title: 2[4]6_zQ175_Untreated_HIP_female_rep1

status: Public on May 05 2026

type: SRA

city: Princeton

first: Jeff

last: Aaronson

state: New Jersey

address: 155 Village Boulevard, Suite 200

department: Discovery & Systems Biology

country: USA

institute: CHDI

description: Library name: zQ175.148.M2054

library_source: transcriptomic

data_processing:
Libraries for RNA-seq were sequenced using an Illumina NovaSeq X Plus and Illumina NovaSeq 6000
Custom genome and gene annotation were created to include transgenic sequences for EGFP, WPRE, nZFP   viral components as well as Htt1a transcript. GRCm38 genome fasta and GRCm38 version 76 gtf were used as a base for the custom genome and annotation.
Pre-alignment QC metrics such as read coverage, percent of un-mapped reads and GC contents were computed in Omicsoft
Omicsoft aligner was used to map the reads to the custom genome and RSEM software from Omicsoft was used to quantify gene and transcript expression
Adapter and quality trimming were performed in Omicsoft using the following settings: Trimming , Mode=TrimByQuality, ReadTrimQuality=2; AverageQualityCutoff=10, EnablePolyRateCutoff=True, PolyRateCutoff=80. FilterSource IlluminaAdapters,Human.rRNA,Human.tRNA,Ercc
Assembly: GRCm38HD.EGFP_WPRE_ZFPs_tdTomatoStiff custom genome assembly and GRCm38.76.Htt1a_EGFP_WPRE_ZFPs_tdTomatoStiff custom gene annotation
Supplementary files format and content: Tab-delimited file containing counts for genes

molecule: total RNA

organism: Mus musculus

source_name: Hippocampus

extract_protocol:
Hippocampal brain tissues were dissected from all mice at 6 or 10 months of age. RNA was extracted using a Qiagen RNeasy kit.
Libraries for RNA-seq were prepared using Illumina RNA preparation with polyA selection

treatment_protocol: The study involved four groups of mice: untreated mice, mice treated with non-targeting siRNA (NTC), mice administrated with HTT-10150 siRNA, and mice treated with both HTT-634 and HTT-486. Three distinct treatment strategies were employed: 2[4]6 - treatment at 2 months, sacrifice at 6 months; 6[4]10 -  treatment at 6 months, sacrifice at 10 months; 2+6[8]10 - treatment at 2 and 6 months, sacrifice at 10 months.

tag: tissue

value: Hippocampus

tag: genotype

tag: treatment

value: Untreated

tag: Sex

value: female

tag: age

value: 6 months

tag: age at_treatment

value: 2 months

tag: sample group


title: 2[4]6_zQ175_HTT-10150_HIP_female_rep3

description: Library name: zQ175.151.M2028


title: 2[4]6_zQ175_Untreated_HIP_female_rep2

description: Library name: zQ175.148.M2059


title: 2[4]6_zQ175_HTT-634.486_HIP_female_rep1

description: Library name: zQ175.148.M2044


title: 2[4]6_zQ175_NTC_HIP_female_rep1

description: Library name: zQ175.148.M2045

value: NTC


title: 2[4]6_zQ175_HTT-10150_HIP_female_rep1

description: Library name: zQ175.148.M2038


title: 2[4]6_zQ175_NTC_HIP_female_rep2

description: Library name: zQ175.149.M2065


title: 2[4]6_zQ175_HTT-634.486_HIP_female_rep2

description: Library name: zQ175.149.M2043


title: 2[4]6_zQ175_HTT-10150_HIP_female_rep2

description: Library name: zQ175.149.M2037


title: 2[4]6_zQ175_Untreated_HIP_female_rep3

description: Library name: zQ175.149.M2057


title: 2[4]6_zQ175_NTC_HIP_female_rep3

description: Library name: zQ175.151.M2032


title: 2[4]6_WT_Untreated_HIP_male_rep1

description: Library name: zQ175.146.M2079

value: Wild Type

value: male


title: 2.6[8]10_zQ175_Untreated_HIP_female_rep4

description: Library name: zQ175.91.215

value: 10 months

value: 2+6 months


title: 2.6[8]10_zQ175_Untreated_HIP_female_rep3

description: Library name: zQ175.87.145


title: 2.6[8]10_zQ175_HTT-10150_HIP_female_rep4

description: Library name: zQ175.88.135


title: 2.6[8]10_WT_NTC_HIP_male_rep4

description: Library name: zQ175.89.27


title: 2.6[8]10_zQ175_NTC_HIP_female_rep4

description: Library name: zQ175.88.151


title: 2.6[8]10_WT_HTT-634.486_HIP_male_rep4

description: Library name: zQ175.89.15


title: 2.6[8]10_zQ175_NTC_HIP_female_rep3

description: Library name: zQ175.87.159


title: 2.6[8]10_WT_Untreated_HIP_male_rep4

description: Library name: zQ175.89.8


title: 2.6[8]10_zQ175_HTT-634.486_HIP_female_rep4

description: Library name: zQ175.88.150


title: 2.6[8]10_zQ175_HTT-634.486_HIP_female_rep3

description: Library name: zQ175.87.158


title: 2.6[8]10_WT_HTT-10150_HIP_male_rep4

description: Library name: zQ175.86.226


title: 2.6[8]10_WT_HTT-10150_HIP_male_rep3

description: Library name: zQ175.85.242


title: 2.6[8]10_WT_HTT-634.486_HIP_male_rep3

description: Library name: zQ175.85.249


title: 2.6[8]10_WT_Untreated_HIP_male_rep3

description: Library name: zQ175.85.241


title: 2.6[8]10_WT_NTC_HIP_male_rep3

description: Library name: zQ175.85.254


title: 2.6[8]10_WT_Untreated_HIP_female_rep4

description: Library name: zQ175.84.45


title: 2.6[8]10_WT_Untreated_HIP_female_rep3

description: Library name: zQ175.83.41


title: 2.6[8]10_zQ175_Untreated_HIP_male_rep3

description: Library name: zQ175.81.64


title: 2.6[8]10_zQ175_HTT-634.486_HIP_male_rep4

description: Library name: zQ175.82.36


title: 2.6[8]10_WT_HTT-10150_HIP_female_rep3

description: Library name: zQ175.83.10


title: 2.6[8]10_zQ175_NTC_HIP_male_rep4

description: Library name: zQ175.82.48


title: 2.6[8]10_zQ175_HTT-10150_HIP_male_rep4

description: Library name: zQ175.82.32


title: 2.6[8]10_WT_HTT-634.486_HIP_female_rep4

description: Library name: zQ175.80.74


title: 2.6[8]10_zQ175_HTT-634.486_HIP_male_rep3

description: Library name: zQ175.81.42


title: 2.6[8]10_WT_HTT-10150_HIP_female_rep4

description: Library name: zQ175.84.1


title: 2.6[8]10_zQ175_HTT-10150_HIP_male_rep3

description: Library name: zQ175.81.40


title: 2.6[8]10_zQ175_NTC_HIP_male_rep3

description: Library name: zQ175.81.55


title: 2.6[8]10_WT_NTC_HIP_female_rep4

description: Library name: zQ175.83.34


title: 2.6[8]10_WT_HTT-634.486_HIP_female_rep2

description: Library name: zQ175.73.14


title: 2.6[8]10_zQ175_Untreated_HIP_female_rep2

description: Library name: zQ175.74.30


title: 2.6[8]10_WT_HTT-634.486_HIP_female_rep3

description: Library name: zQ175.79.54


title: 2.6[8]10_WT_HTT-10150_HIP_female_rep2

description: Library name: zQ175.73.16


title: 2.6[8]10_zQ175_NTC_HIP_male_rep2

description: Library name: zQ175.78.36


title: 2.6[8]10_zQ175_Untreated_HIP_male_rep1

description: Library name: zQ175.72.28


title: 2.6[8]10_WT_NTC_HIP_female_rep2

description: Library name: zQ175.73.17


title: 2.6[8]10_zQ175_HTT-10150_HIP_male_rep1

description: Library name: zQ175.71.27


title: 2.6[8]10_WT_NTC_HIP_female_rep3

description: Library name: zQ175.80.51


title: 2.6[8]10_zQ175_Untreated_HIP_male_rep4

description: Library name: zQ175.82.63


title: 2.6[8]10_zQ175_HTT-634.486_HIP_male_rep1

description: Library name: zQ175.71.26


title: 2.6[8]10_zQ175_NTC_HIP_male_rep1

description: Library name: zQ175.71.21


title: 2.6[8]10_WT_Untreated_HIP_female_rep1

description: Library name: zQ175.73.12


title: 2.6[8]10_WT_HTT-10150_HIP_male_rep1

description: Library name: zQ175.70.19


title: 2.6[8]10_WT_Untreated_HIP_female_rep2

description: Library name: zQ175.80.46


title: 2.6[8]10_WT_Untreated_HIP_male_rep2

description: Library name: zQ175.69.14


title: 2.6[8]10_WT_HTT-634.486_HIP_male_rep1

description: Library name: zQ175.70.16


title: 2.6[8]10_zQ175_Untreated_HIP_female_rep1

description: Library name: zQ175.68.27


title: 2.6[8]10_WT_Untreated_HIP_male_rep1

description: Library name: zQ175.69.13


title: 2.6[8]10_WT_NTC_HIP_female_rep1

description: Library name: zQ175.66.3


title: 2.6[8]10_zQ175_NTC_HIP_female_rep1

description: Library name: zQ175.68.19


title: 2.6[8]10_zQ175_HTT-634.486_HIP_female_rep1

description: Library name: zQ175.68.23


title: 2.6[8]10_zQ175_HTT-10150_HIP_female_rep2

description: Library name: zQ175.68.26


title: 2.6[8]10_zQ175_HTT-10150_HIP_female_rep1

description: Library name: zQ175.68.20


title: 2.6[8]10_WT_HTT-634.486_HIP_female_rep1

description: Library name: zQ175.66.7


title: Control, whole bone

city: Farmington

first: Ernesto

last: Canalis

state: CT

address: 263 Farmington Avenue

department: Orthopaedic Surgery

institute: UConn Health

description: Library name: ControlWholeBone

library_source: transcriptomic single cell

data_processing:
FASTQ files generated using reference genome mm10-2020-A were analyzed on Cell Ranger v9.0 (10x Genomics) for sample demultiplexing, barcode processing and transcript counting and output HTMLs for sample visualization and data quality assessment.
The output was analyzed using Seurat R Package (v5.4) to perform secondary analyses, such as dimensionality reduction, cell clustering and differential gene expression. Cells expressing fewer than 250 transcripts, more than 10% mitochondrial RNA and cells expressing >10,000 genes/cell were excluded manually, and the data set was normalized by employing the NormalizeData function in Seurat. Highly variable functions were identified, and linear dimensional reduction conducted by principal component analysis and non-linear dimensional reduction performed by uniform manifold approximation and projection (UMAP). Doublets were identified and excluded, and cell clusters were identified by the FindClusters function in Seurat. Pseudotime trajectory analysis was constructed by analyzing the Seurat object in Monocle 3. Monocle cell data set was constructed and the learn principal graph from the reduced dimensional space was applied using learn_graph. Cells were organized along their trajectory using Monocle plot_cells and order_cells; marker genes for each cluster were identified using Seurat’s FindVariableFeatures function. Gene ontology and Ingenuity Pathway Analysis (IPA) (Qiagen) of differentially expressed genes was performed on selected clusters and genes prioritized based on ontology and relevance to transcriptional control and signaling pathways. IPA was performed to analyze canonical pathways under Genes and Chemicals category.
Assembly: mm10-2020-A
Supplementary files format and content: .h5

source_name: Whole bone

extract_protocol:
To profile the transcriptome of femurs from Notch2em1Ecan and sex-matched control wild type mice, femoral bones from 2 Notch2em1Ecan and from 2 wild type mice were excised after the epiphyseal ends were removed and the marrow was flushed and discarded. Bones were crushed and cells from mice of each genotype were pooled independently and dispersed by digesting the tissue with collagenase, dispase and DNase. Dispersed cells were recovered and incubated with ACK lysis buffer to remove red blood cells followed by fluorescence-activated cell sorting for the depletion of immune and erythroid cells by double-negative (CD45−; TER119−) selection.
Sorted cells were suspended and live cells counted and analyzed on a cell-by-cell basis through the use of microfluidic partitioning to capture single cells. Cell partitioning and barcoded libraries were prepared using a Chromium X instrument and a Chromium Single-Cell GEM-X Universal 3' gene expression v4 4-plex library and a GEM-X OCM 3' Chip v4 (10x Genomics). cDNA amplification and library generation were performed according to the manufacturer’s protocol and cDNAs from a single-cell had the same barcode, allowing the sequencing reads to be mapped back to the cell of origin. Libraries were validated for length and adapter dimer removal using the Agilent TapeStation D1000 High Sensitivity assay, quantified and sequenced as one sample pool on the AVITI Platform using a 2 x 75 high-output flow cell (AmpSeq). A target read depth of 50,000 transcriptome reads per cell was achieved in each sample.

value: Whole bone

value: Control


title: N2Ex25, whole bone

description: Library name: N2Ex25WholeBone


title: Cowpea infected with B. cinerea isolate_1

city: Davis

first: Daniel

middle: J

last: Kliebenstein

state: CA

address: One Shields Ave

institute: University of California Davis

description: Library name: I1

data_processing:
Raw paired-end sequencing reads were quality-trimmed and filtered using Trimmomatic (Bolger et al. 2014). Adapter sequences were clipped using the ILLUMINACLIP module, allowing up to two seed mismatches, a palindrome clip threshold of 30, and a simple clip threshold of 10. Reads were further processed to remove low-quality bases from the 5' and 3' ends, trim within a sliding window of four bases where the average quality dropped below 15, and discard reads shorter than 20 bases.
Reads were mapped to reference genomes using Hisat2 (Kim et al. 2019). Bulk reads were mapped first to the host genome. The remaining un-mapped reads were mapped to Botrytis B05.10 isolate reference genome.
Read counts were obtained from the mapped reads using RSubread (Shi 2017). Read counts were TMM normalized with the EdgeR package (Robinson et al. 2010). Low expression genes (genes with <1 CPM in <20% of samples within each host) were removed from the dataset.
Assembly: Cowpea: Lonardi et al., 2019; Common Bean: Schmutz et al., 2014; Botrytis cinerea: van Kan et al., 2017.
Supplementary files format and content: csv files include normalized counts for both host and pathogen for each sample

molecule: polyA RNA

organism: Vigna unguiculata

source_name: leaf

extract_protocol:
mRNA isolation was performed with Dynabeads oligo-dT kit.
Libraries were cosntructed as described in Kumar et al. 2012.

value: leaf


title: Cowpea infected with B. cinerea isolate_11

description: Library name: I11


title: Cowpea infected with B. cinerea isolate_19

description: Library name: I19


title: Cowpea infected with B. cinerea isolate_16

description: Library name: I16


title: Cowpea infected with B. cinerea isolate_25

description: Library name: I25


title: Cowpea infected with B. cinerea isolate_27

description: Library name: I27


title: Cowpea infected with B. cinerea isolate_22

description: Library name: I22


title: Cowpea infected with B. cinerea isolate_17

description: Library name: I17


title: Cowpea infected with B. cinerea isolate_14

description: Library name: I14


title: Cowpea infected with B. cinerea isolate_23

description: Library name: I23


title: Cowpea infected with B. cinerea isolate_15

description: Library name: I15


title: Cowpea infected with B. cinerea isolate_13

description: Library name: I13


title: Cowpea infected with B. cinerea isolate_2

description: Library name: I2


title: Cowpea infected with B. cinerea isolate_29

description: Library name: I29


title: Cowpea infected with B. cinerea isolate_20

description: Library name: I20


title: Cowpea infected with B. cinerea isolate_3

description: Library name: I3


title: Cowpea infected with B. cinerea isolate_21

description: Library name: I21


title: Cowpea infected with B. cinerea isolate_4

description: Library name: I4


title: Cowpea infected with B. cinerea isolate_28

description: Library name: I28


title: Cowpea infected with B. cinerea isolate_31

description: Library name: I31


title: Cowpea infected with B. cinerea isolate_30

description: Library name: I30


title: Cowpea infected with B. cinerea isolate_26

description: Library name: I26


title: Cowpea infected with B. cinerea isolate_32

description: Library name: I32


title: Cowpea infected with B. cinerea isolate_18

description: Library name: I18


title: Cowpea infected with B. cinerea isolate_34

description: Library name: I34


title: Cowpea infected with B. cinerea isolate_33

description: Library name: I33


title: Cowpea infected with B. cinerea isolate_35

description: Library name: I35

value: Acacia


title: Cowpea infected with B. cinerea isolate_39

description: Library name: I39


title: Cowpea infected with B. cinerea isolate_37

description: Library name: I37


title: Cowpea infected with B. cinerea isolate_40

description: Library name: I40

value: BMM


title: Cowpea infected with B. cinerea isolate_36

description: Library name: I36


title: Cowpea infected with B. cinerea isolate_5

description: Library name: I5


title: Cowpea infected with B. cinerea isolate_38

description: Library name: I38

value: Ausubel


title: Cowpea infected with B. cinerea isolate_42

description: Library name: I42

value: EsparatoFresa


title: Cowpea infected with B. cinerea isolate_41

description: Library name: I41

value: DavisNavel


title: Cowpea infected with B. cinerea isolate_44

description: Library name: I44


title: Cowpea infected with B. cinerea isolate_43

description: Library name: I43


title: Cowpea infected with B. cinerea isolate_45

description: Library name: I45


title: Cowpea infected with B. cinerea isolate_54

description: Library name: I54


title: Cowpea infected with B. cinerea isolate_46

description: Library name: I46


title: Cowpea infected with B. cinerea isolate_50

description: Library name: I50

value: KatieTomato


title: Cowpea infected with B. cinerea isolate_47

description: Library name: I47


title: Cowpea infected with B. cinerea isolate_48

description: Library name: I48

value: Geranium


title: Cowpea infected with B. cinerea isolate_49

description: Library name: I49

value: Grape


title: Cowpea infected with B. cinerea isolate_53

description: Library name: I53


title: Cowpea infected with B. cinerea isolate_51

description: Library name: I51


title: Cowpea infected with B. cinerea isolate_52

description: Library name: I52


title: Cowpea infected with B. cinerea isolate_57

description: Library name: I57


title: Cowpea infected with B. cinerea isolate_55

description: Library name: I55


title: Cowpea infected with B. cinerea isolate_6

description: Library name: I6


title: Cowpea infected with B. cinerea isolate_58

description: Library name: I58

value: Molly


title: Cowpea infected with B. cinerea isolate_56

description: Library name: I56


title: Cowpea infected with B. cinerea isolate_60

description: Library name: I60

value: NobleRot


title: Cowpea infected with B. cinerea isolate_59

description: Library name: I59

value: Navel


title: Cowpea infected with B. cinerea isolate_68

description: Library name: I68


title: Cowpea infected with B. cinerea isolate_61

description: Library name: I61

value: Peachy


title: Cowpea infected with B. cinerea isolate_65

description: Library name: I65

value: Rasp


title: Cowpea infected with B. cinerea isolate_62

description: Library name: I62

value: Pepper


title: Cowpea infected with B. cinerea isolate_12

description: Library name: I12


title: Cowpea infected with B. cinerea isolate_69

description: Library name: I69


title: Cowpea infected with B. cinerea isolate_63

description: Library name: I63

value: PepperSub


title: Cowpea infected with B. cinerea isolate_8

description: Library name: I8


title: Cowpea infected with B. cinerea isolate_71

description: Library name: I71


title: Cowpea infected with B. cinerea isolate_64

description: Library name: I64

value: PhiloMenlo


title: Cowpea control sample_48h

description: Library name: I74

value: leaf


title: Cowpea infected with B. cinerea isolate_70

description: Library name: I70

value: UKRazz


title: Cowpea infected with B. cinerea isolate_66

description: Library name: I66

value: Rose


title: Cowpea infected with B. cinerea isolate_7

description: Library name: I7


title: Cowpea infected with B. cinerea isolate_72

description: Library name: I72

value: FresaSD


title: Cowpea control sample_0h

description: Library name: I73


title: Cowpea infected with B. cinerea isolate_67

description: Library name: I67

value: Supersteak


title: Cowpea infected with B. cinerea isolate_10

description: Library name: I10


title: Cowpea infected with B. cinerea isolate_9

description: Library name: I9


title: Common Bean infected with B. cinerea isolate_15

description: Library name: U15

organism: Phaseolus vulgaris

value: UC Cran


title: Common Bean infected with B. cinerea isolate_23

description: Library name: U23


title: Common Bean infected with B. cinerea isolate_22

description: Library name: U22


title: Common Bean infected with B. cinerea isolate_25

description: Library name: U25


title: Common Bean infected with B. cinerea isolate_3

description: Library name: U3


title: Common Bean infected with B. cinerea isolate_16

description: Library name: U16


title: Common Bean infected with B. cinerea isolate_12

description: Library name: U12


title: Common Bean infected with B. cinerea isolate_27

description: Library name: U27


title: Common Bean infected with B. cinerea isolate_26

description: Library name: U26


title: Common Bean infected with B. cinerea isolate_11

description: Library name: U11


title: Common Bean infected with B. cinerea isolate_24

description: Library name: U24


title: Common Bean infected with B. cinerea isolate_13

description: Library name: U13


title: Common Bean infected with B. cinerea isolate_20

description: Library name: U20


title: Common Bean infected with B. cinerea isolate_19

description: Library name: U19


title: Common Bean infected with B. cinerea isolate_14

description: Library name: U14


title: Common Bean infected with B. cinerea isolate_18

description: Library name: U18


title: Common Bean infected with B. cinerea isolate_21

description: Library name: U21


title: Common Bean infected with B. cinerea isolate_2

description: Library name: U2


title: U2OS cells, Total RNA-seq, shYTHDC1, HS, rep2

city: Beijing

first: Qidong

last: Deng

address: No.5 Yiheyuan Road Haidian District, Beijing 100871 P.R. China

department: School of Life Sciences

country: China

institute: Peking university

description:
Library name: Sample6
Total_mRNA_Raw_Read_Counts.txt
mRNA_siDC1_HS_2

data_processing:
For RNA-seq analysis, raw sequencing reads from NHS and HS samples were first assessed for quality using FastQC (v0.11.8). Low-quality bases and adapter sequences were trimmed with Trim Galore! (v0.6.7, https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). Clean reads were then aligned to the human reference genome (GRCh38) using HISAT2 (v2.2.1) with default parameters. Mapping quality was evaluated using SAMtools (v1.17). Aligned reads were processed with featureCounts (v2.0.2) to obtain raw read counts for annotated genes. Normalization and differential gene expression analysis were conducted using DESeq2 (v1.36.0) in R (v4.4.0). Genes with p-values < 0.05 and log2 fold change > log2(1.5) were considered differentially expressed. The DEGs were then hierarchically clustered, split into three distinct groups based on their expression patterns, and visualized using the ComplexHeatmap package. Functional annotation of differentially expressed genes (DEGs) was performed using the clusterProfiler package (v4.6.0) in R. Gene Ontology (GO) enrichment analyses were conducted to identify enriched biological processes and pathways. Transcription factor enrichment analysis was performed using the Enrichr web server with default settings, focusing on upregulated genes during the heat shock.
For MeRIP-seq analysis, the cleaned reads were aligned to the human genome (GRCh38) using HISAT2 and were converted into BAM format using Samtools, followed by filtering for high-quality mapped reads. The BAM files were then separated into forward and reverse strands using Samtools. MACS2 was used to perform peak calling separately for the forward and reverse strands, with a threshold parameter of ‘-q 0.05’, to identify enriched regions likely containing m6A modifications and their specific peak intensities. The peaks from both strands were then merged to generate the final peak set. For genes with multiple m6A peaks, the methylation level was defined as the sum of the peak intensities of all identified peaks associated with that gene.
Assembly: hg38
Supplementary files format and content: For RNA-seq, tab-delimited text file includes raw counts for each Sample.
Supplementary files format and content: For MeRIP-seq, bigWig format files.

organism: Homo sapiens

growth_protocol: U2OS cell line was cultured in DMEM medium (Gibco) supplemented with 10% fetal bovine serum and 1% penicillin/ streptomycin at 37°C under 5% CO2.

extract_protocol:
For RNA-seq, Total RNA were extracted using TRIzol™ reagent (Invitrogen, 15596026) according to the manufacturer’s protocol and quantified using NanoDrop One spectrophotometer (Invitrogen). For MeRIP-seq, MeRIP-seq was carried out according to the previously published protocol (DOI: 10.1126/science.aay6018). m6A was immunoprecipitated using the EpiMark N6-Methyladenosine Enrichment Kit (NEB, E1610S), following the manufacturer's protocol.
For RNA-seq, RNA-seq library preparation was performed utilizing VAHTS Universal V8 RNA-seq Library Prep Kit (Vazyme, NR605) following the manufacturer’s protocol with 1 µg initial amount of total RNA for each sample, and sequencing was performed at JMDNA Bio-Medical Technology Corporation on an DNBSEQ-T7 platform. For MeRIP-seq, MeRIP-seq  library preparation was constructed using the SMARTer Stranded Total RNA-Seq Kit v2 (Takara, 634413), both following their manufacturer’s protocols. Sequencing was conducted at Beijing Annoroad Medical Inspection Laboratory on an Illumina NovaSeq 6000 platform.

tag: cell line

value: Total, shYTHDC1, HS


title: U2OS cells, Total RNA-seq, shCtrl, NHS, rep1

description:
Library name: Sample1
Total_mRNA_Raw_Read_Counts.txt
mRNA_siCtrl_NHS_1

value: WT

value: Total, WT, NHS


title: U2OS cells, Total RNA-seq, shCtrl, HS, rep1

description:
Library name: Sample3
Total_mRNA_Raw_Read_Counts.txt
mRNA_siCtrl_HS_1

value: Total, WT, HS


title: U2OS cells, Total RNA-seq, shYTHDC1, HS, rep1

description:
Library name: Sample5
Total_mRNA_Raw_Read_Counts.txt
mRNA_siDC1_HS_1


title: U2OS cells, Total RNA-seq, shCtrl, NHS, rep2

description:
Library name: Sample2
Total_mRNA_Raw_Read_Counts.txt
mRNA_siCtrl_NHS_2


title: U2OS cells, Total RNA-seq, shCtrl, HS, rep2

description:
Library name: Sample4
Total_mRNA_Raw_Read_Counts.txt
mRNA_siCtrl_HS_2


title: Common Bean infected with B. cinerea isolate_28

description: Library name: U28


title: Common Bean infected with B. cinerea isolate_31

description: Library name: U31


title: Common Bean infected with B. cinerea isolate_32

description: Library name: U32


title: Common Bean infected with B. cinerea isolate_30

description: Library name: U30


title: Common Bean infected with B. cinerea isolate_42

description: Library name: U42

value: EsparatoFresa


title: Common Bean infected with B. cinerea isolate_43

description: Library name: U43


title: Common Bean infected with B. cinerea isolate_39

description: Library name: U39


title: Common Bean infected with B. cinerea isolate_40

description: Library name: U40

value: BMM


title: Common Bean infected with B. cinerea isolate_29

description: Library name: U29


title: Common Bean infected with B. cinerea isolate_35

description: Library name: U35

value: Acacia


title: Common Bean infected with B. cinerea isolate_4

description: Library name: U4


title: Common Bean infected with B. cinerea isolate_45

description: Library name: U45


title: Common Bean infected with B. cinerea isolate_36

description: Library name: U36


title: Common Bean infected with B. cinerea isolate_34

description: Library name: U34


title: Common Bean infected with B. cinerea isolate_41

description: Library name: U41

value: DavisNavel


title: Common Bean infected with B. cinerea isolate_37

description: Library name: U37


title: 2.6[8]10_WT_NTC_HIP_male_rep1

description: Library name: zQ175.70.15

value: Hippocampus

value: Wild Type

value: NTC

value: male

value: 10 months

value: 2+6 months


title: Common Bean infected with B. cinerea isolate_38

description: Library name: U38

value: leaf

value: Ausubel


title: Common Bean infected with B. cinerea isolate_44

description: Library name: U44

value: UC Cran


title: Common Bean infected with B. cinerea isolate_49

description: Library name: U49

value: Grape


title: Common Bean infected with B. cinerea isolate_6

description: Library name: U6


title: Common Bean infected with B. cinerea isolate_50

description: Library name: U50

value: KatieTomato


title: Common Bean infected with B. cinerea isolate_46

description: Library name: U46


title: Common Bean infected with B. cinerea isolate_47

description: Library name: U47


title: Common Bean infected with B. cinerea isolate_33

description: Library name: U33


title: Common Bean infected with B. cinerea isolate_52

description: Library name: U52


title: Common Bean infected with B. cinerea isolate_53

description: Library name: U53


title: Common Bean infected with B. cinerea isolate_55

description: Library name: U55


title: Common Bean infected with B. cinerea isolate_7

description: Library name: U7


title: Common Bean infected with B. cinerea isolate_56

description: Library name: U56


title: Common Bean infected with B. cinerea isolate_54

description: Library name: U54


title: Common Bean infected with B. cinerea isolate_57

description: Library name: U57


title: Common Bean infected with B. cinerea isolate_66

description: Library name: U66

value: Rose


title: Common Bean infected with B. cinerea isolate_67

description: Library name: U67

value: Supersteak


title: Common Bean infected with B. cinerea isolate_70

description: Library name: U70

value: UKRazz


title: Common Bean infected with B. cinerea isolate_60

description: Library name: U60

value: NobleRot


title: Common Bean infected with B. cinerea isolate_63

description: Library name: U63

value: PepperSub


title: Common Bean infected with B. cinerea isolate_64

description: Library name: U64

value: PhiloMenlo


title: Common Bean infected with B. cinerea isolate_8

description: Library name: U8


title: Common Bean infected with B. cinerea isolate_68

description: Library name: U68


title: Common Bean infected with B. cinerea isolate_58

description: Library name: U58

value: Molly


title: Common Bean infected with B. cinerea isolate_69

description: Library name: U69


title: Common Bean infected with B. cinerea isolate_72

description: Library name: U72

value: FresaSD


title: Common Bean control sample_48h

description: Library name: U74


title: Common Bean infected with B. cinerea isolate_65

description: Library name: U65

value: Rasp


title: Common Bean infected with B. cinerea isolate_62

description: Library name: U62

value: Pepper


title: Common Bean control sample_0h

description: Library name: U73


title: Common Bean infected with B. cinerea isolate_5

description: Library name: U5


title: Common Bean infected with B. cinerea isolate_10

description: Library name: U10


title: Common Bean infected with B. cinerea isolate_1

description: Library name: U1


title: Common Bean infected with B. cinerea isolate_51

description: Library name: U51


title: Common Bean infected with B. cinerea isolate_61

description: Library name: U61

value: Peachy


title: 2.6[8]10_zQ175_HTT-10150_HIP_female_rep3

description: Library name: zQ175.87.156

value: Hippocampus

value: female

value: 10 months

value: 2+6 months


title: PROTEXI2

type: RNA

city: Cleveland

first: Jin Muk

last: Kang

state: OH

address: 2103 Cornell rd WRB 3501

institute: University Hospitals Cleveland Medical Center

description: Two probes were used to detect each transcript: a reporter probe that carries the fluorescent barcode, and a biotinylated capture probe that immobilizes the complex for data collection. The code set contained 755 probe pairs, each pair specific to a particular nucleic acid target

scan_protocol: Once the cartridge was prepared, it was then loaded onto the nCounter Digital Analyzer and scanned.

data_processing: Sample quality control was conducted according to the manufacturer's instructions to ensure reliable results. Background levels were determined for each sample using mean plus two standard deviations of the included negative control counts. Background subtracted counts were normalized using geometric means of 16 housekeeping genes.

source_name: B16F10 tumor

growth_protocol: B16F10 cells were inoculated subcutaneously into syngeneic C57BL/6 mice.

extract_protocol: The total RNA of tumors wee extracted via RNeasy Mini Kit.

treatment_protocol: DC vaccines were treated at day 3 and 10 after tumor inoculation.

value: Melanoma

tag: strain

value: PROTEXI loaded with Trp2 and OVA323


title: Common Bean infected with B. cinerea isolate_59

description: Library name: U59

value: leaf

value: UC Cran

value: Navel


title: DC-Trp2-2

value: DC vaccine loaded with Trp2 peptide


title: Control2

value: Vehicle


title: PROTEXI1


title: Common Bean infected with B. cinerea isolate_9

description: Library name: U9


title: Control1


title: Common Bean infected with B. cinerea isolate_71

description: Library name: U71


title: Macrophage_control_rep1

city: Buffalo

first: Jessy

last: Alexander

state: NY

address: 875 Ellicott Street

department: Medicine

institute: University at Buffalo

hyb_protocol: Cells were subjected to RBC lysis, washed and plated at a concentration of 2×106 cells/well in RPMI 1640 (+ 10%FBS + Penn/Strep  + 2 mM L-glutamine + 20ng/ml GM-CSF) and grown in 5% CO2 at 37°C. After 24 h, the floating cells were collected, plated and medium was changed every 48 h. At day 7, cells were used for experiments. Cell viability was >90% and were characterized by staining with anti-F4/80 antibody (1:400). RNA was isolated from wildtype and FHKO Mos using TriZol reagent.

scan_protocol: RNA  (RIN ≥ 9.5, 100 ng/sample, n=3/group) was subjected to the mouse myeloid panel (nCounter Analysis System, NanoString Technologies). Analysis was performed using nCounter Software 4.0.

data_processing: Data was normalized for hybridization and counting efficiency. Gene thresholds were calculated as the median of the maxima of the negative control probe measurements. Log transformations were performed in the background before doing a t-test, and all the reported p-values are based on these data (nCounter Software 4.0).

source_name: macrophage control

label_protocol: None.

growth_protocol: 8–10-week-old FH knockout (FHKO) mice, C3aR knockout (C3aRKO) mice, and Ccr2RFPCx3cr1GFP reporter mice maintained in accordance with the Institutional Animal Care and Use Committee, UB guidelines were used for the experiments.

extract_protocol: Femur and tibia were harvested and the bones were flushed with DMEM. Cells were pipetted and filtered to obtain a single cells suspension.

treatment_protocol: None, treatment consists of mice with different genetic backgrounds.

value: Macrophage

value: WT


title: Cowpea infected with B. cinerea isolate_24

description: Library name: I24


title: Macrophage_FHKO_rep3

source_name: macrophage FHKO

value: FHKO


title: Macrophage_FHKO_rep1


title: Macrophage_control_rep2


title: Bulk_Control3

city: Shanghai

first: Chenke

last: Xu

address: No. 2005, Songhu Road, Northwest of Xiangjiangqu City, Yangpu District

institute: Fudan University

description:
Library name: Sample3
bulk_RNA_seq_geneexpression.txt

data_processing:
For RNA-seq, HISAT2 (v2.0.4) and Bowtie2 (v2.2.5) were used to map the reads against GRCh38.p12. Expectation-Maximization (v1.2.8) was used to calculated the gene expression levels. This study performed Gene Set Enrichment Analysis (GSEA) based on all expressed genes between the control and each exposure group. For scRNA-seq, . Downstream integration of scRNA-seq datasets and cellular clustering analyses were conducted using the Seurat toolkit within the R statistical computing environment.
Assembly: GRCh38.p12.
Supplementary files format and content: For RNA-seq,A tab-delimited text file (bulk-RNA-seq-geneexpression.txt)  containing raw gene counts for all samples. The first column is the gene symbol/Ensembl ID, and each subsequent column represents the read counts for one sample. For scRNA-seq, scRNA_Control_barcodes.tsv.gz,scRNA_Control_features.tsv.gz, scRNA_Control_matrix.mtx.gz, scRNA_EHDPP_barcodes.tsv.gz,scRNA_EHDPP_features.tsv.gz, scRNA_EHDPP_matrix.mtx.gz, were provided

source_name: immature kidney organoids

extract_protocol:
For RNA-seq, organoids exposed to EHDPP and negative control (DMSO) were collected by 500 μL TransZol Up (ET111-01, Transgen). After that, 100 μL of chloroform (M1024442500, Merck) was used before vigorous shaking before an 12,000-rpm centrifugation at 20 °C for 10 min. Top layer was aspirated and 300 μL of isopropyl alcohol (1.01040.4008, Merck) was added. And then the samples were gently shaken before an 12,000-rpm centrifugation at 20°C for 10 min. The supernatants were removed, and then 700 μL of 75% ethanol (E801077, Macklin) was used per sample before gentle shaking and centrifugation at same rpm at 20°C for 5 min. After removing the supernatants, each sample was dissolved in 30 μL of DEPC H2O (W274329, Aladdin). For scRNA-seq,For sample preparation, organoids were digested with Accumax (STEMCELL, 07921) for 10 min. Then, cells underwent washing and were subsequently resuspended in calcium- and magnesium-free 1X phosphate-buffered saline supplemented with 0.04% bovine serum albumin.
For RNA-seq, RNA integrity number (RIN) was detected by Agilent 2100, and the RIN of > 7 qualified were used on RNA-seq. RNA-seq was achieved by the Beijing Genomics Institute. Poly A species were used to enrich RNA samples, and the libraries were constructed on the BGISEQ-500 platform (BGI). Sequencing depth of each library was approximate 40 million reads. For scRNA-seq, a total of 15,000 viable cells were then used for scRNA-seq library preparation via the Chromium Next GEM Single Cell 3’ Kit v3.1 (10x Genomics, Catalog No. PN-1000268) and the Chromium Next GEM Chip G Single Cell Kit (10x Genomics, Catalog No. PN-1000127) according to the manufacturer’s protocol. All the libraries were pooled and sequenced via the 150 bp paired-end Illumina NovaSeq 6000 platform. Alignment and transcript quantification of the scRNA sequencing data were executed using the CellRanger count pipeline (version 8.0.1) with the mm39 reference assembly.

value: immature kidney organoids

value: DMSO


title: Bulk_EHDPP3

description:
Library name: Sample6
bulk_RNA_seq_geneexpression.txt

value: EHDPP


title: Bulk_Control1

description:
Library name: Sample1
bulk_RNA_seq_geneexpression.txt


title: Bulk_EHDPP1

description:
Library name: Sample4
bulk_RNA_seq_geneexpression.txt


title: Control_2

city: 天津

first: yingge

last: Lv

state: 天津

address: 天津市和平区气象台路

department: 基础医学院

institute: 天津医科大学

description:
Library name: Sample 2
NormalizedCount_gene_TE_analysis: MCF7CON3
CON3

data_processing:
Reads were aligned to the human genome (UCSC hg38) using STAR (v2.7.9a_2021-06-25) with the default parameters .
Gene and TE expression levels were quantified by TEtranscripts (v2.2.3).
Assembly: GRCh38; TE reference from RepeatMasker
Supplementary files format and content: NormalizedCount_gene_TE_analysis.txt

source_name: breast

growth_protocol: MCF-7 cells were cultured in Dulbecco's modified Eagle’s medium supplemented with 10% fetal bovine serum at 37℃ in a humidified atmosphere with 5% CO2.

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: MCF-7 cells were transfected with control and P-SETDB1-4 PROTAC using PEI transfection reagent.

value: breast

tag: cell type

value: human breast adenocarcinoma cell

value: MCF-7 cells were transfected with control PROTAC.


title: scRNA_Control

description: Library name: Sample7

source_name: kidney organoids

value: kidney organoids


title: scRNA_EHDPP

description: Library name: Sample8


title: P-SETDB1-4_2

description:
Library name: Sample 4
NormalizedCount_gene_TE_analysis: MCF7PRO3
PRO3

value: MCF-7 cells were transfected with P-SETDB1-4.


title: Control_1

description:
Library name: Sample 1
NormalizedCount_gene_TE_analysis: MCF7CON2
CON2


title: P-SETDB1-4_1

description:
Library name: Sample 3
NormalizedCount_gene_TE_analysis: MCF7PRO2
PRO2


title: Bulk_Control2

description:
Library name: Sample2
bulk_RNA_seq_geneexpression.txt


title: Vortex-2

city: Chengdu

first: Du

last: Lingyu

state: Sichuan

address: Yulin Street

institute: Sixhuan University

description: Library name: Sample 8

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing 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.
Reads were mapped to mouse genome assembly GRCm39 (https://ftp.ensembl.org/pub/release-112/fasta/mus_musculus/dna/Mus_musculus.GRCm39.dna.toplevel.fa.gz) using HISAT2.
HTSeq v0.13.5 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. GTF file:https://ftp.ensembl.org/pub/release-112/gtf/mus_musculus/Mus_musculus.GRCm39.112.gtf.gz.
Assembly: GRCm39
Supplementary files format and content: File include Count and  FPKM values for each sample

growth_protocol: The brain-derived endothelial cells.3 (bEnd.3) were purchased from Xiamen Immocell Biotechnology Co, Ltd. The cells were cultured with Low sodium bicarbonate basic medium (ICell), containing 10% fetal bovine serum (FBS, Shanghai Zhongqiao Xinzhou Biotech Co, Ltd.), 100 units/ml and 100 μg/ml penicillin–streptomycin at 37 °C in an incubator with 95% humidified air and 5% carbon dioxide (Heraeus Company, Germany).

extract_protocol:
bEnd.3 was collected from the PSS group, the HSS group and the VSS group respectively. Total RNA was extracted from the samples using TRIzol reagent (Invitrogen, USA). The mixed RNA samples from the three groups were sent to Shanghai Lifegenes Technology Co., Ltd.（Shanghai Lifegenes Technology, China） for transcriptome sequencing analysis.
A total amount of 1.5 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: Cells cultured on glass coverslips were exposed to flow using a parallel-plate flow chamber system (CellShear™, Chengdu Lixiang Biotechnology Co., Ltd., China). By reviewing the literature, we determined the three mechanical magnitudes and methods involved in this study[30]. The PSS group represents the normal physiological cerebrovascular fluid shear force, with a laminar flow size of 10 dyne/cm2; the HSS group represents the early stage of IA, as IA often forms at vascular bifurcations, where there is a higher fluid shear force, so it is set at a laminar flow of 20 dyne/cm2; and the VSS group represents the late stage of IA, at which the tumor forms and enlarges, with a large amount of blood flowing into the tumor cavity in an irregular vortex state, and the shear force is significantly reduced, so it is set at a vortex of 0.5 - 2 dyne/cm2.

value: Vortex


title: HSS-1

description: Library name: Sample 4

value: HSS


title: Vortex-3

description: Library name: Sample 9


title: HSS-2

description: Library name: Sample 5


title: HSS-3

description: Library name: Sample 6


title: PSS-3

description: Library name: Sample 3

value: PSS


title: Vortex-1

description: Library name: Sample 7


title: PSS-1

description: Library name: Sample 1


title: Bulk_EHDPP2

description:
Library name: Sample5
bulk_RNA_seq_geneexpression.txt


title: SK-N-BE(2), c-IDR, rep4

city: Lund

first: Stina

last: Östenberg

address: Sölvegatan 19

country: Sweden

institute: Lund University

description: Library name: BE2c_CIDR_rep4_S15

data_processing:
Raw sequencing reads were quality trimmed using fastp, and ribosomal RNA reads were removed.
Reads were aligned to the human reference genome (GRCh38) using STAR, and transcript quantification was performed with Salmon.
Gene-level counts were generated using featureCounts based on GENCODE v45 annotation.
Data processing was performed using the nf-core/rnaseq pipeline.
Assembly: GRCh38 (Homo sapiens)
Supplementary files format and content: salmon.merged.gene_counts.tsv contains raw read count of all genes.
Supplementary files format and content: salmon.merged.gene_tpm.tsv contains TPM normalized values of all genes.

growth_protocol: Cells were cultured at 37°C, 21% O2, and 5% CO2 in DMEM suplemented with 10% FBS.

extract_protocol:
RNA was extracted using the Qiagen RNeasy Mini Kit according to manufacturer’s instructions.
Total RNA (~250 ng input) was used for library preparation with the Illumina Stranded mRNA Prep kit (poly(A) selection and fragmentation), followed by first- and second-strand cDNA synthesis, end repair, A-tailing, and adapter ligation. Libraries were amplified using 13 PCR cycles and indexed with unique dual indexes. Library quality and concentration were assessed using TapeStation (Agilent) and Qubit fluorometry (Thermo Fisher Scientific).

value: Neuroblastoma

value: cIDR

tag: batch


title: SK-N-BE(2), c-IDR, rep1

description: Library name: BE2c_CIDR_rep1_S3


title: Common Bean infected with B. cinerea isolate_48

description: Library name: U48

value: leaf

value: UC Cran

value: Geranium


title: SK-N-BE(2), c-IDR, rep3

description: Library name: BE2c_CIDR_rep3_S11


title: SK-N-BE(2), c-IDR, rep2

description: Library name: BE2c_CIDR_rep2_S7


title: SK-N-BE(2), N‑CTAD, rep4

description: Library name: BE2c_NTAD_rep4_S14

value: NCTAD


title: SK-N-BE(2), N‑CTAD, rep3

description: Library name: BE2c_NTAD_rep3_S10


title: SK-N-BE(2), WT, rep2

description: Library name: BE2c_CTRL_rep2_S8

value: WT


title: SK-N-BE(2), FL, rep1

description: Library name: BE2c_WT_rep1_S1

value: FL


title: SK-N-BE(2), N‑CTAD, rep1

description: Library name: BE2c_NTAD_rep1_S2


title: SK-N-BE(2), FL, rep4

description: Library name: BE2c_WT_rep4_S13


title: SK-N-BE(2), WT, rep3

description: Library name: BE2c_CTRL_rep3_S12


title: SK-N-BE(2), FL, rep3

description: Library name: BE2c_WT_rep3_S9


title: SK-N-BE(2), WT, rep1

description: Library name: BE2c_CTRL_rep1_S4


title: Common Bean infected with B. cinerea isolate_17

description: Library name: U17


title: Mouse control morula embryo, replicate 5

city: jinan

first: Leoti Jiawei

last: Wang

state: Shandong

address: Wenhua xilu

institute: Shandong UNIVERSITY

description:
Library name: morula_5
Control intact mouse embryo at the morula stage; column name in processed expression matrices: morula_5

data_processing:
Raw sequencing read quality was assessed using FastQC, and quality metrics were summarized using MultiQC.
Adapter sequences and low-quality bases were trimmed using Cutadapt.
Clean reads were aligned to the mouse reference genome Mus musculus GRCm39, Ensembl release 105, using HISAT2.
Gene-level read counts were generated using featureCounts with the corresponding Ensembl gene annotation.
Gene expression was quantified as TPM and log2(TPM+1). Lowly expressed genes were filtered using edgeR before downstream analyses.
Assembly: Mus musculus GRCm39; Ensembl release 105
Supplementary files format and content: tab-delimited matrix containing gene-level raw read counts generated by featureCounts. Rows represent genes and columns represent embryo samples.
Supplementary files format and content: tab-delimited matrix containing TPM-normalized gene expression values. Rows represent genes and columns represent embryo samples.

source_name: preimplantation embryo

growth_protocol: ICR mouse embryos were generated by in vitro fertilization and cultured under 6% CO2 and 5% O2 at 37°C. For split-embryo groups, fully cleaved late two-cell embryos were selected for blastomere separation and subsequent culture in modified sodium hyaluronate gel. Intact control embryos were cultured in parallel.

extract_protocol:
Individual embryo samples were transferred into lysis buffer. Total RNA was reverse-transcribed using an oligo(dT) primer and a template-switching oligonucleotide to generate full-length cDNA.
Smart-seq2 libraries were prepared from amplified full-length cDNA. Amplified cDNA was purified, quantified and used for sequencing library construction. Libraries were pooled and sequenced on an Illumina platform.

treatment_protocol: For split-embryo samples, fully cleaved late two-cell embryos were pretreated in G-PGD embryo biopsy medium, mechanically separated into sister blastomeres by micromanipulation, and each isolated blastomere was cultured individually in modified sodium hyaluronate gel. Control embryos were not separated and were cultured intact under matched conditions.

value: preimplantation embryo


title: Mouse control blastocyst embryo, replicate 1

description:
Library name: blastocyst_1
Control intact mouse embryo at the blastocyst stage; column name in processed expression matrices: blastocyst_1


title: Mouse control morula embryo, replicate 2

description:
Library name: morula_2
Control intact mouse embryo at the morula stage; column name in processed expression matrices: morula_2


title: Mouse split blastocyst embryo, pair 1, blastomere 2

description:
Library name: 2B_1_2
Blastocyst-stage embryo derived from the sister blastomere of the same separated late two-cell mouse embryo as 2B_1_1; column name in processed expression matrices: 2B_1_2


title: Mouse control blastocyst embryo, replicate 2

description:
Library name: blastocyst_2
Control intact mouse embryo at the blastocyst stage; column name in processed expression matrices: blastocyst_2


title: Mouse split blastocyst embryo, pair 3, blastomere 1

description:
Library name: 2B_3_1
Blastocyst-stage embryo derived from one blastomere of a separated late two-cell mouse embryo; column name in processed expression matrices: 2B_3_1


title: Mouse split blastocyst embryo, pair 2, blastomere 1

description:
Library name: 2B_2_1
Blastocyst-stage embryo derived from one blastomere of a separated late two-cell mouse embryo; column name in processed expression matrices: 2B_2_1


title: DSP-1001660008763-C-H03.dcc Patient 3 PanCK Tumor

city: Bordeaux

first: Hamid-Reza

last: Rezvani

address: 2 Rue Dr Hoffmann Martinot

country: France

institute: Bordeaux Institute of Oncology (BRIC)

description: Library name: DSP-1001660008763-C-H03.dcc

data_processing:
Following a pooling purification, the final library was sequenced on a Novaseq6000 (Illumina) using a dual-index workflow.
The quality control (QC) of NGS data was assessed prior analysis to ensure the data robustness and to eliminate problematic AOIs. Different parameters were analyzed and notably the raw read threshold, alignment, and sequencing saturation. Segments with less than 1000 reads, less than 80% of raw reads, and or less than 50% of sequencing saturation were eliminated. Moreover, segments with exceptionally low signal (< 1% of panel genes detected above the limit of quantification, based on negative control probes) were excluded.
Assembly: hg38
Supplementary files format and content: File name is "21019220628_rawdata.csv". File contains the count matrix.
Supplementary files format and content: File name is "21019220628_metadata.csv". File contains the sample metadata.
Library strategy: Spatial Transcriptomics

source_name: PanCK

extract_protocol:
Formalin-fixed, paraffin-embedded (FFPE) skin specimens were obtained from a cohort of three patients with cutaneous squamous cell carcinoma (cSCC). For each patient, tissue blocks contained histologically distinct regions corresponding to (i) healthy skin, (ii) peritumoral skin, (iii) actinic keratosis (AK) and/or in situ cSCC, (iv) advanced tumor core, (v) advanced invasive cSCC. Hematoxylin and eosin–stained sections were reviewed by a board-certified dermatopathologist to confirm diagnoses and to guide region selection.
Spatial transcriptomics was carried out through the Nanostring Technologies GeoMx Digital Spatial Profiling (GeoMx DSP). The protocol has five steps: standard FFPE tissue preparation; tissue incubation with a mixture of visualization markers (VMs) and DSP probes; imaging and region of interest (ROI) selection; ultraviolet (UV) exposure; and oligo collection step. This is then quantified using the Nanostring nCounter® system. Briefly, tissue sections were stained with a CD68/PanCK/Vimentin/Sytox panel to visualize tissue architecture and guide the selection of regions of interest (ROIs) for analysis. For each slide, ROIs were drawn in order to analyze the expression of the WTA gene panel in the healthy regions, AK/cSCC in situ, advanced cSCC, and invasive front. Each ROI was further segmented in 3 to 5 AOIs (area of illumination) based on the PanCK, CD68, and Vimentin staining. AOIs enriched for PanCK marked epithelial/tumor regions; CD68-enriched AOIs captured macrophage-rich regions; and PanCK⁺/Vimentin⁺ AOIs were used as an operational proxy for the invasive front, consistent with the local histopathology. The gene expression of each AOI was analyzed on the GeoMX DSP (NanoString®) using the Whole Transcriptome Atlas (WTA) panel. This panel covers the expression of 18695 protein-coding genes. Slides were incubated overnight with in situ hybridization (ISH) probes conjugated to unique DNA indexing-oligonucleotides via a UV-photocleavable linker. Each AOI was then illuminated with a UV laser to precisely release and collect the DNA barcode in a 96-well plate. GeoMx DSP aspirates in the plate contain photocleaved DNA oligos comprised of an analyte identifier, a unique molecular identifier (UMI) barcode, and primer binding sites. A PCR was performed on these aspirates to add Illumina adapter sequences and unique dual sample indices.

tag: group

value: Tumor

value: PanCK


title: Mouse control morula embryo, replicate 1

description:
Library name: morula_1
Control intact mouse embryo at the morula stage; column name in processed expression matrices: morula_1


title: DSP-1001660008763-C-G12.dcc Patient 3 PanCK Invasive front

description: Library name: DSP-1001660008763-C-G12.dcc

value: Invasive front


title: Mouse split blastocyst embryo, pair 2, blastomere 2

description:
Library name: 2B_2_2
Blastocyst-stage embryo derived from the sister blastomere of the same separated late two-cell mouse embryo as 2B_2_1; column name in processed expression matrices: 2B_2_2


title: Mouse control morula embryo, replicate 4

description:
Library name: morula_4
Control intact mouse embryo at the morula stage; column name in processed expression matrices: morula_4


title: Mouse split blastocyst embryo, pair 3, blastomere 2

description:
Library name: 2B_3_2
Blastocyst-stage embryo derived from the sister blastomere of the same separated late two-cell mouse embryo as 2B_3_1; column name in processed expression matrices: 2B_3_2


title: Mouse control blastocyst embryo, replicate 3

description:
Library name: blastocyst_3
Control intact mouse embryo at the blastocyst stage; column name in processed expression matrices: blastocyst_3


title: Mouse split blastocyst embryo, pair 1, blastomere 1

description:
Library name: 2B_1_1
Blastocyst-stage embryo derived from one blastomere of a separated late two-cell mouse embryo; column name in processed expression matrices: 2B_1_1


title: DSP-1001660008763-C-H02.dcc Patient 3 Macrophages Tumor

description: Library name: DSP-1001660008763-C-H02.dcc

source_name: Macrophages

value: Macrophages


title: DSP-1001660008763-C-G11.dcc Patient 3 Macrophages Invasive front

description: Library name: DSP-1001660008763-C-G11.dcc


title: DSP-1001660008763-C-G10.dcc Patient 3 PanCK Tumor

description: Library name: DSP-1001660008763-C-G10.dcc


title: Mouse split morula embryo, pair 2, blastomere 2

description:
Library name: 2M_2_2
Morula-stage embryo derived from the sister blastomere of the same separated late two-cell mouse embryo as 2M_2_1; column name in processed expression matrices: 2M_2_2


title: DSP-1001660008763-C-G09.dcc Patient 3 Macrophages Tumor

description: Library name: DSP-1001660008763-C-G09.dcc


title: Mouse split morula embryo, pair 3, blastomere 2

description:
Library name: 2M_3_2
Morula-stage embryo derived from the sister blastomere of the same separated late two-cell mouse embryo as 2M_3_1; column name in processed expression matrices: 2M_3_2


title: Macrophage_control_rep3

value: Macrophage


title: PSS-2

description: Library name: Sample 2


title: DSP-1001660008763-C-G04.dcc Patient 3 Macrophages Tumor

description: Library name: DSP-1001660008763-C-G04.dcc


title: DSP-1001660008763-C-G02.dcc Patient 3 Macrophages Peritumoral

description: Library name: DSP-1001660008763-C-G02.dcc

value: Peritumoral


title: Mouse control 8-cell embryo, replicate 1

description:
Library name: 8cell_1
Control intact mouse embryo at the 8-cell stage; column name in processed expression matrices: 8cell_1


title: T6-5

city: Xiamen

first: Guangtong

last: Jiang

address: Xiang'an Campus,4221 Xiang'an South Road, Xiang'an District, Xiamen,Fujian, China.

institute: Xiamen University

description:
Library name: sample10
T6-5_count

data_processing:
Transcript assembly and quantification were performed using StringTie (v1.3.1) and RSEM, with gene expression levels reported in TPM (Transcripts Per Kilobase Million).
Assembly: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

source_name: hippocampus

growth_protocol: All animals were maintained and animal experiments were performed following instructions from the Institutional Animal Care and Use Committee of Xiamen University.

extract_protocol:
Total RNA was extracted from hippocampal tissues of AAV-circTau6 and control-injected hMAPT mice using TRIzol reagent (Invitrogen). RNA integrity was verified with an Agilent 2100 Bioanalyzer, and all samples had RNA integrity number (RIN) > 8.0. Ribosomal RNA was depleted using the Ribo-Zero™ Magnetic Kit (Epicentre).
Strand-specific cDNA libraries were prepared with the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB #7530) and sequenced on an Illumina NovaSeq 6000 platform (150 bp paired-end) by Gene Denovo Biotechnology Co. (Guangzhou, China).

value: hippocampus

value: 6 months

value: hMapt

value: AAV-circTau6 injection


title: Mouse control 8-cell embryo, replicate 4

description:
Library name: 8cell_4
Control intact mouse embryo at the 8-cell stage; column name in processed expression matrices: 8cell_4


title: Mouse split morula embryo, pair 1, blastomere 1

description:
Library name: 2M_1_1
Morula-stage embryo derived from one blastomere of a separated late two-cell mouse embryo; column name in processed expression matrices: 2M_1_1


title: T6-3

description:
Library name: sample8
T6-3_count


title: DSP-1001660008763-C-G07.dcc Patient 3 PanCK Invasive front

description: Library name: DSP-1001660008763-C-G07.dcc


title: DSP-1001660008763-C-F09.dcc Patient 3 Macrophages In situ

description: Library name: DSP-1001660008763-C-F09.dcc

value: In situ


title: Mouse split morula embryo, pair 2, blastomere 1

description:
Library name: 2M_2_1
Morula-stage embryo derived from one blastomere of a separated late two-cell mouse embryo; column name in processed expression matrices: 2M_2_1


title: DSP-1001660008763-C-G06.dcc Patient 3 Macrophages Invasive front

description: Library name: DSP-1001660008763-C-G06.dcc


title: T6-2

description:
Library name: sample7
T6-2_count


title: Mouse control 8-cell embryo, replicate 2

description:
Library name: 8cell_2
Control intact mouse embryo at the 8-cell stage; column name in processed expression matrices: 8cell_2


title: DSP-1001660008763-C-F12.dcc Patient 3 PanCK Invasive front

description: Library name: DSP-1001660008763-C-F12.dcc


title: DSP-1001660008763-C-F11.dcc Patient 3 Macrophages Invasive front

description: Library name: DSP-1001660008763-C-F11.dcc


title: DSP-1001660008763-C-G03.dcc Patient 3 PanCK Peritumoral

description: Library name: DSP-1001660008763-C-G03.dcc


title: Mouse split morula embryo, pair 1, blastomere 2

description:
Library name: 2M_1_2
Morula-stage embryo derived from the sister blastomere of the same separated late two-cell mouse embryo as 2M_1_1; column name in processed expression matrices: 2M_1_2


title: T6-4

description:
Library name: sample9
T6-4_count


title: Mouse control 8-cell embryo, replicate 3

description:
Library name: 8cell_3
Control intact mouse embryo at the 8-cell stage; column name in processed expression matrices: 8cell_3


title: DSP-1001660008763-C-F10.dcc Patient 3 PanCK In situ

description: Library name: DSP-1001660008763-C-F10.dcc


title: DSP-1001660008763-C-G05.dcc Patient 3 PanCK Tumor

description: Library name: DSP-1001660008763-C-G05.dcc


title: T6-1

description:
Library name: sample6
T6-1_count


title: DSP-1001660008763-C-F07.dcc Patient 3 Macrophages Healthy

description: Library name: DSP-1001660008763-C-F07.dcc

value: Healthy


title: con-5

description:
Library name: sample5
con-5_count

value: control


title: DSP-1001660008763-C-F06.dcc Patient 3 PanCK Tumor

description: Library name: DSP-1001660008763-C-F06.dcc


title: DSP-1001660008763-C-F05.dcc Patient 3 Macrophages Tumor

description: Library name: DSP-1001660008763-C-F05.dcc


title: con-2

description:
Library name: sample2
con-2_count


title: con-1

description:
Library name: sample1
con-1_count


title: DSP-1001660008763-C-F01.dcc Patient 3 PanCK Invasive front

description: Library name: DSP-1001660008763-C-F01.dcc


title: DSP-1001660008763-C-E09.dcc Patient 3 PanCK Healthy

description: Library name: DSP-1001660008763-C-E09.dcc


title: Mouse split morula embryo, pair 3, blastomere 1

description:
Library name: 2M_3_1
Morula-stage embryo derived from one blastomere of a separated late two-cell mouse embryo; column name in processed expression matrices: 2M_3_1


title: DSP-1001660008763-C-E07.dcc Patient 3 PanCK Tumor

description: Library name: DSP-1001660008763-C-E07.dcc


title: Diabetic_D2

city: Wuhan

first: Yuan

last: Zhang

address: No.169 Eastern lake Road

institute: Zhongnan hospital of Wuhan university

description: Library name: Sample5

data_processing:
Solexa pipeline v1.8 (Off-Line Base Caller software v1.8) was used for image processing and base calling.
Assembly: GRCm38 (mm10)
Supplementary files format and content: Expression_Gene.txt: plain text file containing gene-level FPKM values for all samples (C1, C2, C3, D1, D2, D3).
Supplementary files format and content: Expression_Transcript.txt: plain text file containing transcript-level FPKM values for all samples (C1, C2, C3, D1, D2, D3).

source_name: Trigeminal ganglia

growth_protocol: Male C57BL/6J mice were housed under standard specific pathogen-free conditions with free access to food and water and allowed to acclimate for one week prior to experimentation.

extract_protocol:
Total RNA from each sample was assessed for integrity by agarose gel electrophoresis, and quantified and further quality-checked using a NanoDrop ND-1000. For each sample, 1–2 μg of total RNA was used for sequencing library construction. Total RNA was  subjected to mRNA enrichment using the NEB Next® Poly(A) mRNA Magnetic Isolation Module.
RNA-seq libraries were constructed from total RNA after oligo(dT) enrichment (or rRNA depletion) using the KAPA Stranded RNA-Seq Library Prep Kit (Roche).

treatment_protocol: Male C57BL/6J mice (6 weeks old) were allowed to acclimate for one week prior to experimentation. At 7 weeks of age, animals were subjected to overnight fasting and subsequently received intraperitoneal injections of streptozotocin (STZ; 90 mg/kg) or an equal volume of citrate buffer as control for two consecutive days. Blood glucose concentrations were assessed five days after the final injection, and mice with levels above 15 mmol/L were defined as diabetic. Experimental analyses were conducted four months after diabetes induction.

value: Trigeminal ganglia

tag: disease state

value: Diabetic


title: Control_C2

description: Library name: Sample2

value: Control


title: Control_C3

description: Library name: Sample3


title: DSP-1001660008763-C-F03.dcc Patient 3 Macrophages Peritumoral

description: Library name: DSP-1001660008763-C-F03.dcc


title: Diabetic_D1

description: Library name: Sample4


title: Diabetic_D3

description: Library name: Sample6


title: DSP-1001660008763-C-F04.dcc Patient 3 PanCK Peritumoral

description: Library name: DSP-1001660008763-C-F04.dcc


title: con-3

description:
Library name: sample3
con-3_count


title: DSP-1001660008763-C-E08.dcc Patient 3 Macrophages Healthy

description: Library name: DSP-1001660008763-C-E08.dcc


title: DSP-1001660008763-C-E06.dcc Patient 3 Macrophages Tumor

description: Library name: DSP-1001660008763-C-E06.dcc


title: DSP-1001660008763-C-F08.dcc Patient 3 PanCK Healthy

description: Library name: DSP-1001660008763-C-F08.dcc


title: DSP-1001660008763-C-E05.dcc Patient 3 PanCK Peritumoral

description: Library name: DSP-1001660008763-C-E05.dcc


title: DSP-1001660008763-C-E12.dcc Patient 3 Macrophages Invasive front

description: Library name: DSP-1001660008763-C-E12.dcc


title: DSP-1001660008763-C-E11.dcc Patient 3 PanCK In situ

description: Library name: DSP-1001660008763-C-E11.dcc


title: DSP-1001660008763-C-E01.dcc Patient 3 Macrophages Invasive front

description: Library name: DSP-1001660008763-C-E01.dcc


title: DSP-1001660008763-C-E04.dcc Patient 3 Macrophages Peritumoral

description: Library name: DSP-1001660008763-C-E04.dcc


title: Mouse control morula embryo, replicate 3

description:
Library name: morula_3
Control intact mouse embryo at the morula stage; column name in processed expression matrices: morula_3

value: preimplantation embryo


title: DSP-1001660008763-C-E02.dcc Patient 3 PanCK Invasive front

description: Library name: DSP-1001660008763-C-E02.dcc


title: Control_C1

description: Library name: Sample1


title: Macrophage_FHKO_rep2

value: FHKO


title: DSP-1001660008763-C-D08.dcc Patient 2 PanCK Tumor

description: Library name: DSP-1001660008763-C-D08.dcc

value: Tumor

value: PanCK


title: DSP-1001660008763-C-D11.dcc Patient 3 Macrophages In situ

description: Library name: DSP-1001660008763-C-D11.dcc

value: Macrophages


title: DSP-1001660008763-C-D12.dcc Patient 3 PanCK In situ

description: Library name: DSP-1001660008763-C-D12.dcc


title: DSP-1001660008763-C-D09.dcc Patient 3 Macrophages Healthy

description: Library name: DSP-1001660008763-C-D09.dcc


title: DSP-1001660008763-C-D04.dcc Patient 2 Macrophages Invasive front

description: Library name: DSP-1001660008763-C-D04.dcc

value: Invasive front


title: DSP-1001660008763-C-D05.dcc Patient 2 PanCK Invasive front

description: Library name: DSP-1001660008763-C-D05.dcc


title: DSP-1001660008763-C-D07.dcc Patient 2 Macrophages Tumor

description: Library name: DSP-1001660008763-C-D07.dcc


title: DSP-1001660008763-C-D10.dcc Patient 3 PanCK Healthy

description: Library name: DSP-1001660008763-C-D10.dcc


title: DSP-1001660008763-C-D03.dcc Patient 2 PanCK Tumor

description: Library name: DSP-1001660008763-C-D03.dcc


title: DSP-1001660008763-C-D02.dcc Patient 2 Macrophages Tumor

description: Library name: DSP-1001660008763-C-D02.dcc


title: DC-Trp2-1

description: Two probes were used to detect each transcript: a reporter probe that carries the fluorescent barcode, and a biotinylated capture probe that immobilizes the complex for data collection. The code set contained 755 probe pairs, each pair specific to a particular nucleic acid target

value: Melanoma

value: DC vaccine loaded with Trp2 peptide


title: DSP-1001660008763-C-C12.dcc Patient 2 PanCK Invasive front

description: Library name: DSP-1001660008763-C-C12.dcc


title: DSP-1001660008763-C-C10.dcc Patient 2 PanCK Tumor

description: Library name: DSP-1001660008763-C-C10.dcc


title: DSP-1001660008763-C-C11.dcc Patient 2 Macrophages Invasive front

description: Library name: DSP-1001660008763-C-C11.dcc


title: RNA-Seq of Mus musculus: tumor WT1

city: Charleston, SC

first: Paramita

last: Chakraborty

address: 171 Ashley Avenue

institute: Medical University of South Carolina

description:
Library name: WT1
WT

data_processing:
Reads were quality-controlled and filtered using TrimGalore. The filtered reads were then aligned to the reference genome using STAR, and FeatureCounts was used to generate the count table from the alignment files. The raw count table was imported into R, where differential expression analysis was performed using DESeq2.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: tumor ascitic fluid

growth_protocol: WT and Sphk2 knockout (KO) mice were injected with EL4 tumor cells to establish in vivo tumor models. Mice were maintained under standard housing conditions and monitored regularly for tumor progression and overall health. Fourteen days after tumor inoculation, mice were euthanized according to approved institutional guidelines. Ascitic fluid was collected, and single-cell suspensions were prepared. Myeloid-derived suppressor cells (MDSCs) were then isolated by flow cytometric sorting using standard surface markers. Freshly sorted tumor-induced MDSCs from WT and Sphk2 KO mice were processed immediately for total RNA isolation and subsequent RNA sequencing.

extract_protocol:
Cells were immediately pelleted by centrifugation at 4°C and resuspended in 1 ml of TRIzol. RNA concentration was measured using a NanoDrop 8000. RNA quality was assessed using an Agilent 4200 TapeStation and RINe values ranged from 9.7 to 10.
Total RNA (250 ng) was used in the construction of libraries with the New England Biolabs NEBNext Poly(A) mRNA Magnetic Isolation Module (catalog no. 7490L) and Ultra II Directional RNA Library Prep Kit for Illumina (catalog no. 7760L) according to the manufacturer’s instructions. Dual-indexed libraries were pooled to and sequenced at VANTAGE (Vanderbilt University Medical Center) on an Illumina NovaSeq 6000 (S4 flow cell), generating paired-end reads for each library.

value: tumor ascitic fluid

value: WT


title: RNA-Seq of Mus musculus: tumor WT2

description:
Library name: WT2
WT


title: RNA-Seq of Mus musculus: tumor Sphk2_KO2

description:
Library name: Sphk2_KO2
KO

value: KO


title: DSP-1001660008763-C-C08.dcc Patient 2 PanCK Peritumoral

description: Library name: DSP-1001660008763-C-C08.dcc

value: Peritumoral


title: DSP-1001660008763-C-C05.dcc Patient 2 PanCK Invasive front

description: Library name: DSP-1001660008763-C-C05.dcc


title: DSP-1001660008763-C-C03.dcc Patient 2 PanCK In situ

description: Library name: DSP-1001660008763-C-C03.dcc

value: In situ


title: DSP-1001660008763-C-C02.dcc Patient 2 Macrophages In situ

description: Library name: DSP-1001660008763-C-C02.dcc


title: Kit2

city: Xi'an

first: Zhiqiang

last: Fang

state: Shaanxi

address: No.169,Changle West Road

institute: Xijing Hospital

description: Library name: Kit2

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis
Short reads alignment tool Bowtie2 (version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation.
An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2.2.4 and other parameters set as a default
The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach
RNAs differential expression analysis was performed by DESeq2 software between two different groups
Assembly: Mus musculus Ensembl_release107
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: liver

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol
RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis. After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads.Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina(NEB #7530,New England Biolabs, Ipswich, MA, USA).The purified double-stranded cDNA fragments were end repaired, A base added, and ligated to Illumina sequencing adapters.The ligation reaction was purified with the AMPure XP Beads(1.0X).Ligated fragments were subjected to size selection by agarose gel electrophoresis and polymerase chain reaction (PCR) amplified.The resulting cDNA library was sequenced using Illumina Novaseq6000.

value: liver

value: primary endothelial cells

value: sorted by c-Kit immunomagnetic beads


title: CT2

description: Library name: CT2

value: After c-Kit immunomagnetic beads sorting，remaining nonparenchymal cells were sorted by CD146 immunomagnetic beads


title: Kit1

description: Library name: Kit1


title: Kit4

description: Library name: Kit4


title: Kit3

description: Library name: Kit3


title: CT3

description: Library name: CT3


title: CT4

description: Library name: CT4


title: con-4

description:
Library name: sample4
con-4_count

value: hippocampus

value: 6 months

value: hMapt

value: control


title: CT1

description: Library name: CT1


title: DSP-1001660008763-C-C01.dcc Patient 2 PanCK Healthy

description: Library name: DSP-1001660008763-C-C01.dcc

value: Healthy

value: PanCK


title: Multiome E8.5 embryonic and extraembryonic cells, GEX, Biol high fat rep 1

city: Toronto

first: Paul

last: Delgado Olguin

state: Ontario

address: 686 Bay Street

department: Translational Medicine

country: Canada

institute: The Hospital for Sick Children

description: Library name: HighFat_1_RNA

data_processing:
Demultiplexing, alignment, filtering, barcode counting, peak calling, and counting of both ATAC and GEX molecules was done using Cell Ranger V2.0.
Assembly: Mus musculus mm10 genome (Ensembl genome annotated assembly GRCh38.98)
Supplementary files format and content: Cellranger output files: filtered_feature_bc_matrix.h5, atac_fragments.tsv.gz, atac_fragments.tsv.gz.tbi, atac_possorted.bam

source_name: E8.5 whole embryo

extract_protocol:
Single nuceli were extracted according to Chromium Nuclei Isolation Kit. Single nuclei were encapsulated in Gel Beads-in-emulsion (GEMs) using the Single Nuclei Multiome ATAC + Gene Expression v1 kit (The Princess Margaret Genomics Centre (PMGC)
Chromium 10x Genomics Next GEM Single Cell Multiome prep v1.0 kit was used to generate libraries following manufactor's instructions. Sequencing using 100 cycle v1.5 kit 10x custom sequencing configuration

value: E8.5 whole embryo

value: Embryonic and extraembryonic cells

value: High fat diet (60% fat)


title: Multiome E8.5 embryonic and extraembryonic cells, GEX, Biol control rep 1

description: Library name: Control_1_RNA

value: Control diet (10% fat)


title: Multiome E8.5 embryonic and extraembryonic cells, ATAC, Biol high fat rep 3

description: Library name: HighFat_3_ATAC

library_source: genomic single cell

molecule: genomic DNA


title: Multiome E8.5 embryonic and extraembryonic cells, ATAC, Biol control rep 1

description: Library name: Control_1_ATAC


title: Multiome E8.5 embryonic and extraembryonic cells, ATAC, Biol control rep 3

description: Library name: Control_3_ATAC


title: Multiome E8.5 embryonic and extraembryonic cells, ATAC, Biol high fat rep 2

description: Library name: HighFat_2_ATAC


title: Multiome E8.5 embryonic and extraembryonic cells, GEX, Biol control rep 3

description: Library name: Control_3_RNA


title: Multiome E8.5 embryonic and extraembryonic cells, GEX, Biol high fat rep 3

description: Library name: HighFat_3_RNA


title: Multiome E8.5 embryonic and extraembryonic cells, GEX, Biol control rep 2

description: Library name: Control_2_RNA


title: SK-N-BE(2), FL, rep2

description: Library name: BE2c_WT_rep2_S5

value: Neuroblastoma

value: FL


title: Multiome E8.5 embryonic and extraembryonic cells, GEX, Biol high fat rep 2

description: Library name: HighFat_2_RNA


title: Multiome E8.5 embryonic and extraembryonic cells, ATAC, Biol high fat rep 1

description: Library name: HighFat_1_ATAC


title: Multiome E8.5 embryonic and extraembryonic cells, ATAC, Biol control rep 2

description: Library name: Control_2_ATAC


title: DSP-1001660008763-C-B12.dcc Patient 2 Macrophages Healthy

description: Library name: DSP-1001660008763-C-B12.dcc

value: Macrophages


title: DSP-1001660008763-C-B09.dcc Patient 2 PanCK Peritumoral

description: Library name: DSP-1001660008763-C-B09.dcc

value: Peritumoral


title: DSP-1001660008763-C-B10.dcc Patient 2 Macrophages Tumor

description: Library name: DSP-1001660008763-C-B10.dcc

value: Tumor


title: DSP-1001660008763-C-C04.dcc Patient 2 Macrophages Invasive front

description: Library name: DSP-1001660008763-C-C04.dcc

value: Invasive front


title: DSP-1001660008763-C-B06.dcc Patient 2 PanCK Invasive front

description: Library name: DSP-1001660008763-C-B06.dcc


title: DSP-1001660008763-C-B11.dcc Patient 2 PanCK Tumor

description: Library name: DSP-1001660008763-C-B11.dcc


title: DSP-1001660008763-C-B08.dcc Patient 2 Macrophages Peritumoral

description: Library name: DSP-1001660008763-C-B08.dcc


title: SK-N-BE(2), N‑CTAD, rep2

description: Library name: BE2c_NTAD_rep2_S6

value: NCTAD


title: DSP-1001660008763-C-B04.dcc Patient 2 PanCK In situ

description: Library name: DSP-1001660008763-C-B04.dcc

value: In situ


title: DSP-1001660008763-C-B05.dcc Patient 2 Macrophages Invasive front

description: Library name: DSP-1001660008763-C-B05.dcc


title: DSP-1001660008763-C-A12.dcc Patient 2 PanCK Tumor

description: Library name: DSP-1001660008763-C-A12.dcc


title: DSP-1001660008763-C-B03.dcc Patient 2 Macrophages In situ

description: Library name: DSP-1001660008763-C-B03.dcc


title: DSP-1001660008763-C-B02.dcc Patient 2 PanCK Healthy

description: Library name: DSP-1001660008763-C-B02.dcc


title: RNA-Seq of Mus musculus: tumor Sphk2_KO1

description:
Library name: Sphk2_KO1
KO

value: tumor ascitic fluid

value: KO


title: DSP-1001660008763-C-B01.dcc Patient 2 Macrophages Healthy

description: Library name: DSP-1001660008763-C-B01.dcc


title: 6[4]10_zQ175_Untreated_HIP_male_rep4

city: Princeton

first: Jeff

last: Aaronson

address: 155 Village Boulevard, Suite 200

institute: CHDI

description: Library name: zQ175.253.115

data_processing:
Libraries for RNA-seq were sequenced using an Illumina NovaSeq X Plus and Illumina NovaSeq 6000
Custom genome and gene annotation were created to include transgenic sequences for EGFP, WPRE, nZFP   viral components as well as Htt1a transcript. GRCm38 genome fasta and GRCm38 version 76 gtf were used as a base for the custom genome and annotation.
Pre-alignment QC metrics such as read coverage, percent of un-mapped reads and GC contents were computed in Omicsoft
Omicsoft aligner was used to map the reads to the custom genome and RSEM software from Omicsoft was used to quantify gene and transcript expression
Adapter and quality trimming were performed in Omicsoft using the following settings: Trimming , Mode=TrimByQuality, ReadTrimQuality=2; AverageQualityCutoff=10, EnablePolyRateCutoff=True, PolyRateCutoff=80. FilterSource IlluminaAdapters,Human.rRNA,Human.tRNA,Ercc
Assembly: GRCm38HD.EGFP_WPRE_ZFPs_tdTomatoStiff custom genome assembly and GRCm38.76.Htt1a_EGFP_WPRE_ZFPs_tdTomatoStiff custom gene annotation
Supplementary files format and content: Tab-delimited file containing counts for genes

source_name: Hippocampus

extract_protocol:
Hippocampal brain tissues were dissected from all mice at 6 or 10 months of age. RNA was extracted using a Qiagen RNeasy kit.
Libraries for RNA-seq were prepared using Illumina RNA preparation with polyA selection

value: Hippocampus

value: Untreated

value: male

value: 10 months

value: 6 months


title: 6[4]10_WT_HTT-10150_HIP_female_rep4

description: Library name: zQ175.250.D24922

value: Wild Type

value: female


title: 6[4]10_zQ175_HTT-10150_HIP_male_rep4

description: Library name: zQ175.251.189


title: 6[4]10_zQ175_HTT-634.486_HIP_male_rep4

description: Library name: zQ175.251.129


title: 6[4]10_zQ175_NTC_HIP_male_rep4

description: Library name: zQ175.251.168

value: NTC


title: DSP-1001660008763-C-C07.dcc Patient 2 Macrophages Peritumoral

description: Library name: DSP-1001660008763-C-C07.dcc


title: DSP-1001660008760-D-D07.dcc Patient 1 Macrophages Tumor

description: Library name: DSP-1001660008760-D-D07.dcc


title: DSP-1001660008763-C-A11.dcc Patient 2 Macrophages Tumor

description: Library name: DSP-1001660008763-C-A11.dcc


title: DSP-1001660008763-C-A05.dcc Patient 2 PanCK In situ

description: Library name: DSP-1001660008763-C-A05.dcc

value: PanCK


title: DSP-1001660008763-C-A09.dcc Patient 2 Macrophages Peritumoral

description: Library name: DSP-1001660008763-C-A09.dcc

value: Macrophages


title: DSP-1001660008763-C-A03.dcc Patient 2 PanCK Healthy

description: Library name: DSP-1001660008763-C-A03.dcc

value: Healthy


title: DSP-1001660008760-D-D08.dcc Patient 1 PanCK Tumor

description: Library name: DSP-1001660008760-D-D08.dcc

value: Tumor


title: 6[4]10_WT_Untreated_HIP_female_rep4

description: Library name: zQ175.249.76


title: DSP-1001660008760-D-D04.dcc Patient 1 Macrophages Invasive front

description: Library name: DSP-1001660008760-D-D04.dcc

value: Invasive front


title: 6[4]10_WT_NTC_HIP_female_rep4

description: Library name: zQ175.249.59


title: 6[4]10_WT_HTT-634.486_HIP_female_rep4

description: Library name: zQ175.249.66


title: DSP-1001660008760-D-D05.dcc Patient 1 PanCK Invasive front

description: Library name: DSP-1001660008760-D-D05.dcc


title: 6[4]10_WT_HTT-10150_HIP_female_rep3

description: Library name: zQ175.249.57


title: DSP-1001660008763-C-A02.dcc Patient 2 Macrophages Healthy

description: Library name: DSP-1001660008763-C-A02.dcc


title: 6[4]10_zQ175_NTC_HIP_female_rep4

description: Library name: zQ175.247.186


title: DSP-1001660008760-D-C11.dcc Patient 1 Macrophages Invasive front

description: Library name: DSP-1001660008760-D-C11.dcc


title: DSP-1001660008760-D-D02.dcc Patient 1 Macrophages Tumor

description: Library name: DSP-1001660008760-D-D02.dcc


title: 6[4]10_zQ175_HTT-10150_HIP_female_rep4

description: Library name: zQ175.247.181


title: DSP-1001660008760-D-D03.dcc Patient 1 PanCK Tumor

description: Library name: DSP-1001660008760-D-D03.dcc


title: 6[4]10_zQ175_Untreated_HIP_female_rep4

description: Library name: zQ175.247.174


title: DSP-1001660008760-D-C10.dcc Patient 1 PanCK Tumor

description: Library name: DSP-1001660008760-D-C10.dcc


title: 6[4]10_zQ175_HTT-634.486_HIP_female_rep4

description: Library name: zQ175.247.158


title: DSP-1001660008760-D-C12.dcc Patient 1 PanCK Invasive front

description: Library name: DSP-1001660008760-D-C12.dcc


title: 6[4]10_WT_HTT-10150_HIP_male_rep4

description: Library name: zQ175.246.169


title: DSP-1001660008763-C-A10.dcc Patient 2 PanCK Peritumoral

description: Library name: DSP-1001660008763-C-A10.dcc

value: Peritumoral


title: DSP-1001660008760-D-C09.dcc Patient 1 Macrophages Tumor

description: Library name: DSP-1001660008760-D-C09.dcc


title: DSP-1001660008760-D-C07.dcc Patient 1 Macrophages Peritumoral

description: Library name: DSP-1001660008760-D-C07.dcc


title: 6[4]10_WT_HTT-634.486_HIP_male_rep4

description: Library name: zQ175.246.149


title: DSP-1001660008760-D-C03.dcc Patient 1 PanCK In situ

description: Library name: DSP-1001660008760-D-C03.dcc

value: In situ


title: DSP-1001660008760-D-C05.dcc Patient 1 PanCK Invasive front

description: Library name: DSP-1001660008760-D-C05.dcc


title: DSP-1001660008760-D-C08.dcc Patient 1 PanCK Peritumoral

description: Library name: DSP-1001660008760-D-C08.dcc


title: 6[4]10_WT_NTC_HIP_male_rep4

description: Library name: zQ175.245.144


title: 6[4]10_WT_HTT-634.486_HIP_male_rep3

description: Library name: zQ175.245.161


title: 6[4]10_WT_Untreated_HIP_male_rep4

description: Library name: zQ175.245.162


title: DSP-1001660008760-D-C04.dcc Patient 1 Macrophages Invasive front

description: Library name: DSP-1001660008760-D-C04.dcc


title: isolated adipocytes, 2-days WNT activated, age p23, bio rep 2

city: Oklahoma City

first: Michael

middle: C.

last: Rudolph

state: OK

address: 975 NE 10th St. BRC North rm 364

department: Biochemistry and Physiology

institute: OUHC

description: Library name: 18361W

data_processing:
Sequenced reads were trimmed using trimmomatic v0.39, aligned using gsnap v2020-12-16, and filtered and sorted using SAMTools v1.9 to generate merged bam files.
Raw FPKM counts were assembled and expression was calculated using cufflinks v2.2.1 using the mm10 genome (GRCm38.79)
a matrix of all genes was imported in to R for statistical analyses using the DESeq2 package (v1.40.1)
Assembly: mm10 (GRCm38.79)
Supplementary files format and content: an Excel workbook containing normalized counts for all genes and all samples passing filtered for genes > 1 in all samples, a per-gene row sum >=15, and variance stabilization transformation.

source_name: dorsal mouse skin

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen). Glycogen was used to increase RNA yield from isolated adipocytes. RNA quality and quantity was quanitified using Agilent Fragment Analyzer 5200.
100 ng of total RNA was used as input to construct sequencing libraries using the Universal Plus mRNA-SEQ kit according to manufacturer protocol (NuGEN, Redwood City, CA)

value: dorsal mouse skin

value: adipocytes

value: EnCre driven beta-catenin overexpression (EngrailedCre/+; Rosa26rtTA/Rosa26rtTA; TetOBcat/+)

value: Doxycycline food (6g/kg) and water (2mg/mL)


title: isolated adipocytes, 5-days WNT activated, age p26, bio rep 2

description: Library name: 18393W


title: isolated adipocytes, 0-days WNT activated, age p26, bio rep 3

description: Library name: 18342C

value: WT (+/+; Rosa26rtTA/Rosa26rtTA; TetOBcat/+)


title: isolated adipocytes, 0-days WNT activated, age p23, bio rep 1

description: Library name: 18362C


title: isolated adipocytes, 0-days WNT activated, age p23, bio rep 2

description: Library name: 18364C


title: isolated adipocytes, 2-days WNT activated, age p23, bio rep 3

description: Library name: 18367W


title: isolated adipocytes, 5-days WNT activated, age p26, bio rep 3

description: Library name: 18394W


title: isolated adipocytes, 0-days WNT activated, age p26, bio rep 2

description: Library name: 18341C


title: isolated adipocytes, 5-days WNT activated, age p26, bio rep 5

description: Library name: 18414W


title: isolated adipocytes, 2-days WNT activated, age p23, bio rep 1

description: Library name: 18436C


title: isolated adipocytes, 5-days WNT activated, age p26, bio rep 4

description: Library name: 18396W


title: isolated adipocytes, 2-days WNT activated, age p23, bio rep 4

description: Library name: 18368W


title: isolated adipocytes, 0-days WNT activated, age p26, bio rep 1

description: Library name: 18340C


title: 6[4]10_WT_HTT-10150_HIP_male_rep3

description: Library name: zQ175.245.143

value: Hippocampus

value: male

value: 10 months


title: isolated adipocytes, 0-days WNT activated, age p23, bio rep 3

description: Library name: 18411C


title: isolated adipocytes, 5-days WNT activated, age p26, bio rep 1

description: Library name: 18337W


title: 6[4]10_WT_NTC_HIP_female_rep3

description: Library name: zQ175.244.2166

value: Wild Type

value: female

value: 6 months


title: DSP-1001660008760-D-B11.dcc Patient 1 PanCK Tumor

description: Library name: DSP-1001660008760-D-B11.dcc

value: PanCK


title: 6[4]10_WT_HTT-10150_HIP_female_rep2

description: Library name: zQ175.244.2163


title: DSP-1001660008760-D-B09.dcc Patient 1 PanCK Peritumoral

description: Library name: DSP-1001660008760-D-B09.dcc


title: 6[4]10_WT_HTT-634.486_HIP_male_rep2

description: Library name: zQ175.242.37


title: 6[4]10_WT_Untreated_HIP_female_rep2

description: Library name: zQ175.243.1474

value: Untreated


title: DSP-1001660008760-D-C01.dcc Patient 1 PanCK Healthy

description: Library name: DSP-1001660008760-D-C01.dcc

value: Healthy


title: DSP-1001660008760-D-B08.dcc Patient 1 Macrophages Peritumoral

description: Library name: DSP-1001660008760-D-B08.dcc

value: Macrophages


title: SK-N-BE(2), WT, rep4

description: Library name: BE2c_CTRL_rep4_S16

value: Neuroblastoma

value: WT


title: DSP-1001660008760-D-B04.dcc Patient 1 PanCK In situ

description: Library name: DSP-1001660008760-D-B04.dcc

value: In situ


title: 6[4]10_WT_NTC_HIP_female_rep2

description: Library name: zQ175.243.2152

value: NTC


title: DSP-1001660008760-D-B10.dcc Patient 1 Macrophages Tumor

description: Library name: DSP-1001660008760-D-B10.dcc

value: Tumor


title: 6[4]10_WT_Untreated_HIP_female_rep3

description: Library name: zQ175.243.2142


title: DSP-1001660008760-D-B06.dcc Patient 1 PanCK Invasive front

description: Library name: DSP-1001660008760-D-B06.dcc

value: Invasive front


title: 6[4]10_WT_Untreated_HIP_male_rep3

description: Library name: zQ175.242.17


title: 6[4]10_WT_NTC_HIP_male_rep2

description: Library name: zQ175.241.15


title: DSP-1001660008760-D-A11.dcc Patient 1 Macrophages Tumor

description: Library name: DSP-1001660008760-D-A11.dcc


title: 6[4]10_WT_NTC_HIP_male_rep1

description: Library name: zQ175.240.107


title: DSP-1001660008760-D-B05.dcc Patient 1 Macrophages Invasive front

description: Library name: DSP-1001660008760-D-B05.dcc


title: 6[4]10_WT_HTT-634.486_HIP_male_rep1

description: Library name: zQ175.241.40


title: 6[4]10_WT_HTT-10150_HIP_male_rep1

description: Library name: zQ175.241.28


title: 6[4]10_zQ175_HTT-634.486_HIP_female_rep3

description: Library name: zQ175.238.83


title: DSP-1001660008760-D-B02.dcc Patient 1 PanCK Healthy

description: Library name: DSP-1001660008760-D-B02.dcc


title: 6[4]10_zQ175_Untreated_HIP_female_rep3

description: Library name: zQ175.238.113


title: 6[4]10_WT_NTC_HIP_male_rep3

description: Library name: zQ175.242.22


title: DSP-1001660008760-D-A05.dcc Patient 1 PanCK In situ

description: Library name: DSP-1001660008760-D-A05.dcc


title: 6[4]10_zQ175_HTT-10150_HIP_female_rep3

description: Library name: zQ175.238.94


title: 6[4]10_WT_Untreated_HIP_male_rep1

description: Library name: zQ175.240.88


title: 6[4]10_WT_HTT-10150_HIP_male_rep2

description: Library name: zQ175.242.16


title: DSP-1001660008760-D-A02.dcc Patient 1 Macrophages Healthy

description: Library name: DSP-1001660008760-D-A02.dcc


title: 6[4]10_zQ175_NTC_HIP_female_rep3

description: Library name: zQ175.237.178


title: DSP-1001660008760-D-A03.dcc Patient 1 PanCK Healthy

description: Library name: DSP-1001660008760-D-A03.dcc


title: DSP-1001660008760-D-A12.dcc Patient 1 PanCK Tumor

description: Library name: DSP-1001660008760-D-A12.dcc


title: 6[4]10_WT_Untreated_HIP_male_rep2

description: Library name: zQ175.241.39


title: DSP-1001660008760-D-B01.dcc Patient 1 Macrophages Healthy

description: Library name: DSP-1001660008760-D-B01.dcc


title: 6[4]10_zQ175_Untreated_HIP_female_rep2

description: Library name: zQ175.237.133


title: 6[4]10_zQ175_HTT-634.486_HIP_female_rep2

description: Library name: zQ175.234.147


title: 6[4]10_zQ175_HTT-10150_HIP_female_rep2

description: Library name: zQ175.237.124


title: 6[4]10_zQ175_NTC_HIP_female_rep2

description: Library name: zQ175.237.84


title: 6[4]10_zQ175_HTT-10150_HIP_female_rep1

description: Library name: zQ175.236.99


title: 6[4]10_zQ175_Untreated_HIP_female_rep1

description: Library name: zQ175.236.142


title: DSP-1001660008760-D-A10.dcc Patient 1 PanCK Peritumoral

description: Library name: DSP-1001660008760-D-A10.dcc

value: Peritumoral


title: DSP-1001660008760-D-A07.dcc Patient 1 PanCK Invasive front

description: Library name: DSP-1001660008760-D-A07.dcc


title: 6[4]10_zQ175_HTT-634.486_HIP_female_rep1

description: Library name: zQ175.236.97

value: Hippocampus


title: U2OS cells, Total MeRIP-seq, WT, IP, rep2

description: Library name: Sample10

data_processing:
library strategy: meRIP-seq
For RNA-seq analysis, raw sequencing reads from NHS and HS samples were first assessed for quality using FastQC (v0.11.8). Low-quality bases and adapter sequences were trimmed with Trim Galore! (v0.6.7, https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). Clean reads were then aligned to the human reference genome (GRCh38) using HISAT2 (v2.2.1) with default parameters. Mapping quality was evaluated using SAMtools (v1.17). Aligned reads were processed with featureCounts (v2.0.2) to obtain raw read counts for annotated genes. Normalization and differential gene expression analysis were conducted using DESeq2 (v1.36.0) in R (v4.4.0). Genes with p-values < 0.05 and log2 fold change > log2(1.5) were considered differentially expressed. The DEGs were then hierarchically clustered, split into three distinct groups based on their expression patterns, and visualized using the ComplexHeatmap package. Functional annotation of differentially expressed genes (DEGs) was performed using the clusterProfiler package (v4.6.0) in R. Gene Ontology (GO) enrichment analyses were conducted to identify enriched biological processes and pathways. Transcription factor enrichment analysis was performed using the Enrichr web server with default settings, focusing on upregulated genes during the heat shock.
For MeRIP-seq analysis, the cleaned reads were aligned to the human genome (GRCh38) using HISAT2 and were converted into BAM format using Samtools, followed by filtering for high-quality mapped reads. The BAM files were then separated into forward and reverse strands using Samtools. MACS2 was used to perform peak calling separately for the forward and reverse strands, with a threshold parameter of ‘-q 0.05’, to identify enriched regions likely containing m6A modifications and their specific peak intensities. The peaks from both strands were then merged to generate the final peak set. For genes with multiple m6A peaks, the methylation level was defined as the sum of the peak intensities of all identified peaks associated with that gene.
Assembly: hg38
Supplementary files format and content: For RNA-seq, tab-delimited text file includes raw counts for each Sample.
Supplementary files format and content: For MeRIP-seq, bigWig format files.

value: Total, WT, m6A IP


title: 6[4]10_zQ175_NTC_HIP_female_rep1

description: Library name: zQ175.236.96

value: 10 months


title: 6[4]10_zQ175_HTT-10150_HIP_male_rep3

description: Library name: zQ175.234.2132

value: male


title: 6[4]10_zQ175_NTC_HIP_male_rep3

description: Library name: zQ175.234.2140


title: U2OS cells, Total MeRIP-seq, WT, Input, rep2

description: Library name: Sample8

value: Total, WT


title: U2OS cells, Total MeRIP-seq, WT, IP, rep1

description: Library name: Sample9


title: 6[4]10_zQ175_HTT-634.486_HIP_male_rep3

description: Library name: zQ175.234.2172

value: 6 months


title: U2OS cells, Total MeRIP-seq, WT, Input, rep1

description: Library name: Sample7


title: 6[4]10_zQ175_NTC_HIP_male_rep2

description: Library name: zQ175.233.184


title: NET, P5, technical replicate 2

city: Berlin

last: Sigal

address: Augustenburger Platz 1

department: Dept. Hepatology and Gastroenterology

country: Germany

institute: Charité Universitätsmedizin

description: Library name: SP084_028

data_processing:
Single-nucleus RNA reads were aligned to the GRCh38-2020-A reference using CellRanger v6.0.1 [PMID: Zheng 28091601], incorporating both exonic and intronic (nuclear pre-mRNA) reads.  Sample P5 was processed as two technical replicates, which were subsequently merged during analysis. The background reads were removed using the R package SoupX [PMID: Young 33367645], with parameters set to tfidfMin = 0.6, soupQuantile = 0.9, and priorRho = 0.1. After background subtraction, expression values were rounded to integers. Cells were filtered based on criteria including fewer than 300 or more than 4000 RNA features, over 5% mitochondrial read content, or genes with fewer than two reads across all samples. Mitochondrial and ribosomal genes were excluded from further analysis to minimize technical noise.
Assembly: Homo sapiens, GRCh38
Supplementary files format and content: Tab separated values files and matrix files

source_name: Tumor tissue

extract_protocol:
Tumor tissue preserved by cryopreservation was disrupted in NP-40 lysis buffer (10 mM Tris-HCl at pH 7.4, 10 mM NaCl, 3 mM MgCl₂, 0.01% NP-40, 1 mM DTT, 2% BSA, 1 U/µl RNAse inhibitor, and Complete EDTA-free protease inhibitor) in a 1.5 ml Eppendorf tube using a plastic pestle. After a 5-minute incubation on ice, the suspension was filtered through a 70 µm pre-separation strainer, then centrifuged at 4°C and resuspended in nuclei wash buffer (PBS, 1% BSA, and 0.4 U/µl RNAse inhibitor). DAPI (3.5 µl) was added, and the mixture was passed through a 40 µm Flowmi cell strainer prior to sorting on a BD Aria Fusion instrument into an Eppendorf tube containing 200 µl of sort buffer (PBS, 2% BSA, 1 U/µl RNAse inhibitor) using a 100 µm nozzle.
Single-nuclei libraries were generated according to the protocol outlined in the Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (Dual Index) user guide (CG0003154) from 10x Genomics. In brief, individual nuclei were encapsulated with gel beads containing barcoded primers in the Chromium controller. Within each droplet, mRNA was reverse-transcribed into barcoded cDNA, which was then amplified. The amplified cDNA was subjected to fragmentation, end-repair, A-tailing, adaptor ligation, and sample index PCR.

value: Tumor tissue


title: 6[4]10_zQ175_Untreated_HIP_male_rep3

description: Library name: zQ175.234.2108

value: Untreated


title: NET, P5, technical replicate 1

description: Library name: SP084_027


title: 6[4]10_zQ175_HTT-634.486_HIP_male_rep2

description: Library name: zQ175.234.2139


title: 6[4]10_zQ175_HTT-10150_HIP_male_rep2

description: Library name: zQ175.233.154


title: NET, P3

description: Library name: SP084_019


title: 6[4]10_zQ175_Untreated_HIP_male_rep2

description: Library name: zQ175.233.121


title: NET, P2

description: Library name: SP084_018


title: NET, P4

description: Library name: SP084_021


title: 6[4]10_zQ175_HTT-10150_HIP_male_rep1

description: Library name: zQ175.230.74


title: 6[4]10_zQ175_Untreated_HIP_male_rep1

description: Library name: zQ175.230.102


title: 6[4]10_WT_NTC_HIP_female_rep1

description: Library name: zQ175.232.K1063

value: Wild Type

value: female


title: 6[4]10_WT_HTT-634.486_HIP_female_rep3

description: Library name: zQ175.232.K1050


title: NET, P1

description: Library name: SP084_007


title: 6[4]10_WT_HTT-634.486_HIP_female_rep2

description: Library name: zQ175.231.K1042


title: DSP-1001660008760-D-A09.dcc Patient 1 Macrophages Peritumoral

description: Library name: DSP-1001660008760-D-A09.dcc

value: Macrophages