title: Tau11i overexpression neuron, biol rep 3, line 25, day55, batch 2

description:
Library name: Sample 17
D55_T11i25C


title: Tau11i overexpression neuron, biol rep 1, line 25, day55, batch 2

status: Public on Dec 26 2025

type: SRA

city: Singapore

first: Yow-Yong

last: Tan

address: 1 Research Link

country: Singapore

institute: Temasek Life Sciences Laboratory

description:
Library name: Sample 15
D55_T11i25A

library_source: transcriptomic

data_processing:
Genome indexes were generated using STAR v2.7.4a with Homo_sapiens.GRCh38.r110 genome before mapping sequencing reads.
The aligned sequencing reads were then counted by using HTseq before differential expression analysis using DESeq2
Assembly: Homo_sapiens.GRCh38.r110
Supplementary files format and content: CSV file includes raw counts for all samples with column name listed in the description

molecule: total RNA

organism: Homo sapiens

source_name: in vitro differentiated neurons

growth_protocol: Isogenic control (XCL-1, SC-001-1V) neuron and Tau overexpression neurons were cultured and differentiated according to manufacturer’s protocols (XCell Science Inc). NSCs were seeded at a density of 0.04×10^6 cells/cm2 on poly-ornithine (20 µg/mL) & laminin (10 µg/mL)-coated plates in NSC maintenance media on Day 0 (D0). Cells were then replenished with neuronal induction media on Day 1, 3 and 5. On Day 6 (D6), neuronal precursor cells (NPCs) were harvested and replated on poly-ornithine/laminin-coated wells with similar density in neuronal maturation medium. Neurons were cultured for designated duration with media change every alternate Day.

extract_protocol:
Total RNA from biological replicates were isolated using RNAzol®RT (Sigma-Aldrich).
Poly-A enriched libraries were prepared and sequenced by NovogeneAIT (Singapore)  via NovaSeq PE150 service according to company protocols.

tag: cell type

value: in vitro differentiated neurons

tag: genotype

value: Tau11i overexpression

tag: batch


title: D4P6_control_S1

city: Pittsburgh

first: Daniella

last: Schwartz

state: PA

address: 200 Lothrop St

country: USA

institute: University of Pittsburgh

description:
Library name: Sample 11
FPKM.Endothelial_cells.txt

data_processing:
Fastq files were processed with bcl2fastq v.2.20.0.422. Reads of 50 bases were processed using the nextflow-core pipeline [9] (https://nf-co.re/rnaseq/2.0). Adaptor sequences were trimmed (Trim Galore) and mapped to mouse transcriptome mm10 or human transcriptome GRCh38 (STAR). Gene expression values (fragments per kilobase exon per million mapped reads; tags per million mapped reads; counts) were generated using RSEM.
Assembly: mm10 (murine Th9 cells)
Assembly: GRCh38 (IL-9-treated endothelial cells)
Supplementary files format and content: tab delimited text (.txt) file (FPKM.*cells.txt) contains Fragments Per Kilobase of transcript per Million mapped reads

source_name: primay human aortic endothelial cells (HAoEC)

growth_protocol:
For murine Th9 cells: N/A
Primary human aortic endothelial cells (HAoEC) from >9 donors (PromoCell) were cultured in endothelial growth media (Promocell) and passaged up to 9 times

extract_protocol:
Sorted cells were lysed in Trizol, and RNA was extracted per the manufacturer's protocol
Libraries for mRNA-sequencing were prepared using the NEBNext Ultra II Directional RNA-seq Library kit. Samples were sequenced on a NovaSeq 6000, paired end (PE), for 50 cycles .
HAoEC were lysed in Trizol, and RNA was extracted per the manufacturer's protocol
Libraries for mRNA-sequencing were prepared using the NEBNext Ultra II Directional RNA-seq Library kit. Samples were sequenced on a NovaSeq 6000, paired end (PE), for 50 cycles .

treatment_protocol:
INFER (IL-9 reporter) mice received daily topical 5% Imiquimod (IMQ, Glenmark 60 mg) or Vanicream on shaved dorsal skin for three 5-day cycles with 13-day recovery periods (6 weeks total).
Spleens were extracted from IL-9 reporter mice (INFER) and homogenized in RPMI with DNAse. After RBC lysis (ACK buffer), organ suspensions were transferred to 96-well plates and stained with DAPI and cell surface antibodies. Live, doublet-excluded cells were sorted for CD45.2+/TCR-beta+/CD4+/CD8-/CD44+ cells, then for GFP+ (Th9) and GFP- (non-Th9) cells.
HAoEC were treated for 14 hours with human recombinant IL-9 100ng/mL vs. vehicle control.

tag: treatment

value: vehicle


title: BBR_3_zone2_3

city: Hangzhou

first: Rongfang

last: Guo

address: 866 Yuhangtang Road, Xihu District

country: China

institute: Zhejiang university

description:
Library name: sample134
DSP-1001660015391-D-D04

data_processing:
FASTQ files were converted to .DCC files and extracted as a matrix using the Nanostring NGS pipeline and GeoMxTools R package
Assembly: Mouse Whole Transcriptome Atlas RNA v1.0
Supplementary files format and content: .dcc: processed counts (used for input in GeoMxTools R package)
Library strategy: Spatial Transcriptomics

organism: Mus musculus

source_name: liver

extract_protocol:
Liver tissues were fixed in 10% neutral formalin for 24 hours and sectioned into 4-µm-thick slices after paraffin embedding. Following deparaffinization, rehydration, and antigen retrieval, sections were incubated overnight with a Mouse Whole Transcriptome Atlas oligonucleotide probe mix at 37 °C. The next day, after washing and blocking, fluorescently labeled antibodies were applied to all slides for morphological staining. After washing, the prepared slides were loaded into GeoMx Digital Spatial Profiler and scanned. Regions of interest (ROIs) were selected and segmented into areas of illumination (AOIs) based on the morphological staining.
Oligonucleotide barcodes were released upon exposure to ultraviolet light, then collected, amplified, and purified. Libraries were constructed and sequenced on the NovaSeq 6000 platform.

tag: tissue

value: liver

tag: group

value: BBR

value: Berberine


title: Tau11i overexpression neuron, biol rep 1, line 6, day55, batch 1

description:
Library name: Sample 18
D55_T11i6A


title: Rb1_3_zone3_2

description:
Library name: sample123
DSP-1001660015391-D-C05

value: Ginsenoside Rb1


title: Rb1_3_zone1_2

description:
Library name: sample121
DSP-1001660015391-D-C03


title: D4P7_control_S7

description:
Library name: Sample 13
FPKM.Endothelial_cells.txt

value: primay human aortic endothelial cells (HAoEC)


title: Rb1_3_zone1_1

description:
Library name: sample118
DSP-1001660015391-D-B12


title: Isogenic control neuron, biol rep 3, day55, batch 2

description:
Library name: Sample 14
D55_CTF

value: Control


title: Isogenic control neuron, biol rep 1, day55, batch 2

description:
Library name: Sample 12
D55_CTD


title: Rb1_3_zone2_1

description:
Library name: sample119
DSP-1001660015391-D-C01


title: RB_3_zone3_3

description:
Library name: sample117
DSP-1001660015391-D-B11

value: RB

value: Ginsenoside Rb1 and berberine


title: Isogenic control neuron, biol rep 3, day55, batch 1

description:
Library name: Sample 11
D55_CTC


title: Isogenic control neuron, biol rep 1, day55, batch 1

description:
Library name: Sample 9
D55_CTA


title: Tau11i overexpression neuron, biol rep 3, line 6, day55, batch 1

description:
Library name: Sample 20
D55_T11i6C


title: RB_3_zone1_3

description:
Library name: sample115
DSP-1001660015391-D-B09


title: Isogenic control neuron, biol rep 2, day55, batch 1

description:
Library name: Sample 10
D55_CTB


title: Tau441 overexpression neuron, biol rep 3, line 8, day21, batch 3

description:
Library name: Sample 8
D21_TFL8C

value: Tau441 overexpression


title: RB_3_zone2_2

description:
Library name: sample113
DSP-1001660015391-D-B07


title: RB_3_zone1_2

description:
Library name: sample112
DSP-1001660015391-D-B06


title: RB_3_zone3_1

description:
Library name: sample111
DSP-1001660015391-D-B05


title: RB_3_zone1_1

description:
Library name: sample109
DSP-1001660015391-D-B03


title: Tau11i overexpression neuron, biol rep 2, line 6, day21, batch 3

description:
Library name: Sample 4
D21_T11i6B


title: Tau441 overexpression neuron, biol rep 1, line 8, day21, batch 3

description:
Library name: Sample 6
D21_TFL8A


title: Rb1_3_zone3_1

description:
Library name: sample120
DSP-1001660015391-D-C02


title: Tau11i overexpression neuron, biol rep 1, line 6, day21, batch 3

description:
Library name: Sample 3
D21_T11i6A


title: Isogenic control neuron, biol rep 2, day21, batch 3

description:
Library name: Sample 2
D21_CTB


title: db/db_3_zone3_3

description:
Library name: sample108
DSP-1001660015391-D-B02

value: model


title: Isogenic control neuron, biol rep 2, day55, batch 2

description:
Library name: Sample 13
D55_CTE


title: db/db_3_zone3_2

description:
Library name: sample105
DSP-1001660015391-D-A11


title: Normal2_RNA

city: Chengdu, Cihna

first: Xaingyu

last: Pan

state: Sichuan

address: No.17 Renming road section3

department: State Key Laboratory of Biotherapy, West China Hospital, Sihcuan University.

institute: Sichuan University

data_processing:
The count model of cellranger (v5.0.1) was used to align the sequencing files generated by Single Cell 5' PE chemistry with the human reference genome of GRCh38-2020-A. The parameter of --include-introns was added in alignment of single nuclei samples processed by Single Cell 3' v3 chemistry. The loupe files were generated by reanalyze model of cellranger (v5.0.1).
The count model of cellranger (v5.0.1) was used to align the sequencing files generated by Single Cell 5' PE chemistry with the human reference genome of GRCh38-2020-A. The parameter of --include-introns was added in alignment of single nuclei samples processed by Single Cell 3' v3 chemistry. The loupe files were generated by reanalyze model of cellranger (v5.0.1).
The FindVariableFeatures was implemented to identify 4,000 high-variable genes with vst model for data scaling and subsequent clustering and dimension reducing. The 25 principal component analysis factors were used to embedding calculation and the 20 principal component analysis factors were used to neighbors’ estimation. The openTSNE, t-SNE, UMAP and force atlas2 (fa2) were used to reduce the dimension following previously reported methods. The major population and subpopulation were identified by classical signatures, and top markers were calculated by FindAllMarkers with wilcox.test.
The analysis of normal adrenal cortex and tumor subpopulation integrated the harmony (v0.1.0) algorithm into remove batch effects from different platform and library construction chemistry for identifying the common molecular features in ACC. The 20 harmony factors were used to cluster and dimension reduce.
Assembly: refdata-gex-GRCh38-2020-A
Supplementary files format and content: MTX
Supplementary files format and content: RDS

source_name: Normal Adrenal gland

extract_protocol:
Under sterile conditions, the tissues of ACC1, ACC2, ACC3 and ACC4 were washed twice with pre-cooled RPMI 1640+0.04%BSA medium. The tissues were fully cut into smaller pieces with surgical scissors and put into the freshly conFigd enzymolysis solution with collagenase II in RPMI 1640. The enzymolysis was digested in a constant temperature incubator at 37℃ for 40 min, and mixed inversely every 5-10min. The digested cell suspension was filtered by BD 40μm cell screen for 1 time, centrifuged at 4℃ and 300g for 5min. After the precipitation was suspended with appropriate medium, the same volume of red blood cell lysate (MACS, No. 130-094-183) was added, mixed, left for 10 min at 4℃, cell suspension 300g centrifuged for 5min, and the supernatant was discarded. The precipitation was washed in the medium once, centrifuged at 300g for 5min, and the supernatant was discarded. Follow the MACS Dead Cell Removal Kit (130-090-101) instructions. The cell suspension was added with 100μl magnetic beads, blown and mixed well, incubated at room temperature for 15min and then passed through the column. The eluted cell suspension was centrifuged at 4℃ and 300g for 5min and washed twice, then re-suspended with 100μl medium and Luna was counted.
The nuclear suspension preparations experiment of Normal1, Normal2, Normal3, ACC5, ACC6, ACC7, ACC8, ACC9 and ACC10 were conducted on ice. Fresh tissue samples were cut in 1ml nuclear lysate (NST), which was divided into 0.1% NP40, 10mM Tris-HCl, 146mM NaCl, 1mM CaCl2, 21mM MgCl2 and 1U/μl RNase inhibitor. The cracking time was 7min. After the nucleolysis was confirmed by Trypan blue microscopy, 1ml ST Wash buffer (10mM Tris-HCl, 146mM NaCl, 1mM CaCl2, 21mM MgCl2) was added. 0.01% BSA (NEB B9000S) and 40U/mL RNase inhibitor). Filtrate was transferred to a 15mL centrifuge tube through a 40µm cell sieve (BD). The filtrate was rinsed with an appropriate amount of ST Wash buffer and combined with the nuclear filtrate. Centrifuge the horizontal rotor 500g at 4℃ for 5 min. The nucleus was re-suspended with 5ml PBS+1%BSA, and after washing and centrifugation, 100µl PBS+1%BSA was re-suspended. Trypan blue staining, microscopic counting. The single-nuclei suspensions were diluted to 700-1200/µl with PBS+1%BSA.
The freshly prepared single-cell suspensions were adjusted to 700-1200 cell/μl, according to 10×Genomics Chromium Next GEM Single Cell 5ʹ Reagent Kits v3.1 (1000020). T Cell V(D)J enrichment was performed in these samples according to the 10×Genomics Chromium™ single-cell V(D)J enrichment kit, human T Cell (1000005) operating instructions, and the library was amplified using Chromium single-cell human TCR amplification kit (1000252).
Machine and cDNA libraries were amplified according to the operating instructions of 10×Genomics Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (1000268). The constructed library was sequenced using the Illumina Nova 6000 platform in PE150 sequencing platform.
10X 5' scRNA+TCR
10X 3' scRNA

value: Normal Adrenal gland


title: RB_3_zone2_1

description:
Library name: sample110
DSP-1001660015391-D-B04


title: db/db_3_zone2_2

description:
Library name: sample104
DSP-1001660015391-D-A10


title: RB_3_zone2_3

description:
Library name: sample116
DSP-1001660015391-D-B10


title: db/db_3_zone2_3

description:
Library name: sample107
DSP-1001660015391-D-B01


title: db/db_3_zone1_3

description:
Library name: sample106
DSP-1001660015391-D-A12


title: Normal3_RNA

description: Machine and cDNA libraries were amplified according to the operating instructions of 10×Genomics Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (1000268). The constructed library was sequenced using the Illumina Nova 6000 platform in PE150 sequencing platform.


title: Normal1_RNA


title: db/db_3_zone1_2

description:
Library name: sample103
DSP-1001660015391-D-A09


title: RB_3_zone3_2

description:
Library name: sample114
DSP-1001660015391-D-B08


title: db/db_3_zone3_1

description:
Library name: sample102
DSP-1001660015391-D-A08


title: ACC9_RNA

source_name: ACC

value: ACC


title: db/db_3_zone2_1

description:
Library name: sample101
DSP-1001660015391-D-A07


title: ACC8_RNA


title: Tau441 overexpression neuron, biol rep 2, line 8, day21, batch 3

description:
Library name: Sample 7
D21_TFL8B


title: Isogenic control neuron, biol rep 1, day21, batch 3

description:
Library name: Sample 1
D21_CTA


title: ACC7_RNA


title: Tau11i overexpression neuron, biol rep 3, line 6, day21, batch 3

description:
Library name: Sample 5
D21_T11i6C


title: db/m_3_zone2_3

description:
Library name: sample98
DSP-1001660015391-D-A04

value: control


title: ACC6_RNA


title: db/m_3_zone3_3

description:
Library name: sample99
DSP-1001660015391-D-A05


title: ACC5_RNA


title: ACC4_TCR

description: 10×Genomics Chromium Next GEM Single Cell 5ʹ Reagent Kits v3.1 (1000020). T Cell V(D)J enrichment was performed in these samples according to the 10×Genomics Chromium™ single-cell V(D)J enrichment kit, human T Cell (1000005) operating instructions, and the library was amplified using Chromium single-cell human TCR amplification kit (1000252).

library_source: other

molecule: other


title: db/m_3_zone1_3

description:
Library name: sample97
DSP-1001660015391-D-A03


title: db/m_3_zone3_2

description:
Library name: sample96
DSP-1001660015391-D-A02


title: ACC4_RNA


title: db/m_3_zone1_2

description:
Library name: sample94
DSP-1001660015390-C-H11


title: db/m_3_zone3_1

description:
Library name: sample93
DSP-1001660015390-C-H10


title: ACC3_TCR


title: db/m_3_zone2_2

description:
Library name: sample95
DSP-1001660015390-C-H12


title: ACC2_RNA


title: db/m_3_zone2_1

description:
Library name: sample92
DSP-1001660015390-C-H09


title: ACC2_TCR


title: ACC1_RNA


title: ACC1_TCR


title: ACC10_RNA


title: db/m_3_zone1_1

description:
Library name: sample91
DSP-1001660015390-C-H08


title: BBR_2_zone3_3

description:
Library name: sample90
DSP-1001660015390-C-H07


title: BBR_2_zone2_3

description:
Library name: sample89
DSP-1001660015390-C-H06


title: db/db_3_zone1_1

description:
Library name: sample100
DSP-1001660015391-D-A06


title: Normal3_spatial

data_processing:
The count model of spaceranger (v1.2.2) was used to align the sequencing files generated by Spatial 3' (v1) with the human reference genome of GRCh38-2020-A using parameter of --reorient-images. The area A1, B1, C1 and D1 in silde of V11D06-026 were used to construct the library of spatial transcriptome sample.  The Seurat (v3.2.3), Matrix (v1.4.1) and spacexr (v2.0.1) were implemented into clustering, cell type annotation and visualization. The FindVariableFeatures was implemented to identify 4,000 high-variable genes with vst model for data scaling. The 30 principal component analysis factors were used to embedding calculation and the 20 principal component analysis factors were used to neighbors’ estimation. The Reference function was used to generate the reference files by inputting the counts of scRNA-seq data, cell annotation information and number of UMI with parameter of n_max_cells= 20000. The RCTD algorithm implemented in spacexr (v2.0.1) was used to deconvolute the potential cell type in each spot of spatial transcriptome data by inputting with spatial counts and parameter of doublet_mode = doublet. And the normalized weights of RCTD results were stored into meta.data in seurat object. The second cell type were regraded as the final annotation results in each spot.
Assembly: refdata-gex-GRCh38-2020-A
Supplementary files format and content: MTX
Supplementary files format and content: RDS
Supplementary files format and content: TIF

extract_protocol:
After cutting normal adrenal tissue of Normal1_spatial, Normal2_spatia and Normal3_spatia and adrenocortical carcinoma of ACC11_spatial, ACC12_spatial, ACC13_spatial and ACC14_spatial into 4-5 mm3 with a dust-free scalpel, dust-free paper was taken to wipe the blood stains from the tissue surface and then fresh tissue was embedded with OCT and placed in -80°C for rapid freezing. The tissues were frozen sectioned (10 µm) on a Lycra frozen sectioning machine and the sections were attached to ST microarrays. Then, HE staining were performed by dehydration with isopropyl alcohol for 1 min. And bright-field images were taken on a 3D HISTECH Pannoramic MIDI FL full-slide scanner at 20X resolution.
Tissue sections were placed in the corresponding capture zones on 10X Visium tissue permeabilization optimization slides. The slides for optimization experiments have 8 capture regions, and by removing the positive and negative controls from them, 6 additional sections are needed for permeabilization optimization experiments. The sections used for optimization are attached to different capture regions and then treated with permeabilizing enzymes for different times. The mRNA released during the permeabilization process binds to primers with poly-dT on the slides to generate fluorescently labeled cDNA. finally, the excess tissue is removed, leaving the fluorescently labeled cDNA to be observed using a fluorescence microscope to determine the optimal permeabilization time. Tissue sections placed in the capture region on gene expression slides are fixed and stained, permeabilized, and cellular mRNA is captured by primers at the gene expression site. The primers capture mRNA at specific sites to generate all cDNAs with a common spatial barcode. Libraries are generated from the cDNAs and sequenced, and the spatial barcodes are then used to correlate read information with tissue section images for spatial gene expression mapping.
10X Visium


title: BBR_2_zone3_2

description:
Library name: sample87
DSP-1001660015390-C-H04


title: BBR_2_zone1_3

description:
Library name: sample88
DSP-1001660015390-C-H05


title: Normal2_spatial

description: 10X Visium tissue permeabilization optimization slides


title: Normal1_spatial


title: ACC14_spatial


title: BBR_2_zone1_2

description:
Library name: sample85
DSP-1001660015390-C-H02


title: ACC13_spatial


title: BBR_2_zone3_1

description:
Library name: sample84
DSP-1001660015390-C-H01


title: ACC11_spatial


title: BBR_2_zone1_1

description:
Library name: sample82
DSP-1001660015390-C-G11


title: BBR_2_zone2_2

description:
Library name: sample86
DSP-1001660015390-C-H03


title: Rb1_2_zone3_3

description:
Library name: sample81
DSP-1001660015390-C-G10


title: Rb1_2_zone3_2

description:
Library name: sample78
DSP-1001660015390-C-G07


title: Rb1_2_zone1_3

description:
Library name: sample79
DSP-1001660015390-C-G08


title: ACC3_RNA

description: 10×Genomics Chromium Next GEM Single Cell 5ʹ Reagent Kits v3.1 (1000020). T Cell V(D)J enrichment was performed in these samples according to the 10×Genomics Chromium™ single-cell V(D)J enrichment kit, human T Cell (1000005) operating instructions, and the library was amplified using Chromium single-cell human TCR amplification kit (1000252).


title: Rb1_2_zone2_2

description:
Library name: sample77
DSP-1001660015390-C-G06


title: BBR_2_zone2_1

description:
Library name: sample83
DSP-1001660015390-C-G12


title: PBMCs from CI treated metastatic melanoma patient 57621 who did not develop CIADM. On-CI Therapy.

city: Westmead

first: Christopher

last: Liddle

state: NSW

address: 176 Hawkesbury Rd

department: Westmead Institute for Medical Research

country: Australia

institute: University of Sydney

description: Library name: S4

data_processing:
RNA quality was assessed using an Agilent TapeStation, TapeStation Analysis Software 4.1.1
Read quality and adapter content was assesed with FastQC 0.12.1
Illumina adapters and low quality sequence were removed using Trimmomatic-0.39 with a minimum trimmed read length of 50 bases.
STAR 2.7.11b, with default alignment options, was used for paired-end alignment and output of a transciptome aligned file using Gencode H45 annotation and the quantMode TranscriptomeSAM option
Gene expression quantitation was performed using RSEM 1.3.3 with the transcriptome aligned file as input.
Assembly: GRCh38.p14
Supplementary files format and content: tab-delimited text with following column headers: gene_id, transcript_id(s), length, effective_length, expected_count, TPM, FPKM

molecule: polyA RNA

source_name: periperal blood mononuclar cells

extract_protocol:
PBMCs from patient blood samples were sorted directly into Takara Bio lysis buffer.
Library was prepared using the Takara Bio Smart-Seq mRNA LP kit followed by paired-end sequencing.

value: periperal blood mononuclar cells

value: Matched Control for patient 33459


title: PBMCs from CI treated metastatic melanoma patient 57621 who did not develop CIADM. Pre-CI treatment.

description: Library name: S3


title: PBMCs from CI treated metastatic melanoma patient 50175 who did not develop CIADM. Pre-CI treatment.

description: Library name: R9

value: Matched Control for patient 13974


title: PBMCs from CI treated metastatic melanoma patient 57475 who developed CIADM. Pre-CI treatment.

description: Library name: S1

value: CI-associated diabetes mellitus case


title: PBMCs from CI treated metastatic melanoma patient 57475 who developed CIADM. On-CI Therapy.

description: Library name: S2


title: PBMCs from CI treated metastatic melanoma patient 55710 who did not develop CIADM. On-CI Therapy.

description: Library name: R16

value: Matched Control for patient 45837


title: PBMCs from CI treated metastatic melanoma patient 55710 who did not develop CIADM. Pre-CI treatment.

description: Library name: R15


title: ACC12_spatial


title: Rb1_2_zone3_1

description:
Library name: sample75
DSP-1001660015390-C-G04

value: liver


title: Rb1_2_zone1_2

description:
Library name: sample76
DSP-1001660015390-C-G05


title: Rb1_2_zone2_1

description:
Library name: sample74
DSP-1001660015390-C-G03


title: Rb1_2_zone1_1

description:
Library name: sample73
DSP-1001660015390-C-G02


title: PBMCs from CI treated metastatic melanoma patient 52405 who developed CIADM. On-CI Therapy.

description: Library name: R13


title: PBMCs from CI treated metastatic melanoma patient 51778 who did not develop CIADM. On-CI Therapy.

description: Library name: R12


title: PBMCs from CI treated metastatic melanoma patient 49697 who did not develop CIADM. On-CI Therapy.

description: Library name: Q8

value: Matched Control for patient 43120


title: PBMCs from CI treated metastatic melanoma patient 51778 who did not develop CIADM. Pre-CI treatment.

description: Library name: R11


title: RB_2_zone3_3

description:
Library name: sample72
DSP-1001660015390-C-G01


title: RB_2_zone2_3

description:
Library name: sample71
DSP-1001660015390-C-F12


title: PBMCs from CI treated metastatic melanoma patient 49697 who did not develop CIADM. Pre-CI treatment.

description: Library name: Q7


title: RB_2_zone1_3

description:
Library name: sample70
DSP-1001660015390-C-F11


title: PBMCs from CI treated metastatic melanoma patient 49445 who did not develop CIADM. On-CI Therapy.

description: Library name: Q6

value: Matched Control for patient 44574


title: Rb1_2_zone2_3

description:
Library name: sample80
DSP-1001660015390-C-G09

value: Ginsenoside Rb1


title: PBMCs from CI treated metastatic melanoma patient 49445 who did not develop CIADM. Pre-CI treatment.

description: Library name: Q5


title: RB_2_zone2_2

description:
Library name: sample68
DSP-1001660015390-C-F09


title: PBMCs from CI treated metastatic melanoma patient 49054 who did not develop CIADM. On-CI Therapy.

description: Library name: Q4


title: PBMCs from CI treated metastatic melanoma patient 49054 who did not develop CIADM. Pre-CI treatment.

description: Library name: Q3


title: PBMCs from CI treated metastatic melanoma patient 48216 who did not develop CIADM. On-CI Therapy.

description: Library name: Q2

value: Matched Control for patient 37100


title: db/db_2_zone3_3

description:
Library name: sample63
DSP-1001660015390-C-F04


title: RB_2_zone2_1

description:
Library name: sample65
DSP-1001660015390-C-F06

value: RB


title: PBMCs from CI treated metastatic melanoma patient 48216 who did not develop CIADM. Pre-CI treatment.

description: Library name: Q1


title: db/db_2_zone2_3

description:
Library name: sample62
DSP-1001660015390-C-F03


title: db/db_2_zone1_3

description:
Library name: sample61
DSP-1001660015390-C-F02


title: PBMCs from CI treated metastatic melanoma patient 47400 who did not develop CIADM. Pre-CI treatment.

description: Library name: P7

value: Matched Control for patient 57475


title: RB_2_zone1_1

description:
Library name: sample64
DSP-1001660015390-C-F05

value: Ginsenoside Rb1 and berberine


title: RB_2_zone1_2

description:
Library name: sample67
DSP-1001660015390-C-F08


title: PBMCs from CI treated metastatic melanoma patient 45837 who developed CIADM. Post diabetes diagnosis.

description: Library name: P6


title: db/db_2_zone3_2

description:
Library name: sample60
DSP-1001660015390-C-F01

value: model


title: PBMCs from CI treated metastatic melanoma patient 44574 who developed CIADM. Post diabetes diagnosis.

description: Library name: P4


title: db/db_2_zone2_2

description:
Library name: sample59
DSP-1001660015390-C-E12


title: db/db_2_zone1_2

description:
Library name: sample58
DSP-1001660015390-C-E11


title: PBMCs from CI treated metastatic melanoma patient 44574 who developed CIADM. Pre-CI treatment.

description: Library name: P2


title: db/db_2_zone3_1

description:
Library name: sample57
DSP-1001660015390-C-E10


title: PBMCs from CI treated metastatic melanoma patient 47400 who did not develop CIADM. On-CI Therapy.

description: Library name: P8


title: PBMCs from CI treated metastatic melanoma patient 44574 who developed CIADM. On-CI Therapy.

description: Library name: P3


title: RB_2_zone3_2

description:
Library name: sample69
DSP-1001660015390-C-F10


title: db/db_2_zone2_1

description:
Library name: sample56
DSP-1001660015390-C-E09


title: PBMCs from CI treated metastatic melanoma patient 43546 who did not develop CIADM. On-CI Therapy.

description: Library name: P1

value: Matched Control for patient 43305


title: db/db_2_zone1_1

description:
Library name: sample55
DSP-1001660015390-C-E08


title: PBMCs from CI treated metastatic melanoma patient 43546 who did not develop CIADM. Pre-CI treatment.

description: Library name: O8


title: PBMCs from CI treated metastatic melanoma patient 43305 who developed CIADM. Post diabetes diagnosis.

description: Library name: O7


title: PBMCs from CI treated metastatic melanoma patient 43305 who developed CIADM. Pre-CI treatment.

description: Library name: O6


title: db/m_2_zone3_3

description:
Library name: sample54
DSP-1001660015390-C-E07


title: RB_2_zone3_1

description:
Library name: sample66
DSP-1001660015390-C-F07


title: PBMCs from CI treated metastatic melanoma patient 43170 who did not develop CIADM. On-CI Therapy.

description: Library name: O5

value: Matched Control for patient 37264


title: db/m_2_zone2_3

description:
Library name: sample53
DSP-1001660015390-C-E06

value: control


title: PBMCs from CI treated metastatic melanoma patient 43170 who did not develop CIADM. Pre-CI treatment.

description: Library name: O4

value: periperal blood mononuclar cells


title: db/m_2_zone1_3

description:
Library name: sample52
DSP-1001660015390-C-E05


title: db/m_2_zone3_2

description:
Library name: sample51
DSP-1001660015390-C-E04


title: PBMCs from CI treated metastatic melanoma patient 45837 who developed CIADM. Pre-CI treatment.

description: Library name: P5


title: db/m_2_zone2_2

description:
Library name: sample50
DSP-1001660015390-C-E03


title: db/m_2_zone1_2

description:
Library name: sample49
DSP-1001660015390-C-E02


title: db/m_2_zone2_1

description:
Library name: sample47
DSP-1001660015390-C-D12


title: PBMCs from CI treated metastatic melanoma patient 43120 who developed CIADM. On-CI Therapy.

description: Library name: O2


title: PBMCs from CI treated metastatic melanoma patient 43120 who developed CIADM. Pre-CI treatment.

description: Library name: O1


title: db/m_2_zone1_1

description:
Library name: sample46
DSP-1001660015390-C-D11


title: PBMCs from CI treated metastatic melanoma patient 42813 who did not develop CIADM. On-CI Therapy.

description: Library name: N9


title: db/m_2_zone3_1

description:
Library name: sample48
DSP-1001660015390-C-E01


title: PBMCs from CI treated metastatic melanoma patient 42259 who did not develop CIADM. On-CI Therapy.

description: Library name: N6

value: Matched Control for patient 38826


title: BBR_1_zone3_3

description:
Library name: sample45
DSP-1001660015390-C-D10

value: BBR

value: Berberine


title: PBMCs from CI treated metastatic melanoma patient 42259 who did not develop CIADM. Pre-CI treatment.

description: Library name: N5


title: PBMCs from CI treated metastatic melanoma patient 41786 who did not develop CIADM. On-CI Therapy.

description: Library name: N4

value: Matched Control for patient 52405


title: BBR_1_zone1_3

description:
Library name: sample43
DSP-1001660015390-C-D08

value: liver


title: BBR_1_zone2_3

description:
Library name: sample44
DSP-1001660015390-C-D09


title: BBR_1_zone3_2

description:
Library name: sample42
DSP-1001660015390-C-D07


title: PBMCs from CI treated metastatic melanoma patient 41737 who did not develop CIADM. Pre-CI treatment.

description: Library name: N1


title: PBMCs from CI treated metastatic melanoma patient 41737 who did not develop CIADM. On-CI Therapy.

description: Library name: N2


title: BBR_1_zone1_2

description:
Library name: sample40
DSP-1001660015390-C-D05


title: PBMCs from CI treated metastatic melanoma patient 41456 who did not develop CIADM. On-CI Therapy.

description: Library name: M8

value: Matched Control for patient 39539


title: BBR_1_zone3_1

description:
Library name: sample39
DSP-1001660015390-C-D04


title: PBMCs from CI treated metastatic melanoma patient 43120 who developed CIADM. Post diabetes diagnosis.

description: Library name: O3

value: CI-associated diabetes mellitus case


title: PBMCs from CI treated metastatic melanoma patient 41456 who did not develop CIADM. Pre-CI treatment.

description: Library name: M7


title: BBR_1_zone2_1

description:
Library name: sample38
DSP-1001660015390-C-D03


title: PBMCs from CI treated metastatic melanoma patient 40961 who did not develop CIADM. On-CI Therapy.

description: Library name: M6


title: PBMCs from CI treated metastatic melanoma patient 40961 who did not develop CIADM. Pre-CI treatment.

description: Library name: M5


title: BBR_1_zone1_1

description:
Library name: sample37
DSP-1001660015390-C-D02


title: Rb1_1_zone3_3

description:
Library name: sample36
DSP-1001660015390-C-D01

value: Ginsenoside Rb1


title: PBMCs from CI treated metastatic melanoma patient 40319 who did not develop CIADM. On-CI Therapy.

description: Library name: M4

value: Matched Control for patient 37061


title: PBMCs from CI treated metastatic melanoma patient 42813 who did not develop CIADM. Pre-CI treatment.

description: Library name: N7

value: Matched Control for patient 45837


title: Rb1_1_zone2_3

description:
Library name: sample35
DSP-1001660015390-C-C12


title: Rb1_1_zone1_3

description:
Library name: sample34
DSP-1001660015390-C-C11


title: Rb1_1_zone3_2

description:
Library name: sample33
DSP-1001660015390-C-C10


title: Rb1_1_zone2_2

description:
Library name: sample32
DSP-1001660015390-C-C09


title: PBMCs from CI treated metastatic melanoma patient 41786 who did not develop CIADM. Pre-CI treatment.

description: Library name: N3


title: PBMCs from CI treated metastatic melanoma patient 39706 who did not develop CIADM. Pre-CI treatment.

description: Library name: M1

value: Matched Control for patient 33459


title: PBMCs from CI treated metastatic melanoma patient 39539 who developed CIADM. Post diabetes diagnosis.

description: Library name: L8


title: PBMCs from CI treated metastatic melanoma patient 39267 who did not develop CIADM. On-CI Therapy.

description: Library name: L5

value: Matched Control for patient 37100


title: PBMCs from CI treated metastatic melanoma patient 39706 who did not develop CIADM. On-CI Therapy.

description: Library name: M2


title: Rb1_1_zone3_1

description:
Library name: sample30
DSP-1001660015390-C-C07


title: Rb1_1_zone1_1

description:
Library name: sample28
DSP-1001660015390-C-C05


title: Rb1_1_zone2_1

description:
Library name: sample29
DSP-1001660015390-C-C06


title: PBMCs from CI treated metastatic melanoma patient 39539 who developed CIADM. Pre-CI treatment.

description: Library name: L6


title: PBMCs from CI treated metastatic melanoma patient 39539 who developed CIADM. On-CI Therapy.

description: Library name: L7


title: PBMCs from CI treated metastatic melanoma patient 39267 who did not develop CIADM. Pre-CI treatment.

description: Library name: L4


title: PBMCs from CI treated metastatic melanoma patient 38968 who did not develop CIADM. On-CI Therapy.

description: Library name: L3

value: Matched Control for patient 29632


title: RB_1_zone2_3

description:
Library name: sample26
DSP-1001660015390-C-C03

value: RB

value: Ginsenoside Rb1 and berberine


title: Tregs， anti-AXL Ab treatment, Day16 (biol rep2)

city: Beijing

first: Zuming

last: Yang

address: No. 30 Shuangqing Road Haidian District

institute: Tsinghua University

description: Library name: 6Treg2

data_processing:
LGC Genomics Workbench
Supplementary files format and content: CSV.files

source_name: Tumor

extract_protocol:
Tumor tissues were harvested, minced into small fragments, and digested in RPMI 1640 containing 1 mg/mL collagenase type IV (Sigma-Aldrich) and 0.5 mg/mL DNase I (Roche) at 37 °C for 30 minutes. The resulting cell suspensions were passed through a 70 μm cell strainer to obtain single-cell suspensions. Cells were resuspended in FACS buffer (PBS supplemented with 2% FBS and 0.05% NaN₃), blocked with anti-mouse CD16/32 antibody (clone 2.4G2) for 20 minutes, and then stained with fluorophore-conjugated antibodies for 30 minutes at 4 °C. Target cell subsets for sequencing were subsequently sorted by flow cytometry, deposited into tubes containing 50 μL of lysis buffer, centrifuged, and immediately frozen at −80 °C.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Tumor

tag: cell line

value: CD45+ cells

value: immune cell

value: WT

value: i.p. anti-AXL Ab


title: Tregs， anti-AXL Ab treatment, Day16 (biol rep1)

description: Library name: 6Treg1


title: PBMCs from CI treated metastatic melanoma patient 38826 who developed CIADM. Post diabetes diagnosis.

description: Library name: L1

value: periperal blood mononuclar cells


title: PD1+Foxp3-CD4+T cells，anti-AXL Ab treatment, Day16 (biol rep3)

description: Library name: 7PDH3


title: PBMCs from CI treated metastatic melanoma patient 40319 who did not develop CIADM. Pre-CI treatment.

description: Library name: M3


title: BBR_1_zone2_2

description:
Library name: sample41
DSP-1001660015390-C-D06

value: liver

value: BBR

value: Berberine


title: RB_1_zone1_3

description:
Library name: sample25
DSP-1001660015390-C-C02


title: PBMCs from CI treated metastatic melanoma patient 37100 who developed CIADM. Post diabetes diagnosis.

description: Library name: K9

value: CI-associated diabetes mellitus case


title: PD1+Foxp3-CD4+T cells，anti-AXL Ab treatment, Day16 (biol rep2)

description: Library name: 7PDH2


title: RB_1_zone3_2

description:
Library name: sample24
DSP-1001660015390-C-C01


title: Rb1_1_zone1_2

description:
Library name: sample31
DSP-1001660015390-C-C08

value: Ginsenoside Rb1


title: PBMCs from CI treated metastatic melanoma patient 38826 who developed CIADM. On-CI Therapy.

description: Library name: K8


title: PD1+Foxp3-CD4+T cells，anti-AXL Ab treatment, Day16 (biol rep1)

description: Library name: 7PDH1


title: RB_1_zone2_2

description:
Library name: sample23
DSP-1001660015390-C-B12


title: PD1-Foxp3-CD4+T cells，anti-AXL Ab treatment, Day16 (biol rep3)

description: Library name: 8PD1-3


title: Tregs， anti-AXL Ab treatment, Day16 (biol rep3)

description: Library name: 6Treg3


title: RB_1_zone1_2

description:
Library name: sample22
DSP-1001660015390-C-B11


title: RB_1_zone3_3

description:
Library name: sample27
DSP-1001660015390-C-C04


title: PBMCs from CI treated metastatic melanoma patient 38568 who did not develop CIADM. On-CI Therapy.

description: Library name: K7

value: Matched Control for patient 39539


title: PBMCs from CI treated metastatic melanoma patient 38568 who did not develop CIADM. Pre-CI treatment.

description: Library name: K6


title: PD1-Foxp3-CD4+T cells，anti-AXL Ab treatment, Day16 (biol rep2)

description: Library name: 8PD1-2


title: PD1-Foxp3-CD4+T cells，anti-AXL Ab treatment, Day16 (biol rep1)

description: Library name: 8PD1-1


title: SiNC_2

city: Nanchang

first: Xubo

last: Chen

email: cchxb560@126.com, ndefy17049@ncu.edu.cn

state: Jiangxi Province

address: Minde Road 1st

institute: The Second Affiliated Hospital of Nanchang University

data_processing:
Raw reads containing more than 2-N bases and short reads less than 16nt were filtered.
Adaptors and low-quality bases were then removed by using FASTX-Toolkit (Version 0.0.13).
clean reads were aligned to the rat genome (Ensembl v6) by using TopHat2(25), allowing four mismatches
Assembly: mRatBN7.2 genome
Supplementary files format and content: tab-delimited text files inculde reads counts for each sample
Supplementary files format and content: tab-delimited text files inculde FPKM values for each sample

organism: Rattus norvegicus

growth_protocol: The cells were cultured at 37 °C with 5% CO2 in Dulbecco's modified eagle medium (DMEM), containing 10% fetal bovine serum and 100 µg/mL streptomycin and penicillin

extract_protocol:
TRIzol (Ambion) solubilization and extraction were used to obtain total RNA. The total RNA was purified by RQ1 DNase (Promega) to remove residual DNA. The RNA quantity and quality were assessed by calculating the absorbance at 260nm/280nm (A260/A280) with Nanodrop One (Thermo).
150 nt paired-end sequencing was performed using Illumina NovaSeq 6000 system

value: Control


title: SiNC_3


title: SiNC_1


title: SiHNRNPD_1

value: AUF1 knock down


title: PBMCs from CI treated metastatic melanoma patient 37100 who developed CIADM. On-CI Therapy.

description: Library name: K1


title: SiHNRNPD_3


title: PBMCs from CI treated metastatic melanoma patient 37264 who developed CIADM. Post diabetes diagnosis.

description: Library name: K5


title: RB_1_zone3_1

description:
Library name: sample21
DSP-1001660015390-C-B10


title: PBMCs from CI treated metastatic melanoma patient 37100 who developed CIADM. Pre-CI treatment.

description: Library name: J8


title: SiHNRNPD_2


title: RB_1_zone2_1

description:
Library name: sample20
DSP-1001660015390-C-B09


title: Susceptible rapeseed control-bio rep 3

city: Yangling

first: Chengyu

last: Yu

state: Shaanxi

address: 3 Taicheng Road

department: College of Agronomy

institute: Northwest A&F University

description: Library name: S-CK3

data_processing:
Based on sequencing-by-synthesis (Sequencing By Synthesis, SBS) technology, cDNA libraries were sequenced on Illumina NovaSeq 6000 platform, generating significant amounts of raw data. Raw data was saved in FASTQ format. Each sample has two FASTQ file, containing cDNA reads measured at both ends respectively.
Clean data with high quality was obtained by filtering Raw data, which removes adapter sequence and reads with low quality. The Raw data of the twelve samples were processed and generated 88.99Gb Clean Data. At least 6.16Gb clean data were generated for each sample, with minimum 91.76% of clean data achieved quality score of Q30.
All the clean sequences were mapped onto the ZS11.v0 rapeseed genome (https://yanglab.hzau.edu.cn/BnIR) using HISAT2 software. The mapping ratio of each sample against reference genome ranged from 89.64% to 93.60%.
Assembly: StringTie was applied to assemble the mapped reads and to discovery of novel transcripts. The mapped reads were assembled and compared with original annotations of the ZS11.v0 rapeseed genome. The transcript regions without annotation obtained by above processes are defined as novel transcripts. Excluding short transcripts(coding peptides with less than 50 amino acids) or those containing only one exons. ASprofile was employed to predict alternative splicing events in each samples and sorting them into 12 types.
Supplementary files format and content: FPKM(Fragments Per Kilobase of transcript per Million fragments mapped) was applied to measure the expression level of a gene or transcript by StringTie using maximum flow algorithm. Differentially expressed genes (DEGs)were identified by the criteria of Fold Change≥ 2.0 and P value<0.01.
Supplementary files format and content: The file 'All_gene_RPKM.txt' shows the RPKM values of each gene in the 12 samples and the file 'Brassica_napus.newGene.longest_transcript.fa' contains the sequences of predicted new genes in fastq format.

organism: Brassica napus

source_name: Young seedling

growth_protocol: Firstly, the healthy seeds after surface sterilization were embedded on two-layer moistened paper in germination boxes. The boxes were placed in growth chambers at day/night temperature of 25℃/22℃, with a 16h/8h light/dark cycle. One week later, when the cotyledons of young seedlings became flat and true leaf just formed, the seedlings were treated by submergence.

extract_protocol:
Total RNA of rapeseed seedling sample was extracted by using Trizol reagent.
RNA quality check, mRNA extraction, cDNA reverse transcription, and preparation of amplicon library were performed by Biomark Biotechnology Co., Ltd (Beijing, China). Purity, concentration and integrity of RNA sample were examined by NanoDrop, Qubit 2.0, Agilent 2100, etc. Qualified RNA were processed for library construction. The procedures include: (1) mRNA was isolated by Oligo(dT)-attached magnetic beads. (2) mRNA was then randomly fragmented in fragmentation buffer. (3) First-strand cDNA was synthesized with fragmented mRNA as template and random hexamers as primers, followed by second-strand synthesis with addition of PCR buffer, dNTPs, RNase H and DNA polymerase I. Purification of cDNA was processed with AMPure XP beads. (4) Double-strand cDNA was subjected to end repair. Adenosine was added to the end and ligated to adapters. AMPure XP beads were applied here to select fragments within size range of 300-400 bp. (5) cDNA library was produced by certain rounds of PCR on cDNA fragments. To ensure the quality of library, Qubit 2.0 and Agilent 2100 were used to examine the concentration of cDNA and insert size. Q-PCR was processed to obtain a more accurate library concentration. Library with concentration larger than 2 nM is acceptable. RNA-seq was conducted on an Illumina NovaSeq6000 platform (Illumina Inc., San Diego, USA) following the standard Illumina PE150 protocol.

treatment_protocol: Distilled water was added to fully submerse the seedlings for 24h.

value: Young seedling

value: Susceptible

value: The young seedlings of resistant and sensitive genotypes were divided into two groups:the control group cultivated under normal conditions and the treatment group submerged in water for 24 hours


title: Susceptible rapeseed control-bio rep 1

description: Library name: S-CK1


title: db/db_1_zone2_3

description:
Library name: sample17
DSP-1001660015390-C-B06

value: model


title: PBMCs from CI treated metastatic melanoma patient 37061 who developed CIADM. On-CI Therapy.

description: Library name: J6


title: Susceptible rapeseed control-bio rep 2

description: Library name: S-CK2


title: Susceptible rapeseed treated by submergence-bio rep 3

description: Library name: S-T3


title: Resistant rapeseed control-bio rep 3

description: Library name: R-CK3

value: Resistant


title: Resistant rapeseed control-bio rep 2

description: Library name: R-CK2


title: db/db_1_zone1_3

description:
Library name: sample16
DSP-1001660015390-C-B05


title: RB_1_zone1_1

description:
Library name: sample19
DSP-1001660015390-C-B08

value: RB

value: Ginsenoside Rb1 and berberine


title: Resistant rapeseed treated by submergence-bio rep 3

description: Library name: R-T3


title: Susceptible rapeseed treated by submergence-bio rep 1

description: Library name: S-T1


title: PBMCs from CI treated metastatic melanoma patient 37061 who developed CIADM. Pre-CI treatment.

description: Library name: J5


title: Resistant rapeseed treated by submergence-bio rep 2

description: Library name: R-T2


title: PBMCs from CI treated metastatic melanoma patient 36837 who did not develop CIADM. On-CI Therapy.

description: Library name: J4

value: Matched Control for patient 29632


title: Susceptible rapeseed treated by submergence-bio rep 2

description: Library name: S-T2


title: db/db_1_zone3_2

description:
Library name: sample15
DSP-1001660015390-C-B04


title: db/db_1_zone2_2

description:
Library name: sample14
DSP-1001660015390-C-B03


title: PBMCs from CI treated metastatic melanoma patient 37061 who developed CIADM. Post diabetes diagnosis.

description: Library name: J7

value: periperal blood mononuclar cells


title: Resistant rapeseed control-bio rep 1

description: Library name: R-CK1


title: PBMCs from CI treated metastatic melanoma patient 36837 who did not develop CIADM. Pre-CI treatment.

description: Library name: J3


title: Resistant rapeseed treated by submergence-bio rep 1

description: Library name: R-T1


title: db/db_1_zone3_3

description:
Library name: sample18
DSP-1001660015390-C-B07

value: liver


title: KO_INPUT

city: Guangzhou

first: Sijia

last: Liang

address: 74 Zhongshan 2 Rd

department: Pharmacology

institute: Sun Yat-Sen University

description: Library name: Sample 8

library_source: genomic

data_processing:
Raw sequencing data were quality‑checked with FastQC, and adapters and low‑quality bases were trimmed using Trimmomatic.
Clean reads were aligned to the mouse genome (GRCm39) with Bowtie2 or BWA, and PCR duplicates were removed.
Peak calling was performed with MACS2 by comparing ChIP samples against input or IgG controls, and statistically significant peaks were annotated to nearby genomic features using HOMER.
Assembly: mm39
Supplementary files format and content: bigWig (except for Input samples)

molecule: genomic DNA

source_name: Primary mous aortic smooth muscle cel

growth_protocol: MAECs were isolated by sequential enzymatic digestion followed by magnetic-bead enrichment using PECAM-1 (BD Biosciences, San Jose, CA) and ICAM-2 (BD Biosciences) antibody–conjugated Dynabeads (Thermo Fisher Scientific, Waltham, MA) and maintained in high-glucose DMEM supplemented with 20% FBS, 1% penicillin/streptomycin, heparin, endothelial cell growth supplement, non-essential amino acids, L-glutamine, sodium pyruvate, and HEPES.

extract_protocol:
Cells (1 × 10⁷) were cross-linked with 1% formaldehyde at 37°C for 10 minutes, and the reaction was quenched with 125 mmol/L glycine for 5 minutes. Nuclei were isolated using lysis buffer and sonicated using a Bioruptor UCD-300 (Diagenode) for 30 minutes (30 s ON/OFF cycle) to generate chromatin fragments ranging from 200 to 500 bp.
Sequencing libraries were constructed using the NEBNext® Ultra DNA Library Prep Kit for Illumina®, including end‑repair, A‑tailing, adapter ligation, size selection (200–500 bp), and PCR amplification.

treatment_protocol: Mice were injected with AAV-PCSK9DY followed by feeding a high-fat diet for 12 weeks. Subsequently, MASMCs were isolated.

value: Primary mous aortic smooth muscle cel

value: KO

value: High-fat diet feeding

tag: chip antibody

value: noe


title: PBMCs from CI treated metastatic melanoma patient 36403 who did not develop CIADM. On-CI Therapy.

description: Library name: J2

value: Matched Control for patient 43120


title: db/db_1_zone1_2

description:
Library name: sample13
DSP-1001660015390-C-B02


title: WT_MAFK

description: Library name: Sample 5

value: WT

value: MAFK (Abcam, #ab229766)


title: PBMCs from CI treated metastatic melanoma patient 36403 who did not develop CIADM. Pre-CI treatment.

description: Library name: J1


title: WT_INPUT

description: Library name: Sample 7


title: KO_MAFK

description: Library name: Sample 6


title: db/db_1_zone3_1

description:
Library name: sample12
DSP-1001660015390-C-B01


title: KO_H3k27ac

description: Library name: Sample 2

value: H3K27ac (Abcam, #ab4729)


title: db/db_1_zone2_1

description:
Library name: sample11
DSP-1001660015390-C-A12


title: WT_H3K4me3

description: Library name: Sample 3

value: H3K4me3 (Abcam, #ab8580)


title: KO_H3K4me3

description: Library name: Sample 4


title: labellum1 from two-year seedling

city: Guiyang

first: Songtao

last: He

state: Guizhou

address: Bachelor's Road, Sunshine Community Service Center, Huaxi District

institute: Guizhou university

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: 005)
Trimmed sequence reads were mappedto GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost 2 insenin cost 3 deletion cost 3lengh fraction: 0.8 similanty 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: tab-delimited text files include RPKM values for each Sample

organism: Dendrobium nobile

source_name: labellum

growth_protocol: Theseedlings were obtained from “Danxia” stone in Chishui, Guizhou, then was cultivated in the media (pycnogenol: vermiculite=3:1) within the greenhouse environment.

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 manufacturers protocols.

treatment_protocol: different tissues

value: labellum

value: tissue

value: chichai No .1

value: different tissues


title: db/db_1_zone1_1

description:
Library name: sample10
DSP-1001660015390-C-A11

value: model


title: stem2 from one-year seedling

source_name: stem

value: stem


title: bud2 from two-year seedling

source_name: bud

value: bud


title: PBMCs from CI treated metastatic melanoma patient 33459 who developed CIADM. Post diabetes diagnosis.

description: Library name: I8

value: periperal blood mononuclar cells

value: CI-associated diabetes mellitus case


title: PBMCs from CI treated metastatic melanoma patient 29632 who developed CIADM. On-CI Therapy.

description: Library name: I5


title: leaf1 from one-year seedling

source_name: leaf

value: leaf


title: db/m_1_zone1_3

description:
Library name: sample7
DSP-1001660015390-C-A08

value: liver

value: control


title: WT_H3k27ac

description: Library name: Sample 1

value: Primary mous aortic smooth muscle cel

value: High-fat diet feeding


title: db/m_1_zone2_3

description:
Library name: sample8
DSP-1001660015390-C-A09


title: PBMCs from CI treated metastatic melanoma patient 33459 who developed CIADM. On-CI Therapy.

description: Library name: I7


title: PBMCs from CI treated metastatic melanoma patient 29632 who developed CIADM. Pre-CI treatment.

description: Library name: I4


title: root2 from one-year seedling

source_name: root

value: root


title: petal1 from two-year seedling

source_name: petal

value: petal


title: PBMCs from CI treated metastatic melanoma patient 29632 who developed CIADM. Post diabetes diagnosis.

description: Library name: I6


title: db/m_1_zone3_2

description:
Library name: sample6
DSP-1001660015390-C-A07


title: leaf2 from one-year seedling


title: T3_3 (2%)

city: Yinchuan

first: Wenyi

last: Ren

address: 489 Helanshan West Road, Xixia District, Yinchuan City, Ningxia

department: College of Animal Science and Technology

institute: Ningxia University

description:
Library name: GSM2345678_Liver_9
T3_3:fpkm

data_processing:
CLC Gencmics Workbench v 11.0.1
Sequence reads were timmed for adaptor sequence/low-aualty sequence using ClC genomic benchwork (parameler- Quality limit: 0 05)
Trimmed sequence reads were mappedto GrCM38/mm 10 using lC genoric benchaok (parnamelers- mismath cost: 2 insericn cost 3 delesion cost 3 lengh facticn 0.8 similarty faction 0.8)
Read count extraction and normalization were performed using ClC genmic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text fles include RPKM values for each Sample

organism: Ovis aries

source_name: Liver

extract_protocol:
Liver  samples were taken immediately after slaughter and stored in liquid nitrogen for testing. The total RNA of the liver  was extracted using TRIzol (Invitrogen, Carlsbad, CA). Then, a NanoDrop spectrophotometer (Thermo Fisher Scientific, Wilmington, MA, USA) was used to quantify the RNA concentration, and the integrity of the RNA samples was evaluated using 1% agarose-formaldehyde gel electrophoresis. RNA concentration was measured using a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 system (Agilent Technologies, Santa Clara, CA, USA). Sequencing libraries were generated using the NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA, USA) according to the manufacturer’s recommendations, and index codes were added to attribute sequences to each sample.
To select cDNA fragments with a length of approximately 240 bp, the library fragments were purified with the AMPure XP system (Beckman Coulter, Beverly, MA, USA). A 3-μl volume of USER Enzyme (New England Biolabs) was incubated with size-selected, adaptor-ligated cDNA at 37 °C for 15 min followed by 5 min at 95 °C. PCR was performed with Phusion High-Fidelity DNA polymerase, universal PCR primers, and index (X) primer. PCR products were purified (AMPure XP system), and library quality was assessed with the Agilent Bioanalyzer 2100. Index-coded samples were clustered on a cBot Cluster Generation System using TruSeq PE Cluster Kit v.4-cBot-HS (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions. After cluster generation, cDNA libraries were sequenced on an Illumina platform, and paired-end reads were generated.

value: Liver

value: basal diet + 2% succinate


title: PBMCs from CI treated metastatic melanoma patient 13974 who developed CIADM. On-CI Therapy.

description: Library name: I2


title: T3_2 (2%)

description:
Library name: GSM2345678_Liver_8
T3_2:fpkm


title: PBMCs from CI treated metastatic melanoma patient 13974 who developed CIADM. Post diabetes diagnosis.

description: Library name: I3


title: db/m_1_zone2_2

description:
Library name: sample5
DSP-1001660015390-C-A06


title: db/m_1_zone3_3

description:
Library name: sample9
DSP-1001660015390-C-A10


title: stem1 from one-year seedling

value: tissue


title: T3_1 (2%)

description:
Library name: GSM2345678_Liver_7
T3_1:fpkm


title: db/m_1_zone3_1

description:
Library name: sample3
DSP-1001660015390-C-A04


title: PBMCs from CI treated metastatic melanoma patient 13974 who developed CIADM. Pre-CI treatment.

description: Library name: I1


title: db/m_1_zone1_2

description:
Library name: sample4
DSP-1001660015390-C-A05


title: PBMCs from CI treated metastatic melanoma patient 34955 who did not develop CIADM. On-CI Therapy.

description: Library name: H1

value: Matched Control for patient 38826


title: bud1R1from two-year seedling

value: chichai No .1

value: different tissues


title: T2_3 (2%)

description:
Library name: GSM2345678_Liver_6
T2_3:fpkm

value: basal diet + 1% succinate


title: root1 from one-year seedling


title: T2_2 (1%)

description:
Library name: GSM2345678_Liver_5
T2_2:fpkm


title: petal2R1from two-year seedling


title: labellum2 from two-year seedling

value: labellum


title: T2_1 (1%)

description:
Library name: GSM2345678_Liver_4
T2_1:fpkm


title: db/m_1_zone1_1

description:
Library name: sample1
DSP-1001660015390-C-A02


title: PBMCs from CI treated metastatic melanoma patient 34955 who did not develop CIADM. Pre-CI treatment.

description: Library name: G1

value: periperal blood mononuclar cells


title: heart, 9mo Het/F 0685, male: H0685M

city: Columbus

first: Jill

last: Rafael-Fortney

state: OH

address: 460 W. 12th Ave

department: Physiology & Cell Biology

institute: The Ohio State University

data_processing:
Novogene In-house Bioinformatics
Novogene Novomagic Software
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean 1 reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2[2] as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts[3] v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: mm39
Supplementary files format and content: excel file containing differential gene counts for each gene for each sample

source_name: heart

extract_protocol:
RNA was extracted with Trizol following manufacturer instructions then Dnase treated and purified. 1uL RNA was used for nanodrop and bioanalyzer quality check before shipping remaining RNA to Novogene
RNA libraries were prepared by Novogene using NEBNext Ultra II RNA Library Prep by Illumina

value: heart

tag: Sex

value: male

value: Het/Fiona


title: JAR+NK_rep2

city: Nagoya

first: Kosuke

last: Yoshida

state: Aichi

address: 65 Tsuruma-cho

country: Japan

institute: Nagoya University

description: Library name: Sample4

data_processing:
Expression levels for each gene were quantified from the sequencing data by Kallisto software.
The tximport package (ver. 1.18.0) was used to summarize the data.
Assembly: Homo_sapiens.GRCh38
Supplementary files format and content: a tsv file includes TPM counts of each sample

source_name: JAR

growth_protocol: JAR cells were co-cultured with NK cells in the presence of 100 IU/mL IL-2 at a ratio of 5:1. As a control, JAR cells were cultured with 100 IU/mL IL-2 without NK cells.

extract_protocol:
After 24 hours of incubation, JAR cells were isolated by flow cytometry. Specifically, CD57-positive NK cells and dead cells were excluded, and viable JAR cells were sorted. Total RNA was then extracted using the miRNeasy Mini Kit.
The library construction and pair-end sequencing were conducted by Novogene. (Beijing, China.)

value: JAR

value: co-culture with NK cells under IL-2


title: heart, 9mo Het/F 0770, male: H0770M


title: db/m_1_zone2_1

description:
Library name: sample2
DSP-1001660015390-C-A03

value: liver

value: control


title: PBMCs from CI treated metastatic melanoma patient 34104 who did not develop CIADM. Pre-CI treatment.

description: Library name: E8

value: Matched Control for patient 52405


title: PBMCs from CI treated metastatic melanoma patient 34104 who did not develop CIADM. On-CI Therapy.

description: Library name: F8


title: C_1 (0%)

description:
Library name: GSM2345678_Liver_1
C_1:fpkm

value: Liver

value: basal diet


title: C_2 (0%)

description:
Library name: GSM2345678_Liver_2
C_2:fpkm


title: heart, 9mo Het/F 0655, female; H0655F

value: female


title: JAR+NK_rep1

description: Library name: Sample3


title: heart, 9mo F/DKO 0698, male: D0698M

value: Fiona/dko


title: SGL-1, beta-cypermethrin-sensitive Aphis gossypii, pooled whole body, repeat1

city: Haikou

first: Yunfei

last: Zhang

address: 58 Renmin Avenue

institute: School of Tropical Agriculture and Forestry, Hainan University

description: Library name: Unknown_AM626-01T0004

data_processing:
Samples are sequenced on the platform to get image files, which are transformed by the software of the sequencing platform, and the original data in FASTQ format (Raw Data) is generated. Sequencing data contains a number of connectors, low-quality Reads, so we use fastp (0.22.0) software to filter the sequencing data to get high quality sequence (Clean Data) for further analysis.
Assembly: The obtained high-quality sequencing data was mapped to the A. gossypii genome ASM401081v1 as a reference using HISAT2
Supplementary files format and content: CSV file including Reads count for each sample
Supplementary files format and content: CSV file including FPKM for each sample

organism: Aphis gossypii

source_name: whole body

extract_protocol:
Total RNA samples were prepared using a RNAiso Plus kit (Takara, Dalian, China) following the manufacturer’s instructions.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: whole body

value: WT


title: RGL-3, beta-cypermethrin-resistant Aphis gossypii, pooled whole body, repeat3

description: Library name: Unknown_AM626-01T0003

value: beta-cypermethrin-resistant srain


title: DMSO

city: New Orleans

first: Jovanny

last: Zabaleta

state: LA

address: 1700 Tulane Ave

department: Interdisciplinary Oncology

institute: LSUHSC

description: 10x Genomics

library_source: transcriptomic single cell

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

source_name: Spleen and lymph nodes (T cells) and bone marrow (MDSC)

extract_protocol:
Activated CD8+ T cells were harvested after 48 hours following in vitro T cell activation and treatment. T cells were lysed with RLT containing 2-mercaptoethanol (Sigma #M7154-24ML) and passed through a QIAshredder (Qiagen #79656) column before extraction using a RNeasy mini kit (Qiagen #74106) following the manufacturer’s instructions with an on-column DNase digestion step (Qiagen #79254)
Chromium next GEM single-cell 3’ reagent kit v3.1 (10x Genomics #1000269) following the manufacturer’s instructions

treatment_protocol:
Murine T cells were activated with 0.1, 0.5, or 1mg/ml plate-bound anti-mouse CD3e (BD Biosciences #553058, clone 145-2C11) and anti-mouse CD28 (BD Biosciences #553294, clone 37.51).GPR84 antagonist GLPG1205 or agonist DL175 were dissolved in DMSO and diluted with cRPMI-1640 to a working concentration of 3µM or 10µM. Treatment was done for 48h before RNA extraction.
GPR84 antagonist GLPG1205 or agonist DL175 were dissolved in DMSO and diluted with cRPMI-1640 to a working concentration of 3µM or 10µM. Treatment was done for 48h before RNA extraction.

value: T cells, BM-MDSC

tag: strain

value: WT C57Bl/6

value: DMSO


title: SGL-2, beta-cypermethrin-sensitive Aphis gossypii, pooled whole body, repeat2

description: Library name: Unknown_AM626-01T0005


title: SGL-3, beta-cypermethrin-sensitive Aphis gossypii, pooled whole body, repeat3

description: Library name: Unknown_AM626-01T0006


title: heart, 9mo F/DKO 0687, male: D0687M

value: heart

value: male


title: RGL-2, beta-cypermethrin-resistant Aphis gossypii, pooled whole body, repeat2

description: Library name: Unknown_AM626-01T0002


title: D10

description: 10x Genomics

value: Spleen and lymph nodes (T cells) and bone marrow (MDSC)

value: agonist DL175


title: C_3 (0%)

description:
Library name: GSM2345678_Liver_3
C_3:fpkm


title: heart, 9mo F/DKO 0672, female: D0672F


title: JAR_rep1

description: Library name: Sample1

value: JAR

value: control (IL-2)


title: OC-3

status: Public on Dec 25 2025

city: Wuhan

first: Yaoting

last: Ji

state: Hubei

address: No.237 Luoyu Road

institute: Wuhan University

description: Library name: Sample 3

data_processing:
RNA-seq
Illumina Casava 1.8 software used for basecalling
Raw data (raw reads) of fastp format were firstly processed through in-house perl scripts..In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Assembly: Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Supplementary files format and content: GRCh38/hg38
Supplementary files format and content: tab-delimited text files include FPKM values and gene count for each Sample

source_name: Bone marrow

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using Fast RNA-seq Lib Prep Kit V2 （Cat.No.RK20306）following manufacturer's protocols.

value: Bone marrow

value: macrophage


title: OC+NBIF-1

description: Library name: Sample 4

value: neobavaisoflavone


title: OC+NBIF-2

description: Library name: Sample 5


title: OC+NBIF-3

description: Library name: Sample 6


title: OC-2

description: Library name: Sample 2


title: (stim2a;stim2b)-/- , replicate 3, scRNA-seq

city: Warsaw

first: Shamba

middle: S.

last: Mondal

address: Księcia Trojdena 4

country: Poland

description: 10x Genomics

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation were done using the Cell Ranger software v6.1.2
Assembly: GRCz11/ danRer11
Supplementary files format and content: Tab-separated values files and matrix files

organism: Danio rerio

source_name: brain

growth_protocol: To create the (stim2a;stim2b) -/- double-knockout zebrafish line, stim2a-/- fish were outcrossed with the stim2b-/- line. Briefly, both stim2a-/- and stim2b-/- lines were created using CRISPR/Cas9 techniques. The stim2a-/- zebrafish line was created by introducing a 5 bp deletion in the 7th exon (Ensembl ID: ENSDART00000114097.4), which gives an early stop codon. The stim2b-/- zebrafish line was created by introducing a 4 nt insertion in exon 3 of stim2b (Ensembl ID: ENDART00000012089). Heterozygous fish of this F1 generation were then in-crossed. To identify homozygous (stim2a;stim2b)-/- fish in the F2 generation, stim2b-/- geno- typing was first performed according to a previously set-up protocol using high-resolution melting (HRM) analysis. From this HRM analysis, (stim2a;stim2b)+/+ and stim2b-/- fish were screened according to a previously set-up protocol for stim2a-/- fish. (stim2a;stim2b)+/+ and (stim2a;stim2b)-/- fish were identified from this screening.

extract_protocol:
5 dpf larvae were anaesthetised by tricaine methanesulfonate (MS222), a neuromuscular blocker (Collymore et al., 2014), and heads were dissected in Dulbecco’s Modified Eagle Medium/Nutrient Mixture F-12 (DMEM/F-12; with Ca2+, and L-glutamine, and without HEPES, and Phenol Red; Gibco) with 10% foetal bovine serum (FBS; Gibco). After eyes were removed promptly, tissue dissociation and single-cell suspension were made according to previously described methods (Bresciani et al., 2018) for zebrafish and placed on ice.  Immediately after isolation of single-cell suspension, the cells were sorted based on GCaMP5G fluorescence (with 488 nm excitation and 510 nm emission) to obtain the cells of neuronal origin. The GCaMP5 was expressed under the elav/Huc promoter, which is an early marker of neuronal cells (Kim et al., 1996, Feng et al., 2019). Cell sorting was performed with a BD FACSAria II (BD Biosciences, Franklin Lakes, NJ) with support from the Core Facility at the International Institute of Molecular and Cell Biology in Warsaw. Cell viability was measured using the trypan blue staining method, and when the viability of cells was ~80%, the cells were immediately loaded on the 10X Chromium system for droplet encapsulation as described previously (Zheng et al., 2016).
Approximately 8000 cells were sorted and suspended in ~40 μl volume. Cells were loaded according to the Chromium single cell 3′ kit’s standard protocol (V3 chemistry). To prepare the cells for droplet-based sequencing, GCaMP5G-positive single-cell suspension was carefully mixed with reverse transcription mix before loading the cells on the 10X Genomics Chromium system, the standard manufacturer’s protocol. During the encapsulation, the cells were lysed within the droplet, and they released polyadenylated RNA bound to the barcoded bead, which was encapsulated with the cell. Following the 10x Genomics user manual’s guidelines, the droplets were directly subjected to reverse transcription, the emulsion was broken, and cDNA was purified using Silane beads. After the amplification of cDNA with 13 cycles, purification and quantification were performed. The 10X Genomics single-cell RNA-sequencing library preparation – involving fragmentation, dA-tailing, adapter ligation, and 12-cycle indexing PCR – was performed. After quantification, the libraries were sequenced at the Nencki Institute of Experimental Biology on an Illumina NextSeq 550 machine using a HighOutput flowcell in paired-end mode (R1: 26 cycles; I1: 8 cycles; R2: 57 cycles), thus generating 80-125 million fragments.

value: brain

value: neuronal origin cells

tag: developmental stage

value: 5 dpf


title: (stim2a;stim2b)-/- , replicate 1, scRNA-seq

institute: International Institute of Molecular and Cell Biology

description: 10x Genomics


title: LEPR+ KC rep2

city: Shanghai

first: Xuege

last: Wang

address: 320 Yueyang Road

institute: Shanghai Institute of Nutrition and Health

description:
Library name: Sample 15
Column name in KCs_gene_exp.txt: LEPR+KC_TPM_rep2

data_processing:
For RNA seq, paired-end reads were aligned to the mouse (GRCm38) reference genome with HISAT2
For scRNA seq, libraries were mapped with Cellranger (version 4.0.0), clustered with Seurat (version 4.3.0).
For stereo seq, sequences were aligned to mouse (GRCm38) reference genome using STAR and down processed with Stereo-Seq Analysis Workflow (SAW).
Assembly: mm10 and hg38
Supplementary files format and content: matrix, bam

source_name: kupffer cells

growth_protocol: For liver metastases sequence, AKP cells were intrasplenically injected to C57BL/6 mice.

extract_protocol:
For mRNA sequence, RNA was extracted from Kupffer cells of AKP liver metastases before and after chemotherapy using Trizol (Invitrogen) and reverse transcribed into cDNA using the HiScript II Q RT SuperMix kit (Vazyme).
For RNA seq, libraries were prepared according to the illumina standard instructions. For scRNA seq, libraries were prepared using the Chromium Single Cell 3’ Reagent Kit v2. For spatial transcriptomics,  libraries were prepared using the Stereo-seq Transcriptomics Set for Chip-on-a-slide (STOmics).

treatment_protocol: treatment with FOLFOX regimen

value: kupffer cells


title: KC-1 rep1

description:
Library name: Sample 10
Column name in KCs_gene_exp.txt: KC-1_TPM_rep1


title: (stim2a;stim2b)-/- , replicate 2, scRNA-seq

description: 10x Genomics


title: JAR_rep2

description: Library name: Sample2


title: KC-2 rep2

description:
Library name: Sample 13
Column name in KCs_gene_exp.txt: KC-2_TPM_rep2


title: Tg control (stim2a;stim2b)+/+, replicate 2, scRNA-seq

description: 10x Genomics


title: Tg control (stim2a;stim2b)+/+, replicate 3, scRNA-seq

description: 10x Genomics


title: ORC_209_PBMC

city: Fort Collins

first: Steven

last: Dow

state: CO

address: 300 W Drake Rd

department: Clinical Sciences

institute: Colorado State University

data_processing:
Partek® Flow® software, v10.0
Reads were trimmed for Phred score of 20, adapters removed using cutadapt
Trimmed reads were aligned using STAR 2.7.3 using EquCab3.0 and annotated with Ensembl EquCab3.0.107
Feature counts were generated with HTseq
Differential analysis was computed using counts normalized to CPM, using DESeq
Assembly: ENSEMBL EquCab3.0
Supplementary files format and content: txt file with median ratio normalized counts

organism: Equus caballus

source_name: PBMC

growth_protocol: To isolate synovial cells for sequencing, synovial fluid samples were digested with hyaluronidase (30 µg/mL) and incubated at 37°C for 15 minutes, then centrifuged at 2000rpm at 8°C for 10 minutes to obtain a cell pellet.

extract_protocol:
RNA was extracted from frozen synovial and PBMC cell pellets using the RNAeasy kit
mRNA was enriched using oligo (dT) beads, followed by cDNA library generation using TruSeq RNA Library Prep Kit (Illumina, San Diego, CA).

value: PBMC

value: Mixed mononulear cells

value: WT

tag: disease

value: Healthy


title: Tg control (stim2a;stim2b)+/+, replicate 1, scRNA-seq

description: 10x Genomics


title: U251cells,ultrasound1

city: Harbin

first: mingming

last: li

address: No. 2075, Qunli Seventh Street

department: Department of Qunli Ultrasound

institute: The First Affiliated Hospital of Harbin Medical University

description:
Library name: sample4
US1

data_processing:
Illumina Casava 1.8 software used for basecalling
Raw data (raw reads) of fastp format were firstly processed through in-house perl scripts..In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values and gene count for each Sample

source_name: Human glioma cell line

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: Human glioma cell line

value: GBM

value: ultrasound,1 W/cm2 for 40 s


title: U251cells,ultrasound3

description:
Library name: sample6
US3


title: OC-1

description: Library name: Sample 1

value: DMSO


title: (stim2a;stim2b)-/- , replicate 4, scRNA-seq

description: 10x Genomics


title: G10

description: 10x Genomics

value: T cells, BM-MDSC

value: Spleen and lymph nodes (T cells) and bone marrow (MDSC)

value: WT C57Bl/6

value: GPR84 antagonist GLPG1205


title: RGL-1, beta-cypermethrin-resistant Aphis gossypii, pooled whole body, repeat1

description: Library name: Unknown_AM626-01T0001

value: whole body

value: beta-cypermethrin-resistant srain


title: ORC_209_SF

source_name: SF

value: SF


title: U251cells,ultrasound2

description:
Library name: sample5
US2


title: Tg control (stim2a;stim2b)+/+, replicate 4, scRNA-seq

description: 10x Genomics

value: brain

value: neuronal origin cells

value: 5 dpf


title: ORC_205_SF

value: Mixed mononulear cells


title: KC-2 rep1

description:
Library name: Sample 12
Column name in KCs_gene_exp.txt: KC-2_TPM_rep1

value: kupffer cells


title: U251cells,control3

description:
Library name: sample3
Con3

value: WT

value: control


title: ORC_208_SF

value: Healthy


title: Untreated-3

first: guozhu

last: xie

address: Shatainan Road No.1023-1063

institute: Southern Medical University

description: Library name: Sample9

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by fastp   Short reads alignment tool Bowtie2 (version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation.  An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2 2.1.0 and other parameters set as a default.
Assembly: hg38
Supplementary files format and content: xls files include TPM and raw counts for each sample

source_name: T cells

extract_protocol:
Total RNA was extracted from 5×10⁶ cells collected from each group (MOCK-T, LV-CAR-T, and CISH-KO-CAR-T) using Trizol reagent (Invitrogen) following the manufacturer's instructions. RNA integrity and quality were verified by agarose gel electrophoresis and assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies).
For library preparation, eukaryotic mRNA was first enriched with Oligo(dT) beads, then fragmented and reverse-transcribed into cDNA using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB #7530). The resulting double-stranded cDNA fragments underwent end repair, adenylation, and Illumina adapter ligation. After purification with AMPure XP Beads (1.0X) and PCR amplification, the constructed libraries were subjected to paired-end sequencing on an Illumina Novaseq 6000 platform at Gene Denovo Biotechnology Co. (Guangzhou, China).

value: T cells


title: ORC_205_PBMC

value: PBMC


title: KC-1 rep2

description:
Library name: Sample 11
Column name in KCs_gene_exp.txt: KC-1_TPM_rep2


title: ORC_208_PBMC


title: Untreated-1

description: Library name: Sample7


title: LEPR+ KC rep1

description:
Library name: Sample 14
Column name in KCs_gene_exp.txt: LEPR+KC_TPM_rep1


title: Untreated-2

description: Library name: Sample8


title: ORC_202_SF


title: ORC_200_PBMC


title: EP-1A10-3

description: Library name: Sample3


title: ORC_202_PBMC


title: LV-1A10-2

description: Library name: Sample5


title: ORC_201_SF


title: ORC_200_SF


title: U251cells,control2

description:
Library name: sample2
Con2

value: Human glioma cell line

value: GBM


title: U251cells,control1

description:
Library name: sample1
Con1


title: ORC_207_PBMC


title: EP-1A10-1

description: Library name: Sample1


title: LV-1A10-1

description: Library name: Sample4


title: ORC_198_SF


title: ORC_197_SF


title: ORC_192_SF


title: EP-1A10-2

description: Library name: Sample2


title: ORC_197_PBMC


title: ORC_192_PBMC


title: ORC_196_SF


title: KU812 resistant cells, 1

city: Kharghar

first: Rukmini

last: Govekar

state: Maharashtra

address: Sector 22, Utsav Chowk-CISF Rd, Owe camp

department: Cancer Research Institute

country: India

institute: Advanced centre for Treatment, Research and Education in Cancer

description: Library name: Sample 7

data_processing:
transcript quantification was performed using Salmon v0.8.1
Gene-level counts were derived from Salmon output via tximport
Differential expression analysis was conducted by comparing each cell line to three normal tissue samples through negative binomial generalized linear modelling. Genes were considered differentially expressed based on a Wald test adjusted p-value < 0.05 and an absolute log fold change > 1.5.
Assembly: Transcriptome index building was performed on transcriptome reference index downloaded from UCSC browser followed by quantification of transcripts. #hg19
Supplementary files format and content: tab-delimited table contains transcript-level quantification from RNA-seq.

source_name: KU812 cells

extract_protocol:
RNA was extracted using AllPrep DNA/RNA/miRNA Universal Kit (Quigen). 200ng of Total RNA was taken as the input for the assay
NEB Ultra RNA-Seq Library Prep kit  (NEB # E7530L) was used to prepare libraries for total RNA sequencing

value: KU812 cells

value: Basophilic cells

value: IM treated

value: Imatinib resistant


title: KU812 sensitive cells, 2

description: Library name: Sample 6

value: Imatinib sensitive


title: ORC_188_SF

value: SF


title: LV-1A10-3

description: Library name: Sample6


title: KU812 sensitive cells, 1

description: Library name: Sample 5


title: OA_9570_SF

value: OA


title: K562 Sensitive cells, 2

description: Library name: Sample 2

source_name: K562 cells

value: K562 cells

value: Erythroid cells


title: K562 resistant cells, 2

description: Library name: Sample 4


title: K562 resistant cells, 1

description: Library name: Sample 3


title: NFIB-knockout HeLa cells, replicate 4

city: Taipa

first: He

last: Song

state: Macau

address: Avenida da Universidade Research Building N22

department: Institute of Chinese Medical Sciences

country: Macau

institute: University of Macau

description: Library name: Sample-8

data_processing:
Paired-end reads were trimmed and aligned to the hg38 genome using STAR aligner (v2.7.11b). Differential expression analysis was performed using the getDifferentialPeaksReplicates.pl script within the HOMER suite and the DESeq2 R package (v1.16.1).
Assembly: hg38
Supplementary files format and content: A tab-delimited text file containing FPKM values for all genes comparing wild-type and NFIB knockout samples

source_name: HeLa

growth_protocol: Cells were maintained in DMEM supplemented with 10% fetal bovine serum, 100 units/mL penicillin, and 100 μg/mL streptomycin (Invitrogen), at 37 °C with an atmosphere of 5% CO2 and 95 % humidity.

extract_protocol:
Total RNA was isolated using the  RNA-easy Isolation Reagent (QIAGEN). 200ng of the total RNA was used for the RNA library preparation.
Paired-end libraries were prepared using the VAHTS® Universal V8 RNA-seq Library Prep Kit (Vazyme Technology Co., Ltd., Nanjing, China) following the manufacture's protocols.

treatment_protocol: HeLa cells and NFIB-knockout HeLa cells generated via CRISPR/Cas9 genome editing (catalog numbers YC-A012 and YKO-XN31872, respectively) were purchased from Guangzhou Yuanjing Biotechnology Co. Ltd.

value: HeLa

value: Immortalized cell line

value: NFIB knockout

value: CRISPR-Cas9 knockout


title: K562 Sensitive cells, 1

description: Library name: Sample 1

value: WT


title: OA_9350_SF

value: Mixed mononulear cells


title: OA_9570_PBMC

value: PBMC


title: KU812 resistant cells, 2

description: Library name: Sample 8


title: NFIB-knockout HeLa cells, replicate 3

description: Library name: Sample-7


title: HCC_L_T

city: Beijing

first: Fengna

last: Yan

address: No. 8 Jingshun East Street, Chaoyang District

department: Beijing Ditan Hospital

institute: Capital Medical University

description:
Library name: sample 4
Hepatocellular Carcinoma, Patient 2, Liver Cancer Tumor Tissue

data_processing:
Raw reads were trimmed of adapters and low-quality bases using Fastp (v0.20.1) and processed with the SeekSoul Tools pipeline to generate a gene-expression matrix. Downstream analyses were performed in Seurat v3: nuclei or cells of high or low quality were filtered based on gene counts, UMI counts, and mitochondrial gene proportions; after normalization, PCA was applied for dimensionality reduction followed by graph-based clustering. Intestinal mucosal cell subpopulations were extracted, and differentially expressed genes (DEGs) between conditions were identified using the Wilcoxon rank-sum test (adjusted p < 0.05). Finally, GO and KEGG pathway enrichment analyses of these DEGs were conducted using ClusterProfiler to elucidate the molecular mechanisms underlying PEDV-induced changes in intestinal mucosal cells.
Assembly: hg38
Supplementary files format and content: tab-separated values files and matrix files

source_name: liver

extract_protocol:
An appropriate number of cells were loaded into the flow channel of the SeekOne MM chip and allowed to settle into microwells by gravity. Unsettled cells were removed, and cell-barcoded magnetic beads (CBBs) were pipetted into the flow channel and allowed to settle into microwells under a magnetic field. Excess CBBs were rinsed away, and cells on the MM chip were lysed to release and capture RNA.
Reverse transcription was carried out at 37 °C for 30 min. The barcoded cDNA on CBBs was hybridized with a random primer containing read-2 SeqPrimer sequences at the 5′ end, enabling extension to form the second strand with a 3′ cell barcode. The resulting second-strand DNA was denatured off the CBBs, purified, and amplified by PCR. The cDNA product was cleaned, ligated to adapters and sample indices, and the indexed sequencing libraries were purified with SPRI beads, quantified, and sequenced on an Illumina NovaSeq.

value: liver


title: HCC_W_PT

description:
Library name: sample 5
Hepatocellular Carcinoma, Patient 3, Adjacent Non-cancerous Liver Tissue


title: HCC_W_T

description:
Library name: sample 6
Hepatocellular Carcinoma, Patient 3, Liver Cancer Tumor Tissue


title: OA_9350_PBMC


title: HCC_L_PT

description:
Library name: sample 3
Hepatocellular Carcinoma, Patient 2, Adjacent Non-cancerous Liver Tissue


title: OA_4110_PBMC


title: NFIB-knockout HeLa cells, replicate 2

description: Library name: Sample-6


title: HCC_J_T

description:
Library name: sample 2
Hepatocellular Carcinoma, Patient 1, Liver Cancer Tumor Tissue


title: NFIB-knockout HeLa cells, replicate 1

description: Library name: Sample-5


title: normosmic control sample 3 TCRseq

city: Durham

first: Sarah

last: Kim

state: NC

address: 481 MSRB1

institute: Duke University

description:
Library name: NORMOSMIC3 TCR
10X Genomics

data_processing:
Raw base call files were analyzed using Cell Ranger v.7.1.0 using the Duke Cluster Computing platform. The ‘mkfastq’ command was used to generate FASTQ files from bcl Illumina sequencer output files.
cellranger-7.1.0 ‘counts’ command was used to generate raw gene-barcode matrices aligned to the GRCh38 v7.0.0 V(D)J human reference genome
Assembly: Human GRCh38 v7.0.0 V(D)J reference
Supplementary files format and content: filtered_contig_annotations
Library strategy: TCR-Seq

source_name: Olfactory epithelium

extract_protocol:
Biopsy specimens were collected in either HBSS + 10% FBS or Hibernate E Media +10% FBS, spun down, then digested using collagenase I, dispase and DNAse, papain, and trypsin. Cells were filtered through a 70 μm strainer, pelleted and washed, and then treated with an erythrocyte lysis buffer and washed again. The cells were then resuspended in PBS with 0.1% bovine serum albumin and 0.2% anti-clumping agent (Invitrogen) and immediately processed for scRNA-seq.
Samples were processed for TCR-seq using Chromium Single Cell 5′ V(D)J-enriched paired-End, Dual-Index Library & Gel Bead Kit v2 (10X Genomics) targeting 10000 cells, then TCR alpha-beta chains were sequenced using NextSeq 6000 (Illumina) flow cells.

value: Olfactory epithelium

value: olfactory epithelial cells

value: control

value: brush


title: HCC_J_PT

description:
Library name: sample 1
Hepatocellular Carcinoma, Patient 1, Adjacent Non-cancerous Liver Tissue


title: ORC_188_PBMC

value: Healthy


title: HeLa cells, replicate 4

description: Library name: Sample-4


title: OA_3850_SF

value: SF


title: normosmic control sample 2 TCRseq

description:
Library name: NORMOSMIC2 TCR
10X Genomics


title: HeLa cells, replicate 3

description: Library name: Sample-3


title: long-covid hyposmic sample 3 TCRseq

description:
Library name: COVID3 TCR
10X Genomics

value: long-COVID


title: OA_3850_PBMC

value: OA


title: long-covid hyposmic sample 2 TCRseq

description:
Library name: COVID2 TCR
10X Genomics


title: HeLa cells, replicate 2

description: Library name: Sample-2


title: OA_2615_SF


title: long-covid hyposmic sample 1 TCRseq

description:
Library name: COVID1 TCR
10X Genomics

value: surgical


title: OA_2615_PBMC


title: normosmic control sample 3 5' GEX

description:
Library name: NORMOSMIC3 5GEX
10X Genomics

data_processing:
Raw base call files were analyzed using Cell Ranger v.8.0.0 using the Duke Cluster Computing platform. The ‘mkfastq’ command was used to generate FASTQ files from bcl Illumina sequencer output files.
CellRanger v.8.0.0 ‘counts’ command was used to generate raw gene-barcode matrices aligned to the GRCh38-2024-A Ensembl 98 human genome
Assembly: GRCh38-2024-A
Supplementary files format and content: barcodes.tsv, features.tsv, matrix.mx

extract_protocol:
Biopsy specimens were collected in either HBSS + 10% FBS or Hibernate E Media +10% FBS, spun down, then digested using collagenase I, dispase and DNAse, papain, and trypsin. Cells were filtered through a 70 μm strainer, pelleted and washed, and then treated with an erythrocyte lysis buffer and washed again. The cells were then resuspended in PBS with 0.1% bovine serum albumin and 0.2% anti-clumping agent (Invitrogen) and immediately processed for scRNA-seq.
Samples were processed for scRNA-seq using Chromium Single Cell 5′ Paired-End, Dual-Index Library & Gel Bead Kit v2 (10X Genomics) targeting 10000 cells, then sequenced using NextSeq 6000 (Illumina) flow cells.


title: HeLa cells, replicate 1

description: Library name: Sample-1

value: HeLa


title: normosmic control sample 2 5' GEX

description:
Library name: NORMOSMIC2 5GEX
10X Genomics


title: Microglia,SPCM_IL,48hours

city: Seoul

first: Tae-won

address: Gamasan-ro 20-gil, 8

department: Medical science

country: South Korea

institute: Korea university

data_processing:
Illumina bcl2fastq (v2.20.0.422) used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and filtered for low-complexity or low-quality sequence(using fastp), then mapped to GRCh38 (NCBI) whole genome using STAR.
Read count extraction using HTSeq-count.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include read count values for each Sample

source_name: Brain

growth_protocol: SV40 human microglia cells were maintained in Prigrow 3 supplemenmted with 10% FBS and 1% P/S in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#015) standard protocols.

treatment_protocol: SV40 human microglia cells were treated with DF12, SPCM, SPILCM for 48 hours.  DF12: DMEM/F12 medium  SPCM: A spheroid was cultured in DMEM/F12 for 48 hours, and the supernatant was collected. The spheroid consisted of 1.8 × 10^4 nucleus pulposus cells and 3.2 × 10^4 annulus fibrosus cells.  SPILCM: A spheroid was cultured in DMEM/F12 with 1 ng/ml of IL-1β for 48 hours, and the supernatant was collected. The spheroid consisted of 1.8 × 10^4 nucleus pulposus cells and 3.2 × 10^4 annulus fibrosus cells.

value: Brain

value: Microglia cell


title: E13.5 G2G3W1 MNP

city: Cincinnati

first: Simon

middle: J. Y.

last: Han

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

description: Library name: Sample 1

data_processing:
The sequencing output data was processing using CellRanger from 10X Genomic's Cloud Platform (http://cloud.10xgenomics.com) to obtain a gene-cell data matrix.
Reads were aligned to mouse genome [mm10] to produce counts of genes across barcodes.
Cells with less than 200 features, more than 6000 features, and more than 10% mitochondrial gene expression were not included in downstream analysis. QC, Filtering, Normalization and Clustering was carried out using Seurat [v4.3.0]
Assembly: mm10
Supplementary files format and content: matrix.mtx.gz

source_name: mandibular prominence

growth_protocol: Mice were maintained in specified pathogen free condition in accordance with institutional guidance.

extract_protocol:
E13.5 mandibles from control CD1 or Gli2f/f;Gli3f/f;Wnt1-Cre mouse embryos were dissected in ice-cold DEPC PBS and minced to a fine paste. 12.5 mg of tissue was placed in a sterile 1.5 mL tube containing 0.5 mL protease solution containing 125 U/mL DNase and 5 mg/mL Bacillus Licheniformis. The samples were incubated at 4C for a total of 10 minutes, with trituration using a wide boar pipette tip every minute after the first two. Protease was inactivated using ice-cold PBS containing 0.02% BSA and filtered using 30 mM filter. The cells were pelleted by centrifugation at 200g for 4 minutes and resuspended in 0.02% BSA in PBS. Cell number and viability were assessed using a hemocytometer and trypan blue staining.
9,600 cells were loaded onto a well on a 10X Chromium Single-Cell instrument (10X Genomics) to target sequencing of 6,000 cells. Barcoding, cDNA amplification, and library construction were performed using the Chromium Single-Cell 3’ Library and Gel Bead Kit v3. Post cDNA amplification and cleanup was performed using SPRI select reagent (Beckman Coulter, Cat# B23318). Post cDNA amplification and post library construction quality control was performed using the Agilent Bioanalyzer High Sensitivity kit (Agilent 5067–4626). Libraries were sequenced using a NovaSeq 6000 and the S2 flow cell. Sequencing parameters used were: Read 1, 28 cycles; Index i7, eight cycles; Read 2, 91 cycles, producing about 300 million reads.

treatment_protocol: Timed mating between Gli2f/f;Gli3f/f and Gli2f/+;Gli3f/+;Wnt1-Cre mice were performed and the date when a plug was detected was considered embryonic day 0.5.

value: mandibular prominence


title: normosmic control sample 1 5' GEX

description:
Library name: NORMOSMIC1 5GEX
10X Genomics


title: Microglia,SPCM,48hours

value: WT

value: SPCM


title: lacrimal gland, NOD, 8 weeks, rep3

first: Siyuan

last: Li

address: No. 1 Dongjiaominxiang, Dongcheng District

institute: Beijing Tongren Hospital

description:
Library name: Sample 12
N8_3

data_processing:
Image processing and base recognition were performed using Solexa pipeline version 1.8 (Off-Line Base Caller software, version 1.8).
Assembly: GRCm38
Supplementary files format and content: The Express file format is xlsx, which analyses the expression of gene and transcript in the lacrimal gland of mice.

source_name: lacrimal gland

extract_protocol:
RNA was harvested using Trizol reagent and  1-2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using KAPA Stranded RNA-Seq Library Prep Kit (Roche) following manufacturer's protocols.

value: lacrimal gland


title: normosmic control sample 1 TCRseq

description:
Library name: NORMOSMIC1 TCR
10X Genomics


title: long-covid hyposmic sample 3 5' GEX

description:
Library name: COVID3 5GEX
10X Genomics


title: OA_1038_SF

value: Mixed mononulear cells


title: OA_1038_PBMC

value: PBMC


title: long-covid hyposmic sample 2 5' GEX

description:
Library name: COVID2 5GEX
10X Genomics

value: Olfactory epithelium

value: olfactory epithelial cells


title: long-covid hyposmic sample 1 5' GEX

description:
Library name: COVID1 5GEX
10X Genomics


title: Microglia,DMEM/F12,48hours


title: lacrimal gland, NOD, 8 weeks, rep2

description:
Library name: Sample 11
N8_2


title: lacrimal gland, NOD, 8 weeks, rep1

description:
Library name: Sample 10
N8_1