title: Bio_Replicate2_ADT

city: Singapore

first: Tongjin

last: WU

address: MD6, 14 Medical Drive

department: Institute for Health Innovation and Technology

institute: National University of Singapore

description:
Surface protein marker and CFSE capture-derived cDNA
Surface protein marker and CFSE staining antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains surface protein-targeted antibody derived tag reads

data_processing:
Raw mRNA-derived cDNA FASTQ data was processed for cell barcodes calling and UMI counting of mRNA library using Cell Ranger v4.0 (10x Genomics) with default parameters. The generated cell barcodes were used to find individual cell barcode-matched expression profile of sample hashtags, surface proteins and CFSE capture using CITE-seq-Count with a Hamming distance of 1 for both cell barcodes calling and UMI counting.
Further processing was done with Seurat package (v4.3.0). Dead cells were removed by filtering out cells expressing > 10% mitochondrial transcript counts, gene features > 1200 but < 8000, and total gene counts > 1000 but < 40000.
Assembly: hg38
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz; CITE-seq-Count output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz.

source_name: PBMC

growth_protocol: Cryopreserved human PBMCs were recovered overnight before NK cells enrichment using EasySep™ Human NK Cell Enrichment Kit (STEMCELL Technologies, 19055) and expanded for 9-10 days using ImmunoCult™ NK Cell Expansion Kit (STEMCELL Technologies, 100-0711).

extract_protocol:
Human primary NK cells were enriched from PBMCs using EasySep™ Human NK Cell Enrichment Kit (STEMCELL Technologies, 19055) and expanded for 9-10 days using ImmunoCult™ NK Cell Expansion Kit (STEMCELL Technologies, 100-0711). For sequencing, expanded NK cells were modified with anti-CFSE capture antibody before co-cultured with or without CFSE-stained K562 at a ratio of 3:1. After 4 hours, cells were collected and pre-blocked by Fc-blocking reagent (Biolegend, 422301). Samples were stained with anti-FITC-PE (Southern Biotech, cat no: 6400-09) while concurrently barcoded with β2M-targeting hashtag before pooled and stained with a cocktail of TotalSeq-A antibodies targeting PE, CD3, CD56, CD16, CD57, CCR7, CD45RA, CD107a, CD69, NKG2D, NKp44, and PD-1. Cells were washed with cold PBS containing 2% FBS for 4 times and re-suspended in PBS before run on the Chromium Controller (10x Genomics) (with duplicate lanes).
The 10x Genomics single cell 3' reagent kits (v3.1 Chemistry) was used to generate single-cell barcoded sequencing libraries following reverse transcription. The recovered material includes complementary DNA (cDNA) of mRNA and protein libraries representative of CFSE capture, surface markers and sample-indicating hashtags. After sample cleanup using silane beads, 35 µl of the eluted DNA sample was pre-amplified following the standard protocol with the addition of two additional primers for surface protein and hashtag and cycled as follows: as follows: 98oC 3 min, 12 cycles of: 98oC 15 s, 63oC 20 s, and 72oC 1 min; Then an extension step of 1 min at 72oC. The 1st-round PCR product was cleaned up and followed by a double size selection step using SPRIselect reagent (Beckman Coulter) to separate protein library from cDNA library. The amplified cDNA product was subjected to final gene expression library construction according to the instructions with the kit. Part of the protein library product (5 µl) was used for the preparation of sequencing libraries corresponding to surface marker and cytokine while additional part (5 µl) was used for the construction of sequencing library of sample hashtags using KAPA HiFi Master Mix (Roche). The 2nd-round P7/read 2 PCR primers used for protein library preparation (the P5/read 1 primer is similar to what was used in cDNA library). The size range and concentration of final library constructions was verified by Agilent 2100 Bioanalyzer. The libraries were pooled and sequenced in Illumina HiSeq platform.
OTHER: PAINTKiller-seq

treatment_protocol: Expanded NK cells were modified with anti-CFSE capture antibody before co-cultured with or without CFSE-stained K562 at a ratio of 3:1 for 4 hours in 12-well cell culture plate.

value: PBMC

value: NK cells


title: Bio_Replicate1_mRNA

status: Public on Jun 14 2023

type: SRA

country: Singapore

description:
mRNA-derived cDNA
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: tissue

tag: cell type


title: NSG_8

city: RTP

first: Xiaojiang

last: Xu

state: North Carolina

address: 111 T. W. Alexander Dr.,

country: USA

institute: NIEHS

data_processing:
RNA-SEQ reads (30-6M per sample) were aligned to the UCSC mm10 reference genome using STAR
The quantification results from FeatureCounts were then analyzed with the Bioconductor package DESeq2, which fits a negative binomial distribution to estimate technical and biological variability.
Genome_build: mm10
Supplementary_files_format_and_content: excel table; log2 transformed and normalized abundance measurements by DESeq2

organism: Mus musculus

source_name: allografted CT26.WT tumors

extract_protocol:
Allografted CT26.WT tumors isolated from mice and total RNA isolated using Qiagen RNeasy mini kit.
The integrity of the total RNA was determined using a bioanalyzer (Agilent) and concentration were assessed by Qubit (ThermoFisher Scientific).  A TruSeq RNA kit (Illumina, San Diego, CA) was utilized to prepare the poly(A)-enriched RNA-seq libraries that were sequenced on the Illumina NextSeq 500 in a 75-base single-end mode according to the manufacturer’s protocol.

treatment_protocol: Allografted CT26.WT tumors isolated from mice fed with either a high methionine diet containing 0.86% methionine (0.86%) or a methionine restricted diet containing 0.172% methionine (0.172%).

tag: background

value: NSG mice

tag: gender

value: Male

value: mouse colon carcinoma cells

tag: timepoint

value: treated with diets for 3-4 weeks

tag: treatment

value: 0.86% high methionine  diet

tag: genotype

value: wild-type


title: Bio_Replicate1_ADT


title: Bio_Replicate1_HTO

description:
HTO-derived cDNA
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag (HTO) reads


title: Bio_Replicate2_mRNA


title: Bio_Replicate2_HTO


title: Input_H3K9me3_T1636_GS8

city: Boston

first: Ben

middle: S.

last: Wittner

state: MA

address: 149 13th Street

department: Center for Cancer Research

institute: Massachusetts General Hospital

library_source: genomic

data_processing:
ULI NChIP-seq and Cut and Run reads were first trimmed by trimgalore (v0.4.3) (https://github.com/FelixKrueger/TrimGalore).
Trimmed reads were mapped to the human genome using BWA men (Li and Durbin, 2009). Duplicated reads were marked by sambamba (Tarasov et al., 2015) and further removed using samtools (Li et al., 2009).
MACS2 (v2.0.10) (Zhang et al., 2008) was used to call the peaks and deepTools (Ramirez et al., 2016) were used to compute the ChIP-seq or Cut and Run signal.
Assembly: hg19 (human)
Supplementary files format and content: bigWig file giving the read coverage at each genomic location

molecule: genomic DNA

source_name: prostate epithelial cell

extract_protocol:
For ULI NChIP-seq, nuclei from different cell lines were isolated in Nuclear Isolation Buffer (Sigma) supplemented with 1% Triton-X 100, 1% Deoxycholate and 1X complete protease inhibitor. Chromatin was digested by MNase enzyme (NEB, 1:10 diluted) at 21°C for 7.5 min.
DNA from ULI NChIP or Cut and Run assay was used to prepare sequencing library using NEBNext Ultra II DNA Library Prep Kit (NEB, Cat#E7645L).

tag: antibody

tag: disease

value: cancer

tag: genome build

tag: patient donor

value: prostate epithelial cell


title: Input_H3K9me3_T1255_GS6


title: Input_H3K9me3_N900

value: normal


title: Input_H3K9me3_T1245_GS6


title: NSG_5

value: 0.172% methionine deficient diet


title: Input_H3K9me3_N1519


title: NSG_1


title: Liver, 5-months post engraftment, LK03C/REDHV, replicate 2, snRNA-seq

city: Westmead

first: Suzanne

last: Scott

state: NSW

address: 214 Hawkesbury Rd

country: Australia

institute: Children's Medical Research Institute

description:
Rod_ASV_3_2
LK03C/REDHV2

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
Assembly: Combined GRCh38, mm10, AAV reference
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

organism:
Homo sapiens
Mus musculus

source_name: Liver

extract_protocol:
To identify and characterize cell states associated with AAV transduction in human heptocytes, we employed a droplet-based (10x chromium) single nucleus transcriptomics approach. Hepatic nuclei were isolated and profiled from (a) human hepatocytes before engraftment, (b) liver samples from FRG mice engrafted with human hepatocytes, and (c) liver samples from FRG mice engrafted with human hepatocytes, treated with two AAV vectors (LLK03, REDH).
Libraries were prepared from single nucei.  Breifly, nuclei were isoalted from flash-frozen chunks of tissue, which were homogenized using a Kimble Dounce tissue grinder, followed by straining with a 40 μm cell strainers, two rounds of centrifugation at 500g.  Nuclei were stained with DAPI and proridium iodide, followed by FACS sorting to isolate PI-positive nuclei. Libraries were then prepared using a 10x Genomics Chromium Single Cell 3’v3 Reagent Kits were used according to manufacturer’s instructions.
snRNA-seq

value: Liver

value: Hepatocytes

value: 5-months post-engraftment, LK03C/REDHV

tag: time

value: 5-months post engraftment


title: ck (mutiple ovarian cells)

city: Guangzhou

first: Zhipeng

last: Sun

state: GuangDong

address: Wushan Distict

country: China

institute: South China Agricultural University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The scRNA-seq data were processed with the Cell Ranger Single Cell Software Suite (v6.1) (http://software.10xgenomics.com/single-cell/overview/welcome) for quality control, sample demultiplexing, barcode processing, and single-cell 3’ gene counting.
Supplementary files format and content: ell Ranger output files (barcodes.tsv, genes.tsv, matrix.mtx)

organism: Drosophila melanogaster

source_name: ovary

extract_protocol:
After dissection, we discarded S-FBS and added 1 mL of PBS to rinse ovaries in a 1.5-ml centrifuge tube, and allowed samples to settle for 5 min, and then rinsed them twice with PBS. Dissociation was carried out at room temperature in 700 μl of dissociation medium by adding 70 μl of 5% (w/v) trypsin (Invitrogen, cat. no. 27250-018) and 70 μl of 2.5% (w/v) collagenase (Invitrogen, cat. no. 17018029) to 560 μl of PBS, and incubated for 15 min with continuous shaking. After incubation, the ovarian cell suspension was pipette into a 40-μm mesh cell strainer, and filtered suspension into a 1.5-ml centrifuge tube containing 500 μl of S-FBS. Then, the empty tube and cell strainer were washed by 100 μl of S-FBS respectively to collect the remaining cells. The cell suspension was collected by centrifuging 5 min at 425 × g, 4°C, and discarded the S-FBS and resuspended the pellets in each tube with 200 μl of serum-free Schneider’s insect medium, after that we combined the suspensions into one tube.
Single-cell libraries were constructed using Chromium single-cell 3’ Library (v2) kit via End Repair, A-tailing, Adaptor Ligation, and PCR according to the manufacturer’s protocol. In brief, the cells of each group were mixed into one sample and adjusted to 1000 cell/μl. Then, the indexed sequencing libraries which contained the P5 and P7 primers were prepared using Chromium single-cell 3’ Reagent kit, and the barcoded sequencing libraries were quantified using a standard curve-based qPCR assay (KAPA Biosystems, USA) and Agilent Bioanalyzer 2100 (Agilent, Loveland, CO, USA).

value: ovary

value: mutiple ovarian cells

value: Wild Type

tag: age


title: Liver, 5-months post engraftment, LK03C/REDHV, replicate 1, snRNA-seq

description:
Rod_ASV_3_1
LK03C/REDHV1


title: Input_H3K9me3_N1245


title: Input_H3K9me3_T826_GS8


title: Input_H3K27me3_T1652_GS8


title: Input_H3K27me3_T1678_GS8


title: Input_H3K27me3_T1646_GS8


title: Input_H3K27me3_T1255_GS6


title: Input_H3K9me3_T1652_GS8


title: Input_H3K9me3_T1484_GS6


title: Input_H3K27me3_N1484


title: H3K9me3_T1678_GS8

value: H3K9me3 (Abcam, Cat#ab8898)


title: Input_H3K27me3_N1519


title: Input_H3K27me3_N1245


title: H3K9me3_T1245_GS6


title: H3K9me3_T1255_GS6


title: H3K9me3_T1652_GS8


title: H3K9me3_T1484_GS6


title: Input_H3K9me3_N1255


title: H3K9me3_N900


title: Input_H3K27me3_T900_GS6


title: H3K9me3_N1519


title: Input_H3K27me3_T826_GS8


title: H3K9me3_N1245


title: H3K9me3_N1255


title: H3K27me3_T1652_GS8

value: H3K27me3 (Active motif, Cat#39155)


title: H3K27me3_T826_GS8


title: H3K27me3_N1519


title: H3K27me3_T1678_GS8


title: H3K27me3_N1255


title: H3K9me3_T1636_GS8


title: H3K27me3_T1255_GS6


title: H3K27me3_T1646_GS8


title: H3K27me3_N1484


title: H3K27me3_T900_GS6


title: H3K9me3_T826_GS8


title: Input_H3K27me3_N1255


title: CR_IgG_vCap

data_processing:
ULI NChIP-seq and Cut and Run reads were first trimmed by trimgalore (v0.4.3) (https://github.com/FelixKrueger/TrimGalore).
Trimmed reads were mapped to the human genome using BWA men (Li and Durbin, 2009). Duplicated reads were marked by sambamba (Tarasov et al., 2015) and further removed using samtools (Li et al., 2009).
MACS2 (v2.0.10) (Zhang et al., 2008) was used to call the peaks and deepTools (Ramirez et al., 2016) were used to compute the ChIP-seq or Cut and Run signal.
Assembly: hg19 (human)
Supplementary files format and content: bigWig file giving the read coverage at each genomic location
Library strategy: CUT&RUN

source_name: vCap

value: IgG (CST, Cat#66362S)

tag: cell line

value: vCap


title: H3K27me3_N1245


title: CR_IgG_LNCap_rep2

source_name: LNCap

value: LNCap


title: CR_IgG_PC3


title: CR_IgG_LNCap_rep1


title: CR_IgG_HPrEC_rep3

source_name: HPrEC

value: HPrEC


title: CR_IgG_BPH-1_rep2


title: CR_IgG_LNCap

value: cancer


title: CR_H3K9me3_vCap

value: prostate epithelial cell


title: CR_IgG_22RV1


title: CR_H3K9me3_PC3


title: CR_IgG_BPH-1_rep1

value: normal


title: CR_H3K9me3_LNCap_rep2


title: CR_H3K9me3_LNCap_rep1


title: CR_H3K9me3_HPrEC_rep3


title: CR_H3K9me3_LNCap


title: CR_H3K9me3_BPH-1_rep2


title: CR_H3K9me3_BPH-1_rep1


title: CR_H3K9me3_22RV1


title: CR_H3K27me3_PC3


title: CR_H3K27me3_LNCap_rep2


title: CR_H3K27me3_vCap


title: 27D_tg_Ab_Hip

city: Catania

first: Sebastiano

last: Cavallaro

address: Via Paolo Gaifami,18

country: Italy

institute: IRIB-CNR

data_processing:
Sequencing data were generated using Torrent Suite Software version 5.4.0 with AmpliSeq RNA plugin (Thermo Fisher Scientific, Waltham, MA, USA) and normalized using reads per million mapped reads (RPM) method. Normalized transcripts were an-alyzed using Transcriptome Analysis Console Software (version 4.0.2), certified for AmpliSeq analysis (Thermo Fisher Scientific, Waltham, MA, USA).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
Supplementary files format and content: Tar archive with log2 normalized counts for all samples available on the series page.

source_name: Hippocampus

growth_protocol: Animals: Heterozygous Tg2576 mice of both genders (Tg-AD), expressing the human Am-yloid Precursor Protein (APP) with the Swedish mutation KM670/671NL which causes an increase in Aβ production and their wild-type (Wt) littermates were used at 6 months of age (n = 8-10 per group) in the immunization regimen. Genotyping was carried out to confirm the presence of human mutant APP DNA sequence by PCR. The N-terminal tau 12A12 monoclonal antibody (26-36aa) was produced and purified from hybridoma supernatants according to standard procedures.

extract_protocol:
Tissue collection: Two days after the last injection of 12A12mAb, animals from three experi-mental groups (wild-type, naive Tg-AD, Tg-AD+mAb) were sacrificed by cervical dis-location, perfused transcardially with ice-cold phosphate buffered saline (PBS), brains and eyes were collected, hippocampi and retinas were dissected, immediately frozen on dry-ice and, then, stored at -80°C until use.   Crude synaptosomal preparations were obtained from mice of three experimental groups (wild-type, naive Tg-AD, Tg-AD+mAb).
High-quality RNA was extracted from hippocampi and retinas of wild-type, naive Tg-AD, Tg-AD+mAb mice (n≥4 biological replicates per experimental group) using Trizol reagent (Sigma-Aldrich, United States) according to the manufacturer's protocol. The quantity and quality of the extracted RNA were checked by using the Agilent 4200 Tape Station using the Agilent High Sensitivity RNA Screen Tape (Agilent Technologies, Santa Clara, CA, USA).
Libraries were prepared using Ion AmpliSeq Transcriptome Mouse Gene Expression Panel, Chef-Ready Kit on Ion Chef (Thermo Fisher Scientific, Waltham, MA, USA) ac-cording to the manufacturer’s instructions. Briefly, 10 ng of total RNA was reverse transcribed using SuperScript VILO cDNA Synthesis Kit (Thermo Fisher Scientific, Waltham, MA, USA) before library preparation on the Ion Chef™ instrument (Thermo Fisher Scientific, Waltham, MA, USA). The resulting cDNA was amplified to prepare barcoded libraries using the Ion Code PCR Plate and the Ion AmpliSeq Transcriptome Mouse Gene Expression Core Panel and Chef-Ready Kit according to the manufacturer’s instructions. Barcoded libraries were quantified using the Ion Library TaqManTM Quantitation Kit (Thermo Fisher Scientific, Waltham, MA, USA) and were combined to a final concentration of 100 pM and used to prepare template-positive Ion Sphere Particles to load on Ion 540 Chips using the Ion 540 Kit-Chef. Sequencing was performed on an Ion S5 sequencer with Torrent Suite Software v6 (Thermo Fisher Scientific, Waltham, MA, USA).

treatment_protocol: The mice were randomized into: (1) wild-type mice treated with saline vehicle; (2) age-matched Tg2576 mice treated with saline vehicle; (3) age-matched Tg2576 mice treated with 12A12mAb (30ug/dose). Animals were infused over 14 days with two weekly injections administered on two alternate days to the lateral vein of the tail. The dose and route of immunization were based on previously-published studies by our and other independent research groups using Tg2576 as AD transgenic mouse model.

value: Hippocampus

value: Tg-AD+mAb

tag: Sex

value: M

value: 6 months


title: 3_D_tg_Ab_Hip

value: F


title: 15S_Tg_Ab_hip


title: 8_S_Tg_Ab_Hip


title: 17S_tg_Ab_hip


title: 25S_tg_Hip

value: Heterozygous Tg2576


title: 25D_Tg_Hip


title: CR_H3K27me3_BPH-1_rep2


title: 3_S_tg_Ab_hip


title: CR_H3K27me3_LNCap


title: CR_H3K27me3_LNCap_rep1


title: 24S_Tg_Hip


title: CR_H3K27me3_22RV1


title: BPH_1_R_H2

data_processing:
Illumina CASAVA version 1.8 were used to do the basecalling.
Reads were trimmed to remove the adapter sequences and low quality bases. For single cell RNA-seq, the cleaned reads were aligned to the human hg19 reference using Tophat (v2.0.12) with default settings and the --no-novel-juncs argument (Trapnell et al., 2009).
PCR duplicates were removed using samtools (v1.3.1)(Li et al., 2009), gene counts were computed using HTseq (v0.6.1) (Anders et al., 2015)
Assembly: hg19
Supplementary files format and content: counts.csv is a comma-separated-values file with rows corresponding to a gene, columns corresponding to a sample, and values giving the number of reads aligned to the gene.

molecule: polyA RNA

source_name: prostate

extract_protocol:
Single cells were picked or sorted into lysate buffer and RNA was released.
single cell cDNA was amplified using SMART-seq2 protocol

value: prostate

tag: patient donor/cell_line


title: scATAC_Day_8_human_stem_cell_model_exp48

city: Seattle

first: Nobuhiko

last: Hamazaki

state: Washington

address: Foege Building S-210 3720 15th Ave NE

department: Genome Sciences

institute: University of Washington

description:
single cell 10x multiome (ATAC)
D8_model_atac_fragments.tsv.gz

library_source: genomic single cell

data_processing:
Raw reads were analyzed using the CellRangerARC pipeline to generate ATAC and RNA fastq files for each sample, and then to align genomic and transcriptomic reads. Matrices were then read into Seurat and Signac using the Read10X_h5 command. For ATAC-seq data, peaks from standard chromosomes were used and peaks were additionally called using macs2 to add an additional Signac assay. Cells with >500 RNA UMI counts, <20% mitochondrial reads, >500 ATAC reads, TSS enrichment >1 and were called as singlets using scDblFinder were retained for downstream analysis. For UMAP projections, SCTransform was used for RNA counts with percent mitochondrial counts and cell cycle scores regressed. PCA and LSI graphs were used to generate a weighted nearest neighbor (wnn) embedding which accounts for both modalities. chromVAR was run to calculate motif accessibility score on the peaks assay.
Assembly: hg38
Supplementary files format and content: Subgroups of RNA/ATAC data were gathered and processed with cellrangerARC (Named "RNA" and "ATAC").
Supplementary files format and content: "peaks" matrix are the output of the macs2 peaks calling of the ATAC data

growth_protocol: All work presented here was approved by the Human Stem Cell Bank Steering Committee and adheres to the regulations of the UK Code of Practice for the Use of Human Stem Cell Lines.  Shef6 human ESCs were cultured on Matrigel-coated plates in mTESR medium (05825, STEMCELL Technologies) at 37°C, 20% O2, 5% CO2. Plates were coated with 1.6% growth-factor reduced Matrigel (356230, BD Biosciences) dissolved in DMEM/F12 (21331-020, Life Technologies) for 1 hour at at 37°C. hESCs were passaged with TrypLE (12604013, ThermoFisher Scientific). For the first 24 hours after passaging, 10 µM ROCK inhibitor Y-27632 (72304, STEMCELL Technologies) was added. Medium was changed every 24 hours. Cells were routinely tested for mycoplasma contamination by PCR (6601, Takara Bio). To convert primed hESCs to RSeT or PXGL culture conditions, cells were passaged to mitomycin-C inactivated CF-1 MEFs (3x103 cells/cm2; GSC-6101G, Amsbio) in media consisting of DMEM/F12 with 20% Knockout Serum Replacement (10828010, ThermoFisher Scientific), 100µM β-mercaptoethanol (31350-010, Thermo Fisher Scientific), 1x GlutaMAX (35050061, Thermo Fisher Scientific), 1x non-essential amino acids, 1x penicillin-streptomycin and 10ng/ml FGF2 (Department of Biochemistry, University of Cambridge) and 10µM ROCK inhibitor Y-27632 (72304, STEMCELL Technologies). For RSeT cells media was switched to RSeT media after 24 hours (05978, STEMCELL Technologies). Cells were maintained in RSeT and passaged as above every 4-5 days. For PXGL cells, conversion was performed as previously described (Bredenkamp, N. et al. 2019). Briefly, cells were cultured in 5% O2, 7% CO2 and media was switched to chemical resetting media 1 (cRM-1) consisting of N2B27 media supplemented with 1µM PD0325901 (University of Cambridge, Stem Cell Institute), 10ng/mL human recombinant LIF (300-05, PeproTech), and 1mM Valproic Acid. N2B27 contains 1:1 DMEM/F12 and Neurobasal A (10888-0222, Thermo Fisher Scientific) supplemented with 0.5x B27 (10889-038, Thermo Fisher Scientific), 0.5x N2 (made in house), 100µM β-mercaptoethanol, 1x GlutaMAX and 1x penicillin-streptomycin. cRM-1 media was changed every 48h for 4 days, after which media was changed to PXGL. PXGL media consists of N2B27 supplemented with 1µM PD0325901, 10ng/mL human recombinant LIF, 2µM Gö6983 (2285, Tocris) and 2µM XAV939 (X3004, Merck). PXGL cells were passaged every 4-6 days using TrypLE (12604013, Thermo Fisher Scientific) for 3 min. 10µM ROCK inhibitor Y-27632 and 1µL/cm2 Geltrex (A1413201, Thermo Fisher Scientific) were added at passage for 24 hours. For yolk sac-like cell or trophoblast differentiation, RSeT cells were passaged onto matrigel coated IBIDI chamber slides. 24 hours later, media was switched to ‘ACL’ (100ng/ml Activin-A, Qk001, QKINE, 3mM CHIR99021, 72052, STEMCELL Technologies, and 10ng/ml human LIF) for hypoblast induction or ‘PA’ (1mM PD0325901 and 1mM A83-01, 72022, STEMCELL Technologies) with or without 500nM lysophosphatidic acid – LPA (3854, Tocris).

extract_protocol:
To collect post-implantation embryo models for single cell sequencing, correctly organized embryoids at day 4, 6 and 8 were picked visually and washed through PBS twice in a 4-well dish before transfer to TrypLE. Samples were agitated by pipetting every 5 minutes for 10-20 minutes until dissociated. Enzymatic activity was inactivated through addition of 20% FBS in PBS at 2x volume. Cells were collected in a falcon tube, pelleted, and resuspended in freeze buffer consisting of 50 mM Tris at pH 8.0 (15-567-027, Fisher Scientific), 25% glycerol (G5516, Sigma-Aldrich), 5 mM Mg(OAc)2 (63052, Sigma-Aldrich), 0.1mM EDTA (15575020, ThermoFisher Scientific), 5mM DTT (R0861, ThermoFisher Scientific), 1x protease inhibitor cocktail (P8340, Sigma-Aldrich), 1:2500 dilution of superasin (AM2694, Invitrogen). For cell lines, 10,000 cells were counted, pelleted, resuspended in the freeze media above, snapped frozen in liquid nitrogen then stored at -80*C. For nuclei isolation and library construction, low input nuclei isolation protocol from 10x Genomics was performed. Briefly, frozen cell pellets were thawed in a 37°C water bath for 30 seconds, centrifuged (500g for 5 minutes at 4°C) to pellet the cells then the supernatant were aspirated. The cell pellets were washed with 200 ul 1x PBS with 0.04% BSA twice, centrifuged and aspirating the supernatant in between washes. Then, chilled lysis buffer (45 ul per sample) was added to the washed cell pellet and placed on ice for 3 minutes, then wash buffer (50 ul per sample) was added.
Washed isolated nuclei were resuspended in a diluted nuclei buffer. In this study, the isolated nuclei were resuspended in 5 ul of diluted nuclei buffer and were directly added to the transposition reaction. All the steps proceeding, 10x Genomics’ Single Cell Multiome ATAC and Gene expression protocol were followed to manufacturer’s specifications and guidelines.
The final libraries were loaded on the NextSeq 2000 using P2 100 cycle kit at 650 pM loading concentration with paired end sequencing following the recommended sequencing reads from 10x Genomics (28/10/10/90 cycles for gene expression libraries and 50/8/24/49 cycles for ATAC libraries).

treatment_protocol: To generate the three-dimensional stem cell-derived model of the post-implantation embryo, RSeT cells between 2 and 6 passages post-conversion to RSeT media were passaged as normal, and the following day (Day -3) the media for extraembryonic-like cells (induced GATA6, induced GATA6-SOX17 or induced GATA3-AP2g) was changed to N2B27 with 5% Knockout Serum Replacement and 1µg/mL DOX. This media was refreshed every 24 hours for 3 days. On day 0 (the day of aggregation), an Aggrewell dish (34415, STEMCELL Technologies) was prepared by pre-coating with anti-adherance solution (07010, STEMCELL Technologies) and centrifuging at 2000g for 5 minutes. Wells were washed twice with PBS prior to the addition of experiment media. This media consists of N2B27 with 5% knockout serum replacement, 1µg/mL doxycycline and 10µM Y-27632. Induced cells and wild type ESCs were enzymatically dissociated 1 hour after addition of 10µM Y-27632 to wells containing cells for post-implantation embryo model generation. Dissociated cells were pelleted and resuspended in experiment media and placed in gelatin-coated wells for MEF depletion. After 15-30 minutes cells were counted, mixed, and plated into an Aggrewell dish with a final calculation of 8 wildtype-ESC, 8 hypoblast-like and 16 trophoblast-like cells plated per microwell in the Aggrewell. On day 1, the media was subjected to two two-third changes of N2B27 with 5% knockout serum replacement and 1µg/mL doxycycline. On day 2, Aggrewells were subjected to a half change with hIVC1 media with 1.25 µg/mL hIGF1 (78022.1 STEMCELL Technologies) and 1µg/mL doxycycline. hIVC1 media consists of Advanced DMEM/F12 (12634-010 ThermoFisher Scientific) supplemented with 20% inactivated FBS (10270106, ThermoFisher Scientific), 1x Glutamax, 1X NEAA, 1x Essential AA, 1x ITS-X, 25U/mL Pen/Strep, 1.8mM Glucose (G8644, Sigma-Aldrich), 0.22% sodium lactate (L7900, Sigma-Aldrich), 8nM b-estradiol (50-28-2, Tocris) and 200ng/mL progesterone (P0130, Sigma-Aldrich). This media is used in half changes each day from day 3. On day 4, aggregates were manually picked using a mouth pipette under a dissecting microscope into individual wells of ultra-low attachment 96 well plates (CLS7007, Corning) in hIVC1 media with IGF1 and doxycycline as above for subsequent culture.

value: Human ESC


title: 13D_Tg_Hip


title: 1_Tg_Hip_D

value: Hippo


title: CR_H3K27me3_BPH-1_rep1

value: H3K27me3 (Active motif, Cat#39155)


title: 20_S_Wt_Ipp

value: WT


title: 18 D_Wt_Ipp


title: BPH_1_R_G3


title: BPH_1_R_F3


title: 19 D_Wt_Ipp


title: BPH_1_R_G2


title: 7 S_Wt_Ipp


title: BPH_1_R_E3


title: BPH_1_R_F2


title: 20_Tg_mAb_R_D

source_name: Retina

value: Retina


title: CR_H3K27me3_HPrEC_rep3


title: 5-D_WT_Ipp


title: BPH_1_R_E2


title: 19_Tg_mAb_R_S


title: 24D_Tg_hip


title: BPH_1_R_D3


title: 17_tg_mAb_R_D


title: Tg_mAb_D


title: BPH_1_R_D2


title: BPH_1_R_C3


title: BPH_1_R_C2


title: 19_tg_mAb_R_D


title: BPH_1_R_B3


title: Tg_14_D


title: tg_13_R


title: BPH_1_R_A3


title: BPH_1_R_B2


title: BPH_1_R_A2


title: HPrEC_R_H3


title: tg_D


title: tg_13_R_s


title: HPrEC_R_H2


title: HPrEC_R_G3


title: Tg_S


title: 6_R_WT


title: 8_R_S_WT


title: 5_R_S_WT


title: 3 R_s_WT


title: HPrEC_R_F3


title: HPrEC_R_G2


title: HPrEC_R_E2


title: HPrEC_R_E3


title: HPrEC_R_D3


title: HPrEC_R_F2


title: HPrEC_R_D2


title: HPrEC_R_C2


title: HPrEC_R_C3


title: HPrEC_R_B3


title: HPrEC_R_B2


title: HPrEC_R_A3


title: R_GU216_180705_CTC7

value: prostate CTC


title: HPrEC_R_A2

value: HPrEC


title: R_GU216_180705_CTC5


title: R_GU216_180705_CTC6


title: R_GU216_180705_CTC4


title: R_GU216_180705_CTC1


title: R_WBC5_HD6_180202

source_name: not prostate

value: WBC

value: not prostate


title: R_GU114_180710_CTC5


title: R_GU114_180710_CTC4


title: R_GU114_180710_CTC1


title: R_WBC5_HD4_180126


title: R_WBC9_HD4_180126


title: Matched healthy tissue sample of male patient 9

city: Firenze

first: Matteo

last: Ramazzotti

address: viale Morgagni 50

department: Experimental and Clinical Biomedical Sciences

institute: University of Florence

data_processing:
[demultiplexing}  from raw data to demultiplexed fastq files please contact IGA Technology Services (Udine, Italy)
[pair merging}  micca mergepairs -i pair1.fastq -r pair2.fastq -o out.joined.fastq -l 30 -d 3
[primer check and trimming}  micca trim -i out.joined.fastq -o out.trimmed.fastq -w CCTACGGGNBGCWSCAG -r GACTACHVGGGTATCTAATCC -W -R -c
[quality check}  micca filter -i out.trimmed.fastq -o out.hiqual.fastq -e 0.5 -m 350 -f fastq
[reads merging}  micca merge -i *.hiqual.fastq -o merged.fastq -f fastq
[abundance table creation}  micca otu -m denovo_greedy -i merged.fasta -o otudata -d 0.97 -c -t 20
[taxonomic assignment (RDP)}  micca classify -m rdp -i otudata/otus.fasta -o otudata/taxa.txt
[further analyses and figure production}  R phyloseq package (see https://github.com/matteoramazzotti/papers/tree/main/2022breast)
Supplementary files format and content: otutable.txt, taxa.txt, otus.fasta

source_name: breast

extract_protocol:
Genomic DNA was extracted using the DNeasy PowerSoil Pro Kit (Qiagen, Hilden, Germany)
Illumina 16S Metagenomic Sequencing Library Preparation protocol ( see https://emea.support.illumina.com)
paired-end (2x300) amplicon sequencing

tag: individual

value: breast

tag: disease state

value: matched healthy tissue


title: R_WBC2_HD6_180202

tag: cell type

tag: tissue


title: R_GU114_180710_CTC2


title: R_WBC3_HD6_180202


title: Matched healthy tissue sample of male patient 10


title: Matched healthy tissue sample of male patient 8


title: Human meningioma, FFPE 8

type: genomic

city: San Francisco

first: William

last: Chen

state: CA

address: 1450 3rd Street, HD 402

institute: UCSF

hyb_protocol: Genomic DNA underwent bisulfite conversion using the EZ DNA Methylation kit (Zymo Research, cat# D5004), followed by amplification, fragmentation, and hybridization to Infinium EPIC 850k Human DNA Methylation BeadChips (Illumina, cat#20020530) according to manufacturer’s instructions at the Molecular Genomics Core at the University of Southern California (Los Angeles,CA).

data_processing: DNA methylation levels are reported as β-values, calculated from mean non-background corrected methylated (M) and unmethylated (U) signal intensities for each locus for each sample using the formula (β=M/(M+U)) and the Illumina BeadStudio software

label: Cy5, Cy3

source_name: Human meningioma, FFPE

extract_protocol: Qiagen FFPE AllPrep Extraction

value: FFPE


title: Matched healthy tissue sample of male patient 7

value: M


title: Human meningioma, FFPE 1

scan_protocol: Genomic DNA underwent bisulfite conversion using the EZ DNA Methylation kit (Zymo Research, cat# D5004), followed by amplification, fragmentation, and hybridization to Infinium EPIC 850k Human DNA Methylation BeadChips (Illumina, cat#20020530) according to manufacturer’s instructions at the Molecular Genomics Core at the University of Southern California (Los Angeles,CA).


title: Human meningioma, FFPE 3

label_protocol: Genomic DNA underwent bisulfite conversion using the EZ DNA Methylation kit (Zymo Research, cat# D5004), followed by amplification, fragmentation, and hybridization to Infinium EPIC 850k Human DNA Methylation BeadChips (Illumina, cat#20020530) according to manufacturer’s instructions at the Molecular Genomics Core at the University of Southern California (Los Angeles,CA).


title: Human meningioma, FFPE 16


title: Human meningioma, FFPE 13


title: Human meningioma, FFPE 12


title: Human meningioma, FFPE 7


title: Human meningioma, FFPE 6


title: Human meningioma, FFPE 15


title: R_WBC1_HD5_180129


title: Human meningioma, FFPE 10


title: R_WBC20_HD6_180202


title: Matched healthy tissue sample of male patient 6


title: Matched healthy tissue sample of male patient 5


title: Matched healthy tissue sample of male patient 3


title: Human meningioma, FFPE 11


title: R_WBC14_HD4_180126


title: Human meningioma, FFPE 2


title: R_WBC4_HD4_180126


title: Human meningioma, FFPE 4


title: Matched healthy tissue sample of male patient 2


title: Human meningioma, FFPE 14


title: Human meningioma, FFPE 9


title: Human meningioma, FFPE 5


title: Tumor sample of male patient 10

value: tumor


title: Control4

city: Xi 'an

first: Mengchang

last: Wang

state: Shaanxi Province

address: No.277, Yanta West Road, Yanta District

institute: The First Affiliated Hospital of Xi 'an Jiaotong University

description:
whole blood
SAMPLE 8

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation850k Beadchip using standard Illumina protocol.

scan_protocol: Arrays were imaged using an Illumina iScan.

data_processing: ChAMP package

label: Cy5 and Cy3

source_name: CD4+ T lymphocytes

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted and purified using QIAamp DNA Mini Kit (QIAGEN)  according to standard instructions.

value: blood

value: healthy


title: Control1

description:
whole blood
SAMPLE 5


title: Control3

description:
whole blood
SAMPLE 7


title: Tumor sample of male patient 6


title: R_GU181_CTC6_180102

value: prostate


title: R_GU181_CTC5_180130


title: Case4

description:
whole blood
SAMPLE 4

value: primary refractory ITP


title: Matched healthy tissue sample of male patient 4


title: R_WBC13_HD4_180126


title: Control2

description:
whole blood
SAMPLE 6


title: R_GU181_CTC2_180102


title: R_WBC15_HD4_180126


title: Matched healthy tissue sample of male patient 1


title: R_GU181_CTC9_180130


title: Case2

description:
whole blood
SAMPLE 2


title: Case3

description:
whole blood
SAMPLE 3


title: R_GU181_CTC11_180130


title: Tumor sample of male patient 2


title: R_GU181_CTC10_180130


title: Tumor sample of male patient 8


title: R_GU181_CTC7_180102


title: Tumor sample of male patient 9


title: R_GU181_CTC6_180130


title: R_GU181_CTC8_180102


title: R_WBC16_HD4_180126


title: Tumor sample of male patient 7


title: R_GU181_CTC4_180102


title: Matched healthy tissue sample of female patient 6

value: F


title: Matched healthy tissue sample of female patient 9


title: Tumor sample of male patient 5


title: Tumor sample of male patient 4


title: R_GURa15_171220_CTC3


title: Tumor sample of male patient 1


title: Matched healthy tissue sample of female patient 3


title: Matched healthy tissue sample of female patient 5


title: Matched healthy tissue sample of female patient 10


title: Matched healthy tissue sample of female patient 2


title: R_GURa15_171220_CTC9


title: Matched healthy tissue sample of female patient 8


title: R_GURa15_171220_CTC6


title: R_GURa15_171220_CTC7


title: Case1

description:
whole blood
SAMPLE 1


title: R_GU181_CTC8_180130


title: Matched healthy tissue sample of female patient 1


title: Tumor sample of female patient 10


title: R_GURa15_171220_CTC5


title: R_GURa15_171220_CTC8


title: R_GURa15_171220_CTC4


title: Matched healthy tissue sample of female patient 7


title: R_GURa15_171220_CTC1


title: Matched healthy tissue sample of female patient 4


title: R_GURa15_171220_CTC2


title: Tumor sample of female patient 9


title: R_GU181_171219_CTC9


title: R_GU181_171219_CTC8


title: R_GU181_CTC3_180130


title: Tumor sample of female patient 7


title: R_GU181_171219_CTC7


title: Tumor sample of female patient 8


title: R_GU181_171219_CTC6


title: Tumor sample of female patient 4


title: Tumor sample of female patient 5


title: R_GU181_171219_CTC4


title: R_GU181_171219_CTC2


title: Tumor sample of female patient 6


title: R_GU181_171219_CTC1


title: Tumor sample of female patient 3


title: R_GU181_171219_CTC13


title: Tumor sample of female patient 1


title: Tumor sample of female patient 2


title: R_GU181_171219_CTC10


title: R_GU181_171219_CTC12


title: R_GU181_171219_CTC11


title: R_GU181_171128_CTC7


title: bulk RNAseq of non-cryoinjured hEHT after 4day cultivation 2

city: WUHAN

first: lihang

last: zhu

state: Hubei province

address: HUBEIWUHAN

institute: HUBEIUniversity

data_processing:
Raw reads were trimmed adaptor sequences and removed low-quality reads by cutadapt (v1.10)
Reads were aligned to the GRCh37/hg19 reference genome by tophat2 (v2.0.13)
Reads were aligned to genes counted by cufflinks (v2.2.1)
The FPKMs are normalized using cuffnorm by cufflinks (v2.2.1)
Assembly: GRCh37
Supplementary files format and content: tab-delimited text includes raw counts for each sample
Supplementary files format and content: tab-delimited text includes FPKM for each sample

source_name: human engineered heart tissue

extract_protocol:
The hEHTs were collected on day 2 and day 4 after cryoinjury and their total RNA was extracted using the RNeasy Fibrous Tissue Mini Kit (Qiagen 74704) according to the manufacturer’s instructions.
The cDNA libraries were constructed using KAPA Hyper Prep Kits (Roche KK8504).

value: human engineered heart tissue

value: WTC

value: Human pluripotent stem cell-derived cardiac cells


title: bulk RNAseq of non-cryoinjured hEHT after 4day cultivation 3


title: bulk RNAseq of non-cryoinjured hEHT after 4day cultivation 1


title: R_GU181_171219_CTC3

value: prostate CTC


title: R_GU181_171128_CTC6


title: bulk RNAseq of non-cryoinjured hEHT after 2day cultivation 3


title: bulk RNAseq of non-cryoinjured hEHT after 2day cultivation 2


title: R_GU181_171128_CTC3


title: R_GU181_171128_CTC5


title: bulk RNAseq of non-cryoinjured hEHT after 2day cultivation 1


title: bulk RNAseq of cryoinjured hEHT after 4day cultivation 1


title: R_GU181_171128_CTC2


title: R_GU181_171128_CTC12


title: R_GU181_171128_CTC11


title: R_GU181_171128_CTC13


title: R_GU181_171128_CTC1


title: R_22Rv1_batch2_8


title: bulk RNAseq of cryoinjured hEHT after 2day cultivation 3


title: R_22Rv1_batch2_7


title: R_GU181_171128_CTC8


title: bulk RNAseq of cryoinjured hEHT after 2day cultivation 2


title: bulk RNAseq of cryoinjured hEHT after 2day cultivation 1


title: MCF-7-TAMR

type: RNA

first: Jing

last: Zhou

state: Guang Dong

address: Yanjiang West Road 107#

institute: Sun Yat-sen University

description: Gene expression of MCF-7-TAMR cells

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Tamoxifen resistant (TAMR) derivatives of MCF-7

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

growth_protocol: MCF-7 cells were cultured in DMEM medium (Life Technologies, USA) supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin mixture. MCF-7-LTED cell lines were cultured in phenol red free RPMI-1640 containing 10% charcoal-stripped steroid-depleted fetal bovine serum and 1% penicillin-streptomycin mixture for over a year and thereafter; MCF-7-TAMR cells were cultured with RPMI-1640 containing 0.1 μM 4-OH tamoxifen for over a year and thereafter.

extract_protocol: RNA was extracted by the TRIZOL-chloroform extraction method from cells.

tag: cell line background

value: Human breast cancer cell lines

value: tamoxifen resistant (TAMR) sub-line


title: R_22Rv1_batch2_6


title: MCF-7-LTED

description: Gene expression of MCF-7-LTED cells

source_name: Long-term estrogen deprivation (LTED) derivatives of MCF-7

value: long-term estrogen deprivation (LTED) sub-line


title: R_22Rv1_batch2_4


title: MCF-7P

description: Gene expression of MCF-7 parent cells

source_name: MCF-7 parent cells

value: parent cells


title: R_22Rv1_batch2_3


title: bulk RNAseq of cryoinjured hEHT after 4day cultivation 3


title: scRNAseq of non-cryoinjured hEHT after 4day cultivation 2

data_processing:
Data were generated and aggregated to the human genome (GRCh37/hg19) by CellRanger software (10x Genomics)
Assembly: GRCh37
Supplementary files format and content: matrix file

extract_protocol:
The cryoinjured hEHTs in day2 and day4 of remodelling process were dissociated by 2 mg/mL collagenase Ⅱ, and 2 mg/mL collagenase Ⅳ for 1 hour. After collagenases were removed, the dispersed hEHTs were further digested into single cells with 0.25% trypsin-EDTA at 37℃. Fluorescence-activated cell sorting was applied to obtain a single-cell suspension, with a high percentage of live cells above 80%.
Single-cell RNA-seq libraries were prepared according to the manufacturer's instructions (Chromium Single Cell 3' Reagent Kits User Guide (v3.1 Chemistry Dual Index)). Briefly, cells at a limiting dilution, barcoded single-cell gel beads, and partitioning oil were combined onto chromium next GEM chip to generate Gel Beads-in-emulsion (GEMs). Then, the gel beads were dissolved and mixed with a master mix containing reverse transcription reagents.


title: scRNAseq of non-cryoinjured hEHT after 4day cultivation 4


title: R_22Rv1_batch2_2


title: scRNAseq of non-cryoinjured hEHT after 4day cultivation 3


title: bulk RNAseq of cryoinjured hEHT after 4day cultivation 2


title: scRNAseq of non-cryoinjured hEHT after 2day cultivation 4


title: R_GU181_171128_CTC9


title: R_22Rv1_batch2_1


title: R_CTC3_GU159_171025


title: R_CTC4_GU159_171025


title: R_CTC6_GU159_171025


title: scRNAseq of non-cryoinjured hEHT after 4day cultivation 1


title: scRNAseq of cryoinjured hEHT after 4day cultivation 4


title: R_CTC2_GU181_171107


title: scRNAseq of cryoinjured hEHT after 4day cultivation 3


title: scRNAseq of cryoinjured hEHT after 4day cultivation 1


title: scRNAseq of cryoinjured hEHT after 2day cultivation 4


title: R_CTC2_GU159_171025


title: scRNAseq of cryoinjured hEHT after 2day cultivation 3


title: CTC1_GU169_170928


title: scRNAseq of hEHT after 3day cultivation 4


title: scRNAseq of cryoinjured hEHT after 2day cultivation 2


title: CTC1_GU216_170914

value: not prostate


title: R_CTC7_GU159_171025


title: R_CTC1_GU159_171025


title: scRNAseq of non-cryoinjured hEHT after 2day cultivation 2


title: scRNAseq of hEHT after 3day cultivation 2


title: scRNAseq of non-cryoinjured hEHT after 2day cultivation 3


title: R_CTC5_GU159_171025


title: scRNAseq of non-cryoinjured hEHT after 2day cultivation 1


title: scRNAseq of cryoinjured hEHT after 2day cultivation 1


title: LNCap_3

value: LNCap


title: LNCap_2


title: scRNAseq of hEHT after 3day cultivation 1


title: scRNAseq of hEHT after 3day cultivation 3


title: R_CTC1_GU181_171107


title: LNCap_1


title: scRNAseq of cryoinjured hEHT after 4day cultivation 2


title: Late-onset pre-eclampsia 5

city: Wenzhou

first: Meng

address: 270 Xueyuan Xi Road

institute: Wenzhou Medical University

data_processing:
The raw data was sequenced on the Nova 6000 platform (Illumina). Fastp (0.20.1) was employed to filter out low-quality reads and junctions from the raw sequencing data.
The filtered clean sequencing reads were aligned to the human genome GRCh 38 obtained from ENSEMBL (release 95) using the miRdeep 2mapper.pl command.
The known miRNAs were then quantified using the miRDeep2.pl command with a miRNA reference file containing mature miRNA sequences and their corresponding precursor sequences downloaded from the miRBase database (https://www.mirbase.org/).
Assembly: GRCh38(hg38)
Supplementary files format and content: tab-delimited text files include RPM values for each Sample

source_name: blood

extract_protocol:
Blood samples were collected from pre-caesarean women who had fasted overnight (approximately 10h) in 10 ml EDTA-coated vacuum blood collection tubes prior to any medical intervention. Within 30 minutes of each collection, 5 mL of blood was separated by centrifugation at 3000 rpm for 15 minutes at 20°C to obtain plasma, and the supernatant was then extracted into a new tube. Leukocytes were purified from an additional 5 ml of blood using an erythrocyte lysis solution (Solarbio, China) according to the manufacturer's protocol. Briefly, 5 ml of blood was mixed with three times the volume of erythrocyte lysis solution and incubated on ice for 15 min. The mixture was centrifuged at 450 x g for 10 min at 4 °C, and the supernatant was discarded to obtain leukocyte precipitates.
For small RNA library preparation, 1 μg of total RNA per sample was utilized as input material. The TruSeq® miRNA Sample Preparation Kit from Illumina® was used to generate sequencing libraries with the manufacturer's recommendations followed, and index codes were added to attribute sequences for each sample. The first-strand cDNA was synthesized using SuperScript II (ThermoFisher), and library quality was assessed on a Qubit system (Invitrogen).


title: Late-onset pre-eclampsia 4


title: Healthy people, biological rep8

city: Tianjin

first: Zhu

last: Li

state: Tianjin

address: No.10 PoYangHu Road, JingHai, District

institute: Tianjin university of TCM

description:
Control-8-713 R094L6B
Expression data from healthy people without intervention.

hyb_protocol: In vitro transcription synthesizes aRNA and incorporates a biotin-conjugated nucleotide (cRNA is also known as amplified RNA or aRNA). The aRNA is then purified to remove unincorporated NTPs, salts, enzymes, and inorganic phosphate. Fragmentation of the biotin-labeled aRNA prepares the sample for hybridization onto GeneChip 3’ expression arrays. GeneChip® HT Hybridization, Wash, and Stain Kit for GeneTitan: Affymetrix, P/N 901406.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 (Affymetrix).

data_processing: AGCC software (Affymetrix GeneChip Command Console version4.0) was used to extract the data from the scan image in .CEL format. This data can be opened by the Expression Console software. The original data were imported into GeneSpring software (version 13.1,Agilent), and the RMA method was used to standardize the results, including the original signal value, the standardized signal value and detailed annotation information.

label: biotin

source_name: Healthy people without intervention

label_protocol: In the GeneChip® 3’ IVT Express Protocol total RNA undergoes reverse transcription to synthesize first-strand cDNA. This cDNA is then converted into a double-stranded DNA template for transcription.

growth_protocol: In each group, the most typical 8 subjects were selected for this research, among which weeks 0 of healthy people and weeks 0 and 8 of patients with coronary heart disease. Patients with CHD were treated with the Danlou Tablets 0.3 g per tablet, five tablets each time, three times a day, and 8 weeks treatment period. Healthy participants in the control group did not receive any treatment. Blood samples for further study were obtained from the antecubital vein of people on the day of enrollment.

extract_protocol: Total RNA was isolated with mirVana™ PARIS™ Kit (Ambion-1556, United States) according to the manufacturers’ instructions. Total RNA was isolated with mirVana™ PARIS™ Kit (Ambion-1556, United States) according to the manufacturers’ instructions. To improve RNA purity for further analysis, RNase Mini Kit (Qiagen p/n 74104, Germany) was used for total RNA clean-up. Total RNA concentration and purity were estimated with NanoDrop1000 (Thermo Scientific, United States). RNA integrity was assessed using the Agilent 2100 bioanalyzer (Agilent Technologies), RNA LabChip® kits and RNA Integrity Number software.

treatment_protocol: Peripheral blood samples (2.5ml) of everyone were collected with PAX gene Vacutainer Tube (BD Biosciences, New York, United States) in the morning, before breakfast.

value: peripheral blood mononuclear cells

tag: diagnosis

tag: agent

tag: gender

value: male

tag: individual id


title: Healthy people, biological rep7

description:
Control-7-419 R094L9X
Expression data from healthy people without intervention.

value: female


title: Healthy people, biological rep6

description:
Control-6-422 R094LC9
Expression data from healthy people without intervention.

value: healthy


title: PC3_3

value: prostate


title: Early-onset pre-eclampsia 1

value: blood


title: Late-onset pre-eclampsia 3


title: CTC1_GU124_170822


title: R_CTC1_GU218_171109


title: PC3_2


title: Late-onset pre-eclampsia 2


title: Early-onset pre-eclampsia 2


title: Early-onset pre-eclampsia 4


title: Early-onset pre-eclampsia 5


title: Late-onset pre-eclampsia 1


title: non-disease control 7


title: Early-onset pre-eclampsia 3


title: PC3_4


title: non-disease control 5


title: Healthy people, biological rep5

description:
Control-5-523 R093Z0M
Expression data from healthy people without intervention.


title: Healthy people, biological rep2

description:
Control-2-519 R094L47
Expression data from healthy people without intervention.


title: non-disease control 3


title: non-disease control 6


title: Healthy people, biological rep4

description:
Control-4-524 R094L3J
Expression data from healthy people without intervention.


title: non-disease control 1


title: CTC2_GU70_170906


title: vCAP_3

value: vCAP


title: CHD patients after treatment, biological rep8

description:
CHD_8-8-507 R094L2B
Expression data from patients with coronary heart disease after Danlou Tablets treatment for eight weeks.

source_name: CHD patients with DLT treatment for eight weeks

value: coronary heart disease

value: Danlou Tablets


title: non-disease control 2


title: Healthy people, biological rep3

description:
Control-3-520 R093Y2C
Expression data from healthy people without intervention.


title: vCAP_2


title: siPTBP1_2

city: Halle

first: Markus

last: Glaß

address: Kurt-Mothes-Str. 3a

department: Institute of Molecular Medicine

country: Germany

institute: Martin Luther University Halle-Wittenberg

data_processing:
Sequenced reads were trimmed for adaptor sequences and low quality sequence using Cutadapt (v 2.8) with parameters -q 20 -O 7 -m 20 --trim-n
Trimmed reads were mapped against the human genome (hg38 UCSC) using HiSat2 (v 2.1.0) with parameters --dta --strandness RF -k 5
secondary alignments were filtered out using samtools (v 1.10)
Mapped reads were summarized using featureCounts (v 2.0.0) with parameters -p -s 2 -M -t exon -g gene_id and Ensembl gene annotations (GRCh 38.100)
Assembly: hg38
Supplementary files format and content: Comma-separated text file containing raw count values for each sample

extract_protocol:
RNA extraction was performed using TRIZOL according to manufacturer's protocol.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was  synthesized using random hexamer primers. Then the second strand cDNA was synthesized using dUTP, instead of dTTP. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification. Following is the workflow of library construction

value: lung cancer derived cell line

tag: genotype

value: PTBP1 knockdown


title: non-disease control 4


title: Tumor sample of male patient 3

value: breast

value: M

value: tumor


title: vCAP_1

tag: genome build


title: siRAVER1_3

value: RAVER1 knockdown


title: siRAVER1_2


title: siPTBP1_1


title: siRAVER1_1


title: Healthy people, biological rep1

description:
Control-1-518 R094L0Y
Expression data from healthy people without intervention.


title: WBC6_donor1

value: WBC

value: not prostate


title: siPTBP1_3


title: PC3_1


title: siC control knockdown_3

value: control knockdown


title: siC control knockdown_2


title: WBC5_donor1


title: siC control knockdown_1


title: WBC4_donor1


title: CTC1_GU70_170906

value: prostate CTC


title: OCIAML3 sgNeg 3d, Input

city: Houston

first: Xiaoping

last: Su

state: Texas

address: 7300 Brompton St, Apt 5633

institute: MD Anderson Cancer Center

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.05
bigWig files were generated using the bamCoverage. narrowPeak and broadPeak files were generated using MACS v2 with default settings.
Assembly: hg38
Supplementary files format and content: broadPeak or narrowPeak

growth_protocol: Culture human AML cells were cultured in 20% FBS containing alpha-MEM media.

extract_protocol:
AML cells (10 million) were treated with 1% formaldehyde for 10 minutes with rotation. The crosslinking reaction was quenched with 2.5 M Glycine for 5 minutes. Chromatin lysates were clarified from ultra-sonicated nuclei and histone-DNA complexes were isolated with H3K27Ac or H3K4me3 antibody, respectively. Following ChIP washes, the  immunoprecipitated DNA fragments were treated with mutant Tn5 transposase for 10 minutes at 37°C to attach sequencing adapters to the DNA. Tagmented DNA was eluted and formaldehyde-induced crosslinks were reversed. Tagmented, eluted DNA was purified over a column and utilized for library preparation.
ChIP-Seq libraries were prepared according to Illumina's instructions accompanying the Nextera DNA Library Prep Kit (Cat. No. FC-121-1030). After adapter ligation, DNA was PCR amplified with Illumina universal primer for 12-15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were isolated utilizing AMP-XP beads. The purified DNA was captured on an Illumina NExt-Seq 500 flow cell for cluster generation. Libraries were sequenced following the manufacturer's protocols.

treatment_protocol: 1 x 10^7 Human AML cells were transfected and cultured for 72 hrs.

value: Cultured AML Cell Line

tag: chip antibody


title: WBC2_donor1


title: OCIAML3 sgNpm1A 3d H3K4me3

value: H3K4me3 (Active Motif) RRID:AB_2793611


title: OCIAML3 sgNeg 3d H3K4me3


title: OCIAML3 sgNpm1A 3d H3K27Ac

value: H3K27Ac (Active Motif) RRID:AB_2793305


title: WBC1_donor1


title: OCIAML3 sgNeg 3d H3K27Ac


title: CHD patients after treatment, biological rep3

description:
CHD_8-3-304R093Z4L
Expression data from patients with coronary heart disease after Danlou Tablets treatment for eight weeks.

value: peripheral blood mononuclear cells

value: male


title: goc10_24_hr_nec_3

city: Chapel Hill

first: Misty

last: Good

state: NC

address: 101 Manning Drive 4th Floor CB 7596

department: Pediatrics

institute: University of North Carolina at Chapel Hill

data_processing:
Basecalling with Illumina RTA 1.9. Demultiplexing with Illumina bcl2fastq software.
Analysis was performed using Partek® Flow® software.
Adapters were removed and reads were aligned to the hg38 assembly with STAR 2.7.3a and quantified to Ensembl transcripts release 91 with an average coverage of 10x.
Reads were normalized to total counts per million. Features containing fewer than 10 reads were not included in the analysis.
Sequencing performance was assessed for the total number of aligned reads, the total number of uniquely aligned reads, and features detected.
The performance of all genes was assessed with plots of the residual standard deviation of every gene to their average log-count with a robustly fitted trend line of the residuals. Differential expression analysis was then performed.
Assembly: hg38
Supplementary files format and content: Gene counts with CPM in excel file

source_name: Small intestine

extract_protocol:
Epithelial RNA was isolated from the top channel of the microfluidic devices using Trizol.
KAPA RiboErase

value: Small intestine

value: Intestinal epithelial cell organoids

tag: treatment

value: Intestinal Bacteria

tag: time

value: 24 hrs


title: Peripheral blood, Lib1

city: York

first: Matthew

middle: Anthony

last: Care

state: North Yorkshire

address: Wentworth Way

department: Department of Biology

country: United Kingdom

institute: The University of York

description:
Reference_extended_genes_EBV_amplicons.fasta
RunSampleTags.txt

data_processing:
Fastq files were processed via the BD Rhapsody Targeted Analysis Pipeline (v1.10.1) on Seven Bridges (https://igor.sbgenomics.com/) using the recommended settings
The BD-Rhapsody pipeline is available here: https://bitbucket.org/CRSwDev/cwl/src/master/
DBEC_molsPerCell and Sample_Tag_Calls files were imported into R (v4.1.2) and processed with the Seurat package (v4.2.0). The data from runs 1 and 2 were analyzed independently. In each case, cells were filtered that were annotated as undetermined or multiplet. Genes were filtered if expressed < 0.1% of cells, and cells were filtered if expressing a number of genes < 1st quartile, the remaining data was log-normalised.
Assembly: Reference_extended_genes_EBV_amplicons.fasta; custom 701 gene targeted panel.
Supplementary files format and content: CSV text files containing the Sample-Tag calls along with DBEC-MolsPerCell per run.

source_name: Peripheral blood

extract_protocol:
Cryopreserved cells were thawed and dead cells removed by lymphoprep density gradient centrifugation. Cells were enumerated on a hemocytometer. The cells from individual donors were labelled with a unique sample tag identifier using the BD Single-Cell Multiplexing Kit. Donors were pooled in equal ratios, with the aim of loading 4000-5000 cells per donor onto a cartridge. Donors 1-4 and 5-8 were run on independent cartridges using a custom designed 701 gene panel. Manufacturers protocols were followed throughout
Libraries were constructed using the BD-Rhapsody Single-Cell Multiplexing kit.

treatment_protocol: Cells were maintained in Iscove’s Modified Dulbecco Medium (IMDM) supplemented with Glutamax and 10% heat-inactivated fetal bovine serum (HIFBS, Invitrogen); Lipid Mixture 1, chemically defined and MEM Amino Acids solution (both at 1x final concentration) were added from day 3 onwards. Day 0 to day 3 – B cells were cultured in 24 well plates at 2.5 X 10^5/ml with IL2 (20 U/ml), IL21 (50 ng/ml), F(ab’)2 goat anti-human IgA, M & IgG (2µg/ml) on γ-irradiated CD40L expressing L-cells (6.25 X 10^4/well). Day 3 to day 6 – At day 3, cells were detached from the CD40L L-cell layer and reseeded at 1 X 10^5/ml in media supplemented with IL2 (20 U/ml) and IL21 (50 ng/ml). Day 6 to day 13 – At day 6, cells were harvested and seeded at 1 X 10^6/ml in media supplemented with IL6 (10ng/ml), IL21 (10 ng/ml) and multimeric-APRIL (100ng/ml). Day 13 onwards – At day 13, cells were harvested and replaced in half the volume of fresh media used at day 6 supplemented with IL6 (10ng/ml) & multimeric-APRIL (100ng/ml). At day 20-24, dead cells were removed by lymphoprep density gradient centrifugation and live cells placed in fresh media for 72 hours. Cells were then cryopreserved.

value: Peripheral blood

tag: donor

value: mixed sample (Donors 1-4)

value: mixed sample (B-cells/Plasma-cells)


title: WBC3_donor1


title: Peripheral blood, Lib5

data_processing:
Fastq files were processed via the BD Rhapsody Targeted Analysis Pipeline (v1.10.1) on Seven Bridges (https://igor.sbgenomics.com/) using the recommended settings
DBEC_molsPerCell and Sample_Tag_Calls files were imported into R (v4.1.2) and processed with the Seurat package (v4.2.0). The data from runs 1 and 2 were analyzed independently. In each case, cells were filtered that were annotated as undetermined or multiplet. Genes were filtered if expressed < 0.1% of cells, and cells were filtered if expressing a number of genes < 1st quartile, the remaining data was log-normalised.
Assembly: Reference_extended_genes_EBV_amplicons.fasta; custom 701 gene targeted panel.
Supplementary files format and content: CSV text files containing the Sample-Tag calls along with DBEC-MolsPerCell per run.
The BD-Rhapsody pipeline is available here: https://bitbucket.org/CRSwDev/cwl/src/master/

value: mixed sample (Donors 5-8)


title: goc10_24_hr_nec_2


title: BPH-1-M-H2

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
All bisulfite sequencing reads were first trimmed to remove adaptors and low quality bases using trim_galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) (parameters: --quality 20 --phred33 –length 50 --paired).
Next, reads that passed quality control were mapped to human reference genome (version: hg19) or mouse reference genome (version: mm9) using bismark (version: 0.7.6) in single-end alignment mode.
Assembly: hg19 (human); mm9 (mouse)
Supplementary files format and content: bigWig (1 if a methylated CpG, 0 if an unmethylated CpG, no value otherwise)

source_name: ATCC cell line cells

extract_protocol:
Single cell were either manully picked or sorted into the scBS lysis buffer by FACS, and DNA was released after proteinase treatment at 50C and then bisulfite converted.
After bislfite purification, DNA was complemented with the biotinated random primer (5’-biotin-CTACACGACGCTCTTCCGATCTNNNNNNNNN-3’) and 50 units of klenow polymerase (3’ to 5’exo-, New England Biolabs). This random priming was repeated 5 times in total. The second strands were synthesized using another random primer (5’-AGACGTGTGCTCTTCCGATCTNNNNNNNNN-3’) and the final libraries were generated after 8-12 cycles PCR amplification with the Illumina universal PCR primer and Illumina indexed primer.

value: ATCC cell line cells

tag: cpg coverage

tag: bisulfite conversion_rate

tag: qc

value: pass


title: CHD patients after treatment, biological rep6

description:
CHD_8-6-504 R094L3M
Expression data from patients with coronary heart disease after Danlou Tablets treatment for eight weeks.

value: coronary heart disease

value: Danlou Tablets

tag: age


title: CHD patients after treatment, biological rep5

description:
CHD_8-5-607 R093Z74
Expression data from patients with coronary heart disease after Danlou Tablets treatment for eight weeks.

value: female


title: CHD patients after treatment, biological rep2

description:
CHD_8-2-303 R093Z2L
Expression data from patients with coronary heart disease after Danlou Tablets treatment for eight weeks.


title: CHD patients after treatment, biological rep4

description:
CHD_8-4-603 R093Z3G
Expression data from patients with coronary heart disease after Danlou Tablets treatment for eight weeks.


title: goc10_24_hr_control_3

tag: cell type


title: goc10_24_hr_control_2

tag: tissue


title: OCIAML3 sgNpm1A 3d, Input

tag: cell line

value: Cultured AML Cell Line


title: CHD patients after treatment, biological rep7

description:
CHD_8-7-506 R094L4W
Expression data from patients with coronary heart disease after Danlou Tablets treatment for eight weeks.

tag: diagnosis


title: CHD patients after treatment, biological rep1

description:
CHD_8-1-302 R093Z26
Expression data from patients with coronary heart disease after Danlou Tablets treatment for eight weeks.

tag: agent


title: CHD patients before treatment, biological rep8

description:
CHD_0-8-507 R094L2D
Expression data from patients with coronary heart disease before Danlou Tablets treatment.

source_name: CHD patients without DLT treatment

tag: gender


title: CHD patients before treatment, biological rep5

description:
CHD_0-5-607 R093Z7B
Expression data from patients with coronary heart disease before Danlou Tablets treatment.

tag: individual id


title: CHD patients before treatment, biological rep6

description:
CHD_0-6-504 R094L4S
Expression data from patients with coronary heart disease before Danlou Tablets treatment.


title: goc5_72_hr_nec_3

value: 72 hrs


title: BPH-1-M-F2

tag: patient donor/cell_line


title: BPH-1-M-G2

tag: genome build


title: goc10_24_hr_nec_1


title: goc5_72_hr_nec_2


title: goc5_72_hr_control_3


title: CHD patients before treatment, biological rep4

description:
CHD_0-4-603 R093Z5Y
Expression data from patients with coronary heart disease before Danlou Tablets treatment.

value: peripheral blood mononuclear cells


title: CHD patients before treatment, biological rep7

description:
CHD_0-7-506 R093YYB
Expression data from patients with coronary heart disease before Danlou Tablets treatment.

value: male


title: BPH-1-M-E2


title: goc5_72_hr_control_2

value: Small intestine


title: Sample 20 - CD12

last: Han

address: No.58 Zhongshan Er Road

department: Division of Gastroenterology

institute: The First Affiliated Hospital, Sun Yat-Sen University

data_processing:
fastqc  v0.11.5 default
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated. About 100M raw reads for each sample were generated. Raw reads of fastq format were firstly processed using fastp[1] and the low quality reads were removed to obtain the clean reads.Then about 95000000 clean reads for each sample were retained for subsequent analyses.
hisat2 2.2.1.0 --rna-strandness rf --fr
The clean reads were mapped to the GRCh38.p12 using HISAT2.
htseq-count 0.9.1 -s reverse
The read counts of each gene were obtained by HTSeq-count[3] and then FPKM[4] of each gene was calculated.PCA analysis were performed using R (v 3.2.0) to evaluate the biological duplication of samples.
Assembly: GRCh38.p12
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
Supplementary files format and content: tab-delimited text files include count values for each Sample

source_name: Mucosal biopsy

extract_protocol:
Total RNA was extracted using the  mirVana miRNA Isolation Kit (Ambion) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
The samples with qualified purity, quantity and integrity were used for subsequent library construction. Ribo-off rRNA Depletion Kit（vazyme, Nanjing, China）was used to remove ribosomal RNA, then the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions. The transcriptome sequencing and analysis were conducted by OE Biotech Co., Ltd. (Shanghai, China).

tag: disease

value: Crohn's disease

tag: Sex

value: Male

value: Mucosal biopsy

tag: biopsy location

value: Transverse colon


title: goc5_72_hr_control_1

value: Intestinal epithelial cell organoids

tag: treatment

tag: time


title: CHD patients before treatment, biological rep3

description:
CHD_0-3-304 R093Z5T
Expression data from patients with coronary heart disease before Danlou Tablets treatment.


title: Sample 19 - CD11


title: BPH-1-M-C2

address: 149 13th Street

institute: Massachusetts General Hospital

tag: cpg coverage

tag: bisulfite conversion_rate

value: fail


title: Sample 18 - CD10

tag: age


title: BPH-1-M-D2

tag: cell type

tag: qc


title: BPH-1-M-B2


title: goc10_24_hr_control_1

tag: tissue

value: 24 hrs


title: patient_derived_ex_vivo_Combo_rep2

city: Denver

first: Lily

last: Nguyen

state: CO

address: 220 Roslyn Street, Apt 706

institute: UNIVERSITY OF COLORADO DENVER

data_processing:
quality assessement using FastQC (v0.11.8) and MultiQC (v1.7)
adapter trimming using BBDuk/BBMap (v38.05)
genome alignment using using hisat2 (v2.1.0)
Assembly: hg38, mm10
Supplementary files format and content: bigwig tracks were generated using the bamCoverage function of deepTools (v3.0.1)

source_name: HGSOC

growth_protocol: Cell Culture- PEO1 (RRID:CVCL_2686), Kuramochi (RRID:CVCL_1345), and OVCA420 (RRID:CVCL_3935) cell lines were provided through the Gynecologic Tumor and Fluid Bank (GTFB). ID8 cell line was kindly gifted from Dr. Iain McNeish lab (Imperial College London). All cells were authenticated via STR at The University of Arizona Arizona Genetics Core (RRID:SCR_012429). All cells undergo monthly mycoplasma testing using Sigma LookOut Mycoplasma Detection kit (Cat. #MP0035) and are only culture up to 20 passages or two months. Cells are cultured in RPMI1640 (Gibco) in 10% FBS (Phoenix Scientific Cat. #PS-100) and Penicillin Streptomycin (Cat. #SV30010) at 37C in 5% CO2. ID8 cells are cultured in DMEM (Gibco, Cat. #11995-065) supplemented with 4% FBS, Penicillin Streptomycin and 1x ITS (Gibco Cat. #41400-045).   Ex vivo Culture - Primary ovarian cancer tumors (Table S1) were collected at The University of Colorado Cancer Center under the Colorado Multiple Institutional Review Board (COMIRB) Gynecologic Tumor and Fluid Bank protocol #07-935. All patients are consented under the GTFB protocol and collected specimens are deidentified. Tumors are collected by the Biorepository Shared Resource and delivered to the lab within one hour of surgical dissection. Tumors are sliced using a Krumdeick Tissue Slicer into 300 micron thick discs and placed in warmed culture media. Tumor sections treated for 72 hours, are either stored at -80C  in RLT plus buffer (Qiagen, Cat. #74136 ) or fixed in 10% buffered formalin. RNA was extracted from tissues stored in the RLT buffer and used for RNA-sequencing. Fixed tissues were embedded in paraffin at the University of Colorado Histopathology Shared Resources.   Cell culture and generation of EHMT1 and 2 overexpression - PEO1 cells were maintained in RPMI+ 10% heat inactivated FBS (Avantor, Cat. #10803-034) + 100 μg/mL Penicilin/Streptomycin (Lonza, Cat. #09-757F). EHMT1 or EHMT2 overexpression cells were obtained by using lentivirus to infect cells with either TRE_EHMT1_hygromycin or TRE_EHMT2_hygromycin. To produce lentivirus, 500,000 Lenti-X 293T cells were seeded on 6-well plate. Twenty-four hours later, the cells were transfected with packaging plasmids (0.5µg pCMV-VSV-G, 1.1µg pD8.9), 0.85µg transfer plasmid, 7.35µg of PEI MAX (Polysciences Inc., Cat. #24765-1) and 10mM HEPES. Media was changed 24 hours later. Supernatant with virus was collected 48 and 72 hours post transfection. The supernatant was filtered using a 0.45µm PES Filter membrane (Whatman Uniflo, Cat. #9914-2504). Cells were then infected using 1mL of supernatant with 5 µg/mL polybrene (EMD Millipore, Cat. #TR-1003-G). Media was changed 24 hours later. 48 hours post transduction, cells were selected using 200μg/ml Hygromycin B (Biosciences, Cat. #31282-04-9). Cells were selected until death of non-transduced cells. Once cells were selected, they were induced for EHMT1 or EHMT2 expression using Doxycycline (1µg/ml, TCI, Cat. #D4116) for four days and collected. Cells were immunoblotted for EHMT1 (Bethyl, Cat. #A301-642A; dilution 1:500), EHMT2 (Cell Signaling, Cat. #3306; RRID:AB_2097647; dilution 1:1000), alpha-tubulin (Cell Signaling Cat. #3873; RRID:AB_1904178; dilution 1:3000), and H3K9me2 (Cell Signaling Cat. #4658; RRID:AB_10544405; diluted 1:1000).

extract_protocol:
RNA was harvested using Zymo Quick-RNA Miniprep Plus Kit (Zymo #R1057). All lysates were frozen at -80°C prior to extraction, and all extracted RNA were stored at -80°C as single-use aliquots.
Sequencing libraries were prepared from RNA harvested from treatment or transfection replicates. Total RNA was extracted using the Quick-RNA Miniprep Plus Kit (Zymo Research, Cat. #D4209). Ribosome depletion and library preparation was performed using the Qiagen Fast-select (Cat. #334375) and KAPA BioSystems mRNA HyperPrep Kit (Cat. #KK8581) according to the manufacturer’s protocols. Briefly, 500ng of RNA was used as input, and KAPA BioSystems single-index adapters were added at a final concentration of 1.5mM. Purified, adapter-ligated library was amplified for a total of 11 cycles following the manufacturer’s protocol. The final libraries were pooled and sequenced on an Illumina NovaSeq 6000 (University of Colorado Genomics Core) as 150 bp paired-end reads.

treatment_protocol: Cells were treated with DMSO, olaparib, UNC0642, or olaparib + UNC0642 for 72 hours

tag: phenotype

tag: timepoint


title: patient_derived_ex_vivo_Combo_rep3


title: BPH-1-M-A2

first: Ben

last: Wittner

value: ATCC cell line cells


title: Sample 17 - CD9

value: Female

value: Descending colon


title: patient_derived_ex_vivo_UNC_rep3


title: patient_derived_ex_vivo_Combo_rep1

source_name: EOC


title: goc5_72_hr_nec_1

value: Intestinal Bacteria


title: patient_derived_ex_vivo_UNC_rep2


title: patient_derived_ex_vivo_UNC_rep1


title: CHD patients before treatment, biological rep2

description:
CHD_0-2-303 R093Z3C
Expression data from patients with coronary heart disease before Danlou Tablets treatment.

tag: diagnosis

value: coronary heart disease

tag: agent

tag: gender


title: patient_derived_ex_vivo_Ola_rep1

value: olaparib


title: patient_derived_ex_vivo_Ola_rep3


title: patient_derived_ex_vivo_DMSO_rep3

value: DMSO


title: T1678_GS8_M_H2

source_name: Single prostate tumor cell

value: Single prostate tumor cell

tag: patient donor/cell_line

tag: genome build


title: patient_derived_ex_vivo_Ola_rep2


title: CHD patients before treatment, biological rep1

description:
CHD_0-1-302 R093Z4R
Expression data from patients with coronary heart disease before Danlou Tablets treatment.

value: peripheral blood mononuclear cells

value: male

tag: individual id


title: Sample 14 - CD6

tag: disease

value: Crohn's disease

tag: Sex

tag: biopsy location


title: T1678_GS8_M_G3

tag: cpg coverage


title: Sample 13 - CD5

value: Male

value: Sigmoid colon


title: Sample 16 - CD8

value: Mucosal biopsy

value: Transverse colon


title: EHMT2_OE_rep2

tag: treatment


title: T1678_GS8_M_H1

tag: bisulfite conversion_rate

value: pass


title: patient_derived_ex_vivo_DMSO_rep2

tag: cell type


title: patient_derived_ex_vivo_DMSO_rep1


title: T1678_GS8_M_G2

tag: qc

value: fail


title: EHMT1_OE_rep2


title: EHMT2_OE_rep1


title: Sample 12 - CD4

tag: age

tag: tissue


title: T1678_GS8_M_G1


title: Sample 15 - CD7


title: Sample 11 - CD3


title: Sample 10 - NC14

value: control


title: T1678_GS8_M_F3


title: EHMT_WT_rep2

tag: phenotype

value: wildtype

tag: timepoint


title: EHMT_WT_rep1


title: T1678_GS8_M_F2


title: EHMT1_OE_rep1


title: OVCAR420_R_Combo_rep3


title: Sample 9 - NC13

value: Female

value: Descending colon


title: OVCAR420_R_Combo_rep2


title: T1678_GS8_M_F1


title: Sample 8 - NC12


title: OVCAR420_R_UNC_rep1


title: Sample 7 - NC11


title: OVCAR420_R_UNC_rep3


title: OVCAR420_R_UNC_rep2


title: T1678_GS8_M_E3


title: Sample 6 - NC10


title: Sample 5 - NC9


title: T1678_GS8_M_D3


title: T1678_GS8_M_E1


title: Sample 4 - NC8


title: OVCAR420_R_Ola_rep2


title: OVCAR420_R_Ola_rep1


title: OVCAR420_R_DMSO_rep2


title: OVCAR420_R_DMSO_rep3


title: OVCAR420_R_DMSO_rep1


title: T1678_GS8_M_D2


title: Kura_R_Combo_rep3

value: Kuramochi


title: OVCAR420_R_Combo_rep1


title: Sample 3 - NC7


title: Kura_R_Combo_rep1


title: Sample 2 - NC6


title: Kura_R_UNC_rep3


title: Kura_R_UNC_rep2


title: T1678_GS8_M_C3


title: OVCAR420_R_Ola_rep3

value: olaparib


title: T1678_GS8_M_E2


title: T1678_GS8_M_D1


title: Kura_R_Ola_rep3


title: Kura_R_Ola_rep2


title: T1678_GS8_M_C2


title: Kura_R_UNC_rep1


title: Kura_R_Ola_rep1


title: T1678_GS8_M_C1


title: OCIAML3_sgNPM1A_2_3d

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw data FASTQ files were generated by standard illumina base calling pipeline. Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, Reads were aligned to hg38 reference genome using STAR with default parameters
STAR was used to generate the "raw count" from an aligned bam againt transcript file
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each annotated gene for each sample

extract_protocol:
Total RNA was isolated with a kit from Ambion, Inc. The RNA was DNAse I treated to eliminate genomic DNA, then the purified RNA was utilized to make libraries for next generation sequencing.
Libraries were constructed following standard Illumina protocols for RNA sequencing in a sequencing and microarray core facility.

treatment_protocol: 1 x 10^6 Human AML cells were transfected and cultured for 72 hrs. Cells were harvested by centrifugation and lysed with a Beta-mercaptoethanol containing RNA lysis buffer.

tag: cell line

value: Cultured AML Cell Line

tag: genotype


title: Kura_R_DMSO_rep3

value: DMSO


title: OCIAML3_sgNeg_2_3d


title: Kura_R_DMSO_rep1


title: PEO1_R_Combo_rep3


title: Kura_R_Combo_rep2


title: T1678_GS8_M_B3

value: Single prostate tumor cell

tag: patient donor/cell_line


title: OCIAML3_sgNPM1A_1_3d


title: Kura_R_DMSO_rep2


title: T1678_GS8_M_B2

tag: genome build


title: T1678_GS8_M_B1


title: Sample 1 - NC5


title: PEO1_R_Combo_rep2


title: PEO1_R_Combo_rep1


title: T1678_GS8_M_A3


title: PEO1_R_UNC_rep3


title: CL_293_HsaSRRM4_ribominus_a

city: Barcelona

first: Manuel

last: Irimia

state: Barcelona

address: Dr. Aiguader, 88

country: Spain

institute: Centre for Genomic Regulation (CRG)

data_processing:
vast-tools was used to map the reads to a library of mRNAs using vast-tools align --expr, for either -sp hg38 or -sp mm10
Assembly: mm10 and hg38

source_name: human embryonic kidney

growth_protocol: Described in Gohr et al, 2022

extract_protocol:
Described in Gohr et al, 2022
Described in Gohr et al, 2022

treatment_protocol: Described in Gohr et al, 2022

value: human embryonic kidney

value: Hek 293


title: NS Human meningioma, FFPE 16

hyb_protocol: 200 ng of total RNA per sample was hybridized to barcoded reporter probes and biotin-conjugated capture probes from a custom codeset targeting genes of interest at 65C for 16 hours according to manufacturer instruction. Hybridization mixtures were washed and target/probe complexes were purified and bound to streptavidin coated cartridges. Cartridges were scanned on the nCounter Digital Analyzer with a FOV setting of 550.

data_processing: Data is positive control normalized mRNA counts, processed with default settings using nSolver.

source_name: Human meningioma, FFPE

value: Tumor


title: PEO1_R_UNC_rep2


title: PEO1_R_UNC_rep1


title: T1678_GS8_M_A2

city: Boston


title: CL_293_GFP_ribominus_a

value: GFP


title: NS Human meningioma, FFPE 14

scan_protocol: 200 ng of total RNA per sample was hybridized to barcoded reporter probes and biotin-conjugated capture probes from a custom codeset targeting genes of interest at 65C for 16 hours according to manufacturer instruction. Hybridization mixtures were washed and target/probe complexes were purified and bound to streptavidin coated cartridges. Cartridges were scanned on the nCounter Digital Analyzer with a FOV setting of 550.


title: NS Human meningioma, FFPE 15

label_protocol: 200 ng of total RNA per sample was hybridized to barcoded reporter probes and biotin-conjugated capture probes from a custom codeset targeting genes of interest at 65C for 16 hours according to manufacturer instruction. Hybridization mixtures were washed and target/probe complexes were purified and bound to streptavidin coated cartridges. Cartridges were scanned on the nCounter Digital Analyzer with a FOV setting of 550.


title: T1652_GS8_M_H2


title: OCIAML3_sgNeg_1_3d


title: CL_293_HsaSRRM4_ribominus_b


title: T1652_GS8_M_H1


title: R17

city: Utrecht

first: Wilbert

last: Vermeij

state: Utrecht

address: Heidelberglaan 25

country: Netherlands

institute: Princess Maxima Center for Pediatric Oncology

data_processing:
Trimmomatic: version 0.39 using default settings
STAR: version 2.7.0f using default settings
featurecounts: (SubRead version 1.6.4) default settings with multimapping
EdgeR: version 3.32.1  using default settings
Assembly: GRCm38.p6.genome.fa; gencode.vMN20.annotation.gtf
Supplementary files format and content: Tab-delimited count file produced by featureCounts

source_name: WT 12 week ketogenic diet male

extract_protocol:
For RNA isolation a part cerebellar cortex containing multiple folia from the hemisphere, paravermis and vermis, but no cerebellar nuclei was rapidly dissected, immediately flash frozen in liquid nitrogen and stored at -80°C. Total RNA was extracted using QIAzol lysis reagent and TissueLyser LT (Qiagen). For increased purity, miRNeasy Mini Kits (Qiagen) with additional on-column DNase treatment were used. Concentration and quality of RNA was measured by Nanodrop One (Thermo Fisher Scientific, USA) and BioAnalyser 2100 (Agilent, USA).
The TruSeq RNA Library prep kit V2 (Illumina) was used to capture poly(A) RNA from 500ng total RNA. Subsequently cDNA was made to which single indexed adapters were ligated. To obtain enough material for sequencing a PCR of 13 cycles was performed. Product size was checked on the Labchip GX (Perkin Elmer) and concentrations were measured with picogreen (Invitrogen).

tag: strain

value: F1 hybrid C57BL6J/FVB

value: cerebellar cortex

value: WT

value: ketogenic diet

value: male

tag: time

value: 12 Weeks


title: R16

source_name: WT 12 week dietary restriction male

value: dietary restriction

tag: Sex


title: NS Human meningioma, FFPE 13

extract_protocol: Qiagen FFPE AllPrep Extraction


title: PEO1_R_Ola_rep1


title: PEO1_R_Ola_rep2


title: PEO1_R_DMSO_rep3


title: T1652_GS8_M_G3

value: fail


title: CL_293_GFP_ribominus_b


title: NS Human meningioma, FFPE 12


title: T1652_GS8_M_G1

value: pass


title: PEO1_R_DMSO_rep2


title: T1652_GS8_M_G2


title: R15

source_name: WT 12 week ad libitum male

value: ad libitum


title: NS Human meningioma, FFPE 11


title: R13


title: R14


title: PEO1_R_DMSO_rep1


title: T1678_GS8_M_A1


title: R12


title: NS Human meningioma, FFPE 10


title: PEO1_R_Combo_IgG_CutTag_rep1

city: Aurora

address: 1635 Aurora Ct

data_processing:
Real-Time Analysis v3.4.4 was used for basecalling.
Adapters and low quality reads were trimmed using BBDuk v38.05 using options ‘ktrim=r k=34 mink=11 hdist=1 tpe tbo qtrim=r trimq=10’. Trimmed reads were aligned to the human assembly using BWA-MEM v0.7.15, and only uniquely mapping reads with a minimum MAPQ of 10 were retained. Peak calling was performed with MACS2 v2.1.1 where peaks were called with paired-end option ‘--format BAMPE’. Bigwig files were prepared from the MACS2 normalized bedgraph files using bedGraphToBigWig v4.
Peaks were normalized to spiked-in yeast DNA
Assembly: hg38
Supplementary files format and content: Normalized signal tracks corresponding to read coverage per 1 million fragments in UCSC bigwig format
Supplementary files format and content: Tab-delimited text files including unfiltered narrowPeaks called by MACS2 in UCSC BED format

growth_protocol: PEO1 (RRID:CVCL_2686) cell lines were provided through the Gynecologic Tumor and Fluid Bank. All cells were authenticated via STR at The University of Arizona Arizona Genetics Core (RRID:SCR_012429). All cells undergo monthly mycoplasma testing using Sigma LookOut Mycoplasma Detection kit (Cat. #MP0035) and are only culture up to 20 passages or two months. Cells are cultured in RPMI1640 (Gibco) in 10% FBS (Phoenix Scientific Cat. #PS-100) and Penicillin Streptomycin (Cat. #SV30010) at 37C in 5% CO2. ID8 cells are cultured in DMEM (Gibco, Cat. #11995-065) supplemented with 4% FBS, Penicillin Streptomycin and 1x ITS (Gibco Cat. #41400-045).

extract_protocol:
CUT&RUN was performed using the CUT&RUN Assay Kit (Cell Signaling Technology, Cat. #86652) using the manufacturer’s protocol. 100,000 cells were used for each Input or IP sample. Input samples were sonicated using a Branson Sonifier 250. To achieve fragmentation with a peak at 300 bp, ice cold cells were pulsed 7 x 10 seconds each at 30% power, with one minute incubations on ice between each pulse. IP was performed using 2 μL EHMT2/G9A antibody (Cell Signaling Technology, Cat. #3306; RRID: AB_2097647), 2 μL H3K4me3 antibody (Cell Signaling Technology, Cat. #9751; RRID: AB_2616028), or 5 μL isotype control antibody (Cell Signaling Technology, Cat. #66362; RRID: AB_2924329). According to the manufacturer’s protocol, Sample Normalization Spike-In Yeast DNA was diluted 1:500 in nuclease-free water, and 5 μL (10 pg) of diluted DNA was added to 1X Stop Buffer prior to DNA digestion and diffusion. IP and Input DNA were purified using ChIP DNA Clean & Concentrator columns (Zymo Research, Cat. #D5205). Elution volume was 30 μL. Prior to library preparation, all samples were analyzed for concentration and fragment size by the University of Colorado Pathology Shared Resource using an Agilent Tapestation with D1000 tape. CUT&TAG was performed following the protocol developed by Kaya-Okur et al (PMID: 32913232) with the following specifications: 500,000 (option A) PEO1-OR cells (treated with DMSO control or 2μM olaparib + 1μM UNC0642 for 72 hours) were used as starting input. The following antibodies were used for primary antibody binding: H3K27Ac (EMD Millipore, Cat. #MABE647; RRID:AB_2893037), H3K4me2 (Epicypher, Cat. #13-0027), no primary antibody (negative control). Guinea Pig anti-Rabbit IgG (Antibodies, Cat. #ABIN101961; RRID:AB_10775589) was used for secondary antibody binding. For CUTAC (using H3K4me2 antibody), the CUTAC tagmentation buffer (10 mM TAPS, 5 mM MgCl2) was used instead of the CUT&TAG tagmentation buffer, and incubated at 37 degrees (step 35iv) for 20 minutes instead of 1 hour. Library sequencing was performed on an Illumnia NovaSEQ 6000 by the University of Colorado Genomics and Microarray Core.
CUT&RUN library were prepared using 5 ng IP DNA or 50 ng Input DNA. SimpleChIP ChIP-seq Multiplex Oligos for Illumina - Single Index Primers (Cell Signaling Technology, Cat. #29580) and the SimpleChIP ChIP-seq DNA Library Prep Kit for Illumina (Cell Signaling Technology, Cat. #56795) were used with protocol modifications for CUT&RUN as recommended by Cell Signaling. The second step of End Prep was performed for 30 minutes at 50 °C, rather than 65 °C. AMPure XP beads (Beckman Coulter, Cat. #A63880) in cleanup steps were used at a 1.1X volume, rather than 0.9X. After washes and prior to resuspension, beads were air dried for 3 minutes. To prevent large fragment amplification during PCR enrichment of adaptor-ligated DNA, the Anneal and Extension step is 65 °C for 15 seconds, rather than 75 seconds. For IP samples, 12 cycles were performed. For Input samples, 6 cycles were performed. To achieve higher final concentration, elution following PCR amplification was performed in 17 μL 10 mM Tris-HCL pH 8.5, with 15 μL final collection volume. Library sequencing was performed on an Illumina NovaSEQ 6000 by the University of Colorado Genomics and Microarray Core.
CUT&RUN and CUT&TAG

tag: antibody

value: IgG, Antibodies, Cat. #ABIN101961; RRID:AB_10775589


title: NS Human meningioma, FFPE 8


title: NS Human meningioma, FFPE 9


title: PEO1_R_Ola_rep3

value: olaparib


title: NS Human meningioma, FFPE 7


title: PEO1_R_Combo_CUTAC_CutTag_rep1

value: H3K4me2, Epicypher, Cat. #13-0027


title: R11


title: R10


title: T1652_GS8_M_F2

value: Single prostate tumor cell

tag: cpg coverage


title: T1652_GS8_M_F3


title: T1652_GS8_M_E3


title: T1652_GS8_M_F1


title: T1652_GS8_M_E2


title: PEO1_R_DMSO_CUTAC_CutTag_rep1

tag: treatment

value: DMSO


title: R8


title: NS Human meningioma, FFPE 6

value: Tumor


title: R7


title: T1652_GS8_M_E1

tag: bisulfite conversion_rate


title: PEO1_R_DMSO_IgG_CutTag_rep1

tag: cell type


title: PEO1_R_DMSO_H3K27Ac_CutTag_rep1

value: H3K27Ac, EMD Millipore, Cat. #MABE647; RRID:AB_2893037


title: PEO1_R_H3K4me3_CutRun_rep1

value: H3K4me3, Cell Signaling Technology, Cat. #9751; RRID:AB_2616028

value: untreated


title: NS Human meningioma, FFPE 4


title: NS Human meningioma, FFPE 3


title: NS Human meningioma, FFPE 5


title: T1652_GS8_M_D3

tag: qc


title: R9

value: F1 hybrid C57BL6J/FVB

value: cerebellar cortex

value: WT


title: PEO1_R_IgG_CutRun_rep1

value: IgG, Cell Signaling Technology, Cat. #66362; RRID:AB_2924329


title: NS Human meningioma, FFPE 2


title: T1652_GS8_M_D2


title: T1652_GS8_M_D1


title: PEO1_R_Combo_H3K27Ac_CutTag_rep1


title: Young (6 month) Vertebrae 9

city: Rochester

first: David

last: Monroe

address: 200 1st St SW

institute: Mayo Clinic

data_processing:
Analysis was performed using the edgeR package in R and normalized expression was used to determine the log fold-change
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw values for each sample

source_name: Vertebrae (L4-5)

extract_protocol:
RNA was harvested using QIAzol reagent and purified using the Rneasy mini plus kit (Qiagen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Lib NEBNEXT Small RNA v2 Kit following manufacturer's protocols.

value: Vertebrae (L4-5)

value: Male

tag: age

value: 6 month


title: Young (6 month) Vertebrae 10

tag: tissue


title: w1118_ZT7_3_S28_

city: Waltham

first: Sebastian

last: Kadener

address: 415 South Street

department: Biology department

institute: Brandeis University

data_processing:
data were aligned to the Drosophila melanogaster dm6 genome and transcriptome version using STAR
quantification was done with ESAT
The circadian analysis was performed using the package MetaCycle
For each circadian timepoint, three replicates were analyzed. Since each replicate was sequenced separately, the counts were divided by the maximum value in each replicate after normalizing by library size. Genes with more than two zero counts at any time point were discarded. The amplitude for each replicate was calculated as the maximum divided by the minimum for each gene. The JTK algorithm was used for the circadian analysis
A gene was considered a cycler if the JTK p-adjusted value was less than 0.05 and the amplitude was more than 2.
Assembly: dm6
Supplementary files format and content: normalized counts

source_name: Brain

growth_protocol: All crosses were performed and raised at 25 °C in a 12:12 Light/Dark cycle (LD) conditions.

extract_protocol:
RNA from the fly brains was extracted using TRIzol reagent (Sigma, T9424) and treated with DnaseI (NEB, M0303L).
150 ng of RNA as input for preparing 3' RNA sequencing libraries following CelSeq2 protocol

value: Brain


title: NS Human meningioma, FFPE 1

address: 1450 3rd Street, HD 402

institute: UCSF


title: T1652_GS8_M_C3

value: pass


title: Young (6 month) Vertebrae 8


title: w1118_ZT3_3_S26_


title: PEO1_R_Combo_G9a_CutRun_rep1

value: G9a, Cell Signaling Technology, Cat. #3306; RRID:AB_2097647


title: PEO1_R_Combo_G9a_CutRun_rep2


title: w1118_ZT19_3_S34_


title: T1652_GS8_M_C2

value: fail


title: Young (6 month) Vertebrae 7


title: PEO1_R_UNC_G9a_CutRun_rep2


title: Young (6 month) Vertebrae 6


title: T1652_GS8_M_C1

value: Single prostate tumor cell


title: T1652_GS8_M_B3


title: w1118_ZT11_3_S30_


title: R6

value: ketogenic diet

value: male

value: 12 Weeks


title: w1118_ZT23_3_S36_


title: PEO1_R_UNC_G9a_CutRun_rep1


title: Young (6 month) Vertebrae 5


title: PEO1_R_Ola_G9a_CutRunrep2

value: olaparib


title: PEO1_R_DMSO_G9a_CutRun_rep2

value: DMSO


title: T1652_GS8_M_B2


title: PEO1_R_Ola_G9a_CutRunrep1


title: w1118_ZT7_2_S16_


title: Young (6 month) Vertebrae 3


title: T1652_GS8_M_B1


title: w1118_ZT15_3_S32_


title: PEO1_R_DMSO_G9a_CutRun_rep1


title: w1118_ZT3_2_S14_


title: T1652_GS8_M_A3


title: BP03, TCRseq

city: Epalinges

first: Mathilde

last: Foglierini-Perez

address: Chemin de Boveresses 155

country: Switzerland

institute: CHUV

description: 10X genomics

data_processing:
BCL-files were demultiplexed into samples using bcl2fastq 2.20
scRNA: The barcoded processing and gene counting were made using the Cell Ranger v6.0.0 software with method count
VDJ: The barcoded processing, V(D)J sequences and annotations were made using the Cell Ranger v6.0.0 software with method vdj
Assembly: mRNA: cellranger gex-GRCh38-2020-A
Assembly: VDJ: cellranger-vdj-GRCh38-alts-ensembl-5.0.0
Assembly: hg38
Supplementary files format and content: mRNA: h5 of count matrix
Supplementary files format and content: VDJ: tsv table of cell annotations (AIRR format)

source_name: biopsed skin

extract_protocol:
4 mm punch biopsies were harvested from the IDR site 24h after skin test from 3 vaccinated controls. Skin biopsies were mechanically and enzymatically digested using DNAse I and collagenase D. Single-cell suspensions were stained with APC conjugated anti-CD45 antibodies. Fluorescence-activated cell sorting (FACS) of CD45-labelled cells was performed on a BD aria sorter for 10x RNA sequencing.
Library construction was performed according to the manufacture's protocol (single cell 5' v2 (dual index) + human TCR amplification). To generate gel beads-in-emulsion (GEMs), T cells were loaded to Chromium Next GEM Chip K together with master mix, gel beads and partitioning oil. After GEM generation, poly-A RNA was retrotranscripted to cDNA and Illumina R1 primer sequence, Unique Molecular Identifier (UMI) and a 10x Barcode were included. For final library construction, pooled cDNA was cleaned up with Silane DynaBeads, further amplified by PCR and size-restricted by using SPRIselect reagent. To generate TCR libraries, a part of the amplified cDNA was used for V(D)J amplification followed by SPRIselect cleanup steps. During final library construction and V(D)J amplification, Illumina R2 primer and paired-end constructs were included. scRNA-seq and TCR seq

value: biopsed skin

value: CD45 immune cell

tag: antibodies/tag

tag: library type

value: mRNA


title: T1652_GS8_M_A2


title: Young (6 month) Vertebrae 1


title: BP03, scRNA

description: 10X genomics


title: Young (6 month) Vertebrae 2


title: T1652_GS8_M_A1


title: Old (24 month) Vertebrae 10

value: 24 month


title: w1118_ZT15_2_S20_


title: Young (6 month) Vertebrae 4

value: Vertebrae (L4-5)


title: Myc-Cap-M-H2

value: ATCC cell line cells

value: Myc-Cap


title: Old (24 month) Vertebrae 9

value: Male


title: Old (24 month) Vertebrae 8


title: w1118_ZT23_2_S24_

value: Brain


title: Myc-Cap-M-G3

value: pass


title: w1118_ZT15_1_S8_


title: Old (24 month) Vertebrae 7


title: Myc-Cap-M-G2


title: BP01, TCRseq

description: 10X genomics


title: BP01, scRNA

description: 10X genomics


title: w1118_ZT3_1_S2_


title: Myc-Cap-M-F3


title: Old (24 month) Vertebrae 6


title: w1118_ZT19_2_S22_


title: Myc-Cap-M-F2


title: Old (24 month) Vertebrae 5


title: w1118_ZT19_1_S10_


title: Old (24 month) Vertebrae 4