title: SAM77_r10_probing_4_igg

address: 401 N Washington St

tag: treatment


title: control_6 850k methylation

status: Public on Jul 01 2022

type: genomic

city: Aurora

first: Ivana

last: Yang

state: CO

country: USA

institute: University of Colorado Anschutz Medical Campus

hyb_protocol: not provided

scan_protocol: not provided

data_processing:
For DNA, Illumina idat signal intensity files were processed using SeSAMe; within-sample normalization with out-of-band probes and dye bias correction were performed {Zhou, 2018, 30085201}. Probes containing a SNP site in our genetic dataset as well as probes with non-unique mapping and off-target hybridization were removed. Additionally, probes with an average detection P value >= .05 across samples and sex chromosome probes were removed prior to analysis.
For DNA methylation, final methylation beta values are included as a processed data file.

label: Cy3, Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: tissue-Explant

label_protocol: not provided

extract_protocol:
DNA was isolated from the same sample of lung tissue using the AllPrep kit (Qiagen).  DNA integrity number (DIN) >5 were used.
1 ug of DNA was bisulfite treated using the Zymo EZ DNA Methylation kit, labeled and hybridized to Illumina Infinium Human MethylationEPIC BeadChip using standard protocols.

tag: tissue

value: lung

tag: center

value: Pittsburgh Lung Donor Core

tag: dx

value: normal

value: control

tag: methylationid

tag: age

tag: Sex

value: m

tag: race

value: white

tag: ethnicity

value: not hispanic or latino

value: Y


title: mES_1Gy_2h_2

type: SRA

city: Leiden

first: Bharath

last: Sampadi

address: Einthovenweg 20

country: Netherlands

institute: Leiden University Medical Center

description: molecule: BrU-labeled RNA

library_source: transcriptomic

data_processing:
Illumina Casava v1.8.2 was used for basecalling.
Reads were mapped to the mouse ribosomal DNA complete repeating unit (GenBank BK000964.1) using Bowtie v.0.12.8 and parameters -n 3 -k 1 -m 1.
Reads that did not map to the ribosomal DNA were mapped to the mm9 genome using TopHat v1.4.1 and parameters –min-isoform-fraction 0, --max-multihits 1, --no-closure-search, --no-coverage-search, --bowtie-n, --initial-read-mismatches 3
A coverage determination was then made for every base in the genome using Bedtools v.2.16.2 such that a base covered by one read was recorded as having a coverage of 1/read_length
Reads Per Kilobase per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files for gene abundance measurements.  Columns are standard BED6 format columns - (1) chr, (2) start, (3) end, (4) name, (5) score (0 as palceholder), strand (6) - and the following additional columns: (7) gene length, (8) num features (introns/exons) in meta-gene, (9) effective length (sum of feature lengths, for measuring RPKM), (10) read counts, (11) density (reads per kb), (12) RPKM

molecule: total RNA

organism: Mus musculus

source_name: mESC

growth_protocol: mESCs were cultured in 10-cm dishes (pre-coated with 0.1%(w/v) gelatin) and maintained in mESC medium – KnockOut DMEM 500 ml [Gibco 10829018] supplemented with  55 ml fetal calf serum, 5.5 ml Pen-strep [Gibco 15140122] , 5.5 ml Sodium Pyruvate [Gibco 11360070], 5.5 ml Glutamax [Gibco 35050061], 1.25 ml b-mercaptoethanol [Gibco 31350010] and 55 ml leukemia inhibitory factor (LIF) [Millipore ESG1107].

extract_protocol:
For Bru-seq experiments, we followed the previously published protocol from Paulsen et al., Methods, 2014. Briefly, bromouridine (BrU) was added to the culture media at a final concentration of 2mM and the dishes were returned to CO2 incubator at 37°C for 30 minutes to label the nascent RNA. Labeling was done in the last 30 minutes of the corresponding incubation times for each experiment. Cells were trypsinized, collected pellets were frozen in liquid nitrogen and stored at -80°C until use. From then on BrU-seq protocol was applied. Cell pellets were then lysed in Trizol, total RNA isolated, BrU-RNA was immunoprecipitated using anti-BrdU antibodies (BD Pharmingen, 555627), strand-specific DNA libraries were prepared with Illumina TruSeq kit [Illumina, RS-122-2001]. Samples were then deep sequenced using Illumina sequencing platform.
Library construction was performed according to the previously published protocol from Paulsen et al., Methods, 2014.
BrU-seq

treatment_protocol: 5-Bromo Uridine [Sigma Aldrich 850187-1G] was directly added to the culture dish with cells 30 minutes prior to trypsinization at a final concentration of 2mM. For BrU-seq experiments, first four passages were done on top of a monolayer of lethally irradiated mouse embryonic fibroblasts and the next three passages were done without feeders for a total of seven passages. Cells were irradiated with X-rays (YXLON  International) for 60 seconds at a dose rate of 0.1 Gy/min for low DNA damage (LD) and at a dose rate of 1 Gy/min for high DNA damage (HD).

tag: cell type

value: embryonic stem cells

tag: labelling agent

value: Bromouridine (BrU)


title: mES_1Gy_0.5h_2

description: molecule: BrU-labeled RNA


title: mES_1Gy_8h_2

description: molecule: BrU-labeled RNA


title: mES_1Gy_1h_2

description: molecule: BrU-labeled RNA


title: SAM77_nop_probing_4_igg

type: protein

city: Rockville

first: Johannes

last: Goll

state: MD

department: Bioinformatics Service Group

institute: The Emmes Company

hyb_protocol: Each serum sample was diluted in protein array blocking buffer (GVS, Sanford, ME) supplemented with E. coli lysate (GenScript, Piscataway, NJ) to a final concentration of 10 mg/mL, and pre-incubated at room temperature (RT) for 30 minutes. Concurrently, arrays were rehydrated in blocking buffer (without lysate) for 30 minutes. Blocking buffer was removed, and arrays were probed with pre-incubated serum samples using sealed chambers to ensure no cross-contamination of sample between pads. Arrays were incubated over-night at 4 °C with gentle agitation. Arrays were then washed at RT five times with TBS-0.05% Tween 20 (T-TBS), followed by incubation with QDot®-conjugated goat anti-human IgG/ IgA diluted 1:200 in blocking buffer for 2 hours at RT. After incubation in secondary antibodies, arrays were then washed three times with TTBS and once with water.

scan_protocol: Chips were air dried by centrifugation at 1,000 g for 5 minutes and scanned on a ArrayCamTM 400-S Microarray Imaging System from Grace Bio-Labs (Bend, OR) for QDot.

data_processing:
Spot and background intensities were measured using an annotated grid (gal) file. For ArrayCamTM a number of different settings were used to attempt to obtain readings. Microarray spot intensities were quantified using software ArrayCamTM (Grace Bio-Labs) utilizing automatic local background subtraction for each spot. The generated signal intensity values were considered raw values.
Prior to the analysis, systematic intensity differences in background reactivity as measured by phosphate buffered saline with tween 20 (PBST) were corrected. This was achieved by subtracting the median raw intensity signal for the 24 PBST intensity measurements for a certain array from the array’s non-PBST antigen intensities. Following background correction, for intensities < 1, an intensity value of 1 was imputed. Global outliers based on PCA and MDS plots were removed.

molecule: protein

source_name: serum

label_protocol: No labeling

extract_protocol: The serum samples originated from future-use consenting participants of parallel avian A(H5N1)/Indonesia/05/2005 influenza vaccine mix and match studies involving MF59® and AS03 adjuvant, also known as DMID Protocols 10-0016 and 10-0017.

treatment_protocol: Only the participants that received the 15 µg dose of H5 vaccine were selected for the microarray analysis; three timepoints from each participant were selected and represent baseline (day 0 or pre-vaccination), day 21 (post-first dose of vaccine), and day 42 (21 days post-second dose of vaccine).

tag: subject id

value: A/H5N1 HA + PBS

tag: day

tag: blocking

value: no peptide


title: case_5 850k methylation

value: UCSF

value: ipf

value: case


title: wt_2_380

city: Ramat Gan

first: Avigail

last: Rein

address: Derech Sheba 2

country: Israel

institute: Sheba Medical Center

data_processing:
Reads were trimmed using cutadapt
After trimming, the reads were mapped to the Mouse genome (GRCm38) using STAR  v2.4.2a (using options alignEndsType EndToEnd and outFilterMismatchNoverLmax set to 0.04)
Counting proceeded over genes annotated in Ensembl release 92, using htseq-count (version 0.6.1p1)
Normalization and differential expression was performed using DESeq2 (Version 1.10.1)
Genome_build: GRCm38
Supplementary_files_format_and_content: Processed files include raw counts.

source_name: lineage negative bone marrow progenitors

extract_protocol:
Femur and tibia of 6-8 week old mice were harvasted and flashed on ice. Fetal livers of 14.5E fetuses were harvasted, purified and crushed into single cells on ice. Lineage negative cells were generated using miltenyi magnetic beads. RNA was obtained using Trizole reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: 6-8 weeks

tag: genotype

value: WT


title: wt_3_381

value: lineage negative bone marrow progenitors


title: mES_0.1Gy_8h_2

description: molecule: BrU-labeled RNA


title: mES_0.1Gy_4h_2

description: molecule: BrU-labeled RNA


title: case_4 850k methylation

value: lung

value: N


title: mES_0.1Gy_2h_2

description: molecule: BrU-labeled RNA


title: SAM01_m10_probing_4_iga

value: Mini HA-10ug/ml


title: mES_0.1Gy_0.5h_2

description: molecule: BrU-labeled RNA


title: case_3 850k methylation

value: m


title: SAM77_m10_probing_4_igg


title: case_2 850k methylation

value: white


title: mES_0.1Gy_1h_2

description: molecule: BrU-labeled RNA


title: mES_Control_2h_2

description: molecule: BrU-labeled RNA


title: SAM01_m50_probing_4_iga

value: Mini HA -50ug/ml


title: mES_Control_4h_2

description: molecule: BrU-labeled RNA


title: control_1 850k methylation

value: Pittsburgh Lung Donor Core

value: normal

value: control

value: not hispanic or latino


title: mES_Control_0.5h_2

description: molecule: BrU-labeled RNA

value: embryonic stem cells

value: Bromouridine (BrU)


title: mES_1Gy_8h_1

description: molecule: BrU-labeled RNA


title: SAM01_r10_probing_4_iga

value: A/H5N1 HA + PBS


title: SAM77_r50_probing_4_igg

value: Y


title: B412_Replicat1_pos_Zn_pos_GSK_RNAseq

city: Marseille

first: Estelle

last: Duprez

address: 27 Boulevard Lei Roure

country: France

institute: CRCM

data_processing:
quality control 1 before mapping:
Sequencing quality control was determined using the FastQC tool
quality control 2 before mapping:
Reads with a Phred quality score less than 30 were filtered out
mapping : Reads were mapped to hg19 genome using subread-align (v1.5.0) with default parameters
Gene expression was determined by counting mapped tags at gene levels using featureCounts
Genome_build: hg19
Supplementary_files_format_and_content: Gene Count csv files

growth_protocol: Human monocytic U937 MT and B412 cell lines were maintained at exponential growth in RPMI with 10% foetal calf serum and 1% penicillin streptomycin

extract_protocol:
Total RNA was extracted using the RNeasy Plus Mini kit (Qiagen)
U937 cDNA was synthesized using a SMART-Seq v3 Ultra Low Input RNA kit for Sequencing (Clontech). ds-cDNA was fragmented using S220 Focused ultrasonicator (Covaris) and libraries were generated using a NEBNext Ultra DNA Library Prep kit (New England Biolabs).

treatment_protocol: For PLZF/RARA expression (U937 B412 cells), cells were pretreated with ZnSO4 0.1mM for 24 hours and then treated for 96 hours with GSK126 2.5µM and ZnSO4 0.1mM

tag: cell line

value: Acute monocytic leukemia

value: Bone marrow

tag: genotype/variation

value: cells expressing the PLZF/RARA oncogenic fusion upon ZnSO4 exposure

value: ZnSO4 0.1mM and GSK126 2.5µM


title: SAM49_m10_probing_4_igg

tag: treatment

value: A/H5N1 HA + AS03

value: N


title: B412_Replicat2_pos_Zn_pos_GSK_RNAseq

tag: tissue


title: mES_Control_1h_2

description: molecule: BrU-labeled RNA


title: mES_1Gy_4h_1

description: molecule: BrU-labeled RNA


title: mES_1Gy_2h_1

description: molecule: BrU-labeled RNA


title: mES_Control_8h_2

description: molecule: BrU-labeled RNA


title: mES_1Gy_1h_1

description: molecule: BrU-labeled RNA


title: mES_1Gy_0.5h_1

description: molecule: BrU-labeled RNA


title: SAM53_r10_probing_4_iga

value: A/H5N1 HA + MF59


title: mES_0.1Gy_8h_1

description: molecule: BrU-labeled RNA


title: B412_Replicat2_pos_Zn_Mock_RNAseq

value: ZnSO4 0.1mM


title: B412_Replicat1_pos_Zn_Mock_RNAseq


title: mES_0.1Gy_4h_1

description: molecule: BrU-labeled RNA


title: SAM53_nop_probing_4_iga

value: no peptide


title: SAM53_m10_probing_4_iga

value: Mini HA-10ug/ml


title: SAM53_r50_probing_4_iga


title: mES_0.1Gy_1h_1

description: molecule: BrU-labeled RNA


title: mES_0.1Gy_0.5h_1

description: molecule: BrU-labeled RNA


title: MT_Replicat3_pos_Zn_Mock_RNAseq

source_name: U937 MT

value: U937 MT

value: parental cells


title: SAM01_r50_probing_4_iga


title: mES_0.1Gy_2h_1

description: molecule: BrU-labeled RNA


title: mES_Control_4h_1

description: molecule: BrU-labeled RNA


title: mES_Control_8h_1

description: molecule: BrU-labeled RNA


title: mES_Control_2h_1

description: molecule: BrU-labeled RNA


title: mES_Control_1h_1

description: molecule: BrU-labeled RNA


title: SAM01_nop_probing_4_iga


title: SAM50_nop_probing_4_iga


title: SAM53_m50_probing_4_iga

value: Mini HA -50ug/ml


title: mES_Control_0.5h_1

description: molecule: BrU-labeled RNA

value: embryonic stem cells


title: H1299 Rep2 Input

city: St. Louis

first: Ting

last: Wang

address: 4515 McKinley Ave

department: Genetics

institute: Washington University in St. Louis

library_source: genomic

data_processing:
Data were processed using the ENCODE ChIP-seq pipeline for transcription factors, outlined in their Github page (github.com/ENCODE-DCC/chip-seq-pipeline2) , and breifly described below:
ChIP-seq reads (fastq files) were trimmed using Cutadapt v1.10, with a minimum length requirement of 20 and -q 20,20
Trimmed paired-end sequencing reads (fastq files) for each ChIP sample and corresponding input were then run through the ENCODE ChIP-seq Pipeline 2, and first aligned to the hg19 genome using Bowtie2 v2.2.6
Macs2 was then run to calculate fold enrichment (signal over input) for both replicates
Fold enrichment files were then z-scored
Assembly: hg19
Supplementary files format and content: z-scored fold change (signal over input) bigWig files

source_name: lymph node-derived

growth_protocol: We cultured H1299 cells in RPMI1640 medium (Gibco, 11875-085) supplemented with 10% fetal bovine serum (Corning, 30-011-CV) and 100 U ml-1 penicillin-streptomycin (Gibco, 15140-122), as previously described in Jang, H. S. et al. Transposable elements drive widespread expression of oncogenes in human cancers. Nat. Genet. 51, 611–617 (2019).

extract_protocol:
The DNA samples were prepared using the SimpleChIP® Plus Enzymatic Chromatin IP Kit (9005, Cell Signaling Technology).
The Illumina standard library construction protocol was used including end repair, A-tailing, adapter ligation and PCR with indexed primers.
The paired end sequencing of ChIP-seq was run on the NextSeq 500 system.

value: lymph node-derived

value: non-small cell lung carcinoma

tag: chip antibody

value: none (input)


title: H1299 EZH2 ChIP, Rep 2


title: WT_25_e_2

first: Karel

last: Naiman

address: BD Lei Roure

data_processing:
library strategy: Pu-Seq (Polymerase-usage Sequencing)
The reads were mapped using bowtie2
Polymerase usage was determined by the tools published and described in detail in Daigaku et al., 2015 and Keszthelyi et al. 2015.
Assembly: Schizosaccharomyces pombe reference sequence (http://www.pombase.org/downloads/genome-datasets) with (1) wildtype genome (2) with inserted subtelomeric region on Chr2 and other subtelomeric regions were removed (3) Two rDNA regions removed and only one kept on left arm Chr3
Supplementary files format and content: CSV files contain read counts corresponding to incorporated rNTPs sorted into 300bp bins on each chromosome. They are in two files for forward and reverse strands separately.

organism: Schizosaccharomyces pombe

source_name: Schizosaccharomyces pombe

growth_protocol: Cells were grown at 25C or 30C or 34C in YE media to log phase. For ‘wt’ datasets two strains were used, both strains containing rnh201 deletion (or rnh201-RED mutant deficient in rNTP recognition) together with either polymerase δ (cdc6-L591G or cdc6-L591M) or polymerase ε (cdc20-M630F) mutations. These strains incorporate more rNTPs on the strands synthetized by the mutant polymerase. These sites can be mapped by Pu-seq.

extract_protocol:
DNA was prepared using the QIAGEN 100/G Genomic-tip. The isolated DNA was then subjected to alkali treatment (0.3 M NaOH, 2h 55°C) which digested the DNA at the positions of rNTP incorporation and also separated the double strands. The resulting ssDNA fragments were size selected on agarose gel (fragments between 300-500bp were isolated).
Polymerase usage sequence (Pu-seq) technique was performed as previously described (Daigaku et al., 2015 and Keszthelyi et al. 2015) with minor modifications: size selection was performed using Blue Pippin (Sage Science). In some instances we used rnh201-RED instead of rnh201::kan (see results).

tag: strain number

value: h- cdc20-M630F  rnh201-RED:kan ade6-704 leu1-32 ura4-D18


title: WT_25_d_2

value: h- cdc6-L591G  rnh201-RED:kan  ade6-704 leu1-32 ura4-D18


title: H1299 Rep1 Input


title: stn_rif_25_e_2

value: rif1{delta} stn1-226 (ts) rnh201{delta}::hphNT1 loxp:cdc20-M630F:loxm3 leu1-32 ura4-


title: SAM50_r10_probing_4_iga


title: SAM50_m50_probing_4_iga


title: H1299 EZH2 ChIP, Rep 1


title: MT_Replicat2_pos_Zn_Mock_RNAseq

value: Acute monocytic leukemia

value: Bone marrow


title: SAM50_r50_probing_4_iga

value: A/H5N1 HA + AS03

value: N


title: K562, LentiLong, Replicate 2, DNA-seq

city: LA JOLLA

first: Carlos

last: Guzman

state: CA

address: 9262 REGENTS RD

institute: UCSD

description: 64 cycles (read 1), 20 cycles (read 2)

data_processing:
TSS-MPRA mapping: A custom genome index made up of all of the sequences in the insert library was generated using STAR version 2.7.9a as follows: “STAR --runMode genomeGenerate --genomeDir <output_directory> --genomeFastaFiles <insert_library_fasta.fa> --genomeSAindexNbases 6”.    Paired-end reads were then mapped to the custom genome index using STAR as follows: “STAR --genomeDir <reference_genome_directory> --readFilesIn <read1_fastq.fq> <read2_fastq.fq> --outFileNamePrefix <output_prefix> --alignEndsType Extend5pOfRead1 --outSAMmultNmax -1 --outReadsUnmapped Fastx --alignEndsProtrude 50 ConcordantPair --seedMultimapNmax 1000000”.
TSS-MPRA quantification: TSS frequencies for both TSS-MPRA and csRNA-seq data was calculated by counting the number of times the 5’ end of read 1 overlapped each nucleotide. Total RNA abundance was calculated as the total number of TSS-MPRA-seq reads (read 2) that mapped to the unique barcode associated with each sequence. Similarly, total DNA abundance was calculated as the total number of DNA-seq reads (read 2) that mapped to the unique barcode associated with each sequence.
TSS-MPRA abundance normalization: After quantification, total RNA and DNA abundances are transformed into CPM values to account for differences in sequencing depth. Insert CPM-transformed RNA values are then normalized by dividing its RNA abundance by its DNA abundance. Thus, insert expression is expressed as the ratio between its total CPM-transformed RNA abundance divided by total CPM-transformed DNA abundance.
TSS-MPRA track visualization: TSS frequencies for all inserts were quantified as explained previously, and single-nucleotide bedgraph files were generated using a custom script (see GitHub). All bedgraph files were visualized using CoolBox(17).
Assembly: hg38
Supplementary files format and content: norm.quant.txt files: first 4k rows includes TSS-MPRA (rep 1 and rep 2) TPM-transformed read counts that are sum to one normalized per insert, as well as RNA and DNA abundance. Last 4k rows includes csRNA-seq (rep 1 and rep 2) TPM-transformed read counts that are sum to one normalized per genomic region, as well as RNA abundance.

growth_protocol: K562 cells were maintained in IMDM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvasted using typical TRIzol LS protocols (Invitrogen)
For TSS-MPRA, starting with 10-15 µg RNA (⅓ of the total), non-capped RNAs were dephosphorylated with Quick CIP (NEB) and DNA digested. Samples were mixed well and incubated at 37°C for 90 minutes. For more complete dephosphorylation of uncapped transcripts, RNA was denatured a second time at 75°C for 30 seconds in a pre-warmed water bath and then quickly chilled on ice for 2 minutes before incubating the sample at 37°C for another 30 minutes. As Quick CIP is thermolabile, the brief heat treatment leaves the enzyme active. Following Cap-enrichment, RNA was purified and then vortexed hard and subsequently spun for 10 minutes at 12k g at RT. Following phase separation, the upper layer was taken, and RNA precipitated. RNA pellets were then resuspended and 5' caps removed. Following decapping, 5’ adapters were ligated by T4RNA Ligase 1 and RNA extracted. RNA pellets were then resuspended and reverse transcribed. Samples were amplified and sequenced paired-end on a NextSeq 500 (additional details available in the manuscript)
TSS-MPRA

value: erythroleukemia

value: WT


title: K562, LentiLong, Replicate 1, DNA-seq

description: 64 cycles (read 1), 20 cycles (read 2)


title: stn_rif_25_d_2

value: rif1{delta} stn1-226 (ts) rnh201{delta}::hphNT1 loxp:cdc6-I591G:loxm3  leu1-32 ura4-


title: K562, EpiLong, Replicate 2, DNA-seq

description: 64 cycles (read 1), 20 cycles (read 2)


title: K562, LentiShort, Replicate 2, DNA-seq

description: 64 cycles (read 1), 20 cycles (read 2)


title: K562, LentiShort, Replicate 1, DNA-seq

description: 64 cycles (read 1), 20 cycles (read 2)


title: MT_Replicat1_pos_Zn_Mock_RNAseq

value: U937 MT

value: ZnSO4 0.1mM


title: stn_25_e_2

value: stn1-226 (ts) rnh201{delta}::hphNT1 loxp:cdc20-M630F:loxm3 leu1-32 ura4-


title: stn_25_d_2

value: stn1-226 (ts) rnh201{delta}::hphNT1 loxp:cdc6-I591G:loxm3  leu1-32 ura4-


title: SAM68_nop_probing_4_iga

value: A/H5N1 HA + PBS

value: no peptide


title: K562, EpiShort, Replicate 2, DNA-seq

description: 64 cycles (read 1), 20 cycles (read 2)


title: K562, EpiShort, Replicate 1, DNA-seq

description: 64 cycles (read 1), 20 cycles (read 2)


title: SAM68_r10_probing_4_iga


title: K562, LentiLong, Replicate 1, TSS-MPRA

description: 64 cycles (read 1), 20 cycles (read 2)


title: WT_34_d-2


title: WT_34_e-2


title: K562, LentiLong, Replicate 2, TSS-MPRA

description: 64 cycles (read 1), 20 cycles (read 2)


title: SAM68_m50_probing_4_iga

value: Mini HA -50ug/ml


title: K562, EpiLong, Replicate 2, TSS-MPRA

description: 64 cycles (read 1), 20 cycles (read 2)


title: K562, EpiLong, Replicate 1, TSS-MPRA

description: 64 cycles (read 1), 20 cycles (read 2)


title: SAM68_m10_probing_4_iga

value: Mini HA-10ug/ml


title: stn_rif_34_e-2


title: K562, LentiShort, Replicate 2, TSS-MPRA

description: 64 cycles (read 1), 20 cycles (read 2)


title: SAM50_m10_probing_4_iga


title: K562, EpiLong, Replicate 1, DNA-seq

description: 64 cycles (read 1), 20 cycles (read 2)


title: stn_rif_34_d_2


title: K562, LentiShort, Replicate 1, TSS-MPRA

description: 64 cycles (read 1), 20 cycles (read 2)


title: SAM68_r50_probing_4_iga


title: SAM61_nop_probing_4_iga

value: A/H5N1 HA + MF59


title: K562, EpiShort, Replicate 2, TSS-MPRA

description: 64 cycles (read 1), 20 cycles (read 2)


title: K562, EpiShort, Replicate 1, TSS-MPRA

description: 64 cycles (read 1), 20 cycles (read 2)


title: stn_34_e_2


title: stn_34_d_2


title: SAM61_m50_probing_4_iga


title: SAM61_m10_probing_4_iga


title: N3-lnc

city: Hefei

first: Liang

last: Chen

state: Anhui

address: NO. 443 Huangshan Road

country: China

institute: University of Science and Technology of China

data_processing:
The Hisat2 and feature counts software were used to map clean reads to reference genome (grcm38) and calculate the gene expression level which was normalized to FPKM.
the find_circ software (v 1.2) was utilized to predict the junction of circRNAs.
FPKMs were calculated by Featurecounts software.
Genome_build: hg19
Supplementary_files_format_and_content: raw counts; circRNA junction counts

source_name: Normal human blood

extract_protocol:
The peripheral blood samples and TRizol reagent(Invitrogen, USA) are evenly mixed in a ratio of 1:3, total of 12 ml. Total RNA was extracted by using Trizol reagent according to the manufacturer’s instructions.
Whole transcriptome libraries were constructed by the TruSeq Ribo Profile Library Prep Kit (Illumina, United States), according to the manufacturer’s instructions. In brief, 10 mg total RNA was depleted rRNA with an Illumina Ribo-Zero Gold kit and purified for end repair and 50-adaptor ligation. Then, reverse transcription was performed with random primers containing 30 adaptor sequences and randomized hexamers. Finally, the cDNAs were purified and amplified with thermo cycler. The PCR products of 300-500 bp were purified, quantified and stored at -80℃ before sequencing. The libraries were subjected to 151 nt paired-end sequencing with an Illumina Nextseq 500 system (Novogene, China). For small RNA (sRNA) sequencing, eight sRNA libraries were generated with TruSeq small RNA (Illumina, United States) according to the manufacturer’s instructions. Then the prepared libraries were sequenced with an Illumina Novaseq 6000 system (Novogene, China).

tag: subject status

value: normal; control

value: peripheral blood


title: SAM61_r10_probing_4_iga


title: N4-lnc


title: N2-lnc


title: N1-lnc


title: rif_25_e_2

value: cdc20- M630F rif1::BSD rnh201::kan ade6-704 leu1-32 ura4-D18


title: C4-lnc

source_name: Human blood with calcification

value: coronary arterial calcification (CAC) patient


title: SAM61_r50_probing_4_iga

value: N


title: rif_34_d_2

value: cdc6- L591G rif1::BSD rnh201::kan ade6-704 leu1-32 ura4-D18


title: C1-lnc


title: C2-lnc


title: N4-circ


title: rif_25_d_2


title: SAM45_nop_probing_4_iga

value: A/H5N1 HA + AS03

value: Y


title: N1-circ


title: N2-circ


title: C4-circ


title: C3-circ


title: C2-circ


title: taz_e_2

value: h- cdc20-M630F  rnh201-RED:kan taz1::NAT ade6-704 leu1-32 ura4-D18


title: rif_34_e_2


title: taz_d_2

value: h- cdc6-L591G  rnh201-RED:kan  taz1::NAT ade6-704 leu1-32 ura4-D18


title: SAM45_r50_probing_4_iga


title: C1-circ


title: taz_e_1


title: C3-lnc


title: TH105a

city: Dallas

first: Yujin

last: Hoshida

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

data_processing:
Raw cDNA reads are aligned to the reference genome (hg19) using the spliced gap aligner STAR, with count-based quantitation carried out via the Subread package featureCounts at the gene levels. The count data were normalized using “Relative Log Expression” normalization (RLE) implemented in the DESeq2 R package. Poor-quality transcriptome profiles were determined based on inter-sample correlation <0.7 and excluded from the subsequent analyses.
Genome_build: hg19
Supplementary_files_format_and_content: .gct file format (tab-delimited text) including normalized gene expression levels.

extract_protocol:
RNA was isolated from 10 micron-thick FFPE tissue using High Pure RNA Paraffin kit (Roche) according to manufacturer’s protocol.
Truseq RNA Exome kit (Illumina, CA) following manufacturer’s protocol.

value: Liver

tag: age

tag: Sex

value: male

tag: fibrosis stage

tag: nafld activity score

tag: pls-nafld-based risk prediction

value: low-risk


title: SAM45_m10_probing_4_iga

tag: subject id


title: N3-circ


title: SAM45_m50_probing_4_iga

tag: day


title: SAM32_m50_probing_4_iga

value: A/H5N1 HA + PBS

tag: blocking


title: SAM32_r10_probing_4_iga


title: KU140a


title: WT_25_e_1

value: h- cdc20-M630F  rnh201-RED:kan ade6-704 leu1-32 ura4-D18


title: TH102a

value: high-risk


title: taz_d_1


title: TH103a


title: KU144a


title: WT_25_d_1

value: h- cdc6-L591G  rnh201-RED:kan  ade6-704 leu1-32 ura4-D18


title: KU138a


title: KU135a


title: SAM45_r10_probing_4_iga


title: SAM32_r50_probing_4_iga


title: KU131a


title: stn_rif_25_e_1

value: rif1{delta} stn1-226 (ts) rnh201{delta}::hphNT1 loxp:cdc20-M630F:loxm3 leu1-32 ura4-


title: KU128a


title: KU124a


title: KU126a


title: SAM32_m10_probing_4_iga

value: Mini HA-10ug/ml


title: stn_rif_25_d_1

value: rif1{delta} stn1-226 (ts) rnh201{delta}::hphNT1 loxp:cdc6-I591G:loxm3  leu1-32 ura4-


title: SAM32_nop_probing_4_iga

value: no peptide


title: KU130a

value: female


title: KU122a


title: KU143a


title: stn_25_e_1

value: stn1-226 (ts) rnh201{delta}::hphNT1 loxp:cdc20-M630F:loxm3 leu1-32 ura4-


title: stn_25_d_1

value: stn1-226 (ts) rnh201{delta}::hphNT1 loxp:cdc6-I591G:loxm3  leu1-32 ura4-


title: SAM69_nop_probing_4_iga

value: A/H5N1 HA + MF59

value: N


title: KU116a


title: KU120a


title: KU121a


title: SAM066_probing_1_iga


title: KU119a


title: KU118a


title: rif_25_e_1

value: cdc20- M630F rif1::BSD rnh201::kan ade6-704 leu1-32 ura4-D18


title: SAM050_probing_1_iga


title: SAM332_probing_1_iga


title: KU111a

value: Liver


title: rif_25_d_1

value: cdc6- L591G rif1::BSD rnh201::kan ade6-704 leu1-32 ura4-D18


title: KU113a

value: low-risk


title: rif_34_e_1


title: SAM319_probing_1_iga

value: Y


title: rif_34_d_1


title: SAM019_probing_1_iga


title: KU102a

value: male


title: KU107a


title: WT_34_e-1

value: h- cdc20-M630F  rnh201-RED:kan ade6-704 leu1-32 ura4-D18


title: SAM351_probing_1_iga

value: A/H5N1 HA + PBS


title: KU101a

value: high-risk


title: KU106a


title: WT_34_d-1

value: h- cdc6-L591G  rnh201-RED:kan  ade6-704 leu1-32 ura4-D18


title: KU115a


title: SAM310_probing_1_iga


title: KU097a


title: SAM154_probing_1_iga


title: KU093a


title: stn_rif_34_e-1

value: rif1{delta} stn1-226 (ts) rnh201{delta}::hphNT1 loxp:cdc20-M630F:loxm3 leu1-32 ura4-


title: KU092a


title: KU109a


title: stn_rif_34_d_1

value: rif1{delta} stn1-226 (ts) rnh201{delta}::hphNT1 loxp:cdc6-I591G:loxm3  leu1-32 ura4-


title: SAM164_probing_1_iga


title: SAM094_probing_1_iga


title: stn_34_e_1


title: stn_34_d_1


title: KU086a


title: KU095a


title: SAM191_probing_1_iga


title: KU085a


title: SAM266_probing_1_iga


title: KU088a


title: KU089a


title: KU100a

value: female


title: KU078a


title: SAM159_probing_1_iga


title: KU081a


title: KU077a


title: KU076a


title: KU079a


title: PGDM_1

city: GUWAHATI

first: SANJAY

middle: K

last: BANERJEE

state: ASSAM

address: CHANGSARI

country: India

institute: NATIONAL INSTITUTE OF PHARMACEUTICAL EDUCATION AND RESEARCH

description: Neonatal hearts derived from diabetic female rats

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence using Cutadapt, and removed the low-quality bases (<q30), then mapped to Rnor_6.0 whole genome usingHisat2.
Cufflinks was used to estimate and calculate transcript abundance. Fragments Per Kilobase of transcript per Million of mapped reads (FPKM) were calculated.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: Transcript abundance text files for every sample

organism: Rattus norvegicus

source_name: Heart

extract_protocol:
Hearts were removed, flash frozen on liquid nitrogen, and RNA was harvested using Trizol reagent. RNA-seq libraries were prepared with NEBNext Ultra directional RNA Library Prep Kit with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: Sprague dawley

value: heart

tag: group

value: Diabetes

value: post natal day 2


title: SAM027_probing_1_iga

value: A/H5N1 HA + MF59

value: N


title: KU087a

value: Liver


title: PGDM_2


title: PGDM_4


title: SAM179_probing_1_iga


title: KU074a


title: Control_4

description: Neonatal hearts derived from control female rats

value: Control


title: KU091a

value: low-risk


title: KU075a

value: male


title: SAM141_probing_1_iga


title: Control_3


title: PGDM_3


title: Control_2


title: KU069a


title: KU065a


title: SAM242_probing_1_iga

value: Y


title: SAM198_probing_1_iga

value: A/H5N1 HA + PBS


title: Control_1


title: KU072a

value: high-risk


title: Seedlings, SUC2::CDF6, 22, Rep3

city: Riverside

first: Dawn

last: Nagel

address: 3401 Watkins Avenue (Batchelor Hall Rm 1123)

department: Botany and Plant Sciences

institute: University of Califonia, Riverside

data_processing:
Basic read processing
Filtering was performed with cutadapt with default settings
RNA-seqeuncing reads were aligned to the Araport11 gff file using HISAT2 (version 2.0.1)
Relative gene expression was calculated using edgeR and limma
Araport 11 GFF (201606)
Genome_build: Excel file ith log2fold-change with false discovery rate and counts per million

organism: Arabidopsis thaliana

source_name: 11-day-old whole seedling tissue

growth_protocol: Arabidopsis plants were grown for 8 days in diurnal light at 22°C, transferred to constant light at 22°C, and then sampled at ZT0

extract_protocol:
GeneJET Plant RNA Purification Kits were used to extract total RNA
Libraries were constructed using protocol adapted from: A high-throughput method for Illumina RNA-Seq library preparation. See Temporal dynamics of temperature stress responses in Arabidopsis for details.

treatment_protocol: Plants were exposed to temperature stress for 1 hour at 0 hours after lights on

value: 11-day-old seedling

value: whole seedling

tag: genotype

tag: temperature

tag: replicate

tag: time


title: KU050a

tag: tissue


title: KU039a


title: SAM078_probing_1_iga

tag: treatment


title: KU061a


title: KU073a


title: SAM352_probing_1_iga


title: KU022a


title: Seedlings, SUC2::CDF6, 22, Rep2


title: KU020a


title: Seedlings, SUC2::CDF6, 22, Rep1


title: KU012a


title: SAM259_probing_1_iga


title: SAM120_probing_1_iga


title: KU068a


title: HUnafld110_2

data_processing:
Raw cDNA reads are aligned to the reference genome (hg19) using the spliced gap aligner STAR, with count-based quantitation carried out via the Subread package featureCounts at the gene levels. The count data were normalized using “Relative Log Expression” normalization (RLE) implemented in the DESeq2 R package. Poor-quality transcriptome profiles were determined based on inter-sample correlation <0.7 and excluded from the subsequent analyses.
Genome_build: hg19
Supplementary_files_format_and_content: .gct file format (tab-delimited text) including normalized gene expression levels normalized within 106 1st biopsy tissues (NAFLD.HUn106.gct) and within the 58 high-risk patients with paired biopsy tissues (NAFLD.HUn164.gct).

tag: biopsy

value: 2nd biopsy

tag: pls-nafld-based risk prediction at 1st biopsy


title: KU002a

tag: age

tag: Sex

value: female


title: HUnafld111_2

tag: fibrosis stage

tag: nafld activity score


title: HUnafld112_2


title: Seedlings, SUC2::CDF6, 10, Rep2


title: KU059a

tag: pls-nafld-based risk prediction


title: SAM378_probing_1_iga

tag: subject id

tag: day


title: KU062a


title: Seedlings, SUC2::CDF6, 10, Rep1


title: SAM315_probing_1_iga


title: HUnafld107_2


title: Seedlings, cdf6, 22, Rep3


title: HUnafld109_2


title: SAM324_probing_1_iga


title: HUnafld106_2


title: Seedlings, cdf6, 22, Rep2


title: HUnafld103_2


title: SAM235_probing_1_iga


title: HUnafld102_2


title: Seedlings, SUC2::CDF6, 10, Rep3


title: Seedlings, cdf6, 22, Rep1


title: SAM249_probing_1_iga


title: HUnafld101_2


title: HUnafld099_2


title: HUnafld098_2


title: Seedlings, cdf6, 10, Rep3


title: SAM170_probing_1_iga


title: SAM269_probing_1_iga

value: A/H5N1 HA + AS03


title: HUnafld096_2


title: Seedlings, cdf6, 10, Rep2


title: HUnafld095_2


title: SAM388_probing_1_iga


title: HUnafld108_2


title: Seedlings, cdf6, 10, Rep1


title: HUnafld092_2


title: HUnafld097_2


title: HUnafld093_2


title: SAM346_probing_1_iga


title: HUnafld091_2


title: Seedlings, WT, 22, Rep3

value: WT


title: Seedlings, WT, 22, Rep2


title: HUnafld090_2


title: HUnafld089_2


title: SAM162_probing_1_iga


title: Seedlings, WT, 22, Rep1


title: HUnafld087_2


title: HUnafld088_2


title: HUnafld085_2


title: HUnafld082_2


title: Seedlings, WT, 10, Rep3


title: HUnafld094_2


title: Seedlings, WT, 10, Rep2


title: SAM088_probing_1_iga


title: SAM384_probing_1_iga


title: Seedlings, WT, 10, Rep1


title: HUnafld081_2


title: ARDS COVID-19, BALF [DE11NGSUKBR115308]

city: Bonn

first: Katarzyna

last: Placek

address: Carl-Troll-Str. 79

country: Germany

institute: Univeristy of Bonn

data_processing:
The RNA-seq 3’ data were processed with nf-core RNA-seq v1.4.2 (Ewels et al., 2020) pipeline using STAR (Dobin et al., 2013) for alignment and featureCounts for gene quantification (Liao et al., 2014).
The library strandedness parameter was set to forward and the reference was set to GRCh38.
Statistical analysis was performed in the R environment (R Core Team, 2019) with the Bioconductor R-package DESeq2 (Huber et al., 2015; Love et al., 2014).
The Benjamini-Hochberg method was used to calculate multiple testing adjusted p-values.
Only genes with at least 20 read counts in at least 3 samples and at least 60 read counts in total across all samples were considered for analysis.
Assembly: hg38
Supplementary files format and content: merged gene count matrix, excel file

source_name: bronchoalveolar lavage fluid (BALF)

extract_protocol:
bronchoalveolar lavage fluid (BALF) was collected via direct bronchoscopy within 24h of ARDS onset. 200 ml sterile NaCl was fractioned injected into the right middle lobe and immediately retracted. Mucus was removed by a 70μm cell strainer. Cells were centrifuged (5 min, 400g, 4°C) and stored at -80°C for later analyzes. RNA was extracted by the NucleoSpin RNA Plus Mini kit (Macherey-Nagel).
After RNA isolation, 100 ng total RNA were used for library preparation using QuantSeq 3´ mRNA-Seq Library Prep kit (Lexogen) according to manufacturer´s instructions
Samples were subjected to RNA-sequencing on a NovaSeq 6000 sequencer (Illumina) with 1x100 bp single-end reads and a mean coverage of 10 million raw reads per sample

value: bronchoalveolar lavage fluid (BALF)

tag: cell type

value: primary cells

tag: disease state

value: severe COVID-19


title: HUnafld078_2


title: HUnafld076_2


title: HUnafld079_2


title: HUnafld075_2


title: SAM043_probing_1_iga


title: HUnafld077_2


title: HUnafld080_2


title: SAM194_probing_1_iga


title: ARDS COVID-19, BALF [DE38NGSUKBR115307]


title: SAM001_probing_1_iga


title: SAM297_probing_1_iga


title: HUnafld074_2


title: HUnafld071_2


title: ARDS COVID-19, BALF [DE65NGSUKBR115306]


title: HUnafld069_2


title: SAM127_probing_1_iga


title: ARDS COVID-19, BALF [DE36NGSUKBR115343]


title: SAM083_probing_1_iga


title: SAM228_probing_1_iga

value: N


title: SAM369_probing_1_iga


title: HUnafld072_2

value: Liver


title: SAM217_probing_1_iga


title: HUnafld068_2


title: HUnafld067_2


title: HUnafld063_2


title: HUnafld066_2


title: ARDS COVID-19, BALF [DE04NGSUKBR115337]


title: HUnafld058_2


title: SAM067_probing_1_iga


title: SAM210_probing_1_iga


title: HUnafld054_2


title: ARDS COVID-19, BALF [DE53NGSUKBR115328]


title: HUnafld059_2


title: ARDS COVID-19, BALF [DE31NGSUKBR115336]


title: HUnafld064_2


title: ARDS COVID-19, BALF [DE10NGSUKBR115326]


title: HUnafld057_2


title: HUnafld052_2


title: ARDS COVID-19, BALF [DE64NGSUKBR115324]


title: SAM303_probing_1_iga


title: HUnafld053_2


title: HUnafld056_2


title: HUnafld050_2


title: HUnafld070_2


title: SAM253_probing_1_iga


title: ARDS COVID-19, BALF [DE91NGSUKBR115323]


title: HUnafld060_2


title: HUnafld049_2


title: HUnafld048_2


title: ARDS COVID-19, BALF [DE20NGSUKBR115340]


title: ARDS COVID-19, BALF [DE21NGSUKBR115322]


title: SAM199_probing_1_iga


title: HUnafld047_2


title: HUnafld046_2


title: SAM292_probing_1_iga


title: SAM261_probing_1_iga


title: ARDS COVID-19, BALF [DE32NGSUKBR115318]


title: HUnafld039_2


title: HUnafld038_2


title: SAM181_probing_1_iga


title: HUnafld035_2


title: HUnafld113

description:
NAFLD.HUn106.gct
NASH.HUn164.gct

value: 1st biopsy


title: ARDS COVID-19, BALF [DE16NGSUKBR115315]


title: HUnafld112_1

description:
NAFLD.HUn106.gct
NASH.HUn164.gct


title: ARDS COVID-19, BALF [DE70NGSUKBR115313]


title: SAM026_probing_1_iga


title: HUnafld111_1

description:
NAFLD.HUn106.gct
NASH.HUn164.gct


title: HUnafld110_1

description:
NAFLD.HUn106.gct
NASH.HUn164.gct


title: ARDS COVID-19, BALF [DE27NGSUKBR115311]


title: HUnafld109_1

description:
NAFLD.HUn106.gct
NASH.HUn164.gct


title: ARDS COVID-19, BALF [DE54NGSUKBR115310]


title: HUnafld108_1

description:
NAFLD.HUn106.gct
NASH.HUn164.gct


title: ARDS COVID-19, BALF [DE75NGSUKBR115320]


title: SAM056_probing_1_iga


title: HUnafld106_1

description:
NAFLD.HUn106.gct
NASH.HUn164.gct


title: HUnafld107_1

description:
NAFLD.HUn106.gct
NASH.HUn164.gct


title: SAM387_probing_1_iga


title: HUnafld105

description:
NAFLD.HUn106.gct
NASH.HUn164.gct

value: low-risk


title: SAM313_probing_1_iga


title: HUnafld103_1

description:
NAFLD.HUn106.gct
NASH.HUn164.gct

value: male


title: ARDS COVID-19, BALF [DE81NGSUKBR115309]


title: ARDS Influenza, BALF [DE71NGSUKBR115295]

value: severe Influenza


title: ARDS Influenza, BALF [DE44NGSUKBR115296]


title: HUnafld104

description:
NAFLD.HUn106.gct
NASH.HUn164.gct


title: SAM126_probing_1_iga

value: Y


title: SAM284_probing_1_iga


title: HUnafld100

description:
NAFLD.HUn106.gct
NASH.HUn164.gct


title: HUnafld101_1

description:
NAFLD.HUn106.gct
NASH.HUn164.gct

value: high-risk


title: HUnafld098_1

description:
NAFLD.HUn106.gct
NASH.HUn164.gct


title: HUnafld102_1

description:
NAFLD.HUn106.gct
NASH.HUn164.gct


title: HUnafld099_1

description:
NAFLD.HUn106.gct
NASH.HUn164.gct


title: SAM336_probing_1_iga

value: A/H5N1 HA + PBS


title: ARDS Influenza, BALF [DE98NGSUKBR115294]


title: HUnafld097_1

description:
NAFLD.HUn106.gct
NASH.HUn164.gct


title: HUnafld096_1

description:
NAFLD.HUn106.gct
NASH.HUn164.gct


title: SAM072_probing_1_iga


title: HUnafld095_1

description:
NAFLD.HUn106.gct
NASH.HUn164.gct


title: HUnafld094_1

description:
NAFLD.HUn106.gct
NASH.HUn164.gct


title: SAM260_probing_1_iga


title: ARDS Influenza, BALF [DE55NGSUKBR115292]


title: ARDS Influenza, BALF [DE82NGSUKBR115291.]


title: HUnafld093_1

description:
NAFLD.HUn106.gct
NASH.HUn164.gct


title: HUnafld092_1

description:
NAFLD.HUn106.gct
NASH.HUn164.gct


title: SAM116_probing_1_iga


title: ARDS Influenza, BALF [DE39NGSUKBR115289]


title: SAM079_probing_1_iga


title: ARDS Influenza, BALF [DE23NGSUKBR115286]


title: HUnafld090_1

description:
NAFLD.HUn106.gct
NASH.HUn164.gct


title: HUnafld091_1

description:
NAFLD.HUn106.gct
NASH.HUn164.gct


title: ARDS Influenza, BALF [DE66NGSUKBR115288]


title: SAM099_probing_1_iga


title: HUnafld088_1

description:
NAFLD.HUn106.gct
NASH.HUn164.gct


title: HUnafld087_1

description:
NAFLD.HUn106.gct
NASH.HUn164.gct


title: HUnafld089_1

description:
NAFLD.HUn106.gct
NASH.HUn164.gct


title: ARDS Influenza, BALF [DE28NGSUKBR115293]


title: SAM362_probing_1_iga


title: HUnafld085_1

description:
NAFLD.HUn106.gct
NASH.HUn164.gct


title: HUnafld083

description:
NAFLD.HUn106.gct
NASH.HUn164.gct


title: TWCM-707

city: Saint Louis

first: Pan

last: Ma

state: United States

address: CSRB, Room 9918, 425 S Euclid, Saint Louis, MO, 63110

institute: Washington University in Saint Louis

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Alignment: Cell Ranger V3, aligned to GRCh38 transcriptome, or custom pre-mrna reference.
QC and Filtering: Seurat V3/V4
Unsupervised Clustering: Seurat V3/V4
Assembly: GRCh38 V3.0.0
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Transmural LV Apex

extract_protocol:
Transmural tissue samples were removed from the left ventricle apex during LVAD implantation or after whole heart explantation. Samples for single nuclei were frozen in liquid nitrogen and stored at -80C until use and processed by mechanical homogenization. All single nuclei suspensions were sorted by FACS to remove debris.
10X Genomics Chromium Single Cell 5’ Reagent V1.1

value: Transmural LV Apex

tag: storage

value: minus 80 degrees

tag: technology

value: Single Nuclei

value: Sarcoidosis


title: HUnafld082_1

description:
NAFLD.HUn106.gct
NASH.HUn164.gct


title: TWCM-761

description: 10x Genomics


title: TWCM-676

description: 10x Genomics


title: SAM305_probing_1_iga


title: SAM013_probing_1_iga

value: A/H5N1 HA + AS03


title: HUnafld081_1

description:
NAFLD.HUn106.gct
NASH.HUn164.gct

value: female


title: HUnafld084

description:
NAFLD.HUn106.gct
NASH.HUn164.gct


title: TWCM-574

description: 10x Genomics


title: HUnafld080_1

description:
NAFLD.HUn106.gct
NASH.HUn164.gct


title: SAM345_probing_1_iga


title: HUnafld079_1

description:
NAFLD.HUn106.gct
NASH.HUn164.gct


title: HUnafld078_1

description:
NAFLD.HUn106.gct
NASH.HUn164.gct


title: SAM262_probing_1_iga


title: HUnafld075_1

description:
NAFLD.HUn106.gct
NASH.HUn164.gct


title: HUnafld077_1

description:
NAFLD.HUn106.gct
NASH.HUn164.gct


title: SAM271_probing_1_iga


title: HUnafld076_1

description:
NAFLD.HUn106.gct
NASH.HUn164.gct


title: HUnafld073

description:
NAFLD.HUn106.gct
NASH.HUn164.gct


title: HUnafld086

description:
NAFLD.HUn106.gct
NASH.HUn164.gct


title: TWCM-11-290

description: 10x Genomics

value: ICM


title: HUnafld074_1

description:
NAFLD.HUn106.gct
NASH.HUn164.gct


title: TWCM-11-173

description: 10x Genomics


title: D14_IA3_S36_L004

address: 1635 Aurora Ct

institute: University of Colorado

data_processing:
base-calling done by Real-Time Analysis software v3.3.3
fastq file demultiplexing done by bcl2fastq2 Conversion Software v2.20.0.422
RNA paired-end reads were aligned at the transcript level to Ensembl GRCh38 using Kallisto with the average mapping rate 90.1%. 120,425 transcripts were detected in the mRNA dataset using Gencode v27
Differential expression was assessed using the DESeq2 package in R
Benjamini-Hochberg false discovery rate (FDR)-adjusted p-values <0.05 were considered significant
Assembly: GENCODE GRCh38 v27
Supplementary files format and content: RNA-seq counts quantified by kallisto are transcript-level pseudo-counts in comma-delimited format

source_name: Primary airway epithelial cells

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit
mRNA libraries were prepared from 500 ng total RNA with TruSeq stranded mRNA library preparation kits
Sequenced at the averaged depth of 92.4M reads on the Illumina NovaSeq 6000

tag: epithelial donor

value: F

tag: epithelial disease_status

value: IPF

tag: fibroblast disease_status

value: No fibroblast

tag: timepoint

value: day 14

value: M

value: Primary airway epithelial cells


title: HUnafld072_1

description:
NAFLD.HUn106.gct
NASH.HUn164.gct

tag: tissue

value: Liver

tag: biopsy

value: 1st biopsy

value: male


title: D14_IA2_S35_L004

value: E

tag: age


title: SAM365_probing_1_iga

tag: treatment

value: N


title: SAM245_probing_1_iga


title: HUnafld071_1

description:
NAFLD.HUn106.gct
NASH.HUn164.gct

tag: Sex

tag: fibrosis stage

tag: pls-nafld-based risk prediction at 1st biopsy

value: high-risk


title: HUnafld070_1

description:
NAFLD.HUn106.gct
NASH.HUn164.gct

tag: nafld activity score


title: HUnafld069_1

description:
NAFLD.HUn106.gct
NASH.HUn164.gct


title: SAM251_probing_1_iga

tag: subject id

tag: day

value: Y


title: D14_IA1_S34_L004

value: D

tag: cell type


title: SAM015_probing_1_iga

value: A/H5N1 HA + PBS


title: D14_CA3_IF_S33_L004

value: C

value: Control


title: HUnafld068_1

description:
NAFLD.HUn106.gct
NASH.HUn164.gct

value: female


title: HUnafld066_1

description:
NAFLD.HUn106.gct
NASH.HUn164.gct


title: HUnafld067_1

description:
NAFLD.HUn106.gct
NASH.HUn164.gct


title: SAM016_probing_1_iga


title: D14_CA1_IF_S31_L004

value: A

value: IPF


title: TWCM-11-193

description: 10x Genomics

value: Transmural LV Apex

tag: storage

value: minus 80 degrees

value: Single Nuclei

tag: disease state

value: ICM


title: D14_CA2_IF_S32_L004

tag: epithelial donor

value: B

value: day 14

value: M

value: Primary airway epithelial cells


title: HUnafld064_1

description:
NAFLD.HUn106.gct
NASH.HUn164.gct

value: Liver

value: 1st biopsy

value: male

value: high-risk


title: HUnafld065

description:
NAFLD.HUn106.gct
NASH.HUn164.gct

value: low-risk


title: HUnafld063_1

description:
NAFLD.HUn106.gct
NASH.HUn164.gct


title: SAM145_probing_1_iga

value: A/H5N1 HA + AS03

value: Y


title: HUnafld062

description:
NAFLD.HUn106.gct
NASH.HUn164.gct

value: female


title: SAM022_probing_1_iga

value: A/H5N1 HA + PBS


title: HUnafld061

description:
NAFLD.HUn106.gct
NASH.HUn164.gct


title: SAM174_probing_1_iga

value: N


title: SAM246_probing_1_iga


title: D14_CA3_CF_S30_L004

value: C

tag: epithelial disease_status

value: Control

value: F


title: HUnafld059_1

description:
NAFLD.HUn106.gct
NASH.HUn164.gct


title: HUnafld060_1

description:
NAFLD.HUn106.gct
NASH.HUn164.gct


title: D14_CA2_CF_S29_L004

value: B

tag: fibroblast disease_status


title: HUnafld058_1

description:
NAFLD.HUn106.gct
NASH.HUn164.gct


title: D14_CA1_CF_S28_L004

value: A

tag: timepoint

value: day 14


title: SAM244_probing_1_iga


title: SAM275_probing_1_iga


title: HUnafld056_1

description:
NAFLD.HUn106.gct
NASH.HUn164.gct

tag: tissue


title: HUnafld057_1

description:
NAFLD.HUn106.gct
NASH.HUn164.gct

tag: biopsy


title: D14_CA3_S27_L004

value: No fibroblast

tag: age

value: Primary airway epithelial cells


title: HUnafld055

description:
NAFLD.HUn106.gct
NASH.HUn164.gct

value: Liver

value: 1st biopsy


title: HUnafld054_1

description:
NAFLD.HUn106.gct
NASH.HUn164.gct

value: high-risk


title: SAM357_probing_1_iga

tag: treatment


title: HUnafld053_1

description:
NAFLD.HUn106.gct
NASH.HUn164.gct

tag: Sex

value: male


title: SAM073_probing_1_iga

value: A/H5N1 HA + AS03


title: D14_CA2_S26_L004

value: M


title: D14_CA1_S25_L004


title: SAM040_probing_1_iga

value: Y


title: HUnafld051

description:
NAFLD.HUn106.gct
NASH.HUn164.gct

tag: fibrosis stage

value: low-risk


title: HUnafld050_1

description:
NAFLD.HUn106.gct
NASH.HUn164.gct

tag: pls-nafld-based risk prediction at 1st biopsy


title: HUnafld048_1

description:
NAFLD.HUn106.gct
NASH.HUn164.gct

tag: nafld activity score


title: D8_IA3_S24_L004

value: IPF

value: day 8


title: SAM373_probing_1_iga

tag: subject id


title: D8_IA2_S23_L004

value: E


title: D8_IA1_S22_L004

value: D


title: HUnafld045

description:
NAFLD.HUn106.gct
NASH.HUn164.gct


title: SAM268_probing_1_iga

tag: day


title: HUnafld044

description:
NAFLD.HUn106.gct
NASH.HUn164.gct


title: SAM238_probing_1_iga

value: A/H5N1 HA + PBS


title: HUnafld047_1

description:
NAFLD.HUn106.gct
NASH.HUn164.gct


title: D8_CA3_IF_S21_L004

value: C

value: Control

value: F

tag: cell type


title: HUnafld046_1

description:
NAFLD.HUn106.gct
NASH.HUn164.gct

value: female


title: HUnafld041

description:
NAFLD.HUn106.gct
NASH.HUn164.gct

value: Liver


title: HUnafld042

description:
NAFLD.HUn106.gct
NASH.HUn164.gct

value: 1st biopsy


title: SAM168_probing_1_iga


title: HUnafld052_1

description:
NAFLD.HUn106.gct
NASH.HUn164.gct

value: high-risk


title: HUnafld040

description:
NAFLD.HUn106.gct
NASH.HUn164.gct


title: D8_CA2_IF_S20_L004

value: B

value: Primary airway epithelial cells


title: D8_CA1_IF_S19_L004

value: A

value: M


title: SAM180_probing_1_iga

value: N


title: HUnafld039_1

description:
NAFLD.HUn106.gct
NASH.HUn164.gct

value: male


title: D8_CA3_CF_S18_L004

value: day 8


title: HUnafld049_1

description:
NAFLD.HUn106.gct
NASH.HUn164.gct


title: D8_CA2_CF_S17_L004


title: SAM376_probing_1_iga

value: A/H5N1 HA + AS03


title: HUnafld036

description:
NAFLD.HUn106.gct
NASH.HUn164.gct

value: low-risk


title: HUnafld038_1

description:
NAFLD.HUn106.gct
NASH.HUn164.gct


title: HUnafld037

description:
NAFLD.HUn106.gct
NASH.HUn164.gct


title: HUnafld043

description:
NAFLD.HUn106.gct
NASH.HUn164.gct


title: HUnafld029

description:
NAFLD.HUn106.gct
NASH.HUn164.gct


title: HUnafld034

description:
NAFLD.HUn106.gct
NASH.HUn164.gct


title: D8_CA1_CF_S16_L004


title: SAM029_probing_1_iga

value: A/H5N1 HA + PBS

value: Y


title: SAM278_probing_1_iga


title: HUnafld027

description:
NAFLD.HUn106.gct
NASH.HUn164.gct


title: HUnafld024

description:
NAFLD.HUn106.gct
NASH.HUn164.gct


title: HUnafld026

description:
NAFLD.HUn106.gct
NASH.HUn164.gct


title: SAM085_probing_1_iga


title: SAM341_probing_1_iga


title: HUnafld023

description:
NAFLD.HUn106.gct
NASH.HUn164.gct


title: SAM163_probing_1_iga


title: D8_CA2_S14_L004

value: Control

value: No fibroblast


title: HUnafld025

description:
NAFLD.HUn106.gct
NASH.HUn164.gct

value: female


title: HUnafld020

description:
NAFLD.HUn106.gct
NASH.HUn164.gct

value: Liver


title: HUnafld021

description:
NAFLD.HUn106.gct
NASH.HUn164.gct

value: 1st biopsy


title: HUnafld019

description:
NAFLD.HUn106.gct
NASH.HUn164.gct


title: SAM302_probing_1_iga


title: HUnafld017

description:
NAFLD.HUn106.gct
NASH.HUn164.gct

value: high-risk


title: D4_IA1_S10_L004

value: D

value: IPF

value: day 4


title: SAM103_probing_1_iga


title: HUnafld018

description:
NAFLD.HUn106.gct
NASH.HUn164.gct


title: D4_IA3_S12_L004

value: F

value: M

value: Primary airway epithelial cells


title: D4_IA2_S11_L004

value: E


title: HUnafld035_1

description:
NAFLD.HUn106.gct
NASH.HUn164.gct

value: male


title: D8_CA3_S15_L004

value: C

value: day 8


title: SAM041_probing_1_iga

value: A/H5N1 HA + AS03

value: N


title: HUnafld016

description:
NAFLD.HUn106.gct
NASH.HUn164.gct

value: low-risk


title: HUnafld015

description:
NAFLD.HUn106.gct
NASH.HUn164.gct

value: female


title: SAM111_probing_1_iga

value: Y


title: HUnafld013

description:
NAFLD.HUn106.gct
NASH.HUn164.gct

value: Liver

value: 1st biopsy


title: D4_CA3_IF_S9_L004

value: Control


title: SAM334_probing_1_iga

value: A/H5N1 HA + PBS


title: HUnafld012

description:
NAFLD.HUn106.gct
NASH.HUn164.gct


title: D8_CA1_S13_L004

value: A

value: No fibroblast


title: D4_CA2_IF_S8_L004

value: B

value: IPF

value: day 4

value: M


title: HUnafld007

description:
NAFLD.HUn106.gct
NASH.HUn164.gct

value: male


title: HUnafld009

description:
NAFLD.HUn106.gct
NASH.HUn164.gct


title: HUnafld008

description:
NAFLD.HUn106.gct
NASH.HUn164.gct


title: D4_CA3_CF_S6_L004

value: C

value: F

value: Primary airway epithelial cells


title: SAM218_probing_1_iga

value: N


title: SAM380_probing_1_iga

value: A/H5N1 HA + AS03


title: HUnafld005

description:
NAFLD.HUn106.gct
NASH.HUn164.gct

value: low-risk


title: SAM118_probing_1_iga


title: HUnafld004

description:
NAFLD.HUn106.gct
NASH.HUn164.gct

value: Liver

value: high-risk


title: HUnafld003

description:
NAFLD.HUn106.gct
NASH.HUn164.gct

value: 1st biopsy


title: D4_CA2_CF_S5_L004

value: Control


title: D4_CA1_CF_S4_L004

value: A


title: HUnafld001

description:
NAFLD.HUn106.gct
NASH.HUn164.gct

value: female


title: HUnafld011

description:
NAFLD.HUn106.gct
NASH.HUn164.gct


title: D4_CA3_S3_L004

value: No fibroblast


title: SAM129_probing_1_iga

value: Y


title: SAM151_probing_1_iga


title: TUnafld059

tag: pls-nafld-based risk prediction


title: HUnafld002

description:
NAFLD.HUn106.gct
NASH.HUn164.gct


title: SAM010_probing_1_iga

value: A/H5N1 HA + PBS


title: HUnafld010

description:
NAFLD.HUn106.gct
NASH.HUn164.gct


title: TUnafld052


title: TUnafld061


title: TUnafld060


title: DH_14_4_S80

source_name: Epithelial cells

tag: disease region

value: distal airway, honeycombed

value: day 14

value: Male

value: Epithelial cells


title: TUnafld050


title: D4_CA1_IF_S7_L004

tag: epithelial donor

value: IPF

value: day 4

value: M

value: Primary airway epithelial cells


title: D4_CA2_S2_L004

value: B

tag: epithelial disease_status


title: SAM161_probing_1_iga

value: N


title: DH_14_3_S79


title: SAM024_probing_1_iga

value: A/H5N1 HA + AS03


title: SAM112_probing_1_iga


title: D4_CA1_S1_L004

value: Control

tag: fibroblast disease_status


title: HUnafld006

description:
NAFLD.HUn106.gct
NASH.HUn164.gct

value: Liver

value: 1st biopsy

value: male

value: high-risk


title: SAM101_probing_1_iga


title: DH_14_1_S77

tag: timepoint


title: TUnafld039

tag: tissue


title: TUnafld048

value: female

value: low-risk


title: TUnafld055


title: TUnafld046


title: TUnafld037


title: SAM377_probing_1_iga

value: A/H5N1 HA + PBS

value: Y


title: TUnafld045


title: SAM028_probing_1_iga


title: TUnafld041


title: DH_14_2_S78

value: distal airway, honeycombed

value: day 14

value: Male

value: Epithelial cells


title: TUnafld040


title: SAM131_probing_1_iga


title: TUnafld032


title: TUnafld038


title: DH_8_1_S73

value: day 8


title: SAM223_probing_1_iga


title: DH_8_4_S76


title: TUnafld026


title: DH_4_3_S71

value: day 4


title: TUnafld035


title: TUnafld024


title: SAM381_probing_1_iga

value: N


title: TUnafld023


title: TUnafld034


title: TUnafld044


title: DH_8_3_S75


title: TUnafld031


title: TUnafld021


title: DH_4_1_S69


title: DH_8_2_S74


title: TUnafld020


title: TUnafld030


title: SAM074_probing_1_iga


title: TUnafld029


title: TUnafld018


title: DH_0_4_S68

value: day 0


title: TUnafld028


title: DH_4_4_S72


title: DH_0_3_S67


title: SAM240_probing_1_iga

value: A/H5N1 HA + AS03


title: TUnafld027

value: Liver


title: TUnafld015


title: TUnafld017


title: SAM036_probing_1_iga


title: TUnafld025


title: SAM215_probing_1_iga


title: DH_4_2_S70


title: DH_0_1_S65


title: TUnafld022


title: DF_14_4_S64

value: distal airway, fibrotic


title: TUnafld012


title: TUnafld019


title: SAM091_probing_1_iga


title: SAM139_probing_1_iga


title: DF_14_3_S63


title: TUnafld006


title: DF_14_1_S61


title: TUnafld005


title: TUnafld004

value: male


title: TUnafld016

value: high-risk


title: SAM033_probing_1_iga


title: TUnafld003


title: SAM039_probing_1_iga


title: DH_0_2_S66


title: DKO_Repliseq_late_rep2

city: Worcester

first: George

last: Spracklin

state: Massachusetts

address: 368 Plantation Street

department: Systems Biology

institute: University of Massachusetts Medical School

description:
processed data file:
DKO_repli.hg38.cov.50000.tsv
DKO_repli.hg38.log2EL.R1R2.50000.zscore.bw
DKO_EL.r1r2_2_state_HMM_colored.bed
diff_repli_domains.thresh_0.75.tsv

data_processing:
library strategy: Repli-seq
FASTQ files were trimmed and assessed for quality with fastp.
Trimmed reads were mapped to hg38 (UCSC) using bwa mem.
Alignment files (BAM format) were filtered using sambamba.
Coverage tracks at different resolutions were generated using bedtools and bioframe.
Coverage tracks were pooled and coverted to standard Z-scores.
Genome_build: hg38
Supplementary_files_format_and_content: Bed files were generated with HMMs
Supplementary_files_format_and_content: bigwig files for genome wide read coverage

source_name: DKO

growth_protocol: HCT116 and DKO cells were cultured in McCoy5A media. DKO cells were grown in the presence of G418, geneticin. All media was supplemented with 10% FBS at 37C/5%CO2

extract_protocol:
Repli-seq was performed and analyzed as described in (Marchal et al., 2018). In brief, asynchronously growing cells were pulse-labeled with 100uM BrdU for 2hrs, trypsinized, ethanol fixed, stained with propidium iodide and FACS sorted (SONY SH-800) based on DNA content (early S v late S). Genomic DNA was purified using Zymo DNA clean and concentrator and sonicated on a Covaris (S2) using the 300bp, 50ul protocol. IPs were performed with anti-BrdU (BD:555627). Libraries were made with Ultra II DNA kits from NEB and sequenced on an Illumina miSeq and/or NextSeq.
Libraries were prepared using NEB UltraII DNA library kit

value: colon cancer cell line

tag: antibody

value: anti-BrdU (BD:555627)


title: TUnafld014

tag: age

value: female

value: low-risk


title: TUnafld008


title: SAM037_probing_1_iga

tag: treatment

value: A/H5N1 HA + PBS

value: Y


title: TUnafld011

tag: Sex


title: SAM283_probing_1_iga


title: TUnafld009

tag: fibrosis stage


title: TUnafld013


title: DF_8_2_S58

value: Male


title: SAM219_probing_1_iga


title: SAM018_probing_1_iga


title: SAM113_probing_1_iga


title: SAM187_probing_1_iga


title: TUnafld007


title: HCT116_Repliseq_late_rep1

description:
processed data file:
HCT_repli.hg38.cov.50000.tsv
HCT_repli.hg38.log2EL.R1R2.50000.zscore.bw
HCT116_EL.r1r2_2_state_HMM_colored.bed
diff_repli_domains.thresh_0.75.tsv


title: DF_8_1_S57

value: Epithelial cells


title: SAM220_probing_1_iga


title: DF_14_2_S62

value: day 14


title: DF_8_4_S60

value: day 8


title: DF_8_3_S59


title: TUnafld010


title: TUnafld001


title: 5Aza_Protectseq_biorep2

data_processing:
library strategy: Protect-seq
We processed ChIP-seq data following steps of the ENCODE pipeline (https://github.com/ENCODE-DCC/chip-seq-pipeline2) with slight modifications using a simplified custom snakemake workflow.
Reads were mapped to hg38 using bwa mem (Li, 2013).
Alignment files (BAM format) were filtered for quality and duplicates using samtools (Li et al., 2009).
Signal track (target over input) generation was performed using MACS2 (Y. Zhang et al., 2008).
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files for genome wide read coverage, bed files for peaks
Supplementary_files_format_and_content: Domains (BED file) were called with HMMs.

growth_protocol: HCT116 and DKO cells were cultured in McCoy5A media. DKO cells were grown in the presence of G418, geneticin. All media was supplemented with 10% FBS at 37C/5%CO2. Cells were grown to ~75% confluency, harvested with trypsin, washed in 1X PBS, and frozen/stored at -80°C. For cross linking, cells were thawed on ice and fixed in 1% formaldehyde and quenched in 0.125M Glycine, then washed twice in 1X PBS.

extract_protocol:
Protect-seq protocol was performed as described in (Spracklin & Pradhan, 2020). Pelleted nuclei were resuspended in 183 μl DNaseI Buffer then 2 μl 100 mM Ca2+ (1 mM final), 5 μl DNase I (10 U), 5 μl MNase (10 000 U) and 5 μl RNase A (20 mg/ml) were added (200 μl final volume). Cells plus the enzyme cocktail were incubated at room temperature (RT) for 30 min. Digested cells were spun 3500 RPM for 3 min and resuspended in 400 μl of 1× NEB buffer 2, then rotated at RT for 15 min. Digested/Wash#1 cells were spun 5000 RPM for 3 min and resuspended in the same 200 μl cocktail mix and incubated again at RT (or 37°C) for 30 min. Digested cells#2 were spun 10 000 RPM for 3 min and resuspended in 400 μl of 1× NEB buffer 2, then rotated at RT for 15 min (save aliquot for microscopy). Spin digested cells#2 10,000 RPM for 3 min and resuspended in 200 μl of 1× NEB buffer 2, 20 μl Proteinase K (SDS optional). Digest overnight at 65°C then purify using phenol/chloroform and ethanol precipitation (compatible with silica-bead purification).
Libraries were prepared using NEB UltraII DNA library kit

value: 5uM 5-azacytidine for 48h

tag: enzyme

value: DNaseI & MNase


title: SAM354_probing_1_iga


title: DKO_Repliseq_early_rep2


title: SAM084_probing_1_iga

value: A/H5N1 HA + AS03


title: DF_4_2_S54

value: day 4


title: SAM323_probing_1_iga


title: DKO_Repliseq_late_rep1


title: DKO_HiC_rep3

description:
processed data file:
HCT116_DKO.hg38.50000.E0-E128.trans.eigvals.pq
HCT116_DKO.hg38.50000.E0-E128.trans.eigvecs.E1.bw
HCT116_DKO.hg38.50000.E0-E128.trans.eigvecs.pq
HCT116_DKO.hg38.mapq_30.50000.expected.cis.tsv
HCT116_DKO.hg38.mapq_30.50000.expected.trans.tsv
DKO.mapq_30.insulation_25kb_100kb.txt
DKO_all.hg38.mapq_30.1000.mcool

data_processing:
Hi-C libraries were trimmed with the fastp package (Chen et al., 2018) to remove low quality reads and sequencing adaptors.
Hi-C datasets were processed using the distiller pipeline (https://github.com/open2c/distiller-nf) written for nextflow (Di Tommaso et al., 2017).
Briefly, we mapped Hi-C sequencing reads to the human reference assembly hg38 using bwa mem (Li, 2013) with flags -SP.
Alignments were parsed, filtered for duplicates and pairs were classified using the pairtools package (https://github.com/open2c/pairtools).
Hi-C pairs were aggregated into contact matrices in the cooler format using the cooler package at multiple resolutions (Abdennur & Mirny, 2020).
All contact matrices were normalized using the iterative correction procedure (Imakaev et al., 2012) after bin-level filtering.
Genome_build: hg38
Supplementary_files_format_and_content: mcool (HDF5, Multiresolution cooler files (https://github.com/open2c/cooler))
Supplementary_files_format_and_content: Compartment Calls (https://github.com/open2c/cooltools)
Supplementary_files_format_and_content: Insulation Boundaries (https://github.com/open2c/cooltools)

extract_protocol:
HiC protocol was performed similar to (Rao et al., 2014). In brief, 4M fixed cells were then resuspended in 500ul lysis buffer (50mM Tris-HCl pH 8.0, 10mM NaCl, 0.2% NP40, 1X PITC) for 30 min on ice with periodic resuspension. Lysed cells were spun 3500 RPM for 3 min and resuspended in 300 μl 1× NEB buffer 2, spun and resuspended in 198 μl 1× NEB buffer 2. 2μl of 10% SDS was added and incubated at 65°C for 10 min. After, 400 μl 1× NEB buffer 2 and 60 μl 10% Triton X-100 were added to quench the SDS. Samples were incubated at 37°C for 15 min. Nuclei were spun 3500 RPM for 3 min and resuspended in 300 μl 1× NEB buffer 2, repeat wash step. Fixed nuclei were then digested with MboI (NEB#R0147M) overnight, 5’ overhangs were filled-in with a biotinylated nucleotide, blunt-ends were ligated, followed by reverse crosslinking overnight. The purified DNA (2 μg) was sonicated using Covaris 50μl 400bp protocol. The sonicated DNA was brought to a volume of 400μl in binding buffer (5 mM Tris-HCl pH7.5; 0.5 mM EDTA; 1M NaCl) and mixed with 20μl of streptavidin magnetic beads (NEB#S1421) and rotated for 1hr at RT. The bead-bound DNA was washed twice with 400μl low-TE and resuspended in 50μl low-TE. NGS libraries were prepared using NEB DNA Ultra II kit (NEB#E7645). End prep: Mix 50μl of sample with 7μl End prep buffer and 3μl End prep enzyme, incubate for 30 min at RT then 30 min at 65°C, wash twice with 400μl low-TE and resuspended in 60μl low-TE. Adaptor ligation: 2.5μl of adaptor and 30μl of ligation mix was incubated at RT for 1-3hrs, washed twice with low-TE and resuspended in 90μl low-TE, following ligation, 3 μl USER was added for 30mins at 37°C, wash twice with 400μl and resuspend in 15μl. PCR: Add 5μl of universal F and index R primer, 25μl Q5 mix, 15μl sample for 5 PCR cycles. Libraries were purified with SPRI beads (0.9X) and quantified on a bioanalyzer and with NEB Illumina quant kit (NEB#E7630). HiC libraries were sequenced on a NextSeq500 either 150bp or 75bp paired-end reads.
Libraries were prepared using NEB UltraII DNA library kit

value: MboI


title: DKO_Repliseq_early_rep1

value: male


title: DF_4_1_S53

value: distal airway, fibrotic


title: SAM276_probing_1_iga

data_processing:
Spot and background intensities were measured using an annotated grid (gal) file. For ArrayCamTM a number of different settings were used to attempt to obtain readings. Microarray spot intensities were quantified using software ArrayCamTM (Grace Bio-Labs) utilizing automatic local background subtraction for each spot. The generated signal intensity values were considered raw values.
Prior to the analysis, systematic intensity differences in background reactivity as measured by phosphate buffered saline with tween 20 (PBST) were corrected. This was achieved by subtracting the median raw intensity signal for the 24 PBST intensity measurements for a certain array from the array’s non-PBST antigen intensities. Following background correction, for intensities < 1, an intensity value of 1 was imputed. Global outliers based on PCA and MDS plots were removed.

value: N


title: DF_4_4_S56


title: DKO_HiC_rep2

value: colon cancer cell line


title: HCT116_Repliseq_early_rep2

value: anti-BrdU (BD:555627)


title: SAM044_probing_1_iga


title: HCT116_Repliseq_early_rep1


title: SAM136_probing_1_iga


title: HCT116_Repliseq_late_rep2


title: 5Aza_Protectseq_biorep3


title: SAM206_probing_1_iga


title: DF_0_4_S52

value: day 0


title: DF_0_3_S51


title: 5Aza_HiC_rep3

description:
processed data file:
HCT116_5Aza.hg38.50000.E0-E128.trans.eigvals.pq
HCT116_5Aza.hg38.50000.E0-E128.trans.eigvecs.E1.bw
HCT116_5Aza.hg38.50000.E0-E128.trans.eigvecs.pq
HCT116_5Aza.hg38.mapq_30.50000.expected.cis.tsv
HCT116_5Aza.hg38.mapq_30.50000.expected.trans.tsv
5Aza.mapq_30.insulation_25kb_100kb.txt
5Aza_r1r2r3.hg38.mapq_30.1000.mcool


title: 5Aza_Protectseq_biorep1


title: SAM034_probing_1_iga


title: 5Aza_HiC_rep1


title: DF_4_3_S55


title: SAM032_probing_1_iga


title: HCT116_HiC_rep1


title: DKO_HiC_rep4


title: 5Aza_ChIPseq_input rep4

data_processing:
We processed ChIP-seq data following the steps of the ENCODE pipeline (https://github.com/ENCODE-DCC/chip-seq-pipeline2) with slight modifications using a simplified custom snakemake workflow.
Reads were mapped to hg38 using bwa mem (Li, 2013).
Alignment files (BAM format) were filtered for quality and duplicates using samtools (Li et al., 2009).
Cross-correlation analysis and fragment length estimation for single-ended datasets was performed using the phantompeakqualtools package (Landt et al., 2012).
Signal track (target over input) generation was performed using MACS2 (Y. Zhang et al., 2008).
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files for genome wide read coverage, bed files for peaks

extract_protocol:
All ChIP-seq experiments used the SimpleChIP® Plus Enzymatic Chromatin IP Kit (Magnetic Beads) #9005 from Cell Signaling Technologies following the manufacturer's recommended protocol. Four million cells per IP. MNase digested chromatin was pooled into a single tube for brief sonication to lyse nuclei. Supernatant was then split evenly between IPs (minus 2% input). Antibodies and chromatin were incubated overnight at 4°C, rotating. DNA was purified using spin columns.
Libraries were prepared using NEB UltraII DNA library kit


title: DKO_HiC_rep1


title: 5Aza_HiC_rep2


title: HCT116_HiC_rep2


title: DF_0_1_S49


title: 5Aza_ChIPseq_input rep3


title: DN_14_4_S48

value: distal airway, normal


title: 5Aza_ChIPseq_input rep2


title: SAM125_probing_1_iga

extract_protocol: The serum samples originated from future-use consenting participants of parallel avian A(H5N1)/Indonesia/05/2005 influenza vaccine mix and match studies involving MF59® and AS03 adjuvant, also known as DMID Protocols 10-0016 and 10-0017.


title: SAM023_probing_1_iga

value: Y


title: 5Aza_ChIPseq_RAD21 rep1

description:
processed data file:
5Aza.RAD21__VS__input.fc.signal.bw

value: anti-RAD21 (abcam:ab992)


title: 5Aza_ChIPseq_input rep1


title: 5Aza_ChIPseq_RAD21 rep2


title: DN_14_2_S46

value: Male

value: Epithelial cells


title: DN_14_3_S47

value: day 14


title: SAM224_probing_1_iga


title: 5Aza_ChIPseq_SMC3 rep2

description:
processed data file:
5Aza.SMC3__VS__input.fc.signal.bw

value: 5uM 5-azacytidine for 48h

value: anti-SMC3 (abcam:ab9263)


title: 5Aza_ChIPseq_SMC3 rep1


title: SAM063_probing_1_iga

value: A/H5N1 HA + AS03


title: 5Aza_ChIPseq_CTCF rep2

description:
processed data file:
5Aza.CTCF__VS__input.fc.signal.bw

value: anti-CTCF (CST:#3418)


title: 5Aza_ChIPseq_H3K9me3 rep2

description:
processed data file:
5Aza.H3K9me3__VS__input.fc.signal.bw


title: 5Aza_ChIPseq_H3K9me3 rep1


title: DN_8_4_S44

value: day 8


title: DN_14_1_S45


title: DF_0_2_S50


title: SAM343_probing_1_iga

value: A/H5N1 HA + PBS


title: SAM165_probing_1_iga


title: 5Aza_ChIPseq_H3K9me2 rep1

description:
processed data file:
5Aza.H3K9me2__VS__input.fc.signal.bw

value: male


title: SAM167_probing_1_iga

value: N


title: DN_8_2_S42


title: 5Aza_ChIPseq_H3K27me3 rep1

description:
processed data file:
5Aza.H3K27me3__VS__input.fc.signal.bw

value: colon cancer cell line


title: SAM270_probing_1_iga


title: 5Aza_ChIPseq_HP1a rep1

description:
processed data file:
5Aza.HP1a__VS__input.fc.signal.bw

value: anti-HP1alpha (CST:2616)


title: 5Aza_ChIPseq_HP1a rep2


title: DN_8_1_S41


title: DKO_ChIPseq_input rep2


title: DN_4_4_S40

value: day 4


title: 5Aza_ChIPseq_CTCF rep1


title: DN_4_3_S39

value: distal airway, normal


title: SAM107_probing_1_iga

value: Y


title: SAM143_probing_1_iga


title: DN_8_3_S43


title: DKO_ChIPseq_RAD21 rep2

description:
processed data file:
DKO.RAD21__VS__input.fc.signal.bw

value: anti-RAD21 (abcam:ab992)


title: DKO_ChIPseq_RAD21 rep1


title: 5Aza_ChIPseq_H3K9me2 rep2


title: DKO_ChIPseq_SMC3 rep2

description:
processed data file:
DKO.SMC3__VS__input.fc.signal.bw


title: DN_4_1_S37

value: Male


title: SAM314_probing_1_iga


title: DKO_ChIPseq_CTCF rep1

description:
processed data file:
DKO.CTCF__VS__input.fc.signal.bw


title: DKO_ChIPseq_SMC3 rep1


title: DKO_ChIPseq_H3K27me3 rep1

description:
processed data file:
DKO.H3K27me3__VS__input.fc.signal.bw


title: DKO_ChIPseq_CTCF rep2


title: SAM335_probing_1_iga


title: DKO_ChIPseq_input rep1


title: 5Aza_ChIPseq_HP1a rep3


title: SAM147_probing_1_iga


title: DKO_ChIPseq_HP1a rep1

description:
processed data file:
DKO.HP1a__VS__input.fc.signal.bw


title: HCT116_ChIPseq_input rep2


title: SAM092_probing_1_iga


title: DN_0_3_S35

value: day 0

value: Epithelial cells


title: SAM295_probing_1_iga


title: HCT116_ChIPseq_RAD21 rep2

description:
processed data file:
HCT.RAD21__VS__input.fc.signal.bw


title: DN_0_2_S34


title: HCT116_ChIPseq_RAD21 rep1


title: DN_4_2_S38


title: HCT116_ChIPseq_SMC3 rep2

description:
processed data file:
HCT.SMC3__VS__input.fc.signal.bw


title: SAM025_probing_1_iga


title: SAM255_probing_1_iga


title: SAM212_probing_1_iga


title: HCT116_ChIPseq_SMC3 rep1


title: HCT116_ChIPseq_CTCF rep1

description:
processed data file:
HCT.CTCF__VS__input.fc.signal.bw


title: SA_14_4_S32

value: small airway

value: day 14


title: DN_0_1_S33


title: HCT116_ChIPseq_H3K27me3 rep1

description:
processed data file:
HCT.H3K27me3__VS__input.fc.signal.bw


title: HCT116_ChIPseq_CTCF rep2


title: SAM184_probing_1_iga

value: A/H5N1 HA + AS03


title: u46T1

city: Hong Kong

first: Qiuyu

last: JING

state: Hong Kong

address: Room 6202C, Academic Building, The Hong Kong University of Science and Technology

department: Division of Life Science

country: Hong Kong

data_processing:
library strategy: metagenomics DNA sequencing library
Illumina Casava1.7 software used for basecalling.
Raw reads were first trimmed to 2x75bp using Cutadapt (version 1.18) and rarefied to 30M to ensure equal library size except for non-template controls due to its low input. Duplicates were then removed using PRINSEQ (version 0.20.4) in a paired-end mode with entropy-based strategy. The threshold of entropy was set as 20. Adapters and bases with quality lower than 20 were then trimmed using BBMap (version 35.74). Reads shorter than 25bp were discarded.
Quality-controlled reads were mapped to human reference GRCh38 downloaded from NCBI RefSeq database using Bowtie2 (version 2.2.6) in a very-sensitive mode. Duplicates were marked and removed using Picard Tools (version 2.18.7). Then both mapped and unmapped reads were extracted using SAMtools (version 1.3.1) for analysis of human fragments and microbial compositions respectively.
Mapped human bam files were firstly sorted using SAMtools (version 1.3.1) and then converted to bed files using BEDtools (version 2.15.0). Human autosome reference was segmented into 1-megabase non-overlap bins using BEDtools. Ratio of fragments of different length overlapped with each bin were calculated using custom script.
Genome_build: GRCh38
Supplementary_files_format_and_content: text file containg the number of fragments with different length within 1M bins across autosomes

source_name: Blood

extract_protocol:
cfDNA was extracted from plasma using QIAamp circulating nucleic acid kit (QIAGEN)
single-strand DNA library preparation with custom sequencing primers

treatment_protocol: Plasma was separated from blood by centrifugation

tag: group

value: Sepsis

tag: 28-day mortality

value: Survivors

tag: time point

value: Blood

tag: molecule type

value: cell-free DNA


title: SA_14_3_S31

tag: cell type


title: SAM150_probing_1_iga

tag: subject id

value: A/H5N1 HA + PBS

tag: day


title: u46T3

institute: The Hong Kong University of Science and Technology


title: HCT116_ChIPseq_input rep1

value: colon cancer cell line

value: male


title: SA_14_2_S30

tag: disease region


title: SAM254_probing_1_iga

value: N


title: u46T0


title: u45T1

value: Non-survivors


title: DN_0_4_S36

value: distal airway, normal


title: u45T0


title: HCT116_ChIPseq_HP1a rep1

value: anti-HP1alpha (CST:2616)


title: SA_8_4_S28

value: day 8

value: Male


title: SAM002_probing_1_iga


title: u44T3


title: SAM052_probing_1_iga

value: Y


title: SA_8_3_S27

value: small airway

value: Epithelial cells


title: u44T2


title: u44T1


title: SAM273_probing_1_iga

value: A/H5N1 HA + AS03


title: SA_8_2_S26


title: u44T0

value: Sepsis


title: SA_8_1_S25


title: u43T3

value: Survivors


title: u43T2

value: Blood


title: u43T1

value: cell-free DNA


title: SA_4_4_S24

value: day 4


title: SA_14_1_S29

value: day 14


title: SAM296_probing_1_iga


title: u43T0


title: SAM318_probing_1_iga

value: A/H5N1 HA + PBS


title: u42T1

value: Non-sepsis


title: SAM068_probing_1_iga


title: SA_4_3_S23


title: u42T0


title: u42T3


title: u41T3


title: SA_4_2_S22


title: u41T2


title: SAM263_probing_1_iga

value: N


title: u41T1


title: SA_4_1_S21


title: SAM325_probing_1_iga


title: u41T0


title: u40T3


title: SA_0_4_S20

value: day 0


title: SA_0_2_S18


title: SA_0_3_S19


title: u40T1


title: u40T0


title: u39T1


title: SAM144_probing_1_iga


title: SAM229_probing_1_iga


title: SA_0_1_S17


title: u39T0


title: SAM241_probing_1_iga


title: u38T0


title: u38T2


title: LA_14_3_S15

value: large airway


title: SAM306_probing_1_iga


title: u36T2


title: u37T0

value: Non-survivors


title: u36T1


title: u35T1


title: LA_14_2_S14

value: Male


title: u34T1


title: SAM146_probing_1_iga

value: Y


title: LA_14_1_S13


title: SAM035_probing_1_iga


title: u40T2


title: SAM353_probing_1_iga


title: u34T0


title: u35T0


title: LA_8_3_S11

value: day 8


title: SAM358_probing_1_iga


title: u32T1


title: SAM108_probing_1_iga


title: u33T1


title: u36T0


title: u33T0


title: LA_14_4_S16

value: Epithelial cells


title: SAM098_probing_1_iga

value: A/H5N1 HA + AS03


title: LA_8_2_S10


title: u32T3

value: Sepsis


title: u32T0

value: Survivors


title: u31T2

value: Blood


title: LA_8_1_S9


title: SAM370_probing_1_iga


title: u30T2

value: cell-free DNA


title: u31T1


title: LA_4_4_S8

value: day 4


title: u30T1


title: u31T0


title: SAM383_probing_1_iga


title: u30T0


title: u29T2


title: LA_8_4_S12


title: SAM193_probing_1_iga


title: u29T0


title: LA_4_2_S6


title: u28T0


title: u27T1


title: LA_4_1_S5


title: SAM186_probing_1_iga


title: u27T0


title: SAM011_probing_1_iga


title: LA_0_4_S4


title: u26T0


title: SAM177_probing_1_iga


title: SAM020_probing_1_iga


title: LA_0_3_S3


title: LA_4_3_S7


title: SAM209_probing_1_iga


title: u24T0


title: u25T0


title: u23T2


title: u29T1


title: SAM252_probing_1_iga


title: LA_0_2_S2


title: u23T1


title: LA_0_1_S1


title: u23T3


title: u23T0


title: SAM175_probing_1_iga


title: Co_Echi_3_IP

city: Beijing

first: Xiao-ning

last: Gao

state: Beijing

address: 28 Fuxing Road

department: Department of Hematology

institute: Chinese PLA General Hospital

data_processing:
fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter.
Then sequence quality of IP and Input samples were also verified using fastp.
We used HISAT2 (http://daehwankimlab.github.io/hisat2) to map reads to the reference genomeHomo sapiens (Version: v101). Mapped reads of IP and input libraries were provided for R package exomePeak (https://bioconductor.org/packages/exomePeak), which identifies m6A peaks with bed or bigwig format that can be adapted for visualization on the IGV software (http://www.igv.org). MEME (http://meme-suite.org) and HOMER (http://homer.ucsd.edu/homer/motif) were used for de novo and known motif finding followed by localization of the motif with respect to peak summit.
Called peaks were annotated by intersection with gene architecture using R package ChIPseeker (https://bioconductor.org/packages/ChIPseeker).

source_name: Homo sapiens

growth_protocol: Kasumi-1 cells were maintained in RPMI 1640 medium supplemented with 50 µg/ml streptomycin, 50 IU/ml penicillin and 10% fetal calf serum.

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure.
The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel. Poly (A) RNA is purified from 50μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 86℃ 7min. Then the cleaved RNA fragments were incubated for 2h at 4℃ with m6A-specific antibody (No. 202003, Synaptic Systems, Germany) in IP buffer (50 mM Tris-HCl, 750 mM NaCl and 0.5% Igepal CA-630). Then the IP RNA was reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.
MeRIP-Seq

treatment_protocol: Kasumi-1 cells was treated with 100uM of CoCl2.6H2O and 10 nM of echinomycin for 24 hours .

value: Homo sapiens

tag: cell line

value: Kasumi-1 cell line

value: acute myeloblastic leukemia cell

tag: genotype

value: WT

value: treated with 100 uM CoCl2 and 10 nM echinomycin for 24 hours


title: u22T3

tag: tissue


title: u22T0


title: u22T2


title: SAM368_probing_1_iga

address: 401 N Washington St

value: N


title: SAM062_probing_1_iga


title: Co_Echi_2_IP


title: u21T3

value: Non-survivors


title: SAM374_probing_1_iga

value: A/H5N1 HA + PBS


title: SAM232_probing_1_iga

value: A/H5N1 HA + MF59


title: u19T1

value: Non-sepsis


title: SAM009_probing_1_iga

value: Y


title: SAM203_probing_1_iga


title: Co_Echi_1_IP


title: u20T3


title: Co_Echi_2_input


title: Co_Echi_1_input


title: u19T0


title: u20T1


title: Co_Echi_3_input


title: u18T3


title: u21T0


title: u20T0


title: u19T3


title: SAM195_probing_1_iga


title: u18T0


title: SAM227_probing_1_iga


title: u17T3


title: u17T2


title: SAM121_probing_1_iga


title: PANC1-WT-3

city: Guangzhou

first: Kaiyuan

last: Ji

address: No.9 Jinsui Road, Guangzhou, China

department: Guangzhou Women and Children’s Medical Center

institute: Guangzhou Medical University

data_processing:
Clean data were generated after removing adapters and low-quality reads. GRCh38 genomes as the reference and the annotation files were downloaded from ENSEMBL database (http://www.ensembl.org/index.html). Bowtie2 v2.2.3 was used for building the genome index, and clean data was then aligned to the reference genome using HISAT2 v2.1.0. Reads count for each gene in each sample was counted by Featurecounts. The differentially expressed genes were analyzed by DESeq2. The adjusted p-value < 0.05 was set as the cut-off value.
Genome_build: hg38
Supplementary_files_format_and_content: TXT files contain raw counts for all genes and samples.

source_name: Wild type PANC1

growth_protocol: PANC1 were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) (Gibco, USA) containing 10% fetal bovine serum (FBS, HyColne, Utah, USA).Cells were cultured at 37℃ in a humidified atmosphere containing 5% CO2 and frequently checked if there is the mycoplasma contamination.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Total RNA was extracted from the cells.RNA libraries were prepared for sequencing using standard Illumina protocols. Paired-end sequencing was completed on an Illumina HiSeq system.

treatment_protocol: CRISPR/Cas9-gRNA system was used to knockout RARG in PANC1 cells. Two expression cassettes encoding the sgRNA sequences (sgRNA1-RARG CCACCCCAATGCCTCTAGCG, sgRNA2-RARG GAAGTGGGCATGTCCAAGGA) flanking the deletion region were cloned into the plasmid that expresses a codon-optimized version of Cas9. Lipofectamine 3000 reagent (Invitrogen, Carlsbad, USA) was used to transfect the plasmid into the PANC1 cells. The transfected PANC1 cells were selected with puromycin for two days. Individual clones were expanded and genotyped. The genotyping primers are following: 5’-TGTGGAATGGCAGGGTCTTC-3’, 5’-GAGGATGACTCCTCGCAGC-3’, 5’-TGGCTACCACTATGGGGTCA-3’.

value: pancreatic cancer


title: PANC1-RARG-KO-1

source_name: PANC1 with RARG-KO

value: The PANC1 cells were stably depleted RARG.


title: PANC1-RARG-KO-2


title: u17T0

value: Sepsis


title: u21T2

value: Blood


title: u18T2

value: cell-free DNA


title: PANC1-RARG-KO-3


title: SAM233_probing_1_iga

source_name: serum


title: PANC1-WT-2


title: PANC1-WT-1


title: SAM301_probing_1_iga


title: u15T3


title: u16T0


title: N3-small

tag: subject status

value: normal; control

value: peripheral blood


title: SAM176_probing_1_iga


title: u15T1


title: u14T1

value: Survivors


title: u17T1


title: u14T3


title: u13T0


title: u15T0


title: SAM333_probing_1_iga


title: N2-small


title: N4-small


title: u13T2


title: u12T1


title: N1-small


title: u12T0


title: u11T3


title: SAM006_probing_1_iga


title: u11T2


title: C4-small

value: coronary arterial calcification (CAC) patient


title: u16T2


title: u11T1


title: SAM221_probing_1_iga


title: u14T0


title: SAM272_probing_1_iga


title: u11T0


title: u10T0


title: C3-small


title: C1-small


title: C2-small


title: SAM140_probing_1_iga


title: u10T1


title: u8T2


title: SAM059_probing_1_iga


title: u9T3


title: u8T3


title: u8T1


title: u8T0


title: cPLS_FFA.Epa50_2

type: RNA

city: Tsu city

first: Naoto

last: Fujiwara

state: Mie

address: 2-174 Edobashi

country: Japan

institute: Mie University

hyb_protocol: Refer to the NanoString nCounter Assay System Manual

data_processing: For each probe, transcript count data were log2 transformed and scaled by geometric mean of the normalization genes by NanoString normalizer module of GenePattern toolkit (www.broadinstitute.org/genepattern) after setting a floor value of 1.1.

label: biotin

growth_protocol: DMSO-differentiated Huh7.5.1 cells (Huh7.5.1dif) and LX2 cells were co-cultured in DMEM with 1% DMSO for 10 days.

extract_protocol: Cells were washed with PBS and lysed with 5 µl of iScript™ RT-qPCR Sample Preparation Reagent (Bio-rad, Hercules, California).

treatment_protocol: Co-cultured DMSO-differentiated Huh7.5.1 cells (Huh7.5.1dif) and LX2 cells were exposed to mock or FFA (800 μM oleic acid and 400 μM palmitic acid) for 3 days, then treated with IDO1 inhibitor, epacadostat or DMSO.

tag: sample type

value: Cell (Huh7.5.1dif+LX2)

tag: exposure to etiological agent

value: Free fatty acid (800 μM oleic acid and 400 μM palmitic acid)

tag: duration with etiological agent

value: 6 days

tag: intervention

value: Epacadostat 50mM

tag: duration of intervention

value: 3 days


title: cPLS_FFA.Epa50_3

scan_protocol: Refer to the NanoString nCounter Assay System Manual


title: SAM222_probing_1_iga

first: Johannes

last: Goll

institute: The Emmes Company

tag: treatment

value: A/H5N1 HA + PBS


title: u7T3

tag: group

tag: 28-day mortality


title: pre-treatment PBMC sample gd TCR

first: Ruoyu

last: Zhang

address: Life Science Park building 1 B220

institute: Innovec Biotherapeutics

data_processing:
Library strategy: TCR-seq
Raw sequencing data were processed by Cell Ranger version 6.0.2 (10X Genomics) to generate gene expression matrix and assemble TCR sequences with human GRCh38 reference genome. scRNA-seq data analysis were performed using Scanpy. In quality control step, cells were filter by the following criteria: 1) mitochondrial abundance < 10%, 2) minimum gene detected > 400, 3) Maximum UMI < 35000. Potential doublets were detected and removed by Scrublet and manual inspections. Principal component analysis (PCA) was applied on the highly variable genes and cells were projected and visualized in 2D dimensions using uniform manifold approximation and projection (UMAP) on the first 30 PCs. Cells were clustered by Leiden algorithm implemented in Scanpy.
Genome_build: human GRCh38
Supplementary_files_format_and_content: 10X matrix or TCR contig

extract_protocol: On the date of experiment, the cells were thaw using a water bath at 37°C and loaded into Chromium microfluidic chips and barcoded within a 10× Chromium Controller (10X Genomics, US). For transcriptome, procedures were performed with reagents: Chromium Next GEM Single Cell 5' Library & Gel Bead Kit v1.1 (10X Genomics, Cat. No. 1000165). TCR enrichment was carried out using the Chromium Single Cell V(D)J Enrichment Kit, Human T Cell (10X Genomics, Cat. No. 1000005) for αβ transcripts, or customer primers for γδ TCR transcripts

tag: patient diagnosis

value: HSTCL

value: pre-treatment

value: PBMC

tag: sequencing type

value: TCR-seq gd TCR


title: u5T1

value: Non-sepsis

tag: time point

tag: molecule type


title: cPLS_FFA.Epa25_2

label_protocol: Refer to the NanoString nCounter Assay System Manual

value: Epacadostat 25mM


title: cPLS_FFA.Epa25_1


title: cPLS_FFA.Epa50_1


title: u7T1

value: Sepsis

value: Blood

value: cell-free DNA


title: post-treatment bone marrow sample gd TCR

value: post-treatment

value: bone marrow


title: u7T0

value: Survivors


title: cPLS_FFA.Epa10_3

value: Cell (Huh7.5.1dif+LX2)

value: Free fatty acid (800 μM oleic acid and 400 μM palmitic acid)

value: Epacadostat 10mM


title: u9T0


title: post-treatment PBMC sample ab TCR

value: TCR-seq ab TCR


title: u5T0


title: u6T0

value: Non-survivors


title: u4T2


title: u7T2


title: post-treatment PBMC sample gd TCR

value: HSTCL


title: Drp1KO EDE-4 [D4_S16]

city: Kansas City

first: Hong-Min

last: Ni

state: KS

address: 3901 Rainbow Blvd, MS-1018

department: Pharmacology, Toxicology and Therapeutics

institute: University of Kansas Medical Center

data_processing:
Raw reads weredemultiplexed into Fastq format allowing up to one mismatch.
Reads were aligned to mouse reference genome (GRCm38.90) , using HISAT v.2.1.0.13.
TPM values were generated using HTSeq (version v0.6.0).
Pairwise differential expression analysis was performed using R package edgeR between the WT and L-DRP1 KO group in control and EtOH conditions.
Assembly: GRCm38.90
Supplementary files format and content: normalized_counts

source_name: Liver

extract_protocol:
Livers were removed and snap frozen in liquid nitrogen. Total RNA was extracted using Trizol reagent and the quality was checked with Qubit quantification and TapeStation gel analysis
RNA libraries were prepared with standard Illumina protocol
RNA-Seq was sequenced as 75bp single reads on Illumina NextSeq 550 machine

treatment_protocol: Liver-specific DRP1 KO mice and paired WT mice were subjected to Gao-Binge alcohol model.

tag: strain

value: Liver

value: L-Dnm1l KO

value: EtOH

tag: age


title: pre-treatment bone marrow sample gd TCR

value: pre-treatment

value: TCR-seq gd TCR


title: u4T3

value: Sepsis


title: Drp1KO EDE-3 [D3_S15]

tag: genotype


title: pre-treatment PBMC sample ab TCR

tag: tissue

value: PBMC


title: u4T1

value: Blood

value: cell-free DNA


title: post-treatment bone marrow sample ab TCR

value: post-treatment

value: bone marrow


title: cPLS_FFA.Epa10_2

value: Cell (Huh7.5.1dif+LX2)

value: 6 days

value: 3 days


title: u4T0

value: Survivors


title: u3T3

value: Non-sepsis


title: pre-treatment bone marrow sample ab TCR

value: HSTCL

value: TCR-seq ab TCR


title: cPLS_FFA.Epa10_1

value: Free fatty acid (800 μM oleic acid and 400 μM palmitic acid)

value: Epacadostat 10mM


title: post-treatment PBMC sample RNA-seq

data_processing:
Raw sequencing data were processed by Cell Ranger version 6.0.2 (10X Genomics) to generate gene expression matrix and assemble TCR sequences with human GRCh38 reference genome. scRNA-seq data analysis were performed using Scanpy. In quality control step, cells were filter by the following criteria: 1) mitochondrial abundance < 10%, 2) minimum gene detected > 400, 3) Maximum UMI < 35000. Potential doublets were detected and removed by Scrublet and manual inspections. Principal component analysis (PCA) was applied on the highly variable genes and cells were projected and visualized in 2D dimensions using uniform manifold approximation and projection (UMAP) on the first 30 PCs. Cells were clustered by Leiden algorithm implemented in Scanpy.
Genome_build: human GRCh38
Supplementary_files_format_and_content: 10X matrix or TCR contig

value: RNA-seq


title: Drp1KO EDE-2 [D2_S14]

value: Liver

value: L-Dnm1l KO

value: EtOH


title: Drp1KO EDE-1 [D1_S13]


title: cPLS_FFA_3

value: DMSO


title: u2T3

value: Sepsis

value: Blood

value: cell-free DNA


title: u3T2


title: pre-treatment bone marrow sample RNA-seq

value: pre-treatment

value: bone marrow


title: post-treatment bone marrow sample RNA-seq

value: post-treatment


title: cPLS_FFA_2

value: Cell (Huh7.5.1dif+LX2)

value: 6 days

value: 3 days


title: pre-treatment PBMC sample RNA-seq

value: HSTCL

value: PBMC


title: Drp1KO CDM-4 [C4_S12]

value: Control


title: u2T2

value: Survivors


title: u3T0

value: Non-sepsis


title: S541-3

first: Xiaoxuan

last: Su

address: 132 East Outer Ring Road

department: School of Pharmaceutical Sciences

institute: Sun Yat-Sen University

data_processing:
Differential expression analysis for mRNA was performed using R package edgeR. Differentially expressed RNAs with |log2(FC)| value >1 and q value <0.05, considered as significantly modulated, were retained for further analysis.
Genome_build: hg38
Supplementary_files_format_and_content: xls files DEGs of each group

source_name: non-small cell lung cancer cell

growth_protocol: A549 cells (Procell, CL-0016, China) were and grown in DMEM medium (Cienry, CR12800, China) complemented with 10% fetal bovine serum (FBS) (ExCell Bio, FSP500, China) and 1% Penicillin-Streptomycin Solution (P/S) (Procell, PB180120, China) at a 37 °C constant-temperature incubator with 5% CO2.

extract_protocol:
The total RNA of each group was isolated by RNAiso Plus, separately.
1. Total RNA extraction. 2. Perform first strand cDNA synthesis. 2.Proceed immediately to second strand cDNA synthesis. 3. Purifiy double-stranded cDNA using DNA clean beads. 4. End prep of cDNA library. 5. Adaptor ligation. 6. Purifiy the Adaptor Ligated DNA Using Beads. 7. PCR Enrichment of Adaptor Ligated DNA. 8. Purification of the PCR reaction using beads.

treatment_protocol: A549 cells were treated with 1.0 µM compounds (S541) or DMSO for 48 h.

tag: cell line

value: treated with compound S541(5n) for 48 hours


title: cPLS_FFA_1

tag: sample type

value: Free fatty acid (800 μM oleic acid and 400 μM palmitic acid)


title: cPLS_mock_3

tag: exposure to etiological agent

value: Mock

value: DMSO


title: Drp1KO CDM-3 [C3_S11]

value: Liver

value: L-Dnm1l KO


title: Drp1KO CDM-2 [C2_S10]


title: cPLS_mock_1

tag: duration with etiological agent


title: u2T1

value: Sepsis

value: Blood

value: cell-free DNA


title: S541-2


title: cPLS_mock_2

value: Cell (Huh7.5.1dif+LX2)

tag: intervention


title: ctrl-3


title: S541-1


title: Drp1WT EDE-3 [B3_S7]

value: WT

value: EtOH


title: u2T0


title: Drp1WT EDE-4 [B4_S8]


title: Drp1WT EDE-2 [B2_S6]


title: ctrl-2


title: u1T3

value: Non-survivors


title: u1T0


title: Drp1KO CDM-1 [C1_S9]


title: Drp1WT EDE-1 [B1_S5]


title: ctrl-1