title: NegELSK_5 [N5]

city: Cambridge

first: Daniel

last: Bode

email: db704@cam.ac.uk, 1danielbode@gmail.com

address: Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge Biomedical Campus

department: Cambridge Stem Cell Institute

institute: University of Cambridge

description:
N5
counts_bulk_rnaseq.txt

data_processing:
bulk RNA-seq: reads were trimmed using trim_galore (parameters: --paired --quality 30 --clip_R2 3) and aligned using STAR (default parameters). Gene counts were acquired using HTSeq (parameters: --format=bam --stranded=reverse --type=exon --mode=intersection-nonempty --additional-attr=gene_name)
scRNA-seq: Raw reads were aligned to the Mus musculous genome build (mm10) using STAR and read counts were computed using featureCounts.
scRNA-seq: Cells from which low-quality libraries with insufficient sequencing depths were generated were excluded by setting the threshold of number of mapped reads to >1e5 and <3e7, with mapped reads comprising nuclear genes, mitochondrial genes and ERCCs. A minimum threshold of 20% for reads mapping to known genes was set, in order to exclude empty wells and dead cells. In addition, the threshold for reads mapping to mitochondrial genes was >0.075, to ensure a minimum of 7.5% of reads to map to non-mitochondrial genes. Finally, an ERCC cutoff of 5% and a high gene cutoff of 1800 were selected.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files containing raw counts for each sample (HT-Seq counts)

growth_protocol: For hibernation cultures, Haematopoietic Stem Cells (HSCs), isolated from primary mouse bone marrow, were cultured in the presence of 20 ng/mL IL-11 but absence of Stem Cell Factor (SCF) and (TPO) to retain HSCs. Expansion cultures (28 days) of single long-term HSCs were performed as previously described (Wilkinson et al., 2019).

extract_protocol:
Haematopoietic Stem Cells (HSCs) were extracted from primary mouse bone marrow, derived from C57BL/6 mice(12-16 weks) for scRNA-seq and Fgd5(ZsGreen•ZsGreen/+) for bulk RNA-seq. To isolate fetal liver HSCs, fetal livers were harvested from E14.5 embryos. All extracted tissues were lineage depleted prior to FACS sorting. HSCs were defined as EPCR-high, CD45+, Sca-1+, CD48-low/neg, CD150+. Expansion cultures were FACS sorted to separate ELSK and nonELSK cell fractions. HSCs in hibernation conditions and freshly isolated fetal liver were FACS sorted to be deposited in 96 well plates (one cell per well), containing lysis buffer and subsequently processed using the previously described Smart-Seq2 protocol (Picelli et al., 2014).
Smart-Seq2 protocol performed as previously described (Picelli et al., 2014). Libraries were prepared using Illumina Nextera libraries, single end reads and 50bp read lengths. The pooled libraries were sequenced on an Illumina HiSeq 4000. Bulk RNA-seq libraries were prepared using the SMARTer Stranded Total RNA-seq Kit v2 – Pico Input mammalian (Takara Bio, CA, USA), paired end and 50bp read length. The libraries were sequenced on an Illumina Novaseq.

treatment_protocol: Hibernating HSCs were cultured in the presence of 20 ng/mL IL-11 but absence of Stem Cell Factor (SCF) and (TPO). Expansion of single HSCs was performed as perviously described (Wilkinson et al., 2019).

value: 12-16 weeks

tag: batch


title: NegELSK_6 [R6_neg]

status: Public on Aug 19 2022

type: SRA

country: United Kingdom

description:
R6_neg
counts_bulk_rnaseq.txt

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

source_name: Bone marrow

tag: age

tag: genotype


title: young_shoots_ddcc_H3K4me1_rep2

city: Wuhan

first: Qiangwei

last: Zhou

state: Hubei

address: Hongshan district, shizishan #1

country: China

institute: Huazhong Agricultural university

library_source: genomic

data_processing:
Trimmomatic fitered the raw reads
ChIP-seq reads were aligned to the TAIR10 genome assembly using bwa mem
Data were filtered using the SAMTOOLS MAPQ30 and filter the  duplication reads
peaks were called using MACS.2.2.1 with narrow(H3K4me3,H3K27ac,PII)/broad(H3K27me3,H3K4me1,H3K9me2) parameters
Genome_build: TAIR10
Supplementary_files_format_and_content: bigWig by deepTools bamCoverage

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: young shoots ddcc

growth_protocol: Plants were grown at 22 °C under a 16 h light/8 h dark photo-period, and two- and five-week-old plants were used for all experiments.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
ChIP-DNA was extracted with phenol:chloroform:isoamyl alcohol (Sigma–Aldrich, P3803), precipitated with ethanol, and resuspended in TE buffer. ChIP DNA libraries were prepared using an NEBNext® Ultra™ II DNA library prep kit for Illumina® (New England BioLabs, E7645). Briefly, ChIP DNA was end-repaired, ligated with an adaptor, and followed by 6–10 cycles of PCR amplification, per the manufacturer’s guidelines. Next, library fragments of 250–650 bp were selected using AMPure XP beads (Beckman, A63881). Finally, the DNA fragments were sequenced using an Illumina HiSeq X Ten system (paired-end 150-bp reads)

treatment_protocol: Tissues were cross-linked with 1% formaldehyde for 10 min and quenched with 0.2 M glycine at room temperature.

tag: tissue

value: young shoots

tag: development stage

value: young shoots from two-week old seedlings

value: ddcc

tag: chip antibody


title: NegNonELSK_1 [N1_neg_2]

description:
N1_neg_2
counts_bulk_rnaseq.txt


title: ELSK_6 [R6]

description:
R6
counts_bulk_rnaseq.txt


title: DLD1 shNC_rep3 IP for acRIP-seq

city: Guangzhou

first: Zhenxing

last: Liang

state: Guangdong

address: 26 Yuancun Erheng Rd

institute: The Sixth Affiliated Hospital, Sun Yat-sen University

description: DLD1 shNC-3-IP-ac4C

data_processing:
library strategy: acRIP-seq
Cutadapt (v2.5) was used to trim adapters and filter for sequences, remaining reads were then aligned to the human Ensemble genome GRCh38 (mouse Ensemble genome GRCm38) using Hisat2 aligner (v2.1.0) under parameters: “--rna-strandness RF”.
ac4C peaks were identified using exomePeak R package (v2.13.2) under parameters:  “PEAK_CUTOFF_PVALUE=0.05,PEAK_CUTOFF_FDR=NA,FRAGMENT_LENGTH=200”.
Differential ac4C peak were identified using exomePeak R package under parameters:“PEAK_CUTOFF_PVALUE=0.05,PEAK_CUTOFF_FDR=NA,FRAGMENT_LENGTH=200” .
GO and KEGG analysis were performed using clusterprofile R package (v3.6.0).
ac4C-RNA-related genomic features were visualized using Guitar R package (v1.16.0).Identified ac4C peaks which p value <0.05 were chosen for the de novo motif analysis using homer (v4.10.4) under parameters:”-len 12 -rna”.
Assembly: GRCh38
Supplementary files format and content: fpkm; peaks

organism: Homo sapiens

source_name: DLD1 cell

growth_protocol: Total RNA was extracted using TRIzol™ Reagent (Invitrogen, 15596018). The concentration of total RNA was measured by Qubit RNA HS assay kit (Invitrogen, Q32852).

extract_protocol:
the fragmented RNA was incubated with Anti-N4-acetylcytidine (ac4C) antibody (abcam, ab252215) for 3 h at 4℃ and then with protein A/G magnetic beads (Thermo Fisher Scientific, 88802) at 4 ℃ for an additional 2 h to obtain immunoprecipitated RNA fragments. The ac4C-enriched RNA was purified by Zymo RNA clean and concentrator-25 kit (Zymo Research, R1017)
The library was prepared by EpiTM mini longRNA-seq kit (Epibiotek, E1802). Both the input samples without IP and the ac4C IP samples were subjected to 150-bp, paired-end sequencing on an Illumina NovaSeq 6000 sequencer.

treatment_protocol: 100μg total RNA was fragmented into 100-200 nt RNA fragments using 10X RNA Fragmentation Buffer (100 mM Tris-HCl, 100 mM ZnCl2 in nuclease-free H2O). The reaction was stopped by adding 10X EDTA (0.5M EDTA). Acetylated RNA immunoprecipitation was performed using EpiTM ac4C immunoprecipitation kit (Epibiotek, R1815).

value: shNC

tag: cell type

value: CRC cell line

tag: passage

tag: cell line

tag: molecule type

value: ac4C RNA


title: young_shoots_ddcc_H3K4me1_rep1


title: Vehicle Nap EtOH bio rep1

city: Leeds

first: LeedsOmics

last: UoLeeds

state: West Yorkshire

address: Clarendon Way

department: Cross-faculty

institute: University of Leeds

data_processing:
Reads were trimmed by Cutadapt and filtered using fastq_quality_filter as part of FASTX-toolkit with parameters including “-q 20” and “-p 90”. The reference genome and gene annotation files of Homo sapiens were retrieved from GENCODE (release 31) (https://www.gencodegenes.org/). Read mapping was performed by means of Subread aligners in Rsubread package with only uniquely mapped reads reported in the final alignment and read summarisation. Principal Component Analysis (PCA) plot was carried out using all protein-coding genes and long noncoding RNAs with RPKM value ≥ 1 in at least one sample. Subsequently, log2(RPKM+1) transformation and quantile normalization were applied.
Quantification was carried out by featureCounts function in R. Significant differences in gene expression were identified using DESeq2 with the following cut-offs: log2FoldChange > 1 (or < -1) and an FDR-adjusted P value of < 0.05. After this analysis, only protein-coding genes were retained based on the gene biotype labels. Overrepresentation enrichment analysis of DEGs were identified using WebGestalt for gene ontology (GO) terms and pathways, with a significance enrichment level set at an FDR < 0.05.
Supplementary files format and content: gene read counts plain text table

source_name: Ishikawa celss

growth_protocol: were cultured (50:50 DMEM/F12, 0.5 % GSP, 10 % charcoal-stripped FBS) at 37 °C and in 5 % CO2. Cells were cultured to 70 % confluence and seeded into 6-well plates.

extract_protocol:
Following treatment, cells were harvested by trypsinization and lysed in QIAzol Lysis Reagent. RNA was extracted using the miRNeasy Mini RNA Extraction kit (Qiagen, UK) as per manufacturer’s instructions.
Total RNA (100 ng) was used for library preparation using the Illumina TruSeq® Stranded Total kit, according to the manufacturer’s guidelines.
The libraries were sequenced by the Next Generation Sequencing Facility at the University of Leeds, using the NextSeq 500 (Illumina, California, USA) to generate single end 75 bp reads.

treatment_protocol: The cultures were treated with either 1) basal media (as above), 2) vehicle control (70 % ethanol, EtOH) or 3), 0.1 mg/ml P4, 4) 1.0 mg/ml P4, or 5) 1.0 mg/ml P4, for 24 hrs.

value: Ishikawa celss

value: Endomerial epithelial adenocarcinoma

tag: treatment

value: Treatment of cells with vehicle control (70% EtOH)  for 24 hrs


title: NegELSK_5 [R5_neg]

description:
R5_neg
counts_bulk_rnaseq.txt


title: ELSK_5 [R5]

description:
R5
counts_bulk_rnaseq.txt


title: DLD1 shNC_rep3 input for acRIP-seq

description: DLD1 shNC-3-input-ac4C

value: totalRNA


title: DLD1 shNC_rep2 IP for acRIP-seq

description: DLD1 shNC-2-IP-ac4C


title: PSAT1_P4 bio rep1

value: Treatment of cells with recombinant human PSAT1 and Progesterone for 24 hrs


title: young_shoots_ddcc_H3K27me3_rep2


title: PSAT1 bio rep1

value: Treatment of cells with recombinant human PSAT1 for 24 hrs


title: young_shoots_ddcc_H3K27me3_rep1


title: NegELSK_4 [R4_neg]

description:
R4_neg
counts_bulk_rnaseq.txt


title: ELSK_4 [R4]

description:
R4
counts_bulk_rnaseq.txt


title: Control bio rep1

value: No treatment of cells control medium


title: DLD1 shNC_rep2 input for acRIP-seq

description: DLD1 shNC-2-input-ac4C


title: DLD1 shNC_rep1 IP for acRIP-seq

description: DLD1 shNC-1-IP-ac4C


title: DLD1 shNAT10_rep1 input for acRIP-seq

description: DLD1 shNAT10-1-input-ac4C


title: young_shoots_ddcc_H3K4me3_rep2


title: Tumor_L

city: Hefei

first: Qidong

last: Li

state: Anhui

address: 443 Huangshan Road, Shushan district

institute: Lianxin Liu Lab

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: hg18
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: distant liver metastasis

growth_protocol: tissue is from one patient

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

value: Liver

value: distant liver metastasis

tag: sample type


title: young_shoots_ddcc_H3K4me3_rep1


title: DLD1 shNC_rep1 input for acRIP-seq

description: DLD1 shNC-1-input-ac4C


title: Normal

source_name: adjacent normal colonic mucosa

value: colon

value: adjacent normal colonic mucosa

value: Normal


title: young_shoots_Col-0_INPUT_rep2

source_name: young shoots Col-0

value: young shoots

value: young shoots from two-week old seedlings

value: wild type


title: NegNonELSK_3 [N3_neg]

description:
N3_neg
counts_bulk_rnaseq.txt

value: 12-16 weeks


title: RSeT_shKLF17_2

city: Beijing

first: Yangming

last: Wang

address: 5 Yiheyuan Road

department: Institute of Molecular Medicine

institute: Peking University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using STAR v2.5.0.
FPKM were calculated using cufflinks v2.2.1.
Genome_build: hg38
Supplementary_files_format_and_content: Text file include FPKM values for each sample.

molecule: polyA RNA

source_name: Embryonic stem cell

growth_protocol: Human naïve ESCs were cultured on feeder with RSET medium, human primed ESCs were cultured on matrigel plate with mTeSR medium.

extract_protocol:
For RNA-seq,cells were treated with TRIzol and followed with phase seperation, RNA precipitation and RNA wash. Finally, RNA were dissolved in DEPC water.
For RNA-seq, poly(A)+ mRNAs were captured by poly-Oligo dT magnet beads followed by fragmentation by bivalent cation buffer at 94 oC for 5min. ds-cDNAs were then synthesized and ligated to adaptors. After PCR amplification, the library was subjected to sequence on an Illumina Nova-seq 6000 sequencing system.

treatment_protocol: Plasimid pB-NC or pB-KLF17 were transfected into human primed ESCs followed hygromycin sellection. Lentiviruses of shRNAs were infected into human naïve ESCs followed puromycin sellection.

value: Human embryonic stem cell

tag: transfection


title: young_shoots_Col-0_INPUT_rep1


title: NegELSK_4 [N4]

description:
N4
counts_bulk_rnaseq.txt


title: RSeT_shKLF17_1


title: Tumor_C

source_name: primary colon adenocarcinoma

value: primary colon adenocarcinoma


title: young_shoots_Col-0_RNAPII_rep2

value: RNAPII


title: NegELSK_2 [R2_neg_2]

description:
R2_neg_2
counts_bulk_rnaseq.txt


title: NegELSK_3 [N3]

description:
N3
counts_bulk_rnaseq.txt


title: RSeT_shNC_2

value: shNC


title: H929_shSITR6_rep2

type: RNA

city: Genoa

first: Michele

last: Cea

state: Genoa

address: viale Benedetto XV, 6

department: Department of Internal Medicine (DiMI)

country: Italy

institute: University of Genoa

hyb_protocol: The fragmented labeled single-stranded DNA target was hybridized for 16 hours and 30 minutes at 45°C on GeneChip ClariomD array, according to the standard protocol, using the GeneChip Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Scanning of the arrays was performed using the GeneChip Scanner 7G

data_processing: Robust Multichip Average (RMA) processing was applied on raw data, that were annotated based on HuGene-2_0-st-v1.na36.hg19.transcript.csv file by means of Transcriptome Analysis Console (TAC 4.0) software.

label: biotin

source_name: Human Myeloma Cell Line

label_protocol: RNA samples were processed using WT PLUS Reagent Kit, according to manifacturer’s protocol (Thermo Fisher Scientific, Waltham, MA, USA).

growth_protocol: HMCLs were purchased from ATCC or DSMZ. Cell lines were Mycoplasma-free and routinely tested for it. Cells were cultured in RPMI-1640 medium containing 10% fetal bovine serum (FBS; GIBCO), 4mM glutamine, 100 U ml−1 penicillin, and 100 μg ml−1 streptomycin (GIBCO).

extract_protocol: Total RNA was extracted from cells using the RNeasy mini kit (Qiagen, #74134d) according to the manufacturer’s instructions.

tag: condition


title: RSeT_shNC_1


title: ELSK_2 [R2_2]

description:
R2_2
counts_bulk_rnaseq.txt


title: mTeSR_pB-KLF17_2


title: NegNonELSK_4 [N4_neg]

description:
N4_neg
counts_bulk_rnaseq.txt


title: young_shoots_Col-0_H3K9me2_rep2


title: young_shoots_Col-0_H3K9me2_rep1


title: ELSK_3 [R3]

description:
R3
counts_bulk_rnaseq.txt


title: NegELSK_2 [R2_neg]

description:
R2_neg
counts_bulk_rnaseq.txt


title: H929_shSITR6_rep1


title: H929_scr_rep1

value: shSCR


title: young_shoots_Col-0_H3K27ac_rep2


title: H929_scr_rep2


title: ELSK_2 [R2]

description:
R2
counts_bulk_rnaseq.txt


title: young_shoots_Col-0_H3K9ac_rep2


title: young_shoots_Col-0_H3K27ac_rep1


title: young_shoots_Col-0_H3K9ac_rep1


title: young_shoots_Col-0_RNAPII_rep1


title: mTeSR_pB-NC_2

value: pB-NC


title: NegNonELSK_2 [N2_neg]

description:
N2_neg
counts_bulk_rnaseq.txt


title: mTeSR_pB-NC_1


title: MM1S_shSITR6_rep2


title: NegELSK_2 [N2]

description:
N2
counts_bulk_rnaseq.txt


title: young_shoots_Col-0_H3K4me1_rep2


title: mTeSR_pB-KLF17_1


title: PNT2, TCR

city: Brussels

first: David

last: Vermijlen

state: non-US Resident

address: Boulevard de Triomphe, accès 2 (CP205/3)

department: Pharmacotherapy and Pharmaceutics

country: Belgium

institute: Université Libre de Bruxelles

data_processing:
Library strategy: TCR-Seq
Single-cell RNA sequencing libraries: Cell Ranger v3.0.2 was used to demultiplex and map sequencing reads against the GRCh38 genome. The resulting count matrices were loaded into R using read10x function form Seurat R package. All downstream analyses were implemented using R v4.0.3 and the package Seurat v3.2.3 (Stuart et al., 2019). Low-quality and doublet cells were filtered using the cutoffs nFeature_RNA > = 200 & nFeature_RNA < 4000 (except for PNT 3 were 3100 was used as it showed a different distribution). Percentage of mitochondrial genes were plotted as well, and outliers were removed to filter out dead cells. Cell cycle score was calculated for all cells and regressed out. Integration vignette from Seurat v3.0 was followed to generate merged Seurat objects (FT: FT1+FT2 & PNT: PNT1+PNT2) using the SCTransform function and regressing mitochondrial genes and trdv & trgv genes. PCA component was performed using pca Seurat function with 30 dimensions. RunUMAP function was used to obtain bidimensional coordinates for each cell. We determined the k-nearest neighbors of each cell using the FindNeighbors function and used this knn graph to construct the SNN graph by calculating the neighborhood overlap (Jaccard index) between every cell and its k.param nearest neighbors. Finally, we used the FindClusters function to cluster cells using the Louvain algorithm based on the same PCs as RunUMAP function.
Single-cell TCR sequencing analysis: Sc TCR libraries were generated by using CellRanger vdj pipeline (v3.0.2). Human genome GRCh38 was used as reference for alignment. Integrated FT and PNT Seurat objects (gene expression data) were combined with their respective sc TCR-seq (TCR sequence) data based on shared 10× cell barcodes and following the script provided here (https://www.biostars.org/p/384640/). Only those cells expressing productive TCR sequences (γ and/or δ chain) from the ‘filtered_contig_annotations’ file were retained for data integration in the Seurat objects.
Genome_build: GRCh38
Supplementary_files_format_and_content: scRNA-seq: matrix.mtx, features.tsv, barcodes.tsv. TCR-seq: TCR_filtered_contig_annotations.csv, TCR_all_contig_annotations.csv.

source_name: ϒδ thymocytes

extract_protocol: Cell suspensions from fetal thymus and pediatric thymus samples were obtained as previously described (Tieppo et al. JEM 2020) and cryopreserved in liquid nitrogen with freezing media (10%DMSO, 90%FBS). When samples were used, cells were thawed and washed twice with RPMI 1640 (Gibco) complete medium, labeled with Zombie NIR dye (BioLegend), and then subsequently stained for cell surface Ags with Abs directed against CD3 (clone UCHT1; BD Biosciences), TCR-γδ (11F2; BD Biosciences), TCR-Vγ9 (IMMU360; Beckman Coulter), TCR-Vδ2 (IMMU389; Beckman Coulter). For the sc experiment, CD3+ γδTCR+ were sorted for “γδ” thymocytes (mean purity 98% of living cells) on a FACS Aria III (BD Biosciences). Libraries for sc RNA and TCR sequencing were generated from 1.5-2*104 FACS-sorted γδ thymocytes using the Chromium Single Cell 5’ Library Gel Bead and Construction kit as well as Chromium Single Cell V(D)J Enrichment Kit (10x Genomics, CA, USA) according to the user guidelines (v1 Chemistry, Single Cell V(D)J protocol number CG000086). Single-cell TCR and gene expression libraries were generated according to Chromium Single Cell V(D)J protocol (10x Genomics). 2μL of cDNA amplified and purified from GEMs (“Gel bead in EMulsion” droplets) were used to amplify γδTCR CDR3 sequences. Custom primers specific for TRDC and TRGC constant gene segments were designed for this purpose. The remaining of cDNA was used for gene expression library construction according to 10X Genomics protocol instructions. Agilent Bioanalyzer High Sensitivity DNA chips were used to check quality control read-outs of scRNA-seq and scTCR-seq libraries using a Bioanalyzer 2100 machine (Agilent Technologies). The scRNA-seq libraries were sequenced on the Illumina NovaSeq 6000 platfotm from BRIGHTcore (Brussels University Alliance).

value: Gamma delta T cell

value: post natal 4.5 years

value: pediatric thymus

tag: group

value: barcoded CDR3 RNA sequences


title: PNT1, TCR

value: post natal 4.0 years


title: MM1S_shSITR6_rep1


title: young_shoots_Col-0_H3K4me1_rep1


title: MM1S_scr_rep2


title: Targeting rep 3

city: Logan

first: Olive

last: Redman

state: UT

address: 0300 Old Main Hill

department: Chemistry and Biochemistry

country: USA

institute: Utah State University

data_processing:
A short RegEx script was used to count the number of reads of each potential NNNNN PAM directly adjacent to a fully correct target sequence. Those count totals are then used to determine a depletion score by comparing the fraction of each PAM in the control (nonselecting) trials to the fraction of that same PAM found in the targetting trials.
Assembly: N/A
Supplementary files format and content: tab-delimited text files contain the PAM read counts for each replicate
Supplementary files format and content: Excel spreadhseet contains the final depletion scores calculated for each PAM taken from the average of all replicates.
Library strategy: PAM screen

organism: Escherichia coli

growth_protocol: Cells containing either a functioning (targeting) or nonfunctioning (control) immune system are prepared to be electrocompetent, and then are transformed with >500ng of a plasmid library containing all combinations of NNNNN PAMs adjacent to a target sequence. Cells are then induced with IPTG to express the CRISPR-Cas system and grown overnight with antibiotic selection for the plasmid library

extract_protocol:
Plasmid DNA was extracted from each replicate by means of an Omega brand Midi-prep kit
The SOI was amiplified using 22 cycles of PCR with Illumina adapter sequences IS1 (5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT 3') added to the forward primer and IS2 (5' GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT 3') added to the reverse primer

tag: strain

value: wt system transplant


title: ELSK_1 [R1]

description:
R1
counts_bulk_rnaseq.txt


title: Targeting rep 2


title: FT2, TCR

value: 21 wk gestation time

value: fetal thymus


title: Targeting rep 1


title: NegELSK_3 [R3_neg]

description:
R3_neg
counts_bulk_rnaseq.txt


title: FT1, TCR

value: 14 wk gestation time


title: MM1S_scr_rep1


title: young_shoots_Col-0_H3K27me3_rep1

value: young shoots

value: young shoots from two-week old seedlings

value: wild type


title: NegELSK_1 [R1_neg]

description:
R1_neg
counts_bulk_rnaseq.txt

value: 12-16 weeks


title: PNT2, GEX

data_processing:
Single-cell RNA sequencing libraries: Cell Ranger v3.0.2 was used to demultiplex and map sequencing reads against the GRCh38 genome. The resulting count matrices were loaded into R using read10x function form Seurat R package. All downstream analyses were implemented using R v4.0.3 and the package Seurat v3.2.3 (Stuart et al., 2019). Low-quality and doublet cells were filtered using the cutoffs nFeature_RNA > = 200 & nFeature_RNA < 4000 (except for PNT 3 were 3100 was used as it showed a different distribution). Percentage of mitochondrial genes were plotted as well, and outliers were removed to filter out dead cells. Cell cycle score was calculated for all cells and regressed out. Integration vignette from Seurat v3.0 was followed to generate merged Seurat objects (FT: FT1+FT2 & PNT: PNT1+PNT2) using the SCTransform function and regressing mitochondrial genes and trdv & trgv genes. PCA component was performed using pca Seurat function with 30 dimensions. RunUMAP function was used to obtain bidimensional coordinates for each cell. We determined the k-nearest neighbors of each cell using the FindNeighbors function and used this knn graph to construct the SNN graph by calculating the neighborhood overlap (Jaccard index) between every cell and its k.param nearest neighbors. Finally, we used the FindClusters function to cluster cells using the Louvain algorithm based on the same PCs as RunUMAP function.
Single-cell TCR sequencing analysis: Sc TCR libraries were generated by using CellRanger vdj pipeline (v3.0.2). Human genome GRCh38 was used as reference for alignment. Integrated FT and PNT Seurat objects (gene expression data) were combined with their respective sc TCR-seq (TCR sequence) data based on shared 10× cell barcodes and following the script provided here (https://www.biostars.org/p/384640/). Only those cells expressing productive TCR sequences (γ and/or δ chain) from the ‘filtered_contig_annotations’ file were retained for data integration in the Seurat objects.
Genome_build: GRCh38
Supplementary_files_format_and_content: scRNA-seq: matrix.mtx, features.tsv, barcodes.tsv. TCR-seq: TCR_filtered_contig_annotations.csv, TCR_all_contig_annotations.csv.

value: barcoded RNA


title: SKBR3, mock 1

city: Pokfulam

first: Lydia

last: Cheung

address: 21 Sassoon Road

department: School of Biomedical Sciences

country: Hong Kong

institute: University of Hong Kong

data_processing:
Sequencing reads were first filtered for adapter sequence, low quality sequence and rRNA sequence. Reads with read length ≥40 bp retained were aligned to the human genome GRCh38 using STAR version 2.5.2. Differentially expressed genes were identified using DESeq2 version 1.26.0.
Assembly: hg38
Supplementary files format and content: tab-delimited text files which include FPKM, TPM, count values and gene ID

source_name: Breast cancer

extract_protocol:
Total RNA was extracted using TRIzol (Invitrogen).
2ug RNA was used for library preparation using KAPA Stranded mRNA-Seq Kit (Roche).
RNA sequencing was performed on the Illumina NovaSeq 6000 system.

value: Breast cancer

value: Breast cancer cells

value: WT


title: NegNonELSK_6 [N6_neg]

description:
N6_neg
counts_bulk_rnaseq.txt


title: young_shoots_Col-0_H3K4me3_rep2


title: Control rep 2

value: -CRISPR knockout


title: young_shoots_Col-0_H3K4me3_rep1


title: Control rep 3


title: FT2, GEX

value: Gamma delta T cell


title: FT1, GEX


title: PNT1, GEX

value: pediatric thymus


title: NegELSK_1 [N1]

description:
N1
counts_bulk_rnaseq.txt


title: Control rep 1


title: Low lac [L6]

status: Public on Aug 18 2022

city: Hong Kong

first: Hui

last: Xiaoyan

address: Chinese University of Hong Kong (CUHK), Shatin, Hong Kong.

department: school of biomedical sciences

institute: The Chinese University of Hong Kong

data_processing:
Raw reads were trimmed of adapters using cutadapt 1.16
Paired-end clean reads were mapped to the reference genome using HISAT2 software
Differential expression analysis was performed with DESeq2 and edgeR R package.
GO enrichment was performed by Metascape
Transcription factor analysis was performed with Enrichr Submissions TF-Gene Coocurrence on Enrichr and diagrammed by Appyters
Assembly: Hg19
Supplementary files format and content: Tab-delimited text files include read counts for each sample

source_name: adipose tissue

extract_protocol:
Total RNA was extracted from human omental adipose tissues using RNeasy Lipid Tissue Mini Kit (Qiagen, #74804)
Libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina (New England Biolabs, #E7530L)

value: adipose tissue

value: Low lactate


title: Low lac [L3]


title: young_shoots_Col-0_H3K27me3_rep2


title: Low lac [L7]


title: Low lac [L2]


title: High lac [H5]

value: High lactate


title: Low lac [L1]


title: High lac [H7]


title: WT Adult

city: Zollikerberg

first: Sonia

last: Tugues

address: 104 Forchstrasse

department: Institute of Experimental Immunology

country: Switzerland

institute: University of Zurich

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
Initial processing was done using Cell Ranger (v3.1.0) mkfastq and count (reads were aligned to GENCODE reference build GRCm38.p6 Release M23). Starting from the filtered gene-cell count matrices produced by CellRranger's built-in cell calling algorithms, we proceeded with Seurat v4 workflow.
Analysis, including quality control (QC), processing, graph-based clustering, visualizations, and differential gene expression analyses of the scRNA-seq data were performed in R using the Seurat pipeline (version 4.0).
Assembly: GRCm38.p6
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Liver

extract_protocol:
1) Livers were cut immediately after dissection and kept in ice-cold digestion buffer (1.0 mg/ml Collagenase IV, 2 mg/ml DNase, 5% FBS in HBSS with Ca2++/Mg2++) to prevent loss of hepatic ILCs due to prolonged exposure to accumulating lactate. Embryos were removed from the uterus of pregnant mice and dissected under a microscope. All organs were digested with gentle rocking at 37°C for 20-30 min. After digestion, cells were passed through a 100 μm filter and washed, followed by 3 min incubation in ACK (Ammonium-Chloride-Potassium, Sigma Aldrich) buffer to lyse erythrocytes 2) For harvesting of bone marrow cells, tibiae and femora were carefully separated from surrounding muscle and connective tissue, crushed in a mortar, and passed through a 100 μm filter, followed by lysis of erythrocytes.
Sorted cells were loaded into 10x Genomics Chromium in parallel. Libraries were prepared following manufacturer's protocol (Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 protocol) and sequenced on an Illumina NovaSeq sequencer according to 10X Genomics recommendations (paired-end reads, R1=28, i7=8, R2=91) to a depth of around 50,000 reads per cell.

value: Group 1 innate lymphoid cells

value: Liver

value: 6-8 weeks old


title: High lac [H6]


title: High lac [H3]


title: High lac [H1]


title: High lac [H2]


title: Low lac [L5]


title: Low lac [L4]


title: NegNonELSK_1 [N1_neg]

description:
N1_neg
counts_bulk_rnaseq.txt


title: WT27_mESC_SE_Capture_Sample 3

city: Oxford

first: Mira

middle: Tony

last: Kassouf

state: England

address: John Radcliffe Hospital, Headly way

department: Weatherall Institute of Molecular Medicine

institute: University of Oxford

description: sequences enriched from a 3C library for their interaction with the Capture points distributed across all superenhancers (SE) identified using the ROSE algorithm in erythroid cells

data_processing:
Trim_galore (to remove sequencing adaptors)
FLASH (to reconstruct paired end reads into single reads where possible)
In silico restriction enzyme digestion of FASTQ file (dpnIIPE.pl)
Alignment to the genome (Bowtie) maintaining strict read order
Removal of PCR duplicates; Parsing of informative reads and mapping to restriction enzyme fragments (CCanalyser2.pl)
Combining data from multiple replicates (custom scripts)
Removal of ploidy regions and off target capture (custom scripts)
Analysis in R to normalise between tracks using the total number of informative interactions
Assembly: mm9
Supplementary files format and content: Custom combined data format (restriction enzyme fragment \t sample 1 \t sample 2 \t etc.)
Library strategy: Capture-C

source_name: E14TG2a.IV mES derived Erythroid cells

extract_protocol:
To produce CD71+ erythroid cells in vitro from differentiated mESCs (WT or mutant mouse ESC line): 24h prior to differentiation, mESCs were induced by passaging into IMDM base media, trypsinised and plated in differentiation media (IMDM suplemented serum and other reagents and growth factors) in either triple vent petri dishes (Thermo Fisher) or flat-bottom 96-well plates (Thermo Fisher) at 3x104 cells in 10 cm dishes or 250 cells per well of a 96-well plate for up to seven days without disruption. EBs were harvested and disaggregated in 0.25% trypsin for 3 minutes at 37°C. CD71-positive cells were isolated by magnetic column separation (LS Column, Miltenyi), according to the manufacturer’s instructions. Briefly, cells (from disaggregated EBs) were labelled with anti-mouse CD71-FITC (eBioscience 11-0711-85; 1:200) in staining buffer (PBS with 10% FCS; 500 ul per 10^7 cells) for 20 minutes at 4°C, washed, then incubated with MACS anti-FITC separation microbeads (Miltenyi; 10 ul  per 10^7 cells, following the manufacturer’s instructions) and bead-labelled cells were retained by LS columns. Cells were then processed for Capture-C as in Davies J et al, Nature Methods.
The protocol used for generation of the 3C libraries was similar to previous methods with minor modifications. Briefly, cells were crosslinked with 2% formaldehyde (10 minutes, room temperature); quenched with cold glycine; washed in phosphate buffered saline; resuspended in cold lysis buffer (tris 10mM, NaCl 10mM, NP40 0.2%, complete proteinase inhibitor (Roche)) and snap frozen to -80.  Cells were thawed on ice, washed in milliq dH2O and Dounce homogenised on ice (x 40 strokes). Cells were then resuspended with 0.25% SDS and restriction enzyme buffer and incubated at 37C for 1h at 1400rpm on a Comfort Thermomixer (Eppendorf) followed by a further incubation of 1h following the addition of triton X100 (final concentration 1.67%). An overnight digestion was performed using Dpn II (500U /ml (NEB) at 37C / 1400 rpm). The digested chromatin was ligated overnight (Fermentas HC Ligase final concentration 10U/ml) at 16 degrees at 1400 rpm on the Thermomixer.  The samples were then decrosslinked overnight at 65C with Proteinase K (Roche) followed by a 30 min incubation at 37C with RNAse (Roche). Phenol/Chloroform extraction was then performed followed by an Ethanol precipitation and a wash with 70% Ethanol. Digestion efficiencys were assessed by gel electrophoresis (1% agarose) and RT-PCR (Taqman), which showed digestion efficiencies in excess of 80%.  DNA content of the Dpn II 3C libraries were quantitated using a Qubit fluorometer (Life technologies) and 5-10ug of each library was sheared using a Covaris S2 in milliq dH2O. Covaris settings used were: duty cycle 10%, Intensity 5, Cycles/burst 200, Time 6 cycles of 60seconds, Set Mode Frequency sweeping Temperature 4 to 7 degrees. Following shearing DNA was purified using AMPureXP beads (Agencourt) and DNA quality assessed on a Bioanalyser 2100 using a DNA High Sensitivity Chip (Agilent). DNA end repair and adapter ligation was performed using the NEB Next or NEB Ultra II DNA sample preparation reagent kits, depending on the amount of DNA available, using the standard protocol.  Biotinylated capture oligonucleotides were designed to the ends of the viewpoint fragments.  Where possible 1-2ug of each adapter ligated library were hybridized with the biotinylated capture oligonucleotides, using  the Nimblegen SeqCap reagents and an adapted protocol.  The quality of the resultant captured library was assessed by Agilent tapestation or bioanalyser (D1000). The resulting libraries were sequenced using Illumina Next-Seq.
The experimental strategy was to generate very high complexity randomly sonicated 3C libraries with ligated Illumina sequencing adaptors (ideally with several hundred thousand fold coverage).  Oligonucleotide capture technology was then used to pull down the restricion fragments containing the viewpoints of interest and their interacting partners, which were subsequently idendified by high throughput sequencing.  The power of the technique is that multiple samples and genes can be analysed simultaneously by using differently indexed samples as we did with all the samples and most prominently with the erythroid SE (183 viewpoints in 6 samples) and promoter (42 viewpoints in 6 samples) captures

value: undifferentiated mouse embryonic stem cells

tag: protocol

value: As detailed in Protocols below

tag: analysis

value: Genome-wide


title: WT12_APHSpleen_SE_Capture_Sample 1

source_name: mouse derived Erythroid cells

value: Ter119+  erythroid cells purified from the spleen of a WT Phenylhydrazine APH-treated mice, sample 1


title: WT25_mESC_SE_Capture_Sample 2


title: WT2_APHSpleen_SE_Capture_Sample 3

value: Ter119+  erythroid cells purified from the spleen of a WT Phenylhydrazine APH-treated mice, sample 3


title: INVEN_APHSpleen_HS4448_CTCF_Capture_Sample 2

description: sequences enriched from a 3C library for their interaction with the Capture point in the Alpha Globin locus as detailed in the sample name

value: Ter119+  erythroid cells purified from the spleen of a WT Phenylhydrazine APH-treated mice, sample 2


title: WT4_APHSpleen_SE_Capture_Sample 2


title: WT23_mESC_SE_Capture_Sample 1


title: INVEN_APHSpleen_Alpha5Pr_Capture_Sample 2


title: WT_APHSpleen_Alpha5Pr_Capture_Sample 1


title: WT_APHSpleen_Alpha5Pr_Capture_Sample 3


title: WT_APHSpleen_HS4448_CTCF_Capture_Sample 2


title: INVEN_APHSpleen_HS4448_CTCF_Capture_Sample 3


title: INVEN_APHSpleen_Alpha5Pr_Capture_Sample 1


title: WT_APHSpleen_Alpha5Pr_Capture_Sample 2


title: High lac [H4]


title: INVEN_APHSpleen_HS3839_CTCF_Capture_Sample 3


title: INVEN_APHSpleen_R1_Enhancer_Capture_Sample 3


title: INVEN_APHSpleen_HS3839_CTCF_Capture_Sample 1


title: INVEN_APHSpleen_R1_Enhancer_Capture_Sample 2


title: INVEN_APHSpleen_HS3839_CTCF_Capture_Sample 2


title: WT_APHSpleen_HS4448_CTCF_Capture_Sample 3


title: INVEN_APHSpleen_Alpha5Pr_Capture_Sample 3


title: INVEN_KO_MpgKO_EBd7 CD71+ R1 Capture sample 2 (INVEN_KO_MpgKO_B12_Enhancers)

value: Chromatin from purified CD71+ erythroid cells derived from differentiated D3839 mES cells, Rhbdf1 and Mpg promoters as Capture point, sample 2

value: Alpha Globin Locus


title: INVEN_APHSpleen_R1_Enhancer_Capture_Sample 1


title: CTCFKO_MpgKO_EBd7 CD71+ R1 Capture sample 3 (INVEN_KO_MpgKO_B7_Enhancers)

value: Chromatin from purified CD71+ erythroid cells derived from differentiated D3839 mES cells, Rhbdf1 and Mpg promoters as Capture point, sample 3


title: INVEN_APHSpleen_HS4448_CTCF_Capture_Sample 1


title: INVEN_KO_MpgKO_EBd7 CD71+ R1 Capture sample 1 (INVEN_KO_MpgKO_B12_Enhancers)

value: Chromatin from purified CD71+ erythroid cells derived from differentiated D3839 mES cells, Rhbdf1 and Mpg promoters as Capture point, sample 1


title: WT_APHSpleen_HS4448_CTCF_Capture_Sample 1


title: CTCFKO_MpgKO_EBd7 CD71+ R1 Capture sample 1 (INVEN_KO_MpgKO_B7_Enhancers)


title: CTCFKO EBd7 CD71+ R1 Capture sample 2 (CTCFKO_A81_Enhancers)

value: Chromatin from purified CD71+ erythroid cells derived from differentiated D3839 mES cells, alpha globin enhancer sequence R1 as Capture point, sample 2


title: CTCFKO EBd7 CD71+ R1 Capture sample 3 (CTCFKO_A82_Enhancers)

value: Chromatin from purified CD71+ erythroid cells derived from differentiated D3839 mES cells, alpha globin enhancer sequence R1 as Capture point, sample 3


title: INVEN_KO CD71+ R1 Capture sample 3 (INVEN_KO_C12_Enhancers)


title: CTCFKO EBd7 CD71+ R1 Capture sample 1 (CTCFKO_A3_Enhancers)

value: Chromatin from purified CD71+ erythroid cells derived from differentiated D3839 mES cells, alpha globin enhancer sequence R1 as Capture point, sample 1


title: Mir_B

city: Derio

first: Ana

middle: Maria

last: Aransay

state: BIZKAIA

address: Parque tecnologico de Bizkaia, Building 801-A

department: Genome Analysis Platform

country: Spain

institute: CIC bioGUNE

description: mirVana PARIS kit (Ambion)

data_processing:
FASTQs were trimmed for the adapters following the recommendations of the NEXTflex™ Small RNA-Seq Kit manufacturers.
We used Bowtie 1.0.1 to align the reads against the human genome (GRCh38), with a mismatch 0, to avoid false positives. We select mirbase v22 to quantify mature micrornas employing Partek Flow application, software version 7.0. Only the miRNAs with 10 or more reads were considered.
Mapped reads were quantified to GENCODE-v26 using Partek E/M method, so the processed data file contains counts values normalized by Partek E/M method
Genome_build: GRCh38
Supplementary_files_format_and_content: read count table

organism: blank sample

source_name: Blank

extract_protocol:
Total RNA from extracellular vesicles from endometrial fluid was extracted using either the mirVana PARIS kit (Ambion) or the Plasma/Serum RNA Purification kit (Norgen), as detailed in the SAMPLES section
Sequencing libraries were prepared following the protocol included with the kit “NEXTflex™ Small RNA-Seq Kit v3,” (©Bioo Scientific Corp. Catalog #5132-05).

treatment_protocol: Endometrial fluid was aspirated with a catheter used for embryo transfer (Frydman, Instrumentos Médicos Estériles SA, Spain) connected to a 10 mL syringe, under abdominal ultrasound guidance. Sample extraction was performed by gentle manual application of negative pressure with the syringe. To prevent contamination with cervical mucus, aspiration was interrupted at the internal cervical os. Aspirate volumes ranged from 5 uL up to 50 uL. After the aspiration, the 10 mL syringe was replaced with a 2 mL syringe containing 1.5 mL saline solution and the aspirates were mixed and expelled in a cryogenic tube (5-50 uL of EF + 1500 uL 1XDPBS (Gibco, Thermo Fisher Scientific #14190250). The mixed samples were centrifuged to remove contaminants at 2,000 x g for 5 min and the supernatants were then frozen at −80 °C until processed. The dilution of the supernatants was 1:30 and they had a volume comprised between 400uL and 1300uL. Extracellular vesicle enrichment was done with Total Exosome Isolation Reagent from cell culture media (Invitrogen by ThermoFisher Scientific, #4478359). The EF supernatants were centrifuged at 3000 g for 30 min at 4 ºC, then 400uL were transferred to a fresh tube and 1 volume of the Total Exosome Isolation Reagent (1:1) was added. The mixture was incubated for 30 min at room temperature and then centrifuged at 10,000 g for 1 hour at 4 ºC. The supernatant was discarded and the EVs that were in the pellet were resuspended in 100 uL of 1 x DPBS.

value: PBS


title: Nor_B

description: Plasma/Serum RNA Purification kit (Norgen)


title: INVEN_KO_MpgKO_EBd7 CD71+ R1 Capture sample 3 (INVEN_KO_MpgKO_B12_Enhancers)


title: EB_CD71_DelR1_INVR2_ATAC_3

description: Genome-wide library of transposed elements

data_processing:
Trim_galore (to remove sequencing adaptors)
Alignment to the genome Bowtie 1 standard parameters with -m set to 2
Removal of PCR duplicates;
plot density of alignments in a moving 300bp window with an moving increment of 30 bp
Assembly: mm9
Supplementary files format and content: BigWig

extract_protocol:
To produce CD71+ erythroid cells in vitro from differentiated mESCs (WT or mutant): 24h prior to differentiation, mESCs were induced by passaging into IMDM base media, trypsinised and plated in differentiation media (IMDM suplemented serum and other reagents and growth factors) in either triple vent petri dishes (Thermo Fisher) or flat-bottom 96-well plates (Thermo Fisher) at 3x104 cells in 10 cm dishes or 250 cells per well of a 96-well plate for up to seven days without disruption. EBs were harvested and disaggregated in 0.25% trypsin for 3 minutes at 37°C. CD71-positive cells were isolated by magnetic column separation (LS Column, Miltenyi), according to the manufacturer’s instructions. Briefly, cells (from disaggregated EBs) were labelled with anti-mouse CD71-FITC (eBioscience 11-0711-85; 1:200) in staining buffer (PBS with 10% FCS; 500 ul per 10^7 cells) for 20 minutes at 4°C, washed, then incubated with MACS anti-FITC separation microbeads (Miltenyi; 10 ul  per 10^7 cells, following the manufacturer’s instructions) and bead-labelled cells were retained by LS columns. Cells were then processed for ATAC-Seq as in (Buenrostro et al, 2013).
Assay for transposition of active chromatin sequencing (ATAC-Seq) was performed as previously published (Buenrostro, 2013). 60000-80000 cells were used per biological replicate. Cells were lysed and nuclei were isolated prior to transposition with Tn5 transposase (Nextera, Illumina) for 30 minutes at 37°C. DNA was purified using a MinElute kit (Qiagen). Libraries were amplified and barcoded using the NEBNext 2xMastermix (NEB) and the custom primers as published in Buenrostro et al., 2013. ATAC-Seq libraries profiles were visualized using D1000 tape on the Tapestation (Agilent). Due to the broad range of DNA fragment sizes found in these libraries, quantitation with the Qubit for DNA concentration was found to be highly variable and was omitted. The libraries were quantified using the universal library quantification kit (KAPA Biosystems). Samples were sequenced using 40 bp paired end reads (NextSeq platform).
The strategy was to survey regions of open chromatin in our cell population of interest (primary mouse derived erythroid cells or CD71+ EB-derived cells) as they mark regulatory genomic regions. The modified Tn5 can in one step identify open chromatin fragments, cut, and ligate adaptors. The fragments can then be multiplexed and sequenced

value: Purified CD71+ erythroid cells derived from Embryoid Bodies (EBs) resulting from mES in vitro differentiation of mutant mES cells deleted for R1 enhancer and inverted enhancer R2, sample 3


title: EB_CD71_DelR1_ATAC_1

value: Purified CD71+ erythroid cells derived from Embryoid Bodies (EBs) resulting from mES in vitro differentiation of mutant mES cells deleted for R1 enhancer, sample 1


title: EB_CD71_DelR1_ATAC_3

value: Purified CD71+ erythroid cells derived from Embryoid Bodies (EBs) resulting from mES in vitro differentiation of mutant mES cells deleted for R1 enhancer, sample 3


title: EB_CD71_DelR1_INVR2_ATAC_2

value: Purified CD71+ erythroid cells derived from Embryoid Bodies (EBs) resulting from mES in vitro differentiation of mutant mES cells deleted for R1 enhancer and inverted enhancer R2, sample 2


title: EB_CD71_INVEN_Mpg_KO_ATAC_3

value: Purified CD71+ erythroid cells derived from Embryoid Bodies (EBs) resulting from INVEN-Mpg KO  (INVEN:homozygous for the inversion of the alpha globin super-enhancer and encompassing both Nprl3 and Mpg genes, ~48kb) and Mpg KO  (deletion of the promoter of the Mpg gene resulting in shutting down of the gene expression) mES in vitro differentiation, sample 3


title: EB_CD71_INVEN_KO_Mpg_KO_ATAC_1

value: Purified CD71+ erythroid cells derived from Embryoid Bodies (EBs) resulting from INVEN KO-Mpg KO (INVEN:homozygous for the inversion of the alpha globin super-enhancer and encompassing both Nprl3 and Mpg genes, ~48kb and deleted for two CTCF sites at the Alpha Globin locus at positions (HS38 and HS39.5)) and Mpg KO  (deletion of the promoter of the Mpg gene resulting in shutting down of the gene expression) mES in vitro differentiation, sample 1


title: EB_CD71_DelR1_ATAC_2

value: Purified CD71+ erythroid cells derived from Embryoid Bodies (EBs) resulting from mES in vitro differentiation of mutant mES cells deleted for R1 enhancer, sample 2


title: EB_CD71_INVEN_Mpg_KO_ATAC_2

value: Purified CD71+ erythroid cells derived from Embryoid Bodies (EBs) resulting from INVEN-Mpg KO  (INVEN:homozygous for the inversion of the alpha globin super-enhancer and encompassing both Nprl3 and Mpg genes, ~48kb) and Mpg KO  (deletion of the promoter of the Mpg gene resulting in shutting down of the gene expression) mES in vitro differentiation, sample 2


title: EB_CD71_INVEN_Mpg_KO_ATAC_1

value: Purified CD71+ erythroid cells derived from Embryoid Bodies (EBs) resulting from INVEN-Mpg KO  (INVEN:homozygous for the inversion of the alpha globin super-enhancer and encompassing both Nprl3 and Mpg genes, ~48kb) and Mpg KO  (deletion of the promoter of the Mpg gene resulting in shutting down of the gene expression) mES in vitro differentiation, sample 1


title: CTCFKO_MpgKO_EBd7 CD71+ R1 Capture sample 2 (INVEN_KO_MpgKO_B7_Enhancers)

value: Chromatin from purified CD71+ erythroid cells derived from differentiated D3839 mES cells, Rhbdf1 and Mpg promoters as Capture point, sample 2

value: As detailed in Protocols below


title: INVEN_KO CD71+ R1 Capture sample 2 (INVEN_KO_C12_Enhancers)

value: Alpha Globin Locus


title: EB_CD71_CTCF_KO_Mpg_KO_ATAC_1

value: Purified CD71+ erythroid cells derived from Embryoid Bodies (EBs) resulting from CTCF KO-Mpg KO mES in vitro differentiation of mutant mES cells deleted for two CTCF sites at the Alpha Globin locus at positions (HS38 and HS39.5), and Mpg KO  (deletion of the promoter of the Mpg gene resulting in shutting down of the gene expression), sample 1


title: Sagittal plane of orchid flowers (bud 8)

city: Shanghai

first: Ji

last: Qi

state: Shanghai

address: E401, Life Science Building, Jiangwan Campus, Fudan University, 2005 Songhu Rd.

department: School of Life Sciences

institute: Fudan University

data_processing:
Sequenced reads were trimmed by SpaceRanger of 10X Genomics (https://support.10xgenomics.com/spatial-gene-expression/software/overview/welcome)
Unique molecular identifiers (UMIs) for each spot were counted to remove PCR duplicates.
For the features.tsv files, the gene annotation models were downloaded from the website of Phalaenopsis aphrodite Genome Resources: http://orchidstra2.abrc.sinica.edu.tw/orchidstra2/padownload.php
Here is the link for GFF file: http://orchidstra2.abrc.sinica.edu.tw/orchidstra2/pagenome/P_aphrodite_genomic_scaffold_v1.0_gene.gff.gz
Genome_build: ASM301322v1
Supplementary_files_format_and_content: Tables with raw gene counts for each gene and each spot

organism: Phalaenopsis aphrodite

source_name: Flower

growth_protocol: Not available

extract_protocol:
Dissections were performed and Phalaenopsis Big Chili flowers at early developing stages were immediately frozen in liquid nitrogen-cooled isopentane and were embedded in pre-cooled OCT. Tissue preparation and optimization were performed on 10X Visium platform, including tissue sectioning, staining, tissue permeabilization, fluorescent cDNA synthesis and imaging, according to the manufacturer’s protocol.
cDNAs of samples were sequenced on Illumina novaseq platform and were subjected to 150 cycles of paired-end (2 × 150 bp) sequencing

treatment_protocol: Not available

tag: cultivar

value: Big Chili

tag: developmental stage

value: bud 8

value: Flower

tag: tissue region

value: Sagittal section


title: EB_CD71_DelR1_INVR2_ATAC_1

value: Purified CD71+ erythroid cells derived from Embryoid Bodies (EBs) resulting from mES in vitro differentiation of mutant mES cells deleted for R1 enhancer and inverted enhancer R2, sample 1


title: EB_CD71_WT_Mpg_KO_ATAC_3

value: Purified CD71+ erythroid cells derived from in vitro differentiationof  Mpg KO  (deletion of the promoter of the Mpg gene resulting in shutting down of the gene expression) mES cells into Embryoid Bodies (EBs) ,  sample 3


title: EB_CD71_WT_Mpg_KO_ATAC_2

value: Purified CD71+ erythroid cells derived from in vitro differentiationof  Mpg KO  (deletion of the promoter of the Mpg gene resulting in shutting down of the gene expression) mES cells into Embryoid Bodies (EBs) ,  sample 2


title: Sagittal plane of orchid flowers (bud 7)

value: bud 7

tag: tissue


title: Sagittal plane of orchid flowers (buds 1-6)

value: bud 1-6


title: EB_CD71_WT_Mpg_KO_ATAC_1

value: Purified CD71+ erythroid cells derived from in vitro differentiationof  Mpg KO  (deletion of the promoter of the Mpg gene resulting in shutting down of the gene expression) mES cells into Embryoid Bodies (EBs) ,  sample 1


title: EB_CD71_INVEN_KO_ATAC_1

value: Purified CD71+ erythroid cells derived from in vitro differentiation of  INVEN KO mES cells into Embryoid Bodies (EBs) ,  sample 1 (INVEN KO:homozygous for the inversion of the alpha globin super-enhancer and encompassing both Nprl3 and Mpg genes, ~48kb and deleted for two CTCF sites at the Alpha Globin locus at positions (HS38 and HS39.5)), sample 1


title: EB_CD71_INVEN_KO_ATAC_2

value: Purified CD71+ erythroid cells derived from in vitro differentiation of  INVEN KO mES cells into Embryoid Bodies (EBs) ,  sample 1 (INVEN KO:homozygous for the inversion of the alpha globin super-enhancer and encompassing both Nprl3 and Mpg genes, ~48kb and deleted for two CTCF sites at the Alpha Globin locus at positions (HS38 and HS39.5)), sample 2


title: EB_CD71_INVEN_ATAC_3

value: Purified CD71+ erythroid cells derived from in vitro differentiationof  INVEN (INVEN:homozygous for the inversion of the alpha globin super-enhancer and encompassing both Nprl3 and Mpg genes, ~48kb) mES cells into Embryoid Bodies (EBs) ,  sample 3


title: Skin containing hair follicle , B6

first: Qi

last: Xiong

address: No.1 Nanhu Yaoyuan, Shizisanjie, Hongsan D

institute: Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Index  of  the  reference  genome  was  built  using  Bowtie  v2.0.6  and paired-end clean reads were aligned to the reference genome using Hisat2
Cufflinks was used to estimate the gene expression levels for each sample using the gene annotation data obtained from ARS1
The read counts that mapped on each gene and the FPKM (fragments per kilobase of transcript per million mapped reads) values were calculated using featureConuts by mapping clean data back onto the transcripts.
Genome_build: ARS1 (ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/vertebrate_mammalian/Capra_hircus/latest_assembly_versions/GCA_001704415.1_ARS1)
Supplementary_files_format_and_content: Microsoft excel format file including readscounts and FPKM values of all gene for each Sample

organism: Capra hircus

source_name: Skin containing hair follicle , B

extract_protocol:
A total amount of 5 μg RNA per sample was isolated from each individual sample using TRIzol reagent (Invitrogen, USA). Purity and quantity of total RNA were measured by using Nanodrop equipment. Ribosomal RNAs were depleted using Epicentre Ribo-zero™ rRNA Removal Kit (Epicentre, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: breed

value: Boer and Macheng Black crossbred goat with black head and white body

value: skin containing hair follicle

tag: region

value: white-coated region


title: Skin containing hair follicle , B5


title: EB_CD71_INVEN_ATAC_2

tag: cell type

value: Purified CD71+ erythroid cells derived from in vitro differentiationof  INVEN (INVEN:homozygous for the inversion of the alpha globin super-enhancer and encompassing both Nprl3 and Mpg genes, ~48kb) mES cells into Embryoid Bodies (EBs) ,  sample 2


title: Skin containing hair follicle , H3

source_name: Skin containing hair follicle , H

value: black-coated region


title: Skin containing hair follicle , H2


title: Skin containing hair follicle , B4


title: INVEN_KO EBd7 CD71+ R1 Capture sample 1 (INVEN_KO_C2_Enhancers)

value: Chromatin from purified CD71+ erythroid cells derived from differentiated D3839 mES cells, Rhbdf1 and Mpg promoters as Capture point, sample 1

value: As detailed in Protocols below

value: Alpha Globin Locus


title: EB_CD71_INVEN_ATAC_1

value: Purified CD71+ erythroid cells derived from in vitro differentiationof  INVEN (INVEN:homozygous for the inversion of the alpha globin super-enhancer and encompassing both Nprl3 and Mpg genes, ~48kb) mES cells into Embryoid Bodies (EBs) ,  sample 1


title: Skin containing hair follicle , H1


title: FHC-4

city: xinxiang

first: Fei

last: Tu

address: 601 Jin Sui Road

institute: xinxiang medical university

description: Gene expression of FHC

hyb_protocol: The labeled cRNAs were hybridized onto the Agilent Human ceRNA Microarray 2019(4*180k,Design ID:086188)

scan_protocol: the arrays were scanned by the Agilent Scanner G2505C

data_processing: Feature Extraction software (version10.7.1.1, Agilent Technologies) was used to analyze array images to get raw data

source_name: normal colorectal epithelial cell

label_protocol: total RNA were transcribed to double strand cDNA, then synthesized into cRNA and labeled with Cyanine-3-CTP.

extract_protocol: Total RNA was extracted from cells using TRIzol® reagent  and quantified by the Nano-Drop ND-2000  and the RNA integrity was assessed using Agilent Bioanalyzer 2100.

tag: cell line

value: FHC

tag: disease state

value: Normal


title: FHC-3

description: Gene expression of FHC


title: EB_CD71_WT_ATAC_3

value: Purified CD71+ erythroid cells derived from in vitro differentiationof  WT mES cells into Embryoid Bodies (EBs) ,  sample 3


title: EB_CD71_WT_ATAC_2

value: Purified CD71+ erythroid cells derived from in vitro differentiationof  WT mES cells into Embryoid Bodies (EBs) ,  sample 2


title: EB_CD71_WT_ATAC_1

value: Purified CD71+ erythroid cells derived from in vitro differentiationof  WT mES cells into Embryoid Bodies (EBs) ,  sample 1


title: HCT116-3

description: Gene expression of HCT116

source_name: human colorectal cancer cell

value: tumor


title: HCT116-4

description: Gene expression of HCT116


title: ATL-43T, bulk ATAC-seq

city: Kashiwa

first: Hiroyoshi

last: Nishikawa

state: Chiba

address: Kahiwanoha 6-5-1

department: Exploratory Oncology Research & Clinical Trial Center

country: Japan

institute: National Cancer Center

data_processing:
Raw Omni-ATAC-seq reads were aligned to the hg38. reference genome using Bowtie 2 with default parameters, and uniquely mapping reads were used for further analysis. All the reads aligning to the positive strand were shifted 4 bp downstream, and all the reads aligning to the negative strand were shifted 5 bp upstream with R package ATACseqQC. ATAC-seq peaks were identified for each sample using MACS2 (with parameters, −q value 0.05 --nomodel --shift 100 --extsise 200). Overlapping peaks in all samples were merged by HOMER mergePeaks.pl, and the merged peak list was produced. The number of raw reads mapped to each merged peak region in the list was counted with featureCounts, and the read counts in all the merged ATAC-seq peaks were quantile-normalized. bigWig files were generated using deepTools
Supplementary files format and content: tab-delimited text files include open chromatin regions and read counts.
Supplementary files format and content: bigWig files

extract_protocol:
Peripheral blood and tumor tissues for Omni-ATAC-seq were obtained from healthy individuals and NSCLC patients who underwent a surgery for curative resection at the National Cancer Center Hospital East. The PBMCs were isolated by the density gradient centrifugation with Ficoll-Paque (GE Healthcare, Chicago, IL, USA). Tumor tissues were cut into small pieces, and single-cell suspensions were prepared with a gentle MACS Dissociator (Miltenyi Biotec, Bergisch Gladbach, Germany) as previously described (PMID: 31028147). Briefly, after filtrating the lung homogenates with a cell strainer (30 μm), the cells were subjected to a density gradient centrifugation with Ficoll-Paque to separate the tumor cells from TILs. Each T cell subset [naive Treg cells (CD45RA+CD25lowFoxP3low CD4+), eTreg cells (CD45RA–CD25highFoxP3highCD4+), naive Tconv cells (CD45RA+CD25-CD4+), effector Tconv cells (CD45RA-CD25-CD4+), naive CD8+ T cells (CD45RA+CCR7+CD8+) and effector memory CD8+ T cells (CD45RA-CCR7-CD8+) from healthy individuals’ PBMCs; and eTreg cells, eTconv cells and effector memory CD8+ T cells from cancer patients’ PMBCs and TILs] was sorted with a BD FACSAria Fusion Cell Sorter (BD Biosciences, San Jose, CA) for subsequent Omni-ATAC-seq analyses. Anti-CD3 (clone: UCTH1), anti-CD4 (clone: RPA-T4) and anti-CD45RA (clone: HI100) mAbs were purchased from BD Biosciences. Anti-CCR7 (clone: G043H7) and anti-CD25 (clone: BC96) mAbs were obtained from BioLegend (San Diego, CA). ATLL cell lines (HuT102, MJ, MT-4, and ATL43T) were maintained in Roswell Park Memorial Institute (RPMI) 1640 medium (FUJIFILM Wako Pure Chemical Corporation, Osaka, Japan) supplemented with 10% fetal calf serum (Biosera, Orange, CA). Recombinant IL-2 (0.5 nmol/L) was added to the culture medium of ATL-43T due to the IL-2-dependency of the cell line.
The Omni-ATAC-seq protocol was performed as described previously with minor modifications (PMID: 28846090). In brief, 5000 to 10000 sorted T cells (for clinical samples), 1000 to 10000 sorted T cells (for murine samples), and 50000 cells (for cell lines) were washed with PBS and then lysed. The cell lysates were resuspended in 50 μl once with TD Buffer containing 2.5 μl of Nextera enzyme (Illumina). The transposition reaction was performed at 37°C for 30 min. The products were then purified with a MinElute polymerase chain reaction (PCR) purification kit (Qiagen, Hilden, Germany), and the fragments for the Omni-ATAC-seq library were amplified for five cycles of PCR. The additional number of PCR cycles was determined for each sample after quantification by real-time PCR. The PCR-amplified products were purified with a MinElute PCR purification kit again.

value: ATLL cell lines


title: HuT102, bulk ATAC-seq


title: MJ, bulk ATAC-seq

source_name: MJ

value: MJ


title: MT-4, bulk ATAC-seq


title: HCT116-1

description: Gene expression of HCT116


title: HD 3, PBMC, nTconv, bulk ATAC-seq

description:
HD_PBMC_nTconv_merged.bw
bulkATACseq_peak_lists.txt
bulkATACseq_counts.txt

source_name: PBMC

value: PBMC

value: nTconv cells


title: HD 3, PBMC, naive CD8+ T, bulk ATAC-seq

description:
HD_PBMC_naive_CD8posT_merged.bw
bulkATACseq_peak_lists.txt
bulkATACseq_counts.txt

value: naive CD8+ T cells


title: HCT116-2

description: Gene expression of HCT116


title: DMSO_761

city: Ottawa

first: Matthew

last: Meier

state: Ontario

address: 251 Sir Frederick Banting Driveway

department: Health Canada

country: Canada

institute: Government of Canada

data_processing:
Base calling was performed by bcl2fastq v 2.20.422
Quality trimming was performed using fastp v0.20.0
Alignment was performed using STAR v2.7.8a
Gene counts were performed with qCount in the QuasR R package v1.30.0
Normalization was performed with DESeq2 v1.30.1
Assembly: Biospyder Human Whole Transcriptome Gene Set
Supplementary files format and content: count_table.csv is a genes by samples count matrix of raw counts from the TempO-Seq data alignments.

source_name: breast cancer

growth_protocol: MCF-7 cells (ATCC, Manassas, VA) were cultured in Dulbecco's modified Eagle's medium (DMEM; Gibco, Thermo Fisher Scientific) supplemented with 10% fetal bovine serum (FBS; Wisent Bioproducts), and 1% penicillin and streptomycin, at 37°C in a humidified atmosphere with 5% CO2.

extract_protocol:
Cell lysates were used directly for TempO-Seq library building
TempO-Seq gene expression analysis was conducted on exposed and control MCF-7 cell lysates. Libraries were prepared in a 96-well plate format using the TempO-Seq® Human Whole Transcriptome Panel reagent kit (BioSpyder Technologies, Carlsbad, CA, USA), following the manufacturer?s protocol. Human Brain Total RNA and qPCR Human Reference Total RNA (Takara Bio, CA, USA) were included as positive assay controls and a no-lysate control (1X TempO-Seq® R Lysis Buffer only) was included as a negative assay control (two replicates per control). In brief, 2 µl cell lysates were hybridized with the targeted detector oligo (DO) probe mix in 1X TempO-Seq® R Lysis Buffer for 10 min at 70oC followed by a temperature gradient with a ramp rate of 0.5oC/min to 45oC over a 50 min period, followed by a nuclease digestion at 37oC for 90 min to remove excess, unbound, or incorrectly bound DOs enzymatically. Ligation of the DO pairs bound to adjacent target sequences was then completed with a 60 min incubation at 37oC, immediately followed with a 15 min enzyme denaturation at 80oC to generate a pool of amplification templates. All amplification templates (i.e., 10 µl of ligated DOs) were transferred to its corresponding well of the 96-well PCR Pre-Mix and Primers plate. Amplification proceeded with a CFX96 Real-Time PCR Detection System (Bio-Rad, Mississauga, ON, Canada) to attach a unique sequence tag and the sequencing adaptors to each sample using the following PCR program settings: 37oC for 10 min, 95oC for 2 min; 6 cycles of 95oC for 30 sec, 54oC for 30 sec, 72oC for 120 sec; 16 cycles of 95oC for 30 sec; 72oC for 2 min; 72oC for 1 min. The TempO-Seq® libraries were pooled (5 µl of all 96 samples) and purified using the Macherey-Nagel NucleoSpin® Gel and PCR Clean-Up kit (Clontech Laboratories Inc., Bethlehem, PA, USA), according to the manufacturer?s instructions for PCR cleanup with three modifications outlined in the TempO-Seq® Assay User Guide. The pooled, purified TempO-Seq® libraries were sequenced using a NextSeq® 500/550 High Output flow cell (v2 kit, 75 cycles) on an Illumina NextSeq® 500 Sequencing platform (Illumina, San Diego, CA, USA).

treatment_protocol: Cells were maintained for 24 hours in phenol red-free DMEM supplemented with 5% charcoal-dextran stripped FBS (CD-FBS) and seeded  into 96-well plates at a density of 2.5 × 104 cells per well in phenol red-free DMEM supplemented with 5% CD-FBS to eliminate estrogenic components. The next day the medium was removed and replaced with DMEM with 5% CD-FBS containing the chemicals of interest. Cells were exposed in quadruplicate in separate 96-well plates to BPA and 15 alternative chemicals at 10 different concentrations (0.0005, 0.001, 0.01,0.1, 0.5, 1, 5, 10, 50, 100 µM), the positive control 17?-estradiol (E2; 0.0001, 0.001, 0.01, 0.1, 1, 10 nM), dexamethasone (Dex ? a non ER-interacting control; 0.0001, 0.001, 0.01, 0.1, 1 µM) alongside solvent controls (0.1% DMSO; four solvent controls per plate) for 48 hours.

value: breast cancer

value: adenocarcinoma cell line

tag: chemical

value: DMSO Pool 2

tag: chemical long_name

value: DMSO 0.1%

tag: dose

tag: treatment

value: DMSO

tag: batch

value: Plate 2D index G

tag: sequencing pool

tag: technical control

value: F

tag: reference rna

tag: solvent control

value: T

tag: well

tag: i7 index_id

tag: index

value: TAGCTCTTC

tag: i5 index_id

value: TCTAACCAT

tag: cas-rn

tag: iupac name


title: DMSO_762

tag: tissue

tag: cell line

tag: cell type

value: ATACGCAGC


title: DMSO_764

tag: chemical

tag: chemical long_name

value: GCACCTATT


title: Cells, no treatment_0_760

value: Cells, no treatment

value: cells, no treatment

tag: dose

tag: treatment

value: Cells, no treatment_0

value: GACTTCATT

value: GGTCTAGCT


title: FHC-2

description: Gene expression of FHC

value: FHC

tag: disease state

value: Normal


title: DMSO_763

value: breast cancer

value: adenocarcinoma cell line

value: DMSO Pool 2

tag: batch

tag: sequencing pool

tag: technical control

value: GCCGTTACA


title: HD 3, PBMC, effector CD8+ T, bulk ATAC-seq

description:
HD_PBMC_effector_CD8posT_merged.bw
bulkATACseq_peak_lists.txt
bulkATACseq_counts.txt

value: PBMC

value: effector CD8+ T cells


title: Cells, no treatment_0_759

value: Plate 2D index G

value: T

tag: reference rna

value: F

tag: solvent control

tag: well

value: CGTAACTTA


title: HD 2, PBMC, naive CD8+ T, bulk ATAC-seq

value: naive CD8+ T cells


title: HD 3, PBMC, eTreg, bulk ATAC-seq

description:
HD_PBMC_eTreg_merged.bw
bulkATACseq_peak_lists.txt
bulkATACseq_counts.txt

value: eTreg cells


title: HD 2, PBMC, nTconv, bulk ATAC-seq

value: nTconv cells


title: Dex_10_755

value: Dex

tag: i7 index_id

tag: index

value: GACTTCATT

tag: i5 index_id


title: FHC-1

description: Gene expression of FHC

value: FHC


title: HD 2, PBMC, nTreg, bulk ATAC-seq

description:
HD_PBMC_nTreg_merged.bw
bulkATACseq_peak_lists.txt
bulkATACseq_counts.txt

tag: tissue

value: nTreg cells


title: Dex_100_756

value: breast cancer

tag: cell line

value: GCACCTATT

tag: cas-rn

tag: iupac name


title: HD 2, PBMC, effector CD8+ T, bulk ATAC-seq

tag: cell type


title: Dex_0.1_753

value: adenocarcinoma cell line

tag: chemical

tag: chemical long_name

tag: dose

value: TCTAACCAT


title: HD 3, PBMC, nTreg, bulk ATAC-seq

value: PBMC


title: Dex_1_754

tag: treatment

tag: batch

value: ATACGCAGC


title: BPA_100_752

value: BPA

value: Plate 2D index G

tag: sequencing pool

tag: technical control

value: TGCATGACA

value: GGTCTAGCT


title: HD 3, PBMC, eTconv, bulk ATAC-seq

description:
HD_PBMC_eTconv_merged.bw
bulkATACseq_peak_lists.txt
bulkATACseq_counts.txt

value: eTconv cells


title: BPS-MPE_100_751

value: BPS-MPE

value: F

tag: reference rna

tag: solvent control

value: CGTAACTTA


title: Cells, no treatment_0_758

value: Cells, no treatment

value: cells, no treatment

value: Cells, no treatment_0

value: T

tag: well

tag: i7 index_id

value: GACTTCATT

value: ATACCGGCA


title: HD 2, PBMC, eTconv, bulk ATAC-seq


title: BTUM_100_749

value: breast cancer

value: adenocarcinoma cell line

value: BTUM

tag: index

tag: i5 index_id

value: GATTGTGTT


title: TGSA_100_750

tag: tissue

tag: cell line

value: TGSA

value: Plate 2D index G


title: HD 1, PBMC, nTconv, bulk ATAC-seq

value: PBMC

value: nTconv cells


title: HD 1, PBMC, naive CD8+ T, bulk ATAC-seq

value: naive CD8+ T cells


title: HD 2, PBMC, eTreg, bulk ATAC-seq

value: eTreg cells


title: HD 1, PBMC, nTreg, bulk ATAC-seq

value: nTreg cells


title: BPAF_100_748

value: BPAF

value: BPAF (Bisphenol AF)

value: F

value: TGCATGACA

value: GCACCTATT

tag: cas-rn

tag: iupac name


title: DCDPS_100_747

tag: cell type

tag: chemical

value: DCDPS

value: Bis (4-chorophenyl) Sulfone

value: GCCGTTACA


title: Dex_1000_757

value: breast cancer

value: adenocarcinoma cell line

value: Dex

tag: chemical long_name

tag: dose

value: GACTTCATT


title: HD 1, PBMC, effector CD8+ T, bulk ATAC-seq

value: PBMC

value: effector CD8+ T cells


title: BPC_100_746

value: BPC

value: BPC (Bisphenol C)

tag: treatment

tag: batch

value: Plate 2D index G

value: ATACGCAGC


title: HD 1, PBMC, eTreg, bulk ATAC-seq

value: eTreg cells


title: HD 1, PBMC, eTconv, bulk ATAC-seq

value: eTconv cells


title: BPA_50_744

value: BPA

tag: sequencing pool

tag: technical control

value: F

value: TAAGGTAGC

value: GGTCTAGCT


title: BPAP_100_745

value: BPAP

value: BPAP (Bisphenol AP)

tag: reference rna

tag: solvent control

value: TGCATGACA

value: TCTAACCAT


title: NSCLC 4, PBMC, effector CD8+ T, bulk ATAC-seq

description:
NSCLC_PBMC_effector_CD8posT_merged.bw
bulkATACseq_peak_lists.txt
bulkATACseq_counts.txt


title: NSCLC 3, PBMC, effector CD8+ T, bulk ATAC-seq


title: BPS-MPE_50_743

value: breast cancer

value: adenocarcinoma cell line

value: BPS-MPE

tag: well

tag: i7 index_id

value: CGTAACTTA


title: NSCLC 4, PBMC, eTreg, bulk ATAC-seq

description:
NSCLC_PBMC_eTreg_merged.bw
bulkATACseq_peak_lists.txt
bulkATACseq_counts.txt

value: PBMC


title: NSCLC 4, PBMC, eTconv, bulk ATAC-seq

description:
NSCLC_PBMC_eTconv_merged.bw
bulkATACseq_peak_lists.txt
bulkATACseq_counts.txt


title: NSCLC 3, PBMC, eTreg, bulk ATAC-seq


title: TGSA_50_742

value: TGSA

value: Plate 2D index G

tag: index

tag: i5 index_id

value: ATACCGGCA


title: DCDPS_50_739

tag: tissue

tag: cell line

value: DCDPS

value: Bis (4-chorophenyl) Sulfone

value: GCCGTTACA


title: BPC_50_738

value: BPC

value: BPC (Bisphenol C)

value: F

value: TAAGGTAGC

value: ATACGCAGC

tag: cas-rn

tag: iupac name


title: NSCLC 3, PBMC, eTconv, bulk ATAC-seq

tag: cell type

value: eTconv cells


title: NSCLC 2, PBMC, effector CD8+ T, bulk ATAC-seq

value: effector CD8+ T cells


title: BPAF_50_740

value: breast cancer

value: adenocarcinoma cell line

tag: chemical

value: BPAF

tag: chemical long_name

value: BPAF (Bisphenol AF)

value: GCACCTATT


title: BTUM_50_741

value: BTUM

tag: dose

tag: treatment

value: Plate 2D index G

value: GATTGTGTT


title: NSCLC 2, PBMC, eTconv, bulk ATAC-seq

value: PBMC


title: NSCLC 1, PBMC, effector CD8+ T, bulk ATAC-seq


title: BPS-MPE_10_735

value: BPS-MPE

tag: batch

tag: sequencing pool

value: TCAGTACAT

value: CGTAACTTA


title: BPA_10_736

value: BPA

tag: technical control

value: F

tag: reference rna

value: GGTCTAGCT


title: BPAP_50_737

value: BPAP

value: BPAP (Bisphenol AP)

tag: solvent control

tag: well

value: TAAGGTAGC

value: TCTAACCAT


title: TGSA_10_734

value: breast cancer

value: adenocarcinoma cell line

value: TGSA

tag: i7 index_id

tag: index

value: ATACCGGCA


title: NSCLC 2, PBMC, eTreg, bulk ATAC-seq

tag: tissue

value: eTreg cells


title: BTUM_10_733

tag: cell line

value: BTUM

value: Plate 2D index G

tag: i5 index_id

value: GATTGTGTT


title: NSCLC 1, PBMC, eTconv, bulk ATAC-seq

value: PBMC

value: eTconv cells


title: NSCLC 4, TIL, eTconv, bulk ATAC-seq

description:
NSCLC_TIL_eTconv_merged.bw
bulkATACseq_peak_lists.txt
bulkATACseq_counts.txt

source_name: tumor

value: tumor


title: NSCLC 4, TIL, effector CD8+ T, bulk ATAC-seq

description:
NSCLC_TIL_effector_CD8posT_merged.bw
bulkATACseq_peak_lists.txt
bulkATACseq_counts.txt

value: effector CD8+ T cells


title: BPAF_10_732

value: BPAF

value: BPAF (Bisphenol AF)

value: F

value: TCAGTACAT

value: GCACCTATT

tag: cas-rn

tag: iupac name


title: BPC_10_730

value: breast cancer

tag: cell type

tag: chemical

value: BPC

value: BPC (Bisphenol C)

value: ATACGCAGC


title: BPAP_10_729

value: adenocarcinoma cell line

value: BPAP

tag: chemical long_name

value: BPAP (Bisphenol AP)

tag: dose

value: TCTAACCAT


title: NSCLC 4, TIL, eTreg, bulk ATAC-seq

description:
NSCLC_TIL_eTreg_merged.bw
bulkATACseq_peak_lists.txt
bulkATACseq_counts.txt

value: eTreg cells


title: DCDPS_10_731

value: DCDPS

value: Bis (4-chorophenyl) Sulfone

tag: treatment

tag: batch

value: Plate 2D index G

value: GCCGTTACA


title: NSCLC 3, TIL, effector CD8+ T, bulk ATAC-seq

value: tumor

value: effector CD8+ T cells


title: BPA_5_728

value: BPA

tag: sequencing pool

tag: technical control

value: F

value: ATTCGCTCT

value: GGTCTAGCT


title: NSCLC 3, TIL, eTconv, bulk ATAC-seq

value: eTconv cells


title: NSCLC 3, TIL, eTreg, bulk ATAC-seq


title: NSCLC 2, TIL, effector CD8+ T, bulk ATAC-seq


title: TGSA_5_726

value: breast cancer

value: TGSA

tag: reference rna

tag: solvent control

value: ATACCGGCA


title: NSCLC 1, PBMC, eTreg, bulk ATAC-seq

value: PBMC


title: NSCLC 1, TIL, effector CD8+ T, bulk ATAC-seq


title: BTUM_5_725

value: adenocarcinoma cell line

value: BTUM

tag: well

tag: i7 index_id

value: GATTGTGTT


title: BPAF_5_724

tag: tissue

value: BPAF

value: BPAF (Bisphenol AF)

tag: index

value: GCACCTATT


title: NSCLC 1, TIL, eTconv, bulk ATAC-seq

value: tumor


title: BPAP_5_721

tag: cell line

value: BPAP

value: BPAP (Bisphenol AP)

value: Plate 2D index G

tag: i5 index_id

value: TCTAACCAT


title: DCDPS_5_723

value: DCDPS

value: Bis (4-chorophenyl) Sulfone

value: F

value: ATTCGCTCT

value: GCCGTTACA

tag: cas-rn

tag: iupac name


title: NSCLC 1, TIL, eTreg, bulk ATAC-seq

tag: cell type

value: eTreg cells


title: BPA_1_720

value: breast cancer

value: adenocarcinoma cell line

tag: chemical

value: BPA

tag: chemical long_name

value: ACTCATGTA

value: GGTCTAGCT


title: BTUM_1_717

value: BTUM

tag: dose

tag: treatment

value: GATTGTGTT


title: BPS-MPE_5_727

value: BPS-MPE

tag: batch

tag: sequencing pool

value: CGTAACTTA


title: HD 3, PBMC, effector CD8+ T, bulk RNA-seq

data_processing:
Bowtie 2 was used to remove reads mapped to ribosomal RNA, and the remaining reads were mapped to the hg38 reference genome using STAR. After mapping, the raw read counts of the mapped reads were counted with featureCounts.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include read counts

source_name: effector CD8+ T cells

extract_protocol: To construct RNA-seq libraries, starting with 100 pg of total RNA, the cDNA was synthesized using a SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio USA, Mountain View, CA) according to the manufacturer’s instructions. One nanogram of amplified cDNA was used to prepare the RNA-seq libraries for Illumina sequencing. The libraries were constructed with a Nextera XT DNA Sample Preparation kit (Illumina, San Diego, CA) according to the manufacturer’s instructions.

treatment_protocol: Peripheral blood and tumor tissues for bulk RNA-seq were obtained from healthy individuals and NSCLC patients who underwent a surgery for curative resection at the National Cancer Center Hospital East. The PBMCs were isolated by the density gradient centrifugation with Ficoll-Paque (GE Healthcare, Chicago, IL, USA). Tumor tissues were cut into small pieces, and single-cell suspensions were prepared with a gentle MACS Dissociator (Miltenyi Biotec, Bergisch Gladbach, Germany) as previously described (PMID: 31028147). Briefly, after filtrating the lung homogenates with a cell strainer (30 μm), the cells were subjected to a density gradient centrifugation with Ficoll-Paque to separate the tumor cells from TILs. Each T cell subset [naive Treg cells (CD45RA+CD25lowFoxP3lowCD4+), eTreg cells (CD45RA–CD25highFoxP3highCD4+), naive Tconv cells (CD45RA+CD25-CD4+), effector Tconv cells (CD45RA-CD25-CD4+), naive CD8+ T cells (CD45RA+CCR7+CD8+) and effector memory CD8+ T cells (CD45RA-CCR7-CD8+) from healthy individuals’ PBMCs; and eTreg cells, eTconv cells and effector memory CD8+ T cells from cancer patients’ PMBCs and TILs] was sorted with a BD FACSAria Fusion Cell Sorter (BD Biosciences, San Jose, CA) for subsequent bulk RNA-seq and Omni-ATAC-seq analyses. Anti-CD3 (clone: UCTH1), anti-CD4 (clone: RPA-T4) and anti-CD45RA (clone: HI100) mAbs were purchased from BD Biosciences. Anti-CCR7 (clone: G043H7) and anti-CD25 (clone: BC96) mAbs were obtained from BioLegend (San Diego, CA). Fixable Viability Dye eFluor 780 was purchased from Thermo Fisher Scientific (Waltham, MA).

value: effector CD8+ T cells


title: TGSA_1_718

value: TGSA

value: Plate 2D index G

tag: technical control

tag: reference rna

value: ATACCGGCA


title: HD 3, PBMC, naive CD8+ T, bulk RNA-seq

source_name: naive CD8+ T cells

value: naive CD8+ T cells


title: HD 3,PBMC, nTconv, bulk RNA-seq

source_name: nTconv cells

value: nTconv cells


title: BPAF_1_716

value: BPAF

value: BPAF (Bisphenol AF)

value: F

tag: solvent control

tag: well

value: GCACCTATT


title: HD 3, PBMC, nTreg, bulk RNA-seq

source_name: nTreg cells

value: nTreg cells


title: BPC_1_714

tag: tissue

value: breast cancer

value: adenocarcinoma cell line

value: BPC

value: BPC (Bisphenol C)

tag: i7 index_id

value: ACTCATGTA

value: ATACGCAGC


title: DCDPS_1_715

tag: cell line

value: DCDPS

value: Bis (4-chorophenyl) Sulfone

tag: index

value: GCCGTTACA


title: NSCLC 2, TIL, eTreg, bulk ATAC-seq

value: tumor

value: eTreg cells


title: BPAP_1_713

value: BPAP

value: BPAP (Bisphenol AP)

value: Plate 2D index G

tag: i5 index_id

value: TCTAACCAT

tag: cas-rn


title: HD 2, PBMC, naive CD8+ T, bulk RNA-seq

tag: cell type

value: naive CD8+ T cells


title: HD 2, PBMC, nTconv, bulk RNA-seq

value: nTconv cells


title: HD 3, PBMC, eTreg, bulk RNA-seq

source_name: eTreg cells


title: HD 2, PBMC, nTreg, bulk RNA-seq

value: nTreg cells


title: HD 2, PBMC,effector CD8+ T, bulk RNA-seq

source_name: effector CD8+ T ce+D62lls

value: effector CD8+ T ce+D62lls


title: NSCLC 2, TIL, eTconv, bulk ATAC-seq

value: eTconv cells


title: BPA_0.5_712

value: breast cancer

value: adenocarcinoma cell line

tag: chemical

value: BPA

value: F

value: GTTTATACT

value: GGTCTAGCT

tag: iupac name


title: HD 2, PBMC, eTconv, bulk RNA-seq

source_name: eTconv cells


title: BPS-MPE_1_719

value: BPS-MPE

tag: chemical long_name

tag: dose

value: ACTCATGTA

value: CGTAACTTA


title: BPC_5_722

value: BPC

value: BPC (Bisphenol C)

tag: treatment

tag: batch

value: ATTCGCTCT

value: ATACGCAGC


title: BPS-MPE_0.5_711

value: Plate 2D index G

tag: sequencing pool

tag: technical control


title: TGSA_0.5_710

value: TGSA

tag: reference rna

tag: solvent control

value: ATACCGGCA


title: BPAF_0.5_708

tag: tissue

value: BPAF

value: BPAF (Bisphenol AF)

tag: well

value: GCACCTATT


title: HD 1, PBMC, naive CD8+ T, bulk RNA-seq

value: naive CD8+ T cells


title: BTUM_0.5_709

value: breast cancer

tag: cell line

value: adenocarcinoma cell line

value: BTUM

value: F

tag: i7 index_id

value: GATTGTGTT


title: HD 1, PBMC, nTconv, bulk RNA-seq

value: nTconv cells


title: HD 1, PBMC, nTreg, bulk RNA-seq

value: nTreg cells


title: HD 1, PBMC, eTreg, bulk RNA-seq

value: eTreg cells


title: HD 1, PBMC, effector CD8+ T, bulk RNA-seq

value: effector CD8+ T cells


title: BPS-MPE_0.1_703

value: BPS-MPE

tag: index

value: GAACTGTAT

tag: i5 index_id

value: CGTAACTTA


title: HD 3, PBMC, eTconv, bulk RNA-seq

tag: cell type

value: eTconv cells


title: HD 1, PBMC, eTconv, bulk RNA-seq


title: BPC_0.5_706

tag: chemical

value: BPC

value: BPC (Bisphenol C)

value: Plate 2D index G

value: GTTTATACT

value: ATACGCAGC

tag: cas-rn


title: DCDPS_0.5_707

value: breast cancer

value: adenocarcinoma cell line

value: DCDPS

tag: chemical long_name

value: Bis (4-chorophenyl) Sulfone

value: GCCGTTACA

tag: iupac name


title: TGSA_0.1_702

value: TGSA

tag: dose

tag: treatment

value: F

value: ATACCGGCA


title: BPA_0.1_704

value: BPA

tag: batch

tag: sequencing pool

value: GGTCTAGCT


title: BTUM_0.1_701

value: BTUM

tag: technical control

tag: reference rna

value: GAACTGTAT

value: GATTGTGTT


title: NSCLC 4, PBMC, eTreg, bulk RNA-seq

value: eTreg cells


title: NSCLC 3, PBMC, eTconv, bulk RNA-seq

value: eTconv cells


title: NSCLC 3, PBMC, effector CD8+ T, bulk RNA-seq

value: effector CD8+ T cells


title: NSCLC 4, PBMC, eTconv, bulk RNA-seq


title: BPAP_0.5_705

tag: tissue

value: BPAP

value: BPAP (Bisphenol AP)

value: Plate 2D index G

tag: solvent control

value: GTTTATACT

value: TCTAACCAT


title: DCDPS_0.1_699

value: breast cancer

tag: cell line

value: adenocarcinoma cell line

value: DCDPS

value: Bis (4-chorophenyl) Sulfone

tag: well

value: GCCGTTACA


title: BPC_0.1_698

value: BPC

value: BPC (Bisphenol C)

value: F

tag: i7 index_id

tag: index

value: ATACGCAGC


title: BPAP_0.1_697

tag: cell type

value: GAACTGTAT

tag: i5 index_id


title: NSCLC 2, PBMC, effector CD8+ T, bulk RNA-seq


title: BPAF_0.1_700

tag: chemical

value: BPAF

value: BPAF (Bisphenol AF)

value: GCACCTATT

tag: cas-rn


title: BTUM_0.01_693

value: BTUM

tag: chemical long_name

value: GGGTTGTTA

value: GATTGTGTT

tag: iupac name


title: NSCLC 1, PBMC, eTconv, bulk RNA-seq

value: eTconv cells


title: NSCLC 1, PBMC, effector CD8+ T, bulk RNA-seq

value: effector CD8+ T cells


title: NSCLC 3, PBMC, eTreg, bulk RNA-seq

value: eTreg cells


title: BPA_0.01_696

value: breast cancer

value: adenocarcinoma cell line

value: BPA

tag: dose

tag: treatment

value: Plate 2D index G

value: GGTCTAGCT


title: NSCLC 2, PBMC, eTreg, bulk RNA-seq


title: BPC_0.01_690

value: BPC

value: BPC (Bisphenol C)

tag: batch

tag: sequencing pool

value: F


title: DCDPS_0.01_691

value: DCDPS

value: Bis (4-chorophenyl) Sulfone

tag: technical control

tag: reference rna

value: GCCGTTACA


title: BPS-MPE_0.01_695

tag: tissue

value: BPS-MPE

tag: solvent control

value: CGTAACTTA


title: TGSA_0.01_694

tag: cell line

value: TGSA

tag: well

value: GGGTTGTTA

value: ATACCGGCA


title: NSCLC 4, PBMC, effector CD8+ T, bulk RNA-seq

value: effector CD8+ T cells


title: NSCLC 2, PBMC, eTconv, bulk RNA-seq

value: eTconv cells


title: NSCLC 1, PBMC, eTreg, bulk RNA-seq

value: eTreg cells


title: NSCLC 6, TIL, effector CD8+ T, bulk RNA-seq


title: BPAF_0.01_692

value: breast cancer

value: adenocarcinoma cell line

value: BPAF

value: BPAF (Bisphenol AF)

tag: i7 index_id

tag: index

value: GCACCTATT


title: BPS-MPE_0.001_687

tag: cell type

value: Plate 2D index G

value: F

value: AAGACTCTT

tag: i5 index_id


title: BPA_0.001_688

tag: chemical

value: BPA

value: GGTCTAGCT

tag: cas-rn


title: NSCLC 6, TIL, eTreg, bulk RNA-seq


title: NSCLC 7, TIL, effector CD8+ T, bulk RNA-seq


title: NSCLC 7, TIL, eTconv, bulk RNA-seq


title: BPAP_0.01_689

value: BPAP

tag: chemical long_name

value: BPAP (Bisphenol AP)

value: TCTAACCAT

tag: iupac name


title: BPAF_0.001_684

tag: dose

tag: treatment


title: NSCLC 7, TIL, eTreg, bulk RNA-seq


title: NSCLC 5, TIL, eTconv, bulk RNA-seq


title: BPC_0.001_682

value: BPC

value: BPC (Bisphenol C)

tag: batch

tag: sequencing pool

value: ATACGCAGC


title: DCDPS_0.001_683

value: DCDPS

value: Bis (4-chorophenyl) Sulfone

tag: technical control

tag: reference rna

value: GCCGTTACA


title: NSCLC 6, TIL, eTconv, bulk RNA-seq

value: eTconv cells


title: NSCLC 4, TIL, eTconv, bulk RNA-seq


title: TGSA_0.001_686

tag: tissue

value: breast cancer

value: adenocarcinoma cell line

value: TGSA

tag: solvent control

value: ATACCGGCA


title: NSCLC 4, TIL, eTreg, bulk RNA-seq

value: eTreg cells


title: BPA_0.0005_680

tag: cell line

value: BPA

value: Plate 2D index G

value: F

tag: well

value: TCCTCAGCC


title: NSCLC 5, TIL, effector CD8+ T, bulk RNA-seq

value: effector CD8+ T cells


title: NSCLC 5, TIL, eTreg, bulk RNA-seq


title: BTUM_0.001_685

value: BTUM

tag: i7 index_id

tag: index

value: AAGACTCTT

value: GATTGTGTT


title: TGSA_0.0005_678

tag: cell type

tag: i5 index_id


title: NSCLC 3, TIL, eTconv, bulk RNA-seq


title: BTUM_0.0005_677

tag: chemical

tag: cas-rn


title: BPAP_0.001_681

value: BPAP

tag: chemical long_name

value: BPAP (Bisphenol AP)

value: TCTAACCAT

tag: iupac name


title: NSCLC 3, TIL, effector CD8+ T, bulk RNA-seq


title: BPS-MPE_0.0005_679

value: BPS-MPE

tag: dose

tag: treatment

value: CGTAACTTA


title: BPC_0.0005_674

value: breast cancer

value: adenocarcinoma cell line

value: BPC

value: BPC (Bisphenol C)

tag: batch

tag: sequencing pool

value: ATACGCAGC


title: NSCLC 2, TIL, eTreg, bulk RNA-seq

value: eTreg cells


title: NSCLC 3 , TIL, eTreg, bulk RNA-seq


title: NSCLC 1, TIL, eTconv, bulk RNA-seq

value: eTconv cells


title: NSCLC 2, TIL, eTconv, bulk RNA-seq


title: No cells; media only_0_672

value: No cells; media only

value: No cells; media only_0

value: Plate 1D index H

tag: technical control

value: T

tag: reference rna

value: F

value: GATAGCGGA

value: GGTCTAGCT


title: DCDPS_0.0005_675

tag: tissue

value: DCDPS

value: Bis (4-chorophenyl) Sulfone

value: Plate 2D index G

tag: solvent control

value: TCCTCAGCC

value: GCCGTTACA


title: NSCLC 4, TIL, effector CD8+ T, bulk RNA-seq

value: effector CD8+ T cells


title: liver tissue, Dengue, Day8 [dengue_5]

first: zheng

last: wenjiang

department: The First Clinical Medical School

institute: Guangzhou University of Chinese Medicine

data_processing:
Libraries were sequenced on the Illumina HiSeq X Ten platform, and 150 bp paired-end reads were 173 generated.
Raw reads in fastq format were first processed using Trimmomatic software (version 0.36), and the low-quality reads were removed to obtain clean reads.
The clean reads were mapped to the Mus musculus genome (GRCm39) using HISAT2 (version 2.2.1.0).
The fragments per kb of transcript per million mapped reads (FPKM) were calculated using Cufflinks software. For the FPKM result see the document named: "Gene expression in each sample FPKM.xls"
The read counts of each gene were obtained with HTSeq-count (version 0.9.1). For the count result see the document named: "Gene expression in each sample counts.xls"
Differential gene expression analysis was performed using the DESeq2 (2014) R package
Assembly: (GRCm39) https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/635/GCF_000001635.27_GRCm39/GCF_000001635.27_GRCm39_genomic.gff.gz
Supplementary files format and content: tab-delimited text files include RPKM and count values for each Sample

source_name: liver

growth_protocol: IFNAR-/- mice on the C57BL/6J background were generated and bred in-house under specific pathogen-free conditions in our laboratory at 21 °C in 55% humidity on a 12:12 h light: dark cycle.

extract_protocol:
Total RNA was extracted from mouse liver tissue using mirVana™ miRNA ISOlation Kit (Ambion-1561) according to the manufacturer’s protocol. 0.5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina (NR604) following the manufacturer's protocols.

treatment_protocol:
Male mice (6-8 weeks old) were challenged intraperitoneally (i.p.) with the DENV-2 TSV01 strain (dengue virus infection group, n=5, 1×10^5 PFU)
Mice injected with an equivalent volume of PBS (mock infection) were used as negative controls (n=5).

value: liver

tag: strain background

tag: genotype

value: IFNAR knockdown

value: dengue virus serotypes -2 (TSV01) i.p.

tag: time

value: Day 8


title: DMSO_667

value: breast cancer

tag: cell line

tag: cell type

value: adenocarcinoma cell line

value: DMSO Pool 2

value: DMSO 0.1%

value: DMSO

tag: well

tag: i7 index_id

tag: index


title: DMSO_668

tag: chemical

tag: chemical long_name

value: Plate 1D index H

value: F

value: T

value: GATAGCGGA

tag: i5 index_id

value: GCACCTATT

tag: cas-rn

tag: iupac name


title: NSCLC 1, TIL, effector CD8+ T, bulk RNA-seq


title: NSCLC 2, TIL, effector CD8+ T, bulk RNA-seq


title: No cells; 1X Lysis buffer_0_671

value: No cells; 1X Lysis buffer

tag: dose

tag: treatment

value: No cells; 1X Lysis buffer_0

tag: batch

tag: sequencing pool

tag: technical control

value: CGTAACTTA


title: No cells; Universal human +ve control_0_669

tag: tissue

value: No cells; Universal human +ve control

value: No cells; Universal human +ve control_0

tag: reference rna

tag: solvent control

value: GATTGTGTT


title: BPAF_0.0005_676

tag: cell line

tag: cell type

value: BPAF

value: BPAF (Bisphenol AF)

value: Plate 2D index G

value: TCCTCAGCC


title: No cells; Brain +ve control_0_670

value: breast cancer

value: adenocarcinoma cell line

value: No cells; Brain +ve control

value: No cells; Brain +ve control_0

tag: well

tag: i7 index_id

value: ATACCGGCA


title: liver tissue, Dengue, Day8 [dengue_1]

value: liver

tag: strain background

tag: genotype

value: IFNAR knockdown

value: dengue virus serotypes -2 (TSV01) i.p.

tag: time

value: Day 8


title: DMSO_666

tag: chemical

value: DMSO Pool 2

tag: chemical long_name

value: DMSO 0.1%

value: DMSO

value: Plate 1D index H

value: F

value: T

tag: index

value: GATAGCGGA

tag: i5 index_id

value: ATACGCAGC

tag: cas-rn


title: liver tissue, Dengue, Day8 [dengue_4]

tag: treatment


title: NSCLC 1, TIL, eTreg, bulk RNA-seq

value: eTreg cells


title: liver tissue, Dengue, Day8 [dengue_2]


title: liver tissue, Dengue, Day8 [dengue_3]


title: 17B-estradiol_10000_662

value: breast cancer

value: adenocarcinoma cell line

tag: dose

tag: batch

tag: sequencing pool

tag: technical control

value: AGCCGATTA

tag: iupac name


title: DMSO_665

tag: tissue

tag: cell line

tag: cell type

tag: reference rna

tag: solvent control

value: TCTAACCAT


title: BPAP_0.0005_673

value: BPAP

value: BPAP (Bisphenol AP)

value: Plate 2D index G

tag: well

tag: i7 index_id

value: TCCTCAGCC


title: Cells, no treatment_0_663

tag: chemical

value: Cells, no treatment

tag: chemical long_name

value: cells, no treatment

value: Cells, no treatment_0

value: CGTAACTTA


title: liver tissue, Control, Day8 [control_2]

value: liver

tag: strain background

tag: genotype

value: IFNAR knockdown

value: PBS i.p.

tag: time

value: Day 8


title: liver tissue, Control, Day8 [control_5]

tag: treatment


title: liver tissue, Control, Day8 [control_3]


title: 17B-estradiol_1000_661

tag: dose

tag: batch

value: Plate 1D index H

value: F

tag: index

tag: i5 index_id

value: GATTGTGTT

tag: cas-rn


title: Cells, no treatment_0_664

tag: tissue

value: breast cancer

tag: cell line

value: adenocarcinoma cell line

tag: sequencing pool

tag: technical control

value: T

value: AGCCGATTA

value: GGTCTAGCT

tag: iupac name


title: liver tissue, Control, Day8 [control_1]


title: 17B-estradiol_100_660

tag: cell type

tag: reference rna

tag: solvent control

tag: well

tag: i7 index_id

value: GCACCTATT


title: 17B-estradiol_10_659

tag: chemical

tag: chemical long_name

value: GCCGTTACA


title: 2,4-BPS_100_655

tag: dose

tag: treatment

value: ACCTGAGGC


title: 17B-estradiol_0.1_657

tag: batch

tag: index

value: TCTAACCAT


title: 17B-estradiol_1_658

tag: i5 index_id

value: ATACGCAGC

tag: cas-rn


title: BADGE_100_652

tag: tissue

tag: cell line

value: BADGE


title: BPS-MAE_100_656

value: BPS-MAE

tag: sequencing pool

tag: technical control


title: Mouse CRC tissue was obtained from wild-type C57 mice with AOM/DSS model, PBS6

city: shanghai

first: Kong

last: Cheng

address: 270 Dong 'an Road

institute: fudan university shanghai cancer center

data_processing:
Using Cell, the official 10X Genomics analysis software Ranger (https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome) to the raw data to identify the data filtering, alignment, quantitative, recycling cells, Finally, the gene expression matrix of each cell was obtained.
The Seurat (https://satijalab.org/seurat/) for further cell filtration, standardization, the classification of the cells, each subgroup analysis and Marker gene screening differentially expressed genes.
Assembly: Mus_musculus.GRCm38.96
Supplementary files format and content: Sample name.gz:contains three files:barcodes.tsv.gz,features.tsv.gz and matrix.mtx.gz.
Supplementary files format and content: cell_batch.tsv.gz:includes cell - sample correspondence.

extract_protocol:
Chromium™ Single Cell 3'Solution is a microfluidics platform built on GemCode technology that combines gel beads with barcodes and primers. Individual cells are encapsulated in oil droplets to form GEM(Gel bead in emulsion).The gel beads in the GEM dissolve and the cells cleave to release mRNA, which is then reverse transcribed to produce cDNA with barcodes for sequencing. After the liquid oil layer is destroyed, cDNA amplification reaction is carried out. After purification, quality inspection is carried out.
Enzymatic digestion interrupted the fragments, end patching was carried out, and base A was added to connect the joints, and the target size fragments were recovered for library quality inspection and quantification.

treatment_protocol: C57BL/6J wild-type (WT) mice were housed and reared in specific pathogen free and barrier conditions with autoclaved food and water. The body weight of mice was measured every week. For AOM/DSS model, 6- to 7-week-old male mice were treated with metronidazole(2mg/ml) in drinking water for 5 consecutive days to ensure the consistency of regular microbiota and facilitate Fn colonization. PBS-resuspended 109 CFU Fn or PBS were administrated into mice by gavage every other day. Then mice were given a single intraperitoneal injection of carcinogen azoxymethane at 12 mg/kg body weight. After 8 days of intraperitoneal injection, 2% dextran sodium sulfate (DSS) was added in the drinking water for 7 consecutive days. Then mice were given regular drinking water. After a week, mice were again given 2% dextran sodium sulfate in drinking water for 7 consecutive days. During the DSS intervention, the bacteria administration was suspended. Bacteria, or PBS administration was given for a period of 10 weeks. To investigate the effect of related therapy on the Fn induced gut tumor progression, At the indicated time intervals, the mice were anaesthetized with 40 mg/kg pentobarbital sodium and sacrificed for tumor statistics.

tag: genotype

value: wild-type mice

value: colorectal tumor tissues PBS administration

tag: agent

value: PBS

tag: strain


title: Mouse CRC tissue was obtained from wild-type C57 mice with AOM/DSS model, PBS3


title: Mouse CRC tissue was obtained from wild-type C57 mice with AOM/DSS model, PBS1


title: liver tissue, Control, Day8 [control_4]

city: Guangzhou

value: liver

tag: strain background

value: IFNAR knockdown

value: PBS i.p.

tag: time

value: Day 8


title: Pergafast201_100_654

value: breast cancer

tag: cell type

value: adenocarcinoma cell line

tag: chemical

value: Pergafast 201

value: Plate 1D index H

value: F

tag: reference rna

tag: solvent control

tag: well

tag: i7 index_id

value: ATACCGGCA

tag: iupac name


title: Mouse CRC tissue was obtained from wild-type C57 mice with AOM/DSS model, FN3

tag: treatment

value: colorectal tumor tissues Fn administration

value: Fusobacterium nucleatum


title: Mouse CRC tissue was obtained from wild-type C57 mice with AOM/DSS model, FN1


title: Mouse CRC tissue was obtained from wild-type C57 mice with AOM/DSS model, FN2


title: BPS_100_651

tag: tissue

value: BPS

tag: chemical long_name

value: Bisphenol S

tag: dose

tag: batch

tag: index

value: ACCTGAGGC

tag: i5 index_id

value: GCCGTTACA

tag: cas-rn


title: D-8_100_650

tag: cell line

tag: sequencing pool

tag: technical control

value: ATACGCAGC


title: 2,4-BPF_100_653

tag: cell type

tag: chemical

value: 2,4-BPF (BPF Analog)

value: GATTGTGTT


title: 4,4-BPF_100_649

value: 4,4-BPF (Bisphenol F)

tag: reference rna

tag: solvent control

value: TCTAACCAT


title: BPS-MAE_50_648

value: breast cancer

value: BPS-MAE

tag: well

tag: i7 index_id

value: TAGCGACAA

value: GGTCTAGCT


title: D-8_50_642

value: adenocarcinoma cell line

tag: treatment

value: Plate 1D index H

value: F

tag: iupac name


title: BPS_50_643

tag: tissue

tag: chemical long_name


title: Pergafast201_50_646

value: Pergafast 201

tag: dose

tag: batch

value: ATACCGGCA