title: HCMVInd

city: Shenyang

first: Jingui

last: Deng

state: Liaoning

address: No.36 Sanhao Street, Heping District

department: Virus Laboratory

institute: the Affiliated Shengjing Hospital, China Medical University

data_processing:
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.16.1).
Gene Ontology (GO) enrichment analysis and KEGG pathways of statistical enrichment of differentially expressed genes was implemented by the clusterProfiler R package
Genome_build: FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Supplementary_files_format_and_content: excel files including differential express gene for each pair sample was achieved for RNA-seq.

source_name: Mesenchymal stem cells

extract_protocol:
Total RNA of each sample was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: SHEDs-derived neuron-like cells with HCMV infection

value: Mesenchymal stem cells

tag: treatment/status

value: differentiated,infected


title: IL21 CBNK GBM Day 9 coculture 124610 ATAC

status: Public on Jul 09 2024

type: SRA

city: HOUSTON

first: Katayoun

last: Rezvani

state: TX

address: 1515 Holcombe Blvd

country: USA

institute: The University of Texas MD Anderson Cancer Center

description:
scATACseq
atac_IL21_15.RDS

library_source: genomic

data_processing:
Cellranger mkfastq v3.01 to generate FASTQ
Cellranger count v3.01 to generate count matrix
Assembly: GRCh38
Supplementary files format and content: [Cellranger files] comprising a MatrixMarket file (matrix.mtx) and two tab separated metadata files (barcodes.tsv, features.tsv)

molecule: genomic DNA

organism: Homo sapiens

source_name: IL-21 NK cells + GSC20 9 days coculture

extract_protocol:
Single‐nucleus libraries were generated using the 10X Genomics Chromium Next GEM ATAC Capture and Library (V1.1), following the manufacturer’s protocol. Nine samples were pooled to give a final concentration of 10 nM. Pooled samples underwent further qPCR prior to sequencing with the NovaSeq 6000 sequencer using the S1, 100 cycles flow cell and sequenced with read 1 for 50 cycles, i7 8 cycles, i5 index 16 cycles, and read 2 for 49 cycles.
By applying RNA  and ATAC sequencing, we want to investigate the epigenetic factors that contributing for IL-21-induced memory formation in NK cells

tag: tissue

value: CBNK

tag: treatment

value: IL-21 NK cells + GSC20 9 days coculture


title: EAS42_2_KI

city: Paris

first: Carole

last: Peyssonnaux

address: 24 rue du Faubourg saint Jacques

country: France

institute: INSERM

library_source: transcriptomic

data_processing:
Libraries were quantified by Q bit and profiles were assessed using the DNA High Sensitivity LabChip kit on an Agilent Bioanalyzer
Libraries were sequenced on an Illumina Nextseq 500 instrument using 75 base-lengths read V2 chemistry in a paired-end mode
After sequencing, a primary analysis based on AOZAN software (ENS, Paris) was applied to demultiplex and control the quality of the raw data (based of FastQC modules / version 0.11.5).
Obtained fastq files were then aligned using STAR algorithm (version 2.5.2b) and quality control of the alignment realized with Picard tools (version 2.8.1).
Reads were then counted using Featurecount (version Rsubread 1.24.1) and the statistical analyses on the read counts were performed with the DESeq2 package version 1.14.1 to determine the proportion of differentially expressed genes between two conditions.
Assembly: Ensembl release 101, GRCm38

molecule: total RNA

organism: Mus musculus

source_name: Skin

extract_protocol:
RNA was harvested using trizol.
The libraries were prepared following the Stranded mRNA Prep protocol from Illumina, starting from 250 ng  of high quality total RNA.

value: Skin

tag: genotype

value: 5 Hamp1-KI ker


title: Ind

country: China

tag: cell type

value: SHEDs-derived neuron-like cells

value: differentiated


title: IL15 CBNK GBM Day 9  coculture 124610 ATAC

description:
scATACseq
atac_IL21_15.RDS

source_name: IL-15 NK cells + GSC20 9 days coculture

value: IL-15 NK cells + GSC20 9 days coculture


title: EAS42_1_WT

value: WT


title: Blank

value: stem cells from human exfoliated deciduous teeth (SHEDs)

value: undifferentiated,uninfected


title: A549_xeno_rep3

city: Shanghai

first: Yin

last: Liu

state: Shanghai

address: Building #2, 507 Zhengmin Road

department: Department of Laboratory Medicine

institute: Shanghai Pulmonary Hospital, Tongji University School of Medicine

description:
processed data file:
PDX_A549_test.gene_summary.txt

data_processing:
MAGeCK and MAGeCK0VISPR softwares were used to analyze CRISPR data.
Raw sequencing data are pre-processed by using MAGeCK to obtain the read counts for each sgRNA. Control sgRNAs are used to normalize the data.
MAGeCK TEST algorithm is used to compare treatment with control samples to obtain the significantly enriched and depleted sgRNAs and genes.
Genes with p value less than 0.001 are canditate hits.
Genome_build: hg38
Supplementary_files_format_and_content: gene_summary.txt

source_name: A549 xenograft

growth_protocol: A549 cells were cultured in RPMI-1640 and supplemented with 10% fetal bovine serum (FBS).

extract_protocol: Genomic DNA was extracted from replicate samples (QIAamp Blood Midi kit) and sgRNA inserts were amplified by PCR. The sgRNAs were designed using the CRISPR-DO tool that accounted for sgRNA specificity and cutting efficiency. sgRNAs were synthesized as 73-mer oligonucleotides (CustomArray, USA), GAAAGGACGAAACACCGNNNNNNNNNNNNNNNNNNNNGTTTTAGAGCTAGAAATAGCAAGTTAAAATAAGGC (N’s denote sgRNA 20 nucleotide target sequence; sense orientation) with a total of 12,472 sequences and amplified by PCR as a pool using the following primers: TAACTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTT GTGGAAAGGACGAAACACCG (Forward) and ACTTTTTCAAGTTGATAACG GACTAGCCTTATTTTAACTTGCTATTTCTAGCTCTAAAAC (Reverse). The PCR product was purified and cloned in the lentiGuide-Puro vector using BsmBI (NEB). Ligation was performed using the NEBuilder® HiFi DNA Assembly Cloning Kit and transformed into an electrocompetent strain (Stbl4; ThermoFisher, USA) to achieve ~300x coverage. Colonies were scraped off Agar plates using LB medium. Plasmid DNA was extracted using NA0310 Sigma GenElute™ HP Plasmid Maxiprep Kit and adequate library representation of each sgRNA was confirmed by NGS.

treatment_protocol: We inoculated the transduced A549 cells to NOD/SCID mice and harvested xenograft tumors at day 14.

value: lung

tag: growth

value: in vivo


title: IL21 CBNK day 7  124610 (baseline) ATAC

description:
scATACseq
atac_IL21_15.RDS

source_name: IL-21 NK cells alone (baseline)

value: IL-21 NK cells alone (baseline)


title: A549_xeno_rep2


title: EAS37_1_WT


title: IL15 CBNK day 7  124610 (baseline) ATAC

description:
scATACseq
atac_IL21_15.RDS

source_name: IL-15 NK cells alone (baseline)

value: IL-15 NK cells alone (baseline)


title: EAS42_6_KI


title: A549_xeno_rep1


title: glial cells, Calcium-free, rep4

city: Würzburg

first: Robert

last: Blum

address: Josef-Schneider-Str. 11

department: Department of Neurology

country: Germany

institute: University Hospital Würzburg

description: block of Calcium entry

data_processing:
Base calling with Illumina NextSeq RTA v2.4.11
FASTQ conversion with bcl2fastq v2.20.0.422
FASTQ quality and adapter trimming using Cutadapt (Martin, 2011) version 1.17 (cutadapt parameters: --nextseq-trim=20 -m 1 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC)
Alignment of trimmed reads to mouse genome using STAR (Dobin et al., 2013)  v2.7.2b with default parameters based on RefSeq annotation version RS_2023_04 for GRCm39
Calculation of read counts on exon level summarized for each gene (RefSeq annotation version RS_2023_04 for GRCm39) using featureCounts v1.6.4 from the Subread package (Liao et al., 2014). Multi-mapping and multi-overlapping reads were counted strand-specific and reversely stranded with a fractional count for each alignment and overlapping feature (command line parameters: -s 2 -t exon -M -O --fraction).
Assembly: GRCm39 (primary assembly and mitochondrion)
Supplementary files format and content: Character (TAB) seperated value file containing mRNA abundance measurements

molecule: polyA RNA

source_name: cortex, postnatal

growth_protocol: Cortical glial cells were prepared from P3 – P5 wt CD1 mice. In brief, frontal cortices from one mouse were dissected and collected in Hank’s buffered saline solution (HBSS). Then, three trituration steps were performed and cells were cultured in basal medium (1:1 mixture of DMEM/F12 with 10% FCS, 5% HS, 1% penicillin/streptomycin, 0.45% glucose) containing B27 (1:50) and 10 ng/ml EGF (PeproTech). Cells were first cultured in a Poly-D L‑ornithine hydrobromide (PORN) coated 75 cm2 culture flask at 37°C, 5% CO2 atmosphere. After 3 days, cells were washed with PBS. At day in vitro (DIV) 7, cells were split with 20% TrpLE (Gibco) and plated at a density of 1 x 105 cells/dish on poly-L-lysine-coated dishes (Marienfeld, Germany). Cells were finally used at DIV 3 – 7, after splitting.

extract_protocol:
Total RNA was extracted from cell cultures using the Qiagen RNeasy Mini Kit.
RNA quality was checked using a 2100 Bioanalyzer with the RNA 6000 Nano kit (Agilent Technologies). The RIN for all samples was >9.3. DNA libraries suitable for sequencing were prepared from 500 ng of total RNA with oligo-dT capture beads for poly-A-mRNA enrichment using the TruSeq Stranded mRNA Library Preparation Kit (Illumina) according to manufacturer’s instructions (½ volume). After 14 cycles of PCR amplification, the size distribution of the barcoded DNA libraries was estimated ~275 bp by electrophoresis on Agilent DNA 1000 Bioanalyzer microfluidic chips.

treatment_protocol: We have investigated three conditions: condition 1 - control, condition 2: 3 µM thapsigargin, 60 min, condition 3: Calcium-free medium / EGTA

value: cortex, postnatal

value: primary cultured astrocytes

value: wildtypic

value: Calcium-free, 60 min


title: A549_day0_rep1

description:
processed data file:
A549_invitro_test.gene_summary.txt

source_name: A549 cell line

value: in vitro


title: EAS37_6_WT

value: Skin


title: glial cells, Calcium-free, rep3

description: block of Calcium entry


title: EAS37_4_KI

value: 5 Hamp1-KI ker


title: HCMV

value: SHEDs with HCMV infection

value: Mesenchymal stem cells

value: infected


title: glial cells, Calcium-free, rep2

description: block of Calcium entry


title: A549_xeno_rep5


title: KPC 53BP1 KO tumor, biol rep 5

city: Boston

first: Jeffrey

last: Patterson-Fortin

state: MA

address: 450 Brookline Avenue

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description:
53BP1_KO_5
Raw_Counts_KPC_53BP1_KO.xls.txt

data_processing:
SOAPnuke (version v.1.5.2)
Sequence reads were filtered as follows: 1. Remove reads containing the adaptor, 2. Remove reads whose N content is greater than 5%, 3. Remove low-quality reads (quality socre less than 15)
Trimmed sequences were mapped to GRCm39 using Hierarchial Indexing for Spliced Alignment of Transcripts (HISAT, version v2.0.4). Parameters: sensitive, no discordant, no mixed, 1, X 1000, p 8, rna-strandness RF)
Read count extraction and normalization were performed using RSEM (v.1.2.8)
Assembly: mm39
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: tumor

growth_protocol: Cell lines were implanted into syngeneic mice resulting in tumor formation.

extract_protocol:
Total RNA was extracted from cells using Qiagen RNeasy kit (#74004)
RNA sequencing and data analysis was performed by the Beijing Genomics Institute

value: tumor

tag: cell line

value: KPC

value: Trp53bp1 KO


title: IL21 CBNK GBM Day 3 coculture 124610 ATAC

description:
scATACseq
atac_IL21_15.RDS

source_name: IL-21 NK cells + GSC20 3 days coculture

value: CBNK

value: IL-21 NK cells + GSC20 3 days coculture


title: KPC 53BP1 KO tumor, biol rep 4

description:
53BP1_KO_4
Raw_Counts_KPC_53BP1_KO.xls.txt


title: IL15 CBNK GBM Day 3 coculture 124610 ATAC

description:
scATACseq
atac_IL21_15.RDS

source_name: IL-15 NK cells + GSC20 3 days coculture

value: IL-15 NK cells + GSC20 3 days coculture


title: glial cells, Calcium-free, rep1

description: block of Calcium entry


title: Chicago Mix H11, PBMC

city: New Haven

first: Xiting

last: Yan

state: Connecticut

address: 300 Cedar Street, Ste S441D

department: Internal Medicine

institute: Yale School of Medicine

description:
H11_HHT
metadata in order of appearance of multiplexed samples

library_source: transcriptomic single cell

data_processing:
The CellRanger v7.0.0 pipeline (mkfastq and count) was used to demultiplex the raw sequencing reads from the single-cell libraries and align them to the GRCh38 reference genome (CellRanger 2020-A).
To demultiplex the mixed samples from Chicago, the fastq files corresponding to the whole-exome sequencing data of these samples were aligned to the CellRanger reference fasta file (refdata-gex-GRCh38-2020-A/genome.fa) using bwa-mem. The resulting .sam files were converted to .bam files using picard. Picard was also used to sort, mark duplicates in, and build indices for the .bam files. The Genome Analysis Toolkit (GATK)’s Best Practices for Germline Short Variant Discovery were followed. These .vcf files were filtered for common single nucleotide polymorphisms (SNPs) with a 5% minor allele frequency cutoff. Demuxlet, implemented in the Demuxafy framework, was used to demultiplex these samples based on their common SNPs [25]. Only samples that had a posterior likelihood of >0.95 were kept.
The feature-barcode matrices for each patient sample were loaded into R and converted into a Seurat (v4.0) object. Cells with fewer than 200 features and those expressing greater than 20% of mitochondrial genes were filtered out to remove dead and dying cells. Samples with fewer than 500 cells were removed to eliminate low-quality samples. The filtered gene expression matrix was normalized using Seurat's NormalizeData function with default settings. Genes with high cell-to-cell variation were identified using the FindVariableFeatures function with the “vst” method. The data was integrated on an assay level (5’ v1 versus v2) using reciprocal PCA to reduce 10X assay-specific effects, and no significant batch effects were noted after this integration. The data were then scaled and centered using the ScaleData function, and the top 3,000 variable features were used for Principal Component Analysis. The top 30 principal components (PCs) were selected based on the elbow plot generated by the ElbowPlot function. Graph-based clustering was performed using the FindNeighbors and FindClusters functions with the selected 30 PCs.
Assembly: Assembly: GRCh38
Supplementary files format and content: Supplementary files format and content: For each sample, processed data include Cell Ranger Count filtered outputs: cell barcodes (barcodes.tsv.gz), genes (features.tsv.gz) and count matrix (matrix.mtx.gz).
Supplementary files format and content: demuxlet-outputs.zip (Chicago Mix A10, B10, C10, etc. include barcodes for multiple samples that were multiplexed together in a single 10X lane. demuxlet-outputs.zip contains the demuxlet.best files for each mix, which are the outputs the demultiplexing software demuxlet, that link each barcode to a specific sample (e.g. A10-demuxlet.best links each barcode to a sample). )

source_name: PBMC

extract_protocol:
At each sample collection site, PBMCs were separated from the whole blood using density gradient centrifugation, and PBMC and BAL samples were cryopreserved in liquid nitrogen as separate samples for single-cell experiments. The PBMCs were cryopreserved in 1.5 ml cryotubes using 10% DMSO in heat-inactivated FBS and were stored long-term in liquid nitrogen. Initial PBMC sample collection, processing, and storage did not differ significantly among the three patient sample collection sites. In Mexico City, bronchoalveolar lavage samples were collected and stored long-term in liquid nitrogen using 10% DMSO in heat-inactivated FBS.
All patient samples were shipped for processing in New Haven, CT, to minimize technical and batch effects arising from sample processing. Samples were randomized based on age, sex, diagnosis, and smoking history into different batches for sample preparation and single-cell library construction. Sixteen samples were processed at a time to reduce batch effects. The sample preparation protocol used was modified from 10X Genomics with the following modifications. Cryopreserved samples were thawed in a 37 °C water bath, and 1.5 ml of 10% FBS in Dulbecco’s Modified Eagle Medium (DMEM) was added to each tube. The cells were centrifuged, the supernatant was removed, and the cells were resuspended in D-PBS with 0.04% bovine serum albumin (BSA). The sample was passed through a 40 µm cell strainer into a 2-mL microcentrifuge tube. The cell concentration was determined using Trypan Blue solution, and Invitrogen Countess Automated Cell Counter. Samples with isolated single cells were diluted, and these cells were loaded into the chip with an anticipated recovery of 10,000 cells according to the manufacturer’s protocol for Chromium Next GEM Single Cell 5’ Reagent Kits v2 (Dual Index) (from samples from New Haven and Mexico City only). To further reduce batch effects, Chicago samples were pooled, such that each chip lane was loaded with two or three patient samples, with an anticipated recovery cell of 20,000 cells to 30,000 cells, respectively. Any leftover samples were fixed in 80% methanol and stored at -20C to preserve nucleotide integrity for downstream DNA extraction and whole-exome sequencing to SNP-demultiplex mixed patient samples from Chicago. All subsequent library construction steps were followed precisely, and all cDNA library QC was performed using an Agilent 2100 Bioanalyzer.
The single-cell cDNA libraries were sequenced using an Illumina HiSeq4000 machine at the Yale Stem Cell Genomics Center (samples from New Haven and Mexico City) and from an Illumina NovaSeq X at the Yale Center for Genomic Analysis (samples from Chicago). Samples were sequenced at a depth of 150 million reads per sample to allow for adequate transcriptome capture.

value: PBMC

tag: cohort

value: Chicago

tag: samples multiplexed_(chicago_only)

value: IPFC7, IPFC8

tag: age (singleton or multiplexed)

tag: sex (singleton or multiplexed)

value: pooled:F, F

tag: disease (singleton or multiplexed)

value: IPF, IPF

tag: smoking status

tag: dlco


title: KPC 53BP1 KO tumor, biol rep 3

description:
53BP1_KO_3
Raw_Counts_KPC_53BP1_KO.xls.txt


title: EAS37_2_KI


title: glial cells, Thapsigargin, rep4

description: ER Calcium depletion

value: cortex, postnatal

value: primary cultured astrocytes

value: wildtypic

value: 3 uM thapsigargin, 60 min


title: Chicago Mix H10 , PBMC

description:
H10_HHT
metadata in order of appearance of multiplexed samples

value: IPFC3, IPFC4

value: pooled:F, M


title: KPC 53BP1 KO tumor, biol rep 2

description:
53BP1_KO_2
Raw_Counts_KPC_53BP1_KO.xls.txt

value: tumor


title: KPC 53BP1 KO tumor, biol rep 1

description:
53BP1_KO_1
Raw_Counts_KPC_53BP1_KO.xls.txt

value: KPC


title: KIT+ cells, E12 FL, scRNAseq

city: Kumamoto

first: Saori

last: Morino-Koga

state: Kumamoto

address: 2-2-1 Honjo, Chuo-ku

department: Institute of Molecular Embryology and Genetics

country: Japan

institute: Kumamoto University

data_processing:
The fastq files were aligned, filtered, and counted by the cellranger count (v5.0.0) (10x Genomics).
Assembly: mm10 (GRCm38)
Supplementary files format and content: tab-separated value files and matrix files

source_name: fetal liver

extract_protocol:
The fetal liver isolated from E12 mouse embryos was mechanically dissociated with a 23G needle. Those obtained cells were stained with KIT antibody and sorted using an SH800 cell sorter (SONY). Sorted KIT-expressing cells were resuspended in 0.04% BSA/PBS.
Library construction was performed by using the Chromium Single Cell 3' v3.1 kit (10x Genomics).

value: fetal liver

value: KIT-expressing cells

tag: strain

tag: age


title: Chicago Mix G11, PBMC

description:
G11_HHT
metadata in order of appearance of multiplexed samples

value: HPC24, HPC25

value: FHP, FHP


title: glial cells, Thapsigargin, rep3

description: ER Calcium depletion


title: Chicago Mix F11, PBMC

description:
F11_HHT
metadata in order of appearance of multiplexed samples

value: PBMC

value: IPFC5, IPFC6

value: pooled:M, F


title: mus_macrophage_lpsmp_rep2

city: Auburn University

first: Xu

last: Wang

state: AL

address: 273 CASIC Building, Auburn Research Park, 559 Devall Dr

department: Pathobiology, College of Veterinary Medicine

institute: Auburn University

description:
Illumina mRNA-seq
LPSMP_rep2

data_processing:
FastQC (version 11.5) software was used for quality check.
Sequenced reads were trimmed for adaptor sequence using Trimmomatic (version 0.36), and masked for low-complexity or low-quality sequence.
The ramaining high-quality clean reads were mapped to mus musculus whole genome using TopHat (version 2.1.1)
HTSeq-count was conducted to calculate the number of aligned reads of each gene overlapping its exons.
DESeq2 and edgeR were employed to calculate the log2-fold change (log2FC), a criterion with |log2FC| ≥ 2 and p-value < 0.05 was used as the threshold for evaluating the DEGs.
Genome_build: Mus musculus genome (GenBank assembly accession GCA_000001635.9)
Supplementary_files_format_and_content: Gzipped, tab-delimiited text file inlcuding raw gene counts for every gene and every sample

source_name: macrophage cell line

extract_protocol:
Quick-DNA/RNA Miniprep Plus Kit (Catalog No. D7003, Zymo Research)
The RNA integrity was evaluated with the LabChip GX Touch HT (PerkinElmer, MA, USA). The RNA library preparation was performed using NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB, MA, USA). Enriched RNAs were fragmented for 10 minutes at 94 °C. The first strand cDNA synthesis, second strand cDNA synthesis, end repair and adaptor ligation according to the manufacturer’s protocol. The library PCR amplification were performed with 16 cycle PCR. The average size of the RNA libraries was approximately 350 bp (including the adapters). The RNA sequencing libraries were checked using the LabChip GX Touch HT (PerkinElmer, MA, USA) and quantified by using Qubit 2.0 Fluorometer (Invitrogen, CA, USA).

value: BALB/c

value: J774A.1 macrophage

value: treated by MP and LPS


title: glial cells, Thapsigargin, rep1

description: ER Calcium depletion

value: cortex, postnatal

value: primary cultured astrocytes


title: mus_macrophage_lpsmp_rep1

description:
Illumina mRNA-seq
LPSMP_rep1


title: KPC tumor, biol rep 4

description:
Ctrl_4
Raw_Counts_KPC.xls.txt

value: WT


title: KPC tumor, biol rep 5

description:
Ctrl_5
Raw_Counts_KPC.xls.txt


title: Chicago Mix F10, PBMC

description:
F10_HHT
metadata in order of appearance of multiplexed samples

value: Chicago

value: HPC12, HPC13

value: pooled:F, F


title: KPC tumor, biol rep 3

description:
Ctrl_3
Raw_Counts_KPC.xls.txt

value: tumor

value: KPC


title: Chicago Mix E11, PBMC

description:
E11_HHT
metadata in order of appearance of multiplexed samples

value: HPC22, HPC23


title: mus_macrophage_lps_rep3

description:
Illumina mRNA-seq
LPS_rep3

value: treated by lipopolysaccharide (LPS)


title: EAS37_3_WT

value: Skin


title: glial cells, control, rep3

description: control condition

value: wildtypic

value: vehicle control


title: mus_macrophage_lps_rep2

description:
Illumina mRNA-seq
LPS_rep2


title: Chicago Mix E10, PBMC

description:
E10_HHT
metadata in order of appearance of multiplexed samples

value: PBMC

value: HPC10, HPC11

value: FHP, FHP


title: mus_macrophage_lpsmp_rep3

description:
Illumina mRNA-seq
LPSMP_rep3

value: BALB/c

value: J774A.1 macrophage

value: treated by MP and LPS


title: KPC tumor, biol rep 1

description:
Ctrl_1
Raw_Counts_KPC.xls.txt

value: WT


title: glial cells, control, rep2

description: control condition

value: cortex, postnatal

value: primary cultured astrocytes


title: Chicago Mix D10, PBMC

description:
D10_HHT
metadata in order of appearance of multiplexed samples

value: Chicago

value: IPFC1, IPFC2

value: pooled:M, F

value: IPF, IPF


title: glial cells, Thapsigargin, rep2

description: ER Calcium depletion

value: 3 uM thapsigargin, 60 min


title: mus_macrophage_lps_rep1

description:
Illumina mRNA-seq
LPS_rep1

value: treated by lipopolysaccharide (LPS)


title: Chicago Mix D11, PBMC

description:
D11_HHT
metadata in order of appearance of multiplexed samples

value: HPC20, HPC21


title: glial cells, control, rep1

description: control condition

value: wildtypic

value: vehicle control


title: treat3

city: hainan

first: Yaochen

last: Cao

address: Xueyuan Road

institute: Hainan Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) 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: mm9 (MGSCv37)
Supplementary_files_format_and_content: all_gene_Expression_matrix.txt: Tab-delimited text file includes raw counts and FPKM values for each Sample.
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each Sample.

source_name: renal

extract_protocol:
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.

value: postnatal day 21

value: kidney

tag: diagnosis

value: acute renal failure


title: ID8 53BP1 KO tumor, biol rep 3

description:
ID8_53BP1_KO3
Raw_Counts_ID8_53BP1_KO.xls.txt

value: tumor

value: Trp53bp1 KO


title: ID8 53BP1 KO tumor, biol rep 2

description:
ID8_53BP1_KO2
Raw_Counts_ID8_53BP1_KO.xls.txt


title: mus_macrophage_mp_rep3

description:
Illumina mRNA-seq
MP_rep3

value: BALB/c

value: J774A.1 macrophage

value: treated by microparticles (MP)


title: Chicago Mix C11, PBMC

description:
C11_HHT
metadata in order of appearance of multiplexed samples

value: PBMC

value: Chicago

value: HPC17, HPC18, HPC19

value: pooled:M, F, F

value: FHP, FHP, FHP


title: mus_macrophage_mp_rep2

description:
Illumina mRNA-seq
MP_rep2


title: treat2


title: glial cells, control, rep4

description: control condition

value: cortex, postnatal

value: primary cultured astrocytes


title: Chicago Mix C10 , PBMC

description:
C10_HHT
metadata in order of appearance of multiplexed samples

value: HPC7, HPC8, HPC9

value: pooled:M, F, M


title: treat1

value: postnatal day 21


title: mus_macrophage_mp_rep1

description:
Illumina mRNA-seq
MP_rep1


title: KPC tumor, biol rep 2

description:
Ctrl_2
Raw_Counts_KPC.xls.txt

value: KPC

value: WT


title: Chicago Mix B11, PBMC

description:
B11_HHT
metadata in order of appearance of multiplexed samples

value: HPC14, HPC15, HPC16

value: pooled:F, M, F


title: ID8 tumor, biol rep 3

description:
ID8_Ctrl3
Raw_Counts_ID8.xls.txt

value: tumor


title: Chicago Mix B10, PBMC

description:
B10_HHT
metadata in order of appearance of multiplexed samples

value: HPC4, HPC5, HPC6


title: mus_macrophage_ctl_rep3

description:
Illumina mRNA-seq
Ctl_rep3

value: BALB/c

value: J774A.1 macrophage

value: untreated


title: control2

value: kidney

value: healthy


title: ID8 tumor, biol rep 2

description:
ID8_Ctrl2
Raw_Counts_ID8.xls.txt


title: mus_macrophage_ctl_rep2

description:
Illumina mRNA-seq
Ctl_rep2


title: Chicago Mix A10, PBMC

description:
A10_HHT
metadata in order of appearance of multiplexed samples

value: PBMC

value: Chicago

value: HPC1, HPC2, HPC3

value: FHP, FHP, FHP


title: ID8 tumor, biol rep 1

description:
ID8_Ctrl1
Raw_Counts_ID8.xls.txt


title: mus_macrophage_ctl_rep1

description:
Illumina mRNA-seq
Ctl_rep1


title: control1


title: ATAC, Dox, rep3

status: Public on Jul 08 2024

first: Qianxia

last: Zhang

address: 3 Blackfan Circle, RM 3117.16

institute: Boston Children's Hospital

data_processing:
QC was performed on demultiplexed sequencing files using FASTQC (v0.11.3). Sequencing reads were trimmed using Trimmomatic (v0.36) and aligned to reference genome (GRCh38 primary assembly) using bwa (v0.7.17). The resulting SAM files were converted to BAM files, sorted and indexed, and reads mapped to mitochondrial DNA were removed using Samtools (v1.6).
Read fragment sizes were checked using the ATACseqQC R package (v3.19). Post PCR duplicate removal, reads were shifted +4bp and –5bp for positive and negative strand respectively, and were further split into nucleosome-free regions (NFR), mono- or di-nucleosome regions using the alignmentSieve function in deepTools (v3.5.1).
Peak calling was performed on bam files containing reads mapped to NFR using MACS2 (v2.2.7.1).
Assembly: hg38
Supplementary files format and content: bigwig files contain nucleosome-free regions

growth_protocol: 4D6 cells were maintained in RPMI supplemented with 10% FBS, 1% L-glutamine

extract_protocol:
100,000 cells were used for each replicate.
ATAC-seq libraries were prepared using ATAC-seq library prep kit (Active Motif) according to the manufacturer’s protocol.

treatment_protocol: 4D6 stable cells were seeded on 150mm plates with or without Dox and grown for 24 hrs.

value: thymic epithelial cells

value: WT AIRE

value: Dox 24hr


title: ATAC, Dox, rep1


title: ATAC, no Dox, rep1

value: no Dox


title: ATAC, Dox, rep2


title: ATAC, no Dox, rep2


title: H3K4me0, no Dox, rep1

data_processing:
QC was performed on demultiplexed sequencing files using FASTQC (v0.11.3). Sequencing reads were trimmed using Trimmomatic (v0.36) and aligned to reference genome (GRCh38 primary assembly) using bwa (v0.7.17). The resulting SAM files were converted to BAM files, sorted and indexed using Samtools (v1.6). Samples with drosophila spike-in chromatins were aligned to a customized reference genome consisting both hg38 and dm6, and the sorted and index BAM files were subsequently split into separate BAM files containing hg38- and dm6-mapped reads, respectively, using plit_bam.py module in the SPIKER tool. hg38- and dm6-mapped reads were deduplicated using the alignmentSieve function in deepTools (v3.5.1), and unique dm6-mapped reads were counted to calculate the scaling factors.
Peak calling was performed using MACS2 (v2.2.7.1) with the following parameters: macs2 callpeak -f BAMPE  -B -g 3.2e+9 --keep-dup 1 --SPMR --nomodel --extsize 250 -q 0.05 --cutoff-analysis. When calling peaks in WT and mutant AIRE ChIP-seq samples, corresponding input controls were included to remove the effect of background noise.
WT and mutant AIRE ChIP-seq BAM files and peaks were imported into DiffBind (v3.8.4), and a census of all AIRE peaks (n=13023, summits +/– 200 bp) were obtained after removing blacklisted and greylisted regions using dba.blacklist and dba.peakset functions. Trimmed Mean of M-values (TMM)-normalized counts-per-million (CPM) reads9 within each peak (summits +/– 200 bp) were obtained using the dba.count function in DiffBind with options.
Peaks called from H3K27ac ChIP-seq (–AIRE expression) were removed of blacklisted regions and subjected to Ranking Ordering of Super Enhancer (ROSE) analysis to obtain putative super-enhancer regions, using 12.5 Kb stitching distance and 2 Kb TSS exclusion parameters.
BAM files were converted to bigwig files using deepTools (v3.5.1). After verification of consistency between replicates, bigwig files were averaged using WiggleTools (v1.2.2) and bedGraphToBigWig (v366) and imported into IGV (v2.15.1) for visualization at specific loci or into deepTools (v3.5.1) for generation of heatmaps and average profiles using the computeMatrix, plotHeatmap and plotProfile functions.
Assembly: hg38, dm6
Supplementary files format and content: bigwig files contain ChIP signals for each sample

extract_protocol:
For anti-FLAG (AIRE) and anti-p300 ChIP-seq, cells were washed 3 times with PBS and then crosslinked with 2mM Disuccinimidyl glutarate (DSG) in PBS for 45 minutes at room temperature. Cells were then washed again 3 times with PBS and then crosslinked with 1% formaldehyde (Sigma, Thermofisher, and Electron Microscopy Sciences) in PBS for 10 minutes at room temperature. For anti-histone mark ChIP-seq, cells were crosslinked with 1% formaldehyde in fresh media for 10 minutes at room temperature. After formaldehyde crosslinking, all cells were washed 1 time with PBS and quenched with 0.125 M glycine in PBS for 5 min at room temperature. Quenched cells were washed with ice cold PBS, then harvested in ice cold PBS supplemented with 0.5 mM PMSF. Cells were spun down at 500 g for 5 minutes and cell pellets were supplemented with 1 µl of 100mM PMSF and 1 µl 1X mammalian protease inhibitor cocktail (G-Biosciences), then flash frozen in liquid nitrogen and stored at -80°C until ready to use. For one ChIP pull-down, ~15x106 cells were used. Cells pellets were thawed on ice for 15 minutes and then resuspended in ice-cold One-Step Lysis Buffer (50 mM Tris H 7.5, 1% SDS, 0.25% Sodium Deoxycholate and 1 X mammalian protease inhibitor cocktail). Cells were incubated on ice for 10 min and then 700 µl ChIP Dilution Buffer (50 mM Tris pH 7.5, 0.01% SDS, 150 mM NaCl, 0.25% Triton-X, 1 X mammalian protease inhibitor cocktail) was added. Chromatin was sheared using with a Covaris M220 ultrasonicator (settings: 5% duty factor, 75W max power, 200 cycles per burst, 20 min) at 6°C. Lysates were spun down in a refrigerated centrifuge for 10 minutes at 18,000 g. Cleared lysate was 3-fold diluted with ChIP Dilution Buffer, spike-in chromatin (600ng per pull-down, Active Motif) was added when cells were treated with p300 inhibitors or DMSO, and 2-3% of the input was saved for later use. Lysates were nutated with antibodies [for each pull-down when indicated, 2.5 µg of anti-FLAG (M2, Sigma); 5 µg anti-H3K4me1, 5 µg anti-H3K27me3, 4 µg of anti-p300 (D2X6N, Cell Signaling Technologies); 4 µg of anti-H3K27Ac (Cell Signaling Technologies); 4 µg of anti-H3K4me0 (Active Motif); an additional 2 µg spike-in antibody (Active Motif) was included when cells had been treated with p300 inhibitors or DMSO] for 16 hrs at 4°C. Protein-DNA complexes were immunoprecipitated using Protein G magnetic beads (Active Motif) with 2 hrs nutation at 4°C. Protein G beads were washed with the following ice-cold buffers: RIPA buffer (0.1% SDS, 0.1% Sodium Deoxycholate, 1% Triton X-100, 1 mM EDTA, 10 mM Tris pH 8, 150 mM NaCl); RIPA supplemented with 350 mM NaCl; LiCl Buffer (10 mM Tris pH 8, 250 mM LiCl, 0.5% Triton X-100, 0.5% Sodium Deoxycholate) and Tris Buffer (10 mM Tris pH 8.5). Protein-DNA complexes were eluted with Elution Buffer (10 mM Tris pH 8, 1 mM EDTA, 0.1% SDS, 150 mM NaCl, 5 mM DTT) with gentle agitation at 65°C for 1 hr. Reserved ChIP inputs were diluted two-fold with Elution Buffer. Dilute inputs and eluted protein-DNA were treated with RNAse (Machery-Nagel) at 37°C for 30 min, then Proteinase K (New England Biolabs) at 65°C for 16 hrs to ensure reverse crosslinking of DNA. Reverse cross-linked DNA was purified using SPRI Select beads (Beckman).
ChIP-seq DNA libraries were prepared using NEBNext Ultra II DNA library Prep Kit for Illumina (New England Biolabs) according to manufacturer’s protocol.

treatment_protocol: 4D6 stable cells were seeded on 150mm plates with or without Dox and grown for 24 hrs. For drug-treated samples, equal volume of DMSO, 3 µm A-485 (Tocris Bioscience), or 0.25 µm dCBP-1 (MedChemExpress) was added to cells 4 hrs prior to harvest.


title: H3K4me0, no Dox, rep2


title: H3K4me0, no Dox, rep3


title: DFLR dBGLF5 LCL, late lytic fraction, c2-3

city: Madison

first: Alejandro

last: Casco

state: WI

address: 1111 Highland Ave

institute: University of Wisconsin-Madison

data_processing:
NASA GeneLab RNA-seq consensus pipeline (PMID: 33870146)
Sequence reads were mapped using STAR v2.7.6a following the parameters outlined in the NASA GeneLab RNA-seq consensus piepline
Read count and normalization was performed using RSEM v1.3.1 following the parameters outlined in the NASA GeneLab RNA-seq consensus pipeline
Assembly: GENCODE GRCh38 primary assembly (p14 genome and v45 annotation)
Assembly: ERCC genome and annotation (Thermo-Fisher
Assembly: DFLR M81 (derived from GenBank: KF373730)
Supplementary files format and content: RSEM output for gene-level expression of individual samples
Supplementary files format and content: RSEM output for isoform-level expression of individual samples

source_name: Blood

growth_protocol: LCLs were maintained in RPMI 1640 supplemented with 10% FBS and 1% penicillin-streptomycin in a humidified atmosphere at 37°C with 5% CO2 at 37°C

extract_protocol:
RNA was harvested using the Direct-Zol RNA mini prep kit (Zymo Research) with the optional on-column DNase treatment.
PolyA-enriched strand-specific libraries were generated using the Illumina TruSeq Stranded mRNA kit, followed by 101 bp paired-end sequencing on the Illumina NovaSeq 6000 system. Library preparation and sequencing was performed by the Yale Center for Genome Analysis.

treatment_protocol:
For BCR stimulation, LCLs were seeded at 300,000 cells/mL in culture media and treated with μg/mL AffiniPure F(ab)2 anti-human pan-Ig antibody (Jackson ImmunoResearch) for 72 hours
40,000 BCR-stimulated LCLs were sorted by FACS directly into TRIzol-LS (Thermo-Fisher) containing 1:125 dilution of 1 μL ERCC Spike-In RNA (Invitrogen)

value: Blood

value: LCL

value: EBV-transformed B cell

tag: fraction

value: Late lytic


title: DFLR dBGLF5 LCL, early lytic fraction, c2-3

tag: tissue

value: Early lytic


title: DFLR dBGLF5 LCL, late lytic fraction, c2-2


title: DFLR dBGLF5 LCL, late lytic fraction, c2-1


title: DFLR dBGLF5 LCL, latent fraction, c2-1

value: Latent


title: DFLR LCL, late lytic fraction, c4-2

value: WT


title: ID8 53BP1 KO tumor, biol rep 1

description:
ID8_53BP1_KO1
Raw_Counts_ID8_53BP1_KO.xls.txt

value: tumor

value: Trp53bp1 KO


title: DFLR LCL, early lytic fraction, c4-2


title: DFLR dBGLF5 LCL, early lytic fraction, c2-2


title: control3

value: postnatal day 21

value: kidney

value: healthy


title: DFLR dBGLF5 LCL, early lytic fraction, c2-1


title: DFLR dBGLF5 LCL, latent fraction, c2-2


title: DFLR LCL, latent fraction, c4-2


title: DFLR LCL, bulk fraction, c4-2

value: Bulk


title: DFLR LCL, late lytic fraction, c4-1


title: DFLR LCL, early lytic fraction, c4-1


title: DFLR LCL, bulk fraction, c4-1


title: DFLR LCL, latent fraction, c4-1


title: DFLR LCL, late lytic fraction, c3-3


title: DFLR dBGLF5 LCL, latent fraction, c2-3


title: DFLR LCL, latent fraction, c3-3


title: DFLR LCL, latent fraction, c3-2


title: DFLR LCL, bulk fraction, c3-2


title: DFLR LCL, late lytic fraction, c3-1


title: DFLR LCL, early lytic fraction, c3-3


title: DFLR LCL, late lytic fraction, c3-2


title: DFLR LCL, latent fraction, c3-1


title: DFLR LCL, bulk fraction, c3-1


title: DFLR LCL, early lytic fraction, c3-2


title: DFLR LCL, early lytic fraction, c3-1


title: DFLR LCL, bulk fraction, c3-3


title: HBE cells treated with smoke extract + Lactobacillus live biotherapeutic product 24h post exposure 2

city: Birmingham

first: Tamas

last: Jilling

address: UAB Station

department: Department of Pediatrics

institute: The University of Alabama at Birmingham

description:
HWI-ST1292
SmokeAB_2

data_processing:
CLC Genomic Workbench 23.0.5
Sequences were trimmed using CLC default parameters
Sequences were mapped to Homo_sapiens_sequence_hg19 (parameters:  Mismatch cost = 2, Insertion cost = 3, Deletion cost = 3, Length fraction = 0.8,  Similarity fraction = 0.8
Read count extraction and normalization was done by CLC genomic workbench
Assembly: Homo_sapiens_sequence_hg19
Supplementary files format and content: Teb-delimited text file containing TPM normalized counts for each sample

source_name: Lung

growth_protocol: Human bronchial epithelial cells (HBEC) (PCS-300-010, ATCC) were grown as sepcified by ATCC

extract_protocol:
RNA was extracted using Qiagen RNEasy mini
150 bp paired end Libraries were produced according to Novogene standard protocol

treatment_protocol: Cells wewre treated as indicated for 24 hours

value: Lung

value: HBEC

value: Human bronchial epithelial

tag: treatment


title: HBE cells treated with Pseudomonas aeruginosa +smoke extract 24h post exposure 3

description:
HWI-ST1284
POASmoke_3

tag: genotype

value: Pseudomonas aeruginosa +smoke extract


title: HBE cells treated with Pseudomonas aeruginosa +Lactobacillus live biotherapeutic product 24h post exposure 3

description:
HWI-ST1281
POA_AB1000_3

tag: cell type


title: HBE cells treated with P. aeruginosa + smoke extract + Lactobacillus live biotherapeutic product 24h post exposure 1

description:
HWI-ST1285
POASmokeAB_1

value: Pseudomonas aeruginosa + smoke extract + Lactobacillus live biotherapeutic product


title: HBE cells treated with Pseudomonas aeruginosa +smoke extract 24h post exposure 1

description:
HWI-ST1282
POASmoke_1


title: HBE cells treated with Pseudomonas aeruginosa +Lactobacillus live biotherapeutic product 24h post exposure 1

description:
HWI-ST1279
POA_AB1000_1


title: HBE cells treated with smoke extract 24h post exposure 2

description:
HWI-ST1289
Smoke_2

value: smoke extract


title: HBE cells treated with P. aeruginosa + smoke extract + Lactobacillus live biotherapeutic product 24h post exposure 3

description:
HWI-ST1287
POASmokeAB_3


title: HBE cells treated with smoke extract + Lactobacillus live biotherapeutic product 24h post exposure 3

description:
HWI-ST1293
SmokeAB_3


title: HBE cells treated with P. aeruginosa + smoke extract + Lactobacillus live biotherapeutic product 24h post exposure 2

description:
HWI-ST1286
POASmokeAB_2


title: HBE cells treated with smoke extract + Lactobacillus live biotherapeutic product 24h post exposure 1

description:
HWI-ST1291
SmokeAB_1


title: HBE cells treated with Pseudomonas aeruginosa 24h post exposure 2

description:
HWI-ST1277
POA_2

value: Pseudomonas aeruginosa


title: HBE cells treated with Pseudomonas aeruginosa 24h post exposure 1

description:
HWI-ST1276
POA_1


title: HBE cells treated with smoke extract 24h post exposure 3

description:
HWI-ST1290
Smoke_3


title: HBE cells treated with Pseudomonas aeruginosa +Lactobacillus live biotherapeutic product 24h post exposure 2

description:
HWI-ST1280
POA_AB1000_2


title: HBE cells treated with Pseudomonas aeruginosa +smoke extract 24h post exposure 2

description:
HWI-ST1283
POASmoke_2


title: HBE cells treated with Pseudomonas aeruginosa 24h post exposure 3

description:
HWI-ST1278
POA_3


title: TT-CITE-11-TCRab

city: Ghent

first: Tom

last: Taghon

address: Corneel Heymanslaan 10

country: Belgium

institute: Ghent University

library_source: other

data_processing:
Fastq files were mapped using Cell Ranger version 7.0.0
Assembly: GRCh38
Supplementary files format and content: "GEX" libraries: raw and filtered h5 files obtained from Cell Ranger (RNA mapped alone)
Supplementary files format and content: "FB" libraries: raw and filtered h5 files obtained from Cell Ranger (combined mapping of RNA and ADT)
Supplementary files format and content: "TCRab" libraries: relevant contig and clonotype files obtained from mapping with Cell Ranger Multi
Library strategy: TCR-seq

molecule: other

source_name: thymus

extract_protocol:
Pediatric thymus from children undergoing cardiac surgery were obtained and used according to and with the approval of the Medical Ethical Commission of Ghent University Hospital (Belgium). Thymus tissue was cut into small pieces and digested with 1.6mg/ml collagenase (Gibco, 17104-019) in IMDM medium for 30min at 37°C to generate a single cell suspension. The reaction was quenched with 10% FBS and the thymocyte suspension was passed through a 70μm filter to remove undigested tissue. Cells were frozen in FBS containing 10% DMSO and stored in liquid nitrogen until needed. Upon thawing, thymocytes were purified with a bead-based dead cell removal kit (Miltenyi, 130-090-101). 2x10^6 cells were blocked with Human TruStain FcX Blocking solution (BioLegend, 422301) and then stained with TotalSeq-C antibodies (customised panel containing TotalSeq-C Human Universal Cocktail 1.0 (BioLegend, 399905) and 13 individual TotalSeq-C antibodies) and anti-CD3-PE. Cells were washed and sorted for CD3. Around 25.000 cells per sample were loaded per well on Chip K (10x Genomics, 1000286) and GEMs were generated using a Chromium Controller (10x Genomics).
Feature barcode (FB), gene expression (GEX) and TCR libraries were prepared according to protocol CG000330 Rev A (10x Genomics) using the Chromium Next GEM Single Cell 5ʹ GEM Kit v2 (10x Genomics, 1000244), Library Construction Kit (10x Genomics, 1000190), 5' Feature Barcode Kit (10x Genomics, 1000256), Human TCR Amplification Kit (10x Genomics, 1000252), Dual Index Kit TT set A (10x Genomics, 1000215) and Dual Index Kit TN set A (10x Genomics, 1000250). The protocol version for >6000 cells was followed and libraries were amplified for 13 cycles (cDNA), 14 cycles (GEX), 8 cycles (FB) or 12+10 cycles (TCR libraries). Library quality and quantity were checked on a Bioanalyzer instrument (Agilent) using a High Sensitivity DNA Assay. Libraries were pooled and sequenced on a Novaseq6000 instrument (Illumina) to a minimum of 25.000 reads/cell for GEX, 10.000 reads/cell for FB, and 5000 reads/cell for TCR libraries.

value: thymus

value: CD3- thymocytes

tag: donor id

tag: donor sex

value: m

tag: donor age_months

tag: library type

value: TCRab


title: TT-CITE-12-TCRab

value: CD3+ thymocytes


title: TT-CITE-10-TCRab

value: f


title: HBE cells treated with smoke extract 24h post exposure 1

description:
HWI-ST1288
Smoke_1

tag: cell line

value: WT


title: TT-CITE-4-TCRab


title: TT-CITE-8-TCRab


title: TT-CITE-9-TCRab


title: TT-CITE-5-TCRab


title: TT-CITE-6-TCRab


title: TT-CITE-3-TCRab


title: TT-CITE-1-TCRab


title: TT-CITE-12-FB

data_processing:
Fastq files were mapped using Cell Ranger version 7.0.0
Assembly: GRCh38
Supplementary files format and content: "GEX" libraries: raw and filtered h5 files obtained from Cell Ranger (RNA mapped alone)
Supplementary files format and content: "FB" libraries: raw and filtered h5 files obtained from Cell Ranger (combined mapping of RNA and ADT)
Supplementary files format and content: "TCRab" libraries: relevant contig and clonotype files obtained from mapping with Cell Ranger Multi
Library strategy: CITE-seq

molecule: protein

value: ADT


title: Liver, Se4

city: Tianjin

first: Jinyang

last: Li

address: No. 32, Xiqi Road, Tianjin Airport Economic Park

institute: Chinese Academy of Sciences

description: mRNA of C57BL/6J mice, Se treated for 14-weeks liver sample 4

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using SOAPnuke (v1.4.0) (parameter– l 15 -q 0.2 -n 0.1)
Clear reads were mapped to Mus musculus genome (GRCm39) using HISAT2 (v2.1.0) with parameters --dta --phred64 unstranded --new-summary -x index -1 read_r1 -2 read_r2（PE）
The counts of reads uniquely mapped to only one gene for each gene were calculated by RSEM (v1.2.8) with default parameters.
The normalized expression values for each gene were calculated by the number of uniquely mapped transcripts per million (TPM) and differential gene expression was determined by DESeq2 package.
Assembly: GCA_000001635.9
Supplementary files format and content: Tab-delimited text files include TPM values for each sample

source_name: liver

growth_protocol: Following a 7-day acclimatization period, six weeks male C57BL/6J specific pathogen-free mice were randomly assigned to normal control group (CON), and selenium-enriched A. oryzae A02 (Se) (daily gavage of 0.5mg/kg Se, dissolved in saline) with 10 replicates mice per group. All mice were fed a normal diet.

extract_protocol:
Total RNA from frozen samples was isolated using TRIzol reagent and an additional clean-up was performed for DNA degradation using the RNeasy mini kit (Qiagen).
RNA libraries for RNA-seq were prepared using standard Illumina protocols.

value: liver

value: hepatocyte

value: Treatment with Se


title: Liver, Se6

description: mRNA of C57BL/6J mice, Se treated for 14-weeks liver sample 6


title: TT-CITE-10-FB


title: TT-CITE-9-FB


title: TT-CITE-8-FB


title: TT-CITE-11-FB


title: TT-CITE-3-FB


title: TT-CITE-4-FB


title: Liver, Se5

description: mRNA of C57BL/6J mice, Se treated for 14-weeks liver sample 5


title: TT-CITE-5-FB


title: Liver, Se1

description: mRNA of C57BL/6J mice, Se treated for 14-weeks liver sample 1


title: Liver, Se3

description: mRNA of C57BL/6J mice, Se treated for 14-weeks liver sample 3


title: Liver, Con6

description: mRNA of C57BL/6J mice, Control for 14-weeks liver sample 6

value: No treatment


title: Liver, Con4

description: mRNA of C57BL/6J mice, Control for 14-weeks liver sample 4


title: TT-CITE-6-FB


title: TT-CITE-1-FB


title: Liver, Con5

description: mRNA of C57BL/6J mice, Control for 14-weeks liver sample 5


title: Liver, Se2

description: mRNA of C57BL/6J mice, Se treated for 14-weeks liver sample 2


title: TT-CITE-12-GEX

value: RNA


title: TT-CITE-11-GEX


title: Liver, Con2

description: mRNA of C57BL/6J mice, Control for 14-weeks liver sample 2


title: TT-CITE-10-GEX


title: Liver, Con3

description: mRNA of C57BL/6J mice, Control for 14-weeks liver sample 3


title: TT-CITE-2-TCRab


title: TT-CITE-8-GEX


title: D7 HTO

city: Melbourne VIC 3004, AU

first: Cameron

middle: Gerard

last: Williams

state: VIC

address: 792 Elizabeth Street

department: Department of Microbiology and Immunology

country: Australia

institute: University of Melbourne

description:
10x Genomics
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz

data_processing:
Data was processed using the “cellranger multi” pipeline from Cell Ranger version 6.1.1 (10x Genomics).
Assembly: mm10
Supplementary files format and content: Tab-separated value files and matrix files

source_name: Spleen

extract_protocol:
Polyclonal CD4+ T cells from spleens were isolated by flow cytometry into a 2% BSA/PBS buffer. Samples from each individual mouse replicate were labelled with a different hashtag reagent, and samples from 5 individual mouse replicates were pooled for isolating CD11a-high/CXCR3+ CD4+ T cells. Polyclonal and TCR transgenic cells were sortedseparately and pooled at a proportion of 9:1. Cells were sorted as single-cells using the Chromium 10x Genomics platform. Approximately 33,000 cells were loaded per channel onto a Chromium controller (10x Genomics) for generation of gel bead-in-emulsions using 10x Genomics Single Cell 5' Reagent Kit v2 (single-cell gene expression and immune repertoire profiling).
Sequencing libraries were prepared using Single Cell 5’ Reagent Kits v2 (10x Genomics) and then converted using the MGIEasy Universal Library Conversion Kit (BGI).

value: Spleen

value: CD4-positive alpha-beta T cell

value: 6-12 weeks


title: TT-CITE-2-FB


title: TT-CITE-6-GEX


title: D7 GEX


title: D7 TCR

description: 10x Genomics


title: TT-CITE-5-GEX


title: LL_WBI_2

city: Guangzhou

first: Shihua

state: Guangdong

address: 651 Dongfeng East Road

department: Collaborative Innovation Center for Cancer Medicine

institute: Sun Yat-sen University Cancer Center

description: low mean dose-rate and low instantaneous dose-rate irradiation

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Fragments Per Kilobase of exon model per Million mapped fragments (FPKM) were calculated.
Assembly: Mouse (GRCm39/mm39)
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Intestine

growth_protocol: Female C57BL6/J mice, aged 7-8 weeks, were purchased from Gempharmatech Co., Ltd (Jiangsu, China) and allowed to acclimate for 1 week before irradiation. All mouse experiments adhered to the approved guidelines of the Institutional Animal Care and Use Committee of Sun Yat-sen University Cancer Center (L102042022060C) and Tsinghua University (22-QR1).

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) according to the manufacturer’s instructions. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 μg of total RNA for the construction of sequencing libraries.
RNA library for lncRNA-seq was prepared as rRNA depletion and stranded method. Briefly, the ribosomal RNA was depleted from total RNA using the rRNA Removal Kit following manufacturer’s instruction. RNA was then fragmented into 250~300 bp fragments, and first strand cDNA was reverse transcribed using fragmented RNA and dNTPs. RNA was degraded using RNase H, and second strand cDNA was synthesized using DNA polymerase I and dNTPs. Remaining overhangs of double-strand cDNA were converted into blunt ends via exonuclease/ polymerase activities. After adenylation of 3’ ends of DNA fragments, sequencing adaptor were ligated to the cDNA. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system. Uridine digestion was performed using Uracil-N-Glycosylase, which was followed by the cDNA amplification using PCR.

treatment_protocol: The HH and mode of irradiation was performed using a compact linear accelerator and the LL mode of irradiations were performed using a clinical Elekta Infinity linac (Elekta AB, Stockholm, Sweden).

value: Intestine

tag: time

tag: Sex

value: Female

value: LL mode irradiation


title: TT-CITE-4-GEX

value: thymus

value: m


title: Liver, Con1

description: mRNA of C57BL/6J mice, Control for 14-weeks liver sample 1


title: TT-CITE-9-GEX

value: CD3- thymocytes


title: HH_WBI_3

description: ultra-high mean dose-rate and ultra-high instantaneous dose-rate irradiation

value: HH mode irradiation


title: LL_Ctrl_2

description: Ctrl

value: untreated


title: TT-CITE-3-GEX


title: HH_WBI_1


title: LL_WBI_1


title: TT-CITE-2-GEX

value: CD3+ thymocytes

value: f


title: LL_Ctrl_3

description: Ctrl


title: LL_WBI_3


title: Donor 26 cultured tissue, fed, rep 2

city: Solna

first: Roland

last: Nilsson

address: Akademiska Stråket 1

department: Dept. of Medicine, Solna

country: Sweden

institute: Karolinska Institutet

data_processing:
Cluster generation and sequencing was carried out by using the Illumina NovaSeq with a read length of 150 nucleotides (paired-end) and aligned to the human transcriptome genome assembly version hg38. Sequencing was performed at either the Vienna Biocenter or by Novogene, as indicated.
Mapped reads were summarized into counts per Ensembl gene (ENSG) using subread v.2.0.3.
Assembly: Human genome hg38
Supplementary files format and content: Total counts per gene (ENSG) and sample in tab-separated text format, as generated by subread v.2.0.3.

source_name: Donor 26

growth_protocol: Tissue samples (~1 cm3) were taken from healthy liver tissue included in the tumor resection, and immediately placed in ice cold preservation solution (Storeprotect Plus, Carnamedica) and processed within 2 hours. Small tissue pieces (~2 mm3) were cut out, washed in ice cold PBS (pH 7.4, Gibco, 10010056) and either snap frozen in dry ice-EtOH bath and stored in -80°C until analysis. The remaining tissue was cut into slices using a vibratome Leica VT1200S (Leica Biosystems; speed: 0.3-0.6 mm/s, amplitude: 3 mm, step size: 150 or 250 um) while submerged in ice-cold preservation solution. The resulting tissue slices were punched with a disposable 8 mm biopsy punch (Kai medical, BP-80F) to obtain slices with a consistent size, transferred onto a cell culture insert (hydrophilic PTFE, 0.4 µm, Millicell, Millipore, PICM03050) in 6-well plates containing 1.3 ml prewarmed custom-synthesized medium and with or without 50% dialyzed human serum and immediately incubated at 37°C and 5% CO2. After a 2h preincubation, the cell culture inserts were transferred to new 6-well plates containing fresh prewarmed medium and returned to the incubator for an additional 22 h. Fresh or cultured liver slices were washed in ice cold PBS, transferred to microcentrifuge tubes, snap frozen and stored in -80°C.

extract_protocol:
Total RNA was extracted from frozen fresh liver tissue pieces and liver slices that had been incubated for 24h. Briefly, the liver samples were homogenized in 2 ml microtubes (Eppendorf, 0030108078) containing 1 ml Qiazol lysis reagent (Qiagen, 79306) together with a 5 mm stainless steel bead (Qiagen, 69989) using a TissueLyzer II (Qiagen) for 2 min at 30 Hz. Then 200 µl chloroform was added to each sample and mixed vigorously by vortex for 15 seconds followed by 3 minutes incubation at RT. Samples were centrifuged at 12,000 g for 15 minutes at 4°C. The upper, colorless aqueous phase containing RNA, were carefully collected. Isolation of total RNA was done on a QIAcube liquid handling system (Qiagen) using RNeasy Mini Kit (Qiagen, 74104) and RNase-Free DNase Set (Qiagen, 79254). All RNA isolation steps were carried out according to the manufacturer’s instructions. Immediately following extraction, the RNA yield and A260:A280 ratio of each sample was determined via NanoDrop 2000 (Thermo Scientific).
RNA was selected using Poly(A) RNA Selection Kit (Lexogen) and sequencing libraries prepared with Lexogen QuantSeq V2. DNA fragments 200-800 bp for RNA-seq were selected.

value: Liver

tag: culture conditions

value: Cultured in fed medium

tag: facility

value: Novogene


title: Donor 26 cultured tissue, fasted, rep 3

value: Cultured in fasted medium


title: Donor 20 cultured tissue, fed, rep 3

source_name: Donor 20


title: HH_WBI_2

tag: strain


title: Donor 26 cultured tissue, fed, rep 3


title: LL_Ctrl_1

description: Ctrl


title: Donor 26 cultured tissue, fasted, rep 2


title: HH_Ctrl_1

description: Ctrl


title: TT-CITE-1-GEX

value: RNA


title: Donor 26 cultured tissue, fed, rep 1


title: Donor 20 cultured tissue, fed, rep 1


title: Donor 26 cultured tissue, fasted, rep 1


title: HH_Ctrl_3

description: Ctrl


title: Donor 20 cultured tissue, fasted, rep 3


title: Donor 20 cultured tissue, fasted, rep 2


title: HH_Ctrl_2

description: Ctrl


title: Kidney, AKI mouse, PTPi@mEVs-administered_3

city: Seoul

first: Hochung

last: Jang

address: 5 Hwarang-ro 14-gil

country: South Korea

institute: Korea Institute of Science and Technology (KIST)

data_processing:
"Timmomatic" was used to trim adapter and low scores of reads.
"STAR" was used to align reads to genome.
"MarkDuplicates" was used to remove duplicates.
"htseq-count" was used to count reads per genes.
Assembly: GRCh38.p14
Supplementary files format and content: The csv file contains the raw counts for each group

source_name: Kidney

extract_protocol:
RNA was harvested using phenol-chloroform based RNA extraction. 100 ng of total RNA was used for the construction of sequencing libraries
RNA libraries for RNA-seq were prepared using Tn5-based NGS Library Prep Kit following manufacturer's protocol

value: Kidney

value: WT


title: Kidney, AKI mouse, PTP@mEVs-administered_2


title: Donor 2 cultured tissue, rep 3

source_name: Donor 2

value: Vienna Biocenter


title: Kidney, Normal mouse (surgery but not IR injury)_2

value: PBS


title: Donor 20 cultured tissue, fasted, rep 1


title: Donor 2 cultured tissue, rep 1


title: Donor 2 fresh liver tissue, rep 1

value: Untreated, freshly resected tissue


title: Donor 2 fresh liver tissue, rep 2


title: Kidney, Normal mouse (surgery but not IR injury)_1


title: Kidney, AKI mouse, PBS-administered_3


title: Kidney, AKI mouse, PTPi@mEVs-administered_1


title: Kidney, Normal mouse (surgery but not IR injury)_3


title: Donor 20 cultured tissue, fed, rep 2


title: Kidney, AKI mouse, PBS-administered_2


title: Kidney, AKI mouse, PBS-administered_1


title: BMP4_human_EB_5D

city: Hang Zhou

first: Tao

last: cheng

state: Zhe Jiang

address: 886 Yuhangtang Road

department: Institute of genetics

institute: Zhejiang University

description: 10x Genomics

data_processing:
Illumina sequencing reads were aligned to the zebrafish (GRCz11) or human mRNA reference genome (GRCh38) using the 10x Genomics CellRanger pipeline (version 3.0.2) with default parameters.
Assembly: GRCz11, GRCh38
Supplementary files format and content: tar archive includes filtered_gene_bc_matrices after running CellRanger pipeline

source_name: embryonic

growth_protocol: Bmp4 explants were cultured in Dulbecco's modified Eagle’s medium (DMEM/F-12 with 10 mM HEPES, 1x MEM with non-essential amino acids, 7 mM CaCl2, 1 mM sodium pyruvate, 50 μg/ml gentamycin, 100 μM 2-mercaptoethanol, 1× antibiotic-antimycotic ,10% serum replacement) and kept at 28.5℃.BMP4 induced human embryoids were cultured in a 96-well U-shaped ultra-low plate with culture medium (TeSR-E6 medium supplemented with 0.5% N2 and 0.5% B27 to support cell growth). Small molecule compounds and recombinant proteins inducing differentiation were added according to the treatment protocol. Samples were collected on day 5 and 6 of differentiation.

extract_protocol:
Single-cell RNA of each sample was extracted by following the Chromium Controller and Chromium Single Cell 30 Library & Gel Bead Kit  v3.1(10x Genomics, PN-1000121) protocol.
Libraries were prepared using Single Cell 3′Library & gel Bead kit v3.1 (10x Genomics, Cat# PN-1000121) according to the manufacturer’s protocol for 10000 cell recovery.

treatment_protocol: To generate bmp4 explants, bmp4 (8-10 pg) mRNA was injected into one animal pole blastomere at the 128-cell stage. Then the animal pole region was explanted and raised to 24hpf. To generate BMP4 induced human embryoids, human embryonic stem cells (hESCs) of the H9 line were grown on Matrigel-coated 12-well plates for a period ranging from 48 to 72 hours, utilizing them when they reached an approximate confluence of 70%. On the initial day of the experiment, both wild-type H9 cells and ihBmp4 cells were treated with accutase to facilitate their dissociation. They were then transferred to 96-well U-bottom low attachment plates for culture. The seeding density was adjusted to 1300 cells per well for H9 cells and 400 cells per well for ihBmp4 cells, using 50 μl of an aggregation medium based on TeSR-E6 and supplemented with the ROCK inhibitor 10μM Y27632. After a 24-hour incubation period, both types of cells formed embryoid bodies (EBs) in their respective wells. These H9 and ihBmp4 EBs were then co-cultured in the same well, with 80 μl of the TeSR-E6 based medium to encourage fusion. Between days 2 and 4 of the culture period, the EBs were subjected to an induction process to enhance Bmp4 expression, which initiated the morphogenesis phase. The culture medium was replaced with a fresh TeSR-E6 medium that included 75 ng ml-1 Doxycycline and 50 ng ml-1 FGF2 to stimulate these processes. Starting from day 4, the Doxycycline and FGF2 were omitted from the culture medium. The EBs were then maintained in a TeSR-E6 based medium for continued growth and development.

value: embryonic

value: human embryonic stem cells

value: stem cell


title: PBS treated BMDMs (untrained control, end of plate) #3

city: Chicago

first: Luis

middle: Bruno

last: Barreiro

state: IL

address: 900 E 57th St

department: Genetic Medicine

institute: University of Chicago

data_processing:
FastQ files from two sequencing runs merged per replicate. Applied NGmerge to remove adapter sequences and bowtie2 to align to the mm10 genome assembly. Samtools was used to remove PCR duplicates and mitochondrial sequences. Call peaks with macs2 and filter out blacklisted regions. Finally, define consensus peaks with beta glucan #3 as reference file using bedtools intersect -wa -a. Generate a raw counts file of these consensus peaks. Generate .bed files for each replicate using bedtools.
Assembly: mm10
Supplementary files format and content: 1- narrowPeak files called by macs2
Supplementary files format and content: 2- tab-delimited text file of raw counts for each replicate
Model differential accessibility with limma. Generate normalized counts (CPM).
Supplementary files format and content: 3- tab-delimited text file of counts per million values for each replicate
Performed transcription factor footprinting with HINT-ATAC from the regulatory genomics toolbox
Supplementary files format and content: 4- tab-delimited text file of hint-atac transcription factor footprinting outputs

source_name: Bone Marrow

growth_protocol: Mature BMDMs were plated at 10e5 cells per well in 200 μL media in 96-well flat-bottomed plates (Corning) and rested overnight at 37°C and 5% CO2 and then trained as described below. On day 5, instead of pre-treatment with IFN- γ, cells instead received fresh media.

extract_protocol:
On day 6, cells were detached from the plate in lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3mM MgCl2, 0.1% IGEPAL CA-630 (abcam)) and transferred to 96-well v-bottomed plates (Corning), then centrifuged at 500 G for 5 minutes.
DNA libraries for ATAC-seq were prepared using Nextera XT DNA Library Preparation Kit (including index v2, set A) following manufacturer specifications.

treatment_protocol: 24 hour incubation with 10μM of either 5-fluoroindole carboxylic acid, fenoterol, hydrocortisone, hydroquinone, myricetin, or nerol; or 100μg/mL of beta glucan; or 20uL of PBS in media.

value: Bone Marrow

value: Bone Marrow Derived Macrophages

value: Macrophages

value: Female

value: Phosphate Buffered Saline


title: PBS treated BMDMs (untrained control, end of plate) #2


title: BMP4_human_EB_6D

description: 10x Genomics


title: WT AIRE 4D6, 24hr Dox, A-485, rep2

description:
QZseq4_12
EUseq24hr_log2FCA485vsDMSO.bw

data_processing:
*library strategy: 5'-ethynyl uridine RNA-seq
QC was performed on demultiplexed sequencing files using FASTQC (v0.11.3).
Sequencing reads were trimmed using Trimmomatic (v0.36) and aligned to reference genome (GRCh38 primary assembly, release v43) using STAR (v2.7.0a).
BAM files generated during the STAR alignment were converted to bigwig files using deepTools (v3.5.1) with the following settings: bamCoverage --scaleFactor "scale factor" --smoothLength 150 --binSize 50 -e 200. "scale factor" was calculated as 1 divided by size factor that was obtained during DEseq2 analysis.
After verification of consistency between replicates, bigwig files were averaged using WiggleTools (v1.2.2) and bedGraphToBigWig (v366). Bigwig files showing log2 fold-changes between two groups were generated using deepTools (v3.5.1) with the bigwigCompare function.
Assembly: hg38
Supplementary files format and content: bigwig files contain EU-seq signals for each sample
Supplementary files format and content: bigwig files showing log2 fold-change between two groups of samples

extract_protocol:
Total RNA was immediately extracted by using Direct-zol RNA Miniprep Kit (Zymo Research, R2052) with DNase I digestion. Ribosomal RNA was depleted using the NEBNext rRNA Depletion Kit v2 (New England Biolabs, E7405L). 5'-EU labeled nascent RNA was biotinylated and pulled down using the Click-iT Nascent RNA Capture Kit (Invitrogen, #C10365) according to the manufacturer's protocol.
5'-EU labeled RNA captured on streptavidin-beads was then immediately used for sequencing library preparation using the NEBNext Ultra II RNA Library Prep Kit (New England Biolabs, E7775S).

treatment_protocol: Dox-inducible AIRE-expressing 4D6 cells were cultured in the absence or presence of 1 µg/mL dox for 24 hrs. Equal volume of DMSO or 3 µM A-485 was added to cells 4 hrs prior, and 0.5 mM 5'-EU was added to the cell culture 30min prior to RNA extraction.

value: thymic epithelial cells

value: WT AIRE

tag: molecule type

value: 5-EU labeled nascernt RNA


title: PBS treated BMDMs (untrained control, end of plate) #1


title: Beta Glucan treated BMDMs #3

value: Beta Glucan

tag: concentration

value: 100 μg/mL


title: WT AIRE 4D6, 24hr Dox, A-485, rep1

description:
QZseq4_6
EUseq24hr_log2FCA485vsDMSO.bw


title: WT AIRE 4D6, 24hr Dox, DMSO, rep2

description:
QZseq4_11
EUseq24hr_log2FCA485vsDMSO.bw

value: 24hr Dox, DMSO


title: Donor 2 cultured tissue, rep 2

value: Liver

value: Cultured in fasted medium

value: Vienna Biocenter


title: WT AIRE 4D6, 24hr Dox, DMSO, rep1

description:
QZseq4_5
EUseq24hr_log2FCA485vsDMSO.bw


title: Beta Glucan treated BMDMs #1


title: Fenoterol treated BMDMs #2

value: Fenoterol

value: 10 μM


title: Fenoterol treated BMDMs #1


title: WT AIRE 4D6, no Dox, DMSO, rep2

description:
QZseq4_7
EUseq24hr_log2FCdox.bw

value: no Dox, DMSO


title: WT AIRE 4D6, no Dox, A-485, rep2

description:
QZseq4_8
EUseq24hr_log2FCdox.bw

value: no Dox, A-485


title: WT AIRE 4D6, no Dox, A-485, rep1

description:
QZseq4_2
EUseq24hr_log2FCdox.bw


title: H3K27ac, Dox, rep1

value: Dox 24hr


title: WT AIRE 4D6, no Dox, DMSO, rep1

description:
QZseq4_1
EUseq24hr_log2FCdox.bw


title: Hydroquinone treated BMDMs #1

value: Bone Marrow

value: Bone Marrow Derived Macrophages

value: Macrophages

value: Hydroquinone


title: Nerol treated BMDMs #3

value: Female

value: Nerol


title: H3K27ac, Dox, rep3

value: thymic epithelial cells

value: WT AIRE


title: Nerol treated BMDMs #1


title: Hydroquinone treated BMDMs #3


title: H3K4me3, Dox, rep3


title: H3K4me3, Dox, rep2


title: H3K27ac, Dox, rep2


title: H3K4me3, Dox, rep1


title: Myricetin treated BMDMs #3

value: Myricetin


title: Nerol treated BMDMs #2


title: H3K4me3, no Dox, rep3

value: no Dox


title: Hydrocortisone treated BMDMs #2

value: Hydrocortisone


title: Hydrocortisone treated BMDMs #1


title: Fenoterol treated BMDMs #3


title: H3K4me3, no Dox, rep2


title: H3K4me3, no Dox, rep1


title: Myricetin treated BMDMs #2


title: 5-Fluoroindole Carboxylic Acid treated BMDMs #3

value: 5-Fluoroindole Carboxylic Acid


title: Myricetin treated BMDMs #1


title: H3K4me1, Dox, rep3


title: H3K4me1, Dox, rep2


title: 5-Fluoroindole Carboxylic Acid treated BMDMs #2


title: Hydrocortisone treated BMDMs #3


title: H3K4me1, Dox, rep1


title: MSC-KSHV-MEM-ST_3

city: La Plata

first: Martin

middle: Carlos

last: Abba

state: Buenos Aires

country: Argentina

institute: School of Medical Sciences - UNLP

data_processing:
The raw short-read sequences  were quality-checked and trimmed to remove adapters and low-quality bases using the Rfastp R/Bioconductor package.
The preprocessed reads were then aligned and mapped to the human genome reference GRCh38 using the Subread aligner algorithm provided by Rsubread R/Bioconductor package.
The aligned reads (BAM files) from each sample were employed to calculate gene expression abundance at gene level using the featureCounts function provided by the Rsubread package.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file of the raw counts per sample
Supplementary files format and content: raw_counts.txt

source_name: MSC rKSHV-219 infected in MEM media, short-term culture, replicate 3

growth_protocol: Human MSCs were isolated from bone marrow aspirates (25–50 mL) purchased from AllCells (Emeryville, CA) under appropriate informed consent and institutional review board approval. The experiments were performed using MSCs in passages 4–7. All human MSC were cultured in MEM alpha media: supplemented with 20% heat-inactivated fetal bovine serum (FBS) (MSC media); or KS-like pro-angiogenic growth medium (KS media).

extract_protocol:
RNA from hMSC was isolated and purified using the RNeasy mini kit (Qiagen). RNA concentration and integrity were measured on an Agilent 2100 Bioanalyzer (Agilent Technologies). Only RNA samples with RNA integrity values (RIN) over 8.0 were considered for subsequent analysis.
We performed paired-end RNA-seq / Trueseq sequencing using the Illumina NovaSeq 6000 platform.

treatment_protocol: The prepared KSHV inoculum (recombinant KSHV 219), MOI of 8, and 8 μg/ml of Polybrene were mixed and added to the cultured cells. After centrifugation at 700 × g for 60 minutes, the inoculum was removed after 3 hours, and 2 ml of culture medium was added to each well. For long-term infection and selection, cells were maintained under puromycin selection for one month until all the culture cells were GFP-positive.

value: Primary hMSC

value: bone marrow-derived human Mesenchymal Stem Cells

tag: infection status

value: rKSHV-219 infected

tag: media

value: MEM media

value: short-term culture


title: 5-Fluoroindole Carboxylic Acid treated BMDMs #1

tag: tissue

value: Bone Marrow

tag: treatment

value: 10 μM


title: MSC-KSHV-MEM-ST_2

source_name: MSC rKSHV-219 infected in MEM media, short-term culture, replicate 2

tag: cell type


title: Flunisolide treated BMDMs #2

value: Bone Marrow Derived Macrophages

value: Macrophages

tag: genotype

value: Flunisolide


title: Flunisolide treated BMDMs #1

value: Female


title: PBS treated BMDMs (untrained control, start of plate) #3

value: Phosphate Buffered Saline


title: MSC-KSHV-MEM-ST_1

source_name: MSC rKSHV-219 infected in MEM media, short-term culture, replicate 1


title: MSC-KSHV-MEM-LT_2

source_name: MSC rKSHV-219 infected in MEM media, long-term culture, replicate 2

value: Long-term culture


title: MSC-KSHV-MEM-LT_3

source_name: MSC rKSHV-219 infected in MEM media, long-term culture, replicate 3


title: MSC-KSHV-MEM-LT_1

source_name: MSC rKSHV-219 infected in MEM media, long-term culture, replicate 1


title: MSC-KSHV-KS-ST_2

source_name: MSC rKSHV-219 infected in KS media, short-term culture, replicate 2

value: KS media


title: PBS treated BMDMs (untrained control, start of plate) #1


title: VSVZ, KO, 8 Weeks, Rep4

city: Toronto

first: Scott

last: Yuzwa

state: Ontario

address: 1 King's College Circle, Medical Sciences Building, Rm 6316

department: Laboratory Medicine and Pathobiology

country: Canada

institute: University of Toronto

data_processing:
Fastq files were generated with bcl2fastq2 v2.20
Fastq files were aligned and reads counted with Salmon.
Assembly: Gencode M29
Supplementary files format and content: tab-delimited text file contains the raw counts for each sample produced from Salmon and summarized by tximport
Supplementary files format and content: Quantification files for each sample produced by Salmon.

source_name: Brain

extract_protocol:
The periventricular area was dissected and RNA was isolated using the Qiagen RNeasy Plus Mini Kit
RNA-seq libraries were prepared with the NEBNext® Ultra™ II DNA Library Prep Kit

value: Brain

value: VSVZ Tissue

value: KO

value: 129 Stain Background


title: PBS treated BMDMs (untrained control, start of plate) #2


title: MSC-KSHV-KS-ST_3

source_name: MSC rKSHV-219 infected in KS media, short-term culture, replicate 3

value: Primary hMSC

value: bone marrow-derived human Mesenchymal Stem Cells


title: VSVZ, KO, 8 Weeks, Rep3

value: Male


title: VSVZ, KO, 8 Weeks, Rep1


title: MSC-KSHV-KS-LT_3

source_name: MSC rKSHV-219 infected in KS media, long-term culture, replicate 3

value: rKSHV-219 infected


title: VSVZ, KO, 8 Weeks, Rep2


title: MSC-KSHV-KS-ST_1

source_name: MSC rKSHV-219 infected in KS media, short-term culture, replicate 1

value: short-term culture


title: MSC-KSHV-KS-LT_2

source_name: MSC rKSHV-219 infected in KS media, long-term culture, replicate 2


title: VSVZ, WT, 8 Weeks, Rep4

value: WT


title: MSC-KSHV-KS-LT_1

source_name: MSC rKSHV-219 infected in KS media, long-term culture, replicate 1


title: MSC-Control-MEM-ST_3

source_name: MSC non-infected in MEM media, short-term culture, replicate 3

value: non-infected

value: MEM media


title: VSVZ, WT, 8 Weeks, Rep3


title: VSVZ, WT, 8 Weeks, Rep2


title: Flunisolide treated BMDMs #3

value: Bone Marrow

value: Bone Marrow Derived Macrophages

value: Macrophages

value: Flunisolide

value: 10 μM


title: MSC-Control-MEM-ST_2

source_name: MSC non-infected in MEM media, short-term culture, replicate 2


title: VSVZ, WT, 8 Weeks, Rep1

value: Brain

value: Female


title: MSC-Control-MEM-ST_1

source_name: MSC non-infected in MEM media, short-term culture, replicate 1


title: JUN  Cut&Tag, WT mESCs (EpiLC-0h), in which JUN was rescued

city: Beijing

first: Xuehui

last: Lv

address: No.5 Yiheyuan Road, Haidian district, Beijing, 100871, China

institute: Peking University

data_processing:
For the bioinformatics analysis, the adapters were cut by Trimmomatic. The data were aligned to mouse genome sequence (mm10) using Bowtie2 with options: –local–very-sensitive-local–no-unal–nomixed–no-discordant–phred33 -I 10 -X 700 . Samtools was used to remove duplication from bam files. The bigWig files were generated by bamCoverage using CPM as normalization method to show IGV examples . The differential peaks between samples were called using Macs2 with default parameters. ComputerMatrix was used to calculate the peak signals around poised-specific genes from bigWig file normalized by CPM, and the results were visualized by plotHeatmap. The read counts in each peak were extracted using bedtools .
Assembly: mm10
Supplementary files format and content: The bigWig files normalized by CPM of each sample were provided to visualize in IGV or UCSC genome browser.

growth_protocol: The mESCs stated as EpiLC 0h/2iLif were cultured in 2i/Lif medium, while  those stated as EB D0/SL were cultured in Serum/Lif medium.ADFNK differentiation medium and N2B27 basal medium were used for EB differentiation and EpiLC differentiation, respectively.

extract_protocol:
Briefly, cells were harvested, counted, and centrifuged for 3 min at 1,000 rpm at room temperature. About 10,000 cells were washed using washing buffer followed by incubation with Concanavalin A beads at room temperature for 10 min. Next, 1 μl primary antibody was incubated with cells on a rotating platform at 4°C overnight. Secondary antibody incubation followed by pA/G-Tn5 incubation were performed on a rotating platform at room temperature each for 1 h. Between each of the above steps, the beads were washed using corresponding buffer. To activate the activity of Tn5, the beads were incubated in Tagmentation buffer at 37°C for 1 h followed by stop tagmentation using EDTA and extract DNA using DNA clean beads.
Cut&Tag libraries preparation using Hyperactive universal CUT&Tag Assay Kit for Illumina (Vazyme, TD903)

value: mESCs

value: FLII and JUN double knockouts


title: MSC-Control-MEM-LT_2

source_name: MSC non-infected in MEM media, long-term culture, replicate 2

value: Primary hMSC

value: Long-term culture


title: MSC-Control-MEM-LT_1

source_name: MSC non-infected in MEM media, long-term culture, replicate 1

value: bone marrow-derived human Mesenchymal Stem Cells


title: 2iLif, KH2-JUN, + Dox 12h, Rep3

data_processing:
For PolyA(+) RNA-seq,Adapteor was removed by trimmomatic-0.39, HISAT2 software was used to align sequencing reads to reference mRNA.,mouse Cdna database(UCSC, NCBI37)  was used for alignment. Reads per Million was calculated for the normalization
Assembly: mm10,hg38
Supplementary files format and content: the txt file provide the CPM of each gene in every sample

growth_protocol: The mESCs stated as EpiLC 0h/2iLif were cultured in 2i/Lif medium, while  those stated as EB D0/SL were cultured in Serum/Lif medium.The human naïve hESCs (WIBR3) were cultured on MEF feeder layer in 5i/L/A medium.ADFNK differentiation medium and N2B27 basal medium were used for EB differentiation and EpiLC differentiation, respectively.

extract_protocol:
TRIzol reagent (Invitrogen) was used to isolate total RNA according to the manufacturer’s instructions.
The RNA was reverse transcribed with superscript IV, followed by 3’ DNA adaptor ligation using T4 RNA ligase (NEB). Libraries were amplified with Q5 2× Master Mix. Finally, the DNA above 175 bp in libraries was isolated by gel-purification.

value: 2iLif, +Dox 12h


title: DGCR8 FLII double knockouts mESC, FLII  and DGCR8 rescue, Rep3

value: DGCR8 FLII double knockouts

value: FLII and DGCR8 rescue


title: 2iLif, KH2-JUN, + Dox 12h, Rep2


title: MSC-Control-KS-ST_3

source_name: MSC non-infected in KS media, short-term culture, replicate 3

value: non-infected

value: KS media

value: short-term culture


title: DGCR8 FLII double knockouts mESC, FLII  and DGCR8 rescue, Rep2


title: MSC-Control-KS-LT_3

source_name: MSC non-infected in KS media, long-term culture, replicate 3


title: MSC-Control-KS-LT_2

source_name: MSC non-infected in KS media, long-term culture, replicate 2


title: MSC-Control-KS-ST_2

source_name: MSC non-infected in KS media, short-term culture, replicate 2


title: MSC-Control-KS-LT_1

source_name: MSC non-infected in KS media, long-term culture, replicate 1


title: EpiLC 6h, KH2-WT, DMSO, Rep3

description:
EpiLC_6h_KH2WT_DMSO.Rep3
EpiLC_MEK_inhibitor.txt

value: EpiLC 6h, DMSO


title: EpiLC 48h, KH2-WT, DMSO, Rep1

description:
EpiLC_48h_KH2WT_DMSO.Rep1
EpiLC_MEK_inhibitor.txt

value: EpiLC 48h, DMSO


title: EpiLC 6h, KH2-WT, PD0325901 1μm, Rep2

description:
EpiLC_6h_KH2WT_MEK_inhibitor.Rep2
EpiLC_MEK_inhibitor.txt

value: EpiLC 6h, PD0325901 1μm


title: EpiLC 6h, KH2-WT, PD0325901 1μm, Rep3

description:
EpiLC_6h_KH2WT_MEK_inhibitor.Rep3
EpiLC_MEK_inhibitor.txt


title: EpiLC 6h, KH2-WT, PD0325901 1μm, Rep1

description:
EpiLC_6h_KH2WT_MEK_inhibitor.Rep1
EpiLC_MEK_inhibitor.txt


title: hESCs transfected with siDGCR8, Rep3

description:
hESC_siDGCR8_5iLA_Rep3
Human_DGCR8_FLII_DROSHA_Knockdown.txt

value: hESCs

value: WT

value: transfected with siDGCR8


title: EpiLC 6h, KH2-WT, DMSO, Rep2

description:
EpiLC_6h_KH2WT_DMSO.Rep2
EpiLC_MEK_inhibitor.txt

value: mESCs


title: hESCs transfected with siDROSHA, Rep3

description:
hESC_siDROSHA_5iLA_Rep3
Human_DGCR8_FLII_DROSHA_Knockdown.txt

value: transfected with siDROSHA


title: hESCs transfected with siDGCR8 and siFLII, Rep3

description:
hESC_siDGCR8FLII_5iLA_Rep3
Human_DGCR8_FLII_DROSHA_Knockdown.txt

value: transfected with siDGCR8 and siFLII


title: hESCs transfected with siNC, Rep3

description:
hESC_siNC_5iLA_Rep3
Human_DGCR8_FLII_DROSHA_Knockdown.txt

value: transfected with siNC


title: EpiLC 0h, KH2-WT, DMSO, Rep1

description:
EpiLC_0h_KH2WT_DMSO_Rep1
EpiLC_MEK_inhibitor.txt

value: EpiLC 0h, DMSO


title: EpiLC 6h, KH2-WT, DMSO, Rep1

description:
EpiLC_6h_KH2WT_DMSO.Rep1
EpiLC_MEK_inhibitor.txt


title: hESCs transfected with siDROSHA, Rep2

description:
hESC_siDROSHA_5iLA_Rep2
Human_DGCR8_FLII_DROSHA_Knockdown.txt


title: hESCs transfected with siDGCR8 and siFLII, Rep2

description:
hESC_siDGCR8FLII_5iLA_Rep2
Human_DGCR8_FLII_DROSHA_Knockdown.txt


title: EpiLC 48h, KH-JUN,+Dox, Rep3

description:
EpiLC_48h_KH2JUN_Dox.Rep3
EpiLC_JUN_overexpression.txt

value: EpiLC 48h, +Dox


title: MSC-Control-MEM-LT_3

source_name: MSC non-infected in MEM media, long-term culture, replicate 3

value: Primary hMSC

value: bone marrow-derived human Mesenchymal Stem Cells

value: MEM media

value: Long-term culture


title: EpiLC 24h, KH-JUN,+Dox, Rep3

description:
EpiLC_24h_KH2JUN_Dox.Rep3
EpiLC_JUN_overexpression.txt

value: EpiLC 24h, +Dox


title: EpiLC 12h, KH-JUN,+Dox, Rep3

description:
EpiLC_12h_KH2JUN_Dox.Rep3
EpiLC_JUN_overexpression.txt

value: EpiLC 12h, +Dox


title: hESCs transfected with siDGCR8, Rep2

description:
hESC_siDGCR8_5iLA_Rep2
Human_DGCR8_FLII_DROSHA_Knockdown.txt


title: MSC-Control-KS-ST_1

source_name: MSC non-infected in KS media, short-term culture, replicate 1

value: non-infected

value: KS media

value: short-term culture


title: EpiLC 6h, KH-JUN,+Dox, Rep3

description:
EpiLC_6h_KH2JUN_Dox.Rep3
EpiLC_JUN_overexpression.txt

value: EpiLC 6h, +Dox


title: hESCs transfected with siDROSHA, Rep1

description:
hESC_siDROSHA_5iLA_Rep1
Human_DGCR8_FLII_DROSHA_Knockdown.txt

value: hESCs

value: WT


title: EpiLC 48h, KH2-WT, PD0325901 1μm, Rep1

description:
EpiLC_48h_KH2WT_MEK_inhibitor.Rep1
EpiLC_MEK_inhibitor.txt

value: mESCs


title: hESCs transfected with siDGCR8 and siFLII, Rep1

description:
hESC_siDGCR8FLII_5iLA_Rep1
Human_DGCR8_FLII_DROSHA_Knockdown.txt

value: transfected with siDGCR8 and siFLII


title: EpiLC 24h, KH-JUN,no Dox, Rep3

description:
EpiLC_24h_KH2JUN_noDox.Rep3
EpiLC_JUN_overexpression.txt

value: EpiLC 24h


title: hESCs transfected with siDGCR8, Rep1

description:
hESC_siDGCR8_5iLA_Rep1
Human_DGCR8_FLII_DROSHA_Knockdown.txt

value: transfected with siDGCR8


title: hESCs transfected with siNC, Rep1

description:
hESC_siNC_5iLA_Rep1
Human_DGCR8_FLII_DROSHA_Knockdown.txt

value: transfected with siNC


title: EpiLC 6h, KH-JUN,no Dox, Rep3

description:
EpiLC_6h_KH2JUN_noDox.Rep3
EpiLC_JUN_overexpression.txt

value: EpiLC 6h


title: EpiLC 48h, KH-JUN,+Dox, Rep2

description:
EpiLC_48h_KH2JUN_Dox.Rep2
EpiLC_JUN_overexpression.txt

value: EpiLC 48h, +Dox


title: BC-Pt01

first: Yihong

address: Zhong shan Er lu

institute: Sun Yat-sen University

data_processing:
The Seurat package (v.4.4.0) (http://satijalab.org/seurat) was used for filtering, data normalization, dimensionality reduction, clustering and further analysis of the single-cell RNA-seq data in R software (v4.2.3).
Assembly: GRCh38
Supplementary files format and content: tsv files containing cell annotation

source_name: primary breast tumor

extract_protocol:
Fresh tumor tissues were washed in ice-cold RPMI 1640, mechanically minced into small pieces and dissociated into single-cell suspension.  Cell count and viability was determined using the fluorescence Cell Analyzer (Countstar® Rigel S2) with acridine orange/propidium iodide (AO/PI) reagent (Cat# CS2-0106, Nexcelom Bioscience) after removal of erythrocytes (Cat# R1010, Solarbio). Cells with > 90% viability were washed twice with RPMI 1640 and resuspended in PBS containing 0.04% BSA at a concentration of 1 × 106 cells/mL .
Libraries were sequenced on an Illumina NovaSeq 6000 with PE150 read length.

value: primary breast tumor

value: female

tag: age


title: EpiLC 24h, KH-JUN,+Dox, Rep2

description:
EpiLC_24h_KH2JUN_Dox.Rep2
EpiLC_JUN_overexpression.txt

value: EpiLC 24h, +Dox


title: SUM-159PT TAZ rep3, ATAC

city: Los Angeles

first: Simon

last: Knott

state: CA

address: 8687 Melrose Ave.

institute: Cedars Sinai

data_processing:
ATAC-seqs were read and aligned to the UCSC hg38 genome reference using ENCODE pipeline.
Peaks were called using MACS2. The consensus peak's read counts were obtained using featureCounts function in Rsubread package in R.
Assembly: hg38
Supplementary files format and content: tab separated values files include ATAC raw counts for each sample.
Supplementary files format and content: tab separated values file includes peak annotation for each peakID

source_name: breast

extract_protocol:
Suspensions of 50,000 cells with viability > 90% were subjected to nuclei isolation, followed by Tn5-mediated transposition.
ATAC-Seq libraries were prepared using the Omni-ATAC-Seq protocol. The Zymo DNA Clean and Concentrator 5 kit was used to clean up the transposed reactions, after which Illumina adapter sequences and barcodes were added to the transposed DNA fragments in a pre-amplification step.  Quantitative PCR was performed to determine the appropriate number of additional PCR amplification cycles, as to not overamplify the reaction.  Amplified libraries were purified using the Zymo DNA Clean and Concentrator 5 kit, followed by a double-sided SPRIselect Bead cleanup (Beckman Coulter, Brea, CA).   Final libraries were analyzed on a 4200 TapeStation (Agilent Technologies, Santa Clara, California) and quantified via quantitative PCR using the Collibri Library Quantification Kit (Thermo Fisher Scientific, Waltham, MA).

value: breast

value: EZH2i (tazemetostat)


title: EpiLC 12h, KH-JUN,+Dox, Rep2

description:
EpiLC_12h_KH2JUN_Dox.Rep2
EpiLC_JUN_overexpression.txt

value: EpiLC 12h, +Dox


title: SUM-159PT TAZ rep2, ATAC


title: EpiLC 6h, KH-JUN,+Dox, Rep2

description:
EpiLC_6h_KH2JUN_Dox.Rep2
EpiLC_JUN_overexpression.txt


title: BC-Pt03


title: EpiLC 24h, KH-JUN,no Dox, Rep2

description:
EpiLC_24h_KH2JUN_noDox.Rep2
EpiLC_JUN_overexpression.txt


title: SUM-159PT DMSO rep3, ATAC

value: DMSO


title: EpiLC 48h, KH-JUN,no Dox, Rep2

description:
EpiLC_48h_KH2JUN_noDox.Rep2
EpiLC_JUN_overexpression.txt

value: EpiLC 48h


title: EpiLC 12h, KH-JUN,no Dox, Rep2

description:
EpiLC_12h_KH2JUN_noDox.Rep2
EpiLC_JUN_overexpression.txt

value: EpiLC 12h


title: SUM-159PT TAZ rep1, ATAC


title: EpiLC 48h, KH-JUN,no Dox, Rep3

description:
EpiLC_48h_KH2JUN_noDox.Rep3
EpiLC_JUN_overexpression.txt


title: SUM-159PT DMSO rep2, ATAC


title: hESCs transfected with siNC, Rep2

description:
hESC_siNC_5iLA_Rep2
Human_DGCR8_FLII_DROSHA_Knockdown.txt

value: hESCs

value: WT


title: EpiLC 48h, KH-JUN,+Dox, Rep1

description:
EpiLC_48h_KH2JUN_Dox.Rep1
EpiLC_JUN_overexpression.txt

value: mESCs


title: SUM-159PT TAZ+IPATA (COMBO) rep3, ATAC

value: EZH2i (tazemetostat) and AKTi (ipatasertib)


title: SUM-159PT TAZ+IPATA (COMBO) rep2, ATAC


title: EpiLC 12h, KH-JUN,no Dox, Rep3

description:
EpiLC_12h_KH2JUN_noDox.Rep3
EpiLC_JUN_overexpression.txt


title: EpiLC 12h, KH-JUN,+Dox, Rep1

description:
EpiLC_12h_KH2JUN_Dox.Rep1
EpiLC_JUN_overexpression.txt


title: EpiLC 6h, KH-JUN,+Dox, Rep1

description:
EpiLC_6h_KH2JUN_Dox.Rep1
EpiLC_JUN_overexpression.txt

value: EpiLC 6h, +Dox


title: SUM-159PT DMSO rep1, ATAC


title: SUM-159PT IPATA rep3, ATAC

value: AKTi (ipatasertib)


title: SUM-159PT IPATA rep2, ATAC


title: EpiLC 48h, KH-JUN,no Dox, Rep1

description:
EpiLC_48h_KH2JUN_noDox.Rep1
EpiLC_JUN_overexpression.txt


title: SUM-159PT IPATA rep1, ATAC


title: BC-Pt02


title: EpiLC 24h, KH-JUN,no Dox, Rep1

description:
EpiLC_24h_KH2JUN_noDox.Rep1
EpiLC_JUN_overexpression.txt

value: EpiLC 24h


title: SUM-149PT TAZ rep3, ATAC


title: EpiLC 6h, KH-JUN,no Dox, Rep1

description:
EpiLC_6h_KH2JUN_noDox.Rep1
EpiLC_JUN_overexpression.txt

value: EpiLC 6h


title: SUM-149PT TAZ rep2, ATAC


title: 2iLif, KH2-JUN, + Dox 48h, Rep1

description:
2ilif_Dox_48h_KH2JUN_Dox.Rep1
EpiLC_JUN_overexpression.txt

value: 2iLif, +Dox 48h


title: EpiLC 6h, KH-JUN,no Dox, Rep2

description:
EpiLC_6h_KH2JUN_noDox.Rep2
EpiLC_JUN_overexpression.txt


title: EpiLC 12h, KH-JUN,no Dox, Rep1

description:
EpiLC_12h_KH2JUN_noDox.Rep1
EpiLC_JUN_overexpression.txt


title: SUM-149PT TAZ rep1, ATAC


title: 2iLif, KH2-JUN, + Dox 12h, Rep1

description:
2ilif_Dox_12h_KH2JUN_Dox.Rep1
EpiLC_JUN_overexpression.txt

value: 2iLif, +Dox 12h


title: EpiLC 24h, KH-JUN,+Dox, Rep1

description:
EpiLC_24h_KH2JUN_Dox.Rep1
EpiLC_JUN_overexpression.txt

value: EpiLC 24h, +Dox


title: 2iLif, KH2-JUN, + Dox 24h, Rep1

description:
2ilif_Dox_24h_KH2JUN_Dox.Rep1
EpiLC_JUN_overexpression.txt

value: 2iLif, +Dox 24h


title: 2iLif, KH2-JUN, + Dox 6h, Rep1

description:
2ilif_Dox_6h_KH2JUN_Dox.Rep1
EpiLC_JUN_overexpression.txt

value: 2iLif, +Dox 6h


title: SUM-149PT IPATA rep3, ATAC

value: breast


title: SUM-149PT IPATA rep2, ATAC


title: SUM-149PT IPATA rep1, ATAC


title: SUM-159PT TAZ+IPATA (COMBO) rep1, ATAC


title: SUM-149PT DMSO rep3, ATAC

value: DMSO


title: EpiLC 48h, KH2-FLII,+ Dox, Rep3

description:
EpiLC_48h_KH2FLII_Dox.Rep3
EpiLC_FLII_overexpression.txt

value: EpiLC 48h, +Dox


title: EpiLC 0h, 2iLif, KH2-JUN, no Dox, Rep1

description:
2ilif_EpiLC_0h_KH2JUN_noDox.Rep1
EpiLC_JUN_overexpression.txt

value: EpiLC 0h, 2iLif,


title: SUM-149PT DMSO rep2, ATAC


title: SUM-149PT DMSO rep1, ATAC


title: EpiLC 6h, KH2-FLII,+ Dox, Rep3

description:
EpiLC_6h_KH2FLII_Dox.Rep3
EpiLC_FLII_overexpression.txt


title: EpiLC 48h, KH2-FLII,no Dox, Rep3

description:
EpiLC_48h_KH2FLII_noDox.Rep3
EpiLC_FLII_overexpression.txt

value: EpiLC 48h


title: SUM-149PT TAZ+IPATA (COMBO) rep2, ATAC


title: SUM-149PT TAZ+IPATA (COMBO) rep3, ATAC


title: EpiLC 12h, KH2-FLII,no Dox, Rep3

description:
EpiLC_12h_KH2FLII_noDox.Rep3
EpiLC_FLII_overexpression.txt

value: EpiLC 12h


title: SUM-149PT TAZ+IPATA (COMBO) rep1, ATAC


title: EpiLC 6h, KH2-FLII,no Dox, Rep3

description:
EpiLC_6h_KH2FLII_noDox.Rep3
EpiLC_FLII_overexpression.txt

value: mESCs


title: MDA-MB-231 TAZ rep3, ATAC

value: EZH2i (tazemetostat)


title: EpiLC 48h, KH2-FLII,+ Dox, Rep2

description:
EpiLC_48h_KH2FLII_Dox.Rep2
EpiLC_FLII_overexpression.txt


title: EpiLC 12h, KH2-FLII,+ Dox, Rep2

description:
EpiLC_12h_KH2FLII_Dox.Rep2
EpiLC_FLII_overexpression.txt

value: EpiLC 12h, +Dox


title: MDA-MB-231 TAZ rep1, ATAC


title: MDA-MB-231 IPATA rep3, ATAC

value: AKTi (ipatasertib)


title: EpiLC 48h, KH2-FLII,no Dox, Rep2

description:
EpiLC_48h_KH2FLII_noDox.Rep2
EpiLC_FLII_overexpression.txt


title: EpiLC 6h, KH2-FLII,+ Dox, Rep2

description:
EpiLC_6h_KH2FLII_Dox.Rep2
EpiLC_FLII_overexpression.txt

value: EpiLC 6h, +Dox


title: EpiLC 12h, KH2-FLII,no Dox, Rep2

description:
EpiLC_12h_KH2FLII_noDox.Rep2
EpiLC_FLII_overexpression.txt


title: EpiLC 12h, KH2-FLII,+ Dox, Rep3

description:
EpiLC_12h_KH2FLII_Dox.Rep3
EpiLC_FLII_overexpression.txt


title: MDA-MB-231 IPATA rep2, ATAC


title: MDA-MB-231 IPATA rep1, ATAC


title: MDA-MB-231 DMSO rep3, ATAC


title: EpiLC 24h, KH2-FLII,+ Dox, Rep1

description:
EpiLC_24h_KH2FLII_Dox.Rep1
EpiLC_FLII_overexpression.txt


title: EpiLC 6h, KH2-FLII,no Dox, Rep2

description:
EpiLC_6h_KH2FLII_noDox.Rep2
EpiLC_FLII_overexpression.txt

value: EpiLC 6h


title: EpiLC 6h, KH2-FLII,+ Dox, Rep1

description:
EpiLC_6h_KH2FLII_Dox.Rep1
EpiLC_FLII_overexpression.txt


title: MDA-MB-231 DMSO rep2, ATAC


title: MDA-MB-231 TAZ+IPATA (COMBO) rep2, ATAC

value: EZH2i (tazemetostat) and AKTi (ipatasertib)


title: EpiLC 12h, KH2-FLII,+ Dox, Rep1

description:
EpiLC_12h_KH2FLII_Dox.Rep1
EpiLC_FLII_overexpression.txt


title: MDA-MB-231 DMSO rep1, ATAC


title: MDA-MB-231 TAZ+IPATA (COMBO) rep3, ATAC


title: MDA-MB-231 TAZ+IPATA (COMBO) rep1, ATAC


title: HCC1937 DMSO rep3, ATAC


title: EpiLC 48h, KH2-FLII,no Dox, Rep1

description:
EpiLC_48h_KH2FLII_noDox.Rep1
EpiLC_FLII_overexpression.txt


title: EpiLC 0h, KH2-FLII,+ Dox, Rep1

description:
EpiLC_0h_KH2FLII_Dox.Rep1
EpiLC_FLII_overexpression.txt

value: EpiLC 0h, +Dox


title: MDA-MB-231 TAZ rep2, ATAC


title: EpiLC 12h, KH2-FLII,no Dox, Rep1

description:
EpiLC_12h_KH2FLII_noDox.Rep1
EpiLC_FLII_overexpression.txt


title: HCC1937 DMSO rep2, ATAC


title: EpiLC 24h, KH2-FLII,no Dox, Rep1

description:
EpiLC_24h_KH2FLII_noDox.Rep1
EpiLC_FLII_overexpression.txt

value: EpiLC 24h


title: EpiLC 6h, KH2-FLII,no Dox, Rep1

description:
EpiLC_6h_KH2FLII_noDox.Rep1
EpiLC_FLII_overexpression.txt


title: HCC1937 DMSO rep1, ATAC


title: EpiLC 48h, KH2-FLII,+ Dox, Rep1

description:
EpiLC_48h_KH2FLII_Dox.Rep1
EpiLC_FLII_overexpression.txt


title: HCC1937 TAZ+IPATA (COMBO) rep2, ATAC


title: EpiLC 0h, KH2-FLII,no Dox, Rep1

description:
EpiLC_0h_KH2FLII_noDox.Rep1
EpiLC_FLII_overexpression.txt

value: EpiLC 0h


title: EpiLC 48h, JUN-/- mESCs, Rep3

description:
EpiLC_48h_JUN_KO.Rep3
EpiLC_FLII_KO_JUN_KO.txt

value: JUN knockout


title: HCC1937 TAZ+IPATA (COMBO) rep1, ATAC

value: breast


title: Histone H4 shutoff strain, 3hr glucose, Rep B

city: Boston

first: Zarmik

last: Moqtaderi

address: 240 Longwood Avenue C2-355

department: BCMP

institute: Harvard Medical School

description:
3' READS
DCB220-1_YP_3hGlucose_READS_RepsABmerged_RelCountsByPosition_1_to_400.txt

data_processing:
Prep fastq files for mapping (discard reads with ambiguous base calls, remove of library adapters, count/remove of initial Ts in each read) python
Map to Sac cer 3 genome, using first 17 nt after adapter and initial T removal; no mismatches allowed, keeping only uniquely mapped reads, Bowtie
Discard reads for which the number of initial Ts could be explained by A residues in the genome adjacent to the mapped position, python
Tally remaining read starts by strand and genomic position, scaling each replicate to 25M total reads (or combined reps scaled to 50M), python
Assembly: Sac cer 3
Supplementary files format and content: Tab-delimited text files giving relative 3' isoform end frequencies by coordinate in the 400nt downstream of each CDS
Supplementary files format and content: Tab-delimited text files of merged A and B replicates giving relative isoform frequencies by genomic coordinate  in the 400nt downstream of each CDS
Library strategy: 3'READS

organism: Saccharomyces cerevisiae

growth_protocol: Exponential growth at 30°C in YPD or YPGal

extract_protocol:
Total RNA extracted with hot acid phenol and subjected to Qiagen RNEasy purification with DNase treatment
3' READS (Jin, Y. et al., 2015 Curr Protoc Mol Biol 110, 4.23.21-24.23.17)

treatment_protocol: As described under "treatment,"  some samples  were treated with 1µM rapamycin for 1 hr for the anchor-away method,  other cells were filtered and switched from YPGal to YPD for 3 hours for shutoff

value: hhf1::TRP1 Kan-pGal1-HHF2

value: YP + 2% glucose for 3hr


title: EpiLC 6h,JUN-/- mESCs, Rep3

description:
EpiLC_6h_JUN_KO.Rep3
EpiLC_FLII_KO_JUN_KO.txt


title: HCC1806 DMSO rep3, ATAC

value: DMSO


title: Histone H4 shutoff strain, 3hr glucose, Rep A


title: Histone shutoff control, 0hr glucose, Rep B

description:
3' READS
DCB220-1_YPGal_0h_READS_RepsABmerged_RelCountsByPosition_1_to_400.txt

value: YP + 2% galactose, before shift to glucose


title: EpiLC 48h, Flii-/- mESCs, Rep3

description:
EpiLC_48h_FLII_KO.Rep3
EpiLC_FLII_KO_JUN_KO.txt

value: FLII knockout

value: EpiLC 48h


title: HCC1806 DMSO rep2, ATAC


title: Histone H3 shutoff strain, 3hr glucose, Rep B

description:
3' READS
DCB200_1_YP_3hGlucose_READS_RepsABmerged_R1_RelCountsByPosition_1_to_400.txt

value: hht1::TRP1 Kan-pGal1-HHT2


title: Histone H3 shutoff strain, 3hr glucose, Rep A


title: EpiLC 6h,Flii-/- mESCs, Rep3

description:
EpiLC_6h_FLII_KO.Rep3
EpiLC_FLII_KO_JUN_KO.txt

value: mESCs


title: SPT6 and SPT16 double Anchor-away strain, 1hr rapamycin, Rep B

description:
3' READS
JZY139_YPD_1hRap_READS_RepsABmerged_RelCountsByPosition_1_to_400.txt

value: YFR1321 parent with SPT6-FRB-KanMX6 SPT16-FRB-KanMX6

value: YPD, 1uM rapamycin for 1 hr


title: HCC1806 DMSO rep1, ATAC