title: 1371-1.TCR.23824.rs102648

description:
Library name: 102648
Fig5.seurat.rds
Fig5.counts.rds

value: Ilio-sacral LN,MesLN,PLN,Spleen


title: 1056-12.GEX.23244.rs93856

status: Public on Aug 12 2026

type: SRA

city: Beaverton

first: Benjamin

middle: N

last: Bimber

state: OR

address: 505 NW 185th Ave

country: USA

description:
Library name: 93856
FigS1.seurat.rds
FigS1.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds

library_source: transcriptomic

data_processing:
CellRanger count
DropletUtils emptyDrops
Seurat Normalize/Scale/PCA
Assembly: GCA_003339765.3
Supplementary files format and content: Sparse count matrix (RDS file)
Supplementary files format and content: Seurat Object (RDS file)

molecule: polyA RNA

organism: Macaca mulatta

source_name: PBMC

extract_protocol: 10x Genomics 5' VDJ scRNA-seq

tag: tissue

value: PBMC


title: EK81_Lv_3.623_PFOA_repl_3

city: Bloomington

first: Jason

middle: M

last: Tennessen

email: tennessenlab@gmail.com, tennlab@iu.edu, jtenness@iu.edu, tourigny@iu.edu

state: IN

address: 1001 E 3rd St

department: Biology

institute: Indiana University

description:
Library name: GSF3307-EK81_S1
Whole body OregonR Drosophila melanogaster larvae exposed to 3.623µM (1500ppb) PFOA, replicate 3
Larval 1500 ppb PFOA repl 3

data_processing:
Read were adapter trimmed using Trimmomatic ver. 0.38 setting the cutoff threshold for average base quality score at 20 over a window of 3 bases, excluding the reads shorter than 20 bases post-trimming. Cleaned reads were aligned to the Drosophila melanogaster reference genome using the RNA-seq aligner, STAR version STAR_2.7.3a. Read pairs mapping concordantly and uniquely to the exon regions of the annotated genes were counted using featureCounts tool ver. 2.0.0  of subread package. Read alignments to the antisense strand, or to multiple regions on the genome or those overlapping with multiple genes were ignored. Differential expression analysis was performed using DESeq2 ver. 1.24.0 and the p-values were corrected for multiple-testing using the Benjamini–Hochberg method.
Assembly: Drosophila melanogaster Flybase r6.47
Supplementary files format and content: EAK Larval PFOA RNA-seq count table

organism: Drosophila melanogaster

source_name: larval whole body

growth_protocol: Fly stocks were maintained on standard Bloomington Drosophila Stock Center (BDSC) food as described (Holsopple et al., 2023). Cultures were maintained at 25 °C with 50% relative humidity under a 12 h light/12 h dark cycle. The following BDSC stocks were used in this study: Oregon-R (RRID:BDSC_25211). For larval exposures mating bottles of adult flies were subjected to a 2 h pre‑lay period to prevent egg retention, followed by a 4 h egg-lay from which embryos were collected. For embryonic exposures, embryos were transferred directly onto PFOA‑supplemented BDSC food. For first‑instar (L1) exposures, embryos were maintained for 24 h on molasses–yeast egg‑laying caps in Petri dishes before transfer to PFOA‑spiked food within 4 h of hatching.

extract_protocol:
RNA was extracted by grinding frozen larval pellets in TRIzol Reagent (Thermo Fisher Scientific, 15596018) using a pellet pestle, following the manufacturer’s instructions. Purified RNA was resuspended in 50 µL of nuclease-free water (HyPure, SH30538.02) and subsequently repurified using a Qiagen RNeasy Plus Micro Kit.
Library consturction was done using Illumina TruSeq Stranded mRNA Library Prep kits

treatment_protocol: First-instar (L1) larvae were collected within 4 h of hatching and transferred to exposure chambers containing BDSC food supplemented with 0, 0.036, or 3.6 µM PFOA (25 larvae per chamber; three chambers per concentration). Sixty hours after hatching (84 h after egg laying [AEL]), third-instar (L3) larvae were collected from individual exposure chambers, transferred to 1.5-mL microcentrifuge tubes, washed three times with ice-cold 1× PBS (pH 7.4), and flash-frozen in liquid nitrogen.

value: larval whole body

tag: genotype

value: OregonR

tag: treatment

value: 3.623 µM PFOA

tag: treatment (pfoa_ppb)

tag: replicate


title: 1056-12.TCR.23244.rs93857

description:
Library name: 93857
FigS1.seurat.rds
FigS1.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: RNA-seq: A549-PTPN13KO Cells infected with EBOV 48hpi replicate 1

city: Cincinnati

first: Matthew

last: Weirauch

state: Ohio

address: 3333 Burnet Avenue

department: Center for Autoimmune Genomics and Etiology (CAGE)

institute: Cincinnati Children's Hospital Medical Center

description: Library name: A549_PTPN13KO_EBOV_48h_rep1

data_processing:
RNA-seq reads were mapped to the hg38-EBOV composite genome using the nf-core RNA-seq pipeline with the default alignment options (STAR and Salmon).
Assembly: hg38
Supplementary files format and content: Aligned reads in BigWig format generated by the nf-core RNA-seq pipeline

molecule: total RNA

organism: Homo sapiens

source_name: Lung

growth_protocol: A549 (CCL-185) cells were purchased from the ATCC and were maintained in Dulbecco’s Modified Eagle’s Medium (DMEM) (Corning) supplemented with 10% v/v fetal bovine serum (FBS) (Corning) and 1% v/v penicillin-streptomycin (Corning). PTPN13 knockout cell lines were generated using the lentiCRISPR v2 plasmid (Addgene #52961) produced by the Feng Zhang lab [PMID: 25075903]. Single-guide RNA was designed using http://crispr.mit.edu:8079/ and targeted the PDZ signaling domain of PTPN13. The sgRNA sequence was cloned into the lentiCRISPR v2 plasmid following the directions described [PMID: 24336571]. To generate the knockout cell lines, 500,000 A549 cells per well and 400,000 293T cells per well were plated in 6-well plates. The cells were transfected with 1 ug of plasmid using Lipofectamine 3000 or Mirus LT-1 respectively according to manufacturer recommendations. The A549 cells had their media replaced after 6 hours. 24-hours post transfection, the media was replaced with DMEM containing 10% FBS and 1.5uM puromycin for selection. Cells were grown in media containing puromycin until viable cell growth was detected. Once cells began growing, they were diluted and plated in 96-well plates to produce single clone colonies. Cells were expanded and then moved up to 6-well plates and finally a T75 flask once almost confluent. Knockout was verified by immunoblot.

extract_protocol:
Wildtype and PTPN13 knockout cells were infected at MOI=5 with EBOV, and RNA was isolated at 24 or 48 hours post infection.
RNA was enriched for Poly(A) RNa from total RNA using oligo(dT)-attached magnetic beads. First- and second-strand synthesis, adaptor ligation, and amplification of the library were performed using the Illumina TruSeq RNA sample preparation kit as recommended by the manufacturer (Illumina). Library quality was evaluated using an Agilent DNA-1000 chip on an Agilent 2100 Bioanalyzer. Quantification of library DNA templates was performed using qRT-PCR and a known-size reference standard. Cluster formation of the library DNA templates was performed using TruSeq PE cluster kit v3 (Illumina) and the Illumina cBot workstation under conditions recommended by the manufacturer.

treatment_protocol: A549  and PTPN13-KO cells were infected with EBOV strain Mayinga-76 originating from the CDC and maintained at the University of Texas Medical Branch at Galveston

value: Lung

tag: cell line

tag: cell type

value: epithelial cell

value: EBOV


title: 1056-12.HTO.23244.rs93855

description:
Library name: 93855
FigS1.seurat.rds
FigS1.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: ut7-Input

city: Suzhou

first: Fang

last: Fang

state: Jiangsu

address: 92 Zhongnan street

country: China

institute: Children’s Hospital of Soochow University

description: ChIP-Seq

library_source: genomic

data_processing:
Raw data of ChIP-Seq was aligned to the reference genome (UCSC hg38) using Bowtie2 (v 2.4.1)
Peaks were identified using MACS2 (v2.0.10)
Assembly: hg38
Supplementary files format and content: bw files for each Sample

molecule: genomic DNA

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared for sequecing using standard Illumina protocols.

value: WT


title: EK80_Lv_3.623_PFOA_repl_2

description:
Library name: GSF3307-EK80_S1
Whole body OregonR Drosophila melanogaster larvae exposed to 3.623µM (1500ppb) PFOA, replicate 2
Larval 1500 ppb PFOA repl 2


title: 1352-5.TCR.26910.rs102284

description:
Library name: 102284
Fig5.seurat.rds
Fig5.counts.rds

source_name: Spleen

value: Spleen


title: 1056-11.TCR.23244.rs93854

description:
Library name: 93854
Fig2.seurat.rds
Fig2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: 1056-11.GEX.23244.rs93853

description:
Library name: 93853
Fig2.seurat.rds
Fig2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: ut7-H3K27ac

description: ChIP-Seq


title: EK79_Lv_3.623_PFOA_repl_1

description:
Library name: GSF3307-EK79_S1
Whole body OregonR Drosophila melanogaster larvae exposed to 3.623µM (1500ppb) PFOA, replicate 1
Larval 1500 ppb PFOA repl 1


title: 1056-11.HTO.23244.rs93852

description:
Library name: 93852
Fig2.seurat.rds
Fig2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: WT_ISL1-WT_ISL1_OE_islet

city: Hinxton

first: MorPhiC

last: Consortium

address: Wellcome Genome Campus

country: United Kingdom

institute: EMBL-EBI

description:
Library name: WT_ISL1
H1 derived islet with ISL1 overexpressed

data_processing:
STAR Suite v1.6.1
https://github.com/morphic-bio/STAR-suite
Assembly: GRCh38 gencode.v44.primary_assembly
Supplementary files format and content: csv files including raw and normalised counts

extract_protocol:
Quick-RNA Purification Kit (Zymo Research, R1055)
SMART-Seq v4 + KAPA EvoPrep

value: ESC

tag: editing strategy

value: WT|overexpression

tag: altered gene_symbol

tag: time

value: 18 days

tag: model system

value: pancreatic islet

tag: parental cell_line


title: 1056-10.TCR.23132.rs93851

description:
Library name: 93851
Fig2.seurat.rds
Fig2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: 1056-10.GEX.23132.rs93850

description:
Library name: 93850
Fig2.seurat.rds
Fig2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: EK78_Lv_0.03623_PFOA_repl_3

description:
Library name: GSF3307-EK78_S1
Whole body OregonR Drosophila melanogaster larvae exposed to 0.03623µM (15ppb) PFOA, replicate 3
Larval 15 ppb PFOA repl 3


title: WT_BFP-WT_control_islet

description:
Library name: WT_BFP
H1 derived islet

value: Not applicable


title: 1056-10.HTO.23132.rs93849

description:
Library name: 93849
Fig2.seurat.rds
Fig2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: EK77_Lv_0.03623_PFOA_repl_2

description:
Library name: GSF3307-EK77_S1
Whole body OregonR Drosophila melanogaster larvae exposed to 0.03623µM (15ppb) PFOA, replicate 2
Larval 15 ppb PFOA repl 2


title: 1056-9.TCR.23244.rs93848

description:
Library name: 93848
FigS1.seurat.rds
FigS1.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: PDX1_ISL1-PDX1_KO_ISL1_islet

description:
Library name: PDX1_ISL1
H1 derived islet with PDX1 KO and ISL1 overexpressed

value: KO|overexpression


title: AMs CD13+ IWC-1

city: Chengdu

first: Yun

last: Shi

address: No 37, Guoxuexiang

institute: West China Hospital, Sichuan University

description: Library name: CD13+-1

data_processing:
The raw reads were filtered using the Trimmomatic software to remove adapter and low quality reads. Quality control was processed by FastQC. The resulting clean reads were aligned to the mouse reference genome (mm10) using Burrows-Wheeler Aligner (BWA) program. The Binary Alignment/Map (BAM) file generated by the unique mapped reads was used as an input file. MACS2 (model-based analysis of ChIPseq) software was applied to call ATAC-seq peak regions with cutoff q-value < 0.05. Peaks were annotated by the function of annotatePeak of ChIPseeker. The target genes for peaks are filtered based on the column "distanceToTSS" (the distance from the peak center to the gene TSS) in the peak annotation analysis results (< 100,000 bp). After perfoming the PCA on the signals of merged peaks from all samples, plotPCA will sort the principal components according to the amount of variability of the data. To identify differential peaks between different samples, the ATAC-seq peaks of each sample were merged using the bedtools software. Then the counts of the reads over the bed was determined for each sample using bedtools multicov, and differential accessible peaks were identified using DESeq2, with the thresholds of | log2FC| > 1 and p < 0.05. Example peak views for key geneswere generated using the Integrative Genomics Viewer (IGV) to visualize changes in chromatin accessibility.
Assembly: mm10
Supplementary files format and content: BigWig,narrowPeak

organism: Mus musculus

source_name: BALF

growth_protocol: None.

extract_protocol:
cells were lysed in cold lysis buffer to extract nuclei (Buenrostro et al., 2015).A total of 40,000 nuclei were treated with transposase (Illumina Nextera) for 30 min at 37°C for transposition reactions.
Transposed DNA was amplified using NEBNext High-Fidelity 2X PCR Master Mix and indexed primers. The transposed DNA fragments were purified with a MinElute PCR Purification Kit (Qiagen) and used to generate the library via PCR amplification with barcoded primers using 1X NEBNext High-Fidelity PCR Master Mix (New England Biolabs, MA). The subsequent libraries were purified with the MinElute PCR Purification Kit (Qiagen) and were sequenced on the Illumina Novaseq 6000 platform with a paired-end read of 150bp.

treatment_protocol: CD45.2+ CD11c+ AMs (3 biological replicates) and CD45.2+ CD13+ AMs (2 biological replicates) were sorted from BALF of IWC-immunized and control CD45.2+ cells were isolated from control CD45.2+ mice using fluorescence-activated cell sorting (FACS). Cells were washed with cold PBS and counted for viability >85% using trypan blue. ATAC-Seq of these cells was done by Shanghai Jiayin Biotechnology Co., Ltd.

value: BALF

value: Alveolar macrophages

value: macrophages

value: IWC immunized CD13+ AMs


title: 1056-9.GEX.23244.rs93847

description:
Library name: 93847
FigS1.seurat.rds
FigS1.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds

value: PBMC


title: EK76_Lv_0.03623_PFOA_repl_1

description:
Library name: GSF3307-EK76_S1
Whole body OregonR Drosophila melanogaster larvae exposed to 0.03623µM (15ppb) PFOA, replicate 1
Larval 15 ppb PFOA repl 1

value: larval whole body

value: OregonR


title: 1056-9.HTO.23244.rs93846

description:
Library name: 93846
FigS1.seurat.rds
FigS1.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: 1056-8.TCR.23244.rs93845

description:
Library name: 93845
Fig2.seurat.rds
Fig2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: EK75_Lv_0uM_PFOA_repl_3

description:
Library name: GSF3307-EK75_S1
Whole body OregonR Drosophila melanogaster larvae exposed to 0µM (0ppb) PFOA, replicate 3
Larval 0 ppb PFOA repl 3

value: 0 µM PFOA


title: 1056-8.GEX.23244.rs93844

description:
Library name: 93844
Fig2.seurat.rds
Fig2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: PDX1_BFP-PDX1_KO_control_islet

description:
Library name: PDX1_BFP
H1 derived islet with PDX1 KO

value: KO


title: PAX6_ISL1-PAX6_KO_ISL1_OE_islet

description:
Library name: PAX6_ISL1
H1 derived islet with PAX6 KO and ISL1 overexpressed


title: 1056-7.TCR.23132.rs93842

description:
Library name: 93842
Fig2.seurat.rds
Fig2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: EK74_Lv_0uM_PFOA_repl_2

description:
Library name: GSF3307-EK74_S1
Whole body OregonR Drosophila melanogaster larvae exposed to 0µM (0ppb) PFOA, replicate 2
Larval 0 ppb PFOA repl 2


title: 1056-7.GEX.23132.rs93841

description:
Library name: 93841
Fig2.seurat.rds
Fig2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: DM-4T1-1

city: Shanghai

first: Rui

last: Zeng

address: Dong An Road

institute: Fudan University

description: Library name: Replicate 1

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values file and matrix files

source_name: Tumor

extract_protocol:
The dura mater with tumors was dissected from the cranium, then was minced into small pieces and digested with 1 mL of 1 mg/mL Collagenase VIII (#C2139, Sigma) and 0.1 mg/mL of DNase I (#DN25, Sigma) in 5%-FBS DMEM in a water bath at 37°C for 20 minutes. The enzymes were neutralized with 5 mL 5%-FBS DMEM, and samples were filtered through a 40 μm cell strainer, followed by centrifugation at 400×g for 5 minutes at 4°C.
Library was performed according to the manufacture's instructions (single cell 3' v2 protocol, 10x Genomics). Briefly, cells were resuspended in the master mix andloaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A  RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Tumor


title: PAX6_BFP-PAX6_KO_control_islet

description:
Library name: PAX6_BFP
H1 derived islet with PAX6 KO


title: 1056-7.HTO.23132.rs93840

description:
Library name: 93840
Fig2.seurat.rds
Fig2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: HMD_input

city: Taiyuan

first: Yuan

last: Fu

state: Shanxi

address: No. 56, Xinjian South Road, Yingze District

department: Department of Biochemistry and Molecular Biology, School of Basic Medicine

institute: Shanxi Medical University

data_processing:
The raw sequencing data were examined using the illumina analysis pipeline.
Using Bowtie2, the data were aligned to the Mus musculus reference genome (University of California, Santa Cruz, mm10).
The data were further analyzed through the ChIP-seq analysis based on the model (MACS) program (https://github.com/taoliu/MACS).
The enriched binding peaks were identified after normalization with the control input.
bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings.
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak

source_name: hippocampus

growth_protocol: C57BL/6 male mice (6-8 weeks old) were purchased from the Experimental Animal Center of Shanxi Medical University and fed with a high-methionine diet for more than 8 weeks.

extract_protocol:
The mice were fed with high-methionine or standard diet for 8 weeks, and the hippocampus of the two groups were isolated after being euthanized by cervical dislocation.
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 30 cycles on the thermocycler. Post amplification libraries were size selected at 250-500bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

treatment_protocol: Two mice per cage were housed at a stable temperature (24±2℃), with 12h/12h light/dark time alternation, and constant humidity. Free food and drinks available at all times.

value: hippocampus

value: high methionine feeding

tag: antibody

value: input


title: EK73_Lv_0uM_PFOA_repl_1

description:
Library name: GSF3307-EK73_S1
Whole body OregonR Drosophila melanogaster larvae exposed to 0µM (0ppb) PFOA, replicate 1
Larval 0 ppb PFOA repl 1


title: 1056-6.TCR.23244.rs93839

description:
Library name: 93839
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: ISL1_ISL1-ISL1_KO_ISL1_OE_islet

description:
Library name: ISL1_ISL1
H1 derived islet with ISL1 KO and ISL1 overexpressed

value: ESC

value: 18 days


title: 1056-6.HTO.23244.rs93837

description:
Library name: 93837
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: 1057-6.HTO.23244.rs93909

description:
Library name: 93909
FigS1.seurat.rds
FigS1.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: 1056-5.TCR.23244.rs93836

description:
Library name: 93836
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: P5A

type: RNA

first: Zhijun

last: Xia

address: No. 506, Fangxielu, Huangpu District

institute: Obstetrics and Gynecology Hospital of Fudan University

description: SAMPLE 10

data_processing: RT-qPCR was performed on an Applied Biosystems Applied Biosystems QuantStudio™ 5 system using SYBR Green Master Mix. Each reaction was run in triplicate. GAPDH was used as the internal reference gene, and relative expression was calculated using the 2⁻ΔΔCt method. Differentially expressed genes were defined as those with |log₂ fold change| > 1 and adjusted P < 0.05 (assessed by Student’s t‑test or Mann-Whitney U test, depending on data normality).

label: SYBR Green

organism: Rattus norvegicus

source_name: After abdominal skin disinfection, the skin was cut along the midline to expose the abdominal wall. A 2 cm × 2 cm area of the abdominal wall was excised to create the defect.

label_protocol: SYBR Green

extract_protocol: Total RNA was extracted from PT-treated HS tissue using TRIzol™ Reagent (Invitrogen, #15596026). To remove genomic DNA contamination, the RNA was treated with DNase I (Thermo Fisher Scientific). The concentration and purity of RNA were measured using a Nanodrop, ensuring an A260/A280 ratio between 1.8 and 2.0. RNA integrity was assessed using an Agilent 2100 Bioanalyzer (RIN value >7.0). Purified RNA was then reverse transcribed into cDNA using random hexamers and reverse transcriptase.

tag: group

value: Control Group Rep 5

value: Abdominal wall tissue

value: Model group (abdominal wall defect created, no repair).


title: 1056-5.GEX.23244.rs93835

description:
Library name: 93835
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: ISL1_BFP-ISL1_KO_control_islet

description:
Library name: ISL1_BFP
H1 derived islet with ISL1 KO

value: pancreatic islet


title: tRNA-derived fragment sequencing of sample AV060

city: New Haven

first: Ramanaiah

last: Mamillapalli

state: CT

address: 310 Cedar Street

department: OBGYN

institute: Yale University

description: Library name: tRF_AV060

data_processing:
Small RNA sequencing count data were analyzed using the DESeq2 package (RRID:SCR_000154) in R (version 4.5.0). Prior to differential expression analysis, low abundance tRFs were filtered to reduce noise and improve statistical power. Specifically, tRFs with fewer than 10 reads in at least two samples were excluded from downstream analyses. Samples with a sequencing depth of at least 750,000 reads were included in the analysis. Individual tRFs were considered detectable if at least one read was identified in a given sample. Differential expression was assessed using a negative binomial generalized linear model as implemented in DESeq2, with experimental group included as the primary factor in the design formula. Size factor normalization was applied to account for differences in library depth across samples. Dispersion parameters were estimated using the local regression fit, which is recommended for datasets with moderate sample size and heterogeneous variance structure. P-values were adjusted for multiple testing using the Benjamini–Hochberg false discovery rate (FDR) procedure. Adjusted p-values (padj) < 0.05 were considered statistically significant. We performed an internal validation of differential expression stability using a leave-one-out (LOO) resampling approach, whereby each sample is excluded in turn and differential expression analysis is repeated to evaluate the consistency of effect directions across runs. To assess robustness, differential expression results were also compared with those obtained using the edgeR quasi-likelihood F-test (RRID:SCR_012802), with concordance of log2 fold changes considered in the interpretation of tRF profiles.
Supplementary files format and content: AllatRF.counts.csv is a csv file that lists the tRF counts for each relevant sample. Allametadata.tRF.csv is a csv file that lists the group (ex. Control. Treatment) for each relevant sample. The reason for the processed data files having less count than the total samples listed in metadata is that not every sample had detected tRF counts above the baseline. Samples with a sequencing depth of at least 750,000 reads were included in the analysis, and are the ones we consider scientifically relevant. Individual tRFs were considered detectable if at least one read was identified in a given sample.

source_name: Serum

extract_protocol:
Total RNA was isolated from serum samples using the Qiagen miRNeasy Mini Kit (cat. #17004, Qiagen, Germantown, MD, USA), following the manufacturer’s protocols. The purified RNA was assessed for concentration and purity by measuring absorbance ratios at 260/280 nm and 260/230 nm on a NanoDrop spectrophotometer. RNA integrity was evaluated using either an Agilent Bioanalyzer or Fragment Analyzer to examine ribosomal RNA peak patterns; samples with satisfactory quality metrics (high integrity and appropriate ratios) were selected for downstream library construction.
Small RNA libraries were generated from the extracted RNA using the Qiagen microRNA Library Prep Kit (Cat# 331505). Each sample was normalized to a defined input range prior to library synthesis. Adapters were ligated sequentially to the 3′ and 5′ ends of small RNAs, followed by reverse transcription. Unique molecular identifiers (UMIs) were incorporated during this process to enable accurate read quantification. The resulting cDNA was purified, amplified, and subjected to a final cleanup step to produce sequencing libraries. Libraries were assessed on an Agilent TapeStation or equivalent platform, and if necessary, size selection was performed to remove adapter dimers. Quantification of libraries was achieved using qPCR with a commercially available kit (KAPA Biosystems) to ensure optimal loading concentrations. Libraries were normalized to 1.2 nM and loaded onto Illumina NovaSeq flow cells in accordance with Illumina’s established protocols. Each lane included a low-level spike-in of a PhiX control library to monitor sequencing performance in real time. Sequencing was performed with 100 bp paired-end reads, and an 8 bp unique dual index was read during dedicated index cycles following the first read. Raw sequencing data were transferred to a high-performance computing environment for downstream analysis. For tRF analysis, read processing and alignment were conducted using an adapted small RNA sequencing pipeline tailored to capture tRF sequences. Reads were trimmed and filtered for quality before mapping to the appropriate small RNA reference. Raw counts representing tRF abundance were generated and used as input for differential expression analysis.

value: Serum

tag: serum volume

tag: age classification

value: adolescent

tag: endometriosis asrm_stage

tag: hormonal treatment


title: 1056-5.HTO.23244.rs93834

description:
Library name: 93834
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds

tag: tissue

value: PBMC


title: P2A

description: SAMPLE 9

value: Control Group Rep 4

tag: treatment


title: 1056-3.TCR.23244.rs93830

description:
Library name: 93830
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: 1056-3.GEX.23244.rs93829

description:
Library name: 93829
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: P23A

description: SAMPLE 8

value: Control Group Rep 3


title: tRNA-derived fragment sequencing of sample AV059

description: Library name: tRF_AV059

value: Stage I

value: yes


title: 1056-2.TCR.23244.rs93827

description:
Library name: 93827
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: 1056-2.GEX.23244.rs93826

description:
Library name: 93826
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: 1056-2.HTO.23244.rs93825

description:
Library name: 93825
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: P22A

description: SAMPLE 7

value: Control Group Rep 2


title: tRNA-derived fragment sequencing of sample AV058

description: Library name: tRF_AV058


title: tRNA-derived fragment sequencing of sample AV057_B

description: Library name: tRF_AV057B


title: 1184-10.HTO.23230.rs97354

description:
Library name: 97354
Fig5.seurat.rds
Fig5.counts.rds

source_name: Ilio-sacral LN,Liver,PBMC,PLN

value: Ilio-sacral LN,Liver,PBMC,PLN


title: RTA7_siNT

city: Memphis

first: Yong-Dong

last: Wang

state: TN

address: 262 Danny Thomas Pl, MS1135

institute: St. Jude Children's Research Hospital

description:
Library name: RTA7_siNT
control siRNAs replicate 3

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and low-quality sequence, then mapped to GRCm39/mm39 whole genome using CLC Genomic Workbench RNA seq tool. TPM for transcripts were reported.
Assembly: mm39
Supplementary files format and content: tab-delimited text files include TPM values for all 8 samples

source_name: skeletal muscles

extract_protocol:
Tissues were homogenized in Trizol and RNA extracted by isopropanol precipitation from the aqueous phase.
RNA sequencing libraries for each sample were prepared with 1 ug total RNA by using the TruSeq RNA Sample Prep v2 Kit (Illumina) per the manufacturer’s instructions, and sequencing was completed on the Illumina NovaSeq 6000.

value: skeletal muscles

value: electroporated with non-targeting (NT) control siRNAs


title: 1184-10.TCR.23230.rs97356

description:
Library name: 97356
Fig5.seurat.rds
Fig5.counts.rds


title: P1A

description: SAMPLE 6

value: Control Group Rep 1


title: 1184-10.GEX.23230.rs97355

description:
Library name: 97355
Fig5.seurat.rds
Fig5.counts.rds


title: tRNA-derived fragment sequencing of sample AV057_A

description: Library name: tRF_AV057A


title: C9A

description: SAMPLE 5

value: Experimental Group Rep 5

value: ADSCs+HVFs group (defect repaired with HAAM scaffold pre-seeded with a 1:1 co-culture of ADSCs and HVFs).


title: 1184-9.TCR.23230.rs97353

description:
Library name: 97353
Fig5.seurat.rds
Fig5.counts.rds

source_name: Bone marrow,Colon,MesLN,Spleen

value: Bone marrow,Colon,MesLN,Spleen


title: C8A

description: SAMPLE 4

value: Experimental Group Rep 4

value: Abdominal wall tissue


title: 1184-9.GEX.23230.rs97352

description:
Library name: 97352
Fig5.seurat.rds
Fig5.counts.rds


title: 1184-9.HTO.23230.rs97351

description:
Library name: 97351
Fig5.seurat.rds
Fig5.counts.rds


title: tRNA-derived fragment sequencing of sample AV056

description: Library name: tRF_AV056

value: Serum


title: 1184-8.TCR.23230.rs97350

description:
Library name: 97350
Fig5.seurat.rds
Fig5.counts.rds

source_name: Bone marrow,Colon,Ilio-sacral LN,PLN

value: Bone marrow,Colon,Ilio-sacral LN,PLN


title: tRNA-derived fragment sequencing of sample AV055

description: Library name: tRF_AV055

value: adolescent


title: C3A

description: SAMPLE 3

value: Experimental Group Rep 3


title: 1184-8.GEX.23230.rs97349

description:
Library name: 97349
Fig5.seurat.rds
Fig5.counts.rds


title: Tdp2 cKO, 6mo, Rep1

city: Dallas

first: Ram

last: Madabhushi

state: TX

address: 5323 Harry Hines Blvd

institute: UT Southwestern Medical Center

description: Library name: cKO1

data_processing:
Raw FASTQ sequencing reads were analyzed for quality control using FastQC, trimmed to remove adapter sequences using Trimmomatic, and aligned to the mm10 (GRCm38.p6) reference genome using TopHat.
Aligned reads were processed by HTSeq-Count to obtain raw read counts, and deSeq2 (p < 0.05, log fold-change > 0.5 or < -0.5) was used to identify differentially regulated transcripts.
BamCoverage was used to convert aligned read files into BigWig signal tracks for visualization.
Assembly: mm10
Supplementary files format and content: tab delimited text file (Raw_Counts) includes raw counts for each sample
Supplementary files format and content: tab delimited text file (TPMs) includes calculated TPM values for each sample
Supplementary files format and content: bigwig files include merged, TPM-normalized RNA-seq signals for each genotype

source_name: Cortex

growth_protocol: Wild-type (Tdp2fl/fl, CAMKII:Cre negative) and Tdp2 conditional knockout (Tdp2fl/fl, CAMKII:Cre positive) mice were maintained in standard housing conditions until 6 months of age.

extract_protocol:
Fresh cortical tissue was dissected from 6-month old WT and Tdp2cKO mice, flash frozen in liquid nitrogen, and stored at -80°C. For RNA purification, samples were dissociated and lysed in 500µL Trizol using a manual homogenizer. RNA was extracted using a standard Trizol procedure, treated with DNase (NEB) for 1 hour at 37℃, and purified using an RNA clean and concentrator kit (Zymo).
The concentration and quality of purified RNA samples were assessed using an Agilent Tapestation 4200 both before and after library construction. Samples with a RIN score of 8 or higher were prepared for sequencing using a paired-end library preparation kit (Illumina) according to the manufacturer’s instructions.

value: Cortex

tag: strain

tag: genotype

value: Tdp2 cKO

tag: age

value: 6 months


title: 1184-8.HTO.23230.rs97348

description:
Library name: 97348
Fig5.seurat.rds
Fig5.counts.rds


title: tRNA-derived fragment sequencing of sample AV053

description: Library name: tRF_AV053


title: C2A

description: SAMPLE 2

value: Experimental Group Rep 2


title: 1184-7.TCR.23230.rs97347

description:
Library name: 97347
Fig5.seurat.rds
Fig5.counts.rds

source_name: Liver,MesLN,PBMC,Spleen

value: Liver,MesLN,PBMC,Spleen


title: C10A

description: SAMPLE 1

value: Experimental Group Rep 1


title: tRNA-derived fragment sequencing of sample AV052

description: Library name: tRF_AV052


title: 1184-7.GEX.23230.rs97346

description:
Library name: 97346
Fig5.seurat.rds
Fig5.counts.rds


title: 1184-7.HTO.23230.rs97345

description:
Library name: 97345
Fig5.seurat.rds
Fig5.counts.rds


title: h-, WT, 24h, biol_rep_3

city: New York

first: Ana

last: Sanchez

state: NY

address: 430 E 67th Street, RRL-865

department: Molecular Biology

institute: Memorial Sloan Kettering Cancer Center

description:
Library name: WT, Strain Sp1, 24h_biol_rep_3
WT_24h_3
count_matrix_INO_starvation.xlsx
WT_24h_DESeq2.xlsx

data_processing:
Base calls from Illumina NovaSeq 6000 or HiSeq 2000 (FASTQ files)
Each replicate was processed separately
The FASTQ files were mapped to the S. pombe genome (current version, source: PomBase) using HISAT2_2.1.0
Resulting SAM files were converted to BAM files using Samtools.
Count files for individual replicated were generated with HTSeq-0.10.0 using exon annotations from PomBase (GFF annotations, genome-version ASM294v2; source ‘ensembl’)
Differential gene expression and fold-change analysis were performed using DESeq2
Assembly: Schizosaccharomyces_pombe_all_chromosomes.fa (Reference sequence, ftp://ftp.pombase.org/pombe/genome_sequence_and_features/genome_sequence/Schizosaccharomyces_pombe_all_chromosomes.fa.gz)
Supplementary files format and content: Matrix file for raw HTSeq counts
Supplementary files format and content: DESeq2 output files that include average (avg) normalized counts

organism: Schizosaccharomyces pombe

source_name: yeast cell

growth_protocol: Log phase cultures of wild-type cells were grown at 30°C in ePMGT(+INO),  transferred to inositol-free medium, and incubated in ePMGT(–INO) medium for 4, 8, 12 or 24 h.

extract_protocol:
Hot acid phenol RNA purification protocol
RNA-seq libraries were prepared from polyA+ RNA using the NEB Ultra II Directional RNA library prep Kit (plus poly A isolation module) accoding to the manufacturer's protocol. Indexed libraries were normalized and pooled for paired-end sequencing performed using an Illumina NovaSeq 6000 instrument at the Weill Cornell Medical College Genome Core Facility (in New York).

tag: cell type

value: yeast cell

tag: growth conditions

value: 24h inositol starved culture, ePMGT–INO medium

tag: developmental stage

value: vegetative growth

value: WT


title: 1184-6.TCR.23230.rs97344

description:
Library name: 97344
Fig5.seurat.rds
Fig5.counts.rds

value: Ilio-sacral LN,Liver,PBMC,PLN


title: tRNA-derived fragment sequencing of sample AV051

description: Library name: tRF_AV051


title: 1184-6.GEX.23230.rs97343

description:
Library name: 97343
Fig5.seurat.rds
Fig5.counts.rds


title: h-, WT, 24h, biol_rep_2

description:
Library name: WT, Strain Sp1, 24h_biol_rep_2
WT_24h_2
count_matrix_INO_starvation.xlsx
WT_24h_DESeq2.xlsx


title: 1184-6.HTO.23230.rs97342

description:
Library name: 97342
Fig5.seurat.rds
Fig5.counts.rds


title: h-, WT, 24h, biol_rep_1

description:
Library name: WT, Strain Sp1, 24h_biol_rep_1
WT_24h_1
count_matrix_INO_starvation.xlsx
WT_24h_DESeq2.xlsx


title: 1184-5.HTO.23230.rs97339

description:
Library name: 97339
Fig5.seurat.rds
Fig5.counts.rds

value: Bone marrow,Colon,MesLN,Spleen


title: 1184-5.TCR.23230.rs97341

description:
Library name: 97341
Fig5.seurat.rds
Fig5.counts.rds


title: 1184-4.TCR.23230.rs97338

description:
Library name: 97338
Fig5.seurat.rds
Fig5.counts.rds


title: h-, WT, 12h, biol_rep_3

description:
Library name: WT, Strain Sp1, 12h_biol_rep_3
WT_12h_3
count_matrix_INO_starvation.xlsx
WT_12h_DESeq2.xlsx

value: 12h inositol starved culture, ePMGT–INO medium


title: 1184-4.HTO.23230.rs97336

description:
Library name: 97336
Fig5.seurat.rds
Fig5.counts.rds


title: tRNA-derived fragment sequencing of sample AV048

description: Library name: tRF_AV048

value: Serum

value: yes


title: tRNA-derived fragment sequencing of sample AV049

description: Library name: tRF_AV049

value: adolescent


title: h-, WT, 12h, biol_rep_2

description:
Library name: WT, Strain Sp1, 12h_biol_rep_2
WT_12h_2
count_matrix_INO_starvation.xlsx
WT_12h_DESeq2.xlsx


title: 1184-3.TCR.23230.rs97335

description:
Library name: 97335
Fig5.seurat.rds
Fig5.counts.rds


title: tRNA-derived fragment sequencing of sample AV050

description: Library name: tRF_AV050


title: tRNA-derived fragment sequencing of sample AV047

description: Library name: tRF_AV047

value: Stage I


title: 1184-3.GEX.23230.rs97334

description:
Library name: 97334
Fig5.seurat.rds
Fig5.counts.rds


title: h-, WT, 12h, biol_rep_1

description:
Library name: WT, Strain Sp1, 12h_biol_rep_1
WT_12h_1
count_matrix_INO_starvation.xlsx
WT_12h_DESeq2.xlsx


title: 1184-2.TCR.23230.rs97332

description:
Library name: 97332
Fig5.seurat.rds
Fig5.counts.rds

source_name: Bone marrow,Colon,Liver,PBMC

value: Bone marrow,Colon,Liver,PBMC


title: tRNA-derived fragment sequencing of sample AV046

description: Library name: tRF_AV046


title: 1184-3.HTO.23230.rs97333

description:
Library name: 97333
Fig5.seurat.rds
Fig5.counts.rds


title: tRNA-derived fragment sequencing of sample AV045

description: Library name: tRF_AV045


title: h-, WT, 8h, biol_rep_3

description:
Library name: WT, Strain Sp1, 8h_biol_rep_3
WT_8h_3
count_matrix_INO_starvation.xlsx
WT_8h_DESeq2.xlsx

value: 8h inositol starved culture, ePMGT–INO medium


title: 1047-5.GEX.26910.rs94893

description:
Library name: 94893
Fig5.seurat.rds
Fig5.counts.rds


title: 1184-1.TCR.23230.rs97329

description:
Library name: 97329
Fig5.seurat.rds
Fig5.counts.rds

source_name: Ilio-sacral LN,MesLN,PLN,Spleen

value: Ilio-sacral LN,MesLN,PLN,Spleen


title: h-, WT, 8h, biol_rep_2

description:
Library name: WT, Strain Sp1, 8h_biol_rep_2
WT_8h_2
count_matrix_INO_starvation.xlsx
WT_8h_DESeq2.xlsx


title: tRNA-derived fragment sequencing of sample AV044

description: Library name: tRF_AV044


title: 1047-3.GEX.26910.rs94888

description:
Library name: 94888
Fig5.seurat.rds
Fig5.counts.rds


title: h-, WT, 8h, biol_rep_1

description:
Library name: WT, Strain Sp1, 8h_biol_rep_1
WT_8h_1
count_matrix_INO_starvation.xlsx
WT_8h_DESeq2.xlsx


title: 1184-1.HTO.23230.rs97327

description:
Library name: 97327
Fig5.seurat.rds
Fig5.counts.rds


title: 1047-6.GEX.26910.rs94886

description:
Library name: 94886
Fig5.seurat.rds
Fig5.counts.rds


title: tRNA-derived fragment sequencing of sample AV043

description: Library name: tRF_AV043


title: 1047-1.GEX.26910.rs94887

description:
Library name: 94887
Fig5.seurat.rds
Fig5.counts.rds


title: SAH12h

first: Haiying

last: Li

address: 188 Shizi Street

department: Department of Neurosurgery

institute: The First Affiliated Hospital of Soo-chow University

description:
Library name: Sample 2
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v 5.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: Mouse mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: brain tissue on the injured side,n=3

growth_protocol: Mice were subjected to subarachnoid hemorrhage (SAH) through the endovascular puncture method. After 12 hours of modeling, the mice were euthanized.

extract_protocol:
The entire nuclear suspension preparation process is conducted on ice. The frozen tissue sample is minced in 1 mL of Nuclei Suspension Buffer (NST), which consists of 0.1% NP40, 10 mM Tris-HCl, 146 mM NaCl, 1 mM CaCl2, 21 mM MgCl2, and 40 U/mL RNase inhibitor. The lysis time is 7 minutes. After confirming complete nuclear lysis through trypan blue staining and microscopic examination, 1 mL of ST Wash buffer is added. The ST Wash buffer contains 10 mM Tris-HCl, 146 mM NaCl, 1 mM CaCl2, 21 mM MgCl2, 0.01% BSA (NEB B9000S), and 40 U/mL RNase inhibitor. The mixture is then filtered through a 40 µm cell strainer (BD). The filtrate is transferred to a 15 mL centrifuge tube, and the cell strainer is rinsed with an appropriate amount of ST Wash buffer, combining the rinse with the nuclear filtrate. The sample is centrifuged at 500g for 5 minutes in a horizontal rotor at 4°C. The nuclei are resuspended in 5 mL of PBS + 1% BSA, washed by centrifugation, and finally resuspended in 100 µL of PBS + 1% BSA. After trypan blue staining, the nuclei are counted under a microscope and diluted with PBS + 1% BSA to a concentration of 700-1200 nuclei/µL.
The single-cell sequencing and cDNA library amplification were performed following the instructions provided in the 10×Genomics Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (1000268). For DNA library construction, the Chromium™ Single Cell 3'/5' Library Construction Kit (1000020) was used. The constructed libraries were then sequenced on the Illumina Nova 6000 platform using the PE150 sequencing mode.

treatment_protocol: The entire brain tissue extraction process was conducted on ice to ensure tissue preservation. After carefully removing the brain from the euthanized mice, the ipsilateral hemisphere (the side affected by SAH) was separated. Subsequently, the brain tissue was dissected from the medial prefrontal cortex (mPFC, starting at 2.34 mm anterior to bregma) to the centrolateral nucleus (CL, ending at 2.18 mm posterior to bregma). Finally, the brain tissues from the same region of three SAH mice and three normal mice were separately pooled, placed into cell freezing medium, and stored at -80°C.

value: brain tissue on the injured side,n=3

value: 6-8 weeks old

tag: Sex

value: male

value: SAH


title: h-, WT, 4h, biol_rep_3

description:
Library name: WT, Strain Sp1, 4h_biol_rep_3
WT_4h_3
count_matrix_INO_starvation.xlsx
WT_4h_DESeq2.xlsx

value: yeast cell

value: 4h inositol starved culture, ePMGT–INO medium


title: tRNA-derived fragment sequencing of sample AV042

description: Library name: tRF_AV042


title: 1047-2.GEX.26910.rs94879

description:
Library name: 94879
Fig5.seurat.rds
Fig5.counts.rds


title: h-, WT, 4h, biol_rep_2

description:
Library name: WT, Strain Sp1, 4h_biol_rep_2
WT_4h_2
count_matrix_INO_starvation.xlsx
WT_4h_DESeq2.xlsx

value: vegetative growth

value: WT


title: 1047-6.HTO.26910.rs93691

description:
Library name: 93691
Fig5.seurat.rds
Fig5.counts.rds

value: Ilio-sacral LN,Liver,PBMC,PLN


title: 1047-6.TCR.26910.rs93693

description:
Library name: 93693
Fig5.seurat.rds
Fig5.counts.rds


title: 1047-5.TCR.26910.rs93690

description:
Library name: 93690
Fig5.seurat.rds
Fig5.counts.rds

value: Bone marrow,Colon,MesLN,Spleen


title: 1047-5.HTO.26910.rs93688

description:
Library name: 93688
Fig5.seurat.rds
Fig5.counts.rds


title: h-, WT, 4h, biol_rep_1

description:
Library name: WT, Strain Sp1, 4h_biol_rep_1
WT_4h_1
count_matrix_INO_starvation.xlsx
WT_4h_DESeq2.xlsx


title: tRNA-derived fragment sequencing of sample AV041

description: Library name: tRF_AV041

value: Serum


title: 1047-4.TCR.26910.rs93687

description:
Library name: 93687
Fig5.seurat.rds
Fig5.counts.rds

value: Bone marrow,Colon,Ilio-sacral LN,PLN


title: tRNA-derived fragment sequencing of sample AV040

description: Library name: tRF_AV040

value: adolescent


title: h-, WT, 0h, biol_rep_3

description:
Library name: WT, Strain Sp1, 0h_biol_rep_3
WT_0h_3
count_matrix_INO_starvation.xlsx

value: log phase culture, ePMGT medium


title: 1047-4.GEX.26910.rs93686

description:
Library name: 93686
Fig5.seurat.rds
Fig5.counts.rds


title: tRNA-derived fragment sequencing of sample AV039

description: Library name: tRF_AV039

value: Stage I

value: yes


title: 1047-4.HTO.26910.rs93685

description:
Library name: 93685
Fig5.seurat.rds
Fig5.counts.rds


title: h-, WT, 0h, biol_rep_2

description:
Library name: WT, Strain Sp1, 0h_biol_rep_2
WT_0h_2
count_matrix_INO_starvation.xlsx


title: 1047-3.TCR.26910.rs93684

description:
Library name: 93684
Fig5.seurat.rds
Fig5.counts.rds

value: Liver,MesLN,PBMC,Spleen


title: tRNA-derived fragment sequencing of sample AV038

description: Library name: tRF_AV038


title: 1047-2.TCR.26910.rs93681

description:
Library name: 93681
Fig5.seurat.rds
Fig5.counts.rds

value: Bone marrow,Colon,Liver,PBMC


title: h-, WT, 0h, biol_rep_1

description:
Library name: WT, Strain Sp1, 0h_biol_rep_1
WT_0h_1
count_matrix_INO_starvation.xlsx


title: tRNA-derived fragment sequencing of sample AV035

description: Library name: tRF_AV035


title: 1047-3.HTO.26910.rs93682

description:
Library name: 93682
Fig5.seurat.rds
Fig5.counts.rds


title: 1047-2.HTO.26910.rs93679

description:
Library name: 93679
Fig5.seurat.rds
Fig5.counts.rds


title: 1047-1.HTO.26910.rs93676

description:
Library name: 93676
Fig5.seurat.rds
Fig5.counts.rds

value: Ilio-sacral LN,MesLN,PLN,Spleen


title: 1102-14.TCR.26814.rs95201

description:
Library name: 95201
Fig2.seurat.rds
Fig2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds

source_name: PBMC

value: PBMC


title: KGN Cells,Cisplatin,48h,rep 2

city: Jinzhou

first: Chao

last: Liu

state: Liaoning

address: Jinzhou Medical University, No. 40, Section 3, Songpo Road, Linghe District, Jinzhou City, Liaoning Province

institute: Jinzhou Medical University

description:
Library name: Sample5
POF2

data_processing:
The raw data obtained from sequencing was filtered using SOAPnuke (v2.2.1).
the Dr. Tom multi-omics data mining system (https://biosys.bgi.com) was utilized for data analysis, visualization, and mining.
The clean data was aligned to the reference genome using HISTA2 (v2.2.1). Subsequently, Ericscript (v0.5.5) was used for gene fusion detection, and rMATS (V4.1.2)[4] was employed for alternative splicing and differential alternative splicing detection.
Clean data were aligned to the reference gene set using Bowtie2 (v2.4.5) . Gene expression quantification was performed using RSEM (v1.3.1) , and the expression levels of genes in different samples were visualized by a clustering heatmap using pheatmap (v1.0.12) .
GO (http://www.geneontology.org/) and KEGG(https://www.kegg.jp/) enrichment analysis on differentially expressed genes using Phyper based on the hypergeometric test, with a threshold of Qvalue≤0.05 . Genes meeting this condition were defined as significantly enriched in the candidate genes.
Assembly: mm10
Supplementary files format and content: FPKM values for each Sample

source_name: ovary

growth_protocol: KGN cells were maintained in DMEM supplemented with 10%fetal bovne serum (FBS) and antibiotics in humidifed atmosphere with 5% CO2 at 37℃

extract_protocol:
Total RNA was extracted from cells using TRIzol (Invitrogen, Carlsbad, California, USA) according to manual instruction and quantified using a Fragment Analyzer or Agilent 2100 Bioanalyzer (Agilent, CA, USA), or Qseq-400 (Bioptic, Taiwan, China).
Library preparation is performed using Optimal Dual-mode mRNA Library Prep Kit (BGI-Shenzhen, China).

value: ovary

tag: cell line

value: KGN

value: Fibroblast


title: 1047-1.TCR.26910.rs93678

description:
Library name: 93678
Fig5.seurat.rds
Fig5.counts.rds


title: KGN Cells,Cisplatin,48h,rep 3

description:
Library name: Sample6
POF3


title: tRNA-derived fragment sequencing of sample AV034

description: Library name: tRF_AV034


title: 1102-14.GEX.26814.rs95200

description:
Library name: 95200
Fig2.seurat.rds
Fig2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds


title: tRNA-derived fragment sequencing of sample AV032

description: Library name: tRF_AV032


title: KGN Cells,Cisplatin,48h,rep 1

description:
Library name: Sample4
POF1


title: 1102-14.HTO.26814.rs95199

description:
Library name: 95199
Fig2.seurat.rds
Fig2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds


title: tRNA-derived fragment sequencing of sample AV031

description: Library name: tRF_AV031


title: 1102-13.TCR.26814.rs95198

description:
Library name: 95198
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: KGN Cells,control,48h,rep 3

description:
Library name: Sample3
Con_3


title: 1102-13.GEX.26814.rs95197

description:
Library name: 95197
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: tRNA-derived fragment sequencing of sample AV030

description: Library name: tRF_AV030


title: KGN Cells,control,48h,rep 2

description:
Library name: Sample2
Con_2


title: 1102-12.TCR.31179.rs95195

description:
Library name: 95195
Fig2.seurat.rds
Fig2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds


title: 1102-12.HTO.31179.rs95193

description:
Library name: 95193
Fig2.seurat.rds
Fig2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds


title: 1102-13.HTO.26814.rs95196

description:
Library name: 95196
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: tRNA-derived fragment sequencing of sample AV029

description: Library name: tRF_AV029


title: KGN Cells,control,48h,rep 1

description:
Library name: Sample1
Con_1


title: 1102-12.GEX.31179.rs95194

description:
Library name: 95194
Fig2.seurat.rds
Fig2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds


title: tRNA-derived fragment sequencing of sample AV028

description: Library name: tRF_AV028


title: ACC2_untreated

type: genomic

city: Augsburg

first: Victoria

middle: Elisabeth

last: Fincke

address: Stenglinstraße 2

country: Germany

institute: Childens Cancer Center - University hospital Augsburg

hyb_protocol: Bisulfite-converted DNA was hybridized to the Infinium HumanMethylation BeadChip (EPIC v2) according to the manufacturer’s instructions (Illumina).

scan_protocol: Arrays were scanned using the Illumina iScan System, and raw image data were processed with Illumina GenomeStudio (Methylation Module).

data_processing:
Raw IDAT files were processed, normalized, filtered and batch effect corrected as described in Capper et. al. 2018 by using the Bioconductor package minfi
[processed value definition] Processed values represent Beta values (β-values), i.e. the ratio of methylated probe intensity to overall intensity (M / [M+U+100]), ranging from 0 (unmethylated) to 1 (fully methylated). Values were derived from IDAT files after background correction and normalization using the minfi.

label: Cy3 and Cy5

source_name: Adrenocortical Carcinoma Cell line

label_protocol: llumina Infinium HD Methylation Assay; single-base extension with biotin- and DNP-labeled nucleotides according to the manufacturer’s protocol.

growth_protocol: Cell lines we cultivated according to published protocols and kept at 37°C with 5% CO2.

extract_protocol: DNA was isolated from the cell lines with the Maxwell® RSC Cultured Cells DNA Kit (Promega) according to the manufactors instruction

treatment_protocol: Entinostat or Decitabine was added to the cell culture medium in according concentrations and incubated for 72h or 168h.

value: Adrenocortical Carcinoma Cell line

value: untreated


title: 1102-11.TCR.26814.rs95192

description:
Library name: 95192
Fig2.seurat.rds
Fig2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds


title: 1102-11.GEX.26814.rs95191

description:
Library name: 95191
Fig2.seurat.rds
Fig2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds


title: tRNA-derived fragment sequencing of sample AV027

description: Library name: tRF_AV027


title: ACC1_untreated


title: 1102-11.HTO.26814.rs95190

description:
Library name: 95190
Fig2.seurat.rds
Fig2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds


title: 1102-10.TCR.26814.rs95189

description:
Library name: 95189
Fig2.seurat.rds
Fig2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds


title: tRNA-derived fragment sequencing of sample AV026

description: Library name: tRF_AV026


title: 1102-10.GEX.26814.rs95188

description:
Library name: 95188
Fig2.seurat.rds
Fig2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds


title: H295R_untreated


title: 1102-10.HTO.26814.rs95187

description:
Library name: 95187
Fig2.seurat.rds
Fig2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds


title: tRNA-derived fragment sequencing of sample AV025

description: Library name: tRF_AV025


title: 1102-9.GEX.26814.rs95185

description:
Library name: 95185
Fig2.seurat.rds
Fig2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds


title: ACC2_Ent_1uM_72h


title: 1102-9.TCR.26814.rs95186

description:
Library name: 95186
Fig2.seurat.rds
Fig2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds


title: 1102-9.HTO.26814.rs95184

description:
Library name: 95184
Fig2.seurat.rds
Fig2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds


title: tRNA-derived fragment sequencing of sample AV024

description: Library name: tRF_AV024


title: ACC1_Ent_1uM_72h


title: tRNA-derived fragment sequencing of sample AV023

description: Library name: tRF_AV023


title: 1102-8.TCR.26814.rs95183

description:
Library name: 95183
Fig2.seurat.rds
Fig2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds


title: 1102-8.GEX.26814.rs95182

description:
Library name: 95182
Fig2.seurat.rds
Fig2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds


title: ACC1_Ent_05uM_168h


title: 1102-8.HTO.26814.rs95181

description:
Library name: 95181
Fig2.seurat.rds
Fig2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds


title: tRNA-derived fragment sequencing of sample AV022

description: Library name: tRF_AV022


title: ACC1_Ent_05uM_72h


title: 1102-7.TCR.26814.rs95180

description:
Library name: 95180
Fig2.seurat.rds
Fig2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds


title: 1102-7.GEX.26814.rs95179

description:
Library name: 95179
Fig2.seurat.rds
Fig2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds


title: tRNA-derived fragment sequencing of sample AV021

description: Library name: tRF_AV021


title: 1102-7.HTO.26814.rs95178

description:
Library name: 95178
Fig2.seurat.rds
Fig2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds


title: H295R_Ent_1uM_72


title: 1102-5.HTO.26814.rs95172

description:
Library name: 95172
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: 1102-5.GEX.26814.rs95173

description:
Library name: 95173
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: 1102-4.TCR.26814.rs95171

description:
Library name: 95171
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: tRNA-derived fragment sequencing of sample AV020

description: Library name: tRF_AV020


title: tRNA-derived fragment sequencing of sample AV019

description: Library name: tRF_AV019


title: 1102-4.GEX.26814.rs95170

description:
Library name: 95170
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: H295R_Ent_05uM_168h


title: H295R_Ent_05uM_72h


title: 1102-4.HTO.26814.rs95169

description:
Library name: 95169
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: tRNA-derived fragment sequencing of sample AV018

description: Library name: tRF_AV018


title: H295R_Dec_1um_72h


title: 1102-3.TCR.26814.rs95168

description:
Library name: 95168
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: 1102-3.HTO.26814.rs95166

description:
Library name: 95166
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: 1102-3.GEX.26814.rs95167

description:
Library name: 95167
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: tRNA-derived fragment sequencing of sample AV017

description: Library name: tRF_AV017


title: 1102-2.GEX.26814.rs95164

description:
Library name: 95164
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: ACC2_Dec_1uM_72h


title: ACC1_Dec_1uM_72h


title: 1102-2.HTO.26814.rs95163

description:
Library name: 95163
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: 1102-1.GEX.26814.rs95161

description:
Library name: 95161
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: tRNA-derived fragment sequencing of sample AV015

description: Library name: tRF_AV015


title: tRNA-derived fragment sequencing of sample AV016

description: Library name: tRF_AV016


title: 1102-1.HTO.26814.rs95160

description:
Library name: 95160
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: 1101-16.TCR.31179.rs95159

description:
Library name: 95159
FigS1.seurat.rds
FigS1.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: AVT@apoEVs@Cap

city: Guangzhou

first: Xian

address: No. 381 Wushan Road, Tianhe District

institute: South China University of Technology

description: Library name: D04613A2

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the DNBC4tools software.
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: Spatial Transcriptomics

source_name: Aorta

extract_protocol:
For aorta tissues, enzymatic and mechanical dissociation was used to obtain viable single-cell suspensions. The resulting cell suspensions was filtered through 40-70 μm strainers to remove debris and aggregates. Cell viablity and concentration were assessed via automated counters.
Single-cell RNA libraries were prepared using the DNBelab C according to the manufacturer's instructions. Briefly, the single-cell suspension was loaded together with partitioning oil and barcoded beads onto a microfluidic chip to generate gel bead-in-emulsions. Cells were lysed and poly-adenylated mRNA molecules were captured onto oligo-dT primers on the surface of the beads. Following mRNA capture, reverse transcription was performed inside the droplets to synthesize full-length cDNA, which incorporated a cell-specific barcode and a Unique Molecular Identifier. The emulsion was then broken, and the barcoded beads were recovered. During the library construction, the amplified cDNA underwent fragmentation, end repair, and adapter ligation, followed by PCR amplification to add sample indices ans sequences compatible with the MGI sequencing platform.

value: Aorta


title: tRNA-derived fragment sequencing of sample AV014

description: Library name: tRF_AV014


title: Saline

description: Library name: D04604G2


title: 1101-16.GEX.31179.rs95158

first: Benjamin

address: 505 NW 185th Ave

description:
Library name: 95158
FigS1.seurat.rds
FigS1.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds

data_processing:
CellRanger count
DropletUtils emptyDrops
Seurat Normalize/Scale/PCA
Assembly: GCA_003339765.3
Supplementary files format and content: Sparse count matrix (RDS file)
Supplementary files format and content: Seurat Object (RDS file)

extract_protocol: 10x Genomics 5' VDJ scRNA-seq


title: tRNA-derived fragment sequencing of sample AV013

description: Library name: tRF_AV013


title: 1101-16.HTO.31179.rs95157

description:
Library name: 95157
FigS1.seurat.rds
FigS1.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: AVT@apoEVs@Cap_3_oligo

description: Library name: Sample 6_oligo

library_source: other

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the DNBC4tools software.
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: other

tag: data type

value: oligo


title: 1101-15.TCR.31179.rs95156

description:
Library name: 95156
Fig2.seurat.rds
Fig2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds


title: 1101-15.HTO.31179.rs95154

description:
Library name: 95154
Fig2.seurat.rds
Fig2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds


title: 1101-15.GEX.31179.rs95155

description:
Library name: 95155
Fig2.seurat.rds
Fig2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds


title: AVT@apoEVs@Cap_3_cDNA

description: Library name: Sample 6_cDNA

value: cDNA


title: tRNA-derived fragment sequencing of sample AV012

description: Library name: tRF_AV012

value: Serum


title: 1101-14.TCR.31179.rs95153

description:
Library name: 95153
FigS1.seurat.rds
FigS1.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: 1101-14.GEX.31179.rs95152

description:
Library name: 95152
FigS1.seurat.rds
FigS1.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: Placenta tissue late stage_ immortalized_method 2_3 (bilayer immortalized TB + fetal vasculature)

city: Rockville

first: Marc

last: Ferrer

state: MD

address: 9800 Medical Center Dr.

department: NCATS (National Center for Advancing Translational Sciences)

institute: NIH (National Institutes of Health)

description:
Library name: YC10044_18
Column name in Placenta_CA_12 samples_raw_count.txt: YC10044_18 (sample name:PB Late_(h+n)_Immortalized_rep3)

data_processing:
Data was all processed in Biowulf using different packages
Use trimmomatic to clean fastq (default setting)
Use STAR alignment with the trimmomatic files
Use HTSeq to get raw count, combine all files into one txt file
Use DESeq2 for filteration and normalization (minCounts=10, minNumSamples=3,sigAdjP=0.05, sigAbsLFC=1), and downstream DEG analysis
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for all 12 samples

source_name: placenta

growth_protocol: In the hPB model, the trophoblast bilayer was grown in differentiation basal media (DMEM/F12 supplemented with 0.1 mM 2-mercaptoethanol, 0.5% penicillin/streptomycin, 0.3% BSA, 1% ITS-X supplement, 2.5 μM Y27632, 4% knockout serum replacement) supplemented with 25µM Forskolin, over 10 days in culture, and replaicing with fresh media every other day. The placental stroma layer was mantained in vascular media. The vascular media formulation consisted of 1:1 ratio of VascuLife culture media and RPE media ( modified Eagle’s alpha-modified medium supplemented with 1% v/v N-2, glutamine, 1% penicillin and streptomycin, 1x non-essential amino acids, 125 mg taurine, 10 µg hydrocortisone, and 0.0065 µg triiodothyronine) , along with the addition of VEGF (21.25 ng/ml), Recombinant Human Angiopoietin‐1 Protein (ANG1, 100 ng/ml), and aprotinin (0.075 U/ml) over 10 days in culture, and replaicing with fresh media every other day.

extract_protocol:
RNA of hPB tissue models (3 replicates for each hPB tissue models) were extracted using Trizol (Zymo, R2050-1) and isolated using Direct-zol-96 RNA Direct-zol-96 RNA, according to the manufacturer’s instructions.
RNA was sent to NHLBI genomic core facility to construct RNA-seq libraries using the Illumina Stranded mRNA Prep kit, which includes poly-A selection of mRNA

treatment_protocol: Early-stage hPB models were exposed to hypoxia conditions (5% oxigen)  for 10 days, under the differentiation basal media with forskolin; while the late-stage hPB models were exposed to hypoxia conditions (5% oxigen)  for 4 days, followed by exposition to normoxia conditions (21% oxigen) for 6 more days, under the differentiation basal media with forskolin.

value: placenta

value: PTC HM3,  GFP-HUVECs, HPlMVPCs

value: Immortalized cytotrophoblast cells, GFP-HUVECs, HPlMVPCs

value: PB Late_h+n_Immortalized

tag: batch


title: AVT@apoEVs@Cap_2_oligo

description: Library name: Sample 5_oligo


title: 1101-14.HTO.31179.rs95151

last: Bimber

description:
Library name: 95151
FigS1.seurat.rds
FigS1.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: Placenta tissue late stage_ immortalized_method 2_2 (bilayer immortalized TB + fetal vasculature)

description:
Library name: YC10044_17
Column name in Placenta_CA_12 samples_raw_count.txt: YC10044_17 (sample name:PB Late_(h+n)_Immortalized_rep2)


title: AVT@apoEVs@Cap_2_cDNA

description: Library name: Sample 5_cDNA


title: 1101-13.TCR.31179.rs95150

description:
Library name: 95150
Fig2.seurat.rds
Fig2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds


title: 1101-13.GEX.31179.rs95149

description:
Library name: 95149
Fig2.seurat.rds
Fig2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds


title: AVT@apoEVs@Cap_1_oligo

description: Library name: Sample 4_oligo


title: Placenta tissue late stage_ immortalized_method 2_1 (bilayer immortalized TB + fetal vasculature)

description:
Library name: YC10044_16
Column name in Placenta_CA_12 samples_raw_count.txt: YC10044_16 (sample name:PB Late_(h+n)_Immortalized_rep1)


title: 1101-13.HTO.31179.rs95148

description:
Library name: 95148
Fig2.seurat.rds
Fig2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds


title: 1101-12.TCR.31179.rs95147

description:
Library name: 95147
FigS1.seurat.rds
FigS1.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: Placenta tissue late stage_primary_method 2_3 (bilayer primary TB + fetal vasculature)

description:
Library name: YC10044_15
Column name in Placenta_CA_12 samples_raw_count.txt: YC10044_15 (sample name:PB Late (h+n)_Primary_rep3)

value: CTBPRO2,  GFP-HUVECs, HPlMVPCs

value: Primary cytotrophoblast, GFP-HUVECs, HPlMVPCs

value: PB Late_h+n_Primary


title: AVT@apoEVs@Cap_1_cDNA

description: Library name: Sample 4_cDNA


title: 1101-12.HTO.31179.rs95145

description:
Library name: 95145
FigS1.seurat.rds
FigS1.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds

value: PBMC


title: 1101-12.GEX.31179.rs95146

description:
Library name: 95146
FigS1.seurat.rds
FigS1.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: Placenta tissue late stage_primary_method 2_2 (bilayer primary TB + fetal vasculature)

description:
Library name: YC10044_14
Column name in Placenta_CA_12 samples_raw_count.txt: YC10044_14 (sample name:PB Late (h+n)_Primary_rep2)


title: Saline_3_oligo

description: Library name: Sample 3_oligo


title: 1101-11.GEX.31179.rs95143

description:
Library name: 95143
Fig2.seurat.rds
Fig2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds


title: 1101-11.TCR.31179.rs95144

description:
Library name: 95144
Fig2.seurat.rds
Fig2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds


title: Placenta tissue late stage_primary_method 2_1 (bilayer primary TB + fetal vasculature)

description:
Library name: YC10044_13
Column name in Placenta_CA_12 samples_raw_count.txt: YC10044_13 (sample name:PB Late (h+n)_Primary_rep1)


title: 1101-11.HTO.31179.rs95142

description:
Library name: 95142
Fig2.seurat.rds
Fig2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds


title: Saline_3_cDNA

description: Library name: Sample 3_cDNA


title: 1101-10.TCR.31179.rs95141

description:
Library name: 95141
FigS1.seurat.rds
FigS1.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: Placenta tissue early stage_ immortalized_3  (bilayer immortalized TB + fetal vasculature)

description:
Library name: YC9783_9
Column name in Placenta_CA_12 samples_raw_count.txt: YC9783_9 (sample name:PB Early_Immortalized_rep3)

value: PB Early_Immortalized


title: Saline_2_oligo

description: Library name: Sample 2_oligo


title: 1101-10.GEX.31179.rs95140

description:
Library name: 95140
FigS1.seurat.rds
FigS1.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: 1101-10.HTO.31179.rs95139

description:
Library name: 95139
FigS1.seurat.rds
FigS1.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: Placenta tissue early stage_ immortalized_2  (bilayer immortalized TB + fetal vasculature)

description:
Library name: YC9783_8
Column name in Placenta_CA_12 samples_raw_count.txt: YC9783_8 (sample name:PB Early_Immortalized_rep2)


title: Saline_2_cDNA

description: Library name: Sample 2_cDNA


title: 1101-9.TCR.31179.rs95138

description:
Library name: 95138
Fig2.seurat.rds
Fig2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds


title: 1101-9.GEX.31179.rs95137

description:
Library name: 95137
Fig2.seurat.rds
Fig2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds


title: Placenta tissue early stage_ immortalized_1  (bilayer immortalized TB + fetal vasculature)

description:
Library name: YC9783_7
Column name in Placenta_CA_12 samples_raw_count.txt: YC9783_7 (sample name:PB Early_Immortalized_rep1)


title: Saline_1_oligo

description: Library name: Sample 1_oligo


title: 1101-9.HTO.31179.rs95136

description:
Library name: 95136
Fig2.seurat.rds
Fig2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds


title: 1101-6.TCR.31179.rs95129

description:
Library name: 95129
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: Placenta tissue early stage_primary_3  (bilayer primary TB + fetal vasculature)

description:
Library name: YC9783_3
Column name in Placenta_CA_12 samples_raw_count.txt: YC9783_3 (sample name:PB Early_Primary_rep3)

value: CTBPRO2, GFP-HUVECs, HPlMVPCs

value: PB Early_Primary


title: 1101-6.GEX.31179.rs95128

description:
Library name: 95128
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: 1101-6.HTO.31179.rs95127

description:
Library name: 95127
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: Placenta tissue early stage_primary_2  (bilayer primary TB + fetal vasculature)

description:
Library name: YC9783_2
Column name in Placenta_CA_12 samples_raw_count.txt: YC9783_2 (sample name:PB Early_Primary_rep2)


title: Saline_1_cDNA

description: Library name: Sample 1_cDNA


title: 1101-4.TCR.31179.rs95123

description:
Library name: 95123
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: 1101-4.GEX.31179.rs95122

description:
Library name: 95122
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: vocal fold, injuried and treated with SOT , 1 week,3

first: Hui

last: Yang

state: sichuan proviince

address: No. 37 Guoxue Xiang, Chengdu, 610041, P.R. China

institute: West Chian Hospital, Sichuan university

description: Library name: H_3

data_processing:
A cDNA library constructed by the pooled RNA was sequenced run with Illumina NovaseqTM 6000 sequence platform.Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads.To get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
we aligned reads of all samples to the Homo sapiens reference genome using HISAT2(https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package
The mapped reads of each sample were assembled using StringTie(http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8).
After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
RNAs differential expression analysis was performed by edgeR software between two different group and two different samples. The genes/transcripts with the parameter of pvalue < 0.05 and fold change > 2 or fold change <0.5.
Assembly: OryCun2.0
Supplementary files format and content: gene expression text files include raw counts and FPKM values for each Sample

organism: Oryctolagus cuniculus

source_name: vocal fold

extract_protocol:
RNA was harvested using RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511). 5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) following manufacturer's protocols.

value: vocal fold

value: Vocal cord histiocytes


title: Placenta tissue early stage_primary_1 (bilayer primary TB + fetal vasculature)

description:
Library name: YC9783_1
Column name in Placenta_CA_12 samples_raw_count.txt: YC9783_1 (sample name:PB Early_Primary_rep1)


title: 1101-2.TCR.31179.rs95117

description:
Library name: 95117
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: 1101-4.HTO.31179.rs95121

description:
Library name: 95121
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: vocal fold, injuried and treated with SOT , 1 week,2

description: Library name: H_2


title: vocal fold, injuried and treated with SOT , 1 week,1

description: Library name: H_1


title: 1101-2.HTO.31179.rs95115

description:
Library name: 95115
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: vocal fold, injuried without treatment, 1week,3

description: Library name: I_3


title: R_3

city: zhejiang jinhua

first: zhang

middle: peng

last: hong

address: xinshijiedao 688

institute: zhejiang normal university

description: Library name: Sample 9

data_processing:
The resulting clean data were aligned to the A. thaliana (TAIR10) reference genome using HISTA2
Differential gene expression analysis was conducted using DESeq2 with a significance threshold of Q value ≤ 0.05 or FDR ≤ 0.001.
Assembly: A. thaliana (TAIR10)
Supplementary files format and content: csv files including read count and FPKMs

organism: Arabidopsis thaliana

source_name: rosette leaves

growth_protocol: 16h light/8h dark, 22°C

extract_protocol:
RNA was harvested using CTAB.
Total RNA was used for the construction of sequencing library.

value: rosette leaves

value: 18 days after germination

value: leaves

value: pskr1 pskr4


title: 1101-2.GEX.31179.rs95116

city: Beaverton

description:
Library name: 95116
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: 936-4.HTO.32069.rs92292

description:
Library name: 92292
Fig1_1of2.seurat.rds
Fig1_2of2.seurat.rds
Fig1_1of2.counts.rds
Fig1_2of2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds

source_name: Bulk CD8s

value: Bulk CD8s


title: 936-1.HTO.32069.rs92289

description:
Library name: 92289
Fig1_1of2.seurat.rds
Fig1_2of2.seurat.rds
Fig1_1of2.counts.rds
Fig1_2of2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: 474-1.TCR.SamplePool.rs39641

description:
Library name: 39641
Fig1_1of2.seurat.rds
Fig1_2of2.seurat.rds
Fig1_1of2.counts.rds
Fig1_2of2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: vocal fold, injuried without treatment, 1week,2

description: Library name: I_2


title: R_2

description: Library name: Sample 8

value: pskr1 pskr3


title: 474-1.GEX.SamplePool.rs39640

description:
Library name: 39640
Fig1_1of2.seurat.rds
Fig1_2of2.seurat.rds
Fig1_1of2.counts.rds
Fig1_2of2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: R_1

description: Library name: Sample 7

value: pskr1 pskr2


title: 474-1.HTO.SamplePool.rs39639

description:
Library name: 39639
Fig1_1of2.seurat.rds
Fig1_2of2.seurat.rds
Fig1_1of2.counts.rds
Fig1_2of2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: E_3

description: Library name: Sample 6


title: 936-4.TCR.32069.rs89553

description:
Library name: 89553
Fig1_1of2.seurat.rds
Fig1_2of2.seurat.rds
Fig1_1of2.counts.rds
Fig1_2of2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: vocal fold, injuried without treatment, 1week,1

description: Library name: I_1


title: 936-4.GEX.32069.rs89552

description:
Library name: 89552
Fig1_1of2.seurat.rds
Fig1_2of2.seurat.rds
Fig1_1of2.counts.rds
Fig1_2of2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: vocal fold, nomal condition 3

description: Library name: N_3

value: vocal fold, nomal condition 3


title: E_2

description: Library name: Sample 5


title: 936-1.TCR.32069.rs89544

description:
Library name: 89544
Fig1_1of2.seurat.rds
Fig1_2of2.seurat.rds
Fig1_1of2.counts.rds
Fig1_2of2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: 936-1.GEX.32069.rs89543

description:
Library name: 89543
Fig1_1of2.seurat.rds
Fig1_2of2.seurat.rds
Fig1_1of2.counts.rds
Fig1_2of2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: vocal fold, nomal condition 2

description: Library name: N_2

value: vocal fold, nomal condition 2


title: 360-3.TCR.SamplePool.rs23861

description:
Library name: 23861
Fig1_1of2.seurat.rds
Fig1_2of2.seurat.rds
Fig1_1of2.counts.rds
Fig1_2of2.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: 360-3.GEX.SamplePool.rs23860

description:
Library name: 23860
Fig1_1of2.seurat.rds
Fig1_2of2.seurat.rds
Fig1_1of2.counts.rds
Fig1_2of2.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: E_1

description: Library name: Sample 4


title: 360-3.HTO.SamplePool.rs23859

description:
Library name: 23859
Fig1_1of2.seurat.rds
Fig1_2of2.seurat.rds
Fig1_1of2.counts.rds
Fig1_2of2.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: WT_3

description: Library name: Sample 3

value: WT


title: vocal fold, nomal condition 1

description: Library name: N_1

value: vocal fold, nomal condition 1


title: H1975 xenograft, isotype, anti-pd-1, anti-ccl20, combination

city: Hong Kong

first: Hoi-Hin

last: Kwok

address: Sassoon Road

institute: The University of Hong Kong

description: Library name: cell mix

data_processing:
FASTQ files were processed with Cell Ranger v7.1.0 (10x Genomics) and using GRCh38-2020-A as reference. Raw reads were aligned to the human genome (hg38) and cells were detected using Cell Ranger count (v7.1.0). Cells detected with less than 200 genes, more than 8,000 genes, more than 10% contamination rate with mitochondrial genes, were filtered out as low-quality cells.
Assembly: Human genome (hg38)
Supplementary files format and content: Tab-separated values files and matrix files

source_name: xenograft

growth_protocol: PBMCs (1 X 107 cells in 100 µl of PBS) were injected in tail vein of mice. After two weeks, H1975 cells (2 X 106 cells in 100 µl of PBS and 100 µl of growth factor reduced basement extract (Trevigen, Gaithersburg, MD, USA)) were injected subcutaneously in the flank regions of mice.

extract_protocol:
Xenografts from humanized mice were harvested and snap frozen. To prepare a single cell suspension, tissue was lysed to release nucleus by adding lysis buffer (Sigma-Aldrich) and pestling. The pellets including released nucleus and undigested tissue were resuspended and the isolated nuclei were filtered through a 20-μm cell strainer (Greiner Bio-OneGmbH, Frickenhausen, Germany). An aliquot of nuclei was stained with DAPI, and concentration and viability were determined on a Cellometer Auto 2000 (Nexcelom Bioscience, Lawrence, MA, USA). The qualified single nuclei were processed to single nuclei RNA-seq. Nuclei were fixed using the demonstrated protocol (CG000478) from 10X Genomics (Pleasanton, CA, USA). After fixation, the nuclei count and quality assessments were intermittently evaluated using a LUNA dual fluorescence cell counter (Logos Biosystems, South Korea).
After Probe Hybridization, uniquely barcoded samples were counted and then pooled in equal nuclei numbers following manufacturer’s protocol (10X Genomics, Chromium fixed RNA profiling multiplexed samples pooling workbook Rev B, CG000565). Pooled nuclei were washed, and 20,000 cells from each sample were targeted to be partitioned into GEMs on a Chip Q, GEM barcoding, GEM recovery and pre-amplification, and library construction. Sequencing libraries were generated following the user guide (CG000527). Libraries were sequenced on an Illumina NovaSeqX with paired-end dual-indexing to a depth of approximately 300 million reads per sample with 2×150 read length. Sequencing libraries were demultiplexed with bcl2fastq conversion software (Illumina Inc., San Diego, CA, USA).

treatment_protocol: When the xenograft  reached the size of 200 mm3 (~ 1 week), mice were injected with anti-PD-1 (#SIM0010, BioXCell, Lebanon, NH, USA, 200 µg per mouse, I.P.) or anti-CCL20 (#MAB360, R&D Systems, Minneapolis, MN, 20 µg per mouse, I.P.)15 diluted in InVivoPure pH7.0 dilution buffer (BioXCell) at the indicated time interval. RecombiMAb human IgG4 (S228P) isotype control (BioXCell) was used as negative control. Mice were sacrificed at day 21.

value: xenograft

value: Epithelial Tumors

value: EGFR L858R/T790M double mutation

value: isotype


title: shy54g21.18-3

city: Zhengzhou City

first: li

last: Mengyu

address: No. 100 Lianhua Street, Fengyang Street, Zhongyuan District

institute: Bioengineering College

description: Library name: dsY3

data_processing:
Raw data quality control was performed using FASTQC software (v0.11.9), followed by WBce1235 genome alignment using HISAT2 software (v2.2.1). FeatureCounts (v1.28.1) generated gene counts. Differentially expressed genes (DEGs) were identified with p value < 0.05 and absolute log2 fold-change >1 or <-1 by DESeq2 R package (v1.16.1) and plotted with R packages ggplot2 (v4.2.3). Pathway enrichment was analyzed using the DAVID database, while Protein-protein interaction and phenotype annotations were analyzed using the STRING database.
Assembly: WBce1235
Supplementary files format and content: excel file includes raw counts for each Sample

organism: Caenorhabditis elegans

source_name: Caenorhabditis elegans

extract_protocol:
Total nematodes RNA was extracted from RNAi rpoa-40 or Y54G2A.18, using TRIzol reagent according to manufacturer’s protocol.
RNA libraries prepared by KindStar (Wuhan) underwent Illumina NovaSeq sequencing.

value: Caenorhabditis elegans


title: WT_2

description: Library name: Sample 2


title: 360-1.GEX.SamplePool.rs23854

description:
Library name: 23854
Fig1_1of2.seurat.rds
Fig1_2of2.seurat.rds
Fig1_1of2.counts.rds
Fig1_2of2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds

value: PBMC


title: 360-1.TCR.SamplePool.rs23855

description:
Library name: 23855
Fig1_1of2.seurat.rds
Fig1_2of2.seurat.rds
Fig1_1of2.counts.rds
Fig1_2of2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: 360-1.HTO.SamplePool.rs23853

description:
Library name: 23853
Fig1_1of2.seurat.rds
Fig1_2of2.seurat.rds
Fig1_1of2.counts.rds
Fig1_2of2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: shy54g2a.18-2

description: Library name: dsY2


title: 314-4.GEX.SamplePool.rs21407

description:
Library name: 21407
Fig1_1of2.seurat.rds
Fig1_2of2.seurat.rds
Fig1_1of2.counts.rds
Fig1_2of2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: WT_1

description: Library name: Sample 1

value: rosette leaves


title: shy54g2a.18-1

description: Library name: dsY1


title: 314-4.TCR.SamplePool.rs21408

description:
Library name: 21408
Fig1_1of2.seurat.rds
Fig1_2of2.seurat.rds
Fig1_1of2.counts.rds
Fig1_2of2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: 314-4.HTO.SamplePool.rs21406

description:
Library name: 21406
Fig1_1of2.seurat.rds
Fig1_2of2.seurat.rds
Fig1_1of2.counts.rds
Fig1_2of2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: Old mice AMs (10 mice) CD11C+CD11b+ S4C

city: San Antonio

first: Larry

middle: S

last: Schlesinger

state: Texas

address: 8715, W Military Drive, Larry Schlesinger Laboratory, Texas Biomedical Research Institute

department: Host Pathogen Interactions program

institute: Texas Biomedical Research Institute

description:
Library name: Sample 12 (S4C)
Mice Flow cytometry sorted BAL cells

data_processing:
Raw sequencing reads were preprocessed using Trim Galore! to trim the adapters and low-quality sequences. Trimmed reads were mapped to the mouse mm10 reference genome using HISAT2.
Read counts for each sample were obtained using featureCounts. Differential gene expression analysis was carried out using  DESeq2.
The Benjamini-Hochberg procedure was used to control the false discovery rate (FDR), and the shrunken log2 fold changes (LFCs) were calculated using the adaptive shrinkage (ash) estimator with an Empirical Bayes approach. Genes with FDR-adjusted p-value <0.05 and LFC of more than 1 or less than -1 were considered to be differentially expressed.
Assembly: mm10
Supplementary files format and content: raw_counts.csv

source_name: Lung

growth_protocol: Alveolar macrophages (AMs) were isolated from both 10 young and 10 old mice. Cells were then stained and sorted by sorted into CD11c+ CD11b- populations from young and old mice, and CD11c- CD11b+ and CD11c+ CD11b+ populations from old mice using the BD FACSAria II flow cytometer flow cytometry using BV421 anti-CD11b (clone M1/70) and PE anti-CD11c (clone N418) antibodies. The post-sorted cells were then verified based on the gating strategy, and the purity of the populations was confirmed through gating.

extract_protocol:
Flowcytometry-sorted CD11c+ CD11b- AMs from young mice and CD11c+ CD11b-, CD11c-CD11b+, and CD11c+ CD11b+ AM populations from old mice were collected and washed at 250 x g for 10 min with 1% PBS. The RNA was isolated using TRIzol reagent (Invitrogen) and a Direct-zol RNA Microprep kit (Zymo Research) according to the manufacturer's instructions. The isolated RNA was quantified using the Qubit 4 Fluorimeter (Invitrogen), and its quality was assessed with the 4200 TapeStation System (Agilent). Samples with an RNA integrity number (RIN) higher than 7 were used for RNA-seq. RNA-seq libraries were prepared from 300 ng of total RNA using the NEB Next RNA Ultra Kit (Qiagen, Redwood City, CA) with poly(A) enrichment, and 50-bp single-read sequencing with approximately 25-30M reads per sample. The RNA sequencing was performed at the Genome Sequencing Facility (GSF) at UTHealth San Antonio using the HiSeq 3000 platform (Illumina).
Then RNA-seq libraries were prepared from 300ng of total RNA using the mRNA-seq library preparation and 50bp single read sequencing with about 25-30M reads per sample in the NEB Next RNA Ultra Kit (Qiagen, Redwood City, CA) with poly (A) enrichment.

value: Lung

value: Primary cells

value: Alveolar macrophages

value: 18 months Old mice

value: CD11c+CD11b+ immigrated alveolar macrophages from old mice were isolated and flow cytometry sorted

value: Replicate batch-3


title: shCtrl-3-y54g2a.18

description: Library name: C3


title: 314-2.TCR.SamplePool.rs21402

description:
Library name: 21402
Fig1_1of2.seurat.rds
Fig1_2of2.seurat.rds
Fig1_1of2.counts.rds
Fig1_2of2.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: 314-2.GEX.SamplePool.rs21401

description:
Library name: 21401
Fig1_1of2.seurat.rds
Fig1_2of2.seurat.rds
Fig1_1of2.counts.rds
Fig1_2of2.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: 1184-2.HTO.23230.rs97330

description:
Library name: 97330
Fig5.seurat.rds
Fig5.counts.rds

value: Bone marrow,Colon,Liver,PBMC


title: Old mice AMs (10 mice) CD11C+CD11b+ S4B

description:
Library name: Sample 11 (S4B)
Mice Flow cytometry sorted BAL cells

value: Replicate batch-2


title: 314-2.HTO.SamplePool.rs21400

description:
Library name: 21400
Fig1_1of2.seurat.rds
Fig1_2of2.seurat.rds
Fig1_1of2.counts.rds
Fig1_2of2.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: shCtrl-2-y54g2a.18

description: Library name: C2


title: 300-4.GEX.32726.rs20823

description:
Library name: 20823
Fig1_1of2.seurat.rds
Fig1_2of2.seurat.rds
Fig1_1of2.counts.rds
Fig1_2of2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: 300-4.TCR.32726.rs20824

description:
Library name: 20824
Fig1_1of2.seurat.rds
Fig1_2of2.seurat.rds
Fig1_1of2.counts.rds
Fig1_2of2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: Old mice AMs (10 mice) CD11C+CD11b+ S4A

description:
Library name: Sample 10 (S4A)
Mice Flow cytometry sorted BAL cells

value: Replicate batch-1


title: 300-4.HTO.32726.rs20822

description:
Library name: 20822
Fig1_1of2.seurat.rds
Fig1_2of2.seurat.rds
Fig1_1of2.counts.rds
Fig1_2of2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: Old mice AMs (10 mice) CD11C-CD11b+ S3C

description:
Library name: Sample 9 (S3C)
Mice Flow cytometry sorted BAL cells

value: CD11c-CD11b+ immigrated alveolar macrophages from old mice were isolated and flow cytometry sorted


title: shCtrl-1-y54g2a.18

description: Library name: C1


title: shRPOA-49-3

description: Library name: dsropa-49-3


title: Old mice AMs (10 mice) CD11C-CD11b+ S3B

description:
Library name: Sample 8 (S3B)
Mice Flow cytometry sorted BAL cells


title: 300-3.GEX.SamplePool.rs20820

description:
Library name: 20820
Fig1_1of2.seurat.rds
Fig1_2of2.seurat.rds
Fig1_1of2.counts.rds
Fig1_2of2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: 300-3.HTO.SamplePool.rs20819

description:
Library name: 20819
Fig1_1of2.seurat.rds
Fig1_2of2.seurat.rds
Fig1_1of2.counts.rds
Fig1_2of2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: shRPOA-49-2

description: Library name: dsropa-49-2


title: 300-3.TCR.SamplePool.rs20821

description:
Library name: 20821
Fig1_1of2.seurat.rds
Fig1_2of2.seurat.rds
Fig1_1of2.counts.rds
Fig1_2of2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: 300-2.TCR.SamplePool.rs20818

description:
Library name: 20818
Fig1_1of2.seurat.rds
Fig1_2of2.seurat.rds
Fig1_1of2.counts.rds
Fig1_2of2.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: Old mice AMs (10 mice) CD11C-CD11b+ S3A

description:
Library name: Sample 7 (S3A)
Mice Flow cytometry sorted BAL cells


title: shRPOA-49-1

description: Library name: dsropa-49-1


title: 300-2.GEX.SamplePool.rs20817

description:
Library name: 20817
Fig1_1of2.seurat.rds
Fig1_2of2.seurat.rds
Fig1_1of2.counts.rds
Fig1_2of2.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: 300-2.HTO.SamplePool.rs20816

description:
Library name: 20816
Fig1_1of2.seurat.rds
Fig1_2of2.seurat.rds
Fig1_1of2.counts.rds
Fig1_2of2.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: Old mice AMs (10 mice) CD11C+CD11b- S2C

description:
Library name: Sample 6 (S2C)
Mice Flow cytometry sorted BAL cells

value: CD11c+ CD11b- resident alveolar macrophages from old mice were isolated and flow cytometry sorted


title: shCtrl-3-RPOA-49

description: Library name: Cc3


title: 300-1.GEX.SamplePool.rs20814

description:
Library name: 20814
Fig1_1of2.seurat.rds
Fig1_2of2.seurat.rds
Fig1_1of2.counts.rds
Fig1_2of2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: 300-1.TCR.SamplePool.rs20815

description:
Library name: 20815
Fig1_1of2.seurat.rds
Fig1_2of2.seurat.rds
Fig1_1of2.counts.rds
Fig1_2of2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: 300-1.HTO.SamplePool.rs20813

description:
Library name: 20813
Fig1_1of2.seurat.rds
Fig1_2of2.seurat.rds
Fig1_1of2.counts.rds
Fig1_2of2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: Old mice AMs (10 mice) CD11C+CD11b- S2B

description:
Library name: Sample 5 (S2B)
Mice Flow cytometry sorted BAL cells


title: 289-4.TCR.SamplePool.rs20767

description:
Library name: 20767
Fig1_1of2.seurat.rds
Fig1_2of2.seurat.rds
Fig1_1of2.counts.rds
Fig1_2of2.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: shCtrl-2-RPOA-49

description: Library name: Cc2


title: 289-4.GEX.SamplePool.rs20766

description:
Library name: 20766
Fig1_1of2.seurat.rds
Fig1_2of2.seurat.rds
Fig1_1of2.counts.rds
Fig1_2of2.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: shCtrl-1-RPOA-49

description: Library name: Cc1


title: Old mice AMs (10 mice) CD11C+CD11b- S2A

description:
Library name: Sample 4 (S2A)
Mice Flow cytometry sorted BAL cells