title: donor 06.21, control


title: donor 07.36, MSA

status: Public on Mar 29 2022

type: SRA

city: Phoenix

first: Ignazio

middle: Stefano

last: Piras

state: Arizona

address: 445 N. Fifth Street, Phoenix

country: USA

institute: Translational Genomic Research Institute

library_source: transcriptomic

data_processing:
Reads alignment:  STAR
Gene level summarization:  featureCounts
Normalization:  DESeq2
Assembly: GRCh37
Supplementary files format and content: *txt, raw counts by gene and sample

molecule: total RNA

organism: Homo sapiens

source_name: post-mortem cerebellum (white matter)

extract_protocol:
Total DNAse-treated RNA was extracted using the Qiagen RNAeasy kit (Qiagen). Quality was assessed by Bioanalyzer (Agilent)
Sequencing libraries were prepared with 250 ng of total RNA using Illumina’s Truseq RNA Sample Preparation Kit v2 (Illumina, Inc.) following the manufacturer’s protocol and purifying poly-A mRNAs with poly-T oligos attached to magnetic beads. The final library was sequenced by 50 bp paired-end sequencing on a HiSeq 2500 (Illumina, Inc.)

tag: tissue

value: post-mortem cerebellum (white matter)

tag: Sex

value: Male

tag: age at death

tag: post mortem interval (hours)

tag: disease state

value: Multiple system atrophy (MSA)

tag: diagnosis

value: MSA

tag: source

value: Brain and Body Donor Program, Sun City, Arizona


title: donor 01.03, MSA

value: Female


title: donor 03.63, control

value: control


title: donor 03.55, MSA


title: Preleukemic stage, Ick:IRF4 fish 5

city: Singapore

first: Tze King

last: Tan

address: 14 Medical Drive

department: Cancer Science Institute

country: Singapore

institute: National University of Singapore

data_processing:
Annotations from Ensembl (GRCz11) for zebrafish genes and transcripts were used and concatenated with mCherry and human IRF4 (ENSG00000137265) gene information.  Single cell data were generated using mkref from cellranger package.
Alignment, barcode assignation, and generation of cell-gene-count matrices were all performed using cellranger count from 10x genomics version 3.1.0
cellranger count --id zv11_{sampleID} --fastqs={directory_scSeq} --sample={sampleID}--transcriptome={mkgtf generated STAR library}
Assembly: GRCz11 Danio Rerio + mCherry + Human IRF4 (ENSG00000137265)
Supplementary files format and content: HDF5 Gene-Barcode Matrix format containing UMI counts of each gene for individual cells.  The data files can be deconvoluted to tsv and mtx files using cellranger reanalyze

organism: Danio rerio

source_name: Zebrafish

growth_protocol: The human IRF4 gene and mCherry fluorescent marker gene were transduced under the zebrafish lck promoter in zebrafish.  The cells were harvested at different stages and sorted by flow cytometry based on mCherry fluorescence expression.  A zebrafish which was transduced only with mCherry was used as a control.

extract_protocol:
After sorting, the cells were washed and processed for barcoding using the 10x Genomics Chromium Single Cell 3' Solution v2 kit following manufacturer's instructions.
Illumina P5 and P7 sequences and sample index sequences are added during the Sample Index PCR. The final library fragments contain the P5, P7, Read 1 and Read 2 sequences used in Illumina bridge amplification and sequencing. Additionally, each fragment contains the 10x Barcode, UMI and cDNA insert sequence used in data analysis.

treatment_protocol: No treatment

tag: cells

value: mCherry sorted cells

tag: transgenic

value: IRF4 overexpression


title: Preleukemic stage, Ick:IRF4 fish 3


title: Preleukemic stage, Ick:IRF4 fish 1


title: Preleukemic stage, Ick:IRF4 fish 4


title: Preleukemic stage, Ick:IRF4 fish 2


title: CP27-DRUG

city: Bristol

first: Elisa

last: Avolio

address: Upper Maudlin Street

department: Bristol Medical School

country: United Kingdom

institute: University of Bristol

data_processing:
RNA-Seq was carried out on an Illumina HiSeq platform, with a 2x150bp configuration, ~20M reads per sample.
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b, and BAM files generated.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted. After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis.
Using DESeq2, a comparison of gene expression between the groups of samples was performed.
Genome_build: Homo sapiens GRCh38 reference genome available on ENSEMBL
Supplementary_files_format_and_content: Count.txt

source_name: patient #3 cardiac pericytes

growth_protocol: Cells were cultured for 10 days with full growth medium (ECGM2 Promocell) and the drug PD0325901 at a final 250nM concentration

extract_protocol:
Total RNA was extracted using ice-cold Qiazol
RNA libraries were prepared for sequencing using standard Illumina protocols. RNA-Seq was carried out on an Illumina HiSeq platform, with a 2x150bp configuration, ~20M reads per sample.

value: Heart

tag: cell type

value: cardiac pericytes

tag: treatment


title: CASMC donor1

source_name: donor #1 coronary artery smooth muscle cells

growth_protocol: Cells were cultured for a few days and RNA collected at confluence

value: coronary artery smooth muscle cells

value: no treatment


title: CP24-DRUG

source_name: patient #1 cardiac pericytes


title: CP27-CTRL

growth_protocol: Cells were cultured for 10 days with full growth medium (ECGM2 Promocell) and DMSO vehicle at the same dilution as the drug

value: DMSO (this is the drug vehicle)


title: CASMC donor2

source_name: donor #2 coronary artery smooth muscle cells


title: CP25-CTRL

source_name: patient #2 cardiac pericytes


title: CP24-CTRL


title: CP25-DRUG


title: Lesional CD4+ T Cells - Obese Control (wt Bl6) Mice given Rosi HFD

city: San Francisco

first: Alexander

last: Marson

state: CA

address: 1650 Owens Street

institute: Gladstone-UCSF Institute of Genomic Immunology

description: scRNAseq for single sample

data_processing:
Raw fastqs were aligned to the `refdata-cellranger-mm10-3.0.0` reference provided by 10x Genomics.
Filtering for expressed genes and high-quality cells was performed as described in the publication.
RNA Velocity estimation was performed with Velocyto (v0.17.17) and attached to merged scRNAseq expression matrices in scVelo (v0.2.2)
Genome_build: mm10
Supplementary_files_format_and_content: Filtered Feature-Barcode Matrices outputted from Cellranger (10x Genomics).

organism: Mus musculus

source_name: sorted lesional skin CD4+ T cells

extract_protocol:
CD4+ T cells were sorted via flow cytometry from a single cell suspension of lesional immune cells
Single cell RNA sequencing libraries were prepared with the 10x Genomics Chromium Single Cell 3’ Reagent Kit (v3).

tag: strain

tag: main figures

tag: agent

value: Rosiglitazone

tag: diet

value: High Fat Diet


title: Lesional CD4+ T Cells - Obese Mice

description: scRNAseq for single sample


title: Lesional CD4+ T Cells - Control (CD4-Cre) Mice - Lean

description: scRNAseq for single sample

value: Normal Chow


title: Lesional CD4+ T Cells - Obese PPARg TKO (CD4-Cre PPARg fl/fl) Mice given Control HFD

description: scRNAseq for single sample


title: Lesional CD4+ T Cells - Obese Control (wt Bl6) Mice given Control HFD

description: scRNAseq for single sample


title: Sorted intestinal crypt epithelial cells from Apln-/- adult mice, biological replicate 3

city: Geneva

first: Isabelle

last: Dupanloup

address: Rue Michel-Servet, 1

country: Switzerland

institute: University of Geneva

data_processing:
Software to map the reads to the mm10 reference genome: STAR v2.6.1
Software to estimate the read counts for each gene: htseq-count
Genome_build: mm10
Supplementary_files_format_and_content: Table of raw gene counts for each gene (rows) and each sample (columns)

growth_protocol: Adult wild-type control (C57Bl/6) or Apln-/- mice were used for experiments

extract_protocol:
Total RNA was isolated using the Qiagen RNeasy Plus Micro Kit (Qiagen) and RNA integrity was verified on a Fragment Analyzer (Advanced Analytical). mRNA was amplified using the Ovation Pico WTA System V2 (Nugen).
RNA-seq libraries were prepared from 100 ng of total RNA using the Nextera DNA Flex Kit (Illumina)

treatment_protocol: Small intestines were harvested and digested with Liberase TL and crypt epithelial cells were sorted as single, live, CD31neg, CD45neg, EpCAM+, CD44+ cells.

tag: genotype

value: Apln-/-

tag: age

value: adult


title: Sorted intestinal crypt epithelial cells from wild-type adult mice, biological replicate 1

value: wild-type control (C57Bl/6)


title: Sorted intestinal crypt epithelial cells from wild-type adult mice, biological replicate 2


title: Sorted intestinal crypt epithelial cells from wild-type adult mice, biological replicate 3


title: Lesional CD4+ T Cells - Obese PPARg TKO (CD4-Cre PPARg fl/fl) Mice given Rosi HFD

description: scRNAseq for single sample


title: Sorted intestinal crypt epithelial cells from Apln-/- adult mice, biological replicate 1


title: Sorted intestinal crypt epithelial cells from Apln-/- adult mice, biological replicate 2


title: Lesional CD4+ T Cells - PPARg TKO (CD4-Cre PPARg fl/fl) Mice - Lean

description: scRNAseq for single sample


title: Lesional CD4+ T Cells - Lean Mice

description: scRNAseq for single sample


title: Mouse_lung-Native-1k-Nextera_TD-55C-Nextera_Tn5-Rep3

city: Tucson

first: Hao

last: Zhang

state: AZ

address: 1230 N Cherry Ave

department: CMM

institute: The University of Arizona

library_source: genomic

data_processing:
The paired-end reads were preprocessed using Trimmomatic v0.36 to trim the Nextera adaptors and low quality reads with the parameter setting as “LEADING:3 TRAILING:3 SLIDINGWINDOW:4:10 MINLEN:20”.
The trimmed reads were mapped to either the hg19 human genome or mm10 mouse genome reference contigent upon the sample source using Bowtie2 v2,2.9 with the parameter setting as “-X 2000 -3 1” to restrict the maximum fragment length of 2000 bp and trim 1 base from the 3’ end of each read before alignment. Following mapping, only the reads confidently (MAPQ ≥ 10) mapped to assembled nuclear chromosomes, and in proper pairs (we used the “-f3” and “-F12” options in SAMtools v1.4) were preserved for downstream analysis.
Picard v2.20.2 “MarkDuplicates” was used to remove duplicate reads and estimate library complexity.
Peaks were called by MACS2 v2.1.2 using deduplicated bed files and considering a 200 bp window centered on the read start using the parameters “--nomodel --keep-dup all --extsize 200 --shift -100”. Because each peak may have multiple summits (and will therefore be listed multiple times in the resulting peak bed file), the peaks output from MACS2 were then merged into a single peak set for each sample using bedtools “merge”.
Genome_build: Data from GM12878 were mapped to hg19 and data from mouse lungs were mapped to mm10
Supplementary_files_format_and_content: Matrix of the number of reads overlapping each peak for each GM12878 sample was generated by "multiBamSummary" (deepTools v3.5.1) using deduplicated bam files and a non-overlapping peak set that combined the peaks identified from each condition. The first column contains the coordinates for each peak.
Supplementary_files_format_and_content: Matrix with deviation scores for each motif and each GM12878 sample was computed by chromVAR v1.12.0. The first column shows the human motif ID from JASPAR CORE database.

molecule: genomic DNA

source_name: lung

growth_protocol: The GM12878 cell line was cultured at 37°C with 5% CO2 in RPMI 1640 medium (GIBCO, cat. no. 11875-093) containing 15% FBS (GIBCO, cat. no. 10437-028), 100 U/ml Penicillin Streptomycin (GIBCO, cat. no. 15140-122). Cells were counted and split to 300,000 cells/ml three times a week

extract_protocol:
1) Nuclei isolation from native GM12878:  ~2 million native cells were collected and washed using 4 ml 1X PBS (pH 7.4, Gibco, cat. no. 10-010-023) supplemented with 0.04% BSA (PBSB), and then resuspended in 200 μl of ATAC-seq lysis buffer. Lysis buffer was made by supplementing ATAC resuspension buffer (RSB) with detergents. RSB buffer is 10 mM Tris-HCl (pH 7.5, Invitrogen, cat. no. 15567027), 10 mM NaCl (Invitrogen, cat. no. AM9759) and 3 mM MgCl2 (Invitrogen, cat. no. AM9530G) in nuclease free water. RSB was made in bulk and stored at 4°C long-term. On the day of the experiment, the ATAC lysis buffer was made by adding 0.1% IGEPAL (Sigma, cat. no. I3021), 0.01% digitonin (Invitrogen, cat. no. BN2006), and 0.1% Tween-20 (Bio-Rad, cat. no. 1610781) to RSB. Detergent percentages reported are final concentrations. After resuspending cell pellets in the lysis buffer, they were incubated on ice for 3 min, and then the lysis was stopped by adding 1 ml RSB containing 0.1% Tween-20. Nuclei were then centrifuged at 500 r.c.f for 10 min at 4 °C and resuspended in 200 ul of PBSB. The nuclei were counted and diluted to 3,100 nuclei/μl with PBSB. Then, 6.6 μl of diluted nuclei (20,460 total nuclei) were transferred to 12.4 μl of transposition reaction (10 μl of 2X Tagmentation buffer, 0.2 μl of 1% digitonin, 0.2 μl of 10% Tween-20, and 2 μl of H2O). We then added 1 μl of transposase to the transposition mix containing nuclei. Tagmentation was carried out on a thermocycler at either 37°C or 55°C for 30 min. Tagmented DNA was cleaned up using Zymo DNA Clean and Concentrator-5 columns with 5X binding buffer (Zymo, cat. no. D4004). 2) Nuclei isolation from fixed GM12878: the frozen, fixed cells (~ 2 million) were incubated in a 37°C water bath until thawed (~ 1 min). After thawing, the cells stored in 1 ml freezing buffer were diluted with 3 ml of PBSB. The fixed cells were collected by centrifuging at 500 r.c.f for 10 min at 4°C, resuspended again in 1 ml PBSB, and then centrifuged at 500 r.c.f for 5 min at 4°C to wash the cells. Following washing, the nuclei were isolated and tagmented as described in the ATAC-seq protocol for native samples described above. After tagmentation, crosslinks were then reversed for the fixed, tagmented nuclei by adding 60 μl of reverse-crosslinking buffer containing 0.067% SDS and 1.33 mg/ml Proteinase K (Qiagen, cat. no. 19133) in Qiagen Buffer EB (final concentration of 0.05% SDS and 1 mg/ml Proteinase K) directly to the tagmentation reactions, and incubating the samples at 65°C for 15 hours in a thermomixer with shaking at 1,000 r.p.m. Following crosslink reversal, tagmented DNA was purified using Zymo DNA Clean and Concentrator-5 columns with 5X binding buffer. 3) The isolation of mouse lung nuclei was performed following the single-nucleus isolation protocol described by Joshi Nikita and Misharin Alexander. In brief, we cut a ~0.1-0.2 g piece from the lung sample removed from -80°C and kept it on dry ice until use. The tissue block was thawed almost completely on ice for 1 min, and then injected with 1 ml of cell lysis buffer, which was made of 1x cOmplete protease inhibitor cocktail (1 tablet per 10 ml solution, Sigma-Aldrich, Cat. 11836153001) in Nuclei EZ prep buffer (Sigma-Aldrich, Cat. NUC101), into the center of the tissue with a 30G needle and syringe. Following lysis buffer injection, the tissue was chopped into small pieces with scissors and then transferred along with the lysing buffer into a gentleMACS C tube (Miltenyi Biotec, Cat. 130-096-334). An additional 1 ml of lysing buffer was added into the C tube to make a final volume of 2 ml. The minced tissue was then homogenized using a gentleMACS tissue dissociator by running the ‘m_lung_01’ program followed by the first 20 sec of the ‘m_lung_02’ program. After homogenization, tissue lysate was briefly centrifuged to reduce foam and then passed through a 40 μm cell strainer in a 50ml tube. After passing the sample through, the strainer was rinsed with 4 ml of washing buffer (PBS with 1% BSA). The nuclei were counted with Trypan blue in the presence of 2X Omni buffer (20 mM Tris HCl (pH 7.5), 10 mM MgCl2 and 20% Dimethyl Formamide), and then collected by centrifugation at 500 r.c.f for 5 min at 4°C. Then, we removed the supernatant and resuspended the nuclei to a concentration of 4-5 million nuclei/ml in a nuclei freezing buffer containing 50 mM Tris-HCI (pH 8.0, Invitrogen, cat. no. 15568025), 5 mM Magnesium Acetate (Sigma, cat. no. 63052), 25% glycerol (VWR, cat. no. RC3290-32), 0.1 mM EDTA (Fisher, cat .no. AM9260G), 5 mM DTT (Fisher, cat. no. P2325), and 2% protease inhibitor (Sigma, cat. no. P8340). 1 ml aliquots of the nuclei were flash frozen in liquid nitrogen and then transferred to a liquid nitrogen dewar for long-term storage.
5 μl of purified DNA out of 10 μl purified product was amplified in a 25 μl PCR reaction containing NEBNext PCR master mix (1X final), 0.5X SYBR Green and 1.25 μM of Ad1 primer from Buenrostro JD. et al., 2013 and 1.25 μM of an N7 primer containing custom barcodes. Samples were amplified on a Bio-Rad CFX Connect Real-time cycler using the following program: 72°C for 5 min; 98°C for 30s; cycling at 98°C for 10 s, 63°C for 30 s, 72°C for 1 min; samples were monitored and stopped when it appeared that their exponential amplification was leveling off. At this point the samples were allowed to incubate at 72°C for an additional minute to fully extend the library. All native samples were stopped after 9 cycles and fixed samples were stopped after 10 cycles. PCR products were cleaned up with Ampure XP beads. A double size selection was performed to remove DNA fragments larger than ~1500 bp (with 0.4X AMPure XP beads) and smaller than ~100 bp (with 1.5X AMPure XP beads). To do this, we added 25 μl of Qiagen Buffer EB to each PCR reaction to bring the volume to 50 μl, and then added 20 μl of beads (homogenizing the mixture well by pipetting), followed by a 5 min incubation at RT. The samples were then put on a magnet stand to bind the beads. 68 μl of the supernatant was transferred to a new 1.5 ml tube and an additional 53 μl of beads were added to the supernatant and resuspended thoroughly (we estimated that 19.4 μl of the 68 μl transferred was bead buffer and 48.6 μl was sample, so to get to 1.5X beads for the second selection we needed to add an additional 72.9 - 19.4 μl of beads, which we rounded off to 53 μl). After another 5 min at RT, the samples were placed on the magnet to clear the beads and the supernatant was discarded. Beads were washed twice with 200 μl of 80% EtOH (made fresh for each experiment). After the second wash, the beads were briefly spun, and any residual ethanol was removed. The beads were then put back on the magnet stand and air dried for 1 min. Then, beads were removed from the magnet and resuspended in 22 μl of Buffer EB, incubated for 2 min at RT and then placed on the magnet stand again. 20 μl of supernatant was transferred to a new tube. The 96 ATAC-seq libraries of the GM12878 cell line and 72 libraries of mouse lungs were pooled separately and sequenced with 2x76 bp reads in two independent runs on an NextSeq 550 Platform using the High Output Kits.

treatment_protocol: For fixation, cells were washed and resuspended in 9.2 ml of RPMI medium without additives, then crosslinked with 270 μl of 37% formaldehyde (1% final, VWR, cat. no. MK501602) for 10 min at room temperature. The fixation reaction was quenched by adding 500 μl of 2.5 M glycine (0.125 M final, Sigma, 50046-50G) and incubated for 5 min at room temperature, and then on ice for 15 min. The fixed cells were collected and resuspend in the freezing buffer, which contains 50 mM Tris-HCI (pH 8.0, Invitrogen, cat. no. 15568025), 5 mM Magnesium Acetate (Sigma, cat. no. 63052), 25% glycerol (VWR, cat. no. RC3290-32), 0.1 mM EDTA (Fisher, cat. no. AM9260G), 5 mM DTT (Fisher, cat. no. P2325), 2% protease inhibitor (Sigma, cat. no. P8340). Then, 2 million cells per aliquot were flash frozen in liquid nitrogen for long-term storage.

tag: tissue

value: Lung

tag: mouse id

tag: nuclei state

value: flash frozen

tag: nuclei input


title: Mouse_lung-Native-1k-Omni_TD-55C-Nextera_Tn5-Rep3


title: Mouse_lung-Native-1k-Nextera_TD-55C-Homemade_Tn5-Rep3


title: Mouse_lung-Native-1k-Omni_TD-55C-Homemade_Tn5-Rep3


title: Mouse_lung-Native-1k-THS_TD-55C-Homemade_Tn5-Rep3


title: Mouse_lung-Native-1k-THS_TD-55C-Nextera_Tn5-Rep3


title: granulosa_cell_1_3

status: Public on Mar 30 2022

city: Guangzhou

first: Xiaoping

last: Liu

address: Shougouling Road

country: China

institute: The Sixth Affliated Hospital of Sun Yat-sen University

data_processing:
RNAs were subjected to first strand and second strand cDNA synthesis following by
adaptor ligation and enrichment with a low-cycle according to instructions of NEBNext® Ultra™ RNA Library
Prep Kit for Illumina (NEB, USA).
Genome_build: hs37d5
Supplementary_files_format_and_content: Excel files include FPKM values for each Sample ...

source_name: granulosa cells

extract_protocol:
Granulosa cells were collected and total RNA were extracted using Trizol reagent. Fragmented  RNA (the average length was approximately 200 bp) were subjected to first strand and second strand cDNA  synthesis following by adaptor ligation and enrichment with a low-cycle according to instructions of NEBNext®  Ultra™ RNA Library Prep Kit for Illumina (NEB, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Five samples were collected from the patients underlying COS protocol and 5 samples from mild protocol

value: mild ovarian stimulation


title: Mouse_lung-Native-1k-THS_TD-37C-Homemade_Tn5-Rep3


title: Mouse_lung-Native-1k-Nextera_TD-37C-Homemade_Tn5-Rep3


title: Mouse_lung-Native-1k-THS_TD-37C-Nextera_Tn5-Rep3


title: Mouse_lung-Native-20k-Nextera_TD-55C-Homemade_Tn5-Rep3


title: Mouse_lung-Native-1k-Nextera_TD-37C-Nextera_Tn5-Rep3


title: Mouse_lung-Native-20k-THS_TD-55C-Nextera_Tn5-Rep3


title: Mouse_lung-Native-20k-Omni_TD-55C-Nextera_Tn5-Rep3


title: Mouse_lung-Native-20k-Omni_TD-37C-Nextera_Tn5-Rep3


title: Mouse_lung-Native-20k-Nextera_TD-37C-Homemade_Tn5-Rep3


title: Mouse_lung-Native-1k-Omni_TD-37C-Nextera_Tn5-Rep3


title: Mouse_lung-Native-20k-THS_TD-55C-Homemade_Tn5-Rep3


title: Mouse_lung-Native-20k-Nextera_TD-55C-Nextera_Tn5-Rep3


title: Mouse_lung-Native-20k-Omni_TD-55C-Homemade_Tn5-Rep3


title: Mouse_lung-Native-20k-THS_TD-37C-Homemade_Tn5-Rep3


title: Mouse_lung-Native-20k-Nextera_TD-37C-Nextera_Tn5-Rep3


title: Mouse_lung-Native-1k-THS_TD-55C-Homemade_Tn5-Rep2


title: Mouse_lung-Native-1k-Omni_TD-55C-Homemade_Tn5-Rep2


title: Mouse_lung-Native-20k-THS_TD-37C-Nextera_Tn5-Rep3


title: Mouse_lung-Native-1k-Nextera_TD-55C-Homemade_Tn5-Rep2


title: Mouse_lung-Native-1k-Omni_TD-37C-Homemade_Tn5-Rep3


title: Mouse_lung-Native-1k-Omni_TD-37C-Homemade_Tn5-Rep2


title: Mouse_lung-Native-1k-THS_TD-37C-Homemade_Tn5-Rep2


title: Mouse_lung-Native-1k-THS_TD-55C-Nextera_Tn5-Rep2


title: Mouse_lung-Native-1k-Omni_TD-55C-Nextera_Tn5-Rep2


title: Mouse_lung-Native-20k-Omni_TD-37C-Homemade_Tn5-Rep3


title: Mouse_lung-Native-1k-THS_TD-37C-Nextera_Tn5-Rep2


title: Mouse_lung-Native-1k-Nextera_TD-55C-Nextera_Tn5-Rep2


title: Mouse_lung-Native-1k-Nextera_TD-37C-Nextera_Tn5-Rep2


title: Mouse_lung-Native-20k-Nextera_TD-55C-Homemade_Tn5-Rep2


title: Mouse_lung-Native-20k-THS_TD-55C-Homemade_Tn5-Rep2


title: Mouse_lung-Native-1k-Omni_TD-37C-Nextera_Tn5-Rep2


title: Mouse_lung-Native-1k-Nextera_TD-37C-Homemade_Tn5-Rep2


title: Mouse_lung-Native-20k-Omni_TD-55C-Homemade_Tn5-Rep2


title: Mouse_lung-Native-20k-THS_TD-37C-Homemade_Tn5-Rep2


title: Mouse_lung-Native-20k-THS_TD-55C-Nextera_Tn5-Rep2


title: Mouse_lung-Native-20k-Omni_TD-55C-Nextera_Tn5-Rep2


title: Mouse_lung-Native-20k-Omni_TD-37C-Nextera_Tn5-Rep2


title: Mouse_lung-Native-20k-Nextera_TD-37C-Homemade_Tn5-Rep2


title: Mouse_lung-Native-20k-THS_TD-37C-Nextera_Tn5-Rep2


title: Mouse_lung-Native-20k-Omni_TD-37C-Homemade_Tn5-Rep2


title: Mouse_lung-Native-20k-Nextera_TD-37C-Nextera_Tn5-Rep2


title: H9_HEP_Heat_12DAH_rep1

city: Kyoto

first: Ken-ichiro

last: Kamei

state: Kyoto

address: Yoshida-Ushinomiya-cho, Sakyo-ku

department: iCeMS

country: Japan

institute: Kyoto University

description: mRNA-seq data from 39˚C-treated cells at 12DAH, replicate 1

data_processing:
Base-calling and demultiplexing were performed with EPI2ME software (Oxford NANOPORE Technologies).
Failed reads were discarded and Fast5 files were converted into FASTQ and FASTA files using EPI2ME software.
Generated FASTQ files were loaded to BioJupies for alignment with human genomes and annotation.
the counts were analysed using TCC in R Bioconducter. Briefly, the counted data set was introduced into the TCC-GUI package.
Genome_build: human_matrix.h5 v2
Supplementary_files_format_and_content: Gene counts were normalized using TMM (Trimmed mean of M values) methods in the edgeR package with the parameters: Number of Iterations = 3; FDR < 0.1; Elimination of Potential DEGs = 0.05.

source_name: Hepatocyte-like cells derived from H9 human embryonic stem cells

growth_protocol: Before inducing differentiation, we coated a cell-culture dish with 0.1% gelatin in phosphate-buffered saline (PBS, Thermo Fisher Scientific) for 30 min at 25˚C. We then aspirated the gelatin solution and introduced a DMEM/F12 medium (Sigma-Aldrich) onto the culture dish for serum coating at 37˚C for 24 h. The medium was supplemented with 10% (v/v) fetal bovine serum (Cell Culture Bioscience, Tokyo, Japan), penicillin/streptomycin (Wako), and 100 µM β-mercaptoethanol (Sigma-Aldrich). The coated dish was then rinsed with fresh medium.  Cultured hPSCs were washed with PBS and treated with TryPLE Express at 37˚C for 5 min, followed by the addition of basal medium and the transfer of the cell suspension into a 15 mL tube to induce endoderm differentiation. Cells were centrifuged at 200 × g for 3 min, the supernatant was removed, and then the cells were resuspended in mTeSR-1 medium supplemented with 10 µM Y27632 and 100 ng mL−1 activin A (R&D Systems, Minneapolis, MN, USA), plated on a serum-coated culture dish, and cultured in a humidified incubator at 37˚C with 5% CO2 for 24 h. At the end of day 1, the medium was replaced with fresh mTeSR-1 medium supplemented with 10 µM Y27632 and 100 ng mL−1 activin A and cultured for another 24 h. On day 2, the medium was replaced with mTeSR-1 medium supplemented with 10 µM Y27632, 100 ng mL−1 activin A, 10 ng mL−1 BMP-4 (R&D Systems), 10 µM LY294002 (Cayman Chemical, Ann Arbor, MI, USA), and 3 µM CHIR99021 (Stemgent, Cambridge, MA, USA), and cells were incubated for 24 h. On day 3, the medium was replaced with mTeSR-1 medium supplemented with 10 µM Y27632, 100 ng mL−1 activin A, 10 ng mL−1 BMP-4, and 10 µM LY294002, and cells were incubated for 24 h. On day 4, the medium was replaced with Roswell Park Memorial Institute (RPMI) medium (Thermo Fisher Scientific) supplemented with B-27 (Thermo Fisher Scientific), 100 ng mL−1 activin A, and 100 ng mL−1 basic FGF, and cells were incubated for 24 h. To induce ADE specification, cells were treated with RPMI medium supplemented with 50 ng mL−1 activin A, with daily medium changes for three days. Cells were then treated with RPMI medium supplemented with 20 ng mL−1 BMP-4 and 10 ng mL−1 FGF-10 (R&D systems), with daily medium changes for four days. On day 12, the medium was replaced with hepatocyte-maturation medium (hepatocyte basal medium (Lonza, Basel, Switzerland) supplemented with 30 ng mL−1 oncostatin M (R&D Systems), 50 ng mL−1 HGF (PeproTech, Rocky Hill, NJ), and 25 mM HEPES (Wako) to induce maturation of the differentiated hepatocytes. On day 14, cells were incubated at 37, 39, or 42˚C, and half the total amount of the medium was changed every day.

extract_protocol:
Total RNA was extracted from hepatocyte-like cells derived from H9 human embryonic stem cells using the RNeasy mini kit (QIAGEN).
To prepare the cDNA library, 10 ng of total RNA was diluted with 9 µL of RNase free water, then mixed with VN primer (Oxford NANOPORE Technologies, UK), 1 µL of 10 mM dNTPs (New England Biolabs Inc. Ipswich, Massachusetts, USA), and incubated at 65˚C for 5 min as the RNA solution. Separately, 4 µL of 5x RT Buffer (Thermo Fisher Scientific), 1 µL of RNaseOUT (Thermo Fisher Scientific), 1 µL of Nuclease-free water and 2 µL of Strand-Switching Primer (Oxford NANOPORE Technologies) was mixed as the strand-switching buffer. The two solutions were mixed at 42˚C for 2 min; then, 1 µL of Maxima H Minus Reverse Transcriptase (Thermo Fisher Scientific) was added, incubated at 42˚C for 90 min, 85˚C for 5 min, and stored at 4˚C until use as the cDNA library. Oxford NANOPORE Technologies Nanopore MinION Flowcell v.9.4.1.

treatment_protocol: On day 14, cells were incubated at 37or 39˚C, and half the total amount of the medium was changed every day.

tag: condition

tag: derived tissue

value: Human hepatocyte-like cells

tag: time point


title: H9_HEP_Heat_12DAH_rep3

description: mRNA-seq data from 39˚C-treated cells at 12DAH, replicate 3


title: H9_HEP_Heat_12DAH_rep2

description: mRNA-seq data from 39˚C-treated cells at 12DAH, replicate 2


title: Mouse_lung-Native-1k-THS_TD-55C-Homemade_Tn5-Rep1


title: H9_HEP_Heat_6DAH_rep2

description: mRNA-seq data from 39˚C-treated cells at 6DAH, replicate 2


title: H9_HEP_Heat_6DAH_rep3

description: mRNA-seq data from 39˚C-treated cells at 6DAH, replicate 3


title: Mouse_lung-Native-1k-Omni_TD-55C-Nextera_Tn5-Rep1


title: Mouse_lung-Native-1k-Nextera_TD-55C-Homemade_Tn5-Rep1


title: Mouse_lung-Native-1k-THS_TD-55C-Nextera_Tn5-Rep1


title: H9_HEP_Heat_6DAH_rep1

description: mRNA-seq data from 39˚C-treated cells at 6DAH, replicate 1


title: H9_HEP_Cont_12DAH_rep3

description: mRNA-seq data from 37˚C-treated cells at 12DAH, replicate 3


title: H9_HEP_Cont_12DAH_rep2

description: mRNA-seq data from 37˚C-treated cells at 12DAH, replicate 2


title: H9_HEP_Cont_12DAH_rep1

description: mRNA-seq data from 37˚C-treated cells at 12DAH, replicate 1


title: Mouse_lung-Native-1k-THS_TD-37C-Homemade_Tn5-Rep1


title: Mouse_lung-Native-20k-Nextera_TD-55C-Nextera_Tn5-Rep2


title: Mouse_lung-Native-1k-Nextera_TD-55C-Nextera_Tn5-Rep1


title: Mouse_lung-Native-1k-Omni_TD-37C-Homemade_Tn5-Rep1


title: H9_HEP_Cont_6DAH_rep3

description: mRNA-seq data from 37˚C-treated cells at 6DAH, replicate 3


title: H9_HEP_Cont_6DAH_rep2

description: mRNA-seq data from 37˚C-treated cells at 6DAH, replicate 2


title: Mouse_lung-Native-1k-Nextera_TD-37C-Homemade_Tn5-Rep1


title: H9_HEP_Cont_0DAH_rep3

description: mRNA-seq data from 37˚C-treated cells at 0DAH, replicate 3


title: H9_HEP_Cont_6DAH_rep1

description: mRNA-seq data from 37˚C-treated cells at 6DAH, replicate 1


title: Mouse_lung-Native-1k-Omni_TD-55C-Homemade_Tn5-Rep1


title: Mouse_lung-Native-1k-Omni_TD-37C-Nextera_Tn5-Rep1


title: H9_HEP_Cont_0DAH_rep2

description: mRNA-seq data from 37˚C-treated cells at 0DAH, replicate 2


title: Mouse_lung-Native-20k-THS_TD-55C-Homemade_Tn5-Rep1


title: Mouse_lung-Native-20k-Omni_TD-55C-Homemade_Tn5-Rep1


title: Mouse_lung-Native-1k-Nextera_TD-37C-Nextera_Tn5-Rep1


title: B16F10_NT_GEX_S2

city: Lebanon

first: Yina

last: Huang

state: NH

address: 1 Medical Center Drive

institute: Dartmouth College

description: NT

data_processing:
Single-cell RNA-seq was performed on the 10X Genomics Chromium Next GEM Single Cell 3ʹ v3.1 platform and base calling was performed with Illumina RTA 2.0.
BCLs were converted to fastqs with the bcl2fastq wrapper in CellRanger 6.0.1: mkfastq.
CellRanger 6.0.1 was used for all alignmanet, counting, and processing.
Assembly: mm10
Supplementary files format and content: filtered_feature_bc_matrices: count matrices, features, and barcodes

source_name: tumor

extract_protocol:
B16F10 tumors were harvested at day 15 post inoculation, filtered through a wet 70 microgram cell strainer and resuspended in RPMI media
10X Genomics Chromium Next GEM Single Cell 3ʹ v3.1 platform

value: Tumor infiltrating leukocytes


title: Mouse_lung-Native-20k-THS_TD-55C-Nextera_Tn5-Rep1


title: B16F10 + TA99 CAR + Super2+IL-33_GEX_S6


title: B16F10 + TA99 CAR + Super2+IL-33_GEX_S3


title: B16F10 + TA99 CAR_GEX_S2

description: CAR


title: Mouse_lung-Native-20k-Nextera_TD-55C-Homemade_Tn5-Rep1


title: B16F10 + TA99 CAR_GEX_S4

description: CAR


title: Mouse_lung-Native-20k-Omni_TD-55C-Nextera_Tn5-Rep1


title: B16F10_NT_GEX_S1

description: NT


title: Mouse_lung-Native-20k-THS_TD-37C-Homemade_Tn5-Rep1


title: Mouse_lung-Native-20k-THS_TD-37C-Nextera_Tn5-Rep1


title: Mouse_lung-Native-20k-Omni_TD-37C-Homemade_Tn5-Rep1


title: Wild type sample, set2

city: Ithica

first: Praveen

last: Sethupathy

state: NY

address: Cornell University College of Veterinary Medicine, Box 17

institute: Cornell University

description:
Separated intestinal cells from 12 month old WT mice - set2
12M_WT_Set_2

data_processing:
Sequenciing was aligned and quantiitated using miRquant2.0.
Genome_build: mm9
Supplementary_files_format_and_content: Processed data contains barcodes, gene list, and counts matrix.

source_name: small intestine

extract_protocol:
Libraries were prepped according to 10X Genomics Chromium library preparation
FACS of various populations of the intestinal epithelium
Libraries were prepared using the TriLink CleanTag Small RNA Ligation kit

value: small intestine


title: Mouse_lung-Native-1k-THS_TD-37C-Nextera_Tn5-Rep1


title: Wild type sample, set1

description:
Separated intestinal cells from 12 month old WT mice - set1
12M_WT_Set_1


title: Mouse_lung-Native-20k-Nextera_TD-37C-Nextera_Tn5-Rep1


title: Mouse_lung-Native-20k-Nextera_TD-37C-Homemade_Tn5-Rep1


title: siPALMD  rep3

first: Dongxing

last: Zhu

state: Guangdong

address: Xinzao, Panyu District

department: School of Basic Medical Sciences

institute: Guangzhou Medical University

data_processing:
Solexa pipeline version 1.8 software used for basecalling.
The trimmed reads (trimmed 5',3'-adaptor bases using cutadapt) were aligned to reference genome using Hisat2 (2.1.0) software
The transcript abundances for each sample was estimated with StringTie (1.3.3)
the FPKM value for gene and transcript level were calculated with R package Ballgown (v2.10.0)
Genome_build: GRCh37
Supplementary_files_format_and_content: The xlsx format file contains the FPKM value of gene in every sample

source_name: Primary human valve interstitial cells

growth_protocol: hVICs were isolated and characterized as we and others’ previously described1-3. In brief, non-calcified regions of aortic valve tissues from CAVD patients were carefully dissected. After incubation with 1 mg/ml trypsin (Gibco, 12605-010) for 10 min, the tissues were gently scraped to remove the valve endothelial layer, and cut into small pieces. Subsequently, the tissues were washed with in HBSS buffer (Hyclone, SC30588.01), and digested in 250 U/ml type II collagenase solution (Worthington, 47D17411A) at 37°C for 7 hrs. The cells subsequently obtained were re-suspended in growth media consisting of α-MEM supplemented with 10% FBS (Gibco, 16000-044), 100 U/mL of penicillin (HyClone, SH40003.01), and 100 mg/ml of streptomycin (Hyclone, SV30010), seeded onto a 25 cm2 flask coated with 0.25 μg/cm2 type I collagen (Gibco, A1048301), and incubated at 37oC with 5% CO2. The media was changed every 2 to 3 days. The cells used for experiments in the present study were between 2 to 4 passages. The purity of isolated hVICs was characterized immunofluorescence staining of vimentin and smooth muscle protein 22 alpha (SM22α) as previously described

extract_protocol:
Total RNA was extracted from cell using TaKaRa MiniBEST Universal RNA Extraction Kit (Takara, 9767).RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis
Libraries were prepared by using KAPA Stranded RNA-Seq Library Prep Kit(Illumina). Briefly,Total RNA of each sample was used to prepare the RNA sequencing library 1)RNA fragment；2)Random primed first strand cDNA synthesis；3)dUTP based second strand cDNA synthesis;4)Adaptor ligation and PCR amplification.

treatment_protocol: hVICs were seeded at the density of 1.0x105 cells/well in 6-well plates and transfected with siRNAs using Lipofectamine RNAiMAX (Invitrogen, 13778) according to the manufacturer’s instructions. A siRNA targeting PALMD (siPALMD)  was used at a concentration of 20 nM. Scrambled siRNA (siScrambled) at a concentration of 20 nM served as a negative control. All siRNAs were obtained from Guangzhou RiboBio Co., Ltd, China. siRNA-mediated knockdown efficiency was confirmed by RT-qPCR and western blotting.

value: Primary human valve interstitial cells

tag: transfection

value: Transfected with 20 nM siPALMD for 48 hrs


title: H9_HEP_Cont_0DAH_rep1

description: mRNA-seq data from 37˚C-treated cells at 0DAH, replicate 1


title: siPALMD rep1


title: Mouse_lung-Native-20k-Omni_TD-37C-Nextera_Tn5-Rep1


title: siScrambled rep1

value: Transfected with 20 nM siScrambled for 48 hrs


title: WAT-HFD-KO6

city: Houston

first: Yulin

last: Dai

state: TX

address: 7000 fannin, suite 600

department: School of Biomedical Informatics

institute: University of Texas health science center at Houston

data_processing:
Raw reads (fastq files) were aligned to mouse reference (mm10) using STAR aligner (version 2.6) with default settings, read count files were generated
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text for gene read count, sample information, and gene annotation

source_name: White adipose tissue

extract_protocol:
White adipose tisseus were collected and flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with total RNA for the construction of sequencing libraries.
RNA libraries were prepared with KAPA mRNA HyperPrep (KK8581, Roche) and KAPA UDI Adapter Kit (KK8727, Roche) following the manufacturer’s instructions.

treatment_protocol: The mice were fed on High fat diet (60% cal from fat) for 14 weeks.

value: White adipose tissue

value: Apn-Cre; Ces1fl/fl

value: High fat diet for 14 weeks


title: WAT-ces3-KO7


title: WAT-HFD-KO2


title: WAT-HFD-KO3


title: WAT-HFD-KO5


title: WAT-HFD-WT6

value: wild type


title: WAT-HFD-WT5


title: control input rep2

city: Shanghai

first: Aiwei

last: Wu

state: Shanghai

address: 800 Dongchuan Road

department: School of Life Sciences and Biotechnology

institute: Shanghai Jiao Tong University

description: control.chip-input.bw

data_processing:
Raw reads were trimmed for adaptor sequence and low-complexity or low-quality sequence were filtered using fastp v0.13.1 with default parameters. ChIP-seq, ATAC-seq, CUT&Tag and 4sUDRB-seq reads were aligned using bowtie2 v2.3.4.1. RNA-seq read were aligned using hisat2 v2.1.0 with parameter --rna-strandness RF.
For ChIP-seq, ATAC-seq, CUT&Tag and 4sUDRB-seq, normalized aboundency in each 50-bp genomic bin were generated into bigWig file using deepTools bamCoverage command with parameter --normalizeUsing CPM. For RNA-seq, read/fragment count were obtained using featureCounts v1.6.1.
Genome_build: Hg38 for RNA-seq, ChIP-seq, ATAC-seq, and CUT&Tag read mapping, hg19 for 4sUDRB-seq.
Supplementary_files_format_and_content: Tab-delimited text files include fragment count values of genes for each sample.
Supplementary_files_format_and_content: BigWig files contains normalized read count (CPM, in 50-bp bins) for ChIP-seq, CUT&Tag and 4sUDRB-seq or normalized insertion count (CPM, in 50-bp bins) for ATAC-seq.

source_name: K562 cell line

growth_protocol: Human cells K562 were cultured in 90% DMEM + 10% FBS+ 2% Penicillin/Streptomycin + 2 mM L-Glutamine.

extract_protocol: For immunoprecipitation, on day 1 antibodies were diluted in RIPA-0.3 and bound to Dynabeads protein A (Thermo, cat. no. 10002D) by incubating at 4 °C for 3 hours. Afterwards, the bead-antibody complexes were washed twice with RIPA-0.3 and then incubated with sonicated chromatin at 4 °C overnight. On day 2, after 2 washes with RIPA-0.5, 1 wash with RIPA-0.3, 1 wash with RIPA-0, 2 washes with LiCl buffer (10 mM Tris-HCl, 1 mM EDTA, 0.25 M LiCl, 0.25% NP-40, and 0.25% NaDOC, pH 7.4), and 2 washes with TE buffer, bound protein-DNA complexes were resuspended in elution buffer (10 mM Tris-HCl, 1mM EDTA, 0.2 M NaCl, and 1% SDS, pH 7.4) supplemented with 10 µg/ml RNase A for both elution and RNA digestion, and incubated at 55 °C for 1 hour. Then Proteinase K was added to a final concentration of 200 µg/ml, and after 30 min incubation the temperature was increased to 65 °C for crosslink reversal. After incubation for 4 to 6 hours, DNA was purified by ChIP DNA Clean & Concentrator (Zymo Research, cat. no. D5205).

treatment_protocol: For double fixation with EGS (Thermo, cat. no. 21565) and formaldehyde, cells were fixed initially with 1.5 mM EGS at room temperature for 30 min, and subsequently with 0.4% formaldehyde at room temperature for 10 min. For sonication, fixed cells were washed twice with PBS and resuspended in ice-cold RIPA-0.3 buffer (10 mM Tris-HCl, 1 mM EDTA, 1% Triton X-100, 0.1% SDS, 0.1% NaDOC, and 0.3 M NaCl, pH 7.4) supplemented with Protease Inhibitor Cocktail (Millipore, cat. no. 535140) at a concentration of 40 million cells/ml; genomic DNA was disrupted to a size range of 100 to 500 bp.

value: control

tag: cell line

value: K562 cell line

tag: antibody

value: input

tag: fixation

value: EGS+FA


title: Mouse_lung-Native-20k-Nextera_TD-55C-Nextera_Tn5-Rep1

value: Lung

tag: strain


title: control TOX4 ChIP-seq rep2

tag: treatment


title: WAT-HFD-WT3


title: control input rep1

description: control.chip-input.bw


title: control TOX4 ChIP-seq rep1


title: siScrambled rep3

tag: cell type


title: siPALMD rep2


title: WAT-HFD-WT2


title: control RNA-seq rep2

extract_protocol:
RNA was extracted from cells using RNeasy Plus Mini Kit (Qiagen, cat. no. 74134) and Quick-RNA MiniPrep Kit (Zymo Research, cat. no. R1054)
the Illumina TruSeq RNA Library preparation protocol: PolyA RNA is captured by oligodT beads and fragmented when eluted from the beads. The first-strand cDNA was synthesized by reverse transcriptase using dNTP, whereas the second-strand cDNA was generated using a dUTP mix . After end-repair, dA-tailing and adapter ligation, the dUTP-containing second strand is digested by uracil DNA glycosylase, rendering it unamplifiable in the subsequent PCR step. Hence the resulting library contains only PCR product of the first-strand cDNA. And then, the barcoded DNA was amplified by 15-cycle PCR.  Libraries were sequenced on Illumina Genome Analyzer II, HiSeq 2000, or HiSeq 2500.


title: control RNA-seq rep1


title: siScrambled rep2


title: TOX4 KO RNA-seq rep2

value: TOX4 knockout


title: PPARg_RIPA

city: La Jolla

first: Ruth

middle: T

last: Yu

address: 10010 N Torrey Pines Rd

department: Gene Expression Lab

institute: Salk Institute

data_processing:
ChIP-seq experiments were conducted multiple times, but only one replicate was used for this publication.  Input was used for background subtraction.  Single end sequencing yielded 13.23M 100bp reads. Bowtie 2 was used for alignment with mm10.  Peak calling, motif analyses, and other data analysis were performed using HOMER, a software suite for ChIP-seq analysis. The methods are freely available at http://biowhat.ucsd.edu/homer/. Only tags that mapped uniquely to the genome were considered for further analysis.
Genome_build: mm10

source_name: mouse TH2 cells

extract_protocol: Nave CD4+ T cells were activated and polarized in TH2 conditions. On day 1 and 2, T cells were transduced with a retroviral vector expressing TY1-tagged Pparg. On day 4, transduced T cells were harvested for ChIP utilizing a TY1 antibody (Sigma, SAB4800032). ChIP-sequencing libraries were constructed and sequenced (50 bp single end reads) as per standard Illumina protocols.

value: In vitro differentiated Th2 cells retrovirally expressing TY1-tagged PPARg

value: TY1 antibody (Sigma, SAB4800032)


title: UNC0638_b

city: Rehovot

first: Noam

last: Stern-Ginossar

address: 234 herzel

department: Molecular Genetics

country: Israel

institute: Weizmann Institute

data_processing:
For the time course libraries, raw sequences were first trimmed at their 3′ end, removing the illumina adapter and polyA tail.
Alignment was performed using Bowtie (allowing up to 2 mismatches) and reads were aligned to concatenation of the human (hg19) and the viral genomes (NCBI EF999921.1). Reads aligned to ribosomal RNA were removed.
Reads that were not aligned to the genome were then aligned to the transcriptome.
Analysis of libraries generated with the MARS-seq protocol was done as previously described . Briefly, 37-bp reads were aligned using Bowtie (allowing up to 2 mismatches) to concatenation of the human (hg19) and the viral genomes (NCBI EF999921.1). Counting of reads per gene was done based on unique molecular identifiers (UMIs) (8 bp).
The transcription units of the virus were based on NCBI annotations, with some changes, including merging several transcripts (considering that the library maps only the 3’ ends of transcripts) and adding some antisense transcripts.
Genome_build: human (hg19) and the viral genomes (NCBI EF999921.1)
Supplementary_files_format_and_content: All processed files are comma delimited files with the number of reads on the transcripts

organism:
Homo sapiens
Human betaherpesvirus 5

source_name: Primary CD14+ monocytes

growth_protocol: Human foreskin fibroblasts (ATCC CRL-1634) were grown in Dulbecco’s Modified Eagle’s Medium (DMEM) with 10% heat-inactivated fetal bovine serum (FBS), 2 mM L-glutamine, and 100 units/ml penicillin and streptomycin (Beit-Haemek, Israel) and maintained at 37°C in a 5% CO2 incubator. Primary CD14+ monocytes were isolated from fresh venous blood, obtained from healthy donors, using a Lymphoprep (StemCell Technologies) density gradient followed by magnetically activated cell sorting with CD14 magnetic beads (Miltenyi Biotec). CD14+ cells were cultured in X-Vivo 15 medium (Lonza) supplemented with 2.25 mM L-glutamine and maintained at 37°C in a 5% CO2 incubator.

extract_protocol:
for cd14 and hff time course experiment as well as TSA time course RNA was extracted using Tri-Reagent (Sigma-Aldrich), total RNA was extracted. poly-A selection was performed using Dynabeads mRNA DIRECT. For MARseq libraries epigenetic treatments RNA was extracted directly from cells using Dynabeads mRNA DIRECT.
Briefly, mRNA samples of ~4ng were subjected to DNaseI treatment and 3′ dephosphorylation using FastAP Thermosensitive Alkaline Phosphatase (Thermo Scientific) and T4 PNK (NEB) followed by 3′ adaptor ligation using T4 ligase (NEB). The ligated products were used for reverse transcription with SSIII (Invitrogen) for first-strand cDNA synthesis. The cDNA products were 3′ ligated with a second adaptor using T4 ligase and amplified with 8 cycles of PCR for final library products of 200–300 base pairs. For epigenetic drug-treated CD14+ monocyte samples, RNA libraries were generated from samples of ~100,000 cells according to the MARS-seq protocol

treatment_protocol: For the time course analysis fibroblasts and CD14+ monocytes were infected with the same stock of HCMV strain TB40E-GFP at a multiplicity of infection (MOI) of 1 and 10, respectively. For all other experiments CD14+ monocytes or THP1 cells were infected with HCMV strain TB40E-GFP at an MOI of 5. Cells were incubated with the virus for 2h, washed, and supplemented with fresh medium. CHX was added to infected fibroblasts and CD14+ monocytes immediately after infection at a final concentration of 100 ug/ml and 200 ug/ml or at 100 ug/ml, respectively. PFA was added to fibroblasts and CD14+ monocytes immediately after infection at a final concentration of 400 ug/ml. for epigenetic drug treatments - 48 hpi, TB40-infected CD14+ monocytes were divided into 1.2 ml tubes containing ~100,000 cells per tube and inhibitors or DMSO for negative control were added to a final concentration of 1uM for 24 hours

tag: virus strain

value: CD14+ monocytes


title: UNC0631_b


title: PPARg_RIPA_input


title: UNC0631_a


title: WAT-ces3-WT4

tag: genotype


title: Progenitor sample 3

description:
Progenitor sorted intestinal cells - sample 3
SI_ISC-types_normalized_miR_counts.csv.gz

extract_protocol:
Libraries were prepared according to the TriLink CleanTag Small RNA Library Preparation Kit protocol
FACS of various populations of the intestinal epithelium
Libraries were prepared using the TriLink CleanTag Small RNA Ligation kit

value: small intestine


title: TOX4 KO RNA-seq rep1


title: Progenitor sample 2

description:
Progenitor sorted intestinal cells - sample 2
SI_ISC-types_normalized_miR_counts.csv.gz


title: Progenitor sample 1

description:
Progenitor sorted intestinal cells - sample 1
SI_ISC-types_normalized_miR_counts.csv.gz


title: TrichostatinA_b

value: TrichostatinA


title: TrichostatinA_a


title: Tenovin6_b


title: Tuft sample 4

description:
Tuft sorted intestinal cells - sample 4
SI_ISC-types_normalized_miR_counts.csv.gz
TU4_S45_R1_001

tag: population

value: Tuft


title: Tuft sample 1

description:
Tuft sorted intestinal cells - sample 1
SI_ISC-types_normalized_miR_counts.csv.gz
TU1_S42_R1_001

tag: tissue


title: Paneth sample 6

description:
Paneth sorted intestinal cells - sample 6
SI_ISC-types_normalized_miR_counts.csv.gz
PN2pos_S50_R1_001

value: Paneth


title: Paneth sample 5

description:
Paneth sorted intestinal cells - sample 5
SI_ISC-types_normalized_miR_counts.csv.gz
PN1pos_S49_R1_001


title: UNC0638_a


title: Tuft sample 3

description:
Tuft sorted intestinal cells - sample 3
SI_ISC-types_normalized_miR_counts.csv.gz
TU3_S44_R1_001


title: Lgr5 High sample 2

description:
Lgr5-High sorted intestinal cells - sample 2
SI_ISC-types_normalized_miR_counts.csv.gz
LH_2_S53_L008_R1_001


title: Tenovin1_b


title: SodiumButyrate_a

value: SodiumButyrate


title: SodiumButyrate_b


title: goblet sample 4

description:
Goblet sorted intestinial cells - sample 4
SI_ISC-types_normalized_miR_counts.csv.gz
GO4_S41_R1_001

value: Goblet


title: Tenovin1_a


title: Rucaparib_a

value: Rucaparib


title: goblet sample 3

description:
Goblet sorted intestinial cells - sample 3
SI_ISC-types_normalized_miR_counts.csv.gz
GO3_S40_R1_001


title: Mirin_a

value: Mirin


title: Tenovin6_a


title: MC1568_b


title: Paneth sample 4

description:
Paneth sorted intestinal cells - sample 4
SI_ISC-types_normalized_miR_counts.csv.gz
D_PC_POS_S50_L006_R1_001


title: GSKJ2_b


title: GSKJ2_a


title: goblet sample 1

description:
Goblet sorted intestinial cells - sample 1
SI_ISC-types_normalized_miR_counts.csv.gz
GO1_S38_R1_001


title: Paneth sample 3

description:
Paneth sorted intestinal cells - sample 3
SI_ISC-types_normalized_miR_counts.csv.gz
C_PC_POS_S48_L006_R1_001


title: CD24Low sample 4

description:
Cd24-Low sorted intestinal cells - sample 4
SI_ISC-types_normalized_miR_counts.csv.gz
CD24Low_4_S45

value: Cd24-Low sorted


title: GSKJ1_b


title: CD24Low sample 2

description:
Cd24-Low sorted intestinal cells - sample 2
SI_ISC-types_normalized_miR_counts.csv.gz
CD24Low_2_S39


title: MC1568_a


title: Etoposide_a

value: Etoposide


title: CD24Low sample 1

description:
Cd24-Low sorted intestinal cells - sample 1
SI_ISC-types_normalized_miR_counts.csv.gz
CD24Low_1_S38


title: CD24Low sample 3

description:
Cd24-Low sorted intestinal cells - sample 3
SI_ISC-types_normalized_miR_counts.csv.gz
CD24Low_3_S44


title: Rucaparib_b


title: Paneth sample 2

description:
Paneth sorted intestinal cells - sample 2
SI_ISC-types_normalized_miR_counts.csv.gz
B_PC_POS_S46_L006_R1_001


title: Gemcitabine_a

value: Gemcitabine


title: Sox9 Low sample 4

description:
Sox9 Low sorted intestinal cells - sample 4
SI_ISC-types_normalized_miR_counts.csv.gz
BC243_chow_Low_GTTTCG_L001_R1
BC243_Low_GTTTCG_L001_R1


title: Lgr5 High sample 1

description:
Lgr5-High sorted intestinal cells - sample 1
SI_ISC-types_normalized_miR_counts.csv.gz
LH_1_S52_L008_R1_001


title: Etoposide_b


title: Mirin_b


title: Cay10591_b


title: Sox9 Negative sample 4

description:
Sox9 Negative sorted intestinal cells - sample 4
SI_ISC-types_normalized_miR_counts.csv.gz
BC243_chow_Neg_GCCAAT_L004_R1
BC243_Neg_GCCAAT_L004_R1


title: goblet sample 2

description:
Goblet sorted intestinial cells - sample 2
SI_ISC-types_normalized_miR_counts.csv.gz
GO2_S39_R1_001


title: DMSO.control


title: Sox9 High sample 4

description:
Sox9 High sorted intestinal cells - sample 4
SI_ISC-types_normalized_miR_counts.csv.gz
BC243_chow_High_TTAGGC_L002_R1
BC243_High_TTAGGC_L002_R1


title: Cay10591_a


title: MCU-5

city: Hershey

first: Yuka

last: Imamura Kawasawa

state: PA

address: 500 University Dr.

department: College of Medicine, Pharmacology

institute: Penn State University

data_processing:
De-multiplexed and adapter-trimmed sequencing reads were generated using Illumina bcl2fastq (released version 2.18.0.12) allowing no mismatches in the index read. BBDuk was used to trim/filter low quality sequences using “qtrim=lr trimq=10 maq=10” option. Next, alignment of the filtered reads to the human reference genome GRCh38) was done using HISAT2 (version 2.1.0) applying --no-mixed and --no-discordant options. Read counts were calculated using HTSeq by supplementing Ensembl gene annotation GRCh38.78).
Assembly: GRCh38
Supplementary files format and content: raw read counts are provided in a csv ifle

source_name: PANC-1 MCU OE cells

growth_protocol: PANC-1 cells were cultured in DMEM medium supplemented with 10% fetal bovine serum and antibiotics.

extract_protocol:
The mRNA was extracted with RNeasy kit (Qiagen) and used for the preparation of RNA sequencing library
The cDNA libraries were prepared using the NEXTflex™ Illumina Rapid Directional RNA-Seq Library Prep Kit (BioO Scientific) as per the manufacturer’s instructions. Briefly, polyA RNA was purified from 200 ng of total RNA using oligo (dT) beads. The extracted mRNA fraction was subjected to fragmentation, reverse transcription, end repair, 3’– end adenylation, and adaptor ligation, followed by PCR amplification and SPRI bead purification (Beckman Coulter). The unique index sequences were incorporated in the adaptors for multiplexed high-throughput sequencing. The final product was assessed for its size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit (Agilent Technologies).
The libraries were pooled and diluted to 3 nM using 10 mM Tris-HCl, pH 8.5 and then denatured using the Illumina protocol. The denatured libraries were loaded onto an S1 flow cell on an Illumina NovaSeq 6000 (Illumina) and run for 2X53 cycles according to the manufacturer's instructions.

treatment_protocol: Before RNA sequencing, cells were treated with culcuture medium with glucose limitation (1mM glcuose) for overnight).

tag: mcu expression status

value: MCU  Overexpressing


title: MCU-1


title: Sox9 Negative sample 3

description:
Sox9 Negative sorted intestinal cells - sample 3
SI_ISC-types_normalized_miR_counts.csv.gz
BC241_HFD_Neg_GTTTCG_L004_R1
BC241_Neg_GTTTCG_L004_R1


title: MCU-4


title: PBS control rep2

city: Changchun

first: Dong

last: Li

address: 126 Xinmin Avenue

department: Department of Immunology

institute: Jilin University

data_processing:
Illumina bcl2fastq software was used for basecalling.
The gene expression analyses were performed with StringTie (v1.3.3b)
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: umbilical vein

growth_protocol: HUVECs were cultrued in DMEM suoplement with 10% FBS

extract_protocol:
HUVEC were havested, flash frozen on dry ice, and RNA was harvested using Trizol reagent. NEBNext Ultra RNA Library Prep Kit for Illumina (Cat#E7530S) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HUVEC cells were seeded in 6-well-plate (2x10^6 cells per well) overnight before the conidia of A. fumigatus were added to the wells at a cells:spores ratio of 1:2. The cell lysates of conidia treated cells and PBC treated cells were harvest 2 and 6 hours post stimulation.

value: umbilical vein

value: Endothelial Cells

value: PBS control


title: Sox9 Negative sample 2

description:
Sox9 Negative sorted intestinal cells - sample 2
SI_ISC-types_normalized_miR_counts.csv.gz
BC183_chow_Neg_GTCCGC_L005_R1
BC183_Neg_GTCCGC_L005_R1


title: PBS control rep3


title: GSKJ1_a


title: Cay10398_a


title: Butyrolactone3_a


title: PBS control rep1


title: BSI201_b


title: Sox9 Low sample 2

description:
Sox9 Low sorted intestinal cells - sample 2
SI_ISC-types_normalized_miR_counts.csv.gz
BC183_chow_Low_CAGATC_L001_R1
BC183_Low_CAGATC_L001_R1


title: 6h post stimulation rep1

value: conidia of A. fumigatus stimulates for 6h


title: 2h post stimulation rep3

value: conidia of A. fumigatus stimulates for 2h


title: control 2

source_name: PANC-1 control cells

value: control


title: 2h post stimulation rep2


title: control 5


title: Sox9 High sample 3

description:
Sox9 High sorted intestinal cells - sample 3
SI_ISC-types_normalized_miR_counts.csv.gz
BC241_HFD_High_GTAGAG_L001_R1
BC241_High_GTAGAG_L001_R1

value: small intestine


title: Sox9 Low sample 3

description:
Sox9 Low sorted intestinal cells - sample 3
SI_ISC-types_normalized_miR_counts.csv.gz
BC241_HFD_Low_GGTAGC_L001_R1
BC241_Low_GGTAGC_L001_R1


title: Butyrolactone3_b

value: CD14+ monocytes


title: Sox9 Negative sample 1

description:
Sox9 Negative sorted intestinal cells - sample 1
SI_ISC-types_normalized_miR_counts.csv.gz
BC180_chow_Neg_CTTGTA_L005_R1
BC180_Neg_CTTGTA_L005_R1


title: Sox9 High sample 2

description:
Sox9 High sorted intestinal cells - sample 2
SI_ISC-types_normalized_miR_counts.csv.gz
BC183_chow_High_CTTGTA_L002_R1
BC183_High_CTTGTA_L002_R1


title: BSI201_a


title: 6h post stimulation rep2


title: CPTH2_b


title: K562 AID-TOX4 ser2p CUT&Tag rep2

data_processing:
Library strategy: CUT&Tag
Raw reads were trimmed for adaptor sequence and low-complexity or low-quality sequence were filtered using fastp v0.13.1 with default parameters. Reads were aligned using bowtie2 v2.3.4.1.
Normalized aboundency in each 50-bp genomic bin were generated into bigWig file using deepTools bamCoverage command with parameter --normalizeUsing CPM.
Genome_build: Hg38
Supplementary_files_format_and_content: BigWig files contains normalized read count (CPM, in 50-bp bins).

extract_protocol:
CUT&Tag experiments were performed as previously described with minor modifications(Kaya-Okur, H.S. et al. ). Briefly, 100,000 cells were used for each experiment. Cells were bound to Concanavalin A-coated beads without fixation and chromatin opening. After primary and secondary antibodies binding, pA-Tn5 transposome binding, and tagmentation, DNA was extracted by PCI.
Library was construct by PCR, NEB Phusion(M0530L) was used as protocol.


title: AGK2_b


title: 2h post stimulation rep1


title: control 1


title: 2PCPA_b


title: K562 control_for_AID-TOX4 ser2p CUT&Tag rep2


title: Paneth sample 1

description:
Paneth sorted intestinal cells - sample 1
SI_ISC-types_normalized_miR_counts.csv.gz
A_PC_POS_S44_L006_R1_001

value: Paneth


title: K562 AID-TOX4 ser5p CUT&Tag rep1


title: Sox9 Low sample 1

description:
Sox9 Low sorted intestinal cells - sample 1
SI_ISC-types_normalized_miR_counts.csv.gz
BC180_chow_Low_GCCAAT_L001_R1
BC180_Low_GCCAAT_L001_R1


title: K562 control_for_AID-TOX4 ser5p CUT&Tag rep1


title: TSA_24

value: TSA


title: K562 AID-TOX4 ser2p CUT&Tag rep1


title: 6h post stimulation rep3


title: JAR cells, treated with 100µm-CoCl2, 6-day timepoint, mRNA, rep 7

city: Boston

first: Erin

last: Ciampa

state: MA

address: 99 Brookline Avenue, RN-345

institute: Beth Israel Deaconess Medical Center

description:
translating mRNA
biological replicate

data_processing:
RNA-Seq data were mapped and quantified using Salmon (Patro et al., 2017)
Gene abundances were summarized from transcript abundances using the tximport package for R (Soneson et al., 2015)
Low expressed genes (log2 CPM≥1) were filtered out, and differentially expressed genes were defined at log2 fold-change (FC) ≥0.6 and log2 false discovery rate (FDR)≤0.05 using EdgeR (Robinson et al., 2010).
Assembly: GRCh38
Supplementary files format and content: tab-separated-values files containing, per-sample, transcript-level quantifications given by Salmon. each file contains (in order): a mapping from the transcript ID to the transcript’s legnth, effective length, the transcripts-per-million mappings observed, and the number of reads mapped to the transcript

source_name: JAR

growth_protocol: JAR choriocarcinoma cells (ATCC) were grown in RPMI1640 media (4.5 g/L glucose) with 10% FBS, and split every 2-3 days as needed to maintain approximately 50-70% confluence

extract_protocol:
Total RNA was isolated using Zymo direct-zol RNA prep. Extracted RNA was treated with NEBNext rRNA Depletion Kit v2.
RNA was converted into double stranded cDNA using NEBNext mRNA Second Strand Synthesis Module. cDNA was tagmented and amplified by using Nextera XT DNA Library Preparation Kit.

treatment_protocol: Cobalt chloride hexahydrate (100 µM CoCl2, Millipore Sigma) dissolved in 1X PBS was added to cell culture medium

value: JAR

value: choriocarcinoma cells


title: K562 control_for_AID-TOX4 Pol II CUT&Tag rep2

value: Pol II


title: AGK2_a


title: K562 AID-TOX4 Pol II CUT&Tag rep2


title: K562 control_for_AID-TOX4 ser2p CUT&Tag rep1


title: JAR cells, treated with 100µm-CoCl2, 6-day timepoint, mRNA, rep 5

description:
translating mRNA
biological replicate


title: K562 TOX4 KO PPP1CB CUT&Tag rep2

value: TOX4 knockout


title: K562 control_for_AID-TOX4 Pol II CUT&Tag rep1


title: Sox9 High sample 1

description:
Sox9 High sorted intestinal cells - sample 1
SI_ISC-types_normalized_miR_counts.csv.gz
BC180_chow_High_CGATGT_L002_R1
BC180_High_CGATGT_L002_R1


title: K562 AID-TOX4 ser5p CUT&Tag rep2


title: K562 TOX4 KO PPP1CB CUT&Tag rep1


title: 2PCPA_a


title: JAR cells, treated with 100µm-CoCl2, 6-day timepoint, mRNA, rep 12

description:
translating mRNA
biological replicate


title: K562 control_for_AID-TOX4 ser5p CUT&Tag rep2


title: K562 AID-TOX4 Pol II CUT&Tag rep1


title: K562 TOX4 KO PPP1CA CUT&Tag rep1


title: K562 TOX4 KO PPP1CA CUT&Tag rep2


title: JAR cells, treated with 100µm-CoCl2, 6-day timepoint, mRNA, rep 2

description:
translating mRNA
biological replicate


title: TSA_12


title: control_b_12


title: K562 control PPP1CA CUT&Tag rep1


title: control_b_0


title: JAR cells, treated with 100µm-CoCl2, 6-day timepoint, mRNA, rep 4

description:
translating mRNA
biological replicate


title: HeLa S3 - rep 1

city: Paris

first: Chunlong

last: Chen

address: 26 rue d’Ulm

country: France

institute: Institut Curie

description: single cell  whole genome sequencing

data_processing:
Data were demultiplexed using IEMFile version 5 and prcessed using Cell Ranger DNA version 1.0.0.
The resultant bam file was subset using 10x Genomics subset-bam version 1.0 to obtain single cell bam files.
Duplicated reads were removed using Picard MarkDuplicates version 2.6.0.
Files were then used as input for the CNV module of Kronos scRT
Genome_build: Hg38
Supplementary_files_format_and_content: Archive containing one file with single cell CNV callings and one file containing single cell statistics

source_name: Cervical carcinoma cells

growth_protocol: MCF7 cells and HeLa S3 cells were culture in DMEM high glucose GlutamaX media with 10% FBS, while JEFF cells were grown in RPMI 1640 GlutamaX supplemented with 5% FBS. All media were supplemented with 50 U/mL penicillin and 50 μg/mL streptomycin. All cell lines are grown in 5% CO2 at 37 °C.

extract_protocol: 10x Genomics Chromium single-cell CNV solution

treatment_protocol: Estrogen (E2) treatment: cells were plated at ~25% confluent in complete media for at least 16 h, rinsed with PBS for 3 times, and then hormone starved for 48 h in hormone-free media (DMEM without phenol red supplemented with 10% charcoal stripped FBS (Dutscher), 50 U/mL penicillin, 50 μg/mL streptomycin and GlutaMAX™ 2 nM) before treated with 100 nM E2 dissolved in EtOH for 24 h.

value: Cervical carcinoma cells


title: K562 control PPP1CB CUT&Tag rep1


title: TSA_0


title: control_b_24


title: JAR cells, untreated, 6-day timepoint, mRNA, rep 8

description:
translating mRNA
biological replicate


title: control_a_12


title: JAR cells, untreated, 6-day timepoint, mRNA, rep 6

description:
translating mRNA
biological replicate


title: TOX4 KO TBP CUT&Tag rep1

description:
CUT&Tag
TOX4_KO.TBP.cuttag.bw

data_processing:
Raw reads were trimmed for adaptor sequence and low-complexity or low-quality sequence were filtered using fastp v0.13.1 with default parameters. ChIP-seq, ATAC-seq, CUT&Tag and 4sUDRB-seq reads were aligned using bowtie2 v2.3.4.1. RNA-seq read were aligned using hisat2 v2.1.0 with parameter --rna-strandness RF. TT-seq reads were aligned using STAR v2.7.9a.
For ChIP-seq, ATAC-seq, CUT&Tag and 4sUDRB-seq, normalized aboundency in each 50-bp genomic bin were generated into bigWig file using deepTools bamCoverage command with parameter --normalizeUsing CPM. For RNA-seq, read/fragment count were obtained using featureCounts v1.6.1. To create scaled, strand-specific BigWig files for TT-seq data, SAMtools was used to split each target BAM file into mappable reads to either forward or reverse strand, and bamCoverage function of deepTools was used with the “-scaleFactor” argument to convert each strand-specific BAM file to a scaled BigWig file.
Genome_build: Hg38 for RNA-seq, ChIP-seq, ATAC-seq, and CUT&Tag read mapping, hg19 for 4sUDRB-seq. Hg38 and sacCer3 for TT-seq read mapping.
Supplementary_files_format_and_content: Tab-delimited text files include fragment count values of genes for each sample.
Supplementary_files_format_and_content: BigWig files contains normalized read count (CPM, in 50-bp bins) for ChIP-seq, CUT&Tag and 4sUDRB-seq, normalized insertion count (CPM, in 50-bp bins) for ATAC-seq, normalized read count (by sequencing read aligned to yeast genome, in 50-bp bins) for TT-seq.

value: TBP


title: TSA_4


title: Jeff - rep 2

description: single cell  whole genome sequencing

source_name: human lymphoblastoid cells

value: Jeff

value: Epstein-Barr-virus-immortalized human B lymphocytes


title: control_b_4


title: JAR cells, untreated, 6-day timepoint, mRNA, rep 5

description:
translating mRNA
biological replicate


title: TOX4 KO 4sUDRB-seq 10min rep2

data_processing:
Library strategy: 4sU-DRB-seq
Raw reads were trimmed for adaptor sequence and low-complexity or low-quality sequence were filtered using fastp v0.13.1 with default parameters. ChIP-seq, ATAC-seq, CUT&Tag and 4sUDRB-seq reads were aligned using bowtie2 v2.3.4.1. RNA-seq read were aligned using hisat2 v2.1.0 with parameter --rna-strandness RF. TT-seq reads were aligned using STAR v2.7.9a.
For ChIP-seq, ATAC-seq, CUT&Tag and 4sUDRB-seq, normalized aboundency in each 50-bp genomic bin were generated into bigWig file using deepTools bamCoverage command with parameter --normalizeUsing CPM. For RNA-seq, read/fragment count were obtained using featureCounts v1.6.1. To create scaled, strand-specific BigWig files for TT-seq data, SAMtools was used to split each target BAM file into mappable reads to either forward or reverse strand, and bamCoverage function of deepTools was used with the “-scaleFactor” argument to convert each strand-specific BAM file to a scaled BigWig file.
Genome_build: Hg38 for RNA-seq, ChIP-seq, ATAC-seq, and CUT&Tag read mapping, hg19 for 4sUDRB-seq. Hg38 and sacCer3 for TT-seq read mapping.
Supplementary_files_format_and_content: Tab-delimited text files include fragment count values of genes for each sample.
Supplementary_files_format_and_content: BigWig files contains normalized read count (CPM, in 50-bp bins) for ChIP-seq, CUT&Tag and 4sUDRB-seq, normalized insertion count (CPM, in 50-bp bins) for ATAC-seq, normalized read count (by sequencing read aligned to yeast genome, in 50-bp bins) for TT-seq.

extract_protocol:
After RNA biotinylation and free biotin removal, biotinylated RNA was purified by streptavidin-coupled Dynabeads (Thermo, cat. no. 11205D). rRNA was depleted before library construction. Sequencing libraries were constructed by following the Illumina TruSeq RNA Library preparation protocol.
Sequencing libraries were constructed by following the Illumina TruSeq RNA Library preparation protocol.

treatment_protocol: 10 million cells were used for each experiment. After DRB (Sigma, cat. no. D1916) treatment and 4sU (Sigma, cat. no. T4509) incorporation, total RNA was extracted.


title: TOX4 KO 4sUDRB-seq 0min rep2


title: control 4sUDRB-seq 20min rep2


title: Jeff - rep 1

description: single cell  whole genome sequencing


title: control 4sUDRB-seq 10min rep2


title: HeLa S3 - rep 2

description: single cell  whole genome sequencing


title: JAR cells, untreated, 6-day timepoint, mRNA, rep 4

description:
translating mRNA
biological replicate


title: control_a_24


title: K562 control PPP1CB CUT&Tag rep2


title: K562 control PPP1CA CUT&Tag rep2


title: MCF7

description: single cell  whole genome sequencing

source_name: Breast cancer cell line

value: Breast cancer cell line


title: JAR cells, untreated, 6-day timepoint, mRNA, rep 2

description:
translating mRNA
biological replicate


title: MCF7 + Estrogen

description: single cell  whole genome sequencing

value: Estrogen Treatment


title: TOX4 KO TBP CUT&Tag rep2

description:
CUT&Tag
TOX4_KO.TBP.cuttag.bw


title: control TBP CUT&Tag rep2

description:
CUT&Tag
control.TBP.cuttag.bw


title: control TBP CUT&Tag rep1

description:
CUT&Tag
control.TBP.cuttag.bw


title: TOX4 KO 4sUDRB-seq 20min rep2


title: hff_8hpi_b

source_name: Human foreskin fibroblasts (ATCC CRL-1634)

value: HFF

tag: time course


title: control_a_0


title: control 4sUDRB-seq 0min rep1


title: hff_8hpi_a


title: TOX4 KO 4sUDRB-seq 0min rep1


title: control 4sUDRB-seq 0min rep2


title: hff_8hpi_200chx_b

value: CHX


title: control ser5p CUT&Tag rep2

data_processing:
Library strategy: CUT&Tag
Raw reads were trimmed for adaptor sequence and low-complexity or low-quality sequence were filtered using fastp v0.13.1 with default parameters. ChIP-seq, ATAC-seq, CUT&Tag and 4sUDRB-seq reads were aligned using bowtie2 v2.3.4.1. RNA-seq read were aligned using hisat2 v2.1.0 with parameter --rna-strandness RF. TT-seq reads were aligned using STAR v2.7.9a.
For ChIP-seq, ATAC-seq, CUT&Tag and 4sUDRB-seq, normalized aboundency in each 50-bp genomic bin were generated into bigWig file using deepTools bamCoverage command with parameter --normalizeUsing CPM. For RNA-seq, read/fragment count were obtained using featureCounts v1.6.1. To create scaled, strand-specific BigWig files for TT-seq data, SAMtools was used to split each target BAM file into mappable reads to either forward or reverse strand, and bamCoverage function of deepTools was used with the “-scaleFactor” argument to convert each strand-specific BAM file to a scaled BigWig file.
Genome_build: Hg38 for RNA-seq, ChIP-seq, ATAC-seq, and CUT&Tag read mapping, hg19 for 4sUDRB-seq. Hg38 and sacCer3 for TT-seq read mapping.
Supplementary_files_format_and_content: Tab-delimited text files include fragment count values of genes for each sample.
Supplementary_files_format_and_content: BigWig files contains normalized read count (CPM, in 50-bp bins) for ChIP-seq, CUT&Tag and 4sUDRB-seq, normalized insertion count (CPM, in 50-bp bins) for ATAC-seq, normalized read count (by sequencing read aligned to yeast genome, in 50-bp bins) for TT-seq.

value: control

value: Pol II (ser5p)


title: control_a_4

value: CD14+ monocytes


title: TOX4 KO 4sUDRB-seq 20min rep1


title: TOX4 KO 4sUDRB-seq 10min rep1


title: hff_8hpi_200chx_a


title: inoc10_3

city: Gent

first: Laurentijn

last: Tilleman

address: Ottergemsesteenweg 460

country: Belgium

institute: Ghent University

data_processing:
Adequate sequencing quality was confirmed using FastQC version 0.11.5 (Andrews, 2010).
Afterward, these reads were trimmed using cutadapt (Martin, 2011) version 1.11 to remove the “QuantSEQ FWD” adaptor sequence. . Potential contamination was checked using FastQ Screen version 0.7.0 (Wingett and Andrews, 2018).
The trimmed reads were mapped to the combined annotated reference genome of V. vinifera (NCBI Reference Sequence: GCF_000003745.3) and L. theobromae strain LA-SOL3 (SUB3910116, Félix et al., unpublished) using the STAR aligning software version 2.5.3a (Dobin et al., 2013).
Following the mapping step, the RSEM software version v1.2.31 (Li and Dewey, 2011), was used to generate the count tables for both V. vinifera and L. theobromae. Please note that the reference genome from Vitis vinifera was combined with the genome of Lasiodiplodia theobromae to have a joined reference genome to characterize the mixed samples of both organisms (VitisVinifera_V3.gff.gz).
Genome_build: V. vinifera GCF_000003745.3; L. theobroma SUB3910116
Supplementary_files_format_and_content: tab-delimited text files include gene_id, transcirpt_id(s), gene length, effective_length, expected_counts, TPM an FPKM for each sample
Genome_build: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/003/745/GCF_000003745.3_12X/GCF_000003745.3_12X_genomic.gff.gz
Genome_build: VitisVinifera_V3.gff.gz

molecule: polyA RNA

organism:
Vitis vinifera
Lasiodiplodia theobromae

source_name: inoc10_green stem

extract_protocol:
Stem tissue samples were ground in liquid nitrogen and total RNA was extracted using CTAB-based extraction protocol according to Gambino et al. (2008) followed by a DNase I treatment (RNase-Free DNase Set, Qiagen). Concentration and quality of the total extracted RNA were checked using the 'Quant-it ribogreen RNA assay' (Life Technologies, Grand Island, NY, USA) and the RNA 6000 nano chip (Agilent Technologies, Santa Clara, CA, USA), respectively.
Illumina mRNA sequencing libraries were made from 200 ng of total RNA of each sample using the QuantSeq 3' mRNA-Seq Library Prep Kit (Lexogen, Vienna, Austria) according to manufacturer's protocol using 15 cycles for the enrichment PCR step. Libraries were quantified by qPCR on a Lightcycler 480 (Roche, Basel, Switzerland), according to Illumina's protocol 'Sequencing Library qPCR Quantification protocol guide', version February 2011. A High Sensitivity DNA chip (Agilent Technologies, Santa Clara, CA, US) was used to control the library's size distribution and quality. The libraries were equimolarly pooled and sequenced at the NXTGNT massively parallel sequencing facility (www.nxtgnt.ugent.be, Ghent University) on an Illumina NextSeq 500 high throughput flow cell, generating single-end 75bp reads.

tag: cultivar

value: Touriga Nacional

tag: age

value: post inoculation day 10

value: Green stem


title: control 4sUDRB-seq 20min rep1


title: hff_8hpi_100chx_b


title: control 4sUDRB-seq 10min rep1


title: hff_8hpi_100chx_a


title: TOX4 KO ser5p CUT&Tag rep2


title: control ser2p CUT&Tag rep1

value: Pol II (ser2p)


title: hff_72PFA_b

value: PFA


title: inoc7_1

source_name: inoc7_green stem

value: post inoculation day 7


title: inoc7_2


title: hff_72PFA_a


title: hff_72hpi_a


title: inoc3_3

source_name: inoc3_green stem

value: post inoculation day 3


title: inoc10_1


title: inoc10_2


title: TOX4 KO ser2p CUT&Tag rep1

value: TOX4 knockout


title: hff_24hpi_b


title: control SPT5 CUT&Tag rep2


title: control SPT5 CUT&Tag rep1


title: inoc7_3


title: inoc3_2


title: hff_24hpi_a


title: TOX4 KO TT-seq rep1

data_processing:
Library strategy: TT-seq
Raw reads were trimmed for adaptor sequence and low-complexity or low-quality sequence were filtered using fastp v0.13.1 with default parameters. ChIP-seq, ATAC-seq, CUT&Tag and 4sUDRB-seq reads were aligned using bowtie2 v2.3.4.1. RNA-seq read were aligned using hisat2 v2.1.0 with parameter --rna-strandness RF. TT-seq reads were aligned using STAR v2.7.9a.
For ChIP-seq, ATAC-seq, CUT&Tag and 4sUDRB-seq, normalized aboundency in each 50-bp genomic bin were generated into bigWig file using deepTools bamCoverage command with parameter --normalizeUsing CPM. For RNA-seq, read/fragment count were obtained using featureCounts v1.6.1. To create scaled, strand-specific BigWig files for TT-seq data, SAMtools was used to split each target BAM file into mappable reads to either forward or reverse strand, and bamCoverage function of deepTools was used with the “-scaleFactor” argument to convert each strand-specific BAM file to a scaled BigWig file.
Genome_build: Hg38 for RNA-seq, ChIP-seq, ATAC-seq, and CUT&Tag read mapping, hg19 for 4sUDRB-seq. Hg38 and sacCer3 for TT-seq read mapping.
Supplementary_files_format_and_content: Tab-delimited text files include fragment count values of genes for each sample.
Supplementary_files_format_and_content: BigWig files contains normalized read count (CPM, in 50-bp bins) for ChIP-seq, CUT&Tag and 4sUDRB-seq, normalized insertion count (CPM, in 50-bp bins) for ATAC-seq, normalized read count (by sequencing read aligned to yeast genome, in 50-bp bins) for TT-seq.

extract_protocol:
Total RNA was extracted using TRNzol according to the manufacturer’s instructions; 1 μg 4-thiouracil (4TU) labeled S. cerevisiae BY4741 RNA was added to 100 μg total human RNA as spike-in; After fragmentation, biotinylation of 4sU-labeled RNA, purification of biotinylated RNA with Dynabeads M-280 streptavidin and rRNA depletion.
Strand-specific RNA-seq libraries were constructed as previously described (Zhong et al., 2011).

treatment_protocol: 35 million cells were used for each experiment; cells were transferred to fresh antibiotics-free medium and cultured for 1 hour before 4-thiouridine (4sU) treatment.


title: TOX4 KO SPT5 CUT&Tag rep2


title: TOX4 KO SPT5 CUT&Tag rep1


title: hff_24PFA_b


title: TOX4 KO TT-seq rep2


title: hff_72hpi_b


title: hff_12hpi_a


title: hff_4hpi_b


title: hff_24PFA_a


title: inoc1_3

source_name: inoc1_green stem

value: post inoculation day 1


title: control TT-seq rep2


title: inoc1_1


title: hff_12hpi_b


title: inoc3_1


title: hff_1hpi_a


title: TOX4 KO NELFE CUT&Tag rep2

data_processing:
Library strategy: CUT&Tag
Raw reads were trimmed for adaptor sequence and low-complexity or low-quality sequence were filtered using fastp v0.13.1 with default parameters. ChIP-seq, ATAC-seq, CUT&Tag and 4sUDRB-seq reads were aligned using bowtie2 v2.3.4.1. RNA-seq read were aligned using hisat2 v2.1.0 with parameter --rna-strandness RF.
For ChIP-seq, ATAC-seq, CUT&Tag and 4sUDRB-seq, normalized abundancy in each 50-bp genomic bin were generated into bigWig file using deepTools bamCoverage command with parameter --normalizeUsing CPM. For RNA-seq, read/fragment count were obtained using featureCounts v1.6.1.
Genome_build: Hg38 for RNA-seq, ChIP-seq, ATAC-seq, and CUT&Tag read mapping, hg19 for 4sUDRB-seq.
Supplementary_files_format_and_content: Tab-delimited text files include fragment count values of genes for each sample.
Supplementary_files_format_and_content: BigWig files contains normalized read count (CPM, in 50-bp bins) for ChIP-seq, CUT&Tag and 4sUDRB-seq or normalized insertion count (CPM, in 50-bp bins) for ATAC-seq.

extract_protocol:
CUT&Tag experiments were performed as previously described with minor modifications (Kaya-Okur, H.S. et al.). Briefly, 100,000 cells were used for each experiment. Cells were bound to Concanavalin A-coated beads without fixation and chromatin opening. After primary and secondary antibodies binding, pA-Tn5 transposome binding, and tagmentation, DNA was extracted by PCI.
Library was constructed by PCR, NEB Phusion (M0530L) was used as protocol.

value: NELFE


title: hff_1hpi_b


title: control TT-seq rep1


title: TOX4 KO NELFE CUT&Tag rep1


title: inoc1_2


title: TOX4 KO pSPT5 CUT&Tag rep2


title: hff_4hpi_a


title: control NELFE CUT&Tag rep2

description: control.NELFE.cuttag.bw


title: control pSPT5 CUT&Tag rep2


title: control NELFE CUT&Tag rep1

description: control.NELFE.cuttag.bw


title: control ATAC-seq rep2

description: control.ATAC-seq.bw

extract_protocol:
ATAC-seq experiments were performed by following a published protocol(Corces, M.R. et al.). Briefly, 50,000 cells were used for each experiment. After nuclei preparation, tagmentation and termination, DNA was extracted by PCI.
Library was construct by PCR, NEB Phusion(M0530L) was used as protocol.

value: K562 cell line


title: APAP_HepKO-2

first: Lin

last: Lei

address: 5333 Xi’an Road, Changchun, Jilin, China

department: State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, College of Veterinary Medicine

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: mmu10
Supplementary files format and content: tab-delimited text files include FPKM for each sample

source_name: Liver

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

treatment_protocol: Mice were fasted overnight to reduce hepatic GSH levels before APAP injection. APAP (IA0030; Solarbio, Beijing, China) was dissolved in warm saline (0.9 % NaCl; 55°C), cooled to 37°C, and injected intraperitoneally at a dose of 300 mg/kg APAP for 24 h. Then the liver samples were harvested for RNA-seq.

tag: genotype/variation

value: Nedd4 HepKO

value: Liver

value: 300 mg/kg APAP (IP) for 24 h


title: APAP_HepKO-3


title: cd14_72PFA_b


title: cd14_72hpi_b


title: cd14_72PFA_a


title: APAP_HepKO-1


title: cd14_48hpi_a


title: cd14_24hpi_b


title: APAP_Flox-3

value: Flox


title: cd14_48hpi_b


title: cd14_72hpi_a


title: TOX4 KO PPP1CC CUT&Tag rep2

data_processing:
Library strategy: CUT&Tag
Raw reads were trimmed for adaptor sequence and low-complexity or low-quality sequence were filtered using fastp v0.13.1 with default parameters. ChIP-seq, ATAC-seq, CUT&Tag and 4sUDRB-seq reads were aligned using bowtie2 v2.3.4.1. RNA-seq read were aligned using hisat2 v2.1.0 with parameter --rna-strandness RF.
For ChIP-seq, ATAC-seq, CUT&Tag and 4sUDRB-seq, normalized aboundency in each 50-bp genomic bin were generated into bigWig file using deepTools bamCoverage command with parameter --normalizeUsing CPM. For RNA-seq, read/fragment count were obtained using featureCounts v1.6.1.
Genome_build: Hg38 for RNA-seq, ChIP-seq, ATAC-seq, and CUT&Tag read mapping, hg19 for 4sUDRB-seq.
Supplementary_files_format_and_content: Tab-delimited text files include fragment count values of genes for each sample.
Supplementary_files_format_and_content: BigWig files contains normalized read count (CPM, in 50-bp bins) for ChIP-seq, CUT&Tag and 4sUDRB-seq or normalized insertion count (CPM, in 50-bp bins) for ATAC-seq.


title: APAP_Flox-2


title: TOX4 KO pSPT5 CUT&Tag rep1


title: control pSPT5 CUT&Tag rep1

value: control


title: cd14_48PFA_b

value: CD14+ monocytes


title: TOX4 KO ATAC-seq rep2


title: cd14_12hpi_b


title: cd14_48PFA_a


title: TOX4 KO ATAC-seq rep1


title: control ATAC-seq rep1

description: control.ATAC-seq.bw


title: B6 + Trib1 WT 3

type: RNA

city: Tokyo

first: Takuro

last: Nakamura

address: 3-8-31 Ariake, Koto-ku

department: The Cancer Institute

institute: Japanese Foundation for Cancer Research

description: Gene expression data from mouse AML

hyb_protocol: Following fragmentation, 7.5 ug of aRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 PM Array. GeneChips were washed and stained in the Affymetrix GeneAtlas Fluidics Station.

scan_protocol: GeneChips were scanned using the Affymetrix GeneAtlas Imaging Station.

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

label: biotin

source_name: AML cell line expressing Trib1

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: B6, Ts1Cje, B6 + Trib1 and Ts1Cje + Trib1 cells were grown in IMDM supplemented with 10% fetal bovine serum, and 5 ng/ml IL-3.

extract_protocol: Total RNA was purified using RNA Easy kit (QIAGEN) according to the manufacturer's protocol

treatment_protocol: No treatment was provided.

value: mouse AML cell

value: expressing Trib1


title: APAP_Flox-1


title: cd14_24hpi_a


title: cd14_8CHX_a

value: CHX


title: Ts1Cje + Trib1 WT 1

description: Gene expression data from mouse AML


title: TOX4 KO Pol II CUT&Tag rep2

source_name: K562 cell line

value: Pol II


title: Ts1Cje + Trib1 WT 3

description: Gene expression data from mouse AML


title: control PPP1CC CUT&Tag rep2


title: cd14_12hpi_a


title: cd14_8CHX_b


title: B6 + Trib1 WT 1

description: Gene expression data from mouse AML


title: control Pol II CUT&Tag rep2

description: control.PolII.cuttag.bw


title: control PPP1CC CUT&Tag rep1


title: Ts1Cje 2

description: Gene expression data from mouse hematopoietic cell

source_name: Ts1Cje mouse hematopoietic cell

value: mouse hematopoietic cell


title: Ts1Cje + Trib1 WT 2

description: Gene expression data from mouse AML


title: B6 + Trib1 WT 2

description: Gene expression data from mouse AML


title: Ts1Cje 3


title: control ser5p CUT&Tag rep1

value: Pol II (ser5p)


title: TOX4 KO ser5p CUT&Tag rep1


title: cd14_8hpi_a

source_name: Primary CD14+ monocytes


title: cd14_8hpi_b


title: TOX4 KO PPP1CC CUT&Tag rep1


title: cd14_4hpi_b


title: GKO-IMM3

city: Toyama

first: Ichiro

last: Takasaki

address: 3190 Gofuku

institute: University of Toyama

description: Gene expression data from B16OVA tumors from OVA-immunized IFN-gamma-deficient mice.

hyb_protocol: Following fragmentation, 5.2 ug of fragmented cRNA were hybridized for 16 hr at 45C on GeneChip MoGene 2.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with GeneSprin (ver. 14) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

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

value: B16 melanoma

value: variant from OVA-immunized IFN-g KO mouse


title: cd14_1hpi_b


title: cd14_1hpi_a


title: ctr10_3

organism: Vitis vinifera

source_name: ctr10_green stem

value: Touriga Nacional

value: post inoculation day 10

value: Green stem


title: cd14_4hpi_a


title: control ser2p CUT&Tag rep2

value: K562 cell line

value: Pol II (ser2p)


title: TOX4 KO Pol II CUT&Tag rep1

value: TOX4 knockout


title: control TOX4 CUT&Tag rep2


title: ctr10_2


title: B6 3

source_name: wild type mouse hematopoietic cell

value: wild type


title: Ts1Cje 1


title: B6 2


title: control Pol II CUT&Tag rep1

description: control.PolII.cuttag.bw

value: control


title: TOX4 KO ser2p CUT&Tag rep2


title: IMM8

description: Gene expression data from B16OVA tumors from OVA-immunized mice.

value: variant from OVA-immunized  B6 mouse


title: 148-1 inner

city: Evry Cedex

first: Robert

last: Olaso

address: 2 rue Gaston Cremieux

department: CNRGH

institute: CEA-DRF

description: SAMPLE 14

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with Beadstudio

source_name: Dcx N°148, internal stratum pyramidale (SPI) CA3 cells

label_protocol: Biotinylated cRNA were prepared with the Ambion Illumina TotalPrep RNA Amplification kit for Illumina arrays

extract_protocol: Total RNA was isolated from pooled microdissected material using an RNA isolation kit (Qiagen RNAeasy microkit) according to manufacturer’s instructions. RNA quantity was measured using a nanodrop spectrophotometer. RNA quality was checked using an Agilent 2100 Bioanalyzer with the RNA 6000 Pico LabChip Kit (5065-4473, Agilent Technologies, Palo Alto) according to the manufacturer’s instructions.

value: Dcx

tag: background strain

tag: developmental stage

value: Adult

value: Brain

tag: brain region


title: 148-2 outer

description: SAMPLE 13

source_name: Dcx  N°148, external stratum pyramidale (SPE) CA3 cells

value: external stratum pyramidale (SPI) CA3 cells


title: B6 1

value: mouse hematopoietic cell


title: GKO-IMM2


title: 166-2 outer

description: SAMPLE 11

source_name: Dcx N°166, external stratum pyramidale (SPE) CA3 cells


title: ctr10_1


title: GKO-IMM1


title: IMM2


title: ctr7_3

source_name: ctr7_green stem

value: post inoculation day 7


title: ctr7_2


title: sigE mutant, rep3

city: Busan 46241, Republic of Korea

first: Yuna

last: Oh

address: Busandaehakro63bun-gil, 2

department: Department of Integrated Biological Science

country: South Korea

institute: Pusan national university

data_processing:
The quality of the obtained data was checked by determining the phred quality score using FastQC v0.11.9.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Trimmomatic v0.38.0, then mapped to the whole genome of M. smegmatis using bowtie v2.4.2 with default setting.
Mapped reads per annotated gene were counted by htseq_count/0.9.1.
Counted values were nomalized in the RPKM method.
Assembly: Mycobacterium smegmatis MC2 155 (GCF_000015005.1_ASM1500v1)
Supplementary files format and content: txt: tab-delimited text files include RPKM values for each sample

organism: Mycolicibacterium smegmatis

source_name: in vitro aerobic culture of the sigE mutant strain

growth_protocol: The M. smegmatis strains were grown aerobically in Middlebrook 7H9 medium supplemented with 0.2% glucose and 0.02% Tween 80 (vol/vol) on a gyratory shaker (200 rpm) at 37°C.

extract_protocol:
The strains were grown until an optical density at 600 nm reached 0.75 to 0.85. Cells were harvested by centrifugation at 4°C with 3500×g for 3 min. The cell pellets were resuspended with 1 ml TRIzol (Invitrogen). Procedures of total RNA extract from the cell pellets were performed using TRIZol purchased from Invitrogen and followed the instructions provided to users. Nine libraries for RNA-seq were prepared using a Truseq standed mRNA Sample Library Prep Kit (Illumina) with the standard high-throughput protocol. Sequencing was performed on an Illumina Novaseq 6000 system.
Nine libraries for RNA-seq were prepared using a Truseq standed mRNA Sample Library Prep Kit (Illumina) with the standard high-throughput protocol.

tag: strain background

value: sigE-

tag: conditions

value: in vitro


title: 166-1 inner

description: SAMPLE 12

source_name: Dcx  N°166, internal stratum pyramidale (SPI) CA3 cells


title: 144 WT

description: SAMPLE 10

source_name: WT N°144, hippocampal CA3 region

value: WT

value: hippocampal CA3 region


title: 165-2 outer

description: SAMPLE 9

source_name: Dcx N°165, external stratum pyramidale (SPE) CA3 cells


title: control TOX4 CUT&Tag rep1

tag: cell line

tag: antibody


title: ctr7_1

value: Touriga Nacional

value: Green stem


title: sigE mutant, rep2


title: sigE mutant, rep1


title: ctr3_3

description:
Detection of L. theobromae genes
RUN345-AC-10_S24

source_name: ctr3_green stem

value: post inoculation day 3


title: NIMM4

description: Gene expression data from B16OVA tumors from non-immunized naïve B6 mice.

tag: strain

tag: cell type

value: B16 melanoma

tag: treatment

value: variant from naive  B6 mouse


title: sigB mutant, rep3

source_name: in vitro aerobic culture of the sigB mutant strain

value: sigB-


title: ctr3_2


title: NIMM3


title: ctr3_1

description:
Detection of L. theobromae genes
RUN345-AC-8_S2


title: IMM1

value: variant from OVA-immunized  B6 mouse


title: sigB mutant, rep2


title: sigB mutant, rep1


title: 199 WT

description: SAMPLE 8

source_name: WT N°199, hippocampal CA3 region

tag: genotype


title: 142 WT

description: SAMPLE 7

source_name: WT N°142, hippocampal CA3 region

tag: tissue


title: WT, rep3

source_name: in vitro aerobic culture of the wild type strain

value: wild type


title: 146-1 inner

description: SAMPLE 6

source_name: Dcx N°146, internal stratum pyramidale (SPI) CA3 cells

value: Dcx

value: Adult


title: Sorted intestinal blood endothelial cells from control mice (WT, Apcfl//fl), biological replicate 3.

city: Geneva

first: Isabelle

last: Dupanloup

address: Rue Michel-Servet, 1

institute: University of Geneva

description: Transcriptomes of intestinal blood endothelial cells (BEC) from mice with acute epithelial Apc deletion.

hyb_protocol: Biotinylated target cDNA were hybridized, washed and stained according to the protocol described in Affymetrix GeneChip Expression Analysis Manual (Fluidics protocol FS450_0007).

scan_protocol: Affymetrix Mouse Gene 2.0 ST arrays were scanned using a GeneChip Scanner 3000 7G (Affymetrix).

data_processing: Raw microarray data (CEL files) were processed using the oligo package from Bioconductor. Background subtraction, normalization, and summarization were performed using the RMA algorithm within the oligo package.

source_name: Sorted intestinal blood endothelial cells from control mice (WT, Apcfl//fl).

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol (Fluidics protocol FS450_0007).

growth_protocol: Control (WT, Apcfl//fl) or Apcfl//fl; Villin-CreERT2 (KO) mice were daily injected subcutaneously with tamoxifen for 5 days.

extract_protocol: Total RNA was isolated using the Qiagen RNeasy Plus Micro Kit (Qiagen) and RNA integrity was verified on a Fragment Analyzer (Advanced Analytical). mRNA was amplified using the Ovation Pico WTA System V2 (Nugen).

treatment_protocol: On day 6 the intestine was harvested and digested with Collagenase IV and BECs were sorted as single, live, CD45neg, EpCAMneg, gp38neg, CD31+ cells. Cells were collected in RLT Buffer (Qiagen), vortexed and snap-frozen.

value: mixed C57BL/6 x 129

value: control mice (WT, Apcfl//fl)


title: Sorted intestinal blood endothelial cells from control mice (WT, Apcfl//fl), biological replicate 1.


title: 146-2 outer

description: SAMPLE 5

source_name: Dcx N°146, external stratum pyramidale (SPE) CA3 cells

value: Brain

value: external stratum pyramidale (SPI) CA3 cells


title: WT, rep2

value: in vitro


title: 206 WT

description: SAMPLE 4

source_name: WT N°206, hippocampal CA3 region

value: WT


title: B16OVA

description: Gene expression data from parent cells.

source_name: cell line

value: parent


title: NIMM1


title: Sorted intestinal blood endothelial cells from Apcfl//fl; Villin-CreERT2 (KO) mice, biological replicate 3.

source_name: Sorted intestinal blood endothelial cells from Apcfl//fl; Villin-CreERT2 (KO) mice.

value: Apcfl//fl; Villin-CreERT2 (KO)


title: ctr1_3

source_name: ctr1_green stem

value: Touriga Nacional

value: post inoculation day 1

value: Green stem


title: ctr1_2


title: ctr1_1


title: Sorted intestinal blood endothelial cells from control mice (WT, Apcfl//fl), biological replicate 2.


title: WT, rep1


title: 147-1 inner

description: SAMPLE 3

source_name: Dcx N°147, internal stratum pyramidale (SPI) CA3 cells


title: Sorted intestinal blood endothelial cells from Apcfl//fl; Villin-CreERT2 (KO) mice, biological replicate 2.