title: CHIPseq_CHIPsample_HAtaggedNPM1_2i

data_processing:
The single-end 100bp ChIPseq reads were aligned to the mouse mm10 reference genome using Bowtie2 (version 2.3.4.3). Read counts were computed and normalized using “bamCoverage” from deepTools (version 3.2.1) using a bin size of 50 bp.NPM1 bound regions were defined using MACS2 by comparing the HA CHIP of tagged NPM1 ESCs and input.
Assembly: mm10 (GRCm38)
Supplementary files format and content: Integrative Genome Viewer (IGV, version 2.5.2) was used to visualize and extract representative ChIPseq tracks in bigwig file format

extract_protocol:
Briefly, 1% formaldehyde was added to cultured cells to cross-link proteins to DNA. Isolated nuclei were then lysed with lysis buffer [(50 mM Tris-HCl, pH 8.1, 10 mM EDTA, pH 8, 1% SDS, 1X cOmplete™ protease inhibitor EDTA-free cocktail (Roche, 1187358001)]. Nuclei were sonicated using a Bioruptor ultrasonic cell disruptor (Diagenode) to shear genomic DNA to an average fragment size of 200 bp. 50ug of chromatin for NPM1 CHIP was diluted to a total volume of 500 μl with ChIP buffer (16.7 mM Tris-HCl, pH 8.1, 167 mM NaCl, 1.2 mM EDTA, 0.01% SDS, 1.1% Triton X-100) and pre-cleared with 10 μl packed Protein A Sepharose CL-4B resin (Cytivia, 17078001) for 2 hours at 4°C. Pre-cleared chromatin was incubated overnight with the ChIP-grade antibody against HA (abcam, ab9110). The next day, Dynabeads™ Protein A (Invitrogen, 10001D)  for HA CHIP was added and incubated for 4 hours at 4°C. After washing, bound chromatin was eluted with the elution buffer (1% SDS, 100 mM NaHCO3). Upon proteinase K (ThermoFisher Scientfic, EO0491) digestion at 50 °C for 3 h and reversion of cross-linking (65 °C, overnight), DNA was purified with phenol/chloroform, ethanol precipitated and quantified.
For ChIPseq library preparation, the quantity and quality of the isolated DNA was determined with Qubit® 4 Fluorometer (Life Technologies). Libraries were prepared using the NEBNext®Ultra™II DNA Library Prep for Illumina (New England Biolabs, E7645S and E7645L) following the manufacturer’s protocol. Briefly, ChIP and input samples (10 ng) were first end-repaired and polyadenylated. Then, the ligation of Illumina compatible adapters containing the index for multiplexing was performed. The quality and quantity of the enriched libraries were evaluated using Qubit®4 Fluorometer and 4200 TapeStation System (Agilent). Sequencing was performed on an Illumina NovaSeq6000 machine with single-end 100 bp reads for NPM1.

value: HA


title: CHIPseq_CHIPsample_WT2i

status: Public on May 22 2025

type: SRA

city: Zurich

first: Raffaella

last: Santoro

address: Winterthurerstrasse 190

department: Dep. of Molecular Mechanisms  of Disease

country: Switzerland

institute: University of Zurich

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

growth_protocol: Mouse embryonic stem cells (E14) were cultured in N2B27 medium with LIF/2i

tag: cell line

tag: cell type

value: Mouse embryonic stem cells (ESCs)

tag: genotype

tag: antibody


title: H3K9me2_CHIPseq_Inputsample_WT2i

data_processing:
The single-end 100bp ChIPseq reads were aligned to the mouse mm10 reference genome using Bowtie2 (version 2.3.4.3).Read counts were computed and normalized using “bamCoverage” from deepTools (version 3.2.1) using a bin size of 50 bp. To calculate read coverage for 20 kb bin region of H3K9me2 ChIPseq, “multiBamSummary” from deepTools was used.
Assembly: mm10 (GRCm38)
Supplementary files format and content: Integrative Genome Viewer (IGV, version 2.5.2) was used to visualize and extract representative ChIPseq tracks in bigwig file format

extract_protocol:
Briefly, 1% formaldehyde was added to cultured cells to cross-link proteins to DNA. Isolated nuclei were then lysed with lysis buffer [(50 mM Tris-HCl, pH 8.1, 10 mM EDTA, pH 8, 1% SDS, 1X cOmplete™ protease inhibitor EDTA-free cocktail (Roche, 1187358001)]. Nuclei were sonicated using a Bioruptor ultrasonic cell disruptor (Diagenode) to shear genomic DNA to an average fragment size of 200 bp. 20 μg of chromatin for H3K9me2 CHIP  was diluted to a total volume of 500 μl with ChIP buffer (16.7 mM Tris-HCl, pH 8.1, 167 mM NaCl, 1.2 mM EDTA, 0.01% SDS, 1.1% Triton X-100) and pre-cleared with 10 μl packed Protein A Sepharose CL-4B resin (Cytivia, 17078001) for 2 hours at 4°C. Pre-cleared chromatin was incubated overnight with the ChIP-grade antibody against H3K9me2 (abcam, ab1220). The next day, Dynabeads™ Protein G (Invitrogen, 10003D) for H3K9me2 CHIP was added and incubated for 4 hours at 4°C. After washing, bound chromatin was eluted with the elution buffer (1% SDS, 100 mM NaHCO3). Upon proteinase K (ThermoFisher Scientfic, EO0491) digestion at 50 °C for 3 h and reversion of cross-linking (65 °C, overnight), DNA was purified with phenol/chloroform, ethanol precipitated and quantified.
For ChIPseq library preparation, the quantity and quality of the isolated DNA was determined with Qubit® 4 Fluorometer (Life Technologies). Libraries were prepared using the NEBNext®Ultra™II DNA Library Prep for Illumina (New England Biolabs, E7645S and E7645L) following the manufacturer’s protocol. Briefly, ChIP and input samples (10 ng) were first end-repaired and polyadenylated. Then, the ligation of Illumina compatible adapters containing the index for multiplexing was performed. The quality and quantity of the enriched libraries were evaluated using Qubit®4 Fluorometer and 4200 TapeStation System (Agilent). Sequencing was performed on an Illumina NovaSeq6000 machine with single end at 100 bp reads for H3K9me2.

treatment_protocol: For CHIP of H3K9me2, 0.4X106 ES cells were seeded into gelatin coated 10 cm dishes 4 hour prior to siRNA transfection using Lipofectamine® RNAiMAX Transfection Reagent  (Invitrogen, 13778150) in Opti‐MEM® GlutaMAX™ (Gibco, 31985062) reduced‐serum medium Transfection Reagent (Invitrogen 13778150) following the manufacturer’s instructions. The cells were harvested post 72 hours for CHIP.

tag: treatment

value: ESCs were transfected with control siRNA and collected 3 days post transfection


title: H3K9me2_CHIPseq_Inputsample_NPM1KD_2i

value: ESCs were transfected with siRNA targeting NPM1 and collected 3 days post transfection


title: SE initiating cells, shFOXO4, rep2

city: Guangzhou

first: Jiafeng

last: Liu

state: Guangdong

address: No.7 Jinsui Road, Tianhe District, Guangzhou

country: China

institute: sun yat-sen university

library_source: transcriptomic

data_processing:
The raw sequenced reads underwent quality testing and were trimmed of adapters using the trimmomatic tool (version 0.39)
The STAR software (version 2.6.1) was utilized to align the trimmed reads to the human hg19 reference genome.
The gene expression levels were quantified and the transcripts per kilobase million (TPM) values were calculated using the RSEM tool (version 1.3.0).
Using DESeq2 (version 1.20.0), differentially expressed genes were identified with a q-value cutoff of ≤ 0.05 and a fold change of ≥ 2.
Assembly: hg19
Supplementary files format and content: excel file includes normalized counts foe each sample

molecule: total RNA

organism: Homo sapiens

extract_protocol:
Total RNA was extracted using the MolPure Cell/Tissue Total RNA Kit (Yeasen)
The TruSeq Stranded mRNA Library Prep kit (Illumina) was used for the RNA-seq libraries construction

value: human embryonic stem cell

value: FOXO4 knockdown

value: SE differentiation


title: CHIPseq_Inputsample_HAtaggedNPM1_2i


title: SE matutating cells, shSP6, rep2

value: SP6 knockdown


title: SE initiating cells, scramble_FOXO4, rep2

value: scramble shRNA-treated


title: SE initiating cells, shFOXO4, rep1


title: SE matutating cells, shSP6, rep1


title: SE matutating cells, shFOXO4, rep1


title: SE matutating cells, scramble_FOXO4, rep1


title: TOXOTRM3 spleen 154dpi (CD8+ T cell-enriched) CSP

city: Toulouse Cedex 3

first: Nicolas

last: Blanchard

address: CHU Purpan BP3028

department: Inserm UMR1291

country: France

institute: Toulouse Institute for Infectious and Inflammatory Diseases (Infinity)

description: CSP library

library_source: other

data_processing:
Fastq files processing was carried out with CellRanger 10X software (version 4.0.0) and reads were mapped against mouse reference genome (version mm10-2020-A). Filtered barcode matrix generated from CellRanger was then loaded into R (version 4.0.3) (R Core Team. R Foundation for Statistical Computing, 2022) and used as input for Seurat R package (version 4.2.1).
Assembly: Mus musculus (version mm10-2020-A)
Supplementary files format and content: .rds file

molecule: other

source_name: spleen

extract_protocol:
Whole brains (including the pia mater, but excluding the dura mater and arachnoid tissue which remain attached to the skull) were collected in complete RPMI supplemented with 10% vol/vol FCS, homogenized using a glass Potter and digested for 45 min at room temperature in HBSS with collagenase D (1 mg/mL) and deoxyribonuclease (DNase) I (20 ug/mL). After digestion, cells were suspended in 30% Percoll (GE Healthcare) and centrifuged at 1590g for 30 min without brake.  Myelin and debris were removed, brain leukocytes were recovered from the interface. Before scRNA-seq, CD103-negative and CD103-positive subpopulations of Kb-OVA dextramer+ CD8+ T cells were separated by Facs-sorting.  For CITE-seq, brain cell suspensions were incubated for 45 min at RT with the following barcoded dextramers diluted in complete RPMI: Kb-SIINFEKL (Immudex cat # JD2163-PfBC, barcode fBC0074: CGGTCTTAGTCGCGC, dilution 1:50), control Kb-SIYRYYGL (Immudex cat # JD2164-PfBC, barcode fBC0068: TTGCGCGGCGTCGTA, dilution 1:50), and then surface labelled for 30 min at 4°C with TotalSeq-C0182 anti-mouse CD3 (clone 17A2, dilution 1:50, Biolegend, cat # 100263) and TotalSeq-C0002 anti-mouse CD8 (clone 53-6.7, dilution 1:50, Biolegend, cat # 100785) diluted in ‘Facs buffer’ (PBS, 2mM EDTA, 0.5% FCS).
Single-cell libraries were generated with Chromium Next GEM Single Cell 5' Kit v2 and 5' Feature Barcode Kit (10X Genomics).
CITE-seq

tag: tissue

value: spleen

value: magnetically enriched CD8+ T cells


title: TOXOTRM3 spleen 154dpi (CD8+ T cell-enriched) RNA

description: GEX library


title: SE initiating cell, shSP6, H3K27ac, ChIP, Rep1

data_processing:
Before alignment, raw reads underwent quality control and adapter trimming using the trimmomatic tool, specifically version 0.39.
The trimmed reads were aligned to the human hg19 reference genome using the BWA software, specifically version 0.7.17.
PCR duplicates were subsequently removed using the Picard tools, specifically version 2.18.16. Peak calling for ChIP-seq data was carried out using MACS2, specifically version 2.1.1.
The Homer mergePeaks program was used to identify overlapping peaks between biological replicates. Additionally, the bedGraph files generated by MACS2 were converted to bigwig format using the deepTools bamCoverage program.
Assembly: hg19
Supplementary files format and content: bigWig

extract_protocol:
Cells grown on 10 cm culture dishes were subjected to crosslinking with 1% formaldehyde at room temperature for a duration of 10 minutes, followed by quenching with 0.125M glycine. Subsequently, the cells were lysed in ice-cold sonication buffer and sonicated using a Covaris M220 focused-ultrasonicator.
The ChIP-seq libraries were prepared by following the manufacturer's instructions with the KAPA Hyper Prep Kit (Kapa Biosystems, KK8502), and were then sequenced on the NovaSeq 6000 platform (Illumina) utilizing 150 bp paired-end reads.


title: SE initiating cells, scramble_FOXO4, rep1


title: RNAseq_ESC_ContsiRNA_rep1

data_processing:
The quality of the 100 bp single end reads generated by the machine was checked by FastQC (Andrews, 2010). The quality of the reads was increased by applying: a) SortMeRNA (Kopylova, 2012) (version 2.1) tool to filter out ribosomal RNA; b) Trimmomatic (Bolger, 2014) (version 0.36) software package to trim the sorted (a) reads. The sorted (a), trimmed (b) reads were mapped against the mouse genome (mm10) using the default parameters of the STAR (Spliced Transcripts Alignment to a Reference, version 2.4.0.1) (Dobin et al., 2013). For each gene, exon coverage was calculated using a custom pipeline and then normalized in reads per kilobase per million (RPKM) (Mortazavi et al., 2008), the method of quantifying gene expression from RNA sequencing data by normalizing for total read length and the number of sequencing reads.
Assembly: mm10 (GRCm38)
Supplementary files format and content: xlsx
Supplementary files format and content: Excel file includes the DESeq2 computed mean of normalized count of all samples based on sequencing depth

extract_protocol:
Total RNA was purified with TRIzol reagent (Life Technologies).
The quality of the isolated RNA was determined with a Qubit® 4 Fluorometer and 4200 Tape Station system. Only those samples with a 260nm/280 nm ratio between 1.8–2.1 and a 28S/18S ratio within 1.5-2 were further processed. The TruSeq Stranded mRNA (Illumina) was used in the succeeding steps. Briefly, total RNA samples (100-1000 ng) were polyA enriched and then reverse-transcribed into double-stranded cDNA. The cDNA samples were fragmented, end-repaired and adenylated before ligation of TruSeq adapters containing unique dual indices (UDI) for multiplexing. Fragments containing TruSeq adapters on both ends were selectively enriched with PCR. The quality and quantity of the enriched libraries were validated using Qubit® 4 Fluorometer. The product is a smear with an average fragment size of approximately 260 bp. Libraries were normalized to 10 nM in Tris-Cl 10 mM, pH8.5 with 0.1% Tween 20. TheIllumina NovaSeq X Pluswas used for cluster generation and sequencing according to standard protocol. Sequencing was single end at 100 bp.

treatment_protocol: 8x10^4 parental ESCs were seeded into gelatin-coated 6 cm plate. Cells were let to attach for 4 hour and then transfected with 2 μl of 40 μM siRNA stock using Lipofectamine RNAiMAX Transfection Reagent (Invitrogen, 13778150) following the manufacturing instructions

value: WT


title: murine hepatocyte 3A Extracellular Vescicles, shPCBP2 Replicate 2

city: Roma

first: Alessio

last: Colantoni

state: RM

address: Piazzale Aldo Moro, 5

department: Dipartimento di Biologia e Biotecnologie "Charles Darwin"

country: Italy

institute: "Sapienza" University of Rome

data_processing:
FastqToolkit version 2.2.5 (available at https://www.illumina.com/products/by-type/informatics-products/basespace-sequence-hub/apps/fastq-toolkit.html) was used to remove adapter sequences from the 3’ end and to filter out reads whose length and average quality after trimming were < 10 and < 30, respectively. Only forward reads were kept for downstream analyses.
The mirPRo software, which utilizes NovoAlign as its alignment engine, was used to align reads to a reference composed of miRNA hairpin sequences downloaded from miRBase v22.1 database with the addition of the spike-in, and to count reads mapping to mature miRNAs.
Assembly: miRBase v22.1 hairpin sequences +  cel-miR-39 Spike-In
Supplementary files format and content: Tab-delimited text file including mature miRNA raw counts (including the spike-in) for each sample.

growth_protocol: Nontumorigenic murine hepatocyte 3A cells  were grown at 37°C, in a humidified atmosphere with 5% CO2, in RPMI 1640 medium supplemented with 10% FBS (Gibco Life Technology), 50 ng/mL epidermal growth factor (EGF), 30 ng/mL insulin growth factor (IGF) II (PeproTech), 10 mg/mL insulin (Roche), and penicillin/streptomycin, on dishes coated with collagen I (Collagen I, Rat Tail; Gibco Life Technology). Extracellular vesicles were prepared according to International Society of Extracellular Vesicles (ISEV) recommendations. Conditioned media (CM) from 150 mm plates each containing 250000 hepatocytes were collected after 72-hrs culture in complete medium containing EV-depleted FBS. Cell-conditioned media were centrifuged at 2000  g for 20 min at 4°C to remove dead cells and then at 20000  g for 30 min at 4°. Cleared supernatants were passed through 0.22 mm filter membranes, ultracentrifuged in a SW32 Ti rotor at 100,000 rpm for 70 min at 4°C, and finally resuspended in PBS. The EVs resuspension was analyzed by EXOID-V1-SC (IZON) for size and concentration characterization.

extract_protocol:
miRNAs were extracted using miRNeasy Mini kit and Rneasy MinElute Cleanup Kit (Qiagen)
miRNA samples, to which the cel-miR-39 Spike-In (59000; NORGEN) was previously added, were sequenced at Procomcure Biotech GmbH. Sequencing libraries were prepared using the NEXTFLEX Small RNA-Seq Kit v4 (PerkinElmer).

treatment_protocol: Stable PCBP2 knockdown was achieved through infection with shRNAs cloned in pSUPER retro puro retroviral vector (Oligoengine). Viral supernatants were collected 48 hrs after transfection of 293gp packaging cells, filtered (0.45 mm), and added to hepatocytes. At 48 hrs post-infection, selection was performed with 2 µg/mL puromycin for at least 1 week before analysis.

value: murine hepatocyte extracellular vescicles


title: input


title: SE initiating cell, scramble, H3K27ac, ChIP, Rep1


title: TOXOTRM3 brain 154dpi (CD8+ T cell-enriched) CSP

description: CSP library

source_name: brain

value: brain


title: murine hepatocyte 3A Extracellular Vescicles, shPCBP2 Replicate 1


title: murine hepatocyte 3A Extracellular Vescicles, shCTRL Replicate 2

value: shCTR


title: SE initiating cell, scramble, H3K27ac, ChIP, Rep2


title: SE initiating cell, shFOXO4, H3K4me3, ChIP, Rep2


title: SE initiating cell, shFOXO4, H3K4me3, ChIP, Rep1


title: murine hepatocyte 3A cells, shPCBP2 2 Replicate 2

value: murine hepatocyte cells


title: TOXOTRM3 brain 154dpi (CD8+ T cell-enriched) RNA

description: GEX library


title: SE initiating cell, scramble, H3K4me3, ChIP, Rep1


title: murine hepatocyte 3A Extracellular Vescicles, shCTRL Replicate 1


title: CHIPseq_Inputsample_WT2i


title: murine hepatocyte 3A cells, shCTRL Replicate 1


title: SE initiating cell, H3K27ac, ChIP, Rep1


title: murine hepatocyte 3A cells, shPCBP2 Replicate 1


title: IgG2 [ChIP-seq]

city: Beijing

first: Yixiao

last: Zhang

address: Xueyuan Road, No.38

institute: Peking Unversity

data_processing:
SnakePipes (v2.5. 1) was used to perform quality control of the downstream data, and then Hisat2 software was used to align the sequences to the mm10 reference genome for comparison analysis,
Sequences that did not align to the reference genome, sequences with low comparison quality, were discarded, Peak detection analysis was then completed using macs2 software (peak calling) and annotation of peaks using Chipseeker,
sequence reads were trmmed for adaptor
identification of conserved feature sequences at peak-enriched sites for motif analysis using Meme software. The distribution of peaks along genomic regions of genes of interest was visualised using the Integrated Genomics Viewer (IGV).
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

source_name: pro-B cell

growth_protocol: B220+IgM-CD43+ pro-B cells were sorted out from bone marrow cell suspensions in mice

extract_protocol:
Cells were fixed with 1% Fomaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using an E220 focused ultrasonicator (Covaris).
ChIP samples were prepared using the PIERCE MAGNETIC CHIP KIT30 RXNS KIT 4725 (Thermo Fisher, 26157) according to the manufacturer's protocol.

value: pro-B cell

tag: chip antibody

value: ms IgG


title: SE initiating cell, H3K4me3, ChIP, Rep1


title: SE initiating cell, shSP6, H3K27ac, ChIP, Rep2


title: SE initiating cell, H3K27ac, ChIP, Rep2


title: SE initiating cell, H3K4me1, ChIP, Rep2


title: SE initiating cell, H3K4me1, ChIP, Rep1


title: IgD1 [ChIP-seq]

value: anti-ms IgD


title: IgD2 [ChIP-seq]


title: SE initiating cell, SP6 , ChIP, Rep2


title: IgG1 [ChIP-seq]


title: SE initiating cell, SP6 , ChIP, Rep1


title: iMEK_B6_replicate3

city: New York

first: Prokopios Alexandros

last: Polyzos

address: 413 E 69th St

country: USA

institute: Weill Cornell Medicine

data_processing:
Paired-end read alignment to mouse genome (mm10 version) was performed with STAR aligner (version 2.7.10) with default setting. Samtools were used for filtering and sorting aligned reads before annotation to “mm10.GRCm38.95.gtf” gene version with htseq-count (0.6.1p1 version). Only protein-coding and long-non-coding RNA transcripts were used for annotation and downstream differential expression analysis was performed with R package DESeq.
Assembly: mm10 and mm10.GRCm38.95.gtf
Supplementary files format and content: raw counts for all samples are submitted in tab delimited format with official gene symbol and ensembl gene id

source_name: ESC

growth_protocol: Mouse ESC's  were maintained in Embryonic Stem cell media (KO-DMEM) in serum/Lif conditions in humidified atmosphere with 5% CO2 at 37C .

extract_protocol:
RNA was extracted using the  Trizol extraction method and then purified using the Zymo Rna Clean and concentrator kit.
Sequencing libraries were prepared using TruSeq Stranded mRNA Library Prep( Illumina)following the manufacturer’s instructions. High-throughput sequencing was performed on an Illumina NovaSeq 6000 platform.

treatment_protocol: DMSO or 1uM of Mek inhibitor (iMEK) was added to the culture from Day0 to Day 5 daily.

value: ESC

tag: Sex

value: male

value: Mek inhibitor


title: DMSO_B6_replicate3

value: DMSO


title: iMEK_B6_replicate2


title: SE initiating cell, FOXO4, ChIP, Rep2

value: human embryonic stem cell

value: SE differentiation


title: SE initiating cell, FOXO4, ChIP, Rep1


title: SE initiating cell, scramble, H3K4me3, ChIP, Rep2

value: scramble shRNA-treated


title: SE initiating cell, shSP6, ATAC, Rep2

data_processing:
Before alignment, raw reads underwent quality control and adapter trimming using the trimmomatic tool, specifically version 0.39.
The trimmed reads were aligned to the human hg19 reference genome using the BWA software, specifically version 0.7.17.
PCR duplicates were subsequently removed using the Picard tools, specifically version 2.18.16. Peak calling for ATAC-seq data was carried out using MACS2, specifically version 2.1.1.
The Homer mergePeaks program was used to identify overlapping peaks between biological replicates. Additionally, the bedGraph files generated by MACS2 were converted to bigwig format using the deepTools bamCoverage program.
Assembly: hg19
Supplementary files format and content: bigWig

extract_protocol:
Cells were harvested and lysed using ice-cold lysis buffer, subsequently, the nuclei were resuspended and allowed to incubate in a transposase reaction mixture (TD501, Vazyme Biotech) at a temperature of 37°C for a duration of 30 minutes. Purification of the transposed DNA fragments was accomplished using the MinElute PCR Purification Kit supplied by QIAGEN.
The construction of the ATAC-seq library, which encompassed steps such as end-repairing, adapter ligation, and PCR amplification, was carried out following the manufacturer's instructions using the TruePrep DNA Library Prep Kit (TD501, Vazyme Biotech).

value: SP6 knockdown


title: murine hepatocyte 3A cells, shCTRL Replicate 2


title: DMSO_B6_replicate2


title: SE initiating cell, H3K4me3, ChIP, Rep2


title: SE initiating cell, shSP6, ATAC, Rep1


title: SE initiating cell, scramble_S, ATAC, Rep1


title: SE initiating cell, scramble_S, ATAC, Rep2


title: iMEK_129_replicate3


title: DMSO_129_replicate3


title: SE initiating cell, shFOXO4, ATAC, Rep1

value: FOXO4 knockdown


title: DMSO_129_replicate2


title: SE initiating cell, shFOXO4, ATAC, Rep2


title: iMEK_129_replicate1


title: SE initiating cell, scramble_F, ATAC, Rep2


title: SE initiating cell, ATAC, Rep1

value: WT


title: SE initiating cell, ATAC, Rep2


title: SE initiating cell, scramble_F, ATAC, Rep1


title: DMSO_129_replicate1


title: Res3_ATAC

city: Chengdu, Cihna

first: Xaingyu

last: Pan

state: Sichuan

address: No.17 Renming road section3

department: State Key Laboratory of Biotherapy, West China Hospital, Sihcuan University.

institute: Sichuan University

data_processing:
To remove adapters from the raw data, NGmerge (v.0.3) was employed. Bowtie2 (v.2.2.1) was used for sequencing reads alignment to the mm10 genome, and samtools (v.1.8) was utilized to generate the .bam files. PCR duplicates were removed using MarkDuplicates, implemented in GATK (v.4.1.3), with the parameter -REMOVE_DUPLICATES = true. Bigwig files were generated using bamCoverage, with bins per million normalizations to account for library size effects. For optimizing peak calling in ATAC-seq data, HMMRATAC (v.1.2.5) was employed as the peak detector to identify peak regions in each sample. ChIPseeker (v.1.22.1) was used to annotate the regions within each peak, and the global transcription start site (TSS) distribution was annotated using TxDb.Mmusculus.UCSC.mm10.knownGene as the reference genome in R (v.3.6.1).
FeatureCounts (RRID:SCR_012919) was employed to quantify the count levels within each peak region. The DESeq2 (v.1.26.0, RRID:SCR_000154) pipeline was utilized to identify significantly differentially expressed peaks based on a p value of < 0.05 and an absolute log2 fold change of > 0.5.
Assembly: mm10
Supplementary files format and content: EXCEL

source_name: NSCLC

extract_protocol:
1. Prepare nuclei. To prepare nuclei, we spun 50,000 cells at 500g for 5 min, which was followed by a wash using 50 µL of cold 1× PBS and centrifugation at 500g for 5 min. Cells were lysed using cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630). Immediately after lysis, nuclei were spun at 500g for 10 min using a refrigerated centrifuge. To avoid losing cells during the nuclei prep, we used a fixedangle centrifuge and carefully pipetted away from the pellet after centrifugations. 2. Transpose and purify. Immediately following the nuclei prep, the pellet was resuspended in the transposase reaction mix (25 µL 2× TD buffer, 2.5 µL transposase (Illumina) and 22.5 µL nucleasefree water). The transposition reaction was carried out for 30 min at 37 °C. Directly following transposition the sample was purified using a Qiagen MinElute kit.3. PCR. Following purification, we amplified library fragments using 1× NEBnext PCR master mix and 1.25 µM of custom Nextera PCR primers 1 and 2 (Supplementary Table 1), using the following PCR conditions: 72 °C for 5 min; 98 °C for 30 s; and thermocycling at 98 °C for 10 s, 63 °C for 30 s and 72 °C for 1 min. To reduce GC and size bias in our PCR, we monitored the PCR reaction using qPCR in order to stop amplification before saturation. To do this, we amplified the full libraries for five cycles, after which we took an aliquot of the PCR reaction and added 10 µl of the PCR cocktail with Sybr Green at a final concentration of 0.6×. We ran this reaction for 20 cycles to determine the additional number of cycles needed for the remaining 45-µL reaction. The libraries were purified using a Qiagen PCR cleanup kit yielding a final library concentration of ~30 nM in 20 µL. Libraries were amplified for a total of 10–12 cycles
The libraries were subsequently sequenced on an Illumina NovaSeq 6000 sequencing machine, producing paired end reads with a length of 150 base pairs (bp).

value: NSCLC


title: Res1_ATAC


title: iMEK_B6_replicate1


title: Sen3_ATAC


title: hESC, ATAC, Rep2


title: DMSO_B6_replicate1


title: Sen2_ATAC


title: Sen1_ATAC


title: hESC, ATAC, Rep1


title: KO3_Erdafitinib

city: WuHan

first: huayuan

last: zhao

state: Hubei Province

address: Jiefang Road, No. 1277

department: Department of Urology

institute: Union Hospital, Tongji Medical College, Huazhong University of Science and Technology

data_processing:
After the library is qualified, the different libraries are pooling according to the effective concentration and the target amount of data off the machine, then being sequenced by the Illumina NovaSeq 6000. The end reading of 150bp pairing is generated. The basic principle of sequencing is to synthesize and sequence at the same time (Sequencing by Synthesis). Four fluorescent labeled dNTP, DNA polymerase and splice primers were added to the sequenced flowcell and amplified. When the sequence cluster extends the complementary chain, each dNTP labeled by fluorescence can release the corresponding fluorescence. The sequencer captures the fluorescence signal and converts the optical signal into the sequencing peak by computer software, so as to obtain the sequence information of the fragment to be tested
The image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition. Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5). We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5). We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools
Assembly: hg38
Supplementary files format and content: processed.data.xls

growth_protocol: All the cell lines were cultured in RPMI-1640 medium (Gibco, USA) supplemented with 10% FBS (Gibco, USA), 1% penicillin/streptomycin (Gibco, USA). Cells were cultured in an incubator at 37°C with humidifified atmosphere of 5% CO2.

extract_protocol:
Total RNA from cell samples was extracted by RNeasy mini kit (Qiagen, Germany) following the manufacturer’s instructions.
Total amounts and integrity of RNA were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, U Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtai

treatment_protocol: DMSO or Erdafitinib

value: bladder cancer cells

value: COPA Knockout

value: Erdafitinib


title: KO2_Erdafitinib


title: iMEK_129_replicate2


title: KO1_Erdafitinib


title: KO1_DMSO


title: CD8+ Tcells, Biol. Replicate 2, scRNAseq

city: Vienna

first: Wilfried

last: Ellmeier

address: Lazarettgasse 19

country: Austria

institute: Medical University of Vienna

description: RNA and hashtag oligo (HTO) sequences are stored in seperate files, two lanes were used (L001, L002) with paired end sequencing (I1, I2, R1, R2)

library_source: transcriptomic single cell

data_processing:
Demultiplexing, barcoded processing, gene counting and aggregation were performed with Cell Ranger v6.1.2
Assembly: mm10
Supplementary files format and content: Tab-seperated-values files and matrix files
Supplementary files format and content: count matrices for all features (genes and hashtag oligos) and barcodes (cells)

extract_protocol:
Single cell suspension from the spleen of either LCMV-Cl13-infected or uninfected WT and HDAC1-cKO mice were prepared. Equal numbers of splenocytes from one female and one male mouse were combined for each scRNA-seq sample per condition. Samples were incubated with fluorescently labeled H2-Db/GP33-41 tetramer, appropriate antibodies against surface markers, oligonucleotide-conjugated antibodies (TotalSeq-A hashtags; Biolegend) and fixable viability dye (Zombie Green; Biolegend). Viable naïve (CD90.2+CD8a+CD44–) and LCMV-specific (CD90.2+CD8a+CD44+GP33-tet+) WT and HDAC1-cKO CD8+ T cells were sorted using a SH800S Cell Sorter (Sony Biotechnology). These four samples were pooled for multiplex sequencing (approx. 30000 cells/run; a total of two runs was performed).
Libraries were generated using the Chromium Controller and the Next GEM Single Cell 3’ Reagent Kit (v3.1, 10x Genomics) according to the manufacturer’s instructions

value: spleen

value: CD8+ Tcells

value: WT and HDAC1-cKO


title: CD8+ Tcells, Biol. Replicate 1, scRNAseq HTO


title: KO3_DMSO


title: KO2_DMSO


title: WT3_Erdafitinib


title: CD8+ Tcells, Biol. Replicate 1, scRNAseq


title: WT2_Erdafitinib


title: CD8+ Tcells, HDAC1-cKO, Tterm, Replicate 3, ATACseq

description: column names in count matrix and annotation file correspond to library name

data_processing:
The resulting pools were sequenced on a NovaSeq 6000 instrument (Illumina, San Diego, CA, USA) in 50 base pair paired-end configuration. Chromatin accessibility mapping by ATAC-seq was done in [two] biological replicates.
NGS reads in unaligned BAM files were converted into FASTQ format with samtools, NGS adapter sequences were removed via fastp (0.23.2, GTCTCGTGGGCTCGG) and the reads were aligned to the GRCm38 (UCSC Genome Browser mm10) assembly with Bowtie2 (2.4.5, --very-sensitive, --no-discordant, --maxins 2000), before deduplicating with samblaster (0.1.24). Alignment statistics and mitochondrial read fractions were collected with samtools. Peaks were called with MACS2 (2.2.7.1, --no-model, --keep-dup auto, –extsize 147) and both, peak annotation and motifs discovery was performed with Homer (4.11). UCSC Track hubs allowed for visual inspection of results. A consensus peak set was compiled and all peaks in mm10 assembly regions blacklisted by the ENCODE project were removed.
Assembly: mm10
Supplementary files format and content: bigWig and narrowPeak files
Supplementary files format and content: csv files containing celltype and genotype annotation of samples, consensus region count matrix and consensus region annotations

extract_protocol:
For each experiment, a maximum of 50,000 sorted cells were collected at 500xg for 5min at 4°C. After centrifugation, the cell pellet was carefully resuspended in transposase reaction mix (12.5µl 2xTD buffer, 2µl TDE1 (Illumina, San Diego, CA, USA), 10.25µl nuclease-free water, and 0.25µl 1% digitonin (Promega, Madison, WI, USA)) for 30min at 37°C.
Following DNA purification (MinElute PCR Purification kit, QIAGEN N.V, Venlo, Netherlands) and eluting in 11µl, 1µl eluate was used in a quantitative PCR (qPCR) reaction to estimate the optimal number of cycles for library amplification. The remaining 10µl of each tagmented sample was then amplified corresponding to the Cq value (i.e., the cycle number at which fluorescence has increased above background levels) in the presence of custom Nextera primers. PCR amplification was followed by SPRI (Beckman Coulter) size selection to exclude fragments larger than 1,200bp. The DNA concertation of each library was assessed with a Qubit 2.0 Fluorometric Quantitation system (Life Technologies, Carlsbad, CA, USA), before pooling in equimolar amounts.

value: CD8+ T cells


title: CD8+ Tcells, HDAC1-cKO, Tterm, Replicate 2, ATACseq


title: Res2_ATAC


title: WT1_Erdafitinib


title: CD8+ Tcells, HDAC1-cKO, Tterm, Replicate 1, ATACseq


title: CD8+ Tcells, HDAC1-cKO, Tprog, Replicate 3, ATACseq


title: WT1_DMSO


title: WT2_DMSO


title: CD8+ Tcells, HDAC1-cKO, Tprog, Replicate 1, ATACseq


title: MHCC97H-2-VRK2 KO+MYC293D, MYC CUT-&TAG

city: Wuhan

first: chen

last: su

address: No. 1095, Jiefang Avenue

institute: Huazhong University of Science and Technology

data_processing:
Sequenced reads were trimmed for adaptor sequence and low-quality bases, then mapped to hg38 whole genome using Bowtie with standard alignment parameters. PCR duplicates were marked with the Picard “Mark Duplicates” utility and removed from further analysis. Bam files were converted to BigWig files using deepTools. Peaks were identified using the MACS2 peak caller with the following parameters: –f BAMPE –keep-dup all –g hs –q 0.01 Assembly: hg38 Supplementary files format and content: wig files were generated using deepTools.
Assembly: hg38
Supplementary files format and content: BigWig files
Library strategy: CUT&Tag

source_name: liver

growth_protocol: cells was cultured in DMEM (Invitrogen, CA, USA) supplemented with 10% fetal bovine serum (FBS) (Gibco, CA, USA) and antibiotics in an incubator at 37°C with 5% CO2.

extract_protocol:
CUT&Tag was performed according to the manufacturer’s protocol (Vazyme, TD-904, China).
The library was constructed by Hyperactive Universal CUT&Tag Assay Kit(TD-904) for Illumina  and PCR amplification

treatment_protocol: transfected with siRNA or plasmid using Lipofectamine  for 48 hours

value: liver

value: human hepatocellular carcinoma

value: VRK2 KO+MYC293D


title: MHCC97H-2-VRK2 KO+MYC293A, MYC CUT-&TAG

value: VRK2 KO+MYC293A


title: CD8+ Tcells, Biol. Replicate 2, scRNAseq HTOP


title: CD8+ Tcells, Wildtype, Tterm, Replicate 3, ATACseq


title: CD8+ Tcells, Wildtype, Tterm, Replicate 2, ATACseq


title: MHCC97H-2-VRK2 KO+MYC281D, MYC CUT-&TAG

value: VRK2 KO+MYC281D


title: MHCC97H-2-VRK2 KO+MYC281A, MYC CUT-&TAG

value: VRK2 KO+MYC281A


title: CD8+ Tcells, Wildtype, Tprog, Replicate 3, ATACseq


title: MHCC97H-2-VRK2 KO+MYC WT, MYC CUT-&TAG

value: VRK2 KO+MYC WT


title: MHCC97H-2-VRK2 KO, MYC CUT-&TAG

value: VRK2 KO


title: CD8+ Tcells, Wildtype, Tterm, Replicate 1, ATACseq

value: WT


title: CD8+ Tcells, Wildtype, Tprog, Replicate 2, ATACseq


title: CD8+ Tcells, Wildtype, Tprog, Replicate 1, ATACseq


title: MHCC97H-2-IgG, gG CUT-&TAG

value: IgG


title: MHCC97H-1-siMYC+MYC293D, MYC CUT-&TAG


title: CD45.2 ADT

city: Saint Louis

first: Daniel

last: Kreisel

state: MO

address: 425 S Euclid Ave

department: Department of Surgery

institute: Washington University School of Medicine

description:
CD452-1008_Ab
immune_naive.rds

data_processing:
Alignment: Cell Ranger V6, aligned to mm10 transcriptome
QC and Filtering: Seurat V4
Unsupervised Clustering: Seurat V4
Assembly: mm10
Supplementary files format and content: .rds objects

molecule: protein

source_name: lung

extract_protocol: Chromium Single Cell 5ʹ Reagent v1.1 kit from 10X Genomics and Chromium Single Cell 3ʹ Reagent v1.1 kit from 10X Genomics

value: lung

value: re-transplant


title: WT3_DMSO

value: bladder cancer cells

value: DMSO


title: CD45.2 GEX

description:
CD452-1008
immune_naive.rds


title: MHCC97H-1-siMYC+MYC293A, MYC CUT-&TAG


title: MHCC97H-2-WT, MYC CUT-&TAG


title: MHCC97H-1-siMYC+MYC281A, MYC CUT-&TAG


title: CD8+ Tcells, HDAC1-cKO, Tprog, Replicate 2, ATACseq

value: spleen


title: CD45.1 ADT

description:
CD451-1008_Ab
immune_naive.rds


title: shTMEM45A_2_2

city: hefei

first: Liang

middle: Jia

last: Hui

address: 218 JiXi Avenue

institute: The First Affiliated Hospital of Anhui Medical University,

data_processing:
Total RNA was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA, Catalog #: E7530L) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEB Next First Strand Synthesis Reaction Buffer(5X).
First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H.
Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEB Next Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beverly, USA).
Then 3 µL USER Enzyme (NEB, USA) was used with size selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. Sequence artifacts, including reads containing adapter contamination, low-quality nucleotides and unrecognizable nucleotide (N), undoubtedly set the barrier for the  subsequent reliable bioinformatics analysis. Hence quality control is an essential step  and applied to guarantee the meaningful downstream analysis. we used Fastp (version  0.23.1) (Chen, S. , et al 2018) to perform basic statistics on the quality of the raw reads.  The steps of data processing were as follows: (1) Discard a paired reads if either one read contains adapter contamination; (2) Discard a paired reads if more than 10% of bases are uncertain in either one read; (3) Discard a paired reads if the proportion of low quality (Phred quality <5) bases is over 50% in either one read.
Assembly: mm10
Supplementary files format and content: Raw Counts.

extract_protocol:
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads.  Fragmentation was carried out using divalent cations under elevated temperature in NEB  Next First Strand Synthesis Reaction Buffer(5X).
Total RNA was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA, Catalog #: E7530L) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEB Next First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEB Next Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beverly, USA). Then 3 µL USER Enzyme (NEB, USA) was used with size selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent 5400 system（Agilent，USA） and quantified by QPCR (1.5 nM). The qualified libraries were pooled and sequenced on Illumina platforms with PE150 strategy in Novogene Bioinformatics Technology Co., Ltd (Beijing, China), according to effective library concentration and data amount required

value: breast

value: invasive breast carcinoma


title: CD45.1 GEX

description:
CD451-1008
immune_naive.rds


title: MHCC97H-1-siMYC+MYC281D, MYC CUT-&TAG

value: liver


title: shTMEM45A_2_3


title: MHCC97H-1-siMYC+MYC WT, MYC CUT-&TAG

value: human hepatocellular carcinoma

value: siMYC+MYC WT


title: MHCC97H-1-siMYC, MYC CUT-&TAG

value: siMYC


title: MHCC97H-1-IgG, IgG CUT-&TAG


title: shTMEM45A_1_2


title: shTMEM45A_1_1


title: MHCC97H-1-siNC, MYC CUT-&TAG

value: siNC


title: MHCC97H-siVRK2-2,RNA-Seq

data_processing:
Sequenced reads were trimmed for adaptor sequence and low-quality bases, then mapped to hg38 whole genome using Bowtie with standard alignment parameters. PCR duplicates were marked with the Picard “Mark Duplicates” utility and removed from further analysis. Bam files were converted to BigWig files using deepTools. Peaks were identified using the MACS2 peak caller with the following parameters: –f BAMPE –keep-dup all –g hs –q 0.01
Assembly: hg38
Supplementary files format and content: FPKM

extract_protocol:
Total RNA extracted using TRIzol was used for library preparation with an Illumina mRNA sequencing (mRNAseq) sample preparation kit. Quality control of the RNA sequencing libraries was performed using a Bioanalyzer 2100 (Agilent, CA, USA) prior to paired-end sequencing on the HiSeq 3000 platform (Illumina, CA, USA)
According to the instructions of the experiment, the purified Total RNA was separated into mRNA, fragmented, first-strand cDNA synthesis, second-strand cDNA synthesis, end repair, adding A to the 3 'end, ligating connector, enrichment and other steps to complete the construction of sequencing sample library.

value: transfected with siRNA or plasmid using Lipofectamine  for 48 hours


title: shTMEM45A_1_3


title: shSHCBP1_2_2


title: shTMEM45A_2_1


title: MHCC97H-siVRK2-1,RNA-Seq


title: shSHCBP1_2_3


title: MHCC97H-siMYC-2,RNA-Seq


title: MHCC97H-siMYC-1,RNA-Seq


title: shSHCBP1_2_1


title: MHCC97H-siNC-2,RNA-Seq


title: MHCC97H-siNC-1,RNA-Seq


title: shSHCBP1_1_2


title: shSHCBP1_1_1


title: NC_3


title: Donor3, cocultured, day 7, ATAC-seq

city: Minneapolis

first: Pedram

last: Motallebnejad

state: MN

address: 421 Washington Ave SE

institute: University of Minnesota

description: ATAC-seq on Donor3, day7

data_processing:
ATAC-seq data analysis was performed following Encode pipeline
Trimmomatic trimmed adapter sequences and low-quality base calls. Reads were mapped to the human reference genome (hg38) using Bowtie2 (parameters: p 2 -X 2000 --very-sensitive), excluding mitochondrial reads, and deduplicated using MarkDuplicates
MACS2 was used to perform peak calling (parameters: -p 0.01 --nomodel --shift -75 --extsize 150 –bdg), and IDR was used to create a reproducible peak list for unstimulated and day 7 samples. Consensus peaks were determined as the union of unstimulated and day 7 peaks.
Raw peak count matrix was obtained using featureCounts. For differential accessibility, GC content bias was corrected using EDASeq, and CPM values were TMM normalized using EdgeR.
Normalized ATAC peak counts were used for PCA analysis and clustering in R. EdgeR identified differentially accessible peaks for day 7 versus unstimulated samples, with criterion of |log2(fold change)|>1 and adj. P value<0.05.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for consensus peaks in each sample

source_name: Peripheral Blood

growth_protocol: K562 cells expressing mb-4-1BBL and mb-IL-21 (referred to as feeder cells, mb stands for membrane-bound) were cultured in RPMI 1640 Medium containing 10% fetal bovine serum. Feeder cells were irradiated at 10,000 rads, cryopreserved and thawed for co-culture with NK cells. Peripheral blood mononuclear cells (PBMCs) were extracted from leukocyte reduction system chambers using Ficoll-Paque Premium (Cytiva). NK cell enrichment was carried out with the EasySep Human NK Cell Enrichment Kit. NK cells were cultured overnight in B0 medium supplemented with 100 U/mL of IL-2 (R&D Systems) for recovery. B0 medium is a 2:1 (vol:vol) mixture of DMEM with 4.5 g/L glucose, L-glutamine, and sodium pyruvate (Gibco) and Ham’s F12 Medium (Corning) supplemented with 20 µM 2-mercaptoethanol (Gibco), 50 µM ethanolamine (Sigma), 10 µg/mL ascorbic acid (Sigma), 1.6 ng/mL sodium selenite (Sigma), 100 U/mL penicillin/streptomycin (Gibco), and 20% heat-inactivated human AB serum (Valley Biomedical).

extract_protocol:
Samples comprised of 50,000 cells were processed following the OMNI-ATAC protocol, and transposed DNA was purified using the MinElute PCR cleanup kit.
dual-indexed ATAC-seq libraries were generated from transposed DNA using Nextera reagents.

treatment_protocol: Enriched NK cells from PBMCs were cultured in media containing IL-2 overnight. Subsequently, NK cells were co-cultured with irradiated feeder cells at 2×105 cells/mL and 4×105 cells/mL, respectively, in B0 media with IL-2 supplementation for 7 days (Figure 1A). Samples were collected right after enrichment (unstimulated) and 7 days after co-culture initiation (day 7) for RNA-seq and ATAC-seq.

value: Peripheral Blood

value: Primary cells

value: Natural Killer Cells

value: Cocultured with feeder cells


title: Donor3, unstimulated, day 0, ATAC-seq

description: ATAC-seq on Donor3, unstimulated

value: WT

value: Unstimulated


title: NC_2


title: Donor2, cocultured, day 7, ATAC-seq

description: ATAC-seq on Donor2, day7


title: Donor2, unstimulated, day 0, ATAC-seq

description: ATAC-seq on Donor2, unstimulated


title: NC_1


title: breast cancer model, serum exosomes, Ctrl-rep2

first: Dong

last: Han

address: 28 Fuxing street

institute: Chinese PLA general hospital

data_processing:
Firstly, fastp software (v0.20.0) was used to trim adaptor and filter low-quality reads to get high-quality clean reads. Then, clean reads from all samples were merged, and miRdeep2 software (v0.1.3) was used to predict novel miRNAs.
The clean reads were then aligned to the merged mouse miRNA databases (miRNA from miRbase v22.1 plus the newly predicted novel miRNAs) using Novoalign software (v3.09.04) with at most one mismatch.
The mapped miRNA read counts were defined as the raw expression levels of that miRNA. The read counts were then normalized by DESeq2 R packages (v1.30.1). Differentially expressed miRNAs between two groups were filtered through fold change and pvalue.
Genome_build: miRBase v22.1
Supplementary_files_format_and_content: miRNA Expression Profiling.xlsx

source_name: serum

extract_protocol: 1) 3'-adaptor ligation; 2) 5'-adaptor ligation; 3) cDNA synthesis; 4) PCR amplification; 5) Size selection of ~150 bp PCR amplicons (corresponding to ~22nt miRNAs). The libraries were denatured as single-stranded DNA molecules, captured on Illumina flow cells, amplified in situ as clusters and finally sequenced for 50 cycles on following the manufacturer's instructions.

tag: disease state

value: breast cancer in situ model

value: serum

value: Control

tag: sample type

value: exosome


title: Donor1, cocultured, day 7, ATAC-seq

description: ATAC-seq on Donor1, day7


title: Donor1 unstimulated, day 0, ATAC-seq

description: ATAC-seq on Donor1, unstimulated


title: Primary CRC tumor samples (FF), CODE925

city: Amsterdam

first: Arezo

last: Torang

address: Meibergdreef 9

country: Netherlands

institute: Amsterdam UMC

data_processing:
Prior to read trimming and alignment, the quality of raw data was assessed using FastQC (v.0.11.9). Trimming was performed on 12 and 11 bases for single-end and pair-end RNAseq data, respectively. To further enhance data quality, bases with a Phred score less than 20 were filtered using Cutadapt (v1.18). The reads were aligned to the reference genome (GRCh38) and gene counts were generated using the STAR (v.2.7.4.a) algorithm. To enable accurate downstream analyses, the count data was log2-transformed and quantile normalization was applied.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw gene count for each Sample

source_name: Primary colorectal cancer

extract_protocol:
For RNA extraction from FF tissue, we followed the manufacturer's protocol using RNA-B and Trizol. Exclusion criteria for samples were set as a tumor percentage of less than 30%. When working with FFPE tissue, we prepared three 10 µm slides that were subjected to H&E staining. De-paraffinisation of tissue was carried out using Xylene, followed by macro-dissection of the specimen to enrich for tumor tissue. RNA extraction was performed using the RNeasy FFPE kit (Qiagen, location) as per the manufacturer's instructions. To assess the quality and quantity of RNA, we used the NanoDrop2000 and Tapestation (Agilent).
RNA libraries for RNA-seq were prepared using KAPA mRNA Hyperprep following manufacturer’s protocol.

value: Primary colorectal cancer

value: Fresh Frozen


title: breast cancer model, serum exosomes, Dox-rep2

value: DOX treatment


title: Primary CRC tumor samples (FF), CODE86


title: slide_2 NeuN+-aoi-004

city: Saskatoon

first: Kundanika

last: Mukherjee

state: Saskatchewan

address: 107 Wiggins Rd,  2D40 Health Sciences Building

department: APP

country: Canada

institute: University of Saskatchewan

description: Library name: DSP-1002990011571-A-C07

data_processing:
dcc-metadata = true
save-interim-files = false
quality-trim-score = 20
2color-trimming = True
adapter1 = AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
adapter2 = AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
adapter-trim-match-length = 10
adapter-trim-max-mismatch = 3
barcode-max-mismatch = 1
stitching-max-mismatch = 2
dedup-hd = 1
threads = 4
Assembly: GeoMx Mouse Whole Transcriptome Atlas
Supplementary files format and content: Digital Count Conversion file (DCC)
Library strategy: Spatial Transcriptomics

organism: Rattus

source_name: Jejunum

extract_protocol:
Fresh frozen jejunal tissues were sectioned in Tissue-Tek® O.C.T. Compound using a Leica microtome at 6 um thickness. The section containing slides were stained with UV- cleavable probes. Slides were loaded into GeoMx DSP instrument and scanned to capture fluorescent images used to select regions of interest (ROIs).
Other: GeoMx DSP SeqCode

treatment_protocol: Mesenteric lymph duct cannulated rats were randomly divided into three groups to receive three different treatments by intracerebroventricular infusion: 1) GLP-2R antagonist (GLP-2(11-33)) 2) MC4R antagonist (SHU9119) 3) saline as control.

value: Jejunum

tag: strain

value: Sprague Dawley

value: Saline (SG)


title: slide_2 SMA+-aoi-004

description: Library name: DSP-1002990011571-A-C06


title: slide_2 CD31+-aoi-004

description: Library name: DSP-1002990011571-A-C05


title: Primary CRC tumor samples (FF), CODE810


title: Primary CRC tumor samples (FF), CODE806


title: slide_2 NeuN+-aoi-003

description: Library name: DSP-1002990011571-A-C04


title: Primary CRC tumor samples (FF), CODE841


title: Primary CRC tumor samples (FF), CODE749


title: slide_2 NeuN+-aoi-002

description: Library name: DSP-1002990011571-A-C01

value: GLP-2R antagonist (GG)


title: Primary CRC tumor samples (FF), CODE717


title: shSHCBP1_1_3

value: breast

value: invasive breast carcinoma


title: slide_2 CD31+-aoi-003

description: Library name: DSP-1002990011571-A-C02


title: slide_2 SMA+-aoi-002

description: Library name: DSP-1002990011571-A-B12


title: slide_2 CD31+-aoi-002

description: Library name: DSP-1002990011571-A-B11


title: Primary CRC tumor samples (FF), CODE691


title: Primary CRC tumor samples (FF), CODE701


title: Primary CRC tumor samples (FF), CODE645


title: Primary CRC tumor samples (FF), CODE669


title: slide_2 SMA+-aoi-001

description: Library name: DSP-1002990011571-A-B09

value: MC4R antagonist (MG)


title: slide_2 NeuN+-aoi-001

description: Library name: DSP-1002990011571-A-B10


title: slide_2 CD31+-aoi-001

description: Library name: DSP-1002990011571-A-B08


title: Primary CRC tumor samples (FF), CODE597


title: slide_1 NeuN+-aoi-006

description: Library name: DSP-1002990011571-A-B07


title: Primary CRC tumor samples (FF), CODE528


title: Primary CRC tumor samples (FF), CODE50


title: slide_1 SMA+-aoi-006

description: Library name: DSP-1002990011571-A-B06


title: Primary CRC tumor samples (FF), CODE473


title: Primary CRC tumor samples (FF), CODE494


title: slide_1 CD31+-aoi-006

description: Library name: DSP-1002990011571-A-B05


title: Infant 4 IL-22

city: Vancouver

first: Pascal

last: Lavoie

state: BRITISH COLUMBIA

address: 950 West 28th Avenue

institute: BC Children's Hospital

data_processing:
Sequencing data was demultiplexed using Illumina's bcl2fastq2
De-multiplexed read sequences were then aligned to the Homo sapiens hg19 reference sequence using STAR aligner.
Assembly and differential expression was estimated using Cufflinks (http://cole-trapnell-lab.github.io/cufflinks/) through bioinformatics apps available on Illumina Sequence Hub
Transcript counts were then normalized by TMM (Trimmed Mean of M-values) by correcting for the library size
Assembly: Homo sapiens (UCSC hg19)
Supplementary files format and content: csv data matrix files with normalized read counts

source_name: ileal enteroid

growth_protocol: Ileal enteroids were cultured in growth medium (advanced DMEM/F12 supplemented with 1X Penicillin/Streptomycin, 1X Glutamax, and 1M HEPES) and 50% WRN supplemented with N2, B27, N-acetylcystine, nicotinamide, mEGF, A83-01, SB 202, Y-27632  was added (400 μL/well) and changed every two days.

extract_protocol:
Enteroids from three to four wells were pooled, resuspended in TRIzol, and lysed at room temperature for 15 minutes. RNA purification was performed with the Direct-zol RNA Microprep Kit (Zymo Research) using the manufacturer’s protocol. A NanoDrop ND-2000 spectrophotometer was used for the quantification of isolated RNA.
Sample quality control was performed using the Agilent 2100 Bioanalyzer. Qualifying samples were then prepped following the standard protocol for the NEBnext Ultra ii Stranded mRNA (New England Biolabs). Sequencing was performed on the Illumina NextSeq2000 with Paired End 59bp × 59bp reads

treatment_protocol: Following culture for 4 days, organoid media was replaced with fresh medium consisting of 70% organoid growth medium and 30% of cRPMI, including recombinant Il-22 (100 ng/ml). On Day 7, organoid cultures were collected, pooled, and harvested for further analysis.

value: ileal enteroid

tag: sequencing batch


title: Primary CRC tumor samples (FF), CODE466


title: slide_2 SMA+-aoi-003

description: Library name: DSP-1002990011571-A-C03


title: slide_1 SMA+-aoi-005

description: Library name: DSP-1002990011571-A-B03


title: Infant 4 ctrl

value: control


title: slide_1 NeuN+-aoi-005

description: Library name: DSP-1002990011571-A-B04


title: Infant 3 ctrl


title: Infant 3 IL-22


title: Primary CRC tumor samples (FF), CODE425


title: slide_1 CD31+-aoi-005

description: Library name: DSP-1002990011571-A-B02


title: Primary CRC tumor samples (FF), CODE421


title: Infant 1 IL-22


title: slide_1 NeuN+-aoi-004

description: Library name: DSP-1002990011571-A-B01


title: Infant 2 ctrl


title: slide_1 SMA+-aoi-004

description: Library name: DSP-1002990011571-A-A12


title: Primary CRC tumor samples (FF), CODE391


title: Primary CRC tumor samples (FF), CODE365


title: Infant 1 ctrl


title: polyIC_naive

city: Los Angeles

first: Alexander

last: Hoffmann

state: California

address: 570 Boyer Hall

department: MIMG

institute: University of California, Los Angeles

description: Library name: Cartridge 2

data_processing:
BD 23-24580(01)
Assembly: GRCh38
Supplementary files format and content: Each cartridge has a barcodes.tsv.gz (cart1_barcodes.tsv.gz and cart2_barcodes.tsv.gz), which contains the cell barcode ids.
Supplementary files format and content: Each cartridge has a features.tsv.gz (cart1_features.tsv.gz and cart2_features.tsv.gz), which contains the gene list.
Supplementary files format and content: Each cartridge has a matrix.mtx.gz (cart1_matrix.mtx..gz and cart2_matrix.mtx.gz), which contains a sparse matrix of the count data, where rows rerpesent genes/features, columns represent cells/barcodes, and entries represent reads in each cell.

molecule: polyA RNA

source_name: macrophages

value: macrophages


title: LPS_TNF

description: Library name: Cartridge 1


title: slide_1 NeuN+-aoi-003

description: Library name: DSP-1002990011571-A-A10


city: Medford

first: rebecca

last: batorsky

state: MA

address: 177 College Ave

department: Tufts Institute of Artificial Intelligence

institute: Tufts University

description:
Library name: Rd1
Drug-seq library of PBMC-derived induced microglia-like cell, batch 1

data_processing:
Raw reads were aligned to reference genome hg38 using STAR v. 2.7.11b (7) using “solo” mode.
Unique molecular identifier count matrices were generated in this step by supplying the list of sequencing barcodes to option –soloCBwhitelist (see file sequencing_barcodes.xlsx)
Assembly: hg38
Supplementary files format and content: count matrix

source_name: PBMC

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated from a half leukapheresis pack (leukopak) sourced from HemaCare Corporation (now part of Charles River Laboratories Cell Solutions) using a standard operating procedure from the AIDS Clinical Trials Group Laboratory Technologist Committee (https://www.hanc.info/content/dam/hanc/documents/laboratory/actgimpaact-laboratorymanual/Leukopak%20PBMC%20Processing%20Standard%20Operating%20Procedure%20v2.0 _22Nov2022.pdf).  Contents of the leukopak were diluted with Hank’s Balanced Salt Solution without Calcium, Magnesium, phenol red (HBSS, Thermo Fisher #14175095) using at least a 1:2 ratio of leukopak to dilutant. 50ml conical tubes were prepared by adding 15ml Density Gradient Medium (DGM, Stemcell Technologies Lymphoprep 07851) to the bottom of each tube. The full volume of the diluted leukopak was split evenly into the 50ml conical tubes, layering the solution on top of the DGM in each tube. Tubes were centrifuged at 400g for 30 minutes, with centrifuge brake set to “off”. The PBMC fractions between the plasma and DGM were transferred to new tubes and diluted with HBSS to a final volume of 45ml each. A series of washing steps followed, starting with a centrifugation at 300g for 10 minutes, again with no brake. The supernatants were discarded, and pellets resuspended in 5ml HBSS, before combining into 2 x 50ml conical tubes. This wash was repeated, and cells were consolidated into a single conical tube with a 20ml volume. Cell concentration was quantified using a Countess II automated cell counter (ThermoFisher), and the volume of Cryostor CS10 medium (Sigma-Aldrich C2874) was calculated to aliquot PBMC’s at  25 million cells/ml. The final centrifugation at 300g for 10 minutes was completed and the pellet was resuspended in the Cryostor cs10 medium, before slow freezing in a Mr. Frosty (ThermoFisher #5100-0001) freezing container at -80C and moving to long term liquid Nitrogen storage the following day. The cells were suspended in Cryostor cs10 at room temperature for a maximum of 10 minutes before being added to the freezer. If the time to aliquot this suspension was estimated to be longer, the cell solution was split into multiple batches before the final centrifugation, and aliquots were prepared one batch at a time. Frozen and aliquoted peripheral blood mononuclear cells (PBMCs) isolated as described above from a healthy control donated half leukopak (Charles River, Lowell MA / Hemacare, Northridge CA) were quick-thawed in a 37C water bath and immediately transferred into RPMI-1640 (Sigma, #R8758) + 10% heat-inactivated fetal bovine serum (Sigma, #12306C) + 1% of Penicillin/Streptomycin (Life Technologies, cat# 15140-122). Cells were washed by centrifugation at 300 g for 5 min with the brake off and resuspended in fresh media, then counted and plated at a density of approximately 400,000 cells/cm2 in a tissue culture treated 6-well plate (Corning, #353046) pre-coated with Geltrex (Gibco, #A1413202) for 1 hour. After incubating for 24 hours, the media was carefully removed and replaced with RPMI-1640 + 1% Penicillin/Streptomycin + 1% Glutamax (Life Technologies, # 35050-061) + 100 ng/ml IL-34 (Biolegend Inc, #577904) + 10 ng/ml GM-CSF (PeproTech, #300-03). After a 10-day incubation period for trans-differentiation, culture media was collected and filtered with a 0.22um SteriflipGP Filter (EMD Millpore #SCGP00525) and retained. PBMC-derived induced microglia-like cells (piMGLCs) were harvested using Accutase (Sigma, #A6964) for 5 minutes at 37C to detach. They were then centrifuged at 300g for 5 min and counted so they could be resuspended in the proper amount of retained and filtered cell culture media to 50,000 cells/ml, and plated into 96-well tissue culture plates (Corning, #3904) at a density of 30,000 cells/cm2 (10,000 cells per well in 200ul) for 4 days before assaying. If the assay plates required a higher volume of cell-culture media than that collected from the batch of 6-well plates, supplementary fresh media of RPMI-1640 with Penicillin/Streptomycin and Glutamax would be used to reach the required seeding volume.

extract_protocol:
96-well multiplexed libraries (DRUG-seq) were prepared using the MERCURIUS™ DRUGseq kit (Alithea Genomics, 10841) following manufacturer instructions. Briefly, cells were washed using 100µL per well of Dulbecco’s Phosphate Buffered Saline (Gibco, 14190-144). Cells were then lysed for 10-15 minutes in 20µL per well of prepared and chilled 1x Cell Lysis Buffer at 4°C.  Lysate was carefully removed from the cell culture plate and transferred to a 96-well PCR plate, then spun at 300xg for 5 min in a centrifuge pre-chilled to 4°C. Up to 20µL of supernatant was then removed to a clean 96-well PCR plate for storage at -80°C for up to one month.
For reverse transcription, stored lysate was thawed at 4°C, then 10µL of lysate from each well was transferred to a 96-well plate containing dry, well position specific barcoded oligo-dT primers (Alithea Genomics, 10513). Upon resuspension of the oligo-dT primers, 10µL of prepared RT Master Mix was added to each well and reverse transcription was carried according to provided instructions (incubation for 30min at 50°C, 10min at 85°C, then cooling to 4°C). Resulting firststrand cDNA was collected and pooled, mixed with 7x volume of DNA binding buffer (Zymo, D4003-1-L), and purified on a Zymo-Spin IC column (Zymo, C1004-50). Purified first-strand cDNA was eluted in 20µL nuclease-free water. Excess oligo-dT was digested from 17µL of eluate by adding Exonuclease I Enzyme and Buffer and incubating for 30min at 37°C, 20 min at 80°C, then cooling to 4°C. Second-strand synthesis was carried out immediately after by adding 7µL of prepared Second Strand Synthesis reaction mix and incubating for 20 min at 37°C, 30 min at 65°C, and then cooling to 4°C.  Resulting second-strand cDNA was purified using CleanNGS DNA & RNA Clean-Up Magnetic Beads (Bulldog Bio, CNGS005) at a ratio of 0.6x bead slurry to cDNA. Bead purification was carried out using a 0.2 mL PCR Strip Magnetic Separator (Permagen, MSR812). Upon purification, cDNA was measured using Qubit 1X dsDNA HS Assay kit (Invitrogen, Q33231) and 50-60ng of cDNA was tagmented in a 20µL reaction with 4µL of provided Tagmentation Enzyme and 4µL of Tagmentation Buffer. After incubating at 55°C for 7 minutes, the tagmented library was brought to 50µL and purified with CleanNGS beads at a ratio of 0.6x bead slurry to cDNA.  Finally, the tagmented library was pre-amplified with provided UDI adapters included in kit for 10 cycles (one cycle composed of 10 seconds at 98°C, 30 seconds at 63°C, and 1 min at 72°C) total. In preparation for sequencing, this pre-amplified library was purified twice with CleanNGS beads at a ratio of 0.7x bead slurry to cDNA and eluted in 20uL. Samples were split over two different sequencing runs, with at least one replicate of each studied compound on each run. Sequencing resulted in 615 million read pairs for run one and 1016 million read pairs for run two.

treatment_protocol: 24 hours before the start of the assay, the media volume per well was brought to 150ul and piMGLCs were pretreated with the 489 screening library compounds (CNS-penetrant compound library, MedChemExpress #HY-LO28) at a final concentration of 10µM, with some exceptions at 2µM), by diluting the compounds in basal RPMI-1640 and adding 50ul of one diluted compound per well. For the primary screen a single dilution per compound was used in a single well per plate, with three replicates split across different plates. DMSO (0.1%) was used as a vehicle control and was used in 3 replicate wells on each plate. The secondary screen included piMGLC plates treated with 47 compounds for 24-hours (see file drugseq_compounds.xlsx).

value: PBMC

value: phagocytosis modulating compounds, see supplementary table 1

tag: batch


title: Primary CRC tumor samples (FF), CODE309


title: Infant 2 IL-22


title: Primary CRC tumor samples (FF), CODE240


title: slide_1 SMA+-aoi-003

description: Library name: DSP-1002990011571-A-A09


title: Primary CRC tumor samples (FF), CODE212


title: scATAC-seq of MH_13-084-D12

city: Seattle

first: Brian

last: Hanratty

state: WA

address: 1100 Fairview Avenue

department: Division of Human Biology

institute: Fred Hutchinson Cancer Cancer

description:
Library name: MH_13-084-D12
10x Genomics

library_source: genomic single cell

data_processing:
scATAC-seq data was processed using Cell Ranger ATAC (v 2.0.0) against genome cellranger-arc-GRCh38-2020-A-2.0.0
Assembly: Human, hg38 (cellranger-arc-GRCh38-2020-A-2.0.0)
Supplementary files format and content: Cellranger output files: peaks.bed, singlecell.csv and fragments.tsv.gz

source_name: tumor tissue

extract_protocol:
Material preparation followed the manufacturer’s protocol for Single-Cell ATAC-Seq and Single-Cell Multiome ATAC (10x Genomics)
Next GEM singlecell ATAC kit V2, Next GEM single cell Multiome ATAC+Gene expression

value: tumor tissue


title: scATAC-seq of MH_13-084-D13

description:
Library name: MH_13-084-D13
10x Genomics


title: slide_1 CD31+-aoi-003

description: Library name: DSP-1002990011571-A-A08


title: scRNA-seq of MH_13-084-D12

data_processing:
Single cell RNA-seq data is aligned and qualitified using the Cell Ranger software (v7.0.0) against genome GRCh38-2020-A.
Assembly: Human hg38 (GRCh38-2020-A)
Supplementary files format and content: Compressed barcodes, features, and matrix files from Cell Ranger (v7.0.0)

molecule: nuclear RNA

extract_protocol:
Material preparation followed the manufacturer’s protocol for Single-Cell RNA-Seq and Single-Cell Multiome GEX (10x Genomics).
Fixed RNA profiling kits, Next GEM Single Cell Multiome ATAC+Gene expression

value: metastatic prostate cancer


title: scATAC-seq of MH_07-042-M2

description:
Library name: MH_07-042-M2
10x Genomics


title: slide_1 NeuN+-aoi-002

description: Library name: DSP-1002990011571-A-A07


title: Primary CRC tumor samples (FF), CODE208

value: Primary colorectal cancer


title: scRNA-seq of MH_13-084-D13


title: Primary CRC tumor samples (FF), CODE201

value: Fresh Frozen


title: slide_1 CD31+-aoi-004

description: Library name: DSP-1002990011571-A-A11


title: 5_RNF20 CRISPR-Trained

city: Blacksburg

first: Timothy

last: Jarome

state: VA

address: 175 W Campus Dr

institute: Virginia Polytechnic Institute and State University

description:
Library name: R5
Train w/RNF20

data_processing:
Sequence is mapped to Rat genome (Rattus_norvegicus mRatBN7.2/rn7)
we use HISAT2 software to alignment for RNA-seq sequencing data analysis
DESeq2 was used for normalization and differential expression analysis
Assembly: GRCr8 (GCA_036323735.1)
Supplementary files format and content: Excel file of raw read count from HISAT2 output
Supplementary files format and content: Excel file of normalized Count from DESeq2

organism: Rattus norvegicus

growth_protocol: Frozen brain tissue from 23 month old Fischer F344 rats

extract_protocol:
RNA was extracted using Allprep Kit (Qiagen)
The Illumina Sequencing Protocol and the NovaSeq X Plus System

treatment_protocol: Stereotaxic injections of CRISPR-dCas9 plasmids into dorsal CA1 area of the hippocampus

value: All brain cell types

value: WT

value: Male

tag: age

value: 23 months

value: RNF20-gRNA+dCas9-VPR Trained


title: slide_1 CD31+-aoi-002

description: Library name: DSP-1002990011571-A-A05

value: Jejunum

value: Sprague Dawley


title: Drug-seq library of PBMC-derived induced microglia-like cell, batch 2

description:
Library name: Rd2
Drug-seq library of PBMC-derived induced microglia-like cell, batch 1


title: Primary CRC tumor samples (FF), CODE186


title: Cartridge 1

city: Oxford

first: Lucy

last: Garner

address: Experimental Medicine, Level 5, John Radcliffe Hospital

department: Nuffield Department of Medicine

country: United Kingdom

institute: University of Oxford

data_processing:
BCL files were converted to FASTQ files using Illumina bcl2fastq. FASTQ files were processed to a gene-by-cell matrix (one per BD Rhapsody Cartridge) using the BD Rhapsody Sequence Analysis Pipeline (v2.2.1). Downstream analysis was performed in R (v4.4.0). A Seurat (v5.1.0) object was generated from distribution-based error correction-adjusted molecule counts (two Cartridges combined) and filtered to retain cells with a defined Sample Tag and to remove doublets (cell labels associated with more than one Sample Tag). Cells with low unique molecular identifier counts (<125) and/or low gene counts (<40) were removed.
Assembly: BD_Rhapsody_Immune_Response_Panel_Hs_FASTA.fasta and 1367_full_KRD1_low_maskORDER_amplicons.fasta
Supplementary files format and content: BD Rhapsody Sequence Analysis Pipeline (v2.2.1) output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz, Sample_Tag_Calls.csv.
Supplementary files format and content: FASTA: BD_Rhapsody_Immune_Response_Panel_Hs_FASTA.fasta
Supplementary files format and content: Custom mRNA FASTA: 1367_full_KRD1_low_maskORDER_amplicons.fasta
Supplementary files format and content: Custom AbSeq FASTA: BDAbSeq_custom.fasta
Supplementary files format and content: Seurat object: seurat_object.rds

source_name: Blood

extract_protocol:
The PBMCs were stained with CD45-PE for 30 min at room temperature. Cells were washed twice in FACS buffer (PBS 2% FBS), incubated with Fc block solution for 15 min at room temperature, then each sample labelled with a separate oligonucleotide-conjugated Sample Tag (BD Flex Single-Cell Multiplexing Kits A-D) for 60 min at 4°C. Cells were washed twice in BD Pharmingen Stain buffer. Twelve samples (3500 cells/sample; n=3 from each group - non-SD HW, non-SD OW/OB, SD HW, SD OW/OB) were pooled and loaded onto one BD Rhapsody Cartridge following manufacturer’s instructions. The remaining 12 samples were pooled and loaded onto a second BD Rhapsody Cartridge.
BD Rhapsody System mRNA Targeted, BD AbSeq, and Sample Tag - 23-24124(02).

tag: samples

value: Blood

value: PBMCs

value: dengue


title: slide_1 SMA+-aoi-002

description: Library name: DSP-1002990011571-A-A06

value: MC4R antagonist (MG)


title: Cartridge 2


title: 4_RNF20 CRISPR-Trained

description:
Library name: R4
Train w/RNF20


title: 2_RNF20 CRISPR-Trained

description:
Library name: R2
Train w/RNF20


title: slide_1 NeuN+-aoi-001

description: Library name: DSP-1002990011571-A-A04


title: 3_RNF20 CRISPR-Trained

description:
Library name: R3
Train w/RNF20


title: 1_RNF20 CRISPR-Trained

description:
Library name: R1
Train w/RNF20


title: slide_1 SMA+-aoi-001

description: Library name: DSP-1002990011571-A-A03


title: Primary CRC tumor samples (FF), CODE150


title: scRNA-seq of MH_07-042-M2

description:
Library name: MH_07-042-M2
10x Genomics


title: 1_Control CRISPR-Trained

description:
Library name: T1
Train

value: RNF20-gRNA Trained


title: Primary CRC tumor samples (FF), CODE146


title: slide_1 CD31+-aoi-001

description: Library name: DSP-1002990011571-A-A02


title: 5_Control CRISPR-Naïve

description:
Library name: N5
Naïve

value: RNF20-gRNA Naïve


title: 4_Control CRISPR-Trained

description:
Library name: T4
Train


title: 2_Control CRISPR-Trained

description:
Library name: T2
Train


title: 3_Control CRISPR-Trained

description:
Library name: T3
Train


title: 3_Control CRISPR-Naïve

description:
Library name: N3
Naïve


title: 4_Control CRISPR-Naïve

description:
Library name: N4
Naïve


title: Primary CRC tumor samples (FF), CODE137


title: Primary CRC tumor samples (FF), CODE116


title: Primary CRC tumor samples (FF), CODE174


title: 1_Control CRISPR-Naïve

description:
Library name: N1
Naïve


title: Primary CRC tumor samples (FF), CODE129


title: Primary CRC tumor samples (FF), P948

value: Female

tag: fixation


title: Primary CRC tumor samples (FF), P848


title: EFAT 18 Cth-/- CysF diet

city: New Haven

first: Lucie

last: Orliaguet

state: CT

address: 310 Cedar Street

institute: Yale University

description:
Library name: Sample 47
Column name in cth.all_gene.rsem.counts.csv: EFAT18

data_processing:
The quality of raw reads was assessed with FastQC [FastQC]. Raw reads were mapped to the GENCODE vM9 mouse reference genome [GENCODE] using STAR aligner [STAR] with the following options: --outFilterMultimapNmax 15 --outFilterMismatchNmax 6 --outSAMstrandField All --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM.
The quality control of mapped reads was performed using in-house scripts that employ Picard tools [Picard]. The list of rRNA genomic intervals that we used for this quality control was prepared on the basis of UCSC mm10 rRNA annotation file [UCSC] and GENCODE primary assembly annotation for vM9 [GENCODE]. rRNA intervals from these two annotations were combined and merged to obtain the final list of rRNA intervals. These intervals were used for the calculation of the percentage of reads mapped to rRNA genomic loci. Strand specificity of the RNA-Seq experiment was determined using an in-house script, on the basis of Picard [Picard] mapping statistics. Expression quantification was performed using RSEM [RSEM]. For the assessment of expression of mitochondrial genes, we used all genes annotated on the mitochondrial chromosome in the GENCODE vM9 mouse reference genome [GENCODE].
Assembly: GENCODE vM9
Supplementary files format and content: csv file with raw counts for each sample

source_name: Visceral adipose tissue

extract_protocol:
Frozen tissues were ground and resuspended in STAT-60. RNA was extracted using Zymo mini kits.
Poly A library prep was performed according to manufeacturers' protocol.

treatment_protocol: Male Cth+/+ and Cth-/- mice were fed with control of cystine deficient diet for 6 days. Adipose depots were collected and snap frozen.

value: Visceral adipose tissue

value: Cth-/-

tag: diet

value: cystine free


title: EFAT 17 Cth-/- CysF diet

description:
Library name: Sample 46
Column name in cth.all_gene.rsem.counts.csv: EFAT17


title: EFAT 16 Cth-/- CysF diet

description:
Library name: Sample 45
Column name in cth.all_gene.rsem.counts.csv: EFAT16


title: EFAT 15 Cth-/- CTRL diet

description:
Library name: Sample 44
Column name in cth.all_gene.rsem.counts.csv: EFAT15

value: control


title: Primary CRC tumor samples (FF), P844

value: Primary colorectal cancer

value: Fresh Frozen


title: RNAseq_ESC_EHMT2siRNA_rep3

city: Zurich

first: Raffaella

last: Santoro

address: Winterthurerstrasse 190

institute: University of Zurich

data_processing:
The quality of the 150 bp paired end reads generated by the machine was checked by FastQC (Andrews, 2010). The quality of the reads was increased by applying: a) SortMeRNA (Kopylova, 2012) (version 2.1) tool to filter out ribosomal RNA; b) Trimmomatic (Bolger, 2014) (version 0.36) software package to trim the sorted (a) reads. The sorted (a), trimmed (b) reads were mapped against the mouse genome (mm10) using the default parameters of the STAR (Spliced Transcripts Alignment to a Reference, version 2.4.0.1) (Dobin et al., 2013). For each gene, exon coverage was calculated using a custom pipeline and then normalized in reads per kilobase per million (RPKM) (Mortazavi et al., 2008), the method of quantifying gene expression from RNA sequencing data by normalizing for total read length and the number of sequencing reads.
Assembly: mm10 (GRCm38)
Supplementary files format and content: xlsx
Supplementary files format and content: Excel file includes the DESeq2 computed mean of normalized count of all samples based on sequencing depth

extract_protocol:
Total RNA was purified with TRIzol reagent (Life Technologies).
The quality of the isolated RNA was determined with a Qubit® 4 Fluorometer and 4200 Tape Station system. Only those samples with a 260nm/280 nm ratio between 1.8–2.1 and a 28S/18S ratio within 1.5-2 were further processed. The TruSeq Stranded mRNA (Illumina) was used in the succeeding steps. Briefly, total RNA samples (100-1000 ng) were polyA enriched and then reverse-transcribed into double-stranded cDNA. The cDNA samples were fragmented, end-repaired and adenylated before ligation of TruSeq adapters containing unique dual indices (UDI) for multiplexing. Fragments containing TruSeq adapters on both ends were selectively enriched with PCR. The quality and quantity of the enriched libraries were validated using Qubit® 4 Fluorometer. The product is a smear with an average fragment size of approximately 260 bp. Libraries were normalized to 10 nM in Tris-Cl 10 mM, pH8.5 with 0.1% Tween 20. TheIllumina NovaSeq X Pluswas used for cluster generation and sequencing according to standard protocol. Sequencing was paired end at 2x150 bp.

tag: cell line

value: Mouse embryonic stem cells (ESCs)

value: EHMT2 knockdown

value: ESCs were transfected with siRNA targeting EHMT2 and collected 3 days post transfection


title: EFAT 14 Cth-/- CTRL diet

description:
Library name: Sample 43
Column name in cth.all_gene.rsem.counts.csv: EFAT14


title: EFAT 13 Cth-/- CTRL diet

description:
Library name: Sample 42
Column name in cth.all_gene.rsem.counts.csv: EFAT13


title: 5_Control CRISPR-Trained

description:
Library name: T5
Train

tag: cell type

value: All brain cell types

value: WT

value: Male

value: 23 months


title: Primary CRC tumor samples (FF), P824


title: EFAT 12 Cth-/- CTRL diet

description:
Library name: Sample 41
Column name in cth.all_gene.rsem.counts.csv: EFAT12

tag: genotype


title: 2_Control CRISPR-Naïve

description:
Library name: N2
Naïve


title: EFAT 20 Cth-/- CysF diet

description:
Library name: Sample 48
Column name in cth.all_gene.rsem.counts.csv: EFAT20


title: Primary CRC tumor samples (FF), P79


title: EFAT 11 Cth+/+ CysF diet

description:
Library name: Sample 40
Column name in cth.all_gene.rsem.counts.csv: EFAT11

value: Cth+/+


title: RNAseq_ESC_EMHT2siRNA_rep1


title: RNAseq_ESC_EHMT2siRNA_rep2


title: EFAT 10 Cth+/+ CysF diet

description:
Library name: Sample 39
Column name in cth.all_gene.rsem.counts.csv: EFAT10


title: Primary CRC tumor samples (FF), P77


title: RNAseq_ESC_ContsiRNA_rep3

value: ESCs were transfected with control siRNA and collected 3 days post transfection


title: EFAT 7 Cth+/+ CysF diet

description:
Library name: Sample 37
Column name in cth.all_gene.rsem.counts.csv: EFAT07


title: Primary CRC tumor samples (FF), P68


title: EFAT 2 Cth+/+ CTRL diet

description:
Library name: Sample 34
Column name in cth.all_gene.rsem.counts.csv: EFAT02


title: EFAT 3 Cth+/+ CTRL diet

description:
Library name: Sample 35
Column name in cth.all_gene.rsem.counts.csv: EFAT03


title: RNAseq_ESC_ContsiRNA_rep2


title: Primary CRC tumor samples (FF), P651


title: SFAT 20 Cth-/- CysF diet

description:
Library name: Sample 32
Column name in cth.all_gene.rsem.counts.csv: SFAT20

source_name: Subcutaneous adipose tissue

value: Subcutaneous adipose tissue


title: Primary CRC tumor samples (FF), P641


title: SFAT 18 Cth-/- CysF diet

description:
Library name: Sample 31
Column name in cth.all_gene.rsem.counts.csv: SFAT18


title: EFAT 1 Cth+/+ CTRL diet

description:
Library name: Sample 33
Column name in cth.all_gene.rsem.counts.csv: EFAT01


title: SFAT 17 Cth-/- CysF diet

description:
Library name: Sample 30
Column name in cth.all_gene.rsem.counts.csv: SFAT17


title: SFAT 15 Cth-/- CTRL diet

description:
Library name: Sample 28
Column name in cth.all_gene.rsem.counts.csv: SFAT15


title: CODE806

type: RNA

description: RCC file not available for this record

hyb_protocol: Samples were hybridized for 16 hours at 65C

scan_protocol: Detection and scanning were performed by the nCounter SPRINT Profiler analysis system.

data_processing: Raw count data from nCounter

label: fluorescence microscope

source_name: CRC tumor

label_protocol: Sample RNA is hybridized with target-specific capture and reporter probes. This creates a library of unique target-probe complexes. Each target is labelled with a specific barcode, which can be detected and counted using an automated fluorescence microscope.

extract_protocol: RNA was extracted from FF tissue using RNA-Bee (Tel-Test inc., USA) and Trizol (ABP Biosciences, Rockville, USA) according to manufacturer’s protocol. Samples with a tumor percentage <30% were excluded. For FFPE tissue, three 10 µm-slides with flanking H&Es were prepared and tissue deparaffinisation was performed with Xylene. Subsequently, tumor tissue was macro-dissected to enrich for tumor tissue. RNA was extracted using the RNeasy FFPE kit (QIAGEN GmbH, Hilden, Germany) according to manufacturer’s instructions. RNA quantity and quality were measured using Tapestation (Agilent).

value: FFPE


title: SFAT 16 Cth-/- CysF diet

description:
Library name: Sample 29
Column name in cth.all_gene.rsem.counts.csv: SFAT16


title: CODE494

description: RCC file not available for this record


title: SFAT 14 Cth-/- CTRL diet

description:
Library name: Sample 27
Column name in cth.all_gene.rsem.counts.csv: SFAT14


title: EFAT 8 Cth+/+ CysF diet

description:
Library name: Sample 38
Column name in cth.all_gene.rsem.counts.csv: EFAT08

value: Visceral adipose tissue


title: Primary CRC tumor samples (FF), P602

value: Female


title: Primary CRC tumor samples (FF), P658


title: SFAT 12 Cth-/- CTRL diet

description:
Library name: Sample 25
Column name in cth.all_gene.rsem.counts.csv: SFAT12

value: Cth-/-


title: CODE425

description: RCC file not available for this record


title: SFAT 13 Cth-/- CTRL diet

description:
Library name: Sample 26
Column name in cth.all_gene.rsem.counts.csv: SFAT13

value: control


title: EFAT 4 Cth+/+ CTRL diet

description:
Library name: Sample 36
Column name in cth.all_gene.rsem.counts.csv: EFAT04


title: RNAseq_ESC_ContsiRNA_rep1


title: Primary CRC tumor samples (FF), P598

value: Primary colorectal cancer


title: CODE208

description: RCC file not available for this record


title: Primary CRC tumor samples (FF), P588

value: Fresh Frozen


title: SFAT 8 Cth+/+ CysF diet

description:
Library name: Sample 22
Column name in cth.all_gene.rsem.counts.csv: SFAT08

value: cystine free


title: CODE309

description: RCC file not available for this record


title: SFAT 11 Cth+/+ CysF diet

description:
Library name: Sample 24
Column name in cth.all_gene.rsem.counts.csv: SFAT11


title: Primary CRC tumor samples (FF), P582


title: SFAT 7 Cth+/+ CysF diet

description:
Library name: Sample 21
Column name in cth.all_gene.rsem.counts.csv: SFAT07


title: Primary CRC tumor samples (FF), P568


title: SFAT 10 Cth+/+ CysF diet

description:
Library name: Sample 23
Column name in cth.all_gene.rsem.counts.csv: SFAT10


title: Primary CRC tumor samples (FF), P633


title: CODE150

description: RCC file not available for this record


title: SFAT 2 Cth+/+ CTRL diet

description:
Library name: Sample 18
Column name in cth.all_gene.rsem.counts.csv: SFAT02


title: SFAT 4 Cth+/+ CTRL diet

description:
Library name: Sample 20
Column name in cth.all_gene.rsem.counts.csv: SFAT04


title: CODE50

description: RCC file not available for this record


title: BAT 20 Cth-/- CysF diet

description:
Library name: Sample 16
Column name in cth.all_gene.rsem.counts.csv: BAT20

source_name: Brown adipose tissue

value: Brown adipose tissue


title: Primary CRC tumor samples (FF), P547


title: CODE701


title: BAT 17 Cth-/- CysF diet

description:
Library name: Sample 14
Column name in cth.all_gene.rsem.counts.csv: BAT17


title: BAT 16 Cth-/- CysF diet

description:
Library name: Sample 13
Column name in cth.all_gene.rsem.counts.csv: BAT16


title: BAT 15 Cth-/- CTRL diet

description:
Library name: Sample 12
Column name in cth.all_gene.rsem.counts.csv: BAT15


title: Primary CRC tumor samples (FF), P538


title: SFAT 3 Cth+/+ CTRL diet

description:
Library name: Sample 19
Column name in cth.all_gene.rsem.counts.csv: SFAT03


title: Primary CRC tumor samples (FF), P524


title: SFAT 1 Cth+/+ CTRL diet

description:
Library name: Sample 17
Column name in cth.all_gene.rsem.counts.csv: SFAT01


title: BAT 12 Cth-/- CTRL diet

description:
Library name: Sample 9
Column name in cth.all_gene.rsem.counts.csv: BAT12


title: CODE528


title: BAT 13 Cth-/- CTRL diet

description:
Library name: Sample 10
Column name in cth.all_gene.rsem.counts.csv: BAT13


title: BAT 11 Cth+/+ CysF diet

description:
Library name: Sample 8
Column name in cth.all_gene.rsem.counts.csv: BAT11


title: BAT 14 Cth-/- CTRL diet

description:
Library name: Sample 11
Column name in cth.all_gene.rsem.counts.csv: BAT14


title: Primary CRC tumor samples (FF), P521


title: CODE174


title: CODE473


title: Primary CRC tumor samples (FF), P492


title: Primary CRC tumor samples (FF), P45


title: BAT 18 Cth-/- CysF diet

description:
Library name: Sample 15
Column name in cth.all_gene.rsem.counts.csv: BAT18


title: BAT 7 Cth+/+ CysF diet

description:
Library name: Sample 5
Column name in cth.all_gene.rsem.counts.csv: BAT07


title: BAT 8 Cth+/+ CysF diet

description:
Library name: Sample 6
Column name in cth.all_gene.rsem.counts.csv: BAT08


title: CODE421


title: CODE212


title: Primary CRC tumor samples (FF), P449


title: BAT 4 Cth+/+ CTRL diet

description:
Library name: Sample 4
Column name in cth.all_gene.rsem.counts.csv: BAT04


title: BAT 3 Cth+/+ CTRL diet

description:
Library name: Sample 3
Column name in cth.all_gene.rsem.counts.csv: BAT03


title: CODE391


title: CODE365


title: BAT 2 Cth+/+ CTRL diet

description:
Library name: Sample 2
Column name in cth.all_gene.rsem.counts.csv: BAT02


title: Primary CRC tumor samples (FF), P447


title: Primary CRC tumor samples (FF), P415


title: Liver, CTRL6h, rep1

city: Barcelona

first: Marina

last: Ruiz-Romero

state: Catalonia

address: Dr. Aiguader 88

country: Spain

institute: CRG

data_processing:
Reads were trimmed in silico to remove adapter sequences and low-quality reads using Trimmomatic.
The reads were aligned to the mouse (mm39) reference genome using Bowtie2
Duplicate reads were removed using Picard
mitochondrial reads and the reads mapping to the ENCODE blacklisted regions were filtered out using BEDTools2
Sambamba92 was used to eliminate fragments larger than 400 bp
Peak calling was performed using MACS293 run in pair-end mode requesting FDR<0.01
Read-depth normalised values (pileup bigwig)  and narrowPeak files were generated by MACS2
Assembly: mm39
Supplementary files format and content: bigwigs, narrowPeak

source_name: Liver

growth_protocol: C57BL/6J wild type (WT) mice were obtained from Jackson Laboratories and housed at IDIBELL (Barcelona, Spain). Animals used were 8 to 16-week-old male and female mice, hosted under a 12h light/dark cycle with free access to food and water

extract_protocol:
10-20mg of frozen liver were homogenised on ice using a glass Tenbroeck and then filtered through a 70µm Flowmi strainer. Nuclei were pelleted 5min 350xg and isolated using Iodixanol density gradient centrifugation (OptiPrepTM). The nuclei band was transferred to a fresh tube and diluted in ATAC-seq resuspension buffer (ATAC-RSB)-Tween
50,000 nuclei were aliquoted per sample and resuspended in transposition mix. Transposition reactions were incubated at 37°C for 30 min. Reactions were cleaned up with Qiagen MinElute PCR purification kit and PCR was performed following Illumina recomendations.

treatment_protocol: Partial hepatectomies (PHx) were performed by removal of two-thirds of the adult mouse liver, and mice that underwent surgery without liver resection (SHAM-operated) were used as control. Mice were euthanised at 6, 24 and 48 hours after surgery, and liver lobes were immediately frozen in liquid nitrogen and stored at -80ºC.

value: Liver

value: Shamsurgery


title: BAT 1 Cth+/+ CTRL diet

description:
Library name: Sample 1
Column name in cth.all_gene.rsem.countss.csv: BAT01


title: Liver, CTRL48h, rep2


title: Liver, CTRL24h, rep1


title: Primary CRC tumor samples (FF), P408


title: Liver, CTRL48h, rep1


title: Primary CRC tumor samples (FF), P404


title: BAT 10 Cth+/+ CysF diet

description:
Library name: Sample 7
Column name in cth.all_gene.rsem.counts.csv: BAT10


title: Liver, PH6h, rep1

value: Partial hepatectomy


title: Liver, PH48h, rep2


title: Liver, PH48h, rep1


title: CODE240


title: KT biol rep4

city: Zhengzhou

first: Lei

last: Zhang

state: Henan

address: No. 7, Weiwu Road

department: Reproductive Medicine Center

institute: Henan Provincial People’s Hospital

data_processing:
Firstly, Fastp (version 0.18.0) was used to remove the adaptor sequence and low-quality bases to obtain clean reads.
Bowtie2 (version 2.2.8) was used to remove ribosome RNA (rRNA) reads.
Then, mapped reads were obtained by comparing clean reads to the reference genome through Hisat2 (version 2.4).
The FPKM value of gene expression (fragment per kilobase of transcript per million mapped reads) was calculated by StringTie (version 1.3.1).
DEseq2 analyzed the gene expression differences between samples. An FDR value (q value) of <0.05 and fold change (FC) of >2 were defined as differential expressions.
Assembly: Ensembl_release100 (GRCm39)
Supplementary files format and content: gene_expression_anno.xls including FPKM values for each sample

source_name: kidney

growth_protocol: After in vitro fertilization (IVF) of fresh and vitrified oocytes, the zygotes were cultured in KSOM medium for 24 hours, and the cleaved embryos were used for embryo transfer. The cleaved embryos were transferred into the fallopian tubes of pseudopregnant female mice by operation. Twenty embryos were transplanted into each female mouse and raised normally until the offspring mice were born. The offspring mice were raised to adulthood (8W) after birth. The feeding environment was 12 h/12 h light/dark, the temperature was 25℃, and the humidity was 50%. The offspring were raised to adulthood (8 weeks old) after birth. The feeding, management, and use of mice complied with the ‘3Rs’ of animal ethics.

extract_protocol:
The offspring mice were raised to adulthood (8W) after birth. After being killed by cervical dislocation, the liver and kidney tissues were retrieved and thoroughly washed with normal saline to remove the blood. Then, the tissue block was cut 0.5 cm×0.5 cm in size with sterile RNase-free surgical scissors, ground into a powder after adding liquid nitrogen, and collected in a sterile RNase-free EP tube. After TRIzol was added and fully lysed, the total RNA in the tissues was obtained for sequencing according to the conventional RNA extraction steps.
The library was built according to standard Illumina protocols, which mainly include the steps of rRNA removal, mRNA isolation and fragmentation, cDNA double-strand synthesis and purification, cDNA terminal repair, 3’ end plus A, adaptor ligation, screening cDNA fragments of around 200 bp, PCR library enrichment and purification, etc.

treatment_protocol: We used the Cryotop method commonly used in ART for vitrification and thawing of oocytes in this study. The thawed oocytes were placed in KSOM at 37℃ and incubated at 100% humidity for 3 hours before IVF. In the control group, except for oocyte vitrification and thawing, the other treatments were the same as those in the vitrification group.

value: CD-1 (ICR)

value: kidney

tag: developmental stage

value: adult offspring

value: derived from vitrified oocytes


title: Liver, PH24h, rep1

tag: treatment


title: CODE669

tag: tissue


title: CODE466


title: CODE597


title: Primary CRC tumor samples (FF), P374


title: Liver, PH6h,rep 2


title: KT biol rep3


title: CODE749


title: Primary CRC tumor samples (FF), P434


title: KT biol rep2


title: CODE691


title: KT biol rep1


title: CODE146


title: Liver, PH24h, rep2


title: Primary CRC tumor samples (FF), P345


title: Primary CRC tumor samples (FF), P373

value: Male


title: Primary CRC tumor samples (FF), P341


title: KC biol rep3

value: derived from fresh oocytes


title: KC biol rep2


title: Primary CRC tumor samples (FF), P316


title: LT biol rep3

source_name: liver

value: liver


title: Primary CRC tumor samples (FF), P309


title: LC biol rep2


title: Primary CRC tumor samples (FF), P3043


title: LT biol rep1


title: LC biol rep3


title: CODE186

description: RCC file not available for this record

value: FFPE


title: Primary CRC tumor samples (FF), P3039


title: Subject 62, paired blood sample, repeat 2, Day P+7

city: Zhubei City, Hsinchu County

first: An

last: Hsu

address: 7F-6, No. 66, Shengyi 5th Road

country: Taiwan

institute: INTI Labs

description:
Library name: Sample 186
molecule: small RNA

data_processing:
Data were preprocessed by performing quality control on raw fastq data, including trimming adapter sequences, and removing low-quality reads using FastQC and Trimmomatic. After trimming low-quality (Q value < 20) ends from reads in addition to adapter removal, reads shorter than 17bps or longer than 55bps were discarded.
Alignment of processed reads to Human Genome Assembly GRCh38 (hg38) reference genome and a specific set of small RNA sequences from miRBase was performed by using aligners such as Bowtie.
Quantification of extracted reads from the data by mapping the aligned reads using samtools and obtained reference annotations using miRBase (total 2656 miRNAs).
Assembly: GRCh38
Supplementary files format and content: csv file include  raw read counts of miRNAs for each sample

source_name: blood

extract_protocol:
Small RNA was isolated from 200–600 μL of plasma with miRNeasy Serum/Plasma Advanced Kit (QIAGEN, Hilden, Germany, Cat. No. 217204) following the manufacturer’s protocol. For each sample, at least 10ng miRNA was used as input for the following library construction.
The miRNA sequencing library was constructed using the QIAseq miRNA Library Kit (QIAGEN, Germany, Cat. No. 331502).

value: blood

value: Progestrone treatment


title: CODE129


title: LC biol rep1


title: KC biol rep1


title: Primary CRC tumor samples (FF), P369

value: Primary colorectal cancer

value: Female