title: Region_12dpn_1


title: V1_ki67+myc+_ROI5_S4_Vehicle

status: Public on Jul 08 2026

type: SRA

city: Umeå

first: Lixiao

last: Wang

state: Sverige

address: Medicinsk biovetenskap, M21, Försörjningsvägen 1

department: Department of Medical Biosciences

country: Sweden

institute: Umeå University

description:
Library name: DSP-1001660037306-B-G07
Tumor V1, Slide S4, ROI 5, Segment ki67+myc+, Replicate V1_ki67+myc+. Raji xenograft in NSG mouse, NanoString GeoMx DSP WTA v1.0.

library_source: transcriptomic

data_processing:
FASTQ files were converted to DCC count files via NanoString GeoMx NGS Pipeline. DCC files loaded into R using GeomxTools (Bioconductor). Segment QC: min 1,000 reads, 75% alignment, 50% saturation, 20 nuclei, 1,000 um2 area. Probe QC: ratio >0.1, Grubbs outlier removal. Aggregated to gene-level by geometric mean.
Counts imported into standR (Bioconductor) as SpatialExperiment. Low-expression genes filtered (sample_fraction=0.9, min_count=5). TMM normalization (edgeR). Batch effects assessed by PCA.
DE analysis: limma-voom with duplicateCorrelation (tumor as block). Treatment comparisons per cell population. Gene set analysis: limma::camera for MYC targets, ribosomal, cell cycle, apoptosis pathways. Significance: BH-adjusted P < 0.05 and |log2FC| > 0.5.
R (v4.4.2), GeomxTools, standR, limma, edgeR, SpatialExperiment (Bioconductor).
Assembly: hg38 (GRCh38)
Supplementary files format and content: DCC files: per-AOI probe-level count files from NanoString GeoMx NGS Pipeline, containing raw/trimmed/stitched/aligned read counts and per-probe expression values
Supplementary files format and content: standR_counts.txt: tab-delimited gene-level raw count matrix (genes x 92 AOIs)
Library strategy: Spatial Transcriptomics

molecule: total RNA

organism: Homo sapiens

source_name: Raji Burkitt lymphoma xenograft

growth_protocol: Raji Burkitt lymphoma cells (ATCC CCL-86, p53 R213Q) were harvested during logarithmic growth, washed, and resuspended in serum-free media. A total of 5x10^6 cells in 200 uL of a 1:1 mixture of Matrigel and medium were injected subcutaneously into the right flank of 6-8-week-old NSG mice (Charles River). Tumors grew to approximately 100-150 mm3 before randomization.

extract_protocol:
FFPE tumor sections were processed on the NanoString GeoMx Digital Spatial Profiler (DSP) at the Genomic Medicine Sweden Center North / Clinical Genomics Umea. Sections were stained with fluorescent antibodies against Ki67 and c-Myc. Within each ROI, cells were segmented into four populations: Ki67+MYC+, Ki67-MYC+, Ki67-MYC-, and Ki67+MYC-. UV-cleavable oligonucleotide tags from each segment (AOI) were collected for library preparation.
Libraries were prepared using the NanoString GeoMx NGS Library Preparation Kit per manufacturer protocol. Human NGS Whole Transcriptome Atlas (WTA v1.0) panel (~18,000 genes). Each AOI received a unique indexing barcode. 92 AOIs across 10 tumors on four slides (S1-S4), each slide containing both conditions.

treatment_protocol: Mice were randomized into milademetan-treated (n=5) and vehicle control (n=5) groups. Milademetan (20 mg/kg) or vehicle was administered daily by oral gavage for 15 days. Tumors were harvested, formalin-fixed, and paraffin-embedded (FFPE).

tag: tissue

value: Raji Burkitt lymphoma xenograft

tag: cell line

value: Raji (ATCC CCL-86)

tag: cell type

tag: genotype

tag: treatment

value: Vehicle

tag: batch


title: V4_ki67+myc+_ROI14_S3_Vehicle

description:
Library name: DSP-1001660037306-B-F12
Tumor V4, Slide S3, ROI 14, Segment ki67+myc+, Replicate V4_ki67+myc+. Raji xenograft in NSG mouse, NanoString GeoMx DSP WTA v1.0.


title: Stool-8w-Apc-5-757

city: Taipei

first: Linda

last: Yu

address: 1 Jen-Ai Rd. Sec. 1

country: Taiwan

institute: National Taiwan University

library_source: genomic

data_processing:
The library was loaded onto the instrument with Sequel Sequencing Kit 2.1 (4 rxn) (Part Number PB 101-310-500) and a Sequel™ SMRT® Cell 1M v2 Tray (4 cells) (Part Number PB101-008-000) for sequencing.
Assembly: The training method of the QIIME2 classifier follows these steps: - Extract all the read datafrom a reference database, in our report, SILVA version 138 with 99% similarity was used.
Supplementary files format and content: File name = abs-abund-table-7 (all 90 samples); Format = excel (.xlsx); Content = raw counts of sequencing reads for the bacteria strain
Supplementary files format and content: File name = rel-table-7 (all 90 samples); Format = excel (.xlsx); Content=relative abundance of sequencing reads for the bacteria strain

molecule: genomic DNA

organism: Mus musculus

source_name: Feces

extract_protocol:
Fecalpellets werecollected asepticallyand placed in sterile eppendorf. Immediately freezing stool in liquid nitrogen (LN) and store at -80°C. Extract stool bacterial DNA followed by QIAamp Fast DNA Stool Kit protocol.
For the PacBio library construction and sequencing, 16S rRNA was amplified by using primer set 27F: AGRGTTYGATYMTGGCTCAG and 1492R: RGYTACCTTGTTACGACTT followed by purification via binding to pre-washed AMPure PB beads (Part Number PB100-265-900)
16S ribosomal RNA (rRNA) gene sequencing

value: Feces

value: ApcMin

value: Untreated

tag: time

value: 8 weeks old


title: V4_ki67+myc+_ROI6_S3_Vehicle

description:
Library name: DSP-1001660037306-B-E12
Tumor V4, Slide S3, ROI 6, Segment ki67+myc+, Replicate V4_ki67+myc+. Raji xenograft in NSG mouse, NanoString GeoMx DSP WTA v1.0.


title: Region_8dpn_2

type: RNA

city: Callaghan

first: M. Fairuz

last: B. Jamaluddin

state: NSW

address: University drive

country: Australia

institute: University of Newcastle

hyb_protocol: A custom Xenium gene expression probe panel (10x Genomics) was hybridized to FFPE tissue sections following the Xenium In Situ Gene Expression FFPE user guide. Hybridization, washing, and signal amplification steps were performed according to the manufacturer’s protocol.

scan_protocol: Slides were imaged on the Xenium Analyzer (10x Genomics) using default acquisition settings for FFPE samples as specified by the Xenium In Situ Gene Expression workflow. Fluorescence imaging was performed across multiple channels to detect hybridized transcripts and morphology.

data_processing: Raw imaging data were processed using the Xenium analysis pipeline (10x Genomics). Transcript detection, cell segmentation, and transcript assignment to cells were performed using default parameters unless otherwise stated. Gene by cell count matrices and spatial coordinate files were generated for downstream analysis.

source_name: Uterus

extract_protocol: FFPE tissue blocks were sectioned and mounted onto Xenium slides according to the Xenium In Situ Gene Expression FFPE protocol (10x Genomics). Sections were baked, deparaffinized, rehydrated, and subjected to target retrieval and protease treatment following the manufacturer’s instructions prior to probe hybridization.

value: Uterus

tag: tissue preservation method

value: 4% PFA


title: DMSO control for ATRA, sorted for CD11b, Replicate 1

city: Solna

first: Bernhard

last: Schmierer

state: (optional)

address: Biomedicum 9B, Solnavagen 9

department: Medical Biochemistry and Biophysics

institute: Karolinska Institutet

description:
Library name: DMSO_ATRA_Rep1
Custom Read1 primer, 20 cycles

data_processing:
MAGeCK v. 0.5.6 read counting
Assembly: hg38
Supplementary files format and content: .txt file containing read counts per guide for all samples
Library strategy: CRISPR Screen

source_name: Blood

extract_protocol:
QIAamp DNA Blood Maxi kit (Qiagen)
PCR

value: Blood

value: Adult acute monocytic leukemia

value: Replicate 1


title: Stool-8w-Apc-4-756


title: V4_ki67+myc+_ROI5_S3_Vehicle

description:
Library name: DSP-1001660037306-B-E11
Tumor V4, Slide S3, ROI 5, Segment ki67+myc+, Replicate V4_ki67+myc+. Raji xenograft in NSG mouse, NanoString GeoMx DSP WTA v1.0.


title: Tn M2 D0 r1

city: Shanghai

first: Ruiqing

last: Ma

address: 2901 Caolang Rd., Jinshan District

country: China

institute: Shanghai Public Health Clinical Center

description:
Library name: M2-1 rep1
input

data_processing:
Basecalling: Illumina GA Pipeline v1.8
Transit v3.0, Transit Pre-Processor (TPP) step for read aligment, Resampling -a for pairwise comparison
Assembly: NC_000962, Mycobacterium tuberculosis H37Rv, complete genome
Supplementary files format and content: *.xlsx files generated by Transit contain log2FoldChange and p-value of the comparison results between two conditions

organism: Mycobacterium tuberculosis

extract_protocol:
CTAB genome extraction method
Tn-seq

tag: sample group

value: Tn M2 D0


title: Female, dsx-RNAi, 11 day, replicate 1

city: Wageningen

first: Julien

last: Rougeot

address: Droevendaalsesteeg 1

department: Plant Science Group

country: Netherlands

institute: Wageningen University and Research (Netherlands)

data_processing:
Raw data filtering was performed to remove reads with adaptor contamination, uncertain nucleotides on more than 10% of the sequence (N>10%) and reads with low-quality nucleotides (<20) on more than 50% of the sequence.
Clean paired-end reads were mapped on the Nasonia vitripennis genome Nvit_psr_1.1 (GCA_009193385.2 Nvit_psr_1.1) using HISAT2 (v2.0.5) and default parameters.
Gene counts were obtained using HTSeq (v0.6.1) and the union method on the annotation GCF_009193385.1_Nvit_psr_1.
Assembly: Nvit_psr_1.1
Supplementary files format and content: tab-delimited text file includes raw counts for each samples

organism: Nasonia vitripennis

source_name: pupae

growth_protocol: Nasonia vitripennis lab strain AsymCX was reared on Calliphora sp. under a 16 hours light / 8 hours dark cycle at 25°C.

extract_protocol:
After 3 days post-injection, five samples with three individuals were collected for each time point and sex and flash-frozen in liquid nitrogen. For adult parts, seven adults were collected one day after emergence, between 7 and 8 days after pupae injection. Adults were flash-frozen in liquid nitrogen, then immediately dissected apart on ice into head, thorax, and abdomen, and finally flash-frozen back in liquid nitrogen. All samples were stored at −80 °C until RNA extraction. For 1 day-old embryo (parental RNAi), F0 female pupae 8 days after oviposition were injected as described above, kept until emergence, and then crossed with uninjected AsymCX males or kept virgin. Every female was then set up individually with one host, changed every 4 hours. Virgin females produce only male progeny while mated females produce between 90-95% females. Batches of 100 embryos were collected  24 hours later by dissecting the host, transfer into a microcentrifugation tube on ice without buffer, flash-frozen in liquid nitrogen, and stored at −80 °C until RNA extraction. Total RNA was extracted with Quick-RNA Tissue/Insect Kit coupled with on column DNase treatment (ZymoResearch - R2030) according to manufacturer's protocol.
Library preparation was performed at the Novogene (HK) Company Limited. Sequencing libraries were generated using NEBNext® Ultra TM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Sequencing libraries were paired-end sequenced (150 bp read-length) on an Illumina NovaSeq platform.

treatment_protocol: Larval RNAi knockdown was induced in AsymCX males or females at 4, 6, and 8 days after oviposition. Larvae at 4 and 6 days were injected on PBS-1%agar plates. After injection, the 4 day-old larvae were transferred back to host (6-8 per host) and sealed with the host shell, while 6 day-old larvae were kept on the PBS-agar plate. Pupae at 8 days were fixed on microscopy slides with double-sided tape, inject, and kept until emergence. Larvae and pupae were injected in the posterior part with 4 μg/μl dsx or GFP dsRNA diluted in milliQ water mixed with red food dye in the ratio 9:1. Injections were performed using custom made capillary needles and a Femtojet (Eppendorf).

value: pupae

tag: strain

value: AsymCX

tag: Sex

value: Female

tag: developmental stage

value: 11 day

value: dsx-RNAi


title: Venetoclax, sorted for dCas9-KRAB-BFP, Replicate 2

description:
Library name: Ven_Rep2
Custom Read1 primer, 20 cycles

value: Replicate 2


title: Region_8dpn_1


title: Stool-8w-Apc-3-755


title: V4_ki67+myc+_ROI4_S3_Vehicle

description:
Library name: DSP-1001660037306-B-E10
Tumor V4, Slide S3, ROI 4, Segment ki67+myc+, Replicate V4_ki67+myc+. Raji xenograft in NSG mouse, NanoString GeoMx DSP WTA v1.0.

value: Raji Burkitt lymphoma xenograft

value: Raji (ATCC CCL-86)

value: Vehicle


title: DMSO control for Venetoclax, sorted for dCas9-KRAB-BFP, Replicate 2

description:
Library name: DMSO_Ven_Rep2
Custom Read1 primer, 20 cycles


title: Region_3dpn_2


title: V2_ki67-myc+_ROI9_S3_Vehicle

description:
Library name: DSP-1001660037306-B-F06
Tumor V2, Slide S3, ROI 9, Segment ki67-myc+, Replicate V2_ki67-myc+. Raji xenograft in NSG mouse, NanoString GeoMx DSP WTA v1.0.


title: Venetoclax, sorted for dCas9-KRAB-BFP, Replicate 1

description:
Library name: Ven_Rep1
Custom Read1 primer, 20 cycles


title: Stool-8w-Apc-2-749

value: Feces

value: ApcMin

value: Untreated


title: Region_3dpn_1

value: Uterus

value: 4% PFA


title: Tn M0 D0 r1

description:
Library name: M0-1 rep1
input

value: Tn M0 D0


title: Stool-8w-Apc-1-748

value: 8 weeks old


title: Stool-20w-Apc-4-773

value: 20 weeks old


title: DMSO control for Venetoclax, sorted for dCas9-KRAB-BFP, Replicate 1

description:
Library name: DMSO_Ven_Rep1
Custom Read1 primer, 20 cycles

value: Blood

value: Adult acute monocytic leukemia

value: Replicate 1


title: V2_ki67+myc+_ROI9_S3_Vehicle

description:
Library name: DSP-1001660037306-B-F05
Tumor V2, Slide S3, ROI 9, Segment ki67+myc+, Replicate V2_ki67+myc+. Raji xenograft in NSG mouse, NanoString GeoMx DSP WTA v1.0.


title: KPC Kmt2df/+ Mouse 12349 Rep 3

city: Rochester

first: Martin

last: Fernandez-Zapico

state: MN

address: 200 First Street SW

country: USA

institute: Mayo Clinic

description:
Library name: 15C_12349
Column name 15_12349_htseq.count

data_processing:
RNA-seq FASTq files were processed and trimmed with Trim Galore 0.6.4.
Read quality was evaluated with FastQC and aligned with STAR 2.7.3a and mm10 genome as reference.
Reads were assigned by HTSeq 0.9.1.
BAM files for biological replicates were merged using SAMtools 1.16.
DESeq2 used to generate normalized read counts from merged BAM files (Galaxy Version 2.11.40.6).
Assembly: mm10
Supplementary files format and content: tabular file of DESeq2 normalized counts for each mouse (merged biological replicates)

source_name: pancreas tumor

growth_protocol: Cells were derived from a genetically engineered mouse model (GEMM) pancreas tumors and cultured in DMEM + 10% FBS + 1% Penn/Strep. Cells were maintained at 37°C and 5% CO2.

extract_protocol:
RNA was extracted with TRIzol reagent and then isolated using Qiagen RNeasy kit per manufacturer instructions.
cDNA libraries were prepared using 200 ng of total RNA according to the manufacturer’s instructions for the Illumina TruSeq Stranded mRNA Sample Prep Kit.

value: pancreas tumor

value: KPC Kmt2df/+

tag: mouse id

value: KPC Kmt2df/+ Mouse 12349


city: London

first: Harry

last: Pink

address: Innovation and Translation Hub, 84 Wood Lane,

country: United Kingdom

institute: Mitra Bio

description:
Library name: M4001
M4001 (subject 121-6 Month Follow Up-Untreated) targeted EM-seq on Twist methylome panel

data_processing:
Data was processed as recommended here - https://www.twistbioscience.com/sites/default/files/resources/2022-06/DOC-001301_TechNote-AnalyzingTargetedMethylSeqDataUsingTwistHumanMethylPanel-REV1-singles (1).pdf
Assembly: hg38
Supplementary files format and content: Beta methylation values (0-100) returned by methyldakel. Gzipped txt format
Library strategy: EM-seq

source_name: forehead tape-strip

growth_protocol: Genomic DNA extracted from ‘tape-strip’ of forehead

extract_protocol:
Genomic DNA was extracted
Extracted gDNA underwent EM-seq enzymatic conversion and subsequent hybridisation to Twist Human Methylome 4M CpG panel - https://www.twistbioscience.com/sites/default/files/resources/2022-06/covered_targets_Twist_Methylome_hg38_annotated_collapsed.bed

treatment_protocol: Participants were exposed to treatment with 1940-nm non-ablative fractional laser (NAFL)

tag: subject id

tag: timepoint

value: 6 Month Follow Up

tag: age

value: forehead tape-strip

tag: gender

value: Female


title: V2_ki67+myc+_ROI8_S3_Vehicle

description:
Library name: DSP-1001660037306-B-F03
Tumor V2, Slide S3, ROI 8, Segment ki67+myc+, Replicate V2_ki67+myc+. Raji xenograft in NSG mouse, NanoString GeoMx DSP WTA v1.0.

tag: tissue

value: Raji Burkitt lymphoma xenograft

value: Raji (ATCC CCL-86)

value: Vehicle


description:
Library name: M4002
M4002 (subject 121-6 Month Follow Up-Treated) targeted EM-seq on Twist methylome panel

value: Treated


title: KPC Kmt2df/+ Mouse 12349 Rep 1

description:
Library name: 15A_12349
Column name 15_12349_htseq.count


title: Stool-8w-WT-3-770

value: Feces

value: Untreated


description:
Library name: M3999
M3999 (subject 121-3 Month Follow Up-Untreated) targeted EM-seq on Twist methylome panel

value: 3 Month Follow Up


title: V2_ki67-myc+_ROI7_S3_Vehicle

description:
Library name: DSP-1001660037306-B-F02
Tumor V2, Slide S3, ROI 7, Segment ki67-myc+, Replicate V2_ki67-myc+. Raji xenograft in NSG mouse, NanoString GeoMx DSP WTA v1.0.

tag: cell line


title: Stool-8w-WT-2-769

value: 8 weeks old


description:
Library name: M4000
M4000 (subject 121-3 Month Follow Up-Treated) targeted EM-seq on Twist methylome panel


title: KPC Kmt2df/+ Mouse 12352 Rep 2

description:
Library name: 14B_12352
Column name 14_12352_htseq.count

value: KPC Kmt2df/+ Mouse 12352


title: Stool-8w-WT-1-766


title: D4_ki67+myc+_ROI13_S3_Milademetan

description:
Library name: DSP-1001660037306-B-F11
Tumor D4, Slide S3, ROI 13, Segment ki67+myc+, Replicate D4_ki67+myc+. Raji xenograft in NSG mouse, NanoString GeoMx DSP WTA v1.0.

tag: cell type

value: Milademetan 20mg/kg


description:
Library name: M3997
M3997 (subject 121-1 Month Follow Up-Untreated) targeted EM-seq on Twist methylome panel

value: 1 Month Follow Up


title: Stool-4w-Apc-5-741

tag: genotype

value: ApcMin

value: 4 weeks old


title: D4_ki67-myc+_ROI12_S3_Milademetan

description:
Library name: DSP-1001660037306-B-F10
Tumor D4, Slide S3, ROI 12, Segment ki67-myc+, Replicate D4_ki67-myc+. Raji xenograft in NSG mouse, NanoString GeoMx DSP WTA v1.0.

tag: treatment


title: KPC Kmt2df/+ Mouse 12352 Rep 1

description:
Library name: 14A_12352
Column name 14_12352_htseq.count

value: pancreas tumor

value: KPC Kmt2df/+

tag: batch


title: Stool-4w-Apc-4-738

tag: time


title: D4_ki67+myc+_ROI12_S3_Milademetan

description:
Library name: DSP-1001660037306-B-F09
Tumor D4, Slide S3, ROI 12, Segment ki67+myc+, Replicate D4_ki67+myc+. Raji xenograft in NSG mouse, NanoString GeoMx DSP WTA v1.0.


title: KPC Kmt2df/+ Mouse 12145 Rep 2

description:
Library name: 13B_12145
Column name 13_12145_htseq.count

value: KPC Kmt2df/+ Mouse 12145


title: Stool-4w-Apc-3-735


title: D4_ki67+myc+_ROI11_S3_Milademetan

description:
Library name: DSP-1001660037306-B-F08
Tumor D4, Slide S3, ROI 11, Segment ki67+myc+, Replicate D4_ki67+myc+. Raji xenograft in NSG mouse, NanoString GeoMx DSP WTA v1.0.


title: Stool-4w-Apc-2-733


title: KPC Kmt2df/+ Mouse 12145 Rep 1

description:
Library name: 13A_12145
Column name 13_12145_htseq.count


title: D4_ki67+myc+_ROI10_S3_Milademetan

description:
Library name: DSP-1001660037306-B-F07
Tumor D4, Slide S3, ROI 10, Segment ki67+myc+, Replicate D4_ki67+myc+. Raji xenograft in NSG mouse, NanoString GeoMx DSP WTA v1.0.


title: M3994 (subject 121-Baseline-Untreated)

description:
Library name: M3994
M3994 (subject 121-Baseline-Untreated) targeted EM-seq on Twist methylome panel

value: Baseline

value: forehead tape-strip

value: Female


title: KPC Kmt2df/+ Mouse 2940 Rep 3

description:
Library name: 12C_2940
Column name 12_2940_htseq.count

value: KPC Kmt2df/+ Mouse 2940


title: Stool-4w-Apc-1-732


description:
Library name: M4090
M4090 (subject 119-6 Month Follow Up-Untreated) targeted EM-seq on Twist methylome panel

value: 6 Month Follow Up


title: KPC Kmt2df/+ Mouse 2940 Rep 2

description:
Library name: 12B_2940
Column name 12_2940_htseq.count


title: Stool-4w-WT-5-742

value: Feces


title: D4_ki67+myc+_ROI3_S3_Milademetan

description:
Library name: DSP-1001660037306-B-E08
Tumor D4, Slide S3, ROI 3, Segment ki67+myc+, Replicate D4_ki67+myc+. Raji xenograft in NSG mouse, NanoString GeoMx DSP WTA v1.0.

value: Raji Burkitt lymphoma xenograft

value: Raji (ATCC CCL-86)


title: KPC Kmt2df/+ Mouse 2940 Rep 1

description:
Library name: 12A_2940
Column name 12_2940_htseq.count


description:
Library name: M4091
M4091 (subject 119-6 Month Follow Up-Treated) targeted EM-seq on Twist methylome panel

value: Treated


title: Stool-4w-WT-4-739

value: Untreated


title: D4_ki67-myc+_ROI2_S3_Milademetan

description:
Library name: DSP-1001660037306-B-E07
Tumor D4, Slide S3, ROI 2, Segment ki67-myc+, Replicate D4_ki67-myc+. Raji xenograft in NSG mouse, NanoString GeoMx DSP WTA v1.0.

value: Milademetan 20mg/kg


title: D4_ki67+myc+_ROI2_S3_Milademetan

description:
Library name: DSP-1001660037306-B-E06
Tumor D4, Slide S3, ROI 2, Segment ki67+myc+, Replicate D4_ki67+myc+. Raji xenograft in NSG mouse, NanoString GeoMx DSP WTA v1.0.


title: KPC Kmt2df/+ Mouse 2500 Rep 2

description:
Library name: 11B_2500
Column name 11_2500_htseq.count

value: KPC Kmt2df/+ Mouse 2500


description:
Library name: M4089
M4089 (subject 119-3 Month Follow Up-Treated) targeted EM-seq on Twist methylome panel

value: 3 Month Follow Up


title: Stool-4w-WT-2-736

value: 4 weeks old


title: KPC Kmt2df/+ Mouse 2500 Rep 1

description:
Library name: 11A_2500
Column name 11_2500_htseq.count

value: pancreas tumor


description:
Library name: M4086
M4086 (subject 119-1 Month Follow Up-Untreated) targeted EM-seq on Twist methylome panel

value: 1 Month Follow Up


title: Stool-4w-WT-1-734


title: D4_ki67+myc+_ROI1_S3_Milademetan

description:
Library name: DSP-1001660037306-B-E04
Tumor D4, Slide S3, ROI 1, Segment ki67+myc+, Replicate D4_ki67+myc+. Raji xenograft in NSG mouse, NanoString GeoMx DSP WTA v1.0.


description:
Library name: M4087
M4087 (subject 119-1 Month Follow Up-Treated) targeted EM-seq on Twist methylome panel


title: KPC Mouse 3622 Rep 3

description:
Library name: 6C_3622
Column name 6_3622_htseq.count

value: KPC

value: KPC Mouse 3622


title: C-epi-20w-Apc-5-775

source_name: colon epithelial cell

value: colon epithelial cell

value: ApcMin

value: 20 weeks old


title: V5_ki67+myc-_ROI9_S2_Vehicle

description:
Library name: DSP-1001660037306-B-D11
Tumor V5, Slide S2, ROI 9, Segment ki67+myc-, Replicate V5_ki67+myc-. Raji xenograft in NSG mouse, NanoString GeoMx DSP WTA v1.0.

value: Vehicle


description:
Library name: M4084
M4084 (subject 119-Post Treatment 1-Untreated) targeted EM-seq on Twist methylome panel

value: Post Treatment 1

value: forehead tape-strip

value: Female


title: C-epi-20w-Apc-4-773


title: KPC Mouse 3622 Rep 2

description:
Library name: 6B_3622
Column name 6_3622_htseq.count


title: V5_ki67+myc+_ROI9_S2_Vehicle

description:
Library name: DSP-1001660037306-B-D10
Tumor V5, Slide S2, ROI 9, Segment ki67+myc+, Replicate V5_ki67+myc+. Raji xenograft in NSG mouse, NanoString GeoMx DSP WTA v1.0.

value: Raji Burkitt lymphoma xenograft

value: Raji (ATCC CCL-86)


description:
Library name: M4085
M4085 (subject 119-Post Treatment 1-Treated) targeted EM-seq on Twist methylome panel

value: Treated


title: KPC Mouse 3622 Rep 1

description:
Library name: 6A_3622
Column name 6_3622_htseq.count


title: V5_ki67+myc-_ROI8_S2_Vehicle

description:
Library name: DSP-1001660037306-B-D09
Tumor V5, Slide S2, ROI 8, Segment ki67+myc-, Replicate V5_ki67+myc-. Raji xenograft in NSG mouse, NanoString GeoMx DSP WTA v1.0.


title: KPC Mouse 12278 Rep 3

description:
Library name: 5C_12278
Column name 5_12278_htseq.count

value: KPC Mouse 12278


title: C-epi-20w-Apc-2-731

value: Untreated


title: Stool-8w-WT-5-772

value: Feces

value: 8 weeks old


title: V2_ki67-myc+_ROI8_S3_Vehicle

description:
Library name: DSP-1001660037306-B-F04
Tumor V2, Slide S3, ROI 8, Segment ki67-myc+, Replicate V2_ki67-myc+. Raji xenograft in NSG mouse, NanoString GeoMx DSP WTA v1.0.


title: Stool-8w-WT-4-771


title: KPC Kmt2df/+ Mouse 12349 Rep 2

description:
Library name: 15B_12349
Column name 15_12349_htseq.count

value: pancreas tumor

value: KPC Kmt2df/+

value: KPC Kmt2df/+ Mouse 12349


title: C-epi-20w-Apc-3-743

value: colon epithelial cell


title: KPC Kmt2df/+ Mouse 12352 Rep 3

description:
Library name: 14C_12352
Column name 14_12352_htseq.count

value: KPC Kmt2df/+ Mouse 12352


title: V5_ki67+myc+_ROI8_S2_Vehicle

description:
Library name: DSP-1001660037306-B-D08
Tumor V5, Slide S2, ROI 8, Segment ki67+myc+, Replicate V5_ki67+myc+. Raji xenograft in NSG mouse, NanoString GeoMx DSP WTA v1.0.


title: V2_ki67+myc+_ROI7_S3_Vehicle

description:
Library name: DSP-1001660037306-B-F01
Tumor V2, Slide S3, ROI 7, Segment ki67+myc+, Replicate V2_ki67+myc+. Raji xenograft in NSG mouse, NanoString GeoMx DSP WTA v1.0.


description:
Library name: M3992
M3992 (subject 116-6 Month Follow Up-Untreated) targeted EM-seq on Twist methylome panel

value: 6 Month Follow Up


title: KPC Mouse 12278 Rep 2

description:
Library name: 5B_12278
Column name 5_12278_htseq.count

value: KPC


title: C-epi-20w-Apc-1-727

value: ApcMin

value: 20 weeks old


description:
Library name: M3993
M3993 (subject 116-6 Month Follow Up-Treated) targeted EM-seq on Twist methylome panel

value: forehead tape-strip

value: Female


title: V5_ki67+myc-_ROI7_S2_Vehicle

description:
Library name: DSP-1001660037306-B-D07
Tumor V5, Slide S2, ROI 7, Segment ki67+myc-, Replicate V5_ki67+myc-. Raji xenograft in NSG mouse, NanoString GeoMx DSP WTA v1.0.

value: Raji Burkitt lymphoma xenograft

value: Raji (ATCC CCL-86)

value: Vehicle


description:
Library name: M3998
M3998 (subject 121-1 Month Follow Up-Treated) targeted EM-seq on Twist methylome panel

value: 1 Month Follow Up

value: Treated


title: M4083 (subject 119-Baseline-Untreated)

description:
Library name: M4083
M4083 (subject 119-Baseline-Untreated) targeted EM-seq on Twist methylome panel

value: Baseline

value: Untreated


title: KPC Mouse 12278 Rep 1

description:
Library name: 5A_12278
Column name 5_12278_htseq.count

value: pancreas tumor

value: KPC Mouse 12278


description:
Library name: M3995
M3995 (subject 121-Post Treatment 1-Untreated) targeted EM-seq on Twist methylome panel

value: Post Treatment 1


title: KPC Kmt2df/+ Mouse 12145 Rep 3

description:
Library name: 13C_12145
Column name 13_12145_htseq.count

value: KPC Kmt2df/+

value: KPC Kmt2df/+ Mouse 12145


title: V5_ki67+myc+_ROI7_S2_Vehicle

description:
Library name: DSP-1001660037306-B-D06
Tumor V5, Slide S2, ROI 7, Segment ki67+myc+, Replicate V5_ki67+myc+. Raji xenograft in NSG mouse, NanoString GeoMx DSP WTA v1.0.


description:
Library name: M3990
M3990 (subject 116-3 Month Follow Up-Untreated) targeted EM-seq on Twist methylome panel

value: 3 Month Follow Up


title: C-epi-20w-WT-5-777

value: colon epithelial cell


title: KPC Mouse 2974 Rep 3

description:
Library name: 3C_2974
Column name 3_2974_htseq.count

value: KPC

value: KPC Mouse 2974


title: C-epi-20w-WT-4-776

value: 20 weeks old


description:
Library name: M3991
M3991 (subject 116-3 Month Follow Up-Treated) targeted EM-seq on Twist methylome panel

value: forehead tape-strip

value: Female


title: D3_ki67-myc-_ROI11_S2_Milademetan

description:
Library name: DSP-1001660037306-B-E03
Tumor D3, Slide S2, ROI 11, Segment ki67-myc-, Replicate D3_ki67-myc-. Raji xenograft in NSG mouse, NanoString GeoMx DSP WTA v1.0.

value: Raji Burkitt lymphoma xenograft

value: Raji (ATCC CCL-86)

value: Milademetan 20mg/kg


title: KPC Mouse 2974 Rep 2

description:
Library name: 3B_2974
Column name 3_2974_htseq.count


title: C-epi-20w-WT-3-774


title: D3_ki67+myc+_ROI11_S2_Milademetan

description:
Library name: DSP-1001660037306-B-E02
Tumor D3, Slide S2, ROI 11, Segment ki67+myc+, Replicate D3_ki67+myc+. Raji xenograft in NSG mouse, NanoString GeoMx DSP WTA v1.0.


description:
Library name: M3988
M3988 (subject 116-1 Month Follow Up-Untreated) targeted EM-seq on Twist methylome panel

value: 1 Month Follow Up


title: KPC Mouse 2974 Rep 1

description:
Library name: 3A_2974
Column name 3_2974_htseq.count


title: C-epi-20w-WT-2-747

value: Untreated


title: D3_ki67-myc-_ROI10_S2_Milademetan

description:
Library name: DSP-1001660037306-B-E01
Tumor D3, Slide S2, ROI 10, Segment ki67-myc-, Replicate D3_ki67-myc-. Raji xenograft in NSG mouse, NanoString GeoMx DSP WTA v1.0.


description:
Library name: M3989
M3989 (subject 116-1 Month Follow Up-Treated) targeted EM-seq on Twist methylome panel

value: Treated


title: Multiome, Thymic Adipocytes, ATAC

city: Salt Lake City

first: Dean

last: Tantin

state: Utah

address: N Campus Dr

institute: University of Utah

description:
Library name: 6mo_F_ATAC
10x Genomics

library_source: genomic single cell

data_processing:
Demultiplexing and feature barcode matrices were obtained using Cellranger Arc (v2.0.2) by the High Throughput Genomics Core at the University of Utah.
Additional thresholding/QC in Seurat (v5.1.0) by unique genes (nFeature_RNA >200 & <2,500), and mitochondrial mRNA content (mt.percent_RNA <20%).
Normalization, PCA, and WNN UMAP generation using Seurat default settings SCTransform() pipeline. Thymic adipocyte and visceral epigonadal WAT objects were merged, integrated, and subset to retain solely adipocyte clusters. The SCTransform() pipeline was re-applied to obtain the final UMAPs/Figures.
Assembly: mm10
Supplementary files format and content: feature_bc_matrix.h5 = barcodes, gene IDs, and expression matrix for 6mo F dataset; barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz = barcodes, gene IDs, and expression matrix for 4mo M dataset
Supplementary files format and content: metadata files contain cell annotations and UMAP coordinates for the 6mo F integrated RNAseq and ATACseq experiment or the integrated thymic adipocyte and visceral WAT 4mo M RNAseq-only experiment.

source_name: Thymus

extract_protocol:
Thymic capsules were cleaned of directly attached perithymic fat and connective tissues, rinsed a final time with PBS, and transferred to a 15mL conical tube for enzymatic digestion with DNase I and Collagenase II in DMEM-F12 10% FBS. Samples were fractionated by sequential centrigugation steps, and the topmost white layer containing mature, floating adipocytes was obtained. Nuclei were isolated as previously described (10X Genomics, Demonstrated Protocol CG000366 Rev D) followed by library preparation and joint RNAseq + ATACseq (6mo F) or RNAseq alone (4mo M) using the 10x Genomics platform by the University of Utah High Throughput Genomics Core.
5,000-10,000 nuclei were targeted for snRNAseq. Libraries were prepared using Library Construction Kit B reagents and sequenced on an Illumina NovaSeq X instrument targeting at least 100 million paired end reads (GEX) and at least 300 million paired end reads (ATAC) of 150 bp.

value: Thymus

value: Adipocyte

value: WT

value: Naïve


title: D4_ki67-myc+_ROI3_S3_Milademetan

description:
Library name: DSP-1001660037306-B-E09
Tumor D4, Slide S3, ROI 3, Segment ki67-myc+, Replicate D4_ki67-myc+. Raji xenograft in NSG mouse, NanoString GeoMx DSP WTA v1.0.


title: C-epi-20w-WT-1-730


description:
Library name: M3986
M3986 (subject 116-Post Treatment 1-Untreated) targeted EM-seq on Twist methylome panel

value: Post Treatment 1


title: D3_ki67+myc+_ROI10_S2_Milademetan

description:
Library name: DSP-1001660037306-B-D12
Tumor D3, Slide S2, ROI 10, Segment ki67+myc+, Replicate D3_ki67+myc+. Raji xenograft in NSG mouse, NanoString GeoMx DSP WTA v1.0.


title: Multiome, Thymic Adipocytes, GEX

description:
Library name: 6mo_F_RNA
10x Genomics

library_source: transcriptomic single cell


title: C-epi-8w-Apc-5-757

value: colon epithelial cell

value: ApcMin

value: 8 weeks old


title: D3_ki67-myc-_ROI6_S2_Milademetan

description:
Library name: DSP-1001660037306-B-D05
Tumor D3, Slide S2, ROI 6, Segment ki67-myc-, Replicate D3_ki67-myc-. Raji xenograft in NSG mouse, NanoString GeoMx DSP WTA v1.0.


description:
Library name: M3987
M3987 (subject 116-Post Treatment 1-Treated) targeted EM-seq on Twist methylome panel


title: snRNAseq, Epigonadal Adipocytes

description:
Library name: 4mo_M_gWAT
10x Genomics

source_name: Epigonadal White Adipose Tissue

value: Epigonadal White Adipose Tissue


title: D3_ki67+myc+_ROI6_S2_Milademetan

description:
Library name: DSP-1001660037306-B-D04
Tumor D3, Slide S2, ROI 6, Segment ki67+myc+, Replicate D3_ki67+myc+. Raji xenograft in NSG mouse, NanoString GeoMx DSP WTA v1.0.


title: C-epi-8w-Apc-4-756


title: M3985 (subject 116-Baseline-Untreated)

description:
Library name: M3985
M3985 (subject 116-Baseline-Untreated) targeted EM-seq on Twist methylome panel

value: Baseline

value: forehead tape-strip


title: snRNAseq, Thymic Adipocytes

description:
Library name: 4mo_M_Thy
10x Genomics


title: C-epi-8w-Apc-3-755


title: D3_ki67+myc-_ROI4_S2_Milademetan

description:
Library name: DSP-1001660037306-B-D03
Tumor D3, Slide S2, ROI 4, Segment ki67+myc-, Replicate D3_ki67+myc-. Raji xenograft in NSG mouse, NanoString GeoMx DSP WTA v1.0.

value: Raji Burkitt lymphoma xenograft


description:
Library name: M4081
M4081 (subject 111-6 Month Follow Up-Untreated) targeted EM-seq on Twist methylome panel

value: 6 Month Follow Up

value: Female


title: C-epi-8w-Apc-2-749


description:
Library name: M4082
M4082 (subject 111-6 Month Follow Up-Treated) targeted EM-seq on Twist methylome panel


title: D3_ki67+myc+_ROI4_S2_Milademetan

description:
Library name: DSP-1001660037306-B-D02
Tumor D3, Slide S2, ROI 4, Segment ki67+myc+, Replicate D3_ki67+myc+. Raji xenograft in NSG mouse, NanoString GeoMx DSP WTA v1.0.

value: Raji (ATCC CCL-86)

value: Milademetan 20mg/kg


title: C-epi-8w-Apc-1-748

value: Untreated


title: FBL2 knockdown 1 background primer set 2

city: Uppsala

first: Rubin

last: Dasgupta

address: Husargatan 3, BMC 582, D9:3

institute: Uppsala University

description: Library name: fbl2_dmso_d560-d559_filt.fastq.gz

library_source: other

data_processing:
After sequencing using PromethIon, basecalling was performed using dorado v1.1.0. The sequence was aligned to the reference sequence using bowtie2 and samtools. The aligned BAM file was used to count the mutations per position using perbase and RNAFramework
Assembly: The sequence was aligned to the reference sequence. There was not genome building or assembly performed
Supplementary files format and content: The processed data is provides as a CSV file containing the nucleotide position, nucleotide identity (A, T, G, or C) as provided in the reference sequence, number of time it was correctly sequenced and mutated to other nucleotide, number of times the identity was not possible and finally number of time the alignment tool classified the position as an insertion or deletion.

molecule: other

extract_protocol:
RNA was purified using the GeneJET RNA Purification Kit (Thermo Scientific, cat. K0732) according to the manufacturer’s instructions. Residual genomic DNA was removed by treatment with TURBO DNase (Invitrogen™, cat. AM1907), followed by ethanol precipitation.
Libraries were prepared using specific primers and Platinum SuperFi II PCR Master Mix (Invitrogen™, cat. 12368010), and dsDNA was purified using the GeneJET Gel Extraction Kit (Thermo Scientific, cat. K0692).

value: human breast cancer


description:
Library name: M4079
M4079 (subject 111-3 Month Follow Up-Untreated) targeted EM-seq on Twist methylome panel

value: 3 Month Follow Up


title: C-epi-8w-WT-5-772


title: FBL2 knockdown 1 background primer set 1

description: Library name: fbl2_dmso_d551-d552_filt.fastq.gz


description:
Library name: M4080
M4080 (subject 111-3 Month Follow Up-Treated) targeted EM-seq on Twist methylome panel

value: Treated


title: FBL2 knockdown 1 primer set 3

description: Library name: fbl2_2a3_d562-d563_filt.fastq.gz


description:
Library name: M4077
M4077 (subject 111-1 Month Follow Up-Untreated) targeted EM-seq on Twist methylome panel

value: 1 Month Follow Up


title: D3_ki67+myc-_ROI2_S2_Milademetan

description:
Library name: DSP-1001660037306-B-C11
Tumor D3, Slide S2, ROI 2, Segment ki67+myc-, Replicate D3_ki67+myc-. Raji xenograft in NSG mouse, NanoString GeoMx DSP WTA v1.0.


title: FBL2 knockdown 1 primer set 2

description: Library name: fbl2_2a3_d560-d559_filt.fastq.gz


title: C-epi-8w-WT-3-770


description:
Library name: M4078
M4078 (subject 111-1 Month Follow Up-Treated) targeted EM-seq on Twist methylome panel


title: C-epi-8w-WT-2-769


description:
Library name: M4075
M4075 (subject 111-Post Treatment 1-Untreated) targeted EM-seq on Twist methylome panel

value: Post Treatment 1


title: FBL1 knockdown 1 background primer set 3

description: Library name: fbl1_dmso_d562-d563_filt.fastq.gz


title: C-epi-8w-WT-1-766

value: colon epithelial cell


title: D3_ki67+myc+_ROI1_S2_Milademetan

description:
Library name: DSP-1001660037306-B-C08
Tumor D3, Slide S2, ROI 1, Segment ki67+myc+, Replicate D3_ki67+myc+. Raji xenograft in NSG mouse, NanoString GeoMx DSP WTA v1.0.


description:
Library name: M4076
M4076 (subject 111-Post Treatment 1-Treated) targeted EM-seq on Twist methylome panel


title: FBL1 knockdown 1 background primer set 2

description: Library name: fbl1_dmso_d560-d559_filt.fastq.gz


title: C-epi-4w-Apc-5-741

value: ApcMin

value: 4 weeks old


title: M4074 (subject 111-Baseline-Untreated)

description:
Library name: M4074
M4074 (subject 111-Baseline-Untreated) targeted EM-seq on Twist methylome panel


title: C-epi-4w-Apc-4-738


title: FBL1 knockdown 1 background primer set 1

description: Library name: fbl1_dmso_d551-d552_filt.fastq.gz


title: V3_ki67+myc+_ROI16_S1_Vehicle

description:
Library name: DSP-1001660037306-B-C06
Tumor V3, Slide S1, ROI 16, Segment ki67+myc+, Replicate V3_ki67+myc+. Raji xenograft in NSG mouse, NanoString GeoMx DSP WTA v1.0.

value: Vehicle


description:
Library name: M3965
M3965 (subject 110-6 Month Follow Up-Untreated) targeted EM-seq on Twist methylome panel


title: Male, GFP-RNAi, Abdomen, replicate 3

source_name: abdomen

value: abdomen

value: AsymCX

value: Male

value: adult

value: GFP-RNAi


title: FBL1 knockdown 1 primer set 3

description: Library name: fbl1_2a3_d562-d563_filt.fastq.gz


title: C-epi-4w-Apc-3-735


title: V3_ki67-myc+_ROI15_S1_Vehicle

description:
Library name: DSP-1001660037306-B-C05
Tumor V3, Slide S1, ROI 15, Segment ki67-myc+, Replicate V3_ki67-myc+. Raji xenograft in NSG mouse, NanoString GeoMx DSP WTA v1.0.

value: Raji Burkitt lymphoma xenograft

value: Raji (ATCC CCL-86)


description:
Library name: M3966
M3966 (subject 110-6 Month Follow Up-Treated) targeted EM-seq on Twist methylome panel

value: 6 Month Follow Up

value: forehead tape-strip

value: Female


title: FBL1 knockdown 1 primer set 2

description: Library name: fbl1_2a3_d560-d559_filt.fastq.gz

value: human breast cancer


title: C-epi-4w-Apc-2-733

value: Untreated


title: V3_ki67+myc+_ROI15_S1_Vehicle

description:
Library name: DSP-1001660037306-B-C04
Tumor V3, Slide S1, ROI 15, Segment ki67+myc+, Replicate V3_ki67+myc+. Raji xenograft in NSG mouse, NanoString GeoMx DSP WTA v1.0.


description:
Library name: M3963
M3963 (subject 110-3 Month Follow Up-Untreated) targeted EM-seq on Twist methylome panel

value: 3 Month Follow Up


title: D3_ki67+myc-_ROI3_S2_Milademetan

description:
Library name: DSP-1001660037306-B-D01
Tumor D3, Slide S2, ROI 3, Segment ki67+myc-, Replicate D3_ki67+myc-. Raji xenograft in NSG mouse, NanoString GeoMx DSP WTA v1.0.

value: Milademetan 20mg/kg


title: D3_ki67+myc+_ROI3_S2_Milademetan

description:
Library name: DSP-1001660037306-B-C12
Tumor D3, Slide S2, ROI 3, Segment ki67+myc+, Replicate D3_ki67+myc+. Raji xenograft in NSG mouse, NanoString GeoMx DSP WTA v1.0.


title: FBL1 knockdown 1 primer set 1

description: Library name: fbl1_2a3_d551-d552_filt.fastq.gz


title: C-epi-4w-Apc-1-732

value: colon epithelial cell

value: ApcMin


title: V3_ki67+myc+_ROI14_S1_Vehicle

description:
Library name: DSP-1001660037306-B-C03
Tumor V3, Slide S1, ROI 14, Segment ki67+myc+, Replicate V3_ki67+myc+. Raji xenograft in NSG mouse, NanoString GeoMx DSP WTA v1.0.

value: Vehicle


title: C-epi-8w-WT-4-771

value: 8 weeks old


description:
Library name: M3964
M3964 (subject 110-3 Month Follow Up-Treated) targeted EM-seq on Twist methylome panel

value: Treated


title: Scrambled background primer set 3

description: Library name: scr_dmso_d562-d563_filt.fastq.gz


title: C-epi-4w-WT-5-742

value: 4 weeks old


title: D3_ki67+myc+_ROI2_S2_Milademetan

description:
Library name: DSP-1001660037306-B-C10
Tumor D3, Slide S2, ROI 2, Segment ki67+myc+, Replicate D3_ki67+myc+. Raji xenograft in NSG mouse, NanoString GeoMx DSP WTA v1.0.


title: V3_ki67+myc+_ROI13_S1_Vehicle

description:
Library name: DSP-1001660037306-B-C02
Tumor V3, Slide S1, ROI 13, Segment ki67+myc+, Replicate V3_ki67+myc+. Raji xenograft in NSG mouse, NanoString GeoMx DSP WTA v1.0.


description:
Library name: M3961
M3961 (subject 110-1 Month Follow Up-Untreated) targeted EM-seq on Twist methylome panel

value: 1 Month Follow Up


title: Scrambled background primer set 2

description: Library name: scr_dmso_d560-d559_filt.fastq.gz


title: C-epi-4w-WT-4-739


title: D3_ki67+myc-_ROI1_S2_Milademetan

description:
Library name: DSP-1001660037306-B-C09
Tumor D3, Slide S2, ROI 1, Segment ki67+myc-, Replicate D3_ki67+myc-. Raji xenograft in NSG mouse, NanoString GeoMx DSP WTA v1.0.


title: FBL2 knockdown 1 primer set 1

description: Library name: fbl2_2a3_d551-d552_filt.fastq.gz


title: V3_ki67-myc-_ROI12_S1_Vehicle

description:
Library name: DSP-1001660037306-B-C01
Tumor V3, Slide S1, ROI 12, Segment ki67-myc-, Replicate V3_ki67-myc-. Raji xenograft in NSG mouse, NanoString GeoMx DSP WTA v1.0.


description:
Library name: M3962
M3962 (subject 110-1 Month Follow Up-Treated) targeted EM-seq on Twist methylome panel


title: Scrambled background primer set 1

description: Library name: scr_dmso_d551-d552_filt.fastq.gz


title: C-epi-4w-WT-3-737


title: V3_ki67-myc+_ROI12_S1_Vehicle

description:
Library name: DSP-1001660037306-B-B12
Tumor V3, Slide S1, ROI 12, Segment ki67-myc+, Replicate V3_ki67-myc+. Raji xenograft in NSG mouse, NanoString GeoMx DSP WTA v1.0.


title: C-epi-4w-WT-2-736


title: Scrambled primer set 3

description: Library name: scr_2a3_d562-d563_filt.fastq.gz


title: V3_ki67+myc+_ROI12_S1_Vehicle

description:
Library name: DSP-1001660037306-B-B11
Tumor V3, Slide S1, ROI 12, Segment ki67+myc+, Replicate V3_ki67+myc+. Raji xenograft in NSG mouse, NanoString GeoMx DSP WTA v1.0.


description:
Library name: M3959
M3959 (subject 110-Post Treatment 1-Untreated) targeted EM-seq on Twist methylome panel

value: Post Treatment 1


description:
Library name: M3960
M3960 (subject 110-Post Treatment 1-Treated) targeted EM-seq on Twist methylome panel


title: Scrambled primer set 2

description: Library name: scr_2a3_d560-d559_filt.fastq.gz


title: C-epi-4w-WT-1-734


title: V3_ki67-myc+_ROI8_S1_Vehicle

description:
Library name: DSP-1001660037306-B-B05
Tumor V3, Slide S1, ROI 8, Segment ki67-myc+, Replicate V3_ki67-myc+. Raji xenograft in NSG mouse, NanoString GeoMx DSP WTA v1.0.

value: Raji Burkitt lymphoma xenograft


title: M3958 (subject 110-Baseline-Untreated)

description:
Library name: M3958
M3958 (subject 110-Baseline-Untreated) targeted EM-seq on Twist methylome panel

value: Baseline


title: Scrambled primer set 1

description: Library name: scr_2a3_d551-d552_filt.fastq.gz


title: Female, dsx-RNAi, 11 day, replicate 5

value: pupae

value: AsymCX

value: 11 day

value: dsx-RNAi


title: V3_ki67-myc+_ROI16_S1_Vehicle

description:
Library name: DSP-1001660037306-B-C07
Tumor V3, Slide S1, ROI 16, Segment ki67-myc+, Replicate V3_ki67-myc+. Raji xenograft in NSG mouse, NanoString GeoMx DSP WTA v1.0.

value: Raji (ATCC CCL-86)


title: V3_ki67+myc+_ROI8_S1_Vehicle

description:
Library name: DSP-1001660037306-B-B04
Tumor V3, Slide S1, ROI 8, Segment ki67+myc+, Replicate V3_ki67+myc+. Raji xenograft in NSG mouse, NanoString GeoMx DSP WTA v1.0.


title: intestinal mucosal cells, mx2s, IBS-D

city: Guangzhou

first: Liyan

last: Ji

address: No. 232 Waihuan East Road, Higher Education Mega Center, Panyu District

institute: Guangzhou university of Traditional Chinese Medicine

description:
Library name: mx2s
10x Genomics

data_processing:
After sequencing, the transcriptome sequencing expression profiles of each single-cell were obtained. The cells were labeled with Barcode, the genes were labeled with UMI, and the expression levels were recorded. Cell RangerTM (v7.1.0) analyzes mRNA to obtain counts. Based on toolkits such as Seurat (v4.0.1), harmony (v0.1.0), SingleR (v1.10.0) and ArchR (v1.0.2) in R (v4.4.1), t-SNE dimension reduction and K-clustering were performed on cell transcriptome data, cell populations were identified based on GSEA analysis, and enrichment analysis was applied to analyze the regulatory signals and phenotypic signals in subpopulation cells.
The slingshot (v2.12.0) was used to estimate the pseudotime prediction using slingshot function.
The cell-cell communication analysis was conducted by CellChat (v1.5.0) package followed the of Cellchat’s protocol.
The gene expression matrix was used for the detection of regulon activity in rat. The transcription factor regulon of cell subpopulations was identified by pySCENIC using mus musculus species. SCENIC grnboost2 was used to quantify the rank of transcription factors. The regulon activiey was calculated by aucell function.
Assembly: mRatBN7.2
Supplementary files format and content: Tab-separated values files and matrix files

organism: Rattus norvegicus

source_name: colon

extract_protocol:
From the 2nd to the 14th day after birth, the suckle rats were separated from the mother rats for 180 minutes each time, once a day. Then from the 15th to the 27th day, the paraffin-lubricated infusion catheter (with a diameter of 1 mm) was inserted through the anus for 1 to 2 cm, and 0.2 to 0.5 ml of 0.087mol/L acetic acid was injected. The dosage of acetic acid was 0.2 ml starting from the 15th day, increasing by 0.1 ml every two days until it remained unchanged at 0.5 ml from the 21st day after birth. Acetic acid was administered to the rectum once a day. After the stimulation, the front shoulder, front upper limb and chest of the rats were immediately bound with paper bags. Restrict the scratching of the head and face with the front upper limb, without limitation of its movement. The restraint time is 1 hour. From the 27th day for two weeks, no operation should be carried out and normal feeding should be conducted. After the modeling was completed, the success of the model was judged through fecal Bristol classification score, abdominal wall retraction reflex (AWR), and in vitro intestinal movement experiments. Samples were collected under terminal anesthesia (4% isoflurane). After anesthetizing the rats, the freed distal colon was cut into small pieces under moist conditions and placed in an Erlenmeyer flask. Each time, 5 ml of digestive enzyme was added to the flask, and the supernatant was stirred with a rotor. Every 15 minutes, the supernatant was transferred to an EP tube containing serum. After digestion, it was passed through a 40 μm cell strainer, then collected and centrifuged. After centrifugation, cells were diluted and sorted by flow cytometry.
The 8-channel microfluidic "double cross" cross-system was applied to combine Gel Beads containing Barcoded RT Primers, the mixture of cells and enzymes, and oil to form GEMs, that is, the oil droplets encapsulating the mixture of Gel Beads, cells and enzymes. GEMs were collected after the reaction (single-cell capture rate ≈65%). After the formation of GEM, the cells lysed, and the gel beads automatically dissolved to release a large number of barcode sequences. Subsequently, the mRNA was reverse transcribed to produce cDNA with Barcode and UMI information. Oil droplet fragmentation, cDNA as template for PCR amplification, followed by cDNA interruption, addition of sequencing connector P5 and sequencing primer R1 and other traditional second-generation sequencing library construction processes for single-cell transcriptome sequencing.

value: colon

value: mucosal cells

value: model


title: Multiplexed 4

city: Chalk River

first: Yi

state: Ontario

address: 286 Plant Road

department: Radiology and Health

country: Canada

institute: Canadian Nuclear Laboratories

description:
Library name: Pool 4
PBMCs from TNBC donors 2 and 3 treated with NK-EVs for 72h (multiplexed in pool 2), raw FASTQ files are multiplexed pools, see config files for demultiplexing information. Pool 4 also contains positive control samples, which were not included in this present analysis.

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Quality control filtering retained cells with 500-4,500 detected genes, 500-14,000 total UMI counts, and <10% mitochondrial gene content. Doublets were identified and removed using scDblFinder. After QC, 88,213 high-quality cells were retained.
Gene expression data were normalized using SCTransform v2 with mitochondrial gene percentage regression. Batch effects were corrected using Harmony integration by donor ID. Dimensionality reduction was performed using PCA followed by UMAP visualization.
Hierarchical clustering was performed using TooManyCells spectral clustering algorithm. Cell type identification used canonical marker genes, e.g.: B cells (MS4A1, CD19, PAX5, IGHD), CD4+ T cells (CD4, CCR4, FOXP3), CD8+ T cells (CD8A, CCR5, GZMH), dendritic cells (CLEC11A, LAMP3, ENPP2), NK cells (NCAM1, KLRD1, PRF1).
Differential expression analysis was conducted using DESeq2 on pseudobulk aggregated data with FDR < 0.05. Pathway analysis was performed using MSigDB C2 collections with Benjamini-Hochberg correction.
Assembly: hg38
Supplementary files format and content: HDF5 (10X Genomics Cell Ranger output): Raw UMI counts, filtered cell barcodes, and gene features
Supplementary files format and content: Pool*_config.csv (4 files): Cell Ranger configuration for sample demultiplexing, probe barcode assignments (BC001 - BC004) mapping to sample IDs

source_name: Peripheral blood

growth_protocol: PBMCs from healthy donors (n=3) and triple-negative breast cancer (TNBC) patients (n=3) were purchased from StemCell Technologies. PBMCs were cultured in serum-free, xeno-free, and feeder-free ImmunoCult-XF T Cell Expansion Medium (StemCell Technologies, cat#10981) and maintained at 3-8 × 10^5 cells/mL. PBMCs were also cultured with 5% Heat-Inactivated Fetal Bovine Serum (HI-FBS, Gibco, cat#12484-028). Cells were incubated at 37°C with 5% CO2.

extract_protocol:
The treated PBMCs were collected into 1.5 mL tubes and centrifuged at 400 x g for 5 min at 4°C. Cells were washed with fresh media, resuspended for counting, then washed with ice-cold PBS. Cells were resuspended in fixation buffer (10X Genomics) and incubated for 22 hours at 4°C. Fixed cells were resuspended in quenching buffer, and enhancer buffer with 10% glycerol was added for sample integrity. Fixed and permeabilized samples were stored at -80°C until library construction.
Library was performed according to the manufacturer's instructions (single cell 3' v2 protocol, 10x Genomics). Briefly, fixed PBMCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscribed to cDNA, which contains an Illumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the appropriated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Illumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added. Libraries were sequenced on NovaSeq X platform generating 0.65-1.07 billion reads per pool.

treatment_protocol: NK-EV treatment: PBMCs were seeded at 2.5 x 10^5 cells per well in U-bottom 96-well plates in ImmunoCult-XF T Cell Expansion Medium (200 µL final volume). Treatment groups received 5 x 10^11 EVs/mL NK-EVs (dosing volume limited to 55% of total assay volume), while control groups received medium only. Cells were incubated at 37°C with 5% CO2 for 72 hours.

value: Peripheral blood

tag: donor id

value: DD2, DD3

value: PBMCs

value: Triple negative breast cancer (TNBC)

value: NK-EV (5e11 EVs/mL, 72h)


title: I-epi-20w-Apc-4-773

source_name: ileum epithelial cell

value: ileum epithelial cell

value: ApcMin

value: Untreated

value: 20 weeks old


title: V3_ki67-myc+_ROI7_S1_Vehicle

description:
Library name: DSP-1001660037306-B-B03
Tumor V3, Slide S1, ROI 7, Segment ki67-myc+, Replicate V3_ki67-myc+. Raji xenograft in NSG mouse, NanoString GeoMx DSP WTA v1.0.

value: Raji Burkitt lymphoma xenograft

value: Vehicle


title: Multiplexed 3

description:
Library name: Pool 3
PBMCs from TNBC patient 1 treated with NK-EVs for 72h (multiplexed in pool 3) and PBMCs from TNBC donors 1, 2, 3 without treatment. Raw FASTQ files are multiplexed pools, see config files for demultiplexing information.

value: DD1, DD2, DD3

value: NK-EV (5e11 EVs/mL, 72h) and untreated control (72h)


title: intestinal mucosal cells, mx1s, IBS-D

description:
Library name: mx1s
10x Genomics


title: I-epi-20w-Apc-3-743


title: V3_ki67+myc+_ROI7_S1_Vehicle

description:
Library name: DSP-1001660037306-B-B02
Tumor V3, Slide S1, ROI 7, Segment ki67+myc+, Replicate V3_ki67+myc+. Raji xenograft in NSG mouse, NanoString GeoMx DSP WTA v1.0.

value: Raji (ATCC CCL-86)


title: Multiplexed 2

description:
Library name: Pool 2
PBMCs from healthy donors 2 and 3 treated with NK-EVs for 72h (multiplexed in pool 2), raw FASTQ files are multiplexed pools, see config files for demultiplexing information. Pool 2 also contains positive control samples, which were not included in this present analysis.

value: HD2, HD3

value: Healthy


title: intestinal mucosal cells, zc3, normal

description:
Library name: zc3
10x Genomics

value: colon

value: mucosal cells

value: normal


title: V3_ki67-myc-_ROI6_S1_Vehicle

description:
Library name: DSP-1001660037306-B-B01
Tumor V3, Slide S1, ROI 6, Segment ki67-myc-, Replicate V3_ki67-myc-. Raji xenograft in NSG mouse, NanoString GeoMx DSP WTA v1.0.


title: I-epi-20w-Apc-2-731


title: intestinal mucosal cells, zc1, normal

description:
Library name: zc1
10x Genomics


title: TBX5 degron + 500 nM dTAGv-1 ligand (24 h) rep 3 - RNAseq

city: San Francisco

first: Benoit

middle: G.

last: Bruneau

state: CA

address: 1650 Owens St

institute: Gladstone Institutes

description:
Library name: dTAGv1_TBX5-degron_24h_RNAseq_rep3
TBX5-degron_dTAGv-1_24h_rep3

data_processing:
The .fastq files were aligned to hg38 reference genome using HISAT2 for alignment and featureCounts (2.0.6) was used to count the reads numbers mapped to each gene. Differential expression analysis for two conditions/groups was performed using the DESeq2 R package(1.42.0). DESeq2 provides statistical programs for determining differential expression in digital gene expression data using models based on negative binomial distribution. The resulting P-value is adjusted using the Benjamini and Hochberg’s methods to control the error discovery rate.
Assembly: hg38
Supplementary files format and content: .txt format of gene counts and fpkm values

molecule: polyA RNA

source_name: atrial cardiomyocyte differentation

growth_protocol: An FKBP12F36V with 2x HA (DOI: 10.1038/s41589-018-0021-8) tag was used to generate a cell line in which TBX5 could be induced for degradation. The tag was inserted immediately after the start methionine codon in the N-terminus of the endogenous TBX5 locus using ribonucleoprotein (RNP) complexes of sgRNA (GCCCTCGTCTGCGTCGGCCA, ordered from Synthego) and SpCas9-NLS ‘HiFi’ protein (QB3 MacroLab, University of California Berkeley). Donor template sequences for each were provided by using HDR Alt-R gene blocks (IDT). 250,000 WTc11 iPSCs were resuspended in 12.2 µl Lonza P3 transfection buffer and nucleofected with 1 µg donor template and 10 µl RNPs using Lonza Nucleofector 4D system in 96-well format using DS-138 settings. Single cell colonies were screened by PCR using primers pairs flanking the whole insertion site (F: 5’-TCCTCAGAGCAGAACCTTGC, R: 5’-CTTACCTGCTGGGTGAAGG). Amplicon from whole insertion site PCR was amplified and verified by Sanger sequencing. All clones used were determined to have a normal karyotype. Cells were grown in 1 well of a 12-well dish per replicate. Atrial (StemCell Technologies #100-0215) kits were used to differentate iPSCs into cardiomyocytes. DMSO or dTAGv-1 samples were treated at d20 with DMSO or 500 nM dTAGv-1 (Tocris, #6914) ligand for 24 h before harvesting.

extract_protocol:
Cells were dissociated in 0.25% Trypsin-EDTA for 10 mins, followed by quenching in 15%FBS in DPBS. Cells were lifted off the dish and resuspended to single cells by repeatedly using P1000 pipette and then transferred to a 1.5 ml tube and centrifuged at 300 x g for 5 min at room temperature. Pellets were snap frozen in dry ice. Total RNA was isolated using Qiagen RNeasy micro kit (Qiagen #74004) with QIAshredder (Qiagen #79656) and eluted in 25 µl water. RNA concentration was determined using Nanodrop and quality was checked using Agilent Bioanalyzer.
Messenger RNA was purified from total RNA using poly-T oligo-attachedmagnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the secondstrand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.

value: atrial cardiomyocyte differentation

value: TBX5-FKBP12-F36V edited WTC11

value: cardiomyocyte

value: 500 nM dTAGv-1 ligand (24 h)


title: Multiplexed 1

description:
Library name: Pool 1
PBMCs from healthy donor 1 treated with NK-EVs for 72h (multiplexed in pool 1) and PBMCs from healthy donors 1, 2, 3 without treatment. Raw FASTQ files are multiplexed pools, see config files for demultiplexing information.

value: Peripheral blood

value: HD1, HD2, HD3

value: PBMCs


title: I-epi-20w-Apc-1-727

value: ileum epithelial cell

value: ApcMin

value: Untreated

value: 20 weeks old


title: WT_rep3

city: Kansas City

first: Shiyuan

middle: (Cynthia)

last: Chen

state: MO

department: Computational Biology

institute: Stowers Institute for Medical Research

description: Library name: WT_rep3

data_processing:
Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18. Reads were aligned to UCSC genome dm6 with TopHat v2.0.13 , default parameters , using Ensembl 87 gene models. FPKM values were generated using Cufflinks v2.2.1 with “-u –max-bundle-frags 100000000”. Read counts were generated using HTSeq-count with “-m intersection-nonempty”.
Assembly: dm6
Supplementary files format and content: FPKM expression table in csv file

organism: Drosophila melanogaster

source_name: Ovary

extract_protocol:
Newly emerged flies expressing UAS-GFP and E-cadherin RNAi driven by c587ts in IGS cells were cultured for 1 week at 29°C. The ovaries were then dissected, placed in Grace’s medium, washed twice with 1X DPBS, and centrifuged at 700 g for 1 minute. Next, the ovaries were incubated in prewarmed collagenase solution at 37°C in a water bath for 3 minutes with gentle shaking, after which the enzymatic reaction was stopped by adding cold 1X DPBS containing 2% FBS. The dissociated samples were washed with 1X DPBS and centrifuged at 700 g and 4°C for 5 minutes. The cell pellet was resuspended in 1X DPBS, filtered through a 70 µm cell strainer, pelleted again by centrifugation, and finally resuspended in 200 µl of 1X DPBS for immediate sorting of GFP-positive cells.
1,000 cells from each of three biological replicates for both the control and E-cadherin RNAi groups were collected. cDNA was synthesized using the SMART-seq v4 Ultra Low Input RNA kit, and libraries were prepared with the Nextera XT DNA Sample Preparation Kit and Index kits. Both cDNA samples and libraries were quality-checked on a Bioanalyzer 2100 before RNA sequencing. Libraries were sequenced as 75-bp paired-end reads on an Illumina NextSeq platform, generating over 20 million FASTQ reads per sample.

value: Ovary

value: IGS cell

value: control


title: V3_ki67-myc+_ROI6_S1_Vehicle

description:
Library name: DSP-1001660037306-B-A12
Tumor V3, Slide S1, ROI 6, Segment ki67-myc+, Replicate V3_ki67-myc+. Raji xenograft in NSG mouse, NanoString GeoMx DSP WTA v1.0.

value: Raji Burkitt lymphoma xenograft

value: Raji (ATCC CCL-86)

value: Vehicle


title: V3_ki67+myc+_ROI6_S1_Vehicle

description:
Library name: DSP-1001660037306-B-A11
Tumor V3, Slide S1, ROI 6, Segment ki67+myc+, Replicate V3_ki67+myc+. Raji xenograft in NSG mouse, NanoString GeoMx DSP WTA v1.0.


title: I-epi-20w-Apc-5-775


title: WT_rep2

description: Library name: WT_rep2


title: TBX5 degron + 500 nM dTAGv-1 ligand (24 h) rep 2 - RNAseq

description:
Library name: dTAGv1_TBX5-degron_24h_RNAseq_rep2
TBX5-degron_dTAGv-1_24h_rep2

value: atrial cardiomyocyte differentation


title: I-epi-20w-WT-4-776


title: V3_ki67+myc+_ROI5_S1_Vehicle

description:
Library name: DSP-1001660037306-B-A10
Tumor V3, Slide S1, ROI 5, Segment ki67+myc+, Replicate V3_ki67+myc+. Raji xenograft in NSG mouse, NanoString GeoMx DSP WTA v1.0.


title: D5_ki67-myc-_ROI11_S1_Milademetan

description:
Library name: DSP-1001660037306-B-B10
Tumor D5, Slide S1, ROI 11, Segment ki67-myc-, Replicate D5_ki67-myc-. Raji xenograft in NSG mouse, NanoString GeoMx DSP WTA v1.0.

value: Milademetan 20mg/kg


title: I-epi-20w-WT-3-774


title: WT_rep1

description: Library name: WT_rep1


title: I-epi-20w-WT-2-747


title: Shg_rep3

description: Library name: Shg_rep3

value: RNAi knockdown of shg


title: TBX5 degron DMSO (24 h) rep 3 - RNAseq

description:
Library name: DMSO_TBX5-degron_24h_RNAseq_rep3
TBX5-degron_DMSO_24h_rep3

value: TBX5-FKBP12-F36V edited WTC11

value: cardiomyocyte

value: DMSO 24 h


title: TBX5 degron DMSO (24 h) rep 2 - RNAseq

description:
Library name: DMSO_TBX5-degron_24h_RNAseq_rep2
TBX5-degron_DMSO_24h_rep2


title: I-epi-20w-WT-1-730


title: Shg_rep2

description: Library name: Shg_rep2


title: D5_ki67+myc+_ROI11_S1_Milademetan

description:
Library name: DSP-1001660037306-B-B08
Tumor D5, Slide S1, ROI 11, Segment ki67+myc+, Replicate D5_ki67+myc+. Raji xenograft in NSG mouse, NanoString GeoMx DSP WTA v1.0.


title: TBX5 degron DMSO (24 h) rep 1 - RNAseq

description:
Library name: DMSO_TBX5-degron_24h_RNAseq_rep1
TBX5-degron_DMSO_24h_rep1


title: D5_ki67-myc+_ROI10_S1_Milademetan

description:
Library name: DSP-1001660037306-B-B07
Tumor D5, Slide S1, ROI 10, Segment ki67-myc+, Replicate D5_ki67-myc+. Raji xenograft in NSG mouse, NanoString GeoMx DSP WTA v1.0.


title: ChIP-seq of Homo sapiens: atrial cardiomyocyte differentiation at D20 from WT WTC11 rep2 - H3K27ac

description: Library name: d20_atrial_CM_H3K27ac_rep2

data_processing:
Fastq files were aligned to the hg38 reference genome using bowtie2. Reads were filtered to include of those with a mapq score of 30 or greater and removing duplicate reads using SAMtools. Blacklisted regions were removed using BEDtools. RAD21 and WT H3K27ac ChIP-seq peaks were called on each individual replicate relative to input using macs2 and the broadpeaks parameter. H3K27ac ChIP-seq data used for differential analysis between WT, TBX5in/+ and TBX5in/del samples were analyzed using the nextflow chip-seq pipeline with the macs2 broadpeaks parameter (DOI: 10.1038/s41587-020-0439-x)
Assembly: hg38
Supplementary files format and content: .narrowPeak of peaks and .bw of signal profiles
Supplementary files format and content: .bed for consensus or merged peaks

growth_protocol: Atrial (StemCell Technologies #100-0215) kits were used to differentate iPSCs into cardiomyocytes. Cells were grown in one 6-well plate per replicate, with all 6 wells pooled together after dissociation for the crosslinking step (approximately 20 million cells). Each plate was one biological replicate.

extract_protocol:
Cells were grown in one 6-well dish per replicate, with all 6 wells pooled together after dissociation for the crosslinking step (approximately 20 million cells). Cells were dissociated in 0.25% Trypsin-EDTA for 10 mins, followed by quenching in 15%FBS in DPBS. Cells were lifted off the dish and resuspended to single cells by repeatedly using P1000 pipette and then transferred to a 15 ml tube and centrifuged at 800 rpm for 5 min at room temperature. Pellets were washed once in 10 ml DPBS plus 1x protease inhibitors (DBPS+PI) before resuspending entire cell pellet in exactly 10 ml DPBS+PI. 16% methanol-free formaldehyde was added to a final concentration of 1% and samples incubated on nutator at room temperature for 10 min. Samples were quenched with 2.5 M glycine to a final concentration of 0.125 M and incubated on nutator at room temperature for 5 min, followed by centrifugation at 500 x g for 5 min at 4˚C. Samples were washed once in ice cold DPBS+PI, before being transferred to 2 ml protein lo-bind tubes, centrifuged at 2500 x g at 4˚C. for 5 min and cell pellets were snap frozen in liquid nitrogen and stored at -80˚C. Cell lysis for 10 min at 4˚C (cell lysis buffer recipe: 20 mM Tris-HCl pH 8.0, 85 mM KCl, 0.5% IGEPAL CA-630 and 1x protease inhibitors in ddH2O). Nuclear lysis for 30 min on ice  (nuclear lysis buffer recipe: 1% SDS, 10 mM EDTA, 50 mM Tris-HCl, pH 8.0, and 1x protease inhibitors in ddH2O). Samples were transferred to 1 ml millitube (Covaris #520130) and sheared using a Covaris S2 sonicator for 15 min at 5% duty cycle, intensity 5, 200 cycles per burst in a water bath maintained at 4˚C. 60 µg of chromatin was used per sample. After diluting in dilution buffer, each ChIP sample was incubated rotating at 4˚C overnight with antibodies (9 µg rabbit anti-RAD21 [Abcam, #ab992] or 10 µg rabbit anti-H3K27ac [Active Motif, #39133] and the following day incubated with 50 µl prewashed Pierce protein A/G beads for 4 hours at 4˚C. Bead washes were performed by resuspending beads in 1 ml buffer using P1000 pipette, spinning briefly and collecting on magnet. Wash buffer 1 recipe (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM EDTA, 0.1% SDS and 1% Triton X-100 in ddH2O), wash buffer 2 recipe (20 mM Tris-HCl pH 8.0, 500 mM NaCl, 2 mM EDTA, 0.1% SDS and 1% Triton X-100 in ddH2O) and wash buffer 3 (250 mM LiCl, 1% IGEPAL CA-630 [Sigma #I8896], 1% sodium deoxycholate, 1 mM EDTA and 10 mM Tris-HCl pH 8.0 in ddH2O) and elution buffer (1% SDS, 100 mM NaHCO3 in ddH2O). Following the bead washes, DNA was eluted in 50 µl shaking at 37˚C, transferring to new tube and repeating bead elution to pool eluates to a total volume of 100 µl. Both ChIP and input samples were incubated at 37˚C for 30 min at 37˚C with 1 µl RNase A, followed addition of 12 µl 5 M NaCl and reverse crosslinking with 1 µl proteinase K at 65˚C overnight. DNA was purified using ChIP DNA Clean and Concentrator kit (Zymo Research #D5205).
For Illumina sequencing library preparation, the entire ChIP sample or 2 µl of each input was used. End repair was performed in a 100 µl reaction with 15 U T4 DNA polymerase (New England Biolabs #M0203L), 5 U Klenow fragment DNA polymerase (New England Biolabs, #M0210L), 50 U T4 PNK (New England Biolabs #M0201L), 400 µM dNTP (Promega #U1511) and 1x T4 DNA ligase buffer w 10 mM ATP (New England Biolabs #B0202S) in nuclease-free water for 30 min at room temperature, followed by 1.6x bead:sample AmpureXP purification. Entire eluate was used for A-tailing in a 50 µl reaction with 1 mM dATP (New England Biolabs #N0440S), 15 U Klenow 3’>5’ exonuclease (New England Biolabs #M0212L) and 1x NEB buffer 2 in nuclease-free water for 30 min at 37˚C, followed by 1.6x bead:sample AMPureXP purification. Entire eluate was used for adapter ligation in a 50 µl reaction with 6000 U T4 DNA ligase (New England Biolabs #M0202L), 20 nM annealed and uniquely indexed adapters and 1x T4 DNA ligase buffer with 10 mM ATP (New England Biolabs #B0202S) in nuclease-free water for 2 hours at room temperature, followed by 1x bead:sample AMPureXP purification. Adapters were prepared by annealing following HPLC purified oligos: 5’-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATC*T and 5’Phos-GATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG where * represents a phosphothiorate bond and NNNNNN is a Truseq index sequence.The entire eluate was used for PCR amplification in a 50 µl reaction with 1x NEB Next High-Fidelity 2x PCR master mix (New England Biolabs #M0541L), 10 µM primers (F: 5’-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGA, R: 5’-CAAGCAGAAGACGGCATACGAGAT) in nuclease free water, using thermocycler settings 98˚C for 30 sec; 16 cycles of 98˚C for 10 sec, 58˚C for 40 sec and 72˚C for 30 sec; 72˚C for 5 min and followed by 0.8x bead:sample AMPureXP purification. DNA was quantified using Qubit Fluorometer and dsDNA HS Assay Kit and quality assessed on Agilent Bioanalyzer. ChIP-seq libraries were sequenced on a NovaSeq X (Illumina) using 50 bp paired-end reads.

value: WT


title: Male, dsx-RNAi, F1 embryo, replicate 4

source_name: embryo

value: embryo

value: AsymCX

value: Male

value: 1 day

value: dsx-RNAi


title: Male, dsx-RNAi, Head, replicate 1

source_name: head

value: head

value: adult


title: ccRCC tumor bulk RNA-seq 8edf

city: PARIS

first: Isaias

last: Hernandez-Verdin

state: Ile-de-France

address: GH PITIE SALPETRIERE ICM IHU A, 47 Boulevard DE L'HOPITAL

department: Genetics and Development of Nervous System Tumors

country: France

institute: Institut du cerveau

description:
8edf
processed data file column header:
8edf

data_processing:
RNA fastq files were aligned to the human reference genome using  kallisto (version 0.46.2)
Assembly: Genome build: GRCh38, release 97
Supplementary files format and content: tab-delimited text files include read counts for each Sample

source_name: Kidney

extract_protocol:
Total RNA was extracted from formalin-fixed paraffin embedded (FFPE) tumours using the Allprep DNA/RNA FFPE Kits according to the manufacturer’s instructions (Qiagen, #80234). The sizing, quantitation, integrity and purity of all samples were measured using the 2100 Bioanalyzer instrument (Agilent).
Sequencing libraries were prepared by IntegraGen as described in Foley et al (Genome Research, 2019) and sequenced with the Illumina NovaSeq.

value: Kidney

tag: disease state

value: renal cell cancer

tag: cancer type

value: Clear cell renal cell carcinoma


title: HCT116, 10Gy radiation, day 2, bio rep 2

city: Toronto

first: Gregory

last: Schwartz

address: 101 College Street

institute: Princess Margaret Cancer Centre

description: Library name: Sample 11

data_processing:
fastp was used for QC and adaptor trimming, reads were aligned with STAR, featureCounts was used to obtain gene counts
Assembly: GRCh38
Supplementary files format and content: tsv files outlining the counts per gene

extract_protocol:
TriZol reagent (Life Technologies, 15596018)
Illumina Stranded mRNA Prep


title: Mixture of MCF10A and HCT116, non-treated, day 2, bio rep 1

description: Library name: Sample 13

source_name: HCT116 + MCF10A

value: HCT116 + MCF10A


title: Cil 1360 P1

city: Pittsburgh

first: Uma

last: Chandran

state: PA

address: 5607 Baum Blvd

institute: University of Pittsburgh

hyb_protocol: 15-μg of purified, amplified, biotin-labeled cRNA was fragmented and hybridized to an Affymetrix Mouse ClariomTM S array (ThermoFisher Scientific 902930) for 18 hours.

scan_protocol: Washing, staining, and scanning of arrays were performed on an Affymetrix Fluidics Station 450 and Scanner 3000 immediately after hybridization according to manufacturer’s instructions (ThermoFisher Scientific 00-0079, 00-0210).

data_processing:
Scanned microchips (in .Cel format) were imported in Transcription Analysis Software (TAC software, ThermoFisher Scientific version 2.0) and compared statistically.
The data were analyzed with Microarray Suite version 2.0  using Affymetrix default analysis settings and global scaling as normalization method. T

label: biotin

source_name: primary fibroblasts

label_protocol: In-vitro transcription was performed with 100 ng of purified total RNA using the MessageAmp Premier Enhanced assay protocol (Fisher Scientific).

growth_protocol: Primary fetal mouse lung fibroblasts were prepared from E18.5 fetal mice, plated in 10cm culture plates and maintained in Waymouth media supplemented with 10% fetal bovine serum.

extract_protocol: Total cellular RNA was isolated from mouse fetal lung fibroblasts following the TRIzol (Ambion, USA) extraction protocol. The concentration and purity (RIN No.) of RNA were determined using a NanoDrop spectrophotometer and the Bioanalyzer.

treatment_protocol: Prepared primary fetal mouse lung fibroblasts were cultured in 6 well plates and treated for 6 hours with 10-6M DES-Cic, dexamethasone and control media.

value: lung E18.5 fetal mouse


title: ChIP-seq of Homo sapiens: atrial cardiomyocyte differentiation at D20 from WT WTC11 rep1 - H3K27ac

description: Library name: d20_atrial_CM_H3K27ac_rep1

value: atrial cardiomyocyte differentation


title: I-epi-8w-Apc-3-755

data_processing:
The library was loaded onto the instrument with Sequel Sequencing Kit 2.1 (4 rxn) (Part Number PB 101-310-500) and a Sequel™ SMRT® Cell 1M v2 Tray (4 cells) (Part Number PB101-008-000) for sequencing.
Assembly: The training method of the QIIME2 classifier follows these steps: - Extract all the read datafrom a reference database, in our report, SILVA version 138 with 99% similarity was used.
Supplementary files format and content: File name = abs-abund-table-7 (all 90 samples); Format = excel (.xlsx); Content = raw counts of sequencing reads for the bacteria strain
Supplementary files format and content: File name = rel-table-7 (all 90 samples); Format = excel (.xlsx); Content=relative abundance of sequencing reads for the bacteria strain

extract_protocol:
Fecalpellets werecollected asepticallyand placed in sterile eppendorf. Immediately freezing stool in liquid nitrogen (LN) and store at -80°C. Extract stool bacterial DNA followed by QIAamp Fast DNA Stool Kit protocol.
For the PacBio library construction and sequencing, 16S rRNA was amplified by using primer set 27F: AGRGTTYGATYMTGGCTCAG and 1492R: RGYTACCTTGTTACGACTT followed by purification via binding to pre-washed AMPure PB beads (Part Number PB100-265-900)
16S ribosomal RNA (rRNA) gene sequencing

value: ileum epithelial cell

value: ApcMin

value: Untreated

value: 8 weeks old


title: D5_ki67-myc-_ROI4_S1_Milademetan

city: Umeå

first: Lixiao

institute: Umeå University

description:
Library name: DSP-1001660037306-B-A09
Tumor D5, Slide S1, ROI 4, Segment ki67-myc-, Replicate D5_ki67-myc-. Raji xenograft in NSG mouse, NanoString GeoMx DSP WTA v1.0.

data_processing:
FASTQ files were converted to DCC count files via NanoString GeoMx NGS Pipeline. DCC files loaded into R using GeomxTools (Bioconductor). Segment QC: min 1,000 reads, 75% alignment, 50% saturation, 20 nuclei, 1,000 um2 area. Probe QC: ratio >0.1, Grubbs outlier removal. Aggregated to gene-level by geometric mean.
Counts imported into standR (Bioconductor) as SpatialExperiment. Low-expression genes filtered (sample_fraction=0.9, min_count=5). TMM normalization (edgeR). Batch effects assessed by PCA.
DE analysis: limma-voom with duplicateCorrelation (tumor as block). Treatment comparisons per cell population. Gene set analysis: limma::camera for MYC targets, ribosomal, cell cycle, apoptosis pathways. Significance: BH-adjusted P < 0.05 and |log2FC| > 0.5.
R (v4.4.2), GeomxTools, standR, limma, edgeR, SpatialExperiment (Bioconductor).
Assembly: hg38 (GRCh38)
Supplementary files format and content: DCC files: per-AOI probe-level count files from NanoString GeoMx NGS Pipeline, containing raw/trimmed/stitched/aligned read counts and per-probe expression values
Supplementary files format and content: standR_counts.txt: tab-delimited gene-level raw count matrix (genes x 92 AOIs)
Library strategy: Spatial Transcriptomics

source_name: Raji Burkitt lymphoma xenograft

extract_protocol:
FFPE tumor sections were processed on the NanoString GeoMx Digital Spatial Profiler (DSP) at the Genomic Medicine Sweden Center North / Clinical Genomics Umea. Sections were stained with fluorescent antibodies against Ki67 and c-Myc. Within each ROI, cells were segmented into four populations: Ki67+MYC+, Ki67-MYC+, Ki67-MYC-, and Ki67+MYC-. UV-cleavable oligonucleotide tags from each segment (AOI) were collected for library preparation.
Libraries were prepared using the NanoString GeoMx NGS Library Preparation Kit per manufacturer protocol. Human NGS Whole Transcriptome Atlas (WTA v1.0) panel (~18,000 genes). Each AOI received a unique indexing barcode. 92 AOIs across 10 tumors on four slides (S1-S4), each slide containing both conditions.

value: Raji Burkitt lymphoma xenograft

value: Raji (ATCC CCL-86)

value: Milademetan 20mg/kg


title: ChIP-seq of Human: atrial CM differentiation at D20 from WTC11 with TBX5in/del rep2 - H3K27ac for differential analyses

description: Library name: TBX5_null_H3K27ac_diff_rep2

value: cardiomyocyte


title: Macrophages_RNA_SCIENCE_6

city: Boston

first: Evgeny

last: Deforzh

state: MA

address: 60 Fenwood Rd, Brigham and Women's Hospital Neurology Department, 9th Floor

department: Neurology

institute: Brigham and Women's Hospital

description: Library name: Sample 12

data_processing:
Duplicate reads were collapsed into a fasta file, with duplicate counts per read calculated using fastx_toolkit (version 0.0.14).
Chimeric reads were aligned to a reference fasta file containing transcript sequences (hg38_Homo_sapiens.GRCh38.100.fasta) using BWA-MEM in local alignment mode considered transcript strand only
Pairs of genes from each chimeric read were identified, and the number of reads for each gene pair was quantified with ChiRA
Assembly: GRCh38/hg38

source_name: primary glioma tumors

extract_protocol:
Nuclei were distributed into 96-well plates by limiting dilution. Nuclear membranes were lysed and chromatin was reverse-crosslinked by incubation with Proteinase K for 4 h at 65 °C followed by 15 min 95 °C to deactivate Proteinase K.  Biotinylated RNA complexes were captured using streptavidin magnetic beads and transferred to fresh wells. For 3′ RNA end repair, bead-enriched RNA–RNA crosslinked material was washed in ice-cold T4 polynucleotide kinase (PNK) buffer and treated with 0.5 U T4 PNK (NEB) in an 80-µL reaction at 37 °C for 4 h. Subsequently, fresh ATP (1 mM final) and an additional 0.5 U T4 PNK were added in a total volume of 100 µL and incubated for 1 h at 37 °C to repair 5′ RNA ends, followed by the removal of the buffer. RNA–RNA chimeras were generated by ligation in T4 RNA ligase buffer (NEB) supplemented with 1 mM ATP, 0.5 U/µL RNase inhibitor, and 2.5 U/µL T4 RNA ligase 1 (NEB) at 37 °C for 1 h with continuous agitation. Reverse crosslinking was completed by UV irradiation at 254 nm for 5 min on ice. RNA on Streptavidine beads was washed once with 1x scRT Buffer (Takara, #634444).
RT and subsequent steps were performed using the SMART-Seq® Stranded Kit (Takara, #634444), following the manufacturer’s instructions.

value: primary glioma tumors

value: WT


title: D5_ki67-myc+_ROI4_S1_Milademetan

last: Wang

address: Medicinsk biovetenskap, M21, Försörjningsvägen 1

description:
Library name: DSP-1001660037306-B-A08
Tumor D5, Slide S1, ROI 4, Segment ki67-myc+, Replicate D5_ki67-myc+. Raji xenograft in NSG mouse, NanoString GeoMx DSP WTA v1.0.


title: Neurons_RNA_SCIENCE

description: Library name: Sample 13


title: I-epi-8w-Apc-1-748

city: Taipei

first: Linda

last: Yu

address: 1 Jen-Ai Rd. Sec. 1

institute: National Taiwan University


title: ChIP-seq of Human: atrial CM differentiation at D20 from WTC11 with TBX5in/del rep1 - H3K27ac for differential analyses

description: Library name: TBX5_null_H3K27ac_diff_rep1


title: D5_ki67+myc+_ROI4_S1_Milademetan

description:
Library name: DSP-1001660037306-B-A07
Tumor D5, Slide S1, ROI 4, Segment ki67+myc+, Replicate D5_ki67+myc+. Raji xenograft in NSG mouse, NanoString GeoMx DSP WTA v1.0.


title: ChIP-seq of Human: atrial CM differentiation at D20 from WTC11 with TBX5in/+ rep2 - H3K27ac for differential analyses

description: Library name: TBX5_Het_H3K27ac_diff_rep2


title: Macrophages_RNA_SCIENCE_5

description: Library name: Sample 11


title: I-epi-8w-WT-5-772


title: D5_ki67-myc+_ROI3_S1_Milademetan

description:
Library name: DSP-1001660037306-B-A06
Tumor D5, Slide S1, ROI 3, Segment ki67-myc+, Replicate D5_ki67-myc+. Raji xenograft in NSG mouse, NanoString GeoMx DSP WTA v1.0.


title: Macrophages_RNA_SCIENCE_4

description: Library name: Sample 10


title: ChIP-seq of Human: atrial CM differentiation at D20 from WTC11 with TBX5in/+ rep1 - H3K27ac for differential analyses

description: Library name: TBX5_Het_H3K27ac_diff_rep1


title: I-epi-8w-WT-4-771


title: D5_ki67+myc+_ROI3_S1_Milademetan

description:
Library name: DSP-1001660037306-B-A05
Tumor D5, Slide S1, ROI 3, Segment ki67+myc+, Replicate D5_ki67+myc+. Raji xenograft in NSG mouse, NanoString GeoMx DSP WTA v1.0.


title: ChIP-seq of Human: atrial CM differentiation at D20 from WT WTC11 rep2 - H3K27ac for differential analyses

description: Library name: TBX5_WT_H3K27ac_diff_rep2


title: I-epi-8w-WT-3-770


title: D5_ki67-myc+_ROI2_S1_Milademetan

description:
Library name: DSP-1001660037306-B-A04
Tumor D5, Slide S1, ROI 2, Segment ki67-myc+, Replicate D5_ki67-myc+. Raji xenograft in NSG mouse, NanoString GeoMx DSP WTA v1.0.


title: ChIP-seq of Human: atrial CM differentiation at D20 from WT WTC11 rep1 - H3K27ac for differential analyses

description: Library name: TBX5_WT_H3K27ac_diff_rep1


title: Macrophages_RNA_SCIENCE_3

description: Library name: Sample 9


title: Wild-type rabbit retina pool, 10 months, 3 biological replicates

city: Ann Arbor

first: Dongshan

last: Yang

address: 2800 Plymouth Rd

institute: University of Michigan

description:
Library name: Pool1_WT
Pooled nuclei from 3 wild-type rabbits at 10 months. Tissue: 5mm retinal visual streak punch (2-3mm ventral to medullary rays). SNP-based demultiplexing with Vireo assigned nuclei to individual animals.

data_processing:
Raw sequencing reads were processed using Cell Ranger v7.0 aligned to rabbit reference genome OryCun2.0. SNP-based demultiplexing performed with cellsnp-lite and Vireo to assign nuclei to individual animals. Quality control filtering retained nuclei with >500 genes, <5% mitochondrial reads, and 500-50,000 total UMI counts. Data integration and cell type annotation performed using Seurat v4.3.0. Differential expression analysis using DESeq2 v1.38.0 with pseudobulk aggregation.
Assembly: OryCun2.0
Supplementary files format and content: Tab-delimited text files. GSE_raw_counts.txt.gz: gene expression matrix with genes as rows and cells as columns (raw UMI counts).
Supplementary files format and content: GSE_umap_coordinates.txt: UMAP dimensional reduction coordinates for visualization.
Supplementary files format and content: GSE_cell_metadata.txt.gz: cell-level metadata including sample ID, genotype, QC metrics(nCount_RNA, nFeature_RNA, percent_mt), cell type annotation, and cluster assignment.

organism: Oryctolagus cuniculus

source_name: retina

extract_protocol:
5mm retinal punch from visual streak region (2-3mm ventral to medullary rays) was collected from each animal and snap-frozen in liquid nitrogen. Nuclei were isolated using 10x Genomics Chromium Nuclei Isolation Kit according to manufacturer's protocol. Nuclei from 3 biological replicates were pooled at equal concentration (target 10,000 nuclei total) prior to library preparation.
10x Genomics Chromium Single Cell 3' v3.1 following manufacturer's protocol.

value: retina

value: retinal nuclei

value: wild-type

value: 10 Months


title: ccRCC tumor bulk RNA-seq 67d9

description:
67d9
processed data file column header:
67d9

value: Kidney

value: renal cell cancer

value: Clear cell renal cell carcinoma


title: D5_ki67+myc+_ROI2_S1_Milademetan

description:
Library name: DSP-1001660037306-B-A03
Tumor D5, Slide S1, ROI 2, Segment ki67+myc+, Replicate D5_ki67+myc+. Raji xenograft in NSG mouse, NanoString GeoMx DSP WTA v1.0.


title: ChIP-seq of Homo sapiens: atrial cardiomyocyte differentiation at D20 from WTC11 with TBX5in/del rep3 - RAD21

description: Library name: TBX5_null_RAD21_rep3

value: atrial cardiomyocyte differentation


title: I-epi-8w-WT-2-769

value: ileum epithelial cell


title: Macrophages_RNA_SCIENCE_1

description: Library name: Sample 7


title: Glioma_RNA_SCIENCE_4

description: Library name: Sample 6


title: ChIP-seq of Homo sapiens: atrial cardiomyocyte differentiation at D20 from WTC11 with TBX5in/del rep2 - RAD21

description: Library name: TBX5_null_RAD21_rep2


title: patient-derived organoids, sample TORG565

first: Jennifer

middle: M

last: Rosenbluth

state: California

address: 10 Koret Way

institute: University of California San Francisco

description: Library name: T565

data_processing:
Methods by Novogene: Data Quality Control. Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing poly-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.
Quantification of gene expression level. Gene expression levels were quantified using RSEM, with reads aligned to the human reference genome (hg38) with Bowtie2 and annotated using the GENCODE 49 gene set, providing transcript abundance estimates for downstream analyses
Assembly: GRCh38.p14
Supplementary files format and content: RSEM (.genes file providing transcript abundance estimates)

source_name: breast cancer

extract_protocol:
Organoids were harvested using TRIzol® reagent (ThermoFisher, Cat. No. 15596018). Cells were lysed using chloroform (SigmaAldrich, Cat. No. C2432-1L) in preparation for using the Purelink RNA Mini Kit® Protocol (ThermoFisher, cat# 12183020). Samples were eluted in 30ul RNA-Free water through two serial elutions. Samples were stored at -80°C until submission for library preparation and sequencing.
Methods by Novogene: 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. 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.

value: breast cancer

value: organoids

value: breast cancer cells


title: ChIP-seq of Homo sapiens: atrial cardiomyocyte differentiation at D20 from WTC11 with TBX5in/del rep1 - RAD21

description: Library name: TBX5_null_RAD21_rep1


title: I-epi-4w-Apc-4-738

value: ApcMin

value: Untreated

value: 4 weeks old


title: patient-derived organoids, sample TORG155

description: Library name: T155


title: I-epi-4w-Apc-3-735


title: ChIP-seq of Homo sapiens: atrial cardiomyocyte differentiation at D20 from WTC11 with TBX5in/+ rep2 - RAD21

description: Library name: TBX5_Het_RAD21_rep2

value: cardiomyocyte


title: 5FdUR_TS_RIP

city: Budapest

first: Angela

last: Bekesi

address: Műegyetem rakpart 3.

department: Department of Applied Biotechnology and Food Science

country: Hungary

institute: Budapest University of Technology and Economics, Faculty of Chemical Technology and Biotechnology

description: Library name: UPL24-005158

data_processing:
Quality was checked using fastQC, residual rRNA-related reads were removed in silico, then polyG, adapter, and low-quality sequences were trimmed using the fastp tool.
A subsampling by random selection of half of the reads (A50) was performed to produce pseudoreplicates for the statistical analysis.
Clean reads were aligned to the human reference genome GRCh38  using HiSAT2 aligner.
Aligned data were filtered for the core chromosomes.
Samples were compared to the corresponding RIPctr samples using the Cufflinks package (cuffnorm and cuffdiff).
Read coverage and log2(fold change) tracks were calculated for the forward and reverse strands, respectively, using the deeptools package. From these tracks, TS-RIP enrichment was also calculated for exons.
Assembly: GRCh38
Supplementary files format and content: The *reverse.filtered.bw and *forward.filtered.bw files contain the strand-selective coverage tracks in bigwig format.
Supplementary files format and content: The *log2.filtered.bw files contain the log2(fold change) signal tracks calculated from the coverage of TS-RIP vs RIPctr samples in bigwig format.
Supplementary files format and content: The *.diff files contain the results of the Cuffdiff analysis comparing TS-RIP and RIPctr samples.

growth_protocol: Cells were maintained in McCoy’s 5A medium supplemented with 10% FBS and 1% PenStrep.

extract_protocol:
Cells were harvested, counted, and resuspended in cytoplasmic extraction buffer then centrifuged; the pellet was extracted with nuclear extraction buffer. Cytoplasmic and nuclear extracts were combined, and glycerol was added. Lysates were pre-cleared with magnetic Protein A/G beads, then subjected to RIP with anti-TS antibody (Proteintech 15047-1-AP) and captured on Protein A/G beads. Beads were washed, eluted in elution buffer (also containing proteinase K) at 60 °C for 30 min, and RNA was purified using the Geneaid VR050 kit. RNA concentration was measured by Qubit and integrity checked by agarose gelelectrophoresis.
The libraries for Illumina sequencing were prepared using xGen RNA Lib Prep Kit (Integrated DNA Technologies, Iowa, USA) according to the Manufacturer's suggestions.

treatment_protocol: Cells were cultured in 6-well plates, treated with 100 nM RTX or 20 µM 5FdUR for 48 hours.

value: colon adenocarcinoma

value: MMR deficient, UGI inhibited

value: 20 µM 5FdUR


title: ChIP-seq of Homo sapiens: atrial cardiomyocyte differentiation at D20 from WTC11 with TBX5in/+ rep3 - RAD21

description: Library name: TBX5_Het_RAD21_rep3


title: Glioma_RNA_SCIENCE_1

description: Library name: Sample 3

value: primary glioma tumors

value: WT


title: I-epi-4w-Apc-2-733


title: ChIP-seq of Homo sapiens: atrial cardiomyocyte differentiation at D20 from WTC11 with TBX5in/+ rep1 - RAD21

description: Library name: TBX5_Het_RAD21_rep1


title: Endothelial_RNA_SCIENCE

description: Library name: Sample 2


title: I-epi-4w-Apc-1-732


title: NT_TS_RIP

description: Library name: UPL24-005156


title: ChIP-seq of Homo sapiens: atrial cardiomyocyte differentiation at D20 from WT WTC11 rep3 - RAD21

description: Library name: TBX5_WT_RAD21_rep3


title: I-epi-4w-WT-5-742


title: Astrocytes_RNA_SCIENCE

description: Library name: Sample 1


title: 5FdUR_negative_control

description: Library name: UPL24-005155


title: Organoids_SOX2_ASO_OPC

description: Library name: Sample 15

data_processing:
Resulting fastq files were demultiplexed based on cell barcodes
Quantification of unique 25 nt long random sequences [Barcode] for each cell
Assembly: GRCh38/hg38

source_name: human brain organoids with glioma stem cells

extract_protocol:
Both dead and viable cell populations were single-cell deposited into individual wells of a 96-well plate, having a PCR-compatible Proteinase K-based lysis buffer (10 mM Tris-HCl (pH 8.0), 50 mM KCl, 2.5 mM MgCl2, 0.45% NP-40, 0.45% Tween-20, Proteinase K (100 µg/mL)), followed by 55°C, 30 min incubation to disrupt both cell and nuclear membranes and then heat-inactivation of the Proteinase K at 95°C for 10 minutes.
ASO Barcodes (DNA) from different wells were amplified for Illumina sequencing with the combination of cell barcodes unique for each well (Illumina DNA/RNA Unique Dual Indexes (UDI)


title: RTX_negative_control

description: Library name: UPL24-005154

value: 100 nM RTX


title: I-epi-4w-WT-4-739


title: Organoids_SOX2_ASO_Oligodendrocytes

description: Library name: Sample 14

value: human brain organoids with glioma stem cells


title: D5_ki67+myc+_ROI1_S1_Milademetan

description:
Library name: DSP-1001660037306-B-A02
Tumor D5, Slide S1, ROI 1, Segment ki67+myc+, Replicate D5_ki67+myc+. Raji xenograft in NSG mouse, NanoString GeoMx DSP WTA v1.0.

value: Raji Burkitt lymphoma xenograft

value: Raji (ATCC CCL-86)

value: Milademetan 20mg/kg


title: I-epi-4w-WT-3-737

value: ileum epithelial cell


title: Glioma_RNA_SCIENCE_3

description: Library name: Sample 5


title: Hi-C of Homo sapiens: D20 of atrial cardiomyocyte (CM) differentiation with 500 nM dTAGv-1 ligand treated for 24h rep2

description: Library name: dTAG_24h_rep2

data_processing:
Hi-C 3.0 data were processed using 4D Nucleome (4DN) Hi-C data Processing Pipeline (v0.2.7) (https://data.4dnucleome.org/resources/data-analysis/hi_c-processing-pipeline), which generated .mcool file with iterative correction and eigenvector decomposition (ICE) normalization.
Reads were mapped to GRCh38 using bwa.
Valid HiC alignments were filtered using pairtools.
Biological replicates were merged using https://github.com/4dn-dcic/docker-4dn-hic/blob/master/scripts/run-merge-pairs.s
The pairs files were converted to cool files using cooler.
Assembly: hg38
Supplementary files format and content: .mcool file of interaction contact frequencies at different resolutions

growth_protocol: An FKBP12F36V with 2x HA (DOI: 10.1038/s41589-018-0021-8) tag was used to generate a cell line in which TBX5 could be induced for degradation. The tag was inserted immediately after the start methionine codon in the N-terminus of the endogenous TBX5 locus using ribonucleoprotein (RNP) complexes of sgRNA (GCCCTCGTCTGCGTCGGCCA, ordered from Synthego) and SpCas9-NLS ‘HiFi’ protein (QB3 MacroLab, University of California Berkeley). Donor template sequences for each were provided by using HDR Alt-R gene blocks (IDT). 250,000 WTc11 iPSCs were resuspended in 12.2 µl Lonza P3 transfection buffer and nucleofected with 1 µg donor template and 10 µl RNPs using Lonza Nucleofector 4D system in 96-well format using DS-138 settings. Single cell colonies were screened by PCR using primers pairs flanking the whole insertion site (F: 5’-TCCTCAGAGCAGAACCTTGC, R: 5’-CTTACCTGCTGGGTGAAGG). Amplicon from whole insertion site PCR was amplified and verified by Sanger sequencing. All clones used were determined to have a normal karyotype.  Atrial (StemCell Technologies #100-0215) kits were used to differentate iPSCs into cardiomyocytes. At d20, each sample was treated with DMSO or dTAGv-1 (Tocris, #6914) ligand for 24 h before harvesting.

extract_protocol:
CMs were grown in 3 wells of a 6-well dish per replicate, with all 3 wells pooled together after dissociation for the crosslinking step (approximately 10 million cells). CMs were dissociated in 0.25% Trypsin-EDTA for 10 mins, followed by quenching in 15%FBS in DPBS. CMs were lifted off the dish and resuspended to single cells by repeatedly using P1000 pipette and then transferred to a 15 ml tube and centrifuged at 800 rpm for 5 min at room temperature. Pellets were washed once in 5 ml HBSS before resuspending entire cell pellet in exactly 10 ml HBSS. 16% methanol-free formaldehyde was added to a final concentration of 1% and samples incubated on nutator at room temperature for 10 min. Samples were quenched with 2.5 M glycine to a final concentration of 0.125 M and incubated on nutator at room temperature for 5 min, then 15 min at 4˚C and followed by centrifugation at 1000 x g for 5 min at room temperature. Samples were washed once in DPBS. Pellets were resuspended in 1 ml of 3 mM DSG in PBS, transferred to 1.5 ml tubes and incubated on nutator for 40 min. Samples were quenched with 2.5 M glycine to a final concentration of 0.125 M and incubated on nutator at room temperature for 5 min. Samples were centrifuged at 2000 x g for 5 min at RT. Cell pellets were resuspended in 5 mg/ml BSA in DPBS, to prevent cells sticking to tube after DSG crosslinking, and centrifuged at 2000 x g for 5 min at 4˚C. Supernatant was carefully removed and cell pellets were snap frozen in liquid nitrogen and stored at -80˚C.
Samples were processed for Hi-C using Arima-HiC+ kit (Arima Genomics). >1 µg per sample was used as determined by Arima’s Estimating Input Amount Protocol using Qubit Fluorometer and dsDNA HS Assay Kit (ThermoFisher Scientific #Q32854) Samples were processed by following manufacturer’s user guide for mammalian cell lines with one exception: DNA was digested using 50 U DpnII (New England Biolabs #R0543M) and 50 U DdeI (New England Biolabs #R0175L) restriction enzymes in 1x NEB Buffer 3.1 for 60 min at 37˚C. All samples passed Arima-QC1 Quality Control. Sequencing libraries were prepared by following Arima’s user guide for Library Prep Using KAPA Hyper Prep Kit (Roche #7962347001). Between 1.5-4 µg of DNA was fragmented in 130 µl microtube (Covaris #520045) using a Covaris S2 sonicator for 55s at 10% duty cycle, intensity 4, 200 cycles per burst in a water bath maintained at 4˚C. An average fragment size of 400 bp was verified using Agilent 2100 Bioanalyzer. Between 400-1000 ng of size-selected DNA was used for biotin enrichment, end repair, dA-tailing and adapter ligation. The number of PCR cycles was determined following Arima-QC2 Quality Control using KAPA Library Quantification Kit (Roche KK4824) and libraries were amplified to at least 10 nM. All samples passed Arima-QC2 Quality Control. DNA cleanup steps were done using Ampure XP beads (Beckman Coulter #A63881). Final libraries were quantified using Qubit Fluorometer and dsDNA HS Assay Kit and assessed on Agilent BioAnalyzer. Pooled, equimolar libraries were sequenced using NovaSeq technology (Illumina).

value: 500 nM dTAGv-1 ligand


title: Organoids_SOX2_ASO_Neurons

description: Library name: Sample 13


title: I-epi-4w-WT-2-736