title: Foxa2 ChIP human normal rep3

data_processing:
Reads were aligned to the mouse genome (mm10; NCBI Build 38) and human genome (hg19; NCBI build 37) using BWA v0.7.12 (Li and Durbin, 2009). Duplicate reads were removed using Picard v 1.134 (http://picard.sourceforge.net). Reads (phred score ≥ 30) that aligned uniquely were used for subsequent analysis.
Data from two murine biological replicates were merged for Foxa2 and lamin B1 ChIP-Seq comparison (2 ND, 2 WD8, 2 WD12). LADs in mouse Lamin B1 ChIP-Seq were determined by SICER (Xu et al., 2014) (mm10 as species, window size 10,000 bp, gap size 10,000 bp, FDR 10%). PeakSeq (Rozowsky et al., 2009) was used to identify Foxa2 bound peaks against input controls (FDR 5%, q-value<1.05E-2;).
Data from three human patients were merged for Foxa2 and Lamin B1 binding (3 normal and 3 NAFLD). Epic peak caller (https://github.com/daler/epic), (Xu et al., 2014), was used to determine Lamin B1 associated domains in human patients (hg19 as species window size of 10kb, gap size of 3, FDR 5%). PeakSeq (Rozowsky et al., 2009) was used to identify Foxa2 bound peaks against input controls (FDR 5%, q-value<0.07).
RNA-Seq reads were aligned using STAR (Dobin et al., 2013) to mouse genome build mm10. Expression levels were calculated using RSEM (Li and Dewey, 2011). Differential expression analysis of RNA-seq (p-value <0.05) was performed in R using EdgeR package (Robinson et al., 2010) with a Benjamini-Hochberg FDR of 5%. Four replicates were sequenced for normal diet at each time point and WD8, 3 replicates for WD12.
Genome_build: mm10 (GRCm38); hg19 (GRCh37)
Supplementary_files_format_and_content: bed files with domain regions called by SICER with following columns: chromosome, start coordinate, end coordinate, p-value.
Supplementary_files_format_and_content: bed files with domain regions called by Epic with following columns: chromosome, start coordinate, end coordinate, p-value.
Supplementary_files_format_and_content: bed files with peak calls from PeakSeq with the following columns: chromosome, start coordinate, end coordinate, q-value.
Supplementary_files_format_and_content: RNA_Seq_WD8.txt: Tab-delimited text file with logFC and logCPM.
Supplementary_files_format_and_content: RNA_Seq_WD12.txt: Tab-delimited text file with logFC and logCPM.
Supplementary_files_format_and_content: Foxa2_ND.bed: bed file with peak coordinates.
Supplementary_files_format_and_content: Foxa2_WD8.bed: bed file with peak coordinates.
Supplementary_files_format_and_content: Foxa2_WD12.bed: bed file with peak coordinates.
Supplementary_files_format_and_content: LaminB1_ND.bed: bed file with domain coordinates.
Supplementary_files_format_and_content: LaminB1_WD8.bed: bed file with domain coordinates.
Supplementary_files_format_and_content: LaminB1_WD12.bed: bed file with domain coordinates.
Supplementary_files_format_and_content: Foxa2_normal_patients.bed: bed file with peak coordinates.
Supplementary_files_format_and_content: Foxa2_NAFLD_patients.bed: bed file with peak coordinates.
Supplementary_files_format_and_content: LaminB1_normal_patients.bed: bed file with domain coordinates.
Supplementary_files_format_and_content: LaminB1_NAFLD_patients.bed: bed file with domain coordinates.

source_name: Liver

value: liver

tag: disease state

value: Normal control


title: 73-AO3_EDM-ER-Rep2

status: Public on Nov 10 2022

type: SRA

city: Leuven

first: Peihua

last: Zhao

address: Herestraat 49

country: Belgium

institute: KU Leuven

library_source: genomic

data_processing:
Paired-end fastq files were aligned to human genome hg38 using STAR
Peak calling was performed by ‘callpeak’ function in the Model-based Analysis of ChIP-Seq (MACS2 2.1.2). Peaks overlapping with the ENCODE blacklist regions were removed.
The genome-wide normalized signal coverage track was generated using MACS2 SPMR peak calling, followed by MACS2 ‘bdgcmp’ with parameter -m FE to calculate fold-enrichment score.
The output BedGraph file was converted to bigWig format by bdg2bw
Assembly: hg38
Supplementary files format and content: bigWig

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: MCF7 cells were maintained in DMEM/F12 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching, chromatin was prepared using SimpleChIP Enzymatic Chromatin Kit from cell signaling.
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit.

treatment_protocol: Cells were cultured under full media for 24 hrs, or starved in charcoal-stripped serum containing media for 72hrs and then stimulated with DMSO or 10nM estradiol for 45 mins.

tag: cell line

tag: cell type

value: ER+ breast cancer cell line

tag: genotype

value: sgNT

tag: chip antibody

value: ER (Millipore, #06-935)


title: Sample 38_fkh1∆dbf4-Zn*1_rep2

city: Los Angeles

first: Meghan

middle: V

last: Petrie

state: CA

address: 1050 Childs Way

department: Molecular Biology

country: USA

institute: University of Southern California

description: BrdU-IP sequencing

data_processing:
library strategy: BrdU-IP-seq
Barcode-splitting: Sequenced reads were first processed using ea-utils which de-multiplexes the reads based on the specified barcode sequences.
Alignment: The raw sequencing reads were then aligned to the indexed genome from Saccharomyces Genome Database using bowtie2.
Data-cleaning: Filterred reads that were mapped to more than one region in the genome using samtools view. Reads were sorted by coordinates of the reference genome using samtools sort. PCR duplicates were removed using samtools rmdup
Binning: sequencing reads were binned over 50bp bins across the genome using coverageBed.
Assembly: S228C
Supplementary files format and content: binned.bed files

organism: Saccharomyces cerevisiae

source_name: Yeast cells

growth_protocol: 10–20 mL of cells were grown per sample to OD ~ 0.5 in YEPD at 23 °C

extract_protocol:
Cells were resuspend in 500 μL genomic lysis buffer and disrupted by bead-beating with FastPrep. Followed by PCI extractracion and ethanol precipitaion.
Samples were end-labeled using KAPA Hyper prep kit with unique barcoded adapters that are compatible with the subsequent library-amplification and sequencing primers for the Illumina sequencing platform.

treatment_protocol: Cells were arrested with α-factor (~5 nM ) and incubated for ~4 h at 23 °C then released in fresh YEPD containing 400 μg/mL BrdU, 200 μg/mL Pronase and 200 mM hydroxyurea. Harvested cells after 60min of incubation.

tag: strain

tag: antibody

value: Non

value: fkh1{delta}dbf4-Zn*1 (C661A C664A)

tag: treatment

value: hydroxyurea


title: CD34+ cells from MDS patient #14, transduced with DDIT3 shRNA#1, differentiated for 7 days

city: Dublin

first: Marina

last: Ainciburu

state: Dublin

address: Foster Avenue

department: Bioinformatics

country: Ireland

institute: NIBRT

library_source: transcriptomic

data_processing:
Samples were demultiplexed with Bcl2fastq (v2.20)
Reads were aligned to the human genome using STAR (v2.6)
Quantification was performed with the R package Rsubread (v1.32.4)
Subsequent analysis was carried out using the R/Bioconductor package DeSeq2
Genome_build: hg38
Supplementary_files_format_and_content: Raw counts matrix (genes x samples) as csv file

molecule: polyA RNA

source_name: CD34+ differentiated ex vivo

extract_protocol:
FACS sorted infected cells were collected at the indicated times
3' RNA sequencing libraries were prepared using the MARS-seq protocol adapted for bulk RNA-seq, with minor modifications

tag: tissue

value: Bone marrow

tag: condition

value: MDS cells, DDIT3 knockdown

tag: initial facs gating prior to cell culture

tag: plasmid used for trasduction of cells

value: pSIH1-H1-copGFP-DDIT3 shRNA#1

tag: time of ex vivo cell expansion

value: 2 days

tag: time of ex vivo erythroid differentiation

value: 7 days

tag: facs gating prior to rna-seq

value: GFP+


title: Sample 20_fkh1∆dbf4-Zn*2_rep2

description: BrdU-IP sequencing

value: anti-BrdU

value: fkh1{delta}dbf4-Zn*2 (H680C)


title: B16-OVA, Isotype IgG + Vehicle, Replicate 1

city: Cambridge

first: Seth

middle: Allen

last: Anderson

state: MA

address: 75 Ames Street

department: Cancer Program

institute: Broad Institute of MIT and Harvard

library_source: transcriptomic single cell

data_processing:
Cellranger v3.0.1 mkfastq command to convert bcl files to fastq files and to demultiplex fastq files
Cellranger v3.0.1 count command to generate raw and filtered count matrices
10X Genomics 3'v2 chemistry; 2x NovaSeq SP flow cells with 2 lanes e/a; raw fastqs from each separate flow cell and lane are included, but included processed files are concatonated across replicate flow cells
Assembly: Assembly: mm10
Supplementary files format and content: Tab-separated values (.tsv.), matrix files (.mtx), hierarchical data file (.h5), and fastq (.fastq)

organism: Mus musculus

source_name: melanoma subcutaneous tumor

growth_protocol: 1E6 B16-OVA cells were resuspended in sterile Ca- and Mg-free PBS (Gibco), mixed 1:1 by volume with Matrigel (Corning) and subcutaneously injected into the flank on day 0.

extract_protocol:
Tumors were dissected on day 14 post-inoculation and disassociated using the Miltenyi Mouse Tumor Dissociation Kit and gentleMACS Octo-Dissociator (Miltenyi) using the m-TKD-1 program. After filtering through a 70-μm filter, live cells were isolated using a density gradient with Lympholyte-M separation media (Cedarlane Labs) per the manufacturer’s specifications. CD45+ tumor-infiltrating immune cells were enriched by positive selection with MicroBeads (Miltenyi) and magnetic separator (Miltenyi).
Four representative samples from each of the Control (Vehicle/IgG-treated), aPD-1 (Vehicle/anti-PD-1-treated), TBK1i (TBK1i/IgG-treated), and αPD-1 + TBK1i (TBK1i/anti-PD-1) groups were selected and droplet-based isolation of single cells was performed with the Chromium Controller (10X Genomics) according to the manufacturer’s specifications. Subsequent generation of 3′ sequencing libraries was performed per manufacturer’s instructions (10X Genomics). Libraries were prepared utilizing Chromium Next GEM Single Cell Reagent Kits 3′v2 chemistry (10X Genomics). Characterization of the sequencing library was performed with TapeStation (Agilent) and Qubit (ThermoFisher) instruments.

treatment_protocol: Mice were randomized into four groups of 10 using the stratified method via Study Log program based on tumor size. Randomization and treatment initiated on Day 1; mean TV at the start of dosing of 110.05 mm3. Vehicle (0.5% hydroxypropyl methylcellulose K100LV / 0.4% Tween 80 / 99.1% 0.05N hydrochloric acid) or TBK1i (Compound 1, Gilead Sciences; 40 mg/kg)14 was administered by oral gavage daily (Days 1-18) and isotype control IgG or anti–PD-1 (10 mg/kg) was administered three times weekly for a total of six doses. Investigators were not blinded to treatment groups.

value: melanoma subcutaneous tumor

value: CD45+ immune cells

value: Isotype IgG + Vehicle


title: Sample 19_fkh1∆dbf4-Zn*2_rep1

description: BrdU-IP sequencing


title: Tumor CD8-IRF2cKO

city: Toronto

first: David

last: Brooks

address: 610, University Ave

country: Canada

institute: Princess Margaret Cancer Centre

data_processing:
For AB-Seq experiment, fastq files were generated using bcl2fastq2 v2.20. Read counts were generated from fastq files using the BD Rhapsody? WTA Analysis Pipeline, available on SevenBridges server, run with default parameters.
For scATAC-Seq experiments, to generated fastq files, we ran Illumina RTA v3.4.4 and we used bcl2fastq 2.20 to convert bcl to fastq files with default parameters, see https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/using/bcl2fastq-direct. For cell ranger analyses, cellranger-atac/2.0.0 count was used with the reference refdata-cellranger-arc-mm10-2020-A-2.0.0 downloaded from the 10x website. We set the chemistry parameter to --chemistry=ARC-v1, since we analysed the scATAC-Seq data of the multiomics data.
For CUT&TAG experiment, samples were aligned to the mm10 genome using bowtie v2.4.1 with the following parameters: ?--local --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700? and preprocessed using samtools v1.10. A bedgraph file was generated by scaling the reads by a scaling factor defined as 1000000/number_of_aligned_reads. Regions overlapping the ENCODE mm10 blacklist regions were removed. Peaks were called using SEACR v1.3 with a signal_threshold of 1 and run in `stringent` and `norm` mode.
Assembly: GRCm38
Supplementary files format and content: For each AB-Seq sample an h5Seurat object contains: raw counts, normalized counts, clustering data, pca and umap data
Supplementary files format and content: For each scATAC-Seq sample a tar file containing:  a fragement and an index file from alignment and a metadata csv file
Supplementary files format and content: For each CUT&TAG experiment, a tar file containing: peaks in 'stringent' and 'norm' mode as called using SEACR v1.4 on blacklist filtered and normalized data

source_name: MC38 tumor

growth_protocol: 2x105 MC38 tumor cells were injected subcutaneously (s.c.) into one hind leg of each mouse. Tumors harvested on day 12 after implantation.

extract_protocol:
For AB-Seq experiment, Tumors were cut into small fragments and digested in RPMI media containing collagenase I, FBS, DnaseI in a gentleMACS dissociator. Tumor ells were filtered and subjected to red blood cell lysis. CD45+ tumor immune cells were FACSorted and the sorted cells  were labelled with sample multi-plexing antibodies and AbSeq Ab-Oligos (antibody-oligonucleotides) using the BD Mouse Immune Single-Cell Multiplexing Kit. For ATAC-Seq experiment, Tumors were cut into small fragments and digested in RPMI media containing collagenase I, FBS, DnaseI in a gentleMACS dissociator. Tumor cells were filtered and subjected to red blood cell lysis. CD8+ tumor immune cells were isolated using autoMACS Pro Separator (Miltenyi Biotec), washed and treated with DNase I, and nuclei isolated according to the 10x Genomics nuclei isolation for single cell ATAC sequencing protocol. For CUT&Tag, naïve CD8+ T cells were isolated from the spleens and lymph nodes of C57BL/6 by negative selection (Stem Cell Technologies). Isolated CD8+ T cells were activated for 3 days using 5ug/mL plate-bound anti-CD3 (16-0031-86 Invitrogen) and 2ug/mL soluble anti-CD28 (16-0281-86 Invitrogen) antibodies in 10% RPMI complete media containing 100U/ml rhIL2 (200-02 PeproTech). Nuclei were isolated and CUT&Tag performed using the protocol from Epicypher (EpiCypher® CUTANA? Direct-to-PCR CUT&Tag Protocol v1.6 Revised: 11.04.2021). Prior to sequencing, samples were normalized based on their DNA concentrations and pooled.
For AB-Seq experiment, Whole transcriptome Analysis (WTA), AbSeq and Sample Tag libraries were constructed using the BD Rhapsody? WTA Amplification Kit from cDNA encoded on beads after cell capture on the BD Rhapsody? Single-Cell Analysis System, using the manufacturer's recommended protocol.. For ATAC-Seq experiment, ATAC libraries were prepared following the 10x Genomics sequencing workflow and protocol. For CUT&Tag library preparetion was performed using the protocol from Epicypher (EpiCypher® CUTANA? Direct-to-PCR CUT&Tag Protocol v1.6 Revised: 11.04.2021).

treatment_protocol: For CUT&Tag: Isolated CD8+ T cells were activated for 3 days using 5ug/mL plate-bound anti-CD3 and 2ug/mL soluble anti-CD28.

value: MC38 tumor

value: MC38 tumor infiltrating CD8 T cells

value: IRF2-/- (CD8 T cells only)


title: GFP-7 IP

city: beijing

first: Yuejiao

last: Ma

address: No. 10.wai xi tou tiao, you an men street.

country: China

description: control KD

data_processing:
The stages of image analysis and base calling were performed using Off-Line Basecaller software (OLB V1.8).
After passing Solexa CHASTITY quality filter, the clean reads were aligned to mouse genome (UCSC mm10) using Hisat2 software
Aligned reads were used for peak calling,LncRNA, mRNA and Small ncRNA associated hMeDIP enriched regions (peaks) with statistically significant were identified for each sample, using a q-value threshold of 10-4 by MACS2 software
LncRNA, mRNA and Small ncRNA associated hMeDIP enriched regions (peaks) were annotated by the nearest gene using the newest UCSC RefSeq database
LncRNA, mRNA and Small ncRNA associated differentially Hydroxymethylated regions (DhMRs) within promoter between two samples/groups with statistically significant were identified by diffReps software [5] (Cutoff: log2FC 1, p-value 10 4)
Enhancer & SuperEnhancer associated Intergenic DhMRs were annotated by the nearest gene using the UCSC RefSeq database.
Genome_build: mm10
Supplementary_files_format_and_content: The All_hMeDIP_Signal file format is xlsx, which analyses LncRNA, mRNA and Small ncRNA associated hMeDIP enriched regions (peaks); the Differentially_HydroxyMethylated file format is xlsx, which analyses the LncRNA, mRNA and Small ncRNA associated differentially Hydroxymethylated regions (DhMRs) within promoter and Enhancer & SuperEnhancer associated Intergenic DhMRs between two samples/groups.

source_name: Liver tissues

extract_protocol:
DNA samples were fragmented to a size range of  200-800bp with a Diagenode Bioruptor.
About 1 g of fragmented DNA was prepared for Illumina HiSeq 4000 sequencing as the following steps: 1) End repair of DNA samples; 2) A single A base was added to the 3' ends; 3) Ligation of Illumina's genomic adapters to DNA fragments; 4) hMeDIP to enrich Hydroxymethylated DNA by anti-5-Hydroxymethylcytosine antibody; 5) PCR amplification to enrich precipitated fragments; 6) Size selection of  300-900bp DNA fragments using AMPure XP beads. The completed libraries were quantified by Agilent 2100 Bioanalyzer. The libraries were denatured  with 0.1 M NaOH to generate single-stranded DNA molecules, captured on Illumina flow cell, amplified in situ. The libraries were then sequenced on the Illumina HiSeq 4000 following the HiSeq 3000/4000 SBS Kit (300 cycles) protocol.

treatment_protocol: The Itgα5 KD groups (n=3) were obtained by the injection of AAV8 vectors packaged with crisp-case9 target liver-specific Itgα5 sgRNA plasmids with LP1 promotor. Control KD groups (n=3) were obtained by the injection of equal dose of control AAV8 vectors. Mice were sacrificed at 4 weeks after tail vein injection.

value: BALB/c

value: liver

tag: group

value: Control


title: CD34+ cells from MDS patient #13, transduced with DDIT3 shRNA#2, differentiated for 7 days

value: Bone marrow

value: pSIH1-H1-copGFP-DDIT3 shRNA#2


title: Foxa2 ChIP human NAFLD Severe rep1

city: Charlottesville

first: Irina

last: Bochkis

state: VA

address: 1340 Jefferson Park Ave

department: Pharmacology

institute: University of Virginia

extract_protocol:
[RNA-Seq] Liver RNA was isolated from mice on control and Western diet (8 weeks and 12 weeks). Quality of RNA samples was analyzed using Agilent RNA 6000 Nano Kit (Bioanalyzer, Agilent Technologies). Samples with RIN scores above 9.5 were used in library preparation. 1 µg of total RNA was used to isolate mRNA (NebNext Poly(A) mRNA Magnetic Isolation Module).
[RNA-Seq] Libraries of resulting mRNA were prepared using NebNext Ultra II RNA library preparation kit. All samples were sequenced on Illumina NextSeq 500.
[ChIP-Seq] Snap-frozen liver (100 mg) from mice on normal and Western diet (8 weeks and 12 weeks) or from normal and NAFLD patients was used to prepare chromatin. Foxa2‐specific rabbit antiserum (Seven Hills Bioreagents, WRAB‐1,200) and rabbit antibody to lamin B1 (Abcam, Ab16048) were used for immunoprecipitation.
[ChIP-Seq] Libraries were prepared according to Illumina's instructions. Briefly, DNAs were blunted with a combination of T4 DNA polymerase, Klenow polymerase, and T4 PNK, then a single 3′-end “A” base was added using Klenow exo (3′-to-5′ exo minus). Multiplex adapters were then ligated to the ends of the modified DNA. After adapter ligation DNA was PCR amplified with Broad custom primers for 16 cycles and library fragments of ~280 bp (~150-bp insert plus ~130-bp adaptor and PCR primer sequences) were isolated using Pippin Prep agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. All libraries were sequenced on Illumina NextSeq 500.

treatment_protocol:
[RNA-Seq] Mice were fed Western diet (WD, 42% kcal from fat and containing 0.1% cholesterol; Harlan TD.88137) with ad libitum consumption of glucose and fructose (SW, 23.1 g/L d-fructose +18.9 g/L d-glucose).
[ChIP-Seq] Mice were fed Western diet (WD, 42% kcal from fat and containing 0.1% cholesterol; Harlan TD.88137) with ad libitum consumption of glucose and fructose (SW, 23.1 g/L d-fructose +18.9 g/L d-glucose).

value: NAFLD


title: 74-AO5_EDM-ER-Rep2

value: ER+ breast cancer cell line

value: ER (Millipore, #06-935)


title: 69-AO3_E2-Input-Rep1

value: sgNT


title: Tumor IRF2-/-


title: CD34+ cells from MDS patient #14, transduced with control shRNA, differentiated for 7 days

value: MDS cells, Control

value: pSIH1-H1-copGFP-Scrambled shRNA

value: 2 days

value: 7 days

value: GFP+


title: Tumor WT

value: MC38 tumor

value: wildtype (WT)


title: CD34+ cells from MDS patient #13, transduced with DDIT3 shRNA#1, differentiated for 7 days

value: MDS cells, DDIT3 knockdown

value: pSIH1-H1-copGFP-DDIT3 shRNA#1


title: GFP-5 IP

description: control KD

value: BALB/c

value: liver


title: CD34+ cells from MDS patient #13, transduced with control shRNA, differentiated for 7 days

value: Bone marrow


title: GFP-7 input

description: control KD

value: Control


title: 65-AO3_EDM-Input-Rep1


title: 66-AO5_EDM-Input-Rep1


title: 64-AO8_E2-ER-Rep1


title: P19, rargKO, BMS641+BMS961, Day 10

city: Evry

first: Marco Antonio

last: Mendoza Parra

address: 2 Gaston Crémieux

country: France

institute: Genoscope

data_processing:
Fastq files were qualified with the NGS-QC Generator tool (Mendoza-Parra et al, 2016b, 2013).
Reads from fastq files were mapped to the mouse mm9 reference genome using Bowtie 2.1.0 under default parameters.
Mapped reads were associated to known genes with featureCounts.  RNA-Seq analyses were done with DESeq2 R-package.
Assembly: mm9
Supplementary files format and content: comma separated files containing differential expression levels (Log2) and confidence p-values (DeSeq2) relative to the WT_EtOHd2 control sample.

molecule: total RNA

growth_protocol: P19 cells were grown in DMEM supplemented with 1 g/L glucose, 5% FCS, and 5% delipidated FCS. P19 EC cells were cultured in monolayer on gelatin-coated culture plates (0.1%).

extract_protocol:
Total RNA was extracted from P19 cells treated with either ATRA or RAR-specific agonists, using the TRIzol RNA isolation reagent (ThermoFisher Scientific ref: 15596026).
RNA-sequencing libraries were produced with the NEBNext® Ultra™ II RNA Library Prep Kit for Illumina (E7770).
poly-T captured mRNA-seq

treatment_protocol: For cell differentiation assays, all-trans retinoic acid (ATRA) was added to plates to a final concentration of 1 μM for different exposure times. For treatment with RAR subtype-specific agonists, cells were incubated with BMS961 (RARg-specific; 0.1 μM), BMS753 (RARa-specific; 1 μM), and/or BMS641 (RARb-specific; 0.1 μM). After four days of treatment with either of the aforementioned retinoids, medium was replaced by neurobasal medium (ThermoFisher Scientific ref: 21103049) supplemented with N2 (ThermoFisher Scientific ref: 17502048) and B27 devoid of vitaminA (ThermoFisher Scientific ref: 12587010) and cultured for 6 more days.

value: carcinoma stem cells

value: rargKO

tag: time

value: Day 10


title: 68-AO8_EDM-Input-Rep1

value: ER+ breast cancer cell line


title: P19, rargKO, BMS641, Day 10


title: CD34+ cells from healthy donor transduced with DDIT3 overexpression plasmid, differentiated for 14 days 2

value: Healthy cells, DDIT3 overexpression

value: 14 days


title: 63-AO6_E2-ER-Rep1

value: ER (Millipore, #06-935)


title: 67-AO6_EDM-Input-Rep1


title: P19, rargKO, BMS753, Day 10


title: Sample 17_fkh1∆dbf4-Zn*1_rep1

description: BrdU-IP sequencing

value: anti-BrdU

value: fkh1{delta}dbf4-Zn*1 (C661A C664A)

value: hydroxyurea


title: P19, rarbKO, BMS641+BMS961, Day 10

value: rarbKO


title: GFP-5 input

description: control KD


title: CD34+ cells from healthy donor transduced with control plasmid, differentiated for 14 days 2

value: Healthy cells, Control

value: 2 days

value: GFP+


title: GFP-3 IP

description: control KD

value: BALB/c

value: liver


title: P19, rargKO, ATRA, Day 10

value: ATRA


title: CD34+ cells from healthy donor transduced with control plasmid, differentiated for 14 days 1

value: Bone marrow


title: AAV-5 input

description: integrin α5 KD

value: Test


title: P19, rarbKO, BMS753, Day 10

value: carcinoma stem cells

value: Day 10


title: GFP-3 input

description: control KD

value: Control


title: 62-AO5_E2-ER-Rep1

value: ER+ breast cancer cell line


title: 61-AO3_E2-ER-Rep1

value: sgNT

value: ER (Millipore, #06-935)


title: P19, rarbKO, BMS961, Day 10


title: 59-AO6_EDM-ER-Rep1


title: CD34+ cells from healthy donor transduced with DDIT3 overexpression plasmid, differentiated for 14 days 1

value: Healthy cells, DDIT3 overexpression

value: 14 days


title: CD34+ cells from healthy donor transduced with DDIT3 overexpression plasmid, differentiated for 10 days 2

value: 10 days


title: ARID1B knockdown, replicate 2

city: Kansas City

first: Madelaine

last: Gogol

state: MO

address: 1000 E. 50th Street

department: Computational Biology Core

institute: Stowers Institute

data_processing:
Paired end reads of 76 bases were sequenced on a NextSeq 500 in mid-output mode. Data was demultiplexed with bcl2fastq2 v2.20.
Data was aligned to the hg38 genome from UCSC using STAR 2.7.3a with annotations from Ensembl 102, with the following parameters (including end to end alignments): --outSAMprimaryFlag OneBestScore --outFilterMultimapNmax 20 --outFilterMismatchNoverLmax 0.1 --outFilterType BySJout --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --readFilesCommand zcat --limitBAMsortRAM 60000000000 --quantMode TranscriptomeSAM GeneCounts --alignEndsType EndToEnd
Downstream analysis was done in R 4.0.0 with edger 3.30.3
Assembly: hg38
Supplementary files format and content: raw gene counts generated by STAR for each sample

source_name: HEK293FRT cells

extract_protocol:
RNA was extracted using Qiagen RNA extraction Kit, followed manufacturers instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: siRNA transfection for 72 hours


title: AAV-5 IP

description: integrin α5 KD


title: P19, raraKO, BMS641+BMS961, Day 10

value: raraKO


title: AAV-17 IP

description: integrin α5 KD


title: 60-AO8_EDM-ER-Rep1


title: 58-AO5_EDM-ER-Rep1


title: AAV-15 input

description: integrin α5 KD


title: P19, raraKO, ATRA, Day 10


title: CD34+ cells from healthy donor transduced with control plasmid, differentiated for 10 days 1

value: Healthy cells, Control

value: 2 days


title: AAV-17 input

description: integrin α5 KD

value: BALB/c


title: CD34+ cells from healthy donor transduced with control plasmid, differentiated for 10 days 2

value: GFP+


title: P19, WT, BMS961, Day 10

value: WT


title: P19, raraKO, BMS961, Day 10


title: 57-AO3_EDM-ER-Rep1


title: AAV-15 IP

description: integrin α5 KD

value: liver


title: CD34+ cells from healthy donor transduced with DDIT3 overexpression plasmid, differentiated for 4 days 1

value: Bone marrow

value: 4 days


title: CD34+ cells from healthy donor transduced with DDIT3 overexpression plasmid, differentiated for 4 days 2


title: 22-AO5_FM-Input-Rep2


title: P19, rarbKO, ATRA, Day 10

value: carcinoma stem cells

value: rarbKO

value: ATRA

value: Day 10


title: CD34+ cells from healthy donor transduced with control plasmid, differentiated for 4 days 2


title: CD34+ cells from healthy donor transduced with DDIT3 overexpression plasmid, differentiated for 10 days 1


title: 24-AO8_FM-Input-Rep2

value: ER+ breast cancer cell line


title: exp female [FMSV275]

city: Rennes

first: Fatima

last: SMAGULOVA

address: 9 av. Prof. Léon Bernard

institute: Irset - U1085

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Sequence reads were mapped to reference genome hg38 using Bowtie v1.2.3 with the following parameters -m 1 --best --strata -v 3
Assembly: hg38
Supplementary files format and content: bigWig files were generated using with an in-house script (Variable step, span=25, reads were elongated to 200b).

source_name: We provided 14 libraries (14 ChIPs) for single-end sequencing (1x50bp). ChIP was performed from chromatin obtained from placenta of human female new borns.

extract_protocol:
50 mg of placenta was chopped and fixed in 1% paraformaldehyde for 10 min at room temperature, quenched with 0.125 M glycine, and pelleted at 900g for 5 min. Tissue was homogenized with Tissue lyser (Qiagen) and samples were filtered in a cell strainer and pelleted. The pellet was washed with the following buffer: 0.25% (vol/vol) Triton X-100, 10 mM EDTA, 0.5 mM EGTA, 10 mM Tris pH8. Samples were centrifugated at 1100 rpm for 5 minutes, 4°C and the pellet, containing cells, was resuspended in 300 μL of SDS lysis buffer (1% (wt/vol) SDS, 10 mM EDTA, and 50 mM TrisCl pH8) containing a protease inhibitor. Sonication was performed using Qsonica 700 sonicator supplied with cup horn 431C2. Sonication was performed in 300 μl in Eppendorf tubes using the following conditions: efficiency 60%, sonication 20 s on, 20 s off, and total time 8 min. The sonicated chromatin was diluted using 1,7 mL of the following buffer: (0.01% (1.1% (vol/vol) Triton X-100, 1.2 mM EDTA, 16.7 mM TrisHCl, 167 mM NaCl). A solution containing 20μL of Dynabeads (10002D, Invitrogen) and 0.5 μg of H3K4me3 (07- 473; Merck Millipore) antibody was added to the sample tubes and incubated overnight at 4°C. After several washes, immunoprecipitated DNA was eluted, treated with proteinase K, and purified using the QIAGEN MinElute kit (28004; QIAGEN).
Sequencing libraries were prepared using NEBNext Ultra DNA Library Prep Kit for Illumina (E7645S; NEB). We used 10 ng DNA for library preparation.

value: diethylphosphate range from 0.11 to 399 nmol/L

tag: Sex

value: female

value: placenta


title: non-exp female [FMSV274]

value: non-detectable level of diethylphosphate


title: P19, WT, EtOH, Day 10

tag: cell line

value: EtOH


title: 19-AO6_FM-NR2F2-Rep2

tag: cell type


title: 23-AO6_FM-Input-Rep2

tag: genotype


title: 21-AO3_FM-Input-Rep2

value: sgNT


title: exp female [FMSV276]


title: P19, WT, EtOH, Day 4

value: Day 4


title: HSCs from healthy donor transduced with DDIT3-overexpression plasmid 1

source_name: HSC

value: Healthy cells, DDIT3 overexpression

value: 2 days

value: GFP+


title: P19, WT, EtOH, Day 2

value: WT

value: Day 2


title: 17-AO3_FM-NR2F2-Rep2

tag: chip antibody


title: HSCs from healthy donor transduced with DDIT3-overexpression plasmid 2

value: Bone marrow


title: HSCs from healthy donor transduced with control plasmid 2

value: Healthy cells, Control


title: P19, WT, BMS641+BMS961, Day 4

value: carcinoma stem cells


title: 16-AO8_FM-ER-Rep2

value: ER (Millipore, #06-935)


title: exp female [FMSV278]


title: P19, WT, BMS641+BMS961, Day 10

value: Day 10


title: HSCs from healthy donor transduced with control plasmid 1


title: exp female [FMSV271]

value: diethylphosphate range from 0.11 to 399 nmol/L


title: 15-AO6_FM-ER-Rep2

value: ER+ breast cancer cell line


title: P19, WT, BMS641+BMS961, Day 2


title: 14-AO5_FM-ER-Rep2


title: CD34+ cells from healthy donor transduced with control plasmid, differentiated for 4 days 1

value: 4 days


title: non-exp female [FMSV273]

value: non-detectable level of diethylphosphate

value: female

value: placenta


title: 13-AO3_FM-ER-Rep2

value: sgNT


title: P19, WT, BMS753, Day 10


title: non-exp female [FMSV272]


title: CD34+ cells; healthy donor tranduced with a control plasmid; erythroid differentiation for 14 days

data_processing:
Demultiplexing, alignment to the hg38 genome and quantification was carried out with Cellranger (v3.1)
Subsequent analysis (quality control, clustering, integration and differential expression) was performed with Seurat v3
Genome_build: hg38
Supplementary_files_format_and_content: HDF5 Feature Barcode matrices

extract_protocol:
Cells were isolated from the ex vivo differentiation system as explained above
Single cell 3' RNA sequencing libraries were prepared using the chromiun controller from 10X Genomics. NEXTGEM Single Cell 3' Reagent Kit v3.1  was used.


title: P19, WT, ATRA, Day 10

value: ATRA


title: P19, WT, BMS753, Day 4

value: Day 4


title: P19, WT, BMS753, Day 2


title: HSCs from untreated MDS patient 12

data_processing:
Samples were demultiplexed with Bcl2fastq (v2.20)
Reads were aligned to the human genome using STAR (v2.6)
Quantification was performed with the R package Rsubread (v1.32.4)
Subsequent analysis was carried out using the R/Bioconductor packages DeSeq2 and MaSigPro
Genome_build: hg38
Supplementary_files_format_and_content: Raw counts matrix (genes x samples) as csv file

extract_protocol:
Cells were sorted from bone marrow aspirates.
3' RNA sequencing libraries were prepared using the MARS-seq protocol adapted for bulk RNA-seq, with minor modifications

value: Untreated MDS patient

tag: facs gating


title: 11-AO6_FM-Input-Rep1


title: HSCs from untreated MDS patient 11


title: exp female [FMSV268]

tag: antibody


title: exp female [FMSV266]


title: 12-AO8_FM-Input-Rep1


title: CD34+ cells; healthy donor tranduced with a DDIT3-overexpression plasmid; erythroid differentiation for 14 days

value: Healthy cells, DDIT3 overexpression

value: 2 days

value: 14 days

value: GFP+


title: HSCs from untreated MDS patient 10

value: Bone marrow


title: exp female [FMSV265]


title: HSCs from untreated MDS patient 8


title: IRF2_KO_GEX

source_name: MC38 tumor cells

tag: strain

tag: tumor


title: exp female [FMSV267]

tag: tissue


title: 10-AO5_FM-Input-Rep1


title: 9-AO3_FM-Input-Rep1


title: non-exp female [FMSV264]


title: 7-AO6_FM-NR2F2-Rep1


title: HSCs from untreated MDS patient 7

tag: condition


title: Input [FMSV216]

source_name: We provided 18 libraries (17 ChIPs + 1 input) for single-end sequencing (1x50bp). ChIP was performed from chromatin obtained from placenta of human male new borns.

value: none, Input

value: male


title: WT_GEX

value: wildtype (WT)


title: B20: Sting1-/- mice+Sting1-/- B16+rMVA rep4

city: New York

first: Ning

last: Yang

state: NY

institute: MSKCC

description: Sting1-/- mice+Sting1-/- B16+rMVA rep4

data_processing:
The samples were sequenced using Illumina NovaSeq6000 sequencer with paired-end 50 bps reads. The raw sequencing reads in BCL format were processed through bcl2fastq 2.19 (Illumina) for FASTQ conversion and demultiplexing.
The RNA reads were aligned and mapped to the GRCm38 human reference genome by STAR (Version2.5.2).
The transcriptome reconstruction was performed by Cufflinks (Version 2.1.1). The abundance of transcripts was measured with Cufflinks in Fragments Per Kilobase of exon model per Million mapped reads (FPKM).
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text file include normalized abundance measurements(FPKM) at gene level for each samples

source_name: Sting1-/- mice+Sting1-/- B16+rMVA

extract_protocol:
RNA was harvested using Qiagen Rneasy Mini kit. Illumina TruSeq RNA Sample Prep Kit  was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Sting1-/- mice

tag: tumor genotype

value: Sting1-/- tumor

value: Sting1-/- mice+Sting1-/- B16+rMVA


title: exp male [FMSV215]

value: diethylphosphate range from 0.11 to 399 nmol/L


title: non-exp male [FMSV214]

value: non-detectable level of diethylphosphate

value: placenta


title: HSCs from untreated MDS patient 6


title: HSCs from untreated MDS patient 5


title: P19, WT, ATRA, Day 2

value: carcinoma stem cells

value: WT

tag: treatment

value: ATRA

value: Day 2


title: 3-AO6_FM-ER-Rep1

value: ER+ breast cancer cell line

value: ER (Millipore, #06-935)


title: non-exp male [FMSV213]


title: 5-AO3_FM-NR2F2-Rep1

value: sgNT


title: 4-AO8_FM-ER-Rep1


title: P19, WT, ATRA, Day 4

value: Day 4


title: B19: Sting1-/- mice+Sting1-/- B16+rMVA rep3

description: Sting1-/- mice+Sting1-/- B16+rMVA rep3


title: non-exp male [FMSV212]


title: HSCs from untreated MDS patient 9

value: Bone marrow

value: Untreated MDS patient


title: B18: Sting1-/- mice+Sting1-/- B16+rMVA rep2

description: Sting1-/- mice+Sting1-/- B16+rMVA rep2


title: HSCs from untreated MDS patient 4


title: B17: Sting1-/- mice+Sting1-/- B16+rMVA rep1

description: Sting1-/- mice+Sting1-/- B16+rMVA rep1


title: HSCs from untreated MDS patient 3


title: 1-AO3_FM-ER-Rep1


title: HSCs from untreated MDS patient 2


title: 2-DKO-FM

extract_protocol: ATAC-seq libraries were prepared using the Nextera XT Library Preparation Kit.


title: 2-AO5_FM-ER-Rep1


title: non-exp male [FMSV211]

value: male


title: B16: Sting1-/- mice+WT B16+rMVA rep4

description: Sting1-/- mice+WT B16+rMVA rep4

source_name: Sting1-/- mice+WT B16+rMVA

value: Sting1-/- mice

value: WT tumor

value: Sting1-/- mice+WT B16+rMVA


title: HSCs from untreated MDS patient 1


title: HSCs from elderly healthy donor 8

value: Elderly healthy donor


title: non-exp male [FMSV210]

value: non-detectable level of diethylphosphate


title: exp male [FMSV208]

value: diethylphosphate range from 0.11 to 399 nmol/L

value: placenta


title: B15: Sting1-/- mice+WT B16+rMVA rep3

description: Sting1-/- mice+WT B16+rMVA rep3


title: exp male [FMSV209]


title: B13: Sting1-/- mice+WT B16+rMVA rep1

description: Sting1-/- mice+WT B16+rMVA rep1


title: 2-sgNF1-FM


title: HSCs from elderly healthy donor 7


title: exp male [FMSV207]


title: 2-sgNT-FM


title: B12: WT mice+Sting1-/- B16+rMVA rep4

description: WT mice+Sting1-/- B16+rMVA rep4

source_name: WT mice+Sting1-/- B16+rMVA

value: Sting1-/- tumor

value: WT mice+Sting1-/- B16+rMVA


title: 1-DKO-FM


title: exp female [FMSV269]

value: female


title: HSCs from elderly healthy donor 6


title: 1-sgNR2F2-FM

value: ER+ breast cancer cell line


title: B11: WT mice+Sting1-/- B16+rMVA rep3

description: WT mice+Sting1-/- B16+rMVA rep3


title: HSCs from elderly healthy donor 5


title: exp male [FMSV206]


title: B10: WT mice+Sting1-/- B16+rMVA rep2

description: WT mice+Sting1-/- B16+rMVA rep2


title: HSCs from elderly healthy donor 4


title: 1-sgNF1-FM


title: exp male [FMSV205]


title: 2-sgNR2F2-FM


title: B14: Sting1-/- mice+WT B16+rMVA rep2

description: Sting1-/- mice+WT B16+rMVA rep2


title: exp male [FMSV204]


title: B9: WT mice+Sting1-/- B16+rMVA rep1

description: WT mice+Sting1-/- B16+rMVA rep1


title: HSCs from elderly healthy donor 3


title: 1-sgNT-FM


title: exp male [FMSV203]


title: B8: WT mice+WT B16-PBS rep4

description: WT mice+WT B16-PBS rep4

source_name: WT mice+WT B16-PBS

value: WT mice+WT B16-PBS


title: HSCs from elderly healthy donor 2


title: B7: WT mice+WT B16-PBS rep3

description: WT mice+WT B16-PBS rep3


title: HSCs from elderly healthy donor 1


title: HSCs from young healthy donor 17

value: Young healthy donor


title: B6: WT mice+WT B16-PBS rep2

description: WT mice+WT B16-PBS rep2


title: exp male [FMSV202]


title: exp male [FMSV201]


title: exp male [FMSV200]


title: Patient 9 KGH263

type: RNA

city: Kingston

last: LeBrun

state: Ontario

address: 88 Stuart street

department: Pathology and Molecular Medicine

institute: Queen's University

description: NanoString codeset was used to enumerate transcripts from 58 KHSC samples. This codeset was designed to quantify expression of 135 genes, including the 92 TCF3 target genes, 35 genes implicated in myelodysplastic syndrome (MDS), and 8 “housekeeping” genes whose expression we expected to be relatively invariant from case to case

hyb_protocol: Transcripts were enumerated using the NanoString nCounter® system (NanoString Technologies, Seattle, WA)

scan_protocol: According to manufacturer's instructions

data_processing: Quality assessment and normalization were performed with NSolver Analysis Software (NanoString Technologies, Inc., v3.0) using geometric mean for background correction and positive control normalization. ARHGAP27, RB1, NRF1, BAALC and ZNF19 showed very low variability among samples and were used as reference genes for normalization. Expression according to probes associated with the same gene (2 probes each for SAMHD1 and EPB41L5) was averaged.

source_name: biopsy

label_protocol: 500 ng of total RNA from each sample was used to enumerate transcripts using the NanoString nCounter® system (NanoString Technologies, Seattle, WA)

extract_protocol: Total RNA was purified from 1 mm cores of FFPE tissue from representative areas of paraffin blocks using the Qiagen AllPrep FFPE kit

tag: diagnosis

value: DLBCL

tag: age at dx

tag: gender

value: F

tag: b symptoms?

value: no

tag: bulky disease?

tag: biopsy site

value: right groin

tag: ipi score

tag: ecog >= 2

tag: ldh > uln

value: yes

tag: extranodal sites > 1

tag: Stage

tag: chemotherapy

value: RCHOP

tag: # of cycles

tag: response chenson

value: partial

tag: relapse?

tag: status

value: Dead

tag: bcl2 by halo

tag: ihc bcl2 high?1=yes,0=no

tag: ihc myc high?1=yes,0=no

tag: myc fish

value: Normal

tag: bcl2 fish

value: CNI

tag: coo by lymph2cx

value: ABC

tag: classification

value: Group A

value: FFPE tissue


title: B5: WT mice+WT B16-PBS rep1

description: WT mice+WT B16-PBS rep1

tag: strain

tag: tumor genotype

value: WT tumor

tag: condition


title: HSCs from young healthy donor 16

tag: tissue

value: Bone marrow

tag: facs gating


title: B4: WT mice+WT B16+rMVA rep4

description: WT mice+WT B16+rMVA rep4

source_name: WT mice+WT B16+rMVA

value: WT mice+WT B16+rMVA


title: exp male [FMSV199]

source_name: We provided 18 libraries (17ChIPs + 1 input) for single-end sequencing (1x50bp). ChIP was performed from chromatin obtained from placenta of human male new borns.

tag: antibody

tag: group

value: diethylphosphate range from 0.11 to 399 nmol/L

tag: Sex

value: male

value: placenta


title: HSCs from young healthy donor 15

value: Young healthy donor


title: siCtrl_739

city: Dresden

first: Ismini

middle: Vasileia

last: Alexaki

state: Saxony

address: Fetscherstraße 74

country: Germany

institute: IKL , Carl Gustav Carus Universitätsklinikum, TU Dresden

data_processing:
Low quality nucleotides were removed by Illumina fastq filter (http://cancan.cshl.edu/labmembers/gordon/fastq_illumina_filter/). Reads were further subjected to adaptor trimming using cutadapt.
lignment of the reads to the human genome was performed using STAR Aligner and the parameters: “--runMode alignReads --outSAMstrandField intronMotif --outSAMtype BAM SortedByCoordinate--readFilesCommand zcat”. Human Genome version GRCh38 (release M12 GENCODE) was used for the alignment.
The parameters: 'htseq-count -f bam -s reverse -m union -a 20', HTSeq-0.6.1p1 were used to count the reads that map to the genes in the aligned sample files. The GTF file (gencode.v34.annotation.gtf) used for reads quantification was downloaded from Gencode (https://www.gencodegenes.org/human/release_34.html).
Assembly: GRCh38

extract_protocol: none provided by the submitter

tag: cell line

tag: cell type

value: human cancer cell line

tag: genotype

value: siCtrl


title: siDKK1_572


title: siDKK1_562


title: siCtrl_571


title: siDKK1_741


title: HSCs from young healthy donor 14


title: B3: WT mice+WT B16+rMVA rep3

description: WT mice+WT B16+rMVA rep3


title: siCtrl_561


title: nucleus pulposus cells, sh_Gli1_3

city: Chongqing

first: Libangxi

last: Liu

address: 183 Xinqiao Main Street Shapingba, Chongqing 400037, People’s  Republic of China

institute: Department of Orthopedics Xinqiao Hospital, Army Medical University

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.

organism: Rattus norvegicus

source_name: Nucleus pulposus cells

growth_protocol: Nucleus pulposus cells were maintained in DMEM/F12 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase, which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I, RNase H and dUTP Solution. An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

treatment_protocol: Nucleus pulposus cells were treated with sh-Gli1 for 72h.Similarly, we treated nucleus pulposus cells with  sh-NC for 72h as the control group

value: SD

value: Nucleus pulposus cells

value: Primary cells

tag: treatment

value: treated with sh-Gli1


title: B2: WT mice+WT B16+rMVA rep2

description: WT mice+WT B16+rMVA rep2


title: nucleus pulposus cells, sh_Gli1_2


title: HSCs from young healthy donor 13


title: Kasumi1, shRNA, H3K27ac, Input

city: Beijing

first: Qian

last: Chen

address: Qinghuayuan Stress

institute: Tsinghua University

data_processing:
Adapters and low-quality bases were trimmed with trim_galore v0.6.4 with default parameters.
Timmed reads were aligned to the hg19 genome with Bowtie2 v2.3.5.1 with default parameters.
Aligned reads stored in SAM format were manipulated to generate bam files using  SAMtools v1.7.
Peaks were called using MACS2 v2.1.1 with default parameters.
RPKM normalized bigwig files were generated using bamCoverage of deepTools v3.3.0.
Assembly: hg19
Supplementary files format and content: bigWig

growth_protocol: RPMI 1640 medium, 10% fetal bovine serum, 1% penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
For AE KD H3K27ac ChIP-seq, cells were collected and treated with Mnase for chromatin fragmentation. For other ChIP-seq data, cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated. Then chromatin was inbubated with antibody/beads, and the DNA/protein complexes were then eluted and reverse crosslinked at 65 °C for 6 h. DNA was purified using phenol/chloroform extraction and ethanol precipitation.
ChIP-seq libraries were prepared using End-It DNA End-Repair Kit, Klenow Fragment (3´→ 5´ exo-) and Quick Ligation kit. Libraries were amplified using 16 cycles on the thermocycler. Post amplification libraries were size selected using AMPure XP beads.

treatment_protocol: For AE KD ChIP-seq, Kasumi-1 cells were infected with shRNA expressing lentiviruses. After 48 h of transduction, puromycin (1 μg/mL) was added into medium for another 48 h to select shRNA expressing cells.

value: Human acute myeloblastic leukemia

tag: chip antibody


title: HSCs from young healthy donor 12


title: nucleus pulposus cells, sh_Gli1_1


title: B1: WT mice+WT B16+rMVA rep1

description: WT mice+WT B16+rMVA rep1


title: Kasumi1, shAE, 3, H3K27ac

value: H3K27ac (Abcam, #ab4729)


title: HSCs from young healthy donor 11


title: nucleus pulposus cells, sh-NC_3

value: treated with sh-NC


title: exp female [FMSV270]

value: female


title: Kasumi1, shAE, 1, H3K27ac


title: HSCs from young healthy donor 10


title: Kasumi1, shNC, 2, H3K27ac


title: nucleus pulposus cells, sh-NC_1


title: HSCs from young healthy donor 9


title: Kasumi1, shNC, 1, H3K27ac


title: WT-AAN-B639

city: Jinan

first: Zhang

address: 44 Wenhua West Road

department: Department of  Pharmacology

institute: Shandong University

data_processing:
Sequenced reads were trimmed for adaptor sequence and masked for low-complexity or low-quality sequence by using Seqtk.
The sample was mapped using Hisat2（version:2.0.4)
The quantification of transcripts expressed for each sequenced samples was performed using Stringtie（version:1.3.0）
Differentially expressed genes were identified using edgeR
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: kidney

extract_protocol:
MJzol animal RNA Extraction Kit(MagBeads)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol:
The sham mice were administered the same amount of PBS. After 28 days, the mice were euthanized and the kidney tissue samples were harvested for histopathological analysis.
Aristolochic acid nephropathy was induced by a one-time intraperitoneal injection of aristolochic acid (5 mg/kg body weight, A5512, Sigma-Aldrich) in PBS. After 28 days, the mice were euthanized and the kidney tissue samples were harvested for histopathological analysis.

value: kidney

value: renal cortex cells

value: WT

value: aristolochic acid

tag: time

value: Day 28

tag: disease state

value: mouse model of AAN


title: WT-AAN-B642


title: WT-AAN-B666


title: nucleus pulposus cells, rShh_2

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Supplementary files format and content: fpkm_expression.txt

treatment_protocol: Nucleus pulposus cells were treated with rShh at 200 ng/ml(dissolved in dmso) for 48h.Similarly, we treated nucleus pulposus cells with the same concentration of DMSO as the control group


title: WT-AAN-B630


title: nucleus pulposus cells, rShh_1

value: rShh at 200 ng/ml(dissolved in dmso) for 48h


title: HSCs from young healthy donor 7

value: Bone marrow

value: Young healthy donor


title: WT-AAN-B614


title: HSCs from young healthy donor 8


title: Kasumi1, shAE, 1, CARM1


title: WT-AAN-A483


title: Kasumi1, shNC, 2, CARM1


title: Kasumi1, shAE, 3, CARM1


title: HSCs from young healthy donor 6


title: Kasumi1, shNC, 1, CARM1


title: WT-sham-H249

value: control


title: nucleus pulposus cells, Control_3

value: SD

value: Nucleus pulposus cells

value: DMSO for 48h


title: nucleus pulposus cells, sh-NC_2

value: Primary cells


title: HSCs from young healthy donor 4


title: WT-sham-B636


title: LC10

city: Shanghai

first: Wei

last: Jin

state: Shanghai

address: 668 Hongqu road

department: Shanghai cancer center

institute: Fudan University

data_processing:
Basecalls performed using CASAVA version 1.8
Umi-tools was utilized to calculate the raw counts and cell whitelist by default parameter
We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria:   MT% < 40%;    Cell Gene Number < 10000;   Cell Gene Number > 200.  PCA and tSNE/UMAP analysis was used for the single cell to cell relation description. Graphcluster and K-mean was utilized for cell clustering and based on the marker gene achieved some cluster was combined. Wilcox rank sum test was then used for marker gene analysis.
Assembly: GRCh38
Supplementary files format and content: TSV file contain counts for each sample

source_name: lung-to-brain metastases

extract_protocol:
Single-cell capture was achieved by random distribution of a single-cell suspension across >200,000 microwells through a limited dilution approach. Beads with oligonucleotide barcodes were added to saturation so that a bead was paired with a cell in a microwell.
Sequencing libraries were conducted using the BD Rhapsody Single-Cell Analysis System (BD Biosciences), following the manufacture's protocol.

tag: diagnosis

value: Lung adenocarcinoma

tag: location/side

value: Frontal / Right


title: nucleus pulposus cells, Control_1

tag: strain


title: HSCs from young healthy donor 3


title: WT-sham-B634


title: LC09

value: Parietal / Left


title: Kasumi1, Histone, Input

value: Human acute myeloblastic leukemia


title: WT-sham-B607

value: kidney

value: renal cortex cells


title: nucleus pulposus cells, rShh_3


title: Sample 36_ctf19∆fkh1∆fkh2-dsm_rep2

description: BrdU-IP sequencing

data_processing:
library strategy: BrdU-IP-seq
Barcode-splitting: Sequenced reads were first processed using ea-utils which de-multiplexes the reads based on the specified barcode sequences.
Alignment: The raw sequencing reads were then aligned to the indexed genome from Saccharomyces Genome Database using bowtie2.
Data-cleaning: Filterred reads that were mapped to more than one region in the genome using samtools view. Reads were sorted by coordinates of the reference genome using samtools sort. PCR duplicates were removed using samtools rmdup
Binning: sequencing reads were binned over 50bp bins across the genome using coverageBed.
Assembly: S228C
Supplementary files format and content: binned.bed files

source_name: Yeast cells

extract_protocol:
Cells were resuspend in 500 μL genomic lysis buffer and disrupted by bead-beating with FastPrep. Followed by PCI extractracion and ethanol precipitaion.
Samples were end-labeled using KAPA Hyper prep kit with unique barcoded adapters that are compatible with the subsequent library-amplification and sequencing primers for the Illumina sequencing platform.

value: Non

value: hydroxyurea


title: HSCs from young healthy donor 1


title: Kasumi1, H3K4me1

value: H3K4me1 (Abcam, #ab8895)


title: Antrum

city: Tokyo

first: Ruslan

last: Deviatiiarov

address: Hongo 2-1-1, Bunkyo-ku

department: Intractable Disease Research Center

country: Japan

institute: Juntendo University

description:
inDrop
conos_primary.rds

data_processing:
The sequenced libraries were demultiplexed using dropEst
Processed with Cellranger using mm10 and hg38 assemblies
Cells with at least 1000 molecules were used for subsequent analysis. The datasets were integrated using Conos, using PCA space, default parameters, using 2000 top overdispersed genes and 30 top eigenvectors per dataset pair.
Annotation was carried out manually with the help of pagoda2 browser (https://github.com/kharchenkolab/pagoda2/), based on the differentially expressed genes and known literature markers.
Sample heterogeneity was estimated by using Cacoa package.
Assembly: hg38, mm10
Supplementary files format and content: rds files with conos objects for R
Supplementary files format and content: bin files for pagoda2 (http://pklab.med.harvard.edu/nikolas/pagoda2/frontend/current/pagodaLocal/index.html)

source_name: primary, antrum, mouse

extract_protocol:
Mouse primary sorted cells were isolated using the previously described protocol, passed through a 40uM filter, and stained for Epcam (clone 9C4, Biolegend), AnnexinV (Biogend), and DAPI using the AnnexinV staining protocol and buffers. Epcam+/AnnexinV-/DAPI- cells were then sorted and GFP or TdTomato was analyzed when applicable. For mouse 2D cells, cells were stained with Epcam and DAPI to exclude irradiated feeders and dead cells. For organoid sorting, DAPI was used to exclude dead cells.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics).

value: antrum

tag: culture method

value: primary


title: Sample 35_ctf19∆fkh1∆fkh2-dsm_rep1

city: Los Angeles

description: BrdU-IP sequencing


title: LC07

value: Frontal / Left


title: LC08


title: Non-diseased nasopharyngal organoids, Infection with P. aeruginosa, 6h post infection NRPA12

city: Singapore

first: Fransiskus

middle: Xaverius

last: Ivan

address: 11 Mandalay Road

department: Lee Kong Chian School of Medicine

country: Singapore

institute: Nanyang Technological University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trimmomatic-0.39 (parameter- /trimmomatic-0.39/adapters/TruSeq3-PE-2.fa:2:30:10:1:TRUE LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:30)
Quality check of sequencing reads using FastQC v0.11.8
Trimmed sequence reads were mapped to hg38 using align function available in Rsubread v2.6.4, which was run in R v4.1.0 software (parameters- type: rna)
Feature count extraction was performed using featureCounts function available in Rsubread v2.6.4, which was run in R v4.1.0 software (parameters- annot.ext: hg38.ensGene.gtf, isGTFAnnotationFile: TRUE, isPairedEnd: TRUE)
Assembly: hg38
Supplementary files format and content: Tab-delimited text files that contain the features and counts for each sample

source_name: Nasopharyngal organoids

growth_protocol: Human nasopharyngeal epithelial cells were isolated from NP swab or BALF, respectively from healthy volunteers or COPD patients, and cultured until confluency was reached. Cells were seeded on transwell inserts and differentiated at air-liquid interface for 2 weeks. Cells from ALI at 2 weeks were detached from the transwell membrane and embedded on matrigel for 3D differentiation for further 4-6 weeks to achieve maturation.

extract_protocol: Organoids were lysed with Qiagen RLT plus buffer and RNA was isolated using Qiagen Rneasy Plus Mini Kit. Stranded mRNA library preparation with oligo dT purification using Illumina TruSeq Stranded mRNA Kit.

treatment_protocol: Non-diseased or COPD nasopharyngeal organoids were either mock-treated or infected with Pseudomonas aeruginosa for 6 hours

value: Nasopharyngal organoids

value: Non-diseased

value: Infection with P. aeruginosa

value: 6h post infection


title: nucleus pulposus cells, Control_2

value: SD

value: Nucleus pulposus cells

value: Primary cells

value: DMSO for 48h


title: HSCs from young healthy donor 2

city: Dublin

value: Bone marrow

tag: condition

value: Young healthy donor


title: Sample 34_fkh1∆fkh2-dsm_rep2

first: Meghan

last: Petrie

address: 1050 Childs Way

institute: University of Southern California

description: BrdU-IP sequencing


title: HSCs from young healthy donor 5

first: Marina

last: Ainciburu

address: Foster Avenue

institute: NIBRT

tag: tissue


title: Sample 33_fkh1∆fkh2-dsm_rep1

description: BrdU-IP sequencing


title: AHb2-4

description:
10x Genomics
conos_human_2d.rds
conosApp_human_2d_samples_10k_cells_Vim.Mt_filtered_cao.bin
conosApp_human-mouse_2D_samples_10k_Vim.Mt_NewEmbeddings_balanced_2.bin

source_name: 2D, corpus, human

value: corpus


title: Kasumi1, H3K27ac

value: Human acute myeloblastic leukemia

value: H3K27ac (Abcam, #ab4729)


title: LC06

value: Lung adenocarcinoma

value: Parietal / Right


title: Non-diseased nasopharyngal organoids, Infection with P. aeruginosa, 6h post infection NRPA11


title: Sample 32_ctf19Δ_rep2

description: BrdU-IP sequencing

value: Non

value: hydroxyurea


title: LC04


title: Non-diseased nasopharyngal organoids, Infection with P. aeruginosa, 6h post infection NRPA10

value: Nasopharyngal organoids


title: COPD nasopharyngal organoids, Infection with P. aeruginosa, 6h post infection NRPA6

value: COPD


title: LC03

value: Occipital / Right


title: Sample 31_ctf19Δ_rep1

description: BrdU-IP sequencing


title: AHb2-2


title: LC02

value: Frontal / Right


title: Sample 30_dbf4-Zn*2_rep2

description: BrdU-IP sequencing


title: COPD nasopharyngal organoids, Infection with P. aeruginosa, 6h post infection NRPA5

value: Infection with P. aeruginosa

value: 6h post infection


title: Corpus

description:
inDrop
conos_primary.rds

source_name: primary, corpus, mouse

value: primary


title: AHb2-1

source_name: 2D, antrum, human

value: antrum


title: COPD nasopharyngal organoids, Infection with P. aeruginosa, 6h post infection NRPA4


title: Sample 29_dbf4-Zn*2_rep1

description: BrdU-IP sequencing


title: LC05

value: Frontal / Left


title: AHb1-8

description:
10x Genomics
conos_mouse_2d_organoid.rds
conosApp_mouse_Set1_samples_10k_Vim.Mt_NewEmbeddings_balanced2_Cao.5.bin
conosApp_mouse_Set2_samples_10k_Vim.Mt_NewEmbeddings_balanced2_Cao.bin

source_name: organoid, corpus, mouse

value: organoid


title: GB04

source_name: gliomas

value: Glioblastoma


title: Non-diseased nasopharyngal organoids, No infection, 6h post infection NRMK12

value: Non-diseased

value: No infection


title: Sample 28_dbf4-Zn*1_rep2

description: BrdU-IP sequencing


title: AHb1-7

source_name: organoid, antrum, mouse


title: Sample 27_dbf4-Zn*1_rep1

description: BrdU-IP sequencing


title: Non-diseased nasopharyngal organoids, No infection, 6h post infection NRMK11


title: GB03

value: High-grade glioma


title: AHb1-6

value: corpus


title: Sample 26_dbf4ΔC_rep2

description: BrdU-IP sequencing

value: Non


title: GB02

value: Oligodendroglioma


title: AHb1-5


title: AHb2-3


title: GB01

value: High-grade diffuse glioma

value: Temporal / Left


title: COPD nasopharyngal organoids, No infection, 6h post infection NRMK6

value: Nasopharyngal organoids

value: COPD


title: Sample 25_dbf4ΔC_rep1

description: BrdU-IP sequencing

value: hydroxyurea


title: COPD nasopharyngal organoids, No infection, 6h post infection NRMK5

value: 6h post infection


title: HCT116 cells, Wild-type transposon with re-engineered hyperactive piggyBac replicate 3

city: Bethesda

first: Pavol

last: Genzor

state: MD

address: 6720A Rockledge Drive, Suite 100

department: ACESO

institute: Henry M Jackson Foundation

data_processing:
To generate *_peaks.bed files: The reads were trimmed twice using cutadapt (v3.4), first to remove the seqeuncing adapters, and second time to remove TIR seqeunce. Trimmed reads were alligned to human genome (hg38) using Hisat aligner (v2.2.1.0) using standard settings. Generated bam files were loaded into R using custom function and paired-end reads converted into read fragments. To call peaks, read fragments were used to generate genomic coverage, and any region with at least five reads coverage was considered as a peak and was reported in the *peaks.bed files. For exact methods and custom code please visit related github fount at https://github.com/HaaseLab.
Assembly: GRCh38.p5.v24
Supplementary files format and content: Tab delimited text files in standard bed format with following colums: chromosome, start, end, peakID, peak_area_under_the_curve, strand, peak_maximum_height, peak_width, total_read_fragments_analyzed_in_sample

source_name: Large intestine, colon

extract_protocol:
RNA was extracted using RNaesy Mini Kit (Qiagen #74106).
Total RNA was reverse-transcribed to cDNA using M-MLV (Promega #M3681) and primer SMART-dT18VN (5`-AAGCAGTGGTATCAACGCAGAGTACGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTVN). Next, cDNA was amplified using different pairs of primers containing regions within specific tranpsoson used in this study (see suplemental information) and primer Smart (5`-AAGCAGTGGTATCAACGCAGAGT). Amplified cDNA was purified using PCR gel purification column (Macherey-Nagel #740609) and 500 ng of purified cDNA was was fragmented and tagged using Illumina DNA Prep (Illumina #20060060). Tagged DNA was PCR amplified (Read1-TnME: 5`-ACACTCTTTCCCTACACGACGCTCTTCCGATCTAGATGTGTATAAGAGACA*G; Read2 primer was specific to transposase species, see suplemental information) and amplicons from 100-500 bp were size selected on 2% agarose gel. Dual index primers (NEB #E7780S) for seqeuncing were added by amplifying tagmented libraries usign Q5 Polymerase (NEB #M0544S) following the NEBnext protocol (NEB #E7645S - Section 4.1). The PCR products were purified using AMPure XP beads (Beckman Coulter #A63881) using 0.9x bead volume. The quality of final library was verified using TapeStation.
See the publication 10.1016/j.cell.2020.06.037 for detailed methods to construct library from self-reporting transposons (SRTs).

treatment_protocol: Cells transfected with different self-reporting transposon construct were grown in presence of 3 µg/ml puromycin for two weeks.

value: Large intestine, colon

value: colorectal carcinoma

tag: transfection

value: transfected with self-reporting transposon (SRT)


title: Sample 24_fkh1∆_rep2

description: BrdU-IP sequencing

tag: antibody


title: AHb1-3

description:
10x Genomics
conos_mouse_2d_organoid.rds
conosApp_mouse_Set1_samples_10k_Vim.Mt_NewEmbeddings_balanced2_Cao.5.bin
conosApp_human-mouse_2D_samples_10k_Vim.Mt_NewEmbeddings_balanced_2.bin
conosApp_mouse_Set3_samples_10k_Vim.Mt_NewEmbeddings_balanced2_Cao.2.bin

source_name: 2D, antrum, mouse

value: antrum


title: COPD nasopharyngal organoids, No infection, 6h post infection NRMK4


title: LC01

value: Lung adenocarcinoma

value: Frontal / Right


title: HCT116 cells, Wild-type transposon with re-engineered hyperactive piggyBac replicate 2


title: HCT116 cells, Wild-type transposon with re-engineered hyperactive piggyBac replicate 1


title: Sample 23_fkh1∆_rep1

description: BrdU-IP sequencing


title: COPD bronchial organoids

data_processing:
Quality check of sequencing reads using FastQC v0.11.8
Alignment of reads and generation of count matrices (feature-barcode matrices) were done with Cell Ranger version 6.0.2
Genome_build: GRCh38 Release 2020
Supplementary_files_format_and_content: Sample_name-barcodes.tsv.gz: gunzipped, tab-separated values (tsv) file containing cell barcode sequence identities for the count matrix.
Supplementary_files_format_and_content: Sample_name-features.tsv.gz: gunzipped, tab-separated values (tsv) file containing table of feature identities for the count matrix (first column: ENSEMBL gene identifiers, second column: HGNC gene symbols; third column: types of features).
Supplementary_files_format_and_content: Sample_name-matrix.mtx.gz: gunzipped, matrix market file containing sparse gene expression UMI count matrix associated with the features (rows) and barcodes (columns).

source_name: Bronchial organoids

growth_protocol: Human nasopharyngeal and bronchial epithelial cells were isolated from NP swab or BALF, respectively from healthy volunteers or COPD patients, and cultured until confluency was reached. Cells were seeded on transwell inserts and differentiated at air-liquid interface for 2 weeks. Cells from ALI at 2 weeks were detached from the transwell membrane and embedded on matrigel for 3D differentiation for further 4-6 weeks to achieve maturation.

extract_protocol:
Organoids were washed once with adDMEM/F12 to eliminate matrigel and then incubated with TrypLE express for 10 mins. Single cell suspensions were next achieved by passing through the large undissociated structures with a P1000 tip repeatedly. Single cells were centrifuged and resuspended in AO medium for cell counting to obtain a density of 1000 cells/µl.
10X Genomics Next GEM Single-Cell RNA v3.1

treatment_protocol: Organoids used for scRNA seq were at stable condition, without any treatment.

value: Bronchial organoids

value: No infection or stimulation


title: Sample 22_WT_rep2

description: BrdU-IP sequencing

value: WT


title: Sample 21_WT_rep1

description: BrdU-IP sequencing

value: Non


title: Non-diseased bronchial organoids

value: Non-diseased


title: AHb1-2

source_name: 2D, corpus, mouse

value: corpus


title: HCT116 cells, Wild-type transposon with re-engineered piggyBac replicate 3


title: mouse antrum/pylorus 2D culture p2  ID AT76

data_processing:
sequenced using HiSeq 2000/2500 in high output mode with V3 kits, paired end 50bp (PE50)
Reads were mapped to mouse mm9 reference genome using the STAR aligner. Read counts for individual transcripts from ENSEMBL annotation were obtained using HTSeq and further normalized using DESeq2. CPM values were calculated using EdgeR.
Assembly: mm9
Supplementary files format and content: CPM Forestomach Corpus Antrum 2D in .xlsx table

source_name: 2D culture antrum/pylorus

growth_protocol: Corpus and antrum was cultured according to the methods section in the accompanying study. Forstomach was cultured according to Mou H. et al., Cell Stem Cell 19, 217–231 (2016)

extract_protocol:
RNA extraction was performed using NEB RNeasy isolation kit according to the protocol
Prepped using Illumina Ribo-Zero zero Kit according to the protocol.

value: 2D culture antrum/pylorus


title: Non-diseased nasopharyngal organoids, No infection, 6h post infection NRMK10

value: Nasopharyngal organoids

value: No infection


title: HCT116 cells, Wild-type transposon with re-engineered piggyBac replicate 2


title: AHb1-1


title: HCT116 cells, Wild-type transposon with re-engineered piggyBac replicate 1


title: mouse antrum/pylorus 2D culture p2  ID AT75


title: mouse corpus 2D culture p2  ID AT76

source_name: 2D culture corpus

value: 2D culture corpus


title: Sample 15_ctf19∆fkh1∆fkh2-dsm_rep1

description: BrdU-IP sequencing

value: anti-BrdU

value: hydroxyurea


title: COPD nasopharyngeal organoids

source_name: Nasopharyngeal organoids

value: COPD


title: Sample 16_ctf19∆fkh1∆fkh2-dsm_rep2

description: BrdU-IP sequencing


title: AHb1-4


title: HCT116 cells, Wild-type transposon with hyperactive piggyBac replicate 3

value: Large intestine, colon

value: colorectal carcinoma

value: transfected with self-reporting transposon (SRT)


title: LF3

city: shenyang

first: Yang

last: Meng

address: Wenhua street num 11

department: College of Life and Health Sciences

institute: Northeastern University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genome using Bowtie 2 suite (version 4.1.2)
Assembly: Cryptococcus neoformans var. grubii H99 .
Supplementary files format and content: tab-delimited text files include reads values for each Sample.

organism: Cryptococcus neoformans H99

source_name: Fungal cells

growth_protocol: WT and isw1∆ strains were inoculated into 50 ml of YPD broth and cultured overnight at 30°C in a shaking incubator. Cells were subcultured in 50 ml fresh YPD broth at OD600=0.2 until the OD600 reached 0.6 to 0.8 with treated or no-treated FLC, respectively. Three independent cultures for each strain were prepared. Every culture was washed three times with PBS and placed in a liquid nitrogen tank for RNA-seq.

extract_protocol:
Total RNA was isolated using the Trizol Reagent (Invitrogen Life Technologies), and the concentration, quality and integrity of total RNA were determined using a NanoDrop spectrophotometer (Thermo Scientific). Three micrograms of RNA were used as input material for the preparations of RNA sample.
Sequencing libraries were constructed using the TruSeq RNA Sample Preparation Kit (Illumina, San Diego, CA, USA).

value: Fungal cells

value: FLC


title: LF2


title: HCT116 cells, Wild-type transposon with hyperactive piggyBac replicate 1


title: mouse forestomach p2 ID AT76

source_name: cultured forestomach epithelia

value: cultured forestomach epithelia


title: mouse corpus 2D culture p2  ID AT75

value: WT


title: Sample 13_fkh1∆fkh2-dsm_rep1

description: BrdU-IP sequencing

source_name: Yeast cells


title: LF1


title: HCT116 cells, Wild-type transposon and piggyBac replicate 3

value: Wild-type transposon and piggyBac


title: Non-diseased nasopharyngeal organoids

value: Non-diseased

value: No infection or stimulation


title: mouse forestomach p2 ID AT75


title: Sample 12_ctf19Δ_rep2

description: BrdU-IP sequencing


title: HF3

value: wild type


title: HCT116 cells, Wild-type transposon and piggyBac replicate 2


title: Sample 10_dbf4-Zn*2_rep2

description: BrdU-IP sequencing


title: HF2


title: HCT116 cells, Wild-type transposon and piggyBac replicate 1


title: ru521 drg injured rep3 [ru 3dpc3]

city: Hong Kong

first: Xu

last: Wang

state: New Territories

address: HKUST

department: LIFS

country: Hong Kong

institute: HKUST

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using TrimGalore with parameters trim_galore -q 20 --phred33 --stringency 5 --length 20 -e 0.1 --paired.
Trimed reads were mapped to GrCM38/mm10 genome using STAR.
Mapped reads (Bam) were quantified using Rsubred package.
Assembly: mm10
Supplementary files format and content: txt file showing raw reads of each sample

source_name: dorsal root ganglion

extract_protocol:
RNA was isolated using RNeasy Kit (Qiagen).
cDNA was generated following the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech) protocol and processed for library generation using Tn5-mediated library generation. Sequencing was carried out in 2 × 100 cycle paired-end mode on a DNBSEQ-G400 sequencer (BGI).

value: dorsal root ganglion

value: L4-L5 DRG

value: wt

value: sciatic nerve injury+RU521


title: HF1


title: Sample 9_dbf4-Zn*2_rep1

description: BrdU-IP sequencing

value: anti-BrdU

value: hydroxyurea


title: HCT116 cells, Wild-type transposon with hyperactive piggyBac replicate 2

value: Large intestine, colon


title: DBTRG-05MG sh-POLR2B_rep2

city: Suzhou

first: Zimu

last: Zhang

state: Jiangsu

address: Zhongnan Street

institute: Children’s Hospital of Soochow University

data_processing:
Illumina Casava2.19 software used for basecalling.
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v2.2.0 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al.. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include readcount values for each Sample …

source_name: DBTRG-05MG cells

extract_protocol:
Cells were harvested, and total RNA was extracted with TRIzol (Invitrogen) according to the manufacturer's protocol. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Glioblastoma cells

tag: knockdown


title: Sample 14_fkh1∆fkh2-dsm_rep2

description: BrdU-IP sequencing


title: DBTRG-05MG sh-POLR2B_rep1


title: ru521 drg injured rep2 [ru 3dpc2]


title: Sample 7_dbf4-Zn*1_rep1

description: BrdU-IP sequencing


title: Sample 11_ctf19Δ_rep1

description: BrdU-IP sequencing


title: DBTRG-05MG sh-NC_rep2

value: scramble shRNA


title: Sample 8_dbf4-Zn*1_rep2

description: BrdU-IP sequencing


title: Sample 6_dbf4ΔC_rep2

description: BrdU-IP sequencing


title: DBTRG-05MG sh-NC_rep1


title: Sample 5_dbf4ΔC_rep1

description: BrdU-IP sequencing


title: Sample 4_fkh1∆_rep2

description: BrdU-IP sequencing


title: cko drg injured rep2 [cko 3dpc2]

value: Ptpn2 KO

value: sciatic nerve injury


title: IFNβ_Flag SP100A

city: Guangzhou

first: hongchang

last: hongchang

state: guangdong

address: East Outer Ring Road, Guangzhou University City, Guangzhou

institute: Sun yat-sen university

data_processing:
Library strategy: CUT&Tag
Paired-end Illumina sequencing was performed on the barcoded libraries following manufacturer’s instructions.
Raw sequences were trimmed using FASTp 0.19.1162 with the following options: length_required=50, n_base_limit=6 to discard adapter and low-quality sequences.
The clean sequences were then aligned to the hg38 by BWA 0.7.12-r1039 with the following parameters: -T 25 -k 18.
Cut &Tag signals in upstream and downstream 3kb areas of transcriptional initiation sites (TSS) were analyzed with the computematrix module of deepTools software (version: 3.0.2)
MACS2 2.1.2 was used to identify the peaks that were significantly enriched in the pairwise comparisons with the following parameters: -q 0.05 --call-summits --nomodel --shift -100 --extsize 200 --keep-dup all65.
Genome_build: hg38
Supplementary_files_format_and_content: peak text files

extract_protocol:
CUT&Tag assay was performed using NovoNGS CUT&Tag 2.0 High-Sensitivity Kit (for Illumina) (Novoprotein scientific Inc, N259-YH01-01A) as previously described 61. In brief, 1X105 HEp-2 or HEp-2 cells transfected with Flag-Sp100A were harvested by trypsin treatment, centrifuged at 800g for 5min at RT, precipated by ConA-magnetic beads, and resuspended in 100mL Dig-wash Buffer (20mM HEPES pH7.5, 150mM NaCl, 0.5mM Spermidine, protease inhibitor cocktail, 0.05% Digitonin) containing 2mM EDTA and primary anti-Flag antibody at 1:100 dilution overnight at 4°C. Beads were washed in Dig-wash Buffer for 3 times and incubated with goat anti-mouse secondary antibody (Abcam, ab6708) for 1hr at a dilution of 1:200. After incubation, the beads were washed for 3 times in Dig-Hisalt Buffer (0.05% Digitonin, 20mM HEPES, pH7.5, 300mM NaCl, 0.5mM Spermidine, protease inhibitor cocktail). Cells were incubated with proteinA-Tn5 transposase at 37°C for 1hr and washed for 3 times in Dig-Hisalt buffer to remove unbound proteinA-Tn5. Next, cells were resuspended in 100uL Tagmentation buffer (10mM MgCl2 in Dig-Hisalt Buffer) and incubated at 37°C for 1hr. The tagmentation was terminated by adding 2.25mL of 0.5M EDTA, 2.75mL of 10% SDS and 0.5mL of 20mg/mL proteinase K at 55°C for 1hr. The DNA fragments were extracted by phenol chloroform, amplified using the provided barcode primers with 15 cycles of PCR. CUT&Tag libraries were cleaned with a single round of Novo NGS DNA clean beads (provided in the kit) at a 1.3 to 1 (vol/vol) ratio of beads to sample, quantified and pooled for sequencing.
The DNA fragments were extracted by phenol chloroform, amplified using the provided barcode primers with 15 cycles of PCR. CUT&Tag libraries were cleaned with a single round of Novo NGS DNA clean beads (provided in the kit) at a 1.3 to 1 (vol/vol) ratio of beads to sample, quantified and pooled for sequencing.

treatment_protocol: 1000u/ml IFNB or MOCK treated for 2h

tag: primary antibody

value: Mouse monoclonal anti-Flag antibody (Abways, AB0008)

tag: secondary antibody

value: Abcam, ab6708


title: cko drg injured rep3 [cko 3dpc3]

tag: cell type


title: Lymph Node, whole tissue cells, KI, Rep6

city: Rennes

first: Delphine

last: Rossille

address: 2 avenue du Pr. Léon Bernard

institute: INSERM U1236-MOBIDIC

data_processing:
The process was completed by Paired-End 150 bases massive parallel sequencing on Illumina MiSeq
Raw sequencing data were checked and visualized for quality using FastQC (v0.11.5).
The RNAseq reads were aligned to the reference genome GRCm39 Release 104 using STAR (v2.5).
Read summarization and gene counts were performed using the featureCounts function from the Subread package (v1.4.6).
Data normalization and differential gene expression were performed with the DESeq2 R package (v1.26.0). Data were filtered using HTSFilter R package (v1.26.0).
Significant genes were defined as p < 0.05 after adjustment for False Discovery Rate (FDR) correction and used for downstream analysis.
Assembly: GRCm39
Supplementary files format and content: Matrix table with normalized gene counts for every gene and every sample reported after HTS Filtering (sheet MATRIX in present xlsx file)

source_name: Lymph Node

extract_protocol:
RNA was extracted from dissociated cells using NucleoSpin RNA Plus XS kit (740990, Macherey-Nagel).
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit (TAKARA bio) following manufacturer's protocols.

treatment_protocol: Iterative mouse ip immunization for 3 months / tissue collected one month after third immunization

value: Lymph Node

value: whole tissue cells

tag: genotype

value: Knock-in (Igk-BCL2)

value: mouse shhep red blood cells i.p. immunization

tag: subject


title: NT_Flag SP100A

tag: treatment


title: Spleen, whole tissue cells, KI, Rep6

source_name: Spleen

value: Spleen


title: subcutaneous xenograft tumor of ctrl mice, biological rep3

first: YingNa

last: Liao

address: No. 25, Lane 2200, Xietu Road, Shanghai

institute: Shanghai Cancer institute

description: Gene expression data from subcutaneous xenograft tumor of ctrl mice.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: A total of 2 × 106 KPC1199 cells were injected subcutaneously in the right back of the mouse once it was pregnant or started breastfeeding. All mice including control mice were sacrificed after injection for 20 days at the same age.

tag: group

value: control


title: subcutaneous xenograft tumor of ctrl mice, biological rep1


title: subcutaneous xenograft tumor of ctrl mice, biological rep2


title: subcutaneous xenograft tumor of lactation mice, biological rep3

description: Gene expression data from subcutaneous xenograft tumor of lactation mice.

value: lactation


title: NC

value: NC


title: subcutaneous xenograft tumor of lactation mice, biological rep1


title: cko drg intact rep3 [cko int3]

value: dorsal root ganglion

value: L4-L5 DRG

value: sham surgery


title: Lymph Node, whole tissue cells, KI, Rep5


title: cko drg intact rep2 [cko int2]


title: Sample 2_WT_rep2

description: BrdU-IP sequencing

treatment_protocol: Cells were arrested with α-factor (~5 nM ) and incubated for ~4 h at 23 °C then released in fresh YEPD containing 400 μg/mL BrdU, 200 μg/mL Pronase and 200 mM hydroxyurea. Harvested cells after 60min of incubation.

value: anti-BrdU

value: WT

value: hydroxyurea


title: ru521 drg injured rep1 [ru 3dpc1]

value: wt

value: sciatic nerve injury+RU521


title: Spleen, whole tissue cells, KI, Rep5


title: Sample 1_WT_rep1

description: BrdU-IP sequencing


title: cko drg injured rep1 [cko 3dpc1]

value: Ptpn2 KO

value: sciatic nerve injury


title: Kasumi-1_UF146-1 (RNA-seq)

first: Jiaying

address: 320 Yue Yang Road

department: CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health

institute: Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences

description: Kasumi-1 UF146 treated

data_processing:
Clean sequenced reads were alignmented to hg19 by bowtie2(2.2.9) with parameters: -N 1; alignmented SAM files were handled using samtools(1.7); peaks were called by macs2(2.1.1.20160309) callpeaks algorithm with default set; BigWig files were generated by deeptols(3.1.2) bamCoverage algorithm with paprameter --normalizeUsing BPM.(ChIP-seq)
Clean sequenced reads were alignmented to hg38  by HISAT2 (2.0.5) with default parameters; alignmented SAM files were handled using samtools(1.7); aligned reads were extracted by Htseq(0.9.1) with default parameters; FPKM were calculated by R script on its defination, differential genes were generated by R package Deseq2(1.22.2).(RNA-seq)
Raw reads were filtered by trimmomatic with parameter: SLIDINGWINDOW:4:15, LEADING:3, TRAILING:3, ILLIMINACLIP:adaper.fa:2:30:7:1:true, HEADCROP:10; clean sequenced reads were alignmented to hg19 by bismark(0.19.0) with parameters: deduplicated alignments were removed by deduplicate_bismark(bismark 0.19.0); coverage files were extracted by bismark_methylation_extractor(bismark 0.19.0); DMR regions were generated by R package DSS(2.26.0). (Bisulfite-Seq)
Genome_build: hg19 & hg38
Supplementary_files_format_and_content: FPKM were calculated by R script on its defination.  BigWig files were generated by deeptols(3.1.2) bamCoverage algorithm with paprameter --normalizeUsing BPM.

source_name: Cell line

growth_protocol: Kasumi-1 and THP-1 cells were cultured in RPMI1640 medium containing 10% FBS.

extract_protocol:
Fluorescence activated Cell Sorting
(For ChIP-seq): Library preparation was according to the manufacture’s guidelines (KAPA Biosystems KK8503) and sequencing procedures were carried out according to Illumina protocols with minor modifications (Illumina, San Diego).  (For RNA-seq): Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.  (For Bisulfite-Seq): A total amount of 5.2 microgram genomic DNA spiked with 26 ng lambda DNA were fragmented by sonication to 200-300bp with Covaris S220, followed by end repair and adenylation. Cytosine-methylated barcodes were ligated to sonicated DNA as per manufacturer’s instructions. Then these DNA fragments were treated twice with bisulfite using EZ DNA Methylation-GoldTM Kit (Zymo Research), before the resulting single-strand DNA fragments were PCR.

treatment_protocol: Kasumi-1 and THP-1 cells were transduced with UHRF1 shRNA and then AML cells were selected by puromycine for 48h,finally these AML cells were subjected to RNA-seq analysis and WGBS. Kasumi-1 and THP-1 cells were treated with UHRF1 inhibitor UF146 for 24h and these cells were subjected to RNA-seq analysis.

value: Blood cell

value: AML patient cell

tag: cell line

tag: agent

tag: chip antibody


title: Kasumi-1_UF146-2 (RNA-seq)

description: Kasumi-1 UF146 treated


title: cko drg intact rep1 [cko int1]


title: Lymph Node, whole tissue cells, Tg, Rep4

value: Lymph Node

value: whole tissue cells

value: Transgenic (3'RR-BCL2)

value: mouse shhep red blood cells i.p. immunization


title: ASFV I73R-3

city: Wuhan

first: Zhou

last: Shen

state: Hubei

address: 1 Shi-zi-shan Street

institute: Huazhong agriculture university

data_processing:
FastQC
Hisat2
Samtools
StringTie
Deseq2
Genome_build: hg19
Supplementary_files_format_and_content: Normalized read count matrix processed by Deseq2

source_name: Human embryo kidney cell

extract_protocol:
Using TRIzol based method following manufactures instruction
Using VAZYME NR612 following manufactures instruction

value: HEK 293T

value: Transfection of ASFV oriented I73R contained pCAGGS


title: subcutaneous xenograft tumor of lactation mice, biological rep2

value: lactation


title: Kasumi-1_DMSO-2 (RNA-seq)

description: Kasumi-1 DMSO treated

value: DMSO


title: Lymph Node, whole tissue cells, Wt, Rep2

value: Wild-type


title: Sample 3_fkh1∆_rep1

description: BrdU-IP sequencing

tag: strain

value: anti-BrdU


title: ASFV I73R-2


title: Lymph Node, whole tissue cells, Tg, Rep3


title: Spleen, whole tissue cells, Tg, Rep4

value: Spleen


title: wt drg injured rep3 [wt 3dpc3]

value: dorsal root ganglion

value: L4-L5 DRG

value: wt


title: wt drg injured rep1 [wt 3dpc1]

value: sciatic nerve injury


title: wt drg injured rep2 [wt 3dpc2]


title: Kasumi-1 _IgG (CUT-TAG)

description: Endogenous

data_processing:
Library strategy: CUT&TAG
Clean sequenced reads were alignmented to hg19 by bowtie2(2.2.9) with parameters: -N 1; alignmented SAM files were handled using samtools(1.7); peaks were called by macs2(2.1.1.20160309) callpeaks algorithm with default set; BigWig files were generated by deeptols(3.1.2) bamCoverage algorithm with paprameter --normalizeUsing BPM.(ChIP-seq)
Clean sequenced reads were alignmented to hg38  by HISAT2 (2.0.5) with default parameters; alignmented SAM files were handled using samtools(1.7); aligned reads were extracted by Htseq(0.9.1) with default parameters; FPKM were calculated by R script on its defination, differential genes were generated by R package Deseq2(1.22.2).(RNA-seq)
Raw reads were filtered by trimmomatic with parameter: SLIDINGWINDOW:4:15, LEADING:3, TRAILING:3, ILLIMINACLIP:adaper.fa:2:30:7:1:true, HEADCROP:10; clean sequenced reads were alignmented to hg19 by bismark(0.19.0) with parameters: deduplicated alignments were removed by deduplicate_bismark(bismark 0.19.0); coverage files were extracted by bismark_methylation_extractor(bismark 0.19.0); DMR regions were generated by R package DSS(2.26.0). (Bisulfite-Seq)
Genome_build: hg19 & hg38
Supplementary_files_format_and_content: FPKM were calculated by R script on its defination.  BigWig files were generated by deeptols(3.1.2) bamCoverage algorithm with paprameter --normalizeUsing BPM.

value: Blood cell


title: wt drg intact rep3 [wt int3]

value: sham surgery


title: pCAGGS-3 empty backbone

value: Transfection of empty backbone


title: pCAGGS-2 empty backbone


title: Spleen, whole tissue cells, Wt, Rep2

value: whole tissue cells


title: pCAGGS-1 empty backbone


title: wt drg intact rep2 [wt int2]


title: wt drg intact rep1 [wt int1]


title: H226

first: sun

middle: yi

last: yun

address: 1YiXue Yuan,Yuzhong District

institute: Chongqing Medical University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequencing fragments are randomly interrupted by mRNA. Use the HISAT2.0.5 software to quickly and accurately compare the Clean Reads after quality control with the reference genome to obtain the location information of the Reads on the reference genome.
Filter the original data: remove reads with adapters; remove reads containing N (N means base information cannot be determined); remove low-quality reads (the number of bases with Qphred<=20 accounts for 50% of the entire read length The above reads).
According to the position information of the gene alignment on the reference genome, the number of reads covered by each gene (including the new predicted gene) from the start to the end is counted. Filter out reads with a comparison quality value lower than 10, reads on unpaired comparisons, and reads that are aligned to multiple regions of the genome. This part of the analysis uses the featureCounts tool in the subread software.
FPKM(expected number of Fragments Per Kilobase of transcript sequence Per Millions base sequenced Fragments) is a set of Fragments from a gene of 1000 bases Per million Fragments.Sequencing depth and gene length were corrected by FPKM to represent gene expression values of RNA-seq.
Genome_build: human NCBI genome build 36
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Lung

extract_protocol:
The total RNA was extracted from cells using TRIzolTM Reagent. After quantitative analysis and quality inspection, the RNA samples were sent to Novogene for RNA sequencing. Briefly, NEBNext® UltraTM RNA Library Prep Kit for Illumina®  was used to construct sequencing libraries. Each sample was subject to DNA sequencing with the Illumina NovaSeq6000 Sequencing System. The raw data was then preprocessed and normalized.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: H226 cells were treated with either 30µM GANT-61 or DMSO control for 48h.

value: Lung squamous cell carcinomas

value: DMSO for 48h


title: Spleen, whole tissue cells, Wt, Rep1

value: mouse shhep red blood cells i.p. immunization


title: Lymph Node, whole tissue cells, Wt, Rep1

value: Lymph Node


title: ASFV I73R-1

value: HEK 293T

value: Transfection of ASFV oriented I73R contained pCAGGS


title: Kasumi-1_DMSO-1 (RNA-seq)

description: Kasumi-1 DMSO treated

value: AML patient cell

value: DMSO