title: 2317 Liver NT FFPE

city: Bethesda

first: Anjali

last: Garg

state: Maryland

address: Building 10, Room 1B53

department: Comparative Oncology Program,NCI

institute: National Institute of Health

description: RNA was profiled using the Canine IO Panel

hyb_protocol: Gene expression profiling was performed using NanoString Canine Immuno-Oncology panel and nCounter instrument according to the manufacturer’s instructions.

data_processing:
Normalization was accomplished using the nanostringr (v.0.4.2) platform using the positive control normalization approach. Sample-specific correlation within each sample lane was also performed using CodeSet context (housekeeping gene) normalization
Normalized gene epression

organism: Canis lupus familiaris

source_name: FFPE

extract_protocol: RNA was extracted using RNeasy Mini reagents and protocol. RNA quality was determined by Agilent 2100 Bioanalyzer’s DV200 analysis.

treatment_protocol: Dogs with osteosarcoma were enrolled in COTC021/022 and received standard of care with or without adjuvant sirolimus (LeBlanc et al., Clinical Cancer Research 2021)

tag: nat tissue

value: Met-free


title: E_mu-Myc lymphoma from cell culture 1

status: Public on Mar 23 2026

type: SRA

city: Bellinzona

first: Santiago

last: Gonzalez

address: Via Francesco Chiesa 5

country: Switzerland

institute: Institute for Research in Biomedicine (IRB)

description: Library name: Sample 1

library_source: transcriptomic

data_processing:
We used FastQC v0.11.9  to assess the quality of raw reads.
Adapters sequences were trimmed using Trimmomatic v0.39.
Reads were subsequently aligned to the mouse genome using HISAT2 v2.1.0.
We then used HTSeq-count v2.0.2 to generate the table of counts.
Assembly: GENCODE vM30 (GRCm39)
Supplementary files format and content: tab-delimited text file including raw counts for each sample

molecule: total RNA

organism: Mus musculus

source_name: Lymph node

extract_protocol:
After dissection, lymph nodes were disrupted into single cell suspension using sterile nuclease free tools. Following Eu-myc lymphoma sorting in sterile condition, Total RNA was extracted using the Direct‐zol RNA Miniprep kit (R2051, Zymo Research, Irvine, CA, USA). RNA quality and concentration were assessed using the Agilent 2100 bioanalyzer (Agilent Technologies Inc., Santa Clara, CA, USA).
NEBNext Ultraexpress RNA Library Prep Kit for Illumina (E3330S - New England BioLabs Inc.) was used with the NEBNext Multiplex Oligos for Illumina (New England BioLabs Inc.) and NEBNext® Poly(A) mRNA Magnetic Isolation Module for cDNA synthesis with the addition of barcode sequences. The pre-pool sequencing was performed using the NextSeq2000 (Illumina, San Diego, CA, USA) with the P2 reagents kit V3 (100cycles; Illumina). Samples were processed starting from stranded, single-ended 120bp-long sequencing reads.

tag: tissue

value: Lymph node

tag: cell line

value: E_mu-Myc lymphoma

tag: cell type

value: B cell


title: HF_4_3_CG

city: Gangnam-gu

first: Hong-Hee

last: Won

address: 81, Irwon-ro

country: South Korea

institute: SungKyunKwan University

description:
Library name: HF_4_3_CG
column name in salmon.merged.gene_counts.tsv: HF_4_3_CG

data_processing:
nf-core/rnaseq v.3.17.0
read alignment using STAR v.2.7.11b, after filtering out alternate loci (ALT), human leukocyte antigen (HLA), and decoy sequence (Decoy) contigs
Isoform expressions of known Ensembl transcripts were quantified using Salmon (v.1.10.3) with GENCODE release 47
QC and generating read counts were performed by the nf-core/rnaseq pipeline with RSeQC, Preseq, Qualimap, dupRadar, DESeq2, Kranken2, and MultiQC
Assembly: GRCh38
Supplementary files format and content: tab-delimited
Supplementary files format and content: files including

organism: Homo sapiens

source_name: skin

growth_protocol: Three types of primary human skin cells were used. Normal Human Epidermal Keratinocytes (Cat. no. PCS-200-010, ATCC, VA, USA) were cultured in Keratinocyte Growth Medium (Lonza, KGMTM Gold, Cat. no. 00192060, BS, Switzerland) supplemented with 10% fetal bovine serum (Gibco, Waltham, MA, USA), 100 U/mL penicillin and 100 µg/mL streptomycin (Gibco). Human Epidermal Melanocytes, neonatal, Light Pigmented (HEMn-LP, Cat. no. C0025C, ThermoFisher Scientific, Waltham, MA, USA) were cultured in Cascade BiologicsTM medium 254 supplemented with Human Melanocyte Growth Supplement (Gibco, S0025). Human Dermal Fibroblasts were cultured in Dulbecco’s modified Eagle’s medium (Sol Bio Pharm, Gyeonggi-do, Korea) supplemented with 10% fetal bovine serum (Gibco), 100 U/mL penicillin and 100 µg/mL streptomycin (Gibco). Cells were maintained in a humidified incubator at 37 °C with 5% CO2. For the assay, Normal Human Epidermal Keratinocytes and HEMn-LP were seeded at 2 × 105 cells/well, and Human Dermal Fibroblasts at 1 × 105 cells/well in 6-well plates. The cells were maintained for 10 h in a humidified incubator at 37 °C with 5% CO2.

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Thermo Fisher Scientific), QIAzol® Lysis Reagent (Qiagen, Germany), and RNeasy® Mini Kit (Qiagen). A library was independently prepared using 0.5 μg of total RNA for each sample.
RNA libraries for RNA-seq were prepared using Illumina TruSeq Stranded Total RNA Library Prep Gold Kit (Illumina, San Diego, CA, USA) following the instructions in the Illumina TruSeq Stranded Total RNA Reference Guide.

treatment_protocol: Chlorogenic acid (Arshine Pharmaceutical Co., Ltd., Changsha, China) and taurine (Qianjiang Yongan Pharmaceutical, Co., Ltd., Qianjiang, China) were treated either individually or in combination at appropriate concentrations, followed by incubation for 24 h under the same conditions. After 24 h, the culture medium was removed, and 1mL of RNAlater (Cat no. AM7020, ThermoFisher Scientific) was added to each well to preserve RNA integrity. The plates were then immediately stored at -80 °C in a deep freezer for high-quality RNA preparation.

value: skin

value: human skin cell line

value: fibroblasts

tag: treatment

value: chlorogenic acid


title: E_mu-Myc lymphoma from cell culture 2

description: Library name: Sample 2


title: PerC_B1_Tpos_612

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

country: USA

institute: Emory University

description: Library name: PerC_B1_Tpos_612

library_source: genomic

data_processing:
Raw sequencing reads were mapped to the mm10 version of the mouse genome using Bowtie2
bigWig files were normalized to reads per million and generated using GenomicRanges and the bedGraphToBigWig function from the UCSC genome browser
Assembly: mm10
Supplementary files format and content: reads per million normalized bigWig files

molecule: genomic DNA

source_name: Peritoneal Cavity

extract_protocol:
Tissue were harvested and cells of each immune population were sorted into tdTomato positive and negative fractions representing early life origin B cells or non-early life origin B cells, respectively.
Cells were centrifuged for 10 minutes at 500xg, and tagmentation was performed by resuspending cells in 25 ul of Tagmentation mix (1X TD buffer (10 mM TAPS-NaOH pH 8.1, 5 mM MgCl2, 10% DMF), 2.5 μl Tn5 transposase, 0.1% Tween 20 and 0.02% Digitonin) and then incubated for 1 h at 37°C. DNA was purified and amplified into a sequencing library with KAPA HiFi Polymerase and the Nextera Indexing Kit Primers (Illumina, Inc).

treatment_protocol: To time-stamp early life origin B cells, Tamoxifen was dissolved in peanut oil at 10 mg/ml and either administered to Mb1Cre-ERT2;R26fl-STOP-tdTomato mice orally (≤ 10-day-old) or injected intraperitoneally (≥10-day-old).

value: Peritoneal Cavity

tag: time stamp

value: Tpos

value: B1 B cell

tag: sorting markers

tag: mouse id


title: PerC_B1_Tneg_612

description: Library name: PerC_B1_Tneg_612

value: Tneg


title: 2317 Kidney Cortex NT FFPE

type: RNA

value: Kidney


title: NK cells from the Hematogenous  model of dissemination 3

description: Library name: Sample 11

extract_protocol:
After dissection, lymph nodes were disrupted into single cell suspension using sterile nuclease free tools. Following NK cell sorting in sterile condition, Total RNA was extracted using the Direct‐zol RNA Microprep kit (R2061 Zymo Research, Irvine, CA, USA). RNA quality and concentration were assessed using the Agilent 2100 bioanalyzer (Agilent Technologies Inc., Santa Clara, CA, USA).
NEBNext Ultraexpress RNA Library Prep Kit for Illumina (E3330S - New England BioLabs Inc.) was used with the NEBNext Multiplex Oligos for Illumina (New England BioLabs Inc.) and NEBNext® Poly(A) mRNA Magnetic Isolation Module for cDNA synthesis with the addition of barcode sequences. The pre-pool sequencing was performed using the NextSeq2000 (Illumina, San Diego, CA, USA) with the P2 reagents kit V3 (100cycles; Illumina). Samples were processed starting from stranded, single-ended 120bp-long sequencing reads.

value: NK cell


title: Spleen_MzB_Tneg_612

description: Library name: Spleen_MzB_Tneg_612

source_name: Spleen

value: Spleen

value: Marginal Zone B cell


title: 2317 Kidney Medulla NT FFPE


title: HF_4_1_CG

description:
Library name: HF_4_1_CG
column name in salmon.merged.gene_counts.tsv: HF_4_1_CG


title: HF_3_2_Tau

description:
Library name: HF_3_2_Tau
column name in salmon.merged.gene_counts.tsv: HF_3_2_Tau

value: taurine


title: 2205 Liver NT FFPE

value: Liver

value: Met-recipient


title: HF_3_3_Tau

description:
Library name: HF_3_3_Tau
column name in salmon.merged.gene_counts.tsv: HF_3_3_Tau


title: E_mu-Myc lymphoma from cell culture 3

description: Library name: Sample 3

value: Lymph node

value: E_mu-Myc lymphoma


title: 2204 Lung NT Frozen

source_name: Frozen

value: Lung

value: Met-free


title: PP_MBC_Tpos_611

description: Library name: PP_MBC_Tpos_611

source_name: Peyer's Patch

value: Peyer's Patch

value: Memory B cell

value: CD19+, IgD–, CD38+


title: Spleen_MzB_Tpos_612

description: Library name: Spleen_MzB_Tpos_612

value: Tpos


title: HF_4_2_CG

description:
Library name: HF_4_2_CG
column name in salmon.merged.gene_counts.tsv: HF_4_2_CG

value: skin

value: human skin cell line

value: fibroblasts

value: chlorogenic acid


title: NK cells from the Lymphatic model of dissemination 2

description: Library name: Sample 6

value: NK cell


title: 2204 Liver NT FFPE


title: PerC_B1_Tneg_611

description: Library name: PerC_B1_Tneg_611

value: Peritoneal Cavity

value: Tneg

value: B1 B cell


title: NK cells from the Hematogenous  model of dissemination 2

description: Library name: Sample 10


title: PP_MBC_Tneg_611

description: Library name: PP_MBC_Tneg_611


title: HF_3_1_Tau

description:
Library name: HF_3_1_Tau
column name in salmon.merged.gene_counts.tsv: HF_3_1_Tau

value: taurine


title: 2205 Liver Met FFPE

value: Liver

value: Met


title: Spleen_FoB_Tpos_612

description: Library name: Spleen_FoB_Tpos_612

value: Spleen

value: Follicular B cells


title: 2204 Kidney NT FFPE

value: Kidney

value: Met-free


title: 2202 Lung NT Frozen

value: Lung

value: Met-recipient


title: HF_2_2_CGA

description:
Library name: HF_2_2_CGA
column name in salmon.merged.gene_counts.tsv: HF_2_2_CGA

value: skin

value: chlorogenic acid and taurine


title: PerC_B1_Tpos_611

description: Library name: PerC_B1_Tpos_611

value: Tpos


title: Spleen_FoB_Tneg_612

description: Library name: Spleen_FoB_Tneg_612


title: HF_1_3_Ctrl

description:
Library name: HF_1_3_Ctrl
column name in salmon.merged.gene_counts.tsv: HF_1_3_Ctrl

value: human skin cell line

value: fibroblasts

value: untreated


title: PP_MBC_Tpos_610

description: Library name: PP_MBC_Tpos_610

value: Peyer's Patch

value: Memory B cell

value: CD19+, IgD–, CD38+


title: HF_2_3_CGA

description:
Library name: HF_2_3_CGA
column name in salmon.merged.gene_counts.tsv: HF_2_3_CGA


title: NK cells from tumor free lymph node 4

description: Library name: Sample 4

value: Lymph node

value: NK cell


title: NK cells from the Hematogenous  model of dissemination 1

description: Library name: Sample 9


title: NK cells from tumor free lymph node 3

description: Library name: Sample 3


title: 2205 Kidney NT FFPE


title: NK cells from the Hematogenous  model of dissemination 4

description: Library name: Sample 12


title: PerC_B1_Tneg_610

description: Library name: PerC_B1_Tneg_610

value: Peritoneal Cavity

value: Tneg

value: B1 B cell


title: HF_1_1_Ctrl

description:
Library name: HF_1_1_Ctrl
column name in salmon.merged.gene_counts.tsv: HF_1_1_Ctrl


title: 2202 Liver NT FFPE

value: Liver


title: NK cells from the Lymphatic model of dissemination 1

description: Library name: Sample 5


title: PP_MBC_Tneg_610

description: Library name: PP_MBC_Tneg_610


title: NK cells from the Lymphatic model of dissemination 3

description: Library name: Sample 7


title: Spleen_MzB_Tpos_610

description: Library name: Spleen_MzB_Tpos_610

value: Spleen

value: Marginal Zone B cell


title: 1015 Liver NT FFPE

value: Met-free


title: Spleen_FoB_Tneg_610

description: Library name: Spleen_FoB_Tneg_610

value: Follicular B cells


title: NK cells from the Lymphatic model of dissemination 4

description: Library name: Sample 8


title: Spleen_MzB_Tneg_610

description: Library name: Spleen_MzB_Tneg_610


title: 2202 Lung Distant NT FFPE

value: Lung

value: Met-recipient


title: HEK293T siUBE2M RNA-seq (biol rep 3)

city: Houston

first: Wenyue

last: Cao

state: TX

address: 7255 Helix Park Ave

institute: Texas A&M University

description:
Library name: Sample 9
HK_E2_S3

data_processing:
Raw reads were quality-trimmed and filtered with fastp to remove adaptor and low-quality bases.
Clean reads were aligned to the human reference genome with HISAT2 v2.0.5 using default parameters.
Strand-specific counting was performed with featureCounts v1.5.0-p3 (-s 2; reverse-stranded) to obtain raw gene-level counts.
Expression values (FPKM) were calculated from gene counts and effective lengths.
Differential expression was analyzed using DESeq2 v1.20.0; significance thresholds were adjusted P < 0.05 and |log₂FC| ≥ 1.
Functional enrichment (GO/KEGG) was performed with clusterProfiler; GSEA was performed with the Broad Institute’s GSEA tool using curated GO and KEGG gene sets.
Assembly: Homo sapiens GRCh38 (hg38); gene annotation from GENCODE (v43)
Supplementary files format and content: Tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: Tab-delimited text file includes FPKM values for each Sample

molecule: polyA RNA

growth_protocol: HEK293T cells were cultured in DMEM (high glucose) supplemented with 10% FBS at 37 °C in a humidified incubator with 5% CO₂. Cells were maintained in antibiotic-free medium prior to transfection and were harvested at ~70–90% confluency.

extract_protocol:
Total RNA extraction was performed by Novogene following the manufacturer’s protocol; RNA quality was assessed by Qubit/NanoDrop and Agilent 2100 Bioanalyzer (RIN ≥ 7.0).
Poly(A)+ mRNA was purified from total RNA using oligo(dT) magnetic beads. Purified mRNA was fragmented, and first-strand cDNA was synthesized with random hexamers followed by second-strand synthesis incorporating dUTP (strand-specific protocol). After end repair, A-tailing, adaptor ligation, size selection, PCR amplification and purification, libraries were QC-checked by Qubit/real-time PCR and Agilent 2100 Bioanalyzer. Libraries were sequenced on an Illumina NovaSeq X Plus platform (paired-end 150 bp).

treatment_protocol: HEK293T cells were seeded in antibiotic-free complete DMEM (10% FBS) and transfected using Lipofectamine™ RNAiMAX (Thermo Fisher, Cat. 13778075) with one of the following siRNAs: URM1 (60 nM; MCE, HY-RS15508), NAE1 (50 nM; MCE, HY-RS09007), or UBE2M (70 nM; MCE, HY-RS15355). Cells were incubated for 48 h post-transfection before harvesting for RNA (and protein) extraction.

value: human embryonic kidney cell line

value: siRNA targeting UBE2M


title: 1012 Liver NT FFPE


title: NK cells from tumor free lymph node 2

description: Library name: Sample 2


title: HF_1_2_Ctrl

description:
Library name: HF_1_2_Ctrl
column name in salmon.merged.gene_counts.tsv: HF_1_2_Ctrl

value: skin

value: human skin cell line

value: fibroblasts

value: untreated


title: 0908 Kidney NT FFPE

value: Kidney


title: HF_2_1_CGA

description:
Library name: HF_2_1_CGA
column name in salmon.merged.gene_counts.tsv: HF_2_1_CGA

value: chlorogenic acid and taurine


title: 2202 Lung Adjacent NT FFPE


title: PerC_B1_Tneg_609

description: Library name: PerC_B1_Tneg_609

value: Peritoneal Cavity

value: Tneg


title: NK cells from tumor free lymph node 1

description: Library name: Sample 1

value: Lymph node

value: NK cell


title: 1913 Kidney NT FFPE


title: control REP4

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

country: Germany

institute: University clinics Freiburg

description: Gene expression from mouse follicular B cells

hyb_protocol: Labeled fragments were hybridized to Affymetrix/Thermo Fisher mouse Clariome D arrays for 16h at 45°C with 60 rpm in an Affymetrix Hybridization oven 645.

scan_protocol: After washing and staining, the arrays were scanned with the Affymetrix GeneChip Scanner 3000 7G. CEL-files were produced from the raw data with Affymetrix GeneChip Command Console Software.

data_processing: CEL files were analysed using the oligo R package. RMA method, log2 transformed were used to normalized the probe intensities.

label: Biotin

source_name: Follicular B cells were sorted from spleen

label_protocol: We used the Affymetrix WT Pico kit for cDNA synthesis, amplification, and second-cycle cDNA synthesis, as well as fragmentation and labeling with Biotin, as described by the manufacturer.

growth_protocol: A single cell suspension was derived from murine spleens by crushing through a 100µm pore filter. They were then frozen in FCS 10% DMSO

extract_protocol: RNA was isolated immediately after sorting using the miRNeasy Mini Kit from Qiagen according to the manufacturer's instructions.

treatment_protocol: After thawing, splenocytes were stained on ice for CD19, B220, CD21 and CD23. Follicular B cells (CD19+;B220+;CD21med;IgM med) were sorted usingMoFlo Astrios cell sorter (Beckman Coulter)

value: SPL

tag: genotype

value: Kindlin-3 fl/fl


title: Kindlin-3 KO REP3

value: Follicular B cells

value: Kindlin-3 fl/fl mb1 Cre


title: HEK293T siURM1 RNA-seq (biol rep 2)

description:
Library name: Sample 11
HK_URM_S2

value: siRNA targeting URM1


title: HEK293T siURM1 RNA-seq (biol rep 1)

description:
Library name: Sample 10
HK_URM_S1

value: human embryonic kidney cell line


title: 2202 Liver Met FFPE

value: Liver

value: Met


title: Spleen_MzB_Tneg_609

description: Library name: Spleen_MzB_Tneg_609

value: Spleen

value: Marginal Zone B cell


title: HEK293T siNAE1 RNA-seq (biol rep 2)

description:
Library name: Sample 5
HK_E1_S2

value: siRNA targeting NAE1


title: Spleen_FoB_Tpos_610

description: Library name: Spleen_FoB_Tpos_610

value: Tpos


title: PerC_B1_Tpos_610

description: Library name: PerC_B1_Tpos_610

value: B1 B cell


title: HEK293T siUBE2M RNA-seq (biol rep 2)

description:
Library name: Sample 8
HK_E2_S2

value: siRNA targeting UBE2M


title: Kindlin-3 KO REP4


title: HEK293T siUBE2M RNA-seq (biol rep 1)

description:
Library name: Sample 7
HK_E2_S1


title: HEK293T siNAE1 RNA-seq (biol rep 3)

description:
Library name: Sample 6
HK_E1_S3


title: 0821 Liver NT FFPE

value: Met-free


title: 0815 Lung NT Frozen

value: Lung


title: PerC_B1_Tpos_609

description: Library name: PerC_B1_Tpos_609

value: Peritoneal Cavity


title: 0821 Lung NT Frozen


title: HEK293T siNAE1 RNA-seq (biol rep 1)

description:
Library name: Sample 4
HK_E1_S1


title: 0814 Kidney NT FFPE

value: Kidney


title: Spleen_FoB_Tneg_609

description: Library name: Spleen_FoB_Tneg_609

value: Tneg


title: IVT 7SK -Larp7 rep2 EtOH

first: Anthony

last: Mustoe

address: 1 Baylor Plaza

institute: Baylor College of Medicine

description: Library name: Larp7_Unbound_Unmod_REP2

library_source: other

data_processing:
Fastq files were aligned and parsed using ShapeMapper2 (v.2.3; https://github.com/Weeks-UNC/shapemapper2)
Parsed mutation files were analyzed using DanceMapper (v1.2; https://github.com/MustoeLab/DanceMapper)
Assembly: sequence files used for alignment are included as supplementary files
Supplementary files format and content: Archives (.tar.gz) include bernouli mixture save files (.bm), normalized N1/3 profiles (profile.txt), and normalized N7 profiles (profile.txtga). A complete description of these files is provided in the DanceMapper and Shapemapper documentation.

molecule: other

source_name: in vitro transcript

extract_protocol:
RNA was extracted from cells using TRIzol reagent (Ambion) or RNeasy Mini Kit (Qiagen).
RNA was converted to cDNA using mutational profiling (MaP) reverse transcription. Amplicon libraries were prepared by 2-step PCR. Ribosomal libaries were prepared via Nextera.

treatment_protocol: RNA modified under variable folding conditions with DMS (or ethanol) for 6 minutes at 37 C, quenched with 20% 2-mercaptoethanol, and ethanol precipitated.

value: EtOH control

value: in vitro transcript


title: HEK293T control siRNA RNA-seq (biol rep 3)

description:
Library name: Sample 3
HK_S3

value: control siRNA


title: IVT 7SK -Larp7 rep3 EtOH

description: Library name: Larp7_Unbound_Unmod_REP3


title: IVT 7SK -Larp7 rep1 EtOH

description: Library name: Larp7_Unbound_Unmod_REP1


title: Kindlin-3 KO REP2

value: Follicular B cells

value: SPL

value: Kindlin-3 fl/fl mb1 Cre


title: Spleen_FoB_Tpos_609

description: Library name: Spleen_FoB_Tpos_609

value: Spleen


title: 0811 Lung NT Frozen

value: Met-recipient


title: Spleen_MzB_Tpos_609

description: Library name: Spleen_MzB_Tpos_609

value: Marginal Zone B cell


title: Kindlin-3 KO REP1


title: 0814 Liver NT FFPE

value: Liver


title: 0811 Kidney NT FFPE


title: control REP2

value: Kindlin-3 fl/fl


title: control REP1


title: HEK293T control siRNA RNA-seq (biol rep 1)

description:
Library name: Sample 1
HK_S1

value: human embryonic kidney cell line


title: 0809 Lung NT Frozen


city: Boston

first: Liang

last: Yang

state: MA

address: 77 Avenue Louis Pasteur

department: Pathology

institute: Harvard Medical School

description:
Library name: I38H9_lung_LCMVarm_D30_allT_P14_SMARTA_mouse0140_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

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: 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 30)

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

value: FALSE

tag: jax

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: 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


description:
Library name: I38H9_lung_LCMVarm_D30_allT_P14_SMARTA_mouse0140_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

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

tag: cell type


title: HEK293T control siRNA RNA-seq (biol rep 2)

description:
Library name: Sample 2
HK_S2

tag: cell line

value: human embryonic kidney cell line

tag: treatment

value: control siRNA


description:
Library name: I38H9_lung_LCMVarm_D30_allT_P14_SMARTA_mouse0140_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

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcode process and gene/ ADT/ hash counts were generated using Cellranger software v7.0.0.
TCRab contig annotations were generating using the cellranger vdj function from Cellranger software v7.0.0. The contigs generated were then mapped to with IMGT, and TRA and TRB chains put back together to create a summary table.
GEX and FBC libraries were processed using Seurat, where RNA, ADT QC was performed, a long with HTO demultiplexing to assign each cell a sample
Assembly: mm10
Supplementary files format and content: Cellranger output files: 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

value: TRUE

value: Pan organ and time course analysis of T cells in acute LCMV (armstrong day 30)

tag: strain

tag: genetics

tag: Sex

tag: age weeks

tag: pool of_mice

tag: jax

tag: infection agent

tag: infection dose

tag: prep description

tag: organ

tag: organ uberon_id


title: 0807 Liver NT FFPE

description: RNA was profiled using the Canine IO Panel

tag: nat tissue

value: Liver

value: Met-free


title: IVT 7SK -Larp7 rep3 DMS

description: Library name: Larp7_Unbound_Mod_REP3

value: DMS treated

tag: tissue

value: in vitro transcript


description:
Library name: I38H8_smallintestineLP_LCMVarm_D30_allT_P14_SMARTA_mouse0140_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: exp name

tag: lab

value: Goldrath

tag: organism name

value: P14 and SMARTA > wt

value: male

value: FALSE

value: LCMV armstrong

value: 2?ó10E5 PFU

value: lamina propria of small intestine

tag: t specificity

tag: target cells

tag: gating strategy

tag: sample comments

tag: batch


title: 0802 Lung NT Frozen

value: Lung

value: Met-recipient


title: IVT 7SK +Larp7 rep3 DMS

description: Library name: Larp7_bound_Mod_REP3

tag: treatment


title: IVT 7SK -Larp7 rep1 DMS

description: Library name: Larp7_Unbound_Mod_REP1


description:
Library name: I38H8_smallintestineLP_LCMVarm_D30_allT_P14_SMARTA_mouse0140_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

tag: age weeks

tag: pool of_mice

tag: jax

tag: infection agent

tag: infection dose

tag: prep description

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

tag: organ

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

tag: cell type

value: T cells


title: IVT 7SK -Larp7 rep2 DMS

description: Library name: Larp7_Unbound_Mod_REP2

value: DMS treated

tag: tissue

value: in vitro transcript


title: IVT 7SK +Larp7 rep2 DMS

description: Library name: Larp7_bound_Mod_REP2


title: C12_WT_Tala

city: Oxford

first: Gwendoline

last: Hoslett

address: MRC Weatherall Institute of Molecular Medicine (Oxford University & John Radcliffe Hospital)

department: Oncology

country: United Kingdom

data_processing:
Original data from Illumina is transformed to sequenced reads by CASAVA base recognition (Base Calling).
Data was filtered to remove reads with adapter contamination, remove reads when uncertain nucleotides constitute more than 10 percent of either read (N > 10%) and remove reads when low quality nucleotides (Base Quality less than 5) constitute more than 50 percent of the read
Assembly: hg38
Supplementary files format and content: .xls file which includes count data and FPKM data for samples which are named in column headers

source_name: Breast

growth_protocol: Cells were maintained in DMEM supplemented with 10% FBS and penicilin/strpetomycin in 37C with 5% CO2

extract_protocol:
RNA was extracted using GeneJet purification kit (K0731, ThermoFisher), according to manufacturer's instructions. 200 ng was sent for seqencing.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using dTTP for non-directional library. For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

treatment_protocol: Talazoparib treated cells were treated with 100 nM Talazoparib for 24 hours. Untreated conditions were reated with DMSO as a veicle control for 24 hours.

value: Breast

tag: cell line

value: epithelial-like

tag: genotype

value: WT

value: talazoparib


title: C12_KO_Tala

institute: MRC Weatherall Institute of Molecular Medicine (Oxford University & John Radcliffe Hospital)

value: TEX264 knockout


description:
Library name: I38H8_smallintestineLP_LCMVarm_D30_allT_P14_SMARTA_mouse0140_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: cite seq

value: TRUE

tag: exp name

value: Pan organ and time course analysis of T cells in acute LCMV (armstrong day 30)

tag: lab

value: Goldrath

tag: organism name

value: P14 and SMARTA > wt

value: male

value: FALSE

value: LCMV armstrong

value: 2?ó10E5 PFU

value: lamina propria of small intestine

tag: organ uberon_id

tag: t specificity

tag: target cells

tag: gating strategy

tag: sample comments


title: C8_KO_Tala

tag: treatment


title: C8_WT_Tala

tag: cell type


title: C12_WT_utd

tag: tissue

value: untreated


title: 0802 Lung Met Frozen

tag: nat tissue

value: Lung

value: Met


title: control REP3

value: Follicular B cells

value: SPL

tag: genotype

value: Kindlin-3 fl/fl


title: 0731 Liver NT FFPE

value: Liver

value: Met-recipient


description:
Library name: I38H7_smallintestineIEL_LCMVarm_D30_allT_P14_SMARTA_mouse0140_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

value: TRUE

tag: strain

tag: genetics

tag: Sex

tag: age weeks

tag: pool of_mice

tag: jax

tag: infection agent

tag: infection dose

tag: prep description

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

tag: organ

value: epithelium of small intestine

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

tag: batch


title: HEK293T in cell 7SK rep4 EtOH

description: Library name: HEK_7SK_07-31_rep2_unmod

tag: treatment

value: EtOH control

tag: cell line


title: IVT 7SK +Larp7 rep1 DMS

description: Library name: Larp7_bound_Mod_REP1

value: DMS treated

tag: tissue

value: in vitro transcript


title: 0731 Liver Met FFPE

tag: nat tissue

value: Met


title: C8_WT_utd

value: Breast

tag: cell type

value: epithelial-like

tag: genotype

value: WT

value: untreated


description:
Library name: I38H7_smallintestineIEL_LCMVarm_D30_allT_P14_SMARTA_mouse0140_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

tag: exp name

value: Pan organ and time course analysis of T cells in acute LCMV (armstrong day 30)

tag: lab

value: Goldrath

tag: organism name

tag: strain

value: P14 and SMARTA > wt

value: male

value: FALSE

value: LCMV armstrong

value: 2?ó10E5 PFU

tag: organ uberon_id

tag: t specificity

tag: target cells

tag: gating strategy

tag: sample comments


title: H4_KO_Tala

source_name: cervix

tag: tissue

value: cervix

tag: cell line

value: HeLa

value: epithelial cell

value: TEX264 knockout

tag: treatment

value: talazoparib


title: 0706 Liver NT FFPE

tag: nat tissue

value: Liver

value: Met-recipient


title: HEK293T in cell 7SK rep3 EtOH

description: Library name: HEK_7SK_07-31_rep1_unmod

value: EtOH control


title: HEK293T in cell 7SK rep4 DMS

description: Library name: HEK_7SK_07-31_rep2_mod

value: DMS treated


title: H4_WT_Tala

tag: cell type

tag: genotype

value: WT


description:
Library name: I38H7_smallintestineIEL_LCMVarm_D30_allT_P14_SMARTA_mouse0140_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

value: TRUE

value: Pan organ and time course analysis of T cells in acute LCMV (armstrong day 30)

tag: genetics

tag: Sex

tag: age weeks

tag: pool of_mice

tag: jax

tag: infection agent

tag: infection dose

tag: prep description

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

tag: organ

value: epithelium of small intestine

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

tag: batch


title: 0628 Kidney NT FFPE

value: Kidney


title: H4_WT_utd

tag: tissue

value: cervix

tag: cell line

value: HeLa

value: epithelial cell

tag: treatment

value: untreated


title: HEK293T in cell 7SK rep2 EtOH

description: Library name: HEK_7SK_04-19_rep2_unmod

value: EtOH control


title: 0621 Lung NT Frozen

tag: nat tissue

value: Lung

value: Met-recipient


description:
Library name: I38H6_LNmesenteric_LCMVarm_D30_allT_P14_SMARTA_mouse0140_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: cite seq

value: TRUE

tag: exp name

tag: lab

value: Goldrath

tag: organism name

tag: strain

value: P14 and SMARTA > wt

value: male

value: FALSE

value: LCMV armstrong

value: 2?ó10E5 PFU

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

value: mesenteric lymph node

tag: organ uberon_id

tag: t specificity

tag: target cells

tag: gating strategy

value: CD45+ CD3e+

tag: sample comments

tag: cell type


title: 0628 Kidney Met FFPE

value: Kidney

value: Met


title: HEK293T in cell 7SK rep3 DMS

description: Library name: HEK_7SK_07-31_rep1_mod

value: DMS treated


description:
Library name: I38H6_LNmesenteric_LCMVarm_D30_allT_P14_SMARTA_mouse0140_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: hashtag number

tag: condition detailed_organ

value: Pan organ and time course analysis of T cells in acute LCMV (armstrong day 30)

tag: genetics

tag: Sex

tag: age weeks

tag: pool of_mice

tag: jax

tag: infection agent

tag: infection dose

tag: prep description

tag: organ

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

tag: batch


title: H2_WT_utd

tag: tissue

value: cervix

tag: cell line

value: HeLa

value: epithelial cell

tag: genotype

value: WT

tag: treatment

value: untreated


title: HEK293T in cell 7SK rep2 DMS

description: Library name: HEK_7SK_04-19_rep2_mod


title: H2_KO_Tala

tag: cell type

value: TEX264 knockout

value: talazoparib


description:
Library name: I38H5_bonemarrow_LCMVarm_D30_allT_P14_SMARTA_mouse0140_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: cite seq

value: TRUE

tag: exp name

tag: lab

value: Goldrath

tag: organism name

tag: strain

value: P14 and SMARTA > wt

value: male

value: FALSE

value: LCMV armstrong

value: 2?ó10E5 PFU

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

value: bone marrow

tag: organ uberon_id

tag: t specificity

tag: target cells

tag: gating strategy

tag: sample comments


title: 0621 Liver NT FFPE

tag: nat tissue

value: Liver

value: Met-recipient


title: HEK293T in cell 7SK rep1 EtOH

description: Library name: HEK_7SK_04-19_rep1_unmod

value: EtOH control

tag: cell line


description:
Library name: I38H6_LNmesenteric_LCMVarm_D30_allT_P14_SMARTA_mouse0140_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: condition detailed_organ

value: Pan organ and time course analysis of T cells in acute LCMV (armstrong day 30)

tag: genetics

tag: Sex

tag: age weeks

tag: pool of_mice

tag: jax

tag: infection agent

tag: infection dose

tag: prep description

tag: organ

value: mesenteric lymph node

value: P14, SMARTA

value: all T including P14 and SMARTA

value: 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


title: H2_WT_Tala

value: cervix

value: HeLa

tag: cell type

value: epithelial cell

tag: genotype

value: WT

tag: treatment

value: talazoparib


title: 0621 Kidney Met FFPE

tag: nat tissue

value: Kidney

value: Met


title: H1_WT_Tala

tag: cell line


description:
Library name: I38H5_bonemarrow_LCMVarm_D30_allT_P14_SMARTA_mouse0140_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: cite seq

value: TRUE

tag: exp name

tag: lab

value: Goldrath

tag: organism name

tag: strain

value: P14 and SMARTA > wt

value: male

value: FALSE

value: LCMV armstrong

value: 2?ó10E5 PFU

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

value: bone marrow

tag: organ uberon_id

tag: t specificity

tag: target cells

tag: gating strategy

tag: sample comments


description:
Library name: I38H5_bonemarrow_LCMVarm_D30_allT_P14_SMARTA_mouse0140_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: condition detailed_organ

value: Pan organ and time course analysis of T cells in acute LCMV (armstrong day 30)

tag: genetics

tag: Sex

tag: age weeks

tag: pool of_mice

tag: jax

tag: infection agent

tag: infection dose

tag: prep description

tag: organ

value: P14, SMARTA

value: all T including P14 and SMARTA

value: CD45+ CD3e+

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: H1_KO_Tala

tag: tissue

value: cervix

tag: cell line

value: HeLa

value: epithelial cell

tag: genotype

value: TEX264 knockout

tag: treatment

value: talazoparib


title: 0601 Liver NT FFPE

tag: nat tissue

value: Liver

value: Met-free


description:
Library name: I38H4_salivarygland_LCMVarm_D30_allT_P14_SMARTA_mouse0140_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

tag: lab

value: Goldrath

tag: organism name

tag: strain

value: P14 and SMARTA > wt

value: male

value: FALSE

value: LCMV armstrong

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

value: submandibular gland

tag: organ uberon_id

tag: t specificity

tag: target cells

tag: gating strategy

value: IV- CD45+ CD3e+

tag: sample comments


title: 0601 Kidney Met FFPE

value: Kidney

value: Met


title: H1975 cells, 9α,11αOH-KA (AL-X), 48 hours

city: Taichung

first: Po-Chen

last: Chu

address: No. 100, Sec. 1, Jingmao Rd., Beitun Dist.

country: Taiwan

institute: China Medical University

description:
Library name: Sample 6
Column name in Gene_counts_All_Samples.txt : H1975_AL_x10

data_processing:
Sequencing data (FASTQ reads) were generated using Welgene Biotech's pipeline based on Illumina's basecalling program bcl2fastq v2.20.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

extract_protocol:
Total RNA was extracted using Trizol® Reagent (Invitrogen, USA) according to the instruction manual.
SureSelect XT HS2 mRNA Library Preparation kit (Agilent, USA) was used for library construction followed by AMPure XP beads (Beckman Coulter, USA) size selection.

tag: cell line

tag: cell type

value: Non-small cell lung cancer

value: WT

value: 9α,11αOH-KA (AL-X)

tag: time

value: 48 hours


title: HCC827 cells, 9α,11αOH-KA (AL-X), 48 hours

description:
Library name: Sample 4
Column name in Gene_counts_All_Samples.txt : HCC827_AL_x10

tag: genotype

tag: treatment


title: 0621 Kidney Medulla NT FFPE

tag: nat tissue

value: Met-recipient


title: 0621 Liver Met FFPE

value: Liver


title: HEK293T in cell 7SK rep1 DMS

description: Library name: HEK_7SK_04-19_rep1_mod

value: DMS treated


title: Control_3

city: Chengdu

first: Bi-Sen

last: Ding

state: Sichuan

address: Wuhou District, Renmin three paragraphs

department: The West China Second UniversityHospital of Sichuan University

country: China

institute: Sichuan University

description:
Library name: Control5
Singleron GEXSCOPE®

data_processing:
The demultiplexing,barcoded processing, gene counting and aggregation were made using the CeleScope software v1.15.0
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Liver

extract_protocol:
Liver samples were obtained through surgical biopsy, preserved in SCelLiVe® Tissue Storage Solution, and minced into small pieces. The tissue was digested at 37°C for 40 minutes using a digestion solution containing 1 mg/ml Collagenase I, 1 mg/ml Collagenase II, 1 mg/ml Dispase II, and 10 U/ml DNase I. After obtaining the cell suspension, red blood cells were removed, and the sample was centrifuged at 50 g for 2 minutes to isolate non-parenchymal cells (NPCs).
Library was performed according to the manufacter's instruction(GEXSCOPE® Single Cell RNA Library Kit)

tag: tissue

value: NPCs

tag: gender

value: Male

tag: age

tag: fibrosis stage


description:
Library name: I38H4_salivarygland_LCMVarm_D30_allT_P14_SMARTA_mouse0140_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

tag: cite seq

value: TRUE

tag: exp name

value: Pan organ and time course analysis of T cells in acute LCMV (armstrong day 30)

tag: lab

value: Goldrath

tag: organism name

tag: genetics

value: P14 and SMARTA > wt

tag: Sex

value: male

tag: age weeks

tag: pool of_mice

tag: jax

tag: infection agent

tag: infection dose

value: 2?ó10E5 PFU

tag: prep description

tag: organ

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

tag: batch


description:
Library name: I38H4_salivarygland_LCMVarm_D30_allT_P14_SMARTA_mouse0140_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: strain

value: FALSE

value: LCMV armstrong

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

value: submandibular gland

tag: organ uberon_id

tag: t specificity

tag: target cells

tag: gating strategy

value: IV- CD45+ CD3e+

tag: sample comments

tag: cell type


title: H1_WT_utd

value: cervix

tag: cell line

value: HeLa

value: epithelial cell

tag: genotype

value: WT

tag: treatment

value: untreated


title: A549 cells, DMSO, 48 hours

description:
Library name: Sample 1
Column name in Gene_counts_All_Samples.txt : A549_DMSO

value: Non-small cell lung cancer

value: DMSO

tag: time

value: 48 hours


title: HCC827 cells, DMSO, 48 hours

description:
Library name: Sample 3
Column name in Gene_counts_All_Samples.txt : HCC827_DMSO


title: 0601 Kidney Distant NT FFPE

description: RNA was profiled using the Canine IO Panel

tag: nat tissue

value: Kidney

value: Met-recipient


title: H1975 cells, DMSO, 48 hours

description:
Library name: Sample 5
Column name in Gene_counts_All_Samples.txt : H1975_DMSO


title: 0327 Lung NT Frozen

value: Lung


description:
Library name: I38H3_prostate_LCMVarm_D30_allT_P14_SMARTA_mouse0140_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: 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 30)

tag: lab

value: Goldrath

tag: organism name

tag: genetics

value: P14 and SMARTA > wt

tag: Sex

value: male

tag: age weeks

tag: pool of_mice

tag: jax

tag: infection agent

tag: infection dose

value: 2?ó10E5 PFU

tag: prep description

value: prostate gland

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: A549 cells, 9α,11αOH-KA (AL-X), 48 hours

description:
Library name: Sample 2
Column name in Gene_counts_All_Samples.txt : A549_AL_x10

tag: cell line

tag: cell type

value: Non-small cell lung cancer

tag: genotype

value: WT

tag: treatment

value: 9α,11αOH-KA (AL-X)


title: Fibrosis_20

description:
Library name: T0061
Singleron GEXSCOPE®

tag: tissue

value: Liver

value: NPCs

tag: gender

value: Female

tag: age

tag: fibrosis stage


title: Control_2

description:
Library name: Control2
Singleron GEXSCOPE®


title: siSRRM2_Biol_rep_2

city: Sant Cugat del Vallés

first: Samuel

last: Bru

state: Barcelona

address: Josep Trueta, s/n

department: Biomedical Sciences

country: Spain

institute: Universitat Internacional de Catalunya

description:
Library name: SRRM2_2
Sc_SRRM2_ReadCount_FPKM_TPM.csv
CLK3_PSI.csv
NUDT3_PSI.csv
PRUNE1_PSI.csv
SRRM2_PSI.csv

data_processing:
Step 1: Raw FASTQ reads were aligned to the human genome (hg38) using VAST-Tools (v2.5.1) with the VASTDB human library (vastdb.hs2.23.06.20).
Step 2: Percent-Spliced-In (PSI) values were quantified for all alternative splicing events (single/complex exon skipping, microexons, alternative 5’/3’ splice sites, and retained introns).
Step 3: Individual sample outputs were combined into a single table using 'vast-tools combine' with default parameters.
Step 4: Differentially spliced events were identified using 'vast-tools compare', applying a filter of |ΔPSI| > 10 and a non-overlapping PSI distribution (minimum range of 5) between groups.
Step 5: Gene-level expression was quantified as raw read counts, FPKM, and TPM values. Alternative splicing was quantified to calculate Percent-Spliced-In (PSI) and delta PSI (dPSI) values. Both types of processed data are provided as CSV files.
Assembly: hg38
Supplementary files format and content: The gene expression matrix (Sc_SRRM2_ReadCount_FPKM_TPM.csv) contains raw read counts, FPKM, and TPM values for the samples.
Supplementary files format and content: The gene expression matrix (Empty_CLK3_NUDT3_PRUNE1_ReadCount.csv) contains raw read counts for the samples. Note: The expression matrix includes additional samples (PPX1) from the same sequencing run that are not part of this study.
Supplementary files format and content: The alternative splicing tables (named [GeneName]_PSI.csv, e.g., NUDT3_PSI.csv) contain Percent-Spliced-In (PSI) and delta PSI (dPSI) values. Each splicing file is filtered to show significant events (|dPSI| > 10) regulated by the specific condition indicated in the filename. To demonstrate event specificity and provide full biological context, these files also include the PSI and dPSI values for those selected events across all sequenced samples in the study.

growth_protocol: HEK293T cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM; Sigma, Cat. D5671) supplemented with 10% fetal bovine serum (FBS; Labclinics, Cat. FBS-12A), 1% GlutaMAX (Labclinics, Cat. X0551-100), and 1% penicillin/streptomycin (Sigma, Cat. P0781-100). Cultures were maintained in a humidified incubator at 37ºC with a 5% CO2 atmosphere until the time of harvest for RNA extraction.

extract_protocol:
Total RNA was isolated 48 hours post-transfection using TRIzol Reagent (Thermo Fisher Scientific) according to the manufacturer's protocol. RNA concentration and purity were determined using a NanoDrop spectrophotometer, and RNA integrity was confirmed before library preparation.
Libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina) following the manufacturer’s protocol (Reference Guide #1000000040498). The process included poly-A selection of mRNA, followed by fragmentation, cDNA synthesis, adapter ligation, and PCR amplification. The resulting libraries were sequenced on an Illumina platform.

treatment_protocol: Cells were transfected using FuGENE (Promega) with either pWPI plasmids (empty or carrying NUDT3, CLK3, or PRUNE1) or siRNAs (Scramble or siSRRM2). Total RNA was extracted 48 hours post-transfection.


title: 0601 Kidney Adjacent NT FFPE

tag: nat tissue

value: Kidney

value: Met-recipient


description:
Library name: I38H3_prostate_LCMVarm_D30_allT_P14_SMARTA_mouse0140_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 day 30)

tag: lab

value: Goldrath

tag: organism name

tag: strain

tag: genetics

value: FALSE

value: LCMV armstrong

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

tag: organ

tag: organ uberon_id

tag: t specificity

tag: target cells

tag: gating strategy

value: IV- CD45+ CD3e+

tag: sample comments

tag: batch


description:
Library name: I38H3_prostate_LCMVarm_D30_allT_P14_SMARTA_mouse0140_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: P14 and SMARTA > wt

tag: Sex

value: male

tag: age weeks

tag: pool of_mice

tag: jax

tag: infection agent

tag: infection dose

value: 2?ó10E5 PFU

tag: prep description

value: prostate gland

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

tag: cell type

value: T cells


title: Fibrosis_21

description:
Library name: T0081
Singleron GEXSCOPE®

value: Liver

value: NPCs

tag: gender

value: Male

tag: age

tag: fibrosis stage


title: Fibrosis_18

description:
Library name: T0058
Singleron GEXSCOPE®

value: Female


title: 0301 Kidney NT FFPE

tag: nat tissue

value: Kidney

value: Met-recipient


title: 0301 Kidney Met FFPE

value: Met


description:
Library name: I38H2_spleen_LCMVarm_D30_allT_P14_SMARTA_mouse0140_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 day 30)

tag: lab

value: Goldrath

tag: organism name

tag: strain

tag: genetics

value: FALSE

value: LCMV armstrong

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

tag: organ

value: spleen

tag: organ uberon_id

tag: t specificity

tag: target cells

value: CD45+ CD3e+


title: siSRRM2_Biol_rep_1

description:
Library name: SRRM2_1
Sc_SRRM2_ReadCount_FPKM_TPM.csv
CLK3_PSI.csv
NUDT3_PSI.csv
PRUNE1_PSI.csv
SRRM2_PSI.csv

tag: cell line

tag: genotype


title: Fibrosis_19

description:
Library name: T0059
Singleron GEXSCOPE®

tag: tissue

tag: cell type

tag: gender

tag: age

tag: fibrosis stage


description:
Library name: I38H2_spleen_LCMVarm_D30_allT_P14_SMARTA_mouse0140_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

value: P14 and SMARTA > wt

tag: Sex

value: male

tag: age weeks

tag: pool of_mice

tag: jax

tag: infection agent

tag: infection dose

value: 2?ó10E5 PFU

tag: prep description

value: P14, SMARTA

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: 0327 Lung Met Frozen

tag: nat tissue

value: Lung

value: Met


title: Control_1

description:
Library name: Control1
Singleron GEXSCOPE®

tag: tissue

value: Liver

tag: cell type

value: NPCs

tag: gender

value: Female

tag: age


description:
Library name: I38H2_spleen_LCMVarm_D30_allT_P14_SMARTA_mouse0140_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

value: TRUE

tag: exp name

value: Pan organ and time course analysis of T cells in acute LCMV (armstrong day 30)

tag: lab

value: Goldrath

tag: organism name

tag: strain

tag: genetics

value: FALSE

tag: organ

tag: organ uberon_id

tag: t specificity

tag: target cells


title: siScramble_control_Biol_rep_2

description:
Library name: Sc_2
Sc_SRRM2_ReadCount_FPKM_TPM.csv
CLK3_PSI.csv
NUDT3_PSI.csv
PRUNE1_PSI.csv
SRRM2_PSI.csv

tag: cell line

tag: genotype

value: WT


title: 0215 Liver NT FFPE

tag: nat tissue

value: Met-free


title: 0213 Liver NT FFPE

value: Met-recipient


title: Fibrosis_16

description:
Library name: T0056
Singleron GEXSCOPE®

tag: tissue

tag: cell type

tag: gender

tag: fibrosis stage


title: siScramble_control_Biol_rep_1

description:
Library name: Sc_1
Sc_SRRM2_ReadCount_FPKM_TPM.csv
CLK3_PSI.csv
NUDT3_PSI.csv
PRUNE1_PSI.csv
SRRM2_PSI.csv


title: I38H1_spleen_allT_mouse0139_TCR

description:
Library name: I38H1_spleen_allT_mouse0139_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

value: spleen

tag: cite seq

value: wt

tag: Sex

value: male

tag: age weeks

tag: pool of_mice

tag: jax

tag: prep description

value: mechanical dissociation alone

value: all T

tag: gating strategy

value: CD45+ CD3e+

tag: batch


title: Fibrosis_17

description:
Library name: T0057
Singleron GEXSCOPE®

value: Liver

tag: age


title: I38H1_spleen_allT_mouse0139_GEX

description:
Library name: I38H1_spleen_allT_mouse0139_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: exp name

tag: lab

tag: organism name

tag: strain

tag: genetics

tag: organ

tag: organ uberon_id

tag: target cells

value: T cells


title: 0207 Kidney Medulla NT FFPE

description: RNA was profiled using the Canine IO Panel

tag: nat tissue

value: Kidney


title: pWPI_PRUNE1_Biol_rep_4

description:
Library name: PRUNE1_4
Empty_CLK3_NUDT3_PRUNE1_ReadCount.csv
CLK3_PSI.csv
NUDT3_PSI.csv
PRUNE1_PSI.csv

tag: cell line

tag: genotype


title: Fibrosis_15

description:
Library name: T0050
Singleron GEXSCOPE®

tag: tissue

tag: cell type

value: NPCs

tag: gender

value: Female

tag: fibrosis stage


title: pWPI_PRUNE1_Biol_rep_3

description:
Library name: PRUNE1_3
Empty_CLK3_NUDT3_PRUNE1_ReadCount.csv
CLK3_PSI.csv
NUDT3_PSI.csv
PRUNE1_PSI.csv


title: 0207 Kidney Cortex NT FFPE


title: I38H1_spleen_allT_mouse0139_FBC

description:
Library name: I38H1_spleen_allT_mouse0139_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

value: Pan organ and time course analysis of T cells in acute LCMV (armstrong day 30)

tag: Sex

tag: age weeks

tag: pool of_mice

tag: jax

tag: prep description

tag: gating strategy

tag: batch


title: Fibrosis_14

description:
Library name: T0049
Singleron GEXSCOPE®

value: Male

tag: age


title: Fibrosis_13

description:
Library name: T0048
Singleron GEXSCOPE®


title: pWPI_PRUNE1_Biol_rep_2

description:
Library name: PRUNE1_2
Empty_CLK3_NUDT3_PRUNE1_ReadCount.csv
CLK3_PSI.csv
NUDT3_PSI.csv
PRUNE1_PSI.csv

tag: cell line

tag: genotype


title: pWPI_PRUNE1_Biol_rep_1

description:
Library name: PRUNE1_1
Empty_CLK3_NUDT3_PRUNE1_ReadCount.csv
CLK3_PSI.csv
NUDT3_PSI.csv
PRUNE1_PSI.csv


title: 8in4 CD8.2 LN T cells - rep3

city: Frederick

first: Jack

last: Chen

state: MD

address: 8560 Progress Drive

institute: Frederick National Laboratory

description: Library name: MS12-8in4-8a.2

data_processing:
Reads were trimmed and aligned to mouse genome (mm10) with STAR aligner. Differentially expression genes (DEG) were selected by the Limma package.
Assembly: mm10
Supplementary files format and content: raw countsin txt format from RSEM

source_name: CD8.2+ H57+CD62L+ LN T cells

extract_protocol:
CD62L+ CD4 or CD8 T cells and CD62L+ CD8.1 or CD8.2 T cells were sorted from lymph nodes of B6 and 8in4 mice.  Total RNA was prepared from pooled sorted cells using RNeasy Plus Mini Kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain

value: CD8 Dual

tag: cell type

value: CD8.2+ H57+CD62L+ LN T cells

value: 6-10 wk-old


title: pWPI_NUDT3_Biol_rep_3

description:
Library name: NUDT3_3
Empty_CLK3_NUDT3_PRUNE1_ReadCount.csv
CLK3_PSI.csv
NUDT3_PSI.csv
PRUNE1_PSI.csv


title: 0201 Liver NT FFPE

tag: nat tissue

value: Met-free


description:
Library name: I38H10_LNmediastinal_LCMVarm_D30_allT_P14_SMARTA_mouse0140_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: exp name

tag: lab

value: Goldrath

tag: organism name

tag: genetics

value: P14 and SMARTA > wt

value: male

value: FALSE

tag: infection agent

value: LCMV armstrong

tag: infection dose

value: 2?ó10E5 PFU

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

tag: organ

value: mediastinal lymph node

tag: organ uberon_id

tag: t specificity

value: P14, SMARTA

tag: target cells

value: all T including P14 and SMARTA

tag: sample comments

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


description:
Library name: I38H10_LNmediastinal_LCMVarm_D30_allT_P14_SMARTA_mouse0140_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: hashtag number

tag: condition detailed_organ

tag: cite seq

value: TRUE

value: Pan organ and time course analysis of T cells in acute LCMV (armstrong day 30)

tag: Sex

tag: age weeks

tag: pool of_mice

tag: jax

tag: prep description

tag: gating strategy

value: CD45+ CD3e+

value: T cells

tag: batch


title: 8in4 CD8.1 LN T cells - rep3

description: Library name: MS11-8in4-8a.1

source_name: CD8.1+ H57+CD62L+ LN T cells

tag: strain

value: CD8 Dual

value: Male

tag: cell type

value: CD8.1+ H57+CD62L+ LN T cells

tag: age

value: 6-10 wk-old


title: Fibrosis_9

description:
Library name: T0023
Singleron GEXSCOPE®

tag: tissue

value: Liver

value: NPCs

tag: gender

value: Female

tag: fibrosis stage


title: 8in4 CD8.2 LN T cells - rep1

description: Library name: MS8-8in4-8a.2

value: CD8.2+ H57+CD62L+ LN T cells


title: Fibrosis_8

description:
Library name: T0017
Singleron GEXSCOPE®


title: 8in4 CD8.1 LN T cells - rep2

description: Library name: MS9-8in4-8a.1


title: pWPI_NUDT3_Biol_rep_2

description:
Library name: NUDT3_2
Empty_CLK3_NUDT3_PRUNE1_ReadCount.csv
CLK3_PSI.csv
NUDT3_PSI.csv
PRUNE1_PSI.csv

tag: cell line

tag: genotype


title: Fibrosis_12

description:
Library name: T0047
Singleron GEXSCOPE®


title: Fibrosis_11

description:
Library name: T0040
Singleron GEXSCOPE®


title: pWPI_NUDT3_Biol_rep_4

description:
Library name: NUDT3_4
Empty_CLK3_NUDT3_PRUNE1_ReadCount.csv
CLK3_PSI.csv
NUDT3_PSI.csv
PRUNE1_PSI.csv


title: ERRaKO 367

city: Shenzhen

first: Tongling

last: Huang

address: Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences  1068 Xueyuan Avenue,Shenzhen University Town,  Nanshan District, Shenzhen, China

description: Library name: Sample 5

data_processing:
Sequencing raw reads were preprocessed by filtering out rRNA reads, sequencing adapters, short-fragment reads and other low-quality reads. We used Hisat2（version:2.0.4）to map the cleaned reads to the GRCm38 reference genome with two mismatches. After genome mapping, Stringtie（version:1.3.0）was run with a reference annotation to generate FPKM values for known gene models. Differentially expressed genes were identified using Stringtie]. The p-value significance threshold in multiple tests was set by the false discovery rate (FDR) . The fold-changes were also estimated according to the FPKM in each sample.The differentially expressed genes were selected using the following filter criteria: FDR ≤0.05 and fold-change ≥2.
Assembly: GRCm38
Supplementary files format and content: xls file includes raw counts, FPKM for each Sample

source_name: gonadal white adipose tissue

extract_protocol:
Gonadal adipose tissue was homogenized and lysed with TRIzol reagent. Following phase separation, the aqueous phase was transferred to spin columns from the PureLink RNA Mini Kit (Vazyme #RC101-01) and processed according to the manufacturer's instructions.
The poly-A containing mRNA molecules were purified using poly-T oligo-attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under 94℃ for 8 min. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then go through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products are then purified and enriched with PCR to create the final cDNA library.

value: gonadal white adipose tissue

value: Non-cell-line-derived cells

value: white adipocyte

value: adipocyte-specific ESRRA deficiency

tag: treatment

value: Gonadal white adipose tissue from mice fed a high-fat high-cholesterol diet for 13 weeks


title: ERRaKO 379

institute: Shenzhen Institute of Advanced Technology

description: Library name: Sample 8


title: ERRaKO 377

description: Library name: Sample 7


title: Fibrosis_10

description:
Library name: T0039
Singleron GEXSCOPE®


title: pWPI_CLK3_Biol_rep_3

description:
Library name: CLK3_3
Empty_CLK3_NUDT3_PRUNE1_ReadCount.csv
CLK3_PSI.csv
NUDT3_PSI.csv
PRUNE1_PSI.csv


title: pWPI_CLK3_Biol_rep_4

description:
Library name: CLK3_4
Empty_CLK3_NUDT3_PRUNE1_ReadCount.csv
CLK3_PSI.csv
NUDT3_PSI.csv
PRUNE1_PSI.csv


title: ERRaFLOX 385

description: Library name: Sample 3

value: wild type


title: ERRaKO 369

description: Library name: Sample 6


title: Fibrosis_5

description:
Library name: T0009
Singleron GEXSCOPE®


title: pWPI_NUDT3_Biol_rep_1

description:
Library name: NUDT3_1
Empty_CLK3_NUDT3_PRUNE1_ReadCount.csv
CLK3_PSI.csv
NUDT3_PSI.csv
PRUNE1_PSI.csv


title: Fibrosis_4

description:
Library name: T0005
Singleron GEXSCOPE®


title: pWPI_CLK3_Biol_rep_2

description:
Library name: CLK3_2
Empty_CLK3_NUDT3_PRUNE1_ReadCount.csv
CLK3_PSI.csv
NUDT3_PSI.csv
PRUNE1_PSI.csv


description:
Library name: I38H10_LNmediastinal_LCMVarm_D30_allT_P14_SMARTA_mouse0140_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 30)

tag: lab

value: Goldrath

tag: organism name

tag: genetics

value: P14 and SMARTA > wt

value: male

value: FALSE

tag: infection agent

value: LCMV armstrong

tag: infection dose

value: 2?ó10E5 PFU

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

tag: organ

value: mediastinal lymph node

tag: organ uberon_id

tag: t specificity

value: P14, SMARTA

tag: target cells

value: all T including P14 and SMARTA

tag: sample comments

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


title: B6 CD8 LN T cells - rep2

description: Library name: MS4-B6-CD8

source_name: CD8+ H57+CD62L+ LN T cells

tag: strain

tag: Sex

value: Male

tag: cell type

value: CD8+ H57+CD62L+ LN T cells

tag: age

value: 6-10 wk-old


title: 8in4 CD8.1 LN T cells - rep1

description: Library name: MS7-8in4-8a.1

value: CD8 Dual

value: CD8.1+ H57+CD62L+ LN T cells


title: ERRaFLOX 389

description: Library name: Sample 4

tag: tissue

value: gonadal white adipose tissue

tag: cell line

value: Non-cell-line-derived cells

value: white adipocyte

tag: genotype

value: wild type

tag: treatment

value: Gonadal white adipose tissue from mice fed a high-fat high-cholesterol diet for 13 weeks


title: 8in4 CD8.2 LN T cells - rep2

description: Library name: MS10-8in4-8a.2

value: CD8.2+ H57+CD62L+ LN T cells


title: Fibrosis_7

description:
Library name: T0013
Singleron GEXSCOPE®

value: Liver

value: NPCs

tag: gender

tag: fibrosis stage


title: ERRaFLOX 357

description: Library name: Sample 1


title: Fibrosis_6

description:
Library name: T0011
Singleron GEXSCOPE®


title: pWPI_control_Biol_rep_3

description:
Library name: Empty_3
Empty_CLK3_NUDT3_PRUNE1_ReadCount.csv
CLK3_PSI.csv
NUDT3_PSI.csv
PRUNE1_PSI.csv

value: WT


title: Fibrosis_2

description:
Library name: T0003
Singleron GEXSCOPE®


title: pWPI_CLK3_Biol_rep_1

description:
Library name: CLK3_1
Empty_CLK3_NUDT3_PRUNE1_ReadCount.csv
CLK3_PSI.csv
NUDT3_PSI.csv
PRUNE1_PSI.csv


title: B6 CD4 LN T cells - rep3

description: Library name: MS5-B6-CD4

source_name: CD4+ H57+CD62L+ LN T cells

value: CD4+ H57+CD62L+ LN T cells


title: B6 CD8 LN T cells - rep3

description: Library name: MS6-B6-CD8


title: Fibrosis_1

description:
Library name: T0001
Singleron GEXSCOPE®


title: pWPI_control_Biol_rep_4

description:
Library name: Empty_4
Empty_CLK3_NUDT3_PRUNE1_ReadCount.csv
CLK3_PSI.csv
NUDT3_PSI.csv
PRUNE1_PSI.csv


title: ERRaFLOX 372

description: Library name: Sample 2


title: Pancreas, P48-Cre control, replicate 1

city: Philadelphia

first: Michael

last: Noji

address: 421 Curie Blvd., BRB II/III, Room 638

department: Cancer Biology

institute: University of Pennsylvania

description:
Library name: Sample 7
P8922_R

data_processing:
Fastq files were trimmed using Fastp
Salmon was used to count the trimmed data.
Assembly: Salmon counted the trimmed data against the Gencode vM35, which was built on the genome GRCm39. Transcriptome count data were annotated and summzred to the gene level with tximeta and further annoteated with biomaRt.
Supplementary files format and content: .txt are TPM counts

source_name: Pancreas

growth_protocol: Male animals were all euthanized at the same age and at the same time of day (5 1/w weeks old at 1:30-2 PM).

extract_protocol:
Total RNA was isolated from frozen pancreata after RNAlater was removed from the sample using Trizol according to the manufacturer's guidelines (Invitrogen).
RNA-seq libraries were generated by Novogene for stanard non-directional library prep for bulk RNA-sequencing at a depth of 6Gb (20M PE reads)

treatment_protocol: Animals were euthanized via cervical dislocation and pancreata were quickly excised and put into RNAlater stabilization solution (Invitrogen) and kept at -20C until extraction.

value: Pancreas

value: 5 1/2 weeks

tag: time of_sac

tag: batch

value: Batch 2


title: pWPI_control_Biol_rep_1

description:
Library name: Empty_1
Empty_CLK3_NUDT3_PRUNE1_ReadCount.csv
CLK3_PSI.csv
NUDT3_PSI.csv
PRUNE1_PSI.csv


title: B6 CD4 LN T cells - rep1

description: Library name: MS1-B6-CD4

value: Male


title: Pancreas, P48-Cre control, replicate 2

description:
Library name: Sample 8
P8924_R


title: Pancreas, P48-Cre;DBTfl/fl, replicate 4

description:
Library name: Sample 6
P8906_R


title: Fibrosis_3

description:
Library name: T0004
Singleron GEXSCOPE®

value: Female


title: gastrocnemius, KIC_2

city: Madrid

first: Manuel

middle: J

last: Gomez

state: Madrid

address: Melchor Fernández Almagro, 3

institute: CNIC

data_processing:
FastQ files for each sample were obtained using CASAVA v1.8 software (Illumina).
Sequencing adapter contaminations were removed using cutadapt, discarding those reads that were shorter than 30 nt after trimming.
Resulting reads were aligned against the GRCm38.91 mouse transcriptome, with RSEM v1.3.1, to obtain expression estimates at gene level.
Expected expression counts were then processed with an analysis pipeline that used Bioconductor package Limma for normalization (using TMM method), considering only those genes for which expression was at least 1 count per million (CPM) in at least 3 samples.
Assembly: GRCm38.91
Supplementary files format and content: TMM-normalized counts (CPM) for genes with expression level of at least 1 count per million (CPM) in at least 3 samples.

source_name: gastrocnemius

extract_protocol:
Total RNA was isolated using the RNeasy Fibrous Tissue Mini Kit (Qiagen) from gastrocnemius samples of mice fed a HFD for 6 weeks. RNA quality was verified using an Agilent 2100 Bioanalyzer, and individual samples with an RNA Integrity Number (RIN) > 8 were included in the study.
Total RNA (100 ng) was used to generate barcoded RNA-seq libraries using the NEBNext Ultra II Directional RNA Library preparation kit (New England Biolabs) according to manufacturer’s instructions. First, poly A+ RNA was purified using poly-T oligo- attached magnetic beads followed by fragmentation and first and second cDNA strand synthesis. Next, cDNA ends were repaired and adenylated. The NEBNext adaptor was then ligated followed by second strand removal, uracile excision from the adaptor and PCR amplification. The size of the libraries was checked using the Agilent 2100 Bioanalyzer and the concentration was determined using the Qubit® fluorometer (ThermoFisher)
Libraries were sequenced on a Illumina MiSeq system to generate 51 base single reads.

value: gastrocnemius

value: control


title: Dentate gyrus cells from P2 hGFAP-Cre;Kdm6bF/F mice

city: San Francisco

first: Eugene

last: Gil

state: CA

address: 1585 5th Avenue, , Apt 301

institute: University of California, San Francisco

description:
Library name: Kdm6b KO
10x Genomics

data_processing:
Libraries were sequenced to a mean depth of approximately 55,000 reads/cell and processed through cellranger 3.0.2 (10x Genomics) with a raw recovery of 5847 cells (3555 WT and 2292 KO).
All subsequent processing analyses were performed using Seurat version 3.
Low-quality cells were filtered out of the dataset: percentage mitochondrial genes >10%, percentage ribosomal genes > 25% and < 5%.
Assembly: refdata-cellranger-mm10-3.0.0
Supplementary files format and content: tab-separated values files and matrix files

source_name: Dentate gyrus

extract_protocol:
DG were microdissected from P2 hGFAP-Cre;Kdm6bF/F mice and littermate controls (2 animals per condition) and dissociated into single cells using the Worthington Papain Dissociation system following all manufacturer protocol steps including ovomucoid gradient.
Single-cell libraries were generated using the 10x Genomics Chromium Single Cell 3’ Assay with a targeted cell recovery of 5000 (2500 cells per condition).

value: Dentate gyrus

value: Dentate gyrus cells

value: Kdm6b KO


title: Polyp_ECRS_CD4_CD45ROposi

city: chiba city

first: Masahiro

last: Kiuchi

state: chiba

address: cyuoku inohana1-8-1

country: Japan

institute: Chiba univercity

description: Library name: Hirasawa_Polyp_ECRS_CD4_CD45ROposi

library_source: genomic single cell

data_processing:
Raw base call (BCL) files were converted to FASTQ files using Cell Ranger ATAC mkfastq.
Sequencing reads were aligned to the human reference genome (hg38) using Cell Ranger ATAC.
Fragment files were generated and PCR duplicates were removed.
Low-quality nuclei were filtered based on fragment counts, transcription start site (TSS) enrichment score, and nucleosome signal.
Peak calling was performed using MACS2 as implemented in Cell Ranger ATAC.
A peak-by-cell count matrix was generated.
Dimensionality reduction using latent semantic indexing (LSI) and clustering were performed.
Visualization was performed using UMAP embedding.
Gene activity scores were computed based on chromatin accessibility at gene bodies and promoter regions.
Differential chromatin accessibility between PBMC-derived and polyp-derived CD4 memory T cells was analyzed.
Assembly: hg38
Supplementary files format and content: Processed data are provided in HDF5 (.h5) format containing peak-by-cell count matrices of chromatin accessibility, including cell barcodes and genomic peak coordinates.

source_name: Nasal Polyp

growth_protocol: Peripheral blood and nasal polyp tissues were obtained from patients diagnosed with ECRS undergoing clinical evaluation or endoscopic sinus surgery. All samples were collected under institutional ethical approval with informed consent.

extract_protocol:
PBMCs were isolated from peripheral blood using density gradient centrifugation. Nasal polyp tissues were mechanically and enzymatically dissociated into single-cell suspensions. CD4 memory T cells were enriched or sorted (e.g., CD3⁺ CD4⁺ CD45RO⁺) using fluorescence-activated cell sorting (FACS) or magnetic bead-based separation. Nuclei were isolated using a lysis buffer optimized for ATAC-seq, followed by filtration and counting prior to library preparation.
scATAC-seq libraries were prepared using the 10x Genomics Chromium Single Cell ATAC platform according to the manufacturer’s instructions. Briefly, isolated nuclei were subjected to Tn5 transposition, followed by droplet-based barcoding, PCR amplification, and library construction. Libraries were sequenced on an Illumina platform to generate paired-end reads.

treatment_protocol: No experimental treatment was applied prior to sample collection.

value: Nasal Polyp

value: CD4T memory

tag: disease

value: ECRS

value: female


title: pWPI_control_Biol_rep_2

description:
Library name: Empty_2
Empty_CLK3_NUDT3_PRUNE1_ReadCount.csv
CLK3_PSI.csv
NUDT3_PSI.csv
PRUNE1_PSI.csv


title: PBMC_ECRS_CD4_CD45ROposi

description: Library name: Hirasawa_PBMC_ECRS_CD4_CD45ROposi

source_name: PBMC

value: PBMC


title: B6 CD4 LN T cells - rep2

description: Library name: MS3-B6-CD4

value: 6-10 wk-old


title: Pancreas, P48-Cre;DBTfl/fl, replicate 3

description:
Library name: Sample 5
P8905_R


title: Dentate gyrus cells from P2 littermate controls

description:
Library name: Kdm6b WT
10x Genomics

value: WT


title: Pancreas, P48-Cre;DBTfl/fl, replicate 1

description:
Library name: Sample 3
P7510

value: Pancreas

value: Batch 1


title: SAM24422624_LIB5461011_C3AR1_KO_PBS

city: Mississauga

first: Justin

middle: JM

last: Wong

address: 7070 Mississauga Road

country: Canada

institute: Hoffmann-La Roche Limited

description: Library name: SAM24422624_LIB5461011

data_processing:
FASTQs were processed with the cellranger pipeline from 10X genomics. Transcript counts for a given gene were based on the number of unique UMIs (up to one mismatch) for reads overlapping exons in sense orientation. Cell barcodes from empty droplets were filtered by requiring a minimum number of detected transcripts. Sample quality was further assessed based on the distribution of per-cell statistics, such as total number of reads, percentage of reads mapping uniquely to the reference genome, percentage of mapped reads overlapping exons, number of detected transcripts (UMIs), number of detected genes, and percentage of mitochondrial transcripts.  After this primary analysis step, cells with less than 1,000 total UMIs or greater than 10% mitochondrial UMIs were discarded. Doublets were identified using Doublet Finder and removed from downstream analyses.
Cell type annotations were determined using markers from: doi:10.1016/j.cell.2018.06.021, doi:10.1016/j.celrep.2017.12.066, doi:10.1016/j.celrep.2022.111189
Assembly: GRCm38
Supplementary files format and content: raw_counts.csv: comma-separated values of annotated gene counts
Supplementary files format and content: cell_info.csv: comma-separated values of mouse identification, biological data, etc.

source_name: mouse hippocampi

growth_protocol: 4~5-month-old WT or C3aRKO mice

extract_protocol:
10x Genomics protocol. Briefly, hippocampi were chopped into small pieces and dissociated with enzyme mixes in a Neural Tissue Dissociation Kit (P) (Miltenyi 130-092-628) in the presence of actinomycin D. After dissociation, cells were resuspended in Hibernate A Low Fluorescence medium (Brainbits) containing 5% FBS, with Calcein Violet AM (Thermo Fisher C34858) and propidium iodide (Thermo Fisher P1304MP). Flow cytometry was used to sort and collect live single-cell suspensions for the single-cell RNAseq study.
Sample processing and library preparation was carried out using the Chromium Next GEM Automated Single Cell 3' Library & Gel Bead Kit v3.1 on the Chromium Connect Instrument according to manufacturer’s instructions. Live cell samples were  prepared to target 10,000 cells per sample and loaded to the instrument. Libraries were sequenced with HiSeq 4000 (Illumina).

treatment_protocol:
1.     WT mice injected with PBS: n = 5
2.     WT mice injected with LPS (1 mg/kg): n = 5
3.     C3aR KO mice injected with PBS: n = 5
4.     C3aR KO mice injected with LPS (1 mg/kg): n = 5

value: mouse hippocampi

value: C3AR1 KO

value: PBS


title: B6 CD8 LN T cells - rep1

description: Library name: MS2-B6-CD8

value: Male

value: CD8+ H57+CD62L+ LN T cells


title: gastrocnemius, KIC_1

value: gastrocnemius

value: control


title: gastrocnemius, KIC_3


title: SAM24422623_LIB5461010_C3AR1_WT_PBS

description: Library name: SAM24422623_LIB5461010

value: C3AR1 WT


title: Pancreas, DBTfl/fl control, replicate 2

description:
Library name: Sample 2
P7359

value: 5 1/2 weeks

value: DBTfl/fl


title: gastrocnemius, HN_2


title: gastrocnemius, HN_1


title: SAM24422622_LIB5461009_C3AR1_KO_LPS

description: Library name: SAM24422622_LIB5461009

value: LPS


title: J.gamma1,shLDHA

city: Nantong

first: Lingling

last: Feng

address: No. 399, Shiji Avenue

institute: Affiliated Maternity and Child Health Care Hospital of Nantong University

description: Library name: G-shLDHA

data_processing:
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated. Raw reads were firstly processed using fastp (v0.22.0) and the low quality reads were removed to obtain the clean reads. The clean reads were mapped to the reference genome using HISAT2 (v2.1.0). FPKM of each gene was calculated and the read counts of each gene were obtained by featureCounts. PCA analysis were performed using R (v 3.2.0) to evaluate the biological duplication of samples.
Assembly: Homo_sapiens_Ensembl_110 (http://asia.ensembl.org/Homo_sapien s/Info/Index)
Supplementary files format and content: csv files include FPKM values for each Sample

source_name: cell line

extract_protocol:
RNA was harvested using Trizol regent. 1 ug of total RNA was used forthe construction of sequencing libraries
1 μg total RNA was used for following library preparation. The poly(A) mRNA isolation was performed using Oligo(dT) beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second-strand cDNA were synthesized. The purified double-stranded cDNA was then treated to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired-end (PE) configuration according to manufacturer’s instructions

value: cell line

value: T cell acute lymphoblastic leukemia


title: gastrocnemius, COW_3


title: Jurkat,shLDHA

description: Library name: J-shLDHA

value: Jurkat


title: gastrocnemius, COW_2


title: Pancreas, P48-Cre;DBTfl/fl, replicate 2

description:
Library name: Sample 4
P7513


title: Monocyte derived alveolar macrophages 14 day post infection 3

city: Newark

first: Alexander

last: Lemenze

state: New Jersey

address: 185 South Orange Ave

institute: Rutgers

description: Library name: MoAM-Nb14-3

data_processing:
Trimming with cutadapt (v2.5)
Alignment with STAR (vSTAR_2.6.1d)
Hit count extraction with featureCounts (v1.6.4)
Assembly: GRCm38
Supplementary files format and content: tab delimited hit count file

source_name: Lung

extract_protocol:
Qiagen
polyA RNA-seq

value: Lung

value: alveolar macrophage

value: Cx3cr1-CreER x Rosa26-TdT

value: tamoxifen treated, post-Nb day 14


title: gastrocnemius, HN_3


title: gastrocnemius, COW_1


title: Jurkat, shControl

description: Library name: J-shNC


title: Homo sapiens, WTAP KD_input_3

city: Anhui

first: shan

last: zhang

address: No. 443, Huangshan Road

institute: University of Science and Technology of China

description: Library name: B3_input

data_processing:
Base calling software: BCL convert
Data filter: fastp(version 0.19.4), remove adapters, repeat sequences and low quality sequences
reads alignment: HISAT2(2.0.4)
Peak calling diffpeak: R package: exomepeak
Peak annotation: ANNOVAR
Transcript assembly and quantification: StringTie(2.1.2)
Differential expression analysis: R package: edgeR(4.1)
Assembly: eq GRCH38
Supplementary files format and content: BVSA_diffPeak_result.xlsx, which contained the result  of differential methylation sites
Supplementary files format and content: BVSA_all_diffPeak_Gene_differential_expression.xlsx contains genes with differential m6A modification and differential expression
Library strategy: MeRIP-Seq

source_name: Cervix

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions. RNA concentration and purity were assessed using a NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific, USA). Polyadenylated mRNA was subsequently purified from total RNA using the GenElute mRNA Miniprep Kit (Sigma, cat. no. MRN10-1KT) through two rounds of enrichment.
the polyA RNA was fragmented at 86 °C for 7 minutes using the Magnesium RNA Fragmentation Module (NEB, cat. no. E6150), then incubated for 2 hours at 4 °C with 5 μg of m6A-specific antibody (Synaptic Systems, cat. no. 202003) in immunoprecipitation buffer (50 mM Tris-HCl, 750 mM NaCl, 0.5% Igepal CA-630). Immunoprecipitated RNA  were extracted, purified, and subjected to reverse transcription to generate cDNA.

value: Cervix

value: HeLa

value: Epithelial Cell

value: WTAP Knockdown


title: Monocyte derived alveolar macrophages 14 day post infection 1

description: Library name: MoAM-Nb14-1


title: Tissue resident alveolar macrophages 14 day post infection 3

description: Library name: TRAM-Nb14-3


title: Homo sapiens, WTAP KD_IP_3

description: Library name: B3_IP


title: Pancreas, DBTfl/fl control, replicate 1

description:
Library name: Sample 1
P7355

value: Pancreas

value: Male

value: Batch 1


title: Homo sapiens, WTAP KD_IP_2

description: Library name: B2_IP


title: J.gamma1,shControl

description: Library name: G-shNC


title: Tissue resident alveolar macrophages 14 day post infection 2

description: Library name: TRAM-Nb14-2


title: Homo sapiens, control_IP_3

description: Library name: A3_IP

value: WT


title: SAM24422620_LIB5461007_C3AR1_KO_LPS

description: Library name: SAM24422620_LIB5461007

value: mouse hippocampi

value: C3AR1 KO


title: in cell ecoli rRNA rep1 EtOH

city: Houston

description: Library name: rRNA-ecoli-unmod-InCellr1

data_processing:
Fastq files were aligned and parsed using ShapeMapper2 (v.2.3; https://github.com/Weeks-UNC/shapemapper2)
Parsed mutation files were analyzed using DanceMapper (v1.2; https://github.com/MustoeLab/DanceMapper)
Assembly: sequence files used for alignment are included as supplementary files
Supplementary files format and content: Archives (.tar.gz) include bernouli mixture save files (.bm), normalized N1/3 profiles (profile.txt), and normalized N7 profiles (profile.txtga). A complete description of these files is provided in the DanceMapper and Shapemapper documentation.

organism: Escherichia coli

value: EtOH control


title: Homo sapiens, WTAP KD_input_2

description: Library name: B2_input


title: Monocyte derived alveolar macrophages 7 day post infection 5

description: Library name: MoAM-Nb7-5


title: SAM24422621_LIB5461008_C3AR1_KO_PBS

description: Library name: SAM24422621_LIB5461008

value: PBS


title: Monocyte derived alveolar macrophages 14 day post infection 2

description: Library name: MoAM-Nb14-2


title: SAM24422615_LIB5461002_C3AR1_WT_PBS

description: Library name: SAM24422615_LIB5461002

value: C3AR1 WT


title: SAM24422619_LIB5461006_C3AR1_WT_LPS

description: Library name: SAM24422619_LIB5461006

value: LPS


title: SAM24422618_LIB5461005_C3AR1_WT_PBS

description: Library name: SAM24422618_LIB5461005


title: Homo sapiens, control_input_2

description: Library name: A2_input


title: in cell ecoli rRNA rep2 EtOH

description: Library name: rRNA-ecoli-unmod-InCellr2


title: cell free -Mg ecoli rRNA rep1 EtOH

description: Library name: rRNA-ecoli-unmod-nomg

source_name: in vitro transcript

value: in vitro transcript


title: SAM24422617_LIB5461004_C3AR1_KO_PBS

description: Library name: SAM24422617_LIB5461004


title: Homo sapiens, control_input_3

description: Library name: A3_input


title: Homo sapiens, WTAP KD_IP_1

description: Library name: B1_IP


title: cell free NoMg ecoli rRNA rep1 DMS

description: Library name: rRNA-ecoli-mod-nomg

value: DMS treated


title: Tissue resident alveolar macrophages 14 day post infection 1

description: Library name: TRAM-Nb14-1

value: Lung

value: alveolar macrophage

value: Cx3cr1-CreER x Rosa26-TdT

value: tamoxifen treated, post-Nb day 14


title: SAM24422616_LIB5461003_C3AR1_KO_PBS

description: Library name: SAM24422616_LIB5461003


title: Monocyte derived alveolar macrophages 7 day post infection 2

description: Library name: MoAM-Nb7-2


title: Monocyte derived alveolar macrophages 7 day post infection 4

description: Library name: MoAM-Nb7-4


title: Homo sapiens, control_IP_2

description: Library name: A2_IP

value: Cervix

value: HeLa

value: Epithelial Cell


title: in cell ecoli rRNA rep2 DMS

description: Library name: rRNA-ecoli-mod-InCellr2


title: SAM24422610_LIB5460997_C3AR1_KO_LPS

description: Library name: SAM24422610_LIB5460997


title: SAM24422613_LIB5461000_C3AR1_KO_LPS

description: Library name: SAM24422613_LIB5461000


title: Monocyte derived alveolar macrophages 7 day post infection 3

description: Library name: MoAM-Nb7-3


title: in cell ecoli rRNA rep1 DMS

description: Library name: rRNA-ecoli-mod-InCellr1