title: scRNA-Seq of Homo sapiens:ESCC_met3 [P11_2]

city: fujian xiamen

first: yangfan

last: Zhou

address: 55 Zhenhai Road, Siming District, Xiamen, Fujian Province

institute: The First Affiliated Hospital of Xiamen University

description: Library name: P11_2

data_processing:
The scRNA-seq FASTQ files were processed using “Cell Ranger” (v.7.1) software. Genome alignment was performed against the hg38 (human) reference to generate 10× expression matrix files for each sample. These 10× expression matrix files were further analyzed using the “Seurat” package
Assembly: hg38
Supplementary files format and content: 10X matirx files

source_name: esophagus

extract_protocol:
The tissue samples were rinsed with phosphate-buffered saline (PBS), minced into small pieces on ice, and the tumor tissue was further fragmented and incubated with 0.5 mg/mL of Digestion Enzyme 1 (prepared by 10K Genomics, Shanghai, China) at 37°C in a water bath for 60 min. The suspension was loaded onto a 10ʹ Chromium Controller (10× Genomics) following the manufacturer’s instructions. Single-cell RNA-seq libraries were prepared using the Chromium Single-Cell 3ʹ-End V3.1 Kit
Single-cell suspensions were processed using a 10× Chromium Controller to generate emulsion droplets, where individual cells in each droplet interacted with gel beads containing unique primers bearing 10× cell barcodes, unique molecular identifiers, and poly(dT) sequences. Full-length barcoded cDNA was synthesized using reverse transcription. Subsequently, the emulsion was disrupted, and cDNA was harvested, amplified, and enriched using reagents from the Chromium Single-Cell 3ʹ V3.1 Kit. Indexed sequencing libraries were constructed as follows: (1) fragmentation, end repair, and A-tailing; (2) size selection of cDNA fragments using SPRI beads; (3) ligation of sequencing adapters; (4) further enrichment of cDNA fragments with SPRI beads; and (5) indexing and final library enrichment using SPRI beads. The number of libraries sequenced was determined based on the cell count and paired-end 150-bp sequencing was performed on NovaSeq 6000 (Illumina).

value: esophagus


title: NEN liver metastasis_patient_005

status: Public on Sep 29 2025

type: genomic

city: Heidelberg

first: Stephanie

last: Roessler

address: Im Neuenheimer Feld 224

country: Germany

institute: Heidelberg University Hospital

description:
Infinium MethylationEPIC
240180

hyb_protocol: supplier protocol (Illumina)

scan_protocol: supplier protocol (Illumina)

data_processing:
Methylation data were processed using the R platform for statistical computing.
Average Beta values in processed data file

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: NEN liver metastasis

label_protocol: supplier protocol (Illumina)

extract_protocol: Genomic DNA of the formalin-fixed paraffin-embedded (FFPE) samples was extracted using the AllPrep DNA/RNA FFPE Kit (Qiagen, Hilden, Germany).

tag: gender

value: female

value: FFPE


title: scRNA-Seq of Homo sapiens:ESCC_met3 [P11_1]

type: SRA

country: China

description: Library name: P11_1

library_source: transcriptomic single cell

molecule: total RNA

tag: tissue


title: scRNA-Seq of Homo sapiens:ESCC_met3 [P11_4]

description: Library name: P11_4


title: NoPCa_18

city: Camperdown

first: Jenna

last: Craddock

state: NSW

address: Johns Hopkins Dr

department: School of Medical Sciences

country: Australia

institute: University of Sydney

description: matrix_sample_id: DOD017

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol.

scan_protocol: Standard Illumina protocol.

data_processing:
All samples were processed and normalised using the RnBeads pipeline using the rnb.execute.normalization() function with methods "scaling.internal" and "sesame.noobsb" for normalisation and background correction, respectively.
Matrix files includes RnBeads computed normalised beta values.

label: Cy3 and Cy5

source_name: prostate tissue

label_protocol: Standard Illumina protocol.

extract_protocol: Snap-frozen tissue cores were retrieved and DNA extracted using the Qiagen AllPrep kit (Qiagen).

value: prostate tissue

tag: Sex

value: male

tag: disease state

value: Non-tumour prostate tissue

tag: treatment

value: treatment-naïve


title: scRNA-Seq of Homo sapiens:ESCC_met2 [P10]

description: Library name: P10


title: NoPCa_17

description: matrix_sample_id: DOD009


title: scRNA-Seq of Homo sapiens:ESCC_met3 [P11_3]

description: Library name: P11_3


title: scRNA-Seq of Homo sapiens:ESCC_met1 [P9]

description: Library name: P9


title: NoPCa_25

description: matrix_sample_id: DOD054


title: NEN colon ascending_patient_003

description:
Infinium MethylationEPIC
240028

source_name: NEN colon ascending


title: NoPCa_16

description: matrix_sample_id: DOD007


title: NoPCa_15

description: matrix_sample_id: DOD006


title: NEN ileum_patient_002

description:
Infinium MethylationEPIC
240002

source_name: NEN ileum


title: scRNA-Seq of Homo sapiens:ESCC2 [P7]

description: Library name: P7


title: scRNA-Seq of Homo sapiens:ESCC3 [P8]

description: Library name: P8


title: NoPCa_14

description: matrix_sample_id: DOD004


title: scRNA-Seq of Homo sapiens:ESCC1 [P6]

description: Library name: P6


title: P_PCa_4

description: matrix_sample_id: DOD002

value: Presumably prostate tumour


title: scRNA-Seq of Homo sapiens:ESCC_normal5 [P5_2]

description: Library name: P5_2


title: scRNA-Seq of Homo sapiens:ESCC_normal5 [P5_1]

description: Library name: P5_1


title: NoPCa_19

description: matrix_sample_id: DOD019


title: NoPCa_10

description: matrix_sample_id: TAF015


title: PCa_102

description: matrix_sample_id: DOD015

value: Prostate tumour


title: NoPCa_11

description: matrix_sample_id: TAF016


title: P_PCa_3

description: matrix_sample_id: TAF017


title: NoPCa_12

description: matrix_sample_id: TAF019


title: NoPCa_9

description: matrix_sample_id: TAF011


title: scRNA-Seq of Homo sapiens:ESCC_normal4 [P4_1]

description: Library name: P4_1


title: scRNA-Seq of Homo sapiens:ESCC_normal5 [P5_4]

description: Library name: P5_4


title: scRNA-Seq of Homo sapiens:ESCC_normal4 [P4_2]

description: Library name: P4_2


title: scRNA-Seq of Homo sapiens:ESCC_normal4 [P4_3]

description: Library name: P4_3


title: NoPCa_8

description: matrix_sample_id: NAM5055


title: scRNA-Seq of Homo sapiens:ESCC_normal4 [P4_4]

description: Library name: P4_4


title: scRNA-Seq of Homo sapiens:ESCC_normal3 [P3_1]

description: Library name: P3_1


title: scRNA-Seq of Homo sapiens:ESCC_normal3 [P3_2]

description: Library name: P3_2


title: PCa_100

description: matrix_sample_id: NAM5054


title: U_1

description: matrix_sample_id: NAM0001

value: Unknown


title: NoPCa_13

description: matrix_sample_id: DOD003


title: scRNA-Seq of Homo sapiens:ESCC_normal3 [P3_3]

description: Library name: P3_3


title: scRNA-Seq of Homo sapiens:ESCC_normal1 [P1]

description: Library name: P1


title: PCa_97

description: matrix_sample_id: 14649


title: PCa_99

description: matrix_sample_id: NAM5051


title: PCa_96

description: matrix_sample_id: 19614


title: scRNA-Seq of Homo sapiens:ESCC_normal3 [P3_4]

description: Library name: P3_4


title: PCa_98

description: matrix_sample_id: 14705


title: PCa_94

description: matrix_sample_id: 19588


title: PCa_95

description: matrix_sample_id: 19607


title: PCa_92

description: matrix_sample_id: 19098


title: scRNA-Seq of Homo sapiens:ESCC_normal5 [P5_3]

description: Library name: P5_3


title: scRNA-Seq of Homo sapiens:ESCC_normal2 [P2]

description: Library name: P2


title: Human T cells treated with TH10785 rep2

city: Magdebrug

first: Dimitrios

last: Mougiakakos

address: Leipziger Str. 44

department: Universitätsklinik für Hämatologie, Onkologie und Zelltherapie

institute: Universitätsklinikum  Magdeburg A.ö.R.

description: Library name: Sample_7_10785

library_source: transcriptomic

data_processing:
Alignment against hg38 using STAR.
Transcripts assembled using StringTie
Transcripts quantified using Salmon
Assembly: hg38
Supplementary files format and content: Salmon output quant.sf files.

molecule: polyA RNA

source_name: T cells

extract_protocol:
Cultures were treated with 7.5 µM TH10785 or DMSO. On days 3 and 7, cultures were refreshed by replacing medium, re-adding Nalm-6 cells, hCD19xCD3, and respective treatments.
Strand-specific cDNA library

treatment_protocol: T cells from healthy donors were isolated and co-cultured with Nalm-6 cells at an effector-to-target (E:T) ratio of 2:1 in the presence of 100 pmol bispecific anti-CD19xCD3 antibody.

tag: cell type

value: T cells

value: treated with TH10785


title: Human T cells treated with TH10785 rep1

description: Library name: Sample_6_10785


title: Untreated control Human T cells rep2

description: Library name: Sample_7

value: Untreated


title: PCa_89

description: matrix_sample_id: 16662


title: Human T cells treated with TH10785 rep4

description: Library name: Sample_30_10785


title: Human T cells treated with TH10785 rep3

description: Library name: Sample_29_10785


title: Untreated control Human T cells rep4

description: Library name: Sample_30


title: PCa_93

description: matrix_sample_id: 19507


title: PCa_101

description: matrix_sample_id: TAF009


title: Untreated control Human T cells rep3

description: Library name: Sample_29


title: PCa_87

description: matrix_sample_id: 14526


title: PCa_90

description: matrix_sample_id: 17123


title: PCa_88

description: matrix_sample_id: 16400


title: Untreated control Human T cells rep1

description: Library name: Sample_6


title: Control sample 4, WM no plaque ROI 12

city: Gainesville

first: Stefan

last: Prokop

state: FL

address: 1275 Center Dr

department: Pathology

country: USA

institute: University of Florida

description:
Library name: DSP-1001660037385-C-H06
Formalin Fixed Spatial transcriptomic sequencing

data_processing:
GeoMx NGS pipeline on DRAGEN from Illumina was used with NovaSeq 6000 as choice of sequencer.
FASTQ files were processesd into DCC files using NanoString NGS Pipeline v2.0.21 on illumina BaseSpace Sequencing Hub according to the manufacturer's instruction
Assembly: hg38
Supplementary files format and content: .dcc: count data from each well of the collection plate, or segment from your study
Supplementary files format and content: SeqCodeIndices.csv: Sample information needed for Illumina demultiplexing
Supplementary files format and content: config.ini: pipeline processing parameters
Library strategy: Spatial Transcriptomics

source_name: brain

extract_protocol:
5 um thick sections of FFPE human brain tissues were cut and processed according to Nanostring protocol
Spatial transcriptomic sequencing libraries were prepared according to Nanostring's GeoMx DSP NGS Readout User Manual

value: brain


title: PCa_83

description: matrix_sample_id: 13586


title: Control sample 4, WM no plaque ROI 15

description:
Library name: DSP-1001660037385-C-H09
Formalin Fixed Spatial transcriptomic sequencing


title: Control sample 4, WM no plaque ROI 10

description:
Library name: DSP-1001660037385-C-H04
Formalin Fixed Spatial transcriptomic sequencing


title: Control sample 4, WM no plaque ROI 14

description:
Library name: DSP-1001660037385-C-H08
Formalin Fixed Spatial transcriptomic sequencing


title: PCa_178

description:
MatrixProcessed_GEO_addition.txt
matrix_sample_id: NAM5001

data_processing:
All samples were processed and normalised using the RnBeads pipeline using the rnb.execute.normalization() function with methods "scaling.internal" and "sesame.noobsb" for normalisation and background correction, respectively.
RnBeads computed normalised beta values.


title: PCa_80

description: matrix_sample_id: 12704


title: Control sample 4, WM no plaque ROI 8

description:
Library name: DSP-1001660037385-C-H02
Formalin Fixed Spatial transcriptomic sequencing


title: PCa_86

description: matrix_sample_id: 14403


title: PCa_85

description: matrix_sample_id: 13775


title: PCa_79

description: matrix_sample_id: DSM044


title: PCa_81

description: matrix_sample_id: 13180


title: Control sample 4, WM no plaque ROI 13

description:
Library name: DSP-1001660037385-C-H07
Formalin Fixed Spatial transcriptomic sequencing


title: Control sample 4, WM no plaque ROI 4

description:
Library name: DSP-1001660037385-C-G10
Formalin Fixed Spatial transcriptomic sequencing


title: PCa_78

description: matrix_sample_id: DOD041


title: Control sample 4, WM no plaque ROI 5

description:
Library name: DSP-1001660037385-C-G11
Formalin Fixed Spatial transcriptomic sequencing


title: PCa_76

description: matrix_sample_id: SMU248


title: PCa_91

description: matrix_sample_id: 17639


title: Control sample 4, WM no plaque ROI 11

description:
Library name: DSP-1001660037385-C-H05
Formalin Fixed Spatial transcriptomic sequencing


title: PCa_74

description: matrix_sample_id: KAL0067


title: PCa_82

description: matrix_sample_id: 13255


title: Control sample 4, GM no plaque ROI 7

description:
Library name: DSP-1001660037385-C-G05
Formalin Fixed Spatial transcriptomic sequencing


title: Control sample 4, GM no plaque ROI 8

description:
Library name: DSP-1001660037385-C-G06
Formalin Fixed Spatial transcriptomic sequencing


title: Control sample 4, WM no plaque ROI 9

description:
Library name: DSP-1001660037385-C-H03
Formalin Fixed Spatial transcriptomic sequencing


title: Control sample 4, GM no plaque ROI 6

description:
Library name: DSP-1001660037385-C-G04
Formalin Fixed Spatial transcriptomic sequencing


title: P_PCa_2

description: matrix_sample_id: DSM083


title: Control sample 4, GM no plaque ROI 5

description:
Library name: DSP-1001660037385-C-G03
Formalin Fixed Spatial transcriptomic sequencing


title: E11 murine podocytes, HF, rep 6

city: Toronto

first: Milica

last: Radisic

state: Ontario

address: 160 College St

country: Canada

institute: University of Toronto

description: Library name: HF6

data_processing:
Original image data file from the Illumina high-throughput sequencing platform was transformed to sequenced reads (called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling).
Raw reads were filtered by: - removing reads with adapter contamination - removing reads when uncertain nucleotides constitute more than 10 percent of either read (N > 10%) - removing reads when low quality nucleotides (Base Quality less than 5) constitute more than 50 percent of the read
Cleaned reads were aligned to the reference mouse genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads mapped to each gene.
Assembly: GRCm39/mm39
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Mus musculus

extract_protocol:
RNA was extracted using the PicoPure RNA extraction and isolation kit (Applied Biosystems).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using dTTP for non-directional library. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries were pooled and sequenced on the Illumina NovaSeq X Plus platform with a read length of 2x150 paired-end reads to a depth of 20 million reads in each direction.

tag: cell line

value: podocyte


title: Control sample 4, WM no plaque ROI 6

description:
Library name: DSP-1001660037385-C-G12
Formalin Fixed Spatial transcriptomic sequencing


title: Control sample 4, GM no plaque ROI 3

description:
Library name: DSP-1001660037385-C-G01
Formalin Fixed Spatial transcriptomic sequencing


title: Control sample 4, GM no plaque ROI 4

description:
Library name: DSP-1001660037385-C-G02
Formalin Fixed Spatial transcriptomic sequencing


title: Control sample 4, GM no plaque ROI 2

description:
Library name: DSP-1001660037385-C-F12
Formalin Fixed Spatial transcriptomic sequencing


title: Control sample 4, WM no plaque ROI 1

description:
Library name: DSP-1001660037385-C-G07
Formalin Fixed Spatial transcriptomic sequencing


title: Control sample 4, GM no plaque ROI 1

description:
Library name: DSP-1001660037385-C-F11
Formalin Fixed Spatial transcriptomic sequencing


title: PCa_72

description: matrix_sample_id: KAL0088


title: E11 murine podocytes, HF, rep 1

description: Library name: HF1


title: Control sample 3, WM no plaque ROI 7

description:
Library name: DSP-1001660037385-C-F10
Formalin Fixed Spatial transcriptomic sequencing


title: E11 murine podocytes, RT, rep 5

description: Library name: RT5


title: Control sample 3, WM no plaque ROI 6

description:
Library name: DSP-1001660037385-C-F09
Formalin Fixed Spatial transcriptomic sequencing


title: Control sample 3, Sparse plaque ROI 5

description:
Library name: DSP-1001660037385-C-F06
Formalin Fixed Spatial transcriptomic sequencing


title: PCa_77

description: matrix_sample_id: SMU237


title: Control sample 4, WM no plaque ROI 3

description:
Library name: DSP-1001660037385-C-G09
Formalin Fixed Spatial transcriptomic sequencing


title: E11 murine podocytes, RT, rep 2

description: Library name: RT2


title: PCa_84

description: matrix_sample_id: 13653


title: Control sample 4, WM no plaque ROI 2

description:
Library name: DSP-1001660037385-C-G08
Formalin Fixed Spatial transcriptomic sequencing


title: PCa_75

description: matrix_sample_id: KAL0075


title: Control sample 4, WM no plaque ROI 7

description:
Library name: DSP-1001660037385-C-H01
Formalin Fixed Spatial transcriptomic sequencing


title: P_PCa_1

description: matrix_sample_id: DSM011


title: Control sample 3, Sparse plaque ROI 6

description:
Library name: DSP-1001660037385-C-F07
Formalin Fixed Spatial transcriptomic sequencing


title: PCa_73

description: matrix_sample_id: KAL0057


title: Control sample 3, WM no plaque ROI 5

description:
Library name: DSP-1001660037385-C-F01
Formalin Fixed Spatial transcriptomic sequencing


title: E11 murine podocytes, NT, rep 2

description: Library name: NT2


title: Control sample 3, WM no plaque ROI 3

description:
Library name: DSP-1001660037385-C-E11
Formalin Fixed Spatial transcriptomic sequencing


title: E11 murine podocytes, HF, rep 5

description: Library name: HF5


title: Control sample 3, Sparse plaque ROI 4

description:
Library name: DSP-1001660037385-C-F05
Formalin Fixed Spatial transcriptomic sequencing


title: E11 murine podocytes, NT, rep 1

description: Library name: NT1


title: E11 murine podocytes, HF, rep 4

description: Library name: HF4


title: E11 murine podocytes, HF, rep 3

description: Library name: HF3


title: E11 murine podocytes, HF, rep 2

description: Library name: HF2


title: Control sample 3, Sparse plaque ROI 7

description:
Library name: DSP-1001660037385-C-F08
Formalin Fixed Spatial transcriptomic sequencing


title: E11 murine podocytes, RT, rep 6

description: Library name: RT6


title: E11 murine podocytes, RT, rep 4

description: Library name: RT4


title: E11 murine podocytes, RT, rep 1

description: Library name: RT1


title: Control sample 3, Sparse plaque ROI 3

description:
Library name: DSP-1001660037385-C-F04
Formalin Fixed Spatial transcriptomic sequencing


title: E11 murine podocytes, RT, rep 3

description: Library name: RT3


title: Control sample 3, Sparse plaque ROI 2

description:
Library name: DSP-1001660037385-C-F03
Formalin Fixed Spatial transcriptomic sequencing


title: D4_PTH17_3_Ctrl

city: wuhan

first: xiaoyu

last: liu

state: 湖北 (Húběi)

address: Donghu Road, No. 115, Wuchang District, Wuhan, Hubei Province

institute: wuhan university

description: Library name: D4_PTH17_3_Ctrl

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software. 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.
Assembly: GCRm38
Supplementary files format and content: tab-delimited text files include raw read count

source_name: spleen and lymph nodes

extract_protocol:
Total RNA was extracted from pTh17 cells or βTH17 cells cultured for 4 days with or without 50 mM fructose using the Direct-zol RNA Microprep Kit (ZYMO Research,R2061).
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-Toligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: spleen and lymph nodes

value: pTh17 cells

tag: genotype

value: wild type


title: Control sample 3, WM no plaque ROI 4

description:
Library name: DSP-1001660037385-C-E12
Formalin Fixed Spatial transcriptomic sequencing


title: D4_PTH17_2_Ctrl

description: Library name: D4_PTH17_2_Ctrl


title: Control sample 3, Sparse plaque ROI 1

description:
Library name: DSP-1001660037385-C-F02
Formalin Fixed Spatial transcriptomic sequencing


title: E11 murine podocytes, NT, rep 5

description: Library name: NT5


title: D4_PTH17_1_Fru

description: Library name: D4_PTH17_1_Fru


title: E11 murine podocytes, NT, rep 4

description: Library name: NT4


title: Control sample 3, WM no plaque ROI 2

description:
Library name: DSP-1001660037385-C-E10
Formalin Fixed Spatial transcriptomic sequencing


title: E11 murine podocytes, NT, rep 3

description: Library name: NT3


title: Control sample 3, GM no plaque ROI 5

description:
Library name: DSP-1001660037385-C-E05
Formalin Fixed Spatial transcriptomic sequencing


title: D4_PTH17_1_Ctrl

description: Library name: D4_PTH17_1_Ctrl


title: D4_PTH17_3_Fru

description: Library name: D4_PTH17_3_Fru


title: Control sample 3, WM no plaque ROI 1

description:
Library name: DSP-1001660037385-C-E09
Formalin Fixed Spatial transcriptomic sequencing


title: Control sample 3, GM no plaque ROI 7

description:
Library name: DSP-1001660037385-C-E07
Formalin Fixed Spatial transcriptomic sequencing


title: Control sample 3, GM no plaque ROI 8

description:
Library name: DSP-1001660037385-C-E08
Formalin Fixed Spatial transcriptomic sequencing


title: D4_PTH17_2_Fru

description: Library name: D4_PTH17_2_Fru


title: D4_CTH17_2_Fru

description: Library name: D4_CTH17_2_Fru

value: beta-Th17 cells


title: Control sample 3, GM no plaque ROI 6

description:
Library name: DSP-1001660037385-C-E06
Formalin Fixed Spatial transcriptomic sequencing


title: Control sample 3, GM no plaque ROI 4

description:
Library name: DSP-1001660037385-C-E04
Formalin Fixed Spatial transcriptomic sequencing


title: D4_CTH17_3_Fru

description: Library name: D4_CTH17_3_Fru


title: D4_CTH17_1_Fru

description: Library name: D4_CTH17_1_Fru


title: Control sample 3, GM no plaque ROI 3

description:
Library name: DSP-1001660037385-C-E03
Formalin Fixed Spatial transcriptomic sequencing


title: Control sample 3, Dense plaque ROI 1

description:
Library name: DSP-1001660037385-C-D12
Formalin Fixed Spatial transcriptomic sequencing


title: D2_PTH17_3_Ctrl

description: Library name: D2_PTH17_3_Ctrl


title: D4_CTH17_3_Ctrl

description: Library name: D4_CTH17_3_Ctrl


title: D4_CTH17_2_Ctrl

description: Library name: D4_CTH17_2_Ctrl


title: Low AD sample 4, Sparse plaque ROI 2

description:
Library name: DSP-1001660037385-C-D07
Formalin Fixed Spatial transcriptomic sequencing


title: Control sample 3, GM no plaque ROI 2

description:
Library name: DSP-1001660037385-C-E02
Formalin Fixed Spatial transcriptomic sequencing


title: D4_CTH17_1_Ctrl

description: Library name: D4_CTH17_1_Ctrl


title: Control sample 3, GM no plaque ROI 1

description:
Library name: DSP-1001660037385-C-E01
Formalin Fixed Spatial transcriptomic sequencing


title: D2_CTH17_3_Ctrl

description: Library name: D2_CTH17_3_Ctrl


title: D2_CTH17_2_Ctrl

description: Library name: D2_CTH17_2_Ctrl


title: D2_CTH17_1_Ctrl

description: Library name: D2_CTH17_1_Ctrl


title: Low AD sample 4, WM plaque ROI 1

description:
Library name: DSP-1001660037385-C-D10
Formalin Fixed Spatial transcriptomic sequencing


title: Low AD sample 4, WM plaque ROI 2

description:
Library name: DSP-1001660037385-C-D11
Formalin Fixed Spatial transcriptomic sequencing


title: Low AD sample 4, GM no plaque ROI 8

description:
Library name: DSP-1001660037385-C-D04
Formalin Fixed Spatial transcriptomic sequencing


title: Low AD sample 4, Sparse plaque ROI 4

description:
Library name: DSP-1001660037385-C-D09
Formalin Fixed Spatial transcriptomic sequencing


title: P1_M, unsorted

city: San Diego

first: Yuejia

last: Liu

state: California

address: DNC 210, The Scripps Research Institute, 9060 Activity Road, Unit F

institute: The Scripps Research Institute

description: 10 x Genomics

data_processing:
BCL files of transcriptome libraries were used to generate FASTQ files using the default 15 parameters by the “cellranger mkfastq” command (Cell Ranger v7.1.0)
Assembly: mm10
Supplementary files format and content: Seurat object file of cell matrix of all conditions.

source_name: neocortex

extract_protocol:
Cortices from P1 pups were micro-dissected in ice-cold dissection medium (Hibernate A medium with B27 supplement and Trehalose under a dissecting microscope. Microdissected cortices were transferred into papain solution with DNase in a cell culture dish and cut into small pieces with a razor blade. The dish was then placed onto a digital rocker in a cell 40 culture incubator for 30 minutes with rocking speed at 30 rpm at 37°C. The digested tissues were collected into a 15 mL tube and triturated with a 10 mL low bind plastic pipette 20 times and the cell suspension was carefully transferred to a new 15 mL tube. 2.7 mL of EBSS, 3 mL of reconstituted Worthington inhibitor solution, and DNase solution were added to the 15 mL tube and mixed gently. Cells were pelleted by centrifugation at 300 g for 5 minutes at 4°C, followed by 45 washing with 8 mL cold dissection medium at 200 g for 5 minutes at 4°C. Cells were resuspended in 0.5 mL ice-cold dissection medium with 10% fetal bovine serum (FBS) and DAPI, and subjected to FACS purification.
The scRNA-seq libraries were constructed using the Chromium Next GEM Single Cell 3' Solution v3.1 kit (10x Genomics) following the manufacturer’s protocol.

value: neocortex

value: unsorted cortical cells


title: D2_PTH17_2_Ctrl

description: Library name: D2_PTH17_2_Ctrl


title: Low AD sample 4, Sparse plaque ROI 3

description:
Library name: DSP-1001660037385-C-D08
Formalin Fixed Spatial transcriptomic sequencing


title: P1_F, estradiol, replicate 1

description: 10 x Genomics

library_source: genomic single cell

data_processing:
The “cellranger-atac count” command (v2.1.0) with default parameters was used to align reads from raw FASTQ files to the mm10 reference genome.
Assembly: mm10
Supplementary files format and content: Seurat object file of cell matrix of all conditions.

extract_protocol:
Animals were anaesthetized on ice, 6 hours post-injection, followed by dissection of the entire neocortex on ice, excluding the amygdalar regions. Followed by a nuclei isolation protocol, GFP+ and 7-AAD+ nuclei were collected into cold PBS with 0.1% BSA by FACS.
The snATAC-seq libraries were constructed using the Chromium Next GEM Single Cell ATAC 40 Reagent Kits v2 (10x Genomics) following the manufacturer’s protocol.

treatment_protocol: Intraperitoneal injection of 5ug estradiol-benzoate or DMSO (vehicle) in sesame oil were administered in female pups at P1 (5-6 animals pooled per condition in each replicate).

value: Estradiol-benzoate in sesame oil


title: D2_PTH17_1_Ctrl

description: Library name: D2_PTH17_1_Ctrl


title: P1_F, vehicle, replicate 1

description: 10 x Genomics

value: DMSO in sesame oil


title: Low AD sample 4, Sparse plaque ROI 1

description:
Library name: DSP-1001660037385-C-D06
Formalin Fixed Spatial transcriptomic sequencing


title: Low AD sample 4, GM no plaque ROI 9

description:
Library name: DSP-1001660037385-C-D05
Formalin Fixed Spatial transcriptomic sequencing


title: Low AD sample 4, GM no plaque ROI 6

description:
Library name: DSP-1001660037385-C-D02
Formalin Fixed Spatial transcriptomic sequencing


title: Low AD sample 4, GM no plaque ROI 7

description:
Library name: DSP-1001660037385-C-D03
Formalin Fixed Spatial transcriptomic sequencing


title: P1_M, GFP_sorted

description: 10 x Genomics

value: GFP sorted cortical cells


title: Low AD sample 4, GM no plaque ROI 4

description:
Library name: DSP-1001660037385-C-C12
Formalin Fixed Spatial transcriptomic sequencing


title: Low AD sample 4, GM no plaque ROI 5

description:
Library name: DSP-1001660037385-C-D01
Formalin Fixed Spatial transcriptomic sequencing


title: Fibroblast, donor, WT

city: Tsukuba

first: Inoue

last: Kimiko

state: Ibaraki

address: 3-1-1 Koyadai

department: BioResource Research Center

country: Japan

institute: RIKEN

description: Library name: Fibroblast

data_processing:
Sequence reads were trimmed for adaptor sequence using fastp.
Trimmed sequence reads were mapped to the common marmoset genome build calJac4 using STAR.
Read count extraction and normalization were performed using featureCounts and Python, respectively.
Assembly: calJac4
Supplementary files format and content: Excel files include TPM values for each samples

organism: Callithrix jacchus

source_name: Somatic cells

growth_protocol: ntESCs were established by following the feeder free protocol that we reported previously (Kishimoto et al., 2021). First, SCNT was performed as follows; MII oocytes were enucleated in HEPES-buffered CZB medium containing cytochalasin B (CB). Fibroblast cell fusion with enucleated oocytes was achieved using HVJ-E (hemagglutinating virus of Japan envelope). After reconstitution, oocytes were rested in POM for 1 hour and then activated by 5-minute exposure to ionomycin, followed by 6-hour culture in medium containing 6-DMAP and trichostatin A (TSA). TSA treatment was continued for an additional 3 hours (8 hours total). Kdm4d mRNA was injected at a concentration of 1500 ng/μl (~10–20 pl per embryo) 5–6 hours post-activation using a piezo device (Matoba et al., 2014, 2018). Embryos were then cultured in Cleav medium until the appropriate stage, followed by transfer to Blast medium to promote blastocyst formation. In some experiments, 1 µM RK-701 (G9a inhibitor) (Matoba et al., 2024) was added at the time of activation and maintained for 24 hours. Next, SCNT blastocysts (Day 8–12) were treated with acidified Tyrode’s solution (1060, Origio, Denmark) to remove the zona pellucida. Embryos were plated onto iMatrix-551 silk-coated plastic culture plates (Nippi, Tokyo, Japan; 0.5 µg/cm²) and cultured in conditioned medium for ESC (CMESC) supplemented with 4 ng/ml bFGF. CMESC was prepared by culturing irradiated MEF feeder cells in Primate ES Cell Medium (RCHEMD001, ReproCELL, Kanagawa, JAPAN) for 24 hours. Outgrowths were observed within 4–10 days. When the cell colonies expanded, they were dissociated using Accutase (12679-54, Nacalai Tesque, Kyoto, Japan) and passaged onto new iMatrix-coated plates. After every passage, Y-27632 (#72308, STEMCELL Technologies Inc., Vancouver, Canada) was added to the culture medium at 10 µM for 1 day to support the survival of dissociated ESCs. Media were replaced every 1–2 days.

extract_protocol:
Total RNA was extracted from 1x10^6 cells of ntESCs, fibroblasts, and embryoid bodies using RNeasy Mini kit (#74104, Qiagen GmbH, Germany).
Library preparation and sequencing were performed using a TruSeq stranded mRNA library prep kit (cat# RS-122-2101, Illumina, San Diego, CA , USA).

treatment_protocol: SCNT embryos were injected with 10 pL of 1500 ng/μL mouse Kdm4d mRNA at 5–6 h post-activation and treated with G9a inhibitors (24h at 1uM) and trichostatin A (TSA; 8h at 25 nM). The established ntESCs were cultured on iMatrix-coated in conditioned medium for ESC (CMESC) supplemented with 4 ng/ml bFGF. CMESC was prepared by culturing irradiated MEF feeder cells in Primate ES Cell Medium (RCHEMD001, ReproCELL, Kanagawa, JAPAN) for 24 hours.

value: Somatic cells

value: Wildtype

value: Donor


title: ntESC, SCNT, WT, #30

description: Library name: ntES30

source_name: ntESC, WT, #30

value: ntESC, WT, #30

value: embryonic stem cells

value: SCNT


title: ESC, IVF, WT, #17

description: Library name: ES17

source_name: ESC, WT, #17

value: ESC, WT, #17

value: IVF


title: Low AD sample 4, GM no plaque ROI 1

description:
Library name: DSP-1001660037385-C-C09
Formalin Fixed Spatial transcriptomic sequencing

value: brain


title: ntESC, SCNT, GFP, #24

description: Library name: ntES24

source_name: ntESC, GFP, #24

value: ntESC, GFP, #24

value: CAG-EGFP Tg


title: Low AD sample 4, GM no plaque ROI 2

description:
Library name: DSP-1001660037385-C-C10
Formalin Fixed Spatial transcriptomic sequencing


title: ESC, IVF, WT, #15

description: Library name: ES15

source_name: ESC, WT, #15

value: ESC, WT, #15


title: ESC, NAT, WT, #37

description: Library name: ES37

source_name: ESC, WT, #37

value: ESC, WT, #37

value: NAT


title: Low AD sample 4, GM no plaque ROI 3

description:
Library name: DSP-1001660037385-C-C11
Formalin Fixed Spatial transcriptomic sequencing


title: Low AD sample 4, Dense plaque ROI 7

description:
Library name: DSP-1001660037385-C-C07
Formalin Fixed Spatial transcriptomic sequencing


title: ESC, NAT, WT, #13

description: Library name: ES13

source_name: ESC, WT, #13

value: ESC, WT, #13


title: Low AD sample 4, Dense plaque ROI 6

description:
Library name: DSP-1001660037385-C-C06
Formalin Fixed Spatial transcriptomic sequencing


title: Low AD sample 4, Dense plaque ROI 8

description:
Library name: DSP-1001660037385-C-C08
Formalin Fixed Spatial transcriptomic sequencing


title: Low AD sample 4, Dense plaque ROI 5

description:
Library name: DSP-1001660037385-C-C05
Formalin Fixed Spatial transcriptomic sequencing


title: Sample12_Microglia Treg co-cultured 3

city: nanjing

first: tao

last: qin

address: hanzhong road 104

institute: The First Affiliated Hospital of Nanjing Medical University

description:
T3 FPKM
Microglia.xlsx

data_processing:
Data filtering The sequencing data was filtered with SOAPnuke by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com).
RNA identification Bowtie2 was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included.
Gene Quantification Differential Expression Analysis Expression level of gene was calculated by RSEM (v1.3.1). The heatmap was drawn by pheatmap (v1.0.8) according to the gene expression difference in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5) (or DEGseq or PoissonDis)with Q value ≤ 0.05 (or FDR ≤ 0.001).
Gene Annotation To take insight to the change of phenotype, GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expression gene was performed by Phyper (https://en.wikipedia.org/wiki/Hypergeometric_distribution) based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05).
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: Treg cells.xlsx file includes FPKM values for sample1-6
Supplementary files format and content: Microglia.xlsx file includes FPKM values for sample7-12

source_name: primary microglia

extract_protocol:
2.1.1 Transfer appropriate tissue sample into corresponding tissue grinding tube (tissue≤30 mg, cell≤1×107). 2.1.2 Add 600 μL Buffer RLT Plus. Homogenize the lysate for using a rotor–stator homogenizer, stay at room temperature for 5 min. 2.1.3 Centrifuge at 12,000×g for 3 min in room temperature, transfer the supernatant to AllPrep DNA spin column. 2.1.4 Centrifuge 12,000×g for 30 s in room temperature, transfer the solution from the collection tube for the RNA purification. 2.1.5 Transfer the DNA spin column to the new collection tube for DNA purification.                                                                                2.3.1 Add the equal volume of 70% ethanol to the collection tube, mix by pipetting. 2.3.2 Transfer 700 μL mixed solution, to a RNeasy spin column placed in a 2 mL collection tube. 2.3.3 Centrifuge at 10,000×g for 30 s and allow it to empty by gravity flow. 2.3.4 Add 700 μL Buffer RW1 to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate. 2.3.5 Add 500 μL Buffer RPE to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate. 2.3.6 Add 500 μL Buffer RPE to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate. 2.3.7 Centrifuge at 16,000×g for 2 min and transfer the RNeasy spin column to the 1.5 mL centrifuge tube. 2.3.8 Add 35 μL RNase-free water to RNeasy spin column. Stay at room temperature for 1min. 2.3.9 Centrifuge at 16,000×g for 2 min at room temperature to collect RNA.
2.Experimental Procedure 2.1 Sample QC Select the corresponding testing methods for quality inspection according to the requirements of samples and products. 2.2 mRNA Isolation A certain amount of RNA samples are denatured at suitable temperature to open their secondary structure, and mRNA is enriched by oligo (dT) -attached magnetic beads. 2.3 mRNA Fragmentation The reaction system is configured. After reacting at the suitable temperature for a fixed period of time, RNAs are fragmented. 2.4 cDNA Synthesis Prepare the first-strand synthesis reaction system, and set up the reaction program, synthesize the first- strand cDNA, prepare the second-strand synthesis reaction system, and set up the reaction program to synthesize the second-strand cDNA. 2.5 End Repair, Add A and Adaptor Ligation After the reaction system and program are configured and set up, double-stranded cDNA fragments are subjected to end-repair, and then a single ‘A’ nucleotide is added to the 3’ ends of the blunt fragments. The reaction system and program for adaptor ligation are subsequently configured and set up to ligate adaptors with the cDNAs. 2.6 PCR The PCR reaction system and program are configured and set up to amplify the product. 2.7 Library QC The corresponding library quality control protocol will be selected depending upon product requirements. 2.8 Circularization Single-stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single-stranded cyclized products are produced, while uncyclized linear DNA molecules are digested. 2.9 Sequencing Single-stranded circle DNA molecules are replicated via rolling cycle amplification, and a DNA nanoball (DNB) which contain multiple copies of DNA is generated. Sufficient quality DNBs are then loaded into patterned nanoarrays using high-intensity DNA nanochip technique and sequenced through combinatorial Probe-Anchor Synthesis (cPAS).

value: primary microglia

value: Treg co-cultured


title: Sample11_Microglia Treg co-cultured 2

description:
T2 FPKM
Microglia.xlsx


title: Low AD sample 4, Dense plaque ROI 4

description:
Library name: DSP-1001660037385-C-C04
Formalin Fixed Spatial transcriptomic sequencing


title: Sample10_Microglia Treg co-cultured 1

description:
T1 FPKM
Microglia.xlsx


title: Low AD sample 4, Dense plaque ROI 3

description:
Library name: DSP-1001660037385-C-C03
Formalin Fixed Spatial transcriptomic sequencing


title: Sample9_Microglia control 3

description:
C3 FPKM
Microglia.xlsx


title: Low AD sample 4, Dense plaque ROI 1

description:
Library name: DSP-1001660037385-C-C01
Formalin Fixed Spatial transcriptomic sequencing


title: Low AD sample 4, Dense plaque ROI 2

description:
Library name: DSP-1001660037385-C-C02
Formalin Fixed Spatial transcriptomic sequencing


title: High AD sample 4, WM plaque ROI 2

description:
Library name: DSP-1001660037385-C-B12
Formalin Fixed Spatial transcriptomic sequencing


title: Sample7_Microglia control 1

description:
C1 FPKM
Microglia.xlsx


title: High AD sample 4, WM plaque ROI 1

description:
Library name: DSP-1001660037385-C-B11
Formalin Fixed Spatial transcriptomic sequencing


title: High AD sample 4, Sparse plaque ROI 4

description:
Library name: DSP-1001660037385-C-B10
Formalin Fixed Spatial transcriptomic sequencing


title: Sample6_Treg spinal cord 3

description:
S3 FPKM
Treg cells.xlsx

source_name: spinal cord

value: spinal cord

value: Treg cells


title: Sample5_Treg spinal cord 2

description:
S2 FPKM
Treg cells.xlsx


title: Sample3_Treg spleen 3

description:
C3 FPKM
Treg cells.xlsx

source_name: spleen

value: spleen


title: High AD sample 4, Sparse plaque ROI 2

description:
Library name: DSP-1001660037385-C-B08
Formalin Fixed Spatial transcriptomic sequencing


title: Sample2_Treg spleen 2

description:
C2 FPKM
Treg cells.xlsx


title: High AD sample 4, Sparse plaque ROI 3

description:
Library name: DSP-1001660037385-C-B09
Formalin Fixed Spatial transcriptomic sequencing


title: High AD sample 4, Sparse plaque ROI 1

description:
Library name: DSP-1001660037385-C-B07
Formalin Fixed Spatial transcriptomic sequencing


title: Sample4_Treg spinal cord 1

description:
S1 FPKM
Treg cells.xlsx


title: High AD sample 4, WM no plaque ROI 4

description:
Library name: DSP-1001660037385-C-B05
Formalin Fixed Spatial transcriptomic sequencing


title: High AD sample 4, WM no plaque ROI 2

description:
Library name: DSP-1001660037385-C-B03
Formalin Fixed Spatial transcriptomic sequencing


title: Sample1_Treg spleen 1

description:
C1 FPKM
Treg cells.xlsx


title: D31-1

city: zhengzhou

first: tingjie

last: wang

state: Henan

address: dongming road

institute: zzu

description:
Library name: D31_1
scRNAseq for harvested 31 days after AKT1/NICD1 injection using MobiCube

data_processing:
The FASTQ files were processed and aligned to mouse GRCm39 genome using MobiVision software (V3.2) with unique molecular identifier (UMI) counts summarized for each barcode.For in-house AKT1/NICD1 and public AKT1/YAP1 ICC single cell data, gene expression matrices were preprocessed using the Seurat R package (V 4.4.0). Quality control measures were employed to remove low-quality cells and genes based on follow criteria: 1) remove ribosomal genes. 2) nCount_RNA > 1000, nCount_RNA < 40000, nFeature_RNA < 6000, nFeature_RNA > 500, percent.mt <20%, min.cells=50. Then, the global-scaling method “LogNormalize” normalized the gene expression measurements for each cell by the total expression. The ScaleData function, “vars.to.regress” option percent mitochondrial content was used to regress out unwanted sources of variation. Top highly variable genes (HVGs, vst, top 2000) were calculated using the Seurat function FindVariableGenes. Performed principal component analysis (PCA) for dimensionality reduction using top 30 components. Clusters were computed using the FindClusters function using top 30 PCAs and then visualized using the uniform manifold approximation and projection (UMAP) implemented in Seurat. Differential expression analysis between clusters was performed using a likelihood-ratio test (RunPrestoAll in presto package) at a family-wise error rate of 5%. Using canonical marker genes (Table S3), SciBet (V1.0) and differentially expressed genes (DEGs) and the associated pathway function to definite the major cell types (Fibroblasts, Endothelial, Macrophage, DC, Neutrophile, T&NK, B, Cholangiocarcinoma and Hepatocyte). Sub-cell types were re-clustered with a resolution parameter set at 0.2 - 0.5, without filtering cells or genes, and the data were processed using the standard workflow to identify the subclusters and their associated differential genes (HVGs, vst,1000 for human macrophage and epithelial cells, 500 for AKT1/NICD1 epithelial cells, 300 for AKT1/NICD1 and AKT1/YAP1 mouse macrophage). In each subtype, if the main cell type marker genes from the first step are simultaneously expressed at a high proportion (>30% of cells) and with high specificity in a cell subpopulation, then that subpopulation is removed. Meanwhile, we used SciBet to remove mixed cells to ensure the accuracy of the final identified cell types. Scibet references downloads from website http://scibet.cancer-pku.cn/scibet_references.html (human:30 major human cell types, mouse: Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris). Finally, based on the functions of the differentially expressed genes and the cell type marker genes, subgroups with similar functions were merged, and the cell types were defined. We collected ICC patients’ data from GSE138709 and GSE189903 (Table S1), and employed the same quality control, normalization and dim reduction as AKT1/NICD1 and AKT1/YAP1. Additionally, we used harmony (V1.1.0) to eliminate batch effects caused by different platforms and sequencing protocols. Cell type definition was the same as AKT1/NICD1 and AKT1/YAP1.
Assembly: GRCm39
Supplementary files format and content: barcodes.tsv.gz,features.tsv.gz,matrix.mtx.gz

source_name: liver

extract_protocol:
Under sterile conditions, the freshly collected liver was washed twice with pre-cooled RPMI1640 medium containing 0.04% BSA. The tissues were then mechanically dissociated into approximately 0.5 mm³ fragments using surgical scissors and transferred into freshly prepared enzymatic digestion solution. The digestion mixture contained RPMI1640 (Conring, cat.no. 10-040-CVR), 0.04% BSA (MACS, cat.no. 1000076), and 0.2% collagenase II (Gibco, cat.no. 17101015). The samples were incubated at 37°C for 30-60 minutes with gentle inversion every 5-10 minutes. The digested cell suspension was filtered through a BD 40 μm cell strainer (Falcon, cat.no. 352340) 1-2 times. The filtrate was centrifuged at 300 × g for 5 minutes at 4°C. The cell pellet was resuspended in appropriate medium, mixed with an equal volume of red blood cell lysis buffer (Miltenyi, cat.no. 130-094-183), and incubated at 4°C for 10 minutes. After centrifugation at 300 × g for 5 minutes, the supernatant was removed. Finally， the cells were re-suspended with 1 ml RPMI 1640 medium (Conring, cat.no.10-040-CVR) with 0.04% BSA added. Single-cell suspension concentration and cell viability were then evaluated by Luna-FL cell counter (Logos Biosystems，Korea) or Trypan Blue staining method.
The freshly prepared single-cell suspension was adjusted to a concentration of 700–1200 cells/μL. Library preparation and loading were performed following the manufacturer’s protocol for the MobiCube High-throughput Single Cell 3 ′ Transcriptome Set V2.1 (cat.no.PN-S050200301). The constructed libraries were sequenced on the DNBSEQ-T7 PE100 platform for high-throughput sequencing.

value: liver

tag: batch


title: High AD sample 4, WM no plaque ROI 3

description:
Library name: DSP-1001660037385-C-B04
Formalin Fixed Spatial transcriptomic sequencing


title: D25-2

description:
Library name: D25_2
scRNAseq for harvested 25 days after AKT1/NICD1 injection using MobiCube


title: D31-3

description:
Library name: D31_3
scRNAseq for harvested 31 days after AKT1/NICD1 injection using MobiCube


title: High AD sample 4, GM no plaque ROI 4

description:
Library name: DSP-1001660037385-C-B01
Formalin Fixed Spatial transcriptomic sequencing


title: High AD sample 4, GM no plaque ROI 3

description:
Library name: DSP-1001660037385-C-A12
Formalin Fixed Spatial transcriptomic sequencing


title: High AD sample 4, GM no plaque ROI 2

description:
Library name: DSP-1001660037385-C-A11
Formalin Fixed Spatial transcriptomic sequencing


title: D15-3

description:
Library name: D15_3
scRNAseq for harvested 15 days after AKT1/NICD1 injection using MobiCube


title: D25-1

description:
Library name: D25_1
scRNAseq for harvested 25 days after AKT1/NICD1 injection using MobiCube


title: High AD sample 4, WM no plaque ROI 5

description:
Library name: DSP-1001660037385-C-B06
Formalin Fixed Spatial transcriptomic sequencing


title: D15-2

description:
Library name: D15_2
scRNAseq for harvested 15 days after AKT1/NICD1 injection using MobiCube


title: High AD sample 4, WM no plaque ROI 1

description:
Library name: DSP-1001660037385-C-B02
Formalin Fixed Spatial transcriptomic sequencing


title: High AD sample 4, GM no plaque ROI 1

description:
Library name: DSP-1001660037385-C-A10
Formalin Fixed Spatial transcriptomic sequencing


title: High AD sample 4, Dense plaque ROI 8

description:
Library name: DSP-1001660037385-C-A09
Formalin Fixed Spatial transcriptomic sequencing


title: D15-1

description:
Library name: D15_1
scRNAseq for harvested 15 days after AKT1/NICD1 injection using MobiCube


title: Sample8_Microglia control 2

description:
C2 FPKM
Microglia.xlsx


title: D7-2

description:
Library name: D7_2
scRNAseq for harvested 7 days after AKT1/NICD1 injection using MobiCube


title: D7-1

description:
Library name: D7_1
scRNAseq for harvested 7 days after AKT1/NICD1 injection using MobiCube


title: High AD sample 4, Dense plaque ROI 7

description:
Library name: DSP-1001660037385-C-A08
Formalin Fixed Spatial transcriptomic sequencing


title: D31-2

description:
Library name: D31_2
scRNAseq for harvested 31 days after AKT1/NICD1 injection using MobiCube


title: High AD sample 4, Dense plaque ROI 3

description:
Library name: DSP-1001660037385-C-A04
Formalin Fixed Spatial transcriptomic sequencing


title: WT-2

description:
Library name: WT_2
scRNAseq for harvested 7 days after Ctrl injection using MobiCube


title: High AD sample 4, Dense plaque ROI 6

description:
Library name: DSP-1001660037385-C-A07
Formalin Fixed Spatial transcriptomic sequencing


title: High AD sample 4, Dense plaque ROI 4

description:
Library name: DSP-1001660037385-C-A05
Formalin Fixed Spatial transcriptomic sequencing


title: WT-1

description:
Library name: WT_1
scRNAseq for harvested 7 days after Ctrl injection using MobiCube


title: V2

city: Guangzhou

first: Jinghui

last: Xu

state: Guangdong

address: NO. 600,Tianhe Road

department: Department of Rehabilitation Medicine

institute: the Third Affiliated Hospital of Sun Yat-sen University

description: Library name: V2

data_processing:
The fastq raw data files were generated using Illumina bcl2fastq software. Differential expression gene (DEG) analyses were performed by HTSeq and DESeq2
GO enrichment and KEGG enrichment were analyzed by TopGO software.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: brain tissue

extract_protocol:
The total RNA was extracted according to the manufacturer’s instructions. Then the mRNA was enriched using magnetic bead, followed by fragmentation with divalent cations under elevated temperature.
The generated cDNA was amplified and used for sequencing library preparation and the clusters were generated. After that, the libraries were sequenced with Illumina NovaSeq6000 platform.

value: brain tissue

tag: sample group

value: V


title: High AD sample 4, Dense plaque ROI 2

description:
Library name: DSP-1001660037385-C-A03
Formalin Fixed Spatial transcriptomic sequencing


title: V3

description: Library name: V3


title: High AD sample 4, Dense plaque ROI 1

description:
Library name: DSP-1001660037385-C-A02
Formalin Fixed Spatial transcriptomic sequencing


title: P3

description: Library name: P3

value: P


title: Low AD sample 3, WM plaque 2

description:
Library name: DSP-1001660037383-B-H09
Formalin Fixed Spatial transcriptomic sequencing


title: P2

description: Library name: P2


title: V1

description: Library name: V1


title: P1

description: Library name: P1


title: No-Template Control 3

description:
Library name: DSP-1001660037385-C-A01
Formalin Fixed Spatial transcriptomic sequencing


title: M3

description: Library name: M3

value: M


title: Low AD sample 3, WM plaque 1

description:
Library name: DSP-1001660037383-B-H08
Formalin Fixed Spatial transcriptomic sequencing

value: brain


title: Low AD sample 3, Sparse plaque ROI 4

description:
Library name: DSP-1001660037383-B-H07
Formalin Fixed Spatial transcriptomic sequencing


title: Low AD sample 3, Sparse plaque ROI 3

description:
Library name: DSP-1001660037383-B-H06
Formalin Fixed Spatial transcriptomic sequencing


title: M1

description: Library name: M1


title: Low AD sample 3, Sparse plaque ROI 2

description:
Library name: DSP-1001660037383-B-H05
Formalin Fixed Spatial transcriptomic sequencing


title: Low AD sample 3, Sparse plaque ROI 1

description:
Library name: DSP-1001660037383-B-H04
Formalin Fixed Spatial transcriptomic sequencing


title: WT SI Rep5

city: Glasgow

first: Kathryn

last: Gilroy

address: Garscube

country: United Kingdom

institute: CRUK Scotland Institute

description: Library name: BUPP-RDT6-1e-WT-Prox-SI-01-05-2023-P2-E2

data_processing:
Trimmed sequences were aligned to mouse genome build GRCm38.98 (mm10) using HISAT2 version 2.1.0
Raw counts per gene were determined using FeatureCounts version 1.6.4 with the following options: --primary -C -t exon -g gene_id.
Assembly: GRCm38
Supplementary files format and content: Matrix of batch corrected raw counts

source_name: Prox. SI

extract_protocol:
After sampling, tissues were stored in RNAlater. RNA was then extracted with an RNeasy Mini Kit according to the manufacturer’s instructions, and then homogenised using a Precellys Evolution machine. RNA quality was assessed by TapeStation and samples were only used if RIN >7.
Library preparation was performed by Azenta using an Illumina mRNA with PolyA selection kit. Libraries were then sequenced using a Novaseq 6000 sequencer.

value: Prox. SI

tag: sample type

value: WT Tissue

value: Male

value: WT

tag: induction method

tag: sampling timepoint


title: WT SI Rep3

description: Library name: BUPP-RDT6-4g-WT-Prox-SI-01-05-2023-P8-B7

value: Female


title: WT SI Rep4

description: Library name: BUPP-RDT6-1d-WT-Prox-SI-01-05-2023-P2-G3


title: Low AD sample 3, WM no plaque ROI 4

description:
Library name: DSP-1001660037383-B-H02
Formalin Fixed Spatial transcriptomic sequencing


title: WT SI Rep2

description: Library name: BUPP-RDT5-1g-WT-Prox-SI-01-05-2023-P4-G7


title: Low AD sample 3, WM no plaque ROI 5

description:
Library name: DSP-1001660037383-B-H03
Formalin Fixed Spatial transcriptomic sequencing


title: High AD sample 4, Dense plaque ROI 5

description:
Library name: DSP-1001660037385-C-A06
Formalin Fixed Spatial transcriptomic sequencing


title: WT Colon Rep5

description: Library name: BUPP-RDT6-1e-WT-Mid-Col-01-05-2023-P1-D2

source_name: Mid. Colon

value: Mid. Colon


title: Low AD sample 3, WM no plaque ROI 2

description:
Library name: DSP-1001660037383-B-G12
Formalin Fixed Spatial transcriptomic sequencing

source_name: brain


title: WT Colon Rep4

description: Library name: BUPP-RDT6-1d-WT-Mid-Col-01-05-2023-P8-D12


title: Low AD sample 3, WM no plaque ROI 1

description:
Library name: DSP-1001660037383-B-G11
Formalin Fixed Spatial transcriptomic sequencing


title: WT Colon Rep2

description: Library name: BUPP-RDT5-1g-WT-Mid-Col-01-05-2023-P1-B10


title: WT Colon Rep3

description: Library name: BUPP-RDT6-4g-WT-Mid-Col-01-05-2023-P8-A9


title: Low AD sample 3, GM no plaque ROI 4

description:
Library name: DSP-1001660037383-B-G10
Formalin Fixed Spatial transcriptomic sequencing


title: Low AD sample 3, GM no plaque ROI 3

description:
Library name: DSP-1001660037383-B-G09
Formalin Fixed Spatial transcriptomic sequencing


title: M2

description: Library name: M2


title: WT Colon Rep1

description: Library name: BUPP-RDT5-1f-WT-Mid-Col-01-05-2023-P2-G11


title: Low AD sample 3, GM no plaque ROI 2

description:
Library name: DSP-1001660037383-B-G08
Formalin Fixed Spatial transcriptomic sequencing


title: Low AD sample 3, GM no plaque ROI 1

description:
Library name: DSP-1001660037383-B-G07
Formalin Fixed Spatial transcriptomic sequencing


title: VilKPN SI Rep7

description: Library name: KPN-RZ6-1b-KPN-SI-01-05-2023-P2-B8

source_name: SI

value: SI

value: Tissue after short term induction

value: VilCreER KRasG12D/+ P53fl/fl Notch1Tg

value: Tamoxifen (IP)

value: Day 30


title: Low AD sample 3, Dense plaque ROI 8

description:
Library name: DSP-1001660037383-B-G06
Formalin Fixed Spatial transcriptomic sequencing


title: Low AD sample 3, Dense plaque ROI 6

description:
Library name: DSP-1001660037383-B-G04
Formalin Fixed Spatial transcriptomic sequencing


title: Low AD sample 3, Dense plaque ROI 7

description:
Library name: DSP-1001660037383-B-G05
Formalin Fixed Spatial transcriptomic sequencing


title: VilKPN SI Rep6

description: Library name: KPN-RZ5-1a-KPN-SI-01-05-2023-P7-B3


title: Low AD sample 3, Dense plaque ROI 5

description:
Library name: DSP-1001660037383-B-G03
Formalin Fixed Spatial transcriptomic sequencing


title: VilKPN SI Rep4

description: Library name: BVKPN-RKAC27-2a-KPN-SI-01-05-2023-P2-D12


title: Low AD sample 3, WM no plaque ROI 3

description:
Library name: DSP-1001660037383-B-H01
Formalin Fixed Spatial transcriptomic sequencing


title: WT SI Rep1

description: Library name: BUPP-RDT5-1f-WT-Prox-SI-01-05-2023-P7-E8


title: VilKPN SI Rep3

description: Library name: KPN-RZ5-1f-KPN-SI-01-05-2023-P5-F4


title: VilKPN SI Rep2

description: Library name: BVKPN-RKAC25-4e-KPN-SI-01-05-2023-P8-C7


title: Low AD sample 3, Dense plaque ROI 2

description:
Library name: DSP-1001660037383-B-F12
Formalin Fixed Spatial transcriptomic sequencing


title: Vil KP SI Rep3

description: Library name: KPN-RZ5-1b-KP-SI-01-05-2023-P4-D1

value: VilCreER KRasG12D/+ P53fl/fl


title: VilKPN SI Rep1

description: Library name: BVKPN-RKAC25-3g-KPN-SI-01-05-2023-P1-C12


title: Low AD sample 3, Dense plaque ROI 1

description:
Library name: DSP-1001660037383-B-F11
Formalin Fixed Spatial transcriptomic sequencing


title: Low AD sample 3, Dense plaque ROI 3

description:
Library name: DSP-1001660037383-B-G01
Formalin Fixed Spatial transcriptomic sequencing


title: Vil BPNA SI Rep5

description: Library name: VANP-RKF51-1b-BPNA-SI-01-05-2023-P8-B3

value: VilCreER BrafV600E/+ P53fl/fl Tgfbr1 fl/fl Notch1Tg

value: Day 20


title: Control sample 2, WM plaque ROI 2

description:
Library name: DSP-1001660037383-B-F10
Formalin Fixed Spatial transcriptomic sequencing


title: Vil KP SI Rep2

description: Library name: KPN-RZ3-1c-KP-SI-01-05-2023-P1-B12


title: Vil BPNA SI Rep4

description: Library name: VANP-RKF50-3b-BPNA-SI-01-05-2023-P1-H1


title: Vil KP SI Rep1

description: Library name: KPN-RZ3-1a-KP-SI-01-05-2023-P6-E5


title: Control sample 2, Sparse plaque ROI 4

description:
Library name: DSP-1001660037383-B-F08
Formalin Fixed Spatial transcriptomic sequencing


title: Vil BPNA SI Rep2

description: Library name: VANP-RKF44-1d-BPNA-SI-01-05-2023-P2-D5


title: VilKPN SI Rep5

description: Library name: BVKPN-RKAC27-2b-KPN-SI-01-05-2023-P8-F1


title: Control sample 2, WM no plaque ROI 5

description:
Library name: DSP-1001660037383-B-F04
Formalin Fixed Spatial transcriptomic sequencing


title: Control sample 2, Sparse plaque ROI 3

description:
Library name: DSP-1001660037383-B-F07
Formalin Fixed Spatial transcriptomic sequencing


title: Control sample 2, WM plaque ROI 1

description:
Library name: DSP-1001660037383-B-F09
Formalin Fixed Spatial transcriptomic sequencing


title: Vil BPNA SI Rep3

description: Library name: VANP-RKF49-2a-BPNA-SI-01-05-2023-P8-E8


title: Vil BP SI Rep7

description: Library name: VBPNOT-RKV46-1b-BP-SI-01-05-2023-P5-F10

value: VilCreER BrafV600E/+ P53fl/fl


title: Vil BPNA SI Rep1

description: Library name: VANP-RKF44-1c-BPNA-SI-01-05-2023-P8-A6


title: Control sample 2, Sparse plaque ROI 2

description:
Library name: DSP-1001660037383-B-F06
Formalin Fixed Spatial transcriptomic sequencing


title: Low AD sample 3, Dense plaque ROI 4

description:
Library name: DSP-1001660037383-B-G02
Formalin Fixed Spatial transcriptomic sequencing


title: Vil BP SI Rep5

description: Library name: VBPNOT-RKV35-1b-BP-SI-01-05-2023-P6-H11


title: Control sample 2, WM no plaque ROI 3

description:
Library name: DSP-1001660037383-B-F02
Formalin Fixed Spatial transcriptomic sequencing


title: Control sample 2, WM no plaque ROI 2

description:
Library name: DSP-1001660037383-B-F01
Formalin Fixed Spatial transcriptomic sequencing


title: MDS17

type: RNA

city: Basel

first: Judith

last: Zaugg

address: Hebelstrasse 20

department: Departement Biomedizin

country: Switzerland

institute: University of Basel

hyb_protocol: Hybridized according to manufacturer protocol.

scan_protocol: Scanned according to manufacturer protocol.

data_processing:
nSolver software package and nSolver Advanced Analysis module (NanoString Technologies) were used to evaluate the determined transcript counts. Quality-checked raw data was normalized utilizing the geometric mean of the housekeeping reference genes and the code sets’ internal positive controls were used to exclude samples that are outliers
Counts normalized utilizing the geometric mean of the housekeeping reference genes.

label: NanoString Oligonucleotide Probe

source_name: Whole bone marrow aspirate

label_protocol: Labeled according to manufacturer protocols.

extract_protocol: Total mRNA was isolated using AllPrep DNA/RNA Mini Kit (Qiagen) following the manufacturer’s instructions. 150-300 ng RNA was extracted per sample.

tag: condition

value: MDS


title: Vil BP SI Rep4

description: Library name: VBPNOT-RKV46-2d-BP-SI-01-05-2023-P5-F7


title: MDS16


title: CHIP9

value: CHIP


title: Control sample 2, WM no plaque ROI 1

description:
Library name: DSP-1001660037383-B-E12
Formalin Fixed Spatial transcriptomic sequencing

value: brain


title: CHIP16


title: Control sample 2, Sparse plaque ROI 1

description:
Library name: DSP-1001660037383-B-F05
Formalin Fixed Spatial transcriptomic sequencing


title: Vil BP SI Rep3

description: Library name: VBPNOT-RKV36-2f-BP-SI-01-05-2023-P7-A6


title: Control16

value: Control


title: Control22


title: CHIP15


title: Control sample 2, GM no plaque ROI 3

description:
Library name: DSP-1001660037383-B-E10
Formalin Fixed Spatial transcriptomic sequencing


title: Control sample 2, WM no plaque ROI 4

description:
Library name: DSP-1001660037383-B-F03
Formalin Fixed Spatial transcriptomic sequencing


title: Control2


title: Control sample 2, GM no plaque ROI 4

description:
Library name: DSP-1001660037383-B-E11
Formalin Fixed Spatial transcriptomic sequencing


title: MDS23


title: MDS2


title: Control sample 2, GM no plaque ROI 2

description:
Library name: DSP-1001660037383-B-E09
Formalin Fixed Spatial transcriptomic sequencing


title: Control13


title: Vil BP SI Rep1

description: Library name: VBPNOT-RKV31-6g-BP-SI-01-05-2023-P6-C4


title: Vil BP SI Rep2

description: Library name: VBPNOT-RKV36-2e-BP-SI-01-05-2023-P7-B10


title: Vil BP Colon Rep7

description: Library name: VBPNOT-RKV46-1b-BP-Col-01-05-2023-P5-G5

source_name: Colon

value: Colon

value: Male


title: Vil BP SI Rep6

description: Library name: VBPNOT-RKV35-1c-BP-SI-01-05-2023-P7-G1


title: MDS22


title: Control sample 2, GM no plaque ROI 1

description:
Library name: DSP-1001660037383-B-E08
Formalin Fixed Spatial transcriptomic sequencing


title: MDS14


title: Vil BP Colon Rep6

description: Library name: VBPNOT-RKV35-1c-BP-Col-01-05-2023-P7-D3


title: MDS11


title: Control sample 2, Dense plaque ROI 8

description:
Library name: DSP-1001660037383-B-E07
Formalin Fixed Spatial transcriptomic sequencing


title: CHIP3


title: CHIP5


title: Vil BP Colon Rep5

description: Library name: VBPNOT-RKV35-1b-BP-Col-01-05-2023-P6-G4


title: CHIP1


title: CHIP14


title: Vil BP Colon Rep4

description: Library name: VBPNOT-RKV46-2d-BP-Col-01-05-2023-P2-D4

value: Female


title: Control sample 2, Dense plaque ROI 7

description:
Library name: DSP-1001660037383-B-E06
Formalin Fixed Spatial transcriptomic sequencing


title: MDS15


title: Control14


title: Control12


title: Vil BP Colon Rep3

description: Library name: VBPNOT-RKV36-2f-BP-Col-01-05-2023-P7-G8


title: Control sample 2, Dense plaque ROI 5

description:
Library name: DSP-1001660037383-B-E04
Formalin Fixed Spatial transcriptomic sequencing


title: Control1


title: MDS4


title: Vil BP Colon Rep2

description: Library name: VBPNOT-RKV36-2e-BP-Col-01-05-2023-P7-G12


title: Control sample 2, Dense plaque ROI 4

description:
Library name: DSP-1001660037383-B-E03
Formalin Fixed Spatial transcriptomic sequencing


title: MDS1


title: MDS6


title: CHIP2


title: Vil Braf Colon Rep5

description: Library name: VBRAFF-RQAC18-4f-B-Col-01-05-2023-P4-G12

value: VilCreER BrafV600E/+


title: CHIP13


title: Control5


title: MDS3


title: CHIP12


title: CHIP11


title: Vil Braf Colon Rep3

description: Library name: VBRAFF-RQAC17-4e-B-Col-01-05-2023-P4-E4


title: Vil BP Colon Rep1

description: Library name: VBPNOT-RKV31-6g-BP-Col-01-05-2023-P1-G12


title: Control sample 2, Dense plaque ROI 6

description:
Library name: DSP-1001660037383-B-E05
Formalin Fixed Spatial transcriptomic sequencing


title: High AD sample 3, WM plaque ROI 2

description:
Library name: DSP-1001660037383-B-D11
Formalin Fixed Spatial transcriptomic sequencing


title: Control31


title: High AD sample 3, WM plaque ROI 1

description:
Library name: DSP-1001660037383-B-D10
Formalin Fixed Spatial transcriptomic sequencing


title: OS457_Primary

city: San Francisco

first: Alex

middle: G

last: Lee

state: CA

address: 1550 4th Street

institute: UCSF

data_processing:
Raw FASTQ files were trimmed for adaptors and low-quality regions using Trimmomatic (v0.36). The processed reads were aligned to the human reference genome (hg38) with STAR aligner (v2.5.1b), using the ‘quantMode’ feature and gene annotations from GENCODE p5 for gene-level expression quantification. Aligned reads were normalized with the TMM method from the EdgeR package (v3.24.3) and transformed to log2(CPM + 1).
Assembly: hg38
Supplementary files format and content: tab delimited

source_name: From osteosarcoma PDX

growth_protocol: All cell lines were routinely tested for mycoplasma and STR tested to confirm identify.  Cells were cultured in standard DMEM media (Corning) supplemented with 10% bovine growth serum (Hyclone SH30541.03) and 1% penicillin–streptomycin–glutamine

extract_protocol:
RNA was harvested when the cells were ~80 confluent.RNA was extracted using the RNAeasy Mini Kit (Qiagen) and on-column DNA digestion with DNaseI according to the manufacturer protocol.
RNA-seq libraries were made using the TruSeq Stranded mRNA Kit (Illumina, RS-122-2101) in accordance with the manufacturer’s instructions. All manufacturer controls were used in preparation of the libraries. Libraries were quantified using the High Sensitivity D1000 ScreenTape (Agilent, 5067-5584) on the TapeStation 4200 (Agilent), the High Sensitivity DNA (Agilent, 5067-4626) on the Bioanalyzer 2100 (Agilent), or the High Sensitivity NGS (Agilent, DNF-474-22) on the Fragment Analyzer

value: From osteosarcoma PDX


title: Control sample 2, Dense plaque ROI 2

description:
Library name: DSP-1001660037383-B-E01
Formalin Fixed Spatial transcriptomic sequencing


title: OS525_Metastasis


title: CHIP10


title: Vil Braf Colon Rep4

description: Library name: VBRAFF-RQAC18-3c-B-Col-01-05-2023-P5-E3

value: Tissue after short term induction


title: Control sample 2, Dense plaque ROI 1

description:
Library name: DSP-1001660037383-B-D12
Formalin Fixed Spatial transcriptomic sequencing


title: Control10


title: Vil Braf Colon Rep2

description: Library name: VBRAFF-RQAC17-4b-B-Col-01-05-2023-P7-G10


title: Control32


title: OS152_Metastasis


title: OS052_Primary


title: VilBPA SI Rep2

description: Library name: VANP-RKF47-2d-BAP-SI-01-05-2023-P8-C1

value: SI

value: VilCreER Braf V600E/+ Tgfbr1 fl/fl P53 fl/fl


title: VilBPA SI Rep1

description: Library name: VANP-RKF47-2c-BAP-SI-01-05-2023-P7-H4

value: Tamoxifen (IP)

value: Day 30


title: Vil Braf Colon Rep1

description: Library name: VBRAFF-RQAC17-4a-B-Col-01-05-2023-P7-A5


title: Control sample 2, Dense plaque ROI 3

description:
Library name: DSP-1001660037383-B-E02
Formalin Fixed Spatial transcriptomic sequencing


title: High AD sample 3, WM no plaque ROI 5

description:
Library name: DSP-1001660037383-B-D05
Formalin Fixed Spatial transcriptomic sequencing


title: High AD sample 3, Sparse plaque ROI 4

description:
Library name: DSP-1001660037383-B-D09
Formalin Fixed Spatial transcriptomic sequencing


title: Osteosarcoma cell line_SaOS2_1

library_source: genomic

data_processing:
Reads were trimmed using NGSUtils. Trimmed reads were aligned to the GRCh38.p5 human genome assembly with Bowtie2 using the ‘--very-sensitive’ parameter. Duplicates and mitochondrial reads were removed using NGSUtils, and reads with high mapping quality (>q30) were retained using Samtools. Peak calling was performed with MACS2, using default options and flags ‘-nomodel –keep-dup all’. Peaks overlapping ENCODE blacklisted features were discarded, and only peaks with FDR q ≤ 0.01 were retained
Assembly: hg38
Supplementary files format and content: bedGraph pileups generated using MACS2

source_name: osteosarcoma cell line

extract_protocol:
Patient derived-xenographs (PDX) were grown in subcutaneos models in NSG mice. A single cell suspension was generated, cell were sorted for human positive cells and use as input in ATAC-seq libraries. Cell lines were harvested using trypsin and used as input in ATAC-seq libraries.
ATAC-seq libraries were prepared with minor modifications as previously described. Briefly, 1x10^5 cells were lysed on ice to isolate nuclei, which were then incubated with Tn5 transposase (Illumina) at 37 °C for 30 minutes with shaking. Libraries were amplified by PCR for 6-11 cycles, purified using SPRI beads, and sequenced at the UCSF CAT facility using HiSeq 4000 with 100-bp paired-end reads. Fresh/frozen PDXs or patient samples followed the same preparation method.

value: osteosarcoma cell line

value: cell line


title: VilBPA SI Rep4

description: Library name: VANP-RKF42-4e-BAP-SI-01-05-2023-P1-C9


title: VilBPA SI Rep3

description: Library name: VANP-RKF42-4b-BAP-SI-01-05-2023-P8-A8


title: OS186_Metastasis


title: High AD sample 3, Sparse plaque ROI 3

description:
Library name: DSP-1001660037383-B-D08
Formalin Fixed Spatial transcriptomic sequencing


title: Osteosarcoma cell line_HOS_2


title: High AD sample 3, Sparse plaque ROI 2

description:
Library name: DSP-1001660037383-B-D07
Formalin Fixed Spatial transcriptomic sequencing


title: High AD sample 3, Sparse plaque ROI 1

description:
Library name: DSP-1001660037383-B-D06
Formalin Fixed Spatial transcriptomic sequencing


title: Osteosarcoma cell line_HuO9_2


title: Control30


title: VilAP SI Rep4

description: Library name: BCVAPK-RCB39-1d-AP-SI-01-05-2023-P2-H9

value: VilCreER Apcfl/fl P53fl/fl

value: Day 4


title: OS526_Primary


title: Osteosarcoma cell line_c143_2


title: VilAP SI Rep2

description: Library name: BCVAPK-RCB30-1c-AP-SI-01-05-2023-P4-H10


title: Osteosarcoma cell line_SaOS2_2


title: High AD sample 3, WM no plaque ROI 3

description:
Library name: DSP-1001660037383-B-D03
Formalin Fixed Spatial transcriptomic sequencing


title: Osteosarcoma cell line_HuO9_1


title: Osteosarcoma cell line_HOS_1


title: Osteosarcoma cell line_SJSA_1


title: High AD sample 3, WM no plaque ROI 1

description:
Library name: DSP-1001660037383-B-D01
Formalin Fixed Spatial transcriptomic sequencing


title: Osteosarcoma cell line_c143_1


title: VilAP SI Rep1

description: Library name: BCVAPK-RCB29-1e-AP-SI-01-05-2023-P2-H7


title: High AD sample 3, WM no plaque ROI 2

description:
Library name: DSP-1001660037383-B-D02
Formalin Fixed Spatial transcriptomic sequencing


title: Osteosarcoma cell line_U2OS_1


title: Osteosarcoma cell line_SJSA_2


title: High AD sample 3, GM no plaque ROI 4

description:
Library name: DSP-1001660037383-B-C12
Formalin Fixed Spatial transcriptomic sequencing


title: Osteosarcoma cell line_U2OS_2


title: VilAP SI Rep3

description: Library name: BCVAPK-RCB39-1b-AP-SI-01-05-2023-P4-A6


title: High AD sample 3, WM no plaque ROI 4

description:
Library name: DSP-1001660037383-B-D04
Formalin Fixed Spatial transcriptomic sequencing


title: VilAKP SI Rep3

description: Library name: BVAKP-RZAO26-5d-AKP-SI-01-05-2023-P2-A6

value: VilCreER Apcfl/fl KRasG12D/+ P53fl/fl

value: Day 3


title: Osteosarcoma cell line_MG63.3_1


title: High AD sample 3, GM no plaque ROI 3

description:
Library name: DSP-1001660037383-B-C11
Formalin Fixed Spatial transcriptomic sequencing

value: brain


title: Osteosarcoma cell line_MG63_1


title: High AD sample 3, GM no plaque ROI 2

description:
Library name: DSP-1001660037383-B-C10
Formalin Fixed Spatial transcriptomic sequencing


title: VilAKP SI Rep4

description: Library name: BCVAPK-RCB34-2a-AKP-SI-01-05-2023-P3-H7


title: Osteosarcoma cell line_MG63.3_2


title: VilAKP SI Rep2

description: Library name: BVAKP-RZAO25-4d-AKP-SI-01-05-2023-P4-H11


title: VilAKP SI Rep1

description: Library name: BVAKP-RZAO24-3i-AKP-SI-01-05-2023-P1-F8


title: Osteosarcoma Patient_p830_2

source_name: Patient sample

value: Patient sample


title: High AD sample 3, GM no plaque ROI 1

description:
Library name: DSP-1001660037383-B-C09
Formalin Fixed Spatial transcriptomic sequencing


title: Osteosarcoma Patient_p830_1


title: Osteosarcoma Patient_p808_1


title: High AD sample 3, Dense plaque ROI 7

description:
Library name: DSP-1001660037383-B-C07
Formalin Fixed Spatial transcriptomic sequencing


title: High AD sample 3, Dense plaque ROI 8

description:
Library name: DSP-1001660037383-B-C08
Formalin Fixed Spatial transcriptomic sequencing


title: Osteosarcoma Patient_p808_2


title: Osteosarcoma Patient_p775_2


title: VilAKP Colon Rep1

description: Library name: BVAKP-RZAO24-3i-AKP-Col-01-05-2023-P6-D11

value: Colon


title: Osteosarcoma Patient_p775_1


title: Osteosarcoma cell line_MG63_2


title: High AD sample 3, Dense plaque ROI 6

description:
Library name: DSP-1001660037383-B-C06
Formalin Fixed Spatial transcriptomic sequencing


title: Osteosarcoma Patient_p774_1


title: Osteosarcoma Patient_p708_2


title: VilApcKras SI Rep8

description: Library name: VARSDH-REAE24-3c-AK-SI-01-05-2023-P2-C12

value: Male

value: VilCreER Apcfl/fl KRasG12D/+


title: Osteosarcoma Patient_p708_1


title: High AD sample 3, Dense plaque ROI 5

description:
Library name: DSP-1001660037383-B-C05
Formalin Fixed Spatial transcriptomic sequencing


title: Osteosarcoma Patient_p152_2


title: VilApcKras SI Rep6

description: Library name: VARSDH-REAE24-1e-AK-SI-01-05-2023-P5-F1

value: Female


title: Osteoblast cell line_hFOB_2

source_name: osteoblast cell line

value: osteoblast cell line


title: High AD sample 3, Dense plaque ROI 3

description:
Library name: DSP-1001660037383-B-C03
Formalin Fixed Spatial transcriptomic sequencing


title: VilApcKras SI Rep7

description: Library name: BVAR-RZF98-5h-AK-SI-01-05-2023-P2-E11

value: SI

value: Tissue after short term induction


title: Osteosarcoma Patient_p186R_2


title: Osteoblast cell line_hFOB_1


title: VilApcKras SI Rep5

description: Library name: VARSDH-REAE23-2g-AK-SI-01-05-2023-P3-B5

value: Tamoxifen (IP)


title: Osteosarcoma Patient_p186R_1


title: Osteosarcoma Patient_p152_1


title: VilAKP Colon Rep3

description: Library name: BVAKP-RZAO26-5d-AKP-Col-01-05-2023-P6-A5


title: High AD sample 3, Dense plaque ROI 2

description:
Library name: DSP-1001660037383-B-C02
Formalin Fixed Spatial transcriptomic sequencing


title: Osteosarcoma Patient_p186M_2


title: VilApcKras SI Rep4

description: Library name: BVAR-RZF99-4b-AK-SI-01-05-2023-P7-F11


title: High AD sample 3, Dense plaque ROI 4

description:
Library name: DSP-1001660037383-B-C04
Formalin Fixed Spatial transcriptomic sequencing


title: Patient derived Xenograph_PDX833_1

source_name: PDX

value: PDX


title: VilAKP Colon Rep2

description: Library name: BVAKP-RZAO25-4d-AKP-Col-01-05-2023-P3-H10


title: Patient derived Xenograph_PDX560_2


title: VilApcKras SI Rep2

description: Library name: BVAR-RZF101-4e-AK-SI-01-05-2023-P6-C1


title: High AD sample 2, Sparse plaque ROI 4

description:
Library name: DSP-1001660037383-B-B10
Formalin Fixed Spatial transcriptomic sequencing


title: VilApcKras Colon Rep4

description: Library name: VARPCA-RIZ5-2a-AK-Col-01-05-2023-P1-H10


title: Osteosarcoma Patient_p774_2


title: Osteosarcoma Patient_p186M_1


title: VilApcKras SI Rep3

description: Library name: BVAR-RZF98-5g-AK-SI-01-05-2023-P6-A4


title: Patient derived Xenograph_PDX833_2


title: Patient derived Xenograph_PDX526_2


title: High AD sample 2, WM plaque ROI 2

description:
Library name: DSP-1001660037383-B-B12
Formalin Fixed Spatial transcriptomic sequencing


title: VilApcKras Colon Rep2

description: Library name: VARPB-RIW10-1i-AK-Col-01-05-2023-P1-A8


title: High AD sample 3, Dense plaque ROI 1

description:
Library name: DSP-1001660037383-B-C01
Formalin Fixed Spatial transcriptomic sequencing


title: Patient derived Xenograph_PDX152


title: High AD sample 2, Sparse plaque ROI 1

description:
Library name: DSP-1001660037383-B-B07
Formalin Fixed Spatial transcriptomic sequencing


title: Patient derived Xenograph_PDX559_2


title: VilApcKras SI Rep1

description: Library name: BVAR-RZF101-4d-AK-SI-01-05-2023-P5-D5


title: VilApcKras Colon Rep1

description: Library name: VARPB-RIW10-1g-AK-Col-01-05-2023-P1-H9


title: High AD sample 2, WM plaque ROI 1

description:
Library name: DSP-1001660037383-B-B11
Formalin Fixed Spatial transcriptomic sequencing


title: Patient derived Xenograph_PDX774_4


title: Patient derived Xenograph_PDX559_1


title: Patient derived Xenograph_PDX384


title: High AD sample 2, Sparse plaque ROI 3

description:
Library name: DSP-1001660037383-B-B09
Formalin Fixed Spatial transcriptomic sequencing


title: Patient derived Xenograph_PDX126_2


title: Patient derived Xenograph_PDX126_1


title: Patient derived Xenograph_PDX560_1


title: Patient derived Xenograph_PDX301


title: VilApcKras Colon Rep3

description: Library name: VARPB-RIW7-2a-AK-Col-01-05-2023-P3-B6


title: Patient derived Xenograph_PDX742_4


title: High AD sample 2, Sparse plaque ROI 2

description:
Library name: DSP-1001660037383-B-B08
Formalin Fixed Spatial transcriptomic sequencing


title: Patient derived Xenograph_PDX526_1


title: Patient derived Xenograph_PDX742_3


title: High AD sample 2, WM no plaque ROI 5

description:
Library name: DSP-1001660037383-B-B06
Formalin Fixed Spatial transcriptomic sequencing


title: Patient derived Xenograph_PDX457_2


title: VilApc SI Rep10

description: Library name: VELP-RLAF17-1b-A-SI-01-05-2023-P2-D2

value: VilCreER Apcfl/fl


title: Patient derived Xenograph_PDX774_3


title: Patient derived Xenograph_PDX566_2


title: VilApc SI Rep9

description: Library name: VELP-RLAF16-1a-A-SI-01-05-2023-P1-D1


title: High AD sample 2, WM no plaque ROI 4

description:
Library name: DSP-1001660037383-B-B05
Formalin Fixed Spatial transcriptomic sequencing


title: Patient derived Xenograph_PDX708_2


title: High AD sample 2, WM no plaque ROI 3

description:
Library name: DSP-1001660037383-B-B04
Formalin Fixed Spatial transcriptomic sequencing


title: Patient derived Xenograph_PDX708_1


title: High AD sample 2, WM no plaque ROI 2

description:
Library name: DSP-1001660037383-B-B03
Formalin Fixed Spatial transcriptomic sequencing


title: Patient derived Xenograph_PDX457_1


title: High AD sample 2, WM no plaque ROI 1

description:
Library name: DSP-1001660037383-B-B02
Formalin Fixed Spatial transcriptomic sequencing


title: VilApc SI Rep7

description: Library name: VELP-RLAF16-5b-A-SI-01-05-2023-P1-G2


title: VilApc SI Rep8

description: Library name: VELP-RLAF15-1c-A-SI-01-05-2023-P5-A12


title: Patient derived Xenograph_PDX566_1


title: VilApc SI Rep4

description: Library name: VELP-RLAF14-1b-A-SI-01-05-2023-P1-A5


title: Patient derived Xenograph_PDX107_2


title: Patient derived Xenograph_PDX186_2


title: High AD sample 2, GM no plaque ROI 2

description:
Library name: DSP-1001660037383-B-A11
Formalin Fixed Spatial transcriptomic sequencing


title: Patient derived Xenograph_PDX107_1


title: High AD sample 2, GM no plaque ROI 4

description:
Library name: DSP-1001660037383-B-B01
Formalin Fixed Spatial transcriptomic sequencing


title: High AD sample 2, GM no plaque ROI 3

description:
Library name: DSP-1001660037383-B-A12
Formalin Fixed Spatial transcriptomic sequencing


title: Patient derived Xenograph_PDX106_1


title: Patient derived Xenograph_PDX106_2


title: VilApc SI Rep6

description: Library name: VELP-RLAF15-3e-A-SI-01-05-2023-P1-D11


title: VilApc SI Rep5

description: Library name: VELP-RLAF17-1d-A-SI-01-05-2023-P2-B10


title: Patient derived Xenograph_PDX186_1


title: VilApc SI Rep2

description: Library name: VELP-RLAF16-5g-A-SI-01-05-2023-P3-B2


title: VilApc SI Rep3

description: Library name: VELP-RLAF16-5i-A-SI-01-05-2023-P4-E10


title: High AD sample 2, GM no plaque ROI 1

description:
Library name: DSP-1001660037383-B-A10
Formalin Fixed Spatial transcriptomic sequencing


title: Patient derived Xenograph_PDX052_2


title: OsteosarcomaPDX-CL_OS833_2

value: From osteosarcoma PDX

value: cell line


title: Patient derived Xenograph_PDX052_1


title: High AD sample 2, Dense plaque ROI 8

description:
Library name: DSP-1001660037383-B-A09
Formalin Fixed Spatial transcriptomic sequencing


title: VilApc SI Rep1

description: Library name: VELP-RLAF15-3i-A-SI-01-05-2023-P3-A12

value: Day 4


title: OsteosarcomaPDX-CL_OS833_1


title: High AD sample 2, Dense plaque ROI 6

description:
Library name: DSP-1001660037383-B-A07
Formalin Fixed Spatial transcriptomic sequencing


title: OsteosarcomaPDX-CL_OS742_2


title: OsteosarcomaPDX-CL_OS766_1


title: OsteosarcomaPDX-CL_OS742_1


title: OsteosarcomaPDX-CL_OS457_2


title: OsteosarcomaPDX-CL_OS774_2


title: High AD sample 2, Dense plaque ROI 4

description:
Library name: DSP-1001660037383-B-A05
Formalin Fixed Spatial transcriptomic sequencing


title: High AD sample 2, Dense plaque ROI 7

description:
Library name: DSP-1001660037383-B-A08
Formalin Fixed Spatial transcriptomic sequencing


title: OsteosarcomaPDX-CL_OS384_2


title: OsteosarcomaPDX-CL_OS457_1


title: High AD sample 2, Dense plaque ROI 3

description:
Library name: DSP-1001660037383-B-A04
Formalin Fixed Spatial transcriptomic sequencing


title: VilApc Colon Rep12

description: Library name: VELP-RLAF16-5b-A-Col-01-05-2023-P4-B11


title: OsteosarcomaPDX-CL_OS774_1


title: OsteosarcomaPDX-CL_OS186_1


title: High AD sample 2, Dense plaque ROI 1

description:
Library name: DSP-1001660037383-B-A02
Formalin Fixed Spatial transcriptomic sequencing


title: VilApc Colon Rep6

description: Library name: VELP-RLAF17-1b-A-Col-01-05-2023-P7-E7


title: OsteosarcomaPDX-CL_OS152_2


title: VilApc Colon Rep11

description: Library name: VELP-RLAF15-3e-A-Col-01-05-2023-P1-E9


title: OsteosarcomaPDX-CL_OS766_2


title: OsteosarcomaPDX-CL_OS152_1


title: VilApc Colon Rep10

description: Library name: VARSDH-REAE24-4a-A-Col-01-05-2023-P8-F5


title: High AD sample 2, Dense plaque ROI 5

description:
Library name: DSP-1001660037383-B-A06
Formalin Fixed Spatial transcriptomic sequencing


title: VilApc Colon Rep5

description: Library name: BVAR-RZF95-1h-A-Col-01-05-2023-P3-D5


title: VilApc Colon Rep9

description: Library name: VARPB-RIW5-2k-A-Col-01-05-2023-P3-D11


title: ntEB, SCNT, GFP, #24

description: Library name: 24-GFP-EB

source_name: ntESC, GFP, #24

value: ntESC, GFP, #24

value: Embryoid bodies

value: CAG-EGFP Tg

value: SCNT


title: VilApc Colon Rep4

description: Library name: VELP-RLAF16-5i-A-Col-01-05-2023-P3-F5

value: Colon


title: OsteosarcomaPDX-CL_OS526_2


title: OsteosarcomaPDX-CL_OS525_2


title: OsteosarcomaPDX-CL_OS384_1


title: VilApc Colon Rep3

description: Library name: VELP-RLAF16-5g-A-Col-01-05-2023-P1-G3


title: OsteosarcomaPDX-CL_OS525_1


title: VilApc Colon Rep8

description: Library name: VARPB-RIW5-2c-A-Col-01-05-2023-P2-C1

value: Male


title: High AD sample 2, Dense plaque ROI 2

description:
Library name: DSP-1001660037383-B-A03
Formalin Fixed Spatial transcriptomic sequencing

value: brain


title: OsteosarcomaPDX-CL_OS052_2


title: OsteosarcomaPDX-CL_OS526_1


title: VilApc Colon Rep7

description: Library name: VELP-RLAF17-1d-A-Col-01-05-2023-P2-H4

value: Female


title: ntEB, SCNT, WT, #61

description: Library name: 61-WT-EB

source_name: ntESC, WT, #61

value: ntESC, WT, #61

value: Wildtype


title: OsteosarcomaPDX-CL_OS186_3


title: VilApc Colon Rep2

description: Library name: VELP-RLAF15-3i-A-Col-01-05-2023-P8-D1

value: Tissue after short term induction


title: No-Template Control 2

description:
Library name: DSP-1001660037383-B-A01
Formalin Fixed Spatial transcriptomic sequencing


title: ntEB, SCNT, GFP, #50

description: Library name: 50-GFP-EB

source_name: ntESC, GFP, #50

value: ntESC, GFP, #50


title: Control sample 1, WM no plaque ROI 7

description:
Library name: DSP-1001660037382-A-H09
Formalin Fixed Spatial transcriptomic sequencing


title: ntEB, SCNT, WT, #30

description: Library name: 30-WT-EB

source_name: ntESC, WT, #30

value: ntESC, WT, #30


title: Control sample 1, WM no plaque ROI 5

description:
Library name: DSP-1001660037382-A-H07
Formalin Fixed Spatial transcriptomic sequencing


title: Control sample 1, WM no plaque ROI 3

description:
Library name: DSP-1001660037382-A-H05
Formalin Fixed Spatial transcriptomic sequencing


title: m2C_Eif1ad3_RIPseq_total_A

first: Zongliang

last: Jiang

address: 2033 Mowry Rd

department: Animal Sciences

data_processing:
Multiplexed sequencing reads that passed filters were trimmed to remove low-quality reads and adaptors by TrimGalore (version 0.6.7) (-q 25 --length 20 --max_n 3 --stringency 3). The quality of reads after filtering was assessed by fastQC, followed by alignment to the mouse genome (GRCm39) by HISAT2 (version 2.2.1) with default parameters. The output SAM files were converted to BAM files and sorted using SAMtools6 (version 1.14). Read counts of all samples were quantified by using FeatureCount (Version 2.0.1) with mouse genome as a reference and were adjusted to provide CPM (Counts per million mapped reads). Principal component analysis (PCA) and cluster analysis were performed by using R (a free software environment for statistical computing and graphics). Differentially expressed genes (DEGs) was identified by using edgeR in R. The genes were considered differentially expressed if they provided a false discovery rate of <0.05 and fold change >2. ClusterProfiler was used to reveal the Gene Ontology (GO) and KEGG pathways in R.
Assembly: GRCm39
Supplementary files format and content: csv, normalized read counts

source_name: 2-cell embryo

extract_protocol:
Samples were collected and used for library construction directly without extration RNA before.
The  libraries were generated from individual fractions by using the Smart-seq2 v4 kit with minor modification from manufacturer’s instructions. Briefly, individual cells were lysed, and mRNA was captured and amplified with the Smart-seq2 v4 kit (Clontech). After AMPure XP beads purification, amplified RNAs were quality checked by using Agilent High Sensitivity D5000 kit (Agilent Technologies). High-quality amplified RNAs were subject to library preparation (Nextera XT DNA Library Preparation Kit; Illumina) and multiplexed by Nextera XT Indexes (Illumina). The concentration of sequencing libraries was determined by using Qubit dsDNA HS Assay Kit (Life Technologies) and KAPA Library Quantification Kits (KAPA Biosystems). The size of sequencing libraries was determined by means of High Sensitivity D5000 Assay in at Tapestation 4200 system (Agilent). Pooled indexed libraries were then sequenced on the Illumina HiSeq X platform with 150-bp paired-end reads.

treatment_protocol: Micromanipulation platform was equipped with a microinjector (FemtoJet 4i, Eppendorf), an inverted microscope (Leica, DMi8), and micromanipulators (Narishige). For Eif1ad3 knockdown experiments, oocytes were microinjected with control or Eif1ad3 antisense morpholino oligos with Cas13d protein. Embryos from control and knockdown groups were collected at 2-cell stage. For RIP experiment, Eif1ad3-HisTag was in vitro transcribed and injected into zygote stage of mouse embryos. RIP experiments were conducted using the EZ-Magna RIP Kit (Millipore Corporation, Billerica, MA). Briefly, 2-cell stage embryos were harvested, lysed and then reacted with RIP buffer containing magnetic beads conjugated with anti-His tag antibody (Millipore) or corresponding negative control IgG (Millipore). After the antibody was recovered using protein A/G beads, the purified RNA were used to perform RNA-seq.

value: 2-cell embryo

value: WT


title: Control sample 1, WM no plaque ROI 6

description:
Library name: DSP-1001660037382-A-H08
Formalin Fixed Spatial transcriptomic sequencing


title: OsteosarcomaPDX-CL_OS052_1

value: From osteosarcoma PDX

value: cell line


title: ntEB, SCNT, WT, #53

description: Library name: 53-WT-EB

source_name: ntESC, WT, #53

value: ntESC, WT, #53


title: EB, NAT, WT, #37

description: Library name: 37-NAT-EB

source_name: ESC, WT, #37

value: ESC, WT, #37

value: Embryoid bodies

value: NAT


title: VilCre SI Rep4

description: Library name: BVBRAF-RAB15-5b-WT-SI-01-05-2023-P3-B7

value: SI

value: VilCreER

value: Tamoxifen (IP)

value: Day 4


title: Control sample 1, WM no plaque ROI 1

description:
Library name: DSP-1001660037382-A-H03
Formalin Fixed Spatial transcriptomic sequencing

value: brain


title: EB, IVF, WT, #17

description: Library name: 17-IVF-EB

source_name: ESC, WT, #17

value: ESC, WT, #17

value: Wildtype

value: IVF


title: Control sample 1, WM no plaque ROI 4

description:
Library name: DSP-1001660037382-A-H06
Formalin Fixed Spatial transcriptomic sequencing

source_name: brain


title: VilCre SI Rep3

description: Library name: BVBRAF-RAB15-5a-WT-SI-01-05-2023-P2-D9

source_name: SI

value: Tissue after short term induction

value: Male


title: VilCre SI Rep2

description: Library name: BVBRAF-RAB16-3d-WT-SI-01-05-2023-P3-B9

value: Female


title: Control sample 1, GM no plaque ROI 15

description:
Library name: DSP-1001660037382-A-H01
Formalin Fixed Spatial transcriptomic sequencing


title: Control sample 1, WM no plaque ROI 2

description:
Library name: DSP-1001660037382-A-H04
Formalin Fixed Spatial transcriptomic sequencing


title: m2C_Eif1ad3_RIPseq_Input_B

value: 2-cell embryo


title: m2C_Eif1ad3_RIPseq_IgG_B


title: m2C_Eif1ad3_RIPseq_Input_A


title: ntESC, SCNT, GFP, #55

description: Library name: ntES55

source_name: ntESC, GFP, #55

value: ntESC, GFP, #55

value: embryonic stem cells

value: CAG-EGFP Tg

value: SCNT


title: VilCre SI Rep1

description: Library name: BVBRAF-RAB16-3c-WT-SI-01-05-2023-P8-C8


title: VilCre Colon Rep4

description: Library name: BVBRAF-RAB15-5a-WT-Col-01-05-2023-P8-F7

source_name: Colon

value: Colon


title: Control sample 1, GM no plaque ROI 14

description:
Library name: DSP-1001660037382-A-G12
Formalin Fixed Spatial transcriptomic sequencing


title: VilApc Colon Rep1

description: Library name: VARPCA-RIZ7-1e-A-Col-01-05-2023-P1-E5

value: VilCreER Apcfl/fl


title: ntESC, SCNT, GFP, #54

description: Library name: ntES54

source_name: ntESC, GFP, #54

value: ntESC, GFP, #54


title: Control sample 1, GM no plaque ROI 13

description:
Library name: DSP-1001660037382-A-G11
Formalin Fixed Spatial transcriptomic sequencing


title: m2C_Eif1ad3_RIPseq_IgG_A


title: m2C_Eif1ad3_RIPseq_total_B

value: WT


title: ntESC, SCNT, GFP, #50

description: Library name: ntES50

value: ntESC, GFP, #50


title: VilCre Colon Rep3

description: Library name: BVBRAF-RAB16-3d-WT-Col-01-05-2023-P3-C2

value: VilCreER

value: Tamoxifen (IP)

value: Day 4


title: m2C_Eif1ad3_RIPseq_His_B


title: Control sample 1, GM no plaque ROI 12

description:
Library name: DSP-1001660037382-A-G10
Formalin Fixed Spatial transcriptomic sequencing

value: brain


title: EB, NAT, WT, #13

description: Library name: 13-NAT-EB

source_name: ESC, WT, #13

value: ESC, WT, #13

value: Embryoid bodies

value: Wildtype

value: NAT


title: m2C_Eif1ad3_RNAseq_KD_B

value: 2-cell embryo


title: Control sample 1, GM no plaque ROI 11

description:
Library name: DSP-1001660037382-A-G09
Formalin Fixed Spatial transcriptomic sequencing


title: ntESC, SCNT, WT, #53

description: Library name: ntES53

value: ntESC, WT, #53

value: embryonic stem cells


title: AhApcMyc SI Rep4

description: Library name: BAAM-97180-AhAMyc-SI-01-05-2023-P1-F1

value: SI

value: Tissue after short term induction

value: Female

value: AhCre+ Apcfl/fl Mycfl/fl

value: B-napthoflavone (IP)


title: Control sample 1, GM no plaque ROI 8

description:
Library name: DSP-1001660037382-A-G06
Formalin Fixed Spatial transcriptomic sequencing


title: Control sample 1, GM no plaque ROI 9

description:
Library name: DSP-1001660037382-A-G07
Formalin Fixed Spatial transcriptomic sequencing


title: m2C_Eif1ad3_RNAseq_Ctrl_B

value: WT


title: Control sample 1, GM no plaque ROI 7

description:
Library name: DSP-1001660037382-A-G05
Formalin Fixed Spatial transcriptomic sequencing


title: undifferentiated USCs

city: Erlangen

first: Steffen

last: Uebe

address: Kussmaulallee 4

department: Humangenetisches Institut

institute: Uniklinikum Erlangen

description:
Library name: AS-U
Parse Bioscience

data_processing:
FASTQ files were processed using TrailmakerTM pipeline module (https://app.trailmaker.parsebiosciences.com/; pipeline v1.5.0, Parse Biosciences).
FASTQ files were demultiplexed sample-wise using the script https://support.parsebiosciences.com/hc/en-us/articles/29780938849044-Partitioning-fastq-files-by-round-1-well-coordinates (last accessed July 9th, 2025)
Assembly: GRCh38-1-1-3c
Supplementary files format and content: all_genes.csv.gz contains genes measured in the experiment. cell_metadata.csv.gz contains metadata for each cell/barcode. count_matrix.mtx.gz stores the raw gene expression matrix in sparse format.

source_name: urine

growth_protocol: Culture medium consisted of a 1:1 mixture of DMEM high glucose (Gibco), containing 1 % NEAA (gibco) and 1 % Penicilin Streptomycin (Gibco), and KSFM (Gibco) with 15 % FBS (Sigma Aldrich or Roth) and 5 ng/mL bFGF (Peprotech) or humankine thermostable bFGF (Sigma). Culture medium was exchanged three times per week.

extract_protocol:
Cell were washed with 1x PBS and treated with accutase (BioLegend) for 20 minutes. Cells were centrifuged for 5 minutes at 300 g and resuspended in PBS with 1 % BSA and 2 mM EDTA.
Cell fixation, barcoding, cDNA amplification and Libraries were prepared using Parse Biosciences Parse Evercode WT V3 Workflow.

treatment_protocol: Chondrogenic differentiation was induced with the StemPro Chondrogenesis Kit (Gibco). Differentation lasted for two weeks with media change three times per week.

value: urine

value: Urine stem cells

value: wildtype


title: m2C_Eif1ad3_RIPseq_His_A


title: Control sample 1, GM no plaque ROI 6

description:
Library name: DSP-1001660037382-A-G04
Formalin Fixed Spatial transcriptomic sequencing

value: brain


title: m2C_Eif1ad3_RNAseq_Ctrl_A


title: ntESC, SCNT, WT, #61

description: Library name: ntES61

value: ntESC, WT, #61

value: SCNT


title: chondrogenic USCs

description:
Library name: AS-C
Parse Bioscience

value: chondrogenic differentation


title: T47D R5020 replicate 3 POLR3G ChIP

city: Aurora

first: Jessica

last: Finlay-Schultz

state: CO

institute: University of Colorado Denver Anschutz Medical Campus

description: Library name: Sample 17

data_processing:
adpater trimming was done using cutadapt
alignment was doneusing Bowtie2 to human hg38
peak calling was done using macs2
Assembly: hg38
Supplementary files format and content: tab separated peaks

source_name: T47D cell line

growth_protocol: T47D cells were maintained in minimal Eagle’s medium, 5% FBS, 1X NEAA, 10^-9 M insulin, 0.1 mg/mL sodium pyruvate, and 2 mM L-glutamine.

extract_protocol:
Cells were fixed with 1% methanol-free formalin in PBS for 5 minutes. After quenching and cell harvest in Szak RIPA buffer, chromatin was fragmented using a Covaris ME220 sonicator
Libraries were prepared for sequencing using the New England Biolabs NEBNext Ultra II Directional DNA Library Prep Kit for Illumina and multiplex oligo set 1 according to manufacturer protocols.

treatment_protocol: Cells were treated with EtOH vehicle or R5020 for 1h

value: T47D cell line

value: ER+PR+ breast cancer

tag: chip antibody


title: m2C_Eif1ad3_RNAseq_KD_A

value: 2-cell embryo


title: AhApcMyc SI Rep3

description: Library name: BAAM-83731-AhAMyc-SI-01-05-2023-P4-B1

value: Day 4


title: AhApcMyc SI Rep1

description: Library name: BAAM-106809-AhAMyc-SI-01-05-2023-P4-A5

value: SI


title: AhApc SI Rep6

description: Library name: AA-218181-AhA-SI-01-05-2023-P6-A6

value: Tissue after short term induction

value: Male

value: AhCre+ Apcfl/fl


title: VilCre Colon Rep1

description: Library name: BVBRAF-RAB15-4a-WT-Col-01-05-2023-P3-G3

value: Colon

value: Female

value: VilCreER

value: Tamoxifen (IP)


title: AhApcMyc SI Rep2

description: Library name: BAAM-78157-AhAMyc-SI-01-05-2023-P3-H5

value: AhCre+ Apcfl/fl Mycfl/fl

value: B-napthoflavone (IP)