title: Hypoxia_AsPC1_Day9_rep3

description: Library name: Hypoxia_AsPC1_Day9_rep3

value: PDAC


title: C26,IGRA-,CD4m,MTB300

status: Public on Dec 03 2025

type: SRA

city: La Jolla

first: Leila

middle: Y

last: Chihab

state: CA

address: 9420 Athena Circle

country: USA

institute: La Jolla Institute for Immunology

description:
Library name: Sample 87
GS1565_V

library_source: transcriptomic

data_processing:
Reads that passed illumina filters were filtered to eliminate reads aligning to tRNA, rRNA, and adapter sequences. The reads were then aligned to GRCh38 reference genome using TopHat. DUST scores were calculated with PRINSEQ Lite and low complexity reads (DUST >4) were removed from the BAM files. The alignment results were parsed via SAMtools to generate SAM files. Read counts for each genomic feature were obtained with the htseq-count program.
Assembly: GRCh38
Supplementary files format and content: abundance measurementas as a matrix table

molecule: total RNA

organism: Homo sapiens

extract_protocol:
RNA was purified using an miRNeasy Micro Kit (QIAGEN).
Purified total RNA (1–5 ng) was amplified following the Smart-Seq2 protocol (16 cycles of cDNA amplification). 1 ng of cDNA was used to prepare a standard Nextera XT sequencing library (Nextera XT DNA sample preparation kit and index kit, Illumina)

treatment_protocol: No specific treatment involved

tag: treatment

tag: cell type

tag: genotype

value: IGRA-


title: Donor 21, 10x 5', Stage III, Indeterminate, Tumor

city: Beijing

first: Zemin

last: Zhang

address: No.5 Yiheyuan Road, Haidian District

country: China

institute: Peking University

description:
D21T
10x Genomics

library_source: transcriptomic single cell

data_processing:
The sequencing reads of scRNA-seq data were aligned against GRCh38 human reference genome by Cell Ranger (version 4.0.0, 10x Genomics Inc) to generate matrixes that record UMI counts of each gene across all cells.
Assembly: hg38
Supplementary files format and content: barcodes.tsv.gz: barcode sequences
Supplementary files format and content: features.tsv.gz: genes
Supplementary files format and content: matrix.mtx.gz: cell x gene count matrix

source_name: Gastric cancer tumor

extract_protocol:
Fresh collected solid tissues (tumour, adjacent normal, and lymph node) were cut into small pieces (~1 mm3) in the RPMI 1640 Medium (Thermo Fisher Scientific Inc., USA) with 10% fetal bovine serum, loaded in gentleMACS C Tubes, and digested with MACS Tumour Dissociation Kit (130095929, Miltenyi Biotec) on a gentleMACS Dissociator with Heaters (Miltenyi Biotec, Germany). Continuous rotation at 37 ℃ for 30 minutes was applied.
Library was performed according to the manufacter's instruction. Roughly 10,000 ~ 20,000 cells were prepared for the 10x 5' and 3' single-cell library construction. The guidance for the library construction is detailed in the manufacturer's protocol (CG000207 and CG000183).

tag: tissue

value: Gastric cancer tumor

tag: cell line

value: Donor 21

tag: Stage

value: Stage III

tag: subtype

value: Indeterminate


title: C27,IGRA-,CD4m,MTB300

description:
Library name: Sample 85
GS1567_V


title: Donor 23, 10x 3', Stage II, Intestinal, Normal

description:
D23N
10x Genomics

source_name: Adjacent normal

value: Adjacent normal

value: Donor 23

value: Stage II

value: Intestinal


title: C28,IGRA-,CD4m,DMSO

description:
Library name: Sample 84
GS1572_X

value: DMSO


title: Hypoxia_AsPC1_Day9_rep2

city: Cambridge

first: Brian

last: Rabe

state: MA

address: 250 Water St

institute: Bristol Myers Squibb

description: Library name: Hypoxia_AsPC1_Day9_rep2

data_processing:
Standard BCL2fastq was used to demultiplex by each plate containing samples with unique TSO barcodes
Plates were further demultiplexed, cDNA sequences aligned, and counts collapsed by UMI using the zUMIs pipeline
Assembly: GRCh38-ensembl93
Supplementary files format and content: Each processed file is a plain-text, tab-delimited table named “<SampleID>.counts.txt”. Column 1: gene_id - Ensembl gene identifier (e.g. ENSG00000141510) Column 2: count - integer UMI-collapsed exon counts for that gene in the sample

molecule: polyA RNA

source_name: cell line

growth_protocol: Panc0203 cells were cultured in RPMI supplemented with 1X GlutaMax, 10 mM HEPES, 10% FBS, 1 mM sodium pyruvate, and 100 U/ml pen-strep. Panc0403 cells were cultured in RPMI supplemented with 1X GlutaMax, 10 mM HEPES, 10% FBS, 20 µg/ml insulin, and 100 U/ml pen-strep. AsPC1 cells were cultured in ATCC modified RPMI supplemented with 10% FBS and 100 U/ml pen-strep. Panc-1 cells were cultured in DMEM supplemented with 10% FBS and 100 U/ml pen-strep. PACADD-188 cells were cultured in a 1:1 mixture of DMEM and KFSM, with KSFM supplements, supplemented with 20% FBS and 100 U/ml pen-strep. All cells were cultured at 37C with humidified atmosphere and 5% CO2, either with atmospheric O2 (normoxia) or 1% O2 (hypoxia).

extract_protocol:
Cells were lysed directly in well with TriReagent and extracted using the Zymo Directzol micro kit according to manufacturer protocols
To generate RNA-seq lite libraries, NEB’s Template Switching RT Enzyme mix was used (NEB Cat# M0466L). 250 ng of total RNA from each sample was brought to a final volume of 8 ul with RT buffer (final concentration 1X), oligodT RT primer with the Illumina Read2 sequence (final concentration of 1 uM), and dNTP mix (NEB Cat# N0447L, final concentration 1 mM each). Samples were then transferred to a thermocycler at 95°C for 2.5 minutes, allowing for Mg2+-mediated RNA fragmentation, and then samples were fast cooled on ice. 0.5 ul of 4X RT buffer, 0.5 ul of 75 uM template switching oligo (TSO, which contained a sample index, UMI, variable length stagger region, and the Illumina Read1 primer sequence), and 1 ul of RT enzyme were added to each sample, and reverse transcription was performed according to manufacturer protocol. Samples with unique TSO-added sample indices were then pooled and treated with RNaseA (NEB Cat# T3018L, 1 ul per pooled sample) for 30 minutes at room temperature, and then cDNA was column purified (Zymo Cat# D4013) using 7 volumes of DNA binding buffer, and eluted in 36 ul of Buffer EB (Qiagen Cat# 19086). 3 ul of each reaction were amplified in a 1/10th scale reaction, as described below, with the addition of 1X EvaGreen (VWR Cat# 76423-472) in a QuantStudio 12k Flex (ThermoFisher Scientific), and the cycle number necessary to reach ~1/3 the maximum amplification was chosen for final pool amplification. The remaining ~30 ul of cDNA was amplified using the NEBNext Ultra™ II Q5 Master Mix (NEB Cat# M0544L) and NEBNext Multiplex Oligos for Illumina (NEB Cat# E7335S) according to manufacturer instructions and using the cycle number determined above. Final sequencing libraries were purified using SPRIselect beads (Beckman Coulter Cat# B23318), with a double-sided size selection (0.5X-0.8X). Libraries were sequenced on a NextSeq 2000 (P3 flowcell kit, 200 cycles, Illumina Cat# 20040560), with a 144 cycle Read1 which contained the sample index, UMI, and cDNA insert.   RNA-lite primers:  RNA-lite_RT-primer: GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT [T-30]VN  RNA-lite_TSO: ACACTCTTTCCCTACACGACGCTCTTCCGATCT[Sample Index-8][UMI-8][Stagger-0-8 bases]rGrGrG

treatment_protocol: Cells cultured in hypoxia were maintained at 1% O2 at all times. All media and solutions were equilibrated overnight to 1% O2 before being applied to cells. Tubes containing cells were tightly sealed with parafilm before being removed from hypoxia glovebox for centrifugation following trypsinization.

value: cell line

value: KRAS G12D

value: Hypoxia

tag: batch

tag: timepoint (day)


title: 4H4

city: Hangzhou

first: jiahong

last: gong

address: Qingchun East Rd. 3

department: Department of Respiratory Care, Regional Medical Center for National Institute of Respiratory Diseases

institute: Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University

description:
Library name: 4H4
Cell specimens obtained from C2C12 cells after 4 hours of cell stretching. Replicate biosample 3

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to mm10  using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes fpkm value for each sample

organism: Mus musculus

source_name: myoblast

extract_protocol:
RNA was extracted from cell lines using TRIzol reagent. Briefly, cells were washed with PBS, lysed in TRIzol, and incubated for 5 min. Chloroform (20% volume) was added, followed by vigorous mixing and centrifugation (12,000 ×g, 15 min, 4°C) to separate phases. The aqueous layer was collected, mixed with isopropanol, and centrifuged (12,000 ×g, 10 min) to precipitate RNA. The pellet was washed twice with 75% ethanol, air-dried, and dissolved in RNase-free water. RNA concentration and integrity (RIN >7) were assessed using Nanodrop and Bioanalyzer. Samples were stored at -80°C to prevent degradation. This method ensures high-quality RNA for transcriptomic analyses such as RNA-seq or qPCR.
Total RNA (1 µg, RIN >7) was enriched for mRNA using poly(A) selection (for eukaryotes) or rRNA depletion (for prokaryotes). The RNA was fragmented (∼200–300 nt) and reverse-transcribed into cDNA using random hexamers and SuperScript IV. Second-strand synthesis was performed with dUTP incorporation (strand-specific libraries). The cDNA was end-repaired, A-tailed, and ligated to Illumina-compatible adapters. Post-ligation cleanup (AMPure XP beads) was followed by size selection (200–500 bp) and uracil digestion (for strand specificity). Library amplification (8–12 cycles) used indexed primers, and final quantification (Qubit) and quality control (Bioanalyzer/TapeStation) ensured optimal fragment size (∼300 bp) and concentration (>10 nM). Libraries were pooled and sequenced (Illumina platforms, 150 bp paired-end).

value: myoblast

value: 4 hours of cell stretching


title: C1

description:
Library name: C1
control group, replicate biosample 1

value: control


title: Hypoxia_AsPC1_Day9_rep1

description: Library name: Hypoxia_AsPC1_Day9_rep1

value: PDAC


title: C24,IGRA-,CD4m,MTB300

description:
Library name: Sample 91
GS1555_V

value: IGRA-


title: C28,IGRA-,CD4m,MTB300

description:
Library name: Sample 83
GS1572_V


title: 4H3

description:
Library name: 4H3
Cell specimens obtained from C2C12 cells after 4 hours of cell stretching. Replicate biosample 2


title: C29,IGRA-,CD4m,DMSO

description:
Library name: Sample 82
GS1579_X


title: Donor 20, 10x 3', Stage III, Diffuse, Core, Tumor

description:
D20T
10x Genomics

value: Gastric cancer tumor

value: Donor 20

value: Diffuse


title: Donor 19, 10x 5', Stage I, Intestinal, Peripheral Blood

description:
D19P
10x Genomics

source_name: Peripheral blood

value: Peripheral blood

value: Donor 19

value: Stage I


title: Hypoxia_AsPC1_Day7_rep3

description: Library name: Hypoxia_AsPC1_Day7_rep3


title: Donor 19, 10x 5', Stage I, Intestinal, Normal

description:
D19N
10x Genomics

value: Adjacent normal


title: C30,IGRA-,CD4m,MTB300

description:
Library name: Sample 80
GS1625_V


title: C29,IGRA-,CD4m,MTB300

description:
Library name: Sample 81
GS1579_V


title: Donor 19, 10x 5', Stage I, Intestinal, Lymph Node

description:
D19L
10x Genomics

source_name: Lymph node

value: Lymph node

value: Intestinal


title: L3

city: Zhuhai

first: Shiying

last: Xie

address: No. 1439, Zhufeng Avenue, Doumen District

institute: The Fifth Affiliated Hospital of Zunyi Medical University, Zhuhai

description: Library name: L3

data_processing:
Raw sequencing reads in FASTQ format were processed using Cutadapt (v1.9.1) to remove technical sequences and low-quality bases.
Clean reads were aligned to the reference genome using HISAT2 (v2.2.1), a splice-aware aligner.
Gene-level counts were quantified using HTSeq (v0.6.1). Reads overlapping exons were counted, and multi-mapping reads or reads overlapping multiple genes were excluded.
Differentially expressed genes were identified using DESeq2 (v1.34.0).
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes count values for each Sample

source_name: liver

growth_protocol: Male C57BL/6J mice (eight weeks old) were purchased from Gempharmatech (Nanjing, China) and maintained in a temperature-controlled room under a 12:12-h light–dark cycle for two weeks, with free access to tap water and standard mouse chow.

extract_protocol:
RNA was havested using TRIzol (Invitrogen) according to manufacturer's' instructions. 1 μg total RNA was used for library preparation.
For mRNA enrichment, poly(A) mRNA isolation was performed using Oligo(dT) beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. Reverse transcriptase was used for first strand cDNA synthesis, followed by second-strand cDNA synthesis. For strand-specific library construction, during the second-strand synthesis the standard dTTP was replaced with dUTP; subsequent treatment with USER enzyme selectively degrades the second strand prior to PCR amplification, thereby preserving strand information. The purified double-stranded cDNA was then treated to repair both ends and add a dA-tail in a single reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers, and the PCR products were validated.

treatment_protocol: All animals were sacrificed 24 h after LPS injection, and liver samples were collected with TRIzol.

value: liver

value: LPS


title: Donor 19, 10x 5', Stage I, Intestinal, Tumor

description:
D19T
10x Genomics


title: 4H1

description:
Library name: 4H1
Cell specimens obtained from C2C12 cells after 4 hours of cell stretching. Replicate biosample 1


title: Hypoxia_PACADD188_Day1_rep1

description: Library name: Hypoxia_PACADD188_Day1_rep1

value: cell line

value: KRAS G12D

value: Hypoxia


title: Hypoxia_AsPC1_Day7_rep1

description: Library name: Hypoxia_AsPC1_Day7_rep1


title: Donor 20, 10x 3', Stage III, Diffuse, Core, Normal

description:
D20N
10x Genomics

value: Stage III


title: Hypoxia_AsPC1_Day3_rep2

description: Library name: Hypoxia_AsPC1_Day3_rep2

value: PDAC


title: L1

description: Library name: L1


title: Donor 18, 10x 5', Stage III, Diffuse, Peripheral Blood

description:
D18P
10x Genomics

value: Donor 18


title: C30,IGRA-,CD4m,DMSO

description:
Library name: Sample 79
GS1625_X

value: DMSO

value: IGRA-


title: Donor 18, 10x 5', Stage III, Diffuse, Lymph Node

description:
D18L
10x Genomics

value: Diffuse


title: C4

description: Library name: C4

value: control


title: Hypoxia_AsPC1_Day3_rep3

description: Library name: Hypoxia_AsPC1_Day3_rep3


title: Hypoxia_AsPC1_Day3_rep1

description: Library name: Hypoxia_AsPC1_Day3_rep1


title: C3

description: Library name: C3


title: I22,IGRA+,CD4m,MTB300

description:
Library name: Sample 78
GS1682_V

value: IGRA+


title: I22,IGRA+,CD4m,DMSO

description:
Library name: Sample 77
GS1682_X


title: Hypoxia_AsPC1_Day14_rep3

description: Library name: Hypoxia_AsPC1_Day14_rep3


title: Donor 18, 10x 5', Stage III, Diffuse, Tumor

description:
D18T
10x Genomics

value: Gastric cancer tumor


title: C32,IGRA-,CD4m,DMSO

description:
Library name: Sample 76
GS1754_X


title: Donor 17, 10x 3', Stage III, Diffuse, Normal

description:
D17N
10x Genomics

value: Adjacent normal

value: Donor 17


title: L2

description: Library name: L2


title: Hypoxia_AsPC1_Day7_rep2

description: Library name: Hypoxia_AsPC1_Day7_rep2


title: C1

description: Library name: C1


title: C32,IGRA-,CD4m,MTB300

description:
Library name: Sample 75
GS1754_V


title: Hypoxia_AsPC1_Day14_rep2

description: Library name: Hypoxia_AsPC1_Day14_rep2


title: Donor 17, 10x 3', Stage III, Diffuse, Tumor

description:
D17T
10x Genomics


title: Donor 16, 10x 5', Stage III, Diffuse, Peripheral Blood

description:
D16P
10x Genomics

value: Peripheral blood

value: Donor 16


title: I23,IGRA+,CD4m,MTB300

description:
Library name: Sample 74
GS1758_V


title: Hypoxia_AsPC1_Day1_rep3

description: Library name: Hypoxia_AsPC1_Day1_rep3


title: Donor 16, 10x 5', Stage III, Diffuse, Lymph Node

description:
D16L
10x Genomics

value: Lymph node


title: I23,IGRA+,CD4m,DMSO

description:
Library name: Sample 73
GS1758_X


title: T9,ATB,CD4m,DMSO

description:
Library name: Sample 72
TS0022_X

value: ATB


title: Hypoxia_AsPC1_Day1_rep1

description: Library name: Hypoxia_AsPC1_Day1_rep1

value: cell line

value: KRAS G12D


title: Donor 15, 10x 3', Stage III, Indeterminate, Tumor

description:
D15T
10x Genomics

value: Donor 15

value: Stage III

value: Indeterminate


title: Donor 16, 10x 5', Stage III, Diffuse, Normal

description:
D16N
10x Genomics


title: Untreated 3

city: Chicago

first: Shashwat

last: Tripathi

state: Illinois

address: 302 e Huron St

department: Neurosurgery

institute: Northwestern

description: Library name: Sample12

data_processing:
Preprocessing of raw sequencing files included alignment to mm10 reference using Cell Ranger (v3.1.0). Next, ambient mRNA and doublets were removed using SoupX (v.1.3.0) and sDblFinder (v1.4.0), respectively. Then, a standard Seurat R Package workflow was applied (34). Cells were cleaned using a mitochondrial DNA threshold of 10% and a UMI range of 100 to 5000. In addition to Seurat functions, the Harmony algorithm was used for batch correction (35).
Assembly: mm10
Supplementary files format and content: FASTQ and matrix files

source_name: Brain

extract_protocol:
At designated time points, tumor-bearing mice were euthanized and brains collected following cardiac perfusion and chopped up using a scalpel, dissociated, and suspended using a mixture of IMDM 1X (Corning) containing 2% inactivated FBS (Millipore Sigma), collagenase (100 μg/mL) and DNase (20 units/mL). Samples were incubated for 35–40 minutes at 37°C with agitation. The tissue was filtered through a 70 μm nylon cell strainer (BD Biosciences) and then underwent centrifugation at 4°C. Half of the pellet representing the whole TME was resuspended in culture media, and the other half in a 20 mL mixture of 5.4 mL Percoll Plus (GE Healthcare) overlaid with 12 mL 1X PBS and 0.6 mL 10X PBS (Corning) for immune enrichment. The tube was centrifuged at 800g for 10 minutes at 4°C, with 9 acceleration and 0 deceleration. After centrifugation, the immune-enriched cell pellet was collected, washed, mixed with the whole TME samples at a ratio of 1:1, stained with Trypan blue dye (MilliporeSigma), and counted using a Countess II FL automated cell counter in a Countess cell-counting chamber (Invitrogen, Thermo Fisher Scientific).
Done through standard protocol by NuSeq Core (Jennifer Chai)

value: Brain

value: Tumor Environment

value: Untreated


title: Hypoxia_AsPC1_Day1_rep2

description: Library name: Hypoxia_AsPC1_Day1_rep2

value: PDAC

value: Hypoxia


title: Untreated 1

description: Library name: Sample10


title: Untreated 2

description: Library name: Sample11


title: T10,ATB,CD4m,MTB300

description:
Library name: Sample 70
TS0023_V


title: C2

description: Library name: C2

value: liver

value: control


title: RT 3

description: Library name: Sample9

value: RT


title: RT 2

description: Library name: Sample8


title: DIOmouse_VHL_GAS_4

city: Torino

first: Emanuele

last: Monteleone

address: Via Nizza, 52

department: Department of Life Sciences and Systems Biology

country: Italy

institute: Universita' di Torino

description: Library name: Sample9

data_processing:
Preprocess and quality control for sequencing data was performed using FastQC tool and the MultiQC framework (https://github.com/MultiQC/MultiQC)
Sequencing reads were trimmed for adpater/ low quality sequence using the fastp tool
Trimmed sequences were mapped to GRcm39 genome suing STAR using the following options: --outSAMtype BAM SortedByCoordinate --outSAMunmapped Within --chimOutType WithinBAM --outFilterType BySJout --outFilterMultimapNmax 200 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000
Read count was performed using the featureCounts utility of the subread package using options: -t exon --extraAttributes gene_name -p -C --countReadPairs. Counts were restricted to last 500 bp of the 3'UTR of each gene to handle biases in sequencing coverage.
Read count normalization and Differential gene expression analysis was performed using  DESeq2
Assembly: GRCm39
Supplementary files format and content: gz compressed tab delimited file includes raw read counts for each sample

source_name: Gastrocnemius

growth_protocol: Randomized 9-week-old male C57BL/6J mice were provided with ad libitum access to high fat diet (D12492i) for 9 weeks until >40 g

extract_protocol:
Mice were dissected at the end of treatment and gastrocnemius muscles were frozen at -80 deg C before RNA extraction. Frozen tissues were homogenized with mortar and pestel in TRIzol reagent. RNA was extracted following TRIzol/chloroform protocol and precipited with isopropanol. The RNA pellet was washed with 75% EtOH solution and resuspended in nuclease-free water
Libraries were prepared with 500 ng of RNA with a RIN value >7 using the Illumina stranded mRNA prep kit. Quality was assessed by TapeStation (280 bp fragments) and quantified using Qubit 1x dsDNA HS kit for sequencing by Illumina NextSeq1000 System

treatment_protocol: Diet-induced obese mice were injected subcutaneously with matched volumes of either 0,9% saline solution or 10 mg/kg anti-miR-22 antisense oligonucleotide once weekly for 14 weeks.

value: Gastrocnemius

value: WT

value: VHL (vehicle)


title: Donor 12, 10x 5', Stage II, Diffuse, Lymph Node

description:
D12L
10x Genomics

value: Lymph node

value: Donor 12

value: Stage II

value: Diffuse


title: T9,ATB,CD4m,MTB300

description:
Library name: Sample 71
TS0022_V

value: ATB


title: RT 1

description: Library name: Sample7


title: Hypoxia_AsPC1_Day14_rep1

description: Library name: Hypoxia_AsPC1_Day14_rep1

value: cell line

value: KRAS G12D


title: T10,ATB,CD4m,DMSO

description:
Library name: Sample 69
TS0023_X

value: DMSO


title: DIOmouse_VHL_GAS_3

description: Library name: Sample8


title: Donor 12, 10x 5', Stage II, Diffuse, Normal

description:
D12N
10x Genomics

value: Adjacent normal


title: Donor 12, 10x 5', Stage II, Diffuse, Tumor

description:
D12T
10x Genomics

value: Gastric cancer tumor


title: T13,ATB,CD4m,DMSO

description:
Library name: Sample 67
TS0030_X


title: 8803 3

description: Library name: Sample6

value: Brain

value: Tumor Environment


title: DIOmouse_VHL_GAS_2

description: Library name: Sample7


title: DIOmouse_VHL_GAS_5

description: Library name: Sample10


title: T14,ATB,CD4m,DMSO

description:
Library name: Sample 66
TS0037_X


title: DIOmouse_VHL_GAS_1

description: Library name: Sample6


title: Donor 11, 10x 5', Stage III, Indeterminate, Peripheral Blood

description:
D11P
10x Genomics

value: Peripheral blood

value: Donor 11

value: Stage III

value: Indeterminate


title: T14,ATB,CD4m,MTB300

description:
Library name: Sample 65
TS0037_V


title: 8803 2

description: Library name: Sample5


title: 8803 1

description: Library name: Sample4


title: DIOmouse_LNA_GAS_4

description: Library name: Sample4

value: Gastrocnemius

value: WT


title: Donor 11, 10x 5', Stage III, Indeterminate, Normal

description:
D11N
10x Genomics


title: Donor 11, 10x 5', Stage III, Indeterminate, Tumor

description:
D11T
10x Genomics


title: DIOmouse_LNA_GAS_5

description: Library name: Sample5


title: RT + 8803 2

description: Library name: Sample2


title: T15,ATB,CD4m,DMSO

description:
Library name: Sample 64
TS0038_X


title: Donor 10, 10x 5', Stage III, Intestinal, Normal

description:
D10N
10x Genomics

value: Donor 10

value: Intestinal


title: Donor 10, 10x 5', Stage III, Intestinal, Lymph Node

description:
D10L
10x Genomics

value: Lymph node


title: DIOmouse_LNA_GAS_3

description: Library name: Sample3


title: RT + 8803 3

description: Library name: Sample3


title: T15,ATB,CD4m,MTB300

description:
Library name: Sample 63
TS0038_V

value: ATB


title: Donor 10, 10x 5', Stage III, Intestinal, Peripheral Blood

description:
D10P
10x Genomics


title: ILC2_4 cultured alone

city: Rome

first: Linda

last: Quatrini

address: Via San Paolo 15

department: Immunology

institute: IRCCS Bambino Gesù Pediatric Hospital

description: Library name: L4

data_processing:
The fastq files were assessed with the fastqc program and cutadapt was used to remove the adapter sequence (if present) and the very short reads (reads length <20).
Assembly: The samples were mapped on reference Homo sapiens genome (HG38) using the bioinformatics tool STAR
Supplementary files format and content: xlsx file includes normalized counts for each sample

source_name: Primary cell culture

extract_protocol:
RNA was prepared from ILC2 with a RNeasy Plus Micro Kit (Qiagen).
The DNA libraries were generated with the TruSeq stranded mRNA prep kit (Illumina, San Diego, Calif), following manufacturer's protocols.

treatment_protocol: ILC2 were cultured alone and with monocyte-derived-macrophages for 4 days in 24 well ultra-low attachment surface plate in RPMI-1640 complete medium plus IL-2 and IL-7 (50 ng/ml each).

value: Primary cell culture


title: Donor 10, 10x 5', Stage III, Intestinal, Tumor

description:
D10T
10x Genomics


title: T16,ATB,CD4m,DMSO

description:
Library name: Sample 62
TS0039_X


title: DIOmouse_LNA_GAS_2

description: Library name: Sample2


title: RT + 8803 1

description: Library name: Sample1


title: Donor 09, 10x 5', Stage III, Indeterminate, Peripheral Blood

description:
D09P
10x Genomics

value: Donor 09


title: DIOmouse_LNA_GAS_1

description: Library name: Sample1


title: T13,ATB,CD4m,MTB300

description:
Library name: Sample 68
TS0030_V


title: Mus musculus, Leydig cells, siprdx1+H2O2, biol repl3

city: Shanghai

first: Fan

last: Dong

address: 845 Lingshan Road

department: Department of Reproductive Medicine

institute: Shanghai Jiao Tong University School of Medicine

description:
Library name: siprdx1-H2O2-3
Column name gene_count.txt: siprdx1-H2O2-3

data_processing:
Before read mapping, clean reads were obtained from the raw reads by removing the adaptor sequences and low-quality reads. The clean reads were then aligned to the mouse genome (mm10, Ensembl100) using the Hisat2. HTseq was used to obtain gene counts.
Assembly: Ensembl100
Supplementary files format and content: Tab separated table count values of genes for each sample

source_name: Leydig cells

growth_protocol: The primary mouse Leydig cells were cultured in DMEM/F-12 medium containing 10% FBS, 100 U/mL penicillin, and 100 μg/mL streptomycin, and maintained at 34℃ with 5% CO2. Cells were transfected with indicated siRNAs using Lipofectamine RNAiMAX Transfection Reagent (Thermo Fisher Scientific).

extract_protocol:
The total RNA of cells in each group was extracted with Trizol (Thermo Fisher Scientific). The RNA with RNA integrity number (RIN) > 7.0 is acceptable for cDNA library construction.
The cDNA libraries were constructed for each RNA sample using the TruSeq Stranded mRNA Library Prep Kit (Illumina, Inc.) according to the manufacturer’s instructions. The libraries were quality controlled with Agilent 2200 and sequenced by NovaSeq 6000 on a 150 bp paired-end run.

value: Leydig cells


title: ILC2_3 cultured alone

description: Library name: L3


title: T16,ATB,CD4m,MTB300

description:
Library name: Sample 61
TS0039_V


title: Mus musculus, Leydig cells, siprdx1+H2O2+FV, biol repl2

description:
Library name: siprdx1-H2O2-FV-2
Column name gene_count.txt: siprdx1-H2O2-FV-2


title: Mus musculus, Leydig cells, siprdx1+H2O2+FV, biol repl3

description:
Library name: siprdx1-H2O2-FV-3
Column name gene_count.txt: siprdx1-H2O2-FV-3


title: ILC2_3 cultured with monocyte-derived-macrophages

description: Library name: C3


title: Mus musculus, Leydig cells, siprdx1+H2O2+FV, biol repl1

description:
Library name: siprdx1-H2O2-FV
Column name gene_count.txt: siprdx1-H2O2-FV


title: Mus musculus, Leydig cells, siprdx1, biol repl3

description:
Library name: siprdx1-3
Column name gene_count.txt: siprdx1-3


title: Donor 09, 10x 5', Stage III, Indeterminate, Tumor

description:
D09T
10x Genomics


title: I47,IGRA+,CD4m,MTB300

description:
Library name: Sample 60
TU0010_V

value: IGRA+


title: I48,IGRA+,CD4m,DMSO

description:
Library name: Sample 58
TU0013_X

value: DMSO


title: Mus musculus, Leydig cells, siprdx1+H2O2, biol repl2

description:
Library name: siprdx1-H2O2-2
Column name gene_count.txt: siprdx1-H2O2-2


title: Donor 09, 10x 5', Stage III, Indeterminate, Normal

description:
D09N
10x Genomics

value: Adjacent normal


title: I48,IGRA+,CD4m,MTB300

description:
Library name: Sample 57
TU0013_V


title: I49,IGRA+,CD4m,DMSO

description:
Library name: Sample 56
TU0022_X


title: K27_NT1_10C

city: Marseille

first: Nori

last: SADOUNI

address: 169 Avenue Luminy

country: France

institute: TAGC INSERM U1090

description: Library name: K27_NT1_10C

library_source: genomic

data_processing:
Base calling was performed using RTA version 2.
Reads were trimmed with Sickle v1.33 and aligned to the hg19 genome assembly using Bowtie v2.3.4.3 and defaults parameters.
Coverage tracks were generated with deepTools v3.2.1.
Peaks were called using Macs2 v2.1.1 and –broad argument.
Assembly: hg38
Supplementary files format and content: bw: RPKM-normalized coverage track
Supplementary files format and content: bed: peaks

molecule: genomic DNA

growth_protocol: K-562 cell line was cultivated in 90% RPMI 1640 cell media complemented with 10% h.i. FBS and 2 mM L-glutamine and maintained in a humidified atmosphere containing 5% CO 2 at 37 °C.

extract_protocol:
5x10 5 cells were seeded in 6-well plates and maintained at 5% CO 2 at 37 °C overnight. The following day, cells were incubated with or without the daunorubicin at a concentration of 1uM for 18h.
The ChIP-Seq analysis targeting the H3K27Ac (Catalogue Number #C15410196, from Diagenode, Serain, Belgium) histone modification was conducted in the K562 cell line utilizing the established BLUEPRINT protocol (http://dcc.blueprint- epigenome.eu/#/md/methods), as described by Cieslak et al. 2020.

treatment_protocol: daunorubicine for 18 hours.

tag: chip antibody


title: Donor 08, 10x 5', Stage I, Intestinal, Lymph Node

description:
D08L
10x Genomics

value: Donor 08

value: Stage I


title: I49,IGRA+,CD4m,MTB300

description:
Library name: Sample 55
TU0022_V


title: Mus musculus, Leydig cells, siprdx1, biol repl2

description:
Library name: siprdx1-2
Column name gene_count.txt: siprdx1-2


title: Donor 08, 10x 5', Stage I, Intestinal, Peripheral Blood

description:
D08P
10x Genomics

value: Peripheral blood


title: I50,IGRA+,CD4m,MTB300

description:
Library name: Sample 54
TU0023_V


title: I47,IGRA+,CD4m,DMSO

description:
Library name: Sample 59
TU0010_X


title: Donor 08, 10x 5', Stage I, Intestinal, Tumor

description:
D08T
10x Genomics

value: Gastric cancer tumor


title: Mus musculus, Leydig cells, siNC+H2O2+FV, biol repl3

description:
Library name: siNC-H2O2-FV-3
Column name gene_count.txt: siNC-H2O2-FV-3


title: INPUT_NT1_10C

description: Library name: INPUT_NT1_10C

value: none, input


title: ILC2_4 cultured with monocyte-derived-macrophages

description: Library name: C4


title: Mus musculus, Leydig cells, siprdx1+H2O2, biol repl1

description:
Library name: siprdx1-H2O2
Column name gene_count.txt: siprdx1-H2O2


title: ILC2_2 cultured alone

description: Library name: L2


title: Donor 08, 10x 5', Stage I, Intestinal, Normal

description:
D08N
10x Genomics


title: ILC2_2 cultured with monocyte-derived-macrophages

description: Library name: C2


title: Donor 09, 10x 5', Stage III, Indeterminate, Lymph Node

description:
D09L
10x Genomics

value: Stage III

value: Indeterminate


title: K27_D1_10C

description: Library name: K27_D1_10C

value: daunorubicine 18h


title: I50,IGRA+,CD4m,DMSO

description:
Library name: Sample 53
TU0023_X


title: Mus musculus, Leydig cells, siNC+H2O2+FV, biol repl1

description:
Library name: siNC-H2O2-FV
Column name gene_count.txt: siNC-H2O2-FV


title: I52,IGRA+,CD4m,DMSO

description:
Library name: Sample 50
TU0046_X


title: Donor 07, 10x 5', Stage III, Indeterminate, Lymph Node

description:
D07L
10x Genomics

value: Donor 07


title: I51,IGRA+,CD4m,MTB300

description:
Library name: Sample 51
TU0024_V


title: Mus musculus, Leydig cells, siNC+H2O2, biol repl3

description:
Library name: siNC-H2O2-3
Column name gene_count.txt: siNC-H2O2-3


title: Donor 07, 10x 5', Stage III, Indeterminate, Peripheral Blood

description:
D07P
10x Genomics


title: Donor 07, 10x 5', Stage III, Indeterminate, Tumor

description:
D07T
10x Genomics


title: I51,IGRA+,CD4m,DMSO

description:
Library name: Sample 52
TU0024_X


title: INPUT_D1_10C

description: Library name: INPUT_D1_10C


title: Mus musculus, Leydig cells, siNC+H2O2+FV, biol repl2

description:
Library name: siNC-H2O2-FV-2
Column name gene_count.txt: siNC-H2O2-FV-2


title: ARPE19-Ad-rTFE3-S-03

city: Bethesda

first: Pablo

middle: S

last: Contreras

state: MD

address: 50 South Dr.

institute: NIH

description: Library name: Sample_9

data_processing:
Basecalling was performed using Real Time Analysis version 2 (RTA2) software.
RTA2 software was used for basecalling and STAR algorithm version 2.5.2b with default settings was used to align the data to the human GRCh38/hg38 genome assembly to generate BAM files.
Differential gene expression analysis was performed using DESeq2 software version v1.14.1.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files include FPKM values for all samples. Matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: Excel file containing DESeq2-normalized gene counts and the results of the performed differential analyses

growth_protocol: ARPE19 cells were cultured in DMEM/F-12 GlutaMAX™ supplemented with 10% (v/v) FBS, 1% (v/v) penicillin-streptomycin at 37°C in 5% CO2.

extract_protocol:
Total RNA was isolated from cells using the Qiagen RNeasy Mini Kit (Qiagen, cat# 74104). For each sample, 0.5 μg of total RNA was then used in Illumina’s TruSeq Stranded mRNA Library kit (Cat# 20020594) for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: ARPE19 cells were infected with Adenovirus-Null, Adenovirus-rTFE3-L or Adenovirus-rTFE3-S 0.2µL/mL for 30 hours.

value: Epithelial cell

value: WT


title: Mus musculus, Leydig cells, siNC+H2O2, biol repl1

description:
Library name: siNC-H2O2
Column name gene_count.txt: siNC-H2O2


title: Donor 06, 10x 5', Stage III, Indeterminate, Peripheral Blood

description:
D06P
10x Genomics

value: Donor 06


title: C48,IGRA-,CD4m,DMSO

description:
Library name: Sample 48
TU0049_X

value: IGRA-


title: Donor 07, 10x 5', Stage III, Indeterminate, Normal

description:
D07N
10x Genomics


title: ARPE19-Ad-rTFE3-S-02

description: Library name: Sample_8


title: I52,IGRA+,CD4m,MTB300

description:
Library name: Sample 49
TU0046_V


title: Mus musculus, Leydig cells, siNC, biol repl2

description:
Library name: siNC-2
Column name gene_count.txt: siNC-2

value: Leydig cells

value: siNC


title: Mus musculus, Leydig cells, siprdx1, biol repl1

description:
Library name: siprdx1
Column name gene_count.txt: siprdx1


title: ARPE19-Ad-rTFE3-L-02

description: Library name: Sample_5


title: C48,IGRA-,CD4m,MTB300

description:
Library name: Sample 47
TU0049_V


title: ARPE19-Ad-rTFE3-S-01

description: Library name: Sample_7


title: Mus musculus, Leydig cells, siNC, biol repl3

description:
Library name: siNC-3
Column name gene_count.txt: siNC-3


title: C50,IGRA-,CD4m,MTB300

description:
Library name: Sample 43
TU0053_V


title: ARPE19-Ad-Null-02

description: Library name: Sample_2

value: Ad-Null


title: Donor 06, 10x 5', Stage III, Indeterminate, Normal

description:
D06N
10x Genomics

value: Adjacent normal


title: Donor 05, 10x 5', Stage III, Indeterminate, Peripheral Blood

description:
D05P
10x Genomics

value: Donor 05


title: Donor 06, 10x 5', Stage III, Indeterminate, Lymph Node

description:
D06L
10x Genomics

value: Lymph node


title: ARPE19-Ad-Null-03

description: Library name: Sample_3


title: PBS5

first: Bo

last: Liu

state: Select a state...

address: 160 Pujian Road

department: Urology

institute: Renji Hospital, School of Medicine, Shanghai Jiao Tong University

description: Library name: F

data_processing:
The transcriptome sequencing and analysis were conducted by OE biotech Co., Ltd. (Shanghai, China). Raw data (raw reads) were processed using Trimmomatic
The reads containing ploy-N and the low quality reads were removed to obtain the clean reads. Then the clean reads were mapped to reference genome using hisat2
FPKM value of each gene was calculated using cufflinks, and the read counts of each gene were obtained by htseq-count
Assembly: mm10
Supplementary files format and content: xls files include FPKM values for each sample

source_name: prostate cancer

growth_protocol: To assess the chemoresistant property of neuroendocrine prostate cancer, we generated an allograft model using tumor tissues from a well-accepted NEPC mouse model (20) (Pb-Cre4: Ptenf/f; Trp53f/f; Rb1f/f), which allowed us to synchronize tumor onset and monitor the response to cisplatin treatment

extract_protocol:
Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) following the manufacturer's protocol.
RNA libraries for RNA-seg were prepared using TruSeq Stranded mRNA LTSample Prep Kit following manufacturer's protocols.

treatment_protocol: Once the tumors were palpable, mice were randomized to receive either cisplatin treatment or PBS vehicle control once a week for four cycles, simulating a clinical treatment regimen. Four weeks later, when tumors in the PBS group reached the ethical endpoint, we collected all the tumors and performed RNA sequencing to investigate the changes after cisplatin treatment

value: prostate cancer

value: Pb-Cre4:Ptenf/f; Trp53f/f; Rb10f/f

value: PBS


title: ARPE19-Ad-Null-01

description: Library name: Sample_1


title: Donor 05, 10x 5', Stage III, Indeterminate, Lymph Node

description:
D05L
10x Genomics

value: Stage III


title: ARPE19-Ad-rTFE3-L-01

description: Library name: Sample_4


title: Mus musculus, Leydig cells, siNC+H2O2, biol repl2

description:
Library name: siNC-H2O2-2
Column name gene_count.txt: siNC-H2O2-2


title: C52,IGRA-,CD4m,MTB300

description:
Library name: Sample 41
TU0056_V


title: C50,IGRA-,CD4m,DMSO

description:
Library name: Sample 44
TU0053_X

value: DMSO


title: Mus musculus, Leydig cells, siNC, biol repl1

description:
Library name: siNC
Column name gene_count.txt: siNC


title: PBS2

description: Library name: D2

value: Pb-Cre4:Ptenf/f; Trp53f/f; Rb7f/f


title: Donor 05, 10x 5', Stage III, Indeterminate, Tumor

description:
D05T
10x Genomics

value: Gastric cancer tumor

value: Indeterminate


title: PBS4

description: Library name: E2

value: Pb-Cre4:Ptenf/f; Trp53f/f; Rb9f/f


title: C52,IGRA-,CD4m,DMSO

description:
Library name: Sample 42
TU0056_X


title: ARPE19-Ad-rTFE3-L-03

description: Library name: Sample_6

value: Epithelial cell

value: WT


title: PBS3

description: Library name: E1

value: Pb-Cre4:Ptenf/f; Trp53f/f; Rb8f/f


title: Donor 06, 10x 5', Stage III, Indeterminate, Tumor

description:
D06T
10x Genomics

value: Donor 06


title: Donor 04, 10x 3', Stage II, Indeterminate, Peripheral Blood

description:
D04P
10x Genomics

value: Peripheral blood

value: Donor 04

value: Stage II


title: Donor 04, 10x 3', Stage II, Indeterminate, Lymph Node

description:
D04L
10x Genomics

value: Lymph node


title: cisplatin4

description: Library name: C1

value: prostate cancer

value: Pb-Cre4:Ptenf/f; Trp53f/f; Rb4f/f

value: cisplatin


title: I53,IGRA+,CD4m,MTB300

description:
Library name: Sample 40
TU0064_V

value: IGRA+


title: Donor 04, 10x 5', Stage II, Indeterminate, Normal

description:
D04N
10x Genomics

value: Adjacent normal


title: PBS1

description: Library name: D1

value: Pb-Cre4:Ptenf/f; Trp53f/f; Rb6f/f

value: PBS


title: I53,IGRA+,CD4m,DMSO

description:
Library name: Sample 39
TU0064_X

value: DMSO


title: C49,IGRA-,CD4m,MTB300

description:
Library name: Sample 45
TU0052_V

value: IGRA-


title: Donor 05, 10x 5', Stage III, Indeterminate, Normal

description:
D05N
10x Genomics

value: Donor 05

value: Stage III

value: Indeterminate


title: C54,IGRA-,CD4m,MTB300

description:
Library name: Sample 38
TU0071_V


title: Donor 04, 10x 3', Stage II, Indeterminate, Tumor

description:
D04T
10x Genomics

value: Gastric cancer tumor


title: Donor 03, 10x 3', Stage III, Intestinal, Lymph Node

description:
D03L
10x Genomics

value: Donor 03

value: Intestinal


title: cisplatin3

description: Library name: B2

value: Pb-Cre4:Ptenf/f; Trp53f/f; Rb3f/f


title: I56,IGRA+,CD4m,MTB300

description:
Library name: Sample 35
TU0078_V


title: C54,IGRA-,CD4m,DMSO

description:
Library name: Sample 37
TU0071_X


title: Donor 03, 10x 5', Stage III, Intestinal, Normal

description:
D03N
10x Genomics


title: C55,IGRA-,CD4m,DMSO

description:
Library name: Sample 34
TU0079_X


title: cisplatin5

description: Library name: C2

value: Pb-Cre4:Ptenf/f; Trp53f/f; Rb5f/f


title: Ctcf_KO, CALM-AF10 AML, input, rep2

city: Toyoake

first: Yoko

last: Kuroki

address: 1-98 Denngakugakubo Kutsukake-cho

country: Japan

institute: Fujita Health University

data_processing:
All data analysis were performed in Galaxy Europe website (https://usegalaxy.eu).
To trim adaptor sequences, sequence reads were processed with the Trimmomatic tool (Garaxy Ver. 0.39) for defalt setting.
Sequence reads were mapped on UCSC mm10 of the mouse genome using the Bowtie2 tool (Galaxy Ver. 2.5.3) for defalt setting.
Aligned sequences were removed PCR duplicates using RmDup samtools (Galaxy Ver. 1.3.1) and sorted into chromosomes using Samtools sort (Galaxy Ver. 1.20) for defalt setting.
To visualize the ChIP-Seq results, modified aligned sequences were converted to BigWig files using deeptools (Galaxy Ver. 3.5.4) for defalt setting.
Assembly: mm10
Supplementary files format and content: BigWig file

source_name: Bone marrow

growth_protocol: Methocult 3234 methylcellulose media, murine IL-3 20 ng/ml, CSF 50 ng/ml, GM-CSF 10ng/ml, and 100 U/ml Penicillin/Streptmycin. Cells were cultured at 37C, at 5 % CO2.

extract_protocol:
CALM-AF10 AML cells were fixed with 1% formaldehyde for 7 minutes. After quenching and cell lysis, chromatin was sonicated using a S220 focused-ultrasonicator (Covaris).
ChIP-Seq libralies were prepared with VAHTS Universal Pro DNA Library Prep Kit (Vazyme) for Illumina.

value: Bone marrow

value: CALM-AF10 leukemia cells

value: none (input)

value: CTCF KO


title: 5th  fraction of S series slicing [5W_Normal]

type: RNA

city: Wako-shi

first: Yuko

last: Okamura-Oho

state: Saitama

address: 2-1, Hirosawa

institute: RIKEN

description: sample for Transcriptome Tomography

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 250 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 GE 028005 Microarrays for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using the one color scan setting for 8x60k array slides (Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Data were normalized using per chip: normalize to 75th percentile.

source_name: 5 micron x 200 sagittal slices (1000 micron width) of the brain, Sf05

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Mice were grown in pathogen-free conditions.

extract_protocol: RNA was prepared using the Mag-max-96 for Microarrays Total RNA Isolation Kit (Ambion) following the manufacturer's recommendations of the spin column protocol. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: strain

value: normal littermate of R6/2

value: brain

tag: gender

value: male

tag: age

value: 5 weeks post-natal age

tag: section

value: sagittal plane

tag: mouse id


title: cisplatin1

description: Library name: A

value: prostate cancer

value: Pb-Cre4:Ptenf/f; Trp53f/f; Rb1f/f

value: cisplatin


title: 8th  fraction of S series slicing [5W_Normal]

description: sample for Transcriptome Tomography

source_name: 5 micron x 200 sagittal slices (1000 micron width) of the brain, Sf08


title: 7th  fraction of S series slicing [5W_Normal]

description: sample for Transcriptome Tomography

source_name: 5 micron x 200 sagittal slices (1000 micron width) of the brain, Sf07


title: 9th  fraction of S series slicing [5W_Normal]

description: sample for Transcriptome Tomography

source_name: 5 micron x 200 sagittal slices (1000 micron width) of the brain, Sf09


title: C55,IGRA-,CD4m,MTB300

description:
Library name: Sample 33
TU0079_V

value: IGRA-


title: 4th  fraction of S series slicing [5W_Normal]

description: sample for Transcriptome Tomography

source_name: 5 micron x 200 sagittal slices (1000 micron width) of the brain, Sf04


title: Donor 03, 10x 3', Stage III, Intestinal, Tumor

description:
D03T
10x Genomics

source_name: Gastric cancer tumor

value: Gastric cancer tumor

value: Donor 03

value: Stage III


title: I56,IGRA+,CD4m,DMSO

description:
Library name: Sample 36
TU0078_X

value: DMSO

value: IGRA+


title: 10th  fraction of S series slicing [5W_Normal]

description: sample for Transcriptome Tomography

source_name: 5 micron x 200 sagittal slices (1000 micron width) of the brain, Sf10


title: Donor 02, 10x 5', Stage III, Indeterminate, Peripheral Blood

description:
D02P
10x Genomics

value: Peripheral blood

value: Donor 02

value: Indeterminate


title: 6th  fraction of S series slicing [5W_Normal]

description: sample for Transcriptome Tomography

source_name: 5 micron x 200 sagittal slices (1000 micron width) of the brain, Sf06

value: normal littermate of R6/2


title: C49,IGRA-,CD4m,DMSO

description:
Library name: Sample 46
TU0052_X


title: Ctcf_KO, CALM-AF10 AML, H3K4me3, rep2

value: Bone marrow

value: CALM-AF10 leukemia cells

value: H3K4me3 (Abcam, ab8580)

value: CTCF KO


title: Donor 02, 10x 5', Stage III, Indeterminate, Lymph Node

description:
D02L
10x Genomics

value: Lymph node


title: 3rd  fraction of S series slicing [5W_Normal]

description: sample for Transcriptome Tomography

source_name: 5 micron x 200 sagittal slices (1000 micron width) of the brain, Sf03

value: brain

value: male

value: 5 weeks post-natal age

value: sagittal plane


title: I57,IGRA+,CD4m,DMSO

description:
Library name: Sample 32
TU0081_X


title: Donor 02, 10x 5', Stage III, Indeterminate, Normal

description:
D02N
10x Genomics

source_name: Adjacent normal

value: Adjacent normal


title: C56,IGRA-,CD4m,DMSO

description:
Library name: Sample 30
TU0084_Y

value: IGRA-


title: Ctcf_WT, CALM-AF10 AML, H3K4me3, rep2

value: CTCF WT


title: Ctcf_KO, CALM-AF10 AML, H3K27ac, rep2

value: H3K27ac (Abcam, ab4729)


title: Donor 02, 10x 5', Stage III, Indeterminate, Tumor

description:
D02T
10x Genomics

value: Gastric cancer tumor

value: Stage III


title: C56,IGRA-,CD4m,MTB300

description:
Library name: Sample 29
TU0084_V


title: 2nd  fraction of S series slicing [5W_Normal]

description: sample for Transcriptome Tomography

source_name: 5 micron x 200 sagittal slices (1000 micron width) of the brain, Sf02


title: 7th  fraction of R series slicing [5W_Normal]

description: sample for Transcriptome Tomography

source_name: 5 micron x 200 right oblique slices (1000 micron width) of the brain, Rf07

value: right oblique plane


title: Donor 01, 10x 5', Stage I, Intestinal, Peripheral Blood

description:
D01P
10x Genomics

source_name: Peripheral blood

value: Peripheral blood

value: Donor 01

value: Stage I

value: Intestinal


title: 6th  fraction of R series slicing [5W_Normal]

description: sample for Transcriptome Tomography

source_name: 5 micron x 200 right oblique slices (1000 micron width) of the brain, Rf06

value: normal littermate of R6/2


title: cisplatin2

description: Library name: B1

value: prostate cancer

value: Pb-Cre4:Ptenf/f; Trp53f/f; Rb2f/f

value: cisplatin


title: I57,IGRA+,CD4m,MTB300

description:
Library name: Sample 31
TU0081_V

value: IGRA+


title: C57,IGRA-,CD4m,DMSO

description:
Library name: Sample 28
TU0094_X

value: DMSO


title: Ctcf_KO, CALM-AF10 AML, H3K27me3, rep2

value: Bone marrow

value: CALM-AF10 leukemia cells

value: CTCF KO


title: Ctcf_WT, CALM-AF10 AML, input, rep2

value: none (input)

value: CTCF WT


title: 5th  fraction of R series slicing [5W_Normal]

description: sample for Transcriptome Tomography

source_name: 5 micron x 200 right oblique slices (1000 micron width) of the brain, Rf05

value: brain

value: male

value: 5 weeks post-natal age


title: C57,IGRA-,CD4m,MTB300

description:
Library name: Sample 27
TU0094_V

value: IGRA-


title: 1st  fraction of S series slicing [5W_Normal]

description: sample for Transcriptome Tomography

source_name: 5 micron x 200 sagittal slices (1000 micron width) of the brain, Sf01

value: sagittal plane


title: Donor 01, 10x 5', Stage I, Intestinal, Tumor

description:
D01T
10x Genomics

value: Gastric cancer tumor

value: Donor 01

value: Stage I

value: Intestinal


title: Ctcf_WT, CALM-AF10 AML, H3K27me3, rep2

source_name: Bone marrow


title: Donor 30, 10x ST, Tumor, Stage III, Diffuse, Core, Replicate 2

description: Fresh frozen Spatial Transcriptome sequencing

data_processing:
*library strategy:  Spatial Transcriptomics
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline to generate FASTQ files
Sequences were aligned to GRCh38 genome for gene expression count using Space Ranger's default settings
Gene expression level of RefSeq coding genes were quantified using Space Ranger's default settings
Assembly: hg38
Supplementary files format and content: filtered_feature_bc_matrix.h5: H5 format that can compress gene expression data
Supplementary files format and content: scalefactors_json.json: scale factors in json format
Supplementary files format and content: tissue_hires_image.png: high resolution of tissue image
Supplementary files format and content: tissue_positions_list.csv: spatial barcodes and their coordinates

extract_protocol:
Fresh tissues were immediately embedded in OCT once leaving the Tissue Storage Solution and cryosectioned at ten μm thickness.
Spatial Transcriptomics sequencing libraries were prepared with 10x Genomics Visium Spatial Gene Expression Slides & Reagents accoridng to manufacturer's protocol

tag: subject id

value: Donor 30

value: Stage III

value: Diffuse

tag: sampling location

value: Core


title: C58,IGRA-,CD4m,DMSO

description:
Library name: Sample 26
TU0110_X

tag: treatment

value: DMSO


title: Donor 30, 10x ST, Tumor, Stage III, Diffuse, Core, Replicate 1


title: Ctcf_KO, CALM-AF10 AML, input, rep1

value: Bone marrow

tag: cell type

value: CALM-AF10 leukemia cells

value: CTCF KO


title: Ctcf_WT, CALM-AF10 AML, input, rep1

value: none (input)

tag: genotype

value: CTCF WT


title: Donor 28, 10x ST, Tumor, Stage II, Indeterminate, In-between, Replicate 1

tag: tissue

value: Donor 28

value: Stage II

value: Indeterminate

value: In-between


title: C58,IGRA-,CD4m,MTB300

description:
Library name: Sample 25
TU0110_V

value: IGRA-


title: Ctcf_WT, CALM-AF10 AML, H3K27ac, rep2

value: H3K27ac (Abcam, ab4729)


title: T48,ATB,CD4m,MTB300

description:
Library name: Sample 24
TU0113_V

value: ATB


title: Ctcf_KO, CALM-AF10 AML, H3K4me3, rep1

value: H3K4me3 (Abcam, ab8580)


title: Ctcf_WT, CALM-AF10 AML, H3K4me3, rep1


title: 2nd  fraction of R series slicing [5W_Normal]

description: sample for Transcriptome Tomography

source_name: 5 micron x 200 right oblique slices (1000 micron width) of the brain, Rf02

value: normal littermate of R6/2

value: brain

value: male

value: 5 weeks post-natal age

value: right oblique plane


title: 8th  fraction of L series slicing [5W_Normal]

description: sample for Transcriptome Tomography

source_name: 5 micron x 200 left oblique slices (1000 micron width) of the brain, Lf08

value: left oblique plane


title: 4th  fraction of R series slicing [5W_Normal]

description: sample for Transcriptome Tomography

source_name: 5 micron x 200 right oblique slices (1000 micron width) of the brain, Rf04


title: T49,ATB,CD4m,MTB300

description:
Library name: Sample 22
TU0122_V


title: Donor 27, 10x ST, Tumor, Stage II, Intestinal, In-between, Replicate 2

value: Gastric cancer tumor

value: Donor 27

value: Intestinal


title: 1st  fraction of R series slicing [5W_Normal]

description: sample for Transcriptome Tomography

source_name: 5 micron x 200 right oblique slices (1000 micron width) of the brain, Rf01


title: Ctcf_KO, CALM-AF10 AML, H3K27ac, rep1

value: Bone marrow

value: CALM-AF10 leukemia cells

value: CTCF KO


title: 3rd  fraction of R series slicing [5W_Normal]

description: sample for Transcriptome Tomography

source_name: 5 micron x 200 right oblique slices (1000 micron width) of the brain, Rf03


title: T48,ATB,CD4m,DMSO

description:
Library name: Sample 23
TU0113_X

value: DMSO


title: T49,ATB,CD4m,DMSO

description:
Library name: Sample 21
TU0122_X


title: Ctcf_WT, CALM-AF10 AML, H3K27ac, rep1

value: CTCF WT


title: 7th  fraction of L series slicing [5W_Normal]

description: sample for Transcriptome Tomography

source_name: 5 micron x 200 left oblique slices (1000 micron width) of the brain, Lf07


title: Ctcf_KO, CALM-AF10 AML, H3K27me3, rep1


title: T50,ATB,CD4m,DMSO

description:
Library name: Sample 20
TU0124_X


title: Ctcf_WT, CALM-AF10 AML, H3K27me3, rep1


title: T50,ATB,CD4m,MTB300

description:
Library name: Sample 19
TU0124_V


title: 5th  fraction of L series slicing [5W_Normal]

description: sample for Transcriptome Tomography

source_name: 5 micron x 200 left oblique slices (1000 micron width) of the brain, Lf05


title: Donor 26, 10x ST, Tumor, Stage II, Intestinal, Edge, Replicate 1

source_name: Gastric cancer tumor

value: Donor 26

value: Stage II

value: Edge


title: Donor 26, 10x ST, Tumor, Stage II, Intestinal, In-between, Replicate 1

value: In-between


title: 6th  fraction of L series slicing [5W_Normal]

description: sample for Transcriptome Tomography

source_name: 5 micron x 200 left oblique slices (1000 micron width) of the brain, Lf06

value: normal littermate of R6/2

value: brain


title: Donor 27, 10x ST, Tumor, Stage II, Intestinal, Edge, Replicate 1


title: WT/sPrdm16_3

city: Yokohama

first: Junji

last: Ikeda

state: Kanagawa

address: 3-9, Fukuura, Kanazawa-ku

department: Pediatrics

institute: Yokohama City University

data_processing:
DRAGEN Bio-IT Platform version 3.6.3 (Illumina)
Assembly: mm10
Supplementary files format and content: xlsx file includes raw counts for each sample

source_name: bone marrow cells

growth_protocol: MA9/control or MA9/sPrdm16 cells were maintained in RPMI1640 medium supplemented with 10% fetal bovine serum (FBS) and 5 ng/ml mouse IL-3 in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen).
RNA libraries for RNA-seq were prepared using Nextera XT DNA Library Prep Kit and Nextera XT Index Kit v2 SetA/B/C/D (Illumina) according to the manufacturer's instructions.

value: bone marrow cells

value: WT

value: sPrdm16-expressing retroviral vector


title: T51,ATB,CD4m,DMSO

description:
Library name: Sample 18
TU0126_X

value: ATB


title: T51,ATB,CD4m,MTB300

description:
Library name: Sample 17
TU0126_V


title: Donor 27, 10x ST, Tumor, Stage II, Intestinal, In-between, Replicate 1

value: Gastric cancer tumor

value: Donor 27


title: 4th  fraction of L series slicing [5W_Normal]

description: sample for Transcriptome Tomography

source_name: 5 micron x 200 left oblique slices (1000 micron width) of the brain, Lf04

value: male

value: 5 weeks post-natal age

value: left oblique plane


title: WT/sPrdm16_2


title: Donor 24, 10x ST, Tumor, Stage II, Intestinal, Edge, Replicate 1

value: Donor 24

value: Intestinal


title: 2nd  fraction of L series slicing [5W_Normal]

description: sample for Transcriptome Tomography

source_name: 5 micron x 200 left oblique slices (1000 micron width) of the brain, Lf02


title: 3rd  fraction of L series slicing [5W_Normal]

description: sample for Transcriptome Tomography

source_name: 5 micron x 200 left oblique slices (1000 micron width) of the brain, Lf03


title: WT/sPrdm16_1


title: Donor 27, 10x ST, Tumor, Stage II, Intestinal, Core, Replicate 1

value: Core


title: T52,ATB,CD4m,MTB300

description:
Library name: Sample 16
TU0129_V


title: Donor 24, 10x ST, Tumor, Stage II, Intestinal, In-between, Replicate 1

value: Stage II


title: 1st  fraction of L series slicing [5W_Normal]

description: sample for Transcriptome Tomography

source_name: 5 micron x 200 left oblique slices (1000 micron width) of the brain, Lf01


title: T52,ATB,CD4m,DMSO

description:
Library name: Sample 15
TU0129_X

value: DMSO


title: Donor 23, 10x ST, Tumor, Stage II, Intestinal, In-between, Replicate 1

value: Donor 23

value: In-between


title: WT/control_3

value: mock


title: 6th  fraction of H series slicing [5W_Normal]

description: sample for Transcriptome Tomography

source_name: 5 micron x 200 holizontal slices (1000 micron width) of the brain, Hf06

value: normal littermate of R6/2

value: brain

value: horizontal plane


title: T53,ATB,CD4m,DMSO

description:
Library name: Sample 14
TU0130_X

value: ATB


title: WT/control_2

value: bone marrow cells

value: WT


title: Donor 22, 10x ST, Tumor, Stage I, Diffuse, In-between, Replicate 1

value: Gastric cancer tumor

value: Donor 22

value: Stage I

value: Diffuse


title: Donor 21, 10x ST, Tumor, Stage III, Indeterminate, Edge, Replicate 2

value: Donor 21

value: Stage III

value: Indeterminate

value: Edge


title: T54,ATB,CD4m,DMSO

description:
Library name: Sample 12
TU0131_X

value: DMSO


title: 5th  fraction of H series slicing [5W_Normal]

description: sample for Transcriptome Tomography

source_name: 5 micron x 200 holizontal slices (1000 micron width) of the brain, Hf05

value: male

value: 5 weeks post-natal age


title: Donor 26, 10x ST, Tumor, Stage II, Intestinal, Core, Replicate 1

value: Donor 26

value: Stage II

value: Intestinal

value: Core


title: MA9/sPrdm16_3

value: bone marrow cells

value: retroviral MLL::AF9 vector

value: sPrdm16-expressing retroviral vector


title: T53,ATB,CD4m,MTB300

description:
Library name: Sample 13
TU0130_V

value: ATB


title: WT/control_1

value: WT

value: mock


title: Donor 21, 10x ST, Tumor, Stage III, Indeterminate, Edge, Replicate 1

value: Gastric cancer tumor

value: Donor 21


title: T54,ATB,CD4m,MTB300

description:
Library name: Sample 11
TU0131_V


title: MA9/sPrdm16_2


title: 3rd  fraction of H series slicing [5W_Normal]

description: sample for Transcriptome Tomography

source_name: 5 micron x 200 holizontal slices (1000 micron width) of the brain, Hf03

value: normal littermate of R6/2

value: brain

value: horizontal plane


title: I58,IGRA+,CD4m,MTB300

description:
Library name: Sample 10
TU0137_V

value: IGRA+


title: 4th  fraction of H series slicing [5W_Normal]

description: sample for Transcriptome Tomography

source_name: 5 micron x 200 holizontal slices (1000 micron width) of the brain, Hf04

value: male

value: 5 weeks post-natal age


title: Donor 21, 10x ST, Tumor, Stage III, Indeterminate, In-between, Replicate 2

value: Stage III

value: Indeterminate

value: In-between


title: Donor 21, 10x ST, Tumor, Stage III, Indeterminate, In-between, Replicate 1


title: 1st  fraction of H series slicing [5W_Normal]

description: sample for Transcriptome Tomography

source_name: 5 micron x 200 holizontal slices (1000 micron width) of the brain, Hf01


title: MA9/sPrdm16_1

value: bone marrow cells


title: 2nd  fraction of H series slicing [5W_Normal]

description: sample for Transcriptome Tomography

source_name: 5 micron x 200 holizontal slices (1000 micron width) of the brain, Hf02


title: MA9/control_3

value: retroviral MLL::AF9 vector


title: Donor 20, 10x ST, Tumor, Stage III, Diffuse, In-between, Replicate 1

value: Donor 20

value: Diffuse


title: I58,IGRA+,CD4m,DMSO

description:
Library name: Sample 9
TU0137_X

value: DMSO


title: MA9/control_2

value: mock


title: MA9/control_1


title: T55,ATB,CD4m,DMSO

description:
Library name: Sample 7
TU0139_X

value: ATB


title: T55,ATB,CD4m,MTB300

description:
Library name: Sample 8
TU0139_V


title: T56,ATB,CD4m,DMSO

description:
Library name: Sample 6
TU0141_X


title: Control fibroblasts Sample 8 = A4126TbRII

city: NYC

first: Izabela

last: Tuleta

state: NY

address: 1545 Rhinelander Ave, Apt. 3K

institute: Albert Einstein College of Medicine

data_processing:
Raw image data file from high-throughput sequencing was transformed to Sequenced Reads by CASAVA base recognition (Base Calling).
The library preparations were sequenced on Illumina NovaSeq 6000 devices, generating 100 bp paired end reads. Adapter, poly-N and low-quality reads from the raw data were excluded to purify the data analysis
Quality Phred Scores, Q20%, Q30% and GC contents of the clean data were calculated, showing high accuracy of reads (>99%, with 0.02 error rate).
Filtered reads were aligned to the C57BL/6J reference genome (December 2011 release of the mouse musculus reference genome (mm10; GRCm38.p6) from Ensembl) using TopHat2 algorithm alignment program v.2.0.
Mapped reads were assembled using both Scripture (beta2) and Cufflinks v.2.1.1 algorithm
HTSeq software v.0.6.1 was used to count the number of reads mapped to each gene. Read count of fragments per kilobase of transcript sequence per millions base pairs sequenced (FPKM), was used to calculate gene expression level, which considered the effects of both sequencing depth and gene length
Assembly: mm10
Supplementary files format and content: txt file including FPKM values counts for every gene and every sample

source_name: heart

growth_protocol: no cell culture, cardiac fibroblasts were isolated by FACS

extract_protocol:
RNA was extracted with Trizol reagent.
RNA sequencing was performed by Novogene. RNA libraries were prepared for sequencing using standard Illumina protocols
Library preparation was performed by Novogene, Inc., using at least 1 ug high-quality total RNA input per sample. mRNA enrichment was performed with poly-T oligo-attached magnetic beads. Libraries were constructed using NEBNext Ultra RNA Library Prep Kit for Illumina.

treatment_protocol: no treatment ex vivo, to achieve fibroblast-specific TbR2 KO tamoxifen i.p. was administrated to the mice (including control mice).

value: heart

value: cardiac fibroblast


title: Donor 18, 10x ST, Tumor, Stage III, Diffuse, In-between, Replicate 1

value: Gastric cancer tumor

value: Donor 18


title: T56,ATB,CD4m,MTB300

description:
Library name: Sample 5
TU0141_V

data_processing:
Reads that passed illumina filters were filtered to eliminate reads aligning to tRNA, rRNA, and adapter sequences. The reads were then aligned to GRCh38 reference genome using TopHat. DUST scores were calculated with PRINSEQ Lite and low complexity reads (DUST >4) were removed from the BAM files. The alignment results were parsed via SAMtools to generate SAM files. Read counts for each genomic feature were obtained with the htseq-count program.
Assembly: GRCh38
Supplementary files format and content: abundance measurementas as a matrix table

extract_protocol:
RNA was purified using an miRNeasy Micro Kit (QIAGEN).
Purified total RNA (1–5 ng) was amplified following the Smart-Seq2 protocol (16 cycles of cDNA amplification). 1 ng of cDNA was used to prepare a standard Nextera XT sequencing library (Nextera XT DNA sample preparation kit and index kit, Illumina)


title: Donor 18, 10x ST, Tumor, Stage III, Diffuse, In-between, Replicate 2


title: Control fibroblasts Sample 7 = A4114TbRII


title: Donor 16, 10x ST, Tumor, Stage III, Diffuse, In-between, Replicate 2

value: Donor 16


title: 10th  fraction of C series slicing [5W_Normal]

description: sample for Transcriptome Tomography

source_name: 5 micron x 200 coronal slices (1000 micron width) of the brain, Cf10

value: normal littermate of R6/2

value: brain

value: male

value: coronal plane


title: 11th  fraction of C series slicing [5W_Normal]

description: sample for Transcriptome Tomography

source_name: 5 micron x 200 coronal slices (1000 micron width) of the brain, Cf11

value: 5 weeks post-natal age


title: Control fibroblasts Sample 6 = A4100TbRII


title: Donor 16, 10x ST, Tumor, Stage III, Diffuse, In-between, Replicate 1

value: Stage III

value: In-between


title: 8th  fraction of C series slicing [5W_Normal]

description: sample for Transcriptome Tomography

source_name: 5 micron x 200 coronal slices (1000 micron width) of the brain, Cf08


title: 7th  fraction of C series slicing [5W_Normal]

description: sample for Transcriptome Tomography

source_name: 5 micron x 200 coronal slices (1000 micron width) of the brain, Cf07


title: 9th  fraction of C series slicing [5W_Normal]

description: sample for Transcriptome Tomography

source_name: 5 micron x 200 coronal slices (1000 micron width) of the brain, Cf09


title: Control fibroblasts Sample 5 = A4088TbRII


title: Donor 20, 10x ST, Tumor, Stage III, Diffuse, Core, Replicate 1

source_name: Gastric cancer tumor

value: Donor 20

value: Core


title: C59,IGRA-,CD4m,MTB300

description:
Library name: Sample 2
TU0146_V

value: IGRA-


title: 12th  fraction of C series slicing [5W_Normal]

description: sample for Transcriptome Tomography

source_name: 5 micron x 200 coronal slices (1000 micron width) of the brain, Cf12


title: Fibroblasts with TbR2 knockout Sample 4 = A4127TbRIIKo


title: T57,ATB,CD4m,DMSO

description:
Library name: Sample 3
TU0145_X

value: DMSO


title: Donor 16, 10x ST, Tumor, Stage III, Diffuse, Core, Replicate 2

value: Diffuse


title: Fibroblasts with TbR2 knockout Sample 3 = A4118TbRIIKo

value: heart


title: Donor 16, 10x ST, Tumor, Stage III, Diffuse, Core, Replicate 1


title: C59,IGRA-,CD4m,DMSO

description:
Library name: Sample 1
TU0146_X


title: 4th  fraction of C series slicing [5W_Normal]

description: sample for Transcriptome Tomography

source_name: 5 micron x 200 coronal slices (1000 micron width) of the brain, Cf04


title: Donor 15, 10x ST, Tumor, Stage III, Indeterminate, In-between, Replicate 1

value: Donor 15

value: Indeterminate


title: 6th  fraction of C series slicing [5W_Normal]

description: sample for Transcriptome Tomography

source_name: 5 micron x 200 coronal slices (1000 micron width) of the brain, Cf06


title: Fibroblasts with TbR2 knockout Sample 2 = A4116TbRIIKo

value: cardiac fibroblast


title: 5th  fraction of C series slicing [5W_Normal]

description: sample for Transcriptome Tomography

source_name: 5 micron x 200 coronal slices (1000 micron width) of the brain, Cf05


title: Donor 27, Bulk, Tumor, Stage II, Intestinal, Core

data_processing:
The raw sequences were processed and the TPM values were caluculated by RSEM.
Assembly: hg38
Supplementary files format and content: counts.txt: tab-delimited text files including TPM values generated by RSEm

extract_protocol:
Ten sections for each tissue block were pooled together, and total RNA was extracted using RNeasy Kits (Qiagen, Germany).
The sequencing libraries was constructed at GENEWIZ (Suzhou, China).

value: Gastric cancer tumor

value: Donor 27

value: Stage II

value: Intestinal


title: Donor 15, 10x ST, Tumor, Stage III, Indeterminate,  Edge, Replicate 1

value: Edge


title: T57,ATB,CD4m,MTB300

description:
Library name: Sample 4
TU0145_V

value: ATB


title: Donor 27, Bulk, Tumor, Stage II, Intestinal, Edge


title: Fibroblasts with TbR2 knockout Sample 1 = A4086TbRIIKo


title: Donor 11, 10x ST, Tumor, Stage III, Indeterminate, In-between, Replicate 2

value: Donor 11

value: Stage III


title: Donor 26, Bulk, Tumor, Stage II, Intestinal, Edge

value: Donor 26


title: 3rd  fraction of C series slicing [5W_Normal]

description: sample for Transcriptome Tomography

source_name: 5 micron x 200 coronal slices (1000 micron width) of the brain, Cf03

value: normal littermate of R6/2

value: brain

value: male

value: 5 weeks post-natal age

value: coronal plane


title: 2nd  fraction of C series slicing [5W_Normal]

description: sample for Transcriptome Tomography

source_name: 5 micron x 200 coronal slices (1000 micron width) of the brain, Cf02


title: Donor 26, Bulk, Tumor, Stage II, Intestinal, In-between

value: In-between


title: Donor 11, 10x ST, Tumor, Stage III, Indeterminate, In-between, Replicate 1

value: Indeterminate


title: RNA_18m_rep2

city: San Diego

first: Kangli

last: Wang

address: 9500 Gilman Drive

institute: University of California San Diego

description: snRNA-seq

data_processing:
The sequencing reads were aligned to mm10 (GRCh38) reference genome and the feature-barcode matrix and fragments was generated using cellranger-arc (v2.0.0).
Assembly: mm10
Supplementary files format and content: Filtered H5 matrix files output from Cell Ranger software.
Supplementary files format and content: Fragments files output from Cell Ranger software.

molecule: nuclear RNA

source_name: brain

extract_protocol:
C57BL/6 mice were purchased from Jackson Laboratories. Brains were extracted from mice and substantia nigra regions were dissected according to the Allen Brain Reference Atlas. For each sample, dissected brain tissues were pooled from 4-5 C57BL/6 mice to obtain enough nuclei for single nucleus multiome for each biological replicate, and two biological replicates were performed for each age stage.
Nucleus were isolated from the directions using the protocol suggested for use with the chromium Next GEM Single Cell Multiome ATAC+Gene Expression protocol (CG000338). Libraries were performed immediately for each sample as per Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide (CG000338).
Chromium Single Cell Multiome ATAC + Gene Expression

tag: tissue region

value: Substantia nigra

tag: number of_animals_pooled

value: 18 months old


title: 1st  fraction of C series slicing [5W_Normal]

description: sample for Transcriptome Tomography

source_name: 5 micron x 200 coronal slices (1000 micron width) of the brain, Cf01


title: Donor 11, 10x ST, Tumor, Stage III, Indeterminate, Core, Replicate 2

value: Gastric cancer tumor

tag: Stage

tag: subtype

value: Core


title: RNA_18m_rep1

description: snRNA-seq


title: ATAC_18m_rep2

description: snATC-seq

library_source: genomic single cell


title: Donor 11, 10x ST, Tumor, Stage III, Indeterminate, Core, Replicate 1


title: ATAC_18m_rep1

description: snATC-seq


title: 10th  fraction of S series slicing [5W_HD]

description: sample for Transcriptome Tomography

source_name: 5 micron x 200 sagittal slices (1000 micron width) of the brain, Sf10

value: Huntington disease model R6/2

value: sagittal plane


title: Donor 24, Bulk, Tumor, Stage II, Intestinal, In-between

value: Donor 24

value: Stage II

value: Intestinal


title: Donor 23, Bulk, Tumor, Stage II, Intestinal, Core/In-between

value: Donor 23

value: Core/In-between


title: Donor 10, 10x ST, Tumor, Stage III, Intestinal, In-between, Replicate 1

value: Donor 10

value: Stage III


title: Donor 07, 10x ST, Tumor, Stage III, Indeterminate, Edge, Replicate 1

value: Donor 07

value: Edge


title: 8th  fraction of S series slicing [5W_HD]

description: sample for Transcriptome Tomography

source_name: 5 micron x 200 sagittal slices (1000 micron width) of the brain, Sf08

value: brain

value: male

value: 5 weeks post-natal age


title: 9th  fraction of S series slicing [5W_HD]

description: sample for Transcriptome Tomography

source_name: 5 micron x 200 sagittal slices (1000 micron width) of the brain, Sf09


title: Donor 10, 10x ST, Tumor, Stage III, Intestinal, Core, Replicate 1


title: ATAC_12m_rep2

description: snATC-seq

value: Substantia nigra

value: 12 months old


title: Donor 03, 10x ST, Tumor, Stage III, Intestinal, Edge, Replicate 1

value: Gastric cancer tumor

value: Donor 03


title: RNA_12m_rep2

description: snRNA-seq


title: Donor 03, 10x ST, Tumor, Stage III, Intestinal, In-between, Replicate 1

value: In-between


title: 6th  fraction of S series slicing [5W_HD]

description: sample for Transcriptome Tomography

source_name: 5 micron x 200 sagittal slices (1000 micron width) of the brain, Sf06

value: Huntington disease model R6/2

value: sagittal plane


title: Donor 26, Bulk, Tumor, Stage II, Intestinal, Core

value: Donor 26

value: Stage II

value: Intestinal

value: Core


title: Donor 16, Bulk, Tumor, Stage III, Diffuse, Core/In-between

value: Donor 16

value: Stage III

value: Diffuse

value: Core/In-between


title: ATAC_6m_rep2

description: snATC-seq

value: brain

value: 6 months old


title: 5th  fraction of S series slicing [5W_HD]

description: sample for Transcriptome Tomography

source_name: 5 micron x 200 sagittal slices (1000 micron width) of the brain, Sf05

value: male

value: 5 weeks post-natal age


title: Donor 01, 10x ST, Tumor, Stage I, Intestinal, Edge, Replicate 1

value: Gastric cancer tumor

value: Donor 01

value: Stage I

value: Edge


title: Donor 10, Bulk, Tumor, Stage III, Intestinal, Core/In-between

value: Donor 10


title: 4th  fraction of S series slicing [5W_HD]

description: sample for Transcriptome Tomography

source_name: 5 micron x 200 sagittal slices (1000 micron width) of the brain, Sf04

value: Huntington disease model R6/2

value: sagittal plane


title: Donor 21, Bulk, Tumor, Stage III, Indeterminate, In-between/Edge

value: Donor 21

value: Indeterminate

value: In-between/Edge


title: Donor 15, Bulk, Tumor, Stage III, Indeterminate, In-between/Edge

value: Donor 15

value: Stage III


title: Donor 11, Bulk, Tumor, Stage III, Indeterminate, Core/In-between

value: Donor 11

value: Core/In-between


title: 7th  fraction of S series slicing [5W_HD]

description: sample for Transcriptome Tomography

source_name: 5 micron x 200 sagittal slices (1000 micron width) of the brain, Sf07

value: brain


title: Donor 01, 10x ST, Tumor, Stage I, Intestinal, In-between, Replicate 1

value: Intestinal

value: In-between


title: RNA_6m_rep1

description: snRNA-seq

value: Substantia nigra

value: 6 months old


title: 2nd  fraction of S series slicing [5W_HD]

description: sample for Transcriptome Tomography

source_name: 5 micron x 200 sagittal slices (1000 micron width) of the brain, Sf02

value: male

value: 5 weeks post-natal age


title: 1st  fraction of S series slicing [5W_HD]

description: sample for Transcriptome Tomography

source_name: 5 micron x 200 sagittal slices (1000 micron width) of the brain, Sf01


title: 3rd  fraction of S series slicing [5W_HD]

description: sample for Transcriptome Tomography

source_name: 5 micron x 200 sagittal slices (1000 micron width) of the brain, Sf03


title: Donor 18, Bulk, Tumor, Stage III, Diffuse, In-between

source_name: Gastric cancer tumor

value: Gastric cancer tumor

value: Donor 18

value: Diffuse


title: Donor 09, Bulk, Tumor, Stage III, Indeterminate, In-between/Edge

value: Donor 09


title: ATAC_2m_rep2

description: snATC-seq

value: 2 months old


title: ATAC_6m_rep1

description: snATC-seq


title: RNA_6m_rep2

description: snRNA-seq


title: RNA_2m_rep2

description: snRNA-seq


title: Donor 27, 10x ST, Tumor, Stage II, Intestinal, Edge

value: Donor 27

value: Stage II

value: Edge


title: 7th  fraction of R series slicing [5W_HD]

description: sample for Transcriptome Tomography

source_name: 5 micron x 200 right oblique slices (1000 micron width) of the brain, Rf07

value: Huntington disease model R6/2

value: right oblique plane


title: Donor 28, 10x ST, Tumor, Stage II, Indeterminate, In-between

value: Donor 28

value: Indeterminate


title: Donor 01, Bulk, Tumor, Stage I, Intestinal, Edge

value: Donor 01

value: Stage I

value: Intestinal


title: RNA_2m_rep1

description: snRNA-seq

value: brain

value: Substantia nigra


title: Donor 27, 10x ST, Tumor, Stage II, Intestinal, Core

value: Gastric cancer tumor

value: Core


title: ATAC_2m_rep1

description: snATC-seq


title: Donor 26, 10x ST, Tumor, Stage II, Intestinal, In-between

value: Donor 26

value: In-between


title: 6th  fraction of R series slicing [5W_HD]

description: sample for Transcriptome Tomography

source_name: 5 micron x 200 right oblique slices (1000 micron width) of the brain, Rf06

value: male

value: 5 weeks post-natal age


title: ATAC_12m_rep1

description: snATC-seq

value: 12 months old


title: Donor 01, Bulk, Tumor, Stage I, Intestinal, In-between


title: KMC037

city: Los Angeles

first: Calvin

last: Pan

address: 675 Charles Young Dr South

institute: UCLA

description: Library name: KMC037

data_processing:
Counts and TPM values were obtained using kallisto v0.46 against the Ensembl mouse transcriptome (v97)
Assembly: mm10
Supplementary files format and content: tab-delimited files contain counts and TPM values

source_name: liver

extract_protocol:
Total RNA from a 20 mg piece of the large lobe of the liver was purified from one mouse per strain of the HMDP, and from 3 mice per diet group in the C57BL6J Control study, using the Qiagen miRNeasy Mini kit (Qiagen cat#217004) per the manufacturer’s instructions. RNA preparation was as previously described (Ma, Fuqua et al. 2019) except that samples were homogenized in QIAzol using a TissueLyzer (Qiagen). All samples had RINe values greater than 8.
RNA sequencing libraries were prepared as described previously (Ma, Fuqua et al. 2019) using the KAPA Stranded mRNA-Seq Kit (cat #KK8421, KAPA Biosystems, Wilmington, MA).

value: liver

tag: Sex

tag: diet

value: 2% carbonyl iron (20,000 ppm); fiber source:cellulose


title: Donor 26, 10x ST, Tumor, Stage II, Intestinal, Edge

first: Zemin

last: Zhang

address: No.5 Yiheyuan Road, Haidian District

institute: Peking University

value: Stage II

value: Edge


title: Donor 24, 10x ST, Tumor, Stage II, Intestinal, Edge

value: Donor 24


title: KMC040

description: Library name: KMC040

tag: strain


title: RNA_12m_rep1

description: snRNA-seq


title: Donor 26, 10x ST, Tumor, Stage II, Intestinal, Core


title: 4th  fraction of R series slicing [5W_HD]

description: sample for Transcriptome Tomography

source_name: 5 micron x 200 right oblique slices (1000 micron width) of the brain, Rf04

value: Huntington disease model R6/2

tag: gender

value: right oblique plane


title: Proximal phalange of hindlimb digit 2, embryos at E17, a pool of 10 individuals

city: Shenyang

first: Wanyi

last: Dang

state: Liaoning

address: 120 Dongling Rd, Shenyang, China

institute: Shenyang Agricultural University

description:
SLH5
E17phalange_Raw_counts.txt
E17phalange_TMM_Normalized_counts.txt

data_processing:
Reads from mRNA-seq data were aligned to NCBI mouse genome (GRCm39) using HISAT2 version 2.2.1.
Transcript assembly by StringTie v2.1.7
Use prepDE.py3 script of StringTie to get raw counts and TMM counts
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes TMM values for each Sample

source_name: Proximal phalange of hindlimb digit 2

growth_protocol: Pregnant mice were raised in a clean environment at 22 to 24℃ and 45% to 55% relative humidity, with an adequate supply of food and water and a 12 h light and 12 h dark cycle (7 pm - 7 am).

extract_protocol:
Total RNA was extracted using the RNeasy Mini kit (Qiagen, Hilden, Germany) and  RNeasy Micro kit (Qiagen, Hilden, Germany), with RNase-Free DNase set to remove contaminating genomic DNA. RNA concentration and purity were measured using NanoDrop 2000 (Thermo Fisher Scientific, Wilmington, DE). RNA integrity was assessed using the RNA Nano 6000 Assay Kit from the Agilent Bioanalyzer 2100 system (Agilent Technologies, Santa Clara, CA).
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample, the library preparations were sequenced on an Illumina platform and paired-end reads were generated.

treatment_protocol: Phalanges of digit 1 and 2 from 20 embryos at E16 and 10 embryos at E17 obtained by using a precise mating time from mice were used to extract RNA.

value: Proximal phalange of hindlimb digit 2

tag: developmental stage

value: embryos at E17


title: Donor 24, 10x ST, Tumor, Stage II, Intestinal, In-between

city: Beijing

value: Intestinal


title: Middle phalange of hindlimb digit 2, embryos at E17, a pool of 10 individuals

description:
SLH4
E17phalange_Raw_counts.txt
E17phalange_TMM_Normalized_counts.txt

source_name: Middle phalange of hindlimb digit 2

value: Middle phalange of hindlimb digit 2


title: KMC038

description: Library name: KMC038


title: 1st  fraction of R series slicing [5W_HD]

description: sample for Transcriptome Tomography

source_name: 5 micron x 200 right oblique slices (1000 micron width) of the brain, Rf01

value: brain

tag: age

tag: section


title: YW-M5-rep2

city: Singapore

first: Gokce

last: OGUZ

address: 60 Biopolis St, GENOME, #02-01

department: Bioinformatics Consulting and Training Platform

country: Singapore

institute: Genome Institute of Singapore

description: 10X Genomics

data_processing:
The demultiplexing, barcoded processing and gene counting were made using the Cell Ranger software v4.0.0
Initial quality control was done to keep cells with nGenes between 300 to 7500, nUMI between 500 to 75000 and pMito < 15%.
Multiplets were identified and removed using DoubletFinder V2.0 assuming a 1% doublet formation rate per 1000 cells.
Secondary QC was conducted based on assessing the pairwise distribution of nGenes, nUMI and pMito for each major cell type.
Assembly: mm10
Supplementary files format and content: QC filtered(initial QC, multiplet filtering, and secondary QC) Seurat object with relevant metadata and UMAP coordinates in R object format

source_name: Dorsal full thickness wound

extract_protocol:
On day 3 post-wounding, mice were sacrificed, and wounds were excised by cutting a 2 mm perimeter around the injured area. For  comparison, distal intact back skin was also excised as a representation of normal unwounded skin. Prior to digestion, the fat tissue layer was gently scraped, and tissues were cut into small pieces using a scalpel. Tissues were transferred into C-tubes and agitated at 37° for 90 minutes in complete RPMI media containing 0.25mg/ml Liberase TL (Roche) and 0.1mg/ml DNase 1 (Sigma). Tissues were disintegrated further using the gentleMACS dissociator m_muscle_01 protocol (Miltenyi). The single cell suspension was passed through a 100μm cell strainer and rinsed with PBS containing 3% FBS and 5mM EDTA. Cells were washed two more times with PBS+ 3% FBS and passed through a 40μm cell strainer. To isolate live single cells, 3μm DAPI was added to the suspension and incubated for 10 minutes in the dark. Live single cells were sorted using a BD Influx cell system.
For single-cell RNA experiments, isolated cells were resuspended in 0.04% BSA in PBS at a concentration of 800 to 1000 cells/μl. Single-cell  experiments were performed using Chromium Next GEM Automated Single Cell 3ʹ cDNA Kit v3.1 on the 10X Genomics Chromium Connect platform (10XGenomics). The 10X Chromium Connect is an integrated system that allows for the automated generation of single-cell libraries from cells with minimum user interference. Firstly, the supplied Gel Bead kits, Library kits, Next GEM Chip G kits and the Single index plate required for GEM generation, cDNA amplification and library construction were loaded onto the machine according to the manufacturer’s instructions. Next, 10μl of each sample (targeted recovery of 5000 cells per sample) was added into the supplied 96-well skirted plate (maximum capacity of 8 samples per run) and carefully placed into the machine. Single-cell libraries were then generated using the system’s automated workflow. A total of 23 libraries from young and aged intact skin and wounds were created and sequenced on the NovaSeq 6000 Illumina platform to an average of 100 000 reads per cell.

value: Dorsal full thickness wound

value: Skin/wound resident  cells

value: Young (8-12 weeks)

value: WT

value: Wounded


title: Donor 23, 10x ST, Tumor, Stage II, Intestinal, In-between

value: Gastric cancer tumor

tag: subject id

value: Donor 23

value: In-between


title: Distal phalange of hindlimb digit 2, embryos at E17, a pool of 10 individuals

description:
SLH3
E17phalange_Raw_counts.txt
E17phalange_TMM_Normalized_counts.txt

source_name: Distal phalange of hindlimb digit 2

value: Distal phalange of hindlimb digit 2


title: 3rd  fraction of R series slicing [5W_HD]

description: sample for Transcriptome Tomography

source_name: 5 micron x 200 right oblique slices (1000 micron width) of the brain, Rf03

value: male

value: 5 weeks post-natal age

tag: mouse id


title: YW-M3-rep2

description: 10X Genomics

tag: treatment


title: 5th  fraction of R series slicing [5W_HD]

description: sample for Transcriptome Tomography

source_name: 5 micron x 200 right oblique slices (1000 micron width) of the brain, Rf05

value: Huntington disease model R6/2

value: right oblique plane


title: Proximal phalange of hindlimb digit 1, embryos at E17, a pool of 10 individuals

description:
SLH2
E17phalange_Raw_counts.txt
E17phalange_TMM_Normalized_counts.txt

source_name: Proximal phalange of hindlimb digit 1

value: Proximal phalange of hindlimb digit 1

value: embryos at E17


title: Donor 22, 10x ST, Tumor, Stage I, Diffuse, In-between

value: Donor 22

value: Stage I

value: Diffuse

tag: sampling location


title: 7th  fraction of L series slicing [5W_HD]

description: sample for Transcriptome Tomography

source_name: 5 micron x 200 left oblique slices (1000 micron width) of the brain, Lf07

value: brain

value: left oblique plane


title: YW-M3-rep1

description: 10X Genomics

value: Dorsal full thickness wound

tag: cell type

value: Skin/wound resident  cells

value: Young (8-12 weeks)

tag: genotype

value: WT


title: 2nd  fraction of R series slicing [5W_HD]

description: sample for Transcriptome Tomography

source_name: 5 micron x 200 right oblique slices (1000 micron width) of the brain, Rf02

tag: tissue


title: Distal phalange of hindlimb digit 1, embryos at E17, a pool of 10 individuals

description:
SLH1
E17phalange_Raw_counts.txt
E17phalange_TMM_Normalized_counts.txt

source_name: Distal phalange of hindlimb digit 1

value: Distal phalange of hindlimb digit 1


title: YW-M1-rep2

description: 10X Genomics

value: Wounded


title: 6th  fraction of L series slicing [5W_HD]

description: sample for Transcriptome Tomography

source_name: 5 micron x 200 left oblique slices (1000 micron width) of the brain, Lf06

value: male


title: YW-M5-rep1

description: 10X Genomics


title: Proximal phalange of forelimb digit 2, embryos at E17, a pool of 10 individuals

description:
SLF5
E17phalange_Raw_counts.txt
E17phalange_TMM_Normalized_counts.txt

source_name: Proximal phalange of forelimb digit 2

value: Proximal phalange of forelimb digit 2


title: 5th  fraction of L series slicing [5W_HD]

description: sample for Transcriptome Tomography

source_name: 5 micron x 200 left oblique slices (1000 micron width) of the brain, Lf05

value: Huntington disease model R6/2

value: 5 weeks post-natal age


title: Donor 21, 10x ST, Tumor, Stage III, Indeterminate, Edge

source_name: Gastric cancer tumor

value: Gastric cancer tumor

value: Donor 21

value: Stage III

value: Indeterminate

value: Edge


title: YW-M1-rep1

description: 10X Genomics


title: 4th  fraction of L series slicing [5W_HD]

description: sample for Transcriptome Tomography

source_name: 5 micron x 200 left oblique slices (1000 micron width) of the brain, Lf04

value: brain


title: Donor 21, 10x ST, Tumor, Stage III, Indeterminate, In-between

value: In-between


title: Middle phalange of forelimb digit 2, embryos at E17, a pool of 10 individuals

description:
SLF4
E17phalange_Raw_counts.txt
E17phalange_TMM_Normalized_counts.txt

source_name: Middle phalange of forelimb digit 2

value: Middle phalange of forelimb digit 2

value: embryos at E17


title: YI-M3

description: 10X Genomics

source_name: Dorsal skin

value: Dorsal skin

value: Skin resident  cells

value: Young (8-12 weeks)

value: Intact


title: Proximal phalange of forelimb digit 1, embryos at E17, a pool of 10 individuals

description:
SLF2
E17phalange_Raw_counts.txt
E17phalange_TMM_Normalized_counts.txt

source_name: Proximal phalange of forelimb digit 1

value: Proximal phalange of forelimb digit 1


title: YI-M5

description: 10X Genomics

value: WT


title: Distal phalange of forelimb digit 1, embryos at E17, a pool of 10 individuals

description:
SLF1
E17phalange_Raw_counts.txt
E17phalange_TMM_Normalized_counts.txt

source_name: Distal phalange of forelimb digit 1

value: Distal phalange of forelimb digit 1


title: Distal phalange of forelimb digit 2, embryos at E17, a pool of 10 individuals

description:
SLF3
E17phalange_Raw_counts.txt
E17phalange_TMM_Normalized_counts.txt

source_name: Distal phalange of forelimb digit 2

value: Distal phalange of forelimb digit 2


title: YI-M1

description: 10X Genomics


title: Donor 20, 10x ST, Tumor, Stage III, Diffuse, Core

value: Gastric cancer tumor

value: Donor 20

value: Diffuse

value: Core


title: 1st  fraction of L series slicing [5W_HD]

description: sample for Transcriptome Tomography

source_name: 5 micron x 200 left oblique slices (1000 micron width) of the brain, Lf01

value: Huntington disease model R6/2

value: male

value: 5 weeks post-natal age

value: left oblique plane


title: 2nd  fraction of L series slicing [5W_HD]

description: sample for Transcriptome Tomography

source_name: 5 micron x 200 left oblique slices (1000 micron width) of the brain, Lf02

value: brain


title: Proximal phalange of hindlimb digit 2, embryos at E16, a pool of 20 individuals

description:
SEH5
E16phalange_Raw_counts.txt
E16phalange_TMM_Normalized_counts.txt

source_name: Proximal phalange of hindlimb digit 2

value: Proximal phalange of hindlimb digit 2

value: embryos at E16


title: YI-P1

description: 10X Genomics

value: Dorsal skin

value: Skin resident  cells

value: Young (8-12 weeks)


title: Donor 20, 10x ST, Tumor, Stage III, Diffuse, In-between

value: Stage III

value: In-between


title: Donor 16, 10x ST, Tumor, Stage III, Diffuse, Core

value: Donor 16


title: 5th  fraction of H series slicing [5W_HD]

description: sample for Transcriptome Tomography

source_name: 5 micron x 200 holizontal slices (1000 micron width) of the brain, Hf05

value: horizontal plane


title: 3rd  fraction of L series slicing [5W_HD]

description: sample for Transcriptome Tomography

source_name: 5 micron x 200 left oblique slices (1000 micron width) of the brain, Lf03


title: Donor 15, 10x ST, Tumor, Stage III, Indeterminate, In-between

value: Gastric cancer tumor

value: Donor 15

value: Indeterminate


title: Proximal phalange of hindlimb digit 1, embryos at E16, a pool of 20 individuals

description:
SEH2
E16phalange_Raw_counts.txt
E16phalange_TMM_Normalized_counts.txt

source_name: Proximal phalange of hindlimb digit 1

value: Proximal phalange of hindlimb digit 1


title: Donor 15, 10x ST, Tumor, Stage III, Indeterminate, Edge

value: Edge


title: AW-M6-rep2

description: 10X Genomics

source_name: Dorsal full thickness wound

value: Dorsal full thickness wound

value: Skin/wound resident  cells

value: Aged (22-24 months)

value: WT

value: Wounded


title: Donor 18, 10x ST, Tumor, Stage III, Diffuse, In-between

value: Donor 18

value: Diffuse


title: AW-M4-rep2

description: 10X Genomics


title: Donor 16, 10x ST, Tumor, Stage III, Diffuse, In-between


title: Middle phalange of hindlimb digit 2, embryos at E16, a pool of 20 individuals

description:
SEH4
E16phalange_Raw_counts.txt
E16phalange_TMM_Normalized_counts.txt

source_name: Middle phalange of hindlimb digit 2

value: Middle phalange of hindlimb digit 2

value: embryos at E16


title: 4th  fraction of H series slicing [5W_HD]

description: sample for Transcriptome Tomography

source_name: 5 micron x 200 holizontal slices (1000 micron width) of the brain, Hf04

value: Huntington disease model R6/2

value: brain

value: male

value: 5 weeks post-natal age


title: AW-M2-rep1

description: 10X Genomics


title: 1st  fraction of H series slicing [5W_HD]

description: sample for Transcriptome Tomography

source_name: 5 micron x 200 holizontal slices (1000 micron width) of the brain, Hf01

value: horizontal plane


title: Distal phalange of hindlimb digit 2, embryos at E16, a pool of 20 individuals

description:
SEH3
E16phalange_Raw_counts.txt
E16phalange_TMM_Normalized_counts.txt

source_name: Distal phalange of hindlimb digit 2

value: Distal phalange of hindlimb digit 2


title: Donor 12, 10x ST, Tumor, Stage II, Diffuse, Core

source_name: Gastric cancer tumor

value: Gastric cancer tumor

value: Donor 12

value: Stage II

value: Core


title: Proximal phalange of forelimb digit 2, embryos at E16, a pool of 20 individuals

description:
SEF5
E16phalange_Raw_counts.txt
E16phalange_TMM_Normalized_counts.txt

source_name: Proximal phalange of forelimb digit 2

value: Proximal phalange of forelimb digit 2


title: YW-P1

description: 10X Genomics

source_name: Dorsal skin

value: Dorsal skin

value: Skin resident  cells

value: Young (8-12 weeks)

value: WT

value: Intact


title: 6th  fraction of H series slicing [5W_HD]

description: sample for Transcriptome Tomography

source_name: 5 micron x 200 holizontal slices (1000 micron width) of the brain, Hf06


title: 3rd  fraction of H series slicing [5W_HD]

description: sample for Transcriptome Tomography

source_name: 5 micron x 200 holizontal slices (1000 micron width) of the brain, Hf03


title: AW-M6-rep1

description: 10X Genomics

value: Dorsal full thickness wound

value: Skin/wound resident  cells

value: Aged (22-24 months)

value: Wounded


title: Donor 12, 10x ST, Tumor, Stage II, Diffuse, In-between

value: Diffuse

value: In-between


title: AW-M2-rep2

description: 10X Genomics


title: Middle phalange of forelimb digit 2, embryos at E16, a pool of 20 individuals

description:
SEF4
E16phalange_Raw_counts.txt
E16phalange_TMM_Normalized_counts.txt

source_name: Middle phalange of forelimb digit 2

value: Middle phalange of forelimb digit 2

value: embryos at E16


title: 12th  fraction of C series slicing [5W_HD]

description: sample for Transcriptome Tomography

source_name: 5 micron x 200 coronal slices (1000 micron width) of the brain, Cf12

value: Huntington disease model R6/2

value: brain

value: male

value: 5 weeks post-natal age

value: coronal plane


title: 2nd  fraction of H series slicing [5W_HD]

description: sample for Transcriptome Tomography

source_name: 5 micron x 200 holizontal slices (1000 micron width) of the brain, Hf02

value: horizontal plane


title: Donor 11, 10x ST, Tumor, Stage III, Indeterminate, Core

description: Fresh frozen Spatial Transcriptome sequencing

value: Gastric cancer tumor

value: Donor 11

value: Stage III

value: Indeterminate

value: Core


title: AW-M4-rep1

description: 10X Genomics

value: Dorsal full thickness wound

value: Skin/wound resident  cells

value: Aged (22-24 months)

value: WT


title: 11th  fraction of C series slicing [5W_HD]

description: sample for Transcriptome Tomography

source_name: 5 micron x 200 coronal slices (1000 micron width) of the brain, Cf11


title: AI-M2-rep2

description: 10X Genomics

value: Dorsal skin

value: Skin resident  cells

value: Intact


title: Donor 10, 10x ST, Tumor, Stage III, Intestinal, In-between

value: Donor 10

value: Intestinal

value: In-between


title: Distal phalange of forelimb digit 2, embryos at E16, a pool of 20 individuals

description:
SEF3
E16phalange_Raw_counts.txt
E16phalange_TMM_Normalized_counts.txt

source_name: Distal phalange of forelimb digit 2

value: Distal phalange of forelimb digit 2

value: embryos at E16


title: Distal phalange of hindlimb digit 1, embryos at E16, a pool of 20 individuals

description:
SEH1
E16phalange_Raw_counts.txt
E16phalange_TMM_Normalized_counts.txt

source_name: Distal phalange of hindlimb digit 1

value: Distal phalange of hindlimb digit 1


title: Proximal phalange of forelimb digit 1, embryos at E16, a pool of 20 individuals

description:
SEF2
E16phalange_Raw_counts.txt
E16phalange_TMM_Normalized_counts.txt

source_name: Proximal phalange of forelimb digit 1

value: Proximal phalange of forelimb digit 1


title: Donor 09, 10x ST, Tumor, Stage III, Indeterminate, Edge

value: Gastric cancer tumor

value: Donor 09

value: Stage III

value: Edge


title: AI-M6-rep2

description: 10X Genomics


title: Donor 09, 10x ST, Tumor, Stage III, Indeterminate, In-between

value: Indeterminate


title: 9th  fraction of C series slicing [5W_HD]

description: sample for Transcriptome Tomography

source_name: 5 micron x 200 coronal slices (1000 micron width) of the brain, Cf09

value: Huntington disease model R6/2

value: brain

value: male

value: 5 weeks post-natal age

value: coronal plane