title: SUNE-1 cells, shLINC01770-rep3

city: GuangZhou

first: xu

last: qingqing

state: GuangDong

address: 651 Dongfeng East Road, Yuexiu District

institute: State Key Laboratory of Oncology in South China

data_processing:
The image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition. Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based onthe clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5). We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
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. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the edgeR R package . edgeR provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . padj<=0.05 and |log2(foldchange)| >= 1 were set as the threshold for significantly differential expression.
Assembly: GRCh38.91
Supplementary files format and content: Gene_Expression.txt - this table include raw gene counts and FPKM for every gene and every sample

source_name: nasopharyngeal carcinoma

extract_protocol:
total RNA was harvested using Trizol reagent
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained.After the construction of the library, the library was initially quantified by Qubit2.0 Fluorometer, then diluted to 1.5ng/ul, and the insert size of the library is detected by Agilent 2100 bioanalyzer.

value: nasopharyngeal carcinoma

value: LINC01770 shRNA


title: NNCSD-031B.a

status: Public on Jul 01 2024

type: RNA

city: Herlev

first: Lauge

last: Kellermann

state: --- Select ---

address: Borgmester Ib Juuls Vej 1

department: Department of Gastroenterology

country: Denmark

institute: Herlev Hospital

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C. GeneChips were washed and stained on the Gene Titan platform (Affymetrix)

scan_protocol: The chips were scanned on the GeneTitan platform (Affymetrix).

data_processing: The Affymetrix raw data (.cel files) were normalized using the robust multichip average (RMA)  algorithm in R environment. Quality assurance was performed using the Bioconductor package  arrayQualityMetrics in R Probe set annotation files were obtained form from Affymetrix NetAffx website (NA35, available online: https: //www.affymetrix.com/analysis/index.affx). For four of the UC patients only one biopsy was analyzed due to quality issues, so in total 152 biopsies were analyzed: tow from each of the 19 healthy controls, tow from 55 UC patients and one biopsy from 4 UC patients, for at total of 152 .cel-files.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Sigmoid colonic tissue

label_protocol: 3'-IVT kit from Affymetrix according to standard protocol. Biotinylated cRNA were prepared from 100 ug total RNA

extract_protocol: RNA  was extracted by mechanical homogenization using a rotor-stator. RNA purification was performed by column purification (Nucleospin miRNA, Macherey–Nagel, Düren, Germany, ref: 740971.250) including DNAse I treatment according to the recommendations of the manufacturer. The RNA concentration was quantified using a NanoDrop spectrometer (Thermo Fisher Scientific, Wilmington, DE, USA). For samples with <10 ng/µL the Ribogreen® RNA assay Kit (Life Technologies, Carlsbad, CA, USA) was used. The Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) was used to assess RNA quality. Samples with a resulting RNA Integrity Number (RIN) value below 6 were excluded.

treatment_protocol: Colonic biopsies were kept in RNAlater (Ambion, Austin, TX, USA) 24–48 h before storage at -80C.

tag: tissue

value: Sigmoid colonic tissue

tag: Sex

value: M

tag: uc or healthy control

value: UC - Active disease

tag: mayoscore

tag: diagnose duration (years)


title: OX_nacl_2

type: SRA

city: Hyeonpung-eup

first: Hyunsu

last: Park

state: Dalseong-gun, Daegu

address: E4-620, 333, Techno jungang-daero

department: New biology

country: South Korea

institute: DGIST

description:
normalized_in_TMM_ERF34.txt
Sample 35

library_source: transcriptomic

data_processing:
Alignment of the resulting reads to the Arabidopsis thaliana genome (TAIR10; Lamesch et al., 2012) was performed using TopHat (Trapnell et al., 2009) with the default option
the abundance was calculated as the fragments per kilobase per million mapped reads (FPKMs) for each transcript using Cufflinks
TMM normalization
Genome_build: Arabidopsis_thaliana.TAIR10.31
Supplementary_files_format_and_content: Tab-delimited text file including TMM values for the individual samples

organism: Arabidopsis thaliana

source_name: Shoot rossette leaf

growth_protocol: Arabidopsis thaliana plants (Col ecotype) were grown in a growth room at 22°C under a 16-h light/8-h dark photoperiod. To generate Arabidopsis transgenic plants that overexpress ERF34, the coding sequence (CDS) of ERF34 was amplified by RT-PCR, subcloned into the pCR-CCD-F vector (Kim et al., 2013), and then recombined into the pCsVMV Gateway binary vector with the CsVMV promoter and N-terminal GFP tag by LR recombination (Invitrogen, USA).

extract_protocol:
mRNA-seq experiments were performed in three independent biological replicates of the Col and ERF34-OX#1 plants. RNA was isolated using WelPrepTM (WelGENE, Korea). Total RNA integrity was checked using an Agilent Technologies 2100 Bioanalyzer with an RNA Integrity Number (RIN) value greater than 7.8.
Poly(A) mRNA was isolated from the RNA (2 µg) and fragmented using Illumina Truseq™ Stranded mRNA LT Sample Prep Kit with poly-T oligo-attached magnetic beads. After the cDNA synthesis from the RNA fragments by using Superscript II reverse transcriptase (Life Technologies), the strand-specific cDNA libraries were generated with adaptor-ligation and sequenced by Illumina HiSeq 2500 system, according to the Illumina Directional RNA-Seq protocol.

treatment_protocol: The detached leaves at 16 DAE were floated on 3 mM MES (pH5.8) containing 100 mM NaCl and placed on 22°C under a 16-h light/8-h dark photoperiod for 1 day.

tag: tissue type

value: third and fourth rosette leaves

tag: cell type

value: Shoot tissue cell

tag: salt stress

value: 1Day after treat Nacl 100mM

tag: genotype/variation

value: Overexpression line of ERF34, Col-0 background Rep2


title: OX_nacl_1

description:
normalized_in_TMM_ERF34.txt
Sample 34

value: Overexpression line of ERF34, Col-0 background Rep1


title: Backfat, control diet, 4

city: Madrid

first: Patricia

last: Palma

address: Carretera de la Coruña, km 7,5

country: Spain

institute: INIA-CSIC

data_processing:
Quality analyses were performed on the reads using FastQC software (Babraham Bioinformatics, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Reads were then mapped against the pig reference genome (Sscrofa11.1) using HISAT2. No additional trimming or filtering of reads was deemed necessary.
Reads counts were performed using HTSeq-count
Assembly: Sscrofa11.1
Supplementary files format and content: tab-delimited text file includes counts per each sample

organism: Sus scrofa

source_name: Backfat

extract_protocol:
RNA was extracted using the RiboPureTM of High Quality total RNA kit (Ambion)
Library preparation and sequencing paired-end libraries were prepared using TruSeq SBS Kit v3-(Illumina)

value: Backfat

tag: genotype

value: Iberian

tag: treatment

value: control diet


title: SUNE-1 cells, shLINC01770-rep2

country: China

tag: cell line


title: Backfat, WCOC diet, 1

value: WCOC diet


title: SUNE-1 cells, NC-rep3

value: control


title: tumor, liver meta, pat001, rep1

city: Seoul

first: Kitae

last: Kim

institute: Seoul National University

data_processing:
The raw paired-end sequencing data were aligned to the human reference genome (hg19) using the Spliced Transcripts Alignment to a Reference (STAR) aligner
RNA sequencing analysis was performed using the bcbio-nextgen pipeline
Gene expression quantification was carried out using the Salmon by tximport
Assembly: hg19
Supplementary files format and content: txt file for gene expression quantification

source_name: Gastric Cancer

extract_protocol:
Total RNA was extracted from the FFPE tissue samples using a commercially available extraction kit (RNeasy FFPE kit, Qiagen, Germany)
TruSeq Stranded Total RNA Library Prep Kit, IlluminaTM, CA, USA

value: Gastric Cancer


title: OX_3

description:
normalized_in_TMM_ERF34.txt
Sample 33

value: Mock

value: Overexpression line of ERF34, Col-0 background Rep3


title: Backfat, control diet, 3


title: NNCSD-026.b

value: UC - Inactive disease


title: SUNE-1 cells, shLINC01770-rep1

value: nasopharyngeal carcinoma

value: LINC01770 shRNA


title: SUNE-1 cells, NC-rep2


title: NNCSD-026.a

value: Sigmoid colonic tissue

value: M


title: OX_1

description:
normalized_in_TMM_ERF34.txt
Sample 31

value: third and fourth rosette leaves

value: Shoot tissue cell


title: OX_nacl_3

description:
normalized_in_TMM_ERF34.txt
Sample 36

value: 1Day after treat Nacl 100mM


title: OX_2

description:
normalized_in_TMM_ERF34.txt
Sample 32

value: Overexpression line of ERF34, Col-0 background Rep2


title: Backfat, control diet, 1

value: Backfat


title: Col_nacl_3

description:
normalized_in_TMM_ERF34.txt
Sample 12

value: wildtype, Columbia-0 background Rep3


title: NNCSD-025.b

value: UC - Active disease


title: Backfat, control diet, 2

value: Iberian

value: control diet


title: SUNE-1 cells, NC-rep1

value: control


title: Col_nacl_2

description:
normalized_in_TMM_ERF34.txt
Sample 11

value: wildtype, Columbia-0 background Rep2


title: WTcal_3

city: Storrs

first: Rahul

middle: N

last: Kanadia

state: CT

address: 75 N. Eagleville Road

department: Physiology and Neurobiology

country: USA

institute: University of Connecticut

data_processing:
Reads were aligned to the GRCz11 Ensembl v99 genome assembly using Hisat2
Retention and alternative splicing analysis was then performed as described before (Baumgartner et al., 2018; Olthof et al., 2019). Briefly, unspliced reads that aligned to exon-intron boundaries of introns of interest were quantified using BEDTools. These counts were utilized to calculate a mis-splicing index (MSI), by dividing them to the total number of spliced reads aligning to the annotated exon-exon boundary. Only introns that passed the filtering criteria (> 4 exon-intron boundary reads, ≥1 read aligning to both the 5′ and 3′ splice site, > 95% intron coverage)  in at least one replicate were considered retained.
Assembly: GRCz11 Ens. V.99
Supplementary files format and content: Tab-delimited txt file with MSI values

molecule: polyA RNA

organism: Danio rerio

source_name: larvae

extract_protocol:
Total RNA was extracted from pools of genotyped 72-hour post fertilization (hpf) larvae using TRIzol
Poly(A)-enriched RNA was used to generate cDNA libraries and sequenced using the Illumina HiSeq by the Australian Genomics Research Facility (AGRF), yielding 100bp single end reads

value: larvae

value: WT

tag: developmental stage

value: 72 hpf larvae


title: Sample_24

city: Boston

first: Hui

last: Pan

address: 1 Joslin Place

department: Bioinformatics and Biostatistics Core

institute: Joslin Diabetes Center

data_processing:
The reads were trimmed for adapters and filtered by sequencing Phred quality (>= Q15) using fastp.
The gene count table was generated by aligning reads to the human transcriptome (Ensembl version 98) using kallisto and converting transcript counts to gene counts using tximport.
Supplementary files format and content: CSV

extract_protocol:
EBs were then harvested, washed with DPBS, and lysed in TRIzol for RNA isolation using RNeasy Kit (Qiagen) according to the manufacturer's instructions.
RNA libraries were prepared using TruSeq Stranded Total Library Prep (Illumina)

value: hESC


title: Col_nacl_1

description:
normalized_in_TMM_ERF34.txt
Sample 10

value: wildtype, Columbia-0 background Rep1


title: Sample_22


title: NNCSD-024.b

value: Sigmoid colonic tissue

value: M


title: NNCSD-030.a

value: F


title: WTcal_2


title: NNCSD-025.a


title: WTcal_1


title: cal_3


title: NNCSD-024.a


title: Col_3

description:
normalized_in_TMM_ERF34.txt
Sample 9

value: third and fourth rosette leaves

value: Shoot tissue cell

value: Mock


title: Sample_21


title: NNCSD-023.b

value: UC - Inactive disease


title: Col_2

description:
normalized_in_TMM_ERF34.txt
Sample 8


title: Sample_19


title: cal_2


title: Col_1

description:
normalized_in_TMM_ERF34.txt
Sample 7


title: cal_1


title: Mtgr1 null D3 enteroid mouse 3

city: Nashville

first: Christopher

last: Williams

state: Tennessee

address: 2215-B Garland Ave, 1075 MRB4

institute: Vanderbilt University Medical Center

description:
3203-CSW-33
DE All w normalized counts D3.csv

data_processing:
Raw reads in FASTQ format were trimmed with fastp (v0.20.0) with default parameters
Quantification was performed using Salmon (v1.3.0) against a decoy transcriptome generated from Mus musculus GENCODE (v21)
Differential expression analysis was performed on raw transcript counts using DESeq2 (v1.26.0) and annotated with AnnotationDbi (v1.46.1)
Assembly: Mus musculus GENCODE v21
Supplementary files format and content: Tab delineated file with normalized read counts per sample

organism: Mus musculus

source_name: Duodenum, small intestine

extract_protocol:
Freshly isolated murine small intestinal crypts were collected and homogenized in TRIzol reagent using a 21g needle. After phenol-chloroform extraction, RNA was isolated using the Rneasy Mini Kit (Qiagen) with on-column DNAse digestion.
mRNA enrichment and cDNA library preparation were performed by the Vanderbilt Technologies for Advanced Genomics (VANTAGE) facility utilizing the Illumina Tru-seq stranded mRNA sample prep kit.

value: Duodenum, small intestine

value: Enteroid

value: Mtgr1-/-, null


title: NNCSD-022.b

value: Healthy control


title: Sample_17


title: WTZMcal_3


title: Mtgr1 null D3 enteroid mouse 2

description:
3203-CSW-30
DE All w normalized counts D3.csv


title: NNCSD-022.a


title: Mtgr1 null D3 enteroid mouse 1

description:
3203-CSW-27
DE All w normalized counts D3.csv


title: NNCSD-021.b

value: UC - Active disease


title: WT D3 enteroid mouse 3

description:
3203-CSW-11
DE All w normalized counts D3.csv

value: Mtgr1+/+, WT


title: WTZMcal_2

value: larvae

value: WT


title: Sample_13

value: hESC

value: SCR


title: ZMcal_3

value: ClbnZM

value: 72 hpf larvae


title: NNCSD-021.a

value: Sigmoid colonic tissue

value: F


title: WT D3 enteroid mouse 2

description:
3203-CSW-7
DE All w normalized counts D3.csv


title: Sample_5


title: NNCSD-020.a

value: M


title: Sample_7


title: Sample_18


title: NNCSD-019.a


title: Sample_4


title: NNCSD-023.a


title: Sample_1


title: Mtgr1 null D1 enteroid mouse 3

description:
3203-CSW-32
DE All w normalized counts D1.csv


title: WTZMcal_1


title: NNCSD-018.b


title: ZMcal_2


title: ZMcal_1


title: CD4, CITE-seq group 6

city: New Haven

first: Ya-Chi

last: Ho

state: Connecticut

address: 295 Congress Avenue,BCMM 354E

institute: Yale University

library_source: other

data_processing:
Raw reads were processed using the Cellranger arc pipeline (version 2.0.1) with default parameters, CITE reads were processed with Kite (https://github.com/pachterlab/kite) and Kallisto (version 0.48.0).
Assembly: hg38
Supplementary files format and content: Matrix files and fragments.tsv files from the cellranger pipeline or Kallisto
Supplementary files format and content: Morphine.Meta.csv contains hashkey, treatment conditions, and timepoint keys
Library strategy: DOGMA-seq

molecule: other

source_name: Peripheral Blood

extract_protocol:
cDNA, transposed cDNA, and CITE cDNA were extracted according to the 10X multiome protocol with the modifications described in Mimitou et al.Nat. Biotechnol. 2021.
Libraries were constructed using the 10X multiome protocol with the modificaitons described in Mimitou et al. Nat. Biotechnol. 2021.

treatment_protocol: Dead cells were removed using a bead based kit (STEMCELL Technologies #17899), and hashed using TotalSeq-A antibodies. Each sample was pooled in equal ratios and stained with the TotalSeq™-A Human Universal Cocktail, V1.0 (Bioledgend #399907). Pools were then lysed on ice with DIG lysis buffer for 5 minutes before washing. Cells werethen loaded into the 10X Chromium controller (10x Genomics) according to the manufacturer protocol. CD4+ T cells samples were additionally negatively selected using Miltenyi Biotech #130-096-533.

value: Peripheral Blood


title: genomic DNA from Patient10_week12

type: genomic

city: Oslo

first: Thomas

last: Fleischer

address: Ullernchausséen 70

department: Department of Cancer Genetics, Institute for Cancer Research

country: Norway

institute: Oslo University Hospital

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
Touleimat and Tost, Epigenomics 2012
Average Beta

label: Cy5 and Cy3

molecule: genomic DNA

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was isolated using the QIAcube and AllPrep DNA/RNA Mini Kit 350 or 600 for biopsies from the first two or the last time point, respectively (Qiagen) according to the company’s standard protocol.

tag: gender

value: Female

tag: sample type

value: Tumor biopsy

tag: disease state

value: Breast cancer

tag: agent

value: Chemotherapy+bevacizumab

tag: timepoint


title: NNCSD-018.a

tag: tissue

tag: Sex

value: UC - Inactive disease


title: Sample_14


title: Mtgr1 null D1 enteroid mouse 1

description:
3203-CSW-26
DE All w normalized counts D1.csv

value: Duodenum, small intestine

value: Enteroid

value: Mtgr1-/-, null


title: CD4, CITE-seq group 5


title: NNCSD-016.b

tag: uc or healthy control

tag: mayoscore


title: genomic DNA from Patient6_week12


title: WT D3 enteroid mouse 1

description:
3203-CSW-3
DE All w normalized counts D3.csv

value: Mtgr1+/+, WT


title: NNCSD-016.a

tag: diagnose duration (years)


title: WT D1 enteroid moue 3

description:
3203-CSW-10
DE All w normalized counts D1.csv

tag: cell type


title: genomic DNA from Patient4_week12


title: PBMC, CITE-seq group 3

value: PBMC


title: WT D1 enteroid mouse 2

description:
3203-CSW-6
DE All w normalized counts D1.csv


title: NNCSD-015.b

value: UC - Active disease


title: CD4, CITE-seq group 4


title: WT D1 enteroid mouse 1

description:
3203-CSW-2
DE All w normalized counts D1.csv


title: genomic DNA from Patient7_week0


title: CD4, CITE-seq group 3


title: NNCSD-014.b


title: genomic DNA from Patient104_week12


title: NNCSD-014.a


title: PBMC, CITE-seq group 2


title: genomic DNA from Patient51_week25


title: Mtgr1 null D1 enteroid mouse 2

description:
3203-CSW-29
DE All w normalized counts D1.csv


title: NNCSD-015.a


title: Mtgr1 null crypt mouse 3

description:
3203-CSW-31
DE All w normalized counts D0.csv

value: Crypt isolate


title: genomic DNA from Patient112_week0

value: Chemotherapy


title: Mtgr1 null crypt mouse 2

description:
3203-CSW-28
DE All w normalized counts D0.csv


title: CD4, CITE-seq group 2


title: genomic DNA from Patient104_week0


title: Mtgr1 null crypt mouse 1

description:
3203-CSW-25
DE All w normalized counts D0.csv


title: NNCSD-012.b

value: Sigmoid colonic tissue

value: Healthy control


title: CD4, CITE-seq group 1


title: genomic DNA from Patient119_week0


title: NNCSD-012.a

value: M


title: PBMC, CITE-seq group 1

value: Peripheral Blood


title: genomic DNA from Patient23_week0

value: Female


title: genomic DNA from Patient66_week0

value: Tumor biopsy


title: CD4, scATAC-seq group 6

library_source: genomic


title: WT crypt mouse 2

description:
3203-CSW-5
DE All w normalized counts D0.csv


title: WT crypt mouse 1

description:
3203-CSW-1
DE All w normalized counts D0.csv


title: NNCSD-011.a

value: F


title: genomic DNA from Patient72_week0

value: Breast cancer


title: genomic DNA from Patient28_week0

value: Chemotherapy+bevacizumab


title: NNCSD-010.a


title: RNA-Seq_GFP+Treg cells_KO1

city: Hangzhou

first: Xiaoqian

last: Liu

address: 866 Yuhangtang Road, Xihu District

institute: Zhejiang University

data_processing:
Raw reads were trimmed using fastp (version 0.23.2) and aligned against mm10 genome reference with HISAT2 (version 2.1.0).
The sam files were sorted and converted into BAM file format usingSamtools(1.10).
Sequencing and PCR duplicates were removed by picard MarkDuplicates (version 2.25.0).
Deduplicated mapped BAM reads were quantified byHTSeq count (0.11.3)
Count files were then fed into DESeqDataSetFromHTSeqCount function in DESeq2 package (1.34.0) to perform differential expression analysis. The significance threshold was set to P-value < .05 and |log2FC| > 0.5.
Assembly: mm10
Supplementary files format and content: excel file includes All.ReadsCount for each sample
Supplementary files format and content: bigWig

source_name: spleen

extract_protocol:
total RNA was extracted from GFP+ Treg cells using the RNeasy Plus Mini Kit (Qiagen, 74134)
libraries construction and sequencing were performed on Haplox (Nanchang, China)

value: spleen

value: Treg cells

value: KO


title: genomic DNA from Patient51_week0


title: PBMC, scATAC-seq group 3


title: NNCSD-009.b


title: RNA-Seq_GFP+Treg cells_KO3


title: CD4, scATAC-seq group 4


title: NNCSD-010.b


title: RNA-Seq_GFP+Treg cells_KO2


title: PBMC, scATAC-seq group 2


title: genomic DNA from Patient90_week0


title: CD4, scATAC-seq group 3


title: NNCSD-009.a


title: RNA-Seq_GFP+Treg cells_WT2

value: WT


title: genomic DNA from Patient53_week0


title: WT crypt mouse 3

description:
3203-CSW-9
DE All w normalized counts D0.csv

value: Duodenum, small intestine

value: Mtgr1+/+, WT


title: NNCSD-011.b

value: UC - Active disease


title: NNCSD-008.b


title: CD4, scATAC-seq group 2


title: genomic DNA from Patient31_week0


title: RNA-Seq_GFP+Treg cells_WT1


title: CD4, scATAC-seq group 5


title: NNCSD-008.a


title: RNA-Seq_GFP+Treg cells_WT3


title: genomic DNA from Patient117_week0

value: Chemotherapy


title: CD4, scATAC-seq group 1


title: Cut&Tag_GFP+Treg cells_RUNX1_rep2

data_processing:
Raw reads were filtered with fastp (version 0.23.2) and aligned to the mm10 mouse genome using Bowtie2 (version 2.3.5.1) with standard alignment parameters.
Apparent PCR duplicates were marked with Picard “Mark Duplicates” function and removed for downstream analysis. Genome browser tracks were generated using deepTools with RPKM normalization (version 3.5.1).
The tracks were visualized using the Integrated Genome Viewer. Peaks were called using MACS2 (version 2.2.7.1) with the following parameters:  -f BAMPE -q 0.001 --keep-dup all.
The genomic distribution of peaks were annotated with ChIPseeker (version 1.28.3).
Heatmaps and read density plots of genomic signal density were generated using Deeptools.
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

extract_protocol:
1ⅹ105 sorted GFP+ Treg cells were washed with 500 µl wash buffer. (Vazyme, TD901)
The library preparation for CUT&Tag was performed according to the manufacturer’s instruction with Hyperactive In-Situ ChIP Library Prep Kit for Illumina (Vazyme, TD901) and sequencing was performed on Haplox (Nanchang, China)


title: NNCSD-006.b

value: Sigmoid colonic tissue


title: Cut&Tag_GFP+Treg cells_RUNX1_rep1


title: genomic DNA from Patient107_week0


title: NNCSD-006.a

value: Healthy control


title: NNCSD-005.b


title: NNCSD-005.a


title: Cut&Tag_GFP+Treg cells_IgG_rep3


title: genomic DNA from Patient94_week0


title: Cut&Tag_GFP+Treg cells_IgG_rep4


title: NNCSD-004.b

value: M


title: Cut&Tag_GFP+Treg cells_IgG_rep2


title: genomic DNA from Patient59_week0


title: genomic DNA from Patient45_week0


title: NNCSD-003.b


title: Cut&Tag_GFP+Treg cells_BAF60b_rep2


title: NNCSD-004.a


title: genomic DNA from Patient64_week0


title: genomic DNA from Patient48_week0


title: NNCSD-003.a


title: Cut&Tag_GFP+Treg cells_BAF60b_rep1


title: NNCSD-002.a


title: NNCSD-002.b


title: PBMC, scATAC-seq group 1

value: Peripheral Blood

value: PBMC


title: genomic DNA from Patient81_week0

value: Female

value: Tumor biopsy


title: ATAC-Seq_GFP+Treg cells_KO1

data_processing:
The pair-end reads were trimmed using fastp(version 0.23.2). After quality control, the reads were mapped to the mm10 mouse genome using Bowtie2(version 2.3.5.1).
The unmapped reads, mitochondrial reads and nonuniquely mapped reads were removed by SAMtools (version 1.10). PCR duplicates were removed by Picard MarkDuplicates (version 2.25.0).
Bigwig tracks were generated using deepTools with RPKM normalization (version 3.5.1). Integrated genomics viewer was used to display coverage tracks.
The read coverage across all genomic regions was calculated by deepTools "computeMatrix" function. The read density at each region was visualized by "plotHeatmap" function(deepTools).
Peaks were identified by MACS2(version 2.2.7.1) with the following parameters: --nomodel –extsize 200 --shift −100. Differential peak analysis between samples was performed using Homer program get Differential Peaks.
Assembly: mm10
Supplementary files format and content: bigWig

extract_protocol:
GFP+ Treg cells were lysed in lysis buffer (10mM Tris-HCl, 10mM NaCl, 3mM MgCl2, 0.1% (v/v) Igepal CA-630) for 5min on ice.
The library preparation for ATAC-Seq was performed according to the manufacturer’s instruction with TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD501)and sequencing was performed on Haplox (Nanchang, China)


title: genomic DNA from Patient25_week0

value: Breast cancer


title: ATAC-Seq_GFP+Treg cells_KO2


title: genomic DNA from Patient10_week0


title: genomic DNA from Patient54_week0


title: H7, GO-APP, scRNAseq

city: Los Angeles

first: Lili

last: Yang

state: California

address: 610 Charles E. Young Dr. East, TLSB 3045

institute: UCLA Lili Yang Lab

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Data analysis was performed using a Cell Ranger Software Suite (10x Genomics). Binary base call (BCL) files were extracted from the sequencer and used as inputs for the Cell Ranger pipeline to generate the digital expression matrix for each sample. Then, cellranger aggr command was used to aggregate all samples into one digital expression matrix.
Assembly: hg38
Supplementary files format and content: Cell-gene matrix as tab-delimited files and barcodes, genes and matrix

source_name: PBMC

extract_protocol:
T cells were activated and expanded from PBMCs with either Beads3/28 (αCD3 and αCD28 on commercial beads) with external IL-2 (30U/ml) or GO-APP3/28 (αCD3 and αCD28 on graphene oxide antigen presenting platform) in absence of external IL-2. T cells were collected 3 days after activation. Cells were quantified using a Cell Countess II automated cell counter (Invitrogen/Thermo Fisher Scientific).
A total of 10,000 cells from each experimental group were loaded on the Chromium platform (10X Genomics), and libraries were constructed using the Chromium Next GEM Single Cell 3' Kit v3.1 and the Chromium Next GEM Chip G Single Cell Kit (10X Genomics), according to the manufacturer’s instructions. Library quality was assessed using the D1000 ScreenTape on a 4200 TapeStation System (Agilent Technologies). Libraries were sequenced on an Illumina NovaSeq using the NovaSeq S4 Reagent Kit (100 cycles; Illumina).

value: PBMC-derived T cells

tag: strain

tag: age

value: random donor


title: ATAC-Seq_GFP+Treg cells_WT2

value: spleen

value: Treg cells

tag: genotype


title: Myhre syndrome_3

first: Hongmei

last: Mou

state: MA

address: 55 Fruit Street, Jackson 1402

department: The Mucosal Immunology & Biology Research Center

institute: Massachusetts General Hospital

data_processing:
Done by Azenta Life Sciences
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts of each sample

source_name: Primary cells

growth_protocol: Human nasal basal epithelial cells were propagated in Small Airway Epithelial Cell Medium (Promocell medium, C-21170) with 5-10 uM ROCKi (Tocris, 1254), 1 uM A-83-01 (Tocris, 2939) and 0.5 uM CHIR99021 (Tocris, 4423) on plates pre-coated with laminin-enriched 804G-conditioned medium. Human nasal epithelial basal cells were trypsinized and seeded onto 0.4 um transwell membranes pre-coated with 804G-conditioned medium with a density of >6000 cells/mm2. The nasal basal epithelial cells were 100% confluent after attachment at this density. Following cell attachment for >12 hours, excess cells were removed, and the medium was replaced with complete Pneumacult-ALI medium (StemCell Technology, Cat. 05001) filling both the upper and lower chambers. The next day, ALI medium was added only in the lower chamber to initiate airway-liquid interface. The ALI medium was changed every 2 days until differentiation was well established. We culture ALI for 14-21 days as a standard protocol.

extract_protocol:
RNA was harvested using RNeasy mini kit (Qiagen, 74104).
RNA libraries for RNA-seq were prepared using mRNA Deep sequencing by Azenta Life Sciences.

value: Primary cells

value: Nasal basal epithelial cells

value: SMAD4 mutant


title: H7, Beads, scRNAseq

description: 10x Genomics


title: Cut&Tag_GFP+Treg cells_IgG_rep1

value: WT


title: RNA_T24_NSD_T0N9 (re-analysis)

city: Lausanne

first: Maxime

last: Jan

state: Suisse

address: University of Lausanne

department: CIG

country: Switzerland

institute: University of Lausanne

description: re-analysis of GSM4159702

data_processing:
Gene quantification was performed as follow for liver samples: Illumina reads were filtered using fastp to keep high quality reads and remove adapter sequences. Reads were aligned on the mouse reference genome mm10 (GRCm38) using STAR v2.7.0e with default parameters. Read counts was done by STAR using “--quantMode GeneCounts”, taking only reverse strand mapped reads. Genes with low counts (mean counts overall samples < 10) were filtered and normalization was performed with edgeR. Batch effects were corrected by ComBat.
Assembly: mm10
Supplementary files format and content: Gene expression [log2 CPM]

source_name: Cortex

growth_protocol: Mice were housed under standard conditions according to the Swiss Animal Protection Act, under a 12h:12h light/dark cycle, with food accessible ad libitum at all times.

extract_protocol:
Mice were anesthetized with isoflurane prior to decapitation. Liver was rapidly dissected and flash frozen in liquid nitrogen. Frozen Liver of each individual was ground in liquid nitrogen and stored at -140°C until further use.
Total RNA was extracted using the miRNeasy kit (Qiagen; Hilden, Germany) following the manufacturer's instructions. RNA-seq libraries were prepared using 10 ng/μl of total RNA and the Illumina TruSeq Stranded mRNA reagents (Illumina; San Diego, CA, USA). Libraries were sequenced on the Illumina HiSeq 4000 sequencer, producing >24 million mappable single-end reads.

treatment_protocol: Mice for tissue collection were divided into two experimental cohorts, sleep deprived (SD) and non-sleep deprived (controls, Ctr). After a one-week habituation to the experimental setting, at the age of 11-12 weeks, the SD mice were sleep-deprived by gentle handling for 6 hours starting at light onset (zeitgeber time ZT0-ZT6), and allowed to recover according to the tissue collection schedule.

value: Cortex

tag: ztime

tag: time

tag: condition

value: NSD

tag: batch


title: Myhre syndrome_1

tag: cell line


title: genomic DNA from Patient75_week0

tag: gender

tag: sample type

tag: disease state

value: Chemotherapy


title: ATAC-Seq_GFP+Treg cells_WT1

tag: tissue


title: Myhre syndrome_2


title: RNA_T0_NSD_T0N8 (re-analysis)

description: re-analysis of GSM4159700


title: Healthy control_3


title: RNA_T24_NSD_T0N5 (re-analysis)

description: re-analysis of GSM4159697


title: U2OS-KRAB-IDR3-TCF3, H3K9me3, ABCAM, rep2

city: Shanghai

first: YING

last: FENG

address: 393 Middle Huaxia Road

institute: Shanghaitech University

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 20, using Trimgalore  v0.6.7, discarding reads left with < 30 bp
ChIP-seq reads were aligned to the UCSC hg19 genome using Bowtie2 version 2.5.0. Only uniquely mapping reads with  were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were  renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Peaks were called uing MACS v2.2.7.1 with the significance cut-off p-value <=0.01
Assembly: hg19
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

growth_protocol: DMEM, 10% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were washed in FBS-free media then cross-linked with 1% formaldehyde for 10 min at room temperature, Cross-linked cells were washed with ice-cold PBS, For each sample, 20 million fixed cells were lysed to prepare nuclear extracts.
For ChIP-Seq, 5ng of purified ChIP DNA were used to generate the sequencing library using a NEB kit and sequenced with the Illumina HiSeq X Ten.

value: Human Bone Osteosarcoma Epihelial Cells

tag: chip antibody

value: H3K9me3 (Abcam, #ab8898)


title: genomic DNA from Patient11_week0

tag: agent

tag: timepoint


title: Healthy control_2


title: H4, Beads, scRNAseq

description: 10x Genomics

value: PBMC


title: U2OS-KRAB-IDR3-TCF3, H3K9me3, ABCAM, rep1


title: genomic DNA from Patient130_week0

value: Female


title: genomic DNA from Patient124_week0

value: Tumor biopsy


title: genomic DNA from Patient96_week0

value: Breast cancer

value: Chemotherapy+bevacizumab


title: RNA_T0_NSD_T0N2 (re-analysis)

description: re-analysis of GSM4159692


title: genomic DNA from Patient121_week0


title: RNA_T0_NSD_T0N1 (re-analysis)

description: re-analysis of GSM4159690


title: T-061-F-C

first: Su-Young

address: 81, Irwon-ro, Gangnam-gu

institute: Samsung Medical Center

data_processing:
mRNA-Seq reads were mapped using TopHat software tool in order to obtain the alignment file.
Differentially expressed gene were determined based on counts from unique and multiple alignments using coverage in Bedtools (Quinlan AR, 2010).
The Read Count data were processed based on Quantile normalization method using EdgeR within R using Bioconductor.
The alignment files also were used for assembling transcripts, estimating their abundances and detecting differential expression of genes or isoforms using cufflinks.
Assembly: hg19
Supplementary files format and content: Excel file includes raw data (Reads Count; RC) and normalized RC for all Sample

source_name: lung

extract_protocol:
Total RNA was isolated using Trizol reagent (Invitrogen). RNA quality was assessed by Agilent 2100 bioanalyzer using the RNA 6000 Nano Chip (Agilent Technologies, Amstelveen, The Netherlands), and RNA quantification was performed using ND-2000 Spectrophotometer (Thermo Inc., DE, USA).
Libraries were prepared from 2ug of total RNA using the SMARTer Stranded RNA-Seq Kit (Clontech Laboratories, Inc., USA). The isolation of mRNA was performed using the Poly(A) RNA Selection Kit (LEXOGEN, Inc., Austria). The isolated mRNAs were used for the cDNA synthesis and shearing, following manufacture’s instruction. Indexing was performed using the Illumina indexes 1-12. The enrichment step was carried out using of PCR. Subsequently, libraries were checked using the Agilent 2100 bioanalyzer (DNA High Sensitivity Kit) to evaluate the mean fragment size. Quantification was performed using the library quantification kit using a StepOne Real-Time PCR System (Life Technologies, Inc., USA).

value: lung

tag: section

value: fibrocavitary

tag: etiology

value: M. avium


title: Healthy control_1

value: Primary cells

tag: cell type


title: genomic DNA from Patient62_week0


title: T-017-F-C


title: EMT Library 4 [C4-CBO]

city: Crawley

first: Jessica

last: King

state: WA

address: 35 Stirling Hwy

department: School of Molecular Sciences

country: Australia

institute: University of Western Australia

description: Channel 4

data_processing:
Fastq files were generated with Illumina bcl2fastq v2.20.0.422, allowing 1 mismatch in each index.
Transcript alignment and generation of gene count and feature barcode matrices were performed using 10x Genomics Cell Ranger count v6.0.2. Output from four channels was combined either with Cell Ranger aggr (for data QC and initial exploration), or Seurat v4.1.0 in R for all further downstream analysis.
Assembly: hg38
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

source_name: HMLE

extract_protocol:
Cells were collected with TryplE and resuspended in 0.04% w/v BSA. Cells from each sample were pooled together in equal numbers at a final concentration of 1,000 cells/μL.
Cells were loaded onto a 10x Genomics Chromium Controller, Chip K (PN  1000286) and libraries were prepared using the Chromium Next GEM single cell 5’ kit v2  (PN1000263/1000265). Libraries from SBOs were prepared using the 5’ Feature Barcode kit (PN 1000256) following  manufacturer guidelines. Illumina iSeq 100 platform was used for initial QC of the libraries and deeper sequencing was conducted on Illumina NovaSeq 6000 in the vendor recommended format to reach up to 50,000 reads per cell.

treatment_protocol: 12 samples were labelled with unique short barcoded oligonucleotides (SBOs) for multiplexing.

value: HMLE

value: Human mammary epithelial cells

tag: library type

value: mRNA

tag: antibodies/tags

value: DNA barcoded oligonucleotides (SBOs)


title: RNA_T30_SD_T30S4 (re-analysis)

description: re-analysis of GSM4159688

value: Cortex

tag: ztime

value: SD


title: T-052-F-UC

value: M. intracellulare


title: U2OS-KRAB-IDR3-TCF3, H3K9me3, ABCAM, input, rep1

value: Human Bone Osteosarcoma Epihelial Cells


title: EMT Library 4 [C4-GEX]

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
Channel 4


title: RNA_T30_SD_T30S3 (re-analysis)

description: re-analysis of GSM4159686

tag: time


title: genomic DNA from Patient85_week0


title: H4, GO-APP, scRNAseq

description: 10x Genomics

value: PBMC-derived T cells

value: PBMC

tag: strain

tag: age

value: random donor


title: genomic DNA from Patient1_week0

value: Female

value: Tumor biopsy

value: Breast cancer


title: RNA_T30_SD_T30S1 (re-analysis)

description: re-analysis of GSM4159684

tag: condition

tag: batch


title: T-027-F-UC

value: lung

value: fibrocavitary


title: RNA_T6_NSD_T6N4 (re-analysis)

description: re-analysis of GSM4159682

value: NSD


title: U2OS-KRAB-IDR3-TCF3, H3K9me3, ABCAM, input, rep2

tag: cell line


title: T-022-F-UC


title: EMT Library 3 [C3-GEX]

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
Channel 3

value: HMLE


title: genomic DNA from Patient38_week0

tag: gender

tag: sample type

tag: disease state

value: Chemotherapy


title: genomic DNA from Patient83_week0

tag: agent


title: RNA_T6_NSD_T6N3 (re-analysis)

description: re-analysis of GSM4159680

tag: tissue


title: T-010-F-UC

tag: section

value: M. avium


title: RNA_T24_NSD_T0N3 (re-analysis)

description: re-analysis of GSM4159694


title: RNA_T6_NSD_T6N2 (re-analysis)

description: re-analysis of GSM4159678


title: EMT Library 2 [C2-GEX]

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
Channel 2

value: Human mammary epithelial cells

value: mRNA

value: DNA barcoded oligonucleotides (SBOs)


title: genomic DNA from Patient103_week0

tag: timepoint


title: genomic DNA from Patient14_week0

value: Chemotherapy+bevacizumab


title: genomic DNA from Patient61_week0


title: EMT Library 2 [C2-CBO]

description: Channel 2

tag: cell type


title: T-007-C

tag: etiology

value: M. intracellulare


title: genomic DNA from Patient57_week0


title: T-003-C


title: EMT Library 1 [C1-CBO]

description: Channel 1

tag: library type

tag: antibodies/tags


title: RNA_T78_SD_T78S4 (re-analysis)

description: re-analysis of GSM4159676

value: Cortex

tag: ztime

tag: time

value: SD


title: RNA_T78_SD_T78S3 (re-analysis)

description: re-analysis of GSM4159674


title: T-048-F-UC


title: T-002-C


title: EMT Library 3 [C3-CBO]

description: Channel 3


title: genomic DNA from Patient87_week0


title: RNA_T78_SD_T78S2 (re-analysis)

description: re-analysis of GSM4159672


title: T-063-F-NB

value: nodular bronchiectatic


title: genomic DNA from Patient44_week0

value: Female


title: EMT Library 1 [C1-GEX]

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
Channel 1


title: genomic DNA from Patient17_week0

value: Tumor biopsy


title: T-060-F-NB


title: RNA_T72_SD_T72S3 (re-analysis)

description: re-analysis of GSM4159668


title: RNA_T72_SD_T72S4 (re-analysis)

description: re-analysis of GSM4159670


title: 7860_ko_D300-1

city: Charleston

first: Aguirre

last: de Cubas

state: SC

address: 86 Jonathan Lucas St

department: Microbiology and Immunology

institute: Medical University of South Carolina

data_processing:
Sequencing reads were aligned against the human GENCODE genome (V28), Version Hg19 (January 2017 freeze, GRCh37, Ensembl 87) using the Spliced Transcripts Alignment to a Reference (STAR) software
Reads were preprocessed and index using SAMtools
Mapped reads were annotated and quantified using featureCounts
Normalization and differential expression was performed using DESeq2
Expression matrix produced using variance stabilized transformation function
Assembly: human GENCODE genome (V28), Version Hg19 (January 2017 freeze, GRCh37, Ensembl 87)
Supplementary files format and content: tab-delimited text files include Raw Counts values for each Sample

source_name: Kidney

growth_protocol: Cells cultured

extract_protocol:
Total RNA was extracted using the miRNeasy Kit (Qiagen)
Illumina libraries prepared using poly-A enrichment.

treatment_protocol: Cells were treated daily with DMSO of Decitabine (100nM or 300nM) for three days. Fresh media added on day 4 and cells were harvested on day 5.

value: Kidney

value: Clear cell renal cell carinoma

tag: genotype

value: SETD2 KO

tag: treatment

value: 300nM Decitabine


title: T-059-F-NB

value: lung


title: 7860_ko_D300-2


title: RNA_T72_SD_T72S2 (re-analysis)

description: re-analysis of GSM4159666

tag: condition

tag: batch


title: 7860_ko_D100-2

tag: cell line

value: 100nM Decitabine


title: 7860_ko_D100-1


title: genomic DNA from Patient67_week0

tag: gender

tag: sample type

value: Breast cancer


title: T-058-F-NB


title: RNA_T66_SD_T66S5 (re-analysis)

description: re-analysis of GSM4159665


title: 7860_ko_D0-2

value: DMSO


title: genomic DNA from Patient32_week0

tag: disease state

tag: agent


title: T-034-F-NB

tag: tissue

tag: section

value: M. avium


title: genomic DNA from Patient19_week0

tag: timepoint


title: T-051-F-NB

tag: etiology


title: 7860_ko_D0-1

tag: cell type


title: RNA_T66_SD_T66S3 (re-analysis)

description: re-analysis of GSM4159664


title: T-030-F-NB


title: BT549 cells, SIK1_S435D

city: Guangzhou

first: sun

last: zicheng

address: zhongshan 2 Road

institute: sun yat-sen university

data_processing: RPKM

source_name: breast

extract_protocol: none provided

value: breast

value: Triple-negative breast cancer


title: RNA_T66_SD_T66S2 (re-analysis)

description: re-analysis of GSM4159662


title: genomic DNA from Patient13_week0

value: Chemotherapy+bevacizumab


title: RNA_T27_SD_T27S5 (re-analysis)

description: re-analysis of GSM4159660

value: Cortex


title: T-029-F-NB


title: BT549 cells, SIK1_WT


title: genomic DNA from Patient118_week0


title: genomic DNA from Patient70_week0


title: RNA_T27_SD_T27S3 (re-analysis)

description: re-analysis of GSM4159658

value: SD


title: CMO_NHDF_72h_IL1b

city: South San Francisco

first: Xin

last: Luo

state: CA

address: 750 Gateway Blvd

department: Research and Development

institute: Amgen Inc

description:
lipid-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains lipid Derived Tag reads
CMO feature barcode from 10X Genomics 3' CellPlex Multiplex Solution

data_processing:
Raw fastq files were aligned to the human GRCh38 reference genome (v) using CellRanger (10x Genomics, v6) multi pipeline with the provided cell multiplexing CMO tags
Subsequent quality control, SCTransform normalization, dimensional reduction, and clustering was performed in Seurat v4.0. Processed data were reference mapped to human CITE-seq fibroblast data within this study by MapQuery function to impute cell annotations.
Assembly: GRCh38
Supplementary files format and content: CellPlex_Multiplex_count_feature_reference.csv with detailed cell multiplexing CMO tags information. 10x Genomics cellranger multi output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

growth_protocol: Human ventricular cardiac fibroblasts (NHCF-V, Lonza, CC-2904), adult human dermal fibroblasts (NHDF-Ad, Lonza, CC-2511), and immortalized human cardiac fibroblasts (iHCF, Applied Biological Materials Inc., T0446) were grown in FibroGRO LS medium supplemented with 2% (NHDF-Ad) or 10% (NHCF-V and iHCF) FBS. Cells were maintained in a humidified atmosphere (95% air, 5% CO2) at 37°C and passaged every 2-3 days.

extract_protocol:
After trypsinization, cell suspensions were labeled with barcoded lipids from the 3' CellPlex Kit Set A (10x Genomics PN:1000261) following manufacturer’s instructions (Protocol CG000391). After labeling, technical replicates were pooled and loaded onto a Chromium Controller (10x Genomics) at a concentration to capture 6-10,000 cells.
Single-cell libraries were prepared using the Single Cell 3’ Kit v3.1 (10x Genomics PN:1000268) according to manufacturer’s instructions (User Guide CG000388). Gene expression and cellplex libraries were indexed with Dual Index Kit TT Set A and NN Set A indexes (PN:1000215, 3000482) respectively.

treatment_protocol: For cytokine treatment, cells were seeded in 6-well plates and allowed to attach for 24hr. Thereafter, cells were equilibrated for 16 hr in low serum medium (0.2% FBS for NHDF-Ad, and 0.5% for NHCF-V and iHCF), and then treated with 10 ng/mL of recombinant human TGF-b (R&D Systems; 240-B-002) or 10 ng/mL of recombinant human IL-1β (R&D Systems; 201-LB-005) for the indicated times.

tag: library type

value: Cell Multiplexing Oligo (CMO)


title: genomic DNA from Patient63_week0

value: Female

value: Chemotherapy


title: RNA_T27_SD_T27S2 (re-analysis)

description: re-analysis of GSM4159656

tag: ztime


title: genomic DNA from Patient99_week0

value: Tumor biopsy


title: CMO_NHDF_72h_TGFb

source_name: Human ventricular cardiac fibroblasts (NHCF-V, Lonza, CC-2904)


title: T-016-F-NB

value: nodular bronchiectatic

value: M. intracellulare


title: CMO_NHDF_72h_Control

value: Human ventricular cardiac fibroblasts (NHCF-V, Lonza, CC-2904)


title: RNA_T3_NSD_T3N4 (re-analysis)

description: re-analysis of GSM4159654

tag: time

value: NSD


title: RNA_T3_NSD_T3N3 (re-analysis)

description: re-analysis of GSM4159652


title: CMO_NHCF_72h_IL1b


title: T-063-F-NL

value: lung

value: unaffected


title: T-009-F-NB


title: genomic DNA from Patient56_week0

value: Breast cancer


title: genomic DNA from Patient39_week0


title: RNA_T3_NSD_T3N2 (re-analysis)

description: re-analysis of GSM4159650


title: T-061-F-NL

value: M. avium


title: CMO_NHCF_72h_Control


title: T-017-F-NL


title: genomic DNA from Patient78_week0


title: RNA_T60_SD_T60S4 (re-analysis)

description: re-analysis of GSM4159648


title: CMO_iHCF_72h_IL1b_lot1

source_name: immortalized human cardiac fibroblasts (iHCF, Applied Biological Materials Inc., T0446)


title: RNA_T60_SD_T60S3 (re-analysis)

description: re-analysis of GSM4159646


title: genomic DNA from Patient60_week0


title: T-060-F-NL


title: T-020-F-NB


title: CMO_iHCF_72h_TGFb_lot1

value: immortalized human cardiac fibroblasts (iHCF, Applied Biological Materials Inc., T0446)


title: RNA_T60_SD_T60S2 (re-analysis)

description: re-analysis of GSM4159644


title: genomic DNA from Patient55_week0


title: RNA_T54_SD_T54S4 (re-analysis)

description: re-analysis of GSM4159642


title: T-058-F-NL


title: RNA_T54_SD_T54S2 (re-analysis)

description: re-analysis of GSM4159640


title: genomic DNA from Patient129_week0


title: T-052-F-NL


title: genomic DNA from Patient46_week0


title: CMO_NHCF_72h_TGFb


title: NHDF_72h_IL1b

description: 3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript

source_name: adult human dermal fibroblasts (NHDF-Ad, Lonza, CC-2511)

value: mRNA


title: genomic DNA from Patient91_week0


title: NHDF_72h_TGFb

value: adult human dermal fibroblasts (NHDF-Ad, Lonza, CC-2511)


title: T-051-F-NL


title: RNA_T54_SD_T54S1 (re-analysis)

description: re-analysis of GSM4159638

value: Cortex


title: RNA_T48_SD_T48S4 (re-analysis)

description: re-analysis of GSM4159636

value: SD


title: NHDF_72h_Control


title: genomic DNA from Patient73_week0


title: T-048-F-NL


title: genomic DNA from Patient126_week0


title: T-034-F-NL


title: NHCF_72h_IL1b


title: T-059-F-NL


title: genomic DNA from Patient88_week0


title: RNA_T48_SD_T48S3 (re-analysis)

description: re-analysis of GSM4159634


title: RNA_T48_SD_T48S1 (re-analysis)

description: re-analysis of GSM4159632


title: CMO_iHCF_72h_Control_lot1

value: Cell Multiplexing Oligo (CMO)


title: NHCF_72h_TGFb


title: genomic DNA from Patient98_week0

value: Female


title: genomic DNA from Patient77_week0

value: Chemotherapy


title: NHCF_72h_Control


title: T-030-F-NL


title: RNA_T42_SD_T42S6 (re-analysis)

description: re-analysis of GSM4159630


title: T-029-F-NL


title: T-027-F-NL


title: genomic DNA from Patient16_week0

value: Tumor biopsy

value: Chemotherapy+bevacizumab


title: iHCF_72h_IL1b_lot1


title: RNA_T42_SD_T42S2 (re-analysis)

description: re-analysis of GSM4159626


title: T-022-F-NL

value: M. intracellulare


title: genomic DNA from Patient35_week0


title: iHCF_72h_IL1b_lot2


title: T-020-F-NL


title: RNA_T18_NSD_T18N8 (re-analysis)

description: re-analysis of GSM4159624


title: iHCF_72h_TGFb_lot1


title: RNA_T18_NSD_T18N7 (re-analysis)

description: re-analysis of GSM4159623


title: T-016-F-NL


title: genomic DNA from Patient9_week0


title: genomic DNA from Patient29_week0


title: iHCF_72h_Control_lot2


title: RNA_T18_NSD_T18N3 (re-analysis)

description: re-analysis of GSM4159619


title: RNA_T18_NSD_T18N4 (re-analysis)

description: re-analysis of GSM4159621


title: T-009-F-NL


title: genomic DNA from Patient105_week0


title: RNA_T42_SD_T42S4 (re-analysis)

description: re-analysis of GSM4159628


title: T-010-F-NL


title: iHCF_72h_Control_lot1


title: RNA_T18_NSD_T18N2 (re-analysis)

description: re-analysis of GSM4159617


title: genomic DNA from Patient106_week0


title: genomic DNA from Patient33_week0


title: T-007-NL


title: Ab_sample41

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
Antibody-derived oligonucleotide (ADT)

data_processing:
Raw fastq files were aligned to the human GRCh38 reference genome (v) using CellRanger (10x Genomics, v6) with the antibody capture tag for the TotalSeqA 277 + two custom oligo-tagged antibodies.
Protein reads were normalized and de-noised using the dsb package in R v4. Subsequent quality control, normalization, dimensional reduction, and clustering was performed in Seurat v4.0. Clusters were annotated using canonical gene and protein markers.
Assembly: GRCh38
Supplementary files format and content: celll.metadata.csv contains meta information of all samples with cells in rows and labels in columns; 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Library strategy: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)

molecule: protein

source_name: Heart

extract_protocol:
Fresh cardiac left ventricular tissue from ex-planted hearts at the time of transplantation, LVAD cores, or donors declared DCD were harvested and perfused. Tissues were minced and digested. After incubating with the TotalSeq A 277 panel (BioLegend) antibodies with custom oligo-labeled FAP and LRRC15 antibodies, single cells were isolated and counted before proceeding with the 10x protocol.
Collected cells were processed using the single Cell 3’ Kit v 3.1 (10x Genomics PN: 1000268). Single-cell libraries were prepared using the single Cell 3’ Kit v 3.1 following a modified 3’ v3.1 assay protocol (User Guide CG000206) to concurrently prepare gene expression and TotalSeq A antibody derived tag (ADT) libraries as recommended by BioLegend. 1 ul of 0.2uM ADT Additive Primer (CCTTGGCACCCGAGAATT*C*C) and 15 ul of cDNA Primers (PN: 2000089) were used to amplify cDNA. ADT libraries were amplified with a final concentration of 0.25 uM SI Primer (AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGC*T*C) and 0.25 uM TrueSeq Small RNA RPI primer (CAAGCAGAAGACGGCATACGAGAT[6nt index]GTGACTGGAGTTCCTTGGCACCCGAGAATTC*C*A) using 15 cycles. Gene expression libraries were indexed using Single Index Kit T Set A (PN: 2000240). Libraries were sequenced on a NovaSeq 6000 S4 flow cell (Illumina).

value: Heart

value: Cardiac Cells

value: ADT

tag: antibodies/tags

value: TotalSeq A 277 panel (BioLegend) antibody cocktail + two custom oligo-tagged antibodies (anti-FAP and anti-LRRC15)


title: RNA_T36_SD_T36S4 (re-analysis)

description: re-analysis of GSM4159615


title: Ab_sample42


title: genomic DNA from Patient40_week0

value: Breast cancer


title: T-003-NL

value: lung

value: unaffected


title: RNA_T36_SD_T36S2 (re-analysis)

description: re-analysis of GSM4159613


title: T-002-NL


title: Ab_sample39


title: iHCF_72h_TGFb_lot2

value: immortalized human cardiac fibroblasts (iHCF, Applied Biological Materials Inc., T0446)

value: mRNA


title: Ab_sample34


title: PA+rapamycin exosomes3

city: Harbin

first: Zhen

last: Tian

address: Baojian Road

institute: Harbin medical university

data_processing:
Raw reads with low quality or more than 10% base information without determination were removed to obtain clean reads. Bowtie was used to locate sRNA after length screening to the reference sequence and analyze the distribution of small RNA on the reference sequence. The reads mapped into the reference sequence above were aligned with the specified range sequences in miRBase to obtain the sequence, length, occurrence times and other information of the miRNA matched in each sample. Then, the DESeq2 R package was used to analyze the differential expression of genes. Genes with adjusted P values <0.05 were considered differentially expressed.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes TPM values for each sample

source_name: epithelial tissue

growth_protocol: Human umbilical vein endothelial cells at approximately 70-80% confluence were cultured in DMEM medium with 10% exosome-depleted FBS (SBI, USA) with or without treatment for 24 h. Cells were incubated at 37 °C in an atmosphere of 5% CO2.

extract_protocol:
Conditioned media was collected and centrifuged serially at 3000 × g for 20 min and 10,000 × g for 30 min at 4 °C.  Then, the supernatants were passed through a 0.22-μm pore polyethersulfone membrane filter (Millipore) and ultracentrifuged at 100,000 × g (Optima XPN-100, Beckman, USA) for 2 h to isolate pelleted exosomes. The pellets were resuspended in PBS and ultracentrifuged at 100,000 × g for 2 h at 4 °C. The isolated exosomes were suspended in PBS for characterization and the following experiments.Total RNA extracted from purified exosomes was prepared, and the RNA total amount and fragment distribution were detected before the establishment of the sequencing library for each sample using the Small RNA Sample Pre Kit.
A total amount of 3 μg total RNA per sample was used as input material for the small RNA library. Sequencing libraries were generated using NEBNext®Multiplex Small RNA Library Prep Set for Illumina®(NEB, USA.)following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: Human umbilical vein endothelial cells were pretreated with rapamycin or pretransfected with Atg7-siRNA for 24h ,then treated with palmitic acid

value: epithelial tissue

value: human umbilical vein endothelial cells

tag: treatment

value: pretreated rapamycin for 26h then treated with palmitic acid


title: RNA_T36_SD_T36S1 (re-analysis)

description: re-analysis of GSM4159611

value: Cortex

tag: condition

value: SD


title: genomic DNA from Patient93_week0

value: Female

value: Tumor biopsy

value: Chemotherapy


title: genomic DNA from Patient80_week0


title: RNA_T12_NSD_T12N6 (re-analysis)

description: re-analysis of GSM4159609

value: NSD

tag: batch


title: PA+rapamycin exosomes2

value: pretreated rapamycin for 25h then treated with palmitic acid


title: Ab_sample33

value: Heart

value: Cardiac Cells

value: ADT


title: Ab_sample32

value: TotalSeq A 277 panel (BioLegend) antibody cocktail + two custom oligo-tagged antibodies (anti-FAP and anti-LRRC15)


title: PA+si-atg7 exosomes3

value: preinfected Atg7 siRNA using Lipofectamine 2000 then treated with palmitic acid


title: genomic DNA from Patient102_week0

value: Breast cancer

value: Chemotherapy+bevacizumab


title: Ab_sample30


title: RNA_T12_NSD_T12N5 (re-analysis)

description: re-analysis of GSM4159607


title: genomic DNA from Patient2_week0


title: Ab_sample29


title: RNA_T12_NSD_T12N2 (re-analysis)

description: re-analysis of GSM4159603


title: PA+si-atg7 exosomes1

value: epithelial tissue


title: genomic DNA from Patient6_week0


title: RNA_T12_NSD_T12N1 (re-analysis)

description: re-analysis of GSM4159601


title: PA+si-atg7 exosomes2

value: human umbilical vein endothelial cells


title: Ab_sample28


title: RNA_T198_SD_J76S3 (re-analysis)

description: re-analysis of GSM4159599


title: genomic DNA from Patient116_week0


title: PA exosome3

value: teated with palmitic acid


title: genomic DNA from Patient21_week0


title: Ab_sample27


title: Ab_sample17


title: RNA_T198_SD_J76S2 (re-analysis)

description: re-analysis of GSM4159597

value: Cortex


title: PA exosome2


title: genomic DNA from Patient125_week0


title: Ab_sample15


title: PA exosome1


title: PA+rapamycin exosomes1

value: pretreated rapamycin for 24h then treated with palmitic acid


title: RNA_T6_NSD_J76N2 (re-analysis)

description: re-analysis of GSM4159593


title: Ab_sample13


title: genomic DNA from Patient4_week0

value: Female


title: RNA_T12_NSD_T12N4 (re-analysis)

description: re-analysis of GSM4159605


title: SKMEL5 cells, shIRF4, day 3,  biological replicate 3

city: Istanbul

first: Tolga

last: Emre

address: Bogazici University, Kuzey Kampus, Kuzey Park Binasi, No 203

country: Turkey

institute: Bogazici University

data_processing:
Reads were aligned with TopHat V2.0.8 and selection of uniquely mapped reads were done with samtools
To quantify mapped reads and determine differentially expressed gene Cuffdiff v2.1.1 software was used.
cuffdiff output was visualized using CummeRbund R package with R v3.0.1
Assembly: GRCh37/hg19 (Feb. 2009 )
Supplementary files format and content: tab-delimited text files include normalized counts for each sample

growth_protocol: SKMEL28 and SKMEL5 cells were maintained in DMEM supplied with 10% FBS, non-essential amino acids, and antibiotics in an incubator at 37°C and 5% CO2

extract_protocol:
RNA was extracted using the Roche High Pure RNA Isolation kit. 1.1 mg total RNA  was used for generating RNA-seq libraries
TruSeq RNA Sample Preparation Kit was used for library preparation step. Briefly, library preparation starts with purification of mRNA by poly-A selection using oligo-dT attached magnetic beads. Following purification, mRNAs are fragmented and copied into first strand cDNA by using random hexamers. Then second strand cDNA synthesis is performed. End repair and addition of adenine base follows the procedure. At the end, adaptors with barcodes are ligated and products are enriched with PCR.

tag: cell line

value: melanoma

tag: genotype

value: lentiviral transduction


title: RNA_T6_NSD_J76N1 (re-analysis)

description: re-analysis of GSM4159591

value: NSD


title: RNA_T198_SD_J76S1 (re-analysis)

description: re-analysis of GSM4159595

value: SD


title: genomic DNA from Patient69_week0

tag: gender

tag: sample type

value: Tumor biopsy

value: Chemotherapy


title: SKMEL5 cells, shIRF4, day 3,  biological replicate 2


title: RNA_T192_SD_J70S3 (re-analysis)

description: re-analysis of GSM4159589


title: genomic DNA from Patient82_week0

tag: disease state

tag: agent


title: Ab_sample9

tag: tissue

value: Heart

value: Cardiac Cells

value: ADT


title: SKMEL5 cells, shIRF4, day 3,  biological replicate 1


title: Ab_sample8

value: TotalSeq A 277 panel (BioLegend) antibody cocktail + two custom oligo-tagged antibodies (anti-FAP and anti-LRRC15)


title: genomic DNA from Patient127_week0

value: Breast cancer

tag: timepoint


title: RNA_T192_SD_J70S2 (re-analysis)

description: re-analysis of GSM4159587


title: genomic DNA from Patient86_week0


title: SKMEL5 cells, shLuc, day 3,  biological replicate 3

value: shLuc(Control)


title: genomic DNA from Patient50_week0


title: RNA_T192_SD_J70S1 (re-analysis)

description: re-analysis of GSM4159585


title: genomic DNA from Patient68_week0

value: Chemotherapy+bevacizumab


title: Ab_sample7


title: SKMEL5 cells, shLuc, day 3,  biological replicate 2


title: genomic DNA from Patient109_week0


title: Ab_sample6


title: RNA_T24_NSD_J70N2 (re-analysis)

description: re-analysis of GSM4159583


title: RNA_T0_NSD_J70N1 (re-analysis)

description: re-analysis of GSM4159581


title: SKMEL5 cells, shLuc, day 3,  biological replicate 1


title: Ab_sample5


title: Dam-LaminDm0 DamID-seq, rep 2

city: Stockholm

first: Artem

last: Ilin

address: Svante Arrhenius väg 20C

department: MBW

country: Sweden

institute: Stockholm University

data_processing:
Two biological replicates of Dam-only, Dam-Elys or Dam-Lam DamID-seq reads were adapter clipped, mapped to the dm3 genome assembly by bowtie2 (Langmead 2012) and counted by ‘HTSeq-count’ software (Anders et al, 2015) on the 300-bp genomic bins. The resulted counts of Dam-Elys and Dam-Lam samples were converted to RPM, normalized to the Dam-only samples counts and log2-transformed. The domain calling was performed with the 3-state HMM algorithm for Dam-Elys and 2-state HMM for Dam-Lam without taking into account the heterochromatin portion of dm3 genome assembly.
Assembly: dm3
Supplementary files format and content: bedgraph files were generated using htseq-count software and R via Rstudio, counts represent RPM values per 300-nt bins; bed files represent Elys and Lam domains in Drosophila embryos after performing 3- or 2-state HMM domain calling, respectively, via custom script in R
Library strategy: DamID-seq

organism: Drosophila melanogaster

source_name: Embryos

growth_protocol: Flies were grown according to standard protocols.

extract_protocol:
Approximately two hundred 16-18-h embryos from these crosses were collected, washed with H2O, dechorionated with 2.5% hypochlorite for 3 min and again washed three times with H2O. Isolation of genomic DNA was performed by DNeasy Blood and Tissue kit (Qiagen), following the protocol for cultured cells. DNA was concentrated by centrifugation in 0.5 ml Amicon-Ultra columns (Millipore) for 10 min at 18000 × g and its concentration was measured using a NanoDrop spectrophotometer. For the selective amplification of methylated GATC-GATC fragments, genomic DNA was first digested by DpnI, followed by ligation of adaptors, DpnII digestion and PCR-amplification as described previously (Vogel et al. 2007) with a minor modification: ~0.5 µg instead of 2.5 µg of genomic DNA was used as an input.We applied 18 cycles of PCR (1 min at 94°C, 1 min at 65°C, 2 min at 68°C) for Dam-only and Dam-Elys and 16 cycles for Dam-Lam DNA samples. Adapters were removed by DpnII digestion for 2 h at 37°C. The amplified methylated DNA fragments were purified using QIAquick PCR Purification kit (Qiagen), concentrated by centrifugation in 0.5 ml Amicon-Ultra columns (Millipore) for 10 min at 18000 × g, and quantified on a NanoDrop spectrophotometer.
0.5 µg of Dam-only, Dam-Elys and Dam-Lam DNA samples (each in two biological replicates) were subjected to next generation sequencing (NGS) on Illumina HiSeq 2500 resulting in ~30 million 100 nt single-end reads per sample.

value: Embryos

value: F1 from nos-Cre x pUAST-attB-hsp70-loxP-stop-loxP-Dam-Lamin


title: Ab_sample12


title: genomic DNA from Patient8_week0

data_processing:
Touleimat and Tost, Epigenomics 2012
Average Beta

extract_protocol: DNA was isolated using the QIAcube and AllPrep DNA/RNA Mini Kit 350 or 600 for biopsies from the first two or the last time point, respectively (Qiagen) according to the company’s standard protocol.


title: genomic DNA from Patient108_week0


title: Dam-LaminDm0 DamID-seq, rep 1


title: 626_NSC-AST_DIV4_input

city: Seattle

middle: H

last: Seward

address: Stubbs Lab, Rm 404, 720 Broadway

institute: Pacific Northwest Research Institute

description: 625+626 are two libraries made from the same input biological sample, for greater read depth, pooled for analysis.

data_processing:
Base calling and demultiplexing into FASTQ files was done using bcl2fastq v1.8.4 software (Illumina).
Read alignment: Bowtie2 to the UCSC Mus musculus mm9 genome, using default settings.
Read quantification: Aligned sequence data were analyzed for peaks using HOMER (Hypergeometric Optimization of Motif EnRichment) v4.7 (Heinz et al. 2010).
BigWiggle pileup files were generated using HOMER’s makeBigWig.pl script with default settings.
Assembly: mm9
Supplementary files format and content: *.bw: BigWig files were generated using HOMER's makeBigWig.pl script with default settings. Scores represent read depth.

source_name: Cultured primary neural stem cells

growth_protocol: Embryos were extracted at E14.5 from C57BL/6J female mice. Frontal cortices were separated from embryonic brains. Tissue was disaggregated and cultured in Complete Embryonic NeuroCult Proliferation Medium at 37C with 5% CO2.

extract_protocol:
2.0 x 10^6 cells were fixed in PBS with 1% formaldehyde for 10 minutes and stopped with 0.125M glycine to 0.125M. Fixed cells were washed 3x with PBS+Protease inhibitor. Washed cells were lysed to nuclei with lysis solution – 50 mM Tris-HCl (pH 8.0), 2 mM EDTA, 0.1% v/v NP-40, 10% v/v glycerol, and PIC – for 30 minutes on ice. Cross-linked chromatin was prepared and sonicated using Bioruptor UCD-200 to generate DNA fragments 200-300 bp in size. 2ug of Rabbit polyclonal antibody raised against H3K27ac (Abcam ab4729) was used to precipitate chromatin from nuclei of approximately 1 x 10^6 cells in biological replicate. DNA was released and quantitated using Qubit 2.0 with dsDNA HS Assay kit, and 10 ng of DNA was used to generate libraries for Illumina sequencing.
ChIP-seq libraries were generated using KAPA LTP Library Preparation Kits to yield two independent ChIP replicates for each antibody. We also generated libraries from sonicated genomic input DNA from the same chromatin preparations as controls. Libraries were bar-coded with Bioo Scientific index adapters and sequenced to generate 20-40 million reads per duplicate sample using the Illumina Hi-Seq 2500 instrument at the University of Illinois W.M. Keck Center for Comparative and Functional Genomics using a HiSeq SBS sequencing kit version 4 according to manufacturer’s instructions.

treatment_protocol: Approximately 5.0 x 10^6 of proliferative mouse neural stem cells were plated to PDL/LMN-coated T-75 flasks. Mouse neuron differentiation medium (Neurobasal medium with 2% B-27 supplement and 2 mM GlutaMAX-1 supplement (Life Technologies, Carlsbad, CA, otherwise mentioned)), oligodendrocyte differentiation medium (Neurobasal medium with 2% B-27 supplement, 2 mM GlutaMAX-1, and 30 ng/mL T3), and astrocyte differentiation medium (Dulbecco’s Modified Eagle Medium with 1% N-2 supplements, 2 mM GlutaMAX-1, and 1% Fetal Bovine Serum) were freshly prepared before use. Upon reaching 70% confluency, complete culture medium was replaced with corresponding cell-type specific differentiation medium after two 1X PBS washes. Differentiation media was changed every 48 hours and samples were collected at Day 0 and Day 4.

value: Frontal cortex

value: Astrocyte

tag: strain

tag: time point

tag: replicate

tag: chip antibody


title: Ab_sample4

tag: cell type

tag: library type


title: Dam-Elys DamID-seq, rep 2

value: F1 from nos-Cre x pUAST-attB-hsp70-loxP-stop-loxP-Dam-Elys


title: 625_NSC-AST_DIV4_input


title: genomic DNA from Patient22_week0

value: Female


title: 499_NSC-OLG_DIV4_input

value: Oligodendrocyte

value: input


title: genomic DNA from Patient15_week0

value: Tumor biopsy


title: Dam-Elys DamID-seq, rep 1

extract_protocol:
Approximately two hundred 16-18-h embryos from these crosses were collected, washed with H2O, dechorionated with 2.5% hypochlorite for 3 min and again washed three times with H2O. Isolation of genomic DNA was performed by DNeasy Blood and Tissue kit (Qiagen), following the protocol for cultured cells. DNA was concentrated by centrifugation in 0.5 ml Amicon-Ultra columns (Millipore) for 10 min at 18000 × g and its concentration was measured using a NanoDrop spectrophotometer. For the selective amplification of methylated GATC-GATC fragments, genomic DNA was first digested by DpnI, followed by ligation of adaptors, DpnII digestion and PCR-amplification as described previously (Vogel et al. 2007) with a minor modification: ~0.5 µg instead of 2.5 µg of genomic DNA was used as an input.We applied 18 cycles of PCR (1 min at 94°C, 1 min at 65°C, 2 min at 68°C) for Dam-only and Dam-Elys and 16 cycles for Dam-Lam DNA samples. Adapters were removed by DpnII digestion for 2 h at 37°C. The amplified methylated DNA fragments were purified using QIAquick PCR Purification kit (Qiagen), concentrated by centrifugation in 0.5 ml Amicon-Ultra columns (Millipore) for 10 min at 18000 × g, and quantified on a NanoDrop spectrophotometer.
0.5 µg of Dam-only, Dam-Elys and Dam-Lam DNA samples (each in two biological replicates) were subjected to next generation sequencing (NGS) on Illumina HiSeq 2500 resulting in ~30 million 100 nt single-end reads per sample


title: GEX_sample42

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
polyA RNA

value: mRNA

tag: antibodies/tags


title: Ab_sample1

value: Heart


title: genomic DNA from Patient30_week0


title: genomic DNA from Patient43_week0

value: Chemotherapy


title: Dam DamID-seq, rep 1

value: F1 from nos-Cre x pUAST-attB-hsp70-loxP-stop-loxP-Dam


title: 497_NSC-OLG_DIV4_H3k27ac

value: H3k27ac (Abcam ab4720)


title: GEX_sample41

value: Cardiac Cells


title: GEX_sample39


title: 495_NSC-AST_DIV4_H3k27ac


title: PK15 cells, PARP11-KO rep3

city: Changchun

first: Chunyun

last: Qi

address: 5333#, Xinzhu Road, Changchun 130062, China

institute: Jilin university

data_processing:
The raw reads were processed with a bioinformatic pipelinetool, BMKCloud(www.biocloud.net) online platform
Assembly: Sus_scrofa.ensembl_release_110.genome.fa
Supplementary files format and content: tab-delimited text file include FPKM values for samples.

source_name: Porcine kidney

extract_protocol:
RNA was isolated with RNAsimple Total RNA Kit (TIANGEN). 1 μg of total RNA  was used  for the construction of sequencing library.
RNA library for RNA-seq were prepared using Hieff NGS Ultima Dual-mode mRNA Library Prep Kit for Illumina (Yeasen) following manufacturer’s protocols.

value: Porcine kidney

value: PK15 cells

value: Porcine Kidney cells

tag: treatment

value: PRV-infected


title: GEX_sample34


title: Ab_sample2

value: ADT

value: TotalSeq A 277 panel (BioLegend) antibody cocktail + two custom oligo-tagged antibodies (anti-FAP and anti-LRRC15)


title: genomic DNA from Patient123_week0

value: Breast cancer

value: Chemotherapy+bevacizumab


title: 494_NSC-AST_DIV4_H3k27ac

first: Christopher

value: Frontal cortex

value: Astrocyte


title: 338_NSC-NEU_DIV4_input

value: Neuron

value: input


title: PK15 cells, PARP11-KO rep2


title: genomic DNA from Patient42_week0

value: Female

value: Tumor biopsy


title: GEX_sample33

value: Heart

value: mRNA


title: genomic DNA from Patient97_week0


title: PK15 cells, PARP11-KO rep1


title: genomic DNA from Patient58_week0

value: Chemotherapy


title: PK15 cells, WT rep3

value: Porcine kidney

value: WT


title: 498_NSC-OLG_DIV4_H3k27ac

value: Oligodendrocyte

value: H3k27ac (Abcam ab4720)


title: 337_NSC-NEU_DIV4_H3k27ac


title: GEX_sample32

value: Cardiac Cells


title: Dam DamID-seq, rep 2

value: Embryos

value: F1 from nos-Cre x pUAST-attB-hsp70-loxP-stop-loxP-Dam


title: 336_NSC-NEU_DIV4_H3k27ac


title: GEX_sample30


title: genomic DNA from Patient113_week0

value: Breast cancer


title: PK15 cells, WT rep2

value: PK15 cells

value: Porcine Kidney cells

value: PRV-infected


title: 320_NSC_DIV0_input

value: Frontal cortex

value: NSC

value: input


title: GEX_sample29

value: Heart


title: 319_NSC_DIV0_H3k27ac


title: PK15 cells, WT rep1


title: genomic DNA from Patient92_week0

value: Female

value: Tumor biopsy

value: Chemotherapy+bevacizumab


title: GEX_sample28

value: mRNA


title: RNA_muscle_CBP_60h_rep3

city: Wuhan

first: Xuan

middle: Wen

last: Wang

state: Hubei Province

address: No. 1 Shizishan Street

institute: Huazhong Agriculture University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trimmomatic
Trimmed sequence reads were mapped to Sscrofa11.1 genome
Read count extraction and normalization were performed using featureCounts
Assembly: Sscrofa11.1
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: muscle

growth_protocol: C3H cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using RNA was harvested using VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina(NR605-02) following manufacturer's protocols.

treatment_protocol: The cells were treated with 5uM/ml SGC-CBP30 for 48h in the proliferation phase and 60h in the differentiation phase

value: muscle

value: muscle satellite cell

value: cell differentiation


title: GEX_sample27

value: Cardiac Cells


title: 318_NSC_DIV0_H3k27ac

value: H3k27ac (Abcam ab4720)


title: genomic DNA from Patient84_week0

first: Thomas

address: Ullernchausséen 70

institute: Oslo University Hospital

value: Breast cancer


title: genomic DNA from Patient5_week0


title: NSC-OLG_DIV4_2_RNA

data_processing:
Base calling and demultiplexing into FASTQ files was done using bcl2fastq v1.8.4 software (Illumina).
Read alignment: Tophat 2.0.8 to the Mus musculus NCBI version 37.2 genome, default parameters.
Read quantification: Reads inside of exon features were counted in union mode using htseq version 0.6.1.
Differential expression: Done in R using the Bioconductor package edgeR. Pairwise comparisons between control and intruder conditions in each tissue and time after challenge were analyzed using the bin.loess version of trended dispersion in edgeR version 3.2.4 in R version 3.0.0.
BigWiggle pileup files were generated on pooled biological replicates using v4.7 of HOMER ’s makeBigWig.pl script with default settings. (Heinz et al. 2010).
Assembly: Mouse NCBI genome build 37.2.
Supplementary files format and content: RNA_CPMs.txt: Tab-delimited text file of the matrix of raw read counts mapped to the mouse genome (Ensembl annotation of the NCBIM37 version of the mouse genome) as created by the edgeR function readDGE. TopHat2 version 2.0.8 (Kim et al. 2013) was used to align reads. Reads inside of exon features were counted in union mode using htseq version 0.6.1 (Anders et al. 2015). Note that the counts include meta tags that are prefixed by "__" that were removed from counts before further processing.
Supplementary files format and content: *.bw: BigWig files were generated using HOMER's makeBigWig.pl script with default settings. Scores represent read depth.

extract_protocol:
About 0.5 x 10^7 cultured cells were disrupted in Trizol with a cell scraper. The aqueous phase was precipitated in isopropanol, resuspended in nuclease-free water, treated with DNase I and cleaned up using a Zymo RNA Clean & Concentrator™-25 kit.
RNA-Seq libraries were prepared from total RNA robotically using TruSeq Stranded mRNA on an epMotion 5075 robot. Libraries were pooled and sequenced on an Illumina HiSeq 2500 using an Illumina TruSeq SBS sequencing kit, version 3.

value: Oligodendrocyte


title: RNA_muscle_CBP_60h_rep1


title: genomic DNA from Patient95_week0


title: GEX_sample15


title: RNA_muscle_CBP_0h_rep3

value: cell proliferation


title: NSC-NEU_DIV4_3_RNA

value: Neuron


title: genomic DNA from Patient101_week0


title: RNA_muscle_CBP_0h_rep2


title: GEX_sample13


title: NSC-NEU_DIV4_2_RNA

value: Frontal cortex


title: genomic DNA from Patient36_week0


title: RNA_muscle_CBP_0h_rep1


title: GEX_sample9


title: NSC-NEU_DIV4_1_RNA


title: GEX_sample12


title: RNA_muscle_WT_60h_rep3


title: genomic DNA from Patient34_week0


title: genomic DNA from Patient120_week0


title: GEX_sample8


title: NSC-AST_DIV4_3_RNA

value: Astrocyte


title: RNA_muscle_WT_60h_rep2


title: RNA_muscle_CBP_60h_rep2


title: NSC-AST_DIV4_2_RNA


title: GEX_sample17


title: RNA_muscle_WT_60h_rep1


title: NSC-OLG_DIV4_1_RNA


title: genomic DNA from Patient41_week0


title: NSC-AST_DIV4_1_RNA


title: RNA_muscle_WT_0h_rep3


title: genomic DNA from Patient3_week0

value: Chemotherapy


title: GEX_sample6

value: Heart


title: GEX_sample5


title: NSC_DIV0_3_RNA

value: NSC


title: RNA_muscle_WT_0h_rep2


title: genomic DNA from Patient111_week0

value: Female

value: Tumor biopsy


title: NSC_DIV0_2_RNA


title: genomic DNA from Patient27_week0

value: Chemotherapy+bevacizumab


title: RNA_muscle_WT_0h_rep1

value: muscle


title: genomic DNA from Patient26_week0


title: GEX_sample2

value: mRNA


title: NSC_DIV0_1_RNA


title: GEX_sample4


title: genomic DNA from Patient114_week0


title: GEX_sample7


title: GEX_sample1


title: genomic DNA from Patient20_week0


title: cut_tag_h3k27ac_muscle_CBP_60h_rep1

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trimmomatic
Trimmed sequence reads were mapped to Sscrofa11.1 genome
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.05
bigWig files were generated using the macs2.  narrowPeak files were generated using MACS v2 with default settings.
Assembly: Sscrofa11.1
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

extract_protocol:
Permeabilized cells in ice-cold NE1 on ice for 10 min, followed by light crosslinking with formaldehyde to fix nuclei. Then, cells nuclei bound to Concanavalin A-coated Magnetic Bead
Performed chromatin profiling with CUT&Tag according to its latest protocol

value: muscle satellite cell


title: IP8_Human_2_METTL3_KO_R1

first: Sandra

last: Melo

address: 1 DNA Way

institute: Genentech, Inc.

description: IP8_Human_2_METTL3_KO_R1.basedon.peaks.l2inputnormnew.bed.compressed.bed

data_processing:
3′-adapters were trimmed from reads using cutadapt (v2.7) 34, and reads shorter than 18 bp in length were removed. Reads were then mapped to a database of human or mouse repetitive elements and rRNA sequences compiled from Dfam 35 and Genbank 36.
All non-repeat mapped reads were mapped to the human genome (hg38) or mouse genome (mm10) using STAR (v2.6.0c). PCR duplicates were removed using umi_tools (v0.5.1) by utilizing UMI sequences from the read names and mapping positions. Peaks were identified within m6A-eCLIP samples using the peak caller CLIPper
Assembly: hg38

source_name: monocyte-derived macs

extract_protocol:
Total RNA was isolated from 20 x 106 cells using Quick-RNA MiniPrep (Zymo) followed by a poly(A) selection using oligo (dT) beads (ThermoFisher) from 50 µg of total RNA
After dephosphorylation with FastAP (ThermoFisher) and T4 PNK (NEB), a barcoded RNA adapter was ligated to the 3′ end (T4 RNA Ligase, NEB).

value: monocyte-derived macs

value: macrophages

tag: antibody


title: cut_tag_h3k27ac_muscle_WT_60h_rep2

tag: cell line


title: Uhrf2 WT LSK 3

city: Fukushima

first: Kazuhiko

last: Ikeda

state: Fukushima

address: 1 Hikariga-oka

department: Blood Transfusion and Transplantation Immunology

country: Japan

institute: Fukushima Medical University

data_processing:
The quality of the libraries was assessed with an Agilent 2200 TapeStation High Sensitivity D1000.
The equally pooled libraries of the samples were sequenced using the Illumina HiSeq system in 51-base-pair (bp) single-end reads.
Sequencing adaptors, low quality reads, and bases were trimmed with Trimmomatic-0.32 tool.
The aligned reads were subjected to downstream analyses using StrandNGS 3.0 software.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: bone marrow

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 8 pM total RNA was used for the construction of sequencing libraries.
Sequencing library construction using Ovation Single Cell RNA-Seq System (NuGEN) according to the manufacture's protocol

value: bone marrow

value: LSK cells

tag: genotype

value: Uhrf2 WT


title: genomic DNA from Patient37_week0

last: Fleischer

tag: gender

value: Breast cancer


title: IP7_Human_2_NTC_WT_R1

description: IP7_Human_2_NTC_WT_R1.basedon.peaks.l2inputnormnew.bed.compressed.bed


title: cut_tag_h3k27ac_muscle_WT_60h_rep1

value: cell proliferation


title: genomic DNA from Patient89_week0

tag: sample type


title: cut_tag_h3k27me3_muscle_CBP_60h_rep2


title: Uhrf2 WT LSK 1


title: genomic DNA from Patient128_week0

tag: disease state


title: Uhrf2 KO LSK 5

value: Uhrf2 KO


title: Uhrf2 WT LSK 5


title: genomic DNA from Patient24_week0

tag: agent


title: IP5_Human_1_ZC3H13_KO_R1

description: IP5_Human_1_ZC3H13_KO_R1.basedon.peaks.l2inputnormnew.bed.compressed.bed


title: cut_tag_h3k27ac_muscle_CBP_60h_rep2

tag: tissue


title: cut_tag_h3k27me3_muscle_WT_60h_rep2


title: Uhrf2 KO LSK 4


title: genomic DNA from Patient71_week0

tag: timepoint


title: IP9_Human_2_ZC3H13_KO_R1

description: IP9_Human_2_ZC3H13_KO_R1.basedon.peaks.l2inputnormnew.bed.compressed.bed


title: cut_tag_h3k27me3_muscle_CBP_60h_rep1


title: IP4_Human_1_METTL3_KO_R1

description: IP4_Human_1_METTL3_KO_R1.basedon.peaks.l2inputnormnew.bed.compressed.bed


title: genomic DNA from Patient110_week0


title: IP3_Human_1_NTC_WT_R1

description: IP3_Human_1_NTC_WT_R1.basedon.peaks.l2inputnormnew.bed.compressed.bed


title: Uhrf2 WT LSK 2


title: cut_tag_h3k4me3_muscle_CBP_60h_rep2


title: IP10_Human_2_WTAP_KO_R1

description: IP10_Human_2_WTAP_KO_R1.basedon.peaks.l2inputnormnew.bed.compressed.bed


title: Uhrf2 KO LSK 2


title: Uhrf2 WT LSK 4


title: cut_tag_h3k4me3_muscle_CBP_60h_rep1


title: Uhrf2 KO LSK 3


title: genomic DNA from Patient131_week0


title: genomic DNA from Patient47_week0


title: Input9_Human_2_ZC3H13_KO_R1

value: input


title: Uhrf2 KO LSK 1


title: IP6_Human_1_WTAP_KO_R1

description: IP6_Human_1_WTAP_KO_R1.basedon.peaks.l2inputnormnew.bed.compressed.bed


title: Input8_Human_2_METTL3_KO_R1


title: genomic DNA from Patient122_week0

value: Chemotherapy


title: cut_tag_h3k4me3_muscle_WT_60h_rep2


title: cut_tag_h3k4me3_muscle_WT_60h_rep1


title: Tet1+/+ TdgN151A/+ ApcMin/+  adenoma 3

city: Camden

first: Jaroslav

last: Jelinek

state: NJ

address: 403 Haddon Avenue

department: Research Labs

institute: Coriell Institute for Medical Research

description: Tet1+/+ TdgN151A/+ ApcMin/+  adenoma

data_processing:
Library strategy: DREAM
Adapter sequences were removed using TrimGalore!
Sequencing reads were mapped using Bowtie2 for each SmaI/XmaI site in the genome and signatures to methylated (5'CCGGG) and unmethylated (5'GGG) CpG were enumerated for each SmaI/XmaI site. The mouse genome mm9 was used.
For every CpG site within the SmaI/XmaI recognition site, the methylation was calculated. Let m be the number of tags corresponding to methylated CpG's (tags starting with CCGGG) and u be the number of tags corresponding to unmethylated CpG's (tags starting with GGG), the methylation percent was calculated as 100*(c*m)/(c*m+u), where c is the correction factor based on the observed vs expected methylation of spiked-in standards.
Genome_build: mm9
Supplementary_files_format_and_content: The processed data are in tab-delimited text file. The columns of the file are: ID_SmaI_mm9 (CCCGGG site ID), chromosome (chromosome of the CCCGGG site), position (position of the CCCGGG site), meth_reads (observed number of reads corresponding to methylated CpG, XmaI), unmeth_reads (observed number of reads corresponding to unmethylated CpG, SmaI), total_reads, raw_methylation (unadjusted methylation value), adjusted_methylation (methylation value adjusted based on spiked in standards).

source_name: Colonic adenoma

growth_protocol: Mutant mice were appropriately crossed to generate experimental mice from four-genotype groups: Tet1-/- Tdg+/+ ApcMin/+; Tet1+/- TdgN151A/+ ApcMin/+ ; Tet1+/+ TdgN151A/+ ApcMin/+; and Tet1+/+ Tdg+/+ ApcMin/+.

extract_protocol:
Genomic DNA was extracted using Puregene Gentra DNA extraction protocol.
Genomic DNA extracted from tissue samples was spiked with methylation standards and sequentially digested with two restriction endonucleases recognizing CCCGGG sites in DNA. SmaI cleaved only unmethylated sites resulting in blunt ended fragments starting with 5’-GGG. Next, XmaI cleaved the remaining methylated sites creating 5’-CmeCGG overhang sequences. Exonuclease-deficient Klenow fragment DNA polymerase was then used to fill in the 3’ recesses left by XmaI and add 3’-dA overhangs to the ends of all fragments. Thus, specific signatures 5’-GGG and 5’-CCGGG were created at unmethylated and methylated CpG sites, respectively. Illumina sequencing adapters were then ligated to the enzyme-treated DNA; sequencing libraries were generated according to Illumina protocols and run on an Illumina HiSeq 2500 instrument at Fox Chase Cancer Center Genomics facility. Sequencing data were aligned to the rat genome (rn4), and the reads with unmethylated and methylated signatures were counted at individual CCCGGG sites. Methylation levels were calculated as the ratio of reads with the methylated signature to all reads mapping to each respective site. DNA methylation values at individual CpG sites were adjusted based on spiked in standards and filtered for the minimum sequencing depth of 100 reads.

treatment_protocol: Mice were sacrificed at 150-160 days, and colonic adenomas were dissected for DNA extraction

tag: strain

value: Tet1 wt TdgN151A/+


title: Tet1+/+ TdgN151A/+ ApcMin/+  adenoma 2

description: Tet1+/+ TdgN151A/+ ApcMin/+  adenoma


title: genomic DNA from Patient100_week0

city: Oslo

value: Female


title: genomic DNA from Patient18_week0

value: Tumor biopsy


title: Input6_Human_1_WTAP_KO_R1


title: Input7_Human_2_NTC_WT_R1


title: cut_tag_h3k27me3_muscle_WT_60h_rep1


title: genomic DNA from Patient74_week0


title: cut_tag_igg_muscle_WT_60h_rep2


title: cut_tag_igg_muscle_CBP_60h_rep1


title: Input5_Human_1_ZC3H13_KO_R1


title: Input4_Human_1_METTL3_KO_R1


title: genomic DNA from Patient65_week0


title: cut_tag_igg_muscle_CBP_60h_rep2


title: Input3_Human_1_NTC_WT_R1


title: genomic DNA from Patient49_week0


title: genomic DNA from Patient112_week25


title: Tet1+/- TdgN151A/+ ApcMin/+  adenoma 2

description: Tet1+/- TdgN151A/+ ApcMin/+  adenoma


title: Tet1+/- TdgN151A/+ ApcMin/+  adenoma 1

description: Tet1+/- TdgN151A/+ ApcMin/+  adenoma


title: Tet1-/- Tdg+/+ Apc-Min/+ adenoma 3

description: Tet1-/- Tdg+/+ Apc-Min/+ adenoma

value: Tet1-/- Tdg wt


title: Tet1+/- TdgN151A/+ ApcMin/+  adenoma 3

description: Tet1+/- TdgN151A/+ ApcMin/+  adenoma


title: cut_tag_igg_muscle_WT_60h_rep1

value: muscle


title: cut_tag_h3k27ac_muscle_CBP_0h_rep1


title: cut_tag_h3k27ac_muscle_CBP_0h_rep2


title: Input10_Human_2_WTAP_KO_R1


title: genomic DNA from Patient104_week25


title: genomic DNA from Patient23_week25


title: Tet1+/+ TdgN151A/+ ApcMin/+  adenoma 1

description: Tet1+/+ TdgN151A/+ ApcMin/+  adenoma


title: Tet1-/- Tdg+/+ Apc-Min/+ adenoma 2

description: Tet1-/- Tdg+/+ Apc-Min/+ adenoma


title: D6

city: Kobe

first: Kazuya

last: Miyagawa

address: 5-7-1 Koji-dai, Nishi

institute: Kobe City Nishi-Kobe Medical Center

data_processing:
Trimmed using FASTQ groomer.
Aligned to the human genome using HISAT2.
Assembly: hg19
Supplementary files format and content: A txt file is generated using DEseq2 on Seqmonk.

source_name: Peripheral blood mononucleor cells

extract_protocol:
Total RNA were extracted using Maxwell® RSC instrument and Maxwell® RSC simply RNA Blood Kit (Promega) according to manufacturer’s instructions
Libraries were prepared with the TruSeq Stranded mRNA Library Prep Kit (Illumina)

tag: subject status

value: early stage non-severe COVID-19 patient

tag: subject group

value: deteriorated based on the subsequent clinical courses

value: Peripheral blood mononucleor cells


title: Tet1-/- Tdg+/+ Apc-Min/+ adenoma 1

description: Tet1-/- Tdg+/+ Apc-Min/+ adenoma


title: cut_tag_h3k27ac_muscle_WT_0h_rep2

value: muscle satellite cell

tag: chip antibody


title: D5

tag: cell type


title: cut_tag_h3k27ac_muscle_WT_0h_rep1


title: cut_tag_h3k27me3_muscle_CBP_0h_rep2


title: Control Apc-Min/+ adenoma 3

description: control Apc-Min adenoma

value: Tet1 wt Tdg wt


title: D4


title: genomic DNA from Patient72_week25


title: Control Apc-Min/+ adenoma 2

description: control Apc-Min adenoma


title: cut_tag_h3k27me3_muscle_CBP_0h_rep1


title: Control Apc-Min/+ adenoma 1

description: control Apc-Min adenoma


title: D2


title: genomic DNA from Patient81_week25

value: Chemotherapy+bevacizumab


title: genomic DNA from Patient28_week25


title: genomic DNA from Patient117_week25


title: D3


title: Ctnnb1-ex3-rep2

city: Milano

first: Diego

last: Pasini

address: Via Adamello, 16

country: Italy

institute: European Institute of Oncology

data_processing:
Transcript abundances were quantified using salmon65 with parameters --gcBias --seqBias –validateMappings. Transcript abundances were imported into DESeq266 using tximport67 to perform differential expression analyses. Fold changes were calculated with DESeq2 with default settings and fold changes and p-values corrected with the bioconductor packages apglm68 and IHW69, respectively. Genes with an absolute log2 fold change >= 1 and FDR < 5% were considered as differentially expressed
Genome_build: mm10
Supplementary_files_format_and_content: differential expression
Supplementary_files_format_and_content: salmon quant
Supplementary_files_format_and_content: raw counts

source_name: intestinal organoids

growth_protocol: Mouse organoids were obtained from small intestines as previously described61. A detailed description can be found in supplementary information. Wild-type organoids were cultured in presence of recombinant Wnt3a (homemade), R-spondin1 (homemade), 0.1 μg/ml Noggin, 0.05 μg/ml EGF.  Apc-/- and CtnnB1-ex3 organoids were only supplemented with 0.1 μg/ml Noggin and 0.05 μg/ml EGF.

extract_protocol: RNA-seq libraries were prepared using a custom Smart-seq2 procedure that was previously described65. A detailed description of the library preparation procedure is available in supplementary information.


title: D1


title: cut_tag_h3k27me3_muscle_WT_0h_rep1


title: cut_tag_h3k27me3_muscle_WT_0h_rep2


title: ND6

value: non-deteriorated, based on the subsequent clinical courses


title: genomic DNA from Patient45_week25

value: Breast cancer


title: cut_tag_h3k4me3_muscle_CBP_0h_rep2

value: cell proliferation


title: genomic DNA from Patient48_week25


title: cut_tag_h3k4me3_muscle_CBP_0h_rep1


title: WT-rep1

value: WT


title: genomic DNA from Patient25_week25


title: ND4


title: D10S

city: Not Hispanic or Latino

first: Sheng

last: Zhao

address: #87, Dingjiaqiao, Gulouqu

department: Biochemistry and Molecular biology

institute: Southeast University

description: The focal regions of caudate putamen ischemia were carefully micro-punched under a cryostat based on the location indicated by T2-weighted magnetic resonance images from the mice. Tissue from 6 animals per time point were mixed as single sample for each time point.

data_processing:
Illumina HiSeq 2500 platform to get the raw data
Clean reads were generated from row reads by Trimmomatic (ver. 0.36) using default parameters
The clean reads were mapped to reference genome (Ensembl Mus_musculus GRCm38.90) with Hisat2 (ver. 2.1.0)
Mapped data were assembled by Stringtie (ver. 1.3.4d) with default parameters
Group comparison using GFold (ver. 1.1.4, sc=0.01) was performed to estimate the differential gene expression by the Reads per kilobase per million mapped reads (RPKM)
Genome_build: Ensembl Mus_musculus GRCm38.90
Supplementary_files_format_and_content: Excel file of differential expressed genes (adjusted p value<0.01, RPKM, Gfold score, and the differential expression data.)  RPKM also provided for all genes at all p-values.

source_name: right focal region 10 day after stroke

growth_protocol: Standard animal care

extract_protocol:
Mixed tissue of each group were then performed standard RNA extraction using Trizol
RNA-seq library construction according to the VAHTSTM Total RNA-seq (H/M/R) Library Prep Kit for Illumina (Vazyme Biotech Co.,Ltd, Nanjing, China)

treatment_protocol: After anesthetization with isoflurane gas, the mouse head was fixed using a small animal stereotactic frame. A scalp incision of 1 cm was made in the midline and a small hole was made on the skull above the caudate putamen (0.5 mm anterior to bregma, +/-2.5 mm lateral to midline). An unjacked optical fiber with 125 μm outer diameter and 50 μm core diameter was placed into a 28-gauge straight stainless steel needle. The other end of the optical fiber was connected to a 532 nm laser source (Shanghai Laser & Optics Century Co., Ltd, China). With the guidance of the needle, the optical fiber was stereotactically positioned to the caudate putamen (3 mm ventral to dura mater) in the mouse brain. 100 mg/kg rose bengal were then injected intraperitoneally (Sigma-Aldrich) 5 min before laser irradiation (another 2 min with 30mW output). On the sham side, all procedures were performed the same as above except applying the laser irradiation before rose bengal injection. After the scalp wound was secured, the mice were released from the stereotactic frame and transferred to a recovery chamber.

value: caudate putamen

value: photothrombotic internal ischemia stroke

tag: time point

value: 10 day after stroke


title: genomic DNA from Patient130_week25

value: Female


title: cut_tag_h3k4me3_muscle_WT_0h_rep1


title: cut_tag_h3k4me3_muscle_WT_0h_rep2


title: D3S

source_name: right focal region 3 day after stroke

value: 3 day after stroke


title: genomic DNA from Patient94_week25

value: Tumor biopsy


title: genomic DNA from Patient76_week25


title: genomic DNA from Patient121_week25


title: cut_tag_igg_muscle_CBP_0h_rep1

value: muscle


title: H4S

source_name: right focal region 4 hour after stroke

value: 4 hour after stroke


title: ND2

value: early stage non-severe COVID-19 patient


title: cut_tag_igg_muscle_CBP_0h_rep2