title: C4_A_FULL...14

description:
Library name: b5ab3928-a72b-451d-acff-eac61b5cf181
A, FULL segment from donor C4


title: C3_M_FULL...13

status: Public on Oct 20 2025

type: SRA

city: GLASGOW

first: Cecilia

last: Ansalone

address: Sir Graeme Davies Building - 120 University Place Glasgow

department: School of Infection & Immunity

country: United Kingdom

institute: University of Glasgow

description:
Library name: 1d38b055-08ea-4f8f-aa5a-a0c45524666f
M, FULL segment from donor C3

library_source: transcriptomic

data_processing:
Sequencing was performed externally, and raw FASTQ files were processed using the NanoString GeoMx NGS Pipeline: – Batch 1: version 2.3.4 – Batch 2: version 2.3.3.10  These pipelines converted FASTQ reads into digital count conversion (DCC) files per segment (ROI), which were imported into GeoMx DSP Analysis Suite (v3.1.0.222). An Initial Dataset was generated with default settings — no background correction, probe QC filtering, or Q3 normalisation was applied.  The Initial Dataset included multiple samples processed in parallel. To isolate only the segments relevant to this study, the exported Excel file was manually filtered to exclude unrelated samples. The resulting curated dataset was saved as a raw  count matrix in CSV format (Raw_Batch1-2_ExpressionMatrix.csv), retaining unnormalised digital counts per gene per segment.  Segment-level annotations were similarly filtered and exported to produce the final SegmentProperties metadata files (Batch1_SegmentProperties.csv, Batch2_SegmentProperties.csv), containing ROI-specific identifiers, region types, tissue compartment annotations, and processing metadata (e.g., nuclei count, detection QC metrics).  Raw digital counts were exported from the DSP Analysis Suite, and technical replicates within the same sample were merged. Quality control (QC) was performed using technical metrics from the GeoMx run. Each ROI was assessed for raw read count, aligned reads, sequencing saturation, nuclei counts, and surface area. ROIs with <50,000 or >1,000,000 raw transcript counts and/or <70% alignment rate were flagged as outliers and excluded from downstream analysis.  Normalised expression matrices were generated in R (v4.2.2) using the DESeq2 package (v1.38.3) to correct for library size and sequencing depth. CD45+ and FULL segments were normalised independently.
Assembly: GeoMx WTA is a probe-based assay targeting 18,000+ genes; no genome alignment is performed.
Supplementary files format and content: Processed data are provided as comma-separated values (.csv) files. – Files processed_CD45_A_em.csv and processed_FULL_areas_em.csv contain DESeq2-normalised expression matrices for CD45+ immune segments and full tissue segments, respectively. – Companion files processed_CD45_A_ss.csv and processed_FULL_areas_ss.csv contain corresponding segment-level statistics (e.g. nuclei counts, detection QC). All expression matrices contain gene symbols as row names and segment identifiers as columns. Segment annotations and sample-level metadata are provided in the accompanying SegmentProperties and clinical data.xlsx files.
Library strategy: Spatial Transcriptomics

molecule: total RNA

organism: Homo sapiens

source_name: temporal artery

extract_protocol:
Tissue sections were processed using the NanoString GeoMx DSP protocol: 5 µm FFPE sections were mounted on slides, deparaffinised, underwent antigen retrieval and proteinase K digestion, followed by overnight hybridisation with the Human Whole Transcriptome Atlas probes. ROIs were selected unsegmented (Full ROI) and segmented based on immunofluorescence (CD45+) and oligonucleotide tags were released by UV photocleavage.
Photocleaved oligonucleotides from each segment were collected into individual wells and underwent PCR amplification with unique i5/i7 dual indices using the GeoMx NGS Library Prep Kit. Indexed libraries were purified using AMPure beads, quantified, and pooled for paired-end sequencing.

tag: tissue

value: temporal artery

tag: batch


title: BRAF Tum, R4

city: Glasgow

first: Patricia

last: Centeno

state: Scotland

address: Switchback Rd, Bearsden, Glasgow

institute: Beatson Institute for Cancer Research

description: Library name: control_rep4

data_processing:
Raw sequence quality control was performed using FastQC (v0.11.8) before and after removing adapters and low-quality base calls (Phred score <20) using TrimGalore with default options (v0.6.6).
Trimmed reads were aligned to GRCm38, release 100 (mouse samples) using Hisat2 (v2.1.0).
RNA-Seq
Gene counts were subsequently estimated using featurecounts (subread/1.6.3).
Assembly: mm10/100
Supplementary files format and content: csv  file includes raw counts for each sample

organism: Mus musculus

source_name: Skin tumour cSCC

growth_protocol: BRAFV600E and SOX2 were induced in IVL+ skin cell specific populations in mice from 7-10 weeks old following tamoxifen inducible CreRT2 recombination.

extract_protocol:
RNA was extracted from fresh frozen tumour samplesusing AllPrep DNA/RNA kit (74104, Qiagen) according to the manufacturer’s instructions.
rRNA-depleted libraries were prepared using 200 ng of total RNA. Total RNA libraries were sequenced using Illumina NovaSeq 6000 XP SP, 200 cycles, paired-end reads (2 x 150 bp) 30 million reads. RNA preparation and sequencing were performed by GENEWIZ Azenta.

treatment_protocol: BRAFV600E and SOX2 overexpression were induced in IVL+ skin population via topical tamoxifen inductions. Tumours were grown until clinical endpoint and frozen in RNA later until extraction.

value: Skin tumour cSCC

tag: cell line

value: Male

tag: cell type

value: squamous cell carcinoma

tag: genotype


title: 697-SCM-CL2-EM-B07

city: Sdyney

first: Yanran

last: Zhao

address: Sydney NSW 2033

country: Australia

institute: UNSW

library_source: transcriptomic single cell

data_processing:
Illumina NextSeq500 was used
Sequenced paired-end reads were trimmed using Trimmomatic (v0.39) (using parameters:  LEADING = 3, TRAILING = 3, SLIDINGWINDOW = 4:10, MINLEN = 50), then aligned to the human reference genome (GRCh38) using STAR (v2.7.3a). Gene expression was then quantified at the counts and TPM level with RSEM (v1.3.1)
Assembly: GRCh38
Supplementary files format and content: .mtx.gz files contain matrices including raw counts, TPM and scaled TPM values for each sample and each gene.
Supplementary files format and content: .txt and and .tsv files contain tab delimited information on sample names and gene names (as per ordering in matrices), and gene annotation information.

source_name: CD8 T

extract_protocol:
Single CMV-specific CD8+ T cells were sorted using flow cytometry, with RNA isolation and sequencing library construction performed according to the Smart-seq2 protocol.
Single cell RNA libraries were prepared for sequencing using standard Illumina protocols

tag: subject

tag: gen1 phenotype

value: SCM

tag: gen2 phenotype

value: EM

tag: clone

tag: epitope

value: NLV

value: CD8 T


title: NR5_A_FULL...18

description:
Library name: 533f45ad-4794-4643-b0d8-5aca800fa748
A, FULL segment from donor NR5


title: 697-SCM-CL2-EFF-C03

value: EFF


title: hIPSC_A_S5D3_1

city: Beijing

first: Cheng-ran

last: Xu

address: NO.5 YIHEYUAN ROAD HAIDIAN DISTRICT, BEIJING, P.R.CHINA

department: School of Basic Medical Sciences

country: China

institute: Peking University

description:
cellname.smartseq3.tsv
genename.smartseq3.tsv
readcount.smartseq3.mtx

data_processing:
We processed Smart-seq3 scRNA-seq data beginning with the removal of index, primer, and adaptor sequences from the paired-end reads, utilizing Trimmomatic software (version 0.39). Post-trimming, the forward reads (Read 1) were aligned to the Homo sapiens reference genome (hg38) employing HISAT2 (version 2.1.0). The aligned reads were then annotated to gene features using the featureCounts tool (version 2.0.0), taking into account both 5' and internal fragments.  For 10x Genomics scRNA-seq data, initial processing was performed with the Cell Ranger software (version 3.0.1) using default parameters and the GRCh38 reference genome (version 3.0.0).The initial processing of raw snATAC-seq data was conducted using the cellranger-atac software, version 1.2.0, employing the standard parameters and referencing the refdata-cellranger-atac-GRCh38-1.2.0 genome assembly.
Assembly: hg38
Supplementary files format and content: sparse matrix: read count
Supplementary files format and content: fragments.tsv

molecule: polyA RNA

source_name: hIPSC

growth_protocol: hESC and hiPSC lines were maintained cultured on surfaces coated with Matrigel (Corning, Cat#354230) and cultured in mTeSR1 media (Stem Cell Technologies, Cat#85850) at 37°C. The cells were passaged using Versene solution (ThermoFisher Scientific, Cat#15040066), and routine screenings for Mycoplasma contamination were performed employing the MycoBlue Mycoplasma Detector Kit (Vazyme, Cat#D101).     For differentiation experiments, hESCs and hiPSCs were dissociated to single-cell suspensions using TrypLE™ Express Enzyme (ThermoFisher Scientific, Cat#12605) and plated at a density of 0.53 x 106 cells/cm2 on surface coated with Matrigel diluted 1:30 (Corning, Cat#356231) in mTeSR1 media. This medium was supplemented with 10 μM Y-27632 (Selleckchem, Cat#S1049) to enhance cell survival. Differentiation was initiated within 24 hours post-seeding. Prior to introducing differentiation media, cells were washed with 1× DPBS without Mg2+ and Ca2+ (Meilunbio, Cat#MA0015). The cells were cultured at 37 °C with 5% (vol/vol) CO2.     The differentiation of stem cells into pancreatic lineages was conducted following modified versions of the protocols established by Rezania et al. and Hogrebe et al., herein referred to as protocols A and B, respectively. Additionally, a novel differentiation protocol developed within this study is referred to as protocol C.

extract_protocol:
SC-derived cells or islets were dissociated into single cells with 0.25% trypsin at 37 °C for 3-5 min, and the digestion was halted by adding 0.4 volumes of FBS. Partially dissociated SC-islets underwent a secondary trypsinization at 37°C for 3 minutes to ensure complete dissociation. Cells from both dissociation steps were pooled for further analysis. Retrieved grafts from the renal capsule were finely minced and enzymatically dissociated using 0.25% trypsin at 37°C for 5 minutes. The enzymatic reaction was halted by adding 0.4 volumes of FBS.
ScRNA-seq via the Smart-seq3 method was carried out in accordance with established procedures. Briefly, individual cells were sorted into 384-well plates containing lysis buffer (0.3 μL per well). The reverse transcription of mRNA was facilitated using a 0.1 μL aliquot of reverse transcription mix, followed by pre-amplification employing a 0.6 μL aliquot of PCR mix. A diluted sample of the resulting cDNA from each cell was analyzed using quantitative PCR (qPCR) employing ChamQ™ SYBR® qPCR Master Mix (Vazyme, Q321-02) and primers targeting ACTB: forward 5’-ACAGAGCCTCGCCTTTGCC-3’ and reverse 5’-GATATCATCATCCATGGTGAGCTGG-3’. Cells exhibiting cycle threshold (Ct) values under 21 for ACTB were selected for library preparation. To differentiate human cells within grafts, GAPDH expression was quantified using specific primers: forward 5’-CTCTGCTCCTCCTGTTCGAC-3’ and reverse 5’-GCGCCCAATACGACCAAATC-3’, considering cells as human if Ct values were below 25 and melting temperatures surpassed 85°C. Library construction was performed utilizing the TruePrep DNA Library Prep Kit (Vazyme, Cat#TD501), and sequencing was conducted on the MGIseq-2000 platform, generating 100 bp paired-end reads.     For 10x Genomics scRNA-seq, cells purified through FACS were processed on a Chromium controller. This step was followed by cDNA synthesis and library preparation in line with the protocols provided with the Single Cell 3′ Reagent Kit v3.1. The prepared libraries were then sequenced using the Illumina HiSeq 4000 system, yielding 150 bp paired-end reads.Cell suspensions were initially stained with DAPI to facilitate the sorting of live single cells utilizing the FACSAria™ Fusion flow cytometer. Subsequent to sorting, nuclei were isolated in accordance with the protocols detailed in the Chromium NEXT GEM Single Cell ATAC Reagent Kits v2 (10x Genomics). The prepared libraries were then subjected to sequencing on the NovaSeq 6000 platform, achieving 50 bp paired-end reads.     In the context of protocol A, one set of samples consisted of a composite of cells from stages S2D2, S4D3, S5D3, and S6D3, combined in a ratio of 1:2:2:3. An alternative set comprised cells from stages S3D2, S4D3, and S5D3, merged in a ratio of 1:2:3. Within the framework of protocol C, one sample amalgamated cells from stages S2D2, S3D3, S4D3, and S5D3, in a ratio of 1:2:2:3, whereas another ensemble included cells from stages S2D4, S3D3, and S4D3, in a ratio of 1:2:3.

value: hIPSC

tag: Stage

tag: treatment

value: A


title: C3_M_FULL...12

description:
Library name: c1013bb3-5297-438d-908d-774dab4bc1dc
M, FULL segment from donor C3


title: 697-SCM-CL2-EFF-C02


title: 697-SCM-CL2-EFF-B09


title: BRAF Tum, R2

description: Library name: control_rep2

value: Female


title: BRAF Tum, R3

description: Library name: control_rep3


title: hIPSC_A_S6D7_1


title: hIPSC_A_S5D1_1


title: hIPSC_A_S4D3_2


title: SR4_M_FULL

description:
Library name: 034b45c9-195d-4508-baa2-68437b82cfd1
M, FULL segment from donor SR4


title: C4_A_FULL...15

description:
Library name: b81fd536-87ec-4fca-b4f6-5c2ecf8e55e3
A, FULL segment from donor C4


title: hIPSC_A_S4D3_1


title: BRAF Tum, R1

description: Library name: control_rep1


title: 697-SCM-CL2-EFF-D09


title: SR4_A_CD45...10

description:
Library name: 49ee4337-c04f-4c8c-be44-29026a5267d7
A, CD45 segment from donor SR4


title: 697-SCM-CL2-EFF-A11


title: 697-SCM-CL2-EFF-C08


title: hIPSC_A_S3D2_2


title: SR4_I_FULL

description:
Library name: a0ef32a7-cb6f-4d47-a31e-a2c4da21f549
I, FULL segment from donor SR4


title: Skeletal muscle, Male, IGF-1R Het, rep 7

city: Boston

first: Alexander

last: Tyshkovskiy

state: Massachusetts

address: 77 Avenue Louis Pasteur

country: USA

institute: Brigham & Women's Hospital, Harvard Medical School

description:
Library name: G_687
Muscle_Male_IGF1R.Het_7

data_processing:
Reads were mapped to mouse genome (GRCm39) with STAR (version 2.7.11b). Genes were counted via featureCounts (version 2.0.6).
Assembly: GRCm39
Supplementary files format and content: comma-separated values file includes gene counts for each sample

source_name: Skeletal muscle

extract_protocol:
RNA was extracted with PureLink RNA Mini Kit.
mRNA library preparation with polyA enrichment was performed by Novogene.

treatment_protocol: C57Bl/6J mice were purchased from Jackson Laboratory and housed with ad libitum diet and drinking water in a barrier facility (biosafety level 2) on 12-hour light-dark cycles. Three- to four-week-old wild-type C57Bl/6J females were superovulated with pregnant mare serum gonadotropin and human chorionic gonadotropin, followed by mating with wild-type stud males. At about 43.5 hours post-HCG administration, two-cell embryos were harvested from successfully mated females and cultured in KSOMAA medium before microinjection. The targeted mutation in mouse embryos was generated by cytoplasmic microinjection of both blastomeres with the mixed CRISPRCas9 reagents. After microinjection, twenty-five to thirty embryos per recipient were transferred into CD1 pseudo-pregnant females. The mice born from the microinjected embryos were genotyped to identify the targeted mutation. The mice carrying the targeted mutation (founder mice, F0) were saved for germline transmission. Natural mating or in vitro fertilization (male founder mice only) of the founders with wild-type mice was performed to produce the F1 generation of mice. The heterozygous mice with the germline-transmitted targeted mutation were identified by genotyping. A heterozygous mouse was further backcrossed to wild-type C57Bl/6J mice to establish its colony. To minimize the risk of off-target effects caused by CRISPR-Cas9, founder mice for knock-in mutation were backcrossed with C57BL/6J wildtype (WT) mice for two generations and selected for the presence of IGF-1R R1096C allele to generate N2 mice, which were later intercrossed to generate N2F1 mice, used for RNA-sequencing.

value: Skeletal muscle

tag: strain

tag: Sex

tag: age

value: 4 months

value: IGF-1R Het

tag: replicate


title: Skeletal muscle, Male, IGF-1R Het, rep 6

description:
Library name: G_686
Muscle_Male_IGF1R.Het_6


title: 697-SCM-CL2-EFF-A10


title: SR4_A_FULL

description:
Library name: 0896211b-9980-434f-b2e6-10fe050f6f0b
A, FULL segment from donor SR4


title: 697-SCM-CL2-EFF-A08


title: SR4_A_CD45...7

description:
Library name: b958b56c-4750-49a1-9416-d843ac4bd3ee
A, CD45 segment from donor SR4


title: hIPSC_A_S2D2_2


title: Skeletal muscle, Male, IGF-1R Het, rep 5

description:
Library name: G_679
Muscle_Male_IGF1R.Het_5


title: 697-SCM-CL2-EFF-A07


title: hIPSC_A_S3D2_1


title: hIPSC_A_S2D2_1


title: SR3_M_FULL

description:
Library name: ea6cff4f-4984-4479-9d8c-2c1d94519e85
M, FULL segment from donor SR3


title: 697-SCM-CL2-EFF-A06


title: hIPSC_A_S1D2_1


title: 697-SCM-CL2-EFF-B06


title: SR3_I_FULL

description:
Library name: 26d505a6-5616-4d7e-9379-b6a7b9ea2711
I, FULL segment from donor SR3


title: 697-SCM-CL2-EFF-A02


title: Skeletal muscle, Male, IGF-1R Het, rep 2

description:
Library name: G_632
Muscle_Male_IGF1R.Het_2


title: SR3_A_FULL

description:
Library name: 89616975-6a65-44c7-b8d8-b28370d24347
A, FULL segment from donor SR3


title: H1_S26d_S3D3_2


title: Skeletal muscle, Male, IGF-1R Het, rep 1

description:
Library name: G_631
Muscle_Male_IGF1R.Het_1


title: SR3_A_CD45

description:
Library name: 54de779d-3659-4535-a926-763e2a175ca5
A, CD45 segment from donor SR3


title: 697-SCM-CL2-CCR7-F11


title: 697-SCM-CL2-CCR7-F02


title: H1_S26d_S3D3_1

description:
cellname.smartseq3.tsv
genename.smartseq3.tsv
readcount.smartseq3.mtx


title: Skeletal muscle, Female, IGF-1R Het, rep 5

description:
Library name: G_677
Muscle_Female_IGF1R.Het_5


title: H1_S26d_S2D6_2


title: 697-SCM-CL2-CCR7-E08


title: Skeletal muscle, Female, IGF-1R Het, rep 4

description:
Library name: G_674
Muscle_Female_IGF1R.Het_4


title: T12.4  StnI100nM 12h replicate 4

city: madrid

first: gonzalo

last: colmenarejo

address: carretera cantoblanco s/n

country: Spain

institute: imdea food

description: Library name: Unknown_AP191-01T0016

data_processing:
In next generation sequencing, e.g. Illumina NovaSeq 6000, etc., bases are inferred from light intensity signals generated by Illumina sequencing platform, which is known as base calling. Data generated directly from base calling is referred to as Raw data or Raw reads. Raw data was normally provided in FASTQ(fq) format, containing sequences and corresponding quality information. A demo FASTQ file is shown as below.Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. First strand cDNA was synthesized, and second strand cDNA synthesis was subsequently performed. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to ensure the quality of library, Qubit 2.0 and Agilent 2100 were used to examine the concentration of cDNA and insert size. Q-PCR was processed to obtain a more accurate library concentration and assure adequate library concentration.
The library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.Qualified libraries were uploaded on Illumina NovaSeq 6000 platform for sequencing with read length of PE150
Assembly: The libraries were sequenced on an Illumina NovaSeq platform to generate 150 bp paired-end reads, according to the manufacturer’s instructions
Supplementary files format and content: tab-delimited text files

source_name: Metastatic; Not specified

growth_protocol: DMEM 10% FBS, 1% penicillin-streptomycin and 1% non-essential aminoacids

extract_protocol:
The cells were then collected, washed with PBS, and RNA extraction was performed within 2h post lysis using Qiagen RNeasy kit (QIAGEN, Venlo, The Netherlands) according to manufacturer’s directions. RNA integrity was checked in 2% agarose gels. RNA purity and concentration were assessed using NanoDrop 2000 (Thermo Fisher Scientific, Waltham, MA USA). The RNA samples were sent for sequencing to Biomarker Technologies (BMKGENE, Beijing, China)
Library preparation for Transcriptome sequencing. A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using Hieff NGS Ultima Dual-mode mRNA Library Prep Kit for Illumina (Yeasen Biotechnology, Shanghai) Co., Ltd.) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: Cellular senescence was induced by incubation with 5 microM palbociclib in 75 cm2 flask. Senescent SKMel103 cells (570x10e3 cell/well) were treated with StnI 100nM following a time course at 0, 3, 6 and 12 h

value: Metastatic; Not specified

value: melanoma Q61R NRAS

value: Q61R NRAS

tag: time point


title: H1_S25d_S3D3_2


title: Skeletal muscle, Male, IGF-1R Het, rep 4

description:
Library name: G_671
Muscle_Male_IGF1R.Het_4

tag: tissue


title: 697-SCM-CL2-CCR7-E04


title: T12.2  StnI100nM 12h replicate 2

description: Library name: Unknown_AP191-01T0014

tag: batch


title: Skeletal muscle, Female, IGF-1R Het, rep 3

description:
Library name: G_668
Muscle_Female_IGF1R.Het_3


title: H1_S25d_S3D3_1

tag: cell line


title: Skeletal muscle, Male, IGF-1R Het, rep 3

description:
Library name: G_633
Muscle_Male_IGF1R.Het_3


title: Skeletal muscle, Female, IGF-1R Het, rep 2

description:
Library name: G_663
Muscle_Female_IGF1R.Het_2


title: H1_S25d_S2D5_2


title: 697-SCM-CL2-CCR7-D07

tag: cell type


title: T12.1 StnI100nM 12h replicate 1

description: Library name: Unknown_AP191-01T0013

tag: genotype


title: 697-SCM-CL2-CCR7-D02

tag: subject


title: T6.4 StnI100nM 6h replicate 4

description: Library name: Unknown_AP191-01T0012


title: H1_S24d_S3D3_2


title: H1_S24d_S3D3_1


title: 697-SCM-CL2-CCR7-C09

tag: gen1 phenotype


title: T6.3 StnI100nM 6h replicate 3

description: Library name: Unknown_AP191-01T0011


title: Skeletal muscle, Male, WT, rep 6

description:
Library name: G_684
Muscle_Male_WT_6

value: WT


title: 697-SCM-CL2-CCR7-B11

tag: gen2 phenotype


title: T6.2 StnI100nM 6h replicate 2

description: Library name: Unknown_AP191-01T0010


title: Skeletal muscle, Male, WT, rep 5

description:
Library name: G_678
Muscle_Male_WT_5

value: Male


title: H1_S24d_S2D4_2


title: 697-SCM-CL2-CCR7-B12

tag: clone


title: T6.1 StnI100nM 6h replicate 1

description: Library name: Unknown_AP191-01T0009


title: H1_S23d_S3D3_2


title: 697-SCM-CL2-CCR7-B05

tag: epitope


title: T12.3  StnI100nM 12h replicate 3

description: Library name: Unknown_AP191-01T0015


title: Skeletal muscle, Male, WT, rep 4

description:
Library name: G_673
Muscle_Male_WT_4


title: H1_S23d_S3D3_1

tag: Stage


title: Skeletal muscle, Male, WT, rep 3

description:
Library name: G_672
Muscle_Male_WT_3


title: 697-SCM-CL2-CCR7-A09


title: H1_S23d_S2D3_2

tag: treatment


title: T3.3 StnI100nM 3h replicate 3

description: Library name: Unknown_AP191-01T0007


title: Skeletal muscle, Female, IGF-1R Het, rep 1

description:
Library name: G_662
Muscle_Female_IGF1R.Het_1

tag: strain


title: T3.2 StnI100nM 3h replicate 2

description: Library name: Unknown_AP191-01T0006


title: 697-SCM-CL1-EM-CM-H11


title: 697-SCM-CL1-EM-CM-H09


title: Skeletal muscle, Male, WT, rep 7

description:
Library name: G_685
Muscle_Male_WT_7

tag: Sex


title: H1_S22d_S4D3_2


title: Skeletal muscle, Male, WT, rep 1

description:
Library name: G_664
Muscle_Male_WT_1

tag: age


title: H1_S22d_S3D2_2


title: T3.1 StnI100nM 3h replicate 1

description: Library name: Unknown_AP191-01T0005

tag: replicate


title: Skeletal muscle, Female, WT, rep 6

description:
Library name: G_751
Muscle_Female_WT_6


title: 697-SCM-CL1-EM-CM-H07


title: H1_S22d_S2D2_1


title: V4 Vehicle replicate 4

description: Library name: Unknown_AP191-01T0004

value: Vehicle


title: V3 Vehicle replicate 3

description: Library name: Unknown_AP191-01T0003


title: T3.4 StnI100nM 3h replicate 4

description: Library name: Unknown_AP191-01T0008

tag: time point


title: 697-SCM-CL1-EM-CM-H06

value: SCM


title: Skeletal muscle, Female, WT, rep 4

description:
Library name: G_728
Muscle_Female_WT_4

tag: tissue


title: Skeletal muscle, Female, WT, rep 5

description:
Library name: G_750
Muscle_Female_WT_5


title: V2 Vehicle replicate 2

description: Library name: Unknown_AP191-01T0002

tag: batch


title: H1_D_S6D7_3

tag: cell line

value: D


title: H1_D_S6D7_4


title: 697-SCM-CL1-EM-CM-E02

value: EM

value: NLV

tag: cell type


title: Skeletal muscle, Male, WT, rep 2

description:
Library name: G_665
Muscle_Male_WT_2

tag: genotype


title: Skeletal muscle, Female, WT, rep 3

description:
Library name: G_680
Muscle_Female_WT_3


title: V1 Vehicle replicate 1

description: Library name: Unknown_AP191-01T0001


title: H1_D_S6D7_2


title: 697-SCM-CL1-EM-CM-C06

tag: subject

value: CD8 T


title: 697-SCM-CL1-EM-CM-B09

tag: gen1 phenotype


title: Skeletal muscle, Female, WT, rep 2

description:
Library name: G_670
Muscle_Female_WT_2


title: 697-SCM-CL1-EM-CM-A05

tag: gen2 phenotype


title: Skeletal muscle, Female, WT, rep 1

description:
Library name: G_628
Muscle_Female_WT_1


title: H1_D_S6D7_1


title: 697-SCM-CL1-EM-CM-A04

tag: clone


title: H1_D_S6D3_4


title: D, scATAC, 2

library_source: genomic single cell

molecule: genomic DNA


title: Pulmonary pleomorphic carcinoma, scRNA-seq, multiplexed

city: Okayama

first: Shuta

last: Tomida

state: Okayama

address: 2-5-1 Shikata-cho, Kita-ku

department: Center for Comprehensive Genomic Medicine

country: Japan

institute: Okayama University Hospital

description: Library name: OPL

data_processing:
The raw FASTQ files generated from sequencing were processed with Cell Ranger (v8.0) using the cellranger-multi pipeline. The reference files used were the Human Transcriptome Reference (GRCh38 - 2024-A) and the Human Transcriptome Probe Set v1.0 (10x Genomics). The analysis was performed using the 3' Cell Multiplexing configuration, and output data was demultiplexed into barcode-specific results.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matlix files.
Supplementary files format and content: The barcodes.tsv, features.tsv, mtx, csv, and h5 files with patients ID at the beginning are demultiplexed and generated by Cell Ranger multi.
Supplementary files format and content: Patients_metadata.csv: Includes patients metadata multiplexed in this library.

source_name: Pulmonary pleomorphic carcinoma

extract_protocol:
Fresh frozen PPC tissue samples (25 mg) from four patients were fixed and dissociated using the Chromium Next GEM Single Cell Fixed RNA Sample Preparation Kit (10x Genomics) according to the manufacturer's protocol. Fixed single-cell suspensions were hybridized with Probe Barcodes from the Chromium Fixed RNA Kit, Human Transcriptome (10x Genomics), for 19 hours at 42°C.
After hybridization, single-cell suspensions were pooled with an equal number of cells from each sample. Gel Beads-in-Emulsion (GEMs) were generated using the Chromium Controller (10x Genomics). GEMs were processed for probe ligation, pre-amplified by PCR, and cleaned using SPRIselect beads (Beckman Coulter). Gene expression libraries were constructed using the Chromium Fixed RNA Profiling Reagent Kits for Multiplexed Samples (10x Genomics). Sample Index PCR was performed with the Dual Index Kit TS Set A (10x Genomics) to add Illumina adapters and indexes. Final libraries were purified, quality-checked and sequenced on the Illumina NovaSeq 6000 platform (150 bp paired-end).

value: Pulmonary pleomorphic carcinoma

value: surgical resection


title: H1_D_S6D3_3


title: Liver, Male, IGF-1R Het, rep 6

description:
Library name: L_679
Liver_Male_IGF1R.Het_6

source_name: Liver

value: Liver


title: D, scATAC, 1


title: Liver, Male, IGF-1R Het, rep 4

description:
Library name: L_633
Liver_Male_IGF1R.Het_4


title: A, scATAC, 2

value: A


title: D, S5D7, posttransplant


title: 697-SCM-CL1-EFF-G02

value: EFF

tag: epitope


title: 697-SCM-CL1-EFF-F11


title: A, scATAC, 1

tag: Stage


title: H1_D_S6D3_2

tag: treatment


title: Liver, Male, IGF-1R Het, rep 3

description:
Library name: L_632
Liver_Male_IGF1R.Het_3

tag: strain

value: 4 months

value: IGF-1R Het


title: H1_D_S6D2_3


title: Liver, Male, IGF-1R Het, rep 2

description:
Library name: L_631
Liver_Male_IGF1R.Het_2

tag: Sex


title: H1_D_S6D3_1


title: 697-SCM-CL1-EFF-F09


title: 697-SCM-CL1-EFF-F05


title: Liver, Male, IGF-1R Het, rep 1

description:
Library name: L_630
Liver_Male_IGF1R.Het_1

tag: age


title: H1_D_S6D2_1


title: H1_D_S6D2_2


title: D, S5D7, pretransplant


title: 697-SCM-CL1-EFF-F03


title: Liver, Female, IGF-1R Het, rep 5

description:
Library name: L_677
Liver_Female_IGF1R.Het_5

value: Female

tag: replicate


title: H1_D_S6D14_4


title: D, S3D3, pretransplant


title: pt_32_KB528

city: Cambridge

first: Walter

last: Lenoir

state: MA

address: 301 Binney St

institute: Kronos Bio

data_processing:
First, reads are preprocessed by BBDuk which removes adapters, trims reads for quality from the 3'-end, and discards reads that are too short after trimming.
Next, preprocessed reads are aligned by STAR aligner. Aligned reads are summarized to gene-level counts by the featureCounts tool.
FastQC reports, alignment statistics, QoRTs QC, RNA-SeQC and rRNA/globin depletion rate QC information is automatically summarized by the MultiQC tool.
Assembly: hg19
Supplementary files format and content: DF_pt_TPM.csv is output genes in TPM format

source_name: blood

growth_protocol: For primary MM cell studies, mononuclear cells that had been fraction separated by Ficoll gradients from the BM aspirates of consenting MM patients were plated at a cell density of 5 × 105 cells/mL in RPMI medium with 20% FBS plus the indicated concentrations of drugs.

extract_protocol: Strand-specific mRNA-Seq (NEB Cat # E7490 and E7765) with Invitrogen ERCC RNA spike-in (Cat # 4456740) addition.

treatment_protocol: Cells were treated with or with 1 µM of KB528, and sampled at 12 hours

value: blood

value: 1 uM KB528 12 Hour


title: H1_D_S6D14_3


title: Liver, Female, IGF-1R Het, rep 4

description:
Library name: L_674
Liver_Female_IGF1R.Het_4


title: 697-SCM-CL1-EFF-E12


title: Liver, Male, IGF-1R Het, rep 5

description:
Library name: L_676
Liver_Male_IGF1R.Het_5

value: Male


title: 697-SCM-CL1-EFF-G10


title: Liver, Female, IGF-1R Het, rep 3

description:
Library name: L_668
Liver_Female_IGF1R.Het_3


title: pt_32_CTRL

value: CTRL

value: control 12 hour


title: 697-SCM-CL1-EFF-C11

value: SCM


title: H1_D_S6D14_2

description:
cellname.smartseq3.tsv
genename.smartseq3.tsv
readcount.smartseq3.mtx

value: D


title: Liver, Female, IGF-1R Het, rep 2

description:
Library name: L_663
Liver_Female_IGF1R.Het_2


title: pt_22_KB528


title: H1_D_S6D14_1


title: 697-SCM-CL1-EFF-B11

value: NLV


title: Liver, Male, WT, rep 6

description:
Library name: L_685
Liver_Male_WT_6

value: WT


title: H1_D_S6D1_4


title: 697-SCM-CL1-EFF-E05

value: CD8 T


title: Liver, Female, IGF-1R Het, rep 1

description:
Library name: L_662
Liver_Female_IGF1R.Het_1


title: pt_22_CTRL


title: pt_18_KB528


title: 697-SCM-CL1-CCR7-H10


title: 697-SCM-CL1-EFF-A08


title: D, S4D3, pretransplant


title: H1_D_S6D1_2


title: Liver, Male, WT, rep 5

description:
Library name: L_684
Liver_Male_WT_5


title: H1_D_S6D1_3


title: pt_18_CTRL


title: Liver, Male, WT, rep 4

description:
Library name: L_678
Liver_Male_WT_4


title: MM1S_KB528_24Hr_input_rep2

library_source: genomic

data_processing:
Align reads using BWA ALN. Default parameters follow the ENCODE ChIP-seq pipeline recommended settings.
Assembly: hg19 + dm3
Supplementary files format and content: none

growth_protocol: Cells were grown in RPMI 1640 media with 10% fetal bovine serum (FBS).

extract_protocol:
Cells were crosslinked using methanol-free formaldehyde using the Covaris truChIP chromatin shearing kit method (Covaris, 520154).
ChIP-Seq libraries were generated from the ChIP-DNA using a custom Illumina library type on an automated system (Apollo 342, Wafergen Biosystems/Takara).

treatment_protocol: MM1.S cells were treated with DMSO or 100nM KB528 for 1, 3, 6 or 24 hours. 10 million cells were used for each ChIP sample, and each ChIP was performed in duplicate. Spike-in normalized ChIP-seq was used for the histone modification ChIP-seq analysis with DMSO or KB528 treatments, where Drosophila S3 cells with an H2Av normalization were used to compare drug effects across treatments, as established by Egan et al PLoS One (2016) . IRF4 (Santa Cruz, cat# sc-6059) and p300 (Active Motif, cat#61401) ChIP-seq was performed on MM1.S cells without drug treatment. Input material was sequenced for each time point. Generally, chromatin preparation and sonication were performed, and chromatin was enriched using the antibodies listed above. Enriched DNA was used to generate sequencing libraries, and Illumina sequencing was performed using single-end 75bp sequencing at an average sequencing depth of 30 million reads per sample. Spike-in normalized ChIP-seq was used for the histone modification ChIP-seq analysis with DMSO or KB528 treatments, where Drosophila S3 cells with an H2Av normalization were used to compare drug effects across treatments, as established by Egan et al PLoS One (2016) . IRF4 (Santa Cruz, cat# sc-6059) and p300 (Active Motif, cat#61401) ChIP-seq was performed on MM1.S cells without drug treatment. Input material was sequenced for each time point. Generally, chromatin preparation and sonication were performed, and chromatin was enriched using the antibodies listed above. Enriched DNA was used to generate sequencing libraries, and Illumina sequencing was performed using single-end 75bp sequencing at an average sequencing depth of 30 million reads per sample.

value: cancer cell line

tag: chip antibody


title: H1_D_S5D7_4


title: 697-SCM-CL1-CCR7-F02

value: CM


title: MM1S_KB528_24Hr_input_rep1


title: 697-SCM-CL1-CCR7-E10


title: MM1S_KB528_6Hr_input_rep2


title: H1_D_S5D7_3


title: Liver, Male, WT, rep 1

description:
Library name: L_629
Liver_Male_WT_1

tag: tissue

value: Liver


title: H1_D_S5D7_2

tag: batch


title: 697-SCM-CL1-CCR7-D04

value: EM


title: Liver, Female, WT, rep 6

description:
Library name: L_751
Liver_Female_WT_6

value: 4 months


title: H1_D_S5D7_1

tag: cell line


title: 697-SCM-CL1-CCR7-C07

tag: cell type


title: MM1S_KB528_6Hr_input_rep1

tag: genotype


title: 697-SCM-CL1-CCR7-H05

tag: subject


title: MM1S_KB528_3Hr_input_rep2


title: H1_D_S6D1_1


title: 697-SCM-CL1-CCR7-C03

tag: gen1 phenotype

value: EFF


title: Liver, Female, WT, rep 5

description:
Library name: L_750
Liver_Female_WT_5

value: Female


title: H1_D_S5D6_4


title: 697-EM-CL1-EFF-H06

tag: gen2 phenotype


title: H1_D_S5D6_3


title: 697-SCM-CL1-CCR7-C05

tag: clone


title: H1_D_S5D6_2


title: Liver, Female, WT, rep 4

description:
Library name: L_680
Liver_Female_WT_4


title: MM1S_KB528_3Hr_input_rep1


title: Liver, Female, WT, rep 3

description:
Library name: L_671
Liver_Female_WT_3


title: MM1S_KB528_1Hr_input_rep1


title: Liver, Female, WT, rep 2

description:
Library name: L_670
Liver_Female_WT_2


title: Liver, Male, WT, rep 3

description:
Library name: L_672
Liver_Male_WT_3


title: Liver, Male, WT, rep 2

description:
Library name: L_665
Liver_Male_WT_2


title: 697-EM-CL1-EFF-G05

tag: epitope


title: H1_D_S5D5_2

tag: Stage


title: MM1S_DMSO_input_rep2

tag: treatment


title: 697-EM-CL1-EFF-G03


title: run2_Day5

city: Turin

first: Andrea

last: Lauria

address: Via Accademia Albertina, 13

department: Life Sciences and Systems Biology

country: Italy

institute: University of Turin

description: Library name: Sample 6

data_processing:
Following quality controls, sequencing reads were quality and adaptor trimmed using Trim Galore! v0.5.0 (parameters: --stringency 3 –q 20). Trimmed reads were next aligned to human reference genome (GRCh38.p13) using Hisat2 [3]. Indexes for transcriptome-guided genome alignment were generated for the human GENCODE release 32 annotation (extract_exons.py and extract_splice_sites.py scripts). Gene expression levels were quantified with featureCounts v1.6.1 (options: -t exon -g gene_name) using the human GENCODE release 32 annotation (https://www.gencodegenes.org/human/release_32.html). Multi-mapped reads were excluded from quantification.
Assembly: GRCh38.p13/hg38
Supplementary files format and content: raw_counts.txt.gz

growth_protocol: HES3-MIXL1-GFP_hESC was cultured in Feeder-free on pre-coated plates with 0.5% growth factor-reduced Matrigel (vol/vol in PBS with MgCl2/CaCl2, Sigma-Aldrich D8662) in E8 medium at 37°C, 5% CO2, 5% O2. For the 3D-hE-Gastruloids, HES3-MIXL1-GFP_hESC was detached as single cells using TrypLETM Select (1X). A well of a Chamber slide was covered with 40µl of pure ice-cold growth factor reduced Matrigel and incubated for 2 minutes at 37°C to allow Matrigel to solidify. 50,000 cells (for each well of a chamber slide) were resuspended in 250μl of E8 medium with 10µM ROCKi. 10 min after plating, the medium was removed and replaced with 250µl of E8 + 10µM ROCKi containing 5% Matrigel. After 24 hours, the medium was changed (E8 medium containing 5% of Matrigel v/v). The 3D structures were grown at 37°C, 5% CO2, 21% O2.

extract_protocol:
For single cell library prep, ~30 3D cysts structures for each time point were collected and dissociated using Trypsin/EDTA for 5 min at room temperature. Cells were then washed with PBS, and the resulting cell suspension was used to sort individual live cells in 96 well plate.
Full length single cell RNA-seq was performed using a modified version of the Smart-seq2 protocol. Briefly, individual cells were sorted into 96 well plates containing lysis buffer in presence of RNase inhibitor, dNTPs and OligodT. Reverse transcription of the polyadenylated RNA was performed with Maxima H Minus Reverse Transcriptase and Template Switching Oligos. The resulting cDNA was amplified with 23 cycles of PCR and libraries were prepared for sequencing with miniaturized NexteraXT Illumina protocol. Libraries were sequenced on Illumina NextSeq 500 System (single-end 75bp reads).

treatment_protocol: After 2 days in E8 media in 3D cultere, the media was changed with E8 + 100ng/ml Activin A (QKINE Qk001).

tag: time


title: H1_D_S5D5_1


title: 697-EM-CL1-EFF-F06


title: run2_Day2

description: Library name: Sample 5


title: H1_D_S5D4_3


title: MM1S_p300_rep2

value: Anti-p300 Active Motif 61401


title: MM1S_IRF4_rep2

value: Anti-IRF4 Santa Cruz sc-6059


title: 697-EM-CL1-EFF-F04


title: run1_Day5

description: Library name: Sample 3


title: 697-EM-CL1-EFF-F02


title: 697-EM-CL1-EFF-H05


title: MM1S_DMSO_input_rep1


title: run2_Day0

description: Library name: Sample 4


title: MM1S_p300_rep1


title: H1_D_S5D4_2


title: H1_D_S5D4_1


title: MM1S_IRF4_rep1


title: 697-EM-CL1-EFF-E06


title: H1_D_S5D3_3


title: run1_Day2

description: Library name: Sample 2


title: MM1S_KB528_24Hr_H3K27me3_rep2

value: Anti-histone H3K27me3 Active Motif 39155


title: H1_D_S5D6_1


title: 697-EM-CL1-EFF-D05


title: Liver, Female, WT, rep 1

description:
Library name: L_628
Liver_Female_WT_1

tag: strain

tag: Sex


title: run1_Day0

description: Library name: Sample 1


title: MM1S_KB528_1Hr_input_rep2


title: 697-EM-CL1-EFF-B02


title: H1_D_S5D3_2


title: H1_D_S5D3_1


title: MM1S_KB528_6Hr_H3K27me3_rep2


title: 697-EM-CL1-EFF-A05


title: H1_D_S5D2_3


title: M-D1-11SN

city: Guangzhou

first: Yamei

last: Tang

state: Guangdong

address: 107 Yan Jiang West Road

department: Department of Neurology

institute: Sun Yat-Sen Memorial Hospital

description:
Library name: M-D1-10SN
5xFAD-iβARK

data_processing:
Cell Ranger (v8.0.1) was used to process raw sequencing reads using the mouse reference genome mm10 (v2.1.0). This included alignment to the reference genome, filtering and counting unique molecular identifiers (UMIs), identifying cell-associated barcodes, and generating a filtered gene-barcode matrix for downstream analyses. The filtered count matrices were imported into Seurat (v4.3.0.9001) in R (v4.2.3 or v4.3.1). Cells with poor quality were removed based on the following criteria: cells with > 10% mitochondrial gene content, total UMI counts exceeding 50,000, or detected gene numbers (nFeature_RNA) greater than 7,500. To further remove ambient RNA contamination, decontX from Celda (v1.20.0) was applied, and cells with an estimated contamination fraction ≥ 0.3 were discarded. Putative doublets were then detected using scrubletR (v0.2.0) with an expected doublet rate of 10%, and predicted doublets were excluded.
Assembly: mm10
Supplementary files format and content: HD5

molecule: nuclear RNA

source_name: mPFC

growth_protocol: Both female and male 5xFAD mice, along with their wild-type age-matched littermates, were housed in a controlled environment, including a 12-hour light/dark cycle, consistent humidity and temperature, and ad libitum access to food and water.

extract_protocol:
The medial prefrontal cortex (mPFC) was microdissected from 500-µm coronal brain sections prepared using adult rodent brain matrices (R&D, 68717). Slices were transferred to ice-cold HBSS, and mPFC-containing regions were identified microscopically and isolated using a 23-gauge needle. For sample preparation, we established two biological replicates per experimental group, with each replicate consisting one male-derived sample (pooled mPFC tissue from 4 male mice) and one female-derived sample (pooled mPFC tissue from 4 female mice). Tissue from each animal was pooled, briefly centrifuged to remove HBSS, and flash-frozen in liquid nitrogen. Nuclei were isolated from frozen mPFC tissue using the Chromium Nuclei Isolation Kit (PN-1000494, 10x Genomics) strictly following the manufacturer's protocol. Tissue samples were homogenized in Lysis Buffer using a pestle and filtered through a column. Debris was removed by centrifugation in Debris Removal Buffer (300g, 10 min). Isolated nuclei were washed, resuspended in Nuclei Buffer, and counted. Nuclei suspensions were loaded directly onto the 10x Genomics Chromium platform.
Single-nucleus RNA sequencing (snRNA-seq) libraries were prepared targeting a capture of approximately 10,000 nuclei. Single-cell gel beads-in-emulsion (GEMs) were generated using the Chromium Single Cell 3' Library & Gel Bead Kit v3.1 (10x Genomics, PN-1000268). Captured nuclei were lysed within GEMs, and released RNA underwent reverse transcription using primers containing a poly-dT sequence, a cell barcode, a unique molecular identifier (UMI), and the Read 1 primer sequence. Barcoded cDNA was recovered, purified, and amplified by PCR. Adapter ligation was then performed to add the sample index and Read 2 primer sequence. Following library quality control assessment, paired-end sequencing (150 bp reads) was performed on an Illumina NovaSeq 6000 platform (Berry Genomics Corporation, Beijing, China).

treatment_protocol: Mice at 3-4 months of age were injected with AAV2/5 carrying either iβARK-mCherry or mCherry control, and transcriptional profiling was performed 45 days post-intervention.

value: mPFC

value: male

value: Whole tissue

value: iβARK


title: MM1S_KB528_3Hr_H3K27me3_rep2


title: M-B1-11SN

description:
Library name: M-B1-10SN
WT-iβARK


title: 697-EM-CL1-EFF-A02

value: NLV


title: M-C1-11SN

description:
Library name: M-C1-10SN
5xFAD-mCherry

value: mCherry


title: 697-EM-CL1-CCR7-G04

value: CD8 T


title: MM1S_KB528_6Hr_H3K27me3_rep1

value: cancer cell line


title: MM1S_KB528_3Hr_H3K27me3_rep1


title: H1_D_S5D2_2

value: D


title: F-D1-11SN

description:
Library name: F-D1-10SN
5xFAD-iβARK

value: female


title: 697-EFF-CL1-EM-H12

value: EM


title: H1_D_S5D1_3


title: H1_D_S5D2_1


title: MM1S_KB528_1Hr_H3K27me3_rep2


title: 697-EFF-CL1-EM-H11


title: F-C1-11SN

description:
Library name: F-C1-10SN
5xFAD-mCherry


title: MM1S_KB528_1Hr_H3K27me3_rep1


title: H1_D_S5D1_2


title: 697-EFF-CL1-EM-G12


title: MM1S_KB528_24Hr_H3K27me3_rep1


title: F-B1-11SN

description:
Library name: F-B1-10SN
WT-iβARK

value: WT


title: H1_D_S5D1_1


title: 697-EFF-CL1-EM-F10

value: EFF


title: MM1S_DMSO_H3K27me3_rep2


title: MM1S_DMSO_H3K27me3_rep1


title: H1_D_S4D3_3


title: 697-EFF-CL1-EM-F09


title: Hashtag expression library CD11b+ enriched myeloid cells from mouse sarcomas, shPostn

city: Houston

first: Jlenia

last: Guarnerio

state: TX

address: 6767 Bertner Ave

department: Genetics

institute: MD Anderson Cancer Center

description: Library name: shPostn-pool-HTO

library_source: other

data_processing:
Fastq files were preprocessed using Cell Ranger (10x Genomics) count and aggr pipelines to produce counts files for both CITE-seq and gene expression.
Single-cell counts files were read into Seurat v5.3 for counts normalization, quality control/filtering, dimensionality reduction, hashtag demultiplexing, clustering, differential expression, and cell cluster annotation. Cells were labeled as dead, ambient, or otherwise failing QC if they: had per-cell percent mitochondrial reads greater than 15%, belonged to a cell cluster in which top 10 DE genes were mostly mitochondrial transcripts, or were marked as a doublet by either HTODemux or scDblFinder.
Assembly: mm10
Supplementary files format and content: cell x feature counts matrix (.h5)
Supplementary files format and content: Processed Seurat object (.rds)
Library strategy: CITE-seq

molecule: other

source_name: Mouse sarcoma tumors

extract_protocol:
Individual mouse tumors (n=5 each group) were digested with Miltenyi Mouse Tumor Dissociation Kit and gentleMACS running 37C_m_TDK_2 protocol. Cells were washed, strained, and red blood cells lysed. Cell suspensions were stained with Biolegend Total-Seq hashtags and fluorescent markers for FACS sorting, and washed 3 times. Cell suspensions were sorted to deplete tumor cells and enrich myeloid cells. Cells were pooled from multiple mice and captured on the 10x Genomics Chromium X controller.
The 10x Genomics NextGEM 3' v3 Kit with Feature Barcoding was used according to manufacturer instructions.

value: Mouse sarcoma tumors

value: CD11b+ myeloid cells


title: M-A1-11SN

description:
Library name: M-A1-10SN
WT-mCherry


title: Gene expression library for CD11b+ enriched myeloid cells from mouse sarcomas, shPostn

description: Library name: shPostn-pool-GEX


title: H1_D_S4D3_2


title: H1_D_S4D3_1


title: MM1S_KB528_24Hr_H3K27ac_rep2

value: Anti-histone H3K27ac Active Motif 39133


title: 697-EFF-CL1-EM-E08


title: MM1S_KB528_24Hr_H3K27ac_rep1


title: H1_D_S4D2_3


title: 697-EFF-CL1-EM-F08


title: 697-EFF-CL1-EM-D10


title: Gene expression library for CD11b+ enriched myeloid cells from mouse sarcomas, shSCR

description: Library name: shSCR-pool-GEX


title: H1_D_S4D2_2


title: MM1S_KB528_6Hr_H3K27ac_rep1


title: MM1S_KB528_6Hr_H3K27ac_rep2


title: IR-Ori6

city: fuzhou

first: qiyuan

last: Yang

state: Fujian Province

address: The First Affiliated Hospital of Fujian Medical University, Taijiang District, Fuzhou City, Fujian Province

description:
Library name: sample18
IR-Ori6_FPKM

data_processing:
In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or  fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt (V1.9.1, phred cutoff: 20, error rate: 0.1, adapter overlap: 1bp, min. length: 75, proportion of N: 0.1) to be high quality clean data
Firstly, reference genome sequences and gene model annotation files of relative species were downloaded from genome website（ ENSEMBL）. Secondly, Hisat2 (v2.2.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.2.1).
Differential expression analysis used the DESeq2 Bioconductor package, a model based on the negative binomial distribution. the estimates of dispersion and logarithmic fold changes incorporate data-driven prior distributions, Padj of genes were setted <=0.05 to detect differential expressed ones.
GOSeq (v1.34.1) was used identifying Gene Ontology (GO) terms that annotate a list of enriched genes with a significant padj less or equal than 0.05. And topGO was used to plot DAG. KEGG (Kyoto Encyclopedia of Genes and Genomes) is a collection of databases dealing with genomes, biological pathways, diseases, drugs, and chemical substances (http://en.wikipedia.org/wiki/KEGG). We used scripts in house to enrich significant differential expression gene in KEGG pathways.
Assembly: GRCm39.107
Supplementary files format and content: gene expression data; FPKM, count

source_name: liver

growth_protocol: After purchase, the mice were allowed to acclimate for 7 days in the experimental animal facility. The ambient temperature was maintained at 22–24 °C with a 12-hour light/12-hour dark cycle, and they were given free access to water.

extract_protocol:
RNA was harvested using MagPure Universal RNA LQ Kit 2. 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using VAHTS® Universal V8 RNA-seq Library Prep Kit  for Illumina following manufacturer's protocols.

treatment_protocol: Except for the sham group—in which the mice were simply anesthetized, disinfected with iodophor, and subjected to laparotomy—non-invasive hemostatic clips were applied to the portal triad in the I/R+Ori and I/R groups to induce ischemia in the median and left lobes (≈70 % of the total liver). After 1 h of ischemia, the clips were removed, and the liver was reperfused for 6 h.

value: liver

value: IR-Ori


title: H1_D_S4D2_1


title: MM1S_KB528_3Hr_H3K27ac_rep2


title: 697-EFF-CL1-EM-C10


title: 697-EFF-CL1-EM-C08


title: IR-Ori5

institute: The First Affiliated Hospital of Fujian Medical University

description:
Library name: sample17
IR-Ori5_FPKM


title: H1_D_S4D1_3


title: F-A1-11SN

description:
Library name: F-A1-10SN
WT-mCherry

value: mPFC


title: 697-EFF-CL1-EM-B11


title: IR-Ori4

description:
Library name: sample16
IR-Ori4_FPKM


title: H1_D_S4D1_2


title: Hashtag expression library CD11b+ enriched myeloid cells from mouse sarcomas, shSCR

description: Library name: shSCR-pool-HTO


title: IR-Ori3

description:
Library name: sample15
IR-Ori3_FPKM


title: 697-EFF-CL1-EM-A12


title: H1_D_S4D1_1


title: 697-EFF-CL1-CCR7-E12


title: MM1S_KB528_1Hr_H3K27ac_rep1


title: H1_D_S3D3_2


title: IR-Ori1

description:
Library name: sample13
IR-Ori1_FPKM


title: 697-EFF-CL1-CCR7-D11


title: MM1S_DMSO_H3K27ac_rep1


title: H1_D_S3D3_1


title: IR6

description:
Library name: sample12
IR6_FPKM

value: IR


title: MM1S_KB528_24Hr_H3K18ac_rep2

value: Anti-histone H3K18ac Active Motif 39764


title: 697-EFF-CL1-CCR7-C11

value: NLV


title: 697-EFF-CL1-CCR7-D07

value: SCM


title: H1_D_S3D2_1


title: H1_D_S3D1_2


title: MM1S_KB528_3Hr_H3K27ac_rep1


title: IR4

description:
Library name: sample10
IR4_FPKM


title: IR5

description:
Library name: sample11
IR5_FPKM


title: 697-EFF-CL1-CCR7-C12

value: CD8 T


title: MM1S_KB528_24Hr_H3K18ac_rep1

value: cancer cell line

value: Anti-histone H3K18ac Active Motif 39763


title: MM1S_KB528_6Hr_H3K18ac_rep2

value: Anti-histone H3K18ac Active Motif 39762


title: MM1S_KB528_1Hr_H3K27ac_rep2


title: IR3

description:
Library name: sample9
IR3_FPKM


title: H1_D_S3D1_1

value: D


title: IR-Ori2

description:
Library name: sample14
IR-Ori2_FPKM

value: WT


title: MM1S_DMSO_H3K27ac_rep2


title: MM1S_KB528_6Hr_H3K18ac_rep1

value: Anti-histone H3K18ac Active Motif 39761


title: IR2

description:
Library name: sample8
IR2_FPKM


title: H1_D_S2D4_2


title: 697-CM-CL1-SCM-H04

value: CM


title: MM1S_KB528_3Hr_H3K18ac_rep2

value: Anti-histone H3K18ac Active Motif 39760


title: H1_D_S3D2_2


title: IR1

description:
Library name: sample7
IR1_FPKM


title: H1_D_S2D4_1


title: MM1S_KB528_3Hr_H3K18ac_rep1

value: Anti-histone H3K18ac Active Motif 39759


title: sham6

description:
Library name: sample6
sham6_FPKM

value: liver

value: sham


title: 697-CM-CL1-SCM-G09


title: H1_D_S2D3_2


title: MM1S_KB528_1Hr_H3K18ac_rep2

value: Anti-histone H3K18ac Active Motif 39758


title: H1_D_S2D3_1


title: 697-CM-CL1-SCM-G03


title: sham5

description:
Library name: sample5
sham5_FPKM


title: sham4

description:
Library name: sample4
sham4_FPKM


title: 697-EFF-CL1-CCR7-B12

value: EFF


title: MM1S_DMSO_H3K18ac_rep2

value: Anti-histone H3K18ac Active Motif 39756


title: MM1S_KB528_1Hr_H3K18ac_rep1

value: Anti-histone H3K18ac Active Motif 39757


title: H1_D_S2D2_2


title: H1_D_S2D2_1


title: sham3

description:
Library name: sample3
sham3_FPKM


title: 697-EFF-CL1-CCR7-A09

value: EM

value: NLV


title: MM1S_DMSO_H3K18ac_rep1

value: cancer cell line

value: Anti-histone H3K18ac Active Motif 39755


title: sham2

description:
Library name: sample2
sham2_FPKM


title: 697-CM-CL1-SCM-E04

value: SCM

value: CD8 T


title: 697-CM-CL1-SCM-C09


title: H1_D_S2D1_1

value: D


title: H1_D_S2D1_2


title: CM_High_line632 [H632]

city: Stanford

first: Joseph

middle: C.

last: Wu

state: California

address: 240 Pasteur Dr

department: Stanford Cardiovascular Institute

institute: Stanford university

data_processing:
Low-quality and adapter sequences have been trimmed from the raw 150 bp paired-end reads by using Trim Galore function within FastQC toolkits Version 0.6 with Phred scoring less than 20.
The trimmed paired-end reads were mapped to either the human reference genome GRCh38, to calculate the gene counts by using STAR version 2.7.10a with the parameters: --runThreadN 12 --quantMode GeneCounts --outFilterMultimapNmax 1 --limitBAMsortRAM 90258540544.
The RNA expression count matrix was merged from the read count tables by using Shell command.
Assembly: GRCh38
Supplementary files format and content: csv file, contain RNA expression count matrix

source_name: iPSC-derived cardiomyocytes

growth_protocol: (1)  Macrophages were differentiated from human iPSCs for 21 days, using a previously published protocol (doi: 10.1016/j.stemcr.2019.05.003). Cells were used when reaching more than 90% confluence. (2) Cardiomyocytes were diffferentiated from human iPSCs for 30 days, using a previously published protocol (doi: 10.1038/nmeth.2999).

extract_protocol:
Cells were lysised in Tirzol and isolated using Direct-zol™ RNA Purification Kit from Zymo Research.
RNA library is formed by polyA capture (or rRNA removal) and reverse transcription of cDNA.

treatment_protocol: (1) For human macrophage samples: human induced pluripotent stem cell-derived macrophages were treated either eitehr BNT162b2 (Pfizer, 3 μg/mL), or mRNA-1273 (Moderna, 10 μg/mL) COVID19 mRNA vaccine. Cells treated with PBS were included as control. were collected 24 hours after treatment and sent for bulk RNA-seq. (2) For human cardiomyocyte samples: human induced pluripotent stem cell-derived cardiomyocytes were treated with a cytokine cocktail of CXCL10 and IFN-γ. Two treatment conditions were tested: a “low” concentration (1 ng/mL of CXCL10 and 0.5 ng/mL of IFN-γ) and a “high” concentration (10 ng/mL CXCL10 and 5 ng/mL IFN-γ). cells treated with PBS were included as control. Cells were collected 48 hours after treatment and sent for bulk RNA-seq.

value: iPSC-derived cardiomyocytes

value: cardiomyocytes

value: Wild type

value: High cytokines


title: CM_High_line477 [H477]


title: p53KO_Vgll3OE model, rep 3

description:
Library name: p53KO_Vgll3_C
vgll3.rep3

data_processing:
Transcripts were quantified with salmon and summarized to gene-level counts using tximport.
Assembly: mm10
Supplementary files format and content: comma-separated values containing gene read counts

source_name: sarcoma cells sorted ex vivo from mouse tumors

growth_protocol: Syngeneic tumor cell lines p53KO Ccne1 OE and p53KO Vgll3 OE were generated in-house. First, mesenchymal stem cells were harvested from female C57/Bl6 p53KO mice, transduced using retroviral vectors for the overexpression of Ccne1 and Vgll3 genes, and expanded in vitro. To generate immortalized tumor cell lines, each was passaged twice through female wild-type (C57/Bl6) recipient mice via subcutaneous transplantation, and re-harvested. Resulting tumor cell lines were briefly expanded in vitro in DMEM+FBS.  Cell lines were transplanted into experimental mice to generate sarcoma tumors. Tumors were harvested and RFP+ tumor cells were sorted for RNA-seq.

extract_protocol:
Total RNA was extracted using TRIzol.
Libraries were constructed and sequenced at the Applied Genomics, Computation & Translational Core at Cedars-Sinai Medical Center.

value: p53 KO Vgll3 OE

value: undifferentiated pleimorphic sarcoma cells


title: CM_High_line114 [H114]


title: H1_Ctrl_S2D4_2

value: Ctrl


title: 697-CM-CL1-SCM-B12

value: CM


title: sham1

description:
Library name: sample1
sham1_FPKM

value: liver

value: WT

value: sham


title: 697-CM-CL1-SCM-F09

value: NLV


title: p53KO_Vgll3OE model, rep 2

description:
Library name: p53KO_Vgll3_B
vgll3.rep2

value: sarcoma cells sorted ex vivo from mouse tumors


title: p53KO_Vgll3OE model, rep 1

description:
Library name: p53KO_Vgll3_A
vgll3.rep1


title: 697-CM-CL1-SCM-E09


title: CM_High_line15 [H015]


title: H1_Ctrl_S2D4_1


title: 697-CM-CL1-SCM-B09


title: 697-CM-CL1-SCM-B04


title: H1_CH3_S2D4_2


title: CM_Low_line632 [L632]

value: Low cytokines


title: p53KO_Ccne1OE model, rep 4

description:
Library name: p53KO_Ccne1_D
ccne1.rep4

value: p53 KO Ccne1 OE


title: CM_Low_line477 [L477]


title: 697-CM-CL1-SCM-A03

value: SCM

value: CD8 T


title: H1_CH3_S2D4_1


title: CM_Low_line114 [L114]

value: iPSC-derived cardiomyocytes


title: p53KO_Ccne1OE model, rep 3

description:
Library name: p53KO_Ccne1_C
ccne1.rep3


title: H1_CH2_S2D4_2


title: 697-CM-CL1-EM-H09

value: EM


title: H1_CH2_S2D4_1


title: 697-CM-CL1-SCM-C04


title: CM_Low_line15 [L015]

value: cardiomyocytes

value: Wild type


title: p53KO_Ccne1OE model, rep 1

description:
Library name: p53KO_Ccne1_A
ccne1.rep1


title: 697-CM-CL1-EM-G12


title: H1_CH1_S2D4_2


title: CM_Control_line632 [C632]

value: Control


title: 697-CM-CL1-EM-G08


title: CM_Control_line477 [C477]


title: H1_C_S6D7_3

value: C


title: 697-CM-CL1-EM-G06


title: BASP1_KO.2

city: Pittsburgh

first: Mark

last: Shlomchik

state: PA

address: The Assembly, 5051 Centre Avenue

department: Department of Immunology

institute: University of Pittsburgh

description:
Library name: Sample 5
Day10_GCBC_BASP1_KO_2

data_processing:
Raw reads quality and adapter sequences were checked using fastqc (v. 0.11.7).
Filtered adaptor and poor quality sequences respectively, using trimgalore(v.0.6.5 )
The reference genome (mm10) based alignment of clean reads were performed using STAR (v.2.6.1a) (Dobin et al., 2013).
Gene-level counts were determined using featureCounts packgae by subread/2.0.1 (Liao et al. 2014).
Raw counts were analyzed for differential expression using the “voom” method (Law et al. 2014) in the “limma” R package (Ritchie et al. 2015).
Assembly: Mus musculus reference genome (mm10).
Supplementary files format and content: tab-delimited text files include log2 normalized expression values for each Sample.

source_name: spleen

growth_protocol: BASP1 fl/fl hCD20TamCre (BASP1-KO) and BASP1 +/+ hCD20TamCre (BASP1-WT) mice were i.p. immunized with NP-KLH, treated with 1 mg tamoxifen on days 5, 7 and 9. Splenocytes were bead purified for B cells and then GC B cells were purified by FACS on BD FacsAria

extract_protocol:
RNA libraries were prepared for sequencing using standard Illumina protocols, using the Illumina TruSeq mRNA  for Sequencing.
RNA-Seq

treatment_protocol: Spleens were processed according to the manuscript. Cells were collected via FACS, washed twice in PBS + 1% FCS, resuspended in 350 ul RLT Plus Buffer (Qiagen) with 1% 2-Me, and frozen at -80 ⁰C.

value: spleen

value: GC B cells

value: BASP1 fl/fl hCD20TamCre+/-


title: CM_Control_line114 [C114]


title: BASP1_KO.1

description:
Library name: Sample 4
Day10_GCBC_BASP1_KO_1


title: 697-CM-CL1-EM-F10

value: CM


title: CM_Control_line15 [C015]


title: H1_C_S6D7_2


title: H1_C_S6D7_1


title: p53KO_Ccne1OE model, rep 2

description:
Library name: p53KO_Ccne1_B
ccne1.rep2

value: undifferentiated pleimorphic sarcoma cells


title: BASP1_WT.3

description:
Library name: Sample 3
Day10_GCBC_BASP1_WT_3

value: BASP1 +/+ hCD20TamCre+/-


title: Macro_Moderna_line632 [F632]

source_name: iPSC-derived macrophages

value: iPSC-derived macrophages

value: macrophage

value: Moderna vaccine


title: Macro_Moderna_line477 [F477]


title: 697-CM-CL1-EM-E05

value: NLV


title: H1_C_S6D5_3


title: 697-CM-CL1-EM-D10

value: CD8 T


title: BASP1_WT.2

description:
Library name: Sample 2
Day10_GCBC_BASP1_WT_2


title: H1_C_S6D5_2


title: BASP1_WT.1

description:
Library name: Sample 1
Day10_GCBC_BASP1_WT_1


title: BASP1_KO.3

description:
Library name: Sample 6
Day10_GCBC_BASP1_KO_3


title: 697-CM-CL1-EM-B07


title: H1_CH1_S2D4_1


title: Macro_Moderna_line114 [F114]


title: Kupffer cells, treated with VSV-M51R 3

city: Hefei

first: Chen

last: Chen

address: huang shan Road 443

institute: university of science and technology of china

description:
Library name: Samples 6
Column name in all_gene.csv: M3

data_processing:
For analysis of transcriptomic data, poor quality reads were first filtered using Trimmomatic.
The raw reads were aligned to the mouse reference genome GRCm38_M13 provided by GENCODE using STAR.
The FeatureCounts tool was used to assign exonic reads to the corresponding genes.
Assembly: GRCm38
Supplementary files format and content: csv files include counts for each sample

growth_protocol: Kupffer cells were isolated by a two-step in situ perfusion procedure.All mice were maintained in a Specific Pathogen–free (SPF) facility at USTC.

extract_protocol:
A total of 20,000 to 50,000 cells were collected, and total RNA was extracted using the RNeasy Micro Kit (QIAGEN, USA).
cDNA libraries were prepared from 2 ng of total RNA using the Smart-Seq v2 protocol.

treatment_protocol: Mice were treated with 3×108 PFU VSV-M51R on day 7 following B16F10 tumor cell inoculation and were harvested on day 10. Kupffer cells were isolated by a two-step in situ perfusion procedure and was resuspended in 1 mL HBSS buffer for antibody staining.Zombie-CD45+TIM4+KCs were sorted using a BD FACSAria III with a purity greater than 95%.

value: Liver

value: Kupffer cell

value: Macrophage

value: WT

value: Metastatic B16F10 melanoma, treated with VSV-M51R


title: Macro_Moderna_line15 [F015]

value: Wild type


title: 697-CM-CL1-EFF-H02

value: EFF


title: Kupffer cells, treated with VSV-M51R 2

description:
Library name: Samples 5
Column name in all_gene.csv: M2


title: 697-CM-CL1-EM-F11

value: EM


title: H1_C_S6D3_2

value: C


title: H1_C_S6D3_1


title: Kupffer cells, treated with VSV-M51R 1

description:
Library name: Samples 4
Column name in all_gene.csv: M1


title: Macro_Pfizer_line632 [D632]

value: Pfizer vaccine


title: Macro_Pfizer_line477 [D477]


title: 697-CM-CL1-EFF-F07

value: CM


title: 697-CM-CL1-EFF-F06


title: Kupffer cells, untreated 3

description:
Library name: Samples 3
Column name in all_gene.csv: C3

value: Metastatic B16F10 melanoma, untreated


title: Kupffer cells, untreated 2

description:
Library name: Samples 2
Column name in all_gene.csv: C2


title: H1_C_S6D1_3


title: 697-CM-CL1-EFF-F04


title: Kupffer cells, untreated 1

description:
Library name: Samples 1
Column name in all_gene.csv: C1


title: 697-CM-CL1-EFF-E10


title: H1_C_S6D1_2


title: Macro_control_line632 [A632]

value: iPSC-derived macrophages

value: Control


title: Macro_Pfizer_line15 [D015]

value: macrophage


title: Macro_Pfizer_line114 [D114]


title: H1_C_S6D5_1


title: 697-CM-CL1-EFF-E03

value: NLV


title: H1_C_S5D4_3


title: 697-CM-CL1-EFF-C06

value: CD8 T


title: H1_C_S6D1_1


title: NormalSkin,R4

data_processing:
Raw sequence quality control was performed using FastQC (v0.11.8) before and after removing adapters and low-quality base calls (Phred score <20) using TrimGalore with default options (v0.6.6).
Trimmed reads were aligned to GRCm38, release 100 (mouse samples) using Hisat2 (v2.1.0).
Gene counts were subsequently estimated using featurecounts (subread/1.6.3).
Assembly: mm10
Supplementary files format and content: csv  file includes raw counts for each sample

source_name: Normal Skin

growth_protocol: BRAFV600E was induced in skin cell specific populations in mice from 7-20 weeks old following tamoxifen inducible CreRT2 recombination.

extract_protocol:
RNA was extracted from fresh frozen tumour samplesusing AllPrep DNA/RNA kit (74104, Qiagen) according to the manufacturer’s instructions.
Indexed poly(A) libraries were prepared using 200 ng of total RNA and 14 cycles of amplification with the Agilent SureSelect Strand-Specific RNA Library Preparation Kit for Illumina Sequencing (G9691B, Agilent). RNA polyA libraries were sequenced using NovaSeq 6000 XP SP, 200 cycles, paired-end reads (2 x 101 bp) 20-30 million reads. RNA preparation and sequencing were performed at CRUK Manchester Institute histology core and sequencing facility and GENEWIZ Azenta.

value: Normal Skin

value: Female

value: skin


title: Macro_control_line477 [A477]


title: Macro_control_line114 [A114]


title: 697-CM-CL1-EFF-C05


title: NormalSkin,R3

value: WT


title: NormalSkin,R2


title: H1_C_S5D4_1


title: 697-CM-CL1-EFF-C03


title: NormalSkin,R1


title: H1_C_S5D3_2


title: 697-CM-CL1-EFF-B05


title: H1_C_S5D3_1


title: Tum, Ivl,R6

source_name: Tumour

value: Tumour

value: squamous cell carcinoma


title: GK4

city: Baltimore

first: Hua

address: 1503 E. Jefferson Street

institute: Johns Hopkins University

description: GEJ TP53/CDKN2A KO organoid 4

data_processing:
An index of the reference genome was built and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
Read counts for each gene were generated by FeatureCounts v1.5.0-p3.
FPKM of each gene was calculated based on the length of the gene and the read count mapped to this gene.
Assembly: hg19
Supplementary files format and content: fpkm_genename.txt: Tab-delimited matrix table includes FPKM values for all Samples.

source_name: GEJ organoid

growth_protocol: Organoid were embedded in Matrigel and maintained in a DME/F12 based organoid condition medium.

extract_protocol:
Total RNA was extracted and treated with DNase I before sequencing.
Libraries were constructed using NEBNet Ultra Directional RNA Library Prep kits.

value: GEJ organoid

value: TP53/CDKN2A KO


title: Tum, K14,R4


title: 697-CM-CL1-CM-H06

data_processing:
Illumina NextSeq500 was used
Sequenced paired-end reads were trimmed using Trimmomatic (v0.39) (using parameters:  LEADING = 3, TRAILING = 3, SLIDINGWINDOW = 4:10, MINLEN = 50), then aligned to the human reference genome (GRCh38) using STAR (v2.7.3a). Gene expression was then quantified at the counts and TPM level with RSEM (v1.3.1)
Assembly: GRCh38
Supplementary files format and content: .mtx.gz files contain matrices including raw counts, TPM and scaled TPM values for each sample and each gene.
Supplementary files format and content: .txt and and .tsv files contain tab delimited information on sample names and gene names (as per ordering in matrices), and gene annotation information.

source_name: CD8 T

extract_protocol:
Single CMV-specific CD8+ T cells were sorted using flow cytometry, with RNA isolation and sequencing library construction performed according to the Smart-seq2 protocol.
Single cell RNA libraries were prepared for sequencing using standard Illumina protocols


title: H1_C_S5D2_3

data_processing:
We processed Smart-seq3 scRNA-seq data beginning with the removal of index, primer, and adaptor sequences from the paired-end reads, utilizing Trimmomatic software (version 0.39). Post-trimming, the forward reads (Read 1) were aligned to the Homo sapiens reference genome (hg38) employing HISAT2 (version 2.1.0). The aligned reads were then annotated to gene features using the featureCounts tool (version 2.0.0), taking into account both 5' and internal fragments.  For 10x Genomics scRNA-seq data, initial processing was performed with the Cell Ranger software (version 3.0.1) using default parameters and the GRCh38 reference genome (version 3.0.0).The initial processing of raw snATAC-seq data was conducted using the cellranger-atac software, version 1.2.0, employing the standard parameters and referencing the refdata-cellranger-atac-GRCh38-1.2.0 genome assembly.
Assembly: hg38
Supplementary files format and content: sparse matrix: read count
Supplementary files format and content: fragments.tsv

extract_protocol:
SC-derived cells or islets were dissociated into single cells with 0.25% trypsin at 37 °C for 3-5 min, and the digestion was halted by adding 0.4 volumes of FBS. Partially dissociated SC-islets underwent a secondary trypsinization at 37°C for 3 minutes to ensure complete dissociation. Cells from both dissociation steps were pooled for further analysis. Retrieved grafts from the renal capsule were finely minced and enzymatically dissociated using 0.25% trypsin at 37°C for 5 minutes. The enzymatic reaction was halted by adding 0.4 volumes of FBS.
ScRNA-seq via the Smart-seq3 method was carried out in accordance with established procedures. Briefly, individual cells were sorted into 384-well plates containing lysis buffer (0.3 μL per well). The reverse transcription of mRNA was facilitated using a 0.1 μL aliquot of reverse transcription mix, followed by pre-amplification employing a 0.6 μL aliquot of PCR mix. A diluted sample of the resulting cDNA from each cell was analyzed using quantitative PCR (qPCR) employing ChamQ™ SYBR® qPCR Master Mix (Vazyme, Q321-02) and primers targeting ACTB: forward 5’-ACAGAGCCTCGCCTTTGCC-3’ and reverse 5’-GATATCATCATCCATGGTGAGCTGG-3’. Cells exhibiting cycle threshold (Ct) values under 21 for ACTB were selected for library preparation. To differentiate human cells within grafts, GAPDH expression was quantified using specific primers: forward 5’-CTCTGCTCCTCCTGTTCGAC-3’ and reverse 5’-GCGCCCAATACGACCAAATC-3’, considering cells as human if Ct values were below 25 and melting temperatures surpassed 85°C. Library construction was performed utilizing the TruePrep DNA Library Prep Kit (Vazyme, Cat#TD501), and sequencing was conducted on the MGIseq-2000 platform, generating 100 bp paired-end reads.     For 10x Genomics scRNA-seq, cells purified through FACS were processed on a Chromium controller. This step was followed by cDNA synthesis and library preparation in line with the protocols provided with the Single Cell 3′ Reagent Kit v3.1. The prepared libraries were then sequenced using the Illumina HiSeq 4000 system, yielding 150 bp paired-end reads.Cell suspensions were initially stained with DAPI to facilitate the sorting of live single cells utilizing the FACSAria™ Fusion flow cytometer. Subsequent to sorting, nuclei were isolated in accordance with the protocols detailed in the Chromium NEXT GEM Single Cell ATAC Reagent Kits v2 (10x Genomics). The prepared libraries were then subjected to sequencing on the NovaSeq 6000 platform, achieving 50 bp paired-end reads.     In the context of protocol A, one set of samples consisted of a composite of cells from stages S2D2, S4D3, S5D3, and S6D3, combined in a ratio of 1:2:2:3. An alternative set comprised cells from stages S3D2, S4D3, and S5D3, merged in a ratio of 1:2:3. Within the framework of protocol C, one sample amalgamated cells from stages S2D2, S3D3, S4D3, and S5D3, in a ratio of 1:2:2:3, whereas another ensemble included cells from stages S2D4, S3D3, and S4D3, in a ratio of 1:2:3.

value: C


title: GK3

description: GEJ TP53/CDKN2A KO organoid 3


title: 697-CM-CL1-CM-H03


title: 697-CM-CL1-CM-G07


title: H1_C_S5D4_2


title: Tum, Ivl,R5


title: GK2

description: GEJ TP53/CDKN2A KO organoid 2


title: Tum, Ivl,R4


title: H1_C_S5D2_1


title: GK1

description: GEJ TP53/CDKN2A KO organoid 1


title: 697-CM-CL1-CM-F05


title: H1_C_S5D1_2


title: H1_C_S5D2_2


title: Tum, K5,R5


title: H1_C_S5D1_1


title: Macro_control_line15 [A015]

value: Wild type


title: 697-CM-CL1-CM-E12

value: CM


title: Tum, K14,R3


title: GN3

description: GEJ organoid 3


title: 697-CM-CL1-CM-D06


title: GN2

description: GEJ organoid 2


title: 697-CM-CL1-CM-D04


title: H1_C_S4D4_3


title: Tum, K5,R3


title: Tum, K5,R4


title: GN1

description: GEJ organoid 1


title: H1_C_S4D4_2


title: H1_C_S4D4_1


title: Tum, K14,R2


title: Tum, K5,R2


title: 697-CM-CL1-CM-C02


title: fusiform 44

city: Chengdu

first: Chengbo

last: Ai

state: Sichuan

address: 37 Guo-Xue-Xiang, Chengdu, 610041, China.

institute: West China Hospital/West China School of Medicine

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic (version 0.36) (parameter- ILLUMINACLIP:{adaptor.fa}:2:30:10  -phred33 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 HEADCROP:0 MINLEN:36 PE)
Clean Reads were further treated with UMI_soft (in-house) to eliminate duplication bias introduced in library preparation and sequencing on using UMI. （Default Parameter developed by Wuhan Seqhealth Co., Ltd.）
The de-duplicated consensus sequences were mapped to GRCh38 using STAR software (version 2.5.3a) (parameters- --outSAMtype BAM SortedByCoordinate)
Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter -T 10 -d 30 -D 1000 -C -s 1 -t {exon} -g {geneid} --primary -O -a {gff_annotation_file}）
Assembly: GRCh38
Supplementary files format and content: ALL_samples_RPKM
Supplementary files format and content: lncRNA

source_name: Extrahepatic dilatations

extract_protocol:
Extrahepatic dilatations were collected, and all specimens were stored in liquid nitrogen after excision. Total RNAs was isolated from frozen tissues using TRIzol (Invitrogen), DNA digestion was carried out by DNaseI. RNA quality was measured by examining A260/A280 with a NanoDrop (Thermo Fisher) and quantified by Qsep-100 (Bioptic). Then, RNA samples were stored at - 80 °C until further use.
2 μg total RNAs were used to prepare KC-Total RNA-seq Library Prep Kit for Illumina® (Catalog NLR086-01, Wuhan Seqhealth Co., Ltd. China)

value: Extrahepatic dilatations


title: fusiform 47


title: H1_C_S4D3_2


title: GN4

description: GEJ organoid 4


title: H1_C_S4D2_3


title: Tum, Ivl,R3


title: H1_C_S4D3_1


title: fusiform 41


title: fusiform 43


title: B-Met-214-1T-R

city: Rome

first: Stefano

last: Scalera

address: Via Elio Chianesi 53

institute: IRCCS Regina Elena National Cancer Institute

data_processing:
RNA-seq data were analyzed with “rnaseq” version 3.9 pipeline of nf-core community (https://nf-co.re/rnaseq). The alignment was performed with STAR and the gene quantification with Salmon. The pipeline was run by using the default parameters.
Assembly: hg19
Supplementary files format and content: tab-delimited text files contains TPM values for all samples. breast_met_tpm_table.txt

source_name: metastasis from breast

extract_protocol:
RNA and genomic DNA were extracted from fresh frozen tissue using the AllPrep DNA/RNA/miRNA Universal Kit (Qiagen, Valencia, CA, USA).
The quality of the RNA was assessed with the Bioanalyzer using the Agilent RNA 6000 Nano Kit. Libraries for RNA-Sequencing were prepared employing the TruSeq RNA Exome kit (Illumina) following the manufacturer’s instructions. The quality of the resulting libraries was controlled via the Bioanalyzer (High Sensitivity DNA Kit). The intermediate library before exon enrichment was quantified with the Bioanalyzer using the Agilent DNA 1000 kit, the final library with qPCR. Samples were sequenced in paired-end mode, sequencing from each side 76 bp on a NextSeq 500 instrument.

value: metastasis from breast

tag: site

value: spine


title: B-Met-225-1T-R

value: soft tissue


title: H1_C_S4D2_1


title: fusiform 38


title: B-Met-229-1T-R


title: B-Met-212-1T-R

value: cutaneous


title: fusiform 33


title: fusiform 46


title: 697-CM-CL1-CM-B06

value: NLV

value: CD8 T


title: Tum, K14,R1

city: Glasgow

first: Patricia

address: Switchback Rd, Bearsden, Glasgow

institute: Beatson Institute for Cancer Research

value: Female


title: H1_C_S4D1_2


title: B-Met-211-1T-R

value: brain


title: Mouse_heart_Genistein_6 [GEN6]

data_processing:
Low-quality and adapter sequences have been trimmed from the raw 150 bp paired-end reads by using Trim Galore function within FastQC toolkits Version 0.6 with Phred scoring less than 20.
The trimmed paired-end reads were mapped to mouse reference genome GRCm39, to calculate the gene counts by using STAR version 2.7.10a with the parameters: --runThreadN 12 --quantMode GeneCounts --outFilterMultimapNmax 1 --limitBAMsortRAM 90258540544.
The RNA expression count matrix was merged from the read count tables by using Shell command.
Assembly: GRCm39
Supplementary files format and content: csv file, contain RNA expression count matrix

growth_protocol: No growth protocol applied for mouse heart samples.

treatment_protocol: For mouse samples: BALB/C mouse were divided into three groups: Control, Cytokine treatment, Cytokine + Genistein. 6 mice in each group. Mice were pretreated for 7 days with Genistein with the Cytokine+Genistein group. Then, cytokines cocktail (2.5 ug of CXCL10 and 2.5 ug IFNr) were injected into mice through tail vein. Mice heart samples were collected 4 hours after cyokines treatment and sent for bulk RNA-seq. Mice treated with vehicle (PBS) were used as control.

value: BALB/c mouse

value: Cytokines+Genistein


title: 697-CM-CL1-CM-C08

city: Sdyney

first: Yanran

address: Sydney NSW 2033

institute: UNSW


title: fusiform 29


title: Mouse_heart_Genistein_5 [GEN5]


title: H1_C_S3D2_3

city: Beijing

first: Cheng-ran

address: NO.5 YIHEYUAN ROAD HAIDIAN DISTRICT, BEIJING, P.R.CHINA

institute: Peking University


title: B-Met-207K-1T-R


title: fusiform 28


title: H1_C_S4D2_2


title: Tum, K5,R1

value: Tumour

value: squamous cell carcinoma


title: B-Met-195-1T-R

value: lung


title: Mouse_heart_Genistein_4 [GEN4]


title: Tum, Ivl,R1


title: fusiform 20


title: H1_C_S4D1_1

value: C


title: H1_C_S3D2_1


title: B-Met-191-1T-R


title: fusiform 19


title: B-Met-163-1T-R

value: lymph node


title: Mouse_heart_Genistein_2 [GEN2]

value: Wild type


title: B-Met-003-1O-R


title: fusiform 15

value: Extrahepatic dilatations


title: B-Met-180-1T-R

value: metastasis from breast


title: H1_C_S2D3_3


title: B-Met-176-1T-R


title: Mouse_heart_Cytokine_6 [CYT6]

value: Cytokines


title: Mouse_heart_Cytokine_5 [CYT5]


title: fusiform 12


title: H1_C_S2D3_2


title: H1_C_S3D1_1


title: fusiform 11


title: H1_C_S3D2_2


title: B-Met-104-1T-R


title: Mouse_heart_Cytokine_4 [CYT4]


title: Mouse_heart_Genistein_3 [GEN3]


title: Tum, Ivl,R2


title: B-Met-160-1T-R

value: liver


title: Mouse_heart_Cytokine_3 [CYT3]


title: H1_C_S2D3_1


title: Mouse_heart_Genistein_1 [GEN1]


title: fusiform 6


title: H1_C_S2D2_2


title: H1_C_S3D1_2


title: fusiform 5


title: B-Met-158L-1T-R


title: fusiform 18


title: B-Met-155-1T-R


title: H1_C_S2D2_1


title: Mouse_heart_Cytokine_1 [CYT1]


title: Cystic 20


title: B-Met-150-1T-R

value: spine


title: H1_C_S2D1_2


title: H1_C_S2D1_1


title: Cystic 19


title: Mouse_heart_Cntrol_5 [CON5]

value: Control


title: H1_C_S1D3_2


title: Mouse_heart_Cntrol_6 [CON6]


title: B-Met-144-1T-R

value: pleura


title: Cystic 18


title: Mouse_heart_Cntrol_4 [CON4]


title: B-Met-139-1T-R


title: Cystic 17


title: Mouse_heart_Cytokine_2 [CYT2]


title: fusiform 9


title: B-Met-138-1T-R


title: H1_C_S1D3_1


title: H1_C_S1D2_2


title: Cystic 16


title: Mouse_heart_Cntrol_2 [CON2]


title: H1_C_S1D2_1


title: B-Met-137-1T-R

value: soft tissue


title: Cystic 14


title: Mouse_heart_Cntrol_3 [CON3]


title: B-Met-136-1T-R

value: cutaneous


title: H1_B_S5D7_2

value: B


title: Mouse_heart_Cntrol_1 [CON1]

value: BALB/c mouse


title: B-Met-132-1T-R


title: oeSir3_HA_fig5_Input_12_doublings_DEX

city: Montpellier

first: Marta

last: Radman-Livaja

address: 1919 route de Mende

department: IGMM

country: France

institute: CNRS

description:
Input from Sir3-HA ChIP timecourse of exit from starvation in a galactose inducible Sir3 overexpression strain
sonication followed by DNA extraction before ChIP
12 doublings after release from starvation into dextrose

data_processing:
Illumina OLB-1.8.0/CASAVA_v1.7.0 were used for base calling
time points  were separated by barcode and the 5bp barcode was removed from the read sequence
reads were mapped to the yeast S288C genome using BLAT
Paired end read count distribution in 10bp windows was determined separately for Watson (marked as F in the processed data files) and Crick (marked as R in the processed data files) strands
the genome average read count value was calculated and the data were normalized to one and the F and R counts were averaged for each bp. ChIP reads were then normalized to their corresponding input.
Assembly: Saccer1
Supplementary files format and content: tab-delimited text files of input normalized read density in 10bp windows for indicated time points. R indicated repetitive regions.

organism: Saccharomyces cerevisiae

source_name: yeast derived from W303 with the a GAL1-Sir3-3xHA cassette in a Sir3D background. (the strain name is THC70)

growth_protocol: Cells were grown in YPD or YPGal (for over expression Sir3 (oeSir3) cells) for 48hrs at 30°C till saturation and growth arrest. In the tag switch experiment, estradiol was added for 16hrs to induce the HA to T7 tag switch. Cells were then released into fresh media (for oeSir3 cells the estradiol step was skipped and cells were kept in starvation for 72hrs) and aliquots were fixed with formaldehyde at indicated times for several cell generations.

extract_protocol:
Cells were washed in water, cell walls were broken with bead beating and spheroplasts were sonicated. Anti-HA, anti-T7 or anti-TAP ChIPs were performed as indicated.
ChIP and input DNA samples, were treated with RNAse A, blunt-ended, A-tailed, and ligated (Epicentre) to Illumina genomic PE adaptors with custom 5bp inline barcodes (first 5bp in raw data read), and PCR amplified and size selected by gel purification.
Illumina multiplex ChIP-seq with custom in line 5bp barcodes

treatment_protocol: Cells were fixed in 1% formaldehyde.

tag: cell cycle

value: exit from starvation after galactose depletion and release into galactose, raffinose or dextrose

value: yeast


title: H1_B_S5D7_1


title: Cystic 12

tag: tissue


title: Cystic 11


title: Cystic 13


title: B-Met-123-1T-R

value: lung


title: oeSir3_HA_fig5_Input_2_doublings_DEX

description:
Input from Sir3-HA ChIP timecourse of exit from starvation in a galactose inducible Sir3 overexpression strain
sonication followed by DNA extraction before ChIP
second doubling after release from starvation into dextrose


title: H1_B_S5D3_4

description:
cellname.smartseq3.tsv
genename.smartseq3.tsv
readcount.smartseq3.mtx

tag: batch


title: B-Met-128-1T-R


title: Cystic 10


title: Cystic 9


title: B-Met-113-1T-R


title: oeSir3_HA_fig5_Input_12_doublings_RAFF

description:
Input from Sir3-HA ChIP timecourse of exit from starvation in a galactose inducible Sir3 overexpression strain
sonication followed by DNA extraction before ChIP
12 doublings after release from starvation into raffinose


title: H1_B_S5D3_2

tag: cell line


title: H1_B_S5D3_1


title: B-Met-110-1T-R


title: B-Met-117-1T-R


title: oeSir3_HA_fig5_Input_2_doublings_RAFF

description:
Input from Sir3-HA ChIP timecourse of exit from starvation in a galactose inducible Sir3 overexpression strain
sonication followed by DNA extraction before ChIP
second doubling after release from starvation into raffinose

tag: cell type


title: Cystic 8


title: Cystic 7


title: H1_B_S5D1_4


title: oeSir3_HA_fig5_Input_2_doublings_GAL

description:
Input from Sir3-HA ChIP timecourse of exit from starvation in a galactose inducible Sir3 overexpression strain
sonication followed by DNA extraction before ChIP
second doubling after release from starvation into galactose


title: oeSir3_HA_fig5_Input_1hr_after_release_DEX

description:
Input from Sir3-HA ChIP timecourse of exit from starvation in a galactose inducible Sir3 overexpression strain
sonication followed by DNA extraction before ChIP
1h after release from starvation into dextrose


title: H1_B_S5D3_3


title: B-Met-108-1T-R


title: H1_B_S5D1_3


title: Cystic 5


title: oeSir3_HA_fig5_Input_48hrs_starvation_GAL

description:
Input from Sir3-HA ChIP timecourse of exit from starvation in a galactose inducible Sir3 overexpression strain
sonication followed by DNA extraction before ChIP
48h incubation starvation cells after growth in galactose


title: Cystic 3


title: B-Met-076-1T-R


title: B-Met-086-1T-R


title: H1_B_S5D1_2


title: oeSir3_HA_fig5_Input_1hr_after_release_GAL

description:
Input from Sir3-HA ChIP timecourse of exit from starvation in a galactose inducible Sir3 overexpression strain
sonication followed by DNA extraction before ChIP
1h after release from starvation into galactose


title: Cystic 4


title: oeSir3_HA_fig5_HA-ChIP_12_doublings_DEX

description:
Sir3-HA ChIP timecourse of exit from starvation in a galactose inducible Sir3 overexpression strain
sonication followed by anti-HA ChIP
12 doublings after release from starvation into dextrose


title: H1_B_S4D4_2


title: B-Met-055-1T-R


title: Cystic 1


title: Cystic 2


title: H1_B_S4D4_1


title: B-Met-052-1T-R


title: oeSir3_HA_fig5_HA-ChIP_1hr_after_release_DEX

description:
Sir3-HA ChIP timecourse of exit from starvation in a galactose inducible Sir3 overexpression strain
sonication followed by anti-HA ChIP
1h after release from starvation into dextrose


title: B-Met-053-1T-R


title: oeSir3_HA_fig5_HA-ChIP_12_doublings_RAFF

description:
Sir3-HA ChIP timecourse of exit from starvation in a galactose inducible Sir3 overexpression strain
sonication followed by anti-HA ChIP
12 doublings after release from starvation into raffinose


title: H1_B_S4D3_2


title: H1_B_S4D3_1


title: RPE-1, siPPP6C, siSETDB1, 2

city: Oxford

first: Emilia

last: Dimitrova

address: South Parks Road

department: Biochemistry

institute: University of Oxford

description: siPPP6CsiSETDB1.vs.siControl.TotalRNAseq_DESeq2.csv

data_processing:
Reads that aligned to the hg19 rDNA genomic sequences were first identified using Bowtie2 with ‘-very-fast’, ‘-no-mixed’ and ‘-no-discordant’ options) and discarded. Unmapped reads were then aligned to the hg19 genome using STAR. To improve mapping of intronic sequences, reads that failed to map using STAR were aligned using Bowtie2 with ‘-sensitive-local’, ‘-no-mixed’ and ‘-no-discordant’ options. Uniquely aligned reads from the last two steps were combined for further analysis and PCR duplicates were removed using Sambamba.
Read counts from biological triplicates were determined and samples were downsampled to the same read depth using custom scripts utilising SAMTools.
Differential analysis was performed using a custom R script adapting DESeq2 (Love et al., 2014). For a change to be called significant, we applied a threshold of p-adj < 0.05 and fold change > 1.5.
Assembly: hg19
Supplementary files format and content: Stranded bigWig files were generated using genomeCoverageBed from BEDTools
Supplementary files format and content: DESeq2 results tables for differential gene expression analysis containing read-count normalised read counts, raw and shrunk log2-fold changes (LFC), and statistical significance levels for hg19 refGene genes.

growth_protocol: HeLa cells were grown in DMEM + 10% (v/v) FBS, and hTERT-RPE-1 cells were grown in DMEM/F12 HAM + 10% (v/v) FBS. Cells cultured at 37 degrees, 5% CO2 in a humidifed cell culture incubator.

extract_protocol:
Cells were washed in PBS, and RNA extracted using the Qiagen Rneasy minikit, following the manufacturer's instructions.
RNA was depleted for ribosomal RNA by the Oxford genomics centre, and library preparation performed using their standard protocols (https://www.well.ox.ac.uk/ogc/guides/)

treatment_protocol: Where siRNA treatment was required, cells were transfected with 4 siRNAs per gene (SMARTPool, Dharmacon). Briefly, 3 µl tranfection reagent (Oligofectamine (HeLa), or Mirus-TX2 (hTERT-RPE-1)) was added to 100 µl OptiMem medium. Following 5 min incubation at room temperature, 60 pM siRNA SMARTPool was added, the tube gently inverted, and incubated at room temperature for 30 mins. Following incubation, siRNA mixes were added drop-wise to cells in a 6-well plate, and incubated for 96 h at 37 degrees, 5% CO2.

tag: genotype

value: SETDB1 siRNA; PPP6C siRNA


title: oeSir3_HA_fig5_HA-ChIP_12_doublings_GAL

description:
Sir3-HA ChIP timecourse of exit from starvation in a galactose inducible Sir3 overexpression strain
sonication followed by anti-HA ChIP
12 doublings after release from starvation into galactose


title: H1_B_S5D1_1


title: B-Met-049-1T-R


title: oeSir3_HA_fig5_HA-ChIP_2_doublings_RAFF

description:
Sir3-HA ChIP timecourse of exit from starvation in a galactose inducible Sir3 overexpression strain
sonication followed by anti-HA ChIP
second doubling after release from starvation into raffinose


title: oeSir3_HA_fig5_Input_12_doublings_GAL

description:
Input from Sir3-HA ChIP timecourse of exit from starvation in a galactose inducible Sir3 overexpression strain
sonication followed by DNA extraction before ChIP
12 doublings after release from starvation into galactose


title: oeSir3_HA_fig5_HA-ChIP_2_doublings_DEX

description:
Sir3-HA ChIP timecourse of exit from starvation in a galactose inducible Sir3 overexpression strain
sonication followed by anti-HA ChIP
second doubling after release from starvation into dextrose


title: B-Met-026-1T-R


title: RPE-1, siSETDB1, 3

description: siSETDB1.vs.siControl.TotalRNAseq_DESeq2.csv

value: SETDB1 siRNA


title: oeSir3_HA_fig5_HA-ChIP_2_doublings_GAL

description:
Sir3-HA ChIP timecourse of exit from starvation in a galactose inducible Sir3 overexpression strain
sonication followed by anti-HA ChIP
second doubling after release from starvation into galactose


title: RPE-1, siSETDB1, 2


title: RPE-1, siPPP6C, siSETDB1, 3


title: B-Met-025-1T-R

value: lymph node


title: B-Met-088-1T-R


title: H1_B_S4D1_2

description:
cellname.smartseq3.tsv
genename.smartseq3.tsv
readcount.smartseq3.mtx


title: RPE-1, siSETDB1, 1


title: oeSir3_HA_fig5_HA-ChIP_1hr_after_release_GAL

description:
Sir3-HA ChIP timecourse of exit from starvation in a galactose inducible Sir3 overexpression strain
sonication followed by anti-HA ChIP
1h after release from starvation into galactose


title: B-Met-008-1T-R

value: brain


title: H1_B_S4D1_1


title: oeSir3_HA_fig5_HA-ChIP_48hrs_starvation_GAL

description:
Sir3-HA ChIP timecourse of exit from starvation in a galactose inducible Sir3 overexpression strain
sonication followed by anti-HA ChIP
48h incubation starvation cells after growth in galactose


title: RPE-1, siPPP6C, 3

description: siPPP6C.vs.siControl.TotalRNAseq_DESeq2.csv

value: PPP6C siRNA


title: RPE-1, siPPP6C, siSETDB1, 1


title: H1_B_S3D2_2


title: Sir3_HAtoT7_switch_figS6_Input_12_doublings

description:
Input from Sir3 tag switch timecourse replicate
sonication followed by DNA extraction before ChIP
12 doublings after release from starvation

source_name: yeast derived from S288C with the loxP-3xHA-loxpP-3xT7 tags switch cassette fused to the Sir3 C-terminus. The strain has the gene for CreEBD78 recombinase integrated into the HIS3 locus.

value: exit from starvation after nutrient depletion


title: B-Met-003-1T-R

value: metastasis from breast


title: H1_B_S4D2_3


title: B-Met-031-1T-R


title: H1_B_S3D2_1


title: Sir3_HAtoT7_switch_figS6_Input_4_doublings

description:
Input from Sir3 tag switch timecourse replicate
sonication followed by DNA extraction before ChIP
4 doublings after release from starvation


title: H1_B_S4D2_2


title: RPE-1, siPPP6C, 2


title: H1_B_S4D2_1


title: H1_B_S3D1_2


title: RPE-1, siControl, 3

value: siRNA Control


title: Sir3_HAtoT7_switch_figS6_Input_3_doublings

description:
Input from Sir3 tag switch timecourse replicate
sonication followed by DNA extraction before ChIP
3 doublings after release from starvation


title: RAW264.7 cells,RANKL+TSH2h

city: Jinan

first: wen

last: Zhang

address: 324 Jing 5 road

institute: Shandong Provincial Hospital

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 GrCM38/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 files include RPKM values for each Sample

growth_protocol: RAW264.7 cells were maintained in aMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: After induced by RANKL for 3 days to generate OCs, OCs were stimulated with 10 mU/mL TSH for 2 h or 24 h

value: RAW264.7 cells

value: WT

value: RANKL+TSH 2h


title: RPE-1, siPPP6C, 1


title: RAW264.7 cells,RANKL+TSH24h

value: RANKL+TSH 24h


title: H1_B_S3D1_1

last: Xu

growth_protocol: hESC and hiPSC lines were maintained cultured on surfaces coated with Matrigel (Corning, Cat#354230) and cultured in mTeSR1 media (Stem Cell Technologies, Cat#85850) at 37°C. The cells were passaged using Versene solution (ThermoFisher Scientific, Cat#15040066), and routine screenings for Mycoplasma contamination were performed employing the MycoBlue Mycoplasma Detector Kit (Vazyme, Cat#D101).     For differentiation experiments, hESCs and hiPSCs were dissociated to single-cell suspensions using TrypLE™ Express Enzyme (ThermoFisher Scientific, Cat#12605) and plated at a density of 0.53 x 106 cells/cm2 on surface coated with Matrigel diluted 1:30 (Corning, Cat#356231) in mTeSR1 media. This medium was supplemented with 10 μM Y-27632 (Selleckchem, Cat#S1049) to enhance cell survival. Differentiation was initiated within 24 hours post-seeding. Prior to introducing differentiation media, cells were washed with 1× DPBS without Mg2+ and Ca2+ (Meilunbio, Cat#MA0015). The cells were cultured at 37 °C with 5% (vol/vol) CO2.     The differentiation of stem cells into pancreatic lineages was conducted following modified versions of the protocols established by Rezania et al. and Hogrebe et al., herein referred to as protocols A and B, respectively. Additionally, a novel differentiation protocol developed within this study is referred to as protocol C.

value: B


title: RAW264.7 cells,RANKL

value: RANKL


title: Sir3_HAtoT7_switch_figS6_Input_1_doubling

description:
Input from Sir3 tag switch timecourse replicate
sonication followed by DNA extraction before ChIP
first doubling after release from starvation


title: H1_B_S2D2_2


title: RPE-1, siControl, 1


title: Tshr −/− mice 3

source_name: bone marrow CD11b+cells

growth_protocol: The bone marrow cells were isolated from tibias of 12-weeks old Tshr+/+ and Tshr −/− mice. CD11b + cells

treatment_protocol: were purified by EasySep™ Mouse CD11b Positive Selection Kit

value: bone marrow CD11b+cells

value: Tshr knockdown

value: osteoclast differentiation


title: RPE-1, siControl, 2


title: Sir3_HAtoT7_switch_figS6_Input_30min_after_release

description:
Input from Sir3 tag switch timecourse replicate
sonication followed by DNA extraction before ChIP
30min after release from starvation

value: yeast


title: HeLa, PPP6CKO, rep3

source_name: HeLa

value: HeLa

value: PPP6C KO


title: B-Met-001-1T-R

value: cutaneous


title: H1_B_S2D2_1


title: H1_B_S2D1_2


title: Tshr −/− mice 2


title: Tshr −/− mice 1


title: Sir3_HAtoT7_switch_figS6_Input_before_switch

description:
Input from Sir3 tag switch timecourse replicate
sonication followed by DNA extraction before ChIP
48h incubation starvation cells


title: Sir3_HAtoT7_switch_figS6_Input_0min_after_release

description:
Input from Sir3 tag switch timecourse replicate
sonication followed by DNA extraction before ChIP
0min after release from starvation


title: H1_B_S2D1_1


title: Sir3_HAtoT7_switch_figS6_Input_midlog

description:
Input from Sir3 tag switch timecourse replicate
sonication followed by DNA extraction before ChIP
cells in log phase before starvation


title: Tshr+/+ mice 3


title: HeLa, PPP6CKO, rep1


title: Tshr+/+ mice 2


title: HeLa, PPP6CKO, rep2


title: Sir3_HAtoT7_switch_figS6_Input_2_doublings

description:
Input from Sir3 tag switch timecourse replicate
sonication followed by DNA extraction before ChIP
second doubling after release from starvation


title: HeLa, SETDB1KO, siPPP6C, rep2

description: SETDB1KO_siPPP6C.vs.WT.TotalRNAseq_DESeq2.csv

value: SETDB1 KO; PPP6C siRNA


title: Sir3_HAtoT7_switch_figS6_T7-ChIP_12_doublings

description:
Sir3-T7 ChIP timecourse of exit from starvation replicate
sonication followed by anti-T7 ChIP
12 doublings after release from starvation

value: exit from starvation after nutrient depletion


title: H1_B_S1D4_1


title: Sir3_HAtoT7_switch_figS6_T7-ChIP_4_doublings

description:
Sir3-T7 ChIP timecourse of exit from starvation replicate
sonication followed by anti-T7 ChIP
4 doublings after release from starvation


title: H1_B_S1D4_2


title: Tshr+/+ mice 1