title: LaubLab_RNAseq_WT_CcPxyl-empty_xyl

status: Public on Apr 30 2022

type: SRA

city: Cambridge

first: Kevin

last: Gozzi

state: MA

address: 31 Ames St

country: USA

institute: Massachusetts Institute of Techonology

library_source: transcriptomic

data_processing:
For samples 1-6, paired-end reads were mapped to Caulobacter crescentus NC011916.1 using Bowtie2 (Langmead and Salzberg) with the following command: bowtie2 -p 6 -x NA1000 -1 *1_sequence.fastq -2 *2_sequence.fastq -S output.sam. Subsequently, reads were ordered with samtools: samtools sort -o *output.sam output_sort.sam. Duplicate reads were removed with: samtools view -f 67 -F 256 *output_sort.sam -o *output_filter.sam. Start and end positions of each read were then extracted from the .sam files and recorded across the genome to calculate read density per base pair, and RPKM was found by summing the read density per base pair within each gene across the genome with custom python scripts.
Genome_build: NC_011916.1
Supplementary_files_format_and_content: File ending with .csv: comma-delimited text file of RPKM per gene from RNA-seq data (column 1: gene name, column 2: function, column 3: WT RPKM, column 4: ΔrogA RPKM, column 5: empty glucose RPKM, column 6: empty xylose RPKM, column 7: gafYZ glucose RPKM, column 8: gafYZ xylose RPKM, column 9: log2(wt), column 10: log2(∆rogA), column 11: log2(empty glucose), column 12: log2(empty xylose), column 13: log2(gafYZ glucose), column 14: log2(gafYZ xylose), column 15: log2(∆rogA/WT), column 16: log2(gafYZ xylose/empty xylose))

molecule: total RNA

organism: Caulobacter vibrioides

source_name: Caulobacter crecentus CB15N

growth_protocol: Cultures of Caulobacter crescentus were grown at 30oC in PYE and supplemented with antibiotics, as necessary, to stationary phase  for all samples. For samples 3-6, additional 0.2% glucose or 0.3% xylose were added to repress or induce, respectively, from the xylose promoter for samples 3-6 as indicated before RNA extraction.

extract_protocol:
For samples 1-6, RNA was isolated with Trizol treatment, Direct-zol RNA purification and further acid-phenol:chlroform extraction. rRNA was removed using Ribo-Zero rRNA Removal Kit in Bacteria from Illumina.
Standard library construction for Illumina NextSeq500 sequencing platform. Standard library construction performed by the BioMicroCenter for PacBio SMRTbell sequencing.

treatment_protocol: Samples 3 and 5 were treated with exogenous 0.2% glucose (final concentration) to repress expression from the plasmid. Samples 4 and 6 were treated with exogenous 0.3% xylose (final concentration) to induce expression from the plasmid.

tag: sample type

value: mixed population, stationary phase

tag: genotype

value: CB15N with pBXMCS-2::Pxyl-empty

tag: treatment

value: 0.3% xylose


title: LaubLab_RNAseq_rogA_CcrogA

value: CB15N delta-rogA


title: LaubLab_RNAseq_WT_CcPxyl-gafYZ_xy

value: CB15N with pBXMCS-2::Pxyl-gafYZ


title: LaubLab_RNAseq_WT_CcPxyl-gafYZ_glu

value: 0.2% glucose


title: LaubLab_RNAseq_WT_CcPxyl-empty_glu


title: 21b-R

city: Dali

first: Lihua

last: Yang

address: No. 5, Wenhua Road, Xiaguan Town, Dali Prefecture, Yunnan Province

country: China

institute: Yunnan Institute for Endemic Disease Control and Prevention

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

organism: Yersinia pestis

source_name: bacilli

growth_protocol: Y. pestis strains EV76 were grown on Luria-Bertani (LB) broth at 21°C or 37°C.

extract_protocol:
The SV Total RNA Isolation System (Promega, USA) was used to isolate the total RNA and the RNA quality and quantity were checked using Bioanalyzer (Anilent, USA) and RNA 6000 Nano kit (Anilent, USA)
rRNA was removed using the Ribo-Zero rRNA removal kit, followed by the construction of the cDNA libraries and sequencing on an illumona HiSeq 2500 sequencer (Illumina, USA), using paired-end 2- by 150-bp reads. Gene expression changes were measured by the Reads Per Kilobase Per Million Read (FPKM) and the false discovery rate (FDR) (q value). Differentially expressed genes (DEGs) between the 21°C or 37°C culture groups were calculated by DESeq, and a fold change value of 1.5 and a q value of 0.05 was determined as DEGs.

treatment_protocol: EV76 was cultured at 21°C or 37°C with shaking until OD600 reaches 0.5. The bacteria were collected by centrifugation, immediately frozen with liquid nitrogen, and then stored at -80°C. Three biological repeats were performed

tag: strain

value: Vaccine strain EV76

tag: cell type

value: bacilli

value: Culture at 21 C


title: 37b-R

value: Culture at 37 C


title: 37a-R


title: 21c-R


title: 21a-R


title: 37c-R


title: Spleen-C

city: WuHan

first: Yin

last: Fan

state: HuBei

address: Shizishan street

institute: Huazhong Agricultural University

library_source: genomic

data_processing:
Library strategy: TraDIS
The clean sequencing reads obtained above were aligned to the ExPEC PCN033 (GenBank: CP006632.1) genome using BWA (mem algorithm)
The resulting bam files were sorted by using Sambamba (default parameter) to exclude redundant sequences
DEseq2 was used to compare the change in the total number of insertion reads for each gene between the input and output libraries
Genome_build: CP006632
Supplementary_files_format_and_content: The total number of insertion reads for each gene between the input and output libraries
Supplementary_files_format_and_content: Matrix of changes in the number of reads per gene

molecule: genomic DNA

organism: Escherichia coli PCN033

source_name: Porcine extraintestinal pathogenic Escherichia coli (ExPEC)

extract_protocol:
Bacterial genomic DNA of input libraries and output libraries recovered from mouse brain, spleen, and lung were extracted from using E.Z.N.A.® Bacterial DNA Kit (Omega Bio-Tek, USA)
The genomic DNA was subjected to fragmentation, end repair, and 3' end dA-tailing. The Illumina universal adaptors were added using the TIANSeq Quick Connect Module (Cat# NG303, TIANGEN Biotech, China) which was then purified using Magic DNA Select Beads (Cat# M3022, Magic Bio, China). Primer pair F-/R- was used in the first round PCR amplification for enrichment of the DNA region flaking the transposon. The PCR product was purified and used as the template for the second round amplification using P5/7 primer pair, and the amplification product was purified which was used to construct Illumina sequencing library by using Magic DNA Select Beads (Cat# M3022, Magic Bio, China). The DNA library was sequenced using an Illumina Novaseq sequencer.

tag: infection

value: mouse infection with a transposon mutagenesis library

tag: library type

value: output

tag: bacteria recovered from

value: Spleen


title: Brain-C

value: Brain


title: Spleen-B


title: Brain-A


title: B11_control

type: RNA

city: Kyoto

first: Osamu

last: Araki

state: Kyoto

address: 54 Shogoin-Kawahara-cho, Sakyo-ku

department: Gastroenterology and Hepatology

country: Japan

institute: Kyoto University Graduate School of Medicine

description: Gene expression data from mouse pancreatic cancer cell line established from pancreatic cancer mouse model (Pdx1-Flp; KrasG12D; Trp53 frt/+)

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Array at 45°C for 16hour.

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix).

data_processing: Array data export processing and analysis was performed using Affymetrix® GeneChip Command Console® Software (AGCC).

label: biotin

organism: Mus musculus

source_name: mouse PDAC cells

label_protocol: The sense cDNA was fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit.

growth_protocol: Mouse pancreatic cancer cell lines was established from pancreatic cancer developed in the mice of Pdx1-Flp; Kras FSF-G12D; Trp53 frt/+; Rosa26 FSF-CreERT2; Brg1 lox/lox genotype and cultured with DMEM at 37C.

extract_protocol: RNA extraction with silica-membrane spin columns were performed according to the manufacturer's instructions.

treatment_protocol: In the Brg1 knockout (KO) group, cancer cells were treated with 4-hydroxytamoxifen for five days to ablate Brg1. In the control group, cancer cells were treated with the solvent (methanol) for five days.

tag: mouse model

value: Pdx1-Flp; KrasG12D; Trp53 frt/+

tag: tissue

value: mouse pancreatic cancer cell line

value: control


title: B1_Brg1 KO

description: Gene expression data from mouse pancreatic cancer cell line established from pancreatic cancer mouse model (Pdx1-Flp; KrasG12D; Trp53 frt/+) 5 days after Brg1 ablation

source_name: mouse PDAC cells with Brg1 ablation

value: Brg1 KO


title: B2_Brg1 KO

source_name: mouse PDAC cells with Brg2 ablation


title: Input-C

value: before mouse infection

value: input


title: Input-B


title: Chinese Simmental_rep3

city: Lanzhou

first: Ya

last: zheng

address: No. 1, Yingmen Village, Anning District

institute: Gansu Agricultural University

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the longissimus dorsi reference genome Bos taurus (assembly ARS-UCD1.2) using HISAT2.2.4 with "-rna-strandness RF" and other parameters set as a default.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Bos taurus (assembly ARS-UCD1.2)
Supplementary_files_format_and_content: tab-delimited excel files include count and FPKM values for each Sample

organism: Bos taurus

source_name: longissimus dorsi

growth_protocol: 18 months  age of  longissimus dorsi

extract_protocol:
12th and 13th ribs were collected, immediately frozen in liquid nitrogen, and total RNA was extracted using Trizol reagent kit. mRNA Seq Kit (Illumina) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Angus cattle and Chinese Simmental cattle

tag: organ

value: 12th and 13th ribs

value: longissimus dorsi

tag: breed

value: Chinese Simmental


title: LaubLab_RNAseq_WT_CcWT

value: mixed population, stationary phase


title: Input-A


title: Angus_rep2

value: Angus


title: Chinese Simmental_rep2


title: Angus_rep3


title: Rings -ZNF4_KO

city: Aachen

first: Che

middle: Julius

last: Ngwa

state: NRW

address: Worringerweg 1

department: Cellular and Applied Infection Biology

country: Germany

institute: RWTH University

data_processing:
STAR v2.5.2b (Dobin et al., 2012) was applied to align the reads to the Plasmodium falciparum 3D7 EPr1 (version 43) with default parameters.
Aligned reads were quantified with Stringtie v1.3.6 as described (Pertea et al., 2015).
Counts for transcripts were counted with featureCounts subread v 1.5.1 (Liao et al., 2014) and differential expression analysis were finally conducted by comparing the transcript levels in the RNA samples of the ZNF4-KO and wildtype parasites for each stage using DESeq2 -R version 3.5.1 (Love et al., 2014).
Supplementary_files_format_and_content: Matrix table include TPM values for each Sample (MGC-WT, MGC-ZNF4_KO, Rings_WT, Rings ZNF4KO) ...

organism: Plasmodium falciparum

source_name: Rings  ZNF4-KO RNA

growth_protocol: Plasmodium falciparum parasites were cultivated in vitro in RPMI 1640/HEPES medium (Gibco) supplemented with 10% heat-inactivated human serum and A+ erythrocytes at 5% hematocrit as described (Ifediba and Vanderberg, 1981)

extract_protocol:
RNA was extrated using the Trizol reagent (Invitrogen) according to the manufacturer’s protocol.
Libraries were generated with TruSeq Stranded mRNA Library Preparation kit (Illumina) from high quality total RNA samples according to the manufacturer´s protocol.


title: Rings _WT

source_name: Rings  WT RNA

value: wild type


title: Angus_rep1


title: Lung-B

value: Lung


title: Lung-A

value: mouse infection with a transposon mutagenesis library


title: Mature gametocytes ZNF4-KO

source_name: Mature gametocytes ZNF4-KO RNA


title: B2_control


title: Mature gametocytes WT

source_name: Mature gametocytes WT RNA


title: Spleen-A

value: output


title: Brain-B


title: Lung-C


title: B1_control


title: B11_Brg1 KO

source_name: mouse PDAC cells with Brg3 ablation


title: p53-STV-3

city: Graz

first: Andreas

last: Prokesch

state: Styria

address: Harrachgasse 21/7

department: Institute of Cell Biology, Histology, and Embryology

country: Austria

institute: Medical University Graz

description: starvation medium: HBSS + 10mM HEPES

data_processing:
FastQ sequencing files were processed and analyzed in R
Alignment with STAR to hg38
Reads per gene were counted using featureCounts
Differentially expressed genes between groups were determined using DESeq2 (https://bioconductor.org/packages/release/bioc/vignettes/DESe  q2/inst/doc/DESeq2.html#data-transformations-andvisualization)
DESeq2 paramters used: Variance stabilizing transformation; Wald-Test on individual genes; Benjamini-Hochberg correction for multiple testing; Output genes with adjusted p-value < 0.05 considered significant
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: TPM values were generated using DESeq2. Identifiers are ENSEMBL gene numbers.

organism: Homo sapiens

growth_protocol: HepG2 cells kept in DMEM high glucose + 10%FCS + penicilin/streptomycin

extract_protocol:
RNA was isolated with RNeasy mini kits (QIAGEN); quality was checked with Agilent Bioanalyzer (RNA Nano 6000 chip, avg RIN: 9)
Illumina TruSeq Standard mRNA Library prep kit; quality was checked with Agilent Bioanalyzer (DNA 7500 chip)

treatment_protocol: Electroporation with empty vector or p53 overexpression vector (addgene Plasmid #10838), followed by medium change with growth medium or stavation medium (HBSS + 10mM HEPES)

tag: cell line

value: hepatoma-derived

value: p53 KO

value: p53re-expression starvation medium


title: EV-STV-3

description: starvation medium: HBSS + 10mM HEPES

value: EVcontrol starvation medium


title: p53-STV-2

description: starvation medium: HBSS + 10mM HEPES


title: EV-STV-2

description: starvation medium: HBSS + 10mM HEPES


title: EV-STV-1

description: starvation medium: HBSS + 10mM HEPES


title: p53-MC-2

value: p53re-expression growth medium


title: p53-STV-1

description: starvation medium: HBSS + 10mM HEPES


title: EV-MC-3

value: EVcontrol growth medium


title: EV-MC-2


title: EV-MC-1


title: TLElab_ChIPseq_antiFLAG_Ccres_delta_rogA_gafZflag_replicate1

data_processing:
For analysis of ChIP-seq data, Hiseq 2500 Illumina short reads (50 bp) were mapped back to the Caulobacter NA1000 reference genome (NCBI Reference Sequence: NC-011916.1) using Bowtie 1 (Langmead et al., 2009) and the following command:bowtie -m 1 -n 1 --best --strata -p 4 --chunkmbs 512 NA1000-bowtie --sam *.fastq > output.sam. Subsequently, the sequencing coverage at each nucleotide position was computed using BEDTools (Quinlan and Hall, 2010) using the following command: bedtools genomecov -d -ibam output.sorted.bam -g NA1000.fna > coverage_output.txt. Finally, ChIP-seq profiles were plotted with the x-axis representing genomic positions and the y-axis is the number of reads per base pair per million mapped reads (RPBPM) using custom R scripts.
Genome_build: NC_011916.1
Supplementary_files_format_and_content: Files ending with _coverage.txt: tab-delimited text file of nucleotide-resolution coverage from ChIP-seq data (column 1: genome ID, column 2: nucleotide position, column 3: coverage)

growth_protocol: Cultures of Caulobacter crescentus were grown at 28oC in PYE and supplemented with antibiotics, as necessary, to either exponential phase (for ChIP-seq of rogA) or to stationary phase (for ChIP-seq of GafY and GafZ). Subsequently, formadehyde (1% final concentration, 30 min) were added to fix cells for ChIP-seq.

extract_protocol:
DNA was isolated using the Qiagen Cell Lysis and Protein Precipitation solutions. Detailed protocols are listed in the Supplementary Materials
Standard library construction for Illumina Hiseq2500 sequencing platform

treatment_protocol:
cells were grown to stationary phase (in PYE at 28 degC) before formadehyde were added to 1% (final concentraation) to fix cells for ChIP-seq.
None

tag: developmental stage

value: CB15N delta-rogA gafZ::gafZ-flag


title: Chinese Simmental_rep1


title: TLElab_ChIPseq_antiFLAG_Ccres_delta_rogA_replicate2

value: CB15N delta-rogA


title: TLElab_ChIPseq_antiFLAG_Ccres_delta_rogA_gafZflag_replicate2


title: TLElab_ChIPseq_antiGafY_Ccres_delta_rogAgafY_replicate2

value: CB15N delta-rogAdelta-gafY


title: TLElab_ChIPseq_antiGafY_Ccres_delta_rogAgafY_replicate1


title: TLElab_ChIPseq_antiRogA_Ccres_delta_rogA_replicate2

treatment_protocol:
cells were grown to exponential phase (in PYE at 28 degC) before formadehyde were added to 1% (final concentraation) to fix cells for ChIP-seq.
None


title: TLElab_ChIPseq_antiGafY_Ccres_delta_rogA_replicate2


title: TLElab_ChIPseq_antiFLAG_Ccres_delta_rogA_replicate1


title: TLElab_ChIPseq_antiGafY_Ccres_delta_rogA_replicate1


title: TLElab_ChIPseq_antiRogA_Ccres_delta_rogA_replicate1


title: TLElab_ChIPseq_antiRogA_CcresWT_replicate2


title: TLElab_ChIPseq_antiRogA_CcresWT_replicate1


title: Dam_empty_rep4

first: Dawei

last: Sun

address: Tennis Court Road

department: The Gurdon Institute

country: United Kingdom

institute: University of Cambridge

data_processing:
Library strategy: DamID-seq
Illumina software used for conventional basecalling.
Reads were mapped to a bowtie2 indexed GRCh38 genome assembly (hg38), binned into 5’-GATC-3’ fragments.
Sox9, ETV4 and ETV5 fusion samples were normalized against a paired Dam-only control derived from the same organoid line (RPM normalization, 300 bp bins)
Macs2 (v2.1.2) was used to call broad peaks for each fusion and Dam-only pair using the bam files generated by the damidseq_pipeline.
Peaks were filtered to only those present in all replicates using bedtools (v2.26.0) and surpassing FDR<10-50 for Sox9 and ETV5; FDR<10-25 for ETV4.
Genome_build: GRCh38 genome assembly (hg38)
Supplementary_files_format_and_content: A bigWig file (.bw format) with the average of the different Dam-only normalized replicates. Bed files with the coordinates of the peaks present in all replicates.

source_name: human foetal lung progenitor organoids

growth_protocol: Organoids were maintained with self-renewing medium, conatining EGF, FGF10, FGF7, Noggin, TGFb inhibitor, R-spondin1 and GSK3b inhibitor (detailed protocol in Nikolic et al., 2017).

extract_protocol:
Genomic DNA was extracted and processed as previously described (Marshall et al., 2016).
See method and Marshall et al., 2016

treatment_protocol: Organoids were infected with lentirvus carry the relavant Dam construct and harvested 48-72 hrs after infection.

value: Human feotal lung derived tip progenitor organoids

tag: Stage

value: 8 pcw

tag: damid type

value: Empty


title: p53-MC-3


title: p53-MC-1


title: Dam_empty_rep3


title: Dam_empty_rep2


title: SOX9-Dam_rep4


title: apoEVs_Control_3

city: Nanjing

first: Rongyao

last: Xu

address: 140 Hanzhong Road, Nanjing, Jiangsu Province 210029, China.

institute: Nanjing medical university

data_processing:
After sequencing, raw reads were filtered using fastp software to remove low quality reads and residual Illumina adapters.
After clipping, miRdeep2 software was used to align known miRNAs, allowing for 1 base mismatch.
miRNA expression corresponding to its reads were counted and calculated using edgeR software, whose significant differentially expression were identified by fold change, p-value and fdr between the two groups.
Supplementary files format and content: tab-delimited text files include RPM values for each Sample

source_name: apoEVs from  SIRT6f/f mice

growth_protocol: To collect apoEVs from the apoOBs, osteoblasts reaching approximately 80-90% confluence were induced to apoptosis and cultured in serum-free αMEM for 48 h. Then, the supernatant was harvested and centrifuged at 300×g for 10 min to remove cell lysate, and 2000×g for 15 min to remove cell debris. Subsequently, the apoEVs were isolated by centrifugation at 100,000×g for 70 min twice, and the final pellet was resuspended with 100 µL PBS and stored at -80 °C.

extract_protocol:
Total RNA was extracted from cells using Trizol reagent
Small RNA libraries for RNA-seq were prepared using KAITAI-BIO Small RNA Library Prep Kit following manufacturer's protocols.

value: extracellular vesicles


title: apoEVs_sirt6_1

source_name: apoEVs from  Prx1cre;SIRT6f/f mice


title: apoEVs_sirt6_2


title: apoEVs_sirt6_3


title: apoEVs_Control_2


title: apoEVs_Control_1


title: Dam_empty_rep1


title: SOX9-Dam_rep3


title: SOX9-Dam_rep2


title: mice_9month-old-WT_rep2

city: Beijing

first: li

last: zeng

state: Beijing

address: Institute of Medical Biotechnology, Tiantan Xili, Dongcheng District, Beijing

institute: Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College

data_processing:
Next, the Illumina HiSeq 2500 at the LC-BIO (Hangzhou, China) was employed for the single-end sequencing according to the manufacturer’s recommendations.
Finally, the clean reads were obtained by Cutadapt V1.14 to remove the 3ʹ-adapter (5ʹ-TGG AAT TCT CGG GTG CCA AGG AAC TC-3ʹ) that controls the length between 17 and 35 bp.
Trimmomatic V0.36 was used to delete the low-quality reads (Q < 20), and Blast V2.6.0 was used to remove the RNA families (ribosomal RNA, transfer RNA, small-nuclear RNA, and small-nucleolar RNA) and repeats using comparison conditions that were defined as a gap- open equal to zero, e-value less than 0.01, and mismatch less than 1.
Raw data were analyzed using the Empirical Analysis of Digital Gene Expression Data (edgeR) in R. The frequency of the miRNA counts was normalized as reads per million to analyze the expression pattern of miRNAs between APP/PS1 mice and WT control mice. The expression difference was evaluated using Student’s t-test. Both a fold change greater than 2.0 and a P-value less than 0.05 were considered as standards to distinguish aberrant miRNAs and mRNAs that were significantly dysregulated between the APP/PS1 mice and WT controls at different age groups.
Genome_build: the mouse reference genome (http://asia.ensembl.org/ index.html)
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: ll the mice were given food and water ad libitum and kept in a constant temperature and humidity environment according to the Guide for the Care and Use of Laboratory Animals.

extract_protocol:
RNA was extracted by Invitrogen’s Trizol reagent (Thermo Fisher Scientific, Waltham, MA, USA). following the manufacturer's recommendations.
One microgram of total RNA was used for the construction of the cDNA library using the TruSeq Small RNA Sample Prep Kits (Illumina) according to the manufacturer’s protocol. Next, the Illumina HiSeq 2500 at the LC-BIO (Hangzhou, China) was employed for the single-end sequencing according to the manufacturer’s recommendations. Finally, the clean reads were obtained by Cutadapt V1.14 to remove the 3ʹ-adapter (5ʹ-TGG AAT TCT CGG GTG CCA AGG AAC TC-3ʹ) that controls the length between 17 and 35 bp. Trimmomatic V0.36 was used to delete the low-quality reads (Q < 20), and Blast V2.6.0 was used to remove the RNA families (ribosomal RNA, transfer RNA, small-nuclear RNA, and small-nucleolar RNA) and repeats using comparison conditions that were defined as a gap- open equal to zero, e-value less than 0.01, and mismatch less than 1. To identify novel miRNAs, miRbase V21.0 was used to screen for known miRNA to make a prediction. The unmapped sequences were further searched using miRDeep2 V2.0.0.8, and the mouse reference genome (http://asia.ensembl.org/ index.html) was used to distinguish novel miRNAs and predict their secondary structure (Friedländer et al., 2012).

treatment_protocol: The mice were then sacrificed by cervical dislocation and their brains were quickly removed and preserved via flash freezing in liquid nitrogen.

value: brain


title: SOX9-Dam_rep1


title: mice_6month-old-WT_rep1


title: mice_9month-old-WT_rep1


title: mice_6month-old-WT_rep2


title: mice_6month-old-WT_rep3


title: AD1_alkb-minus

city: Atlanta

first: Andrew

last: Shafik

address: 615 Michael Street

department: Human Genetics

institute: Emory University

description: In this approach, half the sample is treated with Alkb which removes the m1A methylation. As m1A sites are known to impede reverse transcription, m1A sites are detected as a misincorporation in the -Alkb sample compared to the +Alkb control

data_processing:
Reads were aligned to mouse genome (mm10) using hisat2. Default mapping parameters were used, with the option “--trim5 11 ” to remove the unique molecular identifier sequence.
m1A sites were determined using mplieup and Varscan comparing misincorporation rates bewteen the alkb-minus and alkb-plus treatments.
Assembly: mm10
Supplementary files format and content: xls files containing coordinates of m1A sites and misincorporation rates of +/- Alkb treatments.

source_name: Cortex

extract_protocol: Trizol was used to extract total RNA from all samples.

value: 6 month old

value: familial Alzheimer's disease

value: Cortex


title: AD2_alkb-minus


title: WT3_alkb-minus

value: wild type


title: AD2_alkb-plus


title: mice_3month-old-WT_rep3


title: WT2_alkb-minus


title: AD1_alkb-plus


title: mice_3month-old-WT_rep2


title: WT3_alkb-plus


title: mice_3month-old-WT_rep1


title: mice_1month-old-WT_rep2


title: mice_9month-old-APP/PS1_rep2


title: WT1_alkb-plus


title: mice_9month-old-APP/PS1_rep3


title: WT1_alkb-minus


title: mice_6month-old-APP/PS1_rep3


title: mice_1month-old-WT_rep3


title: mice_9month-old-WT_rep3


title: mice_6month-old-APP/PS1_rep1


title: mice_3month-old-APP/PS1_rep3


title: mice_3month-old-APP/PS1_rep2


title: WT2_alkb-plus


title: mice_9month-old-APP/PS1_rep1


title: mice_6month-old-APP/PS1_rep2


title: HDF cells, PD10 as young cells-2

city: swon

first: Tea jun

last: Park

address: 206, World cup-ro, Yeongtong-gu

department: Biochemistry and Molecular Biology

country: South Korea

institute: Ajou University School of Medicine

data_processing:
MGI DNBSEQ-G400 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence then mapped to hg19 whole genome using STAR (version 2.5.4) with parameters -outFilterIntronMotifs RemoveNoncanonicalUnannotated.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated by Cufflinks packages (version 2.2.1).
Differentially expressed genes were detected using Cuffdiff (version 2.2.1) against Ensemble genes.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: skin

growth_protocol: DMEM high glucose medium with 10%FBS

extract_protocol:
extracting RNA was using NucleoSpin mini kit (Macherey-nagel).
RNA libraries for RNA-seq were prepared using MGIEasy RNA Directional Library Prep Kit

treatment_protocol: No treat

value: skin

value: HDF

value: Human dermal fibroblast

value: WT

value: no treat


title: HDF cells, PD 59 as old cells


title: HDF cells, PD 32 as mid old cells-2


title: HDF cells, PD 32 as Control

treatment_protocol: The mid old cells were treated with 100ng/ml of Slit2 (peprotech) during 2days and cell were harevest for RNA extraction.


title: HDF cells, PD 32 as Slit2 100ng/ml treatment

value: Slit2 100ng/ml


title: HDF cells, PD 32 as mid old cells-1


title: mice_1month-old-APP/PS1_rep3


title: mice_1month-old-APP/PS1_rep2


title: mice_3month-old-APP/PS1_rep1


title: HDF cells, PD10 as young cells-1


title: HDF cells, PD 32, co-cultured with mid old cells as control

value: co-cultured with mid old cells


title: HDF cells, PD 32, co-cultured with young cells

value: co-cultured with young cells


title: mice_1month-old-APP/PS1_rep1


title: mice_1month-old-WT_rep1


title: Organoids WT-3

first: Rong

last: Huang

address: 5 Dong Dan San Tiao

institute: Chinese Academy of Medical Sciences and Peking Union Medical College

data_processing:
Reads were trimmed for low-quality sequence, then mapped to mm10 whole genome using STAR v2.6.1d
Genes were annotated using gencode vM16
Read count were calculated by htseq-count v0.11.2
Differential genes were analyzed from DESeq2 library in R, with |fold change|>=2 and p-value <=0.05
Genome_build: mm10

source_name: colorectal

growth_protocol: mice were mainted in a specific pathogen–free facility.

extract_protocol:
colorectal were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For chronic inflammation model, 6-8 weeks RNF138fl/fl and RNF138-/- mice were given 2% (w/v) DSS drinking water by oral administration for 7 days, followed by 14 days regular water. This cycle was repeated two times and mice were sacriﬁced 4 weeks after the last DSS cycle. For colitis-associated CRC model, 6-8 weeks mice were i.p. injected with 10 mg/kg AOM (Sigma, A5486) and kept on 4 days regular diet and water. After 4 days mice received water with 2% DSS for 7 days and followed for 14 days regular water. After this, mice were subjected to two more DSS treatment cycles. For organoids, the intestinal fragments containing tumors were cut off from colitis-associated CRC model, digested and cultured in matrigel.

value: colorectal

tag: sample group

value: colitis-associated CRC model organoid


title: Organoids RNF138 KO-2


title: Organoids RNF138 KO-1


title: Organoids WT-1


title: AOM DSS-RNF138 KO-3

value: colitis-associated CRC model


title: MOLT4 cells, GATA3

city: Ann Arbor

first: Chenguang

last: Wang

state: Michigan

address: 1500E Medical Center Dr, Room 4411

department: Department of Internal Medicine

institute: University of Michigan

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Cutadapt (v2.3)
Trimmed sequence reads were mapped to GRCh38/hg38 using bwa (v0.7.15), all uniquely matched reads were retained
Mapped reads were blacklist, PCR duplicates and multimapping reads filtered using samtools (v0.1.19).
Peak calling was performed by MACS2 (v2.1.2) to generate bed files with following parameters: --nomodel --extsize 50 -f BAMPE --keep-dup auto --min-length 100 -g hs -q 0.05 -B 18
Bigwig(bw) files were generated by Deeptools (v2.0)
Assembly: hg38
Supplementary files format and content: tab-delimited text files include gene counts for each Sample

growth_protocol: All cell lines were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was digested using a Micrococcal Nuclease (CST). Chromatin DNA was purified using QIAquick PCR purification kit. 500ng DNA were used for library preparation.
ChIP-seq libraries were prepared using NEBNext Ultra II FS DNA Library Prep Kit following manufacturer's protocol.

value: T-cell acute lymphoblastic leukemia

tag: chip antibody


title: Organoids WT-2

tag: genotype


title: CCRF CEM cells, GATA3

source_name: CCRF CEM

value: CCRF CEM


title: CCRF CEM cells, input


title: SUP-T1 cells, input


title: THP6 cells, input


title: THP6 cells, GATA3


title: MOLT4 cells, input


title: SUP-T1 cells, GATA3


title: Mac1 cells, input

value: cutaneous T lymphocyte


title: Myla CD4+ cells, GATA3

source_name: Myla CD4+

value: Myla CD4+


title: AOM DSS-RNF138 KO-2


title: AOM DSS-WT-3


title: AOM DSS-RNF138 KO-1


title: Mac1 cells, GATA3


title: Myla CD4+ cells, input


title: AOM DSS-WT-2


title: H9 cells, GATA3


title: AOM DSS-WT-1


title: THP6 cells, GATA-3 knock-down, replicate 2 [THP6_shGATA3-2]

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Cutadapt (v2.3)
Trimmed sequence reads were mapped to GRCh38/hg38 using STAR (v2.7.8a)
Read count extraction and normalization were performed using RSEM (v1.3.3)
Assembly: hg38
Supplementary files format and content: tab-delimited text files include gene counts for each Sample

molecule: polyA RNA

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 50 ng of total RNA was used for the construction of sequencing libraries. For ChIP-seq, cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was digested using a Micrococcal Nuclease (CST). 500ng were used for library preparation.
RNA libraries for RNA-seq were prepared using NEBNext Poly(A) mRNA Magnetic Isolation Module and xGen Broad-range RNA Library Prep following manufacturer's protocols. ChIP-seq libraries were prepared using NEBNext Ultra II FS DNA Library Prep Kit following manufacturer's protocol.

value: Acute Lymphoblastic Leukemia

value: GATA-3 knock down


title: DSS RNF138 KO-2

value: chronic inflammation model


title: THP6 cells, GATA-3 knock-down, replicate 1 [THP6_shGATA3-1]


title: DSS RNF138 KO-3


title: H9 cells, input


title: Organoids RNF138 KO-3


title: DSS WT-3

value: wild type


title: DSS RNF138 KO-1


title: THP6 cells,control, replicate 2 [THP6_scramble2]


title: THP6 cells,control, replicate 3 [THP6_scramble3]


title: DSS WT-1


title: MOLT4 cells,control, replicate 1 [MOLT4_scramble1]


title: MOLT4 cells, GATA-3 knock-down, replicate 1 [MOLT4_shGATA3-1]


title: MOLT4 cells,control, replicate 2 [MOLT4_scramble2]


title: MOLT4 cells, GATA-3 knock-down, replicate 2 [MOLT4_shGATA3-2]


title: RNA-Seq THP1_macrophages_1440min_R1

city: Bethesda

first: Kathleen

middle: Shaindel Metz

last: Reed

state: MD

address: 41 Medlars Dr, B507

department: Genetics and Molecular Biology

institute: National Cancer Institute, NIH

data_processing:
Adapters and low-quality reads were trimmed from paired-end reads using Trim Galore! (version 0.4.3)
Salmon was used in quant mode to quantify reads to hg19 transcripts (version 1.4.0)
Reads were aligned to the hg19 genome using HISAT2 (version 2.1.0)
Alignments were indexed using samtools (version 1.9)
Replicates were merged with samtools (version 1.9)
Alignments were converted to bigwigs using deeptools (version 3.0.1)
Reads were summarized to a gene level using txImport (R version 3.3.1, tximport version 1.2.0)
Differential analysis was completed in DESeq2 (R version 3.3.1, DESeq version 1.33.5)
Assembly: hg19
Supplementary files format and content: quant.sf: tab-delimited file of transcript-level quantifications including transcript ID, length, effective length, TPM, and NumReads, output from Salmon; .bw: bigwig files of signal tracks; .tsv: tab-delimited text file containing information on gene-summarized information including chromosome, start and end coordinates, ENSEMBL and HGNC IDs, differential cluster, DESeq adjusted LRT p-values and LFC, raw counts, variance-stabilize transformed counts, and Z-scored VST counts

source_name: THP1-derived resting macrophages

growth_protocol: THP1 monocytes were grown and maintained in RPMI media with 10% FBS and 1% penicillin-streptomycin. Monocytes were grown to a density of 2x10^5 cells/mL and then differentiated into macrophages using 25 nM PMA for 24 hours. Media was then aspirated off and replaced with PMA-free media and the cells were left to rest for 72 hours.

extract_protocol:
RNA was extracted using the QIAGEN RNeasy Mini kit. With Dnase I treatment. RNA integrity numbers were confirmed using a Tapestation High-Sensitivity RNA tape (<9.8). Concentration was determined using a Qubit HS assay.
Ribosomal RNA was removed using the NEB rRNA Depletion Kit (Human/Mouse/Rat) using 500 ng of RNA as input. Following depletion, RNA-seq libraries were prepared using the NEB Ultra II Directional RNA Library Prep Kit for Illumina, and NEBNext Multiplex Oligos for Illumina. Library concentration and fragment size was determined using Qubit (dsDNA HS assay) and Tapestation (D1000 tape). Libraries from each time point were pooled to a final DNA concentration of 15 nM, and 75-bp paired-end reads were sequenced on an Illumina NextSeq 500 using a High Output Kit.

treatment_protocol: Resting macrophages were treated with a combination of 10 ng/mL lipopolysaccharide (LPS) and 20 ng/mL interferon gamma (IFNg) in fresh RPMI (10% FBS, 1% PS). Cells were harvested without treatment, or 0.5, 1, 1.5, 2, 4, 6, or 24 hours after LPS/IFNg treatment

tag: treatment

value: 24 hr LPS/IFNg

value: THP1 monocytes (differentiated to macropahges)


title: RNA-Seq THP1_macrophages_0360min_R2

value: 6 hr LPS/IFNg


title: RNA-Seq THP1_macrophages_0360min_R1


title: CCRF-CEM cells, GATA-3 knock-down, replicate 3 [CCRFCEM_shGATA3-3]

source_name: CCRF-CEM

value: CCRF-CEM


title: RNA-Seq THP1_macrophages_1440min_R2


title: THP6 cells,control, replicate 1 [THP6_scramble1]

value: WT


title: CCRF-CEM cells, GATA-3 knock-down, replicate 2 [CCRFCEM_shGATA3-2]


title: RNA-Seq THP1_macrophages_0240min_R2

value: 4 hr LPS/IFNg


title: RNA-Seq THP1_macrophages_0240min_R1


title: CCRF-CEM cells,control, replicate 3 [CCRFCEM_scramble3]


title: CCRF-CEM cells, GATA-3 knock-down, replicate 1 [CCRFCEM_shGATA3-1]


title: CCRF-CEM cells,control, replicate 2 [CCRFCEM_scramble2]


title: RNA-Seq THP1_macrophages_0120min_R2

value: 2 hr LPS/IFNg


title: RNA-Seq THP1_macrophages_0120min_R1


title: RNA-Seq THP1_macrophages_0090min_R2

value: 1.5 hr LPS/IFNg


title: RNA-Seq THP1_macrophages_0090min_R1


title: SUP-T1 cells, GATA-3 knock-down, replicate 3 [SUPT1_shGATA3-3]


title: SUP-T1 cells, GATA-3 knock-down, replicate 1 [SUPT1_shGATA3-1]


title: CCRF-CEM cells,control, replicate 1 [CCRFCEM_scramble1]


title: RNA-Seq THP1_macrophages_0060min_R2

value: 1 hr LPS/IFNg


title: DSS WT-2

tag: strain

value: colorectal


title: RNA-Seq THP1_macrophages_0030min_R2

value: 0.5 hr LPS/IFNg


title: RNA-Seq THP1_macrophages_0030min_R1


title: RNA-Seq THP1_macrophages_0060min_R1


title: SUP-T1 cells, GATA-3 knock-down, replicate 2 [SUPT1_shGATA3-2]

tag: cell type


title: SUP-T1 cells,control, replicate 3 [SUPT1_scramble3]


title: SUP-T1 cells,control, replicate 2 [SUPT1_scramble2]


title: SUP-T1 cells,control, replicate 1 [SUPT1_scramble1]


title: ChIP-Seq THP1_macrophages_1440min_R1

data_processing:
Adapters and low-quality reads were trimmed from paired-end reads using Trim Galore! (version 0.4.3)
Reads were aligned to the hg19 genome using BWA mem (version 0.7.17)
Alignments were sorted using Samtools (version 1.9)
Duplicates were removed with PicardTools (version 2.10.3)
Alignments were index using Samtools (version 1.9)
Replicates were merged with samtools (version 1.9)
Alignments were converted to bigwigs using deeptools (version 3.0.1)
Peaks were called from merged alignments using MACS2 (-f BAM -q 0.01 -g hs --nomodel --extsize 200 --keep-dup all -B --SPMR --shift 0; version 2.1.1.20160309)
Peaks were merged among all timepoints using bedtools (version 2.26)
Counts at ATAC peaks were extacted from replicate H3K27ac ChIP-Seq BAM files using bedtools multicov (version 2.26)
Putative enhancers were identified by overlapping ATAC-Seq and H3K27ac ChIP-Seq peaks using bedtools intersect (version 2.26)
Raw counts were used to identify differential enhancers with DESeq2 (version 1.33.5)
Assembly: hg19
Supplementary files format and content: narrowPeak: tab-delimited BED-style file containing peak information from MACS2, including chromosome, start and end coordinates, peak IDs, a peak score, strand info, signal value, p-value, q-value, and peak summit position; .bw: bigwig signal tracks; .tsv: tab-delimited text file containing information on ATAC peaks including chromosome, start and end coordinates, peak names, differential cluster based on H3K27ac ChIP-Seq counts (including "none" if ATAC peak did not overlap a ChIP peak), DESeq adjusted LRT p-values and LFC, raw H3K27ac ChIP-Seq counts within peaks, variance-stabilize transformed counts, and Z-scored VST counts

extract_protocol:
Cells were crosslinked with 1% formaldehyde in RPMI fro 10 minutes with gentle shaking. Cells were then quenched with 10% 2.0 M cold glycine for 5 minutes. Media was then removed and cells were scraped into cold PBS. Cells from each flask (containing 20 million cells total) was divided into 4 tubes of approximately 5 million cells each. Cells were spun down at 526 G for 5 minutes, resuspended in PBS and respun to wash residual formaldehyde. Cells were then frozen in liquid nitrogen and stored at -80 for library preparation
Four frozen cell pellets (5M cells each) were used for each time point. Pellets were first rinsed in 10 mL rinse buffer 1 (50 mM HEPES pH 8, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, Triton-X), incubated on ice for 10 minutes, and then spun down at 2,400 G at 4°C for 5 minutes. Supernatant was removed and the pellets were rinsed again in rinse buffer 2 (10 mM Tris pH 8, 1 mM EDTA, 0.5 mM EGTA, 200 mM NaCl), and spun at the same settings. Supernatant was removed, and 5 mL of shearing buffer (10 mM Tris pH 8, 2% Triton-X, 1% SDS, 100 mM NaCl, 1 mM EDTA) was added to the tubes to wash out the rinse buffer. The samples were centrifuged at 2,400G at 4°C for 3 minutes, the shearing buffer was removed and this step was repeated. The cell pellets were then resuspended in 88 uL of shearing buffer, 2 uL of protease inhibitor cocktail (PIC), and 10 uL of nanodroplets (Triangle Biotechnology, Inc.) per 10 million cells. Samples were aliquoted into 100 uL tubes and sheared using a Covaris E110 (intensity 6, 210 seconds). Cells were spun down at max speed for 2 minutes and the supernatant was retained. Immunoprecipitation of each sheared sample was completed using the Active Motif ChIP-IT High Sensitivity kit, using 2.8 ug of chromatin from each time point (as determined by the lowest yield samples), and 4 ug of anti-H3K27ac antibody (AbCam ab4729). Following overnight antibody incubation and washing steps, crosslinking was reversed by adding 100 uL of elution buffer (described previously) and 4 uL of 5M NaCl to 100 uL of the IP reactions, vortexing, and then incubating overnight at 65°C. DNA was purified using the Zymo ChIP DNA Clean & Concentrator kit, and quantified using Qubit (dsDNA high-sensitivity (HS) assay), as before. Following the final dilution, libraries were prepared using the NEB Ultra II DNA Library Prep Kit with NEBNext Multiplex Oligos for Illumina with 0.88 ng of DNA as input. Libraries were analyzed using Qubit (dsDNA HS assay) and Tapestation (D1000 tape) and pooled to a final concentration of 12 nM, and then 75-bp paired-end reads were sequenced on an Illumina NextSeq 500 using a High Output Kit.

tag: antibody

value: H3K27ac (AbCam ab4729)


title: ChIP-Seq THP1_macrophages_1440min_R2


title: Mac1 cells, GATA-3 knock-down, replicate 2 [MAC1_shGATA3-2]

value: cutaneous T lymphocyte


title: ChIP-Seq THP1_macrophages_0360min_R1


title: Mac1 cells, GATA-3 knock-down, replicate 1 [MAC1_shGATA3-1]


title: MylaCD4+ cells, GATA-3 knock-down, replicate 2 [Myla_shGATA3-2]

value: Myla CD4+


title: RNA-Seq THP1_macrophages_0000min_R1

value: 0 hr LPS/IFNg


title: Mac1 cells,control, replicate 2 [MAC1_scramble2]


title: Mac1 cells,control, replicate 1 [MAC1_scramble1]


title: MylaCD4+ cells, GATA-3 knock-down, replicate 1 [Myla_shGATA3-1]

value: GATA-3 knock down


title: ChIP-Seq THP1_macrophages_0240min_R1


title: ChIP-Seq THP1_macrophages_0120min_R2


title: MylaCD4+ cells, GATA-3 knock-down, replicate 3 [Myla_shGATA3-3]


title: ChIP-Seq THP1_macrophages_0360min_R2


title: ChIP-Seq THP1_macrophages_0240min_R2


title: ChIP-Seq THP1_macrophages_0090min_R2


title: MylaCD4+ cells,control, replicate 3 [Myla_scramble3]


title: MylaCD4+ cells,control, replicate 1 [Myla_scramble1]


title: ChIP-Seq THP1_macrophages_0120min_R1


title: H9 cells, GATA-3 knock-down, replicate 3 [H9_shGATA3-3]


title: MylaCD4+ cells,control, replicate 2 [Myla_scramble2]


title: ChIP-Seq THP1_macrophages_0090min_R1


title: ChIP-Seq THP1_macrophages_0000min_R2


title: ChIP-Seq THP1_macrophages_0000min_R1


title: H9 cells,control, replicate 1 [H9_scramble1]


title: ChIP-Seq THP1_macrophages_0060min_R2


title: H9 cells, GATA-3 knock-down, replicate 2 [H9_shGATA3-2]


title: ChIP-Seq THP1_macrophages_0060min_R1


title: ChIP-Seq THP1_macrophages_0030min_R2


title: ATAC-Seq THP1_macrophages_1440min_R2

data_processing:
Adapters and low-quality reads were trimmed from paired-end reads using Trim Galore! (version 0.4.3)
Reads were aligned to the hg19 genome using BWA mem (version 0.7.17)
Alignments were sorted using Samtools (version 1.9)
Duplicates were removed with PicardTools (version 2.10.3)
Alignments were index using Samtools (version 1.9)
Replicates were merged with samtools (version 1.9)
Alignments were converted to bigwigs using deeptools (version 3.0.1)
Peaks were called from merged alignments using MACS2 (-f BAM -q 0.01 -g hs --nomodel --extsize 200 --keep-dup all -B --SPMR --shift 0; version 2.1.1.20160309)
Peaks were merged using bedtools (version 2.26)
Counts at merged peaks were extacted from BAM files using bedtools multicov (version 2.26)
Assembly: hg19
Supplementary files format and content: narrowPeak: tab-delimited BED-style file containing peak information from MACS2, including chromosome, start and end coordinates, peak IDs, a peak score, strand info, signal value, p-value, q-value, and peak summit position; .bw: bigwig signal tracks

extract_protocol:
Cells were crosslinked with 1% formaldehyde in RPMI fro 10 minutes with gentle shaking. Cells were then quenched with 10% 2.0 M cold glycine for 5 minutes. Media was then removed and cells were scraped into cold PBS. Cells from each flask (containing 20 million cells total) was divided into 4 tubes of approximately 5 million cells each. Cells were spun down at 526 G for 5 minutes, resuspended in PBS and respun to wash residual formaldehyde. Cells were then frozen in liquid nitrogen and storedat -80 for library preparation
ATAC-Seq libraries were prepared using the Omni ATAC-seq protocol as described in Beunrostro et al 2013. Adherent macrophages were washed once with PBS and lifted off of the plate with EDTA for 5 minutes. EDTA was quenched with RPMI, and library preparation was performed on 50,000 cells. 3.75 µL of Illumina Nextera XT indices were used in PCR and qPCR. After performing the initial 5 cycles of PCR, 5% of the PCR reaction was used in qPCR to determine how many additional cycles were required. 4-7 cycles were determined to be sufficient for the final amplification. A 2-sided bead cleanup with AMPure XP beads was performed (0.5X, then 1.3X). Libraries were quantified using Qubit (dsDNA HS Assay) and the KAPA Library Quantification kit. Libraries from each time point were pooled to a concentration of 8 nM or 10 nM for each biological replicate, and 75-bp paired-end reads were sequenced on an Illumina NextSeq 500 using a High Output Kit.


title: Malignant pleural effusions, CD45+CD235a+CD71+

city: Chongqing

first: Qingzhu

last: Jia

address: Xinqiao

department: Department of Onoclogy

institute: XinQiao Hospital

data_processing:
Data was processed with cellranger pipeline, version 3.0.0
Assembly: mm10 for mouse samples, GRCh38 for human samples
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Malignant pleural effusions

extract_protocol:
Ter119+CD71+ splenic cells from anemic mice (A-EPCs), splenic CD45+Ter119+CD71+CD11b-C-kit- cells (T-EPCs), and intratumoral CD45+Ter119+CD71+CD11b+Gr1+ (EDMCs) and CD11b+Gr-1+ (MDSCs) from mice bearing late-stage tumors were sorted by FACS. For patient samples, CD235a+ bone marrow cells from bone-metastasis-free patients with advanced tumors, or CD45+CD235a+CD71+ cells from MPE were sorted by FACS, as indicated. Single cells were suspendend in calcium- and magnesium-free PBS containing 0.04% weight/volume BSA,then the cell suspension was loaded into Chromium microfluidic chips with 3’ chemistry and barcoded with a 10× Chromium Controller
RNA Libraries were constructed using a Chromium Single Cell 3’ v1 Chemistry kit (10x Genomics) according to the manufacturer’s protocol

value: Malignant pleural effusions

tag: cell subtype

value: tumor-bearing


title: ATAC-Seq THP1_macrophages_0360min_R2

value: THP1 monocytes (differentiated to macropahges)


title: ChIP-Seq THP1_macrophages_0030min_R1


title: RNA-seq, iPSC-induced RPE, biol rep3

city: San Francisco

first: Kirsty

last: Jamieson

address: 400 Parnassus Ave

institute: University of California

data_processing:
For libraries having undergone paired-end sequencing, only the first read was used.
Reads were mapped using STAR and GENCODE V19 transcripts were quantified with RSEM using the standard ENCODE parameters.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files including gene expression estimates from RSEM
Supplementary files format and content: Signal tracks in bigwig format (separated for plus and minus strands)

source_name: WTB

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (QIAGEN #74104) according to its protocol.
The TruSeq Stranded mRNA protocol from Illumina was followed for library construction (catalog #RS-122-2101).

value: WTB

value: iPSC-induced RPE

value: wild-type


title: RNA-seq, primary RPE, biol rep2

source_name: RPE

value: RPE

value: healthy


title: H9 cells, GATA-3 knock-down, replicate 1 [H9_shGATA3-1]


title: ATAC-Seq THP1_macrophages_1440min_R1

value: 24 hr LPS/IFNg


title: ATAC-Seq THP1_macrophages_0240min_R2

value: 4 hr LPS/IFNg


title: ChIP-seq, H3K27ac, iPSC-induced RPE, biol rep2

description: ChIP-seq_H3K27ac_iPSC-induced_RPE.narrowPeak

data_processing:
Reads were trimmed to 50 bp and mapped using bowtie2
Picard Tools was used to remove blacklisted regions and duplicate reads
MACS2 was used to call peaks on merged replicates
Assembly: hg38
Supplementary files format and content: Peaks from merged replicates in narrowPeak format
Supplementary files format and content: Signal tracks in bigwig format

extract_protocol:
Cells were washed with PBS and crosslinked with 1% formaldehyde prior to library construction
Libraries were prepared using Tru-seq adapters and size-selected using SPRIselect beads

value: anti-H3K27ac (Active Motif 39133, Lot 22618011)


title: H9 cells,control, replicate 2 [H9_scramble2]

value: WT


title: ATAC-Seq THP1_macrophages_0360min_R1

value: 6 hr LPS/IFNg


title: ATAC-Seq THP1_macrophages_0240min_R1


title: Bone marrow, CD235a+

source_name: Bone marrow

value: Bone marrow


title: ChIP-seq, input, iPSC-induced RPE, biol rep2


title: ChIP-seq, input, iPSC-induced RPE, biol rep1


title: ChIP-seq, H3K27ac, iPSC-induced RPE, biol rep1


title: ATAC-Seq THP1_macrophages_0120min_R1

value: 2 hr LPS/IFNg


title: Capture HiC, primary RPE, biol rep2

description: KJ189_KJ212_ChiCMaxima_interactions.ibed

data_processing:
Mapped and deduplicated reads were then filtered for ditags between 100 and 1200 bp using HiCUP
Biological replicates originating from either two replicates of iPSC-induced RPE or two replicates of primary RPE were merged
Interactions on the merged data sets were called using ChiCMaxima30 with default parameters
Interactions that were less than 2 kb or greater than 1 Mb were filtered out
Assembly: hg38
Supplementary files format and content: Interaction data in ibed format

extract_protocol:
Cells were harvested, fixed in 2% formaldehyde and DNA was digested with DpnII (New England Biolabs #R0543)
Capture HiC was performed on at least 500 ng of each HiC library using custom biotinylated DNA probes designed for the SureSelectXT Target Enrichment System (Agilent Technologies)
Capture HiC


title: ATAC-Seq THP1_macrophages_0090min_R2

value: 1.5 hr LPS/IFNg


title: Capture HiC, primary RPE, biol rep1


title: ATAC-Seq THP1_macrophages_0090min_R1


title: Capture HiC, iPSC-induced RPE, biol rep2

description: KJ184_KJ211_ChiCMaxima_interactions.ibed

source_name: WTC

value: WTC


title: Capture HiC, iPSC-induced RPE, biol rep1


title: ATAC-seq, primary RPE, biol rep3

data_processing:
All reads were trimmed to 50 bp prior to processing. For libraries having undergone paired-end sequencing, only the first read was used.
All libaries were processed using the ENCODE ATAC-seq pipeline.
Optimal IDR and optimal overlap peaks called by MACS2 were used.
Assembly: hg38
Supplementary files format and content: Narrow peaks called in bed format for merged replicates
Supplementary files format and content: Signal tracks in bigwig format for individual libraries

extract_protocol:
Fresh cells were washed with ice cold PBS containing protease inhibitor and nuclei were extracted prior to library construction.
The standard ATAC-seq protocol was used, with the transposase reaction carried out for 30 minutes at 37C. 8-10 cycles of amplification were performed and dual size selection was performed with Ampure XP beads.


title: ATAC-Seq THP1_macrophages_0060min_R1

value: 1 hr LPS/IFNg


title: ATAC-seq, iPSC-induced RPE, biol rep3


title: pediatric_AT2_CKDCI_MRC5_3

city: Boston

first: Feiya

address: 670 Albany street, 2nd floor

institute: Center for Regenerative Medicine, Boston University

data_processing:
Reads were aligned to the ENSEMBL human reference genome GRCh38.92 using STAR
We used the Bioconductor package edgeR to import, filter and normalize the count matrix, followed by the limma package and voom, for linear model fitting and differential expression testing, using empirical Bayes moderation for estimating gene-wise variability prior to significance testing based on the moderated t-statistic.
Genome_build: GRCh38.92
Supplementary_files_format_and_content: raw counts matrix

source_name: pediatric AT2 cells

extract_protocol:
RNeasy Mini Kit (Qiagen)
poly(A) selection & reverse transcription

tag: media

value: CK+DCI

tag: cultureformat

tag: celltype

value: pediatric AT2


title: ATAC-seq, iPSC-induced RPE, biol rep2

value: WTB


title: ATAC-Seq THP1_macrophages_0000min_R2

value: 0 hr LPS/IFNg

value: THP1 monocytes (differentiated to macropahges)


title: ATAC-seq, iPSC-induced RPE, biol rep1

value: iPSC-induced RPE

value: wild-type


title: RNA-seq, iPSC-induced RPE, biol rep2


title: pediatric_AT2_CKDCI_MRC5_2


title: ATAC-Seq THP1_macrophages_0030min_R2

value: 0.5 hr LPS/IFNg


title: ATAC-seq, primary RPE, biol rep1

tag: tissue

value: RPE

value: healthy


title: ATAC-Seq THP1_macrophages_0120min_R2


title: ATAC-Seq THP1_macrophages_0000min_R1


title: pediatric_AT2_CKDCI_MRC5_1


title: siNC, replicate 2

city: Jinan

first: Shan

address: 107 Wenhuaxi Road, Jinan, Shandong, China

institute: Shandong University Qilu Hospital

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit  version 0.0.13 and Perl version 5.8.8
mRNA-seq reads were aligned to the mm10 genome assembly using Tophat version 2.0.6 with parameters: -r 100 -I 50000  --max-segment-intron 50000 -a 10 -g 10
Gene abundance measurements were generationed and normalized  using Cufflink version 2.0.2.Linux_x86_64 ; The normalized standard were Fragments Per Kilobase of exon per Megabase of library size (FPKM)
Differential expression were analysed  using DEGseq function package in R program version 2.10.0

growth_protocol: Ker-CT cells were maintained in cultured in KGM_x001F_Gold™ BulletKit™ in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was harvested using Rneasy mini plus kit (Qiagen).
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: The M5 (IL-17A, IL-22, oncostatin M, IL-1α, and TNF-α, each at a final concentration of 10 ng/ml; PeproTech, Rocky Hill, USA), a cocktail of cytokines, was used to simulate cells to establish psoriatic model

value: skin

value: Ker-CT cells

value: keratinocytes

tag: group

value: siNC

value: M5 for 24h


title: siNC, replicate 3

tag: cell line


title: ATAC-seq, iPSCs, biol rep1

value: iPSCs


title: PBMCs, ADT-derived cDNA

first: Jessica

last: Neely

state: California

address: 550 16th Street

department: Pediatrics

institute: UCSF

description: ADT counts matrix

data_processing:
CellRanger (v3.1.0) was run to align reads to the GRCh38 genome build and generate counts matrices and binary alignment files (BAMs).
Each BAM was inputted into freemuxlet for donor-of-origin annotation and doublet removal. To assign cells to donors of origin in our multiplexed design, we used the genetic demultiplexing tool freemuxlet and a sample matching script, each being part of the popscle suite of population genetics tools (https://github.com/statgen/popscle) to assign cells to donors
Heterotypic doublets detected by demuxlet were removed, and additional homotypic doublets (i.e. two cells from the same individual co-encapsulated) were removed using doubletdetector.
Gene and protein expression matrices (4 each) were subsequently processed using Scanpy (v1.5.1).  A full description of data processing can be found here: https://www.medrxiv.org/content/10.1101/2021.09.18.21263581v1
Genome_build: hg38
Supplementary_files_format_and_content: counts_for_GEO.csv (RNA counts matrix)
Supplementary_files_format_and_content: adts_for_GEO.csv (ADT counts matrix)
Supplementary_files_format_and_content: metadata_for_GEO.csv (sample metadata)
Supplementary_files_format_and_content: long1_umap_coords.csv (UMAP coordinates to reconstruct UMAP)

molecule: protein

source_name: peripheral blood mononuclear cells

extract_protocol:
PBMCs were isolated and cryopreserved until the day of the experiment.
Our experimental protocol followed the manufacturer’s user guide (10X 3’V3 Document CG000185 Rev B, 10X Genomics) with certain modifications to isolate and amplify antibody-derived DNA tags (ADTs). Full details can be found here: https://www.medrxiv.org/content/10.1101/2021.09.18.21263581v1

tag: individual

value: 4 treatment-naïve JDM (TN-JDM) subjects and 4 subjects with inactive disease

tag: time

value: 4 treatment-naïve JDM (TN-JDM) subjects at baseline, 2, 4, and 6 months

value: peripheral blood mononuclear cells (PBMCs)

tag: data type

value: ADT (protein)


title: iAT2_ALI_CKDCI_2

source_name: SPC2-ST-B2corr iATs

value: CK+DCI

value: ALI


title: iAT2_ALI_CKDCI_3


title: iAT2_3D_CKDCI_2


title: ATAC-seq, primary RPE, biol rep2


title: siNC, replicate 1


title: ATAC-Seq THP1_macrophages_0030min_R1

value: THP1 monocytes (differentiated to macropahges)


title: iAT2_3D_CKDCI_1


title: iAT2_ALI_CKDCI_1


title: iAT2_3D_CKDCI_3


title: adult_AT2_CKDCI_MRC5_2

source_name: adult AT2 cells

value: adult AT2


title: siKMT2C, replicate 2


title: Hi-C THP1_macrophages_1440min_R3

data_processing:
Hi-C maps for each sample were generated using the Juicer pipeline as initially described in Rao et al. 2014 (version 1.5.6).
Merged Hi-C maps for each time point as well as a total "mega" map were generated using Juicer (version 1.5.6)
Loops were called from merged timepoint maps at 5kb resolution using SIP (-g 2 -t 2000 -fdr 0.05, version 1.6.1)
Loops were called from merged mega map at 5kb resolution using SIP (-g 1 -t 2000 -fdr 0.05, version 1.6.1)
Loops were extrapolated to 10kb and concatenated, then merged using DBScan while keeping the mean of modes for anchor coordinates (epsilon = 20kb manhattan distance, version 1.1.8)
Counts for merged loops were extracted from Hi-C files of each sample using strawR (no normalization, 10kb resolution, version 0.0.9)
Raw counts were used as input for differential analysis with DESeq2 (LRT, full design ~techRep + bioRep + time, reduced ~techRep + bioRep, version 1.33.5). Significant results were determined based on an absolute LFC greater than 0.585 (fold-change of ±1.5) and an adjusted p-value below 0.05.
Assembly: hg19
Supplementary files format and content: .hic: chromatin contact matrices; .tsv: tab-delimited text file containing information on HiC loops including anchor chromosome, start and end coordinates, SIP loop-calling outputs, loop names, differential clusters, DESeq adjusted LRT p-values and LFC, maps the loops were called in, raw un-normalized counts within loops, variance-stabilize transformed counts, and Z-scored VST counts

extract_protocol:
Cells were crosslinked with 1% formaldehyde in RPMI fro 10 minutes with gentle shaking. Cells were then quenched with 10% 2.0 M cold glycine for 5 minutes. Media was then removed and cells were scraped into cold PBS. Cells from each flask (containing 20 million cells total) was divided into 4 tubes of approximately 5 million cells each. Cells were spun down at 526 G for 5 minutes, resuspended in PBS and respun to wash residual formaldehyde. Cells were then frozen in liquid nitrogen and stored at -80 for library preparation
Libraries were prepared using the in situ Hi-C protocol as described in Rao et al. 2014. For each sample, two frozen cell pellets (5 million cells each) were used to generate separate libraries as technical replicates. Samples were sheared on a Covaris LE 220 (DF 25, PIP 500, 200 cycles/burst, 90 seconds). Illumina TruSeq Nano (Set A) indices were used, and libraries were pooled to 10 nM. Paired-end 150-bp reads were sequenced on one or two lanes of an Illumina NovaSeq S4.

value: 24 hr LPS/IFNg

tag: biological replicate

tag: technical replicate


title: ATAC-Seq THP1_macrophages_0060min_R2

value: 1 hr LPS/IFNg


title: siKMT2C, replicate 1


title: ATAC-seq, iPSCs, biol rep2

value: WTB

tag: genotype

value: wild-type


title: Air-liquid interface culture with cigarette smoke exposure [KA_smoke]

data_processing:
The sample was processed using the standard Cellranger v.2 pipeline
Reads were mapped to GRCh38 with TdTomato reporter
Downstream analysis and QC done on Seurat
Differential expression using MAST models
Genome_build: GRCh38 with TdTomato reporter
Supplementary_files_format_and_content: the processed files are the standard output from the cellranger count pipeline: count matrices compressed in the HDF5  format

source_name: SPC2corr-ST-B2 iAEC2s

growth_protocol: To generate iAEC2s, we performed PSC directed differentiation via definitive endoderm into NKX2-1 lung progenitors using methods we have previously described (Hawkins et al., JCI 2017; Jacob et al., Cell Stem Cell 2017; Jacob et al., Nat Protoc 2019). In brief, cells maintained in mTeSR1 media were differentiated into definitive endoderm using the STEMdiff Definitive Endoderm Kit (StemCell Technologies) for 3 days (day 0-3) and after the endoderm-induction stage, cells were dissociated with gentle cell dissociation reagent and passaged into 6-well dishes pre-coated with growth factor reduced Matrigel in ‘‘DS/SB’’ anteriorization media, consisting of complete serum-free differentiation media (cSFDM) base as previously described (Jacob et al., Cell Stem Cell 2017; Jacob et al., Nat Protoc 2019), supplemented with 2 µM Dorsomorphin (‘‘DS’’; Stemgent) and 10 µM SB431542 (‘‘SB’’; Tocris). For the first 24 hour after passaging, 10 µM Y-27632 was added to the media. After anteriorization in DS/SB media for 3 days (day 3-6), cells were cultured in ‘‘CBRa’’ lung progenitor-induction media until day 15, as we have previously published (Jacob et al., Cell Stem Cell 2017). ‘‘CBRa’’ media consists of cSFDM base supplemented with 3 µM CHIR99021 (Tocris), 10 ng/ml recombinant human BMP4 (rhBMP4, R&D Systems), and 100 nM retinoic acid (RA, Sigma). On day 15 of differentiation, live cells were sorted on a high-speed cell sorter (MoFlo Legacy or MoFlo Astrios EQ) to isolate NKX2-1+ lung progenitors based on CD47hi/CD26neg gating (Hawkins et al., JCI 2017). Sorted lung progenitors were resuspended in undiluted growth factor reduced 3D Matrigel (Corning) at a concentration of approximately 400 cells/µl and distal/alveolar differentiation of cells was performed in CK+DCI media, consisting of cSFDM base supplemented with 3 µM CHIR99021, 10 ng/mL rhKGF (CK), and 50 nM dexamethasone (Sigma), 0.1 mM 8-Bromoadenosine 30,50-cyclic monophosphate sodium salt (Sigma) and 0.1 mM 3-Isobutyl-1-methylxanthine (IBMX; Sigma) (DCI). On day 30, live SFTPCtdTomato+ positive cells were sorted and encapsulated for scRNA-seq using the 10X Chromium System.

extract_protocol:
10X Chromium system
NextSeq 500

tag: culture

value: Air-liquid interface culture

tag: treatment

value: 5% cigarrete smoke exposure


title: Hi-C THP1_macrophages_1440min_R1


title: adult_AT2_CKDCI_MRC5_3


title: Hi-C THP1_macrophages_1440min_R5


title: adult_AT2_CKDCI_MRC5_1


title: Hi-C THP1_macrophages_1440min_R2


title: Air-liquid interface culture [KA_ALI]

value: air


title: Hi-C THP1_macrophages_0360min_R4

value: 6 hr LPS/IFNg


title: 3D sphere culture [KA_3D]

value: 3D sphere culture


title: 2D submerged culture [KA_2D]

value: 2D submerged culture


title: Hi-C THP1_macrophages_0360min_R2


title: ChIPSC22_replicate_3

city: Gothenburg

first: Lars

last: Palmqvist

address: Sahlgrenska University Hospital

department: Institute of Biomedicine

country: Sweden

institute: University of Gothenburg

data_processing:
RNA sequencing was performed using NextSeq 500 instrument (Illumina). The library prep was done with TruSeq Stranded Total RNA Sample Preparation kit with Ribo-Zero Gold.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genome using STAR (version 2.9.0a) with the following parameters: outSAMtype BAM SortedByCoordinate
Quantification of counts for each gene aligned to exons was carried out using HTSeq-count (Python package HTSeq, python v 3.8.1) software using the following parameters -f bam -r pos -s no -m union with the reference annotation file. The human reference genome and annotation files were obtained from the Ensembl database
Differential gene expression was performed using the R package Deseq2 (version "1.31.14").  Genes with log2 (foldchange) 1 and false discovery rate (FDR) adjusted p-value < 0.05 were considered differentially expressed genes
Genome_build: GRCH38(hg38)
Supplementary_files_format_and_content: Excel sheet with  gene counts, log fold change, p-value and adjusted p-value for every gene.

source_name: induced pluripotent stem cells, ChIPSC22

growth_protocol: The human iPSC line ChiPSC22 (Cellartis/Takara Bio Europe) was maintained in the feeder-free DEF-CS culture system under standard conditions.

extract_protocol:
Total RNA was isolated using the RNeasy Plus Mini kit (Qiagen)
The library preparation was done with TruSeq Stranded Total RNA Sample Preparation kit with Ribo-Zero Gold.

treatment_protocol: The cells were transferred to Corning® Matrigel® (BD Biosciences) and mTeSR1 medium (StemCell Technologies Inc.) for 2-3 passages before differentiation to hematopoietic cells utilizing STEMdiff Hematopoietic kit (Stemcell Technologies Inc.) according to protocol.

tag: clone

value: Wildtype

tag: cell type

value: iPSC differentiated into hematopoietic stem and progentitor cells (HSPC)


title: siKMT2C, replicate 3

source_name: skin

value: skin

value: Ker-CT cells

value: keratinocytes

value: M5 for 24h


title: ChIPSC22_replicate_2


title: ChIPSC22_t(7;12)_clone_24C7

value: t(7;12)(q36;p13) translocation


title: Hi-C THP1_macrophages_0240min_R5

value: 4 hr LPS/IFNg

value: THP1 monocytes (differentiated to macropahges)


title: ChIPSC22_replicate_1


title: ChIPSC22_t(7;12)_clone_23G8


title: Hi-C THP1_macrophages_0360min_R1


title: Hi-C THP1_macrophages_1440min_R4

value: 24 hr LPS/IFNg


title: Hi-C THP1_macrophages_0240min_R2


title: Hi-C THP1_macrophages_0240min_R3


title: Hi-C THP1_macrophages_0240min_R1


title: Hi-C THP1_macrophages_0120min_R5

value: 2 hr LPS/IFNg


title: ChIPSC22_t(7;12)_clone_14D7


title: 10T_Super-engaged

city: Utrecht

first: Maria

last: Alieva

state: Netherlands

address: Heidelberglaan 25

country: Netherlands

institute: Prinses Maxima Centrum

description:
10T_vs_13T_exposed_TEGs_counts
10T_vs_13T_exposed_TEGs_metadata

data_processing:
SORTseq data were mapped and reads were counted, using STAR version 2.6.1a on the Hg38p10 human genome (annotated with GenCode v26). Plate-QC was performed using the Sharq pipeline(Candelli et al.). Percentage of ERCC spike-in reads and mitochondrial mRNA reads versus total read count per cell were applied as QC parameters to identify systemic processing or pipetting errors over the plates. Cells with mitochondrial mRNA reads higher than 15%, ribosomal RNA content higher than 30%, or ERCC reads higher than 25% were excluded from the downstream analysis. Cells with fewer than 650 and higher than 4500 genes captured, and genes captured in fewer than 2 cells per plate were also excluded. After the initial QC steps, the ERCC spike-in reads were removed from the final count tables.
Genome_build: Hg38p10
Supplementary_files_format_and_content: The data are in csv format. The table contains  counts and metadata.

source_name: TEG (Super-engaged)  co-cultured with 10T organoids

growth_protocol: TEGs were co-cultured with 10T organoids and isolated from co-culure after 6 hours. TEGs engaged to organoids were separated by centrifugation (pellet) , and put back in culture for 2 hours. After that the procedure was repeated and cells were digested to separate from the organoids and sorted into indivual plate wells from SORTseq.

extract_protocol:
TEGs (>0,8x106 per condition) were  co-cultured with 10T PDOs (E:T of 1: 3) and separated at 4 hrs into organoid-engaged and organoid non-engaged populations by a slow-spin (30 rcf) centrifugation step, co-cultured for another 2h with or without addition of fresh PDOs, again followed 2 slow-spin (30 rcf) centrifugation steps to obtain non-engagedEnriched and super-engaged TEG populations. To create single-cell suspensions, conditions containing organoids (all ‘engaged’ TEG conditions) were treated with TrypLE for seven minutes at 37°C and washed with adDMEM/F12+++. Cells were then stained in FC buffer (2% FCS in PBS) with anti-CD3-APC conjugated antibodies (1:80; BioLegend) and LIVE/DEAD Fixable Near-IR Dead Cell Stain (1:1000; ThermoFisher) for 30 minutes at 4°C and sorted into 384-wells SORTseq plates using a FACS Aria Cell Sorter (BD Biosciences) and directly stored at -80°C until further processing.
All sorted plates were processed according to the CEL-Seq2 protocol with the total transcriptome amplification via poly-A RNA-capture, library preparation, and sequencing into Illumina sequencing libraries as previously described(Muraro et al., 2016). Paired-end sequencing (read1: 30 bp; read2: 120 bp) was used to sequence the prepared libraries using an Illumina NextSeq sequencer.

value: alphaBeta T cells engineered to express a Vgamma9/Vdelta2 T cell receptor

value: Cultured in organoid medium in presence of 10T organoids

tag: response to teg (% organoids killed in 24h)


title: 13T_Super-engaged 2

description:
10T_vs_13T_exposed_TEGs_counts
10T_vs_13T_exposed_TEGs_metadata
Pseudotime_TEGs_counts
Pseudotime_TEGs_metadata

source_name: TEG (Super-engaged)  co-cultured with 13T organoids

growth_protocol: TEGs were co-cultured with 13T organoids and isolated from co-culure after 6 hours. TEGs engaged to organoids were separated by centrifugation (pellet) , and put back in culture for 2 hours. After that the procedure was repeated and cells were digested to separate from the organoids and sorted into indivual plate wells from SORTseq.

extract_protocol:
TEGs (>0,8x106 per condition) were  co-cultured with 13T PDOs (E:T of 1: 3) and separated at 4 hrs into organoid-engaged and organoid non-engaged populations by a slow-spin (30 rcf) centrifugation step, co-cultured for another 2h with or without addition of fresh PDOs, again followed 2 slow-spin (30 rcf) centrifugation steps to obtain non-engagedEnriched and super-engaged TEG populations. To create single-cell suspensions, conditions containing organoids (all ‘engaged’ TEG conditions) were treated with TrypLE for seven minutes at 37°C and washed with adDMEM/F12+++. Cells were then stained in FC buffer (2% FCS in PBS) with anti-CD3-APC conjugated antibodies (1:80; BioLegend) and LIVE/DEAD Fixable Near-IR Dead Cell Stain (1:1000; ThermoFisher) for 30 minutes at 4°C and sorted into 384-wells SORTseq plates using a FACS Aria Cell Sorter (BD Biosciences) and directly stored at -80°C until further processing.
All sorted plates were processed according to the CEL-Seq2 protocol with the total transcriptome amplification via poly-A RNA-capture, library preparation, and sequencing into Illumina sequencing libraries as previously described(Muraro et al., 2016). Paired-end sequencing (read1: 30 bp; read2: 120 bp) was used to sequence the prepared libraries using an Illumina NextSeq sequencer.

value: Cultured in organoid medium in presence of 13T organoids


title: 10T_Non engager enriched

source_name: TEG (Non-engager enriched) co-cultured with 10T organoids

growth_protocol: TEGs were co-cultured with 10T organoids and isolated from co-culure after 4 hours. TEGs that were not engaged to organoids were separated by centrifugation (supernatant), and sorted into indivual plate wells from SORTseq.


title: Hi-C THP1_macrophages_0120min_R4

source_name: THP1-derived resting macrophages


title: Hi-C THP1_macrophages_0360min_R5

value: 6 hr LPS/IFNg


title: Hi-C THP1_macrophages_0120min_R3


title: Hi-C THP1_macrophages_0120min_R2


title: Hi-C THP1_macrophages_0120min_R1


title: Hi-C THP1_macrophages_0360min_R3


title: Hi-C THP1_macrophages_0090min_R5

value: 1.5 hr LPS/IFNg


title: 13T_Super-engaged 1

description:
Pseudotime_TEGs_counts
Pseudotime_TEGs_metadata


title: TEG_medium_exposed control 2

source_name: TEG (medium-exposed)

growth_protocol: TEGs were grown in organoid medium for 6 hours and subjected to SORTseq

extract_protocol:
TEGs (>0,8x106 per condition) were cultured for six hrs without addition of PDOs (no target control), using 12-wells culture plates (Thermo Fischer) and ‘co-culture medium’. To create single-cell suspensions, conditions containing organoids (all ‘engaged’ TEG conditions) were treated with TrypLE for seven minutes at 37°C and washed with adDMEM/F12+++. Cells were then stained in FC buffer (2% FCS in PBS) with anti-CD3-APC conjugated antibodies (1:80; BioLegend) and LIVE/DEAD Fixable Near-IR Dead Cell Stain (1:1000; ThermoFisher) for 30 minutes at 4°C and sorted into 384-wells SORTseq plates using a FACS Aria Cell Sorter (BD Biosciences) and directly stored at -80°C until further processing.
All sorted plates were processed according to the CEL-Seq2 protocol with the total transcriptome amplification via poly-A RNA-capture, library preparation, and sequencing into Illumina sequencing libraries as previously described(Muraro et al., 2016). Paired-end sequencing (read1: 30 bp; read2: 120 bp) was used to sequence the prepared libraries using an Illumina NextSeq sequencer.

value: Cultured in organoid medium


title: 13T Engaged

source_name: TEG (Engaged)  co-cultured with 13T organoids

growth_protocol: TEGs were co-cultured with 13T organoids and isolated from co-culure after 4 hours. TEGs were separated by centrifugation, digested to separate from the organoids and sorted into indivual plate wells from SORTseq.

extract_protocol:
TEGs (>0,8x106 per condition) were co-cultured with 13T PDOs (E:T of 1:3) and separated into organoid-engaged (engaged) and organoid non-engaged (non-engaged) populations by 2 slow-spin (30 rcf) centrifugation steps at 6 h co-culture. To create single-cell suspensions, conditions containing organoids (all ‘engaged’ TEG conditions) were treated with TrypLE for seven minutes at 37°C and washed with adDMEM/F12+++. Cells were then stained in FC buffer (2% FCS in PBS) with anti-CD3-APC conjugated antibodies (1:80; BioLegend) and LIVE/DEAD Fixable Near-IR Dead Cell Stain (1:1000; ThermoFisher) for 30 minutes at 4°C and sorted into 384-wells SORTseq plates using a FACS Aria Cell Sorter (BD Biosciences) and directly stored at -80°C until further processing.
All sorted plates were processed according to the CEL-Seq2 protocol with the total transcriptome amplification via poly-A RNA-capture, library preparation, and sequencing into Illumina sequencing libraries as previously described(Muraro et al., 2016). Paired-end sequencing (read1: 30 bp; read2: 120 bp) was used to sequence the prepared libraries using an Illumina NextSeq sequencer.


title: Hi-C THP1_macrophages_0090min_R4


title: 13T_Non engager enriched 1

source_name: TEG (Non-engager enriched) co-cultured with 13T organoids

growth_protocol: TEGs were co-cultured with 13T organoids and isolated from co-culure after 4 hours. TEGs that were not engaged to organoids were separated by centrifugation (supernatant), and put back in culture for 2 hours. After that the procedure was repeated and cells were then sorted into indivual plate wells from SORTseq.


title: Hi-C THP1_macrophages_0240min_R4


title: TEG_medium_exposed control 1

extract_protocol:
TEGs (>0,8x106 per condition) were cultured in normal medium without addition of PDOs (no target control), using 12-wells culture plates (Thermo Fischer) . Cells were then stained in FC buffer (2% FCS in PBS) with anti-CD3-APC conjugated antibodies (1:80; BioLegend) and LIVE/DEAD Fixable Near-IR Dead Cell Stain (1:1000; ThermoFisher) for 30 minutes at 4°C and sorted into 384-wells SORTseq plates using a FACS Aria Cell Sorter (BD Biosciences) and directly stored at -80°C until further processing.
All sorted plates were processed according to the CEL-Seq2 protocol with the total transcriptome amplification via poly-A RNA-capture, library preparation, and sequencing into Illumina sequencing libraries as previously described(Muraro et al., 2016). Paired-end sequencing (read1: 30 bp; read2: 120 bp) was used to sequence the prepared libraries using an Illumina NextSeq sequencer.


title: Hi-C THP1_macrophages_0090min_R2


title: Hi-C THP1_macrophages_0090min_R3


title: ChIPSC22_t(7;12)_clone_16F3


title: Hi-C THP1_macrophages_0090min_R1


title: Hi-C THP1_macrophages_0060min_R4

value: 1 hr LPS/IFNg


title: Hi-C THP1_macrophages_0060min_R5


title: TEGs non-exposed to organoids (control condition) SORTseq

description:
Non_exposed_TEGs_counts
Non_exposed_TEGs_metadata

source_name: TEG (non-exposed)

growth_protocol: TEGs were grown under normal conditions and subjected to SORTseq

value: Untreated


title: RNA-Seq THP1_macrophages_0000min_R2

extract_protocol:
RNA was extracted using the QIAGEN RNeasy Mini kit. With Dnase I treatment. RNA integrity numbers were confirmed using a Tapestation High-Sensitivity RNA tape (<9.8). Concentration was determined using a Qubit HS assay.
Ribosomal RNA was removed using the NEB rRNA Depletion Kit (Human/Mouse/Rat) using 500 ng of RNA as input. Following depletion, RNA-seq libraries were prepared using the NEB Ultra II Directional RNA Library Prep Kit for Illumina, and NEBNext Multiplex Oligos for Illumina. Library concentration and fragment size was determined using Qubit (dsDNA HS assay) and Tapestation (D1000 tape). Libraries from each time point were pooled to a final DNA concentration of 15 nM, and 75-bp paired-end reads were sequenced on an Illumina NextSeq 500 using a High Output Kit.

value: 0 hr LPS/IFNg


title: 209M organoids

data_processing:
Reads were been mapped to the GRCh37 version of the human reference genome. Quality control on the bams was done using Picard. Read counts were generated with Htseq-count after which normalization is done using DESeq. RPKMs have been calculated with edgeR.
Genome_build: GRCh37
Supplementary_files_format_and_content: The data are in txt format. The table contains raw counts or normalized counts (*ndata.txt).

source_name: Patient derived breast cancer organoids (209M)

growth_protocol: Organoids were grown in normal conditions and harvested and RNA was isolated according to the manufacturer’s protocol using the RNeasy Mini Kit (QIAGEN)

extract_protocol:
RNA was isolated according to the manufacturer’s protocol using the RNeasy Mini Kit (QIAGEN)
Quality and quantity of the RNA samples and the libraries were measured with Agilent’s Bioanalyzer2100 and Invitrogen™ Qubit™ 3.0 Fluorometer. Quality control was done using FastQC, alignment has been done using STAR (https://github.com/alexdobin/STAR/releases/tag/STAR_2.4.2a  ) and reads have been mapped to the GRCh37 version of the human reference genome. Quality control on the bams was done using Picard. Read counts were generated with Htseq-count after which normalization is done using DESeq. RPKMs have been calculated with edgeR. For the library preparation the TruSeq Stranded mRNA Library Prep kit from Illumina was used. Sequencing was performed on the nextseq500 sequencer (also Illumina) with single-end 75bp reads.

treatment_protocol: NA. Organoids were grown in normal conditions (no TEG exposure) (Dekkers et al 2021, Nature protocols)

value: Breast metastasis derived organoids


title: Hi-C THP1_macrophages_0060min_R3


title: 100T organoids

source_name: Patient derived breast cancer organoids (100T)

value: Breast tumor derived organoids


title: 13T_Non engager enriched 2

growth_protocol: TEGs were co-cultured with 13T organoids and isolated from co-culure after 4 hours. TEGs that were not engaged to organoids were separated by centrifugation (supernatant), and sorted into indivual plate wells from SORTseq.


title: 34T organoids

source_name: Patient derived breast cancer organoids (34T)


title: 27T organoids

source_name: Patient derived breast cancer organoids (27T)


title: Hi-C THP1_macrophages_0060min_R2


title: Hi-C THP1_macrophages_0030min_R5

value: 0.5 hr LPS/IFNg


title: Hi-C THP1_macrophages_0060min_R1


title: Hi-C THP1_macrophages_0030min_R4


title: 36T organoids

source_name: Patient derived breast cancer organoids (36T)


title: Hi-C THP1_macrophages_0030min_R2


title: Hi-C THP1_macrophages_0030min_R1


title: Hi-C THP1_macrophages_0000min_R5


title: 1837M organoids

source_name: Patient derived breast cancer organoids (1837M)


title: 169M organoids

source_name: Patient derived breast cancer organoids (169M)


title: Hi-C THP1_macrophages_0000min_R3


title: Hi-C THP1_macrophages_0000min_R1


title: Hi-C THP1_macrophages_0000min_R2


title: 38T organoids

source_name: Patient derived breast cancer organoids (38T)


title: 25T organoids

source_name: Patient derived breast cancer organoids (25T)


title: Hi-C THP1_macrophages_0030min_R3


title: 13T organoids

source_name: Patient derived breast cancer organoids (13T)


title: 62T organoids

source_name: Patient derived breast cancer organoids (62T)


title: HRT18-highpx-3

city: Cheongju

first: Jiyeong

last: Noh

address: Chungdae-ro 1

institute: Chungbuk National University

data_processing:
Raw sequences were checked the quality of the data  with FastQCv0.11.7 program before proceeding.
The adapter sequences were removed using BBDuk adaptor and quality trimming version 38.84 (Bushnell, B.,2014).
The trimmed reads of the low-passaged and high-passaged virus were mapped to the sequence of shaan virus (GenBank accession number. MG230624.1) using the Geneious Prime Bowtie 2 plugin version 2.3.0.
Transcript expression level in cells infected with shaan virus were calculated based on annotation on a reference shaan virus (MG230624.1). The transcript abundance was counted and normalized to the TPM (Transcript per Million mapped reads) value considering the read count, transcript length, and depth of coverage.
Assembly: Genbank accession no. MG230624.1

growth_protocol: MARC-145 cell lines derived from African green monkey kidney, were cultured in DMEM (Gibco, NY, USA, Cat.11995) supplemented with antibiotic-antimycotic (100 IU/mL penicillin, 100 ug/mL streptomycin, and 0.25 µg/mL amphotericin B, Gibco, NY, USA, Cat.15240) and 10% foetal bovine serum (Hyclone, NY, USA, Cat.SV30207). HEK-293, A549, and HRT18 cell lines of human kidney, lung, and colon origin, were cultured in MEM(Gibco, NY, USA, Cat.10370) and RPMI1640(Gibco, NY, USA, Cat.A10491) media with 10% foetal bovine serum (FBS) and antibiotic-antimycotic, respectively. All cells were maintained in an incubator at 37℃ with 5% CO2. Shaan virus isolate (B16-40, Genbank accession no. MG230624.1) was cultured in MARC-145 cells. To amplify the isolated shaan virus B16-40, 1 × 105/mL of MARC-145 cells were seeded into tissue culture flasks in DMEM (5% FBS) and incubated overnight. A monolayer of MARC-145 cells was infected with shaan virus (B16-40) at a multiplicity of infection (MOI) of 0.1 and the cytopathic effect (CPE) was confirmed in infected cells at 5 days post-inoculation (DPI). The virus harvested by freeze-thawing the infected cells was further used to infect a new monolayer of MARC-145 cells for the next passages.

extract_protocol:
The infected cell pellets were resuspended to 250µl with fresh medium, to extract RNA for the high-throughput sequencing.
The RNA libraries were prepared with illumine TruSeq Strand Total RNA LT kit and illumine NovaSeq6000 plaform form Macrogen, Inc (Seoul, Korea) for high throughput sequencing accroding to the manufacturer's instruction.

treatment_protocol: The prepared low- (p4) and high passaged shaan virus (p44) in MARC-145 cells were inoculated in triplicate to different host cells, HEK-293, A549, and HRT18 cell lines at M.O.I of 0.5 for 2 hours. The infected cells were incubated with the maintenance medium for each cell line for 24hrs.

value: Colon

value: Epithelial cells

value: infected with Shaan virus p43


title: HRT18-lowpx-3

value: infected with Shaan virus p3


title: HRT18-highpx-2


title: 10T organoids

source_name: Patient derived breast cancer organoids (10T)


title: HRT18-lowpx-1


title: Hi-C THP1_macrophages_0000min_R4

source_name: THP1-derived resting macrophages

value: THP1 monocytes (differentiated to macropahges)


title: HEK293-highpx-3

value: kidney


title: HEK293-highpx-2


title: HEK293-highpx-1


title: Human Dermal Endothelial Cells-2

city: Los Angeles

first: Joshua

last: Sasine

state: CA

address: 8700 Beverly Blvd., AHSP, #8110B

institute: Cedars-Sinai Medical Center

hyb_protocol: The samples were  fragmented and hybridised onto Affymetrix GeneChip® Human Genome U133 Plus 2.0 arrays (Affymetrix, High Wycombe, Bucks, UK).

scan_protocol: Arrays were scanned using an Affymetrix Scanner 3000. GCOS software (Affymetrix) was used to monitor scanning and to convert the raw image files into cell intensity files (.CEL).

data_processing: Affymetrix GeneChip® CEL files for the samples assayed were imported into the Affymetrix Expression Console™ software to perform gene level normalization and signal summarizations. Affymetrix Transcriptome Analysis Console (TAC) software was used to analyze the differential gene expression between the cell types. Robust multi-array average (RMA) values generated in the Affymetrix Expression Console software from this gene list were imported into Partek® microarray data analysis software (Partek Inc., St. Louis, MO).

source_name: Human Dermal Endothelial Cells

label_protocol: Biotinylated cRNA probes were prepared from the total RNA samples (1µg) using the microarray target amplification kit and the microarray target RNA synthesis kit (both Roche Applied Sciences) following the manufacturer's instructions.

growth_protocol: Flasks or 24-well plates were precoated with 10% gelatin for 30 minutes, then washed with PBS. Endothelial cells purchased from ATCC were cultured in Endothelial Complete Culture Media (Lonza). Once they were 80% confluent, BMECs were detached using a mixture of 0.05% Trypsin and Versene at a 1:8 ratio. This was inactivated with 5 times the volume of Endothelial Complete Culture Media (Lonza). The cells were then centrifuged and RNA extracted.

extract_protocol: RNA was isolated using the QIAGEN® RNeasy micro kit (QIAGEN, Santa Clarita, CA).Total RNA were assessed for quality with Agilent 2100 Bioanalyzer G2939A (Agilent Technologies,Santa Clara, CA) and Nanodrop 8000 spectrophotometer (Thermo Scientific/Nanodrop, Wilmington, DE).

value: Human Dermal Endothelial Cells


title: Human Dermal Endothelial Cells-6


title: Human Dermal Endothelial Cells-4


title: Human Dermal Endothelial Cells-1


title: HEK293-lowpx-2


title: Human Dermal Endothelial Cells-5


title: HRT18-highpx-1


title: 14T organoids

source_name: Patient derived breast cancer organoids (14T)


title: HRT18-lowpx-2


title: Human Aortic Endothelial Cells-6

source_name: Human Aortic Endothelial Cells

value: Human Aortic Endothelial Cells


title: Human Dermal Endothelial Cells-3


title: Human Aortic Endothelial Cells-5


title: HEK293-lowpx-1


title: 63N

city: Tainan

first: Wenya

address: No.1, University Road

country: Taiwan

institute: NCKU

description: gene expression of surgical liver resection of HCC patients

hyb_protocol: cRNA was hybridized on Agilent-014850 Whole Human Genome Microarray 4x44K.

scan_protocol: Arrays were scanned using the Agilent Microarray Scanner (Agilent G2565BA) according to the manufacturer’s protocol.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Normal - 63

label_protocol: Cyanine-3 (Cya3) labeled cRNA was prepared from 2000 ng RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent).

extract_protocol: Total RNA was extracted from the tumorous and adjacent nontumorous HCC tissues using TRIzol reagent (Sigma-Aldrich) and then reverse transcribed into cDNA.

treatment_protocol: The patients were regularly followed up at clinic visits every 1-3 months after hepatic resection. HCC recurrence was detected by medical imaging and biopsy confirmation. All the patients provided signed informed consent to use their surgical specimens for this research.

value: liver

tag: gender

value: Female

tag: age


title: 63T

source_name: Tumor - 63


title: Human Aortic Endothelial Cells-4


title: Human Aortic Endothelial Cells-3


title: A549-highpx-1

value: Lung


title: A549-highpx-3


title: A549-lowpx-3


title: A549-highpx-2


title: 61T

source_name: Tumor - 61


title: HEK293-lowpx-3


title: A549-lowpx-1


title: Fmr1 KO+RA-3

city: shanghai

first: zhixiong

last: xia

address: yueyang road 320

institute: SIBCBs

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using fastp software. Then sequence were mapped to mm10 whole genome using hisat2 (version 2.1.0) with default parameters.
Reads count were calculated using htseq-count software with default parameters.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: prefrontal cortex

extract_protocol:
prefrontal cortex were removed, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: WT and Fmr1 KO mice (4 weeks old) were administered daily with RA  dissolved in olive oil via oral gavage for one month, at the dosage of 5 mg/kg. The WT group received the olive oil only.

tag: strain

value: prefrontal cortex

value: RA


title: Fmr1 KO+RA-2

tag: tissue


title: A549-lowpx-2


title: Fmr1 KO+Oil-2

value: oil


title: Fmr1 KO+RA-1


title: Human Aortic Endothelial Cells-2


title: Fmr1 KO+Oil-3


title: Fmr1 KO+Oil-1


title: 61N

source_name: Normal - 61


title: 13T_Non engaged

source_name: TEG (non-engaged)  co-cultured with 13T organoids

growth_protocol: TEGs were co-cultured with 13T organoids and isolated from co-culure after 6 hours. TEGs that were not engaged to organoids were separated by centrifugation (supernatant), and sorted into indivual plate wells from SORTseq.

value: alphaBeta T cells engineered to express a Vgamma9/Vdelta2 T cell receptor

value: Cultured in organoid medium in presence of 13T organoids


title: 4N

source_name: Normal - 4

value: Male


title: 4T

source_name: Tumor - 4


title: WT+RA-3

value: wild type


title: Human Aortic Endothelial Cells-1


title: 62N

source_name: Normal - 62


title: WT+RA-1


title: WT+RA-2


title: WT+Oil-3


title: WT+Oil-2


title: RCDII-2

city: Leiden

first: Tessa

last: Dieckman

address: Albinusdreef 2

department: Immunology

institute: LUMC

data_processing:
Pre-processing with Cell Rangr software v2.2.0.
Genome_build: GrCh38
Supplementary_files_format_and_content: Tab-separated value file with barcodes for every cell in every sample
Supplementary_files_format_and_content: Tab-separated value file with names for every gene in every sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: duodenum

extract_protocol:
Intraepithelial lymphocytes (IELs) were isolated from duodenal biopsies by treatment with HBSS/1 mM EDTA (made in-house; J.T. Baker) rolling for 2x 45 min at 37°C. Cells were collected in 20% FCS/RPMI and kept at 4°C. Subsequently, single-cell suspensions were obtained from the lamina propria (LP) by  1.5 hours enzymatic treatment with 10 units/mL collagenase IV (Worthington) and 200 µg/ml DNase I grade II (Roche). For obtainment of single cells, LP cells and IELs were resuspended and passed through a 70 µm cell strainer. Cells were washed with 0.5% FCS/DPBS (Dulbecco’s Phosphate Buffered Saline) (Gibco, Thermo Fisher) by centrifuging at 1650 rpm for 10 min. Hereafter, cells were treated with red blood cell lysis buffer (LUMC pharmacy) and removal of dead cells was performed using microbeads (Miltenyi Biotec). Lastly, live CD45+ cells were positively selected using MACS beads (Miltenyi Biotec).
Chromium 3' Single cell platform (10X Genomics)

value: duodenum

tag: disease state

value: Refractory Celiac Disease type II

value: single intra-epithelial and lamina propria CD45+ lymphoyctes

tag: Sex

value: F

tag: aberrant of total iels

tag: pa

value: Marsh 0

tag: hx of rcdii therapy

value: 2008 small jejunal resection with adjuvant 6x CHOEP


title: RCDII-1

value: M

value: Marsh 3A

value: 2017 anti-IL-15 monoclonal, 2007 auSCT, prev cladribine


title: 28T

source_name: Tumor - 28

value: liver

value: Female


title: J76

city: Guangzhou

first: Lipeng

last: Mao

state: Guangdong

address: No.601, West Huangpu Avenue

department: Department of Microbiology and Immunology

institute: Jinan University

data_processing:
Illumina Casava1.7 software used for basecalling.
The original data of ATAC-seq were considered pre-analysis. The experimental process of ATAC-seq analysis includes pre-alignment quality control (QC), read alignment to a reference genome, and post-alignment QC and processing. The sequence was posted back to the reference genome by Bowtie2 software and the repetitive sequences were removed by SAM tools. In order to facilitate reading and visualization, deep tools were used for visualization, MACS2 for peak calling, data was converted into BAM file format, and then peak annotation, GO enrichment and motif analysis were carried out, respectively
Assembly: Homo sapiens Ensembl 94
Supplementary files format and content: peak files, bw files

source_name: Cell line

growth_protocol: The underlined region corresponds to the double-stranded portion of the adapter-ME sequence identified by the transposase.

extract_protocol:
The number of 293T cells and J76 cells in the logarithmic growth phase was counted by hemacytometer. 50000 cells were added to PCR tubes and centrifuged at 4 ºC at 600 x g for 5 min, discarded the supernatant. The pre-cooled 0.1% NP-40 lysis buffer solution was added to the cell precipitate and pipetted until homogeneous. The cells were lysed on ice for 3 minutes. After centrifugation at 4 ºCa t 550 x g for 5 min, discard the supernatant.
The two kinds of DNA samples were cut by adding the self-made Tn5 transposase mixed system into the precipitation, and the library was constructed before ATAC-seq sequencing. The reaction system was10 µl 5 x TAPS-MgCl2-PEG 8000, 32 µl H2O, 8 µl 0.96 µg/µl Tn5 enzyme. The reaction conditions were the same as 1.2.3 enzyme activity detection.  The DNA of Tn5 reaction system samples was purified by an Omega PCR purification kit. The purified DNA samples were collected and amplified by PCR. The DNA samples were sent to Guangzhou Nuo He Zhi Yuan Company for sequencing. A portion of the DNA was used for Q-PCR to measure the concentration of DNA.

tag: cell line

value: human acute T-lymphoblastic leukemia cells


title: WT+Oil-1

value: prefrontal cortex

value: oil


title: 28N

source_name: Normal - 28