title: 543-1.TCR.SamplePool.rs43862

description: Library name: 43862


title: 543-2.TCR.SamplePool.rs43866

status: Public on Mar 29 2026

type: SRA

city: Beaverton

first: Benjamin

middle: N

last: Bimber

state: OR

address: 505 NW 185th Ave

country: USA

description: Library name: 43866

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
10x Genomics 5' VDJ scRNA-seq

tag: tissue

value: PBMC


title: Female Down syndrome 5,iPSC [E250027128]

city: Chongqing

first: Kai

last: Guo

address: 1 Youyi Road, Yuzhong District

country: China

institute: Chongqing Medical University

description:
Library name: E250027128_L01_N_B_N4A14-3M-Poly-A17_N_B
BGI DNBSEQ-T7
X2-12-5

data_processing:
Raw FASTQ data were preprocessed using Trim Galore to remove low-quality reads (containing adapter sequences, reads with Phred scores <20, or N base proportions >10%), yielding high-quality clean reads for downstream analysis.
Assembly: tab-delimited text file include raw counts for each sample
Supplementary files format and content: csv files include FPKM values for each sample

molecule: total RNA

organism: Homo sapiens

source_name: brain

extract_protocol:
Total RNA was extracted from cells and tissues using TRIzol reagent.
RNA quality was evaluated using an Agilent 2200 Bioanalyzer, and only samples with an RNA integrity number >8.0 were used for library construction. After rRNA depletion, RNA was fragmented to 150–200 bp, and single‑end cDNA libraries were generated using the Ion Total RNA‑Seq Kit v2.0 (Life Technologies) following reverse transcription, adapter ligation, and PCR enrichment. Library concentration was quantified using an Agilent 2200 Bioanalyzer. Sequencing was performed at NovelBio Corp. Laboratory (Shanghai) on an Ion Proton system using Ion PITM Template OT2 200 Kit v2.0 and Ion PI Sequencing 200 Kit v2.0 (Life Technologies).

value: brain

tag: Sex

value: female

tag: cell type

value: induced pluripotent stem cell

tag: genotype

value: Trisomy 21

tag: treatment

tag: batch


title: Female Down syndrome 6,iPSC [E250027128]

description:
Library name: E250027128_L01_N_B_N4A14-3N-Poly-A18_N_B
BGI DNBSEQ-T7
X2-12-6


title: 543-1.GEX.SamplePool.rs43861

description: Library name: 43861


title: Female Down syndrome 4,iPSC [E250027128]

description:
Library name: E250027128_L01_N_B_N4A14-3K-Poly-A16_N_B
BGI DNBSEQ-T7
X2-12-4


title: 543-2.GEX.SamplePool.rs43865

description: Library name: 43865


title: Female Down syndrome 2,iPSC [E250027128]

description:
Library name: E250027128_L01_N_B_N4A14-3H-Poly-A14_N_B
BGI DNBSEQ-T7
X2-12-2


title: 543-2.HTO.SamplePool.rs43863

description: Library name: 43863


title: Female Down syndrome 3,iPSC [E250027128]

description:
Library name: E250027128_L01_N_B_N4A14-3J-Poly-A15_N_B
BGI DNBSEQ-T7
X2-12-3


title: 538-8.TCR.37012.rs43735

description: Library name: 43735

source_name: Bone marrow,MesLN,PLN,Spleen

value: Bone marrow,MesLN,PLN,Spleen


title: 543-1.HTO.SamplePool.rs43859

description: Library name: 43859


title: Female Down syndrome with XIST,doxycycline-treated2,iPSC [E250027128]

description:
Library name: E250027128_L01_N_B_N4A14-3Q-Poly-A32_N_B
BGI DNBSEQ-T7
X2-12ALL-Dox-2

value: doxycycline


title: Female Down syndrome 1,iPSC [E250027128]

description:
Library name: E250027128_L01_N_B_N4A14-3G-Poly-A13_N_B
BGI DNBSEQ-T7
X2-12-1


title: Female Down syndrome with XIST,doxycycline-treated5,iPSC [E250027128]

description:
Library name: E250027128_L01_N_B_N4A14-3T-Poly-A35_N_B
BGI DNBSEQ-T7
X2-12ALL-Dox-5


title: Female Control 6,iPSC [E250027128]

description:
Library name: E250027128_L01_N_B_N4A14-3F-Poly-A12_N_B
BGI DNBSEQ-T7
H9-3-6

value: Euploid


title: 538-7.TCR.36683.rs43731

description: Library name: 43731


title: LICs, KO+BHB3

city: guangzhou

first: Songqi

last: Zhu

state: guangdong

address: No. 74, Zhongshan 2nd Road, Yuexiu District

institute: Sun Yat-sen University

description: Library name: Sample9

data_processing:
RNA-seq reads were aligned to mouse genome mm10 and gene annotation from the Ensembl database.
Low quality reads were removed and the adaptor sequences were trimmed by Trim Galore (v0.5.0).
The remaining pair-end reads were mapped to the mouse genome (GRCm39, Ensembl) via subread (v2.0.6) and bedtools (v2.31.1),
The remaining pair-end reads were mapped to the reference genome by by featureCounts (v2.0.6).
Assembly: GRCm39
Supplementary files format and content: counts.txt.gz

organism: Mus musculus

source_name: Bone Marrow

extract_protocol:
In brief, intact bone marrows from mice at the age of 6-8weeks were flushed from mouse femora and tibiae. Bone marrow cells by pipetting with 1 mL syringe, and then underwent red blood cell lysis using 0.16 M ammonium chloride solution.
RNA libraries for RNA-seq were prepared using TruePrep DNA Library Prep Kit V2 for Illumina TD503.

value: Bone Marrow

value: leukemia-initiating cells

value: HMGCS4 KO+BHB


title: 538-8.HTO.37012.rs43732

description: Library name: 43732


title: 538-7.HTO.36683.rs43728

description: Library name: 43728


title: Female Control 4,iPSC [E250027128]

description:
Library name: E250027128_L01_N_B_N4A14-3D-Poly-A10_N_B
BGI DNBSEQ-T7
H9-3-4


title: 538-6.TCR.36562.rs43727

description: Library name: 43727


title: LICs, KO+BHB2

description: Library name: Sample8

value: HMGCS3 KO+BHB


title: 538-6.HTO.36562.rs43724

description: Library name: 43724


title: Female Control 3,iPSC [E250027128]

description:
Library name: E250027128_L01_N_B_N4A14-3C-Poly-A9_N_B
BGI DNBSEQ-T7
H9-3-3


title: 538-5.HTO.SamplePool.rs43720

description: Library name: 43720


title: LICs, KO+BHB1

description: Library name: Sample7

value: HMGCS2 KO+BHB


title: Female Control 2,iPSC [E250027128]

description:
Library name: E250027128_L01_N_B_N4A14-3B-Poly-A8_N_B
BGI DNBSEQ-T7
H9-3-2


title: 538-4.TCR.35547.rs43719

description: Library name: 43719


title: 538-5.TCR.SamplePool.rs43723

description: Library name: 43723


title: LICs, KO2

description: Library name: Sample5

value: HMHCS2 KO


title: Female Control 1,iPSC [E250027128]

description:
Library name: E250027128_L01_N_B_N4A14-3A-Poly-A7_N_B
BGI DNBSEQ-T7
H9-3-1


title: Female Control 5,iPSC [E250027128]

description:
Library name: E250027128_L01_N_B_N4A14-3E-Poly-A11_N_B
BGI DNBSEQ-T7
H9-3-5


title: LICs, KO1

description: Library name: Sample4

value: HMGCS2 KO


title: 538-3.HTO.38090.rs43712

description: Library name: 43712


title: LICs, WT3

description: Library name: Sample3


title: 538-4.HTO.35547.rs43716

description: Library name: 43716


title: 538-1.HTO.SamplePool.rs43704

description: Library name: 43704


title: Female Down syndrome with XIST,doxycycline-treated5,iPSC [E250027119]

description:
Library name: E250027119_L01_N_B_N4A14-3T-Poly-A35_N_B
BGI DNBSEQ-T7
X2-12ALL-Dox-5


title: 538-2.HTO.38089.rs43708

description: Library name: 43708


title: Female Down syndrome with XIST,doxycycline-treated4,iPSC [E250027119]

description:
Library name: E250027119_L01_N_B_N4A14-3S-Poly-A34_N_B
BGI DNBSEQ-T7
X2-12ALL-Dox-4


title: 538-1.TCR.SamplePool.rs43707

description: Library name: 43707


title: LICs, KO3

description: Library name: Sample6


title: 538-3.TCR.38090.rs43715

description: Library name: 43715


title: 528-8.GEX.36767.rs43702

description: Library name: 43702


title: LICs, WT2

description: Library name: Sample2


title: Female Down syndrome with XIST,doxycycline-treated6,iPSC [E250027119]

description:
Library name: E250027119_L01_N_B_N4A14-3U-Poly-A36_N_B
BGI DNBSEQ-T7
X2-12ALL-Dox-6


title: Female Down syndrome with XIST,doxycycline-treated3,iPSC [E250027119]

description:
Library name: E250027119_L01_N_B_N4A14-3R-Poly-A33_N_B
BGI DNBSEQ-T7
X2-12ALL-Dox-3


title: 538-2.TCR.38089.rs43711

description: Library name: 43711


title: 528-8.HTO.36767.rs43700

description: Library name: 43700


title: Female Down syndrome with XIST,doxycycline-treated1,iPSC [E250027119]

description:
Library name: E250027119_L01_N_B_N4A14-3P-Poly-A31_N_B
BGI DNBSEQ-T7
X2-12ALL-Dox-1


title: Female Down syndrome with XIST,doxycycline-treated2,iPSC [E250027119]

description:
Library name: E250027119_L01_N_B_N4A14-3Q-Poly-A32_N_B
BGI DNBSEQ-T7
X2-12ALL-Dox-2


title: 528-6.GEX.37826.rs43694

description: Library name: 43694


title: LICs, WT1

description: Library name: Sample1


title: 528-6.TCR.37826.rs43695

description: Library name: 43695


title: 528-6.HTO.37826.rs43692

description: Library name: 43692


title: mKate2 control, biol rep2

city: Rehovot

first: Fabian

last: Stamp

address: Herzl St 234

department: department of brain science

country: Israel

institute: The Weziamnn institiute of science

description: Library name: Lior_23

data_processing:
Poly-A/T stretches and Illumina adapters were trimmed from the reads using cutadapt [@cutadapt]; resulting reads shorter than 30bp were discarded. Reads were mapped to the `r input_pars[["intermine_organism"]]` reference genome $$ref_genome using STAR [@STAR], supplied with gene annotations downloaded from Ensembl (and with EndToEnd option and outFilterMismatchNoverLmax was set to 0.04). Reads with the same UMI were removed using the PICARD MarkDuplicate tool using the BARCODE_TAG parameter. Expression levels for each gene were quantified using htseq-count [@htseq, @htseqWeb], using the gtf above. Differentially expressed genes were identified using DESeq2 [@deseq] with the betaPrior, cooksCutoff and independentFiltering parameters set to False. Raw P values were adjusted for multiple testing using the procedure of Benjamini and Hochberg. Pipeline was run using snakemake
Assembly: GRCh38
Supplementary files format and content: TSV with counts

source_name: HEK 293T

extract_protocol:
RNA was isolated using RNeasy plus mini kit (QIAGEN), according to the manufacturer’s protocol.  RNA concentrations were measured by Tape Station.
total RNA was fragmented followed by reverse transcription and second strand cDNA synthesis. The double strand cDNA was subjected to end repair, A base addition, adapter ligation and PCR amplification to create libraries. Libraries were evaluated by Qubit and TapeStation. Sequencing libraries were constructed with barcodes to allow multiplexing of 24 samples

tag: cell line

value: HEK 293T

value: Human embryonic kidney 293T cells

value: WT

value: Transfection (mKate2 control)


title: 528-5.GEX.SamplePool.rs43690

description: Library name: 43690

value: PBMC


title: 528-5.TCR.SamplePool.rs43691

description: Library name: 43691


title: mKate2 control, biol rep1

description: Library name: Lior_22

value: Transfection  (mKate2 control)


title: 528-8.TCR.36767.rs43703

description: Library name: 43703


title: 528-5.HTO.SamplePool.rs43688

description: Library name: 43688


title: 528-4.TCR.37246.rs43687

description: Library name: 43687


title: mKate2 control, biol rep3

description: Library name: Lior_24


title: Female Down syndrome 5,iPSC [E250027119]

description:
Library name: E250027119_L01_N_B_N4A14-3M-Poly-A17_N_B
BGI DNBSEQ-T7
X2-12-5

value: brain

value: female

value: induced pluripotent stem cell

value: Trisomy 21


title: 528-3.TCR.36131.rs43683

description: Library name: 43683

value: Bone marrow,MesLN,PLN,Spleen


title: BD10, biol rep3

description: Library name: Lior_20

value: Transfection (BD10 )


title: BD9, biol rep3

description: Library name: Lior_19

value: Transfection (BD9 )


title: Female Down syndrome 3,iPSC [E250027119]

description:
Library name: E250027119_L01_N_B_N4A14-3J-Poly-A15_N_B
BGI DNBSEQ-T7
X2-12-3


title: 528-4.HTO.37246.rs43684

description: Library name: 43684


title: 528-2.GEX.35112.rs43678

description: Library name: 43678


title: NT, biol rep3

description: Library name: Lior_21

value: NT


title: Female Down syndrome 4,iPSC [E250027119]

description:
Library name: E250027119_L01_N_B_N4A14-3K-Poly-A16_N_B
BGI DNBSEQ-T7
X2-12-4


title: 528-1.TCR.SamplePool.rs43675

description: Library name: 43675


title: 528-3.GEX.36131.rs43682

description: Library name: 43682


title: 528-2.HTO.35112.rs43676

description: Library name: 43676


title: 528-3.HTO.36131.rs43680

description: Library name: 43680


title: Female Down syndrome 2,iPSC [E250027119]

description:
Library name: E250027119_L01_N_B_N4A14-3H-Poly-A14_N_B
BGI DNBSEQ-T7
X2-12-2


title: 528-1.GEX.SamplePool.rs43674

description: Library name: 43674


title: 528-2.TCR.35112.rs43679

description: Library name: 43679


title: BD8, biol rep3

description: Library name: Lior_18

value: Transfection (BD8)


title: Female Down syndrome 1,iPSC [E250027119]

description:
Library name: E250027119_L01_N_B_N4A14-3G-Poly-A13_N_B
BGI DNBSEQ-T7
X2-12-1


title: Female Control 6,iPSC [E250027119]

description:
Library name: E250027119_L01_N_B_N4A14-3F-Poly-A12_N_B
BGI DNBSEQ-T7
H9-3-6

value: Euploid


title: BD7, biol rep3

description: Library name: Lior_17

value: Transfection (BD7 )


title: BD5, biol rep3

description: Library name: Lior_16

value: HEK 293T

value: Transfection (BD5 )


title: Female Down syndrome 6,iPSC [E250027119]

description:
Library name: E250027119_L01_N_B_N4A14-3N-Poly-A18_N_B
BGI DNBSEQ-T7
X2-12-6


title: 533-2.HTO.SamplePool.rs43668

description: Library name: 43668


title: 533-2.TCR.SamplePool.rs43671

description: Library name: 43671


title: 533-1.TCR.SamplePool.rs43667

description: Library name: 43667


title: Female Control 4,iPSC [E250027119]

description:
Library name: E250027119_L01_N_B_N4A14-3D-Poly-A10_N_B
BGI DNBSEQ-T7
H9-3-4


title: NT, biol rep2

description: Library name: Lior_14

value: Human embryonic kidney 293T cells

value: WT


title: BD6, biol rep3

description: Library name: Lior_15

value: Transfection (BD6 )


title: 525-1.TCR.SamplePool.rs43659

description: Library name: 43659

value: PBMC


title: 528-1.HTO.SamplePool.rs43672

description: Library name: 43672


title: 525-2.GEX.SamplePool.rs43662

description: Library name: 43662


title: 525-2.HTO.SamplePool.rs43660

description: Library name: 43660


title: Female Control 3,iPSC [E250027119]

description:
Library name: E250027119_L01_N_B_N4A14-3C-Poly-A9_N_B
BGI DNBSEQ-T7
H9-3-3

value: brain


title: 525-2.TCR.SamplePool.rs43663

description: Library name: 43663


title: Female Control 2,iPSC [E250027119]

description:
Library name: E250027119_L01_N_B_N4A14-3B-Poly-A8_N_B
BGI DNBSEQ-T7
H9-3-2

value: female


title: Female Control 5,iPSC [E250027119]

description:
Library name: E250027119_L01_N_B_N4A14-3E-Poly-A11_N_B
BGI DNBSEQ-T7
H9-3-5

value: induced pluripotent stem cell


title: BD10, biol rep2

description: Library name: Lior_13


title: BD9, biol rep2

description: Library name: Lior_12


title: 514-8.TCR.37448.rs42560

description: Library name: 42560

source_name: Bone marrow,Spleen

value: Bone marrow,Spleen


title: 525-1.HTO.SamplePool.rs43656

description: Library name: 43656


title: BD8, biol rep2

description: Library name: Lior_11


title: 533-1.HTO.SamplePool.rs43664

description: Library name: 43664


title: 514-8.HTO.37448.rs42557

description: Library name: 42557


title: Female Down syndrome with XIST,doxycycline-treated3,NPC

description:
Library name: E250048544_L01_N_B_N4A31-1C-Poly-AN18_N_B
BGI DNBSEQ-T7
X2-12-All-Dox-3

value: neural progenitor cell

value: Trisomy 21

value: doxycycline


title: 514-6.TCR.37167.rs42552

description: Library name: 42552

source_name: Spleen

value: Spleen


title: 514-6.HTO.37167.rs42549

description: Library name: 42549


title: Female Control 1,iPSC [E250027119]

description:
Library name: E250027119_L01_N_B_N4A14-3A-Poly-A7_N_B
BGI DNBSEQ-T7
H9-3-1


title: 525-1.GEX.SamplePool.rs43658

description: Library name: 43658


title: Female Down syndrome with XIST,doxycycline-treated2,NPC

description:
Library name: E250048544_L01_N_B_N4A31-1B-Poly-AN17_N_B
BGI DNBSEQ-T7
X2-12-All-Dox-2


title: 514-5.HTO.SamplePool.rs42545

description: Library name: 42545


title: Female Down syndrome with XIST,doxycycline-treated1,NPC

description:
Library name: E250048544_L01_N_B_N4A31-1A-Poly-AN16_N_B
BGI DNBSEQ-T7
X2-12-All-Dox-1


title: BD5, biol rep2

description: Library name: Lior_9


title: 514-5.TCR.SamplePool.rs42548

description: Library name: 42548


title: BD7, biol rep2

description: Library name: Lior_10


title: BD6, biol rep2

description: Library name: Lior_8


title: 514-4.HTO.37166.rs42541

description: Library name: 42541

value: Bone marrow,MesLN,PLN,Spleen


title: 514-4.TCR.37166.rs42544

description: Library name: 42544


title: Fe-RR-20-2

city: Yibin

first: Xia

last: Zhao

state: Sichuan

address: Daxue road 5

institute: Yibin University

description: Library name: Fe-20d2_FPKM

data_processing:
The raw reads were further processed with a bioinformatic pipelinetool, BMKCloud(www.biocloud.net) online platform.
Assembly: Gene function was annotated based on the following databases: Nr (NCBI non-redundant protein sequences);Pfam (Protein family); KOG/COG (Clusters of Orthologous Groups of proteins); Swiss-Prot (A manually annotated and reviewed protein sequence database); KO (KEGG Ortholog database); GO (Gene Ontology).
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Oryza sativa

source_name: grain

extract_protocol:
The plant total RNA was extracted using the RNAprep Pure Plant Kit (Tiangen, Beijing, China) according the instructions provided by the manufacturer.The animal total RNA was extracted according to the instruction manual of the TRlzol Reagent (Life technologies, California, USA).
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using Hieff NGS Ultima Dual-mode mRNA Library Prep Kit for Illumina (Yeasen Biotechnology (Shanghai) Co., Ltd.) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads.First strand cDNA was synthesized and second strand cDNA synthesis was subsequently performed. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: grain


title: NT, biol rep1

description: Library name: Lior_7

value: NT


title: Fe-RR-20-3

description: Library name: Fe-20d3_FPKM


title: Fe-RR-20-1

description: Library name: Fe-20d1_FPKM


title: Female Control 3,NPC

description:
Library name: E250048544_L01_N_B_N4A31-10-Poly-AN6_N_B
BGI DNBSEQ-T7
H68-3

value: Euploid


title: BD10, biol rep1

description: Library name: Lior_6

value: HEK 293T

value: Transfection (BD10 )


title: Female Control 1,NPC

description:
Library name: E250048544_L01_N_B_N4A31-0Y-Poly-AN4_N_B
BGI DNBSEQ-T7
H68-1


title: BD9, biol rep1

description: Library name: Lior_5

value: Human embryonic kidney 293T cells

value: WT

value: Transfection (BD9 )


title: 514-3.TCR.38180.rs42540

description: Library name: 42540


title: 514-3.HTO.38180.rs42537

description: Library name: 42537


title: CK-RR-20-2

description: Library name: CK-20d2_FPKM


title: BD8, biol rep1

description: Library name: Lior_4

value: Transfection (BD8)


title: CK-RR-20-3

description: Library name: CK-20d3_FPKM


title: 514-1.TCR.SamplePool.rs42532

description: Library name: 42532

value: PBMC


title: Female Down syndrome 2,NPC

description:
Library name: E250048544_L01_N_B_N4A31-0W-Poly-AN2_N_B
BGI DNBSEQ-T7
D8-11-2

value: brain

value: female


title: Fe-RR-3

description: Library name: Fe-15d3_FPKM


title: CK-RR-20-1

description: Library name: CK-20d1_FPKM


title: Female Down syndrome 1,NPC

description:
Library name: E250048544_L01_N_B_N4A31-0V-Poly-AN1_N_B
BGI DNBSEQ-T7
D8-11-1

value: neural progenitor cell


title: BD7, biol rep1

description: Library name: Lior_3

value: Transfection (BD7 )


title: BD5, biol rep1

description: Library name: Lior_2

value: Transfection (BD5 )


title: 511-2.TCR.SamplePool.rs42519

description: Library name: 42519


title: 514-1.HTO.SamplePool.rs42529

description: Library name: 42529


title: Fe-RR-2

description: Library name: Fe-15d2_FPKM


title: 511-2.HTO.SamplePool.rs42516

description: Library name: 42516


title: Panc-1 cells, CAF overexpressing PAI-1, biological replicate 3

city: Tianjin

first: Yu

last: Ren

state: Tianjin

address: No22.Qixiangtai Rd.,Heping Dist

institute: Tianjin Medical University

description: Panc-1 cells co-cultured with CAF overexpressing PAI-1 biological replicate 3

data_processing:
Basecalls performed using MGISEQ-2000
SOAPnuke was used to get the "clean reads".
Mapping clean reads to hg19 whole genome using BWA.
Bowtie2 was used to get the mapping ratio.
Fragments Per Kilobase Million (FPKM) was calculated based on the RSEM.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include fpkm values for each sample

growth_protocol: Panc-1 epithelial cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37°C

extract_protocol:
Cal27 were treated with Stattic or DMSO as a negative control, followed by total RNA extraction with Trizol (Solarbio, R1100) 174 total RNA extraction with Trizol (Solarbio, R1100)
RNA libraries were prepared for sequencing using  oligo -dT beads

treatment_protocol: Panc-1 cells co-cultured with CAF or CAF overexpressing PAI-1 for 72h

value: epithelial cell

value: Co-culture with CAF overexpressing PAI-1

tag: time


title: BD6, biol rep1

description: Library name: Lior_1

value: Transfection (BD6 )


title: Female Down syndrome 3,NPC

description:
Library name: E250048544_L01_N_B_N4A31-0X-Poly-AN3_N_B
BGI DNBSEQ-T7
D8-11-3

value: Trisomy 21


title: Panc-1 cells, CAF overexpressing PAI-1, biological replicate 2

description: Panc-1 cells co-cultured with CAF overexpressing PAI-1 biological replicate 2


title: CARM1 knockdown guide2 rep4

city: Bronx

first: Ronald

last: Cutler

state: NY

address: 1300 Morris Park Ave

department: Genetics & Biochemistry

institute: Albert Einstein College of Medicine

description: Library name: sgCAR2_r4e4

data_processing:
Raw sequence reads were processed using the nf-core rnaseq pipeline (https://nf-co.re/rnaseq/3.14.0) using the star_rsem alignment option and min_mapped_reads set to 5 to align the reads to the GRCh38 primary genome assembly and gene level counts were obtained using the gencode v42 primary assembly annotation
Assembly: GRCh38
Supplementary files format and content: Tab-separated values; Ensemble gene and transcript IDs with gene unnormalized counts or TPM

source_name: patient derived Glioblastoma

growth_protocol: Glioma stem-like cell lines (GSCs) NSC11 and NSC20 were provided as frozen stocks by Dr. Frederick Lang, MD Anderson Cancer Center, Houston, TX. GSCs were grown as neurospheres in stem cell media (DMEM/F12, 50ng/ml EGF and bFGF, 2% B27 without vitamin A, and 1% penicillin-streptomycin) and CD133+ cells were selected by FACS as previously reported [18]. All cell lines were maintained in culture (5% O2 and 5% CO2 incubators) for less than two months from thawing and tested for mycoplasma with PCR. GSCs were authenticated by observation of cell morphology and growth, we also validate NSC11 and NSC20 differences using proteomics.

extract_protocol:
RNA was extracted from cell pellets using the RNeasy kit (Qiagen), quantified using a Qubit kit (Thermo Fisher Scientific) purity was assessed by 260/280 and 260/230 ratios using a Nanodrop (Thermo Fisher Scientific).
Libraries were prepared for mRNA analysis and sequenced on an Illumina Novaseq X using 150bp paired-end mode by Novogene Corp Inc., CA.

treatment_protocol: We used lipofectamine RNAiMAX transfection reagent (ThermoFisher) to generate siRNA knockdowns. We purchased two different siRNA against NFIA and NGFR from ThermoFisher (s9477, s9478, s9540). We followed the RNAiMAX protocol for transfection. In short, 1 x 106 GSCs were seeded into 10ml of stem cell media with 40nM of siRNA-lipofectamine complexes against siRNA of target gene or siCTRL (negative control) and placed in incubator for 24 hours. GSCs were then gently collected, spun down, and reseeded with fresh media without siRNA and placed in incubator for another 4 days. Fresh media was added accordingly.

value: patient derived Glioblastoma

value: Glioblastoma stem-like cells


title: Female Control 2,NPC

description:
Library name: E250048544_L01_N_B_N4A31-0Z-Poly-AN5_N_B
BGI DNBSEQ-T7
H68-2

value: Euploid


title: Panc-1 cells, CAF overexpressing PAI-1, biological replicate 1

description: Panc-1 cells co-cultured with CAF overexpressing PAI-1 biological replicate 1


title: 511-1.TCR.SamplePool.rs42515

description: Library name: 42515


title: Fe-RR-1

description: Library name: Fe-15d1_FPKM

value: grain


title: CK-RR-3

description: Library name: CK-15d3_FPKM


title: CARM1 knockdown guide2 rep2

description: Library name: sgCAR2_r2e4


title: 511-1.HTO.SamplePool.rs42512

description: Library name: 42512


title: CK-RR-2

description: Library name: CK-15d2_FPKM


title: CARM1 knockdown guide1 rep4

description: Library name: sgCAR1_r4e4


title: Panc-1 cells, CAF, biological replicate 3

description: Panc-1 cells co-cultured with CAF biological replicate 3

value: WT

value: Co-culture with CAF


title: Panc-1 cells, CAF, biological replicate 1

description: Panc-1 cells co-cultured with CAF biological replicate 1


title: 499-8.TCR.36622.rs41424

description: Library name: 41424

value: Bone marrow,MesLN,PLN,Spleen


title: 499-8.HTO.36622.rs41421

description: Library name: 41421


title: Fe-BR-3

description: Library name: BR-Fe3_FPKM


title: Panc-1 cells, CAF, biological replicate 2

description: Panc-1 cells co-cultured with CAF biological replicate 2


title: 499-7.TCR.36135.rs41420

description: Library name: 41420


title: CARM1 knockdown guide2 rep1

description: Library name: sgCAR2_r1e4


title: CARM1 knockdown guide1 rep2

description: Library name: sgCAR1_r2e4


title: Fe-BR-1

description: Library name: BR-Fe1_FPKM


title: CARM1 knockdown guide1 rep3

description: Library name: sgCAR1_r3e4


title: CK-BR-3

description: Library name: BR-CK3_FPKM


title: mouse tumor, PD1 treated

city: Houston

first: Salah-Eddine

last: Bentebibel

address: 1515 Holcombe Blvd

institute: MD Anderson Cancer Center

description:
Library name: Tu_PD1
10X Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using cellranger-7.0.0
Assembly: GRCm38
Supplementary files format and content: tab separated values files and matrix files

source_name: tumor

extract_protocol:
B16 melanoma tumors were mashed through 40-mm filters, and red blood cells were lysed with ammonium-chloride-potassium buffer for 5 min at room temperature followed by washing with phosphate-buffered saline containing 2% fetal bovine serum. Single-cell suspensions from 6 mice per group were pooled and incubated with antibodies against CD16 and CD32, stained with anti-CD45 antibody and SYTOX Blue viability dye. Live CD45+ cells were sorted using a BD FACS Aria I (BD Biosciences).
Library preparation were conducted according to 10x Genomics' 5ʹ scRNA-seq guidelines [CG000331_Chromium_Next_GEM_Single_Cell_5-v2_User Guide_RevD].The final libraries were quantified using the Qubit HS dsDNA Assay Kit (Thermo Fisher Scientific), and library profiles were analyzed using High Sensitivity DNA Kit (Agilent).

treatment_protocol: Mice bearing tumors were treated with CD40 Ab (or dilution buffer) intratumorally alone or in combination with PD1 Ab or IgG Ab (i.v.) on day 8 and day 11. Melanoma tumors were dissected 14 days after tumor inoculation.

value: tumor

value: melanoma


title: mouse tumor, CD40 & PD1 treated

description:
Library name: Tu_Comb
10X Genomics


title: CK-BR-2

description: Library name: BR-CK2_FPKM


title: 499-6.TCR.36497.rs41416

description: Library name: 41416

source_name: Bone marrow

value: Bone marrow


title: CARM1 knockdown guide1 rep1

description: Library name: sgCAR1_r1e4


title: mouse tumor, CD40 treated

description:
Library name: Tu_CD40
10X Genomics


title: 499-5.TCR.SamplePool.rs41412

description: Library name: 41412

value: PBMC


title: 499-6.HTO.36497.rs41413

description: Library name: 41413


title: 499-7.HTO.36135.rs41417

description: Library name: 41417


title: scramble control rep3

description: Library name: sgSCR_r3e4

value: non-targeting Crispr sgRNA


title: CK-BR-1

description: Library name: BR-CK1_FPKM


title: scramble control rep4

description: Library name: sgSCR_r4e4


title: JGH3

city: Nan jing

first: 璐

last: 李

state: jiangsu

address: 龙眠大道578号

institute: 江苏康缘药业股份有限公司

description: Library name: Sample 15

data_processing:
Genomics Workbench
Nextseq 2000 was used for sequencing. The principle of sequencing is to sequence while synthesizing. Filter the original data, including removing the reads with connectors; Remove reads containing N; Remove low quality reads.
Compare clean reads to the reference genome, use hisat2 software to compare clean reads with the reference genome, filter out the reads with a comparison quality value of less than 10, and compare the reads with multiple regions of the genome.
The "deseq2" R software package was used to screen the differentially expressed genes (DEGs) between koa samples and normal samples. The screening conditions were p<0.05, 𞓜 log2fc|>2.
The featurecounts tool in subread software is used for analysis.
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include p values for DEG

organism: Rattus norvegicus

source_name: synovium

extract_protocol:
total RNA was extracted using Trizol reagent (thermofisher, 15596018)
Illumina NovaseqTM 6000 sequence platform

value: synovium

value: wild type


title: PBS

city: Cambridge

first: Akash

last: Gupta

state: MA

address: 500 Main Street, Building 76

institute: Massachusetts Institute of Technology

description: Library name: D25-4316

data_processing:
Output data was processed using 10X Genomics cell ranger using default configuration. scRNAseq data was processed by Bioinformatics & Computing Core Facility. Single‐cell RNA sequencing (scRNA‐seq) data were generated on the 10X Genomics Chromium platform from four independent mouse samples which were annotated as “FFL,” “PBS,” “NIK,” and “IRF8,” respectively.
Assembly: mm10-2020-A
Supplementary files format and content: filtered_feature_bc_matrix.tar.gz is archived and compressed folder that contains the gene expression count matrix along with corresponding gene (features) and cell barcode annotations for each sample.
Supplementary files format and content: singlet.integrated.filtered.rds.gz is fully processed and annotated integrated Seurat object.

source_name: immune cells

growth_protocol: B16-F10 and B16-F10-Luc2 were purchased from ATCC. B16-OVA, MC38, and MB49 were purchased from Millipore-Sigma. THP-1 IRF reporter cells were obtained from These cells were routinely screened for murine pathogens and mycoplasma contamination. Cells were cultured in DMEM supplemented with 4.5 g/L D-glucose, GlutaMAX, and 10% fetal bovine serum (FBS) (ThermoFisher). BMDCs were cultured by isolating bone marrow from the femur and tibia of mice. Bone marrow cells were then cultured in RPMI-1640 supplemented with GlutaMAX (ThermoFisher), 10% FBS (ThermoFisher), 100 U/mL penicillin (ThermoFisher), 100 μg/mL streptomycin (ThermoFisher), 50 μM β-mercaptoethanol (Millipore), 200 ng/mL Flt3L-Fc (R&D Systems), and 20 ng/mL GM-CSF (R&D Systems). On day 9, non-adherent cells were harvested and used immediately.

extract_protocol:
Native TE buffer (ThermoFisher) or denaturing TE buffer + 0.5% Triton-X 100 (Millipore-Sigma)
3' RNA libraries were prepared from ~5k cells on using 10X Genomics 3'RNA (GEM-X) chemistry on a ChromiumX using 12 cycles of PCR.

treatment_protocol: Human dendritic cells were differentiated from human primary bone marrow CD34+ cell using a Mouse-OP9 co-culture method as reported in previously established protocols.83 Mouse OP9 cell line (ATCC, Cat no CRL-2749)_were cultured in T75 flasks in OP9 medium (αMEM, 20% FCS, penicillin-streptomycin) at 37 °C and 5% CO₂ and maintained at a density of 4 × 10³–1 × 10⁴ cells/cm² with medium changes every 3–4 days. For plating, OP9 cells were seeded into 96-well U-bottom plates at 5,000 cells/well. Human primary bone marrow CD34⁺ cells (ATCC PCS-800-012) were resuspended at 1.5 × 10⁴ cells/ml in DC differentiation medium (αMEM supplemented with 10% FCS, 1% penicillin–streptomycin, 100 ng/ml Flt3L, 20 ng/ml SCF, and 20 ng/ml GM-CSF). OP9 medium was gently removed and replaced with 200 µl of CD34⁺ cell suspension (3,000 cells/well). Cultures were maintained with half-medium changes on day 6 and subsequently on days 12 and 18. Differentiated cells were harvested on day 19 by gentle pipetting, filtered through 50 µm strainers, and resuspended in appropriate buffers for flow cytometric analysis. Immature human DCs were treated with human NIK, IRF8 and Fluc (control) mRNAs on day 6, 12, and 18 followed by analysis on day 19.

value: immune cells


title: mouse tumor, control

description:
Library name: Tu_CTR
10X Genomics

value: Control


title: scramble control rep1

description: Library name: sgSCR_r1e4


title: 499-4.TCR.35644.rs41408

description: Library name: 41408

source_name: MesLN,PLN

value: MesLN,PLN


title: NIK

description: Library name: D25-4314


title: JGH2

institute: 江苏康缘药业股份有限公司

description: Library name: Sample 14


title: Fe-BR-2

description: Library name: BR-Fe2_FPKM


title: FFL

description: Library name: D25-4315


title: 499-5.HTO.SamplePool.rs41409

description: Library name: 41409


title: JGH1

institute: 江苏康缘药业股份有限公司

description: Library name: Sample 13


title: 499-3.TCR.37636.rs41404

description: Library name: 41404


title: HEK293T cells, ANXA4-targeting paCas13d, post-illumination, rep3

city: tianjin

first: miaomiao

last: gao

address: tianjin

country: Algeria

institute: tianjin university

description:
Library name: Sample6
ANXA4-targeting paCas13d, replicate 3
B3

data_processing:
Sequencing was performed on the Illumina NovaSeq 6000 platform.
Raw reads were processed for quality control prior to alignment.
Clean reads were aligned to the human reference genome (hg38) using STAR.
Gene expression quantification and differential expression analysis were performed
Gene expression quantification and differential expression analysis were performed using DESeq2.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files containing gene-level FPKM values for each sample.

growth_protocol: HEK293T cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin in a humidified incubator with 5% CO2 at 37°C.

extract_protocol:
Total RNA was extracted from HEK293T cells 48 h post-illumination using standard RNA isolation procedures. RNA quality and quantity were assessed prior to library preparation.
RNA-seq libraries were prepared using the NEBNext Ultra RNA Library Prep Kit according to the manufacturer’s instructions.

treatment_protocol: HEK293T cells were transfected with non-targeting control or ANXA4-targeting photoactivatable Cas13d (paCas13d) constructs according to the experimental design. After transfection, cells were subjected to illumination, and samples were collected 48 h post-illumination for RNA sequencing.

value: human embryonic kidney cells

value: transfected with ANXA4-targeting paCas13d


title: 499-4.HTO.35644.rs41405

description: Library name: 41405


title: scRNA-seq of mouse lung tissue (Group C)

city: Harbin

first: Xintong

last: Wang

address: No. 37, Yiyuan Street, Nangang District, Harbin 150001, China

institute: Department of Respiratory and Critical Care Medicine, The Fourth Affiliated Hospital of Harbin Medical University

description:
Library name: WTA_C
Raw fastq files of mouse lung scRNA-seq, Group C.

data_processing:
Raw sequencing data were processed using the BD Rhapsody Analysis Pipeline. Reads were filtered, aligned to the mouse reference genome (mm10), and cell barcodes and UMI counts were extracted.
Gene expression matrices (matrix.mtx, barcodes.tsv, genes.tsv) were generated using the BD Rhapsody pipeline. Quality control, normalization, PCA-based dimensionality reduction, clustering, and differential expression analysis were conducted using Seurat (v4.3.0). Only cells with 400–5000 detected genes, 600–20000 UMIs, and mitochondrial gene content <20% were retained. DEGs were identified with the FindMarkers function, and GO enrichment was performed. CellChat was used for intercellular communication analysis.
Processed data for TCR/BCR repertoires were generated using the scRepertoire R package (v2.0.0), including clonal abundance, diversity, homeostasis, length distribution, overlap, and quantification analyses. Hashtag demultiplexing and clustering results (celltype_count.tsv and seuratcluster_count.tsv) were generated using Seurat (v4.3.0) based on HTO expression and clustering information. All processed files are provided in tab-delimited format as intermediate results from the corresponding pipeline.
Assembly: mm10 (GRCm38, Mus musculus reference genome)
Supplementary files format and content: The processed data includes matrix.mtx, which contains the sparse expression matrix (cells × genes); barcodes.tsv, which lists the single-cell barcodes; and genes.tsv, which provides the gene (or feature) names corresponding to the matrix. These files together represent the aggregated gene expression matrix across all WTA samples.

source_name: Lung

extract_protocol:
Lung tissues containing visible nodules were collected. Samples were mechanically and enzymatically dissociated into single-cell suspensions using collagenase and hyaluronidase digestion. Single cells were filtered, counted, viability assessed, and immediately used for single-cell capture and library preparation.
Single-cell RNA-seq, TCR/BCR immune repertoire, and Hashtag libraries were prepared using the BD Rhapsody system following the manufacturer's protocols. Libraries were sequenced on the Illumina NovaSeq 6000 platform using paired-end sequencing.

value: Lung

value: Lung cells

value: Wild type

value: Smoking cessation (longer)


title: JGM3

institute: 江苏康缘药业股份有限公司

description: Library name: Sample 12


title: scramble control rep2

description: Library name: sgSCR_r2e4

value: patient derived Glioblastoma

value: Glioblastoma stem-like cells


title: scRNA-seq of mouse lung tissue (Group B)

description:
Library name: WTA_B
Raw fastq files of mouse lung scRNA-seq, Group B.

value: Smoking cessation


title: HEK293T cells, ANXA4-targeting paCas13d, post-illumination, rep2

description:
Library name: Sample5
ANXA4-targeting paCas13d, replicate 2
B2

value: WT


title: JGM2

institute: 江苏康缘药业股份有限公司

description: Library name: Sample 11


title: JGM1

institute: 江苏康缘药业股份有限公司

description: Library name: Sample 10


title: 499-3.HTO.37636.rs41401

description: Library name: 41401

value: Bone marrow,MesLN,PLN,Spleen


title: HEK293T cells, ANXA4-targeting paCas13d, post-illumination, rep1

description:
Library name: Sample4
ANXA4-targeting paCas13d, replicate 1
B1


title: scRNA-seq of mouse lung tissue (Group A)

description:
Library name: WTA_A
Raw fastq files of mouse lung scRNA-seq, Group A.

value: Smoking


title: 499-2.TCR.37374.rs41400

description: Library name: 41400


title: JGL3

institute: 江苏康缘药业股份有限公司

description: Library name: Sample 9

value: synovium


title: HEK293T cells, non-targeting control, post-illumination, rep2

description:
Library name: Sample2
non-targeting control, replicate 2
A2

value: transfected with non-targeting control paCas13d


title: JGL2

institute: 江苏康缘药业股份有限公司

description: Library name: Sample 8

value: wild type


title: TCR-seq of mouse lung tissue (Group C)

description:
Library name: TCR_C
Raw fastq files of mouse lung TCR-seq, Group C.

value: T cells


title: HEK293T cells, non-targeting control, post-illumination, rep1

description:
Library name: Sample1
non-targeting control, replicate 1
A1


title: JGL1

institute: 江苏康缘药业股份有限公司

description: Library name: Sample 7


title: 499-1.HTO.SamplePool.rs41393

description: Library name: 41393

value: PBMC


title: Hashtag reads of mouse lung tissue (Group C)

description:
Library name: Tag_C
Raw fastq files of mouse lung Tag-seq, Group C.


title: Female Down syndrome,organoid

description: Library name: D2-12

data_processing:
Raw base calls were demultiplexed to FASTQ files.Reads were aligned and quantified using 10x Genomics Cell Ranger (cellranger count) with default parameters unless otherwise stated. --include-introns=true, --chemistry=auto (Single Cell 3' v4), and BAM file generation enabled. UMI counting and gene-barcode matrix generation were performed by Cell Ranger(8.0.0).
Assembly: GRCh38,Ensembl release 104
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Human fetal brain tissue (24 GW) or organoid (2.5 months culture) are minced and homogenized using a Dounce homogenizer on ice, then washed and filtered through a 40 μm mesh to generate a clean nuclear suspension ready for the 10x Genomics Chromium platform.
snRNA seq libraries were prepared using the 10× Genomics Chromium Controller and Chromium Single Cell 3′ V3.1 reagent kit (10× Genomics, Pleasanton, USA). Isolated nuclei were adjusted to a concentration of 1000 nuclei per uL and loaded onto the Chromium chip to generate single-nucleus Gel Bead-In-Emulsions (GEMs). Reverse transcription was performed within GEMs, followed by GEM disruption and recovery of barcoded cDNA, which was then purified and amplified. The amplified cDNA was fragmented, a tailed, adaptor ligated, and further enriched by index PCR. Library concentration was determined using the Qubit High Sensitivity DNA assay (Thermo Fisher Scientific, USA), and fragment size distribution was assessed with a High Sensitivity DNA chip on a 2100 Bioanalyzer (Agilent, USA). All libraries were sequenced on a NovaSeq 6000 platform (Illumina, USA) using a 150 bp paired end configuration.

value: brain

value: single nucleus

value: Trisomy 21


title: TCR-seq of mouse lung tissue (Group A)

description:
Library name: TCR_A
Raw fastq files of mouse lung TCR-seq, Group A.

value: Lung


title: HEK293T cells, non-targeting control, post-illumination, rep3

description:
Library name: Sample3
non-targeting control, replicate 3
A3

value: human embryonic kidney cells


title: Hashtag reads of mouse lung tissue (Group B)

description:
Library name: Tag_B
Raw fastq files of mouse lung Tag-seq, Group B.

value: Lung cells

value: Wild type


title: Model3

institute: 江苏康缘药业股份有限公司

description: Library name: Sample 6


title: S10D-BDL-CKI-Alb-Cre-DOX-2

city: Shanghai

first: Tao

last: Le

address: LANXI ROAD 164

institute: Shanghai University of traditional Chinese Medicine

description: Library name: SAMPLES5

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence / low - quality sequence using CLC genomic benchwork ( parameter - Quality limit :0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork ( parameters - mismath cost :2 insertion cost :3 deletion cost :3 length fraction :0.8 similarity fraction :0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab - delimited text file includes raw counts for each Sample
Supplementary files format and content: Csv files include FPKM values for each Sample

source_name: liver

growth_protocol: BucheKI/KI-Hep mice were housed in a room at 25℃ with a 12-hour lingh/dark cycle and understricted access to chow food and water

extract_protocol:
RNA was harvested using Rneasy mini plus kit ( Qiagen ).1.3 ug of total RNA was used for the construction of sequencing libraries
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: liver

value: BucheKI/KI-Hep

tag: sample group

value: BDL treatment


title: S10D-BDL-CKI-Alb-Cre-DOX-3

description: Library name: SAMPLES6


title: Hashtag reads of mouse lung tissue (Group A)

description:
Library name: Tag_A
Raw fastq files of mouse lung Tag-seq, Group A.


title: Model2

institute: 江苏康缘药业股份有限公司

description: Library name: Sample 5


title: Normal, CD45+ depleted, scRNA-seq

city: Ann Arbor

first: Lu

last: Lu

state: MI

address: 100 Washtenaw Ave.

department: Department of Computational Medicine and Bioinformatics

institute: University of Michigan, Ann Arbor

description: 10X Genomics

data_processing:
The Cell Ranger ARC pipeline (verison 6.0.1 for non-delpelted samples and version 6.1.2 for depleted samples) with default parameter settings was used to process the raw Chromium Single Cell Gene Expression sequencing data. During alignment steps, reads were mapped to the human reference genome (GRCh38) provided by 10x Genomics.
Assembly: GRCh38
Supplementary files format and content: Cell Ranger output files: filtered_feature_bc_matrix.h5

extract_protocol:
Representative tissue sections from small airway regions were excised using dissection scissors, manually minced, then placed into a digestion solution containing 1mg/mL Collagenase A (Sigma-Aldrich), 1U/mg/mL Elastase (Worthington), and 0.1mg/mL DNase I (Thermo Fisher) in serum-free 1X high-glucose DMEM. Solutions were incubated for 45min-1hr at 37C in a dry incubator on an end-to-end rotator, mechanically disrupted, and incubated a second time for another 15-30min. Cell suspensions were then filtered through 100um strainers and pelleted by centrifugation at 400xg for 10min. After aspiration of digestion solution and resuspension, cells were counted and either frozen or taken for CD45+ depletion.
After initial thawing of frozen bullets of cells on ice, cells were diluted into chilled 1X DMEM supplemented with 10% FBS (Avator), spun down at 400xg for 5min, then resuspended in PBS at a density of 1000 cells/uL and kept on ice prior to submission. A small aliquot of cells was taken at time of submission to monitor cell death. Samples with >70% viability were submitted for 3’ single-cell RNA, taking 10,000 target cells from each sample with a sequencing depth of 50,000 reads/cell.


title: BCR-seq of mouse lung tissue (Group C)

description:
Library name: BCR_C
Raw fastq files of mouse lung BCR-seq, Group C, longer cessation.

value: B cells

value: Smoking cessation (longer)


title: CLAD, CD45+ depleted, scRNA-seq

description: 10X Genomics


title: Model1

institute: 江苏康缘药业股份有限公司

description: Library name: Sample 4

value: synovium


title: TCR-seq of mouse lung tissue (Group B)

description:
Library name: TCR_B
Raw fastq files of mouse lung TCR-seq, Group B.

value: Smoking cessation


title: Sham3

institute: 江苏康缘药业股份有限公司

description: Library name: Sample 3

value: wild type


title: S10D-BDL-CKI-Alb-Cre-DOX-1

description: Library name: SAMPLES4


title: 499-2.HTO.37374.rs41397

description: Library name: 41397

value: Bone marrow,MesLN,PLN,Spleen


title: Normal replicate 2, Non-depleted, scRNA-seq

description: 10X Genomics


title: CLAD, Non-depleted, scRNA-seq

description: 10X Genomics


title: S10D-BDL-CKI-Alb-Cre-PBS-3

description: Library name: SAMPLES3


title: S10D-BDL-CKI-Alb-Cre-PBS-2

description: Library name: SAMPLES2


title: 499-1.TCR.SamplePool.rs41396

description: Library name: 41396

value: PBMC


title: Sham1

institute: 江苏康缘药业股份有限公司

description: Library name: Sample 1


title: BCR-seq of mouse lung tissue (Group B)

description:
Library name: BCR_B
Raw fastq files of mouse lung BCR-seq, Group B, smoking cessation model.


title: Normal replicate 1, Non-depleted, scRNA-seq

description: 10X Genomics


title: S10D-BDL-CKI-Alb-Cre-PBS-1

description: Library name: SAMPLES1


title: HDI+YF replicate 2

status: Public on Mar 28 2026

city: Suzhou

first: Hang

last: Ruan

state: Jiangsu

address: 199 Ren'ai Road

department: IBMS

institute: Soochow University

data_processing:
The samples were sequenced using BGISEQ platform with PE 100 generating about 6.56Gb bases per sample.
The sequencing data was filtered with SOAPnuke (v1.5.2) by removing reads containing sequencing adapter, reads whose low-quality base ratio is more than 20%, and reads whose unknown base ('N' base) ratio is more than 5%.
The resultant clean reads were obtained and stored in FASTQ format and mapped to the reference genome GRCm38.p6 using HISAT2 (v2.0.4). Bowtie2 (v2.2.5) was applied to align the clean reads to the reference coding gene set, and the expression level of genes was calculated with RSEM (v1.2.12).
The differential expression analysis was performed using the DESeq2 (v1.4.5). GO and KEGG enrichment analysis of annotated different expressed genes was performed by DAVID Bioinformatics Resources 6.7.
Assembly: GRCm38.p6
Supplementary files format and content: tab-delimited text file includes raw counts and normalized gene expression for each Sample

extract_protocol:
The total RNA extraction from all the three groups of treated AML12 cells (HDI, YF and YF+HDI) was performed using a TRIzol™ Reagent (Thermo Fisher Scientific, Waltham, MA, USA), following the protocol described by the manufacturer.
BGISEQ platform with PE 100 generating about 6.56Gb bases per sample

value: hepatocytes


title: Female Control,organoid

description: Library name: A93

value: brain

value: single nucleus

value: Euploid


title: BCR-seq of mouse lung tissue (Group A)

description:
Library name: BCR_A
Raw fastq files of mouse lung BCR-seq, Group A, smoking model.

value: Lung

value: Smoking


title: HDI+YF replicate 3


title: Sham2

institute: 江苏康缘药业股份有限公司

description: Library name: Sample 2


title: YF replicate 2


title: YF replicate 3


title: control replicate 2


title: HDI replicate 1


title: HDI replicate 2


title: YF replicate 1


title: control replicate 1


title: control replicate 3


title: NS1mt_Vector_r2

city: Yinchuan

first: Chuchu

last: Tian

address: 1160 Victory Street

institute: Ningxia Medical University

description: Library name: sample 20

data_processing:
Sample 1-21: Dual-indexed 150-bp paired-end sequencing was conducted using combinatorial probe-anchor synthesis (cPAS) technology (DNBSEQ platform, BGI). Raw reads were processed with SOAPnuke to remove low-quality bases and adapter sequences. Clean reads were aligned to the human reference genome (GRCh38/hg38) using HISAT2, and gene expression levels were quantified via RSEM (v1.3.1) with FPKM normalization. Differential expression analysis was performed using DESeq2 (v1.4.5) with thresholds of |log2FC| ≥ 1 and adjusted Q-value ≤ 0.05. Enriched KEGG pathways were identified by hypergeometric testing (Phyper) and considered significant at an FDR-corrected Q-value ≤ 0.05. All analyses were executed on the BGI Tom multi-omics platform (https://biosys.bgi.com).
Assembly: GRCh38/hg38,and HBoV1 genome (GenBank number: U22521.1 or JQ804832.1)
Supplementary files format and content: Sample 1-21: Excel files contain FPKM.

source_name: kidney

growth_protocol: HEK293T cells (ATCC CRL-11268) were cultured in Dulbecco's Modified Eagle Medium (DMEM, Gibco) supplemented with 10% fetal bovine serum (FBS, Gibco) at 37 ℃ in a 5% CO2 environment.

extract_protocol:
Total RNAs were extracted using TRIzol Reagent (Invitrogen, cat. NO 15596026）
Sample 1-21: Briefly, mRNA was enriched using oligo-dT magnetic beads, fragmented, and subjected to quality control. First- and second-strand cDNA synthesis was followed by adenylation of 3′ ends and adapter ligation. For sequencing, circular DNA was amplified into DNA nanoballs (DNBs) via rolling circle amplification and loaded onto patterned nanoarrays.

treatment_protocol: RNA-seq analysis was performed on total RNA extracted from 293T cells transfected with wild-type (WT) HBoV1, NS1-mt, or NS1-mt supplemented with NS1, NS2, NS1-70, or an empty vector respectively, at 48 hours post-transfection.

value: kidney


title: NS1mt_Vector_r3

description: Library name: sample 21


title: NS1mt_NS1_70_r3

description: Library name: sample 18


title: NS1mt_NS2_r3

description: Library name: sample 15


title: NS1mt_Vector_r1

description: Library name: sample 19


title: NS1mt_NS1_70_r1

description: Library name: sample 16


title: NS1mt_NS2_r2

description: Library name: sample 14


title: NS1mt_NS1_70_r2

description: Library name: sample 17


title: HDI replicate 3

value: liver


title: NS1mt_NS1_r3

description: Library name: sample 12


title: HDI+YF replicate 1


title: NS1mt_NS1_r2

description: Library name: sample 11


title: NS1mt_NS1_r1

description: Library name: sample 10


title: NS1mt_NS2_r1

description: Library name: sample 13


title: NS1mt_r3

description: Library name: sample 9


title: NS1mt_r2

description: Library name: sample 8


title: NS1mt_r1

description: Library name: sample 7


title: WT_r3

description: Library name: sample 6


title: Mock_r3

description: Library name: sample 3


title: Mock_r1

description: Library name: sample 1


title: WT_r2

description: Library name: sample 5


title: WT_r1

description: Library name: sample 4


title: IMR90-4 FKD bulkseq Day30_3

city: Nanjing

first: Xu

last: Zhang

address: Longmian Avenue 101

institute: Nanjing Medical University

description: Library name: bulk_KD_3

data_processing:
Alignment, barcode filtering, and counting of unique molecular identifiers (UMIs) were executed using Capitalbiotech Singlecell V1.1.0 software, generating a feature-barcode matrix for downstream analysis.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: brain organoid

extract_protocol:
Day 30 (D30) organoids derived from the IMR90-4 FCT and FKD cell lines were processed for single-cell RNA sequencing (scRNA-seq). For organoid dissociation, tissues were incubated with 1 mL of TrypLE (Life Technologies, Thermo Fisher Scientific) in 1.5 mL Eppendorf (EP) tubes at 37 °C, for incubation durations of 10 minutes (for D6 embryoid bodies [EBs]), 35 minutes (for D30 organoids), or 50 minutes (for D60 or D100 organoids). Gentle agitation was applied every 10 minutes during incubation.
Single-cell RNA-seq libraries were constructed using the sCelluFlu-A Single Cell Transcriptome Library Kit V1.2 following the manufacturer’s protocols. The libraries were sequenced on an MGI DNBSEQ-T7 sequencer with a paired-end 150 bp (PE150) strategy, ensuring a minimum sequencing depth of 20,000 reads per cell.

value: brain organoid

value: cells with neural lineage

value: FABP7 knockdown


title: IMR90-4 FKD bulkseq Day30_1

description: Library name: bulk_KD_1


title: Mock_r2

description: Library name: sample 2


title: IMR90-4 FCT bulkseq Day30_3

description: Library name: bulk_Ctrl_3

value: WT


title: IMR90-4 FCT bulkseq Day30_1

description: Library name: bulk_Ctrl_1


title: IMR90-4 sc_FKD Day30

description: Library name: sc_FKD


title: Papillary renal cancer cells U345, Dasatinib Treated, Rep3

city: BETHESDA

first: Ramaprasad

last: Srinivasan

state: MD

address: 1-W-5888, 10 center drive

department: Urologic Oncology Branch

institute: National Cancer Institute – NIH

description: Library name: U345_DAS_3

data_processing:
Basecalling was performed using RTA version 1.18.64.
Demultiplexing and FASTQ generation was performed using bcl2fastq (version 2.17) allowing 1 mismatch.
Trimming of adapters and low-quality bases was performed using CutAdapt (v.1.16).
Mapping to the human genome (hg38) was performed using STAR 2.5.2b. The following parameters were used: "--outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMstrandField None --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.3 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 clip3pAdapterSeq - --readFilesCommand zcat --runThreadN 32 --outSAMtype BAM Unsorted --chimSegmentMin 20"
Gene-level expression quantification was performed using RSEM (version 1.3.0).
Assembly: hg38
Supplementary files format and content: Tab-delimited text file of raw counts

source_name: Kidney

growth_protocol: The cell lines were cultured in high glucose DMEM containing pyruvate, glutamine, and supplemented with 10% FBS.

extract_protocol:
High-quality RNA was harvested from treated and control cell lines using Qiagen kit. The quality of total RNA was evaluated using the Agilent RNA Screen 2200 Tape Station system (G2964AA). Only samples with a 28S/18S ribosomal peak ratio of 1.8–2.0 and a RIN number >8.0 were considered suitable for sequencing.
RNA-seq libraries were prepared using Illumina® TruSeq mRNA Prep Kit RS-122-2101 and were sequenced using Illumina® HiSeq3000/4000 to obtain 76-bp paired-end reads. The sequencing depth for each sample was >20 million reads.

treatment_protocol: PRCC cells were treated with dasatinib (25nM) or vehicle in 6-well plates and RNA was isolated from these cells after 48 hours of treatment

value: Kidney

value: metastatic renal cancer cells derived from patient pleural effusion

value: germline MET mutation  (p.H1112R)

value: Treated with Dasatinib


title: Papillary renal cancer cells U342, Dasatinib Treated, Rep1

description: Library name: U342_DAS_1

value: metastatic renal cancer cells derived from patient ascites

value: wild type MET gene with gain of chromosome 7


title: Papillary renal cancer cells U345, Dasatinib Treated, Rep2

description: Library name: U345_DAS_2


title: Papillary renal cancer cells U345,Dasatinib Treated, Rep1

description: Library name: U345_DAS_1


title: P7_Exp_OHC_55

city: Beijing

first: Zhiyong

last: Liu

address: Kexueyuan Road

institute: National Institute of Biological Sciences, Beijing

description: Library name: Sample 162

data_processing:
Reads were mapped to the mouse reference genome (mm10) with high quality, using Hisat2 (v2.2.1) with default parameters.
The resulting alignment files were converted, sorted, and indexed using Samtools.
Raw counts were calculated by featureCounts (v2.0.1) software.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Cochlear

extract_protocol:
Cochlear samples were incubated in choline chloride solution containing 20 U/mL papain (Cat# LK003178, Worthington) and 100 U/mL DNase I (Cat# LK003172, Worthington) for 20 min at 37°C, and this was followed by digestion with a protease (Cat# P5147, Sigma; 1 mg/mL) and dispase (Cat# LS02104, Worthington; 1 mg/mL) for 20 min at 25°C. The components of the choline chloride solution contained 92 mM choline chloride, 2.5 mM KCl, 1.2 mM NaH2PO4, 30 mM NaHCO3, 20 mM HEPES, 25 mM glucose, 5 mM sodium ascorbate, 2 mM thiourea, 3 mM sodium pyruvate, 10 mM MgSO4.7H2O, 0.5 mM CaCl2.2H2O, and 12 mM N-acetyl-L-cysteine. Next, the post-digested cochlear samples were gently triturated using fire-polished glass Pasteur pipettes (13-678-20b; Fisher) with 4 different pore sizes (largest size the first, and smallest one the last). The picked endogenous IHCs and iOHCs were immediately subjected to reverse-transcription and cDNA amplification using a Smart-Seq HT kit (Cat# 634437, Takara).
Smart-Seq HT kit (Cat# 634437, Takara) was used to generate full-length cDNA. The cDNAs (1 ng each) were tagmented using a TruePrep DNA Library Prep Kit V2 for Illumina (Cat# TD503-02, Vazyme) and a TruePrep Index Kit V2 for Illumina (Cat# TD202, Vazyme).

value: Cochlear


title: P7_Exp_OHC_53

description: Library name: Sample 160


title: P7_Exp_OHC_54

description: Library name: Sample 161


title: IMR90-4 FCT bulkseq Day30_2

description: Library name: bulk_Ctrl_2


title: P7_Exp_OHC_52

description: Library name: Sample 159


title: P7_Exp_OHC_50

description: Library name: Sample 157


title: P7_Exp_OHC_49

description: Library name: Sample 156


title: IMR90-4 FKD bulkseq Day30_2

description: Library name: bulk_KD_2


title: IMR90-4 sc_FCT Day30

description: Library name: sc_FCT


title: Papillary renal cancer cells U342, Dasatinib Treated, Rep3

description: Library name: U342_DAS_3


title: P7_Exp_OHC_48

description: Library name: Sample 155


title: P7_Exp_OHC_41

description: Library name: Sample 148


title: P7_Exp_OHC_56

description: Library name: Sample 163


title: P7_Exp_OHC_44

description: Library name: Sample 151


title: P7_Exp_OHC_47

description: Library name: Sample 154


title: P7_Exp_OHC_38

description: Library name: Sample 145


title: P7_Exp_OHC_45

description: Library name: Sample 152


title: P7_Exp_OHC_40

description: Library name: Sample 147


title: P7_Exp_OHC_43

description: Library name: Sample 150


title: P7_Exp_OHC_39

description: Library name: Sample 146


title: P7_Exp_OHC_37

description: Library name: Sample 144


title: P7_Exp_OHC_51

description: Library name: Sample 158


title: P7_Exp_OHC_32

description: Library name: Sample 139


title: P7_Exp_OHC_42

description: Library name: Sample 149


title: P7_Exp_OHC_31

description: Library name: Sample 138


title: P7_Exp_OHC_35

description: Library name: Sample 142


title: P7_Exp_OHC_36

description: Library name: Sample 143


title: P7_Exp_OHC_33

description: Library name: Sample 140


title: Papillary renal cancer cells U342, Dasatinib Treated, Rep2

description: Library name: U342_DAS_2


title: P7_Exp_OHC_46

description: Library name: Sample 153


title: P7_Exp_OHC_28

description: Library name: Sample 135


title: P7_Exp_OHC_29

description: Library name: Sample 136


title: P7_Exp_OHC_23

description: Library name: Sample 130


title: P7_Exp_OHC_20

description: Library name: Sample 127


title: P7_Exp_OHC_27

description: Library name: Sample 134


title: P7_Exp_OHC_22

description: Library name: Sample 129


title: P7_Exp_OHC_30

description: Library name: Sample 137


title: P7_Exp_OHC_15

description: Library name: Sample 122


title: P7_Exp_OHC_26

description: Library name: Sample 133


title: P7_Exp_OHC_17

description: Library name: Sample 124


title: P7_Exp_OHC_16

description: Library name: Sample 123


title: P7_Exp_OHC_24

description: Library name: Sample 131


title: P7_Exp_OHC_34

description: Library name: Sample 141


title: P7_Exp_OHC_13

description: Library name: Sample 120


title: P7_Exp_OHC_25

description: Library name: Sample 132


title: P7_Exp_OHC_21

description: Library name: Sample 128


title: P7_Exp_OHC_18

description: Library name: Sample 125


title: P7_Exp_OHC_11

description: Library name: Sample 118


title: P7_Exp_OHC_14

description: Library name: Sample 121


title: P7_Exp_OHC_9

description: Library name: Sample 116


title: P7_Exp_OHC_10

description: Library name: Sample 117


title: P7_Exp_OHC_12

description: Library name: Sample 119


title: P7_Exp_OHC_19

description: Library name: Sample 126


title: P7_Exp_OHC_7

description: Library name: Sample 114


title: P7_Exp_OHC_3

description: Library name: Sample 110


title: P7_Exp_OHC_6

description: Library name: Sample 113


title: P7_Exp_OHC_2

description: Library name: Sample 109


title: P7_Exp_OHC_4

description: Library name: Sample 111


title: P7_Exp_OHC_1

description: Library name: Sample 108


title: P7_Exp_IHC_24

description: Library name: Sample 105


title: P7_Exp_IHC_25

description: Library name: Sample 106


title: P7_Exp_IHC_22

description: Library name: Sample 103


title: P7_Exp_IHC_20

description: Library name: Sample 101


title: P7_Exp_IHC_23

description: Library name: Sample 104


title: P7_Exp_IHC_21

description: Library name: Sample 102


title: P7_Exp_IHC_18

description: Library name: Sample 99


title: P7_Exp_IHC_11

description: Library name: Sample 92


title: P7_Exp_IHC_19

description: Library name: Sample 100


title: P7_Exp_IHC_15

description: Library name: Sample 96


title: P7_Exp_OHC_5

description: Library name: Sample 112


title: P7_Exp_IHC_12

description: Library name: Sample 93


title: P7_Exp_IHC_9

description: Library name: Sample 90


title: P7_Exp_IHC_13

description: Library name: Sample 94


title: P7_Exp_IHC_10

description: Library name: Sample 91


title: P7_Exp_IHC_16

description: Library name: Sample 97


title: P7_Exp_IHC_14

description: Library name: Sample 95


title: P7_Exp_IHC_26

description: Library name: Sample 107


title: P7_Exp_IHC_8

description: Library name: Sample 89


title: P7_Exp_IHC_6

description: Library name: Sample 87


title: P7_Exp_IHC_7

description: Library name: Sample 88


title: P7_Exp_IHC_5

description: Library name: Sample 86


title: P7_Exp_IHC_4

description: Library name: Sample 85


title: P7_Exp_IHC_3

description: Library name: Sample 84


title: P7_Exp_IHC_1

description: Library name: Sample 82


title: P7_Exp_IHC_17

description: Library name: Sample 98


title: P7_Ctrl_OHC_43

description: Library name: Sample 81


title: P7_Exp_IHC_2

description: Library name: Sample 83


title: P7_Ctrl_OHC_42

description: Library name: Sample 80


title: P7_Ctrl_OHC_41

description: Library name: Sample 79


title: P7_Ctrl_OHC_39

description: Library name: Sample 77


title: P7_Ctrl_OHC_40

description: Library name: Sample 78


title: P7_Exp_OHC_8

description: Library name: Sample 115


title: P7_Ctrl_OHC_36

description: Library name: Sample 74


title: P7_Ctrl_OHC_37

description: Library name: Sample 75


title: P7_Ctrl_OHC_29

description: Library name: Sample 67


title: P7_Ctrl_OHC_30

description: Library name: Sample 68


title: P7_Ctrl_OHC_32

description: Library name: Sample 70


title: P7_Ctrl_OHC_31

description: Library name: Sample 69


title: P7_Ctrl_OHC_38

description: Library name: Sample 76


title: P7_Ctrl_OHC_34

description: Library name: Sample 72


title: High affinity sub-population

city: Be'er Sheva

first: Noam

last: Tzuri

address: David Ben Gurion Blvd 1

institute: Ben Gurion University

description:
Library name: HI
Column name in df_summary_raw.csv: count HI

library_source: other

data_processing:
Paired-end reads from the NGS experiments were merged and their quality scores were calculated in the FastQC tool
In the Python script, the sequences were aligned, and sequences were too short, containing extra mutations at nonrandomized positions  were filtered out. Read cound for each remaining variant was calculated
Assembly: bovine pancreatic trypsin inhibitor (BPTI) reference sequence: RPDFCLEPPYTGPCKARIIRYFYNAKAGLCQTFVYGGCRAKRNNFKSAEDCMRT
Supplementary files format and content: csv file contain read cound for each sample

molecule: other

organism: Saccharomyces cerevisiae

growth_protocol: The transformed yeast was grown in SDCAA selective medium (2% dextrose, 0.67% yeast nitrogen base, 0.5% Bacto casamino acids, 1.47% sodium citrate, and 0.429% citric acid monohydrate) overnight at 30°C.

extract_protocol:
The sorted BPTI library fractions (HI, WT, SL and LO affinity fructions) were isolated from the yeast cells using thePrepEase yeast plasmid isolation kit (Affymetrix, Santa Clara, CA) according to the manufacturer’s protocol.
The library was constructed based on the BPTI wild-type gene (PDB ID: 3OTJ), with randomization introduced at twelve positions located at the binding interface with chymotrypsin (T11, G12, P13, K15, A16, R17, I18, V34, Y35, G36, G37, and R39). Mutations were introduced using NNS degenerate codons (where N represents A, C, T, or G, and S represents C or G), encoding all possible amino acids at each position. The library was designed to include all combinations of double mutations across these positions and was divided into 66 sublibraries, each corresponding to a specific pair of positions. Libraries were generated using targeted PCR-based mutagenesis of the BPTI wild-type plasmid, followed by removal of template DNA, purification, and transformation into Escherichia coli. Individual sublibraries were validated and subsequently pooled in equal proportions. The pooled library was then transformed into Saccharomyces cerevisiae for yeast surface display, yielding approximately 6–7 × 10^4 transformants.


title: P7_Ctrl_OHC_35

description: Library name: Sample 73


title: SL affinity sub-population

description:
Library name: SL
Column name in df_summary_raw.csv: count SL


title: WT affinity sub-population

description:
Library name: WT
Column name in df_summary_raw.csv: count WT


title: P7_Ctrl_OHC_25

description: Library name: Sample 63


title: Presort library

description:
Library name: Pre
Column name in df_summary_raw.csv: count Presort


title: P7_Ctrl_OHC_24

description: Library name: Sample 62


title: Human LAA RNA-seq Low MNP burden (L8)

first: Yilin

last: Pan

address: Anzhen Road #2, Chaoyang District

institute: Beijing Anzhen Hospital

description:
Library name: L8
Left atrial appendage tissue collected intraoperatively before cardiopulmonary bypass. Group assignment based on tissue micro(nano)plastic burden quantified by Py-GC/MS.

data_processing:
Adapters/low-quality bases removed using fastp; quality metrics (Q20/Q30/GC) computed.
Paired-end reads were aligned to the human reference genome (GRCh38/hg38) using HISAT2 (v2.0.5) with splice-aware mapping and the corresponding gene annotation (GTF).
Aligned reads assembled with StringTie (v1.3.3b) in reference-guided mode.
Gene-level counts generated using featureCounts (v1.5.0-p3).
Gene-level read counts were used for downstream differential expression analyses; FPKM values were generated only for descriptive purposes/visualization.
Assembly: GRCh38 (hg38).
Supplementary files format and content: Processed data include (i) gene-level raw count table and (ii) gene-level FPKM table (tab-delimited text). Each table contains columns for H1–H9 and L1–L9

source_name: left atrial appendage

growth_protocol: Not applicable (human tissue; no growth protocol).

extract_protocol:
Total RNA was extracted from left atrial appendage tissue using TRIzol reagent (Invitrogen) according to the manufacturer’s instructions. RNA integrity was assessed using an Agilent Bioanalyzer 2100.
mRNA-seq libraries were prepared by Novogene using poly(A)+ mRNA enrichment with oligo(dT) beads, RNA fragmentation, cDNA synthesis, end repair/A-tailing, adapter ligation, size selection, and PCR amplification. Libraries were sequenced on an Illumina platform as paired-end reads (instrument model/read configuration as reported in the raw sequencing metadata).

treatment_protocol: Not applicable (observational study; no experimental treatment prior to collection; groups defined by myocardial micro(nano)plastic burden).

value: left atrial appendage

value: Low MNP burden

value: Novogene


title: P7_Ctrl_OHC_33

description: Library name: Sample 71


title: LO affinity sub-population

description:
Library name: LO
Column name in df_summary_raw.csv: count LO


title: P7_Ctrl_OHC_28

description: Library name: Sample 66


title: Human LAA RNA-seq Low MNP burden (L9)

description:
Library name: L9
Left atrial appendage tissue collected intraoperatively before cardiopulmonary bypass. Group assignment based on tissue micro(nano)plastic burden quantified by Py-GC/MS.


title: P7_Ctrl_OHC_23

description: Library name: Sample 61


title: Human LAA RNA-seq Low MNP burden (L7)

description:
Library name: L7
Left atrial appendage tissue collected intraoperatively before cardiopulmonary bypass. Group assignment based on tissue micro(nano)plastic burden quantified by Py-GC/MS.


title: P7_Ctrl_OHC_21

description: Library name: Sample 59


title: Human LAA RNA-seq Low MNP burden (L6)

description:
Library name: L6
Left atrial appendage tissue collected intraoperatively before cardiopulmonary bypass. Group assignment based on tissue micro(nano)plastic burden quantified by Py-GC/MS.


title: Human LAA RNA-seq Low MNP burden (L4)

description:
Library name: L4
Left atrial appendage tissue collected intraoperatively before cardiopulmonary bypass. Group assignment based on tissue micro(nano)plastic burden quantified by Py-GC/MS.


title: Human LAA RNA-seq Low MNP burden (L5)

description:
Library name: L5
Left atrial appendage tissue collected intraoperatively before cardiopulmonary bypass. Group assignment based on tissue micro(nano)plastic burden quantified by Py-GC/MS.


title: P7_Ctrl_OHC_20

description: Library name: Sample 58


title: P7_Ctrl_OHC_22

description: Library name: Sample 60


title: P7_Ctrl_OHC_26

description: Library name: Sample 64


title: Human LAA RNA-seq High MNP burden (H8)

description:
Library name: H8
Left atrial appendage tissue collected intraoperatively before cardiopulmonary bypass. Group assignment based on tissue micro(nano)plastic burden quantified by Py-GC/MS.

value: High MNP burden


title: Human LAA RNA-seq Low MNP burden (L1)

description:
Library name: L1
Left atrial appendage tissue collected intraoperatively before cardiopulmonary bypass. Group assignment based on tissue micro(nano)plastic burden quantified by Py-GC/MS.


title: P7_Ctrl_OHC_15

description: Library name: Sample 53


title: P7_Ctrl_OHC_13

description: Library name: Sample 51


title: P7_Ctrl_OHC_17

description: Library name: Sample 55


title: Human LAA RNA-seq Low MNP burden (L3)

description:
Library name: L3
Left atrial appendage tissue collected intraoperatively before cardiopulmonary bypass. Group assignment based on tissue micro(nano)plastic burden quantified by Py-GC/MS.


title: P7_Ctrl_OHC_19

description: Library name: Sample 57


title: Human LAA RNA-seq Low MNP burden (L2)

description:
Library name: L2
Left atrial appendage tissue collected intraoperatively before cardiopulmonary bypass. Group assignment based on tissue micro(nano)plastic burden quantified by Py-GC/MS.


title: P7_Ctrl_OHC_18

description: Library name: Sample 56


title: Formative ESC, Kmt2cKO; Kmt2dKO, P300, rep2

city: San Francisco

first: Robert

last: Blelloch

state: CA

address: 35 Medical Center Way

institute: UCSF

description:
Library name: dKO_form_P300_rep2
P300

library_source: genomic

data_processing:
Fastq files for CUT&RUN samples were processed using Nextflow and the nf-core CUT&RUN pipeline v3.1. In brief, adapters were trimmed using Trim Galore. Paired-end alignment was performed using Bowtie2 and peaks were called using SEACR with a peak threshold of 0.05 using spike in calibration performed using the E.coli genome K12.
Assembly: mm10
Supplementary files format and content: bigWig files generated from merging replicates together post processing and used as input into all metagene analyses
Library strategy: CUT&Tag

molecule: genomic DNA

growth_protocol: Mouse ESCs were cultured in Knockout DMEM (Thermo Fisher, CAT#10829018) supplemented with 15% FBS, L-Glutamine, Penicillin/Streptomycin, NEAA, LIF (1000U/mL), and 2i (1uM MEK inhibitor PD0325901 and 3uM GSK3 inhibitor CHIR99021). GRHL2-ERT proof of principle tests were conducted in WT V6.5 ESCs. Clones used to conduct RNA-seq are derived from WT R1 ESCs. CKO ESCs (KMT2C-/-; KMT2Dfl/fl) and KMT2C/D dKO (KMT2C-/-; KMT2D-/-) are derived from a mixed background of C57BL/6J and 129 strains. The plasmid expressing GRHL2-ERT from the hPGK promoter was integrated into CKO and dKO genomes using cotransfection with a transient plasmid expressing PiggyBac transposase. Transfected cells were treated with blasticidin to select for GRHL2-ERT integration and plated at single cell density in 10cm2 plates to isolate and characterize colonies. Formative cells were generated by removal of LIF and 2i. Briefly, 5e4 ESCs were plated per well of a 6 well plate on day −1 in LIF+2i media. To initiate differentiation, LIF and 2i were removed 24 hours after seeding (Day 0). Formative cells were collected on day 3 of differentiation, 63 hours after removal of LIF and 2i. To overcome proliferation defects 7.5e4 KMT2C/D dKO cells were plated per well of a 6 well. Naive cells were passaged and staged appropriately for simultaneous harvest. Lines consistently tested negative for mycoplasm.

extract_protocol:
Following treatment or differentiations, cells were harvested using trypsinization and normalized cell counts were used as input into CUT&Tag protocols
CUT&TAG was conducted using the protocol from Kaya-Okur et al. 2020 with the following modifications: freshly trypsinized cells were bound to Concanavalin A beads at a ratio of 2e5 cells/7ul beads in CR wash at room temp. We used 2e5 cells as input per sample. Bead-bound cells were then incubated rotating overnight at 4C in CT Antibody buffer (CR Wash with 0.05% Digitonin, 2mM EDTA, 1mg/mL BSA) containing primary antibody. We used the following primary antibodies for CUT&TAG: 1:100 Rabbit anti-HA (Abcam, abxxx), 1:100 1:100 Rabbit anti-H3K4me1 (Abcam, ab8895), 1:100 Rabbit anti-H3K4me2 (Abcam, abxxx), 1:100 Rabbit anti-H3K27ac (Abcam, ab4729), 1:100 Rabbit anti-KAT2B (Abcam, ab), 1:100 Rabbit anti-H3.3 (Active Motif, xxxx), and 1:100 Rabbit IgG isotype control (Abcam, ab171870). After primary, samples were washed 3 times for 5 minutes each using CR Dig-wash buffer and resuspended in 1:100 secondary antibody (Guinea pig anti-rabbit, Antibodies Online #ABIN101961) in CR Dig-wash buffer at 4C for 1 hour rotating at 4C. Samples were then incubated for 1 hour at 4C with 50ul of approximately 25nM homemade pA-Tn5 in CT Dig300 wash buffer (20mM HEPES, 300mM NaCl, 0.01% Digitonin, 0.5mM Spermidine with Roche cOmplete protease inhibitors added). Recombinant Tn5 was purified and loaded with adapters as previously described (Kaya-Okur et al. 2019). After Tn5 incubation, samples were washed 3 times for 5 minutes each with CT Dig300 wash buffer. Tagmentation was then initiated for 1hr at 37C in a thermocycler by adding MgCl2 to 10mM final concentration in 50uL volume. The tagmentation reaction was quenched immediately afterwards by adding 1.6ul of 0.5M EDTA, 1ul of 10mg/mL Proteinase K, and 1ul of 5% SDS. Samples were then incubated at 55C for 2 hours in a thermocycler to denature Tn5 and solubilize tagmented chromatin. After incubation, samples were magnetized and the supernatant was transferred to new wells where SPRI bead purification was performed using homemade beads to select all DNA fragment lengths larger than 100bp. Samples were eluted in 0.1X TE and approximately half of each sample was used for library preparation using NEBNext HIFI Polymerase with custom indices synthesized by IDT. An appropriate number of cycles for each target was chosen to prevent overamplification bias. After amplification, libraries were purified with 1.2x homemade SPRI beads to select for fragments >250bp and eluted in 0.1X TE. Quality and concentration of libraries were determined by an Agilent 4200 Tapestation with D1000 reagents before pooling for sequencing. CUT&TAG samples were processed similarly to CUT&RUN samples using the same Nextflow pipeline.

value: Formative ESC

value: Kmt2cKO; Kmt2dKO

value: 63 hours L2i withdrawal

tag: antibody


title: P7_Ctrl_OHC_27

description: Library name: Sample 65


title: Naive ESC, Kmt2cKO; Kmt2dKO, P300, rep1

description:
Library name: dKO_naive_P300_rep1
P300

value: Naive ESC


title: P7_Ctrl_OHC_14

description: Library name: Sample 52


title: Formative ESC, Kmt2cKO; Kmt2dKO, P300, rep1

description:
Library name: dKO_form_P300_rep1
P300


title: Human LAA RNA-seq High MNP burden (H3)

description:
Library name: H3
Left atrial appendage tissue collected intraoperatively before cardiopulmonary bypass. Group assignment based on tissue micro(nano)plastic burden quantified by Py-GC/MS.


title: Human LAA RNA-seq High MNP burden (H7)

description:
Library name: H7
Left atrial appendage tissue collected intraoperatively before cardiopulmonary bypass. Group assignment based on tissue micro(nano)plastic burden quantified by Py-GC/MS.


title: Human LAA RNA-seq High MNP burden (H6)

description:
Library name: H6
Left atrial appendage tissue collected intraoperatively before cardiopulmonary bypass. Group assignment based on tissue micro(nano)plastic burden quantified by Py-GC/MS.


title: P7_Ctrl_OHC_11

description: Library name: Sample 49


title: Formative ESC, Kmt2cKO; Kmtd fl/fl, P300, rep1

description:
Library name: CKO_form_P300_rep1
P300

value: Kmt2cKO; Kmtd fl/fl


title: P7_Ctrl_OHC_10

description: Library name: Sample 48


title: P7_Ctrl_OHC_12

description: Library name: Sample 50


title: Human LAA RNA-seq High MNP burden (H9)

description:
Library name: H9
Left atrial appendage tissue collected intraoperatively before cardiopulmonary bypass. Group assignment based on tissue micro(nano)plastic burden quantified by Py-GC/MS.


title: Human LAA RNA-seq High MNP burden (H2)

description:
Library name: H2
Left atrial appendage tissue collected intraoperatively before cardiopulmonary bypass. Group assignment based on tissue micro(nano)plastic burden quantified by Py-GC/MS.


title: Naive ESC, Kmt2cKO; Kmtd fl/fl, P300, rep2

description:
Library name: CKO_naive_P300_rep2
P300


title: Formative ESC, Kmt2cKO; Kmt2dKO, H3K27ac, rep2

description:
Library name: dKO_form_H3K27ac_rep2
H3K27ac


title: Naive ESC, Kmt2cKO; Kmtd fl/fl, P300, rep1

description:
Library name: CKO_naive_P300_rep1
P300


title: Formative ESC, Kmt2cKO; Kmtd fl/fl, P300, rep2

description:
Library name: CKO_form_P300_rep2
P300


title: P7_Ctrl_OHC_16

description: Library name: Sample 54


title: Human LAA RNA-seq High MNP burden (H4)

description:
Library name: H4
Left atrial appendage tissue collected intraoperatively before cardiopulmonary bypass. Group assignment based on tissue micro(nano)plastic burden quantified by Py-GC/MS.


title: Human LAA RNA-seq High MNP burden (H1)

description:
Library name: H1
Left atrial appendage tissue collected intraoperatively before cardiopulmonary bypass. Group assignment based on tissue micro(nano)plastic burden quantified by Py-GC/MS.


title: P7_Ctrl_OHC_9

description: Library name: Sample 47


title: Formative ESC, Kmt2cKO; Kmtd fl/fl, H3K27ac, rep2

description:
Library name: CKO_form_H3K27ac_rep2
H3K27ac


title: Formative ESC, Kmt2cKO; Kmt2dKO, H3K27ac, rep1

description:
Library name: dKO_form_H3K27ac_rep1
H3K27ac


title: Naive ESC, Kmt2cKO; Kmt2dKO, P300, rep2

description:
Library name: dKO_naive_P300_rep2
P300


title: P7_Ctrl_OHC_8

description: Library name: Sample 46


title: Naive ESC, Kmt2cKO; Kmt2dKO, H3K27ac, rep2

description:
Library name: dKO_naive_H3K27ac_rep2
H3K27ac


title: Human LAA RNA-seq High MNP burden (H5)

description:
Library name: H5
Left atrial appendage tissue collected intraoperatively before cardiopulmonary bypass. Group assignment based on tissue micro(nano)plastic burden quantified by Py-GC/MS.


title: P7_Ctrl_OHC_7

description: Library name: Sample 45


title: P7_Ctrl_OHC_6

description: Library name: Sample 44


title: Formative ESC, Kmt2cKO; Kmtd fl/fl, H3K27ac, rep1

description:
Library name: CKO_form_H3K27ac_rep1
H3K27ac


title: Naive ESC, Kmt2cKO; Kmt2dKO, H3K27ac, rep1

description:
Library name: dKO_naive_H3K27ac_rep1
H3K27ac


title: Naive ESC, Kmt2cKO; Kmtd fl/fl, H3K27ac, rep1

description:
Library name: CKO_naive_H3K27ac_rep1
H3K27ac


title: Formative ESC, Kmt2cKO; Kmt2dKO, IgG control, rep2

description:
Library name: dKO_form_igg_rep2
IgG control

value: IgG control


title: Naive ESC, Kmt2cKO; Kmtd fl/fl, H3K27ac, rep2

description:
Library name: CKO_naive_H3K27ac_rep2
H3K27ac


title: P7_Ctrl_OHC_5

description: Library name: Sample 43


title: Naive ESC, Kmt2cKO; Kmt2dKO, IgG control, rep1

description:
Library name: dKO_naive_igg_rep1
IgG control


title: Spatial-Seq, Synovium, hip OA, OA005

city: Rochester

first: Gulzada

last: Kulzhanova

address: 310 University Park

department: Biomedical Engineering

institute: University of Rochester

description:
Library name: Sample 9
Spatial-seq datasets from OA patient #5
Supplemental File 1_GO terms of top 20 conserved markers for integrated CD45- non-hematopoietic cells.xlsx
Supplemental File 2_DEGs of CD45- non-hematopoietic cells.xlsx
Supplemental File 3_GO terms of top 20 conserved markers for integrated CD45+CD14+ myeloid cells.xlsx
Supplemental File 4_DEGs of CD45+CD14+ myeloid cells.xlsx

data_processing:
Paired-end sequencing reads were processed by Cell Ranger (10x Genomics software, version 2.0.0). Reads were aligned to the GRCh38 (version 90) for genome annotation, demultiplexing, barcode filtering, and gene quantification. Cell Ranger also removes any barcode that has less than 10% of the 99th percentile of total unique molecular identifiers (UMI) counts per barcode as these barcodes are considered to be associated with empty droplets. After this quality control, gene barcode matrices for each sample were generated by counting the number of UMIs for a given gene (as row) in individual cell (as column). For each sample, ~5000-10000 cells were captured.
Assembly: GRCh38 (version 90)
Supplementary files format and content: gene list (_genes.tsv) and cell barcodes (_barcodes.tsv) as well as gene/barcode matrices (_matrix.mtx) are provided for each time sample
Library strategy: Spatial Transcriptomics

extract_protocol:
Human FAI (n = 4) and hip OA (n = 6) synovial tissues were isolated and placed in collection medium (DMEM/F-12, GlutaMAX™ supplement, #10-565-018, Gibco™, with 1% Penicillin-Streptomycin (10,000 U/mL), #15140122, Gibco™, and 10% Fetal Bovine Serum, #F0926-100, Sigma-Aldrich). Harvested synovial tissues were then transferred to 10% neutral buffered formalin solution. Upon 24-hour fixation at room temperature and paraffin embedding, FAI and hip OA synovial samples were sectioned at 8 m in an RNase-free environment (#7003 ThermoFischer) and placed on the individual spatially barcoded capture areas of a 10X Genomics Visium Gene Expression Slide (10X Genomics, Pleasanton, CA). Following tissue placement, slide drying, and overnight incubation in a desiccator, the slide was deparaffinized, H&E stained, and imaged using a VS120 Slide Scanner (Olympic) at 20X magnification.
Sequence ready libraries were then constructed according to the manufacturer’s instructions (10X Genomics, CG000407). Final libraries were sequenced on the NovaSeq 6000 sequencer (Illumina, San Diego, CA) to obtain at least 50,000 reads per spot.

value: synovium

value: human primary cells

value: OA synoviocytes

tag: disease state

value: hip OA

tag: patient

value: OA patient #5


title: Spatial-Seq, Synovium, hip OA, OA003

description:
Library name: Sample 7
Spatial-seq datasets from OA patient #3
Supplemental File 1_GO terms of top 20 conserved markers for integrated CD45- non-hematopoietic cells.xlsx
Supplemental File 2_DEGs of CD45- non-hematopoietic cells.xlsx
Supplemental File 3_GO terms of top 20 conserved markers for integrated CD45+CD14+ myeloid cells.xlsx
Supplemental File 4_DEGs of CD45+CD14+ myeloid cells.xlsx

value: OA patient #3


title: Spatial-Seq, Synovium, hip OA, OA004

description:
Library name: Sample 8
Spatial-seq datasets from OA patient #4
Supplemental File 1_GO terms of top 20 conserved markers for integrated CD45- non-hematopoietic cells.xlsx
Supplemental File 2_DEGs of CD45- non-hematopoietic cells.xlsx
Supplemental File 3_GO terms of top 20 conserved markers for integrated CD45+CD14+ myeloid cells.xlsx
Supplemental File 4_DEGs of CD45+CD14+ myeloid cells.xlsx

value: OA patient #4


title: Formative ESC, Kmt2cKO; Kmt2dKO, IgG control, rep1

description:
Library name: dKO_form_igg_rep1
IgG control


title: P7_Ctrl_OHC_4

description: Library name: Sample 42

value: Cochlear


title: P7_Ctrl_OHC_3

description: Library name: Sample 41


title: Formative ESC, Kmt2cKO; Kmtd fl/fl, IgG control, rep1

description:
Library name: CKO_form_igg_rep1
IgG control


title: Spatial-Seq, Synovium, hip OA, OA002

description:
Library name: Sample 6
Spatial-seq datasets from OA patient #2
Supplemental File 1_GO terms of top 20 conserved markers for integrated CD45- non-hematopoietic cells.xlsx
Supplemental File 2_DEGs of CD45- non-hematopoietic cells.xlsx
Supplemental File 3_GO terms of top 20 conserved markers for integrated CD45+CD14+ myeloid cells.xlsx
Supplemental File 4_DEGs of CD45+CD14+ myeloid cells.xlsx

value: OA patient #2


title: Naive ESC, Kmt2cKO; Kmt2dKO, IgG control, rep2

description:
Library name: dKO_naive_igg_rep2
IgG control


title: Formative ESC, Kmt2cKO; Kmtd fl/fl, IgG control, rep2

description:
Library name: CKO_form_igg_rep2
IgG control


title: Naive ESC, Kmt2cKO; Kmtd fl/fl, IgG control, rep2

description:
Library name: CKO_naive_igg_rep2
IgG control


title: P7_Ctrl_OHC_2

description: Library name: Sample 40


title: Naive ESC, Kmt2cKO; Kmt2dKO;GRHL2-ERT, Tam 8 hours, P300, rep2

description:
Library name: dKOert_Tam_P300_rep2
P300

value: Kmt2cKO; Kmt2dKO;GRHL2-ERT

value: Tam 8 hours


title: Naive ESC, Kmt2cKO; Kmtd fl/fl, IgG control, rep1

description:
Library name: CKO_naive_igg_rep1
IgG control


title: P7_Ctrl_OHC_1

description: Library name: Sample 39


title: Naive ESC, Kmt2cKO; Kmt2dKO;GRHL2-ERT, Tam 8 hours, P300, rep1

description:
Library name: dKOert_Tam_P300_rep1
P300


title: Spatial-Seq, Synovium, hip OA, OA001

description:
Library name: Sample 5
Spatial-seq datasets from OA patient #1
Supplemental File 1_GO terms of top 20 conserved markers for integrated CD45- non-hematopoietic cells.xlsx
Supplemental File 2_DEGs of CD45- non-hematopoietic cells.xlsx
Supplemental File 3_GO terms of top 20 conserved markers for integrated CD45+CD14+ myeloid cells.xlsx
Supplemental File 4_DEGs of CD45+CD14+ myeloid cells.xlsx

value: OA patient #1


title: P7_Ctrl_IHC_38

description: Library name: Sample 38


title: Naive ESC, Kmt2cKO; Kmt2dKO;GRHL2-ERT, EtOH 8 hours, P300, rep1

description:
Library name: dKOert_Eth_P300_rep1
P300

value: EtOH 8 hours


title: Spatial-Seq, Synovium, hip OA, OA006

description:
Library name: Sample 10
Spatial-seq datasets from OA patient #6
Supplemental File 1_GO terms of top 20 conserved markers for integrated CD45- non-hematopoietic cells.xlsx
Supplemental File 2_DEGs of CD45- non-hematopoietic cells.xlsx
Supplemental File 3_GO terms of top 20 conserved markers for integrated CD45+CD14+ myeloid cells.xlsx
Supplemental File 4_DEGs of CD45+CD14+ myeloid cells.xlsx

value: OA patient #6


title: Naive ESC, Kmt2cKO; Kmt2dKO;GRHL2-ERT, EtOH 8 hours, P300, rep2

description:
Library name: dKOert_Eth_P300_rep2
P300

value: Naive ESC


title: Spatial-Seq, Synovium, FAI, FAI006

description:
Library name: Sample 4
Spatial-seq datasets from FAI patient #6
Supplemental File 1_GO terms of top 20 conserved markers for integrated CD45- non-hematopoietic cells.xlsx
Supplemental File 2_DEGs of CD45- non-hematopoietic cells.xlsx
Supplemental File 3_GO terms of top 20 conserved markers for integrated CD45+CD14+ myeloid cells.xlsx
Supplemental File 4_DEGs of CD45+CD14+ myeloid cells.xlsx

value: FAI synoviocytes

value: FAI

value: FAI patient #6


title: Spatial-Seq, Synovium, FAI, FAI005

description:
Library name: Sample 3
Spatial-seq datasets from FAI patient #5
Supplemental File 1_GO terms of top 20 conserved markers for integrated CD45- non-hematopoietic cells.xlsx
Supplemental File 2_DEGs of CD45- non-hematopoietic cells.xlsx
Supplemental File 3_GO terms of top 20 conserved markers for integrated CD45+CD14+ myeloid cells.xlsx
Supplemental File 4_DEGs of CD45+CD14+ myeloid cells.xlsx

value: synovium

value: human primary cells

value: FAI patient #5


title: Naive ESC, Kmt2cKO; Kmtd fl/fl;GRHL2-ERT, Tam 8 hours, P300, rep2

description:
Library name: CKOert_Tam_P300_rep2
P300

value: Kmt2cKO; Kmtd fl/fl;GRHL2-ERT


title: P7_Ctrl_IHC_36

description: Library name: Sample 36


title: Naive ESC, Kmt2cKO; Kmtd fl/fl;GRHL2-ERT, EtOH 8 hours, P300, rep2

description:
Library name: CKOert_Eth_P300_rep2
P300


title: Naive ESC, Kmt2cKO; Kmtd fl/fl;GRHL2-ERT, Tam 8 hours, P300, rep1

description:
Library name: CKOert_Tam_P300_rep1
P300


title: P7_Ctrl_IHC_37

description: Library name: Sample 37


title: Spatial-Seq, Synovium, FAI, FAI002

description:
Library name: Sample 2
Spatial-seq datasets from FAI patient #2
Supplemental File 1_GO terms of top 20 conserved markers for integrated CD45- non-hematopoietic cells.xlsx
Supplemental File 2_DEGs of CD45- non-hematopoietic cells.xlsx
Supplemental File 3_GO terms of top 20 conserved markers for integrated CD45+CD14+ myeloid cells.xlsx
Supplemental File 4_DEGs of CD45+CD14+ myeloid cells.xlsx

value: FAI patient #2


title: Naive ESC, Kmt2cKO; Kmtd fl/fl;GRHL2-ERT, EtOH 8 hours, P300, rep1

description:
Library name: CKOert_Eth_P300_rep1
P300


title: Synovium, hip OA, OA009

description: Library name: Sample 11

data_processing:
Paired-end sequencing reads were processed by Cell Ranger (10x Genomics software, version 2.0.0). Reads were aligned to the GRCh38 (version 90) for genome annotation, demultiplexing, barcode filtering, and gene quantification. Cell Ranger also removes any barcode that has less than 10% of the 99th percentile of total unique molecular identifiers (UMI) counts per barcode as these barcodes are considered to be associated with empty droplets. After this quality control, gene barcode matrices for each sample were generated by counting the number of UMIs for a given gene (as row) in individual cell (as column). For each sample, ~5000-10000 cells were captured.
Assembly: GRCh38 (version 90)
Supplementary files format and content: gene list (_genes.tsv) and cell barcodes (_barcodes.tsv) as well as gene/barcode matrices (_matrix.mtx) are provided for each time sample

extract_protocol:
Human FAI and hip OA synovium samples (3 samples per disease condition per sex) were harvested for scRNA-seq analysis. The FAI synovium samples were minced by hand and digested in 0.3% collagenase medium (DMEM/F-12, GlutaMAX™ supplement, #10-565-018, Gibco™ with 3 ug/mL collagenase II, #LS004177, Worthington Biochemical Corporation, and 10% Fetal Bovine Serum, #F0926-100, Sigma-Aldrich) for three hours at 37C while shaking continuously. The samples were thoroughly vortexed every hour. The OA synovium samples were digested in 0.4% collagenase medium (DMEM/F-12, GlutaMAX™ supplement, #10-565-018, Gibco™ with 4 ug/mL collagenase II, #LS004177, Worthington Biochemical Corporation, and 10% Fetal Bovine Serum, #F0926-100, Sigma-Aldrich) at 37C overnight. Cells were then resuspended in ACK lysing buffer (#A1049201, Gibco) for 1-2 minutes to lyse red blood cells. Afterwards, cells were filtered through 70um (#130-110-916, Miltenyi Biotec) and 30um MACS® SmartStrainers (#130-110-915, Miltenyi Biotec). The cell suspension was later frozen down in freezing medium (DMEM/F-12, GlutaMAX™ supplement, #10-565-018, Gibco™ with 10% Pierce™ Dimethylsulfoxide (DMSO), LC-MS Grade, #85190, ThermoFischer, and 80% Fetal Bovine Serum, #F0926-100, Sigma-Aldrich) until submitted for scRNA-seq.
Samples with greater than 70% viability were submitted to UR Genomics Research Center for scRNA-Seq library preparation using Chromium Next GEM Single Cell 3′ GEM, Library and Gel Bead Kit v3.1 (10x Genomics), per the manufacturer’s recommendations, as summarized below. Samples were loaded on a Chromium Single-Cell Instrument (10x Genomics, Pleasanton, CA, USA) to generate single-cell GEMs (Gel Bead-in-Emulsions). GEM reverse transcription (GEM-RT) was performed to produce a barcoded, full-length cDNA from poly-adenylated mRNA. After incubation, GEMs were broken, the pooled GEM-RT reaction mixtures were recovered, and cDNA was purified with silane magnetic beads (DynaBeads MyOne Silane Beads, ThermoFisher Scientific). The purified cDNA was further amplified by PCR to generate sufficient material for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size and indexed sequencing libraries were constructed by end repair, A-tailing, adaptor ligation, and PCR. The final libraries contain the P5 and P7 priming sites used in Illumina bridge amplification. Sequence data was generated using the Illumina NovaSeq 6000 platform.

value: OA synoviocytes

value: hip OA

value: Human hip synoviocytes from OA patient #5


title: Naive ESC, Kmt2cKO; Kmt2dKO;GRHL2-ERT, Tam 8 hours, H3K27ac, rep1

description:
Library name: dKOert_Tam_H3K27ac_rep1
H3K27ac

value: Kmt2cKO; Kmt2dKO;GRHL2-ERT


title: P7_Ctrl_IHC_34

description: Library name: Sample 34

value: Cochlear


title: Synovium, hip OA, OA010

description: Library name: Sample 12

value: Human hip synoviocytes from OA patient #6


title: P7_Ctrl_IHC_35

description: Library name: Sample 35


title: Synovium, hip OA, OA008

description: Library name: Sample 10

value: Human hip synoviocytes from OA patient #4


title: Naive ESC, Kmt2cKO; Kmt2dKO;GRHL2-ERT, EtOH 8 hours, H3K27ac, rep2

description:
Library name: dKOert_Eth_H3K27ac_rep2
H3K27ac

value: EtOH 8 hours


title: P7_Ctrl_IHC_33

description: Library name: Sample 33


title: Spatial-Seq, Synovium, FAI, FAI001

description:
Library name: Sample 1
Spatial-seq datasets from FAI patient #1
Supplemental File 1_GO terms of top 20 conserved markers for integrated CD45- non-hematopoietic cells.xlsx
Supplemental File 2_DEGs of CD45- non-hematopoietic cells.xlsx
Supplemental File 3_GO terms of top 20 conserved markers for integrated CD45+CD14+ myeloid cells.xlsx
Supplemental File 4_DEGs of CD45+CD14+ myeloid cells.xlsx

value: FAI patient #1


title: Naive ESC, Kmt2cKO; Kmtd fl/fl;GRHL2-ERT, Tam 8 hours, H3K27ac, rep2

description:
Library name: CKOert_Tam_H3K27ac_rep2
H3K27ac

value: Naive ESC

value: Tam 8 hours


title: Naive ESC, Kmt2cKO; Kmt2dKO;GRHL2-ERT, EtOH 8 hours, H3K27ac, rep1

description:
Library name: dKOert_Eth_H3K27ac_rep1
H3K27ac


title: Synovium, hip OA, OA007

description: Library name: Sample 9

value: Human hip synoviocytes from OA patient #3


title: Naive ESC, Kmt2cKO; Kmt2dKO;GRHL2-ERT, Tam 8 hours, H3K27ac, rep2

description:
Library name: dKOert_Tam_H3K27ac_rep2
H3K27ac


title: Naive ESC, Kmt2cKO; Kmtd fl/fl;GRHL2-ERT, EtOH 8 hours, H3K27ac, rep2

description:
Library name: CKOert_Eth_H3K27ac_rep2
H3K27ac


title: Naive ESC, Kmt2cKO; Kmtd fl/fl;GRHL2-ERT, EtOH 8 hours, H3K27ac, rep1

description:
Library name: CKOert_Eth_H3K27ac_rep1
H3K27ac


title: Synovium, hip OA, OA005

description: Library name: Sample 8

value: synovium

value: Human hip synoviocytes from OA patient #2


title: Naive ESC, Kmt2cKO; Kmt2dKO;GRHL2-ERT, Tam 8 hours, H3K4me3, rep2

description:
Library name: dKOert_Tam_H3K4me3_rep2
H3K4me3