title: ChIP_seq_blue_MAC3A_rep3

city: Chicago

first: Bochen

last: Jiang

address: Department of Chemistry

institute: The University of Chicago

description: ChIP seq data of blue MAC3A replicate3

data_processing:
ChIP-seq reads from this study were mapped to the TAIR10 reference genome with Bowtie2.
Only reads with one best hit and no mismatches were deduplicated with Samtools and maintained for the following analyses.
ChIP-seq peaks were identified by MACS2 (v2.1.1) and annotated using ChIPseeker
Assembly: TAIR10
Supplementary files format and content: narrowPeak contains peak files
Supplementary files format and content: bigwig contains normalized ChIP-seq signal

source_name: seedling

growth_protocol: Plant lines expressing MAC3A-GFP were used for ChIP-seq with plant lines expressing only GFP as input control. Around 2-4 grams grown for 6 days under blue light on 1/2 MS medium were collected and ground with liquid nitrogen.

extract_protocol:
Nuclei isolation buffering (50mM Hepes, 1M Sucrose, 5mM KCl, 5mM MgCl2, 0.6% Triton X-100, 0.4mM PMSF, 5mM Benzamidine) containing 1% formaldehyde were used to fix the chromatin for 10 minutes. Fresh-prepared glycine was used to terminate the crossing reaction and sheared via Bioruptor Plus (Diagenode) and immunoprecipitated with the antibody at 4°C overnight. Magnetic Protein A and Protein G Dynabeads (Invitrogen) were added into the samples and incubated at 4 °C for 2 hours. The reverse crosslink was performed at 65 °C overnight. The protein-DNA mix was treated with Protease K (Invitrogen) at 45°C for 4 hours, then the DNA was purified and precipitated with 3M Sodium Acetate (Invitrogen), glycoBlue (Invitrogen), and Ethanol at -20°C overnight.
The precipitated DNA was used for qPCR using the primers listed in Table S1 or library preparation with the Ovation Ultra Low System V2 kit (NuGEN) following the manufacturer’s instructions and sequenced on Illumina NovaSeq.

treatment_protocol: Light-emitting diode (LED) was used to obtain monochromatic blue light.

value: seedling

value: anti-FLAG M2 (Sigma)


title: Skin, excised, cultured, expanded, for lamin A/C ChIP Rep2

status: Public on Aug 21 2023

type: SRA

city: Oslo

first: Philippe

last: Collas

address: PO Box 1112 Blindern

department: Institute of Basic Medical Sciences

country: Norway

institute: University of Oslo

library_source: genomic

data_processing:
Reads were mapped to the hg38 genome with Bowtie2 v2.4.1.
Bigwig tracks were generated from Log2(ChIP/input) ratios in 1 kilobase (kb) bins using bamCompare from Deeptools v3.5.1
Mapped reads were used to call Lamin A/C and H3K9me3 peaks using 10 runs of Enriched Domain Detector with auto-estimation of GapPenalty and BinSize parameters, and mean GapPenalty and BinSize outputs from these runs were used for a final EDD run.
Supplementary files format and content: peaks.bed
Supplementary files format and content: bw

molecule: genomic DNA

organism: Homo sapiens

source_name: Skin

extract_protocol:
Cells were fixed in 1% formaldehyde, lysed in 50 mM Tris-HCl, pH 8, 10 mM EDTA, 1% SDS, protease inhibitors and Na-butyrate, and sonicated into ~200 bp fragments using a Picorupter (Diagenode). After sedimentation,  chromatin was incubated with anti-lamin A/C antibodies at 10 µg/5x10e6 cells or with anti-H3K9me3 antibodies at 2.5 µg/10e6 cells. Cross-links were reversed, DNA purified, eluted in H2= and processed for library preparation.
Libraries were prepared using the Microplex kit (Diagenode)

treatment_protocol:
For myo-conversion, immortalized fibroblasts were transduced with a Tet-on inducible lentiviral vector encoding mouse Myod with a multiplicity of injection of 10 in presence of 4 μg/ml of polybrene (Sigma-Aldrich). Cells were cultured in DMEM, 4.5 g/l glucose, 10% fetal bovine serum and 0.1% Penicil-lin-Streptomycin. Cells were then plated on dishes coated with 1% Matrigel (Sig-ma-Aldrich) at high density and cultured in DMEM, 10 µg/ml insulin and 4 µg/ml doxycycline (Sigma-Aldrich). After 5 days, myo-converted fibroblasts (McF) were harvest-ed for follow-up assays.
For myogenic differentiation, cells were plated on dishes coated with 1% Matrigel (Sigma-Aldrich) at high density in differentiating medium (DMEM, 10 µg/ml insulin, 50 µg/ml Penicillin-Streptomycin). After 5 days, myotubes (MT) were harvested for follow-up assays.

tag: tissue

value: Skin

tag: cell type

value: fibroblast

tag: genotype

value: WT

tag: treatment 1

value: hTRET-immorttalized

tag: treatment 2

value: Myogenic induction

tag: time

value: 5 days

tag: chip antibody

value: Lamin A/C (Santa Cruz sc7292x)

tag: replicate

value: rep 2


title: Heat-3h-2

city: Jinju

first: Seon-In

last: Yeom

address: 501, Jinjou-daero

country: South Korea

institute: Gyeongsang National University

library_source: transcriptomic

data_processing:
A quality control application for high throughput sequence data using FastQC Version 0.11.8
Removes adapter sequences from DNA high-throughput sequencing data using Cutadapt  Version 1.15
A toolkit for the quality control (QC) of next generation sequencing (NGS) data using Trimmomatic Version 0.38
Alignment program for mapping next-generation sequencing reads to Capsicum annuum genome using Hisat2 Version 2-2.1.0
Assembly: Capsicum annuum v1.6
Supplementary files format and content: tab-delimited text files include the values of read count for each sample

molecule: polyA RNA

organism: Capsicum annuum

source_name: Leaves

extract_protocol:
Three biological replicates at each time point per condition were collected. The leaf samples were flash-frozen in liquid nitrogen and stored at ˗80°C until RNA isolation. Total RNA was extracted from pepper leaf samples (100 mg) using the Trizol reagent. Five micrograms of each RNA sample were used for construction of sequencing libraries.
RNA libraries were prepared for sequencing using strand-specfic RNA-seq Illumina protocols

value: Leaves

tag: treatment

value: Heat

tag: timepoint


title: MPP1_GEX_Pert

city: Berlin

first: Frederik

middle: Richard

last: Heinrich

state: Berlin

address: Chariteplatz 1

department: Bioinformatics

country: Germany

description:
4 mice, hashtagged (#1) miR-221/222-proficient, 4 mice, hashtagged (#2) miR-221/222-deficient,
MPP1_no3.h5

data_processing:
Raw data were processed using cellranger-3.1.0 with refdata-gex-mm10-2020-A and refdata-cellranger-vdj_GRCm38_alts_ensembl-mouse-2.2.0 as reference.   .Mkfastq, count and vdj were used in default parameter settings with 3000 expected cells for demultiplexing, detection of intact cells, quantification of gene expression, antibody capture as well as assembly and quantification of T cell receptor sequences.
Assembly: mm10
Supplementary files format and content: h5: aggregated gene count matrix in hdf5 format including antibody counts for CD127,  AntiAPC, CD279, CD197, CD39, CD185, CD31, KLRG1, CD183, CD49d, CD73, FQPQNGQFI, KAVYNFATC, SGVENPGGYCL, CSANNSHHYI, ISHNFCNL as well as hashtag counts for different biological replicates. feature_reference.csv: ADT/HTO reference file, fasta: high-confidence contig sequences of immune receptors with the corresponding cellular barcode and contig-id; csv: results from single cell immune profiling, comprising the annotation of the immune receptor, cellular barcode and contig-id.

molecule: total RNA

organism: Mus musculus

source_name: Bone marrow

extract_protocol:
Bone marrow derived lineage positive (B220+, CD3+, CD4+, CD8+, CD11b+, CD11c+,CD19+, Gr1+, NK1.1+, TER119+) cells from perturbed or unperturbed miR‑221/222 proficient and deficient mice were first depleted on magnetic column (LS from Miltenyi) using 4 mice in each condition. The BM single cell suspensions were labeled separately for preparative FACS, followed by staining with TotalSeq™-C anti-mouse antibodies: Hashtag‑1 for miR‑221/222 proficient and perturbed, Hashtag‑4 for miR‑221/222 proficient and unperturbed, Hashtag-2 for miR‑221/222 deficient and perturbed and Hashtag-5 miR‑221/222 deficient and unperturbed (BioLegned, #1: 155861, #2: 155863, #4: 155867, #5 155869). The unperturbed or perturbed miR221/222-proficient samples were pooled with deficient samples for scRNAseq.
HSC was sorted as live, lineage(CD3, CD4, CD8, CD11b, CD11c, CD19, B220, Ly6g(Gr1), NK1.1, TER119)- CD117(ckit)+ Ly6a/e(Sca1)+ CD34- Flk2- CD150+ CD48- cells; MPP1 was sorted as live, lineage(CD3, CD4, CD8, CD11b, CD11c, CD19, B220, Ly6g(Gr1), NK1.1, TER119)- CD117(ckit)+ Ly6a/e(Sca1)+ CD34+ Flk2- CD150+ CD48- cells; MPP2 was sorted as live, lineage(CD3, CD4, CD8, CD11b, CD11c, CD19, B220, Ly6g(Gr1), NK1.1, TER119)- CD117(ckit)+ Ly6a/e(Sca1)+ CD34+ Flk2- CD150+ CD48+ cells.
The samples were then applied to 10x Genomics workflow for cell capturing and scRNA gene expression (GEX) library preparation using the Chromium Single Cell 5′ Library & Gel Bead Kit as well as the Single Cell 5′ Feature Barcode Library Kit (10x Genomics). After cDNA amplification the CiteSeq libraries were prepared separately using the Single Index Kit N Set A while final GEX libraries were obtained after fragmentation, adapter ligation, and final Index PCR using the Single Index Kit T Set A.
Chromium Single Cell 5′ Library & Gel Bead Kit as well as the Single Cell 5′ Feature Barcode Library Kit (10x Genomics).

tag: strain

value: C57BL/6J background

tag: genotypes

tag: sorting strategy

value: live, lineage(CD3, CD4, CD8, CD11b, CD11c, CD19, B220, Ly6g(Gr1), NK1.1, TER119)- CD117(ckit)+ Ly6a/e(Sca1)+ CD34+ Flk2- CD150+ CD48- MPP1 cells


title: MPP2_GEX_Pert

description:
4 mice, hashtagged (#1) miR-221/222-proficient, 4 mice, hashtagged (#2) miR-221/222-deficient,
MPP2_no3.h5

value: live, lineage(CD3, CD4, CD8, CD11b, CD11c, CD19, B220, Ly6g(Gr1), NK1.1, TER119)- CD117(ckit)+ Ly6a/e(Sca1)+ CD34+ Flk2- CD150+ CD48+ MPP2 cells


title: MPP1_CITE_Pert

library_source: other

molecule: protein


title: Skin, excised, cultured, expanded, for lamin A/C ChIP Rep1

value: rep 1


title: Heat-3h-1


title: HSC_CITE_Pert

description:
4 mice, hashtagged (#1) miR-221/222-proficient, 4 mice, hashtagged (#2) miR-221/222-deficient,
HSC_no3.h5

value: live, lineage(CD3, CD4, CD8, CD11b, CD11c, CD19, B220, Ly6g(Gr1), NK1.1, TER119)- CD117(ckit)+ Ly6a/e(Sca1)+ CD34- Flk2- CD150+ CD48- HSC cells


title: ChIP_seq_blue_MAC3A_rep1

country: USA

description: ChIP seq data of blue MAC3A replicate1

organism: Arabidopsis thaliana

value: seedling


title: SARS-CoV-2_28

city: Hamburg

first: Marcel

middle: Seungsu

last: Woo

state: Hamburg

address: Falkenried 94

department: Neurology

institute: UKE

data_processing:
STAR v.2.4 alignment to genome
featurCounts v.1.5.1 for gene loci counting
DESeq2 for differential expression analysis
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file including raw gene counts of every sample

source_name: vagus nerve

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen)
RNA libraries for RNA-seq were prepared using poly A enrichment with Illumina TruSeq sample prep Kit / Illumina TruSeq SR Cluster Kit v3 HiSeq4000 according to manufacturers protocol.

treatment_protocol:
NA
NA

value: vagus nerve

tag: disease


title: MPP1_CITE_Unpert

description:
4 mice, hashtagged (#4) miR-221/222-proficient, 4 mice, hashtagged (#5) miR-221/222-deficient,
MPP1.h5


title: Cold-72h-2

value: Cold


title: SARS-CoV-2_27


title: ChIP_seq_blue_input_control_rep2

description: ChIP seq data of blue control replicate2

value: anti-FLAG M2 (Sigma)


title: SARS-CoV-2_26


title: MPP1_GEX_Unpert


title: Cold-72h-1

value: WT


title: ChIP_seq_blue_input_control_rep1

description: ChIP seq data of blue control replicate1


title: ChIP_seq_blue_MAC3A_rep2

description: ChIP seq data of blue MAC3A replicate2


title: SARS-CoV-2_25


title: SARS-CoV-2_24


title: HSC_GEX_Unpert

description:
4 mice, hashtagged (#4) miR-221/222-proficient, 4 mice, hashtagged (#5) miR-221/222-deficient,
HSC.h5


title: Pool_TP_miR-221/222-deficient

description: 4 mouse, non-hashtagged

data_processing:
Raw data were processed using cellranger-3.1.0 with refdata-gex-mm10-2020-A and refdata-cellranger-vdj_GRCm38_alts_ensembl-mouse-2.2.0 as reference.   .Mkfastq, count and vdj were used in default parameter settings with 3000 expected cells for demultiplexing, detection of intact cells, quantification of gene expression, antibody capture as well as assembly and quantification of T cell receptor sequences.
Assembly: mm10
Supplementary files format and content: h5: filtered_feature_bc_matrix (gene count matrix) in hdf5 format.

extract_protocol:
The preparative sorted samples were applied to the 10x Genomics workflow using the Chromium Single Cell 5′ Library & Gel Bead Kit and Single Index Kit T Set A.
Chromium Single Cell 5′ Library & Gel Bead Kit as well as the Single Cell 5′ Feature Barcode Library Kit (10x Genomics).

treatment_protocol:
Prior to HSC sorting, bone marrow-derived lineage-positive cells from CD45.2 miR221/222-proficent and deficent mice were depleted using MACS. HSC were then FACS sorted and transplanted twice into lethaly irradiated CD45.1 host mice. After the second transplantation, miR221/222-proficent and deficent donor derived (CD45.2+) HSC, MPP1 and MPP2 were sorted. miR221/222-deficent  HSC, MPP1 and MPP2  were pooled before capture.
HSC was sorted as live, lineage(CD3, CD4, CD8, CD11b, CD11c, CD19, B220, Ly6g(Gr1), NK1.1, TER119)- CD117(ckit)+ Ly6a/e(Sca1)+ CD34- Flk2- CD150+ CD48- cells; MPP1 was sorted as live, lineage(CD3, CD4, CD8, CD11b, CD11c, CD19, B220, Ly6g(Gr1), NK1.1, TER119)- CD117(ckit)+ Ly6a/e(Sca1)+ CD34+ Flk2- CD150+ CD48- cells; MPP2 was sorted as live, lineage(CD3, CD4, CD8, CD11b, CD11c, CD19, B220, Ly6g(Gr1), NK1.1, TER119)- CD117(ckit)+ Ly6a/e(Sca1)+ CD34+ Flk2- CD150+ CD48+ cells. Pooled sample werre separately sorted as HSC, MPP1 and MPP2 cells mentioned before, and pooled after the sorting for scRNA-seq analysis.

value: miR-221/222fl/gamma- Tg(Vav1-icre)J

value: live, lineage(CD3, CD4, CD8, CD11b, CD11c, CD19, B220, Ly6g(Gr1), NK1.1, TER119)- CD117(ckit)+ Ly6a/e(Sca1)+ CD34-/+ Flk2- CD150+ CD48-/+ HSC, MPP1 and MPP2 cellscells


title: ChIP_seq_dark_MAC3A_rep3

description: ChIP seq data of dark MAC3A replicate3


title: Cold-24h-3


title: ChIP_seq_dark_MAC3A_rep2

description: ChIP seq data of dark MAC3A replicate2


title: Ctrl_5

value: Ctrl


title: Cold-24h-1


title: SARS-CoV-2_23


title: Cold-24h-2


title: ChIP_seq_dark_MAC3A_rep1

description: ChIP seq data of dark MAC3A replicate1


title: MPP1_TP_miR-221/222-proficient

description: 4 mouse, non-hashtagged


title: ChIP_seq_dark_input_control_rep3

description: ChIP seq data of dark control replicate3


title: Cold-12h-3


title: MPP2_TP_miR-221/222-proficient

description: 4 mouse, non-hashtagged


title: HSC_GEX_Pert


title: ChIP_seq_blue_input_control_rep3

description: ChIP seq data of blue control replicate3


title: MPP2_GEX_Unpert

description:
4 mice, hashtagged (#4) miR-221/222-proficient, 4 mice, hashtagged (#5) miR-221/222-deficient,
MPP2.h5


title: Ctrl_4


title: Ctrl_3


title: HSC_TP_miR-221/222-proficient

description: 4 mouse, non-hashtagged


title: Cold-72h-3


title: ChIP_seq_dark_input_control_rep2

description: ChIP seq data of dark control replicate2


title: Cold-12h-1


title: Cold-12h-2


title: Ctrl_2


title: Cold-6h-3


title: ChIP_seq_dark_input_control_rep1

description: ChIP seq data of dark control replicate1


title: Ctrl_1


title: Cold-6h-2


title: H2AZ_IP_met1-2

city: Beijing

first: Jincong

last: Zhou

address: Tsinghua Yuan

country: China

institute: Tsinghua University

data_processing:
ssDRIP-seq and ChIP-seq: Reads were trimed using trim_galore.  Trimmed reads were aligned to the TAIR10 genome with Bowtie 2 version 2.3.0 using the default settings, and samtools 1.3.1 was used to remove reads with more than three mismatches and non-uniquely mapped reads. Then total mapped reads were further divided into forward and reverse reads. MACS2 was used to identify peaks and normalized coverage files (bigWig) with 5 bp bin sizes were obtained using bamCoverage from deeptools v2.26.0 to visualize on the Integrative Genomics Viewer. Furthermore, bamCompare or bigwigCompare from deeptools were used to compare immunoprecipitated and input samples for ChIP-seq analysis.
Whole-genome bisulfite-seq: Reads were trimed using trim_galore. Bismark v0.19.0 was used to map the trimmed reads and extract methylation level as described previously. The UCSC application tool wigToBigWig was used to get the bigwig file.
Assembly: TAIR10
Supplementary files format and content: ssDRIP-seq and ChIP-seq: bigwig files were generated using the bamCoverage from deeptools. Whole-genome bisulfite-seq: The UCSC application tool wigToBigWig was used to get the bigwig file.

source_name: seedlings

extract_protocol:
ssDRIP-seq: Nuclei were isolated from Arabidopsis plants with Honda buffer, followed by SDS/proteinase K treatment at 37°C overnight. Genome DNA was extracted by the phenol-chloroform method and precipitated with isopropanol. DNA fragmentation was performed overnight using endonucleases (MboI, MseI, NlaIII, DdeI); the negative control was treated with RNase H (New England Biolabs) overnight. DRIP was performed as described in Xu et al., 2017 and Sun et al., 2013. Briefly, 3.5 ug of DNA was bound with 10 ug of S9.6 antibody in 1 X binding buffer (10 mM NaPO4 pH 7, 140 mM NaCl, 0.05% Triton X-100) overnight at 4˚C. 50 ul Protein G sepharose beads were added for 4 hours. Bound beads were washed 4 times in binding buffer and elution was performed in elution buffer (50 mM Tris pH 8, 10 mM EDTA, Proteinase K) for 45 min at 55˚C. DNA was purified and sonoicated to 150 bp fragments.
Whole-genome bisulfite-seq: Nuclear DNA was extracted from 12 days old seedlings as described in DRIP/DRIP-seq section and sonicated to 250bp with COVARIS. After that Bisulfite conversion and DNA recovery was performed with EZ DNA Methylation-Gold Kit (ZYMO Research) by following the manufacturer instructions. Finally, the sequencing library is made using the EpiArt DNA Methylation Library Kit for Illumina V3 (Vazyme, NE103) by following the manufacturer instructions.
ChIP-seq: To gain the nucleosome resolution, native H2A.Z ChIP without crosslink and sonication was performed as described in (Bernatavichute et al., 2008), with some modifications. In brief, nuclei were extracted from 12 days old seedlings with Honda buffer (0.44 M sucrose, 1.25% Ficoll, 2.5% Dextran T40, 20 mM HEPES–KOH [pH 7.4], 10 mM MgCl2, 0.5% Triton X-100, 5 mM DTT, and protease inhibitors [Roche]). Nuclei were suspended in 1X MNAse buffer (50mM TriHCl pH 7.6, 5mM CaCl2, 0.1mM PMSF) containing 1X proteinase inhibitor cocktail (Roche). After RNase A (Thermo Scientific™) treatment at 37C for 30 minutes, chromatin was digested with MNase enzyme (NEB) for 6 minutes and the reaction was stopped with EDTA (10mM). Then, the nucleosomes were released with the addition of 0.005% SDS while rotating at 4C for 2-3 hours. After that the supernatant was separated and diluted with dilution buffer (0.1% triton, 50mM NaCl, 0.1mM PMSF, 17mM trisHCl, 3.33mM EDTA, 1x Cocktail inhibitor). Chromatin was pre-cleaned with Protein G beads, and immnoprecipitated with anti-H2A.Z antibodies at 4C overnight. The complexes were incubated with protein G beads (Millipore) at 4C for 3 hours with rotation, and washed three times with ChIP wash buffer having different concentration of NaCl in each wash (50mM TrisHCl pH 7.6, 10mM EDTA, 50/100/150 mM NaCl, 0.1mM PMSF, and 1x Cocktail inhibitor). Then DNA was eluted with elution buffer (0.1%SDS and 0.1M NaHCO3) at 65C for 15 minutes. Proteinase K treatment was performed at 55 C for 2 hour. DNA was recovered after phenol:chloroform extraction.
ssDRIP-seq: DRIPed DNA was conducted to library construction using the VAHTS ssDNA Library Prep Kit (Vazyme, ND620). Bisulphite-seq: to use EpiArt DNA Methylation Library Kit for Illumina V3 (Vazyme, NE103) for library construction. ChIP-seq: ChIPed DNA was conducted to library construction using the TruePrep DNA Library Prep Kit V2 (Vazyme, TD502).

value: seedlings

tag: ecotype

value: Columbia

tag: antibody

value: H2A.Z antibody (Luo et al., 2020)


title: H2AZ_IP_met1-1


title: SARS-CoV-2_22


title: Cold-6h-1

value: Leaves


title: H2AZ_IP-wt-2

value: wt


title: Cold-3h-3


title: SARS-CoV-2_21


title: H2AZ_IP-wt-1


title: SARS-CoV-2_20


title: Cold-3h-2


title: Cold-3h-1


title: H2AZ_IP-swc6ddm1-2


title: Abio-mock-72h-3


title: H2AZ_IP-swc6ddm1-1


title: Abio-mock-72h-2


title: H2AZ_IP-pie1ddm1-2


title: Abio-mock-72h-1


title: H2AZ_IP-pie1ddm1-1


title: SARS-CoV-2_17


title: SARS-CoV-2_16


title: SARS-CoV-2_18


title: Abio-mock-24h-3


title: H2AZ_IP-h1ddm1-1


title: SARS-CoV-2_15


title: H2AZ_IP-h1ddm1-2


title: SARS-CoV-2_14


title: Abio-mock-24h-2


title: SARS-CoV-2_13


title: Abio-mock-24h-1


title: SARS-CoV-2_12


title: H2AZ_IP-ddm1-1


title: H2AZ_IP-arp6ddm1-2


title: H2AZ_IP-ddm1-2


title: SARS-CoV-2_19


title: SARS-CoV-2_11


title: Abio-mock-12h-2


title: SARS-CoV-2_10


title: H2AZ_IP-arp6ddm1-1


title: H2AZ_input_met1-2


title: Abio-mock-12h-1


title: SARS-CoV-2_9


title: Abio-mock-6h-3


title: H2AZ_input_met1-1


title: Abio-mock-6h-2


title: SARS-CoV-2_8


title: Abio-mock-6h-1


title: SARS-CoV-2_6


title: SARS-CoV-2_7


title: H2AZ_input-wt-2


title: H2AZ_input-wt-1


title: Abio-mock-12h-3


title: SARS-CoV-2_4


title: Abio-mock-3h-3


title: H2AZ_input-swc6ddm1-2


title: SARS-CoV-2_3


title: H2AZ_input-swc6ddm1-1


title: H2AZ_input-pie1ddm1-2


title: SARS-CoV-2_2


title: SARS-CoV-2_1


title: Abio-mock-0h-3


title: Abio-mock-0h-2


title: H2AZ_input-h1ddm1-2


title: H2AZ_input-pie1ddm1-1


title: ADMSCs, Induction+ghrelin, rep3

city: Mudanjiang

first: Ge

last: Sun

address: No. 15, Dongxiaoyun Street, Aimin District, Mudanjiang 157010, Heilongjiang, China.

institute: Department of Orthopedics, The Second Affiliated Hospital of Mudanjiang Medical University

data_processing:
Real-Time Analysis (version 3.4.4) and bcl2fastq (version 2.19 ).
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp (version 0.23.1).
Trimmed sequence reads were mapped to GRCh38/hg38 using hisat2 with default parameters.
Read count extraction were performed using htseq-count,and normalized counts using FPKM (Fragments Per Kilobase Million).
Assembly: hg38
Supplementary files format and content: processed data.xlsx

source_name: Mesenchymal stem cells

extract_protocol:
RNA was extracted by using TRIzol (Ambion/Invitrogen，USA) reagent.  200 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® UltraTM RNA Library Prep Kit for Illumina®  following manufacturer's protocols.

value: Mesenchymal stem cells

value: Cardiomyocyte differentiation

tag: agent

value: ghrelin


title: ADMSCs, Induction+ghrelin, rep2


title: Flower-2

source_name: Flower

tag: tissue

value: Flower


title: H2AZ_input-ddm1-2


title: Flower-1


title: ADMSCs, Induction+ghrelin, rep1

tag: cell type


title: ADMSCs, Induction, rep3

tag: genotype

value: control


title: Abio-mock-3h-2


title: H2AZ_input-ddm1-1


title: stem-3

source_name: Stem

value: Stem


title: Abio-mock-3h-1


title: stem-2


title: ADMSCs, Induction, rep2


title: stem-1


title: ADMSCs, Induction, rep1


title: root-3

source_name: Root

value: Root


title: H2AZ_input-arp6ddm1-2


title: 293-dKO_SNX7886_3d_Rep4

city: COLUMBIA

first: HAO

last: JI

state: SC

address: 715 SUMTER ST CLS RM 109

department: College of Pharmacy

institute: University of South Carolina

data_processing:
Indexed sequences were checked quality by Fastqc
Indexed sequences were trimmed adaptor sequence by TrimGalore-0.4.5
Reads were mapped to the hg38 reference genome using STAR | version 2.7.2b with default parameters (generation of sam files)
Convert .sam files to .bam files using samtools | version: 1.5 with parameters -bh -F 3840 -q 255
Read counts over annotated genes were obtained using featureCount (subreads | version: 1.5.3) with parameters -p -B -M -O --fraction -T 10
Assembly: GRCh38.98
Supplementary files format and content: tab-delimited text files include gene counts for each sample

growth_protocol: 293-WT and 293-dKO cells were grown in DMEM (High-glucose) media with 10% FBS, 1% penicillin-streptomycin and 2 mM L-glutamine. The cells were plated in 12-well plate at the density of 5x10^4 cells per well.  24 hours post seeding, cells were treated as indicated.

extract_protocol:
RNA was harvested using RNeasy Mini Kit (Qiagen) and RNA quality was validated on RNA-1000 chip using Bioanalyzer (Agilent). 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext Ultra II Directional RNA Library prep Kit following manufacturer's protocols.

treatment_protocol: Cells were treated with vehicle control (0.1% DMSO) or 200nM BI1347 or 200nM SNX7886 for 72 hours.

tag: cell line

value: immortalized human embryonic kidney cells

value: CDK8/CDK19 double-knockout

value: 200nM SNX7886 for 72 hours

value: 3 days


title: H2AZ_input-arp6ddm1-1


title: 293-dKO_SNX7886_3d_Rep3


title: Abio-mock-0h-1

value: WT


title: H2AZ_input-h1ddm1-1

value: seedlings


title: root-1


title: 293-dKO_SNX7886_3d_Rep2


title: root-2


title: cmt3_DRIP_rep2_setG

data_processing:
library strategy: DRIP-seq
ssDRIP-seq and ChIP-seq: Reads were trimed using trim_galore.  Trimmed reads were aligned to the TAIR10 genome with Bowtie 2 version 2.3.0 using the default settings, and samtools 1.3.1 was used to remove reads with more than three mismatches and non-uniquely mapped reads. Then total mapped reads were further divided into forward and reverse reads. MACS2 was used to identify peaks and normalized coverage files (bigWig) with 5 bp bin sizes were obtained using bamCoverage from deeptools v2.26.0 to visualize on the Integrative Genomics Viewer. Furthermore, bamCompare or bigwigCompare from deeptools were used to compare immunoprecipitated and input samples for ChIP-seq analysis.
Whole-genome bisulfite-seq: Reads were trimed using trim_galore. Bismark v0.19.0 was used to map the trimmed reads and extract methylation level as described previously. The UCSC application tool wigToBigWig was used to get the bigwig file.
Assembly: TAIR10
Supplementary files format and content: ssDRIP-seq and ChIP-seq: bigwig files were generated using the bamCoverage from deeptools. Whole-genome bisulfite-seq: The UCSC application tool wigToBigWig was used to get the bigwig file.

value: Columbia


title: 293-dKO_SNX7886_3d_Rep1


title: BCX-102.P0

city: Houston

first: Xiaofeng

last: Zheng

state: TX

address: 7007 Bertner Ave

department: Bioinformatics & Computational Biology

institute: UT MD Anderson Cancer Center

data_processing:
BCL (raw output of Illumina HigSeq) files are processed using Illumina’s Consensus Assessment of sequence And Variation (CASAVA) tool (http://support.illumina.com/sequencing/sequencing_software/casava.html) for demultiplexing/conversion to FASTQ format, which is the standard input for most aligners and downstream analytic tools.
FASTQ files of RNA samples are processed using both STAR (Dobin et. al. 2012) following the two-step alignment procedure and TopHat (Kim and Salzberg 2011) and Cufflinks (Trapnell et. al. 2010).
Additional RNA quantification is conducted using HTSeq (Anders et. al. 2014) analyses.
Supplementary files format and content: tab-delimited text files include read counts and RPKM values for each Sample

source_name: PDX xenograft

extract_protocol: Frozen fragments of breast tumors from patients (BCX P0) and corresponding breast cancer xenografts (BCX P1) were placed in lysis buffer, homogenized, and RNA was isolated using Norgen BIOTEK Total RNA Purification Plus Kit.  RNA quality was assessed with an Agilent Bioanalyzer. Genomic RNA was quantified by Picogreen (Invitrogen) and quality was then assessed using 2200 Tapestation (Agilent).  RNA was converted to doubled stranded complementary DNA (cDNA) using Ovation RNA-Seq System V2 Kit (Nugen).  Libraries of cDNA were made using KAPA kits and capture was performed using Nimblegen whole exome V3 probes.  Libraries were then sequenced on a HiSeq 2000 (Illumina) via a version 3 TruSeq paired end flowcell per manufacturer's instructions.  FASTQ files are aligned to the reference genome (human Hg19) using STAR 64, and HTSeq 65 was used to obtain the read counts of genes.  Qualities of raw reads were assessed using FastQC 66. The read counts were normalized with DESeq2 67.

value: PDX xenograft

value: no treatment


title: PRMG-3

source_name: Pericarp

value: Pericarp


title: met1_DRIP_rep2_setG


title: BCX-100.P1


title: cmt3_DRIP_rep1_setG


title: PRMG-2


title: BCX-100.P0


title: 293-dKO_BI1347_3d_Rep4

value: 200nM BI1347 for 72 hours


title: met1_DRIP_rep1_setG


title: cmt2_DRIP_rep2_setG


title: cmt2_DRIP_rep1_setG


title: h1ddm1_2_DRIP_setF


title: PRBplus5-3


title: h1ddm1_1_DRIP_setF


title: BCX-099.P0


title: PRBplus5-2


title: PRMG-1


title: pie1ddm1_1_DRIP_setE


title: BCX-102.P1


title: 293-dKO_BI1347_3d_Rep3


title: 293-dKO_BI1347_3d_Rep2


title: 293-dKO_Ctrl_3d_Rep4

value: 0.1percent DMSO (vehicle control) for 72 hours


title: BCX-096.P1


title: BCX-099.P1


title: pie1ddm1_2_DRIP_setE


title: PRBplus5-1


title: 293-dKO_Ctrl_3d_Rep3


title: PRBplus10-3


title: ddm1swc6_2_DRIP_setE


title: BCX-095.P1


title: BCX-096.P0


title: PRBplus10-2


title: 293-dKO_Ctrl_3d_Rep1


title: ddm1swc6_1_DRIP_setE


title: BCX-092.P1


title: PRBplus10-1


title: ddm1arp6_2_DRIP_setE


title: 293-WT_SNX7886_3d_Rep4


title: 293-dKO_BI1347_3d_Rep1


title: PRB-3


title: BCX-087.P1


title: 293-WT_SNX7886_3d_Rep3


title: PRB-2


title: 293-WT_SNX7886_3d_Rep2


title: 293-dKO_Ctrl_3d_Rep2


title: ddm1_2_DRIP_setH


title: ddm1_2_DRIP_setF


title: BCX-084.P1


title: BCX-087.P0


title: PR3-3


title: 293-WT_BI1347_3d_Rep3


title: PRB-1


title: 293-WT_SNX7886_3d_Rep1


title: BCX-095.P0


title: PR3-2


title: ddm1_2_DRIP_setE


title: BCX-084.P0


title: ddm1_1_DRIP_setH


title: PR3-1


title: 293-WT_BI1347_3d_Rep2


title: BCX-080.P1


title: 293-WT_Ctrl_3d_Rep4


title: PR2-3


title: BCX-080.P0


title: ddm1_1_DRIP_setF


title: ddm1_1_DRIP_setE


title: ddm1arp6_1_DRIP_setE


title: BCX-092.P0


title: 293-WT_BI1347_3d_Rep1


title: BCX-066.P1


title: BCX-066.P0


title: PR2-2


title: 293-WT_Ctrl_3d_Rep3


title: DDM1-GFP_2_DRIP_setH


title: DDM1-GFP_1_DRIP_setH


title: PR2-1


title: 293-WT_Ctrl_3d_Rep2


title: PR1-4


title: BCX-055.P0


title: PR1-2


title: BCX-055.P1


title: DRIP_input-ddm1-1-1_setI


title: DRIP_input-ddm1-1-2_setI


title: BCX-051.P1


title: DRIP_IP-ddm1-1-1_setI


title: HiC_MEP_rep2

city: Randwick

first: Julie

last: Thoms

state: NSW

address: Level 2, C25 Lowy Cancer Research Centre, UNSW Sydney, High St

department: Adult Cancer Program

country: Australia

institute: UNSW Sydney

description:
MEP_40000.matrix
40000_abs.bed

data_processing:
HiC fastq files were processed and mapped to GRCh38, then PCR duplicates removed and contact matrices generated from the merged valid-pairs files
HOMER was used to identify compartments and TADs from balanced HiC-Pro contact matrice
Assembly: hg38
Supplementary files format and content: .matrix, .bed

source_name: Bone Marrow

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching, cells were lysed and nuclei frozen. Nuclei were sonicated using a Bioruptor Pico to generate chromatin fragments.
Libraries were generated using the Arima Genomics HiC kit (Arima cat#A101020) Biotinylated fragments were enriched and sheared prior to library preparation which was performed using Accel NGS 2S Plus DNA Library kit (Swift Biosciences)

value: Bone Marrow

value: CD34+ HSPC

tag: cell subset

value: MEP


title: HiC_GMP_rep2

description:
GMP_40000.matrix
40000_abs.bed

value: GMP


title: DRIP_IP-ddm1-1-2_setI


title: BCX-017.P1


title: HiC_GMP_rep1

description:
GMP_40000.matrix
40000_abs.bed


title: DRIP_input-ddm1-2-1_setI


title: PLMG-2

source_name: Placenta

value: Placenta


title: PLMG-1


title: 293-WT_Ctrl_3d_Rep1

value: immortalized human embryonic kidney cells

tag: time


title: HiC_HSC_rep2

description:
HSC_40000.matrix
40000_abs.bed

value: HSC


title: BCX-009.P1


title: PLBplus5-3


title: PR1-1


title: BCX-009.P0


title: DRIP_IP-ddm1-2-2_setI


title: DRIP_input-ddm1-2-2_setI


title: BCX-017.P0


title: BCX-051.P0


title: PLBplus5-2


title: HiC_MEP_rep1

description:
MEP_40000.matrix
40000_abs.bed


title: PLMG-3


title: HiC_HSC_rep1

description:
HSC_40000.matrix
40000_abs.bed


title: HiC_CMP_rep2

description:
CMP_40000.matrix
40000_abs.bed

value: CMP


title: PLBplus10-3


title: PLBplus5-1


title: BCX-022.P0


title: HiC_CMP_rep1

description:
CMP_40000.matrix
40000_abs.bed


title: BCX-022.P1


title: DRIP_IP-ddm1-2-1_setI


title: BCX-011.P1


title: DRIP_IP-ddm1-CRI-1_setI


title: PLBplus10-2


title: HiChIP_H3K27AC_MEP_rep2

description:
MEP_annotated_regions_withGenes.xlsx
MEP_sig0.01_loops.txt

data_processing:
HiChIP fastq files were processed and mapped to GRCh38, then PCR duplicates removed and contact matrices generated from the merged valid-pairs files
HiChIP contact matrices were used to generate interaction pairs at 5 kb resolution using MaxHiC,  and the WashU browser was used for loop visualization.
High confidence interactions (FDR ≤ 0.01) were used to generate a final list of promoter- regulator interactions.
Assembly: hg38
Supplementary files format and content: .xlsx, .txt
Library strategy: Hi-ChIP

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching, cells were lysed and nuclei frozen. Nuclei were sonicated using a Bioruptor Pico to generate chromatin fragments.
Libraries were generated using the Arima Genomics HiC kit (Arima cat#A101020) and the H3K27ac antibody. Biotinylated fragments were enriched and sheared prior to library preparation which was performed using Accel NGS 2S Plus DNA Library kit (Swift Biosciences)

tag: chip antibody


title: HiChIP_H3K27AC_MEP_rep1


title: DRIP_input-ddm1-CRI-2_setI


title: PLBplus10-1


title: BCX-011.P0


title: DRIP_IP-ddm1-CRI-2_setI


title: HiChIP_H3K27AC_GMP_rep2

description:
GMP_annotated_regions_withGenes.xlsx
GMP_sig0.01_loops.txt


title: PLB-3


title: BCX-010.P1


title: PLB-2


title: BCX-010.P0


title: HiChIP_H3K27AC_GMP_rep1


title: DRIP_input-ddm1-T-1_setI


title: PLB-1


title: BCX-006.P1


title: DRIP_IP-ddm1-T-1_setI


title: DRIP_input-ddm1-T-2_setI


title: HiChIP_H3K27AC_HSC_rep2

description:
HSC_annotated_regions_withGenes.xlsx
HSC_sig0.01_loops.txt


title: PL3-3


title: HiChIP_H3K27AC_CMP_rep2

description:
CMP_annotated_regions_withGenes.xlsx
CMP_sig0.01_loops.txt


title: BCX-006.P0


title: PL3-2


title: DRIP_input-ddm1-CRI-1_setI


title: HiChIP_H3K27AC_CMP_rep1


title: HiChIP_H3K27AC_HSC_rep1


title: DRIP_IP-wt-1_setI

value: wt


title: DRIP_input-wt-1_setI


title: PL3-1

value: WT


title: ChIP_MEP_H3K4me3

data_processing:
ChipSeq reads were trimmed using TrimGalore. Adaptors were removed using CutAdapt. The reads were aligned to hg38 using BWA.
ChipSeq reads were sorted, indexed using Samtools. Dupicate reads were removed using Picard. Replicates were merged using Samtools.
ChipSeq peak calling was done using MACS 2.0 with a p value of 1e-5
hg38
Supplementary files format and content: bigWig

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching, cells were lysed and nuclei frozen. Nuclei were sonicated using a Bioruptor Pico to generate chromatin fragments.
Antibody-chromatin complexes were recovered using protein G-agarose beads (Roche). After washing, immunoprecipitated DNA was eluted from beads, crosslinks reversed, and DNA purified using phenol-chloroform-isoamyl alcohol.


title: DRIP_IP-ddm1-T-2_setI

value: seedlings


title: PL2-3


title: MP41_rep3

city: Paris Cedex 05

first: Nicolas

last: Servant

address: 26 rue d'ulm

country: France

institute: Institut Curie

data_processing:
Raw sequencing data have been processed with HiC(Pro (v2.8.0). Biological replicates have then been merged to generate the final contact maps.
Raw contact maps have been normalized using the ICE or CAIC normalization according to the resolution.
Assembly: hg19

source_name: PDX of uveal melanoma

growth_protocol: Normal uveal melanocytes from an healthy donors, obtained after enucleations were dissociated and maintained in culture from choroidal membranes from Pr Simon Saule’s lab and Dr Geraldine Liot. After enzymatic (with collagenase) and mechanical dissociation, primary cells were cultured in HAM/F12 supplemented with 10% FBS, Penicillin 100 U/mL, Streptomycin 100 U/mL, 2mM L-glutamine, 2.5µg/mL Amphotericin B. Extemporaneously completed media was supplemented with 0.1mM IBMX, 10ng/µL of Cholera toxin (10 ng/ml final), and 10mg/mL FGF and filter with a 0.22µm filter. Cell were maintained in a humidified atmosphere with 5% CO2 at 37°C , and culture medium was exchanged twice a week.   MP41 and MP46 xenograft tumors were harvested before they reached a volume of 1 cm3 following ethical rules, and processed immediately for dissociation, immunolabelling and sorting based on Crépin R, Gentien D et al. et al protocol (2017).

extract_protocol: Genomic DNA was prepared according the protocol published by Rao et al. Cell 2014)

treatment_protocol: Cells obtained from subcultre or cell sorting were counted and 5 million cells were resuspended in 1xPBS with 1%, v/v freshly opened formaldehyde at a concentration of  1x106 cells per 1ml PBS. Cells were icubated at room temperature for 15 minutes with gentle rocking. A glycine solution was added to a final concentration of 0.125M to quench the reaction. The mixture was incubated at room temperature for 5 minutes on rocker. Cells were centrifuged for 5 minutes at 300xG (1000rpm) at 4°C. The supernatant was discarded  into an appropriate collection container, and cells were resuspended in 1ml of cold 1X PBS and spin for 5 minutes at 00xG (1000rpm) at 4°C. The supernatant was discarded. This washing step was repeated one more time, the supernatant was removed and cell pellets were flash-freezon in a dry ice/ethanol bath and stored at -80°C before starting the in situ HiC protocol (Rao et al. Cell 2014)

value: PDX of uveal melanoma

value: UM sorted cells


title: MP46_rep1


title: DRIP_input-wt-2_setI

value: Columbia


title: ChIP_GMP_H3K4me3


title: MP41_rep2


title: PL2-2


title: ChIP_CMP_H3K4me3


title: DRIP_IP-wt-2_setI


title: ChIP_HSC_H3K4me3


title: MP41_rep1


title: PL2-1


title: wt_2_DRIP_setG


title: 3T3-L1,mouse-LV-Bmp8a_3

city: Qingdao

first: shenjie

last: zhong

address: No. 5, Yushan Road

institute: ocean university of china

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.
Hisat2 tools soft were used to map with reference genome.
Quantification of gene expression levelsGene expression levels were estimated by fragments per kilobase of transcript per million fragments mapped.
Differential expression analysis of two conditions/groups was performed using the DESeq2.
Assembly: GRCz11.103
Supplementary files format and content: TXT files include FPKM values for each Sample

growth_protocol: 3T3-L1 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using RNAeasy™ Small RNA Isolation Kit with Spin Column (beyotime). Total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext Ultra Directional RNA Library Prep Kit for Illumina following manufacturer's protocols. 1ug of total RNA was used for the construction of sequencing libraries.

treatment_protocol: Adipogenic differentiation was induced by treatment of 2-day post confluent cells (designated day 0, D0) with 10ug/ml insulin (Sigma),1uM dexamethasone (Sigma), and 0.5mM isobutylmethylxanthine (Sigma) in the presence of 10% FBS until day 2. Cells were then fed with DMEM supplemented with 10% FBS and 10ug/ml insulin for 2 days, after which they were fed every other day with DMEM containing 10% FBS

value: embryonic fibroblast cells

value: mouse Bmp8a Overexpression

value: adipogenic differentiation

value: Day 8


title: MP46_rep2


title: PL1-2


title: PL1-3


title: wt_2_DRIP_setF


title: ChIP_MEP_H3K27ac

value: Bone Marrow

value: CD34+ HSPC


title: 3T3-L1,mouse-LV-Bmp8a_1


title: ChIP_GMP_H3K27ac

value: GMP


title: 3T3-L1,mouse-LV-Bmp8a_2


title: PL1-1

value: Placenta


title: 3T3-L1,LV-bmp8a_3

value: zebrafish bmp8a Overexpression


title: wt_1_DRIP_setG


title: CM_Pep_3D-3

value: Leaves

value: PepMoV


title: 3T3-L1,LV-bmp8a_2


title: CM_Pep_3D-2


title: ChIP_HSC_H3K27ac

value: HSC


title: ChIPmentation_MEP_H3K27me3

data_processing:
ChipSeq reads were trimmed using TrimGalore. Adaptors were removed using CutAdapt. The reads were aligned to hg38 using BWA.
ChipSeq reads were sorted, indexed using Samtools. Dupicate reads were removed using Picard. Replicates were merged using Samtools.
ChipSeq peak calling was done using MACS 2.0 with a p value of 1e-5
Assembly: hg38
Supplementary files format and content: bigWig
Supplementary files format and content: narrowPeak: BED6+4 files containing peaks called from merged replicates with macs2 using p-value of 1 x 10-5 and the IgG track as the control.
Library strategy: ChIPmentation

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching, cells were lysed and nuclei frozen. Nuclei were sonicated using a Bioruptor Pico to generate chromatin fragments.
Antibody bound chromatin was collected and crosslinked, before library construction using the KAPA HiFi HotStart Ready Mix and size selection using AMPure XP beads.
ChIPmentation/ Low input ChIP seq using tagmentation

value: MEP


title: wt_1_DRIP_setF

value: seedlings

value: wt


title: 3T3-L1,LV-bmp8a_1


title: CM_Pep_3D-1

value: WT


title: ChIPmentation_GMP_H3K27me3


title: BS_swc6ddm1_rep2_setA

value: Columbia


title: CM_Pep_2D-3


title: wt_2_DRIP_setE


title: CM_Pep_2D-2


title: BS_swc6ddm1_rep1_setA


title: ChIPmentation_HSC_H3K27me3


title: ChIPmentation_CMP_H3K27me3

value: CMP


title: 3T3-L1,LV-zsGreen2

value: embryonic fibroblast cells


title: BS_pie1ddm1_rep2_setA


title: ChIP_CMP_H3K27ac


title: 3T3-L1,LV-zsGreen1

value: adipogenic differentiation


title: CM_Pep_2D-1


title: ChIPmentation_MEP_Pol2_rep2

description:
Coverage_Pol2_MEP_merge_clip.bw
Pol2_MEP_peaks.narrowPeak


title: BS_pie1ddm1_rep1_setA


title: CM_Pep_1D-3


title: ChIPmentation_MEP_Pol2_rep1


title: wt_1_DRIP_setE


title: N2A-RNA-Seq-shK7-2

city: Shanghai

first: Yifan

last: Wang

address: 130 Dong An Road

institute: Fudan University

data_processing:
we aligned 150-bp paired-end reads to the mouse mm9 reference (more gene annotations than mm9) using HISAT2 v2.1.0 [47] with default parameters.
We then extracted uniquely mapped reads using grep command with NH:i:1 tag. BAM files were converted to bigwig files and normalized to 1× sequencing depth using bamCoverage in deeptools v2.5.5
We quantified gene expression using transcripts per million (TPM) with StringTie v1.3.3 with the parameter “-A”.
To identify differentially expressed genes, we counted reads overlapping Ensembl genes using HTSeq with the following command: htseq-count -f bam -r pos -s reverse -a 10 -t exon -i gene_id -m union.
We defined genes showing significant differences with log2(fold change) > 1 or < -1 and Benjamini-Hochberg corrected p-value < 0.05 as cutoff using the R package DESeq2excluding genes with zerocoverage in all samples.
Assembly: mm10
Supplementary files format and content: Excel files include TPM values for each Sample and DEG results
Supplementary files format and content: BIGWIG

growth_protocol: N2a cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA samples were prepared with TRIzol reagent (Life Technologies).
RNA libraries for RNA-seq were prepared using NEBNext Ultra II RNA Directional Library Prep Kit following manufacturer's protocols.

value: mouse neuroblasts

value: KDM7A knockdown


title: CM_Pep_1D-2


title: ChIPmentation_GMP_Pol2_rep2

description:
Coverage_Pol2_GMP_merge.bw
Pol2_GMP_peaks.narrowPeak

value: Bone Marrow

value: CD34+ HSPC


title: BS_ddm1_rep2_setA


title: CM_Pep_1D-1


title: N2A-RNA-Seq-shK7-1


title: ChIPmentation_GMP_Pol2_rep1

value: GMP


title: N2A-RNA-Seq-Ctrl-3


title: 3T3-L1,LV-zsGreen3

value: Day 8


title: CM_Pep_4h-3

value: Leaves


title: ChIPmentation_CMP_Pol2_rep2

description:
Coverage_Pol2_CMP_clip_merge.bw
Pol2_CMP_peaks.narrowPeak


title: N2A-RNA-Seq-Ctrl-2


title: CM_Pep_4h-2

value: PepMoV


title: N2A-RNA-Seq-shK7-3


title: ChIPmentation_CMP_Pol2_rep1


title: N2A-RNA-Seq-Ctrl-1


title: CM_Pep_4h-1


title: BS_wt_rep1_setB


title: CM_Pep_30m-3


title: BS_h1ddm1_rep1_setB


title: BS_h1ddm1_rep2_setB


title: CM_Pep_30m-2


title: ChIPmentation_HSC_Pol2_rep2

description:
Coverage_Pol2_HSC_merge_clip.bw
Pol2_HSC_peaks.narrowPeak

value: HSC


title: ChIPmentation_HSC_Pol2_rep1


title: CM_Pep_30m-1


title: ChIPmentation_MEP_STAG2_rep2

description:
Coverage_STAG2_MEP_merge_clip.bw
STAG2_MEP_peaks.narrowPeak

value: MEP


title: BS_WT_rep2_setA

value: seedlings


title: BS_ddm1_rep1_setB


title: BS_ddm1_rep2_setB


title: ChIPmentation_MEP_STAG2_rep1


title: BS_ddm1_rep1_setA


title: CM-P0-3D-3


title: ChIPmentation_GMP_STAG2_rep2

description:
Coverage_STAG2_GMP_merge_clip.bw
STAG2_GMP_peaks.narrowPeak


title: CM-P0-3D-2


title: ChIPmentation_CMP_STAG2_rep2

description:
Coverage_STAG2_CMP_merge_clip.bw
STAG2_CMP_peaks.narrowPeak


title: CM-P0-2D-3


title: BS_WT_rep1_setA

value: wt


title: BS_arp6ddm1_rep2_setA


title: ChIPmentation_CMP_STAG2_rep1


title: ChIPmentation_GMP_STAG2_rep1


title: CM-P0-3D-1

value: WT


title: BS_arp6ddm1_rep1_setA

value: Columbia


title: ChIPmentation_HSC_STAG2_rep2

description:
Coverage_STAG2_HSC.bw
STAG2_HSC_peaks.narrowPeak


title: human_nucleus pulposus_healthy_rep4

type: RNA

first: Zhenhao

last: Chen

address: 12 Mid- Wulumuqi Road

department: Department of Orthopedics

institute: Huashan Hospital, Fudan university

description: Biological replicate 4 of 4

hyb_protocol: The “IP” and “Sup” RNAs were treated with RNase R to eliminate linear RNAs and the resulting RNA was subsequently purified using the RNeasy MinElute Cleanup Kit

scan_protocol: the arrays were scanned in two-color channels by an Agilent Scanner G2505C.

data_processing:
Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images.
Data were analyzed by channel.
Raw intensities of IP (immunoprecipitated, Cy5-labelled) and Sup (supernatant, Cy3-labelled) were normalized with average of log2-scaled Spike-in RNA intensities.

source_name: healthy nucleus pulposus

label_protocol: the total RNAs were immunoprecipitated with anti-N6-methyadenosine (m6A) antibody. The modified RNAs were eluted from the immunoprecipitated magnetic beads as the “IP”. The unmodified RNAs were recovered from the supernatant as “Sup”. The “IP” and “Sup” RNAs were treated with RNase R, and then labeled with Cy5 and Cy3 respectively as cRNAs in separate reactions using Arraystar Super RNA Labeling Kit.

extract_protocol: Total RNAs and DNAs were extracted using the RNeasy Mini Kit

tag: disease state

value: healthy

tag: rna population

value: m6A unmodified RNAs

value: m6A modified RNAs


title: CM-P0-2D-1

data_processing:
A quality control application for high throughput sequence data using FastQC Version 0.11.8
Removes adapter sequences from DNA high-throughput sequencing data using Cutadapt  Version 1.15
A toolkit for the quality control (QC) of next generation sequencing (NGS) data using Trimmomatic Version 0.38
Alignment program for mapping next-generation sequencing reads to Capsicum annuum genome using Hisat2 Version 2-2.1.0
Assembly: Capsicum annuum v1.6
Supplementary files format and content: tab-delimited text files include the values of read count for each sample

tag: treatment

tag: timepoint


title: BS_wt_rep2_setB


title: human_nucleus pulposus_healthy_rep3

description: Biological replicate 3 of 4


title: CM-P0-1D-3


title: human_nucleus pulposus_healthy_rep2

description: Biological replicate 2 of 4


title: ChIPmentation_HSC_STAG2_rep1


title: ChIPmentation_MEP_PU1_rep2

description:
Coverage_PU1_MEP_merge_clip.bw
PU1_MEP_peaks.narrowPeak


title: human_nucleus pulposus_healthy_rep1

description: Biological replicate 1 of 4


title: ChIPmentation_MEP_PU1_rep3


title: VD2-MeDIP

city: SAINT LOUIS

first: Daofeng

last: Li

state: MO

address: 4515 McKinley Avenue

department: Genetics

institute: Washington University in St. Louis

data_processing:
All libraries were sequenced on Illumina HiSeq 2500 platforms.
Reads were aligned to mm9 genome using bowtie.
Genome_build: mm9
Supplementary_files_format_and_content: MeDIP bigWig files represent read density over genome using in-house script
Supplementary_files_format_and_content: MRE bigWig files represent read density over CpG sites using in-house script

source_name: Vitamin D sufficient LDLR-/- GFP+ bone marrow cells

growth_protocol: Pups born both vitamin D-deficient and sufficient were weaned to vitamin D-deficient or sufficient diets for 8 weeks

extract_protocol:
DNA was extracted for bone marrow cells from Vitamin D deficient and sufficient treated mouse  using the standard phenol chloroform method.
MeDIP-seq and MRE-seq were generated using the protocol in the paper: "Tost J. (eds) DNA Methylation Protocols. Methods in Molecular Biology, vol 1708".

treatment_protocol: Vitamin D deficient and sufficient LDLR-/- GFP+

tag: strain

tag: age

value: bone marrow cells

value: LDLR-/- GFP+


title: human_nucleus pulposus_degenerative_rep4

description: Biological replicate 4 of 4

source_name: degenerative nucleus pulposus

value: degenerative


title: VD2-MRE

data_processing:
Library strategy: MRE-seq
All libraries were sequenced on Illumina HiSeq 2500 platforms.
Reads were aligned to mm9 genome using bowtie.
Genome_build: mm9
Supplementary_files_format_and_content: MeDIP bigWig files represent read density over genome using in-house script
Supplementary_files_format_and_content: MRE bigWig files represent read density over CpG sites using in-house script


title: ChIPmentation_MEP_PU1_rep1

value: Bone Marrow

value: CD34+ HSPC


title: CM-P0-1D-2

extract_protocol:
Three biological replicates at each time point per condition were collected. The leaf samples were flash-frozen in liquid nitrogen and stored at ˗80°C until RNA isolation. Total RNA was extracted from pepper leaf samples (100 mg) using the Trizol reagent. Five micrograms of each RNA sample were used for construction of sequencing libraries.
RNA libraries were prepared for sequencing using strand-specfic RNA-seq Illumina protocols


title: VD1-MeDIP

source_name: Vitamin D deficient LDLR-/- GFP+ bone marrow cells


title: VD1-MRE


title: human_nucleus pulposus_degenerative_rep3

description: Biological replicate 3 of 4


title: CM-P0-1D-1

source_name: Leaves


title: CM-P0-2D-2


title: CM-P0-4h-3


title: ChIPmentation_GMP_PU1_rep3

description:
Coverage_PU1_GMP_clip.bw
PU1_GMP_peaks.narrowPeak

value: GMP


title: human_nucleus pulposus_degenerative_rep1

description: Biological replicate 1 of 4


title: R_tha_24m_B6_5

city: San Francisco

first: Tom

last: McMahon

state: CA

address: 1550 4th Street

institute: University of California San Francisco

data_processing:
Paired-end reads were mapped to mouse reference genome (mm10) by Hisat2 (v2.1.0).
Curated genes annotations from RefSeq were used to quantify gene expression as reads count by HTseq (v0.9.1).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *_count.txt: Tab-delimited text files for raw reads count for every gene by HTseq for each sample.

source_name: Hypothalamus

growth_protocol: All experimental animals were singly housed on a LD 12:12 cycle (250lux) and given ad libitum access to food and water. Male mice were used for all experiments.

extract_protocol:
Cervical dislocation then hypothalamus were excised at around ZT6 and placed in RNAlater for 2 days at 4'C. Subsequently, RNAlater was drained from tissues and then tissues flash frozen, and then stored at -80 degree.
Paired-end RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: Sex

value: Male

value: 24 months

value: Hypothalamus


title: CM-P0-4h-2

value: Leaves


title: R_tha_24m_B6_4


title: human_nucleus pulposus_degenerative_rep2

description: Biological replicate 2 of 4


title: ChIPmentation_GMP_PU1_rep2


title: CM-P0-4h-1


title: R_tha_18m_B6_16

value: 18 months


title: CM-P0-30m-3


title: ChIPmentation_GMP_PU1_rep1


title: ChIPmentation_CMP_PU1_rep3

description:
Coverage_PU1_CMP_merge_clip.bw
PU1_CMP_peaks.narrowPeak

value: CMP


title: R_tha_18m_B6_15

value: WT


title: CM-P0-30m-1


title: CM-P0-30m-2


title: R_tha_18m_B6_14


title: ChIPmentation_CMP_PU1_rep2


title: ChIPmentation_HSC_PU1_rep3

description:
Coverage_PU1_HSC.bw
PU1_HSC_peaks.narrowPeak

value: HSC


title: CM-Mock-V-3D-3


title: CM-Mock-V-3D-2


title: R_tha_12mB6_27

value: 12 months


title: R_tha_12mB6_28


title: ChIPmentation_HSC_PU1_rep2


title: R_tha_12mB6_26


title: R_tha_24m_B6_2


title: CM-Mock-V-3D-1


title: ChIPmentation_HSC_PU1_rep1


title: R_6mo_B34

value: 6 months


title: CM-Mock-V-2D-3


title: ChIPmentation_MEP_CTCF_rep3

description:
Coverage_CTCF_MEP_merge_clip.bw
CTCF_MEP_peaks.narrowPeak

value: MEP

value: CTCF


title: ChIPmentation_CMP_PU1_rep1


title: CM-Mock-V-2D-2


title: R_6mo_B33


title: ChIPmentation_MEP_CTCF_rep2


title: R_B13_2mothal

value: 2 months


title: R_6mo_B32


title: ChIPmentation_MEP_CTCF_rep1


title: ChIPmentation_GMP_CTCF_rep3

description:
Coverage_CTCF_GMP_merge_clip.bw
CTCF_GMP_peaks.narrowPeak


title: R_B12_2mothal


title: colorectum_young_AOM+DSS_d21_rep3

city: Chengdu

first: Yi

last: Liu

state: Sichuan Province

address: No. 4 keyuan road, gaopeng avenue

institute: Sichuan University

description: gene expression after 21 days in AOM+DSS-treated young mice's colorectum

hyb_protocol: 0.6 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 13.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

source_name: colorectum from young mice,AOM+DSS,d21,replicate 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: C57 mice (20 g weight, male) were purchased from Beijing HFK Bioscience Co. (Beijing, China) and housed in a specific-pathogen free (SPF) room (25 ˚C) under a 12-h light/dark cycle with ad libitum access to food and water.

extract_protocol: RNA was extracted by mirVanaTM RNA Isolation Kit (Applied Biosystem p/n AM1556 ) following the manufacturer's instructions.

treatment_protocol: Mice were injected intraperitoneally (i.p.) with 10 mg/kg azoxymethane (AOM; Sigma-Aldrich, Germany). After 7 days, the mice received drinking water containing 2% DSS for 7 days followed by normal drinking water for 14 days. Totally, three DSS cycles were performed.

value: colorectum

value: young

tag: time point (days)

tag: group

value: wound healing completed


title: colorectum_young_AOM+DSS_d21_rep1

source_name: colorectum from young mice,AOM+DSS,d21,replicate 1


title: CM-Mock-V-1D-2


title: colorectum_old_AOM+DSS_d21_rep3

description: gene expression after 21 days in AOM+DSS-treated old mice's colorectum

source_name: colorectum from old mice,AOM+DSS,d21,replicate 3

value: old


title: colorectum_old_AOM+DSS_d21_rep2

source_name: colorectum from old mice,AOM+DSS,d21,replicate 2


title: colorectum_old_AOM+DSS_d21_rep1

source_name: colorectum from old mice,AOM+DSS,d21,replicate 1


title: CM-Mock-V-1D-1


title: colorectum_young_AOM+DSS_d10_rep1

description: gene expression after 10 days in AOM+DSS-treated young mice's colorectum

source_name: colorectum from young mice,AOM+DSS,d10,replicate 1

value: wound healing


title: ChIPmentation_GMP_CTCF_rep1

value: Bone Marrow

value: CD34+ HSPC

value: GMP


title: ChIPmentation_GMP_CTCF_rep2


title: CM-Mock-V-2D-1

value: Leaves


title: colorectum_young_AOM+DSS_d10_rep3

source_name: colorectum from young mice,AOM+DSS,d10,replicate 3


title: CM-Mock-V-4h-3


title: th_5W_4

value: Male

value: 5 weeks

value: Hypothalamus


title: CM-Mock-V-1D-3

value: WT


title: ChIPmentation_CMP_CTCF_rep3

description:
Coverage_CTCF_CMP_merge_clip.bw
CTCF_CMP_peaks.narrowPeak

value: CMP


title: th_5W_3


title: colorectum_old_AOM+DSS_d10_rep2

description: gene expression after 10 days in AOM+DSS-treated old mice's colorectum

source_name: colorectum from old mice,AOM+DSS,d10,replicate 2


title: colorectum_young_AOM+DSS_d21_rep2

source_name: colorectum from young mice,AOM+DSS,d21,replicate 2


title: colorectum_old_AOM+DSS_d10_rep3

source_name: colorectum from old mice,AOM+DSS,d10,replicate 3


title: R_B11_2mothal


title: colorectum_young_AOM+DSS_d10_rep2

source_name: colorectum from young mice,AOM+DSS,d10,replicate 2


title: ChIPmentation_CMP_CTCF_rep2

source_name: Bone Marrow


title: CM-Mock-V-4h-2


title: th_5W_2


title: CM-Mock-V-4h-1


title: th_5W_1


title: CM-Mock-V-30m-3


title: ChIPmentation_HSC_CTCF_rep3

description:
Coverage_CTCF_HSC.bw
CTCF_HSC_peaks.narrowPeak

value: HSC


title: ChIPmentation_CMP_CTCF_rep1

value: CTCF


title: th_4W_4

value: 4 weeks


title: CM-Mock-V-30m-2


title: ChIPmentation_HSC_CTCF_rep2


title: colorectum_young_AOM+DSS_d0_rep3

description: gene expression after 0 day in AOM+DSS-treated young mice's colorectum

source_name: colorectum from young mice,AOM+DSS,d0,replicate 3

value: colorectum

value: normal


title: CM-Mock-V-30m-1


title: ChIPmentation_HSC_CTCF_rep1


title: colorectum_young_AOM+DSS_d0_rep2

source_name: colorectum from young mice,AOM+DSS,d0,replicate 2

value: young


title: th_4W_3


title: colorectum_old_AOM+DSS_d10_rep1

source_name: colorectum from old mice,AOM+DSS,d10,replicate 1

value: old


title: Human ASCP RNA-seq, sample 5

city: La Jolla

first: Nirakar

last: Rajbhandari

state: Ca

address: 2880 Torrey Pines Scenic Dr

institute: University of California San Diego

description:
ASCP4
NormalvsASCPsleuthb1fdr5.txt
ASCP_tpm.txt

data_processing:
Library output was aligned and quantified using Kallisto version 0.43.1 with 50 bootstraps for each read and an estimated fragment length of 75 for the single-end reads.
Differential analysis of Kallisto data was performed using the Sleuth Tool (version 0.30.0) (Harold J. Pimentel, Nicolas Bray, Suzette Puente, Páll Melsted and Lior Pachter, Differential analysis of RNA-Seq incorporating quantification uncertainty, Nature Methods (2017), advanced access http://dx.doi.org/10.1038/nmeth.4324.) GSM3415808 samples from GEO were used as a control of healthy pancreatic tissue. The sleuth R package was used for pairwise differential expression using the Wald test, with an FDR <0.05 and a beta value >1.
Assembly: hg38
Supplementary files format and content: Each unprocessed sample condition file has three corresponding processed kallisto output files: abundance.h5, abundance.tsv, and run_info.json
Supplementary files format and content: Sleuth used the samples in this Series and GSE120795 samples (GSM3415808, GSM3415817, GSM3415824) to generate the following output files: NormalvsASCPsleuthb1fdr5.txt, NormalvsACCsleuthb1fdr5.txt, ASCP_tpm.txt, ACC_tpm.txt.

source_name: Pancreatic adenosquamous carcinoma

growth_protocol: Human patient tissue samples.

extract_protocol:
Snap-frozen tumor tissues were sliced into 1-2 mm sized pieces and crushed in an Eppendorf tube with sterile microcentrifuge pestle in the presence of RLT-Plus buffer in the presence ofb-mercaptoethanol. Total RNA was isolated using the RNeasy Micro Plus kit (Qiagen #74034). Total RNA was assessed for quality using an Agilent Tapestation, and all samples had RIN >7.0. RNA libraries were generated from >50 to 100 ng of RNA using Illumina’s TruSeq Stranded mRNA Sample Prep Kit following the manufacturer’s instructions.
RNA libraries were multiplexed and sequenced with 75 base pairs (bp) single-end reads (SR75) or 100 bp paired-end reads to a depth of approximately 30 million reads per sample on an Illumina HiSeq4000 using V4 sequencing chemistry at theUCSD IGM core.

value: Pancreatic adenosquamous carcinoma

value: pancreatic cancer


title: th_4W_2

source_name: Hypothalamus


title: ChIPmentation_MEP_TAL1_rep3

description:
Coverage_TAL1_MEP_merge_clip.bw
TAL1_MEP_peaks.narrowPeak

value: Bone Marrow

value: CD34+ HSPC

value: MEP

value: TAL1 (Abcam)


title: Human ASCP RNA-seq, sample 4

description:
ASCP3
NormalvsASCPsleuthb1fdr5.txt
ASCP_tpm.txt


title: CM-Mock-V-0-2

source_name: Leaves

value: Leaves


title: Human ASCP RNA-seq, sample 3

description:
ASCP2
NormalvsASCPsleuthb1fdr5.txt
ASCP_tpm.txt


title: ChIPmentation_MEP_TAL1_rep2


title: th_3W_3

value: Male

value: 3 weeks

value: Hypothalamus


title: ChIPmentation_MEP_TAL1_rep1


title: th_3W_2

value: WT


title: CM_pi_5D-3


title: ChIPmentation_MEP_RUNX1_rep3

description:
Coverage_RUNX1_MEP_merge_clip.bw
RUNX1_MEP_peaks.narrowPeak

value: RUNX1 (Abcam)


title: colorectum_young_AOM+DSS_d0_rep1

source_name: colorectum from young mice,AOM+DSS,d0,replicate 1


title: th_4W_1

value: 4 weeks


title: Human ACC RNA-seq, sample 88

description:
ACC3
NormalvsACCsleuthb1fdr5.txt
ACC_tpm.txt

source_name: Pancreatic acinar cell carcinoma

value: Pancreatic acinar cell carcinoma


title: Human ASCP RNA-seq, sample 2

description:
ASCP1
NormalvsASCPsleuthb1fdr5.txt
ASCP_tpm.txt


title: th_3W_1


title: colorectum_old_AOM+DSS_d0_rep1

description: gene expression after 0 day in AOM+DSS-treated old mice's colorectum

source_name: colorectum from old mice,AOM+DSS,d0,replicate 1

value: colorectum

value: normal


title: CM-Mock-V-0-3


title: colorectum_old_AOM+DSS_d0_rep2

source_name: colorectum from old mice,AOM+DSS,d0,replicate 2

value: old


title: colorectum_old_AOM+DSS_d0_rep3

source_name: colorectum from old mice,AOM+DSS,d0,replicate 3


title: CM-Mock-V-0-1


title: R_p5_thal_3

value: postnatal day 5


title: Human ACC RNA-seq, sample 87

description:
ACC2
NormalvsACCsleuthb1fdr5.txt
ACC_tpm.txt

value: pancreatic cancer


title: ChIPmentation_MEP_LYL1_rep3

description:
Coverage_LYL1_MEP_merge_clip.bw
LYL1_MEP_peaks.narrowPeak

value: Bone Marrow

value: LYL1 (Abcam)


title: CM_pi_5D-1


title: Human ACC RNA-seq, sample 1

description:
ACC1
NormalvsACCsleuthb1fdr5.txt
ACC_tpm.txt


title: ChIPmentation_MEP_RUNX1_rep2

value: CD34+ HSPC

value: MEP


title: ChIPmentation_MEP_RUNX1_rep1


title: R_p5_thal_1


title: CM_pi_5D-2

value: Leaves


title: ChIPmentation_MEP_LYL1_rep2


title: HeLa, mock, cytosol biol rep 3

city: Rome

first: Savina

last: Apolloni

address: Via della Ricerca Scientifica, 1

department: Department of Biology

country: Italy

institute: University of Rome Tor Vergata

data_processing:
CASAVA 1.8.2 version of the Illumina pipeline was used to processed raw data for both format conversion and de-multiplexing
Trimming using ERNE and Cutadapt softwares
Alignments with STAR
Stringtie4 was used to assemble and quantify full-length transcripts representing multiple spliced variants for each gene locus. Default parameters were used.
Quality control by using RSeqQC package.
Assembly: hg19
Supplementary files format and content: file TAB including FPKM for each sample

molecule: cytoplasmic RNA

source_name: HeLa

extract_protocol:
Nuclear and cytoplasmic RNAs from control and C9orf72 cells were extracted using Trizol, according to the manufacturer's instruction. 1-2 µg of total RNA was used for the construction of sequencing libraries.
TruSeq Stranded mRNA Sample Prep kit

value: HeLa

value: mock


title: CM_pi_3.5D-2

first: Seon-In

last: Yeom

address: 501, Jinjou-daero


title: CM_pi_3.5D-3


title: R_p5_tha_2

value: Male

value: Hypothalamus


title: ChIPmentation_MEP_LYL1_rep1


title: HeLa, G4C231, cytosol, biol rep 3


title: U87 shCCDC50-5 rep2

city: Philadelphia

first: Tian

last: Tian

state: PA

address: 3615 Civic Center Blvd

department: Center of Applied Genomics

institute: Children's Hospital of Philadelphia

data_processing:
Raw fastq files were trimmed by trim-galore to remove adapters and low-quality bases
Trimed reads were aligned to hg38 by Hisat2
Read counts were summarized by StringTie2
Assembly: hg38
Supplementary files format and content: counts

growth_protocol: DMEM medium containing with 10% FBS, 1% L-glutamine (200 mM) and 1% penicillin/streptomycin.

extract_protocol:
The cells were collected and and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Astrocyte tumor cell


title: U87 shCCDC50-1 rep2


title: U87 shCCDC50-5 rep1


title: HeLa, G4C231, nucleus, biol rep 3

molecule: nuclear RNA


title: CM_pi_3.5D-1

city: Jinju

institute: Gyeongsang National University

value: WT


title: CM_pi_2D-3


title: U87 shCCDC50-1 rep1


title: U87 shCtrl rep2

value: wt

value: shRNA control


title: ChIPmentation_MEP_LMO2_rep3

description:
Coverage_LMO2_MEP_merge_clip.bw
LMO2_MEP_peaks.narrowPeak

value: LMO2 (Abcam)


title: ChIPmentation_MEP_LMO2_rep2


title: CM_pi_2D-1


title: HeLa, mock, nucleus, biol rep 3


title: U87 shCtrl rep1


title: HeLa, G4C231 cytosol, biol rep 2


title: CM_pi_1D-2


title: ChIPmentation_MEP_LMO2_rep1


title: HeLa, mock, cytosol, biol rep 2


title: ChIPmentation_MEP_GATA2_rep3

description:
Coverage_GATA2_MEP_merge_clip.bw
GATA2_MEP_peaks.narrowPeak

value: GATA2 (Abcam)


title: HeLa, G4C231, nucleus, biol rep 2


title: CM_pi_1D-1


title: Repli si-2-6R

first: Yongjie

address: No. 1 West Beichen Road, Chaoyang District

institute: Institute of Genetics and Developmental Biology

data_processing:
Adapters were removed using Trimmomatic(version 0.36)
Mapping by Bowtie( version 2.3.4.1) under the parameters -X 2000 --very-sensitive --qc-filter
PCR duplicates reads were removed using Picard
we counted the reads of in sliding windows of 50 kb interval and performed CPM (counts per million) normalization.
Genome-wide quantile normalization and loess smoothing (a span of 300 kb) were futher performed. And loess-smoothed data was export into bedGraph files.
Assembly: hg38/Grhc38
Supplementary files format and content: bedGraph files were transformed into bigwig format by bedGraphToBigWig.
Library strategy: Repli-seq

growth_protocol: U2OS  cells were maintained in DMEM supplemented with 10% FBS in a humidified incubator equilibrated with 5% CO2 at 37°C.

extract_protocol:
Harvest U2OS cells were grown with indicated treatments and count the cells. Cells should be intact and in a homogenous, single-cell suspension.
The cells were collected and lysed immediately in lysis buffer (50 mM Tris-HCl, pH 8.0, 10 mM EDTA, 1 M NaCl, 0.5% SDS, 0.1 mg/ml RNase A, 0.2 mg/ml protease K), and the lysates were incubated at 37 °C for 3 h and then at 55 °C for 8 h before being sonicated for 5 cycles using Bioruptor with 30 s  on and 30 s off for 30 cycles. DNA fragments ranging from 200 bp to 400 bp was selected with AMPure beads (0.6 × to 1.0 ×) (Beckman, A63881). Biotin was conjugated to EdU-labeled DNAs by Click-iT reaction in buffer containing 15 mM Tris, pH 7.5, 400 uM biotin azide; 100 μM: 500 μM CuSO4 (Sigma, 209198):THPTA (Sigma, 762342), 5 mM freshly prepared sodium ascorbate (Sigma, A4034) at 34 °C for 20 min. DNAs were purified with MinElute PCR purification kit (Qiagen, 28004), end-repaired, dA-tailed, and adapter-ligated before being dissolved in 1× TE buffer and incubated with M280 streptavidin beads (Thermo Fisher, 11205D) in binding/washing buffer containing 5 mM Tris-HCl, pH 7.5, 1 M NaCl, 0.5 mM EDTA, pH 8.0 for 20 min. After rinsing in binding/washing buffer containing 0.5% IGEPAL CA-630 (Sigma, I3021) for 6 times, recovered DNAs from beads were used for Repli-seq library construction.

treatment_protocol: U2OS cells treated with control siRNAs or siRNAs against NFIB were synchronized at G1/S transition by thymidine and aphidicolin double treatments. These cells were released for 0  (early S phase) , 4 (middle S phase) or 6 h (later S phase) respectively.

value: U2OS cells with NFIB depletion and release into S phase for 6 h

tag: cell cycle_phase

value: S


title: CM_pi_2D-2

tag: tissue


title: Repli si-1-6R

tag: cell type


title: Repli si-2-1R

value: U2OS cells with NFIB depletion and release into S phase for 0 h


title: ChIPmentation_MEP_GATA2_rep2

value: Bone Marrow


title: HeLa, mock, nucleus, biol rep 2

tag: genotype


title: ChIPmentation_MEP_GATA2_rep1

value: CD34+ HSPC


title: CM_pi_12h-3


title: ChIPmentation_MEP_FLI1_rep3

description:
Coverage_FLI1_MEP_merge_clip.bw
FLI1_MEP_peaks.narrowPeak

value: MEP

value: FLI1 (Abcam)


title: Repli si-1-4R

tag: cell line

value: U2OS cells with NFIB depletion and release into S phase for 4 h


title: HeLa, mock, cytosol, biol rep 1

value: HeLa

value: mock


title: HeLa, G4C231, cytosol, biol rep 1


title: CM_pi_12h-1

value: Leaves


title: CM_pi_12h-2


title: Repli si-1-1R


title: HeLa, G4C231, nucleus, biol rep 1


title: CM_pi_6h-3


title: Repli NC-2-6R

value: U2OS cells without NFIB depletion and release into S phase for 6 h


title: ChIPmentation_MEP_IgG

tag: cell subset

value: IgG (Abcam)


title: ChIPmentation_MEP_FLI1_rep1


title: Repli si-2-4R


title: HeLa, mock, nucleus, biol rep 1


title: CM_pi_6h-2

value: WT


title: Repli NC-2-4R

value: U2OS cells without NFIB depletion and release into S phase for 4 h


title: ChIPmentation_MEP_ERG_rep3

description:
Coverage_ERG_MEP_merge_clip.bw
ERG_MEP_peaks.narrowPeak

value: ERG (Abcam)


title: Control treatment 3

city: Nes-Ziona

first: Yehudit

last: Natan

address: 11 Haharash

country: Israel

institute: Amorphical Ltd.

data_processing:
Reads were trimmed using cutadapt
After trimming the reads were mapped to the human genome using STAR  v2.4.2a (using options outFilterMismatchNmax 2 and alignEndsType EndToEnd)
Counting proceeded over genes annotated in Ensembl release 92, using htseq-count
Normalization was performed using DESeq2
GRCh38
Supplementary files format and content: Excel file includes the normalized counts and DESeq2 output

growth_protocol: A549 cells were cultured in DMEM/F12 complete medium  or with DMEM/F12 calcium depleted medium to which 2mM elemntal calcium as ACC was added, to both mediums 10% fetal bovine serum (FBS) and antibiotics were added. Cell were cultured in a  humidified atmospheric incubator with 5% CO2 at 37C.

extract_protocol:
RNA was extracted using Promega SV Total RNA Isolation System (Promega Corp. Madison, Wisconsin, USA). 2-4.4µg total RNA was used to constract libraries for sequencing.
Inhouse poly A based RNA seq

treatment_protocol: ACC treated cell or control (as described above) were cultured in triplicates for 8 consecutive passages.

value: human lung carcinoma epithelial cells

value: Control


title: Repli NC-2-1R

value: U2OS cells without NFIB depletion and release into S phase for 0 h

value: S


title: ChIPmentation_MEP_ERG_rep2

value: Bone Marrow


title: ChIPmentation_MEP_ERG_rep1

value: CD34+ HSPC


title: CM-TDW_5D-3


title: ChIPmentation_MEP_FLI1_rep2

value: MEP


title: CM-TDW_5D-2


title: ACC treatment 3

value: 2mM ACC


title: Control treatment 2


title: Control treatment 1


title: Repli NC-1-4R


title: ChIPmentation_GMP_TAL1_rep3

description:
Coverage_TAL1_GMP_merge_clip.bw
TAL1_GMP_peaks.narrowPeak

value: GMP

value: TAL1 (Abcam)


title: CM-TDW_5D-1


title: Repli NC-1-1R


title: ACC treatment 2


title: ChIPmentation_GMP_TAL1_rep2


title: CM-TDW_3_5D-3


title: ChIPmentation_GMP_TAL1_rep1


title: CUT&Tag si-S-K9

data_processing:
Adapters were removed using Trimmomatic(version 0.36)
Mapping by Bowtie( version 2.3.4.1) under the parameters -X 2000 --very-sensitive --qc-filter
PCR duplicates reads were removed using Picard
Peak calling was performed with macs2 2.1.2 using ‘macs2 callpeak -f BAMPE --keep-dup all -g hg’
Peak reads counts were calculated by multicov function from BEDTools
Assembly: hg38/Grhc38
Supplementary files format and content: wig files were generated using bamCoverage
Library strategy: H3K9me3 CUT&Tag

extract_protocol:
Harvest U2OS cells were grown with indicated treatments and count the cells. Cells should be intact and in a homogenous, single-cell suspension.
DNA libraries were established by NovoNGS CUT&Tag 2.0 High-Sensitivity Kit.

treatment_protocol: U2OS cells treated with control siRNAs or siRNAs against NFIB were synchronized at G1/S transition by double-thymidine block. These cells were released for 0 (G1 phase) or 4 h (S phase) respectively.

value: U2OS cells with NFIB depletion at S phase


title: ACC treatment 1


title: CM-TDW_3_5D-2

value: Leaves


title: CUT&Tag si-G1-K9

value: U2OS cells with NFIB depletion at G1 phase


title: ChIPmentation_GMP_RUNX1_rep3

description:
Coverage_RUNX1_GMP_merge_clip.bw
RUNX1_GMP_peaks.narrowPeak

value: RUNX1 (Abcam)


title: CM_pi_6h-1

value: WT


title: CM-TDW_3_5D-1


title: ChIPmentation_GMP_RUNX1_rep2


title: CUT&Tag NC-S-K9

value: U2OS cells without NFIB depletion at S phase


title: PM_6

city: Botucatu

first: Geysson Javier

middle: Fernandez

last: Garcia

state: Sao Paulo

address: Departamento morfologia IBB UNESPRubiao Junior

country: Brazil

institute: UNESP

data_processing:
Sequenced reads were performed quality assessment using FastQC. Reads with phred score >30 were accepted
Adapters were removed using trimomatic in the default options
Single-end reads for mRNA were mapped to the GRCh38.p13 genome using STAR with default options
Counts for RefSeq genes were obtained using Featurecounts with the default settings
DESeq2 was used to normalize expression counts.
Assembly: GRCh38.p13
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: blood cells

growth_protocol: Human peripheral blood mononuclear cells from 6 healthy donors mixed with 2% EDTA, were isolated through density gradient with Ficoll-histopaque.

extract_protocol:
Total RNA from untreated or Particulate Matter-treated blood cells was obtained using Direct-zol ™ RNA Miniprep Plus (Zymo Research, Irvine, California) following the manufacturer’s protocol. RNA samples were treated with DNase I column (Zymo Research, Irvine, California) to remove contaminating genomic DNA. RNA was quantifed, and the quality of each RNA sample was checked by spectrophotometry (Thermo Scientifc, Wilmington, DE, USA). Additionally, RNA quality was determined by analysis of ribosomal RNAs, using the Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA).
Libary construction was made using the KAPA Stranded mRNA-Seq Kit (cat #KK8421, KAPA Biosystems, Wilmington, MA)

treatment_protocol: Particulate matter treatment  of human blood cells was performed at  100ug/ml in 5% serum RPMI-1640 medium. Samples were incubated at 37°C with 5% CO2 for 48 h.

value: blood cells

value: Particulate Matter (PM)

value: Healthy

tag: donor

value: Donor 6


title: PM_5

value: Donor 5


title: Repli NC-1-6R

city: Beijing

value: U2OS cells without NFIB depletion and release into S phase for 6 h

value: S


title: CM-TDW_2D-2


title: CUT&Tag NC-G1-K9

value: U2OS cells without NFIB depletion at G1 phase


title: CM-TDW_2D-1


title: CUT&Tag si-K4-S

data_processing:
Adapters were removed using Trimmomatic(version 0.36)
Mapping by Bowtie( version 2.3.4.1) under the parameters -X 2000 --very-sensitive --qc-filter
PCR duplicates reads were removed using Picard
Peak calling was performed with macs2 2.1.2 using ‘macs2 callpeak -f BAMPE --keep-dup all -g hg’
Peak reads counts were calculated by multicov function from BEDTools
Assembly: hg38/Grhc38
Supplementary files format and content: wig files were generated using bamCoverage
Library strategy: H3K4me3 CUT&Tag


title: PM_4

value: Donor 4


title: CM-TDW_1D-3


title: ChIPmentation_GMP_RUNX1_rep1

value: Bone Marrow

value: CD34+ HSPC

value: GMP

tag: chip antibody


title: PM_3

tag: disease state

value: Donor 3


title: ChIPmentation_GMP_LYL1_rep2

description:
Coverage_LYL1_GMP_clip.bw
LYL1_GMP_peaks.narrowPeak

value: LYL1 (Abcam)


title: ChIPmentation_GMP_LYL1_rep3


title: CUT&Tag NC-K4-S


title: PM_2

value: Donor 2


title: PM_1

value: Donor 1


title: CUT&Tag si-K4-G1

value: U2OS cells with NFIB depletion at G1 phase


title: CM-TDW_1D-2

value: Leaves

value: WT


title: ChIPmentation_GMP_LYL1_rep1


title: Control_6

value: blood cells

value: Control

value: Healthy


title: CM-TDW_1D-1


title: ChIPmentation_GMP_LMO2_rep2

description:
Coverage_LMO2_GMP_clip.bw
LMO2_GMP_peaks.narrowPeak

value: LMO2 (Abcam)


title: CUT&Tag NC-K4-G1


title: Control_5

value: Donor 5


title: CM-TDW_2D-3


title: ATAC_si-S-2

data_processing:
Adapters were removed using Trimmomatic(version 0.36)
Mapping by Bowtie( version 2.3.4.1) under the parameters -X 2000 --very-sensitive --qc-filter
PCR duplicates reads were removed using Picard
Peak calling was performed with macs2 2.1.2 using ‘macs2 callpeak -f BAMPE --keep-dup all -g hg’
Peak reads counts were calculated by multicov function from BEDTools
Assembly: hg38/Grhc38
Supplementary files format and content: wig files were generated using bamCoverage

extract_protocol:
Harvest U2OS cells were grown with indicated treatments and count the cells. Cells should be intact and in a homogenous, single-cell suspension. Transposition reaction and purification DNA fragments and amplify transposed DNA fragments by PCR.
ATAC-Seq libraries were prepared using ATAC protocol and DNA fragments were recovered using Qiagen MinElute PCR Purification Kit Purification DNA

value: U2OS cells with NFIB depletion at S phase

value: S


title: ATAC_si-S-1


title: ChIPmentation_GMP_LMO2_rep1

data_processing:
ChipSeq reads were trimmed using TrimGalore. Adaptors were removed using CutAdapt. The reads were aligned to hg38 using BWA.
ChipSeq reads were sorted, indexed using Samtools. Dupicate reads were removed using Picard. Replicates were merged using Samtools.
ChipSeq peak calling was done using MACS 2.0 with a p value of 1e-5
Assembly: hg38
Supplementary files format and content: bigWig
Supplementary files format and content: narrowPeak: BED6+4 files containing peaks called from merged replicates with macs2 using p-value of 1 x 10-5 and the IgG track as the control.
Library strategy: ChIPmentation

value: Bone Marrow


title: CM-TDW_12h-3


title: Control_4

value: Donor 4


title: ChIPmentation_GMP_IgG

value: CD34+ HSPC

value: GMP

value: IgG (Abcam)


title: ATAC_si-G1-2


title: CM-TDW_12h-2


title: ChIPmentation_GMP_GATA2_rep3

description:
Coverage_GATA2_GMP_merge_clip.bw
GATA2_GMP_peaks.narrowPeak

value: GATA2 (Abcam)


title: Control_3

value: Donor 3


title: Control_2

value: Donor 2


title: CM-TDW_12h-1

value: Leaves


title: ATAC_NC-S-2

value: U1OS cells without NFIB depletion at S phase


title: CM-TDW_6h-3

value: WT


title: ATAC_NC-S-1


title: ChIPmentation_GMP_LMO2_rep3


title: CM-TDW_6h-2


title: Control_1

value: blood cells

value: Control

value: Donor 1


title: ChIPmentation_GMP_FLI1_rep3

description:
Coverage_FLI1_GMP_merge_clip.bw
FLI1_GMP_peaks.narrowPeak

value: FLI1 (Abcam)


title: ChIPmentation_GMP_GATA2_rep2


title: CM-TDW_6h-1


title: LNCaP_0nm3

city: Adelaide

first: Nick

last: Warnock

state: South Australia

address: UniSA Bradley Building, North Terrace

department: Centre for Cancer Biology

institute: SA Pathology

description: Replicate 3

data_processing:
Basecalling was performed using bcl-convert, with the following options: --bcl-num-parallel-tiles 1 --bcl-num-conversion-threads 10 --bcl-num-compression-threads 10 --bcl-num-decompression-threads 5 --bcl-sampleproject-subdirectories true --force  --no-lane-splitting true
Adapters were trimmed using cutadapt version 4.1 and the following parameters: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA --minimum-length 18 --error-rate 0.2 --overlap=5
Reads were aligned to the genome using STAR version 2.7.7a
Aligned reads were UMI-deduplicated using UMI-tools version 1.1.2
Deduplicated reads were realigned to the genome using STAR version 2.7.7a, producing gene counts for each sample
Assembly: GCA_000001405.15_GRCh38_no_alt_analysis_set using RefSeq annotations
Supplementary files format and content: *ReadsPerGene.out.tab: tab-separated gene counts file for each sample
Supplementary files format and content: gene_counts.tsv: tab-separated file containing strand-specific gene counts for all samples

source_name: LNCaP (clone FCG)

growth_protocol: PC3 cells were cultured in F12K media supplemented supplemented with 10% FBS. LNCaP cells were cultured in RPMI media supplemented with 10% FBS. Cells were kept in humidified atmosphere with 5% CO2 at 37°C

extract_protocol:
RNA was extracted using PureLink RNA Mini Kit (Thermo Fisher Scientific), followed by DNase I treatment with TURBO DNA-free Kit (Invitrogen).  Quality control was performed with Agilent 2100 Bioanalyser.
RNA libraries for mRNAseq were started by using NEBNext® Poly(A) mRNA Magnetic Isolation Module to enrich the polyA RNA from total RNA, then library prep with KAPA RNA HyperPrep Kits according to the manufacturer’s guidelines

treatment_protocol: LNCaP cells were cultured for 24 h in phenol red-free RPMI media supplemented with 10% charcoal-stripped FBS, followed by 48h treatment with 10 nM dihydrotestosterone (DHT) or vehicle (0.01% ethanol)

value: LNCaP (clone FCG)

value: epithelial

value: Vehicle (0.01% ethanol)


title: LNCaP_0nm2

description: Replicate 2


title: ATAC_NC-G1-2

value: U2OS cells without NFIB depletion at G1 phase


title: CM_pi_0-3


title: ATAC_NC-G1-1


title: ChIPmentation_GMP_FLI1_rep2

value: Bone Marrow

value: CD34+ HSPC


title: LNCaP_0nm1

description: Replicate 1


title: CM_pi_0-2


title: TNFa input ChIP-seq rep3

city: Tucson

first: Casey

last: Romanoski

state: AZ

address: 1230 N Cherry Ave

institute: U. Arizona

data_processing:
demultiplexed ChIP-seq fastq data were aligned to hg38 using Bowtie2 with default parameters
Aligned sam files were made into tagDirectories in HOMER.
ChIP-seq peaks were identified using the findPeaks function.
Assembly: hg38
Supplementary files format and content: comb-control-SREPB2-ChIP-peaks.txt. This is a HOMER-formatted peak file generated using HOMER software. Each of the 4 biological replicate SREBP2 ChIP-seq samples from the control condition were combined into one tagDirectory, and the function 'findPeaks' was perfromed using option "-i" to designate the combined control input samples as background. All other options to findPeaks were default parameters.
Supplementary files format and content: comb-tnfa-SREPB2-ChIP-peaks.txt. This file was generated as described for the control peak file with the exception that TNFa treated replicates were used for the ChIP and input samples.

source_name: non-immunoprecipitated input chromatin

growth_protocol: HUVEC used in this study were primary isolates of ECs collected from donor umbilical cords through Yale School of Medicine's Vascular Biology and Therapeutic core. They were used at early passage (p4) and cultured in EGM-2 media (Lonza) with 10% fetal bovine serum, penicilllin/streptomycin and glutamine (2.8mM) in a 37C incubator with 5% CO2 supply

extract_protocol:
Cells were fixed at room temperature with 2mM disuccinimidyl glutarate (DSG) for 30min before an additional fixation with 1% formaldehyde for 15min and quenched with glycin. Between 5 and 15 million cells were used for each ChIP-seq. Cell lysates were sonicated using a BioRuptor Standord or BioRuptor Pico and then immunoprecipitated using antibodies bound to a 2:1 mixture of Protein A Dynabeads and Protein G Dynabeads.
For ChIP-seq, HUVECs were fixed with DSG for 30 min, then formaldehyde for 15 minutes and quenched with glycine. Lysates were sonicated, a small fraction of chromatin was removed and prepared as inputs, whereas the remaining complexes were immunoprecipitated with antibody.
For ChIP-seq, double-stranded End Repair was performed and inserts were ligated to barcoded  BioO Nextflex adapters and amplified prior to sequencing.

treatment_protocol: Cells were treated with or without 10ng/mL of TNFa for 10 hour

value: Primary Human Umbilical Vein Endothelial Cell (HUVEC)

value: TNFa treatment


title: ATAC_si-G1-1

value: U2OS cells with NFIB depletion at G1 phase


title: LNCaP_10nm3

description: Replicate 3

value: 10 nM DHT


title: CM_pi_0-1

data_processing:
A quality control application for high throughput sequence data using FastQC Version 0.11.8
Removes adapter sequences from DNA high-throughput sequencing data using Cutadapt  Version 1.15
A toolkit for the quality control (QC) of next generation sequencing (NGS) data using Trimmomatic Version 0.38
Alignment program for mapping next-generation sequencing reads to Capsicum annuum genome using Hisat2 Version 2-2.1.0
Assembly: Capsicum annuum v1.6
Supplementary files format and content: tab-delimited text files include the values of read count for each sample

value: Leaves


title: ChIPmentation_GMP_ERG_rep3

first: Julie

address: Level 2, C25 Lowy Cancer Research Centre, UNSW Sydney, High St

institute: UNSW Sydney

description:
Coverage_ERG_GMP_merge_clip.bw
ERG_GMP_peaks.narrowPeak

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching, cells were lysed and nuclei frozen. Nuclei were sonicated using a Bioruptor Pico to generate chromatin fragments.
Antibody bound chromatin was collected and crosslinked, before library construction using the KAPA HiFi HotStart Ready Mix and size selection using AMPure XP beads.
ChIPmentation/ Low input ChIP seq using tagmentation

value: GMP

value: ERG (Abcam)


title: CM-P2-4h-3

value: WT


title: TNFa input ChIP-seq rep2


title: ChIPmentation_GMP_GATA2_rep1

value: GATA2 (Abcam)


title: ChIPmentation_GMP_ERG_rep2


title: control input ChIP-seq rep3

value: control treatment


title: CM-P2-4h-2


title: ChIPmentation_GMP_ERG_rep1


title: CM-P2-4h-1


title: TNFa input ChIP-seq rep1


title: PC3F12K_3

description: Replicate 3


title: control input ChIP-seq rep1


title: PC3F12K_2

description: Replicate 2


title: CM-P2-3D-3


title: CM-P2-3D-2


title: PC3F12K_1

description: Replicate 1


title: ChIPmentation_HSC_TAL1_rep2

description:
Coverage_TAL1_HSC.bw
TAL1_HSC_peaks.narrowPeak

value: HSC

value: TAL1 (Abcam)


title: ChIPmentation_GMP_FLI1_rep1

value: FLI1 (Abcam)


title: ChIPmentation_HSC_TAL1_rep1


title: TNFa SREBP2 ChIP-seq rep4

source_name: ChIP-seq for human SREBP2


title: CM-P2-3D-1


title: ChIPmentation_HSC_RUNX1_rep3

description:
Coverage_RUNX1_HSC.bw
RUNX1_HSC_peaks.narrowPeak

source_name: Bone Marrow

value: RUNX1 (Abcam)


title: LNCaP_10nm2

description: Replicate 2

value: LNCaP (clone FCG)

value: epithelial


title: control SREBP2 ChIP-seq rep4


title: CM-P2-30m-3


title: LNCaP_10nm1

description: Replicate 1


title: control input ChIP-seq rep2


title: control SREBP2 ChIP-seq rep3


title: CM-P2-30m-2


title: ChIPmentation_HSC_RUNX1_rep2

value: Bone Marrow

value: CD34+ HSPC


title: ChIPmentation_HSC_RUNX1_rep1


title: TNFa SREBP2 ChIP-seq rep3

value: Primary Human Umbilical Vein Endothelial Cell (HUVEC)

value: TNFa treatment


title: AMC_LCDM_Case_#37

city: Seoul

first: DONG-MYUNG

last: SHIN

address: Pungnap-2 dong, Songpa-gu

department: Department of Biomedical Sciences

institute: University of Ulsan College of Medicine

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 (UCSC) whole genome using Bowtie2
Read count extraction using bedtools.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include read count values for each Sample

source_name: Laser capture microdissected (LCMD) tumors from the formalin-fixed paraffin-embedded (FFPE) TURBT specimens

growth_protocol: This retrospective study was approved by the Institutional Review Board of Asan Medical Center (AMC; 2020-0064). It included 105 consecutive MIBC (cT2-4aN0M0) patients who underwent TUR with available formalin-fixed paraffin-embedded (FFPE) tumor tissues and at least 3 cycles of NAC between August 2011 and August 2017 at AMC. Among the 105 patients, 60 patients who underwent curative surgery after NAC were designated as validation cohort since their pathologic response of NAC was assessable using the surgical specimens.

extract_protocol:
Laser capture microdissection (LCMD) was performed on hematoxylin-eosin-stained tissue slides using a Leica LMD6500 laser capture dissection microscope (Leica Microsystems) as described by the manufacturer. The urothelial carcinoma areas were meticulously microdissected as close as possible to the perimeter of tumor cells to avoid contamination of stroma and inflammatory cells while avoiding tumor necrotic area. Total RNA from the LCMD tumor tissues was isolated using the RNeasy Mini Kit (QIAGEN, Valencia, CA), including treatment with DNase I (QIAGEN)
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

treatment_protocol: The ASAN cohort was classified into two groups showing marked contrast in NAC response: NAC response (R) patients with the absence of residual invasive tumor and NAC nonresponse (NR) patients with large residual MIBC (4.9 ± 2.5 cm) in the radical/partial cystectomy specimens.

value: Human Bladder cancer

value: NAC non response

tag: patholresponse

value: No


title: AMC_LCDM_Case_#36

value: Laser capture microdissected (LCMD) tumors from the formalin-fixed paraffin-embedded (FFPE) TURBT specimens


title: ChIPmentation_HSC_TAL1_rep3

city: Randwick

last: Thoms


title: ChIPmentation_HSC_LYL1_rep3

description:
Coverage_LYL1_HSC.bw
LYL1_HSC_peaks.narrowPeak

value: LYL1 (Abcam)


title: TNFa SREBP2 ChIP-seq rep2

tag: treatment


title: CM-P2-30m-1

value: Leaves

value: WT

tag: timepoint


title: AMC_LCDM_Case_#35


title: control SREBP2 ChIP-seq rep2

value: control treatment


title: ChIPmentation_HSC_LYL1_rep2

value: HSC


title: CM-P2-2D-2


title: AMC_LCDM_Case_#39


title: ChIPmentation_HSC_LYL1_rep1


title: TNFa SREBP2 ChIP-seq rep1


title: AMC_LCDM_Case_#34


title: AMC_LCDM_Case_#33


title: AMC_LCDM_Case_#38


title: CM-P2-2D-1


title: control SREBP2 ChIP-seq rep1


title: ChIPmentation_HSC_LMO2_rep3

description:
Coverage_LMO2_HSC.bw
LMO2_HSC_peaks.narrowPeak

value: LMO2 (Abcam)


title: CM-P2-1D-3


title: ChIPmentation_HSC_LMO2_rep2


title: shNFIB-NS-RNase

data_processing:
Adapters were removed using Trimmomatic(version 0.36)
Mapping by Bowtie( version 2.3.4.1) under the parameters -X 2000 --very-sensitive --qc-filter
PCR duplicates reads were removed using Picard
Peak calling was performed with macs2 2.1.2 using ‘macs2 callpeak -f BAMPE --keep-dup all -g hg’
Peak reads counts were calculated by multicov function from BEDTools
Assembly: hg38/Grhc38
Supplementary files format and content: wig files were generated using bamCoverage; Scores represent reads counts
Library strategy: NS-Seq

source_name: U2OS cells with NFIB depletion

extract_protocol:
The genomic DNA was extracted by DNAzol. Then the DNA was denatured by boiling 10 mins at 100 °C and loaded onto 30ml neutral 5%-30% sucrose gradients. The mixture was centrifuged in SW28 rotor at 25000rpm for 20 hours. 1 ml-fraction was withdrawn from the top of the gradients. DNA fragments ranged from 0.5-2.5Kb were collected and purified. Half of the total purified DNA was treated with RNAase A (shNFIB-NS-RNase and  NC-NS-RNase sample).
The single strand DNA was converted to double strand DNA by BioPrime Array CGH Genomic Labeling System. DNA library for Immunila was prepared using a NEBNext Ultra DNA Library Prep Kit.

treatment_protocol: U2OS cells were infected with lentiviruses carrying control shRNA or NFIB shRNA.

value: NFIB depletion


title: AMC_LCDM_Case_#32


title: AMC_LCDM_Case_#31


title: shNFIB-NS


title: AMC_LCDM_Case_#30


title: ChIPmentation_HSC_LMO2_rep1


title: CM-P2-1D-2


title: NC-NS-RNase

source_name: U2OS cells without NFIB depletion


title: ChIPmentation_HSC_IgG

value: IgG (Abcam)


title: CM-P2-1D-1


title: CM-P2-2D-3


title: AMC_LCDM_Case_#29


title: NC-NS


title: CM-PC-1D-3


title: ChIPmentation_HSC_GATA2_rep3

description:
Coverage_GATA2_HSC.bw
GATA2_HSC_peaks.narrowPeak

value: GATA2 (Abcam)


title: Microc_S_sh_2

data_processing:
BWA was used mapping DNA sequences against reference genome
pairtools was used to detect ligation junctions, remove PCR duplicates and generate ValidPairs files
mcool files were converted from ValidPairs by Cooler package
hic file were converted from ValidPairs by Juicer tools
Assembly: hg38/Grhc38
Supplementary files format and content: hic file contains all valid Micro-C pairs with mutiple resolutions
Supplementary files format and content: valid paris file contains 1) read name, 2) chromosome of first locus, 3) read position of first locus,  4) chromosome of second locus, 5) read position of second locus,6) strand of first locus,  7) strand of second locus, 8) pair reads type
Library strategy: MicroC

source_name: U2OS cells with NFIB depletion at S phase

extract_protocol:
Cells were digested into a single-cell suspension and then filtered through a 70-μm cell strainer into 15-ml tubes.
Dovetail Micro-C v1.0

treatment_protocol: U2OS cells without or with NFIB depletion at G1/S phase and S phase were synchronized at G1/S boundary by double-thymidine block and followed by release for 4 h to allow cells entering S phase, respectively.

tag: cell cycle phase

value: S phase


title: CM-PC-1D-2

extract_protocol:
Three biological replicates at each time point per condition were collected. The leaf samples were flash-frozen in liquid nitrogen and stored at ˗80°C until RNA isolation. Total RNA was extracted from pepper leaf samples (100 mg) using the Trizol reagent. Five micrograms of each RNA sample were used for construction of sequencing libraries.
RNA libraries were prepared for sequencing using strand-specfic RNA-seq Illumina protocols


title: ChIPmentation_HSC_GATA2_rep2

value: Bone Marrow

value: CD34+ HSPC


title: Microc_S_sh_1


title: CM-PC-1D-1


title: ChIPmentation_HSC_GATA2_rep1


title: AMC_LCDM_Case_#28


title: AMC_LCDM_Case_#27


title: AMC_LCDM_Case_#26


title: Microc_G1_sh_2

source_name: U2OS cells with NFIB depletion at G1/S phase

value: G1/S phase


title: AMC_LCDM_Case_#25

value: Human Bladder cancer


title: ChIPmentation_HSC_FLI1_rep3

description:
Coverage_FLI1_HSC.bw
FLI1_HSC_peaks.narrowPeak

value: FLI1 (Abcam)


title: CM-PC-12h-2

source_name: Leaves


title: Microc_G1_sh_1


title: AMC_LCDM_Case_#24

value: NAC non response

value: No


title: Microc_S_NC_2

source_name: U2OS cells without NFIB depletion at S phase


title: ChIPmentation_HSC_FLI1_rep2


title: ChIPmentation_HSC_FLI1_rep1


title: AMC_LCDM_Case_#23

value: Laser capture microdissected (LCMD) tumors from the formalin-fixed paraffin-embedded (FFPE) TURBT specimens


title: CM-PC-6h-3

value: Leaves


title: ChIPmentation_HSC_ERG_rep3

description:
Coverage_ERG_HSC.bw
ERG_HSC_peaks.narrowPeak

value: ERG (Abcam)


title: Microc_S_NC_1

value: WT


title: AMC_LCDM_Case_#22


title: CM-PC-6h-2


title: ChIPmentation_HSC_ERG_rep2

value: HSC


title: Microc_G1_NC_2

source_name: U2OS cells without NFIB depletion at G1/S phase


title: ChIPmentation_HSC_ERG_rep1


title: CM-PC-6h-1


title: AMC_LCDM_Case_#21

value: Yes


title: CM-PC-4h-3


title: CM-PC-12h-3


title: AMC_LCDM_Case_#19


title: shNFIB-NFIB-Cuttag

data_processing:
Adapters were removed using Trimmomatic(version 0.36)
Mapping by Bowtie( version 2.3.4.1) under the parameters -X 2000 --very-sensitive --qc-filter
PCR duplicates reads were removed using Picard
Peak calling was performed with macs2 2.1.2 using ‘macs2 callpeak -f BAMPE --keep-dup all -g hg’
Peak reads counts were calculated by multicov function from BEDTools
Assembly: hg38/Grhc38
Supplementary files format and content: wig files were generated using bamCoverage; Scores represent reads counts
Library strategy: CUT&Tag

source_name: U2OS cells with NFIB depletion at G1 phase

extract_protocol:
Harvest U2OS cells were grown with indicated treatments and count the cells. Cells should be intact and in a homogenous, single-cell suspension.  Immunoprecipitated using indicated antibodies, transposition reaction and purification DNA fragments and amplify transposed DNA fragments by PCR.
DNA libraries were established by NovoNGS CUT&Tag 2.0 High-Sensitivity Kit.

treatment_protocol: NFIB- or ORC1- associated chromatin were immunoprecipitated in G1 phase U2OS cells which were synchronized at G1/S boundary by double-thymidine block and followed by release for 16 h  without or with NFIB depletion.

value: NFIB depletion

value: G1 phase

tag: ip

value: NFIB


title: shNFIB-ORC1-Cuttag


title: CM-PC-4h-2


title: ChIPmentation_CMP_TAL1_rep3

description:
Coverage_TAL1_CMP_merge_clip.bw
TAL1_CMP_peaks.narrowPeak

value: CMP

value: TAL1 (SCBT)


title: AMC_LCDM_Case_#20


title: CM-PC-12h-1


title: NC-ORC1-Cuttag

source_name: U2OS cells without NFIB depletion at G1 phase


title: AMC_LCDM_Case_#18

value: NAC response