title: HeLa_Input

city: Cambridge

first: Felix

last: Krueger

institute: Altos Labs

data_processing:
Sequencing was carried out on the Illumina Genome Analyzer GAIIx and HiSeq 1000 platforms.
Data collection was performed using Sequencing Control Software v2.6.
Real-time Analysis (RTA) 1.5-1.8 were used for base calling.
Mapping of ChIP-Seq data was performed using Bowtie (v0.12.8; options -n 1 -m 1 --best --strata --chunkmbs  1024) against the human GRCh37 assembly.
Genome_build: GRCh37
Supplementary_files_format_and_content: Seqmonk Probe reports (tab-delimited text) from cell cycle sorted HeLa cells (H3K9ac ChIP in G1, G2M and M) and LCLs (H3K4me3, H3K9ac, H3K27me3 ChIP in G1 and G2M) using 5000bp rolling windows, corrected for read count, log2 transformed.

source_name: HeLa

extract_protocol:
Acetone-fixed cells were washed twice in cold PBS and resuspended in digestion buffer (0.32M sucrose, 50mM Tris/HCl (pH7.4), 4mM MgCl2, 1mM CaCl2, 5mM Na Butyrate, 0.1mM PMSF). Micrococcal nuclease was added to 25units/ml and chromatin digested at 37°C for 5 minutes. The reaction was stopped by the addition of EDTA to 5mM. Chromatin was pre-cleared by incubation with protein A sepharose beads and incubated overnight with antibodies to H3K9ac (in house, R607), H3K4me3 (in house, R612) and H3K27me3 (Millipore, 07-449). Antibody-bound material was isolated on Protein A-Sepharose beads (Invitrogen, UK) and DNA from antibody-bound and input chromatin was purified by PCR purification kit (Qiagen).
Sequencing libraries were prepared from 100ng DNA per sample using the NEBNext Library preparation kit for Illumina (NEB).  Samples were barcoded using the system described by Bronner et al. (2014).  Fragments were PCR amplified with 12–18 cycles using adaptor specific primers (Illumina); fragments ranging between 300 and 500 bp in size were gel-purified before cluster generation and sequencing.

value: HeLa

tag: sorting method

value: centrifugal elutriation

tag: cell cycle phase

tag: chip antibody


title: NG-Capture-C Mouse HS2HS3 fetal liver cells replicate 1

status: Public on Feb 03 2021

type: SRA

city: Oxford

first: Martin

middle: Stephen Charles

last: Larke

state: Oxfordshire

address: Headley Way

department: MRC Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

description: Next generation Capture-C products : 3C library prepartion followed by double oligonucleotide capture

library_source: genomic

data_processing:
Library strategy: Capture-C
Adaptor Removal: Trim Galore
Fragment reconstruction into a single read: Flash
In silico restriction enzyme digestion of FASTQ file (dpnIIPE.pl)
Alignment: Bowtie 2
Processing: Removal of PCR duplicates; Parsing of informative reads and mapping to restriction enzyme fragments (CCanalyser2.pl)
Processing: Combining data from multiple replicates (custom scripts)
Processing: Removal of ploidy regions and off target capture (custom scripts)
Genome_build: mm9
Supplementary_files_format_and_content: custom format: coordinates_fragment_tested, counts_biorep1, counts_biorep2, counts_biorep3

molecule: genomic DNA

organism: Mus musculus

source_name: Differentiated CD117+ mouse fetal liver erythroid cells

growth_protocol: Mouse fetal livers were harvested at E12.5 and disaggregated in expansion media (StemPro (ThermoFisher)) supplemented with Epo (1U/ml), SCF (50ng/ml), Dexamethosone (1μM)). Cells from individual fetal livers were grown for 6 days, maintaining a constant erythroblast cell count of <= 1 x106. Cells were genotyped as wildtype, homozygous R1R2 or homozygous HS2HS3 during expansion. Cells were counted using the nucleocounter before selection for CD117 positive cells using magnetic assisted cell separation LS columns (130-042-401 - Milltenyi) following the manufacturers protocol. Cells were left to recover for 6h in expansion media at a density of 1x10^6 cells/ml. Aliquots of 5x10^6 cells were harvested as the ‘0h’ timepoint corresponding to early erythropoiesis whilst the remaining cells were re-suspended in differentiation media (which is expansion media with the following changes: increased levels of Epo (5U/ml) and transferrin (0.5mg/ml), SCF and Dexamethasone removed). To induce erythroid differentiation cells were grown for 24h before harvesting for the ‘24h’ timepoint.

extract_protocol:
3C Libraries were generated according to the NG Capture-C protocol (Davies et al. 2016). Briefly, cells were crosslinked with 2% formaldehyde (10 minutes, room temperature); quenched with cold glycine; washed in phosphate buffered saline; resuspended in cold lysis buffer (tris 10mM, NaCl 10mM, NP40 0.2%, complete proteinase inhibitor (Roche)) and snap frozen to -80. Cells were thawed on ice, washed in milliq dH2O and Dounce homogenised on ice (x 40 strokes). Cells were then resuspended with 0.25% SDS and restriction enzyme buffer and incubated at 37C for 1h at 1400rpm on a Comfort Thermomixer (Eppendorf) followed by a further incubation of 1h following the addition of triton X100 (final concentration 1.67%). An overnight digestion was performed using Dpn II (500U /ml (NEB) at 37C / 1400 rpm). The digested chromatin was ligated overnight (Fermentas HC Ligase final concentration 10U/ml) at 16 degrees at 1400 rpm on the Thermomixer. The samples were then decrosslinked overnight at 65C with Proteinase K (Roche) followed by a 30 min incubation at 37C with RNAse (Roche). Phenol/Chloroform extraction was then performed followed by an Ethanol precipitation and a wash with 70% Ethanol. Digestion efficiencys were assessed by gel electrophoresis (1% agarose) and RT-PCR (Taqman), which showed digestion efficiencies in excess of 70%. DNA content of the Dpn II 3C libraries were quantitated using a Qubit fluorometer (Life technologies)
5-10ug of each library was sheared using a Covaris S2 in milliq dH2O. Covaris settings used were: duty cycle 10%, Intensity 5, Cycles/burst 200, Time 6 cycles of 60seconds, Set Mode Frequency sweeping Temperature 4 to 7 degrees. Following shearing DNA was purified using AMPureXP beads (Agencourt) and DNA quality assessed on a Bioanalyser 2100 using a DNA High Sensitivity Chip (Agilent). DNA end repair and adapter ligation was performed using the NEB Next or NEB Ultra DNA sample preparation reagent kits, depending on the amount of DNA available, using the standard protocol. Biotinylated capture oligonucleotides were designed to the ends of the viewpoint fragments. Where possible 1-2ug of each adapter ligated library were hybridized with the biotinylated capture oligonucleotides, using the Nimblegen SeqCap reagents and an adapted protocol. The quality of the resultant captured library was assessed by Agilent tapestation or bioanalyser (D1000). The resulting libraries were sequenced using Illumina Nextseq 500 (150 bp paired-end reads)

tag: strain

value: Mixed

tag: tissue

value: Fetal liver cultured ex vivo

tag: developmental stage

value: late erythroid

tag: genotype

value: homozygous deletion of HS2 and HS3 beta-globin enhancers


title: 18_S141: dHC-Train-6d_rep3

city: New York City

first: Alireza

last: Khodadadi-Jamayran

state: NY

address: 550 1st Ave, MSB 304

department: Division of Advanced Research Technologies (DART)

country: USA

institute: New York University, NYU Langone Medical Center

library_source: transcriptomic

data_processing:
RNA-Seq was run on an Illumina HiSeq 4000 as paired end 150 reads.
Alignments were guided by a Gene Transfer File (Ensembl GTF Rnor_6.0.84) and the mean read insert sizes and their standard deviations were calculated using Picard tools (v.1.126)
The Read Per Million (RPM) normalized BigWig files were generated using BEDTools (v2.17.0) and bedGraphToBigWig tool (v4).
DESeq2 was used to generate gene count tables and differential gene analysis.
Genome_build: Rnor_6.0.84
Supplementary_files_format_and_content: count table (txt), bigWig (bw)

molecule: total RNA

organism: Rattus norvegicus

source_name: Dorsal hippocampus

extract_protocol:
Rats were euthanized by decapitation. Their brains were quickly dissected and snap-frozen in pre-chilled isopentane on dry ice. PL (bregma +3.7mm to +2.2mm) and dHC (bregma -2.3mm to -4.52mm) tissue was isolated by punches in a cryostat using a Neuro Punch (19 gauge, Fine Science Tools, Foster City, CA) as described previously (Milekic et al., 2007) and immediately submerged into Qiazol (Qiagen, Venlo, Netherlands). Total RNA was isolated using the RNAeasy Plus Universal Kit following the manufactureâ€™s protocol (Qiagen, Venlo, Netherlands). 500 ng of RNA was reverse-transcribed using QuantiTect Reverse Transcription Kit (Qiagen, Venlo, Netherlands) in order to perform real-time polymerase chain reaction (RT-PCR) on all individual samples to validate immediate early gene c-Fos induction in trained vs. naÃ¯ve animals. RNA samples for naÃ¯ve and both groups of trained animals were pooled into 3 biological replicates (n=5/group per condition) and submitted to the New York University School of Medicine Genome Technology Center for further quality control, quantification and normalization. RNA integrity was tested on an Agilent 2100 Bioanalyzer before library preperation.
RNA-Seq library preps were made using the Illumina TruSeqÂ® Stranded mRNA LT kit (Cat #RS- RS-122-2101 or RS-122-2102), on a Beckman Biomek FX instrument, using 200 ng of total RNA as input, amplified by 12 cycles of PCR, and run on an Illumina 4000, as paired end 150 reads.

value: Long-Evans

value: Brain

value: Adult


title: high elevation lake water microbial gene_1

type: genomic

city: Nanjing

first: Huabing

last: Li

address: East Beijing Road 73

country: China

institute: Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences

description: sample in lake HHZ

hyb_protocol: The dried and labeled DNA was resuspended in 42 μl hybridization solution, which included 1 × HI-RPM hybridization buffer, 1 × a CGH blocking agent, 0.05 μgμl-1 Cot-1 DNA, 10 pM universal standard, and 10% formamide (final concentrations). Hybridizations were performed at 67°C for 24 h with a rotation of 20 rpm in a hybridization oven.

scan_protocol: The scanned images of hybridized GeoChips were converted and extracted by using Agilent Feature Extraction 11.5 software (Agilent Technologies, Inc., CA, USA)

data_processing: Raw data were uploaded to the microarray analysis pipeline (http://ieg.ou.edu/microarray/). In brief, the following steps were performed: (i) spots with a signal to noise ratio (SNR) less than 2 were removed due to poor quality; (ii) for each sample, intensities plus 1 were transformed to logarithm and divided by mean signal intensity.

organism: uncultured microorganism

source_name: water

label_protocol: DNA (500 ng) was labeled with the fluorescent dye Cy-3 (GE Healthcare, CA, USA) by random priming.

extract_protocol: The whole microbial DNA was extracted and puriﬁed using the Wizard DNA clean-up kit.

treatment_protocol: In this study, to investigate the influence of elevation  on microbial functional genes in aquatic environments, we focused on four shallow freshwater lakes at comparable elevations, two HELs (at 4,652 m and 4,608 m, respectively) and two LELs (at 530 m and 525 m, respectively), at Siguniang Mountain in Sichuan province, China. Six sampling sites were set in each lake. At each site, approximately 1 L of water was collected from surface waters (top 50 cm) for microbial Geochip analyses

tag: treatment

value: lake at 4608 m


title: 17_S140: dHC-Train-6d_rep2


title: S-Smc6 Top3-Flag input

city: Milan

first: Dana

last: Branzei

address: Via Adamello 16

country: Italy

institute: IFOM Foundation - The FIRC Institute of Molecular Oncology Foundation

description: Binding pattern of Top3 in S-smc6 background by ChIP-on-chip after arrest of cells in G2/M with Nocodazole

hyb_protocol: Labelled probes were hybridized to Affymetrix S.cerevisiae whole genome tiling R arrays.

scan_protocol: Arrays were scanned on an Affymetrix Scanner.

data_processing: BAR files were produced with Tiling Array Suite 1.1 from the command line with these options: tilecore -analysis -bpmap Sc03b_MR_v04.bpmap -type 1 -n 1 -nt 1 -export 1 -output_type 0 -format_type 1 -band 150 -pval_scale 0 -sig_scale 2 -tail_type 1 -nscale 1 -tgt 500 [files]

label: Dynabeads Protein A invitrogen

organism: Saccharomyces cerevisiae

source_name: G2/M arrest with Nocodazole

label_protocol: Sample preparation and labeling were carried out following the Affymetrix GeneChip Expression Anaysis protocol.

growth_protocol: Cells were grown in YP+Glucose 2% (YPD) media at 25°C in 500 ml flask for a density of 1.2×10^7 cells/ml.

extract_protocol: Binding profiles by ChIP-on-chip were determined as described in (Bermejo et al., 2009).

treatment_protocol: G2/M synchronization was performed by 10-20 μg/ml Nocodazole for 120-180 minutes at 25°C and validated by microscopy. Cells were treated with 0.2 mg/ml of Auxin (stock 50 mg/ml) during the arrest, if mentioned. Cells were collected and fixed with 1% formaldehyde for 30 min at room temperature for further ChIP.

tag: strain genotype

value: W303 MATa S-SMC6::NATMX4, Top3-10FLAG::KANMX4

tag: antibody

value: Anti-FLAG M2 F1804 (SIGMA)


title: Smc6-P4 Top3-Flag input

description: Binding pattern of Top3 in Smc6-P4 background by ChIP-on-chip after arrest of cells in G2/M with Nocodazole

value: W303 MATa smc6-P4-13myc::KAN, Top3-10FLAG::KANMX4


title: HeLa_H3K9ac_M

address: Granta Park

department: Bioinformatics

organism: Homo sapiens

growth_protocol: The AH-LCL lymphoblastoid cell line was cultured in RPMI 1640 medium, 10% foetal bovine serum, supplemented with L-glutamine (2mM) and penicillin/streptomycin (all reagents from Life Technologies) at 37°C, 5% CO2). HeLa cells were cultured in DMEM medium supplemented with 10% foetal bovine serum (Sigma), supplemented with L-glutamine (2mM) and penicillin/streptomycin (Life Technologies).

treatment_protocol: Cells were sorted into cell-cycle phase by several protocols: Fluorescence-activated cell sorting: Lymphoblastoid cells were treated with 0.1µg/ml colcemid for 4 hours to enrich the mitotic fraction. Cells were then harvested by centrifugation, washed three times in PBS and ice cold acetone was added dropwise before freezing to -20°C for at least 2 hours. Cells were then washed and resuspended in ice cold PBS. Propidium iodide was added to a concentration of 10µg/ml and incubated for 30 minutes at 4°C. Cells were sorted into G1 and G2M fraction based on Propidium iodide fluorescence using a MoFlo cell sorter (DakoCytomation). Centrifugal elutriation: a JE-5.0 elutriating centrifuge (Beckman Coulter) was used. HeLa cells were trypsinised, washed in culture medium and resuspended in 10ml of elutriation buffer (5mM EDTA, 1% bovine serum albumin in 0.75x PBS). Cells were passaged through an 18G needle and loaded into the elutriation chamber.Optima G1 fractions were achieved loading at 15ml/min, 1800rpm and the purest G2M fraction at 11ml/min, 1300 rpm. Cell cycle fractions were eluted by gradually increasing the flow rate and collecting 200ml fractions. Eluted cells were centrifuged and acetone-fixed as above for ChIP-seq. Mitotic shak off: HeLa cells in culture were shaken on an orbital shaker at 200 rpm for 1 minute. Medium containing shaken-off cells was collected and cells pelleted by centrifugation. Cells were acetone-fixed as above for ChIP-seq.

tag: cell line

value: mitotic shakeoff

value: Mitosis


title: S-Smc6 Top3-Flag


title: 16_S139: dHC-Train-6d_rep1


title: HeLa_H3K9ac_G1


title: HeLa_H3K9ac_G2M


title: Rrm3-Flag

description: Binding pattern of Rrm3 by ChIP-on-chip after arrest of cells in G2/M with Nocodazole

value: W303 MATa Rrm3-10Flag::KANMX4


title: low elevation lake water microbial gene_11

description: sample in lake BGY

value: lake at 530 m


title: Smc6-P4 Top3-Flag


title: 14_S137: dHC-Naive_rep2


title: 15_S138: dHC-Naive_rep3


title: 13_S136: dHC-Naive_rep1


title: Rrm3-Flag input


title: Smc6-Flag

description: Binding pattern of Smc6 by ChIP-on-chip after arrest of cells in G2/M with Nocodazole

value: W303 MATa RAD5+, Smc6-6xHIS-3FLAG::KANMX4


title: 11_S134: PL-Train-1hr_rep2

source_name: Prelimbic Cortex


title: Rmi1-Flag

description: Binding pattern of Rmi1 by ChIP-on-chip after arrest of cells in G2/M with Nocodazole

value: W303 MATa Rmi1-10FLAG::KANMX4


title: low elevation lake water microbial gene_9

description: sample in lake BGY


title: Rmi1-Flag input


title: 10_S133: PL-Train-1hr_rep1


title: low elevation lake water microbial gene_8

description: sample in lake BGY


title: low elevation lake water microbial gene_7

description: sample in lake BGY


title: Smc6-Flag input


title: Top3-Flag

description: Binding pattern of Top3 by ChIP-on-chip after arrest of cells in G2/M with Nocodazole

value: W303 MATa RAD5+, Top3-10FLAG::KANMX4


title: low elevation lake water microbial gene_6

description: sample in lake MJK

value: lake at 525 m


title: 1_S124: PL-Naive_rep1


title: low elevation lake water microbial gene_5

description: sample in lake MJK


title: Top3-Flag input


title: low elevation lake water microbial gene_4

description: sample in lake MJK


title: 12_S135: PL-Train-1hr_rep3


title: MB8

type: RNA

city: Toronto

first: Marc

last: Angeli

state: Ontario

address: 101 College street

department: Multi Organ Transplant

country: Canada

institute: University Health Network

hyb_protocol: standard Affymetric protocol

scan_protocol: standard Affymetric protocol

data_processing: RMA data

label: biotin

source_name: flow-sorted Kupffer cells isolated from mice 7 days after infected with S. aureus

label_protocol: standard Affymetric protocol

extract_protocol: RNA was isolated from flow-sorted Kupffer cells under the two different conditions (tacrolimus and control) using RNeasy mini kit (Qiagen). Integrity of DNA and RNA was assessed by Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA, USA). 500 nanograms of RNA were used for analysis with Affymetrix Mouse Gene 2.0 ST platform

treatment_protocol: Mice were treated with tacrolimus (1µg/g body weight) through daily intraperitoneal injections for seven days prior to infection experiments. Mice were infected by i.v. injection of 5x107 CFUs S. aureus MW2. They were closely monitored after infection and their health status assessed using an established scoring system. Based on this scoring system, mice were euthanized in case they reached their humane endpoint.

value: Tacrolimus

tag: cell type

value: flow-sorted Kupffer cells


title: low elevation lake water microbial gene_3

description: sample in lake MJK


title: MB7

value: Untreated


title: low elevation lake water microbial gene_1

description: sample in lake MJK


title: MB4


title: low elevation lake water microbial gene_2

description: sample in lake MJK


title: MB2


title: Bisulfite_sequencing_Aphid_72hrs_bioreplicate_2

status: Public on Feb 02 2021

city: Uppsala

first: German

last: Martinez

state: Uppsala

address: Almas Allé 8

department: Plant Biology

country: Sweden

institute: Swedish University of Agricultural Sciences

description:
Bisulfited genomic DNA
Bisulfite_CpG_context_Aphid_72hrs_bioreplicate_2.bedGraph.gz
Bisulfite_CHG_context_Aphid_72hrs_bioreplicate_2.bedGraph.gz
Bisulfite_CHH_context_Aphid_72hrs_bioreplicate_2.bedGraph.gz
Bisulfite_CpG_context_Aphid_72hrs_bioreplicate_2.bigWig
Bisulfite_CHG_context_Aphid_72hrs_bioreplicate_2.bigWig
Bisulfite_CHH_context_Aphid_72hrs_bioreplicate_2.bigWig

data_processing:
sRNAs, PARE and RNA libraries  were trimmed using Trim Galore. For bisulfite sequencing libraries adapters and 10 bases from 5' ends from reads were trimmed using Trimgalore.
All libraries were mapped to the Arabidopsis thaliana chromosome sequences from the TAIR10 genome version. sRNAs were mapped with bowtie allowing 2 mismatches. PARE and RNA seq libaries were mapped using bowtie2 with default parameters. For bisulfite libraries Clean reads were mapped to the reference genome TAIR 10 using bismark, allowing one mismatch per 25 nt seed. Forward and reverse reads were mapped independently. Alignments at the same position were removed using deduplicate_bismark script, including alignments of reads 1 and 2 together.Conversion rate of cytosines were obtained using bismark_methylation_extractor, the first 7 bases from 5' end and 13 from 3' end of each read were ignored.
Genome_build: TAIR10
Supplementary_files_format_and_content: Tabular files were generated using Galaxy. For RNA seq experiments reads were aligned with bowtie with default parameters. SAM files were converted to BAM and count reads per gene or TE were assesed with ht-seq counts. Count files were used to infer differential expression using DESeq2.

organism: Arabidopsis thaliana

source_name: Rosette leaves

growth_protocol: Plants were grown under standard long day conditions at 22 °C.

extract_protocol:
Total RNA was extracted using TRIzol reagent (Life Technologies) following the manufacturer instructions. mRNA for RNA and PARE sequencing was obtained by purification with the NEB mRNA isolation kit (New England Biolabs). RNA for sRNA library preparation was enriched with the mirVana miRNA Isolation Kit (Life Technologies). Genomic DNA was extracted using the DNeasy Plant Mini Kit (Qiagen).
sRNA libraries were produced using the TruSeq Small RNA Sample Preparation Kit (Illumina). PARE libraries were constructed according to Zhai et al (2014). RNA libraries were produced using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs). Bisulfite DNA libraries were produced and sequenced at Novogene (Hong Kong).
sRNA-sequencing, RNA sequencing, PARE sequencing and Bisulfite sequencing

treatment_protocol: 5-week-old plants were infested with 40 wingless M.persicae of second to fourth larval instars and covered with net cage. After 72 hours all aphids were carefully removed by brush and all Arabidopsis rosette leaves were sampled into Falcon tubes extraction bag before being placed in liquid nitrogen. Tissue was collected from all tested mutants. Each frozen plant sample was stored at -70 °C before RNA and DNA extraction.

value: Columbia 0 wild type


title: MB5


title: Bisulfite_sequencing_Aphid_72hrs_bioreplicate_1

description:
Bisulfited genomic DNA
Bisulfite_CpG_context_Aphid_72hrs_bioreplicate_1.bedGraph.gz
Bisulfite_CHG_context_Aphid_72hrs_bioreplicate_1.bedGraph.gz
Bisulfite_CHH_context_Aphid_72hrs_bioreplicate_1.bedGraph.gz
Bisulfite_CpG_context_Aphid_72hrs_bioreplicate_1.bigWig
Bisulfite_CHG_context_Aphid_72hrs_bioreplicate_1.bigWig
Bisulfite_CHH_context_Aphid_72hrs_bioreplicate_1.bigWig


title: Bisulfite_sequencing_Control_bioreplicate_1

description:
Bisulfited genomic DNA
Bisulfite_CpG_context_Control_bioreplicate_1.bedGraph.gz
Bisulfite_CHG_context_Control_bioreplicate_1.bedGraph.gz
Bisulfite_CHH_context_Control_bioreplicate_1.bedGraph.gz
Bisulfite_CpG_context_Control_bioreplicate_1.bigWig
Bisulfite_CHG_context_Control_bioreplicate_1.bigWig
Bisulfite_CHH_context_Control_bioreplicate_1.bigWig


title: NALT-Control and Treated cells

city: Houston

first: Navin

last: Varadarajan

state: Texas

address: 4722 Calhoun Rd

department: Chemical and Biomolecular Engineering

institute: University of Houston

description:
BD Mouse Immune Single-Cell Multiplexing Kit (BD Biosciences, San Jose, CA) was used.  Complete sample-tag sequence is available in "Single Cell Labeling with the BD Single-Cell Multiplexing Kits” protocol.
Cells with SampleTag03_mm are in control group. Cells with SampleTag05_mm are in treated group.

data_processing:
We uploaded and analyzed the FASTQ files on Seven Bridges website (Seven Bridges Genomics) by running the “BD Rhapsody WTA Analysis Pipeline” (BD Biosciences, San Jose, CA).
Alignment, filtering, and sample tag detection were performed by the "BD Rhapsody WTA Analysis Pipeline".
Genome_build: GRCm38
Supplementary_files_format_and_content: CSV file format, molecules per gene per cell based on RSEC
Supplementary_files_format_and_content: CSV file format, assigned Sample Tag for each putative cell

molecule: polyA RNA

source_name: Immune cells from Nasal-associated lymphoid tissue (NALT)

extract_protocol:
We harvested the NALT from the immunized animals at the time of euthanasia and converted them into single-cell suspensions. We subsequently washed the single-cell suspensions with PBS, resuspended them in PBS + 2% FBS, and added 50 nM Helix NP Blue (BioLegend, San Diego, CA) for detection of live/dead cells. We used a BD FACSMelody cell sorter (BD Biosciences, San Jose, CA) to collect live cells.
We labeled each group of NALT cells separately with the Sample-Tags from the BD Mouse Immune Single-Cell Multiplexing Kit (BD Biosciences, San Jose, CA), described in “Single Cell Labeling with the BD Single-Cell Multiplexing Kits” protocol. We then proceeded to library preparation with a mixture of ∼6000 cells (3000 cells from each group). We prepared the whole transcriptome using the BD Rhapsody System following the BD “mRNA Whole Transcriptome Analysis (WTA) and Sample Tag Library Preparation Protocol”. We assessed the quality and quantity of the final library by Agilent 4200 TapeStation system using the Agilent High Sensitivity D5000 ScreenTape (Agilent Technologies, Santa Clara, CA) and a Qubit Fluorometer using the Qubit dsDNA HS Assay, respectively. We diluted the final library to 3 nM concentration and used a HiSeq PE150 sequencer (Illumina, San Diego, CA) to perform the sequencing.
scRNA-Seq

treatment_protocol: Female, 7-9 week-old BALB/c mice were purchased from Charles River Laboratories. We immunized the mice intranasally with different formulations: (1) the control group was administrated with protein only and (2) the Trimer-STINGa group was administrated with protein and liposome-STINGa.    We purchased the STINGa, 2′-3’′cyclic guanosine monophosphate adenosine monophosphate (cGAMP) from Chemietek (Indianapolis, IN). 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), 1,2-dipalmitoyl-sn-glycero-3-phospho-(1’-rac-glycerol) (DPPG), and 1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine-N-[methoxy(polyethylene glycol)-2000] (DPPE-PEG2000) were obtained from Avanti Polar Lipids (Alabaster, AL). Cholesterol was obtained from Sigma Aldrich (St. Louis, MO).  The liposomes were composed of a molar ratio of 10:1:1:1 of DPPC, DPPG, Cholesterol (Chol), and DPPE-PEG2000. To prepare the liposomes, we mixed the lipids in CHCl3 and CH3OH, and the solution was evaporated by a vacuum rotary evaporator for approximately 80 min at 45 °C. We dried the resulting lipid thin film until all organic solvent was evaporated. We hydrated the lipid film by adding a pre-warmed cGAMP solution (0.3 mg/ml in PBS buffer at pH 7.4). The hydrated lipids were mixed at elevated temperature 65 °C for an additional 30 min, then subjected to freeze-thaw cycles. We sonicated the mixture for 60 min using a Brandson Sonicator (40 kHz). The free untrapped cGAMP was removed by Amicon Ultrafiltration units (MW cut off 10kDa). We washed the cGAMP-liposomes three times using PBS buffer. The cGAMP concentration in the filtrates was measured by Take3 Micro-Volume absorbance analyzer of Cytation 5 (BioTek) against a calibration curve of cGAMP at 260 nm. We calculated the final concentration of liposomal encapsulated cGAMP and encapsulation efficiency by subtracting the concentration of free drug in the filtrate.    We mixed the S protein monomer (4 µg) or the trimer (10 µg) with the STINGa-liposomal suspensions at room temperature to allow the adsorption of the protein onto the liposomes. The formulated vaccine was stored at 4 °C and used for up to 2 months. The average particle diameter, polydispersity index, and zeta potential were characterized by Litesizer 500 (Anton Paar) at room temperature.

value: BALB/c

value: Immune cells

value: Immunized by intranasal administration with SARS-CoV-2 spike protein "S protein" (control group), and immunized by intranasal administration with combination of the SARS-CoV-2 spike protein and adjuvant:trimeric stimulator of interferon genes agonists (Trimer-STINGa) liposomes (treated group)


title: Bisulfite_sequencing_Control_bioreplicate_2

description:
Bisulfited genomic DNA
Bisulfite_CpG_context_Control_bioreplicate_2.bedGraph.gz
Bisulfite_CHG_context_Control_bioreplicate_2.bedGraph.gz
Bisulfite_CHH_context_Control_bioreplicate_2.bedGraph.gz
Bisulfite_CpG_context_Control_bioreplicate_2.bigWig
Bisulfite_CHG_context_Control_bioreplicate_2.bigWig
Bisulfite_CHH_context_Control_bioreplicate_2.bigWig


title: CS26 non-diseased sample 264

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

state: MA

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

description: Gene expression data from non-diseased perivascular adipose tissue from patient CS26.

hyb_protocol: The labeled, fragmented DNA was hybridized to the Affymetrix Human Gene 2.0 ST Array for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix Fluidics Station 450.

scan_protocol: After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus.

data_processing: Raw Affymetrix CEL files were normalized to produce Entrez Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy Bioconductor package (version 1.58.0), using R version 3.5.1 and the Brainarray hugene20sthsentrezgcdf R package (version 23.0.0).

source_name: distal mammary adipose tissue

label_protocol: Biotin labeling was performed using the WT Plus reagent kit (Affymetrix, Santa Clara, CA) according to the manufacturer's protocol.

extract_protocol: Adipose tissue samples were collected in All Protect-Reagent (Qiagen) and stored at −80°C. mRNA was isolated using RNeasy-Lipid Tissue Mini-Kit (Qiagen).

tag: patient

tag: diagnosis

value: coronary artery disease

value: mammary adipose tissue

tag: depot

value: non-diseased


title: Dp4_4D_rep3[DNA-seq]

city: Hangzhou

first: Xiaowen

last: Shi

state: Zhejiang

address: 866 Yuhangtang Road NongshenghuanA443

department: College of Agriculture and Biotechnology

institute: Zhejiang University

description:
Dp4_22C_5
Dp4_DNA_counts_combine_RPKM.txt

data_processing:
Library strategy: DNA-Seq
mRNA-seq: Adaptors at the 3' end of the reads were trimmed using cutadapt version 1.16. Low quality reads were removed using the FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/, fastq_quality_filter -Q 33 -q 20 -p 80). mRNA reads were aligned to ERCC sequences using Bowtie 2 with default parameters. The remaining non-ERCC reads were aligned to maize chloroplast and mitochondrial genome using TopHat2 with default parameters so that the organellar transcripts are excluded for further study. The remaining reads were then mapped to the maize reference genome W22v2 along with the maize chloroplast and mitochondrial genome using TopHat2 with default parameters. Normalized read counts were generated by Cuffdiff (--raw-mapped-norm) for each comparison.
DNA-seq: Adaptor trimming and low-quality read removal were performed the same as in mRNA-seq data process. Then the remaining DNA reads were aligned to the maize reference genome W22v2 along with the maize chloroplast and mitochondrial genome using Bowtie 2 with default parameters. A custom perl script was used for extraction of uniquely mapped read counts, which were then subjected to RPKM normalization.
Genome_build: W22v2 along with the maize chloroplast and mitochondrial genome (Springer et al., 2018; Bosacchi et al., 2015; Clifton et al., 2004).
Supplementary_files_format_and_content: Tab-delimited text files including tables showing cuffdiff normalized counts and differential gene expression analyses (mRNA-seq) and tables reporting RPKM normalized counts in DNA-seq.

organism: Zea mays

source_name: Leaf tissue

growth_protocol: 45-day grown in the greenhouse

extract_protocol:
RNA extracted by mirVana™ miRNA Isolation Kit; DNA extracted by DNeasy Plant Mini Kit (QIAGEN)
RNA and DNA libraries were prepared for sequencing using standard Illumina protocols

tag: age

tag: group (aneuploidy vs. whole-ploidy)

value: aneuploidy comparison (Dp4)


title: CS20 diseased sample 205

description: Gene expression data from diseased perivascular adipose tissue from patient CS20.

source_name: aortic adipose tissue

value: aortic adipose tissue

value: diseased


title: CS26 diseased sample 265

description: Gene expression data from diseased perivascular adipose tissue from patient CS26.


title: CS14 non-diseased sample 144

description: Gene expression data from non-diseased perivascular adipose tissue from patient CS14.


title: CTRL

city: Louisville

first: Jae Yeon

last: Hwang

state: Kentucky

address: 505 S. Hancock Street

department: Division of Medical Oncology & Hematology

institute: University of Louisville

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were mapped to Ensembl transcript (release 84) then rn6 whole genome using STAR 2.5.2b with parameters  --chimSegmentMin 2 --outFilterMismatchNmax 3 --alignEndsType EndToEnd --outSAMstrandField intronMotif. Chimeric reads from STAR aligner were then examined to identify circular RNAs.
Fragments Per Kilobase of exon per Million fragments mapped (FPKM) were calculated using cuffdiff v2.2.0 with uniquely and properly mapped pairs.
Genome_build: rn6
Supplementary_files_format_and_content: an excel file includes FPKM values for each Sample.

source_name: Rat retina

extract_protocol:
RNA was extracted using the RNeasy Lipid Tissue Mini Kit (Qiagen). 350ng of total RNA were  used  for RNA-seq library preparation.
Sequencing libraries were prepared using the TrueSeq Stranded Total RNA LT Sample Prep Kit (Illumina) with Ribo-Zero Gold according to the manufacturer's instructions.

value: Retina

value: 2 months

value: Long-Evans Rat

tag: sample type

value: Control


title: HHcy_Ly6c_L2

city: Philadelphia

first: Hong

last: Wang

state: PA

address: 3500 N Broad St. MERB1060

department: CMDR

institute: Temple University Lewis Katz School of Medicine

data_processing:
The processed data were generated by mapping the raw read to the mouse reference transcriptome (mouse cDNA FASTA from ensembl, website http://uswest.ensembl.org/info/data/ftp/index.html) using Kallisto.
Supplementary_files_format_and_content: tab-delimited text files include count per million (CPM) values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Ly6Clow monocyte

extract_protocol:
Flow cytometry sorted CD11b+Ly6G-Ly6Chigh and CD11b+Ly6G-Ly6Clow cells from control and Cbs-/- WBC (200000/MC subset) were collected in 1400 μL QIAzol Lysis Reagent (Qiagen, Germantown, MD) for total RNA extraction.
Samples were quality checked on an Agilent Bioanalyzer 2100 using pico RNA chip for RNA integrity number.
Total RNA (50-100 ng/sample) were used for cDNA library construction after ribosomal cDNA depletion using Takara pico-input kit.
Pooled samples were run for sequencing analysis in duplication on Illumina NextSeq 500 (CT) and Illumina Hiseq 4000 sequencer (HHcy).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Peripheral blood monocyte

tag: genetype

value: Cbs-/-

value: 22 weeks

tag: cell subtype


title: CS10 non-diseased sample 104

description: Gene expression data from non-diseased perivascular adipose tissue from patient CS10.


title: HHcy_Ly6c_L1


title: CS9 diseased sample 95

description: Gene expression data from diseased perivascular adipose tissue from patient CS9.


title: CS10 diseased sample 105

description: Gene expression data from diseased perivascular adipose tissue from patient CS10.


title: CS9 non-diseased sample 94

description: Gene expression data from non-diseased perivascular adipose tissue from patient CS9.


title: CS20 non-diseased sample 204

description: Gene expression data from non-diseased perivascular adipose tissue from patient CS20.


title: CS14 diseased sample 145

description: Gene expression data from diseased perivascular adipose tissue from patient CS14.


title: IR12

value: Ischemic Retina


title: HHcy_Ly6c_H2

source_name: Ly6Chigh monocyte


title: HHcy_Ly6c_H1


title: MB1

value: Untreated

value: flow-sorted Kupffer cells


title: 10L18_2D_rep1[DNA-seq]

description:
10L18-38
10L18_DNA_counts_combine_RPKM.txt

value: aneuploidy comparison (10L18)


title: Tri_2X_rep3[RNA-seq]

description:
3N-7
diff_3X.txt

data_processing:
mRNA-seq: Adaptors at the 3' end of the reads were trimmed using cutadapt version 1.16. Low quality reads were removed using the FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/, fastq_quality_filter -Q 33 -q 20 -p 80). mRNA reads were aligned to ERCC sequences using Bowtie 2 with default parameters. The remaining non-ERCC reads were aligned to maize chloroplast and mitochondrial genome using TopHat2 with default parameters so that the organellar transcripts are excluded for further study. The remaining reads were then mapped to the maize reference genome W22v2 along with the maize chloroplast and mitochondrial genome using TopHat2 with default parameters. Normalized read counts were generated by Cuffdiff (--raw-mapped-norm) for each comparison.
DNA-seq: Adaptor trimming and low-quality read removal were performed the same as in mRNA-seq data process. Then the remaining DNA reads were aligned to the maize reference genome W22v2 along with the maize chloroplast and mitochondrial genome using Bowtie 2 with default parameters. A custom perl script was used for extraction of uniquely mapped read counts, which were then subjected to RPKM normalization.
Genome_build: W22v2 along with the maize chloroplast and mitochondrial genome (Springer et al., 2018; Bosacchi et al., 2015; Clifton et al., 2004).
Supplementary_files_format_and_content: Tab-delimited text files including tables showing cuffdiff normalized counts and differential gene expression analyses (mRNA-seq) and tables reporting RPKM normalized counts in DNA-seq.

value: whole-ploidy comparison(triploid)


title: 6Sa_2D_rep1[DNA-seq]

description:
6SA21
6SA_DNA_counts_combine_RPKM.txt

value: aneuploidy comparison (6Sa)


title: 9Sd_2D_rep3[RNA-seq]

description:
9Sd7
diff_9Sd.txt

value: aneuploidy comparison (TB-9Sd)


title: Tri_3X_rep2[RNA-seq]

description:
3N-3
diff_3X.txt


title: 9Sd_2D_rep4[RNA-seq]

description:
9Sd8
diff_9Sd.txt


title: Tri_3X_rep1[RNA-seq]

description:
3N-1
diff_3X.txt


title: 9Sd_2D_rep2[RNA-seq]

description:
9Sd4
diff_9Sd.txt


title: Dp4_2D_rep4[DNA-seq]

description:
Dp4_20C_7
Dp4_DNA_counts_combine_RPKM.txt

value: aneuploidy comparison (Dp4)


title: 9Sd_1D_rep1[RNA-seq]

description:
9Sd39
diff_9Sd.txt


title: 9Sd_3D_rep2[RNA-seq]

description:
9Sd23
diff_9Sd.txt


title: 9Sd_1D_rep4[RNA-seq]

description:
9Sd43
diff_9Sd.txt


title: 9Sd_3D_rep4[RNA-seq]

description:
9Sd31
diff_9Sd.txt


title: 9Sd_1D_rep2[RNA-seq]

description:
9Sd40
diff_9Sd.txt


title: 9Lc_1D_rep3[RNA-seq]

description:
9Lc43
diff_9Lc.txt

value: aneuploidy comparison (TB-9Lc)


title: 9Sd_3D_rep1[RNA-seq]

description:
9Sd22
diff_9Sd.txt


title: 6Sa_3D_rep2[DNA-seq]

description:
6SA30
6SA_DNA_counts_combine_RPKM.txt


title: 9Lc_3D_rep3[RNA-seq]

description:
9Lc3
diff_9Lc.txt


title: 9Lc_1D_rep4[RNA-seq]

description:
9Lc47
diff_9Lc.txt


title: 9Lc_3D_rep4[RNA-seq]

description:
9Lc5
diff_9Lc.txt


title: 9Lc_2D_rep4[RNA-seq]

description:
9Lc66
diff_9Lc.txt


title: 9Lc_1D_rep2[RNA-seq]

description:
9Lc40
diff_9Lc.txt


title: 9Lc_2D_rep3[RNA-seq]

description:
9Lc36
diff_9Lc.txt


title: low elevation lake water microbial gene_10

description: sample in lake BGY

value: lake at 530 m


title: 9Sd_2D_rep1[RNA-seq]

description:
9Sd1
diff_9Sd.txt


title: 9Lc_2D_rep2[RNA-seq]

description:
9Lc34
diff_9Lc.txt


title: 9Lc_3D_rep2[RNA-seq]

description:
9Lc2
diff_9Lc.txt


title: Tri_2X_rep2[RNA-seq]

description:
3N-6
diff_3X.txt


title: 9Lc_1D_rep1[RNA-seq]

description:
9Lc21
diff_9Lc.txt


title: Tri_2X_rep1[RNA-seq]

description:
3N-4
diff_3X.txt


title: 9Lc_3D_rep1[RNA-seq]

description:
9Lc1
diff_9Lc.txt


title: 8Lc_3D_rep3[RNA-seq]

description:
8Lc8
diff_8Lc.txt

value: aneuploidy comparison (TB-8Lc)


title: 8Lc_3D_rep4[RNA-seq]

description:
8Lc9
diff_8Lc.txt


title: 9Sd_1D_rep3[RNA-seq]

description:
9Sd41
diff_9Sd.txt


title: 10L18_3D_rep1[DNA-seq]

description:
10L18-76
10L18_DNA_counts_combine_RPKM.txt


title: 9Sd_3D_rep3[RNA-seq]

description:
9Sd24
diff_9Sd.txt


title: 8Lc_1D_rep4[RNA-seq]

description:
8Lc37
diff_8Lc.txt


title: 8Lc_1D_rep1[RNA-seq]

description:
8Lc28
diff_8Lc.txt


title: 8Lc_1D_rep2[RNA-seq]

description:
8Lc35
diff_8Lc.txt


title: 8Lc_1D_rep3[RNA-seq]

description:
8Lc36
diff_8Lc.txt


title: 8Lc_2D_rep2[RNA-seq]

description:
8Lc23
diff_8Lc.txt


title: 7Lb_1D_rep4[RNA-seq]

description:
7Lb27
diff_7Lb.txt

value: aneuploidy comparison (TB-7Lb)


title: 7Lb_2D_rep4[RNA-seq]

description:
7Lb6
diff_7Lb.txt


title: 7Lb_2D_rep2[RNA-seq]

description:
7Lb4
diff_7Lb.txt


title: 7Lb_2D_rep1[RNA-seq]

description:
7Lb2
diff_7Lb.txt


title: 8Lc_3D_rep2[RNA-seq]

description:
8Lc11
diff_8Lc.txt


title: 7Lb_1D_rep2[RNA-seq]

description:
7Lb21
diff_7Lb.txt


title: 8Lc_3D_rep1[RNA-seq]

description:
8Lc10
diff_8Lc.txt


title: 7Lb_2D_rep3[RNA-seq]

description:
7Lb5
diff_7Lb.txt


title: 7Lb_3D_rep2[RNA-seq]

description:
7Lb15
diff_7Lb.txt


title: 7Lb_1D_rep1[RNA-seq]

description:
7Lb19
diff_7Lb.txt


title: 8Lc_2D_rep1[RNA-seq]

description:
8Lc17
diff_8Lc.txt


title: 7Lb_3D_rep1[RNA-seq]

description:
7Lb14
diff_7Lb.txt


title: 9Lc_2D_rep1[RNA-seq]

description:
9Lc15
diff_9Lc.txt


title: 4Sa_3D_rep4[RNA-seq]

description:
4Sa7
diff_4Sa.txt

value: aneuploidy comparison (TB-4Sa)


title: 7Lb_1D_rep3[RNA-seq]

description:
7Lb24
diff_7Lb.txt


title: 4Sa_2D_rep4[RNA-seq]

description:
4Sa6
diff_4Sa.txt


title: 4Sa_1D_rep4[RNA-seq]

description:
4Sa53
diff_4Sa.txt


title: 8Lc_2D_rep4[RNA-seq]

description:
8Lc66
diff_8Lc.txt


title: 4Sa_1D_rep3[RNA-seq]

description:
4Sa52
diff_4Sa.txt


title: 4Sa_2D_rep3[RNA-seq]

description:
4Sa55
diff_4Sa.txt


title: 4Sa_1D_rep1[RNA-seq]

description:
4Sa50
diff_4Sa.txt


title: 4Sa_1D_rep2[RNA-seq]

description:
4Sa51
diff_4Sa.txt


title: 8Lc_2D_rep3[RNA-seq]

description:
8Lc24
diff_8Lc.txt


title: 7Lb_3D_rep3[RNA-seq]

description:
7Lb16
diff_7Lb.txt


title: 7Lb_3D_rep4[RNA-seq]

description:
7Lb17
diff_7Lb.txt


title: 4Sa_3D_rep3[RNA-seq]

description:
4Sa5
diff_4Sa.txt


title: 1Sb_1D_rep1[RNA-seq]

description:
1Sb14
diff_1Sb.txt

value: aneuploidy comparison (TB-1Sb)


title: 4Sa_2D_rep1[RNA-seq]

description:
4Sa34
diff_4Sa.txt


title: 4Sa_3D_rep1[RNA-seq]

description:
4Sa25
diff_4Sa.txt


title: 6Lc_1D_rep4[RNA-seq]

description:
6Lc9e
diff_6Lc.txt

value: aneuploidy comparison (TB-6Lc)


title: 1Sb_3D_rep4[RNA-seq]

description:
1Sb7
diff_1Sb.txt


title: 1Sb_1D_rep4[RNA-seq]

description:
1Sb1
diff_1Sb.txt


title: 6Lc_3D_rep4[RNA-seq]

description:
6Lc8H
diff_6Lc.txt


title: 1Sb_3D_rep1[RNA-seq]

description:
1Sb2
diff_1Sb.txt


title: 1Sb_3D_rep2[RNA-seq]

description:
1Sb4
diff_1Sb.txt


title: 1Sb_1D_rep3[RNA-seq]

description:
1Sb18
diff_1Sb.txt


title: 1Sb_1D_rep2[RNA-seq]

description:
1Sb17
diff_1Sb.txt


title: 6Lc_1D_rep3[RNA-seq]

description:
6Lc8e
diff_6Lc.txt


title: 1Sb_2D_rep2[RNA-seq]

description:
1Sb24
diff_1Sb.txt
diff_3Sb.txt
diff_5Lb.txt

value: aneuploidy comparison (TB-1Sb, 3Sb, 5Lb)


title: 4Sa_2D_rep2[RNA-seq]

description:
4Sa43
diff_4Sa.txt


title: 6Lc_3D_rep3[RNA-seq]

description:
6Lc7H
diff_6Lc.txt


title: 1Sb_2D_rep3[RNA-seq]

description:
1Sb25
diff_1Sb.txt
diff_3Sb.txt
diff_5Lb.txt


title: 1Sb_3D_rep3[RNA-seq]

description:
1Sb6
diff_1Sb.txt


title: 1Sb_2D_rep4[RNA-seq]

description:
1Sb26
diff_1Sb.txt
diff_3Sb.txt
diff_5Lb.txt


title: 1Sb_2D_rep1[RNA-seq]

description:
1Sb16
diff_1Sb.txt
diff_3Sb.txt
diff_5Lb.txt


title: 4Sa_3D_rep2[RNA-seq]

description:
4Sa42
diff_4Sa.txt


title: 6Lc_2D_rep4[RNA-seq]

description:
6Lc6e
diff_6Lc.txt


title: 6Lc_2D_rep2[RNA-seq]

description:
6Lc2e
diff_6Lc.txt


title: 6Lc_2D_rep1[RNA-seq]

description:
6Lc1e
diff_6Lc.txt


title: 6Lc_1D_rep1[RNA-seq]

description:
6Lc11e
diff_6Lc.txt


title: 6Lc_2D_rep3[RNA-seq]

description:
6Lc3e
diff_6Lc.txt


title: 6Lc_1D_rep2[RNA-seq]

description:
6Lc12e
diff_6Lc.txt


title: 6Lc_3D_rep2[RNA-seq]

description:
6Lc3H
diff_6Lc.txt


title: 6Lc_3D_rep1[RNA-seq]

description:
6Lc10H
diff_6Lc.txt


title: 5Lb_3D_rep4[RNA-seq]

description:
5Lb48
diff_5Lb.txt

value: aneuploidy comparison (TB-5Lb)


title: 5Lb_1D_rep4[RNA-seq]

description:
5Lb28
diff_5Lb.txt


title: 3Sb_1D_rep2[RNA-seq]

description:
3Sb24
diff_3Sb.txt

value: aneuploidy comparison (TB-3Sb)


title: 3Sb_1D_rep4[RNA-seq]

description:
3Sb6
diff_3Sb.txt


title: 4Lb_2D_rep3[RNA-seq]

description:
4Lb-35
diff_4Lb.txt

value: aneuploidy comparison (TB-4Lb)


title: 3Sb_3D_rep4[RNA-seq]

description:
3Sb8
diff_3Sb.txt


title: 3Sb_3D_rep1[RNA-seq]

description:
3Sb1
diff_3Sb.txt


title: 3Sb_1D_rep1[RNA-seq]

description:
3Sb21
diff_3Sb.txt


title: 3Sb_1D_rep3[RNA-seq]

description:
3Sb25
diff_3Sb.txt


title: 5Lb_1D_rep2[RNA-seq]

description:
5Lb26
diff_5Lb.txt


title: 5Lb_1D_rep1[RNA-seq]

description:
5Lb23
diff_5Lb.txt


title: 5Lb_3D_rep1[RNA-seq]

description:
5Lb17
diff_5Lb.txt


title: 5Lb_3D_rep2[RNA-seq]

description:
5Lb18
diff_5Lb.txt


title: 5Lb_1D_rep3[RNA-seq]

description:
5Lb27
diff_5Lb.txt


title: 4Lb_1D_rep3[RNA-seq]

description:
4Lb-28
diff_4Lb.txt


title: 4Lb_1D_rep4[RNA-seq]

description:
4Lb-30
diff_4Lb.txt


title: 4Lb_1D_rep1[RNA-seq]

description:
4Lb-26
diff_4Lb.txt


title: 4Lb_3D_rep4[RNA-seq]

description:
4Lb-20
diff_4Lb.txt


title: 4Lb_1D_rep2[RNA-seq]

description:
4Lb-27
diff_4Lb.txt


title: 3Sb_3D_rep2[RNA-seq]

description:
3Sb2
diff_3Sb.txt


title: 4Lb_2D_rep4[RNA-seq]

description:
4Lb-37
diff_4Lb.txt


title: 4Lb_3D_rep3[RNA-seq]

description:
4Lb-19
diff_4Lb.txt


title: 5Lb_3D_rep3[RNA-seq]

description:
5Lb1
diff_5Lb.txt


title: 4Lb_2D_rep1[RNA-seq]

description:
4Lb-24
diff_4Lb.txt


title: 4Lb_3D_rep1[RNA-seq]

description:
4Lb-15
diff_4Lb.txt


title: 3La_2D_rep4[RNA-seq]

description:
3La-9
diff_3La.txt

value: aneuploidy comparison (TB-3La)


title: 4Lb_2D_rep2[RNA-seq]

description:
4Lb-25
diff_4Lb.txt


title: 4Lb_3D_rep2[RNA-seq]

description:
4Lb-17
diff_4Lb.txt


title: 3La_2D_rep3[RNA-seq]

description:
3La-8
diff_3La.txt


title: 3La_2D_rep2[RNA-seq]

description:
3La-5
diff_3La.txt


title: 3La_1D_rep4[RNA-seq]

description:
3La-36
diff_3La.txt


title: 3Sb_3D_rep3[RNA-seq]

description:
3Sb5
diff_3Sb.txt


title: 3La_1D_rep3[RNA-seq]

description:
3La-30
diff_3La.txt


title: 3La_3D_rep3[RNA-seq]

description:
3La-22
diff_3La.txt


title: 3La_1D_rep2[RNA-seq]

description:
3La-17
diff_3La.txt


title: 3La_3D_rep1[RNA-seq]

description:
3La-19
diff_3La.txt


title: 3La_3D_rep2[RNA-seq]

description:
3La-21
diff_3La.txt


title: 3La_2D_rep1[RNA-seq]

description:
3La-1
diff_3La.txt


title: 10L18_3D_rep3[RNA-seq]

description:
10L18-76
diff_10L18.txt

value: aneuploidy comparison (TB-10L18)


title: 10L18_2D_rep4[RNA-seq]

description:
10L18-38
diff_10L18.txt


title: 10L18_2D_rep3[RNA-seq]

description:
10L18-30
diff_10L18.txt


title: 3La_3D_rep4[RNA-seq]

description:
3La-24
diff_3La.txt


title: 10L18_2D_rep2[RNA-seq]

description:
10L18-1
diff_10L18.txt


title: 10L18_3D_rep1[RNA-seq]

description:
10L18-59
diff_10L18.txt


title: 10L18_4D_rep2[RNA-seq]

description:
10L18-26
diff_10L18.txt


title: 10L18_3D_rep2[RNA-seq]

description:
10L18-74
diff_10L18.txt


title: 10L18_1D_rep4[RNA-seq]

description:
10L18-106
diff_10L18.txt


title: 3La_1D_rep1[RNA-seq]

description:
3La-16
diff_3La.txt


title: 10L18_4D_rep4[RNA-seq]

description:
10L18-34
diff_10L18.txt


title: 10L18_4D_rep1[RNA-seq]

description:
10L18-13
diff_10L18.txt


title: 10L18_2D_rep1[RNA-seq]

description:
10L18-10
diff_10L18.txt


title: 10L18_1D_rep3[RNA-seq]

description:
10L18-103
diff_10L18.txt


title: 10L18_1D_rep1[RNA-seq]

description:
10L18-101
diff_10L18.txt


title: 10L18_1D_rep2[RNA-seq]

description:
10L18-102
diff_10L18.txt


title: tetra_4X_rep3[RNA-seq]

description:
Z47
diff_4X.txt

value: whole-ploidy comparison(tetraploid)


title: tetra_2X_rep4[RNA-seq]

description:
Z63
diff_4X.txt


title: tetra_2X_rep2[RNA-seq]

description:
Z61
diff_4X.txt


title: tetra_4X_rep2[RNA-seq]

description:
Z38
diff_4X.txt


title: tetra_4X_rep4[RNA-seq]

description:
Z54
diff_4X.txt


title: 10L18_3D_rep4[RNA-seq]

description:
10L18-80
diff_10L18.txt


title: tetra_4X_rep1[RNA-seq]

description:
Z30
diff_4X.txt


title: ha_1X_rep2[RNA-seq]

description:
H22
diff_1X.txt

value: whole-ploidy comparison(haploid)


title: ha_1X_rep3[RNA-seq]

description:
H23
diff_1X.txt


title: ha_1X_rep4[RNA-seq]

description:
H25
diff_1X.txt


title: ha_2X_rep3[RNA-seq]

description:
D25
diff_1X.txt


title: ha_1X_rep1[RNA-seq]

description:
H21
diff_1X.txt


title: 5Sc_2D_rep4[RNA-seq]

description:
5SCS6
diff_5Sc.txt

value: aneuploidy comparison (TB-5Sc)


title: tetra_2X_rep1[RNA-seq]

description:
Z14
diff_4X.txt


title: ha_2X_rep2[RNA-seq]

description:
D22
diff_1X.txt


title: tetra_2X_rep3[RNA-seq]

description:
Z62
diff_4X.txt


title: 10L18_4D_rep3[RNA-seq]

description:
10L18-32
diff_10L18.txt


title: 5Sc_3D_rep4[RNA-seq]

description:
5SCS8
diff_5Sc.txt


title: 5Sc_3D_rep3[RNA-seq]

description:
5SCS42
diff_5Sc.txt


title: 5Sc_1D_rep4[RNA-seq]

description:
5SCS5
diff_5Sc.txt


title: 5Sc_4D_rep4[RNA-seq]

description:
5SCS38
diff_5Sc.txt


title: ha_2X_rep1[RNA-seq]

description:
D21
diff_1X.txt


title: 5Sc_4D_rep2[RNA-seq]

description:
5SCS30
diff_5Sc.txt


title: 5Sc_4D_rep1[RNA-seq]

description:
5SCS20
diff_5Sc.txt


title: 5Sc_3D_rep2[RNA-seq]

description:
5SCS25
diff_5Sc.txt


title: 5Sc_2D_rep3[RNA-seq]

description:
5SCS4
diff_5Sc.txt


title: 5Sc_3D_rep1[RNA-seq]

description:
5SCS24
diff_5Sc.txt


title: 5Sc_1D_rep3[RNA-seq]

description:
5SCS18
diff_5Sc.txt


title: 5Sc_1D_rep2[RNA-seq]

description:
5SCS11
diff_5Sc.txt


title: 5Sc_2D_rep1[RNA-seq]

description:
5SCS17
diff_5Sc.txt


title: 6Sa_4D_rep4[RNA-seq]

description:
6SA61
diff_6Sa.txt

value: aneuploidy comparison (TB-6Sa)


title: 5Sc_1D_rep1[RNA-seq]

description:
5SCS10
diff_5Sc.txt


title: 6Sa_4D_rep3[RNA-seq]

description:
6SA50
diff_6Sa.txt


title: ha_2X_rep4[RNA-seq]

description:
D26
diff_1X.txt


title: 6Sa_3D_rep3[RNA-seq]

description:
6SA33
diff_6Sa.txt


title: 5Sc_2D_rep2[RNA-seq]

description:
5SCS3
diff_5Sc.txt


title: 5Sc_4D_rep3[RNA-seq]

description:
5SCS34
diff_5Sc.txt


title: 6Sa_4D_rep1[RNA-seq]

description:
6SA25
diff_6Sa.txt


title: 6Sa_4D_rep2[RNA-seq]

description:
6SA32
diff_6Sa.txt


title: 6Sa_3D_rep1[RNA-seq]

description:
6SA29
diff_6Sa.txt


title: 6Sa_2D_rep1[RNA-seq]

description:
6SA21
diff_6Sa.txt


title: 6Sa_3D_rep2[RNA-seq]

description:
6SA30
diff_6Sa.txt


title: 6Sa_2D_rep2[RNA-seq]

description:
6SA22
diff_6Sa.txt


title: 6Sa_2D_rep4[RNA-seq]

description:
6SA24
diff_6Sa.txt


title: Starch4h_1

city: Tianjin

first: Jingen

address: Xiqi Dao 32, Tianjin Airport Economic Area

institute: Tianjin institute of industrial biotechnology,Chinses Academy of Sciences

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence with NGSQCToolkit (v2.3).
Clean reads were mapped to Myceliophthora thermophila ATCC 42464 genome using Tophat (version 2.0.8b) with parameters -i 10 -g 1 --segment-length 24 --b2-very-sensitive --no-convert-bam --library-type fr-unstranded.
The counts of reads uniquely mapped to only one gene for each gene were calculated by HTseq-count( v0.5.4p2).
Genome_build: Myceliophthora thermophila ATCC 42464(https://genome.jgi.doe.gov/Spoth2/Spoth2.home.html)
Supplementary_files_format_and_content: Excel file including Reads count and RPKM for each sample.

organism: Thermothelomyces thermophilus

source_name: Myceliophthora thermophila ATCC 42464_starch

growth_protocol: M. thermophila strains were inoculated into 1×Vogel’s salt with 2% glucose and cultivated at 45 °C for 18h. Mycelia were collected and washed three times with 1×Vogel’s salt, and then transferred into the medium with 2% starch or Avicel as the carbon source for an additional 4 h of cultivation.

extract_protocol:
Mycelia were harvested by vacuum filtration with Whatman filter paper, frozen immediately in liquid nitrogen. Total RNA from frozen samples was isolated using TRIzol reagent and an additional clean-up was performed for DNA degradation using the RNeasy mini kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain


title: 6Sa_2D_rep3[RNA-seq]

description:
6SA23
diff_6Sa.txt


title: H3K4me3_ChIPSeq_rep2

first: Jingping

last: Yang

state: Jiangsu

address: 22 Hankou Road

department: Medical School

institute: Nanjing University

data_processing:
ChIPseq: The adaptors were trimmed with cutadapt, the trimmed reads were aligned to the hg19 using Bowtie2 with default parameters, and uniquely mapped reads were used for peak calling with MACS2. HiChIP: HiChIP paired-end reads for each replication were aligned to hg19 genomes using the HiC-Pro pipeline with default parameters. The output from HiC-Pro for replicates were combined and used for loop calling with Hichipper. RNAseq: The reads were mapped to hg38 using HISAT2 with default parameters. Transcript assembly was performed using Stringtie. Expression level estimation was reported as fragments per kilobase of transcript sequence per million mapped fragments (FPKM).
Genome_build: ChIPseq and HiChIP:hg19,RNAseq:hg38

source_name: kidney tubule HK2 cells

growth_protocol: HK2 cell line  maintained in DMEM-F12 medium with 10% FBS (Gibco), 1% penicillin-streptomycin and 0.05% DMSO at 37°C in a 5% (v/v) CO2 humidified incubator.

extract_protocol:
Genomic DNA was extracted with DNA Clean & Concentrator kit(ZYMO).
Libraries were constructed according to the Illumina instruction. DNA sample was first end-repaired by NEBNext End Repair Enzyme Mix. Then used T4 ligase buffer to add adapters.

treatment_protocol: The harvested cells were fixed with 1% formaldehyde for ChIPseq and HiChIP. MboI restriction enzyme was used to digest chromatin in HiChIP. Cells were harvested in Trizol (Invitrogen) for  RNAseq.

value: Proximal tubular epithelial cells

tag: chip antibody

value: H3K4me3, Abcam, ab8580


title: Glucose4h_1

source_name: Myceliophthora thermophila ATCC 42464_glucose


title: Glucose4h_2


title: NoCarbon4h_1

source_name: Myceliophthora thermophila ATCC 42464_carbon starvation


title: NoCarbon4h_2


title: SARS-CoV-2-infected and remdesivir-treated 3

city: Bethesda

first: Eytan

last: Ruppin

address: 9000 Rockville Pike

institute: National Institutes of Health

description: SARS-CoV-2 infection with remdesivir

data_processing:
Reads of the samples were trimmed for adapters and low-quality bases using Cutadapt before alignment with the reference genome and the annotated transcripts using STAR (v2.7.3a).
The gene expression quantification analysis was performed for all samples using STAR/RSEM tools (v1.3.2).
Genome_build: Chlorocebus sabaeus genome (https://useast.ensembl.org/Chlorocebus_sabaeus/Info/Annotation); SARS-CoV-2 genome (https://www.ncbi.nlm.nih.gov/nuccore/NC_045512).
Supplementary_files_format_and_content: The RSEM result for each sample is given in a separate file, containing the expected read count, TPM and FPKM across genes and transcripts

organism: Chlorocebus sabaeus

source_name: SARS-CoV-2-infected Vero E6 cells

growth_protocol: Vero E6 cells were maintained in Dulbecco’s modified eagle medium (DMEM, Gibco) supplemented with 10 % heat-inactivated fetal bovine serum (FBS, Gibco), 50 U/mL penicillin, 50 μg/mL streptomycin, 1 mM sodium pyruvate (Gibco), 10 mM 4-(2-hydroxyethyl)-1- piperazineethanesulfonic acid (HEPES, Gibco), and 1X MEM non-essential amino acids solution (Gibco).

extract_protocol:
Cells were harvested, and total RNA was extracted using the Qiagen RNeasy Plus Mini Kit. The quality of the extracted RNA was assessed with the Agilent 2100 Bioanalyzer.
Libraries were prepared on total RNA following ribosome RNA depletion with standard protocol according to Illumina.

treatment_protocol: 500,000 Vero E6 cells were seeded in 6-well plates. The following day, the cell medium was replaced with fresh medium supplemented with either DMSO or 1 µM remdesivir (Adooq Bioscience), and cells were either mock-infected or infected with SARS-CoV-2 USA-WA1/2020 (MOI=0.3) for 24 hours.

value: Vero E6 cells

tag: infection

tag: time point

tag: agent

value: Remdesivier

tag: drug concentration


title: H3K27ac_ChIPSeq_rep2

value: H3K27ac(Abcam, ab4729)


title: Starch4h_2


title: 6Sa_3D_rep4[RNA-seq]

description:
6SA38
diff_6Sa.txt


title: SARS-CoV-2-infected and remdesivir-treated 1

description: SARS-CoV-2 infection with remdesivir


title: SARS-CoV-2-infected 3

description: SARS-CoV-2 infection with DMSO

value: DMSO


title: SARS-CoV-2-infected 1

description: SARS-CoV-2 infection with DMSO


title: SARS-CoV-2-infected and remdesivir-treated 2

description: SARS-CoV-2 infection with remdesivir


title: Remdesivier-treated 2

description: Control (mock infection) with remdesivir

source_name: Vero E6 cells

value: Control (mock infection)


title: Remdesivier-treated 1


title: SARS-CoV-2-infected 2

description: SARS-CoV-2 infection with DMSO


title: Remdesivier-treated 3


title: Control (mock-infected), DMSO 3

description: Control (mock infection) with DMSO


title: Control (mock-infected), DMSO 2

description: Control (mock infection) with DMSO


title: Control (mock-infected), DMSO 1

description: Control (mock infection) with DMSO


title: H3K27me3_ChIPSeq_rep2

value: H3K27me3, diagenode, C15410069


title: 3hpi-rep1

city: Hong Kong SAR

first: Xiangzhi

last: Meng

address: 21 Sassoon Road

country: Hong Kong

institute: The University of Hong Kong

description:
CFZ_SARS2_rpkm.csv
3h-virus-1

data_processing:
Fastq files from RNA-seq were quality examined by FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Reads were processed by cutadapt to remove reads with low quality and to trim adapters.
Trimmed reads were aligned to hg38 reference genome using Tophat2
Reads assigned to each gene were counted by featureCounts  with refseq gene sets as references.
Genes without at least 1 read mapped on average in each sample were considered undetectable and were filtered out. Read counts were normalized by Trimmed Mean of M-values (TMM) method and RPKM of each gene was calculated using R package edgeR
Genome_build: hg38 for Caco-2 cells; MesAur1.0 for hamster lung tissues
Supplementary_files_format_and_content: CSV files include RPKM values for each sample

organism:
Homo sapiens
Severe acute respiratory syndrome coronavirus 2

growth_protocol: Caco-2 cells were maintained in DMEM culture medium supplemented with 20% heat-inactivated FBS, 50 U/ml penicillin and 50 µg/ml streptomycin

extract_protocol:
Qiagen RNeasy Mini Kit
cDNA libraries were prepared by KAPA mRNA HyperPrep Kit.1 ug of total RNA was used as starting material. Manufacturer’s protocol was followed.

treatment_protocol: For the experiment on Caco-2 cells, cells were infected with/without SARS-CoV-2 virus at MOI=4 for 1 hour, followed by incubation with fresh medium with 10uM clofazimine or DMSO control. After 3 or 6 hours, cells were collected for RNA extraction. For the experiment on golden hamsters, we delivered clofazimine through oral route utilizing corn oil as vehicle. An equivalent hamster dose of 25 mg/kg/day was converted based on body surface area. Prophylactic treatment through oral administration of clofazimine was given at -3, -2 and -1 dpi (25 mg/kg/day), followed by virus challenge at 0dpi through intranasal route (10^5 PFU/hamster); therapeutic post-exposure administration of clofazimine was performed at 1, 2, and 3 dpi applying the same drug dosage and virus inoculum. Lung tissues were collected at 4dpi for prophylactic and therapeutic groups. For uninfected group, clofazimine was given for 3 consecutive days and lung tissues were collected on day 4.

tag: tissue

value: cell line

tag: infection status

value: infected with SARS-CoV-2

tag: clofazimine treatment


title: 3hpi.CFZ-rep1

description:
CFZ_SARS2_rpkm.csv
3h-virusdrug-1

tag: cell line

value: 3 hours clofazimine


title: 3hpi-rep2

description:
CFZ_SARS2_rpkm.csv
3h-virus-2


title: 6hpi-rep3

description:
CFZ_SARS2_rpkm.csv
6h-virus-3


title: 6hpi.CFZ-rep1

description:
CFZ_SARS2_rpkm.csv
6h-virusdrug-1

value: 6 hours clofazimine


title: 6hpi-rep1

description:
CFZ_SARS2_rpkm.csv
6h-virus-1


title: 6hpi-rep2

description:
CFZ_SARS2_rpkm.csv
6h-virus-2


title: 3hpi-rep3

description:
CFZ_SARS2_rpkm.csv
3h-virus-3


title: hamster.therapeutic.CFZ.rep2

description:
hamster_SARS2_rpkm.csv
Ther-drug-3

organism:
Mesocricetus auratus
Severe acute respiratory syndrome coronavirus 2

source_name: tissue

value: lung tissue

value: post-exposure treatment with clofazimine


title: 3hpi.CFZ-rep2

description:
CFZ_SARS2_rpkm.csv
3h-virusdrug-2


title: 6hpi.CFZ-rep2

description:
CFZ_SARS2_rpkm.csv
6h-virusdrug-2


title: hamster.therapeutic.CFZ.rep1

description:
hamster_SARS2_rpkm.csv
Ther-drug-1


title: hamster.therapeutic.vehicle.rep2

description:
hamster_SARS2_rpkm.csv
Ther-DMSO-2


title: hamster.prophylactic.CFZ.rep3

description:
hamster_SARS2_rpkm.csv
Pro-drug-4

value: prophylatic treatment with clofazimine


title: hamster.prophylactic.CFZ.rep2

description:
hamster_SARS2_rpkm.csv
Pro-drug-2


title: hamster.therapeutic.vehicle.rep3

description:
hamster_SARS2_rpkm.csv
Ther-DMSO-4


title: hamster.therapeutic.vehicle.rep1

description:
hamster_SARS2_rpkm.csv
Ther-DMSO-1


title: hamster.prophylactic.vehicle.rep2

description:
hamster_SARS2_rpkm.csv
Pro-DMSO-3


title: hamster.prophylactic.vehicle.rep3

description:
hamster_SARS2_rpkm.csv
Pro-DMSO-4


title: hamster.prophylactic.CFZ.rep1

description:
hamster_SARS2_rpkm.csv
Pro-drug-1


title: 6hpi.CFZ-rep3

description:
CFZ_SARS2_rpkm.csv
6h-virusdrug-3


title: 3hpi.CFZ-rep3

description:
CFZ_SARS2_rpkm.csv
3h-virusdrug-3


title: hamster.prophylactic.vehicle.rep1

description:
hamster_SARS2_rpkm.csv
Pro-DMSO-1


title: UTA39 (∆xrrA) Rep 3

first: Theresa

middle: Marie

last: Koehler

address: 6431 Fannin Street, MSB 1.508

department: Microbiology and Molecular Genetics

institute: McGovern Medical School

description:
Two paired-end sequencing runs were performed
UTA37vsUTA39_CuffDiff.txt

data_processing:
Illumina RTA v2 software was used for base calling.
The quality of the reads was assessed using FastQC (Andrews, 2010).
Low quality bases and Illumina Adapter sequences were removed using Trim Galore! Galaxy Version 0.6.3 (Krueger, 2012).
A second round of FastQC analysis was done to verify the removal of low-quality bases and Illumina Adapter sequences.
Trimmed reads were aligned to the complete Ames Ancestor genome (NCBI accession numbers AE017334.2 for chromosome, AE017336.2 for pXO1, and AE017335.3 for pXO2) using the GCF_000008445.1_ASM844v1_genomic.fna FASTA file obtained from the NCBI website. Bowtie2 Galaxy Version 2.3.4.3 (Langmead & Salzberg, 2012) with default parameters was used to align the paired-end reads to the genome.
BAM files obtained from mapped reads from each of the two sequencing runs were pooled using Convert, Merge, Randomize Galaxy Version 2.4.0.0 (Barnett et al., 2011), resulting in a single BAM file per triplicate per strain.
The Cufflinks/Cuffcompare/CuffDiff pipeline (Trapnell et al., 2010) was used for transcript assembly using the GCF_000008445.1_ASM844v1_genomic.gff reference annotation file from NCBI, count the number of reads mapped to each annotated transcript, and calculate differential transcript expression between the strains. The Fragments Per Kilobase of transcript per Million mapped reads (FPKM) values per assembled transcript were obtained and differential expression was calculated as the log2 (fold-change) in FPKM values between the parent strain and each sRNA-null strain, with an adjusted p-value cut-off for significance of 0.01.
BamCoverage Galaxy Version 3.3.2.0.0 (Ramírez et al., 2016) was used to create BigWig files for visualization of read coverage over the genome on Integrative Genomics Viewer (IGV) (Thorvaldsdóttir et al., 2013).
Genome_build: GCF_000008445.1_ASM844v1
Supplementary_files_format_and_content: Tab-delimited text files showing log2(fold-change) in expression between the parent strain and each sRNA mutant.
Supplementary_files_format_and_content: BigWig files showing read coverage across the genome per DNA strand (F and R) per strain.

organism: Bacillus anthracis

source_name: B. anthracis cell culture

growth_protocol: B. anthracis strains were cultured in 25 ml of casamino acids medium supplemented with 0.1% w/v of glucose at a starting OD600 of 0.08 in 5% atmospheric CO2 (CA-CO2). All cultures were incubated with shaking at 200 r.p.m.

extract_protocol:
At early stationary phase (OD600 = 1.0 – 1.5), cells from 10-ml samples were centrifuged at 10,000 x g for 15 min. Total RNA was extracted using two consecutive treatments of saturated acid phenol (pH 4.3), followed by treatment with chloroform. To precipitate the RNA from the final aqueous phase, 20 ng of glycogen, one-tenth volume of 3 M sodium acetate, and 3 volumes of 100% ice-cold ethanol were added to the samples. RNA was precipitated at -80◦C for one hour, followed by centrifugation. The resulting RNA pellet was washed twice with ice-cold 75% ethanol before resuspending in DEPC-treated sterile water.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Ames ancestor

tag: genotype

value: xrrA-null


title: UTA39 (∆xrrA) Rep 2


title: UTA41 (∆xrrA∆xrrB) Rep 1

description:
Two paired-end sequencing runs were performed
UTA37vsUTA41_CuffDiff.txt

value: xrrA-null, xrrB-null


title: hamster.therapeutic.CFZ.rep3

description:
hamster_SARS2_rpkm.csv
Ther-drug-4


title: UTA41 (∆xrrA∆xrrB) Rep 3


title: UTA39 (∆xrrA) Rep 1


title: UTA37 (Parent) Rep 2

description: Two paired-end sequencing runs were performed

value: Parent


title: Control urine

first: Katalin

last: Susztak

state: Pennsylvania

address: 3400 Civic Center Blvd

department: Department of Medicine

institute: University of Pennsylvania

description: Urine samples from individuals devoid of Diabetic Kidney Disease

data_processing:
FASTQ files from each 10X single cell run were processed by Cell Ranger v3.0.2 (10X Geonmics).
Genome_build: Human genome reference GRCh38
Supplementary_files_format_and_content: Count matrix for all genes and all cells after quality control filtering

source_name: urine

extract_protocol:
All steps were performed on ice or at 4 degree Celsius. The urine volume was measured and the sample was transferred into a 50 ml conical tube and centrifuged at 1000 rpm for 5 minutes. The supernatant was carefully removed leaving about 1ml in the tube. Next, the cells were suspended in 1X D-PBS and centrifuged at 1000 rpm for 5 minutes. This process was repeated twice. The pelleted cells were suspended in 1 ml of 1X D-PBS and passed through a 40um cell strainer. After centrifugation at 1,000 RPM for 5 mins, cell pellet was resuspended in appropriate volume of 1X D-PBS (resuspension volume was approximated based on the pellet size). Cell number and viability were analyzed using Countess Auto Counter (Invitrogen, C10227).
cDNA libraries were prepared according to the manufacturer’s protocol (Single Cell 3’ Reagent Kits v3, 10x Genomics, USA).

tag: disease

value: NO Diabetic Kidney Disease

tag: subject id

value: healthy control

value: urine

tag: barcode suffix


title: UTA38 (∆xrrB) Rep 2

description:
Two paired-end sequencing runs were performed
UTA37vsUTA38_CuffDiff.txt

value: xrrB-null


title: 24hr_urine_patient4_visit1

description: 24h samples refer to 24-hour urine samples. A 24-hour urine collection is done by collecting urine from individuals in a special container over a full 24-hour period.

value: Diabetic Kidney Disease

value: patient 4

tag: barcode prefix


title: UTA37 (Parent) Rep 3


title: UTA41 (∆xrrA∆xrrB) Rep 2


title: UTA38 (∆xrrB) Rep 3


title: UTA38 (∆xrrB) Rep 1


title: 24hr_urine_patient5_visit1

value: patient 5


title: Spot_urine_patient4_visit1

description: Spot samples refer to spot urine samples obtained from the sampling of a single untimed urine specimen, voided spontaneously by the patient.


title: 24hr_urine_patient4_visit2


title: Spot_urine_patient4_visit2


title: 24hr_urine_patient3_visit2

value: patient 3


title: 24hr_urine_patient3_visit1


title: Spot_urine_patient3_visit2


title: Spot_urine_patient3_visit1


title: 24hr_urine_patient2_visit1

value: patient 2


title: 24hr_urine_patient2_visit2


title: Spot_urine_patient2_visit2


title: Spot_urine_patient2_visit1


title: UTA37 (Parent) Rep 1


title: 24hr_urine_patient1_visit2


title: 24hr_urine_patient1_visit1


title: Spot_urine_patient1_visit1


title: CAG-05 [W-05]

city: Changchun

first: Yang

last: Chao

address: Xiantai Street

institute: China-Japan Union Hospital of Jilin University

data_processing:
Paired-end reads were harvested from Illumina HiSeq 4000 sequencer
The high quality reads were aligned to the human reference genome (UCSC hg19) with hisat2 software (v2.0.4)
guided by the Ensembl gtf gene annotation file, cuffdiff software (v2.2.1, part of cufflinks) was used to get the FPKM as the expression profiles of LncRNA and mRNA
Genome_build: hg19
Supplementary_files_format_and_content: FPKM as the expression profiles of LncRNA and mRNA

source_name: CAG_gastric mucosa

extract_protocol:
Briefly, total RNA was used for removing the rRNAs using Ribo-Zero rRNA Removal Kits (Illumina, USA) following the manufacturer's instructions.
RNA libraries were constructed by using rRNA-depleted RNAs with TruSeq Stranded Total RNA Library Prep Kit (Illumina, USA) according to the manufacturer’s instructions.

tag: subject status

value: chronic atrophic gastritis (CAG)

value: Gastric mucosa


title: CAG-04 [W-04]


title: CAG-03 [W-03]


title: CAG-02 [W-02]


title: LPS_OBF1KO_day3_rep1

city: Basel

first: Shuang

last: Song

state: Basel

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

data_processing:
Sequencing reads were aligned using qAlign from the Bioconductor package QuasR [Gaidatzis et al 2015] (package version 1.16.0) to the mouse genome (mm9) with default parameters except for splicedAlignment = TRUE. Alignments were quantified with qCount from the Bioconductor package QuasR [Gaidatzis et al 2015] (package version 1.16.0) for known UCSC genes obtained from the TxDb.Mmusculus.UCSC.mm9.knownGene package (package version 3.2.2) using default parameters.
Genome_build: mm9
Supplementary_files_format_and_content: txt file containing the count table

growth_protocol: Mature B cells were purified from spleens by MACS column using anti-mouse CD19 Microbeads (Miltenyi Biotec). Single cell suspension was prepared by smashing the spleen, and then washing in freshly prepared MACS buffer (0.5% BSA and 2mM EDTA in PBS) (20ml for two spleens) three times. After washing, cell concentration was adjusted to 108 cells/ml. To label the B cells for MACS LS column separation, 10 μl CD19 beads was added to every 107 cells (100 μl), and the mixture was incubated at 4 ℃ for 15min. The anti-CD19-labeled spleen cells were further washed with MACS buffer and then applied to MACS LS column. CD19+ mature B cells were purified according to the standard protocol of Miltenyi Biotec LS column (Cat# 130-042-401). Purified CD19+ mature B cells were subjected to in vitro culture with LPS at 2 × 106 cells/ml.

extract_protocol:
QIAGEN Rneasy Micro kit
The Illumina TruSeq Stranded mRNA protocol was used for library preparation for next generation sequencing.

treatment_protocol: For LPS stimulation, primary spleen mature B cells were cultured in RPMI1640 medium (10% FBS, 50 μm 2-mercaptoethanol (AppliChem), 50 μg/ml LPS (Sigma), 2 mM Glutamine, 1% ITS (Sigma), 1% MEM (Sigma), 1mM Sodium Pyruvate (ThermoFisher Scientific)), medium was changed every day. For anti-CD40 and Interleukin 4 (IL4), primary spleen mature B cells were cultured in RPMI1640 medium (10% FBS, 50 μm 2-mercaptoethanol (AppliChem), 1 ug/ml anti-murine-CD40 + 20 ng/ml IL4, 2 mM Glutamine, 1% ITS (Sigma), 1% MEM (Sigma), 1 mM Sodium Pyruvate (ThermoFisher Scientific)), medium was changed every day. For each stimulation, B cells were harvested after 72 hours.

value: CD19+ B cells

value: OBF1 knockout

tag: mouse strain


title: LPS_WT_day3_rep1

value: wild type


title: LPS_WT_day3_rep2


title: LPS_OBF1KO_day3_rep3


title: WT_for_PU1KO_LPS_r5


title: Small intestine neuroendocrine tumor (SINET), 21

city: Gothenburg

first: Yvonne

last: Arvidsson

address: Box 425

department: Biomedicin

institute: University of Gothenburg

hyb_protocol: SureTag DNA Labeling Kit; Agilent Technologies Inc

scan_protocol: Arrays were scanned using the Agilent G2565BA Microarray Scanner

data_processing: Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

source_name: Tumor

extract_protocol: Genomic DNA was isolated from the biopsies using the DNeasy® Blood and Tissue kit (Qiagen GmbH, Hilden, Germany).

tag: case

tag: gender male (m), female (f)

value: F

value: primary tumor

source_name: Human Reference DNA female (Agilent)

tag: gender reference

value: Male (M), Female (F):F


title: Small intestine neuroendocrine tumor (SINET), 23

label_protocol: SureTag DNA Labeling Kit; Agilent Technologies Inc


title: Small intestine neuroendocrine tumor (SINET), 20


title: WT_for_PU1KO_LPS_r4


title: Small intestine neuroendocrine tumor (SINET), 18


title: WT_for_PU1KO_LPS_r3


title: CAG-01 [W-01]


title: CNAG-05 [F-05]

source_name: CNAG_gastric mucosa

value: chronic nonatrophic gastritis (CNAG)


title: LPS_OBF1KO_day3_rep2


title: Spot_urine_patient1_visit2


title: CNAG-04 [F-04]


title: WT_for_PU1KO_LPS_r2


title: Small intestine neuroendocrine tumor (SINET), 17

value: M

source_name: Human Reference DNA male (Agilent)

value: Male (M), Female (F):M


title: Small intestine neuroendocrine tumor (SINET), 24


title: Small intestine neuroendocrine tumor (SINET), 19


title: Small intestine neuroendocrine tumor (SINET), 22


title: WT_for_PU1KO_LPS_r1


title: LPS_PU1KO_day3_rep5

value: PU1 knockout


title: Small intestine neuroendocrine tumor (SINET), 16


title: CNAG-02 [F-02]


title: LPS_WT_day3_rep3


title: LPS_PU1KO_day3_rep3


title: mouse GC OBF1 rep1

description: mouse GC OBF1 rep1

data_processing:
ChIP-seq sequencing reads were aligned to the mouse genome (mm9) using the qAlign function, which internally uses Bowtie [Langmead et al 2009], from Bioconductor package QuasR [Gaidatzis et al 2015] (package version 1.16.0). Alignments were shifted by 60 bases, corresponding to an estimated fragment length of 120 bp. Peaks of OBF1 and H3K27ac were called in control sample (input) with MACS2 [Zhang et al 2008] (software version 2.1.1) using default parameters. Reads were counted in each peak region using the qCount function in QuasR (with shift set to 60). The read counts per sample were normalized to the mean total mapped number of reads across all samples. CUT&RUN were aligned to the human genome (hg19) using  Bowtie2. Bigwig files were generated using bamCoverage in deepTools [Fidel Ramírez et al 2014].
Genome_build: mm9 / hg19
Supplementary_files_format_and_content: bigwig files containing the enrichment of IP over input

source_name: mouse GC OBF1 rep1

growth_protocol: Burkitt’s lymphoma and DLBCL cell lines (Raji and SUDHL4) were cultured in T75 flasks in RPMI1640 medium (10% FBS, 50 μm 2-mercaptoethanol). B Lymphoma cells were passaged every two to three days.

extract_protocol:
For GC induction: mice were injected i.p. with 100ul 10% SRBC (PBS), and sacrificed at day 7. GC B cells were isolated using PNA beads by MACS. Bio-ChIP-seq was carried out with 4M cells crosslinked with 1% formaldehyde. For primary human GC B cells: MNCs were isolated from tonsils after tonsillectomy and crosslinked with 1% formaldehyde, and subjected to CUT&RUN. GC B cells were purified by FACS under gate CD19+CD38+IgD-. For GC-derived lymphoma cells: cells were crosslinked with 1% formaldehyde, and subjected to CUT&RUN.
libraries were prepared using NEB Ultra II DNA Library Prep Kit for Illumina (E7645S) following the manufacturers instructions

tag: clone

value: Wild type PNA+ GC B cells

value: Primary cells

tag: other

value: Isolated with PNA beads by MACS


title: LPS_PU1KO_day3_rep2


title: Cyt49_GT.ATAC-Seq.replicate.2

city: La Jolla

first: Maike

last: Sander

state: CA

address: 2880 Torrey Pines Scenic Dr.

institute: UC San Diego

data_processing:
For ATAC-seq: adaptors were trimmed from ATAC-Seq reads using the trim_galore package. Reads were mapped to human reference genome hg19 using bwa. Mapped reads were filtered by Samtools, skipping alignment for reads with MAPQ smaller than 30, removing duplicate and mitochondrial reads.
Fragments were normalized to 1e7 bases of library size using Homer
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated

source_name: Cyt49 Control

growth_protocol: CyT49 hESCs were maintained and differentiated as previously described (Kroon et al., 2008; Schulz et al., 2012). H1 cells were maintained and differentiated as previously described (Jin et al. 2019).

extract_protocol:
Genomic DNA was extracted using Dneasy Blood and Tissue Kit from Qiagen.
Cells were collected and lysed using spin lysis buffer mix. Next, transposition reaction was performed using reaction mix and then DNA was purified using Zymo DNA clean and concentrator. Lastly, DNA product was amplified by PCR and then gel purified for tapestation analysis.

tag: cell type

value: differentiated hESCs

tag: developmental stage

value: Gut tube cells


title: Cyt49_PP2.ATAC-Seq.replicate.2

value: Late pancreatic progenitor cells


title: Cyt49_PP1.ATAC-Seq.replicate.2

value: Early pancreatic progenitor cells


title: CNAG-03 [F-03]

tag: tissue

value: Gastric mucosa


title: mouse GC OBF1 rep2

description: mouse GC OBF1 rep2

source_name: mouse GC OBF1 rep2


title: Cyt49_PP1.ATAC-Seq.replicate.1


title: mouse GC H3K27ac

description: mouse GC H3K27ac

source_name: mouse GC H3K27ac


title: Cyt49_GT.ATAC-Seq.replicate.1


title: LPS_PU1KO_day3_rep4

value: CD19+ B cells


title: Cyt49_ES.ATAC-Seq.replicate.1

value: Embyonic stem cells


title: PE+IL-4 replicate 6 [6.6]

city: Ann Arbor

first: Joseph

last: Holoshitz

state: MI

address: 1150 W Medical Center Dr

department: Internal Medicine - Rheumatology

institute: University of Michigan

description:
deSeq2_counts_raw_cells_Il-4_SE_PE.txt
Labeled 0402Il-4-rep3_R1

data_processing:
Raw counts were attained using featureCounts from the Rsubread1.5.0p3 package.
Gencode-M12 gene annotations using only uniquely aligned reads.
DESeq2-1.16.1 within R-3.4.1 was used to perform data normalization and differential expression analysis with an adjusted p-value threshold of 0.05.
Genome_build: Gencode-M12 (GRCm38.p5)
Supplementary_files_format_and_content: deSeq2_counts raw cells_*SE_PE.txt

source_name: RAW264.7 cells

growth_protocol: RAW264.7 cells grown in DMEM.

extract_protocol:
Total RNA was isolated with Trizol and the Direct-ZolTM RNA miniprep from Zymo research. Genomic DNA was removed using the Turbo DNA-Free kit from Ambion. 200 ng total RNA was used to generate libraries with the Illumina TruSeq RNA Sample Prep Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: RAW 264.7 cells were treated with or without IFNγ (5 ng/ml) or IL-4 (5 ng/ml) in the presence or absence of 15-mer peptides 65-79*0401 or 65-79*0402 (100 μg/ml) for 72 hrs. Medium was refreshed once at 48 hrs.

value: Macrophage cell line

tag: treatment

value: 65-79*PE peptide and IL-4 (5ng/ml)

tag: treatment duration

value: 72 hours


title: Cyt49_DE.ATAC-Seq.replicate.2

value: Definitive endoderm cells


title: PE+IL-4 replicate 5 [6.5]

description:
deSeq2_counts_raw_cells_Il-4_SE_PE.txt
Labeled 0402Il-4-rep2_R1

tag: cell line


title: mouse GC Input

description: mouse GC Input

source_name: mouse GC Input


title: Cyt49_DE.ATAC-Seq.replicate.1


title: PE+IL-4 replicate 4 [6.4]

description:
deSeq2_counts_raw_cells_Il-4_SE_PE.txt
Labeled 0402Il-4-rep1_R1


title: HiChIP_H3K27ac_rep2

city: Nanjing

data_processing:
Library strategy: HiChIP
ChIPseq: The adaptors were trimmed with cutadapt, the trimmed reads were aligned to the hg19 using Bowtie2 with default parameters, and uniquely mapped reads were used for peak calling with MACS2.
HiChIP: HiChIP paired-end reads for each replication were aligned to hg19 genomes using the HiC-Pro pipeline with default parameters. The output from HiC-Pro for replicates were combined and used for loop calling with Hichipper.
RNAseq: The reads were mapped to hg38 using HISAT2 with default parameters. Transcript assembly was performed using Stringtie. Expression level estimation was reported as fragments per kilobase of transcript sequence per million mapped fragments (FPKM).
Genome_build: ChIPseq and HiChIP: hg19 (GRCh37); RNAseq: hg38 (GRCh38)
Supplementary_files_format_and_content: bw, bed, hic, gtf

source_name: kidney tubule HK2 cells

growth_protocol: HK2 cell line maintained in DMEM-F12 medium with 10% FBS (Gibco), 1% penicillin-streptomycin and 0.05% DMSO at 37°C in a 5% (v/v) CO2 humidified incubator.

extract_protocol:
Cells were harvested in Trizol (Invitrogen) for RNAseq.
Genomic DNA was extracted with DNA Clean & Concentrator kit (ZYMO).
Libraries were constructed according to the Illumina instruction. DNA sample was first end-repaired by NEBNext End Repair Enzyme Mix. Then used T4 ligase buffer to add adapters.

treatment_protocol: The harvested cells were fixed with 1% formaldehyde for ChIPseq and HiChIP. MboI restriction enzyme was used to digest chromatin in HiChIP.

value: Proximal tubular epithelial cells

tag: restriction enzyme

value: MboI

tag: chip antibody

value: H3K27ac (Abcam, ab4729)


title: RNAseq rep2

description: mRNA

data_processing:
ChIPseq: The adaptors were trimmed with cutadapt, the trimmed reads were aligned to the hg19 using Bowtie2 with default parameters, and uniquely mapped reads were used for peak calling with MACS2.
HiChIP: HiChIP paired-end reads for each replication were aligned to hg19 genomes using the HiC-Pro pipeline with default parameters. The output from HiC-Pro for replicates were combined and used for loop calling with Hichipper.
RNAseq: The reads were mapped to hg38 using HISAT2 with default parameters. Transcript assembly was performed using Stringtie. Expression level estimation was reported as fragments per kilobase of transcript sequence per million mapped fragments (FPKM).
Genome_build: ChIPseq and HiChIP: hg19 (GRCh37); RNAseq: hg38 (GRCh38)
Supplementary_files_format_and_content: bw, bed, hic, gtf


title: PE+IL-4 replicate 2 [6.2]

description:
deSeq2_counts_raw_cells_Il-4_SE_PE.txt
Labeled P


title: PE+IL-4 replicate 3 [6.3]

description:
deSeq2_counts_raw_cells_Il-4_SE_PE.txt
Labeled X


title: Cyt49_PP2.ATAC-Seq.replicate.1


title: HiChIP_H3K27ac_rep1


title: SE+IL-4 replicate 6 [5.6]

description:
deSeq2_counts_raw_cells_Il-4_SE_PE.txt
Labeled 0401Il-4-rep3_R1

value: 65-79*SE peptide and IL-4 (5ng/ml)


title: LPS_PU1KO_day3_rep1

tag: genotype

value: PU1 knockout


title: PE+IL-4 replicate 1 [6.1]

description:
deSeq2_counts_raw_cells_Il-4_SE_PE.txt
Labeled H


title: RNAseq rep1

description: mRNA


title: SE+IL-4 replicate 5 [5.5]

description:
deSeq2_counts_raw_cells_Il-4_SE_PE.txt
Labeled 0401Il-4-rep2_R1


title: SE+IL-4 replicate 4 [5.4]

description:
deSeq2_counts_raw_cells_Il-4_SE_PE.txt
Labeled 0401Il-4-rep1_R1


title: H3K4me3_ChIPSeq

value: H3K4me3 (Abcam, ab8580)


title: Cyt49_ES.ATAC-Seq.replicate.2

value: differentiated hESCs


title: H3K27me3_ChIPSeq


title: SE+IL-4 replicate 2 [5.2]

description:
deSeq2_counts_raw_cells_Il-4_SE_PE.txt
Labeled O


title: H3K27ac_ChIPSeq


title: SE+IL-4 replicate 1 [5.1]

description:
deSeq2_counts_raw_cells_Il-4_SE_PE.txt
Labeled G


title: PBS replicate 6, IL-4 [4.6]

description:
deSeq2_counts_raw_cells_Il-4_SE_PE.txt
Labeled PBS-rep3_R1

value: PBS


title: PBS replicate 4, IL-4 [4.4]

description:
deSeq2_counts_raw_cells_Il-4_SE_PE.txt
Labeled PBS-rep1_R1


title: isw1_B

first: Peter

last: Eriksson

state: Maryland

address: 9000 Rockville Pike, Bldg.6A/2A14

department: NICHD

description: Biological replicate 2

data_processing:
Sequencing data was aligned to the yeast genome (SacCer3) using Bowtie2 with default settings. Occupancy profiles in bedGraph format were generated using bedtools. For further analyses the aligned reads were size-selected as described in the article.
Genome_build: Genome_build: SacCer3
Supplementary_files_format_and_content: bedgraph format

source_name: isw1_nucleosome core particles (MNase)

growth_protocol: Wild-type cells and null mutants were grown to mid-log phase in synthetic complete medium containing 40mg per liter adenine and 2% glucose.

extract_protocol:
Nuclei were prepared from unfixed yeast cells and then digested with MNase.
The DNA was repaired using the DNA repair kit from New England Biolabs (NEB). The repaired DNA was processed for paired-end sequencing according to the Illumina protocol. NEB kits# M0309L, E7370L  , E7335L, E7500L were used.

tag: strain

value: MATa ade2-1 can1-100 his3-11,15 leu2-3,112 trp1-1 ura3-1 RAD5+ isw1-delta::ADE2


title: PBS replicate 5, IL-4 [4.5]

description:
deSeq2_counts_raw_cells_Il-4_SE_PE.txt
Labeled PBS-rep2_R1


title: isw1_A

description: Biological replicate 1


title: chd1ioc2_4_B

description: Biological replicate 2

source_name: chd1ioc2_nucleosome core particles (MNase)

value: MATa ade2-1 can1-100 his3-11,15 leu2-3,112 trp1-1 ura3-1 RAD5+ chd1::HIS3MX6 ioc2::URA3 ioc4::hph1


title: PBS replicate 2, IL-4 [4.2]

description:
deSeq2_counts_raw_cells_Il-4_SE_PE.txt
Labeled I


title: PBS replicate 3, IL-4 [4.3]

description:
deSeq2_counts_raw_cells_Il-4_SE_PE.txt
Labeled Q


title: chd1ioc3_A

description: Biological replicate 1

source_name: chd1ioc3_nucleosome core particles (MNase)

value: MATa ade2-1 can1-100 his3-11,15 leu2-3,112 trp1-1 ura3-1 RAD5+ chd1::HIS3MX6 ioc3::KanMX6


title: chd1ioc2_4_A

description: Biological replicate 1


title: PE+IFNy replicate 6 [3.6]

description:
deSeq2_counts_raw_cells_IFNy_SE_PE.txt
Labeled HLA24

value: 65-79*PE peptide and IFNgamma (5ng/ml)


title: WT111_B

description: Biological replicate 2

source_name: WT111_nucleosome core particles (MNase)

value: MATa ade2-1 can1-100 HIS3 leu2-3,112 trp1-1 ura3-1 RAD5+


title: PE+IFNy replicate 4 [3.4]

description:
deSeq2_counts_raw_cells_IFNy_SE_PE.txt
Labeled HLA8

value: Macrophage cell line


title: chd1_B

description: Biological replicate 2

source_name: chd1_nucleosome core particles (MNase)

value: MATa ade2-1 can1-100 his3-11,15 leu2-3,112 trp1-1 ura3-1 RAD5+ chd1-delta::HIS5


title: input DNA


title: WT111_A

description: Biological replicate 1


title: SE+IL-4 replicate 3 [5.3]

description:
deSeq2_counts_raw_cells_Il-4_SE_PE.txt
Labeled W

value: 72 hours


title: PE+IFNy replicate 3 [3.3]

description:
deSeq2_counts_raw_cells_IFNy_SE_PE.txt
Labeled X


title: PE+IFNy replicate 5 [3.5]

description:
deSeq2_counts_raw_cells_IFNy_SE_PE.txt
Labeled HLA16


title: WT101_A

description: Biological replicate 1

source_name: WT101_nucleosome core particles (MNase)

value: MATalpha lys2 trp1 his3 leu2 ura3 hhf1-hht1<delta>::LEU2 hhf2-hht2<delta>::HIS3 pRS-HHT1-HHF1 (CEN ARS LYS2 plasmid)


title: chd1ioc3_B

description: Biological replicate 2


title: set2_B

description: Biological replicate 2

source_name: set2_nucleosome core particles (MNase)

value: MATa ade2-1 can1-100 leu2-3,112 trp1-1 ura3-1 HIS3+ RAD5+ set2::TRP1


title: SE+IFNy replicate 6 [2.6]

description:
deSeq2_counts_raw_cells_IFNy_SE_PE.txt
Labeled HLA23

value: 65-79*SE peptide and IFNgamma (5ng/ml)


title: set2_A

description: Biological replicate 1


title: PE+IFNy replicate 1 [3.1]

description:
deSeq2_counts_raw_cells_IFNy_SE_PE.txt
Labeled H


title: PE+IFNy replicate 2 [3.2]

description:
deSeq2_counts_raw_cells_IFNy_SE_PE.txt
Labeled P


title: SE+IFNy replicate 5 [2.5]

description:
deSeq2_counts_raw_cells_IFNy_SE_PE.txt
Labeled HLA15


title: set1_B

description: Biological replicate 2

source_name: set1_nucleosome core particles (MNase)

value: MATa ade2-1 can1-100 leu2-3,112 trp1-1 ura3-1 HIS3+ RAD5+ set1::NAT1


title: SE+IFNy replicate 4 [2.4]

description:
deSeq2_counts_raw_cells_IFNy_SE_PE.txt
Labeled HLA7


title: PBS replicate 1, IL-4 [4.1]

description:
deSeq2_counts_raw_cells_Il-4_SE_PE.txt
Labeled A


title: chd1_A

description: Biological replicate 1


title: SE+IFNy replicate 3 [2.3]

description:
deSeq2_counts_raw_cells_IFNy_SE_PE.txt
Labeled W


title: set1_A

description: Biological replicate 1


title: ioc4_A

description: Biological replicate 1

source_name: ioc4_nucleosome core particles (MNase)

value: MATa ade2-1 can1-100 leu2-3,112 trp1-1 ura3-1 HIS3+ RAD5+ ioc4::hph1


title: ioc4_B

description: Biological replicate 2


title: SE+IFNy replicate 1 [2.1]

description:
deSeq2_counts_raw_cells_IFNy_SE_PE.txt
Labeled G


title: ioc2_B

description: Biological replicate 2

source_name: ioc2_nucleosome core particles (MNase)

value: MATa ade2-1 can1-100 leu2-3,112 trp1-1 ura3-1 HIS3+ RAD5+ ioc2<delta>::URA3


title: ioc3_A

description: Biological replicate 1

source_name: ioc3_nucleosome core particles (MNase)

value: MATa ade2-1 can1-100 leu2-3,112 trp1-1 ura3-1 HIS3+ RAD5+ ioc3::KanMX


title: PBS replicate 6, IFNy [1.6]

description:
deSeq2_counts_raw_cells_IFNy_SE_PE.txt
Labeled HLA17


title: SE+IFNy replicate 2 [2.2]

description:
deSeq2_counts_raw_cells_IFNy_SE_PE.txt
Labeled O


title: ioc3_B

description: Biological replicate 2


title: PBS replicate 5, IFNy [1.5]

description:
deSeq2_counts_raw_cells_IFNy_SE_PE.txt
Labeled HLA9


title: PBS replicate 4, IFNy [1.4]

description:
deSeq2_counts_raw_cells_IFNy_SE_PE.txt
Labeled HLA1


title: ioc2_A

description: Biological replicate 1


title: WT101_B

description: Biological replicate 2


title: PBS replicate 3, IFNy [1.3]

description:
deSeq2_counts_raw_cells_IFNy_SE_PE.txt
Labeled Q


title: PBS replicate 2, IFNy [1.2]

description:
deSeq2_counts_raw_cells_IFNy_SE_PE.txt
Labeled I


title: ioc2_4_B

description: Biological replicate 2

source_name: ioc2_3_nucleosome core particles (MNase)

value: MATa ade2-1 can1-100 leu2-3,112 trp1-1 ura3-1 HIS3+ RAD5+ ioc2::URA3 ioc4::hph1


title: ioc2_4_A

description: Biological replicate 1


title: PBS replicate 1, IFNy  [1.1]

description:
deSeq2_counts_raw_cells_IFNy_SE_PE.txt
Labeled A

value: PBS


title: ioc2_3_4_B

description: Biological replicate 2

source_name: ioc2_3_4_nucleosome core particles (MNase)

value: MATa ade2-1 can1-100 leu2-3,112 trp1-1 ura3-1 HIS3+ RAD5+ ioc2::URA3 ioc3::KanMX ioc4::hph1


title: H4Nd_B

description: Biological replicate 2

source_name: H4Nd_nucleosome core particles (MNase)

value: MATalpha lys2 trp1 his3 leu2 ura3 hhf1-hht1<delta>::LEU2 hhf2-hht2<delta>::HIS3 p730 (CEN ARS HHF1delta21-HHT1 LYS2)


title: H4Nd_A

description: Biological replicate 1


title: LPS_day3_rep1

growth_protocol: Mature B cells were purified from spleens by MACS column using anti-mouse CD19 Microbeads (Miltenyi Biotec). Single cell suspension was prepared by smashing the spleen, and then washing in freshly prepared MACS buffer (0.5% BSA and 2mM EDTA in PBS) (20ml for two spleens) three times. After washing, cell concentration was adjusted to 108 cells/ml. To label the B cells for MACS LS column separation, 10 μl CD19 beads was added to every 107 cells (100 μl), and the mixture was incubated at 4 ℃ for 15min. The anti-CD19-labeled spleen cells were further washed with MACS buffer and then applied to MACS LS column. CD19+ mature B cells were purified according to the standard protocol of Miltenyi Biotec LS column (Cat# 130-042-401). Purified CD19+ mature B cells were subjected to in vitro culture with LPS or anti-CD40/IL4 stimulants at 2 × 106 cells/ml.

value: CD19+ splenic B cells

value: treated with LPS for 3 days

value: wild type


title: LPS_day3_rep2


title: CD40IL4_day3_rep3

value: treated with CD40IL4 for 3 days


title: CD40IL4_day3_rep2


title: CD40IL4_day3_rep1


title: ChIP WT LPS H3K27ac rep3 input

description: ChIP WT LPS H3K27ac rep3 input

data_processing:
ChIP-seq and BioChIP-seq sequencing reads were aligned to the mouse genome (mm9) using the qAlign function, which internally uses Bowtie Langmead et al 2009], from Bioconductor package QuasR [Gaidatzis et al 2015] (package version 1.16.0). Alignments were shifted by 60 bases, corresponding to an estimated fragment length of 120 bp. Peaks of OCT1, OCT2, OBF1, PU.1, H3K27ac, H3K4me3 and H3K4me1 were called in control sample (input) with MACS2 [Zhang et al 2008] (software version 2.1.1) using default parameters. Reads were counted in each peak region using the qCount function in QuasR (with shift set to 60). The read counts per sample were normalized to the mean total mapped number of reads across all samples.
Genome_build: mm9
Supplementary_files_format_and_content: wig files containing the enrichment of IP over input

source_name: ChIP WT LPS H3K27ac rep3 input

extract_protocol:
To extract the nuclei of stimulated splenic B cells: cultured CD19+ spleen B cells stimulated with either LPS or anti-CD40/IL4 were used for chromatin immunoprecipitation as described {Choukrallah, 2015 #46}. Immediately after centrifugation, supernatant was discarded, and cells were resuspended and fixed with 10 ml 1% formaldehyde in PBS at room temperature for 10min, followed by quenching with 530μl 2.5 M Glycine at room temperature for 5 min. Cells were lysed for 10 min in 10 ml lysis buffer A (10 mM HEPES, pH8.0, 10 mM EDTA, 0.5 mM EGTA, 0.25% Triton X-100, PI). The supernatant was discarded, and pellets were incubated for 10 min in lysis buffer B (10 mM HEPES, pH8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.01% Triton X-100, PI). Then, the nuclei were resuspended in chromatin lysis buffer (50 mM Tris-HCl, pH 8.0, 10 mM EDTA, 0.5% SDS) for 30 min at 4 ℃. Subsequently, sonication was performed using Bioruptor Next Gen (Diagenode) at high output intensity for 25 cycles (30s on/30s off). Finally, the fragmented chromatin suspension was diluted 5 times with chromatin dilution buffer (50 mM Tris-HCl, pH8.0, 10 mM EDTA, 167 mM NaCl, 1.67% Triton X-100). 30-50 μg chromatin was subjected to immunoprecipitation with 5-10 μg ChIP-grade antibodies and incubated overnight. Subsequently, the samples were incubated with Dynabeads Protein G for 2 hours. The beads were washed with the following buffers: twice with low salt buffer (20 mM Tris pH 8.0, 0.1% SDS, 1% Triton X-100, 2 mM EDTA, 150 mM NaCl), twice with high salt buffer (20 mM Tris pH 8.0, 0.1% SDS, 1% Triton X-100, 2 mM EDTA, 500 mM NaCl), twice with LiCl buffer (10 mM Tris pH 8.0, 250 mM LiCl, 1 mM EDTA, 1% NP-40, 1% Na Deoxychholate) and once with TE (20 mM Tris-HCl, pH8.9, 2 mM EDTA). The protein-DNA complexes were eluted from the beads with 350 μl elution buffer (10 mM Tris-HCl, pH7.5, 1 mM EDTA, 1% SDS, 100 mM NaHCO3) and reverse crosslinked overnight at 65 ℃ with 60 μg Proteinase K and 60 μg RNase A. Immunoprecipitated DNA was recovered using AMPure XP beads.
libraries were prepared using NEB Ultra II DNA Library Prep Kit for Illumina (E7645S) following the manufacturers instructions

value: Wild type

tag: sample type

value: Primary cells

tag: stimulation

value: LPS

tag: antibody

value: none (input)


title: ChIP OBF1KO LPS OCT1 H3K27ac input

description: ChIP OBF1KO LPS OCT1 H3K27ac input

source_name: ChIP OBF1KO LPS OCT1 H3K27ac input


title: ChIP OBF1KO LPS OCT1 rep2

description: ChIP OBF1KO LPS OCT1 rep2

source_name: ChIP OBF1KO LPS OCT1 rep2

value: Bio-ChIP-seq, Dynabeads M-280 Streptavidin, 11205D


title: ChIP OBF1KO LPS H3K27ac

description: ChIP OBF1KO LPS H3K27ac

source_name: ChIP OBF1KO LPS H3K27ac

value: H3K27ac, Active Motif, Cat# 39133


title: ChIP WT LPS H3K27ac rep3

description: ChIP WT LPS H3K27ac rep3

source_name: ChIP WT LPS H3K27ac rep3


title: ChIP OBF1KO LPS OCT1 rep1

description: ChIP OBF1KO LPS OCT1 rep1

source_name: ChIP OBF1KO LPS OCT1 rep1


title: ioc2_3_4_A

description: Biological replicate 1


title: LPS_day3_rep3

tag: mouse strain


title: ChIP WT CD40/IL4 OCT1 OBF1 PU1 H3K27ac H3K4me1 H3K4me3 input rep2


title: ChIP WT CD40/IL4 OCT1 OBF1 PU1 H3K27ac H3K4me1 H3K4me3 input rep1


title: ChIP WT CD40/IL4 H3K4me3 rep2

description: ChIP WT CD40/IL4 H3K4me3 rep2

source_name: ChIP WT CD40/IL4 H3K4me3 rep2

value: H3K4me3, Millipore, Cat# 07-473


title: ChIP WT CD40/IL4 H3K4me1 rep2

description: ChIP WT CD40/IL4 H3K4me1 rep2

source_name: ChIP WT CD40/IL4 H3K4me1 rep2

value: H3K4me1, Abcam, Cat# ab8895


title: ChIP WT CD40/IL4 H3K27ac rep2

description: ChIP WT CD40/IL4 H3K27ac rep2

source_name: ChIP WT CD40/IL4 H3K27ac rep2


title: ChIP WT CD40/IL4 PU1 rep2

description: ChIP WT CD40/IL4 PU1 rep2

source_name: ChIP WT CD40/IL4 PU1 rep2

value: PU.1, Cell Signaling Technology, Cat# 2258


title: ChIP WT CD40/IL4 OBF1 rep2

description: ChIP WT CD40/IL4 OBF1 rep2

source_name: ChIP WT CD40/IL4 OBF1 rep2


title: ChIP WT CD40/IL4 OCT2 rep2

description: ChIP WT CD40/IL4 OCT2 rep2

source_name: ChIP WT CD40/IL4 OCT2 rep2


title: Small intestine neuroendocrine tumor (SINET), 44

source_name: Tumor

tag: case

tag: gender male (m), female (f)

value: F

value: lymph node metastasis

source_name: Human Reference DNA female (Agilent)

tag: gender reference

value: Male (M), Female (F):F


title: Small intestine neuroendocrine tumor (SINET), 40

value: M

value: liver metastasis

source_name: Human Reference DNA male (Agilent)

value: Male (M), Female (F):M


title: Small intestine neuroendocrine tumor (SINET), 43


title: Small intestine neuroendocrine tumor (SINET), 41

value: primary tumor


title: Small intestine neuroendocrine tumor (SINET), 9


title: ChIP WT CD40/IL4 H3K4me3 rep1

description: ChIP WT CD40/IL4 H3K4me3 rep1

source_name: ChIP WT CD40/IL4 H3K4me3 rep1

tag: cell type

value: CD19+ splenic B cells


title: ChIP WT CD40/IL4 H3K4me1 rep1

description: ChIP WT CD40/IL4 H3K4me1 rep1

source_name: ChIP WT CD40/IL4 H3K4me1 rep1

value: Wild type


title: Small intestine neuroendocrine tumor (SINET), 45


title: Small intestine neuroendocrine tumor (SINET), 6


title: ChIP WT CD40/IL4 OCT1 rep2

description: ChIP WT CD40/IL4 OCT1 rep2

source_name: ChIP WT CD40/IL4 OCT1 rep2

value: Primary cells


title: Small intestine neuroendocrine tumor (SINET), 5