title: Human3.1

city: Ann Arbor

first: Qianyi

last: Ma

address: 1141 E Catherine St

institute: University of Michigan

data_processing:
Two paired-end fastq files were converted to one query-sorted bam file using Picard tools v2.6.0 and samtools v1.2.
Sequence reads were tagged with cell and molecular barcodes, filtered for low base quality in cell or molecular barcodes, trimmed for starting sequence and polyA tail using Drop-seq tools v1.12.
The barcode-tagged, filtered and trimmed bam file is converted back to fastq file using Picard tools v2.6.0.
Alignment was performed using Star v2.5.2b.
Aligned reads were tagged with gene exons and cleaned for bead synthesis errors using Drop-seq tools v1.12.
Gene expressoin matrix was generated using Drop-seq tools v1.12.
For mixed-species samples, spike-in mouse cells were separated from other species based on gene expression data and removed from the unaligned fastq file.
Genome_build: GRCh37, Mmul_8.0.1, GRCm38
Supplementary_files_format_and_content: tab-delimited text files include raw UMI counts for each cell (column) and each gene (row)

source_name: Adult Testis

extract_protocol:
Briefly, cells, barcoded microparticle beads and lysis buffer were co-flown into a microfluidic device and captured in nanoliter sized droplets. After droplet collection and breakage, the beads were washed, and cDNA synthesis occurred on the bead. Excess oligos were removed by exonuclease I digestion. cDNA amplification was done from a pool of 2,000 bead. Individual PCRs were purified and pooled for library generation.
A total of 600 pg of amplified cDNA was used for a Nextera XT library preparation (Illumina).

value: Testis

tag: age

value: 30-40 years

tag: source name for spike-in

tag: organism for spike-in


title: Human3.2

status: Public on Jun 12 2020

type: SRA

state: MI

department: Human Genetics

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: tissue


title: Hi-C: G1 control + 4sT

city: Vienna

first: Michael

last: Mitter

address: Dr.-Bohr-Gasse 3

country: Austria

institute: IMBA

description: scsHi-C library of cells synchronized to G1 using thymidine/aphidicoline and not released from aphidicoline block but treated with 4sT; Merge of two replicates. All contacts, cis-sister contacta and trans-sister contacts.

library_source: genomic

data_processing:
Basecalling software: Illumina RTA
Hi-C samples were preprocessed using a custom nextflow pipeline (https://github.com/gerlichlab/scshic_pipeline). Briefly, bcl2 files were first demultiplexed using bcl2tofastq. Then, fastq files were aligned to hg19 with HeLa SNPs using bwa, aligning read pairs independently. Then, pairsam files were constructed using pairtools (https://github.com/mirnylab/pairtools), followed by sorting and deduplicating. Then, reads were split into cis sister and trans sister contacts based on the presence of signature mutations using pairtools select: A read was assigned to the Watson strand if it contained two or more A-to-G mutations and no T-to-C mutations. Similarly, if a read contained two or more T-to-C mutations, but no A-to-G mutations it was assigned to the Crick strand. Then, contacts were classified as cis sister contacts if (after correcting for the opposite read-strandedness of Illumina sequencing of the two mates) both mates mapped to the same strand. Conversely, contacts were classified as trans sister contacts if the two mates mapped to opposing strands. Then, cooler (https://github.com/mirnylab/cooler) was used to construct .cool files. For DNAseq samples,  a custom python script was used to count the number of each point mutation type.
Genome_build: hg19
Supplementary_files_format_and_content: cooler derived .cool files (Mirny lab) containing Hi-C matrices for usage with HiGlass and the cooler ecosystem for Hi-C. For DNAseq data, tables (csv) are provided that indicate the number of each point mutation type, mapping quality and average Phred-score of every sequencing read.
Supplementary_files_format_and_content: cool files were generated using cooler (https://github.com/mirnylab/cooler) using standard parameters. Separate cooler files are provided for all contacts, cis-sister contacts and trans-sister contacts. Csv files were generated using a custom python script to count different point mutation types.

molecule: genomic DNA

source_name: cervical carcinoma

growth_protocol: For Hi-C synchronization, HeLa Kyoto cells were seeded into 25 cm2 flasks and grown for 3 h, then supplemented with 2 mM Thymidine (Sigma). Cells were released 16 h later by washing 2 times with prewarmed WT medium. 8 h later, cells were supplemented with 3 µg/ml aphidicolin (Sigma) and 2 mM 4sT. Cells were released 16 h later by washing 2 times with PBS and addition of medium containing 2 mM 4sT. For Sororin-AID experiments, 500 µM Indole-3-acetic acid (Sigma) was added 1 h prior to S-phase release. For S-phase release experiments, samples were taken at the indicated time-points. For synchronization to G2 and prometaphase, after 4 h release, 9 µg RO-3306 (Sigma) or 200 ng/ml nocodazole (Sigma) were added respectively. For NIPBL-AID experiments, 500 µM Indole-3-acetic acid (Sigma) was added 8 h after released. Samples were processed 16 h later. Cells were harvested by washing with PBS, followed by trypsinisation and resuspension in WT medium. Cells were then spun down, washed again with PBS, followed by fixation for 4 min in 1 % formaldehyde (Sigma). Cell pellets were stored at -20 °C or processed immediately. For DNAseq evaluation of 4sT mediated increase of mutation rate, cells were seeded into a 6-well plate and supplemented either with H20 or 2 mM 4sT for 5 days before harvesting.

extract_protocol:
For Hi-C, fixed cells were permeabilized using ice-cold Hi-C lysis buffer (10 mM TRIS-HCl pH 8 [Sigma], 10 mM NaCl [Sigma], 0.2 % Nonidet P-40 substitute [Sigma], 1x Complete EDTA-free Protease inhibitor [Roche]) for 30 min at 4 °C. Then, cells were spun down (2500 x g for 5 min), supernatant was discarded, and digestion mix was added (375 U DpnII [NEB] in 1x DpnII buffer [NEB]) and cells incubated for 16 h at 37 °C under rotation. Then, cells were spun down, supernatant was discarded and fill-in mix was added (38 µM Biotin-14-dATP [Thermo Fisher Scientific], 38 µM dCTP, dGTP and dCTP [Thermo Fisher Scientific], 50 U Klenow Polymerase [NEB], 1x NEB 2 buffer) and cells incubated for 1 h at 37 °C under rotation. Then, cells were spun down again, and ligation mix was added (1x T4 DNA ligase buffer [Thermo Fisher Scientific], 0.1 % Triton X-100 [Sigma], 100 µg/ml BSA [Sigma], 50 U T4 DNA ligase [Thermo Fisher Scientific]) and incubated at RT for 4 h. Then, cells were spun down, resuspended in 200 µl PBS and gDNA was purified using the DNeasy Blood and Tissue kit (Quiagen). DNA was transferred to a Covaris microTUBE (Covaris) and sheared on a Covaris S2 instrument (Duty cycle 10 %, Intensity 5.0, Cycles/burst 200) for 25 s. Double size selection was performed by employing AMPure XP beads (Beckman Coulter) first at 0.8-fold sample volume according to the standard protocol, followed by transfer of the supernatant and bead application at 0.12-fold sample volume. The resulting DNA was bound to Dynabeads MyOne Streptavidin C1 beads (Thermo Fisher Scientific) in Biotin binding buffer (5 mM Tris-HCl pH 7.5 [Sigma], 0.5 mM EDTA [AppliChem], 1 M NaCl [Merck]) for 1 h at RT. Beads were then washed 2x in Tween wash buffer (5 mM Tris-HCl [Sigma], 0.5 mM EDTA [AppliChem], 1 M NaCl [Merck], 0.05 % Tween-20 [Sigma]) and 1x in H2O. For DNAseq, Cells were harvested by trypsinization, spun down at 1100 x g for 1 min and the supernatant was discarded. Then, cells were spun down, resuspended in 200 µl PBS and gDNA was purified using the DNeasy Blood and Tissue kit (Quiagen). DNA was transferred to Covaris microTUBE (Covaris) and sheared on a Covaris S2 instrument (Duty cycle 10 %, Intensity 5.0, Cycles/burst 200) for 25 s. Double size selection was performed by employing AMPure XP beads (Beckman Coulter) first at 0.8-fold sample volume according to the standard protocol, followed by transfer of the supernatant and bead application at 0.12-fold sample volume.
For Hi-C samples, beads with bound biotinylated DNA were resuspended in H2O and library preparation was performed using the NEBNext Ultra II DNA library prep kit for Illumina [NEB] according to the standard protocol. After this, beads were washed 4x using Tween wash buffer and DNA was eluted using 95 % formamide (Sigma), 10 mM EDTA (AppliChem) at 65 °C for 2 min. DNA was then precipitated using 80 % EtOH (Sigma), washed with 75 % EtOH and resuspended in H2O. Then, 4sT was converted to methyl-cytosine using OsO4 / NH4Cl, followed by qPCR according the NEBUltra Ultra II DNA library prep kit for Illumina [NEB]. The finished libraries were purified using AMPure XP beads (Beckman Coulter) at 0.9x sample volume following the standard protocol. For DNAseq samples, DNA library preparation was performed using the NEBNext Ultra II DNA library prep kit for Illumina [NEB] according to the standard protocol. The unamplified libraries were then treated using OsO4  and amplified according the NEBNext Ultra II DNA library prep kit for Illumina [NEB]. The finished libraries were purified using AMPure XP beads (Beckman Coulter) at 0.9x sample volume following the standard protocol.

treatment_protocol: HeLa cells were either untreated or treated with auxin to deplete target proteins as per the growth protocol.

tag: cell type

value: HeLa Kyoto

tag: diesease state

value: cervical carcinoma

tag: genotype

value: w.t. G1


title: Human4


title: Human2.2

value: 37 years


title: Control_C42816_R1

city: Erie

middle: A

last: Campbell

state: PA

address: 4205 College Drive

department: School of Science

institute: Penn State Erie

description: late ecodormant tissue

data_processing:
fastq files were uploaded to the Galaxy Suite (https://usegalaxy.org) and mapped to the double haploid potato genome (Solanum tuberosum SolTub_ver3) using Tophat2-SE and differential expression of transcripts was determined using Cufflinks v2.2.1a
Genome_build: SolTub_3.0
Supplementary_files_format_and_content: genes.fpkm_tracking

organism: Solanum tuberosum

source_name: tuber meristems

growth_protocol: Tubers were treated in a 9 liter container  for two days

extract_protocol:
Tuber meristems were extracted with a microcurette and frozen in liquid N2, total RNA was isolated using a PureLink RNA Mini Kit (www.thermofisher.com) and quantified on a BioSpecNano (www.ssi.shimadzu.com)
The libraries were made with the Illumina TruSeq Stranded mRNA Kit and sequenced on the HiSeq 2500 in Rapid Mode

treatment_protocol: Tubers received either water at 22.5 ul per 9liters of head space (Control) or 22.5 ul of DMN per 9 liters of head space (treated)

value: tuber meristem

tag: treatment

value: water treated

tag: dormancy status

value: late ecodormant tissue


title: Hi-C: G1 control

description: scsHi-C library of cells synchronized to G1 using thymidine/aphidicoline and not released from aphidicoline block; Merge of two replicates. All contacts, cis-sister contacta and trans-sister contacts.


title: Human2.1


title: Control_C42616_R1

description: late ecodormant tissue


title: 06_F_SN_PBS_IS

city: La Jolla

first: Andrei

last: Chernov

state: CA

address: 9500 Gilman Dr

department: Anesthesiology

institute: University of California San Diego

data_processing:
The reads data were processed using BaseSpace software (Illumina)
Reads were aligned to m. musculus genome (version Mm10) using STAR aligner with default settings.
Statistical data processing and differential transcript expression was determined using the Cufflinks package (http://cufflinks.cbcb.umd.edu/).
Biological pathway analysis and comparison were performed using Ingenuity Pathway Analysis (Qiagen).
Genome_build: mm10

organism: Mus musculus

source_name: sciatic nerve

growth_protocol: Adult female and male C57BL6/J mice (n = 6/group) were obtained from Jackson Labs and housed in a temperature-controlled room (∼22 °C), on a 12-h light/dark cycle with free access to food and water. The procedure and testing were conducted during the light cycle.

extract_protocol:
Total RNA was extracted from mouse tissues using TRI reagent (Zymo Research) and purified using Direct-zol microRNA system (Zymo Research). The RNA purity was estimated by measuring the OD260/280 ratio using a ND-1000 spectrophotometer (Thermo Scientific). RNA integrity was determined using 2100 Bioanalyser (Agilent Technologies).
Poly(A) RNA was enriched using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs). Ribosomal RNA was depleted using NEBNext rRNA Depletion reagents (New England Biolabs). A NEBNext Ultra Directional II RNA Library Preparation Kit for Illumina (New England Biolabs) was used to obtain barcoded cDNA libraries from total RNA. Barcoded libraries were pooled and the High Output v2 kit (IlluminaO) was employed to prepare the sequencing libraries. Libraries were sequenced on a NextSeq 500 DNA sequencer (Illumina).

treatment_protocol: Under isoflurane anesthesia a single intrasciatic bolus injections of the MBP peptides (60 µg in 5 µl PBS each) or PBS carrier were performed into a nerve fascicle using a 33-gauge needle on a Hamilton syringe. In 7 days sciatic nerve segments (injection site), L5 DRG and DSC were collected for RNA-seq. All animal procedures were performed in agreement with the PHS Policy on Humane Care and Use of Laboratory Animals and the protocol approved by the Institutional Animal Care and Use Committee at the VA San Diego Healthcare System.

value: sciatic nerve

tag: strain

tag: Sex

value: female

value: PBS carrier

tag: injection site

value: intrasciatic


title: 05_F_SN_MBPS_IS

value: MBP84-104-SCR (scramble) peptide


title: 10_F_DRG_MBP_IS

source_name: dorsal root ganglia

value: dorsal root ganglia

value: MBP84-104-WT (wild type) peptide


title: Sevi PDX HCI-009 3975

city: Aurora

first: Jessica

last: Christenson

state: CO

department: Pathology

institute: University of Colorado Anschutz Medical Campus

description: Sevi PDX HCI-009 3975

data_processing:
Reads generated were mapped to the human genome (GRCH38) by gSNAP (CITE2)
Expression (FPKM) derived by Cufflinks (CITE2)
Differential expression analyzed with ANOVA in R.

source_name: Patient derived xenograft tumors

growth_protocol: PDX tumors were propogated in the mammary glands of  NOD/SCID/gamma mice

extract_protocol:
mRNA was extracted from frozen tissue using TRIzol and was Bioanalyzed prior to sequencing
RNA libraries were prepared used Illumina HiSeq libraries according to manufacturer’s instructions for the TruSeq Stranded RNA kit

treatment_protocol: PDX tumors were implanted in mice and when mammary tumors reached a volume of 100mm3 mice were administered vehicle control or 150mg/kg/day Sevi daily PO. Tumor tissue was collect 2 weeks later.

tag: pdx

value: HCI-009 TNBC

tag: mouse strain

value: NOD scid gamma

value: Drug:150mg/kd/day Sevi, daily PO, 2wk


title: Human1.5

description: mixed-species samples

value: Testis

value: 20-25 years

value: NIH3T3 cell line

value: Mus musculus


title: Sevi PDX HCI-009 3971

description: Sevi PDX HCI-009 3971


title: Control_C21816_R1

description: early ecodormant tissue

value: tuber meristem

value: early ecodormant tissue


title: 04_F_SN_MBP_IS


title: Sevi PDX HCI-009 3967

description: Sevi PDX HCI-009 3967


title: Human1.4

description: mixed-species samples


title: Control_C21616_R1

description: early ecodormant tissue

value: water treated


title: Human1.3


title: 03_M_SN_PBS_IS

value: sciatic nerve

value: male


title: 07_M_DRG_MBP_IS


title: DMN_D121117_R1

description: DMN dormant tissue

value: 1,4-dimethylnaphthalene treated

value: dormant tissue


title: 02_M_SN_MBPS_IS

value: MBP84-104-SCR (scramble) peptide

value: intrasciatic


title: Ctrl PDX HCI-009 3992

description: Ctrl PDX HCI-009 3992

value: Vehicle:Control, daily PO, 2wk


title: Control_C11117_R1

description: control dormant tissue


title: 01_M_SN_MBP_IS

value: MBP84-104-WT (wild type) peptide


title: Ctrl PDX HCI-009 3990

description: Ctrl PDX HCI-009 3990

value: HCI-009 TNBC

value: NOD scid gamma


title: C1-2

description: nondormant control Feburary

data_processing:
fastq files were uploaded to the Galaxy Suite (https://usegalaxy.org) and mapped to the double haploid potato genome (Solanum tuberosum SolTub_ver3) using Tophat2-SE and differential expression of transcripts was determined using Cufflinks v2.2.1a
Genome_build: SolTub_ver3
Supplementary_files_format_and_content: FPKM


title: Human1.1

value: Testis


title: Human1.2

value: 20-25 years


title: D4-4

description: nondormant DMN April

value: DMN treated

value: late ecodormant tissue


title: Ctrl PDX HCI-009 3991

description: Ctrl PDX HCI-009 3991


title: MDA453 Unstimulated

data_processing:
3000 cells were sequenced with a read-depth of approximately 75,000 reads/cell. Read mapping and expression quantification was performed using a combination of the 10X Cellranger pipeline and custom analytic scripts
Single-cell reads were mapped to the human genome (GRCh38) and assigned to genes using the standard CellRanger pipeline.
The R packages Monocle and Seurat were used for differential expression.

source_name: TNBC cells

growth_protocol: Cells grown in DMEM media supplemented with 10% FBS

extract_protocol:
mRNA was extracted using the 10X Genomics Sample Preparation Protocol
RNA libraries were prepared used Illumina HiSeq libraries according to manufacturer’s instructions for the TruSeq Stranded RNA kit

treatment_protocol: None, unstimulated

value: None, unstimulated

tag: cell line

value: MDA-MB-453 cells


title: D3-4

description: nondormant DMN April

value: tuber meristem


title: AICAR_rep2

city: Cambridge

first: Mohsen

last: Sarikhani

state: MA

address: 7 Divinity,Fairchild 159

department: Stem cell and regenerative biology

institute: Harvard University

data_processing:
Alignment with bowtie2
Convertion to bigwig using igvtools and ucsc tools
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

source_name: iPSC-derived Cardiomyoytes

growth_protocol: iPSC cells differentiated into cardiomcytes using CHIR and IWP4 and at day 9 cells were treated with 1mM AICAR and 10mM NAM then harvested for ATAC-seq assay.

extract_protocol: ATAC-seq experiment was performed using a using a modified protocol (Xu et al., 2019 Immunity). Briefly, 50,000 cells were used for library preparation. The libraries were amplified for 9 cycles, purified with Zymo DNA clean and Concentrator, and sequenced on a NextSeq 500 using a 75 cycle high output V2 kit (Read 1: 38 cycles, Index 1: 8 cycles, Read 2: 38 cycles).

value: Induced pluripotent stem cells


title: AICAR_rep1


title: 518CD4DIS

city: Herston

first: Susanna

last: Ng

state: QLD

address: 300 Herston Road

department: Immunology

country: Australia

institute: QIMR Berghofer Medical Research Institute

data_processing:
Quality control was performed using FastQC.
Reads were mapped to the reference genome GRCh38.p3 and assigned to transcripts (Ensembl v82) using STAR.
Genome_build: GRCh38.p3
Supplementary_files_format_and_content: tab-delimited text files include transcript counts

source_name: Blood

extract_protocol:
MACS-purified CD4+ T cells were homogenised in QIAshredder (QIAGEN) columns, followed by RNA extraction using the RNeasy Mini Kit (QIAGEN) according to manufacturer's instructions. Total RNA was treated with the RNase-free DNase Set (QIAGEN).
mRNA was isolated using the NEBNext Poly(A) mRNA magnetic isolation module (New England Biolabs). Libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs).

treatment_protocol: Patients were treated with Ambisome after diagnosis either by microscopic detection of amastigotes in splenic aspirate smears, or using an rk39 dipstick test

value: CD4+ T cells

tag: cellular source

value: PBMCs

value: Blood

tag: status

value: Day 30 post-treatment (day 30)

tag: disease state

value: visceral leishmaniasis


title: 518CD4D0

value: Infected (day 0)


title: D5-4

description: nondormant DMN April


title: D2-4

description: nondormant DMN April


title: NAM_rep2


title: hESC.Pancreas.mock.2

city: New York

first: David

last: Redmond

state: New York

address: 1300 York Avenue

institute: Weill Cornell Medicine

description: hESC Pancreas Mock

data_processing:
FastQC (v0.11.8) to check FASTQ quality.
Trim Galore (v0.6.4) for adapter trimming
SortMeRNA (v2.1b) to remove rRNA reads.
STAR (v2.6.1d) to align files
Subread (v1.6.4) featureCounts to quantify gene counts
Genome_build: GRCh38
Supplementary_files_format_and_content: Gene count matrix

molecule: polyA RNA

source_name: hESC

growth_protocol:
Protocols for maintenance of hPSCs and generation of lung cells were slightly modified from previous studies (Chen et al., 2019; Huang et al., 2014). The hESC line-RUES2 was cultured on irradiated mouse embryonic fibroblasts (Global Stem, cat. no. GSC-6001G) at a density of 20,000- 25,000 cells/cm2 in a medium of DMEM/F12, 20% knockout serum replacement (Life Technologies), 0.1 mM β-mercaptoethanol (Sigma Aldrich) and 20 ng/ml bFGF (R&D Systems), and medium was changed daily. hESC cultures were maintained in an undifferentiated state at 37 °C in a 5% CO2/air environment until stem cells reached about 90% confluence.
Pancreatic endocrine cell differentiation was performed using INSGFP/W MEL-1 cells. Cells were cultured on Matrigel-coated 6-well plates in StemFlex medium (Gibco Thermo Fisher). Cells were maintained at 37℃ with 5% CO2. hESCs were differentiated using a previously reported strategy (Zeng et al., 2016). In brief, on day 0, cells were exposed to basal medium RPMI 1640 supplemented with 1× Glutamax (Thermo Fisher Scientific), 50 μg/mL Normocin, 100 ng/mL Activin A (R&D systems), and 2 μM of CHIR99021 (GSK3β inhibitor 3, Cayman Chemical ) for 24 h. The medium was changed on day 1 to basal RPMI 1640 medium supplemented with 1× Glutamax (Thermo Fisher Scientific), 50 μg/mL Normocin, 0.2% fetal bovine serum (FBS, Corning), 100 ng/mL Activin A (R&D systems) for 2 days. On day 3, the resulting definitive endoderm cells were cultured in MCDB 131 medium (Thermo Fisher Scientific) supplemented with 1.5 g/L sodium bicarbonate, 1× Glutamax, 10 mM glucose (Sigma Aldrich) at final concentration, 2% bovine serum albumin (BSA, Lampire), 0.25 mM L-ascorbic acid (Sigma Aldrich) and 50 ng/ml of fibroblast growth factor 7 (FGF-7, Peprotech) for 2 days to acquire primitive gut tube. On day 5, the cells were induced to differentiate to posterior foregut in MCDB 131 medium supplemented with 2.5 g/L sodium bicarbonate, 1× Glutamax, 10 mM glucose at final concentration, 2% BSA, 0.25 mM L-ascorbic acid, 50 ng/ml of FGF-7, 1 μM Retinoic acid (RA; Sigma Aldrich), 100 nM LDN193189 (LDN, Axon Medchem), 1:200 ITS-X (Thermo Fisher Scientific), 200 nM TPPB (Tocris Bioscience) and 0.25 μM SANT-1 (Sigma Aldrich) for 2 days. On day 7, the cells were induced to differentiate to pancreatic endoderm in MCDB 131 medium supplemented with 2.5 g/L sodium bicarbonate, 1× Glutamax, 10 mM glucose at final concentration, 2% BSA, 0.25 mM L-ascorbic acid, 2 ng/ml of FGF-7, 0.1 μM RA, 200 nM LDN193189, 1:200 ITS-X, 100 nM TPPB and 0.25 μM SANT-1 for 3 days. On day 10, the cells were induced to differentiate to pancreatic endocrine precursors in MCDB 131 medium supplemented with 1.5 g/L sodium bicarbonate, 1× Glutamax, 20 mM glucose at final concentration, 2% BSA, 0.05 μM RA, 100 nM LDN, 1:200 ITS-X, 0.25 μM SANT-1, 1 mM T3 hormone (Sigma Aldrich), 10 μM ALK5 inhibitor II (Cayman Chemical), 10 μM zinc sulfate heptahydrate (Sigma Aldrich) and 10 μg/ml of heparin (Sigma Aldrich) for 3 days. On day 13, cells were exposed to MCDB 131 medium supplemented with 1.5 g/L sodium bicarbonate, 1× Glutamax, 20 mM glucose at final concentration, 2% BSA, 100 nM LDN193189, 1:200 ITS-X, 1 μM T3, 10 μM ALK5 inhibitor II, 10 μM zinc sulfate, 10 μg/ml of heparin, 100 nM gamma secretase inhibitor XX (Millipore) for the first 7 days. On day 27, cells were exposed to MCDB 131 medium supplemented with 1.5 g/L sodium bicarbonate, 1× Glutamax, 20 mM glucose at final concentration, 2% BSA, 1:200 ITS-X, 1 μM T3, 10 μM ALK5 inhibitor II, 10 μM zinc sulfate heptahydrate, 10 μg/ml of heparin, 1 mM N-acetyl cysteine (Sigma Aldrich), 10 μM Trolox (Millipore), 2 μM R428 (MedchemExpress) for 7-15 days. The medium was subsequently refreshed every day.  The protocol details are summarized in Figure S1B.

extract_protocol:
Organoid infections were performed at an MOI of 0.1 and harvested at 24 hpi in DMEM supplemented with 0.3% BSA, 4.5 g/L D-glucose, 4 mM L-glutamine and 1 μg/ml TPCKtrypsin. Total RNA was extracted in TRIzol (Invitrogen) and DNase I treated using Directzol RNA Miniprep kit (Zymo Research) according to the manufacturer’s instructions.  cDNA libraries were sequenced using an Illumina NextSeq 500 platform.
RNAseq libraries of polyadenylated RNA were prepared using the TruSeq RNA Library Prep Kit v2 (Illumina) or TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturer’s instructions.

treatment_protocol: Mock infected versus SARS-CoV-2 infected

value: hESC Pancreas

tag: infected

value: Mock


title: hESC.Pancreas.mock.3

description: hESC Pancreas Mock


title: NAM_rep1


title: 516CD4D0


title: 515CD4DIS


title: hESC.Pancreas.SARSCoV2.3

description: hESC Pancreas Infected


title: D4-2

description: nondormant DMN Feb

value: early ecodormant tissue


title: D3-2

description: nondormant DMN Feb


title: D6-2

description: nondormant DMN Feb


title: 514CD4D0


title: 515CD4D0


title: D497

city: 重庆

first: Gongwei

last: zhang

address: 重庆市荣昌区学院路160号

country: China

institute: 西南大学

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.
Index of the B. taurus reference genome ARS-UCD1.2 was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two conditions/groups was performed using the DESeq2 R package (1.16.1).
Genome_build: ARS-UCD1.2
Supplementary_files_format_and_content: readcount_18.txt: Tab-delimited text file includes read count values for each Sample.
Supplementary_files_format_and_content: novel_genes.txt: Tab-delimited text file.

organism: Bos taurus

extract_protocol:
Blood was collected from tail veins of healthy cattle and anticoagulated with EDTA. Blood samples (5 ml) were centrifuged at 3000 × g for 15 min at 4 °C and white coat (leukocytes) was transferred to a new 2-ml cryopreservation tube to which 1 ml RNAiso Plus (Takara, Dalian, China) was added before snap freezing in liquid nitrogen for transport. Total RNA was extracted with RNAiso Plus (Takara) according to manufacturer protocols.
All mRNA-Seq libraries were sequenced on an Illumina Novaseq platform (San Diego, CA) following the manufacturer’s protocol. Quantity and purity of RNA and RNA-Seq libraries were determined by Beijing Novogene Bioinformatics Technology (Beijing, China).

tag: breed

value: Droughtmaster

value: female

value: leukocytes

tag: condition

value: heat stress


title: D1-2

description: nondormant DMN Feb

tag: tissue

value: DMN treated


title: L.4: COVID-19 Lung 58L

description: COVID-19 Lung

source_name: Autopsy patient

value: Lung


title: hESC.Pancreas.SARSCoV2.2

description: hESC Pancreas Infected


title: D6007

address: 重庆市荣昌区学院路160号

tag: cell type


title: D4-12

description: dormant DMN

value: tuber meristem

value: dormant tissue


title: D6086

address: 重庆市荣昌区学院路160号


title: D6020

address: 重庆市荣昌区学院路160号


title: D6046

address: 重庆市荣昌区学院路160号


title: hESC.Pancreas.SARSCoV2.1

description: hESC Pancreas Infected


title: 514CD4DIS

value: CD4+ T cells


title: L.3: COVID-19 Lung 56L

description: COVID-19 Lung


title: D2-12

description: dormant DMN


title: 499CD4DIS

value: PBMCs


title: 516CD4DIS

value: Blood


title: H581

address: 重庆市荣昌区学院路160号

value: Red Angus x Droughtmaster


title: L.2: COVID-19 Lung 51L

description: COVID-19 Lung


title: D438

address: 重庆市荣昌区学院路160号


title: D3-12

description: dormant DMN


title: hESC.Pancreas.mock.1

description: hESC Pancreas Mock


title: 496CD4DIS

value: Day 30 post-treatment (day 30)

value: visceral leishmaniasis


title: H545

address: 重庆市荣昌区学院路160号


title: C1-4

description: Nondormant control April

value: water treated

value: late ecodormant tissue


title: X52.22: Liver Organoid Donor 1 SARS-CoV-2 2

description: Liver Organoid Donor 1 SARS-CoV-2

source_name: Organoid

value: Liver Organoid


title: D1-12

description: dormant DMN


title: 496CD4D0

value: Infected (day 0)


title: C3-4

description: Nondormant control April


title: X50.7: Liver Organoid Donor 2 SARS-CoV-2 1 R2

description: Liver Organoid Donor 2 SARS-CoV-2 R2


title: 492CD4D0


title: X50.8: Liver Organoid Donor 2 SARS-CoV-2 2 R2

description: Liver Organoid Donor 2 SARS-CoV-2 R2


title: H555

address: 重庆市荣昌区学院路160号

value: female


title: A562

address: 重庆市荣昌区学院路160号

value: Red Angus

value: leukocytes


title: C2-4

description: Nondormant control April


title: H548

address: 重庆市荣昌区学院路160号

value: heat stress


title: X50.4: Liver Organoid Donor 1 SARS-CoV-2 2 R2

description: Liver Organoid Donor 1 SARS-CoV-2 R2


title: C3-2

description: nondormant control Feburary

value: early ecodormant tissue


title: H490

address: 重庆市荣昌区学院路160号


title: H546

address: 重庆市荣昌区学院路160号


title: 495CD4DIS


title: X50.6: Liver Organoid Donor 2 Mock 2 R2

description: Liver Organoid Donor 2 Mock R2

value: Mock


title: C4-2

description: nondormant control Feburary

value: tuber meristem


title: X50.3: Liver Organoid Donor 1 SARS-CoV-2 1 R2

description: Liver Organoid Donor 1 SARS-CoV-2 R2


title: 499CD4D0

value: CD4+ T cells


title: 492CD4DIS

value: PBMCs


title: C4-4

description: Nondormant control April


title: X50.5: Liver Organoid Donor 2 Mock 1 R2

description: Liver Organoid Donor 2 Mock R2


title: 449CD4DIS

value: Blood


title: Sample_5_RL_CREBBPKO_gRNA1_H3K27Ac_ChIPseq

first: Matt

last: Teater

state: NY

address: 445 E 69th St

institute: Weill Cornell Medical College

data_processing:
Illumina Casava1.8 software used for basecalling.
RNA-seq reads were aligned to hg19 using STAR with default parameters
FPKM were obtained using Rsubread
ChIP-seq reads were aligned to hg19 using BWA with default parameters
Peaks were called using MACS2
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-seq: MACS2 peaks
Supplementary_files_format_and_content: RNA-seq: FPKM

source_name: RL cell line

extract_protocol:
RNA-seq libraries were prepared using the Illumina TruSeq stranded mRNA sample kits, respectively, according to the manufacturer
ChIP-seq ws performed using H3K27Ac antibodies (Active Motif; catalog No. 39133).  ChIPseq libraries were prepared using  KAPA Hyper Prep Kits (Roche) and TruSeq adaptors according to the manufacturer

value: RL

tag: genotype

value: Transfected with CRISPR gRNAs inducing CREBBP frameshift mutation


title: A524

address: 重庆市荣昌区学院路160号


title: 495CD4D0

value: visceral leishmaniasis


title: 449CD4D0


title: X50.2: Liver Organoid Donor 1 Mock 2 R2

description: Liver Organoid Donor 1 Mock R2


title: A507

address: 重庆市荣昌区学院路160号


title: 443CD4DIS

value: Day 30 post-treatment (day 30)


title: X50.1: Liver Organoid Donor 1 Mock 1 R2

description: Liver Organoid Donor 1 Mock R2


title: A522

address: 重庆市荣昌区学院路160号


title: C3-12

description: Dormant Control

tag: treatment

value: water treated

value: dormant tissue


title: A485

address: 重庆市荣昌区学院路160号


title: C2-12

description: Dormant Control

tag: dormancy status


title: 442CD4DIS


title: 442CD4D0

value: Infected (day 0)


title: X45.2: Liver Organoid Donor 1 Mock 2

description: Liver Organoid Donor 1 Mock

value: Liver Organoid


title: C1-12

description: Dormant Control


title: X45.3: Liver Organoid Donor 1 SARS-CoV-2 1

description: Liver Organoid Donor 1 SARS-CoV-2


title: A495

address: 重庆市荣昌区学院路160号

value: Red Angus

value: female


title: C2-2

description: nondormant control Feburary


title: Ad-hACE2.rep3

status: Public on Jun 11 2020

city: GuangZhou

first: Jiangping

last: He

address: Kai yuan avenue 190

institute: Guangzhou Institutes of Biomedicine and Health (GIBH), CAS

data_processing:
bcl2fastq conversion software v2.17 used for basecalling.
Reads were aligned to the ENSEMBL transcriptome using Bowtie2 (version 2.2.5) and RSEM
The gene expression level was calculated by using  EDASeq GC-normalize method
Genome_build: Ensembl v88
Supplementary_files_format_and_content: expr.tsv represents the normalized read counts

source_name: Lung

growth_protocol: the  cells were digested from mouse lung directly

extract_protocol: VAHTS mRNA-seq V2 Library Prep Kit for Illumina was used according to the manufacturer's instruction. Briefly, 1ug total RNA was used and mRNA was enriched using olig-dT dynabeads, followed by fragmentation by divalent cation at elevated temperature. First-strand cDNA synthesis by random hexamers and reverse transcriptase was followed by the second-strand cDNA synthesis. Then the reverse product was purified using AMPure XP beads. The cDNA was end repaired and a dA was added, followed by ligation, two round purification using AMPure XP beads, PCR amplification and PCR product purification. The library was quantified with an Invitrogen Qubit.

treatment_protocol: no treatment

value: Lung


title: 443CD4D0


title: C4-12

description: Dormant Control


title: X45.1: Liver Organoid Donor 1 Mock 1

description: Liver Organoid Donor 1 Mock


title: sonicated-DNA-control-input

city: Tempe

first: Robin

last: Harris

state: AZ

address: 427 E Tyler Mall LSE 229

department: School of Life Sciences

institute: Arizona State University

description: ControlGenomicDNA_q5_sorted_dupsRemoved_noYUHet.bed

data_processing:
Reads were trimmed to 50 bp using cutadapt (Martin, 2011) and aligned to the dm3 reference genome using bowtie 2 (setting: --seed 123, -q –X 2000).
Reads with quality scores below 5 were removed and only reads mapping to Chr2L/2R/3L/3R/4/X were used in subsequent analysis
Peaks were called with MACS2 (setting: -g dm –keep-dup all –shift 9 –nomodel –seed 123), using a sonicated genomic DNA dataset as a control (Zhang et al., 2008).
Signal tracks were generated from individual replicates using Deeptools v2.4.1 (Ramirez et al., 2016).
ATAC peak calls from pooled datasets were ranked by MACS2 q-score. The top 11,500 peaks from each dataset were selected and combined into a union peak set of 46,000 peaks which was subsequently reduced by merging any peaks that overlapped by 1 bp or more using the GenomicRanges Bioconductor package (Gentleman et al., 2004; Lawrence et al., 2013). This resulted in a final union peak set of 14,142 peaks. ATAC-seq reads were counted inside union peaks using featureCounts from Rsubread (setting: isPairedEnd = T, requireBothEndsMapped = T, countChimericFragments = F, allowMultiOverlap = T) (Liao et al., 2013). The resulting count matrix was used as input for DESeq2 analysis (Love et al., 2014). Peaks were called as differentially accessible using the criteria of log2FoldChange>0.5 and padj<0.1.
Genome_build: dm3

organism: Drosophila melanogaster

source_name: whole animal

growth_protocol: Density controlled larvae (50 per vial) grown at 18'C and upshifted to 30'C for 40hrs to induce ablation at either day 7 or day 9 (as per Smith-Bolton et al, 2009). Ablated larvae genotype: w;;rn-GAL4,UAS-egr,GAL80ts. Unablated larvae genotype: w;;rn-GAL4,GAL80ts.

extract_protocol:
Discs were dissected in PBS immediately upon downshift and collected as pools of 100 discs for early L3 samples and 50 discs for late L3 samples.  The 4 samples were placed in lysis buffer (10mM Tris 7.5, 10mM NaCl, 3mM MgCl2, 0.1% IGEPAL CA-630), and pelleted for library prep. Each of the 4 samples was repeated in triplicate from separate repeats of larval ablation.
ATAC-seq libraries were created using Illumina Tn5 transposase, essentially as in Buenrostro et al. 2013.

tag: age

value: control

tag: damage status

tag: repeat #


title: Ad-hACE2.rep1


title: Ad5-Empty.rep1


title: Ad5-Empty.rep2


title: RNA-seq_N0 rep3

city: Birmingham

first: Csilla

last: Varnai

address: Haworth Building

department: Institute of Cancer and Genomic Sciences

country: United Kingdom

institute: University of Birmingham

data_processing:
Paired-end reads were aligned using TopHat (version 2.1.1)
Transcript counts were calculated with HTSeq-count (version 0.9.1) using gene models from Ensembl as reference.
Differential gene expression analysis was carried out using the DESeq2 (version 1.18) and EdgeR (version 3.24)
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited table of read counts per gene

source_name: CD4 T cells

extract_protocol:
CD4 T cells were purfied from the spleen using the MagniSort Mouse CD4 T cell enrichment Kit. Total RNA was extracted using PicoPure™ RNA Isolation Kit (KIT0204) and Ribosomal RNA was depleted using NEBNext rRNA depletion kit (E6310L)
RNA-seq libraries were prepared from 30 ng RNA using the NEBNext Ultra II kit (E7760S) using the NEBNext oligonucleotides (E7335S)

treatment_protocol: Tg4 transgenic mice were tolerized by repeated subcutaneous injection of the 4Y peptide in an escalating dose adminsitered every 3-4 days. Control mice were given a dose of PBS vehicle in the same dosing strategy

tag: strain

value: CD4 T cells

value: Naive - untreated


title: 20190131_SHAM_E_unstim

first: Emily

last: Brown

address: 435 E 30th St

department: Medicine

institute: NYU Langone

description: Bone marrow monocytes isolated 9 days following sham surgery

data_processing:
Align reads to mm10 using STAR
count reads per gene for all samples using FeatCounts
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited files, output of FeatCounts, with unnormalized reads per gene

source_name: Bone marrow monocytes

extract_protocol:
Cells were MACS sorted and RNA was harvested with trizol LS.  RNA library preparation with polyA selection was used with 50-350 ng of total RNA for the construction of sequencing libraries.
RNA library preparation with polyA selection

treatment_protocol: Bone marrow monocytes were isloated from mice 9 days following LAD ligation or sham surgery.

value: 10-12 weeks

value: Bone marrow monocytes

value: SHAM surgery


title: 20190131_LAD_A_unstim

description: Bone marrow monocytes isolated 9 days following LAD ligation

value: LAD ligation


title: 20190131_SHAM_D_unstim


title: SDLN_Xcr1++_rep2

type: RNA

city: Saint Louis

first: Kenneth

last: Murphy

state: MO

address: Clinical Science Research Building, 7th Floor, Room 7701A, Campus Box 8118

department: Pathology & Immunology

institute: Washington University School of Medicine

hyb_protocol: Following fragmentation and labeling, 2.5 ug of cDNA were hybridized onto the Gene 1.0 ST arrays and placed in GeneChip Hybridization Oven 640 for 18 hr at 45C. Gene Chip’s were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data was analyzed with the Affymetrix GeneChip Command Console. Microarray expression data was processed using Command Console (Affymetrix, Inc) and the raw (.CEL) files generated were analyzed using Expression Console software with Affymetrix default RMA Gene analysis settings.(Affymetrix, Inc).  Probe summarization (Robust Multichip Analysis, RMA), quality control analysis, and probe annotation were performed according to recommended guidelines (Expression Console Software, Affymetrix, Inc.).

label: biotin

source_name: Migratory cDC1 from Xcr1++ CD40 fl skin draining lymph nodes

label_protocol: Biotinylated cDNA were prepared according to the Affymetrix WT Pico reagent kit from 100pg-2ng total RNA.

growth_protocol: CD40 fl/fl was crossed to a a cDC1-specific Cre strain, the Xcr1-cre, to generate mice with conditional deletion of CD40 in cDC1s. Spleens and skin draining lymph nodes were isolated from naive Xcr1+/+ CD40fl/fl or Xcr1 Cre/+ CD40fl/fl mice and digested to extract cDC1s.

extract_protocol: Column extraction of total RNA was performed acording to the manufacturer's instructions.

treatment_protocol: B220- MHC IIhigh CD11cint XCR1+ Sirpa- migratory cDC1 (SDLN), or B220- MHC IIhigh CD11chigih XCR1+ Sirpa- cDC1 (spleen) were sort-purified to extract RNA for microarray analysis.

tag: strain background

value: Xcr1++ CD40flfl

value: Skin draining lymph node


title: SDLN_Xcr1Cre+_rep1

source_name: Migratory cDC1 from Xcr1Cre+ CD40 fl skin draining lymph nodes

value: Xcr1Cre+ CD40flfl


title: RNA-seq_N0 rep2


title: SPL_Xcr1Cre+_rep2

source_name: cDC1 from Xcr1Cre+ CD40 fl spleen

value: Spleen


title: SPL_Xcr1Cre+_rep3


title: input

city: Atlanta

first: Roger

middle: B

last: Deal

state: GA

address: 1510 Clifton Rd NE

department: Biology

institute: Emory University

data_processing:
Sequencing reads were mapped to the genome using Bowtie2 software (Langmead and Salzberg, 2012) with default parameters.
Mapped reads in .sam format were converted to .bam format and sorted using Samtools 0.1.19 (Li et al., 2009).
Mapped reads were then filtered using Samtools to retain only those reads with a mapping quality score of 2 or higher (Samtools “view” command with option “-q 2” to set mapping quality cutoff).
For normalization and visualization, the filtered, sorted .bam files were converted to bigwig format using the “bamcoverage” script in deepTools 2.0 (Ramirez et al., 2016) with a bin size of 1 bp and RPKM normalization.
Heatmaps and average plots displaying sequencing data were generated using SeqPlots (Stempor and Ahringer 2016).
Genome_build: TAIR10
Supplementary_files_format_and_content: .bw files contain aligned reads for individual samples at a resolution of 1 bp bin sized windows
Supplementary_files_format_and_content: .bed files contain coordinates of all ChIP-seq peaks called by HOMER for each individual sample

organism: Arabidopsis thaliana

source_name: Non-hair cells

growth_protocol: This study of Arabidopsis root non-hair cells used a stable INTACT transgenic line that has been previously described (Deal and Henikoff, 2010). This line is in the Col-0 background and carries a constitutively expressed biotin ligase gene (ACT2p:BirA) and a transgene conferring cell type-specific expression of the NTF gene from the GLABRA2 promoter in non-hair cells.  Seeds were surface sterilized and sown on 1⁄2-strength Murashige and Skoog (MS) media (Murashige and Skoog, 1962) with 1% (w/v) sucrose in 150 mm diameter Petri plates. Plants were grown vertically on plates for 10 days after germination at 20°C and a 200 μmol/m2/sec during a 16 h light/8 h dark cycle. Then,  1.25 cm segments of root tissue from within the fully differentiated cell zone were harvested and flash frozen in liquid N2, for a total of 3g of root tissue per sample. This segment of the root contains only fully differentiated cells and excludes the root tip below and any lateral roots above.

extract_protocol:
Nuclei were purified from frozen and pulverized tissue as previously described for A. thaliana (Wang and Deal, 2015). Tissue was resuspended in an ice-cold mortar containing 10 mL of freshly prepared nuclei purification buffer (NPB: 20 mM MOPS, 40 mM NaCl, 90 mM KCl, 2 mM EDTA, 0.5 mM EGTA, 0.5 mM spermidine, 0.2 mM spermine, pH, 7.0) containing 200 uL Protease Inhibitor Cocktail (0.4X, Sigma, P9599) per 50 mL of buffer. The homogenized extracts were filtered through a 70 µM nylon mesh to remove cell debris and centrifuged at 1000 x g for 15 min at 4° C to pellet nuclei. Nuclei were resuspended in 1 mL of NPB and 25 µL of M-280 streptavidin-coated Dynabeads (Life Technologies, catalog # 11205D) were added to the nuclei. This mixture was slowly rotated in a cold room at 4° C for 30 min. The nuclei/beads suspension was diluted to 14 mL with NPB supplemented with 0.1% (v/v) Triton X-100 (NPB-T), in a 15 mL Falcon tube, mixed thoroughly and placed in a 15 ml magnet (adapted NEB 50 mL tube magnet) to capture bead-bound nuclei for 1 min at 4° C. The supernatant was carefully removed using a plastic Pasteur pipette, taking care to remove bubbles to avoid disturbing the beads. Beads were resuspended in 14 ml of cold NPB-T, placed on a rotating mixer for 30 sec, and then placed back in the 15 ml magnet to capture the beads-nuclei at 4° C for 1 min. This wash step was repeated and bead-bound nuclei were resuspended in 1 mL of NPB-T and transferred to a new tube.
ChIP-seq libraries were prepared and sequenced as described in (Adli and Bernstein 2011)

tag: nuclei type

value: Non-hair cell nuclei from root epidermal tissue

tag: chip antibody


title: Ad-hACE2.rep2


title: SPL_Xcr1++_rep2

source_name: cDC1 from Xcr1++ CD40 fl spleen


title: SDLN_Xcr1Cre+_rep2


title: SDLN_Xcr1Cre+_rep3


title: 20190131_SHAM_G_unstim


title: SPL_Xcr1Cre+_rep1


title: D20BM_SHAM_9

description: bone marrow Ly6Chigh monocytes isolated 20 days following tumor implantation (17 days post sham surgery)

data_processing:
Align reads to mm10 using bowtie2
call peaks using macs2
Genome_build: mm10
Supplementary_files_format_and_content: bed files of significant peaks called by macs2; 5th column corresponds to the pileup

source_name: Bone marrow CD45+ CD11b+Ly6chighLy6G- monocytes

extract_protocol:
30,000 to 75,000 bone marrow CD45+CD11b+Ly6ChiLy6G– monocytes were flow sorted (pools of 2 mice), then washed in cold PBS and lysed for 1 min in a refrigerated centrifuge.
Transposition reaction (Illumina) was performed at 37°C for 30 min. After purification of the DNA with the MinElute PCR purification kit (Qiagen), material was amplified for 5 cycles. Additional PCR cycles were evaluated by real time PCR. Final product was cleaned with the MinElute PCR purification kit. Libraries were individually checked with the Kapa-Roche quantification kit and size was verified on tapestation high sensitivity screentape.

value: 11-15 weeks

value: E0771 tumor implantation + SHAM surgery


title: SPL_Xcr1++_rep3


title: RNA-seq_N0 rep1


title: SPL_Xcr1++_rep1


title: 20190131_LAD_B_unstim


title: H3

value: H3 (Abcam, ab1791)


title: 20190131_SHAM_C_unstim


title: D20BM_SHAM_8

value: Bone marrow CD45+ CD11b+Ly6chighLy6G- monocytes


title: 20190131_LAD_F_unstim


title: H2A.Z

value: H2A.Z (Deal et al [2007] Plant Cell 19.)


title: 20190131_SHAM_H_unstim


title: D20BM_SHAM_4


title: H3K27me3

value: H3K27me3 (Millipore, 07-449)


title: SDLN_Xcr1++_rep3


title: D20BM_SHAM_3


title: D20BM_LAD_6

description: bone marrow Ly6Chigh monocytes isolated 20 days following tumor implantation (17 days post MI)

value: E0771 tumor implantation + LAD ligation (surgical myocardial infarction)


title: D20BM_LAD_7


title: H3K27ac

value: H3K27ac (Abcam, ab4729)


title: H3K4me3

value: H3K4me3 (Abcam, ab8580)


title: RNA-seq_NAg rep2

value: CD4 T cells

value: Naive + Antigen


title: RNA-seq_NAg rep1


title: 6_S5_L008_STAR_mapAligned

description:
blood Ly6Chigh monocytes isolated 12 days following tumor implantation (9 days post sham surgery)
merge_all_D12Blood_samples.featCounts.txt

source_name: Blood CD45+ CD11b+Ly6chighLy6G- monocytes

extract_protocol:
Cells were flow sorted and RNA was harvested with trizol LS.  NEBNext Ultra RNA library prep with rRNA depletion was used with 50-100 ng of total RNA for the construction of sequencing libraries.
NEBNext Ultra RNA library prep with rRNA depletion (New England Biolabs)


title: 1_S1_L008_STAR_mapAligned

description:
blood Ly6Chigh monocytes isolated 12 days following tumor implantation (9 days post MI)
merge_all_D12Blood_samples.featCounts.txt


title: RNA-seq_PBSPI rep3

value: Naive + PI


title: 15-BM-RNA-MIT10.STARAligned

description:
bone marrow Ly6Chigh monocytes isolated 20 days following tumor implantation (17 days post sham surgery)
merge_all_D20BM_samples.featCounts.txt


title: 5_S4_L008_STAR_mapAligned


title: H3K4me1

value: H3K4me1 (Abcam, ab8895)


title: RNA-seq_PBSPI rep2


title: 13-BM-RNA-MIT10.STARAligned


title: RNA-seq_PBSPI rep1


title: 7-BM-RNA-MIT10.STARAligned


title: 5-BM-RNA-MIT10.STARAligned


title: Healthy control UP#3-0_hour.162280

city: Minneapolis

last: Gale

state: Minnesota

address: 689 23rd Ave SE

department: Microbiology and Immunology

institute: University of Minnesota

data_processing:
Base calls were processed to FASTQs on BaseSpace (Illumina)
A base call trimming step was applied to remove low-confidence base calls from read ends
FASTQs were aligned using STAR v.2.4.2a
Gene counts were generated using htseq-count
QC and metrics was performed using the Picard family of tools (v1.134)
Genome_build: NCBI build37.1
Supplementary_files_format_and_content: counts_raw_gs_skopelja_elkon.txt

extract_protocol:
A 6-mm punch skin biopsy was collected from unexposed skin A 6-mm punch skin biopsy was collected from unexposed skin at 0hr and from skin 6hr and 24hr after UV exposure., and from skin 6hr and 24hr after UV exposure. Tissue was stored in RNA later and samples from PA shipped to UW. Following RNA isolation at UW, the RNA yield was 2-3 ug RNA (all samples had RIN >9.5).
cDNA libraries were prepared from 1 μg of total RNA using the TruSeq Stranded mRNA kit (Illumina, San Diego, CA) and the Sciclone NGSx Workstation (Perkin Elmer, Waltham, MA).

value: skin

value: 1 dose UV light

tag: timepoint (hours)


title: RNA-seq_T0 rep3

value: Tolerant - untreated


title: RNA-seq_NAg rep3


title: Healthy control UP#3-24_hour.162281


title: Healthy control UW05-24_hour.162279


title: 3-BM-RNA-MIT10.STARAligned


title: 2-BM-RNA-MIT10.STARAligned


title: RNA-seq_T0 rep2


title: 4_S3_L008_STAR_mapAligned


title: 19-BM-RNA-MIT10.STARAligned

description:
bone marrow Ly6Chigh monocytes isolated 20 days following tumor implantation (17 days post MI)
merge_all_D20BM_samples.featCounts.txt


title: Healthy control UW05-6_hour.162278


title: 18-BM-RNA-MIT10.STARAligned


title: 4-BM-RNA-MIT10.STARAligned


title: 15-T-RNA-MIT10_STARAligned

description:
tumor mMDSCs isolated from mammary tumors 20 days following tumor implantation (17 days post sham surgery)
merge_all_D20T_samples.featCounts.txt

source_name: tumor CD45+ CD11b+Ly6chighLy6G- mMDSCs


title: 16-BM-RNA-MIT10.STARAligned


title: RNA-seq_TAg rep3

value: Tolerant + Antigen


title: 1-BM-RNA-MIT10.STARAligned

value: 11-15 weeks


title: RNA-seq_TAg rep2


title: Healthy control UW03-24_hour.162276


title: 7-T-RNA-MIT10_STARAligned

value: E0771 tumor implantation + SHAM surgery


title: Healthy control UW03-0_hour.162271


title: 5-T-RNA-MIT10_STARAligned


title: 2_S2_L008_STAR_mapAligned


title: RNA-seq_T0 rep1


title: 3-T-RNA-MIT10_STARAligned


title: Healthy control UW03-6_hour.162272


title: RNA-seq_TPI rep3

value: Tolerant + PI


title: 13-T-RNA-MIT10_STARAligned


title: 2-T-RNA-MIT10_STARAligned


title: 19-T-RNA-MIT10_STARAligned

description:
tumor mMDSCs isolated from mammary tumors 20 days following tumor implantation (17 days post MI)
merge_all_D20T_samples.featCounts.txt


title: Healthy control UW02-0_hour.162269


title: RNA-seq_TPI rep2


title: Healthy control UW02-24_hour.162270


title: 18-T-RNA-MIT10_STARAligned


title: Healthy control UW05-0_hour.162277


title: RNA-seq_TPI rep1


title: 4-T-RNA-MIT10_STARAligned


title: 16-T-RNA-MIT10_STARAligned


title: Healthy control UW01-24_hour.162268


title: DNAse_TM rep2

data_processing:
Library strategy: DNase-seq
Raw sequencing reads were aligned to mm9 using bowtie2 (Galaxy Version 2.3.2.2) with the preset –very-sensitive-local
Peaks were identified using MACs version 1.4.2 using the parameters –g mm –keep-dup auto –w -S
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph file of tag pile-ups produced by MACS v1.4.2

extract_protocol:
CD4 T cells were purfied from the spleen using the MagniSort Mouse CD4 T cell enrichment Kit. Cells were permeabilised and treated with DNase I for three minutes at 22C. DNA was purified by phenol chloroform extraction and small DNA fragments (50-250bp) were purified before library preperation
Libraries were constructed using the Kapa Hyper prep kit according to the manufacturer's instructions

value: Spleen

value: Tolerant - 3 weeks post treatment


title: 1-T-RNA-MIT10_STARAligned


title: Healthy control UW01-6_hour.162267


title: LY500307+PD-1-2

city: Chengdu

first: Shengtao

last: Zhou

address: #17, Renmin South Road

department: Department of Obstetrics and Gynecology

institute: West China Second Hospital, Sichuan University

data_processing:
Basecalls performed using CASAVA version 1.8
RNA seq reads were adaptor-trimmed and mapped to mouse genome(mm9) by bowtie2 software with default parameters.
Analyzed with DeSeq2
Genome_build: mm9
Supplementary_files_format_and_content: FPKM

source_name: 4T1 cells

extract_protocol:
RNA extracted using Trizol by following manufacturer’s instruction (Invitrogen).
RNA libraries were constructed by using rRNA-depleted RNAs with TruSeq Stranded Total RNA Library Prep Kit (Illumina, San Diego, CA,  USA) according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using  the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA).

tag: treatment group

value: LY500307+PD-1 treatment group

tag: cell line


title: LY500307+PD-1-1


title: LY500307+PD-1-3


title: DNAse_TPI rep2


title: Healthy control UW01-0_hour.162266


title: DNAse_TM rep1


title: PD-1-1

value: PD-1 treatment group


title: PBMC Donor 2 LPS rep1

city: Beaverton

first: Victor

last: DeFilippis

state: OR

address: 505 N.W. 185th Avenue

department: Vaccine and Gene Therapy Institute

institute: Oregon Health & Science University

data_processing:
Base call files were converted to fastq format using Bcl2fastq (Illumina).
Illumina adapters trimmed using Trimmomatic.
STAR (v020201) was used to align RNAseq reads to the Homo_sapiens.GRCh38 genome in Ensembl along with its corresponding annotation, release 84. Two-pass mode was used with default parameters.
Genome_build: Homo_sapiens.GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: PBMC from human donor

growth_protocol: PBMCs from two healthy adult donors were obtained from StemCell Technologies, grown in 12 well dishes in RPMI + 10% FBS.

extract_protocol:
Total RNA was isolated using Direct-zol RNA mini-prep kit (Zymo Research) in accordance with manufacturer’s instructions and profiled for intactness on a Bioanalyzer (Agilent).
Tru-Seq RNA Sample Preparation kit (Illumina). Poly(A)+ RNA was isolated from 500 ng of total RNA per sample. The isolated RNA was fragmented using divalent cations and heat. First strand cDNA was generated using random hexamer priming. The RNA template was removed and the second strand was synthesized. The ends of the cDNAs were repaired, followed by adenylation of the 3′ termini. Indexing adapters were ligated to the cDNA ends. The ligation products were amplified using polymerase chain reaction (PCR). The amplification product was cleaned using AMPure XP beads (Beckman Coulter).

treatment_protocol: Cells were treated in duplicate for 6h with 1% DMSO vehicle, 50 μM M04, 100ng/mL LPS, or 15 μg/mL cGAMP.

value: PBMC

value: LPS 100 ng/ml

tag: Sex

value: male


title: PBMC Donor 2 LPS rep2


title: PD-1-3

value: PD-3 treatment group


title: PD-1-2

value: PD-2 treatment group


title: DNAse_TPI rep1

value: CD4 T cells


title: Control-2

value: Control group


title: PBMC Donor 2 M04 rep2


title: DNAse_NPI rep2

value: Naive+ PI


title: Control-1


title: DNAse_NPI rep1


title: PBMC Donor 2 M04 rep1


title: ZR-75-30_RRBS

city: Salt Lake City

first: Katherine

middle: E

last: Varley

state: UT

address: 2000 Circle of Hope, Room 3719

department: Department of Oncological Sciences

institute: Huntsman Cancer Institute University of Utah

data_processing:
We aligned these reads to a modified reference genome sequence that was created to reflect both the reduced representation of the genome due to the MspI restriction digest as well as the sodium bisulfite conversion which creates a T in the sequencing reads rather than a C at all unmethylated bases. To create this reference, we first parsed the hg19 reference genome to identify all of the MspI restriction fragments <500 bp. We then isolated the 36-bp ends of these fragments into a fasta file and converted every C in the reference to a T and recorded the position of these reference cytosines in the name of the reference sequence. To achieve optimal alignment that is not biased by the methylation state of a molecule, we also created a copy of our sequencing read files, converted every C in the read to a T, and recorded the position of these read cytosines in the name of the read. We then used bowtie (Langmead et al. 2009) to align these converted reads to the custom reference sequence and required that the alignment be optimal and unique in the reference and only align to the proper strand (bowtie options –best, -m 1, norc).
We then parsed the alignment file and the encoded read and reference names to determine how many reads covered each reference cytosine position.
For each position with at least 10 reads of coverage, we calculated the percentage of those reads that contained a C and reported the percent of reads that were methylated in the processed data file.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix of percent methylated values

source_name: ZR-75-30 Cell line

growth_protocol: The following cell lines: MDA-MB-231, MDA-MB-157, MDA-MB-361 , MDA-MB-453, and MDA-MB-468, were cultured in DMEM media supplemented with 10% fetal bovine serum, 1 mM sodium pyruvate, and non-essential amino acids. MDA-MB-134 cells were cultured in DMEM, 20% FBS, 1 mM sodium pyruvate, and non-essential amino acids. MDA-MB-436 were cultured in DMEM, 10% FBS, 10 μg/mL insulin, and 16 μg/mL glutathione. 2LMP and DY36T2 cells were cultured in Improved MEM and 10% FBS. HCC70, HCC1187, HCC1937, HCC1143, HCC1569, HCC1599, HCC1954, HCC38, ZR-75-1, and ZR-75-30 cells  were cultured in RPMI media, supplemented with 10% fetal bovine serum, 10 mM HEPES, 1 mM sodium pyruvate, and 4.5 g/l glucose. BT-20 cells were cultured in EMEM, 10% FBS, 1 mM sodium pyruvate, and non-essential amino acids. BT-474, BT-549 and T-47D cells were cultured in RPMI, 10% fetal bovine serum, 10 mM HEPES, 1mM sodium pyruvate, 4.5g/l glucose, and 10µg/ml insulin. MCF-7 cells were cultured in EMEM, 10% fetal bovine serum, 1mM sodium pyruvate, non-essential amino acids and 10µg/ml insulin. SUM159 and SUM149 cells were cultured in Ham’s F12, 5% fetal bovine serum, 1µg/ml hydrocortisone, and 5µg/ml insulin. SUM102 cells were cultured in Ham’s F12, 5 μg/ml insulin, 1 μg/ml hydrocortisone, 10 ng/ml EGF, 5 mM ethanolamine, 10 mM HEPES, 5 μg/ml transferrin, 10 nM triiodothyronine (T3), 50 mM sodium selenite, 1 g/l BSA (2% FBS added for first 24 h after plating to allow cells to attach). SKBR-3 cells were cultured in McCoy’s media and 15% FBS. T-47D cells were cultured in Cells were passaged and harvested at 80% confluence.

extract_protocol:
DNA was extracted with the Qiagen DNeasy Blood and Tissue Kit.
Libraries were constructed using the protocol described in Varley KE, Gertz J, Bowling KM, et al. Dynamic DNA methylation across diverse human cell lines and tissues. Genome Res. 2013;23(3):555‐567. doi:10.1101/gr.147942.112 (PMCID: PMC3589544).

value: breast cancer cell line

tag: method

value: RRBS


title: ZR-75-1_RRBS

source_name: ZR-75-1 Cell line


title: SUM159_RRBS

source_name: SUM159 Cell line


title: PBMC Donor 1 M04 rep2

value: female


title: SK-BR-3_RRBS

source_name: SK-BR-3 Cell line


title: Control-3


title: SUM149_RRBS

source_name: SUM149 Cell line


title: DNAse_NAg rep2

source_name: CD4 T cells

tag: tissue

value: Naive+ Antigen


title: SUM102_RRBS

source_name: SUM102 Cell line

tag: cell type


title: PBMC Donor 2 cGAMP rep2

value: cGAMP 15 ug/ml


title: DNAse_TAg rep1

description: The HiDepth files are technical replicates (resequencing)

value: Spleen

value: Tolerant + Antigen


title: MDA-MB-436_RRBS

source_name: MDA-MB-436 Cell line


title: MDA-MB-468_RRBS

source_name: MDA-MB-468 Cell line


title: PBMC Donor 1 M04 rep1


title: DNAse_NAg rep1


title: MDA-MB-453_RRBS

source_name: MDA-MB-453 Cell line


title: PBMC Donor 2 cGAMP rep1


title: DNAse_T0 rep2

value: Tolerant - untreated


title: MDA-MB-231_RRBS

source_name: MDA-MB-231 Cell line


title: MDA-MB-157_RRBS

source_name: MDA-MB-157 Cell line


title: DNAse_TAg rep2


title: DNAse_T0 rep1


title: PBMC Donor 1 cGAMP rep1


title: MDA-MB-134_RRBS

source_name: MDA-MB-134 Cell line


title: T-47D_RRBS

source_name: T-47D Cell line


title: PBMC Donor 2 DMSO rep2

value: 1% DMSO


title: MCF-7_RRBS

source_name: MCF-7 Cell line


title: HCC70_RRBS

source_name: HCC70 Cell line


title: HCC1954_RRBS

source_name: HCC1954 Cell line


title: HCC38_RRBS

source_name: HCC38 Cell line


title: PBMC Donor 1 DMSO rep2

source_name: PBMC from human donor

value: PBMC


title: DNAse_N0 rep1

value: Naive- untreated


title: HCC1599_RRBS

source_name: HCC1599 Cell line


title: lL3-damaged-ATAC-rep3

description:
Old-Damaged-Rep3_q5_sorted_noYUHet_normalizedToRPGC_zNorm.bw
Old-Damaged_3Reps_POOLED_q5_sorted_noYUHet_normalizedToRPGC_zNorm.bw
Old-Damaged_3Reps_ATAC_PooledPeaks_peaks.xls

source_name: L3 wing imaginal disc

value: late L3

value: damaged


title: MDA-MB-361_RRBS

source_name: MDA-MB-361 Cell line


title: HCC1569_RRBS

source_name: HCC1569 Cell line


title: PBMC Donor 1 cGAMP rep2


title: lL3-damaged-ATAC-rep2

description:
Old-Damaged-Rep2_q5_sorted_noYUHet_normalizedToRPGC_zNorm.bw
Old-Damaged_3Reps_POOLED_q5_sorted_noYUHet_normalizedToRPGC_zNorm.bw
Old-Damaged_3Reps_ATAC_PooledPeaks_peaks.xls


title: HIV-1 infected primary T cell mRNA PA-ac4C-seq

city: Taipei

first: Kevin

last: Tsai

address: 128 Sec. 2, Academia Rd. Nankang

department: Institute of Biomedical Sciences

country: Taiwan

institute: Academia Sinica

description: Aligned to the HIV-1 NL4-3 genome, with one copy of LTR, U3 sequence on the 5' end, R-U5 on the 3' end

data_processing:
CASAVA 1.8.2
fastx toolkit: fastq_quality_filter -Q33| fastx_clipper -Q33 -v -a [index_sequence] -l 15 -c | fastq_to_fasta -Q33
Aligned to the human genome hg19 using Bowtie 0.12.7: bowtie -m 8 -a --best --strata --chunkmbs 10000
hg19 non-aligning reads aligned to the HIV-1 NL4-3 genome using Bowtie 0.12.7: bowtie -m 3 -v 1 -a --best --strata --chunkmbs 10000
Filtered out all reads that lack a TC mutation
The primary T cell PA-ac4C-seq run was preprocessed through: cutadapt --minimum-length=15 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A GATCGTCGGACTGTAGAACTCTGAACGTGTAGATCTCGGTGGTCGCCGTATCATT ; susequent Bowtie alignments were done the same as all other samples with the additional option "--allow-contain"
Awk script to generate bed file, columns are "chromosome, start, end, score, strand"
Genome_build: NL4-3 genomes: 551-9626nt of GenBank AF324493.2
Supplementary_files_format_and_content: bed files, aligned to HIV-1 NL4-3 genome

source_name: Human donor blood purified primary CD4+ T cell

extract_protocol:
PAR-CLIP (PA-ac4C-seq is PAR-CLIP done with the ac4C antibody directly UV crosslinked to it's target RNA)
All samples were processed with the NEB Next small RNA-seq kit

tag: virus

value: HIV-1 NL4-3

value: Human donor primary T cell

tag: technique

tag: pulldown antibody

value: anti-ac4C, Abcam, ab252215, Lot No GR3269449-2


title: DNAse_N0 rep2

source_name: CD4 T cells

value: CD4 T cells

tag: treatment


title: iMit_K243R_Input_control

city: Oxford

first: Pakavarin

last: Louphrasitthiphol

address: Old Road Campus Research Building (off Roosevelt Drive)

department: Nuffield Department of Clinical Medicine

institute: Ludwig Institute for Cancer Research

description: Input control for K243R mutant

data_processing:
Raw fastq files (with base-calling quality score) were obtained form Wellcome Trust Genomics service
Three technical replicates (same library sequence in two separate flow cells) which were stitched together using UNIX to generate a single fastq
Processed fastq files were mapped using STAR {Dobin, 2013 #5946} against hg38 build
Mapped SAM-files were used for peak calling using the Homer package {Heinz, 2010}
Homer was used to generated bedgraphs with bp resolution with counts normalised to 10 million reads
Genome_build: hg38
Supplementary_files_format_and_content: bedgraph of normalised counts for uniqely aligned reads

growth_protocol: All cell lines were grown at 37°C with 10% CO2 in RPMI-1640 (Gibco BRL, Invitrogen) supplemented with penicillin and streptomycin, 10% fetal bovine serum (FBS, Biosera).

extract_protocol:
30x-15cm dishes of 501mel cells were fixed in 0.4% PFA then cheared with a Covaris S220 for 15 minutes (160 W peak incident power, 5% duty cycle and 200 cycles per burst). The sonicated chromatin were precleared and ChIP was performed using 120ug of the indicated antibodies. Purification of the ChIP-DNA was done using QIAGEN PCR clean-up column
Libraries were prepared using recommended Illumina protocols

treatment_protocol: Cells were grown overnight with or without 20ng/ml Doxycycline, prior to fixation in 0.4% PFA in PBS (as described in Louphrasitthiphol et al., 2019)

tag: cell-type

value: melanoma

tag: genotype/variation


title: HCC1143_RRBS

source_name: HCC1143 Cell line

value: breast cancer cell line

value: RRBS


title: iMit_K243R_20ng_Dox_Replicate2

description: HA-MITF-K243R ChIP with 20ng/ml Dox relicate 2

value: 20ng/ml Doxycycline


title: DY36T2_RRBS

source_name: DY36T2 Cell line


title: lL3-undamaged-ATAC-rep3

description:
Old-Undamaged-Rep3_q5_sorted_noYUHet_normalizedToRPGC_zNorm.bw
Old-Undamaged_3Reps_POOLED_q5_sorted_noYUHet_normalizedToRPGC_zNorm.bw
Old-Undamaged_3Reps_ATAC_PooledPeaks_peaks.xls

tag: age

tag: damage status

value: undamaged

tag: repeat #


title: lL3-undamaged-ATAC-rep2

description:
Old-Undamaged-Rep2_q5_sorted_noYUHet_normalizedToRPGC_zNorm.bw
Old-Undamaged_3Reps_POOLED_q5_sorted_noYUHet_normalizedToRPGC_zNorm.bw
Old-Undamaged_3Reps_ATAC_PooledPeaks_peaks.xls


title: iMit_K243R_20ng_Dox_Replicate1

description: HA-MITF-K243R ChIP with 20ng/ml Dox relicate 1

tag: chip antibody


title: HCC1937_RRBS

source_name: HCC1937 Cell line


title: PBMC Donor 2 DMSO rep1

value: male


title: input for H3K27me3

source_name: Non-hair cells

tag: nuclei type

value: Non-hair cell nuclei from root epidermal tissue


title: BT-549_RRBS

source_name: BT-549 Cell line


title: lL3-undamaged-ATAC-rep1

description:
Old-Undamaged-Rep1_q5_sorted_noYUHet_normalizedToRPGC_zNorm.bw
Old-Undamaged_3Reps_POOLED_q5_sorted_noYUHet_normalizedToRPGC_zNorm.bw
Old-Undamaged_3Reps_ATAC_PooledPeaks_peaks.xls


title: PBMC Donor 1 DMSO rep1

value: female


title: eL3-damaged-ATAC-rep3

description:
Young-Damaged-Rep3_q5_sorted_noYUHet_normalizedToRPGC_zNorm.bw
Young-Damaged_3Reps_POOLED_q5_sorted_noYUHet_normalizedToRPGC_zNorm.bw
Young-Damaged_3Reps_ATAC_PooledPeaks_peaks.xls

value: early L3


title: iMit_K243R_0ng_Dox_Replicate2

description: HA-MITF-K243R ChIP with no Dox relicate 2


title: BT-20_RRBS

source_name: BT-20 Cell line


title: iMit_K243R_0ng_Dox_Replicate1

description: HA-MITF-K243R ChIP with no Dox relicate 1


title: eL3-damaged-ATAC-rep2

description:
Young-Damaged-Rep2_q5_sorted_noYUHet_normalizedToRPGC_zNorm.bw
Young-Damaged_3Reps_POOLED_q5_sorted_noYUHet_normalizedToRPGC_zNorm.bw
Young-Damaged_3Reps_ATAC_PooledPeaks_peaks.xls


title: HCC1187_RRBS

source_name: HCC1187 Cell line


title: BT-474_RRBS

source_name: BT-474 Cell line


title: Ad5-Empty.rep3

source_name: Lung

value: control

value: Lung


title: 2LMP_RRBS

source_name: 2LMP Cell line


title: iMit_K243Q_Input_control

description: Input control for K243Q mutant


title: lL3-damaged-ATAC-rep1

description:
Old-Damaged-Rep1_q5_sorted_noYUHet_normalizedToRPGC_zNorm.bw
Old-Damaged_3Reps_POOLED_q5_sorted_noYUHet_normalizedToRPGC_zNorm.bw
Old-Damaged_3Reps_ATAC_PooledPeaks_peaks.xls

value: late L3


title: eL3-damaged-ATAC-rep1

description:
Young-Damaged-Rep1_q5_sorted_noYUHet_normalizedToRPGC_zNorm.bw
Young-Damaged_3Reps_POOLED_q5_sorted_noYUHet_normalizedToRPGC_zNorm.bw
Young-Damaged_3Reps_ATAC_PooledPeaks_peaks.xls

value: damaged


title: iMit_K243Q_20ng_Dox_Replicate2

description: HA-MITF-K243Q ChIP with 20ng/ml Dox relicate 2


title: iMit_K243Q_20ng_Dox_Replicate1

description: HA-MITF-K243Q ChIP with 20ng/ml Dox relicate 1


title: eL3-undamaged-ATAC-rep3

description:
Young-Undamaged-Rep3_q5_sorted_noYUHet_normalizedToRPGC_zNorm.bw
Young-Undamaged_3Reps_POOLED_q5_sorted_noYUHet_normalizedToRPGC_zNorm.bw
Young-Undamaged_3Reps_ATAC_PooledPeaks_peaks.xls


title: iMit_K243Q_0ng_Dox_Replicate2

description: HA-MITF-K243Q ChIP with no Dox relicate 2


title: eL3-undamaged-ATAC-rep2

description:
Young-Undamaged-Rep2_q5_sorted_noYUHet_normalizedToRPGC_zNorm.bw
Young-Undamaged_3Reps_POOLED_q5_sorted_noYUHet_normalizedToRPGC_zNorm.bw
Young-Undamaged_3Reps_ATAC_PooledPeaks_peaks.xls


title: eL3-undamaged-ATAC-rep1

description:
Young-Undamaged-Rep1_q5_sorted_noYUHet_normalizedToRPGC_zNorm.bw
Young-Undamaged_3Reps_POOLED_q5_sorted_noYUHet_normalizedToRPGC_zNorm.bw
Young-Undamaged_3Reps_ATAC_PooledPeaks_peaks.xls


title: iMit_K243Q_0ng_Dox_Replicate1

description: HA-MITF-K243Q ChIP with no Dox relicate 1


title: iMit_WT_20ng_Dox_Replicate2

description: HA-MITF-WT ChIP with 20ng/ml Dox relicate 2

value: wild type


title: iMit_WT_20ng_Dox_Replicate1

description: HA-MITF-WT ChIP with 20ng/ml Dox relicate 1


title: iMit_WT_0ng_Dox_Replicate2

description: HA-MITF-WT ChIP with no Dox relicate 2


title: iMit_WT_0ng_Dox_Replicate1

description: HA-MITF-WT ChIP with no Dox relicate 1


title: pbmc_mono_ko_ss

first: Stephen

last: Sansom

state: Oxfordshire

address: Roosevelt Drive

department: NDORMS

institute: Kennedy Institute of Rheumatology

data_processing:
Data analysis was performed using Python3 pipelines (https://github.com/sansomlab/tenx) written using CGAT-core. Read mapping, quantitation and aggregation of sample count matrices was performed with the 10x Genomics Cell Ranger pipeline (version 3.1.0). For the "cellranger count" step, a custom reference was built using Ensembl annotations (version 91) that included genes with protein coding, lincRNA, macro_lincRNA, immune (IG_*, TR_*), antisense_RNA, and miRNA Ensembl (version 91) biotypes.
Within each dataset, Irf5-/- and wildtype samples were aggregated. No normalisation was applied during the aggregation step. Cells with barcodes common to more than one sample from the same sequencing batch were removed from the analysis to avoid issues associated with index hopping. For each of the experiments, the aggregated count matrices were randomly down-sampled in order to normalise the median number of UMIs per-cell between the Irf5-/- and wildtype samples ("downsampleMatrix" function from the DropletUtils R package) and genes detected in less than 3 cells removed.
For the steady state colon dataset, cells with < 1k genes, > 25k UMIs, > 7.5% mitochondrial UMIs, identified as contaminating B, T or stromal cells (n=75), or with high expression of interferon-induced genes (n=34) were removed. For the steady state PBMC dataset, cells with < 500 genes, > 20k UMIs, > 5% mitochondrial UMIs, with high expression of haemoglobin genes (n=8) or identified as contaminating T cells (n=694) were removed. For each of the datasets either the WT or Irf5-/-cells were randomly down sampled to retain an equal number of cells per genotype.
Genome_build: mm10
Supplementary_files_format_and_content: The "matrix.mtx.gz" MEX file contains the aggregated count matrix (cells in columns, genes in rows). The "barcodes.tsv.gz" TSV file contains the cell barcodes (tissue and genotype are indicated in the cell barcode  with the suffixes "-cLP_wt",  "-cLP_ko",  "-pbmc_wt",  "-pbmc_ko"). The "genes.tsv.gz" file contains the Ensembl gene identifiers and names. These files can be read with the "Read10X" function from the Seurat R package.

source_name: preipheral blood

growth_protocol: Mice were bred and maintained under SPF conditions in accredited animal facilities at the University of Oxford. All procedures were conducted according to the Operations of Animals in Scientific Procedures Act (ASPA) of 1986 and approved by the Kennedy Institute of Rheumatology Ethics Committee. Animals were housed in individually ventilated cages at a constant temperature with food and water ad libitum. Mice were free of known intestinal pathogens and negative for Helicobacter species.

extract_protocol:
(1) Isolation of lamina propria leukocytes: Colons and/or caeca were harvested from mice, washed in PBS/BSA and content flushed with forceps. Intestines were then opened longitudinally and washed once more before blotting to remove mucus. Gut tissue was then cut into 1 cm long pieces and placed in 50 mL centrifuge tube (Greiner) in ice cold PBS + 0.1% BSA. Colons were incubated 2 times at 200 rpm in 40 mL HBSS + 0.1% BSA + 1% Penicillin-Streptomycin (PS, Lonza) + 5mM EDTA (Sigma-Aldrich) at 37 °C for 10 min before the supernatant was aspirated. Tissue was placed in 40 mL PBS + 0.1% BSA + 1% PS for 5 min. Intestines were then incubated with 20 mL RPMI + 10% FCS +1% PS + 2.5 U/mL Collagenase VIII (Sigma-Aldrich) + 2 U/mL DNAse I (Roche), shaking at 200 rpm for 45 mins - 1 hour at 37 °C. Supernatant was filtered through a 70 μm cell strainer to which 30 mL of ice cold PBS + 0.1% BSA + 1% PS + 5 mM EDTA was added to ablate collagenase/DNase activity. Cells were washed in 30 mL PBS/BSA before filtering once more through a 40 μm cell strainer. The cells were then pelleted by centrifugation at 400 rcf for 10 minutes at 4 °C. Colonic lamina propria leukocytes (cLPLs) were isolated by resuspending cells in 4 mL P80 (80% P100 (9:1 percoll:10X PBS) + 20% RPMI) percoll in a 15 mL centrifuge tube (Greiner) before overlaying 4 mL P40 (40% P100 + 60% 1X PBS) layer. Cells were spun at 3000 rpm for 20 min at room temperature, slow acceleration, no brake. Mucus and cellular debris were aspirated from the surface of the P40 layer with a Pasteur pipette and pipetted into 40 mL of ice cold PBS + 0.1% BSA. Cells were pelleted by centrifugation at 400 rcf for 10 min and resuspended in 1 mL RPMI + 10% FCS + 1% PS before counting.    (2) Isolation of blood leukocytes: Blood was harvested by either tail vein bleed or cardiac puncture. Mice were culled by Schedule 1 method in accordance with the project licence. Prior to cardiac puncture a 1 mL syringe was coated with PBS + 2 mM EDTA. Cardiac puncture was performed with a 27G needle. Tail vein bleeds were performed using a #24 blade scalpel (Swann-Morton Ltd.) Collected blood was placed in 1 mL of sterile 2 mM EDTA/PBS solution in a 15 mL centrifuge tube (Greiner). Tubes were topped up with ice-cold PBS + 0.1% BSA. Cells were pelleted by centrifugation at 400 rcf for 10 mins at 4 °C and the supernatant discarded. Erythrocytes were then lysed using 10-20X the blood sample volume of ACK lysis buffer (Gibco) for 3 mins. Tubes were then topped up to 15 mL with ice cold PBS + 0.1% BSA to quench the lysis buffer. Cells were washed in PBS/BSA, resuspended in PBS + 0.1% BSA to the desired cell concentration, and stored at 4 °C until required.
Libraries were generated using 10x Genomics Single Cell 3’ Solution (version 3) kit and subjected to Illumina sequencing (NovaSeq 6000).

tag: strain

value: C57BL/6 SJL

tag: genotype

tag: facs  phenotype

value: CD45+CD11b+ SiglecF-Ly6G-CX3CR1+Dump-

tag: replicate

value: pool of cells from n=5 chimeras


title: pbmc_mono_wt_ss


title: cLP_mph_ko_ss

source_name: colonic lamina propria


title: ZBTB38 WT rep 2

city: Tucson

first: Deepta

last: Bhattacharya

state: Arizona

address: 1656 E. Mabel Street, MRB 217

department: Department of Immunobiology

institute: University of Arizona

data_processing:
Reads were mapped with Salmon v 0.9.1
Differentially expressed genes were quantifed with DESeq2 v 2.11.40.6
Genome_build: Gencode M17 transcriptome
Supplementary_files_format_and_content: .sf files were generated using Salmon and list TPM values for all genes
Supplementary_files_format_and_content: .xlsx files were generated using DESeq2, and list differentially expressed genes between ZBTB38 KO vs. WT, or between ZBTB38 KO vs. WT and HET

source_name: Germinal center B cells

growth_protocol: Primary cells

extract_protocol:
Macherey-Nagel nucleospin XS
Illumina Nextera

treatment_protocol: untreated


title: ZBTB38 KO rep 5

value: Zbtb38fl/fl x Vav-Cre


title: ZBTB38 WT rep 1


title: ZBTB38 KO rep 6


title: iMit_WT_Input_control

description: Input control for WT

value: melanoma


title: cLP_mph_wt_ss


title: ZBTB38 KO rep 4


title: SPF D m6A IP

city: Chciago

first: Chuan

state: IL

address: 929 E 57 th St

institute: University of Chicago

data_processing:
Library strategy: MeRIP-seq
Base-calling performed using CASAVA
Reads were aligned to the mouse transcriptome mm10 using hisat2 (v2.1.0)
m6A peaks are called by RADAR
Genome_build: mm10
Supplementary_files_format_and_content: Treg_Tnaive_m6A.xls and GF_SPF_m6A.xls contain the differentially methylated peaks between indicated cell types called by RADAR

source_name: T Cells

growth_protocol: CD4 + Tnaïve cells were cultured in Advanced RPMI 1640 + 10% FBS + 1% penicillin/streptomycin + 2mM L-glutamine + 20 ng/mL TGFb + 40 ng/mL IL-2 + 1nM all-trans-retinoic-acid for 96 hours to generate induced Treg

extract_protocol:
RNA was isolated with the Trizol reagent and Direct-zol RNA Kit. polyA RNAs were enriched with Dynabeads mRNA Purification Kit and fragmented to 150 nt with a Bioruptor Pico sonicator. 4% fragmented RNA was saved as input. Remaining fragments containing m6A were enriched with the EpiMark N6-methyladenosine Enrichment Kit.
All libraries were constructed with the SMARTer Stranded Total RNA-Seq Kit v2 (Takara)

value: CD4+ T cells

tag: mouse facility

value: Specific pathogen free

tag: antibody

value: anti m6A from EpiMark N6-Methyladenosine Enrichment Kit


title: GF 1689 m6A IP

tag: cell type

value: Gnotobiotics


title: GF 1683 m6A IP


title: GF 1688 m6A IP


title: ZBTB38 KO rep 3


title: ZBTB38 HET rep 2

value: Zbtb38fl/+ x Vav-Cre


title: SDLN_Xcr1++_rep1

source_name: Migratory cDC1 from Xcr1++ CD40 fl skin draining lymph nodes

tag: strain background

value: Xcr1++ CD40flfl

tag: tissue

value: Skin draining lymph node


title: RNA-seq_TAg rep1

value: CD4 T cells

tag: treatment

value: Tolerant + Antigen


title: ZBTB38 Het rep 1


title: SPF C m6A IP


title: SPF B m6A IP


title: SPF A m6A IP


title: ZBTB38 KO rep 2


title: Tnaive H m6A IP

value: Tnaive


title: Tnaive G m6A IP


title: ZBTB38 KO rep 1


title: mazF10

city: Cambridge

first: Michele

last: LeRoux

address: 31 Ames St

institute: MIT

description:
RNA with rRNA subtracted
Overnight cultures of indicated strain were back diluted into M9-glucose and grown 3-4 hours to an OD600 of ~0.3 at 37°C in an orbital shaker at 200 RPM. Cells were washed into M9-glycerol media and diluted to OD ~0.2. After 30 min, arabinose was added to 0.2%. After 10 min, samples were collected for RNA. Cells from pBAD30-mazF and pBAD30-empty were mixed at a ratio of 10:90.
mazF10_ratio.csv

data_processing:
Paired-end reads mapped to MG1655 genome using bowtie2 with default settings. Any adapter sequences were removed prior to mapping.
For each uniquely mapped fragment a count was added at all aligned positions.
Counts were depth normalized to a pseudo-reference sample calculated from all samples
Counts at all positions were log2 transformed and a ratio was calculated (wildtype - ∆10TA) for assessing toxin activity.
Genome_build: NCBI reference sequence: NC_000913.2
Supplementary_files_format_and_content: heatshock_15_ratio.csv, heatshock_60_ratio.csv are log-transformed lists of sequencing depth-normalized counts for every genomic position at both strands for each time point. crMazF100, crMazF1, crMazF5, and crMazF10 are log-transformed lists of sequencing depth-normalized counts for every genomic positions at both strands where the ratio was generated by subtracting MazF0 from each of the relevant datasets.

organism: Escherichia coli

source_name: Bacterial liquid culture

extract_protocol:
RNA was extracted using Trizol (Invitrogen) and Direct-zol RNA MiniPrep kit (Zymo).
See publication for complete protocol. Briefly, ribosomal RNA was substracted (samples 1-6 with Illumina RiboZero kit; samples 7-14 as described in Culviner et. al. 2020 https://doi.org/10.1101/2020.01.06.896837) and resulting RNA was fragmented with RNA fragmentation reagents (Ambion). First strand cDNA synthesis was conducted using random primers and Superscript III (Invitrogen). To enable strand specificity, second strand synthesis was conducted using dUTP instead of dTTP with RNase H, E. coli DNA ligase, and E. coli DNA polymerase. Ends were repaired with T4 DNA polymerase, Klenow DNA polymerase, and T4 PNK. 3’ ends were adenylated with the Klenow fragment (3’>5’ exo-). Y-shaped adapters were ligated and 9-12 cycles of PCR were conducted with standard Illumina primers with multiplexing indexes. Libraries were size selected and submitted for sequencing at the MIT BioMicro Center using standard Illumina protocols.

value: MG1655 pBAD30-mazF/MG1655 pBAD30-empty

tag: time point


title: Tnaive F m6A IP


title: mazF5

description:
RNA with rRNA subtracted
Overnight cultures of indicated strain were back diluted into M9-glucose and grown 3-4 hours to an OD600 of ~0.3 at 37°C in an orbital shaker at 200 RPM. Cells were washed into M9-glycerol media and diluted to OD ~0.2. After 30 min, arabinose was added to 0.2%. After 10 min, samples were collected for RNA. Cells from pBAD30-mazF and pBAD30-empty were mixed at a ratio of 5:95.
mazF5_ratio.csv


title: mazF1

description:
RNA with rRNA subtracted
Overnight cultures of indicated strain were back diluted into M9-glucose and grown 3-4 hours to an OD600 of ~0.3 at 37°C in an orbital shaker at 200 RPM. Cells were washed into M9-glycerol media and diluted to OD ~0.2. After 30 min, arabinose was added to 0.2%. After 10 min, samples were collected for RNA. Cells from pBAD30-mazF and pBAD30-empty were mixed at a ratio of 1:99.
mazF1_ratio.csv


title: iTreg 50 m6A IP

value: induced Treg


title: mazF0

description:
RNA with rRNA subtracted
Overnight cultures of indicated strain were back diluted into M9-glucose and grown 3-4 hours to an OD600 of ~0.3 at 37°C in an orbital shaker at 200 RPM. Cells were washed into M9-glycerol media and diluted to OD ~0.2. After 30 min, arabinose was added to 0.2%. After 10 min, samples were collected for RNA
mazF0_ratio.csv

value: MG1655 pBAD30-empty


title: iTreg 05 m6A IP


title: mazF100

description:
RNA with rRNA subtracted
Overnight cultures of indicated strain were back diluted into M9-glucose and grown 3-4 hours to an OD600 of ~0.3 at 37°C in an orbital shaker at 200 RPM. Cells were washed into M9-glycerol media and diluted to OD ~0.2. After 30 min, arabinose was added to 0.2%. After 10 min, samples were collected for RNA
mazF100_ratio.csv

value: MG1655 pBAD30-mazF


title: iTreg 03 m6A IP


title: Breast cancer PD36050a

type: genomic

city: Lund

first: Johan

last: Staaf

address: Medicon Village

country: Sweden

institute: SCIBLU - Swegene Centre for Integrative Biology at Lund University

hyb_protocol: Bisulfite-converted genomic DNA was hybridised to Illumina EPIC 850K arrays using standard manufacturer protocols

scan_protocol: Standard Illumina scanner and settings

data_processing: Raw signal values extracted using minfi::preprocessRaw() followed by minfi::getUnmeth and minfi::getMeth. Normalized betas were obtained by minfi::preprocessFunnorm(), betas were then scaled to adjust for difference in Infinium I/II beta distribution using the method of Karlsson et al. 2014 (PMID: 25278450), finally Zhou et al. 2016 (PMID: 27924034) annotations (20180909 data freeze) were used to filter out unreliable probes.

source_name: Breast cancer

label_protocol: Standard Illumina protocol

extract_protocol: Standard DNA extraction protocol according to SCAN-B workflow

tag: subtype

value: TNBC

value: Hypermethylated

tag: gender

value: female


title: GF 1689 m6A input

value: CD4+ T cells

value: none (input)


title: wt_heatshock_60

description:
RNA with rRNA subtracted
Overnight cultures were back diluted into M9-glucose media and grown 3-4 hours to an OD600 of ~0.3 at 30°C in an orbital shaker at 200 RPM. Cells were shifted to a shaking incubator set to 45°C and collected for RNA extraction at indicated time point.
heatshock_60_ratio.csv


title: ∆10_heatshock_60

value: MG1655 {delta}10TA


title: GF 1688 m6A input

value: Gnotobiotics


title: Tnaive E m6A IP

value: Specific pathogen free

value: anti m6A from EpiMark N6-Methyladenosine Enrichment Kit


title: Genomic DNA from 203038250014_R02C01

city: New Haven

first: Ke

last: Xu

state: CT

institute: Yale University

description:
Sample 2
Whole blood sample

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human EPIC BeadChip using standard Illumina protocol.

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting.

data_processing: minfi

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol.

extract_protocol: Standard Illumina Protocol.

value: Peripheral blood mononuclear cell

tag: subject


title: Breast cancer PD36057a


title: Genomic DNA from 203038250014_R03C01

description:
Sample 3
Whole blood sample


title: Pancreatic Islets, ICRH122

city: New York

first: Shuibing

last: Chen

address: A 827B, 1300 York Ave

department: Surgery

institute: Weill Cornell Medical College

description: single cell RNA-seq

data_processing:
The sequencing data were primarily analyzed by the 10X cellranger pipeline (v3.0.2)
cellranger mkfastq was used for sample demultiplexing and fastq generation.
cellranger count was used to align reads to the 10X pre-built human reference genome (GRCh38 v3.0.0) and to extract gene expression UMI counts matrix.
Genome_build: GRCh38
Supplementary_files_format_and_content: UMI counts matrix generated by 10X cellranger count; matrix.mtx.gz stores UMI counts per gene per cell; features.tsv.gz stores gene annotations; barcodes.tsv.gz stores cell barcodes.

source_name: Pancreatic Islets

extract_protocol:
Fresh pancreatic islets were dissociated to single cells, Chromium Single Cell 3’ Library & Gel Bead Kit v2 was used to construct the sequencing libraries.
Library was constructed according to the user manual of Chromium Single Cell 3’ Library & Gel Bead Kit v2

value: Pancreatic islet

value: Female

tag: age

value: 46 years


title: ∆10_heatshock_15

description:
RNA with rRNA subtracted
Overnight cultures were back diluted into M9-glucose media and grown 3-4 hours to an OD600 of ~0.3 at 30°C in an orbital shaker at 200 RPM. Cells were shifted to a shaking incubator set to 45°C and collected for RNA extraction at indicated time point.
heatshock_15_ratio.csv


title: Genomic DNA from 203038250014_R04C01

description:
Sample 4
Whole blood sample


title: GF 1683 m6A input

last: He


title: Breast cancer PD36034a


title: CEM virion RNA PA-ac4C-seq

description:
HIV-1 virion packaged RNA
Aligned to the HIV-1 NL4-3 genome, with one copy of LTR, U3 sequence on the 5' end, R-U5 on the 3' end

data_processing:
CASAVA 1.8.2
fastx toolkit: fastq_quality_filter -Q33| fastx_clipper -Q33 -v -a [index_sequence] -l 15 -c | fastq_to_fasta -Q33
Aligned to the human genome hg19 using Bowtie 0.12.7: bowtie -m 8 -a --best --strata --chunkmbs 10000
hg19 non-aligning reads aligned to the HIV-1 NL4-3 genome using Bowtie 0.12.7: bowtie -m 3 -v 1 -a --best --strata --chunkmbs 10000
Filtered out all reads that lack a TC mutation
Awk script to generate bed file, columns are "chromosome, start, end, score, strand"
Genome_build: NL4-3 genomes: 551-9626nt of GenBank AF324493.2
Supplementary_files_format_and_content: bed files, aligned to HIV-1 NL4-3 genome

source_name: CEM virion RNA

tag: cell line

value: CEM

tag: virus

value: hIV-1 NL4-3

tag: genotype/variation

tag: technique

tag: pulldown antibody

value: anti-ac4C, Abcam, ab252215, Lot No GR3269449-2


title: Breast cancer PD36039a


title: Breast cancer PD36037a


title: wt_heatshock_15

tag: strain


title: Breast cancer PD36033a


title: Breast cancer PD36046a


title: HIV-1 infected CEM mRNA PA-ac4C-seq

description:
poly(A)+ RNA
Aligned to the HIV-1 NL4-3 genome, with one copy of LTR, U3 sequence on the 5' end, R-U5 on the 3' end

source_name: HIV-1 infected CEM


title: Genomic DNA from 203038250014_R01C01

description:
Sample 1
Whole blood sample


title: ev2_10_minute_expression

city: Boston

first: Peter

last: Culviner

address: 677 Huntington Ave

department: IID

institute: Harvard School of Public Health

description: RNA with rRNA subtracted

data_processing:
Paired-end reads mapped to MG1655 genome using bowtie2.
For each uniquely mapped fragment, at all aligned positions a count was added.
Counts were depth normalized to a pseudo-reference sample calculated from all samples.
Counts at all positions were log2 transformed and a cleavage ratio was calculated (+ toxin / - empty vector) for assessing cleavage in transcripts.
Genome_build: NCBI reference sequence: NC_000913.2
Supplementary_files_format_and_content: Included csv files show raw counts at each position for uniquely mapped fragments. The first column corresponds to the positive strand and the second column to the negative strand. An additional file with calculated cleavage ratios at all positions for these samples is also included.

growth_protocol: Separate E. coli colonies were picked from LB agar plates for each replicate. Overnight cultures (12-16 hrs) were grown at 37°C in M9 media supplemented with 0.1% casamino acids, 0.4% glycerol, 0.4% glucose, 2 mM MgSO4, and 0.1 mM CaCl2. Overnight cultures were back diluted into fresh media and grown 3-4 hours to an OD600 of ~0.35 at 37°C in an orbital shaker at 200 RPM. Cultures were centrifuged, washed, and back diluted into media lacking glucose. After at least 30 minutes of recovery Para was induced by adding arabinose to quantity described. Titratable strains were grown without glucose present as antitoxin was present for control of toxicity.  Cells were harvested by centrifuging 1 mL of culture for 1 minute at maximum speed on a benchtop centrifuge. Pellets were immediately flash frozen in lN2.

extract_protocol:
RNA was extracted using Trizol (Invitrogen) and Direct-zol RNA MiniPrep kit (Zymo).
Briefly, samples with rRNA subtraction with treated with bacterial Ribo-Zero kit (Illumina) or comparable homebrew kit. Next, RNA was fragmented with RNA fragmentation reagents (Ambion). First strand cDNA synthesis was conducted using random primers and Superscript III (Invitrogen). To enable strand specificity, second strand synthesis was conducted using dUTP instead of dTTP with RNase H, E. coli DNA ligase, and E. coli DNA polymerase. Ends were repaired with T4 DNA polymerase, Klenow DNA polymerase, and T4 PNK. 3’ ends were adenylated with the Klenow fragment (3’>5’ exo-). Y-shaped adapters were ligated and 9-12 cycles of PCR were conducted with standard Illumina primers with multiplexing indexes. Libraries were extracted from an acrylamide gel and submitted for sequencing at the MIT BioMicro Center using standard Illumina protocols.

tag: plasmid

tag: ribosome depletion

value: RiboZero

tag: arabinose concentration

value: 0.2 percent

tag: time induction

value: 10 minutes


title: SPF C m6A input

tag: cell type

tag: mouse facility

tag: antibody


title: Breast cancer PD36058a

tag: subtype

value: TNBC

value: female


title: SPF D m6A input

value: CD4+ T cells

value: none (input)


title: mock infected CEM mRNA PA-ac4C-seq

source_name: mock infected CEM


title: Breast cancer PD36060a

tag: gender


title: ev1_10_minute_expression

description: RNA with rRNA subtracted


title: SPF B m6A input


title: Breast cancer PD36038a

value: Hypermethylated


title: Breast cancer PD36023a


title: HigB_10_minute_expression

description: RNA with rRNA subtracted


title: Breast cancer PD36010a


title: Breast cancer PD36029a


title: CEM-SS virion RNA PA-ac4C-seq

source_name: CEM-SS virion RNA

value: CEM-SS

value: anti-ac4C, Abcam, NCI-184 clone 128 (non-commercially avaliable production of ab252215), Lot No H09131602


title: SupT1 virion RNA PA-ac4C-seq

source_name: SupT1 virion RNA


title: YafO_10_minute_expression

description: RNA with rRNA subtracted


title: Breast cancer PD36013a


title: Breast cancer PD36017a


title: HIV-1 infected CEM-SS mRNA PA-ac4C-seq

source_name: HIV-1 infected CEM-SS


title: SPF A m6A input

value: Specific pathogen free


title: YoeB_10_minute_expression

description: RNA with rRNA subtracted


title: Breast cancer PD36025a


title: Breast cancer PD36026a


title: Tnaive G m6A input

value: Tnaive


title: mock infected CEM-SS mRNA PA-ac4C-seq

source_name: mock infected CEM-SS


title: RelE_10_minute_expression

description: RNA with rRNA subtracted


title: Breast cancer PD36016a


title: Breast cancer PD36007a


title: Tnaive E m6A input


title: Tnaive F m6A input


title: MqsR_10_minute_expression

description: RNA with rRNA subtracted


title: YhaV_10_minute_expression

description: RNA with rRNA subtracted


title: Breast cancer PD36006a


title: iTreg 50 m6A input

value: induced Treg


title: iTreg 05 m6A input


title: HicA_10_minute_expression

description: RNA with rRNA subtracted


title: iTreg 03 m6A input


title: ChpB_10_minute_expression

description: RNA with rRNA subtracted


title: MazF_middle_expression

description: RNA with rRNA subtracted

value: pBAD30-MazF, pKVS45-MazE

value: homebrew

value: 3.13e-5  percent


title: Breast cancer PD36004a


title: empty_vector_middle_expression

description: RNA with rRNA subtracted

value: pBAD30-empty, pKVS45-empty


title: MazF_low_expression

description: RNA with rRNA subtracted

value: 1.57e-5  percent


title: Striatum P3, run 1

city: London

first: Michael

last: Lattke

address: Hammersmith Hospital Campus, Du Cane Road

department: Brain Sciences

institute: Imperial College London

description:
PN2
LAT293A6
PN2_L1

data_processing:
The resulting data was demultiplexed using the 10x cellranger mkfastq function according to manufactuer’s instructions. Reads from individual samples were mapped to the mouse genome (mm10) and quantified with the cell ranger count function (v3.0.2, option --expect-cells=3500).
The generated count matrices were imported into Seurat (v3.1.1) (Stuart et al., 2019) and aggregated using the Seurat “merge” function.
Genome_build: mm10
Supplementary_files_format_and_content: Raw read counts for each gene for each cell; cells from all samples merged (extracted from Seurat)

source_name: striatal astrocytes (MACS-purified)

extract_protocol:
cell suspensions of striatal astrocytes were prepared by anti-ACSA2-MACS. Samples were prepared using the 10x Chromium Next GEM Single Cell 3ʹ v3.1 kit.
Following GEM recovery, cDNA was amplified and final libraries prepared according to the manufactuer’s instructions.
scRNA-Seq

value: mixed

tag: tissue

value: striatum

value: post natal day 7

tag: genotype

value: wild type

value: striatal astrocytes (MACS-purified)

tag: experimental group


title: Striatum P3, run 2

description:
PN2
LAT293A6
PN2_L2

tag: age


title: Striatum 3m, repl 2, run 2

description:
WT2
LAT293A4
WT2_L2

value: 3 months


title: Striatum 3m, repl 2, run 1

description:
WT2
LAT293A4
WT2_L1


title: empty_vector_low_expression

description: RNA with rRNA subtracted

value: 10 minutes


title: Striatum P7, run 4

description:
PN1
LAT293A3
PN1_L4

value: post natal day 3


title: wt_chlor_60

description: RNA with rRNA subtracted

data_processing:
Paired-end reads mapped to MG1655 genome using bowtie2 with default settings. Any adapter sequences were removed prior to mapping.
For each uniquely mapped fragment a count was added at all aligned positions.
Counts were depth normalized to a pseudo-reference sample calculated from all samples
Counts at all positions were log2 transformed and a ratio was calculated (wildtype - ∆10TA) for assessing toxin activity.
Genome_build: NCBI reference sequence: NC_000913.2
Supplementary_files_format_and_content: chlor_15_ratio.csv.gz, chlor_30_ratio.csv.gz, and chlor_60_ratio.csv.gz are log-transformed lists of sequencing depth-normalized counts for every genomic position at both strands for each time point. The files contain 2 rows by 4639675 columns where the first row is the positive strand and the second row is the negative strand.

growth_protocol: Overnight cultures of E. coli MG1655 wildtype or ∆10TA (Goeders, Dreze, Van Melderen 2013 J. Bacteriology) were back diluted into fresh media and grown 3-4 hours to an OD600 of ~0.3 at 37°C in an orbital shaker at 200 RPM. Chloramphenicol was added to a final concentration of 75 µg/mL. Cells were collected for RNA extraction at 15, 30, and 60 min after addition of chloramphenicol.

extract_protocol:
RNA was extracted using Trizol (Invitrogen) and Direct-zol RNA MiniPrep kit (Zymo).
See publication for complete protocol. Briefly, samples were treated with bacterial Ribo-Zero kit (Illumina) and the resulting RNA was fragmented with RNA fragmentation reagents (Ambion). First strand cDNA synthesis was conducted using random primers and Superscript III (Invitrogen). To enable strand specificity, second strand synthesis was conducted using dUTP instead of dTTP with RNase H, E. coli DNA ligase, and E. coli DNA polymerase. Ends were repaired with T4 DNA polymerase, Klenow DNA polymerase, and T4 PNK. 3’ ends were adenylated with the Klenow fragment (3’>5’ exo-). Y-shaped adapters were ligated and 9-12 cycles of PCR were conducted with standard Illumina primers with multiplexing indexes. Libraries were size selected and submitted for sequencing at the MIT BioMicro Center using standard Illumina protocols.

treatment_protocol: Chloramphenicol was added to all cultures to a final concentration of 75 µg/mL.

tag: time point (minutes)


title: Striatum P7, run 3

description:
PN1
LAT293A3
PN1_L3


title: Breast cancer PD35992a

value: TNBC

value: Hypermethylated

value: female


title: ∆10_chlor_30

description: RNA with rRNA subtracted

value: MG1655 delta10TA


title: Breast cancer PD35990a


title: Striatum P7, run 2

description:
PN1
LAT293A3
PN1_L2


title: Breast cancer PD35995a


title: ∆10_chlor_60

description: RNA with rRNA subtracted


title: ∆10_chlor_15

description: RNA with rRNA subtracted


title: wt_chlor_30

description: RNA with rRNA subtracted