title: Nasal swab, COVID19+, Patient 3

description: MM-C_03 column in coverage_all_samples_hsa_un_COVID_al.txt


title: Leaves, rep 2

status: Public on Dec 11 2023

type: SRA

city: Yangling

first: Liping

last: Guo

address: Taicheng Road

country: China

institute: Northwest A&F University

library_source: transcriptomic

data_processing:
Raw reads were filtered by removing adaptor sequences and low quality sequences to obtain high-quality reads
The clean reads were assembled into transcript using Trinity after the adaptors and the low quality reads were removed
The clean reads were separately mapped to the reference transcriptome by TopHat2
Fragments per kilobase per million mapped reads (FPKM) values were calculated using RSEM
Assembly: For de novo transcriptome analysis, RNA-seq reads were assembled into transcripts using the Trinity software.
Supplementary files format and content: Tab-delimited text file includes reads counts for each sample

molecule: total RNA

organism: Delphinium anthriscifolium

source_name: Leaves

extract_protocol:
RNA was extracted using the RNAprep Pure Plant Kit (TIANGEN)
Construction of an RNA sequencing library was uising Fast RNA-seq Lib Prep Kit V2

tag: tissue

value: Leaves

tag: genotype

value: WT


title: Nasal swab, COVID19+, Patient 2

city: Bedford Park

first: Jonathan

last: Gleadle

state: SA

address: 3D226 Renal Lab, Flinders Medical Centre, Flinders Drive

department: College of Medicine and Public Health

country: Australia

institute: Flinders University

description: MM-C_02 column in coverage_all_samples_hsa_un_COVID_al.txt

data_processing:
FastQC (Andrews, 2010) was used to quality check the smRNAseq sequencing reads.
Cutadapt version 2.3 (Martin, 2011) was used to trim reads with adaptors (AAGATCGGAAGAGCACACGTCT), remove low quality reads and remove reads with a length less than 18bp.
The cleaned reads were first aligned to the Homo sapiens genome (GRCh38, Gencode) using Bowtie2 with the following parameters: -q -D 20 -R 3 -N 0 -L 18 -i S,1,0.50.
The unaligned reads were then aligned to SARS-CoV-2 genome (NC_045512.2, NCBI) using Bowtie2 with the following parameters: -q -D 20 -R 3 -N 0 -L 18 -i S,1,0.50.
The whole read coverage was visualised as a circos plot using the Circlize package in R (Gu et al., 2014) with mapped reads divided into different bins and distribution calculated at each position to produce smooth and uniform coverage.
The alignment process was repeated with 18 to 26 nucleotides size selected reads using awk command. The size distribution of SARS CoV-2 mapped reads and the overrepresented smRNAseq patient reads were determined.
Assembly: hg39, SARS-CoV-2
Supplementary files format and content: bigwig files; BAM files generated from unalignment to human followed alignment to COVID-19. It was then filtered for 18-26 nt and normalized to CPM with a bin size of 1 into bigwig format for visualisation. Patient 6 has not alignment to COVID-19.
Supplementary files format and content: txt files; BAM files generated from unalignment to human followed alignment to COVID-19. Coverage for individual genes for each patients were calculated and then normalize for CIRCOS plot

organism:
Homo sapiens
Severe acute respiratory syndrome coronavirus 2

source_name: Nasopharyngeal swab

extract_protocol:
RNA was isolated from 0.5 mL of viral transport fluid using 1.5 mL of Trizol LS (Thermo Fisher Scientific) and chloroform as per the manufacturer’s recommendations. RNA was precipitated with isopropanol supplemented with 20 µg of glycogen (Thermo Fisher Scientific) as a carrier. RNA pellets were washed with 75% ethanol and resuspended in 30 µL 0.1mM nuclease-free EDTA (Thermo Fisher Scientific). RNA concentration was determined using a NanoDrop 8000 Spectrophotometer (Thermo Fisher Scientific) and Qubit Fluorometer (Thermo Fisher Scientific), and LabChip GX Touch 24 (Perkin Elmer) for quality assessment.
Libraries were prepared from nasopharyngeal RNA from SARS-CoV-2 positive patients using the NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (New England Biolabs) as per the manufacturer’s protocol. PCR amplification was performed using 15 cycles and size selection was performed using AMPureXP beads (Beckman Coulter) according to the manufacturer’s protocol. Libraries were QC checked for quality and quantitation of RNA on the Lab Chip (Perkin Elmer). Pooled libraries were sequenced on the Illumina NextSeq 500 1 x 75 cycle High Output kit.

value: Nasopharyngeal swab

tag: disease

value: COVID19 positive

tag: diagnostic ct


title: Nasal swab, COVID19+, Patient 1

description: MM-C_01 column in coverage_all_samples_hsa_un_COVID_al.txt


title: 5679_YM3B_1-5-B11-J10

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Reads trimmed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted hg38 reference genome using Hisat-3n.
The raw BAM files were filtered using samtools to keep only uniquely mapped reads and use Picard to remove PCR duplicates.
From the filtered BAM file, DNA reads are selected by read-level mCH base coverage >= 3 and read-level mCH fraction < 0.5, selected reads will be processed by ALLCools package to produce ALLC files (allcools allc-to-bam function). The ALLC files are Tab-delimited files describing the quantity of unmethylated and methylated cytosine base calls.
Trimmed reads will also be mapped by Hisat2 to map to hg38 reference genome with GENCODE human v37 gene annotation. RNA reads are selected by read-level mCH base coverage >= 3 and read-level mCH fraction > 0.9, selected reads will be processed by featureCount to quantify gene level (exon + intron) RNA counts.
Assembly: hg38
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column.
Library strategy: snmCT-seq

molecule: genomic DNA

organism: Homo sapiens

source_name: YM3B human BA46

extract_protocol: Library prepared following protocol discribed in Luo, Chongyuan, Hanqing Liu, Fangming Xie, Ethan J. Armand, Kimberly Siletti, Trygve E. Bakken, Rongxin Fang, et al. 2019. “Single Nucleus Multi-Omics Links Human Cortical Cell Regulatory Genome Diversity to Disease Risk Variants.” bioRxiv. https://doi.org/10.1101/2019.12.11.873398. https://www.protocols.io/view/snmcat-v1-bwubpesn

tag: brain region

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

tag: age

tag: Sex

value: Male

tag: molecule subtype

value: nuclear RNA + genomic DNA


title: Capture_promoter_WT_rep3

city: Headington

first: Damien

last: Downes

state: Oxfordshire

address: John Radcliffe Hospital

department: MRC Weatherall Institute of Medicine

country: United Kingdom

institute: The University of Oxford

description: DpnII digested 3C library, enriched for fragments of interest by oligonucleotide pulldown

data_processing:
Library Strategy: NG 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: hg38
Supplementary_files_format_and_content: custom format (chr start stop interactions viewpoint)

source_name: Cardiomyocyte

growth_protocol: The iPSC lines were differentiated into cardiomyocytes using protocols adapted from Lian et al.29 and Zhang et al.30. Briefly, cells were seeded at a 1:5 ratio (approximately 200 000 cells/well) on 24 well plates coated 1:50 with reduced factor matrigel (matrigel basement membrane matrix growth factor reduced LDEV-free, Corning). They were then cultured in E8 medium until reaching 90% confluency (day 0).  On day 0, -INS medium (RPMI 1640, Life Technologies Ltd, with N21-MAX insulin free media supplement, Bio-Techne) containing 8µM CHIR-99021 (Stratech Scientific Ltd), 10ng/ml recombinant Activin A (Bio-Techne), and 1:100 reduced factor matrigel were added for 24 hours. Following incubation (day 1), the medium was replaced with -INS medium and cells were cultured for a further 48 hours until day 3. They were then cultured in 1:1 old to fresh -INS medium supplemented with 5uM WNT inhibitor IWP-4 (Stemcell Technologies) until day 5, when the medium was replaced again with -INS medium for 48 hours. On day 7, the medium was switched to +INS medium (RPMI 1640, Life Technologies Ltd, with N21-MAX media supplement, Bio-Techne) and replaced every second day until more than 60% of cells were beating (day 12-15). They then received daily medium changes until harvesting (day 21 for ATAC sequencing and day 38 for RNA and C-capture experiments).

extract_protocol:
3C Libraries were generated according to the NuTi Capture-C protocol (Downes et al. 2020 in press). 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: cell type

value: Cardiomyocyte

tag: day of differentiation

value: Day 38

tag: genotype/variation

value: wild type


title: 5679_YM3B_1-5-B11-I21


title: Capture_promoter_WT_rep1


title: Capture_promoter_WT_rep2


title: 5679_YM3B_1-5-B11-I22


title: 5679_YM3B_1-5-B11-H9


title: Capture_promoter_Mut_C6_rep3

value: mutant


title: Capture_promoter_Mut_C6_rep2


title: 5679_YM3B_1-5-B11-I10


title: 5679_YM3B_1-5-B11-H21


title: Capture_enhancer_WT_rep3


title: 5679_YM3B_1-5-B11-H22


title: Capture_promoter_Mut_C6_rep1


title: 5679_YM3B_1-5-B11-H10


title: 5679_YM3B_1-5-B11-J22


title: 5679_YM3B_1-5-B11-J21


title: 5679_YM3B_1-5-B11-G22


title: Capture_enhancer_Mut_C6_rep2


title: Capture_enhancer_WT_rep1


title: Capture_enhancer_WT_rep2


title: Capture_enhancer_Mut_C6_rep3


title: Capture_enhancer_Mut_C6_rep1


title: 5679_YM3B_1-5-B11-G21


title: ATAC_Mut_CM_C6_d23_unpaced_rep2

description: Genome-wide library of tagmented fragments

data_processing:
Library Strategy: ATAC-seq
Mapping : bowtie -m 2 --maxIns 350, hg9
For un-mapping reads : trimming adaptors trim_galore -- length 10, combining overlapping R1-R2 reads : flash -m 9 -x 0.125
Combining trimmed+flashed and originally mapped reads, mapping again with  bowtie -m 2 --maxIns 350
Removing read pairs overlapping Blacklisted regions
Removing duplicates : samtools rmdup
Reconstructing sequenced fragments from R1+R2 read pairs ( bedtools bedpe | cut -f 1,2,6) - for visualisation
Pileup of fragments (bedtools genomecov -counts)
Generating bigwig tracks
Genome_build: hg38
Supplementary_files_format_and_content: bigWig : (DEEPtools) bamCoverage converison of filtered fragments (reconstructed, duplicate-filtered fragments : see above) from bam to bigwig,  (--binSize 10 --normalizeUsingRPKM --minMappingQuality 30)

extract_protocol:
Assay for transposition of active chromatin sequencing (ATAC-Seq) was performed as previously published (Buenrostro, 2013) on single cell suspensions. 60000-80000 cells were used per biological replicate. Cells were lysed and nuclei were isolated prior to transposition with Tn5 transposase (Nextera, Illumina) for 30 minutes at 37°C. DNA was purified using a MinElute kit (Qiagen).
Libraries were amplified and barcoded using the NEBNext 2xMastermix (NEB) and the custom primers as published in Buenrostro et al., 2013. ATAC-Seq libraries profiles were visualized using D1000 tape on the Tapestation (Agilent). The libraries were quantified using the universal library quantification kit (KAPA Biosystems).

tag: differentiation day

value: Day 23


title: ATAC_Mut_CM_C6_d23_unpaced_rep1


title: 5679_YM3B_1-5-B11-F9


title: 5679_YM3B_1-5-B11-G10


title: 5679_YM3B_1-5-B11-F22


title: 5679_YM3B_1-5-B11-I9


title: 5679_YM3B_1-5-B11-F10


title: 5679_YM3B_1-5-B11-F21


title: 5679_YM3B_1-5-B11-E9


title: 5679_YM3B_1-5-B11-E22


title: 5679_YM3B_1-5-B11-G9


title: 5679_YM3B_1-5-B11-E10


title: 5679_YM3B_1-5-B11-E21


title: 5679_YM3B_1-5-B11-D9


title: 5679_YM3B_1-5-B11-D22


title: 5679_YM3B_1-5-B11-D10


title: 5679_YM3B_1-5-B11-D21


title: 5679_YM3B_1-5-B11-C9


title: 5679_YM3B_1-5-B11-C21


title: 5679_YM3B_1-5-B11-B9


title: 5679_YM3B_1-5-B11-C22


title: 5679_YM3B_1-5-B11-B22


title: 5679_YM3B_1-5-B11-C10


title: 5679_YM3B_1-5-B11-B21


title: 50-week-old SAMP1-1

type: RNA

city: Saitama City

first: Katsunori

last: Yanai

address: 1-847, Amanuma-cho, Omiya-ku

country: Japan

institute: Jichi Medical University, Saitama Medical Center

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent GE hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE 8x60K Ver.2.0 Microarray (Agilent, G4852B) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 12.0.3.1 (Agilent) using default parameters (protocol GE1_1200_Jun14 and Grid 074809_D_F_20200916) to obtain background subtracted and spatially detrended Processed Signal intensities. The 75th percentile shift normalization was performed using Agilent GeneSpring GX 14.9.1. Data were baseline shifted to the median of all samples.

organism: Mus musculus

source_name: 50-week-old, SAMP1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50 ng Total RNA using Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: After crushing 10 mg of the removed cortical tissue piece of kidney tissue in a silicon homogenizer, transfer to a filter column crusher (QIA Shredder; Qiagen, Valencia, CA, USA) and centrifuge at 25 °C, 14,000 × g, 3 minutes. The filtrate was transferred to a new tube and 140 µL of chloroform was added. After that, the protein and nucleic acid were separated by centrifugation at 12,000 × g at 4 °C for 15 minutes. The supernatant was transferred to a new tube and 1.5 times the amount of 100% ethanol was added. Subsequently, DNA and RNA were separated using the miRNeasy Mini Kit (Qiagen), and total RNA was extracted.

value: kidney

tag: gender

value: male


title: KO-dEZH2_H3K27me3_cuttag_rp2

city: Clayton

first: Qi

last: Zhang

address: 23 Innovation Walk

institute: Monash University

description: EZH2 KO/Rescue CUT&TAG-rp2

data_processing:
Library strategy: CUT&TAG
rChIP-seq: short reads were aligned using bowtie with the following flags: --best --chunkmbs 256 -m 1 -n 1 -q. SAM files were converted to BAM files and then bigwig files using samtools and deepTools.
CUT&Tag: First, the --local flag was used for bowtie alignment in order to remove adapter sequences used during the experimental protocol. Second, potential duplicates were removed from the BAM files using the MarkDuplicates function from the Picard toolkit, with these BAM filles were then used to calculate scaling factors for H3K27me3 and H3K27ac datasets using the ChIPseqSpikeInFree R package. These scaling factors were used to generate bigwig files for heatmap, enrichment profiles, and genome browser tracks.
CUT&Tag: CUT&Tag peaks of H3K27me3 were calculated using SEACR (PMID: 31300027) as previously described (dx.doi.org/10.17504/protocols.io.bjk2kkye; PMID: 33191916)
RNAseq: RNA-seq reads were obtained in FASTQ format and were quantified against the hg38 transcriptome index using Salmon (version 0.14.1) with the --gcBias flag. These transcript-level quantifications were then imported into R using the R packages DESeq2 and tximport. Batch effect removal was done with limma, using the function removeBatchEffect().
Assembly: hg38 and mm9
Supplementary files format and content: bed
Supplementary files format and content: bigWig
Supplementary files format and content: abundance measurements

growth_protocol: K562 cells were cultured in RPMI-1640 (Merck #R8758) growth medium supplemented with 10% FBS (Cellsera AU-FBS/SF) and 1% (v/v) penicillin-streptomycin (Thermo Scientific #15140122) and were incubated at 37 °C with 5% CO2. J1 mouse embryonic stem cells (mESCs) were cultured at 37°C with 5% CO2 in DMEM growth medium, supplemented with 10% FBS (Moregate Biotech), 2% penicillin-streptomycin (Thermo Scientific 15140122), EmbryoMax® Nucleosides (Merck ES-008-D), MEM Non-Essential Amino Acids Solution (Thermo Scientific 11140050), Glutamax™ Supplement (Thermo Scientific 35050061), EmbryoMax® 2-Mercaptoethanol (Merck ES-007-E), 0.01% Plasmocin® (Invivogen ant-mpt) and ESGRO® Recombinant Mouse LIF Protein (Merck ESG1107). All tissue culture plates were first incubated with 0.1% gelatin (Sigma G1393) for >10 minutes at 37°C.

extract_protocol:
CUT&TAG was performed according to Bench top CUT&Tag V.3 (protocols.io, Kaya-Okur & Henikoff). RNA was extracted from 1 million cells using RNeasy kit (QIAGEN #74004) as per manufacturer’s instructions. For rChIP, cell lysates were clarified from sonicated nuclei and DNA were isolated with EZH2 (CST #5246) and H3K27me3 (CST #9733 and Millipore #07-449) antibodies w/o RNase A treatment.
Libraries were constructed according to Bench top CUT&Tag V.3 (protocols.io, Kaya-Okur & Henikoff) using PCR primers described in Buenrostro et al. Single-cell chromatin accessibility reveals principles of regulatory variation. Nature  (2015). DNA (ChIP) and RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For EZH2 depletion and rescue experiments, 3x104 K562 cells were transduced in RPMI and 8 µg/mL polybrene using 200 µL of either EZH2 gRNA or AAVS1 gRNA lentivirus, and 200 µL of rescue or empty vector lentivirus to a final volume of 700 µl in a treated 24-well plate (day 0). On the second day 50% of the media was replaced with fresh RPMI, and on the third day the cell suspension was moved to a 10 cm dish with puromycin added to a final concentration of 10 µg/mL. On day 7, cells were sorted by flow cytometry based on EGFP signal, and seeded into a 10 cm dish. On day 14, cells were trypsinized and washed twice with PBS by centrifugation at 500 x rcf for 5 minutes, resuspended in PBS to 1 million/mL before aliquoting them to the downstream applications.

tag: treatment

value: EZH2 KO/Rescue dEZH2

tag: antibody


title: 5679_YM3B_1-5-B11-B10


title: KO-dEZH2_IgG_cuttag_rp2

description: EZH2 KO/Rescue CUT&TAG-rp2

data_processing:
Library strategy: CUT&TAG
rChIP-seq: short reads were aligned using bowtie with the following flags: --best --chunkmbs 256 -m 1 -n 1 -q. SAM files were converted to BAM files and then bigwig files using samtools and deepTools.
CUT&Tag: First, the --local flag was used for bowtie alignment in order to remove adapter sequences used during the experimental protocol. Second, potential duplicates were removed from the BAM files using the MarkDuplicates function from the Picard toolkit, with these BAM filles were then used to calculate scaling factors for H3K27me3 and H3K27ac datasets using the ChIPseqSpikeInFree R package. These scaling factors were used to generate bigwig files for heatmap, enrichment profiles, and genome browser tracks.
RNAseq: RNA-seq reads were obtained in FASTQ format and were quantified against the hg38 transcriptome index using Salmon (version 0.14.1) with the --gcBias flag. These transcript-level quantifications were then imported into R using the R packages DESeq2 and tximport. Batch effect removal was done with limma, using the function removeBatchEffect().
Assembly: hg38 and mm9
Supplementary files format and content: bigWig
Supplementary files format and content: abundance measurements

value: IgG


title: Tx_liver_rep2

city: Tokushima

first: Takaaki

last: Tsunematsu

address: 3-18-15 Kuramoto

department: Oral Molecular Pathology

institute: Tokushima University

description: Gene expression of liver of Tx mice

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and SurePrint G3 Mouse GE v2 8x60K Microarray for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the RNeasy mini kit (Qiagen) following the manufacturer's recommendations.

treatment_protocol: To establish a primary Sjögren's syndrome mouse model, neonatal thymectomy (Tx) was performed to female NFS/sld mice on day 3 after birth.  The gene expression of liver was measured by using liver tissue of female NFS/sld mice at 8 weeks after the Tx surgery. The control mice used in this study were non-thymectomized female NFS/sld mice. Four independent replicate were utilized.

value: Liver

value: Female

tag: disease state

value: Sjögren's syndrome mouse model


title: 10-week-old SAMP1-5

source_name: 10-week-old, SAMP1


title: 5679_YM3B_1-5-B11-A9


title: nonTx_liver_rep4

description: Gene expression of liver of nonTx mice

value: control


title: KO-mt1_H3K27ac_cuttag_rp2

description: EZH2 KO/Rescue CUT&TAG-rp2

value: EZH2 KO/Rescue mt1


title: nonTx_liver_rep3

description: Gene expression of liver of nonTx mice


title: nonTx_liver_rep2

description: Gene expression of liver of nonTx mice


title: nonTx_liver_rep1

description: Gene expression of liver of nonTx mice


title: Tx_liver_rep4

description: Gene expression of liver of Tx mice


title: 50-week-old SAMR1-6

source_name: 50-week-old, SAMR1


title: 50-week-old SAMR1-12


title: Tx_liver_rep1

description: Gene expression of liver of Tx mice


title: 10-week-old SAMP1-4


title: KO-mt1_H3K27me3_cuttag_rp2

description: EZH2 KO/Rescue CUT&TAG-rp2


title: KO-mt1_IgG_cuttag_rp2

description: EZH2 KO/Rescue CUT&TAG-rp2


title: 10-week-old SAMR1-4

source_name: 10-week-old, SAMR1


title: 10-week-old SAMR1-1


title: Tx_liver_rep3

description: Gene expression of liver of Tx mice


title: KO-dEZH2_H3K27ac_cuttag_rp2

description: EZH2 KO/Rescue CUT&TAG-rp2


title: 5679_YM3B_1-5-B11-A10

value: Dorsolateral Prefrontal cortex (Brodmann area 46)


title: 50-week-old SAMP1-4


title: KO-mt2_H3K27ac_cuttag_rp2

description: EZH2 KO/Rescue CUT&TAG-rp2

value: EZH2 KO/Rescue mt2


title: KO-mt2_H3K27me3_cuttag_rp2

description: EZH2 KO/Rescue CUT&TAG-rp2


title: 5679_YM3B_1-5-B11-A22

value: Male

value: nuclear RNA + genomic DNA


title: 5679_YM3B_1-4-B11-P8


title: KO-mt2_IgG_cuttag_rp2

description: EZH2 KO/Rescue CUT&TAG-rp2


title: 5679_YM3B_1-5-B11-A21


title: 5679_YM3B_1-4-B11-P7


title: 5679_YM3B_1-4-B11-O8


title: 5679_YM3B_1-4-B11-P20


title: KO-WT_H3K27ac_cuttag_rp2

description: EZH2 KO/Rescue CUT&TAG-rp2

value: EZH2 KO/Rescue WT


title: 5679_YM3B_1-4-B11-O7


title: 5679_YM3B_1-4-B11-O20


title: 5679_YM3B_1-4-B11-P19


title: KO-WT_IgG_cuttag_rp2

description: EZH2 KO/Rescue CUT&TAG-rp2


title: KO-Ctrl_H3K27ac_cuttag_rp2

description: EZH2 KO/Rescue CUT&TAG-rp2

value: EZH2 KO/Rescue Ctrl


title: 5679_YM3B_1-4-B11-O19


title: Ctrl-Ctrl_H3K27me3_cuttag_rp2

description: EZH2 KO/Rescue CUT&TAG-rp2

value: KO Ctrl/Rescue Ctrl


title: 5679_YM3B_1-4-B11-N8


title: KO-Ctrl_IgG_cuttag_rp2

description: EZH2 KO/Rescue CUT&TAG-rp2


title: 5679_YM3B_1-4-B11-N19


title: 5679_YM3B_1-4-B11-N7


title: 5679_YM3B_1-4-B11-M7


title: 5679_YM3B_1-4-B11-N20


title: 5679_YM3B_1-4-B11-M8


title: Ctrl-Ctrl_IgG_cuttag_rp2

description: EZH2 KO/Rescue CUT&TAG-rp2


title: KO-dEZH2_H3K27ac_cuttag_rp1

description: EZH2 KO/Rescue CUT&TAG-rp1


title: KO-dEZH2_H3K27me3_cuttag_rp1

description: EZH2 KO/Rescue CUT&TAG-rp1


title: KO-WT_H3K27me3_cuttag_rp2

description: EZH2 KO/Rescue CUT&TAG-rp2


title: 5679_YM3B_1-4-B11-M19


title: 5679_YM3B_1-4-B11-M20


title: KO-mt1_H3K27ac_cuttag_rp1

description: EZH2 KO/Rescue CUT&TAG-rp1


title: KO-mt1_H3K27me3_cuttag_rp1

description: EZH2 KO/Rescue CUT&TAG-rp1


title: 5679_YM3B_1-4-B11-L8


title: 5679_YM3B_1-4-B11-L7


title: 5679_YM3B_1-4-B11-L20


title: KO-mt2_H3K27ac_cuttag_rp1

description: EZH2 KO/Rescue CUT&TAG-rp1


title: 5679_YM3B_1-4-B11-L19


title: KO-mt2_H3K27me3_cuttag_rp1

description: EZH2 KO/Rescue CUT&TAG-rp1


title: KO-mt2_IgG_cuttag_rp1

description: EZH2 KO/Rescue CUT&TAG-rp1


title: KO-Ctrl_H3K27me3_cuttag_rp2

description: EZH2 KO/Rescue CUT&TAG-rp2


title: 5679_YM3B_1-4-B11-K8


title: KO-WT_H3K27ac_cuttag_rp1

description: EZH2 KO/Rescue CUT&TAG-rp1


title: Ctrl-Ctrl_H3K27ac_cuttag_rp2

description: EZH2 KO/Rescue CUT&TAG-rp2


title: 5679_YM3B_1-4-B11-K7


title: KO-WT_H3K27me3_cuttag_rp1

description: EZH2 KO/Rescue CUT&TAG-rp1


title: KO-dEZH2_IgG_cuttag_rp1

description: EZH2 KO/Rescue CUT&TAG-rp1


title: 5679_YM3B_1-4-B11-J7


title: 5679_YM3B_1-4-B11-J20


title: 5679_YM3B_1-4-B11-J8


title: 5679_YM3B_1-4-B11-K19


title: Ctrl-Ctrl_H3K27ac_cuttag_rp1

description: EZH2 KO/Rescue CUT&TAG-rp1


title: KO-Ctrl_H3K27me3_cuttag_rp1

description: EZH2 KO/Rescue CUT&TAG-rp1


title: KO-Ctrl_H3K27ac_cuttag_rp1

description: EZH2 KO/Rescue CUT&TAG-rp1


title: KO-Ctrl_IgG_cuttag_rp1

description: EZH2 KO/Rescue CUT&TAG-rp1


title: 5679_YM3B_1-4-B11-J19


title: 5679_YM3B_1-4-B11-I8


title: Ctrl-Ctrl_H3K27me3_cuttag_rp1

description: EZH2 KO/Rescue CUT&TAG-rp1


title: KO-mt1_IgG_cuttag_rp1

description: EZH2 KO/Rescue CUT&TAG-rp1


title: 5679_YM3B_1-4-B11-I7


title: YoGI_324_before_heat_stress [B_15]

city: Heslington, York

first: Sara

last: Franco Ortega

address: Wentworth Way

department: Department of Biology

institute: Centre for Novel Agricultural Products, University of York

description: Column YoGI_324_Before in processed files

data_processing:
Raw reads were then trimmed using Trimmomatic v0.39
Salmon was used to map the trimmed reads to the Triticum aestivum reference genome  (IWGSC). Then TxImport was used to input salmon output in R package to generate a table containing transcript abundance, counts, and length from the Salmon quantification files
Assembly: IWGSC V1.1 reference (http://ftp.ensemblgenomes.org/pub/plants/release-46/)
Supplementary files format and content: Salmon output

organism: Triticum aestivum

growth_protocol: A total of 13 accessions from Barratt et al., 2023 (Co-expression Network Analysis of Diverse Wheat Landraces Reveals Marker of Early Thermotolerance and Candidate Master-regulator of Thermotolerance Genes) were selected for this work. The seeds (from plants selfed at least three generations) were sown in Levington Advance Seed & Modular F2S compost mixed with Aggregate Industries Garside Sands 16/30 sand (80:20 ratio), treated with CaLypso insecticide. Plants were grown in a Percival AR-75L growth cabinet at 22°C/16°C (day/night) on an 18 hour day/night cycle until reaching the 3-leaves stage.

extract_protocol:
For each one of the 13 wheat accessions, 2 cm of leaf tissue was taken at the 3-leaf stage and after the 14 days of heat stress. Total RNA was extracted from <100 mg of individual leaf tissue samples using the E.Z.N.A Plant RNA Kit (Omega Bio-Tek, ) including a DNase treatment, according to the manufacturer’s protocol. RNA concentration was quantified by both NanoDrop ND-1000 Spectrophotometer, and Qubit 4 Fluorometer and the quality was assessed by Agilent Technology 2100 Bioanalyzer. Samples with RNA Integrity Number (RIN) values >7 were used for the sequencing. Replicates were pooled into 1 sample per accession, per group, at equimolar proportions.
The library preparation and sequencing were performed by Novogene UK. The library was obtained using TruSeq Stranded mRNA (Illumina) . The mRNA was purified using poly-T oligo attached magnetic beads, fragmented and the first strand cDNA synthesized using random hexamer primers, whilst the second strand cDNA using dUTP for directional library. End-repair, A-tailing, adapter ligation, size selection,USER enzyme digestion to remove the UTP-containing second strand cDNA, PCR amplification and purification
TruSeq stranded mRNA run in the Illumina Novaseq 6000 platform (Illumina, CA, USA) with an 150bp paired-end sequencing strategy

treatment_protocol: The heat stress was performed by exposing the plants to 35°C/30°C (day/night) for 14 days after reaching the 3-leaf stage. RNA extraction was conducted before and after stress exposure.

value: Leaves

value: YoGI_324=Prague, collection accession identifier 01C0202172


title: 5679_YM3B_1-4-B11-I20


title: Ctrl-Ctrl_IgG_cuttag_rp1

description: EZH2 KO/Rescue CUT&TAG-rp1


title: 5679_YM3B_1-4-B11-I19


title: YoGI_310_before_heat_stress [B_14]

description: Column YoGI_310_Before in processed files

value: YoGI_310=Prague, collection accession identifier 01C0203425


title: 5679_YM3B_1-4-B11-H8


title: YoGI_292_before_heat_stress [B_13]

description: Column YoGI_292_Before in processed files

value: YoGI_292=Watkins, collection accession identifier 1190788


title: 5679_YM3B_1-4-B11-H7


title: YoGI_235_before_heat_stress [B_11]

description: Column YoGI_235_Before in processed files

value: YoGI_235=Watkins, collection accession identifier 1190627


title: 5679_YM3B_1-4-B11-H20


title: YoGI_155_before_heat_stress [B_10]

description: Column YoGI_155_Before in processed files

value: YoGI_155=Watkins, collection accession identifier 1190264


title: KO-WT_IgG_cuttag_rp1

description: EZH2 KO/Rescue CUT&TAG-rp1

value: IgG


title: YoGI_268_before_heat_stress [B_12]

description: Column YoGI_268_Before in processed files

value: YoGI_268=Watkins, collection accession identifier 1190732


title: 5679_YM3B_1-4-B11-K20


title: 5679_YM3B_1-4-B11-H19


title: YoGI_086_before_heat_stress [B_9]

description: Column YoGI_86_Before in processed files

value: YoGI_086=Watkins, collection accession identifier 1190021


title: 5679_YM3B_1-4-B11-G8


title: 5679_YM3B_1-4-B11-F8


title: 5679_YM3B_1-4-B11-G7


title: 5679_YM3B_1-4-B11-G20


title: YoGI_078_before_heat_stress [B_7]

description: Column YoGI_78_Before in processed files

value: YoGI_078=CIMMYT, collection accession identifier CWI 53363


title: YoGI_062_before_heat_stress [B_6]

description: Column YoGI_62_Before in processed files

value: YoGI_062=CIMMYT, collection accession identifier CWI 24954


title: YoGI_057_before_heat_stress [B_5]

description: Column YoGI_57_Before in processed files

value: YoGI_057=CIMMYT, collection accession identifier CWI 13719


title: 5679_YM3B_1-4-B11-G19

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

value: Male


title: 5679_YM3B_1-4-B11-F7

value: nuclear RNA + genomic DNA


title: YoGI_050_before_heat_stress [B_3]

description: Column YoGI_50_Before in processed files

value: YoGI_050=CIMMYT, collection accession identifier CWI 13561


title: 5679_YM3B_1-4-B11-F20


title: YoGI_055_before_heat_stress [B_4]

description: Column YoGI_55_Before in processed files

value: YoGI_055=CIMMYT, collection accession identifier CWI 13661


title: 5679_YM3B_1-4-B11-F19


title: YoGI_033_before_heat_stress [B_1]

description: Column YoGI_33_Before in processed files

value: Leaves

value: YoGI_033=CIMMYT, collection accession identifier CWI 9391


title: YoGI_310_after_heat_stress [A_29]

description: Column YoGI_310_After in processed files

value: YoGI_310=Prague, collection accession identifier 01C0203425

value: heat


title: 5679_YM3B_1-4-B11-E7


title: 5679_YM3B_1-4-B11-E20


title: 5679_YM3B_1-4-B11-E8


title: YoGI_324_after_heat_stress [A_30]

description: Column YoGI_324_After in processed files

value: YoGI_324=Prague, collection accession identifier 01C0202172


title: YoGI_292_after_heat_stress [A_28]

description: Column YoGI_292_After in processed files

value: YoGI_292=Watkins, collection accession identifier 1190788


title: YoGI_268_after_heat_stress [A_27]

description: Column YoGI_268_After in processed files


title: 5679_YM3B_1-4-B11-E19


title: 5679_YM3B_1-4-B11-D20


title: YoGI_155_after_heat_stress [A_25]

description: Column YoGI_155_After in processed files

value: YoGI_155=Watkins, collection accession identifier 1190264


title: YoGI_235_after_heat_stress [A_26]

description: Column YoGI_235_After in processed files

value: YoGI_235=Watkins, collection accession identifier 1190627


title: 5679_YM3B_1-4-B11-D8


title: YoGI_083_before_heat_stress [B_8]

description: Column YoGI_83_Before in processed files

value: YoGI_083=Watkins, collection accession identifier 1190004


title: YoGI_086_after_heat_stress [A_24]

description: Column YoGI_86_After in processed files

value: YoGI_086=Watkins, collection accession identifier 1190021


title: YoGI_078_after_heat_stress [A_22]

description: Column YoGI_78_After in processed files

value: YoGI_078=CIMMYT, collection accession identifier CWI 53363


title: YoGI_083_after_heat_stress [A_23]

description: Column YoGI_83_After in processed files


title: YoGI_062_after_heat_stress [A_21]

description: Column YoGI_62_After in processed files

value: YoGI_062=CIMMYT, collection accession identifier CWI 24954


title: YoGI_057_after_heat_stress [A_20]

description: Column YoGI_57_After in processed files

value: YoGI_057=CIMMYT, collection accession identifier CWI 13719


title: 5679_YM3B_1-4-B11-C8

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

value: Male


title: 5679_YM3B_1-4-B11-C20

value: nuclear RNA + genomic DNA


title: 5679_YM3B_1-4-B11-D19


title: 5679_YM3B_1-4-B11-C7


title: YoGI_055_after_heat_stress [A_19]

description: Column YoGI_55_After in processed files

value: YoGI_055=CIMMYT, collection accession identifier CWI 13661


title: YoGI_050_after_heat_stress [A_18]

description: Column YoGI_50_After in processed files

value: Leaves

value: YoGI_050=CIMMYT, collection accession identifier CWI 13561


title: 5679_YM3B_1-4-B11-B8


title: 5679_YM3B_1-4-B11-B7


title: 5679_YM3B_1-4-B11-C19


title: YoGI_048_before_heat_stress [B_2]

description: Column YoGI_48_Before in processed files

value: YoGI_048=CIMMYT, collection accession identifier CWI 13434


title: YoGI_048_after_heat_stress [A_17]

description: Column YoGI_48_After in processed files

value: heat


title: YoGI_033_after_heat_stress [A_16]

description: Column YoGI_33_After in processed files

value: YoGI_033=CIMMYT, collection accession identifier CWI 9391


title: 5679_YM3B_1-4-B11-B20


title: 5679_YM3B_1-4-B11-D7


title: 5679_YM3B_1-4-B11-A8


title: 5679_YM3B_1-4-B11-A7


title: 5679_YM3B_1-4-B11-B19


title: 5679_YM3B_1-4-B11-A20


title: 5679_YM3B_1-4-B11-A19


title: 5679_YM3B_1-3-B11-P6


title: 7 day post-TBI Microglia, replicate 2, Bulk RNA

city: Chicago

first: Deborah

last: Winter

state: IL

address: 240 E. Huron Street, M300

institute: Northwestern University

data_processing:
The BCL files generated from sequencing were demultiplexed (bcl2fastq)
Trimmed reads were aligned to the mouse genome reference mm10, using STAR (Dobin et al., 2013)
Aligned reads were mapped to exons using the tool HTSeq (Anders et al., 2015)  with the reference transcriptome (mm10).
The merged table of gene expression counts across samples was normalized to counts per million (CPM)
Assembly: mm10
Supplementary files format and content: tab-delimited table of CPM values across all samples

source_name: Brain

growth_protocol: All mice were male and purchased from the Jackson Laboratory and housed at a barrier facility at the Center for Comparative Medicine at Northwestern University (Chicago, IL, USA).  Bone marrow was aseptically harvested from the tibias and femurs of eight week-old B6.SJL-Ptprca Pepcb/BoyJ (CD45.1) mice. Erythrocytes were lysed, and the cells were counted using a Countess automated cell counter. Eight-week-old C57BL/6 (CD45.2) mice received a single 1000-cGy g-irradiation dose using a Cs-137ebasedGammacell 40 irradiator. The mice heads were shielded with a lead bar so as to deliver the irradiation to the body only. Six hours after shielded irradiation, busulfan (30 mg/kg) was administered to completely ablate the bone marrow of the recipient mice. Donor bone marrow (CD45.1) was transplantedi into CD45.2 recipient mice 12 h after busulfan ablation. Shielded bone marrow chimeras were maintained on antibiotics trimethoprim/sulfamethoxazole (40 mg/5 mg, respectively).

extract_protocol:
RNA was extracted from sorted CD45.2 microglia using Picopure RNA isolation kits.
RNA-seq libraries were prepared using the QuantSeq 3’ mRNA sequencing kit and sequenced on an Illumina NextSeq 500 instrument to an average depth of 20x10^6 reads per sample.

treatment_protocol: Sixteen-week-old chimeric mice (n = 9) were used for all RNA-seq experiments. In brief, mice were were anesthetized with 100 mg/kg Ketamine and 10 mg/kg Xylazine via intraperitoneal injection. A 1cm scalp incision was performed and a 5mm craniectomy was performed 2 mm left of the sagittal suture and 2 mm rostral to the coronal suture. The dura was left intact. Mice were then placed in a stereotaxic operating frame and the impactor (Leica Biosystems Inc., Buffalo Grove, IL) was maneuvered into position. A controlled cortical impact was then applied with a 3mm impacting tip at a velocity of 2.5m/s and an impacting depth of 2mm with the dwell time set at 0.1s. Immediately following injury all animals had their scalps sealed with VetBond (3M). All animals received postinjury analgesia with Buprenorphine SR via subcutaneous injection and were allowed to recover in separate cages over a warming pad. Mice were euthanized via carbon dioxide inhalation at 7, 30, and 90 d after TBI and brains were harvested.

value: Brain

tag: time point

value: 7 day post

value: Microglia

value: C57BL/6 (CD45.2 recipient)

value: Traumatic Brain Injury


title: 30 day post-TBI Microglia, replicate 3, Bulk RNA

tag: tissue

value: 30 day post


title: 7 day post-TBI Microglia, replicate 3, Bulk RNA

tag: genotype


title: 30 day post-TBI Microglia, replicate 2, Bulk RNA


title: 30 day post-TBI Microglia, replicate 4, Bulk RNA


title: 5679_YM3B_1-3-B11-P17


title: 90 day post-TBI Microglia, replicate 4, Bulk RNA

value: 90 day post


title: 5679_YM3B_1-3-B11-P18


title: 90 day post-TBI Microglia, replicate 3, Bulk RNA


title: 5679_YM3B_1-3-B11-O6


title: 90 day post-TBI Microglia, replicate 1, Bulk RNA


title: 5679_YM3B_1-3-B11-O5


title: 5679_YM3B_1-3-B11-P5


title: Panc02, percoll seperated tumor, Anti-PD-1 , TCR

city: Baltimore

first: Elana

middle: Judith

last: Fertig

state: MD

address: 670 W. Baltimore Street, 3rd floor

department: Institute for Genome Sciences

institute: University of Maryland, Baltimore

library_source: transcriptomic single cell

data_processing:
Alignment of aggregated fastq files using CellRanger v4.0.0
Import of data into R using Seurat
Integrate TCR-seq data using Scirpy v0.10.1
Log-normalization of RNA counts
Scaling of normalized expression with regression of cell cycle scores
Dimensionality reduction controlling for batch with Harmony
Cell clustering by Louvain clustering
Differential gene expression analysis by MAST test
Assembly: mm10
Supplementary files format and content: .rds; SeuratObject
Supplementary files format and content: .tsv.gz; CellRanger output features and barcodes
Supplementary files format and content: .mtx.gz; CellRanger UMI counts
Supplementary files format and content: .csv; merged CellRanger vdj output

molecule: polyA RNA

source_name: percoll density seperated tumor

growth_protocol: 3*10^6 Panc02 cells were implanted subcutaneosuly in six-seven week-old male C57BL/6 mouse flanks. Treatments began 12 days post implantation, and tumors were harvested on day 38.

extract_protocol:
10x Genomics Chromium
10x Genomics Chromium Single Cell 5’ Library and Gel Bead Kit; 10x Genomics Chromium Single Cell V(D)J Enrichment Kit

treatment_protocol: 50 ug of PancVAX peptides were injected subcutaneously on days 12 and 19 post-implantation. 100 ug of Anti-CTLA-4 antibody was injected subcutaneously on days 15 and 22 post-implantation. 100 ug of Anti-PD-1 antibody was injected subcutaneously twice weekly starting on day 12 post-implantation.

value: percoll density seperated tumor

tag: cell line

value: WT

tag: strain


title: 5679_YM3B_1-3-B11-O18

tag: brain region

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

value: Male


title: Panc02, percoll seperated tumor, Isotype control, RNA

value: Isotype Control


title: Panc02, percoll seperated tumor, Isotype control, TCR


title: 5679_YM3B_1-3-B11-O17

tag: age

value: nuclear RNA + genomic DNA


title: 5679_YM3B_1-3-B11-N6

tag: Sex


title: Panc02, percoll seperated tumor, Anti-CTLA-4, TCR


title: 7 day post-TBI Microglia, replicate 4, Bulk RNA


title: Panc02, percoll seperated tumor, Anti-PD-1 , RNA


title: Panc02, percoll seperated tumor, Anti-CTLA-4, RNA


title: 5679_YM3B_1-3-B11-N18

tag: molecule subtype


title: Panc02, percoll seperated tumor, Anti-PD-1 + Anti-CTLA-4, TCR

value: Anti-PD-1 + Anti-CTLA-4


title: 5679_YM3B_1-3-B11-N17


title: 5679_YM3B_1-3-B11-M5


title: Panc02, percoll seperated tumor, Anti-PD-1 + Anti-CTLA-4, RNA


title: 5679_YM3B_1-3-B11-M18


title: Panc02, percoll seperated tumor, PancVAX + Anti-CTLA-4, TCR

value: PancVAX + Anti-CTLA-4


title: 5679_YM3B_1-3-B11-M6


title: Panc02, percoll seperated tumor, PancVAX + Anti-CTLA-4, RNA


title: 5679_YM3B_1-3-B11-M17


title: Panc02, percoll seperated tumor, PancVAX + Anti-PD-1, TCR

value: PancVAX + Anti-PD-1


title: Panc02, percoll seperated tumor, PancVAX + Anti-PD-1 + Anti-CTLA-4, RNA

value: PancVAX + Anti-PD-1 + Anti-CTLA-4


title: 5679_YM3B_1-3-B11-L6


title: Panc02, percoll seperated tumor, PancVAX + Anti-PD-1 + Anti-CTLA-4, TCR


title: Panc02, percoll seperated tumor, PancVAX, TCR

value: PancVAX


title: 5679_YM3B_1-3-B11-L5


title: 5679_YM3B_1-3-B11-L17


title: 5679_YM3B_1-3-B11-L18


title: 5679_YM3B_1-3-B11-N5


title: 5679_YM3B_1-3-B11-K5


title: 5679_YM3B_1-3-B11-K6


title: 5679_YM3B_1-3-B11-K18


title: 5679_YM3B_1-3-B11-K17


title: Panc02, percoll seperated tumor, PancVAX, RNA


title: 5679_YM3B_1-3-B11-J6


title: Panc02, whole tumor, Isotype control, RNA

source_name: dissociated whole tumor

value: dissociated whole tumor


title: Panc02, whole tumor, Anti-PD-1, RNA


title: Panc02, whole tumor, Anti-PD-1 + Anti-CTLA-4, RNA


title: Panc02, whole tumor, PancVAX + Anti-CTLA-4, RNA


title: 5679_YM3B_1-3-B11-J18


title: 5679_YM3B_1-3-B11-J5


title: Panc02, whole tumor, PancVAX, RNA


title: 5679_YM3B_1-3-B11-I6


title: Panc02, whole tumor, PancVAX + Anti-PD-1, RNA


title: RNA.Testis_Day7

city: Shanghai

first: Yuxuan

last: Zheng

address: 825 Zhangheng Rd.

institute: Fudan University

data_processing:
The paired scRNA-seq and single-cell TCR sequencing data were simultaneously processed with 10× Genomics software CellRanger (version: 3.0). The sequencing data were aligned into the mouse reference genome (mm10) and VDJ database (mm10), and the expected cell number was set to 10,000. After obtaining processed scRNA-seq data, we filtered cells with three following criteria using R packages Seurat (version: 4.0.3): 1) the number of detected genes (expressed in at least three cells) greater than 500 but less than 4,000, 2) the number of Unique Molecular Identifiers (UMIs) less than 20,000, and 3) the percentage of mitochondrial transcripts less than 10%. Only high-quality single cells were retained for the downstream analysis. The gene expression level was quantified with UMI counts per million mapped reads (CPM) as the UMI number of a given gene in a single cell divided by the total UMI number of this cell and then multiplied by 100,000. The gene expression level was then transformed into log2(CPM + 1) in this study.
Assembly: Mus musculus (mm10).
Supplementary files format and content: "barcodes.tsv" files include scRNA-seq barcode information, "features.tsv" files include scRNA-seq gene features and "matrix.mtx" files include scRNA-seq gene expression. "filtered_contig_annotations.csv" files include scTCR-seq annotated contig information, "filtered_contig.fasta" files include scTCR-seq sequence information.

source_name: Testis

extract_protocol:
We applied E294–302 tetramer selection to dissect virus-specific CD8+ T cells within different tissues of ZIKV infected Ifnar1-/- mice, including spleen, PBMCs, brain and testicle, at different onset times (7 and 30 dpi).
We performed single TCR sequencing and single-cell RNA sequencing (scRNA-seq) with 10× Genomics platform. Moreover, we also sequenced TCRs of general CD8+ T cells from the spleen at 0 dpi. After quality control processing and removing non-T cells, 40,371 high-quality single T cells were retained for the downstream analysis.

value: Testis

tag: library

value: scRNA-seq

tag: timepoint

value: 7 dpi


title: RNA.Testis_Day30

value: 30 dpi


title: 5679_YM3B_1-3-B11-I17


title: Panc02, whole tumor, Anti-CTLA-4, RNA


title: 5679_YM3B_1-3-B11-I5


title: 5679_YM3B_1-3-B11-I18


title: RNA.Spleen_Day7

source_name: Spleen

value: Spleen


title: 5679_YM3B_1-3-B11-J17


title: Panc02, percoll seperated tumor, PancVAX + Anti-PD-1, RNA

value: percoll density seperated tumor


title: 5679_YM3B_1-3-B11-H5


title: 5679_YM3B_1-3-B11-H17


title: 5679_YM3B_1-3-B11-G6


title: 5679_YM3B_1-3-B11-H18


title: TCR.Testis_Day7

source_name: Single T cell receptor-seq (scTCR-seq)

value: scTCR-seq


title: 5679_YM3B_1-3-B11-G18

value: Dorsolateral Prefrontal cortex (Brodmann area 46)


title: 5679_YM3B_1-3-B11-G5

value: Male


title: Panc02, whole tumor, PancVAX + Anti-PD-1 + Anti-CTLA-4, RNA

value: WT


title: 5679_YM3B_1-3-B11-F6

value: nuclear RNA + genomic DNA


title: TCR.Spleen_Day30


title: 5679_YM3B_1-3-B11-F5


title: 5679_YM3B_1-3-B11-F18


title: RNA.Brain_Day7

value: Brain


title: RNA.PBMC_Day30

source_name: Peripheral blood mononuclear cell (PBMC)


title: RNA.PBMC_Day7

value: Peripheral blood mononuclear cell (PBMC)


title: RNA.Brain_Day30


title: 5679_YM3B_1-3-B11-H6


title: RNA.Spleen_Day30


title: RNA.Spleen_Day0

value: 0 dpi


title: TCR.Spleen_Day0


title: 5679_YM3B_1-3-B11-F17


title: 5679_YM3B_1-3-B11-E6


title: 5679_YM3B_1-3-B11-E5


title: 5679_YM3B_1-3-B11-E18


title: 5679_YM3B_1-3-B11-E17


title: TCR.Brain_Day30


title: 5679_YM3B_1-3-B11-D6


title: TCR.Testis_Day30


title: 5679_YM3B_1-3-B11-D5


title: mPFC, Rank4, replicate 4, scRNAseq

city: Seoul

first: Murim

last: Choi

address: 103 Daehakro, Jongrogu

country: South Korea

institute: Seoul National University

description: 10x Genomics

data_processing:
Raw sequencing data from each sample were quantified using 10x Genomics Cell Ranger 4.0.0 (Zheng et al., 2017). Mouse mm10 reference recommended and provided by 10x Genomics (Pleasanton, CA) was used.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: medial prefrontal cortex

extract_protocol:
Animals were anesthetized with CO2 and the brains were extracted and transferred into ice-cold Dulbecco's phosphate-buffered saline (DPBS) one day after the last tube test. For single cell dissociation, the brains were sectioned into 1.0 mm coronal slices in ice-cold DPBS with the brain matrix, and the mPFC was collected from each slice using 14-gauge punches (BP-10F, Kai Medical). In total, five pooled independent biological replicates including tissues from two-to-three different mice were analyzed for sequencing. Briefly, the tissues were cut into small pieces and incubated in a dissociation media (Hibernate A without Calcium and Magnesium with 1 mg/ml papain, 50% D-(+)-trehalose dihydrate, 25 mM DL-2-amino-5-phosphonopentanoic acid and DNase I) at 37 °C for 60 min with shaking at 225 RPM. After washing with 5 ml Hibernate A medium, the tissues were mechanically triturated with cutting pipette tips (tip diameter 2 mm and 1 mm) in 2 ml Hibernate A medium, which was repeated for another two times, and filtered through a cell strainer with 70 μm of the pore size to release single cells. The 1.5 ml single-cell suspension was pooled and loaded on a gradient medium (Hibernate A without Calcium and Magnesium with 1 mg/ml papain, 50% D-(+)-trehalose dehydrate, 25 mM DL-2-amino-5-phosphonopentanoic acid, DNase I, and ovomucoid inhibitor-albumin) and centrifuged at 900 RPM for 6 min at 4 °C to remove debris. The cells were then washed with 1 ml Hibernate A medium followed by 1 ml DPBS. The cells were spun down at 1,250 RPM for 6 min and re-suspended in DPBS. Countess II Automated Cell Counter (Invitrogen) was used to count the number of cells after centrifugation.1,000 ~ 1,800 cells/μl or 1,500 ~ 3,200 cells/μl were obtained from samples from two or three pooled mice, respectively.
For single cell RNA-sequencing (scRNA-seq), the cell suspension was diluted to the recommended concentration (700 ~ 1,200 cells/μl) of the manufacturer’s protocol. We prepared cell suspension to 10,000 targeted cell recovery, and it was captured with 10X Chromium platform (10X Genomics, CA). 10x Genomics Chromium platform delivers a microfluidic chip for 3’ digital gene expression by profiling 500-10,000 individual cells per sample. Using Chromium Single Cell 3’ Reagent Kits v3, we prepared single cell master mix and gel beads, and then generated Gel Beads-in-emulsion (GEMs), combining barcoded Single Cell 3’ v3 Gel Beads. Next, the Gel Beads were dissolved, and cDNA was synthesized according to the sequence included in the GEMs. Since cDNA was synthesized, GEMs were broken and silane magnetic beads were used to purify the first-strand cDNA. And then, cDNA was amplified to generate sufficient mass for library for sequencing. Libraries were generated and sequenced from the cDNA and 10x Barcode containing the GEMs. The final libraries contained the P5 and P7 primers used in Illumina bridge amplification and the concentration was 1.7~2.7ug.

value: medial prefrontal cortex

value: over 2 months old

value: male


title: TCR.Spleen_Day7


title: 5679_YM3B_1-3-B11-D18


title: 5679_YM3B_1-3-B11-D17


title: mPFC, Rank4, replicate 2, scRNAseq

description: 10x Genomics


title: mPFC, Rank4, replicate 3, scRNAseq

description: 10x Genomics


title: mPFC, Rank4, replicate 1, scRNAseq

description: 10x Genomics


title: mPFC, Rank1, replicate 5, scRNAseq

description: 10x Genomics


title: 5679_YM3B_1-3-B11-C17


title: TCR.PBMC_Day7


title: 5679_YM3B_1-3-B11-C18


title: 5679_YM3B_1-3-B11-B6


title: 5006

city: Oxford

first: Thomas

last: Monfeuga

address: Innovation Building, Old Road Campus, Roosevelt Drive

institute: Novo Nordisk Research Centre Oxford

data_processing:
Adaptor trimming with Trim Galore! (v. 0.6.4_dev)
Alignement with Salmon (v. 1.9.0)
Gene levels counts obtained with tximeta (v. 1.10.0)
Assembly: GRCm38, release M23
Supplementary files format and content: text files with gene-level count values for each sample

source_name: Liver

extract_protocol:
Lysis of tissue was performed using a MP FastPrep system. Briefly, 15-20 mg liver biopsy was homogenized and used for RNA extraction on NucleoSpin Plus RNA columns (Macherey-Nagel) as recommended by the supplier. The quantity of the RNA was assessed using a NanoDrop 2000 spectrophotometer (ThermoScientific). The purified RNA was stored at -80c
NeoPrep™ Library Prep System

value: Liver


title: 5679_YM3B_1-3-B11-C6


title: mPFC, Rank1, replicate 3, scRNAseq

description: 10x Genomics


title: mPFC, Rank1, replicate 4, scRNAseq

description: 10x Genomics


title: TCR.PBMC_Day30


title: 5679_YM3B_1-3-B11-C5


title: 5679_YM3B_1-3-B11-B5


title: TCR.Brain_Day7


title: mPFC, Rank1, replicate 2, scRNAseq

description: 10x Genomics


title: mPFC, Rank1, replicate 1, scRNAseq

description: 10x Genomics


title: 5004


title: 5679_YM3B_1-3-B11-B18


title: 4897

value: Semaglutide


title: 5679_YM3B_1-3-B11-A6


title: 4895


title: 4894


title: 5679_YM3B_1-3-B11-A18


title: 4893


title: 5679_YM3B_1-3-B11-A17


title: 4801


title: mPFC, Rank4, replicate 5, scRNAseq

description: 10x Genomics


title: 5679_YM3B_1-2-B11-P4


title: 4799


title: 4798


title: 5679_YM3B_1-2-B11-P16


title: 4797


title: 5679_YM3B_1-2-B11-P15


title: 5679_YM3B_1-2-B11-O4


title: 4783


title: 4790


title: 5679_YM3B_1-2-B11-O16


title: 4786


title: 4780


title: 5679_YM3B_1-3-B11-B17


title: 5679_YM3B_1-2-B11-O15


title: 5679_YM3B_1-3-B11-A5


title: 4779


title: 4657


title: 5679_YM3B_1-2-B11-N3


title: 5679_YM3B_1-2-B11-N15


title: 4654


title: 5679_YM3B_1-2-B11-N4


title: 5679_YM3B_1-2-B11-N16


title: 4656


title: 4653


title: 5679_YM3B_1-2-B11-M4


title: 5679_YM3B_1-2-B11-M3


title: 5679_YM3B_1-2-B11-M16


title: 5679_YM3B_1-2-B11-M15


title: 4652


title: 4649


title: 5679_YM3B_1-2-B11-P3


title: 4646


title: 4643


title: 5679_YM3B_1-2-B11-L4


title: 5679_YM3B_1-2-B11-L16


title: 5679_YM3B_1-2-B11-L3


title: 4641


title: 5679_YM3B_1-2-B11-L15


title: 5679_YM3B_1-2-B11-K4


title: 4638


title: 5679_YM3B_1-2-B11-K3


title: 4431


title: 5679_YM3B_1-2-B11-K16


title: 4635


title: 4430


title: 4433


title: 4429


title: 5679_YM3B_1-2-B11-J3


title: 5679_YM3B_1-2-B11-J16


title: 4423


title: 4426


title: 4420


title: 4418


title: 5679_YM3B_1-2-B11-K15


title: 5679_YM3B_1-2-B11-I16


title: 4415


title: 4642


title: 4419


title: 5679_YM3B_1-2-B11-I4


title: 5679_YM3B_1-2-B11-I15


title: 4411


title: 4409


title: 5679_YM3B_1-2-B11-H3


title: 4408


title: 5679_YM3B_1-2-B11-H4


title: 4407


title: 5679_YM3B_1-2-B11-H16


title: 5679_YM3B_1-2-B11-H15


title: 4354


title: 5679_YM3B_1-2-B11-J4


title: 5679_YM3B_1-2-B11-G4


title: 4353


title: 4404


title: 5679_YM3B_1-2-B11-G3


title: 5679_YM3B_1-2-B11-J15


title: 4349


title: 5679_YM3B_1-2-B11-I3


title: RNAseq_B6_HFD_7 [F_B6_16_4]

city: Kuopio

first: Juho

middle: Mikael

last: Mononen

address: Yliopistonranta 1E

department: Faculty of Health Sciences

country: Finland

institute: University of Eastern Finland

data_processing:
Raw reads were trimmed with Trimmomatic (v0.36) using long TruSeq3-SE.v2 adapters and as essential settings: ILLUMINACLIP:0:30:10, LEADING:3, TRAILING:3, MINLEN:35.
Bowtie (v.2.2.3) was used to identify reads that align to known possible contaminants, which were then discarded.
Reads were then aligned to strain specific genomes, generated with g2gtools (v0.2.9) and MGPv5 SNPs and InDels, using STAR (v2.5.4b). Alignment was done using manual two-pass alignment: After first alignment the splice junctions were collected and used on the second pass alignment with ‘–sjdbFileChrStartEnd’ parameter along with the 2nd pass index generated with the splice junctions. STAR parameters were as follows: --outFilterMultimapNmax 100 –outFilterMismatchNmax 33 –seedSearchStartLmax 12 –alignSJoverhangMin 15 –outFilterMatchNminOverLread 0 –outFilterScoreMinOverLread 0.3 –outFilterType BySJout).
Genome_build: mm10
Supplementary_files_format_and_content: Raw counts: Read counts for genes were generated using STARs ‘-quantMode GeneCounts’ option. Gene IDs are ENSEMBL IDs from Gencode M17 annotation.
Supplementary_files_format_and_content: VST normalized counts: Normalized counts were generated using DESeq2 (v1.26.0) for blind VST normalization.

extract_protocol:
Total RNA from mouse liver tissue was extracted using the miRNeasy Mini Kit (QIAGEN) and QIAzol Lysis Reagent (QIAGEN) according to the manufacturer's protocol. Extracted RNA was treated with DNase using RNase-Free DNase (QIAGEN).
Ribosomal RNA was depleted using the NEBNext rRNA Depletion Kit (New England BioLabs). Libraries were prepared using a NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England BioLabs) following the manufacturer’s instructions.

tag: diet

value: HFD

tag: mouse id

tag: replicate


title: 5679_YM3B_1-2-B11-G16


title: 5679_YM3B_1-2-B11-F15


title: RNAseq_B6_HFD_6 [F_B6_16_3]


title: RNAseq_B6_HFD_5 [F_B6_16_1]


title: 4352

tag: treatment


title: 5679_YM3B_1-2-B11-F16


title: 5679_YM3B_1-2-B11-G15


title: 5679_YM3B_1-2-B11-F3


title: 5679_YM3B_1-2-B11-F4


title: 5679_YM3B_1-2-B11-E4


title: RNAseq_B6_HFD_3 [F_B6_1_4]


title: RNAseq_B6_HFD_2 [F_B6_1_3]


title: 5679_YM3B_1-2-B11-E16


title: RNAseq_B6_HFD_1 [F_B6_1_1]


title: 5679_YM3B_1-2-B11-D4


title: RNAseq_B6_Chow_6 [C_B6_61_4]

value: Chow


title: 5679_YM3B_1-2-B11-D3


title: 5679_YM3B_1-2-B11-D16


title: 5679_YM3B_1-2-B11-E3


title: RNAseq_B6_HFD_4 [F_B6_1_5]


title: 5679_YM3B_1-2-B11-E15


title: RNAseq_B6_Chow_5 [C_B6_61_2]


title: 4346


title: 5679_YM3B_1-2-B11-C4


title: 5679_YM3B_1-2-B11-D15


title: 5679_YM3B_1-2-B11-C3


title: RNAseq_B6_Chow_2 [C_B6_58_3]


title: RNAseq_B6_Chow_4 [C_B6_61_1]


title: 5679_YM3B_1-2-B11-B4


title: 5679_YM3B_1-2-B11-C16


title: RNAseq_SV_HFD_5 [F_SV_113_3]


title: RNAseq_SV_HFD_6 [F_SV_113_5]


title: RNAseq_SV_HFD_3 [F_SV_109_5]


title: 5679_YM3B_1-2-B11-B3


title: RNAseq_SV_HFD_4 [F_SV_113_1]


title: RNAseq_SV_HFD_2 [F_SV_109_3]


title: 5679_YM3B_1-2-B11-B15


title: 5679_YM3B_1-2-B11-A4


title: RNAseq_SV_HFD_1 [F_SV_109_2]


title: 5679_YM3B_1-2-B11-A3


title: RNAseq_SV_Chow_4 [C_SV_120_1]


title: RNAseq_B6_Chow_3 [C_B6_58_4]


title: RNAseq_SV_Chow_3 [C_SV_119_3]


title: 5679_YM3B_1-2-B11-A15


title: 5679_YM3B_1-1-B11-P2


title: RNAseq_SV_Chow_2 [C_SV_119_2]


title: RNAseq_B6_Chow_1 [C_B6_58_1]


title: RNAseq_SV_Chow_1 [C_SV_119_1]


title: TCF7L2_SV_HFD_2 [F_SV_113_5]

data_processing:
Reads were then trimmed with Trimmomatic (v0.36) using long TruSeq3-SE.v2 adapters and as essential settings: ILLUMINACLIP:0:30:10, LEADING:3, TRAILING:3, MINLEN:35.
Alignment was done using to strain-specific genomes, generated with g2gtools (v0.2.9) and MGPv5 SNPs and InDels, using STAR (v2.5.4b) with ‘--alignIntronMax 1 --alignEndsType "EndToEnd"’.
Reads were filtered for true pairs and MAPQ>20 with Samtools (v1.9) and duplicates were removed using Picard (v2.8.13) MarkDuplicates.
Peaks were called with MACS2 (v2.2.7.1) using ‘-g mm -B --call-summits --keep-dup auto’. For H3K27ac ‘-q 0.05’, TCF7L2 ‘-q 0.01’ and CTCF ‘-q 0.001’ were used with MACS2.
Genome_build: mm10
Supplementary_files_format_and_content: Sample-wise peaks: For TCF7L2 and H3K27ac summits were widened to peaks with Bedtools (v2.27.1) using ‘slop -b 75’. Peaks were shifted to mm10 coordinates using g2gtools. ENCODE blacklisted regions were removed from the regions.
Supplementary_files_format_and_content: TCF7L2 raw counts: Consensus peak set was formed from the peak centers using modified kernel density estimation -based approach (Tuoresmäki et al. PLoS One 2014;9(4):e96105). csaw was used for counting by using ‘correlateReads’ to determine average fragments length and extending reads to this length before counting.
Supplementary_files_format_and_content: H3K27ac ChIP-R regions & raw counts: ChIP-R (v1.1.0) was used to get group-wise H3K27ac regions (CHIPR-bed files) which were merged using Bedtools to create consensus peak set. csaw (v1.28.0) function ‘correlateReads’ was used to determine average fragments length and reads were extended to this length before counting with csaw.
Supplementary_files_format_and_content: BigWigs: BAM files shifted to mm10 coordinates were downsampled after and merged by group using Samtools. BigWigs were generated using Deeptools (v3.4.2) bamCoverage with '--normalizeUsing CPM --outFileFormat bigwig --binSize 10'.

extract_protocol:
Frozen tissues were Dounce homogenized with loose pestle A in 1× PBS with 1× protease inhibitors (cOmplete, Roche). Tissue suspension was centrifuged at 2000 rpm for 5 min and the pellet was resuspended in 1 ml PBS containing 1 % formaldehyde for 10 min and quenched with glycine 150 mmol/L for 5 min at room temperature. Samples were washed twice with ice-cold 1× PBS with 1× protease inhibitors. Cells were lysed by pelleting and diluting twice in ice-cold SDS lysis buffer (50 mM Tris/HCl, 0.5% SDS, and 10 mM EDTA, 1 × protease inhibitor) and incubating for 10 min at 4°C with gentle mixing. The cell lysate was then Dounce homogenized with tight pestle B in 1 ml ice-cold of SDS lysis buffer and the homogenate was filtered through a 100 µm cell strainer. Samples were split into 3 × 300 µl aliquots in 1.5 sonication tubes and incubated on ice for 10 min. Chromatin was sheared with Bioruptor Plus sonicator (Diagenode) for 35 cycles at high setting. Once cycle was 30s ON, 30s OFF and after each 10 cycles the sonicator was allowed to cool down for 5 min. To neutralize SDS, Triton-X-100 was added to final concentration of 1% along with 50× protease inhibitors (final 1×). All the aliquots were combined and centrifuged at 13,000 rpm for 20 min. Supernatant with sheared chromatin was collected.
ChIP and library preparation were performed using the recently described ChIPmentation protocol (Gustafsson C et al. BMC Genomics. 2019;20(1):59) with minor modifications. For ChIP, 2 µg of rabbit polyclonal anti-CTCF antibody, 5µl of rabbit monoclonal anti-TCF4/TCF7L2 antibody or 2 µg of Anti-Histone H3 (acetyl K27) antibody was added to 50 µl Protein G-coupled Dynabeads (Thermo Fisher Scientific) in 1 × PBS with 0.5% bovine serum albumin (BSA) and rotated at 40 rpm for 4 h at 4°C. Dynabeads were washed three times with PBS with 0.5% BSA and then mixed with 190 µl chromatin samples in 1.5 ml tubes. The samples were rotated at 40 rpm overnight at 4°C. Chromatin was washed with 150 µl of low-salt buffer (50 mM Tris/HCl, 150 mM NaCl, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, and 1 mM EDTA), high-salt buffer (50 mM Tris/HCl, 500 mM NaCl, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, and 1 mM EDTA) and LiCl buffer (10 mM Tris/HCl, 250 mM LiCl, 0.5% IGEPAL CA-630, 0.5% sodium deoxycholate, and 1 mM EDTA), followed by two washes with TE buffer (10 mM Tris/HCl and 1 mM EDTA) and two washes with ice-cold Tris/HCl pH 8. Chromatin was resuspended in 30 µl of 2 × TD buffer and 1 µl of transposase (Nextera, Illumina) for tagmentation. Samples were incubated at 37°C for 10 min followed by two washes with low-salt buffer. Bead bound tagmented chromatin was diluted in 23 µl of water and 25 µl of 2 × Ultra II Q5 Master Mix (New England BioLabs, M0544S) and 1 µl of both amplification primers (Buenrostro et al, 2013; 0.125 µM final concentration) were added. The libraries were incubated as follows: 72 °C 5 min (adapter extension); 95 °C 5 min (reverse cross-linking); followed by 11 cycles of 98 °C 10s, 63 °C 30s and 72 °C 3 min. After PCR amplification, double-sided purification was performed using SPRIselect beads (Beckman Coulter). To prepare input controls, 2 μl of 50 mM MgCl2 was added to 10 μl sonicated lysate to neutralize the EDTA in the SDS lysis buffer. Tagmentation and amplification was done as described above.

tag: chip antibody

value: TCF4/TCF7L2 (Cell Signaling, C48H11)


title: C33A-E7-2

city: Aglantzia

first: Vasilis

middle: J

last: Promponas

state: Nicosia

address: 1 Panepistimiou Avenue

department: Department of Biological Sciences

country: Cyprus

institute: University of Cyprus

data_processing:
The raw bam files, one for each RNA-Seq sample, were summarized to a 3’UTR read counts table, using the Bioconductor package GenomicRanges
The gene counts table was normalized for inherent systematic or experimental biases (e.g.sequencing depth, gene length, GC content bias etc. using the Bioconductor package DESeq after removing genes that had zero counts over all the RNA-Seq samples (36808 genes).Gene read counts were filtered for possible artifacts that may affect the subsequent statistical testing procedures.
Genes/transcripts presenting any of the following were excluded from further analysis: i) genes with length less than 500bp (2644 genes), ii) genes whose average numbers of reads per 100 bp was less than the 25thquantile of the total normalized distribution of average reads per 100bp (0 genes with cutoff value 0.07471 average reads per 100 bp), iii) genes with read counts below the median read counts of the total normalized count distribution (10382 genes with cutoff value 8 normalized read counts), iv) genes whose biotype matched the following: unprocessed_pseudogene, unitary_pseudogene, IG_V_pseudogene, rRNA, IG_J_pseudogene, IG_C_pseudogene, pseudogene, TR_V_pseudogene, Mt_tRNA, Mt_rRNA, TR_J_pseudogene (245 genes), v) genes which in 50% of samples did not exceed 5 counts (12390 genes) condition-wise. The total number of genes excluded due to the application of gene filters was 16652.
In order to combine the statistical significance from multiple algorithms and perform meta-analysis, the PANDORA weighted p-value across results method was applied.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw counts
Supplementary files format and content: The raw bam files, one for each RNA-Seq sample, were summarized to a 3’UTR read counts table, using the Bioconductor package GenomicRanges. In the final read counts table, each row represented each column one RNA-Seq sample and each cell, the corresponding read counts associated with each row and column.The gene counts table was normalized for inherent systematic or experimental biases (e.g. sequencing depth, gene length, GC content bias etc. using the Bioconductor package DESeq after removing genes that had zero counts over all the RNA-Seq samples (36808 genes). The output of the normalization algorithm was a table with normalized counts, which can be used for differential expression analysis with statistical algorithms developed specifically for count data.

source_name: Cervix

growth_protocol: C33A cells are preserved in DMEM media supplemented with 10% FBS and 1% Penstrep antibiotics and kept at 37 degrees incubator with 5% CO2.

extract_protocol:
48-hours post transfection, cells were collected and RNA was extracted with the Qiagen Rneasy Kit
RNA libraries were normalised with PANDORA

treatment_protocol: Cells at 80% confluency were transfected with Oct4 and/or E7 plasmids. Trasnfection reagent is Fugene-6 from Promega.

value: Cervix

tag: cell type

value: Epithelial

value: Oct4 + E7 expression


title: C33A-E7-3


title: 5679_YM3B_1-2-B11-C15

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

value: Male


title: C33A-E7-1


title: 5679_YM3B_1-2-B11-B16

value: nuclear RNA + genomic DNA


title: 5679_YM3B_1-1-B11-P1


title: TCF7L2_SV_HFD_1 [F_SV_109_2]


title: 5679_YM3B_1-1-B11-P13


title: 5679_YM3B_1-1-B11-O13


title: TCF7L2_B6_HFD_2 [F_B6_16_3]


title: 5679_YM3B_1-1-B11-O1


title: 5679_YM3B_1-1-B11-O2


title: 5679_YM3B_1-1-B11-P14


title: C33A-3

value: Oct4 expression


title: 5679_YM3B_1-1-B11-O14


title: 5679_YM3B_1-1-B11-N2


title: RNAseq_SV_Chow_5 [C_SV_120_4]


title: C33A-2


title: BLM(M2 D135)

city: Madrid

first: Rafael

last: Samaniego

address: Calle Dr Esquerdo 46

country: Spain

institute: Fundación para la Investigación Biomédica del Hospital Gregorio Marañón

description: Human melanoma BLM cell line cocultured for 24h with healthy donor monocyte-derived macrophages differentiated with M-CSF

data_processing:
DNBseq-G400 platform
Low quality reads (More than 20% of the bases qualities are lower than 10), reads with adaptors and reads with unknown bases (N bases more than 5%) were filtered to get the clean reads.Sequences were mapped to GRCh38 genome using  Bowtie2 with the following parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant  -p 1 -k 200
Gene expression levels were determined with software RSEM
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include gene ID and FPKM values for each sample

source_name: BLM - human melanoma

growth_protocol: Cells were cultured in 10% STF RPMI in a 37ºC and 5% CO2 atmosphere.

extract_protocol:
Total RNA was extracted using the NucleoSpin RNA purification kit from Macherey-Nagel
RNA libraries were prepared for sequencing using standard BGI protocols

treatment_protocol: CD14+ monocytes were isolated from PBMCs of healthy donors and differentiated to macrophages adding 1000 U/ml GM-CSF or M-CSF for 7 days renewing cytokines every 3 days. BLM melanoma cell line was cocultured for 24h with these in vitro-generated macrophages before negative selection with CD14 beads and RNA purification.

value: BLM - human melanoma

value: Coculture with healthy donor monocyte-derived M-CSF macrophages for 24h


title: 5679_YM3B_1-1-B11-N1

data_processing:
Reads trimmed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted hg38 reference genome using Hisat-3n.
The raw BAM files were filtered using samtools to keep only uniquely mapped reads and use Picard to remove PCR duplicates.
From the filtered BAM file, DNA reads are selected by read-level mCH base coverage >= 3 and read-level mCH fraction < 0.5, selected reads will be processed by ALLCools package to produce ALLC files (allcools allc-to-bam function). The ALLC files are Tab-delimited files describing the quantity of unmethylated and methylated cytosine base calls.
Trimmed reads will also be mapped by Hisat2 to map to hg38 reference genome with GENCODE human v37 gene annotation. RNA reads are selected by read-level mCH base coverage >= 3 and read-level mCH fraction > 0.9, selected reads will be processed by featureCount to quantify gene level (exon + intron) RNA counts.
Assembly: hg38
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column.
Library strategy: snmCT-seq

source_name: YM3B human BA46


title: TCF7L2_B6_HFD_1 [F_B6_1_1]


title: 5679_YM3B_1-2-B11-A16


title: TCF7L2_SV_Chow_2 [C_SV_120_4]


title: TCF7L2_SV_Chow_1 [C_SV_119_3]


title: C33A-1


title: BLM(M2 D134)


title: BLM(M2 D133)


title: BLM_3

description: Human melanoma cell line

value: Control


city: Palo alto

first: Jeffrey

last: Goldberg

state: Ca

address: 1651 page mill rd rm 2200

department: Ophthalmology

institute: Stanford University

description: Synchronization of proliferating astrocytes with nodocazole that interferes with microtubule polymerization and induces mitosis arrest.

data_processing:
Illumina sequencing reads were trimmed for adaptor sequences / low-quality sequences with Trimmomatic
The trimmed sequences were mapped to hg38 human genome with STAR.
The aligned sequences were counted with RSEM on GENCODE annotated genes of hg38.
The differentially expressed genes were called with Limma-Voom.
The gene set enrichment analysis was performed with FGSEA and displayed in GraphPad Prism.
Assembly: hg38
Supplementary files format and content: DEG-Integrated.xls
Supplementary files format and content: DEG-Aph.xls
Supplementary files format and content: DEG-Aph-KH7.xls
Supplementary files format and content: DEG-KH7.xls
Supplementary files format and content: DEG-Noc.xls

source_name: Astrocytes

growth_protocol: Human astrocytes were seeded on PDL-coated 100x25mm tissue culture dishes (Corning 353003) at a density of 1x106 cells per dish and incubated for 48 hours to allow for adherence and expansion.

extract_protocol: Frozen cell pellets were shipped to Genewiz (genewiz.com) for RNA extraction, library construction, and RNA sequencing.

treatment_protocol: Astrocytes were treated with KH7 (10 µM; Sigma-Aldrich, K3394), aphidicolin (10 µM; Tocris, 5736), nocodazole (1 µM; Tocris, 1228), or DMSO (vehicle; Sigma, D8418) diluted in fresh human astrocyte media and incubated for 20 hrs at 37ºC. The following day, astrocytes were washed twice with ice cold 1X PBS, scraped down in 500 µL 1X PBS, and transferred to 1.5mL Eppendorf tubes. Astrocytes were spun down at 800g, supernatant decanted, and cell pellets snap frozen on dry ice.

value: Astrocytes

value: WT

value: Nocodazole


title: 5679_YM3B_1-1-B11-N13

extract_protocol: Library prepared following protocol discribed in Luo, Chongyuan, Hanqing Liu, Fangming Xie, Ethan J. Armand, Kimberly Siletti, Trygve E. Bakken, Rongxin Fang, et al. 2019. “Single Nucleus Multi-Omics Links Human Cortical Cell Regulatory Genome Diversity to Disease Risk Variants.” bioRxiv. https://doi.org/10.1101/2019.12.11.873398. https://www.protocols.io/view/snmcat-v1-bwubpesn


title: TCF7L2_B6_Chow_2 [C_B6_61_2]

value: Liver


title: 5679_YM3B_1-1-B11-M2


title: Astrocytes were treated with KH7

description: Astrocytes were treated with KH7.


title: TCF7L2_B6_Chow_1 [C_B6_58_4]


description: Astrocytes were treated with DMSO (vehicle).

value: DMSO


title: 5679_YM3B_1-1-B11-M1


title: BLM_2

description: Human melanoma cell line


title: Input_SV_HFD_1 [F_SV_109_3]

value: HFD


title: BLM_1

description: Human melanoma cell line


description: Syncronization of proliferating astrocytes cell cultures by inhibition of DNA polymerase alpha with aphidicolin.

value: Aphidicolin


title: 5679_YM3B_1-1-B11-M14


title: BLM(M1 D135)

description: Human melanoma BLM cell line cocultured for 24h with healthy donor monocyte-derived macrophages differentiated with GM-CSF

value: Coculture with healthy donor monocyte-derived GM-CSF macrophages for 24h


title: Input_B6_Chow_2 [C_B6_58_3]

value: Chow


title: 5679_YM3B_1-1-B11-M13


title: Input_SV_Chow_1 [C_SV_119_2]


title: 5679_YM3B_1-1-B11-N14


title: si_CTRL_3

city: Hangzhou

first: Yunkun

last: Lu

state: Zhejiang

address: No. 3, Qingchun East Rd

department: Sir Run Run Shaw Hospital

institute: Zhejiang University

data_processing:
Raw RNA-seq data were trimmed by fastp (v0.20.1) to remove adapter sequence and reads with low sequencing quality, paired-end sequencing was carried out with the Illumina HiSeq 2500 with paired-end 150-bp read length.
Clean reads were aligned to the human genome (hg38) using HISAT2 software (v2.1.0) with the default parameter settings.
Transcript assembly was performed by stringtie software (v2.0) and expression of transcripts sharing each gene_id was quantified as transcripts Per Million (TPM).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

growth_protocol: HCCLM3-SR cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
Cells were havested and total RNA was isolated using trizol (Invitrogen, USA).
3 μg RNA per sample were used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina®

treatment_protocol: With the treatment of 5μM sorafenib, control samples were transfected with siCTRL and cDCBLD2 knockdown samples were transfected with si-cDCBLD2 for 3 days.

value: control

value: siRNA transfection


title: si_CTRL_2


title: Input_B6_Chow_1 [C_B6_58_1]


title: BLM(M1 D133)


title: H3K27ac_SV_HFD_4 [F_SV_113_5]


title: 5679_YM3B_1-1-B11-L1

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

value: Male


title: 5679_YM3B_1-1-B11-L14

value: nuclear RNA + genomic DNA


title: si_CTRL_1


title: 5679_YM3B_1-1-B11-L2


title: si_circRNA_3

value: cDCBLD2 knockdown


title: H3K27ac_SV_HFD_3 [F_SV_109_5]


description: Astrocyte cell cycle arrest at the border of G1 to S phases by aphidicolin, followed by the treatment with KH7.

value: Aphidicolin and KH7


title: 5679_YM3B_1-1-B11-L13


title: H3K27ac_SV_HFD_2 [F_SV_109_3]


title: Lung Normoxia

city: Palo Alto

first: Yu

last: Liu

address: 1215 Welch Road

department: CVI

data_processing:
The read counts of each cell was calculated by using Cellranger
The analysis of single cell RNAseq data was performed by Seurat
Assembly: mm10
Supplementary files format and content: Normoxia_barcodes.tsv.gz
Supplementary files format and content: Normoxia_features.tsv.gz
Supplementary files format and content: Normoxia_matrix.mtx.gz
Supplementary files format and content: Hypoxia_barcodes.tsv.gz
Supplementary files format and content: Hypoxia_features.tsv.gz
Supplementary files format and content: Hypoxia_matrix.mtx.gz

source_name: Lung

extract_protocol:
After sacrificing 2-4 month old C57/B6, the lung lobes were flushed away blood by 1X PBS and harvested and digested using Miltenyi gentleMACS dissociator and lung tissue dissociation kit (Miltenyi Biotec, Germany). After dissociation, 5% fetal bovine serum (FBS) in PBS (FBS/PBS) was added to the digested cell suspension to achieve a total volume of 10mL and then passed through a BD Falcon 70μm cell strainer (BD Biosciences, Franklin Lakes, NJ) to remove any undigested tissue. The sample was centrifuged at 400 x g  for five minutes and the cell pellet washed with 0.1% FBS/PBS. After repeat centrifuge, the cell pellet was suspended in 1mL of 0.1% FBS/PBS and transferred into an Eppendorf tube containing the pre-prepared CD45 IgG-coated Dynabeads and gently rotated at 4°C for 30 min. After thirty minutes, the Dynabeads were placed on a magnetic stand for 2 min and the cell suspension (CD45 negative cells) was resuspended in CD326-IgG coated Dynabeads and rotated again for 30 min at 4°C. The Dynabeads were placed on a magnetic stand for 2 min and the cell suspension (CD45 negative and CD326 negative cells) as the non-binding suspension was collected. Cell viability (>85%) was measured using the Automated Cell Counter (Thermo Fisher, MQAF1000) and cell suspension was subject to Chromium Next GEM Single Cell 3' Kit v3.1 (10x Genomics). Sequencing platform is NovaSeq (PE150)
The library was performed according to the manufacturer’s instructions (10X Genomics).

value: Lung

value: Normoxia


title: Lung Hypoxia

value: Hypoxia


title: si_circRNA_2


title: BLM(M1 D134)

value: BLM - human melanoma


title: H3K27ac_SV_HFD_1 [F_SV_109_2]

value: Liver


title: H3K27ac_B6_HFD_4 [F_B6_16_3]


title: si_circRNA_1


title: 5679_YM3B_1-1-B11-K2

city: La Jolla

first: Joseph

last: Ecker

address: 10010 North Torrey Pines Road


title: 5679_YM3B_1-1-B11-K1


title: IM-HYA-3

city: Chuo-ku, Kobe City, Hyogo

last: Hirata

address: 7-5-1 Kusunoki-cho

department: Department of Internal Medicine Division of Diabetes and Endocrinology

institute: Kobe University Graduate School of Medicine

data_processing:
Illumina bcl2fastq2-v2.20.0 software used for basecalling.
Trimmomatic program is used to remove adapter sequences and bases with base quality lower than three from the ends. Also using sliding window method, bases of reads that does not qualify for window size 4, and mean quality 15 are trimmed. Afterwards, reads with length shorter than 36bp are dropped to produce trimmed data.
Sequenced reads were mapped to GRCm38 (mm10) whole genome by using HISAT2 version 2.1.0 with parameter -p 20 -dta --rna-strandness RF --novel-splicesite-outfile -x -1 -2
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated by using StringTie version 2.1.3b, with parameter --rf -p 20 -l -o -G -A -C -e
Assembly: GRCm38 (mm10)
Supplementary files format and content: The excel file includes read counts, FPKM values, and TPM values for each sample.

source_name: colon tissue

growth_protocol: Mice were maintained on a 12-hour light/dark cycle and allowed free access to food and water.

extract_protocol:
Total RNA was extracted from the cells with the use of an RNeasy Mini Kit (Qiagen) .
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: The anesthetized mice were subjected to hindlimb cast-immobilization with plastic tubes and adhesive tape for 10 days.

value: colon

value: wild type

value: HYA-containing diet, IM


title: IM-HYA-2


title: IM-HYA-1


title: IM-3

value: Normal diet, IM


title: 5679_YM3B_1-1-B11-K14

institute: HHMI-Salk-Institute


title: 5679_YM3B_1-1-B11-K13


title: H3K27ac_B6_HFD_3 [F_B6_1_5]

value: HFD


title: KNSEN01-C

city: Piscataway

first: Ronald

middle: P.

last: Hart

state: NJ

address: 604 Allison Rd Rm B430

department: Cell Biology & Neuroscience

institute: Rutgers University

data_processing:
Fastq files were cleaned and trimmed with fastp
Fastq files were aligned with Ensembl cDNA reference using Kallisto
Abundance.h5 files were imported into a DESeq2 object using tximport
Groups were compared by Wald testing in DESeq2
Normalized counts were exported using DEseq2 counts() with normalized=TRUE
Assembly: GRCh38/release-104
Supplementary files format and content: Ensembl transcript ID version x sample ID, tab-delimited text file

growth_protocol: Human fibroblast cultures were grown in DMEM supplemented with D-glucose, pyruvate, and 10% fetal calf serum

extract_protocol:
Total RNA was extracted using TriZol
RNA was delivered to Azenta/GeneWiz for library construction using Illumina TruSeq kits

value: Fibroblast

value: Nudt2 174G>T; E58D


title: KNSE20003-C

value: Nudt2 34C>T; R12X


title: IM-2


title: H3K27ac_B6_HFD_2 [F_B6_1_3]


title: 5679_YM3B_1-1-B11-J2

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

value: Male


title: Control C

description: Con-C

source_name: Control

value: Control


title: IM-1


title: KNSE20003-B


title: H3K27ac_B6_HFD_1 [F_B6_1_1]


title: H3K27ac_SV_Chow_4 [C_SV_120_4]

value: Chow


title: CT-3

value: Normal diet, control


title: 5679_YM3B_1-1-B11-J14

value: nuclear RNA + genomic DNA


title: CT-2


title: KNSEN01-B


title: Control B

description: Con-B


title: H3K27ac_SV_Chow_3 [C_SV_119_3]


title: H3K27ac_SV_Chow_2 [C_SV_119_2]


title: 5679_YM3B_1-1-B11-J13


title: 5679_YM3B_1-1-B11-I2


title: CT-1


title: KNSE20003-A


title: KNSEN01-A


title: 5679_YM3B_1-1-B11-I1


title: H3K27ac_B6_Chow_4 [C_B6_61_2]


title: ADAM9_WT_Pan18

city: Taichung

first: Wei-Chung

last: Cheng

address: No.91, Hsueh-Shih Road

department: Research Center for Tumor Medical Science

country: Taiwan

institute: China Medical University

data_processing:
1. trim adapter: trimmomatic
2. Alignment: Hisat2
3. Expression profiling: stringtie
hisat2_index: V97
Assembly: Mus_musculus.GRCm38
Supplementary files format and content: tab-delimited text file includes FPKM value for each sample

extract_protocol:
RNA was harvested using TRIzol (Invitrogen)
The library synthesis was using TruSeq Stranded mRNA Library Prep Kit (Illumina) following the manufacturer's protocols

treatment_protocol: Serum starvation for 24 hours

value: Pancreatic cancer cell

value: ADAM9 WT


title: Control A

description: Con-A


title: Farnesol-3

city: Debrecen

first: Agnes

last: Jakab

address: Nagyerdei krt 98.

country: Hungary

institute: University of Debrecen

data_processing:
The FastQC package (http://www.bioinformatics.babraham.ac.uk/projects/fastqc) was used for quality control.
Reads were aligned to the genome of C. auris B8441
The DESeq algorithm (StrandNGS software) was used to obtain normalized gene transcription values.
Gene transcription differences between treated and control groups were compared by a moderated t test; the Benjamini-Hochberg false discovery rate was used for multiple-testing correction, and a corrected P value of <0.05 was considered significant.
Assembly: genome: https://fungi.ensembl.org/_candida_auris_gca_002759435/Info/Index; features: http://www.candidagenome.org/download/gff/C_auris_B8441/archive/C_auris_B8441_version_s01-m01-r11_features_with_chromosome_sequences.gff.gz
Supplementary files format and content: excell file includes log fold change values and raw data for each Sample

organism: Candidozyma auris

source_name: fungal cells

growth_protocol: C. auris isolate was subcultured on YPD agar for 48 hours at 37 °C. Fungal cells were harvested by centrifugation at 3000 × g for 5 min and were washed three times with sterile physiological saline. After the final washing, pellets were re-suspended in physiological saline and the cell density was adjusted to 1 × 10^6 cells/ml in RPMI-1640 media for each experiment using Burker’s chamber. The 550 μl suspensions of C. auris cells were placed on the bottom of 24-well polystyrene plates (TPP, Trasadingen, Switzerland) to 450 μl RPMI-1640 media and reincubated statically for 24 hours at 37 °C. After the incubation time, culture medium was aspired and non-adherent cells were removed by washing the biofilms with sterile physiological saline.

extract_protocol:
Total RNA was isolated from lyophilized samples with Trisol reagent.
RNA libraries for RNA-seq were prepared using TruSeq RNA Sample preparation kit (Illumina) following manufacturer's protocols.

treatment_protocol: Tyrosol and farnesol in 15 mM and 75 μM concentrations were added to preformed one-day-old biofilms and then the plates were incubated for 24 hours at 37 °C.

value: fungal cells

value: Isolate 12

value: Farnesol treated


title: 5679_YM3B_1-1-B11-I14


title: H3K27ac_SV_Chow_1 [C_SV_119_1]

value: Liver


title: 5679_YM3B_1-1-B11-J1


title: 5679_YM3B_1-1-B11-I13


title: Farnesol-2


title: H3K27ac_B6_Chow_2 [C_B6_58_3]


title: sAC KO 3dpc

first: Evan

middle: G

last: Cameron

address: 1651 Page Mill Road

department: Department of Ophthalmology

description: 10x genomics

data_processing:
The demultiplexing, barcoded processing, and gene counting were made using the Cell Ranger software v7.1.0 with the reference genome of mm10-2020-A(https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tap-seperated values files and matrix files

source_name: optic nerve

extract_protocol:
Whole optic nerves were dissected and enzymatically dissociated into single cells before passing through a magnetic myelin removal column and 10X capture.
Libraries were prepared according to the manufacturer's instructions (10x Chromium Next GEM Single Cell 3' Reagent Kit v 3.1)

value: optic nerve

value: optic nerve crush


title: 5679_YM3B_1-1-B11-H2


title: sAC KO 7dpc

description: 10x genomics


title: H3K27ac_B6_Chow_1 [C_B6_58_1]


title: Farnesol-1


title: WT 7dpc

description: 10x genomics

value: WT


title: Tyrosol-3

value: Tyrosol treated


title: 5679_YM3B_1-1-B11-H1


title: CTCF_SV_HFD_2 [F_SV_113_5]

value: HFD

value: CTCF (Diagenode, #C15410210)


title: WT 3dpc 2

description: 10x genomics


title: 5679_YM3B_1-1-B11-H14

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

value: Male


title: WT control 2

description: 10x genomics


title: Tyrosol-2


title: ADAM9_KO_Pan18

value: ADAM9 KO


title: CTCF_SV_HFD_1 [F_SV_109_2]


title: H3K27ac_B6_Chow_3 [C_B6_58_4]

value: Chow


title: 5679_YM3B_1-1-B11-G2

value: nuclear RNA + genomic DNA


title: 5679_YM3B_1-1-B11-H13


title: Control-3

value: untreated


title: 5679_YM3B_1-1-B11-G1


title: WT 3dpc 1

description: 10x genomics


title: CTCF_B6_HFD_1 [F_B6_1_1]


title: CTCF_SV_Chow_2 [C_SV_120_4]


title: Control-2


title: WT control 1

description: 10x genomics


title: 5679_YM3B_1-1-B11-G14


title: WAT, high-fat diet, tea, rep5

city: Ya'an

first: Songqi

last: Duan

state: Sichuan

address: No.46, Xinkang Road, Yucheng District

department: College of Food Science

institute: Sichuan Agricultural University

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp (v0.23.2) with default parameters.
Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 (v2.2.1).
The gene expression levels were quantified using featureCounts (v2.0.6) based on the aligned BAM files generated by HISAT2.
Assembly: mm10
Supplementary files format and content: tab-delimited text files contain raw counts values for each sample

source_name: White adipose tissue

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent according the manufacturer’s instructions. Then RNA quality was determined by 5300 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample(OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, >1μg) was used to construct sequencing library.
RNA-seq transcriptome librariy was prepared following Illumina® Stranded mRNA Prep, Ligation from Illumina (San Diego, CA) using 1μg of total RNA.

value: White adipose tissue

value: high fat diet

tag: group

value: tea


title: CTCF_SV_Chow_1 [C_SV_119_3]

tag: tissue


title: Control-1

value: fungal cells

tag: genotype

value: Isolate 12


title: CTCF_B6_Chow_2 [C_B6_61_2]

value: Liver


title: 5679_YM3B_1-1-B11-G13


title: WAT, high-fat diet, tea, rep3


title: CTCF_B6_HFD_2 [F_B6_16_3]


title: 5679_YM3B_1-1-B11-F1


title: WAT, high-fat diet, tea, rep2


title: CTCF_B6_Chow_1 [C_B6_58_4]


title: tumor-bearing liver, vehicle treated

city: Dallas

first: Mingrui

last: zhu

state: TX

address: 5323 Harry Hines Blvd

department: Pathology

institute: UTSouthwestern Medical Center

data_processing:
The Cell Ranger Single-Cell Software suite was used for demultiplexing, barcode processing, alignment, and initial clustering of the raw scRNA-seq profiles. The Loupe Browser 6.3.0 was used for data visualization and for intuitive primary analysis of single cell RNA sequencing data.
Assembly: mm10
Supplementary files format and content: aligned bam file and processed cloupe

source_name: liver

extract_protocol:
mouse livers were minced, digested and filtered for single cell sequencing
About 8-10K single cells with viability score of >70% were input in each library. The 10x Genomics Chromium controller instrument was used for Gel Bead- in Emulsion (GEMs) preparation. Chromium Next GEM Single Cell 3' Kit v3.1 (PC-1000269), Chromium Next GEM Chip G Single Cell Kit (PC-1000127) and Dual Index Kit TT Set A Kit (PC-1000215) were used for Single-Cell Library Preparation. cDNA and final barcoded sequencing libraries were generated as per the manufacturer's specifications and their quality and concentration was assessed using the Bioanalyzer 2100 and qPCR, respectively. Quality pass single cell libraries were sequenced on NextSeq550 sequencer using the paired-end 75bp sequencing kit.

value: liver

tag: cell line

value: mouse SCLC

value: Vehicle


title: tumor-bearing liver, 6ThiodG treated

value: WT


title: ATAC_F1_4 [ATAC_F1_no4]

data_processing:
For ATAC-seq samples from the C57Bl/6J and 129S1/SvImJ strains reads were trimmed with Trimmomatic (v0.36) using long TruSeq3-SE.v2 adapters and as essential settings: ILLUMINACLIP:0:30:10, LEADING:3, TRAILING:3, MINLEN:35.
Alignment was done using to strain-specific genomes, generated with g2gtools (v0.2.9) and MGPv5 SNPs and InDels, using STAR (v2.5.4b) with ‘--alignIntronMax 1 --alignEndsType "EndToEnd"’.
Reads were filtered for true pairs and MAPQ>20 with Samtools v 1.9. Duplicates were removed using Picard (v2.8.13) MarkDuplicates.
Peaks were called with HMMRATAC (v1.2.10) using ‘--means 75,200,400,600 --upper 20 --lower 10’.
For F1 samples we used ASEReadCounter* pipeline (https://github.com/gimelbrantlab/ASEReadCounter_star).
Genome_build: mm10
Supplementary_files_format_and_content: Sample-wise peaks: Summits were widened to peaks with Bedtools (v2.27.1) using ‘slop -b 75’. Peaks were shifted to mm10 coordinates using g2gtools. ENCODE blacklisted regions were removed from the regions.
Supplementary_files_format_and_content: Raw counts: Consensus peak set was formed from the peak centers using modified kernel density estimation -based approach (Tuoresmäki et al. PLoS One 2014;9(4):e96105). Reads were shortened to 1bp tags at 5’-ends and counted using csaw (v1.28.0).
Supplementary_files_format_and_content: F1 allelic counts: Counts were obtained from ASEReadCounter* pipeline. Counts were generated using the consensus peak set from ATAC-seq samples from the C57Bl/6J and 129S1/SvImJ strains. The table contains counts for peaks and aggregated counts for SNPs in these peaks.
Supplementary_files_format_and_content: BigWigs: BAM files shifted to mm10 coordinates were downsampled after and merged by group using Samtools. BigWigs were generated using Deeptools (v3.4.2) bamCoverage with '--normalizeUsing CPM --outFileFormat bigwig --binSize 10'.

extract_protocol:
Nuclei were isolated using a Dounce homogenizer and 1× homogenization buffer (320 mM sucrose, 0.1 mM EDTA, 0.1% NP40, 5 mM CaCl2, 3 mM Mg(Ac)2, 10 mM Tris pH 7.8, 1× protease inhibitors (Roche, cOmplete), and 1 mM β-mercaptoethanol). After tissue homogenization, nuclei were recovered by OptiPrep/iodixanol (Sigma-Aldrich) density gradient centrifugation.
Libraries were generated following Omni-ATAC protocol (Corces MR. et al. Nat Methods. 2017;14(10):959-962) with minor adjustments. Nuclei were resuspended in transposition mix (25 µl 2× TD buffer, 2.5 µl transposase, 16.5 µl PBS, 0.5 µl 1% digitonin, 0.5 µl 10% Tween-20, 5 µl H2O). After the transposition reaction, DNA was purified with DNA Clean & Concentrator-5 Kit (Zymo Research). Ten microliters of purified transposed DNA were amplified for 9-11 cycles (predetermined) using 25µl of 2 × Ultra II Q5 Master Mix (New England BioLabs) and 1 µl of both amplification primers (Buenrostro JD et al. Nat Methods. 2013;10(12):1213-1218; 1.25 μM final concentration). For cleanup and to remove primer dimers and large (>1,000 bp) fragments from the libraries, SPRIselect beads (Beckman Coulter) were used.

tag: strain

value: F1 (129S1/SvImJ x C57BL/6J)


title: Tyrosol-1

value: Tyrosol treated


title: 5679_YM3B_1-1-B11-F14

tag: brain region

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

value: Male


title: ATAC_F1_3 [ATAC_F1_no3]