 2 μL (1:100) ERCC Spike-in (Thermo Fisher Scientific, 4456740) was added to each sample. Libraries were prepared using NEBNext UltraII Directional RNA Library Prep Kit (NEB, E7760) with polyA enrichment.

tag: cell line

value: immortalized mammary epithelial cells

tag: genotype

value: MSL3 KO

value: Acute deletion of the indicated gene via crRNA transfection in Cas9 expressing cells


title: HME_MSL3_2

description: Library name: HME_MSL3_2


description:
Library name: I40H5_bonemarrow_LCMVarm_D60_allT_P14_SMARTA_mouse0142_TCR
Two separate 10x lanes of 10 individually hashed samples: Control_spleen, Bone.Marrow.LCMV.D7, IEL.LCMV.D7, LPL.LCMV.D7, Lung.Draining.LN, Lung.LCMV.D7, Mesenteric.LN.LCMV.D7, Prostate.LCMV.D7, Salivary.LCMV.d7, Spleen.LCMV.D7.M

data_processing:
The demultiplexing, barcode process and gene/ ADT/ hash counts were generated using Cellranger software v7.0.0.
TCRab contig annotations were generating using the cellranger vdj function from Cellranger software v7.0.0. The contigs generated were then mapped to with IMGT, and TRA and TRB chains put back together to create a summary table.
GEX and FBC libraries were processed using Seurat, where RNA, ADT QC was performed, a long with HTO demultiplexing to assign each cell a sample
Assembly: mm10
Supplementary files format and content: Cellranger output files: IGT36_cells.tsv, IGT36_matrix_rna.mtx, genes.tsv, IGT36_matrix_protein.mtx, proteins.tsv,  - Processed data from GEX, ADT and HTO libraries for IGT36.
Supplementary files format and content: Cellranger output files: IGT36_summary_table.csv - Mapped TCR contigs with TCR gene annotations for VDJ library of IGT36
Supplementary files format and content: Cellranger output files: IGT38_cells.tsv, IGT38_matrix_rna.mtx, genes.tsv, IGT38_matrix_protein.mtx, proteins.tsv,  - Processed data from GEX, ADT and HTO libraries for IGT38.
Supplementary files format and content: Cellranger output files: IGT38_summary_table.csv - Mapped TCR contigs with TCR gene annotations for VDJ library of IGT38
Supplementary files format and content: Cellranger output files: IGT40_cells.tsv, IGT40_matrix_rna.mtx, genes.tsv, IGT40_matrix_protein.mtx, proteins.tsv,  - Processed data from GEX, ADT and HTO libraries for IGT40.
Supplementary files format and content: Cellranger output files: IGT40_summary_table.csv - Mapped TCR contigs with TCR gene annotations for VDJ library of IGT40
Library strategy: TCR-seq

value: siIEL, siLPL, prostate, SG, lung, bone marrow, spleen, mesenteric lymph nodes, mediastinal lymph nodes

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

value: TRUE

tag: exp name

value: Pan organ and time course analysis of T cells in acute LCMV (armstrong day 60)

value: Goldrath

value: P14 and SMARTA > wt

value: male

tag: infection agent

tag: infection dose

tag: prep description

tag: organ

value: bone marrow

tag: organ uberon_id

tag: t specificity

tag: target cells

tag: batch


description:
Library name: I40H5_bonemarrow_LCMVarm_D60_allT_P14_SMARTA_mouse0142_GEX
Two separate 10x lanes of 10 individually hashed samples: Control_spleen, Bone.Marrow.LCMV.D7, IEL.LCMV.D7, LPL.LCMV.D7, Lung.Draining.LN, Lung.LCMV.D7, Mesenteric.LN.LCMV.D7, Prostate.LCMV.D7, Salivary.LCMV.d7, Spleen.LCMV.D7.M

tag: tissue

tag: lab

tag: organism name

tag: strain

tag: genetics

tag: Sex

tag: age weeks

tag: pool of_mice

value: FALSE

tag: jax

value: LCMV armstrong

value: 2?ó10E5 PFU

value: anti-CD45 IV injection before tissue harvest, mechanical dissociation alone

value: P14, SMARTA

value: all T including P14 and SMARTA

tag: gating strategy

tag: sample comments


title: sg2_0_3

city: Shanghai

first: Luzhang

last: Ji

address: 1239 Siping Rd.

country: China

institute: Tongji University

description: Library name: sg2_0_3

data_processing:
Pair-end FASTQ files were mapped to the Mus_musculus.GRCm38.101 reference genomes, via using the HISAT2 package. Then, the FPKM values were calculated with StringTie and Ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html). Differential gene expression was analyzed using DESeq2, with genes having a P value ≤ 0.05 and absolute fold change ≥ 2 recognized as differentially expressed genes (DEGs). Heatmaps were generated, and Gene Ontology (GO) and KEGG pathway analyses were performed on DEGs using the OmicStudio tools at https://www.omicstudio.cn/tool. Gene set enrichment analysis (GSEA) was conducted using GSEA (v4.1.0) and MSigDB to identify gene sets involved in specific pathways.
Assembly: Mus_musculus.GRCm38.101
Supplementary files format and content: Excel file including FRKM values for each sample

source_name: smooth muscle cell

extract_protocol:
High-throughput mRNA sequencing was performed by the LC-Bio Technology co.ltd., (HangZhou, China). The quality of total RNAs was assessed by BioAnalyzer 2100 (Agilent Technologies).
RNA libraries were constructed with TruSeq Stranded Total RNA Library Prep kit (Illumina). Libraries were quality-controlled for size distribution and quantified with Qubit Fluorometer (Thermo Fisher Scientific). The libraries were sequenced on an Illumina HiSeq sequencer for 150-bp paired-end reads according to the manufacturer’s instructions.

tag: cell line

value: smooth muscle cell

tag: genotype

tag: treatment

value: Vehicle


title: Single nuclei, Subacute Day 7 post injection of saline,  biol rep 3

value: Cardiac

tag: disease state

value: IR surgery

value: Intramyocardial injection of saline


title: Single nuclei, Subacute Day 7 post injection of saline,  biol rep 1 and 2


title: sg2_0_2

description: Library name: sg2_0_2


title: HME_MSL3_1

description: Library name: HME_MSL3_1

tag: cell type

value: immortalized mammary epithelial cells

value: MSL3 KO

value: Acute deletion of the indicated gene via crRNA transfection in Cas9 expressing cells


title: 92_pos

city: Geneva

first: Celine

last: Delucinge

address: 1 rue Michel Servet

department: iGE3 Genomics Platform

country: Switzerland

institute: University of Geneva

description: Library name: Sample 4

data_processing:
Illumina bcl2fastq software (v.2.20.0) used for basecalling.
Sequenced reads were mapped to UCSC hg38 whole genome using STAR v2.7.0f with default parameters
Raw counts are produced by htseq-count (HTSeq v.0.9.1)
Normalization and differential expression analysis were performed with edgeR v.3.38.4
Assembly: UCSC hg38
Supplementary files format and content: rawcounts.txt = tab-delimited text files include rawcount values for each Sample
Supplementary files format and content: log2normcounts.txt = tab-delimited text files include normalized expression values(log 2 cpm = count per millions) for each Sample

growth_protocol: fresh PBMC isolation, FACS sorted c-Met+ CD4 T cells

extract_protocol:
Venous blood was collected in vacutainer K2E tubes containing EDTA (Becton Dickinson) and CSF was collected in 15 mL Falcon tubes via lumbar puncture from MS and NIND patients. CSF was collected and kept on ice until processing, then centrifuged at 400 g for 10 minutes. The cell pellet was gently resuspended in ice-cold phosphate-buffered saline (PBS; Thermo-Fisher #10010072) for flow cytometry staining, performed within 2 hours after lumbar puncture. Whole blood was processed for the isolation of PBMCs by density gradient centrifugation using Ficoll Paque Plus (GE Healthcare). A fraction of PBMCs was resuspended in ice-cold PBS for flow cytometric analysis, and the remaining cells were cryopreserved using 10% DMSO in fetal bovine serum (Gibco) and stored in liquid nitrogen. CD4 T cells were magnetically isolated from PBMCs using CD4 microbeads (Miltenyi Biotec), stained with anti-human CD3 (UCHT1, Biolegend), anti-human CD4 (SK3, BD Biosciences), anti-human c-Met (95106, R&D), and DAPI, and sorted on a FACSAria™ II to >95% purity for use in transmigration assays and RNA isolation for bulk RNA sequencing. FACS-sorted T cell subsets were washed with PBS and resuspended in RNA lysis solution with 1% DTT, and total RNA was extracted using the Nucleospin RNA kit (Macherey-Nagel). Complementary DNA was synthesized from total RNA using a reaction mix containing Tris-aminoMethane (200 mM), KCl (500 mM), MgCl₂ (0.2 M; Sigma-Aldrich), DTT (100 mM; Invitrogen), random hexamers (50 mM; Invitrogen), oligo(dT)₁₅ primer (100 mg/ml; Promega), dNTP mix (10 mM; Promega), RNAsin (40 U/ml; Promega), and SuperScript™ II (200 U/ml; Invitrogen). After incubation at 42 °C for 50 minutes and inactivation at 99 °C for 3 minutes, cDNA was diluted and stored at −20 °C until use. Bulk RNA sequencing was performed on sorted c-Met⁻ and c-Met⁺ CD4 T cells using the SMART-Seq v4 kit (Clontech) for reverse transcription and cDNA amplification according to the manufacturer’s instructions, starting with 1 ng total RNA. 200 pg of cDNA were used for library preparation with the Nextera XT kit (Illumina), and library molarity and quality were assessed with the Qubit and Tapestation using a DNA High Sensitivity chip (Agilent Technologies). Libraries were sequenced on a NovaSeq 6000 Illumina sequencer for SR100 reads, with an average depth of approximately 35 million reads per sample.
Illumina TruSeq HT stranded mRNA

tag: subject


title: HME_MSL2_3

description: Library name: HME_MSL2_3

value: MSL2 KO


title: sg2_0_1

description: Library name: sg2_0_1


description:
Library name: I40H4_salivarygland_LCMVarm_D60_allT_P14_SMARTA_mouse0142_TCR
Two separate 10x lanes of 10 individually hashed samples: Control_spleen, Bone.Marrow.LCMV.D7, IEL.LCMV.D7, LPL.LCMV.D7, Lung.Draining.LN, Lung.LCMV.D7, Mesenteric.LN.LCMV.D7, Prostate.LCMV.D7, Salivary.LCMV.d7, Spleen.LCMV.D7.M

tag: tissue

value: siIEL, siLPL, prostate, SG, lung, bone marrow, spleen, mesenteric lymph nodes, mediastinal lymph nodes

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

value: TRUE

tag: exp name

value: Pan organ and time course analysis of T cells in acute LCMV (armstrong day 60)

value: Goldrath

value: P14 and SMARTA > wt

value: male

tag: infection agent

tag: infection dose

tag: prep description

value: anti-CD45 IV injection before tissue harvest, collagenase I

tag: organ

value: submandibular gland

tag: organ uberon_id

tag: t specificity

tag: target cells

value: IV- CD45+ CD3e+

value: 100x10E3 SMARTA (male, CD45.1.2) and 50x10E3 P14 (male, CD45.1), intravenous, 1 day before infection

value: T cells

tag: batch


description:
Library name: I40H4_salivarygland_LCMVarm_D60_allT_P14_SMARTA_mouse0142_GEX
Two separate 10x lanes of 10 individually hashed samples: Control_spleen, Bone.Marrow.LCMV.D7, IEL.LCMV.D7, LPL.LCMV.D7, Lung.Draining.LN, Lung.LCMV.D7, Mesenteric.LN.LCMV.D7, Prostate.LCMV.D7, Salivary.LCMV.d7, Spleen.LCMV.D7.M

tag: lab

tag: organism name

tag: strain

tag: genetics

tag: Sex

tag: age weeks

tag: pool of_mice

value: FALSE

tag: jax

value: LCMV armstrong

value: 2?ó10E5 PFU

value: P14, SMARTA

value: all T including P14 and SMARTA

tag: gating strategy

tag: sample comments


title: 81_pos

description: Library name: Sample 2

tag: cell type

tag: subject


title: HME_MSL2_2

description: Library name: HME_MSL2_2

tag: cell line

value: immortalized mammary epithelial cells

tag: genotype

value: MSL2 KO

tag: treatment

value: Acute deletion of the indicated gene via crRNA transfection in Cas9 expressing cells


title: sg2_R_1

description: Library name: sg2_R_1

value: smooth muscle cell

value: rhCTHRC1 treatment


title: HME_MSL2_1

description: Library name: HME_MSL2_1


title: R26_R_2

description: Library name: R26_R_2


title: 81_neg

description: Library name: Sample 1


description:
Library name: I40H4_salivarygland_LCMVarm_D60_allT_P14_SMARTA_mouse0142_FBC
Two separate 10x lanes of 10 individually hashed samples: Control_spleen, Bone.Marrow.LCMV.D7, IEL.LCMV.D7, LPL.LCMV.D7, Lung.Draining.LN, Lung.LCMV.D7, Mesenteric.LN.LCMV.D7, Prostate.LCMV.D7, Salivary.LCMV.d7, Spleen.LCMV.D7.M

data_processing:
The demultiplexing, barcode process and gene/ ADT/ hash counts were generated using Cellranger software v7.0.0.
TCRab contig annotations were generating using the cellranger vdj function from Cellranger software v7.0.0. The contigs generated were then mapped to with IMGT, and TRA and TRB chains put back together to create a summary table.
GEX and FBC libraries were processed using Seurat, where RNA, ADT QC was performed, a long with HTO demultiplexing to assign each cell a sample
Assembly: mm10
Supplementary files format and content: Cellranger output files: IGT36_cells.tsv, IGT36_matrix_rna.mtx, genes.tsv, IGT36_matrix_protein.mtx, proteins.tsv,  - Processed data from GEX, ADT and HTO libraries for IGT36.
Supplementary files format and content: Cellranger output files: IGT36_summary_table.csv - Mapped TCR contigs with TCR gene annotations for VDJ library of IGT36
Supplementary files format and content: Cellranger output files: IGT38_cells.tsv, IGT38_matrix_rna.mtx, genes.tsv, IGT38_matrix_protein.mtx, proteins.tsv,  - Processed data from GEX, ADT and HTO libraries for IGT38.
Supplementary files format and content: Cellranger output files: IGT38_summary_table.csv - Mapped TCR contigs with TCR gene annotations for VDJ library of IGT38
Supplementary files format and content: Cellranger output files: IGT40_cells.tsv, IGT40_matrix_rna.mtx, genes.tsv, IGT40_matrix_protein.mtx, proteins.tsv,  - Processed data from GEX, ADT and HTO libraries for IGT40.
Supplementary files format and content: Cellranger output files: IGT40_summary_table.csv - Mapped TCR contigs with TCR gene annotations for VDJ library of IGT40
Library strategy: CITE-seq

tag: tissue

value: siIEL, siLPL, prostate, SG, lung, bone marrow, spleen, mesenteric lymph nodes, mediastinal lymph nodes

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

value: TRUE

tag: exp name

value: Pan organ and time course analysis of T cells in acute LCMV (armstrong day 60)

value: Goldrath

value: P14 and SMARTA > wt

tag: infection agent

tag: infection dose

tag: prep description

tag: organ

tag: organ uberon_id

tag: t specificity

tag: target cells


title: R26_R_3

description: Library name: R26_R_3


title: HME_MSL1_3

description: Library name: HME_MSL1_3

tag: cell type

value: MSL1 KO


description:
Library name: I40H3_prostate_LCMVarm_D60_allT_P14_SMARTA_mouse0142_TCR
Two separate 10x lanes of 10 individually hashed samples: Control_spleen, Bone.Marrow.LCMV.D7, IEL.LCMV.D7, LPL.LCMV.D7, Lung.Draining.LN, Lung.LCMV.D7, Mesenteric.LN.LCMV.D7, Prostate.LCMV.D7, Salivary.LCMV.d7, Spleen.LCMV.D7.M

tag: lab

tag: organism name

tag: strain

tag: genetics

tag: Sex

value: male

tag: age weeks

tag: pool of_mice

tag: jax

value: anti-CD45 IV injection before tissue harvest, collagenase I

value: prostate gland

tag: gating strategy

value: IV- CD45+ CD3e+

tag: sample comments

value: 100x10E3 SMARTA (male, CD45.1.2) and 50x10E3 P14 (male, CD45.1), intravenous, 1 day before infection

value: T cells

tag: batch


title: R26_0_3

description: Library name: R26_0_3

tag: cell line

tag: genotype

tag: treatment

value: Vehicle


title: HME_MSL1_2

description: Library name: HME_MSL1_2

value: immortalized mammary epithelial cells


title: R26_R_1

description: Library name: R26_R_1


title: HME_TNP2_3

description: Library name: HME_TNP2_3

value: Ctrl KO

value: Acute deletion of the indicated gene via crRNA transfection in Cas9 expressing cells


description:
Library name: I40H3_prostate_LCMVarm_D60_allT_P14_SMARTA_mouse0142_GEX
Two separate 10x lanes of 10 individually hashed samples: Control_spleen, Bone.Marrow.LCMV.D7, IEL.LCMV.D7, LPL.LCMV.D7, Lung.Draining.LN, Lung.LCMV.D7, Mesenteric.LN.LCMV.D7, Prostate.LCMV.D7, Salivary.LCMV.d7, Spleen.LCMV.D7.M

tag: tissue

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

tag: exp name

value: FALSE

tag: infection agent

value: LCMV armstrong

tag: infection dose

value: 2?ó10E5 PFU

tag: prep description

tag: organ

tag: organ uberon_id

tag: t specificity

value: P14, SMARTA

value: all T including P14 and SMARTA


title: D6-18-2-4

city: Athens

first: Chad

middle: Michael

last: Paton

state: Georgia

address: 100 Cedar St.

department: Nutritional Sciences

institute: University of Georgia

data_processing:
Single-read sequencing was performed on Illumina (Illumina, San Diego, CA) NexSeq 500 (PE75)
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic with following settings: adapters/TruSeq3-SE.fa:2:30:10 LEADING:10 TRAILING:10 SLIDINGWINDOW:4:15 MINLEN:30.
Trimmed, filtered reads were then mapped against MM39 using the STAR aligner, ver. 2.7.1a.
HTSeq, ver. 0.9.1 (33) was used to extract raw count data from each BAM file and output files containing gene-to-count information for each sample were concatenated to generate a raw count matrix that was manually filtered to remove rows containing zero counts or rows whose summation of counts was less than 50.
Count matrix normalization, DESeq2
Assembly: mm39
Supplementary files format and content: Excel sheet including DESeq values for each sample

source_name: C2C12 cells, 18:2, Day6

growth_protocol: C2C12 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
100uM of bovine serum albumin-conjugated linoleic acid (18:2n6) or 10 ng/mL of recombinant mouse ANGPTL4 was added to the cellls during differentiation.
RNA was harvested and total RNA (RIN value >7.0) was submitted.
RNA-Seq libraries were synthesized using a QuantSeq 3’ mRNA-Seq library kit following manufacturer's protocols.

treatment_protocol: Skeletal muscle differentiation was induced by changing 10% FBS to 2% Horse serum.

value: C2C12 cells

tag: cell type

value: Mouse myoblast

value: WT

value: 18:2 linoleic acid

tag: time

value: Day 6


description:
Library name: I40H5_bonemarrow_LCMVarm_D60_allT_P14_SMARTA_mouse0142_FBC
Two separate 10x lanes of 10 individually hashed samples: Control_spleen, Bone.Marrow.LCMV.D7, IEL.LCMV.D7, LPL.LCMV.D7, Lung.Draining.LN, Lung.LCMV.D7, Mesenteric.LN.LCMV.D7, Prostate.LCMV.D7, Salivary.LCMV.d7, Spleen.LCMV.D7.M

value: siIEL, siLPL, prostate, SG, lung, bone marrow, spleen, mesenteric lymph nodes, mediastinal lymph nodes

value: TRUE

value: Pan organ and time course analysis of T cells in acute LCMV (armstrong day 60)

tag: lab

value: Goldrath

tag: organism name

tag: strain

tag: genetics

value: P14 and SMARTA > wt

tag: Sex

value: male

tag: age weeks

tag: pool of_mice

tag: jax

value: anti-CD45 IV injection before tissue harvest, mechanical dissociation alone

value: bone marrow

tag: target cells

tag: gating strategy

value: CD45+ CD3e+

tag: sample comments

tag: batch


title: Donor_3_alveolar

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

institute: University of Basel

description: alveolar basal cells cultured from transbronchial biopsies

data_processing:
Read quality was assessed with the FastQC tool (version 0.11.5)
STARsolo (version 2.7.9a) was used to perform sample and cell demultiplexing, and alignment of reads to the human genome (hg38) and UMI counting on gene models from Ensembl 102. The options --outFilterType=BySJout --outFilterMultimapNmax=10 --outSAMmultNmax=1 --outFilterScoreMin=30 --soloCBmatchWLtype=1MM_multi_Nbase_pseudocounts --soloUMIfiltering=MultiGeneUMI_CR --soloUMIdedup=1MM_CR --soloType=CB_UMI_Simple –soloStrand=Reverse were used.
Processing of the UMI counts matrix was performed using the Bioconductor packages DropletUtils (version 1.16.0; function emptyDrops using 5000 iterations, the option test.ambient=TRUE, a lower threshold of 100 UMIs and an FDR threshold of 0.1%), scran (version 1.24.1) and scater (version 1.24.0), following mostly the steps illustrated in the OSCA book (http://bioconductor.org/books/3.15/OSCA/). Cells with less than 5% or more than 20% of UMI counts attributed to mitochondrial genes, with less than 10% or more than 30% of UMI counts attributed to ribosomal protein genes, with less than 4000 UMI counts, or with less than 2500 detected genes were excluded. The presence of doublet cells was investigated with the scDblFinder package (version 1.10.0), and suspicious cells were filtered out (score > 0.9).
Assembly: hg38
Supplementary files format and content: UMIsMatrix.txt.gz: TSV file (tab separated values) including UMI counts for each cell and gene (ENSEMBL ID release 102). Column headers include the sample ID and cell barcode sequence separated by a dash (e.g., "BSSE_QGF_173112-AAACCCAAGGTCACAG")
Supplementary files format and content: CellMetadata.txt.gz: TSV file (tab separated values) including metadata for cells used in the paper. The information include the cluster assignment and tSNE coordinates, before and after MNN corrrection for sample-specific effects.

source_name: basal cells

growth_protocol: Biopsies were placed into cell culture-treated plastic dishes containing an epithelial cell-specific growth medium (Cnt-PR-A). After 5-7 days, tissue was removed and the outgrown cells were trypsinized and expanded.

extract_protocol:
Cultured cells were harvested at passage 1 for scRNA-seq
Cell suspensions from each sample were loaded each into a single channel of a 10× Genomics Chromium Single Cell Controller. Single-cell capture and cDNA and library preparation were performed at the Genomics Facility Basel of the ETH Zurich, Basel, with a Single Cell 3’ v3 Reagent Kit (10× Genomics) according to manufacturer’s instructions.

treatment_protocol: No treatment

tag: donor

value: basal cells

tag: disease

value: interstitial lung disease

value: female


title: 92_neg

description: Library name: Sample 3

tag: subject


title: Donor_2_airway

description: airway basal cells cultured from airway mucosal biopsies

tag: cell type


description:
Library name: I40H3_prostate_LCMVarm_D60_allT_P14_SMARTA_mouse0142_FBC
Two separate 10x lanes of 10 individually hashed samples: Control_spleen, Bone.Marrow.LCMV.D7, IEL.LCMV.D7, LPL.LCMV.D7, Lung.Draining.LN, Lung.LCMV.D7, Mesenteric.LN.LCMV.D7, Prostate.LCMV.D7, Salivary.LCMV.d7, Spleen.LCMV.D7.M

tag: tissue

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

tag: exp name

value: FALSE

tag: infection agent

value: LCMV armstrong

tag: infection dose

value: 2?ó10E5 PFU

tag: prep description

value: anti-CD45 IV injection before tissue harvest, collagenase I

tag: organ

value: prostate gland

tag: organ uberon_id

tag: t specificity

value: P14, SMARTA

value: all T including P14 and SMARTA

value: IV- CD45+ CD3e+

value: 100x10E3 SMARTA (male, CD45.1.2) and 50x10E3 P14 (male, CD45.1), intravenous, 1 day before infection

value: T cells


title: R26_0_2

description: Library name: R26_0_2

tag: cell line

value: smooth muscle cell

tag: genotype

tag: treatment

value: Vehicle


title: HME_MSL1_1

description: Library name: HME_MSL1_1

value: immortalized mammary epithelial cells

value: MSL1 KO

value: Acute deletion of the indicated gene via crRNA transfection in Cas9 expressing cells


title: Donor_2_alveolar

tag: donor

value: basal cells

tag: disease

value: interstitial lung disease

tag: Sex

value: male


description:
Library name: I40H2_spleen_LCMVarm_D60_allT_P14_SMARTA_mouse0142_TCR
Two separate 10x lanes of 10 individually hashed samples: Control_spleen, Bone.Marrow.LCMV.D7, IEL.LCMV.D7, LPL.LCMV.D7, Lung.Draining.LN, Lung.LCMV.D7, Mesenteric.LN.LCMV.D7, Prostate.LCMV.D7, Salivary.LCMV.d7, Spleen.LCMV.D7.M

tag: tissue

value: siIEL, siLPL, prostate, SG, lung, bone marrow, spleen, mesenteric lymph nodes, mediastinal lymph nodes

tag: immgent igt_10xlane_id

value: TRUE

value: Pan organ and time course analysis of T cells in acute LCMV (armstrong day 60)

tag: lab

value: Goldrath

tag: organism name

tag: strain

tag: genetics

value: P14 and SMARTA > wt

tag: age weeks

tag: pool of_mice

value: FALSE

tag: jax

value: LCMV armstrong

value: anti-CD45 IV injection before tissue harvest, mechanical dissociation alone

value: spleen

tag: target cells

tag: gating strategy

value: CD45+ CD3e+

tag: sample comments

tag: cell type

tag: batch


title: HME1_MSL3ko_EdU_HUseq_Rep2

description: Library name: HME1_MSL3ko_EdU_HUseq_Rep2

library_source: genomic

data_processing:
*library strategy: EdU-Huseq
EdU-HUseq reads were aligned to the hg38 genome using nf-core/chipseq pipeline version 2.0.0 with bwa aligner.
BigWig files were generated within the nf-core/chipseq pipeline
Assembly: hg38
Supplementary files format and content: bigWig of aligned samples for genome browser visualization

molecule: genomic DNA

extract_protocol:
Stable Ctrl-KO, MSL3-KO and Myc overexpressing HME1 cells were seeded in T150 flasks. When 50% confluency was reached, cells were treated with 2μM Palbociclib (Universal Biologicals, S116) for 20 hours to synchronize them in G1/S. Cells were washed twice with medium and treated with 10mM Hydroxyurea (Merck Life Science, H8627) for 7 hours to stop them at the entry of S phase. After two washes with medium, cells were released in medium containing 25μM EdU (Universal Biologicals, 10540) for 90 minutes. Cells were collected and fixed in 90% MetOH. EdU-labelled DNA was isolated as previously described[5]. Briefly, cells were permeabilized in 0.2% Triton-X100 in PBS for 30 minutes and EdU was detected using a biotin-azide click reaction by incubating cells in click-it reaction cocktail (100 mM TrisHCl pH 8, 4mM CuSO4, 100mM sodium-L-ascorbate, 50µM Biotin Azide - Thermo Fisher Scientific, B10184) for 30 minutes. After washes, cells were incubated in lysis buffer (10 mM Tris-HCl, pH 8, 10 mM EDTA, 0.5% SDS, 0.2 mg/ml Proteinase K) for 3 hours at 50ºC. DNA was purified using phenol/chloroform/isoamyl alcohol, resuspended in TE and sonicated using Bioruptor Pico. EdU-labelled DNA was captured using Dynabeads MyOne Streptavidin C1 (Thermo Fisher Scientific, 65001), washed and eluted from beads using 2% β-mercaptoethanol. DNA was purified with solid-phase reversible immobilization (SPRI) beads (Agencourt AMPure XP, Beckman Coulter), and then quantified with QuantiFluor (Promega, E2670). For HighResEdU-HUseq sample, stable Ctrl-KO HME1 cells were seeded in T150 flasks. When 50% confluency was reached, cells were treated with 100ng/ml Nocodazole (Merck Life Science, SML1665) for 8 hours. Cells in mitosis were detached by shake-off in the same culture medium, pelleted, washed once with PBS and plated in medium containing 25μM EdU (Universal Biologicals, 10540) and 10mM Hydroxyurea (Merck Life Science, H8627). After 16 hours, cells were collected and fixed in 90% MetOH. EdU-labelled DNA isolation and library preparation were carried out as described for EdU-HUseq.
DNA libraries were prepared using the NEBNext UltraII DNA Library Prep Kit for Illumina (New England Biolabs, E7645L).

tag: pull down

value: EdU

tag: cell line

tag: genotype

value: MSL3 KO


title: HME1_WT_HighResEdU_HUseq

description: Library name: HME1_WT_HighResEdU_HUseq

value: immortalized mammary epithelial cells

value: Ctrl KO


title: HME1_MSL3ko_EdU_HUseq_Rep1

description: Library name: HME1_MSL3ko_EdU_HUseq_Rep1


title: WT_T_0_R_2

description: Library name: WT_T_0_R_2

value: smooth muscle cell

value: WT

tag: treatment

value: rhCTHRC1 treatment


title: WT_T_0_R_3

description: Library name: WT_T_0_R_3


description:
Library name: I40H2_spleen_LCMVarm_D60_allT_P14_SMARTA_mouse0142_FBC
Two separate 10x lanes of 10 individually hashed samples: Control_spleen, Bone.Marrow.LCMV.D7, IEL.LCMV.D7, LPL.LCMV.D7, Lung.Draining.LN, Lung.LCMV.D7, Mesenteric.LN.LCMV.D7, Prostate.LCMV.D7, Salivary.LCMV.d7, Spleen.LCMV.D7.M

tag: tissue

value: siIEL, siLPL, prostate, SG, lung, bone marrow, spleen, mesenteric lymph nodes, mediastinal lymph nodes

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

tag: exp name

tag: Sex

value: male

tag: infection agent

tag: infection dose

value: 2?ó10E5 PFU

tag: prep description

tag: organ

tag: organ uberon_id

tag: t specificity

value: P14, SMARTA

value: all T including P14 and SMARTA

value: 100x10E3 SMARTA (male, CD45.1.2) and 50x10E3 P14 (male, CD45.1), intravenous, 1 day before infection

value: T cells


title: R26_0_1

description: Library name: R26_0_1

value: Vehicle


title: Donor_1_alveolar

tag: donor

tag: cell type

value: basal cells

tag: disease

value: interstitial lung disease

value: female


title: WT_T_0_R_1

description: Library name: WT_T_0_R_1

tag: cell line

tag: genotype

tag: treatment


title: HME1_WT_EdU_HUseq_Rep2

description: Library name: HME1_WT_EdU_HUseq_Rep2

tag: pull down

value: EdU


title: I40H1_spleen_allT_mouse0141_TCR

description:
Library name: I40H1_spleen_allT_mouse0141_TCR
Two separate 10x lanes of 10 individually hashed samples: Control_spleen, Bone.Marrow.LCMV.D7, IEL.LCMV.D7, LPL.LCMV.D7, Lung.Draining.LN, Lung.LCMV.D7, Mesenteric.LN.LCMV.D7, Prostate.LCMV.D7, Salivary.LCMV.d7, Spleen.LCMV.D7.M

tag: tissue

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

value: spleen

value: TRUE

value: Pan organ and time course analysis of T cells in acute LCMV (armstrong day 60)

tag: lab

value: Goldrath

tag: organism name

tag: strain

tag: genetics

value: wt

tag: age weeks

tag: pool of_mice

value: FALSE

tag: jax

value: mechanical dissociation alone

tag: target cells

value: all T

tag: gating strategy

value: CD45+ CD3e+

tag: batch


title: WT40-2-2

city: Berlin

first: Marco

last: Preussner

address: Takustrasse 6

country: Germany

institute: FU berlin

data_processing:
For alignment and quantification of gene.tpm and psi files we used the Whippet-quant function of Whippet v0.11. This aligns and quantifies in one step
As supplemenatry files the primary rMATS output for pairwise comparisons of skipped exon events is provided
Assembly: hg38
Supplementary files format and content: contains whippet derived gene expression information in transcripts per million per gene
Supplementary files format and content: contains whippet-derived percentage splie in

molecule: polyA RNA

source_name: HeLa

growth_protocol: HeLa or Hek293 cells were grown in DMEM supplemented with 10% fetal bovine serum and 1% Penicillin/Streptomycin (Invitrogen).

extract_protocol:
Trizol (Bio&Sell) was used for RNA extraction as described in the user manual. Pure RNA was optained using DNAseI digestion and repurification.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Two clones of HeLa cells were were incubated for 24-hours at 32, 37 or 40°C. Hek293 cells were incubated at 39°C for 12-hours, then treated with ocadaic acid (OA) or DMSO as a control for further 2-hours at 33°C or 39°C. RNA was extracted and analyzed by RNA-Seq.

tag: cell line

value: HeLa


title: Donor_3_airway

tag: donor

tag: cell type

tag: disease

tag: Sex


title: HME1_WT_EdU_HUseq_Rep1

description: Library name: HME1_WT_EdU_HUseq_Rep1

tag: pull down

value: immortalized mammary epithelial cells

tag: genotype

value: Ctrl KO


title: WT_C_0_0_3

description: Library name: WT_C_0_0_3

value: smooth muscle cell

value: WT

tag: treatment

value: Vehicle


title: I40H1_spleen_allT_mouse0141_GEX

description:
Library name: I40H1_spleen_allT_mouse0141_GEX
Two separate 10x lanes of 10 individually hashed samples: Control_spleen, Bone.Marrow.LCMV.D7, IEL.LCMV.D7, LPL.LCMV.D7, Lung.Draining.LN, Lung.LCMV.D7, Mesenteric.LN.LCMV.D7, Prostate.LCMV.D7, Salivary.LCMV.d7, Spleen.LCMV.D7.M

tag: tissue

value: siIEL, siLPL, prostate, SG, lung, bone marrow, spleen, mesenteric lymph nodes, mediastinal lymph nodes

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

tag: exp name

tag: lab

tag: organism name

value: male

tag: prep description

tag: organ

tag: organ uberon_id

value: T cells


title: WT40-2-1

tag: cell line


title: HME1_Myc_EdU_HUseq_Rep2

description: Library name: HME1_Myc_EdU_HUseq_Rep2

value: EdU

tag: cell type

value: Ctrl KO + Myc overexpression


title: I40H1_spleen_allT_mouse0141_FBC

description:
Library name: I40H1_spleen_allT_mouse0141_FBC
Two separate 10x lanes of 10 individually hashed samples: Control_spleen, Bone.Marrow.LCMV.D7, IEL.LCMV.D7, LPL.LCMV.D7, Lung.Draining.LN, Lung.LCMV.D7, Mesenteric.LN.LCMV.D7, Prostate.LCMV.D7, Salivary.LCMV.d7, Spleen.LCMV.D7.M

value: spleen

value: TRUE

value: Pan organ and time course analysis of T cells in acute LCMV (armstrong day 60)

value: Goldrath

tag: strain

tag: genetics

tag: Sex

tag: age weeks

tag: pool of_mice

tag: jax

tag: target cells

tag: gating strategy

tag: batch


title: WT40-1-2

tag: treatment


title: WT_C_0_0_2

description: Library name: WT_C_0_0_2

tag: genotype


title: Donor_1_airway

tag: donor

value: basal cells

tag: disease

value: interstitial lung disease

value: female


title: WT_C_0_0_1

description: Library name: WT_C_0_0_1


description:
Library name: I40H10_LNmediastinal_LCMVarm_D60_allT_P14_SMARTA_mouse0142_TCR
Two separate 10x lanes of 10 individually hashed samples: Control_spleen, Bone.Marrow.LCMV.D7, IEL.LCMV.D7, LPL.LCMV.D7, Lung.Draining.LN, Lung.LCMV.D7, Mesenteric.LN.LCMV.D7, Prostate.LCMV.D7, Salivary.LCMV.d7, Spleen.LCMV.D7.M

tag: tissue

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

tag: exp name

tag: lab

tag: organism name

value: P14 and SMARTA > wt

value: FALSE

tag: infection agent

value: LCMV armstrong

tag: infection dose

value: 2?ó10E5 PFU

tag: prep description

value: anti-CD45 IV injection before tissue harvest, mechanical dissociation alone

tag: organ

value: mediastinal lymph node

tag: t specificity

value: P14, SMARTA

value: all T including P14 and SMARTA

value: CD45+ CD3e+

tag: sample comments

value: 100x10E3 SMARTA (male, CD45.1.2) and 50x10E3 P14 (male, CD45.1), intravenous, 1 day before infection


description:
Library name: I40H2_spleen_LCMVarm_D60_allT_P14_SMARTA_mouse0142_GEX
Two separate 10x lanes of 10 individually hashed samples: Control_spleen, Bone.Marrow.LCMV.D7, IEL.LCMV.D7, LPL.LCMV.D7, Lung.Draining.LN, Lung.LCMV.D7, Mesenteric.LN.LCMV.D7, Prostate.LCMV.D7, Salivary.LCMV.d7, Spleen.LCMV.D7.M

value: siIEL, siLPL, prostate, SG, lung, bone marrow, spleen, mesenteric lymph nodes, mediastinal lymph nodes

tag: strain

tag: genetics

tag: Sex

value: male

tag: age weeks

tag: pool of_mice

tag: jax

value: spleen

tag: organ uberon_id

tag: target cells

tag: gating strategy

tag: cell type

value: T cells

tag: batch


title: WT40-1-1

tag: cell line

value: HeLa

tag: treatment


title: A_R_3

description: Library name: A_R_3

value: smooth muscle cell

tag: genotype

value: WT

value: ADAM9i treatment+rhCTHRC1


title: CScreen_MAP3K7

city: bethesda

first: Seolkyoung

last: Jung

state: MD

address: 10 Center Dr

department: NIAMS

institute: NIH

description: Library name: CScreen_MAP3K7

data_processing:
base calling: illumina CASAVA 1.8.2
CRISPR screen: build index on artificial genome which have  specific sgRNA sequence and common template sequence with stagger sequence
CRISPR screen: bowtie/1.1.2 with -S -m 1 -p 4 -a --best --strata -n 2 -l 80
CRISPR screen: samtools idxstats and custom perl script to generate table for counts and fraction on each gene
ChIP-Seq_density: alignment: bowtie-1.1.1/bowtie -S -m 1 -p 20 -a --best --strata -n 2 -l 50
ChIP-Seq_density: filtering (uniquely aligned reads): samtools-0.1.19-1.2/samtools view -S -b -F4
ChIP-Seq_density: normalized tag density: custom script, maximum 2 reads with the same start position allowed
mRNA-Seq_density:alignment: gsnap --use-sarray=0 --novelsplicing=0 --use-splicing refseq.splices.iit --format=sam -B 4
mRNA-Seq_density: filtering: samtools-1.2/samtools view -S -b -F132 -q 20
mRNA-Seq density: normalized tag density: bedtools-2.25/genomeCoverageBed -ibam -bg -split -scale normalization_factor, ucsc-314/bedGraphToBigWig
Assembly: hg19
Supplementary files format and content: Tab-separated values files
Supplementary files format and content: bigwig file
Library strategy: CRISPR screen

growth_protocol: SU-DHL-4 cells with doxycycline inducible Cas9 were described previously (Phelan et al. 2018). Cells were cultured in advanced RPMI-1640 media supplemented with 5% FBS (Gemini), 1% GlutaMAX, and 1% Penicillin-Streptomycin (Thermo Fisher Scientific). Peripheral blood mononuclear cells from healthy blood donors (NIH blood bank) were isolated over Ficoll and cryopreserved. Naïve CD19+ human B cells were isolated with EasySep Human Naïve B Cell Isolation Kit according to the manufacture’s instructions (Stemcell Technologies). Isolated B cells were grown in IMDM media supplemented with 10% FBS (Gemini), 50 µM of beta-mercaptoethanol, and 1% Penicillin-Streptomycin (Thermo Fisher Scientific). All cells were cultured at 37°C and 5% CO2 in a humidified incubator.

extract_protocol:
CRISPR screens:
SU-DHL-4 reporter cells were transduced with the Brunello library. For each screen, 6 replicates with 15 million cells (90 million in total) were transduced at a density of 5 million cells/ml in a 6 well plate. The amount of virus was adjusted according to the viral titer to obtain a multiplicity of infection (MOI) of 0.3. Cells were transduced by spinfection (1,460g for 90 min and 30°C) in the presence of 6 µg/ml polybrene. Infected cells were puromycin selected 24h post infection at a final concentration of 4 µg/ml. On day 3 post infection, the MOI was verified and cells were split in medium containing 200 ng/ml doxycycline. Cells were split every other day with fresh doxycycline containing medium. On day 10 post infection, for each of the six replicates 60 million cells were sorted using BD FACS Aria or Fusion cell sorters based on reporter fluorescence to capture the bottom and top 5% expressing cells. On average, for each screen 286 million cells were sorted yielding ~9 million low or high expressing cells (Table S1B). For the three mTORC1 inhibited CRISPR screens in BTG2, CD79B and OCAB reporter cell lines, 5 nM rapamycin was added on day 8 and cells were sorted on day 10 as for the other screens. Genomic DNA from sorted cells was extracted using DNeasy Blood and Tissue kit (Qiagen) according to the manufacturer’s instructions.
RNA-seq
Cells were either unperturbed, transduced with sgRNA, or treated with inhibitors as described above. Cells were split every other day and seeded at 200,000 cells/ml the day before harvest. Inhibitor treated cells were harvested on day 2 post-treatment and sgRNA transduced cells on day 10 post-infection. On the day of harvest, half a million cells were pelleted and lysed in 100 µl of the Ambion RNAqueous lysis solution. RNA was extracted and treated with DNase according to the RNAqueous-Micro Total RNA Isolation Kit protocol (Thermo Fisher Scientific). RNA-seq libraries were prepared from 500 ng of RNA using NEBNext Poly(A) mRNA Magnetic Isolation and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs).
ChIP-seq
Cells for ChIP-seq analysis were either unperturbed or transduced with sgRNA for 10 days before harvesting. The day before harvest, cells were diluted to 200,000 cells/ml. Cultured cells were fixed at room temperature for 10 min with 1% formaldehyde (Sigma) and the reaction was quenched with 125 mM glycine (Sigma). Fixed cells were washed with PBS, snap-frozen, and stored at -80°C until further processing. For ChIP, 20 million cells were resuspended in 1 ml of RIPA buffer (10 mM Tris pH 7.6, 1 mM EDTA, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, and freshly added Complete Mini EDTA free proteinase inhibitor (Roche)). Chromatin was sheared by sonication on ice using a Branson Sonifier with an amplitude of 35% and 12 cycles of 20 sec sonication followed by 30 sec of pause. Supernatant was precleared with 20 µl Dynabeads Protein A (Thermo Fisher Scientific) for 1 hour at 4°C under rotation. Precleared chromatin was incubated with BRD4 (Abcam, ab128874) or FLI1 (Abcam, ab133485) antibody overnight at 4°C under rotation. The antibody-protein solution was then captured with 40 µl of Dynabeads Protein A for 1 hour at 4°C under rotation. Antibody-bound beads were washed twice with RIPA buffer, twice with RIPA buffer containing 0.3 M NaCl, once with LiCl buffer (0.25M LiCl, 0.5% NP-40, 0.5% sodium deoxycholate), once with TE pH 8.0 containing 0.2% Triton X-100, and once with TE pH 8.0. Crosslinks were reversed by incubating the beads at 65°C for 4 hours in the presence of 0.3% SDS and 1 mg/ml Proteinase K (Thermo Fisher Scientific). ChIP DNA was column purified with ChIP DNA Clean and Concentrator kit (Zymo research).
RNA-seq
Libraries were prepared from 500 ng of RNA using NEBNext Poly(A) mRNA Magnetic Isolation and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs). Single 50 cycles of sequencing data were acquired on HiSeq3000, NovaSeq6000, NovaSeqXplus (illumina).
ChIP-Seq
Libraries were prepared using the Ovation Ultralow Library System V2. Single 50 cycles of sequencing data were acquired on NextSeq550, NovaSeq6000 (illumina)
CRISPR screen
Libraries were prepared using staggered GeCKO readout primers following the recommended instructions (Shalem et al. 2014). Deep sequencing was performed on NextSeq550 and NovaSeq6000 (Illumina) using 75bp single-end reads.

treatment_protocol:
primary human B cells:
Cells were activated with 100 ng/ml MEGACD40L (Enzo Life Sciences), 1 µg/ml CpG oligodeoxynucleotide ODN 2006 (Invivogen), 50 ng/ml human IL-2, 50 ng/ml human IL-10, and 10 ng/ml human IL-15 (all interleukins from PeproTech). Every other day the medium was fully removed and cells diluted in fresh activation medium.
Inhibitor treatments:
SU-DHL-4 or primary B cells were seeded at 0.2 million cells/ml and treated with DMSO or inhibitors. Inhibitors were purchased from MedChemExpress or Selleck Chemicals and dissolved in DMSO. Inhibitors were titrated and used at the following concentrations: rapamycin (5 nM), MK2206 (250 nM), AS1842856 (50 nM), LY2090314 (2 nM), CHIR99021 (1 µM). After two days of treatment, cells were analyzed by flow cytometry or harvested for RNA-seq.

value: B cell lymphoma

value: no


title: HME1_WT_Input

description: Library name: HME1_WT_Input

tag: pull down

value: immortalized mammary epithelial cells

value: Ctrl KO


description:
Library name: I40H10_LNmediastinal_LCMVarm_D60_allT_P14_SMARTA_mouse0142_GEX
Two separate 10x lanes of 10 individually hashed samples: Control_spleen, Bone.Marrow.LCMV.D7, IEL.LCMV.D7, LPL.LCMV.D7, Lung.Draining.LN, Lung.LCMV.D7, Mesenteric.LN.LCMV.D7, Prostate.LCMV.D7, Salivary.LCMV.d7, Spleen.LCMV.D7.M

tag: tissue

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

value: TRUE

tag: exp name

value: Pan organ and time course analysis of T cells in acute LCMV (armstrong day 60)

tag: lab

value: Goldrath

tag: organism name

value: P14 and SMARTA > wt

value: FALSE

tag: infection agent

value: LCMV armstrong

tag: infection dose

value: 2?ó10E5 PFU

tag: prep description

value: anti-CD45 IV injection before tissue harvest, mechanical dissociation alone

tag: organ

value: mediastinal lymph node

tag: t specificity


title: WT37-2-2

tag: cell line

value: HeLa


title: HME1_MSL3ko_Input

description: Library name: HME1_MSL3ko_Input

tag: cell type

value: MSL3 KO


description:
Library name: I40H10_LNmediastinal_LCMVarm_D60_allT_P14_SMARTA_mouse0142_FBC
Two separate 10x lanes of 10 individually hashed samples: Control_spleen, Bone.Marrow.LCMV.D7, IEL.LCMV.D7, LPL.LCMV.D7, Lung.Draining.LN, Lung.LCMV.D7, Mesenteric.LN.LCMV.D7, Prostate.LCMV.D7, Salivary.LCMV.d7, Spleen.LCMV.D7.M

value: siIEL, siLPL, prostate, SG, lung, bone marrow, spleen, mesenteric lymph nodes, mediastinal lymph nodes

tag: strain

tag: genetics

tag: Sex

value: male

tag: age weeks

tag: pool of_mice

tag: jax

tag: organ uberon_id

value: P14, SMARTA

tag: target cells

value: all T including P14 and SMARTA

tag: gating strategy

value: CD45+ CD3e+

tag: sample comments

value: 100x10E3 SMARTA (male, CD45.1.2) and 50x10E3 P14 (male, CD45.1), intravenous, 1 day before infection

value: T cells

tag: batch


title: HME1_MSL3ko_H4K16acAb2_Rep2

description: Library name: HME1_MSL3ko_H4K16acAb2_Rep2

data_processing:
ChIPseq reads were aligned to the hg38 genome using nf-core/chipseq pipeline version 2.0.0 with bwa aligner. In the case of H4K16ac ChIP, reads were aligned to a composite genome containing Homo sapiens hg38 and Drosophila melanogaster BDGP6 genome assemblies
BigWig files were generated within the nf-core/chipseq pipeline
For H4K16ac datasets only: replicates were merged using SAMtools merge. DeepTool multiBamSummary was used to compute the number of reads covering the top 10000 common peaks in each sample. Derived scaling factors were used to generate BigWig files through deepTools bamCoverage and WT over MSL KO corrected BigWig files were obtained through bigwigCompare with parameters --operation subtract --skipNAs -bs 1 --skipZeroOverZero. Since negative signals would not be biologically meaningful, bigWigToBedGraph and bedGraphToBigWig from UCSC tolls were applied to bring negative signals to zero.
Assembly: hg38
Supplementary files format and content: bigWig of aligned samples for genome browser visualization
Supplementary files format and content: For H4K16ac datasets only: bigWig of corrected signal after replicate merging and removal of non-specific signal retained in the KO samples

extract_protocol:
2x106 cells per pull down were cross-linked using 1% formaldehyde for 10 min. The reaction was stopped by incubation for 5 min with 0.125M glycine. After nuclear extraction and chromatin shearing by sonication, lysates were incubated overnight at 4°C with protein G Dynabeads (Thermo Fisher Scientific, 10003D) coupled with one of the following antibodies: anti-H4K16ac (Millipore, 07-329, 5g), anti-H4K16ac (Cell Signaling Technology, 13534; 1g) anti-H3K36me3 (Cell Signaling Technology, 4909S, 5l). After immunoprecipitation, beads were recovered using a magnet and washed; chromatin was eluted and cross-links reverted overnight at 65°C. DNA was purified with solid-phase reversible immobilization (SPRI) beads (Agencourt AMPure XP, Beckman Coulter), and then quantified with QuantiFluor (Promega, E2670). For H4K16ac pull-downs, Drosophila spike-in was added to normalize signal between Ctrl-KO and MSL3-KO cells. S2 Drosophila cells were processed as described above and lysates were quantified using DC Protein Assay Kit I (Bio-Rad Laboratories Ltd, 5000111). 5% chromatin was added to HME1 lysates and pull-down was carried on.
DNA libraries were prepared using the NEBNext UltraII DNA Library Prep Kit for Illumina (New England Biolabs, E7645L).

tag: chip antibody

value: Cell Signaling Technology, 13534

value: immortalized mammary epithelial cells

tag: genotype


title: WT37-2-1

tag: treatment


title: A_R_1

description: Library name: A_R_1

value: smooth muscle cell

value: WT

value: ADAM9i treatment+rhCTHRC1


description:
Library name: I36H9_lung_LCMVarm_D7_allT_P14_SMARTA_mouse0127_TCR
Two separate 10x lanes of 10 individually hashed samples: Control_spleen, Bone.Marrow.LCMV.D7, IEL.LCMV.D7, LPL.LCMV.D7, Lung.Draining.LN, Lung.LCMV.D7, Mesenteric.LN.LCMV.D7, Prostate.LCMV.D7, Salivary.LCMV.d7, Spleen.LCMV.D7.M

tag: tissue

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

value: TRUE

tag: exp name

value: Pan organ and time course analysis of T cells in acute LCMV (armstrong) infection (day 7)

tag: lab

value: Goldrath

tag: organism name

value: P14 and SMARTA > wt

value: FALSE

tag: infection agent

value: LCMV armstrong

tag: infection dose

value: 2?ó10E5 PFU

tag: prep description

value: anti-CD45 IV injection before tissue harvest, collagenase I

tag: organ

value: lung

tag: t specificity

value: IV- CD45+ CD3e+


title: HME1_MSL3ko_H4K16acAb2_Rep1

description: Library name: HME1_MSL3ko_H4K16acAb2_Rep1

tag: cell line

tag: cell type

value: MSL3 KO


title: A_0_3

description: Library name: A_0_3

tag: genotype

value: ADAM9i treatment+Vehicle


title: WT37-1-2

value: HeLa

tag: treatment


description:
Library name: I36H9_lung_LCMVarm_D7_allT_P14_SMARTA_mouse0127_GEX
Two separate 10x lanes of 10 individually hashed samples: Control_spleen, Bone.Marrow.LCMV.D7, IEL.LCMV.D7, LPL.LCMV.D7, Lung.Draining.LN, Lung.LCMV.D7, Mesenteric.LN.LCMV.D7, Prostate.LCMV.D7, Salivary.LCMV.d7, Spleen.LCMV.D7.M

tag: tissue

value: siIEL, siLPL, prostate, SG, lung, bone marrow, spleen, mesenteric lymph nodes, mediastinal lymph nodes

tag: strain

tag: genetics

tag: Sex

value: male

tag: age weeks

tag: pool of_mice

tag: jax

tag: organ uberon_id

value: P14, SMARTA

tag: target cells

value: all T including P14 and SMARTA

tag: gating strategy

tag: sample comments

value: 100x10E3 SMARTA (male, CD45.1.2) and 50x10E3 P14 (male, CD45.1), intravenous, 1 day before infection

value: T cells

tag: batch


title: HME1_WT_H4K16acAb2_Rep2

description:
Library name: HME1_WT_H4K16acAb2_Rep2
HME1_Corrected_H4K16acAb2.bigWig

tag: chip antibody

value: Cell Signaling Technology, 13534

value: immortalized mammary epithelial cells

value: Ctrl KO


title: D2-ANGPTL4-4

source_name: C2C12 cells, ANGPTL4, Day2

tag: cell line

value: C2C12 cells

value: Mouse myoblast

value: WT

tag: time

value: Day 2


title: WT37-1-1


title: HME1_Myc_EdU_HUseq_Rep1

description: Library name: HME1_Myc_EdU_HUseq_Rep1

tag: pull down

value: EdU

tag: cell type

tag: genotype

value: Ctrl KO + Myc overexpression


title: A_0_2

description: Library name: A_0_2

value: smooth muscle cell

tag: treatment

value: ADAM9i treatment+Vehicle


description:
Library name: I36H9_lung_LCMVarm_D7_allT_P14_SMARTA_mouse0127_FBC
Two separate 10x lanes of 10 individually hashed samples: Control_spleen, Bone.Marrow.LCMV.D7, IEL.LCMV.D7, LPL.LCMV.D7, Lung.Draining.LN, Lung.LCMV.D7, Mesenteric.LN.LCMV.D7, Prostate.LCMV.D7, Salivary.LCMV.d7, Spleen.LCMV.D7.M

tag: tissue

value: siIEL, siLPL, prostate, SG, lung, bone marrow, spleen, mesenteric lymph nodes, mediastinal lymph nodes

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

value: TRUE

tag: exp name

value: Pan organ and time course analysis of T cells in acute LCMV (armstrong) infection (day 7)

tag: lab

value: Goldrath

tag: organism name

tag: strain

tag: genetics

value: P14 and SMARTA > wt

value: FALSE

tag: infection agent

value: LCMV armstrong

tag: infection dose

value: 2?ó10E5 PFU

tag: prep description

value: anti-CD45 IV injection before tissue harvest, collagenase I

tag: organ

value: lung

tag: t specificity

value: IV- CD45+ CD3e+


title: WT32-2-2

tag: cell line

value: HeLa


title: HME1_WT_H4K16acAb2_Rep1

description:
Library name: HME1_WT_H4K16acAb2_Rep1
HME1_Corrected_H4K16acAb2.bigWig

tag: chip antibody

value: Cell Signaling Technology, 13534

tag: cell type

value: immortalized mammary epithelial cells

tag: genotype

value: Ctrl KO


description:
Library name: I36H8_smallintestineLP_LCMVarm_D7_allT_P14_SMARTA_mouse0127_TCR
Two separate 10x lanes of 10 individually hashed samples: Control_spleen, Bone.Marrow.LCMV.D7, IEL.LCMV.D7, LPL.LCMV.D7, Lung.Draining.LN, Lung.LCMV.D7, Mesenteric.LN.LCMV.D7, Prostate.LCMV.D7, Salivary.LCMV.d7, Spleen.LCMV.D7.M

tag: tissue

tag: immgent igt_10xlane_id

tag: hashtag number

tag: Sex

value: male

tag: age weeks

tag: pool of_mice

tag: jax

value: lamina propria of small intestine

tag: organ uberon_id

value: P14, SMARTA

tag: target cells

value: all T including P14 and SMARTA

tag: gating strategy

tag: sample comments

value: 100x10E3 SMARTA (male, CD45.1.2) and 50x10E3 P14 (male, CD45.1), intravenous, 1 day before infection

value: T cells

tag: batch


title: WT32-2-1

tag: treatment


title: A_0_1

description: Library name: A_0_1

tag: cell line

value: smooth muscle cell

value: WT

value: ADAM9i treatment+Vehicle


title: HME1_MSL3ko_H4K16acAb1_Rep2

description: Library name: HME1_MSL3ko_H4K16acAb1_Rep2

tag: chip antibody

value: Millipore, 07-329

value: MSL3 KO


title: WT_T3

description: Library name: WT_T3

source_name: aorta

value: aorta

value: Ang-II/BAPN


title: A_R_2

description: Library name: A_R_2

value: ADAM9i treatment+rhCTHRC1


description:
Library name: I36H8_smallintestineLP_LCMVarm_D7_allT_P14_SMARTA_mouse0127_GEX
Two separate 10x lanes of 10 individually hashed samples: Control_spleen, Bone.Marrow.LCMV.D7, IEL.LCMV.D7, LPL.LCMV.D7, Lung.Draining.LN, Lung.LCMV.D7, Mesenteric.LN.LCMV.D7, Prostate.LCMV.D7, Salivary.LCMV.d7, Spleen.LCMV.D7.M

value: siIEL, siLPL, prostate, SG, lung, bone marrow, spleen, mesenteric lymph nodes, mediastinal lymph nodes

tag: condition detailed_organ

tag: cite seq

value: TRUE

tag: exp name

value: Pan organ and time course analysis of T cells in acute LCMV (armstrong) infection (day 7)

tag: lab

value: Goldrath

tag: organism name

tag: strain

tag: genetics

value: P14 and SMARTA > wt

value: FALSE

tag: infection agent

value: LCMV armstrong

tag: infection dose

value: 2?ó10E5 PFU

tag: prep description

value: anti-CD45 IV injection before tissue harvest, collagenase I

tag: organ

tag: t specificity

value: IV- CD45+ CD3e+

tag: cell type


title: WT32-1-2

value: HeLa


title: HME1_MSL3ko_H4K16acAb1_Rep1

description: Library name: HME1_MSL3ko_H4K16acAb1_Rep1

value: immortalized mammary epithelial cells

tag: genotype


description:
Library name: I36H8_smallintestineLP_LCMVarm_D7_allT_P14_SMARTA_mouse0127_FBC
Two separate 10x lanes of 10 individually hashed samples: Control_spleen, Bone.Marrow.LCMV.D7, IEL.LCMV.D7, LPL.LCMV.D7, Lung.Draining.LN, Lung.LCMV.D7, Mesenteric.LN.LCMV.D7, Prostate.LCMV.D7, Salivary.LCMV.d7, Spleen.LCMV.D7.M

tag: tissue

tag: immgent igt_10xlane_id

tag: hashtag number

tag: Sex

value: male

tag: age weeks

tag: pool of_mice

tag: jax

value: lamina propria of small intestine

tag: organ uberon_id

value: P14, SMARTA

tag: target cells

value: all T including P14 and SMARTA

tag: gating strategy

tag: sample comments

value: 100x10E3 SMARTA (male, CD45.1.2) and 50x10E3 P14 (male, CD45.1), intravenous, 1 day before infection

value: T cells

tag: batch


title: WT_T2

description: Library name: WT_T2

value: aorta

value: WT

tag: treatment

value: Ang-II/BAPN


title: WT_T1

description: Library name: WT_T1


title: HME1_WT_H4K16acAb1_Rep2

description:
Library name: HME1_WT_H4K16acAb1_Rep2
HME1_Corrected_H4K16acAb1.bigWig

tag: chip antibody

value: Millipore, 07-329

tag: cell line

value: Ctrl KO


description:
Library name: I36H7_smallintestineIEL_LCMVarm_D7_allT_P14_SMARTA_mouse0127_TCR
Two separate 10x lanes of 10 individually hashed samples: Control_spleen, Bone.Marrow.LCMV.D7, IEL.LCMV.D7, LPL.LCMV.D7, Lung.Draining.LN, Lung.LCMV.D7, Mesenteric.LN.LCMV.D7, Prostate.LCMV.D7, Salivary.LCMV.d7, Spleen.LCMV.D7.M

value: siIEL, siLPL, prostate, SG, lung, bone marrow, spleen, mesenteric lymph nodes, mediastinal lymph nodes

tag: condition detailed_organ

tag: cite seq

value: TRUE

tag: exp name

value: Pan organ and time course analysis of T cells in acute LCMV (armstrong) infection (day 7)

tag: lab

value: Goldrath

tag: organism name

tag: strain

tag: genetics

value: P14 and SMARTA > wt

value: FALSE

tag: infection agent

value: LCMV armstrong

tag: infection dose

tag: prep description

value: anti-CD45 IV injection before tissue harvest, DTE

tag: organ

value: epithelium of small intestine

tag: t specificity

tag: cell type


title: MCF10A cells, MYADM, rep2

city: taipei

first: Tai-Lung

last: Cha

state: taipei

address: 11490 No.161, Sec. 6, Minquan E. Rd., Neihu Dist., Taipei City 114, Taiwan (R.O.

department: National Institute of Cancer Research

country: Taiwan

institute: National Defense Medical Center

description:
Library name: Smaple 36
Column name in MCF10A_raw_counts.txt :MCF10A_MY_rep2

data_processing:
RNAseq:RNA-seq data were aligned to the UCSC reference genome using Bowtie2 (v2.4.5). The human genome (GRCh37/hg19) and mouse genome (GRCm38/mm10) assemblies from the UCSC Genome Browser were used as references. Aligned reads were processed with SAMtools (v1.3) to generate a read count table for each gene.
ATACsaq: Reads were mapped to the human genome (hg19) and mouse genome (mm10) using Bowtie2. PCR duplicates were removed using Picard Tools. For peak calling, biological replicates were merged and processed using MACS2. Peaks from all replicates were further merged using SAMtools. Variance-stabilizing transformation and principal component analysis (PCA) were performed using SeqMonk, based on the DESeq2 model. Visualization of ATAC-seq signals across specific genes was performed using the Integrative Genomics Viewer (IGV).
Assembly: hg19 and mm10
Supplementary files format and content: text files inculed raw counts for each sample
Supplementary files format and content: csv files include FPKM value for each sample

source_name: breast

growth_protocol: Cell lines were cultured in media recommended by the American Type Culture Collection (ATCC) and maintained at 37°C in a humidified incubator with 5% CO₂. Bone marrow cells were isolated from mouse femurs and tibias by PBS flushing, followed by red blood cell lysis with Tris-ammonium chloride. Cells were filtered through a 70-μm strainer and cultured in RPMI-1640 supplemented with 10% heat-inactivated FBS. For stimulation, cells were seeded at 0.5 × 10⁶ cells/ml with 20 ng/ml M-CSF. Fresh cytokine-containing medium was added on day 2, and cells were collected over a 5-day period.

extract_protocol:
Total RNA was extracted using the RNeasy Plus Mini Kit (QIAGEN). RNA-seq libraries were prepared from pretreated RNA using the TruSeq Stranded Total RNA Library Prep Kit (Illumina) according to the manufacturer’s instructions. For ATAC-seq, 1×10⁶ cells were collected, washed with PBS, and lysed in cold ATAC RSB lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl₂, 0.1% NP-40, 0.1%Tween-20, and 0.01% digitonin). Nuclei were washed with ATAC RSB containing 0.1% Tween-20 and resuspended in transposition mix containing Tn5 transposase (Illumina). Transposition was carried out at 37°C for 30 min with shaking at 300 rpm. DNA was purified using the Qiagen MinElute PCR Purification Kit and libraries were amplified using NEBNext PCR master mix (NEB).
RNA-seq libraries were quantified using Qubit (Invitrogen), denatured to single-stranded DNA, loaded onto Illumina flow cells, amplified by in situ cluster generation, and sequenced for 150 cycles on an Illumina HiSeq 2500 platform following the manufacturer's instructions. ATAC-seq libraries were sequenced on an Illumina NextSeq 550 system using paired-end reads.

tag: tissue

value: breast

value: human mammary epithelial cell

tag: genotype

value: MYADM overexpression


title: WT_C3

description: Library name: WT_C3

value: aorta

tag: treatment

value: PBS


description:
Library name: I36H7_smallintestineIEL_LCMVarm_D7_allT_P14_SMARTA_mouse0127_GEX
Two separate 10x lanes of 10 individually hashed samples: Control_spleen, Bone.Marrow.LCMV.D7, IEL.LCMV.D7, LPL.LCMV.D7, Lung.Draining.LN, Lung.LCMV.D7, Mesenteric.LN.LCMV.D7, Prostate.LCMV.D7, Salivary.LCMV.d7, Spleen.LCMV.D7.M

tag: immgent igt_10xlane_id

tag: hashtag number

tag: Sex

value: male

tag: age weeks

tag: pool of_mice

tag: jax

value: 2?ó10E5 PFU

tag: organ uberon_id

value: P14, SMARTA

tag: target cells

value: all T including P14 and SMARTA

tag: gating strategy

value: IV- CD45+ CD3e+

tag: sample comments

value: 100x10E3 SMARTA (male, CD45.1.2) and 50x10E3 P14 (male, CD45.1), intravenous, 1 day before infection

value: T cells

tag: batch


title: HME1_WT_H4K16acAb1_Rep1

description:
Library name: HME1_WT_H4K16acAb1_Rep1
HME1_Corrected_H4K16acAb1.bigWig

tag: chip antibody

value: Millipore, 07-329

tag: cell line

value: immortalized mammary epithelial cells

value: Ctrl KO


title: MCF10A cells, MYADM, rep1

description:
Library name: Smaple 35
Column name in MCF10A_raw_counts.txt :MCF10A_MY_rep1

tag: cell type


title: HME1_H3K36me3

description: Library name: HME1_H3K36me3

value: Cell Signaling Technology, 4909S

value: WT


title: WT_C2

description: Library name: WT_C2

tag: tissue


description:
Library name: I36H7_smallintestineIEL_LCMVarm_D7_allT_P14_SMARTA_mouse0127_FBC
Two separate 10x lanes of 10 individually hashed samples: Control_spleen, Bone.Marrow.LCMV.D7, IEL.LCMV.D7, LPL.LCMV.D7, Lung.Draining.LN, Lung.LCMV.D7, Mesenteric.LN.LCMV.D7, Prostate.LCMV.D7, Salivary.LCMV.d7, Spleen.LCMV.D7.M

value: siIEL, siLPL, prostate, SG, lung, bone marrow, spleen, mesenteric lymph nodes, mediastinal lymph nodes

tag: condition detailed_organ

tag: cite seq

value: TRUE

tag: exp name

value: Pan organ and time course analysis of T cells in acute LCMV (armstrong) infection (day 7)

tag: lab

value: Goldrath

tag: organism name

tag: strain

tag: genetics

value: P14 and SMARTA > wt

value: FALSE

tag: infection agent

value: LCMV armstrong

tag: infection dose

tag: prep description

value: anti-CD45 IV injection before tissue harvest, DTE

tag: organ

value: epithelium of small intestine

tag: t specificity


title: MCF10A cells, vector, rep2

description:
Library name: Smaple 34
Column name in MCF10A_raw_counts.txt :MCF10A_Vector_rep2

value: breast

value: human mammary epithelial cell

tag: genotype

value: wild-type

tag: treatment

value: vector control


title: WT_C1

description: Library name: WT_C1

value: aorta

value: PBS


description:
Library name: I36H6_LNmesenteric_LCMVarm_D7_allT_P14_SMARTA_mouse0127_TCR
Two separate 10x lanes of 10 individually hashed samples: Control_spleen, Bone.Marrow.LCMV.D7, IEL.LCMV.D7, LPL.LCMV.D7, Lung.Draining.LN, Lung.LCMV.D7, Mesenteric.LN.LCMV.D7, Prostate.LCMV.D7, Salivary.LCMV.d7, Spleen.LCMV.D7.M

tag: immgent igt_10xlane_id

tag: hashtag number

tag: Sex

value: male

tag: age weeks

tag: pool of_mice

tag: jax

value: 2?ó10E5 PFU

value: anti-CD45 IV injection before tissue harvest, mechanical dissociation alone

value: mesenteric lymph node

tag: organ uberon_id

value: P14, SMARTA

tag: target cells

value: all T including P14 and SMARTA

tag: gating strategy

value: CD45+ CD3e+

tag: sample comments

value: 100x10E3 SMARTA (male, CD45.1.2) and 50x10E3 P14 (male, CD45.1), intravenous, 1 day before infection

value: T cells

tag: batch


title: MCF10A cells, vector, rep1

description:
Library name: Smaple 33
Column name in MCF10A_raw_counts.txt :MCF10A_Vector_rep1

tag: tissue

tag: cell line

tag: cell type


title: Input_MSL3ko

description: Library name: Input_MSL3ko

data_processing:
*library strategy: REPLIseq
REPLIseq reads were aligned to the hg38 genome using nf-core/chipseq pipeline version 2.0.0 with bwa aligner.
BigWig files were generated within the nf-core/chipseq pipeline
For REPLIseq samples, replicates were merged using SAMtool. bigWig were generated using bamCoverage and bigwigCompare within DeepTools was used to generate log2Early/Late bigwig files for genome browsing and visualization via IGV. Default –-operation parameter was applied (log2) with –binSize 20
Assembly: hg38
Supplementary files format and content: bigWig of aligned samples for genome browser visualization
Supplementary files format and content: bigWig of log2Early/Late ratios for genome browser visualization

extract_protocol:
Stable Ctrl-KO and MSL3-KO HME1 cells were seeded in T150 flasks. While growing in exponential phase, asynchronous cells were pulsed with 25μM EdU (Universal Biologicals, 10540) for 30 minutes. After fixation with 90% MetOH and permeabilization, Biotin Click it reaction was performed by incubating cells in click-it reaction cocktail (100 mM TrisHCl pH 8, 4mM CuSO4, 100mM sodium-L-ascorbate, 50µM Biotin Azide - Thermo Fisher Scientific, B10184) for 30 minutes. After washes, DNA was stained using PI (propidium iodide). Two population of cells, corresponding to early and late S phase cells were sorted using Beckman Coulter - MoFlo™ XDP. Cells were pelleted and incubated in lysis buffer (10 mM Tris-HCl, pH 8, 10 mM EDTA, 0.5% SDS, 0.2 mg/ml Proteinase K) for 3 hours at 50ºC. DNA was purified using phenol/chloroform/isoamyl alcohol, resuspended in TE and sonicated using Bioruptor Pico. EdU-labelled DNA was captured using Dynabeads MyOne Streptavidin C1 (Thermo Fisher Scientific, 65001), washed and eluted from beads using 2% β-mercaptoethanol. DNA was purified with solid-phase reversible immobilization (SPRI) beads (Agencourt AMPure XP, Beckman Coulter), and then quantified with QuantiFluor (Promega, E2670).
DNA libraries were prepared using the NEBNext UltraII DNA Library Prep Kit for Illumina (New England Biolabs, E7645L).

tag: pull down

value: immortalized mammary epithelial cells

value: MSL3 KO


description:
Library name: I36H6_LNmesenteric_LCMVarm_D7_allT_P14_SMARTA_mouse0127_GEX
Two separate 10x lanes of 10 individually hashed samples: Control_spleen, Bone.Marrow.LCMV.D7, IEL.LCMV.D7, LPL.LCMV.D7, Lung.Draining.LN, Lung.LCMV.D7, Mesenteric.LN.LCMV.D7, Prostate.LCMV.D7, Salivary.LCMV.d7, Spleen.LCMV.D7.M

value: siIEL, siLPL, prostate, SG, lung, bone marrow, spleen, mesenteric lymph nodes, mediastinal lymph nodes

tag: condition detailed_organ

tag: cite seq

value: TRUE

tag: exp name

value: Pan organ and time course analysis of T cells in acute LCMV (armstrong) infection (day 7)

tag: lab

value: Goldrath

tag: organism name

tag: strain

tag: genetics

value: P14 and SMARTA > wt

value: FALSE

tag: infection agent

value: LCMV armstrong

tag: infection dose

tag: prep description

tag: organ

tag: t specificity


title: CL1-5 cells , rep2

description:
Library name: Smaple 32
Column name in CL1_raw_counts.txt :CL1_5_rep2

source_name: lung

value: lung

value: human lung adenocarcinoma cell

tag: genotype

value: wild-type

tag: treatment

value: no treatment (wild-type, differing metastatic potential)


title: KO_T3

description: Library name: KO_T3

tag: tissue

value: aorta

value: Ang-II/BAPN


title: KO_T2

description: Library name: KO_T2


title: WT32-1-1

tag: cell line

value: HeLa


description:
Library name: I36H6_LNmesenteric_LCMVarm_D7_allT_P14_SMARTA_mouse0127_FBC
Two separate 10x lanes of 10 individually hashed samples: Control_spleen, Bone.Marrow.LCMV.D7, IEL.LCMV.D7, LPL.LCMV.D7, Lung.Draining.LN, Lung.LCMV.D7, Mesenteric.LN.LCMV.D7, Prostate.LCMV.D7, Salivary.LCMV.d7, Spleen.LCMV.D7.M

tag: immgent igt_10xlane_id

tag: hashtag number

tag: Sex

value: male

tag: age weeks

tag: pool of_mice

tag: jax

value: 2?ó10E5 PFU

value: anti-CD45 IV injection before tissue harvest, mechanical dissociation alone

value: mesenteric lymph node

tag: organ uberon_id

value: P14, SMARTA

tag: target cells

value: all T including P14 and SMARTA

tag: gating strategy

value: CD45+ CD3e+

tag: sample comments

value: 100x10E3 SMARTA (male, CD45.1.2) and 50x10E3 P14 (male, CD45.1), intravenous, 1 day before infection

tag: cell type

value: T cells

tag: batch


title: REPLIseq_MSL3ko_late_R2

description:
Library name: REPLIseq_MSL3ko_late_R2
REPLIseq_MSL3ko_Early_vs_Late.bw

tag: pull down

value: EdU

value: immortalized mammary epithelial cells

value: MSL3 KO


title: KO_T1

description: Library name: KO_T1

tag: genotype


title: CL1-5 cells , rep1

description:
Library name: Smaple 31
Column name in CL1_raw_counts.txt :CL1_5_rep1

value: lung

value: human lung adenocarcinoma cell

value: wild-type

tag: treatment


title: CL1-3 cells , rep2

description:
Library name: Smaple 30
Column name in CL1_raw_counts.txt :CL1_3_rep2

tag: tissue

value: no treatment (wild-type, differing metastatic potential)


title: REPLIseq_MSL3ko_late_R1

description:
Library name: REPLIseq_MSL3ko_late_R1
REPLIseq_MSL3ko_Early_vs_Late.bw

tag: cell line


title: KO-C3

description: Library name: KO-C3

value: aorta

value: PBS


description:
Library name: I36H5_bonemarrow_LCMVarm_D7_allT_P14_SMARTA_mouse0127_TCR
Two separate 10x lanes of 10 individually hashed samples: Control_spleen, Bone.Marrow.LCMV.D7, IEL.LCMV.D7, LPL.LCMV.D7, Lung.Draining.LN, Lung.LCMV.D7, Mesenteric.LN.LCMV.D7, Prostate.LCMV.D7, Salivary.LCMV.d7, Spleen.LCMV.D7.M

value: siIEL, siLPL, prostate, SG, lung, bone marrow, spleen, mesenteric lymph nodes, mediastinal lymph nodes

tag: immgent igt_10xlane_id

tag: condition detailed_organ

tag: cite seq

value: TRUE

tag: exp name

value: Pan organ and time course analysis of T cells in acute LCMV (armstrong) infection (day 7)

tag: lab

value: Goldrath

tag: organism name

tag: strain

tag: genetics

value: P14 and SMARTA > wt

value: male

value: FALSE

tag: infection agent

value: LCMV armstrong

tag: infection dose

value: 2?ó10E5 PFU

tag: prep description

tag: organ

value: bone marrow

tag: t specificity


title: PDAC CAFs, control, replicate 3

city: Stanford

first: Daniel

last: Delitto

address: 257 Campus Dr

institute: Stanford University

description: Samples were actually sequenced with the Singular Genomics G4 sequencer (https://singulargenomics.com/g4/)

data_processing:
Bulk RNA-seq library quality control, processing, and alignment were performed using nf-core/rnaseq, with Ensemble’s GRCh38 assembly as the reference genome and salmon for transcript quantification. The quant.sf and tx2gene.tsv files were processed with R package tximport for downstream analysis with DESeq2.
Assembly: Ensemble’s GRCh38 assembly
Supplementary files format and content: Output directory from Salmon quantification, containing quant.sf file (transcript-level quantification) and quant.genes.sf file (gene-level quantification) and other metadata for every sample. Tx2gene.tsv contains gene to transcripts ids mappings.

source_name: Fibroblast

growth_protocol: PDAC CAFs were isolated from surgical specimens using the Human Tumor Dissociation Kit (Miltenyi Biotec) under an institutional review board approved protocol with patient informed consent. Tumors were minced into 2-4 mm pieces in a petri dish containing a small volume of DMEM/F-12 to maintain specimen moisture. The minced tissue was then added to a gentleMACS C tube containing weight-based enzyme mixture as per manufacturer’s protocol (Miltenyi Biotec). Following dissociation, cells were filtered through a 100 µm and then a 40 µm filter, spun down at 300 RCF for 5 minutes in a 4°C centrifuge, and resuspended in 1 ml of growth medium with 20% FBS. Cells were plated in a gelatin (Sigma-Aldrich) coated flask at a concentration of 2000 cells/cm2. After 24 hours, the media was changed to growth medium with 10% FBS, with additional media changes every 2-3 days as needed. After 2-3 passages, cells were frozen in Bambanker (NIPPON Genetics) at roughly 1 million cells per vial. Prior to further experimentation, cells were thawed and maintained in sterile conditions in growth medium.

extract_protocol:
Total RNA was extracted from the cells using the RNeasy Mini kit (QIAGEN) per the manufacturer’s protocol.
Library preparation was performed using the NEBNext Ultra II Directional RNA Library Prep Kit with rRNA Depletion Kit v2 (New England Biolabs). Library conversion was done with Singular Genomics Library Compatibility Kit (Singular Genomics). Libraries were sequenced on the Singular Genomics G4 sequencer on F3 flow cells, with one lane per library, at 75 bp pair-end for 100 cycles.

treatment_protocol: Passage 4-7 fibroblasts were plated in a 12-well plate (105 cells per well, three replicates per condition), allowed to adhere overnight, and then treated with fresh media (control), or fresh media containing LPS (InvivoGen) at 100 ng/ml. After 24 hours, the cells were harvested.

tag: cell type

value: Fibroblast


title: REPLIseq_WT_late_R2

description:
Library name: REPLIseq_WT_late_R2
REPLIseq_WT_Early_vs_Late.bw

tag: pull down

value: EdU

value: immortalized mammary epithelial cells

tag: genotype

value: Ctrl KO


description:
Library name: I36H5_bonemarrow_LCMVarm_D7_allT_P14_SMARTA_mouse0127_GEX
Two separate 10x lanes of 10 individually hashed samples: Control_spleen, Bone.Marrow.LCMV.D7, IEL.LCMV.D7, LPL.LCMV.D7, Lung.Draining.LN, Lung.LCMV.D7, Mesenteric.LN.LCMV.D7, Prostate.LCMV.D7, Salivary.LCMV.d7, Spleen.LCMV.D7.M

tag: tissue

tag: hashtag number

tag: Sex

tag: age weeks

tag: pool of_mice

tag: jax

value: anti-CD45 IV injection before tissue harvest, mechanical dissociation alone

tag: organ uberon_id

value: P14, SMARTA

tag: target cells

value: all T including P14 and SMARTA

tag: gating strategy

value: CD45+ CD3e+

tag: sample comments

value: 100x10E3 SMARTA (male, CD45.1.2) and 50x10E3 P14 (male, CD45.1), intravenous, 1 day before infection

value: T cells

tag: batch


title: KO-C2

description: Library name: KO-C2

value: aorta

tag: treatment

value: PBS


description:
Library name: I36H5_bonemarrow_LCMVarm_D7_allT_P14_SMARTA_mouse0127_FBC
Two separate 10x lanes of 10 individually hashed samples: Control_spleen, Bone.Marrow.LCMV.D7, IEL.LCMV.D7, LPL.LCMV.D7, Lung.Draining.LN, Lung.LCMV.D7, Mesenteric.LN.LCMV.D7, Prostate.LCMV.D7, Salivary.LCMV.d7, Spleen.LCMV.D7.M

value: siIEL, siLPL, prostate, SG, lung, bone marrow, spleen, mesenteric lymph nodes, mediastinal lymph nodes

tag: immgent igt_10xlane_id

tag: condition detailed_organ

tag: cite seq

value: TRUE

tag: exp name

value: Pan organ and time course analysis of T cells in acute LCMV (armstrong) infection (day 7)

tag: lab

value: Goldrath

tag: organism name

tag: strain

tag: genetics

value: P14 and SMARTA > wt

value: male

tag: infection agent

tag: infection dose

tag: prep description

tag: organ


title: CL1-1 cells , rep2

description:
Library name: Smaple 28
Column name in CL1_raw_counts.txt :CL1_1_rep2

tag: tissue

value: lung

tag: cell line

tag: cell type

value: human lung adenocarcinoma cell

tag: genotype

value: wild-type

value: no treatment (wild-type, differing metastatic potential)


title: KO-C1

description: Library name: KO-C1

tag: treatment


title: HME1_Input

description: Library name: HME1_Input

tag: chip antibody

value: immortalized mammary epithelial cells

value: WT


title: REPLIseq_WT_late_R1

description:
Library name: REPLIseq_WT_late_R1
REPLIseq_WT_Early_vs_Late.bw

tag: pull down

value: EdU

value: Ctrl KO


description:
Library name: I36H4_salivarygland_LCMVarm_D7_allT_P14_SMARTA_mouse0127_TCR
Two separate 10x lanes of 10 individually hashed samples: Control_spleen, Bone.Marrow.LCMV.D7, IEL.LCMV.D7, LPL.LCMV.D7, Lung.Draining.LN, Lung.LCMV.D7, Mesenteric.LN.LCMV.D7, Prostate.LCMV.D7, Salivary.LCMV.d7, Spleen.LCMV.D7.M

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

tag: Sex

tag: age weeks

tag: pool of_mice

value: FALSE

tag: jax

value: LCMV armstrong

value: 2?ó10E5 PFU

value: anti-CD45 IV injection before tissue harvest, collagenase I

value: submandibular gland

tag: organ uberon_id

tag: t specificity

value: P14, SMARTA

tag: target cells

value: all T including P14 and SMARTA

tag: gating strategy

value: IV- CD45+ CD3e+

tag: sample comments

value: 100x10E3 SMARTA (male, CD45.1.2) and 50x10E3 P14 (male, CD45.1), intravenous, 1 day before infection

value: T cells

tag: batch


title: CL1-1 cells , rep1

description:
Library name: Smaple 27
Column name in CL1_raw_counts.txt :CL1_1_rep1

tag: tissue

value: lung

tag: cell line

tag: cell type

value: human lung adenocarcinoma cell

tag: genotype

tag: treatment


title: REPLIseq_MSL3ko_early_R2

description:
Library name: REPLIseq_MSL3ko_early_R2
REPLIseq_MSL3ko_Early_vs_Late.bw

tag: pull down

value: MSL3 KO


title: FWT_T3

description: Library name: FWT_T3

value: aorta

value: Ang-II/BAPN


description:
Library name: I36H4_salivarygland_LCMVarm_D7_allT_P14_SMARTA_mouse0127_GEX
Two separate 10x lanes of 10 individually hashed samples: Control_spleen, Bone.Marrow.LCMV.D7, IEL.LCMV.D7, LPL.LCMV.D7, Lung.Draining.LN, Lung.LCMV.D7, Mesenteric.LN.LCMV.D7, Prostate.LCMV.D7, Salivary.LCMV.d7, Spleen.LCMV.D7.M

value: siIEL, siLPL, prostate, SG, lung, bone marrow, spleen, mesenteric lymph nodes, mediastinal lymph nodes

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

value: TRUE

tag: exp name

value: Pan organ and time course analysis of T cells in acute LCMV (armstrong) infection (day 7)

tag: lab

value: Goldrath

tag: organism name

tag: strain

tag: genetics

value: P14 and SMARTA > wt

value: male

tag: infection agent

tag: infection dose

tag: prep description

tag: organ


title: Input_WT

description: Library name: Input_WT

tag: cell line

tag: cell type

value: immortalized mammary epithelial cells

value: Ctrl KO


title: CL1-0 cells , rep2

description:
Library name: Smaple 26
Column name in CL1_raw_counts.txt :CL1_0_rep2

tag: tissue

tag: genotype

value: wild-type

tag: treatment

value: no treatment (parental CL1-1)


title: FWT_T2

description: Library name: FWT_T2

value: WT


title: REPLIseq_WT_early_R2

description:
Library name: REPLIseq_WT_early_R2
REPLIseq_WT_Early_vs_Late.bw

tag: pull down

value: EdU


description:
Library name: I36H4_salivarygland_LCMVarm_D7_allT_P14_SMARTA_mouse0127_FBC
Two separate 10x lanes of 10 individually hashed samples: Control_spleen, Bone.Marrow.LCMV.D7, IEL.LCMV.D7, LPL.LCMV.D7, Lung.Draining.LN, Lung.LCMV.D7, Mesenteric.LN.LCMV.D7, Prostate.LCMV.D7, Salivary.LCMV.d7, Spleen.LCMV.D7.M

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: Sex

tag: age weeks

tag: pool of_mice

value: FALSE

tag: jax

value: LCMV armstrong

value: 2?ó10E5 PFU

value: anti-CD45 IV injection before tissue harvest, collagenase I

value: submandibular gland

tag: organ uberon_id

tag: t specificity

value: P14, SMARTA

tag: target cells

value: all T including P14 and SMARTA

tag: gating strategy

value: IV- CD45+ CD3e+

tag: sample comments

value: 100x10E3 SMARTA (male, CD45.1.2) and 50x10E3 P14 (male, CD45.1), intravenous, 1 day before infection

value: T cells

tag: batch


title: REPLIseq_MSL3ko_early_R1

description:
Library name: REPLIseq_MSL3ko_early_R1
REPLIseq_MSL3ko_Early_vs_Late.bw

tag: cell line

tag: cell type

value: MSL3 KO


title: CL1-0 cells , rep1

description:
Library name: Smaple 25
Column name in CL1_raw_counts.txt :CL1_0_rep1

tag: tissue

value: lung

value: human lung adenocarcinoma cell

tag: genotype

tag: treatment

value: no treatment (parental CL1-0)


description:
Library name: I36H3_prostate_LCMVarm_D7_allT_P14_SMARTA_mouse0127_GEX
Two separate 10x lanes of 10 individually hashed samples: Control_spleen, Bone.Marrow.LCMV.D7, IEL.LCMV.D7, LPL.LCMV.D7, Lung.Draining.LN, Lung.LCMV.D7, Mesenteric.LN.LCMV.D7, Prostate.LCMV.D7, Salivary.LCMV.d7, Spleen.LCMV.D7.M

value: siIEL, siLPL, prostate, SG, lung, bone marrow, spleen, mesenteric lymph nodes, mediastinal lymph nodes

tag: immgent igt_10xlane_id

tag: hashtag number

tag: cite seq

value: TRUE

tag: exp name

value: Pan organ and time course analysis of T cells in acute LCMV (armstrong) infection (day 7)

tag: lab

value: Goldrath

tag: organism name

tag: strain

tag: genetics

value: P14 and SMARTA > wt

value: male

tag: infection agent

tag: infection dose

tag: prep description

tag: organ

value: prostate gland


title: REPLIseq_WT_early_R1

description:
Library name: REPLIseq_WT_early_R1
REPLIseq_WT_Early_vs_Late.bw

tag: pull down

value: EdU

tag: cell line

value: immortalized mammary epithelial cells

value: Ctrl KO


title: LL cells, rep2

description:
Library name: Smaple 24
Column name in ACHN_LL_raw_counts.txt :LL_rep2

source_name: kidney

tag: tissue

value: kidney

value: LL

tag: cell type

value: human renal carcinoma cell

value: wild-type

value: no treatment (wild-type, differing metastatic potential)


title: FWT_C3

description: Library name: FWT_C3

value: aorta

tag: genotype

value: WT

tag: treatment

value: PBS


description:
Library name: I36H3_prostate_LCMVarm_D7_allT_P14_SMARTA_mouse0127_TCR
Two separate 10x lanes of 10 individually hashed samples: Control_spleen, Bone.Marrow.LCMV.D7, IEL.LCMV.D7, LPL.LCMV.D7, Lung.Draining.LN, Lung.LCMV.D7, Mesenteric.LN.LCMV.D7, Prostate.LCMV.D7, Salivary.LCMV.d7, Spleen.LCMV.D7.M

value: siIEL, siLPL, prostate, SG, lung, bone marrow, spleen, mesenteric lymph nodes, mediastinal lymph nodes

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

value: TRUE

tag: Sex

tag: age weeks

tag: pool of_mice

value: FALSE

tag: jax

value: LCMV armstrong

value: 2?ó10E5 PFU

value: anti-CD45 IV injection before tissue harvest, collagenase I

tag: organ uberon_id

tag: t specificity

value: P14, SMARTA

tag: target cells

value: all T including P14 and SMARTA

tag: gating strategy

value: IV- CD45+ CD3e+

tag: sample comments

value: 100x10E3 SMARTA (male, CD45.1.2) and 50x10E3 P14 (male, CD45.1), intravenous, 1 day before infection

value: T cells

tag: batch


title: CL1-3 cells , rep1

description:
Library name: Smaple 29
Column name in CL1_raw_counts.txt :CL1_3_rep1

tag: tissue

value: lung

tag: cell line

value: human lung adenocarcinoma cell


title: FWT_T1

description: Library name: FWT_T1

tag: genotype

value: Ang-II/BAPN


title: LL cells, rep1

description:
Library name: Smaple 23
Column name in ACHN_LL_raw_counts.txt :LL_rep1

value: kidney

value: LL

tag: cell type

value: human renal carcinoma cell

value: wild-type

tag: treatment

value: no treatment (wild-type, differing metastatic potential)


title: 231 -G EV, rep2

city: wuhan

first: Wei

last: Yan

state: Hubei

address: Bayi Street 229 in Wuchang district

department: College of life science

institute: Wuhan University

description: 231-G EV-2

data_processing:
Image analysis and base calling are performed using Solexa pipeline v1.8 (Off-Line Base Caller soft-ware, v1.8).
Sequencing quality are examined by FastQC and trimmed reads (pass Illumina quality filter, trimmed 5’,3‘-adaptor bases by cutadapt) are aligned allowing for 1 mismatch only to the mature miRNA sequences, then reads that do not map are aligned allowing for 1 mismatch only to precursor miRNA sequences with bowtie software.
The remaining reads are aligned allowing for 1 mismatch only to miRNA reference sequences with miRDeep2. The abundance of miRNA are evaluated using their sequencing counts and is normalized as counts per million of total aligned reads(CPM).
The miRNAs differentially expressed are screened based on the count value with R package edgeR.
For 231 EV-2 and 231-G EV-2, after cluster generation, the library preparations were sequenced on an Illumina platform and 50 bp single-end reads were generated. The raw paired end reads were trimmed and quality controlled by SeqPrep and Sickle with default parameters. Then clean reads were separately aligned to reference genome with orientation mode using HIASAT software. The mapped reads of each sample were assembled by StringTie in a reference-based approach. Low-quality bases (Sanger base quality of < 20) of the 3’ end were trimmed using in-house perl scripts, and then the sequencing adapters were removed with the fastx toolkit software.All identical sequences of sizes ranging from 18 to 32nt were counted and eliminated from the initial data set.The assembled unique sequences were used for a BLAST search of the Rfam database, version 10.1, to remove non-miRNA sequences (rRNA, tRNA, snoRNA etc.). Bowtie2 was used to annotate the chromosomal location against the reference genome data. Through a BLAST search of the miRbase, version 21.0, the highly matched sequences were used to count and analyze the known miRNA expression profile. The characteristics of hairpin structure of miRNA precursor could be used to predict novel miRNA. Mireap or miRDeep2 were used to predict novel miRNA, and the Dicer cleavage site and the minimum free energy of the small RNA tags were unannotated in the former steps. Meanwhile, in-house scripts were used to obtain the identified miRNA base bias on the first position with certain length and on each position of all identified miRNA.The expression level of each miRNA was calculated according to the transcripts TPM method.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include counts and CPM/TPM values for each Sample

growth_protocol: MDA-MB-231 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37°C

extract_protocol:
Total RNA samples were first pretreated as following to remove some RNA modifications that interfere with small RNA-seq library construction: 3‘-aminoacyl (charged)deacylation to 3‘-OH for 3’-adaptor ligation, 3‘-cP (2’,3‘-cyclic phosphate) removal to 3’-OH for 3‘-adaptor ligation, 5’-OH (hydroxyl group) phosphorylation to 5‘-P for 5’-adaptor ligation, m1A and m3C demethylation for efficient reverse transcription. For 231 EV-2 and 231-G EV-2, RNA was prepared following TruSeq RNA sample preparation Kit from Illumina (San Diego, CA) using 1 μg of total RNA.
1) 3’-adapter ligation; 2) 5‘-adapter ligation; 3) cDNA synthesis; 4) PCR amplification; 5) size selection of 134∼160bp PCR amplified fragments (corresponding to 14∼40nt small RNA size range).For 231 EV-2 and 231-G EV-2, sequencing libraries were generated using NEBNext Multiplex Small RNA Library Prep Set for Illumina (NEB) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: When MDA-MB-231 cells fusion reaches 90%, replace with EV free DMEM or glucose free medium and continue to culture for 12 h. The medium was collected and pre-cleared by centrifugation at 500 × g for 15 min and then at 10,000 × g for 20 min.EVs were pelleted by ultracentrifugation at 110,000 × g for 70 min, and resuspended in PBS.

value: epithelial cell

value: WT


description:
Library name: I36H3_prostate_LCMVarm_D7_allT_P14_SMARTA_mouse0127_FBC
Two separate 10x lanes of 10 individually hashed samples: Control_spleen, Bone.Marrow.LCMV.D7, IEL.LCMV.D7, LPL.LCMV.D7, Lung.Draining.LN, Lung.LCMV.D7, Mesenteric.LN.LCMV.D7, Prostate.LCMV.D7, Salivary.LCMV.d7, Spleen.LCMV.D7.M

value: siIEL, siLPL, prostate, SG, lung, bone marrow, spleen, mesenteric lymph nodes, mediastinal lymph nodes

tag: immgent igt_10xlane_id

tag: hashtag number

tag: cite seq

value: TRUE

tag: exp name

value: Pan organ and time course analysis of T cells in acute LCMV (armstrong) infection (day 7)

tag: lab

value: Goldrath

tag: organism name

tag: strain

tag: genetics

value: P14 and SMARTA > wt

value: male

value: FALSE

tag: infection agent

value: LCMV armstrong

tag: infection dose

value: 2?ó10E5 PFU

tag: prep description

tag: organ

value: prostate gland


title: AL cells, rep2

description:
Library name: Smaple 22
Column name in ACHN_LL_raw_counts.txt :AL_rep2

tag: tissue

value: kidney

value: AL


title: FWT_C2

description: Library name: FWT_C2

value: aorta

value: PBS


title: 231 EV, rep2

description: 231 EV-2

tag: cell line


description:
Library name: I36H2_spleen_LCMVarm_D7_allT_P14_SMARTA_mouse0127_TCR
Two separate 10x lanes of 10 individually hashed samples: Control_spleen, Bone.Marrow.LCMV.D7, IEL.LCMV.D7, LPL.LCMV.D7, Lung.Draining.LN, Lung.LCMV.D7, Mesenteric.LN.LCMV.D7, Prostate.LCMV.D7, Salivary.LCMV.d7, Spleen.LCMV.D7.M

tag: condition detailed_organ

tag: Sex

tag: age weeks

tag: pool of_mice

tag: jax

value: mechanical dissociation alone

value: spleen

tag: organ uberon_id

tag: t specificity

value: P14, SMARTA

tag: target cells

value: all T including P14 and SMARTA

tag: gating strategy

value: CD45+ CD3e+

tag: sample comments

value: 100x10E3 SMARTA (male, CD45.1.2) and 50x10E3 P14 (male, CD45.1), intravenous, 1 day before infection

value: T cells

tag: batch


title: AL cells, rep1

description:
Library name: Smaple 21
Column name in ACHN_LL_raw_counts.txt :AL_rep1

tag: cell type

value: human renal carcinoma cell

tag: genotype

value: wild-type

tag: treatment

value: no treatment (wild-type, differing metastatic potential)


title: FKO_T3

description: Library name: FKO_T3

value: Ang-II/BAPN