title: ETO-3

city: WuHan

first: chenchao

last: yan

state: Hubei Province

address: Donghu Road, No. 115

institute: WuHan university

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, the clean data were mapped to human genome (hg38) using HISAT2 (v2.1.0)
Raw reads were counted using FeatureCounts (v1.6.4)
Assembly: GRCh38

growth_protocol: Human ESC line HUES8  was cultured on Matrigel (Corning, Cat# 354277)-coated plates in mTeSR1 (StemCell Technologies, Cat# 85850) at 37℃ with 5% CO2. To induce definitive endoderm (DE) differentiation, human ESCs were seeded on growth factor-reduced Matrigel (Corning, Cat# 354230)-coated 24-well plates in mTeSR1 at the density of 1×105 cells/well. After 2 days’ maintaining to achieve 80% confluence, mTeSR1 was replaced by DMEM/F12 (DF12, Gibco, Cat# C11995500BT) supplemented with 100 ng/mL Activin A (PeproTech, Cat# 120-14P), 50 ng/mL Wnt-3a (R&D, Cat# 5036-WN), and 0.2% fatty acid free bovine serum albumin (Yeasen Biotechnology, Cat# 36104ES25) for 2 days, then the Wnt-3a was removed for the following 1-2 days.

extract_protocol:
The cells were washed by DPBS and harvested by buffer RL. The HiPure Total RNA Mini Kit (Magen, Cat# R4111-03) was used to extract total RNA following the manufacturer’s instructions and the RNA was quantitated with nanodrop 2000 (ThermoFisher).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: human definitive endoderm

value: WT


title: mantle_3

status: Public on Jul 02 2023

type: SRA

city: Ningbo

first: Zhaoshou

last: Ran

state: Zhejiang

address: Fenghua Road 818, Jiangbei Districta

department: Institute of Marine Science

country: China

institute: Ningbo University

library_source: transcriptomic

data_processing:
The library preparations were sequenced on an Illumina Hiseq 4000 platform in Novogene Bioinformatics Technology Co., Ltd (Beijing, China).
Raw data of fastq format were firstly processed through inhouse perl scripts.
Transcriptome assembly was accomplished by using Trinity with min_kmer_cov set to 2 by default and all other parameters set default.
Gene function was annotated based on the following seven databases: Nr (non-redundant protein sequences), Nt (non-redundant nucleotide sequences), Swiss Prot, KOG (eukaryotic Orthology Groups; BLASTx, version v2.2.26, E-value = 1 × 10-5), Pfam (Protein family; HMMER 3.0 Package, hmmscan, E-value = 0.01), KO (KEGG Ortholog; KEGG Automatic Annotation Server, E-value = 1 × 10-10) and GO (Gene Ontology; Blast2GO v2.5, E-value = 1 × 10-6). Thereafter, the homology of deduced proteins with other organisms, gene categorizing, functional phylogenetic classification and biological pathways were further analyzed based on NR, GO, KOG and KEGG, respectively.
To estimate the expression level of each gene, the transcriptome obtained from Trinity was used as the reference sequence (REF), the clean reads from each sample were mapped to REF by using RSEM software (bowtie2, default parameters). The count of mapped reads of each gene was further estimated using expected number of fragments per kilobase of transcript per millions base pairs sequenced (FPKM). The analyses of DEGs between tissues were performed using the DESeq R package (1.10.1).
Supplementary files format and content: FPKM values for each sample

molecule: total RNA

organism: Sinonovacula constricta

source_name: mantle

extract_protocol:
RNA was isolated using the TRIzol reagent (Invitrogen, USA). The resulting RNA was further treated with RNase-free DNase I (Invitrogen, USA) to remove any contaminating genomic DNA.
Approximately 1.5 μg RNA per sample was used as input material for the RNA sample preparations. The sequence libraries were generated using NEB Next® Ultra™ RNA Library Prep Kit for Illumina® (NEB) following the manufacturer's recommendations.

tag: tissue

value: mantle


title: HCT116_WT-CSTF2+Serum

city: Nanjing

first: Xiaoxu

last: Liu

state: Jiangsu

address: 2 Sipailou

department: Institute of Life Sciences

institute: Southeast University

library_source: genomic

data_processing:
Clean reads were aligned to the Human genome (UCSC genome, GRCh37/hg19) using Bowtie2 (v2.2.5) with default mode . Peak calling was performed with MACS2.
For peaks, associated control samples were used to determine statistical enrichment at a p < 1e-8 and FDR < 0.05. For Pol II peaks, the enrichments were determined at p < 1e-8 and FDR < 0.05.
The ChIP-seq enrichment is displayed as reads per million (RPM). Gene annotations and transcript start site information were from Human genome (UCSC genome, GRCh37/hg19) by R package ChIPseeker.
Assembly: hg19

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: DMEM (HyClone) supplemented with 10% FBS (Ex-Cell Bio) and 1% Penicillin-Streptomycin (HyClone), at 37°C with 5% CO2 in a humidified incubator and routinely passaged 2-3 times a week.

extract_protocol:
For ChIP-seq,cells were crosslinked with 1% formaldehyde for 10 min and quenched with glycine for 5 min at the room temperature. Fixed cells were sonicated and immunoprecipitated with the mixture of beads and antibody overnight at 4 ℃. ChIP-DNA was purified using PCR purification kit (Qiagen) and performed for qPCR using iTaq™ Universal SYBR® Green Supermix (Bio-Rad) on CFX96 (Bio-Rad).
The ChIP-seq libraries were prepared with VAHTS Universal DNA Library Prep Kit for Illumina V3

treatment_protocol: For serum induction, the complete medium of 60%-70% confluent HCT116 cells was replaced with fresh medium without FBS after washed by PBS for three times. The starved cells were incubated for 40 hours. The incomplete medium was changed with pre-heated complete medium and the cells were incubated for 30 minutes before fixation for ChIP-seq.

tag: cell line

tag: cell type

value: human colon cancer cells

tag: treatment

value: Serum induction

tag: chip antibody

value: abclonal


title: T47D_Clone28_1hour_rep4

city: Charlottesville

first: Thomas

middle: G

last: Scott

state: VA

address: 1340 Jefferson Park Ave, Pinn Hall 6225

department: Biochemistry and Molecular Genetics

country: USA

institute: University of Virginia

data_processing:
Adapter trimming: cutadapt v1.8.1
UMI trimming and reverse complementing: seqtk v1.3
FASTQ deduplication: https://github.com/guertinlab/fqdedup v1.0.0
FASTQ pairing: fastq_pair v1.0
Alignment: bowtie2 v2.4.4
File manipulation: samtools v1.9
File manipulation: https://github.com/guertinlab/seqOutBias v1.3.1
All details and code: https://guertinlab.github.io/TRPS1_ER/Vignette.html
Assembly: hg38
Supplementary files format and content: Stranded bigWig counts files
Supplementary files format and content: Gene counts files

growth_protocol: T47D cells (RRID:CVCL_0553) (ATCC) were cultured in RPMI 1640 medium (Gibco) supplemented with 10% fetal bovine serum (Gemini) and 10ug/ml insulin from bovine pancreas (Sigma, made as a 1000x solution in 1% aqueous glacial acetic acid).

extract_protocol:
Cell permeabilization was performed as previously described (Mahat et al. 2016), with modifications. At the time of harvest, cells were scraped in 10mL ice cold PBS and washed in 5mL buffer W (10mM Tris-HCl pH 7.5, 10mM KCl, 150mM sucrose, 5mM MgCl2, 0.5mM CaCl2, 0.5mM DTT, 0.004U/mL SUPERaseIN RNase inhibitor (Invitrogen), Complete protease inhibitors (Roche)). Cells were permeabilized by incubating with buffer P (10 mM Tris-HCl pH 7.5, KCl 10 mM, 250 mM sucrose , 5 mM MgCl2, 1 mM EGTA, 0.05% Tween-20, 0.1% NP40, 0.5 mM DTT, 0.004 units/mL SUPERaseIN RNase inhibitor (Invitrogen), Complete protease inhibitors (Roche)) for 3 minutes on ice. Cells were washed with 10 mL buffer W before being transferred into 1.5mL tubes using wide bore pipette tips. Finally, cells were resuspended in 50μL buffer F (50mM Tris-HCl pH 8, 5mM MgCl2, 0.1mM EDTA, 50% Glycerol, 0.5 mM DTT). Cells were snap frozen in liquid nitrogen and stored at -80°C.
PRO-seq libraries were prepared as previously described (Judd et al. 2020), with modifications. RNA extraction after the run-on reaction was performed with 500μL Trizol LS (Thermo Fisher) followed by 130μL chloroform (Sigma). The equivalent of 1μL of 50μM for each adapter was used. A random eight base unique molecular identifier (UMI) was included at the 5′ end of the adapter ligated to the 3′ end of the nascent RNA. 37°C incubations were performed with rotation with 1.5mL tubes placed in 50mL conical tubes in a hybridization oven. For the reverse transcription reac- tion, RP1 was used at 100μM and dNTP mix was used at 10mM each. Libraries were amplified by PCR for a total of 8 cycles in 100μL reactions with Phusion polymerase (New England Biolabs). No PAGE purification was performed to ensure that our libraries were not biased against short nascent RNA insertions.

treatment_protocol: 4 replicates were performed from cells treated and collected at different times in the same day. 8*106 cells per sample were plated in 15cm dishes 2 days before harvest. Cells were treated with DMSO or 50nM dTAG-13 and 50nM dTAGV-1 in DMSO at various time points and collected simultaneously.

value: 50nM dTAG-13 + 50nM dTAG-V-1 for 1 hour


title: T47D_Clone28_4hour_rep1

value: 50nM dTAG-13 + 50nM dTAG-V-1 for 4 hours


title: ETO-2

tag: genotype


title: mantle_1


title: T47D_Clone28_2hour_rep4

value: 50nM dTAG-13 + 50nM dTAG-V-1 for 2 hours


title: lips_3

source_name: labial palp

value: labial palp


title: muscle_3

source_name: foot muscle

value: foot muscle


title: T47D_Clone28_1hour_rep2


title: T47D_Clone28_1hour_rep3


title: lips_2


title: T47D_Clone28_0.5hour_rep4

value: 50nM dTAG-13 + 50nM dTAG-V-1 for 30 minutes


title: C75-2


title: C75-1


title: Intest_3

source_name: intestine

value: intestine


title: C75-3


title: T47D_Clone28_0.5hour_rep3


title: Intest_2


title: DE-3


title: DE-2


title: gill_3

source_name: gill

value: gill


title: Intest_1


title: ETO-1


title: DE-1


title: T47D_Clone28_0.5hour_rep2


title: T47D_Clone28_0hour_rep4

value: 0.1% v/v DMSO for 24 hours


title: T47D_Clone28_0.5hour_rep1


title: mouse cells, PTGES-KO, #2

city: Houston

first: Suhendan

last: Ekmekcioglu

state: TX

address: 1515 Holcombe Blvd

department: Melanoma Medical Oncology

institute: University of Texas, MD Anderson Cancer Center

data_processing:
BCL were converted to fastq files using Illumina BaseSpace.
Assembly: mm10
Supplementary files format and content: Tab-delimited files included RPKM values for each Sample

organism: Mus musculus

source_name: C57BL/6 murine BrafV600E melanoma

growth_protocol: Cells were cultivated in D-MEM supplemented with 10% heat-inactivated fetal bovine serum (FBS), 100 U/mL penicillin, and 100 µg/mL streptomycin. Cell cultures were maintained in 5% CO2 at 37°C.

extract_protocol:
RNA-Seq libraries were constructed using Illumina TruSeq RNA sample Preparation Kit v2 following standard procedures
mRNA libraries were generated with a Bioo Scientific NEXTflex Rapid Directional RNA-seq Library Prep Kit. The mRNA libraries were then sequenced on an Illumina HiSeq 2500 in rapid mode using 101 bp paired-end reads.

treatment_protocol: The RNA extraction was performed using Direct-zol RNA MiniPrep kit (Zymo Research, Irvine, CA, USA), following the manufacturer's recommendations.

value: C57BL/6 murine BrafV600E melanoma

value: PTGES-KO

value: Replicate 2


title: mouse cells, PTGES KO, #3

value: Replicate 3


title: CPT2KO-2

source_name: Embryonic stem cell

value: Embryonic stem cell

value: ESC

value: CPT2 KO

value: WT


title: T47D_Clone28_0hour_rep3


title: mouse cells, PTGS2-KO, #3


title: CPT2KO-1


title: gill_2


title: T47D_Clone28_1hour_rep1

value: 50nM dTAG-13 + 50nM dTAG-V-1 for 1 hour


title: mouse cells, PTGES-KO, #1

value: Replicate 1


title: T47D_Clone28_0hour_rep2


title: gill_1


title: siphon_3

source_name: siphon

value: siphon


title: ES-2


title: siphon_2


title: ES-1


title: T47D_Clone28_0hour_rep1


title: mouse cells, PTGS2-KO, #2


title: mouse cells, PTGS2-KO, #1


title: siphon_1


title: mouse cells, PTGS-1 KO, #3


title: Hi-C th1 replicate 2

city: Shanghai

first: Ge

last: Zhang

address: Yueyang Road 320

institute: Shanghai Institute of Nutrition and Health,CAS

data_processing:
Paired-end sequencing reads were mapped to mm10 using HiC-Pro (v2.11.4) pipeline.
The raw contact matrices were generated for each replicate at binning resolutions of 5kb,10kb,20kb,25kb,40kb,100kb. To correct bias, the raw contact matrices were normalized using the iterative correction and eigenvector decomposition (ICE) method.
Assembly: mm10
Supplementary files format and content: allValidPairs.gz

extract_protocol:
For Hi-C, nuclei were extraced after fixing using a cell lysis buffer and DNA was digested with DpnII restriction endonuclease.
All Hi-C libraries were constructed following illumina insctructions accompanying Truseq sample preparation kit.


title: RNA-seq.PR16EXON4KO-EB2

city: Ann Arbor

first: Fengbiao

last: Mao

state: Michigan

address: 1301 Catherine St

department: Department of Pathology

institute: University of Michigan

data_processing:
All RNA-seq data were mapped to the mm10 genome of human using Tophat2 (2.1.1), which was shown to be accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Then, duplicated reads for pair-end data were removed by SAMtools (v1.5).
For RNA-seq, the bigwig files for visualization in Integrative Genomics Viewer (IGV) were generated from BAM files by using “bamCoverage” from deepTools with parameters “--ignoreDuplicates --normalizeUsingRPKM --skipNonCoveredRegions --binSize 50”.
Aligned reads were assembled using Cufflinks (v2.2.1) and assembled transcriptome catalog were used as input for Cuffdiff2 to determine expression levels (FPKM, Fragments Per Kilobase per Million mapped reads) and differential expression between conditions using default options. Genes with p<0.01 were considered to be differentially expressing genes.
Genome_build: mm10
Supplementary_files_format_and_content: Normalized read counts and FPKM values data

growth_protocol: EB were cultured in Knock-out DMEM supplemented with 10%  FBS ,1% NEAA, 1% L-Glutamine and 0.01mM 2-mercaptoethanol.

extract_protocol:
The RNA was extracted using Trizol reagent (Ambion) and further purified according to instructions of RNeasy Mini Kit, QIAGEN
RNA libraries were prepared with the Illumina TruSeq protocol according to the manufacturer’s protocol for RNA-seq libraries.

tag: strain background

value: PR domain KO

value: EB differentiation at day 9th form ES cells


title: RNA-seq.PR16EXON4KO-EB1


title: HCT116_WT_Ser5P+Serum

data_processing:
Clean reads were aligned to the Human genome (UCSC genome, GRCh37/hg19) using Bowtie2 (v2.2.5) with default mode . Peak calling was performed with MACS2.
For AFF1 and AFF4 peaks, associated control samples were used to determine statistical enrichment at a p < 1e-8 and FDR < 0.05. For Pol II peaks, the enrichments were determined at p < 1e-8 and FDR < 0.05.
The ChIP-seq enrichment is displayed as reads per million (RPM). Gene annotations and transcript start site information were from Human genome (UCSC genome, GRCh37/hg19) by R package ChIPseeker.
Assembly: hg19

value: Human colon cancer cells

value: Serum induction

value: Abcam #ab5131


title: wild-type regenerating liver

city: Dallas

first: Prashant

last: Mishra

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

library_source: transcriptomic single cell

data_processing:
Raw reads were processed by 10x Genomics Cell Ranger v7.0 for sample demultiplexing, barcode processing and single-nucleus gene counting.
Assembly: mm10
Supplementary files format and content: Raw read counts per cell in an excel file.

molecule: nuclear RNA

source_name: Liver

growth_protocol: Animals were maintained on standard chow diet, ad libitum, under a standard 12 hr light-dark cycle.

extract_protocol:
In anesthetized mice, livers were perfused  in Liver Perfusion medium (Gibco 17701038) and digest in Liver Digestion medium (Gibco 17703034). The liver cell suspenseion was strained through a 70 um strainer, and nuclei isolation was performed using the 10x Genomics nucleir isolation protocol (CG000365). 7000 nuclei per sample were used for library preparation.
3'RNA-seq libraries were prepared on a 10x Genomics Chromium Contoller using a Chromium Next GEM Single Cell 3' kit v3.1 (10x Genomics, PN-1000629).

treatment_protocol: AAV8-GFP or AAV8-Cre (5x10^10 GC, once) was adminstered by retroorbital injection to mice containing the Cox10-floxed conditional allele. Four weeks later, mice were subjected to a 70% partial hepatectomy protocol. Four days after partial hepatectomy, regenerating livers were dissected for further analysis.

value: Liver

tag: time

value: 4 weeks post partial hepatectomy

value: wild-type


title: HCT116_AFF4 MT_Ser2P+Serum

value: Abcam #ab5095


title: Hi-C th1 replicate 1


title: Hi-C th17 replicate 2


title: Cox10-/- regenerating liver


title: lips_1

value: labial palp


title: RNA-seq.PR16EXON4wt-EB2


title: HCT116_WT_Ser2P+Serum


title: mouse cells, PTGS1-KO, #1

value: C57BL/6 murine BrafV600E melanoma


title: HCT116_AFF4 MT-3-Pol II+Serum

value: Homemade #233


title: mouse cells, scramble, #3

value: Control

value: Replicate 3


title: mouse cells, scramble, #2

value: Replicate 2


title: Hi-C th17 replicate 1


title: RNA-seq.PR16EXON4wt-EB1

value: WT


title: Hi-C naïve CD4+ T cell replicate 2

source_name: naive CD4+ T cells

value: naive CD4+ T cells


title: HCT116_AFF4 KO-2-Pol II+Serum


title: RNA-seq.PR16KO-EB2

value: PRDM16 KO


title: Hi-C naïve CD4+ T cell replicate 1


title: mouse cells, scramble, #1

value: Replicate 1


title: RNA-seq.PR16KO-EB1

value: EB differentiation at day 9th form ES cells


title: HCT116_WT-2-Pol II+Serum

value: Human colon cancer cells

value: Serum induction


title: ATAC-Seq th1 replicate 2

data_processing:
ATAC-Seq reads were mapped to the mm10 with Bowtie2 (v2.3.5.1) using parameter '-X 2000 --no-discordant --no-mixed --no-unal'.
Aligned reads were filtered for a minimum MAPQ of 10, and duplicates were removed using SAMtools.
MACS2  was applied on each merged bam file to call peaks  with option '--nomodel --extsize 200 --shift 100'.
The bigwig files were generated by Deeptools using RPKM option of bamCoverage command.
Assembly: mm10
Supplementary files format and content: bigWig

extract_protocol:
Cells were lysed in lysis buffer (10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2 and NP-40) for 10 min on ice to prepare the nuclei. The optimized concentration of NP-40 is 0.5% for all Th cell types. Immediately after lysis, nuclei were spun at 500g for 5 min to remove the supernatant. Nuclei were then incubated with the Tn5 transposome and tagmentation buffer at 37 °C for 30 min (Vazyme Biotech). After the tagmentation, the stop buffer was added directly into the reaction to end the tagmentation.
PCR was performed to amplify the library for 13 cycles using the following PCR conditions: 72 °C for 3 min; 98 °C for 30 s; and thermocycling at 98 °C for 15 s, 60 °C for 30 s and 72 °C for 3 min; following by 72 °C 5 min. After the PCR reaction, libraries were purified with the 1.2× AMPure (Beckman) beads.


title: LM3-SI-3A

city: Hangzhou

first: Boqiang

address: 3rd Qingchun East Road, Han

institute: Zhejiang University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: hg38
Supplementary files format and content: tab-delimited file includes raw counts for each sample
Supplementary files format and content: tab-delimited file includes RPKM values for each sample

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacture's protocols.

value: HCC cells


title: HCT116_AFF1 KO-1-Pol II+Serum


title: ATAC-Seq th1 replicate 1


title: RNA-seq.PR16wt-EB2


title: HCT116_WT-1-Pol II+Serum


title: ATAC-Seq th17 replicate 2


title: A549_AFF4 shRNA-2_Pol II

value: human alveolar basal epithelial cells

value: AFF4 shRNA


title: A549_NonT shRNA-2_Pol II

value: Non-targeting shRNA


title: LM3-NC-3A

value: si-NC


title: spindrop mouse brain E105 sorted

city: Cambridge

first: Florian

last: Hollfelder

address: 80 tennis court road

country: United Kingdom

institute: University of Cambridge

description: spindrop

data_processing:
FastQC quality control
Pheniqs for demultiplexing
zUMIs to generate gene expression matrices using mouse and human references with Ensembl v99 annotations
Seurat v3 for data integration and analysis
Assembly: GRCm38 genome (Ensembl 99) and GRCh38 genome (Ensembl 99)
Supplementary files format and content: UMI quantified reads mapping to intronic and exonic regions. Downsampled to 20,000 reads per cell when indicated in the file header.

source_name: Embryos at E10.5, brain

extract_protocol:
HEK293T cultured in DMEM supplemented with 10% FBS, mESC cells cultured in 2i/LIF. HEK293T were dissociated with Trypsin-EDTA for 5 minutes at 37C , mESCs were dissociated with Accutase. Mouse brain dissections were dissociated with  with TrypLE Express for 15 minutes at 37C. For nuclei preparations the Nuclei EZ prep kit. For the paraformaldehyde (PFA) treatment, 4% PFA was used. Live celsl were stained with Calcein-AM, PFA-fixed cells and nuclei were stained with Vybrant green.
Bead barcoding: indrop v3 protocol, encapsulation: spinDrop protocol, downstream library preparation: inDrop v3 protocol
inDrop v3 protocol

value: Embryos at E10.5, brain

value: embryos

value: Sample was dissected and , cells were dissociated with TrypLE Express for 15 minutes at 37C, stained with Calcein-AM and sequenced using spindrop.


title: LM3-NC-2A


title: spindrop mouse brain E105 unsorted

description: spindrop without sorting

value: Sample was dissected and , cells were dissociated with TrypLE Express for 15 minutes at 37C, stained with Calcein-AM and sequenced using spindrop without sorting.


title: LM3-SI-2A


title: indrop HEK293T

description: indrop

source_name: kidney, Embryo

value: kidney, Embryo

value: cultured cells

value: cultured in DMEM supplemented with 10% FBS, cells were dissociated with Trypsin-EDTA for 5 minutes at 37C, stained with Calcein-AM and sequenced using  indrop.


title: indrop sorted HEK293T

description: sorted indrop

value: WT

value: cultured in DMEM supplemented with 10% FBS, cells were dissociated with Trypsin-EDTA for 5 minutes at 37C, stained with Calcein-AM and sequenced using sorted indrop.


title: A549_NonT shRNA_AFF4

value: Homemade #110


title: ATAC-Seq naïve CD4+ T cell replicate 1

value: naive CD4+ T cells


title: LM3-SI-1A


title: LM3-NC-1A


title: RNA-Seq th1 replicate 2

data_processing:
RNA-Seq reads were mapped to the mm10 reference genome using hisat2 (v2.2.1) with the parameters '--dta --no-discordant --no-mixed'.
Duplicates were removed, and aligned reads were calculated for each protein-coding gene using HTSeq (v0.13.5) with default parameters.
Fragments Per Kilobase of exon model per Million mapped fragments (FPKM) was calculated by stringtie (v2.1.7) with the default parameters.
DESeq2 (v1.34.0) was applied to identify the differentially expressed genes by using raw read count.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw read count for each sample and bigWig

extract_protocol:
Total RNA was isolated by using the RNeasy kit (Qiagen) while the concentrations and integrity were quantified by Bioanalyzer (Agilent); and the polyadenylated mRNAs were captured with PolyT primers, the Smart-seq2 reverse transcription reactions were performed.
RNA libraries for RNA-seq were preAfter pre-amplification and AMPure XP bead purification, cDNAs were sheared with Covaris and were subject to Illumina TruSeq library preparation. All libraries were sequenced on Illumina HiSeq X Ten according to the manufacturer’s instructions.


title: spindrop HEK293T

description: spindrop

value: cultured in DMEM supplemented with 10% FBS, cells were dissociated with Trypsin-EDTA for 5 minutes at 37C, stained with Calcein-AM and sequenced using spinDrop.


title: HU7-SI-3A

value: HCC cells


title: A549_AFF1

value: human alveolar basal epithelial cells

value: Homemade #218


title: HU7-SI-2A


title: ATAC-Seq th17 replicate 1


title: spindrop maxima HEK293T

description: spindrop

value: cultured in DMEM supplemented with 10% FBS, cells were dissociated with Trypsin-EDTA for 5 minutes at 37C, stained with Calcein-AM and sequenced using spinDrop, but using the Maxima H- reverse transcriptase rather than Superscript III.


title: spindrop no peg HEK293T

description: spindrop

value: cultured in DMEM supplemented with 10% FBS, cells were dissociated with Trypsin-EDTA for 5 minutes at 37C and then stained with Calcein-AM before being processed using spinDrop without the addition of PEG8000 to the reaction mixture, but without proteinaseK added to the lysis mix.


title: HCT116_AFF4 MT_Ser5P+Serum

value: Human colon cancer cells

value: Serum induction

value: Abcam #ab5131


title: HU7-SI-1A


title: A549_AFF1 shRNA_AFF4

data_processing:
Clean reads were aligned to the Human genome (UCSC genome, GRCh37/hg19) using Bowtie2 (v2.2.5) with default mode . Peak calling was performed with MACS2.
For AFF1 and AFF4 peaks, associated control samples were used to determine statistical enrichment at a p < 1e-8 and FDR < 0.05. For Pol II peaks, the enrichments were determined at p < 1e-8 and FDR < 0.05.
The ChIP-seq enrichment is displayed as reads per million (RPM). Gene annotations and transcript start site information were from Human genome (UCSC genome, GRCh37/hg19) by R package ChIPseeker.
Assembly: hg19
Supplementary files format and content: bw

value: Human alveolar basal epithelial cells

value: AFF1 shRNA


title: HU7-NC-3A

value: si-NC


title: RNA-Seq th17 replicate 1


title: HU7-NC-2A


title: RNA-Seq naïve CD4+ T cell replicate 2


title: RNA-Seq naïve CD4+ T cell replicate 1


title: spindrop peg HEK293T

description: spindrop

value: kidney, Embryo

value: cultured cells

value: cultured in DMEM supplemented with 10% FBS, cells were dissociated with Trypsin-EDTA for 5 minutes at 37C and then stained with Calcein-AM before being processed using spinDrop with the addition of PEG8000 to the reaction mixture, but without proteinaseK added to the lysis mix.


title: ATAC-Seq naïve CD4+ T cell replicate 2


title: NB4 ChIP-seq GFI1

first: Yun

last: Tan

state: Shanghai

address: Room 1109, Building 11, 197 Ruijin Er Rd

department: Shanghai Institute of Hematology

institute: Ruijin Hospital, Shanghai Jiao Tong University School of Medicine

data_processing:
Sequencing reads were aligned to hg38 by Bowtie2 (version 2.2.9). The uniquely mapped and non-redundant reads were left to conduct peak calling.
ChIP-seq peak regions were called using MACS (version 1.4.2) at a p-value cut off of 10e-8.
Genome_build: hg38
Supplementary_files_format_and_content: peak.bed files were generated by MACS software

source_name: NB4 cells

growth_protocol: NB4 cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS) in a humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
Cells were washed once with PBS buffer and 3 times with lysis buffer (10 mM Tris-HCl, PH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.5% NP-40, 1 mM PMSF). The pellets were then re-suspended in ChIP buffer (Active motif) containing 1 mM PMSF and proteinase inhibitor cocktail (Sigma). Chromatin shearing was performed using a Biorupter Pico ultrasonicator device (Diagenode) with 30s ON then 30s OFF for 30 cycles. Solubilized chromatin was used for immunoprecipitation by incubating overnight at 4 °C with 5 μg antibodies against PML/RARα fusion protein. The immunoprecipitation reaction was transferred to the Protein G agarose Column (53039, Active Motif) and incubated for 2 hours at 4 °C, then each column was washed 4 times with 900 μL Wash Buffer AM1 (Active motif). The ChIPed sample was eluted using 100 μL 37 °C Elution Buffer AM4 (Active Motif). Cross-linking was reversed by adding 5 μL Proteinase K and the sample was incubated overnight at 65 °C. Input and ChIPed DNA were purified using a DNA purification column (Active Motif).
DNA libraries were prepared with the MicroPlex Library Preparation Kit (Diagenode) according to the manufacturer’s instructions.

treatment_protocol: NB4 cells were cross-linked with 1% formaldehyde in Phosphate Buffered Saline (PBS) buffer for 10min at room temperature, and the fixation reactions were quenched by adding glycine to a final concentration of 0.125 M.

value: acute promyelocytic leukemia cell line


title: RNA-seq.PR16wt-EB1

value: WT

value: EB differentiation at day 9th form ES cells


title: HU7-NC-1A

value: HCC cells


title: spindrop PFA fixed HEK293T

description: spindrop

value: cultured in DMEM supplemented with 10% FBS, cells were dissociated with Trypsin-EDTA for 5 minutes at 37C and then fixed with 4% paraformaldehyde before staining with Vybrant Green and sequencing using spinDrop.


title: mother-derived iPSC rep3

status: Public on Jul 01 2023

city: Tokyo

first: Long

last: Guo

address: 4-6-1 Shirokanedai, Minato-ku

country: Japan

institute: RIKEN

description:
m173
peripheral blood lymphocytes

data_processing:
Read quality was assessed using FastQC, and adapters were removed by Cutadapt 2.9.
The reads from the RNA-seq were aligned to the human genome using HISAT2 v 2.2.0.
Aligned reads were quantified using featureCounts 2.6.0.
TPM was calculated by Python package bioinfokit v2.0.8.
Assembly: GRCh38
Supplementary files format and content: all.tpm.xlsx: Excel file includes TPM values for each Sample.

source_name: iPSC

extract_protocol:
Total RNA was extracted using the SV Total RNA Isolation System (Promega) according to the manufacturer’s instructions.
rRNA was removed by NEBNext Poly(A) mRNA Magnetic Isolation Module (New England biolabs). cDNA synthesis followed by RNA-Seq library preparation were conducted using MGIEasy RNA Directional Library Prep Set V2.0 (MGI tech).

value: iPSC

tag: condition

value: chondrogenic differentiation at day 8


title: patient-derived iPSC rep2

description:
p342
peripheral blood lymphocytes


title: patient-derived iPSC rep3

description:
p343
peripheral blood lymphocytes


title: mother-derived iPSC rep2

description:
m172
peripheral blood lymphocytes


title: mother-derived iPSC rep1

description:
m171
peripheral blood lymphocytes


title: RNA-Seq th1 replicate 1

extract_protocol:
Total RNA was isolated by using the RNeasy kit (Qiagen) while the concentrations and integrity were quantified by Bioanalyzer (Agilent); and the polyadenylated mRNAs were captured with PolyT primers, the Smart-seq2 reverse transcription reactions were performed.
RNA libraries for RNA-seq were preAfter pre-amplification and AMPure XP bead purification, cDNAs were sheared with Covaris and were subject to Illumina TruSeq library preparation. All libraries were sequenced on Illumina HiSeq  X Ten according to the manufacturer’s instructions.


title: NB4 ChIP-seq GFI2


title: RNA-Seq th17 replicate 2


title: A549_AFF1 shRNA-1_Pol II

value: Homemade #233


title: VT80-b

first: Guosong

last: Jiang

address: Jiefang Road, No. 1277

department: Department of Urology

institute: Union Hospital, Tongji Medical College, Huazhong University of Science and Technology

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Trimmomatic-0.36 with parameters LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:20
To evaluate the quality of clean reads , fastqc was used  with default parameters
clean reads were mapped to vitis vinifera genome(ftp://ftp.ensemblgenomes.org/pub/plants/release-25/fasta/vitis_vinifera/) by tophat2 using default paremeters and fpkm values were calculated by cufflinks
DEGs were identified by R package EdgeR
Genome_build: vitis vinifera
Supplementary_files_format_and_content: tab-delimited text files include FPKM values  for each Sample

organism: Vitis vinifera

source_name: fruit

extract_protocol:
Total RNA was extracted using a Plant RNA EASYspin Plus Kit (aidlab, Peking, China) according to the instructions of the manufacturer, and treated with RQ1 DNase (Promega) to remove DNA. The quality and quantity of the purified RNA were determined by measuring the absorbance at 260 nm and 280 nm (A260 and A280) using SmartSpec Plus (BioRad, USA). RNA integrity was further verified by electrophoresis using a 1.5% agrose gel. To avoid individual variation, we selected three biological replicates for each sample, and extracted total RNA separately, and then we pooled the replicates together for the following experiments.
Construction of cDNA library was independently prepared using 10 ug of total RNA. Polyadenylated RNAs were purified and concentrated with oligo (dT)-conjugated magnetic beads (Invitrogen) before being used for the directional RNA-seq library preparation. Purified mRNAs were iron fragmented at 95oC followed by end repair and 5' adaptor ligation. Then reverse transcription was performed with RT primer harboring 3' adaptor sequence and randomized hexamer. The cDNAs were purified and amplified and PCR products corresponding to 200-500 bps were purified, quantified and stored at -80 oC until used for sequencing.

value: fruit

tag: cultivar

value: Victoria

tag: age

value: 80 days after full blooming


title: VT80-c


title: patient-derived iPSC rep1

description:
p341
peripheral blood lymphocytes


title: VT60-c

value: 60 days after full blooming


title: VT50-b

value: 50 days after full blooming


title: VT80-a


title: mouse cells, PTGS1-KO, #2

value: C57BL/6 murine BrafV600E melanoma

value: Replicate 2


title: VT50-c


title: VT60-b


title: VT60-a


title: FS80-b

value: Flame Seedless


title: FS80-c


title: A549_NonT shRNA-1_Pol II

value: human alveolar basal epithelial cells

value: Non-targeting shRNA


title: VT50-a


title: VT40-b

value: 40 days after full blooming


title: VT40-a


title: FS50-c


title: FS40-a


title: FS80-a


title: FS60-c


title: FS60-b


title: FS40-c


title: FS40-b


title: FS60-a


title: FS50-b


title: VT40-c


title: FS50-a


title: Genomic DNA from Endometrial Tissue T12

type: genomic

city: Provo

first: Timothy

last: Jenkins

state: UT

address: 4005 Life Sciences Building

department: Cell Biology and Physiology

institute: Brigham Young University

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450K Beadchip using standard Illumina protocol

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

data_processing: Data was processed using the minfi R package, and normalized using SWAN normalization.

label: Cy5 and Cy3

source_name: Endometrial Tissue

label_protocol: Standard Illumina Protocol

extract_protocol: Samples were extracted using Qiagen DNeasy extraction kit

tag: group

value: Treatment

tag: sample type

value: Endometrial Tissue


title: Genomic DNA from Endometrial Tissue T8


title: Genomic DNA from Endometrial Tissue C10

value: Control


title: Genomic DNA from Endometrial Tissue C8


title: Sample 43 CRC

city: Melbourne

first: Jihoon

middle: Eric

last: Joo

state: Vic

address: 305 Grattan Street

department: Clinical Pathology

country: Australia

institute: University of Melbourne

description: Lynch syndrome CRC

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing: the data was preprocessed using minfi Bioconductor package.

source_name: FFPE CRC

extract_protocol: FFPE extraction using Qiagen column-based extracion method

tag: crc subgroup

value: Lynch syndrome CRC


title: Genomic DNA from Endometrial Tissue T11


title: Sample 41 Normal

description: Double MMR somatic mutation

source_name: FFPE normal mucosa

value: Double MMR somatic mutation


title: Genomic DNA from Endometrial Tissue C1


title: Sample 39 CRC

description: Lynch syndrome CRC


title: Genomic DNA from Endometrial Tissue C11


title: Sample 42 CRC

description: Double MMR somatic mutation


title: Genomic DNA from Endometrial Tissue C3


title: Genomic DNA from Endometrial Tissue C7


title: Genomic DNA from Endometrial Tissue T7


title: Sample 40 CRC

description: Double MMR somatic mutation


title: Genomic DNA from Endometrial Tissue T9


title: Genomic DNA from Endometrial Tissue C4


title: Genomic DNA from Endometrial Tissue C5


title: Genomic DNA from Endometrial Tissue T1


title: Genomic DNA from Endometrial Tissue C9


title: Genomic DNA from Endometrial Tissue T3


title: Genomic DNA from Endometrial Tissue T5


title: Sample 41 CRC

description: Double MMR somatic mutation


title: Genomic DNA from Endometrial Tissue C12


title: Genomic DNA from Endometrial Tissue C6


title: Genomic DNA from Endometrial Tissue C2


title: Genomic DNA from Endometrial Tissue T6


title: Genomic DNA from Endometrial Tissue T4


title: Genomic DNA from Endometrial Tissue T10


title: Genomic DNA from Endometrial Tissue T2


title: Sample 38 Normal

description: Double MMR somatic mutation


title: Sample 38 CRC

description: Double MMR somatic mutation


title: Sample 37 CRC

description: Double MMR somatic mutation


title: Sample 35 Normal

description: MLH1: c-[28A>G;7C>T]

value: MLH1 VUS carrier


title: Sample 34 CRC

description: MLH1: c-11C>T


title: Sample 36 CRC

description: MLH1 methylated CRC

value: MLH1 methylated CRC


title: Sample 35 CRC

description: MLH1: c-[28A>G;7C>T]


title: Sample 31 CRC

description: MLH1 methylated EOCRC

value: MLH1 methylated EOCRC


title: Sample 36 Normal

description: MLH1 methylated CRC


title: Sample 28 CRC 2

description: Primary MLH1 epimutation carrier

value: Primary MLH1 epimutation carrier


title: Sample 33 CRC

description: MLH1: c.-27C>A

value: Secondary MLH1 epimutation carrier


title: Sample 32 Normal

description: MLH1 methylated CRC


title: Sample 30 CRC

description: MLH1 methylated EOCRC


title: Sample 34 Normal

description: MLH1: c-11C>T


title: Sample 31 Normal

description: MLH1 methylated EOCRC


title: Sample 32 CRC

description: MLH1 methylated CRC


title: Sample 30 Normal

description: MLH1 methylated EOCRC


title: Sample 29 CRC

description: MLH1: c.-27C>A


title: Sample 29 Normal

description: MLH1: c.-27C>A


title: Sample 28 CRC

description: Primary MLH1 epimutation carrier


title: Sample 26 CRC

description: MLH1: c-11C>T


title: Sample 20 CRC

description: MMR-proficient CRC

value: MMR-proficient CRC


title: Sample 23 CRC

description: MLH1 methylated EOCRC


title: Sample 27 CRC

description: MLH1 methylated CRC


title: Sample 24 CRC

description: Primary MLH1 epimutation carrier


title: Sample 22 CRC

description: Primary MLH1 epimutation carrier


title: Sample 25 Normal

description: MLH1 methylated CRC


title: Sample 26 Normal


title: Sample 21 CRC

description: MMR-proficient CRC


title: IgG, control, repC (Sample 30)

city: New York

first: Bjorn

middle: FC

last: Kafsack

state: NY

address: 1300 York Avenue

department: Microbiology & Immunology

institute: Weill Cornell Medicine

data_processing:
Library strategy: CUT&RUN
After sequencing, raw reads were trimmed using Trimmomatic v0.38 47 to remove residual adapter sequences and low quality leading and trailing bases. Both paired and unpaired reads were retained for read lengths that were at least 30 bases after trimming. Trimmed paired reads were aligned to the PlasmoDB version 46 P. falciparum 3D7 reference genome 26 using BWA v.0.7.1 48.  SAMtools v.1.10 49 was used to remove low quality alignments as well as sort and index sample files. Normalized fold enrichment tracks were generated by using the MACS2 v.2.2.7.1 50 callpeak function with settings: -f BAMPE -B -g 2.3e7 -q 0.05 –nomodel –broad –keep-dup auto –max gap 500. Bedgraph outputs were then passed into the bdgcmp function with the setting -m FE (fold enrichment) to generate signal tracks to profile histone modification enrichment levels compared to whole genome. Peak sets from replicates were compared with Bedtools intersect v2.26.0 51, and peaks that overlapped by at least 1 bp were considered shared. Fold enrichment bedgraphs and peak sets were then output to RStudio Server (v1.4.1717) for further analysis using the GenomicRanges Package v.1.44.0 52 and visualized with the GViz  v1.38.1 package 53 within the Bioconductor project (release 3.13) 54
Genome_build: Plasmodium falciparum 3D7 v51 from PlasmoDB
Supplementary_files_format_and_content: bedgraph, bed
X*.bedgraph files (bedgraph of enrichment foldchange versus matched IgG control)
delta*.bedgraph files (bedgraph of difference in K9 enrichment)
bed file of called peaks

organism: Plasmodium falciparum

source_name: asexual blood stages

growth_protocol: The parasite strains used for this study were NF54 obtained from BEI Resources and the Pf-peg4-tdTomato 43. Cultures were maintained using established culturing techniques. Standard complete media was RPMI-1640 supplemented with 25 mM HEPES, 368 μM hypoxanthine, 1 mM sodium hydroxide, 24 mM sodium bicarbonate, 21 μM gentamycin (Millipore Sigma), with Albumax II Lipid-Rich BSA (Gibco), unless otherwise stated. Concentrations for choline and lysoPC supplementation were used according to 14. See Supplementary Table 1 for changes to media compositions used throughout this manuscript. RBCs or cultures were washed three times with respective experimental media conditions at the start of each change in media condition

extract_protocol:
H3K9me3 and H3K4me3 abundances were measured by Cleavage Under Targets & Release Using Nuclease (CUT & RUN) 46 adapted for P.  falciparum. Approximately 1 x 10^7 percoll/sorbitol isolated schizonts (34-38 hpi) per sample were washed three times with 1 ml wash buffer (20 mM HEPES at pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, and 1 × Roche complete protease inhibitor) at room temperature and resuspended in 225ul of wash buffer. 25ul of Concanavalin A-coated beads were washed and resuspended in binding buffer (20 mM HEPES–KOH at pH 7.5, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2) before being added to each sample. Samples were then rotated for 10 minutes at room temperature. Then, samples were placed on a magnetic stand to clear (30s to 2 minutes) and remove all the liquid. Samples were washed 3x’s with DIG wash buffer (wash buffer with 0.025% digitonin). For each sample, 150μl of antibody wash buffer was added (wash buffer, 0.025% digitonin, and 2 mM EDTA at pH 8.0) with H3K4me3 (0.005μg/μl, C15410003-50, Diagenode), H3K9me3 (0.005μg/μl, ab8898, abcam), or IgG isotype control (0.005μg/μl, 02-6102, ThermoFisher) was added to the sample tube and incubated at 4 °C, rotating, overnight. Following antibody incubation, samples were placed on a magnetic stand to clear and pull off the liquid, then washed 3 x’s with DIG wash buffer, 150 μl of ProteinA/G-MNASE fusion protein (dilution 1:60, 15-1016, EpiCypher) in DIG wash buffer and rotated at 4 °C for 1 hour. After washing samples 3x’s with DIG wash buffer, samples were then washed 3x’s with Low Salt Rinse Buffer (20 mM HEPES–NaOH at pH 7.5, 0.025% digitonin, 0.5 mM spermidine). 200 μl of ice-cold incubation buffer (3.5 mM HEPES–NaOH at pH 7.5, 100mM CaCl2, 0.025% DIG) was added and samples were equilibrated at 0 °C for 30 minutes to achieve targeted digestion. Digestion was then stopped by adding 200 μl of stop buffer (170 mM NaCl, 20 mM EGTA at pH 8.0, 20 mM EGTA, 0.0.25% digitonin, 25 μg/mL glycogen, 50 μg/mL RNase A). After incubation at 37 °C for 30 minutes to release soluble fragments, samples were digested by adding 2.5 μL proteinase K (20 mg/ml) and 2 μL 10% SDS, and then incubated at 50 °C for 1 hour. DNA fragments were purified with phenol–chloroform–isoamyl alcohol and washed by ethanol precipitation, and finally dissolved in 30 μL TE buffer (1mM Tris-HCl pH 8, 0.1 mM EDTA).
Library construction was carried out using NEBNext Ultra II DNA Library Prep Kit for Illumina (E7645S, NEB). 4ng of fragmented DNA was used for end-repair/A-tailing, ligation, and post ligation cleanup with 1.7x volumes of AMPure XP beads (Catalog number, company). Following cleanup, PtdChoR amplification was performed using 2x KAPA HotStart ready mix (Catalog number, company) and NETFLEX primer mix (Catalog number, Bio Scientific) with PtdChoR program: 1 min @ 98o C/15 cycles: 10 sec @ 98o C/1 min @ 65o C// 5min @ 65o C// hold 4o C. PtdChoR products were size selected with 0.8x volumes, then 1.2x volumes of AMPure XP beads. Beads were then washed twice with 80% ethanol and DNA eluted with 0.1x TE and used for sequencing in a Nextseq2000 system as paired-end reads, following quality control.

treatment_protocol: Synchronous P. falciparum parasites were grown from 8hpi to 34hpi ± 6 hpi (100mL, 3% hematocrit, 5-6% parasitemia) under the indicated growth conditions. Infected red blood cells (iRBC) were then purified to > 90% purity using a 70/40% percoll/sorbitol density gradient and centrifugation (4700 G for 15 minutes at room temperature), then washed three times with minimal RPMI. Following isolation, equal numbers of isolated iRBC, as determined by the Beckman Coulter Z1 Coulter Particle Counter, were then re-incubated in their respective treatment conditions for four more hours to allow parasites to recover from percoll/sorbitol isolation. Following recovery, the purity of iRBCs was assessed using flow cytometry,

tag: strain

tag: developmental stage

value: asexual blood stages

value: IgG Isotype antibody Control Rabbit IgG, ThermoFisher Catalog #02-6102

value: schizonts


title: Sample 22 Normal

description: Primary MLH1 epimutation carrier


title: IgG, control, repB (Sample 28)


title: IgG, control, repC (Sample 26)


title: IgG, control, repC (Sample 29)

value: +Met+Cho


title: IgG, control, repA (Sample 24)

value: -Met-Cho


title: IgG, control, repB (Sample 27)


title: Sample 25 CRC

description: MLH1 methylated CRC


title: IgG, control, repA (Sample 25)


title: IgG, control, repA (Sample 23)


title: H3K4me3,  +MC+3DZA, repC (Sample 22)

value: H3K4me3 antibody ChIP Grade (polyclonal) Rabbit IgG, Diagenode Catalog #C15410003-50


title: Sample 14 CRC

description: MMR-proficient CRC


title: PBMCpie1_snATAC

first: Jin-Gyu

last: Cheong

description:
nuclei RNA and genomic DNA fragment
Chromium Single Cell Multiome ATAC + Gene Expression
BM_PBMC_PIE_RNA_norm_count.mtx
BM_PBMC_PIE_metadata.csv

library_source: other

data_processing:
All preprocessing steps were performed by 10X Genomics Cell Ranger ARC software
Assembly: hg38 for human, mm10 for mouse
Supplementary files format and content: h5 file for feature-barcode matrix
Library strategy: MultiomeRNA

molecule: other

source_name: PBMC

extract_protocol:
10X Genomics CG000365
10X Genomics CG000338

value: PBMC

value: mononuclear cell


title: Sample 10 CRC

description: MLH1 methylated CRC


title: Sample 5 CRC

description: MMR-proficient CRC


title: H3K4me3,  +MC, repC (Sample 21)


title: BMMCpie1_snATAC

source_name: Bone Marrow

value: Bone Marrow


title: Sample 17 CRC

description: Lynch syndrome CRC

value: Lynch syndrome CRC


title: Sample 11 CRC

description: MLH1 methylated CRC


title: Sample 16 CRC

description: Lynch syndrome CRC


title: H3K4me3,  +MC+3DZA, repB (Sample 20)


title: Sample 19 CRC

description: Lynch syndrome CRC


title: Sample 15 CRC

description: MMR-proficient CRC


title: Sample 9 CRC

description: MLH1 methylated CRC


title: Sample 18 CRC

description: Lynch syndrome CRC


title: PBMCpie1_snATAC [MultiomeATAC-seq]

description:
nuclei RNA and genomic DNA fragment
Chromium Single Cell Multiome ATAC + Gene Expression
BM_PBMC_PIE_peaks_norm_count.mtx
BM_PBMC_PIE_metadata.csv

library_source: genomic single cell

data_processing:
All preprocessing steps were performed by 10X Genomics Cell Ranger ARC software
Assembly: hg38 and mm10
Supplementary files format and content: mtx file for peak-barcode count matrix
Supplementary files format and content: bam file for post-sort cells

extract_protocol: 10X Genomics CG000338


title: BMMCpie1_snATAC [MultiomeATAC-seq]


title: H3K4me3,  +MC+3DZA, repA (Sample 18)


title: Sample 4 Normal

description: MMR-proficient CRC


title: H3K4me3,  +MC, repB (Sample 19)


title: siFSCN1_3

city: Urumqi

first: Qingchao

last: Sun

state: Xinshi District

address: 137 Liyushan South Road

institute: The First Affiliated Hospital of Xinjiang Medical University

data_processing:
Illumina bcl2fastq software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) and low quality bases trimmed using FASTX-Toolkit (Version 0.0.13). the short reads less than 16nt were also dropped.
The dataset containing the clean reads was aligned to the GRch38 genome by tophat2 allowing 4 mismatches.
Uniquely mapped reads were used for gene reads number counting and FPKM calculation (fragments per kilobase of transcript per million fragments mapped)
The alternative splicing events (ASEs) and regulated alternative splicing events (RASEs) between the samples were defined and quantified using the ABLas pipeline.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include gene FPKM values for each Sample
Supplementary files format and content: tab-delimited text files include gene reads values for each Sample

molecule: polyA RNA

extract_protocol:
Total RNA was treated with RQ1 DNase (Promega) to remove DNA. The quality and quantity of the purified RNA were determined by measuring the absorbance at 260nm/280nm (A260/A280) using smartspec plus (BioRad).
mRNAs were captured by VAHTS mRNA capture Beads（Vazyme, N401. The purified RNA was treated with RQ1 DNase (Promega) to remove DNA before used for directional VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina （NR605） Polyadenylated mRNAs were purified and fragmented. Fragmented mRNAs were converted into double strand cDNA.
After purification of ligation product and size fractioning to 300-500bps , the ligated products were amplified and purified, quantified and stored at -80℃ before sequencing. The strand marked with dUTP (the 2nd cDNA strand) is not amplified, allowing strand-specific sequencing.

value: NSCLC cells

value: FSCN1 silence expression in NSCLC cells


title: H3K4me3,  +MC, repA (Sample 17)


title: siFSCN1_2


title: Sample 12 CRC

description: MLH1 methylated CRC

value: MLH1 methylated CRC


title: H3K9me3,  +MC+3DZA, repC (Sample 16)

value: H3K9me3 antibody ChIP Grade (polyclonal) Rabbit IgG, Abcam Catalog #ab8898


title: Sample 7 CRC

description: MMR-proficient CRC


title: Sample 6 CRC

description: MMR-proficient CRC


title: siFSCN1_1


title: Sample 9 Normal

description: MLH1 methylated CRC


title: Sample 1 CRC

description: MMR-proficient CRC


title: Sample 3 CRC

description: Lynch syndrome CRC


title: NC_ 3

value: NSCLC  cells(control plasmid)


title: H3K9me3,  +MC, repB (Sample 13)


title: Sample 2 CRC

description: Lynch syndrome CRC


title: H3K9me3,  +MC, repC (Sample 15)


title: H3K9me3,  +MC+3DZA, repB (Sample 14)


title: H3K9me3,  +MC+3DZA, repA (Sample 12)


title: Sample 13 CRC

description: Lynch syndrome CRC


title: NC _2


title: NC _1


title: Sample 2 Normal

description: Lynch syndrome CRC


title: FSCN1-IP-1

data_processing:
the supernatant was incubated overnight at 4°C with 10 μg FLAG antibody (sigma: F7425) and control IgG-antibody (AC005).
Incubate the suspension for 30 min in a heat block at 70°C to release the immunoprecipitated RBP with crosslinked RNA and vortex.
Remove the magnetic beads on the separator and transfer the supernatant to a clean 1.5 ml microfuge tube. Add Proteinase K (Sangon Biotech) into the 10% input（without immunoprecipitated）and immunoprecipitated RBP with crosslinked RNA, with final concentration of 1.2 mg/ml. Incubate for 120 min at 55°C. The RNA was purified with Phenol: chloroform: isopentyl alcohol (25:24:1 pH<5) reagent (Solarbio).
cDNA libraries were prepared with the KAPA RNA Hyper Prep Kit (KAPA, KK8544) according the manufacturer’s procedure.
For high-throughput sequencing, the libraries were prepared following the manufacturer's instructions and applied to Illumina NovaSeq6000 system for 150 nt paired-end sequencing
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include peak information for IP_1 group.
Supplementary files format and content: tab-delimited text files include peak information for IP_2 group.

extract_protocol:
A549 cells were irradiated once for 400 mJ/cm2 , and lysed in ice-cold wash buffer. Cells lysis was performed in cold Wash buffer (1×PBS, 0.5% SDS, 0.5% NP-40 and 0.5% sodium deoxycholate) supplemented with a 400 U/mL RNase inhibitor (Takara) and protease inhibitor cocktail (Bimake) and incubate on ice for 30 min. Add RQ I (Promega, 1 U/μl) to a final concentration of 0.1 U/μl and incubate in a heat block for 30 min at 37°C. The mixture was then vibrated vigorously and centrifuged at 13,000 xg at 4℃ for 15 min to remove cell debris
For immunoprecipitation, the supernatant was incubated overnight at 4°C with 10 μg FLAG antibody (sigma: F7425) and control IgG-antibody (AC005). The immunuprecipitates were further incubated with protein A/G Dynabeads (Thermo Scientific) for 2h at 4°C. After applying to magnet and removing the supernatants, the beads were sequentially washed with lysis buffer (1× PBS, 0.1% SDS, 0.5% NP-40 and 0.5% sodium deoxycholate), high-salt buffer (250 mM Tris 7.4, 750 mM NaCl, 10 mM EDTA, 0.1% SDS, 0.5% NP-40 and 0.5 deoxycholate), and PNK buffer (50 mM Tris, 20 mM EGTA and 0.5% NP-40) for two times, respectively. Resuspend the beads in of Elution buffer (50 mM Tris 8.0, 10 mM EDTA and 1% SDS). Incubate the suspension for 30 min in a heat block at 70°C to release the immunoprecipitated RBP with crosslinked RNA and vortex. Remove the magnetic beads on the separator and transfer the supernatant to a clean 1.5 ml microfuge tube. Add Proteinase K (Sangon Biotech) into the 10% input（without immunoprecipitated）and immunoprecipitated RBP with crosslinked RNA, with final concentration of 1.2 mg/ml. Incubate for 120 min at 55°C. The RNA was purified with Phenol: chloroform: isopentyl alcohol (25:24:1 pH<5) reagent (Solarbio).

value: NSCLC cells(IP)


title: H3K9me3,  +MC, repA (Sample 11)


title: H3K4me3,  +MC, repC (Sample 9)


title: FSCN1_input-2

value: NSCLC cells (input plasmid)


title: H3K4me3,  -MC, repC (Sample 10)

value: asexual blood stages


title: FSCN1_input-1

value: NSCLC  cells (input)


title: H3K4me3,  -MC, repB (Sample 8)

value: schizonts


title: A172 GBM cell line

city: Munich

first: Kristian

last: Unger

address: Marchioninistr. 15

department: Department of radiation oncology

country: Germany

institute: LMU University Hospital

description: glioblastoma cell line

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

data_processing: BeadStudio software v3.2

source_name: Human glioblastoma cell line

growth_protocol: The human GBM cell lines A172, LN18, LN229, T98G, U87-MG, U138-MG and U251-MG were analyzed in this study. A172, LN18, LN229, U87-MG and T98G were obtained from the American type culture collection (ATCC, Manassas, Virginia, USA), U138-MG and U251-MG from the cell line repository CLS (Eppelheim, Germany). The cells were cultivated at 37°C and 7,5% CO2 in DMEM Glutamax (ThermoFisher, Waltham, MA, USA) supplemented with 10% FCS and 1% penicillin/streptomycin and kept at low passage numbers (<10).

extract_protocol: Genomic DNA was extracted from cell line pellets using the Qiagen Allprep kit.


title: Sample 8 CRC

description: MLH1 methylated CRC


title: HCT116, shNELFE, EPZ-5676, HMBA, replicate2

city: Seoul

first: Junyoung

last: Park

address: 84, Heukseok-ro

department: Department of Life Science

country: South Korea

institute: Chung-Ang University

data_processing:
Low-quality reads were filtered based on the following criteria: reads containing more than 10% of skipped bases (marked as ‘N’s), reads containing more than 40% of bases with quality scores of less than 20, and reads with average quality scores for each read of less than 20.
The filtering process was performed using in-house scripts. Filtered reads were mapped to the reference genome related to the species using the aligner STAR v.2.4.0b.
Gene expression levels were measured using Cufflinks v2.1.1 and the gene annotation database of the species. For differentially expressed gene (DEG) analysis, gene-level count data were generated using HTSeq-count v0.6.1p1. Based on the calculated read count data, DEGs were identified using the R package ‘TCC’.
The normalization factors were calculated using the iterative DEGES/edgeR method. The Q-value was calculated based on the P-value using the p.adjust function of the R package, with default parameter settings. The DEGs were identified based on a Q-value threshold of less than 0.05 for correcting errors caused by multiple testing.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include read counts for each sample

source_name: colon

extract_protocol:
RNA was extracted using TruSeq Stranded mRNA Sample Prep Kit (Illumina)
mRNA molecules were purified and fragmented from 0.1-1 ug of total RNA using oligo (dT) magnetic beads. Fragmented mRNAs were synthesized as single-stranded cDNAs through random hexamer priming. Double-stranded cDNA was prepared by using this cDNA as a template for second strand synthesis. After a sequential process of end repair, A-tailing, and adpter ligation, cDNA libraries were amplifed using PCR.

value: colon

value: Colorectal carcinoma

value: NELFE knockdown

value: EPZ-5676, HMBA


title: FSCN1-IP-2


title: U87-MG GBM cell line

description: glioblastoma cell line


title: HCT116, shCTL, EPZ-5676, HMBA, replicate2

value: Control


title: H3K4me3,  +MC, repB (Sample 7)

value: H3K4me3 antibody ChIP Grade (polyclonal) Rabbit IgG, Diagenode Catalog #C15410003-50

value: +Met+Cho


title: H3K4me3,  +MC, repA (Sample 5)


title: LN229 GBM cell line

description: glioblastoma cell line


title: HCT116, shCTL, EPZ-5676, HMBA, replicate1


title: H3K9me3,  +MC, repB (Sample 3)


title: H3K4me3,  -MC, repA (Sample 6)

value: -Met-Cho


title: HCT116, shCTL, HMBA, replicate2

value: HMBA


title: H3K9me3,  +MC, repA (Sample 1)


title: H3K9me3,  -MC, repA (Sample 2)


title: H3K9me3,  -MC, repB (Sample 4)


title: HCT116, shNELFE, HMBA, replicate2


title: Sample 4 CRC

description: MMR-proficient CRC

value: MMR-proficient CRC


title: HCT116, shNELFE, HMBA, replicate1


title: U138-MG GBM cell line

description: glioblastoma cell line


title: HCT116, shCTL, HMBA, replicate1


title: HCT116, shNELFE, EPZ-5676, replicate2


title: HCT116, shNELFE, EPZ-5676, replicate1


title: HCT116, shNELFE, DMSO, replicate2

value: DMSO


title: U251-MG GBM cell line

description: glioblastoma cell line


title: D37712_dRNA_Pool

city: Hinxton

first: Alexander

last: Predeus

address: Wellcome Trust Genome Campus

institute: Wellcome Sanger Institute

description: Salmonella enterica subsp. enterica serovar Typhimurium str. D37712

data_processing:
RNA-Seq data quality control, alignment, quantification, and statistics calculations were done using the “simple” workflow of Bacpipe RNA-seq processing pipeline v0.6.0 (https://github.com/apredeus/multi-bacpipe).
RNA-seq samples were aligned to the genome sequence using STAR v2.6.0c using “--alignIntronMin 20 --alignIntronMax 19 --outFilterMultimapNmax 20” options.
Read counting was done by featureCounts v1.6.4, using options “-O -M --fraction -t gene -g ID -s 1”.
TPMs were calculated using raw read counts obtained in featureCounts, with effective gene length equal to gene length in annotation.
Genome_build: Assembly ASM1425033v1 was used for strain D37712 genome build.
Supplementary_files_format_and_content: TPM and raw read count values in tab-separated text columns

organism: Salmonella enterica subsp. enterica

source_name: in vitro culture

growth_protocol: Growth conditions and treatment for 16 in vitro conditions are described previously (PMID 24331466). Growth conditions for intra-macrophage transcriptome are described in PMID 26561851.

extract_protocol:
Transcription and RNA turnover were stopped using 2/5 volumes of the cell suspension using ice-cold ‘‘stop solution’’ (19% ethanol, 1% acidic phenol [pH 4.3]) and incubated on ice for 30 min to prevent RNA degradation. RNA was isolated using TRIzol (Invitrogen) and digested with DNase I.
For RNA-seq, cDNA libraries were prepared and sequenced by Vertis Biotechnologie AG (Freising, Germany). RNA samples were fragmented with ultrasound (4 pulses of 30 sec at 4°C), treated with antarctic phosphatase, and rephosphorylated with polynucleotide kinase (PNK). RNA fragments were poly(A)-tailed and a RNA adapter was ligated to the 5'-phosphate of the RNA. First-strand cDNA synthesis was carried out using an oligo(dT)-adapter primer and M-MLV reverse transcriptase. cDNA was subsequently amplified by PCR to 20-30 ng/μL, and purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics). cDNA samples were pooled in equimolar amounts, size-selected to 150 - 500 bp and sequenced on an Illumina HiSeq 2000 or Illumina NextSeq 500 system (single-end 50, 75, or 100 bp reads).

value: wildtype

tag: protocol


title: D37712_Oxygen_shock

treatment_protocol: Growth conditions and treatment for 16 in vitro conditions are described previously (PMID 24331466). Growth conditions for intra-macrophage transcriptome are described in PMID 26561851.


title: LN18 GBM cell line

description: glioblastoma cell line


title: D37712_NonSPI2


title: T98G GBM cell line

description: glioblastoma cell line


title: D37712_Peroxide_shock_InSPI2


title: HCT116, shCTL, DMSO, replicate2

tag: tissue


title: D37712_NO_shock_InSPI2


title: D37712_NaCl_shock


title: D37712_MEP

value: MEP


title: D37712_RNA_Pool


title: HCT116, shNELFE, EPZ-5676, HMBA, replicate1

tag: cell line


title: HCT116, shCTL, DMSO, replicate1

tag: cell type


title: D37712_LSP

value: LSP


title: NKAP_KDRNAPolIIChIP

first: Xing

address: Insititute of Genetics, Zhejiang University, 866 Yuhangtang Rd

department: Institute of Genetics

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 > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie version 1.1.2.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01
bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

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

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, the pellet was washed two times in lysis buffer and prepared for sonication using a Bioruptor (30 s on, 30 s off, 10 rounds of 10 min) at 4 °C. .
After the DNA samples quality control， the purified DNA was used NEBNext® Ultra™ II
DNA Library Prep Kit （NEB, USA, Catalog #: E7645L） for ChIP-seq library preparation.
(1) The DNA fragments are repaired, dA-tailed.
(2) The DNA fragments with A tail are ligated to sequencing adaptors.
(3) The final DNA library is obtained by size selection and PCR amplification. Libraries
were analyzed for size distribution by Agilent 5400 system（Agilent, USA） and quantified
by QPCR (1.5 nM).
The qualified libraries were pooled and sequenced on Illumina platforms with PE150
strategy in Novogene Bioinformatics Technology Co., Ltd (Beijing, China), according to
effective library concentration and data amount required.

treatment_protocol: U2OS cells were transfected with siRNAs through Lipofectamine RNAiMAX for 48 h.

value: Human Bone Osteosarcoma Epithelial Cells

value: RNA polymerase II (Active Motif, 91151)

tag: treatment

value: siRNA transfection for 48h

value: NKAP KD


title: NCRNAPolIIChIP

tag: chip antibody

value: control


title: D37712_Low_Fe_shock

tag: genotype


title: D37712_LEP

value: LEP


title: HCT116, shCTL, EPZ-5676, replicate1

value: colon

value: Colorectal carcinoma


title: D37712_Low_Mg_InSPI2


title: InputNKAP


title: HCT116, shCTL, EPZ-5676, replicate2

value: Control


title: D37712_InSPI2


title: GC6_TCR

city: Seocho-gu

first: June-Young

last: Koh

state: Seoul

address: 2575 Nambusunhwan-ro,

institute: GENOME INSIGHT

description: 10x Genomics

data_processing:
10x Genomics
Assembly: GRCH38
Supplementary files format and content: 10x Genomics output files: filtered_feature_bc_matrix.h5, filtered_contig_annotations.csv
Library strategy: scTCR-seq

extract_protocol:
PBMCs were isolated by Ficoll-Paque (GE Healthcare, Uppsala, Sweden) density-gradient centrifugation
Libraries for scRNA-seq were generated using the Chromium Next GEM Single Cell 5' Kit v2 (10× Genomics, Pleasanton, CA, USA) and Chromium Single Cell Human TCR Amplification Kit (10× Genomics) to read 5'-mRNA and full-length paired T-cell and B-cell receptor sequences following the manufacturer’s instructions
Libraries were constructed and sequenced at a depth of approximately 50,000 reads per cell using the Novaseq 6000 platform (Illumina, San Diego, CA, USA).

value: PBMC

value: mononuclear cell

tag: library type

value: TCR

tag: patient id

tag: patient id 2

value: Patients #15, Patients #22, Patients #23, Patients #24

tag: disease state

value: advanced gastric cancer; advanced gastric cancer; advanced gastric cancer; advanced gastric cancer

tag: antibiotics usage

value: Not used; Used; Not used; Used

tag: patient sex

value: F; F; F; F


title: InputNC


title: GC5_TCR

description: 10x Genomics

value: Patients #13, Patients #14, Patients #20, Patients #21

tag: age

value: Not used; Not used; Used; Used

value: F; M; F; F


title: D37712_EEP

value: wildtype

value: EEP


title: D37712_ESP

value: ESP


title: GC4_TCR

description: 10x Genomics

value: Patients #5, Patients #8, Patients #12, Patients #16

value: Used; Not used; Not used; Used

value: M; M; M; F


title: HCT116, shNELFE, DMSO, replicate1

value: colon

value: Colorectal carcinoma

value: NELFE knockdown

value: DMSO


title: GC3_TCR

description: 10x Genomics

value: PBMC

value: mononuclear cell

value: TCR

value: Patients #3, Patients #4, Patients #6, Patients #7

value: Used; Used; Not used; Not used

value: M; M; F; M


title: D37712_25C


title: GC1_TCR

description: 10x Genomics

value: Patients #1, Patients #2, Patients #17, Patients #118

value: advanced gastric cancer; advanced gastric cancer; advanced gastric cancer; advanced gastric cancer

value: F; M; M; M


title: D37712_Anaerobic_shock

value: wildtype


title: D37712_Anaerobic_growth


title: GC2_TCR

description: 10x Genomics

value: Patients #9, Patients #10, Patients #11, Patients #19

value: F; F; F; M


title: GC6_GEX

description: 10x Genomics

data_processing:
10x Genomics
Assembly: GRCH38
Supplementary files format and content: 10x Genomics output files: filtered_feature_bc_matrix.h5, filtered_contig_annotations.csv

value: mRNA

value: Patients #15, Patients #22, Patients #23, Patients #24

value: Not used; Used; Not used; Used

value: F; F; F; F


title: GC5_GEX

description: 10x Genomics

value: Patients #13, Patients #14, Patients #20, Patients #21

value: Not used; Not used; Used; Used

value: F; M; F; F


title: DU145 cells, taraxasterol  1

city: Dali

first: Jinqiu

last: Yang

state: Yunnan Province

address: Wanhua Street

institute: Dali University

data_processing:
Basecall_T7_GPU_1.2.0.26_
Sequence reads were trimmed for adaptor sequence/low-quality sequence using  Fastp v 0.20.1 (reads will be filtered out ：<100bp or Q30<60% or N>10bp)
Trimmed sequence reads were mapped to GRCh38 using Hisat2 v 2.2.0
Using BLAST v 2.2.31+ as basic local alignment search tool
Using StringTie v 2.1.2 for transcript assembly
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

growth_protocol: DU145 cells were cultured in MEM medium supplemented with 10% FBS and 1% Pen Strep at 37℃ under a humidity incubator of 5% CO2

extract_protocol:
Total RNAs were isolated using Trizol reagent(Invitrogen, Carlsbad, CA)
RNA libraries for RNA-seq were prepared using Hieff NGS® Ultima Dual-mode mRNA Library Prep Kit for Illumina following manufacturer's protocols.

treatment_protocol: DU145 cells were treated by MEM medium or taraxasterol(IC50) (ChemFaces,Wuhan, China) for 48 h

value: prostate cancer cells

value: WT

value: taraxasterol for 48h


title: DU145 cells, control 3

value: medium for 48h


title: DU145 cells, taraxasterol  3


title: GC4_GEX

description: 10x Genomics

value: PBMC

value: mononuclear cell

value: Patients #5, Patients #8, Patients #12, Patients #16

value: Used; Not used; Not used; Used

value: M; M; M; F


title: GC3_GEX

description: 10x Genomics

value: Patients #3, Patients #4, Patients #6, Patients #7

value: advanced gastric cancer; advanced gastric cancer; advanced gastric cancer; advanced gastric cancer

value: Used; Used; Not used; Not used

value: M; M; F; M


title: DU145 cells, control 1


title: T263-12

city: Gainesville

first: Daiqing

last: Liao

state: Florida

address: 2033 Mowry Road

department: Anatomy and Cell Biology

institute: University of Florida

description:
Sample 30
T263_count_matrix.csv

data_processing:
Sequence reads were mapped to GrCM38/mm10 using HISAT2 for alignment
Picard for count deduplication
HTSeq for extract count
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes count values for all T112 samples
Supplementary files format and content: comma-separated values file includes count values for all T240 and T263 samples

source_name: triple-negative breast cancer

growth_protocol: MDA-MB-231 cells were maintained in DMEM supplemented with 10% bovine calf serum and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 250 ng of total RNA was used for the construction of sequencing libraries.
NEBNext Ultra II Directional RNA Library Prep Kit

treatment_protocol: Cells were treated with DMSO control (samples 1-3) or UF010 (10 µM, samples 4-6) for 24 hours. Samples were treated with DMSO (samples 7-9, and 19-21), YX968 (50 nM, samples 10-12, and 22-24), YX968-NC (samples 13-15, and 25-27), or YXYX26862 (samples 16-18, and 28-30) for 6h (samples 7-18) or 24h (samples 19-30).

value: triple-negative breast cancer


title: T263-10

description:
Sample 28
T263_count_matrix.csv


title: GC2_GEX

description: 10x Genomics

value: mRNA

value: Patients #9, Patients #10, Patients #11, Patients #19

value: F; F; F; M


title: T263-11

description:
Sample 29
T263_count_matrix.csv


title: GC1_GEX

description: 10x Genomics

value: Patients #1, Patients #2, Patients #17, Patients #18

value: F; M; M; M


title: hMF.413.Control

city: Madrid

first: Lisardo

last: Bosca

state: Madrid

address: Arturo Duperier 4

department: Metabolism and cellular Signaling

country: Spain

institute: Instituto Investigaciones Biomedicas Alberto Sols

data_processing:
Raw reads were analyzed for data quality using FastQC v0.11.5 (Babraham Bioinformatics) and filtered using skewer v0.2.2 (Jiang etal,2014) for removing the low-quality reads and trimming the Illumina adapter.
Mapping of the reads were obtained using the STAR program against human genome (hg38) and the quantification of genes and transcripts were done with the RSEM program using GENCODE v26.
Assembly: hg38
Supplementary files format and content: Excel file includes Entrez Gene ID and Log2 Fold Change values for differential expression of case vs control

source_name: Monocyte-derived macrophages

growth_protocol: Monocyte-derived human macrophages were isolated from buffy coats by a ficoll gradient, cells were seeded 1h in DMEM without FBS and then cell media was replaced by DMEM+10%FBS for a week until differentiation was observed visually.

extract_protocol:
Total RNA was extracted using TRI Reagent TM Solution (Invitrogen) protocol.
RNA libraries were prepared for sequencing using standard BGI protocols

treatment_protocol: Differentiated macrophages were treated with CK (IL1β, IL-6, IL8, TNFα, IFNƴ and GM-CSF)20ng/mL for 24h, DETANONOATE 500µM (D500µM) 24h or CK (1h)+DETANONOATE 500µM 24h (D500µM) in RPMI+2%FBS or vehicle (controls RPMI+2%FBS)

tag: group

value: Monocyte-derived macrophages

value: Vehicle


title: hMF.413.CKs.D500uM

value: CK (IL1β, IL-6, IL8, TNFα, IFNƴ and GM-CSF 20ng/mL) 1h, then DETA NONOATE 500µM 24h


title: T263-8

description:
Sample 26
T263_count_matrix.csv

value: YX968-NC 50 nM for 24h


title: hMF.410.CKs

value: CK (IL1β, IL-6, IL8, TNFα, IFNƴ and GM-CSF 20ng/mL) 24h


title: T263-7

description:
Sample 25
T263_count_matrix.csv


title: hMF.410.D500uM

value: DETA NONOATE 500µM 24h


title: DU145 cells, taraxasterol  2

value: prostate cancer cells

value: WT

value: taraxasterol for 48h


title: T263-4

description:
Sample 22
T263_count_matrix.csv

value: YX968 50 nM for 24h


title: T263-9

description:
Sample 27
T263_count_matrix.csv


title: hMF.319.D500uM


title: T263-6

description:
Sample 24
T263_count_matrix.csv


title: hMF.410.Control


title: T263-5

description:
Sample 23
T263_count_matrix.csv


title: T263-3

description:
Sample 21
T263_count_matrix.csv

value: DMSO for 24h


title: hMF.319.CKs


title: hMF.318.CKs.D500uM


title: T263-1

description:
Sample 19
T263_count_matrix.csv

value: triple-negative breast cancer


title: hMF.318.CKs


title: DU145 cells, control 2

value: medium for 48h


title: hMF.318.D500uM


title: hMF.319.Control


title: T240-12

description:
Sample 18
T240_count_matrix.csv

value: YX26862 50 nM for 6h


title: T263-2

description:
Sample 20
T263_count_matrix.csv


title: T240-11

description:
Sample 17
T240_count_matrix.csv


title: T240-9

description:
Sample 15
T240_count_matrix.csv

value: YX968-NC 50 nM for 6h


title: hMF.317.CKs.D500uM


title: hMF.317.CKs


title: T240-8

description:
Sample 14
T240_count_matrix.csv


title: T240-10

description:
Sample 16
T240_count_matrix.csv


title: 5 day deligated stroma-enriched murine  submandibular salivary gland_1

city: Albany

first: Melinda

last: Larsen

address: 1400 Washington Ave., LSRB 10

department: Dept. of Biological Science

institute: University at Albany, SUNY

description: 10X Genomics

data_processing:
The demultiplexing, barcoded processing, and gene counting  were made using the Cell Ranger software v6.0.1 (deligated) and 7.0.0 (homeostatic) at the University at Albany Center for Functional Genomics.
The raw sequencing files from Cell Ranger were loaded into R Studio, where we removed doublets and dead cells using the Seurat package with the feature cutoffs >200 and <6000 and mt genes <6%.
The two biological replicates of the deligated glands were merged using 16 dimensions with a resolution of 0.8. The two technical replicates of thehomeostatic datasets were merged using 16 dimensions with a resolution of 0.8. The merged datasets were scaled and normalized using the Seurat package.
Assembly: mm10

source_name: Submandibular Salivary Gland

extract_protocol:
Two deligated or homeostatic submandibular and sublingual glands were harvested, and excess fat and interstitial tissue was removed. The glands were then transferred to a dish containing 1X PBS, liberase TL Research Grade low Thermolysin (Roche), DNase I, and dispase and microdissected for 7-9 minutes. The sample was then incubated in a 37°C incubator for 15 minutes and triturated. After trituration, the sample was incubated for an additional 5 minutes in a 37°C incubator and triturated once more. A 15 mL conical tube was placed on ice and the entire sample was transferred to the conical tube and incubated for 10 minutes. The supernatant was isolated and transferred to a fresh conical tube and was centrifuged for 5? minutes at 450xg. The supernatant was removed and discarded, and the cell pellet was resuspended in isolation buffer composed of sterile-filtered Ca2+- and Mg2+-free 1X PBS, 0.1% bovine serum albumin, and 2mM ethylenediaminetetraacetic acid. 5 mg of EpCAM-A647 (catalog: 118212, BioLegend) and Ter119 (catalog: 50-133-27, eBioscience/ThermoFisher) was added to the cell suspension and incubated at 4°C for 10 minutes for depletion of epithelial and red blood cells, respectively. The cell suspension was washed using isolation buffer and centrifuged at 450xg for 5 minutes. The supernatant was discarded, and the cell pellet was resuspended in 1 mL of isolation buffer and 25 uL of sheep anti-rat Dynabeads, which bind to the EpCAM and Ter119 labeled cells, (catalog: 11035, Invitrogen) before incubating on ice for 20 minutes on a rocker. The sample was placed on a microcentrifuge magnet for 2 minutes, and the supernatant was transferred to a fresh microcentrifuge tube to remove labeled epithelial and red blood cells. An additional epithelial and red blood cell depletion was performed. The sample was then depleted of dead cells using a dead cell removal kit (catalog: 130-090-101, Miltenyi Biotec) following manufacturer’s instructions. Cells were counted and resuspended to a concentration of 1000 cells/mL. Homeostatic libraries were prepared in two technical replicates, while the deligated libraries were from two biological replicates. Following the manufacturer’s protocol for the Chromium Next GEM Single Cell 3’ Reagent kits v3.1, scRNAseq libraries were generated.
Library was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics).

treatment_protocol: Mice underwent either a 14 day ligation surgery followed by a 5 day deligation surgery, where a metal clip was applied to the main ducts of the submandibular and sublingual glands and remained in place for 14 days followed by a second surgery to remove the metal clip for 5 days prior to harvest or were harvested at 12-weeks-old with no treatment or surgical manipulation performed (homeostatic)

tag: strain

tag: Sex

value: Female

value: 14 weeks

value: Submandibular Salivary Gland

value: Stromal Enriched

value: 14 day ligation surgery followed by 5 day deligation surgery


title: 5 day deligated stroma-enriched murine  submandibular salivary gland_2

description: 10X Genomics


title: homeostatic stroma-enriched murine  submandibular salivary gland_1

description: 10X Genomics

value: 12 weeks

value: homeostatic salivary glands


title: hMF.319.CKs.D500uM

value: Monocyte-derived macrophages

value: CK (IL1β, IL-6, IL8, TNFα, IFNƴ and GM-CSF 20ng/mL) 1h, then DETA NONOATE 500µM 24h


title: homeostatic stroma-enriched murine  submandibular salivary gland_2

description: 10X Genomics


title: hMF.317.D500uM

value: DETA NONOATE 500µM 24h


title: T240-7

description:
Sample 13
T240_count_matrix.csv


title: D37712_NonSPI2-5

value: wildtype

tag: protocol


title: D37712_NonSPI2-4


title: hMF.316.CKs.D500uM


title: hMF.317.Control

value: Vehicle


title: D37712_NonSPI2-3


title: D37712_NonSPI2-2


title: T240-5

description:
Sample 11
T240_count_matrix.csv

tag: tissue

value: YX968 50 nM for 6h


title: D37712_InSPI2-4


title: D37712_Macrophage-1

source_name: macrophage co-culture


title: T240-4

description:
Sample 10
T240_count_matrix.csv

value: triple-negative breast cancer

tag: cell line


title: D37712_InSPI2-3


title: hMF.316.D500uM

tag: cell type


title: hMF.318.Control

tag: treatment


title: hMF.316.CKs

value: CK (IL1β, IL-6, IL8, TNFα, IFNƴ and GM-CSF 20ng/mL) 24h


title: D37712_InSPI2-2


title: D37712_ESP-4


title: T240-3

description:
Sample 9
T240_count_matrix.csv

value: DMSO for 6h


title: hMF.316.Control


title: D37712_ESP-3


title: T240-2

description:
Sample 8
T240_count_matrix.csv


title: hMF.314.CKs.D500uM


title: D37712_Anaerobic_growth-5


title: D37712_ESP-2


title: D37712_Anaerobic_growth-4


title: T240-1

description:
Sample 7
T240_count_matrix.csv


title: D37712_Anaerobic_growth-3


title: T240-6

description:
Sample 12
T240_count_matrix.csv


title: hMF.314.D500uM


title: T112-6

description:
Sample 6
T112_count_matrix.txt

value: UF010, 10 µM for 24h


title: D37712_Anaerobic_growth-2


title: hMF.314.CKs


title: D37712_Anaerobic_shock-2


title: T112-5

description:
Sample 5
T112_count_matrix.txt


title: KO, macroH2A1, HSV-1 12 hpi, Rep3

city: Seattle

first: Daphne

last: Avgousti

state: WA

address: 1100 Fairview Avenue North C1-201

department: Human Biology

institute: Fred Hutchinson Cancer Research Center

data_processing:
CUT&Tag raw sequencing data were aligned to a custom genome made by concatenating human (hg38), HSV (JN555585.1), and E. coli (U00096.3 Escherichia coli str. K-12 substr. MG1655, complete genome). We performed alignments using bowtie2.
Coverage at 100 bp windows of the human hg38 reference genome was calculated as number of reads of given length (120-1000 bp for the analyses presented here) that mapped at that window normalized by the factor N:   N= 10,000/(Total number of reads that mapped to E. coli genome)   Here 10,000 is an arbitrarily chosen number. The normalized coverage at each base-pair from each replicate was averaged when combining multiple replicates.
The normalized read density in 100 bp bins were then smoothed with a running average over the bins spanning +/- 1000 bp around each bin.
Assembly: hg38
Assembly: HSV-1 strain 17 JN555585.1
Library strategy: CUT&Tag

organism:
Homo sapiens
Human alphaherpesvirus 1

source_name: Skin

extract_protocol:
Cells were harvested using trypsin, washed three times with ice-cold phosphate-buffered saline (PBS) via centrifugation at 600 xg for 3 minutes and counted using a hemocytometer. Nuclei from six hundred thousand cells were isolated by hypotonic lysis in 1 mL buffer NE1 (20 mM HEPES-KOH pH 7.9; 10 mM KCl; 0.5 mM spermidine; 0.1% Triton X-100; 20% Glycerol; Roche EDTA-free protease inhibitor) for 10 minutes on ice followed by centrifugation at 1300 xg for 4 minutes. Nuclei were resuspended in Wash buffer (20 mM HEPES-NaOH pH 7.5; 150 mM NaCl; 0.5 mM spermidine; Roche EDTA-free protease inhibitor) and counted using a hemocytometer. BioMag Plus Concanavalin A coated beads (Polysciences 86057-3) were equilibrated with Binding buffer (20 mM HEPES-KOH pH 7.9; 10 mM KCL; 1mM CaCl2; 1 mM MnCl2). The beads (5 µL) were mixed with aliquots of seventy-five thousand nuclei and incubated at room temperature (RT) for 10 minutes, then were placed on a magnet stand to clear (1 min) and be decanted through removal of liquid with a pipettor. The beads were resuspended in 50 µL primary antibody (anti-mH2A1, anti-H3K27me3, anti-mouse IgG 1:100) in Wash buffer supplemented with 2 mM EDTA and 0.1% bovine serum albumin (BSA) and incubated on a nutator at 4 °C for 5 days. The beads were decanted on a magnet stand then resuspended in 50 µL secondary antibody (Guinea pig anti-rabbit IgG 1:100) in Wash buffer supplemented with 2 mM EDTA and 0.1% BSA and incubated on a nutator at room temperature for 1 hr. The beads were decanted on a magnet stand and washed with 200 µL Wash buffer, then were resuspended in 50 µL pA-Tn5 (1:200) in 300-Wash buffer (Wash buffer containing 300 mM NaCl) and incubated on a nutator at room temperature for 1 hr. The beads were decanted on a magnet stand and washed twice with 200 µL 300-Wash buffer, then resuspended in 50 µL Tagmentation buffer (300-Wash buffer supplemented with 10 mM MgCl2) and incubated at 37 °C for 1 hr. Following tagmentation, the beads were decanted on a magnet stand and washed with 50 µL TAPS wash buffer (10 mM TAPS pH 8.5, 0.2 mM EDTA), then resuspended in 5 µL TAPS wash buffer supplemented with 0.1% SDS and incubated at 58 °C C for 1 hr. Tubes were placed on ice and SDS was neutralized with 15 µL 0.67% Triton-X100
2 µL of 10 mM indexed P5 and P7 primer solutions and 25 µL NEBnext High-Fidelity 2X Master Mix were added. Gap-filling and 15 cycles of PCR were performed using an MJ PTC-200 Thermocycler. Library clean-up was performed by incubating beads with 65 µL SPRI bead slurry for 5-10 minutes, then magnetization and two washes with 200 µL 80% ethanol. Libraries were eluted with 22 µL Tris-HCl pH 8.0 and 2 µL was used for Agilent 4200 Tapestation analysis. The barcoded libraries were mixed to achieve equimolar representation as desired aiming for a final concentration as recommended by the manufacturer for sequencing on an Illumina HiSeq 2500 2-lane Turbo flow cell.

value: Skin

value: mH2A1 KO HFF-T

value: macroH2A1 knockout tert-immortalized human foreskin fibroblast

tag: cut&tag antibody

value: HSV-1 infection

tag: time

value: 12 hours post-infection


title: T112-4

description:
Sample 4
T112_count_matrix.txt


title: hMF.314.Control


title: KO, macroH2A1, Mock, Rep3

value: Mock (no infection)


title: KO, macroH2A1, HSV-1 8 hpi, Rep3

value: 8 hours post-infection


title: T112-3

description:
Sample 3
T112_count_matrix.txt

value: DMSO for 24h


title: KO, macroH2A1, HSV-1 4 hpi, Rep3

value: 4 hours post-infection


title: KO, macroH2A1, HSV-1 12 hpi, Rep2


title: hMF.301.CKs.D500uM

value: Monocyte-derived macrophages

value: CK (IL1β, IL-6, IL8, TNFα, IFNƴ and GM-CSF 20ng/mL) 1h, then DETA NONOATE 500µM 24h


title: KO, macroH2A1, HSV-1 8 hpi, Rep2


title: hMF.301.CKs


title: T112-2

description:
Sample 2
T112_count_matrix.txt


title: hMF.301.D500uM

value: DETA NONOATE 500µM 24h


title: KO, macroH2A1, Mock, Rep2


title: KO, H3K27me3, HSV-1 12 hpi, Rep3


title: T112-1

description:
Sample 1
T112_count_matrix.txt


title: KO, H3K27me3, HSV-1 8 hpi, Rep3


title: KO, H3K27me3, Mock, Rep3


title: hMF.294.CKs.D500uM


title: hBM-MSC-TERT4, 1d adipogenic differentiation, BANF1-antibody-ab129184

city: Odense

last: Rauch

address: Campusvej 55

department: Department of Clinical Research

country: Denmark

institute: University of Southern Denmark and Odense University Hospital

data_processing:
ChIP-seq reads were aligned to the hg19 genome using STAR aligner (Dobin A, et al., Bioinformatics 29:15-21) with the following parameters: --outSJfilterIntronMaxVsReadN 0 --alignIntronMax 1 --alignSJDBoverhangMin 200, with all other parameters set at default. Only one read per position and read length was kept.
Peak calling, annotation and tag quatification was done using HOMER (Heinz S, et al. 2010. Molecular Cell 38: 576-589) and human ENCODE blacklisted sites were removed using BedTools.
Assembly: hg19
Supplementary files format and content: BigWig files were created using HOMER for visualization of BANF1 binding in genome browser. BANF1 tag count was quantified at BANF1 or DNase1 peaks (Rauch A, et al. 2019. Nature Genetics 51: 716-727) using HOMER with  option noadj (BANF1_antibodies_at_BANF1peaks.txt) or without (BANF1_DNase_at_DNasepeaks.txt; BANF1_DNase_at_BANF1peaks_NormalizedToTenMillionTags.txt)

growth_protocol: Telomerase-immortalized human mesenchymal stromal cells of bone marrow (BM-hMSC-TERT4)  origin were grown under standard cell culture conditions in α-MEM supplemented with 10 % fetal calf serum (FCS) and 1 % penicillin/streptomycin (P/S).

extract_protocol:
Chromatin was prepared from 150 mm culture dishes first by crosslinking in 1% formaldehyde in PBS (10 minutes, RT). Cross-linking was stopped by adding glycine to a final concentration of 0.125 M (10 minutes, RT). The cells were washed twice in ice-cold PBS, and harvested in ice-cold lysis buffer (0.1% SDS, 1% Triton X-100, 0.15 M NaCl, 1 mM EDTA, 20 mM Tris pH=8) and sonicated at high setting in a Bioruptor-Twin (Diagenode) at a volume of 1.5 ml in 15-mL tubes for 40 cycles of 30 seconds on and 30 seconds off. The chromatin IPs were performed as described in (Nielsen R, et al. 2014. Methods in Enzymology 537: 261-279).
ChIP-seq libraries were constructed from 10 to 20 ng of genomic DNA according to the manufacturer's instructions (Illumina) as described in (Nielsen R, et al. 2014. Methods in Enzymology 537: 261-279).

treatment_protocol: Two days post confluency cells were induced to undergo osteoblast or adipocyte differentiation by switching to α-MEM supplemented with 10% FCS, 10 mM dexamethasone, 10 nM vitamin D, 10 mM β-glycerolphosphate, and 50 µg/ml ascorbic acid or to DMEM supplemented with 10% fetal serum, 10ug/mL insulin, 1µM rosiglitazone, 100 mM dexamethasone, and 500 µM isobutylmethylxanthine. Media was replaced on day 2, 4, 7, 9 and 11.

value: 24 hrs

tag: antibody

value: adipogenic differentiation


title: KO, H3K27me3, HSV-1 4 hpi, Rep3


title: KO, H3K27me3, HSV-1 8 hpi, Rep2


title: KO, H3K27me3, HSV-1 4 hpi, Rep2


title: KO, H3K27me3, HSV-1 12 hpi, Rep2


title: hMF.294.CKs

value: CK (IL1β, IL-6, IL8, TNFα, IFNƴ and GM-CSF 20ng/mL) 24h


title: hBM-MSC-TERT4, undifferentiated, BANF1-antibody-ab129184

value: 0 hrs

value: undifferentiated


title: KO, H3K27me3, Mock, Rep2

value: Skin


title: KO, macroH2A1, HSV-1 4 hpi, Rep2

value: mH2A1 KO HFF-T


title: hMF.294.D500uM


title: hBM-MSC-TERT4, undifferentiated, BANF1-antibody-sc166324


title: hMF.293.CKs.D500uM


title: hMF.293.CKs


title: hMF.301.Control

value: Vehicle


title: hMF.294.Control


title: KO, IgG, HSV-1 4 hpi, Rep2

value: macroH2A1 knockout tert-immortalized human foreskin fibroblast

value: IgG

value: HSV-1 infection


title: KO, IgG, Mock, Rep3

value: Mock (no infection)


title: KO, IgG, HSV-1 4 hpi, Rep3


title: KO, IgG, HSV-1 8 hpi, Rep2

value: 8 hours post-infection


title: KO, IgG, Mock, Rep2


title: hMF.293.D500uM


title: hUC-MSCs,+CoQ10 biol rep 3

city: Shanghai, China

first: Liming

last: Ouyang

address: East China University of Science and Technology, 130 Meilong Road, Xuhui District, Shanghai, China

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
paired-end clean reads were aligned to the Homo Sapiens(GRCh38/hg38) using hisat2 (v2.0.5)
featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample.

source_name: umbilical cord

growth_protocol: Human umbilical cord mesenchymal stem cells are cultured in serum-free medium in an incubator containing 5% carbon dioxide, 37 °C

extract_protocol:
Then total RNA of cells was extracted by Trizol reagent method. Total amounts and integrity of RNA were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA) .
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® or NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® following manufacture's protocols.

treatment_protocol: hUC-MSCs were cultured in medium containing NMN (10μM) or CoQ10 (50μM) or none (control) for 24 hours.

value: umbilical cord

tag: genotype

value: WT

value: No serum culture

tag: agent

value: CoQ10 treat


title: hUC-MSCs,+CoQ10 biol rep 2

institute: East China University of Science and Technology

value: Human umbilical cord mesenchymal stem cells


title: HFF, macroH2A1, HSV-1 12 hpi, Rep3

value: HFF

value: Primary human foreskin fibroblast

value: 12 hours post-infection


title: KO, IgG, HSV-1 8 hpi, Rep3


title: KO, IgG, HSV-1 12 hpi, Rep3


title: KO, IgG, HSV-1 12 hpi, Rep2


title: hMF.293.Control

value: Monocyte-derived macrophages


title: hUC-MSCs,+CoQ10 biol rep 1


title: hBM-MSC-TERT4, 1d osteogenic differentiation, BANF1-antibody-ab129184

value: 24 hrs

value: osteogenic differentiation


title: hUC-MSCs,+NMN biol rep 3

value: NMN treat


title: HFF, macroH2A1, HSV-1 8 hpi, Rep3

value: Skin


title: hUC-MSCs,+NMN biol rep 2


title: hUC-MSCs,+NMN biol rep 1


title: DSCs-control

city: Guangzhou

first: Yang

address: Nanfang Hospital

institute: Nanfang Hospital, Southern Medical University

description: DSCs in control group

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh38 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: hair

growth_protocol: DPCs and DSCs were routinely generated by re-plating  (typically 5 × 105 cells into a T25 flask) in DMEM medium (Gibico, Grand Island, USA)

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard protocols

treatment_protocol: DPCs and DSCs were transfected with miR-221 angomir or control sequence

value: hair

value: Dermal sheath cells

value: tranfected with control sequence


title: DSCs-miR-221

description: DSCs with miR-221 overexpression

value: tranfected with miR-221 angomir


title: HFF, macroH2A1, Mock, Rep3

value: HSV-1 infection

value: Mock (no infection)


title: HFF, macroH2A1, HSV-1 8 hpi, Rep2

value: 8 hours post-infection


title: HFF, macroH2A1, HSV-1 12 hpi, Rep2


title: hUC-MSCs,Control biol rep 3

value: umbilical cord

value: WT

value: No serum culture

value: control


title: HFF, macroH2A1, Mock, Rep2

value: HFF

value: Primary human foreskin fibroblast


title: DPCs-control

description: DPCs in control group

value: Dermal papilla cells


title: HFF, H3K27me3, HSV-1 12 hpi, Rep3

value: 12 hours post-infection


title: HFF, H3K27me3, HSV-1 8 hpi, Rep3


title: DPCs-miR-221

description: DPCs with miR-221 overexpression


title: hUC-MSCs,Control biol rep 1

value: Human umbilical cord mesenchymal stem cells


title: hUC-MSCs,Control biol rep 2


title: HFF, H3K27me3, Mock, Rep3

value: Skin


title: HFF, macroH2A1, HSV-1 4 hpi, Rep3

value: 4 hours post-infection