title: mpra_A-NPC_2

extract_protocol:
To perform the MPRA in cell lines, an MPRA lentiviral library titration was performed to determine the volume of concentrated lentivirus needed to achieve a high infection rate without negatively affecting cell growth. Titration was also performed to test the optimal concentration of blastocidin S HCl needed for a 48 hour selection. For each sample, 10 million cells were transduced with 700µL of the MPRA lentiviral library and 5 µg/mL polybrene. Cells were plated into two 10cm plates (5 million cells/plate) and cultured overnight. Approximately 24 hours post transduction, cells were lifted and plated into two 15cm plates in media supplemented with blasticidin S HCl. Non-transduced cells were fully selected within 48 hours. After 72 hours of drug selection, cells were collected and lysed in Qiagen buffer RLT Plus containing 2-mercaptoethanol. Transductions were performed in triplicate. Lysates were frozen at -80°C prior to performing RNA isolation using a Qiagen RNeasy Plus Mini Kit (Qiagen cat. no. 74136).
Both the plasmid library and cDNA libraries were sequenced. The plasmid library was sequenced to assess oligo frequencies. Briefly, Illumina adaptors were PCRed onto the plasmid libraries, upstream and downstream of the oligo inserts. Final libraries concentrations were assessed by Kapa Library Quantification Kit (Roche) and sequenced on an Illumina MiSeq instrument using 30 cycles for read 1 (barcode) and 115 cycles for read 2 (genomic instance). Paired-end sequencing was used to assess template switching.  cDNA libraries were synthesized from total RNA.  Briefly, SuperScript IV was used to synthesize cDNA with a sample specific primer that annealed to the MPRA mRNA transcript. A 12 bp random sequence was included in the primer to serve as a transcript UMI. cDNA synthesis reactions were size selected using SPRIselect beads (Beckman) to remove the cDNA synthesis oligo. Partial Illumina sequencing adaptors were added using PrimeSTAR Max DNA Polymerase (Takara) in a PCR1 consisting of five cycles. Full adapters and sample indices were added in a PCR2 and monitored by qPCR on a Stratagene MX3005P machine. Amplification was terminated while qPCR curves were still in the linear phase to avoid library-over amplification and minimize library skew. The final library was gel purified in a 2% agarose gel. Library concentrations were determined using a Kapa Library Quantification Kit (Roche) and on an Agilent Bioanalyzer. Average molarity was used to equally mix a final cDNA library. Libraries were sequenced on an Illumina MiSeq instrument to ensure each sample had adequate coverage. Deeper sequencing runs were performed on an Illumina Novaseq 6000 SP flow cell (Novogene) with 50 read 1 cycles, 8 index 1 cycles, and 20 index 2 cycles.


title: LV Tissue WT [WLV_6]

status: Public on Dec 23 2022

type: SRA

city: BALTIMORE

first: Kirill

middle: V

last: Tarasov

state: Maryland

address: 251 Bayview Boulevard, Room 9B133, Room 9B133

department: NIA

country: USA

institute: NIH

library_source: transcriptomic

data_processing:
Analysis was performed by DNA Link USA, Inc.
Basecalling Software: RTA2.0;  Fastq Quality Score: ASCII Qscore Offset 64
Trimmed reads were aligned to the reference genome using TopHat v2.1.1
Cufflinks v.2.1.1 was used to calculate FPKM for each sample. Differential gene expression analysis was performed with a Cuffdiff package (Cufflinks v2.1.1)
Assembly: UCSC mm10 mouse reference genome; ADCY8HS - https://www.ncbi.nlm.nih.gov/gene/?term=NM_001115
Supplementary files format and content: Excel file w/the following columns: tracking_id, gene_id, gene_short_name, locus, FPKM for each sample, statistics

molecule: total RNA

organism: Mus musculus

source_name: Left Ventricles

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).
RNA libraries for RNA-seq were prepared using SMARTer Stranded Total RNA-Seq Kit - Pico Input Mammalian (Takara Bio USA, Inc.) following manufacturer's protocols.

tag: tissue

value: Left Ventricles

tag: genotype

value: WT

tag: strain background


title: Acute_Hippocampus_H20

city: Leiden

first: Eva

last: Viho

email: e.viho@lumc.nl, viho.eva@gmail.com

address: Albinusdreef 2

country: Netherlands

institute: Leiden University Medical Center

description:
H20
Acute_rawcounts.csv, DNBSEQ-PE100

data_processing:
The BioWDL pipeline was used for reads quality control, alignment, and quantification.
Quality control was performed using FastQC and MultiQC.
Reads were aligned to mm10 using STAR and gene-read quantification was performed using HTSeq-count
Assembly: mm10
Supplementary files format and content: Matrix tables with gene raw counts for every feature according to Ensembl97 for each sample

source_name: hippocampus

extract_protocol:
Total RNA was isolated from frozen hippocampus and liver tissue using the NucleoSpin® RNA kit (Macherey-Nagel)
mRNA was enriched and purified and a stranded library was constructed for 100 bp paired-end sequencing on BGI's DNBseq platform

value: hippocampus

value: AS

tag: treatment

value: acute corticosterone


title: mpra_A-NPC_1

city: Stanford

first: Margaret

last: Guo

state: CA

address: 269 Campus Dr. CCSR Room 2150

institute: Stanford University

data_processing:
To count number of reads per unique barcode sequence, we took the read 1 sequence, extracted the 20bp region corresponding to the random barcode, and aligned the sequence to the reference MPRA library using bowtie212. Barcodes were allowed a maximum of one mismatch during alignment. The barcodes were counted to determine barcode-oligo frequencies in the plasmid library. Similar alignment was done with read 2 to align the sequence to the genomic instance of the variant to assess for template switching.
Assembly: hg19
Supplementary files format and content: tab-delimited files include barcode counts for each cell type for each repliccate
Library strategy: MPRA-seq

organism: Homo sapiens

tag: cell type

value: neuron

tag: cell line

tag: growth

value: Stem cells were plated in clumps in the presence of Y27632 (10mg/ml, 1000x, Axon MedChem). The hES colonies were allowed to grow in mTESR for another day before the media was switch to differentiation media (1X N2, 1X B27, DMEM/F12:Neurobasal=1:1 (Invitrogen), 0.1mM Ascorbic acid (Sigma)) with small molecules [SB431542, LDN193189 and CHIR99021 (Final concentration:10µM, 100nM and 3µM from Stemgent and Tocris)]. To obtain anterior or posterior neural stem cells, SB431542/LDN194189 and SB431542/LDN193189/CHIR99021 were added respectively. The cells were allowed to differentiate in the media for 6 days before they were dissociated with Accutase and plated at the density of 1 million cells per well of 6 wells for infection. For Ngn2 day 2 post-dox induction cells, TetO-Ngn2-t2a-puro and FUW-rtTA were infected at day 0 in differentiation media followed by adding doxycycline and puromycin the next day. The cells were selected for two days in puromycin before collection for downstream HiChIP experiment.


title: Invitro_BMDM_Strep_3_L1

city: St Louis

first: Felipe

last: Almeida de Pinho Ribeiro

state: MO

address: 4515 McKinley Ave

institute: Washington University in St Louis

description:
tx2gene.rda
txi.rda

data_processing:
For bulk RNA-seq (in vitro samples) data, the raw data was converted to fastq files using bcl2fastq 2.17.1.14 with options “--minimum-trimmed-read-length 10 --mask-short-adapter-reads 10”. Transcript quantification was done using Salmon 1.9.0 with the mm10 mouse genome annotation, and transcript counts were then converted to gene counts and normalized TPM values using the R package tximport (Soneson et al., 2015). Differential gene expression analysis was performed in sequencing datasets using the R package DESeq2.
For single-cell RNA-sequencing samples, Cell Ranger (10x Genomics) analysis pipelines were used to demultiplex raw sequencing data and to perform alignment, filtering, and counting of barcodes and UMIs. Reference mouse genome mm10 version 2020-A was used. Count matrices generated by Cell Ranger imported into R (v.4.0.3) for further analysis using Seurat package (v. 4.1.0). Analysis was performed using only high-quality cells that had UMI counts between 4000 and 70000 and less than 25% of their genes corresponding to the mitochondrial genome. Samples were normalized and scaled using Seurat’s SCTransform function followed by Principal component analysis (PCA). Clustering and visualization were performed by running Uniform Manifold Approximation and Projection (UMAP) dimensional reduction of 15 principal components for each cluster resolution of 0.3. Cell types were defined by comparing cluster marker genes with previously published single-cell RNA-sequencing datasets of mouse meninges. Visualization of genes illustrating expression levels was performed using R/Seurat commands (DoHeatmap, FeaturePlot, and DotPlot) and R/Nebulosa package. Differential gene expression analysis was performed in sequencing datasets using Seurat.
Assembly: mm10

molecule: polyA RNA

source_name: Bone marrow-derived macrophages

extract_protocol:
Four biologically independent replicates were sequenced. After incubation, supernatant was removed and replaced by 500 μL of Trizol, and plates were frozen at −80°C until RNA extraction. For total RNA extraction, samples were thawed at room temperature, mixed with 100 μL of chloroform, and centrifuged at 12,000 g for 15 min at 4°C. The aqueous phase was collected to a new tube and combined with equal parts of isopropyl alcohol, mixed well, and centrifuged at 12,000 g for 10 min at 4°C. After discarding the supernatant, 500 μL of 75% ethanol was added to the samples, vortexed well, and centrifuged at 7,500 g for 5 min. Supernatant was then discarded and the pellet containing RNA was resuspended in 50 μL of nuclease-free water. RNA-seq library preparation (Kapa mRNA Hyperprep, Roche) and sequencing (NovaSeq SP, 2x50bp, Illumina) was conducted by the Bauer Sequencing Core at Harvard University.
Meningeal cells were processed using Liberase TL and subsequently enriched for CD45 positive and negative cells using CD45 MicroBeads (Miltenyi Biotec).
see library construction protocol for each sample above

treatment_protocol: BMDM co-incubated for 4h with vehicle, S. pneumoniae, or Spneumoniae+CGRP

tag: strain

tag: lane

tag: s. pneumoniae-stimulated

value: Yes

tag: cgrp-treated

value: No

tag: in vitro vs. in vivo

value: In vitro

tag: rna-seq method

value: Bulk RNA-seq


title: LV Tissue WT [WLV_5]


title: Acute_Hippocampus_H19

description:
H19
Acute_rawcounts.csv, DNBSEQ-PE100


title: mpra_HEK293_3

value: cell line

value: HEK293T (Takara, cat. no. 632180) cells were cultured in DMEM (Thermo Fisher Scientific cat. no. 11995065) supplemented with 10% FBS and 1X Penicillin-Streptomycin (Thermo Fisher Scientific cat. no. 15140122) at 37°C with 5% CO2. Cell were lifted using 0.05% trypsin (Thermo Fisher Scientific cat. no. 25300054) and passaged 1:10 once they reached 80-90% confluence.


title: SC-beta, -ifn, biol rep 1

city: Cambridge

first: Dario

last: Gerace

address: 7 Divinity Ave

institute: Harvard University

data_processing:
Image analysis and base calling were conducted by the HiSeq Control Software (HCS). Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into FASTQ files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification.
After investigating the quality of the raw data, sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Homo sapiens reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step. Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis. Using DESeq2, a comparison of gene expression between the groups of samples was performed. The Wald test was used to generate p-values and Log2 fold changes. Genes with adjusted p-values < 0.05 and absolute log2 fold changes > 1 were called as differentially expressed genes for each comparison.

growth_protocol: SC-endothelial and CD49a+ SC-beta cells were magnetically-enriched and seeded at a concentration of 1M cells/well of a matrigel-coated 6-well plate and incubated at 370C/5% CO2 for 24 h.

extract_protocol:
Total RNA was extracted from cell pellet samples using RNeasy Plus Mini Kit (Qiagen, Germantown, MD, USA) and quantified using Qubit Fluorometer (Life Technologies, Carlsbad, CA, USA).
SMART-Seq v4 Ultra Low Input Kit for Sequencing was used for full-length cDNA synthesis and amplification (Clontech, Mountain View, CA), and Illumina Nextera XT library was used for sequencing library preparation. Multiplexed sequencing libraries were loaded on the Illumina HiSeq instrument and sequenced using a 2x150 Paired End (PE) configuration.

treatment_protocol: After 24 h of culture, the medium was replaced and IFN-G (10ng/ml) added to half the wells containing SC-beta or SC-EC, and the cells incubated for a further 24 h at 370C/5% CO2.

value: beta cell

value: No treatment


title: LV Tissue WT [WLV_4]


title: mpra_HEK293_2


title: Acute_Hippocampus_H18

description:
H18
Acute_rawcounts.csv, DNBSEQ-PE100

value: Veh


title: Invitro_BMDM_StrepCGRP_1_L1

description:
tx2gene.rda
txi.rda


title: Invitro_BMDM_Strep_2_L1

description:
tx2gene.rda
txi.rda


title: LV Tissue WT [WLV_3]


title: Acute_Hippocampus_H17

description:
H17
Acute_rawcounts.csv, DNBSEQ-PE100


title: LV Tissue WT [WLV_8]


title: Invitro_BMDM_Strep_1_L2

description:
tx2gene.rda
txi.rda


title: Invitro_BMDM_Strep_4_L2

description:
tx2gene.rda
txi.rda


title: LV Tissue WT [WLV_2]


title: mpra_N-D10_4

tag: age

value: day 10


title: Invitro_BMDM_Strep_1_L1

description:
tx2gene.rda
txi.rda


title: Acute_Hippocampus_H16

description:
H16
Acute_rawcounts.csv, DNBSEQ-PE100


title: Invitro_BMDM_Vehicle_4_L2

description:
tx2gene.rda
txi.rda


title: Acute_Hippocampus_H14

description:
H14
Acute_rawcounts.csv, DNBSEQ-PE100


title: LV Tissue TGAC8 [MLV_8]

value: Left Ventricles


title: Acute_Hippocampus_H15

description:
H15
Acute_rawcounts.csv, DNBSEQ-PE100


title: LV Tissue WT [WLV_1]

value: WT


title: mpra_N-D10_2


title: Invitro_BMDM_Vehicle_4_L1

description:
tx2gene.rda
txi.rda


title: Invitro_BMDM_Strep_3_L2

description:
tx2gene.rda
txi.rda


title: Invitro_BMDM_Strep_2_L2

description:
tx2gene.rda
txi.rda


title: LV Tissue TGAC8 [MLV_7]


title: LV Tissue TGAC8 [MLV_6]


title: Invitro_BMDM_Vehicle_3_L2

description:
tx2gene.rda
txi.rda


title: mpra_HEK293_1


title: Acute_Hippocampus_H13

description:
H13
Acute_rawcounts.csv, DNBSEQ-PE100

value: hippocampus


title: mpra_N-D4_3

value: day 4


title: mpra_N-D10_1


title: Invitro_BMDM_Vehicle_3_L1

description:
tx2gene.rda
txi.rda


title: LV Tissue TGAC8 [MLV_5]


title: mpra_N-D4_2


title: Acute_Hippocampus_H12

description:
H12
Acute_rawcounts.csv, DNBSEQ-PE100

value: acute corticosterone


title: Acute_Hippocampus_H11

description:
H11
Acute_rawcounts.csv, DNBSEQ-PE100


title: Invitro_BMDM_Vehicle_2_L2

description:
tx2gene.rda
txi.rda


title: Acute_Hippocampus_H10

description:
H10
Acute_rawcounts.csv, DNBSEQ-PE100


title: mpra_N-D4_1

value: neuron


title: mpra_N-D10_3

value: Stem cells were plated in clumps in the presence of Y27632 (10mg/ml, 1000x, Axon MedChem). The hES colonies were allowed to grow in mTESR for another day before the media was switch to differentiation media (1X N2, 1X B27, DMEM/F12:Neurobasal=1:1 (Invitrogen), 0.1mM Ascorbic acid (Sigma)) with small molecules [SB431542, LDN193189 and CHIR99021 (Final concentration:10µM, 100nM and 3µM from Stemgent and Tocris)]. To obtain anterior or posterior neural stem cells, SB431542/LDN194189 and SB431542/LDN193189/CHIR99021 were added respectively. The cells were allowed to differentiate in the media for 6 days before they were dissociated with Accutase and plated at the density of 1 million cells per well of 6 wells for infection. For Ngn2 day 2 post-dox induction cells, TetO-Ngn2-t2a-puro and FUW-rtTA were infected at day 0 in differentiation media followed by adding doxycycline and puromycin the next day. The cells were selected for two days in puromycin before collection for downstream HiChIP experiment.


title: Invitro_BMDM_Vehicle_2_L1

description:
tx2gene.rda
txi.rda


title: LV Tissue TGAC8 [MLV_3]


title: Acute_Hippocampus_H9

description:
H9
Acute_rawcounts.csv, DNBSEQ-PE100


title: Acute_Hippocampus_H8

description:
H8
Acute_rawcounts.csv, DNBSEQ-PE100


title: LV Tissue TGAC8 [MLV_2]


title: Invitro_BMDM_Vehicle_1_L1

description:
tx2gene.rda
txi.rda


title: Acute_Hippocampus_H7

description:
H7
Acute_rawcounts.csv, DNBSEQ-PE100


title: LV Tissue TGAC8 [MLV_1]


title: mpra_N-D2_2

value: day 2


title: Peds CD Ileum 205

city: Ithaca

first: Praveen

last: Sethupathy

email: as3999@cornell.edu, pr46@cornell.edu

state: NY

address: T7 006D Veterinary Research Tower, Box 17

department: Department of Biomedical Sciences

institute: Cornell University

description:
Ileum_Peds_normalized_counts.csv
PB205 D1

data_processing:
miRquant 2.0 used for 3' adapter trimming (Cutadapt), two tier read alignment (Bowtie and SHRiMP), and miRNA annotation (miRBase, GtRNAdb, and GENCODE). Normalization and differential analysis was then performed using DESeq2.
RNA-seq data were mapped to the mm6 genome with STAR.Transcripts were quantified with Salmon using GENCODE release 25 transcript annotations. Normalization and differential analysis was then performed using DESeq2.
Assembly: Genome_build: hg19 (GRCh37) for small-RNA seq. mm6 genome for RNA-seq.
Supplementary files format and content: Normalized counts

source_name: CD, Terminal ileum mucosal biopsy

growth_protocol: FFPE samples from the index colonoscopies from treatment naive pediatric patients were collected as part of the University of North Carolina IRB protocol 15-0024.

extract_protocol:
Small RNA libraries were generated using Illumina TruSeq Small RNA Sample Preparation Kit (San Diego, CA).
miRNA was enriched from FFPE tissue samples using the Roche High Pure miRNA Isolation Kit (Penzberg, Germany). RNA purity and integrity were assessed with Thermo Scientific NanoDrop 2000 (Waltham, MA) and Agilent 2100 Bio- analyzer (Santa Clara, CA), respectively.
Single-end (50 bp) sequencing was performed on the Illumina HiSeq 2500 platform.

value: Pediatric

value: Terminal ileum mucosal biopsy

tag: phenotypic status

value: Crohn's disease

value: Naïve


title: Acute_Hippocampus_H6

description:
H6
Acute_rawcounts.csv, DNBSEQ-PE100


title: S2_ChIATAC_50k_SD_B1T3

city: Seattle

first: Chia-Lin

last: Wei

state: WA

address: 3720 15th Ave NE

department: The Northwest Genomics Center (NWGC)

institute: University of Washington

description: ChIATAC

library_source: genomic

data_processing:
Library strategy: ChIATAC
ChIATAC and ChIA-PET data were processed using ChIA-PIPE pipeline (Lee et al., 2020) on hg38 reference genome. Interaction data or loops with significant (called with Chiasig method by Paulsen 2014; PMID: 25114054) PETs >= 3 and PET distance > 8 kb are used for downstream analyses. The peak intensity from MACS2 (Liu, 2014) output is normalized with “-SPMR” option (signal per million reads). Both ChIATAC and ChIA-PET data can be visualized on Juicebox as 2D contact maps by using Juicer software (Durand et al., 2016) version 1.6.2 to create .hic file format.
ChIATAC data was processed by ChIA-PET Utilities (CPU) (https://github.com/cheehongsg/CPU). CPU (options: stat -s -p -T 18 -t 16) removed the adaptors, and grouped the reads into three categories: PET reads, single tag reads and no-linker reads. Tags identified (>=16bp) and reads without linkers were mapped to hg38 using BWA alignment and mem according to the tag/read length. CPU further separated the mapping results into uniquely-mapped, multiply-mapped, and unmapped classes with the pairing consideration (options: pair -S -t 16) and removed duplicates generated by PCR amplification (dedup -g -t 16). Next, the non-redundant uniquely-mapped reads from 3 categories were merged and used for peak calling with MACS v2.1.1.20160309 (options: --keep-dup all --nomodel --extsize 250 -B --SPMR -g hs). CPU further clustered the non-redundant uniquely-mapped pair-end tags and grouped them as intra-chromosomal PET clusters (cis-interactions) and inter-chromosomal PET clusters (trans-interactions) (options: cluster -s 8000 -M -B 1000 -5 5, -20 -3 5, 480 -t 16 -O). The cis-interaction significance was assessed with ChiaSigScaled (https://github.com/cheehongsg/ChiaSigScaled ; options: -c 3 -t 16 -p -m 8000). Cis-interactions with member size >=3 and FDR < 0.05 were reported. The complete list trans interaction was reported here while additional filtering were applied (e.g. exclude singletons) for corresponding analyses in publication. (see details in publication).
Genome_build: hg38
Supplementary_files_format_and_content: Significant intrachromosomal interactions with frequency at least 3 PETs. Format: text file with 7-column (coordinates of 2 anchors at the first six columns, interaction frequency at the 7th).

molecule: genomic DNA

organism: Drosophila melanogaster

growth_protocol: Drosophila Schneider 2 (S2) cells (derived from a primary culture of late-stage Drosophila melanogaster embryos) were cultured in Express Five® SFM (ThermoFisher Scientific; 10486025) with 1:100 L-Glutamine (ThermoFisher Scientific; 25030081) at 27 °C.

extract_protocol: ChIATAC libraries were performed by combining ChIAPET (Wang et al., 2021) and ATAC-seq protocol. Briefly, crosslinked cells are permeabilized, restriction enzyme digested, and ligated. Then the nuclei were subjected to in situ transposition, DNA were purified and amplified by PCR.

tag: cell numbers


title: mpra_N-D2_1


title: Acute_Hippocampus_H5

description:
H5
Acute_rawcounts.csv, DNBSEQ-PE100


title: S2_ChIATAC_50k_SD_B1T2

description: ChIATAC


title: LV Tissue TGAC8 [MLV_4]


title: mpra_ES_2

value: day 0


title: mpra_ES_1


title: S2_ChIATAC_50k_SD_B1T1

description: ChIATAC


title: Isolated Cardiomyocytes, Mutant, 8 weeks, H3K36me2, CUT&Tag, Replicate 1

city: Toronto

first: Paul

last: Delgado-Olguin

state: Ontario

department: Molecular Genetics

country: Canada

institute: University of Toronto

data_processing:
Raw sequence reads were trimmed using FASTP v0.20.0 and aligned to the reference mouse genome (mm10) using Bowtie2 v2.1.0.
Assembly: mm10
Supplementary files format and content: bigwig for each sample
Library strategy: CUT&Tag

source_name: Heart

extract_protocol:
Cardiomyocytes isolated from 2-month-old hearts were processed using the CUT&Tag-IT Assay Kit (Active Motif)
Libraries were constructed using the CUT&Tag-IT Assay Kit (Active Motif)

value: Heart

value: isolated cardiomyocytes

value: Kdm8 knockout

value: 8 weeks

tag: chip antibody

value: H3K36me2 (Active Motif, 39255 + Cell Signalling, 2901)


title: Isolated Cardiomyocytes, Mutant, 8 weeks, H3K36me2, CUT&Tag, Replicate 3

tag: tissue


title: Isolated Cardiomyocytes, Mutant, 8 weeks, H3K36me2, CUT&Tag, Replicate 2

tag: genotype


title: Acute_Hippocampus_H4

description:
H4
Acute_rawcounts.csv, DNBSEQ-PE100

value: WT

value: Veh


title: Isolated Cardiomyocytes, Wildtype, 8 weeks, H3K36me2, CUT&Tag, Replicate 3


title: Acute_Hippocampus_H3

description:
H3
Acute_rawcounts.csv, DNBSEQ-PE100

value: hippocampus


title: mpra-AST_2

source_name: primary

value: primary astrocytes

value: primary

value: Normal Human Astrocytes (Lonza, CC-2565) were cultured in Lonza Astrocyte Growth Media containing astrocyte basal medium, 7.5% FBS, ascorbic acid, rhEGF, GA-1000 (gentamicin sulfate-amphotericin), insulin, and L-glutamine. Astrocytes were seeded at a 5,000 cells/cm^2 density and maintained up to 70% confluence before splitting at 37C and 5% CO2. Growth medium was changed the day after seeding and every other day thereafter.


title: mpra_N-D2_4

value: neuron

value: day 2

value: Stem cells were plated in clumps in the presence of Y27632 (10mg/ml, 1000x, Axon MedChem). The hES colonies were allowed to grow in mTESR for another day before the media was switch to differentiation media (1X N2, 1X B27, DMEM/F12:Neurobasal=1:1 (Invitrogen), 0.1mM Ascorbic acid (Sigma)) with small molecules [SB431542, LDN193189 and CHIR99021 (Final concentration:10µM, 100nM and 3µM from Stemgent and Tocris)]. To obtain anterior or posterior neural stem cells, SB431542/LDN194189 and SB431542/LDN193189/CHIR99021 were added respectively. The cells were allowed to differentiate in the media for 6 days before they were dissociated with Accutase and plated at the density of 1 million cells per well of 6 wells for infection. For Ngn2 day 2 post-dox induction cells, TetO-Ngn2-t2a-puro and FUW-rtTA were infected at day 0 in differentiation media followed by adding doxycycline and puromycin the next day. The cells were selected for two days in puromycin before collection for downstream HiChIP experiment.


title: WT_stim_rep3

city: Amsterdam

first: Heinz

last: Jacobs

address: Plesmanlaan 121

institute: Netherlands Cancer Institute

data_processing:
RNAseq samples were aligned single-end using hisat2 against GRCm38.
Using itreecount reads per gene were counted considering strand, as annotated in an Ensembl GRCm38.100 gtf.
The DEseq2 package in R was used to calculate p values and LFC
Assembly: Mouse reference genome GRCm38
Supplementary files format and content: Tab-delimited text files with the adjusted p values and log 2 fold change per gene per condition comparison

source_name: B cells

extract_protocol:
RNA was isolated using Qiagen RNeasy column purification and DNAse
libraries were prepared using the HiSeq® HOM SR Cluster Kit v4 - cBot™, according to the manufacturer’s instructions.

value: wild-type

value: stimulated for 3 days with LPS+CD40+IL4+IgD-Dextran for 3 days


title: mpra_N-D2_3


title: Isolated Cardiomyocytes, Wildtype, 8 weeks, H3K36me2, CUT&Tag, Replicate 2


title: Invitro_BMDM_Vehicle_1_L2

description:
tx2gene.rda
txi.rda

value: No

value: In vitro

value: Bulk RNA-seq


title: mpra-AST_1


title: Acute_Hippocampus_H2

description:
H2
Acute_rawcounts.csv, DNBSEQ-PE100


title: Isolated Cardiomyocytes, Wildtype, 8 weeks, H3K36me2, CUT&Tag, Replicate 1

value: Heart

value: isolated cardiomyocytes


title: Acute_Hippocampus_H1

description:
H1
Acute_rawcounts.csv, DNBSEQ-PE100


title: T24 cells, sgOTUD1_3

city: Wuhan

first: Guanlan

last: Fan

address: Donghu Road, No. 115, Wuchang District

country: China

institute: Wuhan University

data_processing:
FeatureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis was performed using the DESeq2 R package (1.20.0).
The GSEA analysis tool http://www.broadinstitute.org/gsea/index.jsp was used for GSEA independently.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Bladder cancer cells

growth_protocol: T24 cells were maintained in RPMI1640 medium (Sigma) supplemented with 10% fetal bovine serum (FBS) and at 37 °C in humid air with 5% CO2 condition.

extract_protocol:
Total amounts and integrity of RNA were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA)
Sequencing libraries were constructed by NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA). Qubit2.0 Fluorometer, Agilent 2100 bioanalyzer and Quantitative real-time PCR (Q-PCR) were carried out successively to ensure the quality of the library.

value: Bladder cancer cells

value: OTUD1 knockout


title: T24 cells, sgOTUD1_2


title: Huwe1_unstim_rep3

value: untreated


title: Continuous_Liver_L20

description:
L20
Continuous_rawcounts.csv, DNBSEQ-PE100

source_name: liver

value: liver

value: WT

value: continuous corticosterone


title: Whole ventricles, Mutant, 24 weeks , RNA-Seq, Replicate 3

description:
24wk_Kdm8_counts.txt
MUT3_24wks

data_processing:
For RNA-Seq, sequence reads were trimmed and aligned to the reference mouse genome (mm10 - Ensembl release 104) using Trimmomatic 0.36 and STAR version 2.7.9 as previously described. For analysis of expression in iCells, reads were aligned to the reference human genome hg38 - Ensembl release 104.
Assembly: mm10, hg38
Supplementary files format and content: tab-delimited text files include count values for each Sample

source_name: whole ventricles

extract_protocol:
Whole ventricles were dissected and frozen in TriZOL (Invitrogen) immediately after dissection. Tissue was homogenized at 30 kHz for 2 min using the TissueLyserII (Qiagen). Bead-homogenized samples were centrifuged to pellet insoluble tissue. DNA-free RNA was isolated using the Direct-zol™ RNA MiniPrep kit (Zymo Research).
Poly(A) mRNA was isolated from 1 ug of total RNA of adult heart using NEBNext Poly(A) Magnetic Isolation Module (New England Biolabs). mRNA was used to prepare RNA-seq libraries using the NEBNext Ultra™ II RNA Library Prep Kit for Illumina (New England Biolabs).

value: whole ventricles

value: Kdm8 knockout

value: 24 weeks


title: Huwe1_unstim_rep2


title: Whole ventricles, Mutant, 24 weeks , RNA-Seq, Replicate 2

description:
24wk_Kdm8_counts.txt
MUT2_24wks


title: Whole ventricles, Mutant, 24 weeks , RNA-Seq, Replicate 1

description:
24wk_Kdm8_counts.txt
MUT1_24wks


title: T24 cells, sgNC_3

value: empty vector as negative control


title: Huwe1_unstim_rep1


title: Continuous_Liver_L19

description:
L19
Continuous_rawcounts.csv, DNBSEQ-PE100

value: AS

value: vehicle


title: WT1_unstim_rep3

value: wild-type


title: T24 cells, sgOTUD1_1


title: Continuous_Liver_L17

description:
L17
Continuous_rawcounts.csv, DNBSEQ-PE100


title: WT_stim_rep2

value: stimulated for 3 days with LPS+CD40+IL4+IgD-Dextran for 3 days


title: Whole ventricles, Wildtype, 24 weeks, RNA-Seq, Replicate 2

description:
24wk_Kdm8_counts.txt
WT2_24wks


title: T24 cells, sgNC_1


title: WT1_unstim_rep2


title: Whole ventricles, Wildtype, 24 weeks, RNA-Seq, Replicate 3

description:
24wk_Kdm8_counts.txt
WT3_24wks


title: Whole ventricles, Wildtype, 24 weeks, RNA-Seq, Replicate 1

description:
24wk_Kdm8_counts.txt
WT1_24wks


title: WT_stim_rep1


title: iPSC-CM transfected with TBX15 OHu33746C pcDNA3.1(+)-N-6His , RNA-Seq, Replicate 3

description:
icell_counts.txt
TBX3_icell

source_name: Human induced pluripotent stem cell-derived cardiomyocytes, iCell Cardiomyocytes

value: iPSC-CMs

value: Transfected with TBX15 OHu33746C pcDNA3.1(+)-N-6His


title: Continuous_Liver_L15

description:
L15
Continuous_rawcounts.csv, DNBSEQ-PE100


title: Whole ventricles, Mutant, 16 weeks , NAD Injection, RNA-Seq, Replicate 3

description:
16wk_Kdm8_counts.txt
MUTNAD3_16wks

value: 16 weeks

value: NAD injection


title: WT1_unstim_rep1


title: Huwe1_stim_rep3


title: iPSC-CM transfected with TBX15 OHu33746C pcDNA3.1(+)-N-6His , RNA-Seq, Replicate 2

description:
icell_counts.txt
TBX2_icell


title: Continuous_Liver_L14

description:
L14
Continuous_rawcounts.csv, DNBSEQ-PE100


title: Whole ventricles, Mutant, 16 weeks , NAD Injection, RNA-Seq, Replicate 2

description:
16wk_Kdm8_counts.txt
MUTNAD2_16wks


title: Huwe1_stim_rep2


title: Continuous_Liver_L18

description:
L18
Continuous_rawcounts.csv, DNBSEQ-PE100


title: Continuous_Liver_L13

description:
L13
Continuous_rawcounts.csv, DNBSEQ-PE100


title: T24 cells, sgNC_2

value: Bladder cancer cells


title: Huwe1_stim_rep1


title: iPSC-CM transfected with GFP-OE plasmid, RNA-Seq, Replicate 3

description:
icell_counts.txt
CNTRL3_icell

value: Transfected with GFP-OE Plasmid


title: iPSC-CM transfected with TBX15 OHu33746C pcDNA3.1(+)-N-6His , RNA-Seq, Replicate 1

description:
icell_counts.txt
TBX1_icell


title: Whole ventricles, Mutant, 16 weeks , NAD Injection, RNA-Seq, Replicate 1

description:
16wk_Kdm8_counts.txt
MUTNAD1_16wks


title: Whole ventricles, Mutant, 16 weeks , untreated, RNA-Seq, Replicate 3

description:
16wk_Kdm8_counts.txt
MUT3_16wks


title: Continuous_Liver_L12

description:
L12
Continuous_rawcounts.csv, DNBSEQ-PE100

value: liver


title: Continuous_Liver_L11

description:
L11
Continuous_rawcounts.csv, DNBSEQ-PE100


title: Continuous_Liver_L16

description:
L16
Continuous_rawcounts.csv, DNBSEQ-PE100


title: Continuous_Liver_L10

description:
L10
Continuous_rawcounts.csv, DNBSEQ-PE100


title: iPSC-CM transfected with GFP-OE plasmid, RNA-Seq, Replicate 1

description:
icell_counts.txt
CNTRL1_icell


title: MKN45, sensitive, rep2

city: Barcelona

first: Lara

last: Nonell

address: C/ NATZARET, 115-117

department: VHIOinformatics

country: Spain

institute: Vall d'Hebron Institute of Oncology (VHIO)

data_processing:
nf-core rnaseq pipeline vesion 3.5
Differential gene expression was assessed with the voom+limma strategy in the limma package (ME.Ritchie and GK.Smyth 2015, version 3.48.3 ).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file including raw counts for each Sample

growth_protocol: MKN45 and derivative cells were maintained in DMEM/F-12 supplemented with 10% fetal bovine serum (FBS), 1% glutamine, and 1% antibiotics (P/S) in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
The RNASeq libraries were prepared using the Stranded Total RNA Prep with Ribo-Zero Plus (Illumina) following the manufacturer´s recommendations and the final library was validated on an Agilent 2100 Bioanalyzer with the DNA 7500 assay (Agilent).

value: Gastric tumor cells

tag: condition


title: Continuous_Liver_L9

description:
L9
Continuous_rawcounts.csv, DNBSEQ-PE100

tag: treatment


title: Whole ventricles, Mutant, 8 weeks, RNA-Seq, Replicate 1

description:
8wk_Kdm8_counts.txt
MUT1_8wks

value: 8 weeks


title: Whole ventricles, Wildtype, 8 weeks, RNA-Seq, Replicate 2

description:
8wk_Kdm8_counts.txt
WT2_8wks

value: whole ventricles

value: WT


title: Whole ventricles, Wildtype, 16 weeks , NAD Injection, RNA-Seq, Replicate 3

description:
16wk_Kdm8_counts.txt
WTNAD3_16wks


title: Whole ventricles, Mutant, 16 weeks , untreated, RNA-Seq, Replicate 2

description:
16wk_Kdm8_counts.txt
MUT2_16wks

value: Kdm8 knockout


title: Whole ventricles, Wildtype, 8 weeks, RNA-Seq, Replicate 1

description:
8wk_Kdm8_counts.txt
WT1_8wks


title: MKN45, sensitive, rep1

tag: cell type


title: Whole ventricles, Wildtype, 16 weeks , NAD Injection, RNA-Seq, Replicate 2

description:
16wk_Kdm8_counts.txt
WTNAD2_16wks


title: Whole ventricles, Mutant, 8 weeks, RNA-Seq, Replicate 2

description:
8wk_Kdm8_counts.txt
MUT2_8wks


title: Whole ventricles, Mutant, 16 weeks , untreated, RNA-Seq, Replicate 1

description:
16wk_Kdm8_counts.txt
MUT1_16wks


title: MKN-CEAR, CEACAM5-TCB resistant, rep2

tag: cell line


title: Continuous_Liver_L8

description:
L8
Continuous_rawcounts.csv, DNBSEQ-PE100

value: continuous corticosterone


title: Continuous_Liver_L7

description:
L7
Continuous_rawcounts.csv, DNBSEQ-PE100

value: AS


title: Whole ventricles, Wildtype, 16 weeks , NAD Injection, RNA-Seq, Replicate 1

description:
16wk_Kdm8_counts.txt
WTNAD1_16wks


title: iPSC-CM transfected with GFP-OE plasmid, RNA-Seq, Replicate 2

description:
icell_counts.txt
CNTRL2_icell


title: IG5_01302017

city: Boston

first: Ionita

middle: Calin

last: Ghiran

state: MA

address: 3 Blackfan Circle

department: Medicine

institute: Beth Israel Deaconess Medical Center

data_processing:
All FASTQ files were processed uniformly through the extra-cellular RNA processing toolkit (exceRpt), with an adapter sequence of [] and random barcode length [] (on []). Information about exceRpt is available at https://github.gersteinlab.org/exceRpt/.
Assembly: hg19
Supplementary files format and content: *.tar: Each processed data file is a core results archive generated by exceRpt. The core results archive contains read counts for alignments to the different transcriptome libraries used by exceRpt (miRNA / piRNA / tRNA / GENCODE annotations / circRNA), taxonomy trees for exogenous rRNA and genomic reads aligned by exceRpt, and a variety of other files generated by exceRpt.

source_name: Plasma

extract_protocol:
RNA Isolation kit was miRcury biofluids (Exiqon).
Library construction kit was NEBNext small RNA library prep (NEB). Samples were not multiplexed. Type of Starting Material was total RNA.

tag: donor

tag: disease state

value: Healthy

value: Plasma

tag: concentration lysed rbc

tag: anatomical location

value: Entire cardiovascular system

tag: rna source

value: total cell-free biofluid RNA

tag: rna isolation kit

value: miRcury biofluids (Exiqon)


title: Continuous_Liver_L6

description:
L6
Continuous_rawcounts.csv, DNBSEQ-PE100

value: vehicle


title: IG3_01302017


title: MKN-CEAR, CEACAM5-TCB resistant, rep1


title: IG1_01302017


title: Whole ventricles, Wildtype, 16 weeks , untreated, RNA-Seq, Replicate 5

description:
16wk_Kdm8_counts.txt
WT5_16wks

value: 16 weeks


title: MKN-HER2, HER2-TCB resistant, rep1


title: IG16_01302017


title: Continuous_Liver_L5

description:
L5
Continuous_rawcounts.csv, DNBSEQ-PE100


title: Whole ventricles, Wildtype, 16 weeks , untreated, RNA-Seq, Replicate 4

description:
16wk_Kdm8_counts.txt
WT4_16wks


title: Whole ventricles, Wildtype, 16 weeks , untreated, RNA-Seq, Replicate 6

description:
16wk_Kdm8_counts.txt
WT6_16wks


title: IG7_01302017


title: Continuous_Liver_L4

description:
L4
Continuous_rawcounts.csv, DNBSEQ-PE100


title: Continuous_Liver_L3

description:
L3
Continuous_rawcounts.csv, DNBSEQ-PE100


title: siLGALS1 3

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

data_processing:
The raw RNA-seq reads were filtered to obtain high-quality data by removing N-containing reads, trimming adaptors and low-quality bases, and discarding short reads (< 16nt) using FASTX-Toolkit (Version 0.0.13).
The high-quality reads were then aligned onto human GRCh38 genome by HISAT2 allowing no more than 4 mismatches.
Aligned reads with uniquely genomic location were used for gene expression level FPKM (fragments per kilobase of transcript per million fragments mapped) calculation.
We then used DESeq2 package from R Bioconductor to predict differentially expressed genes (DEGs) with corrected p-value (FDR) <0.05 and fold change>2 as the criteria.
The alternative splicing events (ASEs) and galectin-1-regulated ASEs (RASEs) between siLGALS1 and Ctrl groups were predicted and quantified using the ABLas pipeline as described previously.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
Supplementary files format and content: tab-delimited text files include reads counts for each Sample

source_name: human umbilical vein endothelial cells (HUVECs)

growth_protocol: The HUVECs (ScienCell, USA) were cultured at 37℃ with 5% CO2 in endothelial cell medium (ECM, ScienCell), which contained 10% fetal bovine serum (FBS), 100 µg/mL streptomycin, 100 U/mL penicillin.

extract_protocol:
After harvesting siLGALS1 and control cells, genomic DNA were removed RQ1 DNase (Promega) and we obtained total RNAs. The qualified RNAs in quality and quantity, which were measured by the absorbance at 260nm/280nm (A260/A280) using smartspec plus (BioRad), were used for following experiment by 1.5% agarose gel electrophoresis method. One μg RNA was captured by by VAHTS mRNA capture Beads (Vazyme, N401) for siLGALS1 and control samples with three biological replicates.
Polyadenylated RNAs by oligo(dT) were used for RNA-seq library preparation by KAPA Stranded Kit for the Illumina® Platforms. After size selection (300-500bps), the cDNA products were processed and stored at -80°C fridge, and then used for high-throughput sequencing (RNA-seq) by Illumina Novaseq 6000 system, and finally 150 nt paired-end sequencing reads were obtained.

treatment_protocol: The siRNA transfection targeting LGALS1 was completed using Lipofectamine 2000 (Invitrogen, Carlsbad, CA, USA) according to the manufacturer's protocol. After 48h, the transfected HUVECs were harvested to validate the repressed expression of LGALS1 by RT-qPCR analysis, which was completed following published procedure and 2-ΔΔCT method.

value: LGALS1 knockdown

value: siRNA transfection targeting LGALS1


title: Whole ventricles, Wildtype, 16 weeks , untreated, RNA-Seq, Replicate 3

description:
16wk_Kdm8_counts.txt
WT3_16wks


title: siLGALS1 2

value: human umbilical vein endothelial cells (HUVECs)


title: Whole ventricles, Wildtype, 16 weeks , untreated, RNA-Seq, Replicate 2

description:
16wk_Kdm8_counts.txt
WT2_16wks


title: IG8_01302017


title: Continuous_Liver_L2

description:
L2
Continuous_rawcounts.csv, DNBSEQ-PE100

value: liver


title: IG13_01302017


title: Continuous_Liver_L1

description:
L1
Continuous_rawcounts.csv, DNBSEQ-PE100


title: Whole ventricles, Wildtype, 16 weeks , untreated, RNA-Seq, Replicate 1

description:
16wk_Kdm8_counts.txt
WT1_16wks


title: siLGALS1 1


title: MKN-HER2, HER2-TCB resistant, rep2

value: Gastric tumor cells


title: IG14_01302017


title: Ctrl 3

value: control siRNA

value: Non-targeting control siRNA


title: Fltp+ late

city: Munich

first: Karin

last: Hrovatin

address: Ingolstädter Landstraße 1

department: Institute of Computational Biology

country: Germany

institute: Helmholtz Munich

library_source: transcriptomic single cell

data_processing:
Cell Ranger
Assembly: Ensembl release 94 mm10 with custom genes for mTmG reporter
Supplementary files format and content: Raw UMI count matrix (feature x droplet barcode) from 10X Genomics single cell RNAseq experiments. Gzipped collection of count matrix in market matrix format, droplet barcodes as tab-delimited text file, and feature names as tab-delimited text file.

source_name: pancreas - islets of Langerhans

extract_protocol:
Islets of Langerhans have been isolated using a standard protocol (Corbin et al., 2021; https://doi.org/10.1186/s12575-021-00143-x; D.-S. Li et al., 2009; https://doi.org/10.1038/nprot.2009.150). We sorted Fltp negative (tomato positive), Fltp lineage positive (GFP positive), and Fltp transient (double positive) populations and generated separate libraries for each population. Male and female mice were pulled together after sorting.
Libraries of single cells were produced using the Chromium Single-Cell 3′ library and 10XGenomics gel bead kit v3.1 (PN #1000121). Briefly, 10,000 cells were loaded per channel of a 10x chip to produce gel bead-in-emulsions (GEMs). Then the samples underwent reverse transcription to barcode RNA followed by cleanup, cDNA amplification, enzymatic fragmentation, 5′ adaptor, and sample index attachment. The samples were sequenced using a NovaSeq6000 (Illumina) with 100 bp paired-end sequencing.

value: pancreas - islets of Langerhans

tag: strain

value: Fltp iCre mTmG

tag: cell sorting

value: mGFP

tag: Sex

value: mixed male and female

value: at least 2 years


title: Ctrl 2


title: Continuous_Hippocampus_H19

description:
H19
Continuous_rawcounts.csv, DNBSEQ-PE100

value: hippocampus

value: AS


title: IG15_01302017

value: Healthy

value: Plasma

value: Entire cardiovascular system

value: total cell-free biofluid RNA

value: miRcury biofluids (Exiqon)


title: Continuous_Hippocampus_H20

description:
H20
Continuous_rawcounts.csv, DNBSEQ-PE100

value: WT

value: continuous corticosterone


title: IG6_01302017


title: Fltp+ early

value: mTmG

tag: age


title: Fltp-

value: mRFP


title: Ctrl 1

value: human umbilical vein endothelial cells (HUVECs)

value: control siRNA

value: Non-targeting control siRNA


title: Continuous_Hippocampus_H17

description:
H17
Continuous_rawcounts.csv, DNBSEQ-PE100

value: vehicle


title: CD4_IL2_RNA-seq_B1T2

data_processing:
The raw sequencing reads were trimmed using Trim Galore version 0.4.3 (options: --stringency 3 -q 20 -e .20 --length 15 --paired) and aligned to the hg38 genome using hisat 2.1.0. The transcripts were quantified with htseq-count (option -q -s reverse -m union --secondary-alignments ignore --supplementary-alignments ignore) using gencodev36 (comprised only protcoding & miRNA)
Genome_build: hg38
Supplementary_files_format_and_content: Gene quantification from HTseq-count output.

source_name: Blood

growth_protocol: Resting CD4+ T cell isolation: A buffycoat was obtained from Blood Bank in National Institute of Health. Human CD4+ T cells were purified by EasySep Human CD4+ T cell isolation kit (StemCell Technology; 17952).

extract_protocol: Total RNA was extracted with RNeasy mini kit (Qiagen, 74106) from primary total CD4+ T cells or total CD4+ T cells with the TCR activation.

treatment_protocol: TCR activation: The isolated primary CD4+ T cells were cultured in RPMI medium supplemented with 10% FBS/penicillin-streptomycin at 37 °C incubator and activated by 2 ug/ml of plate-bound anti-CD3 and 1 ug/ml of suspended anti-CD28 for 72 hours. IL-2 stimulation: The above TCR-activated T cells were rested overnight. Two hundred International Units of IL-2 were added to the cells for 4 hours.

value: IL2 induced CD4+ TCR activated T cells


title: Blood sample from COVID-19 patient P5 at day 7

city: Genoa

first: Paolo

last: Uva

address: Via Gerolamo Gaslini, 5

country: Italy

institute: IRCCS Istituto Giannina Gaslini

data_processing:
Basecalling was performed using bcl2fastq version 2.20.0.
Reads were trimmed for low-quality ends with TrimGalore version 0.6.6
Reads were aligned to the hg38 reference transcriptome and transcript abundance was estimated with Kallisto version 0.43.
Kallisto counts were normalized by the regularized log (rlog) transformation using the DeSeq2 R Package
Genome_build: hg38
Supplementary_files_format_and_content: Comma-delimited text files include rlog values for each sample and time point

source_name: Blood sample

extract_protocol:
RNA was extracted with Paxgene ® Blood RNA Kit (Qiagen, Hilden, Germany).
Poly-A enriched libraries were generated with Illumina TruSeq mRNA Stranded kit according to the manufacturer’s instructions.

tag: individual

value: patient P5

tag: infection

value: anakinra

tag: time

value: day 7

value: Whole blood


title: CD4_IL2_RNA-seq_B1T1


title: Blood sample from COVID-19 patient P5 at day 0

value: Untreated

value: day 0

tag: tissue


title: Continuous_Hippocampus_H16

description:
H16
Continuous_rawcounts.csv, DNBSEQ-PE100

value: hippocampus

tag: genotype

value: AS

tag: treatment


title: IG2_01302017

value: Healthy

value: Plasma

value: Entire cardiovascular system

value: total cell-free biofluid RNA

value: miRcury biofluids (Exiqon)


title: IG4_01302017


title: CD4_activation_RNA-seq_B1T2

tag: cell type

value: TCR activated CD4+ T cells


title: Continuous_Hippocampus_H15

description:
H15
Continuous_rawcounts.csv, DNBSEQ-PE100

value: WT

value: continuous corticosterone


title: Blood sample from COVID-19 patient P3 at day 7

value: patient P3


title: CD4_activation_RNA-seq_B1T1


title: Continuous_Hippocampus_H14

description:
H14
Continuous_rawcounts.csv, DNBSEQ-PE100

value: vehicle


title: Blood sample from COVID-19 patient P3 at day 0


title: CD4_activation_ATAC-seq_B1T1

data_processing:
The raw paired-end reads were quality trimmed using Trim Galore version 0.6.6 (options: --stringency 3 -q 30 -e .20 --length 16) and mapped to the hg38 genome using BWA 0.7.17 (command: mem). The duplicate reads were removed from the alignment file and MACS v2.2.7.1 callpeak command was used to generate bedgraph (options: --nomodel --extsize 150 --shift -75 -B --SPMR) which then converted to bigwig format.
Genome_build: hg38
Supplementary_files_format_and_content: ATAC-seq coverage; bigwig format.

extract_protocol: not provided

tag: cell numbers


title: Continuous_Hippocampus_H18

description:
H18
Continuous_rawcounts.csv, DNBSEQ-PE100

data_processing:
The BioWDL pipeline was used for reads quality control, alignment, and quantification.
Quality control was performed using FastQC and MultiQC.
Reads were aligned to mm10 using STAR and gene-read quantification was performed using HTSeq-count
Assembly: mm10
Supplementary files format and content: Matrix tables with gene raw counts for every feature according to Ensembl97 for each sample


title: Continuous_Hippocampus_H13

description:
H13
Continuous_rawcounts.csv, DNBSEQ-PE100


title: Blood sample from COVID-19 patient P2 at day 7

value: patient P2

value: anakinra


title: CD4_activation_RNAPIIChIAPET_B1T1

description: RNAPII ChIAPET

data_processing:
Library strategy: ChIAPET
ChIATAC and ChIA-PET data were processed using ChIA-PIPE pipeline (Lee et al., 2020) on hg38 reference genome. Interaction data or loops with significant (called with Chiasig method by Paulsen 2014; PMID: 25114054) PETs >= 3 and PET distance > 8 kb are used for downstream analyses. The peak intensity from MACS2 (Liu, 2014) output is normalized with “-SPMR” option (signal per million reads). Both ChIATAC and ChIA-PET data can be visualized on Juicebox as 2D contact maps by using Juicer software (Durand et al., 2016) version 1.6.2 to create .hic file format.
ChIA-PETdata was processed by ChIA-PET Utilities (CPU) (https://github.com/cheehongsg/CPU). CPU (options: stat -s -p -T 18 -t 16) removed the adaptors, and grouped the reads into three categories: PET reads, single tag reads and no-linker reads. Tags identified (>=16bp) and reads without linkers were mapped to hg38 using BWA alignment and mem according to the tag/read length. CPU further separated the mapping results into uniquely-mapped, multiply-mapped, and unmapped classes with the pairing consideration (options: pair -S -t 16) and removed duplicates generated by PCR amplification (dedup -g -t 16). Next, the non-redundant uniquely-mapped reads from 3 categories were merged and used for peak calling with MACS v2.1.1.20160309 (options: --keep-dup all --nomodel --extsize 250 -B --SPMR -g hs). CPU further clustered the non-redundant uniquely-mapped pair-end tags and grouped them as intra-chromosomal PET clusters (cis-interactions) and inter-chromosomal PET clusters (trans-interactions) (options: cluster -s 8000 -M -B 1000 -5 5, -20 -3 5, 480 -t 16 -O). The cis-interaction significance was assessed with ChiaSigScaled (https://github.com/cheehongsg/ChiaSigScaled ; options: -c 3 -t 16 -p -m 8000). Cis-interactions with member size >=3 and FDR < 0.05 were reported. The complete list trans interaction was reported here while additional filtering were applied (e.g. exclude singletons) for corresponding analyses in publication. (see details in publication).
Genome_build: hg38
Supplementary_files_format_and_content: Significant intrachromosomal interactions with frequency at least 3 PETs. Format: text file with 7-column (coordinates of 2 anchors at the first six columns, interaction frequency at the 7th).

extract_protocol: In situ ChIA-PET libraries with antibody against RNAPII or CTCF were constructed using 10,000,000 FA-EGS-crosslinked cells from GM12878 cell cultures, following the in situ ChIA-PET protocol (Wang et al., 2021).

tag: antibody

value: anti-RNAPII antibody (BioLegend, 664912)


title: Continuous_Hippocampus_H12

description:
H12
Continuous_rawcounts.csv, DNBSEQ-PE100

extract_protocol:
Total RNA was isolated from frozen hippocampus and liver tissue using the NucleoSpin® RNA kit (Macherey-Nagel)
mRNA was enriched and purified and a stranded library was constructed for 100 bp paired-end sequencing on BGI's DNBseq platform


title: Blood sample from COVID-19 patient P2 at day 0

value: Untreated

value: Whole blood


title: CD4_resting_RNAPIIChIAPET_B1T1

description: RNAPII ChIAPET

value: Resting CD4+ T cells


title: CD4_IL2_ChIATAC_50k_DD_B1T2

description: ChIATAC

value: IL2 induced CD4+ TCR activated T cells


title: Continuous_Hippocampus_H10

description:
H10
Continuous_rawcounts.csv, DNBSEQ-PE100

value: hippocampus

value: AS


title: Blood sample from COVID-19 patient P1 at day 0

value: patient P1

value: day 0


title: Continuous_Hippocampus_H9

description:
H9
Continuous_rawcounts.csv, DNBSEQ-PE100


title: CD4_IL2_ChIATAC_50k_DD_B1T1

description: ChIATAC


title: Continuous_Hippocampus_H8

description:
H8
Continuous_rawcounts.csv, DNBSEQ-PE100


title: CD4_activation_ChIATAC_50k_DD_B1T2

description: ChIATAC

data_processing:
Library strategy: ChIATAC
ChIATAC and ChIA-PET data were processed using ChIA-PIPE pipeline (Lee et al., 2020) on hg38 reference genome. Interaction data or loops with significant (called with Chiasig method by Paulsen 2014; PMID: 25114054) PETs >= 3 and PET distance > 8 kb are used for downstream analyses. The peak intensity from MACS2 (Liu, 2014) output is normalized with “-SPMR” option (signal per million reads). Both ChIATAC and ChIA-PET data can be visualized on Juicebox as 2D contact maps by using Juicer software (Durand et al., 2016) version 1.6.2 to create .hic file format.
Raw fastq files from 2 libraries (THN0009 & THN0010) are merged then processed by ChIA-PET Utilities (CPU) (https://github.com/cheehongsg/CPU). CPU (options: stat -s -p -T 18 -t 16) removed the adaptors, and grouped the reads into three categories: PET reads, single tag reads and no-linker reads. Tags identified (>=16bp) and reads without linkers were mapped to hg38 using BWA alignment and mem according to the tag/read length. CPU further separated the mapping results into uniquely-mapped, multiply-mapped, and unmapped classes with the pairing consideration (options: pair -S -t 16) and removed duplicates generated by PCR amplification (dedup -g -t 16). Next, the non-redundant uniquely-mapped reads from 3 categories were merged and used for peak calling with MACS v2.1.1.20160309 (options: --keep-dup all --nomodel --extsize 250 -B --SPMR -g hs). CPU further clustered the non-redundant uniquely-mapped pair-end tags and grouped them as intra-chromosomal PET clusters (cis-interactions) and inter-chromosomal PET clusters (trans-interactions) (options: cluster -s 8000 -M -B 1000 -5 5, -20 -3 5, 480 -t 16 -O). The cis-interaction significance was assessed with ChiaSigScaled (https://github.com/cheehongsg/ChiaSigScaled ; options: -c 3 -t 16 -p -m 8000). Cis-interactions with member size >=3 and FDR < 0.05 were reported. The complete list trans interaction was reported here while additional filtering were applied (e.g. exclude singletons) for corresponding analyses in publication. (see details in publication).
Genome_build: hg38
Supplementary_files_format_and_content: Significant intrachromosomal interactions with frequency at least 3 PETs. Format: text file with 7-column (coordinates of 2 anchors at the first six columns, interaction frequency at the 7th).


title: Continuous_Hippocampus_H7

description:
H7
Continuous_rawcounts.csv, DNBSEQ-PE100


title: d3_Gcn5 OE whole fly_2

city: Shanghai

first: Jingshu

last: Li

address: 100 Hai Ke Rd., Pudong

institute: Chinese Academy of Sciences

description: Gcn5 overexpression flies

data_processing:
Trim Galore (version 0.6.6) was used for quality control of fastq files with parameters ‘--nextseq 30 --paired’. Sequencing reads were mapped to the reference genome dmel_r6.36 with STAR-2.7.6a by default parameter. The read counts for each gene were calculated by featureCounts (version 2.0.1) with parameters ‘-p -B -C’. The count files were used as input to R package DESeq2 for normalization and the differential expression analysis. The criterion for differential expression genes was the absolute fold-change of counts between groups > 2 and adjusted p-value < 0.05.
Assembly: dmel_r6.36
Supplementary files format and content: DESeq2 was used for calling differential expression.tab-delimited text files include foldChange,pvalue

source_name: Whole fly

extract_protocol:
Total RNA was extracted and purified using RNAiso Plus (TaKaRa, catalog: 9108)
RNA libraries were prepared according to instructions of Abclonal mRNA-seq Library Prep Kit for Illumina (RK20302)
RNA-Seq; Sample1-24: 100bp single-end; Sample25-39: 150bp paired-end

value: gcn5c450, tub-GAL4/c450, UAS-HA-Gcn5


title: CD4_activation_ChIATAC_50k_DD_B1T1

description: ChIATAC

value: TCR activated CD4+ T cells


title: Continuous_Hippocampus_H11

description:
H11
Continuous_rawcounts.csv, DNBSEQ-PE100


title: CD4_resting_ChIATAC_50k_DD_B1T2

description: ChIATAC

data_processing:
Library strategy: ChIATAC
ChIATAC and ChIA-PET data were processed using ChIA-PIPE pipeline (Lee et al., 2020) on hg38 reference genome. Interaction data or loops with significant (called with Chiasig method by Paulsen 2014; PMID: 25114054) PETs >= 3 and PET distance > 8 kb are used for downstream analyses. The peak intensity from MACS2 (Liu, 2014) output is normalized with “-SPMR” option (signal per million reads). Both ChIATAC and ChIA-PET data can be visualized on Juicebox as 2D contact maps by using Juicer software (Durand et al., 2016) version 1.6.2 to create .hic file format.
Raw fastq files from 2 libraries (THN0017 & THN0018) are merged then processed by ChIA-PET Utilities (CPU) (https://github.com/cheehongsg/CPU). CPU (options: stat -s -p -T 18 -t 16) removed the adaptors, and grouped the reads into three categories: PET reads, single tag reads and no-linker reads. Tags identified (>=16bp) and reads without linkers were mapped to hg38 using BWA alignment and mem according to the tag/read length. CPU further separated the mapping results into uniquely-mapped, multiply-mapped, and unmapped classes with the pairing consideration (options: pair -S -t 16) and removed duplicates generated by PCR amplification (dedup -g -t 16). Next, the non-redundant uniquely-mapped reads from 3 categories were merged and used for peak calling with MACS v2.1.1.20160309 (options: --keep-dup all --nomodel --extsize 250 -B --SPMR -g hs). CPU further clustered the non-redundant uniquely-mapped pair-end tags and grouped them as intra-chromosomal PET clusters (cis-interactions) and inter-chromosomal PET clusters (trans-interactions) (options: cluster -s 8000 -M -B 1000 -5 5, -20 -3 5, 480 -t 16 -O). The cis-interaction significance was assessed with ChiaSigScaled (https://github.com/cheehongsg/ChiaSigScaled ; options: -c 3 -t 16 -p -m 8000). Cis-interactions with member size >=3 and FDR < 0.05 were reported. The complete list trans interaction was reported here while additional filtering were applied (e.g. exclude singletons) for corresponding analyses in publication. (see details in publication).
Genome_build: hg38
Supplementary_files_format_and_content: Significant intrachromosomal interactions with frequency at least 3 PETs. Format: text file with 7-column (coordinates of 2 anchors at the first six columns, interaction frequency at the 7th).


title: Continuous_Hippocampus_H6

description:
H6
Continuous_rawcounts.csv, DNBSEQ-PE100

value: WT


title: Blood sample from COVID-19 patient P1 at day 7

value: day 7


title: d3_Gcn5 OE whole fly_1

description: Gcn5 overexpression flies


title: Continuous_Hippocampus_H5

description:
H5
Continuous_rawcounts.csv, DNBSEQ-PE100

value: continuous corticosterone


title: Mesothelioma_60211

type: genomic

city: Nagoya

first: Shinya

last: Toyokuni

state: Aichi

address: 65 Tsuruma-Cho, Showa-Ku

department: Pathology

country: Japan

institute: Nagoya University

hyb_protocol: The labeled DNA was hybridized with Agilent SurePrint G3 Mouse CGH 4x180k microarray at 67°C for 24 hours according to the manufacturer's protocol (Version 8.0).

scan_protocol: The slides were scanned in an Agilent DNA microarray scanner with SureScan High-Resolution Technology (G2565CA).

data_processing: The scanned images were analyzed with Agilent Feature Extraction Software 10.7 using default parameters (CGH_107_Sep09 protocol).

organism: Rattus norvegicus

source_name: normal kidney cortex

label_protocol: The extracted genomic DNA was labeled using Aagilent Sure tag DNA labeling kit according to the manufacturer's protocol (Version 8.0).

extract_protocol: Genomic DNA was extracted using DNeasy Blood & Tissue Kit (QIAGEN).

treatment_protocol: Male and female wild-type and BRCA1+/- rats at 5,6,7 weeks of age were injected intraperitoneally with 3,3,4 mg crocidolite or chrysotile. The rats were euthanized when they were dying.

value: Jcl:SD wild-type

value: Female

value: Chrysotile, 10mg


title: Mesothelioma_60203


title: Mesothelioma_70402

value: Male


title: Mesothelioma_70455

value: Untreated


title: Mesothelioma_62922


title: d3_gcn5-/- whole fly_4

description: Gcn5 loss-of-functon flies


title: Mesothelioma_62401

value: Jcl:SD BRCA1+/-


title: Mesothelioma_52522


title: d3_Gcn5 OE whole fly_4

description: Gcn5 overexpression flies


title: d3_gcn5-/- whole fly_3

description: Gcn5 loss-of-functon flies


title: CD4_resting_ChIATAC_50k_DD_B1T1

description: ChIATAC

value: Resting CD4+ T cells


title: d3_Gcn5 OE whole fly_3

description: Gcn5 overexpression flies


title: GM12878_CTCFChIAPET_B1T2

description: CTCF ChIAPET

growth_protocol: The GM12878 cells were cultured in RPMI 1640 (ThermoFisher; A10491), supplemented with 15% fetal bovine serum (ThermoFisher; 10082147). The cells were cultured at 37 °C, 5% CO2, and ambient oxygen levels as described by the Coriell Institute of Medical Research.

tag: cell line

value: anti-CTCF antibody (Abcam, ab70303)


title: Mesothelioma_52416

value: Crocidolite, 10mg


title: Continuous_Hippocampus_H4

description:
H4
Continuous_rawcounts.csv, DNBSEQ-PE100

source_name: hippocampus

value: hippocampus

value: vehicle


title: GM12878_CTCFChIAPET_B1T1

description: CTCF ChIAPET


title: Mesothelioma_60204


title: Continuous_Hippocampus_H3

description:
H3
Continuous_rawcounts.csv, DNBSEQ-PE100


title: d3_gcn5-/- whole fly_2

description: Gcn5 loss-of-functon flies


title: GM12878_RNAPIIChIAPET_B1T2

description: RNAPII ChIAPET

value: anti-RNAPII antibody (BioLegend, 664912)


title: Mesothelioma_60212


title: d3_gcn5-/- whole fly_1

description: Gcn5 loss-of-functon flies


title: Continuous_Hippocampus_H2

description:
H2
Continuous_rawcounts.csv, DNBSEQ-PE100

value: AS


title: d3_WT whole fly_3

description: WT flies


title: d3_WT whole fly_4

description: WT flies


title: Continuous_Hippocampus_H1

description:
H1
Continuous_rawcounts.csv, DNBSEQ-PE100


title: GM12878_RNAPIIChIAPET_B1T1

description: RNAPII ChIAPET


title: GM12878_ChIATAC_1k_DD_B1T2

description: ChIATAC

data_processing:
Library strategy: ChIATAC
ChIATAC and ChIA-PET data were processed using ChIA-PIPE pipeline (Lee et al., 2020) on hg38 reference genome. Interaction data or loops with significant (called with Chiasig method by Paulsen 2014; PMID: 25114054) PETs >= 3 and PET distance > 8 kb are used for downstream analyses. The peak intensity from MACS2 (Liu, 2014) output is normalized with “-SPMR” option (signal per million reads). Both ChIATAC and ChIA-PET data can be visualized on Juicebox as 2D contact maps by using Juicer software (Durand et al., 2016) version 1.6.2 to create .hic file format.
ChIATAC data was processed by ChIA-PET Utilities (CPU) (https://github.com/cheehongsg/CPU). CPU (options: stat -s -p -T 18 -t 16) removed the adaptors, and grouped the reads into three categories: PET reads, single tag reads and no-linker reads. Tags identified (>=16bp) and reads without linkers were mapped to hg38 using BWA alignment and mem according to the tag/read length. CPU further separated the mapping results into uniquely-mapped, multiply-mapped, and unmapped classes with the pairing consideration (options: pair -S -t 16) and removed duplicates generated by PCR amplification (dedup -g -t 16). CPU further clustered the non-redundant uniquely-mapped pair-end tags and grouped them as intra-chromosomal PET clusters (cis-interactions) and inter-chromosomal PET clusters (trans-interactions) (options: cluster -s 8000 -M -B 1000 -5 5, -20 -3 5, 480 -t 16 -O).
Genome_build: hg38
Supplementary_files_format_and_content: Intrachromosomal interaction with frequency at least 2 PETs. Format: text file with 7-column (coordinates of 2 anchors at the first six columns, interaction frequency at the 7th).


title: Hi-C_20h_rep2

first: Baibai

last: Gao

address: 1 Shizishan Street, Hongshan District

institute: National Key Laboratory of Crop Genetic Improvement

description: PM.allValidPairs.hic

data_processing:
Hi-C raw reads were processed using HiC-Pro pipeline.
Assembly: MH63
Supplementary files format and content: .hic files

organism: Oryza sativa Indica Group

source_name: MH63 mature leaf

growth_protocol: Rice [Oryza sativa L. ssp. indica cv. Minghui 63 (MH63)] seeds were sown on May 19, 2017 in a paddy field. At 20 days after germination, the seedlings were transplanted into a paddy field of Huazhong Agricultural University at Wuhan, China, and grown under normal agricultural conditions. In the paddy field, the plants were transplanted at a density of one plant per 15 × 30 cm area.

extract_protocol:
In total, 0.5 g of homogenized tissue powder produced via grinding fixed tissues with liquid nitrogen was used for one round of library prep. The extracted nuclei were resuspended with 150 µl 0.5% SDS and split equally into three tubes. The nuclei were incubated at 62 °C for 5 min, after which the SDS molecules were quenched by adding 145 µl water and 25µl 10% Triton X-100, and incubated at 37 °C for 15 min. The DNA in the nuclei in each tube was digested by adding 25µl 10x NEB buffer 3 (100 mM NaCl, 50 mM Tris-HCl, 10 mM MgCl2, 1 mM DTT, pH 7.9) and 50 U of MboI, and incubated at 37 °C overnight. On the next day, the MboI enzyme was inactivated at 62 °C for 20 min. Next, the cohesive ends were filled in by adding 1 µl of 10 mM dTTP, 1 µl of 10 mM dATP, 1 µl of 10 mM dGTP, 25µl of 0.4 mM biotin-14-dCTP, 14µl water and 4µl (40 U) Klenow, and incubated at 37 °C for 2 h. Subsequently, 663 µl water, 120 µl 10x blunt-end ligation buffer (300 mM Tris-HCl, 100 mM MgCl2, 100 mM DTT, 1 mM ATP, pH 7.8), 100 µl 10% Triton X-100 and 20 U T4 DNA ligase were added to start proximity ligation. The ligation reaction was placed at room temperature for 4 h. Next, the reaction mixture was centrifuged at 1000 g for 3 min, and the nuclei pellet was resuspended with 750 µl SDS buffer (50 mM Tris-HCl, 1% SDS, 10 mM EDTA, pH 8.0) and incubated with 200 µg proteinase K at 55 °C for 30 min.
The formaldehyde cross-link was reversed by adding 30 μl 5 M NaCl to the solution followed by incubation at 65 °C overnight. Amplification of library molecules was performed according to the standard BGI library preparation protocol. The final library was sequenced on a BGI MGISEQ-2000 instrument with 2 ×150 base pair (bp) reads.

treatment_protocol: Rice leaves were cross-linked with 1% formaldehyde for 20 min and quenched with 0.2 M glycine.

tag: cultivar

value: Minghui 63

value: mature leaf

tag: development stage

value: mature leaves harvested at 20:00 at floral induction stage


title: GM12878_ChIATAC_1k_DD_B1T1

description: ChIATAC

extract_protocol: ChIATAC libraries were performed by combining ChIAPET (Wang et al., 2021) and ATAC-seq protocol. Briefly, crosslinked cells are permeabilized, restriction enzyme digested, and ligated. Then the nuclei were subjected to in situ transposition, DNA were purified and amplified by PCR.


title: d3_WT whole fly_2

description: WT flies

value: WT


title: d3_WT whole fly_1

description: WT flies


title: Hi-C_20h_rep1

description: PM.allValidPairs.hic


title: Hi-C_8h_rep2

description: AM.allValidPairs.hic

value: mature leaves harvested at 8:00 at floral induction stage


title: GM12878_ChIATAC_5k_DD_B1T1

description: ChIATAC


title: ylf-3

city: kunming

first: Bin

last: Qi

state: 云南

address: Yunnan University, Kunming, China

department: School of Life Sciences

institute: yunnan university

data_processing:
1, filter connector, low quality: fastp parameters: -q 10-u 50-y-g-Y 10-e 20-l 100-b 150-B 150
2, Filter rRNA, mRNA is 0.1, use soap comparison, soap parameters are as follows: soap -a 1.fq -b 2.fq -D /share/nas2/database/sRNA_database/current/ncRNA_integer.fasta.index -o out.pe -2 out.se -m 100 -x 1000 -u unmap.fa
Assembly: Caenorhabditis_elegans.GCF_000002985.6_WBcel235.genome.fa
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Caenorhabditis elegans

source_name: Adult animal

extract_protocol:
Total RNA was extracted from the worms using TRIzol ® Reagent according the manufacturer’s instructions (Invitrogen Cat #15596018). RNA concentration and purity was measured using NanoDrop 2000(Thermo Fisher Scientific, Wilmington, DE). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
RNA libraries for RNA-seq were prepared using  VAHTS Universal V6 RNA-seg Library Prep Kit for Illumina® Kit following manufacturer's protocols.

value: Adult animal

value: bcf-1(ylf1) mutant


title: GM12878_ChIATAC_5k_DD_B1T2

description: ChIATAC


title: Mesothelioma_60201

value: Female

value: Chrysotile, 10mg


title: Mesothelioma_62404

value: Jcl:SD BRCA1+/-

value: Male

value: Untreated


title: GM12878_ChIATAC_25k_DD_B1T1

description: ChIATAC


title: Mesothelioma_52406


title: Hi-C_8h_rep1

description: AM.allValidPairs.hic


title: Mesothelioma_52413


title: Mesothelioma_52813

value: Crocidolite, 10mg


title: Prostate tumor_nTKO_Rep1

type: RNA

city: South Bend

first: Xin

middle: Lu

last: Lu

state: Indiana

address: 113 Galvin Life Science Center

department: Biological Department

institute: University of notre dame

description: mouse id 471842

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: The data were analyzed with Transcriptome Analysis Console, Summarization Method: RMA

label: biotin

source_name: Probasin PtenL/L/Smad4L/LPygo2L/L prostate tumor cells

label_protocol: Affymetrix protocol

extract_protocol: total RNA was extracted using RNeasy Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: All the procedure including tumor dissociation and tumor cell purification were performed on ice

value: Prostate


title: Prostate tumor_nTKO_Rep2

description: mouse id 485862

value: 16 week


title: Mesothelioma_52805


title: Input DNA

data_processing:
Library strategy: CUT&RUN
All the data analysis were performed in https://usegalaxy.org/
The reads were first mapped using the module Bowtie2 in galaxy.
The unaligned reads then were filtered using the module samtool_filter2 in galaxy.
Peaks were called using MACS2 module in galaxy with the following setting: input were used as control, not buld shiftting model, shift size 100bp, use the default for all the other parameters.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bigwig files were generated using CONVERTER_bedgraph_to_bigwig module in galaxy using the wig file generated in peak calling.

source_name: Mouse prostate Pten/Smad4 KO (PS) cell line

growth_protocol: DMEM:F12 supplemented with FBS (5%), penicillin/streptomycin (1%), EGF (10 ng/ml), adenine (20 μg/ml), HEPES (15 mM), insulin (5 μg/ml), hydrocortisone (0.32 μg/m) and ROCK inhibitor (10 μ M Y-27632).

extract_protocol:
The samples are prepared according to the instruction of CUT&RUN Assay Kit (CST #86652). The input samples were sonicated for 12min with Covaris S220 Ultrasonicator System to get the fragment size between 150-300bp.
Library were prepared according to the instruction of SimpleChIP® ChIP-seq DNA Library Prep Kit for Illumina® (CST #56795).

treatment_protocol: No treatment.

value: PS

value: Prostate tumor cell line established from pDKO tumor

value: untreated


title: ylf-1


title: N2-3

value: wild-type


title: GM12878_ChIATAC_25k_SD_B1T1

description: ChIATAC


title: ylf-2


title: Prostate tumor_nDKO_Rep2

description: mouse id 490760

source_name: Probasin PtenL/L/Smad4L/L prostate tumor cells


title: GM12878_ChIATAC_50k_DD_B1T2

description: ChIATAC

data_processing:
Library strategy: ChIATAC
ChIATAC and ChIA-PET data were processed using ChIA-PIPE pipeline (Lee et al., 2020) on hg38 reference genome. Interaction data or loops with significant (called with Chiasig method by Paulsen 2014; PMID: 25114054) PETs >= 3 and PET distance > 8 kb are used for downstream analyses. The peak intensity from MACS2 (Liu, 2014) output is normalized with “-SPMR” option (signal per million reads). Both ChIATAC and ChIA-PET data can be visualized on Juicebox as 2D contact maps by using Juicer software (Durand et al., 2016) version 1.6.2 to create .hic file format.
ChIATAC data was processed by ChIA-PET Utilities (CPU) (https://github.com/cheehongsg/CPU). CPU (options: stat -s -p -T 18 -t 16) removed the adaptors, and grouped the reads into three categories: PET reads, single tag reads and no-linker reads. Tags identified (>=16bp) and reads without linkers were mapped to hg38 using BWA alignment and mem according to the tag/read length. CPU further separated the mapping results into uniquely-mapped, multiply-mapped, and unmapped classes with the pairing consideration (options: pair -S -t 16) and removed duplicates generated by PCR amplification (dedup -g -t 16). Next, the non-redundant uniquely-mapped reads from 3 categories were merged and used for peak calling with MACS v2.1.1.20160309 (options: --keep-dup all --nomodel --extsize 250 -B --SPMR -g hs). CPU further clustered the non-redundant uniquely-mapped pair-end tags and grouped them as intra-chromosomal PET clusters (cis-interactions) and inter-chromosomal PET clusters (trans-interactions) (options: cluster -s 8000 -M -B 1000 -5 5, -20 -3 5, 480 -t 16 -O). The cis-interaction significance was assessed with ChiaSigScaled (https://github.com/cheehongsg/ChiaSigScaled ; options: -c 3 -t 16 -p -m 8000). Cis-interactions with member size >=3 and FDR < 0.05 were reported. The complete list trans interaction was reported here while additional filtering were applied (e.g. exclude singletons) for corresponding analyses in publication. (see details in publication).
Genome_build: hg38
Supplementary_files_format_and_content: Significant intrachromosomal interactions with frequency at least 3 PETs. Format: text file with 7-column (coordinates of 2 anchors at the first six columns, interaction frequency at the 7th).


title: GM12878_ChIATAC_50k_DD_B1T1

description: ChIATAC


title: GM12878_ChIATAC_50k_SD_B1T2

description: ChIATAC


title: p53


title: N2-1


title: Prostate tumor_nDKO_Rep3

description: mouse id 490761


title: H322 with EGF

city: kashiwa

first: Eri

last: Sugiyama

address: 6-5-1 kashiwanoha

department: Division of Cancer Immunology

institute: National Cancer Center

description: Gene expression data from H322 with EGF

hyb_protocol: Following fragmentation, biotinylated cRNA were hybridized for 17 hr on Clariom S Array, human.

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3000 7G System (cartridge) Gene Titan Multi-channel.

data_processing: The data were analyzed using Affymetrix GeneChip Command Consle Software and Affymetrix Expression Console.

source_name: non-small cell lung cancer

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA.

growth_protocol: Two EGFR-mutated cell lines (PC-9 and HCC827) and an EGFR wild type cell line (H322) were cultured with mediun+TNFa and were treated with 0.01uM erlotinib and 100ug/ml EGF for 6 hours, respectively.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

value: EGF


title: Pygo2

value: Pygo2(3I4) (gift from Dr. Kenneth R. Kao lab)


title: GM12878_ChIATAC_50k_SD_B1T1

description: ChIATAC


title: H3K4-Me3


title: skin, golden, rep3 miRNA

status: Public on Dec 22 2022

city: Wuxi

first: Mingkun

last: Luo

state: Jiangsu

address: East Shanshui Road 9

department: Wuxi Fisheries College

institute: Nanjing Agricultural University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: Carassius auratus (goldfish)
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Carassius auratus

source_name: skin

extract_protocol:
RNA was harvested using TRIzol (Invitrogen, UK)., and genomic DNA was removed using Dnase I (New England Biolabs), 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: skin

tag: group

value: golden

value: female


title: HCC827 with erlotinib

description: Gene expression data from HCC827 with erlotinib

value: EGFR mutant

value: erlotinib


title: skin, golden, rep2 miRNA


title: skin, greenish grey, rep2 miRNA

value: greenish grey


title: skin, greenish grey, rep3 miRNA


title: skin, greenish grey, rep1 miRNA


title: HCC827 with control

description: Gene expression data from HCC827 with control

value: control


title: H322 with control

description: Gene expression data from H322 with control


title: WT-2 K9 ChIP Rep1

city: Melbourne

first: Attila

last: Horvath

state: Victoria

address: 305 Grattan St

country: Australia

institute: Peter MacCallum Cancer Centre

description: H3K9me2 ChIP DNA was directly used for library preparation

data_processing:
Paired-end illumina reads were subjected to a thorough Quality Control (QC) and the FastQC 0.11.8 was used to generate QC reports. Low complexity regions were filtered out with prinseq-lite.pl from PRINSEQ-lite 0.20.4 (maximum dust was set to 3)  and the remaining sequences were trimmed using Trimmomatic (SLIDINGWINDOW: 4 nt; phred quality cut-off: 15, MINLEN=36).
QC filtered were aligned with BWA MEM -0.7.17. Aligned bam files were sorted and indexed using samtools 1.3.1.
Potential PCR duplications were removed with samtools using the rmdup option
Genome_build: ASM294v2
Bigwig tracks were generated using bamCoverage to the pombe genome (ASM294v2) with the parameter “—binSize 1”. Bigwig tracks were normalised by the sum of the raw signals of chromosome I and II multiplied by 100 million. Further, bigwig tracks of a dusty filtering of 4 was used for further analysis and screenshots.

organism: Schizosaccharomyces pombe

source_name: S. pombe grown in YEA liquid culture to an OD600 of 0.5-0.8

growth_protocol: S. pombe strains used for the study were grown in YEA liquid culture to an OD of 0.8 - 2.2 according to experiment performed.

extract_protocol:
ChIP DNA: The collected lysate was used for chromatin shearing to a median size of ~300bp by sonication using Covaris S2. The samples were then incubated overnight  with H3K9me2 antibody (mAbcam 1220) followed by an incubation with an appropriate bead slurry (nProtein A Sepharose, GE Healthcare, 5280-01). Post washing , the bound protein and chromatin fractions were eluted using elution buffer. The samples were then decrosslinked and the DNA was purified using Phenol: Chloroform: Isomyl alcohol method following RNase treatment.
ChIP seq: The purified DNA pellet was used for library preparation using NEBNext Ultra II DNA library prep kit for Illumina (NEB, E7645) following manufacturer instructions.

treatment_protocol: Samples for ChIP seq. was treated using formaldehyde solution to a final concentration of 1% at room temperature (RT) for 15 min and quenched by addition of glycine to a final concentration of 150 mM for 5 min at RT

tag: strain number

value: MatMsmt0, leu1-32, ura4-D18, ade6-216


title: WT-2 K9 ChIP Rep2


title: Prostate tumor_nDKO_Rep1

description: mouse id 485865

tag: strain


title: red1288-345DEL total Rep2

data_processing:
Paired-end illumina reads were aligned with hisat 2.1.0,allowing introns with a maximum length of 2,000 nt (‘--max.intronlen 2000’).
Aligned bam files were then sorted and indexed using samtools 1.3.1
Strand-specific bigwig tracks were generated using bamCoverage to the pombe genome (ASM294v2) with the parameter ‘—binSize 1’.
Genome_build: ASM294v2
Bigwig tracks were generated after normalisation by the sum of the raw signals of chromosome I and II multiplied by 100 million.

source_name: S. pombe grown in YEA liquid culture to an OD600 of 0.8

extract_protocol:
poly(A)+ and total RNA: RNA was isolated using TriReagent (Sigma-Aldrich, T9424) and precipitated using 2-propanol (Sigma-Aldrich). 10ug of this isolated RNA was used for DNase treatment using NEB DNase 1 (M0303), and purified using the RNA Clean and Concentrator Kit (Zymo Research, R1015/R1017).
Total RNA seq.: 100ng of total RNA samples were directly proceeded for cDNA library preparation using NEBNext Ultra II directional RNA library kit (NEB, E7760) following the manufacturers library preparation protocol.


title: red1288-345DEL polyA Rep1

description: OligodT purified poly(A) selected RNA was used for cDNA library preparation

extract_protocol:
poly(A)+ and total RNA: RNA was isolated using TriReagent (Sigma-Aldrich, T9424) and precipitated using 2-propanol (Sigma-Aldrich). 10ug of this isolated RNA was used for DNase treatment using NEB DNase 1 (M0303), and purified using the RNA Clean and Concentrator Kit (Zymo Research, R1015/R1017).
poly(A)+RNA seq.:1 ug of RNA samples were OligodT purified (NEB, E7490) and the recovered poly(A) selected RNA was used for cDNA library preparation using NEBNext Ultra II directional RNA library kit (NEB, E7760) following manufacturers library preparation protocol.


title: red1288-345 DELpolyA Rep2

description:
OligodT purified poly(A) selected RNA was used for cDNA library preparation
Processed data for Rep2 was combined with Rep1 and is available on GSM6243403.


title: red1KO total Rep2

description: total RNA samples were directly proceeded for cDNA library preparation

value: MatMsmt0, leu1-32, ura4-D18, ade6-M210, red1KO::kanMX6


title: N2-2

value: Adult animal


title: PC-9 with erlotinib

description: Gene expression data from PC-9 with erlotinib


title: red1KO polyA Rep1


title: red1KO total Rep1


title: PC-9 with control

description: Gene expression data from PC-9 with control


title: red1288-345DEL total Rep1


title: red1W298A/F305A polyA Rep2

description:
OligodT purified poly(A) selected RNA was used for cDNA library preparation
Processed data for Rep2 was combined with Rep1 and is available on GSM6243394.


title: red1W298A/F305A total Rep1


title: red1W298A/F305A polyA Rep1


title: red1W298A/F305A total Rep2


title: WT total Rep1

value: MatMsmt0, leu1-32, ura4-D18, ade6-M210, red1::natNT2 (+3'UTR)


title: WT total Rep2


title: WT polyA Rep2

description:
OligodT purified poly(A) selected RNA was used for cDNA library preparation
Processed data for Rep2 was combined with Rep1 and is available on GSM6243391.


title: skin, golden, rep1 miRNA

tag: Sex


title: WT polyA Rep1


title: WT K9 ChIP Rep1


title: red1W298A/F305A K9 ChIP Rep1


title: WT K9 ChIP Rep2


title: red1W298A/F305A K9 ChIP Rep2


title: red1KO K9 ChIP Rep2


title: red1KO K9 ChIP Rep1


title: WT-3 K9 ChIP Rep1

value: MatMsmt0, leu1-32, ura4 DS/E, ade6-210, his2, Otr1R::Ura4 (SphI)


title: red1288-345DEL K9 ChIP Rep2


title: F3

city: Palo Alto

first: Goonho

last: Park

address: 3801 Miranda Avenue

institute: Stanford University

description:
F-3
RNA seq_Thapsigargin FPKM.xlsx

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2) and clean reads were mapped using HISAT2 (v2.0.4) to  the reference genome (Homo_sapiens_GCF_000001405.38_GRCh38.p12 reference assembly). The expression levels of the genes were calculated by RSEM (v1.2.12)
Differential expression analysis and statistical significance calculations between condition and experiment groups were assessed using R based software, DESeq2 (v 1.4.5). The FDR q-value for the DESeq analysis is 0.1.
Assembly: GRCh38.p12
Supplementary files format and content: each excel file include 5 replicate FPKM values for each experiment group

source_name: Biosensor cells, Thapsigargin 0.3uM

growth_protocol: Biosensor cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics 1% P/S in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA-Seq (Quantification) uses a new generation of high-throughput sequencing technology to study the gene expression pattern of eukaryotic cells and provide accurate digital expression profile detection by sequencing and comparing transcripts.   Transcriptome research is the basis and starting point of gene function and structure research. Through the new generation of high-throughput sequencing, almost all transcripts of a specific tissue or organ of a species can be obtained comprehensively and quickly
Single-stranded circle DNA molecules are replicated via rolling cycle amplification, and a DNA nanoball (DNB) which contain multiple copies of DNA is generated. Sufficient quality DNBs are then loaded into patterned nanoarrays using high-intensity DNA nanochip technique and sequenced through combinatorial Probe-Anchor Synthesis (cPAS).

treatment_protocol: Biosensor cells were transfected by brain lysate extraction of WT and PS19 and treated with thapsigragin.

value: Biosensor cell

value: HEK

value: human embryo kiney

value: WT endogeneously expressing TauRD(P301S)-YFP

value: Thapsigargin


title: C5

description:
C-5
RNA seq_PS19 FPKM.xlsx

source_name: Biosensor cells, PS19 brain

value: PS19 brain lysate


title: F2

description:
F-2
RNA seq_Thapsigargin FPKM.xlsx


title: C2

description:
C-2
RNA seq_PS19 FPKM.xlsx


title: C1

description:
C-1
RNA seq_PS19 FPKM.xlsx


title: C4

description:
C-4
RNA seq_PS19 FPKM.xlsx


title: C3

description:
C-3
RNA seq_PS19 FPKM.xlsx


title: B2

description:
B-2
RNA seq_Control FPKM.xlsx

source_name: Biosensor cells, Control brain

value: Control brain lysate


title: B1

description:
B-1
RNA seq_Control FPKM.xlsx


title: B3

description:
B-3
RNA seq_Control FPKM.xlsx


title: B5

description:
B-5
RNA seq_Control FPKM.xlsx


title: placenta, FET02

city: China

first: Yuan

last: Zhu

address: Hankou Road 22, Nanjing 210008

institute: Nanjing University medical school

data_processing:
Use the BGISEQ-500 sequencing platform for high-throughput sequencing procedures of mRNA and lncRNA.
Use SOAPnuke (v1.5.2) to filter sequencing data
Use HISAT2 (v2.0.4) to map the filtered high-quality reads with the reference gene set database established by BGI
Use Bowtie2 (v2.2.5) for lncRNA and mRNA identification
Use RSEM (v1.2.12) to standardize the expression of lncRNA and mRNA with fragments per kilobase per million mapped read fragments (Fragments Per Kilobase per Million, FPKM).
Supplementary_files_format_and_content: Excel file includes FPKM values for each Sample

source_name: mouse placenta

extract_protocol:
The total RNA of mouse placenta tissue was collected according to the method described in the instructions of Trizol reagent (Invitrogen, USA), and identified and quantified using Agilent 2100 bioanalyzer (ThermoFisher Science, USA). After a qualified specific RNA library was established, it was sequenced on the computer. SOAPnuke (v1.5.2) was used to filter the sequencing data, HISAT2 (v2.0.4) was used to map the filtered high-quality reads with the reference gene set database established by BGI, and Bowtie2 (v2.2.5) was used for lncRNA and mRNA identification. Then RSEM (v1.2.12) was used to standardize the expression of lncRNA and mRNA with fragments per kilobase per million (Fragments Per Kilobase per Million, FPKM).
RNA libraries were prepared for sequencing using standard lllumina protoclos

value: ICR

value: placenta

value: frozen embryo transfer


title: placenta, freshET01

value: fresh embryo transfer


title: placenta, FET01


title: B4

description:
B-4
RNA seq_Control FPKM.xlsx


title: red1288-345DEL K9 ChIP Rep1


title: F4

description:
F-4
RNA seq_Thapsigargin FPKM.xlsx


title: F5

description:
F-5
RNA seq_Thapsigargin FPKM.xlsx


title: F1

description:
F-1
RNA seq_Thapsigargin FPKM.xlsx


title: WT-3 K9 ChIP Rep2


title: infected, cerebrum, male

city: Beijing

first: Qiang

last: Ma

address: Datun Road, #15

institute: Institute of Biophysics, Chinese Academy of Sciences

description: infected animal #2, male

data_processing:
Illumina Casava1.8 software used for basecalling
Reads were aligned to macaca mulatta pre-mRNA reference genome by Cell Ranger count (v3.1.0).
Alignment results of macaque data were aggragated by Cell Ranger aggr (v3.1.0).
Aggragated data of macaque were read into scanpy.
Assembly: macaca mulatta (release 95) pre-mRNA
Supplementary files format and content: The file Macaca_global_integration.h5ad is formatted by h5ad (created by scanpy), contains all samples in this study.

organism: Macaca mulatta

source_name: cerebrum

extract_protocol:
Tissue blocks that stored at -80 refrigerators were homogenized and performed density gradient centrifugation to cleanup, single-nucleus suspension is the final product for 10X Genomics system.
Library construction was carried out in according to manufacturer's protocol.

value: cerebrum

value: male

tag: animal

value: infected animal #2


title: placenta, freshET02


title: infected, liver, male

description: infected animal #2, male

source_name: liver

value: liver


title: infected, lung, male, rep1

description: infected animal #2, male

source_name: lung

value: lung


title: infected, cerebrum, female

description: infected animal #1, female

value: female

value: infected animal #1


title: infected, lung, male, rep2

description: infected animal #2, male


title: infected, kidney, female

description: infected animal #1, female

source_name: kidney

value: kidney


title: infected, liver, female

description: infected animal #1, female


title: infected, lung, female, rep2

description: infected animal #1, female


title: healthy, cerebrum, ctrl2

description: healthy animal #2, male

value: healthy control

value: healthy animal #2


title: infected, lung, female, rep1

description: infected animal #1, female


title: healthy, liver, ctrl1

description: healthy animal #1, male

value: healthy animal #1


title: healthy, lung, ctrl1

description: healthy animal #1, male


title: healthy, cerebrum, ctrl1

description: healthy animal #1, male


title: healthy, kidney, ctrl1

description: healthy animal #1, male


title: IL-10+TGFb treated macrophages replicate 2

city: Hannover

first: Maximilian

last: Schinke

address: Nikolai-Fuchs-Str. 1

institute: Fraunhofer ITEM

hyb_protocol: 500 ng of each fluorescently labeled cRNA population were used for cRNA fragmentation, hybridization, and washing steps carried out as recommended in the ‘One-Color Microarray-Based Gene Expression Analysis Protocol V5.7’.

scan_protocol: Slides were scanned on the Agilent Micro Array Scanner G2565CA (pixel resolution 3 µm, bit depth 20).

data_processing: Data extraction was performed with the ‘Feature Extraction Software V10.7.3.1’ using the extraction protocol file ‘GE1_107_Sep09.xml’, except that ‘Multiplicative detrending’ algorithm was inactivated.

label: Alexa Fluor 555

label_protocol: 30 ng of total RNA was used to prepare aminoallyl-UTP-modified (aaUTP) cRNA (Life Technologies) as directed by the company. The labeling of aaUTP-cRNA was performed by use of Alexa Fluor 555 Reactive Dye ( LifeTechnologies).

growth_protocol: Differentiation of human iPSC into macrophages was performed as described in Schinke et al. Polarization of human iPSC-derived macrophages directs their immunological response to secondary pro-inflammatory stimuli. Journal of Immunology and Regenerative Medicine. 2022; 17:100061

extract_protocol: Cells were washed with PBS. Subsequently, RNA lysis buffer was applied to collect cells and RNA isolation was  performed with RNAeasy micro Kit (Qiagen, Hilden, Germany) according to manufacturer’s instructions

treatment_protocol: Terminally differentiated iPSC-Mac were washed and starved overnight in complete X–VIVO medium (X–VIVO15 medium containing 1% P/S and 1% LG). The next day, medium was changed to complete X–VIVO medium supplemented with either 25 ng/mL hIFNγ  for M1/M(IFNγ) polarization, 10 ng/mL hIL-4 for M2a/M(IL-4) polarization or 10 ng/mL hIL-10 and 10 ng/mL hTGFβ for M2c/M(IL10/TGFβ) polarization. Cells were cultured for 24h.

tag: agent


title: IL-4 treated macrophages replicate 2


title: untreated macrophages replicate 1

value: untreated


title: IFNg treated macrophages replicate 2

value: IFNg


title: IL-10+TGFb treated macrophages replicate 1


title: untreated macrophages replicate 2


title: IL-4 treated macrophages replicate 1


title: H9c2 cells day 14 with RA, replicate 1

city: Monterrey

first: Victor

last: Trevino

state: Nuevo León

address: Ave. Eugenio Garza Sada 2501 Sur

department: Investigación e Innovación

country: Mexico

institute: Tecnológico de Monterrey

data_processing:
FASTQ files uploaded to GALAXY platform
QC, Trimming in GALAXY
Mapped to Rat genome in GALAXY using HiSat2
Reads counted by FeatureCounts tool in GALAXY
Transcripts not showing reads in any sample were removed.
Assembly: Rattus norvegicus Rnor_6.0.98

source_name: Heart; Myocardium

growth_protocol: The H9c2 cell line obtained from ATCC (Manassas, VA, USA) was cultured in Dulbecco´s modified Eagle´s medium (DMEM) (SIGMA), supplemented with 3.7 g/L sodium bicarbonate (SIGMA S5761), 10% fetal bovine serum (FBS), 100 U/ml penicillin, and 100 μg/ml streptomycin in 75 cm2 tissue culture flasks at 37°C in a humidified atmosphere of 5% CO2. Cells were fed every 2–3 days and subcultured when reaching 70–80% confluence to prevent the loss of the differentiation potential. Cell differentiation was initiated by H9c2 cells at a density of 35,000 cells/ml in 25 cm2 tissue culture flasks for 24 hours for cell attachment. Then, decreasing FBS from 10% to 1% in the media, followed by Retinoic Acid (RA) supplementation [1, 5].

extract_protocol:
The collection of total RNA extracts was performed following the TRIzol™ reagent protocol instructions (Invitrogen). Add 0.3–0.4 mL of TRIzol™ reagent per 1 × 105-107 cells directly to the culture dish to lyse the cells. The suspension was homogenized pipetting the lysate up and down several times and incubating for 5 min at room temperature to permit the complete dissociation of the nucleoproteins complex. After this time, 0.2 mL of chloroform was added per 1 mL of TRIzol™ reagent used for lysis and incubated for 3 min on ice. Samples were centrifuged for 15 min at 12,000 x g at 4°C, and the aqueous phase that contained the RNA was transferred to a new tube. For the RNA precipitation, we added 0.5 mL of isopropanol to the aqueous phase per 1 mL of TRIzol™ reagent used for lysis, and the sample was incubated for 10 min on ice. The samples were then centrifuged for 10 min at 12,000 x g at 4°C. The supernatant was discarded, and the pellet was resuspended in 1 mL of 75% ethanol per 1 mL of TRIzol™ reagent used for lysis. The sample was vortexed for 5 sec and immediately centrifuged for 5 min at 7500 x g at 4°C; the supernatant was discarded, and the RNA pellet was dried for 10 min on ice. Pellet was resuspended in 50 µL of RNase-free water. Total RNA was quantified using a UV analysis Synergy™ HT Multi-Detection Microplate Reader (Biotek Instruments). To examine RNA integrity and DNA contamination, 0.5 μg of RNA was electrophoretically separated in an agarose gel. Samples were then saved at -80°C.
TruSeq Stranded mRNA Sample Preparation Kit (Illumina, San Diego, CA, USA) following the manufacturer’s instructions.

treatment_protocol: The RA (1 μM) addition was performed daily in dark conditions for 14 days. All-trans-RA was prepared in DMSO and stored at -20°C in dark conditions to avoid degradation [1]. For Ca2+ signaling experiments, cells were plated in 6-well plates with coverslips at a density of 15,000 cells/ 400 µL. Cells were incubated at 37°C for 30 minutes, afterward added 600 µL of DMEM supplemented with 10 % FBS. After 24 hours, FBS was decreased to 1 % and treated with 1 μM daily for 7 or 14 days, as previously stated.

value: Heart; Myocardium

value: myoblast

value: WT

value: retinoc acid (RA)

value: Day 14

tag: replicate


title: infected, kidney, male

description: infected animal #2, male

tag: infection

value: male


title: H9c2 cells day 7 with RA, replicate 3

tag: tissue

tag: time

value: Day 7


title: H9c2 cells day 14 with RA, replicate 3

tag: genotype

tag: treatment


title: H9c2 cells day 14 without RA, replicate 2

tag: cell type

value: culture time


title: H9c2 cells day 14 without RA, replicate 3


title: H9c2 cells day 7 with RA, replicate 1


title: IFNg treated macrophages replicate 1


title: H9c2 cells day 14 with RA, replicate 2


title: H9c2 cells day 7 without RA, replicate 2


title: H9c2 cells day 7 with RA, replicate 2


title: H9c2 cells day 7 without RA, replicate 3


title: H9c2 cells day 0 without RA, replicate 2

value: control

value: Day 0


title: H9c2 cells day 0 without RA, replicate 3


title: H9c2 cells day 7 without RA, replicate 1


title: H9c2 cells day 14 without RA, replicate 1