title: Melanoma human, 3pRNA, dabrafenib+trametinib, 24h, rep1


title: Serum exosome miRNA, PD, 2020, 29

status: Public on Jul 26 2024

type: SRA

city: Bunkyo

first: Zhiyang

last: Yu

state: Tokyo to

address: Hongo 2-1-1

department: Department of Neurology

country: Japan

institute: Juntendo University

library_source: transcriptomic

data_processing:
Generated sequencing data was aligned and mapped to miRBase using the Bowtie2.
Assembly: hg19(whole genome) miRBase(miRNA)
Supplementary files format and content: xlsx file containing raw counts and RPM values for all samples

molecule: total RNA

organism: Homo sapiens

source_name: Serum exosome

extract_protocol:
Total Exosome RNA and Protein Isolation Kit (Thermo Fisher Scientific, Waltham, MA) was utilised to extract total RNA from serum exosomes, following the manufacturer's instructions.
Small RNA library construction, alignment and mapping were performed by staff at Thermo Fisher Scientific. The small RNA libraries were prepared with the Ion Total RNA-Seq Kit version 2 on the Ion PGM System (Thermo Fisher Scientific, Waltham, MA). Quality control of the generated small RNA library was carried out using the Agilent High Sensitivity DNA kit on the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Serum samples were collected from participants at the outpatient department of Juntendo University Hospital. Upon collection, the serum samples were immediately stored at −80°C until use.

tag: tissue

value: Serum exosome

tag: disease state

value: PD

tag: cell type

value: Extracellular vesicles


title: Melanoma human, no stimulation, dabrafenib+trametinib, 24h, rep1

city: Bonn

first: Thais

middle: Marina

last: Schlee-Guimarães

address: Venusberg-Campus 1

department: Institute of Clinical Chemistry and Clinical Pharmacology

country: Germany

institute: University Hospital, University of Bonn

data_processing:
Next, sequencing reads were aligned to the human reference genome using STAR (Dobin et al., 2013).
Quantifying  with HTSeq (G Putri, S Anders, PT Pyl, JE Pimanda, F Zanini Analysing high-throughput sequencing data in Python with HTSeq 2.0 ).
Gene expression analysis was performed with the statical R-package edgeR (Robinson MD, McCarthy DJ, Smyth GK (2010).
Assembly: GRCh38.109
Supplementary files format and content: counts csv files

growth_protocol: Kept at 37°C 5% CO2  A375 cell line was cultured in DMEM  with 10 % (v/v) fetal calf serum (FCS) and 100 units penicillin and 100µg streptomycin per mL Media (p/s).

extract_protocol:
Qiagen, RNeasy Mini Kit, accodring to manufacturers recomandation
mRNA was purified by poly-A enrichment using NEBNext® Poly(A) mRNA Magnetic Isolation Module. For library preparation NEBNext® Ultra™ II Directional RNA Library Prep with Sample Purification Beads with NEBNext® Multiplex Oligos for Illumina® were used.

treatment_protocol: For RIG-I stimulation a chemically synthesized dsRNA with a 3p end was used. CA21 control RNA (5’-CACACACACACACACACACAC-3’) was used als transfection control. For transfection RNA was complexed to Lipofectamine 2000 (Invitrogen) according to the manufactures protocol. Dabrafenib and Trametinib were dissolved in Dimethylsulfoxid (DMSO) and added at indicated concentrations. DMSO at highest used concentration served as vehicle control.

tag: cell line

value: melanoma

tag: genotype

value: BRAF mut

tag: group

value: no stimulation

tag: treatment

value: dabrafenib 1000 nM + trametinib 100 nM


title: Serum exosome miRNA, PD, 2020, 31


title: Melanoma human, transfection control, vehicle, 24h, rep1

value: transfection control

value: vehicle


title: Serum exosome miRNA, PD, 2020, 28


title: Melanoma human, 3pRNA, vehicle, 24h, rep1


title: Serum exosome miRNA, PD, 2020, 27


title: Melanoma human, 3pRNA, trametinib, 24h, rep1

value: trametinib 100 nM


title: Serum exosome miRNA, PD, 2020, 25


title: Serum exosome miRNA, PD, 2020, 38


title: Serum exosome miRNA, PD, 2020, 26


title: Serum exosome miRNA, PD, 2020, 24


title: Melanoma human, 3pRNA, dabrafenib, 24h, rep1

value: dabrafenib 1000 nM


title: Melanoma human, no stimulation, trametinib, 24h, rep1


title: Serum exosome miRNA, PD, 2020, 23


title: Serum exosome miRNA, PD, 2020, 22


title: Melanoma human, transfection control, no inhibitor, 24h, rep1

value: no inhibitor


title: Melanoma human, transfection control, dabrafenib, 24h, rep1


title: Serum exosome miRNA, PD, 2020, 20


title: Melanoma human, 3pRNA, no inhibitor, 24h, rep1


title: Melanoma human, no stimulation, dabrafenib, 24h, rep1


title: Serum exosome miRNA, PD, 2020, 21


title: Serum exosome miRNA, PD, 2020, 19


title: Serum exosome miRNA, PD, 2020, 18


title: Serum exosome miRNA, PD, 2020, 17


title: Serum exosome miRNA, PD, 2020, 16


title: Melanoma human, no stimulation, vehicle, 24h, rep1


title: Serum exosome miRNA, PD, 2020, 15


title: Serum exosome miRNA, PD, 2020, 14


title: Melanoma human, transfection control, trametinib, 24h, rep1


title: HEK293, IgG, 32°C, replicate 2, SMYD5-KD

city: Reykjavik

first: Hans

middle: Tomas

last: Bjornsson

state: Hofudborgarsvaedid

address: Sturlugata 8

department: Faculty of Medicine

country: Iceland

institute: University of Iceland

library_source: genomic

data_processing:
We demultiplexed the fastq files and trimmed the raw Fastq reads in paired mode with TrimGalore (v.0.6.7)
Bowtie2 (v.2.4.4.) to align the reads to Hg38 and E. Coli reference genome, downloaded from UCSC
aligned Sam files were then converted to Bam files, indexed, and sorted via SAMtools (v.1.15) and BedGraphtoBigWig (v.4) from BEDTools (v.2.3)
SEACR (v.1.3) for peak calling after normalization with the normalization factor calculated as 1/(percent alignment to E. coli). We also used MACS3 callpeak function to call peaks on individual bam files for each replicate against merged IgG files for each condition, with the following settings: --broad --broad-cutoff 0.05 --outdir MASC3 (v.3.0.0) -B --keep-dup all --max-gap 20 --format BAMPE for H3K36me3. For H3K4me3 we used --broad --broad-cutoff 0.05 --outdir MASC3 -B --keep-dup all --max-gap 300 and --format BAMPE.  For the differential peak analysis we used DiffBind (v.3.9.6) where we used the default normalization and analyzing mode. ChIPseeker (v.1.35.3), TxDb.Hsapiens.UCSC.hg38.knownGene (v.3.4.6) and org.Hs.eg.db (v.3.8.2) were used for annotation, all in R.
We used DiffBind (v.3.9.6) for the differential peak analysis, ChIPseeker (v.1.35.3), TxDb.Hsapiens.UCSC.hg38.knownGene (v.3.4.6) and org.Hs.eg.db (v.3.8.2) for annotation. We used  deepTools (v. 3.5.1) computeMatrix, plotProfile and bamCoverage (binSize 5, normalized using RPGC),  for making bigwig files for visualization in the UCSC Genome Browser as well as visualizing the Plot Profile of distinct modifications.  For further analysis and image creation we used deepTools (v.3.5.1.) as well as R.
Assembly: Hg38 and E. coli downloaded from UCSC
Supplementary files format and content: bedgraph file, normalized to e.coli, containing peaks for SEACR calling
Supplementary files format and content: bigwig file made from merged bam files, alignments, for replicate 1 and 2, normalized to genome size
Supplementary files format and content: bigwig file made from bam files, alignments, for each replicate, normalized to genome size
Supplementary files format and content: peak file made with MACS3 peakcall function
Library strategy: CUT&RUN

molecule: genomic DNA

growth_protocol: HEK293WT cells were  cultured in DMEM/F12 with GlutaMAX (Gibco, 10565018) with 10% filtered FBS (Gibco, 10270106) under 5% CO2. Cells were sub-cultured when they had reached 70-90% confluence and media was changed every other day. Human iPS cells (ATCC, ACS-1019)  were used to generate NPCs by neural induction of iPSCs using dual SMAD inhibition and embryoid body generation (StemCell Technologies; 08581, 05832, 05838)77, prior to experiments described here the NPCs were cultured in STEMdiff Neural Progenitor Medium (StemCell Technologies, 05833) on Matrigel (Corning, 354234).

extract_protocol:
We followed the Epicypher CUTANA protocol (v.1.7) on 300.000 cells per sample. We permeabilized the cells with 0.01% digitonin (Sigma, D141). For normalization we spiked in E. Coli DNA (Epicypher, 23618-1401) at the final concentration of 0.2 ng per sample.
The library preparation was performed with TrueSeq-Chip Sample preparation Kit (Illumina, IP-202-9001). We also used a NextSeq 550 using the NextSeq 500/550 Mid Output Kit v2.5 (20024904) with 75 bp paired-end sequencing

treatment_protocol: Cells were exposed to 32°C for 6h or kept at 37°C. For siRNA knockdown we transfected the HEK293 cells with predesigned DsiRNA (IDT, hs.Ri.SMYD5.13.8) and Negative control using Lipofectamine 3000 (Thermo Fisher Scientific, L3000015) based on the manufacturer´s protocol. After 48 hours of transfection, the cells were placed in 32°C and 37°C for 6 hours post which they were harvested for CUT&RUN and RT-qPCR (for validation of the knockdown of SMYD5).

value: 32C, SMYD5 KD

tag: antibody

value: IgG


title: HEK293, IgG, 37°C, replicate 4


title: HEK293, IgG, 37°C, replicate 1, SMYD5-KD

value: 37C, SMYD5 KD


title: HEK293, IgG, 32°C, replicate 1, SMYD5-KD


title: Serum exosome miRNA, PD, 2020, 13


title: HEK293, H3K36me3, 37°C, replicate 2, SMYD5-KD


title: HEK293, H3K36me3, 37°C, replicate 3, SMYD5-KD


title: Serum exosome miRNA, PD, 2020, 12


title: HEK293, H3K36me3, 37°C, replicate 1, SMYD5-KD


title: HEK293, H3K36me3, 6 h at 32°C, replicate 3, SMYD5-KD

value: 6h of 32C, SMYD5 KD


title: Serum exosome miRNA, PD, 2020, 11


title: Serum exosome miRNA, PD, 2020, 10


title: HEK293, H3K36me3, 6 h at 32°C, replicate 2, SMYD5-KD


title: Serum exosome miRNA, PD, 2020, 09


title: Melanoma human, no stimulation, no inhibitor, 24h, rep1


title: Serum exosome miRNA, PD, 2020, 08


title: HEK293, H3K36me3, 37°C, replicate 6


title: Serum exosome miRNA, PD, 2020, 07


title: HEK293, H3K36me3, 6 h at 32°C, replicate 1, SMYD5-KD


title: Serum exosome miRNA, PD, 2020, 06


title: HEK293, H3K36me3, 37°C, replicate 5


title: Serum exosome miRNA, PD, 2020, 05


title: HEK293, H3K36me3, 37°C, replicate 4


title: HEK293, H3K36me3, 6 h at 32°C, replicate 6

value: 6h of 32C


title: Serum exosome miRNA, PD, 2020, 04

value: Serum exosome


title: Serum exosome miRNA, PD, 2020, 03

value: PD


title: HEK293, H3K36me3, 6 h at 32°C, replicate 4


title: HEK293, H3K4me3, 37°C, replicate 2, SMYD5-KD


title: HEK293, H3K36me3, 6 h at 32°C, replicate 5


title: wt3

city: Geneva

first: Athanasia

last: Tzika

address: Athanasia Tzika, LANE - Sciences III, 30 quai Ernest Ansermet, 1211 Genève 4, Switzerland

country: Switzerland

institute: University of Geneva

description:
TruSeq stranded mRNA library
Ter_WT3

data_processing:
Bulk RNA-seq samples were aligned to the corn snake genome (GCF_001185365.1) with STAR (v2.7.0d) using default parameters for paired-end libraries. Gene expression quantification was performed using the featureCounts function implemented in the R package Rsubread (v2.2.1) counting uniquely mapped paired-end reads.
Normalization, processing and differential expression analyses were performed using DEseq2
Assembly: GCF_001185365.1
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

molecule: polyA RNA

organism: Pantherophis guttatus

source_name: embryonic dorsal skin

extract_protocol:
Direct-zol RNA MiniPrep total RNA extraction
TruSeq stranded mRNA library

value: embryonic dorsal skin


title: Serum exosome miRNA, PD, 2020, 01

value: Extracellular vesicles


title: HEK293, H3K4me3, 37°C, replicate 1, SMYD5-KD


title: HEK293, H3K4me3, 37°C, replicate 3, SMYD5-KD


title: Serum exosome miRNA, PD, 2020, 02


title: Serum exosome miRNA, Control, 2020, 25

value: Control


title: wt2

description:
TruSeq stranded mRNA library
Ter_WT2


title: HEK293, H3K4me3, 6 h at 32°C, replicate 3, SMYD5-KD


title: wt1

description:
TruSeq stranded mRNA library
Ter_WT1


title: HEK293, H3K4me3, 6 h at 32°C, replicate 2, SMYD5-KD


title: terrazzo3

description:
TruSeq stranded mRNA library
Ter_Homo3

value: tz/tz


title: 3_2 | 003 | Full ROI

city: Norfolk

first: Clinton

last: Enos

state: Virginia

address: 721 Fairfax Avenue, Suite 200

department: Dermatology

country: USA

institute: Eastern Virginia Medical School

data_processing:
The sequencing data were processed with the GeoMx NGS Pipeline (DND) according to the GeoMx¬Æ-DSP user manual (MAN-10153-01). Briefly, the pipeline was performed for trimming, merging, and aligning the reads to a list of indexing oligos to identify the source probe. The unique molecular identifier (UMI) region of each read was used to remove PCR duplicate reads. This program then converted FASTQ files to DCCs, i.e., converting reads into digital counts.
The zipped folder containing the DCC files were transferred back to GeoMx DSP to obtain the read counts.
After uploading the files to GeoMx DSP, the sequencing quality (quality control) allowed for specifying the parameters for evaluating the quality of NGS data and to qualify segments by number of cells or by area. Read counts were filtered setting the threshold for the limit of detection (LoD) in an ROI. This was defined based on the mean and standard deviation (s.d.) of 𝑙𝑜𝑔−10 normalized target group genes. The calculation is: LoD = mean + (2 × s.d.). A gene was filtered/counted as detected only if it exceeded the LoD in at least 10% of all ROIs. ROIs that did not have the filtering criteria were excluded from further analyses
Assembly: GeoMx® Human Whole Transcriptome Atlas
Supplementary files format and content: DCC files are converted from fastq files from the GeoMX NGS Pipeline
Supplementary files format and content: Normalized_Counts.xlsx contains read counts from all ROI over the 10% LoD threshold and after Q3 normalization.
Library strategy: Spatial Transcriptomics

source_name: HS_Epi Mid Tunnel

extract_protocol:
Slides were processed using the Nanostring GeoMx DSP manual slide preparation GeoMx¬Æ-DSP protocol (MAN-10150-01). Antigen retrieval of the FFPE tissue was performed for 20 minutes followed by deparaffinization and rehydration.Then, the slides were incubated with proteinase K for 20 minutes and RNA probes were placed on slides for overnight in situ hybridization. day2:slides were washed to remove off-target probes for 90 minutes.
Morphology markers pancytokeratin (FITCH/525nm), SYTO 13 (Cy3/568nm), CD138 (Texas Red/615nm), and CD31 (Cy5/666nm) were aded for 1-hour incubation. Slides were loaded onto the GeoMx DSP instrument and after scanning, ROI (region of interest) selection and probe collection were performed according to the GeoMx-DSP user manual protocol (MAN-10088-03). Samples were collected in a 96-well probe aspirate collection plate and each ROI representing a compartment from a patient tumor core was collected in a well.

value: Skin

tag: patient

tag: disease

value: HS

tag: region of_interest_(roi)

value: Epi Mid Tunnel

tag: roi nuclei_count

tag: roi surface_area


title: HEK293, H3K4me3, 6 h at 32°C, replicate 1, SMYD5-KD


title: 3_2 | 004 | Full ROI

source_name: Healthy Control_Epidermis

value: Healthy Control

value: Epidermis


title: 3_2 | 001 | Full ROI


title: terrazzo2

description:
TruSeq stranded mRNA library
Ter_Homo2


title: HEK293, H3K4me3, 37°C, replicate 5


title: 2_2 | 013 | Full ROI

source_name: Cyst_Cyst Stroma

value: Cyst

value: Cyst Stroma


title: 6wkFollowUp43, miRNA

city: Toronto

first: Mohit

last: Kapoor

state: Ontario

address: 60 Leonard Ave

country: Canada

institute: Schroeder Arthritis Institute

data_processing:
Demultiplexing of .bcl files and conversion into Fastq files was performed, followed by quality assessment for each sample using the bcl2fastq conversion tool (v2.19.1.403).
UMI tags were extracted from raw files using UMI-tools software.
The first round of alignment using Bowtie1 was performed against human miRBase (v22.1), and then unaligned reads from this step are aligned to the human reference genome to obtain reads falling in miRBase chromosomal coordinates only.
Reads were collapsed according to associated UMI to remove PCR amplification bias.
UMI-based counts for each miRNA in a sample were generated from both alignments and summed to generate a final table of miRNA expression levels for each sample.
Inference was performed on the raw counts using a negative binomial regression estimated by quasi-likelihood with trended dispersion and normalized by total aligned sequences.
Assembly: GRCh38
Supplementary files format and content: 1 combined comma separated values file includes raw count values for each sample.

source_name: plasma

growth_protocol: No growth

extract_protocol:
RNA was extracted from 200 µL of human plasma using the QIAcube following Qiagen's instructions for sample setup of the miRNeasy Serum/Plasma Advanced Kit (Cat #217204) following manufacturer instructions (Cat #56900).
miRNA libraries for miRNA-seq were prepared using Qiagen's QIAseq miRNA Library Kit optimized for biofluid samples (Cat # 331505). Individual libraries were quantified using a fluorometric high-sensitivity dsDNA assay and assessed using Bioanalyzer high sensitivity assay.

treatment_protocol: No treatment

tag: subject id

tag: batch

tag: timepoint

value: 6-week Followup

tag: Sex

value: MALE

tag: procedure

value: ACL reconstruction

value: plasma


title: terrazzo1

description:
TruSeq stranded mRNA library
Ter_Homo1

tag: tissue


title: 3_2 | 005 | Full ROI

source_name: HS_Epi Deep Tunnel

value: Epi Deep Tunnel


title: HEK293, H3K4me3, 37°C, replicate 4


title: HEK293, H3K4me3, 37°C, replicate 3


title: HEK293, H3K4me3, 6 h at 32°C, replicate 5

value: 6h of 32C


title: 6wkFollowUp42, miRNA


title: 3_2 | 002 | Full ROI


title: HEK293, H3K4me3, 6 h at 32°C, replicate 3


title: 2_2 | 005 | Full ROI

source_name: SCC_SCC Stroma

value: SCC

value: SCC Stroma


title: Baseline43, miRNA

value: Baseline


title: 2_2 | 010 | Full ROI

source_name: Cyst_Cyst Wall

value: Cyst Wall


title: Baseline40, miRNA

value: FEMALE


title: 2wkFollowUp42, miRNA

value: 2-week Followup


title: Baseline42, miRNA


title: 2_2 | 008 | Full ROI

source_name: SCC_SCC Epi

value: Skin

value: SCC Epi


title: 2_2 | 009 | Full ROI


title: 2wkFollowUp39, miRNA


title: 6wkFollowUp41, miRNA


title: 2_2 | 007 | Full ROI


title: Baseline39, miRNA


title: 2wkFollowUp41, miRNA


title: 1_4 | 011 | Full ROI

source_name: HS_Plasma Cell Poor

value: HS

value: Plasma Cell Poor


title: HEK293, H3K4me3, 6 h at 32°C, replicate 4


title: 2_2 | 006 | Full ROI


title: 6wkFollowUp40, miRNA


title: Baseline41, miRNA


title: 2_2 | 003 | Full ROI

value: Cyst

value: Infundibulum


title: 2wkFollowUp43, miRNA

value: MALE


title: 2_2 | 012 | Full ROI

value: Cyst Stroma


title: 2_2 | 011 | Full ROI


title: 2wkFollowUp38, miRNA

value: ACL reconstruction

value: plasma


title: 2_2 | 001 | Full ROI


title: 1_4 | 012 | Full ROI

source_name: HS_CD31 Rich

value: CD31 Rich


title: 6wkFollowUp37, miRNA

value: 6-week Followup


title: Baseline38, miRNA


title: 1_4 | 007 | Full ROI


title: 6wkFollowUp38, miRNA


title: 1_4 | 010 | Full ROI

source_name: HS_CD31 RIch

value: CD31 RIch


title: 1_4 | 005 | Full ROI


title: 2_2 | 002 | Full ROI

source_name: Cyst_CD31 Rich


title: 2_2 | 004 | Full ROI

value: SCC


title: 6wkFollowUp39, miRNA


title: 2wkFollowUp40, miRNA


title: 2wkFollowUp36, miRNA


title: 1_4 | 009 | Full ROI


title: 1_4 | 008 | Full ROI

source_name: HS_Plasma Cell Rich

value: Plasma Cell Rich


title: 1_4 | 002 | Full ROI

value: Epi Deep Tunnel


title: 1_4 | 006 | Full ROI

source_name: HS_Plasma Cell RIch

value: Plasma Cell RIch


title: 2wkFollowUp37, miRNA

value: 2-week Followup


title: 1_4 | 001 | Full ROI

value: Skin


title: Baseline37, miRNA

value: Baseline


title: 6wkFollowUp36, miRNA


title: 6wkFollowUp35, miRNA


title: Baseline36, miRNA


title: 1_3 | 017 | Full ROI

source_name: HS_Stroma Mid Tunnel

value: HS

value: Stroma Mid Tunnel


title: 6wkFollowUp34, miRNA


title: Baseline35, miRNA


title: 2wkFollowUp35, miRNA


title: 1_3 | 018 | Full ROI


title: 1_3 | 015 | Full ROI

source_name: HS_Stroma Deep Tunnel

value: Stroma Deep Tunnel


title: 1_4 | 004 | Full ROI


title: Baseline34, miRNA

value: MALE


title: 1_3 | 014 | Full ROI


title: 2wkFollowUp34, miRNA


title: 1_3 | 016 | Full ROI


title: 1_3 | 013 | Full ROI


title: 1_3 | 012 | Full ROI


title: 6wkFollowUp33, miRNA


title: 2wkFollowUp32, miRNA

value: FEMALE


title: 1_4 | 003 | Full ROI

value: Plasma Cell Poor


title: 1_3 | 011 | Full ROI

source_name: HS_Stroma Infundibulum

value: Stroma Infundibulum


title: 2wkFollowUp33, miRNA

value: ACL reconstruction

value: plasma


title: Baseline33, miRNA


title: 1_3 | 010 | Full ROI


title: 6wkFollowUp32, miRNA

value: 6-week Followup


title: 6wkFollowUp31, miRNA


title: 1_3 | 007 | Full ROI


title: Baseline32, miRNA


title: 1_3 | 008 | Full ROI

value: Epidermis


title: Baseline31, miRNA


title: 1_3 | 004 | Full ROI


title: 1_3 | 005 | Full ROI


title: 6wkFollowUp30, miRNA


title: 2wkFollowUp30, miRNA


title: 6wkFollowUp29, miRNA


title: 2wkFollowUp31, miRNA


title: 1_3 | 006 | Full ROI

source_name: HS_Epi Mid Tunnel

value: Epi Mid Tunnel


title: 2wkFollowUp29, miRNA


title: 1_3 | 003 | Full ROI

value: Infundibulum


title: 1_3 | 002 | Full ROI


title: Baseline30, miRNA


title: Baseline29, miRNA


title: 1_3 | 009 | Full ROI


title: 2wkFollowUp28, miRNA


title: Baseline28, miRNA


title: 1_3 | 001 | Full ROI


title: 6wkFollowUp28, miRNA


title: AAVrh10-C5

city: Columbus

first: Scott

last: Harper

state: Ohio

address: Center for Gene Therapy, 575 Children’s Crossroads Room WC3740

institute: The Research Institute at Nationwide Children's Hospital

data_processing:
BCL files demultiplexing into FASTQ files
Data trimming and mapping
Host-virus chimeric site detection
Vaariant detection
Assembly: Performed by Azenta Life Sciences Inc.
Supplementary files format and content: .csv file for each sample containing aligned sequences

organism: synthetic construct

source_name: vector

growth_protocol: AAV production performed by Andelyn Biosciences

extract_protocol:
Performed by Azenta Life Sciences Inc.
Illumina library prep performed by Azenta Life Sciences Inc.

tag: cell type

value: vector


title: AAVrh74-C1

treatment_protocol: AAV production performed by Andelyn Biosciences


title: AAV9-C5


title: AAVrh10-C1


title: 6wkFollowUp27, miRNA


title: 2wkFollowUp27, miRNA

value: 2-week Followup


title: B35T1NC2 [TP63 CUT&Tag]

city: Beijing

first: Yi

last: Hu

address: No. 28 Fuxing Rd， Haidian district，Beijing

country: China

institute: Chinese PLA General Hospital

library_source: other

data_processing:
Sequence alignment to the hg19 reference genome was performed using Bowtie2 v2.1.0.
TP63 CUT&Tag peak calling was performed with MACS2 v2.2.6 using the parameter “-- nomodel" and default parameters otherwise.
Assembly: hg19
Supplementary files format and content: bigwig

molecule: other

source_name: bronchial epithelium

growth_protocol: The cells were cultured in serum-free LHC-8 medium (Gibco, USA) at 37°C in an atmosphere containing 95% air and 5% CO2. The culture medium was changed every 3 days. When cells reached 90% confluency, they were detached by using trypsin (Sigma-Aldrich, USA) for 5 min, and the suspension was separated by centrifugation to collect the cells. The cells were then subjected to subculturing.

extract_protocol:
DNA was extracted, purified and amplified with TruePrepTM Index Kit V2 for Illumina® (Vazyme)
Libraries were analyzed for size distribution by Agilent 2100 Bioanalyzer and quantified by real-time PCR.Finally, DNA libraries were sequenced on the Illumina Novaseq platform and 150 bp paired-end reads were generated.

value: bronchial epithelium

tag: cell line


title: B35T1NC1 [TP63 CUT&Tag]


title: AAVrh7410-C5


title: Baseline27, miRNA

source_name: plasma

value: Baseline


title: 6wkFollowUp26, miRNA


title: AAV8-C5


title: 2wkFollowUp26, miRNA


title: Baseline26, miRNA


title: AAV8-C1


title: 6wkFollowUp25, miRNA


title: 2wkFollowUp25, miRNA


title: BEP2DNC2 [TP63 CUT&Tag]


title: Baseline25, miRNA


title: AAV6-C5


title: 6wkFollowUp24, miRNA


title: BEP2DOE1 [TP63 CUT&Tag]


title: BEP2DNC1 [TP63 CUT&Tag]


title: AAV6-C1


title: 2wkFollowUp24, miRNA


title: Baseline24, miRNA


title: B35T1NC2 [STAG2 CUT&Tag]

data_processing:
Sequence alignment to the hg19 reference genome was performed using Bowtie2 v2.1.0.
STAG2 CUT&Tag peak calling was performed with MACS2 v2.2.6 using the parameter “-- nomodel" and default parameters otherwise.
Assembly: hg19
Supplementary files format and content: bigwig


title: 6wkFollowUp23, miRNA


title: AAV5-C5


title: Baseline23, miRNA


title: AAV9-C1


title: BEP2DOE2 [TP63 CUT&Tag]


title: 6wkFollowUp22, miRNA


title: AAV5-C1


title: Baseline22, miRNA


title: BEP2DOE1 [STAG2 CUT&Tag]


title: 2wkFollowUp22, miRNA


title: 6wkFollowUp21, miRNA


title: AAV1-C5


title: 2wkFollowUp21, miRNA


title: BEP2DNC2 [STAG2 CUT&Tag]


title: AAV2-C5


title: B35T1NC4 [Micro-C]

data_processing:
Micro-C data was processed using dovetail-genomics pipeline https://micro-c.readthedocs.io/en/latest/index.html
Assembly: hg19
Supplementary files format and content: hic


title: 2wkFollowUp20, miRNA


title: 6wkFollowUp20, miRNA


title: AAV2-C4


title: Baseline20, miRNA


title: B35T1NC1 [STAG2 CUT&Tag]


title: 2wkFollowUp23, miRNA


title: B35T1NC3 [Micro-C]


title: 6wkFollowUp19, miRNA


title: 2wkFollowUp19, miRNA


title: AAV2-C3


title: Baseline19, miRNA


title: BEP2DOE2 [STAG2 CUT&Tag]


title: 6wkFollowUp18, miRNA


title: AAV2-C1


title: 2wkFollowUp18, miRNA


title: AAV2-C2


title: B35T1NC2 [Micro-C]


title: 6wkFollowUp17, miRNA


title: AAV1-C1


title: B35T1NC1 [Micro-C]


title: Baseline21, miRNA


title: Baseline18, miRNA


title: BEP2DOE4 [Micro-C]


title: BEP2DNC1 [STAG2 CUT&Tag]


title: 2wkFollowUp17, miRNA


title: Vehicle scBCR-seq

city: Houston

first: Zhongming

last: Zhao

state: TX

address: 7000 Fannin St Suite 600

department: McWilliams School of Biomedical Informatics

institute: The University of Texas Health Science Center at Houston

description: Vehicle-treated sample, BCR sequenced using 10x Genomics Chromium Single Cell Immune Profiling protocol

data_processing:
We processed the raw data from paired single-cell RNA library, single-cell TCR library, and single-cell BCR library using Cell Ranger (v7.0.0) multi pipeline. The RNA library was aligned to mm10-2020-A reference genome, and the TCR and BCR libraries were aligned to GRCm38-alts-ensembl-7.0.0 provided by 10x Genomics. As we detected ambient RNA contamination from acinar and PanIN cells, we used CellBender (v3.0.0) to correct the raw UMI count matrix from Cell Ranger output. The corrected UMI count matrix h5 files from CellBender were used for analysis.
Assembly: mm10
Supplementary files format and content: h5 files (RNA): CellBender output count matrix files
Supplementary files format and content: filtered_contig_annotations.csv (TCR and BCR): CellRanger output comma-separated contig annotation files

organism: Mus musculus

source_name: pancreas

extract_protocol:
Pancreas tissue from two mice per group was collected. The two tissues from each respective group were combined and submitted as one sample per group to the Cancer Genomics Center at UTHealth after processing. After collection, tissue was placed in ice-cold PBS, then minced thoroughly on a glass surface on ice for about 2 minutes until it was a fine paste. Tissue was added to 1 mL Type 4 collagenase enzyme mix (50 μL Type 4 collagenase 100 mg/mL, 5 μL DNAse, 10 μL RNAse inhibitor, 5 μL 1 M CaCl2, 10 μL 10% BSA/PBS, 930 μL DPBS). Samples were incubated on ice and shaken gently every 30 seconds for two minutes. Then we triturated 10 times per minute for 20 minutes. Chunks were allowed to settle over ice for one minute. 750 microliters of supernatant containing whole cells were filtered on a 30 μM filter over a 50 mL conical tube. The filter was rinsed with 5 mL ice-cold PBS/BSA 0.04%. To the remaining tissue chunks, 1 mL type 4 collagenase enzyme mix was added and triturated on ice ten times every minute for 30 minutes. The entire volume of the sample was added onto the same filter over the 50 mL conical and rinsed with 5 mL ice-cold PBS/BSA 0.04%. Flow through was transferred to 15 mL conical and centrifuged at 300 g for 5 minutes at 4°C. The supernatant was removed, and the pellet was resuspended in 100 μL ice-cold PBS/BSA 0.04%. 10 mL ice-cold PBS/BSA 0.04% was added, and the sample was centrifuged for 5 minutes at 300 g at 4°C. The supernatant was removed, and the pellet was resuspended in 100 μL ice-cold PBS/BSA 0.04%. The single cells were filtered using a 40-μm cell strainer and examined under a microscope to confirm successful dissociation into individual cells before sequencing.
The single cell capture and library construction were performed by following the Chromium Next GEM Single cell 5ʹ Reagent Kits v2 protocol (CG000331). Briefly, cells were resuspended in PBS with 0.04% BSA at a concentration of 700-1200 cells/µl and more than 85% viability. The single cells were loaded onto Chromium Next GEM Chip K with partitioning oil and barcoded singe cell gel beads. Approximately 3,000 cells per sample were captured. The barcoded and full-length cDNA is produced after incubation of the gel beads-in-emulsion (GEMs) and amplified via PCR for library construction. The library preparation is performed by following the protocol of Chromium Next GEM Single Cell 5ʹ GEM, Library & Gel Bead Kit v2 (PN-1000267). The RNA libraries and the TCR/BCR libraries were generated from the same cells and have the same cell barcodes. The quality of the final libraries was examined using Agilent High Sensitive DNA Kit (#5067-4626) on an Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, USA).

treatment_protocol: AB-680 (HY-125286) was dissolved in 20% SBE-β-CD (MedChem Express, HY-17031/CS-0731) and DMSO (Sigma-Aldrich, D8418) and administered oral gavage 10mg/kg three days a week. The Vehicle Control was DMSO in 20% SBE-β-CD and administered oral gavage three days a week.

value: pancreas

tag: genotype

value: DMSO


title: 6wkFollowUp16, miRNA


title: Baseline17, miRNA


title: Baseline16, miRNA


title: BEP2DOE3 [Micro-C]


title: Vehicle scRNA-seq

description: Vehicle-treated sample, RNA sequenced using 10x Genomics Chromium Single Cell Immune Profiling protocol

library_source: transcriptomic single cell


title: BEP2DOE2 [Micro-C]


title: Vehicle scTCR-seq

description: Vehicle-treated sample, TCR sequenced using 10x Genomics Chromium Single Cell Immune Profiling protocol


title: BEP2DOE1 [Micro-C]


title: AB680 scBCR-seq

description: AB-680 treated sample, BCR sequenced using 10x Genomics Chromium Single Cell Immune Profiling protocol


title: 2wkFollowUp15, miRNA


title: 2wkFollowUp14, miRNA


title: Baseline15, miRNA


title: AB680 scTCR-seq

description: AB-680 treated sample, TCR sequenced using 10x Genomics Chromium Single Cell Immune Profiling protocol


title: 6wkFollowUp14, miRNA


title: 6wkFollowUp15, miRNA


title: BEP2DNC4 [Micro-C]


title: 6wkFollowUp13, miRNA


title: BEP2DNC3 [Micro-C]


title: Day14-4

city: Hohhot

first: Jiamin

address: zhaowuda road

institute: Inner Mongolia Agricultural University

description: replicate sample 4

data_processing:
Raw reads of fastq format were firstly processed using fastp  and the low quality reads were removed to obtain the clean reads.
Q value < 0.05 and foldchange > 2 or foldchange < 0.5 was set as the threshold for significantly differential expression gene (DEGs)
R (v 3.2.0) was used to draw the column diagram, the chord diagram and bubble diagram of the significant enrichment term
Assembly: mm10
Supplementary files format and content: tab-delimited text files include Raw_gene_counts_matrix
Supplementary files format and content: tab-delimited text files include RPKM values for each sample

source_name: skin

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Then the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

value: skin

tag: time

value: Natural wound healing


title: 6wkFollowUp12, miRNA

value: MALE


title: BEP2DNC2 [Micro-C]


title: 2wkFollowUp12, miRNA


title: Baseline14, miRNA


title: 2wkFollowUp16, miRNA

value: FEMALE


title: AB680 scRNA-seq

description: AB-680 treated sample, RNA sequenced using 10x Genomics Chromium Single Cell Immune Profiling protocol

tag: treatment


title: Baseline13, miRNA


title: Baseline12, miRNA


title: 2wkFollowUp13, miRNA


title: BEP2DNC1 [Micro-C]


title: B35T1NC1 [CTCF CUT&Tag]

data_processing:
Sequence alignment to the hg19 reference genome was performed using Bowtie2 v2.1.0.
CTCF CUT&Tag peak calling was performed with MACS2 v2.2.6 using the parameter “-- nomodel" and default parameters otherwise.
Assembly: hg19
Supplementary files format and content: bigwig


title: Day14-1

description: replicate sample 1


title: Day14-3

description: replicate sample 3


title: B35T1NC2 [CTCF CUT&Tag]


title: 2wkFollowUp11, miRNA


title: Day12-4

description: replicate sample 4


title: Baseline11, miRNA


title: 6wkFollowUp10, miRNA


title: 6wkFollowUp11, miRNA


title: BEP2DOE [CTCF CUT&Tag]


title: Day12-3

description: replicate sample 3


title: 2wkFollowUp10, miRNA


title: Baseline10, miRNA


title: 6wkFollowUp9, miRNA


title: BEP2DNC2 [CTCF CUT&Tag]


title: Day12-2

description: replicate sample 2


title: 2wkFollowUp9, miRNA


title: B35T1NC2 [ATAC-seq]

data_processing:
Sequence alignment to the hg19 reference genome was performed using Bowtie2 v2.1.0.
ATAC-seq peak calling was performed with MACS2 v2.2.6 using the parameter “-- nomodel" and default parameters otherwise.
Assembly: hg19
Supplementary files format and content: bigwig


title: 2wkFollowUp8, miRNA


title: Baseline9, miRNA


title: Day12-1

description: replicate sample 1


title: Day14-2

description: replicate sample 2


title: Day10-4

description: replicate sample 4


title: Baseline8, miRNA


title: 6wkFollowUp7, miRNA


title: BEP2DOE2 [ATAC-seq]


title: B35T1NC1 [ATAC-seq]


title: 2wkFollowUp7, miRNA


title: Day10-3

description: replicate sample 3


title: 6wkFollowUp6, miRNA


title: 2wkFollowUp6, miRNA


title: BEP2DOE1 [ATAC-seq]


title: 2wkFollowUp5, miRNA


title: 6wkFollowUp8, miRNA


title: BEP2DNC1 [ATAC-seq]


title: Day7-3

description: replicate sample 3


title: Baseline5, miRNA


title: Day10-1

description: replicate sample 1


title: 6wkFollowUp4, miRNA


title: Baseline6, miRNA


title: BEP2DNC2 [ATAC-seq]


title: Day10-2

description: replicate sample 2


title: BEP2DNC1 [CTCF CUT&Tag]


title: Day7-2

description: replicate sample 2


title: Day7-4

description: replicate sample 4


title: 2wkFollowUp3, miRNA


title: Baseline3, miRNA


title: 2wkFollowUp2, miRNA


title: Day5-4

description: replicate sample 4


title: HTR-8/SVneo cell, lenti overexpression,3

city: Shanghai

first: Yaoxi

last: Xiong

state: i

address: Jinqian Road No.1567

institute: The International Peace Maternity and Child Health Hospital, School of Medicine

data_processing:
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated.  Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads. The clean reads were mapped to the reference genome using HISAT. FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count. PCA analysis were performed using R (v 3.2.0) to evaluate the biological duplication of samples.Differential expression analysis was performed using the DESeq2. Q value < 0.05 and foldchange > 2 or foldchange < 0.5 was set as the threshold for significantly differential expression gene (DEGs). Hierarchical cluster analysis of DEGs was performed using R (v 3.2.0) to demonstrate the expression pattern of genes in different groups and samples. The radar map of top 30 genes was drew to show the expression of up-regulated or down-regulated DEGs using R packet ggradar . Based on the hypergeometric distribution, GO, KEGG pathway, Reactome and WikiPathways enrichment analysis of DEGs were performed to screen the significant enriched term using R (v 3.2.0), respectively. R (v 3.2.0) was used to draw the column diagram, the chord diagram and bubble diagram of the significant enrichment term. Gene Set Enrichment Analysis (GSEA) was performed using GSEA software. The analysis was www.oebiotech.com used a predefined gene set, and the genes were ranked according to the degree of differential expression in the two types of samples. Then it is tested whether the predefined gene set was enriched at the top or bottom of the ranking list.
After reads ressembled by StringTie2, gene structure extension and novel transcripts identification were performed by comparing the reference genome and the known annotated genesusing Cuffcompare software. ASprofile was used to analyse the alternatively splicing of differentially regulated transcripts isoforms or exons. SNPs and InDels were called using SAMtools and BCFtools, and the details were shown on SAMtools webpage (http://samtools.sourceforge.net/mpileup.shtml). Then SnpEff14annotates and predicts the effects of variants on genes (such as amino acid changes).
Assembly: mm10
Supplementary files format and content: tab-delimited text files includes FPKM valus for each sample

source_name: Placenta

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Then the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions. The transcriptome sequencing and analysis were conducted by OE Biotech Co., Ltd. (Shanghai, China).

value: Placenta

value: trophoblast

value: LncRNA-LPE overexpression

value: lentiviral transfection


title: HTR-8/SVneo cell, control,3

value: WT


title: 2wkFollowUp4, miRNA

value: ACL reconstruction

value: plasma


title: HTR-8/SVneo cell, lenti overexpression,2


title: Baseline7, miRNA


title: 6wkFollowUp3, miRNA

value: 6-week Followup


title: Baseline4, miRNA


title: 6wkFollowUp1, miRNA


title: Day7-1

description: replicate sample 1


title: 2wkFollowUp1, miRNA

value: 2-week Followup


title: Day5-2

description: replicate sample 2


title: Baseline1, miRNA


title: HTR-8/SVneo cell, lenti overexpression,1


title: 6wkFollowUp2, miRNA


title: 6wkFollowUp5, miRNA


title: Day5-3

description: replicate sample 3


title: Baseline2, miRNA


title: HTR-8/SVneo cell, control,2


title: KO.M2.D.1

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

description: KO M2 BMDM, Control

data_processing:
RSEM along with Bowtie2 used for alignment
All reads within any transcript’s coding part of a gene were counted to get expression for each gene
Raw counts were tested for differential expression using DESeq2 method
DESeq2 normalized count values were used for heatmap visualization of expression differences (genes with at least 10 raw counts in at least one sample were considered)
Enrichment analysis, PCA analysis

source_name: bone marrow hematopoietic stem cells

growth_protocol: Thioglycolate macrophages were isolated from intact B6 mice 4 days after injecting 1 ml 3% Thioglycolate intraperitoneally. F4/80+ Cells were sorted by magnetic beads (Miltenyi Biotec). Ascites macrophages were isolated from ID8 tumor-bearing mice by peritoneal washes 45 days after injecting ID8 tumor cells. F4/80+ Cells were sorted by magnetic beads (Miltenyi Biotec). Bone Marrow-derived macrophages were generated from hematopoietic stem cells by culturing with 10 ng/mL M-CSF (PeproTech, Cranbury, NJ) for 6 days. Then cells were incubated for additional 24 hours with LPS (100 ng/mL) and murine IFN-γ (50 ng/mL) for M1 type polarization or murine IL-4 (10 ng/mL) and murine IL-13 (10 ng/mL) for M2 type polarization, respectively.

extract_protocol:
RNA was isolated with Zymo Microkit (cat. #1050)
3’ mRNA-Seq libraries were generated from 100 ng of DNAse I treated total RNA using the QuantSeq FWD Library Preparation kit (Lexogen, Vienna, Austria), according to manufacturer’s directions. Overall library size was determined using the Agilent Tapestation and the DNA 5000 Screentape (Agilent, Santa Clara, CA). Libraries were quantitated using real-time PCR (Kapa Biosystems, Wilmington, MA). Libraries were pooled and Single read, 75 base pair Next Generation Sequencing was done on a P2 flow cell using the NextSeq 2000 (Illumina, San Diego, CA).

treatment_protocol: Cells were incubated with 10 uM AP-3-84 or equivalent amount of DMSO for 4 hours

tag: strain

value: bone marrow hematopoietic stem cells

value: Bone Marrow-derived macrophages

value: wild-type C57BL/6

value: Vehicle Control


title: HEK293, H3K4me3, 6 h at 32°C, replicate 1

value: 6h of 32C

tag: antibody


title: KO.M1.D.2

description: KO M1 BMDM, Control


title: HTR-8/SVneo cell, control,1


title: Day5-1

description: replicate sample 1

value: skin

value: Natural wound healing


title: KO.M2.A.2

description: KO M2 BMDM, AP-3-84-treated

value: 10 uM AP-3-84 for 4 hours


title: HEK293, H3K4me3, 37°C, replicate 2


title: KO.M2.A.3

description: KO M2 BMDM, AP-3-84-treated


title: HEK293, H3K4me3, 37°C, replicate 1


title: KO.M2.A.1

description: KO M2 BMDM, AP-3-84-treated


title: Day3-4

description: replicate sample 4


title: KO.M1.D.1

description: KO M1 BMDM, Control


title: KO.M0.A.3

description: KO M0 BMDM, AP-3-84-treated


title: KO.M2.D.3

description: KO M2 BMDM, Control


title: KO.M2.D.2

description: KO M2 BMDM, Control


title: Day3-3

description: replicate sample 3


title: KO.M1.A.1

description: KO M1 BMDM, AP-3-84-treated


title: HEK293, H3K4me3, 6 h at 32°C, replicate 2


title: Day3-2

description: replicate sample 2


title: KO.M0.D.3

description: KO M0 BMDM, Control


title: KO.M1.A.2

description: KO M1 BMDM, AP-3-84-treated


title: KO.M1.A.3

description: KO M1 BMDM, AP-3-84-treated


title: Day3-1

description: replicate sample 1


title: HEK293, H4K20me3, 37°C, replicate 2


title: HEK293, H4K20me3, 37°C, replicate 3


title: KO.M1.D.3

description: KO M1 BMDM, Control


title: Day0-4

description: replicate sample 4


title: Day0-3

description: replicate sample 3


title: HEK293, H4K20me3, 37°C, replicate 1


title: KO.M0.A.2

description: KO M0 BMDM, AP-3-84-treated


title: HEK293, H4K20me3, 6 h at 32°C, replicate 1


title: Day0-2

description: replicate sample 2


title: KO.M0.A.1

description: KO M0 BMDM, AP-3-84-treated


title: WT.M2.D.1

description: WT M2 BMDM, Control


title: HEK293, H4K20me3, 6 h at 32°C, replicate 3


title: HEK293, H3K9me3, 37°C, replicate 2


title: Day0-1

description: replicate sample 1


title: KO.M0.D.2

description: KO M0 BMDM, Control


title: HEK293, H4K20me3, 6 h at 32°C, replicate 2


title: KO.M0.D.1

description: KO M0 BMDM, Control


title: WT.M1.A.3

description: WT M1 BMDM, AP-3-84-treated


title: WT.M1.A.2

description: WT M1 BMDM, AP-3-84-treated


title: WT.M2.A.3

description: WT M2 BMDM, AP-3-84-treated


title: WT.M2.A.2

description: WT M2 BMDM, AP-3-84-treated


title: soleus skeletal muscle, wild-type, rep3

city: Solna

first: Igor

last: Cervenka

address: Solnavägen 9

department: Physiology and Pharmacology

country: Sweden

institute: Karolinska Institutet

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm38 whole genome using STAR 2.7.3a with extra arguments --outFilterMultimapNmax 50   --outFilterMultimapScoreRange 3   --outFilterScoreMinOverLread 0.7   --outFilterMatchNminOverLread 0.7   --outFilterMismatchNmax 10   --alignIntronMax 500000   --alignMatesGapMax 1000000   --sjdbScore 2
Reads aligning to gene exons were counted using featureCounts v2.0.0 program from Subread package, summarized at gene level
Differential gene expression at FDR level 0.1 was obtained using DESeq2 R package, genes with total raw counts less then 10 across all samples were excluded from analysis
Assembly: GRCm38.p6
Supplementary files format and content: tab-delimited text file includes raw read counts for all samples
Supplementary files format and content: tab-delimited text file includes differetial gene expression analysis output from DESeq2

source_name: soleus skeletal muscle

extract_protocol:
Total RNA was extracted from mice soleus muscles using Trizol reagent
Strand-specific cDNA library

value: male

value: soleus skeletal muscle

tag: muscle

value: soleus

value: wild-type

tag: condition


title: WT.M1.D.3

description: WT M1 BMDM, Control


title: mDO_2220_ctrl

city: Stanford

first: Anthony

last: Oro

state: CA

address: 269 Campus Drvie

institute: Stanford University

data_processing:
STAR used for alignment.
Homer for raw counts and RPKM values
DESEQ2 used for differential expression
Assembly: mm10
Supplementary files format and content: text file, raw counts

source_name: mouse BCC organoids

growth_protocol: Mouse primary BCC tumor tissues were embedded as small pieces in basement membrane extract and grown in organoid medium for 7 days.

extract_protocol:
RNA samples were obtained from mouse organoids using RNeasy Plus Mini Kit from Qiagen according to manufacturer’s instructions.
The RNAseq libraries were constructed by TruSeq Stranded mRNA Library Prep kit (Illumina) and sequenced on an Illumina NovaSeq sequencer.

treatment_protocol: Cells were treated with either PBS control or Il1 and Osm ligand combination for 7 days in organoid medium.

value: mouse BCC organoids

value: WT

value: control group


title: HEK293, H3K9me3, 37°C, replicate 3


title: HEK293, H3K9me3, 6 h at 32°C, replicate 3


title: mDO_2251_ligand

value: treatment group


title: WT.M2.A.1

description: WT M2 BMDM, AP-3-84-treated


title: mDO_2220_ligand


title: WT.M2.D.3

description: WT M2 BMDM, Control


title: WT.M1.D.2

description: WT M1 BMDM, Control


title: mDO_2251_ctrl


title: WT.M2.D.2

description: WT M2 BMDM, Control


title: soleus skeletal muscle, wild-type, rep1


title: HEK293, H3K9me3, 6 h at 32°C, replicate 1


title: WT.M1.A.1

description: WT M1 BMDM, AP-3-84-treated


title: WT.M0.A.3

description: WT M0 BMDM, AP-3-84-treated


title: WT.M1.D.1

description: WT M1 BMDM, Control


title: soleus skeletal muscle, wild-type, rep2


title: WT.M0.D.3

description: WT M0 BMDM, Control


title: HEK293, H3K9me3, 37°C, replicate 1


title: WT.M0.A.2

description: WT M0 BMDM, AP-3-84-treated


title: HEK293, H3K9me3, 6 h at 32°C, replicate 2


title: soleus skeletal muscle, HECTD1-mKO, rep1


title: WT.M0.D.2

description: WT M0 BMDM, Control


title: WT.M0.A.1

description: WT M0 BMDM, AP-3-84-treated


title: 9.Thio-Macs_control_replicate3

description: Thioglycolate Macrophages, Control

source_name: peritoneal macrlphages

value: peritoneal macrlphages

value: Thioglycolate-induced macrophages


title: soleus skeletal muscle, HECTD1-mKO, rep2


title: soleus skeletal muscle, HECTD1-mKO, rep3


title: SW620 (colon cancer) cells, L-pampo™ 1x, 3 hours, replicate 3

city: Seoul

first: Sera

last: Park

state: Seocho-gu

address: 15-19 Gangnam-daero 41-gil

country: South Korea

institute: MOGAM Institute for Biomedical Research

data_processing:
Trimming adapter sequences using TrimGalore (Cutadapt version 0.6.10)
Alignment by STAR (version 2.7.10b)
Quantification of transcript abundances using RSEM (version 1.2.28)
Assembly: GRCh38
Supplementary files format and content: comma-delimited text file includes TPM values for each sample

source_name: Large intestine; Colon

growth_protocol: THP-1 cells were grown in RPMI1640 medium (Gibco) containing 10% fetal bovine serum (Gibco), 1% antibiotics (100 mg/L streptomycin, 100 U/mL penicillin), and 0.4% 2-Mercaptoethanol (Sigma Aldrich). THP-1 cells were differentiated into macrophage-like cells in a medium with 1% phorbol 12-myristate 13-acetate (PMA) (Sigma Aldrich) for 72 h. PC-3 and SW620 cells were cultured in a DMEM medium (Gibco) containing 10% fetal bovine serum and 1% antibiotics. All Cells were cultured at 37°C in a 5% CO2 atmosphere.

extract_protocol:
The cells were washed twice using 1x DPBS (WelGENE) to extract the total RNA. After removing all the DPBS, 1ml of TRIzol (Invitrogen, Waltham, MA, USA) was added to each well. The TRIzol/cell lysate was collected in a 1.5 mL EP tube after briefly scraping each well and incubated at room temperature for 5 min. Then, 250 µl chloroform was added into the EP tube and shaken vigorously ten times. The EP tube was centrifuged at 14,000 rpm at 4°C for 5 min. The cleared supernatant was transferred to a new EP tube, and 500 µl of isopropanol was added, mixing it carefully. The EP tube was centrifuged at 14,000 rpm at 4°C for 20 min. The isopropanol was discarded, and the pellets were allowed to air dry.
Libraries were generated using the Illumina TruSeq Stranded mRNA kit (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.

treatment_protocol: After replacing the fresh complete media and incubating for 1hr, the diluted L-pampo™ was treated to each cell line at a concentration of 1x (40 µg/ml) and cultured for 3 and 6 h, respectively.

value: Large intestine; Colon

value: Colon cancer cell

value: L-pampo


title: SW620 (colon cancer) cells, L-pampo™ 1x, 6 hours, replicate 3


title: SW620 (colon cancer) cells, L-pampo™ 1x, 3 hours, replicate 2


title: SW620 (colon cancer) cells, L-pampo™ 1x, 6 hours, replicate 2


title: 12.Thio-Macs_AP3-84_replicate3

description: Thioglycolate Macrophages, AP-3-84-treated

value: wild-type C57BL/6


title: WT.M0.D.1

description: WT M0 BMDM, Control

value: bone marrow hematopoietic stem cells

value: Bone Marrow-derived macrophages

value: Vehicle Control


title: Hippocampus, 37°C, replicate 4

data_processing:
Fastq files were pseudo-aligned to the GRCm39 mouse transcriptome, downloaded from NCBI, using Kallisto (v.0.48.0) with paired-end mode on and 100 bootstraps.
Kallisto output files were imported into R using the tximport package. Transcripts were assigned to genes using the TxDb.Mmusculus.UCSC.mm10.ensGene package (v.3.4.0) in R . Differential expression analysis was performed using the DESeq2 package (v.3.16) in R after discarding transcripts with less than 10 counts. Differentially expressed genes were defined as those with an adjusted p-value less than 0.1.
Assembly: mm39,  downloaded from NCBI
Supplementary files format and content: HDF5 binary file containing run info, abundance esimates, bootstrap estimates, and transcript length information length.
Supplementary files format and content: csv file containing result from DESeq such as; count and p-value and logfoldchange

source_name: Brain

growth_protocol: C57BL6 mice (Jackson) were bred to create a litter (n=2). At P10, we split littermates into two groups. One group (n=6) was cooled to a core temperature of 32°C and other (n=6) were maintained at 37°C, for 6 hours respectively. These animals were then euthanized, and their brains were isolated immediately after the cooling period and flashed with PBS. One of the hemispheres was immersed in 4% PFA for 72-96 h for fixation and the other hemisphere was dissected for the cerebellum, thalamus/basal ganglia, hippocampus, anterior and posterior cortex. After fixation, samples were cryopreserved in a sucrose gradient and then flash-frozen.

extract_protocol:
RNA was isolated using Qiagen's RNeasy Mini Kit (Qiagen, 74104).
Isolated RNA was constructed with directional mRNA library preparation (poly A enrichment) and then sequencing was performed by Novogene on a NovaSeq PE150 paired-end, generating over 80 million reads per sample.

treatment_protocol: Neonatal mice (P10) were injured with cerebral HI and treated with normothermia (37°C) or cooling (32°C) for 6h.

value: Brain

value: Hippocampal cells

value: 37C, cerebral HI


title: 11.Thio-Macs_AP3-84_replicate2

value: 10 uM AP-3-84 for 4 hours


title: Hippocampus, 37°C, replicate 6


title: Hippocampus, 37°C, replicate 5


title: 10.Thio-Macs_AP3-84_replicate1


title: SW620 (colon cancer) cells, L-pampo™ 1x, 3 hours, replicate 1


title: 6.Ascites_AP3-84_replicate3

description: Ascites Macrophages, AP-3-84-treated

source_name: peritoneal ascites

value: peritoneal ascites

value: ID8-induced ascites macrophages


title: 4.Ascites_AP3-84_replicate1

description: Ascites Macrophages, AP-3-84-treated


title: SW620 (colon cancer) cells, Non-treatment, 0 hour, replicate 3


title: 5.Ascites_AP3-84_replicate2

description: Ascites Macrophages, AP-3-84-treated


title: Hippocampus, 37°C, replicate 3

value: 32C 6h, cerebral HI


title: 3.Ascites_control_replicate3

description: Ascites Macrophages, Control


title: 2.Ascites_control_replicate2

description: Ascites Macrophages, Control


title: SW620 (colon cancer) cells, L-pampo™ 1x, 6 hours, replicate 1


title: 8.Thio-Macs_control_replicate2

description: Thioglycolate Macrophages, Control


title: 1.Ascites_control_replicate1

description: Ascites Macrophages, Control


title: SW620 (colon cancer) cells, Non-treatment, 0 hour, replicate 2


title: Sequencing Pool 5,HTO

city: New York

first: Jahan

last: Rahman

state: New York

address: 417 E 68th St

department: Center for Hematologic Malignancies

institute: Memorial Sloan Kettering

data_processing:
FASTQ sequencing reads were processed using the Cell Ranger pipeline, which extracts cell barcodes, unique molecular identifiers (UMIs), and cDNA or antibody barcodes. It aligns cDNA reads to the human GRCh38 reference genome and generates gene and antibody UMI count matrices.
Assembly: Human reference, GRCh38 (GENCODE v32/Ensembl 98)
Supplementary files format and content: Raw count matrices:  RNA_counts.csv.gz,ADT_counts.csv.gz
Supplementary files format and content: Demultiplexing tables: cell_sample_assign.csv.gz
Supplementary files format and content: ADT and HTO feature information: feature_README.txt
Library strategy: CITE-Seq

source_name: AML PDX

extract_protocol:
Healthy and leukemic bone marrow samples were thawed using prewarmed RPMI with 10% FBS and cultured overnight. Subsequently, viable cells were subject to RNP-based CRISPR editting.  Cells were washed twice with cold PBS before labeling with unique TotalSeqA-compatible HashTags (BioLegend). CRISPR editted samples were incubated with human Fc receptor-blocking agent (BioLegend) and labeled with DAPI for live cell sorting by flow cytometry using an Aria cytometer (BD Biosciences). After sorting, equal numbers of cells were washed once with cold PBS before application of the TotalSeqA cocktail (BioLegend) and subsequently a custom ADT-tagged anti-CD10, CD90 and CD34 antibody (BioLegend). Cells were washed three times with cold PBS and submitted to the MSKCC Integrative Genomics Core for sequencing.
A 10X Genomics Chromium machine was used for 3000–5000 single-cell capture. Cells were washed and partitioned into nanoliter-scale Gel Bead-In-Emulsions (GEMs), where all generated cDNA share a common 10x Genomics Barcode but uses a pool of ~750,000 barcodes to separately index each cell’s transcriptome and ADT-barcode. The silane magnetic beads and Solid Phase Reversible Immobilization beads were used to clean up the GEM reaction mixture and the barcoded cDNA and antibodies was then amplified in a PCR step. Libraries were prepared using the Chromium Single Cell 3′ Reagent Kits (v3.1): Single Cell 3′ Library & Gel Bead Kit v3.1, Single Cell 3′ Chip G Kit v3.1 and Single Index kit T Set A (10x Genomics). Libraries were sequenced on an Illumina Nova Seq to achieve 75 bp reads. The P7 and R2 primers were added during the GEM incubation and the P5 and R1 during library construction via end repair, A-tailing, adapter ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification.

value: AML PDX

tag: library type

value: Multiplexing Capture

tag: antibodies/tags

value: Total-Seq A Hashing Oligos


title: Hippocampus, 37°C, replicate 1


title: SW620 (colon cancer) cells, Non-treatment, 0 hour, replicate 1

value: Large intestine; Colon


title: Sequencing Pool 5,RNA

value: mRNA-Seq


title: 7.Thio-Macs_control_replicate1

description: Thioglycolate Macrophages, Control

value: peritoneal macrlphages

value: Thioglycolate-induced macrophages


title: Hippocampus, 32°C, replicate 6


title: PC-3 (prostate cancer) cells, L-pampo™ 1x, 6 hours, replicate 3

source_name: Prostate

value: Prostate

value: Prostate cancer cell

value: L-pampo


title: Sequencing Pool 4,HTO


title: Hippocampus, 32°C, replicate 5

value: Brain


title: Sequencing Pool 4,ADT

value: Antibody Capture

value: Total-Seq A ADT Cocktail


title: Sequencing Pool 3,ADT


title: PC-3 (prostate cancer) cells, L-pampo™ 1x, 6 hours, replicate 1


title: Sequencing Pool 4,RNA


title: Hippocampus, 32°C, replicate 3

value: Hippocampal cells


title: PC-3 (prostate cancer) cells, L-pampo™ 1x, 3 hours, replicate 3


title: Sequencing Pool 2,HTO


title: Hippocampus, 37°C, replicate 2


title: Hippocampus, 32°C, replicate 2


title: Sequencing Pool 2,ADT


title: Sequencing Pool 2,RNA


title: Sequencing Pool 5,ADT


title: Hippocampus, 32°C, replicate 1


title: PC-3 (prostate cancer) cells, L-pampo™ 1x, 3 hours, replicate 1


title: PC-3 (prostate cancer) cells, Non-treatment, 0 hour, replicate 3


title: Sequencing Pool 1,HTO


title: Cortex, 37°C, replicate 6

value: cortical cells

value: 37C, cerebral HI


title: Whole blood, ID54_Day60

city: Canyon

first: Matthew

middle: Adam

last: Scott

address: 3201 Russell Long Blvd

department: Large Animal Clinical Sciences

institute: Texas A&M University

data_processing:
Illumina RTA v3 software was used for basecalling.
Read quality was assessed in FastQC v0.11.9
Read trimming was performed with Trimmomatic v0.39 with parameters for a 4-base pair sliding window and removing read segments below a minimum base quality score of 20, read length of less than 28 bases, leading and trailing basepairs below a quality score of 3, and removal of all Illumina adaptors.
Read mapping and indexing was performed with HISAT2 v2.1.1, using the bovine whole genome assembly ARS-UCD1.3; parameters -p 14 --dta -x GCF_002263795.2_ARS-UCD1.3
Read assembly and quantification was performed with StringTie v2.2.0 with parameters -p 14 -G GCF_002263795.2_ARS-UCD1.3_genomic.gff, followed by stringtie --merge -p 14 -G GCF_002263795.2_ARS-UCD1.3_genomic.gff -o mergefile.gtf, and stringtie -e -p 14 -G mergefile.gtf -o. A read count matrix was generated with prepDE3.py with parameters python prepDE3.py  -l 150 -i mergelist.txt. Differential expression analysis was performed with edgeR v3.36.0, glmmSeq v0.2.0, and EBSeq-HMM v1.32.0.
Assembly: GCF_002263795.2
Supplementary files format and content: Comma-delimited text file of raw gene counts for each sample

organism: Bos taurus

source_name: Whole blood

extract_protocol:
Total RNA was isolated from Tempus Blood Tubes with Tempus Spin RNA Isolation Kit per product instruction.
RNA libraries were prepared for sequencing using Illumina Stranded mRNA Prep kits, using standard Illumina protocols.

treatment_protocol: All  samples were collected in Tempus blood RNA tubes (Applied Biosystem). Samples were stored per product recommendation.

value: Whole blood

tag: time point

value: COMBO

tag: pen

tag: individual id

tag: disease

value: Yes


title: Sequencing Pool 1,RNA

value: AML PDX


title: PC-3 (prostate cancer) cells, Non-treatment, 0 hour, replicate 2


title: Hippocampus, 32°C, replicate 4


title: Whole blood, ID57_Day60

value: No


title: Sequencing Pool 1,ADT


title: Cortex, 37°C, replicate 4


title: Whole blood, ID49_Day60

value: AAC


title: PC-3 (prostate cancer) cells, L-pampo™ 1x, 6 hours, replicate 2


title: Sequencing Pool 3,HTO

value: Multiplexing Capture

value: Total-Seq A Hashing Oligos


title: Whole blood, ID50_Day60

value: INR


title: Cortex, 37°C, replicate 5


title: Sequencing Pool 3,RNA

value: mRNA-Seq


title: Whole blood, ID48_Day60


title: PC-3 (prostate cancer) cells, L-pampo™ 1x, 3 hours, replicate 2

value: Prostate

value: Prostate cancer cell

value: L-pampo


title: Whole blood, ID43_Day60


title: Cortex, 37°C, replicate 3

value: Brain

value: 32C 6h, cerebral HI


title: PC-3 (prostate cancer) cells, Non-treatment, 0 hour, replicate 1


title: Whole blood, ID46_Day60


title: differentiated THP-1 (monocyte) cells, L-pampo™ 1x, 6 hours, replicate 2

source_name: Peripheral blood

value: Peripheral blood

value: Myeloid immune cell


title: differentiated THP-1 (monocyte) cells, L-pampo™ 1x, 6 hours, replicate 3


title: Cortex, 37°C, replicate 2

value: cortical cells


title: Whole blood, ID42_Day60

value: Whole blood

value: COMBO


title: differentiated THP-1 (monocyte) cells, L-pampo™ 1x, 6 hours, replicate 1


title: Whole blood, ID40_Day60

value: Yes


title: Cortex, 37°C, replicate 1


title: Cortex, 32°C, replicate 5

value: 37C, cerebral HI


title: differentiated THP-1 (monocyte) cells, L-pampo™ 1x, 3 hours, replicate 3


title: Whole blood, ID34_Day60

value: AAC

value: No


title: Cortex, 32°C, replicate 6


title: Whole blood, ID31_Day60


title: Whole blood, ID39_Day60


title: differentiated THP-1 (monocyte) cells, L-pampo™ 1x, 3 hours, replicate 2


title: Cortex, 32°C, replicate 4


title: Whole blood, ID30_Day60


title: Whole blood, ID23_Day60


title: differentiated THP-1 (monocyte) cells, L-pampo™ 1x, 3 hours, replicate 1


title: Whole blood, ID29_Day60


title: differentiated THP-1 (monocyte) cells, Non-treatment, 0 hour, replicate 3


title: Whole blood, ID21_Day60


title: Whole blood, ID27_Day60


title: Cortex, 32°C, replicate 3


title: Whole blood, ID18_Day60


title: Whole blood, ID41_Day60


title: Cortex, 32°C, replicate 2


title: differentiated THP-1 (monocyte) cells, Non-treatment, 0 hour, replicate 2


title: Whole blood, ID9_Day60


title: Whole blood, ID17_Day60


title: Whole blood, ID7_Day60


title: Whole blood, ID16_Day60


title: Cortex, 32°C, replicate 1


title: 322761_2-KO

city: schwerzenbach

first: jing

last: zhang

state: Schwerzenbach

address: schorenstrasse 16

department: Department Health Sciences and Technology

institute: DHEST

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software version 5.0.0 and 6.0.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCm39.p6
Supplementary files format and content: Tab-separated values files and matrix files

source_name: skeletal muscle

extract_protocol:
For isolation of cells for scRNAseq, skeletal muscle was collected and minced in a petri dish on ice using scissors and a surgical blade. Minced samples were transferred into a digestion buffer (4 mL digestion buffer per 100 mg of muscle) containing 2 mg/ml Dispase II (D4693 Sigma-Aldrich) and 2 mg/ml Collagenase IV (17104019 Thermo Fisher Scientific) in HBSS buffer (14025100 Thermo Fisher Scientific) at 37°C for 25 minutes, with gentle shaking every 5 minutes. After digestion, the reaction was stopped by adding an equal volume of 20% heat-inactivated FBS (10500064 Thermo Fisher Scientific) in HBSS (14025100 Thermo Fisher Scientific) and the suspension was passed through a series of 70-µm cell strainers (#352360, Corning, New York, USA) and 40-μm cell strainers (#352350, Corning, New York, USA) to remove tissue debris. Cell suspension was centrifuged at 450 g for 5 minutes at 4°C and the supernatant was discarded. The pellet was resuspended 2% FBS (10500064 Thermo Fisher Scientific) in DPBS (14190250 Thermo Fisher Scientific) and incubated with anti-CD31 and anti-CD45 antibodies for 15 minutes on ice. Thereafter, cells were washed and subjected for sorting.
Metabolically active (Calcein+) human muscle mononuclear cells were FACS sorted and loaded into the 10X Chromium Next GEM Chip G, aiming the recovery of ~10000 cells per sample. scRNAseq libraries were generated according to 10X Chromium Next Gem Single Cell 3’ Reagent Kits v3.1 (CG000204 Rev D) and sequenced on the Illumina Novaseq 6000 system

value: skeletal muscle

value: muscle cell

value: knockout


title: Whole blood, ID54_Day45


title: mECDglut1-4

data_processing:
Bulk RNA-seq libraries were obtained following the Takara Clontech PicoMammalian v2 recommended protocol. Libraires were sequenced on the Novaseq 6000 (Ilummina) instrument and sequenced data were processed using Kallisto to generate a count file matrix for each individual sample. Samples were pooled together on a single dataset for downstream analysis and genes with one count or less across all samples were filtered out. Following DESeq2 analysis workflow 67, gene expression values were computed with the function feature Counts from the R package Rsubread. A minimum expression of each gene (mean of counts > 1) was applied as a cut off before analysis. Differential gene expression were computed using Negative Binomial model implemented in the Bioconductor package DESeq. Significantly differentially expressed genes was defined as a pvalue < 0.01 with a false discovery ratio (FDR) < 0.1. FDR values were calculated using the Benjamini–Hochberg method. Pathway analysis was performed using the clusterProfiler R package.
Kallisto
Assembly: GRCm39
Supplementary files format and content: Normalized Counts include RPKM values for each sample

growth_protocol: Beads isolated mECs were subjected to RNA extraction inmediately.

extract_protocol:
RNA was isolated with using Rneasy Plus Kit. 10ng of RNA was used for the construction of sequencing.
RNA library for Bulk-RNAseq was prepared by using "Takara Clontech PicoMammalian v2" and following the instruction of kit.

treatment_protocol: no special treatment

value: primary muscle endothelial cell


title: HEPG2 replicate 2

middle: C

last: Pahl

address: 3615 Civic Center Blvd

department: Center for Spatial and Functional Genomics

institute: Children's Hospital of Philadelphia

data_processing:
The fastq files of technical replicates were concatenated.  Paired-end reads from two replicates were pre-processed using the HICUP pipeline v0.7.4 , with bowtie as aligner and hg38 as the reference genome.
Significant promoter interactions at 1-DpnII fragment resolution were called using CHiCAGO (v1.1.8) [3] with default parameters except for binsize set to 2500. Significant interactions at 4-DpnII fragment resolution were also called using CHiCAGO with artificial.baitmap and .rmap files in which DpnII fragments were concatenated in silico into 4 consecutive fragments using default parameters except for removeAdjacent set to False. The significant interactions (CHiCAGO score > 5) from both 1-fragment and 4-fragment resolutions were exported in.ibed format.
Assembly: hg38
Supplementary files format and content: ibed (interaction bed files)

growth_protocol: EndoC BH1 cells were expanded in DMEM low glucose (1g/mL), 2% Albumin Bovine Serum fraction V, 50uM 2 (beta)-mercaptoethanol, 10mM Nicotinamide, 5.5uM Transferrin, 6.7ng/mL sodium selenite, 100 U penicillin/100ug/mL streptomycin/0.25ug/mL amphotericin B (1x Gibco). Plates were coated with either Matrigel or MaxGel ECM (Sigma) and 2 ug/mL fibronectin according to manufacturer’s instructions: Cells were passaged when confluence was observed or otherwise passaged by two-thirds every two weeks. The other cell lines were maintained under standard conditions. HepG2 Cells (ATCC,  HB¬8065TM) were maintained in Eagle's Minimum Essential Medium  supplemented with 10% heat inactivated fetal bovine serum and 1X Antibiotic-Antimycotic at standard tissue culture conditions; 37C and 5% CO2.

extract_protocol:
For each library, 10^7 fixed cells were thawed at 37C, followed by centrifugation at RT for 5 mins at 1845 xg. The cell pellet was resuspended in 1 mL of dH2O supplemented with 5 uL 200X protease inhibitor cocktail, incubated on ice for 10 mins, then centrifuged. The cell pellet was resuspended to a total volume of 650 uL in dH2O. Samples underwent a pre-digestion incubation in a Thermomixer (BenchMark) with the addition of 0.3%SDS, 1x NEB DpnII restriction buffer, and dH2O for 1hr at 37ºC shaking at 1,000 rpm. A 1.7% solution of Triton X-100 was added to each tube and shaking was continued for another hour. After pre-digestion incubation, 10 ul of DpnII (NEB, 50 U/µL) was added to each sample tube only and continued shaking until the end of the day. An additional 10 µL of DpnII was added to each digestion reaction and digested overnight.  The next day, a further 10 µL DpnII was added and continue shaking for another 2-3 hours.  The samples were incubated at 1000 rpm in a MultiTherm for 20 min at 65°C to inactivate the DpnII, and cooled on ice for 20 additional minutes. Digested samples were ligated with 8 uL of T4 DNA ligase (HC ThermoFisher, 30 U/µL) and 1X ligase buffer at 1,000 rpm overnight at 16°C in a MultiTherm. The next day, an additional 2 µL of T4 DNA ligase was spiked in to each sample and incubated for another few hours. The ligated samples were then de-crosslinked overnight at 65°C with Proteinase K (20 mg/mL, Denville Scientific) along with pre-digestion and digestion control. The following morning, both controls and ligated samples were incubated for 30 min at 37°C with RNase A (Millipore), followed by phenol/chloroform extraction, ethanol precipitation at -20°C, the 3C libraries were centrifuged at 1000 xg for 45 min at 4°C to pellet the samples. The controls were centrifuged at 1845 xg. The pellets were resuspended in 70% ethanol and centrifuged as described above. The pellets of 3C libraries and controls were resuspended in 300uL and 20μL dH2O, respectively, and stored at −20°C. Sample concentrations were measured by Qubit. Digestion and ligation efficiencies were assessed by gel electrophoresis on a 0.9% agarose gel and also by quantitative PCR (SYBR green, Thermo Fisher). The HepG2 libraries were prepared following the Arima Promoter Capture HiC protocol, using two restriction enzymes (targeting ^GATC and G^ANTC as restriction sites).
For Promoter focused Capture C, isolated DNA from 3C libraries was quantified using a Qubit fluorometer (Life technologies), and 10 μg of each library was sheared in dH2O using a QSonica Q800R to an average fragment size of 350bp 26,28–31.  QSonica settings used were 60% amplitude, 30s on, 30s off, 2 min intervals, for a total of 5 intervals at 4 °C. After shearing, DNA was purified using AMPureXP beads (Agencourt). DNA size was assessed on a Bioanalyzer 2100 using a DNA 1000 Chip (Agilent) and DNA concentration was checked via Qubit. SureSelect XT library prep kits (Agilent) were used to repair DNA ends and for adaptor ligation following the manufacturer protocol. Excess adaptors were removed using AMPureXP beads. Size and concentration were checked by Bioanalyzer using a DNA 1000 Chip and by Qubit fluorometer before hybridization. One microgram of adaptor-ligated library was used as input for the SureSelect XT capture kit using manufacturer protocol and our custom-designed 41K promoter Capture-C library. The quantity and quality of the captured library was assessed by Bioanalyzer using a high sensitivity DNA Chip and by Qubit fluorometer. SureSelect XT libraries were then paired-end sequenced either the Illumina HiSeq 4000 or on Illumina NovaSeq 6000 platform (51 bp read length). EndoC-BH1, SGBS_undiff, and SGBS_diff libraries were generated in triplicate, while HepG2 were generated in duplicate.

treatment_protocol: SGBS differentiation began by washing cells with phosphate buffered saline (PBS) three times and changing to a serum- and albumin-free differentiation medium (DMEM/F12 supplemented with 2 μmol/l rosiglitazone, 25 nmol/l dexamethasone, 0.5 mmol/l methylisobuthylxantine, 0.1 μmol/l cortisol, 0.01 mg/ml transferrin, 0.2 nmol/l triiodotyronin, and 20 nmol/l human insulin). After 4 days, the differentiation medium was changed, and cells were further cultured in DMEM/F12 supplemented with 0.1 μmol/l cortisol, 0.01 mg/ml transferrin, 0.2 nmol/l triiodotyronin, and 20 nmol/l human insulin. Successful differentiation was assessed by the presence of lipid droplets.

value: Hepatoma cell line


title: Whole blood, ID6_Day60


title: Whole blood, ID50_Day45

value: INR


title: Whole blood, ID57_Day45


title: mECDglut1-3


title: Whole blood, ID48_Day45


title: Whole blood, ID46_Day45


title: SGBS Undifferentiated replicate 1

source_name: SGBS

value: SGBS

value: Preadipocyte cell line


title: Whole blood, ID49_Day45


title: mECDglut1-2


title: SGBS Undifferentiated replicate 2


title: mECDglut1-1


title: Whole blood, ID10_Day60


title: Whole blood, ID43_Day45


title: HEPG2 replicate 1


title: SGBS Undifferentiated replicate 3


title: 322761_1-WT

description: 10x Genomics

value: wild type


title: Whole blood, ID3_Day60


title: differentiated THP-1 (monocyte) cells, Non-treatment, 0 hour, replicate 1

value: Peripheral blood

value: Myeloid immune cell


title: Whole blood, ID42_Day45

value: Whole blood


title: Whole blood, ID40_Day45


title: SGBS Differentiated replicate 3

value: Adipocyte cell line


title: EndoC-BH1 Hi-C replicate B, technical replicate 1

data_processing:
Paired-end reads from two replicates were pre-processed using the HICUP pipeline v0.7.4 , with bowtie as aligner and hg38 as the reference genome. The alignment .bam file were parsed to .pairs format using pairtools v0.3.0 and converted to pre-binned Hi-C matrix in .cool format by cooler v0.8.10 with multiple resolutions (1kbp, 2kbp, 4kbp). These matrices were merged with cooler merge and normalized with the ICE method
For each cell stage, significant intra-chromosomal interaction loops were determined under multiple resolutions (1kb, 2kb and 4kb) using the Hi-C loop callers Mustache V1.01 or Fit-HiC2 v2.0.7  (FDR<1e-6) on merged replicates matrix.
Assembly: hg38
Supplementary files format and content: bedpe file, coordinates of loops and associated statistics
Supplementary files format and content: tab deliminated bedpe files, significant contact coordinates in hg38 and read count and FDR adjusted P value at the indicated resolutions.  Mustache files, are FDR corrected P values and mustache scale value

source_name: Islet-like

extract_protocol:
Hi-C library preparation on two replicates of Endo-C BH1 cells was performed using the Arima-HiC kit according to the manufacturer’s protocols. Briefly, cells were crosslinked using formaldehyde. Crosslinked cells were then subject to the Arima-HiC protocol, which utilizes multiple restriction enzymes (targeting ^GATC and G^ANTC) to digest chromatin. Arima-HiC sequencing libraries were prepared by first shearing purified proximally-ligated DNA and then size-selecting 200–600 bp DNA fragments using AmpureXP beads. The size-selected fragments were then enriched using enrichment beads (provided in the Arima-HiC kit).
The resulting fragments were converted into Illumina-compatible sequencing libraries with the Swift Accel-NGS 2S Plus DNA Library Kit and Swift 2S Indexing Kit. The purified, PCR-amplified DNA underwent standard QC (qPCR, Bioanalyzer, and KAPA Library Quantification) and was sequenced with unique single indexes on the Illumina NovaSeq 6000 Sequencing System at 2x101 base pairs.

value: Islet-like

value: Pancreatic Beta cell line


title: Whole blood, ID41_Day45

value: AAC

value: Yes


title: Whole blood, ID39_Day45


title: Whole blood, ID34_Day45

value: No


title: mECwt-3

value: skeletal muscle


title: SGBS Undifferentiated RNA-Seq replicate 1

data_processing:
The fastq files of technical replicates were concatenated.  Reads were aligned to hg38 using STAR v2.7.9a. Reads were assigned to genes from the gencodeV30 annotation using HTSeq 2.0.2
TPM values were calculated using the effective gene length.
Assembly: hg38
Supplementary files format and content: TPM values annotated to gencodeV30

source_name: Preadipocyte Like cell line

extract_protocol:
A total of 50,000 to 100,000 cells were centrifuged at 550g for 5min at 4°C. The cell pellet was washed with cold PBS and resuspended in 50μL cold lysis buffer (10mM Tris-HCl, pH7.4, 10mM  NaCl, 3mM MgCl2, 0.1% NP-40/IGEPAL CA-630) and immediately centrifuged at 550g for 10min at 4°C. Nuclei were resuspended in the Nextera transposition reaction mix (25μL 2x TD Buffer, 2.5μL Nextera Tn5 transposase (Illumina Cat #FC-121-1030), and 22.5μL nuclease free H2O) on ice, then incubated for 45min at 37°C.
The tagmented DNA was then purified using the Qiagen MinElute kit eluted with 10.5μL Elution Buffer (EB). Ten microliters of purified tagmented DNA was PCR amplified using Nextera primers for 12cycles to generate each library. PCR reaction was subsequently cleaned up using 1.5x AMPureXP beads (Agencourt) and concentrations were measured by Qubit. Libraries were paired-end sequenced on the Illumina Libraries were paired-end sequenced on the Illumina Novaseq 6000 platform (100bp read length).

value: Preadipocyte Like cell line


title: Il1a + Osm 48h 2

data_processing:
STAR used for alignment.
Homer for raw counts and RPKM values
DESEQ2 used for differential expression
Assembly: mm10
Supplementary files format and content: text file, rpkm

growth_protocol: ASZ-001 cells (mouse BCC cell line) were grown in M154CF (Thermo Fisher Scientific, Waltham, MA) supplemented with 2% chelated FBS, 1% Penicillin-Streptomycin and 0.05mM CaCl2 (So et al. 2006).

extract_protocol:
RNA samples were obtained from adherent cells using RNeasy Plus Mini Kit from Qiagen according to manufacturer’s instructions.
The RNAseq libraries were constructed by TruSeq Stranded mRNA Library Prep kit (Illumina) and sequenced on an Illumina NovaSeq sequencer.

treatment_protocol: Cells were treated with either PBS control or Il1 or Osm ligands (or in combination) for 24 and 48 hours.

value: WT

value: treatment group 9


title: Whole blood, ID31_Day45


title: HEPG2 RNA-Seq replicate 2

source_name: hepatocellular carcinoma cell line

value: hepatocellular carcinoma cell line

value: Hepatoma cell line


title: Whole blood, ID27_Day45

value: INR


title: mECwt-1

value: primary muscle endothelial cell

value: wild type


title: HEPG2 RNA-Seq replicate 3


title: Whole blood, ID21_Day45


title: Whole blood, ID18_Day45

value: COMBO


title: Whole blood, ID17_Day45

value: Whole blood


title: Il1b + Osm 48h 1

value: treatment group 10


title: EndoC-BH1 Hi-C replicate A, technical replicate 1

value: Islet-like


title: Il1b + Osm 48h 2


title: Whole blood, ID6_Day45


title: HEPG2 RNA-Seq replicate 1


title: Whole blood, ID29_Day45


title: Whole blood, ID9_Day45


title: Osm 48h 1

value: treatment group 8


title: Whole blood, ID7_Day45


title: Whole blood, ID23_Day45


title: Whole blood, ID3_Day45


title: Whole blood, ID30_Day45


title: SGBS Differentiated RNA-Seq replicate 1

source_name: Adipocyte Like cell line

value: Adipocyte Like cell line

value: SGBS

value: Adipocyte cell line


title: mECwt-2

value: skeletal muscle


title: SGBS Differentiated RNA-Seq replicate 2


title: Whole blood, ID16_Day45

value: Yes


title: Il1a + Osm 48h 1

value: WT


title: Whole blood, ID10_Day45

value: No


title: SGBS Undifferentiated RNA-Seq replicate 2

value: Preadipocyte Like cell line

value: Preadipocyte cell line


title: Osm 48h 2


title: Whole blood, ID57_Day28


title: Il1b 48h 2

value: treatment group 7


title: Whole blood, ID54_Day28


title: Whole blood, ID50_Day28

value: INR


title: EndoC-BH1 RNA-Seq replicate 3

source_name: Islet-like cell line

value: Islet-like cell line

value: Pancreatic Beta cell line


title: EndoC-BH1 RNA-Seq replicate 2


title: Il1a 48h 2

value: treatment group 6


title: Whole blood, ID46_Day28

value: Whole blood

value: AAC


title: EndoC-BH1 RNA-Seq replicate 1


title: Whole blood, ID49_Day28


title: Whole blood, ID42_Day28

value: COMBO


title: Il1b 48h 1


title: Il1a 48h 1


title: HCT116 cells, MTHFD2-KO

city: Barcelona

first: Luca

last: Cozzuto

state: Barcelona

address: Carrer Dr. Aiguader 88

department: Bioinformatics facility

country: Spain

institute: Centre for genomic regulation (CRG)

description: PromethIon 24 (Oxford Nanopore)

data_processing:
Raw fast5 nanopore data were analyzed using Master of Pores suite.
Basecalling was performed with Guppy and alignment with Winnowmap.
Methylation analysis was performed with methylKit R package.
Structural variation analysis was performed with CuteSV.
Assembly: T2T
Supplementary files format and content: bedgraph file includes differential methylation information KO vs WT. Columns are: chromosome, start coordinate, end coordinate, change of methylation, adjusted p-value.
Supplementary files format and content: Output from cuteSV in vcf format.

source_name: colon

growth_protocol: HCT116 were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
High molecular weight genomic DNA (HMW gDNA) was extracted following the manufacturer’s protocol of Nanobind tissue kit (Circulomics).
Libraries were prepared using the 1D Sequencing kit SQK-LSK110 from Oxford Nanopore Technologies (ONT).

treatment_protocol: HCT116 knock-out cells were generated by CRISPR-Cas9, a single knock-out clone was isolated, and gDNA samples were then harvested.

value: colon


title: Whole blood, ID43_Day28


title: HEPG2 ATAC-Seq replicate 1

data_processing:
The fastq files of technical replicates were concatenated.  ATAC-seq peaks were called using the ENCODE ATAC-seq pipeline (https://www.encodeproject.org/atac-seq/). Briefly, pair-end reads from 2-3 replicates for each cell type were aligned to hg38 genome using bowtie2 , and duplicate reads were removed from the alignment. Narrow peaks were called independently for each replicate using macs2 (-p 0.01 --nomodel --shift -75 --extsize 150 -B --SPMR --keep-dup all --call-summits) and ENCODE blacklist regions (ENCSR636HFF) were removed from peaks in individual replicates. Reproducible peaks, peaks called in at least two replicates, were used to generate a consensus peakset.
For bigwig files, individual replicate bam files were merged and indexed with samtools 1.7 and then converted to bigwig deeptools bamCoverage v3.5.1 with parameters --RPGC, --effectiveGenomeSize 2864785220 --binsize 10 --extend reads
Assembly: hg38
Supplementary files format and content: bigwig files

value: hepatocellular carcinoma cell line

value: Hepatoma cell line


title: HEPG2 ATAC-Seq replicate 3


title: HEPG2 ATAC-Seq replicate 2


title: Il1b + Osm 24h 1

value: treatment group 5


title: HCT116 cells, MTHFD2-WT

description: PromethIon 24 (Oxford Nanopore)


title: HOM_3

city: Madrid

first: Jaime

last: Martinez de Villarreal

state: Madrid

address: Melchor Fernández Almagro, 3

department: Molecular Oncology Programme

institute: CNIO

data_processing:
Reads were aligned using STAR aligner
count matrix was built using featureCounts
normalization and differential expression analysis was carried out using DESeq2
Assembly: mm10
Supplementary files format and content: raw count matrix tsv format

source_name: Pancreas

extract_protocol:
RNA was isolated using the phenol-chloroform method (Chirgwin et al., 1979). Total RNA was then treated with DNase I (DNA-free DNase Treatment & Removal Reagents, Ambion) according to manufacturerʼs instructions.
Total RNA samples (500ng; RQS/RIN average 5.6, range 4.7-6.5) were converted into cDNA sequencing libraries with the "QuantSeq 3‘ mRNA-Seq Library Prep Kit (FWD) for Illumina" (Lexogen, Cat.No. 015). Briefly, library generation is initiated by reverse transcription with oligodT priming, followed by a random-primed second strand synthesis. Primers from both steps contain Illumina-compatible sequences. Libraries were completed by PCR, and sequenced on an Illumina instrument (see below) by following manufacturer's protocols. {This library preparation kit generates directional libraries stranded in the sense orientation (the read1 (the only read in single read format) has the sense orientation (--library-type fr-secondstrand in TopHat, --stranded=yes in HTSeq)}

value: Pancreas


title: HOM_2


title: Whole blood, ID41_Day28

value: Yes


title: Il1a + Osm 24h 2

value: WT

value: treatment group 4


title: Whole blood, ID48_Day28

value: No


title: Whole blood, ID39_Day28


title: SGBS Undifferentiated ATAC-Seq replicate 2

value: Preadipocyte Like cell line

value: SGBS

value: Preadipocyte cell line


title: HOM_1


title: SGBS Undifferentiated ATAC-Seq replicate 3


title: SGBS Undifferentiated ATAC-Seq replicate 1


title: Il1a + Osm 24h 1


title: HET_3


title: Il1b + Osm 24h 2


title: Osm 24h 2

value: treatment group 3


title: Whole blood, ID40_Day28

value: INR


title: Whole blood, ID34_Day28

value: Whole blood


title: HET_1


title: SGBS Differentiated ATAC-Seq replicate 2

value: Adipocyte Like cell line

value: Adipocyte cell line


title: Il1b 24h 2

value: treatment group 2


title: Il1b 24h 1


title: HET_2


title: Whole blood, ID29_Day28


title: SGBS Differentiated ATAC-Seq replicate 1


title: Osm 24h 1


title: Il1a 24h 2

value: treatment group 1


title: Whole blood, ID30_Day28


title: WT_3


title: Whole blood, ID31_Day28

value: AAC


title: WT_2


title: Il1a 24h 1


title: Whole blood, ID23_Day28


title: WT_1


title: EndoC-BH1 ATAC-Seq replicate 2

value: Islet-like cell line

value: Pancreatic Beta cell line


title: PBS 2

value: control group


title: EndoC-BH1 ATAC-Seq replicate 1


title: Whole blood, ID21_Day28

value: Yes


title: HEK293WT+Cas9, control, replicate 4

city: Reykjavik

first: Hans

last: Bjornsson

address: Sturlugata 8

institute: University of Iceland

description:
80 cycles and 8 indexing cycles with PhiX spike in of 20%
CTRLvsLOW4Replicates.countsummary.txt/CTRLvsHIGH4Replicates.countsummary.txt
16_7_20_control_R1_001.fastq.gz

data_processing:
Cat command to merge fastq files for samples 1-3
mageck count -l Human_GeCKOv2_Library_combine.csv
mageck test -k CTRLvsHIGH4Replicates.count.txt --sort-criteria pos --norm-method control --control *HIGH*nontargetingsgrna.txt --paired
Assembly: Reference sequence downloaded from Library site (addgene), named  "Human_GeCKOv2_Library_combine.csv"
Supplementary files format and content: text file, counts of sgRNA in library in all replicates of control and low/high sorted cells
Supplementary files format and content: text file, counts of sgRNA in library normalized to internal control count in all replicates of control and low/high sorted cells
Supplementary files format and content: text file, information on vaues e.g. P-value, RRA score and more for all genes in library
Supplementary files format and content: text file, information on vaues e.g. P-value, RRA score and more for all sgRNAs in library
Library strategy: CRISPR Screen

growth_protocol: HEK293WT cells were  cultured in DMEM/F12 with GlutaMAX (Gibco, 10565018) with 10% filtered FBS (Gibco, 10270106) under 5% CO2. Cells were sub-cultured when they had reached 70-90% confluence and media was changed every other day. We selected for stable sgRNAs with puromycin selection for 6 days and 8 hours and exposesd to 32°C the last 16h before FACS

extract_protocol:
genomic DNA extracted with DNA mediprep kit from Zymo Research.
Custom library amplification protocol ac. To Joung et al. Nat Protoc. 2017
sgRNA-sec, genome wide CRISPR-Cas9 library screening

treatment_protocol: 6 days and 6 h selection with puromycin before 16 hours exposure of 32°C

value: 16 h of 32degreeC


title: SGBS Differentiated ATAC-Seq replicate 3


title: Whole blood, ID18_Day28

value: COMBO


title: Ligand2

data_processing:
bowtie2.3.4.1 used for alignment.
duplicate fragments were removed using samtools1.8
macs2 used for peak calling
bedtools2.27.1 multicov to generate normalized counts
DESEQ2 used for differential peak calling
Assembly: mm10
Supplementary files format and content: bigwig

extract_protocol:
Cells were removed from the plate with Trypsin. Nuclear DNA was extracted following ATAC-seq the protocol in Buenrostro et al. 2015. Briefly, 7x104 cells were washed with cold PBS and lysed in 0.1% NP40 RSB buffer. Nuclei were Tn5 transposed with Nextera Transposase at 37°C for 30 minutes, then purified with the Qiagen MinElute PCR Purification Kit.
Libraries were amplified for 9-15 total cycles using the Nextera Ad1 and Ad 2.1-2.16 barcodes. Libraries were purified and eluted using the Min-Elute columns (Qiagen). Library concentrations were determined with Bioanalyzer High-Sensitivity DNA analysis (Agilent).

treatment_protocol: Cells were treated with either PBS control or a combination of  Il1a and Osm ligands for 48 hours.

value: WT

value: treatment group


title: ICoVax_132_i30

city: Lausanne

first: Yannick

middle: D

last: Muller

state: Vaud

address: Rue du Bugnon 46

department: Center for Human Immunology and Vaccinology

institute: Lausanne University Hospital (CHUV)

data_processing:
RNA-sequencing libraries were aligned to the human genome (GRCh38.96) using STAR (2.4.0j).
Only uniquely mapped reads were kept for downstream steps.
Gene expression quantification was performed with featureCounts for reads overlapping protein-coding genes.
Low-count genes were filtered out with the filtered.data() function from the NOISeq R package using the following parameters: method = 1, norm = FALSE, cv.cutoff = 100, cpm = 1.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file containing raw counts for each sample.

source_name: whole blood

extract_protocol:
Blood samples were collected in PAXgene Blood RNA Tube (BD Biosciences). RNA extraction was performed using the PAXgene Blood miRNA Kit (BD) on the QIAcube instrument (QIAGEN) following the manufacturer’s instructions.
RNA concentration and quality were assessed by using the Qubit instrument (Invitrogen) and the Agilent 2100 Bioanalyzer, respectively. The Stranded Total RNA Ribo-Zero Plus kit from Illumina was used for the library preparation with 100 ng of total RNA as input. Library molarity and quality were assessed with the Qubit and Tapestation using a DNA High sensitivity chip (Agilent Technologies). Libraries were pooled at 2 nM for clustering and sequenced on an Illumina HiSeq4000 sequencer for a minimum of 30 million single-end 100 reads per sample.

value: whole blood

value: ICoVax


title: ICoVax_130_i30


title: ICoVax_126_i30


title: Ligand1


title: ICoVax_122_i30


title: Whole blood, ID27_Day28

value: INR


title: Whole blood, ID17_Day28

value: Whole blood


title: HEK293WT+Cas9+SP1-MHI, 5% high sorted, replicate 4

description:
80 cycles and 8 indexing cycles with PhiX spike in of 20%
CTRLvsHIGH4Replicates.countsummary.txt
CTRLvsHIGH4Replicates.count_normalized.txt
normCTRLvsHIGH4Replicates.gene_summary.txt
normCTRLvsHIGH4Replicates.sgrna_summary.txt
16_7_20_high_R1_001.fastq.gz


title: EndoC-BH1 ATAC-Seq replicate 3


title: ICoVax_119_i30


title: HEK293WT+Cas9+SP1-MHI, 5% low sorted, replicate 4

description:
80 cycles and 8 indexing cycles with PhiX spike in of 20%
CTRLvsLOW4Replicates.countsummary.txt
CTRLvsLOW4Replicates.count_normalized.txt
normCTRLvsLOW4Replicates.gene_summary.txt
normCTRLvsLOW4Replicates.sgrna_summary.txt
16_7_20_low_R1_001.fastq.gz


title: ICoVax_117_i30


title: HEK293WT+Cas9, control, replicate 3

description:
80 cycles and 8 indexing cycles with PhiX spike in of 20%
CTRLvsLOW4Replicates.countsummary.txt/CTRLvsHIGH4Replicates.countsummary.txt
15_7_20_control_R1_001.fastq.gz


title: Whole blood, ID9_Day28


title: Whole blood, ID10_Day28

value: No


title: HEK293WT+Cas9+SP1-MHI, 5% low sorted, replicate 3

description:
80 cycles and 8 indexing cycles with PhiX spike in of 20%
CTRLvsLOW4Replicates.countsummary.txt
CTRLvsLOW4Replicates.count_normalized.txt
normCTRLvsLOW4Replicates.gene_summary.txt
normCTRLvsLOW4Replicates.sgrna_summary.txt
15_7_20_low_R1_001.fastq.gz


title: PBS2


title: PBS 1


title: Whole blood, ID7_Day28


title: HEK293WT+Cas9+SP1-MHI, 5% high sorted, replicate 3

description:
80 cycles and 8 indexing cycles with PhiX spike in of 20%
CTRLvsHIGH4Replicates.countsummary.txt
CTRLvsHIGH4Replicates.count_normalized.txt
normCTRLvsHIGH4Replicates.gene_summary.txt
normCTRLvsHIGH4Replicates.sgrna_summary.txt
15_7_20_high_R1_001.fastq.gz


title: ICoVax_109_i30


title: Ligand_NFKB1_1

data_processing:
bowtie2.3.4.1 used for alignment.
duplicate fragments were removed using samtools1.8
macs2 used for peak calling
Assembly: mm10
Supplementary files format and content: bigwig
Library strategy: CUT&Run

extract_protocol:
Briefly, cells were harvested, washed, and bound to activated Concanavalin A-coated magnetic beads and permeabilized. The bead-cell complex was incubated overnight with either an anti-NFKB1 antibody or an IgG antibody control at 4°C. Cells were then washed with digitonin buffer, resuspended in 50 µl of pAG/Mnase and incubated for 2h at 4°C. Enriched DNA fragments were purified using QIAGEN MinElute PCR Purification Kit.
CUT&RUN libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina according to manufacturer’s protocol.

tag: chip antibody


title: Ligand_NFKB1_2


title: ICoVax_106_i30

tag: tissue


title: HEK293WT+Cas9, control, replicate 2

description:
80 cycles and 8 indexing cycles with PhiX spike in of 20%
CTRLvsLOW4Replicates.countsummary.txt/CTRLvsHIGH4Replicates.countsummary.txt
12_6_20_control_R1_001.fastq.gz

tag: cell type


title: Whole blood, ID16_Day28


title: PBS_NFKB1_2


title: ICoVax_104_i30


title: Whole blood, ID3_Day28


title: HEK293WT+Cas9+SP1-MHI, 5% low sorted, replicate 2

description:
80 cycles and 8 indexing cycles with PhiX spike in of 20%
CTRLvsLOW4Replicates.countsummary.txt
CTRLvsLOW4Replicates.count_normalized.txt
normCTRLvsLOW4Replicates.gene_summary.txt
normCTRLvsLOW4Replicates.sgrna_summary.txt
12_6_20_low_R1_001.fastq.gz

tag: cell line


title: ICoVax_105_i30


title: Whole blood, ID57_Day13


title: PBS_NFKB1_1

tag: genotype


title: HEK293WT+Cas9+SP1-MHI, 5% high sorted, replicate 2

description:
80 cycles and 8 indexing cycles with PhiX spike in of 20%
CTRLvsHIGH4Replicates.countsummary.txt
CTRLvsHIGH4Replicates.count_normalized.txt
normCTRLvsHIGH4Replicates.gene_summary.txt
normCTRLvsHIGH4Replicates.sgrna_summary.txt
12_6_20_high_R1_001.fastq.gz


title: Whole blood, ID54_Day13


title: ICoVax_114_i30


title: ICoVax_101_i30


title: HEK293WT+Cas9+SP1-MHI, 5% low sorted, replicate 1

description:
80 cycles and 8 indexing cycles with PhiX spike in of 20%
CTRLvsLOW4Replicates.countsummary.txt
CTRLvsLOW4Replicates.count_normalized.txt
normCTRLvsLOW4Replicates.gene_summary.txt
normCTRLvsLOW4Replicates.sgrna_summary.txt
10_6_20_low_merge


title: NPC, 32°C, replicate 4

growth_protocol: Mouse NPCs were isolated from the cortex of E17.5 C57BL6/NTac embryos. The protocol was adapted from Bernas et al, 2017105. Embryo cortices were manually dissected from brains and the tissue was dissociated in 1X TrypLE™ Select Enzyme (Thermo Fisher Scientific, A1217701) for 10 min, with manual dissociation using a 1000 µL pipette. The cell suspension was washed in Neurobasal medium (Thermo Fisher Scientific, 21103049) and filtered through a 70 µm cell strainer (Miltenyi Biotech, 130-110-916). Cells were washed twice in 5 mL Neurobasal medium (Gibco, 21103049) by centrifugation at 200 xg for 10 min. Cells were resuspended in 1 mL Neurobasal growth medium containing 1X B27 supplement (Thermo Fisher Scientific, 17504044), 1X Penicillin/Streptomycin (Thermo Fisher Scientific, 15140122), 1X Glutamax (Thermo Fisher Scientific, 35050038), 20ng/mL FGF-2 (Peprotech, 100-18B), 20 ng/mL EFG (Peprotech, AF-100-15), and 2 µg/mL Heparin (MP Biomedicals, 210193125). Cells were seeded onto 12-well plates, previously coated for 2 h at 37°C in 1:100 dilution of Matrigel (Corning, 354234). After passaging, NPCs were cultured in media described above on plates coated overnight in poly-D-lysine (Sigma, P7280), and then coated for 2 h in laminin (Sigma, L2020). Cells were either sub-cultured or media was changed every 2 days. Primary mouse NPC lines from 4 separate embryos were seeded 0.3 x 106 cells per well, in two batches, in a poly-D-lysine/laminin coated 6-well plate after 9 days in vitro.

extract_protocol:
Cells from both 37°C and 32°C conditions were harvested in tri-reagent and RNA was isolated using the Direct-zol RNA Microprep kit (Zymo Research, R2063).
RNAseq library construction and Illumina next generation sequencing was performed by Novogene on a PE150 flow cell, generating 30 million paired-end reads per sample.

treatment_protocol: Following 36 h of incubation at 37°C, one plate with 4 lines was incubated at 32°C for 6 h.

value: Brain

value: cortical mNPC

value: nouse neural progenitor cells

value: 32degreeC 6h


title: Whole blood, ID6_Day28


title: HEK293WT+Cas9+SP1-MHI, 5% high sorted, replicate 1

description:
80 cycles and 8 indexing cycles with PhiX spike in of 20%
CTRLvsHIGH4Replicates.countsummary.txt
CTRLvsHIGH4Replicates.count_normalized.txt
normCTRLvsHIGH4Replicates.gene_summary.txt
normCTRLvsHIGH4Replicates.sgrna_summary.txt
10_6_20_high_merge


title: NPC, 32°C, replicate 3


title: PBS1


title: Whole blood, ID46_Day13

value: AAC


title: NPC, 32°C, replicate 1


title: ICoVax_100_i30


title: Whole blood, ID49_Day13


title: ICoVax_85_i30


title: ICoVax_65_i30