title: plaque cells from M-LipaKI mice

description:
Library name: HF04
10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were performed using the Cell Ranger software v3.0.1.
The outputs of Cell Ranger were analyzed using Seurat 4.3.0.1 in R.
Samples were filtered based on the number of genes per cell (> 1500 and < 6000), number of Unique Molecular Identifiers (< 20000), and percentage of mitochondrial genes (< 10%).
Two-dimensional Uniform Manifold Approximation and Projection (UMAP) was constructed with 25 nearest neighbors and the first 40 principal components as input. Clusters were identified with a resolution of 0.6. Differential expressing genes among clusters were performed using the MAST 1.26.0 test with min.pct threshold as 0.1.
Genes with an absolute fold change > 1.2 and Bonferroni-corrected P < 0.05 were defined as differentially expressed (DE).
Assembly: mm10
Supplementary files format and content: HF03_barcodes.tsv.gz: list of barcode for HF03
Supplementary files format and content: HF03_features.tsv.gz: list of gene IDs for HF03
Supplementary files format and content: HF03_matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format for HF03
Supplementary files format and content: HF04_barcodes.tsv.gz: list of barcode for HF04
Supplementary files format and content: HF04_features.tsv.gz: list of gene IDs for HF04
Supplementary files format and content: HF04_matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format for HF04

source_name: atherosclerotic plaque cells

extract_protocol:
The ascending aorta, aortic arch, and descending thoracic aorta were excised, cleaned of perivascular adipose tissue, and cut into small pieces to facilitate enzymatic digestion. The aortic tissues were digested into single cells in 1 mL RPMI medium containing 4 U/mL of Liberase TM (Sigma, 5401127001), 60 U/mL of hyaluronidase (Sigma, H3506), and 60 U/mL of DNase I (Worthington Biochemical Corporation, LS006333) at 37°C for 40 min. The enzymes were then neutralized by adding 4 mL of RPMI medium supplemented with 10% FBS. The obtained cell suspensions were filtered through 100 μm cell strainers and stained in 500 μL FACS buffer including DRAQ5 (BioLegend, 424101,1:1000) and DAPI (BioLegend, 422801, 1:3000) for 10 min on ice. Viable singlets (DRAQ5+DAPI-) were collected into DMEM/F12 medium (Cytiva SH30261.01) containing 10% FBS, and immediately submitted to the Single Cell Analysis
Samples were prepared using the 10x Genomics Chromium Single Cell 3’ Reagent Kits v2 (mouse samples) according to the manufacturer's instructions by Single Cell Analysis Core at the JP Sulzberger Columbia Genome Center.

value: atherosclerotic plaque cells


title: E12_PBC_subject5_PDC-E2_Tconv

status: Public on Aug 01 2025

type: SRA

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

country: USA

institute: Benaroya Research Institute

library_source: transcriptomic

data_processing:
Reads were trimmed by 1 base at the 3′ end, and then trimmed from both ends until base calls had a minimum quality score of at least 30 (Galaxy FASTQ Trimmer tool v1.0.0). FastqMcf (v1.1.2) was used to remove any remaining adapter sequence. To align the trimmed reads, we used the STAR aligner (v2.4.2a) with the GRCh38 reference genome and gene annotations from ensembl release 91. Gene counts were generated using HTSeq-count (v0.4.1). Quality metrics were compiled from PICARD (v1.134), FASTQC (v0.11.3), Samtools (v1.2), and HTSeq-count (v0.4.1). To identify TCR chains, the Trinity assembler was used to generate contigs. TCR sequences were identified and annotated using MiXCR (v2.1.3).
Assembly: GRCh38
Supplementary files format and content: P461_genecounts.txt: Library by Gene Count Matrix
Supplementary files format and content: P461_tcrs.txt: tab-delimited text file with sequences and metadata

molecule: total RNA

organism: Homo sapiens

source_name: PBMC

growth_protocol: PBMCs were isolated from fresh whole blood by Ficoll-Hypaque centrifugation and then immediately used in AIM assay.

extract_protocol:
To optimize recovery, PDC-E2-reactive T cells were sorted at single-cell purity directly into individual wells of a 96-well PCR plate with 5μl reaction buffer from the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara Bio) as previously described
Sequencing libraries were constructed using the NexteraXT DNA sample preparation kit (Illumina) to generate Illumina-compatible barcoded libraries.
Libraries were pooled and quantified using a Qubit® Fluorometer (Life Technologies). Dual-index, single-read sequencing of pooled libraries was carried out on a NextSeq 2000 sequencer (Illumina) with 58-base reads, using HiSeq v4 Cluster and SBS kits (Illumina) with a target depth of 1 million reads per sample.

treatment_protocol: . For each sample, the gate in antigen-stimulated cultures was set based on the DMSO-treated culture. CEFX stimulation was used as positive control, but not sorted. FOXP3 and Helios were not used to identify Tregs for sorting since permeabilization and fixation are incompatible with scRNA-seq.

tag: tissue

value: PBMC

value: Tconv

tag: group

value: PBC

tag: stimulation

value: PDC-E2 peptides

tag: subject


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 0, 35911

city: Minneapolis

first: Michael

last: Gale

state: Minnesota

address: 689 23rd Ave SE

department: Microbiology and Immunology

institute: University of Minnesota

description: Library name: G022_O06_ABL2_A2_35911_D0

data_processing:
Trimgalorev0.6.4 used to remove low quality reads and bases
Filtered out globin and rRNA reads using bowtie2v2.1.0
Aligned reads with STARv2.7.3
quantified read counts with  htseqv0.11.2
Assembly: Rhesus macaques version 10 Ensembl annoation v98
Supplementary files format and content: ount matrix

organism: Macaca mulatta

source_name: Whole blood

extract_protocol:
Isolation of RNA from Whole Blood Using the RNAdvance Blood Kit – for NHP samples
mRNA Library Prep for RNA from Whole Blood using KAPA HyperPrep Reagents

treatment_protocol: A prime and boost of one of the 4 modified RhCMV/SIV vectors were given to Rhesus macaques

value: Whole blood

tag: treatment

tag: time

value: day 0

tag: animal id

tag: Sex

value: male

tag: dose

tag: treatment outcome

value: protected


title: E11_PBC_subject5_PDC-E2_Tconv


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 0, 35827

description: Library name: G018_O06_ABL2_A2_35827_D0

value: notprotected


title: plaque cells from Control mice

city: New York

first: Fang

last: Li

state: NY

department: Medicine

institute: Columbia University Irving Medical Center

description:
Library name: HF03
10X Genomics

library_source: transcriptomic single cell

organism: Mus musculus

tag: genotype

value: LysMCre-/-, LipaKI/WT, Ldlr-/-


title: E8_PBC_subject5_PDC-E2_Tconv


title: E10_PBC_subject5_PDC-E2_Tconv


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 0, 35883

description: Library name: G019_O06_ABL2_A2_35883_D0


title: E9_PBC_subject5_PDC-E2_Tconv


title: E7_PBC_subject5_PDC-E2_Tconv


title: F2_PBC_subject5_PDC-E2_Tconv


title: E6_PBC_subject5_PDC-E2_Tconv


title: E4_PBC_subject5_PDC-E2_Tconv


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 0, 35820

description: Library name: G017_O06_ABL2_A2_35820_D0


title: PG_NTG_Colon_10M_04

city: Taipei

first: Chia-Lang

last: Hsu

address: No. 7, Zhongshan S. Rd.

department: Department of Medical Research

country: Taiwan

institute: National Taiwan University Hospital

description: Library name: CG_PG_NTG4

data_processing:
Raw sequencing reads were controlled for quality using FASTQC (v 0.11.9), and adaptor sequences were trimmed with cutadapt (v 3.5).
The qualified reads were aligned to the mouse reference genome GRCm38 using STAR with the 2-pass aligned mode (v 2.7.8a).
Gene counts were generated using featureCounts (v 1.6.4) based on the GENCODE vM25 annotation.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include read count values for each sample

source_name: Colon

extract_protocol:
Total RNA was isolated by using the AllPrep DNA/RNA Mini Kit (Qiagen, Hilden, Germany)
Libraries were constructed using KAPA RNA HyperPrep Kit with RiboErase according to the manufacturer's instructions (Cat# KK8560)

value: Colon

value: WT

value: Parabacteroides goldsteinii MTS01


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 0, 33864

description: Library name: G016_O06_ABL2_A2_33864_D0


title: E1_PBC_subject5_PDC-E2_Tconv


title: E3_PBC_subject5_PDC-E2_Tconv


title: PG_NTG_Colon_10M_03

description: Library name: CG_PG_NTG3


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 0, 33543

description: Library name: G021_O06_ABL2_A2_33543_D0


title: PG_NTG_Colon_10M_02

description: Library name: CG_PG_NTG2


title: D12_PBC_subject5_PDC-E2_Tconv


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 0, 32509

description: Library name: G015_O06_ABL2_A2_32509_D0


title: PG_NTG_Colon_10M_01

description: Library name: CG_PG_NTG1


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 0, 32119

description: Library name: G014_O06_ABL2_A2_32119_D0


title: E5_PBC_subject5_PDC-E2_Tconv


title: D9_PBC_subject5_PDC-E2_Tconv


title: D8_PBC_subject5_PDC-E2_Tconv


title: D10_PBC_subject5_PDC-E2_Tconv


title: GF_NTG_Colon_10M_02

description: Library name: CG_GF_NTG2

value: germ-free


title: D7_PBC_subject5_PDC-E2_Tconv


title: D6_PBC_subject5_PDC-E2_Tconv


title: GF_NTG_Colon_10M_04

description: Library name: CG_GF_NTG4


title: D5_PBC_subject5_PDC-E2_Tconv


title: E2_PBC_subject5_PDC-E2_Tconv


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 0, 32017

description: Library name: G013_O06_ABL2_A2_32017_D0


title: GF_NTG_Colon_10M_03

description: Library name: CG_GF_NTG3


title: D4_PBC_subject5_PDC-E2_Tconv


title: GF_NTG_Colon_10M_01

description: Library name: CG_GF_NTG1


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 0, 35916

description: Library name: G012_O06_ABL2_A1_35916_D0


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 0, 35890

description: Library name: G011_O06_ABL2_A1_35890_D0


title: D1_PBC_subject5_PDC-E2_Tconv


title: D2_PBC_subject5_PDC-E2_Tconv


title: D3_PBC_subject5_PDC-E2_Tconv


title: PG_HET_Colon_10M_04

description: Library name: CG_PG_HET4

value: LRRK2 G2019S


title: F12_PBC_subject5_PDC-E2_Tconv


title: C12_PBC_subject5_PDC-E2_Tconv


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 0, 35808

description: Library name: G009_O06_ABL2_A1_35808_D0


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 0, 35815

description: Library name: G010_O06_ABL2_A1_35815_D0


title: C11_PBC_subject5_PDC-E2_Tconv


title: PG_HET_Colon_10M_03

description: Library name: CG_PG_HET3


title: D11_PBC_subject5_PDC-E2_Tconv


title: C10_PBC_subject5_PDC-E2_Tconv


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 0, 33900

description: Library name: G008_O06_ABL2_A1_33900_D0


title: PG_HET_Colon_10M_02

description: Library name: CG_PG_HET2


title: C8_PBC_subject5_PDC-E2_Tconv


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 0, 33879

description: Library name: G007_O06_ABL2_A1_33879_D0


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 0, 32814

description: Library name: G006_O06_ABL2_A1_32814_D0


title: C7_PBC_subject5_PDC-E2_Tconv


title: C5_PBC_subject5_PDC-E2_Tconv


title: C6_PBC_subject5_PDC-E2_Tconv


title: PG_HET_Colon_10M_01

description: Library name: CG_PG_HET1


title: C4_PBC_subject5_PDC-E2_Tconv


title: GF_HET_Colon_10M_04

description: Library name: CG_GF_HET4


title: B12_PBC_subject5_PDC-E2_Tconv


title: GF_HET_Colon_10M_02

description: Library name: CG_GF_HET2


title: C3_PBC_subject5_PDC-E2_Tconv


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 0, 32778

description: Library name: G005_O06_ABL2_A1_32778_D0


title: GF_HET_Colon_10M_01

description: Library name: CG_GF_HET1


title: GF_HET_Colon_10M_03

description: Library name: CG_GF_HET3


title: C1_PBC_subject5_PDC-E2_Tconv


title: B11_PBC_subject5_PDC-E2_Tconv


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 0, 32321

description: Library name: G003_O06_ABL2_A1_32321_D0


title: B9_PBC_subject5_PDC-E2_Tconv


title: B10_PBC_subject5_PDC-E2_Tconv


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 0, 32215

description: Library name: G002_O06_ABL2_A1_32215_D0


title: B8_PBC_subject5_PDC-E2_Tconv


title: PG_HET_Colon_5M_03

description: Library name: N1121212


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 0, 32019

description: Library name: G001_O06_ABL2_A1_32019_D0


title: C9_PBC_subject5_PDC-E2_Tconv


title: B7_PBC_subject5_PDC-E2_Tconv


title: C2_PBC_subject5_PDC-E2_Tconv


title: B6_PBC_subject5_PDC-E2_Tconv


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 0, 32485

description: Library name: G004_O06_ABL2_A1_32485_D0


title: B5_PBC_subject5_PDC-E2_Tconv


title: PG_HET_Colon_5M_01

description: Library name: N1121210


title: B3_PBC_subject5_PDC-E2_Tconv


title: B4_PBC_subject5_PDC-E2_Tconv


title: B2_PBC_subject5_PDC-E2_Tconv


title: PBMCs, IL15, 48h, 40ng/ml, 31954, Two

description: Library name: 224_O10_31954_40_48h_2

data_processing:
Trimgalorev0.6.10 used to remove low quality reads and bases
Filtered out globin and rRNA reads using bowtie2v2.4.4
Aligned reads with STARv2.7.10b to rhesus macaque genome
Assembly: Macaca mulatta version 10 Ensembl annoation v110
Supplementary files format and content: individual count files for each sample

source_name: PBMCs

extract_protocol:
RNeasy Micro Kit
TruSeq mRNA / Biomek

treatment_protocol: Ex-vivo PBMCs from rhesus macaques  were treated with IL-15/IL-15Ra at 4ng and 40ng/ml

value: PBMCs

tag: replicate

value: Two


title: PBMCs, IL15, 48h, 40ng/ml, 31954, Three

description: Library name: 225_O10_31954_40_48h_3

value: Three


title: GF_HET_Colon_5M_02

description: Library name: N1121208


title: A11_PBC_subject5_PDC-E2_Tconv

value: PBMC

value: Tconv


title: A12_PBC_subject5_PDC-E2_Tconv

value: PBC

value: PDC-E2 peptides


title: PBMCs, IL15, 24h, 40ng/ml, 31954, Two

description: Library name: 221_O10_31954_40_24h_2


title: A10_PBC_subject5_PDC-E2_Tconv


title: A9_PBC_subject5_PDC-E2_Tconv


title: GF_HET_Colon_5M_01

description: Library name: N1121207


title: A8_PBC_subject5_PDC-E2_Tconv


title: PBMCs, IL15, 24h, 40ng/ml, 31954, One

description: Library name: 220_O10_31954_40_24h_1

value: One


title: PBMCs, IL15, 12h, 40ng/ml, 31954, Three

description: Library name: 219_O10_31954_40_12h_3

value: male


title: A6_PBC_subject5_PDC-E2_Tconv


title: A7_PBC_subject5_PDC-E2_Tconv


title: A5_PBC_subject5_PDC-E2_Tconv


title: PG_HET_Colon_5M_02

description: Library name: N1121211


title: PG_NTG_Colon_5M_02

description: Library name: N1121205


title: PG_NTG_Colon_5M_01

description: Library name: N1121204


title: PBMCs, IL15, 12h, 40ng/ml, 31954, Two

description: Library name: 218_O10_31954_40_12h_2


title: A4_PBC_subject5_PDC-E2_Tconv


title: GF_HET_Colon_5M_03

description: Library name: N1121209


title: A3_PBC_subject5_PDC-E2_Tconv


title: GF_NTG_Colon_5M_03

description: Library name: N1121203


title: B1_PBC_subject5_PDC-E2_Tconv


title: PBMCs, IL15, 48h, 40ng/ml, 31954, One

description: Library name: 223_O10_31954_40_48h_1


title: PBMCs, IL15, 24h, 40ng/ml, 31954, Three

description: Library name: 222_O10_31954_40_24h_3


title: GF_NTG_Colon_5M_02

description: Library name: N1121202


title: PG_NTG_Colon_5M_03

description: Library name: N1121206


title: E5_HC_subject5_PDC-E2_Treg

value: Treg

value: HC


title: PBMCs, IL15, 12h, 40ng/ml, 31954, One

description: Library name: 217_O10_31954_40_12h_1


title: A2_PBC_subject5_PDC-E2_Tconv


title: A1_PBC_subject5_PDC-E2_Tconv


title: GF_NTG_Colon_5M_01

description: Library name: N1121201


title: PBMCs, IL15, 6h, 40ng/ml, 31954, Three

description: Library name: 216_O10_31954_40_6h_3


title: E4_HC_subject5_PDC-E2_Treg


title: E2_HC_subject5_PDC-E2_Treg


title: E1_HC_subject5_PDC-E2_Treg


title: PG_HET_Brain_10M_03

description: Library name: N1103915

source_name: Brain

value: Brain


title: PBMCs, IL15, 6h, 40ng/ml, 31954, One

description: Library name: 214_O10_31954_40_6h_1


title: PBMCs, IL15, 6h, 40ng/ml, 31954, Two

description: Library name: 215_O10_31954_40_6h_2


title: D11_HC_subject5_PDC-E2_Treg


title: D10_HC_subject5_PDC-E2_Treg


title: PG_HET_Brain_10M_01

description: Library name: N1103913


title: D12_HC_subject5_PDC-E2_Treg


title: PG_HET_Brain_10M_02

description: Library name: N1103914


title: D8_HC_subject5_PDC-E2_Treg


title: D9_HC_subject5_PDC-E2_Treg


title: PBMCs, IL15, 2h, 40ng/ml, 31954, Two

description: Library name: 212_O10_31954_40_2h_2


title: D7_HC_subject5_PDC-E2_Treg


title: PG_NTG_Brain_10M_04

description: Library name: N1103912


title: PBMCs, IL15, 2h, 40ng/ml, 31954, One

description: Library name: 211_O10_31954_40_2h_1


title: D6_HC_subject5_PDC-E2_Treg


title: PG_NTG_Brain_10M_03

description: Library name: N1103911


title: D5_HC_subject5_PDC-E2_Treg


title: D4_HC_subject5_PDC-E2_Treg


title: PBMCs, IL15, 48h, 4ng/ml, 31954, Three

description: Library name: 210_O10_31954_4_48h_3


title: D3_HC_subject5_PDC-E2_Treg


title: E3_HC_subject5_PDC-E2_Treg


title: D1_HC_subject5_PDC-E2_Treg


title: PBMCs, IL15, 48h, 4ng/ml, 31954, Two

description: Library name: 209_O10_31954_4_48h_2


title: D2_HC_subject5_PDC-E2_Treg


title: PBMCs, IL15, 2h, 40ng/ml, 31954, Three

description: Library name: 213_O10_31954_40_2h_3


title: PG_NTG_Brain_10M_01

description: Library name: N1103909


title: C12_HC_subject5_PDC-E2_Treg


title: PBMCs, IL15, 48h, 4ng/ml, 31954, One

description: Library name: 208_O10_31954_4_48h_1


title: GF_HET_Brain_10M_03

description: Library name: N1103907


title: C10_HC_subject5_PDC-E2_Treg


title: PBMCs, IL15, 24h, 4ng/ml, 31954, Three

description: Library name: 207_O10_31954_4_24h_3


title: C9_HC_subject5_PDC-E2_Treg


title: GF_HET_Brain_10M_02

description: Library name: N1103906


title: PBMCs, IL15, 24h, 4ng/ml, 31954, Two

description: Library name: 206_O10_31954_4_24h_2


title: C11_HC_subject5_PDC-E2_Treg


title: C8_HC_subject5_PDC-E2_Treg


title: GF_HET_Brain_10M_01

description: Library name: N1103905


title: PBMCs, IL15, 24h, 4ng/ml, 31954, One

description: Library name: 205_O10_31954_4_24h_1


title: C6_HC_subject5_PDC-E2_Treg


title: C7_HC_subject5_PDC-E2_Treg


title: PG_NTG_Brain_10M_02

description: Library name: N1103910


title: C5_HC_subject5_PDC-E2_Treg


title: C4_HC_subject5_PDC-E2_Treg


title: GF_NTG_Brain_10M_03

description: Library name: N1103903


title: C3_HC_subject5_PDC-E2_Treg


title: PBMCs, IL15, 12h, 4ng/ml, 31954, Three

description: Library name: 204_O10_31954_4_12h_3


title: PBMCs, IL15, 12h, 4ng/ml, 31954, Two

description: Library name: 203_O10_31954_4_12h_2


title: B12_HC_subject5_PDC-E2_Treg


title: GF_NTG_Brain_10M_02

description: Library name: N1103902


title: PBMCs, IL15, 12h, 4ng/ml, 31954, One

description: Library name: 202_O10_31954_4_12h_1


title: PBMCs, IL15, 6h, 4ng/ml, 31954, Three

description: Library name: 201_O10_31954_4_6h_3


title: B10_HC_subject5_PDC-E2_Treg


title: B11_HC_subject5_PDC-E2_Treg


title: C1_HC_subject5_PDC-E2_Treg


title: GF_NTG_Brain_10M_01

description: Library name: N1103901


title: B9_HC_subject5_PDC-E2_Treg


title: B8_HC_subject5_PDC-E2_Treg


title: PG_HET_Brain_5M_03

description: Library name: N1121224


title: PG_HET_Brain_5M_02

description: Library name: N1121223


title: B6_HC_subject5_PDC-E2_Treg


title: B7_HC_subject5_PDC-E2_Treg


title: GF_NTG_Brain_10M_04

description: Library name: N1103904


title: PBMCs, IL15, 6h, 4ng/ml, 31954, One

description: Library name: 199_O10_31954_4_6h_1


title: PBMCs, IL15, 6h, 4ng/ml, 31954, Two

description: Library name: 200_O10_31954_4_6h_2


title: B4_HC_subject5_PDC-E2_Treg


title: PG_HET_Brain_5M_01

description: Library name: N1121222


title: B5_HC_subject5_PDC-E2_Treg


title: B3_HC_subject5_PDC-E2_Treg


title: PBMCs, IL15, 2h, 4ng/ml, 31954, Three

description: Library name: 198_O10_31954_4_2h_3


title: PBMCs, IL15, 2h, 4ng/ml, 31954, Two

description: Library name: 197_O10_31954_4_2h_2


title: GF_HET_Brain_5M_03

description: Library name: N1121221


title: C2_HC_subject5_PDC-E2_Treg


title: B2_HC_subject5_PDC-E2_Treg


title: GF_HET_Brain_5M_02

description: Library name: N1121220


title: B1_HC_subject5_PDC-E2_Treg


title: PBMCs, IL15, 2h, 0ng/ml, 31954, One

description: Library name: 196_O10_31954_4_2h_1


title: A12_HC_subject5_PDC-E2_Treg


title: GF_HET_Brain_5M_01

description: Library name: N1121219


title: A10_HC_subject5_PDC-E2_Treg


title: A11_HC_subject5_PDC-E2_Treg


title: A9_HC_subject5_PDC-E2_Treg


title: PBMCs, Control, 48h, 0ng/ml, 31954, Two

description: Library name: 194_O10_31954_0_48h_2

value: Control


title: PG_NTG_Brain_5M_03

description: Library name: N1121218

value: WT


title: PBMCs, Control, 48h, 0ng/ml, 31954, Three

description: Library name: 195_O10_31954_0_48h_3


title: PG_NTG_Brain_5M_01

description: Library name: N1121216

value: Parabacteroides goldsteinii MTS01


title: A8_HC_subject5_PDC-E2_Treg


title: PBMCs, Control, 24h, 0ng/ml, 31954, Three

description: Library name: 192_O10_31954_0_24h_3


title: A4_HC_subject5_PDC-E2_Treg


title: PG_NTG_Brain_5M_02

description: Library name: N1121217


title: GF_NTG_Brain_5M_03

description: Library name: N1121215

value: germ-free


title: A3_HC_subject5_PDC-E2_Treg


title: A7_HC_subject5_PDC-E2_Treg


title: A2_HC_subject5_PDC-E2_Treg


title: H12_HC_subject5_PDC-E2_Tconv


title: GF_NTG_Brain_5M_02

description: Library name: N1121214


title: A1_HC_subject5_PDC-E2_Treg


title: PBMCs, Control, 24h, 0ng/ml, 31954, Two

description: Library name: 191_O10_31954_0_24h_2


title: GF_NTG_Brain_5M_01

description: Library name: N1121213


title: PBMCs, Control, 24h, 0ng/ml, 31954, One

description: Library name: 190_O10_31954_0_24h_1


title: H11_HC_subject5_PDC-E2_Tconv


title: PBMCs, Control, 12h, 0ng/ml, 31954, Three

description: Library name: 189_O10_31954_0_12h_3


title: A6_HC_subject5_PDC-E2_Treg


title: H10_HC_subject5_PDC-E2_Tconv


title: H9_HC_subject5_PDC-E2_Tconv


title: PBMCs, Control, 12h, 0ng/ml, 31954, Two

description: Library name: 188_O10_31954_0_12h_2


title: H8_HC_subject5_PDC-E2_Tconv


title: PBMCs, Control, 12h, 0ng/ml, 31954, One

description: Library name: 187_O10_31954_0_12h_1


title: PBMCs, Control, 48h, 0ng/ml, 31954, One

description: Library name: 193_O10_31954_0_48h_1


title: A5_HC_subject5_PDC-E2_Treg


title: BMDMs, β-glucan-trained BMDM rep3

city: Guangzhou

first: Mengyun

address: Xingang Road

country: China

institute: SYSU

library_source: genomic

data_processing:
Illumina high-throughput sequencing results initially exist as raw image data files. After sequence base recognition by bcl-convert software, they are converted into raw sequencing sequences (Sequenced Reads), which we call Raw Data or Raw Reads. The results are expressed in FASTQ ( Referred to as fq) file format storage. The FASTQ file contains the name, base sequence and corresponding sequencing quality information of each sequencing sequence (Read).
Quality control was performed with FastQC  in Linux and with ATACseqQC (Version 1.16.0) in R.
reads were aligned to the reference mouse genome GRCm38/mm10 using HISTA2, to creat ATAC-seq coverage blots, the location of Chip-Seq reads were extended to 500bp,
ATAC-seq peaks were called using MACS3 software，peaks with low counts (consensus peaks with a median across treatments of counts-per-million less than 1) were  filtered out from further analysis submitted to Diffbind~3.8.4
Assembly: GRCm38/mm10
Supplementary files format and content: bigwig

molecule: genomic DNA

source_name: BMDMs isolated from mice adminstrated with β-glucan

growth_protocol: RPMI 1640, 10%FBS, 10% L929, 1%pen/strep. Cells were cultured at 37℃ with 5% CO2

extract_protocol:
Genomice DNA was extracted according to the instruction from a commercial kit. This kit is named High-Sensitivity Open Chromatin Profile Kit 2.0 (for Illumina); Novoprotein, Cat#N248
library construction was also completed according to the instruction from the commercial kit. (Novoprotein, N248)

tag: cell type

value: bone marrow derived macrophages (BMDMs)

value: wild type

value: β-glucan


title: PBMCs, Control, 6h, 0ng/ml, 31954, Three

description: Library name: 186_O10_31954_0_6h_3

value: PBMCs

value: Three


title: G9_HC_subject5_PDC-E2_Tconv

value: PBMC

value: Tconv


title: G10_HC_subject5_PDC-E2_Tconv

value: PDC-E2 peptides


title: G8_HC_subject5_PDC-E2_Tconv


title: BMDMs, β-glucan-trained BMDM rep1


title: G7_HC_subject5_PDC-E2_Tconv


title: PBMCs, Control, 6h, 0ng/ml, 31954, Two

description: Library name: 185_O10_31954_0_6h_2

value: Two


title: BMDMs, untrained BMDMs rep3

source_name: BMDMs isolated from mice adminstrated with placebo

value: placebo


title: G6_HC_subject5_PDC-E2_Tconv


title: BMDMs, β-glucan with alisertib trained BMDM rep3

source_name: BMDMs isolated from mice adminstrated with β-glucan and alisertib

value: β-glucan and alisertib


title: PBMCs, Control, 2h, 0ng/ml, 31954, Three

description: Library name: 183_O10_31954_0_2h_3

value: male


title: G5_HC_subject5_PDC-E2_Tconv

value: HC


title: G3_HC_subject5_PDC-E2_Tconv


title: BMDMs, untrained BMDMs rep2


title: G4_HC_subject5_PDC-E2_Tconv


title: PBMCs, Control, 6h, 0ng/ml, 31954, One

description: Library name: 184_O10_31954_0_6h_1

value: Control

value: One


title: G1_HC_subject5_PDC-E2_Tconv


title: G2_HC_subject5_PDC-E2_Tconv


title: OE-TDP43.2C.2

city: Hangzhou

first: Heng-yu

last: Fan

state: Zhejiang

address: Yuhangtang Road

institute: Life Sciences  Institute

data_processing:
Raw reads were trimmed by using trim-galore (v.0.6.10) and mapped to the mm10 genome (gencode, vM25) by using STAR (v.2.7.10a). Uniquely mapped reads were quantified by using FeatureCounts (v.2.0.2) and further calibrated with the ERCC spike-in as described before. Differential expression genes (DEG, adjusted P value < 0.01, average |log2 fold change| ≥ 1) were analyzed by using DESeq2 R package for further analysis.
Assembly: mm10
Supplementary files format and content: Count_list_WT-CKO.xlsx
Supplementary files format and content: Count_list_OE-TDP43.xlsx

molecule: polyA RNA

source_name: embryos

extract_protocol:
The embryos were washed in 0.2 BSA in 1X PBS and collected for lysis in 4.2 μl lysis buffer (0.2% Triton X-100, RNase inhibitor, deoxyribonucleotide triphosphate (dNTPs), oligo-dT primers, and 1:1000 ERCC spike-in).
The samples were reverse transcribed and amplificated using the Smart-seq2 method, as described previously. Sequencing libraries were constructed from 500 pg of amplified cDNA using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD503). Barcoded libraries were pooled and sequenced on the HiSeq X Ten platform with 150-bp paired-end reads.

value: embryos


title: PBMCs, Control, 2h, 0ng/ml, 31954, Two

description: Library name: 182_O10_31954_0_2h_2


title: F12_HC_subject5_PDC-E2_Tconv


title: OE-TDP43.2C.1


title: BMDMs, β-glucan with alisertib trained BMDM rep2


title: G11_HC_subject5_PDC-E2_Tconv


title: TDP43-MUT.2C.3


title: F10_HC_subject5_PDC-E2_Tconv


title: PBMCs, Control, 2h, 0ng/ml, 31954, One

description: Library name: 181_O10_31954_0_2h_1


title: F11_HC_subject5_PDC-E2_Tconv


title: PBMCs, IL15, 48h, 40ng/ml, 34100, Three

description: Library name: 180_O10_34100_40_48h_3


title: F9_HC_subject5_PDC-E2_Tconv


title: TDP43-MUT.2C.2


title: F8_HC_subject5_PDC-E2_Tconv


title: TDP43-MUT.2C.1


title: F5_HC_subject5_PDC-E2_Tconv


title: G9.2C.3


title: PBMCs, IL15, 48h, 40ng/ml, 34100, One

description: Library name: 178_O10_34100_40_48h_1


title: F4_HC_subject5_PDC-E2_Tconv


title: F3_HC_subject5_PDC-E2_Tconv


title: G9.2C.2


title: PBMCs, IL15, 24h, 40ng/ml, 34100, Three

description: Library name: 177_O10_34100_40_24h_3


title: PBMCs, IL15, 24h, 40ng/ml, 34100, Two

description: Library name: 176_O10_34100_40_24h_2


title: F2_HC_subject5_PDC-E2_Tconv


title: G9.2C.1


title: E12_HC_subject5_PDC-E2_Tconv


title: E10_HC_subject5_PDC-E2_Tconv


title: WT.2C.3


title: PBMCs, IL15, 24h, 40ng/ml, 34100, One

description: Library name: 175_O10_34100_40_24h_1


title: F1_HC_subject5_PDC-E2_Tconv


title: WT.2C.2


title: E9_HC_subject5_PDC-E2_Tconv


title: PBMCs, IL15, 12h, 40ng/ml, 34100, Three

description: Library name: 174_O10_34100_40_12h_3


title: PBMCs, IL15, 12h, 40ng/ml, 34100, One

description: Library name: 172_O10_34100_40_12h_1


title: G12_HC_subject5_PDC-E2_Tconv


title: PBMCs, IL15, 48h, 40ng/ml, 34100, Two

description: Library name: 179_O10_34100_40_48h_2


title: F7_HC_subject5_PDC-E2_Tconv


title: WT.2C.1


title: F6_HC_subject5_PDC-E2_Tconv


title: E6_HC_subject5_PDC-E2_Tconv


title: PBMCs, IL15, 6h, 40ng/ml, 34100, Three

description: Library name: 171_O10_34100_40_6h_3


title: E5_HC_subject5_PDC-E2_Tconv


title: G9.1C.3


title: E4_HC_subject5_PDC-E2_Tconv


title: E3_HC_subject5_PDC-E2_Tconv


title: E11_HC_subject5_PDC-E2_Tconv


title: PBMCs, IL15, 6h, 40ng/ml, 34100, Two

description: Library name: 170_O10_34100_40_6h_2


title: E2_HC_subject5_PDC-E2_Tconv


title: G9.1C.2


title: PBMCs, IL15, 6h, 40ng/ml, 34100, One

description: Library name: 169_O10_34100_40_6h_1


title: E1_HC_subject5_PDC-E2_Tconv


title: D11_HC_subject5_PDC-E2_Tconv


title: PBMCs, IL15, 2h, 40ng/ml, 34100, Three

description: Library name: 168_O10_34100_40_2h_3


title: G9.1C.1


title: WT.1C.3


title: E8_HC_subject5_PDC-E2_Tconv


title: D12_HC_subject5_PDC-E2_Tconv


title: D9_HC_subject5_PDC-E2_Tconv


title: D10_HC_subject5_PDC-E2_Tconv


title: WT.1C.2


title: PBMCs, IL15, 2h, 40ng/ml, 34100, One

description: Library name: 166_O10_34100_40_2h_1


title: D8_HC_subject5_PDC-E2_Tconv


title: PBMCs, IL15, 48h, 4ng/ml, 34100, Three

description: Library name: 165_O10_34100_4_48h_3


title: D7_HC_subject5_PDC-E2_Tconv


title: WT.1C.1


title: E7_HC_subject5_PDC-E2_Tconv


title: D6_HC_subject5_PDC-E2_Tconv


title: D5_HC_subject5_PDC-E2_Tconv


title: 2C.FLAG.3

data_processing:
Raw reads were trimmed by using trim-galore (v.0.6.10) and mapped to the mm10 genome (gencode, vM25) by using STAR (v.2.7.10a). Uniquely mapped reads were quantified by using FeatureCounts (v.2.0.2) and further calibrated with the ERCC spike-in as described before. Differential expression genes (DEG, adjusted P value < 0.01, average |log2 fold change| ≥ 1) were analyzed by using DESeq2 R package for further analysis.
Assembly: mm10
Supplementary files format and content: FPKM_RIP-seq.xlsx

extract_protocol:
400 2-cells for each sample were washed three times with 0.2% bovine serum albumin (BSA) in PBS and lysed in the lysis buffer (50 mM Tris–HCl [pH 7.4], 1% Triton X‐100, 150 mM NaCl, 5 mM EDTA, protease inhibitor cocktail, and RNase inhibitor). 90% cell lysate supernatant was used for immunoprecipitation with agarose beads conjugated with IgG or FLAG antibodies, while the residual cell lysate supernatant was used as the “input”. After incubation at 4°C for 4 h, bead‐bound RNAs were collected and reverse‐transcribed using the random primer.
The samples were reverse transcribed and amplificated using the Smart-seq2 method, as described previously. Sequencing libraries were constructed from 500 pg of amplified cDNA using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD503). Barcoded libraries were pooled and sequenced on the HiSeq X Ten platform with 150-bp paired-end reads.


title: PBMCs, IL15, 48h, 4ng/ml, 34100, Two

description: Library name: 164_O10_34100_4_48h_2


title: PBMCs, IL15, 48h, 4ng/ml, 34100, One

description: Library name: 163_O10_34100_4_48h_1


title: D3_HC_subject5_PDC-E2_Tconv


title: 2C.FLAG.2


title: C12_HC_subject5_PDC-E2_Tconv


title: D2_HC_subject5_PDC-E2_Tconv


title: PBMCs, IL15, 24h, 4ng/ml, 34100, Three

description: Library name: 162_O10_34100_4_24h_3


title: PBMCs, IL15, 24h, 4ng/ml, 34100, Two

description: Library name: 161_O10_34100_4_24h_2


title: C10_HC_subject5_PDC-E2_Tconv


title: 2C.FLAG.1


title: PBMCs, IL15, 24h, 4ng/ml, 34100, One

description: Library name: 160_O10_34100_4_24h_1


title: 2C.FLAG-TDP43.3


title: 2C.FLAG-TDP43.1


title: C5_HC_subject5_PDC-E2_Tconv


title: C7_HC_subject5_PDC-E2_Tconv


title: C9_HC_subject5_PDC-E2_Tconv


title: C6_HC_subject5_PDC-E2_Tconv


title: C4_HC_subject5_PDC-E2_Tconv


title: C8_HC_subject5_PDC-E2_Tconv


title: cKO

city: Beijing

first: Pu

last: Xing

address: No.52 Fucheng Road

institute: Peking University Cancer Hospital & Institute

description: 10x Genomics

data_processing:
Cell Ranger software was employed for comprehensive data processing, encompassing alignment, filtering, barcode enumeration, and unique molecular identifier counting via the count module. This streamlined process generated a feature-barcode matrix and identified clusters, which were then converted into Seurat objects using the Seurat package (v3.0). Cells exhibiting a low gene count (< 200), high gene expression rank (top 1% percentile), or excessive mitochondrial gene contributions (>25%) were flagged as abnormal and excluded from further analysis. Dimensionality reduction was applied through principal component analysis, while data visualization was accomplished by tSNE.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Intestine

extract_protocol:
Fresh tumor samples obtained from groups of MTCH2fl/fl and MTCH2cKO mice were pooled, rinsed with PBS, minced, and dissociated with 1× Trypsin-EDTA solution for 20 minutes at 37°C. A Countstar Fluorescence Cell Analyzer was used to assess the cell viability of dissociated single cells.
The cDNA synthesis and library construction for scRNA-seq strictly adhered to the protocols of the respective manufacturers. Briefly, unique RNAs released from individual cells underwent barcoding by reverse transcription in individual gel bead-in emulsions. This process yielded cDNA, which was then amplified and quality-checked to ensure accuracy.
Subsequently, the libraries were sequenced on an Illumina Novaseq6000 platform, employing a pair-end 150-bp strategy that achieved a minimum sequencing depth of 100,000 reads per cell to guarantee comprehensive coverage and analysis, by CapitalBio Technology.

value: Intestine

value: Mtch2fl/fl VilCre

value: AOM-DSS


title: PBMCs, IL15, 12h, 4ng/ml, 34100, Two

description: Library name: 158_O10_34100_4_12h_2


title: D4_HC_subject5_PDC-E2_Tconv


title: PBMCs, IL15, 12h, 4ng/ml, 34100, Three

description: Library name: 159_O10_34100_4_12h_3


title: PBMCs, IL15, 12h, 4ng/ml, 34100, One

description: Library name: 157_O10_34100_4_12h_1


title: C3_HC_subject5_PDC-E2_Tconv


title: 2C.FLAG-TDP43.2


title: C2_HC_subject5_PDC-E2_Tconv


title: C1_HC_subject5_PDC-E2_Tconv


title: WT

description: 10x Genomics


title: D1_HC_subject5_PDC-E2_Tconv


title: C11_HC_subject5_PDC-E2_Tconv


title: B12_HC_subject5_PDC-E2_Tconv


title: PBMCs, IL15, 6h, 4ng/ml, 34100, Two

description: Library name: 155_O10_34100_4_6h_2


title: B11_HC_subject5_PDC-E2_Tconv


title: PBMCs, IL15, 6h, 4ng/ml, 34100, One

description: Library name: 154_O10_34100_4_6h_1


title: B9_HC_subject5_PDC-E2_Tconv


title: M3cKOPNX, scRNAsq

city: Chengdu

first: Jie

last: Ma

address: No.17 People's South Road

institute: Sichuan university

data_processing:
Sample data were aggregated using Cell Ranger software and raw data were processed further in R (version 3.4.4). The whole workflow included quality control, data normalization, sample integration, clustering and visualization.
Assembly: mm10
Supplementary files format and content: Table-separated values and matrix market files

source_name: lung

extract_protocol:
Briefly, the Sheep anti Rat magnetic beads were pre-coated with CD31 and CD45 respectively. Harvested mouse lungs were washed with pre-cooled DPBS, cut into pieces, digested with digestion buffer containing type 1 collagenase (2mg/mL) in 37°C for 40min. After erythrocytes were lysed, lung cells were incubated with CD45 coated magnetic beads in 4°C for 30 min. The CD45 positive cells were absorbed by magnetic rack, the remaining cell suspension was incubated with CD31 coated magnetic beads in 4°C for 30 min, and CD31-positive and CD45-negative lung endothelial cells were obtained by elution of magnetic beads.
Library was performed according to manufactors' instruction: GEM generation,  Barcoding, GEM-RT clean-up, cDNA amplification and library construction.  Sequencing was performed on Illumina Nova-seq 6000 (Illumina, America),  followed by de-multiplexing and mapping to the mouse genome (build mm10)  using Cell Ranger (10x Genomics, version 2.1.1).

value: lung

value: endothelial cell


title: WTPNX, scRNAsq


title: B8_HC_subject5_PDC-E2_Tconv


title: PBMCs, IL15, 2h, 4ng/ml, 34100, Three

description: Library name: 153_O10_34100_4_2h_3

value: PBMCs

value: Three


title: PBMCs, IL15, 6h, 4ng/ml, 34100, Three

description: Library name: 156_O10_34100_4_6h_3


title: B10_HC_subject5_PDC-E2_Tconv

value: PBMC

value: Tconv


title: B7_HC_subject5_PDC-E2_Tconv

value: PDC-E2 peptides


title: B4_HC_subject5_PDC-E2_Tconv


title: B5_HC_subject5_PDC-E2_Tconv


title: Sham, scRNAsq


title: PBMCs, Control, 48h, 0ng/ml, 34100, Three

description: Library name: 150_O10_34100_0_48h_3


title: Nf1-Cdkn2a_DKO cell line 3 rep 3

city: Iowa City

first: Rebecca

last: Dodd

state: IA

address: 375 Newton Rd MERF 5241D

department: Internal Medicine

institute: University of Iowa

data_processing:
Original image data file from high-throughput sequencing (like Illumina) is transformed into sequenced reads (called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling). Raw data are stored in FASTQ(fq) format files.
The sequenced reads/raw reads often contain low quality reads or reads with adaptors, which will affect the quality of downstream analysis. To avoid this, it's necessary to filter the raw reads and get the clean reads. (1)Remove reads with adaptor contamination. (2)Remove reads when uncertain nucleotides constitute more than 10 percent of either read (N > 10%). (3)Remove reads when low quality nucleotides (Base Quality less than 20) constitute more than 50 percent of the read. The Qscore (Quality value) of over 50% bases of these read is <= 5. P5 Adaptor Sequence P5-AATGATACGGCGACCACCGAGA (5’-3’) P5'-TTACTATGCCGCTGGTGGCTCT (3’-5’) P7 Adaptor Sequence CGTATGCCGTCTTCTGCTTG-P7' (5’-3’) GCATACGGCAGAAGACGAAC-P7 (3’-5’)
STAR v2.5 software is used to accomplish the mapping. The alignment by STAR performs precise and effective in positioning junction reads for RNA sequencing data analysis. Mapped to GRCm38_mm10
Quantification was conducted with HTSeq2 v0.6.1 with -m union parameter
Differential Analysis conducted with DESeq2 v1.14.1, padj<0.05
Assembly: GRCm38_mm10
Supplementary files format and content: Processed_RNAseq_data_Read_Counts.txt

source_name: Mouse MPNST tumor

growth_protocol: Primary mouse MPNST cells maintained in DMEM + 10% FBS + 1% penicillin + 1% sodium pyruvate, 5% CO2 @37 degrees Celsius

extract_protocol:
Sample extracted with 500 uL Trizol reagent, purified with Zyme Research Direct-zol RNA miniprep kit, followed by Monach RNA clean-up kit (50ug)
Library prepped by Novogene

treatment_protocol: Samples were plated in DMEM + 10% FBS + 1% penicillin + 1% sodium pyruvate

value: Mouse MPNST tumor

tag: cell line

value: Primary tumor-derived cell line

value: mesenchymal


title: Foxo1cKOPNX, scRNAsq


title: B6_HC_subject5_PDC-E2_Tconv

value: HC


title: B3_HC_subject5_PDC-E2_Tconv


title: B2_HC_subject5_PDC-E2_Tconv


title: PBMCs, IL15, 2h, 4ng/ml, 34100, One

description: Library name: 151_O10_34100_4_2h_1

value: male


title: PBMCs, Control, 48h, 0ng/ml, 34100, Two

description: Library name: 149_O10_34100_0_48h_2

value: Control

value: Two


title: PBMCs, Control, 48h, 0ng/ml, 34100, One

description: Library name: 148_O10_34100_0_48h_1

value: One


title: B1_HC_subject5_PDC-E2_Tconv


title: Nf1-Cdkn2a_DKO cell line 3 rep 2


title: A11_HC_subject5_PDC-E2_Tconv


title: Nf1-Cdkn2a_DKO cell line 3 rep 1


title: Nf1-Cdkn2a_DKO cell line 2 rep 3


title: A10_HC_subject5_PDC-E2_Tconv


title: PBMCs, Control, 24h, 0ng/ml, 34100, Three

description: Library name: 147_O10_34100_0_24h_3


title: A9_HC_subject5_PDC-E2_Tconv


title: PBMCs, Control, 24h, 0ng/ml, 34100, Two

description: Library name: 146_O10_34100_0_24h_2


title: Nf1-Cdkn2a_DKO cell line 2 rep 1


title: A6_HC_subject5_PDC-E2_Tconv


title: A5_HC_subject5_PDC-E2_Tconv


title: Nf1-Cdkn2a_DKO cell line 2 rep 2


title: A12_HC_subject5_PDC-E2_Tconv


title: PBMCs, Control, 24h, 0ng/ml, 34100, One

description: Library name: 145_O10_34100_0_24h_1


title: Nf1-Cdkn2a_DKO cell line 1 rep 3


title: A3_HC_subject5_PDC-E2_Tconv


title: A1_HC_subject5_PDC-E2_Tconv


title: PBMCs, Control, 12h, 0ng/ml, 34100, Three

description: Library name: 144_O10_34100_0_12h_3


title: PBMCs, Control, 12h, 0ng/ml, 34100, One

description: Library name: 142_O10_34100_0_12h_1


title: A4_HC_subject5_PDC-E2_Tconv


title: F8_HC_subject2_PDC-E2_Treg

value: Treg


title: Nf1-p53_DKO cell line 3 rep 3


title: F10_HC_subject2_PDC-E2_Treg


title: F12_HC_subject2_PDC-E2_Treg


title: Nf1-p53_DKO cell line 3 rep 2


title: Nf1-Cdkn2a_DKO cell line 1 rep 2


title: F9_HC_subject2_PDC-E2_Treg


title: PBMCs, Control, 12h, 0ng/ml, 34100, Two

description: Library name: 143_O10_34100_0_12h_2


title: PBMCs, Control, 6h, 0ng/ml, 34100, Three

description: Library name: 141_O10_34100_0_6h_3


title: PBMCs, Control, 6h, 0ng/ml, 34100, Two

description: Library name: 140_O10_34100_0_6h_2


title: Nf1-Cdkn2a_DKO cell line 1 rep 1


title: A8_HC_subject5_PDC-E2_Tconv


title: Nf1-p53_DKO cell line 2 rep 3


title: A7_HC_subject5_PDC-E2_Tconv


title: F5_HC_subject2_PDC-E2_Treg


title: F3_HC_subject2_PDC-E2_Treg


title: PBMCs, Control, 2h, 0ng/ml, 34100, Three

description: Library name: 138_O10_34100_0_2h_3


title: PBMCs, Control, 6h, 0ng/ml, 34100, One

description: Library name: 139_O10_34100_0_6h_1


title: Nf1-p53_DKO cell line 3 rep 1


title: F6_HC_subject2_PDC-E2_Treg


title: Nf1-p53_DKO cell line 2 rep 2


title: F1_HC_subject2_PDC-E2_Treg


title: PBMCs, Control, 2h, 0ng/ml, 34100, One

description: Library name: 136_O10_34100_0_2h_1


title: E12_HC_subject2_PDC-E2_Treg


title: E9_HC_subject2_PDC-E2_Treg


title: E10_HC_subject2_PDC-E2_Treg


title: PBMCs, IL15, 48h, 40ng/ml, 34024, Three

description: Library name: 135_O10_34024_40_48h_3


title: E8_HC_subject2_PDC-E2_Treg


title: Nf1-p53_DKO cell line 1 rep 2


title: PBMCs, IL15, 48h, 40ng/ml, 34024, Two

description: Library name: 134_O10_34024_40_48h_2


title: E11_HC_subject2_PDC-E2_Treg


title: Nf1-p53_DKO cell line 1 rep 3


title: E6_HC_subject2_PDC-E2_Treg


title: Nf1-p53_DKO cell line 1 rep 1


title: E7_HC_subject2_PDC-E2_Treg


title: A2_HC_subject5_PDC-E2_Tconv


title: F7_HC_subject2_PDC-E2_Treg


title: F4_HC_subject2_PDC-E2_Treg


title: F2_HC_subject2_PDC-E2_Treg


title: PBMCs, Control, 2h, 0ng/ml, 34100, Two

description: Library name: 137_O10_34100_0_2h_2


title: PBMCs, IL15, 48h, 40ng/ml, 34024, One

description: Library name: 133_O10_34024_40_48h_1


title: Nf1-p53_DKO cell line 2 rep 1


title: E4_HC_subject2_PDC-E2_Treg


title: E3_HC_subject2_PDC-E2_Treg


title: PBMCs, IL15, 24h, 40ng/ml, 34024, Three

description: Library name: 132_O10_34024_40_24h_3


title: E2_HC_subject2_PDC-E2_Treg


title: E5_HC_subject2_PDC-E2_Treg


title: young,deletion,scRNAseq

first: Dandan

last: Zong

address: No.106, Zhongshan 2nd Road

institute: Guangdong Provincial People’s Hospital

description:
F/M
10x Genomics

data_processing:
the raw data was analyzed using 10x cellranger
Assembly: hg38，mm10
Supplementary files format and content: Tab-separated text files include count values, features and barcodes

source_name: Thyroid tissue-specific Bmal1 deletion

extract_protocol:
cells were trypsined and filtered using a 0.4uM filter in order to obtain a mix composed of single cells.
the single cell mixture was processed using the 10X Chromium Single Cell 3' Reagent Kits User Guide

value: Thyroid tissue-specific Bmal1 deletion

tag: age

value: 3 months

value: NO


title: E1_HC_subject2_PDC-E2_Treg


title: F11_HC_subject2_PDC-E2_Treg


title: old,wild-type,scRNAseq

description:
F/M
10x Genomics

source_name: Normal thyroid tissue

value: Normal thyroid tissue

value: 21-22 months


title: PBMCs, IL15, 12h, 40ng/ml, 34024, Three

description: Library name: 129_O10_34024_40_12h_3

value: PBMCs

value: Three


title: D10_HC_subject2_PDC-E2_Treg

value: PBMC

value: PDC-E2 peptides


title: D9_HC_subject2_PDC-E2_Treg


title: D11_HC_subject2_PDC-E2_Treg


title: PBMCs, IL15, 24h, 40ng/ml, 34024, One

description: Library name: 130_O10_34024_40_24h_1


title: Run 6: combined group with 2d, 4d, 7d and naïve astrocytes

first: Elisa

middle: E

last: Konofagou

department: Biomedical Engineering

institute: Columbia University

description:
Hashtag multiplexed samples from all treatment conditions
R1 files not available for this sample

data_processing:
cellranger-5.0.1
Assembly: mm10-2020-A
Supplementary files format and content: .zip files for each library

source_name: brain

growth_protocol: The cells were maintained on ice throughout FACS and scRNA sequencing processing

extract_protocol:
At the appropriate timepoint post-FUS-BBBO (2, 4 or 7 days) animals were euthanized with naïve control animals by cardiac perfusion with sterile saline.  The hippocampi of each animal were dissected out and timepoint-matched male and female tissue was pooled.  The tissue was minced with a sterile razor and underwent enzymatic digestion according to the manufacturer’s protocol using a Postnatal Neuron Neural Tissue Dissociation Kit (Miltenyi, # 130-094-802).  Following enzymatic digestion the tissue was filtered using a 70-μm cell strainer and pelleted by centrifuging at 300xG for 10 minutes at room temperature.  The pellet was then resuspended in 900 μL MACS buffer (Miltenyi, #130-091-376), and incubated with 100 μL Myelin II removal beads (Miltenyi, #130-096-433) for 15 minutes at 4°C, flicking to mix the solution every 5 minutes.  The cells were pelleted at 4°C by centrifuging for 1 minute at 9,300 RCF.  The supernatant was discarded, and the pellet was resuspended in 1 mL of MACS buffer.  This cell suspension was then passed through LS columns (Miltenyi, #130-042-401) on a magnet to extract the magnetic myelin beads.  The cells were pelleted again for 1 minute at 9,300 RCF, and resuspended in staining buffer, consisting of a 1:100 dilution of ACSA-II-PE conjugated antibody (Miltenyi, #130-123-284) and a 1:500 dilution of a unique hash tag antibody (Biolegend, #155801-8) for each timepoint group in 1xPBS.  Cells were incubated with this staining solution for 30 minutes at 4°C.  The cells were then pelleted, the supernatant was discarded, and the cells were resuspended in flow cytometry buffer consisting of a 1:1000 dilution of DAPI, 1:1000 Vybrant DyeCycle Ruby (Invitrogen, #V10309) and 1:500 DNase (from 4 mg/mL stock) in 1x PBS.  The cells were then taken to the Columbia Stem Cell Initiative Flow Cytometry Core and live, ACSA-II+ astrocytes were sorted for each condition.  These sorted cells were then brought to the Columbia Genome Center for single-cell RNA sequencing on a 10x Genomics Chromium Single Cell 3’ flow cell.
The 10x Genomics Chromium platform was used to generate low-depth data, which was procseed using the Cell Ranger analysis pipeline to align reads and generate feature-barcode matricies.

treatment_protocol: Focused ultrasound blood-brain barrier opening

value: brain

value: Astrocyte

value: Focused Ultrasound Blood-Brain barrier opening


title: Run 7: combined group with 2d, 4d, 7d and naïve astrocytes

description: Hashtag multiplexed samples from all treatment conditions


title: young,wild-type,scRNAseq

description:
F/M
10x Genomics


title: PBMCs, IL15, 12h, 40ng/ml, 34024, Two

description: Library name: 128_O10_34024_40_12h_2

value: male


title: D12_HC_subject2_PDC-E2_Treg

value: HC


title: Run 5: combined group with 2d, 4d, 7d and naïve astrocytes

description:
Hashtag multiplexed samples from all treatment conditions
processed data not available for this sample; R1 files not available for this sample


title: D7_HC_subject2_PDC-E2_Treg


title: PBMCs, IL15, 12h, 40ng/ml, 34024, One

description: Library name: 127_O10_34024_40_12h_1


title: D8_HC_subject2_PDC-E2_Treg


title: Run 4: combined group with 2d, 4d, 7d and naïve astrocytes


title: D5_HC_subject2_PDC-E2_Treg


title: D4_HC_subject2_PDC-E2_Treg


title: D1_HC_subject2_PDC-E2_Treg


title: PBMCs, IL15, 24h, 40ng/ml, 34024, Two

description: Library name: 131_O10_34024_40_24h_2

value: Two


title: D3_HC_subject2_PDC-E2_Treg


title: Run 1: combined group with 2d, 4d, 7d and naïve astrocytes


title: PBMCs, IL15, 6h, 40ng/ml, 34024, One

description: Library name: 124_O10_34024_40_6h_1

value: One


title: C11_HC_subject2_PDC-E2_Treg

value: Treg


title: Run 3: combined group with 2d, 4d, 7d and naïve astrocytes


title: PBMCs, IL15, 6h, 40ng/ml, 34024, Two

description: Library name: 125_O10_34024_40_6h_2


title: Run 2: combined group with 2d, 4d, 7d and naïve astrocytes


title: C12_HC_subject2_PDC-E2_Treg


title: D2_HC_subject2_PDC-E2_Treg


title: C10_HC_subject2_PDC-E2_Treg


title: D6_HC_subject2_PDC-E2_Treg


title: C8_HC_subject2_PDC-E2_Treg


title: C9_HC_subject2_PDC-E2_Treg


title: PBMCs, IL15, 2h, 40ng/ml, 34024, Three

description: Library name: 123_O10_34024_40_2h_3


title: Murine LT-HSC CUX1 Knockdown Replicate B CMO

city: Chicago

first: Tanner

middle: Clark

last: Martinez

state: IL

address: 900 E 57th Street Chicago, IL, 5220A LB35

department: Pathology

institute: University of Chicago

description:
CMO
HT: Read 1 contains cell barcode and UMI. Read 2 contains antibody-derived tag seqeunce.

library_source: other

data_processing:
The cellranger 7.1.0 multi pipeline (10X Genomics) was used to align FASTQ reads and generate the Gene Expression, ADT, and CMO matrices
Assembly: mm10
Supplementary files format and content: Bigwig files are provided for each sample.

molecule: protein

source_name: Bone marrow

growth_protocol: Cells were sorted and cultured in Phenol-free IMDM supplemented with 1x penicillin-streptomycin-glutamine, 100 ng/mL murine TPO, and 10 ng/mL murine SCF, 50uM 2-ME, and 20% BIT. Media was supplemented with 1 µg/mL doxycycline to insuce shRNA.

extract_protocol:
Single-cell libraries were prepared according to the manufacturer’s protocol using the Chromium Single Cell 3’ Reagent Kits (v3)
Libraries were perpared according to the 10X Chromium 3' single cell RNA with CMO protocol. Appropriate library construction was verified prior to sequencing.

treatment_protocol: Cells were cultured with 1 µg/mL doxycycline.

value: Bone marrow

value: LT-HSC

value: CUX1mCherry/mCherry shControl and shCUX4

value: Mixed Sample

tag: library type

value: CMO

tag: hto

value: TotalSeq-B301 anti-mouse Hashtag 1, TotalSeq-B302 anti-mouse Hashtag 2, TotalSeq-B303 anti-mouse Hashtag 3, TotalSeq-B304 anti-mouse Hashtag 4


title: C4_HC_subject2_PDC-E2_Treg

tag: tissue


title: Murine LT-HSC CUX1 Knockdown Replicate A CMO

value: CUX1mCherry/mCherry shControl and shCUX2


title: Murine LT-HSC CUX1 Knockdown Replicate B mRNA

description:
polyA mRNA
GEX (3' mRNA): Read 1 contains cell barcode and UMI. Read 2 contains transcript

value: CUX1mCherry/mCherry shControl and shCUX3

value: mRNA


title: C6_HC_subject2_PDC-E2_Treg

value: PBMC

tag: group

value: PDC-E2 peptides


title: Murine LT-HSC CUX1 Knockdown Replicate A mRNA

value: CUX1mCherry/mCherry shControl and shCUX1


title: C2_HC_subject2_PDC-E2_Treg

tag: stimulation


title: PBMCs, IL15, 2h, 40ng/ml, 34024, Two

description: Library name: 122_O10_34024_40_2h_2

value: PBMCs

value: male


title: PBMCs, IL15, 2h, 40ng/ml, 34024, One

description: Library name: 121_O10_34024_40_2h_1


title: C5_HC_subject2_PDC-E2_Treg

value: HC

tag: subject


title: C3_HC_subject2_PDC-E2_Treg


title: PBMCs, IL15, 48h, 4ng/ml, 34024, Three

description: Library name: 120_O10_34024_4_48h_3

tag: treatment

value: Three


title: PBMCs, IL15, 6h, 40ng/ml, 34024, Three

description: Library name: 126_O10_34024_40_6h_3

tag: time


title: C1_HC_subject2_PDC-E2_Treg

value: Treg


title: PBMCs, IL15, 48h, 4ng/ml, 34024, Two

description: Library name: 119_O10_34024_4_48h_2

tag: animal id

value: Two


title: Murine Hematopoietic Progenitors CMO_ADT

description:
CMO and ADT
HT: Read 1 contains cell barcode and UMI. Read 2 contains antibody-derived tag seqeunce.

value: Bone marrow

value: Progenitor

value: CMO, ADT

tag: adt

value: anti-CD74—TotalSeqB1043 (In-1) , anti-CD86—TotalSeqB0200 (GL-1) , anti-CD201—TotalSeqB0439 (RCR-16) , anti-NGFR—TotalSeqB0816 (ME20.4), anti-CD274—TotalSeqB0190 (MIH6) , anti-I-E/I-A—TotalSeqB0117 (M5/114.15.2) , Mouse IgG1κ Isotype Control—TotalSeqB0090 (MOPC-21)


title: C7_HC_subject2_PDC-E2_Treg


title: B11_HC_subject2_PDC-E2_Treg


title: Murine Hematopoietic Progenitors mRNA

value: Mixed Sample


title: PBMCs, IL15, 48h, 4ng/ml, 34024, One

description: Library name: 118_O10_34024_4_48h_1

tag: Sex

value: One

tag: dose


title: B9_HC_subject2_PDC-E2_Treg


title: PBMCs, IL15, 24h, 4ng/ml, 34024, Three

description: Library name: 117_O10_34024_4_24h_3


title: Murine LT-HSC mRNA

value: LT-HSC

tag: genotype


title: B6_HC_subject2_PDC-E2_Treg


title: PBMCs, IL15, 24h, 4ng/ml, 34024, One

description: Library name: 115_O10_34024_4_24h_1

tag: replicate


title: Murine LT-HSC CMO_ADT

tag: cell type

value: TotalSeq-B301 anti-mouse Hashtag 1, TotalSeq-B302 anti-mouse Hashtag 2, TotalSeq-B303 anti-mouse Hashtag 3, TotalSeq-B304 anti-mouse Hashtag 4


title: CUX1Bright shCUX1 Replicate D

description:
RNA-Seq
Sample 35

data_processing:
Sequenced reads were aligned to the mm10 reference genome with STAR aligner. Differential gene expression analysis was conducted with DESeq2 (Love et al. 2014). Adjusted p-values were calculated with the Benjamini-Hochberg method. Genes with adjusted p-values less than  0.01 were used in downstream analyses.
Gene rank lists were calculated by multiplying the fold-change, -log10(pvalue), and sign of change. Rank lists were used to assess gene set enrichment (Subramanian et al. 2005).
Assembly: mm10
Supplementary files format and content: Reporter_featurecounts.txt corresponds to Samples 1-12. ReporterKnockdown_featurecounts.txt corresponds to Samples 13-35.

growth_protocol: Cells were grown on fibronectin-coated plates  Ham's F12 nutrient mix supplemented with 10 mM HEPES, 1x Insulin-Transferrin-Selenium-Ethanolamine, 1 mg/mL polyvinyl alcohol, 1x penicillin-streptomycin-glutamine, 100 ng/mL murine TPO, and 10 ng/mL murine SCF. In both cases media was supplemented with 1 µg/mL doxycycline to insuce shRNA.

extract_protocol:
LT-HSCs were sorted directly into lysis buffer supplemented with 2-ME, and total RNA was extracted with Absolutely RNA Nanoprep Kit (Agilent).
Barcoded libraries were created by the University of Chicago Functional Genomics Facility

treatment_protocol: Cells were cultured with 1.5 µg/mL doxycycline to induce shRNA.

value: CUX1mCherry/mCherry shCUX1


title: B7_HC_subject2_PDC-E2_Treg

value: PBMC

value: PDC-E2 peptides


title: B4_HC_subject2_PDC-E2_Treg


title: B8_HC_subject2_PDC-E2_Treg


title: B10_HC_subject2_PDC-E2_Treg


title: B3_HC_subject2_PDC-E2_Treg


title: CUX1Int shCUX1 Replicate D

description:
RNA-Seq
Sample 34


title: B2_HC_subject2_PDC-E2_Treg


title: B5_HC_subject2_PDC-E2_Treg


title: B1_HC_subject2_PDC-E2_Treg


title: PBMCs, IL15, 24h, 4ng/ml, 34024, Two

description: Library name: 116_O10_34024_4_24h_2

value: PBMCs


title: PBMCs, IL15, 12h, 4ng/ml, 34024, Three

description: Library name: 114_O10_34024_4_12h_3

value: male


title: CUX1Dim shCUX1 Replicate D

description:
RNA-Seq
Sample 33


title: B12_HC_subject2_PDC-E2_Treg

value: HC


title: A12_HC_subject2_PDC-E2_Treg


title: PBMCs, IL15, 12h, 4ng/ml, 34024, One

description: Library name: 112_O10_34024_4_12h_1


title: A11_HC_subject2_PDC-E2_Treg


title: CUX1Bright shControl Replicate D

description:
RNA-Seq
Sample 32

value: CUX1mCherry/mCherry shControl


title: PBMCs, IL15, 6h, 4ng/ml, 34024, Three

description: Library name: 111_O10_34024_4_6h_3

value: Three


title: CUX1Int shControl Replicate D

description:
RNA-Seq
Sample 31


title: A9_HC_subject2_PDC-E2_Treg

value: Treg


title: A10_HC_subject2_PDC-E2_Treg


title: A8_HC_subject2_PDC-E2_Treg


title: A7_HC_subject2_PDC-E2_Treg


title: A6_HC_subject2_PDC-E2_Treg


title: PBMCs, IL15, 6h, 4ng/ml, 34024, One

description: Library name: 109_O10_34024_4_6h_1


title: A5_HC_subject2_PDC-E2_Treg


title: CUX1Bright shCUX1 Replicate C

description:
RNA-Seq
Sample 29

value: Bone marrow


title: A4_HC_subject2_PDC-E2_Treg


title: PBMCs, IL15, 2h, 4ng/ml, 34024, Three

description: Library name: 108_O10_34024_4_2h_3


title: CUX1Int shCUX1 Replicate C

description:
RNA-Seq
Sample 28


title: A3_HC_subject2_PDC-E2_Treg


title: PBMCs, IL15, 12h, 4ng/ml, 34024, Two

description: Library name: 113_O10_34024_4_12h_2

value: Two


title: PBMCs, IL15, 2h, 4ng/ml, 34024, Two

description: Library name: 107_O10_34024_4_2h_2


title: PBMCs, Control, 48h, 0ng/ml, 34024, Three

description: Library name: 105_O10_34024_0_48h_3

value: Control


title: A2_HC_subject2_PDC-E2_Treg


title: G3_HC_subject2_PDC-E2_Tconv

value: Tconv


title: G2_HC_subject2_PDC-E2_Tconv


title: CUX1Bright shControl Replicate C

description:
RNA-Seq
Sample 26


title: A1_HC_subject2_PDC-E2_Treg


title: CUX1Dim shControl Replicate D

description:
RNA-Seq
Sample 30


title: PBMCs, Control, 48h, 0ng/ml, 34024, Two

description: Library name: 104_O10_34024_0_48h_2


title: G1_HC_subject2_PDC-E2_Tconv


title: PBMCs, IL15, 6h, 4ng/ml, 34024, Two

description: Library name: 110_O10_34024_4_6h_2


title: CUX1Int shControl Replicate C

description:
RNA-Seq
Sample 25


title: F12_HC_subject2_PDC-E2_Tconv


title: PBMCs, Control, 48h, 0ng/ml, 34024, One

description: Library name: 103_O10_34024_0_48h_1


title: CUX1Dim shCUX1 Replicate C

description:
RNA-Seq
Sample 27


title: F11_HC_subject2_PDC-E2_Tconv


title: F10_HC_subject2_PDC-E2_Tconv


title: F9_HC_subject2_PDC-E2_Tconv


title: CUX1Dim shControl Replicate C

description:
RNA-Seq
Sample 24


title: CUX1Bright shCUX1 Replicate B

description:
RNA-Seq
Sample 23


title: F8_HC_subject2_PDC-E2_Tconv


title: F7_HC_subject2_PDC-E2_Tconv


title: PBMCs, Control, 24h, 0ng/ml, 34024, One

description: Library name: 100_O10_34024_0_24h_1


title: F6_HC_subject2_PDC-E2_Tconv


title: CUX1Dim shCUX1 Replicate B

description:
RNA-Seq
Sample 21


title: PBMCs, Control, 24h, 0ng/ml, 34024, Three

description: Library name: 102_O10_34024_0_24h_3


title: G4_HC_subject2_PDC-E2_Tconv


title: F5_HC_subject2_PDC-E2_Tconv


title: F4_HC_subject2_PDC-E2_Tconv


title: PBMCs, Control, 12h, 0ng/ml, 34024, Three

description: Library name: 099_O10_34024_0_12h_3


title: F3_HC_subject2_PDC-E2_Tconv


title: CUX1Bright shControl Replicate B

description:
RNA-Seq
Sample 20


title: F2_HC_subject2_PDC-E2_Tconv


title: PBMCs, Control, 12h, 0ng/ml, 34024, One

description: Library name: 097_O10_34024_0_12h_1


title: F1_HC_subject2_PDC-E2_Tconv


title: E12_HC_subject2_PDC-E2_Tconv


title: PBMCs, Control, 6h, 0ng/ml, 34024, Three

description: Library name: 096_O10_34024_0_6h_3


title: E11_HC_subject2_PDC-E2_Tconv


title: CUX1Int shControl Replicate B

description:
RNA-Seq
Sample 19


title: CUX1Bright shCUX1 Replicate A

description:
RNA-Seq
Sample 18


title: PBMCs, Control, 24h, 0ng/ml, 34024, Two

description: Library name: 101_O10_34024_0_24h_2


title: E10_HC_subject2_PDC-E2_Tconv


title: E8_HC_subject2_PDC-E2_Tconv


title: CUX1Int shCUX1 Replicate A

description:
RNA-Seq
Sample 17


title: PBMCs, Control, 6h, 0ng/ml, 34024, One

description: Library name: 094_O10_34024_0_6h_1


title: PBMCs, Control, 6h, 0ng/ml, 34024, Two

description: Library name: 095_O10_34024_0_6h_2


title: PBMCs, Control, 2h, 0ng/ml, 34024, Two

description: Library name: 092_O10_34024_0_2h_2


title: E7_HC_subject2_PDC-E2_Tconv


title: E9_HC_subject2_PDC-E2_Tconv


title: CUX1Bright shControl Replicate A

description:
RNA-Seq
Sample 15


title: E3_HC_subject2_PDC-E2_Tconv


title: E5_HC_subject2_PDC-E2_Tconv


title: E6_HC_subject2_PDC-E2_Tconv


title: CUX1Int shControl Replicate A

description:
RNA-Seq
Sample 14


title: E2_HC_subject2_PDC-E2_Tconv


title: PBMCs, IL15, 48h, 40ng/ml, 33047, Three

description: Library name: 090_O10_33047_40_48h_3


title: E4_HC_subject2_PDC-E2_Tconv


title: CUX1Dim shControl Replicate A

description:
RNA-Seq
Sample 13


title: E1_HC_subject2_PDC-E2_Tconv


title: D12_HC_subject2_PDC-E2_Tconv


title: D10_HC_subject2_PDC-E2_Tconv


title: D9_HC_subject2_PDC-E2_Tconv


title: PBMCs, IL15, 48h, 40ng/ml, 33047, Two

description: Library name: 089_O10_33047_40_48h_2


title: CUX1Int Replicate D

description:
RNA-Seq
Sample 11


title: PBMCs, IL15, 48h, 40ng/ml, 33047, One

description: Library name: 088_O10_33047_40_48h_1


title: D8_HC_subject2_PDC-E2_Tconv


title: CUX1Bright Replicate D

description:
RNA-Seq
Sample 12


title: D7_HC_subject2_PDC-E2_Tconv


title: D6_HC_subject2_PDC-E2_Tconv


title: D5_HC_subject2_PDC-E2_Tconv


title: PBMCs, Control, 2h, 0ng/ml, 34024, One

description: Library name: 091_O10_34024_0_2h_1


title: CUX1Int shCUX1 Replicate B

description:
RNA-Seq
Sample 22


title: PBMCs, IL15, 24h, 40ng/ml, 33047, Two

description: Library name: 086_O10_33047_40_24h_2


title: CUX1Bright Replicate C

description:
RNA-Seq
Sample 9


title: CUX1Dim shCUX1 Replicate A

description:
RNA-Seq
Sample 16


title: D4_HC_subject2_PDC-E2_Tconv


title: D3_HC_subject2_PDC-E2_Tconv


title: D1_HC_subject2_PDC-E2_Tconv


title: CUX1Int Replicate C

description:
RNA-Seq
Sample 8


title: C12_HC_subject2_PDC-E2_Tconv


title: CUX1Dim Replicate D

description:
RNA-Seq
Sample 10


title: PBMCs, IL15, 12h, 40ng/ml, 33047, Two

description: Library name: 083_O10_33047_40_12h_2


title: C11_HC_subject2_PDC-E2_Tconv


title: PBMCs, IL15, 24h, 40ng/ml, 33047, One

description: Library name: 085_O10_33047_40_24h_1


title: CUX1Dim Replicate C

description:
RNA-Seq
Sample 7


title: PBMCs, IL15, 24h, 40ng/ml, 33047, Three

description: Library name: 087_O10_33047_40_24h_3


title: PBMCs, IL15, 12h, 40ng/ml, 33047, One

description: Library name: 082_O10_33047_40_12h_1


title: D11_HC_subject2_PDC-E2_Tconv


title: CUX1Bright Replicate B

description:
RNA-Seq
Sample 6


title: C10_HC_subject2_PDC-E2_Tconv


title: C9_HC_subject2_PDC-E2_Tconv


title: C8_HC_subject2_PDC-E2_Tconv


title: CUX1Int Replicate B

description:
RNA-Seq
Sample 5


title: PBMCs, IL15, 6h, 40ng/ml, 33047, Three

description: Library name: 081_O10_33047_40_6h_3


title: CUX1Dim Replicate B

description:
RNA-Seq
Sample 4


title: C6_HC_subject2_PDC-E2_Tconv


title: D2_HC_subject2_PDC-E2_Tconv


title: CUX1Bright Replicate A

description:
RNA-Seq
Sample 3


title: C4_HC_subject2_PDC-E2_Tconv


title: C5_HC_subject2_PDC-E2_Tconv


title: C2_HC_subject2_PDC-E2_Tconv


title: CUX1Int Replicate A

description:
RNA-Seq
Sample 2


title: C3_HC_subject2_PDC-E2_Tconv


title: PBMCs, IL15, 2h, 40ng/ml, 33047, Three

description: Library name: 078_O10_33047_40_2h_3


title: CUX1Dim Replicate A

description:
RNA-Seq
Sample 1


title: B12_HC_subject2_PDC-E2_Tconv


title: C1_HC_subject2_PDC-E2_Tconv


title: B11_HC_subject2_PDC-E2_Tconv


title: B10_HC_subject2_PDC-E2_Tconv


title: PBMCs, IL15, 2h, 40ng/ml, 33047, One

description: Library name: 076_O10_33047_40_2h_1


title: B8_HC_subject2_PDC-E2_Tconv


title: B9_HC_subject2_PDC-E2_Tconv


title: PBMCs, IL15, 2h, 40ng/ml, 33047, Two

description: Library name: 077_O10_33047_40_2h_2


title: B7_HC_subject2_PDC-E2_Tconv


title: PBMCs, IL15, 48h, 4ng/ml, 33047, Three

description: Library name: 075_O10_33047_4_48h_3


title: C7_HC_subject2_PDC-E2_Tconv


title: ATAC_SK11

description: ATAC-Seq

data_processing:
FASTQ reads were aligned to the mm10 genome using bwa-mem. Reads were filtered to exclude low quality (q<30), mitochondrial, blacklist (mm10 v2), and PCR duplicate reads using samtools.
Differential accessibility was performed using the edgeR implementation in csaw.
Assembly: mm10
Supplementary files format and content: Bigwig files are provided for each sample.

extract_protocol:
ATAC-Seq libraries were prepared according to the OMNI-ATAC protocol (Corces et al. 2017).
Transposition reaction was carried out using the Nextera DNA Library Prep Kit. DNA was isolated using the Qiagen MinElute Reaction Cleanup Kit (Qiagen) and amplified using NEBNext High-Fidelity PCR Master Mix (NEB) for five cycles of PCR and adjusted using qPCR.

value: CUX1Bright shControl


title: ATAC_SK10

description: ATAC-Seq


title: B6_HC_subject2_PDC-E2_Tconv


title: PBMCs, IL15, 48h, 4ng/ml, 33047, Two

description: Library name: 074_O10_33047_4_48h_2


title: PBMCs, IL15, 6h, 40ng/ml, 33047, Two

description: Library name: 080_O10_33047_40_6h_2


title: ATAC_SK09

description: ATAC-Seq

value: CUX1Bright shCUX1


title: PBMCs, IL15, 6h, 40ng/ml, 33047, One

description: Library name: 079_O10_33047_40_6h_1

value: One


title: PBMCs, IL15, 48h, 4ng/ml, 33047, One

description: Library name: 073_O10_33047_4_48h_1


title: B5_HC_subject2_PDC-E2_Tconv


title: ATAC_SK08

description: ATAC-Seq

value: LT-HSC


title: B4_HC_subject2_PDC-E2_Tconv


title: B2_HC_subject2_PDC-E2_Tconv


title: B3_HC_subject2_PDC-E2_Tconv


title: ATAC_SK07

description: ATAC-Seq


title: PBMCs, IL15, 24h, 4ng/ml, 33047, Three

description: Library name: 072_O10_33047_4_24h_3


title: B1_HC_subject2_PDC-E2_Tconv


title: ATAC_SK12

description: ATAC-Seq


title: A12_HC_subject2_PDC-E2_Tconv


title: A11_HC_subject2_PDC-E2_Tconv


title: A10_HC_subject2_PDC-E2_Tconv


title: ATAC_SK06

description: ATAC-Seq

value: CUX1Dim shControl


title: A7_HC_subject2_PDC-E2_Tconv

value: PBMC


title: ATAC_SK05

description: ATAC-Seq


title: A8_HC_subject2_PDC-E2_Tconv

value: PDC-E2 peptides


title: A6_HC_subject2_PDC-E2_Tconv


title: PBMCs, IL15, 12h, 4ng/ml, 33047, Three

description: Library name: 069_O10_33047_4_12h_3

value: PBMCs


title: ATAC_SK04

description: ATAC-Seq


title: A9_HC_subject2_PDC-E2_Tconv


title: ATAC_SK03

description: ATAC-Seq

value: CUX1Dim shCUX1


title: PBMCs, IL15, 24h, 4ng/ml, 33047, One

description: Library name: 070_O10_33047_4_24h_1

value: male


title: A5_HC_subject2_PDC-E2_Tconv

value: HC


title: A4_HC_subject2_PDC-E2_Tconv


title: PBMCs, IL15, 12h, 4ng/ml, 33047, Two

description: Library name: 068_O10_33047_4_12h_2


title: A3_HC_subject2_PDC-E2_Tconv


title: ATAC_SK02

description: ATAC-Seq


title: A2_HC_subject2_PDC-E2_Tconv


title: PBMCs, IL15, 12h, 4ng/ml, 33047, One

description: Library name: 067_O10_33047_4_12h_1


title: A1_HC_subject2_PDC-E2_Tconv


title: KR_c

first: Douglas

last: Barrows

address: 1230 York Ave

institute: Rockefeller University

description: rep 3

data_processing:
Combined mm10 and hg38 fasta and GTF files were retrieved from the 10X Genomics public reference repository (version 2024-A, build information: https://www.10xgenomics.com/support/software/cell-ranger/downloads/cr-ref-build-steps). Fastq files were aligned to the combined reference with STAR (v2.5.2b) using default settings except the ‘outSAMmultNmax’ argument was set to 1. The reads that preferentially aligned to the hg38 chromosomes were extracted from the BAM file using the ‘view’ function from Samtools (v1.10), and gene level counts were obtained using the ‘summarizeOverlaps’ function from the GenomicAlignments R Bioconductor package (v1.28.0)
Assembly: hg38
Supplementary files format and content: raw counts from DESeq2

source_name: MCF7 6KR MED1

extract_protocol:
Cells were harvested, washed with PBS, and flash frozen in liquid nitrogen. RNA was isolated using QIAGEN RNeasy kit.
Libraries were generated using mRNA TruSeq stranded 350bp

tag: cell line

value: MCF7 6KR MED1

value: xenograft of breast cancer cell line

value: ectopic 6KR MED1


title: ATAC_SK01

description: ATAC-Seq

value: Bone marrow


title: PBMCs, IL15, 6h, 4ng/ml, 33047, Three

description: Library name: 066_O10_33047_4_6h_3

value: Three


title: PBMCs, IL15, 6h, 4ng/ml, 33047, Two

description: Library name: 065_O10_33047_4_6h_2

value: Two


title: PBMCs, IL15, 24h, 4ng/ml, 33047, Two

description: Library name: 071_O10_33047_4_24h_2


title: KR_a

description: rep 1


title: KR_b

description: rep 2


title: WT_b

description: rep 2

source_name: MCF7 WT MED1

value: MCF7 WT MED1

value: ectopic WT MED1


title: RAW 264.7 cells, replicate 2, RMF treatment group

city: Shanghai

first: Li

last: Yingze

address: Zhennan Road

institute: Tongji University

data_processing:
Raw data (raw reads) of FASTQ format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing following reads: (1) reads with adapter; (2) reads with more than 3 N; (3) reads with more than 20% nucleotides with Qphred<=5; At the same time, Q20, Q30 and GC content of the clean data were calculated. Then, map the clean reads to the silva database to remove the rRNA. All the downstream analyses were based on the clean data without rRNA.
Paired-end clean reads were aligned to the reference genome using Hisat2. Featurecount was used to count the reads numbers mapped to each gene.
EdgeR was used for differential expression analysis. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with |log2 (Fold Change)| > 1 & q value < 0.05 were assigned as differentially expressed.
GO and KEGG enrichment analysis of differentially expressed gene sets were implemented by the topG (http://www.bioconductor.org/packages/release/bioc/html/topGO.html) and KOBAS package, respectively.
Assembly: GRCm38.p6
Supplementary files format and content: tab-delimited text file includes readcounts for each Sample

extract_protocol:
RNA was harvested using 2×SG Fast qPCR Master Mix kit (Sangon Biotech).  2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: macrophage cell lines


title: PBMCs, IL15, 6h, 4ng/ml, 33047, One

description: Library name: 064_O10_33047_4_6h_1

value: One


title: PBMCs, IL15, 2h, 4ng/ml, 33047, Three

description: Library name: 063_O10_33047_4_2h_3


title: WT_a

description: rep 1


title: RAW 264.7 cells, replicate 3, control group


title: PBMCs, IL15, 2h, 4ng/ml, 33047, Two

description: Library name: 062_O10_33047_4_2h_2


title: hFF, control (titanium surface), rep 2

city: Seattle

first: Xinru

last: Wang

state: Washington

address: 3946 W Stevens Way NE

department: Biochemistry

institute: University of Washington

data_processing:
demultiplexing was performed with bcl2fastq. Alignment was done through biojupies with standard parameters to hg38. Raw counts were normalized to log10-Counters per million (logCPM) by dividing each column by the total sum of its counts, multiplying it by 10^6, followed by the application of a log10-transform.
Assembly: hg38
Supplementary files format and content: fastqs

source_name: foreskin

growth_protocol: MCF10A cells were cultured in media described previously50,51; briefly, the media consisted of DMEM/F12 (Gibco, 11330032), 5% horse serum (Gibco, 16050130), 20 ng/mL EGF (Sigma-Aldrich, SRP3027), 0.5 mg/mL hydrocortisone (Sigma-Aldrich, H4001), 100 ng/mL cholera toxin (Millipore, C8052), 10 µg/mL insulin (Sigma-Aldrich,11070-73-8) and 1% penicillin–streptomycin (Gibco, 15140122). MCF10A cells were starved in the same media without EGF and contained 2% horse serum (assay media) for 16 hours before signaling experiments. Human bone marrow-derived mesenchymal stem cells (MSCs; ATCC) and human osteoblasts (OBs; Sigma-Aldrich) were cultured in Advanced DMEM medium supplemented with 10% FBS, 20 mM HEPES, penicillin/streptomycin (50 U/mL and 50 µg/mL, respectively) and 2 mM L-glutamine (all components from ThermoFisher Scientific). Cells from passage 5 were used in all experiments. Human foreskin fibroblasts (FFs; Millipore) were cultured in DMEM medium supplemented with 10% FBS, 20 mM HEPES, 50 U mL-1 penicillin, 50 µg mL-1 streptomycin and 2 mM L-glutamine, all from ThermoFisher Scientific. FFs from passage 10 were used in all experiments.

extract_protocol:
RNAeasy plus (Qiagen)
Illumina Stranded mRNA prep

treatment_protocol: MCF10A cells (5X 103) were plated onto 12 wells plate in assay media. These cells were treated with the increasing concentration (0, 20, 200, 500 nM) of integrin mini binder (mb) after 12 h of attachment.MSCs, FFs, and OBs were cultured in serum-free conditions at a concentration of 25,000 cells/disc and allowed to adhere for 4 h on the grafted titanium discs.

value: foreskin

value: foreskin fibroblasts

value: WT

value: control


title: hFF, binder, rep 2

value: binder


title: PBMCs, IL15, 2h, 4ng/ml, 33047, One

description: Library name: 061_O10_33047_4_2h_1

value: PBMCs

value: male


title: hFF, control (titanium surface), rep 1


title: hFF, binder, rep 1


title: RAW 264.7 cells, replicate 2, control group


title: hFF, fibronectin, rep 2

value: Fibronectin


title: PBMCs, Control, 48h, 0ng/ml, 33047, Three

description: Library name: 060_O10_33047_0_48h_3

value: Control


title: RAW 264.7 cells, replicate 1, control group


title: hOBS, control (titanium surface), rep 1

source_name: bone

value: bone

value: osteoblasts


title: PBMCs, Control, 48h, 0ng/ml, 33047, Two

description: Library name: 059_O10_33047_0_48h_2

source_name: PBMCs


title: hFF, fibronectin, rep 1


title: RAW 264.7 cells, replicate 3, RMF treatment group


title: GRIS-BD_Experiment_18-WTA

city: Xinxiang

first: Tianhan

state: Henan

address: No.601, Hualan Road

institute: Xinxiang Medical University

description: BD Rhapsody

data_processing:
Set up BD rhapsody local pepline on linux operating system according to the manufacter's instruction, then load with WTA and TAG raw data and run, finally analysis the processed data (“_RSEC_MolsPerCell.csv” and “_Sample_Tag_Calls.csv”) using Segeq software.
Assembly: GRCm39
Supplementary files format and content: tab-separated values file and matrix files

source_name: spleen

extract_protocol:
sort CD3+CD5+ cells from single cell suspension of spleen
each group was labelled with sample tag, then built the whole transcriptome analysis (WTA) and sample tag library (TAG) according to the manufacter's instructions (BD Rhapsody™ Single-Cell Analysis System Instrument User Guide (Doc ID 214062))

treatment_protocol: 8-9 weeks old LatY136F mice and LatY136F CD45-KO mice

value: spleen

value: CD3+CD5+ cell from spleen

value: 8-9 weeks old LatY136F CD45-KO mice


title: hOBS, binder, rep 1


title: hOBS, binder, rep2


title: GRIS-BD_Experiment_17-WTA

description: BD Rhapsody

value: 8-9 weeks old LatY136F mice


title: hOBS, fibronectin, rep 2


title: hOBS, fibronectin, rep1


title: RAW 264.7 cells, replicate 1, RMF treatment group

value: macrophage cell lines


title: GRIS-BD Experiment22-TAG-2

description: BD Rhapsody

extract_protocol:
CD45.2+CD5-CD19-Ly6G- cells from spleen were sorted
each group was labelled with sample tag, then built the whole transcriptome analysis (WTA) and sample tag library (TAG) according to the manufacter's instructions (BD Rhapsody™ Single-Cell Analysis System Instrument User Guide (Doc ID 214062))

treatment_protocol: 7 to 8-week old ApoE−/−, Lipa+/− ApoE−/− and Lipa−/−ApoE−/−mice were fed with a high-fat diet for 12 weeks

value: immune cells

value: CD45.2+CD5-CD19-Ly6G- cells


title: hMSC, control (titanium surface), rep 2

source_name: mesenchyme

value: mesenchyme

value: mesenchymal stem cells


title: hMSC, control (titanium surface), rep 1

value: WT

value: control


title: hMSC, binder, rep 2

value: binder


title: hMSC, binder, rep 1


title: PBMCs, Control, 24h, 0ng/ml, 33047, Two

description: Library name: 056_O10_33047_0_24h_2

extract_protocol:
RNeasy Micro Kit
TruSeq mRNA / Biomek

value: PBMCs

value: male

value: Two


title: PBMCs, Control, 24h, 0ng/ml, 33047, One

description: Library name: 055_O10_33047_0_24h_1

value: Control

value: One


title: hMSC, fibronectin, rep 2

value: Fibronectin


title: alveolar macrophages, Printex90, overload, biol rep3

city: Woluwé

first: Jérôme

last: Ambroise

address: Avenue Hippocrate 54

department: Institut de Recherche Expérimentale et Clinique

country: Belgium

institute: Université catholique de Louvain

data_processing:
All sequencing data were analyzed using the Automated Reproducible MOdular workflow for preprocessing and differential analysis of RNA-seq data (ARMOR v1.5.4) pipeline48.
In this pipeline, reads underwent a quality check using FastQC (Babraham Bioinformatics). Quantification and quality control results were summarized in a MultiQC report before being mapped using Salmon to the transcriptome index which was built using all Ensembl cDNA sequences obtained in the Mus_musculus.GRCm39.cdna.all.fa file.
Assembly: Mus_musculus.GRCm39.cdna.all.fa
Supplementary files format and content: excell file with the counts matrix

source_name: Primary alveolar macrophages

growth_protocol: Primary alveolar macrophages were maintained during 5 days in DMEM supplemented with 10% fetal bovine serum (FBS) and 1 % antibiotic-antimycotic (AA) in humidified atmosphere with 5% CO2 at 37°C

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (Qiagen) following the manufacturer’s instructions. Residual DNA was removed by on-column DNase digestion using the RNAse-Free DNase Set (Qiagen)
The Libraries were prepared starting from 150 ng of total RNA using the KAPA RNA HyperPrep Kit with RiboErase (HMR) (KAPA Biosystems, KK8560) following the manufacturer’s recommendations (KR1351 – v1.16).

treatment_protocol: Cells were exposed during 4 days to control, non-overload or overload conditions of G1-1 or Printex90 particles

value: Primary alveolar macrophages

tag: strain

value: Male

value: 4 days


title: hMSC, fibronectin, rep 1


title: alveolar macrophages, Printex90, overload, biol rep2


title: PBMCs, Control, 12h, 0ng/ml, 33047, Three

description: Library name: 054_O10_33047_0_12h_3

data_processing:
Trimgalorev0.6.10 used to remove low quality reads and bases
Filtered out globin and rRNA reads using bowtie2v2.4.4
Aligned reads with STARv2.7.10b to rhesus macaque genome
Assembly: Macaca mulatta version 10 Ensembl annoation v110
Supplementary files format and content: individual count files for each sample

value: Three


title: alveolar macrophages, Printex90, overload, biol rep1


title: MCF 10A, fibronectin, rep 2

source_name: breast/mammary gland

value: breast/mammary gland

value: MCF 10A

value: breast epithelial cell


title: MCF 10A, fibronectin + binder, rep 1

value: Fibronectin + binder


title: PBMCs, Control, 12h, 0ng/ml, 33047, Two

description: Library name: 053_O10_33047_0_12h_2


title: MCF 10A, fibronectin, rep1

value: WT


title: PBMCs, Control, 24h, 0ng/ml, 33047, Three

description: Library name: 057_O10_33047_0_24h_3


title: PBMCs, Control, 12h, 0ng/ml, 33047, One

description: Library name: 052_O10_33047_0_12h_1


title: TOM interactome, COQ3_repeat, rep2

city: Pasadena

first: Zikun

last: Zhu

state: CA

address: 1200 E California Blvd

institute: California Institute of Technology

description: 3' adaptor sequence: CGTAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC

data_processing:
3’ adaptor sequences were trimmed from sequencing reads with Cutadapt v4.1 using the following command: cutadapt --cores=0 -q20 -m24 -M42 --discard-untrimmed -O6 --no-indels -a adaptor_sequence -o outfile.fastq.gz infile.fastq.gz 1> Cutadapt_report.txt
Unique molecular identifiers (UMIs, two random 5' nucleotides and five random 3' nucleotides) were trimmed from each read using a Julia script (Script1) from (M. Bertolini, et. al., Science, 2021). This generates an output fastq file containing the 7-nucelotide UMI information in the read name.
The UMI-trimmed reads were mapped to the human ribosomal RNA sequences with Bowtie2 v2.4.5 using the following command: bowtie2 -p 32 -t -x rRNA_index -q infile.fastq.gz -p 16 --un outfile.fastq.gz -S /dev/null > Bowtie2.report.txt
Reads that did not align to ribosomal RNA sequences were mapped to human reference genome (GRCh38p13 downloaded from NCBI) with STAR 2.7.10a using the following command: STAR --runThreadN 32 --genomeDir indexed_genome --readFilesIn infile.fastq.gz --outFilterMultimapNmax 1 --outFilterType BySJout --alignIntronMin 5 --outFileNamePrefix Prefix --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --outSAMattributes All XS --quantMode GeneCounts --twopassMode Basic
For each gene, the transcript with the longest coding sequence was selected, and ribosome density was assigned to the p-site of each read using a Julia script (Script2) from (M. Bertolini, et. al., Science, 2021).
Assembly: GRCh38p13
Supplementary files format and content: The files are in HDF5 format containing one data set per gene. Each data set consists of a 2-row matrix, with the 1-based nucleotide position within the CDS and the detected p-site reads at this position. The data set attributes contain additional information including gene and protein names, transcript isoform used for position assignment, CDS length, chromosome and strand location of the gene.
Library strategy: ribosome profiling

growth_protocol: HEK293-T cells were cultured in high glucose DMEM media supplemented with GlutaMAX™ and pyruvate (Gibco) + 10% fetal bovine serum (Gibco). Cells were grown at 37 °C and passaged regularly using Trypsin-EDTA for dissociation.

extract_protocol:
RNA was extracted using the Direct-zol kit (Zymo) according to manufacturer’s instructions.
Ribosome profiling libraries were prepared as described in (Z. Zhu, S. Wang, S. Shan, Nat. Commun., 2022) with an additional rRNA depletion step. rRNA depletion was performed on the linker-ligated RNA footprints using the riboPOOL Ribo-Seq (human) kit (Galen) according to the manufacturer’s instructions.

value: Human embroynic kidney

value: TOM22-Twinstrep, COQ3-repeat knockin


title: alveolar macrophages, Printex90, non-overload, biol rep3


title: Translatome, COQ3_repeat, rep2


title: alveolar macrophages, Printex90, non-overload, biol rep2


title: GRIS-BD Experimen22-WTA

description: BD Rhapsody

value: spleen

value: immune cells

value: CD45.2+CD5-CD19-Ly6G- cells

value: 7 to 8-week old ApoE-/-, Lipa+/- ApoE-/- and Lipa-/-ApoE-/-mice were fed with a high-fat diet for 12 weeks


title: TOM interactome, COQ3_repeat, rep1


title: PBMCs, Control, 6h, 0ng/ml, 33047, Two

first: Michael

institute: University of Minnesota

description: Library name: 050_O10_33047_0_6h_2

value: PBMCs

value: Control

value: male

value: Two


title: Translatome, COQ3_repeat, rep1


title: MCF 10 A, fibronectin + binder, rep 2


title: TOM interactome, auxin, rep2

description: 3' adaptor sequence: CTAGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC

value: TOM22-Twinstrep, BTF3-AID, AtAFB2 knockin

value: 100 microg/mL IAA, 4.5hr, 37 degreeC


title: alveolar macrophages, Printex90, non-overload, biol rep1

value: Primary alveolar macrophages

value: Male

value: 4 days


title: TOM interactome, auxin, rep1


title: PBMCs, Control, 2h, 0ng/ml, 33047, Three

description: Library name: 048_O10_33047_0_2h_3

value: Three


title: PBMCs, Control, 6h, 0ng/ml, 33047, One

description: Library name: 049_O10_33047_0_6h_1

value: One


title: alveolar macrophages, Printex90, control, biol rep2


title: TOM interactome, 15minCHX, rep2

description: 3' adaptor sequence: AGCTAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC

value: Human embroynic kidney

value: 100 microg/ml cycloheximide, 15 min, 37 degreeC


title: alveolar macrophages, Printex90, control, biol rep1


title: Translatome, auxin, rep1


title: PBMCs, Control, 2h, 0ng/ml, 33047, Two

description: Library name: 047_O10_33047_0_2h_2


title: Translatome, 15minCHX, rep2


title: Translatome, auxin, rep2


title: PBMCs, Control, 6h, 0ng/ml, 33047, Three

description: Library name: 051_O10_33047_0_6h_3


title: Translatome, 15minCHX, rep1


title: PBMCs, Control, 2h, 0ng/ml, 33047, One

description: Library name: 046_O10_33047_0_2h_1


title: TOM interactome, 15minCHX, rep1


title: alveolar macrophages, G1-1, overload, biol rep3


title: TOM interactome, DSP, rep2

value: 250 microM DSP, 5min RT


title: alveolar macrophages, Printex90, control, biol rep3


title: alveolar macrophages, G1-1, overload, biol rep2


title: Translatome, DSP, rep2


title: TOM interactome, DSP, rep1


title: alveolar macrophages, G1-1, overload, biol rep1


title: PBMCs, IL15, 48h, 40ng/ml, 32062, One

description: Library name: 043_O10_32062_40_48h_1


title: TOM interactome, rep3


title: Translatome, DSP, rep1


title: Translatome, rep3


title: TOM interactome, rep2


title: alveolar macrophages, G1-1, non-overload, biol rep3


title: PBMCs, IL15, 24h, 40ng/ml, 32062, Three

description: Library name: 042_O10_32062_40_24h_3


title: Translatome, rep2


title: TOM interactome, rep1


title: PBMCs, IL15, 24h, 40ng/ml, 32062, Two

description: Library name: 041_O10_32062_40_24h_2


title: alveolar macrophages, G1-1, non-overload, biol rep1


title: Translatome, rep1

description: 3' adaptor sequence: ATCGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC


title: PBMCs, IL15, 24h, 40ng/ml, 32062, One

description: Library name: 040_O10_32062_40_24h_1


title: PBMCs, IL15, 12h, 40ng/ml, 33047, Three

description: Library name: 084_O10_33047_40_12h_3


title: PBMCs, IL15, 48h, 40ng/ml, 32062, Three

description: Library name: 045_O10_32062_40_48h_3


title: EHM, hiPSC,TC1133

city: Maastricht

first: Jana

last: Hegenbarth

state: Limburg

address: Universiteitssingel 50

department: Department of Molecular Genetics

country: Netherlands

institute: Maastricht University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processig, gene counting and aggregation were made using the Cell Ranger software v5.0.0
Assembly: GrCh38/Ensembl98
Supplementary files format and content: Cell Ranger feature matrix and value files

source_name: hiPSC

extract_protocol:
For single cell dissociation, d3, d10, d25 and EHM were treated with digestion medium (Accutase, Trypsin and DNase1) for up to 30 min at room temperature. Cell suspensions were gently dissociated by pipetting, centrifuged (100xg, 10min @RT) and resuspended in PBS. Similarly, hiPSC (d0) were washed with PBS twice and incubated in Versene for 5-10 min, arrested with pre-warmed medium, mechanically dissociated, centrifuged and resuspended in PBS. All cell suspensions were checked for viability (>90%), counted and passaged through a 30 μm mesh to ensure compatibility with the 10x Genomics pipeline.
Library was constructed according to manufacter's instructions (Chromium Single Cell 3’ Gene Expression Solution v2, 10x Genomics).

value: hiPSC

value: cardiomyocytes


title: alveolar macrophages, G1-1, control, biol rep3


title: d0, hiPSC,TC1133

description: 10x Genomics


title: PBMCs, IL15, 12h, 40ng/ml, 32062, Three

description: Library name: 039_O10_32062_40_12h_3


title: d0, hiPSC,BXS0116

description: 10x Genomics


title: d25, hiPSC,BXS0116

description: 10x Genomics


title: PBMCs, IL15, 48h, 40ng/ml, 32062, Two

description: Library name: 044_O10_32062_40_48h_2


title: d10, hiPSC,BXS0116

description: 10x Genomics

value: cardiac cells


title: PBMCs, IL15, 12h, 40ng/ml, 32062, Two

description: Library name: 038_O10_32062_40_12h_2

value: PBMCs


title: alveolar macrophages, G1-1, control, biol rep2


title: WT_c

description: rep 3

value: MCF7 WT MED1

value: xenograft of breast cancer cell line

value: ectopic WT MED1


title: d25, hiPSC,TC1133

description: 10x Genomics


title: alveolar macrophages, G1-1, non-overload, biol rep2


title: d3, hiPSC,BXS0116

description: 10x Genomics

value: mesodermal cells