title: TYLCV-CPmut biol rep 4

city: Tübingen

first: Rosa

last: Lozano-Durán

address: Auf der Morgenstelle 32

institute: University of Tübingen

description:
Library name: TYLCV-CPmut-4
Column name in FPKM.txt:TYLCV_CPmut_4

data_processing:
The paired-end reads were cleaned by Trimimomatic (version 0.36). Clean read pairs were retained for further analysis after trimming the adapter sequence, removing low quality bases, and filtering short reads. Clean reads were mapped to the genome sequence by HISAT (version 2.1.0) with default parameters. The number of reads that were mapped to each N. benthamiana gene was calculated with the htseq-count script in HTSeq. Differentially expressed genes (DEGs) with at least 1.5 fold change in expression and a FDR < 0.05 between control and experiment samples were identified by using EdgeR.
Assembly: The N. benthamiana draft genome sequence (v1.0.1) from solgenomics.net was used.
Supplementary files format and content: txt file contained FPKM values for each sample. Description, Gene ontology and Arabidopsis thaliana ortholog is also included for each gene.

organism: Nicotiana benthamiana

source_name: leaves

extract_protocol:
Total RNA was extracted from 8 mm leaf discs using the RNeasy plant mini kit (Qiagen) following the manufacturer’s instructions.
Total RNA (1 μg) from each sample was used for library preparation with NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England BioLabs, E7420L) following the manufacturer’s instructions. Prepared libraries were assessed for quality using NGS High-Sensitivity kit on a Fragment Analyzer (AATI) and for quantity using Qubit 2.0 fluorometer (Thermo Fisher Scientific).

value: leaves

value: WT

value: TYLCV-CPmut


title: T47D R5020 replicate 3 POLR3GL ChIP

status: Public on Sep 29 2025

type: SRA

city: Aurora

first: Jessica

last: Finlay-Schultz

state: CO

department: Pathology

country: USA

institute: University of Colorado Denver Anschutz Medical Campus

description: Library name: Sample 18

library_source: genomic

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

molecule: genomic DNA

organism: Homo sapiens

source_name: T47D cell line

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

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

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

tag: cell line

value: T47D cell line

tag: cell type

value: ER+PR+ breast cancer

tag: treatment

tag: chip antibody


title: VilCre Colon Rep2

city: Glasgow

first: Kathryn

last: Gilroy

address: Garscube

country: United Kingdom

institute: CRUK Scotland Institute

description: Library name: BVBRAF-RAB16-3c-WT-Col-01-05-2023-P6-A3

library_source: transcriptomic

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

molecule: total RNA

organism: Mus musculus

source_name: Colon

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

tag: tissue

value: Colon

tag: sample type

value: Tissue after short term induction

tag: Sex

value: Female

tag: genotype

value: VilCreER

tag: induction method

value: Tamoxifen (IP)

tag: sampling timepoint

value: Day 4


title: Control sample 1, GM no plaque ROI 5

city: Gainesville

first: Stefan

last: Prokop

state: FL

address: 1275 Center Dr

institute: University of Florida

description:
Library name: DSP-1001660037382-A-G03
Formalin Fixed Spatial transcriptomic sequencing

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

source_name: brain

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

value: brain


title: Control sample 1, GM no plaque ROI 10

description:
Library name: DSP-1001660037382-A-G08
Formalin Fixed Spatial transcriptomic sequencing


title: T47D R5020 replicate 2 POLR3GL ChIP

description: Library name: Sample 15


title: Control sample 1, GM no plaque ROI 4

description:
Library name: DSP-1001660037382-A-G02
Formalin Fixed Spatial transcriptomic sequencing


title: TYLCV-CPmut biol rep 2

country: Germany

description:
Library name: TYLCV-CPmut-2
Column name in FPKM.txt:TYLCV_CPmut_2


title: AhApc SI Rep4

description: Library name: AA-106603-AhA-SI-01-05-2023-P2-B5

source_name: SI

value: SI

value: Male

value: AhCre+ Apcfl/fl

value: B-napthoflavone (IP)


title: Control sample 1, GM no plaque ROI 3

description:
Library name: DSP-1001660037382-A-G01
Formalin Fixed Spatial transcriptomic sequencing


title: TYLCV-CPmut biol rep 1

description:
Library name: TYLCV-CPmut-1
Column name in FPKM.txt:TYLCV_CPmut_1


title: T47D R5020 replicate 2 POLR3C ChIP

description: Library name: Sample 13

value: EtOH 1h

value: POLR3C (Bethyl Laboratories A303-063A, lot #1)


title: Control sample 1, GM no plaque ROI 2

description:
Library name: DSP-1001660037382-A-F12
Formalin Fixed Spatial transcriptomic sequencing


title: AhApc SI Rep3

description: Library name: AA-217570-AhA-SI-01-05-2023-P1-G4


title: AhApc SI Rep1

description: Library name: AA-106614-AhA-SI-01-05-2023-P3-H6


title: TYLCV-C2mut biol rep 4

description:
Library name: TYLCV-C2mut-4
Column name in FPKM.txt:TYLCV_C2mut_4

value: leaves

value: WT


title: T47D R5020 replicate 1 POLR3G ChIP

description: Library name: Sample 11

value: T47D cell line


title: T47D R5020 replicate 1 POLR3GL ChIP

description: Library name: Sample 12

value: ER+PR+ breast cancer


title: Control sample 1, GM no plaque ROI 1

description:
Library name: DSP-1001660037382-A-F11
Formalin Fixed Spatial transcriptomic sequencing


title: TYLCV-C2mut biol rep 2

description:
Library name: TYLCV-C2mut-2
Column name in FPKM.txt:TYLCV_C2mut_2


title: T47D R5020 replicate 3 POLR3C ChIP

description: Library name: Sample 16


title: AhApc SI Rep5

description: Library name: AA-217563-AhA-SI-01-05-2023-P6-A2


title: cd4tcells_propanol_4

city: Odense

first: Lars

last: Grøntved

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

description: Library name: cd4t.pro4

data_processing:
Data alinged using STAR (V.2.7.9). Reads in genes (Ensembl gene transcripts GRCm39.104.gtf) were quantified using featureCounts within the Subread package (V.2.0.3).
Assembly: GRCm39
Supplementary files format and content: count matrix text file generated by featureCounts

molecule: polyA RNA

source_name: lung cd4t cells

extract_protocol:
RNA was isolated using an RNA purification kit (Qiagen)
RNA quality was assessed using the Agilent 2100 Bioanalyzer. Total RNA (500 ng) was prepared for sequencing using polydT-mediated cDNA synthesis according to the manufacturer´s (Illumina) instructions. Subsequent library preparation was performed using the NEBNext RNA library preparation kit for Illumina. Library quality was assessed using the Fragment Analyzer (AATI) followed by library quantification (Illumina library quantification kit). Sequencing was carried out on a NovaSeq 6000 platform (Illumina).

value: lung cd4t cells

value: Propranolol


title: TYLCV-CPmut biol rep 3

description:
Library name: TYLCV-CPmut-3
Column name in FPKM.txt:TYLCV_CPmut_3

value: TYLCV-CPmut


title: TYLCV-C2mut biol rep 1

description:
Library name: TYLCV-C2mut-1
Column name in FPKM.txt:TYLCV_C2mut_1


title: Low AD sample 2, WM plaque ROI 1

description:
Library name: DSP-1001660037382-A-F09
Formalin Fixed Spatial transcriptomic sequencing


title: T47D R5020 replicate 1 POLR3C ChIP

description: Library name: Sample 10


title: T47D OH replicate 3 POLR3G ChIP

description: Library name: Sample 8


title: T47D OH replicate 3 POLR3GL ChIP

description: Library name: Sample 9


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

description:
Library name: DSP-1001660037382-A-F07
Formalin Fixed Spatial transcriptomic sequencing


title: cd4tcells_propanol_3

description: Library name: cd4t.pro3


title: TYLCV biol rep 4

description:
Library name: TYLCV-4
Column name in FPKM.txt:TYLCV_4

value: TYLCV


title: cd4tcells_propanol_1

description: Library name: cd4t.pro1


title: Low AD sample 2, WM plaque ROI 2

description:
Library name: DSP-1001660037382-A-F10
Formalin Fixed Spatial transcriptomic sequencing


title: T47D OH replicate 3 POLR3C ChIP

description: Library name: Sample 7


title: TYLCV-C2mut biol rep 3

description:
Library name: TYLCV-C2mut-3
Column name in FPKM.txt:TYLCV_C2mut_3


title: cd4tcells_propanol_2

description: Library name: cd4t.pro2


title: TYLCV biol rep 3

description:
Library name: TYLCV-3
Column name in FPKM.txt:TYLCV_3


title: T47D R5020 replicate 2 POLR3G ChIP

description: Library name: Sample 14


title: TYLCV biol rep 2

description:
Library name: TYLCV-2
Column name in FPKM.txt:TYLCV_2


title: AhApc SI Rep2

description: Library name: AA-106616-AhA-SI-01-05-2023-P5-G12

value: Tissue after short term induction

value: Female


title: TYLCV biol rep 1

description:
Library name: TYLCV-1
Column name in FPKM.txt:TYLCV_1


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

description:
Library name: DSP-1001660037382-A-F05
Formalin Fixed Spatial transcriptomic sequencing

value: brain


title: cd4tcells_control_3

description: Library name: cd4t.ctl3

value: no treatment


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

description:
Library name: DSP-1001660037382-A-F06
Formalin Fixed Spatial transcriptomic sequencing


title: T47D OH replicate 2 POLR3G ChIP

description: Library name: Sample 5


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

description:
Library name: DSP-1001660037382-A-F08
Formalin Fixed Spatial transcriptomic sequencing


title: T47D OH replicate 2 POLR3GL ChIP

description: Library name: Sample 6


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

description:
Library name: DSP-1001660037382-A-F04
Formalin Fixed Spatial transcriptomic sequencing


title: cd4tcells_control_2

description: Library name: cd4t.ctl2


title: T47D OH replicate 2 POLR3C ChIP

description: Library name: Sample 4


title: C2+CP biol rep 4

description:
Library name: C2+CP-4
Column name in FPKM.txt: C2+CP_4


title: C2+CP biol rep 3

description:
Library name: C2+CP-3
Column name in FPKM.txt: C2+CP_3


title: Low AD sample 2, Sparse plaque ROI 4

description:
Library name: DSP-1001660037382-A-F03
Formalin Fixed Spatial transcriptomic sequencing


title: cd4tcells_control_1

description: Library name: cd4t.ctl1


title: T47D OH replicate 1 POLR3G ChIP

description: Library name: Sample 2


title: T47D OH replicate 1 POLR3GL ChIP

description: Library name: Sample 3


title: Low AD sample 2, Sparse plaque ROI 3

description:
Library name: DSP-1001660037382-A-F02
Formalin Fixed Spatial transcriptomic sequencing


title: C2C12 cells, Day 10, control-treated myotubes Rep4

city: Berlin

first: Suzuka

last: Nakagawa

address: Robert-Rössle Str. 10

institute: MDC

description:
Library name: Sample 24
Column in processed files: MT_Ctrl72_4

data_processing:
For gene expression analysis, samples were demultiplexed and read length quantified using salmon, via pseudoalignment against all transcripts and on reference chromosomes in the gencode vM12 mouse transcriptome annotations using parameters: “salmon quant –I ISR –seqBias –gcBias – validateMappings”. RNA-just seq fold changes were calculated using the tximport package with default settings for isoform aware quantification, and DEseq
For isoform analysis, RNA-seq reads were pseudo-aligned and quantified using Kallisto (version 0.51.1) with the mouse reference transcriptome corresponding to genome assembly GRCm39. The resulting transcript-level abundance estimates (TPM and estimated counts) were imported into R using the `importIsoformExpression()` function from the IsoformSwitchAnalyzeR package.
Assembly: GRCm39
Supplementary files format and content: Transcript-level abundance output of kallisto

growth_protocol: C2C12 cells were maintained in 10% FBS 1% P/S high glucose DMEM at 5% CO2, 37C.

extract_protocol:
RNA was extracted Zymo Direct-zol RNA Miniprep Plus kit according to manufacturer's instructions. Modifications included all centrifugation steps at 20,817 x g and an additional spin step before elution without buffer to elute residual wash buffer.
RNA libraries were prepared using TruSeq® Stranded mRNA Library Prep kit (Illumina, # 20020595) according to manufacturer's protocol. 1µg of RNA was used per sample.

treatment_protocol: At day of 80-90% confluence, cells were either harvested (Day 0 myoblasts, MB) or switched to differentiation medium (2% FBS 1% P/S high glucose DMEM) and cultured for 7 days in 5% CO2 37C. On day 7, medium was switched to vehicle containing control medium (1% EtOH 2% FBS 1%P/S high glucose medium) or atrophy medium (100 µM Dexamethasone, 2% FBS 1%P/S high glucose DMEM) and cultured for an additional 72 hrs

value: Myotube

value: Differentiation, vehicle control

tag: time point

value: Day 10


title: C2+CP biol rep 2

description:
Library name: C2+CP-2
Column name in FPKM.txt: C2+CP_2


title: cd4tcells_control_4

description: Library name: cd4t.ctl4


title: Low AD sample 2, Sparse plaque ROI 2

description:
Library name: DSP-1001660037382-A-F01
Formalin Fixed Spatial transcriptomic sequencing


title: Low AD sample 2, Sparse plaque ROI 1

description:
Library name: DSP-1001660037382-A-E12
Formalin Fixed Spatial transcriptomic sequencing


title: CP biol rep 4

description:
Library name: CP-4
Column name in FPKM.txt: CP_4

value: CP


title: T47D OH replicate 1 POLR3C ChIP

description: Library name: Sample 1

value: EtOH 1h

value: POLR3C (Bethyl Laboratories A303-063A, lot #1)


title: C2C12 cells, Day 10, atrophied myotubes Rep4

description:
Library name: Sample 23
Column in processed files: MT_A72_4

value: WT

value: Differentiation, Dexamethasone atrophy


title: C2C12 cells, Day 8, control-treated myotubes Rep4

description:
Library name: Sample 22
Column in processed files: MT_Ctrl24_4

value: Day 8


title: C2+CP biol rep 1

description:
Library name: C2+CP-1
Column name in FPKM.txt: C2+CP_1

value: leaves


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

description:
Library name: DSP-1001660037382-A-E11
Formalin Fixed Spatial transcriptomic sequencing


title: MV4-11, LAA+ATRA, RNA-seq, rep7

city: Miami

first: Luisa

last: Cimmino

state: Florida

address: 1501 NW 10th Ave, BRB 711

institute: University of Miami

description: Library name: mv4_com7

data_processing:
FASTQ files were quantified against a decoy-aware transcriptome made from GRCh38 genome and gencode v40 transcripts using Salmon (v1.8.0) using automatic library tuype inference and default Salmon parameters
Gene counts were summarized using tximport (v1.30.0) and tximeta (v1.20.1)
Differential analysis and fpkm normalization was performed with DESeq2  (v1.42.0)
Assembly: GRCh38
Supplementary files format and content: Gene count estimates per sample from tximeta containing the Ensembl gene IDs
Supplementary files format and content: FPKM of genes (Ensembl and symbol) per sample calculated by DESeq2

growth_protocol: MV4-11 cells were cultured in vitro with RPMI 1640, 10% fetal bovine serum, and 10 units/mL penicillin and 10µg/mL streptomycin in a humidified incubator at 37˚C and 5% CO2.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Plus kit (QIAGEN 74134)
mRNA was enriched from total RNA using poly-T oligo magnetic beads. Libraries were constructed from reverse transcribing the enriched mRNA using random hexamer primers, end repairing, A-tailing, adapter ligating, size selecting, PCR amplification and purification using the NEBNext Ultra II RNA library prep kit (NEB E7770)

treatment_protocol: Cells were treated for 72hr with 250µM L-ascorbic acid (LAA; Sigma A4544; dissolved in PBS), 1µM all-trans retinoic acid (ATRA; Sigma R2625; dissolved in DMSO), the combination thereof, or vehicle controls (PBS+DMSO).

value: macrophage

value: LAA + ATRA


title: CP biol rep 3

description:
Library name: CP-3
Column name in FPKM.txt: CP_3


title: MV4-11, LAA+ATRA, RNA-seq, rep6

description: Library name: mv4_com6


title: C2C12 cells, Day 7 myotubes Rep4

description:
Library name: Sample 20
Column in processed files: MT_4

value: Differentiation

value: Day 7


title: CP biol rep 2

description:
Library name: CP-2
Column name in FPKM.txt: CP_2


title: MV4-11, LAA+ATRA, RNA-seq, rep5

description: Library name: mv4_com5


title: CP biol rep 1

description:
Library name: CP-1
Column name in FPKM.txt: CP_1


title: C2C12 cells, Day 8, atrophied myotubes Rep4

description:
Library name: Sample 21
Column in processed files: MT_A24_4


title: C2C12 cells, Day 0 myoblasts Rep4

description:
Library name: Sample 19
Column in processed files: MB_4

value: Myoblast

value: Undifferentiated

value: Day 0


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

description:
Library name: DSP-1001660037382-A-E09
Formalin Fixed Spatial transcriptomic sequencing

value: brain


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

description:
Library name: DSP-1001660037382-A-E08
Formalin Fixed Spatial transcriptomic sequencing


title: C2C12 cells, Day 10, control-treated myotubes Rep3

description:
Library name: Sample 18
Column in processed files: MT_Ctrl72_3

value: Myotube

value: Differentiation, vehicle control


title: C2 biol rep 4

description:
Library name: C2-4
Column name in FPKM.txt: C2_4


title: MV4-11, ATRA, RNA-seq, rep7

description: Library name: mv4_atra7

value: All-trans retinoic acid (ATRA, 1µM)


title: MV4-11, ATRA, RNA-seq, rep6

description: Library name: mv4_atra6


title: C2 biol rep 3

description:
Library name: C2-3
Column name in FPKM.txt: C2_3


title: Low AD sample 2, Dense plaque ROI 7

description:
Library name: DSP-1001660037382-A-E06
Formalin Fixed Spatial transcriptomic sequencing


title: C2C12 cells, Day 10, atrophied myotubes Rep3

description:
Library name: Sample 17
Column in processed files: MT_A72_3

value: Day 10


title: C2 biol rep 2

description:
Library name: C2-2
Column name in FPKM.txt: C2_2


title: C2C12 cells, Day 8, control-treated myotubes Rep3

description:
Library name: Sample 16
Column in processed files: MT_Ctrl24_3


title: MV4-11, ATRA, RNA-seq, rep5

description: Library name: mv4_atra5


title: Low AD sample 2, Dense plaque ROI 6

description:
Library name: DSP-1001660037382-A-E05
Formalin Fixed Spatial transcriptomic sequencing


title: MV4-11, LAA, RNA-seq, rep7

description: Library name: mv4_laa7

value: L-ascorbic acid (LAA, 250µM)


title: EV biol rep 4

description:
Library name: EV-4
Column name in FPKM.txt: EV_4

value: WT

value: EV


title: C2C12 cells, Day 8, atrophied myotubes Rep3

description:
Library name: Sample 15
Column in processed files: MT_A24_3

value: Differentiation, Dexamethasone atrophy

value: Day 8


title: Low AD sample 2, Dense plaque ROI 5

description:
Library name: DSP-1001660037382-A-E04
Formalin Fixed Spatial transcriptomic sequencing


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

description:
Library name: DSP-1001660037382-A-E10
Formalin Fixed Spatial transcriptomic sequencing


title: MV4-11, LAA, RNA-seq, rep5

description: Library name: mv4_laa5

value: macrophage


title: C2C12 cells, Day 7 myotubes Rep3

description:
Library name: Sample 14
Column in processed files: MT_3


title: Low AD sample 2, Dense plaque ROI 4

description:
Library name: DSP-1001660037382-A-E03
Formalin Fixed Spatial transcriptomic sequencing


title: C2C12 cells, Day 0 myoblasts Rep3

description:
Library name: Sample 13
Column in processed files: MB_3


title: MV4-11, vehicle, RNA-seq, rep7

description: Library name: mv4_veh7

value: Vehicle


title: EV biol rep 3

description:
Library name: EV-3
Column name in FPKM.txt: EV_3

value: leaves


title: Low AD sample 2, Dense plaque ROI 3

description:
Library name: DSP-1001660037382-A-E02
Formalin Fixed Spatial transcriptomic sequencing


title: C2C12 cells, Day 10, control-treated myotubes Rep2

description:
Library name: Sample 12
Column in processed files: MT_Ctrl72_2


title: Low AD sample 2, Dense plaque ROI 2

description:
Library name: DSP-1001660037382-A-E01
Formalin Fixed Spatial transcriptomic sequencing


title: EV biol rep 1

description:
Library name: EV-1
Column name in FPKM.txt: EV_1


title: C2C12 cells, Day 10, atrophied myotubes Rep2

description:
Library name: Sample 11
Column in processed files: MT_A72_2


title: MV4-11, vehicle, RNA-seq, rep5

description: Library name: mv4_veh5


title: Low AD sample 2, Dense plaque ROI 8

description:
Library name: DSP-1001660037382-A-E07
Formalin Fixed Spatial transcriptomic sequencing


title: C2C12 cells, Day 8, control-treated myotubes Rep2

description:
Library name: Sample 10
Column in processed files: MT_Ctrl24_2


title: C2 biol rep 1

description:
Library name: C2-1
Column name in FPKM.txt: C2_1


title: Low AD sample 1, WM plaque ROI 2

description:
Library name: DSP-1001660037382-A-D11
Formalin Fixed Spatial transcriptomic sequencing


title: MV4-11, LAA, RNA-seq, rep6

description: Library name: mv4_laa6


title: SaB200uM3

city: Beijing

first: Yongli

last: Zhang

address: Sunny South Street, Fangshan District

country: China

institute: Beijing University of Chinese Medicine

description: Library name: Sample9

data_processing:
Raw sequencing reads were quality checked using FastQC. Clean reads were aligned to the Homo sapiens reference genome (GRCh38) using HISAT2 with default parameters. Gene-level read counts were generated using featureCounts. Raw count matrices were used for downstream differential expression analysis with DESeq2. Read counts are provided as processed data.
Assembly: GRCh38 (hg38)
Supplementary files format and content: raw_readcount.txt — a tab-delimited text file containing raw gene-level read counts for each sample. Rows represent genes (with Ensembl Gene IDs and Gene Symbols) and columns represent individual samples from the control and treatment groups.
Supplementary files format and content: DEGs_list.csv — a comma-separated values (CSV) file containing FPKM-normalized expression values and differential expression results for each gene, including gene IDs, gene symbols, fold changes, p-values, and adjusted p-values.

growth_protocol: A375 human melanoma cells were cultured in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin at 37°C in a humidified atmosphere containing 5% CO₂.

extract_protocol:
Total RNA was extracted from A375 cells using TRIzol reagent (Invitrogen) according to the manufacturer’s instructions.
RNA libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB) following the manufacturer’s instructions. Briefly, mRNA was enriched using poly-T oligo-attached magnetic beads, fragmented, reverse transcribed into cDNA, end repaired, A-tailed, ligated with sequencing adapters, and PCR amplified to generate the final cDNA libraries.

treatment_protocol: A375 melanoma cells were treated with Salvianolic Acid B (Sal B) at final concentrations of 100 µM or 200 µM for 48 hours. Control cells were cultured under the same conditions without Sal B treatment.

value: human melanoma cell line

value: Sal B 200 µM 48h

tag: batch


title: sgRARA U-937, LAA+ATRA, rep2

description: Library name: dRA_Combo_02

data_processing:
Only read 1 (R1) was used for mapping and analysis
FASTQ files were trimmed with cutadapt (v4.9) to remove adaptor sequence with 2 additional bases
Trimmed reads were aligned to GRCh38 with Bismark (v0.24.2)
CpG sites were destranded with bsseq (v1.36.0)
Differential hydroxymethylation was calculated with methylSig (v1.12.0), restricting to CpGs with 10-400X coverage.
Assembly: GRCh38
Supplementary files format and content: Bismark CpG reports containing genomic loci, their hydroxymethylated and unmethylated counts, and di- and tri-nucleotide cytosine contexts

growth_protocol: Puromycin-selected CRISPR knockout NTG and sgRARA U-937 cells were cultured in vitro with RPMI 1640, 10% fetal bovine serum, and 10 units/mL penicillin and 10µg/mL streptomycin in a humidified incubator at 37˚C and 5% CO2.

extract_protocol:
Cells were collected and pelleted after treatment, digested with RNase in a 10% SDS buffer for 30minutes, followed by overnight proteinase K digestion at 55°C. Lysate was phenol-chloroform extracted, ethanol-salt precipitated, and genomic DNA resuspended in buffer EB.
Genomic DNA was MspI digested to enrich for CpGs. Libraries were prepared using the NEBNext® Enzymatic 5hmC-seq Kit (NEB, E3350)

treatment_protocol: Cells were treated for 72hr with the combination of 250µM L-ascorbic acid (LAA; Sigma A4544; dissolved in PBS) + 1µM all-trans retinoic acid (ATRA; Sigma R2625; dissolved in DMSO)f, or vehicle controls (PBS+DMSO).

value: monocyte

value: CRISPR sgRARA

value: LAA + ATRA


title: SaB200uM2

description: Library name: Sample8


title: C2C12 cells, Day 7 myotubes Rep2

description:
Library name: Sample 8
Column in processed files: MT_2

value: Myotube

value: Differentiation

value: Day 7


title: Low AD sample 1, WM no plaque ROI 5

description:
Library name: DSP-1001660037382-A-D09
Formalin Fixed Spatial transcriptomic sequencing

value: brain


title: Low AD sample 1, WM plaque ROI 1

description:
Library name: DSP-1001660037382-A-D10
Formalin Fixed Spatial transcriptomic sequencing


title: C2C12 cells, Day 0 myoblasts Rep2

description:
Library name: Sample 7
Column in processed files: MB_2

value: Myoblast

value: Undifferentiated

value: Day 0


title: SaB100uM3

description: Library name: Sample6

value: Sal B 100 µM 48h


title: EV biol rep 2

description:
Library name: EV-2
Column name in FPKM.txt: EV_2

value: WT

value: EV


title: MV4-11, vehicle, RNA-seq, rep6

description: Library name: mv4_veh6

value: macrophage

value: Vehicle


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

description:
Library name: DSP-1001660037382-A-D08
Formalin Fixed Spatial transcriptomic sequencing


title: SaB100uM2

description: Library name: Sample5

value: human melanoma cell line


title: sgRARA U-937, vehicle, rep2

description: Library name: dRA_Veh_02


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

description:
Library name: DSP-1001660037382-A-D07
Formalin Fixed Spatial transcriptomic sequencing


title: SaB100uM1

description: Library name: Sample4


title: Low AD sample 2, Dense plaque ROI 1

description:
Library name: DSP-1001660037382-A-D12
Formalin Fixed Spatial transcriptomic sequencing


title: sgRARA U-937, vehicle, rep1

description: Library name: dRA_Veh_01


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

description:
Library name: DSP-1001660037382-A-D06
Formalin Fixed Spatial transcriptomic sequencing


title: C2C12 cells, Day 10, atrophied myotubes Rep1

description:
Library name: Sample 5
Column in processed files: MT_A72_1

value: Differentiation, Dexamethasone atrophy

value: Day 10


title: con3

description: Library name: Sample3

value: untreated


title: sgRARA U-937, LAA+ATRA, rep3

description: Library name: dRA_Combo_03

value: monocyte

value: CRISPR sgRARA

value: LAA + ATRA


title: C2C12 cells, Day 8, control-treated myotubes Rep1

description:
Library name: Sample 4
Column in processed files: MT_Ctrl24_1

value: Myotube

value: Differentiation, vehicle control

value: Day 8


title: C2C12 cells, Day 8, atrophied myotubes Rep2

description:
Library name: Sample 9
Column in processed files: MT_A24_2


title: NTG U-937, LAA+ATRA, rep3

description: Library name: NTG_Combo_03

value: CRISPR Non-target guide


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

description:
Library name: DSP-1001660037382-A-D05
Formalin Fixed Spatial transcriptomic sequencing

value: brain


title: SaB200uM1

description: Library name: Sample7

value: Sal B 200 µM 48h


title: con2

description: Library name: Sample2


title: sgRARA U-937, LAA+ATRA, rep1

description: Library name: dRA_Combo_01


title: Low AD sample 1, Sparse plaque ROI 4

description:
Library name: DSP-1001660037382-A-D04
Formalin Fixed Spatial transcriptomic sequencing


title: NTG U-937, LAA+ATRA, rep2

description: Library name: NTG_Combo_02


title: C2C12 cells, Day 7 myotubes Rep1

description:
Library name: Sample 2
Column in processed files: MT_1

value: WT

value: Differentiation

value: Day 7


title: NTG U-937, LAA+ATRA, rep1

description: Library name: NTG_Combo_01


title: C2C12 cells, Day 10, control-treated myotubes Rep1

description:
Library name: Sample 6
Column in processed files: MT_Ctrl72_1


title: Low AD sample 1, Sparse plaque ROI 3

description:
Library name: DSP-1001660037382-A-D03
Formalin Fixed Spatial transcriptomic sequencing


title: C2C12 cells, Day 8, atrophied myotubes Rep1

description:
Library name: Sample 3
Column in processed files: MT_A24_1


title: sgRARA U-937, vehicle, rep3

description: Library name: dRA_Veh_03

value: Vehicle


title: con1

description: Library name: Sample1

value: human melanoma cell line


title: T47D P4 replicate 3 PR ChIP

description: Library name: Sample 13

extract_protocol:
Cells were prepared using the ActiveMotif ChIP-IT® Express Chromatin Immunoprecipitation Kit according to manufacturer protocols, chromatin was fragmented using a Covaris S220 sonicator
Libraries were prepared for sequencing using the Illumina TruSeq ChIP-seq kit according to manufacturer protocol

treatment_protocol: Cells were treated with EtOH vehicle or P4 for 1h

value: T47D cell line

value: ER+PR+ breast cancer

value: PR Ab-8 (ThermoFisher MS-298-P1-A, lot #298P1806G)

value: P4 1h


title: NTG U-937, vehicle, rep2

description: Library name: NTG_Veh_02

value: monocyte


title: Low AD sample 1, Sparse plaque ROI 1

description:
Library name: DSP-1001660037382-A-D01
Formalin Fixed Spatial transcriptomic sequencing


title: NTG U-937, vehicle, rep3

description: Library name: NTG_Veh_03


title: T47D P4 replicate 2 POLR3A ChIP

description: Library name: Sample 12


title: NTG U-937, vehicle, rep1

description: Library name: NTG_Veh_01


title: T47D P4 replicate 3 POLR3A ChIP

description: Library name: Sample 14


title: C2C12 cells, Day 0 myoblasts Rep1

description:
Library name: Sample 1
Column in processed files: MB_1

value: Myoblast

value: Undifferentiated

value: Day 0


title: AKTP MTO, RM-044, replicate 2

city: Barcelona

first: Adria-Jaume

last: Roura

address: Carrer de Baldiri Reixac, 10

country: Spain

institute: IRB Barcelona

description: Library name: Sample 5

data_processing:
Mapping was performed according to a fragment-based strategy as previously described {Imakaev, 2012, PubMed:22941365} to the reference genome mouse June 2020 mouse reference genome (GRCm39/mm39).
TADbit filtering module was used to remove noninformative contacts and to create contact matrices. PCR duplicates were removed, and the Hi-C filters applied corresponded to potential nondigested fragments (extra-dangling ends), non-ligated fragments (dangling ends), self-circles, and random breaks.
Contact matrices were normalized for sequencing depth and genomic biases using cooler balance {Abdennur, 2020, PubMed:31290943}.
Assembly: GRCm39/mm39
Supplementary files format and content: fastq.gz and mcool

source_name: Mouse Tumor Organoids (MTO)

extract_protocol:
For cell lysis, 600 μl lysis buffer (10 mM Tris-HCl Ph=8, 10 mM NaCl, 0.2% IGEPAL CA-630, 1x protease inhibitor complex (Roche, 11873580001) in water) was added to each pellet. Cells were incubated for 30 min on ice and immediately centrifuged for 5 min at 950 g at 4 ºC. All centrifugations throughout the protocol were done under the same conditions. Pellets were washed with 1x NEBuffer 2 (NEB, B7002S), resuspended in 190 μl 1x NEBuffer 2 and 10 μl 10% SDS and incubated for 10 min at 65 ºC 350 rpm. SDS effect was quenched with 400 μl 1x NEBuffer 2 and 120 μl 10% Triton X-100 (Merck, 648466) for 30 min at 37 ºC 300 rpm. Nuclei were spun down, washed with 1x NEBuffer 2 and resuspended in 300 μl 1x NEBuffer 2 with 400 Units of MboI (NEB, R0147M). Chromatin was digested overnight at 37 ºC 300 rpm.
1 ug of DNA was sheared in a Bioruptor Pico (Diagenode, B01080010) and pull-down of the biotin tagged Hi-C fragments was done through binding to Dynabeads MyOne Streptavidin T1 beads (ThermoFisher Scientific, 65601). Hi-C libraries were prepared using the NEBNext End Repair Module (E6050L), NEBNext dA-Tailing Module (E6053L) and NEBNext Quick Ligation Reaction Buffer 5X (B6058S). PCR amplification (8 cycles) was done with UDIs (E6440S) and NEBNext High-Fidelity 2x PCR Master Mix (M0541S). Amplified libraries were purified with 0.9x volume AMPure beads and eluted in water. Library concentration and size were assessed with Qubit HS dsDNA (Invitrogen, Q33321) and Tapestation (Agilent, 5067-5589, 5067-5590), respectively, and sequencing was done with Illumina NovaSeq 6000 2x150 bp paired-end sequencing for at least 1,000 M reads.

value: Mouse Tumor Organoids (MTO)

value: Epithelial malignant cells

value: AKTP mutant

value: RM-044 KRASi


title: RM-044 treated liver metastasis Epcam+/CD45- sorted epithelial cells

description:
Library name: Sample 2
10X Genomics

library_source: transcriptomic single cell

data_processing:
Cellular transcriptome was profiled using 10X Genomics CellRanger software (v.8.0.1). Reads were mapped to the mouse reference transcriptome, mm10 (GENCODE vM23/Ensembl 98) in which the EGFP sequence was incorporated to track its expression.
Quality control of the raw data included checking the number of genes, UMIs (Unique Molecular Identifiers), and the percentage of mitochondrial RNA per cell. Filtering of low-quality cells was performed by calculating the median absolute deviation (MAD) for the number of features (nFeatures) and the number of reads (nCounts) per sample. Only cells within a maximum threshold of 5×MAD were retained. Additionally, cells with a minimum of 200 nFeatures and a mitochondrial RNA percentage below 20% were included in the analysis.
After quality control, we preprocessed the data using the Seurat package (v5.0.2). This process involved normalizing gene expression measurements for each cell using the SCTransform function (SCT method, v2), while regressing out the percentage of mitochondrial reads to mitigate their potential influence.
Assembly: mm10
Supplementary files format and content: Tab-separated barcodes, features and matrix files

source_name: liver

extract_protocol:
FACS-sorted Epcam+/CD45- epithelial cells were concentrated by centrifugation (500g for 10 min at 4ºC) and counted. Cells were partitioned into Gel Bead In Emulsions (GEMs) with a target of 10.000 cells per sample using the Chromium Controller system (10X Genomics).
cDNA sequencing libraries were prepared using the Chromium Single Cell 3ʹ Kit v3 (PN-1000075). cDNA was amplified, quality checked, and quantified on an Agilent Bioanalyzer High Sensitivity chip (Agilent Technologies), then used for Gene Expression (GEX) library preparation (PN-220103 Chromium i7 Sample Index Plate). Final libraries were indexed by PCR and verified for size and concentration. Sequencing was performed on an Illumina NovaSeq 6000 to obtain approximately 40.000 reads per cell.

value: liver


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

description:
Library name: DSP-1001660037382-A-C12
Formalin Fixed Spatial transcriptomic sequencing

value: brain


title: Vehicle liver metastasis Epcam+/CD45- sorted epithelial cells

description:
Library name: Sample 1
10X Genomics


title: T47D P4 replicate 2 PR ChIP

description: Library name: Sample 11


title: MV4, LAA+ATRA, 5hmC-seq, rep4

description: Library name: mv4_com_4.fastq.gz

data_processing:
Only read 1 (R1) was used for mapping and analysis
FASTQ files were trimmed with cutadapt (v4.9) to remove adaptor sequence with 2 additional bases
Trimmed reads were aligned to GRCh38 with Bismark (v0.24.2)
CpG sites were destranded with bsseq (v1.36.0)
Differential hydroxymethylation was calculated with methylSig (v1.12.0), restricting to CpGs with 10-400X coverage.
Assembly: GRCh38
Supplementary files format and content: Bismark CpG reports containing cytosine loci, their hydroxymethylated and unmethylated counts, and di- and tri-nucleotide contexts

value: macrophage

value: LAA + ATRA


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

description:
Library name: DSP-1001660037382-A-C11
Formalin Fixed Spatial transcriptomic sequencing


title: AKTP MTO, RM-044, replicate 1

description: Library name: Sample 4


title: T47D P4 replicate 1 POLR3A ChIP

description: Library name: Sample 10


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

description:
Library name: DSP-1001660037382-A-C10
Formalin Fixed Spatial transcriptomic sequencing


title: MV4, LAA+ATRA, 5hmC-seq, rep3

description: Library name: mv4_com_3.fastq.gz


title: T47D P4 replicate 1 PR ChIP

description: Library name: Sample 9


title: AKTP MTO, vehicle control, replicate 2

description: Library name: Sample 2


title: Low AD sample 1, Sparse plaque ROI 2

description:
Library name: DSP-1001660037382-A-D02
Formalin Fixed Spatial transcriptomic sequencing


title: MV4, LAA+ATRA, 5hmC-seq, rep1

description: Library name: mv4_com_1.fastq.gz


title: AKTP MTO, vehicle control, replicate 1

description: Library name: Sample 1


title: MV4, ATRA, 5hmC-seq, rep4

description: Library name: mv4_atra_4.fastq.gz

value: All-trans retinoic acid (ATRA, 1µM)


title: T47D Veh replicate 3 POLR3A ChIP

description: Library name: Sample 7

value: T47D cell line

value: EtOH 1h


title: Low AD sample 1, Dense plaque ROI 8

description:
Library name: DSP-1001660037382-A-C08
Formalin Fixed Spatial transcriptomic sequencing


title: T47D P4 pooled input

description: Library name: Sample 8

value: ER+PR+ breast cancer


title: WT rep3

city: Yangzhou

first: Hongzhou

last: Guo

state: Jiangsu

address: No. 12, Wenhui East Road, Hanjiang District

institute: COLLEGE OF VETERINARY MED-LIB

description: Library name: Sample6

data_processing:
The reference genome was indexed, and the paired-end clean reads were aligned to it using HISAT2 software (version 2.0.5).
Assembly: GRCm38 (GenBank Assembly ID: GCA_000001635.8)
Supplementary files format and content: Raw sequencing reads in FASTQ format (compressed with gzip). Includes read IDs, sequences, and quality scores.

source_name: testis

extract_protocol:
Total RNA was extracted from mouse testis using TRIzol reagent (Invitrogen), followed by DNase I treatment. RNA integrity was verified by Bioanalyzer (RIN ≥ 8.0).
Briefly, magnetic beads with poly-T oligo were utilized to isolate mRNA from total RNA. After the process of fragmentation, a library for transcriptome sequencing was created and its quality was evaluated using an Agilent Bioanalyzer 2100 system. The index-coded samples were clustered using a cBot Cluster Generation System and a TruSeq PE Cluster kit v3-cBot-HS (Illumina), following the manufacturer’s guidelines. After cluster generation, the library preparations were sequenced using the Illumina NovaSeq platform.

value: testis


title: WT rep2

description: Library name: Sample5


title: MV4, ATRA, 5hmC-seq, rep1

description: Library name: mv4_atra_1.fastq.gz


title: MV4, ATRA, 5hmC-seq, rep3

description: Library name: mv4_atra_3.fastq.gz


title: Low AD sample 1, Dense plaque ROI 6

description:
Library name: DSP-1001660037382-A-C06
Formalin Fixed Spatial transcriptomic sequencing


title: WT rep1

description: Library name: Sample4


title: T47D Veh replicate 2 PR ChIP

description: Library name: Sample 4

value: PR Ab-8 (ThermoFisher MS-298-P1-A, lot #298P1806G)


title: Low AD sample 1, Dense plaque ROI 7

description:
Library name: DSP-1001660037382-A-C07
Formalin Fixed Spatial transcriptomic sequencing


title: T47D Veh replicate 3 PR ChIP

description: Library name: Sample 6


title: T47D Veh replicate 2 POLR3A ChIP

description: Library name: Sample 5


title: Low AD sample 1, Dense plaque ROI 4

description:
Library name: DSP-1001660037382-A-C04
Formalin Fixed Spatial transcriptomic sequencing


title: cKO rep3

description: Library name: Sample3


title: MV4, LAA, 5hmC-seq, rep3

description: Library name: mv4_laa_3.fastq.gz

value: L-ascorbic acid (LAA, 250µM)


title: MV4, LAA, 5hmC-seq, rep4

description: Library name: mv4_laa_4.fastq.gz


title: Low AD sample 1, Dense plaque ROI 5

description:
Library name: DSP-1001660037382-A-C05
Formalin Fixed Spatial transcriptomic sequencing


title: cKO rep2

description: Library name: Sample2


title: MV4, LAA, 5hmC-seq, rep1

description: Library name: mv4_laa_1.fastq.gz


title: T47D Veh replicate 1 PR ChIP

description: Library name: Sample 2


title: T47D Veh replicate 1 POLR3A ChIP

description: Library name: Sample 3


title: cKO rep1

description: Library name: Sample1


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

description:
Library name: DSP-1001660037382-A-C09
Formalin Fixed Spatial transcriptomic sequencing


title: MV4, vehicle, 5hmC-seq, rep4

description: Library name: mv4_veh_4.fastq.gz

value: Vehicle


title: Low AD sample 1, Dense plaque ROI 3

description:
Library name: DSP-1001660037382-A-C03
Formalin Fixed Spatial transcriptomic sequencing


title: T47D Veh pooled input

description: Library name: Sample 1


title: Blastocyst_F10_C

first: Zongliang

last: Jiang

address: 2033 Mowry Rd

department: Animal Sciences

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

source_name: oocyte or embryo

extract_protocol:
Ten equal fractions were recovered and subjected to RNA isolation by Trizol reagent (Sigma).
The RNA-seq libraries were generated from individual fractions by using the Smart-seq2 v4 kit with minor modification from manufacturer’s instructions. Briefly, individual cells were lysed, and mRNA was captured and amplified with the Smart-seq2 v4 kit (Clontech). After AMPure XP beads purification, amplified RNAs were quality checked by using Agilent High Sensitivity D5000 kit (Agilent Technologies). High-quality amplified RNAs were subject to library preparation (Nextera XT DNA Library Preparation Kit; Illumina) and multiplexed by Nextera XT Indexes (Illumina). The concentration of sequencing libraries was determined by using Qubit dsDNA HS Assay Kit (Life Technologies) and KAPA Library Quantification Kits (KAPA Biosystems). The size of sequencing libraries was determined by means of High Sensitivity D5000 Assay in at Tapestation 4200 system (Agilent). Pooled indexed libraries were then sequenced on the Illumina HiSeq X platform with 150-bp paired-end reads.

treatment_protocol: Approximately 100 oocytes (GV or MII oocyte) or embryos at different developmental stages (zygote, 2-, 4-, 8-cell, morula, and blastocyst) were combined with lysis buffer containing 10 mM HEPES (pH 7.5), 5 mM KCL, 5 mM MgCL2, 2 mM DTT, 1% Triton X-100, 100 μg/ml cycloheximide, complete EDTA-free protease inhibitor (Roche), and 40 U/ml RNase inhibitor. Oocytes and embryos were disrupted by zirconium silica beads (Sigma) in the mixer mill apparatus MM301 (shake frequency 30, total time 45s, Retsch). Lysates were cleaned by centrifugation in 10,000 x g for 5 min at 4°C and the supernatants were loaded into 10-40 % linear sucrose gradients containing 10 mM HEPES (pH7.5), 100 mM KCL, 5 mM MgCl2, 2mM DTT, 100 μg/ml cycloheximide, complete EDTA-free protease inhibitor, and 5 U/ml RNase inhibitor. Ultracentrifugation was carried out with a SW55Ti rotor and Optima L-90 Ultracentrifuge (Beckman Coulter). Ribosome profiles were recorded by ISCO UV absorbance reader. The overall quality of particular ribosome fractionation experiment was monitored by analysis of a parallel Hek293 cells sample.

value: oocyte or embryo


title: MV4, vehicle, 5hmC-seq, rep3

description: Library name: mv4_veh_3.fastq.gz


title: Blastocyst_F10_B


title: Low AD sample 1, Dense plaque ROI 2

description:
Library name: DSP-1001660037382-A-C02
Formalin Fixed Spatial transcriptomic sequencing


title: Low AD sample 1, Dense plaque ROI 1

description:
Library name: DSP-1001660037382-A-C01
Formalin Fixed Spatial transcriptomic sequencing


title: Lung, uncontrolled, ROI8

city: Mountain View

first: Lester

last: Kobzik

state: California

address: 320 Logue Avenue

institute: Cellecta, Inc

description: Library name: Uncontrolled8

data_processing:
To obtain raw counts, raw sequencing files were converted to .DCC files via Nanostring geomxngspipeline function. The DCC files were uploaded to the DSP instrument and automatically associated with individual scans.  Sequencing and Probe QC was performed using default parameters.
Assembly: GRCm38.p6
Supplementary files format and content: RawCountTableControlledvsUncontrolled.txt: Count table for 8 controlled and 8 uncontrolled lesions with gene names and probe details
Library strategy: Spatial Transcriptomics

source_name: Lung

extract_protocol:
Formalin-fixed paraffin-embedded lung sections were prepared for spatial analysis.
Spatial transcriptomics libraries were prepared using samples corresponding to ROI (regions of interest) of controlled and uncontrolled lesions as per manufacturer’s instructions.

treatment_protocol: Mice were injected into their hocks with 10E6 M. Tb Erdman strain, followed by euthanasia 14 weeks later with harvesting and fixation of lungs.

value: Lung

value: Tuberculosis infection


title: MV4, vehicle, 5hmC-seq, rep1

description: Library name: mv4_veh_1.fastq.gz


title: Blastocyst_F10_A


title: Lung, uncontrolled, ROI7

description: Library name: Uncontrolled7


title: CD271+ MSC Plate5

city: Basel

first: Judith

last: Zaugg

address: Hebelstrasse 20

department: Departement Biomedizin

country: Switzerland

institute: University of Basel

description: Library name: Plate5

data_processing:
A hybrid genome reference and annotation was prepared by combining human genome reference GRCh38 and a gene annotation from Gencode Release 32 with the reference sequences and annotation of the Ambion ERCC RNA Spike-In Mix (Thermo Fisher Scientific). Raw Fastq files were aligned against the hybrid reference using STAR aligner (v2.7.10b).
Resulting BAM files were filtered to remove reads without an assigned cell barcode or UMI using SAMtools and GNU grep. Filtered BAM files were used to create the gene count tables using the dropEst pipeline (v0.8.6) with adjusted settings for CEL-Seq2 experiment and counting of any UMIs that overlap either exonic or intronic regions. The results were additionally corrected for UMI collisions and sequencing errors using dropEst.
Assembly: GRCh38 + ERCC RNA Spike-In Mix (Thermo Fisher Scientific).
Supplementary files format and content: RDS files with gene counts corrected with dropEst.

source_name: Bone marrow

extract_protocol:
CD45-CD14-CD235a-CD71-CD38-CD271+ single cells were sorted in 5 384-well plates containing 5 μl of CEL-Seq2 primer solution in mineral oil (24 bp polyT stretch, a 4 bp random molecular barcode (UMI), a cell-specific barcode, the 5'-Illumina TruSeq small RNA kit adapter, and a T7 promoter), provided by Single Cell Discoveries (Utrecht, the Netherlands). After sorting, the plates were centrifuged for 1 min at 1000g and immediately placed on ice and stored at −70°C.
Single Cell Discoveries further processed the plates. In brief, ERCC Spike-in RNA Mix (Ambion, 0.02 μl of 1:50,000 dilution) was added to each well before cell lysis with heat shocking. Reverse transcription and second-strand synthesis reagents were dispensed using the Nanodrop II (GC biotech). After generation of cDNA from the original mRNA, all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. To generate sequencing libraries, RPI-series index primers were used for library PCR. Libraries were sequenced on an Illumina Nextseq500 using 75 bp paired-end sequencing.

value: Bone marrow

value: CD271+ MSC


title: Lung, uncontrolled, ROI6

description: Library name: Uncontrolled6


title: CD271+ MSC Plate4

description: Library name: Plate4


title: High AD sample 1, WM plaque ROI 1

description:
Library name: DSP-1001660037382-A-B11
Formalin Fixed Spatial transcriptomic sequencing


title: High AD sample 1, WM plaque ROI 2

description:
Library name: DSP-1001660037382-A-B12
Formalin Fixed Spatial transcriptomic sequencing


title: Blastocyst_F9_B


title: CD271+ MSC Plate3

description: Library name: Plate3


title: Blastocyst_F9_C


title: Lung, uncontrolled, ROI5

description: Library name: Uncontrolled5


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

description:
Library name: DSP-1001660037382-A-B09
Formalin Fixed Spatial transcriptomic sequencing


title: Lung, uncontrolled, ROI4

description: Library name: Uncontrolled4


title: High AD sample 1, WM no plaque ROI 5

description:
Library name: DSP-1001660037382-A-B10
Formalin Fixed Spatial transcriptomic sequencing


title: Blastocyst_F9_A


title: CD271+ MSC Plate2

description: Library name: Plate2


title: Lung, uncontrolled, ROI3

description: Library name: Uncontrolled3


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

description:
Library name: DSP-1001660037382-A-B08
Formalin Fixed Spatial transcriptomic sequencing


title: Blastocyst_F8_C


title: CD271+ MSC Plate1

description: Library name: Plate1


title: Lung, uncontrolled, ROI2

description: Library name: Uncontrolled2


title: Blastocyst_F8_B


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

description:
Library name: DSP-1001660037382-A-B07
Formalin Fixed Spatial transcriptomic sequencing


title: T cells + HSPC CHIP2+MDS2+MDS4 multiplexed

description: Library name: SIGAE4

data_processing:
Reads were aligned to the GRCh38 (v.2020-A) reference genome and quantified using cellranger count (10x Genomics, v.7.0.0).
Assembly: GRCh38
Supplementary files format and content: H5 feature bc matrices produced by cellranger

extract_protocol:
BM aspirates from a representative subset of donors in this study (3 age-matched controls, 3 CHIP, and 4 MDS donors), curated as part of the BoHemE study (NCT02867085), were included for scRNA-seq. The samples were thawed in 100% FCS + 100 µg/ml DNAse I, centrifuged at 300g for 5 min and suspended in DMEM + 10% FCS + 100 µg/ml DNAse I. When necessary, cell pellets were treated with 1X Red Blood Cell Lysis for 10 min at RT . Cells were washed with 2% FCS/PBS. Live/dead staining (FV780, Thermo Fisher) was performed in PBS, followed by antibody staining for 30 min at 4°C in CellCover (Anacyte Laboratories). Stained cells were sorted into PBS + 5% BSA with a FACSAria™ Fusion (BD Biosciences) equipped with a 130 µm nozzle into BSA-coated LoBind 1.5 ml tubes (Eppendorf).
The HSPC and T cell fractions were combined and subjected to scRNA-seq in parallel with the stromal fraction, ensuring clean separation of the populations and minimizing contamination of blood or immune cells in the stromal fractions. 10x Genomics was performed using the Chromium Next GEM (Gel Bead-In Emulsions) Single Cell 3’ kit (v3.1, 10x Genomics) according to the manufacturer's instructions. We pooled the T cells (CD45highCD34-CD14-CD235a-CD71-CD3+) and HSPC (CD45dimCD34+CD14-CD235a-CD71-) fractions in 1 lane and the stromal cells (CD34-CD45-CD14-CD235a-CD71-CD38-) in a separate lane. Sorting and single cell processing was performed in 3 batches on different days, with each batch consisting of a mix of control, CHIP, and MDS donors to correct for batch effects. Libraries were prepared based on manufacturer’s instructions, with 13-14 PCR cycles for the final library generation. Following, the libraries were equimolarly pooled and sequenced using Illumina NextSeq 2000 with P2 and P3 flow cells.


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

description:
Library name: DSP-1001660037382-A-B06
Formalin Fixed Spatial transcriptomic sequencing


title: Lung, uncontrolled, ROI1

description: Library name: Uncontrolled1


title: Stroma CHIP2+MDS2+MDS4 multiplexed

description: Library name: SIGAE3


title: High AD sample 1, Sparse plaque ROI 4

description:
Library name: DSP-1001660037382-A-B05
Formalin Fixed Spatial transcriptomic sequencing


title: Blastocyst_F8_A


title: High AD sample 1, Sparse plaque ROI 3

description:
Library name: DSP-1001660037382-A-B04
Formalin Fixed Spatial transcriptomic sequencing


title: T cells + HSPC Control2+CHIP1+MDS3 multiplexed

description: Library name: SIGAE2


title: Lung, controlled, ROI8

description: Library name: Controlled8


title: Blastocyst_F7_C


title: Lung, controlled, ROI7

description: Library name: Controlled7


title: Stroma Control2+CHIP1+MDS3 multiplexed

description: Library name: SIGAE1


title: Stroma CHIP2+MDS4 multiplexed

description: Library name: SIGAD9


title: Blastocyst_F7_B


title: High AD sample 1, Sparse plaque ROI 1

description:
Library name: DSP-1001660037382-A-B02
Formalin Fixed Spatial transcriptomic sequencing


title: Blastocyst_F7_A


title: Blastocyst_F6_C


title: T cells + HSPC Control3+CHIP1 multiplexed

description: Library name: SIGAD8


title: T cells + HSPC Control1+MDS1 multiplexed

description: Library name: SIGAD12


title: High AD sample 1, Sparse plaque ROI 2

description:
Library name: DSP-1001660037382-A-B03
Formalin Fixed Spatial transcriptomic sequencing


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

description:
Library name: DSP-1001660037382-A-B01
Formalin Fixed Spatial transcriptomic sequencing


title: Lung, controlled, ROI5

description: Library name: Controlled5


title: Lung, controlled, ROI4

description: Library name: Controlled4


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

description:
Library name: DSP-1001660037382-A-A12
Formalin Fixed Spatial transcriptomic sequencing


title: Lung, controlled, ROI3

description: Library name: Controlled3


title: Blastocyst_F6_B


title: Blastocyst_F6_A


title: Lung, controlled, ROI2

description: Library name: Controlled2


title: Blastocyst_F5_C


title: Stroma Control1+MDS1 multiplexed

description: Library name: SIGAD11


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

description:
Library name: DSP-1001660037382-A-A11
Formalin Fixed Spatial transcriptomic sequencing


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

description:
Library name: DSP-1001660037382-A-A10
Formalin Fixed Spatial transcriptomic sequencing


title: T cells + HSPC CHIP2+MDS4 multiplexed

description: Library name: SIGAD10


title: Blastocyst_F5_B


title: Lung, controlled, ROI6

description: Library name: Controlled6


title: Blastocyst_F5_A


title: V4_Control

city: Belmont

first: Evon

last: Poon

state: Surrey

address: 15, Cotswold Road, Godstone Road

department: Clinical Studies

institute: Institute of Cancer Research

data_processing:
cufflinks for couting expression levels
Assembly: mm10
Supplementary files format and content: txt file includes raw counts

source_name: neuroblastoma tumor

extract_protocol:
RNA was extracted using Rneasy Plus kit (Qiagen)
NEBNext directional rna-seq kit

treatment_protocol: in vivo dose-escalating treatment of temozolomide up to 13.5 mg/kg

value: neuroblastoma tumor

value: TH-MYCN ++ naive treatment

value: no treatment


title: High AD sample 1, Dense plaque ROI 7

description:
Library name: DSP-1001660037382-A-A09
Formalin Fixed Spatial transcriptomic sequencing

value: brain


title: Human T cells_TP53_WT5_rep12

city: München

first: Kieron

last: White

address: Genzentrum, Feodor-Lynen-Straße 25

department: Gene Center

institute: LMU

description: Library name: Human T cells_TP53_WT5

data_processing:
Quality assesment of the fastq data files was conducted using fastqc (v0.11.5), followed by poly A trimming using cutadapt (v4.1). Subsequent read filtering, mapping, and conducting were performed using the zUMIs pipeline (v.2.9.7), with reads mapped to the human genome (hg38). Bulk-fastq data was sample-demultiplexed using deML.
Assembly: hg38
Supplementary files format and content: raw counts for each sample
Supplementary files format and content: csv files

source_name: Bone Marrow

extract_protocol:
RNA isolation and library preparation were performed according to the Prime-seq protocol. RNA was isolated from cell lysates and cDNA synthesized using Maxima H Minus Reverse Transcriptase (Thermo Fisher Scientific, EP0753) with barcoded oligo-dT primers (E3V7NEXT) and a custom template-switching oligo. Libaries were prepared from 30 ng of pooled cDNA.
Libraries were prepared using the NEBNext Ultra II FS DNA Library Prep Kit for Illumina (New England Biolabs, E7805S) using a prime-seq specific custom ligation-adapter and dual-indexing with TruSeq i5 and Nextera i7 primers via PCR.

value: Bone Marrow

value: T cells


title: High AD sample 1, Dense plaque ROI 6

description:
Library name: DSP-1001660037382-A-A08
Formalin Fixed Spatial transcriptomic sequencing


title: Blastocyst_F4_C


title: High AD sample 1, Dense plaque ROI 5

description:
Library name: DSP-1001660037382-A-A07
Formalin Fixed Spatial transcriptomic sequencing


title: Blastocyst_F4_B


title: V1_Control


title: V3_Control


title: Human T cells_TP53_WT1_rep11

description: Library name: Human T cells_TP53_WT1


title: Human T cells_TP53_KD5_rep9

description: Library name: Human T cells_TP53_KD5


title: Human T cells_TP53_WT6_rep10

description: Library name: Human T cells_TP53_WT6


title: Blastocyst_F4_A


title: High AD sample 1, Dense plaque ROI 4

description:
Library name: DSP-1001660037382-A-A05
Formalin Fixed Spatial transcriptomic sequencing


title: High AD sample 1, Dense plaque ROI 3

description:
Library name: DSP-1001660037382-A-A04
Formalin Fixed Spatial transcriptomic sequencing


title: T8_Low

value: TH-MYCN ++ low resistant

value: dose-escalating treatment of temozolomide up to 13.5 mg/kg


title: Blastocyst_F3_C


title: Lung, controlled, ROI1

description: Library name: Controlled1


title: High AD sample 1, Dense plaque ROI 2

description:
Library name: DSP-1001660037382-A-A03
Formalin Fixed Spatial transcriptomic sequencing


title: Human T cells_TP53_KD6_rep7

description: Library name: Human T cells_TP53_KD6


title: Human T cells_TP53_KD4_rep8

description: Library name: Human T cells_TP53_KD4


title: High AD sample 1, Dense plaque ROI 1

description:
Library name: DSP-1001660037382-A-A02
Formalin Fixed Spatial transcriptomic sequencing


title: T4_Low


title: T6_Low


title: Stroma Control3+CHIP1 multiplexed

description: Library name: SIGAC12


title: Blastocyst_F3_A


title: Human T cells_TP53_KD2_rep6

description: Library name: Human T cells_TP53_KD2


title: T3_High

value: TH-MYCN ++ high resistant


title: No-Template Control 1

description:
Library name: DSP-1001660037382-A-A01
Formalin Fixed Spatial transcriptomic sequencing


title: Blastocyst_F2_C


title: V2_Control


title: T2_High


title: Human T cells_TP53_WT2_rep5

description: Library name: Human T cells_TP53_WT2


title: HIV-infected methamphetamine treated macrophages from donor coded JW100 biological replicate 3

city: Bronx

last: Weiselberg

state: NY

address: 1300 Morris Park Avenue, Forchheimer 727

institute: Albert Einstein College of Medicine

description: Library name: JW100HIVMA3

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean 2 reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools. featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: GRCh38/hg38
Supplementary files format and content: gene counts for each sample for each condition, in Excel format

source_name: PBMC

growth_protocol: PBMC or isolated monocytes were isolated and cultured in media containing DMEM, 10% fetal bovine serum, 5% human serum, 1% penicillin-streptomycin, 1% GlutaMax, 1% HEPES, and 10ng/ml macrophage colonoy stimulating factor. Media is changed every three days. After six days, cells are fully differentiated into macrophages.

extract_protocol:
Trizol extraction
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the directional library, it was ready after end repair, A tailing, adapter ligation, siz e selection, USER enzyme digestion , amplification, and purification. The library was checked with Qubit and real time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount. The clustering of the index coded samples was performed according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform and paired end reads were generated.

treatment_protocol: For HIV-infected samples, samples were infected after six days in culture with 20ng/mL HIVADA. On day three post-infection, cells began daily treatments with 50uM methamphetamine. Uninfetced cells began treatment at the same timepoint. Cells were treated daily for five days, after which RNA was extracted.

value: PBMC

value: Primary human

value: Macrophage

value: Infection with HIVADA and treated with 50uM methamphetamine for five days


title: Blastocyst_F2_B

value: oocyte or embryo


title: Human T cells_TP53_KD1_rep4

description: Library name: Human T cells_TP53_KD1


title: HIV-infected methamphetamine treated macrophages from donor coded JW100 biological replicate 2

description: Library name: JW100HIVMA2


title: T1_High


title: HIV-infected methamphetamine treated macrophages from donor coded JW100 biological replicate 1

description: Library name: JW100HIVMA1


title: Human T cells_TP53_KD3_rep3

description: Library name: Human T cells_TP53_KD3


title: HIV-infected untreated macrophages from donor coded JW100 biological replicate 3

description: Library name: JW100HIVUn3

value: Infection with HIVADA and untreated


title: Human T cells_TP53_WT4_rep2

description: Library name: Human T cells_TP53_WT4


title: T10_MYCN

data_processing:
Sequenced reads were aligned to mm10 referenece genome using bowtie2 with default parameters with the exception of '-k 1'
Peaks were called using MACS1.4.2 with  p-val =1e-9 and background datasets as described in characteristic: input
Assembly: mm10
Supplementary files format and content: Processed ChIP-Seq data files are in Bedgraph format

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared using Tn5 enzyme and amplified using 2x NEBNext HiFi master mix.
ChIPmentation (Schmidl et a., 2015; PMC4589892)

value: MYCN


title: Blastocyst_F1_B


title: Blastocyst_F1_C


title: T10_H3K27ac


title: Blastocyst_F3_B


title: Human T cells_TP53_WT3_rep1

description: Library name: Human T cells_TP53_WT3


title: Blastocyst_F1_A


title: T9_MYCN


title: RKI1 n=3 PRDM9 Knock Out_CMPD1

city: Camperdown

first: George

middle: Louis

last: Joun

state: NSW

address: John Hopkins Drive

department: School of Medical Sciences

country: Australia

institute: The University of Sydney

data_processing:
Dragen RNA pipeline
Assembly: Homo Sapiens HG19
Supplementary files format and content: Batch corrected rlog normalised counts. Batch correction was performed using RUV and a set of stably expressed genes. (https://academic.oup.com/gigascience/article/8/9/giz106/5570567)

source_name: Cell Line

growth_protocol: Stem Pro Neural Stem Cell Serum Free Media (ThermoFisher Scientific, Cat # A1286001) plated on 0.15% matrigel/PBS coated flasks. Incubation: 37 degrees Celsius, 5% CO2.

extract_protocol:
Qiagen RNeasy Minikit, manufacturer's protocol
Illumina mRNA stranded library preparation kit, manufacturer's protocol

treatment_protocol: RKI1 PRDM9 knock-out and NTC Glioblastoma stem cell lines were plated, and left to attach to the dish for 24 hours, at 15,000 cells/cm^2. The media was changed, according to treatment condition, with CMPD1 at 10µM for 72 hours, or time-matched untreated control. The experiment was performed with three biological replicates

value: Cell Line

value: Glioblastoma Stem Cell

value: PRDM9 Knock-out

value: 10µM CMPD1, 72 hours


title: HIV-infected untreated macrophages from donor coded JW100 biological replicate 1

description: Library name: JW100HIVUn1


title: T9_H3K27ac

value: neuroblastoma tumor


title: Morula_F10_C


title: RKI1 n=3 PRDM9 Knock Out_UT

value: Untreated


title: Methampehtamine treated uninfected macrophages from donor coded JW100 biological replicate 3

description: Library name: JW100UnMA3

value: Treated with 50uM methamphetamine for five days


title: T8_MYCN

value: TH-MYCN ++ low resistant


title: Morula_F10_B


title: RKI1 n=3 NTC_CMPD1

value: Parent


title: Morula_F10_A


title: Blastocyst_F2_A


title: RKI1 n=3 NTC_UT


title: Methampehtamine treated uninfected macrophages from donor coded JW100 biological replicate 1

description: Library name: JW100UnMA1


title: Uninfected untreated macrophages from donor coded JW100 biological replicate 2

description: Library name: JW100UnUn2


title: T6_MYCN

value: dose-escalating treatment of temozolomide up to 13.5 mg/kg


title: HIV-infected untreated macrophages from donor coded JW100 biological replicate 2

description: Library name: JW100HIVUn2

value: PBMC


title: RKI1 n=2 PRDM9 Knock Out_CMPD1


title: RKI1 n=2 PRDM9 Knock Out_UT


title: T6_H3K27ac


title: Uninfected untreated macrophages from donor coded JW100 biological replicate 1

description: Library name: JW100UnUn1

value: Primary human


title: T4_MYCN


title: Morula_F9_A


title: HIV-infected methamphetamine treated macrophages from donor coded JW98

description: Library name: JW98HIVMA

value: Macrophage


title: Morula_F9_B


title: RKI1 n=2 NTC_CMPD1

description:
Sample failed quality control (did not correctly cluster in PCA analysis) and was therefore not included in downstream analysis
Sample006


title: T4_H3K27ac


title: Morula_F8_C


title: T3_MYCN

value: TH-MYCN ++ high resistant


title: Morula_F8_B

value: oocyte or embryo


title: RKI1 n=1 PRDM9 Knock Out_CMPD1


title: T8_H3K27ac


title: RKI1 n=1 PRDM9 Knock Out_ UT


title: Methampehtamine treated uninfected macrophages from donor coded JW100 biological replicate 2

description: Library name: JW100UnMA2


title: Morula_F8_A


title: Uninfected untreated macrophages from donor coded JW98

description: Library name: JW98UnUn


title: Morula_F7_C


title: T2_MYCN


title: Morula_F9_C


title: RKI1 n=1 NTC_UT


title: HIV-infected methamphetamine treated macrophages from donor coded JW84

description: Library name: JW84HIVMA

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean 2 reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools. featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Supplementary files format and content: GRCh38/hg38
Supplementary files format and content: gene counts for each sample for each condition, in Excel format

extract_protocol:
For HIV-infected samples, samples were infected after six days in culture with 20ng/mL HIVADA. On day three post-infection, cells began daily treatments with 50uM methamphetamine. Uninfetced cells began treatment at the same timepoint. Cells were treated daily for five days, after which RNA was extracted.
Trizol extraction
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the directional library, it was ready after end repair, A tailing, adapter ligation, siz e selection, USER enzyme digestion , amplification, and purification. The library was checked with Qubit and real time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount. The clustering of the index coded samples was performed according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform and paired end reads were generated.

treatment_protocol: PBMC or isolated monocytes were isolated and cultured in media containing DMEM, 10% fetal bovine serum, 5% human serum, 1% penicillin-streptomycin, 1% GlutaMax, 1% HEPES, and 10ng/ml macrophage colonoy stimulating factor. Media is changed every three days. After six days, cells are fully differentiated into macrophages.

value: Infection with HIVADA and treated with 50uM methamphetamine for five days


title: HIV-infected untreated macrophages from donor coded JW84

description: Library name: JW84HIVUntx

value: Infection with HIVADA and untreated


title: PRDM9 (1) C10 n=2 H3K4me3 ChIP

description: H3K4me3 ChIP

data_processing:
Dragen BCL Convert
Assembly: Homo Sapiens hg38
Supplementary files format and content: bigWig

extract_protocol:
After harvesting, cell pellets were cross-linked with 0.75% PFA/PBS for 10 min, quenched in 1 M glycine, washed in PBS, and cell pellets snap frozen in liquid nitrogen. Cells were lysed in ChIP lysis buffer (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA pH 8, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS, Protease Inhibitor Cocktail) and sonicated to shear chromatin to approximately 300bp DNA fragment size.
Input and ChIP fragments were quantified using QUBIT dsDNA kit and 25ng DNA fragments was subjected to library preparation using NEBNext Ultra II DNA library preparation kit for Illumina.

treatment_protocol: RKI1 PRDM9 knock-out and NTC Glioblastoma stem cell lines were plated, and left to attach to the dish for 24 hours, at 15,000 cells/cm^2. The media was changed, according to treatment condition, with CMPD1 at 10uM for 72 hours, or time-matched untreated control. The experiment was performed with two biological replicates


title: Morula_F7_A


title: RKI1 n=2 NTC_UT

value: Cell Line


title: TL360_T1_MYCN

value: MYCN


title: Uninfected untreated macrophages from donor coded JW84

description: Library name: JW84UnUntx


title: HIV-infected untreated macrophages from donor coded JW98

description: Library name: JW98HIVUn


title: Morula_F6_C


title: Morula_F7_B


title: Methampehtamine treated uninfected macrophages from donor coded JW84

description: Library name: JW84UnMA


title: Morula_F6_B


title: PRDM9 (1) UT n=2 H3K4me3 ChIP

description: H3K4me3 ChIP

value: Glioblastoma Stem Cell

value: PRDM9 Knock-out


title: V8_MYCN

value: neuroblastoma tumor

value: TH-MYCN ++ naive treatment

value: no treatment


title: TL359_T1_H3K27ac


title: HIV-infected methamphetamine treated macrophages from donor coded JW82

description: Library name: JW82HIVMA


title: Methampehtamine treated uninfected macrophages from donor coded JW98

description: Library name: JW98UnMA

value: Treated with 50uM methamphetamine for five days


title: NTC C10 n=2 H3K4me3 ChIP

description: H3K4me3 ChIP

value: Parent

value: 10µM CMPD1, 72 hours


title: T3_H3K27ac

value: dose-escalating treatment of temozolomide up to 13.5 mg/kg


title: Morula_F6_A


title: HIV-infected untreated macrophages from donor coded JW82

description: Library name: JW82HIVUntx

value: PBMC

value: Primary human


title: V8_H3K27ac


title: NTC UT n=2 H3K4me3 ChIP

description: H3K4me3 ChIP_This sample was excluded from downstream analysis.

value: Untreated


title: RKI1 n=1 NTC_CMPD1


title: V7_MYCN


title: Methampehtamine treated uninfected macrophages from donor coded JW82

description: Library name: JW82UnMA

value: Macrophage


title: Morula_F5_C

value: oocyte or embryo


title: PRDM9 (1) C10 n=1 H3K4me3 ChIP

description: H3K4me3 ChIP


title: T2_H3K27ac

value: TH-MYCN ++ high resistant


title: Uninfected untreated macrophages from donor coded JW82

description: Library name: JW82UnUntx


title: V7_H3K27ac


title: PRDM9 (1) UT n=1 H3K4me3 ChIP

description: H3K4me3 ChIP


title: Morula_F5_B


title: Morula_F5_A


title: V6_MYCN


title: NTC C10 n=1 H3K4me3 ChIP

description: H3K4me3 ChIP


title: HIV-infected methamphetamine treated macrophages from donor coded JW81

description: Library name: JW81HIVMA

value: Infection with HIVADA and treated with 50uM methamphetamine for five days


title: HIV-infected untreated macrophages from donor coded JW81

description: Library name: JW81HIVUntx

value: Infection with HIVADA and untreated


title: Methampehtamine treated uninfected macrophages from donor coded JW81

description: Library name: JW81UnMA


title: PRDM9 (1) C10 n=2 INPUT

description: Input

value: Glioblastoma Stem Cell


title: Morula_F4_B


title: Morula_F4_C


title: NTC UT n=1 H3K4me3 ChIP

description: H3K4me3 ChIP


title: PRDM9 (1) UT n=2 INPUT

description: Input

value: PRDM9 Knock-out


title: V6_H3K27ac

value: neuroblastoma tumor


title: V5_H3K27ac

value: TH-MYCN ++ naive treatment


title: Morula_F4_A


title: V5_MYCN

value: no treatment

value: MYCN


title: Uninfected untreated macrophages from donor coded JW81

description: Library name: JW81UnUntx


title: Morula_F3_C


title: NTC C10 n=2 INPUT

description: Input

value: Parent


title: Morula_F3_B


title: NTC UT n=2 INPUT

description: Input


title: YS_p2_run3_NB70

city: Manchester

first: Georges

last: Lacaud

state: England

address: Wilmslow Raod

department: Stem Cell Biology

institute: Cancer Research UK Manchester Institute

description: Library name: YS_p2_run3_NB70_GL69_376_WN-S6-2_G17_YS_E9-0_HE_Runx1_S376

data_processing:
Nanopore sequencing data were basecalled using Dorado (v0.9.1) using the high-accuracy model (dna_r10.4.1_e8.2_400bps_hac@v5.0.0). Raw reads were trimmed for SMARTseq adapters using bbduk.sh (v39.08). Chimeric reads were filtered from the data using YACRD (v1.0.0) and porechop (v0.2.4). Cleaned reads were aligned to GENCODE transcripts (Release 37) using Minimap2 (v2.26), retaining a maximum of 10 alignments per read. Alignments were quantified using Nanocount (v1.0.0.post6). Abundance files were read into R (v4.3.0) filtered for low library size samples using findOutliers (scuttle v1.10.3; type = "lower", nmads = 1) and normalised using DESeq2 (v1.40.2). Estimated and normalised counts were subject to analysis using IsoformSwitchAnalyzeR and SplicingFactory as previously described.
Assembly: GENCODE transcripts (Release 37)
Supplementary files format and content: nanoCount_trans_Estcount.txt; nanoCount Estimated counts as TSV
Supplementary files format and content: nanoCount_trans_tpm.txt; nanoCount TPM as TSV

source_name: mouse embryo yolk sac

growth_protocol: fresh samples (AGM and Yolksac) were harvested from mouse embryos and directly processed for sequencing

extract_protocol:
Single cells were FACS sorted into wells of a 384-well plate containing lysis buffer and snap-frozen.
10ng full-length purified amplified cDNA from a miniaturised Smart-seq2 cDNA was purified using a 0.7x volume of AMPure XP reagent (Beckman Coulter). Purified amplification product was quantified by Qubit (ThermoFisher) and sized / quality checked by Fragment Analyzer (Agilent). 200fmol was used as input for the Ligation sequencing amplicons - Native Barcoding Kit 24 V14 (SQK-NBD114.24) protocol (revision H) (Oxford Nanopore). Sequencing was performed on a PromethION P2 Solo (Oxford Nanopore) using flow cell FLO-PRO114M

treatment_protocol: No treatments were performed. Cells were directly harvested from Embryos and FACS sorted into lyses buffer for sequence library preparation.

value: mouse embryo yolk sac

value: primary material

value: early YS hematopoietic progenitor (EMP skewed)


title: Morula_F3_A


title: YS_p2_run3_NB73

description: Library name: YS_p2_run3_NB73_GL69_644_WN-S6-3_B3_YS_E9-5_HE_Runx1_S644


title: YS_p2_run3_NB48

description: Library name: YS_p2_run3_NB48_GL69_540_WN-S6-2_G13_YS_E9-0_HE_Runx1_S540


title: osteogenic USCs biol rep 3

city: Erlangen

first: Steffen

last: Uebe

address: Kussmaulallee 4

department: Humangenetisches Institut

institute: Uniklinikum Erlangen

description: Library name: OsteoLAMA5_WT_3

data_processing:
Raw data was converted into reads and demultiplexed using Illumina Dragen Software (v. 3.8.4).
Unwanted RNA was filtered from the reads using bwa mem (version 0.7.17-r1188, arXiv:1303.3997) in combination with samtools (version 1.1770) and converted back into fastq format using the SamToFastq tool from GATK (version 4.2.1.071).
Reads from each sequencing lane were aligned individually to the hg38 reference genome with Ensembl (release 11072) gene annotations using STAR (version 2.7.10a73).
For each sample, resulting alignments were combined using the MergeSamFiles command from Picard (version 2.25.4, http://broadinstitute.github.io/picard/). Gene quantification in form of a count matrix was generated using featureCounts (version 2.0.174) and Ensembl gene annotations corresponding to those of the alignment reference. Alignment and quantification levels were used for quality assessment.
Assembly: hg38
Supplementary files format and content: comma separated value file containing raw counts for each sample

source_name: urine

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

extract_protocol:
RNA was extracted from USC samples with RNeasy Mini Kit (Qiagen)with DNAse digestion, according to manufacturer.
A cDNA library was generated for each sample using the Illumina stranded mRNA kit.

treatment_protocol: Chondrogenic differentiation was induced with the StemPro Chondrogenesis Kit (Gibco). Osteogenic induction was facilitated with an osteogenic medium described by zhang et al (PMID: 32015680). Differentation lasted for two weeks with media change three times per week.

value: urine

value: Urine stem cells

value: wildtype

value: osteogenic differentation


title: osteogenic USCs biol rep 1

description: Library name: OsteoLAMA5_WT_1


title: YS_p2_run3_NB41

description: Library name: YS_p2_run3_NB41_GL69_584_WN-S6-2_I6_YS_E9-5_HE_Runx1_S584


title: PRDM9 (1) UT n=1 INPUT

description: Input

value: Untreated


title: chondrogenic USCs biol rep 3

description: Library name: CHONDR_WT_3

value: chondrogenic differentation


title: Morula_F2_B

value: oocyte or embryo


title: PRDM9 (1) C10 n=1 INPUT

description: Input

value: Glioblastoma Stem Cell

value: 10µM CMPD1, 72 hours


title: YS_p2_run3_NB25

description: Library name: YS_p2_run3_NB25_GL69_462_WN-S6-2_C3_YS_E9-5_HE_Runx1_S462


title: NTC C10 n=1 INPUT

description: Input


title: Morula_F2_A


title: chondrogenic USCs biol rep 1

description: Library name: CHONDR_WT_1


title: NTC UT n=1 INPUT

description: Input


title: Morula_F1_C


title: USCs biol rep 3

description: Library name: WT_3


title: YS_p2_run2_NB68

description: Library name: YS_p2_run2_NB68_GL69_514_WN-S6-2_F13_YS_E9-0_HE_Runx1_S514


title: chondrogenic USCs biol rep 2

description: Library name: CHONDR_WT_2


title: Morula_F1_B


title: YS_p2_run3_NB15

description: Library name: YS_p2_run3_NB15_GL69_522_WN-S6-2_O5_YS_E9-5_HE_Runx1_S522


title: CMPD1+MRK-740_n=2_H3K4me3

growth_protocol: Stem Pro Neural Stem Cell Serum Free Media (ThermoFisher Scientific).

extract_protocol:
After harvesting, cell pellets were cross-linked with 0.75% PFA/PBS for 10 min, quenched in 1 M glycine, washed in PBS, and cell pellets snap frozen in liquid nitrogen. Cells were lysed in ChIP lysis buffer (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA pH 8, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS, Protease Inhibitor Cocktail) and sonicated to shear chromatin to approximately 300bp DNA fragment size.
Input and ChIP fragments were quantified using QUBIT dsDNA kit and 5 ng DNA fragments was subjected to library preparation using NEBNext Ultra II DNA library preparation kit for Illumina.

value: WT

value: CMPD1 10uM + MRK-740 3uM, 72 hours


title: USCs biol rep 2

description: Library name: WT_2


title: CMPD1_n=2_H3K4me3

value: CMPD1 10uM, 72 hours


title: osteogenic USCs biol rep 2

description: Library name: OsteoLAMA5_WT_2


title: Morula_F1_A


title: YS_p2_run2_NB47

description: Library name: YS_p2_run2_NB47_GL69_177_WN-S6-4_C9_YS_E10-5_HE_Runx1_S177


title: USCs biol rep 1

description: Library name: WT_1


title: 8C_F10_C


title: Morula_F2_C


title: CMPD1_n=2_Input

value: none (input)


title: YS_p2_run3_NB17

description: Library name: YS_p2_run3_NB17_GL69_608_WN-S6-2_F19_YS_E9-0_HE_Runx1_S608


title: 8C_F10_B


title: 8C_F10_A


title: MRK-740_n=2_H3K4me3

value: MRK-740 3uM, 72 hours


title: YS_p2_run2_NB16

description: Library name: YS_p2_run2_NB16_GL69_0901_WN-S6-3_E20_YS_E10-5_HE_Runx1_S133

value: mouse embryo yolk sac


title: YS_p2_run2_NB01

description: Library name: YS_p2_run2_NB01_GL69_679_WN-S6-2_N8_YS_E9-5_HE_Runx1_S679

value: primary material


title: Parent_n=2_H3K4me3


title: FPW1_Parent_n=3

description:
Library name: Sample 3
In the counts file, Parent = Untreated, DTP = 14 days CMPD1 25uM

data_processing:
FASTQ reads were aligned, genes were counted, using DESeq2
Assembly: hg38
Supplementary files format and content: Contains the raw counts for each gene, within each samples

growth_protocol: FPW1 Glioblastoma stem cells were grown in Stem Pro Neural Stem Cell Serum Free Media (ThermoFisher Scientific) on matrigel coated flasks (0.15% Matrigel/PBS).

extract_protocol:
RNA extraction using Qiagen Rneasy Minikit
NEBNext® UltraTM RNALibrary Prep Kit for Illumina (NEB, USA) following manufacturers instructions

treatment_protocol: 24 hours after plating, cells were collected (Parent, untreated) or treated for 14 days with CMPD1 25uM). Media and drug was replaced twice per week. At the end of the treatment timecourse, samples were harvested, RNA extracted, and subject to library preperation.


title: Parent_n=2_Input


title: CMPD1+MRK-740_n=2_Input


title: FPW1_Parent_n=2

description:
Library name: Sample 2
In the counts file, Parent = Untreated, DTP = 14 days CMPD1 25uM


title: FPW1_DTP_n=1

description:
Library name: Sample 4
In the counts file, Parent = Untreated, DTP = 14 days CMPD1 25uM

value: CMPD1 25uM, 14 days


title: YS_p2_run1_NB72

description: Library name: YS_p2_run1_NB72_GL69_288_WN-S6-4_A11_YS_E10-5_HE_Runx1_S288

value: early YS hematopoietic progenitor (EMP skewed)


title: 8C_F9_A


title: YS_p2_run2_NB65

description: Library name: YS_p2_run2_NB65_GL69_695_WN-S6-1_L7_YS_E10-5_HE_Runx1_S695


title: FPW1_Parent_n=1

description:
Library name: Sample 1
In the counts file, Parent = Untreated, DTP = 14 days CMPD1 25uM


title: 8C_F8_C


title: CMPD1+MRK-740_n=1_H3K4me3


title: YS_p2_run1_NB49

description: Library name: YS_p2_run1_NB49_GL69_0905_WN-S6-4_I07_YS_E10-5_HE_Runx1_S137


title: YS_p2_run1_NB58

description: Library name: YS_p2_run1_NB58_GL69_035_WN-S6-2_G12_YS_E9-0_HE_Runx1_S35


title: CMPD1+MRK-740_n=1_Input


title: YS_p2_run2_NB23

description: Library name: YS_p2_run2_NB23_GL69_036_WN-S6-2_C6_YS_E9-5_HE_Gfi1_S36


title: FPW1_DTP_n=3

description:
Library name: Sample 6
In the counts file, Parent = Untreated, DTP = 14 days CMPD1 25uM


title: MCF7-COX2, H2O2, 48hr, Rep3

city: Brandon

first: Mousumi

last: Majumder

state: Manitoba

address: 270 18th Street

department: Biology

country: Canada

institute: Brandon University

description: Library name: Sample 36

data_processing:
In Linux, raw '.fastq' files were trimmed with Trimmomatic (v0.39). Trimmed files were aligned with STAR (v2.7.11b) (Human reference genome GRCh38.p14) sorted by coordinates. Alignments were counted with HTSeq (v2.0.8).
Assembly: GRCh38.p14
Supplementary files format and content: Tab-delimited text file containing raw counts for each sample (HTSeq)

source_name: Breast

growth_protocol: Cells were cultured in Roswell Park Memorial Institute (RPMI)-1640 media, supplemented with 10% fetal bovine serum and 1% Pen-Strep. Cells were incubated at 37˚C with 5% CO2. Transfected cells were maintained with 200ng/mL Geneticin (Cat. No: G418, Biobasic).

extract_protocol:
Samples were homogenized in Qiazol before shipment on dry ice to the third party sequencing service provider (Centre d'expertise et de services Génome Québec (CES) (McGill University, Montréal, Canada)). RNA extraction and QC checks were outsourced to a third party (Centre d'expertise et de services Génome Québec (CES) (McGill University, Montréal, Canada)). All samples passed QC with RNA Integrity Numbers (RINs) of 8.5 or higher.
PolyA-Enriched

treatment_protocol: Cells treated with  either H2O2 (216uM), DOX (0.8uM) or DMSO for 48 hours. Three biological replicates performed per cell line and condition.

value: Breast

value: Adenocarcinoma


title: YS_p2_run2_NB22

description: Library name: YS_p2_run2_NB22_GL69_747_WN-S6-2_F5_YS_E9-5_HE_Runx1_S747


title: FPW1_DTP_n=2

description:
Library name: Sample 5
In the counts file, Parent = Untreated, DTP = 14 days CMPD1 25uM


title: 8C_F8_B


title: MRK-740_n=2_Input


title: CMPD1_n=1_H3K4me3


title: MCF7-COX2, H2O2, 48hr, Rep2

description: Library name: Sample 35


title: YS_p2_run1_NB36

description: Library name: YS_p2_run1_NB36_GL69_270_WN-S6-2_B11_YS_E9-5_HE_Runx1_S270


title: 8C_F9_C


title: 8C_F9_B


title: 8C_F8_A


title: MCF7-COX2, H2O2, 48hr, Rep1

description: Library name: Sample 34


title: CMPD1_n=1_Input


title: MCF7-miR655, H2O2, 48hr, Rep3

description: Library name: Sample 33


title: YS_p2_run1_NB19

description: Library name: YS_p2_run1_NB19_GL69_323_WN-S6-2_F10_YS_E9-5_HE_Runx1_S323


title: 8C_F7_C


title: MRK-740_n=1_H3K4me3


title: 8C_F7_B


title: MRK-740_n=1_Input


title: MCF7-miR655, H2O2, 48hr, Rep2

description: Library name: Sample 32


title: YS_p2_run1_NB04

description: Library name: YS_p2_run1_NB04_GL69_1066_WN-S6-4_I09_YS_E10-5_HE_Gfi1_S298


title: 8C_F7_A


title: 8C_F6_C


title: Parent_n=1_H3K4me3


title: YS_p1_run3_NB69

description: Library name: YS_p1_run3_NB69_GL69_1123_WN-S7-1_E05_YS_E9-5_HE_Gfi1_S32

value: early YS hematopoietic progenitor (LMP skewed)


title: MCF7-miR655, H2O2, 48hr, Rep1

description: Library name: Sample 31


title: Parent_n=1_Input

value: Untreated


title: MCF7-miR526b, H2O2, 48hr, Rep3

description: Library name: Sample 30


title: CMPD1+MRK-740-n=3

data_processing:
Dragen RNA pipeline
Assembly: Homo Sapiens HG38
Supplementary files format and content: Raw Counts


title: CMPD1+MRK-740_n=2


title: 8C_F6_B


title: MCF7-miR526b, H2O2, 48hr, Rep1

description: Library name: Sample 28


title: YS_p1_run3_NB52

description: Library name: YS_p1_run3_NB52_GL69_646_WN-S6-2_C8_YS_E9-5_HE_Gfi1_S646


title: 8C_F5_C


title: 8C_F6_A


title: MCF7-miR526b, H2O2, 48hr, Rep2

description: Library name: Sample 29


title: YS_p1_run3_NB67

description: Library name: YS_p1_run3_NB67_GL69_1038_WN-S6-4_M06_YS_E10-5_HE_Runx1_S270


title: YS_p2_run1_NB16

description: Library name: YS_p2_run1_NB16_GL69_1083_WN-S6-3_J13_YS_E10-5_HE_Runx1_S315


title: MCF7, H2O2, 48hr, Rep3

description: Library name: Sample 27


title: 8C_F5_B


title: CMPD1_n=3


title: MCF7, H2O2, 48hr, Rep2

description: Library name: Sample 26


title: 8C_F5_A


title: CMPD1+MRK-740_n=1


title: CMPD1_n=2


title: YS_p1_run2_NB67

description: Library name: YS_p1_run2_NB67_GL69_1049_WN-S6-4_G12_YS_E10-5_HE_Gfi1_S281


title: MCF7, H2O2, 48hr, Rep1

description: Library name: Sample 25


title: YS_p1_run3_NB10

description: Library name: YS_p1_run3_NB10_GL69_072_WN-S6-4_K9_YS_E10-5_HE_Runx1_S72


title: YS_p1_run3_NB34

description: Library name: YS_p1_run3_NB34_GL69_214_WN-S6-1_M7_YS_E10-5_HE_Gfi1_S214


title: 8C_F4_C


title: CMPD1_n=1


title: YS_p1_run2_NB66

description: Library name: YS_p1_run2_NB66_GL69_084_WN-S6-3_C18_YS_E10-5_HE_Runx1_S84


title: PSP20-HS3

city: London

first: Tallulah

middle: Suzanne

last: Andrews

state: Ontario

address: 1151 Richmond St.

institute: University of Western Ontario

description:
Library name: 22-11-GL_D1
10X Visium FFPE Chemistry (Human Probe Set v2.0)

data_processing:
Reads were aligned to target probeset (Visium_Human_Transcriptome_Probe_Set_v2.0_GRCh38-2020-A, this file in included in the processed data as "probe_set.tsv") using spaceranger v2.0.1 (martian v4.0.10), reference genome used was 2020-GRCh38 from the 10X website.
Spots were filtered to remove low quality spots (<100 genes/spot) and edges of certain slides were excluded to do marginal quality (<200 genes/spot).
Data was clustered using the standard Seurat clustering pipeline: sctransform, 20 PCs, 20 sNN graph, Louvain clustering at various resolutions
Data was deconvovled using DWLS, and the Pineda et al. (2024) Cell data as reference.
Cortical layers were manually annotated.
Assembly: GRCh38
Supplementary files format and content: Processed files include raw and filtered spot count matrices (.mtx + barcodes.tsv + features.tsv). Complete compressed "spatial" directories that include spot-coordinates and low/hi resolution image files, and scaling files. Final metadata for the filtered spots including layer annotations, raw clustering results, and deconvolution results
Supplementary files format and content: a README.txt file that includes a description and explanation of all columns in the metadata file.
Library strategy: Spatial Transcriptomics

source_name: brain:primary motor cortex

growth_protocol: NA - clinical samples

extract_protocol:
Primary motor cortex FFPE tissue blocks from 4 PSP patients with DV200 > 50% were selected for sectioning. Appropriate-sized sections were placed within the frames of capture areas on the Visium Spatial Gene Expression Slide (PN-1000188, 10x Genomics) with one section in each capture area (6.5 × 6.5 mm). Tissues were deparaffinized, stained and decross-linked, followed by probe hybridization, ligation, release, and extension. Visium spatial gene expression FFPE libraries were constructed with a Visium Human Transcriptome Probe kit (PN-1000363, 10x Genomics) and Visium FFPE Reagent kit (PN-1000361, 10x Genomics) following the manufacturer’s guidance and sequenced on the Illumina NovaSeq 6000 platforms to achieve a depth of at least 25,000 mean read pairs.
10X Visium FFPE Probe-based library construction

value: brain:primary motor cortex

tag: disease

value: PSP (high seeder)


title: 8C_F4_B

city: Gainesville

institute: University of Florida

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

extract_protocol:
Ten equal fractions were recovered and subjected to RNA isolation by Trizol reagent (Sigma).
The RNA-seq libraries were generated from individual fractions by using the Smart-seq2 v4 kit with minor modification from manufacturer’s instructions. Briefly, individual cells were lysed, and mRNA was captured and amplified with the Smart-seq2 v4 kit (Clontech). After AMPure XP beads purification, amplified RNAs were quality checked by using Agilent High Sensitivity D5000 kit (Agilent Technologies). High-quality amplified RNAs were subject to library preparation (Nextera XT DNA Library Preparation Kit; Illumina) and multiplexed by Nextera XT Indexes (Illumina). The concentration of sequencing libraries was determined by using Qubit dsDNA HS Assay Kit (Life Technologies) and KAPA Library Quantification Kits (KAPA Biosystems). The size of sequencing libraries was determined by means of High Sensitivity D5000 Assay in at Tapestation 4200 system (Agilent). Pooled indexed libraries were then sequenced on the Illumina HiSeq X platform with 150-bp paired-end reads.

value: oocyte or embryo


title: PSP23-HS5

description:
Library name: 21-11-GL_D1
10X Visium FFPE Chemistry (Human Probe Set v2.0)


title: YS_p1_run3_NB50

description: Library name: YS_p1_run3_NB50_GL69_0903_WN-S6-3_K18_YS_E10-5_HE_Runx1_S135


title: YS_p1_run2_NB58

description: Library name: YS_p1_run2_NB58_GL69_116_WN-S6-4_E7_YS_E10-5_HE_Runx1_S116


title: MRK-740_n=3

value: Glioblastoma Stem Cell


title: 8C_F4_A


title: YS_p1_run2_NB38

description: Library name: YS_p1_run2_NB38_GL69_232_WN-S6-4_G7_YS_E10-5_HE_Runx1_S232


title: YS_p1_run2_NB56

description: Library name: YS_p1_run2_NB56_GL69_0906_WN-S6-3_E22_YS_E10-5_HE_Runx1_S138


title: MRK-740_n=2

value: WT


title: 8C_F3_C


title: MRK-740_n=1


title: PSP25-LS5

description:
Library name: 20-13-GR_A1
10X Visium FFPE Chemistry (Human Probe Set v2.0)

value: PSP (low seeder)


title: PSP17-LS4

description:
Library name: 19-01-GL_A1
10X Visium FFPE Chemistry (Human Probe Set v2.0)


title: 8C_F3_B


title: MCF7-COX2, DOX, 48hr, Rep3

description: Library name: Sample 24

treatment_protocol: Cells treated with either doxorubicn (0.8uM) or DMSO for 48 hours. Three biological replicates performed per cell line and condition.

value: DOX, 48hr


title: Parent_n=3


title: 8C_F3_A


title: YS_p1_run2_NB36

description: Library name: YS_p1_run2_NB36_GL69_159_WN-S6-3_B14_YS_E10-5_HE_Runx1_S159


title: Parent_n=2